[med-svn] [crux] 03/05: New upstream version 3.1
Andreas Tille
tille at debian.org
Tue Dec 5 12:44:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository crux.
commit e02afacb34c834e07ec4926b4b9bdafb27a71a4f
Author: Andreas Tille <tille at debian.org>
Date: Tue Dec 5 13:20:39 2017 +0100
New upstream version 3.1
---
AUTHORS | 5 +
CMakeLists.txt | 163 +
COPYRIGHT | 1 +
CPackConfig.cmake | 68 +
CPackSourceConfig.cmake | 73 +
INSTALL | 34 +
Makefile | 472 +
NEWS | 2 +
README | 8 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/Makefile | 207 +
.../doc/assign-confidence.html | 147 +
.../ZIP/crux-3.1.Linux.x86_64/doc/barista.html | 163 +
.../ZIP/crux-3.1.Linux.x86_64/doc/bullseye.html | 158 +
.../crux-3.1.Linux.x86_64/doc/cascade-search.html | 215 +
.../crux-3.1.Linux.x86_64/doc/cmake_install.cmake | 38 +
.../doc/comet-options/activation_method.html | 23 +
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.../doc/comet-options/add_B_user_amino_acid.html | 19 +
.../doc/comet-options/add_C_cysteine.html | 21 +
.../doc/comet-options/add_Cterm_peptide.html | 15 +
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.../doc/comet-options/add_E_glutamic_acid.html | 15 +
.../doc/comet-options/add_F_phenylalanine.html | 15 +
.../doc/comet-options/add_G_glycine.html | 15 +
.../doc/comet-options/add_H_histidine.html | 15 +
.../doc/comet-options/add_I_isoleucine.html | 15 +
.../doc/comet-options/add_J_user_amino_acid.html | 19 +
.../doc/comet-options/add_K_lysine.html | 15 +
.../doc/comet-options/add_L_leucine.html | 15 +
.../doc/comet-options/add_M_methionine.html | 15 +
.../doc/comet-options/add_N_asparagine.html | 15 +
.../doc/comet-options/add_Nterm_peptide.html | 15 +
.../doc/comet-options/add_Nterm_protein.html | 15 +
.../doc/comet-options/add_O_ornithine.html | 15 +
.../doc/comet-options/add_P_proline.html | 15 +
.../doc/comet-options/add_Q_glutamine.html | 15 +
.../doc/comet-options/add_R_arginine.html | 15 +
.../doc/comet-options/add_S_serine.html | 15 +
.../doc/comet-options/add_T_threonine.html | 15 +
.../doc/comet-options/add_U_user_amino_acid.html | 19 +
.../doc/comet-options/add_V_valine.html | 15 +
.../doc/comet-options/add_W_tryptophan.html | 15 +
.../doc/comet-options/add_X_user_amino_acid.html | 19 +
.../doc/comet-options/add_Y_tyrosine.html | 15 +
.../doc/comet-options/add_Z_user_amino_acid.html | 19 +
.../doc/comet-options/allowed_missed_cleavage.html | 18 +
.../doc/comet-options/clear_mz_range.html | 24 +
.../doc/comet-options/clip_nterm_methionine.html | 22 +
.../doc/comet-options/combined.html | 23 +
.../doc/comet-options/comet.params | 160 +
.../doc/comet-options/content.html | 1 +
.../doc/comet-options/convertCometPHPs.py | 55 +
.../doc/comet-options/database_name.html | 21 +
.../doc/comet-options/decoy_prefix.html | 22 +
.../doc/comet-options/decoy_search.html | 29 +
.../doc/comet-options/digest_mass_range.html | 23 +
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.../doc/comet-options/mass_type_fragment.html | 20 +
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.../max_variable_mods_in_peptide.html | 18 +
.../doc/comet-options/minimum_intensity.html | 23 +
.../doc/comet-options/minimum_peaks.html | 21 +
.../doc/comet-options/ms_level.html | 20 +
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.../doc/comet-options/num_output_lines.html | 26 +
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.../doc/comet-options/output_sqtstream.html | 19 +
.../doc/comet-options/output_suffix.html | 25 +
.../doc/comet-options/output_txtfile.html | 52 +
.../doc/comet-options/override_charge.html | 25 +
.../doc/comet-options/peptide_mass_tolerance.html | 17 +
.../doc/comet-options/peptide_mass_units.html | 20 +
.../doc/comet-options/precursor_charge.html | 30 +
.../doc/comet-options/print_expect_score.html | 24 +
.../doc/comet-options/remove_precursor_peak.html | 25 +
.../comet-options/remove_precursor_tolerance.html | 19 +
.../doc/comet-options/require_variable_mod.html | 22 +
.../crux-3.1.Linux.x86_64/doc/comet-options/runall | 24 +
.../doc/comet-options/sample_enzyme_number.html | 22 +
.../doc/comet-options/scan_range.html | 23 +
.../doc/comet-options/search_enzyme_number.html | 46 +
.../doc/comet-options/show_fragment_ions.html | 20 +
.../doc/comet-options/skip_researching.html | 25 +
.../doc/comet-options/spectrum_batch_size.html | 28 +
.../comet-options/theoretical_fragment_ions.html | 32 +
.../doc/comet-options/topmenu.html | 1 +
.../doc/comet-options/use_A_ions.html | 18 +
.../doc/comet-options/use_B_ions.html | 18 +
.../doc/comet-options/use_C_ions.html | 18 +
.../doc/comet-options/use_NL_ions.html | 18 +
.../doc/comet-options/use_X_ions.html | 18 +
.../doc/comet-options/use_Y_ions.html | 18 +
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.../doc/comet-options/use_sparse_matrix.html | 26 +
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.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet.html | 297 +
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.../doc/commands/hardklor_standalone_to_crux.html | 127 +
.../crux-3.1.Linux.x86_64/doc/contributors.html | 177 +
.../crux-3.1.Linux.x86_64/doc/create-docs.cmake | 127 +
.../ZIP/crux-3.1.Linux.x86_64/doc/create-docs.html | 125 +
.../ZIP/crux-3.1.Linux.x86_64/doc/default.params | 1832 +
.../ZIP/crux-3.1.Linux.x86_64/doc/demos/demo1.sh | 34 +
.../crux-3.1.Linux.x86_64/doc/demos/tsv2html.py | 77 +
.../ZIP/crux-3.1.Linux.x86_64/doc/deploy-to-web.sh | 9 +
.../ZIP/crux-3.1.Linux.x86_64/doc/download.html | 741 +
.../doc/example-files/default.params | 1676 +
.../doc/example-files/demo.ms2 | 54667 ++++
.../doc/example-files/search.target.txt | 721 +
.../doc/example-files/small-yeast.fasta | 165 +
.../doc/example-files/target.sqt | 33 +
.../crux-3.1.Linux.x86_64/doc/extract-columns.html | 131 +
.../crux-3.1.Linux.x86_64/doc/extract-rows.html | 134 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/faq.html | 638 +
.../doc/file-formats/barista-xml-format.html | 249 +
.../doc/file-formats/fasta-format.html | 169 +
.../doc/file-formats/features.html | 398 +
.../doc/file-formats/ms2-format.html | 283 +
.../doc/file-formats/parameter-file.html | 129 +
.../doc/file-formats/sample.fasta | 17 +
.../doc/file-formats/sqt-format.html | 329 +
.../doc/file-formats/txt-format.html | 1363 +
.../ZIP/crux-3.1.Linux.x86_64/doc/fileformats.html | 387 +
.../doc/generate-peptides.html | 166 +
.../doc/get-ms2-spectrum.html | 143 +
.../ZIP/crux-3.1.Linux.x86_64/doc/glossary.html | 165 +
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.../ZIP/crux-3.1.Linux.x86_64/doc/pipeline.html | 460 +
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.../doc/print-processed-spectra.html | 141 +
.../ZIP/crux-3.1.Linux.x86_64/doc/psm-convert.html | 142 +
.../ZIP/crux-3.1.Linux.x86_64/doc/q-ranker.html | 160 +
.../crux-3.1.Linux.x86_64/doc/read-tide-index.html | 128 +
.../crux-3.1.Linux.x86_64/doc/release-notes.html | 1849 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/doc/runall | 28 +
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.../doc/tutorials/gettingstarted.html | 218 +
.../doc/tutorials/install.html | 805 +
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.../doc/tutorials/spectralcounts.html | 182 +
.../doc/xlink-assign-ions.html | 145 +
.../doc/xlink-score-spectrum.html | 158 +
.../Linux/ZIP/crux-3.1.Linux.x86_64/license.txt | 12 +
cmake_install.cmake | 58 +
crux_version.h | 1 +
crux_version.h.txt | 1 +
debian/changelog | 5 -
debian/compat | 1 -
debian/control | 24 -
debian/copyright | 17 -
debian/rules | 7 -
debian/source/format | 1 -
debian/upstream/metadata | 21 -
debian/watch | 3 -
doc/Doxyfile | 1551 +
doc/PWIZ_README | 142 +
doc/crux-report.doc | Bin 0 -> 61952 bytes
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doc/logs/README | 12 +
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doc/user/CMakeLists.txt | 29 +
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doc/user/assign-confidence.html | 147 +
doc/user/barista.html | 163 +
doc/user/bullseye.html | 158 +
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doc/user/comet-options/add_Cterm_protein.html | 15 +
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doc/user/comet-options/add_O_ornithine.html | 15 +
doc/user/comet-options/add_P_proline.html | 15 +
doc/user/comet-options/add_Q_glutamine.html | 15 +
doc/user/comet-options/add_R_arginine.html | 15 +
doc/user/comet-options/add_S_serine.html | 15 +
doc/user/comet-options/add_T_threonine.html | 15 +
doc/user/comet-options/add_U_user_amino_acid.html | 19 +
doc/user/comet-options/add_V_valine.html | 15 +
doc/user/comet-options/add_W_tryptophan.html | 15 +
doc/user/comet-options/add_X_user_amino_acid.html | 19 +
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ext/download_pbuffers.cmake | 65 +
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ext/fdstream.hpp | 184 +
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ext/patches/boost/asio.hpp | 121 +
ext/patches/boost/asio/async_result.hpp | 96 +
ext/patches/boost/asio/basic_datagram_socket.hpp | 951 +
ext/patches/boost/asio/basic_deadline_timer.hpp | 520 +
ext/patches/boost/asio/basic_io_object.hpp | 242 +
ext/patches/boost/asio/basic_raw_socket.hpp | 942 +
ext/patches/boost/asio/basic_seq_packet_socket.hpp | 567 +
ext/patches/boost/asio/basic_serial_port.hpp | 697 +
ext/patches/boost/asio/basic_signal_set.hpp | 386 +
ext/patches/boost/asio/basic_socket.hpp | 1520 +
ext/patches/boost/asio/basic_socket_acceptor.hpp | 1138 +
ext/patches/boost/asio/basic_socket_iostream.hpp | 288 +
ext/patches/boost/asio/basic_socket_streambuf.hpp | 569 +
ext/patches/boost/asio/basic_stream_socket.hpp | 854 +
ext/patches/boost/asio/basic_streambuf.hpp | 371 +
ext/patches/boost/asio/basic_streambuf_fwd.hpp | 35 +
ext/patches/boost/asio/basic_waitable_timer.hpp | 521 +
ext/patches/boost/asio/buffer.hpp | 2241 +
ext/patches/boost/asio/buffered_read_stream.hpp | 246 +
.../boost/asio/buffered_read_stream_fwd.hpp | 27 +
ext/patches/boost/asio/buffered_stream.hpp | 260 +
ext/patches/boost/asio/buffered_stream_fwd.hpp | 27 +
ext/patches/boost/asio/buffered_write_stream.hpp | 238 +
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ext/patches/boost/asio/buffers_iterator.hpp | 483 +
ext/patches/boost/asio/completion_condition.hpp | 220 +
ext/patches/boost/asio/connect.hpp | 825 +
ext/patches/boost/asio/coroutine.hpp | 330 +
ext/patches/boost/asio/datagram_socket_service.hpp | 434 +
ext/patches/boost/asio/deadline_timer.hpp | 42 +
ext/patches/boost/asio/deadline_timer_service.hpp | 173 +
ext/patches/boost/asio/detail/addressof.hpp | 40 +
ext/patches/boost/asio/detail/array.hpp | 40 +
ext/patches/boost/asio/detail/array_fwd.hpp | 34 +
ext/patches/boost/asio/detail/assert.hpp | 32 +
ext/patches/boost/asio/detail/atomic_count.hpp | 47 +
.../asio/detail/base_from_completion_cond.hpp | 70 +
ext/patches/boost/asio/detail/bind_handler.hpp | 491 +
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.../boost/asio/detail/buffer_sequence_adapter.hpp | 385 +
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ext/patches/boost/asio/detail/call_stack.hpp | 127 +
.../boost/asio/detail/chrono_time_traits.hpp | 192 +
.../boost/asio/detail/completion_handler.hpp | 83 +
ext/patches/boost/asio/detail/config.hpp | 906 +
.../boost/asio/detail/consuming_buffers.hpp | 294 +
ext/patches/boost/asio/detail/cstdint.hpp | 48 +
ext/patches/boost/asio/detail/date_time_fwd.hpp | 34 +
.../boost/asio/detail/deadline_timer_service.hpp | 229 +
ext/patches/boost/asio/detail/dependent_type.hpp | 38 +
ext/patches/boost/asio/detail/descriptor_ops.hpp | 119 +
.../boost/asio/detail/descriptor_read_op.hpp | 121 +
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ext/patches/boost/asio/detail/dev_poll_reactor.hpp | 212 +
ext/patches/boost/asio/detail/epoll_reactor.hpp | 244 +
ext/patches/boost/asio/detail/event.hpp | 50 +
.../asio/detail/eventfd_select_interrupter.hpp | 85 +
ext/patches/boost/asio/detail/fd_set_adapter.hpp | 41 +
ext/patches/boost/asio/detail/fenced_block.hpp | 78 +
ext/patches/boost/asio/detail/function.hpp | 40 +
.../boost/asio/detail/gcc_arm_fenced_block.hpp | 91 +
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.../boost/asio/detail/gcc_sync_fenced_block.hpp | 65 +
.../boost/asio/detail/gcc_x86_fenced_block.hpp | 99 +
.../boost/asio/detail/handler_alloc_helpers.hpp | 82 +
.../boost/asio/detail/handler_cont_helpers.hpp | 45 +
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ext/patches/boost/asio/detail/handler_tracking.hpp | 161 +
.../asio/detail/handler_type_requirements.hpp | 490 +
ext/patches/boost/asio/detail/hash_map.hpp | 333 +
.../asio/detail/impl/buffer_sequence_adapter.ipp | 120 +
.../boost/asio/detail/impl/descriptor_ops.ipp | 453 +
.../boost/asio/detail/impl/dev_poll_reactor.hpp | 80 +
.../boost/asio/detail/impl/dev_poll_reactor.ipp | 447 +
.../boost/asio/detail/impl/epoll_reactor.hpp | 78 +
.../boost/asio/detail/impl/epoll_reactor.ipp | 664 +
.../detail/impl/eventfd_select_interrupter.ipp | 167 +
.../boost/asio/detail/impl/handler_tracking.ipp | 307 +
.../boost/asio/detail/impl/kqueue_reactor.hpp | 82 +
.../boost/asio/detail/impl/kqueue_reactor.ipp | 465 +
.../asio/detail/impl/pipe_select_interrupter.ipp | 126 +
ext/patches/boost/asio/detail/impl/posix_event.ipp | 49 +
ext/patches/boost/asio/detail/impl/posix_mutex.ipp | 48 +
.../boost/asio/detail/impl/posix_thread.ipp | 76 +
.../boost/asio/detail/impl/posix_tss_ptr.ipp | 48 +
.../detail/impl/reactive_descriptor_service.ipp | 210 +
.../detail/impl/reactive_serial_port_service.ipp | 153 +
.../detail/impl/reactive_socket_service_base.ipp | 269 +
.../asio/detail/impl/resolver_service_base.ipp | 132 +
.../boost/asio/detail/impl/select_reactor.hpp | 89 +
.../boost/asio/detail/impl/select_reactor.ipp | 315 +
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.../boost/asio/detail/impl/service_registry.ipp | 190 +
.../boost/asio/detail/impl/signal_set_service.ipp | 649 +
ext/patches/boost/asio/detail/impl/socket_ops.ipp | 3395 +
.../asio/detail/impl/socket_select_interrupter.ipp | 177 +
.../boost/asio/detail/impl/strand_service.hpp | 120 +
.../boost/asio/detail/impl/strand_service.ipp | 178 +
.../boost/asio/detail/impl/task_io_service.hpp | 80 +
.../boost/asio/detail/impl/task_io_service.ipp | 476 +
ext/patches/boost/asio/detail/impl/throw_error.ipp | 47 +
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.../boost/asio/detail/impl/timer_queue_set.ipp | 103 +
ext/patches/boost/asio/detail/impl/win_event.ipp | 69 +
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.../boost/asio/detail/impl/win_iocp_io_service.hpp | 132 +
.../boost/asio/detail/impl/win_iocp_io_service.ipp | 540 +
.../detail/impl/win_iocp_serial_port_service.ipp | 182 +
.../detail/impl/win_iocp_socket_service_base.ipp | 730 +
ext/patches/boost/asio/detail/impl/win_mutex.ipp | 80 +
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.../boost/asio/detail/impl/win_static_mutex.ipp | 120 +
ext/patches/boost/asio/detail/impl/win_thread.ipp | 141 +
ext/patches/boost/asio/detail/impl/win_tss_ptr.ipp | 59 +
.../detail/impl/winrt_ssocket_service_base.ipp | 614 +
.../asio/detail/impl/winrt_timer_scheduler.hpp | 81 +
.../asio/detail/impl/winrt_timer_scheduler.ipp | 124 +
.../boost/asio/detail/impl/winsock_init.ipp | 84 +
ext/patches/boost/asio/detail/io_control.hpp | 136 +
ext/patches/boost/asio/detail/keyword_tss_ptr.hpp | 72 +
ext/patches/boost/asio/detail/kqueue_reactor.hpp | 221 +
ext/patches/boost/asio/detail/limits.hpp | 26 +
.../boost/asio/detail/local_free_on_block_exit.hpp | 59 +
.../boost/asio/detail/macos_fenced_block.hpp | 63 +
ext/patches/boost/asio/detail/mutex.hpp | 50 +
ext/patches/boost/asio/detail/noncopyable.hpp | 45 +
ext/patches/boost/asio/detail/null_event.hpp | 90 +
.../boost/asio/detail/null_fenced_block.hpp | 47 +
ext/patches/boost/asio/detail/null_mutex.hpp | 66 +
ext/patches/boost/asio/detail/null_reactor.hpp | 69 +
.../boost/asio/detail/null_signal_blocker.hpp | 71 +
.../boost/asio/detail/null_socket_service.hpp | 499 +
.../boost/asio/detail/null_static_mutex.hpp | 62 +
ext/patches/boost/asio/detail/null_thread.hpp | 63 +
ext/patches/boost/asio/detail/null_tss_ptr.hpp | 70 +
ext/patches/boost/asio/detail/object_pool.hpp | 148 +
.../boost/asio/detail/old_win_sdk_compat.hpp | 216 +
ext/patches/boost/asio/detail/op_queue.hpp | 158 +
ext/patches/boost/asio/detail/operation.hpp | 40 +
.../boost/asio/detail/pipe_select_interrupter.hpp | 91 +
ext/patches/boost/asio/detail/pop_options.hpp | 105 +
ext/patches/boost/asio/detail/posix_event.hpp | 128 +
.../boost/asio/detail/posix_fd_set_adapter.hpp | 120 +
ext/patches/boost/asio/detail/posix_mutex.hpp | 78 +
.../boost/asio/detail/posix_signal_blocker.hpp | 87 +
.../boost/asio/detail/posix_static_mutex.hpp | 66 +
ext/patches/boost/asio/detail/posix_thread.hpp | 107 +
ext/patches/boost/asio/detail/posix_tss_ptr.hpp | 81 +
ext/patches/boost/asio/detail/push_options.hpp | 138 +
.../asio/detail/reactive_descriptor_service.hpp | 324 +
.../boost/asio/detail/reactive_null_buffers_op.hpp | 90 +
.../asio/detail/reactive_serial_port_service.hpp | 236 +
.../asio/detail/reactive_socket_accept_op.hpp | 138 +
.../asio/detail/reactive_socket_connect_op.hpp | 108 +
.../boost/asio/detail/reactive_socket_recv_op.hpp | 125 +
.../asio/detail/reactive_socket_recvfrom_op.hpp | 135 +
.../asio/detail/reactive_socket_recvmsg_op.hpp | 127 +
.../boost/asio/detail/reactive_socket_send_op.hpp | 122 +
.../asio/detail/reactive_socket_sendto_op.hpp | 125 +
.../boost/asio/detail/reactive_socket_service.hpp | 459 +
.../asio/detail/reactive_socket_service_base.hpp | 452 +
ext/patches/boost/asio/detail/reactor.hpp | 32 +
ext/patches/boost/asio/detail/reactor_fwd.hpp | 42 +
ext/patches/boost/asio/detail/reactor_op.hpp | 63 +
ext/patches/boost/asio/detail/reactor_op_queue.hpp | 170 +
ext/patches/boost/asio/detail/regex_fwd.hpp | 35 +
.../boost/asio/detail/resolve_endpoint_op.hpp | 123 +
ext/patches/boost/asio/detail/resolve_op.hpp | 133 +
ext/patches/boost/asio/detail/resolver_service.hpp | 131 +
.../boost/asio/detail/resolver_service_base.hpp | 131 +
ext/patches/boost/asio/detail/scoped_lock.hpp | 103 +
ext/patches/boost/asio/detail/scoped_ptr.hpp | 81 +
.../boost/asio/detail/select_interrupter.hpp | 48 +
ext/patches/boost/asio/detail/select_reactor.hpp | 221 +
ext/patches/boost/asio/detail/service_registry.hpp | 158 +
ext/patches/boost/asio/detail/shared_ptr.hpp | 40 +
ext/patches/boost/asio/detail/signal_blocker.hpp | 46 +
ext/patches/boost/asio/detail/signal_handler.hpp | 84 +
ext/patches/boost/asio/detail/signal_init.hpp | 49 +
ext/patches/boost/asio/detail/signal_op.hpp | 51 +
.../boost/asio/detail/signal_set_service.hpp | 218 +
ext/patches/boost/asio/detail/socket_holder.hpp | 100 +
ext/patches/boost/asio/detail/socket_ops.hpp | 336 +
ext/patches/boost/asio/detail/socket_option.hpp | 318 +
.../asio/detail/socket_select_interrupter.hpp | 93 +
ext/patches/boost/asio/detail/socket_types.hpp | 406 +
.../boost/asio/detail/solaris_fenced_block.hpp | 63 +
ext/patches/boost/asio/detail/static_mutex.hpp | 54 +
ext/patches/boost/asio/detail/std_event.hpp | 178 +
ext/patches/boost/asio/detail/std_mutex.hpp | 75 +
ext/patches/boost/asio/detail/std_static_mutex.hpp | 83 +
ext/patches/boost/asio/detail/std_thread.hpp | 67 +
ext/patches/boost/asio/detail/strand_service.hpp | 144 +
ext/patches/boost/asio/detail/task_io_service.hpp | 203 +
.../asio/detail/task_io_service_operation.hpp | 78 +
.../asio/detail/task_io_service_thread_info.hpp | 42 +
ext/patches/boost/asio/detail/thread.hpp | 58 +
ext/patches/boost/asio/detail/thread_info_base.hpp | 93 +
ext/patches/boost/asio/detail/throw_error.hpp | 55 +
ext/patches/boost/asio/detail/throw_exception.hpp | 53 +
ext/patches/boost/asio/detail/timer_queue.hpp | 334 +
ext/patches/boost/asio/detail/timer_queue_base.hpp | 70 +
.../boost/asio/detail/timer_queue_ptime.hpp | 95 +
ext/patches/boost/asio/detail/timer_queue_set.hpp | 68 +
ext/patches/boost/asio/detail/timer_scheduler.hpp | 35 +
.../boost/asio/detail/timer_scheduler_fwd.hpp | 42 +
ext/patches/boost/asio/detail/tss_ptr.hpp | 71 +
ext/patches/boost/asio/detail/type_traits.hpp | 60 +
.../boost/asio/detail/variadic_templates.hpp | 63 +
ext/patches/boost/asio/detail/wait_handler.hpp | 85 +
ext/patches/boost/asio/detail/wait_op.hpp | 47 +
ext/patches/boost/asio/detail/weak_ptr.hpp | 40 +
ext/patches/boost/asio/detail/win_event.hpp | 128 +
.../boost/asio/detail/win_fd_set_adapter.hpp | 151 +
ext/patches/boost/asio/detail/win_fenced_block.hpp | 91 +
.../boost/asio/detail/win_iocp_handle_read_op.hpp | 111 +
.../boost/asio/detail/win_iocp_handle_service.hpp | 324 +
.../boost/asio/detail/win_iocp_handle_write_op.hpp | 103 +
.../boost/asio/detail/win_iocp_io_service.hpp | 317 +
.../boost/asio/detail/win_iocp_null_buffers_op.hpp | 121 +
.../boost/asio/detail/win_iocp_operation.hpp | 97 +
.../boost/asio/detail/win_iocp_overlapped_op.hpp | 90 +
.../boost/asio/detail/win_iocp_overlapped_ptr.hpp | 146 +
.../asio/detail/win_iocp_serial_port_service.hpp | 230 +
.../asio/detail/win_iocp_socket_accept_op.hpp | 167 +
.../asio/detail/win_iocp_socket_connect_op.hpp | 126 +
.../boost/asio/detail/win_iocp_socket_recv_op.hpp | 117 +
.../asio/detail/win_iocp_socket_recvfrom_op.hpp | 125 +
.../asio/detail/win_iocp_socket_recvmsg_op.hpp | 118 +
.../boost/asio/detail/win_iocp_socket_send_op.hpp | 111 +
.../boost/asio/detail/win_iocp_socket_service.hpp | 527 +
.../asio/detail/win_iocp_socket_service_base.hpp | 526 +
.../boost/asio/detail/win_iocp_thread_info.hpp | 36 +
ext/patches/boost/asio/detail/win_mutex.hpp | 80 +
.../asio/detail/win_object_handle_service.hpp | 185 +
ext/patches/boost/asio/detail/win_static_mutex.hpp | 76 +
ext/patches/boost/asio/detail/win_thread.hpp | 141 +
ext/patches/boost/asio/detail/win_tss_ptr.hpp | 81 +
ext/patches/boost/asio/detail/wince_thread.hpp | 118 +
.../boost/asio/detail/winrt_async_manager.hpp | 296 +
ext/patches/boost/asio/detail/winrt_async_op.hpp | 67 +
ext/patches/boost/asio/detail/winrt_resolve_op.hpp | 119 +
.../boost/asio/detail/winrt_resolver_service.hpp | 185 +
.../boost/asio/detail/winrt_socket_connect_op.hpp | 92 +
.../boost/asio/detail/winrt_socket_recv_op.hpp | 112 +
.../boost/asio/detail/winrt_socket_send_op.hpp | 103 +
.../boost/asio/detail/winrt_ssocket_service.hpp | 234 +
.../asio/detail/winrt_ssocket_service_base.hpp | 357 +
.../boost/asio/detail/winrt_timer_scheduler.hpp | 133 +
ext/patches/boost/asio/detail/winrt_utils.hpp | 108 +
ext/patches/boost/asio/detail/winsock_init.hpp | 130 +
ext/patches/boost/asio/detail/wrapped_handler.hpp | 293 +
ext/patches/boost/asio/error.hpp | 336 +
ext/patches/boost/asio/generic/basic_endpoint.hpp | 195 +
.../boost/asio/generic/datagram_protocol.hpp | 125 +
ext/patches/boost/asio/generic/detail/endpoint.hpp | 135 +
.../boost/asio/generic/detail/impl/endpoint.ipp | 111 +
ext/patches/boost/asio/generic/raw_protocol.hpp | 123 +
.../boost/asio/generic/seq_packet_protocol.hpp | 124 +
ext/patches/boost/asio/generic/stream_protocol.hpp | 129 +
ext/patches/boost/asio/handler_alloc_hook.hpp | 83 +
.../boost/asio/handler_continuation_hook.hpp | 56 +
ext/patches/boost/asio/handler_invoke_hook.hpp | 87 +
ext/patches/boost/asio/handler_type.hpp | 114 +
ext/patches/boost/asio/high_resolution_timer.hpp | 65 +
.../boost/asio/impl/buffered_read_stream.hpp | 360 +
.../boost/asio/impl/buffered_write_stream.hpp | 340 +
ext/patches/boost/asio/impl/connect.hpp | 430 +
ext/patches/boost/asio/impl/error.ipp | 130 +
ext/patches/boost/asio/impl/handler_alloc_hook.ipp | 79 +
ext/patches/boost/asio/impl/io_service.hpp | 156 +
ext/patches/boost/asio/impl/io_service.ipp | 157 +
ext/patches/boost/asio/impl/read.hpp | 755 +
ext/patches/boost/asio/impl/read_at.hpp | 812 +
ext/patches/boost/asio/impl/read_until.hpp | 1149 +
ext/patches/boost/asio/impl/serial_port_base.hpp | 61 +
ext/patches/boost/asio/impl/serial_port_base.ipp | 556 +
ext/patches/boost/asio/impl/spawn.hpp | 338 +
ext/patches/boost/asio/impl/src.cpp | 25 +
ext/patches/boost/asio/impl/src.hpp | 73 +
ext/patches/boost/asio/impl/use_future.hpp | 174 +
ext/patches/boost/asio/impl/write.hpp | 767 +
ext/patches/boost/asio/impl/write_at.hpp | 827 +
ext/patches/boost/asio/io_service.hpp | 772 +
ext/patches/boost/asio/ip/address.hpp | 202 +
ext/patches/boost/asio/ip/address_v4.hpp | 243 +
ext/patches/boost/asio/ip/address_v6.hpp | 248 +
ext/patches/boost/asio/ip/basic_endpoint.hpp | 265 +
ext/patches/boost/asio/ip/basic_resolver.hpp | 270 +
ext/patches/boost/asio/ip/basic_resolver_entry.hpp | 96 +
.../boost/asio/ip/basic_resolver_iterator.hpp | 262 +
ext/patches/boost/asio/ip/basic_resolver_query.hpp | 246 +
ext/patches/boost/asio/ip/detail/endpoint.hpp | 141 +
ext/patches/boost/asio/ip/detail/impl/endpoint.ipp | 206 +
ext/patches/boost/asio/ip/detail/socket_option.hpp | 571 +
ext/patches/boost/asio/ip/host_name.hpp | 44 +
ext/patches/boost/asio/ip/icmp.hpp | 117 +
ext/patches/boost/asio/ip/impl/address.hpp | 55 +
ext/patches/boost/asio/ip/impl/address.ipp | 228 +
ext/patches/boost/asio/ip/impl/address_v4.hpp | 55 +
ext/patches/boost/asio/ip/impl/address_v4.ipp | 180 +
ext/patches/boost/asio/ip/impl/address_v6.hpp | 55 +
ext/patches/boost/asio/ip/impl/address_v6.ipp | 300 +
ext/patches/boost/asio/ip/impl/basic_endpoint.hpp | 57 +
ext/patches/boost/asio/ip/impl/host_name.ipp | 56 +
ext/patches/boost/asio/ip/multicast.hpp | 193 +
ext/patches/boost/asio/ip/resolver_query_base.hpp | 132 +
ext/patches/boost/asio/ip/resolver_service.hpp | 178 +
ext/patches/boost/asio/ip/tcp.hpp | 157 +
ext/patches/boost/asio/ip/udp.hpp | 113 +
ext/patches/boost/asio/ip/unicast.hpp | 72 +
ext/patches/boost/asio/ip/v6_only.hpp | 71 +
ext/patches/boost/asio/is_read_buffered.hpp | 61 +
ext/patches/boost/asio/is_write_buffered.hpp | 61 +
ext/patches/boost/asio/local/basic_endpoint.hpp | 241 +
ext/patches/boost/asio/local/connect_pair.hpp | 106 +
ext/patches/boost/asio/local/datagram_protocol.hpp | 82 +
ext/patches/boost/asio/local/detail/endpoint.hpp | 135 +
.../boost/asio/local/detail/impl/endpoint.ipp | 130 +
ext/patches/boost/asio/local/stream_protocol.hpp | 92 +
ext/patches/boost/asio/placeholders.hpp | 125 +
ext/patches/boost/asio/posix/basic_descriptor.hpp | 492 +
.../boost/asio/posix/basic_stream_descriptor.hpp | 364 +
ext/patches/boost/asio/posix/descriptor_base.hpp | 99 +
ext/patches/boost/asio/posix/stream_descriptor.hpp | 39 +
.../boost/asio/posix/stream_descriptor_service.hpp | 262 +
ext/patches/boost/asio/raw_socket_service.hpp | 434 +
ext/patches/boost/asio/read.hpp | 633 +
ext/patches/boost/asio/read_at.hpp | 666 +
ext/patches/boost/asio/read_until.hpp | 925 +
.../boost/asio/seq_packet_socket_service.hpp | 382 +
ext/patches/boost/asio/serial_port.hpp | 38 +
ext/patches/boost/asio/serial_port_base.hpp | 169 +
ext/patches/boost/asio/serial_port_service.hpp | 255 +
ext/patches/boost/asio/signal_set.hpp | 30 +
ext/patches/boost/asio/signal_set_service.hpp | 136 +
ext/patches/boost/asio/socket_acceptor_service.hpp | 304 +
ext/patches/boost/asio/socket_base.hpp | 522 +
ext/patches/boost/asio/spawn.hpp | 267 +
ext/patches/boost/asio/ssl.hpp | 30 +
ext/patches/boost/asio/ssl/basic_context.hpp | 42 +
ext/patches/boost/asio/ssl/context.hpp | 789 +
ext/patches/boost/asio/ssl/context_base.hpp | 169 +
ext/patches/boost/asio/ssl/context_service.hpp | 42 +
.../asio/ssl/detail/buffered_handshake_op.hpp | 112 +
ext/patches/boost/asio/ssl/detail/engine.hpp | 166 +
ext/patches/boost/asio/ssl/detail/handshake_op.hpp | 70 +
ext/patches/boost/asio/ssl/detail/impl/engine.ipp | 328 +
.../boost/asio/ssl/detail/impl/openssl_init.ipp | 147 +
ext/patches/boost/asio/ssl/detail/io.hpp | 349 +
ext/patches/boost/asio/ssl/detail/openssl_init.hpp | 103 +
.../boost/asio/ssl/detail/openssl_types.hpp | 28 +
.../boost/asio/ssl/detail/password_callback.hpp | 74 +
ext/patches/boost/asio/ssl/detail/read_op.hpp | 75 +
ext/patches/boost/asio/ssl/detail/shutdown_op.hpp | 62 +
ext/patches/boost/asio/ssl/detail/stream_core.hpp | 128 +
.../boost/asio/ssl/detail/verify_callback.hpp | 70 +
ext/patches/boost/asio/ssl/detail/write_op.hpp | 75 +
ext/patches/boost/asio/ssl/error.hpp | 72 +
ext/patches/boost/asio/ssl/impl/context.hpp | 73 +
ext/patches/boost/asio/ssl/impl/context.ipp | 952 +
ext/patches/boost/asio/ssl/impl/error.ipp | 59 +
.../boost/asio/ssl/impl/rfc2818_verification.ipp | 168 +
ext/patches/boost/asio/ssl/impl/src.hpp | 28 +
ext/patches/boost/asio/ssl/old/basic_context.hpp | 436 +
ext/patches/boost/asio/ssl/old/context_service.hpp | 176 +
.../ssl/old/detail/openssl_context_service.hpp | 388 +
.../asio/ssl/old/detail/openssl_operation.hpp | 526 +
.../asio/ssl/old/detail/openssl_stream_service.hpp | 573 +
ext/patches/boost/asio/ssl/old/stream.hpp | 503 +
ext/patches/boost/asio/ssl/old/stream_service.hpp | 186 +
.../boost/asio/ssl/rfc2818_verification.hpp | 102 +
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src/util/GlobalParams.cpp | 197 +
src/util/GlobalParams.h | 97 +
src/util/MathUtil.cpp | 20 +
src/util/MathUtil.h | 15 +
src/util/Params.cpp | 2849 +
src/util/Params.h | 399 +
src/util/StringUtils.cpp | 139 +
src/util/StringUtils.h | 167 +
src/util/WinCrux.cpp | 193 +
src/util/WinCrux.h | 65 +
src/util/crux-utils.cpp | 1669 +
src/util/crux-utils.h | 483 +
src/util/linked_list.cpp | 370 +
src/util/linked_list.h | 145 +
src/util/mass.cpp | 307 +
src/util/mass.h | 132 +
src/util/modifications.cpp | 993 +
src/util/modifications.h | 419 +
src/util/peptide_modifications.cpp | 814 +
src/util/peptide_modifications.h | 160 +
src/util/utils.cpp | 469 +
src/util/utils.h | 247 +
src/util/windirent.h | 369 +
1273 files changed, 685777 insertions(+), 79 deletions(-)
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..72c573e
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,5 @@
+Crux was developed in the Department of Genome Sciences at the
+University of Washington under the leadership of Dr. William S. Noble
+and guidance of Dr. Michael J. MacCoss. For a detailed list of Crux
+contributors, see doc/user/contributors.html.
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..4c43f82
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,163 @@
+project(crux)
+cmake_minimum_required(VERSION 2.8.4)
+cmake_policy(VERSION 2.8.4)
+
+set (CRUX_VERSION_MAJOR "3")
+set (CRUX_VERSION_MINOR "1")
+set (CRUX_VERSION ${CRUX_VERSION_MAJOR}.${CRUX_VERSION_MINOR})
+
+message(
+ "-- Creating build files for Crux ${CRUX_VERSION} for system ${CMAKE_SYSTEM} "
+ "(short name ${CMAKE_SYSTEM_NAME})"
+)
+
+add_subdirectory(doc/user)
+add_subdirectory(ext)
+add_subdirectory(src)
+
+# Only process smoke tests directory if it exiists
+if (EXISTS "${CMAKE_SOURCE_DIR}/test/smoke-tests/runall")
+ add_subdirectory(test/smoke-tests)
+endif (EXISTS "${CMAKE_SOURCE_DIR}/test/smoke-tests/runall")
+
+# Only process performance tests directory if it exiists
+if (EXISTS "${CMAKE_SOURCE_DIR}/test/performance-tests/runall")
+ add_subdirectory(test/performance-tests)
+endif (EXISTS "${CMAKE_SOURCE_DIR}/test/performance-tests/runall")
+
+install(FILES license.txt DESTINATION .)
+
+add_custom_target(
+ deep-clean
+ COMMAND ${CMAKE_COMMAND} --build . --target clean
+ COMMAND ${CMAKE_COMMAND} -E remove CMakeCache.txt
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/build
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/downloads
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/include/CometSearch
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/include/MSToolkit
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/include/boost
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/include/gflags-2.1.2
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/include/google
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/include/pwiz
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/include/xercesc
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/include/xsd
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/lib/pkgconfig
+ COMMAND ${CMAKE_COMMAND} -E remove ext/lib/*.a
+ COMMAND ${CMAKE_COMMAND} -E remove ext/lib/*.la
+ COMMAND ${CMAKE_COMMAND} -E remove ext/lib/*.lib
+ COMMAND ${CMAKE_COMMAND} -E remove_directory ext/share
+ COMMENT "Cleaning project tree."
+ COMMENT "Deleting all files for external tools."
+)
+
+add_custom_target(
+ externals-only
+ COMMAND ${CMAKE_MAKE_PROGRAM}
+ WORKING_DIRECTORY ext
+ COMMENT "Building only external dependendcies."
+)
+
+add_custom_target(
+ no-externals
+ COMMAND ${CMAKE_MAKE_PROGRAM} crux xlink-score-spectrum xlink-assign-ions
+ WORKING_DIRECTORY src
+ COMMENT "Not building external dependendcies."
+)
+
+# a custom target for obtaining the SVN revision number
+add_custom_target(crux_version ALL DEPENDS crux_version_header )
+
+# creates crux_version.h using cmake script
+add_custom_command(
+ OUTPUT crux_version_header
+ ${CMAKE_CURRENT_BINARY_DIR}/crux_version.h
+ COMMAND
+ ${CMAKE_COMMAND}
+ -DSOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}
+ -DCRUX_VERSION=${CRUX_VERSION}
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/make-version-header.cmake
+)
+
+add_dependencies(barista comet)
+add_dependencies(bullseye hardklor)
+add_dependencies(comet ProteoWizard)
+add_dependencies(crux barista)
+add_dependencies(crux bullseye)
+add_dependencies(crux crux-support)
+add_dependencies(crux hardklor)
+add_dependencies(crux percolator)
+add_dependencies(crux tide-support)
+add_dependencies(crux xlink)
+add_dependencies(crux-support crux_version)
+add_dependencies(crux-support percolator)
+add_dependencies(hardklor comet)
+add_dependencies(percolator comet)
+add_dependencies(tide-support comet)
+add_dependencies(tide-support protobuf-2.5.0)
+add_dependencies(tide-support gflags-2.1.2)
+add_dependencies(xlink comet)
+add_dependencies(xlink percolator)
+add_dependencies(xlink ProteoWizard)
+add_dependencies(create-docs crux)
+
+# build a CPack driven installer package
+include (InstallRequiredSystemLibraries)
+
+if (WIN32 AND NOT CYGWIN)
+ # If windows build we need to select 32/64 bit platform
+ if (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ SET(BUILD_PROCESSOR "AMD64")
+ else (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ SET(BUILD_PROCESSOR "i386")
+ endif (CMAKE_GENERATOR MATCHES "^.*Win64$")
+else (WIN32 AND NOT CYGWIN)
+ SET(BUILD_PROCESSOR ${CMAKE_SYSTEM_PROCESSOR})
+endif (WIN32 AND NOT CYGWIN)
+
+set (CPACK_GENERATOR ZIP)
+set (CPACK_SOURCE_GENERATOR TGZ)
+set (CPACK_PACKAGE_VERSION_MAJOR ${CRUX_VERSION_MAJOR})
+set (CPACK_PACKAGE_VERSION_MINOR ${CRUX_VERSION_MINOR})
+set (CRUX_VERSION ${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR})
+set(CPACK_PACKAGE_FILE_NAME
+ ${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CMAKE_SYSTEM_NAME}.${BUILD_PROCESSOR})
+set(CPACK_SOURCE_PACKAGE_FILE_NAME
+ "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.Source")
+set (
+ CPACK_SOURCE_IGNORE_FILES
+ /\\\\..*$;
+ \\\\./_CPack_Packages/;
+ /benchmark/;
+ /bin/;
+ /results/;
+ /doc/developer/;
+ /doc/guispec/;
+ /doc/mods/;
+ /doc/user/download/;
+ /doc/user/open_source_download/;
+ /test/;
+ /src/CruxGui/;
+ /ext/bin/;
+ /ext/build/;
+ /ext/downloads/;
+ /ext/include/;
+ /ext/lib/;
+ /ext/share/;
+ /src/python/;
+ /CMakeCache.txt$;
+ /CMakeFiles/;
+ \\\\.gz$;
+ \\\\.swp$;
+ \\\\.zip$;
+ ${CPACK_SOURCE_IGNORE_FILES}
+)
+
+# Generate checksum files for binary and source packages.
+add_custom_target(
+ checksum
+ COMMAND ${CMAKE_COMMAND} -E md5sum ${CPACK_PACKAGE_FILE_NAME}.zip > ${CPACK_PACKAGE_FILE_NAME}.zip.md5sum.txt
+ COMMAND ${CMAKE_COMMAND} -E md5sum ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz > ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz.md5sum.txt
+ COMMENT "Creating checksum files."
+)
+
+include (CPack)
diff --git a/COPYRIGHT b/COPYRIGHT
new file mode 100644
index 0000000..6f01e99
--- /dev/null
+++ b/COPYRIGHT
@@ -0,0 +1 @@
+Crux is Copyright 2007-2016 University of Washington
diff --git a/CPackConfig.cmake b/CPackConfig.cmake
new file mode 100644
index 0000000..63d9364
--- /dev/null
+++ b/CPackConfig.cmake
@@ -0,0 +1,68 @@
+# This file will be configured to contain variables for CPack. These variables
+# should be set in the CMake list file of the project before CPack module is
+# included. The list of available CPACK_xxx variables and their associated
+# documentation may be obtained using
+# cpack --help-variable-list
+#
+# Some variables are common to all generators (e.g. CPACK_PACKAGE_NAME)
+# and some are specific to a generator
+# (e.g. CPACK_NSIS_EXTRA_INSTALL_COMMANDS). The generator specific variables
+# usually begin with CPACK_<GENNAME>_xxxx.
+
+
+SET(CPACK_BINARY_BUNDLE "")
+SET(CPACK_BINARY_CYGWIN "")
+SET(CPACK_BINARY_DEB "")
+SET(CPACK_BINARY_DRAGNDROP "")
+SET(CPACK_BINARY_NSIS "")
+SET(CPACK_BINARY_OSXX11 "")
+SET(CPACK_BINARY_PACKAGEMAKER "")
+SET(CPACK_BINARY_RPM "")
+SET(CPACK_BINARY_STGZ "")
+SET(CPACK_BINARY_TBZ2 "")
+SET(CPACK_BINARY_TGZ "")
+SET(CPACK_BINARY_TZ "")
+SET(CPACK_BINARY_WIX "")
+SET(CPACK_BINARY_ZIP "")
+SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
+SET(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
+SET(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
+SET(CPACK_GENERATOR "ZIP")
+SET(CPACK_INSTALL_CMAKE_PROJECTS "/data/TeamCity/buildAgent/work/779d99b0241b2175;crux;ALL;/")
+SET(CPACK_INSTALL_PREFIX "/usr/local")
+SET(CPACK_MODULE_PATH "")
+SET(CPACK_NSIS_DISPLAY_NAME "crux 3.1.1")
+SET(CPACK_NSIS_INSTALLER_ICON_CODE "")
+SET(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
+SET(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
+SET(CPACK_NSIS_PACKAGE_NAME "crux 3.1.1")
+SET(CPACK_OUTPUT_CONFIG_FILE "/data/TeamCity/buildAgent/work/779d99b0241b2175/CPackConfig.cmake")
+SET(CPACK_PACKAGE_DEFAULT_LOCATION "/")
+SET(CPACK_PACKAGE_DESCRIPTION_FILE "/net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/share/cmake-2.8/Templates/CPack.GenericDescription.txt")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "crux built using CMake")
+SET(CPACK_PACKAGE_FILE_NAME "crux-3.1.Linux.x86_64")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "crux 3.1.1")
+SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "crux 3.1.1")
+SET(CPACK_PACKAGE_NAME "crux")
+SET(CPACK_PACKAGE_RELOCATABLE "true")
+SET(CPACK_PACKAGE_VENDOR "Humanity")
+SET(CPACK_PACKAGE_VERSION "3.1.1")
+SET(CPACK_PACKAGE_VERSION_MAJOR "3")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_RESOURCE_FILE_LICENSE "/net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/share/cmake-2.8/Templates/CPack.GenericLicense.txt")
+SET(CPACK_RESOURCE_FILE_README "/net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/share/cmake-2.8/Templates/CPack.GenericDescription.txt")
+SET(CPACK_RESOURCE_FILE_WELCOME "/net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/share/cmake-2.8/Templates/CPack.GenericWelcome.txt")
+SET(CPACK_SET_DESTDIR "OFF")
+SET(CPACK_SOURCE_CYGWIN "")
+SET(CPACK_SOURCE_GENERATOR "TGZ")
+SET(CPACK_SOURCE_IGNORE_FILES "/\\..*$;\\./_CPack_Packages/;/benchmark/;/bin/;/results/;/doc/developer/;/doc/guispec/;/doc/mods/;/doc/user/download/;/doc/user/open_source_download/;/test/;/src/CruxGui/;/ext/bin/;/ext/build/;/ext/downloads/;/ext/include/;/ext/lib/;/ext/share/;/src/python/;/CMakeCache.txt$;/CMakeFiles/;\\.gz$;\\.swp$;\\.zip$")
+SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/data/TeamCity/buildAgent/work/779d99b0241b2175/CPackSourceConfig.cmake")
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "crux-3.1.Source")
+SET(CPACK_SOURCE_TBZ2 "")
+SET(CPACK_SOURCE_TGZ "")
+SET(CPACK_SOURCE_TZ "")
+SET(CPACK_SOURCE_ZIP "")
+SET(CPACK_SYSTEM_NAME "Linux")
+SET(CPACK_TOPLEVEL_TAG "Linux")
+SET(CPACK_WIX_SIZEOF_VOID_P "8")
diff --git a/CPackSourceConfig.cmake b/CPackSourceConfig.cmake
new file mode 100644
index 0000000..6e99ba6
--- /dev/null
+++ b/CPackSourceConfig.cmake
@@ -0,0 +1,73 @@
+# This file will be configured to contain variables for CPack. These variables
+# should be set in the CMake list file of the project before CPack module is
+# included. The list of available CPACK_xxx variables and their associated
+# documentation may be obtained using
+# cpack --help-variable-list
+#
+# Some variables are common to all generators (e.g. CPACK_PACKAGE_NAME)
+# and some are specific to a generator
+# (e.g. CPACK_NSIS_EXTRA_INSTALL_COMMANDS). The generator specific variables
+# usually begin with CPACK_<GENNAME>_xxxx.
+
+
+SET(CPACK_BINARY_BUNDLE "")
+SET(CPACK_BINARY_CYGWIN "")
+SET(CPACK_BINARY_DEB "")
+SET(CPACK_BINARY_DRAGNDROP "")
+SET(CPACK_BINARY_NSIS "")
+SET(CPACK_BINARY_OSXX11 "")
+SET(CPACK_BINARY_PACKAGEMAKER "")
+SET(CPACK_BINARY_RPM "")
+SET(CPACK_BINARY_STGZ "")
+SET(CPACK_BINARY_TBZ2 "")
+SET(CPACK_BINARY_TGZ "")
+SET(CPACK_BINARY_TZ "")
+SET(CPACK_BINARY_WIX "")
+SET(CPACK_BINARY_ZIP "")
+SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
+SET(CPACK_COMPONENT_UNSPECIFIED_HIDDEN "TRUE")
+SET(CPACK_COMPONENT_UNSPECIFIED_REQUIRED "TRUE")
+SET(CPACK_GENERATOR "TGZ")
+SET(CPACK_IGNORE_FILES "/\\..*$;\\./_CPack_Packages/;/benchmark/;/bin/;/results/;/doc/developer/;/doc/guispec/;/doc/mods/;/doc/user/download/;/doc/user/open_source_download/;/test/;/src/CruxGui/;/ext/bin/;/ext/build/;/ext/downloads/;/ext/include/;/ext/lib/;/ext/share/;/src/python/;/CMakeCache.txt$;/CMakeFiles/;\\.gz$;\\.swp$;\\.zip$")
+SET(CPACK_INSTALLED_DIRECTORIES "/data/TeamCity/buildAgent/work/779d99b0241b2175;/")
+SET(CPACK_INSTALL_CMAKE_PROJECTS "")
+SET(CPACK_INSTALL_PREFIX "/usr/local")
+SET(CPACK_MODULE_PATH "")
+SET(CPACK_NSIS_DISPLAY_NAME "crux 3.1.1")
+SET(CPACK_NSIS_INSTALLER_ICON_CODE "")
+SET(CPACK_NSIS_INSTALLER_MUI_ICON_CODE "")
+SET(CPACK_NSIS_INSTALL_ROOT "$PROGRAMFILES")
+SET(CPACK_NSIS_PACKAGE_NAME "crux 3.1.1")
+SET(CPACK_OUTPUT_CONFIG_FILE "/data/TeamCity/buildAgent/work/779d99b0241b2175/CPackConfig.cmake")
+SET(CPACK_PACKAGE_DEFAULT_LOCATION "/")
+SET(CPACK_PACKAGE_DESCRIPTION_FILE "/net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/share/cmake-2.8/Templates/CPack.GenericDescription.txt")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "crux built using CMake")
+SET(CPACK_PACKAGE_FILE_NAME "crux-3.1.Source")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "crux 3.1.1")
+SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "crux 3.1.1")
+SET(CPACK_PACKAGE_NAME "crux")
+SET(CPACK_PACKAGE_RELOCATABLE "true")
+SET(CPACK_PACKAGE_VENDOR "Humanity")
+SET(CPACK_PACKAGE_VERSION "3.1.1")
+SET(CPACK_PACKAGE_VERSION_MAJOR "3")
+SET(CPACK_PACKAGE_VERSION_MINOR "1")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_RESOURCE_FILE_LICENSE "/net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/share/cmake-2.8/Templates/CPack.GenericLicense.txt")
+SET(CPACK_RESOURCE_FILE_README "/net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/share/cmake-2.8/Templates/CPack.GenericDescription.txt")
+SET(CPACK_RESOURCE_FILE_WELCOME "/net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/share/cmake-2.8/Templates/CPack.GenericWelcome.txt")
+SET(CPACK_SET_DESTDIR "OFF")
+SET(CPACK_SOURCE_CYGWIN "")
+SET(CPACK_SOURCE_GENERATOR "TGZ")
+SET(CPACK_SOURCE_IGNORE_FILES "/\\..*$;\\./_CPack_Packages/;/benchmark/;/bin/;/results/;/doc/developer/;/doc/guispec/;/doc/mods/;/doc/user/download/;/doc/user/open_source_download/;/test/;/src/CruxGui/;/ext/bin/;/ext/build/;/ext/downloads/;/ext/include/;/ext/lib/;/ext/share/;/src/python/;/CMakeCache.txt$;/CMakeFiles/;\\.gz$;\\.swp$;\\.zip$")
+SET(CPACK_SOURCE_INSTALLED_DIRECTORIES "/data/TeamCity/buildAgent/work/779d99b0241b2175;/")
+SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "/data/TeamCity/buildAgent/work/779d99b0241b2175/CPackSourceConfig.cmake")
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "crux-3.1.Source")
+SET(CPACK_SOURCE_TBZ2 "")
+SET(CPACK_SOURCE_TGZ "")
+SET(CPACK_SOURCE_TOPLEVEL_TAG "Linux-Source")
+SET(CPACK_SOURCE_TZ "")
+SET(CPACK_SOURCE_ZIP "")
+SET(CPACK_STRIP_FILES "")
+SET(CPACK_SYSTEM_NAME "Linux")
+SET(CPACK_TOPLEVEL_TAG "Linux-Source")
+SET(CPACK_WIX_SIZEOF_VOID_P "8")
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 0000000..f0a6721
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,34 @@
+Full directions for installing Crux can be found in doc/users/install-tutorial.html.
+
+Building Crux from source requires a C++ compiler and standard libraries. It
+also requires the programs 'cmake' and 'svn'. To build Crux from a source
+distribution or a copy checked out from the SVN repository:
+
+1. Run 'cmake .'. This generates all the final 'Makefile' from the 'CMakeLists.txt'.
+ See text below for a description of some useful 'cmake' options.
+2. Run 'make'. This will build Crux. Crux depends on the Proteowizard libraries
+ (http://proteowizard.sourceforge.net). These will automatically be obtained
+ from the Proteowizard SVN repository.
+3. Run 'make install'.
+
+The 'cmake' program accepts several command line options. These are described
+in the CMake documentation, available at http://www.cmake.org. Three of the
+most useful options are described below.
+
+By default CMake will install Crux in /usr/local. To specify a different
+installation directory use:
+
+cmake -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+
+where you should replace '<install directory>' with the full path to the
+root directory where Crux should be installed.
+
+By default CMake will perform a non-debug build of Crux. To turn on debugging
+symbols use:
+
+cmake -DCMAKE_BUILD_TYPE=Debug .
+
+By default CMake will hide most of the processing messages from the compiler
+and linker. To turn on 'verbose' messages use:
+
+cmake -DCMAKE_VERBOSE_MAKEFILE=ON .
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..d76e09d
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,472 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+# A target that is always out of date.
+cmake_force:
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake
+
+# The command to remove a file.
+RM = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -E remove -f
+
+# Escaping for special characters.
+EQUALS = =
+
+# The program to use to edit the cache.
+CMAKE_EDIT_COMMAND = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+#=============================================================================
+# Targets provided globally by CMake.
+
+# Special rule for the target edit_cache
+edit_cache:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake cache editor..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : edit_cache
+
+# Special rule for the target edit_cache
+edit_cache/fast: edit_cache
+.PHONY : edit_cache/fast
+
+# Special rule for the target install
+install: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -P cmake_install.cmake
+.PHONY : install
+
+# Special rule for the target install
+install/fast: preinstall/fast
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -P cmake_install.cmake
+.PHONY : install/fast
+
+# Special rule for the target install/local
+install/local: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local
+
+# Special rule for the target install/local
+install/local/fast: install/local
+.PHONY : install/local/fast
+
+# Special rule for the target install/strip
+install/strip: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
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+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/assign-confidence.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/assign-confidence.html
new file mode 100644
index 0000000..8249447
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/assign-confidence.html
@@ -0,0 +1,147 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>assign-confidence</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>assign-confidence</h1>
+<h2>Usage:</h2>
+<p><code>crux assign-confidence [options] <target input>+</code></p>
+<h2>Description:</h2>
+<p>Given target and decoy scores, estimate a q-value for each target score. The q-value is analogous to a p-value but incorporates false discovery rate multiple testing correction. The q-value associated with a score threshold T is defined as the minimal false discovery rate (FDR) at which a score of T is deemed significant. In this setting, the q-value accounts for the fact that we are analyzing a large collection of scores. For confidence estimation afficionados, please note that this [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>target input+</code> – One or more files, each containing a collection of peptide-spectrum matches (PSMs) in <a href="../file-formats/txt-format.html">tab-delimited text</a>, <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">PepXML</a>, or <a href="http://www.psidev.info/mzidentml">mzIdentML</a> format. In tab-delimited text format, only the specified score column is required. However if --estimation-method is tdc, then the columns "scan" and [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>assign-confidence.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> that contains the targets, sorted by score. The file will contain one new column, named "<method> q-value", where <method> is either "tdc" or "mix-max".</li>
+ <li><code>assign-confidence.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>assign-confidence.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>assign-confidence options</h3>
+<ul>
+ <li class="nobullet"><code>--estimation-method mix-max|tdc|peptide-level</code> – Specify the method used to estimate q-values. The mix-max procedure or target-decoy competition apply to PSMs. The peptide-level option eliminates any PSM for which there exists a better scoring PSM involving the same peptide, and then uses decoys to assign confidence estimates. Default = <code>tdc</code>.</li>
+ <li class="nobullet"><code>--score <string></code> – Specify the column (for tab-delimited input) or tag (for XML input) used as input to the q-value estimation procedure. If this parameter is unspecified, then the program searches for "xcorr score", "evalue" (comet), "exact p-value" score fields in this order in the input file. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--sidak T|F</code> – Adjust the score using the Sidak adjustment and reports them in a new column in the output file. Note that this adjustment only makes sense if the given scores are p-values, and that it requires the presence of the "distinct matches/spectrum" feature for each PSM. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-charge-states T|F</code> – Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-modified-peptides T|F</code> – Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/barista.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/barista.html
new file mode 100644
index 0000000..f5b1d92
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/barista.html
@@ -0,0 +1,163 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>barista</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>barista</h1>
+<h2>Usage:</h2>
+<p><code>crux barista [options] <database> <fragmentation spectra> <search results></code></p>
+<h2>Description:</h2>
+<p>Barista is a protein identification algorithm that combines two different tasks–peptide-spectrum match (PSM) verification and protein inference–into a single learning algorithm. The program requires three inputs: a set of MS2 spectra, a protein database, and the results of searching the spectra against the database. Barista produces as output three ranked lists of proteins, peptides and PSMs, based on how likely the proteins and peptides are to be present in the sample and [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>database</code> – The program requires the FASTA format protein database files against which the search was performed. The protein database input may be a concatenated database or separate target and decoy databases; the latter is supported with the --separate-searches option, described below. In either case, Barista distinguishes between target and decoy proteins based on the presence of a decoy prefix on the sequence identifiers (see the --decoy-prefix option, below). [...]
+ <li><code>fragmentation spectra</code> – The fragmentation spectra must be provided in <a href="../file-formats/ms2-format.html">MS2</a>, mzXML, or MGF format.</li>
+ <li><code>search results</code> – Search results in the <a href="../file-formats/txt-format.html">tab-delimited text format</a> produced by Crux or in <a href="../file-formats/sqt-format.html">SQT format</a>. Like the spectra, the search results can be provided as a single file, a list of files or a directory of files. Note, however, that the input mode for spectra and for search results must be the same; i.e., if you provide a list of files for the spectra, then you must also pr [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>barista.xml</code> – an <a href="../file-formats/barista-xml-format.html">XML file</a> that contains four information about proteins, subset proteins, peptides, and PSMs.</li>
+ <li><code>barista.target.proteins.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited file</a> containing a ranked list of groups of indistinguishable target proteins with associated Barista scores and q-values and with peptides that contributed to the identification of the protein group.</li>
+ <li><code>barista.target.subset-proteins.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited file</a> containing groups of indistinguishable proteins.</li>
+ <li><code>barista.target.peptides.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited file</a> containing a ranked list of target peptides with the associated Barista scores and q-values.</li>
+ <li><code>barista.target.psm.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited file format</a> containing a ranked list of target peptide-spectrum matches with the associated Barista scores and q-values.</li>
+ <li><code>barista.log.txt</code> – a file where the program reports its progress.</li>
+ <li><code>barista.params.txt</code> – a file with the values of all the options given to the current run.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>barista options</h3>
+<ul>
+ <li class="nobullet"><code>--separate-searches <string></code> – If the target and decoy searches were run separately, rather than using a concatenated database, then the program will assume that the database search results provided as a required argument are from the target database search. This option then allows the user to specify the location of the decoy search results. Like the required arguments, these search results can be provided as a single file, a list of files [...]
+ <li class="nobullet"><code>--skip-cleanup T|F</code> – Analysis begins with a pre-processsing step that creates a set of lookup tables which are then used during training. Normally, these lookup tables are deleted at the end of the analysis, but setting this option to T prevents the deletion of these tables. Subsequently, analyses can be repeated more efficiently by specifying the --re-run option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--re-run <string></code> – Re-run a previous analysis using a previously computed set of lookup tables. For this option to work, the --skip-cleanup option must have been set to true when the program was run the first time. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--use-spec-features T|F</code> – Use an enriched feature set, including separate features for each ion type. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--optimization protein|peptide|psm</code> – Specifies whether to do optimization at the protein, peptide or psm level. Default = <code>protein</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-out T|F</code> – Output the computed features in <a href="../file-formats/features.html">tab-delimited text format</a>. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/bullseye.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/bullseye.html
new file mode 100644
index 0000000..e73bf1e
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/bullseye.html
@@ -0,0 +1,158 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>bullseye</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
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+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>bullseye</h1>
+<h2>Usage:</h2>
+<p><code>crux bullseye [options] <MS1 spectra> <MS2 spectra></code></p>
+<h2>Description:</h2>
+<p>Bullseye assigns high resolution precursor m/z values to fragmentation (MS2) spectra. Bullseye uses the Hardklör algorithm to identify persistent isotope distributions (PPIDs) in precursor (MS1) scans. For each PPID, MS2 scans that occur within a specified time and m/z range are assigned the average monoisotopic m/z from the PPID assigned as the precursor m/z. A detailed description of the Bullseye algorithm is given in </p><quote>Hsieh EJ, Hoopmann MR, Maclean B, MacCoss MJ. <a [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>MS1 spectra</code> – The name of a file from which to parse high-resolution spectra of intact peptides. The file may be in MS1 (.ms1), binary MS1 (.bms1), compressed MS1 (.cms1), or mzXML (.mzXML) format. Bullseye will search for PPIDs in these spectra.</li>
+ <li><code>MS2 spectra</code> – The name of a file from which to parse peptide fragmentation spectra. The file may be in MS2 (.ms2), binary MS2 (.bms2), compressed MS2 (.cms2) or mzXML (.mzXML) format. Bullseye will assign high-resolution precursor masses to these spectra.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>bullseye.pid.<format></code> – a file containing the fragmentation spectra for which accurate masses were successfully inferred. Unless otherwise specified (with the --spectrum-format option), the output file format is ".ms2". Note that if the output format is ".ms2," then a single spectrum may have multiple "Z" lines, each indicating a charge state and accurate mass. In addition, Bullseye inserts an "I" line (for charge-dependent analysis) corresponding to each "Z" lin [...]
+ <li><code>bullseye.no-pid.<format></code> – a file containing the fragmentation spectra for which accurate masses were not inferred.</li>
+ <li><code>hardklor.mono.txt</code> – a tab-delimited text file containing one line for each isotope distribution, as described <a href="hardklor.html">here</a>.</li>
+ <li><code>bullseye.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>bullseye.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Identifying PPIDs in MS1 spectra</h3>
+<ul>
+ <li class="nobullet"><code>--max-persist <float></code> – Ignore PPIDs that persist for longer than this length of time in the MS1 spectra. The unit of time is whatever unit is used in your data file (usually minutes). These PPIDs are considered contaminants. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--persist-tolerance <float></code> – Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--gap-tolerance <integer></code> – Allowed gap size when checking for PPIDs across consecutive MS1 scans. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--scan-tolerance <integer></code> – Total number of MS1 scans over which a PPID must be observed to be considered real. Gaps in persistence are allowed by setting --gap-tolerance. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--bullseye-max-mass <float></code> – Only consider PPIDs below this maximum mass in daltons. Default = <code>8000</code>.</li>
+ <li class="nobullet"><code>--bullseye-min-mass <float></code> – Only consider PPIDs above this minimum mass in daltons. Default = <code>600</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Matching PPIDs to MS2 spectra</h3>
+<ul>
+ <li class="nobullet"><code>--exact-match T|F</code> – When true, require an exact match (as defined by --exact-tolerance) between the center of the precursor isolation window in the MS2 scan and the base isotopic peak of the PPID. If this option is set to false and no exact match is observed, then attempt to match using a wider m/z tolerance. This wider tolerance is calculated using the PPID's monoisotopic mass and charge (the higher the charge, the smaller the window). Default = [...]
+ <li class="nobullet"><code>--exact-tolerance <float></code> – Set the tolerance (+/-ppm) for --exact-match. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--retention-tolerance <float></code> – Set the tolerance (+/-units) around the retention time over which a PPID can be matches to the MS2 spectrum. The unit of time is whatever unit is used in your data file (usually minutes). Default = <code>0.5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--spectrum-format |ms2|bms2|cms2|mgf</code> – The format to write the output spectra to. If empty, the spectra will be output in the same format as the MS2 input. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
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+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
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+<!DOCTYPE html>
+<html>
+<head>
+<title>cascade-search</title>
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+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
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+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>cascade-search</h1>
+<h2>Usage:</h2>
+<p><code>crux cascade-search [options] <tide spectra file>+ <database-series></code></p>
+<h2>Description:</h2>
+<p>Cascade-search is a general procedure for incorporating information about peptide groups into the database search and confidence estimation procedure. Peptides may be grouped according to, for example, their enzymatic properties (zero, one, or two enzymatic termini) or the presence of different types of numbers of variable modifications. The algorithm works on a series of databases, each corresponding to a different peptide group. The database is searched in series, and after each sea [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>tide spectra file+</code> – The name of one or more files from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard. Alternatively, the argument may be one or more binary spectrum files produced by a previous run of crux tide-search using the store-spectra parameter.</li>
+ <li><code>database-series</code> – A comma-separated list of databases, each generated by tide-index. Cascade-search will search the given spectra against these databases in the given order.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>cascade-search.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> containing the target PSMs accepted at a pre-defined fdr.</li>
+ <li><code>cascade-search.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>cascade-search.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>cascade-search options</h3>
+<ul>
+ <li class="nobullet"><code>--q-value-threshold <float></code> – The q-value threshold used by cascade search. Each spectrum identified in one search with q-value less than this threshold will be excluded from all subsequent searches. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--estimation-method mix-max|tdc|peptide-level</code> – Specify the method used to estimate q-values. The mix-max procedure or target-decoy competition apply to PSMs. The peptide-level option eliminates any PSM for which there exists a better scoring PSM involving the same peptide, and then uses decoys to assign confidence estimates. Default = <code>tdc</code>.</li>
+ <li class="nobullet"><code>--score <string></code> – Specify the column (for tab-delimited input) or tag (for XML input) used as input to the q-value estimation procedure. If this parameter is unspecified, then the program searches for "xcorr score", "evalue" (comet), "exact p-value" score fields in this order in the input file. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--sidak T|F</code> – Adjust the score using the Sidak adjustment and reports them in a new column in the output file. Note that this adjustment only makes sense if the given scores are p-values, and that it requires the presence of the "distinct matches/spectrum" feature for each PSM. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-charge-states T|F</code> – Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-modified-peptides T|F</code> – Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Precursor selection</h3>
+<ul>
+ <li class="nobullet"><code>--precursor-window <float></code> – Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto-precursor-window false|warn|fail</code> – Automatically estimate optimal value for the precursor-window parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> – Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not avail [...]
+ <li class="nobullet"><code>--max-precursor-charge <integer></code> – The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-min-mz <float></code> – The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum-max-mz <float></code> – The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
+ <li class="nobullet"><code>--min-peaks <integer></code> – The minimum number of peaks a spectrum must have for it to be searched. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--spectrum-charge 1|2|3|all</code> – The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge state will be searched. Default = <code>all</code>.</li>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--compute-sp T|F</code> – Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spe [...]
+ <li class="nobullet"><code>--remove-precursor-peak T|F</code> – If true, all peaks around the precursor m/z will be removed, within a range specified by the --remove-precursor-tolerance option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--exact-p-value T|F</code> – Enable the calculation of exact p-values for the XCorr score as described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this article</a>. Calculation of p-values increases the running time but increases the number of identifications at a fixed confidence threshold. The p-values will be reported in a new column with header "exact p-value", and the "xcorr score" column will be replaced with a "refactored xcorr" colu [...]
+ <li class="nobullet"><code>--use-neutral-loss-peaks T|F</code> – Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+ <li class="nobullet"><code>--auto-mz-bin-width false|warn|fail</code> – Automatically estimate optimal value for the mz-bin-width parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-offset <float></code> – In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--peptide-centric-search T|F</code> – Carries out a peptide-centric search. For each peptide the top-scoring spectra are reported, in contrast to the standard spectrum-centric search where the top-scoring peptides are reported. Note that in this case the "xcorr rank" column will contain the rank of the given spectrum with respect to the given candidate peptide, rather than vice versa (which is the default). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--isotope-error <string></code> – List of positive, non-zero integers. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--skip-preprocessing T|F</code> – Skip preprocessing steps on spectra. Default = F. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>CPU threads</h3>
+<ul>
+ <li class="nobullet"><code>--num-threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--store-spectra <string></code> – Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir). This option is not valid if multiple input spectrum files are given. Default = <code><e [...]
+ <li class="nobullet"><code>--store-index <string></code> – When providing a FASTA file as the index, the generated binary index will be stored at the given path. This option has no effect if a binary index is provided as the index. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--concat T|F</code> – When set to T, target and decoy search results are reported in a single file, and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--print-search-progress <integer></code> – Show search progress by printing every n spectra searched. Set to 0 to show no search progress. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--sqt-output T|F</code> – Outputs an SQT results file to the output directory. Note that if sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mzid-output T|F</code> – Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pin-output T|F</code> – Output a Percolator input (PIN) file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--file-column T|F</code> – Include the file column in tab-delimited output. Default = <code>true</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/cmake_install.cmake b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/cmake_install.cmake
new file mode 100644
index 0000000..f038400
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/cmake_install.cmake
@@ -0,0 +1,38 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/doc/user
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+ FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/doc" TYPE DIRECTORY FILES "/data/TeamCity/buildAgent/work/779d99b0241b2175/doc/user/." REGEX "/CMakeLists\\.txt$" EXCLUDE REGEX "/download$" EXCLUDE)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/activation_method.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/activation_method.html
new file mode 100644
index 0000000..f21a03d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/activation_method.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: activation_method</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: activation_method</h2>
+
+ <ul>
+ <li>This parameter specifies which scan types are searched.
+ <li>If "ALL" is specified, no filtering based on the activation method
+ is applied.
+ <li>If any other allowed entry is chosen, only spectra with activation
+ method matching the specified entry are searched.
+ <li>This parameter is valid only for mzXML, mzML and mz5 input.
+ <li>Allowed values are: ALL, CID, ECD, ETD, PQD, HCD, IRMPD
+ <li>The default value is "ALL" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>activation_method = ALL</tt>
+ <br><tt>activation_method = CID</tt>
+ <br><tt>activation_method = ETD</tt>
+ <br><tt>activation_method = HCD</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_A_alanine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_A_alanine.html
new file mode 100644
index 0000000..392f658
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_A_alanine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_A_alanine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_A_alanine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue A.
+ <li>The specified mass is added to the unmodified mass of A.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_A_alanine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_B_user_amino_acid.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_B_user_amino_acid.html
new file mode 100644
index 0000000..1a74ce3
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_B_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_B_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_B_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'B' in the input FASTA file and specify its mass here.
+ <li>The letter 'B' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'B' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_B_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_C_cysteine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_C_cysteine.html
new file mode 100644
index 0000000..757e1be
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_C_cysteine.html
@@ -0,0 +1,21 @@
+<html><head><title>comet parameter: add_C_cysteine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_C_cysteine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue C.
+ <li>The specified mass is added to the unmodified mass of C.
+ <li>The default value is "0.0" if this parameter is missing.
+ If Comet was compiled for
+ <a href="noble.gs.washington.edu/proj/crux/">Crux</a> compatibility,
+ the default value is "57.021464".
+ Note that in the example parameter file produced by Comet using the "-p"
+ command line option, this parameter entry has a value of 57.021464 for
+ cysteine carbamidomethylation.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_C_cysteine = 57.021464</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Cterm_peptide.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Cterm_peptide.html
new file mode 100644
index 0000000..f796288
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Cterm_peptide.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Cterm_peptide</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Cterm_peptide</h2>
+
+ <ul>
+ <li>Specify a static modification to the C-terminus of all peptides.
+ <li>The specified mass is added to the unmodified C-terminal mass (mass of OH or 17.00274).
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Cterm_peptide = 14.01</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Cterm_protein.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Cterm_protein.html
new file mode 100644
index 0000000..1d617e0
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Cterm_protein.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Cterm_protein</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Cterm_protein</h2>
+
+ <ul>
+ <li>Specify a static modification to the C-terminal peptide of each protein entry.
+ <li>The specified mass is added to the unmodified C-terminal mass (mass of OH or 17.00274).
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Cterm_protein = 14.01</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_D_aspartic_acid.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_D_aspartic_acid.html
new file mode 100644
index 0000000..dc85968
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_D_aspartic_acid.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_D_aspartic_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_D_aspartic_acid</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue D.
+ <li>The specified mass is added to the unmodified mass of D.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_D_cysteine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_E_glutamic_acid.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_E_glutamic_acid.html
new file mode 100644
index 0000000..d95b244
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_E_glutamic_acid.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_E_glutamic_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_E_glutamic_acid</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue E.
+ <li>The specified mass is added to the unmodified mass of E.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_E_cysteine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_F_phenylalanine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_F_phenylalanine.html
new file mode 100644
index 0000000..82952d4
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_F_phenylalanine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_F_phenylalanine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_F_phenylalanine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue F.
+ <li>The specified mass is added to the unmodified mass of F.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_F_phenylalanine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_G_glycine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_G_glycine.html
new file mode 100644
index 0000000..62d8a24
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_G_glycine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_G_glycine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_G_glycine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue G.
+ <li>The specified mass is added to the unmodified mass of G.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_G_cysteine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_H_histidine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_H_histidine.html
new file mode 100644
index 0000000..8984a28
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_H_histidine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_H_histidine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_H_histidine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue H.
+ <li>The specified mass is added to the unmodified mass of H.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_H_histidine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_I_isoleucine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_I_isoleucine.html
new file mode 100644
index 0000000..90d6de0
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_I_isoleucine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_I_isoleucine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_I_isoleucine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue I.
+ <li>The specified mass is added to the unmodified mass of I.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_I_isoleucine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_J_user_amino_acid.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_J_user_amino_acid.html
new file mode 100644
index 0000000..3806f3a
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_J_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_J_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_J_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'J' in the input FASTA file and specify its mass here.
+ <li>The letter 'J' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'J' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_J_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_K_lysine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_K_lysine.html
new file mode 100644
index 0000000..a52206d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_K_lysine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_K_lysine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_K_lysine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue K.
+ <li>The specified mass is added to the unmodified mass of K.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_K_lysine = 14.01</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_L_leucine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_L_leucine.html
new file mode 100644
index 0000000..58d84bf
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_L_leucine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_L_leucine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_L_leucine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue L.
+ <li>The specified mass is added to the unmodified mass of L.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_L_leucine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_M_methionine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_M_methionine.html
new file mode 100644
index 0000000..2abd014
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_M_methionine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_M_methionine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_M_methionine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue M.
+ <li>The specified mass is added to the unmodified mass of M.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_M_methionine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_N_asparagine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_N_asparagine.html
new file mode 100644
index 0000000..a296025
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_N_asparagine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_N_asparagine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_N_asparagine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue N.
+ <li>The specified mass is added to the unmodified mass of N.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_N_cysteine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Nterm_peptide.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Nterm_peptide.html
new file mode 100644
index 0000000..617217d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Nterm_peptide.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Nterm_peptide</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Nterm_peptide</h2>
+
+ <ul>
+ <li>Specify a static modification to the N-terminus of all peptides.
+ <li>The specified mass is added to the unmodified N-terminal mass (mass of H or 1.007825).
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Nterm_peptide = 14.01</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Nterm_protein.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Nterm_protein.html
new file mode 100644
index 0000000..3f41d87
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Nterm_protein.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Nterm_protein</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Nterm_protein</h2>
+
+ <ul>
+ <li>Specify a static modification to the N-terminal peptide of each protein entry.
+ <li>The specified mass is added to the unmodified N-terminal mass (mass of H or 1.007825).
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Nterm_protein = 14.01</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_O_ornithine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_O_ornithine.html
new file mode 100644
index 0000000..32b3b38
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_O_ornithine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_O_ornithine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_O_ornithine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue O.
+ <li>The specified mass is added to the unmodified mass of O.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_O_ornithine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_P_proline.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_P_proline.html
new file mode 100644
index 0000000..c27daf0
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_P_proline.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_P_proline</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_P_proline</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue P.
+ <li>The specified mass is added to the unmodified mass of P.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_P_proline = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Q_glutamine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Q_glutamine.html
new file mode 100644
index 0000000..37227f2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Q_glutamine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Q_glutamine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Q_glutamine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue Q.
+ <li>The specified mass is added to the unmodified mass of Q.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Q_glutamine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_R_arginine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_R_arginine.html
new file mode 100644
index 0000000..d668719
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_R_arginine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_R_arginine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_R_arginine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue R.
+ <li>The specified mass is added to the unmodified mass of R.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_R_arginine = 28.03</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_S_serine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_S_serine.html
new file mode 100644
index 0000000..6f7b93e
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_S_serine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_S_serine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_S_serine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue S.
+ <li>The specified mass is added to the unmodified mass of s.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_S_serine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_T_threonine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_T_threonine.html
new file mode 100644
index 0000000..68aef74
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_T_threonine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_T_threonine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_T_threonine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue T.
+ <li>The specified mass is added to the unmodified mass of T.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_T_threonine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_U_user_amino_acid.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_U_user_amino_acid.html
new file mode 100644
index 0000000..ab71e4a
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_U_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_U_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_U_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'U' in the input FASTA file and specify its mass here.
+ <li>The letter 'U' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'U' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_U_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_V_valine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_V_valine.html
new file mode 100644
index 0000000..5749b4c
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_V_valine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_V_valine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_V_valine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue V.
+ <li>The specified mass is added to the unmodified mass of V.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_V_valine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_W_tryptophan.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_W_tryptophan.html
new file mode 100644
index 0000000..ee0558b
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_W_tryptophan.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_W_tryptophan</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_W_tryptophan</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue W.
+ <li>The specified mass is added to the unmodified mass of W.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_W_tryptophan = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_X_user_amino_acid.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_X_user_amino_acid.html
new file mode 100644
index 0000000..6309a5a
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_X_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_X_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_X_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'X' in the input FASTA file and specify its mass here.
+ <li>The letter 'X' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'X' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_X_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Y_tyrosine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Y_tyrosine.html
new file mode 100644
index 0000000..d1eb52d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Y_tyrosine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Y_tyrosine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Y_tyrosine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue Y.
+ <li>The specified mass is added to the unmodified mass of Y.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Y_tyrosine = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Z_user_amino_acid.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Z_user_amino_acid.html
new file mode 100644
index 0000000..dc0d808
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/add_Z_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_Z_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Z_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'Z' in the input FASTA file and specify its mass here.
+ <li>The letter 'Z' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'Z' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Z_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/allowed_missed_cleavage.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/allowed_missed_cleavage.html
new file mode 100644
index 0000000..7a03d24
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/allowed_missed_cleavage.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: allowed_missed_cleavage</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: allowed_missed_cleavage</h2>
+
+ <ul>
+ <li>Number of allowed missed enzyme cleavages in a peptide.
+ <li>Parameter is not applied of the no-enzyme option is specified
+ in the <a href="search_enzyme_number.php">search_enzyme_number</a>
+ parameter.
+ <li>The default value is "2" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>allowed_missed_cleavage = 0</tt> <i>for no missed cleavages</i>
+ <br><tt>allowed_missed_cleavage = 2</tt> <i>allow two missed cleavages</i>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/clear_mz_range.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/clear_mz_range.html
new file mode 100644
index 0000000..6845854
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/clear_mz_range.html
@@ -0,0 +1,24 @@
+<html><head><title>comet parameter: clear_mz_range</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: clear_mz_range</h2>
+
+ <ul>
+ <li>This parameter is intended for iTRAQ/TMT type data where one might
+ want to remove the reporter ion signals in the MS/MS spectra prior to searching.
+ <li>Defines the m/z range to clear out in each MS/MS spectra
+ <li>This parameter has two decimal values.
+ <li>The first value is the lower mass cutoff and the second value is
+ the high mass cutoff.
+ <li>Valid values are two decimal numbers where the first number must
+ be less or equal to the second number.
+ <li>All peaks between the two decimal values are cleared out.
+ <li>The default value is "0.0 0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>clear_mz_range = 0.0 0.0</tt> <i>parameter is ignored</i>
+ <br><tt>clear_mz_range = 112.5 121.5</tt> <i>ignore all peaks between 112.5 and 121.5 m/z for iTRAQ 8-plex</i>
+ <br><tt>clear_mz_range = 125.5 131.5</tt> <i>ignore all peaks between 125.5 and 131.5 m/z for TMT</i>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/clip_nterm_methionine.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/clip_nterm_methionine.html
new file mode 100644
index 0000000..82826fb
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/clip_nterm_methionine.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: clip_nterm_methionine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: clip_nterm_methionine</h2>
+
+ <ul>
+ <li>This parameter controls whether Comet will automatically remove
+ the N-terminal methionine from a sequence entry.
+ <li>If set to 0, the sequence is analyzed as-is.
+ <li>If set to 1, any sequence with an N-terminal methionine will be
+ analyzed as-is as well as with the methionine removed. This means
+ that any N-terminal modifications will also apply (if appropriate)
+ to the peptide that is generated after the removal of the methionine.
+ <li>Valid values are 0 and 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>clip_nterm_methionine = 0</tt>
+ <br><tt>clip_nterm_methionine = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/combined.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/combined.html
new file mode 100644
index 0000000..f21a03d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/combined.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: activation_method</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: activation_method</h2>
+
+ <ul>
+ <li>This parameter specifies which scan types are searched.
+ <li>If "ALL" is specified, no filtering based on the activation method
+ is applied.
+ <li>If any other allowed entry is chosen, only spectra with activation
+ method matching the specified entry are searched.
+ <li>This parameter is valid only for mzXML, mzML and mz5 input.
+ <li>Allowed values are: ALL, CID, ECD, ETD, PQD, HCD, IRMPD
+ <li>The default value is "ALL" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>activation_method = ALL</tt>
+ <br><tt>activation_method = CID</tt>
+ <br><tt>activation_method = ETD</tt>
+ <br><tt>activation_method = HCD</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/comet.params b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/comet.params
new file mode 100644
index 0000000..b7105d5
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/comet.params
@@ -0,0 +1,160 @@
+# comet_version 2013.02 rev. 0
+# Comet MS/MS search engine parameters file.
+# Everything following the '#' symbol is treated as a comment.
+
+database_name = /some/path/db.fasta
+decoy_search = 0 # 0=no (default), 1=concatenated search, 2=separate search
+
+num_threads = 0 # 0=poll CPU to set num threads; else specify num threads directly (max 32)
+
+#
+# masses
+#
+peptide_mass_tolerance = 3.00
+peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm
+mass_type_parent = 1 # 0=average masses, 1=monoisotopic masses
+mass_type_fragment = 1 # 0=average masses, 1=monoisotopic masses
+precursor_tolerance_type = 0 # 0=MH+ (default), 1=precursor m/z
+isotope_error = 0 # 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)
+
+#
+# search enzyme
+#
+search_enzyme_number = 1 # choose from list at end of this params file
+num_enzyme_termini = 2 # valid values are 1 (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term
+allowed_missed_cleavage = 2 # maximum value is 5; for enzyme search
+
+#
+# Up to 6 variable modifications are supported
+# format: <mass> <residues> <0=variable/1=binary> <max mods per a peptide>
+# e.g. 79.966331 STY 0 3
+#
+variable_mod1 = 15.9949 M 0 3
+variable_mod2 = 0.0 X 0 3
+variable_mod3 = 0.0 X 0 3
+variable_mod4 = 0.0 X 0 3
+variable_mod5 = 0.0 X 0 3
+variable_mod6 = 0.0 X 0 3
+max_variable_mods_in_peptide = 5
+
+#
+# fragment ions
+#
+# ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), theoretical_fragment_ions = 1
+# high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), theoretical_fragment_ions = 0
+#
+fragment_bin_tol = 1.0005 # binning to use on fragment ions
+fragment_bin_offset = 0.4 # offset position to start the binning (0.0 to 1.0)
+theoretical_fragment_ions = 1 # 0=default peak shape, 1=M peak only
+use_A_ions = 0
+use_B_ions = 1
+use_C_ions = 0
+use_X_ions = 0
+use_Y_ions = 1
+use_Z_ions = 0
+use_NL_ions = 1 # 0=no, 1=yes to consider NH3/H2O neutral loss peaks
+use_sparse_matrix = 0
+
+#
+# output
+#
+output_sqtstream = 0 # 0=no, 1=yes write sqt to standard output
+output_sqtfile = 0 # 0=no, 1=yes write sqt file
+output_txtfile = 0 # 0=no, 1=yes write tab-delimited txt file
+output_pepxmlfile = 1 # 0=no, 1=yes write pep.xml file
+output_pinxmlfile = 0 # 0=no, 1=yes write pin.xml file
+output_outfiles = 0 # 0=no, 1=yes write .out files
+print_expect_score = 1 # 0=no, 1=yes to replace Sp with expect in out & sqt
+num_output_lines = 5 # num peptide results to show
+show_fragment_ions = 0 # 0=no, 1=yes for out files only
+
+sample_enzyme_number = 1 # Sample enzyme which is possibly different than the one applied to the search.
+ # Used to calculate NTT & NMC in pepXML output (default=1 for trypsin).
+
+#
+# mzXML parameters
+#
+scan_range = 0 0 # start and scan scan range to search; 0 as 1st entry ignores parameter
+precursor_charge = 0 0 # precursor charge range to analyze; does not override mzXML charge; 0 as 1st entry ignores parameter
+ms_level = 2 # MS level to analyze, valid are levels 2 (default) or 3
+activation_method = ALL # activation method; used if activation method set; allowed ALL, CID, ECD, ETD, PQD, HCD, IRMPD
+
+#
+# misc parameters
+#
+digest_mass_range = 600.0 5000.0 # MH+ peptide mass range to analyze
+num_results = 50 # number of search hits to store internally
+skip_researching = 1 # for '.out' file output only, 0=search everything again (default), 1=don't search if .out exists
+max_fragment_charge = 3 # set maximum fragment charge state to analyze (allowed max 5)
+max_precursor_charge = 6 # set maximum precursor charge state to analyze (allowed max 9)
+nucleotide_reading_frame = 0 # 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six
+clip_nterm_methionine = 0 # 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine
+spectrum_batch_size = 0 # max. # of spectra to search at a time; 0 to search the entire scan range in one loop
+decoy_prefix = DECOY_ # decoy entries are denoted by this string which is pre-pended to each protein accession
+
+#
+# spectral processing
+#
+minimum_peaks = 10 # minimum num. of peaks in spectrum to search (default 10)
+minimum_intensity = 0 # minimum intensity value to read in
+remove_precursor_peak = 0 # 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD)
+remove_precursor_tolerance = 1.5 # +- Da tolerance for precursor removal
+clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range
+
+#
+# additional modifications
+#
+
+variable_C_terminus = 0.0
+variable_N_terminus = 0.0
+variable_C_terminus_distance = -1 # -1=all peptides, 0=protein terminus, 1-N = maximum offset from C-terminus
+variable_N_terminus_distance = -1 # -1=all peptides, 0=protein terminus, 1-N = maximum offset from N-terminus
+
+add_Cterm_peptide = 0.0
+add_Nterm_peptide = 0.0
+add_Cterm_protein = 0.0
+add_Nterm_protein = 0.0
+
+add_G_glycine = 0.0000 # added to G - avg. 57.0513, mono. 57.02146
+add_A_alanine = 0.0000 # added to A - avg. 71.0779, mono. 71.03711
+add_S_serine = 0.0000 # added to S - avg. 87.0773, mono. 87.03203
+add_P_proline = 0.0000 # added to P - avg. 97.1152, mono. 97.05276
+add_V_valine = 0.0000 # added to V - avg. 99.1311, mono. 99.06841
+add_T_threonine = 0.0000 # added to T - avg. 101.1038, mono. 101.04768
+add_C_cysteine = 57.021464 # added to C - avg. 103.1429, mono. 103.00918
+add_L_leucine = 0.0000 # added to L - avg. 113.1576, mono. 113.08406
+add_I_isoleucine = 0.0000 # added to I - avg. 113.1576, mono. 113.08406
+add_N_asparagine = 0.0000 # added to N - avg. 114.1026, mono. 114.04293
+add_D_aspartic_acid = 0.0000 # added to D - avg. 115.0874, mono. 115.02694
+add_Q_glutamine = 0.0000 # added to Q - avg. 128.1292, mono. 128.05858
+add_K_lysine = 0.0000 # added to K - avg. 128.1723, mono. 128.09496
+add_E_glutamic_acid = 0.0000 # added to E - avg. 129.1140, mono. 129.04259
+add_M_methionine = 0.0000 # added to M - avg. 131.1961, mono. 131.04048
+add_O_ornithine = 0.0000 # added to O - avg. 132.1610, mono 132.08988
+add_H_histidine = 0.0000 # added to H - avg. 137.1393, mono. 137.05891
+add_F_phenylalanine = 0.0000 # added to F - avg. 147.1739, mono. 147.06841
+add_R_arginine = 0.0000 # added to R - avg. 156.1857, mono. 156.10111
+add_Y_tyrosine = 0.0000 # added to Y - avg. 163.0633, mono. 163.06333
+add_W_tryptophan = 0.0000 # added to W - avg. 186.0793, mono. 186.07931
+add_B_user_amino_acid = 0.0000 # added to B - avg. 0.0000, mono. 0.00000
+add_J_user_amino_acid = 0.0000 # added to J - avg. 0.0000, mono. 0.00000
+add_U_user_amino_acid = 0.0000 # added to U - avg. 0.0000, mono. 0.00000
+add_X_user_amino_acid = 0.0000 # added to X - avg. 0.0000, mono. 0.00000
+add_Z_user_amino_acid = 0.0000 # added to Z - avg. 0.0000, mono. 0.00000
+
+#
+# COMET_ENZYME_INFO _must_ be at the end of this parameters file
+#
+[COMET_ENZYME_INFO]
+0. No_enzyme 0 - -
+1. Trypsin 1 KR P
+2. Trypsin/P 1 KR -
+3. Lys_C 1 K P
+4. Lys_N 0 K -
+5. Arg_C 1 R P
+6. Asp_N 0 D -
+7. CNBr 1 M -
+8. Glu_C 1 DE P
+9. PepsinA 1 FL P
+10. Chymotrypsin 1 FWYL P
+
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/content.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/content.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/content.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/convertCometPHPs.py b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/convertCometPHPs.py
new file mode 100644
index 0000000..bc19af5
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/convertCometPHPs.py
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+# AUTHOR: William Stafford Noble
+# CREATE DATE: May Day, 2013
+import sys
+
+USAGE = """USAGE: convertCometPHP.py <php file>
+
+ This is a goofy little helper script that takes as input one of the
+ parameter PHP files distributed with Jimmy Eng's Comet search
+ engine, strips off some of the unnecessary text, adds HTML headers
+ and prints the result to standard output. The idea is to allow
+ automatic incorporation of any changes Jimmy makes to his
+ documentation into Crux. This is brittle, because it's based on
+ hand-designed parsing code. A better solution would be for Jimmy to
+ store his parameter docs in, say, XML, and then use an existing
+ parser.
+
+"""
+
+# Parse the command line.
+if (len(sys.argv) != 2):
+ sys.stderr.write(USAGE)
+ exit(1)
+phpFileName = sys.argv[1]
+
+phpFile = open(phpFileName, "r")
+
+# Find the start of the interesting section.
+for line in phpFile:
+ if ("<h2>" in line):
+
+ # Get the name of the parameter.
+ words = line.rstrip().split()
+ if ((len(words) != 3) or
+ (words[0] != "<h2>Comet") or
+ (words[2][-5:] != "</h2>")):
+ sys.stderr.write("Can't parse %s." % line)
+ sys.exit(1)
+ parameter = words[2][:-5]
+
+ # Print the HTML header.
+ sys.stdout.write("<html><head><title>comet parameter: %s</title>\n" % parameter)
+ sys.stdout.write("<link href=\"../crux.css\" rel=\"styleSheet\" type=\"text/css\">\n")
+ sys.stdout.write("</title><body>\n")
+ sys.stdout.write("<h2>Comet parameter: %s</h2>\n" % parameter)
+ break
+
+# Print the body of the file.
+for line in phpFile:
+ if "</div" in line:
+ break
+ sys.stdout.write(line)
+phpFile.close()
+
+sys.stdout.write("</body></html>\n")
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/database_name.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/database_name.html
new file mode 100644
index 0000000..3517f6f
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/database_name.html
@@ -0,0 +1,21 @@
+<html><head><title>comet parameter: database_name</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: database_name</h2>
+
+ <ul>
+ <li>A full or relative path to the sequence database, in FASTA format, to search. Example databases
+ include RefSeq or UniProt.
+ <li>Database can contain amino acid sequences or nucleic acid sequences. If sequences are amino acid
+ sequences, set the parameter "nucleotide_reading_frame = 0". If the sequences are nucleic acid
+ sequences, you must instruct Comet to translate these to amino acid sequences. Do this by setting
+ "nucleotide_reading_frame" to a value between 1 and 9.
+ <li>There is no default value if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>database_name = /usr/local/db/yeast.fasta</tt>
+ <br><tt>database_name = c:\local\db\yeast.fasta</tt>
+ <br><tt>database_name = yeast.fasta</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/decoy_prefix.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/decoy_prefix.html
new file mode 100644
index 0000000..0780628
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/decoy_prefix.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: decoy_prefix</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: decoy_prefix</h2>
+
+ <ul>
+ <li>This parameter specifies the prefix string that is pre-pended to
+ the protein identifier and reported for decoy hits.
+ <li>This parameter is only valid when a <a href="decoy_search.php">decoy_search</a>
+ is performed.
+ <li>For example, if the prefix parameter is set to "decoy_prefix = reverse_",
+ a match to a decoy peptide from protein "ALBU_HUMAN" would return
+ "reverse_ALBU_HUMAN" as the protein identifier.
+ <li>The default value is "DECOY_" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>decoy_prefix = DECOY_</tt>
+ <br><tt>decoy_prefix = rev_</tt>
+ <br><tt>decoy_prefix = --any_string_you_want_without_spaces--</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/decoy_search.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/decoy_search.html
new file mode 100644
index 0000000..ebf7962
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/decoy_search.html
@@ -0,0 +1,29 @@
+<html><head><title>comet parameter: decoy_search</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: decoy_search</h2>
+
+ <ul>
+ <li>This parameter controls whether or not an internal decoy search is performed.
+ <li>Comet generates decoys by reversing each target peptide sequence, keeping the
+ N-terminal or C-terminal amino acid in place (depending on the "sense" value of the
+ digestion enzyme specified by <a href="search_enzyme_number.php">search_enzyme_number</a>).
+ For example, peptide DIGSESTK becomes decoy peptide TSESGIDK for a tryptic search
+ and peptide DVINHKGGA becomes DAGGKHNIV for an Asp-N search.
+ <li>Valid parameter values are 0, 1, or 2:
+ <ul>
+ <li>0 = no decoy search (default)
+ <li>1 = concatenated decoy search. Target and decoy entries will be scored against
+ each other and a single result is performed for each spectrum query.
+ <li>2 = separate decoy search. Target and decoy entries will be scored separately
+ and separate target and decoy search results will be reported.
+ </ul>
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>decoy_search = 0</tt>
+ <br><tt>decoy_search = 1</tt>
+ <br><tt>decoy_search = 2</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/digest_mass_range.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/digest_mass_range.html
new file mode 100644
index 0000000..f225dcf
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/digest_mass_range.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: digest_mass_range</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: digest_mass_range</h2>
+
+ <ul>
+ <li>Defines the mass range of peptides to search (based on MH+ or the singly
+ protonated mass).
+ <li>This parameter has two decimal values.
+ <li>The first value is the lower mass cutoff and the second value is
+ the high mass cutoff.
+ <li>Only spectra with experimental MH+ masses in within the defined
+ mass ranges are searched.
+ <li>Valid values are two decimal numbers where the first number must
+ be less or equal to the second number.
+ <li>The default value is "0.0 10000.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>digest_mass_range = 600.0 5000.0</tt> <i>search only 600.0 to 5000.0 mass range</i>
+ <br><tt>digest_mass_range = 0.0 6500.0</tt> <i>search all spectra with peptide masses between 0.0 and 6000.0</i>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/footer.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/footer.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/footer.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/fragment_bin_offset.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/fragment_bin_offset.html
new file mode 100644
index 0000000..052ca15
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/fragment_bin_offset.html
@@ -0,0 +1,31 @@
+<html><head><title>comet parameter: fragment_bin_offset</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: fragment_bin_offset</h2>
+
+ <ul>
+ <li>This parameter controls how each fragment bin of size <a href="fragment_bin_tol.php">fragment_bin_tol</a>
+ is defined in terms of where each bin starts.
+ <li>For example, assume a <a href="fragment_bin_tol.php">fragment_bin_tol</a> of 1.0. Most intuitively,
+ the fragment bins would be 0.0 to 1.0, 1.0 to 2.0, 2.0 to 3.0, etc.
+ This set of bins corresponds to a fragment_bin_offset of 0.0. However,
+ consider if we set fragment_bin_offset to 0.5; this would cause the
+ bins to be 0.5 to 1.5, 1.5 to 2.5, 2.5 to 3.5, etc.
+ <li>So this fragment_bin_offset gives one a mechanism to define
+ where each bin starts and is centered.
+ <li>For ion trap data with a <a href="fragment_bin_tol.php">fragment_bin_tol</a> of 1.0005,
+ it is recommended to set fragment_bin_offset to 0.4.
+ <li>For high-res MS/MS data, one might use a <a href="fragment_bin_tol.php">fragment_bin_tol</a> of 0.02
+ and a corresponding fragment_bin_offset of 0.0.
+ <li>Allowed values are between 0.0 and 1.0. The actual offset value is
+ scaled by the <a href="fragment_bin_tol.php">fragment_bin_tol</a> value.
+ <li>I know this is esoteric and any normal user should not give this
+ parameter any thought beyond using the recommended settings.
+ <li>The default value is "0.4" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>fragment_bin_offset = 0.4</tt>
+ <br><tt>fragment_bin_offset = 0.0</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/fragment_bin_tol.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/fragment_bin_tol.html
new file mode 100644
index 0000000..4ab7e38
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/fragment_bin_tol.html
@@ -0,0 +1,30 @@
+<html><head><title>comet parameter: fragment_bin_tol</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: fragment_bin_tol</h2>
+
+ <ul>
+ <li>This parameter controls the bin size associated with fragment ions.
+ <li>The bin size defines the mass width associated with a single MS/MS peak
+ as it is stored internally in an array element.
+ <li>Although it's not explicitly a fragment ion tolerance, it's probably
+ easiest to think of it as such.
+ <li>Note, there is a direct correlation between the value selected for
+ the fragment_bin_tol and the memory used in a search. The lower the
+ fragment_bin_tol setting, the more memory a search will use. A test of
+ 4,515 query spectra used ~700MB RAM with a 0.4 fragment_bin_tol value,
+ ~1.5GB RAM with a 0.10 value, and ~9GB RAM with a 0.01 value. For small
+ fragment_bin_tol values where computer memory becomes an issue, either
+ set <a href="use_sparse_matrix.php">use_sparse_matrix</a> to true and/or
+ make use of the <a href="spectrum_batch_size.php">spectrum_batch_size</a>
+ parameter
+ <li>The minimum allowed value is 0.01.
+ <li>The default value is "1.0005" if the parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>fragment_bin_tol = 1.0005</tt>
+ <br><tt>fragment_bin_tol = 0.4</tt>
+ <br><tt>fragment_bin_tol = 0.02</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/head.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/head.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/head.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/index.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/index.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/index.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/isotope_error.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/isotope_error.html
new file mode 100644
index 0000000..4409115
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/isotope_error.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: isotope_error</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: isotope_error</h2>
+
+ <ul>
+ <li>This parameter controls whether the <a href="peptide_mass_tolerance.php">peptide_mass_tolerance</a>
+ takes into account possible isotope errors in the precursor mass measurement.
+ <li>It is possible that an accurately read precursor mass is not measured on the monoisotopic
+ peak of a precursor isotopic pattern. In these cases, the precursor mass is measured on the
+ first isotope peak (one C13 atom) or possibly even the second or third isotope peak. To address
+ this problem, this "isotope_error" parameter allows you to perform an accurate mass search
+ (say 10 ppm) even if the precursor mass measurement is off by one or more C13 offsets.
+ <li>Valid values are 0, 1, and 2:
+ <ul>
+ <li>0 performs no isotope error searches
+ <li>1 searches -1, 0, +1, +2, and +3 isotope offsets
+ <li>2 searches -8, -4, 0, +4, +8 isotope offsets (for +4/+8 stable isotope labeling)
+ </ul>
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>isotope_error = 0</tt>
+ <br><tt>isotope_error = 1</tt>
+ <br><tt>isotope_error = 2</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/mass_type_fragment.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/mass_type_fragment.html
new file mode 100644
index 0000000..469c36d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/mass_type_fragment.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: mass_type_fragment</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: mass_type_fragment</h2>
+
+ <ul>
+ <li>Controls the mass type, average or monoisotopic, applied to fragment ion calculations.
+ <li>Valid values are 0 or 1:
+ <ul>
+ <li>0 for average masses
+ <li>1 for monoisotopic masses
+ </ul>
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>mass_type_fragment = 0</tt>
+ <br><tt>mass_type_fragment = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/mass_type_parent.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/mass_type_parent.html
new file mode 100644
index 0000000..c242786
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/mass_type_parent.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: mass_type_parent</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: mass_type_parent</h2>
+
+ <ul>
+ <li>Controls the mass type, average or monoisotopic, applied to peptide mass calculations.
+ <li>Valid values are 0 or 1:
+ <ul>
+ <li>0 for average masses
+ <li>1 for monoisotopic masses
+ </ul>
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>mass_type_parent = 0</tt>
+ <br><tt>mass_type_parent = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_fragment_charge.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_fragment_charge.html
new file mode 100644
index 0000000..0e6dee4
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_fragment_charge.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: max_fragment_charge</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: max_fragment_charge</h2>
+
+ <ul>
+ <li>This parameter sets the maximum fragment charge state that will
+ be considered in the analysis.
+ <li>Typically, the fragment charge state range that is analyzed is
+ from 1+ to one charge less than the precursor charge state.
+ <li>For high precursor charge states (i.e. 6+), the default behavior
+ would analyze fragment ions with 1+ through 5+ charges on them. This
+ parameter is a mechanism to limit the fragment charge range that is
+ analyzed.
+ <li>For example, if max_fragment_charge is set to 3 then the maximum
+ fragment charge state that will be analyzed is 3+. However, the default
+ rule will still limit 1+ and 2+ precursor ions to only have
+ 1+ fragments considered. And similarly 3+ precursors will still only
+ have 1+ and 2+ fragments considered.
+ <li>Valid values are any non-zero integer.
+ <li>The default value is "3" if this parameter is missing. A maximum
+ allowed value of "5" is enforced for this parameter.
+ </ul>
+
+ <p>Example:
+ <br><tt>max_fragment_charge = 3</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_precursor_charge.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_precursor_charge.html
new file mode 100644
index 0000000..269cd79
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_precursor_charge.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: max_precursor_charge</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: max_precursor_charge</h2>
+
+ <ul>
+ <li>This parameter defines the maximum precursor charge state that
+ will be analyzed.
+ <li>Only spectra with this number of precursor charges or less will be searched.
+ <li>Valid values are any integer greater than 1.
+ <li>The default value is "6" if this parameter is missing. A maximum
+ allowed value of "9" is enforced for this parameter.
+ </ul>
+
+ <p>Example:
+ <br><tt>max_precursor_charge = 5</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_variable_mods_in_peptide.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_variable_mods_in_peptide.html
new file mode 100644
index 0000000..edcbcd7
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/max_variable_mods_in_peptide.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: max_variable_mods_in_peptide</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: max_variable_mods_in_peptide</h2>
+
+ <ul>
+ <li>Specifies the total/maximum number of residues that can be modified in a peptide.
+ <li>As opposed to specifying the maximum number of variable modifications for each
+ of the 6 possible variable modifications, this entry limits the global number
+ of variable mods possible in each peptide.
+ <li>The default value is "10" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>max_variable_mods_in_peptide = 6</tt>
+ <br><tt>max_variable_mods_in_peptide = 10</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/minimum_intensity.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/minimum_intensity.html
new file mode 100644
index 0000000..f0c1fe5
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/minimum_intensity.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: minimum_intensity</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: minimum_intensity</h2>
+
+ <ul>
+ <li>A floating point number indicating the minimum intensity value
+ for input the input peaks.
+ <li>If an experimental MS/MS peak intensity is less than this value,
+ it will not be read in and used in the analysis.
+ <li>This is one mechanism to get rid of systemmatic background noise
+ that has a near contant peak intensity.
+ <li>If a peak does not pass this minimum intensity threshold, it will
+ also not be counted towards the <a href="minimum_peaks.php">minimum_peaks</a>
+ parameter.
+ <li>Valid values are any floating point number.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>minimum_intensity = 100.0</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/minimum_peaks.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/minimum_peaks.html
new file mode 100644
index 0000000..0650c83
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/minimum_peaks.html
@@ -0,0 +1,21 @@
+<html><head><title>comet parameter: minimum_peaks</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: minimum_peaks</h2>
+
+ <ul>
+ <li>An integer value indicating the minimum number of m/z-intensity pairs
+ that must be present in a spectrum before it is searched.
+ <li>This parameter can be used to avoid searching nearly sparse spectra
+ that will not likely yield an indentification.
+ <li>This parameter is checked against the spectrum after
+ <a href="clear_mz_range.php">clear_mz_range</a> is applied but before
+ any other spectral processing occurs (i.e. <a href="remove_precursor_peak.php">remove_precursor_peak</a>).
+ <li>Valid values are any integer number.
+ <li>The default value is "10" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>minimum_peaks = 10</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/ms_level.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/ms_level.html
new file mode 100644
index 0000000..16d19b1
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/ms_level.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: ms_level</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: ms_level</h2>
+
+ <ul>
+ <li>This parameter specifies which scans are searched.
+ <li>An input value of 2 will search MS/MS scans.
+ <li>An input value of 3 will search MS3 scans.
+ <li>This parameter is only valid for mzXML, mzML, and mz5 input files.
+ <li>Allowed values are 2 or 3.
+ <li>The default value is "2" if this parameter is missing or any value
+ other than 2 or 3 is entered.
+ </ul>
+
+ <p>Example:
+ <br><tt>ms_level = 2</tt>
+ <br><tt>ms_level = 3</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/nucleotide_reading_frame.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/nucleotide_reading_frame.html
new file mode 100644
index 0000000..4b5b6c3
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/nucleotide_reading_frame.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: nucleotide_reading_frame</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: nucleotide_reading_frame</h2>
+
+ <ul>
+ <li>This parameter is used to search nucleotide sequence databases.
+ <li>It controls how the nucleotides are translated specifically
+ which sets of reading frames are translated.
+ <li>Valid values are 0 through 9.
+ <li>Set this parameter to 0 for a protein sequence database.
+ <li>Set this parameter to 1 to search the 1st forward reading frame.
+ <li>Set this parameter to 2 to search the 2nd forward reading frame.
+ <li>Set this parameter to 3 to search the 3rd forward reading frame.
+ <li>Set this parameter to 4 to search the 1st reverse reading frame.
+ <li>Set this parameter to 5 to search the 2nd reverse reading frame.
+ <li>Set this parameter to 6 to search the 3rd reverse reading frame.
+ <li>Set this parameter to 7 to search all 3 forward reading frames.
+ <li>Set this parameter to 8 to search all 3 reverse reading frames.
+ <li>Set this parameter to 9 to search all 6 reading frames.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>nucleotide_reading_frame = 0</tt>
+ <br><tt>nucleotide_reading_frame = 9</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_enzyme_termini.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_enzyme_termini.html
new file mode 100644
index 0000000..2af8498
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_enzyme_termini.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: num_enzyme_termini</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: num_enzyme_termini</h2>
+
+ <ul>
+ <li>This parameter specifies the number of enzyme termini a peptide must
+ have.
+ <li>For example, if trypsin were specified as the search enzyme, only
+ fully tryptic peptides would be analyzed if "num_enzyme_termini = 2"
+ whereas semi-tryptic peptides would be analyzed if "num_enzyme_termini = 1".
+ <li>This parameter is unused if a no-enzyme search is specified.
+ <li>Valid values are 1, 2, 8, 9.
+ <li>Set this parameter to 1 for a semi-enzyme search.
+ <li>Set this parameter to 2 for a full-enzyme search.
+ <li>Set this parameter to 8 for a semi-enzyme search, unspecific cleavage on peptide's N-terminus.
+ <li>Set this parameter to 9 for a semi-enzyme search, unspecific cleavage on peptide's C-terminus.
+ <li>The default value is "2" if this parameter is missing.
+ </ul>
+
+
+ <p>Example:
+ <br><tt>num_enzyme_termini = 1</tt>
+ <br><tt>num_enzyme_termini = 2</tt>
+ <br><tt>num_enzyme_termini = 8</tt>
+ <br><tt>num_enzyme_termini = 9</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_output_lines.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_output_lines.html
new file mode 100644
index 0000000..39b1bdc
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_output_lines.html
@@ -0,0 +1,26 @@
+<html><head><title>comet parameter: num_output_lines</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: num_output_lines</h2>
+
+ <ul>
+ <li>This parameter controls the number of search result
+ hits (peptides) that are reported for each spectrum query.
+ <li>If you are only interested in seeing one top hit each
+ per query, set this value to 1.
+ <li>This parameter value cannot be larger than the value
+ entered for "<a href="num_results.php">num_results</a>"
+ which itself is limited to a maximum value of 100.
+ <li>This parameter does not apply to the text output as
+ defined by "<a href="output_txtfile.php">output_txtfile</a>".
+ <li>Valid values are any positive integer 1 or greater.
+ <li>If a value less than 1 is entered, this parameter is set to 1.
+ <li>The default value is "10" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>num_output_lines = 1</tt>
+ <br><tt>num_output_lines = 5</tt>
+ <br><tt>num_output_lines = 10</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_results.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_results.html
new file mode 100644
index 0000000..8cffff2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_results.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: num_results</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: num_results</h2>
+
+ <ul>
+ <li>This parameter controls the number of peptide search results that
+ are stored internally.
+ <li>Depending on what post-processing tools are used, one may want to
+ set this to the same value as <a href="num_output_lines.php">num_output_lines</a>.
+ <li>When this parameter is set to a value greater than
+ <a href="num_output_lines.php">num_output_lines</a>, it allows
+ the SpRank value to span a larger range which may be helpful for
+ tools like PeptideProphet or Percolator (not likely though).
+ <li>Valid values are any integer between 1 and 100.
+ <li>The default value is "100" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>num_results = 50</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_threads.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_threads.html
new file mode 100644
index 0000000..2eb596f
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/num_threads.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: num_threads</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: num_threads</h2>
+
+ <ul>
+ <li>This parameter controls the number of processing threads that will be spawned for a search.
+ Ideally the number of threads is set to the same value as the number of CPU cores available.
+ <li>Valid values range for this parameter are numbers ranging from 0 to 64.
+ <li>A value of 0 will cause Comet to poll the system and launch the same number of threads
+ as CPU cores.
+ <li>To set an explicit thread count, enter any value between 1 and 64.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>num_threads = 0</tt>
+ <br><tt>num_threads = 8</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_outfiles.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_outfiles.html
new file mode 100644
index 0000000..5c10786
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_outfiles.html
@@ -0,0 +1,16 @@
+<html><head><title>comet parameter: output_outfiles</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_outfiles</h2>
+
+ <ul>
+ <li>Controls whether to output search results as individual .out files.
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_outfiles = 0</tt>
+ <br><tt>output_outfiles = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_pepxmlfile.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_pepxmlfile.html
new file mode 100644
index 0000000..25980bd
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_pepxmlfile.html
@@ -0,0 +1,16 @@
+<html><head><title>comet parameter: output_pepxmlfile</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_pepxmlfile</h2>
+
+ <ul>
+ <li>Controls whether to output search results in a pepXML file.
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_pepxmlfile = 0</tt>
+ <br><tt>output_pepxmlfile = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_percolatorfile.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_percolatorfile.html
new file mode 100644
index 0000000..aca9843
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_percolatorfile.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: output_percolatorfile</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_percolatorfile</h2>
+
+ <ul>
+ <li>Controls whether to output search results in a <a href="http://per-colator.com">Percolator's</a>
+ tab-delimited input format.
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ <li>The created file will have a ".tsv" file extension.
+ <li>This parameter replaces the now defunct "output_pinxmlfile".
+ </ul>
+
+ <p>Example:
+ <br><tt>output_percolatorfile = 0</tt>
+ <br><tt>output_percolatorfile = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_sqtfile.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_sqtfile.html
new file mode 100644
index 0000000..5a18492
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_sqtfile.html
@@ -0,0 +1,16 @@
+<html><head><title>comet parameter: output_sqtfile</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_sqtfile</h2>
+
+ <ul>
+ <li>Controls whether to output search results into an SQT file (.sqt).
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_sqtfile = 0</tt>
+ <br><tt>output_sqtfile = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_sqtstream.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_sqtstream.html
new file mode 100644
index 0000000..8ed1505
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_sqtstream.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: output_sqtstream</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_sqtstream</h2>
+
+ <ul>
+ <li>Controls whether to output search results to standard out
+ (i.e. to the screen unless otherwise directed) in SQT format.
+ <li>Just the search results (M and L lines and not any H lines)
+ are output to standard out.
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_sqtstream = 0</tt>
+ <br><tt>output_sqtstream = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_suffix.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_suffix.html
new file mode 100644
index 0000000..dca2425
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_suffix.html
@@ -0,0 +1,25 @@
+<html><head><title>comet parameter: output_suffix</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_suffix</h2>
+
+ <ul>
+ <li>This parameter specifies the suffix string that is appended to
+ the base output name for the pep.xml, pin.xml, txt and sqt output files.
+ <li>Use this parameter to give output files a unique suffix base name.
+ <li>For example, if the output_suffix parameter is set to
+ "output_suffix = _000", then a search of the file base.mzXML
+ will generate output files named base_000.pep.xml, base_000.pin.xml,
+ base_000.txt, and/or base_000.sqt.
+ <li>Note that using this parameter could break downstream tools that
+ expect the output base name to be the same as the input file base name.
+ <li>The default value is blank if this parameter is missing i.e.
+ base.mzXML will generate base.pep.xml.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_suffix = </tt>
+ <br><tt>output_suffix = _some_suffix</tt>
+ <br><tt>output_suffix = any_string_you_want_without_spaces</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_txtfile.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_txtfile.html
new file mode 100644
index 0000000..390b363
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/output_txtfile.html
@@ -0,0 +1,52 @@
+<html><head><title>comet parameter: output_txtfile</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_txtfile</h2>
+
+ <ul>
+ <li>Controls whether to output search results into a tab-delimited text file (.txt).
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_txtfile = 0</tt>
+ <br><tt>output_txtfile = 1</tt>
+
+ <p>Here's snippet of sample output below. The first line of the output file is a
+ header line which contains the Comet version, search start time/date, and search
+ database. The second line contains the column headers. Only the top hit for each
+ search is reported in the text output; the parameter
+ "<a href="num_output_lines.php">num_output_lines</a>" does not apply to the text output.
+
+<pre>CometVersion 2013.02 rev. 0 100 10/04/2013, 08:37:09 AM /net/pr/vol1/ProteomicsResource/dbase/SGD/SGDyeast.fasta.20101117
+scan charge exp_neutral_mass calc_neutral_mass e-value xcorr delta_cn sp_score ions_matched ions_total plain_peptide peptide prev_aa next_aa protein duplicate_protein_count
+5129 1 599.9698 602.3136 1.73E+01 0.6847 0.0995 44.3 4 8 DAKNR R.DAKNR.I R I YML019W 0
+5385 1 601.3290 603.3228 1.73E+01 0.5316 0.1905 70.9 3 8 NLTEK R.NLTEK.T R T YBL024W 1
+5496 1 601.3358 599.3755 1.67E+01 0.4527 0.1315 6.6 2 8 VVNIR R.VVNIR.L R L YJL012C 0
+5430 1 602.3329 605.2591 2.33E+01 0.4222 0.0854 73.2 4 8 DVGCR K.DVGCR.I K I YER085C 0
+5829 1 616.4184 615.3414 5.26E+01 0.4321 0.0658 8.5 2 8 KPPMK -.KPPM*K.Q - Q DECOY__YBR025C 2
+
+</pre></p>
+
+ <p>Comet's text output is different if Comet was compiled for
+ <a href="noble.gs.washington.edu/proj/crux/">Crux</a> compatibility.
+ Here's the example text output if you are running Comet in Crux.
+ Note that up to 5 hits per spectrum are reported and there is just
+ a single column header line.
+
+<pre>scan charge spectrum precursor m/z spectrum neutral mass matches/spectrum peptide mass e-value xcorr score xcorr rank delta_cn sp score sp rank b/y ions matched b/y ions total sequence flanking aa protein id
+5129 1 600.9771 599.9698 5440 602.3136 1.73E+01 0.6847 1 0.0995 44.3 19 4 8 DAKNR RI YML019W
+5129 1 600.9771 599.9698 5440 602.3249 1.96E+01 0.6714 2 0.1016 46.1 17 5 10 RTGGGR RI YGR054W
+5129 1 600.9771 599.9698 5440 602.3136 1.99E+01 0.6698 3 0.1131 77.6 6 5 8 NISNR KV YMR033W
+5129 1 600.9771 599.9698 5440 601.2820 2.16E+01 0.6612 4 0.1240 38.6 22 4 8 EPSNR RD YPL161C
+5129 1 600.9771 599.9698 5440 600.3231 0.00E+00 0.6532 5 0.1389 104.6 3 6 8 IESPR KM YLL021W
+5385 1 602.3363 601.3290 6518 603.3228 1.73E+01 0.5316 1 0.1905 70.9 2 3 8 NLTEK RT YBL024W
+5385 1 602.3363 601.3290 6518 600.3707 1.86E+01 0.5249 2 0.2022 31.0 8 3 8 ARNIK KT DECOY_YIL159W
+5385 1 602.3363 601.3290 6518 602.3249 2.02E+01 0.5173 3 0.2134 47.4 4 3 8 ARNSR KI DECOY_YLL040C
+5385 1 602.3363 601.3290 6518 601.3184 2.19E+01 0.5100 4 0.2148 7.1 19 2 10 GAVNNK KS DECOY_YMR125W
+5385 1 602.3363 601.3290 6518 599.4119 0.00E+00 0.5091 5 0.2148 28.3 9 3 8 ALLKR RI YML107C
+</pre></p>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/override_charge.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/override_charge.html
new file mode 100644
index 0000000..b93b267
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/override_charge.html
@@ -0,0 +1,25 @@
+<html><head><title>comet parameter: override_charge</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: override_charge</h2>
+
+ <ul>
+ <li>This parameter specifies the whether to override existing precursor
+ charge state information when present in the files with the charge
+ range specified by the
+ "<a href="precursor_charge.php">precursor_charge</a>" parameter.
+ <li>Valid values are 0 and 1.
+ <li>To keep any known charge state values in the input files,
+ set the value to 0.
+ <li>To ignore any known charge values in the input files and instead
+ use the charge state range specified by the
+ "<a href="precursor_charge.php">precursor_charge</a>" parameter,
+ set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>override_charge = 0</tt>
+ <br><tt>override_charge = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/peptide_mass_tolerance.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/peptide_mass_tolerance.html
new file mode 100644
index 0000000..d795294
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/peptide_mass_tolerance.html
@@ -0,0 +1,17 @@
+<html><head><title>comet parameter: peptide_mass_tolerance</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: peptide_mass_tolerance</h2>
+
+ <ul>
+ <li>This parameter controls the mass tolerance value.
+ <li>The mass tolerance is set at +/- the specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0 tolerance.
+ <li>The units of the mass tolerance is controlled by the parameter "<a href="peptide_mass_units.php">peptide_mass_units</a>".
+ <li>The default value is "1.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>peptide_mass_tolerance = 3.0</tt>
+ <br><tt>peptide_mass_tolerance = 10.0</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/peptide_mass_units.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/peptide_mass_units.html
new file mode 100644
index 0000000..f2483a2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/peptide_mass_units.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: peptide_mass_units</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: peptide_mass_units</h2>
+
+ <ul>
+ <li>This parameter controls the units applied to the <a href="peptide_mass_tolerance.php">peptide_mass_tolerance</a> parameter.
+ <li>Valid values are 0, 1, and 2.
+ <li>Set this parameter to 0 for amu.
+ <li>Set this parameter to 1 for mmu.
+ <li>Set this parameter to 2 for ppm.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>peptide_mass_units = 0</tt>
+ <br><tt>peptide_mass_units = 1</tt>
+ <br><tt>peptide_mass_units = 2</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/precursor_charge.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/precursor_charge.html
new file mode 100644
index 0000000..752671a
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/precursor_charge.html
@@ -0,0 +1,30 @@
+<html><head><title>comet parameter: precursor_charge</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: precursor_charge</h2>
+
+ <ul>
+ <li>This parameter specifies the precursor charge range to search.
+ <li>This parameter expects to integer values as input.
+ <li>If the first input value is 0 then this parameter is ignored and all charge
+ states are searched
+ <li>Only in the case where a spectrum does not have a precursor charge will all charges
+ in the specified charge range be searched.
+ <li>If the first input value is not 0 then all charge states between (and inclusive of)
+ the first and second input values are searched. Again, only for those spectra with no
+ specified precursor charge state.
+ <li>If a precursor charge is present for a particular spectrum, this parameter will
+ not override that charge state and that spectrum will always be searched.
+ <li>With the default "0 0" values and a spectrum with no precursor charge, Comet will
+ either search the spectrum as a 1+ or a 2+/3+.
+ <li>The default value is "0 0" if this parameter is missing.
+
+ </ul>
+
+ <p>Example:
+ <br><tt>precursor_charge = 0 0</tt> <i>search all charge ranges</i>
+ <br><tt>precursor_charge = 0 2</tt> <i>search all charge ranges (because first entry is 0)</i>
+ <br><tt>precursor_charge = 2 6</tt> <i>search 2+ to 6+ precursors</i>
+ <br><tt>precursor_charge = 3 3</tt> <i>search 3+ precursors</i>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/print_expect_score.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/print_expect_score.html
new file mode 100644
index 0000000..122ad18
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/print_expect_score.html
@@ -0,0 +1,24 @@
+<html><head><title>comet parameter: print_expect_score</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: print_expect_score</h2>
+
+ <ul>
+ <li>A boolean flag this determines whether or not the expectation
+ score (E-value) is reported in .out and SQT formats. Note that the
+ E-value is always reported in pepXML output.
+ <li>This parameter is only pertinant for results reported in .out and SQT formats.
+ <li>If expect scores are chosen to be reported (i.e. value set to 1), they will replace
+ the number reported for the traditional "spscore" i.e. "spscore" will
+ be replaced by an E-value. Also an expectation value histogram will
+ be output at the end of each .out file; this histogram is not present
+ for SQT output.
+ <li>Valid values are 0 and 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>print_expect_score = 0</tt>
+ <br><tt>print_expect_score = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/remove_precursor_peak.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/remove_precursor_peak.html
new file mode 100644
index 0000000..dab6a7a
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/remove_precursor_peak.html
@@ -0,0 +1,25 @@
+<html><head><title>comet parameter: remove_precursor_peak</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: remove_precursor_peak</h2>
+
+ <ul>
+ <li>This parameter controls excluding/removing any precursor signals
+ from the input MS/MS spectrum.
+ <li>An input value of 0 will not perform any precursor removal.
+ <li>An input value of 1 will remove all peaks around the precursor m/z.
+ <li>An input value of 2 will remove all charge reduced precursor peaks
+ as expected to be present for ETD/ECD spectra.
+ <li>This parameter works in conjuction with
+ <a href="remove_precursor_tolerance.php">remove_precursor_tolerance</a>
+ to specify the tolerance around each precuror m/z that will be removed.
+ <li>Valid values are 0, 1, and 2.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>remove_precursor_peak = 0</tt>
+ <br><tt>remove_precursor_peak = 1</tt>
+ <br><tt>remove_precursor_peak = 2</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/remove_precursor_tolerance.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/remove_precursor_tolerance.html
new file mode 100644
index 0000000..857d504
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/remove_precursor_tolerance.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: remove_precursor_tolerance</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: remove_precursor_tolerance</h2>
+
+ <ul>
+ <li>This parameter specifies the mass tolerance around each precursor m/z
+ that would be removed when the <a href="remove_precursor_peak.php">remove_precursor_peak</a>
+ option is invoked.
+ <li>The mass tolerance units is in Da (or Th if you prefer).
+ <li>Any non-negative, non-zero floating point number is valid.
+ <li>The default value is "1.5" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>remove_precursor_tolerance = 0.75</tt>
+ <br><tt>remove_precursor_tolerance = 1.5</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/require_variable_mod.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/require_variable_mod.html
new file mode 100644
index 0000000..eeef8ed
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/require_variable_mod.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: require_variable_mod</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: require_variable_mod</h2>
+
+ <ul>
+ <li>This parameter takes in one input value.
+ <li>The input value is an integer that controls whether the analyzed peptides
+ must contain at least one variable modification i.e. force all reported peptides
+ to have a variable modifiation.
+ <ul>
+ <li>0 = consider both modified and unmodified peptides (default)
+ <li>1 = analyze only peptides that contain a variable modification
+ </ul>
+ </ul>
+
+ <p>Example:
+ <br><tt>require_variable_mod = 0</tt> ... <i>modifications not required</i>
+ <br><tt>require_variable_mod = 1</tt> ... <i>peptides must contain a variable modification</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/runall b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/runall
new file mode 100644
index 0000000..b2ec284
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/runall
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+
+
+# The parameters files are in the binary release of comet, in a file
+# called paramters_<release>.zip.
+
+to_remove=`ls *.html | grep -v index.html | grep -v header.html | grep -v footer.html | grep -v topmenu.html | grep -v head.html`
+
+rm $to_remove
+
+rm -rf ~/tmp
+mkdir ~/tmp
+svn checkout svn://svn.code.sf.net/p/comet-ms/code/www/parameters/parameters_201501 ~/tmp/comet-params
+
+files=`ls ~/tmp/comet-params/*.php`
+
+for file in $files; do
+ if [[ -e $file ]]; then # Some symlinks point to missing files.
+ echo Converting $file
+ basename=`basename $file`
+ ./convertCometPHPs.py $file > ${basename%.php}.html
+ fi
+done
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/sample_enzyme_number.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/sample_enzyme_number.html
new file mode 100644
index 0000000..14beb94
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/sample_enzyme_number.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: sample_enzyme_number</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: sample_enzyme_number</h2>
+
+ <ul>
+ <li>This parameter is relevant only for pepXML output i.e. when
+ <a href="output_pepxmlfile.php">output_pepxmlfile</a> is set to 1.
+ <li>The pepXML format encodes the enzyme that is applied to the sample
+ i.e. trypsin. This enzyme is written to the "sample_enzyme" element.
+ <li>The sample enzyme could be different from the search enzyme i.e.
+ the sample enzyme is "trypsin" yet the search enzyme is "No-enzyme"
+ for a non-specific search. Hence the need for this separate parameter.
+ <li>Valid values are any integer represented in the enzyme list.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>sample_enzyme_number = 1</tt>
+ <br><tt>sample_enzyme_number = 3</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/scan_range.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/scan_range.html
new file mode 100644
index 0000000..28f0989
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/scan_range.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: scan_range</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: scan_range</h2>
+
+ <ul>
+ <li>Defines the scan range to search. Only spectra within (and inclusive) of the specified
+ scan range are searched.
+ <li>This parameter works only with mzXML and mzML inputs files.
+ <li>Two digits are specified for this parameter. The first digit is the start scan and the
+ second digit is the end scan.
+ <li>When the start scan is set to 0, this parameter setting is ignored irrespective of what
+ the end scan is set to.
+ <li>When the end scan is less than the start scan, this parameter setting is ignored.
+ <li>The default value is "0 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>scan_range = 0 0</tt> <i>search all scans</i>
+ <br><tt>scan_range = 0 1000</tt> <i>search all scans (because first entry is 0)</i>
+ <br><tt>scan_range = 1000 1500</tt> <i>search only scans 1000 to 1500</i>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/search_enzyme_number.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/search_enzyme_number.html
new file mode 100644
index 0000000..09da2d8
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/search_enzyme_number.html
@@ -0,0 +1,46 @@
+<html><head><title>comet parameter: search_enzyme_number</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: search_enzyme_number</h2>
+
+ <ul>
+ <li>The search enzyme is specified by this parameter.
+ <li>The list of search enzymes is specified at the end of the comet.params file
+ beginning with the line <tt>[COMET_ENZYME_INFO]</tt>. The actual enzyme list and
+ digestion parameters are read here. So one can edit/add/delete enzyme definitions
+ simply be changing the enzyme information.
+ <li>This parameter works in conjection with the <a href="num_enzyme_termini.php">num_enzyme_termini</a>
+ parameter to define the cleavage rule for fully-digested vs. semi-digested search options.
+ <li>This parameter works in conjection with the <a href="allowed_missed_cleavage.php">allowed_missed_cleavage</a>
+ parameter to define the miss cleavage rule.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>search_enzyme_number = 0</tt> <i>typically no-enzyme</i>
+ <br><tt>search_enzyme_number = 1</tt> <i>typically trypsin</i></p>
+
+
+ <li>The format of the parameter definition looks like the following:
+ <p><pre>[COMET_ENZYME_INFO]
+0. No_enzyme 0 - -
+1. Trypsin 1 KR P
+2. Trypsin/P 1 KR -
+3. Lys_C 1 K P
+4. Lys_N 0 K -
+5. Arg_C 1 R P
+6. Asp_N 0 D -
+7. CNBr 1 M -
+8. Glu_C 1 DE P
+9. PepsinA 1 FL P
+10. Chymotrypsin 1 FWYL P</pre></p>
+
+ <p>The first column of the parameter definition is the enzyme number. This number list
+ must start from 0 and sequentially increase by 1. The second column is the enzyme name;
+ no spaces are allowed in this name field. The third column is the digestion "sense"
+ i.e. a value of "0" specifies cleavage N-teriminal to (before) the specified residues
+ in column 4 and a value of "1" specifies cleavage C-terminal to (after) the specified
+ residues in column 4. Column 4 contains the residue(s) that the enzyme cleaves at.
+ Column 5 contains the flanking residue(s) that negate cleavage.
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/show_fragment_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/show_fragment_ions.html
new file mode 100644
index 0000000..bb1f1cc
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/show_fragment_ions.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: show_fragment_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: show_fragment_ions</h2>
+
+ <ul>
+ <li>This parameter affects .out files only i.e.
+ <a href="output_outfiles.php">output_outfiles</a> set to 1.
+ <li>This parameter controls whether or not the theoretical
+ fragment ion masses for the top peptide hit are calculated
+ and dislayed at the end of an .out file.
+ <li>Valid values are 0 and 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>show_fragment_ions = 0</tt>
+ <br><tt>show_fragment_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/skip_researching.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/skip_researching.html
new file mode 100644
index 0000000..4a2957b
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/skip_researching.html
@@ -0,0 +1,25 @@
+<html><head><title>comet parameter: skip_researching</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: skip_researching</h2>
+
+ <ul>
+ <li>This parameter is valid only when <a href="output_outfiles.php">output_outfiles</a> is set
+ to 1 and each of
+ <a href="output_pepxmlfile.php">output_pepxmlfile</a>,
+ <a href="output_sqtfile.php">output_sqtfile</a>, and
+ <a href="output_sqtstream.php">output_sqtstream</a> are set to 0.
+ <li>When .out files only are set to be exported, this parameter will look to see if
+ an .out file already exists for each query spectrum. If so, it will not re-search
+ that particular spectrum.
+ <li>When set to 0, all spectra are re-searched. When set to 1, the search is skipped
+ for those spectra where an .out file already exists.
+ <li>Valid values are 0 and 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>skip_researching = 0</tt>
+ <br><tt>skip_researching = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/spectrum_batch_size.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/spectrum_batch_size.html
new file mode 100644
index 0000000..760fe14
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/spectrum_batch_size.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: spectrum_batch_size</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: spectrum_batch_size</h2>
+
+ <ul>
+ <li>When this parameter is set to a non-zero value, say 5000, this causes Comet
+ to load and search about 5000 spectra at a time, looping through sets of 5000
+ spectra until all data have been analyzed.
+ <li>This parameter was implemented to simplify searching large datasets that
+ might not fit into memory if searched all at once.
+ <li>The loaded batch sizes might be a little larger than the specified parameter
+ value (i.e. 5014 spectra loaded when the parameter is set to 5000) due to both
+ threading and potential charge state considerations when precursor charge state
+ is not known.
+ <li>Valid values are 0 or any positive integer.
+ <li>Set this parameter to 0 to load and search all spectra at once.
+ <li>Set this parameter to any other positive integer to loop through searching
+ this number of spectra at a time until all spectra have been analyzed.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>spectrum_batch_size = 0</tt>
+ <br><tt>spectrum_batch_size = 1000</tt>
+ <br><tt>spectrum_batch_size = 5000</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/theoretical_fragment_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/theoretical_fragment_ions.html
new file mode 100644
index 0000000..60b57d4
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/theoretical_fragment_ions.html
@@ -0,0 +1,32 @@
+<html><head><title>comet parameter: theoretical_fragment_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: theoretical_fragment_ions</h2>
+
+ <ul>
+ <li>This parameter specifies how theoretical fragment ion peaks are
+ represented.
+ <li>Even though Comet does not generate/store a theoretical spectrum,
+ it does calculate fragment ion masses and this parameter controls how
+ the acquired spectrum intensities at these theoretical mass locations
+ contribute to the correlation score.
+ <li>A value of 0 indicates that the fast correlation score will be
+ a sum of the intensities at each theortical fragment mass bin and half
+ the intensity of each flanking bin.
+ <li>A value of 1 indicates that the fast correlation score will be
+ the sum of the intensities at each theoretical fragment mass bin.
+ <li>For extremely coarse <a href="fragment_bin_tol.php">fragment_bin_tol</a>
+ values such as the historical ~1 Da bins, a theoretical_fragment_ions
+ value of 1 is optimal.
+ <li>But for narrower bins, such as ~0.3 for ion trap data or ~0.03 for
+ high-res MS/MS spectra, a value of 0 is optimal to incorporate
+ intensities from the flanking bins.
+ <li>Allowed values are 0 or 1.
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>theoretical_fragment_ions = 0</tt>
+ <br><tt>theoretical_fragment_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/topmenu.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/topmenu.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/topmenu.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_A_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_A_ions.html
new file mode 100644
index 0000000..2eb9a48
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_A_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_A_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_A_ions</h2>
+
+ <ul>
+ <li>Controls whether or not A-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use A-ions, set the value to 0.
+ <li>To use A-ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_A_ions = 0</tt>
+ <br><tt>use_A_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_B_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_B_ions.html
new file mode 100644
index 0000000..ad78694
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_B_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_B_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_B_ions</h2>
+
+ <ul>
+ <li>Controls whether or not B-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use B-ions, set the value to 0.
+ <li>To use B-ions, set the value to 1.
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_B_ions = 0</tt>
+ <br><tt>use_B_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_C_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_C_ions.html
new file mode 100644
index 0000000..c2a7eb6
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_C_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_C_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_C_ions</h2>
+
+ <ul>
+ <li>Controls whether or not C-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use C-ions, set the value to 0.
+ <li>To use C-ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_C_ions = 0</tt>
+ <br><tt>use_C_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_NL_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_NL_ions.html
new file mode 100644
index 0000000..fe88f3d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_NL_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_NL_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_NL_ions</h2>
+
+ <ul>
+ <li>Controls whether or not neutral loss ions (-NH3 and -H2O from b- and y-ions) are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use neutral loss ions, set the value to 0.
+ <li>To use neutral loss ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_NL_ions = 0</tt>
+ <br><tt>use_NL_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_X_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_X_ions.html
new file mode 100644
index 0000000..cf91b63
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_X_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_X_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_X_ions</h2>
+
+ <ul>
+ <li>Controls whether or not X-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use X-ions, set the value to 0.
+ <li>To use X-ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_X_ions = 0</tt>
+ <br><tt>use_X_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_Y_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_Y_ions.html
new file mode 100644
index 0000000..83ed9dc
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_Y_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_Y_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_Y_ions</h2>
+
+ <ul>
+ <li>Controls whether or not Y-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use Y-ions, set the value to 0.
+ <li>To use Y-ions, set the value to 1.
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_Y_ions = 0</tt>
+ <br><tt>use_Y_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_Z_ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_Z_ions.html
new file mode 100644
index 0000000..6e9c5f2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_Z_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_Z_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_Z_ions</h2>
+
+ <ul>
+ <li>Controls whether or not Z-dot ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use Z-dot ions, set the value to 0.
+ <li>To use Z-dot ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_Z_ions = 0</tt>
+ <br><tt>use_Z_ions = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_sparse_matrix.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_sparse_matrix.html
new file mode 100644
index 0000000..ef9f1e4
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/use_sparse_matrix.html
@@ -0,0 +1,26 @@
+<html><head><title>comet parameter: use_sparse_matrix</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_sparse_matrix</h2>
+
+ <ul>
+ <li>Controls whether or not internal sparse matrix data representation is used.
+ <li>The sparse matrix data representation will use a <em>significantly</em> smaller amount
+ of memory/RAM for small <a href="fragment_bin_tol.php">fragment_bin_tol</a> settings such
+ as 0.05 or 0.01. We're talking going from tens of GB (gigabytes) down to a few hundred
+ megabytes (MB)!
+ <li>In this release, the sparse matrix searches will always be slower than the classical
+ data representation (i.e. use_sparse_matrix = 0). So it should be used only when
+ memory is an issue. Alternately, the <a href="spectrum_batch_size.php">spectrum_batch_size</a>
+ parameter can also be used to mitigate memory issues.
+ <li>Valid values are 0 and 1.
+ <li>To not use sparse matrix, set the value to 0.
+ <li>To use sparse matrix, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_sparse_matrix = 0</tt>
+ <br><tt>use_sparse_matrix = 1</tt>
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod01.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod01.html
new file mode 100644
index 0000000..4940708
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod01.html
@@ -0,0 +1,62 @@
+<html><head><title>comet parameter: variable_mod01</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod01</h2>
+
+ <ul>
+ <li>This parameter specifies the 1st of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies whichprotein terminus the distance constraint is applied to:
+ <ul>
+ <li>0 = protein N-terminus
+ <li>1 = protein C-terminus
+ <li>2 = peptide N-terminus
+ <li>3 = peptide C-terminus
+ </ul>
+ <li>The seventh entry specifies whether peptides are must contain this modification
+ <ul>
+ <li>0 = not forced to be present
+ <li>1 = modification is required
+ </ul>
+
+ </ul>
+ <li>In the output, this first modification is encoded with the character '*' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod01 = 15.9949 M 0 3 -1 0 0</tt>
+ <br><tt>variable_mod01 = 79.966331 STY 0 3 -1 0 0</tt> ... <i>possible phosphorylation on any S, T, Y residue</i>
+ <br><tt>variable_mod01 = 79.966331 STY 0 3 -1 0 1</tt> ... <i>force peptide IDs to contain at least one phosphorylation mod</i>
+ <br><tt>variable_mod01 = 42.010565 nK 0 3 -1 0 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod01 = 15.994915 n 0 3 0 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod01 = 28.0 c 0 3 8 1 0</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod01 = -17.026549 Q 0 1 0 2</tt> ... <i>cyclization of N-terminal glutamine to form pyroglutamic acid (elimination of NH3)</i>
+ <br><tt>variable_mod01 = -18.010565 E 0 1 0 2</tt> ... <i>cyclization of N-terminal glutamic acid to form pyroglutamic acid (elimination of H2O)</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod02.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod02.html
new file mode 100644
index 0000000..31107c7
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod02.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod02</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod02</h2>
+
+ <ul>
+ <li>This parameter specifies the 2nd of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '#' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod02 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod02 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod02 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod02 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod02 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod02 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod03.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod03.html
new file mode 100644
index 0000000..76b8f5d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod03.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod03</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod03</h2>
+
+ <ul>
+ <li>This parameter specifies the 3rd of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '@' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod03 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod03 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod03 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod03 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod03 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod03 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod04.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod04.html
new file mode 100644
index 0000000..8548a34
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod04.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod04</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod04</h2>
+
+ <ul>
+ <li>This parameter specifies the 4th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '^' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod04 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod04 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod04 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod04 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod04 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod04 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod05.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod05.html
new file mode 100644
index 0000000..fa5d180
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod05.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod05</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod05</h2>
+
+ <ul>
+ <li>This parameter specifies the 5th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '~' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod05 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod05 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod05 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod05 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod05 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod05 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod06.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod06.html
new file mode 100644
index 0000000..cad626d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod06.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod06</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod06</h2>
+
+ <ul>
+ <li>This parameter specifies the 6th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '$' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod06 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod06 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod06 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod06 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod06 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod06 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod07.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod07.html
new file mode 100644
index 0000000..c976fb1
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod07.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod07</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod07</h2>
+
+ <ul>
+ <li>This parameter specifies the 7th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '%' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod07 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod07 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod07 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod07 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod07 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod07 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod08.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod08.html
new file mode 100644
index 0000000..34aae4e
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod08.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod08</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod08</h2>
+
+ <ul>
+ <li>This parameter specifies the 8th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '!' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod08 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod08 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod08 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod08 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod08 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod08 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod09.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod09.html
new file mode 100644
index 0000000..8c2d93d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/comet-options/variable_mod09.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod09</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod09</h2>
+
+ <ul>
+ <li>This parameter specifies the 9th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '+' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod09 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod09 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod09 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod09 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod09 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod09 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
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+<!DOCTYPE html>
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+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>comet</h1>
+<h2>Usage:</h2>
+<p><code>crux comet [options] <input spectra>+ <database_name></code></p>
+<h2>Description:</h2>
+<p>This command searches a protein database with a set of spectra, assigning peptide sequences to the observed spectra. This search engine was developed by Jimmy Eng at the University of Washington Proteomics Resource.</p><p>Although its history goes back two decades, the Comet search engine was first made publicly available in August 2012 on SourceForge. Comet is multithreaded and supports multiple input and output formats.</p><blockquote><a href="http://onlinelibrary.wiley.com/doi/10.1 [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>input spectra+</code> – The name of the file from which to parse the spectra. Valid formats include mzXML, mzML, mz5, raw, ms2, and cms2. Files in mzML or mzXML may be compressed with gzip. RAW files can be parsed only under windows and if the appropriate libraries were included at compile time.</li>
+ <li><code>database_name</code> – A full or relative path to the sequence database, in FASTA format, to search. Example databases include RefSeq or UniProt. The database can contain amino acid sequences or nucleic acid sequences. If sequences are amino acid sequences, set the parameter "nucleotide_reading_frame = 0". If the sequences are nucleic acid sequences, you must instruct Comet to translate these to amino acid sequences. Do this by setting nucleotide_reading_frame" to a va [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>comet.target.txt</code> – a tab-delimited text file containing the target PSMs. See <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>comet.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>comet.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Database</h3>
+<ul>
+ <li class="nobullet"><code>--decoy_search <integer></code> – 0=no, 1=concatenated search, 2=separate search. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>CPU threads</h3>
+<ul>
+ <li class="nobullet"><code>--num_threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Masses</h3>
+<ul>
+ <li class="nobullet"><code>--peptide_mass_tolerance <float></code> – Controls the mass tolerance value. The mass tolerance is set at +/- the specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0 tolerance. The units of the mass tolerance is controlled by the parameter "peptide_mass_units". Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto_peptide_mass_tolerance false|warn|fail</code> – Automatically estimate optimal value for the peptide_mass_tolerancel parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--peptide_mass_units <integer></code> – 0=amu, 1=mmu, 2=ppm. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--mass_type_parent <integer></code> – 0=average masses, 1=monoisotopic masses. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--mass_type_fragment <integer></code> – 0=average masses, 1=monoisotopic masses. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--precursor_tolerance_type <integer></code> – 0=singly charged peptide mass, 1=precursor m/z. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--isotope_error <integer></code> – 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8 labeling). Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search enzyme</h3>
+<ul>
+ <li class="nobullet"><code>--search_enzyme_number <integer></code> – Specify a search enzyme from the end of the parameter file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--num_enzyme_termini <integer></code> – valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--allowed_missed_cleavage <integer></code> – Maximum value is 5; for enzyme search. Default = <code>2</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fragment ions</h3>
+<ul>
+ <li class="nobullet"><code>--fragment_bin_tol <float></code> – Binning to use on fragment ions. Default = <code>1.000507</code>.</li>
+ <li class="nobullet"><code>--fragment_bin_offset <float></code> – Offset position to start the binning (0.0 to 1.0). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--auto_fragment_bin_tol false|warn|fail</code> – Automatically estimate optimal value for the fragment_bin_tol parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--theoretical_fragment_ions <integer></code> – 0=default peak shape, 1=M peak only. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_A_ions <integer></code> – Controls whether or not A-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_B_ions <integer></code> – Controls whether or not B-ions are considered in the search (0 - no, 1 - yes). Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_C_ions <integer></code> – Controls whether or not C-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_X_ions <integer></code> – Controls whether or not X-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_Y_ions <integer></code> – Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes). Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_Z_ions <integer></code> – Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_NL_ions <integer></code> – 0=no, 1= yes to consider NH3/H2O neutral loss peak. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>mzXML/mzML parameters</h3>
+<ul>
+ <li class="nobullet"><code>--scan_range <string></code> – Start and scan scan range to search; 0 as first entry ignores parameter. Default = <code>0 0</code>.</li>
+ <li class="nobullet"><code>--precursor_charge <string></code> – Precursor charge range to analyze; does not override mzXML charge; 0 as first entry ignores parameter. Default = <code>0 0</code>.</li>
+ <li class="nobullet"><code>--override_charge <integer></code> – Specifies the whether to override existing precursor charge state information when present in the files with the charge range specified by the "precursor_charge" parameter. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--ms_level <integer></code> – MS level to analyze, valid are levels 2 or 3. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--activation_method ALL|CID|ECD|ETD|PQD|HCD|IRMPD</code> – Specifies which scan types are searched. Default = <code>ALL</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Miscellaneous parameters</h3>
+<ul>
+ <li class="nobullet"><code>--digest_mass_range <string></code> – MH+ peptide mass range to analyze. Default = <code>600.0 5000.0</code>.</li>
+ <li class="nobullet"><code>--num_results <integer></code> – Number of search hits to store internally. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--skip_researching <integer></code> – For '.out' file output only, 0=search everything again, 1=don't search if .out exists. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--max_fragment_charge <integer></code> – Set maximum fragment charge state to analyze (allowed max 5). Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--max_precursor_charge <integer></code> – Set maximum precursor charge state to analyze (allowed max 9). Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--nucleotide_reading_frame <integer></code> – 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--clip_nterm_methionine <integer></code> – 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum_batch_size <integer></code> – Maximum number of spectra to search at a time; 0 to search the entire scan range in one loop. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--decoy_prefix <string></code> – Specifies the prefix of the protein names that indicates a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--output_suffix <string></code> – Specifies the suffix string that is appended to the base output name for the pep.xml, pin.xml, txt and sqt output files. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--mass_offsets <string></code> – Specifies one or more mass offsets to apply. This value(s) are effectively subtracted from each precursor mass such that peptides that are smaller than the precursor mass by the offset value can still be matched to the respective spectrum. Default = <code><empty></code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Spectral processing</h3>
+<ul>
+ <li class="nobullet"><code>--minimum_peaks <integer></code> – Minimum number of peaks in spectrum to search. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--minimum_intensity <float></code> – Minimum intensity value to read in. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--remove_precursor_peak <integer></code> – 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--remove_precursor_tolerance <float></code> – +- Da tolerance for precursor removal. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--clear_mz_range <string></code> – For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range. Default = <code>0.0 0.0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Variable modifications</h3>
+<ul>
+ <li class="nobullet"><code>--variable_mod01 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod02 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod03 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod04 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod05 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod06 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod07 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod08 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod09 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--max_variable_mods_in_peptide <integer></code> – Specifies the total/maximum number of residues that can be modified in a peptide. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--require_variable_mod <integer></code> – Controls whether the analyzed peptides must contain at least one variable modification. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Static modifications</h3>
+<ul>
+ <li class="nobullet"><code>--add_Cterm_peptide <float></code> – Specifiy a static modification to the c-terminus of all peptides. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Nterm_peptide <float></code> – Specify a static modification to the n-terminus of all peptides. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Cterm_protein <float></code> – Specify a static modification to the c-terminal peptide of each protein. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Nterm_protein <float></code> – Specify a static modification to the n-terminal peptide of each protein. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_A_alanine <float></code> – Specify a static modification to the residue A. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_B_user_amino_acid <float></code> – Specify a static modification to the residue B. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_C_cysteine <float></code> – Specify a static modification to the residue C. Default = <code>57.021464</code>.</li>
+ <li class="nobullet"><code>--add_D_aspartic_acid <float></code> – Specify a static modification to the residue D. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_E_glutamic_acid <float></code> – Specify a static modification to the residue E. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_F_phenylalanine <float></code> – Specify a static modification to the residue F. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_G_glycine <float></code> – Specify a static modification to the residue G. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_H_histidine <float></code> – Specify a static modification to the residue H. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_I_isoleucine <float></code> – Specify a static modification to the residue I. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_J_user_amino_acid <float></code> – Specify a static modification to the residue J. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_K_lysine <float></code> – Specify a static modification to the residue K. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_L_leucine <float></code> – Specify a static modification to the residue L. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_M_methionine <float></code> – Specify a static modification to the residue M. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_N_asparagine <float></code> – Specify a static modification to the residue N. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_O_ornithine <float></code> – Specify a static modification to the residue O. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_P_proline <float></code> – Specify a static modification to the residue P. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Q_glutamine <float></code> – Specify a static modification to the residue Q. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_R_arginine <float></code> – Specify a static modification to the residue R. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_S_serine <float></code> – Specify a static modification to the residue S. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_T_threonine <float></code> – Specify a static modification to the residue T. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_U_selenocysteine <float></code> – Specify a static modification to the residue U. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_V_valine <float></code> – Specify a static modification to the residue V. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_W_tryptophan <float></code> – Specify a static modification to the residue W. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_X_user_amino_acid <float></code> – Specify a static modification to the residue X. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Y_tyrosine <float></code> – Specify a static modification to the residue Y. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Z_user_amino_acid <float></code> – Specify a static modification to the residue Z. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--output_sqtfile <integer></code> – 0=no, 1=yes write sqt file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--output_txtfile <integer></code> – 0=no, 1=yes write tab-delimited text file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--output_pepxmlfile <integer></code> – 0=no, 1=yes write pep.xml file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--output_percolatorfile <integer></code> – 0=no, 1=yes write percolator file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--output_outfiles <integer></code> – 0=no, 1=yes write .out files. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--print_expect_score <integer></code> – 0=no, 1=yes to replace Sp with expect in out & sqt. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--num_output_lines <integer></code> – num peptide results to show. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--show_fragment_ions <integer></code> – 0=no, 1=yes for out files only. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--sample_enzyme_number <integer></code> – Sample enzyme which is possibly different than the one applied to the search. Used to calculate NTT & NMC in pepXML output. Default = <code>1</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/commands/bullseye_standalone_to_crux.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/commands/bullseye_standalone_to_crux.html
new file mode 100644
index 0000000..382c4d2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/commands/bullseye_standalone_to_crux.html
@@ -0,0 +1,74 @@
+ <table border="1">
+ <tr>
+ <td><b>Bullseye Parameter</b></td>
+ <td><b>crux bullseye parameter</b></td>
+ <td><b>datatype</b></td>
+ <td><b>default</b></td>
+
+ </tr>
+ <tr>
+ <td>-c</td>
+ <td>--max-persist</td>
+ <td>double</td>
+ <td>2.0</td>
+ </tr>
+
+ <tr>
+ <td>-e</td>
+ <td>--exact-match</td>
+ <td>boolean</td>
+ <td>false</td>
+ </tr>
+ <tr>
+
+ <td>-g</td>
+ <td>--gap-tolerance</td>
+ <td>integer</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>-m</td>
+
+ <td>--max-mass</td>
+ <td>double</td>
+ <td>8000.0</td>
+ </tr>
+ <tr>
+ <td>-n</td>
+ <td>--min-mass</td>
+
+ <td>double</td>
+ <td>600.0</td>
+ </tr>
+ <tr>
+ <td>-p</td>
+ <td>--exact-tolerance</td>
+ <td>double</td>
+
+ <td>10.0</td>
+ </tr>
+ <tr>
+ <td>-r</td>
+ <td>--persist-tolerance</td>
+ <td>double</td>
+ <td>10.0</td>
+
+ </tr>
+ <tr>
+ <td>-s</td>
+ <td>--scan-tolerance</td>
+ <td>integer</td>
+ <td>3</td>
+ </tr>
+
+ </tr>
+ <tr>
+ <td>-t</td>
+ <td>--retention-tolerance</td>
+ <td>float</td>
+ <td>0.5</td>
+ </tr>
+
+
+ </table>
+
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/commands/hardklor_standalone_to_crux.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/commands/hardklor_standalone_to_crux.html
new file mode 100644
index 0000000..553064e
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/commands/hardklor_standalone_to_crux.html
@@ -0,0 +1,127 @@
+ <table border="1">
+ <tr>
+ <td><b>Hardklör parameter</b></td>
+ <td><b>crux hardklor parameter</b></td>
+ <td><b>datatype</b></td>
+ <td><b>default</b></td>
+
+ </tr>
+ <tr>
+ <td>-a</td>
+ <td>--hardklor-algorithm</td>
+ <td>string</td>
+ <td>fast-fewesst-peptides</td>
+ </tr>
+
+ <tr>
+ <td>-cdm</td>
+ <td>--cdm</td>
+ <td>char</td>
+ <td>Q</td>
+ </tr>
+ <tr>
+ <td>-chMin</td>
+ <td>--min-charge</td>
+ <td>integer</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>-chMax</td>
+ <td>--max-charge</td>
+ <td>integer</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>-corr</td>
+ <td>--corr</td>
+ <td>double</td>
+ <td>0.85</td>
+ </tr>
+ <tr>
+ <td>-d</td>
+ <td>--depth</td>
+ <td>integer</td>
+
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>-da</td>
+ <td>--distribution-area</td>
+ <td>boolean</td>
+ <td>F</td>
+
+ </tr>
+ <tr>
+ <td>-m</td>
+ <td>--averagine-mod</td>
+ <td>string</td>
+ <td>Empty string</td>
+ </tr>
+ <tr>
+ <td>-mF</td>
+ <td>--mzxml-filter</td>
+ <td>string</td>
+ <td>none</td>
+ </tr>
+ <tr>
+ <td>-p</td>
+ <td>--max-p</td>
+ <td>integer</td>
+ <td>10</td>
+ </tr>
+ <tr>
+ <td>-res</td>
+ <td>--resolution</td>
+ <td>float</td>
+ <td>100000</td>
+ </tr>
+ <tr>
+ <td>-res</td>
+ <td>--instrument</td>
+ <td>string</td>
+ <td>fticr</td>
+ </tr>
+ <tr>
+ <td>-sc</td>
+ <td>--scan-number</td>
+ <td>number range</td>
+ <td>search all</td>
+ </tr>
+ <tr>
+ <td>-sl</td>
+ <td>--sensitivity</td>
+ <td>0|1|2|3</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>-sn</td>
+ <td>--signal-to-noise</td>
+ <td>float</td>
+ <td>1.0</td>
+ </tr>
+ <tr>
+ <td>-snWin</td>
+ <td>--sn-window</td>
+ <td>float</td>
+ <td>250.0</td>
+ </tr>
+ <tr>
+ <td>-snWin</td>
+ <td>--static-sn</td>
+ <td>boolean</td>
+ <td>true</td>
+ </tr>
+ <tr>
+ <td>-w</td>
+ <td>--mz-window</td>
+ <td>double-double</td>
+ <td>0-max</td>
+ </tr>
+ <tr>
+ <td>-win</td>
+ <td>--max-width</td>
+ <td>float</td>
+ <td>4.0</td>
+ </tr>
+ </table>
+
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/contributors.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/contributors.html
new file mode 100644
index 0000000..3c7e5f1
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/contributors.html
@@ -0,0 +1,177 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux contributors</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Crux contributors</h2>
+ <p>
+ The current Crux development team consists of the following people:</p>
+
+ <ul>
+
+ <li>
+ Charles Grant, February 2008—present</li>
+
+ <li>
+ Sean McIlwain, January 2009—present</li>
+
+ <li>
+ Kaipo Tamura, October 2012—present</li>
+
+ <li>
+ J. Jeffry Howbert, October 2011—present</li>
+
+ <li>
+ Alice Cheng, March 2014—present</li>
+
+ </ul>
+
+ <p>
+ Former Crux contributors include</p>
+
+ <ul>
+
+ <li>
+ Chris Park, June 2006—August 2007</li>
+
+ <li>
+ Aaron Klammer, June 2006—June 2008</li>
+
+ <li>
+ Lukas Käll, November 2007—July 2008</li>
+
+ <li>
+ Michael Mathews, June 2010—December 2010</li>
+
+ <li>
+ Benjamin Diament, July 2010—September 2011</li>
+
+ <li>
+ Kha Nguyen, April 2011—July 2011</li>
+
+ <li>
+ Manijeh Naseri, January 2012—September 2012</li>
+
+ <li>
+ Marina Spivak, September 2009—September 2012</li>
+
+ <li>
+ Barbara Frewen, October 2007—September 2014</li>
+
+ <li>
+ Attila Kertesz-Farkas, September 2013—September 2015</li>
+
+ <li>
+ Jared Moore, September 2015—June 2016</li>
+
+ <li>
+ Atul Pai, September 2015—June 2016</li>
+
+ <li>
+ Zijin Zhang, September 2015—June 2016</li>
+
+ </ul>
+
+ <p>
+ The Crux project is overseen and directed by Michael MacCoss and
+ William Stafford Noble.</p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/create-docs.cmake b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/create-docs.cmake
new file mode 100644
index 0000000..5c98f75
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/create-docs.cmake
@@ -0,0 +1,127 @@
+# This script generates the documentation for the Crux commands using the
+# 'crux create-docs' command.
+
+# Create the list of documents to create
+execute_process(
+ COMMAND ${CRUX_PATH} create-docs --no-analytics T list
+ RESULT_VARIABLE status
+ OUTPUT_VARIABLE doc_list
+ ERROR_VARIABLE error_message
+)
+if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to create list of documents "
+ "\nError message: ${error_message}"
+ "\nCreation of documents failed."
+ )
+endif (NOT ${status} EQUAL 0)
+
+# Documents are separated by newlines, convert to CMake list
+STRING(REGEX REPLACE "\n" ";" doc_list "${doc_list}")
+
+# Generate each document
+foreach (doc ${doc_list})
+ execute_process(
+ COMMAND ${CRUX_PATH} create-docs --no-analytics T ${doc}
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_FILE "${doc}.html"
+ )
+ if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to generate ${doc}.html"
+ "\nError message: ${error_message}"
+ "\nCreation of documents failed."
+ )
+ endif (NOT ${status} EQUAL 0)
+ message(STATUS "Created ${doc}.html")
+ if (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+ # If building out of source copy doc files back to
+ # source doc directory.
+ execute_process(
+ COMMAND ${CMAKE_COMMAND}
+ -E copy ${doc}.html ${DOC_DIR}
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ )
+ if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to copy ${doc}.html to ${DOC_DIR}"
+ "\nError message: ${error_message}"
+ "\nCreation of documents failed."
+ )
+ endif (NOT ${status} EQUAL 0)
+ endif (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+endforeach (doc ${doc_list})
+
+# Create the parameter table
+execute_process(
+ COMMAND ${CRUX_PATH} create-docs --no-analytics T param-table
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_FILE param-table.html
+)
+if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to generate param-table.html"
+ "\nError message: ${error_message}"
+ "\nCreation of param-table failed."
+ )
+endif (NOT ${status} EQUAL 0)
+message(STATUS "Created param-table.html")
+if (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+ # If building out of source copy doc files back to
+ # source doc directory.
+ execute_process(
+ COMMAND ${CMAKE_COMMAND}
+ -E copy param-table.html ${DOC_DIR}
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ )
+ if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to copy param-table.html to ${DOC_DIR}"
+ "\nError message: ${error_message}"
+ "\nCreation of param-table failed."
+ )
+ endif (NOT ${status} EQUAL 0)
+endif (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+# Create the default.params file
+execute_process(
+ COMMAND ${CRUX_PATH} create-docs --no-analytics T default-params
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_FILE default.params
+)
+if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to generate default.params"
+ "\nError message: ${error_message}"
+ "\nCreation of default.params failed."
+ )
+endif (NOT ${status} EQUAL 0)
+message(STATUS "Created default.params")
+if (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+ # If building out of source copy doc files back to
+ # source doc directory.
+ execute_process(
+ COMMAND ${CMAKE_COMMAND}
+ -E copy default.params ${DOC_DIR}
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ )
+ if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to copy default.params to ${DOC_DIR}"
+ "\nError message: ${error_message}"
+ "\nCreation of param-table failed."
+ )
+ endif (NOT ${status} EQUAL 0)
+endif (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/create-docs.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/create-docs.html
new file mode 100644
index 0000000..47fa916
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/create-docs.html
@@ -0,0 +1,125 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>create-docs</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>create-docs</h1>
+<h2>Usage:</h2>
+<p><code>crux create-docs [options] <tool-name></code></p>
+<h2>Description:</h2>
+<p>This command prints to standard output an HTML formatted version of the documentation for a specified Crux command.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tool-name</code> – Specifies the Crux tool to generate documentation for. If the value is 'list', then a list of available tools will be given. If the value is 'default-params', then a default parameter file will be given.If the value is 'param-table' then a table will be printed showing which parameters are associated with which commands.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – The command prints to standard output the HTML documentation for the specified Crux tool.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<p>This command does not support any optional parameters.</p>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/default.params b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/default.params
new file mode 100644
index 0000000..3791557
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/default.params
@@ -0,0 +1,1832 @@
+################################################################################
+# Sample parameter file
+#
+# On each line, anything after a '#' will be ignored.
+# The format is:
+#
+# <parameter-name>=<value>
+#
+################################################################################
+
+# Crux parameter file (generated by Crux version 3.1)
+# Full documentation available at http://cruxtoolkit.sourceforge.net/
+# comet_version 2016.01 rev. 1
+# Everything following the '#' symbol is treated as a comment.
+
+# Path where pin file will be written instead of make-pin.pin.
+# It is optional for make-pin
+output-file=
+
+# Specify the verbosity of the current processes. Each level prints the
+# following messages, including all those at lower verbosity levels: 0-fatal
+# errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of
+# execution, 40-more progress information, 50-debug info, 60-detailed debug
+# info.
+# Available for all crux programs.
+verbosity=30
+
+# A file containing parameters.
+# Available for all crux programs. Any options specified on the command line
+# will override values in the parameter file.
+parameter-file=
+
+# Replace existing files if true or fail when trying to overwrite a file if
+# false.
+# Available for all crux programs. Applies to parameter file as well as index,
+# search, and analysis output files.
+overwrite=false
+
+# The minimum length of peptides to consider.
+# Used from the command line or parameter file by crux-generate-peptides, and
+# crux tide-index.
+min-length=6
+
+# The maximum length of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides, crux
+# tide-index.
+max-length=50
+
+# The minimum mass (in Da) of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides and
+# crux tide-index.
+min-mass=200
+
+# The maximum mass (in Da) of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides and
+# crux tide-index.
+max-mass=7200
+
+# The minimum number of peaks a spectrum must have for it to be searched.
+# Available for tide-search.
+min-peaks=20
+
+# Specify the enzyme used to digest the proteins in silico. Available enzymes
+# (with the corresponding digestion rules indicated in parentheses) include
+# no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin
+# ([FWYL]|{P}), elastase ([ALIV]|{P}), clostripain ([R]|[]), cyanogen-bromide
+# ([M]|[]), iodosobenzoate ([W]|[]), proline-endopeptidase ([P]|[]),
+# staph-protease ([E]|[]), asp-n ([]|[D]), lys-c ([K]|{P}), lys-n ([]|[K]),
+# arg-c ([R]|{P}), glu-c ([DE]|{P}), pepsin-a ([FL]|{P}),
+# elastase-trypsin-chymotrypsin ([ALIVKRWFY]|{P}). Specifying --enzyme no-enzyme
+# yields a non-enzymatic digest. Warning: the resulting index may be quite
+# large.
+# Available for crux-generate-peptides and crux tide-index.
+enzyme=trypsin
+
+# Specify rules for in silico digestion of protein sequences. Overrides the
+# enzyme option. Two lists of residues are given enclosed in square brackets or
+# curly braces and separated by a |. The first list contains residues
+# required/prohibited before the cleavage site and the second list is residues
+# after the cleavage site. If the residues are required for digestion, they are
+# in square brackets, '[' and ']'. If the residues prevent digestion, then they
+# are enclosed in curly braces, '{' and '}'. Use X to indicate all residues. For
+# example, trypsin cuts after R or K but not before P which is represented as
+# [RK]|{P}. AspN cuts after any residue but only before D which is represented
+# as [X]|[D].
+#
+custom-enzyme=
+
+# Specify whether every peptide in the database must have two enzymatic termini
+# (full-digest) or if peptides with only one enzymatic terminus are also
+# included (partial-digest).
+# Available for crux-generate-peptides and crux tide-index.
+digestion=full-digest
+
+# Maximum number of missed cleavages per peptide to allow in enzymatic
+# digestion.
+# Available from command line or parameter file for crux-generate-peptides. When
+# used with enzyme=<trypsin|elastase|chymotrypsin> includes peptides containing
+# one or more potential cleavage sites.
+missed-cleavages=0
+
+# Tolerance used for matching peptides to spectra. Peptides must be within +/-
+# 'precursor-window' of the spectrum value. The precursor window units depend
+# upon precursor-window-type.
+# Available for tide-search and crux-generate-peptides.
+precursor-window=3
+
+# Specify the units for the window that is used to select peptides around the
+# precursor mass location (mass, mz, ppm). The magnitude of the window is
+# defined by the precursor-window option, and candidate peptides must fall
+# within this window. For the mass window-type, the spectrum precursor m+h value
+# is converted to mass, and the window is defined as that mass +/-
+# precursor-window. If the m+h value is not available, then the mass is
+# calculated from the precursor m/z and provided charge. The peptide mass is
+# computed as the sum of the average amino acid masses plus 18 Da for the
+# terminal OH group. The mz window-type calculates the window as spectrum
+# precursor m/z +/- precursor-window and then converts the resulting m/z range
+# to the peptide mass range using the precursor charge. For the
+# parts-per-million (ppm) window-type, the spectrum mass is calculated as in the
+# mass type. The lower bound of the mass window is then defined as the spectrum
+# mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as
+# spectrum mass / (1.0 - (precursor-window / 1000000)).
+# Available for search-for-xlinks and tide-search.
+precursor-window-type=mass
+
+# Automatically estimate optimal value for the precursor-window parameter from
+# the spectra themselves. false=no estimation, warn=try to estimate but use the
+# default value in case of failure, fail=try to estimate and quit in case of
+# failure.
+# Available for tide-search.
+auto-precursor-window=false
+
+# Specify the parser to use for reading in MS/MS spectra.
+# Available for search-for-xlinks.
+spectrum-parser=pwiz
+
+# Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor
+# mass information from the "S" line or the "Z" line.
+# Available when spectrum-parser = pwiz.
+use-z-line=true
+
+# When creating decoy peptides using decoy-format=shuffle or
+# decoy-format=peptide-reverse, this option specifies whether the N-terminal and
+# C-terminal amino acids are kept in place or allowed to be shuffled or
+# reversed. For a target peptide "EAMPK" with decoy-format=peptide-reverse,
+# setting keep-terminal-aminos to "NC" will yield "EPMAK"; setting it to "C"
+# will yield "PMAEK"; setting it to "N" will yield "EKPMA"; and setting it to
+# "none" will yield "KPMAE".
+# Available for tide-index.
+keep-terminal-aminos=NC
+
+# Create in the output directory a text file listing of all the peptides in the
+# database, along with their neutral masses, one per line. If decoys are
+# generated, then a second file will be created containing the decoy peptides.
+# Decoys that also appear in the target database are marked with an asterisk in
+# a third column.
+# Available for tide-index.
+peptide-list=false
+
+# Stop after the specified pre-processing step.
+# Available for print-processed-spectra.
+stop-after=xcorr
+
+# Specify the output units for processed spectra.
+# Available for print-processed-spectra
+output-units=bin
+
+# Outputs an SQT results file to the output directory. Note that if sqt-output
+# is enabled, then compute-sp is automatically enabled and cannot be overridden.
+# Available for tide-search.
+sqt-output=false
+
+# Output an mzIdentML results file to the output directory.
+# Available for tide-search, percolator.
+mzid-output=false
+
+# Output a Percolator input (PIN) file to the output directory.
+# Available for tide-search.
+pin-output=false
+
+# Output a Percolator pout.xml format results file to the output directory.
+# Available for percolator.
+pout-output=false
+
+# Output a pepXML results file to the output directory.
+# Available for tide-search, q-ranker, barista, percolator.
+pepxml-output=false
+
+# Output a tab-delimited results file to the output directory.
+# Available for tide-search, percolator, q-ranker, barista.
+txt-output=true
+
+# Compute the preliminary score Sp for all candidate peptides. Report this score
+# in the output, along with the corresponding rank, the number of matched ions
+# and the total number of ions. This option is recommended if results are to be
+# analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp
+# is automatically enabled and cannot be overridden. Note that the Sp
+# computation requires re-processing each observed spectrum, so turning on this
+# switch involves significant computational overhead.
+# Available for tide-search.
+compute-sp=false
+
+# Estimate the parameters of the score distribution for each spectrum by fitting
+# to a Weibull distribution, and compute a p-value for each xlink product. This
+# option is only available when use-old-xlink=F.
+# Currently only implemented for XCORR.
+compute-p-values=false
+
+# A single scan number or a range of numbers to be searched. Range should be
+# specified as 'first-last' which will include scans 'first' and 'last'.
+# The search range x-y is inclusive of x and y.
+scan-number=
+
+# Before calculation of the XCorr score, the m/z axes of the observed and
+# theoretical spectra are discretized. This parameter specifies the size of each
+# bin. The exact formula for computing the discretized m/z value is
+# floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z
+# value. For low resolution ion trap ms/ms data 1.0005079 and for high
+# resolution ms/ms 0.02 is recommended.
+# Available for tide-search and xlink-assign-ions.
+mz-bin-width=1.0005079
+
+# In the discretization of the m/z axes of the observed and theoretical spectra,
+# this parameter specifies the location of the left edge of the first bin,
+# relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the
+# first bin will be located at +0.xx Da).
+# Available for tide-search.
+mz-bin-offset=0.4
+
+# Automatically estimate optimal value for the mz-bin-width parameter from the
+# spectra themselves. false=no estimation, warn=try to estimate but use the
+# default value in case of failure, fail=try to estimate and quit in case of
+# failure.
+# Available for tide-search.
+auto-mz-bin-width=false
+
+# Include flanking peaks around singly charged b and y theoretical ions. Each
+# flanking peak occurs in the adjacent m/z bin and has half the intensity of the
+# primary peak.
+# Available for the tide-search and search-for-xlinks commands.
+use-flanking-peaks=false
+
+# The lowest spectrum m/z to search in the ms2 file.
+# Available for tide-search.
+spectrum-min-mz=0
+
+# The highest spectrum m/z to search in the ms2 file.
+# Available for tide-search.
+spectrum-max-mz=1e+09
+
+# The spectrum charges to search. With 'all' every spectrum will be searched and
+# spectra with multiple charge states will be searched once at each charge
+# state. With 1, 2, or 3 only spectra with that charge state will be searched.
+# Used by tide-search.
+spectrum-charge=all
+
+# The fileroot string will be added as a prefix to all output file names.
+# Available for all commands that produce an output directory.
+fileroot=
+
+# The name of the directory where output files will be created.
+# Available for most commands.
+output-dir=crux-output
+
+# The name of the directory where temporary files will be created. If this
+# parameter is blank, then the system temporary directory will be used
+# Available for tide-index.
+temp-dir=
+
+# Specify the number of matches to report for each spectrum.
+# Available for tide-search and crux percolator
+top-match=5
+
+# When given a unsigned integer value seeds the random number generator with
+# that value. When given the string "time" seeds the random number generator
+# with the system time.
+# Available for all Crux commands.
+seed=1
+
+# Specify which isotopes to use in calculating fragment ion mass.
+# Used by crux-predict-peptide-ions.
+fragment-mass=mono
+
+# Specify the type of isotopic masses to use when calculating the peptide mass.
+# Used from command line or parameter file by crux-generate-peptides.
+isotopic-mass=mono
+
+# The minimum number of modifications that can be applied to a single peptide.
+# Available for tide-index.
+min-mods=0
+
+# The maximum number of modifications that can be applied to a single peptide.
+# Available for tide-index.
+max-mods=255
+
+# The maximum number of modified amino acids that can appear in one peptide.
+# Each aa can be modified multiple times.
+#
+max-aas-modified=255
+
+# Specify how sequence modifications are reported in various output files. Each
+# modification is reported as a number enclosed in square braces following the
+# modified residue; however, the number may correspond to one of three different
+# masses: (1) 'mod-only' reports the value of the mass shift induced by the
+# modification; (2) 'total' reports the mass of the residue with the
+# modification (residue mass plus modification mass); (3) 'separate' is the same
+# as 'mod-only', but multiple modifications to a single amino acid are reported
+# as a comma-separated list of values. For example, suppose amino acid D has an
+# unmodified mass of 115 as well as two moifications of masses +14 and +2. In
+# this case, the amino acid would be reported as D[16] with 'mod-only', D[131]
+# with 'total', and D[14,2] with 'separate'.
+# Available for generate-peptides.
+mod-mass-format=mod-only
+
+# Consider a-ions in the search? Note that an a-ion is equivalent to a neutral
+# loss of CO from the b-ion. Peak height is 10 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-a-ions=false
+
+# Consider b-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-b-ions=true
+
+# Consider c-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-c-ions=false
+
+# Consider x-ions in the search? Peak height is 10 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-x-ions=false
+
+# Consider y-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-y-ions=true
+
+# Consider z-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-z-ions=false
+
+# Set the precision for scores written to sqt and text files.
+# Available for all commands.
+precision=8
+
+# Set the precision for masses and m/z written to sqt and .txt files. Note that
+# this parameter only takes effect when specified in the parameter file.
+# Available for all commands.
+mass-precision=4
+
+# Show search progress by printing every n spectra searched. Set to 0 to show no
+# search progress.
+# Available for tide-search
+print-search-progress=1000
+
+# Specify the type of target-decoy search. Using 'auto', percolator attempts to
+# detect the search type automatically. Using 'separate' specifies two
+# searches: one against target and one against decoy protein db. Using
+# 'concatenated' specifies a single search on concatenated target-decoy protein
+# db.
+# Available for percolator
+search-input=auto
+
+# When given a unsigned integer value seeds the random number generator with
+# that value. When given the string "time" seeds the random number generator
+# with the system time.
+# Available for all percolator
+percolator-seed=1
+
+# Output the computed features in tab-delimited text format.
+# Available for percolator and q-ranker.
+feature-file-out=false
+
+# Include decoys (PSMs, peptides, and/or proteins) in the XML output.
+# Available for crux percolator
+decoy-xml-output=false
+
+# Specifies the prefix of the protein names that indicate a decoy.
+# Available for percolator
+decoy-prefix=decoy_
+
+# Output final weights to a file named "percolator.weights.txt".
+# Available for crux percolator
+output-weights=false
+
+# Read initial weights from the given file (one per line).
+# Available for crux percolator
+init-weights=
+
+# Only train Percolator on a subset of PSMs, and use the resulting score vector
+# to evaluate the other PSMs. Recommended when analyzing huge numbers (>1
+# million) of PSMs. When set to 0, all PSMs are used for training as normal.
+# Available for crux percolator
+subset-max-train=0
+
+# Penalty for mistakes made on positive examples. If this value is set to 0,
+# then it is set via cross validation over the values {0.1, 1, 10}, selecting
+# the value that yields the largest number of PSMs identified at the q-value
+# threshold set via the --test-fdr parameter.
+# Available for crux percolator
+c-pos=0
+
+# Penalty for mistake made on negative examples. If not specified, then this
+# value is set by cross validation over {0.1, 1, 10}.
+# Available for crux percolator
+c-neg=0
+
+# False discovery rate threshold to define positive examples in training.
+# Available for crux percolator
+train-fdr=0.01
+
+# False discovery rate threshold used in selecting hyperparameters during
+# internal cross-validation and for reporting the final results.
+# Available for crux percolator.
+test-fdr=0.01
+
+# Apply the specified threshold to PSM, peptide and protein probabilities to
+# obtain a faster estimate of the alpha, beta and gamma parameters.
+# Available for crux percolator.
+fido-fast-gridsearch=0
+
+# Do not approximate the posterior distribution by allowing large graph
+# components to be split into subgraphs. The splitting is done by duplicating
+# peptides with low probabilities. Splitting continues until the number of
+# possible configurations of each subgraph is below 2^18
+# Available for crux percolator
+fido-no-split-large-components=false
+
+# To speed up inference, proteins for which none of the associated peptides has
+# a probability exceeding the specified threshold will be assigned probability =
+# 0.
+# Available for crux percolator
+fido-protein-truncation-threshold=0.01
+
+# Use target-decoy competition to assign q-values and PEPs. When set to F, the
+# mix-max method, which estimates the proportion pi0 of incorrect target PSMs,
+# is used instead.
+# Available for crux percolator
+tdc=true
+
+# Maximum number of iterations for training.
+# Available for crux percolator
+maxiter=10
+
+# Quicker execution by reduced internal cross-validation.
+# Available for crux percolator
+quick-validation=false
+
+# In its initial round of training, Percolator uses one feature to induce a
+# ranking of PSMs. By default, Percolator will select the feature that produces
+# the largest set of target PSMs at a specified FDR threshold (cf. --train-fdr).
+# This option allows the user to specify which feature is used for the initial
+# ranking, using the name as a string. The name can be preceded by a hyphen
+# (e.g. "-XCorr") to indicate that a lower value is better.
+# Available for crux percolator
+default-direction=
+
+# Use unit normalization (i.e., linearly rescale each PSM's feature vector to
+# have a Euclidean length of 1), instead of standard deviation normalization.
+# Available for crux percolator.
+unitnorm=false
+
+# Measure performance on test set each iteration.
+# Available for crux percolator.
+test-each-iteration=false
+
+# When set to T, interpret the input file as a PIN file.
+# Available for crux percolator.
+feature-file-in=false
+
+# Use the picked protein-level FDR to infer protein probabilities, provide the
+# fasta file as the argument to this flag.
+# Available for crux percolator
+picked-protein=
+
+# Type of enzyme
+# Available for crux percolator
+protein-enzyme=trypsin
+
+# By default, if the peptides associated with protein A are a proper subset of
+# the peptides associated with protein B, then protein A is eliminated and all
+# the peptides are considered as evidence for protein B. Note that this
+# filtering is done based on the complete set of peptides in the database, not
+# based on the identified peptides in the search results. Alternatively, if this
+# option is set and if all of the identified peptides associated with protein B
+# are also associated with protein A, then Percolator will report a
+# comma-separated list of protein IDs, where the full-length protein B is first
+# in the list and the fragment protein A is listed second. Not available for
+# Fido.
+# Available for crux percolator
+protein-report-fragments=false
+
+# If multiple database proteins contain exactly the same set of peptides, then
+# Percolator will randomly discard all but one of the proteins. If this option
+# is set, then the IDs of these duplicated proteins will be reported as a
+# comma-separated list. Not available for Fido.
+# Available for crux percolator
+protein-report-duplicates=false
+
+# Use the Fido algorithm to infer protein probabilities. Must be true to use any
+# of the Fido options.
+# Available for crux percolator
+protein=false
+
+# Specify the probability with which a present protein emits an associated
+# peptide. Set by grid search (see --fido-gridsearch-depth parameter) if not
+# specified.
+# Available for crux percolator if --protein T is set.
+fido-alpha=0
+
+# Specify the probability of the creation of a peptide from noise. Set by grid
+# search (see --fido-gridsearch-depth parameter) if not specified.
+# Available for crux percolator if --protein T is set.
+fido-beta=0
+
+# Specify the prior probability that a protein is present in the sample. Set by
+# grid search (see --fido-gridsearch-depth parameter) if not specified.
+# Available for crux percolator if --protein T is set.
+fido-gamma=0
+
+# Estimate empirical p-values and q-values for proteins using target-decoy
+# analysis.
+# Available for crux percolator if --protein T is set.
+fido-empirical-protein-q=false
+
+# Set depth of the grid search for alpha, beta and gamma estimation.
+# Available for crux percolator if --protein T is set.
+fido-gridsearch-depth=0
+
+# Q-value threshold that will be used in the computation of the MSE and ROC AUC
+# score in the grid search.
+# Available for crux percolator if --protein T is set.
+fido-gridsearch-mse-threshold=0.05
+
+# By default, Percolator will examine the learned weights for each feature, and
+# if the weight appears to be problematic, then percolator will discard the
+# learned weights and instead employ a previously trained, static score vector.
+# This switch allows this error checking to be overriden.
+# Available for crux percolator.
+override=false
+
+# Use retention time features calculated as in "Improving tandem mass spectrum
+# identification using peptide retention time prediction across diverse
+# chromatography conditions" by Klammer AA, Yi X, MacCoss MJ and Noble WS.
+# (Analytical Chemistry. 2007 Aug 15;79(16):6111-8.).
+# Available for crux percolator
+klammer=false
+
+# Do not remove redundant peptides; keep all PSMs and exclude peptide level
+# probability.
+# Available for crux percolator
+only-psms=false
+
+# Include a decoy version of every peptide by shuffling or reversing the target
+# sequence or protein. In shuffle or peptide-reverse mode, each peptide is
+# either reversed or shuffled, leaving the N-terminal and C-terminal amino acids
+# in place. Note that peptides appear multiple times in the target database are
+# only shuffled once. In peptide-reverse mode, palindromic peptides are
+# shuffled. Also, if a shuffled peptide produces an overlap with the target or
+# decoy database, then the peptide is re-shuffled up to 5 times. Note that,
+# despite this repeated shuffling, homopolymers will appear in both the target
+# and decoy database. The protein-reverse mode reverses the entire protein
+# sequence, irrespective of the composite peptides.
+# Available for tide-index
+decoy-format=shuffle
+
+# Expression for static and variable mass modifications to include. Specify a
+# comma-separated list of modification sequences of the form:
+# C+57.02146,2M+15.9949,1STY+79.966331,...
+# Available for tide-index
+mods-spec=C+57.02146
+
+# Specifies N-terminal static and variable mass modifications on peptides.
+# Specify a comma-separated list of N-terminal modification sequences of the
+# form: 1E-18.0106,C-17.0265
+# Available for tide-index
+nterm-peptide-mods-spec=
+
+# Specifies C-terminal static and variable mass modifications on peptides.
+# Specify a comma-separated list of C-terminal modification sequences of the
+# form: X+21.9819
+# Available for tide-index
+cterm-peptide-mods-spec=
+
+# Specify the name of the file where the binarized fragmentation spectra will be
+# stored. Subsequent runs of crux tide-search will execute more quickly if
+# provided with the spectra in binary format. The filename is specified relative
+# to the current working directory, not the Crux output directory (as specified
+# by --output-dir). This option is not valid if multiple input spectrum files
+# are given.
+# Available for tide-search
+store-spectra=
+
+# Enable the calculation of exact p-values for the XCorr score. Calculation of
+# p-values increases the running time but increases the number of
+# identifications at a fixed confidence threshold. The p-values will be reported
+# in a new column with header "exact p-value", and the "xcorr score" column will
+# be replaced with a "refactored xcorr" column. Note that, currently, p-values
+# can only be computed when the mz-bin-width parameter is set to its default
+# value. Variable and static mods are allowed on non-terminal residues in
+# conjunction with p-value computation, but currently only static mods are
+# allowed on the N-terminus, and no mods on the C-terminus.
+# Available for tide-search
+exact-p-value=false
+
+# When providing a FASTA file as the index, the generated binary index will be
+# stored at the given path. This option has no effect if a binary index is
+# provided as the index.
+# Available for tide-search
+store-index=
+
+# When set to T, target and decoy search results are reported in a single file,
+# and only the top-scoring N matches (as specified via --top-match) are reported
+# for each spectrum, irrespective of whether the matches involve target or decoy
+# peptides.
+# Available for tide-search
+concat=false
+
+# Include the file column in tab-delimited output.
+# Available for tide-search
+file-column=true
+
+# If true, all peaks around the precursor m/z will be removed, within a range
+# specified by the --remove-precursor-tolerance option.
+# Available for tide-search.
+remove-precursor-peak=false
+
+# This parameter specifies the tolerance (in Th) around each precursor m/z that
+# is removed when the --remove-precursor-peak option is invoked.
+# Available for print-processed spectra and tide-search.
+remove-precursor-tolerance=1.5
+
+# When set to T, for each protein that begins with methionine, tide-index will
+# put two copies of the leading peptide into the index, with and without the
+# N-terminal methionine.
+# Available for tide-index.
+clip-nterm-methionine=false
+
+# Prevent duplicate peptides between the target and decoy databases. When set to
+# "F", the program keeps all target and previously generated decoy peptides in
+# memory. A shuffled decoy will be re-shuffled multiple times to avoid
+# duplication. If a non-duplicated peptide cannot be generated, the decoy is
+# skipped entirely. When set to "T", every decoy is added to the database
+# without checking for duplication. This option reduces the memory requirements
+# significantly.
+# Available for tide-index.
+allow-dups=false
+
+# Controls whether neutral loss ions are considered in the search. Two types of
+# neutral losses are included and are applied only to singly charged b- and
+# y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each
+# neutral loss peak has intensity 1/5 of the primary peak.
+# Available for tide-search.
+use-neutral-loss-peaks=true
+
+# The maximum charge state of a spectra to consider in search.
+# Available for tide-search.
+max-precursor-charge=5
+
+# Carries out a peptide-centric search. For each peptide the top-scoring spectra
+# are reported, in contrast to the standard spectrum-centric search where the
+# top-scoring peptides are reported. Note that in this case the "xcorr rank"
+# column will contain the rank of the given spectrum with respect to the given
+# candidate peptide, rather than vice versa (which is the default).
+# Available for tide-search.
+peptide-centric-search=false
+
+# Skip preprocessing steps on spectra. Default = F.
+# Available for tide-search
+skip-preprocessing=false
+
+# List of positive, non-zero integers.
+# Isotope errors to include. Specify a comma-separated list of isotope errors of
+# the form: 1,2,3,...Available for tide-search
+isotope-error=
+
+# 0=poll CPU to set num threads; else specify num threads directly.
+# Available for tide-search tab-delimited files only.
+num-threads=0
+
+# Analysis begins with a pre-processsing step that creates a set of lookup
+# tables which are then used during training. Normally, these lookup tables are
+# deleted at the end of the analysis, but setting this option to T prevents the
+# deletion of these tables. Subsequently, analyses can be repeated more
+# efficiently by specifying the --re-run option.
+# Available for q-ranker and barista.
+skip-cleanup=false
+
+# Re-run a previous analysis using a previously computed set of lookup tables.
+# For this option to work, the --skip-cleanup option must have been set to true
+# when the program was run the first time.
+# Available for q-ranker and barista.
+re-run=
+
+# Use an enriched feature set, including separate features for each ion type.
+# Available for q-ranker and barista.
+use-spec-features=true
+
+# If the target and decoy searches were run separately, rather than using a
+# concatenated database, then the program will assume that the database search
+# results provided as a required argument are from the target database search.
+# This option then allows the user to specify the location of the decoy search
+# results. Like the required arguments, these search results can be provided as
+# a single file, a list of files or a directory. However, the choice (file, list
+# or directory) must be consistent for the MS2 files and the target and decoy
+# tab-delimited files. Also, if the MS2 and tab-delimited files are provided in
+# directories, then Q-ranker will use the MS2 filename (foo.ms2) to identify
+# corresponding target and decoy tab-delimited files with names like
+# foo*.target.txt and foo*.decoy.txt. This naming convention allows the target
+# and decoy txt files to reside in the same directory.
+# Available for q-ranker and barista.
+separate-searches=
+
+# Specify that the search results are provided as lists of files, rather than as
+# individual files.
+# Available for barista and percolator.
+list-of-files=false
+
+# Specifies whether to do optimization at the protein, peptide or psm level.
+# Available for barista.
+optimization=protein
+
+# Specify the method used to estimate q-values. The mix-max procedure or
+# target-decoy competition apply to PSMs. The peptide-level option eliminates
+# any PSM for which there exists a better scoring PSM involving the same
+# peptide, and then uses decoys to assign confidence estimates.
+# Used by assign-confidence.
+estimation-method=tdc
+
+# Adjust the score using the Sidak adjustment and reports them in a new column
+# in the output file. Note that this adjustment only makes sense if the given
+# scores are p-values, and that it requires the presence of the "distinct
+# matches/spectrum" feature for each PSM.
+# Used by assign-confidence.
+sidak=false
+
+# Specify the column (for tab-delimited input) or tag (for XML input) used as
+# input to the q-value estimation procedure. If this parameter is unspecified,
+# then the program searches for "xcorr score", "evalue" (comet), "exact p-value"
+# score fields in this order in the input file.
+# Used by assign-confidence.
+score=
+
+# Specify this parameter to T in order to combine charge states with peptide
+# sequencesin peptide-centric search. Works only if estimation-method =
+# peptide-level.
+# Used by assign-confidence.
+combine-charge-states=false
+
+# Specify this parameter to T in order to treat peptides carrying different or
+# no modifications as being the same. Works only if estimation = peptide-level.
+# Used by assign-confidence.
+combine-modified-peptides=false
+
+# The q-value threshold used by cascade search. Each spectrum identified in one
+# search with q-value less than this threshold will be excluded from all
+# subsequent searches.
+# Used by Cascade-Search
+q-value-threshold=0.01
+
+# Predict the specified primary ion series. 'a' indicates a-ions only, 'b'
+# indicates b-ions only, 'y' indicates y-ions only, 'by' indicates both b and y,
+# 'bya' indicates b, y, and a.
+# Only available for crux-predict-peptide-ions. Set automatically to 'by' for
+# searching.
+primary-ions=by
+
+# Predict the precursor ions, and all associated ions (neutral losses, multiple
+# charge states) consistent with the other specified options.
+# Only available for crux-predict-peptide-ions.
+precursor-ions=false
+
+# Predict the given number of isotope peaks (0|1|2).
+# Only available for crux-predict-peptide-ion. Automatically set to 0 for Sp
+# scoring and 1 for xcorr scoring.
+isotope=0
+
+# Predict flanking peaks for b- and y ions.
+# Only available for crux-predict-peptide-ion.
+flanking=false
+
+# Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the
+# charge state of the peptide ("peptide"). If the max-ion-charge is greater than
+# the charge state of the peptide, then the maximum is the peptide charge.
+# Available for predict-peptide-ions and search-for-xlinks. Set to 'peptide' for
+# search.
+max-ion-charge=peptide
+
+# Include among the predicted peaks b/y ions with up to n losses of nh3. For
+# example, for --nh3 2, predict a peak for each b- and y-ion with the loss of
+# one nh3 group and predict a second peak for each b- and y-ion with the loss of
+# two nh3 groups. These peaks will have 1 and 2, respectively, in the NH3 column
+# of the output.
+# Only available for crux-predict-peptide-ions.
+nh3=0
+
+# Include in the predicted peaks, b/y ions with the loss of 1 to n water
+# molecules. See --nh3 for an example.
+# Only available for crux-predict-peptide-ions.
+h2o=0
+
+# The name of the file in FASTA format.
+# Option for spectral-counts
+protein-database=
+
+# Type of analysis to make on the match results: (RAW|NSAF|dNSAF|SIN|EMPAI).
+# With exception of the RAW metric, the database of sequences need to be
+# provided using --protein-database.
+# Available for spectral-counts. RAW is raw counts, NSAF is Normalized Spectral
+# Abundance Factor, dNSAF is Distributed Spectral Abundance Factor, SIN is
+# Spectral Index Normalized and EMPAI is Exponentially Modified Protein
+# Abundance Index
+measure=NSAF
+
+# Ignore peptides that map to multiple proteins.
+# Available for spectral-counts.
+unique-mapping=false
+
+# Quantification at protein or peptide level.
+# Available for spectral-counts and either NSAF and SIN.
+quant-level=protein
+
+# Perform a parsimony analysis on the proteins, and report a "parsimony rank"
+# column in the output file. This column contains integers indicating the
+# protein's rank in a list sorted by spectral counts. If the parsimony analysis
+# results in two proteins being merged, then their parsimony rank is the same.
+# In such a case, the rank is assigned based on the largest spectral count of
+# any protein in the merged meta-protein. The "simple" parsimony algorithm only
+# merges two proteins A and B if the peptides identified in protein A are the
+# same as or a subset of the peptides identified in protein B. The "greedy"
+# parsimony algorithm does additional merging, using the peptide q-values to
+# greedily assign each peptide to a single protein.
+# Available for spectral-counts.
+parsimony=none
+
+# Determines what type of threshold to use when filtering matches. none : read
+# all matches, qvalue : use calculated q-value from percolator or q-ranker,
+# custom : use --custom-threshold-name and --custom-threshold-min parameters.
+# used for crux spectral-counts
+threshold-type=qvalue
+
+# Only consider PSMs with a threshold value. By default, q-values are
+# thresholded using a specified threshold value. This behavior can be changed
+# using the --custom-threshold and --threshold-min parameters.
+# Available for spectral-counts. All PSMs with higher (or lower) than this will
+# be ignored.
+threshold=0.01
+
+# Specify which field to apply the threshold to. The direction of the threshold
+# (<= or >=) is governed by --custom-threshold-min. By default, the threshold
+# applies to the q-value, specified by "percolator q-value", "q-ranker q-value",
+# "decoy q-value (xcorr)", or "barista q-value".
+# Available for spectral-counts.
+custom-threshold-name=
+
+# When selecting matches with a custom threshold, custom-threshold-min
+# determines whether to filter matches with custom-threshold-name values that
+# are greater-than or equal (F) or less-than or equal (T) than the threshold.
+# Available for spectral-counts.
+custom-threshold-min=true
+
+# MS2 file corresponding to the psm file. Required to measure the SIN. Ignored
+# for NSAF, dNSAF and EMPAI.
+# Available for spectral-counts with measure=SIN.
+input-ms2=
+
+# Use mzid's passThreshold attribute to filter matches.
+# Used when parsing mzIdentML files.
+mzid-use-pass-threshold=false
+
+# Change the mass of all amino acids 'A' by the given amount.
+#
+A=0
+
+# Change the mass of all amino acids 'C' by the given amount.
+#
+C=57.021464
+
+# Change the mass of all amino acids 'D' by the given amount.
+#
+D=0
+
+# Change the mass of all amino acids 'E' by the given amount.
+#
+E=0
+
+# Change the mass of all amino acids 'F' by the given amount.
+#
+F=0
+
+# Change the mass of all amino acids 'G' by the given amount.
+#
+G=0
+
+# Change the mass of all amino acids 'H' by the given amount.
+#
+H=0
+
+# Change the mass of all amino acids 'I' by the given amount.
+#
+I=0
+
+# Change the mass of all amino acids 'K' by the given amount.
+#
+K=0
+
+# Change the mass of all amino acids 'L' by the given amount.
+#
+L=0
+
+# Change the mass of all amino acids 'M' by the given amount.
+#
+M=0
+
+# Change the mass of all amino acids 'N' by the given amount.
+#
+N=0
+
+# Change the mass of all amino acids 'P' by the given amount.
+#
+P=0
+
+# Change the mass of all amino acids 'Q' by the given amount.
+#
+Q=0
+
+# Change the mass of all amino acids 'R' by the given amount.
+#
+R=0
+
+# Change the mass of all amino acids 'S' by the given amount.
+#
+S=0
+
+# Change the mass of all amino acids 'T' by the given amount.
+#
+T=0
+
+# Change the mass of all amino acids 'V' by the given amount.
+#
+V=0
+
+# Change the mass of all amino acids 'W' by the given amount.
+#
+W=0
+
+# Change the mass of all amino acids 'Y' by the given amount.
+#
+Y=0
+
+# Legal values are auto, tsv, sqt, pepxml or mzidentml format.
+# option, for psm-convert
+input-format=auto
+
+# Whether matches/ion are distinct (as opposed to total).
+# option, for psm-convert.
+distinct-matches=true
+
+# Rather than the spectrum, output summary statistics to standard output. Each
+# statistic is placed on a separate line, in the format <name>:<value> (e.g.
+# "TIC:1000.0").
+# Available only for crux-get-ms2-spectrum. Does not affect contents of the
+# output file.
+stats=false
+
+# write out the weibull training points for thespectrum,charge
+# Available for crux search-for-xlinks
+write-weibull-points=false
+
+# Print the theoretical spectrum
+# Available for xlink-predict-peptide-ions.
+print-theoretical-spectrum=false
+
+# Use the old version of xlink-searching algorithm. When false, a new version of
+# the code is run. The new version supports variable modifications and can
+# handle more complex databases. This new code is still in development and
+# should be considered a beta release.
+# Available for search-for-xlinks program.
+use-old-xlink=true
+
+# Score method for xlink {composite, modification, concatenated}.
+# Available for xlink-score-spectrum.
+xlink-score-method=composite
+
+# Provides a list of isotopic windows to search. For example, -1,0,1 will search
+# in three disjoint windows: (1) precursor_mass - neutron_mass +/- window, (2)
+# precursor_mass +/- window, and (3) precursor_mass + neutron_mass +/- window.
+# The window size is defined from the precursor-window and precursor-window-type
+# parameters. This option is only available when use-old-xlink=F.
+# Used for crux search-for-xlinks
+isotope-windows=0
+
+# Top-n open-mod peptides to consider in the second pass, value of 0 will search
+# all candiates.
+# Available for crux search-for-xlinks
+xlink-top-n=250
+
+# If there is no cross-link candidate found, then don't bother looking for
+# linear, self-loop, and dead-link candidates.
+# Available for crux search-for-xlinks program.
+require-xlink-candidate=false
+
+# Include linear peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-linears=true
+
+# Include dead-end peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-deadends=true
+
+# Include self-loop peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-selfloops=true
+
+# Include intra-protein cross-link candiates within the search.
+# Available for crux search-for-xlinks program.
+xlink-include-intra=true
+
+# Include inter-protein cross-link candidates within the search.
+# Available for crux search-for-xlinks program.
+xlink-include-inter=true
+
+# Include crosslink candidates that are both inter and intra.
+# Available for crux search-for-xlinks program.
+xlink-include-inter-intra=true
+
+# List of amino acids for which the cross-linker can prevent cleavage. This
+# option is only available when use-old-xlink=F.
+# Available for search-for-xlinks program.
+xlink-prevents-cleavage=K
+
+# Specify the maximum number of modifications allowed on a crosslinked peptide.
+# This option is only available when use-old-xlink=F.
+# Available for crux search-for-xlinks
+max-xlink-mods=255
+
+# Search decoy peptides within +/- precursor-window-weibull of the precursor
+# mass. The resulting scores are used only for fitting the Weibull distribution
+# Available for crux search-for-xlinks.
+precursor-window-weibull=20
+
+# Window type to use in conjunction with the precursor-window-weibull parameter.
+# Available for crux search-for-xlinks
+precursor-window-type-weibull=mass
+
+# Keep shuffling and collecting XCorr scores until the minimum number of points
+# for weibull fitting (using targets and decoys) is achieved.
+# Available for crux search-for-xlinks
+min-weibull-points=4000
+
+# Determines which spectral feature detection algorithm to use. Different
+# results are possible with each algorithm, and there are pros and cons to each.
+# Available for crux hardklor
+hardklor-algorithm=version1
+
+# Defines alternative averagine models in the analysis that incorporate
+# additional atoms and/or isotopic enrichments. Modifications are represented as
+# text strings. Inclusion of additional atoms in the model is done using by
+# entering an atomic formula, such as: PO2 or Cl. Inclusion of isotopic
+# enrichment to the model is done by specifying the percent enrichment (as a
+# decimal) followed by the atom being enriched and an index of the isotope. For
+# example, 0.75H1 specifies 75% enrichment of the first heavy isotope of
+# hydrogen. In other words, 75% deuterium enrichment. Two or more modifications
+# can be combined into the same model, and separated by spaces: B2 0.5B1
+# Available for crux hardklor
+averagine-mod=
+
+# Boxcar averaging is a sliding window that averages n adjacent spectra prior to
+# feature detection. Averaging generally improves the signal-to-noise ratio of
+# features in the spectra, as well as improving the shape of isotopic envelopes.
+# However, averaging will also change the observed peak intensities. Averaging
+# with too wide a window will increase the occurrence of overlapping features
+# and broaden the chromatographic profiles of observed features. The number
+# specified is the total adjacent scans to be combined, centered on the scan
+# being analyzed. Therefore, an odd number is recommended to center the boxcar
+# window. For example, a value of 3 would produce an average of the scan of
+# interest, plus one scan on each side. A value of 0 disables boxcar averaging.
+# Available for crux hardklor
+boxcar-averaging=0
+
+# This parameter is only functional when boxcar-averaging is used. The filter
+# will remove any peaks not seen in n scans in the boxcar window. The effect is
+# to reduce peak accumulation due to noise and reduce chromatographic broadening
+# of peaks. Caution should be used as over-filtering can occur. The suggested
+# number of scans to set for filtering should be equal to or less than the
+# boxcar-averaging window size. A value of 0 disables filtering.
+# Available for crux hardklor
+boxcar-filter=0
+
+# This parameter is only functional when boxcar-filter is used. The value
+# specifies the mass tolerance in ppm for declaring a peak the same prior to
+# filtering across all scans in the boxcar window.
+# Available for crux hardklor
+boxcar-filter-ppm=10
+
+# Indicates whether the data contain profile or centroided peaks.
+# Available for crux hardklor
+centroided=false
+
+# Choose the charge state determination method.
+# Available for crux hardklor
+cdm=Q
+
+# Specifies the minimum charge state to allow when finding spectral features. It
+# is best to set this value to the lowest assumed charge state to be present. If
+# set higher than actual charge states that are present, those features will not
+# be identified or incorrectly assigned a different charge state and mass.
+# Available for crux hardklor
+min-charge=1
+
+# Specifies the maximum charge state to allow when finding spectral features. It
+# is best to set this value to a practical number (i.e. do not set it to 20 when
+# doing a tryptic shotgun analysis). If set higher than actual charge states
+# that are present, the algorithm will perform significantly slower without any
+# improvement in results.
+# Available for crux hardklor
+max-charge=5
+
+# Sets the correlation threshold (cosine similarity) for accepting each
+# predicted feature.
+# Available for crux hardklor
+corr=0.85
+
+# Sets the depth of combinatorial analysis. For a given set of peaks in a
+# spectrum, search for up to this number of combined peptides that explain the
+# observed peaks. The analysis stops before depth is reached if the current
+# number of deconvolved features explains the observed peaks with a correlation
+# score above the threshold defined with the correlation parameter.
+# Available for crux hardklor
+depth=3
+
+# When reporting each feature, report abundance as the sum of all isotope peaks.
+# The value reported is the estimate of the correct peak heights based on the
+# averagine model scaled to the observed peak heights.
+# Available for crux hardklor
+distribution-area=false
+
+# Specifies an ASCII text file that defines symbols for the periodic table.
+# Available for crux hardklor
+hardklor-data-file=
+
+# Indicates the type of instrument used to collect data. This parameter,
+# combined with the resolution parameter, define how spectra will be centroided
+# (if you provide profile spectra) and the accuracy when aligning observed peaks
+# to the models.
+# Available for crux hardklor
+instrument=fticr
+
+# Specifies an ASCII text file that can be read to override the natural isotope
+# abundances for all elements.
+# Available for crux hardklor
+isotope-data-file=
+
+# Specifies the maximum number of models to build for a set of peaks being
+# analyzed. Regardless of the setting, the number of models will never exceed
+# the number of peaks in the current set. However, as many of the low abundance
+# peaks are noise or tail ends of distributions, defining models for them is
+# detrimental to the analysis.
+# Available for crux hardklor
+max-features=10
+
+# Filters the spectra prior to analysis for the requested MS/MS level. For
+# example, if the data contain MS and MS/MS spectra, setting mzxml-filter = 1
+# will analyze only the MS scan events. Setting mzxml-filter = 2 will analyze
+# only the MS/MS scan events.
+# Available for crux hardklor
+mzxml-filter=1
+
+# Constrains the search in each spectrum to signals below this value in
+# Thomsons. Setting to 0 disables this feature.
+# Available for crux hardklor
+mz-max=0
+
+# Constrains the search in each spectrum to signals above this value in
+# Thomsons. Setting to 0 disables this feature.
+# Available for crux hardklor
+mz-min=0
+
+# Only used when algorithm = version1. Defines the maximum window size in
+# Thomsons to analyze when deconvolving peaks in a spectrum into features.
+# Available for crux hardklor
+mz-window=4
+
+# Specifies the resolution of the instrument at 400 m/z for the data being
+# analyzed.
+# Available for crux hardklor
+resolution=100000
+
+# Used to restrict analysis to spectra with scan numbers below this parameter
+# value. A value of 0 disables this feature.
+# Available for crux hardklor
+scan-range-max=0
+
+# Used to restrict analysis to spectra with scan numbers above this parameter
+# value. A value of 0 disables this feature.
+# Available for crux hardklor
+scan-range-min=0
+
+# Set the sensitivity level. There are four levels: 0 (low), 1 (moderate), 2
+# (high), and 3 (max). Increasing the sensitivity will increase computation
+# time, but will also yield more isotope distributions.
+# Available for crux hardklor
+sensitivity=2
+
+# Filters spectra to remove peaks below this signal-to-noise ratio prior to
+# finding features.
+# Available for crux hardklor
+signal-to-noise=1
+
+# Uses Savitzky-Golay smoothing on profile peak data prior to centroiding the
+# spectra. This parameter is recommended for low resolution spectra only.
+# Smoothing data causes peak depression and broadening. Only use odd numbers for
+# the degree of smoothing (as it defines a window centered on each data point).
+# Higher values will produce smoother peaks, but with greater depression and
+# broadening. Setting this parameter to 0 disables smoothing.
+# Available for crux hardklor
+smooth=0
+
+# Set the signal-to-noise window length (in m/z). Because noise may be
+# non-uniform across a spectrum, this value adjusts the segment size considered
+# when calculating a signal-over-noise ratio.
+# Available for crux hardklor
+sn-window=250
+
+# Applies the lowest noise threshold of any sn_window across the entire mass
+# range for a spectrum. Setting this parameter to 0 turns off this feature, and
+# different noise thresholds will be used for each local mass window in a
+# spectrum.
+# Available for crux hardklor
+static-sn=true
+
+# Ignore PPIDs that persist for longer than this length of time in the MS1
+# spectra. The unit of time is whatever unit is used in your data file (usually
+# minutes). These PPIDs are considered contaminants.
+# Available for crux bullseye
+max-persist=2
+
+# When true, require an exact match (as defined by --exact-tolerance) between
+# the center of the precursor isolation window in the MS2 scan and the base
+# isotopic peak of the PPID. If this option is set to false and no exact match
+# is observed, then attempt to match using a wider m/z tolerance. This wider
+# tolerance is calculated using the PPID's monoisotopic mass and charge (the
+# higher the charge, the smaller the window).
+# Available for crux bullseye
+exact-match=false
+
+# Allowed gap size when checking for PPIDs across consecutive MS1 scans.
+# Available for crux bullseye
+gap-tolerance=1
+
+# Only consider PPIDs above this minimum mass in daltons.
+# Available for crux bullseye
+bullseye-min-mass=600
+
+# Only consider PPIDs below this maximum mass in daltons.
+# Available for crux bullseye
+bullseye-max-mass=8000
+
+# Set the tolerance (+/-ppm) for --exact-match.
+# Available for crux bullseye
+exact-tolerance=10
+
+# Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans.
+# Available for crux bullseye
+persist-tolerance=10
+
+# Total number of MS1 scans over which a PPID must be observed to be considered
+# real. Gaps in persistence are allowed by setting --gap-tolerance.
+# Available for crux bullseye
+scan-tolerance=3
+
+# Set the tolerance (+/-units) around the retention time over which a PPID can
+# be matches to the MS2 spectrum. The unit of time is whatever unit is used in
+# your data file (usually minutes).
+# Available for crux bullseye
+retention-tolerance=0.5
+
+# The format to write the output spectra to. If empty, the spectra will be
+# output in the same format as the MS2 input.
+# Available for crux bullseye
+spectrum-format=
+
+# Sort in ascending (T) or descending (F) order.
+# Available for sort-by-column
+ascending=true
+
+# Specify the input and output delimiter to use when processing the delimited
+# file. The argument can be either a single character or the keyword 'tab.'
+# Available for the delimited utility programs.
+delimiter=tab
+
+# Print the header line of the file, in addition to the columns that match.
+# Available for crux extract-columns and extract-rows
+header=true
+
+# Specifies the data type of the column, either an integer (int), a floating
+# point number (real), or a string.
+# Available for crux extract-rows
+column-type=string
+
+# Specify the operator that is used to compare an entry in the specified column
+# to the value given on the command line.
+# Available for crux extract-rows
+comparison=eq
+
+# Run the Bullseye algorithm on the given MS data, using it to assign
+# high-resolution precursor values to the MS/MS data. If a spectrum file ends
+# with .ms2 or .cms2, matching .ms1/.cms1 files will be used as the MS1 file.
+# Otherwise, it is assumed that the spectrum file contains both MS1 and MS2
+# scans.
+# Available for crux pipeline
+bullseye=false
+
+# Specify which search engine to use.
+# Available for crux pipeline
+search-engine=tide-search
+
+# Specify which post-processor to apply to the search results.
+# Available for crux pipeline
+post-processor=percolator
+
+# Minimum precursor m/z value to use in measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-min-precursor-mz=400
+
+# Minimum precursor m/z value to use in measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-max-precursor-mz=1800
+
+# Minimum fragment m/z value to use in measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-min-frag-mz=150
+
+# Maximum fragment m/z value to use in measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-max-frag-mz=1800
+
+# Minimum fragment peaks an MS/MS scan must contain to be used in measurement
+# error estimation.
+# Available for param-medic and tide-search and comet
+pm-min-scan-frag-peaks=40
+
+# Maximum ppm distance between precursor m/z values to consider two scans
+# potentially generated by the same peptide for measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-max-precursor-delta-ppm=50
+
+# Precursor charge state to consider MS/MS spectra from, in measurement error
+# estimation. Ideally, this should be the most frequently occurring charge state
+# in the given data.
+# Available for param-medic and tide-search and comet
+pm-charge=2
+
+# Number of most-intense fragment peaks to consider for measurement error
+# estimation, per MS/MS spectrum.
+# Available for param-medic and tide-search and comet
+pm-top-n-frag-peaks=30
+
+# Number of fragment peaks per spectrum pair to be used in fragment error
+# estimation.
+# Available for param-medic and tide-search and comet
+pm-pair-top-n-frag-peaks=5
+
+# Number of the most-intense peaks that two spectra must share in order to
+# potentially be generated by the same peptide, for measurement error
+# estimation.
+# Available for param-medic and tide-search and comet
+pm-min-common-frag-peaks=20
+
+# Maximum number of scans two spectra can be separated by in order to be
+# considered potentially generated by the same peptide, for measurement error
+# estimation.
+# Available for param-medic and tide-search and comet
+pm-max-scan-separation=1000
+
+# Minimum number of peak pairs (for precursor or fragment) that must be
+# successfully paired in order to attempt to estimate measurement error
+# distribution.
+# Available for param-medic and tide-search and comet
+pm-min-peak-pairs=100
+
+# Consider modifications on any amino acid in aa list with at most
+# max-per-peptide in one peptide. The parameter takes the form
+# <mass change>:<aa list>:<max per
+# peptide>:<prevents cleavage>:<prevents cross-link>. This parameter
+# may be included with different values multiple times so long as the
+# total number of mod, cmod, and nmod parameters does not exceed 11. The
+# "prevents cleavage" and "prevents cross-link" arguments are optional
+# T/F arguments for describing whether the modification prevents
+# enzymatic cleavage of cross-linking, respectively. This option is only
+# available when use-old-xlink=F. Note that this parameter only takes
+# effect when specified in the parameter file.
+# Available for search-for-xlinks.
+mod=NO MODS
+
+# Specify a variable modification to apply to N-terminus of peptides.
+# <mass change>:<max distance from protein n-term (-1 for no max)> Note
+# that this parameter only takes effect when specified in the parameter
+# file.
+# Available for search-for-xlinks.
+nmod=NO MODS
+
+# Specify a variable modification to apply to C-terminus of peptides.
+# <mass change>:<max distance from protein c-term (-1 for no max)>. Note
+# that this parameter only takes effect when specified in the parameter
+# file.
+# Available for search-for-xlinks.
+cmod=NO MODS
+
+####################
+# Comet Parameters #
+####################
+# 0=no, 1=concatenated search, 2=separate search.
+# Available for comet.
+decoy_search=0
+
+# 0=poll CPU to set num threads; else specify num threads directly.
+# Available for comet.
+num_threads=0
+
+# Controls the mass tolerance value. The mass tolerance is set at +/- the
+# specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0
+# tolerance. The units of the mass tolerance is controlled by the parameter
+# "peptide_mass_units".
+# Available for comet.
+peptide_mass_tolerance=3
+
+# 0=amu, 1=mmu, 2=ppm.
+# Available for comet.
+peptide_mass_units=0
+
+# Automatically estimate optimal value for the peptide_mass_tolerancel parameter
+# from the spectra themselves. false=no estimation, warn=try to estimate but use
+# the default value in case of failure, fail=try to estimate and quit in case of
+# failure.
+# Available for comet.
+auto_peptide_mass_tolerance=false
+
+# 0=average masses, 1=monoisotopic masses.
+# Available for comet.
+mass_type_parent=1
+
+# 0=average masses, 1=monoisotopic masses.
+# Available for comet.
+mass_type_fragment=1
+
+# 0=singly charged peptide mass, 1=precursor m/z.
+# Available for comet.
+precursor_tolerance_type=0
+
+# 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8
+# labeling).
+# Available for comet.
+isotope_error=0
+
+# Specify a search enzyme from the end of the parameter file.
+# Available for comet.
+search_enzyme_number=1
+
+# valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term.
+# Available for comet.
+num_enzyme_termini=2
+
+# Maximum value is 5; for enzyme search.
+# Available for comet.
+allowed_missed_cleavage=2
+
+# Binning to use on fragment ions.
+# Available for comet.
+fragment_bin_tol=1.000507
+
+# Offset position to start the binning (0.0 to 1.0).
+# Available for comet.
+fragment_bin_offset=0.4
+
+# Automatically estimate optimal value for the fragment_bin_tol parameter from
+# the spectra themselves. false=no estimation, warn=try to estimate but use the
+# default value in case of failure, fail=try to estimate and quit in case of
+# failure.
+# Available for comet.
+auto_fragment_bin_tol=false
+
+# 0=default peak shape, 1=M peak only.
+# Available for comet.
+theoretical_fragment_ions=1
+
+# Controls whether or not A-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_A_ions=0
+
+# Controls whether or not B-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_B_ions=1
+
+# Controls whether or not C-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_C_ions=0
+
+# Controls whether or not X-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_X_ions=0
+
+# Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_Y_ions=1
+
+# Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_Z_ions=0
+
+# 0=no, 1= yes to consider NH3/H2O neutral loss peak.
+# Available for comet.
+use_NL_ions=1
+
+# 0=no, 1=yes write sqt file.
+# Available for comet.
+output_sqtfile=0
+
+# 0=no, 1=yes write tab-delimited text file.
+# Available for comet.
+output_txtfile=1
+
+# 0=no, 1=yes write pep.xml file.
+# Available for comet.
+output_pepxmlfile=1
+
+# 0=no, 1=yes write percolator file.
+# Available for comet.
+output_percolatorfile=0
+
+# 0=no, 1=yes write .out files.
+# Available for comet.
+output_outfiles=0
+
+# 0=no, 1=yes to replace Sp with expect in out & sqt.
+# Available for comet.
+print_expect_score=1
+
+# num peptide results to show.
+# Available for comet.
+num_output_lines=5
+
+# 0=no, 1=yes for out files only.
+# Available for comet.
+show_fragment_ions=0
+
+# Sample enzyme which is possibly different than the one applied to the search.
+# Used to calculate NTT & NMC in pepXML output.
+# Available for comet.
+sample_enzyme_number=1
+
+# Start and scan scan range to search; 0 as first entry ignores parameter.
+# Available for comet.
+scan_range=0 0
+
+# Precursor charge range to analyze; does not override mzXML charge; 0 as first
+# entry ignores parameter.
+# Available for comet.
+precursor_charge=0 0
+
+# Specifies the whether to override existing precursor charge state information
+# when present in the files with the charge range specified by the
+# "precursor_charge" parameter.
+# Available for comet.
+override_charge=0
+
+# MS level to analyze, valid are levels 2 or 3.
+# Available for comet.
+ms_level=2
+
+# Specifies which scan types are searched.
+# Available for comet.
+activation_method=ALL
+
+# MH+ peptide mass range to analyze.
+# Available for comet.
+digest_mass_range=600.0 5000.0
+
+# Number of search hits to store internally.
+# Available for comet.
+num_results=50
+
+# For '.out' file output only, 0=search everything again, 1=don't search if .out
+# exists.
+# Available for comet.
+skip_researching=1
+
+# Set maximum fragment charge state to analyze (allowed max 5).
+# Available for comet.
+max_fragment_charge=3
+
+# Set maximum precursor charge state to analyze (allowed max 9).
+# Available for comet.
+max_precursor_charge=6
+
+# 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six.
+# Available for comet.
+nucleotide_reading_frame=0
+
+# 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine.
+# Available for comet.
+clip_nterm_methionine=0
+
+# Maximum number of spectra to search at a time; 0 to search the entire scan
+# range in one loop.
+# Available for comet.
+spectrum_batch_size=0
+
+# Specifies the prefix of the protein names that indicates a decoy.
+# Available for comet.
+decoy_prefix=decoy_
+
+# Specifies the suffix string that is appended to the base output name for the
+# pep.xml, pin.xml, txt and sqt output files.
+# Available for comet.
+output_suffix=
+
+# Specifies one or more mass offsets to apply. This value(s) are effectively
+# subtracted from each precursor mass such that peptides that are smaller than
+# the precursor mass by the offset value can still be matched to the respective
+# spectrum.
+# Available for comet.
+mass_offsets=
+
+# Minimum number of peaks in spectrum to search.
+# Available for comet.
+minimum_peaks=10
+
+# Minimum intensity value to read in.
+# Available for comet.
+minimum_intensity=0
+
+# 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD).
+# Available for comet.
+remove_precursor_peak=0
+
+# +- Da tolerance for precursor removal.
+# Available for comet.
+remove_precursor_tolerance=1.5
+
+# For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range.
+# Available for comet.
+clear_mz_range=0.0 0.0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod01=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod02=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod03=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod04=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod05=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod06=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod07=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod08=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod09=0.0 null 0 4 -1 0 0
+
+# Specifies the total/maximum number of residues that can be modified in a
+# peptide.
+# Available for comet.
+max_variable_mods_in_peptide=5
+
+# Controls whether the analyzed peptides must contain at least one variable
+# modification.
+# Available for comet.
+require_variable_mod=0
+
+# Specifiy a static modification to the c-terminus of all peptides.
+# Available for comet.
+add_Cterm_peptide=0
+
+# Specify a static modification to the n-terminus of all peptides.
+# Available for comet.
+add_Nterm_peptide=0
+
+# Specify a static modification to the c-terminal peptide of each protein.
+# Available for comet.
+add_Cterm_protein=0
+
+# Specify a static modification to the n-terminal peptide of each protein.
+# Available for comet.
+add_Nterm_protein=0
+
+# Specify a static modification to the residue A.
+# Available for comet.
+add_A_alanine=0
+
+# Specify a static modification to the residue B.
+# Available for comet.
+add_B_user_amino_acid=0
+
+# Specify a static modification to the residue C.
+# Available for comet.
+add_C_cysteine=57.021464
+
+# Specify a static modification to the residue D.
+# Available for comet.
+add_D_aspartic_acid=0
+
+# Specify a static modification to the residue E.
+# Available for comet.
+add_E_glutamic_acid=0
+
+# Specify a static modification to the residue F.
+# Available for comet.
+add_F_phenylalanine=0
+
+# Specify a static modification to the residue G.
+# Available for comet.
+add_G_glycine=0
+
+# Specify a static modification to the residue H.
+# Available for comet.
+add_H_histidine=0
+
+# Specify a static modification to the residue I.
+# Available for comet.
+add_I_isoleucine=0
+
+# Specify a static modification to the residue J.
+# Available for comet.
+add_J_user_amino_acid=0
+
+# Specify a static modification to the residue K.
+# Available for comet.
+add_K_lysine=0
+
+# Specify a static modification to the residue L.
+# Available for comet.
+add_L_leucine=0
+
+# Specify a static modification to the residue M.
+# Available for comet.
+add_M_methionine=0
+
+# Specify a static modification to the residue N.
+# Available for comet.
+add_N_asparagine=0
+
+# Specify a static modification to the residue O.
+# Available for comet.
+add_O_ornithine=0
+
+# Specify a static modification to the residue P.
+# Available for comet.
+add_P_proline=0
+
+# Specify a static modification to the residue Q.
+# Available for comet.
+add_Q_glutamine=0
+
+# Specify a static modification to the residue R.
+# Available for comet.
+add_R_arginine=0
+
+# Specify a static modification to the residue S.
+# Available for comet.
+add_S_serine=0
+
+# Specify a static modification to the residue T.
+# Available for comet.
+add_T_threonine=0
+
+# Specify a static modification to the residue U.
+# Available for comet.
+add_U_selenocysteine=0
+
+# Specify a static modification to the residue V.
+# Available for comet.
+add_V_valine=0
+
+# Specify a static modification to the residue W.
+# Available for comet.
+add_W_tryptophan=0
+
+# Specify a static modification to the residue X.
+# Available for comet.
+add_X_user_amino_acid=0
+
+# Specify a static modification to the residue Y.
+# Available for comet.
+add_Y_tyrosine=0
+
+# Specify a static modification to the residue Z.
+# Available for comet.
+add_Z_user_amino_acid=0
+
+#
+# COMET_ENZYME_INFO _must_ be at the end of this parameters file
+#
+[COMET_ENZYME_INFO]
+0. No_enzyme 0 - -
+1. Trypsin 1 KR P
+2. Trypsin/P 1 KR -
+3. Lys_C 1 K P
+4. Lys_N 0 K -
+5. Arg_C 1 R P
+6. Asp_N 0 D -
+7. CNBr 1 M -
+8. Glu_C 1 DE P
+9. PepsinA 1 FL P
+10. Chymotrypsin 1 FWYL P
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/demos/demo1.sh b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/demos/demo1.sh
new file mode 100644
index 0000000..7c90a03
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/demos/demo1.sh
@@ -0,0 +1,34 @@
+#!/bin/bash -x
+# AUTHOR: WSN
+# CREATE DATE: 18 December 2013, Tokyo Narita airport
+
+# This file implements the commands described in ../search-tutorial.html.
+
+if [[ -e ../../../src/crux ]]; then
+ CRUX=../../../src/crux
+else
+ CRUX=../../../release/src/crux
+fi
+
+rm -rf yeast-index crux-output
+chmod +x ./tsv2html.py
+cp ../example-files/demo.ms2 .
+cp ../example-files/small-yeast.fasta .
+
+$CRUX tide-index small-yeast.fasta yeast-index
+
+$CRUX tide-search --compute-sp T demo.ms2 yeast-index
+$CRUX sort-by-column --column-type real --ascending F \
+ crux-output/tide-search.target.txt "xcorr score" \
+ > crux-output/tide-search.target.sort.txt
+head -11 crux-output/tide-search.target.sort.txt \
+ | ./tsv2html.py - \
+ > crux-output/tide-search.target.sort.html
+
+$CRUX percolator crux-output/tide-search.target.txt
+$CRUX sort-by-column --column-type real --ascending F \
+ crux-output/percolator.target.psms.txt "percolator score" \
+ > crux-output/percolator.target.psms.sort.txt
+head -11 crux-output/percolator.target.psms.sort.txt \
+ | ./tsv2html.py - \
+ > crux-output/percolator.target.psms.sort.html
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/demos/tsv2html.py b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/demos/tsv2html.py
new file mode 100644
index 0000000..06914a1
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/demos/tsv2html.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+# AUTHOR: William Stafford Noble
+# CREATE DATE: 13 Sep 2015
+import sys
+
+USAGE = """USAGE: tsv2html.py [options] <tab-delimited file>
+
+ Convert a tab-delimited text file an HTML table. Use "-" to read
+ from stdin.
+
+ Options:
+ --title <string>
+ --table-only
+"""
+
+title = ""
+tableOnly = False
+
+# Parse the command line.
+sys.argv = sys.argv[1:]
+while (len(sys.argv) > 1):
+ nextArg = sys.argv[0]
+ sys.argv = sys.argv[1:]
+ if (nextArg == "--title"):
+ title = sys.argv[1]
+ sys.argv = sys.argv[1:]
+ elif (nextArg == "--table-only"):
+ tableOnly = True
+ else:
+ sys.stderr.write("Invalid option (%s).\n" % nextArg)
+ sys.exit(1)
+if (len(sys.argv) != 1):
+ sys.stderr.write(USAGE)
+ sys.exit(1)
+tsvFileName = sys.argv[0]
+
+# Open the input file.
+if (tsvFileName == "-"):
+ tsvFile = sys.stdin
+else:
+ tsvFile = open(tsvFileName, "r")
+
+# Print the header.
+if (not tableOnly):
+ sys.stdout.write("<html>\n")
+ sys.stdout.write("<head>\n")
+ if (title != ""):
+ sys.stdout.write("<title>%s</title>\n" % title)
+ sys.stdout.write("</head>\n")
+ sys.stdout.write("<body bgcolor=\"#ffffff\">\n")
+ if (title != ""):
+ sys.stdout.write("<h1>%s</h1>" % title)
+sys.stdout.write("<table border cellspacing=0>\n")
+
+# Read and display header row
+fields = tsvFile.readline().rstrip().split("\t")
+for field in fields:
+ sys.stdout.write("<td><b>%s</b></td>" % field)
+sys.stdout.write("</tr>\n")
+
+# Process lines.
+for line in tsvFile:
+
+ fields = line.rstrip().split("\t")
+ sys.stdout.write("<tr>\n")
+ for field in fields:
+ if (field == ""):
+ field = " "
+ sys.stdout.write("<td>%s</td>" % field)
+ sys.stdout.write("</tr>\n")
+tsvFile.close()
+
+# Print tail info.
+sys.stdout.write("</table>\n")
+if not tableOnly:
+ sys.stdout.write("</body>\n")
+ sys.stdout.write("</html>\n")
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/deploy-to-web.sh b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/deploy-to-web.sh
new file mode 100644
index 0000000..4fcfe88
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/deploy-to-web.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+scp *.html charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp *.png charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp *.gif charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp crux.html charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs/index.html
+scp crux.css charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp -r data charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp -r demos charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp -r download charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/download.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/download.html
new file mode 100644
index 0000000..5b6fa90
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/download.html
@@ -0,0 +1,741 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Download Crux</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+<style type="text/css">
+.inset {
+ position:relative;
+ left:20px;
+}
+
+.lic-div {
+ border:1px solid black;
+ height:150px;
+ width:600px;
+ margin-left:10px;
+ margin-top:10px;
+ margin-bottom:10px;
+ overflow-y:scroll;
+ overflow-x:hidden;
+}
+ p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p2 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: center; font: 14.0px Arial}
+ p.p3 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px Arial}
+ p.p4 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px Arial; min-height: 11.0px}
+ p.p5 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 12.0px Arial}
+ p.p6 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 12.0px Arial; min-height: 14.0px}
+ p.p7 {margin: 0.0px 0.0px 0.0px 18.0px; text-align: justify; text-indent: -18.0px; font: 10.0px Arial}
+ p.p8 {margin: 0.0px 0.0px 0.0px 13.5px; text-align: justify; text-indent: -13.5px; font: 10.0px Arial}
+ p.p9 {margin: 0.0px 0.0px 0.0px 18.0px; text-align: justify; text-indent: -18.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p10 {margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Arial}
+ p.p11 {margin: 0.0px 0.0px 0.0px 14.2px; font: 10.0px Arial}
+ p.p12 {margin: 0.0px 0.0px 0.0px 0.0px; text-indent: 36.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p13 {margin: 0.0px 0.0px 0.0px 18.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p14 {margin: 0.0px 0.0px 0.0px 36.0px; font: 10.0px Arial}
+ p.p15 {margin: 0.0px 0.0px 0.0px 0.0px; text-indent: 36.0px; font: 10.0px Arial}
+ p.p16 {margin: 0.0px 0.0px 0.0px 36.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p17 {margin: 0.0px 0.0px 0.0px 31.5px; text-indent: -31.5px; font: 10.0px Arial}
+ p.p18 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px Verdana; min-height: 12.0px}
+ p.p19 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px 'Times New Roman'; min-height: 11.0px}
+ p.p20 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: center; font: 12.0px Arial}
+ p.p21 {margin: 0.0px 0.0px 0.0px 0.0px; font: 7.0px Arial; min-height: 7.0px}
+ li.li3 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px Arial}
+ span.Apple-tab-span {white-space:pre}
+ ol.ol1 {list-style-type: decimal}
+ .page-wrap:after { /*hacky just for download page. content is all over the place need this to fix footer*/
+ content: "";
+ display: none;
+ }
+</style>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+
+<form action="http://noble.gs.washington.edu/crux-downloads/download.php" method="post">
+
+<h2> Get Crux Toolkit (3 steps)</H2>
+<div class="inset">
+
+<H3> Step 1, Choose Download Type: </H3>
+<UL>
+<SELECT NAME="downloadtype">
+ <optgroup label="For End Users">
+ <OPTION value="Linux32"> Linux 32 bit binaries (NO vendor reader support)</OPTION>
+ <OPTION value="Linux64"> Linux 64 bit binaries (NO vendor reader support)</OPTION>
+ <OPTION value="OSX"> Macintosh binaries (NO vendor reader support)</OPTION>
+ <OPTION value="Windows64"> Windows 64-bit(includes vendor reader support)</OPTION>
+ <OPTION value="Windows32"> Windows 32-bit(includes vendor reader support)</OPTION>
+ </optgroup>
+ <optgroup label="For Developers">
+ <OPTION value="Source"> Source, CMake build (includes vendor reader support)</OPTION>
+ </optgroup>
+</SELECT>
+
+</UL>
+
+<H3> Step 2, Read License Agreements</H3>
+
+Crux is covered by an
+<a href="http://www.apache.org/licenses/LICENSE-2.0" >Apache license</a>
+but depends on several libraries that have other licences.
+You must read and agree to these other licenses before downloading Crux.
+<ul>
+ <li>ProteoWizard Core:</li>
+<div class="lic-div">
+ADDENDUM TO APACHE LICENSE
+
+<p>To the best of our ability we deliver this software to you under the Apache 2.0 License listed below (the source code is available in the ProteoWizard project). This software does, however, depend on other software libraries which place further restrictions on its use and redistribution. By accepting the license terms for this software, you agree to comply with the restrictions imposed on you by the license agreements of the software libraries on which it depends:</p>
+
+<p>
+<B>Agilent Mass Hunter Data Access Component Library <br />
+Waters Raw Data Access Component Library <br />
+Bruker CompassXtract <br />
+Thermo-Scientific MSFileReader Library <br />
+Waters Raw Data Access Component Library <br />
+AB Sciex WIFF Reader Library </B><br /><br />
+
+
+NOTE: If you do not plan to redistribute this software yourself, then you are the "end-user" in the above agreements.</p>
+
+<hr />
+<p>Apache License - Covers Core ProteoWizard Tools and Library<br></br>Version 2.0, January 2004<br></br>
+<a href="http://www.apache.org/licenses/">http://www.apache.org/licenses/</a> </p>
+<p>TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION</p>
+<p><strong><a name="definitions">1. Definitions</a></strong>.</p>
+<p>"License" shall mean the terms and conditions for use, reproduction, and
+distribution as defined by Sections 1 through 9 of this document.</p>
+<p>"Licensor" shall mean the copyright owner or entity authorized by the
+copyright owner that is granting the License.</p>
+<p>"Legal Entity" shall mean the union of the acting entity and all other
+entities that control, are controlled by, or are under common control with
+that entity. For the purposes of this definition, "control" means (i) the
+power, direct or indirect, to cause the direction or management of such
+entity, whether by contract or otherwise, or (ii) ownership of fifty
+percent (50%) or more of the outstanding shares, or (iii) beneficial
+ownership of such entity.</p>
+<p>"You" (or "Your") shall mean an individual or Legal Entity exercising
+permissions granted by this License.</p>
+<p>"Source" form shall mean the preferred form for making modifications,
+including but not limited to software source code, documentation source,
+and configuration files.</p>
+<p>"Object" form shall mean any form resulting from mechanical transformation
+or translation of a Source form, including but not limited to compiled
+object code, generated documentation, and conversions to other media types.</p>
+<p>"Work" shall mean the work of authorship, whether in Source or Object form,
+made available under the License, as indicated by a copyright notice that
+is included in or attached to the work (an example is provided in the
+Appendix below).</p>
+<p>"Derivative Works" shall mean any work, whether in Source or Object form,
+that is based on (or derived from) the Work and for which the editorial
+revisions, annotations, elaborations, or other modifications represent, as
+a whole, an original work of authorship. For the purposes of this License,
+Derivative Works shall not include works that remain separable from, or
+merely link (or bind by name) to the interfaces of, the Work and Derivative
+Works thereof.</p>
+<p>"Contribution" shall mean any work of authorship, including the original
+version of the Work and any modifications or additions to that Work or
+Derivative Works thereof, that is intentionally submitted to Licensor for
+inclusion in the Work by the copyright owner or by an individual or Legal
+Entity authorized to submit on behalf of the copyright owner. For the
+purposes of this definition, "submitted" means any form of electronic,
+verbal, or written communication sent to the Licensor or its
+representatives, including but not limited to communication on electronic
+mailing lists, source code control systems, and issue tracking systems that
+are managed by, or on behalf of, the Licensor for the purpose of discussing
+and improving the Work, but excluding communication that is conspicuously
+marked or otherwise designated in writing by the copyright owner as "Not a
+Contribution."</p>
+<p>"Contributor" shall mean Licensor and any individual or Legal Entity on
+behalf of whom a Contribution has been received by Licensor and
+subsequently incorporated within the Work.</p>
+<p><strong><a name="copyright">2. Grant of Copyright License</a></strong>. Subject to the
+terms and conditions of this License, each Contributor hereby grants to You
+a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+copyright license to reproduce, prepare Derivative Works of, publicly
+display, publicly perform, sublicense, and distribute the Work and such
+Derivative Works in Source or Object form.</p>
+<p><strong><a name="patent">3. Grant of Patent License</a></strong>. Subject to the terms
+and conditions of this License, each Contributor hereby grants to You a
+perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+(except as stated in this section) patent license to make, have made, use,
+offer to sell, sell, import, and otherwise transfer the Work, where such
+license applies only to those patent claims licensable by such Contributor
+that are necessarily infringed by their Contribution(s) alone or by
+combination of their Contribution(s) with the Work to which such
+Contribution(s) was submitted. If You institute patent litigation against
+any entity (including a cross-claim or counterclaim in a lawsuit) alleging
+that the Work or a Contribution incorporated within the Work constitutes
+direct or contributory patent infringement, then any patent licenses
+granted to You under this License for that Work shall terminate as of the
+date such litigation is filed.</p>
+<p><strong><a name="redistribution">4. Redistribution</a></strong>. You may reproduce and
+distribute copies of the Work or Derivative Works thereof in any medium,
+with or without modifications, and in Source or Object form, provided that
+You meet the following conditions:</p>
+<ol>
+<li>
+<p>You must give any other recipients of the Work or Derivative Works a
+copy of this License; and</p>
+</li>
+<li>
+<p>You must cause any modified files to carry prominent notices stating
+that You changed the files; and</p>
+</li>
+<li>
+<p>You must retain, in the Source form of any Derivative Works that You
+distribute, all copyright, patent, trademark, and attribution notices from
+the Source form of the Work, excluding those notices that do not pertain to
+any part of the Derivative Works; and</p>
+</li>
+<li>
+<p>If the Work includes a "NOTICE" text file as part of its distribution,
+then any Derivative Works that You distribute must include a readable copy
+of the attribution notices contained within such NOTICE file, excluding
+those notices that do not pertain to any part of the Derivative Works, in
+at least one of the following places: within a NOTICE text file distributed
+as part of the Derivative Works; within the Source form or documentation,
+if provided along with the Derivative Works; or, within a display generated
+by the Derivative Works, if and wherever such third-party notices normally
+appear. The contents of the NOTICE file are for informational purposes only
+and do not modify the License. You may add Your own attribution notices
+within Derivative Works that You distribute, alongside or as an addendum to
+the NOTICE text from the Work, provided that such additional attribution
+notices cannot be construed as modifying the License.
+You may add Your own copyright statement to Your modifications and may
+provide additional or different license terms and conditions for use,
+reproduction, or distribution of Your modifications, or for any such
+Derivative Works as a whole, provided Your use, reproduction, and
+distribution of the Work otherwise complies with the conditions stated in
+this License.</p>
+</li>
+</ol>
+<p><strong><a name="contributions">5. Submission of Contributions</a></strong>. Unless You
+explicitly state otherwise, any Contribution intentionally submitted for
+inclusion in the Work by You to the Licensor shall be under the terms and
+conditions of this License, without any additional terms or conditions.
+Notwithstanding the above, nothing herein shall supersede or modify the
+terms of any separate license agreement you may have executed with Licensor
+regarding such Contributions.</p>
+<p><strong><a name="trademarks">6. Trademarks</a></strong>. This License does not grant
+permission to use the trade names, trademarks, service marks, or product
+names of the Licensor, except as required for reasonable and customary use
+in describing the origin of the Work and reproducing the content of the
+NOTICE file.</p>
+<p><strong><a name="no-warranty">7. Disclaimer of Warranty</a></strong>. Unless required by
+applicable law or agreed to in writing, Licensor provides the Work (and
+each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT
+WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including,
+without limitation, any warranties or conditions of TITLE,
+NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You
+are solely responsible for determining the appropriateness of using or
+redistributing the Work and assume any risks associated with Your exercise
+of permissions under this License.</p>
+<p><strong><a name="no-liability">8. Limitation of Liability</a></strong>. In no event and
+under no legal theory, whether in tort (including negligence), contract, or
+otherwise, unless required by applicable law (such as deliberate and
+grossly negligent acts) or agreed to in writing, shall any Contributor be
+liable to You for damages, including any direct, indirect, special,
+incidental, or consequential damages of any character arising as a result
+of this License or out of the use or inability to use the Work (including
+but not limited to damages for loss of goodwill, work stoppage, computer
+failure or malfunction, or any and all other commercial damages or losses),
+even if such Contributor has been advised of the possibility of such
+damages.</p>
+<p><strong><a name="additional">9. Accepting Warranty or Additional Liability</a></strong>.
+While redistributing the Work or Derivative Works thereof, You may choose
+to offer, and charge a fee for, acceptance of support, warranty, indemnity,
+or other liability obligations and/or rights consistent with this License.
+However, in accepting such obligations, You may act only on Your own behalf
+and on Your sole responsibility, not on behalf of any other Contributor,
+and only if You agree to indemnify, defend, and hold each Contributor
+harmless for any liability incurred by, or claims asserted against, such
+Contributor by reason of your accepting any such warranty or additional
+liability.</p>
+<HR />
+</div>
+ <li>AB Sciex WiffReader</li>
+<div class="lic-div">
+
+<p class="p1"><br></p>
+<p class="p2"><b>AB Sciex LLC</b></p>
+<p class="p2"><b>END USER BETA SOFTWARE LICENSE AGREEMENT</b></p>
+<p class="p2"><b>and</b></p>
+<p class="p2"><b>LIMITED DEVELOPER LICENSE</b></p>
+<p class="p2"><i>WIFF Reader Distributable Beta SDK</i></p>
+<p class="p1"><br></p>
+<p class="p1"><br></p>
+<p class="p3"><b>NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY.<span class="Apple-converted-space"> </span>THIS IS THE CONTRACT BETWEEN YOU AND AB SCIEX REGARDING THIS SOFTWARE PRODUCT.<span class="Apple-converted-space"> </span>THIS AGREEMENT INCLUDES LICENSE TERMS AND RESTRICTIONS, WARRANTY AND LIABILITY DISCLAIMERS, AND LIMITATIONS.</b></p>
+<p class="p4"><b></b><br></p>
+<p class="p3"><b>YOUR INSTALLATION AND USE OF THIS AB SCIEX SDK IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT.</b></p>
+<p class="p4"><b></b><br></p>
+<p class="p3">This AB Sciex End User Software License Agreement (EULA) and Limited Developer & Redistribution License accompanies this AB Sciex WIFF Reader Distributable Beta SDK product ("Software") and related explanatory materials ("Documentation"). The term "SDK" also includes any upgrades, modified versions, updates, additions and copies of the SDK licensed to you by AB Sciex.<span class="Apple-converted-space"> </span>The term “AB Sciex,” as used in this License, means AB Scie [...]
+<p class="p4"><br></p>
+<p class="p4"><br></p>
+<p class="p5"><b>Third Party Products</b></p>
+<p class="p3">This Software may include software products licensed by third party provider(s). In addition, the Software may enable you to run multiple instances of third-party software and application programs. You are responsible for reviewing and complying with any licenses necessary to use any such third-party software.<span class="Apple-converted-space"> </span>Such licenses may be included in your AB Sciex installation package.</p>
+<p class="p4"><br></p>
+<p class="p5"><b>TITLE</b></p>
+<p class="p3">Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with AB Sciex and its subsidiaries, and their suppliers.<span class="Apple-converted-space"> </span>All rights not specifically granted by this License, including Federal and international copyrights, are reserved by AB Sciex or their respective owners.</p>
+<p class="p6"><b></b><br></p>
+<p class="p5"><b>COPYRIGHT</b></p>
+<p class="p3">The Software, including its structure, organization, code, user interface and associated Documentation, is a proprietary product of AB Sciex or its suppliers, and is protected by international laws of copyright. The law provides for civil and criminal penalties for anyone in violation of the laws of copyright.</p>
+<p class="p4"><br></p>
+<p class="p5"><b>LICENSE</b></p>
+<p class="p3"><b>Use of the Software</b></p>
+<ol class="ol1">
+ <li class="li3">As a Developer License, AB Sciex grants to you one (1) personal, nontransferable, nonexclusive, license to use copies of the Software and install such Software on your machine(s) for your single concurrent internal use.</li>
+</ol>
+<p class="p7">2.<span class="Apple-tab-span"> </span>You may make one copy of the Software in machine-readable form solely for backup or archival purposes.<span class="Apple-converted-space"> </span>You must reproduce on any such copy all copyright notices and any other proprietary legends found on the original.<span class="Apple-converted-space"> </span>You may not make any other copies of the Software.</p>
+<p class="p7">3.<span class="Apple-tab-span"> </span>From time to time, AB Sciex may change the terms of this Agreement.<span class="Apple-converted-space"> </span>AB Sciex will notify you of such change.<span class="Apple-converted-space"> </span>Your continued use of the Software will indicate your agreement to the change.</p>
+<p class="p4"><br></p>
+<p class="p3"><b>Use Restrictions</b></p>
+<p class="p7">1.<span class="Apple-converted-space"> </span>You may not use the Software, Documentation, or any associated documentation, in whole or in part, except as expressly permitted in this Agreement.</p>
+<p class="p7">2.<span class="Apple-converted-space"> </span>You may not sublicense, copy, merge, modify, sell, resell, rent, lease, assign, transfer (except temporarily in the event of a computer malfunction or as expressly permitted under the Section “Use of the Software”), or distribute this license or the Software, or create derivative works based on the Software (except as outlined in the Distribution Rights below), or any part thereof or any interest therein. <span class="Apple-con [...]
+<p class="p7">3.<span class="Apple-converted-space"> </span>You may not reverse assemble, decompile, modify, create any derivative works, or otherwise attempt, cause, or permit any reverse engineering of the Software or any part thereof.</p>
+<p class="p8">4.<span class="Apple-converted-space"> </span>You acknowledge that the Software in human-readable (source code) form, including its structure, sequence, and organization, is and remains the confidential trade secret of AB Sciex.<span class="Apple-converted-space"> </span>You agree that you shall not attempt, cause or permit the reverse engineering, modification, decompiliation, disassembly of the Software to any human readable or perceivable form, or creation of any deriv [...]
+<p class="p8">5.<span class="Apple-converted-space"> </span>You may not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation and you acknowledge that the Software in human-readable (source code) form, including its structure, sequence, and organization, is and remains the confidential trade secret of AB Sciex.</p>
+<p class="p7">6.<span class="Apple-converted-space"> </span>You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities.<span class="Apple-converted-space"> </span>You agree that you will not export or reexport, directly or indirectly, the Software into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law.</p>
+<p class="p9"><br></p>
+<p class="p10"><b>Distribution of the Distributable Components (DCs)</b></p>
+<p class="p10">1.<span class="Apple-converted-space"> </span><b>Distributable Components.</b> The Software contains Distributable Components that you are permitted<span class="Apple-converted-space"> </span></p>
+<p class="p11">to distribute for non-commercial purposes provided that: (a) the Distributable Components are bundled as part of, and for the sole purpose of running programs developed by you and supplied by you; and (b) you comply with all other terms in this EULA.<span class="Apple-converted-space"> </span>As used herein commercial purposes include, but are not limited to, charging a purchase price, license fee, maintenance fee, subscription fee, or providing software incorporating Dis [...]
+<p class="p1"><br></p>
+<p class="p10">2.<span class="Apple-converted-space"> </span><b>Right to Use and Distribute.</b> The code and text files listed in Appendix A are “Distributable<span class="Apple-converted-space"> </span></p>
+<p class="p10"><span class="Apple-converted-space"> </span>Components”.<span class="Apple-converted-space"> </span>All other code and text files of the Software are not distributable.</p>
+<p class="p12"><br></p>
+<p class="p10">3.<span class="Apple-converted-space"> </span><b>Third Party Distribution.</b> You may not permit distributors of your programs or end users of your<span class="Apple-converted-space"> </span></p>
+<p class="p10"><span class="Apple-converted-space"> </span>programs to copy and distribute the Distributable Components as part of those or their programs.</p>
+<p class="p13"><br></p>
+<p class="p10">4. <b>Distribution Requirements, General.</b> For any Distributable Component you distribute, you must:</p>
+<p class="p14">(a) embed the license key in your program such that it is obscured from end users seeing it.<span class="Apple-converted-space"> </span>In the event that your program is open source, this license key must not be part of the open source;</p>
+<p class="p15">(b) add significant primary functionality to it in your programs;</p>
+<p class="p14">(c) for any Distributable Component having a filename extension of .lib, distribute only the results of running such Distributable Component through a linker with your program;</p>
+<p class="p14">(d) distribute Distributable Components included in a setup program only as part of that setup program without modification;</p>
+<p class="p14">(e) require distributors and external end users to agree to terms that protect it at least as much as this EULA; and</p>
+<p class="p15">(f) display your valid copyright notice on your programs.</p>
+<p class="p16"><br></p>
+<p class="p17">5. <b>Distribution Requirement, Indemnification.<span class="Apple-converted-space"> </span></b>For any Distributable Component you distribute, you must and you hereby agree to: indemnify, defend, and hold harmless AB Sciex from any and all claims and costs, including attorneys’ fees, related to the distribution or use of your programs.</p>
+<p class="p16"><br></p>
+<p class="p10">6.<span class="Apple-converted-space"> </span><b>Distribution Restrictions.</b> You may not:</p>
+<p class="p15">(a) alter any copyright, trademark or patent notice in the Distributable Component;</p>
+<p class="p14">(b) use AB Sciex or AB Sciex’s trademarks in your programs’ names or in a way that suggests your programs come from or are endorsed by AB Sciex;</p>
+<p class="p15">(c) include Distributable Components in malicious, deceptive or unlawful programs; or</p>
+<p class="p14">(d) modify or distribute the source code of any Distributable Component so that any part of it becomes subject to an Excluded License. An Excluded License is one that requires, as a condition of use, modification or distribution, that (i) the code be disclosed or distributed in source code form; and/or (ii) others have the right to modify it.</p>
+<p class="p4"><br></p>
+<p class="p3"><b>Trial</b></p>
+<p class="p3">If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period.</p>
+<p class="p4"><br></p>
+<p class="p3"><b>Termination</b></p>
+<p class="p3">You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to AB Sciex.<span class="Apple-converted-space"> </span>AB Sciex may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Softwar [...]
+<p class="p4"><b></b><br></p>
+<p class="p3"><b>U.S. Government End Users</b></p>
+<p class="p3">The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein.<span class="Apple-converted-space"> </span></p>
+<p class="p4"><b></b><br></p>
+<p class="p3"><b>European Community End Users</b></p>
+<p class="p3">If this Software is used within a country of the European Community, nothing in this Agreement shall be construed as restricting any rights available under the European Community Software Directive, O.J. Eur. Comm. (No. L. 122) 42 (1991).</p>
+<p class="p4"><br></p>
+<p class="p3"><b>Regulated Uses</b></p>
+<p class="p3">You acknowledge that the Software has not been cleared, approved, registered or otherwise qualified (collectively, “Approval”) by AB Sciex<b> </b>with any regulatory agency, including without limitation for use in diagnostic or therapeutic procedures or any other use requiring compliance with any federal or state law regulating diagnostic or therapeutic products, blood products, medical devices or any similar product (hereafter collectively referred to as "federal or state [...]
+<p class="p4"><b></b><br></p>
+<p class="p5"><b>NO WARRANTY and LIMITATION OF REMEDIES</b></p>
+<p class="p3">AB SCIEX MAKES NO WARRANTIES OF ANY KIND WHATSOEVER, EXPRESS OR IMPLIED, WITH RESPECT TO THE SOFTWARE OR DOCUMENTATION, INCLUDING BUT NOT LIMITED TO WARRANTIES OF FITNESS FOR A PARTICULAR PURPOSE OR MERCHANTABILITY OR THAT THE SOFTWARE OR DOCUMENTATION IS NON-INFRINGING.<span class="Apple-converted-space"> </span>ALL OTHER WARRANTIES ARE EXPRESSLY DISCLAIMED.<span class="Apple-converted-space"> </span>WITHOUT LIMITING THE GENERALITY OF THE FOREGOING, AB SCIEX MAKES NO WAR [...]
+<p class="p4"><br></p>
+<p class="p5"><b>Limitation of Liability</b></p>
+<p class="p3">IN NO EVENT SHALL AB SCIEX OR ITS AGENTS, CONSULTANTS, CONTRACTORS OR SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE OR DOCUMENTATION, EVEN IF AB [...]
+<p class="p4"><br></p>
+<p class="p3">Some states, countries or jurisdictions limit the scope of or preclude limitations or exclusion of remedies or damages, or of liability, such as liability for gross negligence or willful misconduct, as or to the extent set forth above, OR do not allow implied warranties TO BE EXCLUDED.<span class="Apple-converted-space"> </span>In such states, countries or jurisdictions, the limitation or exclusion of warranties, remedies, damages or liability set forth above may not apply [...]
+<p class="p4"><br></p>
+<p class="p5"><b>GENERAL</b></p>
+<p class="p3">This Agreement shall be governed by laws of the Commonwealth of Massachusetts, U.S.A., exclusive of its conflict of laws provisions.<span class="Apple-converted-space"> </span>This Agreement shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods.<span class="Apple-converted-space"> </span>This Agreement contains the complete agreement between the parties with respect to the subject matter hereof, and supersedes all prior or [...]
+<p class="p18"><br></p>
+<p class="p19"><br></p>
+<p class="p3">Unpublished rights reserved under the copyright laws of the United States.</p>
+<p class="p3">AB Sciex LLC, 500 Old Connecticut Path, Framingham, MA 01701 U.S.A.</p>
+<p class="p4"><br></p>
+<p class="p3">For Research Use Only. Not for use in diagnostic procedures.<span class="Apple-converted-space"> </span>The trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective owners.<span class="Apple-converted-space"> </span>AB SCIEX™ is being used under license.</p>
+<p class="p3">© 2012 AB SCIEX</p>
+<p class="p20"><b>APPENDIX A</b></p>
+<p class="p20"><b>DISTRIBUTABLE COMPONENTS OF THE SOFTWARE</b></p>
+<p class="p21"><br></p>
+<p class="p10">Clearcore2.Compression.dll</p>
+<p class="p10">Clearcore2.Data.AnalystDataProvider.dll</p>
+<p class="p10">Clearcore2.Data.CommonInterfaces.dll</p>
+<p class="p10">Clearcore2.Data.dll</p>
+<p class="p10">Clearcore2.Data.WiffReader.dll</p>
+<p class="p10">Clearcore2.InternalRawXYProcessing.dll</p>
+<p class="p10">Clearcore2.Muni.dll</p>
+<p class="p10">Clearcore2.ProjectUtilities.dll</p>
+<p class="p10">Clearcore2.RawXYProcessing.dll</p>
+<p class="p10">Clearcore2.StructuredStorage.dll</p>
+<p class="p10">Clearcore2.Utility.dll</p>
+<p class="p1"><br></p>
+</div>
+ <li>Agilent MHDAC</li>
+<div class="lic-div">
+<strong><p>END-USER LICENSE TERMS FOR AGILENT MHDAC</p></strong>
+<strong>
+<p>AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE TERMS <strong>FOR THE MASSHUNTER DATA ACCESS COMPONENT RUNTIME VERSION</strong></p>
+</strong>
+<p><strong>ATTENTION: USE OF THE SOFTWARE IS SUBJECT TO THE LICENSE TERMS SET FORTH BELOW.</strong></p>
+<p>IF YOU DO NOT AGREE TO THESE LICENSE TERMS, THEN (A) DO NOT INSTALL OR USE THE SOFTWARE, AND (B) YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. NOTWITHSTANDING ANYTHING TO THE CONTRARY IN THIS NOTICE, INSTALLING OR OTHERWISE USING THE SOFTWARE INDICATES YOUR ACCEPTANCE OF THESE TERMS. </p>
+<p>AGILENT SOFTWARE LICENSE TERMS</p>
+<p><strong><u>Software</u></strong>. “Software” means the Masshunter Data Access Component Runtime computer program in object code format.</p>
+<p><strong><u>License Grant</u></strong>. Agilent grants you a non-exclusive, non-transferable license to (a) use one copy of the Software for internal purposes in accordance with these License Terms and the documentation provided with the Software or (b) to distribute the Software for non-commercial purposes only and only bundled as part of, and for the sole purpose of running, products supplied by you. This Software is licensed for internal concurrent or network use of an unlimited n [...]
+<p><strong><u>License Restrictions</u></strong>. You may make copies or adaptations of the Software only for archival purposes or only when copying or adaptation is an essential step in the authorized use of the Software. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not offer or provide unrestricted access to this Software on any public or distributed network.</p>
+<p><strong><u>Upgrades</u></strong>. This license does not entitle you to receive upgrades, updates or technical support. Such services may be purchased separately. </p>
+<p><strong><u>Ownership</u></strong>. <strong> </strong>The Software and all copies thereof are owned and copyrighted by Agilent. Agilent retains all right, title and interest in the Software. Agilent and its third party suppliers may protect their rights in the Software in the event of any violation of these License Terms.<strong><u></u></strong></p>
+<p><strong><u>No Disassembly</u></strong>. <strong> </strong>You may not disassemble, decompile or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly, decompilation or modification.</p>
+<p><strong><u>High Risk Activities</u></strong>.<strong> </strong>The Software is not specifically designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. </p>
+<p><strong><u>Termination</u></strong>. Agilent may terminate your license upon notice for breach of these License Terms. Upon termination, you must immediately destroy all copies of the Software.<strong><u></u></strong></p>
+<p><strong><u>No Warranty</u></strong>. THIS SOFTWARE IS LICENSED "AS IS" AND WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY, AND FITNESS FOR A PARTICULAR PURPOSE.
+</p>
+<p><strong><u>Limitation of Liability</u></strong>. TO THE EXTENT NOT PROHIBITED BY LAW, IN NO EVENT WILL AGILENT BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR SPECIAL, INDIRECT, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF OR RELATED TO THE USE OF OR INABILITY TO USE SOFTWARE, EVEN IF AGILENT HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. In no event will Agilent's liability to you, whether in contract [...]
+<p><strong><u>Export Requirements</u></strong>. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations.</p>
+<p><strong><u>U.S. Government Restricted Rights</u></strong>.<strong> </strong>Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data – Commercial Items) and DFARS 227.7202-3 (Rights [...]
+<hr />
+
+
+</div>
+ <li>Bruker CompassXtract</li>
+ <div class="lic-div">
+<div class=WordSection1>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>SOFTWARE LICENSE AGREEMENT for <span class=SpellE>CompassXtract</span> and <span
+class=SpellE>CompassXtract</span> Libraries</span></b></p>
+ <p style='text-autospace:none'><span class=SpellE><span style='font-family:Helvetica;'>Bruker</span></span><span style='font-family:
+Helvetica;'> <span
+class=SpellE>Daltonik</span> GmbH (hereinafter referred to as
+ "Licensor") has developed the <span class=SpellE>CompassXtract</span> software program (hereinafter referred to as "<span class=SpellE>CompassXtract</span>"),
+ which consists of documentation and individual <span class=SpellE>CompassXtract</span> libraries (hereinafter referred to as "<span class=SpellE>CompassXtract</span> <b>Libraries"). </b>These license terms constitute an agreement (hereinafter referred to as
+ "Agreement") between you and Licensor and shall be the legal basis
+ for any non-commercial usage of Licensor's <span class=SpellE>CompassXtract</span>.
+ These license terms also apply to any updates or supplements for <span
+class=SpellE>CompassXtract</span> or separable parts of <span class=SpellE>CompassXtract</span> such as <span class=SpellE>CompassXtract</span> Libraries, unless other terms
+ accompany those items, in which case those terms apply<span class=GramE>.
</span>You
+ may only use <span class=SpellE>CompassXtract</span> as a whole, if you have
+ downloaded it from Licensor's Webserver at http://www.bdal.de/compassxtract and
+ accepted this Agreement as binding between Licensor and you. However, <span
+class=GramE>certain individual <span class=SpellE>CompassXtract</span> Libraries might be conveyed to you by others</span>. In both cases, you may
+ only legally use <span class=SpellE>CompassXtract</span> or any of the <span
+class=SpellE>CompassXtract</span> Libraries conveyed to you after having
+ accepted this Agreement as binding between Licensor and you.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>1. Purpose of <span class=SpellE>CompassXtract</span> and License</span></b></p>
+ <p style='text-autospace:none'><span class=SpellE><span style='font-family:Helvetica;'>CompassXtract</span></span><span style='font-family:Helvetica;'> is provided as it is, in a trial and development stage, not yet marketable and
+ without any warranties regarding fitness for any purpose whatsoever. It may
+ contain errors and defects. The aim and purpose of providing it free of charge
+ and under the terms of this Agreement is to discover such errors and defects.
+ It is, inter alia but not limited to, not designed, manufactured or intended
+ for any use requiring fail-safe performance in which the failure of <span
+class=SpellE>CompassXtract</span> could lead to death, personal injury or
+ physical and environmental damage, such as the operation of medical facilities.
+ Nor is it, inter alia but not limited to, designed to perform any queries or
+ operations which might require reliable results and/or which might be the basis
+ for business and/or medical decisions. You agree not to use <span class=SpellE>CompassXtract</span> in connection with any such activities.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>2. Rights
+ Granted</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>You may
+ install and use <span class=SpellE>CompassXtract</span> on any of your
+ computing devices.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>3. Use
+ Restrictions</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>3.1 You may
+ not decompile, disassemble, reverse engineer or modify <span class=SpellE>CompassXtract</span>.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>3.2 You may
+ not distribute <span class=SpellE>CompassXtract</span> to others, breach of
+ which terminates the rights granted under this agreement. This also applies to
+ any integration or implementation of <span class=SpellE>CompassXtract</span> to
+ software developed by you or by others on your behalf (hereinafter referred to
+ as Own <b>Software) </b>or any distribution of which <span class=SpellE>CompassXtract</span> is <span class=GramE>part of.</span> However, you may distribute Own <span
+class=GramE>Software which requires the usage of</span> or links to <span
+class=SpellE>CompassXtract</span> Libraries if you comply with the requirements
+ set down in Section 4 of this Agreement.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>4.
+ Requirements for Distribution of your own Software using <span class=SpellE>CompassXtract</span> Libraries</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>You may only
+ distribute <span class=SpellE>CompassXtract</span> Libraries to others if all
+ of the following conditions are met: 4.1 <span class=GramE>You</span> distribute <span class=SpellE>CompassXtract</span> Libraries as part of Own
+ Software which you license to third parties</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>(<span
+class=GramE>hereinafter</span> "Your <b>Licensees");
</b>4.2
+ Your Own Software requires all the <span class=SpellE>CompassXtract</span> Libraries distributed by you in order to function</span></p>
+ <p style='text-autospace:none'><span class=GramE><span style='font-family:Helvetica;'>properly</span></span><span style='font-family:
+Helvetica;'> when used by
+ Your Licensees;</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>4.3 You
+ provide to Your Licensee a URL to Licensor's Webserver at
+ http://www.bdal.de/compassxtract and require Your Licensees, as condition for
+ being granted the right to use your Own Software, to acquire the usage rights
+ for <span class=SpellE>CompassXtract</span> directly from Licensor by agreeing
+ to the terms of this Agreement, which you distribute in unmodified form with
+ your Own Software.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>4.4 In your
+ Own Software's "About" box the following text is displayed: "This software uses <span class=SpellE>CompassXtract</span> software. <span class=GramE>Copyright $copy;
+ 2011 by <span class=SpellE>Bruker</span> <span class=SpellE>Daltonik</span> GmbH.</span> All rights reserved."</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>5.
+ Restrictions for Distribution of your own Products</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>5.1 You may
+ not use the Licensor's trademarks in a way that suggests your software
+ components and/or programs are provided by or are endorsed by the Licensor.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>5.2 You may
+ not commercially exploit <span class=SpellE>CompassXtract</span>, <span
+class=SpellE>CompassXtract</span> Libraries or products that require the usage
+ of or link to <span class=SpellE>CompassXtract</span> or <span class=SpellE>CompassXtract</span> Libraries. Commercial exploitation includes, but is not limited to, charging a
+ purchase price, license fee, maintenance fee, or subscription fee.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>5.3 Your
+ rights to <span class=SpellE>CompassXtract</span> do not include any license,
+ right, power or authority to subject <span class=SpellE>CompassXtract</span> in
+ whole or in part to any of the terms of an Excluded License. <b>"Excluded
+ License" </b>means any license that requires as a condition of use,
+ modification and/or distribution of software that such software or other
+ software combined and/or distributed with such software shall be (a) disclosed
+ or distributed in source code form; or (b) licensed for the purpose of making
+ derivative works. Without limiting the foregoing obligation, you are
+ specifically prohibited from distributing <span class=SpellE>CompassXtract</span> or <span class=SpellE>CompassXtract</span> Libraries with any software that is
+ subject to the General Public License (GPL) or similar license in a manner that
+ would create a combined work.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>6. Liability</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>6.1 As
+ Licensor delivers the software for free, Licensor is not liable for any kind of
+ damage, direct or indirect, which may arise due to simple negligence (Section
+ 521 German Civil Code). In the event, that there should be – for whatever
+ reason – a statutory liability of Licensor for simple <span class=SpellE>negliegence</span>,
+ the aforementioned exclusion of liability applies nevertheless, but with the
+ exception of damages to life, body or health.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>6.2 You
+ indemnify, defend and hold harmless the Licensor from any liability claims,
+ including attorney fees, of third parties in connection with your usage of <span
+class=SpellE>CompassXtract</span> as well as the distribution of your Own <span
+class=GramE>Software which</span> requires usage of or links to <span
+class=SpellE>CompassXtract</span> Libraries and other circumstances for which
+ you are responsible.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>7. Additional
+ Terms Applicable to <span class=SpellE>CompassXtract</span></span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.1 <span
+class=SpellE>CompassXtract</span> is licensed, not sold. This License only
+ gives you some rights to use <span class=SpellE>CompassXtract</span> and the <span
+class=SpellE>CompassXtract</span> Libraries; the Licensor reserves all other
+ rights. Unless applicable law gives you more rights despite this limitation,
+ you may use <span class=SpellE>CompassXtract</span> and the <span class=SpellE>CompassXtract</span> Libraries only as expressly permitted in this License.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.2 Licensor
+ has no obligation to fix, update, supplement or support <span class=SpellE>CompassXtract</span> and/or the <span class=SpellE>CompassXtract</span> Libraries.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.3 Your
+ rights under this License terminate automatically if you breach this License in
+ any way. Termination of this License will not affect any of your obligations or
+ liabilities arising prior to termination. The following sections of this
+ License shall survive termination: 3.1, 3.2, 5.1, 5.2, 5.3, 6.1<span
+class=GramE>.,</span> 6.2.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.4 No
+ subsidiary agreements of this Agreement have been made. Supplements and
+ amendments to this Agreement must be made in writing as prescribed by law in
+ order to be valid. The requirement of written form under this Agreement may be
+ waived in writing only.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.5 This
+ Agreement is governed by German law to the exclusion of the UN Convention on
+ Contracts for the International Sale of Goods. If you are a consumer, this does
+ not apply if legal provisions, in particular consumer protection legislation,
+ conflict with this choice. The courts of Bremen shall have exclusive
+ jurisdiction. If you are not a merchant, a legal entity under public law or a
+ public-law special fund in the sense Section 38 of the German Code of Civil
+ Procedure (ZPO), the <span class=GramE>agreement on the place of jurisdiction
+ is replaced by the legal provisions</span>.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.6 If
+ individual provisions of this Agreement are or become invalid or contain a <span
+class=GramE>gap which</span> needs to be filled, the validity of the remaining
+ provisions of the Agreement will not be affected thereby. The Parties hereby
+ undertake to substitute the invalid or lacking provision with a valid <span
+class=GramE>provision which</span> comes closest to the documented intentions
+ of the Parties.</span></p>
+</div>
+ </div>
+ <li>Thermo msFileReader</li>
+ <div class="lic-div">
+<p><strong>SOFTWARE LICENSE AGREEMENT (“License”) FOR MSFileReader</strong></p>
+<p>These License terms are an agreement between you and Thermo Finnigan LLC ("Licensor"). They apply to Licensor’s MSFileReader software program (“Software”), which includes documentation and any media on which you received it. These terms also apply to any updates or supplements for this Software, unless other terms accompany those items, in which case those terms apply. <strong>If you use this Software, you accept this License. If you do not accept this Lice [...]
+<p>1. Rights Granted:</p>
+<p>1.1. You may install and use this Software on any of your computing devices.</p>
+<p>1.2. You may distribute this Software to others, but only in combination with other software components and/or programs that you provide. </p>
+<p>2. Use Restrictions:</p>
+<p>2.1. You may not decompile, disassemble, reverse engineer or modify this Software.</p>
+<p>3. Distribution Requirements:</p>
+<p>If you distribute this Software to others, you agree to:</p>
+<p>3.1. Indemnify, defend and hold harmless the Licensor from any claims, including attorneys’ fees, related to the distribution or use of this Software;</p>
+<p>3.2. Display the following text in your software’s “About” box: “MSFileReader file reading tool. Copyright © 2009 by Thermo Fisher Scientific, Inc. All rights reserved.”;</p>
+<p>3.3. Require your end users to agree to a license agreement that prohibits them from redistributing this Software to others.</p>
+<p>4. Distribution Restrictions:</p>
+<p>4.1. You may not use the Licensor’s trademarks in a way that suggests your software components and/or programs are provided by or are endorsed by the Licensor; and</p>
+<p>4.2. You may not <a name="OLE_LINK1" id="OLE_LINK1">commercially exploit </a>this Software or products that incorporate this Software. Commercial exploitation includes, but is not limited to, charging a purchase price, license fee, maintenance fee, or subscription fee.</p>
+<p>4.3. Your rights to this Software do not include any license, right, power or authority to subject this Software in whole or in part to any of the terms of an Excluded License. "Excluded License" means any license that requires as a condition of use, modification and/or distribution of software subject to the Excluded License, that such software or other software combined and/or distributed with such software be (a) disclosed or distributed in source code form; or (b) licens [...]
+<p>5. Additional Terms Applicable to Software:</p>
+<p>5.1. This Software is licensed, not sold. This License only gives you some rights to use this Software; the Licensor reserves all other rights. Unless applicable law gives you more rights despite this limitation, you may use this Software only as expressly permitted in this License.</p>
+<p>5.2. Licensor has no obligation to fix, update, supplement or support this Software.</p>
+<p>5.3. This Software is not designed, manufactured or intended for any use requiring fail-safe performance in which the failure of this Software could lead to death, serious personal injury or severe physical and environmental damage (“High Risk Activities”), such as the operation of aircraft, medical or nuclear facilities. You agree not to use, or license the use of, this Software in connection with any High Risk Activities.</p>
+<p>5.4. Your rights under this License terminate automatically if you breach this License in any way. Termination of this License will not affect any of your obligations or liabilities arising prior to termination. The following sections of this License shall survive termination: 2.1, 3.1, 3.2, 3.3, 4.1, 4.2, 4.3, 5.1, 5.2, 5.3, 5.5, 5.6, 5.7, 5.8, and 5.9.</p>
+<p>5.5. This Software is subject to United States export laws and regulations. You agree to comply with all domestic and international export laws and regulations that apply to this Software. These laws include restrictions on destinations, end users and end use.</p>
+<p>5.6. This License shall be construed and controlled by the laws of the State of California, U.S.A., without regard to conflicts of law. You consent to the jurisdiction of the state and federal courts situated in the State of California in any action arising under this License. The application of the U.N. Convention on Contracts for the International Sale of Goods to this License is hereby expressly excluded. If any provision of this License shall be deemed unenforceable or contrary to [...]
+<p>5.7. THIS SOFTWARE IS LICENSED "AS IS". YOU BEAR ALL RISKS OF USING IT. LICENSOR GIVES NO EXPRESS WARRANTIES, REPRESENTATIONS OR GUARANTEES. YOU MAY HAVE ADDITIONAL CONSUMER RIGHTS UNDER YOUR LOCAL LAWS WHICH THIS LICENSE CANNOT CHANGE. TO THE EXTENT PERMITTED UNDER YOUR LOCAL LAWS, LICENSOR EXCLUDES THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT.</p>
+<p>5.8. LICENSOR’S LIABILITY TO YOU FOR DIRECT DAMAGES ARISING UNDER THIS LICENSE IS LIMITED TO U.S. $1.00. YOU CANNOT RECOVER ANY OTHER DAMAGES, INCLUDING CONSEQUENTIAL, LOST PROFITS, SPECIAL, INDIRECT OR INCIDENTAL DAMAGES, EVEN IF LICENSOR IS EXPRESSLY MADE AWARE OF THE POSSIBILITY THEREOF OR IS NEGLIGENT. THIS LIMITATION APPLIES TO ANYTHING RELATED TO THIS SOFTWARE, SERVICES, CONTENT (INCLUDING CODE) ON THIRD PARTY INTERNET SITES, OR THIRD PARTY PROGRAMS, AND CLAIMS FOR BREACH [...]
+<p>5.9. Use, duplication or disclosure of this Software by the U.S. Government is subject to the restricted rights applicable to commercial computer software (under FAR 52.227019 and DFARS 252.227-7013 or parallel regulations). The manufacturer for this purpose is Thermo Finnigan LLC, 355 River Oaks Parkway, San Jose, California 95134, U.S.A.</p>
+ </div>
+ <li>Waters WRDAC</li>
+ <div class="lic-div">
+<p align="center"><strong>END-USER SOFTWARE LICENSE TERMS FOR WATERS WRDAC SOFTWARE</strong></p>
+<p>Waters grants you a nonexclusive and terminable license to (i) use the software to perform internal information and data processing in connection with Waters and other non-Waters instrumentation products for non-commercial purposes only and (ii) distribute the software as part of the ProteoWizard Software version 2.1 for non-commercial purposes only. You may not incorporate the software into a commercial application nor charge any fee for the software. The software is protected by [...]
+<p>THE SOFTWARE IS PROVIDED “AS IS” AND WITHOUT ANY WARRANTY, EXPRESS OR IMPLIED, BY STATUTE OR OTHERWISE, REGARDING THE WRDAC, INCLUDING WITHOUT LIMITATION THE WARRANTIES OF NON-INFRINGEMENT, FITNESS FOR A PARTICULAR PURPOSE AND MERCHANTABILITY. Waters shall not be liable for any direct, indirect, special, consequential or punitive damages of any kind arising out of or in connection with the software. In the event that the foregoing disclaimers are not effective under appl [...]
+<p>You agree to comply fully with all relevant export laws and regulations of the United States ("Export Laws") to ensure that the software is (a) not exported directly or indirectly in violation of Export Laws and (b) not intended to be used for any purposes prohibited by the Export Laws. If you are a branch of the United States government, you shall have "restricted rights" to use, duplicate, or disclose the software as set forth in subdivision (c)(1)(ii) of Rights [...]
+<p> </p>
+</div>
+</ul>
+
+<br />
+<H3> Step 3, Click below to agree to Licenses and get Crux</H3>
+
+<div style="width:600px;margin-left:10px;margin-top:10px;margin-bottom:10px;border:1px solid black;">
+The most recent build of Crux is temporarily unavailable for OS X.
+If you need a copy of Crux for OS X, please download release 3.0.
+</div>
+
+<input
+ type="submit"
+ name="release_button"
+ value="I agree to the licensing terms, download release 3.0 of Crux"
+/>
+<br/>
+<input
+ type="submit"
+ name="daily_button"
+ value="I agree to the licensing terms, download the most recent build of Crux"
+/>
+</form>
+
+<br>
+<br>
+<br>
+
+ <p>
+Note that you can access the most recent source code from the Crux main development
+trunk using the following Git command:<br>
+<code> git clone https://github.com/crux-toolkit/crux-toolkit.git crux-toolkit</code></p>
+
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
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+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
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+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/default.params b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/default.params
new file mode 100644
index 0000000..5e447aa
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/default.params
@@ -0,0 +1,1676 @@
+################################################################################
+# Sample parameter file
+#
+# On each line, anything after a '#' will be ignored.
+# The format is:
+#
+# <parameter-name>=<value>
+#
+################################################################################
+
+# Crux parameter file (generated by Crux version 2.1)
+# Full documentation available at http://cruxtoolkit.sourceforge.net/
+# comet_version 2016.01 rev. 1
+# Everything following the '#' symbol is treated as a comment.
+
+# Path where pin file will be written instead of make-pin.pin.
+# It is optional for make-pin
+output-file=
+
+# Specify the verbosity of the current processes. Each level prints the
+# following messages, including all those at lower verbosity levels: 0-fatal
+# errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of
+# execution, 40-more progress information, 50-debug info, 60-detailed debug
+# info.
+# Available for all crux programs.
+verbosity=30
+
+# A file containing parameters.
+# Available for all crux programs. Any options specified on the command line
+# will override values in the parameter file.
+parameter-file=
+
+# Replace existing files if true or fail when trying to overwrite a file if
+# false.
+# Available for all crux programs. Applies to parameter file as well as index,
+# search, and analysis output files.
+overwrite=false
+
+# The minimum length of peptides to consider.
+# Used from the command line or parameter file by crux-generate-peptides, and
+# crux tide-index.
+min-length=6
+
+# The maximum length of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides, crux
+# tide-index.
+max-length=50
+
+# The minimum mass (in Da) of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides and
+# crux tide-index.
+min-mass=200
+
+# The maximum mass (in Da) of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides and
+# crux tide-index.
+max-mass=7200
+
+# The minimum number of peaks a spectrum must have for it to be searched.
+# Available for tide-search.
+min-peaks=20
+
+# Specify the enzyme used to digest the proteins in silico. Available enzymes
+# (with the corresponding digestion rules indicated in parentheses) include
+# no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin
+# ([FWYL]|{P}), elastase ([ALIV]|{P}), clostripain ([R]|[]), cyanogen-bromide
+# ([M]|[]), iodosobenzoate ([W]|[]), proline-endopeptidase ([P]|[]),
+# staph-protease ([E]|[]), asp-n ([]|[D]), lys-c ([K]|{P}), lys-n ([]|[K]),
+# arg-c ([R]|{P}), glu-c ([DE]|{P}), pepsin-a ([FL]|{P}),
+# elastase-trypsin-chymotrypsin ([ALIVKRWFY]|{P}). Specifying --enzyme no-enzyme
+# yields a non-enzymatic digest. Warning: the resulting index may be quite
+# large.
+# Available for crux-generate-peptides and crux tide-index.
+enzyme=trypsin
+
+# Specify rules for in silico digestion of protein sequences. Overrides the
+# enzyme option. Two lists of residues are given enclosed in square brackets or
+# curly braces and separated by a |. The first list contains residues
+# required/prohibited before the cleavage site and the second list is residues
+# after the cleavage site. If the residues are required for digestion, they are
+# in square brackets, '[' and ']'. If the residues prevent digestion, then they
+# are enclosed in curly braces, '{' and '}'. Use X to indicate all residues. For
+# example, trypsin cuts after R or K but not before P which is represented as
+# [RK]|{P}. AspN cuts after any residue but only before D which is represented
+# as [X]|[D].
+#
+custom-enzyme=
+
+# Specify whether every peptide in the database must have two enzymatic termini
+# (full-digest) or if peptides with only one enzymatic terminus are also
+# included (partial-digest).
+# Available for crux-generate-peptides and crux tide-index.
+digestion=full-digest
+
+# Maximum number of missed cleavages per peptide to allow in enzymatic
+# digestion.
+# Available from command line or parameter file for crux-generate-peptides. When
+# used with enzyme=<trypsin|elastase|chymotrypsin> includes peptides containing
+# one or more potential cleavage sites.
+missed-cleavages=0
+
+# Tolerance used for matching peptides to spectra. Peptides must be within +/-
+# 'precursor-window' of the spectrum value. The precursor window units depend
+# upon precursor-window-type.
+# Available for tide-search and crux-generate-peptides.
+precursor-window=3
+
+# Specify the units for the window that is used to select peptides around the
+# precursor mass location (mass, mz, ppm). The magnitude of the window is
+# defined by the precursor-window option, and candidate peptides must fall
+# within this window. For the mass window-type, the spectrum precursor m+h value
+# is converted to mass, and the window is defined as that mass +/-
+# precursor-window. If the m+h value is not available, then the mass is
+# calculated from the precursor m/z and provided charge. The peptide mass is
+# computed as the sum of the average amino acid masses plus 18 Da for the
+# terminal OH group. The mz window-type calculates the window as spectrum
+# precursor m/z +/- precursor-window and then converts the resulting m/z range
+# to the peptide mass range using the precursor charge. For the
+# parts-per-million (ppm) window-type, the spectrum mass is calculated as in the
+# mass type. The lower bound of the mass window is then defined as the spectrum
+# mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as
+# spectrum mass / (1.0 - (precursor-window / 1000000)).
+# Available for search-for-xlinks and tide-search.
+precursor-window-type=mass
+
+# Specify the parser to use for reading in MS/MS spectra.
+# Available for search-for-xlinks.
+spectrum-parser=pwiz
+
+# Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor
+# mass information from the "S" line or the "Z" line.
+# Available when spectrum-parser = pwiz.
+use-z-line=true
+
+# When creating decoy peptides using decoy-format=shuffle or
+# decoy-format=peptide-reverse, this option specifies whether the N-terminal and
+# C-terminal amino acids are kept in place or allowed to be shuffled or
+# reversed. For a target peptide "EAMPK" with decoy-format=peptide-reverse,
+# setting keep-terminal-aminos to "NC" will yield "EPMAK"; setting it to "C"
+# will yield "PMAEK"; setting it to "N" will yield "EKPMA"; and setting it to
+# "none" will yield "KPMAE".
+# Available for tide-index.
+keep-terminal-aminos=NC
+
+# Create in the output directory a text file listing of all the peptides in the
+# database, along with their neutral masses, one per line. If decoys are
+# generated, then a second file will be created containing the decoy peptides.
+# Decoys that also appear in the target database are marked with an asterisk in
+# a third column.
+# Available for tide-index.
+peptide-list=false
+
+# Stop after the specified pre-processing step.
+# Available for print-processed-spectra.
+stop-after=xcorr
+
+# Specify the output units for processed spectra.
+# Available for print-processed-spectra
+output-units=bin
+
+# Outputs an SQT results file to the output directory. Note that if sqt-output
+# is enabled, then compute-sp is automatically enabled and cannot be overridden.
+# Available for tide-search.
+sqt-output=false
+
+# Output an mzIdentML results file to the output directory.
+# Available for tide-search, percolator.
+mzid-output=false
+
+# Output a Percolator input (PIN) file to the output directory.
+# Available for tide-search.
+pin-output=false
+
+# Output a Percolator pout.xml format results file to the output directory.
+# Available for percolator.
+pout-output=false
+
+# Output a pepXML results file to the output directory.
+# Available for tide-search, q-ranker, barista, percolator.
+pepxml-output=false
+
+# Output a tab-delimited results file to the output directory.
+# Available for tide-search, percolator, q-ranker, barista.
+txt-output=true
+
+# Compute the preliminary score Sp for all candidate peptides. Report this score
+# in the output, along with the corresponding rank, the number of matched ions
+# and the total number of ions. This option is recommended if results are to be
+# analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp
+# is automatically enabled and cannot be overridden. Note that the Sp
+# computation requires re-processing each observed spectrum, so turning on this
+# switch involves significant computational overhead.
+# Available for tide-search.
+compute-sp=false
+
+# Estimate the parameters of the score distribution for each spectrum by fitting
+# to a Weibull distribution, and compute a p-value for each xlink product. This
+# option is only available when use-old-xlink=F.
+# Currently only implemented for XCORR.
+compute-p-values=false
+
+# A single scan number or a range of numbers to be searched. Range should be
+# specified as 'first-last' which will include scans 'first' and 'last'.
+# The search range x-y is inclusive of x and y.
+scan-number=
+
+# Before calculation of the XCorr score, the m/z axes of the observed and
+# theoretical spectra are discretized. This parameter specifies the size of each
+# bin. The exact formula is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where
+# x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079
+# and for high resolution ms/ms 0.02 is recommended.
+# Available for tide-search and xlink-assign-ions.
+mz-bin-width=1.0005079
+
+# In the discretization of the m/z axes of the observed and theoretical spectra,
+# this parameter specifies the location of the left edge of the first bin,
+# relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the
+# first bin will be located at +0.xx Da).
+# Available for tide-search.
+mz-bin-offset=0.4
+
+# Include flanking peaks around singly charged b and y theoretical ions. Each
+# flanking peak occurs in the adjacent m/z bin and has half the intensity of the
+# primary peak.
+# Available for the tide-search and search-for-xlinks commands.
+use-flanking-peaks=false
+
+# The lowest spectrum m/z to search in the ms2 file.
+# Available for tide-search.
+spectrum-min-mz=0
+
+# The highest spectrum m/z to search in the ms2 file.
+# Available for tide-search.
+spectrum-max-mz=1e+009
+
+# The spectrum charges to search. With 'all' every spectrum will be searched and
+# spectra with multiple charge states will be searched once at each charge
+# state. With 1, 2, or 3 only spectra with that charge state will be searched.
+# Used by tide-search.
+spectrum-charge=all
+
+# The fileroot string will be added as a prefix to all output file names.
+# Available for all commands that produce an output directory.
+fileroot=
+
+# The name of the directory where output files will be created.
+# Available for most commands.
+output-dir=crux-output
+
+# Specify the number of matches to report for each spectrum.
+# Available for tide-search and crux percolator
+top-match=5
+
+# When given a unsigned integer value seeds the random number generator with
+# that value. When given the string "time" seeds the random number generator
+# with the system time.
+# Available for all Crux commands.
+seed=1
+
+# Specify which isotopes to use in calculating fragment ion mass.
+# Used by crux-predict-peptide-ions.
+fragment-mass=mono
+
+# Specify the type of isotopic masses to use when calculating the peptide mass.
+# Used from command line or parameter file by crux-generate-peptides.
+isotopic-mass=mono
+
+# The minimum number of modifications that can be applied to a single peptide.
+# Available for tide-index.
+min-mods=0
+
+# The maximum number of modifications that can be applied to a single peptide.
+# Available for tide-index.
+max-mods=255
+
+# Specify how sequence modifications are reported in various output files. Each
+# modification is reported as a number enclosed in square braces following the
+# modified residue; however, the number may correspond to one of three different
+# masses: (1) 'mod-only' reports the value of the mass shift induced by the
+# modification; (2) 'total' reports the mass of the residue with the
+# modification (residue mass plus modification mass); (3) 'separate' is the same
+# as 'mod-only', but multiple modifications to a single amino acid are reported
+# as a comma-separated list of values. For example, suppose amino acid D has an
+# unmodified mass of 115 as well as two moifications of masses +14 and +2. In
+# this case, the amino acid would be reported as D[16] with 'mod-only', D[131]
+# with 'total', and D[14,2] with 'separate'.
+# Available for generate-peptides.
+mod-mass-format=mod-only
+
+# Consider a-ions in the search? Note that an a-ion is equivalent to a neutral
+# loss of CO from the b-ion. Peak height is 10 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-a-ions=false
+
+# Consider b-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-b-ions=true
+
+# Consider c-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-c-ions=false
+
+# Consider x-ions in the search? Peak height is 10 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-x-ions=false
+
+# Consider y-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-y-ions=true
+
+# Consider z-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-z-ions=false
+
+# Set the precision for scores written to sqt and text files. Note that this
+# parameter only takes effect when specified in the parameter file.
+# Available percolator.
+precision=8
+
+# Set the precision for masses and m/z written to sqt and .txt files. Note that
+# this parameter only takes effect when specified in the parameter file.
+# Available for all commands.
+mass-precision=4
+
+# Show search progress by printing every n spectra searched. Set to 0 to show no
+# search progress.
+# Available for tide-search
+print-search-progress=1000
+
+# When given a unsigned integer value seeds the random number generator with
+# that value. When given the string "time" seeds the random number generator
+# with the system time.
+# Available for all percolator
+percolator-seed=1
+
+# Output the computed features in tab-delimited text format.
+# Available for percolator and q-ranker.
+feature-file-out=false
+
+# Include decoys (PSMs, peptides, and/or proteins) in the XML output.
+# Available for crux percolator
+decoy-xml-output=false
+
+# Specifies the prefix of the protein names that indicate a decoy.
+# Available for percolator
+decoy-prefix=decoy_
+
+# Output final weights to a file named "percolator.weights.txt".
+# Available for crux percolator
+output-weights=false
+
+# Read initial weights from the given file (one per line).
+# Available for crux percolator
+init-weights=
+
+# Penalty for mistakes made on positive examples. If this value is not
+# specified, then it is set via cross validation over the values {0.1, 1, 10},
+# selecting the value that yields the largest number of PSMs identified at the
+# q-value threshold set via the --test-fdr parameter.
+# Available for crux percolator
+c-pos=0.01
+
+# Penalty for mistake made on negative examples. This parameter requires the
+# c-pos is set explicitly; otherwise, --c-neg will have no effect. If not
+# specified, then this value is set by cross validation over {0.1, 1, 10}.
+# Available for crux percolator
+c-neg=0
+
+# False discovery rate threshold to define positive examples in training.
+# Available for crux percolator
+train-fdr=0.01
+
+# False discovery rate threshold used in selecting hyperparameters during
+# internal cross-validation and for reporting the final results.
+# Available for crux percolator.
+test-fdr=0.01
+
+# Apply the specified threshold to PSM, peptide and protein probabilities to
+# obtain a faster estimate of the alpha, beta and gamma parameters.
+# Available for crux percolator.
+fido-fast-gridsearch=0
+
+# Approximate the posterior distribution by allowing large graph components to
+# be split into subgraphs. The splitting is done by duplicating peptides with
+# low probabilities. Splitting continues until the number of possible
+# configurations of each subgraph is below 2^18
+# Available for crux percolator
+fido-split-large-components=false
+
+# To speed up inference, proteins for which none of the associated peptides has
+# a probability exceeding the specified threshold will be assigned probability =
+# 0.
+# Available for crux percolator
+fido-protein-truncation-threshold=0.01
+
+# Replace the target-decoy competition with the method qvality to assign
+# q-values and PEPs. Note that this option only has an effect if the input PSMs
+# are from separate target and decoy searches.
+# Available for crux percolator
+post-processing-qvality=false
+
+# Maximum number of iterations for training.
+# Available for crux percolator
+maxiter=10
+
+# Quicker execution by reduced internal cross-validation.
+# Available for crux percolator
+quick-validation=false
+
+# In its initial round of training, Percolator uses one feature to induce a
+# ranking of PSMs. By default, Percolator will select the feature that produces
+# the largest set of target PSMs at a specified FDR threshold (cf. --train-fdr).
+# This option allows the user to specify which feature is used for the initial
+# ranking, using the name as a string. The name can be preceded by a hyphen
+# (e.g. "-XCorr") to indicate that a lower value is better.
+# Available for crux percolator
+default-direction=
+
+# Use unit normalization (i.e., linearly rescale each PSM's feature vector to
+# have a Euclidean length of 1), instead of standard deviation normalization.
+# Available for crux percolator.
+unitnorm=false
+
+# Measure performance on test set each iteration.
+# Available for crux percolator.
+test-each-iteration=false
+
+# When set to T, interpret the input file as a PIN file.
+# Available for crux percolator.
+feature-file-in=false
+
+# Use the Fido algorithm to infer protein probabilities. Must be true to use any
+# of the Fido options.
+# Available for crux percolator
+protein=false
+
+# Specify the probability with which a present protein emits an associated
+# peptide. Set by grid search (see --fido-gridsearch-depth parameter) if not
+# specified.
+# Available for crux percolator if --protein T is set.
+fido-alpha=0
+
+# Specify the probability of the creation of a peptide from noise. Set by grid
+# search (see --fido-gridsearch-depth parameter) if not specified.
+# Available for crux percolator if --protein T is set.
+fido-beta=0
+
+# Specify the prior probability that a protein is present in the sample. Set by
+# grid search (see --fido-gridsearch-depth parameter) if not specified.
+# Available for crux percolator if --protein T is set.
+fido-gamma=0
+
+# Use pi_0 value when calculating empirical q-values
+# Available for crux percolator if --protein T is set.
+fido-protein-level-pi0=false
+
+# Estimate empirical p-values and q-values for proteins using target-decoy
+# analysis.
+# Available for crux percolator if --protein T is set.
+fido-empirical-protein-q=false
+
+# Set depth of the grid search for alpha, beta and gamma estimation.
+# Available for crux percolator if --protein T is set.
+fido-gridsearch-depth=0
+
+# Use target-decoy competition to assign q-values and PEPs.
+# Available for crux percolator
+post-processing-tdc=false
+
+# Q-value threshold that will be used in the computation of the MSE and ROC AUC
+# score in the grid search.
+# Available for crux percolator if --protein T is set.
+fido-gridsearch-mse-threshold=0.05
+
+# By default, Percolator will examine the learned weights for each feature, and
+# if the weight appears to be problematic, then percolator will discard the
+# learned weights and instead employ a previously trained, static score vector.
+# This switch allows this error checking to be overriden.
+# Available for crux percolator.
+override=false
+
+# Use retention time features calculated as in "Improving tandem mass spectrum
+# identification using peptide retention time prediction across diverse
+# chromatography conditions" by Klammer AA, Yi X, MacCoss MJ and Noble WS.
+# (Analytical Chemistry. 2007 Aug 15;79(16):6111-8.).
+# Available for crux percolator
+klammer=false
+
+# Do not remove redundant peptides; keep all PSMs and exclude peptide level
+# probability.
+# Available for crux percolator
+only-psms=false
+
+# Include a decoy version of every peptide by shuffling or reversing the target
+# sequence or protein. In shuffle or peptide-reverse mode, each peptide is
+# either reversed or shuffled, leaving the N-terminal and C-terminal amino acids
+# in place. Note that peptides appear multiple times in the target database are
+# only shuffled once. In peptide-reverse mode, palindromic peptides are
+# shuffled. Also, if a shuffled peptide produces an overlap with the target or
+# decoy database, then the peptide is re-shuffled up to 5 times. Note that,
+# despite this repeated shuffling, homopolymers will appear in both the target
+# and decoy database. The protein-reverse mode reverses the entire protein
+# sequence, irrespective of the composite peptides.
+# Available for tide-index
+decoy-format=shuffle
+
+# Expression for static and variable mass modifications to include. Specify a
+# comma-separated list of modification sequences of the form:
+# C+57.02146,2M+15.9949,1STY+79.966331,...
+# Available for tide-index
+mods-spec=C+57.02146
+
+# Specifies N-terminal static and variable mass modifications on peptides.
+# Specify a comma-separated list of N-terminal modification sequences of the
+# form: 1E-18.0106,C-17.0265
+# Available for tide-index
+nterm-peptide-mods-spec=
+
+# Specifies C-terminal static and variable mass modifications on peptides.
+# Specify a comma-separated list of C-terminal modification sequences of the
+# form: X+21.9819
+# Available for tide-index
+cterm-peptide-mods-spec=
+
+# Specify the name of the file where the binarized fragmentation spectra will be
+# stored. Subsequent runs of crux tide-search will execute more quickly if
+# provided with the spectra in binary format. The filename is specified relative
+# to the current working directory, not the Crux output directory (as specified
+# by --output-dir). This option is not valid if multiple input spectrum files
+# are given.
+# Available for tide-search
+store-spectra=
+
+# Enable the calculation of exact p-values for the XCorr score. Calculation of
+# p-values increases the running time but increases the number of
+# identifications at a fixed confidence threshold. The p-values will be reported
+# in a new column with header "exact p-value", and the "xcorr score" column will
+# be replaced with a "refactored xcorr" column. Note that, currently, p-values
+# can only be computed when the mz-bin-width parameter is set to its default
+# value. Variable and static mods are allowed on non-terminal residues in
+# conjunction with p-value computation, but currently only static mods are
+# allowed on the N-terminus, and no mods on the C-terminus.
+# Available for tide-search
+exact-p-value=false
+
+# When providing a FASTA file as the index, the generated binary index will be
+# stored at the given path. This option has no effect if a binary index is
+# provided as the index.
+# Available for tide-search
+store-index=
+
+# When set to T, target and decoy search results are reported in a single file,
+# and only the top-scoring N matches (as specified via --top-match) are reported
+# for each spectrum, irrespective of whether the matches involve target or decoy
+# peptides.
+# Available for tide-search
+concat=false
+
+# Include the file column in tab-delimited output.
+# Available for tide-search
+file-column=true
+
+# If true, all peaks around the precursor m/z will be removed, within a range
+# specified by the --remove-precursor-tolerance option.
+# Available for tide-search.
+remove-precursor-peak=false
+
+# This parameter specifies the tolerance (in Th) around each precursor m/z that
+# is removed when the --remove-precursor-peak option is invoked.
+# Available for print-processed spectra and tide-search.
+remove-precursor-tolerance=1.5
+
+# When set to T, for each protein that begins with methionine, tide-index will
+# put two copies of the leading peptide into the index, with and without the
+# N-terminal methionine.
+# Available for tide-index.
+clip-nterm-methionine=false
+
+# Prevent duplicate peptides between the target and decoy databases. When set to
+# "F", the program keeps all target and previously generated decoy peptides in
+# memory. A shuffled decoy will be re-shuffled multiple times to avoid
+# duplication. If a non-duplicated peptide cannot be generated, the decoy is
+# skipped entirely. When set to "T", every decoy is added to the database
+# without checking for duplication. This option reduces the memory requirements
+# significantly. Default = F.
+# Available for tide-index.
+allow-dups=false
+
+# Controls whether neutral loss ions are considered in the search. Two types of
+# neutral losses are included and are applied only to singly charged b- and
+# y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each
+# neutral loss peak has intensity 1/5 of the primary peak.
+# Available for tide-search.
+use-neutral-loss-peaks=true
+
+# The maximum charge state of a spectra to consider in search.
+# Available for tide-search.
+max-precursor-charge=5
+
+# Carries out a peptide-centric search. For each peptide the top-scoring spectra
+# are reported, in contrast to the standard spectrum-centric search where the
+# top-scoring peptides are reported. Note that in this case the "xcorr rank"
+# column will contain the rank of the given spectrum with respect to the given
+# candidate peptide, rather than vice versa (which is the default).
+# Available for tide-search.
+peptide-centric-search=false
+
+# 0=poll CPU to set num threads; else specify num threads directly.
+# Available for tide-search tab-delimited files only.
+num-threads=0
+
+# Analysis begins with a pre-processsing step that creates a set of lookup
+# tables which are then used during training. Normally, these lookup tables are
+# deleted at the end of the analysis, but setting this option to T prevents the
+# deletion of these tables. Subsequently, analyses can be repeated more
+# efficiently by specifying the --re-run option.
+# Available for q-ranker and barista.
+skip-cleanup=false
+
+# Re-run a previous analysis using a previously computed set of lookup tables.
+# For this option to work, the --skip-cleanup option must have been set to true
+# when the program was run the first time.
+# Available for q-ranker and barista.
+re-run=
+
+# Use an enriched feature set, including separate features for each ion type.
+# Available for q-ranker and barista.
+use-spec-features=true
+
+# If the target and decoy searches were run separately, rather than using a
+# concatenated database, then the program will assume that the database search
+# results provided as a required argument are from the target database search.
+# This option then allows the user to specify the location of the decoy search
+# results. Like the required arguments, these search results can be provided as
+# a single file, a list of files or a directory. However, the choice (file, list
+# or directory) must be consistent for the MS2 files and the target and decoy
+# tab-delimited files. Also, if the MS2 and tab-delimited files are provided in
+# directories, then Q-ranker will use the MS2 filename (foo.ms2) to identify
+# corresponding target and decoy tab-delimited files with names like
+# foo*.target.txt and foo*.decoy.txt. This naming convention allows the target
+# and decoy txt files to reside in the same directory.
+# Available for q-ranker and barista.
+separate-searches=
+
+# Specify that the search results are provided as lists of files, rather than as
+# individual files.
+# Available for barista and percolator.
+list-of-files=false
+
+# Specifies whether to do optimization at the protein, peptide or psm level.
+# Available for barista.
+optimization=protein
+
+# Specify the method used to estimate q-values: the mix-max procedure or
+# target-decoy competition. peptide-level is applied for spectrum-centric
+# search. Eliminates any PSMS for which there exists a better scoring PSM
+# involving the same peptide.
+# Used by assign-confidence.
+estimation-method=tdc
+
+# Adjust the score using the Sidak adjustment and reports them in a new column
+# in the output file. Note that this adjustment only makes sense if the given
+# scores are p-values, and that it requires the presence of the "distinct
+# matches/spectrum" feature for each PSM.
+# Used by assign-confidence.
+sidak=false
+
+# Specify the column (for tab-delimited input) or tag (for XML input) used as
+# input to the q-value estimation procedure. If this parameter is unspecified,
+# then assign-confidence tries to seach for "xcorr score", "evalue" (comet),
+# "exact p-value" score fields in this order in the input file.
+# Used by assign-confidence.
+score=
+
+# Specify this parameter to T in order to combine charge states with peptide
+# sequencesin peptide-centric search. Works only if peptide-level=T.
+# Used by assign-confidence.
+combine-charge-states=false
+
+# Specify this parameter to T in order to treat peptides carrying different or
+# no modifications as being the same. Works only if peptide-level=T.
+# Used by assign-confidence.
+combine-modified-peptides=false
+
+# The q-value threshold used by cascade search. Spectra identified with q-value
+# less than this threshold in one search will be excluded from all subsequent
+# searches.
+# Used by Cascade-Search
+q-value-threshold=0.01
+
+# Predict the specified primary ion series. 'a' indicates a-ions only, 'b'
+# indicates b-ions only, 'y' indicates y-ions only, 'by' indicates both b and y,
+# 'bya' indicates b, y, and a.
+# Only available for crux-predict-peptide-ions. Set automatically to 'by' for
+# searching.
+primary-ions=by
+
+# Predict the precursor ions, and all associated ions (neutral losses, multiple
+# charge states) consistent with the other specified options.
+# Only available for crux-predict-peptide-ions.
+precursor-ions=false
+
+# Predict the given number of isotope peaks (0|1|2).
+# Only available for crux-predict-peptide-ion. Automatically set to 0 for Sp
+# scoring and 1 for xcorr scoring.
+isotope=0
+
+# Predict flanking peaks for b- and y ions.
+# Only available for crux-predict-peptide-ion.
+flanking=false
+
+# Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the
+# charge state of the peptide ("peptide"). If the max-ion-charge is greater than
+# the charge state of the peptide, then the maximum is the peptide charge.
+# Available for predict-peptide-ions and search-for-xlinks. Set to 'peptide' for
+# search.
+max-ion-charge=peptide
+
+# Include among the predicted peaks b/y ions with up to n losses of nh3. For
+# example, for --nh3 2, predict a peak for each b- and y-ion with the loss of
+# one nh3 group and predict a second peak for each b- and y-ion with the loss of
+# two nh3 groups. These peaks will have 1 and 2, respectively, in the NH3 column
+# of the output.
+# Only available for crux-predict-peptide-ions.
+nh3=0
+
+# Include in the predicted peaks, b/y ions with the loss of 1 to n water
+# molecules. See --nh3 for an example.
+# Only available for crux-predict-peptide-ions.
+h2o=0
+
+# The name of the file in FASTA format.
+# Option for spectral-counts
+protein-database=
+
+# Type of analysis to make on the match results: (RAW|NSAF|dNSAF|SIN|EMPAI).
+# With exception of the RAW metric, the database of sequences need to be
+# provided using --protein-database.
+# Available for spectral-counts. RAW is raw counts, NSAF is Normalized Spectral
+# Abundance Factor, dNSAF is Distributed Spectral Abundance Factor, SIN is
+# Spectral Index Normalized and EMPAI is Exponentially Modified Protein
+# Abundance Index
+measure=NSAF
+
+# Ignore peptides that map to multiple proteins.
+# Available for spectral-counts.
+unique-mapping=false
+
+# Quantification at protein or peptide level.
+# Available for spectral-counts and either NSAF and SIN.
+quant-level=protein
+
+# Perform a parsimony analysis on the proteins, and report a "parsimony rank"
+# column in the output file. This column contains integers indicating the
+# protein's rank in a list sorted by spectral counts. If the parsimony analysis
+# results in two proteins being merged, then their parsimony rank is the same.
+# In such a case, the rank is assigned based on the largest spectral count of
+# any protein in the merged meta-protein. The "simple" parsimony algorithm only
+# merges two proteins A and B if the peptides identified in protein A are the
+# same as or a subset of the peptides identified in protein B. The "greedy"
+# parsimony algorithm does additional merging, using the peptide q-values to
+# greedily assign each peptide to a single protein.
+# Available for spectral-counts.
+parsimony=none
+
+# Determines what type of threshold to use when filtering matches. none : read
+# all matches, qvalue : use calculated q-value from percolator or q-ranker,
+# custom : use --custom-threshold-name and --custom-threshold-min parameters.
+# used for crux spectral-counts
+threshold-type=qvalue
+
+# Only consider PSMs with a threshold value. By default, q-values are
+# thresholded using a specified threshold value. This behavior can be changed
+# using the --custom-threshold and --threshold-min parameters.
+# Available for spectral-counts. All PSMs with higher (or lower) than this will
+# be ignored.
+threshold=0.01
+
+# Specify which field to apply the threshold to. The direction of the threshold
+# (<= or >=) is governed by --custom-threshold-min. By default, the threshold
+# applies to the q-value, specified by "percolator q-value", "q-ranker q-value",
+# "decoy q-value (xcorr)", or "barista q-value".
+# Available for spectral-counts.
+custom-threshold-name=
+
+# When selecting matches with a custom threshold, custom-threshold-min
+# determines whether to filter matches with custom-threshold-name values that
+# are greater-than or equal (F) or less-than or equal (T) than the threshold.
+# Available for spectral-counts.
+custom-threshold-min=true
+
+# MS2 file corresponding to the psm file. Required to measure the SIN. Ignored
+# for NSAF, dNSAF and EMPAI.
+# Available for spectral-counts with measure=SIN.
+input-ms2=
+
+# Use mzid's passThreshold attribute to filter matches.
+# Used when parsing mzIdentML files.
+mzid-use-pass-threshold=false
+
+# Change the mass of all amino acids 'A' by the given amount.
+#
+A=0
+
+# Change the mass of all amino acids 'C' by the given amount.
+#
+C=57.021464
+
+# Change the mass of all amino acids 'D' by the given amount.
+#
+D=0
+
+# Change the mass of all amino acids 'E' by the given amount.
+#
+E=0
+
+# Change the mass of all amino acids 'F' by the given amount.
+#
+F=0
+
+# Change the mass of all amino acids 'G' by the given amount.
+#
+G=0
+
+# Change the mass of all amino acids 'H' by the given amount.
+#
+H=0
+
+# Change the mass of all amino acids 'I' by the given amount.
+#
+I=0
+
+# Change the mass of all amino acids 'K' by the given amount.
+#
+K=0
+
+# Change the mass of all amino acids 'L' by the given amount.
+#
+L=0
+
+# Change the mass of all amino acids 'M' by the given amount.
+#
+M=0
+
+# Change the mass of all amino acids 'N' by the given amount.
+#
+N=0
+
+# Change the mass of all amino acids 'P' by the given amount.
+#
+P=0
+
+# Change the mass of all amino acids 'Q' by the given amount.
+#
+Q=0
+
+# Change the mass of all amino acids 'R' by the given amount.
+#
+R=0
+
+# Change the mass of all amino acids 'S' by the given amount.
+#
+S=0
+
+# Change the mass of all amino acids 'T' by the given amount.
+#
+T=0
+
+# Change the mass of all amino acids 'V' by the given amount.
+#
+V=0
+
+# Change the mass of all amino acids 'W' by the given amount.
+#
+W=0
+
+# Change the mass of all amino acids 'Y' by the given amount.
+#
+Y=0
+
+# Legal values are auto, tsv, sqt, pin, pepxml or mzidentml format.
+# option, for psm-convert
+input-format=auto
+
+# Whether matches/ion are distinct (as opposed to total).
+# option, for psm-convert.
+distinct-matches=true
+
+# Rather than the spectrum, output summary statistics to standard output. Each
+# statistic is placed on a separate line, in the format <name>:<value> (e.g.
+# "TIC:1000.0").
+# Available only for crux-get-ms2-spectrum. Does not affect contents of the
+# output file.
+stats=false
+
+# Print the theoretical spectrum
+# Available for xlink-predict-peptide-ions.
+print-theoretical-spectrum=false
+
+# Use the old version of xlink-searching algorithm. When false, a new version of
+# the code is run. The new version supports variable modifications and can
+# handle more complex databases. This new code is still in development and
+# should be considered a beta release.
+# Available for search-for-xlinks program.
+use-old-xlink=true
+
+# Score method for xlink {composite, modification, concatenated}.
+# Available for xlink-score-spectrum.
+xlink-score-method=composite
+
+# Provides a list of isotopic windows to search. For example, -1,0,1 will search
+# in three disjoint windows: (1) precursor_mass - neutron_mass +/- window, (2)
+# precursor_mass +/- window, and (3) precursor_mass + neutron_mass +/- window.
+# The window size is defined from the precursor-window and precursor-window-type
+# parameters. This option is only available when use-old-xlink=F.
+# Used for crux search-for-xlinks
+isotope-windows=0
+
+# Include linear peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-linears=true
+
+# Include dead-end peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-deadends=true
+
+# Include self-loop peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-selfloops=true
+
+# Include intra-protein cross-link candiates within the search.
+# Available for crux search-for-xlinks program.
+xlink-include-intra=true
+
+# Include inter-protein cross-link candidates within the search.
+# Available for crux search-for-xlinks program.
+xlink-include-inter=true
+
+# Include crosslink candidates that are both inter and intra.
+# Available for crux search-for-xlinks program.
+xlink-include-inter-intra=true
+
+# List of amino acids for which the cross-linker can prevent cleavage. This
+# option is only available when use-old-xlink=F.
+# Available for search-for-xlinks program.
+xlink-prevents-cleavage=K
+
+# Specify the maximum number of modifications allowed on a crosslinked peptide.
+# This option is only available when use-old-xlink=F.
+# Available for crux search-for-xlinks
+max-xlink-mods=0
+
+# Search decoy peptides within +/- precursor-window-weibull of the precursor
+# mass. The resulting scores are used only for fitting the Weibull distribution
+# Available for crux search-for-xlinks.
+precursor-window-weibull=20
+
+# Window type to use in conjunction with the precursor-window-weibull parameter.
+# Available for crux search-for-xlinks
+precursor-window-type-weibull=mass
+
+# Keep shuffling and collecting XCorr scores until the minimum number of points
+# for weibull fitting (using targets and decoys) is achieved.
+# Available for crux search-for-xlinks
+min-weibull-points=4000
+
+# Determines which spectral feature detection algorithm to use. Different
+# results are possible with each algorithm, and there are pros and cons to each.
+# Available for crux hardklor
+hardklor-algorithm=version1
+
+# Defines alternative averagine models in the analysis that incorporate
+# additional atoms and/or isotopic enrichments. Modifications are represented as
+# text strings. Inclusion of additional atoms in the model is done using by
+# entering an atomic formula, such as: PO2 or Cl. Inclusion of isotopic
+# enrichment to the model is done by specifying the percent enrichment (as a
+# decimal) followed by the atom being enriched and an index of the isotope. For
+# example, 0.75H1 specifies 75% enrichment of the first heavy isotope of
+# hydrogen. In other words, 75% deuterium enrichment. Two or more modifications
+# can be combined into the same model, and separated by spaces: B2 0.5B1
+# Available for crux hardklor
+averagine-mod=
+
+# Boxcar averaging is a sliding window that averages n adjacent spectra prior to
+# feature detection. Averaging generally improves the signal-to-noise ratio of
+# features in the spectra, as well as improving the shape of isotopic envelopes.
+# However, averaging will also change the observed peak intensities. Averaging
+# with too wide a window will increase the occurrence of overlapping features
+# and broaden the chromatographic profiles of observed features. The number
+# specified is the total adjacent scans to be combined, centered on the scan
+# being analyzed. Therefore, an odd number is recommended to center the boxcar
+# window. For example, a value of 3 would produce an average of the scan of
+# interest, plus one scan on each side. A value of 0 disables boxcar averaging.
+# Available for crux hardklor
+boxcar-averaging=0
+
+# This parameter is only functional when boxcar-averaging is used. The filter
+# will remove any peaks not seen in n scans in the boxcar window. The effect is
+# to reduce peak accumulation due to noise and reduce chromatographic broadening
+# of peaks. Caution should be used as over-filtering can occur. The suggested
+# number of scans to set for filtering should be equal to or less than the
+# boxcar-averaging window size. A value of 0 disables filtering.
+# Available for crux hardklor
+boxcar-filter=0
+
+# This parameter is only functional when boxcar-filter is used. The value
+# specifies the mass tolerance in ppm for declaring a peak the same prior to
+# filtering across all scans in the boxcar window.
+# Available for crux hardklor
+boxcar-filter-ppm=10
+
+# Indicates whether the data contain profile or centroided peaks.
+# Available for crux hardklor
+centroided=false
+
+# Choose the charge state determination method.
+# Available for crux hardklor
+cdm=Q
+
+# Specifies the minimum charge state to allow when finding spectral features. It
+# is best to set this value to the lowest assumed charge state to be present. If
+# set higher than actual charge states that are present, those features will not
+# be identified or incorrectly assigned a different charge state and mass.
+# Available for crux hardklor
+min-charge=1
+
+# Specifies the maximum charge state to allow when finding spectral features. It
+# is best to set this value to a practical number (i.e. do not set it to 20 when
+# doing a tryptic shotgun analysis). If set higher than actual charge states
+# that are present, the algorithm will perform significantly slower without any
+# improvement in results.
+# Available for crux hardklor
+max-charge=5
+
+# Sets the correlation threshold (cosine similarity) for accepting each
+# predicted feature.
+# Available for crux hardklor
+corr=0.85
+
+# Sets the depth of combinatorial analysis. For a given set of peaks in a
+# spectrum, search for up to this number of combined peptides that explain the
+# observed peaks. The analysis stops before depth is reached if the current
+# number of deconvolved features explains the observed peaks with a correlation
+# score above the threshold defined with the correlation parameter.
+# Available for crux hardklor
+depth=3
+
+# When reporting each feature, report abundance as the sum of all isotope peaks.
+# The value reported is the estimate of the correct peak heights based on the
+# averagine model scaled to the observed peak heights.
+# Available for crux hardklor
+distribution-area=false
+
+# Specifies an ASCII text file that defines symbols for the periodic table.
+# Available for crux hardklor
+hardklor-data-file=
+
+# Indicates the type of instrument used to collect data. This parameter,
+# combined with the resolution parameter, define how spectra will be centroided
+# (if you provide profile spectra) and the accuracy when aligning observed peaks
+# to the models.
+# Available for crux hardklor
+instrument=fticr
+
+# Specifies an ASCII text file that can be read to override the natural isotope
+# abundances for all elements.
+# Available for crux hardklor
+isotope-data-file=
+
+# Specifies the maximum number of models to build for a set of peaks being
+# analyzed. Regardless of the setting, the number of models will never exceed
+# the number of peaks in the current set. However, as many of the low abundance
+# peaks are noise or tail ends of distributions, defining models for them is
+# detrimental to the analysis.
+# Available for crux hardklor
+max-features=10
+
+# Filters the spectra prior to analysis for the requested MS/MS level. For
+# example, if the data contain MS and MS/MS spectra, setting mzxml-filter = 1
+# will analyze only the MS scan events. Setting mzxml-filter = 2 will analyze
+# only the MS/MS scan events.
+# Available for crux hardklor
+mzxml-filter=1
+
+# Constrains the search in each spectrum to signals below this value in
+# Thomsons. Setting to 0 disables this feature.
+# Available for crux hardklor
+mz-max=0
+
+# Constrains the search in each spectrum to signals above this value in
+# Thomsons. Setting to 0 disables this feature.
+# Available for crux hardklor
+mz-min=0
+
+# Only used when algorithm = version1. Defines the maximum window size in
+# Thomsons to analyze when deconvolving peaks in a spectrum into features.
+# Available for crux hardklor
+mz-window=4
+
+# Specifies the resolution of the instrument at 400 m/z for the data being
+# analyzed.
+# Available for crux hardklor
+resolution=100000
+
+# Used to restrict analysis to spectra with scan numbers below this parameter
+# value. A value of 0 disables this feature.
+# Available for crux hardklor
+scan-range-max=0
+
+# Used to restrict analysis to spectra with scan numbers above this parameter
+# value. A value of 0 disables this feature.
+# Available for crux hardklor
+scan-range-min=0
+
+# Set the sensitivity level. There are four levels: 0 (low), 1 (moderate), 2
+# (high), and 3 (max). Increasing the sensitivity will increase computation
+# time, but will also yield more isotope distributions.
+# Available for crux hardklor
+sensitivity=2
+
+# Filters spectra to remove peaks below this signal-to-noise ratio prior to
+# finding features.
+# Available for crux hardklor
+signal-to-noise=1
+
+# Uses Savitzky-Golay smoothing on profile peak data prior to centroiding the
+# spectra. This parameter is recommended for low resolution spectra only.
+# Smoothing data causes peak depression and broadening. Only use odd numbers for
+# the degree of smoothing (as it defines a window centered on each data point).
+# Higher values will produce smoother peaks, but with greater depression and
+# broadening. Setting this parameter to 0 disables smoothing.
+# Available for crux hardklor
+smooth=0
+
+# Set the signal-to-noise window length (in m/z). Because noise may be
+# non-uniform across a spectrum, this value adjusts the segment size considered
+# when calculating a signal-over-noise ratio.
+# Available for crux hardklor
+sn-window=250
+
+# Applies the lowest noise threshold of any sn_window across the entire mass
+# range for a spectrum. Setting this parameter to 0 turns off this feature, and
+# different noise thresholds will be used for each local mass window in a
+# spectrum.
+# Available for crux hardklor
+static-sn=true
+
+# Ignore PPIDs that persist for longer than this length of time in the MS1
+# spectra. The unit of time is whatever unit is used in your data file (usually
+# minutes). These PPIDs are considered contaminants.
+# Available for crux bullseye
+max-persist=2
+
+# When true, require an exact match (as defined by --exact-tolerance) between
+# the center of the precursor isolation window in the MS2 scan and the base
+# isotopic peak of the PPID. If this option is set to false and no exact match
+# is observed, then attempt to match using a wider m/z tolerance. This wider
+# tolerance is calculated using the PPID's monoisotopic mass and charge (the
+# higher the charge, the smaller the window).
+# Available for crux bullseye
+exact-match=false
+
+# Allowed gap size when checking for PPIDs across consecutive MS1 scans.
+# Available for crux bullseye
+gap-tolerance=1
+
+# Only consider PPIDs above this minimum mass in daltons.
+# Available for crux bullseye
+bullseye-min-mass=600
+
+# Only consider PPIDs below this maximum mass in daltons.
+# Available for crux bullseye
+bullseye-max-mass=8000
+
+# Set the tolerance (+/-ppm) for --exact-match.
+# Available for crux bullseye
+exact-tolerance=10
+
+# Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans.
+# Available for crux bullseye
+persist-tolerance=10
+
+# Total number of MS1 scans over which a PPID must be observed to be considered
+# real. Gaps in persistence are allowed by setting --gap-tolerance.
+# Available for crux bullseye
+scan-tolerance=3
+
+# Set the tolerance (+/-units) around the retention time over which a PPID can
+# be matches to the MS2 spectrum. The unit of time is whatever unit is used in
+# your data file (usually minutes).
+# Available for crux bullseye
+retention-tolerance=0.5
+
+# The format to write the output spectra to. If empty, the spectra will be
+# output in the same format as the MS2 input.
+# Available for crux bullseye
+spectrum-format=
+
+# Sort in ascending (T) or descending (F) order.
+# Available for sort-by-column
+ascending=true
+
+# Specify the input and output delimiter to use when processing the delimited
+# file. The argument can be either a single character or the keyword 'tab.'
+# Available for the delimited utility programs.
+delimiter=tab
+
+# Print the header line of the file, in addition to the columns that match.
+# Available for crux extract-columns and extract-rows
+header=true
+
+# Specifies the data type of the column, either an integer (int), a floating
+# point number (real), or a string.
+# Available for crux extract-rows
+column-type=string
+
+# Specify the operator that is used to compare an entry in the specified column
+# to the value given on the command line.
+# Available for crux extract-rows
+comparison=eq
+
+# Run the Bullseye algorithm on the given MS data, using it to assign
+# high-resolution precursor values to the MS/MS data. If a spectrum file ends
+# with .ms2 or .cms2, matching .ms1/.cms1 files will be used as the MS1 file.
+# Otherwise, it is assumed that the spectrum file contains both MS1 and MS2
+# scans.
+# Available for crux pipeline
+bullseye=false
+
+# Specify which search engine to use.
+# Available for crux pipeline
+search-engine=tide-search
+
+# Specify which post-processor to apply to the search results.
+# Available for crux pipeline
+post-processor=percolator
+
+# Consider modifications on any amino acid in aa list with at most
+# max-per-peptide in one peptide. The parameter takes the form
+# [[html:<mass change>:<aa list>:<max per
+# peptide>:<prevents cleavage>:<prevents cross-link>]].
+# This parameter may be included with different values multiple times so
+# long as the total number of mod, cmod, and nmod parameters does not
+# exceed 11. The "prevents cleavage" and "prevents cross-link" arguments
+# are optional T/F arguments for describing whether the modification
+# prevents enzymatic cleavage of cross-linking, respectively. This
+# option is only available when use-old-xlink=F. Note that this
+# parameter only takes effect when specified in the parameter file.
+# Available for search-for-xlinks.
+mod=NO MODS
+
+# Specify a variable modification to apply to N-terminus of peptides.
+# <mass change>:<max distance from protein n-term (-1 for no max)> Note
+# that this parameter only takes effect when specified in the parameter
+# file.
+# Available for search-for-xlinks.
+nmod=NO MODS
+
+# Specify a variable modification to apply to C-terminus of peptides.
+# <mass change>:<max distance from protein c-term (-1 for no max)>. Note
+# that this parameter only takes effect when specified in the parameter
+# file.
+# Available for search-for-xlinks.
+cmod=NO MODS
+
+####################
+# Comet Parameters #
+####################
+# 0=no, 1=concatenated search, 2=separate search.
+# Available for comet.
+decoy_search=0
+
+# 0=poll CPU to set num threads; else specify num threads directly.
+# Available for comet.
+num_threads=0
+
+# Controls the mass tolerance value. The mass tolerance is set at +/- the
+# specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0
+# tolerance. The units of the mass tolerance is controlled by the parameter
+# "peptide_mass_units".
+# Available for comet.
+peptide_mass_tolerance=3
+
+# 0=amu, 1=mmu, 2=ppm.
+# Available for comet.
+peptide_mass_units=0
+
+# 0=average masses, 1=monoisotopic masses.
+# Available for comet.
+mass_type_parent=1
+
+# 0=average masses, 1=monoisotopic masses.
+# Available for comet.
+mass_type_fragment=1
+
+# 0=singly charged peptide mass, 1=precursor m/z.
+# Available for comet.
+precursor_tolerance_type=0
+
+# 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8
+# labeling).
+# Available for comet.
+isotope_error=0
+
+# Specify a search enzyme from the end of the parameter file.
+# Available for comet.
+search_enzyme_number=1
+
+# valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term.
+# Available for comet.
+num_enzyme_termini=2
+
+# Maximum value is 5; for enzyme search.
+# Available for comet.
+allowed_missed_cleavage=2
+
+# Binning to use on fragment ions.
+# Available for comet.
+fragment_bin_tol=1.000507
+
+# Offset position to start the binning (0.0 to 1.0).
+# Available for comet.
+fragment_bin_offset=0.4
+
+# 0=default peak shape, 1=M peak only.
+# Available for comet.
+theoretical_fragment_ions=1
+
+# Controls whether or not A-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_A_ions=0
+
+# Controls whether or not B-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_B_ions=1
+
+# Controls whether or not C-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_C_ions=0
+
+# Controls whether or not X-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_X_ions=0
+
+# Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_Y_ions=1
+
+# Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_Z_ions=0
+
+# 0=no, 1= yes to consider NH3/H2O neutral loss peak.
+# Available for comet.
+use_NL_ions=1
+
+# 0=no, 1=yes write sqt file.
+# Available for comet.
+output_sqtfile=0
+
+# 0=no, 1=yes write tab-delimited text file.
+# Available for comet.
+output_txtfile=1
+
+# 0=no, 1=yes write pep.xml file.
+# Available for comet.
+output_pepxmlfile=1
+
+# 0=no, 1=yes write percolator file.
+# Available for comet.
+output_percolatorfile=0
+
+# 0=no, 1=yes write .out files.
+# Available for comet.
+output_outfiles=0
+
+# 0=no, 1=yes to replace Sp with expect in out & sqt.
+# Available for comet.
+print_expect_score=1
+
+# num peptide results to show.
+# Available for comet.
+num_output_lines=5
+
+# 0=no, 1=yes for out files only.
+# Available for comet.
+show_fragment_ions=0
+
+# Sample enzyme which is possibly different than the one applied to the search.
+# Used to calculate NTT & NMC in pepXML output.
+# Available for comet.
+sample_enzyme_number=1
+
+# Start and scan scan range to search; 0 as first entry ignores parameter.
+# Available for comet.
+scan_range=0 0
+
+# Precursor charge range to analyze; does not override mzXML charge; 0 as first
+# entry ignores parameter.
+# Available for comet.
+precursor_charge=0 0
+
+# Specifies the whether to override existing precursor charge state information
+# when present in the files with the charge range specified by the
+# "precursor_charge" parameter.
+# Available for comet.
+override_charge=0
+
+# MS level to analyze, valid are levels 2 or 3.
+# Available for comet.
+ms_level=2
+
+# Specifies which scan types are searched.
+# Available for comet.
+activation_method=ALL
+
+# MH+ peptide mass range to analyze.
+# Available for comet.
+digest_mass_range=600.0 5000.0
+
+# Number of search hits to store internally.
+# Available for comet.
+num_results=50
+
+# For '.out' file output only, 0=search everything again, 1=don't search if .out
+# exists.
+# Available for comet.
+skip_researching=1
+
+# Set maximum fragment charge state to analyze (allowed max 5).
+# Available for comet.
+max_fragment_charge=3
+
+# Set maximum precursor charge state to analyze (allowed max 9).
+# Available for comet.
+max_precursor_charge=6
+
+# 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six.
+# Available for comet.
+nucleotide_reading_frame=0
+
+# 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine.
+# Available for comet.
+clip_nterm_methionine=0
+
+# Maximum number of spectra to search at a time; 0 to search the entire scan
+# range in one loop.
+# Available for comet.
+spectrum_batch_size=0
+
+# Specifies the prefix of the protein names that indicates a decoy.
+# Available for comet.
+decoy_prefix=decoy_
+
+# Specifies the suffix string that is appended to the base output name for the
+# pep.xml, pin.xml, txt and sqt output files.
+# Available for comet.
+output_suffix=
+
+# Specifies one or more mass offsets to apply. This value(s) are effectively
+# subtracted from each precursor mass such that peptides that are smaller than
+# the precursor mass by the offset value can still be matched to the respective
+# spectrum.
+# Available for comet.
+mass_offsets=
+
+# Minimum number of peaks in spectrum to search.
+# Available for comet.
+minimum_peaks=10
+
+# Minimum intensity value to read in.
+# Available for comet.
+minimum_intensity=0
+
+# 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD).
+# Available for comet.
+remove_precursor_peak=0
+
+# +- Da tolerance for precursor removal.
+# Available for comet.
+remove_precursor_tolerance=1.5
+
+# For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range.
+# Available for comet.
+clear_mz_range=0.0 0.0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod01=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod02=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod03=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod04=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod05=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod06=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod07=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod08=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod09=0.0 null 0 4 -1 0 0
+
+# Specifies the total/maximum number of residues that can be modified in a
+# peptide.
+# Available for comet.
+max_variable_mods_in_peptide=5
+
+# Controls whether the analyzed peptides must contain at least one variable
+# modification.
+# Available for comet.
+require_variable_mod=0
+
+# Specifiy a static modification to the c-terminus of all peptides.
+# Available for comet.
+add_Cterm_peptide=0
+
+# Specify a static modification to the n-terminus of all peptides.
+# Available for comet.
+add_Nterm_peptide=0
+
+# Specify a static modification to the c-terminal peptide of each protein.
+# Available for comet.
+add_Cterm_protein=0
+
+# Specify a static modification to the n-terminal peptide of each protein.
+# Available for comet.
+add_Nterm_protein=0
+
+# Specify a static modification to the residue A.
+# Available for comet.
+add_A_alanine=0
+
+# Specify a static modification to the residue B.
+# Available for comet.
+add_B_user_amino_acid=0
+
+# Specify a static modification to the residue C.
+# Available for comet.
+add_C_cysteine=57.021464
+
+# Specify a static modification to the residue D.
+# Available for comet.
+add_D_aspartic_acid=0
+
+# Specify a static modification to the residue E.
+# Available for comet.
+add_E_glutamic_acid=0
+
+# Specify a static modification to the residue F.
+# Available for comet.
+add_F_phenylalanine=0
+
+# Specify a static modification to the residue G.
+# Available for comet.
+add_G_glycine=0
+
+# Specify a static modification to the residue H.
+# Available for comet.
+add_H_histidine=0
+
+# Specify a static modification to the residue I.
+# Available for comet.
+add_I_isoleucine=0
+
+# Specify a static modification to the residue J.
+# Available for comet.
+add_J_user_amino_acid=0
+
+# Specify a static modification to the residue K.
+# Available for comet.
+add_K_lysine=0
+
+# Specify a static modification to the residue L.
+# Available for comet.
+add_L_leucine=0
+
+# Specify a static modification to the residue M.
+# Available for comet.
+add_M_methionine=0
+
+# Specify a static modification to the residue N.
+# Available for comet.
+add_N_asparagine=0
+
+# Specify a static modification to the residue O.
+# Available for comet.
+add_O_ornithine=0
+
+# Specify a static modification to the residue P.
+# Available for comet.
+add_P_proline=0
+
+# Specify a static modification to the residue Q.
+# Available for comet.
+add_Q_glutamine=0
+
+# Specify a static modification to the residue R.
+# Available for comet.
+add_R_arginine=0
+
+# Specify a static modification to the residue S.
+# Available for comet.
+add_S_serine=0
+
+# Specify a static modification to the residue T.
+# Available for comet.
+add_T_threonine=0
+
+# Specify a static modification to the residue U.
+# Available for comet.
+add_U_selenocysteine=0
+
+# Specify a static modification to the residue V.
+# Available for comet.
+add_V_valine=0
+
+# Specify a static modification to the residue W.
+# Available for comet.
+add_W_tryptophan=0
+
+# Specify a static modification to the residue X.
+# Available for comet.
+add_X_user_amino_acid=0
+
+# Specify a static modification to the residue Y.
+# Available for comet.
+add_Y_tyrosine=0
+
+# Specify a static modification to the residue Z.
+# Available for comet.
+add_Z_user_amino_acid=0
+
+#
+# COMET_ENZYME_INFO _must_ be at the end of this parameters file
+#
+[COMET_ENZYME_INFO]
+0. No_enzyme 0 - -
+1. Trypsin 1 KR P
+2. Trypsin/P 1 KR -
+3. Lys_C 1 K P
+4. Lys_N 0 K -
+5. Arg_C 1 R P
+6. Asp_N 0 D -
+7. CNBr 1 M -
+8. Glu_C 1 DE P
+9. PepsinA 1 FL P
+10. Chymotrypsin 1 FWYL P
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/demo.ms2 b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/demo.ms2
new file mode 100644
index 0000000..9359011
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/demo.ms2
@@ -0,0 +1,54667 @@
+H CreationDate 2/14/2007 6:19:18 PM
+H Extractor MakeMS2
+H ExtractorVersion 1.0
+H Comments MakeMS2 written by Michael J. MacCoss, 2004
+H ExtractorOptions MS2/MS1
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+Z 2 1271.67
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diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/search.target.txt b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/search.target.txt
new file mode 100644
index 0000000..b4193e0
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/search.target.txt
@@ -0,0 +1,721 @@
+scan charge spectrum precursor m/z spectrum neutral mass peptide mass delta_cn sp score sp rank xcorr score xcorr rank b/y ions matched b/y ions total matches/spectrum sequence cleavage type protein id flanking aa unshuffled sequence
+10 2 636.3400 1270.6644 1270.4917 0 56.458275 1 0.843481 1 5 22 6 SGLIVEIQGVQK trypsin-full-digest YDR093W KE
+10 2 636.3400 1270.6644 1273.4087 0.50464863 49.409576 2 0.41781947 2 4 20 6 TVLDLEVNNTR trypsin-full-digest YDR093W RT
+10 2 636.3400 1270.6644 1272.5227 0.82345378 22.858458 4 0.1489134 3 4 22 6 MSVEPVVVIDGK trypsin-full-digest YIL133C -G
+10 2 636.3400 1270.6644 1271.5254 0.99421889 7.6680117 5 0.0048762476 4 2 20 6 KPQVYPALLSR trypsin-full-digest YLR371W KV
+10 2 636.3400 1270.6644 1270.3618 1.2562495 42.079628 3 -0.21614161 5 4 20 6 TDLPEGEEKPR trypsin-full-digest YPL106C KI
+11 2 745.2700 1488.5244 1489.7319 0 2799.7004 1 4.9665937 1 21 24 5 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+11 2 745.2700 1488.5244 1486.6195 0.78361297 150.82512 2 1.0747064 2 8 26 5 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+11 2 745.2700 1488.5244 1490.6510 0.92498112 27.513174 5 0.37258846 3 3 24 5 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+11 2 745.2700 1488.5244 1488.7063 0.95597595 86.188286 3 0.21864961 4 5 24 5 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+11 2 745.2700 1488.5244 1485.6539 0.98590338 70.940605 4 0.070012115 5 5 22 5 QEAIYEVYITEK trypsin-full-digest YLR371W RN
+12 3 472.5600 1414.6565 1411.7252 0 107.23654 1 0.70944363 1 12 44 8 IISYAQGFMLIR trypsin-full-digest YHR183W KE
+12 3 472.5600 1414.6565 1412.5806 0.29089656 67.485161 3 0.50306892 2 11 44 8 IVNMYGTTETQR trypsin-full-digest YBR115C RA
+12 3 472.5600 1414.6565 1414.5780 0.30653799 39.472534 6 0.49197221 3 8 40 8 NTLEEYIYTLR trypsin-full-digest YPL106C KG
+12 3 472.5600 1414.6565 1414.6240 0.33313781 55.1306 4 0.47310114 4 9 44 8 VLEFHPFDPVSK trypsin-full-digest YGL008C KK
+12 3 472.5600 1414.6565 1413.6769 0.51874274 94.480415 2 0.34142488 5 11 48 8 YGPLLVDIIDPAK trypsin-full-digest YKL127W KA
+13 1 717.0600 716.0522 717.8204 0 41.040947 2 0.6652953 1 4 10 16 SLEITR trypsin-full-digest YLR371W KD
+13 1 717.0600 716.0522 716.8506 0.065693147 47.344681 1 0.62158996 2 4 12 16 DVMPAGK trypsin-full-digest YBR115C KG
+13 1 717.0600 716.0522 715.9341 0.07201229 21.613161 4 0.61738586 3 3 10 16 LLPFVK trypsin-full-digest YLR340W KG
+13 1 717.0600 716.0522 713.7887 0.64012295 39.931419 3 0.23942451 4 4 12 16 NPAVGEK trypsin-full-digest YGL245W KK
+13 1 717.0600 716.0522 716.7893 0.67106682 5.8860817 10 0.21883771 5 2 12 16 EAAELGK trypsin-full-digest YBR118W KG
+14 2 559.1000 1116.1843 1119.1559 0 66.227585 1 0.53043324 1 5 16 11 YHIEEEGSR trypsin-full-digest YCR012W RK
+14 2 559.1000 1116.1843 1118.2635 0.13069028 23.070383 3 0.46111077 2 4 16 11 FFCALFDAK trypsin-full-digest YKL127W KK
+14 2 559.1000 1116.1843 1116.1615 0.29996294 12.308622 6 0.37132293 3 3 16 11 YDGAFDCLR trypsin-full-digest YBL030C KK
+14 2 559.1000 1116.1843 1117.3536 0.48043215 23.054535 4 0.27559605 4 5 18 11 FLDGQIALLK trypsin-full-digest YBL076C KK
+14 2 559.1000 1116.1843 1116.2769 0.61405927 10.694719 7 0.2047158 5 3 18 11 LVDEVVDSLK trypsin-full-digest YMR235C RF
+14 3 559.1000 1674.2765 1675.6885 0 63.059669 1 0.767111 1 13 60 5 ATAGDTHLGGEDFDNR trypsin-full-digest YLL024C KL
+14 3 559.1000 1674.2765 1671.7804 1.2015421 33.726143 2 -0.15460518 2 8 48 5 ITYSSDYFDELYR trypsin-full-digest YOR168W KL
+14 3 559.1000 1674.2765 1676.9332 1.3099092 29.03307 3 -0.23773479 3 7 56 5 YLTNTGNLLLASQIR trypsin-full-digest YBL076C KH
+14 3 559.1000 1674.2765 1673.7159 1.5774156 10.770131 5 -0.44294184 4 6 56 5 HEAEWSGLSNDATTR trypsin-full-digest YDL223C RN
+14 3 559.1000 1674.2765 1673.7625 1.8034767 21.514181 4 -0.61635584 5 7 64 5 TTHPVSHGHSGSSTGPK trypsin-full-digest YDL223C KS
+15 2 732.1300 1462.2444 1462.7675 0 1342.2397 1 3.8226082 1 19 24 5 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+15 2 732.1300 1462.2444 1460.6036 0.92579734 21.992445 3 0.28364772 2 4 22 5 EEPDLENLLFNK trypsin-full-digest YHR183W RF
+15 2 732.1300 1462.2444 1463.5709 0.93476593 3.2144897 4 0.24936424 3 2 24 5 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+15 2 732.1300 1462.2444 1460.4707 0.94384331 46.283249 2 0.2146651 4 6 24 5 ELGDAYVSSDEEF trypsin-full-digest YLR249W K-
+15 2 732.1300 1462.2444 1459.6195 0.98524964 2.9621341 5 0.056384861 5 2 26 5 SQVDEIVLVGGSTR trypsin-full-digest YLL024C KI
+16 1 713.0700 712.0622 713.7887 0 40.185627 2 0.4695082 1 4 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+16 1 713.0700 712.0622 710.7880 0.34402412 97.301079 1 0.30798605 2 6 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+16 1 713.0700 712.0622 714.8626 0.65348947 8.9418478 5 0.16268952 3 2 10 9 ALPTWK trypsin-full-digest YMR235C KD
+16 1 713.0700 712.0622 710.8309 1.0855368 13.639264 3 -0.040160265 4 2 10 9 AFAQFK trypsin-full-digest YJR069C KE
+16 1 713.0700 712.0622 712.8472 1.3372214 9.0141134 4 -0.15832822 5 2 12 9 TPGGILR trypsin-full-digest YER056C-A KA
+17 2 495.2500 988.4844 989.0935 0 94.401619 2 0.65849799 1 5 16 3 SLEASVIDR trypsin-full-digest YBR115C KN
+17 2 495.2500 988.4844 988.1950 0.14087622 47.611462 3 0.56573129 2 4 18 3 TPLPPAPAPK trypsin-full-digest YBL030C KK
+17 2 495.2500 988.4844 987.0771 0.40132889 150.00021 1 0.39422372 3 6 16 3 YSFLEGGSK trypsin-full-digest YGL009C KL
+18 3 1032.4000 3094.1765 3095.2366 0 1794.3577 1 4.4612322 1 41 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+18 3 1032.4000 3094.1765 3095.4709 0.91822755 28.71706 2 0.364806 2 10 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+19 2 604.2900 1206.5643 1207.4535 0 4.0179791 2 0.085511789 1 2 18 2 DTLKPMAIYR trypsin-full-digest YLR371W RV
+19 2 604.2900 1206.5643 1204.3109 1.6698694 10.554982 1 -0.057281736 2 3 20 2 VNGDAHVISHR trypsin-full-digest YGR157W RA
+19 3 604.2900 1809.8464 1808.0363 0 139.71983 1 0.43815228 1 14 68 4 GYLVAMTGDGVNDAPSLK trypsin-full-digest YGL008C RK
+19 3 604.2900 1809.8464 1810.0775 0.73968351 45.731903 3 0.11405826 2 9 68 4 LQDGVPDSIALLAEAGIK trypsin-full-digest YDR093W RL
+19 3 604.2900 1809.8464 1810.0824 1.4776366 58.53331 2 -0.20927754 3 8 52 4 LLNFIDELTNWYIR trypsin-full-digest YBL076C KF
+19 3 604.2900 1809.8464 1812.0063 1.701064 40.476826 4 -0.30717278 4 10 64 4 YTVSFIEGDGIGPEISK trypsin-full-digest YOR136W KS
+20 2 450.9000 899.7844 902.0154 0 14.423851 3 0.1545447 1 3 16 12 STVVSANPK trypsin-full-digest YOR267C KK
+20 2 450.9000 899.7844 897.0107 0.43213871 30.959551 2 0.087759949 2 3 12 12 LDDEFMK trypsin-full-digest YMR309C RS
+20 2 450.9000 899.7844 898.0265 0.48145139 5.8385301 5 0.080138937 3 2 14 12 FFADAVTK trypsin-full-digest YHR183W KA
+20 2 450.9000 899.7844 896.9524 0.78898019 50.266438 1 0.032611992 4 3 14 12 SSFNDISK trypsin-full-digest YMR309C KL
+20 2 450.9000 899.7844 902.0586 1.8137401 13.619667 4 -0.12575921 5 3 16 12 QGVTSLGIK trypsin-full-digest YML092C KA
+21 1 805.0000 803.9922 804.8956 0 124.69447 1 0.80470002 1 5 12 20 ESTIDIK trypsin-full-digest YOR267C KI
+21 1 805.0000 803.9922 804.8957 0.14753152 83.322594 2 0.68598139 2 4 12 20 ESVTEIK trypsin-full-digest YGR157W KA
+21 1 805.0000 803.9922 803.8675 0.27760506 22.862658 9 0.58131123 3 3 12 20 ELDTAQK trypsin-full-digest YGR192C KH
+21 1 805.0000 803.9922 805.9292 0.56622195 59.186016 3 0.34906122 4 5 12 20 FSPSQLK trypsin-full-digest YMR073C KN
+21 1 805.0000 803.9922 804.8577 0.63594806 38.015034 6 0.2929526 5 3 10 20 EWNQTK trypsin-full-digest YDR093W KF
+22 1 1489.8500 1488.8422 1489.7319 0 374.82031 1 3.0246928 1 14 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+22 1 1489.8500 1488.8422 1486.6195 0.84436226 36.411674 2 0.47075641 2 6 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+22 1 1489.8500 1488.8422 1490.6510 1.00218 3.5401781 4 -0.0065939161 3 2 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+22 1 1489.8500 1488.8422 1488.7063 1.0877013 4.2567067 3 -0.26526943 4 2 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+23 1 805.0000 803.9922 804.8957 0 151.28577 1 0.60042703 1 6 12 20 ESVTEIK trypsin-full-digest YGR157W KA
+23 1 805.0000 803.9922 803.8675 0.23424846 53.851978 4 0.45977792 2 4 12 20 ELDTAQK trypsin-full-digest YGR192C KH
+23 1 805.0000 803.9922 804.8956 0.25316995 72.456558 2 0.44841695 3 4 12 20 ESTIDIK trypsin-full-digest YOR267C KI
+23 1 805.0000 803.9922 804.9012 0.29283255 23.882532 11 0.42460245 4 3 12 20 VAHTSYK trypsin-full-digest YML092C KR
+23 1 805.0000 803.9922 804.8987 0.47863716 46.161007 5 0.31304035 5 4 12 20 VSTTLER trypsin-full-digest YDR093W RR
+24 3 830.6200 2488.8364 2490.7063 0 26.858793 1 0.14122425 1 13 84 2 AAGQLDQLVEDYINDELEIVSR trypsin-full-digest YBR115C RI
+24 3 830.6200 2488.8364 2489.7822 1.78395 18.704006 2 -0.11071275 2 10 84 2 VMPYSTGLTTPLSNFEAQQNYK trypsin-full-digest YBL076C KD
+25 2 745.5500 1489.0844 1489.7319 0 1807.792 1 4.2164721 1 19 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+25 2 745.5500 1489.0844 1486.6195 0.81398946 106.51873 3 0.78430814 2 7 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+25 2 745.5500 1489.0844 1488.7063 0.82931358 207.0804 2 0.71969455 3 8 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+25 2 745.5500 1489.0844 1490.6510 0.85102826 25.70677 4 0.62813509 4 3 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+26 2 692.3800 1382.7444 1382.4467 0 2156.4043 1 3.8436441 1 20 24 5 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+26 2 692.3800 1382.7444 1381.6099 0.87371606 76.68457 2 0.48539051 2 5 22 5 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+26 2 692.3800 1382.7444 1381.5258 0.90621096 30.044098 3 0.36049169 3 4 22 5 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+26 2 692.3800 1382.7444 1380.6042 1.055408 21.984407 4 -0.21296872 4 3 22 5 EVVELPLLSPER trypsin-full-digest YKL145W RF
+26 2 692.3800 1382.7444 1383.6108 1.0793326 2.7308655 5 -0.30492619 5 1 26 5 NVIVSGIVLAADGR trypsin-full-digest YBL076C KK
+27 2 732.5500 1463.0844 1462.7675 0 1126.2389 1 2.6634736 1 17 24 4 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+27 2 732.5500 1463.0844 1460.6036 0.81959116 66.824799 3 0.48051417 2 6 22 4 EEPDLENLLFNK trypsin-full-digest YHR183W RF
+27 2 732.5500 1463.0844 1460.4707 0.88409299 92.661507 2 0.30871528 3 7 24 4 ELGDAYVSSDEEF trypsin-full-digest YLR249W K-
+27 2 732.5500 1463.0844 1463.5709 0.96493638 15.490486 4 0.093391061 4 3 24 4 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+28 2 613.2600 1224.5044 1222.3203 0 26.820997 2 0.5495218 1 4 22 5 GGEGEVSVFVSR trypsin-full-digest YDR037W KV
+28 2 613.2600 1224.5044 1223.4375 0.018783558 28.635321 1 0.53919983 2 4 20 5 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+28 2 613.2600 1224.5044 1224.3788 0.8169654 6.3640132 5 0.1005815 3 2 18 5 LAFLENQDFK trypsin-full-digest YBR115C RL
+28 2 613.2600 1224.5044 1227.4233 0.84511566 13.379468 3 0.085112311 4 3 18 5 IEVLEQELVR trypsin-full-digest YGR086C KA
+28 2 613.2600 1224.5044 1223.2670 0.96065545 8.3532753 4 0.021620696 5 2 18 5 YYGGNEHIDR trypsin-full-digest YLR058C RM
+29 2 614.2600 1226.5044 1229.3525 0 21.443193 1 0.31570217 1 3 20 3 EILGTDEPTVR trypsin-full-digest YKL127W KT
+29 2 614.2600 1226.5044 1224.3788 0.23751414 15.323318 2 0.24071844 2 3 18 3 LAFLENQDFK trypsin-full-digest YBR115C RL
+29 2 614.2600 1226.5044 1227.4233 1.4932648 2.4419763 3 -0.15572478 3 1 18 3 IEVLEQELVR trypsin-full-digest YGR086C KA
+30 1 715.0700 714.0622 716.7460 0 23.359188 1 0.30748594 1 3 10 12 KPDDDK trypsin-full-digest YKL145W KI
+30 1 715.0700 714.0622 716.7893 0.64147574 6.6294503 3 0.11024117 2 2 12 12 EAAELGK trypsin-full-digest YBR118W KG
+30 1 715.0700 714.0622 713.7887 0.78619045 4.9657464 4 0.065743424 3 2 12 12 NPAVGEK trypsin-full-digest YGL245W KK
+30 1 715.0700 714.0622 716.8852 0.82486218 1.6637436 9 0.05385242 4 1 10 12 ALLICK trypsin-full-digest YDR093W KG
+30 1 715.0700 714.0622 712.8472 0.84074181 8.0855684 2 0.048969656 5 2 12 12 TPGGILR trypsin-full-digest YER056C-A KA
+31 3 501.2200 1500.6365 1500.4829 0 75.014168 1 0.738213 1 9 44 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+31 3 501.2200 1500.6365 1497.7600 0.61014986 57.982483 2 0.28779244 2 8 48 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+31 3 501.2200 1500.6365 1500.7172 0.6992386 25.314043 3 0.22202596 3 5 48 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+32 3 1032.7900 3095.3467 3095.2366 0 1021.062 1 4.1811695 1 33 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+32 3 1032.7900 3095.3467 3095.4709 1.08211 25.482035 2 -0.34331581 2 8 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+33 2 433.7900 865.5644 868.0007 0 24.923223 2 0.27615401 1 3 14 13 EPGVPTIR trypsin-full-digest YDR399W KI
+33 2 433.7900 865.5644 863.9689 0.25559467 20.780163 4 0.20557052 2 2 12 13 EYQVIGR trypsin-full-digest YMR242C KR
+33 2 433.7900 865.5644 863.9843 0.3070561 21.143938 3 0.19135924 3 3 14 13 MSSNAQVK trypsin-full-digest YBL030C -T
+33 2 433.7900 865.5644 864.9566 0.67410392 11.694733 7 0.089997508 4 2 12 13 NIQHPEK trypsin-full-digest YDL223C KN
+33 2 433.7900 865.5644 868.0435 0.77937192 10.029391 8 0.060927331 5 2 12 13 AYVQFLK trypsin-full-digest YKL127W KE
+33 3 433.7900 1298.3466 1295.5011 0 142.93625 1 0.74851775 1 11 44 5 TSFFQALGVPTK trypsin-full-digest YLR340W KI
+33 3 433.7900 1298.3466 1300.4741 1.1231706 11.750471 5 -0.092195369 2 3 40 5 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+33 3 433.7900 1298.3466 1298.5687 1.2744842 56.905846 2 -0.20545629 3 6 40 5 LNNPAIALMWR trypsin-full-digest YHR183W KG
+33 3 433.7900 1298.3466 1299.4120 1.2848094 14.490228 4 -0.21318488 4 4 36 5 FEELCADLFR trypsin-full-digest YLL024C RS
+33 3 433.7900 1298.3466 1299.4670 1.4924383 46.446587 3 -0.36859885 5 7 40 5 MPYTLSDAHHK trypsin-full-digest YLR058C -L
+34 2 750.9200 1499.8243 1500.4829 0 35.232906 1 0.51629972 1 4 22 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+34 2 750.9200 1499.8243 1500.7172 0.51376176 11.712827 3 0.25104466 2 2 24 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+34 2 750.9200 1499.8243 1497.7600 0.79214215 14.823524 2 0.10731694 3 3 24 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+35 1 709.0700 708.0622 708.7692 0 14.558948 3 0.26784292 1 2 10 8 DFQTAK trypsin-full-digest YMR309C KD
+35 1 709.0700 708.0622 709.8869 0.36011532 11.018554 4 0.17138858 2 2 10 8 SIHILK trypsin-full-digest YMR242C RV
+35 1 709.0700 708.0622 710.8309 0.46457091 52.933228 1 0.14341089 3 3 10 8 AFAQFK trypsin-full-digest YJR069C KE
+35 1 709.0700 708.0622 710.7880 0.66859102 16.86434 2 0.088765554 4 2 12 8 HIDAGAK trypsin-full-digest YGR192C KK
+35 1 709.0700 708.0622 707.7845 0.86462736 2.7231455 5 0.036258604 5 1 10 8 FESAVR trypsin-full-digest YOR168W RK
+36 2 427.3800 852.7444 853.0293 0 107.2902 1 0.787049 1 6 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+36 2 427.3800 852.7444 852.0445 0.28271866 70.995552 2 0.56453556 2 5 14 13 HASLILAK trypsin-full-digest YMR235C KA
+36 2 427.3800 852.7444 852.8194 0.68353808 50.631237 3 0.24907105 3 3 12 13 DSCTENK trypsin-full-digest YNL166C KE
+36 2 427.3800 852.7444 855.0451 0.69871479 31.401226 4 0.23712622 4 4 14 13 LLGPQLSK trypsin-full-digest YGL135W RA
+36 2 427.3800 852.7444 852.0011 0.70649135 10.25797 8 0.2310057 5 2 14 13 LPLNPNGK trypsin-full-digest YBR115C KV
+37 2 652.3400 1302.6644 1301.4161 0 613.67346 1 2.9785695 1 18 22 8 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+37 2 652.3400 1302.6644 1301.4161 0.77743554 51.197414 3 0.66292375 2 6 22 8 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+37 2 652.3400 1302.6644 1303.4968 0.8709349 69.481659 2 0.3844294 3 8 22 8 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+37 2 652.3400 1302.6644 1304.4626 0.90986937 19.165369 5 0.26846039 4 5 22 8 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+37 2 652.3400 1302.6644 1300.4741 0.92362046 8.7759972 6 0.22750174 5 3 20 8 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+38 3 1032.3900 3094.1465 3095.2366 0 1161.2994 1 4.266221 1 34 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+38 3 1032.3900 3094.1465 3095.4709 0.91375649 57.854763 2 0.36793384 2 12 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+39 2 613.1300 1224.2444 1223.4375 0 19.768681 2 0.47953755 1 3 20 5 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+39 2 613.1300 1224.2444 1222.3203 0.55245852 38.796162 1 0.21461295 2 5 22 5 GGEGEVSVFVSR trypsin-full-digest YDR037W KV
+39 2 613.1300 1224.2444 1221.2867 0.68277049 5.8917556 5 0.15212347 3 2 22 5 TTTPAATSEQSK trypsin-full-digest YDL223C KV
+39 2 613.1300 1224.2444 1223.2670 0.94518626 8.5665131 4 0.026285237 4 2 18 5 YYGGNEHIDR trypsin-full-digest YLR058C RM
+39 2 613.1300 1224.2444 1224.3788 1.0179251 15.589462 3 -0.0085957637 5 3 18 5 LAFLENQDFK trypsin-full-digest YBR115C RL
+40 2 636.3700 1270.7244 1270.4917 0 35.940578 2 0.80229896 1 4 22 6 SGLIVEIQGVQK trypsin-full-digest YDR093W KE
+40 2 636.3700 1270.7244 1273.4087 0.023744045 95.220009 1 0.78324914 2 6 20 6 TVLDLEVNNTR trypsin-full-digest YDR093W RT
+40 2 636.3700 1270.7244 1272.5227 0.83309722 23.839369 3 0.13390592 3 4 22 6 MSVEPVVVIDGK trypsin-full-digest YIL133C -G
+40 2 636.3700 1270.7244 1271.5254 0.85973752 0.86187017 6 0.11253244 4 1 20 6 KPQVYPALLSR trypsin-full-digest YLR371W KV
+40 2 636.3700 1270.7244 1272.3778 1.3148003 14.258236 4 -0.25256389 5 4 22 6 VTAVVESPEGER trypsin-full-digest YGL008C KI
+41 2 1003.8400 2005.6644 2006.3051 0 419.7645 1 3.8897491 1 16 34 3 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+41 2 1003.8400 2005.6644 2004.0973 0.74423027 39.264839 2 0.99488002 2 5 36 3 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+41 2 1003.8400 2005.6644 2005.2764 1.0753206 9.034647 3 -0.29297847 3 4 34 3 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+42 3 1032.2600 3093.7566 3095.2366 0 1344.3297 1 4.2084866 1 36 108 3 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+42 3 1032.2600 3093.7566 3095.4709 1.0023168 51.772331 2 -0.0097504091 2 11 112 3 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+42 3 1032.2600 3093.7566 3090.7644 1.1557556 13.163209 3 -0.65549535 3 6 112 3 NIVPVIMAGIIAIYGLVVSVLVCYSLGQK trypsin-full-digest YEL027W KQ
+43 1 713.0700 712.0622 710.7880 0 35.014496 3 0.36360914 1 4 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+43 1 713.0700 712.0622 714.7765 0.043656271 37.214542 2 0.34773532 2 4 12 9 SGPTPTR trypsin-full-digest YDL223C KS
+43 1 713.0700 712.0622 713.7887 0.12476196 39.507935 1 0.31824455 3 4 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+43 1 713.0700 712.0622 710.8309 1.0670638 12.245291 4 -0.024385018 4 2 10 9 AFAQFK trypsin-full-digest YJR069C KE
+43 1 713.0700 712.0622 714.8626 1.256899 9.9744434 5 -0.093410835 5 2 10 9 ALPTWK trypsin-full-digest YMR235C KD
+44 2 1002.5200 2003.0244 2000.2000 0 4.9326487 2 0.64485914 1 3 28 4 FESIIHEFDPWFNYR trypsin-full-digest YGL022W KA
+44 2 1002.5200 2003.0244 2005.2764 0.12105732 35.548817 1 0.56679422 2 6 34 4 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+44 2 1002.5200 2003.0244 2000.1700 0.99633354 3.1540933 3 0.0023643672 3 2 34 4 ESDTGLAPSHLWDIMGDR trypsin-full-digest YKL145W KQ
+44 2 1002.5200 2003.0244 2004.0973 1.272543 2.1951361 4 -0.17575185 4 2 36 4 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+45 2 419.3200 836.6244 837.9280 0 120.29333 1 0.93879902 1 8 12 10 ETSNFIK trypsin-full-digest YBR118W KK
+45 2 419.3200 836.6244 839.0054 0.21616718 73.09761 2 0.73586148 2 6 14 10 IAGLNPVR trypsin-full-digest YPL106C RI
+45 2 419.3200 836.6244 835.9554 0.55938864 40.067127 4 0.41364554 3 5 12 10 FDNLLSK trypsin-full-digest YDL198C R-
+45 2 419.3200 836.6244 835.0110 0.65359831 45.420536 3 0.32520157 4 4 12 10 EYILGLK trypsin-full-digest YDL198C KD
+45 2 419.3200 836.6244 835.9554 0.72016436 31.306742 5 0.26270941 5 5 14 10 IGDYAGIK trypsin-full-digest YMR303C KW
+46 2 613.8100 1225.6044 1224.3788 0 7.4563694 3 0.28366849 1 2 18 4 LAFLENQDFK trypsin-full-digest YBR115C RL
+46 2 613.8100 1225.6044 1223.4375 0.78064227 9.3816624 2 0.06222488 2 2 20 4 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+46 2 613.8100 1225.6044 1227.4233 0.89254183 12.353053 1 0.030482505 3 2 18 4 IEVLEQELVR trypsin-full-digest YGR086C KA
+46 2 613.8100 1225.6044 1223.2670 1.9748561 3.6607263 4 -0.27653596 4 1 18 4 YYGGNEHIDR trypsin-full-digest YLR058C RM
+47 2 731.7700 1461.5244 1462.7675 0 977.83374 1 2.9550073 1 16 24 5 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+47 2 731.7700 1461.5244 1460.6036 0.76668084 39.054245 4 0.68945986 2 5 22 5 EEPDLENLLFNK trypsin-full-digest YHR183W RF
+47 2 731.7700 1461.5244 1459.6195 0.77189511 53.278816 3 0.67405158 3 6 26 5 SQVDEIVLVGGSTR trypsin-full-digest YLL024C KI
+47 2 731.7700 1461.5244 1460.4707 0.88700467 20.282669 5 0.333902 4 3 24 5 ELGDAYVSSDEEF trypsin-full-digest YLR249W K-
+47 2 731.7700 1461.5244 1463.5709 0.93729258 89.043457 2 0.18530098 5 7 24 5 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+48 2 692.1400 1382.2644 1382.4467 0 1650.222 1 3.2511344 1 19 24 7 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+48 2 692.1400 1382.2644 1379.3623 0.91646332 111.14242 2 0.27158907 2 7 24 7 FDDGAGGDNEVQR trypsin-full-digest YKL145W RT
+48 2 692.1400 1382.2644 1381.6099 0.94984984 56.814457 3 0.16304493 3 5 22 7 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+48 2 692.1400 1382.2644 1381.5258 1.0133696 15.170854 4 -0.043466073 4 3 22 7 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+48 2 692.1400 1382.2644 1379.5791 1.0143504 13.739942 5 -0.046654966 5 3 24 7 LIVTAHSSSHSIK trypsin-full-digest YLR371W RY
+49 2 652.2200 1302.4243 1301.4161 0 1331.3566 1 2.9836347 1 19 22 9 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+49 2 652.2200 1302.4243 1301.4161 0.47995821 476.32742 2 1.5516148 2 13 22 9 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+49 2 652.2200 1302.4243 1300.4741 0.68522078 147.28616 3 0.93918622 3 8 20 9 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+49 2 652.2200 1302.4243 1303.4968 0.76649767 98.610008 4 0.69668561 4 7 22 9 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+49 2 652.2200 1302.4243 1304.4626 0.83955383 96.138992 5 0.47871277 5 7 22 9 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+50 2 651.2900 1300.5643 1301.4161 0 1851.6044 1 4.5879292 1 20 22 10 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+50 2 651.2900 1300.5643 1301.4161 0.68850791 133.35484 2 1.4291036 2 8 22 10 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+50 2 651.2900 1300.5643 1303.4968 0.83599889 122.15955 3 0.75242537 3 7 22 10 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+50 2 651.2900 1300.5643 1298.5687 0.91140366 20.537592 6 0.40647364 4 3 20 10 LNNPAIALMWR trypsin-full-digest YHR183W KG
+50 2 651.2900 1300.5643 1300.4741 0.93134964 60.500343 4 0.31496304 5 5 20 10 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+51 2 498.7000 995.3844 996.0446 0 619.99927 1 2.5252917 1 13 18 14 NGFQTGSASK trypsin-full-digest YLR185W KA
+51 2 498.7000 995.3844 993.0570 0.73925728 16.682711 7 0.65845144 2 3 14 14 GEINCCLK trypsin-full-digest YOR267C RQ
+51 2 498.7000 995.3844 998.1502 0.76451415 156.03938 2 0.59467053 3 8 20 14 IAAVGAANGVR trypsin-full-digest YKL127W KK
+51 2 498.7000 995.3844 998.1038 0.81507969 33.531857 5 0.46697778 4 4 16 14 SSIQLGEHK trypsin-full-digest YLR371W KK
+51 2 498.7000 995.3844 993.2323 0.85587269 60.745483 3 0.36396354 5 5 14 14 VSILMFQR trypsin-full-digest YPL266W RE
+52 2 501.1300 1000.2444 999.1753 0 142.79124 1 1.1606123 1 8 16 10 EALGELVIR trypsin-full-digest YPL215W KA
+52 2 501.1300 1000.2444 998.1502 0.34597751 99.963516 2 0.75906658 2 7 20 10 IAAVGAANGVR trypsin-full-digest YKL127W KK
+52 2 501.1300 1000.2444 1003.0769 0.72584987 20.871323 6 0.31818202 3 3 16 10 NLDGETNLK trypsin-full-digest YDR093W KV
+52 2 501.1300 1000.2444 1003.1383 0.7358076 44.979645 4 0.30662498 4 5 18 10 AVNTGMEPGK trypsin-full-digest YLR340W RT
+52 2 501.1300 1000.2444 1000.1217 0.74814993 32.278728 5 0.29230028 5 4 12 10 EAYYWLR trypsin-full-digest YGL022W RM
+52 3 501.1300 1500.3666 1500.7172 0 43.558441 1 0.55699539 1 8 48 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+52 3 501.1300 1500.3666 1500.4829 1.2666898 20.81834 2 -0.14854498 2 6 44 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+52 3 501.1300 1500.3666 1497.7600 2.3426661 5.7192822 3 -0.74785888 3 3 48 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+53 2 745.7500 1489.4844 1489.7319 0 2781.0261 1 5.3343987 1 21 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+53 2 745.7500 1489.4844 1486.6195 0.76325125 235.51993 2 1.2629123 2 10 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+53 2 745.7500 1489.4844 1490.6510 0.9047128 25.391062 4 0.50830007 3 3 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+53 2 745.7500 1489.4844 1488.7063 0.95565957 74.514969 3 0.23652941 4 5 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+54 3 410.2000 1227.5765 1227.4233 0 56.159355 1 0.036128547 1 6 36 2 IEVLEQELVR trypsin-full-digest YGR086C KA
+54 3 410.2000 1227.5765 1229.3525 5.2370372 44.455582 2 -0.153078 2 7 40 2 EILGTDEPTVR trypsin-full-digest YKL127W KT
+55 2 475.8100 949.6044 949.0466 0 26.808455 2 0.71967018 1 4 14 9 MSQQDNVK trypsin-full-digest YDR037W -A
+55 2 475.8100 949.6044 950.1027 0.18550882 35.054756 1 0.58616501 2 5 14 9 SFLESVIR trypsin-full-digest YBR009C KD
+55 2 475.8100 949.6044 950.0160 0.27314121 11.84093 6 0.52309859 3 3 14 9 QTNPESFK trypsin-full-digest YDL198C RG
+55 2 475.8100 949.6044 951.0929 0.44186732 13.180162 5 0.40167144 4 3 14 9 EHAPWALK trypsin-full-digest YGL009C RD
+55 2 475.8100 949.6044 949.1149 0.47345805 13.361526 4 0.37893653 5 3 14 9 IFENVSIK trypsin-full-digest YDR205W KA
+56 2 902.9600 1803.9044 1801.9713 0 271.61176 1 1.4312 1 12 32 2 AEAESLVAEAQLSNITR trypsin-full-digest YGR086C RS
+56 2 902.9600 1803.9044 1805.0215 0.91516519 30.447412 2 0.12141556 2 5 32 2 LSAIESLAGVEILCSDK trypsin-full-digest YGL008C KT
+57 2 564.6800 1127.3444 1126.2928 0 1.6282531 8 0.38786855 1 1 18 9 GDVVMIYSSR trypsin-full-digest YBR115C RG
+57 2 564.6800 1127.3444 1129.2966 0.69543523 16.327734 3 0.1181311 2 4 18 9 NVVAVEMDPR trypsin-full-digest YPL266W KM
+57 2 564.6800 1127.3444 1126.2004 0.80020344 2.7844698 7 0.077494793 3 1 18 9 CTINGVSYGR trypsin-full-digest YDR093W KA
+57 2 564.6800 1127.3444 1125.2004 0.85385883 19.824213 2 0.056683555 4 3 20 9 YESATASALVN trypsin-full-digest YDR064W K-
+57 2 564.6800 1127.3444 1126.2340 0.9029569 32.730118 1 0.037639961 5 3 16 9 DEGLFNLYR trypsin-full-digest YDL198C RG
+58 2 565.6500 1129.2844 1130.2659 0 10.387362 3 0.17425571 1 2 18 6 NSPWVVDSVK trypsin-full-digest YOR168W KN
+58 2 565.6500 1129.2844 1129.2966 0.032992441 7.5589361 6 0.16850659 2 2 18 6 NVVAVEMDPR trypsin-full-digest YPL266W KM
+58 2 565.6500 1129.2844 1131.1674 0.27751508 33.858917 1 0.12589712 3 4 20 6 IDQASGAAQDR trypsin-full-digest YLR371W RH
+58 2 565.6500 1129.2844 1126.2928 1.4995954 21.486506 2 -0.087057345 4 3 18 6 GDVVMIYSSR trypsin-full-digest YBR115C RG
+58 2 565.6500 1129.2844 1129.3646 2.1613607 8.9149437 5 -0.20237374 5 2 18 6 GITIDIALWK trypsin-full-digest YBR118W RF
+59 2 474.3000 946.5844 945.0836 0 163.22826 1 0.79811859 1 6 14 7 LQTIIDSR trypsin-full-digest YMR309C RG
+59 2 474.3000 946.5844 946.0281 0.48343256 26.635284 6 0.41228208 2 4 16 7 LSVATADNR trypsin-full-digest YLR249W KH
+59 2 474.3000 946.5844 949.0466 0.51973206 79.889168 3 0.38331077 3 6 14 7 MSQQDNVK trypsin-full-digest YDR037W -A
+59 2 474.3000 946.5844 949.1149 0.74977499 81.326645 2 0.19970922 4 4 14 7 IFENVSIK trypsin-full-digest YDR205W KA
+59 2 474.3000 946.5844 945.0836 0.7771157 41.841644 4 0.1778881 5 5 20 7 LLGSGAGGSVK trypsin-full-digest YOR267C KV
+59 3 474.3000 1419.8765 1417.4955 0 122.20961 1 0.76713252 1 13 56 7 ADTGIAVEGATDAAR trypsin-full-digest YGL008C KS
+59 3 474.3000 1419.8765 1419.5200 0.60215867 52.378551 3 0.30519703 2 9 44 7 GEDELWCVINGK trypsin-full-digest YMR073C KV
+59 3 474.3000 1419.8765 1420.7550 0.64994532 79.130165 2 0.26853833 3 9 48 7 GVDLMVCVMGVLK trypsin-full-digest YBR115C RA
+59 3 474.3000 1419.8765 1420.5975 0.78942293 27.125801 5 0.16154051 4 7 44 7 LLARPGDSLYCR trypsin-full-digest YPL266W RL
+59 3 474.3000 1419.8765 1422.5168 0.95424658 50.471569 4 0.035098951 5 7 44 7 NFHNAIDEFSTK trypsin-full-digest YDR093W KE
+60 1 713.3600 712.3522 710.7880 0 24.40822 1 0.43409193 1 4 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+60 1 713.3600 712.3522 713.7887 0.54279155 22.626112 3 0.1984705 2 3 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+60 1 713.3600 712.3522 713.7881 0.66906232 1.9599029 6 0.14365739 3 1 12 9 TLYGFGG trypsin-full-digest YBR009C R-
+60 1 713.3600 712.3522 714.8626 0.7312721 13.145251 4 0.1166526 4 2 10 9 ALPTWK trypsin-full-digest YMR235C KD
+60 1 713.3600 712.3522 714.7765 1.0561372 24.213102 2 -0.024368707 5 4 12 9 SGPTPTR trypsin-full-digest YDL223C KS
+61 2 1004.4300 2006.8444 2006.3051 0 871.86584 1 3.8326077 1 18 34 4 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+61 2 1004.4300 2006.8444 2004.0973 0.74373084 43.846146 3 0.98217922 2 5 36 4 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+61 2 1004.4300 2006.8444 2009.1975 1.0181385 50.501587 2 -0.069518089 3 6 38 4 YDSPVSSPITSASELGSIAK trypsin-full-digest YNL166C KL
+61 2 1004.4300 2006.8444 2005.2764 1.057922 4.156528 4 -0.22199231 4 2 34 4 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+62 2 745.8600 1489.7043 1489.7319 0 2761.3391 1 5.301578 1 21 24 3 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+62 2 745.8600 1489.7043 1490.6510 0.86824602 44.483547 3 0.69850397 2 4 24 3 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+62 2 745.8600 1489.7043 1488.7063 0.96409976 82.697823 2 0.19032791 3 5 24 3 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+63 2 444.4100 886.8044 886.9603 0 26.139324 4 0.71276307 1 3 14 8 DLDRPGSK trypsin-full-digest YOR063W RF
+63 2 444.4100 886.8044 886.9292 0.39397162 26.822899 3 0.43195465 2 3 12 8 SHTLCNR trypsin-full-digest YLR185W KC
+63 2 444.4100 886.8044 887.0439 0.68880337 42.980015 1 0.22180946 3 3 14 8 ELQSLLGK trypsin-full-digest YCR012W KD
+63 2 444.4100 886.8044 886.0563 0.75538975 41.696362 2 0.17434917 4 4 14 8 ALLDEVVK trypsin-full-digest YCR012W KS
+63 2 444.4100 886.8044 887.0092 0.8485781 12.152888 5 0.10792796 5 2 12 8 RPTNPFR trypsin-full-digest YNL166C RV
+64 2 676.1000 1350.1843 1348.5188 0 29.814545 1 0.20261776 1 4 22 2 LVETLPSSYPSR trypsin-full-digest YBR115C KE
+64 2 676.1000 1350.1843 1351.3583 2.6623373 0 2 -0.33681905 2 0 20 2 DETCESNPFPR trypsin-full-digest YLR298C RL
+64 3 676.1000 2025.2765 2027.1876 0 24.818066 1 0.08459115 1 7 80 1 NVIAETGAGQHGVATATACAK trypsin-full-digest YGL026C KF
+65 2 452.8500 903.6844 904.0949 0 97.185295 4 0.74056631 1 5 14 20 HAFMGTLK trypsin-full-digest YOR063W KK
+65 2 452.8500 903.6844 904.9293 0.022225995 153.16431 1 0.72410649 2 7 14 20 EQPESTSK trypsin-full-digest YDL223C KN
+65 2 452.8500 903.6844 904.8859 0.29299486 40.426414 9 0.52358419 3 4 14 20 ESTPDNDK trypsin-full-digest YOR267C KE
+65 2 452.8500 903.6844 903.0921 0.32120171 101.14278 3 0.50269514 4 6 14 20 NLALLFGR trypsin-full-digest YLR371W RS
+65 2 452.8500 903.6844 905.1050 0.45861647 20.786068 15 0.4009304 5 3 16 20 IALIAGYGK trypsin-full-digest YGR086C KA
+66 2 427.3800 852.7444 853.0293 0 86.936096 2 0.80033225 1 5 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+66 2 427.3800 852.7444 855.0049 0.097246684 152.10268 1 0.72250259 2 7 16 13 SALVPGGVR trypsin-full-digest YLR058C KI
+66 2 427.3800 852.7444 851.9758 0.47781974 63.129513 3 0.4179177 3 5 14 13 SSMGPAFR trypsin-full-digest YGL135W KL
+66 2 427.3800 852.7444 852.8194 0.61674178 31.039164 4 0.30673394 4 3 12 13 DSCTENK trypsin-full-digest YNL166C KE
+66 2 427.3800 852.7444 852.0011 0.80157036 15.659703 9 0.15880965 5 3 14 13 LPLNPNGK trypsin-full-digest YBR115C KV
+67 2 692.1500 1382.2844 1382.4467 0 1821.1417 1 4.1942277 1 19 24 7 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+67 2 692.1500 1382.2844 1381.5258 0.82534504 46.728306 3 0.73254275 2 5 22 7 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+67 2 692.1500 1382.2844 1381.6099 0.88650858 119.8332 2 0.47600889 3 6 22 7 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+67 2 692.1500 1382.2844 1379.5791 0.92010963 43.565853 4 0.33507845 4 5 24 7 LIVTAHSSSHSIK trypsin-full-digest YLR371W RY
+67 2 692.1500 1382.2844 1379.3623 0.940844 29.001404 5 0.24811386 5 4 24 7 FDDGAGGDNEVQR trypsin-full-digest YKL145W RT
+68 2 468.8000 935.5844 935.0446 0 49.533195 4 0.74895662 1 6 14 11 LNLEGDFK trypsin-full-digest YGL245W KK
+68 2 468.8000 935.5844 933.9707 0.16079384 12.465908 7 0.62852901 2 4 16 11 NTISEAGDK trypsin-full-digest YLL024C KL
+68 2 468.8000 935.5844 935.1315 0.23179226 71.465187 2 0.57535428 3 5 16 11 VLPGPEVPK trypsin-full-digest YHR183W KD
+68 2 468.8000 935.5844 935.8565 0.28700686 98.048073 1 0.53400093 4 6 14 11 EDDSNNDK trypsin-full-digest YOR267C KE
+68 2 468.8000 935.5844 937.0202 0.62856978 36.394066 6 0.27818513 5 4 16 11 SDGVAGLYR trypsin-full-digest YBL030C KG
+68 3 468.8000 1403.3765 1404.5829 0 40.724213 2 0.37462369 1 9 44 6 TTLHYALSELEK trypsin-full-digest YDR399W RD
+68 3 468.8000 1403.3765 1404.4968 0.58936948 13.110674 6 0.15383191 2 7 56 6 VASANATAAESDVAK trypsin-full-digest YIL133C KQ
+68 3 468.8000 1403.3765 1405.7032 0.81445163 74.083321 1 0.069510803 3 11 48 6 GFLPSVVGIVVYR trypsin-full-digest YBL030C RG
+68 3 468.8000 1403.3765 1402.6282 1.1776992 21.763506 3 -0.066570319 4 8 44 6 MTSGYYLGELLR trypsin-full-digest YFR053C KL
+68 3 468.8000 1403.3765 1405.4899 1.3059314 15.813335 4 -0.11460918 5 6 44 6 STSTVNLNNHYR trypsin-full-digest YOR267C KA
+69 2 652.4800 1302.9443 1301.4161 0 866.42224 1 3.2185082 1 16 22 8 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+69 2 652.4800 1302.9443 1301.4161 0.61322856 165.8327 2 1.2448272 2 8 22 8 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+69 2 652.4800 1302.9443 1303.4968 0.75579822 75.887726 4 0.7859655 3 6 22 8 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+69 2 652.4800 1302.9443 1300.4741 0.77344012 113.19061 3 0.72918487 4 7 20 8 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+69 2 652.4800 1302.9443 1304.4626 0.87005603 46.928429 5 0.4182258 5 5 22 8 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+70 2 691.9500 1381.8844 1382.4467 0 1932.3346 1 3.9032106 1 19 24 7 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+70 2 691.9500 1381.8844 1381.5258 0.84123105 49.488419 4 0.61970872 2 5 22 7 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+70 2 691.9500 1381.8844 1379.3623 0.87033457 72.380486 3 0.5061115 3 6 24 7 FDDGAGGDNEVQR trypsin-full-digest YKL145W RT
+70 2 691.9500 1381.8844 1381.6099 0.89363277 82.036919 2 0.41517377 4 5 22 7 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+70 2 691.9500 1381.8844 1380.6042 0.98013854 8.8494978 6 0.077523351 5 2 22 7 EVVELPLLSPER trypsin-full-digest YKL145W RF
+71 2 488.7600 975.5044 974.1251 0 51.582912 1 0.57350701 1 5 16 10 STSANILLR trypsin-full-digest YDR205W KL
+71 2 488.7600 975.5044 974.0044 0.23152198 34.17643 2 0.44072753 2 4 14 10 DQPGLCER trypsin-full-digest YDR037W RF
+71 2 488.7600 975.5044 974.0121 0.52275521 6.3304238 6 0.27370325 3 2 12 10 HHHNHHR trypsin-full-digest YDL223C KH
+71 2 488.7600 975.5044 978.1595 0.53639543 6.1636882 7 0.26588047 4 2 16 10 HTAIVNPVK trypsin-full-digest YGL245W RI
+71 2 488.7600 975.5044 975.0636 0.64310586 7.7996826 5 0.20468129 5 2 16 10 DISTPDLSK trypsin-full-digest YDR093W KV
+72 2 651.6300 1301.2444 1301.4161 0 1339.0245 1 3.3731258 1 18 22 10 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+72 2 651.6300 1301.2444 1301.4161 0.61750263 258.82028 2 1.2902117 2 9 22 10 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+72 2 651.6300 1301.2444 1303.4968 0.82103974 53.011913 3 0.60365552 3 5 22 10 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+72 2 651.6300 1301.2444 1298.5687 0.86949509 32.90501 4 0.44020939 4 4 20 10 LNNPAIALMWR trypsin-full-digest YHR183W KG
+72 2 651.6300 1301.2444 1300.4741 0.89867258 29.368866 6 0.3417902 5 3 20 10 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+73 2 452.8500 903.6844 902.0586 0 56.347805 2 1.0837035 1 6 16 20 QGVTSLGIK trypsin-full-digest YML092C KA
+73 2 452.8500 903.6844 906.0465 0.21322978 68.521774 1 0.85262567 2 5 14 20 FDIGDLVK trypsin-full-digest YLR298C RA
+73 2 452.8500 903.6844 904.0338 0.41111323 23.418583 9 0.63817865 3 3 14 20 VSHTVSFK trypsin-full-digest YOR168W KS
+73 2 452.8500 903.6844 902.0587 0.5519315 24.958044 8 0.48557344 4 4 16 20 VIAVTNGTK trypsin-full-digest YGL026C KT
+73 2 452.8500 903.6844 904.8859 0.60063833 11.533216 15 0.43278965 5 3 14 20 ESTPDNDK trypsin-full-digest YOR267C KE
+73 3 452.8500 1355.5265 1354.3092 0 97.742645 1 0.66088116 1 10 48 7 GDDEANGATSFDR trypsin-full-digest YOR063W KT
+73 3 452.8500 1355.5265 1355.5164 0.41827905 96.809456 2 0.38444841 2 10 44 7 YQVTVIDAPGHR trypsin-full-digest YBR118W KD
+73 3 452.8500 1355.5265 1355.6616 0.59096551 21.397329 7 0.27032319 3 5 44 7 GMLNVQLLVVNR trypsin-full-digest YBR115C KN
+73 3 452.8500 1355.5265 1357.6157 0.76384509 52.985188 3 0.15607032 4 9 48 7 APIVAYAELIAAR trypsin-full-digest YGL245W KI
+73 3 452.8500 1355.5265 1354.4875 0.84334892 43.882256 4 0.10352775 5 7 40 7 GEYHFFQGITR trypsin-full-digest YJR069C RG
+74 2 427.3800 852.7444 853.0293 0 46.593933 3 0.44586661 1 4 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+74 2 427.3800 852.7444 854.0171 0.19086304 46.874577 2 0.36076716 2 4 14 13 THILSGVK trypsin-full-digest YDR093W RN
+74 2 427.3800 852.7444 849.9823 0.44673637 43.607098 5 0.24668178 3 4 12 13 IADQYLK trypsin-full-digest YPL215W RD
+74 2 427.3800 852.7444 852.0445 0.4754456 8.7929144 11 0.23388129 4 2 14 13 HASLILAK trypsin-full-digest YMR235C KA
+74 2 427.3800 852.7444 852.8194 0.49826011 39.332458 6 0.22370906 5 3 12 13 DSCTENK trypsin-full-digest YNL166C KE
+75 2 877.2700 1752.5244 1752.8573 0 1072.6307 1 3.9823563 1 16 26 4 LVSWYDNEYGYSTR trypsin-full-digest YGR192C KV
+75 2 877.2700 1752.5244 1753.9385 1.020926 7.8260818 2 -0.083334833 2 3 30 4 ACIIFFDEIDAVGGAR trypsin-full-digest YKL145W KF
+75 2 877.2700 1752.5244 1750.8798 1.100632 4.3475466 3 -0.4007521 3 2 30 4 AEETIAWLDSNTTATK trypsin-full-digest YLL024C KE
+75 2 877.2700 1752.5244 1754.9578 1.1276983 0 4 -0.50854033 4 0 34 4 ISHVSTGGGASLELLEGK trypsin-full-digest YCR012W KE
+76 2 731.8100 1461.6044 1462.7675 0 1339.4905 1 3.6146004 1 19 24 5 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+76 2 731.8100 1461.6044 1463.5709 0.89022428 15.232876 4 0.3967953 2 4 24 5 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+76 2 731.8100 1461.6044 1460.6036 0.90547442 10.096539 5 0.34167209 3 3 22 5 EEPDLENLLFNK trypsin-full-digest YHR183W RF
+76 2 731.8100 1461.6044 1460.4707 0.94390142 21.407425 2 0.2027739 4 4 24 5 ELGDAYVSSDEEF trypsin-full-digest YLR249W K-
+76 2 731.8100 1461.6044 1459.6195 0.97492385 21.211966 3 0.090640165 5 5 26 5 SQVDEIVLVGGSTR trypsin-full-digest YLL024C KI
+77 2 745.4300 1488.8444 1489.7319 0 2646.4438 1 4.6354041 1 21 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+77 2 745.4300 1488.8444 1486.6195 0.80580199 209.53319 2 0.9001863 2 9 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+77 2 745.4300 1488.8444 1490.6510 0.8935802 27.22241 4 0.49329877 3 3 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+77 2 745.4300 1488.8444 1488.7063 0.9329536 57.869457 3 0.31078729 4 4 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+78 2 452.2200 902.4244 902.0586 0 102.61301 1 0.80108744 1 7 16 19 QGVTSLGIK trypsin-full-digest YML092C KA
+78 2 452.2200 902.4244 904.9293 0.10703871 74.167198 2 0.71534008 2 5 14 19 EQPESTSK trypsin-full-digest YDL223C KN
+78 2 452.2200 902.4244 903.0513 0.43047881 35.246094 5 0.45623627 3 4 12 19 QFWLGPR trypsin-full-digest YBR115C RD
+78 2 452.2200 902.4244 903.9957 0.504062 42.685417 4 0.39728969 4 4 14 19 GWGWTAAR trypsin-full-digest YDL198C RN
+78 2 452.2200 902.4244 901.9256 0.5203054 7.4105458 15 0.38427731 5 2 14 19 APLEDDDK trypsin-full-digest YKL145W KK
+78 3 452.2200 1353.6365 1354.4875 0 109.16689 2 0.85549891 1 10 40 7 GEYHFFQGITR trypsin-full-digest YJR069C RG
+78 3 452.2200 1353.6365 1355.6616 0.046028499 77.322945 4 0.81612158 2 9 44 7 GMLNVQLLVVNR trypsin-full-digest YBR115C KN
+78 3 452.2200 1353.6365 1354.3092 0.4786047 101.63564 3 0.44605312 3 10 48 7 GDDEANGATSFDR trypsin-full-digest YOR063W KT
+78 3 452.2200 1353.6365 1355.5164 0.55555004 147.19391 1 0.38022646 4 11 44 7 YQVTVIDAPGHR trypsin-full-digest YBR118W KD
+78 3 452.2200 1353.6365 1355.4419 0.86263269 69.608704 5 0.11751757 5 8 48 7 FDSGTSGSQNMPK trypsin-full-digest YDL223C KA
+79 2 559.1000 1116.1843 1119.1559 0 22.954494 2 0.23699306 1 3 16 11 YHIEEEGSR trypsin-full-digest YCR012W RK
+79 2 559.1000 1116.1843 1118.3104 0.074480131 12.163911 5 0.21934178 2 3 16 11 INMIEELEK trypsin-full-digest YDR037W RV
+79 2 559.1000 1116.1843 1113.3398 0.39199558 8.6371117 6 0.14409283 3 3 18 11 AIMVNFGYAK trypsin-full-digest YOR168W KY
+79 2 559.1000 1116.1843 1113.1975 0.57595927 14.989534 4 0.10049471 4 4 16 11 DYFGAHTFR trypsin-full-digest YHR183W RV
+79 2 559.1000 1116.1843 1117.3536 0.65604508 35.847515 1 0.081514932 5 6 18 11 FLDGQIALLK trypsin-full-digest YBL076C KK
+80 2 509.2700 1016.5244 1017.1068 0 150.40614 1 0.90325707 1 6 16 9 ITSGQELNR trypsin-full-digest YDL198C KV
+80 2 509.2700 1016.5244 1017.1035 0.1405158 98.749428 2 0.77633518 2 5 16 9 VSSAEYYAK trypsin-full-digest YIL133C KK
+80 2 509.2700 1016.5244 1015.1717 0.84938502 54.884029 3 0.13604406 3 4 16 9 LDAELVLDK trypsin-full-digest YNL166C KF
+80 2 509.2700 1016.5244 1017.2080 0.85867649 17.96553 6 0.12765144 4 2 16 9 MTAFYSGIK trypsin-full-digest YMR309C RV
+80 2 509.2700 1016.5244 1018.0887 1.0889183 2.9468262 8 -0.080316156 5 1 14 9 LEEIETER trypsin-full-digest YMR235C KL
+81 2 427.3800 852.7444 853.0293 0 40.234848 3 0.71672249 1 3 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+81 2 427.3800 852.7444 854.0171 0.1037989 48.62289 2 0.64232749 2 4 14 13 THILSGVK trypsin-full-digest YDR093W RN
+81 2 427.3800 852.7444 852.0445 0.55270237 26.911837 6 0.32058826 3 3 14 13 HASLILAK trypsin-full-digest YMR235C KA
+81 2 427.3800 852.7444 851.9758 0.58951396 66.419243 1 0.29420456 4 5 14 13 SSMGPAFR trypsin-full-digest YGL135W KL
+81 2 427.3800 852.7444 851.8712 0.75772524 33.243809 4 0.17364377 5 4 12 13 FQTGEDR trypsin-full-digest YLR249W RE
+82 2 452.8500 903.6844 904.8859 0 64.193161 2 0.5262 1 4 14 20 ESTPDNDK trypsin-full-digest YOR267C KE
+82 2 452.8500 903.6844 906.0465 0.11277704 56.972046 3 0.46685672 2 4 14 20 FDIGDLVK trypsin-full-digest YLR298C RA
+82 2 452.8500 903.6844 904.9293 0.2270361 47.524639 5 0.4067336 3 4 14 20 EQPESTSK trypsin-full-digest YDL223C KN
+82 2 452.8500 903.6844 903.0002 0.42635316 51.255814 4 0.30185297 4 4 16 20 DTGVVDAVK trypsin-full-digest YNL166C KV
+82 2 452.8500 903.6844 904.0338 0.52230549 64.921379 1 0.25136286 5 4 14 20 VSHTVSFK trypsin-full-digest YOR168W KS
+82 3 452.8500 1355.5265 1355.5164 0 156.55568 2 0.72244394 1 10 44 7 YQVTVIDAPGHR trypsin-full-digest YBR118W KD
+82 3 452.8500 1355.5265 1355.4419 0.25582105 104.23301 4 0.53762758 2 10 48 7 FDSGTSGSQNMPK trypsin-full-digest YDL223C KA
+82 3 452.8500 1355.5265 1354.3928 0.72055531 159.81966 1 0.20188312 3 11 48 7 SGDAETAAYDNIK trypsin-full-digest YDL223C KN
+82 3 452.8500 1355.5265 1355.6616 0.78724837 51.907604 6 0.15370114 4 6 44 7 GMLNVQLLVVNR trypsin-full-digest YBR115C KN
+82 3 452.8500 1355.5265 1357.6157 1.0172542 42.36615 7 -0.012465239 5 7 48 7 APIVAYAELIAAR trypsin-full-digest YGL245W KI
+83 2 468.8000 935.5844 937.0202 0 165.04073 1 0.70322478 1 8 16 11 SDGVAGLYR trypsin-full-digest YBL030C KG
+83 2 468.8000 935.5844 937.0635 0.051904984 157.04977 2 0.66672391 2 7 14 11 LTSQGIYR trypsin-full-digest YGR157W KY
+83 2 468.8000 935.5844 935.1315 0.23450169 68.503082 4 0.53831738 3 5 16 11 VLPGPEVPK trypsin-full-digest YHR183W KD
+83 2 468.8000 935.5844 935.0446 0.30850619 18.517334 6 0.48627558 4 3 14 11 LNLEGDFK trypsin-full-digest YGL245W KK
+83 2 468.8000 935.5844 935.8565 0.42743704 51.483372 5 0.40264046 5 4 14 11 EDDSNNDK trypsin-full-digest YOR267C KE
+83 3 468.8000 1403.3765 1404.4968 0 43.463505 3 0.39917707 1 11 56 6 VASANATAAESDVAK trypsin-full-digest YIL133C KQ
+83 3 468.8000 1403.3765 1404.5829 0.13736853 77.41394 1 0.34434271 2 10 44 6 TTLHYALSELEK trypsin-full-digest YDR399W RD
+83 3 468.8000 1403.3765 1405.7032 0.552109 64.443207 2 0.17878783 3 9 48 6 GFLPSVVGIVVYR trypsin-full-digest YBL030C RG
+83 3 468.8000 1403.3765 1405.4899 1.5814054 3.3649597 6 -0.23208369 4 2 44 6 STSTVNLNNHYR trypsin-full-digest YOR267C KA
+83 3 468.8000 1403.3765 1402.6282 1.6719476 5.7472043 5 -0.26822606 5 4 44 6 MTSGYYLGELLR trypsin-full-digest YFR053C KL
+84 2 440.0600 878.1044 877.0109 0 18.001448 6 0.8047384 1 4 14 12 QGIYGLAR trypsin-full-digest YKL127W KS
+84 2 440.0600 878.1044 877.0080 0.18432704 45.319706 2 0.65640336 2 5 14 12 LSTSVGWK trypsin-full-digest YIL133C KY
+84 2 440.0600 878.1044 876.0233 0.21106918 59.926601 1 0.63488293 3 6 14 12 FVVGLGER trypsin-full-digest YKL145W KV
+84 2 440.0600 878.1044 875.8907 0.38777286 23.468019 5 0.4926827 4 4 12 12 LEEQDSR trypsin-full-digest YMR145C KR
+84 2 440.0600 878.1044 877.0135 0.43924966 8.4855242 9 0.45125732 5 2 12 12 NFGVWVR trypsin-full-digest YMR242C KY
+85 3 497.6200 1489.8365 1489.7319 0 2629.9929 1 5.015099 1 28 48 3 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+85 3 497.6200 1489.8365 1488.7063 0.84448564 590.96753 2 0.77991986 2 17 48 3 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+85 3 497.6200 1489.8365 1490.6510 0.92268771 84.568672 3 0.3877289 3 9 48 3 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+86 1 713.0700 712.0622 713.7887 0 42.898697 1 0.25811729 1 4 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+86 1 713.0700 712.0622 710.7880 0.43596756 26.317953 2 0.14558652 2 3 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+86 1 713.0700 712.0622 713.7881 0.89537442 14.902379 3 0.027005678 3 2 12 9 TLYGFGG trypsin-full-digest YBR009C R-
+86 1 713.0700 712.0622 714.7765 1.1662105 13.06544 4 -0.042901821 4 2 12 9 SGPTPTR trypsin-full-digest YDL223C KS
+86 1 713.0700 712.0622 709.8033 1.3344504 6.7109046 5 -0.086327426 5 2 14 9 AHGGVAAK trypsin-full-digest YCR034W RV
+87 2 501.1300 1000.2444 998.1502 0 82.180992 1 0.94085401 1 6 20 10 IAAVGAANGVR trypsin-full-digest YKL127W KK
+87 2 501.1300 1000.2444 999.1753 0.0071040629 52.168655 3 0.93417013 2 5 16 10 EALGELVIR trypsin-full-digest YPL215W KA
+87 2 501.1300 1000.2444 1003.0769 0.31822187 32.207912 4 0.64145368 3 4 16 10 NLDGETNLK trypsin-full-digest YDR093W KV
+87 2 501.1300 1000.2444 1003.1383 0.40787295 56.638897 2 0.55710512 4 6 18 10 AVNTGMEPGK trypsin-full-digest YLR340W RT
+87 2 501.1300 1000.2444 998.1038 0.58649296 12.313833 6 0.38904974 5 3 16 10 SSIQLGEHK trypsin-full-digest YLR371W KK
+87 3 501.1300 1500.3666 1500.7172 0 41.45351 1 0.32945254 1 8 48 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+87 3 501.1300 1500.3666 1497.7600 1.226549 22.535898 2 -0.074637152 2 6 48 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+87 3 501.1300 1500.3666 1500.4829 1.4662495 19.797424 3 -0.15360707 3 6 44 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+88 2 419.3200 836.6244 835.8872 0 24.406082 2 0.40368167 1 3 12 10 SDNVMDR trypsin-full-digest YBL076C KW
+88 2 419.3200 836.6244 834.0013 0.31547526 12.321632 4 0.27633008 2 2 12 10 LSMSQLR trypsin-full-digest YOR267C KS
+88 2 419.3200 836.6244 839.0054 0.49235049 17.52681 3 0.2049288 3 3 14 10 IAGLNPVR trypsin-full-digest YPL106C RI
+88 2 419.3200 836.6244 835.0110 0.76761371 2.3227963 9 0.093810096 4 1 12 10 EYILGLK trypsin-full-digest YDL198C KD
+88 2 419.3200 836.6244 837.9280 0.8460986 7.1517234 5 0.062127165 5 2 12 10 ETSNFIK trypsin-full-digest YBR118W KK
+89 2 452.8500 903.6844 906.0465 0 67.909523 1 0.66419196 1 5 14 20 FDIGDLVK trypsin-full-digest YLR298C RA
+89 2 452.8500 903.6844 904.8859 0.11163299 46.654369 2 0.59004623 2 5 14 20 ESTPDNDK trypsin-full-digest YOR267C KE
+89 2 452.8500 903.6844 903.0513 0.32041824 4.8063245 13 0.45137274 3 2 12 20 QFWLGPR trypsin-full-digest YBR115C RD
+89 2 452.8500 903.6844 900.9867 0.48289984 21.544519 4 0.34345376 4 3 12 20 ITADYYR trypsin-full-digest YLR298C RN
+89 2 452.8500 903.6844 905.0593 0.5430572 1.1933155 18 0.30349773 5 1 16 20 VSSTSLALK trypsin-full-digest YLR371W RR
+89 3 452.8500 1355.5265 1355.4419 0 115.35501 2 1.0529802 1 13 48 7 FDSGTSGSQNMPK trypsin-full-digest YDL223C KA
+89 3 452.8500 1355.5265 1354.3092 0.6454857 152.35396 1 0.37329653 2 12 48 7 GDDEANGATSFDR trypsin-full-digest YOR063W KT
+89 3 452.8500 1355.5265 1357.6157 0.64984179 32.56052 6 0.36870968 3 8 48 7 APIVAYAELIAAR trypsin-full-digest YGL245W KI
+89 3 452.8500 1355.5265 1355.6616 0.69778049 44.920116 4 0.31823114 4 7 44 7 GMLNVQLLVVNR trypsin-full-digest YBR115C KN
+89 3 452.8500 1355.5265 1354.3928 0.86221355 78.549049 3 0.14508639 5 11 48 7 SGDAETAAYDNIK trypsin-full-digest YDL223C KN
+90 3 1032.0000 3092.9766 3095.2366 0 1014.6406 1 4.1437883 1 32 108 3 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+90 3 1032.0000 3092.9766 3095.4709 0.99053985 48.36216 2 0.039200895 2 12 112 3 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+90 3 1032.0000 3092.9766 3090.7644 1.2211008 8.0220041 3 -0.91619474 3 5 112 3 NIVPVIMAGIIAIYGLVVSVLVCYSLGQK trypsin-full-digest YEL027W KQ
+91 2 466.0900 930.1644 932.2044 0 65.519272 2 0.60412568 1 5 14 9 MIAPMIEK trypsin-full-digest YLR043C KF
+91 2 466.0900 930.1644 933.0876 0.026813155 100.87474 1 0.58792716 2 6 14 9 MSIPETQK trypsin-full-digest YMR303C -A
+91 2 466.0900 930.1644 930.0287 0.048423041 58.461544 3 0.57487208 3 4 14 9 QVSDIVNR trypsin-full-digest YGR157W RI
+91 2 466.0900 930.1644 931.0996 0.40841615 30.83877 5 0.357391 4 4 14 9 LWVLTGDK trypsin-full-digest YDR093W KV
+91 2 466.0900 930.1644 930.0690 0.71705782 42.043987 4 0.17093264 5 4 14 9 IETGELIR trypsin-full-digest YLR371W KC
+92 3 497.2800 1488.8165 1489.7319 0 1872.1616 1 3.8966787 1 24 48 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+92 3 497.2800 1488.8165 1486.6195 0.83217859 344.51291 2 0.65394616 2 14 52 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+92 3 497.2800 1488.8165 1488.7063 0.84458709 281.42068 3 0.60559422 3 13 48 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+92 3 497.2800 1488.8165 1490.6510 1.0214745 92.455688 4 -0.083679095 4 9 48 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+93 2 693.0300 1384.0444 1382.4467 0 1282.8864 1 3.071521 1 18 24 5 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+93 2 693.0300 1384.0444 1381.5258 0.82522219 24.710701 3 0.53683364 2 4 22 5 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+93 2 693.0300 1384.0444 1381.6099 0.92968917 132.91029 2 0.21596114 3 7 22 5 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+93 2 693.0300 1384.0444 1386.6718 1.0372562 2.1949697 5 -0.11443344 4 1 20 5 LAEMIPQFFYK trypsin-full-digest YDR093W RN
+93 2 693.0300 1384.0444 1383.6108 1.0673972 2.2312288 4 -0.20701215 5 1 26 5 NVIVSGIVLAADGR trypsin-full-digest YBL076C KK
+94 3 669.4400 2005.2965 2006.3051 0 676.56519 1 2.6910779 1 27 68 3 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+94 3 669.4400 2005.2965 2004.0973 0.97163469 106.12769 2 0.076333262 2 14 72 3 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+94 3 669.4400 2005.2965 2005.2764 1.1398195 27.866337 3 -0.37626526 3 8 68 3 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+95 2 1004.4600 2006.9044 2006.3051 0 723.72211 1 3.9027524 1 16 34 4 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+95 2 1004.4600 2006.9044 2004.0973 0.82395792 26.607611 3 0.68704855 2 4 36 4 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+95 2 1004.4600 2006.9044 2009.1975 0.9481867 26.953934 2 0.2022146 3 4 38 4 YDSPVSSPITSASELGSIAK trypsin-full-digest YNL166C KL
+95 2 1004.4600 2006.9044 2005.2764 0.99055701 8.0184507 4 0.036853641 4 3 34 4 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+96 2 652.2400 1302.4644 1301.4161 0 1587.1769 1 4.1044731 1 18 22 9 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+96 2 652.2400 1302.4644 1301.4161 0.77718401 146.15948 2 0.9145422 2 7 22 9 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+96 2 652.2400 1302.4644 1303.4968 0.78656965 136.04576 3 0.87601912 3 7 22 9 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+96 2 652.2400 1302.4644 1301.4192 0.8966037 43.772213 5 0.42438722 4 4 22 9 DALPSVTSEQVR trypsin-full-digest YBL076C KE
+96 2 652.2400 1302.4644 1304.4626 0.9150939 87.347191 4 0.34849483 5 6 22 9 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+97 2 433.7800 865.5444 863.9689 0 22.758293 3 0.22999756 1 2 12 13 EYQVIGR trypsin-full-digest YMR242C KR
+97 2 433.7800 865.5444 865.1040 0.27651593 141.54544 1 0.16639957 2 5 10 13 FLWMIR trypsin-full-digest YGL022W KI
+97 2 433.7800 865.5444 862.9965 1.1270387 31.535526 2 -0.029218594 3 3 14 13 IMDTAGQK trypsin-full-digest YHR183W KG
+97 2 433.7800 865.5444 867.9752 1.3190436 0 8 -0.073379271 4 0 12 13 MANFETR trypsin-full-digest YNL166C KR
+97 2 433.7800 865.5444 863.9843 1.572087 18.824604 5 -0.13157864 5 3 14 13 MSSNAQVK trypsin-full-digest YBL030C -T
+97 3 433.7800 1298.3165 1295.5011 0 108.83713 1 0.50911599 1 9 44 5 TSFFQALGVPTK trypsin-full-digest YLR340W KI
+97 3 433.7800 1298.3165 1300.4741 0.5583092 77.047203 3 0.22487184 2 8 40 5 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+97 3 433.7800 1298.3165 1299.4670 0.79660463 95.325806 2 0.10355183 3 9 40 5 MPYTLSDAHHK trypsin-full-digest YLR058C -L
+97 3 433.7800 1298.3165 1298.5687 1.2789003 34.471161 5 -0.1419926 4 5 40 5 LNNPAIALMWR trypsin-full-digest YHR183W KG
+97 3 433.7800 1298.3165 1299.4120 1.4781585 36.938969 4 -0.24343814 5 5 36 5 FEELCADLFR trypsin-full-digest YLL024C RS
+98 2 751.2800 1500.5444 1500.4829 0 85.739204 1 0.73663002 1 6 22 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+98 2 751.2800 1500.5444 1497.7600 0.39315757 57.672653 2 0.44701836 2 6 24 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+98 2 751.2800 1500.5444 1500.7172 1.3417306 5.9268188 3 -0.25172904 3 2 24 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+99 3 581.9500 1742.8265 1740.0070 0 95.88134 1 0.48460686 1 11 56 3 MNSLVTQYAAPLFER trypsin-full-digest YCR034W -Y
+99 3 581.9500 1742.8265 1742.9492 0.37074959 43.33564 2 0.30493906 2 7 56 3 SLLNIDPHSSDYLIR trypsin-full-digest YMR309C KL
+99 3 581.9500 1742.8265 1742.9031 1.6881881 9.5394077 3 -0.33350065 3 4 56 3 ESLVEVNFADLYTSR trypsin-full-digest YMR235C RL
+100 1 763.1100 762.1022 764.9664 0 10.836562 7 0.33078977 1 2 12 15 LVLVHGK trypsin-full-digest YDR093W RW
+100 1 763.1100 762.1022 759.8577 0.046465401 32.205807 1 0.3154195 2 4 14 15 SGDAALVK trypsin-full-digest YBR118W KF
+100 1 763.1100 762.1022 762.9196 0.28373277 20.508097 2 0.23693387 3 3 12 15 MAAELTK trypsin-full-digest YPL266W RR
+100 1 763.1100 762.1022 761.8761 0.46104947 18.759415 4 0.17827933 4 3 10 15 DPVIYR trypsin-full-digest YGL245W RC
+100 1 763.1100 762.1022 764.8363 0.46744531 19.572428 3 0.17616364 5 3 12 15 YGADALR trypsin-full-digest YBL076C KL
+101 1 833.2400 832.2322 829.9922 0 25.544271 2 0.28301004 1 3 14 16 DIVSAVVK trypsin-full-digest YMR303C KA
+101 1 833.2400 832.2322 834.0013 0.083209559 14.410157 3 0.2594609 2 2 12 16 LSMSQLR trypsin-full-digest YOR267C KS
+101 1 833.2400 832.2322 832.9573 0.3484197 67.488708 1 0.18440376 3 3 12 16 NAPAWFK trypsin-full-digest YDR064W RL
+101 1 833.2400 832.2322 835.0112 0.46711424 2.5795839 10 0.15081201 4 1 12 16 TIFVVEK trypsin-full-digest YMR309C KG
+101 1 833.2400 832.2322 834.9862 0.69176388 4.319622 8 0.087233908 5 1 16 16 AAATAAMTK trypsin-full-digest YLR249W KA
+102 2 733.2200 1464.4243 1462.7675 0 963.87823 1 3.3292608 1 16 24 3 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+102 2 733.2200 1464.4243 1463.5709 0.91493738 1.7641164 3 0.28319573 2 1 24 3 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+102 2 733.2200 1464.4243 1466.6692 0.93777496 36.194633 2 0.20716341 3 4 22 3 DFMVEQELLNTK trypsin-full-digest YFR053C KD
+103 2 559.1000 1116.1843 1119.1559 0 27.676226 1 0.44975054 1 3 16 11 YHIEEEGSR trypsin-full-digest YCR012W RK
+103 2 559.1000 1116.1843 1114.1895 0.19610925 9.8223457 3 0.3615503 2 3 16 11 TLQPNPECR trypsin-full-digest YDR093W RF
+103 2 559.1000 1116.1843 1116.1615 0.39587018 7.9366827 4 0.27170771 3 3 16 11 YDGAFDCLR trypsin-full-digest YBL030C KK
+103 2 559.1000 1116.1843 1113.1975 0.65997499 0.809264 11 0.15292643 4 1 16 11 DYFGAHTFR trypsin-full-digest YHR183W RV
+103 2 559.1000 1116.1843 1115.2114 0.77206689 17.480232 2 0.10251305 5 4 18 11 DVSNSKPNVR trypsin-full-digest YMR073C RF
+104 2 565.2200 1128.4243 1129.2966 0 8.6711378 3 0.40850091 1 2 18 7 NVVAVEMDPR trypsin-full-digest YPL266W KM
+104 2 565.2200 1128.4243 1126.2340 0.37231663 18.984291 1 0.25640923 2 2 16 7 DEGLFNLYR trypsin-full-digest YDL198C RG
+104 2 565.2200 1128.4243 1126.2928 0.73227251 7.3460369 4 0.10936692 3 2 18 7 GDVVMIYSSR trypsin-full-digest YBR115C RG
+104 2 565.2200 1128.4243 1131.1674 1.013297 15.935033 2 -0.0054318211 4 3 20 7 IDQASGAAQDR trypsin-full-digest YLR371W RH
+104 2 565.2200 1128.4243 1126.2004 1.2105 3.8605995 5 -0.085989423 5 1 18 7 CTINGVSYGR trypsin-full-digest YDR093W KA
+105 2 483.1200 964.2244 964.0862 0 29.478136 2 0.52027655 1 4 14 9 SDTPLLYR trypsin-full-digest YBL076C RS
+105 2 483.1200 964.2244 965.1637 0.12127268 45.200874 1 0.45718122 2 4 14 9 VLVHTQIR trypsin-full-digest YOR063W RK
+105 2 483.1200 964.2244 967.0465 0.58198601 15.500867 4 0.21748286 3 3 16 9 GADSVIYSR trypsin-full-digest YDR093W KL
+105 2 483.1200 964.2244 962.1570 0.77023834 26.160965 3 0.1195396 4 3 14 9 LFTLEAIR trypsin-full-digest YOR168W RR
+105 2 483.1200 964.2244 962.1136 0.78001142 1.991576 5 0.1144549 5 1 14 9 LALIDDFR trypsin-full-digest YGL022W KE
+106 1 713.0700 712.0622 713.7887 0 19.851704 2 0.24297184 1 3 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+106 1 713.0700 712.0622 710.7880 0.56537306 9.3046618 4 0.10560211 2 2 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+106 1 713.0700 712.0622 714.8626 0.81795621 2.3578839 9 0.044231515 3 1 10 9 ALPTWK trypsin-full-digest YMR235C KD
+106 1 713.0700 712.0622 710.8309 0.96226132 9.7281923 3 0.0091694407 4 2 10 9 AFAQFK trypsin-full-digest YJR069C KE
+106 1 713.0700 712.0622 709.8033 1.3992343 6.9487085 5 -0.097002678 5 2 14 9 AHGGVAAK trypsin-full-digest YCR034W RV
+107 2 433.7800 865.5444 866.0430 0 2.096514 11 0.18164477 1 1 12 13 NDFIMVK trypsin-full-digest YOR063W KG
+107 2 433.7800 865.5444 863.9689 0.0033280628 54.479156 1 0.18104024 2 3 12 13 EYQVIGR trypsin-full-digest YMR242C KR
+107 2 433.7800 865.5444 864.9566 0.31438479 3.6916726 8 0.12453841 3 1 12 13 NIQHPEK trypsin-full-digest YDL223C KN
+107 2 433.7800 865.5444 864.0271 0.50945479 18.027445 5 0.089104973 4 2 12 13 LAEWMSK trypsin-full-digest YBR115C RY
+107 2 433.7800 865.5444 867.8272 0.59848398 17.266714 6 0.072933286 5 2 12 13 DSDDNFR trypsin-full-digest YOR267C RL
+107 3 433.7800 1298.3165 1295.5011 0 217.9725 1 0.61248285 1 10 44 5 TSFFQALGVPTK trypsin-full-digest YLR340W KI
+107 3 433.7800 1298.3165 1299.4670 0.57715613 143.61385 2 0.25898463 2 9 40 5 MPYTLSDAHHK trypsin-full-digest YLR058C -L
+107 3 433.7800 1298.3165 1298.5687 1.2572666 93.581177 3 -0.15757143 3 7 40 5 LNNPAIALMWR trypsin-full-digest YHR183W KG
+107 3 433.7800 1298.3165 1299.4120 1.3784283 34.675423 4 -0.23178086 4 5 36 5 FEELCADLFR trypsin-full-digest YLL024C RS
+107 3 433.7800 1298.3165 1300.4741 1.4784603 26.163458 5 -0.29304871 5 4 40 5 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+108 3 1032.5000 3094.4766 3095.2366 0 612.73865 1 3.6182745 1 28 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+108 3 1032.5000 3094.4766 3095.4709 0.90336043 41.487244 2 0.34966859 2 10 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+109 2 419.3200 836.6244 835.8872 0 24.110601 5 0.3558453 1 3 12 10 SDNVMDR trypsin-full-digest YBL076C KW
+109 2 419.3200 836.6244 839.0054 0.1598686 21.904999 6 0.29895681 2 3 14 10 IAGLNPVR trypsin-full-digest YPL106C RI
+109 2 419.3200 836.6244 835.0110 0.52057219 15.567754 8 0.17060213 3 3 12 10 EYILGLK trypsin-full-digest YDL198C KD
+109 2 419.3200 836.6244 835.9554 0.6000371 95.850708 1 0.14232492 4 6 14 10 IGDYAGIK trypsin-full-digest YMR303C KW
+109 2 419.3200 836.6244 837.9280 0.63456231 5.9988446 9 0.13003929 5 2 12 10 ETSNFIK trypsin-full-digest YBR118W KK
+110 2 613.1900 1224.3644 1222.3203 0 20.85313 1 0.51401627 1 3 22 4 GGEGEVSVFVSR trypsin-full-digest YDR037W KV
+110 2 613.1900 1224.3644 1223.4375 0.0089263823 11.477989 3 0.50942796 2 2 20 4 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+110 2 613.1900 1224.3644 1223.2670 0.44400001 14.988181 2 0.28579304 3 2 18 4 YYGGNEHIDR trypsin-full-digest YLR058C RM
+110 2 613.1900 1224.3644 1224.3788 0.87815511 8.9747524 4 0.062630266 4 2 18 4 LAFLENQDFK trypsin-full-digest YBR115C RL
+111 3 1033.0200 3096.0366 3095.2366 0 934.97644 1 4.0064011 1 31 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+111 3 1033.0200 3096.0366 3095.4709 0.9004131 97.407951 2 0.39898497 2 13 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+112 2 403.3000 804.5844 803.8675 0 66.118599 2 0.9786734 1 5 12 20 ELDTAQK trypsin-full-digest YGR192C KH
+112 2 403.3000 804.5844 803.9288 0.26627362 49.190113 6 0.71807849 2 5 14 20 GSMADVPK trypsin-full-digest YFR053C KE
+112 2 403.3000 804.5844 804.8577 0.52704316 56.694237 3 0.46287027 3 5 10 20 EWNQTK trypsin-full-digest YDR093W KF
+112 2 403.3000 804.5844 801.9383 0.61698544 10.482521 12 0.37484616 4 3 14 20 LSPGITSK trypsin-full-digest YGL009C KD
+112 2 403.3000 804.5844 804.8957 0.67115271 76.747498 1 0.32183412 5 6 12 20 ESVTEIK trypsin-full-digest YGR157W KA
+112 3 403.3000 1206.8765 1204.3109 0 33.421028 1 0.73118997 1 6 40 2 VNGDAHVISHR trypsin-full-digest YGR157W RA
+112 3 403.3000 1206.8765 1207.4535 0.65048796 28.29888 2 0.25555971 2 6 36 2 DTLKPMAIYR trypsin-full-digest YLR371W RV
+113 2 751.4200 1500.8243 1500.4829 0 2.2083549 1 0.20484404 1 2 22 2 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+113 2 751.4200 1500.8243 1500.7172 1.3362254 0.41176486 2 -0.068873771 2 1 24 2 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+114 3 670.5500 2008.6265 2006.3051 0 431.85522 1 2.2389128 1 24 68 2 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+114 3 670.5500 2008.6265 2009.1975 0.7732603 74.17244 2 0.50765038 2 14 76 2 YDSPVSSPITSASELGSIAK trypsin-full-digest YNL166C KL
+115 2 452.8500 903.6844 905.0214 0 68.137947 2 0.39396563 1 4 12 20 HHEELLK trypsin-full-digest YOR267C RE
+115 2 452.8500 903.6844 904.9293 0.15361577 75.46859 1 0.33344629 2 5 14 20 EQPESTSK trypsin-full-digest YDL223C KN
+115 2 452.8500 903.6844 903.0513 0.26712555 40.726894 6 0.28872734 3 4 12 20 QFWLGPR trypsin-full-digest YBR115C RD
+115 2 452.8500 903.6844 905.1050 0.30531314 38.380623 7 0.27368274 4 4 16 20 IALIAGYGK trypsin-full-digest YGR086C KA
+115 2 452.8500 903.6844 903.0921 0.33805606 49.166584 4 0.26078317 5 5 14 20 NLALLFGR trypsin-full-digest YLR371W RS
+116 2 613.3100 1224.6044 1224.3788 0 30.347525 2 0.61062574 1 4 18 5 LAFLENQDFK trypsin-full-digest YBR115C RL
+116 2 613.3100 1224.6044 1222.3203 0.40603259 55.583378 1 0.36269179 2 5 22 5 GGEGEVSVFVSR trypsin-full-digest YDR037W KV
+116 2 613.3100 1224.6044 1223.4375 0.463314 28.741871 3 0.32771429 3 3 20 5 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+116 2 613.3100 1224.6044 1223.2670 1.3308802 4.6025863 4 -0.20204397 4 1 18 5 YYGGNEHIDR trypsin-full-digest YLR058C RM
+116 2 613.3100 1224.6044 1227.4233 1.5334202 3.0746751 5 -0.32572013 5 1 18 5 IEVLEQELVR trypsin-full-digest YGR086C KA
+117 2 652.5200 1303.0244 1301.4161 0 1256.421 1 3.6139576 1 18 22 8 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+117 2 652.5200 1303.0244 1301.4161 0.77656871 141.89146 2 0.80747122 2 7 22 8 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+117 2 652.5200 1303.0244 1300.4741 0.85818648 125.72668 3 0.51250803 3 8 20 8 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+117 2 652.5200 1303.0244 1304.4626 0.90605557 53.969692 5 0.3395111 4 5 22 8 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+117 2 652.5200 1303.0244 1303.4968 0.91972971 114.00854 4 0.29009345 5 7 22 8 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+118 3 1031.9399 3092.7964 3095.2366 0 2070.8057 1 4.5130448 1 42 108 3 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+118 3 1031.9399 3092.7964 3095.4709 0.9686414 41.307964 2 0.14152278 2 10 112 3 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+118 3 1031.9399 3092.7964 3090.7644 1.0997559 28.020123 3 -0.45020282 3 9 112 3 NIVPVIMAGIIAIYGLVVSVLVCYSLGQK trypsin-full-digest YEL027W KQ
+119 2 651.7700 1301.5244 1301.4161 0 1300.1331 1 3.780313 1 17 22 11 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+119 2 651.7700 1301.5244 1301.4161 0.71379524 221.25522 2 1.0819436 2 9 22 11 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+119 2 651.7700 1301.5244 1298.5687 0.81658727 125.39308 4 0.69335759 3 7 20 11 LNNPAIALMWR trypsin-full-digest YHR183W KG
+119 2 651.7700 1301.5244 1303.4968 0.84427452 163.24036 3 0.58869106 4 8 22 11 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+119 2 651.7700 1301.5244 1304.4626 0.85154969 104.09963 5 0.56118876 5 7 22 11 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+120 2 409.2100 816.4044 818.8417 0 124.02093 1 0.57712847 1 5 12 9 QSNDSLR trypsin-full-digest YOR267C KS
+120 2 409.2100 816.4044 815.9681 0.20467918 48.632717 3 0.45900229 2 3 12 9 SLNLTLR trypsin-full-digest YOR136W RK
+120 2 409.2100 816.4044 814.8504 0.22414759 34.387234 4 0.44776651 3 3 12 9 APELDDR trypsin-full-digest YBR115C KN
+120 2 409.2100 816.4044 816.9555 0.3102152 25.83992 6 0.39809445 4 2 12 9 HLSSVFK trypsin-full-digest YPL266W KF
+120 2 409.2100 816.4044 818.9838 0.33361226 99.746979 2 0.38459134 5 4 12 9 LEEAMVK trypsin-full-digest YMR309C KL
+121 2 651.5800 1301.1444 1301.4161 0 1479.4915 1 4.3240523 1 18 22 10 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+121 2 651.5800 1301.1444 1303.4968 0.78806555 74.371384 3 0.91641569 2 5 22 10 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+121 2 651.5800 1301.1444 1300.4741 0.86330932 74.331306 4 0.5910576 3 5 20 10 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+121 2 651.5800 1301.1444 1301.4161 0.86501253 103.94946 2 0.58369279 4 6 22 10 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+121 2 651.5800 1301.1444 1301.4192 0.88314486 54.668568 5 0.50528789 5 5 22 10 DALPSVTSEQVR trypsin-full-digest YBL076C KE
+122 1 760.2200 759.2122 759.8577 0 70.539841 1 0.42828295 1 5 14 13 SGDAALVK trypsin-full-digest YBR118W KF
+122 1 760.2200 759.2122 758.7892 0.059807912 19.467524 5 0.40266824 2 3 12 13 GSSQQPR trypsin-full-digest YEL027W RL
+122 1 760.2200 759.2122 756.8137 0.21858351 17.001827 6 0.33466735 3 3 12 13 SHSEGLK trypsin-full-digest YMR235C KV
+122 1 760.2200 759.2122 758.8753 0.24966337 23.554132 4 0.32135639 4 3 10 13 IGWDLR trypsin-full-digest YGL026C KF
+122 1 760.2200 759.2122 759.8577 0.46435907 69.700447 2 0.22940588 5 5 12 13 NSTIPTK trypsin-full-digest YLL024C RK
+123 2 565.0300 1128.0444 1129.2966 0 15.687304 2 0.33831081 1 3 18 7 NVVAVEMDPR trypsin-full-digest YPL266W KM
+123 2 565.0300 1128.0444 1125.2004 0.22678033 19.670055 1 0.26158857 2 4 20 7 YESATASALVN trypsin-full-digest YDR064W K-
+123 2 565.0300 1128.0444 1130.2659 0.40167227 10.035781 4 0.20242074 3 2 18 7 NSPWVVDSVK trypsin-full-digest YOR168W KN
+123 2 565.0300 1128.0444 1126.2340 0.41678071 10.784776 3 0.19730939 4 2 16 7 DEGLFNLYR trypsin-full-digest YDL198C RG
+123 2 565.0300 1128.0444 1126.2004 1.3182964 10.035781 4 -0.10768311 5 2 18 7 CTINGVSYGR trypsin-full-digest YDR093W KA
+124 2 495.0600 988.1044 987.0771 0 147.71281 1 1.242798 1 7 16 3 YSFLEGGSK trypsin-full-digest YGL009C KL
+124 2 495.0600 988.1044 989.0935 0.68469864 6.1323128 3 0.39185587 2 2 16 3 SLEASVIDR trypsin-full-digest YBR115C KN
+124 2 495.0600 988.1044 988.1950 0.79839063 12.011983 2 0.25055972 3 3 18 3 TPLPPAPAPK trypsin-full-digest YBL030C KK
+125 1 805.0000 803.9922 804.8957 0 67.403206 1 0.68201995 1 4 12 20 ESVTEIK trypsin-full-digest YGR157W KA
+125 1 805.0000 803.9922 802.9286 0.3362076 46.575958 2 0.45271966 2 4 12 20 THAIFSK trypsin-full-digest YGR157W KI
+125 1 805.0000 803.9922 804.8956 0.49661425 22.291025 6 0.34331912 3 2 12 20 ESTIDIK trypsin-full-digest YOR267C KI
+125 1 805.0000 803.9922 804.8577 0.50674599 32.34922 4 0.33640909 4 3 10 20 EWNQTK trypsin-full-digest YDR093W KF
+125 1 805.0000 803.9922 803.8675 0.57547224 26.311508 5 0.28953642 5 3 12 20 ELDTAQK trypsin-full-digest YGR192C KH
+126 2 745.2600 1488.5044 1489.7319 0 573.63257 1 3.4199548 1 14 24 5 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+126 2 745.2600 1488.5044 1486.6195 0.79367924 34.449203 4 0.70560771 2 5 26 5 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+126 2 745.2600 1488.5044 1488.7063 0.84733301 35.298698 3 0.52211416 3 4 24 5 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+126 2 745.2600 1488.5044 1485.6539 0.94492072 53.523678 2 0.18836875 4 5 22 5 QEAIYEVYITEK trypsin-full-digest YLR371W RN
+126 2 745.2600 1488.5044 1490.6510 0.97745997 6.6915894 5 0.077085875 5 2 24 5 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+127 2 474.7400 947.4644 947.0990 0 49.968937 1 0.57516605 1 4 14 8 LTWLADTK trypsin-full-digest YGL245W KD
+127 2 474.7400 947.4644 949.1149 0.36377129 24.094387 5 0.36593714 2 4 14 8 IFENVSIK trypsin-full-digest YDR205W KA
+127 2 474.7400 947.4644 945.0836 0.50043005 19.564295 6 0.28733566 3 3 14 8 LQTIIDSR trypsin-full-digest YMR309C RG
+127 2 474.7400 947.4644 945.0836 0.73157567 26.662403 4 0.15438858 4 4 20 8 LLGSGAGGSVK trypsin-full-digest YOR267C KV
+127 2 474.7400 947.4644 950.1027 0.78049624 49.048164 2 0.12625112 5 5 14 8 SFLESVIR trypsin-full-digest YBR009C KD
+128 1 711.0700 710.0622 709.8869 0 12.085135 3 0.16219591 1 2 10 9 SIHILK trypsin-full-digest YMR242C RV
+128 1 711.0700 710.0622 710.7880 0.71393204 8.2783346 4 0.046399057 2 2 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+128 1 711.0700 710.0622 710.8309 0.72429669 23.710316 1 0.044717953 3 3 10 9 AFAQFK trypsin-full-digest YJR069C KE
+128 1 711.0700 710.0622 712.8472 0.97089922 19.031324 2 0.0047200308 4 3 12 9 TPGGILR trypsin-full-digest YER056C-A KA
+128 1 711.0700 710.0622 708.8125 1.0198404 2.5368099 6 -0.0032180157 5 1 10 9 FSLQSK trypsin-full-digest YMR145C RS
+129 2 523.2900 1044.5643 1045.1577 0 46.084091 1 0.65602416 1 4 16 6 ELEELTGVR trypsin-full-digest YBL076C KN
+129 2 523.2900 1044.5643 1044.1908 0.96237737 15.760937 4 0.024681358 2 3 16 6 QTHSMAELK trypsin-full-digest YOR267C KR
+129 2 523.2900 1044.5643 1045.2443 1.032151 5.7093325 5 -0.021091802 3 2 18 6 LNITGTVLSK trypsin-full-digest YOR168W RR
+129 2 523.2900 1044.5643 1047.2213 1.041258 3.3512132 6 -0.027066199 4 1 12 6 YWYFLQK trypsin-full-digest YMR242C RL
+129 2 523.2900 1044.5643 1046.2346 1.1082737 16.434448 3 -0.071030214 5 3 16 6 YKPGEAILR trypsin-full-digest YOR168W KM
+130 2 733.0300 1464.0444 1462.7675 0 1393.9764 1 3.6638756 1 19 24 3 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+130 2 733.0300 1464.0444 1463.5709 0.95259821 6.5836983 3 0.17367421 2 3 24 3 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+130 2 733.0300 1464.0444 1466.6692 0.96637368 7.5720978 2 0.12320261 3 2 22 3 DFMVEQELLNTK trypsin-full-digest YFR053C KD
+131 2 745.8500 1489.6843 1489.7319 0 2819.5974 1 5.3028259 1 21 24 3 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+131 2 745.8500 1489.6843 1488.7063 0.8833434 85.206764 2 0.61860967 2 5 24 3 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+131 2 745.8500 1489.6843 1490.6510 0.90654737 26.993124 3 0.49556294 3 3 24 3 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+132 2 474.7400 947.4644 945.0836 0 54.108074 1 0.59248811 1 4 14 8 LQTIIDSR trypsin-full-digest YMR309C RG
+132 2 474.7400 947.4644 947.0990 0.13254599 25.854864 6 0.51395619 2 3 14 8 LTWLADTK trypsin-full-digest YGL245W KD
+132 2 474.7400 947.4644 950.1027 0.17679264 34.256989 3 0.48774058 3 4 14 8 SFLESVIR trypsin-full-digest YBR009C KD
+132 2 474.7400 947.4644 949.0466 0.2716538 48.32312 2 0.43153647 4 4 14 8 MSQQDNVK trypsin-full-digest YDR037W -A
+132 2 474.7400 947.4644 946.0281 0.31869599 26.415321 5 0.40366453 5 4 16 8 LSVATADNR trypsin-full-digest YLR249W KH
+133 2 483.1200 964.2244 965.1637 0 66.851875 1 0.60504568 1 6 14 9 VLVHTQIR trypsin-full-digest YOR063W RK
+133 2 483.1200 964.2244 962.1136 0.27866718 28.080624 3 0.43643931 2 4 14 9 LALIDDFR trypsin-full-digest YGL022W KE
+133 2 483.1200 964.2244 962.1570 0.71846265 42.350151 2 0.17034295 3 5 14 9 LFTLEAIR trypsin-full-digest YOR168W RR
+133 2 483.1200 964.2244 967.0465 0.89122903 6.9606466 4 0.065811396 4 2 16 9 GADSVIYSR trypsin-full-digest YDR093W KL
+133 2 483.1200 964.2244 966.0991 1.1542394 4.0717926 6 -0.093321867 5 2 14 9 DLTEFLTK trypsin-full-digest YGR157W KV
+134 2 457.5500 913.0844 914.1131 0 103.68198 1 1.1871964 1 7 16 11 QTVAVGVIK trypsin-full-digest YBR118W RS
+134 2 457.5500 913.0844 915.0573 0.51189619 31.804583 4 0.5794751 2 4 16 11 QGQAAIISK trypsin-full-digest YLR371W KT
+134 2 457.5500 913.0844 914.1532 0.54558873 37.778015 3 0.53947538 3 4 14 11 SIILLIDK trypsin-full-digest YLR371W KK
+134 2 457.5500 913.0844 914.0292 0.57700694 22.956854 5 0.50217581 4 3 14 11 QNNIAVQK trypsin-full-digest YMR309C KR
+134 2 457.5500 913.0844 914.0289 0.78891629 38.178898 2 0.2505978 5 4 14 11 AFHVTPDK trypsin-full-digest YLR058C KW
+135 2 1004.9900 2007.9644 2006.3051 0 933.36005 1 4.2101994 1 19 34 3 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+135 2 1004.9900 2007.9644 2009.1975 1.0327803 34.554996 2 -0.13801165 2 5 38 3 YDSPVSSPITSASELGSIAK trypsin-full-digest YNL166C KL
+135 2 1004.9900 2007.9644 2005.2764 1.0644609 3.5093601 3 -0.27139318 3 2 34 3 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+136 1 717.0700 716.0622 716.7893 0 33.504017 6 0.72184199 1 4 12 16 EAAELGK trypsin-full-digest YBR118W KG
+136 1 717.0700 716.0622 714.7765 0.10004064 114.26469 1 0.64962846 2 6 12 16 SGPTPTR trypsin-full-digest YDL223C KS
+136 1 717.0700 716.0622 717.8204 0.1884166 23.559481 8 0.58583498 3 3 10 16 SLEITR trypsin-full-digest YLR371W KD
+136 1 717.0700 716.0622 718.7643 0.38262898 39.344013 5 0.44564432 4 4 10 16 GAEWEK trypsin-full-digest YGL009C KA
+136 1 717.0700 716.0622 713.7887 0.49265304 44.671604 4 0.36622435 5 4 12 16 NPAVGEK trypsin-full-digest YGL245W KK
+137 3 497.2900 1488.8466 1489.7319 0 1202.3578 1 3.5980604 1 22 48 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+137 3 497.2900 1488.8466 1488.7063 0.81239575 238.33492 2 0.67501152 2 13 48 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+137 3 497.2900 1488.8466 1490.6510 0.91495377 106.84063 3 0.30600145 3 10 48 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+137 3 497.2900 1488.8466 1486.6195 0.96376705 104.79422 4 0.13036823 4 9 52 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+138 1 719.0600 718.0522 716.8506 0 52.676434 1 0.83089995 1 4 12 13 DVMPAGK trypsin-full-digest YBR115C KG
+138 1 719.0600 718.0522 717.8204 0.24423222 27.570053 4 0.62796742 2 3 10 13 SLEITR trypsin-full-digest YLR371W KD
+138 1 719.0600 718.0522 718.8077 0.44881228 42.191254 2 0.45798185 3 3 10 13 FDNVPK trypsin-full-digest YGL009C KR
+138 1 719.0600 718.0522 717.8817 0.54288805 30.408899 3 0.37981433 4 3 10 13 QSKPMK trypsin-full-digest YDR093W RD
+138 1 719.0600 718.0522 718.7643 0.58580309 26.714539 5 0.34415618 5 2 10 13 GAEWEK trypsin-full-digest YGL009C KA
+139 3 1032.0900 3093.2463 3095.2366 0 1460.1478 1 3.9592109 1 39 108 3 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+139 3 1032.0900 3093.2463 3095.4709 0.89455146 39.019924 2 0.41749313 2 11 112 3 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+139 3 1032.0900 3093.2463 3090.7644 1.1534919 13.67534 3 -0.60770655 3 6 112 3 NIVPVIMAGIIAIYGLVVSVLVCYSLGQK trypsin-full-digest YEL027W KQ
+140 1 717.0600 716.0522 716.7893 0 31.130041 3 0.59465551 1 4 12 16 EAAELGK trypsin-full-digest YBR118W KG
+140 1 717.0600 716.0522 716.7460 0.0037337129 23.396549 6 0.59243524 2 3 10 16 KPDDDK trypsin-full-digest YKL145W KI
+140 1 717.0600 716.0522 714.7765 0.42896518 40.463547 2 0.339569 3 4 12 16 SGPTPTR trypsin-full-digest YDL223C KS
+140 1 717.0600 716.0522 718.8077 0.43547797 48.258392 1 0.33569613 4 4 10 16 FDNVPK trypsin-full-digest YGL009C KR
+140 1 717.0600 716.0522 717.8817 0.44567406 29.726236 4 0.32963297 5 3 10 16 QSKPMK trypsin-full-digest YDR093W RD
+141 3 497.2900 1488.8466 1489.7319 0 1504.3676 1 4.4072876 1 24 48 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+141 3 497.2900 1488.8466 1486.6195 0.81095272 174.72479 3 0.83318573 2 12 52 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+141 3 497.2900 1488.8466 1488.7063 0.8131507 369.57693 2 0.82349861 3 15 48 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+141 3 497.2900 1488.8466 1490.6510 0.96138328 67.817703 4 0.17019501 4 8 48 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+142 1 715.0700 714.0622 716.7893 0 72.108284 1 0.72181535 1 5 12 12 EAAELGK trypsin-full-digest YBR118W KG
+142 1 715.0700 714.0622 713.7887 0.55028677 11.598034 6 0.32460991 2 2 12 12 NPAVGEK trypsin-full-digest YGL245W KK
+142 1 715.0700 714.0622 714.7765 0.71276796 21.419298 3 0.20732848 3 3 12 12 SGPTPTR trypsin-full-digest YDL223C KS
+142 1 715.0700 714.0622 716.8506 0.7541483 8.9955482 8 0.17745954 4 2 12 12 DVMPAGK trypsin-full-digest YBR115C KG
+142 1 715.0700 714.0622 715.9341 0.7584759 12.551558 4 0.17433582 5 2 10 12 LLPFVK trypsin-full-digest YLR340W KG
+143 2 452.8500 903.6844 906.0465 0 200.59422 1 0.94311553 1 8 14 20 FDIGDLVK trypsin-full-digest YLR298C RA
+143 2 452.8500 903.6844 905.0214 0.28600335 74.133629 3 0.67338133 2 5 12 20 HHEELLK trypsin-full-digest YOR267C RE
+143 2 452.8500 903.6844 904.0949 0.36352864 52.860504 6 0.60026604 3 5 14 20 HAFMGTLK trypsin-full-digest YOR063W KK
+143 2 452.8500 903.6844 904.0338 0.41108957 83.931282 2 0.55541056 4 6 14 20 VSHTVSFK trypsin-full-digest YOR168W KS
+143 2 452.8500 903.6844 904.9293 0.41509125 34.957909 12 0.55163652 5 4 14 20 EQPESTSK trypsin-full-digest YDL223C KN
+144 3 497.2900 1488.8466 1489.7319 0 1053.226 1 3.5541759 1 21 48 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+144 3 497.2900 1488.8466 1488.7063 0.86864299 272.68655 2 0.46686584 2 13 48 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+144 3 497.2900 1488.8466 1486.6195 1.0075978 137.61798 3 -0.027004087 3 11 52 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+144 3 497.2900 1488.8466 1490.6510 1.0094203 64.820557 4 -0.033481151 4 7 48 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+145 1 717.0600 716.0522 714.7765 0 58.588223 1 0.90983647 1 5 12 16 SGPTPTR trypsin-full-digest YDL223C KS
+145 1 717.0600 716.0522 715.9341 0.44376087 41.323978 3 0.50608665 2 4 10 16 LLPFVK trypsin-full-digest YLR340W KG
+145 1 717.0600 716.0522 716.7893 0.48714566 22.007057 7 0.46661359 3 3 12 16 EAAELGK trypsin-full-digest YBR118W KG
+145 1 717.0600 716.0522 713.7887 0.49324587 33.729961 4 0.46106339 4 4 12 16 NPAVGEK trypsin-full-digest YGL245W KK
+145 1 717.0600 716.0522 717.8204 0.53495586 9.8458958 9 0.42311412 5 2 10 16 SLEITR trypsin-full-digest YLR371W KD
+146 2 692.6800 1383.3444 1382.4467 0 2011.0013 1 3.8734953 1 19 24 5 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+146 2 692.6800 1383.3444 1381.6099 0.68104291 337.00198 2 1.2354789 2 10 22 5 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+146 2 692.6800 1383.3444 1381.5258 0.88333881 9.5191793 3 0.45188648 3 2 22 5 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+146 2 692.6800 1383.3444 1380.6042 1.0289 3.3277209 5 -0.11194392 4 1 22 5 EVVELPLLSPER trypsin-full-digest YKL145W RF
+146 2 692.6800 1383.3444 1383.6108 1.1577057 7.8270969 4 -0.61087209 5 2 26 5 NVIVSGIVLAADGR trypsin-full-digest YBL076C KK
+147 2 614.5800 1227.1444 1227.4233 0 7.4682322 1 0.01874348 1 2 18 3 IEVLEQELVR trypsin-full-digest YGR086C KA
+147 2 614.5800 1227.1444 1224.3788 3.5171313 1.7642522 3 -0.0471798 2 1 18 3 LAFLENQDFK trypsin-full-digest YBR115C RL
+147 2 614.5800 1227.1444 1229.3525 6.4989333 4.1427054 2 -0.10306915 3 2 20 3 EILGTDEPTVR trypsin-full-digest YKL127W KT
+148 1 713.0700 712.0622 713.7887 0 24.496252 4 0.33537182 1 3 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+148 1 713.0700 712.0622 713.7881 0.33931932 46.403988 3 0.22157368 2 4 12 9 TLYGFGG trypsin-full-digest YBR009C R-
+148 1 713.0700 712.0622 710.7880 0.54243892 48.601635 2 0.1534531 3 4 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+148 1 713.0700 712.0622 712.8472 0.59844357 11.41906 5 0.1346707 4 3 12 9 TPGGILR trypsin-full-digest YER056C-A KA
+148 1 713.0700 712.0622 710.8309 0.78597832 59.82716 1 0.071776837 5 4 10 9 AFAQFK trypsin-full-digest YJR069C KE
+149 2 733.7700 1465.5244 1462.7675 0 1203.868 1 3.1824079 1 18 24 3 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+149 2 733.7700 1465.5244 1466.6692 0.92764938 7.8815074 2 0.23024926 2 2 22 3 DFMVEQELLNTK trypsin-full-digest YFR053C KD
+149 2 733.7700 1465.5244 1463.5709 0.96620041 1.0003113 3 0.10756414 3 1 24 3 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+150 1 832.2400 831.2322 834.0013 0 12.4148 2 0.15348957 1 2 12 12 LSMSQLR trypsin-full-digest YOR267C KS
+150 1 832.2400 831.2322 832.9573 0.33006737 31.373159 1 0.10282768 2 2 12 12 NAPAWFK trypsin-full-digest YDR064W RL
+150 1 832.2400 831.2322 832.9578 0.37659156 10.274959 3 0.095686696 3 2 14 12 VAINGFGR trypsin-full-digest YGR192C RI
+150 1 832.2400 831.2322 830.9366 0.58833861 3.6209517 5 0.063185729 4 1 12 12 VTDVIER trypsin-full-digest YDR093W KE
+150 1 832.2400 831.2322 829.9922 1.1218611 2.9467273 6 -0.018704401 5 1 14 12 DIVSAVVK trypsin-full-digest YMR303C KA
+151 2 651.6200 1301.2244 1301.4161 0 1202.2273 1 4.0469213 1 17 22 10 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+151 2 651.6200 1301.2244 1301.4192 0.77860552 43.713001 5 0.89596611 2 5 22 10 DALPSVTSEQVR trypsin-full-digest YBL076C KE
+151 2 651.6200 1301.2244 1301.4161 0.77958488 94.108009 3 0.89200252 3 6 22 10 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+151 2 651.6200 1301.2244 1303.4968 0.78279489 228.81261 2 0.87901193 4 9 22 10 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+151 2 651.6200 1301.2244 1300.4741 0.85280436 85.688034 4 0.59568912 5 6 20 10 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+152 2 531.2200 1060.4243 1059.2889 0 26.479269 2 0.6205802 1 3 16 8 MNLQELLAK trypsin-full-digest YDR205W -V
+152 2 531.2200 1060.4243 1060.2126 0.056052148 86.054985 1 0.58579534 2 5 18 8 GTIEIVSDVK trypsin-full-digest YLR340W RV
+152 2 531.2200 1060.4243 1060.1289 0.84516138 11.819891 7 0.096089773 3 2 16 8 EISDAQEIR trypsin-full-digest YMR145C KL
+152 2 531.2200 1060.4243 1058.1594 0.8702845 24.158962 4 0.080498867 4 3 18 8 DQKPGTSGLR trypsin-full-digest YKL127W KK
+152 2 531.2200 1060.4243 1062.1960 1.003428 7.30264 8 -0.0021273475 5 2 16 8 FANWIANAR trypsin-full-digest YBL076C RD
+153 2 613.7900 1225.5643 1224.3788 0 5.6870127 2 0.16703272 1 2 18 4 LAFLENQDFK trypsin-full-digest YBR115C RL
+153 2 613.7900 1225.5643 1223.4375 1.2733541 7.349463 1 -0.045659065 2 2 20 4 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+153 2 613.7900 1225.5643 1223.2670 2.1510031 2.7957928 4 -0.19225518 3 1 18 4 YYGGNEHIDR trypsin-full-digest YLR058C RM
+153 2 613.7900 1225.5643 1227.4233 2.5895705 4.6158304 3 -0.26551029 4 2 18 4 IEVLEQELVR trypsin-full-digest YGR086C KA
+154 1 717.0600 716.0522 716.8506 0 215.65358 1 0.59496731 1 6 12 16 DVMPAGK trypsin-full-digest YBR115C KG
+154 1 717.0600 716.0522 716.7460 0.072602049 154.65167 2 0.55177146 2 5 10 16 KPDDDK trypsin-full-digest YKL145W KI
+154 1 717.0600 716.0522 716.7893 0.41614333 80.299057 4 0.34737563 3 4 12 16 EAAELGK trypsin-full-digest YBR118W KG
+154 1 717.0600 716.0522 715.9341 0.48545897 47.664581 7 0.30613509 4 3 10 16 LLPFVK trypsin-full-digest YLR340W KG
+154 1 717.0600 716.0522 717.8817 0.5674172 68.329742 6 0.25737262 5 3 10 16 QSKPMK trypsin-full-digest YDR093W RD
+155 2 419.3200 836.6244 835.8872 0 69.90876 1 0.78055704 1 5 12 10 SDNVMDR trypsin-full-digest YBL076C KW
+155 2 419.3200 836.6244 835.9554 0.60037106 41.898266 2 0.31193319 2 4 14 10 IGDYAGIK trypsin-full-digest YMR303C KW
+155 2 419.3200 836.6244 834.8437 0.75223875 8.1968241 7 0.19339177 3 2 12 10 YDSTHGR trypsin-full-digest YGR192C KY
+155 2 419.3200 836.6244 839.0054 0.80877531 7.8815541 8 0.14926179 4 2 14 10 IAGLNPVR trypsin-full-digest YPL106C RI
+155 2 419.3200 836.6244 834.0013 0.8121413 29.737709 3 0.14663443 5 3 12 10 LSMSQLR trypsin-full-digest YOR267C KS
+156 3 1032.4399 3094.2964 3095.2366 0 1813.374 1 5.0189385 1 42 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+156 3 1032.4399 3094.2964 3095.4709 0.96011585 39.488911 2 0.20017597 2 10 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+157 2 509.3200 1016.6244 1017.1068 0 158.00694 1 1.1119214 1 7 16 9 ITSGQELNR trypsin-full-digest YDL198C KV
+157 2 509.3200 1016.6244 1017.1035 0.43675607 28.964193 3 0.62628299 2 3 16 9 VSSAEYYAK trypsin-full-digest YIL133C KK
+157 2 509.3200 1016.6244 1018.1962 0.61605942 23.395197 4 0.42691177 3 3 16 9 MQSVIDLGR trypsin-full-digest YBL076C RN
+157 2 509.3200 1016.6244 1018.0887 0.80515426 42.167759 2 0.21665314 4 3 14 9 LEEIETER trypsin-full-digest YMR235C KL
+157 2 509.3200 1016.6244 1018.1529 0.98998845 10.166105 8 0.011132082 5 2 16 9 VALNGEEMR trypsin-full-digest YDR093W KR
+158 2 427.3800 852.7444 852.0445 0 280.23941 1 1.6478953 1 8 14 13 HASLILAK trypsin-full-digest YMR235C KA
+158 2 427.3800 852.7444 852.8194 0.72617084 44.829403 4 0.45124179 2 4 12 13 DSCTENK trypsin-full-digest YNL166C KE
+158 2 427.3800 852.7444 849.9823 0.72882479 92.955452 2 0.44686839 3 5 12 13 IADQYLK trypsin-full-digest YPL215W RD
+158 2 427.3800 852.7444 853.0293 0.75062484 38.825851 5 0.41094413 4 4 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+158 2 427.3800 852.7444 852.0011 0.82441694 10.621344 11 0.28934249 5 2 14 13 LPLNPNGK trypsin-full-digest YBR115C KV
+159 2 745.7500 1489.4844 1489.7319 0 1736.3658 1 4.2195272 1 18 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+159 2 745.7500 1489.4844 1486.6195 0.81333941 176.23169 2 0.78761947 2 8 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+159 2 745.7500 1489.4844 1490.6510 0.92798012 23.23929 4 0.30388993 3 3 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+159 2 745.7500 1489.4844 1488.7063 0.95878029 29.159029 3 0.17392777 4 3 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/small-yeast.fasta b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/small-yeast.fasta
new file mode 100644
index 0000000..2d25ef0
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/small-yeast.fasta
@@ -0,0 +1,165 @@
+>YBL030C PET9 SGDID:S000000126, Chr II from 164000-163044, reverse complement, Verified ORF, "Major ADP/ATP carrier of the mitochondrial inner membrane, exchanges cytosolic ADP for mitochondrially synthesized ATP; required for viability in many common lab strains carrying a mutation in the polymorphic SAL1 gene"
+MSSNAQVKTPLPPAPAPKKESNFLIDFLMGGVSAAVAKTAASPIERVKLLIQNQDEMLKQGTLDRKYAGILDCFKRTATQEGVISFWRGNTANVIRYFPTQALNFAFKDKIKAMFGFKKEEGYAKWFAGNLASGGAAGALSLLFVYSLDYARTRLAADSKSSKKGGARQFNGLIDVYKKTLKSDGVAGLYRGFLPSVVGIVVYRGLYFGMYDSLKPLLLTGSLEGSFLASFLLGWVVTTGASTCSYPLDTVRRRMMMTSGQAVKYDGAFDCLRKIVAAEGVGSLFKGCGANILRGVAGAGVISMYDQLQMILFGKKFK
+
+>YBL076C ILS1 SGDID:S000000172, Chr II from 84259-81041, reverse complement, Verified ORF, "Cytoplasmic isoleucine-tRNA synthetase, target of the G1-specific inhibitor reveromycin A"
+MSESNAHFSFPKEEEKVLSLWDEIDAFHTSLELTKDKPEFSFFDGPPFATGTPHYGHILASTIKDIVPRYATMTGHHVERRFGWDTHGVPIEHIIDKKLGITGKDDVFKYGLENYNNECRSIVMTYASDWRKTIGRLGRWIDFDNDYKTMYPSFMESTWWAFKQLHEKGQVYRGFKVMPYSTGLTTPLSNFEAQQNYKDVNDPAVTIGFNVIGQEKTQLVAWTTTPWTLPSNLSLCVNADFEYVKIYDETRDRYFILLESLIKTLYKKPKNEKYKIVEKIKGSDLVGLKYEPLFPYFAEQFHETAFRVISDDYVTSDSGTGIVHNAPAFGEEDNAACLKNGVISEDSVLPNAIDDLGRFTKDVPDFEGVYVKDADKLIIKYLTNTGNLLLASQIRHSYPFCWRSDTPLLYRSVPAWFVRVKNIVPQMLDSVMKSHWVPNTIKEKRFANWIANARDWNVSRNRYWGTPIPLWVSDDFEEVVCVGSIKELEELT [...]
+
+>YBR009C HHF1 SGDID:S000000213, Chr II from 255682-255371, reverse complement, Verified ORF, "One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity"
+MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
+
+>YBR115C LYS2 SGDID:S000000319, Chr II from 473920-469742, reverse complement, Verified ORF, "Alpha aminoadipate reductase, catalyzes the reduction of alpha-aminoadipate to alpha-aminoadipate 6-semialdehyde, which is the fifth step in biosynthesis of lysine; activation requires posttranslational phosphopantetheinylation by Lys5p"
+MTNEKVWIEKLDNPTLSVLPHDFLRPQQEPYTKQATYSLQLPQLDVPHDSFSNKYAVALSVWAALIYRVTGDDDIVLYIANNKILRFNIQPTWSFNELYSTINNELNKLNSIEANFSFDELAEKIQSCQDLERTPQLFRLAFLENQDFKLDEFKHHLVDFALNLDTSNNAHVLNLIYNSLLYSNERVTIVADQFTQYLTAALSDPSNCITKISLITASSKDSLPDPTKNLGWCDFVGCIHDIFQDNAEAFPERTCVVETPTLNSDKSRSFTYRDINRTSNIVAHYLIKTGIKRGDVVMIYSSRGVDLMVCVMGVLKAGATFSVIDPAYPPARQTIYLGVAKPRGLIVIRAAGQLDQLVEDYINDELEIVSRINSIAIQENGTIEGGKLDNGEDVLAPYDHYKDTRTGVVVGPDSNPTLSFTSGSEGIPKGVLGRHFSLAYYFNWMSKRFNLTENDKFTMLSGIAHDPIQRDMFTPLFLGAQLYVPTQDDIGT [...]
+
+>YBR118W TEF2 SGDID:S000000322, Chr II from 477665-479041, Verified ORF, "Translational elongation factor EF-1 alpha; also encoded by TEF1; functions in the binding reaction of aminoacyl-tRNA (AA-tRNA) to ribosomes"
+MGKEKSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDKTEKAAKVTKAAQKAAKK
+
+>YCR012W PGK1 SGDID:S000000605, Chr III from 137744-138994, Verified ORF, "3-phosphoglycerate kinase, catalyzes transfer of high-energy phosphoryl groups from the acyl phosphate of 1,3-bisphosphoglycerate to ADP to produce ATP; key enzyme in glycolysis and gluconeogenesis"
+MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKK
+
+>YCR034W FEN1 SGDID:S000000630, Chr III from 190588-191631, Verified ORF, "Fatty acid elongase, involved in sphingolipid biosynthesis; acts on fatty acids of up to 24 carbons in length; mutations have regulatory effects on 1,3-beta-glucan synthase, vacuolar ATPase, and the secretory pathway"
+MNSLVTQYAAPLFERYPQLHDYLPTLERPFFNISLWEHFDDVVTRVTNGRFVPSEFQFIAGELPLSTLPPVLYAITAYYVIIFGGRFLLSKSKPFKLNGLFQLHNLVLTSLSLTLLLLMVEQLVPIIVQHGLYFAICNIGAWTQPLVTLYYMNYIVKFIEFIDTFFLVLKHKKLTFLHTYHHGATALLCYTQLMGTTSISWVPISLNLGVHVVMYWYYFLAARGIRVWWKEWVTRFQIIQFVLDIGFIYFAVYQKAVHLYFPILPHCGDCVGSTTATFAGCAIISSYLVLFISFYINVYKRKGTKTSRVVKRAHGGVAAKVNEYVNVDLKNVPTPSPSPKPQHRRKR
+
+>YDL198C GGC1 SGDID:S000002357, Chr IV from 104552-103650, reverse complement, Verified ORF, "Mitochondrial GTP/GDP transporter, essential for mitochondrial genome maintenance; has a role in mitochondrial iron transport; member of the mitochondrial carrier family"
+MPHTDKKQSGLARLLGSASAGIMEIAVFHPVDTISKRLMSNHTKITSGQELNRVIFRDHFSEPLGKRLFTLFPGLGYAASYKVLQRVYKYGGQPFANEFLNKHYKKDFDNLFGEKTGKAMRSAAAGSLIGIGEIVLLPLDVLKIKRQTNPESFKGRGFIKILRDEGLFNLYRGWGWTAARNAPGSFALFGGNAFAKEYILGLKDYSQATWSQNFISSIVGACSSLIVSAPLDVIKTRIQNRNFDNPESGLRIVKNTLKNEGVTAFFKGLTPKLLTTGPKLVFSFALAQSLIPRFDNLLSK
+
+>YDL223C HBT1 SGDID:S000002382, Chr IV from 60406-57266, reverse complement, Verified ORF, "Substrate of the Hub1p ubiquitin-like protein that localizes to the shmoo tip (mating projection); mutants are defective for mating projection formation, thereby implicating Hbt1p in polarized cell morphogenesis"
+MNMNESISKDGQGEEEQNNFSFGGKPGSYDSNSDSAQRKKSFSTTKPTEYNLPKEQPESTSKNLETKAKNILLPWRKKHNKDSETPHEDTEADANRRANVTSDVNPVSADTKSSSGPNATITTHGYSYVKTTTPAATSEQSKVKTSPPTSHEHSNIKASPTAHRHSKGDAGHPSIATTHNHSTSKAATSPVTHTHGHSSATTSPVTHTHGHASVKTTSPTNTHEHSKANTGPSATATTHGHINVKTTHPVSHGHSGSSTGPKSTAAAQDHSSTKTNPSVTHGHTSVKDNSSATKGYSNTDSNSDRDVIPGSFRGMTGTDVNPVDPSVYTSTGPKSNVSSGMNAVDPSVYTDTSSKSADRRKYSGNTATGPPQDTIKEIAQNVKMDESEQTGLKNDQVSGSDAIQQQTMEPEPKAAVGTSGFVSQQPSYHDSNKNIQHPEKNKVDNKNISERAAEKFNIERDDILESADDYQQKNIKSKTDSNWGPIEYSSSA [...]
+
+>YDR037W KRS1 SGDID:S000002444, Chr IV from 525437-527212, Verified ORF, "Lysyl-tRNA synthetase; also identified as a negative regulator of general control of amino acid biosynthesis "
+MSQQDNVKAAAEGVANLHLDEATGEMVSKSELKKRIKQRQVEAKKAAKKAAAQPKPASKKKTDLFADLDPSQYFETRSRQIQELRKTHEPNPYPHKFHVSISNPEFLAKYAHLKKGETLPEEKVSIAGRIHAKRESGSKLKFYVLHGDGVEVQLMSQLQDYCDPDSYEKDHDLLKRGDIVGVEGYVGRTQPKKGGEGEVSVFVSRVQLLTPCLHMLPADHFGFKDQETRYRKRYLDLIMNKDARNRFITRSEIIRYIRRFLDQRKFIEVETPMMNVIAGGATAKPFITHHNDLDMDMYMRIAPELFLKQLVVGGLDRVYEIGRQFRNEGIDMTHNPEFTTCEFYQAYADVYDLMDMTELMFSEMVKEITGSYIIKYHPDPADPAKELELNFSRPWKRINMIEELEKVFNVKFPSGDQLHTAETGEFLKKILVDNKLECPPPLTNARMLDKLVGELEDTCINPTFIFGHPQMMSPLAKYSRDQPGLCERFEVF [...]
+
+>YDR064W RPS13 SGDID:S000002471, Chr IV from 579456-579476,580016-580450, Verified ORF, "Protein component of the small (40S) ribosomal subunit; has similarity to E. coli S15 and rat S13 ribosomal proteins"
+MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN
+
+>YDR093W DNF2 SGDID:S000002500, Chr IV from 631279-636117, Verified ORF, "Aminophospholipid translocase (flippase) that localizes primarily to the plasma membrane; contributes to endocytosis, protein transport and cell polarity; type 4 P-type ATPase"
+MSSPSKPTSPFVDDIEHESGSASNGLSSMSPFDDSFQFEKPSSAHGNIEVAKTGGSVLKRQSKPMKDISTPDLSKVTFDGIDDYSNDNDINDDDELNGKKTEIHEHENEVDDDLHSFQATPMPNTGGFEDVELDNNEGSNNDSQADHKLKRVRFGTRRNKSGRIDINRSKTLKWAKKNFHNAIDEFSTKEDSLENSALQNRSDELRTVYYNLPLPEDMLDEDGLPLAVYPRNKIRTTKYTPLTFFPKNILFQFHNFANIYFLILLILGAFQIFGVTNPGFASVPLIVIVIITAIKDGIEDSRRTVLDLEVNNTRTHILSGVKNENVAVDNVSLWRRFKKANTRALIKIFEYFSENLTAAGREKKLQKKREELRRKRNSRSFGPRGSLDSIGSYRMSADFGRPSLDYENLNQTMSQANRYNDGENLVDRTLQPNPECRFAKDYWKNVKVGDIVRVHNNDEIPADMILLSTSDVDGACYVETKNLDGETNLKVR [...]
+
+>YDR205W MSC2 SGDID:S000002613, Chr IV from 859343-861517, Verified ORF, "Member of the cation diffusion facilitator family, localizes to the endoplasmic reticulum and nucleus; mutations affect the cellular distribution of zinc and also confer defects in meiotic recombination between homologous chromatids"
+MNLQELLAKVPLLLSYPTIILSSNLIVPSHNDLISRAASTSAAEYADEKLIFFSTDHAIRLIFLPTFVASSFNLFAHYFNFINYSSRRKYYVLFTAIYFLSILTAIFHPIQSTCITLLIIKLLTTADESSPKIALNFKTILKTFVPFITLTLVILRWDPSFDASSGDVNKISTSLAAYALLILTLRYASPLILSTLSSSIGVVSKDTSVAQHSISRNKRFPLILVLPIFSFVLLYLMTIVNKTYNIQLLMVFVFFGCLSIFFLSLKDLFTEDGNQKKGGQEDEYCRMFDIKYMISYLWLTRFTILLTGIMAIVVHFLSFNEITSSIKTDLLSLLFVVVAEYVSSFSNKQPDSHSHNHAHHHSHLTDSLPLENESMFKQMALNKDTRSIFSFLLLNTAFMFVQLLYSFRSKSLGLLSDSLHMALDCTSLLLGLIAGVLTKKPASDKFPFGLNYLGTLAGFTNGVLLLGIVCGIFVEAIERIFNPIHLHATNEL [...]
+
+>YDR399W HPT1 SGDID:S000002807, Chr IV from 1270060-1270725, Verified ORF, "Dimeric hypoxanthine-guanine phosphoribosyltransferase, catalyzes the formation of both inosine monophosphate and guanosine monophosphate; mutations in the human homolog HPRT1 can cause Lesch-Nyhan syndrome and Kelley-Seegmiller syndrome"
+MSANDKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYEDLNSVGSEVEEVGVKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQEHKQ
+
+>YEL027W CUP5 SGDID:S000000753, Chr V from 100769-101251, Verified ORF, "Proteolipid subunit of the vacuolar H(+)-ATPase V0 sector (subunit c; dicyclohexylcarbodiimide binding subunit); required for vacuolar acidification and important for copper and iron metal ion homeostasis"
+MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC
+
+>YER056C-A RPL34A SGDID:S000002135, Chr V from 270183-270147,269749-269421, reverse complement, Verified ORF, "Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl34Bp and has similarity to rat L34 ribosomal protein"
+MAQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIVKKVVKEQTEAAKKSEKKAKK
+
+>YFR053C HXK1 SGDID:S000001949, Chr VI from 255036-253579, reverse complement, Verified ORF, "Hexokinase isoenzyme 1, a cytosolic protein that catalyzes phosphorylation of glucose during glucose metabolism; expression is highest during growth on non-glucose carbon sources; glucose-induced repression involves the hexokinase Hxk2p"
+MVHLGPKKPQARKGSMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKKGGNIPMIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKLSGNHTFDTTQSKYKLPHDMRTTKHQEELWSFIADSLKDFMVEQELLNTKDTLPLGFTFSYPASQNKINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKRELPIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKLEGKLADDIPSNSPMAINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQAFEKMTSGYYLGELLRLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARIEDDPFENLEDTDDIFQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGIAAICQKRGYKTGHIAADGSVYNKYPGFKEAAAKGLRDIYGWTGDASKDPITIVPAEDGSGAGAAVIAALSEKRIAEGKSLGIIGA
+
+>YGL008C PMA1 SGDID:S000002976, Chr VII from 482671-479915, reverse complement, Verified ORF, "Plasma membrane H+-ATPase, pumps protons out of the cell; major regulator of cytoplasmic pH and plasma membrane potential; part of the P2 subgroup of cation-transporting ATPases"
+MTDTSSSSSSSSASSVSAHQPTQEKPAKTYDDAASESSDDDDIDALIEELQSNHGVDDEDSDNDGPVAAGEARPVPEEYLQTDPSYGLTSDEVLKRRKKYGLNQMADEKESLVVKFVMFFVGPIQFVMEAAAILAAGLSDWVDFGVICGLLMLNAGVGFVQEFQAGSIVDELKKTLANTAVVIRDGQLVEIPANEVVPGDILQLEDGTVIPTDGRIVTEDCFLQIDQSAITGESLAVDKHYGDQTFSSSTVKRGEGFMVVTATGDNTFVGRAAALVNKAAGGQGHFTEVLNGIGIILLVLVIATLLLVWTACFYRTNGIVRILRYTLGITIIGVPVGLPAVVTTTMAVGAAYLAKKQAIVQKLSAIESLAGVEILCSDKTGTLTKNKLSLHEPYTVEGVSPDDLMLTACLAASRKKKGLDAIDKAFLKSLKQYPKAKDALTKYKVLEFHPFDPVSKKVTAVVESPEGERIVCVKGAPLFVLKTVEEDHPIPE [...]
+>YGL009C LEU1 SGDID:S000002977, Chr VII from 478657-476318, reverse complement, Verified ORF, "Isopropylmalate isomerase, catalyzes the second step in the leucine biosynthesis pathway"
+MVYTPSKGPRTLYDKVFDAHVVHQDENGSFLLYIDRHLVHEVTSPQAFEGLENAGRKVRRVDCTLATVDHNIPTESRKNFKSLDTFIKQTDSRLQVKTLENNVKQFGVPYFGMSDARQGIVHTIGPEEGFTLPGTTVVCGDSHTSTHGAFGSLAFGIGTSEVEHVLATQTIIQAKSKNMRITVNGKLSPGITSKDLILYIIGLIGTAGGTGCVIEFAGEAIEALSMEARMSMCNMAIEAGARAGMIKPDETTFQYTKGRPLAPKGAEWEKAVAYWKTLKTDEGAKFDHEINIEAVDVIPTITWGTSPQDALPITGSVPDPKNVTDPIKKSGMERALAYMGLEPNTPLKSIKVDKVFIGSCTNGRIEDLRSAAAVVRGQKLASNIKLAMVVPGSGLVKKQAEAEGLDKIFQEAGFEWREAGCSICLGMNPDILDAYERCASTSNRNFEGRQGALSRTHLMSPAMAAAAGIAGHFVDIREFEYKDQDQSSPKVE [...]
+
+>YGL022W STT3 SGDID:S000002990, Chr VII from 452409-454565, Verified ORF, "Subunit of the oligosaccharyltransferase complex of the ER lumen, which catalyzes asparagine-linked glycosylation of newly synthesized proteins; forms a subcomplex with Ost3p and Ost4p and is directly involved in catalysis"
+MGSDRSCVLSVFQTILKLVIFVAIFGAAISSRLFAVIKFESIIHEFDPWFNYRATKYLVNNSFYKFLNWFDDRTWYPLGRVTGGTLYPGLMTTSAFIWHALRNWLGLPIDIRNVCVLFAPLFSGVTAWATYEFTKEIKDASAGLLAAGFIAIVPGYISRSVAGSYDNEAIAITLLMVTFMFWIKAQKTGSIMHATCAALFYFYMVSAWGGYVFITNLIPLHVFLLILMGRYSSKLYSAYTTWYAIGTVASMQIPFVGFLPIRSNDHMAALGVFGLIQIVAFGDFVKGQISTAKFKVIMMVSLFLILVLGVVGLSALTYMGLIAPWTGRFYSLWDTNYAKIHIPIIASVSEHQPVSWPAFFFDTHFLIWLFPAGVFLLFLDLKDEHVFVIAYSVLCSYFAGVMVRLMLTLTPVICVSAAVALSKIFDIYLDFKTSDRKYAIKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVVLPSQTPDGKLAL [...]
+
+>YGL026C TRP5 SGDID:S000002994, Chr VII from 448540-446417, reverse complement, Verified ORF, "Tryptophan synthase involved in tryptophan biosynthesis, regulated by the general control system of amino acid biosynthesis"
+MSEQLRQTFANAKKENRNALVTFMTAGYPTVKDTVPILKGFQDGGVDIIELGMPFSDPIADGPTIQLSNTVALQNGVTLPQTLEMVSQARNEGVTVPIILMGYYNPILNYGEERFIQDAAKAGANGFIIVDLPPEEALKVRNYINDNGLSLIPLVAPSTTDERLELLSHIADSFVYVVSRMGTTGVQSSVASDLDELISRVRKYTKDTPLAVGFGVSTREHFQSVGSVADGVVIGSKIVTLCGDAPEGKRYDVAKEYVQGILNGAKHKVLSKDEFFAFQKESLKSANVKKEILDEFDENHKHPIRFGDFGGQYVPEALHACLRELEKGFDEAVADPTFWEDFKSLYSYIGRPSSLHKAERLTEHCQGAQIWLKREDLNHTGSHKINNALAQVLLAKRLGKKNVIAETGAGQHGVATATACAKFGLTCTVFMGAEDVRRQALNVFRMRILGAKVIAVTNGTKTLRDATSEAFRFWVTNLKTTYYVVGSAIGPH [...]
+
+>YGL135W RPL1B SGDID:S000003103, Chr VII from 254646-255299, Verified ORF, "N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl1Ap and has similarity to E. coli L1 and rat L10a ribosomal proteins; rpl1a rpl1b double null mutation is lethal"
+MSKITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLVNQILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRLY
+
+>YGL245W GUS1 SGDID:S000003214, Chr VII from 39023-41149, Verified ORF, "Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm"
+MPSTLTINGKAPIVAYAELIAARIVNALAPNSIAIKLVDDKKAPAAKLDDATEDVFNKITSKFAAIFDNGDKEQVAKWVNLAQKELVIKNFAKLSQSLETLDSQLNLRTFILGGLKYSAADVACWGALRSNGMCGSIIKNKVDVNVSRWYTLLEMDPIFGEAHDFLSKSLLELKKSANVGKKKETHKANFEIDLPDAKMGEVVTRFPPEPSGYLHIGHAKAALLNQYFAQAYKGKLIIRFDDTNPSKEKEEFQDSILEDLDLLGIKGDRITYSSDYFQEMYDYCVQMIKDGKAYCDDTPTEKMREERMDGVASARRDRSVEENLRIFTEEMKNGTEEGLKNCVRAKIDYKALNKTLRDPVIYRCNLTPHHRTGSTWKIYPTYDFCVPIVDAIEGVTHALRTIEYRDRNAQYDWMLQALRLRKVHIWDFARINFVRTLLSKRKLQWMVDKDLVGNWDDPRFPTVRGVRRRGMTVEGLRNFVLSQGPSRNVINL [...]
+
+>YGR086C PIL1 SGDID:S000003318, Chr VII from 650621-649602, reverse complement, Verified ORF, "Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Lsp1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways"
+MHRTYSLRNSRAPTASQLQNPPPPPSTTKGRFFGKGGLAYSFRRSAAGAFGPELSRKLSQLVKIEKNVLRSMELTANERRDAAKQLSIWGLENDDDVSDITDKLGVLIYEVSELDDQFIDRYDQYRLTLKSIRDIEGSVQPSRDRKDKITDKIAYLKYKDPQSPKIEVLEQELVRAEAESLVAEAQLSNITRSKLRAAFNYQFDSIIEHSEKIALIAGYGKALLELLDDSPVTPGETRPAYDGYEASKQIIIDAESALNEWTLDSAQVKPTLSFKQDYEDFEPEEGEEEEEEDGQGRWSEDEQEDGQIEEPEQEEEGAVEEHEQVGHQQSESLPQQTTA
+
+>YGR157W CHO2 SGDID:S000003389, Chr VII from 802445-805054, Verified ORF, "Phosphatidylethanolamine methyltransferase (PEMT), catalyzes the first step in the conversion of phosphatidylethanolamine to phosphatidylcholine during the methylation pathway of phosphatidylcholine biosynthesis"
+MSSCKTTLSEMVGSVTKDRGTINVEARTRSSNVTFKPPVTHDMVRSLFDPTLKKSLLEKCIALAIISNFFICYWVFQRFGLQFTKYFFLVQYLFWRIAYNLGIGLVLHYQSHYETLTNCAKTHAIFSKIPQNKDANSNFSTNSNSFSEKFWNFIRKFCQYEIRSKMPKEYDLFAYPEEINVWLIFRQFVDLILMQDFVTYIIYVYLSIPYSWVQIFNWRSLLGVILILFNIWVKLDAHRVVKDYAWYWGDFFFLEESELIFDGVFNISPHPMYSIGYLGYYGLSLICNDYKVLLVSVFGHYSQFLFLKYVENPHIERTYGDGTDSDSQMNSRIDDLISKENYDYSRPLINMGLSFNNFNKLRFTDYFTIGTVAALMLGTIMNARFINLNYLFITVFVTKLVSWLFISTILYKQSQSKWFTRLFLENGYTQVYSYEQWQFIYNYYLVLTYTLMIIHTGLQIWSNFSNINNSQLIFGLILVALQTWCDKETRLA [...]
+
+>YGR192C TDH3 SGDID:S000003424, Chr VII from 883815-882817, reverse complement, Verified ORF, "Glyceraldehyde-3-phosphate dehydrogenase, isozyme 3, involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate; detected in the cytoplasm and cell-wall "
+MVRVAINGFGRIGRLVMRIALSRPNVEVVALNDPFITNDYAAYMFKYDSTHGRYAGEVSHDDKHIIVDGKKIATYQERDPANLPWGSSNVDIAIDSTGVFKELDTAQKHIDAGAKKVVITAPSSTAPMFVMGVNEEKYTSDLKIVSNASCTTNCLAPLAKVINDAFGIEEGLMTTVHSLTATQKTVDGPSHKDWRGGRTASGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTVDVSVVDLTVKLNKETTYDEIKKVVKAAAEGKLKGVLGYTEDAVVSSDFLGDSHSSIFDASAGIQLSPKFVKLVSWYDNEYGYSTRVVDLVEHVAKA
+
+>YHR021C RPS27B SGDID:S000001063, Chr VIII from 148662-148660,148109-147864, reverse complement, Verified ORF, "Protein component of the small (40S) ribosomal subunit; nearly identical to Rps27Ap and has similarity to rat S27 ribosomal protein"
+MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCSTVLCTPTGGKAKLSEGTSFRRK
+
+>YHR183W GND1 SGDID:S000001226, Chr VIII from 470960-472429, Verified ORF, "6-phosphogluconate dehydrogenase (decarboxylating), catalyzes an NADPH regenerating reaction in the pentose phosphate pathway; required for growth on D-glucono-delta-lactone and adaptation to oxidative stress"
+MSADFGLIGLAVMGQNLILNAADHGFTVCAYNRTQSKVDHFLANEAKGKSIIGATSIEDFISKLKRPRKVMLLVKAGAPVDALINQIVPLLEKGDIIIDGGNSHFPDSNRRYEELKKKGILFVGSGVSGGEEGARYGPSLMPGGSEEAWPHIKNIFQSISAKSDGEPCCEWVGPAGAGHYVKMVHNGIEYGDMQLICEAYDIMKRLGGFTDKEISDVFAKWNNGVLDSFLVEITRDILKFDDVDGKPLVEKIMDTAGQKGTGKWTAINALDLGMPVTLIGEAVFARCLSALKNERIRASKVLPGPEVPKDAVKDREQFVDDLEQALYASKIISYAQGFMLIREAAATYGWKLNNPAIALMWRGGCIIRSVFLGQITKAYREEPDLENLLFNKFFADAVTKAQSGWRKSIALATTYGIPTPAFSTALSFYDGYRSERLPANLLQAQRDYFGAHTFRVLPECASDNLPVDKDIHINWTGHGGNVSSSTYQA
+
+>YIL133C RPL16A SGDID:S000001395, Chr IX from 99416-99386,99095-98527, reverse complement, Verified ORF, "N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p"
+MSVEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVASANATAAESDVAKQLAALGY
+
+>YJR069C HAM1 SGDID:S000003830, Chr X from 569392-568799, reverse complement, Verified ORF, "Protein of unknown function that is involved in DNA repair; mutant is sensitive to the base analog, 6-N-hydroxylaminopurine, while gene disruption does not increase the rate of spontaneous mutagenesis"
+MSNNEIVFVTGNANKLKEVQSILTQEVDNNNKTIHLINEALDLEELQDTDLNAIALAKGKQAVAALGKGKPVFVEDTALRFDEFNGLPGAYIKWFLKSMGLEKIVKMLEPFENKNAEAVTTICFADSRGEYHFFQGITRGKIVPSRGPTTFGWDSIFEPFDSHGLTYAEMSKDAKNAISHRGKAFAQFKEYLYQNDF
+
+>YKL127W PGM1 SGDID:S000001610, Chr XI from 203185-204897, Verified ORF, "Phosphoglucomutase, minor isoform; catalyzes the conversion from glucose-1-phosphate to glucose-6-phosphate, which is a key step in hexose metabolism"
+MSLLIDSVPTVAYKDQKPGTSGLRKKTKVFMDEPHYTENFIQATMQSIPNGSEGTTLVVGGDGRFYNDVIMNKIAAVGAANGVRKLVIGQGGLLSTPAASHIIRTYEEKCTGGGIILTASHNPGGPENDLGIKYNLPNGGPAPESVTNAIWEASKKLTHYKIIKNFPKLNLNKLGKNQKYGPLLVDIIDPAKAYVQFLKEIFDFDLIKSFLAKQRKDKGWKLLFDSLNGITGPYGKAIFVDEFGLPAEEVLQNWHPLPDFGGLHPDPNLTYARTLVDRVDREKIAFGAASDGDGDRNMIYGYGPAFVSPGDSVAIIAEYAPEIPYFAKQGIYGLARSFPTSSAIDRVAAKKGLRCYEVPTGWKFFCALFDAKKLSICGEESFGTGSNHIREKDGLWAIIAWLNILAIYHRRNPEKEASIKTIQDEFWNEYGRTFFTRYDYEHIECEQAEKVVALLSEFVSRPNVCGSHFPADESLTVIDCGDFSYRDLDGSI [...]
+
+>YKL145W RPT1 SGDID:S000001628, Chr XI from 174218-175621, Verified ORF, "One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; required for optimal CDC20 transcription; interacts with Rpn12p and the E3 ubiquitin-protein ligase Ubr1p"
+MPPKEDWEKYKAPLEDDDKKPDDDKIVPLTEGDIQVLKSYGAAPYAAKLKQTENDLKDIEARIKEKAGVKESDTGLAPSHLWDIMGDRQRLGEEHPLQVARCTKIIKGNGESDETTTDNNNSGNSNSNSNQQSTDADEDDEDAKYVINLKQIAKFVVGLGERVSPTDIEEGMRVGVDRSKYNIELPLPPRIDPSVTMMTVEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATEKDFLKAVDKVISGYKKFSSTSRYMQYN
+>YKL145W-A YKL145W-A SGDID:S000028841, Chr XI from 174963-175055, Dubious ORF, "Dubious open reading frame, unlikely to encode a protein; completely overlaps the verified essential gene RPT1; identified by expression profiling and mass spectrometry"
+MGHLVLVRHYVLVLLLIELMQLLLGSLGLS
+
+>YLL024C SSA2 SGDID:S000003947, Chr XII from 97484-95565, reverse complement, Verified ORF, "ATP binding protein involved in protein folding and vacuolar import of proteins; member of heat shock protein 70 (HSP70) family; associated with the chaperonin-containing T-complex; present in the cytoplasm, vacuolar membrane and cell wall"
+MSKAVGIDLGTTYSCVAHFSNDRVDIIANDQGNRTTPSFVGFTDTERLIGDAAKNQAAMNPANTVFDAKRLIGRNFNDPEVQGDMKHFPFKLIDVDGKPQIQVEFKGETKNFTPEQISSMVLGKMKETAESYLGAKVNDAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKGKEEHVLIFDLGGGTFDVSLLSIEDGIFEVKATAGDTHLGGEDFDNRLVNHFIQEFKRKNKKDLSTNQRALRRLRTACERAKRTLSSSAQTSVEIDSLFEGIDFYTSITRARFEELCADLFRSTLDPVEKVLRDAKLDKSQVDEIVLVGGSTRIPKVQKLVTDYFNGKEPNRSINPDEAVAYGAAVQAAILTGDESSKTQDLLLLDVAPLSLGIETAGGVMTKLIPRNSTIPTKKSEVFSTYADNQPGVLIQVFEGERAKTKDNNLLGKFELSGIPPAPRGVPQIEVTFDVDSNGILNVSAVEKGT [...]
+
+>YLR043C TRX1 SGDID:S000004033, Chr XII from 232014-231703, reverse complement, Verified ORF, "Cytoplasmic thioredoxin isoenzyme of the thioredoxin system which protects cells against both oxidative and reductive stress, forms LMA1 complex with Pbi2p, acts as a cofactor for Tsa1p, required for ER-Golgi transport and vacuole inheritance"
+MVTQFKTASEFDSAIAQDKLVVVDFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIAANA
+
+>YLR058C SHM2 SGDID:S000004048, Chr XII from 259402-257993, reverse complement, Verified ORF, "Cytosolic serine hydroxymethyltransferase, involved in one-carbon metabolism"
+MPYTLSDAHHKLITSHLVDTDPEVDSIIKDEIERQKHSIDLIASENFTSTSVFDALGTPLSNKYSEGYPGARYYGGNEHIDRMEILCQQRALKAFHVTPDKWGVNVQTLSGSPANLQVYQAIMKPHERLMGLYLPDGGHLSHGYATENRKISAVSTYFESFPYRVNPETGIIDYDTLEKNAILYRPKVLVAGTSAYCRLIDYKRMREIADKCGAYLMVDMAHISGLIAAGVIPSPFEYADIVTTTTHKSLRGPRGAMIFFRRGVRSINPKTGKEVLYDLENPINFSVFPGHQGGPHNHTIAALATALKQAATPEFKEYQTQVLKNAKALESEFKNLGYRLVSNGTDSHMVLVSLREKGVDGARVEYICEKINIALNKNSIPGDKSALVPGGVRIGAPAMTTRGMGEEDFHRIVQYINKAVEFAQQVQQSLPKDACRLKDFKAKVDEGSDVLNTWKKEIYDWAGEYPLAV
+
+>YLR185W RPL37A SGDID:S000004175, Chr XII from 522665-522671,523031-523290, Verified ORF, "Protein component of the large (60S) ribosomal subunit, has similarity to Rpl37Bp and to rat L37 ribosomal protein"
+MGKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA
+
+>YLR249W YEF3 SGDID:S000004239, Chr XII from 636782-639916, Verified ORF, "Translational elongation factor, stimulates the binding of aminoacyl-tRNA (AA-tRNA) to ribosomes by releasing EF-1 alpha from the ribosomal complex; contains two ABC cassettes; binds and hydrolyses ATP"
+MSDSQQSIKVLEELFQKLSVATADNRHEIASEVASFLNGNIIEHDVPEHFFGELAKGIKDKKTAANAMQAVAHIANQSNLSPSVEPYIVQLVPAICTNAGNKDKEIQSVASETLISIVNAVNPVAIKALLPHLTNAIVETNKWQEKIAILAAISAMVDAAKDQVALRMPELIPVLSETMWDTKKEVKAAATAAMTKATETVDNKDIERFIPSLIQCIADPTEVPETVHLLGATTFVAEVTPATLSIMVPLLSRGLNERETGIKRKSAVIIDNMCKLVEDPQVIAPFLGKLLPGLKSNFATIADPEAREVTLRALKTLRRVGNVGEDDAIPEVSHAGDVSTTLQVVNELLKDETVAPRFKIVVEYIAAIGADLIDERIIDQQAWFTHITPYMTIFLHEKKAKDILDEFRKRAVDNIPVGPNFDDEEDEGEDLCNCEFSLAYGAKILLNKTQLRLKRARRYGICGPNGCGKSTLMRAIANGQVDGFPTQEECRT [...]
+
+>YLR298C YHC1 SGDID:S000004289, Chr XII from 725418-724723, reverse complement, Verified ORF, "Component of the U1 snRNP complex required for pre-mRNA splicing; putative ortholog of human U1C protein, which is involved in formation of a complex between U1 snRNP and the pre-mRNA 5' splice site"
+MTRYYCEYCHSYLTHDTLSVRKSHLVGKNHLRITADYYRNKARDIINKHNHKRRHIGKRGRKERENSSQNETLKVTCLSNKEKRHIMHVKKMNQKELAQTSIDTLKLLYDGSPGYSKVFVDANRFDIGDLVKASKLPQRANEKSAHHSFKQTSRSRDETCESNPFPRLNNPKKLEPPKILSQWSNTIPKTSIFYSVDILQTTIKESKKRMHSDGIRKPSSANGYKRRRYGN
+
+>YLR340W RPP0 SGDID:S000004332, Chr XII from 805887-806825, Verified ORF, "Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302"
+MGGIREKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKLLPFVKGNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRAVNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQVFPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLINNYKDLLAVAIAASYHYPEIEDLVDRIENPEKYAAAAPAATSAASGDAAPAEEAAAEEEEESDDDMGFGLFD
+
+>YLR371W ROM2 SGDID:S000004363, Chr XII from 862713-866783, Verified ORF, "GDP/GTP exchange protein (GEP) for Rho1p and Rho2p; mutations are synthetically lethal with mutations in rom1, which also encodes a GEP"
+MSETNVDSLGDRNDIYSQIFGVERRPDSFATFDSDSHGDISSQLLPNRIENIQNLNVLLSEDIANDIIIAKQRRRSGVEAAIDDSDIPNNEMKGKSSNYILSQQTNIKEVPDTQSLSSADNTPVSSPKKARDATSSHPIVHAKSMSHIYSTSNSASRQAKHYNDHPLPPMSPRNEVYQKNKSTTAFVPKRKPSLPQLALAGLKKQSSFSTGSASTTPTQARKSPLQGFGFFSRPSSKDLHEQHQHHQHIQHNNINNHNNNNTNNNGAHYQVGSSNSNYPQHSHSISSRSMSLNSSTLKNIASSFQSKTSNSRKATQKYDITSNPFSDPHHHHHHHHSSNSHSSLNNVHGSGNSSSVMGSSSNIGLGLKTRVSSTSLALKRYTSVSGTSLSSPRRSSMTPLSASRPVMSASSKKPQVYPALLSRVATKFKSSIQLGEHKKDGLVYRDAFTGQQAVDVICAIIRTSDRNLALLFGRSLDAQKLFHDVVYEHRLR [...]
+
+>YML092C PRE8 SGDID:S000004557, Chr XIII from 86739-85987, reverse complement, Verified ORF, "20S proteasome beta-type subunit"
+MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL
+
+>YMR073C YMR073C SGDID:S000004677, Chr XIII from 412872-412267, reverse complement, Uncharacterized ORF, "Putative protein of unknown function; proposed to be involved in resistance to carboplatin and cisplatin; shares similarity to a human cytochrome oxidoreductase"
+MSSDGMNRDVSNSKPNVRFAAPQRLSVAHPAISSPLHMPMSKSSRKPLVRTKIRLDPGHSALDWHSLTSNPANYYTKFVSLQLIQDLLDDPVFQKDNFKFSPSQLKNQLLVQKIPLYKIMPPLRINRKIVKKHCKGEDELWCVINGKVYDISSYLKFHPGGTDILIKHRNSDDLITYFNKYHQWVNYEKLLQVCFIGVVCE
+
+>YMR145C NDE1 SGDID:S000004753, Chr XIII from 556474-554792, reverse complement, Verified ORF, "Mitochondrial external NADH dehydrogenase, catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p are involved in providing the cytosolic NADH to the mitochondrial respiratory chain"
+MIRQSLMKTVWANSSRFSLQSKSGLVKYAKNRSFHAARNLLEDKKVILQKVAPTTGVVAKQSFFKRTGKFTLKALLYSALAGTAYVSYSLYREANPSTQVPQSDTFPNGSKRKTLVILGSGWGSVSLLKNLDTTLYNVVVVSPRNYFLFTPLLPSTPVGTIELKSIVEPVRTIARRSHGEVHYYEAEAYDVDPENKTIKVKSSAKNNDYDLDLKYDYLVVGVGAQPNTFGTPGVYEYSSFLKEISDAQEIRLKIMSSIEKAASLSPKDPERARLLSFVVVGGGPTGVEFAAELRDYVDQDLRKWMPELSKEIKVTLVEALPNILNMFDKYLVDYAQDLFKEEKIDLRLKTMVKKVDATTITAKTGDGDIENIPYGVLVWATGNAPREVSKNLMTKLEEQDSRRGLLIDNKLQLLGAKGSIFAIGDCTFHPGLFPTAQVAHQEGEYLAQYFKKAYKIDQLNWKMTHAKDDSEVARLKNQIVKTQSQIEDFKYN [...]
+
+>YMR235C RNA1 SGDID:S000004848, Chr XIII from 742734-741511, reverse complement, Verified ORF, "GTPase activating protein (GAP) for Gsp1p, involved in nuclear transport"
+MATLHFVPQHEEEQVYSISGKALKLTTSDDIKPYLEELAALKTCTKLDLSGNTIGTEASEALAKCIAENTQVRESLVEVNFADLYTSRLVDEVVDSLKFLLPVLLKCPHLEIVNLSDNAFGLRTIELLEDYIAHAVNIKHLILSNNGMGPFAGERIGKALFHLAQNKKAASKPFLETFICGRNRLENGSAVYLALGLKSHSEGLKVVKLYQNGIRPKGVATLIHYGLQYLKNLEILDLQDNTFTKHASLILAKALPTWKDSLFELNLNDCLLKTAGSDEVFKVFTEVKFPNLHVLKFEYNEMAQETIEVSFLPAMEKGNLPELEKLEINGNRLDEDSDALDLLQSKFDDLEVDDFEEVDSEDEEGEDEEDEDEDEKLEEIETERLEKELLEVQVDDLAERLAETEIK
+
+>YMR242C RPL20A SGDID:S000004855, Chr XIII from 754196-754178,753741-753224, reverse complement, Verified ORF, "Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Bp and has similarity to rat L18a ribosomal protein"
+MPQKWKMAHFKEYQVIGRRLPTESVPEPKLFRMRIFASNEVIAKSRYWYFLQKLHKVKKASGEIVSINQINEAHPTKVKNFGVWVRYDSRSGTHNMYKEIRDVSRVAAVETLYQDMAARHRARFRSIHILKVAEIEKTADVKRQYVKQFLTKDLKFPLPHRVQKSTKTFSYKRPSTFY
+
+>YMR303C ADH2 SGDID:S000004918, Chr XIII from 874336-873290, reverse complement, Verified ORF, "Glucose-repressible alcohol dehydrogenase II, catalyzes the conversion of ethanol to acetaldehyde; involved in the production of certain carboxylate esters; regulated by ADR1"
+MSIPETQKAIIFYESNGKLEHKDIPVPKPKPNELLINVKYSGVCHTDLHAWHGDWPLPTKLPLVGGHEGAGVVVGMGENVKGWKIGDYAGIKWLNGSCMACEYCELGNESNCPHADLSGYTHDGSFQEYATADAVQAAHIPQGTDLAEVAPILCAGITVYKALKSANLRAGHWAAISGAAGGLGSLAVQYAKAMGYRVLGIDGGPGKEELFTSLGGEVFIDFTKEKDIVSAVVKATNGGAHGIINVSVSEAAIEASTRYCRANGTVVLVGLPAGAKCSSDVFNHVVKSISIVGSYVGNRADTREALDFFARGLVKSPIKVVGLSSLPEIYEKMEKGQIAGRYVVDTSK
+
+>YMR309C NIP1 SGDID:S000004926, Chr XIII from 895425-892987, reverse complement, Verified ORF, "Subunit of the eukaryotic translation initiation factor 3 (eIF3), involved in the assembly of preinitiation complex and start codon selection"
+MSRFFSSNYEYDVASSSSEEDLLSSSEEDLLSSSSSESELDQESDDSFFNESESESEADVDSDDSDAKPYGPDWFKKSEFRKQGGGSNKFLKSSNYDSSDEESDEEDGKKVVKSAKEKLLDEMQDVYNKISQAENSDDWLTISNEFDLISRLLVRAQQQNWGTPNIFIKVVAQVEDAVNNTQQADLKNKAVARAYNTTKQRVKKVSRENEDSMAKFRNDPESFDKEPTADLDISANGFTISSSQGNDQAVQEDFFTRLQTIIDSRGKKTVNQQSLISTLEELLTVAEKPYEFIMAYLTLIPSRFDASANLSYQPIDQWKSSFNDISKLLSILDQTIDTYQVNEFADPIDFIEDEPKEDSDGVKRILGSIFSFVERLDDEFMKSLLNIDPHSSDYLIRLRDEQSIYNLILRTQLYFEATLKDEHDLERALTRPFVKRLDHIYYKSENLIKIMETAAWNIIPAQFKSKFTSKDQLDSADYVDNLIDGLSTILSK [...]
+
+>YNL166C BNI5 SGDID:S000005110, Chr XIV from 323567-322221, reverse complement, Verified ORF, "Protein involved in organization of septins at the mother-bud neck, may interact directly with the Cdc11p septin, localizes to bud neck in a septin-dependent manner"
+MGLDQDKIKKRLSQIEIDINQMNQMIDENLQLVEPAEDEAVEDNVKDTGVVDAVKVAETALFSGNDGADSNPGDSAQVEEHKTAQVHIPTENEANKSTDDPSQLSVTQPFIAKEQITHTAIAIGDSYNSFVANSAGNEKAKDSCTENKEDGTVNIDQNRGEADVEIIENNDDEWEDEKSDVEEGRVDKGTEENSEIESFKSPMPQNNTLGGENKLDAELVLDKFSSANKDLDIQPQTIVVGGDNEYNHESSRLADQTPHDDNSENCPNRSGGSTPLDSQTKIFIPKKNSKEDGTNINHFNSDGDGQKKMANFETRRPTNPFRVISVSSNSNSRNGSRKSSLNKYDSPVSSPITSASELGSIAKLEKRHDYLSMKCIKLQKEIDYLNKMNAQGSLSMEDGKRLHRAVVKLQEYLDKKTKEKYEVGVLLSRHLRKQIDRGENGQFWIGTK
+
+>YOR063W RPL3 SGDID:S000005589, Chr XV from 444688-445851, Verified ORF, "Protein component of the large (60S) ribosomal subunit, has similarity to E. coli L3 and rat L3 ribosomal proteins; involved in the replication and maintenance of killer double stranded RNA virus"
+MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL
+
+>YOR136W IDH2 SGDID:S000005662, Chr XV from 580251-581360, Verified ORF, "Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle"
+MLRNTFFRNTSRRFLATVKQPSIGRYTGKPNPSTGKYTVSFIEGDGIGPEISKSVKKIFSAANVPIEWESCDVSPIFVNGLTTIPDPAVQSITKNLVALKGPLATPIGKGHRSLNLTLRKTFGLFANVRPAKSIEGFKTTYENVDLVLIRENTEGEYSGIEHIVCPGVVQSIKLITRDASERVIRYAFEYARAIGRPRVIVVHKSTIQRLADGLFVNVAKELSKEYPDLTLETELIDNSVLKVVTNPSAYTDAVSVCPNLYGDILSDLNSGLSAGSLGLTPSANIGHKISIFEAVHGSAPDIAGQDKANPTALLLSSVMMLNHMGLTNHADQIQNAVLSTIASGPENRTGDLAGTATTSSFTEAVIKRL
+
+>YOR168W GLN4 SGDID:S000005694, Chr XV from 649304-651733, Verified ORF, "Glutamine tRNA synthetase, monomeric class I tRNA synthetase that catalyzes the specific glutaminylation of tRNA(Glu); N-terminal domain proposed to be involved in enzyme-tRNA interactions"
+MSSVEELTQLFSQVGFEDKKVKEIVKNKKVSDSLYKLIKETPSDYQWNKSTRALVHNLASFVKGTDLPKSELIVNGIINGDLKTSLQVDAAFKYVKANGEASTKMGMNENSGVGIEITEDQVRNYVMQYIQENKERILTERYKLVPGIFADVKNLKELKWADPRSFKPIIDQEVLKLLGPKDERDLIKKKTKNNEKKKTNSAKKSSDNSASSGPKRTMFNEGFLGDLHKVGENPQAYPELMKEHLEVTGGKVRTRFPPEPNGYLHIGHSKAIMVNFGYAKYHNGTCYLRFDDTNPEKEAPEYFESIKRMVSWLGFKPWKITYSSDYFDELYRLAEVLIKNGKAYVCHCTAEEIKRGRGIKEDGTPGGERYACKHRDQSIEQNLQEFRDMRDGKYKPGEAILRMKQDLNSPSPQMWDLIAYRVLNAPHPRTGTKWRIYPTYDFTHCLVDSMENITHSLCTTEFYLSRESYEWLCDQVHVFRPAQREYGRLNIT [...]
+
+>YOR267C HRK1 SGDID:S000005793, Chr XV from 824866-822587, reverse complement, Verified ORF, "Protein kinase implicated in activation of the plasma membrane H(+)-ATPase Pma1p in response to glucose metabolism; plays a role in ion homeostasis"
+MPNLLSRNPFHGHHNDHHHDRENSSNNPPQLIRSSKSFLNFIGRKQSNDSLRSEKSTDSMKSTTTTTNYTTTNLNNNTHSHSNATSISTNNYNNNYETNHHHNISHGLHDYTSPASPKQTHSMAELKRFFRPSVNKKLSMSQLRSKKHSTHSPPPSKSTSTVNLNNHYRAQHPHGFTDHYAHTQSAIPPSTDSILSLSNNINIYHDDCILAQKYGKLGKLLGSGAGGSVKVLVRPTDGATFAVKEFRPRKPNESVKEYAKKCTAEFCIGSTLHHPNVIETVDVFSDSKQNKYYEVMEYCPIDFFAVVMTGKMSRGEINCCLKQLTEGVKYLHSMGLAHRDLKLDNCVMTSQGILKLIDFGSAVVFRYPFEDGVTMAHGIVGSDPYLAPEVITSTKSYDPQCVDIWSIGIIYCCMVLKRFPWKAPRDSDDNFRLYCMPDDIEHDYVESARHHEELLKERKEKRQRFLNHSDCSAINQQQPAHESNLKTVQNQV [...]
+
+>YPL106C SSE1 SGDID:S000006027, Chr XVI from 352272-350191, reverse complement, Verified ORF, "ATPase that is a component of the heat shock protein Hsp90 chaperone complex; binds unfolded proteins; member of the heat shock protein 70 (HSP70) family; localized to the cytoplasm"
+MSTPFGLDLGNNNSVLAVARNRGIDIVVNEVSNRSTPSVVGFGPKNRYLGETGKNKQTSNIKNTVANLKRIIGLDYHHPDFEQESKHFTSKLVELDDKKTGAEVRFAGEKHVFSATQLAAMFIDKVKDTVKQDTKANITDVCIAVPPWYTEEQRYNIADAARIAGLNPVRIVNDVTAAGVSYGIFKTDLPEGEEKPRIVAFVDIGHSSYTCSIMAFKKGQLKVLGTACDKHFGGRDFDLAITEHFADEFKTKYKIDIRENPKAYNRILTAAEKLKKVLSANTNAPFSVESVMNDVDVSSQLSREELEELVKPLLERVTEPVTKALAQAKLSAEEVDFVEIIGGTTRIPTLKQSISEAFGKPLSTTLNQDEAIAKGAAFICAIHSPTLRVRPFKFEDIHPYSVSYSWDKQVEDEDHMEVFPAGSSFPSTKLITLNRTGDFSMAASYTDITQLPPNTPEQIANWEITGVQLPEGQDSVPVKLKLRCDPSGLHTI [...]
+
+>YPL215W CBP3 SGDID:S000006136, Chr XVI from 147415-148422, Verified ORF, "Mitochondrial protein required for assembly of ubiquinol cytochrome-c reductase complex (cytochrome bc1 complex); interacts with Cbp4p and function is partially redundant with that of Cbp4p"
+MMSVNRFTSGRLPVFLRKSPFYYSRAYLHQTCVFKQNKETAQDSPELLAKSSHLNSKPLDVSNKAPVKTAQNKIPLAHSKYESSKYELPKWKEALGELVIRAFHLDMDRVRAGPVAGSYYYKICKEQGLQYEDEPLSETAKYFYEDLKLPRTFSQWFQITVLHEWILFVRMRAMPFKYGRNYQQKLVDRTFSDIELRLFEEMKVNSGRIADQYLKDFNTQLRGAIFAYDEGFATDDGTLATAVWRNLFGGRKNIDMVHLESVVRYIYSQLYVLSRLSDREFATGKFKFVPPGVKVEKLTPKQEEELKAKTIAKYEALDKDPKTLPSERSRLSYTN
+
+>YPL266W DIM1 SGDID:S000006187, Chr XVI from 39121-40077, Verified ORF, "Essential 18S rRNA dimethylase, responsible for conserved m6(2)Am6(2)A dimethylation in 3'-terminal loop of 18 S rRNA, part of 90S and 40S pre-particles in nucleolus, involved in pre-ribosomal RNA processing"
+MGKAAKKKYSGATSSKQVSAEKHLSSVFKFNTDLGQHILKNPLVAQGIVDKAQIRPSDVVLEVGPGTGNLTVRILEQAKNVVAVEMDPRMAAELTKRVRGTPVEKKLEIMLGDFMKTELPYFDICISNTPYQISSPLVFKLINQPRPPRVSILMFQREFALRLLARPGDSLYCRLSANVQMWANVTHIMKVGKNNFRPPPQVESSVVRLEIKNPRPQVDYNEWDGLLRIVFVRKNRTISAGFKSTTVMDILEKNYKTFLAMNNEMVDDTKGSMHDVVKEKIDTVLKETDLGDKRAGKCDQNDFLRLLYAFHQVGIHFS
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/target.sqt b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/target.sqt
new file mode 100644
index 0000000..3c4e472
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/example-files/target.sqt
@@ -0,0 +1,33 @@
+H SQTGenerator Crux
+H SQTGeneratorVersion 1.0
+H Comment Crux was written by...
+H Comment ref...
+H StartTime Tue Dec 2 15:22:50 2008
+H EndTime
+H Database test_crux_index/test-binary-fasta
+H DBSeqLength ?
+H DBLocusCount 4
+H PrecursorMasses average
+H FragmentMasses mono
+H Alg-PreMasTol 3.0
+H Alg-FragMassTol 0.50
+H Alg-XCorrMode 0
+H Comment preliminary algorithm sp
+H Comment final algorithm xcorr
+H StaticMod C=160.139
+H Alg-DisplayTop 5
+H EnzymeSpec tryptic
+H Line fields: S, scan number, scan number,charge, 0, precursor m/z, 0, 0, number of matches
+H Line fields: M, rank by xcorr score, rank by sp score, peptide mass, deltaCn, xcorr score, sp score, number ions matched, total ions compared, sequence
+S 14 14 2 0.00 server 500.41 0.00 0.00 1
+M 1 1 1001.15 0.00 0.29 98.43 6 14 K.FHLELSQK.D U
+L gi|6381999|ref|NP_009311.2|
+S 14 14 3 0.00 server 500.41 0.00 0.00 1
+M 1 1 1495.81 0.00 -0.09 55.08 8 44 R.VMFTTFYMITNK.Y U
+L gi|6382000|ref|NP_009314.2|
+S 15 15 2 0.00 server 488.82 0.00 0.00 1
+M 1 1 973.09 0.00 -0.10 0.00 0 16 K.SGATAYIYK.A U
+L gi|6381999|ref|NP_009311.2|
+S 15 15 3 0.00 server 488.82 0.00 0.00 1
+M 1 1 1464.81 0.00 0.13 15.58 5 44 K.QYLLLNIAYLLK.L U
+L gi|6381999|ref|NP_009311.2|
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/extract-columns.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/extract-columns.html
new file mode 100644
index 0000000..0d799f5
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/extract-columns.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>extract-columns</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>extract-columns</h1>
+<h2>Usage:</h2>
+<p><code>crux extract-columns [options] <tsv file> <column names></code></p>
+<h2>Description:</h2>
+<p>Given a tab-delimited file and a comma-delimited list of column names, extract the requested columns.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tsv file</code> – A tab-delimited file, with column headers in the first row. Use "-" to read from standard input.</li>
+ <li><code>column names</code> – A comma-delimited list of column names.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – the requested columns in tab-delimited format. The columns are printed in the same order that they appear in the input column list.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--delimiter <string></code> – Specify the input and output delimiter to use when processing the delimited file. The argument can be either a single character or the keyword 'tab.' Default = <code>tab</code>.</li>
+ <li class="nobullet"><code>--header T|F</code> – Print the header line of the file, in addition to the columns that match. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/extract-rows.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/extract-rows.html
new file mode 100644
index 0000000..033c1f9
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/extract-rows.html
@@ -0,0 +1,134 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>extract-rows</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>extract-rows</h1>
+<h2>Usage:</h2>
+<p><code>crux extract-rows [options] <tsv file> <column name> <column value></code></p>
+<h2>Description:</h2>
+Given a tab-delimited file, a column name and a column cell value, extract the rows that have the matching values for that column.
+<h2>Input:</h2>
+<ul>
+ <li><code>tsv file</code> – A tab-delimited file, with column headers in the first row. Use "-" to read from standard input.</li>
+ <li><code>column name</code> – A column name.</li>
+ <li><code>column value</code> – A cell value for a column.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – the rows for which the value observed in the specified column of the input file match the <column value> given on the command line.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--delimiter <string></code> – Specify the input and output delimiter to use when processing the delimited file. The argument can be either a single character or the keyword 'tab.' Default = <code>tab</code>.</li>
+ <li class="nobullet"><code>--header T|F</code> – Print the header line of the file, in addition to the columns that match. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--comparison eq|gt|gte|lt|lte|neq</code> – Specify the operator that is used to compare an entry in the specified column to the value given on the command line. Legal values are as follows:<ul><li>eq – The two values are equal</li><li>lt – The file value is less than the argument value</li><li>lte – The file value is less than or equal to the argument value</li><li>gt – The file value is greater than the argument value</li><li>gt [...]
+ <li class="nobullet"><code>--column-type int|real|string</code> – Specifies the data type of the column, either an integer (int), a floating point number (real), or a string. Default = <code>string</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
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+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux FAQs</title>
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+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Crux Frequently Asked Questions</h2>
+
+ <ol>
+
+ <li>
+ <b>What is the difference between Tide and Comet?</b></li>
+
+ <p>
+ The differences are as follows:
+ <ul>
+ <li>
+ Tide converts your FASTA file to an index (either as part
+ of <code>tide-search</code> or by using <code>tide-index</code>),
+ whereas Comet does searching directly from the FASTA file. The
+ indexing step allows Tide to pre-compute many parts of the search
+ procedure, thereby making the search faster.
+ <li>
+ Comet is multi-threaded, whereas Tide runs on a single thread. On
+ multi-threaded CPUs, this feature can offset the speed difference
+ between Comet and Tide.</li>
+ <li>
+ For each match, Comet reports the <i>total</i> number of candidate
+ peptides, whereas Tide reports the number of <i>distinct</i> candidate
+ peptides.</li>
+ <li>
+ Comet provides an option to report an E-value in addition to the raw
+ XCorr score, whereas Tide provides an option to report a p-value. The
+ methods for computing these two statistical confidence measures are
+ quite different.</li>
+ <li>
+ Some options are available only in Comet (various options related to
+ different types of theoretical fragment ions, max_fragment_charge,
+ nucleotide_reading_frame, etc.) whereas others are only available in
+ Tide (e.g., keep-terminal-aminos).</li>
+ </ul></p>
+
+ <p>
+ Overall, for a given set of spectra, the XCorr scores computed by
+ Comet and by Tide should be quite similar to one another, assuming
+ that the various search parameters are set similarly between the two
+ algorithms. Below is a table summarizing the correspondence between
+ the two sets of parameters. The specified values will yield nearly
+ identical XCorr scores from the two search engines.</p>
+
+ <table border="1">
+ <tr>
+ <td>
+ <b>Tide parameter</b></td>
+ <td>
+ <b>Tide value</b></td>
+ <td>
+ <b>Comet parameter</b></td>
+ <td>
+ <b>Comet value</b></td>
+ </tr>
+
+ <tr>
+ <td>
+ enzyme</td>
+ <td>
+ trypsin</td>
+ <td>
+ search_enzyme_number</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ digestion</td>
+ <td>
+ full-digest</td>
+ <td>
+ num_enzyme_termini</td>
+ <td>
+ 2</td>
+ </tr>
+
+ <tr>
+ <td>
+ missed-cleavages</td>
+ <td>
+ 0</td>
+ <td>
+ allowed_missed_cleavage</td>
+ <td>
+ 0</td>
+ </tr>
+
+ <tr>
+ <td>
+ min-peaks</td>
+ <td>
+ 10</td>
+ <td>
+ minimum_peaks</td>
+ <td>
+ 10</td>
+ </tr>
+
+ <tr>
+ <td>
+ precursor-window</td>
+ <td>
+ 3</td>
+ <td>
+ peptide_mass_tolerance</td>
+ <td>
+ 3</td>
+ </tr>
+
+ <tr>
+ <td>
+ precursor-window-type</td>
+ <td>
+ mass</td>
+ <td>
+ peptide_mass_units</td>
+ <td>
+ 0</td>
+ </tr>
+
+ <tr>
+ <td>
+ fragment-mass</td>
+ <td>
+ mono</td>
+ <td>
+ mass_type_fragment</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ decoy-format</td>
+ <td>
+ peptide-reverse</td>
+ <td>
+ N/A</td>
+ <td>
+ </td>
+ </tr>
+
+ <tr>
+ <td>
+ keep-terminal-aminos</td>
+ <td>
+ C</td>
+ <td>
+ N/A</td>
+ <td>
+ </td>
+ </tr>
+
+ <tr>
+ <td>
+ concat</td>
+ <td>
+ T</td>
+ <td>
+ decoy_search</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ top-match</td>
+ <td>
+ 5</td>
+ <td>
+ num_results, num_output_lines</td>
+ <td>
+ 6, 5</td>
+ </tr>
+
+ <tr>
+ <td>
+ remove-precursor-peak</td>
+ <td>
+ T</td>
+ <td>
+ remove_precursor_peak</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ remove-precursor-tolerance</td>
+ <td>
+ 15</td>
+ <td>
+ remove_precursor_tolerance</td>
+ <td>
+ 15</td>
+ </tr>
+
+ <tr>
+ <td>
+ use-flanking-peaks</td>
+ <td>
+ F</td>
+ <td>
+ theoretical_fragment_ions</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ use-neutral-loss-peaks</td>
+ <td>
+ F</td>
+ <td>
+ use_NL_ions</td>
+ <td>
+ F</td>
+ </tr>
+
+ <tr>
+ <td>
+ mz-bin-width</td>
+ <td>
+ 1.0005079</td>
+ <td>
+ fragment_bin_tol</td>
+ <td>
+ 1.0005079</td>
+ </tr>
+
+ <tr>
+ <td>
+ mz-bin-offset</td>
+ <td>
+ 0.4</td>
+ <td>
+ fragment_bin_offset</td>
+ <td>
+ 0.4</td>
+ </tr>
+
+ <tr>
+ <td>
+ min-mass, max-mass</td>
+ <td>
+ 200, 7200</td>
+ <td>
+ digest_mass_range</td>
+ <td>
+ 200 7200</td>
+ </tr>
+
+ <tr>
+ <td>
+ N/A</td>
+ <td>
+ </td>
+ <td>
+ max_fragment_charge</td>
+ <td>
+ 2</td>
+ </tr>
+
+ </table>
+
+ <p>
+ Here is a scatter plot of XCorr scores from a search run with the
+ parameters listed above:</p>
+
+ <img src="images/stored-xcorr.png">
+
+
+ <li>
+ <b>What operating systems does Crux work with?</b></li>
+
+ <p>
+ Crux is written in C++, so in principle it should work on virtually
+ any modern operating system. We provide pre-compiled binaries for
+ Linux, MacOS and Windows.</p>
+
+ <li>
+ <b>How does Crux compute the masses of peptides and peptide
+ fragments?</b></li>
+
+ <p>
+ <ul>
+
+ <li>
+ Each amino acid can be characterized either by its monoisotopic mass,
+ which is the mass of the most abundant isotopic form of that amino acid,
+ or the average mass, which is a weighted average of the masses of all
+ the isotopic forms. By default, Crux uses average mass to calculate
+ peptide masses, though this behavior can be controlled by the
+ <code>isotopic-mass</code> option to <code>tide-index</code> and the
+ <code>mass_type_parent</code> option to <code>comet</code>. For
+ fragments, <code>tide-search</code> always uses the monoisotopic mass,
+ whereas <code>comet</code> allows selection
+ via <code>mass_type_fragment</code>.</li>
+
+ <li>
+ The neutral mass of a peptide is not the sum of the masses of its
+ amino acids. The N-terminus and C-terminus of the peptide together
+ contribute an additional water molecule, whose mass is either
+ 18.010564684 Da (monoisotopic) or 18.0153 Da (average).</li>
+ <li>
+ A charged peptide has an additional approximately 1 Da mass for each
+ charge, corresponding to the mass of a hydrogen atom. The exact mass
+ to be added depends on whether we are using the monoisotopic mass
+ (1.007825035) or average mass (1.00794).</li>
+
+ <li>When a peptide fragments, each b-ion will have a mass equal to
+ the sum of its amino acids plus one hydrogen for each charge on the
+ fragment, while each y-ion will have a mass equal to the sum of its
+ amino acids plus water plus one hydrogen for each charge on the
+ fragment.</li>
+
+ <li>
+ By default, both Tide and Comet add a static modification of
+ 57.021464 Da to all cysteines. This is because in most protein
+ preparation protocols the peptides are alkylated with iodoacetamide,
+ resulting in carbamidomethylation of cysteine. The alkylation step
+ prevents the reformation of disulfide bonds. Other alykylation
+ reagents may be used, in which case the appropriate mass shift can be
+ specified with the <code>C=[mass]</code> option
+ to <code>tide-index</code> or the <code>add_C_cysteine</code> option
+ to <code>comet</code>.</li>
+
+ </ul>
+ </p>
+
+ <li>
+ <b>How does Crux assign fragment masses to bins prior to computing
+ the XCorr score?</b>
+ </li>
+
+ <p>The XCorr score is essentially a dot product between a preprocessed
+ form of the observed spectrum and the theoretical spectrum derived
+ from the candidate peptide. In order to compute this dot product, the
+ masses of the fragments in both spectra are assigned to discrete mass
+ bins. This can be viewed as a form of rounding, but with more control
+ over the discrete masses. Two parameters, <code>mz-bin-width</code> and
+ <code>mz-bin-offset</code>, control the size and location of the bins,
+ and are used to convert fragment masses according to this formula:</p>
+
+ <p align=center>binned mass = floor( ( original mass / <code>bin-width</code> ) + 1.0 - <code>bin-offset</code> )</p>
+
+ <p>
+ The default values <code>bin-width</code>=1.0005079
+ and <code>bin-offset</code>=0.40 are suitable for most low-resolution
+ datasets.
+ </p>
+
+ <li>
+ <b>How does Crux estimate the possible charge states of the peptides when the
+ information is not provided within the spectra file?</b>
+ </li>
+
+ <p>
+ Crux calculates the ratio of two values: (1) the sum of the
+ intensities from the peaks in the fragmentation spectrum whose m/z is
+ greater than the precursor m/z versus (2) the sum of the peaks whose
+ m/z is smaller than the precursor. If this ratio is greater than or
+ equal to a calculated threshold based upon the location of the
+ precursor m/z and the max m/z in the spectrum, Crux then assigns both
+ +2 and +3 as possible charge states to the spectrum. Otherwise, Crux
+ assigns +1 as the charge state. The algorithm is based upon the
+ observation that fragmentation spectra collected from +1 peptides
+ should have no peaks above the precursor m/z. In contrast, a peptide
+ of charge state greater than +1 can generate fragment ions of lower
+ charge whose m/z is greater than the precursor m/z, thus indicating a
+ multiply charged precursor.</p>
+
+ <p>
+ Note that, in addition, <code>comet</code> includes
+ a <code>precursor_charge</code> parameter. If the first number in
+ this parameter is set to 0, i.e., <code>precursor_charge = 0 0</code>,
+ then the charge state rule above is applied. However, if a user
+ specifies a precursor charge range, i.e., <code>precursor_charge = 1
+ 5</code>, then Comet will search every spectrum through this range of
+ assumed charge states for every spectrum whose precursor charge
+ is unknown.</p>
+
+ <li>
+ <b>How does Crux create peptides from the given set of proteins in the
+ database?</b></li>
+
+ <p>
+ The options <code>enzyme</code> (for <code>tide-index</code>)
+ and <code>search_enzyme_number</code> (for <code>comet</code>) define
+ the enzymatic cleavage rules. When <code>enzyme=no-enzyme</code>
+ or <code>search_enzyme_number=0</code>, then any subsequence of a
+ protein may be considered as a candidate peptide. For other values of
+ these parameters, the residues at the termini of the protein
+ subsequence must follow specific rules. For example, trypsin requires
+ that the preceeding residue must be an R or K and the following
+ residue may not be a P.</p>
+
+ <p>
+ When <code>digestion=full-digest</code> (for <code>tide-index</code>)
+ or <code>num_enzyme_termini=2</code> (for <code>comet</code>), then
+ these rules must be true at both ends of the peptide. When it
+ is <code>digestion=partial-digest</code>
+ or <code>num_enzyme_termini=1</code>, then the rules must be true at
+ at least one of the ends. The <code>missed-cleavages</code>
+ and <code>allowed_missed_cleavages</code> parameters control the
+ maximum number of cleavage sites that may lie within the peptide
+ sequence.</p>
+
+ <p>
+ Note that if <code>enzyme=no-enzyme</code>
+ or <code>search_enzyme_number=0</code>, then
+ the <code>digestion</code>, <code>num_enzyme_termini</code>, <code>missed-cleavages</code>
+ and <code>allowed_missed_cleaveages</code> parameters are not used.</p>
+
+
+ <li>
+ <b>How does Crux select candidate peptides from the database?</b></li>
+
+ <p>
+ The Crux search tools (<code>tide-index</code> and <code>comet</code>)
+ select candidate peptides for each spectrum based on its precursor
+ singly charged mass (m+h) or the mass-to-charge (m/z) and an assumed
+ charge state (specified in the input file). If the m+h and charge is
+ provided in the input file (e.g., from the Z lines of an MS2 file),
+ then the precursor mass is calculated from the m+h minus the mass of a
+ proton. Otherwise, the precursor mass is calculated from the precursor
+ m/z and an assumed charge. A mass window is defined in one of three
+ ways based on the
+ <code>precursor-window-type</code> and <code>precursor-window</code>
+ options.</p>
+
+ <ul>
+ <li>
+ If the <code>precursor-window-type</code> is set to <code>mz</code>,
+ then the window is calculated as spectrum precursor m/z ±
+ <code>precursor-window</code> and the resulting range is converted
+ to mass using the charge state with the formula:<br>
+ Mass=m/z * charge - MASS_PROTON * charge, where MASS_PROTON=1.00727646677
+ </li>
+
+ <li>
+ If the <code>precursor-window-type</code> is set to <code>mass</code>, then
+ the window is defined as the precursor mass ±
+ <code>precursor-window</code>.
+ </li>
+
+ <li>
+ If the <code>precursor-window-type</code> is set to <code>ppm</code>
+ (parts per million), then the window spans from the precursor mass /
+ (1.0 + window * 1e-6) to precursor mass / (1.0 - window * 1e-6).</li>
+ </ul>
+
+ <p>
+ Candidate peptides are those whose mass falls within the defined
+ window. The peptide mass is computed as the sum of the average amino
+ acid masses plus 18 Da for the terminal OH group. Candidate peptides
+ can also be constrained by minimum and maximum allowed length. </p>
+
+ <li>
+ <b>How can I search my ITRAQ data?</b></li>
+
+ <p>
+ ITRAQ and other tagged seaches can be done by using terninal
+ modifications. For example, if your tag has a mass of 304.199040, add
+ these lines to your parameter file:
+ <pre>
+nmod=304.199040:-1
+cmod=304.199040:-1
+ </pre>
+ <p>
+ Crux will then generate peptides with this modification (+304.199904)
+ on the n-terminus, the c-terminus and on both termini. The -1 in the
+ option means to add the modification regardless of where the peptide
+ terminus lies relative to the rest of the protein.
+
+ <li>
+ <b>What happens if I decrease the size of the precursor window during
+ searching?</b></li>
+
+ <p>
+ Reducing the precursor mass tolerance has two main benefits. One is
+ reduced search time, and the other is improved statistical power to
+ detect matches. With a smaller window, fewer candidates are tested
+ against a spectrum. As a result, the statistical confidence measure
+ calculated after multiple testing correction will be more significant.
+ Of course, the flipside is that if you make the precursor window too
+ small, then you may end up throwing out correct identifications.
+ Control over the size of the window is provided by the using
+ the <code>precursor-window</code> and
+ <code>precursor-window-type</code> options.</p>
+
+ <li>
+ <b>How can I run many jobs in parallel?</b>
+
+
+ <p>
+ In combination with GNU parallel, parallelization of Crux can be
+ achieved rather painlessly. For example, to run tide-search on a set
+ of spectrum files, you can just get your spectra files into a filelist:</p>
+
+ <pre>
+find . -name "*.mzXML" > file.list
+ </pre>
+
+ <p>
+ Then, with a bit of bash magic, run parallel as follows (assuming
+ there are 100 files in file.list):</p>
+
+ <pre>
+parallel --xapply crux tide-search <options> --fileroot {1} {2} database.db ::: $(seq 1 100) ::: $(cat file.list)
+ </pre>
+
+ <p>
+ <i>Thanks to Ben Temperton for this answer.</i></p>
+
+ <li>
+ <b>How can I contribute to Crux?</b></li>
+
+ <p>
+ Patches implementing new features can be emailed to the development
+ team at crux-support at uw.edu for review and inclusion in subsequent
+ releases of Crux.</p>
+
+ <li>
+ <b>Where does the name "Crux" come from?</b></li>
+
+ <p>
+ Thin air. The name is not an acronym or a reference to anything in
+ particular.</p>
+
+ </ol>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/barista-xml-format.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/barista-xml-format.html
new file mode 100644
index 0000000..5e007d9
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/barista-xml-format.html
@@ -0,0 +1,249 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>barista.xml </h2>
+ <p>
+ The barista.xml is an XML files that used to record four main
+ parts:
+ </p>
+ <pre>
+< proteins > ... < /proteins >
+< subset_proteins > ... < /subset_proteins >
+< peptides > ... < /peptides >
+< psms > ... < /psms >
+ </pre>
+ <p>
+ <ol>
+ <li>
+ <b>Proteins:</b>contains the ranked list of groups of indistinguishable
+ target proteins. Each protein entry includes the following fields:
+ <ol>
+ <li>
+ <b>protein group:</b> a number that identifies a group. </li>
+ <li>
+ <b>q-value: </b>The minimal protein-level false discovery rate at which this
+ protein is deemed significant. This q-value is computed based on the
+ ranking of the proteins induced by the Barista score.</li>
+ <li>
+ <b>score:</b> The score assigned to the proteins by Barista. Higher values
+ correspond to more confident identifications.</code>
+ <li>
+ <b>protein_ids:</b> proteins in the protein group. </li>
+ <li>
+ <b>alternative_peptide_id: </b>peptides are considered indistinguishable if
+ they have identical amino acid sequences or they differ only by I/L or
+ T/S in the same position in the peptide. If the peptides shared by the
+ group are not identical, they are listed immediately after the
+ proteins they belong to. </li>
+ <li><b>
+ peptide_ids:</b> belong to each of the proteins in the
+ group.</li>
+ </ol>
+
+ <br>
+ For example, suppose that
+ <dl>
+ <dd> <b> protein_a </b> has peptide <b> KLEAEVEALKK </b>       // 'L' in second position </dd>
+ <dd> and peptide <b> VLGAK </b> </dd>
+ <dd> <b> protein_b </b> has peptide <b> KIEAEVEALKK </b>       // 'I' in second position
+ <dd> and peptide <b> VLGAK </b> </dd>
+ </dl>
+
+ <br>
+ Then the xml entry could look like this <br />
+ <pre>
+< proteins >
+< q_value > 0 < /q_value >
+< score > 8.9 > < /score >
+< protein_group group_id="1" >
+< protein_ids >
+< protein_id > protein_a < /protein_id >
+< alternative_peptide_id > KLEAEVEALKK < /alternative_peptide_id >
+< protein_id > protein_b < /protein_id >
+< alternative_peptide_id > KIEAEVEALKK < /alternative_peptide_id >
+< /protein_ids >
+< peptide_ids >
+< peptide_id > VLGAK < /peptide_id >
+< /peptide_ids >
+< /protein_group >
+< /proteins >
+ </pre>
+ </li>
+ </p>
+ <li>
+ <p>
+ <b>Subset proteins</b> contains groups of indistinguishable proteins, which
+ constitute a subset of some group in the proteins section in
+ terms of the peptides identified in these proteins. Each entry includes
+ <ol>
+ <li>
+ group id and parent group id: the identifier of the group and the
+ identifier of the protein group which has the superset of the peptide
+ set belonging the current group
+ </li>
+ <li>
+ protein_ids : proteins that belong to the group
+ </li>
+ <li>
+ peptide_ids: peptides that belong to the proteins in the group.
+ </li>
+ </ol>
+ </li>
+ </p>
+ <li>
+ <p>
+ <b>Peptides</b> contains a ranked list of target peptides. Each peptide entry
+ includes:
+ <ol>
+ <li>
+ peptide: Peptide amino acid sequence.
+ <li>
+ q-value: The minimal peptide-level false discovery rate at which this
+ peptide is deemed significant. This q-value is computed based on the
+ ranking of the peptides induced by the Barista score.</li>
+ <li>
+ score: The score assigned to the peptide by Barista. Higher values
+ correspond to more confident identifications.</li>
+ <li>
+ main_psm_id: The PSM identifier based on which the peptide received
+ its score. A peptide score is the maximum over all the PSMs that
+ contain this peptide. </li>
+ <li>
+ psm_ids: The identifiers of all the PMS that contain this peptide .</li>
+ <li>
+ protein_ids: All the proteins that contain this peptide and were
+ infered based on some PSMs from the database search. </li>
+ </ol>
+
+ </li>
+ </p>
+ <li>
+ <p>
+ <b>PSMs</b> contains ranked list of target peptide-spectrum matches. The
+ following columns are included:
+ <ol>
+ <li>
+ psm_id: PSM identifier. </li>
+ <li>
+ q-value: The minimal PSM-level false discovery rate at which this PSM
+ is deemed significant. This q-value is computed based on the ranking
+ of the PSMs induced by the Barista score.</li>
+ <li>
+ score: The score assigned to the PSM by Barista. Higher values
+ correspond to more confident identifications.</code>
+ <li>
+ scan: the scan number</li>
+ <li>
+ charge: the inferred charge state</li>
+ <li>
+ precursor_mass: precrusor mass as recorded during the MS1 scan </li>
+ <li>
+ peptide: the peptide sequence</li>
+ <li>
+ filename: name of the file in which the PSM appears</li>
+ </ol>
+ </p>
+ </ol>
+ </li>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/fasta-format.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/fasta-format.html
new file mode 100644
index 0000000..13cb395
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/fasta-format.html
@@ -0,0 +1,169 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <H2>FASTA file format</H2>
+
+ <p>
+ Crux searches protein sequence databases given in FASTA format. The
+ format is very simple. Every entry consists of a sequence identifier
+ (ID), an optional comment (COMMENT), and a sequence (SEQUENCE). The
+ format looks like this:
+ </p>
+
+ <pre>
+>ID COMMENT
+SEQUENCE
+ </pre>
+
+ <p>
+ The special character ">" marks the beginning of a new sequence.
+ The ">" character is followed immediately by the sequence
+ identifier. The rest of that line is occupied by the optional
+ comment. Subsequent lines contain the sequence itself.
+ </p>
+
+ <p>Some rules about representing sequences:</p>
+
+ <ul style="padding:0; font-size:14px;">
+
+ <li>
+ A single protein sequence can span multiple lines. The > character
+ occurring at the beginning of the line indicates the end of the
+ sequence.</li>
+
+ <li>
+ Case doesn't matter. Crux Suite converts everything to uppercase.</li>
+
+ <li>
+ White space (spaces and newlines) within the sequence are
+ ignored.</li>
+
+ <li>
+ Characters should be from the amino acid alphabet, which contains
+ twenty characters for amino acids ("ACDEFGHIKLMNPQRSTVWY") and is
+ augmented by four more ambiguous characters ("BUXZ"):</li>
+
+ <pre>
+A alanine P proline
+B aspartate or asparagine Q glutamine
+C cystine R arginine
+D aspartate S serine
+E glutamate T threonine
+F phenylalanine U any
+G glycine V valine
+H histidine W tryptophan
+I isoleucine Y tyrosine
+K lysine Z glutamate or glutamine
+L leucine X any
+M methionine
+N asparagine
+ </pre>
+
+ </ul>
+
+ <p>
+ <a href="sample.fasta">Here</a> is an example of three sequences in
+ FASTA format.</p>
+
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/features.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/features.html
new file mode 100644
index 0000000..eb81b6a
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/features.html
@@ -0,0 +1,398 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <div id="content">
+ <h2>Features used by percolator and q-ranker</h2>
+
+ <p>
+ Following is a list of the features used by the <span class="code">crux
+ percolator</span> and <span class="code">crux q-ranker</span> commands to represent
+ each peptide-spectrum match (PSM).</p>
+
+
+ <table border="1" align="center" id="featurestable">
+ <tr>
+ <!--table header-->
+ <th>Number</th>
+ <th>Name</th>
+ <th>Type</th>
+ <th>Description</th>
+ <th>Percolator</th>
+ <th>q-ranker</th>
+ <th>barista</th>
+ </tr>
+ <!--tr backgoud(grey)"#DEDEDE"-->
+ <!--check mark : "✓" or "✔, not supported use: -->
+
+ <tr bgcolor="#DEDEDE" >
+ <td>1</td>
+ <td><code>lnrSp</code></td>
+ <td>Float</td>
+ <td>The natural logarithm of the rank of the match
+ based on the Sp score</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr>
+ <td>2</td>
+ <td><code>deltLCn</code></td>
+ <td>Float</td>
+ <td>The difference between this PSM's XCorr and the
+ XCorr of the <i>last-ranked</i> PSM for this spectrum, divided by
+ this PSM's XCorr or 1, whichever is larger.</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE" >
+ <td>3</td>
+ <td><code>deltCn</code></td>
+ <td>Float</td>
+ <td>The difference between this PSM's XCorr and the
+ XCorr of the <i>next-ranked</i> PSM for this spectrum, divided by
+ this PSM's XCorr or 1, whichever is larger.
+ Note that this definition differs from that of the
+ standard delta Cn reported by SEQUEST<sup>®</sup>.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>4</td>
+ <td><code>Xcorr / XCorr Score</code></td>
+ <td>Float</td>
+ <td>The SEQUEST cross-correlation score</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>5</td>
+ <td><code>Sp / Sp score</code></td>
+ <td>Float</td>
+ <td>The preliminary SEQUEST score.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>6</td>
+ <td><code>IonFrac</code></td>
+ <td>Float</td>
+ <td>The fraction of b and y ions theoretical ions matched to the spectrum</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>7</td>
+ <td><code>Mass</code></td>
+ <td>Float</td>
+ <td>The observed mass [M+H]<sup>+</sup></td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>8</td>
+ <td><code>PepLen</code></td>
+ <td>Integer</td>
+ <td>The length of the matched peptide, in residues</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>9-11</td>
+ <td><code>Charge[n]</code></td>
+ <td>Boolean</td>
+ <td>Is this a 1+/2+/3+ charged spectrum?</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>12</td>
+ <td><code>enzN</code></td>
+ <td>Boolean</td>
+ <td>Is the peptide preceded by an enzymatic (tryptic) site?</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>13</td>
+ <td><code>enzC</code></td>
+ <td>Boolean</td>
+ <td>Does the peptide have an enzymatic (tryptic) C-terminus?</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>14</td>
+ <td><code>enzInt</code></td>
+ <td>Integer</td>
+ <td>Number of missed internal enzymatic (tryptic) sites</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>15</td>
+ <td><code>lnNumSP</code></td>
+ <td>Float</td>
+ <td>The natural logarithm of the number of database
+ peptides within the specified precursor range</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr>
+ <td>16</td>
+ <td><code>dM</code></td>
+ <td>Float</td>
+ <td>The difference between the calculated and observed mass</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>17</td>
+ <td><code>absdM</code></td>
+ <td>Float</td>
+ <td>The absolute value of the difference between the calculated and observed mass</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>18</td>
+ <td><code>label</code></td>
+ <td>Boolean</td>
+ <td>Is this decoy or target?</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+
+ <tr bgcolor="#DEDEDE">
+ <td>19</td>
+ <td><code>xcorr rank</code></td>
+ <td>Integer</td>
+ <td>The rank of this PSM when sorted by xcorr</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>20</td>
+ <td><code>Sp rank</code></td>
+ <td>Integer</td>
+ <td>The rank of this PSM when sorted by sp score.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE" >
+ <td>21</td>
+ <td><code>missed cleavage</code></td>
+ <td>Boolean</td>
+ <td>Does the peptide contain one or more missed cleavage sites?</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>22</td>
+ <td><code>number of sequence comparisons</code></td>
+ <td>Integer</td>
+ <td>The number of sequence comparisons</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>23</td>
+ <td><code>delta mass</code></td>
+ <td>Float</td>
+ <td>Difference between measured and calculated mass</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr-->
+
+ <tr>
+ <td>24</td>
+ <td><code>abs(delta mass)</code></td>
+ <td>Float</td>
+ <td>Absolute value of delta mass</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>25</td>
+ <td><code>b ions</code></td>
+ <td>Float</td>
+ <td>The XCorr from the theoretical b-ions.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>26</td>
+ <td><code>y ions</code></td>
+ <td>Float</td>
+ <td>The XCorr from the theoretical y-ions.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>27</td>
+ <td><code>flanking</code></td>
+ <td>Float</td>
+ <td>The XCorr from the flanking peaks</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td><b>Total</b></td>
+ <td> </td>
+ <td> </td>
+ <td></td>
+ <td><b>17</td>
+ <td><b>20</td>
+ <td><b>20</b></td>
+ </tr>
+ </table>
+ </div>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/ms2-format.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/ms2-format.html
new file mode 100644
index 0000000..a5d385a
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/ms2-format.html
@@ -0,0 +1,283 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>MS2 file format</h2>
+ <p>
+ The MS2 file format is used to record MS/MS spectra.
+ A full description of the MS2 file format may be found in:
+ <cite>
+ McDonald,W.H. et al.
+ MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage
+ of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom.
+ <b>18</b>, 2162-2168 (2004).
+ </cite>
+ </p>
+ <p>
+ An MS2 file consists of a header followed by one or more sets of scan data.
+ The header and scan data are broken into records, one record per line.
+ The fields within a record are separated by white space.
+ The header records list information applicable to all the scans in the file.
+ Each scan begins with a few records describing the parameters for that scan.
+ This is followed by pairs of m/z and intensity values, one pair per line.
+ </p>
+ <p>
+ A sample MS2 file may be found <a href="../example-files/demo.ms2">here</a>.
+ </p>
+ <h3>Header details</h3>
+ <p>
+ Each line in the header must begin with an <code>H</code>.
+ This is followed by a field label, and then a field value,
+ all separated by white space.
+ The field label must be one of the labels listed below,
+ while the field value can be an aribrary string.
+ A typical header is shown below.
+ </p>
+ <pre>
+H CreationDate 2/14/2007 6:19:18 PM
+H Extractor MakeMS2
+H ExtractorVersion 1.0
+H Comments MakeMS2 written by Michael J. MacCoss, 2004
+H ExtractorOptions MS2/MS1
+ </pre>
+ <p>
+ The following field labels must appear in the header:
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Required header field labels</caption>
+ <thead>
+ <tr>
+ <th>Field Label</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>CreationDate</td><td>The date and time when the file was created</td>
+ </tr>
+ <tr>
+ <td>Extractor</td><td>The name of the software used to create the MS2 file</td>
+ </tr>
+ <tr>
+ <td>ExtractorVersion</td><td>The version number of the Extractor software</td>
+ </tr>
+ <tr>
+ <td>ExtractorOptions</td><td>The options used in running the extractor software</td>
+ </tr>
+ </tbody>
+ </table>
+ <p>
+ The following field labels are optional, and may appear in the header:
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Optional header field labels</caption>
+ <thead>
+ <tr>
+ <th>Field Label</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>IAnalyzer</td>
+ <td>Name of software used to conduct charge-state independent analysis of the spectra</td>
+ </tr>
+ <tr>
+ <td>IAnalyzerVersion</td>
+ <td>The version number of the IAnalyzer software</td>
+ </tr>
+ <tr>
+ <td>IAnalyzerOptions</td>
+ <td>The options used in running the IAnalyzer software</td>
+ </tr>
+ <tr>
+ <td>DAnalyzer</td>
+ <td>Name of software used to conduct charge-state dependent analysis of the spectra</td>
+ </tr>
+ <tr>
+ <td>DAnalyzerVersion</td>
+ <td>The version number of the DAnalyzer software</td>
+ </tr>
+ <tr>
+ <td>DAnalyzerOptions</td>
+ <td>The options used in running the DAnalyzer software</td>
+ </tr>
+ <tr>
+ <td>SortedBy</td>
+ <td>Name of field use to sort spectra<td>
+ </tr>
+ <tr>
+ <td>InstrumentType</td>
+ <td>The type of mass analyzer used<td>
+ </tr>
+ <tr>
+ <td>Comment</td>
+ <td>Remarks. Multiple comment lines are allowed<td>
+ </tr>
+ <tr>
+ <td>InstrumentSN</td>
+ <td>Serial number of the mass spectrometer used<td>
+ </tr>
+ </tbody>
+ </table>
+ <h3>Scan details</h3>
+ <p>
+ Each scan begins with a few records listing the parameters describing the spectrum.
+ These lines must begin with S, I, Z, or D.
+ The records are followed by pairs of m/z and intensity values, one pair per line.
+ A fragment of a typical scan is shown below.
+ </p>
+ <pre>
+S 10 10 636.34
+Z 2 1271.67
+187.4 12.5
+193.1 19.5
+194.3 13.7
+198.3 29.8
+199.1 12.2
+ </pre>
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Record types for scans</caption>
+ <thead>
+ <tr>
+ <th>Symbol</th>
+ <th>Description</th>
+ <th>Generic form</th>
+ <th>Required</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>S</td>
+ <td>scan</td>
+ <td><code>S [first scan] [second scan] [pre m/z]</code></td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>I</td>
+ <td>Charge independent analysis</td>
+ <td><code>I [field label] [field value]</code></td>
+ <td>no</td>
+ </tr>
+ <tr>
+ <td>Z</td>
+ <td>Charge</td>
+ <td><code>I [charge] [mass]</code></td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>D</td>
+ <td>Charge dependent analysis</td>
+ <td><code>I [field label] [field value]</code></td>
+ <td>no</td>
+ </tr>
+ <tr>
+ <td>[data]</td>
+ <td>m/z intensity paris</td>
+ <td><code>[m/z] [intensity]</code></td>
+ <td>yes</td>
+ </tr>
+ </tbody>
+ </table>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/parameter-file.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/parameter-file.html
new file mode 100644
index 0000000..6c4fe1d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/parameter-file.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Crux parameter files</h2>
+
+ <b>Description:</b>
+ <p>A file containing parameters and their arguments passed to a crux
+ program to control various aspects of execution. Every command-line
+ option and many additional options can be read from a parameter
+ file. If an option is specified in a file and on the command line,
+ the command line value will be used.
+ </p>
+
+ <b>Usage:</b>
+ <p><span class="code"><program name> --parameter-file <file name> [<argument>+]</span></p>
+
+ <b>Format:</b>
+ <p>The parameter file can contain parameter lines, comment lines and
+ blank lines. Parameter lines are name-value pairs separated by an
+ equal sign, '=' with no spaces in between. Comment lines must begin
+ with '#'. Blank lines should contain no spaces or tabs before the newline.
+ </p>
+
+ <p>
+ <a href="../commands/default.params">Here</a> is a sample parameter file
+ containing the default values for every parameter/option available to
+ all crux programs.</p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/sample.fasta b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/sample.fasta
new file mode 100644
index 0000000..1f51f20
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/sample.fasta
@@ -0,0 +1,17 @@
+>ICYA_MANSE
+GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKY
+DGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVN
+LVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD
+NVLKTFSHLIDASKFISNDFSEAACQYSTTYSLTGPDRH
+
+>LACB_BOVIN
+MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDA
+QSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKI
+DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE
+KFDKALKALPMHIRLSFNPTQLEEQCHI
+
+>BBP_PIEBR
+NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPE
+GKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFN
+VLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI
+GSPVVDSQKLVYSDFSEAACKVN
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/sqt-format.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/sqt-format.html
new file mode 100644
index 0000000..1540f6d
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/sqt-format.html
@@ -0,0 +1,329 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>SQT file format</h2>
+ <p>
+ The SQT file format is used to record the matches between MS/MS spectra
+ and a sequence database.
+ A full description of the SQT file format may be found in:</p>
+
+ McDonald, W.H. et al.
+ <a href="http://onlinelibrary.wiley.com/doi/10.1002/rcm.1603/abstract">"MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage
+ of shotgun proteomic spectra and identifications."</a> <i>Rapid
+ Communications in Mass Spectrometry.</i> <b>18</b>, 2162-2168 (2004).
+ </blockquote>
+
+ <p>
+ An SQT file consists of a header followed by one or more spectrum matches.
+ The header and match data are broken into records, one record per line.
+ Fields within a record are separated by white space.
+ </p>
+ <p>
+ A sample SQT file may be found <a href="../example-files/target.sqt">here</a>.
+ </p>
+
+ <h3>Header details</h3>
+ <p>
+ Each line in the header must begin with an <code>H</code>.
+ This is followed by a field label, and then a field value,
+ all separated by white space.
+ The field label must be one of the labels listed below,
+ while the field value can be an aribrary string.
+ A typical header is shown below.
+ </p>
+ <pre>
+H SQTGenerator Crux
+H SQTGeneratorVersion 1.0
+H Comment Crux was written by...
+H Comment ref...
+H StartTime Tue Dec 2 15:22:50 2008
+H EndTime
+H Database test_crux_index/test-binary-fasta
+H DBSeqLength ?
+H DBLocusCount 4
+H PrecursorMasses average
+H FragmentMasses mono
+H Alg-PreMasTol 3.0
+H Alg-FragMassTol 0.50
+H Alg-XCorrMode 0
+H Comment preliminary algorithm sp
+H Comment final algorithm xcorr
+H StaticMod C=160.139
+H Alg-DisplayTop 5
+H EnzymeSpec tryptic
+ </pre>
+ <p>
+ The following field labels must appear in the header:
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Required header field labels</caption>
+ <thead>
+ <tr>
+ <th>Field Label</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>SQTGenerator</td><td>The name of the software used to create the SQT file</td>
+ </tr>
+ <tr>
+ <td>SQTGeneratorVersion</td><td>The version number of the SQTGenerator software</td>
+ </tr>
+ <tr>
+ <td>Database</td><td>Path to sequence database used to generate the SQT file</td>
+ </tr>
+ <tr>
+ <td>FragmentMasses</td>
+ <td>Were average or mono-istopic residue masses used to predict the fragment ion mass</td>
+ </tr>
+ <tr>
+ <td>PrecursorMasses</td>
+ <td>Were average or mono-istopic residue masses used to predict the precursor ion mass</td>
+ </tr>
+ <tr>
+ <td>StartTime</td><td>Time when SQT file was created</td>
+ </tr>
+ <tr>
+ <td>StaticMod</td>
+ <td>Non-standard amino-acid masses used in identification
+ (repeat this record if there are multiple non-standard masses)</td>
+ </tr>
+ <tr>
+ <td>DynamicMod</td>
+ <td>List of dynamic modifications used in identification</td>
+ </tr>
+ </tbody>
+ </table>
+ <p>
+ The following field labels are optional, and may appear in the header:
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Optional header field labels</caption>
+ <thead>
+ <tr>
+ <th>Field Label</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>Comment</td>
+ <td>Remarks. Multiple comment lines are allowed<td>
+ </tr>
+ <tr>
+ <td>DBSeqLength</td>
+ <td>Number of aminio acids in sequence database</td>
+ </tr>
+ <tr>
+ <td>DBLocusCount</td>
+ <td>Number of proteins in sequence database</td>
+ </tr>
+ <tr>
+ <td>DBMD5Sum</td>
+ <td>MD5 checksum of sequence database</td>
+ </tr>
+ <tr>
+ <td>SortedBy</td>
+ <td>Name of field use to sort spectra<td>
+ </tr>
+ <tr>
+ <td>Alg-</td>
+ <td>Field names begining with Alg- are algorithm specific<td>
+ </tr>
+ <tr>
+ <td>*</td>
+ <td>Other field names are allowed, but may not contain white-space<td>
+ </tr>
+ </tbody>
+ </table>
+
+ <h3>Match details</h3>
+ <p>
+ Each spectrum match begins with a spectrum (S) record,
+ each S record is followed by one or more match (M) records,
+ and each M record is followed by one or more Locus (L) records.
+ The S record contains the scan number and other details for the spectum,
+ the M records contains the highest scoring peptide matches for the parent spectrum,
+ and the L records give the names of proteins containing the parent match peptide.
+ </p>
+ <pre>
+S 45894 45894 2 1 maccoss007 2038.59 9199.5 147.1 153628
+M 1 27 2040.244 0.0000 1.5881 245.6 11 34 V.YKCAADKQDATVVELTNL.T U
+L YCR102C
+M 2 68 2038.265 0.0116 1.5698 208.4 11 36 S.TQSGIVAEQALLHSLNENL.S U
+L YGR080W
+M 3 34 2039.247 0.1582 1.3369 239.3 11 36 I.NEKTSPALVIPTPDAENEI.S U
+L YLR035C
+M 4 322 2040.365 0.1699 1.3183 160.0 9 36 I.LKESKSVQPGKAIPDIIES.P U
+L YJL126W
+M 5 74 2039.453 0.2288 1.2248 203.6 10 32 D.MISVDLKTPLVIFKCHH.G U
+L YAL002W
+M 65 1 2041.246 0.4179 0.9245 370.2 13 32 S.CCGLSLPGLHDLLRHYE.E U
+L YLR403W
+S 45904 45904 3 1 maccoss007 2834.54 10103.7 246.4 152668
+M 1 237 2833.059 0.0000 1.9175 273.1 20 108 N.NSGSDTVDPLAGLNNLRNSIKSAGNGME.N U
+L YDR505C
+M 2 223 2834.278 0.1390 1.6510 274.8 18 96 G.HLSRISNIDDILISMRMDAFDSLIG.Y U
+L YLR247C
+M 3 52 2835.100 0.1503 1.6292 324.1 20 96 S.KSTTEPIQLNNKHDLHLGQELTEST.V U
+L YDR098C-B
+L YDR365W-B
+L YER138C
+L YGR027W-B
+ </pre>
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Record types for scans</caption>
+ <thead>
+ <tr>
+ <th>Symbol</th>
+ <th>Description</th>
+ <th>Generic form</th>
+ <th>Required</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>S</td>
+ <td>Spectrum</td>
+ <td><code>S [low scan] [high scan] [charge] [process time]
+ <br />
+ [server] [experimental neutral mass] [total ion intensity] [lowest Sp] [# of seq. matched]
+ </code></td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>M</td>
+ <td>Match</td>
+ <td><code>M [rank by Xcorr] [rank by Sp] [calculated mass]
+ <br />
+ [DeltaCN] [Xcorr] [Sp] [matched ions] [expected ions] [sequence matched]
+ <br />
+ [validation status U = unknown, Y = yes, N = no, M = Maybe]
+ </code></td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>L</td>
+ <td>Locus</td>
+ <td><code>L [locus name] [description if available]</code></td>
+ <td>yes</td>
+ </tr>
+ </tbody>
+ </table>
+
+ <h3>Differences between Crux's SQT format and the published
+ version</h3>
+
+ <ul>
+ <li>
+ Relative to the original specification of SQT, Crux expects an
+ additional field [total ion intensity] in the "S" lines.</li>
+ <li>
+ In the original specification, the FragmentMasses and PrecursorMasses
+ header lines used the values "AVG" or "MONO", but Crux uses "average"
+ and "mono".</li>
+ </ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/txt-format.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/txt-format.html
new file mode 100644
index 0000000..690a9fe
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/file-formats/txt-format.html
@@ -0,0 +1,1363 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Tab-delimited File Format</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Tab-delimited file format</h2>
+ <p>
+ Various programs in Crux report their output and read inputs in tab-delimited text format. Each such file consists of a single line containing the tab-separated names of fields, followed by one or more lines giving the corresponding field values.
+ </p>
+ <table border="1" id="tabformat">
+ <!-- table headers-->
+ <tr>
+ <th rowspan="2">Name</th>
+ <th rowspan="2">Description</th>
+ <th rowspan="2">comet</th>
+ <th rowspan="2">tide</th>
+ <th rowspan="2">cascade-search</th>
+ <th rowspan="2">search-for-xlinks</th>
+ <th rowspan="2">search-for-xlinks (new)</th>
+ <th colspan="4">barista</th>
+ <th rowspan="2">q-ranker</th>
+ <th colspan="3">percolator</th>
+ <th rowspan="2">spectral-counts</th>
+ </tr>
+
+ <tr>
+ <!--barista-->
+ <th>PSM</th>
+ <th>peptides</th>
+ <th>proteins</th>
+ <th>sub-proteins</th>
+ <!--percolator-->
+ <th>PSM</th>
+ <th>peptides</th>
+ <th>proteins</th>
+ </tr>
+
+ <!--"✓"= "✓" or "✔"-->
+ <!--"✕"= "✕" or "✖"-->
+ <!--"–"=–-->
+
+ <tr bgcolor="#DEDEDE">
+ <td>file</td>
+ <td>The name of the file containing the scan.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>fileidx</td>
+ <td>The integer index of the file containing the scan.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>scan</td>
+ <td>The identifying number of each scan.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>charge</td>
+ <td>The charge state for this spectrum in this PSM.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>spectrum precursor m/z</td>
+ <td>The observed m/z of the spectrum precursor ion.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>spectrum neutral mass</td>
+ <td>The computed mass of the spectrum precursor at the given charge state. This is equal to the precursor m/z minus the mass of a proton (1.00727646677 Da), all multiplied by the charge.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>peptide mass</td>
+ <td>The mass of the peptide sequence, computed as the sum of the the amino acid masses plus the mass of water (18.010564684 Da or 18.0153 Da, depending on whether we are using monoisotopic or average mass).</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>delta_cn</td>
+ <td>The normalized difference in XCorr for this PSM
+ relative to the next ranked PSM for the same spectrum
+ and charge. The denominator for normalization is the
+ minimum of the current XCorr and 1.0.
+ If <code>exact-p-value=T</code>, then the difference
+ is computed between -log(p-value) rather than XCorr,
+ and no normalization is applied.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>delta_lcn</td>
+ <td>Similar to delta_cn, except that the difference
+ is computed with respect to the lowest reported XCorr
+ score for a given spectrum and charge state.</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>sp score</td>
+ <td>The SEQUEST-type preliminary score.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>sp rank</td>
+ <td>The rank of this PSM when sorted by Sp score. Note that,
+ in <code>tide-search</code>, the Sp score is only computed for PSMs
+ that are reported to the user. Hence, the rank of the Sp score
+ will be in the range from 1 to <i>n</i>, where the value
+ of <i>n</i> is determined by the <code>--top-match</code> parameter.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>xcorr score</td>
+ <td>The SEQUEST-type cross correlation score.
+ This column only appears when <code>exact-p-value=F</code>.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>exact p-value</td>
+ <td>The p-value computed as described in
+ <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">"Computing Exact p-values
+ for a Cross-correlation Shotgun Proteomics Score Function"</a>.
+ This column only appears when <code>exact-p-value=T</code>.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>refactored xcorr</td>
+ <td>A discretized version of XCorr, used to compute the p-value.
+ This column only appears when <code>exact-p-value=T</code>.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>xcorr rank</td>
+ <td>The rank of this PSM when sorted by xcorr.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>p-value</td>
+ <td>The p-value computed from the estimated Weibull parameters of the score distribution for this spectrum.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>percolator score</td>
+ <td>The discriminant score assigned by percolator.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>percolator q-value</td>
+ <td>The q-value assigned by percolator.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>percolator PEP</td>
+ <td>The posterior error probability assigned by percolator.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>q-ranker score</td>
+ <td>The discriminant score assigned by q-ranker.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>q-ranker q-value</td>
+ <td>The q-value assigned by q-ranker.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>q-ranker PEP</td>
+ <td>The posterior error probability estimated from the q-ranker score</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>barista score</td>
+ <td>The discriminant score assigned by barista.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>barista q-value</td>
+ <td>The q-value assigned by barista.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>barista PEP</td>
+ <td>The PEP assigned by barista</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>b/y ions matched</td>
+ <td>The number of b-ions and y-ions in the peptide that have a corresponding peak in the spectrum.</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>b/y ions total</td>
+ <td>The total number of b- and y-ions predicted for this peptide.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>total matches/spectrum</td>
+ <td>The number of candidate peptides in the database found for this
+ spectrum, including duplicates. Note that this is always the number of target candidate
+ peptides, even if the PSM involves a decoy peptide.</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>distinct matches/spectrum</td>
+ <td>The number of unique candidate peptides in the database found for this
+ spectrum. Note that this is always the number of target candidate
+ peptides, even if the PSM involves a decoy peptide.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+
+ <tr>
+ <td>sequence</td>
+ <td>The peptide sequence, not including any modifications.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>modified sequence</td>
+ <td>The peptide sequence, with modifications included.</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>modifications</td>
+ <!-- This description needs to be expanded considerably. -->
+ <td>Variable modifications applied to the sequence.</td>
+ <td></td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>cleavage type</td>
+ <td>The cleavage rules for generating this peptide based on the user-specified enzyme specificity.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>protein id</td>
+ <td>A comma-separated list of proteins in which this peptide
+ appears. Optionally, the protein name may be followed by a number in parentheses giving the start position of the peptide in the protein.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>flanking aa</td>
+ <td>The amino acids that precede and follow this
+ peptide in the parent protein ID. If the peptide
+ occurs in more than one protein, then this column
+ will contain a comma-separated list of pairs of amino
+ acids.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>original target sequence</td>
+ <td>The unmodified target sequence. For a target PSM,
+ the value in this column will be identical to the
+ value in the "sequence" column. For a decoy PSM,
+ this column will contain the corresponding target
+ sequence.</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>RAW</td>
+ <td>The raw (unnormalized) count of spectra per peptide</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>SIN</td>
+ <td>A protein quantification score</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>NSAF</td>
+ <td>The normalized spectral abundace factor</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>dNSAF</td>
+ <td>The distributed normalized spectral abundace factor</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>EMPAI</td>
+ <td>The exponentially modified protein abundance index</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td> parsimony rank</td>
+ <td>The protein rank based on its spectral-counts score.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>psm_id</td>
+ <td>PSM identifier.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>protein group number</td>
+ <td>Protein group index</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>peptides-scan.charge</td>
+ <td>Peptides belonging to each protein in the group, with scan and charge (for example, EAMPK-001285.2)</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>proteins</td>
+ <td>Proteins in the protein group. Each protein can be followed by peptides in parenthesis, if they belong only to this particular protein in the group. Since peptides are considered indistinguishable if they have identical amino acid sequences or they differ only by I/L or T/S in the same position in the peptide, the peptides shared by the group may not all be identical.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>parent group numbers</td>
+ <td>The numbers of the protein groups in the barista.target.proteins.txt that are supersets of this group in terms of peptides.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>peptide mass mono</td>
+ <td>Monoisotopic peptide mass</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>peptide mass average</td>
+ <td>Average peptide mass</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>mass error(ppm)</td>
+ <td>The mass error (in ppm) between the observed precursor mass and the
+ cross-link peptide product</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>protein id(loc)</td>
+ <td>List of protein IDs that give rise to the first and second peptide in the
+ cross-link peptide product. (loc) indicates the location of the
+ peptide in the protein. The ";" separates the protein ids from the
+ first and second peptide.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>protein id(loc) 1</td>
+ <td>List of protein IDs that give rise to the first peptide in the
+ cross-link peptide product. (loc) indicates the location of the
+ peptide in the protein</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>protein id(loc) 2</td>
+ <td>List of protein IDs that give rise to the second peptide in the
+ cross-link peptide product. (loc) indicates the location of the
+ peptide in the protein</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>by total</td>
+ <td>Total number of b-y ions in product</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>by observable (0-1200)</td>
+ <td>Total number of b and y ions observable in the 0-1200 m/z range</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>by observable bin (0-1200)</td>
+ <td>Total number of b and y ions observable in the 0-1200 m/z range
+ using 1 Da bins</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>by observable (0-max)</td>
+ <td>Total number of b and y ions observable in the entire m/z range</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>by observable bin (0-max)</td>
+ <td>Total number of b and y ions observable in the entire m/z range
+ using 1 Da bins</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>by observed bin</td>
+ <td>Total number of b-y ions observed in spectrum</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>ion current total</td>
+ <td>Total ion current for spectrum</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>ion current observed</td>
+ <td>Total ion current observed for matching b-y ions</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>ions observable bin (0-1200)</td>
+ <td>Total ions observable (b, y, flanks, and neutral losses) within 0-1200 m/z range</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ </table>
+<!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/fileformats.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/fileformats.html
new file mode 100644
index 0000000..51aaf71
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/fileformats.html
@@ -0,0 +1,387 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux File Formats</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <div id="content">
+ <h2>File formats</h2>
+
+ <table id="fileFormatsTable">
+ <tr>
+ <td> </td>
+ <td>bullseye</td>
+ <td>tide-index</td>
+ <td>tide-search</td>
+ <td>comet</td>
+ <td>percolator</td>
+ <td>q-ranker</td>
+ <td>barista</td>
+ <td>search-for-xlinks</td>
+ <td>spectral-counts</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/ms2-format.html">MS1</a>
+ </td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/ms2-format.html">MS2</a>
+ (<a href="example-files/demo.ms2">sample</a>) / CMS2
+ </td>
+ <td>in/out</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://www.matrixscience.com/help/data_file_help.html">MGF</a>
+ </td>
+ <td>in/out</td>
+ <td> </td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://www.psidev.info/mzml_1_0_0">mzML</a>,
+ <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML">mzXML</a>
+ </td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ Thermo .raw files
+ (Windows only)
+ </td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://proteowizard.sourceforge.net/formats.shtml">Other
+ proprietary vendor formats</a> (Windows only)
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/fasta-format.html">FASTA</a>
+ (<a href="file-formats/sample.fasta">sample</a>)
+ </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>in</td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ database index
+ </td>
+ <td> </td>
+ <td>out</td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/txt-format.html">Tab-delimited text</a>
+ (<a href="example-files/search.target.txt">sample</a>)
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td>out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>out</td>
+ <td>in/out</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">
+ pepXML</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td>out</td>
+ <td>in/out</td>
+ <td>out</td>
+ <td>out</td>
+ <td> </td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="https://github.com/percolator/percolator/wiki/Interface">PIN</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td> </td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="https://github.com/percolator/percolator/wiki/Interface">POUT</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://www.psidev.info/mzidentml">mzIdentML</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td>out</td>
+ <td>out</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/sqt-format.html">SQT</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td>out</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/features.html">Feature file</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>in/out</td>
+ <td>out</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/barista-xml-format.html">Barista XML</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/parameter-file.html">Crux parameters</a>
+ (<a href="example-files/default.params">sample</a>)
+ </td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ </tr>
+
+ </table>
+ </div>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/generate-peptides.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/generate-peptides.html
new file mode 100644
index 0000000..dc0ec41
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/generate-peptides.html
@@ -0,0 +1,166 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>generate-peptides</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>generate-peptides</h1>
+<h2>Usage:</h2>
+<p><code>crux generate-peptides [options] <protein fasta file></code></p>
+<h2>Description:</h2>
+<p>This command takes as input a protein FASTA file and outputs the corresponding list of peptides, as well as a matched list of decoy peptides and decoy proteins. Decoys are generated either by reversing or shuffling the non-terminal amino acids of each peptide. The program will shuffle each peptide multiple times to attempt to ensure that there is no overlap between the target and decoy peptides. For homopolymers, this is not possible. In this case, the occurrence of these target/decoy [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>protein fasta file</code> – The name of the file in FASTA format from which to retrieve proteins.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>generate-peptides.target.txt</code> – A text file containing the target peptides, one per line. Each line has three tab-delimited columns, containing the peptide sequence, the m+h mass of the unmodified peptide, and a comma-delimited list of protein IDs in which the peptide occurs.</li>
+ <li><code>generate-peptides.decoy.txt</code> – A text file containing the decoy peptides, one per line. Each line has three tab-delimited columns, containing the peptide sequence, the m+h mass of the unmodified peptide, and a comma-delimited list of protein IDs in which the peptide occurs. There is a one-to-one correspondence between targets and decoys.</li>
+ <li><code>generate-peptides.proteins.decoy.txt</code> – a FASTA format file containing decoy proteins, in which all of the peptides have been replaced with their shuffled or reversed counterparts. Note that this file will only be created if the enzyme specificity is "full-digest" and no missed cleavages are allowed.</li>
+ <li><code>generate-peptides.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>generate-peptides.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Peptide properties</h3>
+<ul>
+ <li class="nobullet"><code>--min-mass <float></code> – The minimum mass (in Da) of peptides to consider. Default = <code>200</code>.</li>
+ <li class="nobullet"><code>--max-mass <float></code> – The maximum mass (in Da) of peptides to consider. Default = <code>7200</code>.</li>
+ <li class="nobullet"><code>--min-length <integer></code> – The minimum length of peptides to consider. Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--max-length <integer></code> – The maximum length of peptides to consider. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--isotopic-mass average|mono</code> – Specify the type of isotopic masses to use when calculating the peptide mass. Default = <code>mono</code>.</li>
+ <li class="nobullet"><code>--clip-nterm-methionine T|F</code> – When set to T, for each protein that begins with methionine, tide-index will put two copies of the leading peptide into the index, with and without the N-terminal methionine. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Decoy database generation</h3>
+<ul>
+ <li class="nobullet"><code>--seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--decoy-format none|shuffle|peptide-reverse|protein-reverse</code> – Include a decoy version of every peptide by shuffling or reversing the target sequence or protein. In shuffle or peptide-reverse mode, each peptide is either reversed or shuffled, leaving the N-terminal and C-terminal amino acids in place. Note that peptides appear multiple times in the target database are only shuffled once. In peptide-reverse mode, palindromic peptides are shuffled. [...]
+ <li class="nobullet"><code>--keep-terminal-aminos N|C|NC|none</code> – When creating decoy peptides using decoy-format=shuffle or decoy-format=peptide-reverse, this option specifies whether the N-terminal and C-terminal amino acids are kept in place or allowed to be shuffled or reversed. For a target peptide "EAMPK" with decoy-format=peptide-reverse, setting keep-terminal-aminos to "NC" will yield "EPMAK"; setting it to "C" will yield "PMAEK"; setting it to "N" will yield "EKPMA" [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+ <li class="nobullet"><code>--custom-enzyme <string></code> – Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. If the residues are required for digestion, they are in square brackets, '[' and ']'. If the re [...]
+ <li class="nobullet"><code>--digestion full-digest|partial-digest|non-specific-digest</code> – Specify whether every peptide in the database must have two enzymatic termini (full-digest) or if peptides with only one enzymatic terminus are also included (partial-digest). Default = <code>full-digest</code>.</li>
+ <li class="nobullet"><code>--missed-cleavages <integer></code> – Maximum number of missed cleavages per peptide to allow in enzymatic digestion. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/get-ms2-spectrum.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/get-ms2-spectrum.html
new file mode 100644
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--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/get-ms2-spectrum.html
@@ -0,0 +1,143 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>get-ms2-spectrum</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>get-ms2-spectrum</h1>
+<h2>Usage:</h2>
+<p><code>crux get-ms2-spectrum [options] <ms2 file></code></p>
+<h2>Description:</h2>
+<p>Extract one or more MS-MS spectra from an MS2 file by scan number. Optionally output summary statistics for each spectrum.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – the requested spectrum or spectra in MS2 format.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>get-ms2-spectrum options</h3>
+<ul>
+ <li class="nobullet"><code>--stats T|F</code> – Rather than the spectrum, output summary statistics to standard output. Each statistic is placed on a separate line, in the format <name>:<value> (e.g. "TIC:1000.0").<br>The following statistics are reported for the entire spectrum:<ul><li>Precursor m/z</li><li>Total Ion Current</li><li>Base Peak Intensity</li><li>Number of peaks</li><li>Minimum m/z</li><li>Maximum m/z</li></ul>In addition, for each possible spectrum charge state, t [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/glossary.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/glossary.html
new file mode 100644
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--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/glossary.html
@@ -0,0 +1,165 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux glossary</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Crux glossary</h2>
+
+ <h3>Mass spectrometry terminology</h3>
+
+ <ul>
+
+ <li><b>c-term peptide</b>: The last peptide in the protein,
+ occurring at the c-terminal end of the protein.</li>
+
+ <li><b>decoy peptide</b>: A shuffled, reversed or randomly
+ generated peptide sequence. Matches to decoy peptides are used
+ for two purposes: to estimate statistical confidence measures
+ such as the false discovery rate, and to train machine learning
+ methods to recognize correctly identified spectra.</li>
+
+ <li><b>modification</b>: A chemical modification of a single amino
+ acid, typically corresponding to the addition of a molecular
+ group to the amino acid side chain.</li>
+
+ <li><b>n-term peptide</b>: The first peptide in the protein,
+ occurring at the n-terminal end of the protein.</li>
+
+ <li><b>peptide</b>: A subsequence of a protein.</li>
+
+ <li><b>peptide-spectrum match (PSM)</b>: An observed spectrum
+ paired with a peptide sequence, along with a score quantifying
+ the quality of the match.</li>
+
+ <li><b>static modification</b>: A chemical modification of a
+ single amino that is expected to occur on every instance of that
+ amino acid. A common example is carbamidomethylation of
+ cysteine, which adds 57.02146 Da to the mass of every
+ cysteine.</li>
+
+ <li><b>target peptide</b>: A real peptide, usually drawn from a
+ protein database.</li>
+
+ <li><b>trypsin</b>: An enzyme used to cleave a protein into
+ peptides.</li>
+
+ <li><b>variable modification</b>: A chemical modification of a
+ single amino that is expected to occur on some instances of that
+ amino acid but not others. A common example is phosphorylation
+ of serine, threonine or tyrosine, which adds a mass of 79.966331
+ Da to each of those amino acids.</li>
+
+ </ul>
+
+ <h3>Analysis terminology</h3>
+
+ <ul>
+
+ <li><b>false discovery rate (FDR)</b>: Estimated proportion of
+ incorrectly identifications among a set of PSMs, peptides or
+ proteins.</li>
+
+ <li><b>support vector machine (SVM)</b>: A machine learning method
+ that learns to classify data objects into two groups.</li>
+
+ </ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/hardklor.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/hardklor.html
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+<!DOCTYPE html>
+<html>
+<head>
+<title>hardklor</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
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+ if(w > 320 && menu.is(':hidden')) {
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+<body>
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+ <li><a href="../fileformats.html">File Formats</a></li>
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+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>hardklor</h1>
+<h2>Usage:</h2>
+<p><code>crux hardklor [options] <spectra></code></p>
+<h2>Description:</h2>
+<p>Hardklör analyzes high-resolution mass spectra, identifying protein or peptide isotope distributions and determining the corresponding monoisotopic masses and charge states. The algorithm aims to identify persistence peptide isotope distribution (PPIDs), i.e., isotope distributions that recur over multiple scans. Hardklör is specifically designed to handle overlapping isotope distributions in a single spectrum. A detailed description of the Hardklör algorithm is given i [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>spectra</code> – The name of a file from which to parse high-resolution spectra. The file may be in MS1 (.ms1), binary MS1 (.bms1), compressed MS1 (.cms1), or mzXML (.mzXML) format.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>hardklor.mono.txt</code> – a tab-delimited text file containing one line for each isotope distribution. The columns appear in the following order:<ol><li><strong>scan</strong>: The scan number assigned to this spectrum in the input file.</li><li><strong>retention time</strong>: The time (in seconds) at which the spectrum was collected.</li><li><strong>mass</strong>: The uncharged monoisotopic mass of the protein or peptide.</li><li><strong>charge</strong>: The inferred [...]
+ <li><code>hardklor.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>hardklor.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>hardklor options</h3>
+<ul>
+ <li class="nobullet"><code>--hardklor-algorithm basic|version1|version2</code> – Determines which spectral feature detection algorithm to use. Different results are possible with each algorithm, and there are pros and cons to each. There are three algorithms to choose from:<ul><li>basic – Performs unoptimized deconvolution and is provided for legacy purposes only.</li><li>version1 – Uses the optimizations developed during the 1.0+ series. It is very accurate, but has [...]
+ <li class="nobullet"><code>--averagine-mod <string></code> – Defines alternative averagine models in the analysis that incorporate additional atoms and/or isotopic enrichments. Modifications are represented as text strings. Inclusion of additional atoms in the model is done using by entering an atomic formula, such as: PO2 or Cl. Inclusion of isotopic enrichment to the model is done by specifying the percent enrichment (as a decimal) followed by the atom being enriched and [...]
+ <li class="nobullet"><code>--boxcar-averaging <integer></code> – Boxcar averaging is a sliding window that averages n adjacent spectra prior to feature detection. Averaging generally improves the signal-to-noise ratio of features in the spectra, as well as improving the shape of isotopic envelopes. However, averaging will also change the observed peak intensities. Averaging with too wide a window will increase the occurrence of overlapping features and broaden the chromatog [...]
+ <li class="nobullet"><code>--boxcar-filter <integer></code> – This parameter is only functional when boxcar-averaging is used. The filter will remove any peaks not seen in n scans in the boxcar window. The effect is to reduce peak accumulation due to noise and reduce chromatographic broadening of peaks. Caution should be used as over-filtering can occur. The suggested number of scans to set for filtering should be equal to or less than the boxcar-averaging window size. A va [...]
+ <li class="nobullet"><code>--boxcar-filter-ppm <float></code> – This parameter is only functional when boxcar-filter is used. The value specifies the mass tolerance in ppm for declaring a peak the same prior to filtering across all scans in the boxcar window. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--centroided T|F</code> – Indicates whether the data contain profile or centroided peaks. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--cdm B|F|P|Q|S</code> – Choose the charge state determination method. There are five methods to choose from:<ul><li>B – Basic method, assume all charge states are possible.</li><li>F – Fast Fourier transform.</li><li>P – Patterson algorithm.</li><li>Q – QuickCharge method, uses inverse peak distances.</li><li>S – Senko method, or combined Fast Fourier Transform and Patterson algorithm.</li></ul> Default = <code>Q</code>.</li>
+ <li class="nobullet"><code>--min-charge <integer></code> – Specifies the minimum charge state to allow when finding spectral features. It is best to set this value to the lowest assumed charge state to be present. If set higher than actual charge states that are present, those features will not be identified or incorrectly assigned a different charge state and mass. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--max-charge <integer></code> – Specifies the maximum charge state to allow when finding spectral features. It is best to set this value to a practical number (i.e. do not set it to 20 when doing a tryptic shotgun analysis). If set higher than actual charge states that are present, the algorithm will perform significantly slower without any improvement in results. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--corr <float></code> – Sets the correlation threshold (cosine similarity) for accepting each predicted feature. Default = <code>0.85</code>.</li>
+ <li class="nobullet"><code>--depth <integer></code> – Sets the depth of combinatorial analysis. For a given set of peaks in a spectrum, search for up to this number of combined peptides that explain the observed peaks. The analysis stops before depth is reached if the current number of deconvolved features explains the observed peaks with a correlation score above the threshold defined with the correlation parameter. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--distribution-area T|F</code> – When reporting each feature, report abundance as the sum of all isotope peaks. The value reported is the estimate of the correct peak heights based on the averagine model scaled to the observed peak heights. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--hardklor-data-file <string></code> – Specifies an ASCII text file that defines symbols for the periodic table. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--instrument fticr|orbitrap|tof|qit</code> – Indicates the type of instrument used to collect data. This parameter, combined with the resolution parameter, define how spectra will be centroided (if you provide profile spectra) and the accuracy when aligning observed peaks to the models. Default = <code>fticr</code>.</li>
+ <li class="nobullet"><code>--isotope-data-file <string></code> – Specifies an ASCII text file that can be read to override the natural isotope abundances for all elements. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--max-features <integer></code> – Specifies the maximum number of models to build for a set of peaks being analyzed. Regardless of the setting, the number of models will never exceed the number of peaks in the current set. However, as many of the low abundance peaks are noise or tail ends of distributions, defining models for them is detrimental to the analysis. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--mzxml-filter <integer></code> – Filters the spectra prior to analysis for the requested MS/MS level. For example, if the data contain MS and MS/MS spectra, setting mzxml-filter = 1 will analyze only the MS scan events. Setting mzxml-filter = 2 will analyze only the MS/MS scan events. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--mz-max <float></code> – Constrains the search in each spectrum to signals below this value in Thomsons. Setting to 0 disables this feature. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--mz-min <float></code> – Constrains the search in each spectrum to signals above this value in Thomsons. Setting to 0 disables this feature. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--mz-window <float></code> – Only used when algorithm = version1. Defines the maximum window size in Thomsons to analyze when deconvolving peaks in a spectrum into features. Default = <code>4</code>.</li>
+ <li class="nobullet"><code>--resolution <float></code> – Specifies the resolution of the instrument at 400 m/z for the data being analyzed. Default = <code>100000</code>.</li>
+ <li class="nobullet"><code>--scan-range-max <integer></code> – Used to restrict analysis to spectra with scan numbers below this parameter value. A value of 0 disables this feature. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--scan-range-min <integer></code> – Used to restrict analysis to spectra with scan numbers above this parameter value. A value of 0 disables this feature. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--sensitivity <integer></code> – Set the sensitivity level. There are four levels: 0 (low), 1 (moderate), 2 (high), and 3 (max). Increasing the sensitivity will increase computation time, but will also yield more isotope distributions. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--signal-to-noise <float></code> – Filters spectra to remove peaks below this signal-to-noise ratio prior to finding features. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--smooth <integer></code> – Uses Savitzky-Golay smoothing on profile peak data prior to centroiding the spectra. This parameter is recommended for low resolution spectra only. Smoothing data causes peak depression and broadening. Only use odd numbers for the degree of smoothing (as it defines a window centered on each data point). Higher values will produce smoother peaks, but with greater depression and broadening. Setting this parameter to 0 dis [...]
+ <li class="nobullet"><code>--sn-window <float></code> – Set the signal-to-noise window length (in m/z). Because noise may be non-uniform across a spectrum, this value adjusts the segment size considered when calculating a signal-over-noise ratio. Default = <code>250</code>.</li>
+ <li class="nobullet"><code>--static-sn T|F</code> – Applies the lowest noise threshold of any sn_window across the entire mass range for a spectrum. Setting this parameter to 0 turns off this feature, and different noise thresholds will be used for each local mass window in a spectrum. Default = <code>true</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
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+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
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+</html>
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+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux tandem mass spectrometry analysis software</title>
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+ <map name="commands-files" id="schematic_map">
+ <area shape="rect" coords="253,135,349,169" alt="tide-index" href="commands/tide-index.html">
+ <area shape="rect" coords="260,247,342,278" alt="bullseye" href="commands/bullseye.html">
+ <area shape="rect" coords="510,100,612,132" alt="tide-search" href="commands/tide-search.html">
+ <area shape="rect" coords="528,191,595,222" alt="comet" href="commands/comet.html">
+ <area shape="rect" coords="512,281,613,335" alt="search-for-xlinks" href="commands/search-for-xlinks.html">
+ <area shape="rect" coords="776,100,873,132" alt="percolator" href="commands/percolator.html">
+ <area shape="rect" coords="791,160,861,192" alt="barista" href="commands/barista.html">
+ <area shape="rect" coords="783,222,866,252" alt="q-ranker" href="commands/q-ranker.html">
+ <area shape="rect" coords="784,281,867,334" alt="spectral-counts" href="commands/spectral-counts.html">
+ </map>
+ <img src="images/crux-logo.png" style="width:200px; float:left; padding:10px;">
+ <p>The Crux mass spectrometry analysis toolkit is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. The toolkit includes several search engines for both standard and cross-linked database search, as well as a variety of pre- and post-processing engines for assigning high-resolution precursor masses to spectra, assigning statistical confidence estimates to spectra, peptides and proteins, and [...]
+ <br />
+ <span class="indentcitation">Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael
+ J. MacCoss and William Stafford
+ Noble. <a href="http://noble.gs.washington.edu/papers/park2008rapid.html">"Rapid
+ and accurate peptide identification from tandem mass spectra."</a>
+ <i>Journal of Proteome Research.</i> 7(7):3022-3027, 2008.</li></span>
+ <br /><br />
+
+ For a more up-to-date description of Crux, please read:<br />
+
+ <span class="indentcitation">Sean McIlwain, Kaipo Tamura, Attila Kertesz-Farkas,
+ Charles E. Grant, Benjamin Diament, Barbara Frewen, J. Jeffry
+ Howbert, Michael R. Hoopmann, Lukas Käll, Jimmy K. Eng, Michael
+ J. MacCoss and William Stafford
+ Noble. <a href="http://pubs.acs.org/doi/abs/10.1021/pr500741y">"Crux:
+ rapid open source protein tandem mass spectrometry
+ analysis."</a> <i>Journal of Proteome Research.</i>
+ 13(10):4488-4491, 2014.</span>
+ </p>
+ </div>
+
+
+ <br />
+ <p/>
+ Crux is provided as a single executable that supports the following
+ commands:</p>
+ <table id="commandstable">
+
+ <tr>
+ <td colspan="2"><b>Primary commands</b></td>
+ </tr>
+
+ <tr>
+ <td><a href="commands/bullseye.html">bullseye</a></td>
+ <td>Assign high resolution precursor m/z values to MS/MS data using the Hardklör algorithm.
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/tide-index.html">tide-index</a></td>
+ <td>
+ Create an index of all peptides in a fasta file, for use in subsequent
+ calls to <code>tide-search</code>.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/tide-search.html">tide-search</a></td>
+ <td>
+ Search a collection of spectra against a sequence database, provided
+ either as a FASTA file or an index, returning a collection of
+ peptide-spectrum matches (PSMs). This is a fast search engine, but it
+ runs most quickly if provided with a peptide index built
+ with <code>tide-index</code>.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/cascade-search.html">cascade-search</a></td>
+ <td>
+ An iterative procedure for incorporating information about peptide
+ groups into the database search and confidence estimation
+ procedure.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/comet.html">comet</a></td>
+ <td>
+ Search a collection of spectra against a sequence database, returning
+ a collection of PSMs. This search engine runs directly on a protein
+ database in FASTA format.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/percolator.html">percolator</a></td>
+ <td>
+ Re-rank and assign confidence estimates to a collection of PSMs using
+ the Percolator algorithm. Optionally, also produce protein rankings
+ using the Fido algorithm.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/q-ranker.html">q-ranker</a></td>
+ <td>
+ Re-rank a collection of PSMs using the Q-ranker algorithm.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/barista.html">barista</a></td>
+ <td>
+ Rank PSMs, peptides and proteins, assigning a confidence measure to each
+ identification.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/search-for-xlinks.html">search-for-xlinks</a></td>
+ <td>
+ Search a collection of spectra against a sequence database, finding
+ cross-linked peptide matches.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/spectral-counts.html">spectral-counts</a></td>
+ <td>
+ Quantify peptides or proteins using one of three spectral counting
+ methods.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/pipeline.html">pipeline</a></td>
+ <td>
+ Given one or more sets of tandem mass spectra as well as a protein
+ database, this command runs a series of Crux tools and reports all of
+ the results in a single output directory.
+ </td></tr>
+
+ <tr>
+ <td colspan="2"><b>Utilities</b></td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/assign-confidence.html">assign-confidence</a></td>
+ <td>
+ Assign statistical confidence measures to each PSM in a given set.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/generate-peptides.html">generate-peptides</a></td>
+ <td>
+ Extract from a given set of protein sequences a list of target and
+ decoy peptides fitting the specified criteria.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/get-ms2-spectrum.html">get-ms2-spectrum</a></td>
+ <td>
+ Extract one or more fragmentation spectra, specified by scan number, from
+ an <code>MS2</code> file.</td>
+ </tr>
+
+ <tr>
+ <td><a href="commands/hardklor.html">hardklör</a></td>
+ <td>Identify isotopic distributions from high-resolution mass spectra.</td>
+ </tr>
+
+ <tr>
+ <td><a href="commands/make-pin.html">make-pin</a></td>
+ <td>Given a set of search results files, generate a pin file for input to
+ <code>crux percolator</code></td>
+ </tr>
+
+ <tr>
+ <td><a href="commands/param-medic.html">param-medic</a></td>
+ <td>Examine the spectra in a file to estimate the best precursor
+ and fragment error tolerances for database search.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/predict-peptide-ions.html">predict-peptide-ions</a></td>
+ <td>
+ Given a peptide and a charge state, predict the m/z values of the
+ resulting fragment ions.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/print-processed-spectra.html">print-processed-spectra</a></td>
+ <td>
+ Process spectra as for scoring xcorr and print the results to a file.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/psm-convert.html">psm-convert</a></td>
+ <td>
+ Convert a file containing peptide-spectrum matches (PSMs) from one
+ format to another.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/subtract-index.html">subtract-index</a></td>
+ <td>Subtract one index file from another, assuming both were generated
+ by tide-index.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/xlink-assign-ions.html">xlink-assign-ions</a></td>
+ <td>Given a spectrum and a pair of cross-linked peptides, assign theoretical
+ ion type labels to peaks in the observed spectrum.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/xlink-score-spectrum.html">xlink-score-spectrum</a></td>
+ <td>Takes a defined cross-linked peptide, a spectra file, and a scan number,
+ and will calculate the XCorr score a number of different ways.</td>
+ </tr>
+
+ <tr>
+ <td>
+ version</td>
+ <td>
+ Print the Crux version number to standard output, then exit.</td>
+ </tr>
+
+ <tr>
+ <td colspan="2"><b>Utilities for processing tab-delimited text files</b>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/extract-columns.html">extract-columns</a></td>
+ <td>Print specified columns from a tab-delimited file.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/extract-rows.html">extract-rows</a></td>
+ <td>Print specified rows from a tab-delimited file.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/stat-column.html">stat-column</a></td>
+ <td>Collect summary statistics from a column in a tab-delimited file.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/sort-by-column.html">sort-by-column</a></td>
+ <td>Sort a tab-delimited file by a column.</td>
+ </tr>
+
+ </table>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/make-pin.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/make-pin.html
new file mode 100644
index 0000000..dbf3496
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/make-pin.html
@@ -0,0 +1,139 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>make-pin</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>make-pin</h1>
+<h2>Usage:</h2>
+<p><code>crux make-pin [options] <target input></code></p>
+<h2>Description:</h2>
+<p>Make-pin is a utility program that combines a collection of target and decoy peptide-spectrum matches (PSMs) into a single file in pin format, according to <a href="https://github.com/percolator/percolator/wiki/Interface">this format</a>. The resulting file can be provided as input to <code><a href="percolator.html">crux percolator</a></code>.</p><p><code>make-pin</code> requires as input two sets of PSMs, one set derived from matching observed spectra against real ("target" [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>target input</code> – One or more files, each containing a collection of peptide-spectrum matches (PSMs) in <a href="../file-formats/txt-format.html">tab-delimited text</a>, <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">PepXML</a>, or <a href="http://www.psidev.info/mzidentml">mzIdentML</a> format. In tab-delimited text format, only the specified score column is required. However if --estimation-method is tdc, then the columns "scan" and [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>make-pin.pin</code> – a tab-delimited file containing the input target and decoy PSMs in pin format. This file can be changed to an absolute path (see --output-file option).</li>
+ <li><code>make-pin.params.txt</code> – a file containing the name and value of all parameters for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>make-pin.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--output-file <string></code> – Path where pin file will be written instead of make-pin.pin. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/mstoolkit.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/mstoolkit.html
new file mode 100644
index 0000000..06696e6
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/mstoolkit.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>MSToolKit</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>MSToolkit</h2>
+ <p>
+ MSToolkit is a library for handling mass spectrometry data in various file
+ formats. Crux is capable of using MSToolkit to parse spectrum files. The
+ ProteoWizard parser is used by default, but the MSToolkit parser can be used by
+ commands that support the <span class="code">spectrum-parser</span> parameter.
+ </p>
+ <p>
+ The following is a list of spectrum file formats supported by MSToolkit.
+ </p>
+ <ul>
+ <li>MS1/CMS1/BMS1</li>
+ <li><a href="file-formats/ms2-format.html">MS2</a>/CMS2/BMS2</li>
+ <li>ZS</li>
+ <li>UZS</li>
+ <li>MSMAT</li>
+ <li>RAW</li>
+ <li><a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML">MZXML[.GZ]</a></li>
+ <li>MZ5</li>
+ <li><a href="http://www.psidev.info/mzml_1_0_0">MZML[.GZ]</a></li>
+ <li><a href="http://www.matrixscience.com/help/data_file_help.html">MGF</a> (Mascot Generic Format)</li>
+ <li>SQLITE3</li>
+ <li>PSM</li>
+ </ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/param-medic.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/param-medic.html
new file mode 100644
index 0000000..894cd35
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/param-medic.html
@@ -0,0 +1,146 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>param-medic</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>param-medic</h1>
+<h2>Usage:</h2>
+<p><code>crux param-medic [options] <spectrum-file>+</code></p>
+<h2>Description:</h2>
+<p>Examine the spectra in a file to estimate the best precursor and fragment error tolerances for database search.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>spectrum-file+</code> – File from which to parse fragmentation spectra.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – the estimated parameter values for precursor mass tolerance (in ppm) and fragment bin size (in Th), as well as the standard deviations of the estimated error distributions for precursor and fragment masses.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/param-table.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/param-table.html
new file mode 100644
index 0000000..ae72dd0
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/param-table.html
@@ -0,0 +1,678 @@
+<!DOCTYPE HTML>
+<html><head><meta charset="UTF-8">
+<title>Crux parameters</title>
+<link href="../crux.css" rel="styleSheet" type="text/css"></head>
+<body><h1>Crux parameters</h1>
+<table border="1" align="center">
+<tr><td> </td><td>assign-confidence</td><td>barista</td><td>cascade-search</td><td>comet</td><td>create-docs</td><td>bullseye</td><td>hardklor</td><td>extract-columns</td><td>extract-rows</td><td>generate-peptides</td><td>get-ms2-spectrum</td><td>make-pin</td><td>param-medic</td><td>percolator</td><td>pipeline</td><td>predict-peptide-ions</td><td>print-processed-spectra</td><td>psm-convert</td><td>q-ranker</td><td>read-tide-index</td><td>search-for-xlinks</td><td>sort-by-column</td> [...]
+<tr bgcolor="#DEDEDE">
+<td>estimation-method</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>decoy-prefix</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>score</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>sidak</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>verbosity</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> [...]
+<tr>
+<td>parameter-file</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>overwrite</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td></tr>
+<tr>
+<td>output-dir</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>list-of-files</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>combine-charge-states</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>combine-modified-peptides</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>fileroot</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>enzyme</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>separate-searches</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>pepxml-output</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr>
+<td>txt-output</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>skip-cleanup</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>re-run</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>use-spec-features</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
+<td>override_charge</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>ms_level</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>activation_method</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>digest_mass_range</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>num_results</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>skip_researching</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>max_fragment_charge</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>max_precursor_charge</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
+<td>max_variable_mods_in_peptide</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<td>require_variable_mod</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<td>add_Cterm_peptide</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<td>add_Nterm_peptide</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_Cterm_protein</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_Nterm_protein</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_A_alanine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_B_user_amino_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_C_cysteine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_D_aspartic_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_E_glutamic_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_F_phenylalanine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_G_glycine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_H_histidine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_I_isoleucine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_J_user_amino_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_K_lysine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_L_leucine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_M_methionine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_N_asparagine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_O_ornithine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_P_proline</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_Q_glutamine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_R_arginine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_S_serine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr>
+<td>add_Z_user_amino_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
+<td>hardklor-algorithm</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr>
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+<tr>
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+<td>cdm</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<td>depth</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr bgcolor="#DEDEDE">
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+<td>instrument</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<td>max-features</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
+<td>delimiter</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>header</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>comparison</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>column-type</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>min-mass</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>max-mass</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>min-length</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>max-length</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>custom-enzyme</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>digestion</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>missed-cleavages</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>isotopic-mass</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>seed</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>clip-nterm-methionine</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>decoy-format</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>keep-terminal-aminos</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>stats</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>top-match</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>output-file</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>pout-output</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>feature-file-in</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<tr bgcolor="#DEDEDE">
+<td>protein-enzyme</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>protein-report-fragments</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
+<td>decoy-xml-output</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr bgcolor="#DEDEDE">
+<td>c-pos</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>c-neg</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>train-fdr</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>test-fdr</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>maxiter</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr>
+<td>unitnorm</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>fido-alpha</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr bgcolor="#DEDEDE">
+<td>fido-gamma</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr bgcolor="#DEDEDE">
+<td>override</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
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+<tr bgcolor="#DEDEDE">
+<td>klammer</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>only-psms</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<td>W</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>Y</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>ascending</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>parsimony</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>threshold</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>threshold-type</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>input-ms2</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>unique-mapping</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>quant-level</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>measure</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>custom-threshold-name</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>custom-threshold-min</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>mzid-use-pass-threshold</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>precision</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td></tr>
+<tr>
+<td>peptide-list</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>mods-spec</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>cterm-peptide-mods-spec</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>nterm-peptide-mods-spec</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>min-mods</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>allow-dups</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>temp-dir</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>xlink-score-method</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td></tr>
+</table></body></html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/percolator.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/percolator.html
new file mode 100644
index 0000000..06119a2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/percolator.html
@@ -0,0 +1,209 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>percolator</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
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+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>percolator</h1>
+<h2>Usage:</h2>
+<p><code>crux percolator [options] <peptide-spectrum matches></code></p>
+<h2>Description:</h2>
+<p>Percolator is a semi-supervised learning algorithm that dynamically learns to separate target from decoy peptide-spectrum matches (PSMs). The algorithm is described in this article:</p><blockquote> Lukas Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and Michael J. MacCoss. <a href="http://noble.gs.washington.edu/papers/kall2007semi-supervised.html">"Semi-supervised learning for peptide identification from shotgun proteomics datasets."</a> <em>Nature Metho [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>peptide-spectrum matches</code> – A collection of target and decoy peptide-spectrum matches (PSMs). Input may be in one of five formats: PIN, SQT, pepXML, <a href="../file-formats/txt-format.html">Crux tab-delimited text</a>, or a list of files (when list-of-files=T). Note that if the input is provided as SQT, pepXML, or Crux tab-delimited text, then a PIN file will be generated in the output directory prior to execution.Crux determines the format of the input file by e [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>percolator.target.proteins.txt</code> – a tab-delimited file containing the target protein matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.proteins.txt</code> – a tab-delimited file containing the decoy protein matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.target.peptides.txt</code> – a tab-delimited file containing the target peptide matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.peptides.txt</code> – a tab-delimited file containing the decoy peptide matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.target.psms.txt</code> – a tab-delimited file containing the target PSMs. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.psms.txt</code> – a tab-delimited file containing the decoy PSMs. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.params.txt</code> – a file containing the name and value of all parameters for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>percolator.pep.xml</code> – a file containing the PSMs in <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">pepXML format</a>. This file can be used as input to some of the tools in the <a href="http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP">Transproteomic Pipeline</a>.</li>
+ <li><code>percolator.mzid</code> – a file containing the protein, peptide, and spectrum matches in <a href="http://www.psidev.info/mzidentml">mzIdentML format</a>.</li>
+ <li><code>percolator.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Protein inference options</h3>
+<ul>
+ <li class="nobullet"><code>--picked-protein <string></code> – Use the picked protein-level FDR to infer protein probabilities, provide the fasta file as the argument to this flag. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--protein-enzyme no_enzyme|elastase|pepsin|proteinasek|thermolysin|trypsinp|chymotrypsin|lys-n|lys-c|arg-c|asp-n|glu-c|trypsin</code> – Type of enzyme Default = <code>trypsin</code>.</li>
+ <li class="nobullet"><code>--protein-report-fragments T|F</code> – By default, if the peptides associated with protein A are a proper subset of the peptides associated with protein B, then protein A is eliminated and all the peptides are considered as evidence for protein B. Note that this filtering is done based on the complete set of peptides in the database, not based on the identified peptides in the search results. Alternatively, if this option is set and if all of the ident [...]
+ <li class="nobullet"><code>--protein-report-duplicates T|F</code> – If multiple database proteins contain exactly the same set of peptides, then Percolator will randomly discard all but one of the proteins. If this option is set, then the IDs of these duplicated proteins will be reported as a comma-separated list. Not available for Fido. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fido options</h3>
+<ul>
+ <li class="nobullet"><code>--protein T|F</code> – Use the Fido algorithm to infer protein probabilities. Must be true to use any of the Fido options. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fido-alpha <float></code> – Specify the probability with which a present protein emits an associated peptide. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-beta <float></code> – Specify the probability of the creation of a peptide from noise. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-gamma <float></code> – Specify the prior probability that a protein is present in the sample. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-empirical-protein-q T|F</code> – Estimate empirical p-values and q-values for proteins using target-decoy analysis. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fido-gridsearch-depth <integer></code> – Set depth of the grid search for alpha, beta and gamma estimation. The values considered, for each possible value of the --fido-gridsearch-depth parameter, are as follows:<ul><li>0: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36, 0.5}; beta = {0.0, 0.01, 0.15, 0.025, 0.035, 0.05, 0.1}; gamma = {0.1, 0.25, 0.5, 0.75}.</li><li>1: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36}; beta = {0.0, 0.01, 0.15, 0.025, 0.0 [...]
+ <li class="nobullet"><code>--fido-gridsearch-mse-threshold <float></code> – Q-value threshold that will be used in the computation of the MSE and ROC AUC score in the grid search. Default = <code>0.05</code>.</li>
+ <li class="nobullet"><code>--fido-fast-gridsearch <float></code> – Apply the specified threshold to PSM, peptide and protein probabilities to obtain a faster estimate of the alpha, beta and gamma parameters. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-protein-truncation-threshold <float></code> – To speed up inference, proteins for which none of the associated peptides has a probability exceeding the specified threshold will be assigned probability = 0. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--fido-no-split-large-components T|F</code> – Do not approximate the posterior distribution by allowing large graph components to be split into subgraphs. The splitting is done by duplicating peptides with low probabilities. Splitting continues until the number of possible configurations of each subgraph is below 2^18 Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>General options</h3>
+<ul>
+ <li class="nobullet"><code>--only-psms T|F</code> – Do not remove redundant peptides; keep all PSMs and exclude peptide level probability. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--tdc T|F</code> – Use target-decoy competition to assign q-values and PEPs. When set to F, the mix-max method, which estimates the proportion pi0 of incorrect target PSMs, is used instead. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--search-input auto|separate|concatenated</code> – Specify the type of target-decoy search. Using 'auto', percolator attempts to detect the search type automatically. Using 'separate' specifies two searches: one against target and one against decoy protein db. Using 'concatenated' specifies a single search on concatenated target-decoy protein db. Default = <code>auto</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>SVM training options</h3>
+<ul>
+ <li class="nobullet"><code>--subset-max-train <integer></code> – Only train Percolator on a subset of PSMs, and use the resulting score vector to evaluate the other PSMs. Recommended when analyzing huge numbers (>1 million) of PSMs. When set to 0, all PSMs are used for training as normal. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--c-pos <float></code> – Penalty for mistakes made on positive examples. If this value is set to 0, then it is set via cross validation over the values {0.1, 1, 10}, selecting the value that yields the largest number of PSMs identified at the q-value threshold set via the --test-fdr parameter. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--c-neg <float></code> – Penalty for mistake made on negative examples. If not specified, then this value is set by cross validation over {0.1, 1, 10}. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--train-fdr <float></code> – False discovery rate threshold to define positive examples in training. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--test-fdr <float></code> – False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--maxiter <integer></code> – Maximum number of iterations for training. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--quick-validation T|F</code> – Quicker execution by reduced internal cross-validation. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--test-each-iteration T|F</code> – Measure performance on test set each iteration. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--percolator-seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>SVM feature input options</h3>
+<ul>
+ <li class="nobullet"><code>--output-weights T|F</code> – Output final weights to a file named "percolator.weights.txt". Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--init-weights <string></code> – Read initial weights from the given file (one per line). Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--default-direction <string></code> – In its initial round of training, Percolator uses one feature to induce a ranking of PSMs. By default, Percolator will select the feature that produces the largest set of target PSMs at a specified FDR threshold (cf. --train-fdr). This option allows the user to specify which feature is used for the initial ranking, using the name as a string from <a href="../file-formats/features.html">this table</a>. The name [...]
+ <li class="nobullet"><code>--unitnorm T|F</code> – Use unit normalization (i.e., linearly rescale each PSM's feature vector to have a Euclidean length of 1), instead of standard deviation normalization. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--override T|F</code> – By default, Percolator will examine the learned weights for each feature, and if the weight appears to be problematic, then percolator will discard the learned weights and instead employ a previously trained, static score vector. This switch allows this error checking to be overriden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--klammer T|F</code> – Use retention time features calculated as in "Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions" by Klammer AA, Yi X, MacCoss MJ and Noble WS. (<em>Analytical Chemistry</em>. 2007 Aug 15;79(16):6111-8.). Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--pout-output T|F</code> – Output a Percolator <a href="https://github.com/percolator/percolator/blob/master/src/xml/percolator_out.xsd">pout.xml</a> format results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mzid-output T|F</code> – Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-out T|F</code> – Output the computed features in <a href="../file-formats/features.html">tab-delimited text format</a>. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--feature-file-in T|F</code> – When set to T, interpret the input file as a PIN file. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-xml-output T|F</code> – Include decoys (PSMs, peptides, and/or proteins) in the XML output. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
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+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
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+<!DOCTYPE html>
+<html>
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+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
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+ <li><a href="../index.html">Home</a></li>
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+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>pipeline</h1>
+<h2>Usage:</h2>
+<p><code>crux pipeline [options] <mass spectra>+ <peptide source></code></p>
+<h2>Description:</h2>
+<p>Given one or more sets of tandem mass spectra as well as a protein database, this command runs a series of Crux tools and reports all of the results in a single output directory. There are three steps in the pipeline:</p><ol><li><a href="bullseye.html">Bullseye</a> to assign high-resolution precursor m/z values to MS/MS data. This step is optional.</li><li>Database searching using either <a href="tide-search.html">Tide-search</a> or <a href="comet.html">Comet</a>. The database can be [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>mass spectra+</code> – The name of the file(s) from which to parse the fragmentation spectra, in any of the <a href="http://proteowizard.sourceforge.net/tools.shtml">file formats supported by ProteoWizard</a>. Alteratively, with Tide-search, these files may be binary spectrum files produced by a previous run of <code>crux tide-search</code> using the <code>store-spectra</code> parameter.</li>
+ <li><code>peptide source</code> – Either the name of a file in fasta format from which to retrieve proteins and peptides or an index created by a previous run of <code>crux tide-index</code> (for Tide searching).</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>bullseye.pid.<format></code> – a file containing the fragmentation spectra for which accurate masses were successfully inferred. Unless otherwise specified (with the --spectrum-format option), the output file format is ".ms2". Note that if the output format is ".ms2," then a single spectrum may have multiple "Z" lines, each indicating a charge state and accurate mass. In addition, Bullseye inserts an "I" line (for charge-dependent analysis) corresponding to each "Z" lin [...]
+ <li><code>bullseye.no-pid.<format></code> – a file containing the fragmentation spectra for which accurate masses were not inferred.</li>
+ <li><code>hardklor.mono.txt</code> – a tab-delimited text file containing one line for each isotope distribution, as described <a href="hardklor.html">here</a>.</li>
+ <li><code>bullseye.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>bullseye.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+ <li><code>tide-search.target.txt</code> – a tab-delimited text file containing the target PSMs. See <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>tide-search.decoy.txt</code> – a tab-delimited text file containing the decoy PSMs. This file will only be created if the index was created with decoys.</li>
+ <li><code>tide-search.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other Crux programs.</li>
+ <li><code>tide-search.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+ <li><code>comet.target.txt</code> – a tab-delimited text file containing the target PSMs. See <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>comet.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>comet.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+ <li><code>percolator.target.proteins.txt</code> – a tab-delimited file containing the target protein matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.proteins.txt</code> – a tab-delimited file containing the decoy protein matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.target.peptides.txt</code> – a tab-delimited file containing the target peptide matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.peptides.txt</code> – a tab-delimited file containing the decoy peptide matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.target.psms.txt</code> – a tab-delimited file containing the target PSMs. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.psms.txt</code> – a tab-delimited file containing the decoy PSMs. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.params.txt</code> – a file containing the name and value of all parameters for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>percolator.pep.xml</code> – a file containing the PSMs in <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">pepXML format</a>. This file can be used as input to some of the tools in the <a href="http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP">Transproteomic Pipeline</a>.</li>
+ <li><code>percolator.mzid</code> – a file containing the protein, peptide, and spectrum matches in <a href="http://www.psidev.info/mzidentml">mzIdentML format</a>.</li>
+ <li><code>percolator.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+ <li><code>assign-confidence.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> that contains the targets, sorted by score. The file will contain one new column, named "<method> q-value", where <method> is either "tdc" or "mix-max".</li>
+ <li><code>assign-confidence.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>assign-confidence.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>pipeline options</h3>
+<ul>
+ <li class="nobullet"><code>--bullseye T|F</code> – Run the Bullseye algorithm on the given MS data, using it to assign high-resolution precursor values to the MS/MS data. If a spectrum file ends with .ms2 or .cms2, matching .ms1/.cms1 files will be used as the MS1 file. Otherwise, it is assumed that the spectrum file contains both MS1 and MS2 scans. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--search-engine comet|tide-search</code> – Specify which search engine to use. Default = <code>tide-search</code>.</li>
+ <li class="nobullet"><code>--post-processor percolator|assign-confidence|none</code> – Specify which post-processor to apply to the search results. Default = <code>percolator</code>.</li>
+ <li class="nobullet"><code>--estimation-method mix-max|tdc|peptide-level</code> – Specify the method used to estimate q-values. The mix-max procedure or target-decoy competition apply to PSMs. The peptide-level option eliminates any PSM for which there exists a better scoring PSM involving the same peptide, and then uses decoys to assign confidence estimates. Default = <code>tdc</code>.</li>
+ <li class="nobullet"><code>--score <string></code> – Specify the column (for tab-delimited input) or tag (for XML input) used as input to the q-value estimation procedure. If this parameter is unspecified, then the program searches for "xcorr score", "evalue" (comet), "exact p-value" score fields in this order in the input file. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--sidak T|F</code> – Adjust the score using the Sidak adjustment and reports them in a new column in the output file. Note that this adjustment only makes sense if the given scores are p-values, and that it requires the presence of the "distinct matches/spectrum" feature for each PSM. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-charge-states T|F</code> – Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-modified-peptides T|F</code> – Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Identifying PPIDs in MS1 spectra</h3>
+<ul>
+ <li class="nobullet"><code>--max-persist <float></code> – Ignore PPIDs that persist for longer than this length of time in the MS1 spectra. The unit of time is whatever unit is used in your data file (usually minutes). These PPIDs are considered contaminants. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--persist-tolerance <float></code> – Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--gap-tolerance <integer></code> – Allowed gap size when checking for PPIDs across consecutive MS1 scans. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--scan-tolerance <integer></code> – Total number of MS1 scans over which a PPID must be observed to be considered real. Gaps in persistence are allowed by setting --gap-tolerance. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--bullseye-max-mass <float></code> – Only consider PPIDs below this maximum mass in daltons. Default = <code>8000</code>.</li>
+ <li class="nobullet"><code>--bullseye-min-mass <float></code> – Only consider PPIDs above this minimum mass in daltons. Default = <code>600</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Matching PPIDs to MS2 spectra</h3>
+<ul>
+ <li class="nobullet"><code>--exact-match T|F</code> – When true, require an exact match (as defined by --exact-tolerance) between the center of the precursor isolation window in the MS2 scan and the base isotopic peak of the PPID. If this option is set to false and no exact match is observed, then attempt to match using a wider m/z tolerance. This wider tolerance is calculated using the PPID's monoisotopic mass and charge (the higher the charge, the smaller the window). Default = [...]
+ <li class="nobullet"><code>--exact-tolerance <float></code> – Set the tolerance (+/-ppm) for --exact-match. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--retention-tolerance <float></code> – Set the tolerance (+/-units) around the retention time over which a PPID can be matches to the MS2 spectrum. The unit of time is whatever unit is used in your data file (usually minutes). Default = <code>0.5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Precursor selection</h3>
+<ul>
+ <li class="nobullet"><code>--precursor-window <float></code> – Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto-precursor-window false|warn|fail</code> – Automatically estimate optimal value for the precursor-window parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> – Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not avail [...]
+ <li class="nobullet"><code>--max-precursor-charge <integer></code> – The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-min-mz <float></code> – The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum-max-mz <float></code> – The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
+ <li class="nobullet"><code>--min-peaks <integer></code> – The minimum number of peaks a spectrum must have for it to be searched. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--spectrum-charge 1|2|3|all</code> – The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge state will be searched. Default = <code>all</code>.</li>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--compute-sp T|F</code> – Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spe [...]
+ <li class="nobullet"><code>--remove-precursor-peak T|F</code> – If true, all peaks around the precursor m/z will be removed, within a range specified by the --remove-precursor-tolerance option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--exact-p-value T|F</code> – Enable the calculation of exact p-values for the XCorr score as described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this article</a>. Calculation of p-values increases the running time but increases the number of identifications at a fixed confidence threshold. The p-values will be reported in a new column with header "exact p-value", and the "xcorr score" column will be replaced with a "refactored xcorr" colu [...]
+ <li class="nobullet"><code>--use-neutral-loss-peaks T|F</code> – Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+ <li class="nobullet"><code>--auto-mz-bin-width false|warn|fail</code> – Automatically estimate optimal value for the mz-bin-width parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-offset <float></code> – In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--peptide-centric-search T|F</code> – Carries out a peptide-centric search. For each peptide the top-scoring spectra are reported, in contrast to the standard spectrum-centric search where the top-scoring peptides are reported. Note that in this case the "xcorr rank" column will contain the rank of the given spectrum with respect to the given candidate peptide, rather than vice versa (which is the default). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--isotope-error <string></code> – List of positive, non-zero integers. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--skip-preprocessing T|F</code> – Skip preprocessing steps on spectra. Default = F. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Protein inference options</h3>
+<ul>
+ <li class="nobullet"><code>--picked-protein <string></code> – Use the picked protein-level FDR to infer protein probabilities, provide the fasta file as the argument to this flag. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--protein-enzyme no_enzyme|elastase|pepsin|proteinasek|thermolysin|trypsinp|chymotrypsin|lys-n|lys-c|arg-c|asp-n|glu-c|trypsin</code> – Type of enzyme Default = <code>trypsin</code>.</li>
+ <li class="nobullet"><code>--protein-report-fragments T|F</code> – By default, if the peptides associated with protein A are a proper subset of the peptides associated with protein B, then protein A is eliminated and all the peptides are considered as evidence for protein B. Note that this filtering is done based on the complete set of peptides in the database, not based on the identified peptides in the search results. Alternatively, if this option is set and if all of the ident [...]
+ <li class="nobullet"><code>--protein-report-duplicates T|F</code> – If multiple database proteins contain exactly the same set of peptides, then Percolator will randomly discard all but one of the proteins. If this option is set, then the IDs of these duplicated proteins will be reported as a comma-separated list. Not available for Fido. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fido options</h3>
+<ul>
+ <li class="nobullet"><code>--protein T|F</code> – Use the Fido algorithm to infer protein probabilities. Must be true to use any of the Fido options. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fido-alpha <float></code> – Specify the probability with which a present protein emits an associated peptide. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-beta <float></code> – Specify the probability of the creation of a peptide from noise. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-gamma <float></code> – Specify the prior probability that a protein is present in the sample. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-empirical-protein-q T|F</code> – Estimate empirical p-values and q-values for proteins using target-decoy analysis. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fido-gridsearch-depth <integer></code> – Set depth of the grid search for alpha, beta and gamma estimation. The values considered, for each possible value of the --fido-gridsearch-depth parameter, are as follows:<ul><li>0: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36, 0.5}; beta = {0.0, 0.01, 0.15, 0.025, 0.035, 0.05, 0.1}; gamma = {0.1, 0.25, 0.5, 0.75}.</li><li>1: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36}; beta = {0.0, 0.01, 0.15, 0.025, 0.0 [...]
+ <li class="nobullet"><code>--fido-gridsearch-mse-threshold <float></code> – Q-value threshold that will be used in the computation of the MSE and ROC AUC score in the grid search. Default = <code>0.05</code>.</li>
+ <li class="nobullet"><code>--fido-fast-gridsearch <float></code> – Apply the specified threshold to PSM, peptide and protein probabilities to obtain a faster estimate of the alpha, beta and gamma parameters. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-protein-truncation-threshold <float></code> – To speed up inference, proteins for which none of the associated peptides has a probability exceeding the specified threshold will be assigned probability = 0. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--fido-no-split-large-components T|F</code> – Do not approximate the posterior distribution by allowing large graph components to be split into subgraphs. The splitting is done by duplicating peptides with low probabilities. Splitting continues until the number of possible configurations of each subgraph is below 2^18 Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Database</h3>
+<ul>
+ <li class="nobullet"><code>--decoy_search <integer></code> – 0=no, 1=concatenated search, 2=separate search. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>CPU threads</h3>
+<ul>
+ <li class="nobullet"><code>--num-threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--num_threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Masses</h3>
+<ul>
+ <li class="nobullet"><code>--peptide_mass_tolerance <float></code> – Controls the mass tolerance value. The mass tolerance is set at +/- the specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0 tolerance. The units of the mass tolerance is controlled by the parameter "peptide_mass_units". Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto_peptide_mass_tolerance false|warn|fail</code> – Automatically estimate optimal value for the peptide_mass_tolerancel parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--peptide_mass_units <integer></code> – 0=amu, 1=mmu, 2=ppm. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--mass_type_parent <integer></code> – 0=average masses, 1=monoisotopic masses. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--mass_type_fragment <integer></code> – 0=average masses, 1=monoisotopic masses. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--precursor_tolerance_type <integer></code> – 0=singly charged peptide mass, 1=precursor m/z. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--isotope_error <integer></code> – 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8 labeling). Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search enzyme</h3>
+<ul>
+ <li class="nobullet"><code>--search_enzyme_number <integer></code> – Specify a search enzyme from the end of the parameter file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--num_enzyme_termini <integer></code> – valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--allowed_missed_cleavage <integer></code> – Maximum value is 5; for enzyme search. Default = <code>2</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fragment ions</h3>
+<ul>
+ <li class="nobullet"><code>--fragment_bin_tol <float></code> – Binning to use on fragment ions. Default = <code>1.000507</code>.</li>
+ <li class="nobullet"><code>--fragment_bin_offset <float></code> – Offset position to start the binning (0.0 to 1.0). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--auto_fragment_bin_tol false|warn|fail</code> – Automatically estimate optimal value for the fragment_bin_tol parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--theoretical_fragment_ions <integer></code> – 0=default peak shape, 1=M peak only. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_A_ions <integer></code> – Controls whether or not A-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_B_ions <integer></code> – Controls whether or not B-ions are considered in the search (0 - no, 1 - yes). Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_C_ions <integer></code> – Controls whether or not C-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_X_ions <integer></code> – Controls whether or not X-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_Y_ions <integer></code> – Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes). Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_Z_ions <integer></code> – Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_NL_ions <integer></code> – 0=no, 1= yes to consider NH3/H2O neutral loss peak. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>mzXML/mzML parameters</h3>
+<ul>
+ <li class="nobullet"><code>--scan_range <string></code> – Start and scan scan range to search; 0 as first entry ignores parameter. Default = <code>0 0</code>.</li>
+ <li class="nobullet"><code>--precursor_charge <string></code> – Precursor charge range to analyze; does not override mzXML charge; 0 as first entry ignores parameter. Default = <code>0 0</code>.</li>
+ <li class="nobullet"><code>--override_charge <integer></code> – Specifies the whether to override existing precursor charge state information when present in the files with the charge range specified by the "precursor_charge" parameter. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--ms_level <integer></code> – MS level to analyze, valid are levels 2 or 3. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--activation_method ALL|CID|ECD|ETD|PQD|HCD|IRMPD</code> – Specifies which scan types are searched. Default = <code>ALL</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Miscellaneous parameters</h3>
+<ul>
+ <li class="nobullet"><code>--digest_mass_range <string></code> – MH+ peptide mass range to analyze. Default = <code>600.0 5000.0</code>.</li>
+ <li class="nobullet"><code>--num_results <integer></code> – Number of search hits to store internally. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--skip_researching <integer></code> – For '.out' file output only, 0=search everything again, 1=don't search if .out exists. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--max_fragment_charge <integer></code> – Set maximum fragment charge state to analyze (allowed max 5). Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--max_precursor_charge <integer></code> – Set maximum precursor charge state to analyze (allowed max 9). Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--nucleotide_reading_frame <integer></code> – 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--clip_nterm_methionine <integer></code> – 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum_batch_size <integer></code> – Maximum number of spectra to search at a time; 0 to search the entire scan range in one loop. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--decoy_prefix <string></code> – Specifies the prefix of the protein names that indicates a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--output_suffix <string></code> – Specifies the suffix string that is appended to the base output name for the pep.xml, pin.xml, txt and sqt output files. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--mass_offsets <string></code> – Specifies one or more mass offsets to apply. This value(s) are effectively subtracted from each precursor mass such that peptides that are smaller than the precursor mass by the offset value can still be matched to the respective spectrum. Default = <code><empty></code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Spectral processing</h3>
+<ul>
+ <li class="nobullet"><code>--minimum_peaks <integer></code> – Minimum number of peaks in spectrum to search. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--minimum_intensity <float></code> – Minimum intensity value to read in. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--remove_precursor_peak <integer></code> – 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--remove_precursor_tolerance <float></code> – +- Da tolerance for precursor removal. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--clear_mz_range <string></code> – For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range. Default = <code>0.0 0.0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Variable modifications</h3>
+<ul>
+ <li class="nobullet"><code>--variable_mod01 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod02 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod03 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod04 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod05 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod06 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod07 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod08 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod09 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--max_variable_mods_in_peptide <integer></code> – Specifies the total/maximum number of residues that can be modified in a peptide. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--require_variable_mod <integer></code> – Controls whether the analyzed peptides must contain at least one variable modification. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Static modifications</h3>
+<ul>
+ <li class="nobullet"><code>--add_Cterm_peptide <float></code> – Specifiy a static modification to the c-terminus of all peptides. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Nterm_peptide <float></code> – Specify a static modification to the n-terminus of all peptides. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Cterm_protein <float></code> – Specify a static modification to the c-terminal peptide of each protein. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Nterm_protein <float></code> – Specify a static modification to the n-terminal peptide of each protein. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_A_alanine <float></code> – Specify a static modification to the residue A. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_B_user_amino_acid <float></code> – Specify a static modification to the residue B. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_C_cysteine <float></code> – Specify a static modification to the residue C. Default = <code>57.021464</code>.</li>
+ <li class="nobullet"><code>--add_D_aspartic_acid <float></code> – Specify a static modification to the residue D. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_E_glutamic_acid <float></code> – Specify a static modification to the residue E. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_F_phenylalanine <float></code> – Specify a static modification to the residue F. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_G_glycine <float></code> – Specify a static modification to the residue G. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_H_histidine <float></code> – Specify a static modification to the residue H. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_I_isoleucine <float></code> – Specify a static modification to the residue I. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_J_user_amino_acid <float></code> – Specify a static modification to the residue J. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_K_lysine <float></code> – Specify a static modification to the residue K. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_L_leucine <float></code> – Specify a static modification to the residue L. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_M_methionine <float></code> – Specify a static modification to the residue M. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_N_asparagine <float></code> – Specify a static modification to the residue N. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_O_ornithine <float></code> – Specify a static modification to the residue O. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_P_proline <float></code> – Specify a static modification to the residue P. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Q_glutamine <float></code> – Specify a static modification to the residue Q. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_R_arginine <float></code> – Specify a static modification to the residue R. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_S_serine <float></code> – Specify a static modification to the residue S. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_T_threonine <float></code> – Specify a static modification to the residue T. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_U_selenocysteine <float></code> – Specify a static modification to the residue U. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_V_valine <float></code> – Specify a static modification to the residue V. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_W_tryptophan <float></code> – Specify a static modification to the residue W. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_X_user_amino_acid <float></code> – Specify a static modification to the residue X. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Y_tyrosine <float></code> – Specify a static modification to the residue Y. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Z_user_amino_acid <float></code> – Specify a static modification to the residue Z. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>General options</h3>
+<ul>
+ <li class="nobullet"><code>--only-psms T|F</code> – Do not remove redundant peptides; keep all PSMs and exclude peptide level probability. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--tdc T|F</code> – Use target-decoy competition to assign q-values and PEPs. When set to F, the mix-max method, which estimates the proportion pi0 of incorrect target PSMs, is used instead. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--search-input auto|separate|concatenated</code> – Specify the type of target-decoy search. Using 'auto', percolator attempts to detect the search type automatically. Using 'separate' specifies two searches: one against target and one against decoy protein db. Using 'concatenated' specifies a single search on concatenated target-decoy protein db. Default = <code>auto</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>SVM training options</h3>
+<ul>
+ <li class="nobullet"><code>--subset-max-train <integer></code> – Only train Percolator on a subset of PSMs, and use the resulting score vector to evaluate the other PSMs. Recommended when analyzing huge numbers (>1 million) of PSMs. When set to 0, all PSMs are used for training as normal. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--c-pos <float></code> – Penalty for mistakes made on positive examples. If this value is set to 0, then it is set via cross validation over the values {0.1, 1, 10}, selecting the value that yields the largest number of PSMs identified at the q-value threshold set via the --test-fdr parameter. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--c-neg <float></code> – Penalty for mistake made on negative examples. If not specified, then this value is set by cross validation over {0.1, 1, 10}. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--train-fdr <float></code> – False discovery rate threshold to define positive examples in training. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--test-fdr <float></code> – False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--maxiter <integer></code> – Maximum number of iterations for training. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--quick-validation T|F</code> – Quicker execution by reduced internal cross-validation. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--test-each-iteration T|F</code> – Measure performance on test set each iteration. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--percolator-seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>SVM feature input options</h3>
+<ul>
+ <li class="nobullet"><code>--output-weights T|F</code> – Output final weights to a file named "percolator.weights.txt". Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--init-weights <string></code> – Read initial weights from the given file (one per line). Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--default-direction <string></code> – In its initial round of training, Percolator uses one feature to induce a ranking of PSMs. By default, Percolator will select the feature that produces the largest set of target PSMs at a specified FDR threshold (cf. --train-fdr). This option allows the user to specify which feature is used for the initial ranking, using the name as a string from <a href="../file-formats/features.html">this table</a>. The name [...]
+ <li class="nobullet"><code>--unitnorm T|F</code> – Use unit normalization (i.e., linearly rescale each PSM's feature vector to have a Euclidean length of 1), instead of standard deviation normalization. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--override T|F</code> – By default, Percolator will examine the learned weights for each feature, and if the weight appears to be problematic, then percolator will discard the learned weights and instead employ a previously trained, static score vector. This switch allows this error checking to be overriden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--klammer T|F</code> – Use retention time features calculated as in "Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions" by Klammer AA, Yi X, MacCoss MJ and Noble WS. (<em>Analytical Chemistry</em>. 2007 Aug 15;79(16):6111-8.). Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--spectrum-format |ms2|bms2|cms2|mgf</code> – The format to write the output spectra to. If empty, the spectra will be output in the same format as the MS2 input. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--store-spectra <string></code> – Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir). This option is not valid if multiple input spectrum files are given. Default = <code><e [...]
+ <li class="nobullet"><code>--store-index <string></code> – When providing a FASTA file as the index, the generated binary index will be stored at the given path. This option has no effect if a binary index is provided as the index. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--concat T|F</code> – When set to T, target and decoy search results are reported in a single file, and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--print-search-progress <integer></code> – Show search progress by printing every n spectra searched. Set to 0 to show no search progress. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--sqt-output T|F</code> – Outputs an SQT results file to the output directory. Note that if sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mzid-output T|F</code> – Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pin-output T|F</code> – Output a Percolator input (PIN) file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--file-column T|F</code> – Include the file column in tab-delimited output. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--output_sqtfile <integer></code> – 0=no, 1=yes write sqt file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--output_txtfile <integer></code> – 0=no, 1=yes write tab-delimited text file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--output_pepxmlfile <integer></code> – 0=no, 1=yes write pep.xml file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--output_percolatorfile <integer></code> – 0=no, 1=yes write percolator file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--output_outfiles <integer></code> – 0=no, 1=yes write .out files. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--print_expect_score <integer></code> – 0=no, 1=yes to replace Sp with expect in out & sqt. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--num_output_lines <integer></code> – num peptide results to show. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--show_fragment_ions <integer></code> – 0=no, 1=yes for out files only. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--sample_enzyme_number <integer></code> – Sample enzyme which is possibly different than the one applied to the search. Used to calculate NTT & NMC in pepXML output. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--pout-output T|F</code> – Output a Percolator <a href="https://github.com/percolator/percolator/blob/master/src/xml/percolator_out.xsd">pout.xml</a> format results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-out T|F</code> – Output the computed features in <a href="../file-formats/features.html">tab-delimited text format</a>. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-in T|F</code> – When set to T, interpret the input file as a PIN file. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-xml-output T|F</code> – Include decoys (PSMs, peptides, and/or proteins) in the XML output. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
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+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/predict-peptide-ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/predict-peptide-ions.html
new file mode 100644
index 0000000..552c290
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/predict-peptide-ions.html
@@ -0,0 +1,141 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>predict-peptide-ions</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>predict-peptide-ions</h1>
+<h2>Usage:</h2>
+<p><code>crux predict-peptide-ions [options] <peptide sequence> <charge state></code></p>
+<h2>Description:</h2>
+<p>Given a peptide and a charge state, predict the corresponding fragment ions according to the provided options.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>peptide sequence</code> – The peptide sequence.</li>
+ <li><code>charge state</code> – The charge state of the peptide.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – a series of lines, describing how the ions were predicted. <blockquote style="font-family: monospace;"># PEPTIDE: <peptide sequence><br># CHARGE: <peptide charge></blockquote>The program then prints a one-line header that labels the tab-delimited columns, followed by one line per ion:<blockquote style="font-family: monospace;">m/z mass charge ion-series peptide-bond-index nh3 h2o isotope flank</blockquo [...]
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>predict-peptide-ions options</h3>
+<ul>
+ <li class="nobullet"><code>--primary-ions a|b|y|by|bya</code> – Predict the specified primary ion series. 'a' indicates a-ions only, 'b' indicates b-ions only, 'y' indicates y-ions only, 'by' indicates both b and y, 'bya' indicates b, y, and a. Default = <code>by</code>.</li>
+ <li class="nobullet"><code>--precursor-ions T|F</code> – Predict the precursor ions, and all associated ions (neutral losses, multiple charge states) consistent with the other specified options. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--isotope <integer></code> – Predict the given number of isotope peaks (0|1|2). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--flanking T|F</code> – Predict flanking peaks for b- and y ions. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--nh3 <integer></code> – Include among the predicted peaks b/y ions with up to n losses of nh3. For example, for --nh3 2, predict a peak for each b- and y-ion with the loss of one nh3 group and predict a second peak for each b- and y-ion with the loss of two nh3 groups. These peaks will have 1 and 2, respectively, in the NH3 column of the output. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--h2o <integer></code> – Include in the predicted peaks, b/y ions with the loss of 1 to n water molecules. See --nh3 for an example. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--max-ion-charge <string></code> – Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state of the peptide ("peptide"). If the max-ion-charge is greater than the charge state of the peptide, then the maximum is the peptide charge. Default = <code>peptide</code>.</li>
+ <li class="nobullet"><code>--fragment-mass average|mono</code> – Specify which isotopes to use in calculating fragment ion mass. Default = <code>mono</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/print-processed-spectra.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/print-processed-spectra.html
new file mode 100644
index 0000000..1ba0ca2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/print-processed-spectra.html
@@ -0,0 +1,141 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>print-processed-spectra</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>print-processed-spectra</h1>
+<h2>Usage:</h2>
+<p><code>crux print-processed-spectra [options] <ms2 file> <output file></code></p>
+<h2>Description:</h2>
+<p>Pre-process each spectrum in a given file in preparation for computing XCorr. The pre-processing steps are described in detail in this paper:</p><blockquote>J. K. Eng, B. Fischer, J. Grossman and M. J. MacCoss. <a href="http://pubs.acs.org/doi/abs/10.1021/pr800420s">"A fast SEQUEST cross correlation algorithm process the peaks as for computing."</a> <em>Journal of Proteome Research</em>. 7(10):4598-4602, 2008.</blockquote><p>The output of this program is equivalent to the sp [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+ <li><code>output file</code> – File where spectrum will be written.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>output file</code> – The name of the file in which the processed spectra will be printed in MS2 format.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>print-processed-spectra options</h3>
+<ul>
+ <li class="nobullet"><code>--stop-after remove-precursor|square-root|remove-grass|ten-bin|xcorr</code> – Stop after the specified pre-processing step. Default = <code>xcorr</code>.</li>
+ <li class="nobullet"><code>--output-units mz|bin</code> – Specify the output units for processed spectra. Default = <code>bin</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/psm-convert.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/psm-convert.html
new file mode 100644
index 0000000..296d0d6
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/psm-convert.html
@@ -0,0 +1,142 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>psm-convert</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>psm-convert</h1>
+<h2>Usage:</h2>
+<p><code>crux psm-convert [options] <input PSM file> <output format></code></p>
+<h2>Description:</h2>
+Reads in a file containing peptide-spectrum matches (PSMs) in one of the variety of supported formats and outputs the same PSMs in a different format
+<h2>Input:</h2>
+<ul>
+ <li><code>input PSM file</code> – The name of a PSM file in tab-delimited text, SQT, pepXML or mzIdentML format</li>
+ <li><code>output format</code> – The desired format of the output file. Legal values are tsv, html, sqt, pin, pepxml, mzidentml.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>psm-convert.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>psm-convert.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>psm-convert options</h3>
+<ul>
+ <li class="nobullet"><code>--input-format auto|tsv|sqt|pepxml|mzidentml</code> – Legal values are auto, tsv, sqt, pepxml or mzidentml format. Default = <code>auto</code>.</li>
+ <li class="nobullet"><code>--distinct-matches T|F</code> – Whether matches/ion are distinct (as opposed to total). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--protein-database <string></code> – The name of the file in FASTA format. Default = <code><empty></code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/q-ranker.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/q-ranker.html
new file mode 100644
index 0000000..0a4abc2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/q-ranker.html
@@ -0,0 +1,160 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>q-ranker</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>q-ranker</h1>
+<h2>Usage:</h2>
+<p><code>crux q-ranker [options] <fragmentation spectra> <search results></code></p>
+<h2>Description:</h2>
+<p>Q-ranker dynamically learns to separate target from decoy PSMs. The algorithm is described in this article:</p><blockquote>Marina Spivak, Jason Weston, Leon Bottou and William Stafford Noble. <a href="http://noble.gs.washington.edu/papers/spivak2009improvements.html">"Direct <em>q</em> value optimization methods for peptide identification from shotgun proteomics data sets."</a> <em>Journal of Proteome Research</em>. 8(7):3737-3745, 2009.</blockquote><p>For more on q-values a [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>fragmentation spectra</code> – The fragmentation spectra must be provided in <a href="../file-formats/ms2-format.html">MS2</a>, mzXML, or MGF format.</li>
+ <li><code>search results</code> – Search results in the <a href="../file-formats/txt-format.html">tab-delimited text format</a> produced by Crux or in <a href="../file-formats/sqt-format.html">SQT format</a>. Like the spectra, the search results can be provided as a single file, a list of files or a directory of files. Note, however, that the input mode for spectra and for search results must be the same; i.e., if you provide a list of files for the spectra, then you must also pr [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>qranker.target.pep.xml</code> – An xml file containing ranked list of target peptide-spectrum matches. Thefollowing entries are included: scan, charge, psm_id, q-value, score, precursor_mass, peptide, filename.</li>
+ <li><code>qranker.decoy.pep.xml</code> – An xml file containing ranked list of decoy peptide-spectrum matches.</li>
+ <li><code>qranker.target.psm.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text format</a> containing a ranked list of target peptide-spectrum matches with the associated Q-ranker scores and q-values.</li>
+ <li><code>qranker.decoy.psm.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text format</a> containing a ranked list of decoy peptide-spectrum matches with the associated Q-ranker scores and q-values.</li>
+ <li><code>qranker.log.txt</code> – a file where the program reports its progress.</li>
+ <li><code>qranker.params.txt</code> – a file with the values of all the options given to the current run.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>q-ranker options</h3>
+<ul>
+ <li class="nobullet"><code>--separate-searches <string></code> – If the target and decoy searches were run separately, rather than using a concatenated database, then the program will assume that the database search results provided as a required argument are from the target database search. This option then allows the user to specify the location of the decoy search results. Like the required arguments, these search results can be provided as a single file, a list of files [...]
+ <li class="nobullet"><code>--skip-cleanup T|F</code> – Analysis begins with a pre-processsing step that creates a set of lookup tables which are then used during training. Normally, these lookup tables are deleted at the end of the analysis, but setting this option to T prevents the deletion of these tables. Subsequently, analyses can be repeated more efficiently by specifying the --re-run option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--re-run <string></code> – Re-run a previous analysis using a previously computed set of lookup tables. For this option to work, the --skip-cleanup option must have been set to true when the program was run the first time. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--use-spec-features T|F</code> – Use an enriched feature set, including separate features for each ion type. Default = <code>true</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-out T|F</code> – Output the computed features in <a href="../file-formats/features.html">tab-delimited text format</a>. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/read-tide-index.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/read-tide-index.html
new file mode 100644
index 0000000..12ed72e
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/read-tide-index.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>read-tide-index</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>read-tide-index</h1>
+<h2>Usage:</h2>
+<p><code>crux read-tide-index [options] <tide database></code></p>
+<h2>Description:</h2>
+Reads an index generated by tide-index and outputs information about the peptides it contains.
+<h2>Input:</h2>
+<ul>
+ <li><code>tide database</code> – Either a FASTA file or a directory containing a database index created by a previous run of crux tide-index.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>read-tide-index.peptides.txt</code> – a tab-delimited file containing two columns with headers: the peptide, and a semicolon-delimited list of IDs of the proteins that peptide occurs in.</li>
+ <li><code>read-tide-index.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>read-tide-index.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<p>This command does not support any optional parameters.</p>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/release-notes.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/release-notes.html
new file mode 100644
index 0000000..750d3d5
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/release-notes.html
@@ -0,0 +1,1849 @@
+<html>
+<head>
+<title>Release notes for Crux</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <blockquote>
+ <h2>Release notes for Crux</h2>
+
+<h3>Version 3.1</h3> January 10, 2017
+
+<h4>Major changes</h4>
+
+<ul>
+
+ <li>8 Nov 2016: Updated Percolator to use the latest version on GitHub.</li>
+ <li>31 Oct 2016: Added param-medic options to Comet and Tide</li>
+ <li>11 Oct 2016: Added the param-medic command.</li>
+ <li>07 Sept 2016: Added isotope-error parameter to Tide.</li>
+ <li>30 Aug 2016: Updated Percolator to version 3.00.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+ <li>
+ 9 Jan 2017: Added search-input option to Percolator.</li>
+
+ <li>
+ 29 Dec 2016: Allow assign-confidence to rank by Percolator score.</li>
+
+ <li>
+ 1 Nov 2016: Added tdc and subset-max-train options to Percolator.</li>
+
+ <li>
+ 20 Sept 2016: Percolator changed to use a modified version of its
+ native output.</li>
+
+ <li>
+ 30 Nov 2016: Added +1 to the numerator of the FDR estimation when
+ carrying out target-decoy competition. This correction was
+ proposed by Barber and
+ Candes, <a href="https://arxiv.org/abs/1404.5609"><i>Annals of
+ Statistics</i></a>, 2015, as well as by He et al.,
+ <a href="http://arxiv.org/abs/1501.00537"</a>arXiv:1501.00537</a>,
+ 2015.</li>
+
+ <li>
+ 8 Aug 2016: Fixed incorrect default value for the cpos parameter
+ to percolator.</li>
+
+ <li>Many other minor bug fixes and enhancements.</li>
+
+</ul>
+
+<hr/>
+
+<h3>Version 3.0</h3> August 1, 2016
+
+<h4>Major changes</h4>
+
+<ul>
+
+<li>
+The <code>tide-search</code> command now supports threading. See the
+<code>num-threads</code> parameter for details.</li>
+
+<li>
+Added the <code>pipeline</a> command to run a series of commands, and
+the <code>cascade-search</code> to run searches across a series of
+databases.</li>
+
+<li>
+Renamed the command <code>calibrate-scores</code>
+to <code>assign-confidence</code> and completely revamped its
+functionality.</li>
+
+<li>
+The <code>search-for-xlinks</code> command offers parameters to
+control categories of
+candidates: <code>xlink-include-inter</code>, <code>xlink-include-intra</code>,
+and
+<code>xlink-include-inter-intra</code>.</li>
+
+<li>
+Added the <code>peptide-centric-search</code> option to tide-search.</li>
+
+<li>
+Compiling the Mac OS version now requires OS X Yosemite. It can be built
+from source using the Clang compilers distributed with the latest version of
+XCode.</li>
+
+<li>
+32-bit and 64-bit Windows versions are now available, built using Visual Studio 2013.</li>
+
+<li>
+Updated Percolator to version 2.10.</li>
+
+<li>
+Updated Hardklor to version 2.30.</li>
+
+<li>
+Updated Comet to version 2016.01 rev. 1.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The Windows version of Crux can be built with support for vendor specific file
+formats disabled.</li>
+
+<li>
+Added the <code>temp-dir</code> option
+to <code>tide-index</code>.</li>
+
+<li>
+The utilities <code>create-docs</code>, <code>subtract-index</code>,
+and <code>psm-convert</code> were added to Crux.</li>
+
+<li>The <code>generate-peptides</code> application has been revamped.</li>
+
+<li>Fixed a bug in <code>barista</code> that occurred when the number of
+peptides exceeded the number of PSMs.</li>
+
+<li>Precursor mass selection is fixed in <code>tide-search</code> when units
+are m/z.</li>
+
+<li><code>hardklor</code> and <code>bullseye</code> now use standard logging.</li>
+
+<li>Version number added to log files. Additionally, the version numbers of
+<code>percolator</code>, <code>comet</code>, and <code>boost</code> are shown
+in the output of the <code>version</code> command.</li>
+
+<li>
+Short usage message is displayed on error (the full usage message is still
+displayed when a command is entered with no arguments).</li>
+
+<li>
+<code>feature-in-file</code> parameter added to <code>percolator</code>.</li>
+
+<li>
+The <code>seed</code> parameter for <code>percolator</code> has been renamed
+to <code>percolator-seed</code>.</li>
+
+<li>
+<code>comet</code> exits with return code 1 on failure, rather than 0.</li>
+
+<li>
+Default value for <code>use_sparse_matrix</code> changed to <code>1</code>.</li>
+
+<li>
+Default value for <code>use-neutral-loss-peaks<code> changed to <code>true</code>.</li>
+
+<li>
+<code>xlink-score-method</code> parameter added to <code>xlink-score-spectrum</code>.</li>
+
+<li>
+deltaLCn column added to <code>tide-search</code> tab-delimited output.</li>
+
+<li>
+Bug fixed in reporting flanking amino acids in <code>PostProcessProtein.cpp</code>.</li>
+
+<li>
+<code>Mix-max</code> procedure is updated to handle ties among target and decoy scores.</li>
+
+<li>
+Default value of <code>use-neutral-loss-peaks</code> changed to <code>true</code></li>
+
+<li>
+<code>Exact p-value</code> calculation takes into account the flanking and neutral loss peaks. </li>
+
+<li>
+A bug was fixed in the naming of the Percolator input (.pin) file that
+is produced by Comet when the <code>output_percolatorfile</code>
+option is turned on. Previously, the file was named "comet.tsv"; now
+it is "comet.target.pin."</li>
+
+<li>
+<code>Assign-confidence</code> can take multiple input files.
+</li>
+
+<li>
+The <code>comet</code> command can take multiple input files.
+</li>
+
+<li>
+The <code>sidak</code> option has been added
+to <code>assign-confidence</code> to perform a Sidak adjustment.
+</li>
+
+<li>
+The <code>peptide-level</code> option has been added
+to <code>assign-confidence</code>.
+</li>
+
+<li>
+The refactored XCorr score has been re-scaled (by dividing by 20) to
+put it into a range that is comparable to that of the original XCorr score.</li>
+
+<li>
+The default value of <code>mz-bin-offset</code> has been changed from
+0.68 to 0.40.</li>
+
+<li>
+The <code>percolator</code> command outputs the <code>pout</code> XML format
+again (controlled by the <code>pout-output</code> parameter).</li>
+
+<li>
+The <code>percolator</code> command can output its native output by using the
+<code>original-output</code> parameter.</li>
+
+<li>
+Fixed a bug in <code>tide-search</code> causing it to fail when
+<code>remove-precursor-peak</code> removed all peaks in a spectrum.</li>
+
+<li>
+The <code>max-precursor-charge</code> parameter
+for <code>tide-search</code> has been introduced.</li>
+
+<li>
+Fixed a bug in candidate peptide selection when m/z tolerance is
+used.</li>
+
+<li>
+Added the <code>read-tide-index</code> command, which reads an index produced
+by <code>tide-index</code> and prints a list of peptides it contains.</li>
+
+<li>
+Added the <code>stop-after</code> option to print-processed-spectra, which
+controls the point at which to stop preprocessing.</li>
+
+<li>
+The <code>tide-search</code> command now accepts multiple spectrum input files.
+</li>
+
+<li>
+Added the <code>use-z-line</code> option to specify whether precursor
+information is taken from the S or Z line when parsing MS2 files using
+ProteoWizard.</li>
+
+<li>
+Added missing options to the <code>percolator</code> command.</li>
+
+<li>
+The <code>tide-search</code> command may now accept a FASTA database in
+place of the index, in which case <code>tide-index</code> will be run prior to
+the search. The <code>store-index</code> option allows the generated index
+to be saved.</li>
+
+<li>
+The <code>assign-confidence</code> command will automatically detect
+score type if the <code>score</code> parameter is not specified, searching for
+xcorr, e-value, or exact p-values.</li>
+
+<li>
+The <code>cascade-search</code> will report the source index database of the
+peptide for all identified PSMs.</li>
+
+<li>
+The <code>top-match</code> parameter has been removed from
+<code>cascade-search</code>.</li>
+
+<li>
+<code>Assign-confidence</code> has got new options: "combine-modified-peptide"
+and "combine-charge-states".</li>
+
+<li>
+<code>Assign-confidence</code> now supports top-match>1 in peptide-level filtering
+mode.</li>
+
+<li>
+<code>Assign-confidence</code> can use smoothed-p-value scores for PSM ranking.</li>
+
+<li>
+<code>Assign-confidence</code> now does not carry out target-decoy competition in
+peptide-level filtering mode.</li>
+
+<li>
+Added the <code>xlink-assign-ions</code> and <code>xlink-score-spectrum
+</code> commands.</li>
+
+<li>
+Rearranged estimation methods in <code>assign-confidence</code>.</li>
+
+<li>
+Added top-match option for <code>estimation-method=peptide-level</code>
+case in <code>assign-confidence</code>.</li>
+
+<li>
+Modified assign-confidence so that ties during target-decoy
+competition are broken randomly.</li>
+
+<li>
+Changed the Percolator output feature "file" to contain the name of
+ the file containing the spectrum (if available), rather than the
+ name of the file containing the PSM.</li>
+
+<li>
+Added to <code>search-for-xlinks</code>, <code>xlink-assign-ions</code>
+ and <code>xlink-score-spectrum</code> parameters of the form
+ "use-a-ion" for a, b, c, x, y, and z-ions.</li>
+
+<li>Various other minor bug/leak fixes and performance enhancements.</li>
+
+<li>Added the <code>allow-dups</code> option to tide-index.</li>
+
+</ul>
+
+<hr></hr>
+
+
+<h3>Version 2.1</h3> October 8, 2014
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+The <code>tide-search</code> command now supports calculation of exact
+p-values via dynamic programming, as described
+in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this
+article</a>. The p-value calculation is controlled with
+the <code>exact-p-value</code> parameter.</li>
+
+<li>
+<code>search-for-xlinks</code> now supports variable modifications and
+larger protein databases. This new code is disabled by default, but
+can be turned on by setting the
+parameter <code>use-old-xlink=F</code>.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The default value of <code>mz_bin_offset</code> has been changed to 0.40 from 0.68.</li>
+
+<li>
+The <code>centroided</code> parameter for the <code>hardklor</code> command is
+now implemented.</li>
+
+<li>
+The <code>spectrum-format</code> parameter for the <code>bullseye</code> command
+works properly.</li>
+
+<li>
+The <code>tide-search</code> command now uses information from the Z line rather
+than the S line when reading spectrum files in the MS2 file format.</li>
+
+<li>
+The <code>tide-search</code> command now accepts the
+<code>spectrum-parser</code> parameter.</li>
+
+<li>
+The <code>protein-database</code> parameter
+to <code>spectral-counts</code> now only accepts fasta files. Parsing
+of a protein index is no longer supported.</li>
+
+<li>
+A bug was fixed in the <code>spectral-counts</code> command that prevented
+<code>tide-search</code> output files from being parsed correctly.</li>
+
+<li>
+The <code>default-direction</code> parameter now takes a string value of the feature
+name rather than an integer.
+</li>
+
+<li>
+The parameters <code>mz-bin-width</code> and <code>mz-bin-offset</code> have been added
+to <code>tide-search</code>.</li>
+
+<li>
+Percolator output now includes, for each PSM, the name of the file
+in which the spectrum resides.
+</li>
+
+<li>
+The parameters <code>clip-nterm-methionine</code>, <code>keep-terminal-aminos</code>, and <code>min-mods</code> have been added to <code>tide-index</code>.
+</li>
+
+<li>
+The parameters <code>use-flanking-peaks</code>
+and <code>use-neutral-loss-peaks</code> have been added to
+<code>tide-search</code>.</li>
+
+<li>
+The calculation of XCorr was simplified in Tide. In the new version,
+<code>tide-index</code> only generates peptides and sorts them,
+leaving the generation of theoretical peaks to be done entirely on the
+fly by <code>tide-search</code>.</li>
+
+<li>
+The <code>tide-search</code> command now prints search progress reports both to
+the screen and to the log file. The interval at which progress is printed can
+be controlled using the <code>print-search-progress</code> parameter.</li>
+
+<li>
+The <code>calibrate-scores</code> command now outputs files with the stem
+"calibrate-scores" rather than "qvalue."</li>
+
+<li>
+The <code>use-flanking-peaks</code> parameter now has a default value of
+false.</li>
+
+<li>
+The Comet search engine was updated to version 2014011.</li>
+
+<li>
+The MSToolkit parser was updated to the latest version (r73).</li>
+
+<li>
+The <code>version</code> command now outputs the revision number.</code>
+
+<li>
+Various improvements in performance and error handling were implemented.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 2.0</h3> June 6, 2014
+<h4>Major enhancements</h4>
+<ul>
+
+<li>
+Two new search engines are now included in Crux: Comet and Tide. The
+old search engine, search-for-matches, has been retired.</li>
+
+<li>Percolator has been updated to version 2.07.</li>
+
+<li>
+Crux now compiles in native Windows, rather than requiring
+Cygwin. Consequently, Crux running under Windows can parse vendor
+proprietary formats using the appropriate Proteowizard libraries.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The "enyzme" parameters "lysc", "lysn", "arg_c", "glue_c", and
+"pepsin_a" were renamed to "lys-c", "lys-n", "arg-c", "glue-c", and
+"pepsin-a".</li>
+
+<li>
+Percolator outputs decoy files in addition to target files.</li>
+
+<li>
+Percolator tab-delimited peptides output now contain a posterior error
+probability (PEP) column.</li>
+
+<li>
+The Percolator tab-delimited peptide output has been corrected to show
+the PSM with the best score, rather than the worst.</li>
+
+<li>
+The Percolator tab-delimited PSMs output "matches/spectrum" value has
+been corrected.</li>
+
+<li>
+A new utility command, <code>make-pin</code>, is provided to create
+input files for use by Percolator.</li>
+
+<li>
+The <code>spectrum-min-mass</code> and <code>spectrum-max-mass</code>
+options have been renamed to <code>spectrum-min-mz</code> and
+<code>spectrum-max-mz</code>, respectively.</li>
+
+<li>
+A <code>spectrum-parser</code> option was added to <code>q-ranker</code> and
+<code>barista</code>.</li>
+
+<li>
+A bug was fixed in <code>q-ranker</code> and <code>barista</code> when
+reading peptides with modifications.</li>
+
+<li>
+Fixed the <code>q-ranker</code> tab delimited output so that, for a
+given peptide, flanking amino acids are reported for each protein that
+contains that peptide, rather than only reporting one set of flanking
+amino acids.</li>
+
+<li>
+A bug was fixed in <code>percolator</code>, wherein the first and last
+two characters were being truncated from peptide sequences when the
+input was missing the flanking amino acids or when the charge state
+was not indicated in the PSM IDs.</li>
+
+<li>
+The crux spectrum parser has been removed.</li>
+
+<li>
+Q-ranker now outputs decoy files.</li>
+
+<li>
+The Boost.Random library is now being used for random number
+generation.</li>
+
+<li>
+<code>calibrate-scores</code> no longer requires a protein input.</li>
+
+<li>
+<code>calibrate-scores</code> now only takes the top match per
+spectrum and charge.</li>
+
+<li>
+<code>get-ms2-spectrum</code> now prints z-lines with Bullseye
+files.</li>
+
+<li>
+Various performance and error handling improvements.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.40</h3> May 22, 2013
+<h4>Major enchancements</h4>
+<ul>
+
+<li>
+Crux Percolator was updated from version 1.05 to the latest release,
+version 2.04.</li>
+
+</ul>
+<h4>Minor changes</h4>
+<ul>
+
+<li>
+<p>The formula that is used to convert fragment m/z values from real
+numbers into integers was modified. Previously, the conversion was<br>
+<pre>
+ floor( (x / mz-bin-size) + 0.5 + mz-bin-offset )
+</pre>
+<br>The new conversion formula is <br>
+<pre>
+ floor( (x / mz-bin-size) + 1.0 - mz-bin-offset )
+</pre>
+<br>The default values of the two parameters (mz-bin-size and
+mz-bin-offset) have not changed. The allowed range of the
+mz-bin-offset parameter was previously [-1,1], but has been changed to
+[0,1].</p>
+
+<p>
+To understand the motivation for the changed formula, note that the
+mz-bin-offset parameter controls the location of bin edges, relative
+to integer masses on the mass scale. In general, mz-bin-offset should
+be chosen so that bin edges fall between the expected clusters of
+fragment masses. For fragments with 1+ charge, masses will cluster
+near integer values (after dividing by mz-bin-width), and the ideal
+value of mz-bin-offset would be 0.5. For mixtures of fragments with
+1+ and 2+ charges, masses will cluster near integer and half-integer
+values, so mz-bin-offset near 0.25 or 0.75 would produce bin edges
+that best avoid the clusters of fragment masses. The old conversion
+formula did not correctly locate bin edges, given a chosen
+mz-bin-offset. The new conversion formula produces a proper
+translation of mz-bin-offset into bin edge locations.</p></li>
+
+<li>
+The <code>seed</code> parameter is now available to control the
+seeding of random number generator. The default value is 1.
+<code>seed</code> is available as a parameter from all applications.
+It can be set as a command line option for
+<code>crux search-for-matches</code>
+and
+<code>crux percolator</code>.
+</li>
+
+<li>
+The default value of the <code>decoys</code> parameter for <code>crux
+search-for-matches</code> was incorrectly documented. The default is
+actually <code>peptide-shuffle</code>, but the documentation said the
+default was <code>protein-shuffle</code>. The documentation has been
+corrected.</li>
+
+<li>
+The incorrectly labeled column header <code>xcorr rank</code> in barista and
+q-ranker feature files has been corrected to <code>xcorr score</code>.
+</li>
+
+<li>
+The q-ranker output file <code>qranker_output.xml</code> has been renamed to
+<code>qranker.xml</code>.
+</li>
+
+<li>
+The deltaCn computation has been modified to be consistent with
+Percolator. Rather than using
+<br /><pre>
+ deltaCn<sub>i</sub> = (xcorr<sub>1</sub> - xcorr<sub>i+1</sub>) / xcorr<sub>1</sub>
+</pre><br />
+it is now computed using<br />
+<pre>
+ deltaCn<sub>i</sub> = (xcorr<sub>i</sub> - xcorr<sub>i+1</sub>) / max(xcorr<sub>i</sub>, 1.0)
+</pre><br />
+</li>
+
+<li>
+Percolator now accepts inputs in SQT, PepXML, and tab-delimited formats in addition to
+the PinXML format.
+</li>
+
+<li>
+Flags were added to several commands allowing the user to control
+whether various results files are created in the output directory:
+<ul>
+ <li><code>--sqt-output <T|F></code> (search-for-matches)</li>
+ <li><code>--mzid-output <T|F></code> (search-for-matches, percolator)</li>
+ <li><code>--pinxml-output <T|F></code> (search-for-matches)</li>
+ <li><code>--pepxml-output <T|F></code> (search-for-matches, q-ranker, barista, percolator)</li>
+ <li><code>--txt-output <T|F></code> (search-for-matches, q-ranker, barista, percolator)</li>
+</ul>
+By default, all of these flags are set to false except <code>txt-output</code>.
+</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.39</h3> October 6, 2012
+
+<h4>Major enchancements</h4>
+
+<ul>
+
+<li>
+Crux is now released under an Apache license for all users.
+</li>
+
+
+<li>
+Parsing MS/MS spectra is now supported using <a href="http://proteowizard.sourceforge.net/">Proteowizard</a> (v. 3.0.3950).
+This allows Crux to
+handle MS/MS spectra in mzML (1.0 and 1.1), mzXML, MGF, MS2 and CMS2
+formats.
+Use <code>spectrum-parser=pwiz</code> to enable Proteowizard parsing.</li>
+<li>
+Crux now uses <code>cmake</code> for the build process rather than
+<code>autoconf</code>/<code>automake</code>.
+</li>
+</ul>
+<h3>Minor changes</h3>
+<ul>
+
+<li>
+The Tide database search software is no longer distributed as part of Crux because its license is not compatible with the new Crux license.
+</li>
+
+<li>
+Support for PIN XML output was added to <code>crux
+search-for-matches</code>.
+</li>
+<li>
+Fixed a bug in <code>crux create-index</code> on Windows and Cygin
+that caused the program to fail with the message:
+<br /><pre>
+WARNING: Cannot rename directory
+FATAL: Failed to create index
+</pre>
+</li>
+<li>
+The parameter <code>protein database</code> is now an option rather than a required argument for <code>crux spectral-counts</code>.
+</li>
+<li>
+mzIdentML file support has been added for <code>crux spectral-counts</code>.
+</li>
+<li>
+PepXML file support has been fixed for <code>crux spectral-counts</code> .
+</li>
+<li>
+Fixed bug in packedNorm() that sometimes generated incorrect values for the posterior error probability.
+</li>
+<li>
+Fixed bug in <code>crux create-index</code> on Windows and Cygwin that caused it to fail on Windows and Cygin.
+</li>
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.38</h3> July 20, 2012
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+Hardklor and Bullseye, tools for analyzing high-resolution precursor
+spectra, are now incorporated into Crux.</li>
+
+<li>
+Barista has been modified extensively so that it more closely
+resembles the other tools in Crux:</li>
+
+<ul>
+<li>
+Barista and Q-ranker accept search results in tab-delimited format, in addition to
+SQT format.</li>
+<li>
+Barista now reports posterior error probabilities, in addition to
+q-values, for PSMs, peptides and proteins.</li>
+<li>
+Barista's pep.xml output has been updated to be compatible with the
+TransProteomic Pipeline (TPP).</li>
+</ul>
+
+<li>
+The <code>sequest-search</code> command has been removed. The
+functionality of this command is still available using options for
+the <code>search-for-matches</code> command (see
+the <a href="faq.html">frequently asked questions list</a> for
+details).</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+<code>crux predict-peptide-ions</code> calculates the mass shift
+resulting from the nh3 or h2o neutral loss correctly. Previously, a
+neutral loss resulted in an addition of mass rather than subtraction.
+</li>
+
+<li>
+<code>crux predict-peptide-ions</code> reports ion-type as
+'b','y','a', or 'p' rather than a number (i.e. 0, 1, 2, 3).</li>
+
+<li>
+<code>crux predict-peptide-ions</code> now only allows one type of
+neutral loss modification per ion. Previously, multiple different
+types of neutral loss could be applied simultaneously to a single
+ion.</li>
+
+<li>
+The <code>neutral-losses</code> option was removed from <code>crux
+predict-peptide-ions</code>, due to its redundancy with the supported
+the <code>--nh3</code> and <code>--h2o</code> options.</li>
+
+<li>
+<code>crux predict-peptide-ions</code> supports 'bya' in the
+<code>--primary-ions</code> parameter, which will generate
+the a-ion series in addition to the 'b' and 'y' ions.</li>
+
+<li>
+The spectrum parsing is updated so that peaks with zero intensity are
+ignored.</li>
+
+<li>
+<code>crux spectral-counts</code> now has an option to compute the raw
+spectral count.</li>
+
+<li>
+<code>crux spectral-counts</code> now has an option to compute dNSAF
+values.</li>
+
+<li>
+A bug in <code>crux spectral-counts</code> was fixed so that it now
+properly normalizes the NSAF value.</li>
+
+<li>
+Multiple missed cleavages are now handled by <code>crux
+search-for-xlinks</code> using the missed-cleavages parameter.
+Previously, this was unsupported.</li>
+
+<li>
+Ambiguous amino acids are handled differently. 'J' is interpreted to
+indicate 'I' or 'L'. Peptides containing B, Z, and X are no longer be
+allowed, and a warning is issued when these amino acid codes are
+encountered.</li>
+
+<li>
+The stand-alone <code>crux-predict-peptide-ions</code>
+and <code>crux-generate-peptides</code> applications have been integrated
+into the main <code>crux</code> application.</li>
+
+<li>
+A bug has been fixed that affected the intensity adjustment of
+observed spectra when the bin width was set much larger or smaller
+than 1.</li>
+
+<li>
+Beginning with version 1.37, q-ranker erroneously included decoy PSMs
+along with target PSMs in the q-ranker.target.psms.txt file. All PSMs
+were sorted by q-ranker score so the targets and decoys were mixed
+together with no accompanying labels. This bug has been fixed so that
+Q-ranker once again returns only target PSMs.</li>
+
+<li>
+The search option <code>display-summed-masses</code> has been replaced by
+<code>mod-mass-format</code>. With this option, there is a new format
+for reporting modificiations: the mass in the square braces is that of the
+preceeding amino acid plus the modification mass. This format is compliant
+with TPP pep.xml output.</li>
+
+<li>
+Modifications are reported differently in the pep.xml header to be
+compliant with the TPP.</li>
+
+<li>
+The command <code>crux compute-q-values</code> now reports posterior
+error probabilities in addition to q-values. Consequently, the
+command was renamed <code>crux calibrate-scores</code>.</li>
+
+<li>
+Crux now provides an explicit error message when an incorrectly
+formatted MS2 file is parsed. Previously, crux simply reported that
+no spectra were found.</li>
+
+<li>
+Several additional scores were added to the <code>q-ranker</code>
+pep.xml files.</li>
+
+<li>Fixed the build procedure to work on both Lion and pre-Lion versions of OS X.</li>
+
+<li>Fixed a bug in the normalization of the observed spectra.
+Previously, after the 10-bin normalization of intensities, peaks with
+heights below 5% of the maximum were not being removed.</li>
+
+<li>
+When a fragmentation spectra file is read, the assumed
+peptide charge state information can be missing for the scans.
+In cases where this information has not been provided,
+Crux will now estimate the possible charge states.
+</li>
+
+<li>
+The feature files for Q-ranker and Barista now contain a header
+describing each feature.
+</li>
+
+<li>
+Q-ranker and Barista now output all of the fields provided in the
+input search files.
+</li>
+
+</ul>
+
+<hr></hr>
+
+
+<h3>Version 1.37</h3> December 22, 2011
+
+<h4>Major enhancements</h4>
+
+<ul>
+<li>
+Added <code>crux barista</code>, a tool for inferring protein
+identifications.</li>
+
+<li>
+Reimplemented <code>crux q-ranker</code> with new outputs and
+command-line syntax.</li>
+
+<li>
+Percolator and compute-q-values now compute and report posterior error
+probabilities, in addition to q-values.</li>
+
+<li>
+<code>crux create-index</code> now generates and store decoy
+peptides in the index. Decoys can still be generated on-the-fly when
+searching .fasta files.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+A pair of options, <code>cterm-fixed</code>
+and <code>nterm-fixed</code>, allow fixed terminal peptide
+modifications, i.e., a mass shift applied to every peptide on either or
+both termini.</li>
+
+<li>
+A bug in the spectrum processing code was fixed, which was erroneously
+eliminating a few of the highest m/z fragment peaks. Xcorrs have
+changed slightly as a result.</li>
+
+<li>
+Simplified the <code>--mz-bin-width</code> and
+</code>--mz-offset</code> parameters so that <code>--xcorr-var-bin</code>
+is no longer needed.</li>
+
+<li>
+Indexes now store information about any static mods used when they
+were created.</li>
+
+<li>
+In the tab-delimited output files the 'matches/spectrum' column gives
+the number of target peptides compared to the spectrum and the decoy
+file has an additional column, 'decoy matches/spectrum' that gives the
+number of decoy peptides compared to the spectrum. These two numbers
+may differ when decoys are not generated on-the-fly.</li>
+<li>
+The header lines of Barista and QRanker include all of the columns
+in the search results.</li>
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.36</h3> August 4, 2011
+
+<h4>Tide changes</h4>
+
+<ul>
+
+<li>
+Added support for user-specifiable variable and static amino acid
+modifications.</li>
+
+<li>
+Tide's version of XCorr has been modified so that it is always
+identical to those of a recent version SEQUEST<sup>®</sup>.</li>
+
+<li>
+Added support for user-specifiable maximum number of missed enzyme
+cleavage points.</li>
+
+<li>
+Tide now performs basic charge state inference when this information
+is missing from the spectrum input files.</li>
+
+<li>
+User-specifiable output formatting, using new
+the <code>tide-results</code> utility, including
+ <ul>
+ <li>Text format with user-specifiable fields.
+ <li>SQT format.
+ <li>PepXML format.
+ <li>Choose whether to display all proteins in which each peptide occurs or
+just one representative.
+ </ul>
+
+<li>
+Note that new file formats are created
+by <code>tide-index</code>. Index files created by previous versions
+of Tide should not be used with the new version.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+<li>
+Q-ranker now reports q-values instead of false discovery rates.</li>
+
+<li>
+Corrected several errors in the pep.xml output, related to reporting
+the spectrum filename, charge, and neutral mass.</li>
+
+<li>
+Changed the <code>missed-cleavages</code> option to allow specifying
+the maximum number of missed cleavages in a peptide rather than
+specifying none/any.</li>
+
+<li>
+Fixed a bug that did not print the spectrum file name correctly in the
+pep.xml files.</li>
+
+<li>
+Improved the error message produced by <code>crux
+spectral-counts</code> when the input PSM file does not contain the
+required q-values.</li>
+
+<li>
+Previously, Crux's theoretical spectrum includes two flanking peaks
+around each b- and y-ion. The new
+Boolean flag <code>use-flanking-peaks</code>, allows these to be
+either on or off. Flanking peaks are by default in
+<code>crux sequest-search</code> but are not used by default
+in <code>crux search-for-matches</code>.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.35</h3> March 23, 2011
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+Added the <code>crux spectral-counts</code> command for estimating
+protein quantification.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The spectrum neutral mass is now calculated from the m+h value
+provided by the Z-lines of an MS2 file. Also, multiple z-lines of a
+spectrum that have the same charge are now supported. With these
+changes, <code>crux search-for-matches</code> and <code>crux
+sequest-search</code> can now take advantage of accurate precursor
+masses in MS2 files generated by Bullseye (Hsieh et al. <i>J. Proteome
+Res.</i> 9(2):1138-43, 2010).</li>
+
+<li>
+Made the <code>pep.xml</code> file header produced by Crux compatible
+with the Transproteomic Pipeline.</li>
+
+<li>
+Introduced several changes to improve performance on MacOS X.</li>
+
+<li>
+Added an <code>nterm</code> option to the link argument of <code>crux
+search-for-xlinks</code>.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.34</h3> December 22, 2010
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The default value of the "pi-zero" parameter has been changed from 0.9
+to 1.0.</li>
+
+<li>
+A new option <code>--peptide-list</code> has been added to <code>crux
+create-index</code>. When set to T, this option causes an ASCII
+file of peptides to be included in the output directory. Each line
+of the file lists the peptide sequence and its neutral mass.</li>
+
+<li>
+The default bin offset was returned to 0.68. It had erroneously been
+changed to 0 in version 1.33.</li>
+
+<li>
+A new option <code>--compute-sp</code> has been added to <code>crux
+search-for-matches</code>. When set to true, all candidate peptides
+will be scored by Sp in addition to xcorr. This option is recommended
+for generating input to <code>percolator</code>
+or <code>q-ranker</code>.</li>
+
+<li>
+Added <code>max-ion-charge</code> parameter to designate the maximum
+charge for theoretical ions in <code>crux search-for-xlinks</code> and
+<code>crux xlink-assign-ions</code>.
+
+<li>
+Modifications may optionally indicate if they prevent cleavage or
+prevent cross linking.
+
+<li>
+Results are printed to .pep.xml files in addition to .txt files.
+
+<li>
+Added a <code>mass-precision</code> option which sets how many digits
+are written for all mass and m/z values in .txt, .sqt, and .ms2 files.
+
+<li>
+The columns printed to the .txt files now vary with the
+<code>crux</code> command being run and the settings so that unused
+columns are not printed.
+
+<li>
+Fixed a bug that limited what files were used as input for post-search
+commands (e.g. <code>crux percolator</code>) based on fileroot. Now
+files with different fileroots can be analyzed together.
+
+<li>
+Fixed a bug that caused searches using fasta files to search peptides
+multiple times if they appeared in a file multiple times.
+
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.33</h3> July 7, 2010
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+The command line syntax
+for <code>compute-q-values</code>, <code>percolator</code>
+and <code>q-ranker</code> was modified to allow the programs to read
+from and write to separate directories.</li>
+
+<li>
+A bug in q-ranker and percolator was fixed. This bug was introduced
+several versions ago, and it led to erroneously many PSMs receiving
+very small q-values. The problem relates to the scaling of the delta
+Cn feature, and the fix is a temporary stopgap: we remove the feature
+entirely. The next version should have the corrected feature in
+place.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+A new option <code>--min-peaks</code> has been added to set a filter
+for the minimum number of peaks a spectrum must have in order for it
+to be searched. The default minimum is 20 peaks.</li>
+
+<li>
+The hardcoded limit for the number of proteins allowed in a database
+has been removed.</li>
+
+<li>
+The hardcoded limit for the number of spectra and the number of
+peaks/spectrum has been removed.</li>
+
+<li>
+A new option <code>--xcorr-var-bin</code> has been added to toggle the
+new binning of the m/z axis. The default bin offset was returned back
+to 0, but the default bin width is still 1.000508. (<i>Note: this
+erroneous change was subsequently reverted in version 1.34</i>.)
+</li>
+
+<li>
+The option <code>--max-ion-charge</code> now places a limit on the
+maximum charge state of the ions generated for the xcorr theoretical
+spectra for <code>crux search-for-xlinks</code>. This change is also
+supported by <code>xlink-assign-ions</code>.
+
+<li>
+The option <code>--no-xval</code> was added to q-ranker, allowing
+faster execution by skipping the internal cross-validation to select
+hyperparameters.</li>
+
+<li>
+The precision of modification masses written to the .txt files now matches
+the maximum precision given in the parameter file.
+
+<li>
+Sub-options <code>prevents cleavage</code> and
+<code>prevents cross-link</code> have been added to variable modifications
+and support has been provided for the <code>"prevents cleavage"</code>
+sub-option.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.32</h3> July 6, 2010
+
+<h4>Major enhancement</h4>
+
+<ul>
+
+<li>
+Version 1.32 includes changes only to Tide. A new binary is introduced
+— a modified version of ProteoWizard's <b>msconvert</b> program
+— that is capable of converting spectrum data from a wide range
+of file formats into Tide-readable <i>.spectrumrecords</i> input
+files.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+<b>tide-import-spectra</b> is removed from the distribution. Although
+it was faster than msconvert, it was specific to ms2 files, whereas
+msconvert now works with any ProteoWizard-supported file format.</li>
+
+<li>
+A standalone utility for reading binary <i>.spectrumrecords</i> files
+is introduced, called <b>read-spectrumrecords</b>. This program is
+useful, for example, for visually checking the output of msconvert.</li>
+
+<li>
+Demo input files <b>worm-06-10000.spectrumrecords</b>
+and <b>yeast-02-10000.spectrumrecords</b> now replace their
+counterparts worm-06-10000.ms2 and yeast-02-10000.ms2. With the
+introduction of Tide-compatible msconvert, ms2 files are in no way
+special to Tide anymore. Any ProteoWizard-supported file format can be
+converted to the <i>.spectrumrecords</i> format for use with
+Tide. Starting with data files in Tide's spectrumrecords format
+eliminates the conversion step in the Tide search demo.</li>
+
+<li>
+The old demo scripts worm-demo.sh and yeast-demo.sh have each been
+replaced by a pair of new scripts that demonstrate the indexing and
+searching steps separately. This is in order to highlight the two-step
+process and the fact that indexing needs to be done just once for each
+fasta file, whereafter the index may be reused indefinitely to perform
+searches.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.31</h3> June 2, 2010
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+This version of Crux is released with a demo version of a new search
+engine, Tide. Tide is an independent
+reimplementation of the SEQUEST<sup>®</sup> algorithm. The
+immediate ancestor of Tide is the Crux <code>search-for-matches</code>
+command, but Tide has been completely re-engineered to achieve a
+thousandfold improvement in speed while exactly replicating Crux XCorr
+scores. Currently, Tide is not fully integrated with Crux, and is
+available only in binary executable format.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+<li>
+Two options have been added to <code>crux search-for-matches</code>
+(<code>--mz-bin-width</code> and <code>--mz-bin-offset</code>) to
+allow control of the binning of the m/z axis.</li>
+
+<li>
+The <code>ion-tolerance</code> option was removed from the search
+tools.</li>
+
+<li>
+The default location of the left edge of the first bin along the m/z
+axis is 0.68, rather than 0.0. This change makes bin edges less
+likely to fall near fragment peak locations. The default bin width
+has also changed from 1.001141 to 1.000508</li>
+
+<li>
+The log file now includes information about the date and time that the
+command was issued, the name of the computer on which the command was
+run, and the elapsed wall clock time at the end of the run.</li>
+
+<li>
+The command line option <code>--version T</code> has been replaced
+with a command <code>crux version</code> that prints the version
+number to standard output and then exits.</li>
+
+<li>
+The header for the feature file produced optionally by
+<code>crux percolator</code> and <code>crux q-ranker</code> now includes names
+for the first two columns, scan number and label (i.e. target or decoy peptide).
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.30</h3> May 5, 2010
+
+<h4>Major enhancements</h4>
+
+<ul>
+<li>
+A new command, <code>xlink-search</code>, has been added. This command
+searches a collection of spectra against a sequence database, finding
+cross-linked peptide matches. The algorithm was described in the
+following article:</li>
+
+<blockquote>
+Sean McIlwain, Paul Draghicescu, Pragya Singh, David R. Goodlett and
+William Stafford
+Noble. <a href="http://noble.gs.washington.edu/proj/xhhc/">"Detecting
+cross-linked peptides by searching against a database of cross-linked
+peptide pairs."</a> <i>Journal of Proteome Research</i>. 2010.
+</blockquote>
+
+<li>
+A new search command, <code>sequest-search</code>, was added. The
+original command, <code>search-for-matches</code>, behaves as before
+except that no .sqt files are printed and no Sp scoring is performed.
+The new <code>sequest-search</code> emulates SEQUEST<sup>®</sup>
+searching. It first scores all candidate peptides with the Sp score,
+then ranks and filters the results by that score, scoring the
+remaining candidates with xcorr. Results are printed to .txt and .sqt
+files.</li>
+
+<li>
+The .mzXML file format is now supported for crux search-for-matches
+and crux sequest-search when the <code>--use-mstoolkit</code> option
+is set to TRUE.</li>
+
+<li>
+The .csm output files from <code>search-for-matches</code> are no
+longer produced and post-search operations take .txt files as input.
+</li>
+
+</ul>
+
+<h4>
+Minor changes</h4>
+
+<ul>
+
+<li>
+Replaced <code>mass-window</code> parameter with <code>
+precursor-window</code> and added <code>precursor-window-type</code>
+for selecting windows of type mass, m/z, or ppm.
+</li>
+
+<li>
+The <code>feature-file</code> option is now true/false instead of
+taking a file name. The file is named '<fileroot>.<qranker|
+percolator>.features.txt'. A header with the column names was
+added to the file.</li>
+
+<li>
+The new option, <code>--scan-number</code>, performs a search on a
+specified subset of the spectra in the given file.</li>
+
+<li>
+When only one decoy file is produced, the name is now 'decoy.txt'
+instead of 'decoy-1.txt'
+
+<li>
+In the .txt files, protein names are now followed by the start index
+of the peptide.
+
+<li>
+Modified sequences are reported differently in the .txt files.
+Instead of modifications being represented by symbols (*,@,#, etc.)
+they are indicated with the mass shift of the modification within
+square brackets. As before, the modification information follows the
+residue that is modified. If multiple modifications appear on one
+residue, the masses may either be summed together or printed
+separately in a comma separated list. This behavior is controlled by
+the <code>--display-summed-mod-masses</code> option.</li>
+
+<li>
+The modified decoy sequences are generated differently. Before, all
+modified peptides were generated and each one was shuffled to create a
+decoy peptide. Now a peptide is shuffled once for each peptide_mod
+and all modifications are applied to that same shuffled peptide.</li>
+
+<li>
+The 'percolator rank' column is now based on percolator scores instead
+of percolator q-values. For cases where two PSMs have different
+percolator scores but the same q-value, the ranks will reflect the
+score differences.</li>
+
+<li>
+The Weibull parameters used for computing p-values are now printed to
+the .txt files.</li>
+
+<li>
+The reporting of DeltaCn has changed. For PSMs of rank i, deltaCn
+used to computed be as deltaCn_i = (xcorr_0 - xcorr_i) / xcorr_0.
+Thus, deltaCn for the top-ranked PSM was always 0. Now deltaCn_i =
+(xcorr_0 - xcorr_i+1) / xcorr_0. This change only
+affects <code>search-for-matches</code>,
+not <code>sequest-search</code>. It also means that
+<code>q-ranker</code> and <code>percolator</code> use the correct
+DeltaCn values.
+</li>
+
+<li>
+A new command, <code>print-processed-spectra</code>, performs
+XCorr-style pre-processing on all spectra in a given file.</li>
+
+<li>
+A small bug was fixed, in which even if the user requested average
+mass, the search programs still used monoisotopic mass in the
+calculation of XCorr and Sp.</li>
+
+<li>
+Protein fasta files are now parsed protein-by-protein so that parsing
+large files does not use excessive amounts of memory.</li>
+
+<li>
+A limit was removed on how many peptides a protein can produce.</li>
+
+<li>
+Crux is now built with g++ instead of gcc.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.22</h3> September 16, 2009
+
+<h4>
+Major enhancements</h4>
+
+<ul>
+
+<li>
+Crux is now distributed in two versions, a full version that is
+covered by the same type of license as before (free to non-profit
+users, and via a licensing fee to commercial users), as well as a
+stripped-down version that is released under an open source license.
+The stripped-down version does not include the database search
+functionality but does include all of the post-processing tools. We
+are unable to release the entire Crux package under an open source
+license due to intellectual property issues. Both versions of Crux
+are available via the Crux web
+page: <a href="http://noble.gs.washington.edu/proj/crux/">http://noble.gs.washington.edu/proj/crux/</a>.</li>
+
+<li>
+A new tool, q-ranker, is available for estimating peptide-spectrum
+match q-values. This tool was described in the following article:
+
+<blockquote>
+Marina Spivak, Jason Weston, Leon Bottou, Lukas Käll and William
+Stafford Noble. "Improvements to the Percolator algorithm for peptide
+identification from shotgun proteomics data sets." <i>Journal of
+Proteome Research.</i></blockquote></li>
+
+<li>
+Version 1.05 of <code>percolator</code> has now been integrated into
+the Crux source tree. A separate installation
+of <code>percolator</code> is no longer needed for basic
+<code>percolator</code> functionality. Note, however,
+that <code>percolator</code> remains under active development. You
+may therefore wish to install the current, stand-alone version
+of <code>percolator</code> and run it separately to take advantage of
+new features.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The internal normalization of the observed spectra has been modifed to
+drop those peaks whose intensity is less than 1/20 of the maximum
+intensity in the spectrum. This brings the xcorr score
+for <code>crux</code> into closer agreement with the xcorr score
+for SEQUEST<sup>®</sup>.</li>
+
+<li>
+Compute-q-values now generates three different q-values (1) from
+p-values using an analytical null model, (2) from decoys and xcorr
+using an empirical null model, or (3) from decoys and p-values using
+an empirical null model. All three types of q-values are computed
+when p-values and decoys are present in the search results.</li>
+
+<li>
+A parameter file is now automatically written to the output
+directory.</li>
+
+<li>
+A log file recording messages sent to stderr has been added for
+<code>search-for-matches</code>, <code>compute-q-values</code>,
+and <code>percolator</code>.</li>
+
+<li>
+The <code>--use-mz-window</code> parameter is now available for
+<code>search-for-matches</code>. When enabled, peptides must be
+within +/- 'm/z-window' of the spectrum m/z. The m/z-window value is
+taken from <code>mass-window</code>.</li>
+
+<li>
+A numerical bug in the Weibull p-value calculation was fixed, which
+had previously caused occasional erroneous NaNs to be output.</li>
+
+<li>
+The Weibull estimated p-values generated
+by <code>search-for-matches</code> are now returned as p-values
+instead of as -log(p-value). The corresponding q-values returned from
+<code>compute-q-values</code> are also now returned without the -log
+transform.</li>
+
+<li>
+The <code>--precision</code> option has been changed to control the
+total number of significant digits printed instead of the number of
+digits after the decimal point. The default precision has changed
+from 6 to 8.</li>
+
+<li>
+The parameters estimated for the Weibull distribution (used for
+computing p-values) now use the xcorrs from all PSMs for a spectrum
+instead of a random selection of 500.</li>
+
+<li>
+The estimation of Weibull distribution parameters requires a minimum
+number of scored PSMs. In the previous version, spectra with fewer
+PSMs than the minimum were not given a p-value. Crux will now
+generate extra decoys until there are enough scores.</li>
+
+<li>
+The p-values for decoy PSMs are now generated from the same Weibull
+distribution parameters as are used for the targets of the same
+spectrum.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.21</h3> May 14, 2009
+
+<ul>
+
+<li>
+The output for <code>search-for-matches</code>,
+<code>compute-q-values</code>, and <code>percolator</code>
+has been revised extensively.
+<code>crux</code> will now create a directory, and all output files
+will be created in that directory.
+By default the directory will be named <code>crux-output</code>,
+but this can be changed using the new <code>output-dir</code> option.
+<br>
+The output files for <code>search-for-matches</code> will be:
+<ul>
+<li><code>search.target.csm</code></li>
+<li><code>search.decoy-?.csm</code></li>
+<li><code>search.target.sqt</code></li>
+<li><code>search.target.txt</code></li>
+</ul>
+The output files for <code>compute-q-values</code> will be:
+<ul>
+<li><code>qvalues.target.sqt</code></li>
+<li><code>qvalues.target.txt</code></li>
+</ul>
+The output files for <code>percolator</code> will be:
+<ul>
+<li><code>percolator.target.sqt</code></li>
+<li><code>percolator.target.txt</code></li>
+</ul>
+</li>
+<li>
+The <code>fileroot</code> option has been added.
+This option is used to specify a string which will be added as a prefix
+to all output files.
+</li>
+<li>
+The option <code>cleavages</code> was replaced with two
+options, <code>enzyme</code> which specifies the name of an enzyme
+(e.g.trypsin) and <code>digestion</code> which indicates
+the degree of specificity, partial or full digest. The full list of
+available enzymes is in the html docs and in the usage statement.
+See also <code>custom-enzyme</code> below.
+
+<li>
+The option <code>custom-enzyme</code> allows users to define arbitrary
+digestion rules. This overrides the <code>enzyme</code> option.
+Syntax for the custom digestion rule is the same the syntax used by
+X!Tandem and is described in the html docs.
+
+<li>
+The number of PSMs per spectrum printed to the output files is now
+controlled by one option, <code>top-match</code>. This
+makes <code>max-sqt-result</code> obsolete.
+
+<li>
+It is now possible to control how many decoy sequences are generated
+and in which file(s) they are returned. There is a new
+option, <code>num-decoys-per-target</code>, which can be used to
+generate more than one shuffled peptide per spectrum. This
+replaces <code>number-decoy-set</code>.
+
+<li>
+A new option, <code>decoy-location</code> has been introduced. The
+three possible values are 'target-file' where all PSMs (target and
+decoys) are sorted together for each spectrum and returned in one
+file, 'one-decoy-file' where target PSMs are printed to one file and
+all decoys are printed to another, and 'separate-decoy-files' where
+there are as many decoy files as there are decoys per target.
+
+<li>
+Protein names for decoy matches are now prepended with 'rand_' in the
+SQT files as in
+'L rand_Y45678'.
+
+<li>
+The option <code>unique-peptides</code> only applies
+to <code>crux-generate-matches</code>. Each peptide is stored in the
+index exactly once with references to all protein sources. Searches with
+fasta files print each peptide only once.
+
+<li>
+The precision of the masses and scores printed to the sqt and text
+files can now be specified by the user. The default precision changed
+from 2 to 6.</li>
+
+<li>
+Search progress is now reported by printing every 10th spectrum that is
+searched. The verbosity can be adjusted with the parameter
+<code>print-search-progress</code>.
+
+<li>
+Decoy (shuffled) sequences now keep the first and last residue the
+same as the target sequence that was shuffled to produce it. This is
+a reversion to previous behavior.
+
+<li>
+It is now possible to skip the Sp score and score all PSMs with xcorr.
+The default procedure is still to score all peptides for one spectrum
+with Sp, rank by Sp, and eliminate all but the best-ranking PSMs (by
+default, the top 500). The remaining PSMs are scored by xcorr,
+re-ranked by xcorr and the top results returned. By setting
+max-rank-preliminary=0, the Sp scoring is skipped and xcorr is
+computed for all PSMs.</li>
+
+<li>
+A new parameter <code>reverse-sequence</code> can be used to generate
+decoy peptides by reversing them rather than shuffling. The first and
+last residues are left unmoved. If the sequence is a palindrome ,
+then a decoy will be generated by shuffling and a note to that effect
+will be printed at the DETAILED INFO level of output (verbosity =
+40).</li>
+
+<li>
+P-values are now computed for decoy peptides.</li>
+
+<li>
+The algorithm used to calculated the xcorr score has been modified so
+that xcorr score will be in better agreement with scores generated by
+SEQUEST<sup>®</sup>.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.20</h3> January 6, 2009
+
+<ul>
+
+<li>
+Generating peptides and searching with up to eleven different dynamic
+modifications is now possible. New options associated with this
+feature are mod, cmod, nmod, max-mods, max-aas-modified.
+
+<li>
+The format of the .csm files has changed and files written by older
+versions of crux are not readable with crux version 1.2.
+
+<li>
+When the option <code>cleavages</code> is set to <code>all</code>,
+peptide generation ignores all tryptic cleavage sites, effectively setting
+the <code>missed-cleavages</code> option to <code>TRUE</code>
+regardless of user settings.
+
+<li>
+When one spectrum has identical xcorr scores for different sequences,
+the rank of all those matches will be the same. Matches with the next
+highest score will rank one below.
+
+<li>
+The options for setting the preliminary and primary score type have
+been removed and are fixed as Sp and xcorr, respectively. A new
+option, <code>compute-p-values=<T | F></code>, was added to
+control p-value computation.
+
+<li>
+The SQT file contains the spectrum calculated mass instead of observed
+mass/charge on the S line.
+
+<li>
+There is now a test for confirming that the file downloaded from the
+crux website was not corrupted. See installation instructions for
+details.
+
+<li>
+Calculating a p-value requires a minimum of 40 matches. Spectra with
+fewer than 40 matches will have p-value scores returned as NaN and a
+warning will be printed at the DETAILED_INFO level (40) of verbosity.
+
+<li>
+Fixed error in generating neutral-loss peaks created as part of the
+theoretical spectrum.
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.02</h3> December 1, 2008
+
+<ul>
+
+<li>
+Three programs, <code>crux-create-index</code>,
+<code>crux-search-for-matches</code>,
+and <code>crux-analyze-matches</code>, were merged into one program
+named
+<code>crux</code>.</li>
+
+<li>
+Percolator is now truly optional as all Crux programs will build
+without it.</li>
+
+<li>
+Fragment masses can now be calculated as average or mono-isotopic.
+This is controlled by the <code>fragment-mass</code> option in the
+parameter file.</li>
+
+<li>
+The name of the score-type option that calculates p-values was changed
+from xcorr-logp to xcorr-pvalue.</li>
+
+<li>
+SQT files have two new lines in the header which describe the
+arrangement of values in the results.</li>
+
+<li>
+HTML documentation was updated to reflect the above changes.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.01</h3>
+
+<p>October 15, 2008</p>
+
+<ul>
+
+<li>
+A bug limiting the length of the name of an index file was fixed.</li>
+
+<li>
+Modifications were made so that Crux will build with version
+1.05 of Percolator. This is the only supported version of
+Percolator.</li>
+
+<li>
+Memory leaks in <code>crux-search-for-matches</code> were patched.</li>
+
+<li>
+The <code>--version</code> option was added.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.0</h3>
+
+<p>March 4, 2008</p>
+
+<blockquote>
+Initial release
+</blockquote>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
+
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/runall b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/runall
new file mode 100644
index 0000000..94d37db
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/runall
@@ -0,0 +1,28 @@
+#!/bin/bash -x
+
+# These three options make it harder to for some part of a script to
+# fail without you recognizing it. nounset means that references to an
+# unset variable result in an error. This means that you can no longer
+# do stuff like this if VAR is potentially unset, because "$VAR" returns
+# an error rather than "":
+#
+# if [ "$VAR" ]; then
+#
+# fi
+#
+# To explicitly indicate that you are OK with the variable potentially
+# being empty you can instead use ${VAR:-}.
+
+# To avoid errexit for a single command, use "|| true", e.g.,
+# diff foo foobar || true
+
+set -o nounset
+set -o pipefail
+set -o errexit
+set -o xtrace
+
+CRUX=../../src/crux
+for command in `$CRUX create-docs list`; do
+ $CRUX create-docs $command > $command.html
+done
+$CRUX create-docs default-params > default.params
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/search-for-xlinks.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/search-for-xlinks.html
new file mode 100644
index 0000000..0af3430
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/search-for-xlinks.html
@@ -0,0 +1,256 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>search-for-xlinks</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>search-for-xlinks</h1>
+<h2>Usage:</h2>
+<p><code>crux search-for-xlinks [options] <ms2 file> <protein fasta file> <link sites> <link mass></code></p>
+<h2>Description:</h2>
+<p>This command compares a set of spectra to cross-linked peptides derived from a protein database in FASTA format. For each spectrum, the program generates a list of candidate molecules, including linear peptides, dead-end products, self-loop products and cross-linked products, with masses that lie within a specified range of the spectrum's precursor mass. These candidate molecules are ranked using XCorr, and the XCorr scores are assigned statistical confidence estimates using an empiri [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+ <li><code>protein fasta file</code> – The name of the file in FASTA format from which to retrieve proteins.</li>
+ <li><code>link sites</code> – A comma delimited list of the amino acids to allow cross-links with. For example, "A:K,A:D" means that the cross linker can attach A to K or A to D. Cross-links involving the N-terminus of a protein can be specified as a link site by using "nterm". For example, "nterm:K" means that a cross-link can attach a protein's N-terminus to a lysine.</li>
+ <li><code>link mass</code> – The mass modification of the linker when attached to a peptide.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>search-for-xlinks.target.txt</code> – a tab-delimited text file containing the peptide-spectrum matches (PSMs). See the <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>search-for-xlinks.decoy.txt</code> – a tab-delimited text file containing the decoy PSMs. See the <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>search-for-xlinks.qvalues.txt</code> – a tab-delimited text file containing the top ranked PSMs with calculated q-values. See the <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>search-for-xlinks.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>search-for-xlinks.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>search-for-xlinks options</h3>
+<ul>
+ <li class="nobullet"><code>--require-xlink-candidate T|F</code> – If there is no cross-link candidate found, then don't bother looking for linear, self-loop, and dead-link candidates. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--xlink-top-n <integer></code> – Top-n open-mod peptides to consider in the second pass, value of 0 will search all candiates. Default = <code>250</code>.</li>
+ <li class="nobullet"><code>--cmod <string></code> – Specify a variable modification to apply to C-terminus of peptides. <mass change>:<max distance from protein c-term (-1 for no max)>. Note that this parameter only takes effect when specified in the parameter file. Default = <code>NO MODS</code>.</li>
+ <li class="nobullet"><code>--nmod <string></code> – Specify a variable modification to apply to N-terminus of peptides. <mass change>:<max distance from protein n-term (-1 for no max)> Note that this parameter only takes effect when specified in the parameter file. Default = <code>NO MODS</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Peptide properties</h3>
+<ul>
+ <li class="nobullet"><code>--min-mass <float></code> – The minimum mass (in Da) of peptides to consider. Default = <code>200</code>.</li>
+ <li class="nobullet"><code>--max-mass <float></code> – The maximum mass (in Da) of peptides to consider. Default = <code>7200</code>.</li>
+ <li class="nobullet"><code>--min-length <integer></code> – The minimum length of peptides to consider. Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--max-length <integer></code> – The maximum length of peptides to consider. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--isotopic-mass average|mono</code> – Specify the type of isotopic masses to use when calculating the peptide mass. Default = <code>mono</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Amino acid modifications</h3>
+<ul>
+ <li class="nobullet"><code>--mod <string></code> – Consider modifications on any amino acid in aa list with at most max-per-peptide in one peptide. The parameter takes the form <mass change>:<aa list>:<max per peptide>:<prevents cleavage>:<prevents cross-link>. This parameter may be included with different values multiple times so long as the total number of mod, cmod, and nmod parameters does not exceed 11. The "prevents cleavage" and "prevent [...]
+ <li class="nobullet"><code>--max-mods <integer></code> – The maximum number of modifications that can be applied to a single peptide. Default = <code>255</code>.</li>
+ <li class="nobullet"><code>--A <float></code> – Change the mass of all amino acids 'A' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--C <float></code> – Change the mass of all amino acids 'C' by the given amount. Default = <code>57.021464</code>.</li>
+ <li class="nobullet"><code>--D <float></code> – Change the mass of all amino acids 'D' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--E <float></code> – Change the mass of all amino acids 'E' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--F <float></code> – Change the mass of all amino acids 'F' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--G <float></code> – Change the mass of all amino acids 'G' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--H <float></code> – Change the mass of all amino acids 'H' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--I <float></code> – Change the mass of all amino acids 'I' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--K <float></code> – Change the mass of all amino acids 'K' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--L <float></code> – Change the mass of all amino acids 'L' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--M <float></code> – Change the mass of all amino acids 'M' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--N <float></code> – Change the mass of all amino acids 'N' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--P <float></code> – Change the mass of all amino acids 'P' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--Q <float></code> – Change the mass of all amino acids 'Q' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--R <float></code> – Change the mass of all amino acids 'R' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--S <float></code> – Change the mass of all amino acids 'S' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--T <float></code> – Change the mass of all amino acids 'T' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--V <float></code> – Change the mass of all amino acids 'V' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--W <float></code> – Change the mass of all amino acids 'W' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--Y <float></code> – Change the mass of all amino acids 'Y' by the given amount. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Decoy database generation</h3>
+<ul>
+ <li class="nobullet"><code>--seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+ <li class="nobullet"><code>--custom-enzyme <string></code> – Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. If the residues are required for digestion, they are in square brackets, '[' and ']'. If the re [...]
+ <li class="nobullet"><code>--digestion full-digest|partial-digest|non-specific-digest</code> – Specify whether every peptide in the database must have two enzymatic termini (full-digest) or if peptides with only one enzymatic terminus are also included (partial-digest). Default = <code>full-digest</code>.</li>
+ <li class="nobullet"><code>--missed-cleavages <integer></code> – Maximum number of missed cleavages per peptide to allow in enzymatic digestion. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Precursor selection</h3>
+<ul>
+ <li class="nobullet"><code>--precursor-window <float></code> – Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> – Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not avail [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-min-mz <float></code> – The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum-max-mz <float></code> – The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
+ <li class="nobullet"><code>--spectrum-charge 1|2|3|all</code> – The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge state will be searched. Default = <code>all</code>.</li>
+ <li class="nobullet"><code>--compute-sp T|F</code> – Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spe [...]
+ <li class="nobullet"><code>--precursor-window-weibull <float></code> – Search decoy peptides within +/- precursor-window-weibull of the precursor mass. The resulting scores are used only for fitting the Weibull distribution Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type-weibull mass|mz|ppm</code> – Window type to use in conjunction with the precursor-window-weibull parameter. Default = <code>mass</code>.</li>
+ <li class="nobullet"><code>--min-weibull-points <integer></code> – Keep shuffling and collecting XCorr scores until the minimum number of points for weibull fitting (using targets and decoys) is achieved. Default = <code>4000</code>.</li>
+ <li class="nobullet"><code>--max-ion-charge <string></code> – Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state of the peptide ("peptide"). If the max-ion-charge is greater than the charge state of the peptide, then the maximum is the peptide charge. Default = <code>peptide</code>.</li>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+ <li class="nobullet"><code>--mz-bin-offset <float></code> – In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--mod-mass-format mod-only|total|separate</code> – Specify how sequence modifications are reported in various output files. Each modification is reported as a number enclosed in square braces following the modified residue; however, the number may correspond to one of three different masses: (1) 'mod-only' reports the value of the mass shift induced by the modification; (2) 'total' reports the mass of the residue with the modification (residue mass plus [...]
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fragment-mass average|mono</code> – Specify which isotopes to use in calculating fragment ion mass. Default = <code>mono</code>.</li>
+ <li class="nobullet"><code>--isotope-windows <string></code> – Provides a list of isotopic windows to search. For example, -1,0,1 will search in three disjoint windows: (1) precursor_mass - neutron_mass +/- window, (2) precursor_mass +/- window, and (3) precursor_mass + neutron_mass +/- window. The window size is defined from the precursor-window and precursor-window-type parameters. This option is only available when use-old-xlink=F. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--compute-p-values T|F</code> – Estimate the parameters of the score distribution for each spectrum by fitting to a Weibull distribution, and compute a p-value for each xlink product. This option is only available when use-old-xlink=F. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fragment ion parameters</h3>
+<ul>
+ <li class="nobullet"><code>--use-a-ions T|F</code> – Consider a-ions in the search? Note that an a-ion is equivalent to a neutral loss of CO from the b-ion. Peak height is 10 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-b-ions T|F</code> – Consider b-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-c-ions T|F</code> – Consider c-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-x-ions T|F</code> – Consider x-ions in the search? Peak height is 10 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-y-ions T|F</code> – Consider y-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-z-ions T|F</code> – Consider z-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Cross-linking parameters</h3>
+<ul>
+ <li class="nobullet"><code>--use-old-xlink T|F</code> – Use the old version of xlink-searching algorithm. When false, a new version of the code is run. The new version supports variable modifications and can handle more complex databases. This new code is still in development and should be considered a beta release. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-linears T|F</code> – Include linear peptides in the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-deadends T|F</code> – Include dead-end peptides in the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-selfloops T|F</code> – Include self-loop peptides in the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-inter T|F</code> – Include inter-protein cross-link candidates within the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-intra T|F</code> – Include intra-protein cross-link candiates within the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-inter-intra T|F</code> – Include crosslink candidates that are both inter and intra. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-prevents-cleavage <string></code> – List of amino acids for which the cross-linker can prevent cleavage. This option is only available when use-old-xlink=F. Default = <code>K</code>.</li>
+ <li class="nobullet"><code>--max-xlink-mods <integer></code> – Specify the maximum number of modifications allowed on a crosslinked peptide. This option is only available when use-old-xlink=F. Default = <code>255</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/sort-by-column.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/sort-by-column.html
new file mode 100644
index 0000000..81fc8f2
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/sort-by-column.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>sort-by-column</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>sort-by-column</h1>
+<h2>Usage:</h2>
+<p><code>crux sort-by-column [options] <tsv file> <column name></code></p>
+<h2>Description:</h2>
+<p>Sort the rows of a tab-delimited file according to the values in a specified column.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tsv file</code> – A tab-delimited file, with column headers in the first row. Use "-" to read from standard input.</li>
+ <li><code>column name</code> – A column name.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – a copy of the given file, with rows sorted according to the values in the specified column.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--delimiter <string></code> – Specify the input and output delimiter to use when processing the delimited file. The argument can be either a single character or the keyword 'tab.' Default = <code>tab</code>.</li>
+ <li class="nobullet"><code>--header T|F</code> – Print the header line of the file, in addition to the columns that match. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--column-type int|real|string</code> – Specifies the data type of the column, either an integer (int), a floating point number (real), or a string. Default = <code>string</code>.</li>
+ <li class="nobullet"><code>--ascending T|F</code> – Sort in ascending (T) or descending (F) order. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/spectral-counts.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/spectral-counts.html
new file mode 100644
index 0000000..f95b686
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/spectral-counts.html
@@ -0,0 +1,152 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>spectral-counts</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>spectral-counts</h1>
+<h2>Usage:</h2>
+<p><code>crux spectral-counts [options] <input PSMs></code></p>
+<h2>Description:</h2>
+<p>Given a collection of scored PSMs, produce a list of proteins or peptides ranked by a quantification score. Spectral-counts supports four types of quantification: Normalized Spectral Abundance Factor (NSAF), Distributed Normalized Spectral Abundance (dNSAF), Normalized Spectral Index (SI<sub>N</sub>) and Exponentially Modified Protein Abundance Index (emPAI). The NSAF method is from <a href="http://www.ncbi.nlm.nih.gov/pubmed/17138671">Paoletti et al. (2006)</a>. The SI<sub>N</sub> me [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>input PSMs</code> – A PSM file in either tab delimited text format (as produced by percolator, q-ranker, or barista) or pepXML format.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>spectral-counts.target.txt</code> – a tab-delimited text file containing the protein IDs and their corresponding scores, in sorted order.</li>
+ <li><code>spectral-counts.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other Crux programs.</li>
+ <li><code>spectral-counts.log.txt</code> – All messages written to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>spectral-counts options</h3>
+<ul>
+ <li class="nobullet"><code>--parsimony none|simple|greedy</code> – Perform a parsimony analysis on the proteins, and report a "parsimony rank" column in the output file. This column contains integers indicating the protein's rank in a list sorted by spectral counts. If the parsimony analysis results in two proteins being merged, then their parsimony rank is the same. In such a case, the rank is assigned based on the largest spectral count of any protein in the merged meta-protein [...]
+ <li class="nobullet"><code>--threshold <float></code> – Only consider PSMs with a threshold value. By default, q-values are thresholded using a specified threshold value. This behavior can be changed using the --custom-threshold and --threshold-min parameters. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--threshold-type none|qvalue|custom</code> – Determines what type of threshold to use when filtering matches. none : read all matches, qvalue : use calculated q-value from percolator or q-ranker, custom : use --custom-threshold-name and --custom-threshold-min parameters. Default = <code>qvalue</code>.</li>
+ <li class="nobullet"><code>--input-ms2 <string></code> – MS2 file corresponding to the psm file. Required to measure the SIN. Ignored for NSAF, dNSAF and EMPAI. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--unique-mapping T|F</code> – Ignore peptides that map to multiple proteins. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--quant-level protein|peptide</code> – Quantification at protein or peptide level. Default = <code>protein</code>.</li>
+ <li class="nobullet"><code>--measure RAW|NSAF|dNSAF|SIN|EMPAI</code> – Type of analysis to make on the match results: (RAW|NSAF|dNSAF|SIN|EMPAI). With exception of the RAW metric, the database of sequences need to be provided using --protein-database. Default = <code>NSAF</code>.</li>
+ <li class="nobullet"><code>--custom-threshold-name <string></code> – Specify which field to apply the threshold to. The direction of the threshold (<= or >=) is governed by --custom-threshold-min. By default, the threshold applies to the q-value, specified by "percolator q-value", "q-ranker q-value", "decoy q-value (xcorr)", or "barista q-value". Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--custom-threshold-min T|F</code> – When selecting matches with a custom threshold, custom-threshold-min determines whether to filter matches with custom-threshold-name values that are greater-than or equal (F) or less-than or equal (T) than the threshold. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--mzid-use-pass-threshold T|F</code> – Use mzid's passThreshold attribute to filter matches. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--protein-database <string></code> – The name of the file in FASTA format. Default = <code><empty></code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/stat-column.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/stat-column.html
new file mode 100644
index 0000000..71d8dc9
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/stat-column.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>stat-column</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>stat-column</h1>
+<h2>Usage:</h2>
+<p><code>crux stat-column [options] <tsv file> <column name></code></p>
+<h2>Description:</h2>
+<p>Given a tab-delimited file, collect summary statistics on the values within a specified column. The specified column must contain numeric values.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tsv file</code> – A tab-delimited file, with column headers in the first row. Use "-" to read from standard input.</li>
+ <li><code>column name</code> – A column name.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – The program prints to standard output the following statistics for the specified column: number of rows, minimum, maximum, sum, average, and median of the data values.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--delimiter <string></code> – Specify the input and output delimiter to use when processing the delimited file. The argument can be either a single character or the keyword 'tab.' Default = <code>tab</code>.</li>
+ <li class="nobullet"><code>--header T|F</code> – Print the header line of the file, in addition to the columns that match. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--precision <integer></code> – Set the precision for scores written to sqt and text files. Default = <code>8</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/styles.css b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/styles.css
new file mode 100644
index 0000000..6eb6d2b
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/styles.css
@@ -0,0 +1,570 @@
+ at import url(https://fonts.googleapis.com/css?family=Roboto:400,300,600);
+
+* {
+ margin: 0;
+}
+a {
+ border: none;
+ text-decoration: none;
+}
+html {
+ font-size: 100%; /* 1 */
+ -webkit-text-size-adjust: 100%; /* 2 */
+ -ms-text-size-adjust: 100%; /* 2 */
+}
+
+body {
+ background-color: #ece8e5;
+ margin: 0;
+ padding: 0;
+
+}
+
+/*Sticky Footer*/
+html, body {
+ height: 100%;
+ font-family: Arial,Verdana,sans-serif;
+ font-size:14px;
+}
+
+table {
+ border-collapse: collapse;
+}
+table > thead, th{
+ border: 1px solid #000;
+ padding:5px;
+ background: #4d87a2;
+ color:#f3f3f7;
+ font-weight: 400;
+ font-family: 'Roboto', sans-serif;
+}
+caption
+{ font-weight: 400;
+ font-family: 'Roboto', sans-serif;
+ padding-left:10px;
+}
+table tr:nth-child(even) {
+ background: #f3f3f7;
+}
+
+.code {
+ background:#F8F8FF;
+ border:black dashed 1px;
+ padding:1px;
+ font:monospace;
+ padding-left:3px;
+ padding-right:3px;
+ padding-bottom:0px;
+ display: inline-block; /* box only as wide as content */
+}
+code {
+ font-family: monospace;
+}
+.page-wrap {
+ min-height: 100%;
+ margin-bottom: -180px; /* equal to footer height */
+ width:100%;
+}
+.page-wrap:after {
+ content: "";
+ display: block;
+}
+pre {
+ white-space: pre-wrap; /* Since CSS 2.1 */
+ white-space: -moz-pre-wrap; /* Mozilla, since 1999 */
+ white-space: -pre-wrap; /* Opera 4-6 */
+ white-space: -o-pre-wrap; /* Opera 7 */
+ word-wrap: break-word; /* Internet Explorer 5.5+ */
+ padding: 10px;
+ background: #eee;
+ border-radius: 5px;
+ overflow-x: auto;
+ background: #f3f3f7;
+ border: 1px solid #dedee3;
+ margin-bottom: 22px;
+ font-family: monospace;
+ font-size: 12px;
+ overflow-x: auto;
+ white-space: pre-wrap;
+ padding-bottom:0px;
+ display: inline-block;
+ padding-right:20px;
+}
+/* Content STYLES */
+#content {
+ background-color: #FFF;
+ min-height: calc(100vh - 280px);
+ width:80%;
+ margin:auto;
+ min-width:320px;
+ overflow: break-word;
+ padding:10px;
+ padding-bottom:20px;
+}
+#content p {
+ font-size:14px;
+ padding-top:5px;
+ padding-bottom:5px;
+}
+#content h2 {
+ font-size:30px;
+ color:#034463;
+ font-size: 30px;
+ font-weight: 600;
+ line-height: 30px;
+ margin: 5px;
+ text-align: center;
+ font-family: 'Roboto', sans-serif;
+}
+#content h3 {
+ font-size:20px;
+ padding:5px;
+ padding-top:15px;
+ padding-bottom:2px;
+ font-weight:400;
+ font-family: 'Roboto', sans-serif;
+}
+#content h4 {
+ font-size:16px;
+ padding:2px;
+ padding-left:5px;
+}
+#content a {
+ color: #2188b8;
+}
+#content a:hover {
+ color: #AA2244;
+}
+#content ul > li {
+
+}
+.nobullet {
+ list-style-type: none;
+}
+/*END content STYLES*/
+#centerfooter {
+ display: inline-block;
+}
+.site-footer, .page-wrap:after {
+ height: 180px;
+ text-align: center;
+}
+.site-footer {
+ background: #FFF;
+ color: #076FA2;
+ font-size:12px !important;
+ padding-top:30px;
+ /*margin-top:20px;*/
+ border-top: 2px solid #69B2D5;
+ font-family:Arial,Verdana,sans-serif !important;
+}
+.site-footer a{
+ color: #076FA2;
+ text-decoration: none;
+}
+.site-footer a:hover{
+ color: #2682AF;
+ text-decoration: none;
+}
+.site-footer h3 {
+ color:#034463;
+ font-size:16px;
+ line-height:22px;
+ border-bottom: 2px solid #B3DAED;
+ width:200px;
+}
+.site-footer img {
+ float:left;
+ padding-right:6px;
+}
+.footerimportantlinks {
+ float:left;
+ margin-left:50px;
+ height:100px;
+ text-align: left;
+}
+.footerimportantlinks ul{
+ float:left;
+ list-style-type: none;
+ margin-left:-40px;
+ margin-top:4px;
+ -moz-column-count: 2;
+ -moz-column-gap: 10px;
+ -webkit-column-count: 2;
+ -webkit-column-gap: 10px;
+ column-count: 2;
+ column-gap: 10px;
+
+}
+.footerimportantlinks li{
+ margin-top:5px;
+ width:150px;
+}
+.tutoriallinks {
+ margin-left:50px;
+}
+.tutoriallinks ul {
+ -moz-column-count: 1;
+ -moz-column-gap: 10px;
+ -webkit-column-count: 1;
+ -webkit-column-gap: 10px;
+ column-count: 1;
+ column-gap: 10px;
+}
+.tutoriallinks li {
+ width:300px;
+}
+#footertext {
+ float:left;
+ margin-top:20px;
+ padding-top:5px;
+ margin-left:20px;
+ height:100px;
+ width:300px;
+ border-top: 2px solid #B3DAED;
+}
+#footertext p {
+ text-align: center;
+ font-size:11px;
+}
+#footertext a {
+ color: #05577F;
+ text-decoration: underline;
+}
+/*******************/
+/* Responsive Menu */
+nav {
+ height: 100px;
+ overflow: show;
+ width: 100%;
+ background: #FFF;
+ font-size: 13pt;
+ font-weight: bold;
+ position: relative;
+ border-bottom: 2px solid #69B2D5;
+ min-width:300px;
+}
+
+#navitems a {
+ display: inline-block;
+ text-align: center;
+ text-decoration: none;
+ line-height: 40px;
+ padding-left:10px;
+ padding-right:10px;
+ color:#4f8bac;
+ /*text-shadow: 1px 1px 0px #283744;*/
+}
+
+nav header {
+ display: none;
+
+}
+
+nav ul {
+ padding: 0;
+ width:100%;
+ /*margin-left:370px;*/
+ float:left;
+ padding-left: 20px;
+ /*margin: 0 auto; /* CENTER MENU */
+ width: 400px;
+ height: 40px;
+ margin-top:60px;
+ background: #FFF;
+}
+nav li {
+ display: inline;
+ float: left;
+}
+
+#logo{
+ float:left;
+ height:100px;
+ margin-left:10%;
+}
+
+nav li a {
+ border-right: 1px solid #4199C4;
+ box-sizing:border-box;
+ -moz-box-sizing:border-box;
+ -webkit-box-sizing:border-box;
+}
+
+nav li:last-child a {
+ border-right: 0;
+}
+#navitems a:hover, #navitems a:active {
+ background-color: #B3DAED;
+}
+
+ at media screen and (max-width: 1124px) {
+ .page-wrap {
+ min-height: 100%;
+ margin-bottom: -250px; /* equal to footer height */
+ }
+ .site-footer, .page-wrap:after {
+ height: 250px;
+ }
+ #footertext {
+ padding-top:40px;
+ border:none;
+ margin-top:20px;
+ display: inline;
+ width:90%;
+ padding-left: 20px;
+ padding-right:20px;
+ text-align: center;
+ }
+}
+/*Styles for 780px (footer changes)*/
+ at media screen and (max-width: 780px) {
+ table {
+ margin:0;
+ }
+ #content {
+ width:100%;
+ }
+ body {
+ background-color: #FFF;
+ }
+ nav {
+ height: 140px;
+ }
+
+ nav ul {
+ width: 100%;
+ display: block;
+ height: auto;
+ margin-top:0px;
+ }
+
+ .footerimportantlinks {
+ margin-left:50px;
+ margin-top:10px;
+ }
+ .page-wrap {
+ min-height: 100%;
+ margin-bottom: -300px; /* equal to footer height */
+ }
+ .site-footer, .page-wrap:after {
+ height: 300px;
+ }
+}
+ at media screen and (max-width: 730px) {
+ .page-wrap {
+ min-height: 100%;
+ margin-bottom: -380px; /* equal to footer height */
+ }
+ .site-footer, .page-wrap:after {
+ height: 380px;
+ }
+}
+/*Styles for screen 600px and lower*/
+ at media screen and (max-width: 600px) {
+ nav {
+ height: 182px;
+ }
+
+ nav ul {
+ width: 100%;
+ display: block;
+ height: auto;
+ }
+ nav li {
+ width: 50%;
+ float: left;
+ position: relative;
+ }
+ nav li a {
+ border: none;
+ }
+ #navitems a {
+ text-align: left;
+ width: 100%;
+ text-indent: 25px;
+ background: #FFF;
+ }
+}
+
+/*Styles for screen 515px and lower*/
+ at media only screen and (max-width : 515px) {
+ #logo {
+ height: 33px;
+ padding-top:0px;
+ }
+
+ nav {
+ border-bottom: 0;
+ width: 100%;
+ height: 33px;
+ padding: 7px 0 0 0;
+
+ }
+ nav ul {
+ display: none;
+ height: auto;
+ padding: 0 0 0 0;
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+ float: none;
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+ }
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+
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+/***********/
+blockquote {
+ font-family:monospace;
+}
+.indentcitation {
+ border-left:4px solid #034463;
+ padding: 0px 10px;
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+ background-color:#f9f9f9;
+}
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+ width:calc(100% + 20px);
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+ padding:5px;
+ border:none;
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+#commandstable td:nth-child(even) {
+ padding-left:10px;
+ font-family: Arial;
+}
+/* fileformats.html */
+#fileFormatsTable {
+ border-collapse: collapse;
+ margin-left:auto;
+ margin-right: auto;
+ padding:0;
+}
+#fileFormatsTable tr:nth-child(even) {
+ background: #DEDEDE;
+}
+#fileFormatsTable th, td {
+ padding-top:5px;
+ padding-bottom: 5px;
+ padding-left:3px;
+ border: 1px solid #000;
+}
+
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+#featurestable {
+ text-align: left;
+ font-size:14px;
+}
+
+#featurestable td{
+ padding-left:3px;
+}
+
+/*txt-format.html*/
+#tabformat td {
+ padding:3px;
+ font-size:14px;
+}
+
+/*search.html*/
+.searchtable td {
+ padding:2px 4px 2px 4px;
+ border:1px solid #000;
+ font-size:12px;
+ word-wrap: break-word;
+}
+
+/*STYLES FOR ALL AUTOGENERATED CONTENT*/
+.autogenerated h1 {
+ font-size:30px;
+ color:#034463;
+ font-size: 30px;
+ font-weight: 600;
+ line-height: 30px;
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+ font-family: 'Roboto', sans-serif;
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+.autogenerated h2, h3, h4 {
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diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/subtract-index.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/subtract-index.html
new file mode 100644
index 0000000..8a925b0
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/subtract-index.html
@@ -0,0 +1,138 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>subtract-index</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>subtract-index</h1>
+<h2>Usage:</h2>
+<p><code>crux subtract-index [options] <tide index 1> <tide index 2> <output index></code></p>
+<h2>Description:</h2>
+<p>This command takes two peptide indices, created by the tide-index command, and subtracts the second index from the first. The result is an output index that contains peptides that appear in the first index but not the second.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tide index 1</code> – A peptide index produced using tide-index</li>
+ <li><code>tide index 2</code> – A second peptide index, to be subtracted from the first index.</li>
+ <li><code>output index</code> – A new peptide index containing all peptides that occur in thefirst index but not the second.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>subtract-index.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> containing the target peptides.</li>
+ <li><code>subtract-index.decoy.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> containing the decoy peptides.</li>
+ <li><code>subtract-index.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>subtract-index.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--peptide-list T|F</code> – Create in the output directory a text file listing of all the peptides in the database, along with their neutral masses, one per line. If decoys are generated, then a second file will be created containing the decoy peptides. Decoys that also appear in the target database are marked with an asterisk in a third column. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/template.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/template.html
new file mode 100644
index 0000000..6ba71fa
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/template.html
@@ -0,0 +1,105 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tide-index.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tide-index.html
new file mode 100644
index 0000000..770cc21
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tide-index.html
@@ -0,0 +1,177 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>tide-index</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>tide-index</h1>
+<h2>Usage:</h2>
+<p><code>crux tide-index [options] <protein fasta file> <index name></code></p>
+<h2>Description:</h2>
+<p>Tide is a tool for identifying peptides from tandem mass spectra. It is an independent reimplementation of the SEQUEST<sup>®</sup> algorithm, which assigns peptides to spectra by comparing the observed spectra to a catalog of theoretical spectra derived from a database of known proteins. Tide's primary advantage is its speed. Our published paper provides more detail on how Tide works. If you use Tide in your research, please cite:</p><blockquote>Benjamin J. Diament and William Sta [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>protein fasta file</code> – The name of the file in FASTA format from which to retrieve proteins.</li>
+ <li><code>index name</code> – The desired name of the binary index.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>index</code> – A binary index, using the name specified on the command line.</li>
+ <li><code>tide-index.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>tide-index.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Peptide properties</h3>
+<ul>
+ <li class="nobullet"><code>--max-length <integer></code> – The maximum length of peptides to consider. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--max-mass <float></code> – The maximum mass (in Da) of peptides to consider. Default = <code>7200</code>.</li>
+ <li class="nobullet"><code>--min-length <integer></code> – The minimum length of peptides to consider. Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--min-mass <float></code> – The minimum mass (in Da) of peptides to consider. Default = <code>200</code>.</li>
+ <li class="nobullet"><code>--isotopic-mass average|mono</code> – Specify the type of isotopic masses to use when calculating the peptide mass. Default = <code>mono</code>.</li>
+ <li class="nobullet"><code>--clip-nterm-methionine T|F</code> – When set to T, for each protein that begins with methionine, tide-index will put two copies of the leading peptide into the index, with and without the N-terminal methionine. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Amino acid modifications</h3>
+<ul>
+ <li class="nobullet"><code>--mods-spec <string></code> – The general form of a modification specification has three components, as exemplified by <span style="color: red;">1</span><span style="color: green;">STY</span>+<span style="color: blue">79.966331</span>.<br>The three components are: [<span style="color: red;">max_per_peptide</span>]<span style="color: green;">residues</span>[+/-]<span style-"color: blue;">mass_change</span><br>In the example, <span style="color: red [...]
+ <li class="nobullet"><code>--cterm-peptide-mods-spec <string></code> – Specify peptide c-terminal modifications. See nterm-peptide-mods-spec for syntax. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--nterm-peptide-mods-spec <string></code> – Specify peptide n-terminal modifications. Like --mods-spec, this specification has three components, but with a slightly different syntax. The <span style="color: red;">max_per_peptide</span> can be either "1", in which case it defines a variable terminal modification, or missing, in which case the modification is static. The <span style="color: green;">residues</span> field indicates which amino acids a [...]
+ <li class="nobullet"><code>--max-mods <integer></code> – The maximum number of modifications that can be applied to a single peptide. Default = <code>255</code>.</li>
+ <li class="nobullet"><code>--min-mods <integer></code> – The minimum number of modifications that can be applied to a single peptide. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Decoy database generation</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-format none|shuffle|peptide-reverse|protein-reverse</code> – Include a decoy version of every peptide by shuffling or reversing the target sequence or protein. In shuffle or peptide-reverse mode, each peptide is either reversed or shuffled, leaving the N-terminal and C-terminal amino acids in place. Note that peptides appear multiple times in the target database are only shuffled once. In peptide-reverse mode, palindromic peptides are shuffled. [...]
+ <li class="nobullet"><code>--keep-terminal-aminos N|C|NC|none</code> – When creating decoy peptides using decoy-format=shuffle or decoy-format=peptide-reverse, this option specifies whether the N-terminal and C-terminal amino acids are kept in place or allowed to be shuffled or reversed. For a target peptide "EAMPK" with decoy-format=peptide-reverse, setting keep-terminal-aminos to "NC" will yield "EPMAK"; setting it to "C" will yield "PMAEK"; setting it to "N" will yield "EKPMA" [...]
+ <li class="nobullet"><code>--seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--allow-dups T|F</code> – Prevent duplicate peptides between the target and decoy databases. When set to "F", the program keeps all target and previously generated decoy peptides in memory. A shuffled decoy will be re-shuffled multiple times to avoid duplication. If a non-duplicated peptide cannot be generated, the decoy is skipped entirely. When set to "T", every decoy is added to the database without checking for duplication. This option reduces the m [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+ <li class="nobullet"><code>--custom-enzyme <string></code> – Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. If the residues are required for digestion, they are in square brackets, '[' and ']'. If the re [...]
+ <li class="nobullet"><code>--digestion full-digest|partial-digest|non-specific-digest</code> – Specify whether every peptide in the database must have two enzymatic termini (full-digest) or if peptides with only one enzymatic terminus are also included (partial-digest). Default = <code>full-digest</code>.</li>
+ <li class="nobullet"><code>--missed-cleavages <integer></code> – Maximum number of missed cleavages per peptide to allow in enzymatic digestion. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--peptide-list T|F</code> – Create in the output directory a text file listing of all the peptides in the database, along with their neutral masses, one per line. If decoys are generated, then a second file will be created containing the decoy peptides. Decoys that also appear in the target database are marked with an asterisk in a third column. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--temp-dir <string></code> – The name of the directory where temporary files will be created. If this parameter is blank, then the system temporary directory will be used Default = <code><empty></code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
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+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
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+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
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+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>tide-search</h1>
+<h2>Usage:</h2>
+<p><code>crux tide-search [options] <tide spectra file>+ <tide database></code></p>
+<h2>Description:</h2>
+<p>Tide is a tool for identifying peptides from tandem mass spectra. It is an independent reimplementation of the SEQUEST<sup>®</sup> algorithm, which assigns peptides to spectra by comparing the observed spectra to a catalog of theoretical spectra derived from a database of known proteins. Tide's primary advantage is its speed. Our published paper provides more detail on how Tide works. If you use Tide in your research, please cite:</p><blockquote>Benjamin J. Diament and William Sta [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>tide spectra file+</code> – The name of one or more files from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard. Alternatively, the argument may be one or more binary spectrum files produced by a previous run of crux tide-search using the store-spectra parameter.</li>
+ <li><code>tide database</code> – Either a FASTA file or a directory containing a database index created by a previous run of crux tide-index.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>tide-search.target.txt</code> – a tab-delimited text file containing the target PSMs. See <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>tide-search.decoy.txt</code> – a tab-delimited text file containing the decoy PSMs. This file will only be created if the index was created with decoys.</li>
+ <li><code>tide-search.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other Crux programs.</li>
+ <li><code>tide-search.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Precursor selection</h3>
+<ul>
+ <li class="nobullet"><code>--precursor-window <float></code> – Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto-precursor-window false|warn|fail</code> – Automatically estimate optimal value for the precursor-window parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> – Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not avail [...]
+ <li class="nobullet"><code>--max-precursor-charge <integer></code> – The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-min-mz <float></code> – The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum-max-mz <float></code> – The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
+ <li class="nobullet"><code>--min-peaks <integer></code> – The minimum number of peaks a spectrum must have for it to be searched. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--spectrum-charge 1|2|3|all</code> – The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge state will be searched. Default = <code>all</code>.</li>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--compute-sp T|F</code> – Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spe [...]
+ <li class="nobullet"><code>--remove-precursor-peak T|F</code> – If true, all peaks around the precursor m/z will be removed, within a range specified by the --remove-precursor-tolerance option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--exact-p-value T|F</code> – Enable the calculation of exact p-values for the XCorr score as described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this article</a>. Calculation of p-values increases the running time but increases the number of identifications at a fixed confidence threshold. The p-values will be reported in a new column with header "exact p-value", and the "xcorr score" column will be replaced with a "refactored xcorr" colu [...]
+ <li class="nobullet"><code>--use-neutral-loss-peaks T|F</code> – Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+ <li class="nobullet"><code>--auto-mz-bin-width false|warn|fail</code> – Automatically estimate optimal value for the mz-bin-width parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-offset <float></code> – In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--peptide-centric-search T|F</code> – Carries out a peptide-centric search. For each peptide the top-scoring spectra are reported, in contrast to the standard spectrum-centric search where the top-scoring peptides are reported. Note that in this case the "xcorr rank" column will contain the rank of the given spectrum with respect to the given candidate peptide, rather than vice versa (which is the default). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--isotope-error <string></code> – List of positive, non-zero integers. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--skip-preprocessing T|F</code> – Skip preprocessing steps on spectra. Default = F. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>CPU threads</h3>
+<ul>
+ <li class="nobullet"><code>--num-threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--store-spectra <string></code> – Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir). This option is not valid if multiple input spectrum files are given. Default = <code><e [...]
+ <li class="nobullet"><code>--store-index <string></code> – When providing a FASTA file as the index, the generated binary index will be stored at the given path. This option has no effect if a binary index is provided as the index. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--concat T|F</code> – When set to T, target and decoy search results are reported in a single file, and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--print-search-progress <integer></code> – Show search progress by printing every n spectra searched. Set to 0 to show no search progress. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--sqt-output T|F</code> – Outputs an SQT results file to the output directory. Note that if sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mzid-output T|F</code> – Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pin-output T|F</code> – Output a Percolator input (PIN) file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--file-column T|F</code> – Include the file column in tab-delimited output. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
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+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/customizedsearch.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/customizedsearch.html
new file mode 100644
index 0000000..7f75f4c
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/customizedsearch.html
@@ -0,0 +1,299 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Customization and search options</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Customization and search options</h2>
+
+ <p><span class="prog">Crux</span> allows the user the flexibility to
+ change many of the search and analysis parameters. Attributes like
+ the output format and which peptides are selected from the protein
+ database are controlled through numerous options. This page
+ starts with some general information about options and then describe
+ the use of some key <span class="prog">crux</span> options.
+ </p>
+
+ <a name="intro"></a>
+ <h3>Introduction to options</h3>
+
+ <p>
+ A <span class="prog">crux</span> command is made up of four parts:
+ executable name, command, options, and required arguments. Let's use
+ a <span class="prog">crux tide-search</span> command as an example.
+ Here is the general form.</p>
+
+ <div class="code"><code>
+ $ crux tide-search [options] <mass spectra> <peptide index>
+ </code>
+ </div>
+
+ <p>
+ In this case, the command is <span class="prog">tide-search</span>.
+ This is followed by zero or more optional arguments. Finally, the
+ required arguments, listed above inside angle brackets, include the
+ name of the file containing the spectra to be identified and the name
+ of a peptide index produced previously by
+ the <span class="prog">tide-index</span> command.</p>
+
+ <p>
+ All of the available options are described for each command on
+ the <a href="../index.html">documentation</a> pages. You can also get a
+ list of available options by running a command with no arguments.
+ For example, the command</p>
+
+ <div class="code"><code>
+ $ crux tide-search</code>
+ </div>
+
+ <p>
+ will produce output that looks like this:</p>
+
+ <pre>
+bash-3.2$ ~/proj/crux/trunk/src/c/crux tide-search
+FATAL: Error in command line. Error # 5
+The required argument <tide spectra file> is missing.
+
+USAGE:
+
+ crux tide-search [options] <tide spectra file> <tide database index>
+
+REQUIRED ARGUMENTS:
+
+ <tide spectra file> The name of the file from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard. Alternatively, the argument may be a binary spectrum file produced by a previous run of crux tide-search using the store-spectra parameter.
+ <tide database index> A directory containing a database index created by a previous run of crux tide-index.
+
+OPTIONAL ARGUMENTS:
+
+ [--precursor-window <double>]
+ Search peptides within +/- 'precursor-window' of the spectrum mass.
+ Definition of precursor window depends upon precursor-window-type.
+ Default=3.0.
+ [--precursor-window-type <string>]
+ Window type to use for selecting candidate peptides.
+ <string>=mass|mz|ppm. Default=mass.
+ [--spectrum-min-mz <double>]
+ The lowest spectrum m/z to search. Default=0.0.
+ [--spectrum-max-mz <double>]
+ The highest spectrum m/z to search. Default=no maximum.
+ [--min-peaks <int>]
+ The minimum number of peaks a spectrum must have for it to be
+ searched. Default=20.
+...
+ </pre>
+
+ <p>The first three lines are telling you that you forgot the required
+ arguments and are reminding you what they are. The following lines
+ list all the options (only five of which are shown
+ above). <span class="prog">Crux</span> options all begin with two
+ dashes followed by the option name. The name is followed by a space
+ and the appropriate argument. This example increases the verbosity to
+ 40:
+ </p>
+
+ <div class="code"><code>
+ $ crux tide-search --verbosity 40 sample.ms2 yeast.fasta</code>
+ </div>
+
+ <a name="file"></a>
+ <h3>Specifying options via a parameter file</h3>
+
+ <p>
+ The second option listed
+ above, <span class="out">--parameter-file</span>, is available for all
+ Crux commands. The parameter file allows multiple options to be
+ specified in a file. All of the command line options can be put in a
+ parameter file, but the format is slightly different. In the
+ parameter file, the two leading dashes are removed from the option
+ name, and the option name and value must be separated by an equal sign
+ instead of a space:
+ </p>
+ <div class=code><code>
+ <option name>=<argument></code>
+ </div>
+
+ <p>
+ The above example, in which we changed the verbosity, would look like this
+ in a parameter file:</p>
+
+ <div class="code"><code>
+ verbosity=40
+ </code>
+ </div>
+
+ <p>
+ The parameter file allows only one option per line. Lines beginning
+ with "#" are considered comments and are ignored. A sample parameter
+ file can be found <a href="../file-formats/parameter-file.html">here</a>. Command
+ line and parameter file options may be used separately or together.
+ If an option is specified in both places, then value on the command
+ line will be used.
+ </p>
+
+ <p>
+ During execution of any Crux command, a parameter file containing the
+ name and value of all the options for the current operation
+ will be automatically be saved in the output directory. Note that not
+ all parameters in the file may have been used in the operation. The
+ parameter file will be named
+ <code><command>.params.txt</code>,
+ where <code><tag></code> is the name of the command that was
+ executed.</p>
+
+ <a name="shared"></a>
+ <h3>Shared options</h3>
+
+ <p>
+ In addition to <code>--parameter-file</code>, Crux includes several
+ other options that are shared across all, or nearly all, Crux commands.
+ </p>
+
+ <ul>
+ <li>
+ <code>--output-dir <filename></code> –
+ The name of the directory where output files will be created.
+ Default = crux-output.</li>
+
+ <li>
+ <code>--fileroot <string></code> –
+ The <code>fileroot</code> string will be added as a prefix to all
+ output file names. Default = none.</li>
+
+ <li>
+ <code>--overwrite <T|F></code> – By default, if Crux
+ detects that the output file it is about to produce already exists,
+ then Crux will exit with an error. This option allows Crux to
+ overwrite existing files.</li>
+
+ <li>
+ <code>--verbosity <0-100></code> – Specify the verbosity
+ of the current command. Each level prints the following messages,
+ including all those at lower verbosity levels: 0-fatal errors,
+ 10-non-fatal errors, 20-warnings, 30-information on the progress of
+ execution, 40-more progress information, 50-debug info, 60-detailed
+ debug info. Default = 30.</li>
+
+ <li>
+ In addition, many Crux commands include various options of the form
+ <code>--<format>-output</code>. These options take Boolean
+ arguments (specified as "T" or "F") and indicate whether output files
+ in the specified format should be produced. For example, in addition
+ to tab-delimited text format, <code>tide-search</code> can produce
+ output in PepXML, MZid, SQT and PINxml formats.</li>
+
+ </ul>
+
+ <a name="index"></a>
+ <h3>Changing the indexing and searching parameters</h3>
+
+ <p>
+ Various options to <span class="prog">tide-index</span> control how
+ the proteins in the database are converted to peptides. These options
+ fall into several categories, allowing specification of peptide
+ properties such as minimum and maximum length, enzymatic digestion
+ rules, decoy database generation and specification of various static
+ and variable modifications. These options are fully
+ documented <a href="../commands/tide-index.html">here</a>. Similarly,
+ the <code><a href="../commands/tide-search.html">tide-search</a></code>
+ documentation describes options for selecting which spectra to score,
+ the rules for selecting candidate peptides for a given spectrum, and
+ for deciding what kinds of scores to report.</p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/gettingstarted.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/gettingstarted.html
new file mode 100644
index 0000000..023bacb
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/gettingstarted.html
@@ -0,0 +1,218 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Getting started with Crux</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Getting started with Crux</h2>
+
+ <p> This page will talk about setting up your environment and choosing
+ your input files. Be sure to have completed the software <a
+ href="install.html">installation</a> first.
+ </p>
+
+ <a name="env"></a>
+ <h3>Your environment</h3>
+ <p>For this tutorial, we'll assume you are working in a Linux/Unix
+ type shell (<a href="http://www.cygwin.com/">cygwin</a> is a good
+ choice for Windows users) and already know some basic
+ commands for changing directories, listing files, and other simple
+ tasks. To successfully run the sample commands, you'll need to work from
+ a directory for which you have write permission. Anywhere
+ in your home directory should work. Create a new directory and
+ navigate to it.</p>
+ <div class=code><code>
+ $ mkdir crux-demo<br>
+ $ cd crux-demo</code>
+ </div>
+ <p>
+ We will refer to this directory, <code>'crux-demo'</code>, as the
+ <em>working directory</em>.</p>
+ <p>Next, make sure that the computer knows where to look for the
+ <span class=prog>crux</span> programs. Try this command. </p>
+ <div class=code><code>
+ $ which crux</code>
+ </div>
+ <p>
+ If it returns a single line with a path ending in <span
+ class=out>crux</span>, then you are set. If not,
+ review the <a href="install.html#path">installation instructions</a> on setting your
+ <span class=code>$PATH</span> environment variable.
+
+ </p>
+
+ <a name=ms2></a>
+ <h3>Input file: mass spectra</h3>
+ <p>Included in the <span class=prog>crux</span> distribution in the
+ <span class=file>doc/example-files</span> directory are some
+ sample files containing mass spectra. We will use the <a
+ href="../example-files/demo.ms2">demo.ms2</a> for this tutorial. Locate the
+ file and copy it to the current working directory.
+ </p>
+ <p>The beginning of the file looks like this.
+ </p>
+ <pre>
+H CreationDate 2/14/2007 6:19:18 PM
+H Extractor MakeMS2
+H ExtractorVersion 1.0
+H Comments MakeMS2 written by Michael J. MacCoss, 2004
+H ExtractorOptions MS2/MS1
+S 10 10 636.34
+Z 2 1271.67
+187.4 12.5
+193.1 19.5
+194.3 13.7
+ </pre>
+ <div class=note><em>NOTE: There are two kinds of optional lines which
+ may be included for each spectrum. Lines beginning with </em><span
+ class=file>I</span><em> are contain information independent of the
+ charge state. Following a </em> <span class=file>Z</span><em> line may
+ be one beginning with </em><span class=file>D</span><em> containing
+ information specific to the above charge state. </em>
+ </div>
+
+ <p>
+ The first lines beginning with <span class=file>H</span> are the
+ header lines and contain information about the program that generated
+ the file, the date it was created, and so on. The line starting with
+ <span class=file>S</span> begins the information about the first
+ spectrum. Following the <span class=file>S</span> is the scan number
+ (twice) and the m/z of the precursor ion. The lines beginning with
+ <span class=file>Z</span> list the possible charge states of the
+ spectrum (in this case 2) and the mass of the peptide at that
+ charge state. Following the <span class=file>Z</span> lines is the
+ list of peaks for the spectrum. The subsequent spectra in the file
+ repeat this pattern of <span class=file>S</span> line, <span
+ class=file>Z</span> line(s), and peak list. <span
+ class=file>demo.ms2</span> contains 150 spectra.
+ </p>
+
+ <a name="fasta"></a>
+ <h3>Input file: protein database (fasta file)</h3>
+ <p>The second input file you will need is a protein database.
+ This file is in fasta format and contains
+ a list of proteins you expect to find in your sample and their
+ sequences. A sample fasta file is also comes with the distribution in
+ <span class=file>doc/example-files</span>. We will use <a
+ href="../example-files/small-yeast.fasta">small-yeast.fasta</a>. Copy it to your
+ current working directory.
+ </p>
+
+ <p>The beginning of the file looks like this.
+ </p>
+
+ <pre>
+>YBL030C PET9 SGDID:S000000126, Chr II from 164000-163044, reverse complement, Verified ORF, "Major ADP/ATP carrier of the mitochondrial inner membrane, exchanges cytosolic ADP for mitochondrially synthesized ATP; required for viability in many common lab strains carrying a mutation in the polymorphic SAL1 gene"
+MSSNAQVKTPLPPAPAPKKESNFLIDFLMGGVSAAVAKTAASPIERVKLLIQNQDEML
+KQGTLDRKYAGILDCFKRTATQEGVISFWRGNTANVIRYFPTQALNFAFKDKIKAMFG
+FKKEEGYAKWFAGNLASGGAAGALSLLFVYSLDYARTRLAADSKSSKKGGARQFNGLI
+DVYKKTLKSDGVAGLYRGFLPSVVGIVVYRGLYFGMYDSLKPLLLTGSLEGSFLASFL
+LGWVVTTGASTCSYPLDTVRRRMMMTSGQAVKYDGAFDCLRKIVAAEGVGSLFKGCGA
+NILRGVAGAGVISMYDQLQMILFGKKFK
+ </pre>
+
+ <p>Lines beginning with <span class=file>></span> give the name of
+ a protein. The first word is the protein name followed by an optional
+ description of any length. The following lines contain the protein
+ sequence. Proteins may or may not be separated by blank lines.
+ <span class=file>small-yeast.fasta</span> contains 56 proteins.
+ </p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/install.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/install.html
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+ <li><a href="../download.html">Download</a></li>
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+ <div id="content">
+ <!-- START CONTENT -->
+ <div id="main">
+ <h2>Crux Installation Instructions</h2>
+
+ <p/>
+ This page will walk you through the steps of
+ installing <span class=prog>crux<span/> on your computer.
+ Seperate sections describe the installation for
+ <a href="#LINUX">Linux</a>,
+ <a href="#OSX">OS X</a>,
+ and
+ <a href="#WINDOWS">Windows</a>.
+ You have the choice of installing precompiled binaries or building
+ Crux from the source code.
+ The compiled binaries offer the easiest installation option.
+
+ <a name="LINUX"></a>
+ <h3>Linux</h3>
+ <b>Note:</b> when typing the commands shown in these instructions
+ do not type the
+ leading <code>$</code> before each command; it indicates the
+ prompt. These instructions will refer to your home directory as
+ <code>$HOME</code>. You can type <code>$HOME</code> in the commands
+ or you can use the fully qualified path to your home directory which
+ may be something like <code>/home/yourname/</code>. Note that you can
+ find out the location of your home directory by logging in and
+ typing <code>pwd</code> or <code>echo $HOME</code>.
+ <h3>Installing Pre-compiled Crux Binaries on Linux</h3>
+ <ul>
+ <li><b>Download the files</b>
+ <p/>
+ <span class=prog>Crux</span> is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license</a>.
+ On the download page click on the link "Linux [architecture]
+ Build (zipped)" to download them to your computer.
+ If your computer is running a 32-bit version of Linux select the
+ i686 version.
+ If your computer is running a 64-bit version of Linux select the
+ x86_64 version.
+ If a window pops
+ up, select the "Save" button.
+ To check that the file was
+ transfered correctly, run this command
+
+ <div class=code><code>
+ $ md5sum <i>[downloaded file]</i></code>
+ </div>
+ <p/>
+ and compare the output to the "MD5 checksum" link next to the file you
+ downloaded.
+ <p/>
+ </li>
+
+ <li><b>Unpack and install the files</b>
+ <p/>
+ The file you downloaded
+ should be named something like
+ <span class=file>crux-x.xx-XXXX-GNU-Linux.zip</span>
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ and
+ <span class=file>XXXX</span> is either i686 or x86_64.
+ Move this file
+ to a convenient location and unpack the file with this command.
+
+ <div class=code><code>
+ $ unzip crux-x.xx-XXXX-GNU-Linux.zip</code>
+ </div>
+ <p/>
+ You should now have a new directory,
+ <span class=file>crux-x.xx-XXXX-GNU-Linux</span>,
+ with two subdirectories <span class=file>bin</span>, and <span
+ class=file>doc</span>. The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> directory. You may want to move
+ these files somewhere
+ more convenient for you, but otherwise, that completes the
+ installation! Skip ahead to
+ <a href="#linux_path">Setting the PATH on Linux and OS X</a>
+ for notes on how to run the executables.
+ </ul>
+ <h3>Building Crux From Source on Linux</h3>
+ <ul>
+ <li><b>Prerequisites</b>
+ <p/>
+ To build Crux from source on Linux you must have installed the
+ following software:
+ <ul>
+ <li><code>gcc</code></li>
+ <li><code>g++</code></li>
+ <li><code>cmake</code></li>
+ <li><code>make</code></li>
+ <li><code>svn</code></li>
+ <li><code>wget</code> (must support SSL)</li>
+ </ul>
+ <p/>
+ Building <span class=prog>crux</span> also requires the
+ <a href="http://proteowizard.sourceforge.net"><span class=prog>Proteowizard</span></a>
+ and
+ <a href="http://per-colator.com"><span class=prog>Percolator</span></a>
+ libraries.
+ These will automatically be copied from the <span class=prog>Proteowizard</span>
+ and <span class=prog>Percolator</span>
+ repositories and statically linked into <span class=prog>crux</span>.
+
+ <li><b>Download the files</b>
+ <p/>
+ The <span class=prog>Crux</span> source is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license></a>.
+ On the download page click on the link "Source (tarred, gzipped)",
+ and choose save to disk if prompted.
+ To check that the file was
+ transfered correctly, run this command
+
+ <div class=code><code>
+ $ md5sum <i>[downloaded file]</i></code>
+ </div>
+ <p/>
+ and compare the output to the "MD5 checksum" link next to the file you
+ selected on the Crux download page.
+ <p/>
+ The file you downloaded should be named something like
+ <span class=file>crux-x.xx.source.tar.gz</span>,
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ <li><b>Unpack the files</b>
+ <p/>
+ Move the downloaded file to a
+ convenient location and unpack it with this command.
+
+ <div class=code>
+ $ tar -zxvf crux-x.xx.Source.tar.gz
+ </div>
+ A new directory named <span class=file>crux-x.xx.Source</span> will be
+ created and a long list of files will stream by as they are being put
+ into the new directory.
+ <p/>
+ </li>
+
+ <li><b>Configure the build</b>
+ <p/>
+ Move into the <span class=file>crux-x.xx.Source</span>
+ directory from step 1.
+ Run the command
+ <div class=code><code>
+ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+ </code>
+ </div>
+ <p/>
+ where <span class=file><install directory></span> is
+ the location where you wish to install the <span class=prog>crux</span> programs.
+ If you want <span class=prog>crux</span> to go in <span class=file>$HOME/bin</span>,
+ then <span class=file><install directory></span> would be <span class=file>$HOME</span>.
+ The installation process will automatically put the programs in a directory called
+ <span class=file>bin</span>.
+ <p/>
+ Note, this configuration will build with optimizations turned on,
+ and will not include debug symbols.
+ To build with optimizations turned off,
+ and debug symbols included,
+ use the command:
+ <div class=code><code>
+ cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+ </code>
+ </div>
+ </li>
+ <p/>
+ <li><b>Build and install</b>
+ <p/>
+ To complete the process, run these two commands.</li>
+ <div class=code><code>
+ $ make<br>
+ $ make install
+ </code>
+ </div>
+ <p/>
+ The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> subdirectory
+ of the
+ <span class=file><install directory></span>
+ That completes the installation! Skip ahead to
+ <a href="#linux_path">Setting the PATH on Linux and OS X</a>
+ for notes on how to run the executables.
+ </ul>
+ <a name="OSX"></a>
+ <h3>OS X</h3>
+ <span class=prog>Crux</span> requires OS X Yosemite or later.
+ <p/>
+ <b>Note:</b>
+ when typing the commands shown in these instructions do not type the
+ leading <code>$</code> before each command; it indicates the
+ prompt. These instructions will refer to your home directory as
+ <code>$HOME</code>. You can type <code>$HOME</code> in the commands
+ or you can use the fully qualified path to your home directory which
+ may be something like <code>/home/yourname/</code>. Note that you can
+ find out the location of your home directory by logging in and
+ typing <code>pwd</code> or <code>echo $HOME</code>.
+ <p/>
+ To install and use <code>crux</code> on OS X
+ you'll need to be familiar with the <span class=code>Terminal</span>
+ application.
+ <h3>Installing Pre-compiled Crux Binaries on OS X</h3>
+ <ul>
+ <li><b>Download the files</b>
+ <p/>
+ <span class=prog>Crux</span> is freely
+ available for download under an
+ <a href=""http://www.apache.org/licenses/LICENSE-2.0>Apache 2.0 license</a>.
+ On the download page click on the link "OS X x86_64 Build (zipped)"
+ to download them to your computer.
+ If a window pops
+ up, select the "Save" button.
+ To check that the file was
+ transfered correctly, run this command
+
+ <div class=code><code>
+ $ md5 <i>[downloaded file]</i></code>
+ </div>
+ <p/>
+ and compare the output to the "MD5 checksum" link next to the file you
+ downloaded.
+ <p/>
+ </li>
+
+ <li><b>Unpack and install the files</b>
+ <p/>
+ The file you downloaded
+ should be named something like
+ <span class=file>crux-x.xx.Darwin.x86_64.zip</span>
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ Move this file
+ to a convenient location and unpack the file with this command.
+
+ <div class=code><code>
+ $ unzip crux-x.xx.Darwin.x86_64.zip</code>
+ </div>
+ <p/>
+ You should now have a new directory,
+ <span class=file>crux-x.xx.Darwin.x86_64</span>,
+ with two subdirectories <span class=file>bin</span>, and <span
+ class=file>doc</span>. The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> directory. You may want to move
+ these files somewhere
+ more convenient for you, but otherwise, that completes the
+ installation! Skip ahead to
+ <a href="#linux_path">Setting the PATH on Linux and OS X</a>
+ for notes on how to run the executables.
+ </ul>
+ <h3>Building Crux From Source on OS X</h3>
+ <ul>
+ <li><b>Prerequisites</b>
+ <p/>
+ To build Crux from source on OS X you must have installed the
+ following software:
+ <ul>
+ <li><code>OS X Yosemite or later</code></li>
+ <li><code>XCode 6.3.1 or later</code></li>
+ <li><code>XCode Command Line Tools</code></li>
+ <li><code>cmake</code></li>
+ <li><code>make</code></li>
+ <li><code>svn</code></li>
+ <li><code>wget</code> (must support SSL)</li>
+ <li><code>gnutar</code> (Apple's version of tar is incompatible with GNU's
+ version of tar)</li>
+ </ul>
+ <p/>
+ Building <span class=prog>crux</span> also requires the
+ <a href="http://proteowizard.sourceforge.net"><span class=prog>Proteowizard</span></a>
+ and
+ <a href="http://per-colator.com"><span class=prog>Percolator</span></a>
+ libraries.
+ These will automatically be copied from the <span class=prog>Proteowizard</span>
+ and <span class=prog>Percolator</span>
+ repositories and statically linked into <span class=prog>crux</span>.
+ <p />
+ Building <span class=prog>Crux</span> on OS X requires a current version of
+ <span class=prog>XCode</span>, and the XCode command line tools.
+ Earlier versions of <span class=prog>Crux</span>
+ had to be built using the GCC compilers.
+ which are no supported by Apple.
+ If you have the both the GCC and Apple compilers installed, you'll need to
+ adjust the <span class=prog>PATH</span> environment variable so that the
+ Apple compilers are found first.
+ Alternatively, you can specify which compilers should be used by setting
+ the <span class=prog>CC</span>, and <span class=prog>CXX</span>.
+ For example,
+ <div class=code>
+ <code>
+ export CC=/usr/bin/gcc
+ <br />
+ export CXX=/usr/bin/g++
+ </code>
+ </div>
+ <p/>
+ The programs
+ <span class=prog>cmake</span>,
+ <span class=prog>svn</span>,
+ and
+ <span class=prog>wget</span>,
+ can be installed from
+ <a href="https://www.macports.org">MacPorts</a>
+ or
+ <a href="http://brew.sh">Homebrew</a>.
+ Note that you must install the <span class=prog>ssl</span> variant of
+ <span class=prog>wget</span>:
+ <div class=code>
+ <code>
+ $ sudo port install wget +ssl
+ </code>
+ </div>
+ <p/>
+ <li><b>Download the files</b>
+ <p/>
+ The <span class=prog>Crux</span> source is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license></a>.
+ On the download page click on the link "Source (tarred, gzipped)",
+ and choose save to disk if prompted.
+ To check that the file was
+ transfered correctly, run this command
+
+ <div class=code><code>
+ $ md5sum <i>[downloaded file]</i></code>
+ </div>
+ <p/>
+ and compare the output to the "MD5 checksum" link next to the file you
+ selected on the Crux download page.
+ <p/>
+ The file you downloaded should be named something like
+ <span class=file>crux-x.xx.source.tar.gz</span>,
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ <li><b>Unpack the files</b>
+ <p/>
+ Move the downloaded file to a
+ convenient location and unpack it with this command.
+
+ <div class=code>
+ $ tar -zxvf crux-x.xx.Source.tar.gz
+ </div>
+ A new directory named <span class=file>crux-x.xx.Source</span> will be
+ created and a long list of files will stream by as they are being put
+ into the new directory.
+ <p/>
+ </li>
+
+ <li><b>Configure the build</b>
+ <p/>
+ Move into the <span class=file>crux-x.xx.Source</span>
+ directory from step 1.
+ Run the command
+ <div class=code><code>
+ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+ </code>
+ </div>
+ <p/>
+ where <span class=file><install directory></span> is
+ the location where you wish to install the <span class=prog>crux</span> programs.
+ If you want <span class=prog>crux</span> to go in <span class=file>$HOME/bin</span>,
+ then <span class=file><install directory></span> would be <span class=file>$HOME</span>.
+ The installation process will automatically put the programs in a directory called
+ <span class=file>bin</span>.
+ <p/>
+ Note, this configuration will build with optimizations turned on,
+ and will not include debug symbols.
+ To build with optimizations turned off,
+ and debug symbols included,
+ use the command:
+ <div class=code><code>
+ cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+ </code>
+ </div>
+ </li>
+ <p/>
+ <li><b>Build and install</b>
+ <p/>
+ To complete the process, run these two commands.</li>
+ <div class=code><code>
+ $ make<br>
+ $ make install
+ </code>
+ </div>
+ <p/>
+ The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> subdirectory
+ of the
+ <span class=file><install directory></span>
+ That completes the installation! Skip ahead to
+ <a href="#linux_path">Setting the PATH on Linux and OS X</a>
+ for notes on how to run the executables.
+ </ul>
+
+ <a name="linux_path"></a>
+ <h3>Setting the PATH on Linux and OS X</h3>
+ <ul>
+ <li>
+ <p/>
+ On Linux and OS X systems you can always run any of the programs by specifying its full
+ path. For example,</p>
+
+ <div class=code><code>
+ $ <em><install directory></em>/bin/crux comet</code>
+ </div>
+
+ <p>In this final step of the installation, we'll set things up so that
+ you can also run any of the programs by just typing its name. This is
+ done with an environment variable called <span
+ class=code>$PATH</span>. <span class=code>$PATH</span> is a list of
+ places that the computer looks for executable programs. Find out what
+ is in the current list with this command:
+
+ <div class=code><code>
+ $ echo $PATH</code><br>
+ </div>
+ <p>The value returned might look something like this:
+ <code>
+ /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games
+ </code>
+ <p>The first directory in this colon-separated list, <span
+ class=out>/usr/local/bin</span>, is the first place the computer looks
+ for a program. If it doesn't find the program there it tries <span
+ class=out>/usr/bin</span> and so on down the list. You can either
+ move the crux executable files into one of these directories already
+ in your PATH, or you can add <span
+ class=code><em><install directory></em></span> to PATH with this
+ command. (Remember to replace the word <em><install directory></em> with the
+ actual location of your installation)</p>
+
+ <div class=code><code>
+ $ export PATH=$PATH:<install directory>/bin</code>
+ </div>
+
+ <p>Try '<span class=code>echo $PATH</span>' again to see that the
+ change was made. <em><install directory>/bin</em> should be at the end of the
+ list. Now you can
+ run the <span class=prog>crux</span> programs by just typing their
+ names. Try this.</p>
+
+ <div class=code><code>
+ $ crux comet</code>
+ </div>
+
+ <p>The change to <span class=code>$PATH</span> is only temporary. As
+ soon as you close the window, the change will disappear. In order to
+ make the change every time you log on, add the line <span
+ class=code>export PATH=$PATH:<install directory>/bin</span> to the file <span
+ class=out>.bashrc</span> located in your home directory. You will
+ have to log on again for the change to take effect.
+ </ul>
+ <a name="WINDOWS"></a>
+ <h3>Windows</h3>
+ <h3>Installing Pre-compiled Crux Binaries on Windows</h3>
+
+ <ul>
+ <li><b>Prerequisites</b>
+ <p/>
+ To run Crux with support for vendor specific file formats
+ on Windows you must have installed the following software:
+ <ul>
+ <li>
+ <a href="https://thermo.flexnetoperations.com/control/thmo/login">
+ <code>Thermo MSFileReader</code></a>
+ </li>
+ <li>
+ <a href="https://www.microsoft.com/en-us/download/details.aspx?id=40784">
+ <code>Visual C++ 2013 Runtime Libraries</code></a>
+ </li>
+ </ul>
+ <p/>
+ <li><b>Download the files</b>
+ <p/>
+ <span class=prog>Crux</span> is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license</a>.
+ On the download page click on the link "Windows x86
+ Build (zipped)" to download them to your computer.
+ If a window pops up, select the "Save" button.
+ </li>
+ <li><b>Unpack and install the files</b>
+ <p/>
+ Browse to the downloaded file in Windows Explorer.
+ Right click on the file and choose "Expand All ...".
+ You should now have a new directory,
+ <span class=file>crux-x.xx</span>,
+ with two subdirectories <span class=file>bin</span>, and <span
+ class=file>doc</span>. The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> directory. You may want to move
+ these files somewhere
+ more convenient for you, but otherwise, that completes the
+ installation! Skip ahead to
+ <a href="#windows_path">Setting the PATH on Windows</a>
+ for notes on how to run the executables.
+ </ul>
+
+ <h3>Building Crux From Source on Windows</h3>
+ <ul>
+ <li><b>Prerequisites</b>
+ <p/>
+ To build Crux from source on Windows you must have installed the
+ following software:
+ <ul>
+ <li><code>
+ <a
+ href="http://www.visualstudio.com/downloads/download-visual-studio-vs#DownloadFamilies_4">Microsoft
+ Visual C++ 2013</a></code></li>
+ <li><a href="http://www.cmake.org/cmake/resources/software.html"><code>CMake</code></a></li>
+ <li><a href="http://sourceforge.net/projects/win32svn/"><code>SVN</code></a></li>
+ <li><a href="http://getgnuwin32.sourceforge.net"><code>wget</code> (must support SSL)</a></li>
+ <li><a
+ href="https://thermo.flexnetoperations.com/control/thmo/login">
+ <code>Thermo MSFileReader</code></a> (This may be omitted if support for
+ vendor specific file formats is disabled.)</li>
+ </ul>
+ <p/>
+ <b>Other verions of Visual Studio will not be able to build Crux!</b>
+ You must have Visual Studio 2013.
+ Visual Studio 2013 Express for Windows Desktop does work.
+ <p/>
+ <span class=code>wget</span> is available as part of the GnuWin32 package.
+ The easiest way to install this is via the
+ <a href="http://getgnuwin32.sourceforge.net"><code>GetGnuWin32</code></a>
+ package manager.
+ <span class=code>wget</span> must support SSL, so install the optional
+ packages provided by
+ <a href="http://getgnuwin32.sourceforge.net"><code>GetGnuWin32</code></a> .
+ <p/>
+ <span class=code>wget</span> and
+ <span class=code>svn</span> must be included in the execution PATH
+ for your system.
+ See the section <i>Setting the PATH on Windows</i> for more information.
+ <p/>
+ <li><b>Download the file</b>
+ <p/>
+ The <span class=prog>Crux</span> source is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license></a>.
+ On the download page click on the link "Source (zipped)",
+ and choose save to disk if prompted.
+ <p/>
+ The file you downloaded should be named something like
+ <span class=file>crux-x.xx.Source.zip</span>,
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ <p />
+ <li><b>Unpack the files</b>
+ <p />
+ Unpack the downloaded file using Windows Explorer.
+ Right click on the file icon and click on "Extract All ...".
+ A new directory named <span class=file>crux-x.xx.Source</span> will be
+ created containing the source code and documentation for Crux.
+ <p/>
+ <b>Note</b> Windows has a fixed maximum path length of 270 characters.
+ The Crux build creates several levels of directories so it
+ is very easy to exceed this limit.
+ This will cause the build to fail.
+ To avoid this problem we recommend keeping the Crux source and build trees
+ very near the disk root (typically
+ <span class=code>C:\</span>
+
+ </li>
+ <li>
+ <p/>
+ <b>Open the command line development environment.</b>
+ <p/>
+ Under the "Start" button
+ open the "Visual Studio 2013" folder, then open the "Visual Studio Tools"
+ folder, and double-click on "Developer Command Prompt for VS2013".
+ This will launch a
+ <span class=file>cmd</span> shell configured to use the
+ Microsoft development tools.
+ </li>
+ <li><b>Configure</b>
+ <p/>
+ In the <span class=file>cmd</span> shell you just opened,
+ move into the <span class=file>crux-x.xx.Source</span>
+ directory from step 1.
+ Run the command
+ <div class=code><code>
+ cmake -DCMAKE_INSTALL_PREFIX:PATH=<install directory> -G "Visual Studio
+ 12 Win64" .
+ </code>
+ </div>
+ <p/>
+ where <span class=file><install directory></span> is
+ the location where you wish to install the <span class=prog>crux</span> programs.
+ Note that, somewhat confusingly, Visual Studio 2013 is version 12.
+ <p/>
+ If you wish to disable support for vendor specific file formats,
+ use this command instead
+ <p/>
+ <div class=code><code>
+ cmake
+ -DCMAKE_INSTALL_PREFIX:PATH=<install directory> -DINCLUDE_VENDOR_LIBRARIES=FALSE -G "Visual Studio 12 Win64" .
+ </code>
+ </div>
+ <p/>
+ <li><b>Build and install</b>
+ <p/>
+ To complete the process run the commands</li>
+ <div class=code><code>
+ cmake --build . --config Release --target ALL_BUILD
+ <br/>
+ cmake --build . --config Release --target INSTALL
+ </code>
+ <p/>
+ Once you've run the configuration step
+ you can also build and debug Crux from within the Visual Studio IDE.
+ CMake will generate a file named
+ <span class=file>crux.sln</span>.
+ Open this file in Visual Studio.
+ You can select the build configuration: Release or Debug
+ in the combo box under the menu bar.
+ <p/>
+ <b>Note</b> The Crux build will not automatically generate
+ debugging symbols even if you've selected the Debug configuration.
+ Right click on the Crux folder in the "Solution Explorer" and
+ select "Properties" from the pop-up menu.
+ In the "Properties" page select the "Debugging" item under the "Linker"
+ properties. Set "Generate Debug Info" to "Yes".
+ <p/>
+ Changes made to the Visual Studio solution and project files will be lost
+ the next time CMake regenerates the project.
+ </div>
+ <p/>
+
+ </ul>
+ </ul>
+
+ <a name="windows_path"></a>
+ <h3>Setting the PATH on Windows</h3>
+ <ul>
+ <li>
+ On Windows systems you can always run any of the programs by specifying its full
+ path. For example,</p>
+
+ <div class=code><code>
+ C:\ <em><install directory></em>\bin\crux comet</code>
+ </div>
+
+ <p>In this final step of the installation, we'll set things up so that
+ you can also run any of the programs by just typing its name. This is
+ done with an environment variable called <span
+ class=code>PATH</span>. <span class=code>PATH</span> is a list of
+ directoires that the computer looks for executable programs. Find out what
+ is in the current list with this command:
+ <p/>
+ <div class=code><code>
+ C:\ echo %PATH%</code><br>
+ </div>
+ <p/>
+ <p>The value returned might look something like this:
+ <p/>
+ <div class=code><code>
+ <code>
+ C:\Windows;C:\Windows\system32;c:\Program Files\Microsoft Visual
+ Studio 10.0\Common7\IDE\;c:\Program Files\Microsoft
+ Visual Studio 10.0\VC\BIN;C:\Program Files\Common Files\Microsoft Shared\
+ Windows Live;C:\Windows\System32\Wbem;C:\Windows\S
+ ystem32\WindowsPowerShell\v1.0\;c:\Program files\Notepad++;C:\Program Files\Tort
+ oiseSVN\bin;C:\Program Files\Windows Live\Shared;C:\Program Files\CMake 2.8\bin;
+ C:\Program Files\PuTTY;C:\Program Files\Subversion\bin;C:\GnuWin32\bin;
+ </code>
+ </div>
+ <p>The first directory in this semicolon-separated list, <span
+ class=out>C:\Windows</span>, is the first place the computer looks
+ for a program. If it doesn't find the program there it tries <span
+ class=out>C:\WIndows\system32</span> and so on down the list. You can either
+ move the crux executable files into one of these directories already
+ in your PATH, or you can add <span
+ class=code><em><install directory></em></span> to PATH with this
+ command. (Remember to replace the word <em><install directory></em> with the
+ actual location of your installation)</p>
+ <div class=code><code>
+ set PATH=%PATH%;<install directory>\bin;</code><br>
+ </div>
+ <p>The change to <span class=code>PATH</span> is only temporary.
+ To make a permanent change to the path follow the following steps:
+ <ol>
+ <li>Open the "Control Panel".</li>
+ <li>Click on "System and Security".</li>
+ <li>Click on "Advanced System Settings" in the list on the left
+ (you may be asked to give an administrative password).
+ <li>
+ You'll presented with a dialog box titled "System Properties".
+ Click on the button labeled "Environment Variables".
+ <li>
+ You'll be presented with a new dialog box containing two list boxes: one for user
+ environment variables, and one for system environment variables.
+ Select the
+ <span class=code>PATH</span>
+ variable in the system variables list, and click on the "Edit ..." button.
+ <li>
+ Add the full path to the directory containing the Crux executables to the
+ list of directories. Remember that each
+ <span class=code>PATH</span>
+ entry should end with a semi-colon.
+ </ol>
+
+ </div>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/search.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/search.html
new file mode 100644
index 0000000..2788a27
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/search.html
@@ -0,0 +1,422 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Running a Simple Search Using Tide and Percolator</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
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+
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+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Running a Simple Search Using Tide and Percolator</h2>
+
+ <p>
+ Now that you have your environment <a href="gettingstarted.html">set
+ up</a> and the two input files in your working directory, you can
+ conduct the search. The search process compares each spectrum
+ in <span class=file>demo.ms2</span> to peptides (subsequences of the
+ proteins) in fasta files provided in a
+ dirctory, <span class=file>yeast-index/</span>. Peptides whose
+ precursor mass is close to that of the observed spectrum are scored
+ against that spectrum, and the top scores are reported in the output.
+ To conduct the search, we first create a peptide index
+ using <code>tide-index</code> and then execute the search
+ using <code>tide-search</code>.</p>
+
+ <ol>
+ <li>
+ <div class=code>
+ <code>$ crux tide-index small-yeast.fasta yeast-index </code>
+ </div>
+
+ <p>
+ While generating the peptide index, you will see output like this:</p>
+
+ <pre>
+INFO: CPU: pyrrolysine.gs.washington.edu
+INFO: Crux version: 2.1
+INFO: Fri Feb 5 11:24:02 PST 2016
+COMMAND LINE: ./crux tide-index small-yeast.fasta yeast-index
+INFO: Running tide-index...
+INFO: Writing results to output directory 'yeast-index'.
+INFO: Reading small-yeast.fasta and computing unmodified peptides...
+INFO: Writing decoy fasta...
+INFO: Reading proteins
+INFO: Precomputing theoretical spectra...
+INFO: Elapsed time: 0.0973 s
+INFO: Finished crux tide-index.
+INFO: Return Code:0
+ </pre>
+
+ <p>
+ This command produces the peptide index in <code>yeast-index</code>
+ and also produces a directory <code>crux-output</code> containing
+ the following files:
+ <ol>
+
+ <li>
+ tide-index.decoy.fasta – a set of decoy proteins, derived from
+ the proteins in the input set,</li>
+
+ <li>
+ tide-search.params.txt – a record of all the parameters used in
+ the search, and</li>
+
+ <li>tide-search.log.txt – a log file containing a copy of all
+ the messages printed to the screen during the search.</li>
+ </ol>
+
+ <p>
+ Now you can run this command:</p></li>
+
+ <div class=code>
+ <li><code>$ crux tide-search --compute-sp T demo.ms2 yeast-index</code>
+ </div>
+
+ <p>While the search is running, you will see output like this:</p>
+
+ <pre>
+INFO: CPU: pyrrolysine.gs.washington.edu
+INFO: Crux version: 2.1
+INFO: Fri Feb 5 11:24:23 PST 2016
+COMMAND LINE: ./crux tide-search --compute-sp T demo.ms2 yeast-index
+INFO: Running tide-search...
+INFO: Reading index yeast-index
+INFO: Converting demo.ms2 to spectrumrecords format
+INFO: Reading spectra file crux-output/demo.ms2.spectrumrecords.tmp
+INFO: Sorting spectra
+INFO: Running search
+INFO: Time per spectrum-charge combination: 0.002318 s.
+INFO: Average number of candidates per spectrum-charge combination: 15.204820
+INFO: Elapsed time: 0.389 s
+INFO: Finished crux tide-search.
+INFO: Return Code:0
+ </pre>
+
+ <p>
+ The <span class=file>crux-output</span> directory now contains four new files
+ containing the search results:
+
+ <ol>
+
+ <li>
+ tide-search.target.txt – search results
+ in <a href="../file-formats/txt-format.html">tab-delimited format</a>.</li>
+
+ <li>
+ tide-search.decoy.txt – search results from a decoy database
+ in <a href="../file-formats/txt-format.html">tab-delimited format</a>.</li>
+
+ <li>
+ tide-search.params.txt – a record of all the parameters used in
+ the search.</li>
+
+ <li>tide-search.log.txt – a log file containing a copy of all
+ the messages printed to the screen during the search.</li>
+ </ol>
+
+ </p>
+ </li>
+
+ <p>
+ Note that the peptide-spectrum matches (PSMs) in the
+ tide-search.target.txt are sorted by the precursor m/z value
+ associated with the spectrum. If you want to see which PSMs got the
+ highest XCorr scores, you can do so like this:</p>
+
+ <div class=code>
+ <li><code>$ crux sort-by-column --column-type real --ascending T crux-output/tide-search.target.txt "xcorr score" > crux-output/tide-search.target.sort.txt</code>
+ </div>
+
+ <p>
+ The first lines of the resulting sorted output file should look like this:</p>
+
+ <table class="searchtable">
+ <td><b>file</b></td><td><b>scan</b></td><td><b>charge</b></td><td><b>spectrum precursor m/z</b></td><td><b>spectrum neutral mass</b></td><td><b>peptide mass</b></td><td><b>delta_cn</b></td><td><b>sp score</b></td><td><b>sp rank</b></td><td><b>xcorr score</b></td><td><b>xcorr rank</b></td><td><b>b/y ions matched</b></td><td><b>b/y ions total</b></td><td><b>distinct matches/spectrum</b></td><td><b>sequence</b></td><td><b>cleavage type</b></td><td><b>protein id</b></td><td><b>flanking aa< [...]
+ <tr>
+ <td>demo.ms2</td><td>85</td><td>3</td><td>497.618</td><td>1489.83</td><td>1488.82</td><td>0.936932</td><td>2430.56</td><td>1</td><td>5.20757</td><td>1</td><td>27</td><td>48</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W(27)</td><td>RN</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>118</td><td>3</td><td>1031.94</td><td>3092.8</td><td>3093.41</td><td>0.949698</td><td>2383.16</td><td>1</td><td>4.76204</td><td>1</td><td>44</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>156</td><td>3</td><td>1032.44</td><td>3094.3</td><td>3093.41</td><td>0.938358</td><td>1929.77</td><td>1</td><td>4.7476</td><td>1</td><td>43</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>18</td><td>3</td><td>1032.4</td><td>3094.18</td><td>3093.41</td><td>0.902056</td><td>1732.23</td><td>1</td><td>4.48933</td><td>1</td><td>40</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>11</td><td>2</td><td>745.269</td><td>1488.52</td><td>1488.82</td><td>0.822851</td><td>2816.6</td><td>1</td><td>4.44855</td><td>1</td><td>21</td><td>24</td><td>4</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W(27)</td><td>RN</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>53</td><td>2</td><td>745.749</td><td>1489.48</td><td>1488.82</td><td>0.935648</td><td>2797.78</td><td>1</td><td>4.39828</td><td>1</td><td>21</td><td>24</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W(27)</td><td>RN</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>38</td><td>3</td><td>1032.39</td><td>3094.15</td><td>3093.41</td><td>0.975741</td><td>1460.28</td><td>1</td><td>4.39627</td><td>1</td><td>37</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>42</td><td>3</td><td>1032.26</td><td>3093.76</td><td>3093.41</td><td>1.0216</td><td>1509.47</td><td>1</td><td>4.35676</td><td>1</td><td>38</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>111</td><td>3</td><td>1033.02</td><td>3096.04</td><td>3093.41</td><td>0.952727</td><td>1366.71</td><td>1</td><td>4.3498</td><td>1</td><td>36</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>62</td><td>2</td><td>745.859</td><td>1489.7</td><td>1488.82</td><td>0.913711</td><td>2766.65</td><td>1</td><td>4.34057</td><td>1</td><td>21</td><td>24</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W(27)</td><td>RN</td></tr>
+ </table>
+
+
+ <p>
+ The final step is to post-process the search results using Percolator.
+ Each spectrum has been compared to many peptides and we would like to
+ return only the best match for each spectrum. We also expect that
+ some fraction of the spectra will not be identifiable as peptides (due
+ to chemical noise, multiple peptides co-eluting, poor fragmentation,
+ etc.). The analysis step filters out those spectra and ranks the
+ matches by quality.
+ </p></li>
+
+ <li>
+ <div class=code><code>
+ $ crux percolator crux-output/tide-search.target.txt</code>
+ </div>
+
+ <p>While the analysis is running, you will see output like this
+ </p>
+
+ <pre>
+INFO: CPU: pyrrolysine.gs.washington.edu
+INFO: Crux version: 2.1
+INFO: Fri Feb 5 11:25:51 PST 2016
+COMMAND LINE: ./crux percolator crux-output/tide-search.target.txt
+INFO: Reading file crux-output/tide-search.target.txt
+INFO: Running make-pin
+INFO: Parsing crux-output/tide-search.target.txt
+INFO: Parsing crux-output/tide-search.decoy.txt
+INFO: There are 690 target matches and 690 decoys
+INFO: Finished make-pin.
+INFO: Percolator version 2.09, Build Date Sep 22 2015 14:29:11
+INFO: Copyright (c) 2006-9 University of Washington. All rights reserved.
+INFO: Written by Lukas Käll (lukall at u.washington.edu) in the
+INFO: Department of Genome Sciences at the University of Washington.
+INFO: Issued command:
+INFO: percolator -r crux-output/percolator.target.peptides.txt -v 2 -P decoy_ --seed 1 -p 0.01 -n 0 --trainFDR 0.01 --testFDR 0.01 --maxiter 10 -s crux-output/make-pin.pin
+INFO: Started Fri Feb 5 11:25:52 2016
+INFO: on pyrrolysine.gs.washington.edu
+INFO: Hyperparameters selectionFdr=0.01, Cpos=0.01, Cneg=0, maxNiter=10
+INFO: Reading Tab delimited input from datafile crux-output/make-pin.pin
+INFO: Features:
+INFO: lnrSp deltCn XCorr Sp IonFrac PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM
+INFO: Train/test set contains 690 positives and 690 negatives, size ratio=1 and pi0=1
+INFO: selecting cneg by cross validation
+INFO: Selected feature number 4 as initial search direction, could separate 39 positives in that direction
+INFO: Selected feature number 3 as initial search direction, could separate 38 positives in that direction
+INFO: Selected feature number 3 as initial search direction, could separate 30 positives in that direction
+INFO: Estimating 53 over q=0.01 in initial direction
+INFO: Reading in data and feature calculation took 0.03 cpu seconds or 0 seconds wall time
+INFO: ---Training with Cpos=0.01, Cneg selected by cross validation, fdr=0.01
+INFO: Iteration 1 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 2 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 3 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 4 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 5 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 6 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 7 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 8 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 9 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 10 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Obtained weights (only showing weights of first cross validation set)
+INFO: # first line contains normalized weights, second line the raw weights
+INFO: lnrSp deltCn XCorr Sp IonFrac PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM m0
+INFO: 0.0352 0.0014 0.1465 0.2956 -0.0130 0.0224 0.0051 -0.0025 -0.0020 0.0000 0.0000 -0.0001 -0.0049 -0.0055 0.0169 -0.9248
+INFO: 0.0580 0.0069 0.2096 0.0010 -0.0922 0.0052 0.0136 -0.0052 -0.0053 0.0000 0.0000 -0.0006 -0.0077 -0.0059 0.0300 -1.1931
+INFO: After all training done, 56 target PSMs with q<0.0100 were found when measuring on the test set
+INFO: Found 56 target PSMs scoring over 1.0000% FDR level on testset
+INFO: Merging results from 3 datasets
+INFO: Target Decoy Competition yielded 116 target PSMs and 50 decoy PSMs
+INFO: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
+INFO: Calibrating statistics - calculating q values
+INFO: Merged list gives 9 peptides over q=0.0100
+INFO: Calibrating statistics - calculating Posterior error probabilities (PEPs)
+INFO: Processing took 0.67 cpu seconds or 0 seconds wall time
+INFO: Elapsed time: 0.933 s
+INFO: Finished crux percolator.
+INFO: Return Code:0
+ </pre>
+
+ <p>
+ The <span class=file>crux-output</span> directory will now contain
+ eight new files:</p>
+ <ol>
+
+ <li>
+ percolator.target.psms.txt – a list of peptide-spectrum matches
+ (PSMs), ranked by quality,</li>
+
+ <li>
+ percolator.target.peptides.txt – a list of peptides, ranked by
+ quality,</li>
+
+ <li>
+ percolator.decoy.psms.txt – a ranked list of decoy PSMs, </li>
+
+ <li>
+ percolator.decoy.peptides.txt – a ranked list of decoy peptides,</li>
+
+ <li>
+ percolator.pout.xml – a single XML output file containing all of
+ the Percolator results,</li>
+
+ <li>
+ make-pin.pin.xml: an intermediate XML format file that is used by
+ Percolator.</li>
+
+ <li>
+ percolator.params.txt – parameter file, and</li>
+
+ <li>
+ percolator.log.txt – log file.</li>
+
+ </ol>
+ </p>
+
+ <p>
+ As before, you might want to sort the Percolator output files, this
+ time by the "percolator score" column:</p>
+
+
+ <li>
+ <div class=code><code>
+ $ crux sort-by-column --column-type real --ascending T crux-output/percolator.target.psms.txt "percolator score" > crux-output/percolator.target.psms.sort.txt
+ </code>
+ </div>
+
+ <p>
+ The beginning of the resulting percolator.target.psms.sort.txt file will look like
+ this:</p>
+
+ <table class="searchtable">
+ <td><b>file</b></td><td><b>file_idx</b></td><td><b>scan</b></td><td><b>charge</b></td><td><b>spectrum precursor m/z</b></td><td><b>spectrum neutral mass</b></td><td><b>peptide mass</b></td><td><b>percolator score</b></td><td><b>percolator rank</b></td><td><b>percolator q-value</b></td><td><b>total matches/spectrum</b></td><td><b>sequence</b></td><td><b>cleavage type</b></td><td><b>protein id</b></td><td><b>flanking aa</b></td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>118</td><td>3</td><td>1031.9407</td><td>3092.8000</td><td>3095.2366</td><td>8.6190662</td><td>1</td><td>0</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C</td><td>KD</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>26</td><td>2</td><td>692.3773</td><td>1382.7400</td><td>1382.4467</td><td>7.0481362</td><td>2</td><td>0</td><td>6</td><td>TASEFDSAIAQDK</td><td>trypsin-full-digest</td><td>YLR043C</td><td>KL</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>53</td><td>2</td><td>745.7473</td><td>1489.4800</td><td>1489.7318</td><td>6.7469611</td><td>3</td><td>0</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W</td><td>RN</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>62</td><td>2</td><td>745.8572</td><td>1489.7000</td><td>1489.7318</td><td>6.6489625</td><td>4</td><td>0</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W</td><td>RN</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>146</td><td>2</td><td>692.6772</td><td>1383.3400</td><td>1382.4467</td><td>6.6027999</td><td>5</td><td>0</td><td>5</td><td>TASEFDSAIAQDK</td><td>trypsin-full-digest</td><td>YLR043C</td><td>KL</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>131</td><td>2</td><td>745.8473</td><td>1489.6801</td><td>1489.7318</td><td>6.5627294</td><td>6</td><td>0</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W</td><td>RN</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>50</td><td>2</td><td>651.2873</td><td>1300.5601</td><td>1301.4160</td><td>6.3757763</td><td>7</td><td>0</td><td>10</td><td>LDVDELGDVAQK</td><td>trypsin-full-digest</td><td>YLR043C</td><td>KN</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>42</td><td>3</td><td>1032.2606</td><td>3093.7600</td><td>3095.2366</td><td>5.8047724</td><td>8</td><td>0</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C</td><td>KD</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>90</td><td>3</td><td>1032.0006</td><td>3092.9800</td><td>3095.2366</td><td>5.4775882</td><td>9</td><td>0</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C</td><td>KD</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>111</td><td>3</td><td>1033.0206</td><td>3096.0400</td><td>3095.2366</td><td>5.4364419</td><td>10</td><td>0</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C</td><td>KD</td></tr>
+ </table>
+
+ <p>
+ In this output, the PSMs are ranked by "percolator score," with higher
+ scores indicating a higher quality match. The associated statistical
+ confidence estimate is reported as a "percolator q-value," interpreted
+ as the minimal false discovery rate threshold at which this match is
+ deemed significant. In the list above, all of the matches have
+ q-values of 0, meaning that they are highly significant.
+ The meanings of the remaining columns are
+ described <a href="../file-formats/txt-format.html">here</a>. Note that when you run
+ Percolator on your own computer, the results may be somewhat
+ different than the ones reported here. This is because Percolator
+ involves randomly subdividing the data in a cross-validation scheme
+ (described in detail
+ <a href="http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-S16-S3">here</a>.)</p>
+ </li>
+ </ol>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/spectralcounts.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/spectralcounts.html
new file mode 100644
index 0000000..4e5be1c
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/tutorials/spectralcounts.html
@@ -0,0 +1,182 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Using spectral-counts</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
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+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Using spectral-counts</h2>
+
+ <p>
+ After you have run a <a href="search.html">search</a> and
+ assigned confidence to your identified PSMs, you can now calculate
+ relative quantification values for the proteins by running the
+ command:<br>
+
+ <div class=code>
+ <code>$ crux spectral-counts --protein-database small-yeast.fasta ./crux-output/percolator.target.psms.txt</code>
+ </div>
+ <br>
+ Alternatively, you can use the pepXML output by q-ranker using the command:<br>
+ <br>
+ <div class=code>
+ <code>$ crux spectral-counts --protein-database small-yeast.fasta ./crux-output/percolator.target.psms.txt</code>
+ </div>
+
+ <p>While the command is running, you will see output like this
+ </p>
+
+ <pre>
+INFO: Beginning spectral-counts.
+INFO: Total proteins found: 56
+INFO: Number of matches passed the threshold 116
+ </pre>
+
+ <p>When the command is finished, it will print</p>
+ <pre>
+INFO: Finished crux spectral-counts.
+ </pre>
+
+ <p>
+ Within the <code>crux-output</code> directory, there will be three new files:
+ <li>spectral-counts.target.txt – tab-delimited file of the <code>spectral-counts</code> results</li>
+ <li>spectral-counts.params.txt – the parameters used for running <code>spectral-counts</code></li>
+ <li>spectral-counts.log.txt – the log output of <code>spectral-counts</code></li>
+ </p>
+
+ <p>The spectral-counts.target.txt file will look something like:<br>
+ <pre>
+protein id NSAF
+YLR043C 0.61643416
+YGL135W 0.17810018
+YEL027W 0.10352074
+YGL009C 0.035437137
+YLR185W 0.031369921
+YJR069C 0.014012959
+YGR192C 0.0083149187
+YMR235C 0.0067826854
+YBR118W 0.0060274079
+ </pre>
+
+ <p>
+ In this output, the first field is the identifier and the second field
+ is the spectral-counting measure (NSAF, dNSAF, SIN, or EMPAI) result
+ for each protein. To select which measure is computed, see the
+ <a href="../commands/spectral-counts.html">crux spectral-counts</a> documentation.</p>
+
+
+ <h3>Using peptideprophet probability from pepXML</h3>
+ <p><code>crux spectral-counts</code> also supports using the Peptide Prophet probability provided in the pepXML file. Use the command:<br>
+ <br>
+ <div class=code>
+ <code>$ crux spectral-counts --protein-database small-yeast.fasta --threshold-type custom --custom-threshold-name peptideprophet --threshold 0.9 --custom-threshold-min F target.pep.xml</code>
+ </div>
+ This code will filter out matches whose Peptide Prophet probability is < 0.9 and calculate NSAF for the proteins of the remaining PSMs.<br>
+
+ <h3>Using mzIdentML files with spectral-counts</h3>
+ <p><code>crux spectral-counts</code> also supports mzIdentML as input. For example, </p>
+ <div class="code">
+ $ crux spectral-counts --measure RAW file.mzid
+ </div>
+ <p>
+ If the protein sequences are not provided in the mzIdentML file, then you will have to provide
+ a database using the <span class="code">protein-database</span> parameter for the NSAF, dNSAF, EMPAI, and SIN metrics.
+ </p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/xlink-assign-ions.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/xlink-assign-ions.html
new file mode 100644
index 0000000..84897bb
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/xlink-assign-ions.html
@@ -0,0 +1,145 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>xlink-assign-ions</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>xlink-assign-ions</h1>
+<h2>Usage:</h2>
+<p><code>crux xlink-assign-ions [options] <peptide A> <peptide B> <pos A> <pos B> <link mass> <charge state> <scan number> <ms2 file></code></p>
+<h2>Description:</h2>
+Given a spectrum and a pair of cross-linked peptides, assign theoretical ion type labels to peaks in the observed spectrum.
+<h2>Input:</h2>
+<ul>
+ <li><code>peptide A</code> – The sequence of peptide A.</li>
+ <li><code>peptide B</code> – The sequence of peptide B.</li>
+ <li><code>pos A</code> – Position of cross-link on peptide A</li>
+ <li><code>pos B</code> – Position of cross-link on peptide B</li>
+ <li><code>link mass</code> – The mass modification of the linker when attached to a peptide.</li>
+ <li><code>charge state</code> – The charge state of the peptide.</li>
+ <li><code>scan number</code> – Scan number identifying the spectrum.</li>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – tab-delimited text in which each row is a peak in the observed spectrum, and the columns are <ol><li>The m/z value.</li><li>The observed intensity.</li><li>The matched intensity.</li><li>The calculated m/z value of the theoretical peak.</li><li>The mass associated with the observed peak.</li><li>The mass difference (in ppm) between the observed and theoretical peaks.</li><li>The ion type, specified as b or y, followed by the charge state in parentheses.< [...]
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--fragment-mass average|mono</code> – Specify which isotopes to use in calculating fragment ion mass. Default = <code>mono</code>.</li>
+ <li class="nobullet"><code>--max-ion-charge <string></code> – Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state of the peptide ("peptide"). If the max-ion-charge is greater than the charge state of the peptide, then the maximum is the peptide charge. Default = <code>peptide</code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--precision <integer></code> – Set the precision for scores written to sqt and text files. Default = <code>8</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/xlink-score-spectrum.html b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/xlink-score-spectrum.html
new file mode 100644
index 0000000..be37984
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/doc/xlink-score-spectrum.html
@@ -0,0 +1,158 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>xlink-score-spectrum</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>xlink-score-spectrum</h1>
+<h2>Usage:</h2>
+<p><code>crux xlink-score-spectrum [options] <peptide A> <peptide B> <pos A> <pos B> <link mass> <charge state> <scan number> <ms2 file></code></p>
+<h2>Description:</h2>
+Given a cross-linked peptide and a spectrum calculate the corresponding XCorr score a number of different ways, depending upon the xlink-score-method parameter:<ul><li>composite – compute a combined XCorr score</li><li>modification - score the two peptides separately, treating the second peptide as a variable modification on the first peptide</li><li>concatenated - score as the concatenation of the two peptides. Note that this mode gives four scores, corresponding to the two relat [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>peptide A</code> – The sequence of peptide A.</li>
+ <li><code>peptide B</code> – The sequence of peptide B.</li>
+ <li><code>pos A</code> – Position of cross-link on peptide A</li>
+ <li><code>pos B</code> – Position of cross-link on peptide B</li>
+ <li><code>link mass</code> – The mass modification of the linker when attached to a peptide.</li>
+ <li><code>charge state</code> – The charge state of the peptide.</li>
+ <li><code>scan number</code> – Scan number identifying the spectrum.</li>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – XCorr score(s) in descending order</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>xlink-score-spectrum options</h3>
+<ul>
+ <li class="nobullet"><code>--xlink-score-method composite|modification|concatenated</code> – Score method for xlink {composite, modification, concatenated}. Default = <code>composite</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fragment ion parameters</h3>
+<ul>
+ <li class="nobullet"><code>--use-a-ions T|F</code> – Consider a-ions in the search? Note that an a-ion is equivalent to a neutral loss of CO from the b-ion. Peak height is 10 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-b-ions T|F</code> – Consider b-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-c-ions T|F</code> – Consider c-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-x-ions T|F</code> – Consider x-ions in the search? Peak height is 10 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-y-ions T|F</code> – Consider y-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-z-ions T|F</code> – Consider z-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/license.txt b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/license.txt
new file mode 100644
index 0000000..9176754
--- /dev/null
+++ b/_CPack_Packages/Linux/ZIP/crux-3.1.Linux.x86_64/license.txt
@@ -0,0 +1,12 @@
+Copyright 2007-2013 University of Washington
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
diff --git a/cmake_install.cmake b/cmake_install.cmake
new file mode 100644
index 0000000..45930ad
--- /dev/null
+++ b/cmake_install.cmake
@@ -0,0 +1,58 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+ FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/." TYPE FILE FILES "/data/TeamCity/buildAgent/work/779d99b0241b2175/license.txt")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_LOCAL_ONLY)
+ # Include the install script for each subdirectory.
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/doc/user/cmake_install.cmake")
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/ext/cmake_install.cmake")
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/src/cmake_install.cmake")
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/test/smoke-tests/cmake_install.cmake")
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/test/performance-tests/cmake_install.cmake")
+
+ENDIF(NOT CMAKE_INSTALL_LOCAL_ONLY)
+
+IF(CMAKE_INSTALL_COMPONENT)
+ SET(CMAKE_INSTALL_MANIFEST "install_manifest_${CMAKE_INSTALL_COMPONENT}.txt")
+ELSE(CMAKE_INSTALL_COMPONENT)
+ SET(CMAKE_INSTALL_MANIFEST "install_manifest.txt")
+ENDIF(CMAKE_INSTALL_COMPONENT)
+
+FILE(WRITE "/data/TeamCity/buildAgent/work/779d99b0241b2175/${CMAKE_INSTALL_MANIFEST}" "")
+FOREACH(file ${CMAKE_INSTALL_MANIFEST_FILES})
+ FILE(APPEND "/data/TeamCity/buildAgent/work/779d99b0241b2175/${CMAKE_INSTALL_MANIFEST}" "${file}\n")
+ENDFOREACH(file)
diff --git a/crux_version.h b/crux_version.h
new file mode 100644
index 0000000..08a753d
--- /dev/null
+++ b/crux_version.h
@@ -0,0 +1 @@
+#define CRUX_VERSION "3.1"
diff --git a/crux_version.h.txt b/crux_version.h.txt
new file mode 100644
index 0000000..08a753d
--- /dev/null
+++ b/crux_version.h.txt
@@ -0,0 +1 @@
+#define CRUX_VERSION "3.1"
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 9bbad5b..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,5 +0,0 @@
-crux (3.1-1) UNRELEASED; urgency=low
-
- * Initial release (Closes: #<bug>)
-
- -- Andreas Tille <tille at debian.org> Tue, 29 Sep 2015 15:21:50 +0200
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index f599e28..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-10
diff --git a/debian/control b/debian/control
deleted file mode 100644
index df0aa8d..0000000
--- a/debian/control
+++ /dev/null
@@ -1,24 +0,0 @@
-Source: crux
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 10)
-Standards-Version: 4.1.1
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/crux-toolkit/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/crux-toolkit/trunk/
-Homepage: http://crux.ms/
-
-Package: crux-toolkit
-Architecture: any
-Depends: ${misc:Depends},
- ${shlibs:Depends}
-Description: toolkit for tandem mass spectrometry analysis
- The Crux mass spectrometry analysis toolkit is an open source project
- that aims to provide users with a cross-platform suite of analysis tools
- for interpreting protein mass spectrometry data. The toolkit includes
- several search engines for both standard and cross-linked database
- search, as well as a variety of pre- and post-processing engines for
- assigning high-resolution precursor masses to spectra, assigning
- statistical confidence estimates to spectra, peptides and proteins, and
- performing label free quantification.
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index 8faf75d..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,17 +0,0 @@
-Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: Crux
-Source: http://sourceforge.net/p/cruxtoolkit/code/HEAD/tree/crux-toolkit/
-
-Files: *
-Copyright: 2008-2014
-License: Apache-2.0
-Comment: License is specified at Sourceforge page
- http://sourceforge.net/projects/cruxtoolkit/
-
-Files: debian/*
-Copyright: 2015 Andreas Tille <tille at debian.org>
-License: Apache-2.0
-
-License: Apache-2.0
- On Debian systems you can find the full text of the Apache License V2.0
- at /usr/share/common-licenses/Apache-2.0
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index 440a381..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,7 +0,0 @@
-#!/usr/bin/make -f
-
-# DH_VERBOSE := 1
-
-%:
- dh $@
-
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index 9efcec4..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,21 +0,0 @@
-Reference:
- - Author: Sean McIlwain and Kaipo Tamura and Attila Kertesz-Farkas and Charles E. Grant and Benjamin Diament and Barbara Frewen and J. Jeffry Howbert and Michael R. Hoopmann and Lukas Käll and Jimmy K. Eng and Michael J. MacCoss and William Stafford Noble
- Title: "Crux: rapid open source protein tandem mass spectrometry analysis"
- Journal: 2014
- Year: Journal of Proteome Research
- Volume: 13
- Number: 10
- Pages: 4488-4491
- DOI: 10.1021/pr500741y
- PMID: 25182276
- URL: http://pubs.acs.org/doi/abs/10.1021/pr500741y
- - Author: Christopher Y. Park and Aaron A. Klammer and Lukas Kall and Michael MacCoss and William Stafford Noble
- Title: Rapid and accurate peptide identification from tandem mass spectra
- Journal: Journal of Proteome Research
- Year: 2008
- Volume: 7
- Number: 7
- Pages: 3022-3027
- DOI: 10.1021/pr800127y
- PMID: 18505281
- URL: http://pubs.acs.org/doi/abs/10.1021/pr800127y
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index f0f636b..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,3 +0,0 @@
-version=4
-
-https://github.com/crux-toolkit/crux-toolkit/releases .*/archive/crux at ANY_VERSION@@ARCHIVE_EXT@
\ No newline at end of file
diff --git a/doc/Doxyfile b/doc/Doxyfile
new file mode 100644
index 0000000..c449aef
--- /dev/null
+++ b/doc/Doxyfile
@@ -0,0 +1,1551 @@
+# Doxyfile 1.6.3
+
+# This file describes the settings to be used by the documentation system
+# doxygen (www.doxygen.org) for a project
+#
+# All text after a hash (#) is considered a comment and will be ignored
+# The format is:
+# TAG = value [value, ...]
+# For lists items can also be appended using:
+# TAG += value [value, ...]
+# Values that contain spaces should be placed between quotes (" ")
+
+#---------------------------------------------------------------------------
+# Project related configuration options
+#---------------------------------------------------------------------------
+
+# This tag specifies the encoding used for all characters in the config file
+# that follow. The default is UTF-8 which is also the encoding used for all
+# text before the first occurrence of this tag. Doxygen uses libiconv (or the
+# iconv built into libc) for the transcoding. See
+# http://www.gnu.org/software/libiconv for the list of possible encodings.
+
+DOXYFILE_ENCODING = UTF-8
+
+# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
+# by quotes) that should identify the project.
+
+PROJECT_NAME = crux
+
+# The PROJECT_NUMBER tag can be used to enter a project or revision number.
+# This could be handy for archiving the generated documentation or
+# if some version control system is used.
+
+PROJECT_NUMBER =
+
+# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
+# base path where the generated documentation will be put.
+# If a relative path is entered, it will be relative to the location
+# where doxygen was started. If left blank the current directory will be used.
+
+OUTPUT_DIRECTORY = ../../doc/
+
+# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
+# 4096 sub-directories (in 2 levels) under the output directory of each output
+# format and will distribute the generated files over these directories.
+# Enabling this option can be useful when feeding doxygen a huge amount of
+# source files, where putting all generated files in the same directory would
+# otherwise cause performance problems for the file system.
+
+CREATE_SUBDIRS = NO
+
+# The OUTPUT_LANGUAGE tag is used to specify the language in which all
+# documentation generated by doxygen is written. Doxygen will use this
+# information to generate all constant output in the proper language.
+# The default language is English, other supported languages are:
+# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
+# Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
+# Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
+# messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
+# Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak,
+# Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
+
+OUTPUT_LANGUAGE = English
+
+# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
+# include brief member descriptions after the members that are listed in
+# the file and class documentation (similar to JavaDoc).
+# Set to NO to disable this.
+
+BRIEF_MEMBER_DESC = YES
+
+# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
+# the brief description of a member or function before the detailed description.
+# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
+# brief descriptions will be completely suppressed.
+
+REPEAT_BRIEF = YES
+
+# This tag implements a quasi-intelligent brief description abbreviator
+# that is used to form the text in various listings. Each string
+# in this list, if found as the leading text of the brief description, will be
+# stripped from the text and the result after processing the whole list, is
+# used as the annotated text. Otherwise, the brief description is used as-is.
+# If left blank, the following values are used ("$name" is automatically
+# replaced with the name of the entity): "The $name class" "The $name widget"
+# "The $name file" "is" "provides" "specifies" "contains"
+# "represents" "a" "an" "the"
+
+ABBREVIATE_BRIEF =
+
+# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
+# Doxygen will generate a detailed section even if there is only a brief
+# description.
+
+ALWAYS_DETAILED_SEC = NO
+
+# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
+# inherited members of a class in the documentation of that class as if those
+# members were ordinary class members. Constructors, destructors and assignment
+# operators of the base classes will not be shown.
+
+INLINE_INHERITED_MEMB = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
+# path before files name in the file list and in the header files. If set
+# to NO the shortest path that makes the file name unique will be used.
+
+FULL_PATH_NAMES = NO
+
+# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
+# can be used to strip a user-defined part of the path. Stripping is
+# only done if one of the specified strings matches the left-hand part of
+# the path. The tag can be used to show relative paths in the file list.
+# If left blank the directory from which doxygen is run is used as the
+# path to strip.
+
+STRIP_FROM_PATH =
+
+# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
+# the path mentioned in the documentation of a class, which tells
+# the reader which header file to include in order to use a class.
+# If left blank only the name of the header file containing the class
+# definition is used. Otherwise one should specify the include paths that
+# are normally passed to the compiler using the -I flag.
+
+STRIP_FROM_INC_PATH =
+
+# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
+# (but less readable) file names. This can be useful is your file systems
+# doesn't support long names like on DOS, Mac, or CD-ROM.
+
+SHORT_NAMES = NO
+
+# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
+# will interpret the first line (until the first dot) of a JavaDoc-style
+# comment as the brief description. If set to NO, the JavaDoc
+# comments will behave just like regular Qt-style comments
+# (thus requiring an explicit @brief command for a brief description.)
+
+JAVADOC_AUTOBRIEF = NO
+
+# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
+# interpret the first line (until the first dot) of a Qt-style
+# comment as the brief description. If set to NO, the comments
+# will behave just like regular Qt-style comments (thus requiring
+# an explicit \brief command for a brief description.)
+
+QT_AUTOBRIEF = NO
+
+# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
+# treat a multi-line C++ special comment block (i.e. a block of //! or ///
+# comments) as a brief description. This used to be the default behaviour.
+# The new default is to treat a multi-line C++ comment block as a detailed
+# description. Set this tag to YES if you prefer the old behaviour instead.
+
+MULTILINE_CPP_IS_BRIEF = NO
+
+# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
+# member inherits the documentation from any documented member that it
+# re-implements.
+
+INHERIT_DOCS = YES
+
+# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
+# a new page for each member. If set to NO, the documentation of a member will
+# be part of the file/class/namespace that contains it.
+
+SEPARATE_MEMBER_PAGES = NO
+
+# The TAB_SIZE tag can be used to set the number of spaces in a tab.
+# Doxygen uses this value to replace tabs by spaces in code fragments.
+
+TAB_SIZE = 8
+
+# This tag can be used to specify a number of aliases that acts
+# as commands in the documentation. An alias has the form "name=value".
+# For example adding "sideeffect=\par Side Effects:\n" will allow you to
+# put the command \sideeffect (or @sideeffect) in the documentation, which
+# will result in a user-defined paragraph with heading "Side Effects:".
+# You can put \n's in the value part of an alias to insert newlines.
+
+ALIASES =
+
+# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
+# sources only. Doxygen will then generate output that is more tailored for C.
+# For instance, some of the names that are used will be different. The list
+# of all members will be omitted, etc.
+
+OPTIMIZE_OUTPUT_FOR_C = NO
+
+# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
+# sources only. Doxygen will then generate output that is more tailored for
+# Java. For instance, namespaces will be presented as packages, qualified
+# scopes will look different, etc.
+
+OPTIMIZE_OUTPUT_JAVA = NO
+
+# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
+# sources only. Doxygen will then generate output that is more tailored for
+# Fortran.
+
+OPTIMIZE_FOR_FORTRAN = NO
+
+# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
+# sources. Doxygen will then generate output that is tailored for
+# VHDL.
+
+OPTIMIZE_OUTPUT_VHDL = NO
+
+# Doxygen selects the parser to use depending on the extension of the files it parses.
+# With this tag you can assign which parser to use for a given extension.
+# Doxygen has a built-in mapping, but you can override or extend it using this tag.
+# The format is ext=language, where ext is a file extension, and language is one of
+# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP,
+# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat
+# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran),
+# use: inc=Fortran f=C. Note that for custom extensions you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
+
+EXTENSION_MAPPING =
+
+# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
+# to include (a tag file for) the STL sources as input, then you should
+# set this tag to YES in order to let doxygen match functions declarations and
+# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
+# func(std::string) {}). This also make the inheritance and collaboration
+# diagrams that involve STL classes more complete and accurate.
+
+BUILTIN_STL_SUPPORT = NO
+
+# If you use Microsoft's C++/CLI language, you should set this option to YES to
+# enable parsing support.
+
+CPP_CLI_SUPPORT = NO
+
+# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
+# Doxygen will parse them like normal C++ but will assume all classes use public
+# instead of private inheritance when no explicit protection keyword is present.
+
+SIP_SUPPORT = NO
+
+# For Microsoft's IDL there are propget and propput attributes to indicate getter
+# and setter methods for a property. Setting this option to YES (the default)
+# will make doxygen to replace the get and set methods by a property in the
+# documentation. This will only work if the methods are indeed getting or
+# setting a simple type. If this is not the case, or you want to show the
+# methods anyway, you should set this option to NO.
+
+IDL_PROPERTY_SUPPORT = YES
+
+# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
+# tag is set to YES, then doxygen will reuse the documentation of the first
+# member in the group (if any) for the other members of the group. By default
+# all members of a group must be documented explicitly.
+
+DISTRIBUTE_GROUP_DOC = NO
+
+# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
+# the same type (for instance a group of public functions) to be put as a
+# subgroup of that type (e.g. under the Public Functions section). Set it to
+# NO to prevent subgrouping. Alternatively, this can be done per class using
+# the \nosubgrouping command.
+
+SUBGROUPING = YES
+
+# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
+# is documented as struct, union, or enum with the name of the typedef. So
+# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
+# with name TypeT. When disabled the typedef will appear as a member of a file,
+# namespace, or class. And the struct will be named TypeS. This can typically
+# be useful for C code in case the coding convention dictates that all compound
+# types are typedef'ed and only the typedef is referenced, never the tag name.
+
+TYPEDEF_HIDES_STRUCT = NO
+
+# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
+# determine which symbols to keep in memory and which to flush to disk.
+# When the cache is full, less often used symbols will be written to disk.
+# For small to medium size projects (<1000 input files) the default value is
+# probably good enough. For larger projects a too small cache size can cause
+# doxygen to be busy swapping symbols to and from disk most of the time
+# causing a significant performance penality.
+# If the system has enough physical memory increasing the cache will improve the
+# performance by keeping more symbols in memory. Note that the value works on
+# a logarithmic scale so increasing the size by one will rougly double the
+# memory usage. The cache size is given by this formula:
+# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
+# corresponding to a cache size of 2^16 = 65536 symbols
+
+SYMBOL_CACHE_SIZE = 0
+
+#---------------------------------------------------------------------------
+# Build related configuration options
+#---------------------------------------------------------------------------
+
+# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
+# documentation are documented, even if no documentation was available.
+# Private class members and static file members will be hidden unless
+# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
+
+EXTRACT_ALL = NO
+
+# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
+# will be included in the documentation.
+
+EXTRACT_PRIVATE = NO
+
+# If the EXTRACT_STATIC tag is set to YES all static members of a file
+# will be included in the documentation.
+
+EXTRACT_STATIC = NO
+
+# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
+# defined locally in source files will be included in the documentation.
+# If set to NO only classes defined in header files are included.
+
+EXTRACT_LOCAL_CLASSES = YES
+
+# This flag is only useful for Objective-C code. When set to YES local
+# methods, which are defined in the implementation section but not in
+# the interface are included in the documentation.
+# If set to NO (the default) only methods in the interface are included.
+
+EXTRACT_LOCAL_METHODS = NO
+
+# If this flag is set to YES, the members of anonymous namespaces will be
+# extracted and appear in the documentation as a namespace called
+# 'anonymous_namespace{file}', where file will be replaced with the base
+# name of the file that contains the anonymous namespace. By default
+# anonymous namespace are hidden.
+
+EXTRACT_ANON_NSPACES = NO
+
+# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
+# undocumented members of documented classes, files or namespaces.
+# If set to NO (the default) these members will be included in the
+# various overviews, but no documentation section is generated.
+# This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_MEMBERS = NO
+
+# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
+# undocumented classes that are normally visible in the class hierarchy.
+# If set to NO (the default) these classes will be included in the various
+# overviews. This option has no effect if EXTRACT_ALL is enabled.
+
+HIDE_UNDOC_CLASSES = NO
+
+# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
+# friend (class|struct|union) declarations.
+# If set to NO (the default) these declarations will be included in the
+# documentation.
+
+HIDE_FRIEND_COMPOUNDS = NO
+
+# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
+# documentation blocks found inside the body of a function.
+# If set to NO (the default) these blocks will be appended to the
+# function's detailed documentation block.
+
+HIDE_IN_BODY_DOCS = NO
+
+# The INTERNAL_DOCS tag determines if documentation
+# that is typed after a \internal command is included. If the tag is set
+# to NO (the default) then the documentation will be excluded.
+# Set it to YES to include the internal documentation.
+
+INTERNAL_DOCS = NO
+
+# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
+# file names in lower-case letters. If set to YES upper-case letters are also
+# allowed. This is useful if you have classes or files whose names only differ
+# in case and if your file system supports case sensitive file names. Windows
+# and Mac users are advised to set this option to NO.
+
+CASE_SENSE_NAMES = YES
+
+# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
+# will show members with their full class and namespace scopes in the
+# documentation. If set to YES the scope will be hidden.
+
+HIDE_SCOPE_NAMES = NO
+
+# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
+# will put a list of the files that are included by a file in the documentation
+# of that file.
+
+SHOW_INCLUDE_FILES = YES
+
+# If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
+# will list include files with double quotes in the documentation
+# rather than with sharp brackets.
+
+FORCE_LOCAL_INCLUDES = NO
+
+# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
+# is inserted in the documentation for inline members.
+
+INLINE_INFO = YES
+
+# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
+# will sort the (detailed) documentation of file and class members
+# alphabetically by member name. If set to NO the members will appear in
+# declaration order.
+
+SORT_MEMBER_DOCS = YES
+
+# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
+# brief documentation of file, namespace and class members alphabetically
+# by member name. If set to NO (the default) the members will appear in
+# declaration order.
+
+SORT_BRIEF_DOCS = NO
+
+# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the (brief and detailed) documentation of class members so that constructors and destructors are listed first. If set to NO (the default) the constructors will appear in the respective orders defined by SORT_MEMBER_DOCS and SORT_BRIEF_DOCS. This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
+
+SORT_MEMBERS_CTORS_1ST = NO
+
+# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
+# hierarchy of group names into alphabetical order. If set to NO (the default)
+# the group names will appear in their defined order.
+
+SORT_GROUP_NAMES = NO
+
+# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
+# sorted by fully-qualified names, including namespaces. If set to
+# NO (the default), the class list will be sorted only by class name,
+# not including the namespace part.
+# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
+# Note: This option applies only to the class list, not to the
+# alphabetical list.
+
+SORT_BY_SCOPE_NAME = NO
+
+# The GENERATE_TODOLIST tag can be used to enable (YES) or
+# disable (NO) the todo list. This list is created by putting \todo
+# commands in the documentation.
+
+GENERATE_TODOLIST = YES
+
+# The GENERATE_TESTLIST tag can be used to enable (YES) or
+# disable (NO) the test list. This list is created by putting \test
+# commands in the documentation.
+
+GENERATE_TESTLIST = YES
+
+# The GENERATE_BUGLIST tag can be used to enable (YES) or
+# disable (NO) the bug list. This list is created by putting \bug
+# commands in the documentation.
+
+GENERATE_BUGLIST = YES
+
+# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
+# disable (NO) the deprecated list. This list is created by putting
+# \deprecated commands in the documentation.
+
+GENERATE_DEPRECATEDLIST= YES
+
+# The ENABLED_SECTIONS tag can be used to enable conditional
+# documentation sections, marked by \if sectionname ... \endif.
+
+ENABLED_SECTIONS =
+
+# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
+# the initial value of a variable or define consists of for it to appear in
+# the documentation. If the initializer consists of more lines than specified
+# here it will be hidden. Use a value of 0 to hide initializers completely.
+# The appearance of the initializer of individual variables and defines in the
+# documentation can be controlled using \showinitializer or \hideinitializer
+# command in the documentation regardless of this setting.
+
+MAX_INITIALIZER_LINES = 30
+
+# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
+# at the bottom of the documentation of classes and structs. If set to YES the
+# list will mention the files that were used to generate the documentation.
+
+SHOW_USED_FILES = YES
+
+# If the sources in your project are distributed over multiple directories
+# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
+# in the documentation. The default is NO.
+
+SHOW_DIRECTORIES = NO
+
+# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
+# This will remove the Files entry from the Quick Index and from the
+# Folder Tree View (if specified). The default is YES.
+
+SHOW_FILES = YES
+
+# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
+# Namespaces page.
+# This will remove the Namespaces entry from the Quick Index
+# and from the Folder Tree View (if specified). The default is YES.
+
+SHOW_NAMESPACES = YES
+
+# The FILE_VERSION_FILTER tag can be used to specify a program or script that
+# doxygen should invoke to get the current version for each file (typically from
+# the version control system). Doxygen will invoke the program by executing (via
+# popen()) the command <command> <input-file>, where <command> is the value of
+# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
+# provided by doxygen. Whatever the program writes to standard output
+# is used as the file version. See the manual for examples.
+
+FILE_VERSION_FILTER =
+
+# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by
+# doxygen. The layout file controls the global structure of the generated output files
+# in an output format independent way. The create the layout file that represents
+# doxygen's defaults, run doxygen with the -l option. You can optionally specify a
+# file name after the option, if omitted DoxygenLayout.xml will be used as the name
+# of the layout file.
+
+LAYOUT_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to warning and progress messages
+#---------------------------------------------------------------------------
+
+# The QUIET tag can be used to turn on/off the messages that are generated
+# by doxygen. Possible values are YES and NO. If left blank NO is used.
+
+QUIET = NO
+
+# The WARNINGS tag can be used to turn on/off the warning messages that are
+# generated by doxygen. Possible values are YES and NO. If left blank
+# NO is used.
+
+WARNINGS = YES
+
+# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
+# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
+# automatically be disabled.
+
+WARN_IF_UNDOCUMENTED = YES
+
+# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
+# potential errors in the documentation, such as not documenting some
+# parameters in a documented function, or documenting parameters that
+# don't exist or using markup commands wrongly.
+
+WARN_IF_DOC_ERROR = YES
+
+# This WARN_NO_PARAMDOC option can be abled to get warnings for
+# functions that are documented, but have no documentation for their parameters
+# or return value. If set to NO (the default) doxygen will only warn about
+# wrong or incomplete parameter documentation, but not about the absence of
+# documentation.
+
+WARN_NO_PARAMDOC = NO
+
+# The WARN_FORMAT tag determines the format of the warning messages that
+# doxygen can produce. The string should contain the $file, $line, and $text
+# tags, which will be replaced by the file and line number from which the
+# warning originated and the warning text. Optionally the format may contain
+# $version, which will be replaced by the version of the file (if it could
+# be obtained via FILE_VERSION_FILTER)
+
+WARN_FORMAT = "$file:$line: $text"
+
+# The WARN_LOGFILE tag can be used to specify a file to which warning
+# and error messages should be written. If left blank the output is written
+# to stderr.
+
+WARN_LOGFILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the input files
+#---------------------------------------------------------------------------
+
+# The INPUT tag can be used to specify the files and/or directories that contain
+# documented source files. You may enter file names like "myfile.cpp" or
+# directories like "/usr/src/myproject". Separate the files or directories
+# with spaces.
+
+INPUT =
+
+# This tag can be used to specify the character encoding of the source files
+# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
+# also the default input encoding. Doxygen uses libiconv (or the iconv built
+# into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
+# the list of possible encodings.
+
+INPUT_ENCODING = UTF-8
+
+# If the value of the INPUT tag contains directories, you can use the
+# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank the following patterns are tested:
+# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
+# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
+
+FILE_PATTERNS =
+
+# The RECURSIVE tag can be used to turn specify whether or not subdirectories
+# should be searched for input files as well. Possible values are YES and NO.
+# If left blank NO is used.
+
+RECURSIVE = NO
+
+# The EXCLUDE tag can be used to specify files and/or directories that should
+# excluded from the INPUT source files. This way you can easily exclude a
+# subdirectory from a directory tree whose root is specified with the INPUT tag.
+
+EXCLUDE =
+
+# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
+# directories that are symbolic links (a Unix filesystem feature) are excluded
+# from the input.
+
+EXCLUDE_SYMLINKS = NO
+
+# If the value of the INPUT tag contains directories, you can use the
+# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
+# certain files from those directories. Note that the wildcards are matched
+# against the file with absolute path, so to exclude all test directories
+# for example use the pattern */test/*
+
+EXCLUDE_PATTERNS =
+
+# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
+# (namespaces, classes, functions, etc.) that should be excluded from the
+# output. The symbol name can be a fully qualified name, a word, or if the
+# wildcard * is used, a substring. Examples: ANamespace, AClass,
+# AClass::ANamespace, ANamespace::*Test
+
+EXCLUDE_SYMBOLS =
+
+# The EXAMPLE_PATH tag can be used to specify one or more files or
+# directories that contain example code fragments that are included (see
+# the \include command).
+
+EXAMPLE_PATH =
+
+# If the value of the EXAMPLE_PATH tag contains directories, you can use the
+# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
+# and *.h) to filter out the source-files in the directories. If left
+# blank all files are included.
+
+EXAMPLE_PATTERNS =
+
+# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
+# searched for input files to be used with the \include or \dontinclude
+# commands irrespective of the value of the RECURSIVE tag.
+# Possible values are YES and NO. If left blank NO is used.
+
+EXAMPLE_RECURSIVE = NO
+
+# The IMAGE_PATH tag can be used to specify one or more files or
+# directories that contain image that are included in the documentation (see
+# the \image command).
+
+IMAGE_PATH =
+
+# The INPUT_FILTER tag can be used to specify a program that doxygen should
+# invoke to filter for each input file. Doxygen will invoke the filter program
+# by executing (via popen()) the command <filter> <input-file>, where <filter>
+# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
+# input file. Doxygen will then use the output that the filter program writes
+# to standard output.
+# If FILTER_PATTERNS is specified, this tag will be
+# ignored.
+
+INPUT_FILTER =
+
+# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
+# basis.
+# Doxygen will compare the file name with each pattern and apply the
+# filter if there is a match.
+# The filters are a list of the form:
+# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
+# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
+# is applied to all files.
+
+FILTER_PATTERNS =
+
+# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
+# INPUT_FILTER) will be used to filter the input files when producing source
+# files to browse (i.e. when SOURCE_BROWSER is set to YES).
+
+FILTER_SOURCE_FILES = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to source browsing
+#---------------------------------------------------------------------------
+
+# If the SOURCE_BROWSER tag is set to YES then a list of source files will
+# be generated. Documented entities will be cross-referenced with these sources.
+# Note: To get rid of all source code in the generated output, make sure also
+# VERBATIM_HEADERS is set to NO.
+
+SOURCE_BROWSER = NO
+
+# Setting the INLINE_SOURCES tag to YES will include the body
+# of functions and classes directly in the documentation.
+
+INLINE_SOURCES = NO
+
+# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
+# doxygen to hide any special comment blocks from generated source code
+# fragments. Normal C and C++ comments will always remain visible.
+
+STRIP_CODE_COMMENTS = YES
+
+# If the REFERENCED_BY_RELATION tag is set to YES
+# then for each documented function all documented
+# functions referencing it will be listed.
+
+REFERENCED_BY_RELATION = YES
+
+# If the REFERENCES_RELATION tag is set to YES
+# then for each documented function all documented entities
+# called/used by that function will be listed.
+
+REFERENCES_RELATION = YES
+
+# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
+# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
+# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
+# link to the source code.
+# Otherwise they will link to the documentation.
+
+REFERENCES_LINK_SOURCE = YES
+
+# If the USE_HTAGS tag is set to YES then the references to source code
+# will point to the HTML generated by the htags(1) tool instead of doxygen
+# built-in source browser. The htags tool is part of GNU's global source
+# tagging system (see http://www.gnu.org/software/global/global.html). You
+# will need version 4.8.6 or higher.
+
+USE_HTAGS = NO
+
+# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
+# will generate a verbatim copy of the header file for each class for
+# which an include is specified. Set to NO to disable this.
+
+VERBATIM_HEADERS = YES
+
+#---------------------------------------------------------------------------
+# configuration options related to the alphabetical class index
+#---------------------------------------------------------------------------
+
+# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
+# of all compounds will be generated. Enable this if the project
+# contains a lot of classes, structs, unions or interfaces.
+
+ALPHABETICAL_INDEX = NO
+
+# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
+# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
+# in which this list will be split (can be a number in the range [1..20])
+
+COLS_IN_ALPHA_INDEX = 5
+
+# In case all classes in a project start with a common prefix, all
+# classes will be put under the same header in the alphabetical index.
+# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
+# should be ignored while generating the index headers.
+
+IGNORE_PREFIX =
+
+#---------------------------------------------------------------------------
+# configuration options related to the HTML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
+# generate HTML output.
+
+GENERATE_HTML = YES
+
+# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `html' will be used as the default path.
+
+HTML_OUTPUT = html
+
+# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
+# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
+# doxygen will generate files with .html extension.
+
+HTML_FILE_EXTENSION = .html
+
+# The HTML_HEADER tag can be used to specify a personal HTML header for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard header.
+
+HTML_HEADER =
+
+# The HTML_FOOTER tag can be used to specify a personal HTML footer for
+# each generated HTML page. If it is left blank doxygen will generate a
+# standard footer.
+
+HTML_FOOTER =
+
+# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
+# style sheet that is used by each HTML page. It can be used to
+# fine-tune the look of the HTML output. If the tag is left blank doxygen
+# will generate a default style sheet. Note that doxygen will try to copy
+# the style sheet file to the HTML output directory, so don't put your own
+# stylesheet in the HTML output directory as well, or it will be erased!
+
+HTML_STYLESHEET =
+
+# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
+# page will contain the date and time when the page was generated. Setting
+# this to NO can help when comparing the output of multiple runs.
+
+HTML_TIMESTAMP = YES
+
+# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
+# files or namespaces will be aligned in HTML using tables. If set to
+# NO a bullet list will be used.
+
+HTML_ALIGN_MEMBERS = YES
+
+# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
+# documentation will contain sections that can be hidden and shown after the
+# page has loaded. For this to work a browser that supports
+# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
+# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
+
+HTML_DYNAMIC_SECTIONS = NO
+
+# If the GENERATE_DOCSET tag is set to YES, additional index files
+# will be generated that can be used as input for Apple's Xcode 3
+# integrated development environment, introduced with OSX 10.5 (Leopard).
+# To create a documentation set, doxygen will generate a Makefile in the
+# HTML output directory. Running make will produce the docset in that
+# directory and running "make install" will install the docset in
+# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
+# it at startup.
+# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
+
+GENERATE_DOCSET = NO
+
+# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
+# feed. A documentation feed provides an umbrella under which multiple
+# documentation sets from a single provider (such as a company or product suite)
+# can be grouped.
+
+DOCSET_FEEDNAME = "Doxygen generated docs"
+
+# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
+# should uniquely identify the documentation set bundle. This should be a
+# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
+# will append .docset to the name.
+
+DOCSET_BUNDLE_ID = org.doxygen.Project
+
+# If the GENERATE_HTMLHELP tag is set to YES, additional index files
+# will be generated that can be used as input for tools like the
+# Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
+# of the generated HTML documentation.
+
+GENERATE_HTMLHELP = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
+# be used to specify the file name of the resulting .chm file. You
+# can add a path in front of the file if the result should not be
+# written to the html output directory.
+
+CHM_FILE =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
+# be used to specify the location (absolute path including file name) of
+# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
+# the HTML help compiler on the generated index.hhp.
+
+HHC_LOCATION =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
+# controls if a separate .chi index file is generated (YES) or that
+# it should be included in the master .chm file (NO).
+
+GENERATE_CHI = NO
+
+# If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
+# is used to encode HtmlHelp index (hhk), content (hhc) and project file
+# content.
+
+CHM_INDEX_ENCODING =
+
+# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
+# controls whether a binary table of contents is generated (YES) or a
+# normal table of contents (NO) in the .chm file.
+
+BINARY_TOC = NO
+
+# The TOC_EXPAND flag can be set to YES to add extra items for group members
+# to the contents of the HTML help documentation and to the tree view.
+
+TOC_EXPAND = NO
+
+# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER
+# are set, an additional index file will be generated that can be used as input for
+# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated
+# HTML documentation.
+
+GENERATE_QHP = NO
+
+# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
+# be used to specify the file name of the resulting .qch file.
+# The path specified is relative to the HTML output folder.
+
+QCH_FILE =
+
+# The QHP_NAMESPACE tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#namespace
+
+QHP_NAMESPACE = org.doxygen.Project
+
+# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
+# Qt Help Project output. For more information please see
+# http://doc.trolltech.com/qthelpproject.html#virtual-folders
+
+QHP_VIRTUAL_FOLDER = doc
+
+# If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to add.
+# For more information please see
+# http://doc.trolltech.com/qthelpproject.html#custom-filters
+
+QHP_CUST_FILTER_NAME =
+
+# The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the custom filter to add.For more information please see
+# <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">Qt Help Project / Custom Filters</a>.
+
+QHP_CUST_FILTER_ATTRS =
+
+# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this project's
+# filter section matches.
+# <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">Qt Help Project / Filter Attributes</a>.
+
+QHP_SECT_FILTER_ATTRS =
+
+# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
+# be used to specify the location of Qt's qhelpgenerator.
+# If non-empty doxygen will try to run qhelpgenerator on the generated
+# .qhp file.
+
+QHG_LOCATION =
+
+# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
+# will be generated, which together with the HTML files, form an Eclipse help
+# plugin. To install this plugin and make it available under the help contents
+# menu in Eclipse, the contents of the directory containing the HTML and XML
+# files needs to be copied into the plugins directory of eclipse. The name of
+# the directory within the plugins directory should be the same as
+# the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before the help appears.
+
+GENERATE_ECLIPSEHELP = NO
+
+# A unique identifier for the eclipse help plugin. When installing the plugin
+# the directory name containing the HTML and XML files should also have
+# this name.
+
+ECLIPSE_DOC_ID = org.doxygen.Project
+
+# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
+# top of each HTML page. The value NO (the default) enables the index and
+# the value YES disables it.
+
+DISABLE_INDEX = NO
+
+# This tag can be used to set the number of enum values (range [1..20])
+# that doxygen will group on one line in the generated HTML documentation.
+
+ENUM_VALUES_PER_LINE = 4
+
+# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
+# structure should be generated to display hierarchical information.
+# If the tag value is set to YES, a side panel will be generated
+# containing a tree-like index structure (just like the one that
+# is generated for HTML Help). For this to work a browser that supports
+# JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
+# Windows users are probably better off using the HTML help feature.
+
+GENERATE_TREEVIEW = NO
+
+# By enabling USE_INLINE_TREES, doxygen will generate the Groups, Directories,
+# and Class Hierarchy pages using a tree view instead of an ordered list.
+
+USE_INLINE_TREES = NO
+
+# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
+# used to set the initial width (in pixels) of the frame in which the tree
+# is shown.
+
+TREEVIEW_WIDTH = 250
+
+# Use this tag to change the font size of Latex formulas included
+# as images in the HTML documentation. The default is 10. Note that
+# when you change the font size after a successful doxygen run you need
+# to manually remove any form_*.png images from the HTML output directory
+# to force them to be regenerated.
+
+FORMULA_FONTSIZE = 10
+
+# When the SEARCHENGINE tag is enabled doxygen will generate a search box for the HTML output. The underlying search engine uses javascript
+# and DHTML and should work on any modern browser. Note that when using HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) there is already a search function so this one should
+# typically be disabled. For large projects the javascript based search engine
+# can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
+
+SEARCHENGINE = NO
+
+# When the SERVER_BASED_SEARCH tag is enabled the search engine will be implemented using a PHP enabled web server instead of at the web client using Javascript. Doxygen will generate the search PHP script and index
+# file to put on the web server. The advantage of the server based approach is that it scales better to large projects and allows full text search. The disadvances is that it is more difficult to setup
+# and does not have live searching capabilities.
+
+SERVER_BASED_SEARCH = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the LaTeX output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
+# generate Latex output.
+
+GENERATE_LATEX = NO
+
+# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `latex' will be used as the default path.
+
+LATEX_OUTPUT = latex
+
+# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
+# invoked. If left blank `latex' will be used as the default command name.
+# Note that when enabling USE_PDFLATEX this option is only used for
+# generating bitmaps for formulas in the HTML output, but not in the
+# Makefile that is written to the output directory.
+
+LATEX_CMD_NAME = latex
+
+# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
+# generate index for LaTeX. If left blank `makeindex' will be used as the
+# default command name.
+
+MAKEINDEX_CMD_NAME = makeindex
+
+# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
+# LaTeX documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_LATEX = NO
+
+# The PAPER_TYPE tag can be used to set the paper type that is used
+# by the printer. Possible values are: a4, a4wide, letter, legal and
+# executive. If left blank a4wide will be used.
+
+PAPER_TYPE = a4wide
+
+# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
+# packages that should be included in the LaTeX output.
+
+EXTRA_PACKAGES =
+
+# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
+# the generated latex document. The header should contain everything until
+# the first chapter. If it is left blank doxygen will generate a
+# standard header. Notice: only use this tag if you know what you are doing!
+
+LATEX_HEADER =
+
+# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
+# is prepared for conversion to pdf (using ps2pdf). The pdf file will
+# contain links (just like the HTML output) instead of page references
+# This makes the output suitable for online browsing using a pdf viewer.
+
+PDF_HYPERLINKS = NO
+
+# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
+# plain latex in the generated Makefile. Set this option to YES to get a
+# higher quality PDF documentation.
+
+USE_PDFLATEX = NO
+
+# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
+# command to the generated LaTeX files. This will instruct LaTeX to keep
+# running if errors occur, instead of asking the user for help.
+# This option is also used when generating formulas in HTML.
+
+LATEX_BATCHMODE = NO
+
+# If LATEX_HIDE_INDICES is set to YES then doxygen will not
+# include the index chapters (such as File Index, Compound Index, etc.)
+# in the output.
+
+LATEX_HIDE_INDICES = NO
+
+# If LATEX_SOURCE_CODE is set to YES then doxygen will include source code with syntax highlighting in the LaTeX output. Note that which sources are shown also depends on other settings such as SOURCE_BROWSER.
+
+LATEX_SOURCE_CODE = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the RTF output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
+# The RTF output is optimized for Word 97 and may not look very pretty with
+# other RTF readers or editors.
+
+GENERATE_RTF = NO
+
+# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `rtf' will be used as the default path.
+
+RTF_OUTPUT = rtf
+
+# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
+# RTF documents. This may be useful for small projects and may help to
+# save some trees in general.
+
+COMPACT_RTF = NO
+
+# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
+# will contain hyperlink fields. The RTF file will
+# contain links (just like the HTML output) instead of page references.
+# This makes the output suitable for online browsing using WORD or other
+# programs which support those fields.
+# Note: wordpad (write) and others do not support links.
+
+RTF_HYPERLINKS = NO
+
+# Load stylesheet definitions from file. Syntax is similar to doxygen's
+# config file, i.e. a series of assignments. You only have to provide
+# replacements, missing definitions are set to their default value.
+
+RTF_STYLESHEET_FILE =
+
+# Set optional variables used in the generation of an rtf document.
+# Syntax is similar to doxygen's config file.
+
+RTF_EXTENSIONS_FILE =
+
+#---------------------------------------------------------------------------
+# configuration options related to the man page output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
+# generate man pages
+
+GENERATE_MAN = NO
+
+# The MAN_OUTPUT tag is used to specify where the man pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `man' will be used as the default path.
+
+MAN_OUTPUT = man
+
+# The MAN_EXTENSION tag determines the extension that is added to
+# the generated man pages (default is the subroutine's section .3)
+
+MAN_EXTENSION = .3
+
+# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
+# then it will generate one additional man file for each entity
+# documented in the real man page(s). These additional files
+# only source the real man page, but without them the man command
+# would be unable to find the correct page. The default is NO.
+
+MAN_LINKS = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the XML output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_XML tag is set to YES Doxygen will
+# generate an XML file that captures the structure of
+# the code including all documentation.
+
+GENERATE_XML = NO
+
+# The XML_OUTPUT tag is used to specify where the XML pages will be put.
+# If a relative path is entered the value of OUTPUT_DIRECTORY will be
+# put in front of it. If left blank `xml' will be used as the default path.
+
+XML_OUTPUT = xml
+
+# The XML_SCHEMA tag can be used to specify an XML schema,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_SCHEMA =
+
+# The XML_DTD tag can be used to specify an XML DTD,
+# which can be used by a validating XML parser to check the
+# syntax of the XML files.
+
+XML_DTD =
+
+# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
+# dump the program listings (including syntax highlighting
+# and cross-referencing information) to the XML output. Note that
+# enabling this will significantly increase the size of the XML output.
+
+XML_PROGRAMLISTING = YES
+
+#---------------------------------------------------------------------------
+# configuration options for the AutoGen Definitions output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
+# generate an AutoGen Definitions (see autogen.sf.net) file
+# that captures the structure of the code including all
+# documentation. Note that this feature is still experimental
+# and incomplete at the moment.
+
+GENERATE_AUTOGEN_DEF = NO
+
+#---------------------------------------------------------------------------
+# configuration options related to the Perl module output
+#---------------------------------------------------------------------------
+
+# If the GENERATE_PERLMOD tag is set to YES Doxygen will
+# generate a Perl module file that captures the structure of
+# the code including all documentation. Note that this
+# feature is still experimental and incomplete at the
+# moment.
+
+GENERATE_PERLMOD = NO
+
+# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
+# the necessary Makefile rules, Perl scripts and LaTeX code to be able
+# to generate PDF and DVI output from the Perl module output.
+
+PERLMOD_LATEX = NO
+
+# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
+# nicely formatted so it can be parsed by a human reader.
+# This is useful
+# if you want to understand what is going on.
+# On the other hand, if this
+# tag is set to NO the size of the Perl module output will be much smaller
+# and Perl will parse it just the same.
+
+PERLMOD_PRETTY = YES
+
+# The names of the make variables in the generated doxyrules.make file
+# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
+# This is useful so different doxyrules.make files included by the same
+# Makefile don't overwrite each other's variables.
+
+PERLMOD_MAKEVAR_PREFIX =
+
+#---------------------------------------------------------------------------
+# Configuration options related to the preprocessor
+#---------------------------------------------------------------------------
+
+# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
+# evaluate all C-preprocessor directives found in the sources and include
+# files.
+
+ENABLE_PREPROCESSING = YES
+
+# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
+# names in the source code. If set to NO (the default) only conditional
+# compilation will be performed. Macro expansion can be done in a controlled
+# way by setting EXPAND_ONLY_PREDEF to YES.
+
+MACRO_EXPANSION = NO
+
+# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
+# then the macro expansion is limited to the macros specified with the
+# PREDEFINED and EXPAND_AS_DEFINED tags.
+
+EXPAND_ONLY_PREDEF = NO
+
+# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
+# in the INCLUDE_PATH (see below) will be search if a #include is found.
+
+SEARCH_INCLUDES = YES
+
+# The INCLUDE_PATH tag can be used to specify one or more directories that
+# contain include files that are not input files but should be processed by
+# the preprocessor.
+
+INCLUDE_PATH =
+
+# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
+# patterns (like *.h and *.hpp) to filter out the header-files in the
+# directories. If left blank, the patterns specified with FILE_PATTERNS will
+# be used.
+
+INCLUDE_FILE_PATTERNS =
+
+# The PREDEFINED tag can be used to specify one or more macro names that
+# are defined before the preprocessor is started (similar to the -D option of
+# gcc). The argument of the tag is a list of macros of the form: name
+# or name=definition (no spaces). If the definition and the = are
+# omitted =1 is assumed. To prevent a macro definition from being
+# undefined via #undef or recursively expanded use the := operator
+# instead of the = operator.
+
+PREDEFINED = DOXYGEN_SHOULD_SKIP_THIS
+
+# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
+# this tag can be used to specify a list of macro names that should be expanded.
+# The macro definition that is found in the sources will be used.
+# Use the PREDEFINED tag if you want to use a different macro definition.
+
+EXPAND_AS_DEFINED =
+
+# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
+# doxygen's preprocessor will remove all function-like macros that are alone
+# on a line, have an all uppercase name, and do not end with a semicolon. Such
+# function macros are typically used for boiler-plate code, and will confuse
+# the parser if not removed.
+
+SKIP_FUNCTION_MACROS = YES
+
+#---------------------------------------------------------------------------
+# Configuration::additions related to external references
+#---------------------------------------------------------------------------
+
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+PERL_PATH = /usr/bin/perl
+
+#---------------------------------------------------------------------------
+# Configuration options related to the dot tool
+#---------------------------------------------------------------------------
+
+# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
+# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
+# or super classes. Setting the tag to NO turns the diagrams off. Note that
+# this option is superseded by the HAVE_DOT option below. This is only a
+# fallback. It is recommended to install and use dot, since it yields more
+# powerful graphs.
+
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+
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+# command. Doxygen will then run the mscgen tool (see
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+
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+# If set to YES, the inheritance and collaboration graphs will hide
+# inheritance and usage relations if the target is undocumented
+# or is not a class.
+
+HIDE_UNDOC_RELATIONS = YES
+
+# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
+# available from the path. This tool is part of Graphviz, a graph visualization
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+
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+# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
+# which can be done by putting it in a standard location or by setting the
+# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
+# containing the font.
+
+DOT_FONTNAME = FreeSans
+
+# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
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+
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+
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+
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+# indirect inheritance relations. Setting this tag to YES will force the
+# the CLASS_DIAGRAMS tag to NO.
+
+CLASS_GRAPH = YES
+
+# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for each documented class showing the direct and
+# indirect implementation dependencies (inheritance, containment, and
+# class references variables) of the class with other documented classes.
+
+COLLABORATION_GRAPH = YES
+
+# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
+# will generate a graph for groups, showing the direct groups dependencies
+
+GROUP_GRAPHS = YES
+
+# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
+# collaboration diagrams in a style similar to the OMG's Unified Modeling
+# Language.
+
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+
+# If set to YES, the inheritance and collaboration graphs will show the
+# relations between templates and their instances.
+
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+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
+# tags are set to YES then doxygen will generate a graph for each documented
+# file showing the direct and indirect include dependencies of the file with
+# other documented files.
+
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+
+# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
+# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
+# documented header file showing the documented files that directly or
+# indirectly include this file.
+
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+
+# If the CALL_GRAPH and HAVE_DOT options are set to YES then
+# doxygen will generate a call dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable call graphs
+# for selected functions only using the \callgraph command.
+
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+
+# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then
+# doxygen will generate a caller dependency graph for every global function
+# or class method. Note that enabling this option will significantly increase
+# the time of a run. So in most cases it will be better to enable caller
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+
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+
+# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
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+
+# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
+# then doxygen will show the dependencies a directory has on other directories
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+
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+
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+# visualized by representing a node as a red box. Note that doxygen if the
+# number of direct children of the root node in a graph is already larger than
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+# option to 1 or 2 may greatly reduce the computation time needed for large
+# code bases. Also note that the size of a graph can be further restricted by
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+
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+# enabling this option may lead to badly anti-aliased labels on the edges of
+# a graph (i.e. they become hard to read).
+
+DOT_TRANSPARENT = YES
+
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+# files in one run (i.e. multiple -o and -T options on the command line). This
+# makes dot run faster, but since only newer versions of dot (>1.8.10)
+# support this, this feature is disabled by default.
+
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+# arrows in the dot generated graphs.
+
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diff --git a/doc/PWIZ_README b/doc/PWIZ_README
new file mode 100644
index 0000000..1a10724
--- /dev/null
+++ b/doc/PWIZ_README
@@ -0,0 +1,142 @@
+Notes on how pwiz stores spectrum data
+
+A spectrum has an isolation window which corresponds to what the
+instrument selected for fragmentation. A spectrum has one precursor
+per isolation window. A precursor has a selected ion which
+corresponds to a peptide that was isoated and fragmented. If more
+than one peptide was fragmented, the spectrum will have more than one
+selected ion.
+
+Hardklor/Bullseye identifies the peptides selected/isolated/fragmented
+in each MS/MS spectrum. That information is contained in the EZ lines
+and duplicated in the Z lines. A pwiz spectrum object from these
+files will have one precursor and one selected ion for each Z line.
+The selected ion will store the charge as it appears in the file, the
+accurate mass as it appears in the file and the m/z computed from the
+accurate mass and the charge. The accurate mass is the singly charged
+mass (M+H).
+
+A default .ms2 file has not been processed with Bullseye. It will
+have a Z line for each possible charge state and the corresponding
+mass computed from the isolated m/z. A pwiz spectrum object from
+these files will have one precursor, and one selected ion. The
+selected ion will have one possible charge state for each z line. The
+selected ion will also have selected_ion_m_z which is the precursor
+m/z.
+
+The SpectrumInfo struct can be used to access common fields from a
+spectrum object. The struct fills the precursor m/z filed from the
+selected_ion_mz from the first selected ion.
+
+Notes on crux's use of pwiz
+
+The pwiz parser is only used when 'use-pwiz=T' is included in a
+parameter file. We may want to change it to be the default, or have
+the parser selected at runtime. So far, the following tests have been
+run using crux search-for-matches:
+
+1. demo.ms2, small-yeast.fasta, use-pwiz=F
+2. demo.ms2, small-yeast.fasta, use-pwiz=T
+3. demo.cms2, small-yeast.fast, use-pwiz=T
+4. wormyraw-1.ms2, small-yeast.fasta, use-pwiz=F
+5. wormyraw-1.ms2, small-yeast.fasta, use-pwiz=T
+6. wormyraw-1.cms2, small-yeast.fasta, use-pwiz=T
+
+wormyraw-1 was processed by Bullseye so it contains accurate masses.
+The search.target.txt file has been compared between various pairs of
+tests with these results.
+
+1 vs 2: Spectrum neutral mass is slightly different for +2 and +3.
+With the crux parser, we used the singly charged mass on the Z line
+and converted to neutral mass. With the pwiz parser, we are using the
+precursor m/z and converting it with the assumed charge to neutral
+mass.
+
+2 vs 3: Identical.
+
+4 vs 5: Identical.
+
+5 vs 6: Spectrum neutral mass is mostly the same (some small
+differences), but the xcorrs are different. A quick test suggested
+that both parsers (ms2 and cms2) are returning the same number of
+peaks. It remains to be tested if the peaks are the same.
+
+In the crux code, we are using the presence of charge vs possible
+charge and the presence of accurate mass to determine if teh file has
+been run through Bullsye. Ideally, the pwiz parser would set a
+parameter to indicate that it has.
+
+As of April 12, 2012, the pwiz parser has not been tested with .mgf,
+.mzXML, or .mzML files.
+
+SVN revisions up to 5669 have been code reviewed.
+
+
+Notes on how to manage the pwiz dependency.
+
+The proteowizard project is stored in the crux repository as a
+tarball of source code. To build crux, the pwiz tarball must be
+unpacked and built. This should only need to happen once for a clean
+check out.
+
+When it is time to update the version of pwiz, go to the website and
+download one of their files (called artifacts). They come in several
+flavors; the ones with no tests and no vendor API's have everything we
+need.
+
+We might want to consider extracting a subset of the pwiz tarball to
+save in the repository. We use only a small fraction of the code.
+For example, we don't need anything in pwiz_tools. It would save some
+space, but would require an extra step each time a new version of pwiz
+is introduced.
+
+Ideally, the unpacking and building of pwiz should happen as part of
+the configure and make process. Until then, it can be done with the
+following steps:
+
+1. In crux/src/external/proteowizard, unpack with the command
+ $ tar -jxvf pwiz-src-without-tv-<version>.tar.bz2
+
+2. Build the project.
+ $ ./quickbuild.sh --without-mz5 pwiz/data/msdata/ \
+ pwiz/data/identdata/ 1> out 2> er
+
+Check the end of out to see if there were any failures. It will say
+something like "At least one target failed to build" if there were
+errors. If it says "...updated 42 targets..." then everything's fine.
+
+** Note about --without-mz5. See Jamroot.jam for notes on some useful
+ options. The tarball I checked in happened to be built without the
+ mz5 support so it requires that you build without it. If you
+ download a new tarball from the website, you won't need this
+ option.
+
+3. Install the libraries and include files in a convenient location.
+ $ ./quickbuild.sh --without-mz5 libraries --prefix=install
+
+This will create a new directory, install, with subdirectories include
+and lib. We will point the compiler/linker to these locations when
+building crux.
+
+** Note about library names. In proteowizard/install/lib will be some
+ boost libraries. The library names will include the compiler name
+ and version. This is a function of how pwiz builds them. Boost by
+ itself can be built with generic names (e.g. libboost_system.a),
+ but I have never figured out how to make that work within the pwiz
+ system.
+
+4. Now you should be able to build crux as usual. If you get errors
+about not finding boost libraries, you may have a different version of
+gcc installed (see note above). Look in proteowizard/install/lib for
+the correct name of the libraries and update crux/src/c/Makefile.am
+accordingly.
+
+Additional notes.
+
+I have made a few changes to the pwiz code to silence the compiler
+warnings-as-errors. Look for comments with BF for the changes.
+
+Steps 2 and 3 can be combined by adding 'libraries --prefix=install'
+to the command in step 2. The order of arguments doesn't seem to
+matter for bjam.
+
diff --git a/doc/crux-report.doc b/doc/crux-report.doc
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diff --git a/doc/logo/README b/doc/logo/README
new file mode 100644
index 0000000..df5cf59
--- /dev/null
+++ b/doc/logo/README
@@ -0,0 +1 @@
+Photoshop says the RGB value for the logo is 2188b8 = (33, 136, 220).
diff --git a/doc/logo/crux-cmyk.eps b/doc/logo/crux-cmyk.eps
new file mode 100644
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diff --git a/doc/logo/crux.ai b/doc/logo/crux.ai
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diff --git a/doc/logo/design-transfer-agreement-454896-en_US.pdf b/doc/logo/design-transfer-agreement-454896-en_US.pdf
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+This directory contains the log of Crux distribution downloads from the Crux
+Sourceforge web site.
+
+The log file, downloads.txt, is downloaded from the Crux web site using:
+
+scp -r crux-toolkit at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs/download/downloads.txt .
+
+This log file is generated on the Crux SourceForge site by the PHP script
+doc/user/download/download.php. This script gets installed to
+/home/project-web/cruxtoolkit/htdocs/download/download.php on the website,
+and is run whenever a user clicks on one of the download buttons in
+doc/user/download.html.
diff --git a/doc/logs/analyze-log.py b/doc/logs/analyze-log.py
new file mode 100755
index 0000000..6763bb3
--- /dev/null
+++ b/doc/logs/analyze-log.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+
+
+import operator
+import socket
+from sys import argv
+from collections import defaultdict
+
+host_counts = defaultdict(int)
+app_counts = defaultdict(int)
+
+for filename in argv[1:]:
+ input_file = open(filename)
+ for line in input_file:
+ if "zip" in line or "gz" in line:
+ values = line.split(",")
+ date_time = values[0]
+ ip_address = values[1]
+ file = values[2]
+ platform = None
+ if "Windows.i386" in line: platform = "Windows 32-bit"
+ if "Windows.ix86" in line: platform = "Windows 32-bit"
+ if "Windows.AMD64" in line: platform = "Windows 64-bit"
+ if "Linux.i686" in line: platform = "Linux 32-bit"
+ if "Linux.x86_64" in line: platform = "Linux 64-bit"
+ if "Darwin" in line: platform = "Mac OS"
+ if "Source" in line: platform = "Source"
+ if platform == None:
+ print line
+ hostname = "Unknown"
+ try:
+ hostname = socket.gethostbyaddr(ip_address)[0]
+ except:
+ pass
+ host_counts[hostname] += 1
+ app_counts[platform] += 1
+ input_file.close()
+
+sorted_host_counts = sorted(host_counts.items(), key=operator.itemgetter(1))
+for key, count in sorted_host_counts[-20:]:
+ print key, count
+
+sorted_app_counts = sorted(app_counts.items(), key=operator.itemgetter(1))
+sum = 0
+for key, count in sorted_app_counts:
+ sum += count
+ print key, count
+print "Total Downloads", sum
diff --git a/doc/logs/downloads.txt b/doc/logs/downloads.txt
new file mode 100644
index 0000000..8452aa1
--- /dev/null
+++ b/doc/logs/downloads.txt
@@ -0,0 +1,926 @@
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+"2015-09-11 00:31:14",127.0.0.1,daily/crux-2.1.16786.Linux.i686.zip
+"2015-09-11 00:39:26",127.0.0.1,daily/crux-2.1.16786.Windows.AMD64.zip
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+"2015-09-14 14:34:46",127.0.0.1,daily/crux-2.1.16789.Windows.AMD64.zip
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+"2015-09-16 19:38:23",127.0.0.1,daily/crux-2.1.16790.Source.tar.gz
+"2015-09-17 00:45:54",127.0.0.1,crux-2.1/crux-2.1.Linux.i686.zip
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+"2015-09-20 03:06:18",127.0.0.1,daily/crux-2.1.16800.Windows.AMD64.zip
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diff --git a/doc/user/CMakeLists.txt b/doc/user/CMakeLists.txt
new file mode 100644
index 0000000..99d91c6
--- /dev/null
+++ b/doc/user/CMakeLists.txt
@@ -0,0 +1,29 @@
+cmake_minimum_required(VERSION 2.8.1)
+cmake_policy(VERSION 2.8.1)
+
+# Generate documentation
+if (UNIX)
+ set(CRUX_PATH "${PROJECT_BINARY_DIR}/src/crux")
+elseif(WIN32)
+ set(CMAKE_MSVCIDE_RUN_PATH ${PROJECT_BINARY_DIR}/ext/lib)
+ set(CRUX_PATH "$<TARGET_FILE:crux>")
+endif (UNIX)
+add_custom_target(
+ create-docs
+ ALL
+ WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/doc/user
+ COMMAND
+ ${CMAKE_COMMAND}
+ -DPROJECT_SOURCE_DIR=${PROJECT_SOURCE_DIR}
+ -DPROJECT_BINARY_DIR=${PROJECT_BINARY_DIR}
+ -DCRUX_PATH:PATH=${CRUX_PATH}
+ -DDOC_DIR:PATH=${PROJECT_SOURCE_DIR}/doc/user/commands
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/create-docs.cmake
+)
+
+install(
+ DIRECTORY .
+ DESTINATION doc
+ PATTERN "CMakeLists.txt" EXCLUDE
+ PATTERN "download" EXCLUDE
+)
diff --git a/doc/user/Makefile b/doc/user/Makefile
new file mode 100644
index 0000000..0f38c7b
--- /dev/null
+++ b/doc/user/Makefile
@@ -0,0 +1,207 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+# A target that is always out of date.
+cmake_force:
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake
+
+# The command to remove a file.
+RM = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -E remove -f
+
+# Escaping for special characters.
+EQUALS = =
+
+# The program to use to edit the cache.
+CMAKE_EDIT_COMMAND = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+#=============================================================================
+# Targets provided globally by CMake.
+
+# Special rule for the target edit_cache
+edit_cache:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake cache editor..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : edit_cache
+
+# Special rule for the target edit_cache
+edit_cache/fast: edit_cache
+.PHONY : edit_cache/fast
+
+# Special rule for the target install
+install: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -P cmake_install.cmake
+.PHONY : install
+
+# Special rule for the target install
+install/fast: preinstall/fast
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -P cmake_install.cmake
+.PHONY : install/fast
+
+# Special rule for the target install/local
+install/local: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local
+
+# Special rule for the target install/local
+install/local/fast: install/local
+.PHONY : install/local/fast
+
+# Special rule for the target install/strip
+install/strip: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
+.PHONY : install/strip
+
+# Special rule for the target install/strip
+install/strip/fast: install/strip
+.PHONY : install/strip/fast
+
+# Special rule for the target list_install_components
+list_install_components:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
+.PHONY : list_install_components
+
+# Special rule for the target list_install_components
+list_install_components/fast: list_install_components
+.PHONY : list_install_components/fast
+
+# Special rule for the target package
+package: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Run CPack packaging tool..."
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cpack --config ./CPackConfig.cmake
+.PHONY : package
+
+# Special rule for the target package
+package/fast: package
+.PHONY : package/fast
+
+# Special rule for the target package_source
+package_source:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Run CPack packaging tool for source..."
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cpack --config ./CPackSourceConfig.cmake /data/TeamCity/buildAgent/work/779d99b0241b2175/CPackSourceConfig.cmake
+.PHONY : package_source
+
+# Special rule for the target package_source
+package_source/fast: package_source
+.PHONY : package_source/fast
+
+# Special rule for the target rebuild_cache
+rebuild_cache:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake to regenerate build system..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : rebuild_cache
+
+# Special rule for the target rebuild_cache
+rebuild_cache/fast: rebuild_cache
+.PHONY : rebuild_cache/fast
+
+# The main all target
+all: cmake_check_build_system
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -E cmake_progress_start /data/TeamCity/buildAgent/work/779d99b0241b2175/CMakeFiles /data/TeamCity/buildAgent/work/779d99b0241b2175/doc/user/CMakeFiles/progress.marks
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 doc/user/all
+ $(CMAKE_COMMAND) -E cmake_progress_start /data/TeamCity/buildAgent/work/779d99b0241b2175/CMakeFiles 0
+.PHONY : all
+
+# The main clean target
+clean:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 doc/user/clean
+.PHONY : clean
+
+# The main clean target
+clean/fast: clean
+.PHONY : clean/fast
+
+# Prepare targets for installation.
+preinstall: all
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 doc/user/preinstall
+.PHONY : preinstall
+
+# Prepare targets for installation.
+preinstall/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 doc/user/preinstall
+.PHONY : preinstall/fast
+
+# clear depends
+depend:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
+.PHONY : depend
+
+# Convenience name for target.
+doc/user/CMakeFiles/create-docs.dir/rule:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 doc/user/CMakeFiles/create-docs.dir/rule
+.PHONY : doc/user/CMakeFiles/create-docs.dir/rule
+
+# Convenience name for target.
+create-docs: doc/user/CMakeFiles/create-docs.dir/rule
+.PHONY : create-docs
+
+# fast build rule for target.
+create-docs/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f doc/user/CMakeFiles/create-docs.dir/build.make doc/user/CMakeFiles/create-docs.dir/build
+.PHONY : create-docs/fast
+
+# Help Target
+help:
+ @echo "The following are some of the valid targets for this Makefile:"
+ @echo "... all (the default if no target is provided)"
+ @echo "... clean"
+ @echo "... depend"
+ @echo "... create-docs"
+ @echo "... edit_cache"
+ @echo "... install"
+ @echo "... install/local"
+ @echo "... install/strip"
+ @echo "... list_install_components"
+ @echo "... package"
+ @echo "... package_source"
+ @echo "... rebuild_cache"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+
diff --git a/doc/user/assign-confidence.html b/doc/user/assign-confidence.html
new file mode 100644
index 0000000..8249447
--- /dev/null
+++ b/doc/user/assign-confidence.html
@@ -0,0 +1,147 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>assign-confidence</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>assign-confidence</h1>
+<h2>Usage:</h2>
+<p><code>crux assign-confidence [options] <target input>+</code></p>
+<h2>Description:</h2>
+<p>Given target and decoy scores, estimate a q-value for each target score. The q-value is analogous to a p-value but incorporates false discovery rate multiple testing correction. The q-value associated with a score threshold T is defined as the minimal false discovery rate (FDR) at which a score of T is deemed significant. In this setting, the q-value accounts for the fact that we are analyzing a large collection of scores. For confidence estimation afficionados, please note that this [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>target input+</code> – One or more files, each containing a collection of peptide-spectrum matches (PSMs) in <a href="../file-formats/txt-format.html">tab-delimited text</a>, <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">PepXML</a>, or <a href="http://www.psidev.info/mzidentml">mzIdentML</a> format. In tab-delimited text format, only the specified score column is required. However if --estimation-method is tdc, then the columns "scan" and [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>assign-confidence.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> that contains the targets, sorted by score. The file will contain one new column, named "<method> q-value", where <method> is either "tdc" or "mix-max".</li>
+ <li><code>assign-confidence.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>assign-confidence.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>assign-confidence options</h3>
+<ul>
+ <li class="nobullet"><code>--estimation-method mix-max|tdc|peptide-level</code> – Specify the method used to estimate q-values. The mix-max procedure or target-decoy competition apply to PSMs. The peptide-level option eliminates any PSM for which there exists a better scoring PSM involving the same peptide, and then uses decoys to assign confidence estimates. Default = <code>tdc</code>.</li>
+ <li class="nobullet"><code>--score <string></code> – Specify the column (for tab-delimited input) or tag (for XML input) used as input to the q-value estimation procedure. If this parameter is unspecified, then the program searches for "xcorr score", "evalue" (comet), "exact p-value" score fields in this order in the input file. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--sidak T|F</code> – Adjust the score using the Sidak adjustment and reports them in a new column in the output file. Note that this adjustment only makes sense if the given scores are p-values, and that it requires the presence of the "distinct matches/spectrum" feature for each PSM. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-charge-states T|F</code> – Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-modified-peptides T|F</code> – Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/barista.html b/doc/user/barista.html
new file mode 100644
index 0000000..f5b1d92
--- /dev/null
+++ b/doc/user/barista.html
@@ -0,0 +1,163 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>barista</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>barista</h1>
+<h2>Usage:</h2>
+<p><code>crux barista [options] <database> <fragmentation spectra> <search results></code></p>
+<h2>Description:</h2>
+<p>Barista is a protein identification algorithm that combines two different tasks–peptide-spectrum match (PSM) verification and protein inference–into a single learning algorithm. The program requires three inputs: a set of MS2 spectra, a protein database, and the results of searching the spectra against the database. Barista produces as output three ranked lists of proteins, peptides and PSMs, based on how likely the proteins and peptides are to be present in the sample and [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>database</code> – The program requires the FASTA format protein database files against which the search was performed. The protein database input may be a concatenated database or separate target and decoy databases; the latter is supported with the --separate-searches option, described below. In either case, Barista distinguishes between target and decoy proteins based on the presence of a decoy prefix on the sequence identifiers (see the --decoy-prefix option, below). [...]
+ <li><code>fragmentation spectra</code> – The fragmentation spectra must be provided in <a href="../file-formats/ms2-format.html">MS2</a>, mzXML, or MGF format.</li>
+ <li><code>search results</code> – Search results in the <a href="../file-formats/txt-format.html">tab-delimited text format</a> produced by Crux or in <a href="../file-formats/sqt-format.html">SQT format</a>. Like the spectra, the search results can be provided as a single file, a list of files or a directory of files. Note, however, that the input mode for spectra and for search results must be the same; i.e., if you provide a list of files for the spectra, then you must also pr [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>barista.xml</code> – an <a href="../file-formats/barista-xml-format.html">XML file</a> that contains four information about proteins, subset proteins, peptides, and PSMs.</li>
+ <li><code>barista.target.proteins.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited file</a> containing a ranked list of groups of indistinguishable target proteins with associated Barista scores and q-values and with peptides that contributed to the identification of the protein group.</li>
+ <li><code>barista.target.subset-proteins.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited file</a> containing groups of indistinguishable proteins.</li>
+ <li><code>barista.target.peptides.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited file</a> containing a ranked list of target peptides with the associated Barista scores and q-values.</li>
+ <li><code>barista.target.psm.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited file format</a> containing a ranked list of target peptide-spectrum matches with the associated Barista scores and q-values.</li>
+ <li><code>barista.log.txt</code> – a file where the program reports its progress.</li>
+ <li><code>barista.params.txt</code> – a file with the values of all the options given to the current run.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>barista options</h3>
+<ul>
+ <li class="nobullet"><code>--separate-searches <string></code> – If the target and decoy searches were run separately, rather than using a concatenated database, then the program will assume that the database search results provided as a required argument are from the target database search. This option then allows the user to specify the location of the decoy search results. Like the required arguments, these search results can be provided as a single file, a list of files [...]
+ <li class="nobullet"><code>--skip-cleanup T|F</code> – Analysis begins with a pre-processsing step that creates a set of lookup tables which are then used during training. Normally, these lookup tables are deleted at the end of the analysis, but setting this option to T prevents the deletion of these tables. Subsequently, analyses can be repeated more efficiently by specifying the --re-run option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--re-run <string></code> – Re-run a previous analysis using a previously computed set of lookup tables. For this option to work, the --skip-cleanup option must have been set to true when the program was run the first time. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--use-spec-features T|F</code> – Use an enriched feature set, including separate features for each ion type. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--optimization protein|peptide|psm</code> – Specifies whether to do optimization at the protein, peptide or psm level. Default = <code>protein</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-out T|F</code> – Output the computed features in <a href="../file-formats/features.html">tab-delimited text format</a>. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/bullseye.html b/doc/user/bullseye.html
new file mode 100644
index 0000000..e73bf1e
--- /dev/null
+++ b/doc/user/bullseye.html
@@ -0,0 +1,158 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>bullseye</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
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+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>bullseye</h1>
+<h2>Usage:</h2>
+<p><code>crux bullseye [options] <MS1 spectra> <MS2 spectra></code></p>
+<h2>Description:</h2>
+<p>Bullseye assigns high resolution precursor m/z values to fragmentation (MS2) spectra. Bullseye uses the Hardklör algorithm to identify persistent isotope distributions (PPIDs) in precursor (MS1) scans. For each PPID, MS2 scans that occur within a specified time and m/z range are assigned the average monoisotopic m/z from the PPID assigned as the precursor m/z. A detailed description of the Bullseye algorithm is given in </p><quote>Hsieh EJ, Hoopmann MR, Maclean B, MacCoss MJ. <a [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>MS1 spectra</code> – The name of a file from which to parse high-resolution spectra of intact peptides. The file may be in MS1 (.ms1), binary MS1 (.bms1), compressed MS1 (.cms1), or mzXML (.mzXML) format. Bullseye will search for PPIDs in these spectra.</li>
+ <li><code>MS2 spectra</code> – The name of a file from which to parse peptide fragmentation spectra. The file may be in MS2 (.ms2), binary MS2 (.bms2), compressed MS2 (.cms2) or mzXML (.mzXML) format. Bullseye will assign high-resolution precursor masses to these spectra.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>bullseye.pid.<format></code> – a file containing the fragmentation spectra for which accurate masses were successfully inferred. Unless otherwise specified (with the --spectrum-format option), the output file format is ".ms2". Note that if the output format is ".ms2," then a single spectrum may have multiple "Z" lines, each indicating a charge state and accurate mass. In addition, Bullseye inserts an "I" line (for charge-dependent analysis) corresponding to each "Z" lin [...]
+ <li><code>bullseye.no-pid.<format></code> – a file containing the fragmentation spectra for which accurate masses were not inferred.</li>
+ <li><code>hardklor.mono.txt</code> – a tab-delimited text file containing one line for each isotope distribution, as described <a href="hardklor.html">here</a>.</li>
+ <li><code>bullseye.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>bullseye.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Identifying PPIDs in MS1 spectra</h3>
+<ul>
+ <li class="nobullet"><code>--max-persist <float></code> – Ignore PPIDs that persist for longer than this length of time in the MS1 spectra. The unit of time is whatever unit is used in your data file (usually minutes). These PPIDs are considered contaminants. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--persist-tolerance <float></code> – Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--gap-tolerance <integer></code> – Allowed gap size when checking for PPIDs across consecutive MS1 scans. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--scan-tolerance <integer></code> – Total number of MS1 scans over which a PPID must be observed to be considered real. Gaps in persistence are allowed by setting --gap-tolerance. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--bullseye-max-mass <float></code> – Only consider PPIDs below this maximum mass in daltons. Default = <code>8000</code>.</li>
+ <li class="nobullet"><code>--bullseye-min-mass <float></code> – Only consider PPIDs above this minimum mass in daltons. Default = <code>600</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Matching PPIDs to MS2 spectra</h3>
+<ul>
+ <li class="nobullet"><code>--exact-match T|F</code> – When true, require an exact match (as defined by --exact-tolerance) between the center of the precursor isolation window in the MS2 scan and the base isotopic peak of the PPID. If this option is set to false and no exact match is observed, then attempt to match using a wider m/z tolerance. This wider tolerance is calculated using the PPID's monoisotopic mass and charge (the higher the charge, the smaller the window). Default = [...]
+ <li class="nobullet"><code>--exact-tolerance <float></code> – Set the tolerance (+/-ppm) for --exact-match. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--retention-tolerance <float></code> – Set the tolerance (+/-units) around the retention time over which a PPID can be matches to the MS2 spectrum. The unit of time is whatever unit is used in your data file (usually minutes). Default = <code>0.5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--spectrum-format |ms2|bms2|cms2|mgf</code> – The format to write the output spectra to. If empty, the spectra will be output in the same format as the MS2 input. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
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+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
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+</body>
+</html>
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+<!DOCTYPE html>
+<html>
+<head>
+<title>cascade-search</title>
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+ <li><a href="../fileformats.html">File Formats</a></li>
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+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>cascade-search</h1>
+<h2>Usage:</h2>
+<p><code>crux cascade-search [options] <tide spectra file>+ <database-series></code></p>
+<h2>Description:</h2>
+<p>Cascade-search is a general procedure for incorporating information about peptide groups into the database search and confidence estimation procedure. Peptides may be grouped according to, for example, their enzymatic properties (zero, one, or two enzymatic termini) or the presence of different types of numbers of variable modifications. The algorithm works on a series of databases, each corresponding to a different peptide group. The database is searched in series, and after each sea [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>tide spectra file+</code> – The name of one or more files from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard. Alternatively, the argument may be one or more binary spectrum files produced by a previous run of crux tide-search using the store-spectra parameter.</li>
+ <li><code>database-series</code> – A comma-separated list of databases, each generated by tide-index. Cascade-search will search the given spectra against these databases in the given order.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>cascade-search.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> containing the target PSMs accepted at a pre-defined fdr.</li>
+ <li><code>cascade-search.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>cascade-search.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>cascade-search options</h3>
+<ul>
+ <li class="nobullet"><code>--q-value-threshold <float></code> – The q-value threshold used by cascade search. Each spectrum identified in one search with q-value less than this threshold will be excluded from all subsequent searches. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--estimation-method mix-max|tdc|peptide-level</code> – Specify the method used to estimate q-values. The mix-max procedure or target-decoy competition apply to PSMs. The peptide-level option eliminates any PSM for which there exists a better scoring PSM involving the same peptide, and then uses decoys to assign confidence estimates. Default = <code>tdc</code>.</li>
+ <li class="nobullet"><code>--score <string></code> – Specify the column (for tab-delimited input) or tag (for XML input) used as input to the q-value estimation procedure. If this parameter is unspecified, then the program searches for "xcorr score", "evalue" (comet), "exact p-value" score fields in this order in the input file. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--sidak T|F</code> – Adjust the score using the Sidak adjustment and reports them in a new column in the output file. Note that this adjustment only makes sense if the given scores are p-values, and that it requires the presence of the "distinct matches/spectrum" feature for each PSM. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-charge-states T|F</code> – Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-modified-peptides T|F</code> – Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Precursor selection</h3>
+<ul>
+ <li class="nobullet"><code>--precursor-window <float></code> – Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto-precursor-window false|warn|fail</code> – Automatically estimate optimal value for the precursor-window parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> – Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not avail [...]
+ <li class="nobullet"><code>--max-precursor-charge <integer></code> – The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-min-mz <float></code> – The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum-max-mz <float></code> – The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
+ <li class="nobullet"><code>--min-peaks <integer></code> – The minimum number of peaks a spectrum must have for it to be searched. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--spectrum-charge 1|2|3|all</code> – The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge state will be searched. Default = <code>all</code>.</li>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--compute-sp T|F</code> – Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spe [...]
+ <li class="nobullet"><code>--remove-precursor-peak T|F</code> – If true, all peaks around the precursor m/z will be removed, within a range specified by the --remove-precursor-tolerance option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--exact-p-value T|F</code> – Enable the calculation of exact p-values for the XCorr score as described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this article</a>. Calculation of p-values increases the running time but increases the number of identifications at a fixed confidence threshold. The p-values will be reported in a new column with header "exact p-value", and the "xcorr score" column will be replaced with a "refactored xcorr" colu [...]
+ <li class="nobullet"><code>--use-neutral-loss-peaks T|F</code> – Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+ <li class="nobullet"><code>--auto-mz-bin-width false|warn|fail</code> – Automatically estimate optimal value for the mz-bin-width parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-offset <float></code> – In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--peptide-centric-search T|F</code> – Carries out a peptide-centric search. For each peptide the top-scoring spectra are reported, in contrast to the standard spectrum-centric search where the top-scoring peptides are reported. Note that in this case the "xcorr rank" column will contain the rank of the given spectrum with respect to the given candidate peptide, rather than vice versa (which is the default). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--isotope-error <string></code> – List of positive, non-zero integers. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--skip-preprocessing T|F</code> – Skip preprocessing steps on spectra. Default = F. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>CPU threads</h3>
+<ul>
+ <li class="nobullet"><code>--num-threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--store-spectra <string></code> – Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir). This option is not valid if multiple input spectrum files are given. Default = <code><e [...]
+ <li class="nobullet"><code>--store-index <string></code> – When providing a FASTA file as the index, the generated binary index will be stored at the given path. This option has no effect if a binary index is provided as the index. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--concat T|F</code> – When set to T, target and decoy search results are reported in a single file, and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--print-search-progress <integer></code> – Show search progress by printing every n spectra searched. Set to 0 to show no search progress. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--sqt-output T|F</code> – Outputs an SQT results file to the output directory. Note that if sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mzid-output T|F</code> – Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pin-output T|F</code> – Output a Percolator input (PIN) file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--file-column T|F</code> – Include the file column in tab-delimited output. Default = <code>true</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/cmake_install.cmake b/doc/user/cmake_install.cmake
new file mode 100644
index 0000000..f038400
--- /dev/null
+++ b/doc/user/cmake_install.cmake
@@ -0,0 +1,38 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/doc/user
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+ FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/doc" TYPE DIRECTORY FILES "/data/TeamCity/buildAgent/work/779d99b0241b2175/doc/user/." REGEX "/CMakeLists\\.txt$" EXCLUDE REGEX "/download$" EXCLUDE)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
diff --git a/doc/user/comet-options/activation_method.html b/doc/user/comet-options/activation_method.html
new file mode 100644
index 0000000..f21a03d
--- /dev/null
+++ b/doc/user/comet-options/activation_method.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: activation_method</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: activation_method</h2>
+
+ <ul>
+ <li>This parameter specifies which scan types are searched.
+ <li>If "ALL" is specified, no filtering based on the activation method
+ is applied.
+ <li>If any other allowed entry is chosen, only spectra with activation
+ method matching the specified entry are searched.
+ <li>This parameter is valid only for mzXML, mzML and mz5 input.
+ <li>Allowed values are: ALL, CID, ECD, ETD, PQD, HCD, IRMPD
+ <li>The default value is "ALL" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>activation_method = ALL</tt>
+ <br><tt>activation_method = CID</tt>
+ <br><tt>activation_method = ETD</tt>
+ <br><tt>activation_method = HCD</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_A_alanine.html b/doc/user/comet-options/add_A_alanine.html
new file mode 100644
index 0000000..392f658
--- /dev/null
+++ b/doc/user/comet-options/add_A_alanine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_A_alanine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_A_alanine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue A.
+ <li>The specified mass is added to the unmodified mass of A.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_A_alanine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_B_user_amino_acid.html b/doc/user/comet-options/add_B_user_amino_acid.html
new file mode 100644
index 0000000..1a74ce3
--- /dev/null
+++ b/doc/user/comet-options/add_B_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_B_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_B_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'B' in the input FASTA file and specify its mass here.
+ <li>The letter 'B' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'B' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_B_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_C_cysteine.html b/doc/user/comet-options/add_C_cysteine.html
new file mode 100644
index 0000000..757e1be
--- /dev/null
+++ b/doc/user/comet-options/add_C_cysteine.html
@@ -0,0 +1,21 @@
+<html><head><title>comet parameter: add_C_cysteine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_C_cysteine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue C.
+ <li>The specified mass is added to the unmodified mass of C.
+ <li>The default value is "0.0" if this parameter is missing.
+ If Comet was compiled for
+ <a href="noble.gs.washington.edu/proj/crux/">Crux</a> compatibility,
+ the default value is "57.021464".
+ Note that in the example parameter file produced by Comet using the "-p"
+ command line option, this parameter entry has a value of 57.021464 for
+ cysteine carbamidomethylation.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_C_cysteine = 57.021464</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_Cterm_peptide.html b/doc/user/comet-options/add_Cterm_peptide.html
new file mode 100644
index 0000000..f796288
--- /dev/null
+++ b/doc/user/comet-options/add_Cterm_peptide.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Cterm_peptide</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Cterm_peptide</h2>
+
+ <ul>
+ <li>Specify a static modification to the C-terminus of all peptides.
+ <li>The specified mass is added to the unmodified C-terminal mass (mass of OH or 17.00274).
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Cterm_peptide = 14.01</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_Cterm_protein.html b/doc/user/comet-options/add_Cterm_protein.html
new file mode 100644
index 0000000..1d617e0
--- /dev/null
+++ b/doc/user/comet-options/add_Cterm_protein.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Cterm_protein</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Cterm_protein</h2>
+
+ <ul>
+ <li>Specify a static modification to the C-terminal peptide of each protein entry.
+ <li>The specified mass is added to the unmodified C-terminal mass (mass of OH or 17.00274).
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Cterm_protein = 14.01</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_D_aspartic_acid.html b/doc/user/comet-options/add_D_aspartic_acid.html
new file mode 100644
index 0000000..dc85968
--- /dev/null
+++ b/doc/user/comet-options/add_D_aspartic_acid.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_D_aspartic_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_D_aspartic_acid</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue D.
+ <li>The specified mass is added to the unmodified mass of D.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_D_cysteine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_E_glutamic_acid.html b/doc/user/comet-options/add_E_glutamic_acid.html
new file mode 100644
index 0000000..d95b244
--- /dev/null
+++ b/doc/user/comet-options/add_E_glutamic_acid.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_E_glutamic_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_E_glutamic_acid</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue E.
+ <li>The specified mass is added to the unmodified mass of E.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_E_cysteine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_F_phenylalanine.html b/doc/user/comet-options/add_F_phenylalanine.html
new file mode 100644
index 0000000..82952d4
--- /dev/null
+++ b/doc/user/comet-options/add_F_phenylalanine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_F_phenylalanine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_F_phenylalanine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue F.
+ <li>The specified mass is added to the unmodified mass of F.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_F_phenylalanine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_G_glycine.html b/doc/user/comet-options/add_G_glycine.html
new file mode 100644
index 0000000..62d8a24
--- /dev/null
+++ b/doc/user/comet-options/add_G_glycine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_G_glycine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_G_glycine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue G.
+ <li>The specified mass is added to the unmodified mass of G.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_G_cysteine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_H_histidine.html b/doc/user/comet-options/add_H_histidine.html
new file mode 100644
index 0000000..8984a28
--- /dev/null
+++ b/doc/user/comet-options/add_H_histidine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_H_histidine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_H_histidine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue H.
+ <li>The specified mass is added to the unmodified mass of H.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_H_histidine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_I_isoleucine.html b/doc/user/comet-options/add_I_isoleucine.html
new file mode 100644
index 0000000..90d6de0
--- /dev/null
+++ b/doc/user/comet-options/add_I_isoleucine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_I_isoleucine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_I_isoleucine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue I.
+ <li>The specified mass is added to the unmodified mass of I.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_I_isoleucine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_J_user_amino_acid.html b/doc/user/comet-options/add_J_user_amino_acid.html
new file mode 100644
index 0000000..3806f3a
--- /dev/null
+++ b/doc/user/comet-options/add_J_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_J_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_J_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'J' in the input FASTA file and specify its mass here.
+ <li>The letter 'J' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'J' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_J_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_K_lysine.html b/doc/user/comet-options/add_K_lysine.html
new file mode 100644
index 0000000..a52206d
--- /dev/null
+++ b/doc/user/comet-options/add_K_lysine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_K_lysine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_K_lysine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue K.
+ <li>The specified mass is added to the unmodified mass of K.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_K_lysine = 14.01</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_L_leucine.html b/doc/user/comet-options/add_L_leucine.html
new file mode 100644
index 0000000..58d84bf
--- /dev/null
+++ b/doc/user/comet-options/add_L_leucine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_L_leucine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_L_leucine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue L.
+ <li>The specified mass is added to the unmodified mass of L.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_L_leucine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_M_methionine.html b/doc/user/comet-options/add_M_methionine.html
new file mode 100644
index 0000000..2abd014
--- /dev/null
+++ b/doc/user/comet-options/add_M_methionine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_M_methionine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_M_methionine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue M.
+ <li>The specified mass is added to the unmodified mass of M.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_M_methionine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_N_asparagine.html b/doc/user/comet-options/add_N_asparagine.html
new file mode 100644
index 0000000..a296025
--- /dev/null
+++ b/doc/user/comet-options/add_N_asparagine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_N_asparagine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_N_asparagine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue N.
+ <li>The specified mass is added to the unmodified mass of N.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_N_cysteine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_Nterm_peptide.html b/doc/user/comet-options/add_Nterm_peptide.html
new file mode 100644
index 0000000..617217d
--- /dev/null
+++ b/doc/user/comet-options/add_Nterm_peptide.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Nterm_peptide</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Nterm_peptide</h2>
+
+ <ul>
+ <li>Specify a static modification to the N-terminus of all peptides.
+ <li>The specified mass is added to the unmodified N-terminal mass (mass of H or 1.007825).
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Nterm_peptide = 14.01</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_Nterm_protein.html b/doc/user/comet-options/add_Nterm_protein.html
new file mode 100644
index 0000000..3f41d87
--- /dev/null
+++ b/doc/user/comet-options/add_Nterm_protein.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Nterm_protein</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Nterm_protein</h2>
+
+ <ul>
+ <li>Specify a static modification to the N-terminal peptide of each protein entry.
+ <li>The specified mass is added to the unmodified N-terminal mass (mass of H or 1.007825).
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Nterm_protein = 14.01</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_O_ornithine.html b/doc/user/comet-options/add_O_ornithine.html
new file mode 100644
index 0000000..32b3b38
--- /dev/null
+++ b/doc/user/comet-options/add_O_ornithine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_O_ornithine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_O_ornithine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue O.
+ <li>The specified mass is added to the unmodified mass of O.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_O_ornithine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_P_proline.html b/doc/user/comet-options/add_P_proline.html
new file mode 100644
index 0000000..c27daf0
--- /dev/null
+++ b/doc/user/comet-options/add_P_proline.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_P_proline</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_P_proline</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue P.
+ <li>The specified mass is added to the unmodified mass of P.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_P_proline = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_Q_glutamine.html b/doc/user/comet-options/add_Q_glutamine.html
new file mode 100644
index 0000000..37227f2
--- /dev/null
+++ b/doc/user/comet-options/add_Q_glutamine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Q_glutamine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Q_glutamine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue Q.
+ <li>The specified mass is added to the unmodified mass of Q.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Q_glutamine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_R_arginine.html b/doc/user/comet-options/add_R_arginine.html
new file mode 100644
index 0000000..d668719
--- /dev/null
+++ b/doc/user/comet-options/add_R_arginine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_R_arginine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_R_arginine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue R.
+ <li>The specified mass is added to the unmodified mass of R.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_R_arginine = 28.03</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_S_serine.html b/doc/user/comet-options/add_S_serine.html
new file mode 100644
index 0000000..6f7b93e
--- /dev/null
+++ b/doc/user/comet-options/add_S_serine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_S_serine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_S_serine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue S.
+ <li>The specified mass is added to the unmodified mass of s.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_S_serine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_T_threonine.html b/doc/user/comet-options/add_T_threonine.html
new file mode 100644
index 0000000..68aef74
--- /dev/null
+++ b/doc/user/comet-options/add_T_threonine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_T_threonine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_T_threonine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue T.
+ <li>The specified mass is added to the unmodified mass of T.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_T_threonine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_U_user_amino_acid.html b/doc/user/comet-options/add_U_user_amino_acid.html
new file mode 100644
index 0000000..ab71e4a
--- /dev/null
+++ b/doc/user/comet-options/add_U_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_U_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_U_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'U' in the input FASTA file and specify its mass here.
+ <li>The letter 'U' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'U' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_U_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_V_valine.html b/doc/user/comet-options/add_V_valine.html
new file mode 100644
index 0000000..5749b4c
--- /dev/null
+++ b/doc/user/comet-options/add_V_valine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_V_valine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_V_valine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue V.
+ <li>The specified mass is added to the unmodified mass of V.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_V_valine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_W_tryptophan.html b/doc/user/comet-options/add_W_tryptophan.html
new file mode 100644
index 0000000..ee0558b
--- /dev/null
+++ b/doc/user/comet-options/add_W_tryptophan.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_W_tryptophan</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_W_tryptophan</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue W.
+ <li>The specified mass is added to the unmodified mass of W.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_W_tryptophan = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_X_user_amino_acid.html b/doc/user/comet-options/add_X_user_amino_acid.html
new file mode 100644
index 0000000..6309a5a
--- /dev/null
+++ b/doc/user/comet-options/add_X_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_X_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_X_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'X' in the input FASTA file and specify its mass here.
+ <li>The letter 'X' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'X' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_X_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_Y_tyrosine.html b/doc/user/comet-options/add_Y_tyrosine.html
new file mode 100644
index 0000000..d1eb52d
--- /dev/null
+++ b/doc/user/comet-options/add_Y_tyrosine.html
@@ -0,0 +1,15 @@
+<html><head><title>comet parameter: add_Y_tyrosine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Y_tyrosine</h2>
+
+ <ul>
+ <li>Specify a static modification to the residue Y.
+ <li>The specified mass is added to the unmodified mass of Y.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Y_tyrosine = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/add_Z_user_amino_acid.html b/doc/user/comet-options/add_Z_user_amino_acid.html
new file mode 100644
index 0000000..dc0d808
--- /dev/null
+++ b/doc/user/comet-options/add_Z_user_amino_acid.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: add_Z_user_amino_acid</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: add_Z_user_amino_acid</h2>
+
+ <ul>
+ <li>This parameter allows users to define their own custom residue. Just
+ encode the letter 'Z' in the input FASTA file and specify its mass here.
+ <li>The letter 'Z' has no default mass. So the mass entered here will
+ be its residue mass.
+ <li>The default value is "0.0" if this parameter is missing. If any peptide
+ contains the letter 'Z' while this parameter value is set to 0.0, that
+ peptide will not be analyzed.
+ </ul>
+
+ <p>Example:
+ <br><tt>add_Z_user_amino_acid = 100.8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/allowed_missed_cleavage.html b/doc/user/comet-options/allowed_missed_cleavage.html
new file mode 100644
index 0000000..7a03d24
--- /dev/null
+++ b/doc/user/comet-options/allowed_missed_cleavage.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: allowed_missed_cleavage</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: allowed_missed_cleavage</h2>
+
+ <ul>
+ <li>Number of allowed missed enzyme cleavages in a peptide.
+ <li>Parameter is not applied of the no-enzyme option is specified
+ in the <a href="search_enzyme_number.php">search_enzyme_number</a>
+ parameter.
+ <li>The default value is "2" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>allowed_missed_cleavage = 0</tt> <i>for no missed cleavages</i>
+ <br><tt>allowed_missed_cleavage = 2</tt> <i>allow two missed cleavages</i>
+
+</body></html>
diff --git a/doc/user/comet-options/clear_mz_range.html b/doc/user/comet-options/clear_mz_range.html
new file mode 100644
index 0000000..6845854
--- /dev/null
+++ b/doc/user/comet-options/clear_mz_range.html
@@ -0,0 +1,24 @@
+<html><head><title>comet parameter: clear_mz_range</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: clear_mz_range</h2>
+
+ <ul>
+ <li>This parameter is intended for iTRAQ/TMT type data where one might
+ want to remove the reporter ion signals in the MS/MS spectra prior to searching.
+ <li>Defines the m/z range to clear out in each MS/MS spectra
+ <li>This parameter has two decimal values.
+ <li>The first value is the lower mass cutoff and the second value is
+ the high mass cutoff.
+ <li>Valid values are two decimal numbers where the first number must
+ be less or equal to the second number.
+ <li>All peaks between the two decimal values are cleared out.
+ <li>The default value is "0.0 0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>clear_mz_range = 0.0 0.0</tt> <i>parameter is ignored</i>
+ <br><tt>clear_mz_range = 112.5 121.5</tt> <i>ignore all peaks between 112.5 and 121.5 m/z for iTRAQ 8-plex</i>
+ <br><tt>clear_mz_range = 125.5 131.5</tt> <i>ignore all peaks between 125.5 and 131.5 m/z for TMT</i>
+
+</body></html>
diff --git a/doc/user/comet-options/clip_nterm_methionine.html b/doc/user/comet-options/clip_nterm_methionine.html
new file mode 100644
index 0000000..82826fb
--- /dev/null
+++ b/doc/user/comet-options/clip_nterm_methionine.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: clip_nterm_methionine</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: clip_nterm_methionine</h2>
+
+ <ul>
+ <li>This parameter controls whether Comet will automatically remove
+ the N-terminal methionine from a sequence entry.
+ <li>If set to 0, the sequence is analyzed as-is.
+ <li>If set to 1, any sequence with an N-terminal methionine will be
+ analyzed as-is as well as with the methionine removed. This means
+ that any N-terminal modifications will also apply (if appropriate)
+ to the peptide that is generated after the removal of the methionine.
+ <li>Valid values are 0 and 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>clip_nterm_methionine = 0</tt>
+ <br><tt>clip_nterm_methionine = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/combined.html b/doc/user/comet-options/combined.html
new file mode 100644
index 0000000..f21a03d
--- /dev/null
+++ b/doc/user/comet-options/combined.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: activation_method</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: activation_method</h2>
+
+ <ul>
+ <li>This parameter specifies which scan types are searched.
+ <li>If "ALL" is specified, no filtering based on the activation method
+ is applied.
+ <li>If any other allowed entry is chosen, only spectra with activation
+ method matching the specified entry are searched.
+ <li>This parameter is valid only for mzXML, mzML and mz5 input.
+ <li>Allowed values are: ALL, CID, ECD, ETD, PQD, HCD, IRMPD
+ <li>The default value is "ALL" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>activation_method = ALL</tt>
+ <br><tt>activation_method = CID</tt>
+ <br><tt>activation_method = ETD</tt>
+ <br><tt>activation_method = HCD</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/comet.params b/doc/user/comet-options/comet.params
new file mode 100644
index 0000000..b7105d5
--- /dev/null
+++ b/doc/user/comet-options/comet.params
@@ -0,0 +1,160 @@
+# comet_version 2013.02 rev. 0
+# Comet MS/MS search engine parameters file.
+# Everything following the '#' symbol is treated as a comment.
+
+database_name = /some/path/db.fasta
+decoy_search = 0 # 0=no (default), 1=concatenated search, 2=separate search
+
+num_threads = 0 # 0=poll CPU to set num threads; else specify num threads directly (max 32)
+
+#
+# masses
+#
+peptide_mass_tolerance = 3.00
+peptide_mass_units = 0 # 0=amu, 1=mmu, 2=ppm
+mass_type_parent = 1 # 0=average masses, 1=monoisotopic masses
+mass_type_fragment = 1 # 0=average masses, 1=monoisotopic masses
+precursor_tolerance_type = 0 # 0=MH+ (default), 1=precursor m/z
+isotope_error = 0 # 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2= -8/-4/0/4/8 (for +4/+8 labeling)
+
+#
+# search enzyme
+#
+search_enzyme_number = 1 # choose from list at end of this params file
+num_enzyme_termini = 2 # valid values are 1 (semi-digested), 2 (fully digested, default), 8 N-term, 9 C-term
+allowed_missed_cleavage = 2 # maximum value is 5; for enzyme search
+
+#
+# Up to 6 variable modifications are supported
+# format: <mass> <residues> <0=variable/1=binary> <max mods per a peptide>
+# e.g. 79.966331 STY 0 3
+#
+variable_mod1 = 15.9949 M 0 3
+variable_mod2 = 0.0 X 0 3
+variable_mod3 = 0.0 X 0 3
+variable_mod4 = 0.0 X 0 3
+variable_mod5 = 0.0 X 0 3
+variable_mod6 = 0.0 X 0 3
+max_variable_mods_in_peptide = 5
+
+#
+# fragment ions
+#
+# ion trap ms/ms: 1.0005 tolerance, 0.4 offset (mono masses), theoretical_fragment_ions = 1
+# high res ms/ms: 0.02 tolerance, 0.0 offset (mono masses), theoretical_fragment_ions = 0
+#
+fragment_bin_tol = 1.0005 # binning to use on fragment ions
+fragment_bin_offset = 0.4 # offset position to start the binning (0.0 to 1.0)
+theoretical_fragment_ions = 1 # 0=default peak shape, 1=M peak only
+use_A_ions = 0
+use_B_ions = 1
+use_C_ions = 0
+use_X_ions = 0
+use_Y_ions = 1
+use_Z_ions = 0
+use_NL_ions = 1 # 0=no, 1=yes to consider NH3/H2O neutral loss peaks
+use_sparse_matrix = 0
+
+#
+# output
+#
+output_sqtstream = 0 # 0=no, 1=yes write sqt to standard output
+output_sqtfile = 0 # 0=no, 1=yes write sqt file
+output_txtfile = 0 # 0=no, 1=yes write tab-delimited txt file
+output_pepxmlfile = 1 # 0=no, 1=yes write pep.xml file
+output_pinxmlfile = 0 # 0=no, 1=yes write pin.xml file
+output_outfiles = 0 # 0=no, 1=yes write .out files
+print_expect_score = 1 # 0=no, 1=yes to replace Sp with expect in out & sqt
+num_output_lines = 5 # num peptide results to show
+show_fragment_ions = 0 # 0=no, 1=yes for out files only
+
+sample_enzyme_number = 1 # Sample enzyme which is possibly different than the one applied to the search.
+ # Used to calculate NTT & NMC in pepXML output (default=1 for trypsin).
+
+#
+# mzXML parameters
+#
+scan_range = 0 0 # start and scan scan range to search; 0 as 1st entry ignores parameter
+precursor_charge = 0 0 # precursor charge range to analyze; does not override mzXML charge; 0 as 1st entry ignores parameter
+ms_level = 2 # MS level to analyze, valid are levels 2 (default) or 3
+activation_method = ALL # activation method; used if activation method set; allowed ALL, CID, ECD, ETD, PQD, HCD, IRMPD
+
+#
+# misc parameters
+#
+digest_mass_range = 600.0 5000.0 # MH+ peptide mass range to analyze
+num_results = 50 # number of search hits to store internally
+skip_researching = 1 # for '.out' file output only, 0=search everything again (default), 1=don't search if .out exists
+max_fragment_charge = 3 # set maximum fragment charge state to analyze (allowed max 5)
+max_precursor_charge = 6 # set maximum precursor charge state to analyze (allowed max 9)
+nucleotide_reading_frame = 0 # 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six
+clip_nterm_methionine = 0 # 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine
+spectrum_batch_size = 0 # max. # of spectra to search at a time; 0 to search the entire scan range in one loop
+decoy_prefix = DECOY_ # decoy entries are denoted by this string which is pre-pended to each protein accession
+
+#
+# spectral processing
+#
+minimum_peaks = 10 # minimum num. of peaks in spectrum to search (default 10)
+minimum_intensity = 0 # minimum intensity value to read in
+remove_precursor_peak = 0 # 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD)
+remove_precursor_tolerance = 1.5 # +- Da tolerance for precursor removal
+clear_mz_range = 0.0 0.0 # for iTRAQ/TMT type data; will clear out all peaks in the specified m/z range
+
+#
+# additional modifications
+#
+
+variable_C_terminus = 0.0
+variable_N_terminus = 0.0
+variable_C_terminus_distance = -1 # -1=all peptides, 0=protein terminus, 1-N = maximum offset from C-terminus
+variable_N_terminus_distance = -1 # -1=all peptides, 0=protein terminus, 1-N = maximum offset from N-terminus
+
+add_Cterm_peptide = 0.0
+add_Nterm_peptide = 0.0
+add_Cterm_protein = 0.0
+add_Nterm_protein = 0.0
+
+add_G_glycine = 0.0000 # added to G - avg. 57.0513, mono. 57.02146
+add_A_alanine = 0.0000 # added to A - avg. 71.0779, mono. 71.03711
+add_S_serine = 0.0000 # added to S - avg. 87.0773, mono. 87.03203
+add_P_proline = 0.0000 # added to P - avg. 97.1152, mono. 97.05276
+add_V_valine = 0.0000 # added to V - avg. 99.1311, mono. 99.06841
+add_T_threonine = 0.0000 # added to T - avg. 101.1038, mono. 101.04768
+add_C_cysteine = 57.021464 # added to C - avg. 103.1429, mono. 103.00918
+add_L_leucine = 0.0000 # added to L - avg. 113.1576, mono. 113.08406
+add_I_isoleucine = 0.0000 # added to I - avg. 113.1576, mono. 113.08406
+add_N_asparagine = 0.0000 # added to N - avg. 114.1026, mono. 114.04293
+add_D_aspartic_acid = 0.0000 # added to D - avg. 115.0874, mono. 115.02694
+add_Q_glutamine = 0.0000 # added to Q - avg. 128.1292, mono. 128.05858
+add_K_lysine = 0.0000 # added to K - avg. 128.1723, mono. 128.09496
+add_E_glutamic_acid = 0.0000 # added to E - avg. 129.1140, mono. 129.04259
+add_M_methionine = 0.0000 # added to M - avg. 131.1961, mono. 131.04048
+add_O_ornithine = 0.0000 # added to O - avg. 132.1610, mono 132.08988
+add_H_histidine = 0.0000 # added to H - avg. 137.1393, mono. 137.05891
+add_F_phenylalanine = 0.0000 # added to F - avg. 147.1739, mono. 147.06841
+add_R_arginine = 0.0000 # added to R - avg. 156.1857, mono. 156.10111
+add_Y_tyrosine = 0.0000 # added to Y - avg. 163.0633, mono. 163.06333
+add_W_tryptophan = 0.0000 # added to W - avg. 186.0793, mono. 186.07931
+add_B_user_amino_acid = 0.0000 # added to B - avg. 0.0000, mono. 0.00000
+add_J_user_amino_acid = 0.0000 # added to J - avg. 0.0000, mono. 0.00000
+add_U_user_amino_acid = 0.0000 # added to U - avg. 0.0000, mono. 0.00000
+add_X_user_amino_acid = 0.0000 # added to X - avg. 0.0000, mono. 0.00000
+add_Z_user_amino_acid = 0.0000 # added to Z - avg. 0.0000, mono. 0.00000
+
+#
+# COMET_ENZYME_INFO _must_ be at the end of this parameters file
+#
+[COMET_ENZYME_INFO]
+0. No_enzyme 0 - -
+1. Trypsin 1 KR P
+2. Trypsin/P 1 KR -
+3. Lys_C 1 K P
+4. Lys_N 0 K -
+5. Arg_C 1 R P
+6. Asp_N 0 D -
+7. CNBr 1 M -
+8. Glu_C 1 DE P
+9. PepsinA 1 FL P
+10. Chymotrypsin 1 FWYL P
+
diff --git a/doc/user/comet-options/content.html b/doc/user/comet-options/content.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/doc/user/comet-options/content.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/doc/user/comet-options/convertCometPHPs.py b/doc/user/comet-options/convertCometPHPs.py
new file mode 100644
index 0000000..bc19af5
--- /dev/null
+++ b/doc/user/comet-options/convertCometPHPs.py
@@ -0,0 +1,55 @@
+#!/usr/bin/env python
+# AUTHOR: William Stafford Noble
+# CREATE DATE: May Day, 2013
+import sys
+
+USAGE = """USAGE: convertCometPHP.py <php file>
+
+ This is a goofy little helper script that takes as input one of the
+ parameter PHP files distributed with Jimmy Eng's Comet search
+ engine, strips off some of the unnecessary text, adds HTML headers
+ and prints the result to standard output. The idea is to allow
+ automatic incorporation of any changes Jimmy makes to his
+ documentation into Crux. This is brittle, because it's based on
+ hand-designed parsing code. A better solution would be for Jimmy to
+ store his parameter docs in, say, XML, and then use an existing
+ parser.
+
+"""
+
+# Parse the command line.
+if (len(sys.argv) != 2):
+ sys.stderr.write(USAGE)
+ exit(1)
+phpFileName = sys.argv[1]
+
+phpFile = open(phpFileName, "r")
+
+# Find the start of the interesting section.
+for line in phpFile:
+ if ("<h2>" in line):
+
+ # Get the name of the parameter.
+ words = line.rstrip().split()
+ if ((len(words) != 3) or
+ (words[0] != "<h2>Comet") or
+ (words[2][-5:] != "</h2>")):
+ sys.stderr.write("Can't parse %s." % line)
+ sys.exit(1)
+ parameter = words[2][:-5]
+
+ # Print the HTML header.
+ sys.stdout.write("<html><head><title>comet parameter: %s</title>\n" % parameter)
+ sys.stdout.write("<link href=\"../crux.css\" rel=\"styleSheet\" type=\"text/css\">\n")
+ sys.stdout.write("</title><body>\n")
+ sys.stdout.write("<h2>Comet parameter: %s</h2>\n" % parameter)
+ break
+
+# Print the body of the file.
+for line in phpFile:
+ if "</div" in line:
+ break
+ sys.stdout.write(line)
+phpFile.close()
+
+sys.stdout.write("</body></html>\n")
diff --git a/doc/user/comet-options/database_name.html b/doc/user/comet-options/database_name.html
new file mode 100644
index 0000000..3517f6f
--- /dev/null
+++ b/doc/user/comet-options/database_name.html
@@ -0,0 +1,21 @@
+<html><head><title>comet parameter: database_name</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: database_name</h2>
+
+ <ul>
+ <li>A full or relative path to the sequence database, in FASTA format, to search. Example databases
+ include RefSeq or UniProt.
+ <li>Database can contain amino acid sequences or nucleic acid sequences. If sequences are amino acid
+ sequences, set the parameter "nucleotide_reading_frame = 0". If the sequences are nucleic acid
+ sequences, you must instruct Comet to translate these to amino acid sequences. Do this by setting
+ "nucleotide_reading_frame" to a value between 1 and 9.
+ <li>There is no default value if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>database_name = /usr/local/db/yeast.fasta</tt>
+ <br><tt>database_name = c:\local\db\yeast.fasta</tt>
+ <br><tt>database_name = yeast.fasta</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/decoy_prefix.html b/doc/user/comet-options/decoy_prefix.html
new file mode 100644
index 0000000..0780628
--- /dev/null
+++ b/doc/user/comet-options/decoy_prefix.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: decoy_prefix</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: decoy_prefix</h2>
+
+ <ul>
+ <li>This parameter specifies the prefix string that is pre-pended to
+ the protein identifier and reported for decoy hits.
+ <li>This parameter is only valid when a <a href="decoy_search.php">decoy_search</a>
+ is performed.
+ <li>For example, if the prefix parameter is set to "decoy_prefix = reverse_",
+ a match to a decoy peptide from protein "ALBU_HUMAN" would return
+ "reverse_ALBU_HUMAN" as the protein identifier.
+ <li>The default value is "DECOY_" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>decoy_prefix = DECOY_</tt>
+ <br><tt>decoy_prefix = rev_</tt>
+ <br><tt>decoy_prefix = --any_string_you_want_without_spaces--</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/decoy_search.html b/doc/user/comet-options/decoy_search.html
new file mode 100644
index 0000000..ebf7962
--- /dev/null
+++ b/doc/user/comet-options/decoy_search.html
@@ -0,0 +1,29 @@
+<html><head><title>comet parameter: decoy_search</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: decoy_search</h2>
+
+ <ul>
+ <li>This parameter controls whether or not an internal decoy search is performed.
+ <li>Comet generates decoys by reversing each target peptide sequence, keeping the
+ N-terminal or C-terminal amino acid in place (depending on the "sense" value of the
+ digestion enzyme specified by <a href="search_enzyme_number.php">search_enzyme_number</a>).
+ For example, peptide DIGSESTK becomes decoy peptide TSESGIDK for a tryptic search
+ and peptide DVINHKGGA becomes DAGGKHNIV for an Asp-N search.
+ <li>Valid parameter values are 0, 1, or 2:
+ <ul>
+ <li>0 = no decoy search (default)
+ <li>1 = concatenated decoy search. Target and decoy entries will be scored against
+ each other and a single result is performed for each spectrum query.
+ <li>2 = separate decoy search. Target and decoy entries will be scored separately
+ and separate target and decoy search results will be reported.
+ </ul>
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>decoy_search = 0</tt>
+ <br><tt>decoy_search = 1</tt>
+ <br><tt>decoy_search = 2</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/digest_mass_range.html b/doc/user/comet-options/digest_mass_range.html
new file mode 100644
index 0000000..f225dcf
--- /dev/null
+++ b/doc/user/comet-options/digest_mass_range.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: digest_mass_range</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: digest_mass_range</h2>
+
+ <ul>
+ <li>Defines the mass range of peptides to search (based on MH+ or the singly
+ protonated mass).
+ <li>This parameter has two decimal values.
+ <li>The first value is the lower mass cutoff and the second value is
+ the high mass cutoff.
+ <li>Only spectra with experimental MH+ masses in within the defined
+ mass ranges are searched.
+ <li>Valid values are two decimal numbers where the first number must
+ be less or equal to the second number.
+ <li>The default value is "0.0 10000.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>digest_mass_range = 600.0 5000.0</tt> <i>search only 600.0 to 5000.0 mass range</i>
+ <br><tt>digest_mass_range = 0.0 6500.0</tt> <i>search all spectra with peptide masses between 0.0 and 6000.0</i>
+
+</body></html>
diff --git a/doc/user/comet-options/footer.html b/doc/user/comet-options/footer.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/doc/user/comet-options/footer.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/doc/user/comet-options/fragment_bin_offset.html b/doc/user/comet-options/fragment_bin_offset.html
new file mode 100644
index 0000000..052ca15
--- /dev/null
+++ b/doc/user/comet-options/fragment_bin_offset.html
@@ -0,0 +1,31 @@
+<html><head><title>comet parameter: fragment_bin_offset</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: fragment_bin_offset</h2>
+
+ <ul>
+ <li>This parameter controls how each fragment bin of size <a href="fragment_bin_tol.php">fragment_bin_tol</a>
+ is defined in terms of where each bin starts.
+ <li>For example, assume a <a href="fragment_bin_tol.php">fragment_bin_tol</a> of 1.0. Most intuitively,
+ the fragment bins would be 0.0 to 1.0, 1.0 to 2.0, 2.0 to 3.0, etc.
+ This set of bins corresponds to a fragment_bin_offset of 0.0. However,
+ consider if we set fragment_bin_offset to 0.5; this would cause the
+ bins to be 0.5 to 1.5, 1.5 to 2.5, 2.5 to 3.5, etc.
+ <li>So this fragment_bin_offset gives one a mechanism to define
+ where each bin starts and is centered.
+ <li>For ion trap data with a <a href="fragment_bin_tol.php">fragment_bin_tol</a> of 1.0005,
+ it is recommended to set fragment_bin_offset to 0.4.
+ <li>For high-res MS/MS data, one might use a <a href="fragment_bin_tol.php">fragment_bin_tol</a> of 0.02
+ and a corresponding fragment_bin_offset of 0.0.
+ <li>Allowed values are between 0.0 and 1.0. The actual offset value is
+ scaled by the <a href="fragment_bin_tol.php">fragment_bin_tol</a> value.
+ <li>I know this is esoteric and any normal user should not give this
+ parameter any thought beyond using the recommended settings.
+ <li>The default value is "0.4" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>fragment_bin_offset = 0.4</tt>
+ <br><tt>fragment_bin_offset = 0.0</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/fragment_bin_tol.html b/doc/user/comet-options/fragment_bin_tol.html
new file mode 100644
index 0000000..4ab7e38
--- /dev/null
+++ b/doc/user/comet-options/fragment_bin_tol.html
@@ -0,0 +1,30 @@
+<html><head><title>comet parameter: fragment_bin_tol</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: fragment_bin_tol</h2>
+
+ <ul>
+ <li>This parameter controls the bin size associated with fragment ions.
+ <li>The bin size defines the mass width associated with a single MS/MS peak
+ as it is stored internally in an array element.
+ <li>Although it's not explicitly a fragment ion tolerance, it's probably
+ easiest to think of it as such.
+ <li>Note, there is a direct correlation between the value selected for
+ the fragment_bin_tol and the memory used in a search. The lower the
+ fragment_bin_tol setting, the more memory a search will use. A test of
+ 4,515 query spectra used ~700MB RAM with a 0.4 fragment_bin_tol value,
+ ~1.5GB RAM with a 0.10 value, and ~9GB RAM with a 0.01 value. For small
+ fragment_bin_tol values where computer memory becomes an issue, either
+ set <a href="use_sparse_matrix.php">use_sparse_matrix</a> to true and/or
+ make use of the <a href="spectrum_batch_size.php">spectrum_batch_size</a>
+ parameter
+ <li>The minimum allowed value is 0.01.
+ <li>The default value is "1.0005" if the parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>fragment_bin_tol = 1.0005</tt>
+ <br><tt>fragment_bin_tol = 0.4</tt>
+ <br><tt>fragment_bin_tol = 0.02</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/head.html b/doc/user/comet-options/head.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/doc/user/comet-options/head.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/doc/user/comet-options/index.html b/doc/user/comet-options/index.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/doc/user/comet-options/index.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/doc/user/comet-options/isotope_error.html b/doc/user/comet-options/isotope_error.html
new file mode 100644
index 0000000..4409115
--- /dev/null
+++ b/doc/user/comet-options/isotope_error.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: isotope_error</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: isotope_error</h2>
+
+ <ul>
+ <li>This parameter controls whether the <a href="peptide_mass_tolerance.php">peptide_mass_tolerance</a>
+ takes into account possible isotope errors in the precursor mass measurement.
+ <li>It is possible that an accurately read precursor mass is not measured on the monoisotopic
+ peak of a precursor isotopic pattern. In these cases, the precursor mass is measured on the
+ first isotope peak (one C13 atom) or possibly even the second or third isotope peak. To address
+ this problem, this "isotope_error" parameter allows you to perform an accurate mass search
+ (say 10 ppm) even if the precursor mass measurement is off by one or more C13 offsets.
+ <li>Valid values are 0, 1, and 2:
+ <ul>
+ <li>0 performs no isotope error searches
+ <li>1 searches -1, 0, +1, +2, and +3 isotope offsets
+ <li>2 searches -8, -4, 0, +4, +8 isotope offsets (for +4/+8 stable isotope labeling)
+ </ul>
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>isotope_error = 0</tt>
+ <br><tt>isotope_error = 1</tt>
+ <br><tt>isotope_error = 2</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/mass_type_fragment.html b/doc/user/comet-options/mass_type_fragment.html
new file mode 100644
index 0000000..469c36d
--- /dev/null
+++ b/doc/user/comet-options/mass_type_fragment.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: mass_type_fragment</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: mass_type_fragment</h2>
+
+ <ul>
+ <li>Controls the mass type, average or monoisotopic, applied to fragment ion calculations.
+ <li>Valid values are 0 or 1:
+ <ul>
+ <li>0 for average masses
+ <li>1 for monoisotopic masses
+ </ul>
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>mass_type_fragment = 0</tt>
+ <br><tt>mass_type_fragment = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/mass_type_parent.html b/doc/user/comet-options/mass_type_parent.html
new file mode 100644
index 0000000..c242786
--- /dev/null
+++ b/doc/user/comet-options/mass_type_parent.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: mass_type_parent</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: mass_type_parent</h2>
+
+ <ul>
+ <li>Controls the mass type, average or monoisotopic, applied to peptide mass calculations.
+ <li>Valid values are 0 or 1:
+ <ul>
+ <li>0 for average masses
+ <li>1 for monoisotopic masses
+ </ul>
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>mass_type_parent = 0</tt>
+ <br><tt>mass_type_parent = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/max_fragment_charge.html b/doc/user/comet-options/max_fragment_charge.html
new file mode 100644
index 0000000..0e6dee4
--- /dev/null
+++ b/doc/user/comet-options/max_fragment_charge.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: max_fragment_charge</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: max_fragment_charge</h2>
+
+ <ul>
+ <li>This parameter sets the maximum fragment charge state that will
+ be considered in the analysis.
+ <li>Typically, the fragment charge state range that is analyzed is
+ from 1+ to one charge less than the precursor charge state.
+ <li>For high precursor charge states (i.e. 6+), the default behavior
+ would analyze fragment ions with 1+ through 5+ charges on them. This
+ parameter is a mechanism to limit the fragment charge range that is
+ analyzed.
+ <li>For example, if max_fragment_charge is set to 3 then the maximum
+ fragment charge state that will be analyzed is 3+. However, the default
+ rule will still limit 1+ and 2+ precursor ions to only have
+ 1+ fragments considered. And similarly 3+ precursors will still only
+ have 1+ and 2+ fragments considered.
+ <li>Valid values are any non-zero integer.
+ <li>The default value is "3" if this parameter is missing. A maximum
+ allowed value of "5" is enforced for this parameter.
+ </ul>
+
+ <p>Example:
+ <br><tt>max_fragment_charge = 3</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/max_precursor_charge.html b/doc/user/comet-options/max_precursor_charge.html
new file mode 100644
index 0000000..269cd79
--- /dev/null
+++ b/doc/user/comet-options/max_precursor_charge.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: max_precursor_charge</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: max_precursor_charge</h2>
+
+ <ul>
+ <li>This parameter defines the maximum precursor charge state that
+ will be analyzed.
+ <li>Only spectra with this number of precursor charges or less will be searched.
+ <li>Valid values are any integer greater than 1.
+ <li>The default value is "6" if this parameter is missing. A maximum
+ allowed value of "9" is enforced for this parameter.
+ </ul>
+
+ <p>Example:
+ <br><tt>max_precursor_charge = 5</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/max_variable_mods_in_peptide.html b/doc/user/comet-options/max_variable_mods_in_peptide.html
new file mode 100644
index 0000000..edcbcd7
--- /dev/null
+++ b/doc/user/comet-options/max_variable_mods_in_peptide.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: max_variable_mods_in_peptide</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: max_variable_mods_in_peptide</h2>
+
+ <ul>
+ <li>Specifies the total/maximum number of residues that can be modified in a peptide.
+ <li>As opposed to specifying the maximum number of variable modifications for each
+ of the 6 possible variable modifications, this entry limits the global number
+ of variable mods possible in each peptide.
+ <li>The default value is "10" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>max_variable_mods_in_peptide = 6</tt>
+ <br><tt>max_variable_mods_in_peptide = 10</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/minimum_intensity.html b/doc/user/comet-options/minimum_intensity.html
new file mode 100644
index 0000000..f0c1fe5
--- /dev/null
+++ b/doc/user/comet-options/minimum_intensity.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: minimum_intensity</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: minimum_intensity</h2>
+
+ <ul>
+ <li>A floating point number indicating the minimum intensity value
+ for input the input peaks.
+ <li>If an experimental MS/MS peak intensity is less than this value,
+ it will not be read in and used in the analysis.
+ <li>This is one mechanism to get rid of systemmatic background noise
+ that has a near contant peak intensity.
+ <li>If a peak does not pass this minimum intensity threshold, it will
+ also not be counted towards the <a href="minimum_peaks.php">minimum_peaks</a>
+ parameter.
+ <li>Valid values are any floating point number.
+ <li>The default value is "0.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>minimum_intensity = 100.0</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/minimum_peaks.html b/doc/user/comet-options/minimum_peaks.html
new file mode 100644
index 0000000..0650c83
--- /dev/null
+++ b/doc/user/comet-options/minimum_peaks.html
@@ -0,0 +1,21 @@
+<html><head><title>comet parameter: minimum_peaks</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: minimum_peaks</h2>
+
+ <ul>
+ <li>An integer value indicating the minimum number of m/z-intensity pairs
+ that must be present in a spectrum before it is searched.
+ <li>This parameter can be used to avoid searching nearly sparse spectra
+ that will not likely yield an indentification.
+ <li>This parameter is checked against the spectrum after
+ <a href="clear_mz_range.php">clear_mz_range</a> is applied but before
+ any other spectral processing occurs (i.e. <a href="remove_precursor_peak.php">remove_precursor_peak</a>).
+ <li>Valid values are any integer number.
+ <li>The default value is "10" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>minimum_peaks = 10</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/ms_level.html b/doc/user/comet-options/ms_level.html
new file mode 100644
index 0000000..16d19b1
--- /dev/null
+++ b/doc/user/comet-options/ms_level.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: ms_level</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: ms_level</h2>
+
+ <ul>
+ <li>This parameter specifies which scans are searched.
+ <li>An input value of 2 will search MS/MS scans.
+ <li>An input value of 3 will search MS3 scans.
+ <li>This parameter is only valid for mzXML, mzML, and mz5 input files.
+ <li>Allowed values are 2 or 3.
+ <li>The default value is "2" if this parameter is missing or any value
+ other than 2 or 3 is entered.
+ </ul>
+
+ <p>Example:
+ <br><tt>ms_level = 2</tt>
+ <br><tt>ms_level = 3</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/nucleotide_reading_frame.html b/doc/user/comet-options/nucleotide_reading_frame.html
new file mode 100644
index 0000000..4b5b6c3
--- /dev/null
+++ b/doc/user/comet-options/nucleotide_reading_frame.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: nucleotide_reading_frame</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: nucleotide_reading_frame</h2>
+
+ <ul>
+ <li>This parameter is used to search nucleotide sequence databases.
+ <li>It controls how the nucleotides are translated specifically
+ which sets of reading frames are translated.
+ <li>Valid values are 0 through 9.
+ <li>Set this parameter to 0 for a protein sequence database.
+ <li>Set this parameter to 1 to search the 1st forward reading frame.
+ <li>Set this parameter to 2 to search the 2nd forward reading frame.
+ <li>Set this parameter to 3 to search the 3rd forward reading frame.
+ <li>Set this parameter to 4 to search the 1st reverse reading frame.
+ <li>Set this parameter to 5 to search the 2nd reverse reading frame.
+ <li>Set this parameter to 6 to search the 3rd reverse reading frame.
+ <li>Set this parameter to 7 to search all 3 forward reading frames.
+ <li>Set this parameter to 8 to search all 3 reverse reading frames.
+ <li>Set this parameter to 9 to search all 6 reading frames.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>nucleotide_reading_frame = 0</tt>
+ <br><tt>nucleotide_reading_frame = 9</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/num_enzyme_termini.html b/doc/user/comet-options/num_enzyme_termini.html
new file mode 100644
index 0000000..2af8498
--- /dev/null
+++ b/doc/user/comet-options/num_enzyme_termini.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: num_enzyme_termini</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: num_enzyme_termini</h2>
+
+ <ul>
+ <li>This parameter specifies the number of enzyme termini a peptide must
+ have.
+ <li>For example, if trypsin were specified as the search enzyme, only
+ fully tryptic peptides would be analyzed if "num_enzyme_termini = 2"
+ whereas semi-tryptic peptides would be analyzed if "num_enzyme_termini = 1".
+ <li>This parameter is unused if a no-enzyme search is specified.
+ <li>Valid values are 1, 2, 8, 9.
+ <li>Set this parameter to 1 for a semi-enzyme search.
+ <li>Set this parameter to 2 for a full-enzyme search.
+ <li>Set this parameter to 8 for a semi-enzyme search, unspecific cleavage on peptide's N-terminus.
+ <li>Set this parameter to 9 for a semi-enzyme search, unspecific cleavage on peptide's C-terminus.
+ <li>The default value is "2" if this parameter is missing.
+ </ul>
+
+
+ <p>Example:
+ <br><tt>num_enzyme_termini = 1</tt>
+ <br><tt>num_enzyme_termini = 2</tt>
+ <br><tt>num_enzyme_termini = 8</tt>
+ <br><tt>num_enzyme_termini = 9</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/num_output_lines.html b/doc/user/comet-options/num_output_lines.html
new file mode 100644
index 0000000..39b1bdc
--- /dev/null
+++ b/doc/user/comet-options/num_output_lines.html
@@ -0,0 +1,26 @@
+<html><head><title>comet parameter: num_output_lines</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: num_output_lines</h2>
+
+ <ul>
+ <li>This parameter controls the number of search result
+ hits (peptides) that are reported for each spectrum query.
+ <li>If you are only interested in seeing one top hit each
+ per query, set this value to 1.
+ <li>This parameter value cannot be larger than the value
+ entered for "<a href="num_results.php">num_results</a>"
+ which itself is limited to a maximum value of 100.
+ <li>This parameter does not apply to the text output as
+ defined by "<a href="output_txtfile.php">output_txtfile</a>".
+ <li>Valid values are any positive integer 1 or greater.
+ <li>If a value less than 1 is entered, this parameter is set to 1.
+ <li>The default value is "10" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>num_output_lines = 1</tt>
+ <br><tt>num_output_lines = 5</tt>
+ <br><tt>num_output_lines = 10</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/num_results.html b/doc/user/comet-options/num_results.html
new file mode 100644
index 0000000..8cffff2
--- /dev/null
+++ b/doc/user/comet-options/num_results.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: num_results</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: num_results</h2>
+
+ <ul>
+ <li>This parameter controls the number of peptide search results that
+ are stored internally.
+ <li>Depending on what post-processing tools are used, one may want to
+ set this to the same value as <a href="num_output_lines.php">num_output_lines</a>.
+ <li>When this parameter is set to a value greater than
+ <a href="num_output_lines.php">num_output_lines</a>, it allows
+ the SpRank value to span a larger range which may be helpful for
+ tools like PeptideProphet or Percolator (not likely though).
+ <li>Valid values are any integer between 1 and 100.
+ <li>The default value is "100" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>num_results = 50</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/num_threads.html b/doc/user/comet-options/num_threads.html
new file mode 100644
index 0000000..2eb596f
--- /dev/null
+++ b/doc/user/comet-options/num_threads.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: num_threads</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: num_threads</h2>
+
+ <ul>
+ <li>This parameter controls the number of processing threads that will be spawned for a search.
+ Ideally the number of threads is set to the same value as the number of CPU cores available.
+ <li>Valid values range for this parameter are numbers ranging from 0 to 64.
+ <li>A value of 0 will cause Comet to poll the system and launch the same number of threads
+ as CPU cores.
+ <li>To set an explicit thread count, enter any value between 1 and 64.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>num_threads = 0</tt>
+ <br><tt>num_threads = 8</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/output_outfiles.html b/doc/user/comet-options/output_outfiles.html
new file mode 100644
index 0000000..5c10786
--- /dev/null
+++ b/doc/user/comet-options/output_outfiles.html
@@ -0,0 +1,16 @@
+<html><head><title>comet parameter: output_outfiles</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_outfiles</h2>
+
+ <ul>
+ <li>Controls whether to output search results as individual .out files.
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_outfiles = 0</tt>
+ <br><tt>output_outfiles = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/output_pepxmlfile.html b/doc/user/comet-options/output_pepxmlfile.html
new file mode 100644
index 0000000..25980bd
--- /dev/null
+++ b/doc/user/comet-options/output_pepxmlfile.html
@@ -0,0 +1,16 @@
+<html><head><title>comet parameter: output_pepxmlfile</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_pepxmlfile</h2>
+
+ <ul>
+ <li>Controls whether to output search results in a pepXML file.
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_pepxmlfile = 0</tt>
+ <br><tt>output_pepxmlfile = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/output_percolatorfile.html b/doc/user/comet-options/output_percolatorfile.html
new file mode 100644
index 0000000..aca9843
--- /dev/null
+++ b/doc/user/comet-options/output_percolatorfile.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: output_percolatorfile</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_percolatorfile</h2>
+
+ <ul>
+ <li>Controls whether to output search results in a <a href="http://per-colator.com">Percolator's</a>
+ tab-delimited input format.
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ <li>The created file will have a ".tsv" file extension.
+ <li>This parameter replaces the now defunct "output_pinxmlfile".
+ </ul>
+
+ <p>Example:
+ <br><tt>output_percolatorfile = 0</tt>
+ <br><tt>output_percolatorfile = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/output_sqtfile.html b/doc/user/comet-options/output_sqtfile.html
new file mode 100644
index 0000000..5a18492
--- /dev/null
+++ b/doc/user/comet-options/output_sqtfile.html
@@ -0,0 +1,16 @@
+<html><head><title>comet parameter: output_sqtfile</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_sqtfile</h2>
+
+ <ul>
+ <li>Controls whether to output search results into an SQT file (.sqt).
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_sqtfile = 0</tt>
+ <br><tt>output_sqtfile = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/output_sqtstream.html b/doc/user/comet-options/output_sqtstream.html
new file mode 100644
index 0000000..8ed1505
--- /dev/null
+++ b/doc/user/comet-options/output_sqtstream.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: output_sqtstream</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_sqtstream</h2>
+
+ <ul>
+ <li>Controls whether to output search results to standard out
+ (i.e. to the screen unless otherwise directed) in SQT format.
+ <li>Just the search results (M and L lines and not any H lines)
+ are output to standard out.
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_sqtstream = 0</tt>
+ <br><tt>output_sqtstream = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/output_suffix.html b/doc/user/comet-options/output_suffix.html
new file mode 100644
index 0000000..dca2425
--- /dev/null
+++ b/doc/user/comet-options/output_suffix.html
@@ -0,0 +1,25 @@
+<html><head><title>comet parameter: output_suffix</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_suffix</h2>
+
+ <ul>
+ <li>This parameter specifies the suffix string that is appended to
+ the base output name for the pep.xml, pin.xml, txt and sqt output files.
+ <li>Use this parameter to give output files a unique suffix base name.
+ <li>For example, if the output_suffix parameter is set to
+ "output_suffix = _000", then a search of the file base.mzXML
+ will generate output files named base_000.pep.xml, base_000.pin.xml,
+ base_000.txt, and/or base_000.sqt.
+ <li>Note that using this parameter could break downstream tools that
+ expect the output base name to be the same as the input file base name.
+ <li>The default value is blank if this parameter is missing i.e.
+ base.mzXML will generate base.pep.xml.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_suffix = </tt>
+ <br><tt>output_suffix = _some_suffix</tt>
+ <br><tt>output_suffix = any_string_you_want_without_spaces</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/output_txtfile.html b/doc/user/comet-options/output_txtfile.html
new file mode 100644
index 0000000..390b363
--- /dev/null
+++ b/doc/user/comet-options/output_txtfile.html
@@ -0,0 +1,52 @@
+<html><head><title>comet parameter: output_txtfile</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: output_txtfile</h2>
+
+ <ul>
+ <li>Controls whether to output search results into a tab-delimited text file (.txt).
+ <li>Valid values are 0 (do not output) or 1 (output).
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>output_txtfile = 0</tt>
+ <br><tt>output_txtfile = 1</tt>
+
+ <p>Here's snippet of sample output below. The first line of the output file is a
+ header line which contains the Comet version, search start time/date, and search
+ database. The second line contains the column headers. Only the top hit for each
+ search is reported in the text output; the parameter
+ "<a href="num_output_lines.php">num_output_lines</a>" does not apply to the text output.
+
+<pre>CometVersion 2013.02 rev. 0 100 10/04/2013, 08:37:09 AM /net/pr/vol1/ProteomicsResource/dbase/SGD/SGDyeast.fasta.20101117
+scan charge exp_neutral_mass calc_neutral_mass e-value xcorr delta_cn sp_score ions_matched ions_total plain_peptide peptide prev_aa next_aa protein duplicate_protein_count
+5129 1 599.9698 602.3136 1.73E+01 0.6847 0.0995 44.3 4 8 DAKNR R.DAKNR.I R I YML019W 0
+5385 1 601.3290 603.3228 1.73E+01 0.5316 0.1905 70.9 3 8 NLTEK R.NLTEK.T R T YBL024W 1
+5496 1 601.3358 599.3755 1.67E+01 0.4527 0.1315 6.6 2 8 VVNIR R.VVNIR.L R L YJL012C 0
+5430 1 602.3329 605.2591 2.33E+01 0.4222 0.0854 73.2 4 8 DVGCR K.DVGCR.I K I YER085C 0
+5829 1 616.4184 615.3414 5.26E+01 0.4321 0.0658 8.5 2 8 KPPMK -.KPPM*K.Q - Q DECOY__YBR025C 2
+
+</pre></p>
+
+ <p>Comet's text output is different if Comet was compiled for
+ <a href="noble.gs.washington.edu/proj/crux/">Crux</a> compatibility.
+ Here's the example text output if you are running Comet in Crux.
+ Note that up to 5 hits per spectrum are reported and there is just
+ a single column header line.
+
+<pre>scan charge spectrum precursor m/z spectrum neutral mass matches/spectrum peptide mass e-value xcorr score xcorr rank delta_cn sp score sp rank b/y ions matched b/y ions total sequence flanking aa protein id
+5129 1 600.9771 599.9698 5440 602.3136 1.73E+01 0.6847 1 0.0995 44.3 19 4 8 DAKNR RI YML019W
+5129 1 600.9771 599.9698 5440 602.3249 1.96E+01 0.6714 2 0.1016 46.1 17 5 10 RTGGGR RI YGR054W
+5129 1 600.9771 599.9698 5440 602.3136 1.99E+01 0.6698 3 0.1131 77.6 6 5 8 NISNR KV YMR033W
+5129 1 600.9771 599.9698 5440 601.2820 2.16E+01 0.6612 4 0.1240 38.6 22 4 8 EPSNR RD YPL161C
+5129 1 600.9771 599.9698 5440 600.3231 0.00E+00 0.6532 5 0.1389 104.6 3 6 8 IESPR KM YLL021W
+5385 1 602.3363 601.3290 6518 603.3228 1.73E+01 0.5316 1 0.1905 70.9 2 3 8 NLTEK RT YBL024W
+5385 1 602.3363 601.3290 6518 600.3707 1.86E+01 0.5249 2 0.2022 31.0 8 3 8 ARNIK KT DECOY_YIL159W
+5385 1 602.3363 601.3290 6518 602.3249 2.02E+01 0.5173 3 0.2134 47.4 4 3 8 ARNSR KI DECOY_YLL040C
+5385 1 602.3363 601.3290 6518 601.3184 2.19E+01 0.5100 4 0.2148 7.1 19 2 10 GAVNNK KS DECOY_YMR125W
+5385 1 602.3363 601.3290 6518 599.4119 0.00E+00 0.5091 5 0.2148 28.3 9 3 8 ALLKR RI YML107C
+</pre></p>
+
+
+</body></html>
diff --git a/doc/user/comet-options/override_charge.html b/doc/user/comet-options/override_charge.html
new file mode 100644
index 0000000..b93b267
--- /dev/null
+++ b/doc/user/comet-options/override_charge.html
@@ -0,0 +1,25 @@
+<html><head><title>comet parameter: override_charge</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: override_charge</h2>
+
+ <ul>
+ <li>This parameter specifies the whether to override existing precursor
+ charge state information when present in the files with the charge
+ range specified by the
+ "<a href="precursor_charge.php">precursor_charge</a>" parameter.
+ <li>Valid values are 0 and 1.
+ <li>To keep any known charge state values in the input files,
+ set the value to 0.
+ <li>To ignore any known charge values in the input files and instead
+ use the charge state range specified by the
+ "<a href="precursor_charge.php">precursor_charge</a>" parameter,
+ set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>override_charge = 0</tt>
+ <br><tt>override_charge = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/peptide_mass_tolerance.html b/doc/user/comet-options/peptide_mass_tolerance.html
new file mode 100644
index 0000000..d795294
--- /dev/null
+++ b/doc/user/comet-options/peptide_mass_tolerance.html
@@ -0,0 +1,17 @@
+<html><head><title>comet parameter: peptide_mass_tolerance</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: peptide_mass_tolerance</h2>
+
+ <ul>
+ <li>This parameter controls the mass tolerance value.
+ <li>The mass tolerance is set at +/- the specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0 tolerance.
+ <li>The units of the mass tolerance is controlled by the parameter "<a href="peptide_mass_units.php">peptide_mass_units</a>".
+ <li>The default value is "1.0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>peptide_mass_tolerance = 3.0</tt>
+ <br><tt>peptide_mass_tolerance = 10.0</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/peptide_mass_units.html b/doc/user/comet-options/peptide_mass_units.html
new file mode 100644
index 0000000..f2483a2
--- /dev/null
+++ b/doc/user/comet-options/peptide_mass_units.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: peptide_mass_units</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: peptide_mass_units</h2>
+
+ <ul>
+ <li>This parameter controls the units applied to the <a href="peptide_mass_tolerance.php">peptide_mass_tolerance</a> parameter.
+ <li>Valid values are 0, 1, and 2.
+ <li>Set this parameter to 0 for amu.
+ <li>Set this parameter to 1 for mmu.
+ <li>Set this parameter to 2 for ppm.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>peptide_mass_units = 0</tt>
+ <br><tt>peptide_mass_units = 1</tt>
+ <br><tt>peptide_mass_units = 2</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/precursor_charge.html b/doc/user/comet-options/precursor_charge.html
new file mode 100644
index 0000000..752671a
--- /dev/null
+++ b/doc/user/comet-options/precursor_charge.html
@@ -0,0 +1,30 @@
+<html><head><title>comet parameter: precursor_charge</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: precursor_charge</h2>
+
+ <ul>
+ <li>This parameter specifies the precursor charge range to search.
+ <li>This parameter expects to integer values as input.
+ <li>If the first input value is 0 then this parameter is ignored and all charge
+ states are searched
+ <li>Only in the case where a spectrum does not have a precursor charge will all charges
+ in the specified charge range be searched.
+ <li>If the first input value is not 0 then all charge states between (and inclusive of)
+ the first and second input values are searched. Again, only for those spectra with no
+ specified precursor charge state.
+ <li>If a precursor charge is present for a particular spectrum, this parameter will
+ not override that charge state and that spectrum will always be searched.
+ <li>With the default "0 0" values and a spectrum with no precursor charge, Comet will
+ either search the spectrum as a 1+ or a 2+/3+.
+ <li>The default value is "0 0" if this parameter is missing.
+
+ </ul>
+
+ <p>Example:
+ <br><tt>precursor_charge = 0 0</tt> <i>search all charge ranges</i>
+ <br><tt>precursor_charge = 0 2</tt> <i>search all charge ranges (because first entry is 0)</i>
+ <br><tt>precursor_charge = 2 6</tt> <i>search 2+ to 6+ precursors</i>
+ <br><tt>precursor_charge = 3 3</tt> <i>search 3+ precursors</i>
+
+</body></html>
diff --git a/doc/user/comet-options/print_expect_score.html b/doc/user/comet-options/print_expect_score.html
new file mode 100644
index 0000000..122ad18
--- /dev/null
+++ b/doc/user/comet-options/print_expect_score.html
@@ -0,0 +1,24 @@
+<html><head><title>comet parameter: print_expect_score</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: print_expect_score</h2>
+
+ <ul>
+ <li>A boolean flag this determines whether or not the expectation
+ score (E-value) is reported in .out and SQT formats. Note that the
+ E-value is always reported in pepXML output.
+ <li>This parameter is only pertinant for results reported in .out and SQT formats.
+ <li>If expect scores are chosen to be reported (i.e. value set to 1), they will replace
+ the number reported for the traditional "spscore" i.e. "spscore" will
+ be replaced by an E-value. Also an expectation value histogram will
+ be output at the end of each .out file; this histogram is not present
+ for SQT output.
+ <li>Valid values are 0 and 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>print_expect_score = 0</tt>
+ <br><tt>print_expect_score = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/remove_precursor_peak.html b/doc/user/comet-options/remove_precursor_peak.html
new file mode 100644
index 0000000..dab6a7a
--- /dev/null
+++ b/doc/user/comet-options/remove_precursor_peak.html
@@ -0,0 +1,25 @@
+<html><head><title>comet parameter: remove_precursor_peak</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: remove_precursor_peak</h2>
+
+ <ul>
+ <li>This parameter controls excluding/removing any precursor signals
+ from the input MS/MS spectrum.
+ <li>An input value of 0 will not perform any precursor removal.
+ <li>An input value of 1 will remove all peaks around the precursor m/z.
+ <li>An input value of 2 will remove all charge reduced precursor peaks
+ as expected to be present for ETD/ECD spectra.
+ <li>This parameter works in conjuction with
+ <a href="remove_precursor_tolerance.php">remove_precursor_tolerance</a>
+ to specify the tolerance around each precuror m/z that will be removed.
+ <li>Valid values are 0, 1, and 2.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>remove_precursor_peak = 0</tt>
+ <br><tt>remove_precursor_peak = 1</tt>
+ <br><tt>remove_precursor_peak = 2</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/remove_precursor_tolerance.html b/doc/user/comet-options/remove_precursor_tolerance.html
new file mode 100644
index 0000000..857d504
--- /dev/null
+++ b/doc/user/comet-options/remove_precursor_tolerance.html
@@ -0,0 +1,19 @@
+<html><head><title>comet parameter: remove_precursor_tolerance</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: remove_precursor_tolerance</h2>
+
+ <ul>
+ <li>This parameter specifies the mass tolerance around each precursor m/z
+ that would be removed when the <a href="remove_precursor_peak.php">remove_precursor_peak</a>
+ option is invoked.
+ <li>The mass tolerance units is in Da (or Th if you prefer).
+ <li>Any non-negative, non-zero floating point number is valid.
+ <li>The default value is "1.5" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>remove_precursor_tolerance = 0.75</tt>
+ <br><tt>remove_precursor_tolerance = 1.5</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/require_variable_mod.html b/doc/user/comet-options/require_variable_mod.html
new file mode 100644
index 0000000..eeef8ed
--- /dev/null
+++ b/doc/user/comet-options/require_variable_mod.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: require_variable_mod</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: require_variable_mod</h2>
+
+ <ul>
+ <li>This parameter takes in one input value.
+ <li>The input value is an integer that controls whether the analyzed peptides
+ must contain at least one variable modification i.e. force all reported peptides
+ to have a variable modifiation.
+ <ul>
+ <li>0 = consider both modified and unmodified peptides (default)
+ <li>1 = analyze only peptides that contain a variable modification
+ </ul>
+ </ul>
+
+ <p>Example:
+ <br><tt>require_variable_mod = 0</tt> ... <i>modifications not required</i>
+ <br><tt>require_variable_mod = 1</tt> ... <i>peptides must contain a variable modification</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/runall b/doc/user/comet-options/runall
new file mode 100644
index 0000000..b2ec284
--- /dev/null
+++ b/doc/user/comet-options/runall
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+
+
+# The parameters files are in the binary release of comet, in a file
+# called paramters_<release>.zip.
+
+to_remove=`ls *.html | grep -v index.html | grep -v header.html | grep -v footer.html | grep -v topmenu.html | grep -v head.html`
+
+rm $to_remove
+
+rm -rf ~/tmp
+mkdir ~/tmp
+svn checkout svn://svn.code.sf.net/p/comet-ms/code/www/parameters/parameters_201501 ~/tmp/comet-params
+
+files=`ls ~/tmp/comet-params/*.php`
+
+for file in $files; do
+ if [[ -e $file ]]; then # Some symlinks point to missing files.
+ echo Converting $file
+ basename=`basename $file`
+ ./convertCometPHPs.py $file > ${basename%.php}.html
+ fi
+done
diff --git a/doc/user/comet-options/sample_enzyme_number.html b/doc/user/comet-options/sample_enzyme_number.html
new file mode 100644
index 0000000..14beb94
--- /dev/null
+++ b/doc/user/comet-options/sample_enzyme_number.html
@@ -0,0 +1,22 @@
+<html><head><title>comet parameter: sample_enzyme_number</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: sample_enzyme_number</h2>
+
+ <ul>
+ <li>This parameter is relevant only for pepXML output i.e. when
+ <a href="output_pepxmlfile.php">output_pepxmlfile</a> is set to 1.
+ <li>The pepXML format encodes the enzyme that is applied to the sample
+ i.e. trypsin. This enzyme is written to the "sample_enzyme" element.
+ <li>The sample enzyme could be different from the search enzyme i.e.
+ the sample enzyme is "trypsin" yet the search enzyme is "No-enzyme"
+ for a non-specific search. Hence the need for this separate parameter.
+ <li>Valid values are any integer represented in the enzyme list.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>sample_enzyme_number = 1</tt>
+ <br><tt>sample_enzyme_number = 3</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/scan_range.html b/doc/user/comet-options/scan_range.html
new file mode 100644
index 0000000..28f0989
--- /dev/null
+++ b/doc/user/comet-options/scan_range.html
@@ -0,0 +1,23 @@
+<html><head><title>comet parameter: scan_range</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: scan_range</h2>
+
+ <ul>
+ <li>Defines the scan range to search. Only spectra within (and inclusive) of the specified
+ scan range are searched.
+ <li>This parameter works only with mzXML and mzML inputs files.
+ <li>Two digits are specified for this parameter. The first digit is the start scan and the
+ second digit is the end scan.
+ <li>When the start scan is set to 0, this parameter setting is ignored irrespective of what
+ the end scan is set to.
+ <li>When the end scan is less than the start scan, this parameter setting is ignored.
+ <li>The default value is "0 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>scan_range = 0 0</tt> <i>search all scans</i>
+ <br><tt>scan_range = 0 1000</tt> <i>search all scans (because first entry is 0)</i>
+ <br><tt>scan_range = 1000 1500</tt> <i>search only scans 1000 to 1500</i>
+
+</body></html>
diff --git a/doc/user/comet-options/search_enzyme_number.html b/doc/user/comet-options/search_enzyme_number.html
new file mode 100644
index 0000000..09da2d8
--- /dev/null
+++ b/doc/user/comet-options/search_enzyme_number.html
@@ -0,0 +1,46 @@
+<html><head><title>comet parameter: search_enzyme_number</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: search_enzyme_number</h2>
+
+ <ul>
+ <li>The search enzyme is specified by this parameter.
+ <li>The list of search enzymes is specified at the end of the comet.params file
+ beginning with the line <tt>[COMET_ENZYME_INFO]</tt>. The actual enzyme list and
+ digestion parameters are read here. So one can edit/add/delete enzyme definitions
+ simply be changing the enzyme information.
+ <li>This parameter works in conjection with the <a href="num_enzyme_termini.php">num_enzyme_termini</a>
+ parameter to define the cleavage rule for fully-digested vs. semi-digested search options.
+ <li>This parameter works in conjection with the <a href="allowed_missed_cleavage.php">allowed_missed_cleavage</a>
+ parameter to define the miss cleavage rule.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>search_enzyme_number = 0</tt> <i>typically no-enzyme</i>
+ <br><tt>search_enzyme_number = 1</tt> <i>typically trypsin</i></p>
+
+
+ <li>The format of the parameter definition looks like the following:
+ <p><pre>[COMET_ENZYME_INFO]
+0. No_enzyme 0 - -
+1. Trypsin 1 KR P
+2. Trypsin/P 1 KR -
+3. Lys_C 1 K P
+4. Lys_N 0 K -
+5. Arg_C 1 R P
+6. Asp_N 0 D -
+7. CNBr 1 M -
+8. Glu_C 1 DE P
+9. PepsinA 1 FL P
+10. Chymotrypsin 1 FWYL P</pre></p>
+
+ <p>The first column of the parameter definition is the enzyme number. This number list
+ must start from 0 and sequentially increase by 1. The second column is the enzyme name;
+ no spaces are allowed in this name field. The third column is the digestion "sense"
+ i.e. a value of "0" specifies cleavage N-teriminal to (before) the specified residues
+ in column 4 and a value of "1" specifies cleavage C-terminal to (after) the specified
+ residues in column 4. Column 4 contains the residue(s) that the enzyme cleaves at.
+ Column 5 contains the flanking residue(s) that negate cleavage.
+
+</body></html>
diff --git a/doc/user/comet-options/show_fragment_ions.html b/doc/user/comet-options/show_fragment_ions.html
new file mode 100644
index 0000000..bb1f1cc
--- /dev/null
+++ b/doc/user/comet-options/show_fragment_ions.html
@@ -0,0 +1,20 @@
+<html><head><title>comet parameter: show_fragment_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: show_fragment_ions</h2>
+
+ <ul>
+ <li>This parameter affects .out files only i.e.
+ <a href="output_outfiles.php">output_outfiles</a> set to 1.
+ <li>This parameter controls whether or not the theoretical
+ fragment ion masses for the top peptide hit are calculated
+ and dislayed at the end of an .out file.
+ <li>Valid values are 0 and 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>show_fragment_ions = 0</tt>
+ <br><tt>show_fragment_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/skip_researching.html b/doc/user/comet-options/skip_researching.html
new file mode 100644
index 0000000..4a2957b
--- /dev/null
+++ b/doc/user/comet-options/skip_researching.html
@@ -0,0 +1,25 @@
+<html><head><title>comet parameter: skip_researching</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: skip_researching</h2>
+
+ <ul>
+ <li>This parameter is valid only when <a href="output_outfiles.php">output_outfiles</a> is set
+ to 1 and each of
+ <a href="output_pepxmlfile.php">output_pepxmlfile</a>,
+ <a href="output_sqtfile.php">output_sqtfile</a>, and
+ <a href="output_sqtstream.php">output_sqtstream</a> are set to 0.
+ <li>When .out files only are set to be exported, this parameter will look to see if
+ an .out file already exists for each query spectrum. If so, it will not re-search
+ that particular spectrum.
+ <li>When set to 0, all spectra are re-searched. When set to 1, the search is skipped
+ for those spectra where an .out file already exists.
+ <li>Valid values are 0 and 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>skip_researching = 0</tt>
+ <br><tt>skip_researching = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/spectrum_batch_size.html b/doc/user/comet-options/spectrum_batch_size.html
new file mode 100644
index 0000000..760fe14
--- /dev/null
+++ b/doc/user/comet-options/spectrum_batch_size.html
@@ -0,0 +1,28 @@
+<html><head><title>comet parameter: spectrum_batch_size</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: spectrum_batch_size</h2>
+
+ <ul>
+ <li>When this parameter is set to a non-zero value, say 5000, this causes Comet
+ to load and search about 5000 spectra at a time, looping through sets of 5000
+ spectra until all data have been analyzed.
+ <li>This parameter was implemented to simplify searching large datasets that
+ might not fit into memory if searched all at once.
+ <li>The loaded batch sizes might be a little larger than the specified parameter
+ value (i.e. 5014 spectra loaded when the parameter is set to 5000) due to both
+ threading and potential charge state considerations when precursor charge state
+ is not known.
+ <li>Valid values are 0 or any positive integer.
+ <li>Set this parameter to 0 to load and search all spectra at once.
+ <li>Set this parameter to any other positive integer to loop through searching
+ this number of spectra at a time until all spectra have been analyzed.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>spectrum_batch_size = 0</tt>
+ <br><tt>spectrum_batch_size = 1000</tt>
+ <br><tt>spectrum_batch_size = 5000</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/theoretical_fragment_ions.html b/doc/user/comet-options/theoretical_fragment_ions.html
new file mode 100644
index 0000000..60b57d4
--- /dev/null
+++ b/doc/user/comet-options/theoretical_fragment_ions.html
@@ -0,0 +1,32 @@
+<html><head><title>comet parameter: theoretical_fragment_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: theoretical_fragment_ions</h2>
+
+ <ul>
+ <li>This parameter specifies how theoretical fragment ion peaks are
+ represented.
+ <li>Even though Comet does not generate/store a theoretical spectrum,
+ it does calculate fragment ion masses and this parameter controls how
+ the acquired spectrum intensities at these theoretical mass locations
+ contribute to the correlation score.
+ <li>A value of 0 indicates that the fast correlation score will be
+ a sum of the intensities at each theortical fragment mass bin and half
+ the intensity of each flanking bin.
+ <li>A value of 1 indicates that the fast correlation score will be
+ the sum of the intensities at each theoretical fragment mass bin.
+ <li>For extremely coarse <a href="fragment_bin_tol.php">fragment_bin_tol</a>
+ values such as the historical ~1 Da bins, a theoretical_fragment_ions
+ value of 1 is optimal.
+ <li>But for narrower bins, such as ~0.3 for ion trap data or ~0.03 for
+ high-res MS/MS spectra, a value of 0 is optimal to incorporate
+ intensities from the flanking bins.
+ <li>Allowed values are 0 or 1.
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>theoretical_fragment_ions = 0</tt>
+ <br><tt>theoretical_fragment_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/topmenu.html b/doc/user/comet-options/topmenu.html
new file mode 100644
index 0000000..62b274f
--- /dev/null
+++ b/doc/user/comet-options/topmenu.html
@@ -0,0 +1 @@
+</body></html>
diff --git a/doc/user/comet-options/use_A_ions.html b/doc/user/comet-options/use_A_ions.html
new file mode 100644
index 0000000..2eb9a48
--- /dev/null
+++ b/doc/user/comet-options/use_A_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_A_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_A_ions</h2>
+
+ <ul>
+ <li>Controls whether or not A-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use A-ions, set the value to 0.
+ <li>To use A-ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_A_ions = 0</tt>
+ <br><tt>use_A_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/use_B_ions.html b/doc/user/comet-options/use_B_ions.html
new file mode 100644
index 0000000..ad78694
--- /dev/null
+++ b/doc/user/comet-options/use_B_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_B_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_B_ions</h2>
+
+ <ul>
+ <li>Controls whether or not B-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use B-ions, set the value to 0.
+ <li>To use B-ions, set the value to 1.
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_B_ions = 0</tt>
+ <br><tt>use_B_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/use_C_ions.html b/doc/user/comet-options/use_C_ions.html
new file mode 100644
index 0000000..c2a7eb6
--- /dev/null
+++ b/doc/user/comet-options/use_C_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_C_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_C_ions</h2>
+
+ <ul>
+ <li>Controls whether or not C-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use C-ions, set the value to 0.
+ <li>To use C-ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_C_ions = 0</tt>
+ <br><tt>use_C_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/use_NL_ions.html b/doc/user/comet-options/use_NL_ions.html
new file mode 100644
index 0000000..fe88f3d
--- /dev/null
+++ b/doc/user/comet-options/use_NL_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_NL_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_NL_ions</h2>
+
+ <ul>
+ <li>Controls whether or not neutral loss ions (-NH3 and -H2O from b- and y-ions) are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use neutral loss ions, set the value to 0.
+ <li>To use neutral loss ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_NL_ions = 0</tt>
+ <br><tt>use_NL_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/use_X_ions.html b/doc/user/comet-options/use_X_ions.html
new file mode 100644
index 0000000..cf91b63
--- /dev/null
+++ b/doc/user/comet-options/use_X_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_X_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_X_ions</h2>
+
+ <ul>
+ <li>Controls whether or not X-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use X-ions, set the value to 0.
+ <li>To use X-ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_X_ions = 0</tt>
+ <br><tt>use_X_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/use_Y_ions.html b/doc/user/comet-options/use_Y_ions.html
new file mode 100644
index 0000000..83ed9dc
--- /dev/null
+++ b/doc/user/comet-options/use_Y_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_Y_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_Y_ions</h2>
+
+ <ul>
+ <li>Controls whether or not Y-ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use Y-ions, set the value to 0.
+ <li>To use Y-ions, set the value to 1.
+ <li>The default value is "1" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_Y_ions = 0</tt>
+ <br><tt>use_Y_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/use_Z_ions.html b/doc/user/comet-options/use_Z_ions.html
new file mode 100644
index 0000000..6e9c5f2
--- /dev/null
+++ b/doc/user/comet-options/use_Z_ions.html
@@ -0,0 +1,18 @@
+<html><head><title>comet parameter: use_Z_ions</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_Z_ions</h2>
+
+ <ul>
+ <li>Controls whether or not Z-dot ions are considered in the search.
+ <li>Valid values are 0 and 1.
+ <li>To not use Z-dot ions, set the value to 0.
+ <li>To use Z-dot ions, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_Z_ions = 0</tt>
+ <br><tt>use_Z_ions = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/use_sparse_matrix.html b/doc/user/comet-options/use_sparse_matrix.html
new file mode 100644
index 0000000..ef9f1e4
--- /dev/null
+++ b/doc/user/comet-options/use_sparse_matrix.html
@@ -0,0 +1,26 @@
+<html><head><title>comet parameter: use_sparse_matrix</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: use_sparse_matrix</h2>
+
+ <ul>
+ <li>Controls whether or not internal sparse matrix data representation is used.
+ <li>The sparse matrix data representation will use a <em>significantly</em> smaller amount
+ of memory/RAM for small <a href="fragment_bin_tol.php">fragment_bin_tol</a> settings such
+ as 0.05 or 0.01. We're talking going from tens of GB (gigabytes) down to a few hundred
+ megabytes (MB)!
+ <li>In this release, the sparse matrix searches will always be slower than the classical
+ data representation (i.e. use_sparse_matrix = 0). So it should be used only when
+ memory is an issue. Alternately, the <a href="spectrum_batch_size.php">spectrum_batch_size</a>
+ parameter can also be used to mitigate memory issues.
+ <li>Valid values are 0 and 1.
+ <li>To not use sparse matrix, set the value to 0.
+ <li>To use sparse matrix, set the value to 1.
+ <li>The default value is "0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>use_sparse_matrix = 0</tt>
+ <br><tt>use_sparse_matrix = 1</tt>
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod01.html b/doc/user/comet-options/variable_mod01.html
new file mode 100644
index 0000000..4940708
--- /dev/null
+++ b/doc/user/comet-options/variable_mod01.html
@@ -0,0 +1,62 @@
+<html><head><title>comet parameter: variable_mod01</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod01</h2>
+
+ <ul>
+ <li>This parameter specifies the 1st of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies whichprotein terminus the distance constraint is applied to:
+ <ul>
+ <li>0 = protein N-terminus
+ <li>1 = protein C-terminus
+ <li>2 = peptide N-terminus
+ <li>3 = peptide C-terminus
+ </ul>
+ <li>The seventh entry specifies whether peptides are must contain this modification
+ <ul>
+ <li>0 = not forced to be present
+ <li>1 = modification is required
+ </ul>
+
+ </ul>
+ <li>In the output, this first modification is encoded with the character '*' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod01 = 15.9949 M 0 3 -1 0 0</tt>
+ <br><tt>variable_mod01 = 79.966331 STY 0 3 -1 0 0</tt> ... <i>possible phosphorylation on any S, T, Y residue</i>
+ <br><tt>variable_mod01 = 79.966331 STY 0 3 -1 0 1</tt> ... <i>force peptide IDs to contain at least one phosphorylation mod</i>
+ <br><tt>variable_mod01 = 42.010565 nK 0 3 -1 0 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod01 = 15.994915 n 0 3 0 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod01 = 28.0 c 0 3 8 1 0</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod01 = -17.026549 Q 0 1 0 2</tt> ... <i>cyclization of N-terminal glutamine to form pyroglutamic acid (elimination of NH3)</i>
+ <br><tt>variable_mod01 = -18.010565 E 0 1 0 2</tt> ... <i>cyclization of N-terminal glutamic acid to form pyroglutamic acid (elimination of H2O)</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod02.html b/doc/user/comet-options/variable_mod02.html
new file mode 100644
index 0000000..31107c7
--- /dev/null
+++ b/doc/user/comet-options/variable_mod02.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod02</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod02</h2>
+
+ <ul>
+ <li>This parameter specifies the 2nd of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '#' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod02 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod02 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod02 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod02 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod02 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod02 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod03.html b/doc/user/comet-options/variable_mod03.html
new file mode 100644
index 0000000..76b8f5d
--- /dev/null
+++ b/doc/user/comet-options/variable_mod03.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod03</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod03</h2>
+
+ <ul>
+ <li>This parameter specifies the 3rd of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '@' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod03 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod03 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod03 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod03 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod03 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod03 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod04.html b/doc/user/comet-options/variable_mod04.html
new file mode 100644
index 0000000..8548a34
--- /dev/null
+++ b/doc/user/comet-options/variable_mod04.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod04</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod04</h2>
+
+ <ul>
+ <li>This parameter specifies the 4th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '^' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod04 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod04 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod04 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod04 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod04 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod04 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod05.html b/doc/user/comet-options/variable_mod05.html
new file mode 100644
index 0000000..fa5d180
--- /dev/null
+++ b/doc/user/comet-options/variable_mod05.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod05</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod05</h2>
+
+ <ul>
+ <li>This parameter specifies the 5th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '~' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod05 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod05 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod05 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod05 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod05 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod05 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod06.html b/doc/user/comet-options/variable_mod06.html
new file mode 100644
index 0000000..cad626d
--- /dev/null
+++ b/doc/user/comet-options/variable_mod06.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod06</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod06</h2>
+
+ <ul>
+ <li>This parameter specifies the 6th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '$' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod06 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod06 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod06 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod06 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod06 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod06 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod07.html b/doc/user/comet-options/variable_mod07.html
new file mode 100644
index 0000000..c976fb1
--- /dev/null
+++ b/doc/user/comet-options/variable_mod07.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod07</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod07</h2>
+
+ <ul>
+ <li>This parameter specifies the 7th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '%' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod07 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod07 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod07 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod07 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod07 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod07 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod08.html b/doc/user/comet-options/variable_mod08.html
new file mode 100644
index 0000000..34aae4e
--- /dev/null
+++ b/doc/user/comet-options/variable_mod08.html
@@ -0,0 +1,48 @@
+<html><head><title>comet parameter: variable_mod08</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod08</h2>
+
+ <ul>
+ <li>This parameter specifies the 8th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '!' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod08 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod08 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod08 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod08 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod08 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod08 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/doc/user/comet-options/variable_mod09.html b/doc/user/comet-options/variable_mod09.html
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+<html><head><title>comet parameter: variable_mod09</title>
+<link href="../crux.css" rel="styleSheet" type="text/css">
+</title><body>
+<h2>Comet parameter: variable_mod09</h2>
+
+ <ul>
+ <li>This parameter specifies the 9th of 9 variable modifications.
+ <li>There are 6 entries/settings that are associated with this parameter:
+ <ul>
+ <li>The first entry is a decimal value specifying the modification mass difference.
+ <li>The second entry is the residue(s) that the modifications are possibly applied to.
+ If more than a single residue is modified by the same mass difference, list them
+ all as a string. Use 'n' for N-terminal modfication and 'c' for C-terminal modification.
+ <li>The third entry is a integer 0 or 1 to specify whether the modification is a
+ variable modification (0) or a binary modification (1).
+ <ul>
+ <li>A variable modification analyzes all permutations of modified and unmodified
+ residues.
+ <li>A binary modification analyzes peptides where all residues are either
+ modified or all residues are not modified.
+ </ul>
+ <li>The fourth entry is an integer specifying the maximum number of modified residues
+ possible in a peptide for this modification entry.
+ <li>The fifth entry specifies the distance the modification is applied to from the
+ respective protein terminus:
+ <ul>
+ <li>-1 = no distance contraint
+ <li>0 = only applies to terminal residue
+ <li>1 = only applies to terminal residue and next residue
+ <li>2 = only applies to terminal residue through next 2 residues
+ <li><i>N</i> = only applies to terminal residue through next <i>N</i> residues where <i>N</i> is a positive integer
+ </ul>
+ <li>The sixth entry specifies which protein terminus the distance constraint is applied to N-terminus (0) or C-terminus (1).
+ </ul>
+ <li>In the output, this first modification is encoded with the character '+' in the peptide string.
+ <li>The default value is "0.0 null 0 4 -1 0" if this parameter is missing.
+ </ul>
+
+ <p>Example:
+ <br><tt>variable_mod09 = 15.9949 M 0 3 -1 0</tt>
+ <br><tt>variable_mod09 = 79.966331 STY 0 3 -1 0</tt>
+ <br><tt>variable_mod09 = 42.010565 nK 0 3 -1 0</tt> ... <i>acetylation mod to lysine and N-terminus of all peptides</i>
+ <br><tt>variable_mod09 = 15.994915 n 0 3 0 0</tt> ... <i>oxidation of protein's N-terminus</i>
+ <br><tt>variable_mod09 = 28.0 c 0 3 8 1</tt> ... <i>modification applied to C-terminus as lon as the C-term residue is one of last 9 residues in protein</i>
+ <br><tt>variable_mod09 = -17.02549 Q 0 1 0 0</tt> ... <i>protein N-terminal Q eliminating NH3 to form N-terminal pyrolidone carboxylic acid</i>
+
+
+</body></html>
diff --git a/doc/user/comet.html b/doc/user/comet.html
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+<!DOCTYPE html>
+<html>
+<head>
+<title>comet</title>
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+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>comet</h1>
+<h2>Usage:</h2>
+<p><code>crux comet [options] <input spectra>+ <database_name></code></p>
+<h2>Description:</h2>
+<p>This command searches a protein database with a set of spectra, assigning peptide sequences to the observed spectra. This search engine was developed by Jimmy Eng at the University of Washington Proteomics Resource.</p><p>Although its history goes back two decades, the Comet search engine was first made publicly available in August 2012 on SourceForge. Comet is multithreaded and supports multiple input and output formats.</p><blockquote><a href="http://onlinelibrary.wiley.com/doi/10.1 [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>input spectra+</code> – The name of the file from which to parse the spectra. Valid formats include mzXML, mzML, mz5, raw, ms2, and cms2. Files in mzML or mzXML may be compressed with gzip. RAW files can be parsed only under windows and if the appropriate libraries were included at compile time.</li>
+ <li><code>database_name</code> – A full or relative path to the sequence database, in FASTA format, to search. Example databases include RefSeq or UniProt. The database can contain amino acid sequences or nucleic acid sequences. If sequences are amino acid sequences, set the parameter "nucleotide_reading_frame = 0". If the sequences are nucleic acid sequences, you must instruct Comet to translate these to amino acid sequences. Do this by setting nucleotide_reading_frame" to a va [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>comet.target.txt</code> – a tab-delimited text file containing the target PSMs. See <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>comet.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>comet.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Database</h3>
+<ul>
+ <li class="nobullet"><code>--decoy_search <integer></code> – 0=no, 1=concatenated search, 2=separate search. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>CPU threads</h3>
+<ul>
+ <li class="nobullet"><code>--num_threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Masses</h3>
+<ul>
+ <li class="nobullet"><code>--peptide_mass_tolerance <float></code> – Controls the mass tolerance value. The mass tolerance is set at +/- the specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0 tolerance. The units of the mass tolerance is controlled by the parameter "peptide_mass_units". Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto_peptide_mass_tolerance false|warn|fail</code> – Automatically estimate optimal value for the peptide_mass_tolerancel parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--peptide_mass_units <integer></code> – 0=amu, 1=mmu, 2=ppm. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--mass_type_parent <integer></code> – 0=average masses, 1=monoisotopic masses. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--mass_type_fragment <integer></code> – 0=average masses, 1=monoisotopic masses. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--precursor_tolerance_type <integer></code> – 0=singly charged peptide mass, 1=precursor m/z. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--isotope_error <integer></code> – 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8 labeling). Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search enzyme</h3>
+<ul>
+ <li class="nobullet"><code>--search_enzyme_number <integer></code> – Specify a search enzyme from the end of the parameter file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--num_enzyme_termini <integer></code> – valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--allowed_missed_cleavage <integer></code> – Maximum value is 5; for enzyme search. Default = <code>2</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fragment ions</h3>
+<ul>
+ <li class="nobullet"><code>--fragment_bin_tol <float></code> – Binning to use on fragment ions. Default = <code>1.000507</code>.</li>
+ <li class="nobullet"><code>--fragment_bin_offset <float></code> – Offset position to start the binning (0.0 to 1.0). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--auto_fragment_bin_tol false|warn|fail</code> – Automatically estimate optimal value for the fragment_bin_tol parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--theoretical_fragment_ions <integer></code> – 0=default peak shape, 1=M peak only. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_A_ions <integer></code> – Controls whether or not A-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_B_ions <integer></code> – Controls whether or not B-ions are considered in the search (0 - no, 1 - yes). Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_C_ions <integer></code> – Controls whether or not C-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_X_ions <integer></code> – Controls whether or not X-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_Y_ions <integer></code> – Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes). Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_Z_ions <integer></code> – Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_NL_ions <integer></code> – 0=no, 1= yes to consider NH3/H2O neutral loss peak. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>mzXML/mzML parameters</h3>
+<ul>
+ <li class="nobullet"><code>--scan_range <string></code> – Start and scan scan range to search; 0 as first entry ignores parameter. Default = <code>0 0</code>.</li>
+ <li class="nobullet"><code>--precursor_charge <string></code> – Precursor charge range to analyze; does not override mzXML charge; 0 as first entry ignores parameter. Default = <code>0 0</code>.</li>
+ <li class="nobullet"><code>--override_charge <integer></code> – Specifies the whether to override existing precursor charge state information when present in the files with the charge range specified by the "precursor_charge" parameter. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--ms_level <integer></code> – MS level to analyze, valid are levels 2 or 3. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--activation_method ALL|CID|ECD|ETD|PQD|HCD|IRMPD</code> – Specifies which scan types are searched. Default = <code>ALL</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Miscellaneous parameters</h3>
+<ul>
+ <li class="nobullet"><code>--digest_mass_range <string></code> – MH+ peptide mass range to analyze. Default = <code>600.0 5000.0</code>.</li>
+ <li class="nobullet"><code>--num_results <integer></code> – Number of search hits to store internally. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--skip_researching <integer></code> – For '.out' file output only, 0=search everything again, 1=don't search if .out exists. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--max_fragment_charge <integer></code> – Set maximum fragment charge state to analyze (allowed max 5). Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--max_precursor_charge <integer></code> – Set maximum precursor charge state to analyze (allowed max 9). Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--nucleotide_reading_frame <integer></code> – 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--clip_nterm_methionine <integer></code> – 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum_batch_size <integer></code> – Maximum number of spectra to search at a time; 0 to search the entire scan range in one loop. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--decoy_prefix <string></code> – Specifies the prefix of the protein names that indicates a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--output_suffix <string></code> – Specifies the suffix string that is appended to the base output name for the pep.xml, pin.xml, txt and sqt output files. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--mass_offsets <string></code> – Specifies one or more mass offsets to apply. This value(s) are effectively subtracted from each precursor mass such that peptides that are smaller than the precursor mass by the offset value can still be matched to the respective spectrum. Default = <code><empty></code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Spectral processing</h3>
+<ul>
+ <li class="nobullet"><code>--minimum_peaks <integer></code> – Minimum number of peaks in spectrum to search. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--minimum_intensity <float></code> – Minimum intensity value to read in. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--remove_precursor_peak <integer></code> – 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--remove_precursor_tolerance <float></code> – +- Da tolerance for precursor removal. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--clear_mz_range <string></code> – For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range. Default = <code>0.0 0.0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Variable modifications</h3>
+<ul>
+ <li class="nobullet"><code>--variable_mod01 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod02 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod03 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod04 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod05 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod06 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod07 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod08 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod09 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--max_variable_mods_in_peptide <integer></code> – Specifies the total/maximum number of residues that can be modified in a peptide. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--require_variable_mod <integer></code> – Controls whether the analyzed peptides must contain at least one variable modification. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Static modifications</h3>
+<ul>
+ <li class="nobullet"><code>--add_Cterm_peptide <float></code> – Specifiy a static modification to the c-terminus of all peptides. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Nterm_peptide <float></code> – Specify a static modification to the n-terminus of all peptides. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Cterm_protein <float></code> – Specify a static modification to the c-terminal peptide of each protein. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Nterm_protein <float></code> – Specify a static modification to the n-terminal peptide of each protein. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_A_alanine <float></code> – Specify a static modification to the residue A. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_B_user_amino_acid <float></code> – Specify a static modification to the residue B. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_C_cysteine <float></code> – Specify a static modification to the residue C. Default = <code>57.021464</code>.</li>
+ <li class="nobullet"><code>--add_D_aspartic_acid <float></code> – Specify a static modification to the residue D. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_E_glutamic_acid <float></code> – Specify a static modification to the residue E. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_F_phenylalanine <float></code> – Specify a static modification to the residue F. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_G_glycine <float></code> – Specify a static modification to the residue G. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_H_histidine <float></code> – Specify a static modification to the residue H. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_I_isoleucine <float></code> – Specify a static modification to the residue I. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_J_user_amino_acid <float></code> – Specify a static modification to the residue J. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_K_lysine <float></code> – Specify a static modification to the residue K. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_L_leucine <float></code> – Specify a static modification to the residue L. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_M_methionine <float></code> – Specify a static modification to the residue M. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_N_asparagine <float></code> – Specify a static modification to the residue N. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_O_ornithine <float></code> – Specify a static modification to the residue O. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_P_proline <float></code> – Specify a static modification to the residue P. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Q_glutamine <float></code> – Specify a static modification to the residue Q. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_R_arginine <float></code> – Specify a static modification to the residue R. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_S_serine <float></code> – Specify a static modification to the residue S. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_T_threonine <float></code> – Specify a static modification to the residue T. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_U_selenocysteine <float></code> – Specify a static modification to the residue U. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_V_valine <float></code> – Specify a static modification to the residue V. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_W_tryptophan <float></code> – Specify a static modification to the residue W. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_X_user_amino_acid <float></code> – Specify a static modification to the residue X. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Y_tyrosine <float></code> – Specify a static modification to the residue Y. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Z_user_amino_acid <float></code> – Specify a static modification to the residue Z. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--output_sqtfile <integer></code> – 0=no, 1=yes write sqt file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--output_txtfile <integer></code> – 0=no, 1=yes write tab-delimited text file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--output_pepxmlfile <integer></code> – 0=no, 1=yes write pep.xml file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--output_percolatorfile <integer></code> – 0=no, 1=yes write percolator file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--output_outfiles <integer></code> – 0=no, 1=yes write .out files. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--print_expect_score <integer></code> – 0=no, 1=yes to replace Sp with expect in out & sqt. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--num_output_lines <integer></code> – num peptide results to show. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--show_fragment_ions <integer></code> – 0=no, 1=yes for out files only. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--sample_enzyme_number <integer></code> – Sample enzyme which is possibly different than the one applied to the search. Used to calculate NTT & NMC in pepXML output. Default = <code>1</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/commands/bullseye_standalone_to_crux.html b/doc/user/commands/bullseye_standalone_to_crux.html
new file mode 100644
index 0000000..382c4d2
--- /dev/null
+++ b/doc/user/commands/bullseye_standalone_to_crux.html
@@ -0,0 +1,74 @@
+ <table border="1">
+ <tr>
+ <td><b>Bullseye Parameter</b></td>
+ <td><b>crux bullseye parameter</b></td>
+ <td><b>datatype</b></td>
+ <td><b>default</b></td>
+
+ </tr>
+ <tr>
+ <td>-c</td>
+ <td>--max-persist</td>
+ <td>double</td>
+ <td>2.0</td>
+ </tr>
+
+ <tr>
+ <td>-e</td>
+ <td>--exact-match</td>
+ <td>boolean</td>
+ <td>false</td>
+ </tr>
+ <tr>
+
+ <td>-g</td>
+ <td>--gap-tolerance</td>
+ <td>integer</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>-m</td>
+
+ <td>--max-mass</td>
+ <td>double</td>
+ <td>8000.0</td>
+ </tr>
+ <tr>
+ <td>-n</td>
+ <td>--min-mass</td>
+
+ <td>double</td>
+ <td>600.0</td>
+ </tr>
+ <tr>
+ <td>-p</td>
+ <td>--exact-tolerance</td>
+ <td>double</td>
+
+ <td>10.0</td>
+ </tr>
+ <tr>
+ <td>-r</td>
+ <td>--persist-tolerance</td>
+ <td>double</td>
+ <td>10.0</td>
+
+ </tr>
+ <tr>
+ <td>-s</td>
+ <td>--scan-tolerance</td>
+ <td>integer</td>
+ <td>3</td>
+ </tr>
+
+ </tr>
+ <tr>
+ <td>-t</td>
+ <td>--retention-tolerance</td>
+ <td>float</td>
+ <td>0.5</td>
+ </tr>
+
+
+ </table>
+
diff --git a/doc/user/commands/hardklor_standalone_to_crux.html b/doc/user/commands/hardklor_standalone_to_crux.html
new file mode 100644
index 0000000..553064e
--- /dev/null
+++ b/doc/user/commands/hardklor_standalone_to_crux.html
@@ -0,0 +1,127 @@
+ <table border="1">
+ <tr>
+ <td><b>Hardklör parameter</b></td>
+ <td><b>crux hardklor parameter</b></td>
+ <td><b>datatype</b></td>
+ <td><b>default</b></td>
+
+ </tr>
+ <tr>
+ <td>-a</td>
+ <td>--hardklor-algorithm</td>
+ <td>string</td>
+ <td>fast-fewesst-peptides</td>
+ </tr>
+
+ <tr>
+ <td>-cdm</td>
+ <td>--cdm</td>
+ <td>char</td>
+ <td>Q</td>
+ </tr>
+ <tr>
+ <td>-chMin</td>
+ <td>--min-charge</td>
+ <td>integer</td>
+ <td>1</td>
+ </tr>
+ <tr>
+ <td>-chMax</td>
+ <td>--max-charge</td>
+ <td>integer</td>
+ <td>5</td>
+ </tr>
+ <tr>
+ <td>-corr</td>
+ <td>--corr</td>
+ <td>double</td>
+ <td>0.85</td>
+ </tr>
+ <tr>
+ <td>-d</td>
+ <td>--depth</td>
+ <td>integer</td>
+
+ <td>3</td>
+ </tr>
+ <tr>
+ <td>-da</td>
+ <td>--distribution-area</td>
+ <td>boolean</td>
+ <td>F</td>
+
+ </tr>
+ <tr>
+ <td>-m</td>
+ <td>--averagine-mod</td>
+ <td>string</td>
+ <td>Empty string</td>
+ </tr>
+ <tr>
+ <td>-mF</td>
+ <td>--mzxml-filter</td>
+ <td>string</td>
+ <td>none</td>
+ </tr>
+ <tr>
+ <td>-p</td>
+ <td>--max-p</td>
+ <td>integer</td>
+ <td>10</td>
+ </tr>
+ <tr>
+ <td>-res</td>
+ <td>--resolution</td>
+ <td>float</td>
+ <td>100000</td>
+ </tr>
+ <tr>
+ <td>-res</td>
+ <td>--instrument</td>
+ <td>string</td>
+ <td>fticr</td>
+ </tr>
+ <tr>
+ <td>-sc</td>
+ <td>--scan-number</td>
+ <td>number range</td>
+ <td>search all</td>
+ </tr>
+ <tr>
+ <td>-sl</td>
+ <td>--sensitivity</td>
+ <td>0|1|2|3</td>
+ <td>2</td>
+ </tr>
+ <tr>
+ <td>-sn</td>
+ <td>--signal-to-noise</td>
+ <td>float</td>
+ <td>1.0</td>
+ </tr>
+ <tr>
+ <td>-snWin</td>
+ <td>--sn-window</td>
+ <td>float</td>
+ <td>250.0</td>
+ </tr>
+ <tr>
+ <td>-snWin</td>
+ <td>--static-sn</td>
+ <td>boolean</td>
+ <td>true</td>
+ </tr>
+ <tr>
+ <td>-w</td>
+ <td>--mz-window</td>
+ <td>double-double</td>
+ <td>0-max</td>
+ </tr>
+ <tr>
+ <td>-win</td>
+ <td>--max-width</td>
+ <td>float</td>
+ <td>4.0</td>
+ </tr>
+ </table>
+
diff --git a/doc/user/contributors.html b/doc/user/contributors.html
new file mode 100644
index 0000000..3c7e5f1
--- /dev/null
+++ b/doc/user/contributors.html
@@ -0,0 +1,177 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux contributors</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Crux contributors</h2>
+ <p>
+ The current Crux development team consists of the following people:</p>
+
+ <ul>
+
+ <li>
+ Charles Grant, February 2008—present</li>
+
+ <li>
+ Sean McIlwain, January 2009—present</li>
+
+ <li>
+ Kaipo Tamura, October 2012—present</li>
+
+ <li>
+ J. Jeffry Howbert, October 2011—present</li>
+
+ <li>
+ Alice Cheng, March 2014—present</li>
+
+ </ul>
+
+ <p>
+ Former Crux contributors include</p>
+
+ <ul>
+
+ <li>
+ Chris Park, June 2006—August 2007</li>
+
+ <li>
+ Aaron Klammer, June 2006—June 2008</li>
+
+ <li>
+ Lukas Käll, November 2007—July 2008</li>
+
+ <li>
+ Michael Mathews, June 2010—December 2010</li>
+
+ <li>
+ Benjamin Diament, July 2010—September 2011</li>
+
+ <li>
+ Kha Nguyen, April 2011—July 2011</li>
+
+ <li>
+ Manijeh Naseri, January 2012—September 2012</li>
+
+ <li>
+ Marina Spivak, September 2009—September 2012</li>
+
+ <li>
+ Barbara Frewen, October 2007—September 2014</li>
+
+ <li>
+ Attila Kertesz-Farkas, September 2013—September 2015</li>
+
+ <li>
+ Jared Moore, September 2015—June 2016</li>
+
+ <li>
+ Atul Pai, September 2015—June 2016</li>
+
+ <li>
+ Zijin Zhang, September 2015—June 2016</li>
+
+ </ul>
+
+ <p>
+ The Crux project is overseen and directed by Michael MacCoss and
+ William Stafford Noble.</p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/create-docs.cmake b/doc/user/create-docs.cmake
new file mode 100644
index 0000000..5c98f75
--- /dev/null
+++ b/doc/user/create-docs.cmake
@@ -0,0 +1,127 @@
+# This script generates the documentation for the Crux commands using the
+# 'crux create-docs' command.
+
+# Create the list of documents to create
+execute_process(
+ COMMAND ${CRUX_PATH} create-docs --no-analytics T list
+ RESULT_VARIABLE status
+ OUTPUT_VARIABLE doc_list
+ ERROR_VARIABLE error_message
+)
+if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to create list of documents "
+ "\nError message: ${error_message}"
+ "\nCreation of documents failed."
+ )
+endif (NOT ${status} EQUAL 0)
+
+# Documents are separated by newlines, convert to CMake list
+STRING(REGEX REPLACE "\n" ";" doc_list "${doc_list}")
+
+# Generate each document
+foreach (doc ${doc_list})
+ execute_process(
+ COMMAND ${CRUX_PATH} create-docs --no-analytics T ${doc}
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_FILE "${doc}.html"
+ )
+ if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to generate ${doc}.html"
+ "\nError message: ${error_message}"
+ "\nCreation of documents failed."
+ )
+ endif (NOT ${status} EQUAL 0)
+ message(STATUS "Created ${doc}.html")
+ if (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+ # If building out of source copy doc files back to
+ # source doc directory.
+ execute_process(
+ COMMAND ${CMAKE_COMMAND}
+ -E copy ${doc}.html ${DOC_DIR}
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ )
+ if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to copy ${doc}.html to ${DOC_DIR}"
+ "\nError message: ${error_message}"
+ "\nCreation of documents failed."
+ )
+ endif (NOT ${status} EQUAL 0)
+ endif (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+endforeach (doc ${doc_list})
+
+# Create the parameter table
+execute_process(
+ COMMAND ${CRUX_PATH} create-docs --no-analytics T param-table
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_FILE param-table.html
+)
+if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to generate param-table.html"
+ "\nError message: ${error_message}"
+ "\nCreation of param-table failed."
+ )
+endif (NOT ${status} EQUAL 0)
+message(STATUS "Created param-table.html")
+if (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+ # If building out of source copy doc files back to
+ # source doc directory.
+ execute_process(
+ COMMAND ${CMAKE_COMMAND}
+ -E copy param-table.html ${DOC_DIR}
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ )
+ if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to copy param-table.html to ${DOC_DIR}"
+ "\nError message: ${error_message}"
+ "\nCreation of param-table failed."
+ )
+ endif (NOT ${status} EQUAL 0)
+endif (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+# Create the default.params file
+execute_process(
+ COMMAND ${CRUX_PATH} create-docs --no-analytics T default-params
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_FILE default.params
+)
+if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to generate default.params"
+ "\nError message: ${error_message}"
+ "\nCreation of default.params failed."
+ )
+endif (NOT ${status} EQUAL 0)
+message(STATUS "Created default.params")
+if (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
+ # If building out of source copy doc files back to
+ # source doc directory.
+ execute_process(
+ COMMAND ${CMAKE_COMMAND}
+ -E copy default.params ${DOC_DIR}
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ )
+ if (NOT ${status} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to copy default.params to ${DOC_DIR}"
+ "\nError message: ${error_message}"
+ "\nCreation of param-table failed."
+ )
+ endif (NOT ${status} EQUAL 0)
+endif (NOT ${PROJECT_SOURCE_DIR} MATCHES ${PROJECT_BINARY_DIR})
diff --git a/doc/user/create-docs.html b/doc/user/create-docs.html
new file mode 100644
index 0000000..47fa916
--- /dev/null
+++ b/doc/user/create-docs.html
@@ -0,0 +1,125 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>create-docs</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>create-docs</h1>
+<h2>Usage:</h2>
+<p><code>crux create-docs [options] <tool-name></code></p>
+<h2>Description:</h2>
+<p>This command prints to standard output an HTML formatted version of the documentation for a specified Crux command.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tool-name</code> – Specifies the Crux tool to generate documentation for. If the value is 'list', then a list of available tools will be given. If the value is 'default-params', then a default parameter file will be given.If the value is 'param-table' then a table will be printed showing which parameters are associated with which commands.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – The command prints to standard output the HTML documentation for the specified Crux tool.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<p>This command does not support any optional parameters.</p>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/default.params b/doc/user/default.params
new file mode 100644
index 0000000..3791557
--- /dev/null
+++ b/doc/user/default.params
@@ -0,0 +1,1832 @@
+################################################################################
+# Sample parameter file
+#
+# On each line, anything after a '#' will be ignored.
+# The format is:
+#
+# <parameter-name>=<value>
+#
+################################################################################
+
+# Crux parameter file (generated by Crux version 3.1)
+# Full documentation available at http://cruxtoolkit.sourceforge.net/
+# comet_version 2016.01 rev. 1
+# Everything following the '#' symbol is treated as a comment.
+
+# Path where pin file will be written instead of make-pin.pin.
+# It is optional for make-pin
+output-file=
+
+# Specify the verbosity of the current processes. Each level prints the
+# following messages, including all those at lower verbosity levels: 0-fatal
+# errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of
+# execution, 40-more progress information, 50-debug info, 60-detailed debug
+# info.
+# Available for all crux programs.
+verbosity=30
+
+# A file containing parameters.
+# Available for all crux programs. Any options specified on the command line
+# will override values in the parameter file.
+parameter-file=
+
+# Replace existing files if true or fail when trying to overwrite a file if
+# false.
+# Available for all crux programs. Applies to parameter file as well as index,
+# search, and analysis output files.
+overwrite=false
+
+# The minimum length of peptides to consider.
+# Used from the command line or parameter file by crux-generate-peptides, and
+# crux tide-index.
+min-length=6
+
+# The maximum length of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides, crux
+# tide-index.
+max-length=50
+
+# The minimum mass (in Da) of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides and
+# crux tide-index.
+min-mass=200
+
+# The maximum mass (in Da) of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides and
+# crux tide-index.
+max-mass=7200
+
+# The minimum number of peaks a spectrum must have for it to be searched.
+# Available for tide-search.
+min-peaks=20
+
+# Specify the enzyme used to digest the proteins in silico. Available enzymes
+# (with the corresponding digestion rules indicated in parentheses) include
+# no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin
+# ([FWYL]|{P}), elastase ([ALIV]|{P}), clostripain ([R]|[]), cyanogen-bromide
+# ([M]|[]), iodosobenzoate ([W]|[]), proline-endopeptidase ([P]|[]),
+# staph-protease ([E]|[]), asp-n ([]|[D]), lys-c ([K]|{P}), lys-n ([]|[K]),
+# arg-c ([R]|{P}), glu-c ([DE]|{P}), pepsin-a ([FL]|{P}),
+# elastase-trypsin-chymotrypsin ([ALIVKRWFY]|{P}). Specifying --enzyme no-enzyme
+# yields a non-enzymatic digest. Warning: the resulting index may be quite
+# large.
+# Available for crux-generate-peptides and crux tide-index.
+enzyme=trypsin
+
+# Specify rules for in silico digestion of protein sequences. Overrides the
+# enzyme option. Two lists of residues are given enclosed in square brackets or
+# curly braces and separated by a |. The first list contains residues
+# required/prohibited before the cleavage site and the second list is residues
+# after the cleavage site. If the residues are required for digestion, they are
+# in square brackets, '[' and ']'. If the residues prevent digestion, then they
+# are enclosed in curly braces, '{' and '}'. Use X to indicate all residues. For
+# example, trypsin cuts after R or K but not before P which is represented as
+# [RK]|{P}. AspN cuts after any residue but only before D which is represented
+# as [X]|[D].
+#
+custom-enzyme=
+
+# Specify whether every peptide in the database must have two enzymatic termini
+# (full-digest) or if peptides with only one enzymatic terminus are also
+# included (partial-digest).
+# Available for crux-generate-peptides and crux tide-index.
+digestion=full-digest
+
+# Maximum number of missed cleavages per peptide to allow in enzymatic
+# digestion.
+# Available from command line or parameter file for crux-generate-peptides. When
+# used with enzyme=<trypsin|elastase|chymotrypsin> includes peptides containing
+# one or more potential cleavage sites.
+missed-cleavages=0
+
+# Tolerance used for matching peptides to spectra. Peptides must be within +/-
+# 'precursor-window' of the spectrum value. The precursor window units depend
+# upon precursor-window-type.
+# Available for tide-search and crux-generate-peptides.
+precursor-window=3
+
+# Specify the units for the window that is used to select peptides around the
+# precursor mass location (mass, mz, ppm). The magnitude of the window is
+# defined by the precursor-window option, and candidate peptides must fall
+# within this window. For the mass window-type, the spectrum precursor m+h value
+# is converted to mass, and the window is defined as that mass +/-
+# precursor-window. If the m+h value is not available, then the mass is
+# calculated from the precursor m/z and provided charge. The peptide mass is
+# computed as the sum of the average amino acid masses plus 18 Da for the
+# terminal OH group. The mz window-type calculates the window as spectrum
+# precursor m/z +/- precursor-window and then converts the resulting m/z range
+# to the peptide mass range using the precursor charge. For the
+# parts-per-million (ppm) window-type, the spectrum mass is calculated as in the
+# mass type. The lower bound of the mass window is then defined as the spectrum
+# mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as
+# spectrum mass / (1.0 - (precursor-window / 1000000)).
+# Available for search-for-xlinks and tide-search.
+precursor-window-type=mass
+
+# Automatically estimate optimal value for the precursor-window parameter from
+# the spectra themselves. false=no estimation, warn=try to estimate but use the
+# default value in case of failure, fail=try to estimate and quit in case of
+# failure.
+# Available for tide-search.
+auto-precursor-window=false
+
+# Specify the parser to use for reading in MS/MS spectra.
+# Available for search-for-xlinks.
+spectrum-parser=pwiz
+
+# Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor
+# mass information from the "S" line or the "Z" line.
+# Available when spectrum-parser = pwiz.
+use-z-line=true
+
+# When creating decoy peptides using decoy-format=shuffle or
+# decoy-format=peptide-reverse, this option specifies whether the N-terminal and
+# C-terminal amino acids are kept in place or allowed to be shuffled or
+# reversed. For a target peptide "EAMPK" with decoy-format=peptide-reverse,
+# setting keep-terminal-aminos to "NC" will yield "EPMAK"; setting it to "C"
+# will yield "PMAEK"; setting it to "N" will yield "EKPMA"; and setting it to
+# "none" will yield "KPMAE".
+# Available for tide-index.
+keep-terminal-aminos=NC
+
+# Create in the output directory a text file listing of all the peptides in the
+# database, along with their neutral masses, one per line. If decoys are
+# generated, then a second file will be created containing the decoy peptides.
+# Decoys that also appear in the target database are marked with an asterisk in
+# a third column.
+# Available for tide-index.
+peptide-list=false
+
+# Stop after the specified pre-processing step.
+# Available for print-processed-spectra.
+stop-after=xcorr
+
+# Specify the output units for processed spectra.
+# Available for print-processed-spectra
+output-units=bin
+
+# Outputs an SQT results file to the output directory. Note that if sqt-output
+# is enabled, then compute-sp is automatically enabled and cannot be overridden.
+# Available for tide-search.
+sqt-output=false
+
+# Output an mzIdentML results file to the output directory.
+# Available for tide-search, percolator.
+mzid-output=false
+
+# Output a Percolator input (PIN) file to the output directory.
+# Available for tide-search.
+pin-output=false
+
+# Output a Percolator pout.xml format results file to the output directory.
+# Available for percolator.
+pout-output=false
+
+# Output a pepXML results file to the output directory.
+# Available for tide-search, q-ranker, barista, percolator.
+pepxml-output=false
+
+# Output a tab-delimited results file to the output directory.
+# Available for tide-search, percolator, q-ranker, barista.
+txt-output=true
+
+# Compute the preliminary score Sp for all candidate peptides. Report this score
+# in the output, along with the corresponding rank, the number of matched ions
+# and the total number of ions. This option is recommended if results are to be
+# analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp
+# is automatically enabled and cannot be overridden. Note that the Sp
+# computation requires re-processing each observed spectrum, so turning on this
+# switch involves significant computational overhead.
+# Available for tide-search.
+compute-sp=false
+
+# Estimate the parameters of the score distribution for each spectrum by fitting
+# to a Weibull distribution, and compute a p-value for each xlink product. This
+# option is only available when use-old-xlink=F.
+# Currently only implemented for XCORR.
+compute-p-values=false
+
+# A single scan number or a range of numbers to be searched. Range should be
+# specified as 'first-last' which will include scans 'first' and 'last'.
+# The search range x-y is inclusive of x and y.
+scan-number=
+
+# Before calculation of the XCorr score, the m/z axes of the observed and
+# theoretical spectra are discretized. This parameter specifies the size of each
+# bin. The exact formula for computing the discretized m/z value is
+# floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z
+# value. For low resolution ion trap ms/ms data 1.0005079 and for high
+# resolution ms/ms 0.02 is recommended.
+# Available for tide-search and xlink-assign-ions.
+mz-bin-width=1.0005079
+
+# In the discretization of the m/z axes of the observed and theoretical spectra,
+# this parameter specifies the location of the left edge of the first bin,
+# relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the
+# first bin will be located at +0.xx Da).
+# Available for tide-search.
+mz-bin-offset=0.4
+
+# Automatically estimate optimal value for the mz-bin-width parameter from the
+# spectra themselves. false=no estimation, warn=try to estimate but use the
+# default value in case of failure, fail=try to estimate and quit in case of
+# failure.
+# Available for tide-search.
+auto-mz-bin-width=false
+
+# Include flanking peaks around singly charged b and y theoretical ions. Each
+# flanking peak occurs in the adjacent m/z bin and has half the intensity of the
+# primary peak.
+# Available for the tide-search and search-for-xlinks commands.
+use-flanking-peaks=false
+
+# The lowest spectrum m/z to search in the ms2 file.
+# Available for tide-search.
+spectrum-min-mz=0
+
+# The highest spectrum m/z to search in the ms2 file.
+# Available for tide-search.
+spectrum-max-mz=1e+09
+
+# The spectrum charges to search. With 'all' every spectrum will be searched and
+# spectra with multiple charge states will be searched once at each charge
+# state. With 1, 2, or 3 only spectra with that charge state will be searched.
+# Used by tide-search.
+spectrum-charge=all
+
+# The fileroot string will be added as a prefix to all output file names.
+# Available for all commands that produce an output directory.
+fileroot=
+
+# The name of the directory where output files will be created.
+# Available for most commands.
+output-dir=crux-output
+
+# The name of the directory where temporary files will be created. If this
+# parameter is blank, then the system temporary directory will be used
+# Available for tide-index.
+temp-dir=
+
+# Specify the number of matches to report for each spectrum.
+# Available for tide-search and crux percolator
+top-match=5
+
+# When given a unsigned integer value seeds the random number generator with
+# that value. When given the string "time" seeds the random number generator
+# with the system time.
+# Available for all Crux commands.
+seed=1
+
+# Specify which isotopes to use in calculating fragment ion mass.
+# Used by crux-predict-peptide-ions.
+fragment-mass=mono
+
+# Specify the type of isotopic masses to use when calculating the peptide mass.
+# Used from command line or parameter file by crux-generate-peptides.
+isotopic-mass=mono
+
+# The minimum number of modifications that can be applied to a single peptide.
+# Available for tide-index.
+min-mods=0
+
+# The maximum number of modifications that can be applied to a single peptide.
+# Available for tide-index.
+max-mods=255
+
+# The maximum number of modified amino acids that can appear in one peptide.
+# Each aa can be modified multiple times.
+#
+max-aas-modified=255
+
+# Specify how sequence modifications are reported in various output files. Each
+# modification is reported as a number enclosed in square braces following the
+# modified residue; however, the number may correspond to one of three different
+# masses: (1) 'mod-only' reports the value of the mass shift induced by the
+# modification; (2) 'total' reports the mass of the residue with the
+# modification (residue mass plus modification mass); (3) 'separate' is the same
+# as 'mod-only', but multiple modifications to a single amino acid are reported
+# as a comma-separated list of values. For example, suppose amino acid D has an
+# unmodified mass of 115 as well as two moifications of masses +14 and +2. In
+# this case, the amino acid would be reported as D[16] with 'mod-only', D[131]
+# with 'total', and D[14,2] with 'separate'.
+# Available for generate-peptides.
+mod-mass-format=mod-only
+
+# Consider a-ions in the search? Note that an a-ion is equivalent to a neutral
+# loss of CO from the b-ion. Peak height is 10 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-a-ions=false
+
+# Consider b-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-b-ions=true
+
+# Consider c-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-c-ions=false
+
+# Consider x-ions in the search? Peak height is 10 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-x-ions=false
+
+# Consider y-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-y-ions=true
+
+# Consider z-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-z-ions=false
+
+# Set the precision for scores written to sqt and text files.
+# Available for all commands.
+precision=8
+
+# Set the precision for masses and m/z written to sqt and .txt files. Note that
+# this parameter only takes effect when specified in the parameter file.
+# Available for all commands.
+mass-precision=4
+
+# Show search progress by printing every n spectra searched. Set to 0 to show no
+# search progress.
+# Available for tide-search
+print-search-progress=1000
+
+# Specify the type of target-decoy search. Using 'auto', percolator attempts to
+# detect the search type automatically. Using 'separate' specifies two
+# searches: one against target and one against decoy protein db. Using
+# 'concatenated' specifies a single search on concatenated target-decoy protein
+# db.
+# Available for percolator
+search-input=auto
+
+# When given a unsigned integer value seeds the random number generator with
+# that value. When given the string "time" seeds the random number generator
+# with the system time.
+# Available for all percolator
+percolator-seed=1
+
+# Output the computed features in tab-delimited text format.
+# Available for percolator and q-ranker.
+feature-file-out=false
+
+# Include decoys (PSMs, peptides, and/or proteins) in the XML output.
+# Available for crux percolator
+decoy-xml-output=false
+
+# Specifies the prefix of the protein names that indicate a decoy.
+# Available for percolator
+decoy-prefix=decoy_
+
+# Output final weights to a file named "percolator.weights.txt".
+# Available for crux percolator
+output-weights=false
+
+# Read initial weights from the given file (one per line).
+# Available for crux percolator
+init-weights=
+
+# Only train Percolator on a subset of PSMs, and use the resulting score vector
+# to evaluate the other PSMs. Recommended when analyzing huge numbers (>1
+# million) of PSMs. When set to 0, all PSMs are used for training as normal.
+# Available for crux percolator
+subset-max-train=0
+
+# Penalty for mistakes made on positive examples. If this value is set to 0,
+# then it is set via cross validation over the values {0.1, 1, 10}, selecting
+# the value that yields the largest number of PSMs identified at the q-value
+# threshold set via the --test-fdr parameter.
+# Available for crux percolator
+c-pos=0
+
+# Penalty for mistake made on negative examples. If not specified, then this
+# value is set by cross validation over {0.1, 1, 10}.
+# Available for crux percolator
+c-neg=0
+
+# False discovery rate threshold to define positive examples in training.
+# Available for crux percolator
+train-fdr=0.01
+
+# False discovery rate threshold used in selecting hyperparameters during
+# internal cross-validation and for reporting the final results.
+# Available for crux percolator.
+test-fdr=0.01
+
+# Apply the specified threshold to PSM, peptide and protein probabilities to
+# obtain a faster estimate of the alpha, beta and gamma parameters.
+# Available for crux percolator.
+fido-fast-gridsearch=0
+
+# Do not approximate the posterior distribution by allowing large graph
+# components to be split into subgraphs. The splitting is done by duplicating
+# peptides with low probabilities. Splitting continues until the number of
+# possible configurations of each subgraph is below 2^18
+# Available for crux percolator
+fido-no-split-large-components=false
+
+# To speed up inference, proteins for which none of the associated peptides has
+# a probability exceeding the specified threshold will be assigned probability =
+# 0.
+# Available for crux percolator
+fido-protein-truncation-threshold=0.01
+
+# Use target-decoy competition to assign q-values and PEPs. When set to F, the
+# mix-max method, which estimates the proportion pi0 of incorrect target PSMs,
+# is used instead.
+# Available for crux percolator
+tdc=true
+
+# Maximum number of iterations for training.
+# Available for crux percolator
+maxiter=10
+
+# Quicker execution by reduced internal cross-validation.
+# Available for crux percolator
+quick-validation=false
+
+# In its initial round of training, Percolator uses one feature to induce a
+# ranking of PSMs. By default, Percolator will select the feature that produces
+# the largest set of target PSMs at a specified FDR threshold (cf. --train-fdr).
+# This option allows the user to specify which feature is used for the initial
+# ranking, using the name as a string. The name can be preceded by a hyphen
+# (e.g. "-XCorr") to indicate that a lower value is better.
+# Available for crux percolator
+default-direction=
+
+# Use unit normalization (i.e., linearly rescale each PSM's feature vector to
+# have a Euclidean length of 1), instead of standard deviation normalization.
+# Available for crux percolator.
+unitnorm=false
+
+# Measure performance on test set each iteration.
+# Available for crux percolator.
+test-each-iteration=false
+
+# When set to T, interpret the input file as a PIN file.
+# Available for crux percolator.
+feature-file-in=false
+
+# Use the picked protein-level FDR to infer protein probabilities, provide the
+# fasta file as the argument to this flag.
+# Available for crux percolator
+picked-protein=
+
+# Type of enzyme
+# Available for crux percolator
+protein-enzyme=trypsin
+
+# By default, if the peptides associated with protein A are a proper subset of
+# the peptides associated with protein B, then protein A is eliminated and all
+# the peptides are considered as evidence for protein B. Note that this
+# filtering is done based on the complete set of peptides in the database, not
+# based on the identified peptides in the search results. Alternatively, if this
+# option is set and if all of the identified peptides associated with protein B
+# are also associated with protein A, then Percolator will report a
+# comma-separated list of protein IDs, where the full-length protein B is first
+# in the list and the fragment protein A is listed second. Not available for
+# Fido.
+# Available for crux percolator
+protein-report-fragments=false
+
+# If multiple database proteins contain exactly the same set of peptides, then
+# Percolator will randomly discard all but one of the proteins. If this option
+# is set, then the IDs of these duplicated proteins will be reported as a
+# comma-separated list. Not available for Fido.
+# Available for crux percolator
+protein-report-duplicates=false
+
+# Use the Fido algorithm to infer protein probabilities. Must be true to use any
+# of the Fido options.
+# Available for crux percolator
+protein=false
+
+# Specify the probability with which a present protein emits an associated
+# peptide. Set by grid search (see --fido-gridsearch-depth parameter) if not
+# specified.
+# Available for crux percolator if --protein T is set.
+fido-alpha=0
+
+# Specify the probability of the creation of a peptide from noise. Set by grid
+# search (see --fido-gridsearch-depth parameter) if not specified.
+# Available for crux percolator if --protein T is set.
+fido-beta=0
+
+# Specify the prior probability that a protein is present in the sample. Set by
+# grid search (see --fido-gridsearch-depth parameter) if not specified.
+# Available for crux percolator if --protein T is set.
+fido-gamma=0
+
+# Estimate empirical p-values and q-values for proteins using target-decoy
+# analysis.
+# Available for crux percolator if --protein T is set.
+fido-empirical-protein-q=false
+
+# Set depth of the grid search for alpha, beta and gamma estimation.
+# Available for crux percolator if --protein T is set.
+fido-gridsearch-depth=0
+
+# Q-value threshold that will be used in the computation of the MSE and ROC AUC
+# score in the grid search.
+# Available for crux percolator if --protein T is set.
+fido-gridsearch-mse-threshold=0.05
+
+# By default, Percolator will examine the learned weights for each feature, and
+# if the weight appears to be problematic, then percolator will discard the
+# learned weights and instead employ a previously trained, static score vector.
+# This switch allows this error checking to be overriden.
+# Available for crux percolator.
+override=false
+
+# Use retention time features calculated as in "Improving tandem mass spectrum
+# identification using peptide retention time prediction across diverse
+# chromatography conditions" by Klammer AA, Yi X, MacCoss MJ and Noble WS.
+# (Analytical Chemistry. 2007 Aug 15;79(16):6111-8.).
+# Available for crux percolator
+klammer=false
+
+# Do not remove redundant peptides; keep all PSMs and exclude peptide level
+# probability.
+# Available for crux percolator
+only-psms=false
+
+# Include a decoy version of every peptide by shuffling or reversing the target
+# sequence or protein. In shuffle or peptide-reverse mode, each peptide is
+# either reversed or shuffled, leaving the N-terminal and C-terminal amino acids
+# in place. Note that peptides appear multiple times in the target database are
+# only shuffled once. In peptide-reverse mode, palindromic peptides are
+# shuffled. Also, if a shuffled peptide produces an overlap with the target or
+# decoy database, then the peptide is re-shuffled up to 5 times. Note that,
+# despite this repeated shuffling, homopolymers will appear in both the target
+# and decoy database. The protein-reverse mode reverses the entire protein
+# sequence, irrespective of the composite peptides.
+# Available for tide-index
+decoy-format=shuffle
+
+# Expression for static and variable mass modifications to include. Specify a
+# comma-separated list of modification sequences of the form:
+# C+57.02146,2M+15.9949,1STY+79.966331,...
+# Available for tide-index
+mods-spec=C+57.02146
+
+# Specifies N-terminal static and variable mass modifications on peptides.
+# Specify a comma-separated list of N-terminal modification sequences of the
+# form: 1E-18.0106,C-17.0265
+# Available for tide-index
+nterm-peptide-mods-spec=
+
+# Specifies C-terminal static and variable mass modifications on peptides.
+# Specify a comma-separated list of C-terminal modification sequences of the
+# form: X+21.9819
+# Available for tide-index
+cterm-peptide-mods-spec=
+
+# Specify the name of the file where the binarized fragmentation spectra will be
+# stored. Subsequent runs of crux tide-search will execute more quickly if
+# provided with the spectra in binary format. The filename is specified relative
+# to the current working directory, not the Crux output directory (as specified
+# by --output-dir). This option is not valid if multiple input spectrum files
+# are given.
+# Available for tide-search
+store-spectra=
+
+# Enable the calculation of exact p-values for the XCorr score. Calculation of
+# p-values increases the running time but increases the number of
+# identifications at a fixed confidence threshold. The p-values will be reported
+# in a new column with header "exact p-value", and the "xcorr score" column will
+# be replaced with a "refactored xcorr" column. Note that, currently, p-values
+# can only be computed when the mz-bin-width parameter is set to its default
+# value. Variable and static mods are allowed on non-terminal residues in
+# conjunction with p-value computation, but currently only static mods are
+# allowed on the N-terminus, and no mods on the C-terminus.
+# Available for tide-search
+exact-p-value=false
+
+# When providing a FASTA file as the index, the generated binary index will be
+# stored at the given path. This option has no effect if a binary index is
+# provided as the index.
+# Available for tide-search
+store-index=
+
+# When set to T, target and decoy search results are reported in a single file,
+# and only the top-scoring N matches (as specified via --top-match) are reported
+# for each spectrum, irrespective of whether the matches involve target or decoy
+# peptides.
+# Available for tide-search
+concat=false
+
+# Include the file column in tab-delimited output.
+# Available for tide-search
+file-column=true
+
+# If true, all peaks around the precursor m/z will be removed, within a range
+# specified by the --remove-precursor-tolerance option.
+# Available for tide-search.
+remove-precursor-peak=false
+
+# This parameter specifies the tolerance (in Th) around each precursor m/z that
+# is removed when the --remove-precursor-peak option is invoked.
+# Available for print-processed spectra and tide-search.
+remove-precursor-tolerance=1.5
+
+# When set to T, for each protein that begins with methionine, tide-index will
+# put two copies of the leading peptide into the index, with and without the
+# N-terminal methionine.
+# Available for tide-index.
+clip-nterm-methionine=false
+
+# Prevent duplicate peptides between the target and decoy databases. When set to
+# "F", the program keeps all target and previously generated decoy peptides in
+# memory. A shuffled decoy will be re-shuffled multiple times to avoid
+# duplication. If a non-duplicated peptide cannot be generated, the decoy is
+# skipped entirely. When set to "T", every decoy is added to the database
+# without checking for duplication. This option reduces the memory requirements
+# significantly.
+# Available for tide-index.
+allow-dups=false
+
+# Controls whether neutral loss ions are considered in the search. Two types of
+# neutral losses are included and are applied only to singly charged b- and
+# y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each
+# neutral loss peak has intensity 1/5 of the primary peak.
+# Available for tide-search.
+use-neutral-loss-peaks=true
+
+# The maximum charge state of a spectra to consider in search.
+# Available for tide-search.
+max-precursor-charge=5
+
+# Carries out a peptide-centric search. For each peptide the top-scoring spectra
+# are reported, in contrast to the standard spectrum-centric search where the
+# top-scoring peptides are reported. Note that in this case the "xcorr rank"
+# column will contain the rank of the given spectrum with respect to the given
+# candidate peptide, rather than vice versa (which is the default).
+# Available for tide-search.
+peptide-centric-search=false
+
+# Skip preprocessing steps on spectra. Default = F.
+# Available for tide-search
+skip-preprocessing=false
+
+# List of positive, non-zero integers.
+# Isotope errors to include. Specify a comma-separated list of isotope errors of
+# the form: 1,2,3,...Available for tide-search
+isotope-error=
+
+# 0=poll CPU to set num threads; else specify num threads directly.
+# Available for tide-search tab-delimited files only.
+num-threads=0
+
+# Analysis begins with a pre-processsing step that creates a set of lookup
+# tables which are then used during training. Normally, these lookup tables are
+# deleted at the end of the analysis, but setting this option to T prevents the
+# deletion of these tables. Subsequently, analyses can be repeated more
+# efficiently by specifying the --re-run option.
+# Available for q-ranker and barista.
+skip-cleanup=false
+
+# Re-run a previous analysis using a previously computed set of lookup tables.
+# For this option to work, the --skip-cleanup option must have been set to true
+# when the program was run the first time.
+# Available for q-ranker and barista.
+re-run=
+
+# Use an enriched feature set, including separate features for each ion type.
+# Available for q-ranker and barista.
+use-spec-features=true
+
+# If the target and decoy searches were run separately, rather than using a
+# concatenated database, then the program will assume that the database search
+# results provided as a required argument are from the target database search.
+# This option then allows the user to specify the location of the decoy search
+# results. Like the required arguments, these search results can be provided as
+# a single file, a list of files or a directory. However, the choice (file, list
+# or directory) must be consistent for the MS2 files and the target and decoy
+# tab-delimited files. Also, if the MS2 and tab-delimited files are provided in
+# directories, then Q-ranker will use the MS2 filename (foo.ms2) to identify
+# corresponding target and decoy tab-delimited files with names like
+# foo*.target.txt and foo*.decoy.txt. This naming convention allows the target
+# and decoy txt files to reside in the same directory.
+# Available for q-ranker and barista.
+separate-searches=
+
+# Specify that the search results are provided as lists of files, rather than as
+# individual files.
+# Available for barista and percolator.
+list-of-files=false
+
+# Specifies whether to do optimization at the protein, peptide or psm level.
+# Available for barista.
+optimization=protein
+
+# Specify the method used to estimate q-values. The mix-max procedure or
+# target-decoy competition apply to PSMs. The peptide-level option eliminates
+# any PSM for which there exists a better scoring PSM involving the same
+# peptide, and then uses decoys to assign confidence estimates.
+# Used by assign-confidence.
+estimation-method=tdc
+
+# Adjust the score using the Sidak adjustment and reports them in a new column
+# in the output file. Note that this adjustment only makes sense if the given
+# scores are p-values, and that it requires the presence of the "distinct
+# matches/spectrum" feature for each PSM.
+# Used by assign-confidence.
+sidak=false
+
+# Specify the column (for tab-delimited input) or tag (for XML input) used as
+# input to the q-value estimation procedure. If this parameter is unspecified,
+# then the program searches for "xcorr score", "evalue" (comet), "exact p-value"
+# score fields in this order in the input file.
+# Used by assign-confidence.
+score=
+
+# Specify this parameter to T in order to combine charge states with peptide
+# sequencesin peptide-centric search. Works only if estimation-method =
+# peptide-level.
+# Used by assign-confidence.
+combine-charge-states=false
+
+# Specify this parameter to T in order to treat peptides carrying different or
+# no modifications as being the same. Works only if estimation = peptide-level.
+# Used by assign-confidence.
+combine-modified-peptides=false
+
+# The q-value threshold used by cascade search. Each spectrum identified in one
+# search with q-value less than this threshold will be excluded from all
+# subsequent searches.
+# Used by Cascade-Search
+q-value-threshold=0.01
+
+# Predict the specified primary ion series. 'a' indicates a-ions only, 'b'
+# indicates b-ions only, 'y' indicates y-ions only, 'by' indicates both b and y,
+# 'bya' indicates b, y, and a.
+# Only available for crux-predict-peptide-ions. Set automatically to 'by' for
+# searching.
+primary-ions=by
+
+# Predict the precursor ions, and all associated ions (neutral losses, multiple
+# charge states) consistent with the other specified options.
+# Only available for crux-predict-peptide-ions.
+precursor-ions=false
+
+# Predict the given number of isotope peaks (0|1|2).
+# Only available for crux-predict-peptide-ion. Automatically set to 0 for Sp
+# scoring and 1 for xcorr scoring.
+isotope=0
+
+# Predict flanking peaks for b- and y ions.
+# Only available for crux-predict-peptide-ion.
+flanking=false
+
+# Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the
+# charge state of the peptide ("peptide"). If the max-ion-charge is greater than
+# the charge state of the peptide, then the maximum is the peptide charge.
+# Available for predict-peptide-ions and search-for-xlinks. Set to 'peptide' for
+# search.
+max-ion-charge=peptide
+
+# Include among the predicted peaks b/y ions with up to n losses of nh3. For
+# example, for --nh3 2, predict a peak for each b- and y-ion with the loss of
+# one nh3 group and predict a second peak for each b- and y-ion with the loss of
+# two nh3 groups. These peaks will have 1 and 2, respectively, in the NH3 column
+# of the output.
+# Only available for crux-predict-peptide-ions.
+nh3=0
+
+# Include in the predicted peaks, b/y ions with the loss of 1 to n water
+# molecules. See --nh3 for an example.
+# Only available for crux-predict-peptide-ions.
+h2o=0
+
+# The name of the file in FASTA format.
+# Option for spectral-counts
+protein-database=
+
+# Type of analysis to make on the match results: (RAW|NSAF|dNSAF|SIN|EMPAI).
+# With exception of the RAW metric, the database of sequences need to be
+# provided using --protein-database.
+# Available for spectral-counts. RAW is raw counts, NSAF is Normalized Spectral
+# Abundance Factor, dNSAF is Distributed Spectral Abundance Factor, SIN is
+# Spectral Index Normalized and EMPAI is Exponentially Modified Protein
+# Abundance Index
+measure=NSAF
+
+# Ignore peptides that map to multiple proteins.
+# Available for spectral-counts.
+unique-mapping=false
+
+# Quantification at protein or peptide level.
+# Available for spectral-counts and either NSAF and SIN.
+quant-level=protein
+
+# Perform a parsimony analysis on the proteins, and report a "parsimony rank"
+# column in the output file. This column contains integers indicating the
+# protein's rank in a list sorted by spectral counts. If the parsimony analysis
+# results in two proteins being merged, then their parsimony rank is the same.
+# In such a case, the rank is assigned based on the largest spectral count of
+# any protein in the merged meta-protein. The "simple" parsimony algorithm only
+# merges two proteins A and B if the peptides identified in protein A are the
+# same as or a subset of the peptides identified in protein B. The "greedy"
+# parsimony algorithm does additional merging, using the peptide q-values to
+# greedily assign each peptide to a single protein.
+# Available for spectral-counts.
+parsimony=none
+
+# Determines what type of threshold to use when filtering matches. none : read
+# all matches, qvalue : use calculated q-value from percolator or q-ranker,
+# custom : use --custom-threshold-name and --custom-threshold-min parameters.
+# used for crux spectral-counts
+threshold-type=qvalue
+
+# Only consider PSMs with a threshold value. By default, q-values are
+# thresholded using a specified threshold value. This behavior can be changed
+# using the --custom-threshold and --threshold-min parameters.
+# Available for spectral-counts. All PSMs with higher (or lower) than this will
+# be ignored.
+threshold=0.01
+
+# Specify which field to apply the threshold to. The direction of the threshold
+# (<= or >=) is governed by --custom-threshold-min. By default, the threshold
+# applies to the q-value, specified by "percolator q-value", "q-ranker q-value",
+# "decoy q-value (xcorr)", or "barista q-value".
+# Available for spectral-counts.
+custom-threshold-name=
+
+# When selecting matches with a custom threshold, custom-threshold-min
+# determines whether to filter matches with custom-threshold-name values that
+# are greater-than or equal (F) or less-than or equal (T) than the threshold.
+# Available for spectral-counts.
+custom-threshold-min=true
+
+# MS2 file corresponding to the psm file. Required to measure the SIN. Ignored
+# for NSAF, dNSAF and EMPAI.
+# Available for spectral-counts with measure=SIN.
+input-ms2=
+
+# Use mzid's passThreshold attribute to filter matches.
+# Used when parsing mzIdentML files.
+mzid-use-pass-threshold=false
+
+# Change the mass of all amino acids 'A' by the given amount.
+#
+A=0
+
+# Change the mass of all amino acids 'C' by the given amount.
+#
+C=57.021464
+
+# Change the mass of all amino acids 'D' by the given amount.
+#
+D=0
+
+# Change the mass of all amino acids 'E' by the given amount.
+#
+E=0
+
+# Change the mass of all amino acids 'F' by the given amount.
+#
+F=0
+
+# Change the mass of all amino acids 'G' by the given amount.
+#
+G=0
+
+# Change the mass of all amino acids 'H' by the given amount.
+#
+H=0
+
+# Change the mass of all amino acids 'I' by the given amount.
+#
+I=0
+
+# Change the mass of all amino acids 'K' by the given amount.
+#
+K=0
+
+# Change the mass of all amino acids 'L' by the given amount.
+#
+L=0
+
+# Change the mass of all amino acids 'M' by the given amount.
+#
+M=0
+
+# Change the mass of all amino acids 'N' by the given amount.
+#
+N=0
+
+# Change the mass of all amino acids 'P' by the given amount.
+#
+P=0
+
+# Change the mass of all amino acids 'Q' by the given amount.
+#
+Q=0
+
+# Change the mass of all amino acids 'R' by the given amount.
+#
+R=0
+
+# Change the mass of all amino acids 'S' by the given amount.
+#
+S=0
+
+# Change the mass of all amino acids 'T' by the given amount.
+#
+T=0
+
+# Change the mass of all amino acids 'V' by the given amount.
+#
+V=0
+
+# Change the mass of all amino acids 'W' by the given amount.
+#
+W=0
+
+# Change the mass of all amino acids 'Y' by the given amount.
+#
+Y=0
+
+# Legal values are auto, tsv, sqt, pepxml or mzidentml format.
+# option, for psm-convert
+input-format=auto
+
+# Whether matches/ion are distinct (as opposed to total).
+# option, for psm-convert.
+distinct-matches=true
+
+# Rather than the spectrum, output summary statistics to standard output. Each
+# statistic is placed on a separate line, in the format <name>:<value> (e.g.
+# "TIC:1000.0").
+# Available only for crux-get-ms2-spectrum. Does not affect contents of the
+# output file.
+stats=false
+
+# write out the weibull training points for thespectrum,charge
+# Available for crux search-for-xlinks
+write-weibull-points=false
+
+# Print the theoretical spectrum
+# Available for xlink-predict-peptide-ions.
+print-theoretical-spectrum=false
+
+# Use the old version of xlink-searching algorithm. When false, a new version of
+# the code is run. The new version supports variable modifications and can
+# handle more complex databases. This new code is still in development and
+# should be considered a beta release.
+# Available for search-for-xlinks program.
+use-old-xlink=true
+
+# Score method for xlink {composite, modification, concatenated}.
+# Available for xlink-score-spectrum.
+xlink-score-method=composite
+
+# Provides a list of isotopic windows to search. For example, -1,0,1 will search
+# in three disjoint windows: (1) precursor_mass - neutron_mass +/- window, (2)
+# precursor_mass +/- window, and (3) precursor_mass + neutron_mass +/- window.
+# The window size is defined from the precursor-window and precursor-window-type
+# parameters. This option is only available when use-old-xlink=F.
+# Used for crux search-for-xlinks
+isotope-windows=0
+
+# Top-n open-mod peptides to consider in the second pass, value of 0 will search
+# all candiates.
+# Available for crux search-for-xlinks
+xlink-top-n=250
+
+# If there is no cross-link candidate found, then don't bother looking for
+# linear, self-loop, and dead-link candidates.
+# Available for crux search-for-xlinks program.
+require-xlink-candidate=false
+
+# Include linear peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-linears=true
+
+# Include dead-end peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-deadends=true
+
+# Include self-loop peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-selfloops=true
+
+# Include intra-protein cross-link candiates within the search.
+# Available for crux search-for-xlinks program.
+xlink-include-intra=true
+
+# Include inter-protein cross-link candidates within the search.
+# Available for crux search-for-xlinks program.
+xlink-include-inter=true
+
+# Include crosslink candidates that are both inter and intra.
+# Available for crux search-for-xlinks program.
+xlink-include-inter-intra=true
+
+# List of amino acids for which the cross-linker can prevent cleavage. This
+# option is only available when use-old-xlink=F.
+# Available for search-for-xlinks program.
+xlink-prevents-cleavage=K
+
+# Specify the maximum number of modifications allowed on a crosslinked peptide.
+# This option is only available when use-old-xlink=F.
+# Available for crux search-for-xlinks
+max-xlink-mods=255
+
+# Search decoy peptides within +/- precursor-window-weibull of the precursor
+# mass. The resulting scores are used only for fitting the Weibull distribution
+# Available for crux search-for-xlinks.
+precursor-window-weibull=20
+
+# Window type to use in conjunction with the precursor-window-weibull parameter.
+# Available for crux search-for-xlinks
+precursor-window-type-weibull=mass
+
+# Keep shuffling and collecting XCorr scores until the minimum number of points
+# for weibull fitting (using targets and decoys) is achieved.
+# Available for crux search-for-xlinks
+min-weibull-points=4000
+
+# Determines which spectral feature detection algorithm to use. Different
+# results are possible with each algorithm, and there are pros and cons to each.
+# Available for crux hardklor
+hardklor-algorithm=version1
+
+# Defines alternative averagine models in the analysis that incorporate
+# additional atoms and/or isotopic enrichments. Modifications are represented as
+# text strings. Inclusion of additional atoms in the model is done using by
+# entering an atomic formula, such as: PO2 or Cl. Inclusion of isotopic
+# enrichment to the model is done by specifying the percent enrichment (as a
+# decimal) followed by the atom being enriched and an index of the isotope. For
+# example, 0.75H1 specifies 75% enrichment of the first heavy isotope of
+# hydrogen. In other words, 75% deuterium enrichment. Two or more modifications
+# can be combined into the same model, and separated by spaces: B2 0.5B1
+# Available for crux hardklor
+averagine-mod=
+
+# Boxcar averaging is a sliding window that averages n adjacent spectra prior to
+# feature detection. Averaging generally improves the signal-to-noise ratio of
+# features in the spectra, as well as improving the shape of isotopic envelopes.
+# However, averaging will also change the observed peak intensities. Averaging
+# with too wide a window will increase the occurrence of overlapping features
+# and broaden the chromatographic profiles of observed features. The number
+# specified is the total adjacent scans to be combined, centered on the scan
+# being analyzed. Therefore, an odd number is recommended to center the boxcar
+# window. For example, a value of 3 would produce an average of the scan of
+# interest, plus one scan on each side. A value of 0 disables boxcar averaging.
+# Available for crux hardklor
+boxcar-averaging=0
+
+# This parameter is only functional when boxcar-averaging is used. The filter
+# will remove any peaks not seen in n scans in the boxcar window. The effect is
+# to reduce peak accumulation due to noise and reduce chromatographic broadening
+# of peaks. Caution should be used as over-filtering can occur. The suggested
+# number of scans to set for filtering should be equal to or less than the
+# boxcar-averaging window size. A value of 0 disables filtering.
+# Available for crux hardklor
+boxcar-filter=0
+
+# This parameter is only functional when boxcar-filter is used. The value
+# specifies the mass tolerance in ppm for declaring a peak the same prior to
+# filtering across all scans in the boxcar window.
+# Available for crux hardklor
+boxcar-filter-ppm=10
+
+# Indicates whether the data contain profile or centroided peaks.
+# Available for crux hardklor
+centroided=false
+
+# Choose the charge state determination method.
+# Available for crux hardklor
+cdm=Q
+
+# Specifies the minimum charge state to allow when finding spectral features. It
+# is best to set this value to the lowest assumed charge state to be present. If
+# set higher than actual charge states that are present, those features will not
+# be identified or incorrectly assigned a different charge state and mass.
+# Available for crux hardklor
+min-charge=1
+
+# Specifies the maximum charge state to allow when finding spectral features. It
+# is best to set this value to a practical number (i.e. do not set it to 20 when
+# doing a tryptic shotgun analysis). If set higher than actual charge states
+# that are present, the algorithm will perform significantly slower without any
+# improvement in results.
+# Available for crux hardklor
+max-charge=5
+
+# Sets the correlation threshold (cosine similarity) for accepting each
+# predicted feature.
+# Available for crux hardklor
+corr=0.85
+
+# Sets the depth of combinatorial analysis. For a given set of peaks in a
+# spectrum, search for up to this number of combined peptides that explain the
+# observed peaks. The analysis stops before depth is reached if the current
+# number of deconvolved features explains the observed peaks with a correlation
+# score above the threshold defined with the correlation parameter.
+# Available for crux hardklor
+depth=3
+
+# When reporting each feature, report abundance as the sum of all isotope peaks.
+# The value reported is the estimate of the correct peak heights based on the
+# averagine model scaled to the observed peak heights.
+# Available for crux hardklor
+distribution-area=false
+
+# Specifies an ASCII text file that defines symbols for the periodic table.
+# Available for crux hardklor
+hardklor-data-file=
+
+# Indicates the type of instrument used to collect data. This parameter,
+# combined with the resolution parameter, define how spectra will be centroided
+# (if you provide profile spectra) and the accuracy when aligning observed peaks
+# to the models.
+# Available for crux hardklor
+instrument=fticr
+
+# Specifies an ASCII text file that can be read to override the natural isotope
+# abundances for all elements.
+# Available for crux hardklor
+isotope-data-file=
+
+# Specifies the maximum number of models to build for a set of peaks being
+# analyzed. Regardless of the setting, the number of models will never exceed
+# the number of peaks in the current set. However, as many of the low abundance
+# peaks are noise or tail ends of distributions, defining models for them is
+# detrimental to the analysis.
+# Available for crux hardklor
+max-features=10
+
+# Filters the spectra prior to analysis for the requested MS/MS level. For
+# example, if the data contain MS and MS/MS spectra, setting mzxml-filter = 1
+# will analyze only the MS scan events. Setting mzxml-filter = 2 will analyze
+# only the MS/MS scan events.
+# Available for crux hardklor
+mzxml-filter=1
+
+# Constrains the search in each spectrum to signals below this value in
+# Thomsons. Setting to 0 disables this feature.
+# Available for crux hardklor
+mz-max=0
+
+# Constrains the search in each spectrum to signals above this value in
+# Thomsons. Setting to 0 disables this feature.
+# Available for crux hardklor
+mz-min=0
+
+# Only used when algorithm = version1. Defines the maximum window size in
+# Thomsons to analyze when deconvolving peaks in a spectrum into features.
+# Available for crux hardklor
+mz-window=4
+
+# Specifies the resolution of the instrument at 400 m/z for the data being
+# analyzed.
+# Available for crux hardklor
+resolution=100000
+
+# Used to restrict analysis to spectra with scan numbers below this parameter
+# value. A value of 0 disables this feature.
+# Available for crux hardklor
+scan-range-max=0
+
+# Used to restrict analysis to spectra with scan numbers above this parameter
+# value. A value of 0 disables this feature.
+# Available for crux hardklor
+scan-range-min=0
+
+# Set the sensitivity level. There are four levels: 0 (low), 1 (moderate), 2
+# (high), and 3 (max). Increasing the sensitivity will increase computation
+# time, but will also yield more isotope distributions.
+# Available for crux hardklor
+sensitivity=2
+
+# Filters spectra to remove peaks below this signal-to-noise ratio prior to
+# finding features.
+# Available for crux hardklor
+signal-to-noise=1
+
+# Uses Savitzky-Golay smoothing on profile peak data prior to centroiding the
+# spectra. This parameter is recommended for low resolution spectra only.
+# Smoothing data causes peak depression and broadening. Only use odd numbers for
+# the degree of smoothing (as it defines a window centered on each data point).
+# Higher values will produce smoother peaks, but with greater depression and
+# broadening. Setting this parameter to 0 disables smoothing.
+# Available for crux hardklor
+smooth=0
+
+# Set the signal-to-noise window length (in m/z). Because noise may be
+# non-uniform across a spectrum, this value adjusts the segment size considered
+# when calculating a signal-over-noise ratio.
+# Available for crux hardklor
+sn-window=250
+
+# Applies the lowest noise threshold of any sn_window across the entire mass
+# range for a spectrum. Setting this parameter to 0 turns off this feature, and
+# different noise thresholds will be used for each local mass window in a
+# spectrum.
+# Available for crux hardklor
+static-sn=true
+
+# Ignore PPIDs that persist for longer than this length of time in the MS1
+# spectra. The unit of time is whatever unit is used in your data file (usually
+# minutes). These PPIDs are considered contaminants.
+# Available for crux bullseye
+max-persist=2
+
+# When true, require an exact match (as defined by --exact-tolerance) between
+# the center of the precursor isolation window in the MS2 scan and the base
+# isotopic peak of the PPID. If this option is set to false and no exact match
+# is observed, then attempt to match using a wider m/z tolerance. This wider
+# tolerance is calculated using the PPID's monoisotopic mass and charge (the
+# higher the charge, the smaller the window).
+# Available for crux bullseye
+exact-match=false
+
+# Allowed gap size when checking for PPIDs across consecutive MS1 scans.
+# Available for crux bullseye
+gap-tolerance=1
+
+# Only consider PPIDs above this minimum mass in daltons.
+# Available for crux bullseye
+bullseye-min-mass=600
+
+# Only consider PPIDs below this maximum mass in daltons.
+# Available for crux bullseye
+bullseye-max-mass=8000
+
+# Set the tolerance (+/-ppm) for --exact-match.
+# Available for crux bullseye
+exact-tolerance=10
+
+# Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans.
+# Available for crux bullseye
+persist-tolerance=10
+
+# Total number of MS1 scans over which a PPID must be observed to be considered
+# real. Gaps in persistence are allowed by setting --gap-tolerance.
+# Available for crux bullseye
+scan-tolerance=3
+
+# Set the tolerance (+/-units) around the retention time over which a PPID can
+# be matches to the MS2 spectrum. The unit of time is whatever unit is used in
+# your data file (usually minutes).
+# Available for crux bullseye
+retention-tolerance=0.5
+
+# The format to write the output spectra to. If empty, the spectra will be
+# output in the same format as the MS2 input.
+# Available for crux bullseye
+spectrum-format=
+
+# Sort in ascending (T) or descending (F) order.
+# Available for sort-by-column
+ascending=true
+
+# Specify the input and output delimiter to use when processing the delimited
+# file. The argument can be either a single character or the keyword 'tab.'
+# Available for the delimited utility programs.
+delimiter=tab
+
+# Print the header line of the file, in addition to the columns that match.
+# Available for crux extract-columns and extract-rows
+header=true
+
+# Specifies the data type of the column, either an integer (int), a floating
+# point number (real), or a string.
+# Available for crux extract-rows
+column-type=string
+
+# Specify the operator that is used to compare an entry in the specified column
+# to the value given on the command line.
+# Available for crux extract-rows
+comparison=eq
+
+# Run the Bullseye algorithm on the given MS data, using it to assign
+# high-resolution precursor values to the MS/MS data. If a spectrum file ends
+# with .ms2 or .cms2, matching .ms1/.cms1 files will be used as the MS1 file.
+# Otherwise, it is assumed that the spectrum file contains both MS1 and MS2
+# scans.
+# Available for crux pipeline
+bullseye=false
+
+# Specify which search engine to use.
+# Available for crux pipeline
+search-engine=tide-search
+
+# Specify which post-processor to apply to the search results.
+# Available for crux pipeline
+post-processor=percolator
+
+# Minimum precursor m/z value to use in measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-min-precursor-mz=400
+
+# Minimum precursor m/z value to use in measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-max-precursor-mz=1800
+
+# Minimum fragment m/z value to use in measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-min-frag-mz=150
+
+# Maximum fragment m/z value to use in measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-max-frag-mz=1800
+
+# Minimum fragment peaks an MS/MS scan must contain to be used in measurement
+# error estimation.
+# Available for param-medic and tide-search and comet
+pm-min-scan-frag-peaks=40
+
+# Maximum ppm distance between precursor m/z values to consider two scans
+# potentially generated by the same peptide for measurement error estimation.
+# Available for param-medic and tide-search and comet
+pm-max-precursor-delta-ppm=50
+
+# Precursor charge state to consider MS/MS spectra from, in measurement error
+# estimation. Ideally, this should be the most frequently occurring charge state
+# in the given data.
+# Available for param-medic and tide-search and comet
+pm-charge=2
+
+# Number of most-intense fragment peaks to consider for measurement error
+# estimation, per MS/MS spectrum.
+# Available for param-medic and tide-search and comet
+pm-top-n-frag-peaks=30
+
+# Number of fragment peaks per spectrum pair to be used in fragment error
+# estimation.
+# Available for param-medic and tide-search and comet
+pm-pair-top-n-frag-peaks=5
+
+# Number of the most-intense peaks that two spectra must share in order to
+# potentially be generated by the same peptide, for measurement error
+# estimation.
+# Available for param-medic and tide-search and comet
+pm-min-common-frag-peaks=20
+
+# Maximum number of scans two spectra can be separated by in order to be
+# considered potentially generated by the same peptide, for measurement error
+# estimation.
+# Available for param-medic and tide-search and comet
+pm-max-scan-separation=1000
+
+# Minimum number of peak pairs (for precursor or fragment) that must be
+# successfully paired in order to attempt to estimate measurement error
+# distribution.
+# Available for param-medic and tide-search and comet
+pm-min-peak-pairs=100
+
+# Consider modifications on any amino acid in aa list with at most
+# max-per-peptide in one peptide. The parameter takes the form
+# <mass change>:<aa list>:<max per
+# peptide>:<prevents cleavage>:<prevents cross-link>. This parameter
+# may be included with different values multiple times so long as the
+# total number of mod, cmod, and nmod parameters does not exceed 11. The
+# "prevents cleavage" and "prevents cross-link" arguments are optional
+# T/F arguments for describing whether the modification prevents
+# enzymatic cleavage of cross-linking, respectively. This option is only
+# available when use-old-xlink=F. Note that this parameter only takes
+# effect when specified in the parameter file.
+# Available for search-for-xlinks.
+mod=NO MODS
+
+# Specify a variable modification to apply to N-terminus of peptides.
+# <mass change>:<max distance from protein n-term (-1 for no max)> Note
+# that this parameter only takes effect when specified in the parameter
+# file.
+# Available for search-for-xlinks.
+nmod=NO MODS
+
+# Specify a variable modification to apply to C-terminus of peptides.
+# <mass change>:<max distance from protein c-term (-1 for no max)>. Note
+# that this parameter only takes effect when specified in the parameter
+# file.
+# Available for search-for-xlinks.
+cmod=NO MODS
+
+####################
+# Comet Parameters #
+####################
+# 0=no, 1=concatenated search, 2=separate search.
+# Available for comet.
+decoy_search=0
+
+# 0=poll CPU to set num threads; else specify num threads directly.
+# Available for comet.
+num_threads=0
+
+# Controls the mass tolerance value. The mass tolerance is set at +/- the
+# specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0
+# tolerance. The units of the mass tolerance is controlled by the parameter
+# "peptide_mass_units".
+# Available for comet.
+peptide_mass_tolerance=3
+
+# 0=amu, 1=mmu, 2=ppm.
+# Available for comet.
+peptide_mass_units=0
+
+# Automatically estimate optimal value for the peptide_mass_tolerancel parameter
+# from the spectra themselves. false=no estimation, warn=try to estimate but use
+# the default value in case of failure, fail=try to estimate and quit in case of
+# failure.
+# Available for comet.
+auto_peptide_mass_tolerance=false
+
+# 0=average masses, 1=monoisotopic masses.
+# Available for comet.
+mass_type_parent=1
+
+# 0=average masses, 1=monoisotopic masses.
+# Available for comet.
+mass_type_fragment=1
+
+# 0=singly charged peptide mass, 1=precursor m/z.
+# Available for comet.
+precursor_tolerance_type=0
+
+# 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8
+# labeling).
+# Available for comet.
+isotope_error=0
+
+# Specify a search enzyme from the end of the parameter file.
+# Available for comet.
+search_enzyme_number=1
+
+# valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term.
+# Available for comet.
+num_enzyme_termini=2
+
+# Maximum value is 5; for enzyme search.
+# Available for comet.
+allowed_missed_cleavage=2
+
+# Binning to use on fragment ions.
+# Available for comet.
+fragment_bin_tol=1.000507
+
+# Offset position to start the binning (0.0 to 1.0).
+# Available for comet.
+fragment_bin_offset=0.4
+
+# Automatically estimate optimal value for the fragment_bin_tol parameter from
+# the spectra themselves. false=no estimation, warn=try to estimate but use the
+# default value in case of failure, fail=try to estimate and quit in case of
+# failure.
+# Available for comet.
+auto_fragment_bin_tol=false
+
+# 0=default peak shape, 1=M peak only.
+# Available for comet.
+theoretical_fragment_ions=1
+
+# Controls whether or not A-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_A_ions=0
+
+# Controls whether or not B-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_B_ions=1
+
+# Controls whether or not C-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_C_ions=0
+
+# Controls whether or not X-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_X_ions=0
+
+# Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_Y_ions=1
+
+# Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_Z_ions=0
+
+# 0=no, 1= yes to consider NH3/H2O neutral loss peak.
+# Available for comet.
+use_NL_ions=1
+
+# 0=no, 1=yes write sqt file.
+# Available for comet.
+output_sqtfile=0
+
+# 0=no, 1=yes write tab-delimited text file.
+# Available for comet.
+output_txtfile=1
+
+# 0=no, 1=yes write pep.xml file.
+# Available for comet.
+output_pepxmlfile=1
+
+# 0=no, 1=yes write percolator file.
+# Available for comet.
+output_percolatorfile=0
+
+# 0=no, 1=yes write .out files.
+# Available for comet.
+output_outfiles=0
+
+# 0=no, 1=yes to replace Sp with expect in out & sqt.
+# Available for comet.
+print_expect_score=1
+
+# num peptide results to show.
+# Available for comet.
+num_output_lines=5
+
+# 0=no, 1=yes for out files only.
+# Available for comet.
+show_fragment_ions=0
+
+# Sample enzyme which is possibly different than the one applied to the search.
+# Used to calculate NTT & NMC in pepXML output.
+# Available for comet.
+sample_enzyme_number=1
+
+# Start and scan scan range to search; 0 as first entry ignores parameter.
+# Available for comet.
+scan_range=0 0
+
+# Precursor charge range to analyze; does not override mzXML charge; 0 as first
+# entry ignores parameter.
+# Available for comet.
+precursor_charge=0 0
+
+# Specifies the whether to override existing precursor charge state information
+# when present in the files with the charge range specified by the
+# "precursor_charge" parameter.
+# Available for comet.
+override_charge=0
+
+# MS level to analyze, valid are levels 2 or 3.
+# Available for comet.
+ms_level=2
+
+# Specifies which scan types are searched.
+# Available for comet.
+activation_method=ALL
+
+# MH+ peptide mass range to analyze.
+# Available for comet.
+digest_mass_range=600.0 5000.0
+
+# Number of search hits to store internally.
+# Available for comet.
+num_results=50
+
+# For '.out' file output only, 0=search everything again, 1=don't search if .out
+# exists.
+# Available for comet.
+skip_researching=1
+
+# Set maximum fragment charge state to analyze (allowed max 5).
+# Available for comet.
+max_fragment_charge=3
+
+# Set maximum precursor charge state to analyze (allowed max 9).
+# Available for comet.
+max_precursor_charge=6
+
+# 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six.
+# Available for comet.
+nucleotide_reading_frame=0
+
+# 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine.
+# Available for comet.
+clip_nterm_methionine=0
+
+# Maximum number of spectra to search at a time; 0 to search the entire scan
+# range in one loop.
+# Available for comet.
+spectrum_batch_size=0
+
+# Specifies the prefix of the protein names that indicates a decoy.
+# Available for comet.
+decoy_prefix=decoy_
+
+# Specifies the suffix string that is appended to the base output name for the
+# pep.xml, pin.xml, txt and sqt output files.
+# Available for comet.
+output_suffix=
+
+# Specifies one or more mass offsets to apply. This value(s) are effectively
+# subtracted from each precursor mass such that peptides that are smaller than
+# the precursor mass by the offset value can still be matched to the respective
+# spectrum.
+# Available for comet.
+mass_offsets=
+
+# Minimum number of peaks in spectrum to search.
+# Available for comet.
+minimum_peaks=10
+
+# Minimum intensity value to read in.
+# Available for comet.
+minimum_intensity=0
+
+# 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD).
+# Available for comet.
+remove_precursor_peak=0
+
+# +- Da tolerance for precursor removal.
+# Available for comet.
+remove_precursor_tolerance=1.5
+
+# For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range.
+# Available for comet.
+clear_mz_range=0.0 0.0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod01=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod02=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod03=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod04=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod05=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod06=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod07=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod08=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod09=0.0 null 0 4 -1 0 0
+
+# Specifies the total/maximum number of residues that can be modified in a
+# peptide.
+# Available for comet.
+max_variable_mods_in_peptide=5
+
+# Controls whether the analyzed peptides must contain at least one variable
+# modification.
+# Available for comet.
+require_variable_mod=0
+
+# Specifiy a static modification to the c-terminus of all peptides.
+# Available for comet.
+add_Cterm_peptide=0
+
+# Specify a static modification to the n-terminus of all peptides.
+# Available for comet.
+add_Nterm_peptide=0
+
+# Specify a static modification to the c-terminal peptide of each protein.
+# Available for comet.
+add_Cterm_protein=0
+
+# Specify a static modification to the n-terminal peptide of each protein.
+# Available for comet.
+add_Nterm_protein=0
+
+# Specify a static modification to the residue A.
+# Available for comet.
+add_A_alanine=0
+
+# Specify a static modification to the residue B.
+# Available for comet.
+add_B_user_amino_acid=0
+
+# Specify a static modification to the residue C.
+# Available for comet.
+add_C_cysteine=57.021464
+
+# Specify a static modification to the residue D.
+# Available for comet.
+add_D_aspartic_acid=0
+
+# Specify a static modification to the residue E.
+# Available for comet.
+add_E_glutamic_acid=0
+
+# Specify a static modification to the residue F.
+# Available for comet.
+add_F_phenylalanine=0
+
+# Specify a static modification to the residue G.
+# Available for comet.
+add_G_glycine=0
+
+# Specify a static modification to the residue H.
+# Available for comet.
+add_H_histidine=0
+
+# Specify a static modification to the residue I.
+# Available for comet.
+add_I_isoleucine=0
+
+# Specify a static modification to the residue J.
+# Available for comet.
+add_J_user_amino_acid=0
+
+# Specify a static modification to the residue K.
+# Available for comet.
+add_K_lysine=0
+
+# Specify a static modification to the residue L.
+# Available for comet.
+add_L_leucine=0
+
+# Specify a static modification to the residue M.
+# Available for comet.
+add_M_methionine=0
+
+# Specify a static modification to the residue N.
+# Available for comet.
+add_N_asparagine=0
+
+# Specify a static modification to the residue O.
+# Available for comet.
+add_O_ornithine=0
+
+# Specify a static modification to the residue P.
+# Available for comet.
+add_P_proline=0
+
+# Specify a static modification to the residue Q.
+# Available for comet.
+add_Q_glutamine=0
+
+# Specify a static modification to the residue R.
+# Available for comet.
+add_R_arginine=0
+
+# Specify a static modification to the residue S.
+# Available for comet.
+add_S_serine=0
+
+# Specify a static modification to the residue T.
+# Available for comet.
+add_T_threonine=0
+
+# Specify a static modification to the residue U.
+# Available for comet.
+add_U_selenocysteine=0
+
+# Specify a static modification to the residue V.
+# Available for comet.
+add_V_valine=0
+
+# Specify a static modification to the residue W.
+# Available for comet.
+add_W_tryptophan=0
+
+# Specify a static modification to the residue X.
+# Available for comet.
+add_X_user_amino_acid=0
+
+# Specify a static modification to the residue Y.
+# Available for comet.
+add_Y_tyrosine=0
+
+# Specify a static modification to the residue Z.
+# Available for comet.
+add_Z_user_amino_acid=0
+
+#
+# COMET_ENZYME_INFO _must_ be at the end of this parameters file
+#
+[COMET_ENZYME_INFO]
+0. No_enzyme 0 - -
+1. Trypsin 1 KR P
+2. Trypsin/P 1 KR -
+3. Lys_C 1 K P
+4. Lys_N 0 K -
+5. Arg_C 1 R P
+6. Asp_N 0 D -
+7. CNBr 1 M -
+8. Glu_C 1 DE P
+9. PepsinA 1 FL P
+10. Chymotrypsin 1 FWYL P
diff --git a/doc/user/demos/demo1.sh b/doc/user/demos/demo1.sh
new file mode 100755
index 0000000..7c90a03
--- /dev/null
+++ b/doc/user/demos/demo1.sh
@@ -0,0 +1,34 @@
+#!/bin/bash -x
+# AUTHOR: WSN
+# CREATE DATE: 18 December 2013, Tokyo Narita airport
+
+# This file implements the commands described in ../search-tutorial.html.
+
+if [[ -e ../../../src/crux ]]; then
+ CRUX=../../../src/crux
+else
+ CRUX=../../../release/src/crux
+fi
+
+rm -rf yeast-index crux-output
+chmod +x ./tsv2html.py
+cp ../example-files/demo.ms2 .
+cp ../example-files/small-yeast.fasta .
+
+$CRUX tide-index small-yeast.fasta yeast-index
+
+$CRUX tide-search --compute-sp T demo.ms2 yeast-index
+$CRUX sort-by-column --column-type real --ascending F \
+ crux-output/tide-search.target.txt "xcorr score" \
+ > crux-output/tide-search.target.sort.txt
+head -11 crux-output/tide-search.target.sort.txt \
+ | ./tsv2html.py - \
+ > crux-output/tide-search.target.sort.html
+
+$CRUX percolator crux-output/tide-search.target.txt
+$CRUX sort-by-column --column-type real --ascending F \
+ crux-output/percolator.target.psms.txt "percolator score" \
+ > crux-output/percolator.target.psms.sort.txt
+head -11 crux-output/percolator.target.psms.sort.txt \
+ | ./tsv2html.py - \
+ > crux-output/percolator.target.psms.sort.html
diff --git a/doc/user/demos/tsv2html.py b/doc/user/demos/tsv2html.py
new file mode 100755
index 0000000..06914a1
--- /dev/null
+++ b/doc/user/demos/tsv2html.py
@@ -0,0 +1,77 @@
+#!/usr/bin/env python
+# AUTHOR: William Stafford Noble
+# CREATE DATE: 13 Sep 2015
+import sys
+
+USAGE = """USAGE: tsv2html.py [options] <tab-delimited file>
+
+ Convert a tab-delimited text file an HTML table. Use "-" to read
+ from stdin.
+
+ Options:
+ --title <string>
+ --table-only
+"""
+
+title = ""
+tableOnly = False
+
+# Parse the command line.
+sys.argv = sys.argv[1:]
+while (len(sys.argv) > 1):
+ nextArg = sys.argv[0]
+ sys.argv = sys.argv[1:]
+ if (nextArg == "--title"):
+ title = sys.argv[1]
+ sys.argv = sys.argv[1:]
+ elif (nextArg == "--table-only"):
+ tableOnly = True
+ else:
+ sys.stderr.write("Invalid option (%s).\n" % nextArg)
+ sys.exit(1)
+if (len(sys.argv) != 1):
+ sys.stderr.write(USAGE)
+ sys.exit(1)
+tsvFileName = sys.argv[0]
+
+# Open the input file.
+if (tsvFileName == "-"):
+ tsvFile = sys.stdin
+else:
+ tsvFile = open(tsvFileName, "r")
+
+# Print the header.
+if (not tableOnly):
+ sys.stdout.write("<html>\n")
+ sys.stdout.write("<head>\n")
+ if (title != ""):
+ sys.stdout.write("<title>%s</title>\n" % title)
+ sys.stdout.write("</head>\n")
+ sys.stdout.write("<body bgcolor=\"#ffffff\">\n")
+ if (title != ""):
+ sys.stdout.write("<h1>%s</h1>" % title)
+sys.stdout.write("<table border cellspacing=0>\n")
+
+# Read and display header row
+fields = tsvFile.readline().rstrip().split("\t")
+for field in fields:
+ sys.stdout.write("<td><b>%s</b></td>" % field)
+sys.stdout.write("</tr>\n")
+
+# Process lines.
+for line in tsvFile:
+
+ fields = line.rstrip().split("\t")
+ sys.stdout.write("<tr>\n")
+ for field in fields:
+ if (field == ""):
+ field = " "
+ sys.stdout.write("<td>%s</td>" % field)
+ sys.stdout.write("</tr>\n")
+tsvFile.close()
+
+# Print tail info.
+sys.stdout.write("</table>\n")
+if not tableOnly:
+ sys.stdout.write("</body>\n")
+ sys.stdout.write("</html>\n")
diff --git a/doc/user/deploy-to-web.sh b/doc/user/deploy-to-web.sh
new file mode 100755
index 0000000..4fcfe88
--- /dev/null
+++ b/doc/user/deploy-to-web.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+scp *.html charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp *.png charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp *.gif charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp crux.html charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs/index.html
+scp crux.css charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp -r data charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp -r demos charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
+scp -r download charlesegrant at web.sourceforge.net:/home/project-web/cruxtoolkit/htdocs
diff --git a/doc/user/download.html b/doc/user/download.html
new file mode 100644
index 0000000..5b6fa90
--- /dev/null
+++ b/doc/user/download.html
@@ -0,0 +1,741 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Download Crux</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+<style type="text/css">
+.inset {
+ position:relative;
+ left:20px;
+}
+
+.lic-div {
+ border:1px solid black;
+ height:150px;
+ width:600px;
+ margin-left:10px;
+ margin-top:10px;
+ margin-bottom:10px;
+ overflow-y:scroll;
+ overflow-x:hidden;
+}
+ p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p2 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: center; font: 14.0px Arial}
+ p.p3 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px Arial}
+ p.p4 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px Arial; min-height: 11.0px}
+ p.p5 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 12.0px Arial}
+ p.p6 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 12.0px Arial; min-height: 14.0px}
+ p.p7 {margin: 0.0px 0.0px 0.0px 18.0px; text-align: justify; text-indent: -18.0px; font: 10.0px Arial}
+ p.p8 {margin: 0.0px 0.0px 0.0px 13.5px; text-align: justify; text-indent: -13.5px; font: 10.0px Arial}
+ p.p9 {margin: 0.0px 0.0px 0.0px 18.0px; text-align: justify; text-indent: -18.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p10 {margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Arial}
+ p.p11 {margin: 0.0px 0.0px 0.0px 14.2px; font: 10.0px Arial}
+ p.p12 {margin: 0.0px 0.0px 0.0px 0.0px; text-indent: 36.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p13 {margin: 0.0px 0.0px 0.0px 18.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p14 {margin: 0.0px 0.0px 0.0px 36.0px; font: 10.0px Arial}
+ p.p15 {margin: 0.0px 0.0px 0.0px 0.0px; text-indent: 36.0px; font: 10.0px Arial}
+ p.p16 {margin: 0.0px 0.0px 0.0px 36.0px; font: 10.0px Arial; min-height: 11.0px}
+ p.p17 {margin: 0.0px 0.0px 0.0px 31.5px; text-indent: -31.5px; font: 10.0px Arial}
+ p.p18 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px Verdana; min-height: 12.0px}
+ p.p19 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px 'Times New Roman'; min-height: 11.0px}
+ p.p20 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: center; font: 12.0px Arial}
+ p.p21 {margin: 0.0px 0.0px 0.0px 0.0px; font: 7.0px Arial; min-height: 7.0px}
+ li.li3 {margin: 0.0px 0.0px 0.0px 0.0px; text-align: justify; font: 10.0px Arial}
+ span.Apple-tab-span {white-space:pre}
+ ol.ol1 {list-style-type: decimal}
+ .page-wrap:after { /*hacky just for download page. content is all over the place need this to fix footer*/
+ content: "";
+ display: none;
+ }
+</style>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+
+<form action="http://noble.gs.washington.edu/crux-downloads/download.php" method="post">
+
+<h2> Get Crux Toolkit (3 steps)</H2>
+<div class="inset">
+
+<H3> Step 1, Choose Download Type: </H3>
+<UL>
+<SELECT NAME="downloadtype">
+ <optgroup label="For End Users">
+ <OPTION value="Linux32"> Linux 32 bit binaries (NO vendor reader support)</OPTION>
+ <OPTION value="Linux64"> Linux 64 bit binaries (NO vendor reader support)</OPTION>
+ <OPTION value="OSX"> Macintosh binaries (NO vendor reader support)</OPTION>
+ <OPTION value="Windows64"> Windows 64-bit(includes vendor reader support)</OPTION>
+ <OPTION value="Windows32"> Windows 32-bit(includes vendor reader support)</OPTION>
+ </optgroup>
+ <optgroup label="For Developers">
+ <OPTION value="Source"> Source, CMake build (includes vendor reader support)</OPTION>
+ </optgroup>
+</SELECT>
+
+</UL>
+
+<H3> Step 2, Read License Agreements</H3>
+
+Crux is covered by an
+<a href="http://www.apache.org/licenses/LICENSE-2.0" >Apache license</a>
+but depends on several libraries that have other licences.
+You must read and agree to these other licenses before downloading Crux.
+<ul>
+ <li>ProteoWizard Core:</li>
+<div class="lic-div">
+ADDENDUM TO APACHE LICENSE
+
+<p>To the best of our ability we deliver this software to you under the Apache 2.0 License listed below (the source code is available in the ProteoWizard project). This software does, however, depend on other software libraries which place further restrictions on its use and redistribution. By accepting the license terms for this software, you agree to comply with the restrictions imposed on you by the license agreements of the software libraries on which it depends:</p>
+
+<p>
+<B>Agilent Mass Hunter Data Access Component Library <br />
+Waters Raw Data Access Component Library <br />
+Bruker CompassXtract <br />
+Thermo-Scientific MSFileReader Library <br />
+Waters Raw Data Access Component Library <br />
+AB Sciex WIFF Reader Library </B><br /><br />
+
+
+NOTE: If you do not plan to redistribute this software yourself, then you are the "end-user" in the above agreements.</p>
+
+<hr />
+<p>Apache License - Covers Core ProteoWizard Tools and Library<br></br>Version 2.0, January 2004<br></br>
+<a href="http://www.apache.org/licenses/">http://www.apache.org/licenses/</a> </p>
+<p>TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION</p>
+<p><strong><a name="definitions">1. Definitions</a></strong>.</p>
+<p>"License" shall mean the terms and conditions for use, reproduction, and
+distribution as defined by Sections 1 through 9 of this document.</p>
+<p>"Licensor" shall mean the copyright owner or entity authorized by the
+copyright owner that is granting the License.</p>
+<p>"Legal Entity" shall mean the union of the acting entity and all other
+entities that control, are controlled by, or are under common control with
+that entity. For the purposes of this definition, "control" means (i) the
+power, direct or indirect, to cause the direction or management of such
+entity, whether by contract or otherwise, or (ii) ownership of fifty
+percent (50%) or more of the outstanding shares, or (iii) beneficial
+ownership of such entity.</p>
+<p>"You" (or "Your") shall mean an individual or Legal Entity exercising
+permissions granted by this License.</p>
+<p>"Source" form shall mean the preferred form for making modifications,
+including but not limited to software source code, documentation source,
+and configuration files.</p>
+<p>"Object" form shall mean any form resulting from mechanical transformation
+or translation of a Source form, including but not limited to compiled
+object code, generated documentation, and conversions to other media types.</p>
+<p>"Work" shall mean the work of authorship, whether in Source or Object form,
+made available under the License, as indicated by a copyright notice that
+is included in or attached to the work (an example is provided in the
+Appendix below).</p>
+<p>"Derivative Works" shall mean any work, whether in Source or Object form,
+that is based on (or derived from) the Work and for which the editorial
+revisions, annotations, elaborations, or other modifications represent, as
+a whole, an original work of authorship. For the purposes of this License,
+Derivative Works shall not include works that remain separable from, or
+merely link (or bind by name) to the interfaces of, the Work and Derivative
+Works thereof.</p>
+<p>"Contribution" shall mean any work of authorship, including the original
+version of the Work and any modifications or additions to that Work or
+Derivative Works thereof, that is intentionally submitted to Licensor for
+inclusion in the Work by the copyright owner or by an individual or Legal
+Entity authorized to submit on behalf of the copyright owner. For the
+purposes of this definition, "submitted" means any form of electronic,
+verbal, or written communication sent to the Licensor or its
+representatives, including but not limited to communication on electronic
+mailing lists, source code control systems, and issue tracking systems that
+are managed by, or on behalf of, the Licensor for the purpose of discussing
+and improving the Work, but excluding communication that is conspicuously
+marked or otherwise designated in writing by the copyright owner as "Not a
+Contribution."</p>
+<p>"Contributor" shall mean Licensor and any individual or Legal Entity on
+behalf of whom a Contribution has been received by Licensor and
+subsequently incorporated within the Work.</p>
+<p><strong><a name="copyright">2. Grant of Copyright License</a></strong>. Subject to the
+terms and conditions of this License, each Contributor hereby grants to You
+a perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+copyright license to reproduce, prepare Derivative Works of, publicly
+display, publicly perform, sublicense, and distribute the Work and such
+Derivative Works in Source or Object form.</p>
+<p><strong><a name="patent">3. Grant of Patent License</a></strong>. Subject to the terms
+and conditions of this License, each Contributor hereby grants to You a
+perpetual, worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+(except as stated in this section) patent license to make, have made, use,
+offer to sell, sell, import, and otherwise transfer the Work, where such
+license applies only to those patent claims licensable by such Contributor
+that are necessarily infringed by their Contribution(s) alone or by
+combination of their Contribution(s) with the Work to which such
+Contribution(s) was submitted. If You institute patent litigation against
+any entity (including a cross-claim or counterclaim in a lawsuit) alleging
+that the Work or a Contribution incorporated within the Work constitutes
+direct or contributory patent infringement, then any patent licenses
+granted to You under this License for that Work shall terminate as of the
+date such litigation is filed.</p>
+<p><strong><a name="redistribution">4. Redistribution</a></strong>. You may reproduce and
+distribute copies of the Work or Derivative Works thereof in any medium,
+with or without modifications, and in Source or Object form, provided that
+You meet the following conditions:</p>
+<ol>
+<li>
+<p>You must give any other recipients of the Work or Derivative Works a
+copy of this License; and</p>
+</li>
+<li>
+<p>You must cause any modified files to carry prominent notices stating
+that You changed the files; and</p>
+</li>
+<li>
+<p>You must retain, in the Source form of any Derivative Works that You
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+</li>
+<li>
+<p>If the Work includes a "NOTICE" text file as part of its distribution,
+then any Derivative Works that You distribute must include a readable copy
+of the attribution notices contained within such NOTICE file, excluding
+those notices that do not pertain to any part of the Derivative Works, in
+at least one of the following places: within a NOTICE text file distributed
+as part of the Derivative Works; within the Source form or documentation,
+if provided along with the Derivative Works; or, within a display generated
+by the Derivative Works, if and wherever such third-party notices normally
+appear. The contents of the NOTICE file are for informational purposes only
+and do not modify the License. You may add Your own attribution notices
+within Derivative Works that You distribute, alongside or as an addendum to
+the NOTICE text from the Work, provided that such additional attribution
+notices cannot be construed as modifying the License.
+You may add Your own copyright statement to Your modifications and may
+provide additional or different license terms and conditions for use,
+reproduction, or distribution of Your modifications, or for any such
+Derivative Works as a whole, provided Your use, reproduction, and
+distribution of the Work otherwise complies with the conditions stated in
+this License.</p>
+</li>
+</ol>
+<p><strong><a name="contributions">5. Submission of Contributions</a></strong>. Unless You
+explicitly state otherwise, any Contribution intentionally submitted for
+inclusion in the Work by You to the Licensor shall be under the terms and
+conditions of this License, without any additional terms or conditions.
+Notwithstanding the above, nothing herein shall supersede or modify the
+terms of any separate license agreement you may have executed with Licensor
+regarding such Contributions.</p>
+<p><strong><a name="trademarks">6. Trademarks</a></strong>. This License does not grant
+permission to use the trade names, trademarks, service marks, or product
+names of the Licensor, except as required for reasonable and customary use
+in describing the origin of the Work and reproducing the content of the
+NOTICE file.</p>
+<p><strong><a name="no-warranty">7. Disclaimer of Warranty</a></strong>. Unless required by
+applicable law or agreed to in writing, Licensor provides the Work (and
+each Contributor provides its Contributions) on an "AS IS" BASIS, WITHOUT
+WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied, including,
+without limitation, any warranties or conditions of TITLE,
+NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A PARTICULAR PURPOSE. You
+are solely responsible for determining the appropriateness of using or
+redistributing the Work and assume any risks associated with Your exercise
+of permissions under this License.</p>
+<p><strong><a name="no-liability">8. Limitation of Liability</a></strong>. In no event and
+under no legal theory, whether in tort (including negligence), contract, or
+otherwise, unless required by applicable law (such as deliberate and
+grossly negligent acts) or agreed to in writing, shall any Contributor be
+liable to You for damages, including any direct, indirect, special,
+incidental, or consequential damages of any character arising as a result
+of this License or out of the use or inability to use the Work (including
+but not limited to damages for loss of goodwill, work stoppage, computer
+failure or malfunction, or any and all other commercial damages or losses),
+even if such Contributor has been advised of the possibility of such
+damages.</p>
+<p><strong><a name="additional">9. Accepting Warranty or Additional Liability</a></strong>.
+While redistributing the Work or Derivative Works thereof, You may choose
+to offer, and charge a fee for, acceptance of support, warranty, indemnity,
+or other liability obligations and/or rights consistent with this License.
+However, in accepting such obligations, You may act only on Your own behalf
+and on Your sole responsibility, not on behalf of any other Contributor,
+and only if You agree to indemnify, defend, and hold each Contributor
+harmless for any liability incurred by, or claims asserted against, such
+Contributor by reason of your accepting any such warranty or additional
+liability.</p>
+<HR />
+</div>
+ <li>AB Sciex WiffReader</li>
+<div class="lic-div">
+
+<p class="p1"><br></p>
+<p class="p2"><b>AB Sciex LLC</b></p>
+<p class="p2"><b>END USER BETA SOFTWARE LICENSE AGREEMENT</b></p>
+<p class="p2"><b>and</b></p>
+<p class="p2"><b>LIMITED DEVELOPER LICENSE</b></p>
+<p class="p2"><i>WIFF Reader Distributable Beta SDK</i></p>
+<p class="p1"><br></p>
+<p class="p1"><br></p>
+<p class="p3"><b>NOTICE TO USER: PLEASE READ THIS DOCUMENT CAREFULLY.<span class="Apple-converted-space"> </span>THIS IS THE CONTRACT BETWEEN YOU AND AB SCIEX REGARDING THIS SOFTWARE PRODUCT.<span class="Apple-converted-space"> </span>THIS AGREEMENT INCLUDES LICENSE TERMS AND RESTRICTIONS, WARRANTY AND LIABILITY DISCLAIMERS, AND LIMITATIONS.</b></p>
+<p class="p4"><b></b><br></p>
+<p class="p3"><b>YOUR INSTALLATION AND USE OF THIS AB SCIEX SDK IS SUBJECT TO THE TERMS AND CONDITIONS CONTAINED IN THIS END USER SOFTWARE LICENSE AGREEMENT.</b></p>
+<p class="p4"><b></b><br></p>
+<p class="p3">This AB Sciex End User Software License Agreement (EULA) and Limited Developer & Redistribution License accompanies this AB Sciex WIFF Reader Distributable Beta SDK product ("Software") and related explanatory materials ("Documentation"). The term "SDK" also includes any upgrades, modified versions, updates, additions and copies of the SDK licensed to you by AB Sciex.<span class="Apple-converted-space"> </span>The term “AB Sciex,” as used in this License, means AB Scie [...]
+<p class="p4"><br></p>
+<p class="p4"><br></p>
+<p class="p5"><b>Third Party Products</b></p>
+<p class="p3">This Software may include software products licensed by third party provider(s). In addition, the Software may enable you to run multiple instances of third-party software and application programs. You are responsible for reviewing and complying with any licenses necessary to use any such third-party software.<span class="Apple-converted-space"> </span>Such licenses may be included in your AB Sciex installation package.</p>
+<p class="p4"><br></p>
+<p class="p5"><b>TITLE</b></p>
+<p class="p3">Title, ownership rights and intellectual property rights in and to the Software and Documentation shall at all times remain with AB Sciex and its subsidiaries, and their suppliers.<span class="Apple-converted-space"> </span>All rights not specifically granted by this License, including Federal and international copyrights, are reserved by AB Sciex or their respective owners.</p>
+<p class="p6"><b></b><br></p>
+<p class="p5"><b>COPYRIGHT</b></p>
+<p class="p3">The Software, including its structure, organization, code, user interface and associated Documentation, is a proprietary product of AB Sciex or its suppliers, and is protected by international laws of copyright. The law provides for civil and criminal penalties for anyone in violation of the laws of copyright.</p>
+<p class="p4"><br></p>
+<p class="p5"><b>LICENSE</b></p>
+<p class="p3"><b>Use of the Software</b></p>
+<ol class="ol1">
+ <li class="li3">As a Developer License, AB Sciex grants to you one (1) personal, nontransferable, nonexclusive, license to use copies of the Software and install such Software on your machine(s) for your single concurrent internal use.</li>
+</ol>
+<p class="p7">2.<span class="Apple-tab-span"> </span>You may make one copy of the Software in machine-readable form solely for backup or archival purposes.<span class="Apple-converted-space"> </span>You must reproduce on any such copy all copyright notices and any other proprietary legends found on the original.<span class="Apple-converted-space"> </span>You may not make any other copies of the Software.</p>
+<p class="p7">3.<span class="Apple-tab-span"> </span>From time to time, AB Sciex may change the terms of this Agreement.<span class="Apple-converted-space"> </span>AB Sciex will notify you of such change.<span class="Apple-converted-space"> </span>Your continued use of the Software will indicate your agreement to the change.</p>
+<p class="p4"><br></p>
+<p class="p3"><b>Use Restrictions</b></p>
+<p class="p7">1.<span class="Apple-converted-space"> </span>You may not use the Software, Documentation, or any associated documentation, in whole or in part, except as expressly permitted in this Agreement.</p>
+<p class="p7">2.<span class="Apple-converted-space"> </span>You may not sublicense, copy, merge, modify, sell, resell, rent, lease, assign, transfer (except temporarily in the event of a computer malfunction or as expressly permitted under the Section “Use of the Software”), or distribute this license or the Software, or create derivative works based on the Software (except as outlined in the Distribution Rights below), or any part thereof or any interest therein. <span class="Apple-con [...]
+<p class="p7">3.<span class="Apple-converted-space"> </span>You may not reverse assemble, decompile, modify, create any derivative works, or otherwise attempt, cause, or permit any reverse engineering of the Software or any part thereof.</p>
+<p class="p8">4.<span class="Apple-converted-space"> </span>You acknowledge that the Software in human-readable (source code) form, including its structure, sequence, and organization, is and remains the confidential trade secret of AB Sciex.<span class="Apple-converted-space"> </span>You agree that you shall not attempt, cause or permit the reverse engineering, modification, decompiliation, disassembly of the Software to any human readable or perceivable form, or creation of any deriv [...]
+<p class="p8">5.<span class="Apple-converted-space"> </span>You may not remove any proprietary, copyright, trade secret or warning legend from the Software or any Documentation and you acknowledge that the Software in human-readable (source code) form, including its structure, sequence, and organization, is and remains the confidential trade secret of AB Sciex.</p>
+<p class="p7">6.<span class="Apple-converted-space"> </span>You agree to comply fully with all export laws and restrictions and regulations of the United States or applicable foreign agencies or authorities.<span class="Apple-converted-space"> </span>You agree that you will not export or reexport, directly or indirectly, the Software into any country prohibited by the United States Export Administration Act and the regulations thereunder or other applicable United States law.</p>
+<p class="p9"><br></p>
+<p class="p10"><b>Distribution of the Distributable Components (DCs)</b></p>
+<p class="p10">1.<span class="Apple-converted-space"> </span><b>Distributable Components.</b> The Software contains Distributable Components that you are permitted<span class="Apple-converted-space"> </span></p>
+<p class="p11">to distribute for non-commercial purposes provided that: (a) the Distributable Components are bundled as part of, and for the sole purpose of running programs developed by you and supplied by you; and (b) you comply with all other terms in this EULA.<span class="Apple-converted-space"> </span>As used herein commercial purposes include, but are not limited to, charging a purchase price, license fee, maintenance fee, subscription fee, or providing software incorporating Dis [...]
+<p class="p1"><br></p>
+<p class="p10">2.<span class="Apple-converted-space"> </span><b>Right to Use and Distribute.</b> The code and text files listed in Appendix A are “Distributable<span class="Apple-converted-space"> </span></p>
+<p class="p10"><span class="Apple-converted-space"> </span>Components”.<span class="Apple-converted-space"> </span>All other code and text files of the Software are not distributable.</p>
+<p class="p12"><br></p>
+<p class="p10">3.<span class="Apple-converted-space"> </span><b>Third Party Distribution.</b> You may not permit distributors of your programs or end users of your<span class="Apple-converted-space"> </span></p>
+<p class="p10"><span class="Apple-converted-space"> </span>programs to copy and distribute the Distributable Components as part of those or their programs.</p>
+<p class="p13"><br></p>
+<p class="p10">4. <b>Distribution Requirements, General.</b> For any Distributable Component you distribute, you must:</p>
+<p class="p14">(a) embed the license key in your program such that it is obscured from end users seeing it.<span class="Apple-converted-space"> </span>In the event that your program is open source, this license key must not be part of the open source;</p>
+<p class="p15">(b) add significant primary functionality to it in your programs;</p>
+<p class="p14">(c) for any Distributable Component having a filename extension of .lib, distribute only the results of running such Distributable Component through a linker with your program;</p>
+<p class="p14">(d) distribute Distributable Components included in a setup program only as part of that setup program without modification;</p>
+<p class="p14">(e) require distributors and external end users to agree to terms that protect it at least as much as this EULA; and</p>
+<p class="p15">(f) display your valid copyright notice on your programs.</p>
+<p class="p16"><br></p>
+<p class="p17">5. <b>Distribution Requirement, Indemnification.<span class="Apple-converted-space"> </span></b>For any Distributable Component you distribute, you must and you hereby agree to: indemnify, defend, and hold harmless AB Sciex from any and all claims and costs, including attorneys’ fees, related to the distribution or use of your programs.</p>
+<p class="p16"><br></p>
+<p class="p10">6.<span class="Apple-converted-space"> </span><b>Distribution Restrictions.</b> You may not:</p>
+<p class="p15">(a) alter any copyright, trademark or patent notice in the Distributable Component;</p>
+<p class="p14">(b) use AB Sciex or AB Sciex’s trademarks in your programs’ names or in a way that suggests your programs come from or are endorsed by AB Sciex;</p>
+<p class="p15">(c) include Distributable Components in malicious, deceptive or unlawful programs; or</p>
+<p class="p14">(d) modify or distribute the source code of any Distributable Component so that any part of it becomes subject to an Excluded License. An Excluded License is one that requires, as a condition of use, modification or distribution, that (i) the code be disclosed or distributed in source code form; and/or (ii) others have the right to modify it.</p>
+<p class="p4"><br></p>
+<p class="p3"><b>Trial</b></p>
+<p class="p3">If this license is granted on a trial basis, you are hereby notified that license management software may be included to automatically cause the Software to cease functioning at the end of the trial period.</p>
+<p class="p4"><br></p>
+<p class="p3"><b>Termination</b></p>
+<p class="p3">You may terminate this Agreement by discontinuing use of the Software, removing all copies from your computers and storage media, and returning the Software and Documentation, and all copies thereof, to AB Sciex.<span class="Apple-converted-space"> </span>AB Sciex may terminate this Agreement if you fail to comply with all of its terms, in which case you agree to discontinue using the Software, remove all copies from your computers and storage media, and return the Softwar [...]
+<p class="p4"><b></b><br></p>
+<p class="p3"><b>U.S. Government End Users</b></p>
+<p class="p3">The Software is a "commercial item," as that term is defined in 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer software" and "commercial computer software documentation," as such terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48 C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995), all U.S. Government End Users acquire the Software with only those rights set forth herein.<span class="Apple-converted-space"> </span></p>
+<p class="p4"><b></b><br></p>
+<p class="p3"><b>European Community End Users</b></p>
+<p class="p3">If this Software is used within a country of the European Community, nothing in this Agreement shall be construed as restricting any rights available under the European Community Software Directive, O.J. Eur. Comm. (No. L. 122) 42 (1991).</p>
+<p class="p4"><br></p>
+<p class="p3"><b>Regulated Uses</b></p>
+<p class="p3">You acknowledge that the Software has not been cleared, approved, registered or otherwise qualified (collectively, “Approval”) by AB Sciex<b> </b>with any regulatory agency, including without limitation for use in diagnostic or therapeutic procedures or any other use requiring compliance with any federal or state law regulating diagnostic or therapeutic products, blood products, medical devices or any similar product (hereafter collectively referred to as "federal or state [...]
+<p class="p4"><b></b><br></p>
+<p class="p5"><b>NO WARRANTY and LIMITATION OF REMEDIES</b></p>
+<p class="p3">AB SCIEX MAKES NO WARRANTIES OF ANY KIND WHATSOEVER, EXPRESS OR IMPLIED, WITH RESPECT TO THE SOFTWARE OR DOCUMENTATION, INCLUDING BUT NOT LIMITED TO WARRANTIES OF FITNESS FOR A PARTICULAR PURPOSE OR MERCHANTABILITY OR THAT THE SOFTWARE OR DOCUMENTATION IS NON-INFRINGING.<span class="Apple-converted-space"> </span>ALL OTHER WARRANTIES ARE EXPRESSLY DISCLAIMED.<span class="Apple-converted-space"> </span>WITHOUT LIMITING THE GENERALITY OF THE FOREGOING, AB SCIEX MAKES NO WAR [...]
+<p class="p4"><br></p>
+<p class="p5"><b>Limitation of Liability</b></p>
+<p class="p3">IN NO EVENT SHALL AB SCIEX OR ITS AGENTS, CONSULTANTS, CONTRACTORS OR SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, THE SOFTWARE OR DOCUMENTATION, EVEN IF AB [...]
+<p class="p4"><br></p>
+<p class="p3">Some states, countries or jurisdictions limit the scope of or preclude limitations or exclusion of remedies or damages, or of liability, such as liability for gross negligence or willful misconduct, as or to the extent set forth above, OR do not allow implied warranties TO BE EXCLUDED.<span class="Apple-converted-space"> </span>In such states, countries or jurisdictions, the limitation or exclusion of warranties, remedies, damages or liability set forth above may not apply [...]
+<p class="p4"><br></p>
+<p class="p5"><b>GENERAL</b></p>
+<p class="p3">This Agreement shall be governed by laws of the Commonwealth of Massachusetts, U.S.A., exclusive of its conflict of laws provisions.<span class="Apple-converted-space"> </span>This Agreement shall not be governed by the United Nations Convention on Contracts for the International Sale of Goods.<span class="Apple-converted-space"> </span>This Agreement contains the complete agreement between the parties with respect to the subject matter hereof, and supersedes all prior or [...]
+<p class="p18"><br></p>
+<p class="p19"><br></p>
+<p class="p3">Unpublished rights reserved under the copyright laws of the United States.</p>
+<p class="p3">AB Sciex LLC, 500 Old Connecticut Path, Framingham, MA 01701 U.S.A.</p>
+<p class="p4"><br></p>
+<p class="p3">For Research Use Only. Not for use in diagnostic procedures.<span class="Apple-converted-space"> </span>The trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective owners.<span class="Apple-converted-space"> </span>AB SCIEX™ is being used under license.</p>
+<p class="p3">© 2012 AB SCIEX</p>
+<p class="p20"><b>APPENDIX A</b></p>
+<p class="p20"><b>DISTRIBUTABLE COMPONENTS OF THE SOFTWARE</b></p>
+<p class="p21"><br></p>
+<p class="p10">Clearcore2.Compression.dll</p>
+<p class="p10">Clearcore2.Data.AnalystDataProvider.dll</p>
+<p class="p10">Clearcore2.Data.CommonInterfaces.dll</p>
+<p class="p10">Clearcore2.Data.dll</p>
+<p class="p10">Clearcore2.Data.WiffReader.dll</p>
+<p class="p10">Clearcore2.InternalRawXYProcessing.dll</p>
+<p class="p10">Clearcore2.Muni.dll</p>
+<p class="p10">Clearcore2.ProjectUtilities.dll</p>
+<p class="p10">Clearcore2.RawXYProcessing.dll</p>
+<p class="p10">Clearcore2.StructuredStorage.dll</p>
+<p class="p10">Clearcore2.Utility.dll</p>
+<p class="p1"><br></p>
+</div>
+ <li>Agilent MHDAC</li>
+<div class="lic-div">
+<strong><p>END-USER LICENSE TERMS FOR AGILENT MHDAC</p></strong>
+<strong>
+<p>AGILENT TECHNOLOGIES, INC. SOFTWARE LICENSE TERMS <strong>FOR THE MASSHUNTER DATA ACCESS COMPONENT RUNTIME VERSION</strong></p>
+</strong>
+<p><strong>ATTENTION: USE OF THE SOFTWARE IS SUBJECT TO THE LICENSE TERMS SET FORTH BELOW.</strong></p>
+<p>IF YOU DO NOT AGREE TO THESE LICENSE TERMS, THEN (A) DO NOT INSTALL OR USE THE SOFTWARE, AND (B) YOU MAY RETURN THE SOFTWARE FOR A FULL REFUND, OR, IF THE SOFTWARE IS SUPPLIED AS PART OF ANOTHER PRODUCT, YOU MAY RETURN THE ENTIRE PRODUCT FOR A FULL REFUND. NOTWITHSTANDING ANYTHING TO THE CONTRARY IN THIS NOTICE, INSTALLING OR OTHERWISE USING THE SOFTWARE INDICATES YOUR ACCEPTANCE OF THESE TERMS. </p>
+<p>AGILENT SOFTWARE LICENSE TERMS</p>
+<p><strong><u>Software</u></strong>. “Software” means the Masshunter Data Access Component Runtime computer program in object code format.</p>
+<p><strong><u>License Grant</u></strong>. Agilent grants you a non-exclusive, non-transferable license to (a) use one copy of the Software for internal purposes in accordance with these License Terms and the documentation provided with the Software or (b) to distribute the Software for non-commercial purposes only and only bundled as part of, and for the sole purpose of running, products supplied by you. This Software is licensed for internal concurrent or network use of an unlimited n [...]
+<p><strong><u>License Restrictions</u></strong>. You may make copies or adaptations of the Software only for archival purposes or only when copying or adaptation is an essential step in the authorized use of the Software. You must reproduce all copyright notices in the original Software on all permitted copies or adaptations. You may not offer or provide unrestricted access to this Software on any public or distributed network.</p>
+<p><strong><u>Upgrades</u></strong>. This license does not entitle you to receive upgrades, updates or technical support. Such services may be purchased separately. </p>
+<p><strong><u>Ownership</u></strong>. <strong> </strong>The Software and all copies thereof are owned and copyrighted by Agilent. Agilent retains all right, title and interest in the Software. Agilent and its third party suppliers may protect their rights in the Software in the event of any violation of these License Terms.<strong><u></u></strong></p>
+<p><strong><u>No Disassembly</u></strong>. <strong> </strong>You may not disassemble, decompile or otherwise modify the Software without written authorization from Agilent, except as permitted by law. Upon request, you will provide Agilent with reasonably detailed information regarding any permitted disassembly, decompilation or modification.</p>
+<p><strong><u>High Risk Activities</u></strong>.<strong> </strong>The Software is not specifically designed, manufactured or intended for use in the planning, construction, maintenance or direct operation of a nuclear facility, nor for use in on line control or fail safe operation of aircraft navigation, control or communication systems, weapon systems or direct life support systems. </p>
+<p><strong><u>Termination</u></strong>. Agilent may terminate your license upon notice for breach of these License Terms. Upon termination, you must immediately destroy all copies of the Software.<strong><u></u></strong></p>
+<p><strong><u>No Warranty</u></strong>. THIS SOFTWARE IS LICENSED "AS IS" AND WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY, AND FITNESS FOR A PARTICULAR PURPOSE.
+</p>
+<p><strong><u>Limitation of Liability</u></strong>. TO THE EXTENT NOT PROHIBITED BY LAW, IN NO EVENT WILL AGILENT BE LIABLE FOR ANY LOST REVENUE, PROFIT OR DATA, OR FOR SPECIAL, INDIRECT, CONSEQUENTIAL, INCIDENTAL OR PUNITIVE DAMAGES, HOWEVER CAUSED REGARDLESS OF THE THEORY OF LIABILITY, ARISING OUT OF OR RELATED TO THE USE OF OR INABILITY TO USE SOFTWARE, EVEN IF AGILENT HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. In no event will Agilent's liability to you, whether in contract [...]
+<p><strong><u>Export Requirements</u></strong>. If you export, re-export or import Software, technology or technical data licensed hereunder, you assume responsibility for complying with applicable laws and regulations and for obtaining required export and import authorizations. Agilent may terminate this license immediately if you are in violation of any applicable laws or regulations.</p>
+<p><strong><u>U.S. Government Restricted Rights</u></strong>.<strong> </strong>Software and technical data rights granted to the federal government include only those rights customarily provided to end user customers. Agilent provides this customary commercial license in Software and technical data pursuant to FAR 12.211 (Technical Data) and 12.212 (Computer Software) and, for the Department of Defense, DFARS 252.227-7015 (Technical Data – Commercial Items) and DFARS 227.7202-3 (Rights [...]
+<hr />
+
+
+</div>
+ <li>Bruker CompassXtract</li>
+ <div class="lic-div">
+<div class=WordSection1>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>SOFTWARE LICENSE AGREEMENT for <span class=SpellE>CompassXtract</span> and <span
+class=SpellE>CompassXtract</span> Libraries</span></b></p>
+ <p style='text-autospace:none'><span class=SpellE><span style='font-family:Helvetica;'>Bruker</span></span><span style='font-family:
+Helvetica;'> <span
+class=SpellE>Daltonik</span> GmbH (hereinafter referred to as
+ "Licensor") has developed the <span class=SpellE>CompassXtract</span> software program (hereinafter referred to as "<span class=SpellE>CompassXtract</span>"),
+ which consists of documentation and individual <span class=SpellE>CompassXtract</span> libraries (hereinafter referred to as "<span class=SpellE>CompassXtract</span> <b>Libraries"). </b>These license terms constitute an agreement (hereinafter referred to as
+ "Agreement") between you and Licensor and shall be the legal basis
+ for any non-commercial usage of Licensor's <span class=SpellE>CompassXtract</span>.
+ These license terms also apply to any updates or supplements for <span
+class=SpellE>CompassXtract</span> or separable parts of <span class=SpellE>CompassXtract</span> such as <span class=SpellE>CompassXtract</span> Libraries, unless other terms
+ accompany those items, in which case those terms apply<span class=GramE>.
</span>You
+ may only use <span class=SpellE>CompassXtract</span> as a whole, if you have
+ downloaded it from Licensor's Webserver at http://www.bdal.de/compassxtract and
+ accepted this Agreement as binding between Licensor and you. However, <span
+class=GramE>certain individual <span class=SpellE>CompassXtract</span> Libraries might be conveyed to you by others</span>. In both cases, you may
+ only legally use <span class=SpellE>CompassXtract</span> or any of the <span
+class=SpellE>CompassXtract</span> Libraries conveyed to you after having
+ accepted this Agreement as binding between Licensor and you.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>1. Purpose of <span class=SpellE>CompassXtract</span> and License</span></b></p>
+ <p style='text-autospace:none'><span class=SpellE><span style='font-family:Helvetica;'>CompassXtract</span></span><span style='font-family:Helvetica;'> is provided as it is, in a trial and development stage, not yet marketable and
+ without any warranties regarding fitness for any purpose whatsoever. It may
+ contain errors and defects. The aim and purpose of providing it free of charge
+ and under the terms of this Agreement is to discover such errors and defects.
+ It is, inter alia but not limited to, not designed, manufactured or intended
+ for any use requiring fail-safe performance in which the failure of <span
+class=SpellE>CompassXtract</span> could lead to death, personal injury or
+ physical and environmental damage, such as the operation of medical facilities.
+ Nor is it, inter alia but not limited to, designed to perform any queries or
+ operations which might require reliable results and/or which might be the basis
+ for business and/or medical decisions. You agree not to use <span class=SpellE>CompassXtract</span> in connection with any such activities.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>2. Rights
+ Granted</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>You may
+ install and use <span class=SpellE>CompassXtract</span> on any of your
+ computing devices.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>3. Use
+ Restrictions</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>3.1 You may
+ not decompile, disassemble, reverse engineer or modify <span class=SpellE>CompassXtract</span>.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>3.2 You may
+ not distribute <span class=SpellE>CompassXtract</span> to others, breach of
+ which terminates the rights granted under this agreement. This also applies to
+ any integration or implementation of <span class=SpellE>CompassXtract</span> to
+ software developed by you or by others on your behalf (hereinafter referred to
+ as Own <b>Software) </b>or any distribution of which <span class=SpellE>CompassXtract</span> is <span class=GramE>part of.</span> However, you may distribute Own <span
+class=GramE>Software which requires the usage of</span> or links to <span
+class=SpellE>CompassXtract</span> Libraries if you comply with the requirements
+ set down in Section 4 of this Agreement.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>4.
+ Requirements for Distribution of your own Software using <span class=SpellE>CompassXtract</span> Libraries</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>You may only
+ distribute <span class=SpellE>CompassXtract</span> Libraries to others if all
+ of the following conditions are met: 4.1 <span class=GramE>You</span> distribute <span class=SpellE>CompassXtract</span> Libraries as part of Own
+ Software which you license to third parties</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>(<span
+class=GramE>hereinafter</span> "Your <b>Licensees");
</b>4.2
+ Your Own Software requires all the <span class=SpellE>CompassXtract</span> Libraries distributed by you in order to function</span></p>
+ <p style='text-autospace:none'><span class=GramE><span style='font-family:Helvetica;'>properly</span></span><span style='font-family:
+Helvetica;'> when used by
+ Your Licensees;</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>4.3 You
+ provide to Your Licensee a URL to Licensor's Webserver at
+ http://www.bdal.de/compassxtract and require Your Licensees, as condition for
+ being granted the right to use your Own Software, to acquire the usage rights
+ for <span class=SpellE>CompassXtract</span> directly from Licensor by agreeing
+ to the terms of this Agreement, which you distribute in unmodified form with
+ your Own Software.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>4.4 In your
+ Own Software's "About" box the following text is displayed: "This software uses <span class=SpellE>CompassXtract</span> software. <span class=GramE>Copyright $copy;
+ 2011 by <span class=SpellE>Bruker</span> <span class=SpellE>Daltonik</span> GmbH.</span> All rights reserved."</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>5.
+ Restrictions for Distribution of your own Products</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>5.1 You may
+ not use the Licensor's trademarks in a way that suggests your software
+ components and/or programs are provided by or are endorsed by the Licensor.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>5.2 You may
+ not commercially exploit <span class=SpellE>CompassXtract</span>, <span
+class=SpellE>CompassXtract</span> Libraries or products that require the usage
+ of or link to <span class=SpellE>CompassXtract</span> or <span class=SpellE>CompassXtract</span> Libraries. Commercial exploitation includes, but is not limited to, charging a
+ purchase price, license fee, maintenance fee, or subscription fee.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>5.3 Your
+ rights to <span class=SpellE>CompassXtract</span> do not include any license,
+ right, power or authority to subject <span class=SpellE>CompassXtract</span> in
+ whole or in part to any of the terms of an Excluded License. <b>"Excluded
+ License" </b>means any license that requires as a condition of use,
+ modification and/or distribution of software that such software or other
+ software combined and/or distributed with such software shall be (a) disclosed
+ or distributed in source code form; or (b) licensed for the purpose of making
+ derivative works. Without limiting the foregoing obligation, you are
+ specifically prohibited from distributing <span class=SpellE>CompassXtract</span> or <span class=SpellE>CompassXtract</span> Libraries with any software that is
+ subject to the General Public License (GPL) or similar license in a manner that
+ would create a combined work.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>6. Liability</span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>6.1 As
+ Licensor delivers the software for free, Licensor is not liable for any kind of
+ damage, direct or indirect, which may arise due to simple negligence (Section
+ 521 German Civil Code). In the event, that there should be – for whatever
+ reason – a statutory liability of Licensor for simple <span class=SpellE>negliegence</span>,
+ the aforementioned exclusion of liability applies nevertheless, but with the
+ exception of damages to life, body or health.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>6.2 You
+ indemnify, defend and hold harmless the Licensor from any liability claims,
+ including attorney fees, of third parties in connection with your usage of <span
+class=SpellE>CompassXtract</span> as well as the distribution of your Own <span
+class=GramE>Software which</span> requires usage of or links to <span
+class=SpellE>CompassXtract</span> Libraries and other circumstances for which
+ you are responsible.</span></p>
+ <p style='text-autospace:none'><b><span style='font-family:
+Helvetica;'>7. Additional
+ Terms Applicable to <span class=SpellE>CompassXtract</span></span></b></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.1 <span
+class=SpellE>CompassXtract</span> is licensed, not sold. This License only
+ gives you some rights to use <span class=SpellE>CompassXtract</span> and the <span
+class=SpellE>CompassXtract</span> Libraries; the Licensor reserves all other
+ rights. Unless applicable law gives you more rights despite this limitation,
+ you may use <span class=SpellE>CompassXtract</span> and the <span class=SpellE>CompassXtract</span> Libraries only as expressly permitted in this License.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.2 Licensor
+ has no obligation to fix, update, supplement or support <span class=SpellE>CompassXtract</span> and/or the <span class=SpellE>CompassXtract</span> Libraries.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.3 Your
+ rights under this License terminate automatically if you breach this License in
+ any way. Termination of this License will not affect any of your obligations or
+ liabilities arising prior to termination. The following sections of this
+ License shall survive termination: 3.1, 3.2, 5.1, 5.2, 5.3, 6.1<span
+class=GramE>.,</span> 6.2.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.4 No
+ subsidiary agreements of this Agreement have been made. Supplements and
+ amendments to this Agreement must be made in writing as prescribed by law in
+ order to be valid. The requirement of written form under this Agreement may be
+ waived in writing only.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.5 This
+ Agreement is governed by German law to the exclusion of the UN Convention on
+ Contracts for the International Sale of Goods. If you are a consumer, this does
+ not apply if legal provisions, in particular consumer protection legislation,
+ conflict with this choice. The courts of Bremen shall have exclusive
+ jurisdiction. If you are not a merchant, a legal entity under public law or a
+ public-law special fund in the sense Section 38 of the German Code of Civil
+ Procedure (ZPO), the <span class=GramE>agreement on the place of jurisdiction
+ is replaced by the legal provisions</span>.</span></p>
+ <p style='text-autospace:none'><span style='font-family:
+Helvetica;'>7.6 If
+ individual provisions of this Agreement are or become invalid or contain a <span
+class=GramE>gap which</span> needs to be filled, the validity of the remaining
+ provisions of the Agreement will not be affected thereby. The Parties hereby
+ undertake to substitute the invalid or lacking provision with a valid <span
+class=GramE>provision which</span> comes closest to the documented intentions
+ of the Parties.</span></p>
+</div>
+ </div>
+ <li>Thermo msFileReader</li>
+ <div class="lic-div">
+<p><strong>SOFTWARE LICENSE AGREEMENT (“License”) FOR MSFileReader</strong></p>
+<p>These License terms are an agreement between you and Thermo Finnigan LLC ("Licensor"). They apply to Licensor’s MSFileReader software program (“Software”), which includes documentation and any media on which you received it. These terms also apply to any updates or supplements for this Software, unless other terms accompany those items, in which case those terms apply. <strong>If you use this Software, you accept this License. If you do not accept this Lice [...]
+<p>1. Rights Granted:</p>
+<p>1.1. You may install and use this Software on any of your computing devices.</p>
+<p>1.2. You may distribute this Software to others, but only in combination with other software components and/or programs that you provide. </p>
+<p>2. Use Restrictions:</p>
+<p>2.1. You may not decompile, disassemble, reverse engineer or modify this Software.</p>
+<p>3. Distribution Requirements:</p>
+<p>If you distribute this Software to others, you agree to:</p>
+<p>3.1. Indemnify, defend and hold harmless the Licensor from any claims, including attorneys’ fees, related to the distribution or use of this Software;</p>
+<p>3.2. Display the following text in your software’s “About” box: “MSFileReader file reading tool. Copyright © 2009 by Thermo Fisher Scientific, Inc. All rights reserved.”;</p>
+<p>3.3. Require your end users to agree to a license agreement that prohibits them from redistributing this Software to others.</p>
+<p>4. Distribution Restrictions:</p>
+<p>4.1. You may not use the Licensor’s trademarks in a way that suggests your software components and/or programs are provided by or are endorsed by the Licensor; and</p>
+<p>4.2. You may not <a name="OLE_LINK1" id="OLE_LINK1">commercially exploit </a>this Software or products that incorporate this Software. Commercial exploitation includes, but is not limited to, charging a purchase price, license fee, maintenance fee, or subscription fee.</p>
+<p>4.3. Your rights to this Software do not include any license, right, power or authority to subject this Software in whole or in part to any of the terms of an Excluded License. "Excluded License" means any license that requires as a condition of use, modification and/or distribution of software subject to the Excluded License, that such software or other software combined and/or distributed with such software be (a) disclosed or distributed in source code form; or (b) licens [...]
+<p>5. Additional Terms Applicable to Software:</p>
+<p>5.1. This Software is licensed, not sold. This License only gives you some rights to use this Software; the Licensor reserves all other rights. Unless applicable law gives you more rights despite this limitation, you may use this Software only as expressly permitted in this License.</p>
+<p>5.2. Licensor has no obligation to fix, update, supplement or support this Software.</p>
+<p>5.3. This Software is not designed, manufactured or intended for any use requiring fail-safe performance in which the failure of this Software could lead to death, serious personal injury or severe physical and environmental damage (“High Risk Activities”), such as the operation of aircraft, medical or nuclear facilities. You agree not to use, or license the use of, this Software in connection with any High Risk Activities.</p>
+<p>5.4. Your rights under this License terminate automatically if you breach this License in any way. Termination of this License will not affect any of your obligations or liabilities arising prior to termination. The following sections of this License shall survive termination: 2.1, 3.1, 3.2, 3.3, 4.1, 4.2, 4.3, 5.1, 5.2, 5.3, 5.5, 5.6, 5.7, 5.8, and 5.9.</p>
+<p>5.5. This Software is subject to United States export laws and regulations. You agree to comply with all domestic and international export laws and regulations that apply to this Software. These laws include restrictions on destinations, end users and end use.</p>
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+<p>5.7. THIS SOFTWARE IS LICENSED "AS IS". YOU BEAR ALL RISKS OF USING IT. LICENSOR GIVES NO EXPRESS WARRANTIES, REPRESENTATIONS OR GUARANTEES. YOU MAY HAVE ADDITIONAL CONSUMER RIGHTS UNDER YOUR LOCAL LAWS WHICH THIS LICENSE CANNOT CHANGE. TO THE EXTENT PERMITTED UNDER YOUR LOCAL LAWS, LICENSOR EXCLUDES THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT.</p>
+<p>5.8. LICENSOR’S LIABILITY TO YOU FOR DIRECT DAMAGES ARISING UNDER THIS LICENSE IS LIMITED TO U.S. $1.00. YOU CANNOT RECOVER ANY OTHER DAMAGES, INCLUDING CONSEQUENTIAL, LOST PROFITS, SPECIAL, INDIRECT OR INCIDENTAL DAMAGES, EVEN IF LICENSOR IS EXPRESSLY MADE AWARE OF THE POSSIBILITY THEREOF OR IS NEGLIGENT. THIS LIMITATION APPLIES TO ANYTHING RELATED TO THIS SOFTWARE, SERVICES, CONTENT (INCLUDING CODE) ON THIRD PARTY INTERNET SITES, OR THIRD PARTY PROGRAMS, AND CLAIMS FOR BREACH [...]
+<p>5.9. Use, duplication or disclosure of this Software by the U.S. Government is subject to the restricted rights applicable to commercial computer software (under FAR 52.227019 and DFARS 252.227-7013 or parallel regulations). The manufacturer for this purpose is Thermo Finnigan LLC, 355 River Oaks Parkway, San Jose, California 95134, U.S.A.</p>
+ </div>
+ <li>Waters WRDAC</li>
+ <div class="lic-div">
+<p align="center"><strong>END-USER SOFTWARE LICENSE TERMS FOR WATERS WRDAC SOFTWARE</strong></p>
+<p>Waters grants you a nonexclusive and terminable license to (i) use the software to perform internal information and data processing in connection with Waters and other non-Waters instrumentation products for non-commercial purposes only and (ii) distribute the software as part of the ProteoWizard Software version 2.1 for non-commercial purposes only. You may not incorporate the software into a commercial application nor charge any fee for the software. The software is protected by [...]
+<p>THE SOFTWARE IS PROVIDED “AS IS” AND WITHOUT ANY WARRANTY, EXPRESS OR IMPLIED, BY STATUTE OR OTHERWISE, REGARDING THE WRDAC, INCLUDING WITHOUT LIMITATION THE WARRANTIES OF NON-INFRINGEMENT, FITNESS FOR A PARTICULAR PURPOSE AND MERCHANTABILITY. Waters shall not be liable for any direct, indirect, special, consequential or punitive damages of any kind arising out of or in connection with the software. In the event that the foregoing disclaimers are not effective under appl [...]
+<p>You agree to comply fully with all relevant export laws and regulations of the United States ("Export Laws") to ensure that the software is (a) not exported directly or indirectly in violation of Export Laws and (b) not intended to be used for any purposes prohibited by the Export Laws. If you are a branch of the United States government, you shall have "restricted rights" to use, duplicate, or disclose the software as set forth in subdivision (c)(1)(ii) of Rights [...]
+<p> </p>
+</div>
+</ul>
+
+<br />
+<H3> Step 3, Click below to agree to Licenses and get Crux</H3>
+
+<div style="width:600px;margin-left:10px;margin-top:10px;margin-bottom:10px;border:1px solid black;">
+The most recent build of Crux is temporarily unavailable for OS X.
+If you need a copy of Crux for OS X, please download release 3.0.
+</div>
+
+<input
+ type="submit"
+ name="release_button"
+ value="I agree to the licensing terms, download release 3.0 of Crux"
+/>
+<br/>
+<input
+ type="submit"
+ name="daily_button"
+ value="I agree to the licensing terms, download the most recent build of Crux"
+/>
+</form>
+
+<br>
+<br>
+<br>
+
+ <p>
+Note that you can access the most recent source code from the Crux main development
+trunk using the following Git command:<br>
+<code> git clone https://github.com/crux-toolkit/crux-toolkit.git crux-toolkit</code></p>
+
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
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+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/example-files/default.params b/doc/user/example-files/default.params
new file mode 100644
index 0000000..5e447aa
--- /dev/null
+++ b/doc/user/example-files/default.params
@@ -0,0 +1,1676 @@
+################################################################################
+# Sample parameter file
+#
+# On each line, anything after a '#' will be ignored.
+# The format is:
+#
+# <parameter-name>=<value>
+#
+################################################################################
+
+# Crux parameter file (generated by Crux version 2.1)
+# Full documentation available at http://cruxtoolkit.sourceforge.net/
+# comet_version 2016.01 rev. 1
+# Everything following the '#' symbol is treated as a comment.
+
+# Path where pin file will be written instead of make-pin.pin.
+# It is optional for make-pin
+output-file=
+
+# Specify the verbosity of the current processes. Each level prints the
+# following messages, including all those at lower verbosity levels: 0-fatal
+# errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of
+# execution, 40-more progress information, 50-debug info, 60-detailed debug
+# info.
+# Available for all crux programs.
+verbosity=30
+
+# A file containing parameters.
+# Available for all crux programs. Any options specified on the command line
+# will override values in the parameter file.
+parameter-file=
+
+# Replace existing files if true or fail when trying to overwrite a file if
+# false.
+# Available for all crux programs. Applies to parameter file as well as index,
+# search, and analysis output files.
+overwrite=false
+
+# The minimum length of peptides to consider.
+# Used from the command line or parameter file by crux-generate-peptides, and
+# crux tide-index.
+min-length=6
+
+# The maximum length of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides, crux
+# tide-index.
+max-length=50
+
+# The minimum mass (in Da) of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides and
+# crux tide-index.
+min-mass=200
+
+# The maximum mass (in Da) of peptides to consider.
+# Available from command line or parameter file for crux-generate-peptides and
+# crux tide-index.
+max-mass=7200
+
+# The minimum number of peaks a spectrum must have for it to be searched.
+# Available for tide-search.
+min-peaks=20
+
+# Specify the enzyme used to digest the proteins in silico. Available enzymes
+# (with the corresponding digestion rules indicated in parentheses) include
+# no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin
+# ([FWYL]|{P}), elastase ([ALIV]|{P}), clostripain ([R]|[]), cyanogen-bromide
+# ([M]|[]), iodosobenzoate ([W]|[]), proline-endopeptidase ([P]|[]),
+# staph-protease ([E]|[]), asp-n ([]|[D]), lys-c ([K]|{P}), lys-n ([]|[K]),
+# arg-c ([R]|{P}), glu-c ([DE]|{P}), pepsin-a ([FL]|{P}),
+# elastase-trypsin-chymotrypsin ([ALIVKRWFY]|{P}). Specifying --enzyme no-enzyme
+# yields a non-enzymatic digest. Warning: the resulting index may be quite
+# large.
+# Available for crux-generate-peptides and crux tide-index.
+enzyme=trypsin
+
+# Specify rules for in silico digestion of protein sequences. Overrides the
+# enzyme option. Two lists of residues are given enclosed in square brackets or
+# curly braces and separated by a |. The first list contains residues
+# required/prohibited before the cleavage site and the second list is residues
+# after the cleavage site. If the residues are required for digestion, they are
+# in square brackets, '[' and ']'. If the residues prevent digestion, then they
+# are enclosed in curly braces, '{' and '}'. Use X to indicate all residues. For
+# example, trypsin cuts after R or K but not before P which is represented as
+# [RK]|{P}. AspN cuts after any residue but only before D which is represented
+# as [X]|[D].
+#
+custom-enzyme=
+
+# Specify whether every peptide in the database must have two enzymatic termini
+# (full-digest) or if peptides with only one enzymatic terminus are also
+# included (partial-digest).
+# Available for crux-generate-peptides and crux tide-index.
+digestion=full-digest
+
+# Maximum number of missed cleavages per peptide to allow in enzymatic
+# digestion.
+# Available from command line or parameter file for crux-generate-peptides. When
+# used with enzyme=<trypsin|elastase|chymotrypsin> includes peptides containing
+# one or more potential cleavage sites.
+missed-cleavages=0
+
+# Tolerance used for matching peptides to spectra. Peptides must be within +/-
+# 'precursor-window' of the spectrum value. The precursor window units depend
+# upon precursor-window-type.
+# Available for tide-search and crux-generate-peptides.
+precursor-window=3
+
+# Specify the units for the window that is used to select peptides around the
+# precursor mass location (mass, mz, ppm). The magnitude of the window is
+# defined by the precursor-window option, and candidate peptides must fall
+# within this window. For the mass window-type, the spectrum precursor m+h value
+# is converted to mass, and the window is defined as that mass +/-
+# precursor-window. If the m+h value is not available, then the mass is
+# calculated from the precursor m/z and provided charge. The peptide mass is
+# computed as the sum of the average amino acid masses plus 18 Da for the
+# terminal OH group. The mz window-type calculates the window as spectrum
+# precursor m/z +/- precursor-window and then converts the resulting m/z range
+# to the peptide mass range using the precursor charge. For the
+# parts-per-million (ppm) window-type, the spectrum mass is calculated as in the
+# mass type. The lower bound of the mass window is then defined as the spectrum
+# mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as
+# spectrum mass / (1.0 - (precursor-window / 1000000)).
+# Available for search-for-xlinks and tide-search.
+precursor-window-type=mass
+
+# Specify the parser to use for reading in MS/MS spectra.
+# Available for search-for-xlinks.
+spectrum-parser=pwiz
+
+# Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor
+# mass information from the "S" line or the "Z" line.
+# Available when spectrum-parser = pwiz.
+use-z-line=true
+
+# When creating decoy peptides using decoy-format=shuffle or
+# decoy-format=peptide-reverse, this option specifies whether the N-terminal and
+# C-terminal amino acids are kept in place or allowed to be shuffled or
+# reversed. For a target peptide "EAMPK" with decoy-format=peptide-reverse,
+# setting keep-terminal-aminos to "NC" will yield "EPMAK"; setting it to "C"
+# will yield "PMAEK"; setting it to "N" will yield "EKPMA"; and setting it to
+# "none" will yield "KPMAE".
+# Available for tide-index.
+keep-terminal-aminos=NC
+
+# Create in the output directory a text file listing of all the peptides in the
+# database, along with their neutral masses, one per line. If decoys are
+# generated, then a second file will be created containing the decoy peptides.
+# Decoys that also appear in the target database are marked with an asterisk in
+# a third column.
+# Available for tide-index.
+peptide-list=false
+
+# Stop after the specified pre-processing step.
+# Available for print-processed-spectra.
+stop-after=xcorr
+
+# Specify the output units for processed spectra.
+# Available for print-processed-spectra
+output-units=bin
+
+# Outputs an SQT results file to the output directory. Note that if sqt-output
+# is enabled, then compute-sp is automatically enabled and cannot be overridden.
+# Available for tide-search.
+sqt-output=false
+
+# Output an mzIdentML results file to the output directory.
+# Available for tide-search, percolator.
+mzid-output=false
+
+# Output a Percolator input (PIN) file to the output directory.
+# Available for tide-search.
+pin-output=false
+
+# Output a Percolator pout.xml format results file to the output directory.
+# Available for percolator.
+pout-output=false
+
+# Output a pepXML results file to the output directory.
+# Available for tide-search, q-ranker, barista, percolator.
+pepxml-output=false
+
+# Output a tab-delimited results file to the output directory.
+# Available for tide-search, percolator, q-ranker, barista.
+txt-output=true
+
+# Compute the preliminary score Sp for all candidate peptides. Report this score
+# in the output, along with the corresponding rank, the number of matched ions
+# and the total number of ions. This option is recommended if results are to be
+# analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp
+# is automatically enabled and cannot be overridden. Note that the Sp
+# computation requires re-processing each observed spectrum, so turning on this
+# switch involves significant computational overhead.
+# Available for tide-search.
+compute-sp=false
+
+# Estimate the parameters of the score distribution for each spectrum by fitting
+# to a Weibull distribution, and compute a p-value for each xlink product. This
+# option is only available when use-old-xlink=F.
+# Currently only implemented for XCORR.
+compute-p-values=false
+
+# A single scan number or a range of numbers to be searched. Range should be
+# specified as 'first-last' which will include scans 'first' and 'last'.
+# The search range x-y is inclusive of x and y.
+scan-number=
+
+# Before calculation of the XCorr score, the m/z axes of the observed and
+# theoretical spectra are discretized. This parameter specifies the size of each
+# bin. The exact formula is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where
+# x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079
+# and for high resolution ms/ms 0.02 is recommended.
+# Available for tide-search and xlink-assign-ions.
+mz-bin-width=1.0005079
+
+# In the discretization of the m/z axes of the observed and theoretical spectra,
+# this parameter specifies the location of the left edge of the first bin,
+# relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the
+# first bin will be located at +0.xx Da).
+# Available for tide-search.
+mz-bin-offset=0.4
+
+# Include flanking peaks around singly charged b and y theoretical ions. Each
+# flanking peak occurs in the adjacent m/z bin and has half the intensity of the
+# primary peak.
+# Available for the tide-search and search-for-xlinks commands.
+use-flanking-peaks=false
+
+# The lowest spectrum m/z to search in the ms2 file.
+# Available for tide-search.
+spectrum-min-mz=0
+
+# The highest spectrum m/z to search in the ms2 file.
+# Available for tide-search.
+spectrum-max-mz=1e+009
+
+# The spectrum charges to search. With 'all' every spectrum will be searched and
+# spectra with multiple charge states will be searched once at each charge
+# state. With 1, 2, or 3 only spectra with that charge state will be searched.
+# Used by tide-search.
+spectrum-charge=all
+
+# The fileroot string will be added as a prefix to all output file names.
+# Available for all commands that produce an output directory.
+fileroot=
+
+# The name of the directory where output files will be created.
+# Available for most commands.
+output-dir=crux-output
+
+# Specify the number of matches to report for each spectrum.
+# Available for tide-search and crux percolator
+top-match=5
+
+# When given a unsigned integer value seeds the random number generator with
+# that value. When given the string "time" seeds the random number generator
+# with the system time.
+# Available for all Crux commands.
+seed=1
+
+# Specify which isotopes to use in calculating fragment ion mass.
+# Used by crux-predict-peptide-ions.
+fragment-mass=mono
+
+# Specify the type of isotopic masses to use when calculating the peptide mass.
+# Used from command line or parameter file by crux-generate-peptides.
+isotopic-mass=mono
+
+# The minimum number of modifications that can be applied to a single peptide.
+# Available for tide-index.
+min-mods=0
+
+# The maximum number of modifications that can be applied to a single peptide.
+# Available for tide-index.
+max-mods=255
+
+# Specify how sequence modifications are reported in various output files. Each
+# modification is reported as a number enclosed in square braces following the
+# modified residue; however, the number may correspond to one of three different
+# masses: (1) 'mod-only' reports the value of the mass shift induced by the
+# modification; (2) 'total' reports the mass of the residue with the
+# modification (residue mass plus modification mass); (3) 'separate' is the same
+# as 'mod-only', but multiple modifications to a single amino acid are reported
+# as a comma-separated list of values. For example, suppose amino acid D has an
+# unmodified mass of 115 as well as two moifications of masses +14 and +2. In
+# this case, the amino acid would be reported as D[16] with 'mod-only', D[131]
+# with 'total', and D[14,2] with 'separate'.
+# Available for generate-peptides.
+mod-mass-format=mod-only
+
+# Consider a-ions in the search? Note that an a-ion is equivalent to a neutral
+# loss of CO from the b-ion. Peak height is 10 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-a-ions=false
+
+# Consider b-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-b-ions=true
+
+# Consider c-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-c-ions=false
+
+# Consider x-ions in the search? Peak height is 10 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-x-ions=false
+
+# Consider y-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-y-ions=true
+
+# Consider z-ions in the search? Peak height is 50 (in arbitrary units).
+# Available for search-for-xlinks and xlink-score-spectrum.
+use-z-ions=false
+
+# Set the precision for scores written to sqt and text files. Note that this
+# parameter only takes effect when specified in the parameter file.
+# Available percolator.
+precision=8
+
+# Set the precision for masses and m/z written to sqt and .txt files. Note that
+# this parameter only takes effect when specified in the parameter file.
+# Available for all commands.
+mass-precision=4
+
+# Show search progress by printing every n spectra searched. Set to 0 to show no
+# search progress.
+# Available for tide-search
+print-search-progress=1000
+
+# When given a unsigned integer value seeds the random number generator with
+# that value. When given the string "time" seeds the random number generator
+# with the system time.
+# Available for all percolator
+percolator-seed=1
+
+# Output the computed features in tab-delimited text format.
+# Available for percolator and q-ranker.
+feature-file-out=false
+
+# Include decoys (PSMs, peptides, and/or proteins) in the XML output.
+# Available for crux percolator
+decoy-xml-output=false
+
+# Specifies the prefix of the protein names that indicate a decoy.
+# Available for percolator
+decoy-prefix=decoy_
+
+# Output final weights to a file named "percolator.weights.txt".
+# Available for crux percolator
+output-weights=false
+
+# Read initial weights from the given file (one per line).
+# Available for crux percolator
+init-weights=
+
+# Penalty for mistakes made on positive examples. If this value is not
+# specified, then it is set via cross validation over the values {0.1, 1, 10},
+# selecting the value that yields the largest number of PSMs identified at the
+# q-value threshold set via the --test-fdr parameter.
+# Available for crux percolator
+c-pos=0.01
+
+# Penalty for mistake made on negative examples. This parameter requires the
+# c-pos is set explicitly; otherwise, --c-neg will have no effect. If not
+# specified, then this value is set by cross validation over {0.1, 1, 10}.
+# Available for crux percolator
+c-neg=0
+
+# False discovery rate threshold to define positive examples in training.
+# Available for crux percolator
+train-fdr=0.01
+
+# False discovery rate threshold used in selecting hyperparameters during
+# internal cross-validation and for reporting the final results.
+# Available for crux percolator.
+test-fdr=0.01
+
+# Apply the specified threshold to PSM, peptide and protein probabilities to
+# obtain a faster estimate of the alpha, beta and gamma parameters.
+# Available for crux percolator.
+fido-fast-gridsearch=0
+
+# Approximate the posterior distribution by allowing large graph components to
+# be split into subgraphs. The splitting is done by duplicating peptides with
+# low probabilities. Splitting continues until the number of possible
+# configurations of each subgraph is below 2^18
+# Available for crux percolator
+fido-split-large-components=false
+
+# To speed up inference, proteins for which none of the associated peptides has
+# a probability exceeding the specified threshold will be assigned probability =
+# 0.
+# Available for crux percolator
+fido-protein-truncation-threshold=0.01
+
+# Replace the target-decoy competition with the method qvality to assign
+# q-values and PEPs. Note that this option only has an effect if the input PSMs
+# are from separate target and decoy searches.
+# Available for crux percolator
+post-processing-qvality=false
+
+# Maximum number of iterations for training.
+# Available for crux percolator
+maxiter=10
+
+# Quicker execution by reduced internal cross-validation.
+# Available for crux percolator
+quick-validation=false
+
+# In its initial round of training, Percolator uses one feature to induce a
+# ranking of PSMs. By default, Percolator will select the feature that produces
+# the largest set of target PSMs at a specified FDR threshold (cf. --train-fdr).
+# This option allows the user to specify which feature is used for the initial
+# ranking, using the name as a string. The name can be preceded by a hyphen
+# (e.g. "-XCorr") to indicate that a lower value is better.
+# Available for crux percolator
+default-direction=
+
+# Use unit normalization (i.e., linearly rescale each PSM's feature vector to
+# have a Euclidean length of 1), instead of standard deviation normalization.
+# Available for crux percolator.
+unitnorm=false
+
+# Measure performance on test set each iteration.
+# Available for crux percolator.
+test-each-iteration=false
+
+# When set to T, interpret the input file as a PIN file.
+# Available for crux percolator.
+feature-file-in=false
+
+# Use the Fido algorithm to infer protein probabilities. Must be true to use any
+# of the Fido options.
+# Available for crux percolator
+protein=false
+
+# Specify the probability with which a present protein emits an associated
+# peptide. Set by grid search (see --fido-gridsearch-depth parameter) if not
+# specified.
+# Available for crux percolator if --protein T is set.
+fido-alpha=0
+
+# Specify the probability of the creation of a peptide from noise. Set by grid
+# search (see --fido-gridsearch-depth parameter) if not specified.
+# Available for crux percolator if --protein T is set.
+fido-beta=0
+
+# Specify the prior probability that a protein is present in the sample. Set by
+# grid search (see --fido-gridsearch-depth parameter) if not specified.
+# Available for crux percolator if --protein T is set.
+fido-gamma=0
+
+# Use pi_0 value when calculating empirical q-values
+# Available for crux percolator if --protein T is set.
+fido-protein-level-pi0=false
+
+# Estimate empirical p-values and q-values for proteins using target-decoy
+# analysis.
+# Available for crux percolator if --protein T is set.
+fido-empirical-protein-q=false
+
+# Set depth of the grid search for alpha, beta and gamma estimation.
+# Available for crux percolator if --protein T is set.
+fido-gridsearch-depth=0
+
+# Use target-decoy competition to assign q-values and PEPs.
+# Available for crux percolator
+post-processing-tdc=false
+
+# Q-value threshold that will be used in the computation of the MSE and ROC AUC
+# score in the grid search.
+# Available for crux percolator if --protein T is set.
+fido-gridsearch-mse-threshold=0.05
+
+# By default, Percolator will examine the learned weights for each feature, and
+# if the weight appears to be problematic, then percolator will discard the
+# learned weights and instead employ a previously trained, static score vector.
+# This switch allows this error checking to be overriden.
+# Available for crux percolator.
+override=false
+
+# Use retention time features calculated as in "Improving tandem mass spectrum
+# identification using peptide retention time prediction across diverse
+# chromatography conditions" by Klammer AA, Yi X, MacCoss MJ and Noble WS.
+# (Analytical Chemistry. 2007 Aug 15;79(16):6111-8.).
+# Available for crux percolator
+klammer=false
+
+# Do not remove redundant peptides; keep all PSMs and exclude peptide level
+# probability.
+# Available for crux percolator
+only-psms=false
+
+# Include a decoy version of every peptide by shuffling or reversing the target
+# sequence or protein. In shuffle or peptide-reverse mode, each peptide is
+# either reversed or shuffled, leaving the N-terminal and C-terminal amino acids
+# in place. Note that peptides appear multiple times in the target database are
+# only shuffled once. In peptide-reverse mode, palindromic peptides are
+# shuffled. Also, if a shuffled peptide produces an overlap with the target or
+# decoy database, then the peptide is re-shuffled up to 5 times. Note that,
+# despite this repeated shuffling, homopolymers will appear in both the target
+# and decoy database. The protein-reverse mode reverses the entire protein
+# sequence, irrespective of the composite peptides.
+# Available for tide-index
+decoy-format=shuffle
+
+# Expression for static and variable mass modifications to include. Specify a
+# comma-separated list of modification sequences of the form:
+# C+57.02146,2M+15.9949,1STY+79.966331,...
+# Available for tide-index
+mods-spec=C+57.02146
+
+# Specifies N-terminal static and variable mass modifications on peptides.
+# Specify a comma-separated list of N-terminal modification sequences of the
+# form: 1E-18.0106,C-17.0265
+# Available for tide-index
+nterm-peptide-mods-spec=
+
+# Specifies C-terminal static and variable mass modifications on peptides.
+# Specify a comma-separated list of C-terminal modification sequences of the
+# form: X+21.9819
+# Available for tide-index
+cterm-peptide-mods-spec=
+
+# Specify the name of the file where the binarized fragmentation spectra will be
+# stored. Subsequent runs of crux tide-search will execute more quickly if
+# provided with the spectra in binary format. The filename is specified relative
+# to the current working directory, not the Crux output directory (as specified
+# by --output-dir). This option is not valid if multiple input spectrum files
+# are given.
+# Available for tide-search
+store-spectra=
+
+# Enable the calculation of exact p-values for the XCorr score. Calculation of
+# p-values increases the running time but increases the number of
+# identifications at a fixed confidence threshold. The p-values will be reported
+# in a new column with header "exact p-value", and the "xcorr score" column will
+# be replaced with a "refactored xcorr" column. Note that, currently, p-values
+# can only be computed when the mz-bin-width parameter is set to its default
+# value. Variable and static mods are allowed on non-terminal residues in
+# conjunction with p-value computation, but currently only static mods are
+# allowed on the N-terminus, and no mods on the C-terminus.
+# Available for tide-search
+exact-p-value=false
+
+# When providing a FASTA file as the index, the generated binary index will be
+# stored at the given path. This option has no effect if a binary index is
+# provided as the index.
+# Available for tide-search
+store-index=
+
+# When set to T, target and decoy search results are reported in a single file,
+# and only the top-scoring N matches (as specified via --top-match) are reported
+# for each spectrum, irrespective of whether the matches involve target or decoy
+# peptides.
+# Available for tide-search
+concat=false
+
+# Include the file column in tab-delimited output.
+# Available for tide-search
+file-column=true
+
+# If true, all peaks around the precursor m/z will be removed, within a range
+# specified by the --remove-precursor-tolerance option.
+# Available for tide-search.
+remove-precursor-peak=false
+
+# This parameter specifies the tolerance (in Th) around each precursor m/z that
+# is removed when the --remove-precursor-peak option is invoked.
+# Available for print-processed spectra and tide-search.
+remove-precursor-tolerance=1.5
+
+# When set to T, for each protein that begins with methionine, tide-index will
+# put two copies of the leading peptide into the index, with and without the
+# N-terminal methionine.
+# Available for tide-index.
+clip-nterm-methionine=false
+
+# Prevent duplicate peptides between the target and decoy databases. When set to
+# "F", the program keeps all target and previously generated decoy peptides in
+# memory. A shuffled decoy will be re-shuffled multiple times to avoid
+# duplication. If a non-duplicated peptide cannot be generated, the decoy is
+# skipped entirely. When set to "T", every decoy is added to the database
+# without checking for duplication. This option reduces the memory requirements
+# significantly. Default = F.
+# Available for tide-index.
+allow-dups=false
+
+# Controls whether neutral loss ions are considered in the search. Two types of
+# neutral losses are included and are applied only to singly charged b- and
+# y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each
+# neutral loss peak has intensity 1/5 of the primary peak.
+# Available for tide-search.
+use-neutral-loss-peaks=true
+
+# The maximum charge state of a spectra to consider in search.
+# Available for tide-search.
+max-precursor-charge=5
+
+# Carries out a peptide-centric search. For each peptide the top-scoring spectra
+# are reported, in contrast to the standard spectrum-centric search where the
+# top-scoring peptides are reported. Note that in this case the "xcorr rank"
+# column will contain the rank of the given spectrum with respect to the given
+# candidate peptide, rather than vice versa (which is the default).
+# Available for tide-search.
+peptide-centric-search=false
+
+# 0=poll CPU to set num threads; else specify num threads directly.
+# Available for tide-search tab-delimited files only.
+num-threads=0
+
+# Analysis begins with a pre-processsing step that creates a set of lookup
+# tables which are then used during training. Normally, these lookup tables are
+# deleted at the end of the analysis, but setting this option to T prevents the
+# deletion of these tables. Subsequently, analyses can be repeated more
+# efficiently by specifying the --re-run option.
+# Available for q-ranker and barista.
+skip-cleanup=false
+
+# Re-run a previous analysis using a previously computed set of lookup tables.
+# For this option to work, the --skip-cleanup option must have been set to true
+# when the program was run the first time.
+# Available for q-ranker and barista.
+re-run=
+
+# Use an enriched feature set, including separate features for each ion type.
+# Available for q-ranker and barista.
+use-spec-features=true
+
+# If the target and decoy searches were run separately, rather than using a
+# concatenated database, then the program will assume that the database search
+# results provided as a required argument are from the target database search.
+# This option then allows the user to specify the location of the decoy search
+# results. Like the required arguments, these search results can be provided as
+# a single file, a list of files or a directory. However, the choice (file, list
+# or directory) must be consistent for the MS2 files and the target and decoy
+# tab-delimited files. Also, if the MS2 and tab-delimited files are provided in
+# directories, then Q-ranker will use the MS2 filename (foo.ms2) to identify
+# corresponding target and decoy tab-delimited files with names like
+# foo*.target.txt and foo*.decoy.txt. This naming convention allows the target
+# and decoy txt files to reside in the same directory.
+# Available for q-ranker and barista.
+separate-searches=
+
+# Specify that the search results are provided as lists of files, rather than as
+# individual files.
+# Available for barista and percolator.
+list-of-files=false
+
+# Specifies whether to do optimization at the protein, peptide or psm level.
+# Available for barista.
+optimization=protein
+
+# Specify the method used to estimate q-values: the mix-max procedure or
+# target-decoy competition. peptide-level is applied for spectrum-centric
+# search. Eliminates any PSMS for which there exists a better scoring PSM
+# involving the same peptide.
+# Used by assign-confidence.
+estimation-method=tdc
+
+# Adjust the score using the Sidak adjustment and reports them in a new column
+# in the output file. Note that this adjustment only makes sense if the given
+# scores are p-values, and that it requires the presence of the "distinct
+# matches/spectrum" feature for each PSM.
+# Used by assign-confidence.
+sidak=false
+
+# Specify the column (for tab-delimited input) or tag (for XML input) used as
+# input to the q-value estimation procedure. If this parameter is unspecified,
+# then assign-confidence tries to seach for "xcorr score", "evalue" (comet),
+# "exact p-value" score fields in this order in the input file.
+# Used by assign-confidence.
+score=
+
+# Specify this parameter to T in order to combine charge states with peptide
+# sequencesin peptide-centric search. Works only if peptide-level=T.
+# Used by assign-confidence.
+combine-charge-states=false
+
+# Specify this parameter to T in order to treat peptides carrying different or
+# no modifications as being the same. Works only if peptide-level=T.
+# Used by assign-confidence.
+combine-modified-peptides=false
+
+# The q-value threshold used by cascade search. Spectra identified with q-value
+# less than this threshold in one search will be excluded from all subsequent
+# searches.
+# Used by Cascade-Search
+q-value-threshold=0.01
+
+# Predict the specified primary ion series. 'a' indicates a-ions only, 'b'
+# indicates b-ions only, 'y' indicates y-ions only, 'by' indicates both b and y,
+# 'bya' indicates b, y, and a.
+# Only available for crux-predict-peptide-ions. Set automatically to 'by' for
+# searching.
+primary-ions=by
+
+# Predict the precursor ions, and all associated ions (neutral losses, multiple
+# charge states) consistent with the other specified options.
+# Only available for crux-predict-peptide-ions.
+precursor-ions=false
+
+# Predict the given number of isotope peaks (0|1|2).
+# Only available for crux-predict-peptide-ion. Automatically set to 0 for Sp
+# scoring and 1 for xcorr scoring.
+isotope=0
+
+# Predict flanking peaks for b- and y ions.
+# Only available for crux-predict-peptide-ion.
+flanking=false
+
+# Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the
+# charge state of the peptide ("peptide"). If the max-ion-charge is greater than
+# the charge state of the peptide, then the maximum is the peptide charge.
+# Available for predict-peptide-ions and search-for-xlinks. Set to 'peptide' for
+# search.
+max-ion-charge=peptide
+
+# Include among the predicted peaks b/y ions with up to n losses of nh3. For
+# example, for --nh3 2, predict a peak for each b- and y-ion with the loss of
+# one nh3 group and predict a second peak for each b- and y-ion with the loss of
+# two nh3 groups. These peaks will have 1 and 2, respectively, in the NH3 column
+# of the output.
+# Only available for crux-predict-peptide-ions.
+nh3=0
+
+# Include in the predicted peaks, b/y ions with the loss of 1 to n water
+# molecules. See --nh3 for an example.
+# Only available for crux-predict-peptide-ions.
+h2o=0
+
+# The name of the file in FASTA format.
+# Option for spectral-counts
+protein-database=
+
+# Type of analysis to make on the match results: (RAW|NSAF|dNSAF|SIN|EMPAI).
+# With exception of the RAW metric, the database of sequences need to be
+# provided using --protein-database.
+# Available for spectral-counts. RAW is raw counts, NSAF is Normalized Spectral
+# Abundance Factor, dNSAF is Distributed Spectral Abundance Factor, SIN is
+# Spectral Index Normalized and EMPAI is Exponentially Modified Protein
+# Abundance Index
+measure=NSAF
+
+# Ignore peptides that map to multiple proteins.
+# Available for spectral-counts.
+unique-mapping=false
+
+# Quantification at protein or peptide level.
+# Available for spectral-counts and either NSAF and SIN.
+quant-level=protein
+
+# Perform a parsimony analysis on the proteins, and report a "parsimony rank"
+# column in the output file. This column contains integers indicating the
+# protein's rank in a list sorted by spectral counts. If the parsimony analysis
+# results in two proteins being merged, then their parsimony rank is the same.
+# In such a case, the rank is assigned based on the largest spectral count of
+# any protein in the merged meta-protein. The "simple" parsimony algorithm only
+# merges two proteins A and B if the peptides identified in protein A are the
+# same as or a subset of the peptides identified in protein B. The "greedy"
+# parsimony algorithm does additional merging, using the peptide q-values to
+# greedily assign each peptide to a single protein.
+# Available for spectral-counts.
+parsimony=none
+
+# Determines what type of threshold to use when filtering matches. none : read
+# all matches, qvalue : use calculated q-value from percolator or q-ranker,
+# custom : use --custom-threshold-name and --custom-threshold-min parameters.
+# used for crux spectral-counts
+threshold-type=qvalue
+
+# Only consider PSMs with a threshold value. By default, q-values are
+# thresholded using a specified threshold value. This behavior can be changed
+# using the --custom-threshold and --threshold-min parameters.
+# Available for spectral-counts. All PSMs with higher (or lower) than this will
+# be ignored.
+threshold=0.01
+
+# Specify which field to apply the threshold to. The direction of the threshold
+# (<= or >=) is governed by --custom-threshold-min. By default, the threshold
+# applies to the q-value, specified by "percolator q-value", "q-ranker q-value",
+# "decoy q-value (xcorr)", or "barista q-value".
+# Available for spectral-counts.
+custom-threshold-name=
+
+# When selecting matches with a custom threshold, custom-threshold-min
+# determines whether to filter matches with custom-threshold-name values that
+# are greater-than or equal (F) or less-than or equal (T) than the threshold.
+# Available for spectral-counts.
+custom-threshold-min=true
+
+# MS2 file corresponding to the psm file. Required to measure the SIN. Ignored
+# for NSAF, dNSAF and EMPAI.
+# Available for spectral-counts with measure=SIN.
+input-ms2=
+
+# Use mzid's passThreshold attribute to filter matches.
+# Used when parsing mzIdentML files.
+mzid-use-pass-threshold=false
+
+# Change the mass of all amino acids 'A' by the given amount.
+#
+A=0
+
+# Change the mass of all amino acids 'C' by the given amount.
+#
+C=57.021464
+
+# Change the mass of all amino acids 'D' by the given amount.
+#
+D=0
+
+# Change the mass of all amino acids 'E' by the given amount.
+#
+E=0
+
+# Change the mass of all amino acids 'F' by the given amount.
+#
+F=0
+
+# Change the mass of all amino acids 'G' by the given amount.
+#
+G=0
+
+# Change the mass of all amino acids 'H' by the given amount.
+#
+H=0
+
+# Change the mass of all amino acids 'I' by the given amount.
+#
+I=0
+
+# Change the mass of all amino acids 'K' by the given amount.
+#
+K=0
+
+# Change the mass of all amino acids 'L' by the given amount.
+#
+L=0
+
+# Change the mass of all amino acids 'M' by the given amount.
+#
+M=0
+
+# Change the mass of all amino acids 'N' by the given amount.
+#
+N=0
+
+# Change the mass of all amino acids 'P' by the given amount.
+#
+P=0
+
+# Change the mass of all amino acids 'Q' by the given amount.
+#
+Q=0
+
+# Change the mass of all amino acids 'R' by the given amount.
+#
+R=0
+
+# Change the mass of all amino acids 'S' by the given amount.
+#
+S=0
+
+# Change the mass of all amino acids 'T' by the given amount.
+#
+T=0
+
+# Change the mass of all amino acids 'V' by the given amount.
+#
+V=0
+
+# Change the mass of all amino acids 'W' by the given amount.
+#
+W=0
+
+# Change the mass of all amino acids 'Y' by the given amount.
+#
+Y=0
+
+# Legal values are auto, tsv, sqt, pin, pepxml or mzidentml format.
+# option, for psm-convert
+input-format=auto
+
+# Whether matches/ion are distinct (as opposed to total).
+# option, for psm-convert.
+distinct-matches=true
+
+# Rather than the spectrum, output summary statistics to standard output. Each
+# statistic is placed on a separate line, in the format <name>:<value> (e.g.
+# "TIC:1000.0").
+# Available only for crux-get-ms2-spectrum. Does not affect contents of the
+# output file.
+stats=false
+
+# Print the theoretical spectrum
+# Available for xlink-predict-peptide-ions.
+print-theoretical-spectrum=false
+
+# Use the old version of xlink-searching algorithm. When false, a new version of
+# the code is run. The new version supports variable modifications and can
+# handle more complex databases. This new code is still in development and
+# should be considered a beta release.
+# Available for search-for-xlinks program.
+use-old-xlink=true
+
+# Score method for xlink {composite, modification, concatenated}.
+# Available for xlink-score-spectrum.
+xlink-score-method=composite
+
+# Provides a list of isotopic windows to search. For example, -1,0,1 will search
+# in three disjoint windows: (1) precursor_mass - neutron_mass +/- window, (2)
+# precursor_mass +/- window, and (3) precursor_mass + neutron_mass +/- window.
+# The window size is defined from the precursor-window and precursor-window-type
+# parameters. This option is only available when use-old-xlink=F.
+# Used for crux search-for-xlinks
+isotope-windows=0
+
+# Include linear peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-linears=true
+
+# Include dead-end peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-deadends=true
+
+# Include self-loop peptides in the search.
+# Available for crux search-for-xlinks program.
+xlink-include-selfloops=true
+
+# Include intra-protein cross-link candiates within the search.
+# Available for crux search-for-xlinks program.
+xlink-include-intra=true
+
+# Include inter-protein cross-link candidates within the search.
+# Available for crux search-for-xlinks program.
+xlink-include-inter=true
+
+# Include crosslink candidates that are both inter and intra.
+# Available for crux search-for-xlinks program.
+xlink-include-inter-intra=true
+
+# List of amino acids for which the cross-linker can prevent cleavage. This
+# option is only available when use-old-xlink=F.
+# Available for search-for-xlinks program.
+xlink-prevents-cleavage=K
+
+# Specify the maximum number of modifications allowed on a crosslinked peptide.
+# This option is only available when use-old-xlink=F.
+# Available for crux search-for-xlinks
+max-xlink-mods=0
+
+# Search decoy peptides within +/- precursor-window-weibull of the precursor
+# mass. The resulting scores are used only for fitting the Weibull distribution
+# Available for crux search-for-xlinks.
+precursor-window-weibull=20
+
+# Window type to use in conjunction with the precursor-window-weibull parameter.
+# Available for crux search-for-xlinks
+precursor-window-type-weibull=mass
+
+# Keep shuffling and collecting XCorr scores until the minimum number of points
+# for weibull fitting (using targets and decoys) is achieved.
+# Available for crux search-for-xlinks
+min-weibull-points=4000
+
+# Determines which spectral feature detection algorithm to use. Different
+# results are possible with each algorithm, and there are pros and cons to each.
+# Available for crux hardklor
+hardklor-algorithm=version1
+
+# Defines alternative averagine models in the analysis that incorporate
+# additional atoms and/or isotopic enrichments. Modifications are represented as
+# text strings. Inclusion of additional atoms in the model is done using by
+# entering an atomic formula, such as: PO2 or Cl. Inclusion of isotopic
+# enrichment to the model is done by specifying the percent enrichment (as a
+# decimal) followed by the atom being enriched and an index of the isotope. For
+# example, 0.75H1 specifies 75% enrichment of the first heavy isotope of
+# hydrogen. In other words, 75% deuterium enrichment. Two or more modifications
+# can be combined into the same model, and separated by spaces: B2 0.5B1
+# Available for crux hardklor
+averagine-mod=
+
+# Boxcar averaging is a sliding window that averages n adjacent spectra prior to
+# feature detection. Averaging generally improves the signal-to-noise ratio of
+# features in the spectra, as well as improving the shape of isotopic envelopes.
+# However, averaging will also change the observed peak intensities. Averaging
+# with too wide a window will increase the occurrence of overlapping features
+# and broaden the chromatographic profiles of observed features. The number
+# specified is the total adjacent scans to be combined, centered on the scan
+# being analyzed. Therefore, an odd number is recommended to center the boxcar
+# window. For example, a value of 3 would produce an average of the scan of
+# interest, plus one scan on each side. A value of 0 disables boxcar averaging.
+# Available for crux hardklor
+boxcar-averaging=0
+
+# This parameter is only functional when boxcar-averaging is used. The filter
+# will remove any peaks not seen in n scans in the boxcar window. The effect is
+# to reduce peak accumulation due to noise and reduce chromatographic broadening
+# of peaks. Caution should be used as over-filtering can occur. The suggested
+# number of scans to set for filtering should be equal to or less than the
+# boxcar-averaging window size. A value of 0 disables filtering.
+# Available for crux hardklor
+boxcar-filter=0
+
+# This parameter is only functional when boxcar-filter is used. The value
+# specifies the mass tolerance in ppm for declaring a peak the same prior to
+# filtering across all scans in the boxcar window.
+# Available for crux hardklor
+boxcar-filter-ppm=10
+
+# Indicates whether the data contain profile or centroided peaks.
+# Available for crux hardklor
+centroided=false
+
+# Choose the charge state determination method.
+# Available for crux hardklor
+cdm=Q
+
+# Specifies the minimum charge state to allow when finding spectral features. It
+# is best to set this value to the lowest assumed charge state to be present. If
+# set higher than actual charge states that are present, those features will not
+# be identified or incorrectly assigned a different charge state and mass.
+# Available for crux hardklor
+min-charge=1
+
+# Specifies the maximum charge state to allow when finding spectral features. It
+# is best to set this value to a practical number (i.e. do not set it to 20 when
+# doing a tryptic shotgun analysis). If set higher than actual charge states
+# that are present, the algorithm will perform significantly slower without any
+# improvement in results.
+# Available for crux hardklor
+max-charge=5
+
+# Sets the correlation threshold (cosine similarity) for accepting each
+# predicted feature.
+# Available for crux hardklor
+corr=0.85
+
+# Sets the depth of combinatorial analysis. For a given set of peaks in a
+# spectrum, search for up to this number of combined peptides that explain the
+# observed peaks. The analysis stops before depth is reached if the current
+# number of deconvolved features explains the observed peaks with a correlation
+# score above the threshold defined with the correlation parameter.
+# Available for crux hardklor
+depth=3
+
+# When reporting each feature, report abundance as the sum of all isotope peaks.
+# The value reported is the estimate of the correct peak heights based on the
+# averagine model scaled to the observed peak heights.
+# Available for crux hardklor
+distribution-area=false
+
+# Specifies an ASCII text file that defines symbols for the periodic table.
+# Available for crux hardklor
+hardklor-data-file=
+
+# Indicates the type of instrument used to collect data. This parameter,
+# combined with the resolution parameter, define how spectra will be centroided
+# (if you provide profile spectra) and the accuracy when aligning observed peaks
+# to the models.
+# Available for crux hardklor
+instrument=fticr
+
+# Specifies an ASCII text file that can be read to override the natural isotope
+# abundances for all elements.
+# Available for crux hardklor
+isotope-data-file=
+
+# Specifies the maximum number of models to build for a set of peaks being
+# analyzed. Regardless of the setting, the number of models will never exceed
+# the number of peaks in the current set. However, as many of the low abundance
+# peaks are noise or tail ends of distributions, defining models for them is
+# detrimental to the analysis.
+# Available for crux hardklor
+max-features=10
+
+# Filters the spectra prior to analysis for the requested MS/MS level. For
+# example, if the data contain MS and MS/MS spectra, setting mzxml-filter = 1
+# will analyze only the MS scan events. Setting mzxml-filter = 2 will analyze
+# only the MS/MS scan events.
+# Available for crux hardklor
+mzxml-filter=1
+
+# Constrains the search in each spectrum to signals below this value in
+# Thomsons. Setting to 0 disables this feature.
+# Available for crux hardklor
+mz-max=0
+
+# Constrains the search in each spectrum to signals above this value in
+# Thomsons. Setting to 0 disables this feature.
+# Available for crux hardklor
+mz-min=0
+
+# Only used when algorithm = version1. Defines the maximum window size in
+# Thomsons to analyze when deconvolving peaks in a spectrum into features.
+# Available for crux hardklor
+mz-window=4
+
+# Specifies the resolution of the instrument at 400 m/z for the data being
+# analyzed.
+# Available for crux hardklor
+resolution=100000
+
+# Used to restrict analysis to spectra with scan numbers below this parameter
+# value. A value of 0 disables this feature.
+# Available for crux hardklor
+scan-range-max=0
+
+# Used to restrict analysis to spectra with scan numbers above this parameter
+# value. A value of 0 disables this feature.
+# Available for crux hardklor
+scan-range-min=0
+
+# Set the sensitivity level. There are four levels: 0 (low), 1 (moderate), 2
+# (high), and 3 (max). Increasing the sensitivity will increase computation
+# time, but will also yield more isotope distributions.
+# Available for crux hardklor
+sensitivity=2
+
+# Filters spectra to remove peaks below this signal-to-noise ratio prior to
+# finding features.
+# Available for crux hardklor
+signal-to-noise=1
+
+# Uses Savitzky-Golay smoothing on profile peak data prior to centroiding the
+# spectra. This parameter is recommended for low resolution spectra only.
+# Smoothing data causes peak depression and broadening. Only use odd numbers for
+# the degree of smoothing (as it defines a window centered on each data point).
+# Higher values will produce smoother peaks, but with greater depression and
+# broadening. Setting this parameter to 0 disables smoothing.
+# Available for crux hardklor
+smooth=0
+
+# Set the signal-to-noise window length (in m/z). Because noise may be
+# non-uniform across a spectrum, this value adjusts the segment size considered
+# when calculating a signal-over-noise ratio.
+# Available for crux hardklor
+sn-window=250
+
+# Applies the lowest noise threshold of any sn_window across the entire mass
+# range for a spectrum. Setting this parameter to 0 turns off this feature, and
+# different noise thresholds will be used for each local mass window in a
+# spectrum.
+# Available for crux hardklor
+static-sn=true
+
+# Ignore PPIDs that persist for longer than this length of time in the MS1
+# spectra. The unit of time is whatever unit is used in your data file (usually
+# minutes). These PPIDs are considered contaminants.
+# Available for crux bullseye
+max-persist=2
+
+# When true, require an exact match (as defined by --exact-tolerance) between
+# the center of the precursor isolation window in the MS2 scan and the base
+# isotopic peak of the PPID. If this option is set to false and no exact match
+# is observed, then attempt to match using a wider m/z tolerance. This wider
+# tolerance is calculated using the PPID's monoisotopic mass and charge (the
+# higher the charge, the smaller the window).
+# Available for crux bullseye
+exact-match=false
+
+# Allowed gap size when checking for PPIDs across consecutive MS1 scans.
+# Available for crux bullseye
+gap-tolerance=1
+
+# Only consider PPIDs above this minimum mass in daltons.
+# Available for crux bullseye
+bullseye-min-mass=600
+
+# Only consider PPIDs below this maximum mass in daltons.
+# Available for crux bullseye
+bullseye-max-mass=8000
+
+# Set the tolerance (+/-ppm) for --exact-match.
+# Available for crux bullseye
+exact-tolerance=10
+
+# Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans.
+# Available for crux bullseye
+persist-tolerance=10
+
+# Total number of MS1 scans over which a PPID must be observed to be considered
+# real. Gaps in persistence are allowed by setting --gap-tolerance.
+# Available for crux bullseye
+scan-tolerance=3
+
+# Set the tolerance (+/-units) around the retention time over which a PPID can
+# be matches to the MS2 spectrum. The unit of time is whatever unit is used in
+# your data file (usually minutes).
+# Available for crux bullseye
+retention-tolerance=0.5
+
+# The format to write the output spectra to. If empty, the spectra will be
+# output in the same format as the MS2 input.
+# Available for crux bullseye
+spectrum-format=
+
+# Sort in ascending (T) or descending (F) order.
+# Available for sort-by-column
+ascending=true
+
+# Specify the input and output delimiter to use when processing the delimited
+# file. The argument can be either a single character or the keyword 'tab.'
+# Available for the delimited utility programs.
+delimiter=tab
+
+# Print the header line of the file, in addition to the columns that match.
+# Available for crux extract-columns and extract-rows
+header=true
+
+# Specifies the data type of the column, either an integer (int), a floating
+# point number (real), or a string.
+# Available for crux extract-rows
+column-type=string
+
+# Specify the operator that is used to compare an entry in the specified column
+# to the value given on the command line.
+# Available for crux extract-rows
+comparison=eq
+
+# Run the Bullseye algorithm on the given MS data, using it to assign
+# high-resolution precursor values to the MS/MS data. If a spectrum file ends
+# with .ms2 or .cms2, matching .ms1/.cms1 files will be used as the MS1 file.
+# Otherwise, it is assumed that the spectrum file contains both MS1 and MS2
+# scans.
+# Available for crux pipeline
+bullseye=false
+
+# Specify which search engine to use.
+# Available for crux pipeline
+search-engine=tide-search
+
+# Specify which post-processor to apply to the search results.
+# Available for crux pipeline
+post-processor=percolator
+
+# Consider modifications on any amino acid in aa list with at most
+# max-per-peptide in one peptide. The parameter takes the form
+# [[html:<mass change>:<aa list>:<max per
+# peptide>:<prevents cleavage>:<prevents cross-link>]].
+# This parameter may be included with different values multiple times so
+# long as the total number of mod, cmod, and nmod parameters does not
+# exceed 11. The "prevents cleavage" and "prevents cross-link" arguments
+# are optional T/F arguments for describing whether the modification
+# prevents enzymatic cleavage of cross-linking, respectively. This
+# option is only available when use-old-xlink=F. Note that this
+# parameter only takes effect when specified in the parameter file.
+# Available for search-for-xlinks.
+mod=NO MODS
+
+# Specify a variable modification to apply to N-terminus of peptides.
+# <mass change>:<max distance from protein n-term (-1 for no max)> Note
+# that this parameter only takes effect when specified in the parameter
+# file.
+# Available for search-for-xlinks.
+nmod=NO MODS
+
+# Specify a variable modification to apply to C-terminus of peptides.
+# <mass change>:<max distance from protein c-term (-1 for no max)>. Note
+# that this parameter only takes effect when specified in the parameter
+# file.
+# Available for search-for-xlinks.
+cmod=NO MODS
+
+####################
+# Comet Parameters #
+####################
+# 0=no, 1=concatenated search, 2=separate search.
+# Available for comet.
+decoy_search=0
+
+# 0=poll CPU to set num threads; else specify num threads directly.
+# Available for comet.
+num_threads=0
+
+# Controls the mass tolerance value. The mass tolerance is set at +/- the
+# specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0
+# tolerance. The units of the mass tolerance is controlled by the parameter
+# "peptide_mass_units".
+# Available for comet.
+peptide_mass_tolerance=3
+
+# 0=amu, 1=mmu, 2=ppm.
+# Available for comet.
+peptide_mass_units=0
+
+# 0=average masses, 1=monoisotopic masses.
+# Available for comet.
+mass_type_parent=1
+
+# 0=average masses, 1=monoisotopic masses.
+# Available for comet.
+mass_type_fragment=1
+
+# 0=singly charged peptide mass, 1=precursor m/z.
+# Available for comet.
+precursor_tolerance_type=0
+
+# 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8
+# labeling).
+# Available for comet.
+isotope_error=0
+
+# Specify a search enzyme from the end of the parameter file.
+# Available for comet.
+search_enzyme_number=1
+
+# valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term.
+# Available for comet.
+num_enzyme_termini=2
+
+# Maximum value is 5; for enzyme search.
+# Available for comet.
+allowed_missed_cleavage=2
+
+# Binning to use on fragment ions.
+# Available for comet.
+fragment_bin_tol=1.000507
+
+# Offset position to start the binning (0.0 to 1.0).
+# Available for comet.
+fragment_bin_offset=0.4
+
+# 0=default peak shape, 1=M peak only.
+# Available for comet.
+theoretical_fragment_ions=1
+
+# Controls whether or not A-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_A_ions=0
+
+# Controls whether or not B-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_B_ions=1
+
+# Controls whether or not C-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_C_ions=0
+
+# Controls whether or not X-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_X_ions=0
+
+# Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_Y_ions=1
+
+# Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes).
+# Available for comet.
+use_Z_ions=0
+
+# 0=no, 1= yes to consider NH3/H2O neutral loss peak.
+# Available for comet.
+use_NL_ions=1
+
+# 0=no, 1=yes write sqt file.
+# Available for comet.
+output_sqtfile=0
+
+# 0=no, 1=yes write tab-delimited text file.
+# Available for comet.
+output_txtfile=1
+
+# 0=no, 1=yes write pep.xml file.
+# Available for comet.
+output_pepxmlfile=1
+
+# 0=no, 1=yes write percolator file.
+# Available for comet.
+output_percolatorfile=0
+
+# 0=no, 1=yes write .out files.
+# Available for comet.
+output_outfiles=0
+
+# 0=no, 1=yes to replace Sp with expect in out & sqt.
+# Available for comet.
+print_expect_score=1
+
+# num peptide results to show.
+# Available for comet.
+num_output_lines=5
+
+# 0=no, 1=yes for out files only.
+# Available for comet.
+show_fragment_ions=0
+
+# Sample enzyme which is possibly different than the one applied to the search.
+# Used to calculate NTT & NMC in pepXML output.
+# Available for comet.
+sample_enzyme_number=1
+
+# Start and scan scan range to search; 0 as first entry ignores parameter.
+# Available for comet.
+scan_range=0 0
+
+# Precursor charge range to analyze; does not override mzXML charge; 0 as first
+# entry ignores parameter.
+# Available for comet.
+precursor_charge=0 0
+
+# Specifies the whether to override existing precursor charge state information
+# when present in the files with the charge range specified by the
+# "precursor_charge" parameter.
+# Available for comet.
+override_charge=0
+
+# MS level to analyze, valid are levels 2 or 3.
+# Available for comet.
+ms_level=2
+
+# Specifies which scan types are searched.
+# Available for comet.
+activation_method=ALL
+
+# MH+ peptide mass range to analyze.
+# Available for comet.
+digest_mass_range=600.0 5000.0
+
+# Number of search hits to store internally.
+# Available for comet.
+num_results=50
+
+# For '.out' file output only, 0=search everything again, 1=don't search if .out
+# exists.
+# Available for comet.
+skip_researching=1
+
+# Set maximum fragment charge state to analyze (allowed max 5).
+# Available for comet.
+max_fragment_charge=3
+
+# Set maximum precursor charge state to analyze (allowed max 9).
+# Available for comet.
+max_precursor_charge=6
+
+# 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six.
+# Available for comet.
+nucleotide_reading_frame=0
+
+# 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine.
+# Available for comet.
+clip_nterm_methionine=0
+
+# Maximum number of spectra to search at a time; 0 to search the entire scan
+# range in one loop.
+# Available for comet.
+spectrum_batch_size=0
+
+# Specifies the prefix of the protein names that indicates a decoy.
+# Available for comet.
+decoy_prefix=decoy_
+
+# Specifies the suffix string that is appended to the base output name for the
+# pep.xml, pin.xml, txt and sqt output files.
+# Available for comet.
+output_suffix=
+
+# Specifies one or more mass offsets to apply. This value(s) are effectively
+# subtracted from each precursor mass such that peptides that are smaller than
+# the precursor mass by the offset value can still be matched to the respective
+# spectrum.
+# Available for comet.
+mass_offsets=
+
+# Minimum number of peaks in spectrum to search.
+# Available for comet.
+minimum_peaks=10
+
+# Minimum intensity value to read in.
+# Available for comet.
+minimum_intensity=0
+
+# 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD).
+# Available for comet.
+remove_precursor_peak=0
+
+# +- Da tolerance for precursor removal.
+# Available for comet.
+remove_precursor_tolerance=1.5
+
+# For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range.
+# Available for comet.
+clear_mz_range=0.0 0.0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod01=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod02=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod03=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod04=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod05=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod06=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod07=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod08=0.0 null 0 4 -1 0 0
+
+# Up to 9 variable modifications are supported; format: "<mass> <residues>
+# <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3.
+# Available for comet.
+variable_mod09=0.0 null 0 4 -1 0 0
+
+# Specifies the total/maximum number of residues that can be modified in a
+# peptide.
+# Available for comet.
+max_variable_mods_in_peptide=5
+
+# Controls whether the analyzed peptides must contain at least one variable
+# modification.
+# Available for comet.
+require_variable_mod=0
+
+# Specifiy a static modification to the c-terminus of all peptides.
+# Available for comet.
+add_Cterm_peptide=0
+
+# Specify a static modification to the n-terminus of all peptides.
+# Available for comet.
+add_Nterm_peptide=0
+
+# Specify a static modification to the c-terminal peptide of each protein.
+# Available for comet.
+add_Cterm_protein=0
+
+# Specify a static modification to the n-terminal peptide of each protein.
+# Available for comet.
+add_Nterm_protein=0
+
+# Specify a static modification to the residue A.
+# Available for comet.
+add_A_alanine=0
+
+# Specify a static modification to the residue B.
+# Available for comet.
+add_B_user_amino_acid=0
+
+# Specify a static modification to the residue C.
+# Available for comet.
+add_C_cysteine=57.021464
+
+# Specify a static modification to the residue D.
+# Available for comet.
+add_D_aspartic_acid=0
+
+# Specify a static modification to the residue E.
+# Available for comet.
+add_E_glutamic_acid=0
+
+# Specify a static modification to the residue F.
+# Available for comet.
+add_F_phenylalanine=0
+
+# Specify a static modification to the residue G.
+# Available for comet.
+add_G_glycine=0
+
+# Specify a static modification to the residue H.
+# Available for comet.
+add_H_histidine=0
+
+# Specify a static modification to the residue I.
+# Available for comet.
+add_I_isoleucine=0
+
+# Specify a static modification to the residue J.
+# Available for comet.
+add_J_user_amino_acid=0
+
+# Specify a static modification to the residue K.
+# Available for comet.
+add_K_lysine=0
+
+# Specify a static modification to the residue L.
+# Available for comet.
+add_L_leucine=0
+
+# Specify a static modification to the residue M.
+# Available for comet.
+add_M_methionine=0
+
+# Specify a static modification to the residue N.
+# Available for comet.
+add_N_asparagine=0
+
+# Specify a static modification to the residue O.
+# Available for comet.
+add_O_ornithine=0
+
+# Specify a static modification to the residue P.
+# Available for comet.
+add_P_proline=0
+
+# Specify a static modification to the residue Q.
+# Available for comet.
+add_Q_glutamine=0
+
+# Specify a static modification to the residue R.
+# Available for comet.
+add_R_arginine=0
+
+# Specify a static modification to the residue S.
+# Available for comet.
+add_S_serine=0
+
+# Specify a static modification to the residue T.
+# Available for comet.
+add_T_threonine=0
+
+# Specify a static modification to the residue U.
+# Available for comet.
+add_U_selenocysteine=0
+
+# Specify a static modification to the residue V.
+# Available for comet.
+add_V_valine=0
+
+# Specify a static modification to the residue W.
+# Available for comet.
+add_W_tryptophan=0
+
+# Specify a static modification to the residue X.
+# Available for comet.
+add_X_user_amino_acid=0
+
+# Specify a static modification to the residue Y.
+# Available for comet.
+add_Y_tyrosine=0
+
+# Specify a static modification to the residue Z.
+# Available for comet.
+add_Z_user_amino_acid=0
+
+#
+# COMET_ENZYME_INFO _must_ be at the end of this parameters file
+#
+[COMET_ENZYME_INFO]
+0. No_enzyme 0 - -
+1. Trypsin 1 KR P
+2. Trypsin/P 1 KR -
+3. Lys_C 1 K P
+4. Lys_N 0 K -
+5. Arg_C 1 R P
+6. Asp_N 0 D -
+7. CNBr 1 M -
+8. Glu_C 1 DE P
+9. PepsinA 1 FL P
+10. Chymotrypsin 1 FWYL P
diff --git a/doc/user/example-files/demo.ms2 b/doc/user/example-files/demo.ms2
new file mode 100644
index 0000000..9359011
--- /dev/null
+++ b/doc/user/example-files/demo.ms2
@@ -0,0 +1,54667 @@
+H CreationDate 2/14/2007 6:19:18 PM
+H Extractor MakeMS2
+H ExtractorVersion 1.0
+H Comments MakeMS2 written by Michael J. MacCoss, 2004
+H ExtractorOptions MS2/MS1
+S 10 10 636.34
+Z 2 1271.67
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diff --git a/doc/user/example-files/search.target.txt b/doc/user/example-files/search.target.txt
new file mode 100644
index 0000000..b4193e0
--- /dev/null
+++ b/doc/user/example-files/search.target.txt
@@ -0,0 +1,721 @@
+scan charge spectrum precursor m/z spectrum neutral mass peptide mass delta_cn sp score sp rank xcorr score xcorr rank b/y ions matched b/y ions total matches/spectrum sequence cleavage type protein id flanking aa unshuffled sequence
+10 2 636.3400 1270.6644 1270.4917 0 56.458275 1 0.843481 1 5 22 6 SGLIVEIQGVQK trypsin-full-digest YDR093W KE
+10 2 636.3400 1270.6644 1273.4087 0.50464863 49.409576 2 0.41781947 2 4 20 6 TVLDLEVNNTR trypsin-full-digest YDR093W RT
+10 2 636.3400 1270.6644 1272.5227 0.82345378 22.858458 4 0.1489134 3 4 22 6 MSVEPVVVIDGK trypsin-full-digest YIL133C -G
+10 2 636.3400 1270.6644 1271.5254 0.99421889 7.6680117 5 0.0048762476 4 2 20 6 KPQVYPALLSR trypsin-full-digest YLR371W KV
+10 2 636.3400 1270.6644 1270.3618 1.2562495 42.079628 3 -0.21614161 5 4 20 6 TDLPEGEEKPR trypsin-full-digest YPL106C KI
+11 2 745.2700 1488.5244 1489.7319 0 2799.7004 1 4.9665937 1 21 24 5 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+11 2 745.2700 1488.5244 1486.6195 0.78361297 150.82512 2 1.0747064 2 8 26 5 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+11 2 745.2700 1488.5244 1490.6510 0.92498112 27.513174 5 0.37258846 3 3 24 5 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+11 2 745.2700 1488.5244 1488.7063 0.95597595 86.188286 3 0.21864961 4 5 24 5 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+11 2 745.2700 1488.5244 1485.6539 0.98590338 70.940605 4 0.070012115 5 5 22 5 QEAIYEVYITEK trypsin-full-digest YLR371W RN
+12 3 472.5600 1414.6565 1411.7252 0 107.23654 1 0.70944363 1 12 44 8 IISYAQGFMLIR trypsin-full-digest YHR183W KE
+12 3 472.5600 1414.6565 1412.5806 0.29089656 67.485161 3 0.50306892 2 11 44 8 IVNMYGTTETQR trypsin-full-digest YBR115C RA
+12 3 472.5600 1414.6565 1414.5780 0.30653799 39.472534 6 0.49197221 3 8 40 8 NTLEEYIYTLR trypsin-full-digest YPL106C KG
+12 3 472.5600 1414.6565 1414.6240 0.33313781 55.1306 4 0.47310114 4 9 44 8 VLEFHPFDPVSK trypsin-full-digest YGL008C KK
+12 3 472.5600 1414.6565 1413.6769 0.51874274 94.480415 2 0.34142488 5 11 48 8 YGPLLVDIIDPAK trypsin-full-digest YKL127W KA
+13 1 717.0600 716.0522 717.8204 0 41.040947 2 0.6652953 1 4 10 16 SLEITR trypsin-full-digest YLR371W KD
+13 1 717.0600 716.0522 716.8506 0.065693147 47.344681 1 0.62158996 2 4 12 16 DVMPAGK trypsin-full-digest YBR115C KG
+13 1 717.0600 716.0522 715.9341 0.07201229 21.613161 4 0.61738586 3 3 10 16 LLPFVK trypsin-full-digest YLR340W KG
+13 1 717.0600 716.0522 713.7887 0.64012295 39.931419 3 0.23942451 4 4 12 16 NPAVGEK trypsin-full-digest YGL245W KK
+13 1 717.0600 716.0522 716.7893 0.67106682 5.8860817 10 0.21883771 5 2 12 16 EAAELGK trypsin-full-digest YBR118W KG
+14 2 559.1000 1116.1843 1119.1559 0 66.227585 1 0.53043324 1 5 16 11 YHIEEEGSR trypsin-full-digest YCR012W RK
+14 2 559.1000 1116.1843 1118.2635 0.13069028 23.070383 3 0.46111077 2 4 16 11 FFCALFDAK trypsin-full-digest YKL127W KK
+14 2 559.1000 1116.1843 1116.1615 0.29996294 12.308622 6 0.37132293 3 3 16 11 YDGAFDCLR trypsin-full-digest YBL030C KK
+14 2 559.1000 1116.1843 1117.3536 0.48043215 23.054535 4 0.27559605 4 5 18 11 FLDGQIALLK trypsin-full-digest YBL076C KK
+14 2 559.1000 1116.1843 1116.2769 0.61405927 10.694719 7 0.2047158 5 3 18 11 LVDEVVDSLK trypsin-full-digest YMR235C RF
+14 3 559.1000 1674.2765 1675.6885 0 63.059669 1 0.767111 1 13 60 5 ATAGDTHLGGEDFDNR trypsin-full-digest YLL024C KL
+14 3 559.1000 1674.2765 1671.7804 1.2015421 33.726143 2 -0.15460518 2 8 48 5 ITYSSDYFDELYR trypsin-full-digest YOR168W KL
+14 3 559.1000 1674.2765 1676.9332 1.3099092 29.03307 3 -0.23773479 3 7 56 5 YLTNTGNLLLASQIR trypsin-full-digest YBL076C KH
+14 3 559.1000 1674.2765 1673.7159 1.5774156 10.770131 5 -0.44294184 4 6 56 5 HEAEWSGLSNDATTR trypsin-full-digest YDL223C RN
+14 3 559.1000 1674.2765 1673.7625 1.8034767 21.514181 4 -0.61635584 5 7 64 5 TTHPVSHGHSGSSTGPK trypsin-full-digest YDL223C KS
+15 2 732.1300 1462.2444 1462.7675 0 1342.2397 1 3.8226082 1 19 24 5 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+15 2 732.1300 1462.2444 1460.6036 0.92579734 21.992445 3 0.28364772 2 4 22 5 EEPDLENLLFNK trypsin-full-digest YHR183W RF
+15 2 732.1300 1462.2444 1463.5709 0.93476593 3.2144897 4 0.24936424 3 2 24 5 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+15 2 732.1300 1462.2444 1460.4707 0.94384331 46.283249 2 0.2146651 4 6 24 5 ELGDAYVSSDEEF trypsin-full-digest YLR249W K-
+15 2 732.1300 1462.2444 1459.6195 0.98524964 2.9621341 5 0.056384861 5 2 26 5 SQVDEIVLVGGSTR trypsin-full-digest YLL024C KI
+16 1 713.0700 712.0622 713.7887 0 40.185627 2 0.4695082 1 4 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+16 1 713.0700 712.0622 710.7880 0.34402412 97.301079 1 0.30798605 2 6 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+16 1 713.0700 712.0622 714.8626 0.65348947 8.9418478 5 0.16268952 3 2 10 9 ALPTWK trypsin-full-digest YMR235C KD
+16 1 713.0700 712.0622 710.8309 1.0855368 13.639264 3 -0.040160265 4 2 10 9 AFAQFK trypsin-full-digest YJR069C KE
+16 1 713.0700 712.0622 712.8472 1.3372214 9.0141134 4 -0.15832822 5 2 12 9 TPGGILR trypsin-full-digest YER056C-A KA
+17 2 495.2500 988.4844 989.0935 0 94.401619 2 0.65849799 1 5 16 3 SLEASVIDR trypsin-full-digest YBR115C KN
+17 2 495.2500 988.4844 988.1950 0.14087622 47.611462 3 0.56573129 2 4 18 3 TPLPPAPAPK trypsin-full-digest YBL030C KK
+17 2 495.2500 988.4844 987.0771 0.40132889 150.00021 1 0.39422372 3 6 16 3 YSFLEGGSK trypsin-full-digest YGL009C KL
+18 3 1032.4000 3094.1765 3095.2366 0 1794.3577 1 4.4612322 1 41 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+18 3 1032.4000 3094.1765 3095.4709 0.91822755 28.71706 2 0.364806 2 10 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+19 2 604.2900 1206.5643 1207.4535 0 4.0179791 2 0.085511789 1 2 18 2 DTLKPMAIYR trypsin-full-digest YLR371W RV
+19 2 604.2900 1206.5643 1204.3109 1.6698694 10.554982 1 -0.057281736 2 3 20 2 VNGDAHVISHR trypsin-full-digest YGR157W RA
+19 3 604.2900 1809.8464 1808.0363 0 139.71983 1 0.43815228 1 14 68 4 GYLVAMTGDGVNDAPSLK trypsin-full-digest YGL008C RK
+19 3 604.2900 1809.8464 1810.0775 0.73968351 45.731903 3 0.11405826 2 9 68 4 LQDGVPDSIALLAEAGIK trypsin-full-digest YDR093W RL
+19 3 604.2900 1809.8464 1810.0824 1.4776366 58.53331 2 -0.20927754 3 8 52 4 LLNFIDELTNWYIR trypsin-full-digest YBL076C KF
+19 3 604.2900 1809.8464 1812.0063 1.701064 40.476826 4 -0.30717278 4 10 64 4 YTVSFIEGDGIGPEISK trypsin-full-digest YOR136W KS
+20 2 450.9000 899.7844 902.0154 0 14.423851 3 0.1545447 1 3 16 12 STVVSANPK trypsin-full-digest YOR267C KK
+20 2 450.9000 899.7844 897.0107 0.43213871 30.959551 2 0.087759949 2 3 12 12 LDDEFMK trypsin-full-digest YMR309C RS
+20 2 450.9000 899.7844 898.0265 0.48145139 5.8385301 5 0.080138937 3 2 14 12 FFADAVTK trypsin-full-digest YHR183W KA
+20 2 450.9000 899.7844 896.9524 0.78898019 50.266438 1 0.032611992 4 3 14 12 SSFNDISK trypsin-full-digest YMR309C KL
+20 2 450.9000 899.7844 902.0586 1.8137401 13.619667 4 -0.12575921 5 3 16 12 QGVTSLGIK trypsin-full-digest YML092C KA
+21 1 805.0000 803.9922 804.8956 0 124.69447 1 0.80470002 1 5 12 20 ESTIDIK trypsin-full-digest YOR267C KI
+21 1 805.0000 803.9922 804.8957 0.14753152 83.322594 2 0.68598139 2 4 12 20 ESVTEIK trypsin-full-digest YGR157W KA
+21 1 805.0000 803.9922 803.8675 0.27760506 22.862658 9 0.58131123 3 3 12 20 ELDTAQK trypsin-full-digest YGR192C KH
+21 1 805.0000 803.9922 805.9292 0.56622195 59.186016 3 0.34906122 4 5 12 20 FSPSQLK trypsin-full-digest YMR073C KN
+21 1 805.0000 803.9922 804.8577 0.63594806 38.015034 6 0.2929526 5 3 10 20 EWNQTK trypsin-full-digest YDR093W KF
+22 1 1489.8500 1488.8422 1489.7319 0 374.82031 1 3.0246928 1 14 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+22 1 1489.8500 1488.8422 1486.6195 0.84436226 36.411674 2 0.47075641 2 6 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+22 1 1489.8500 1488.8422 1490.6510 1.00218 3.5401781 4 -0.0065939161 3 2 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+22 1 1489.8500 1488.8422 1488.7063 1.0877013 4.2567067 3 -0.26526943 4 2 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+23 1 805.0000 803.9922 804.8957 0 151.28577 1 0.60042703 1 6 12 20 ESVTEIK trypsin-full-digest YGR157W KA
+23 1 805.0000 803.9922 803.8675 0.23424846 53.851978 4 0.45977792 2 4 12 20 ELDTAQK trypsin-full-digest YGR192C KH
+23 1 805.0000 803.9922 804.8956 0.25316995 72.456558 2 0.44841695 3 4 12 20 ESTIDIK trypsin-full-digest YOR267C KI
+23 1 805.0000 803.9922 804.9012 0.29283255 23.882532 11 0.42460245 4 3 12 20 VAHTSYK trypsin-full-digest YML092C KR
+23 1 805.0000 803.9922 804.8987 0.47863716 46.161007 5 0.31304035 5 4 12 20 VSTTLER trypsin-full-digest YDR093W RR
+24 3 830.6200 2488.8364 2490.7063 0 26.858793 1 0.14122425 1 13 84 2 AAGQLDQLVEDYINDELEIVSR trypsin-full-digest YBR115C RI
+24 3 830.6200 2488.8364 2489.7822 1.78395 18.704006 2 -0.11071275 2 10 84 2 VMPYSTGLTTPLSNFEAQQNYK trypsin-full-digest YBL076C KD
+25 2 745.5500 1489.0844 1489.7319 0 1807.792 1 4.2164721 1 19 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+25 2 745.5500 1489.0844 1486.6195 0.81398946 106.51873 3 0.78430814 2 7 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+25 2 745.5500 1489.0844 1488.7063 0.82931358 207.0804 2 0.71969455 3 8 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+25 2 745.5500 1489.0844 1490.6510 0.85102826 25.70677 4 0.62813509 4 3 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+26 2 692.3800 1382.7444 1382.4467 0 2156.4043 1 3.8436441 1 20 24 5 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+26 2 692.3800 1382.7444 1381.6099 0.87371606 76.68457 2 0.48539051 2 5 22 5 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+26 2 692.3800 1382.7444 1381.5258 0.90621096 30.044098 3 0.36049169 3 4 22 5 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+26 2 692.3800 1382.7444 1380.6042 1.055408 21.984407 4 -0.21296872 4 3 22 5 EVVELPLLSPER trypsin-full-digest YKL145W RF
+26 2 692.3800 1382.7444 1383.6108 1.0793326 2.7308655 5 -0.30492619 5 1 26 5 NVIVSGIVLAADGR trypsin-full-digest YBL076C KK
+27 2 732.5500 1463.0844 1462.7675 0 1126.2389 1 2.6634736 1 17 24 4 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+27 2 732.5500 1463.0844 1460.6036 0.81959116 66.824799 3 0.48051417 2 6 22 4 EEPDLENLLFNK trypsin-full-digest YHR183W RF
+27 2 732.5500 1463.0844 1460.4707 0.88409299 92.661507 2 0.30871528 3 7 24 4 ELGDAYVSSDEEF trypsin-full-digest YLR249W K-
+27 2 732.5500 1463.0844 1463.5709 0.96493638 15.490486 4 0.093391061 4 3 24 4 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+28 2 613.2600 1224.5044 1222.3203 0 26.820997 2 0.5495218 1 4 22 5 GGEGEVSVFVSR trypsin-full-digest YDR037W KV
+28 2 613.2600 1224.5044 1223.4375 0.018783558 28.635321 1 0.53919983 2 4 20 5 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+28 2 613.2600 1224.5044 1224.3788 0.8169654 6.3640132 5 0.1005815 3 2 18 5 LAFLENQDFK trypsin-full-digest YBR115C RL
+28 2 613.2600 1224.5044 1227.4233 0.84511566 13.379468 3 0.085112311 4 3 18 5 IEVLEQELVR trypsin-full-digest YGR086C KA
+28 2 613.2600 1224.5044 1223.2670 0.96065545 8.3532753 4 0.021620696 5 2 18 5 YYGGNEHIDR trypsin-full-digest YLR058C RM
+29 2 614.2600 1226.5044 1229.3525 0 21.443193 1 0.31570217 1 3 20 3 EILGTDEPTVR trypsin-full-digest YKL127W KT
+29 2 614.2600 1226.5044 1224.3788 0.23751414 15.323318 2 0.24071844 2 3 18 3 LAFLENQDFK trypsin-full-digest YBR115C RL
+29 2 614.2600 1226.5044 1227.4233 1.4932648 2.4419763 3 -0.15572478 3 1 18 3 IEVLEQELVR trypsin-full-digest YGR086C KA
+30 1 715.0700 714.0622 716.7460 0 23.359188 1 0.30748594 1 3 10 12 KPDDDK trypsin-full-digest YKL145W KI
+30 1 715.0700 714.0622 716.7893 0.64147574 6.6294503 3 0.11024117 2 2 12 12 EAAELGK trypsin-full-digest YBR118W KG
+30 1 715.0700 714.0622 713.7887 0.78619045 4.9657464 4 0.065743424 3 2 12 12 NPAVGEK trypsin-full-digest YGL245W KK
+30 1 715.0700 714.0622 716.8852 0.82486218 1.6637436 9 0.05385242 4 1 10 12 ALLICK trypsin-full-digest YDR093W KG
+30 1 715.0700 714.0622 712.8472 0.84074181 8.0855684 2 0.048969656 5 2 12 12 TPGGILR trypsin-full-digest YER056C-A KA
+31 3 501.2200 1500.6365 1500.4829 0 75.014168 1 0.738213 1 9 44 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+31 3 501.2200 1500.6365 1497.7600 0.61014986 57.982483 2 0.28779244 2 8 48 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+31 3 501.2200 1500.6365 1500.7172 0.6992386 25.314043 3 0.22202596 3 5 48 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+32 3 1032.7900 3095.3467 3095.2366 0 1021.062 1 4.1811695 1 33 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+32 3 1032.7900 3095.3467 3095.4709 1.08211 25.482035 2 -0.34331581 2 8 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+33 2 433.7900 865.5644 868.0007 0 24.923223 2 0.27615401 1 3 14 13 EPGVPTIR trypsin-full-digest YDR399W KI
+33 2 433.7900 865.5644 863.9689 0.25559467 20.780163 4 0.20557052 2 2 12 13 EYQVIGR trypsin-full-digest YMR242C KR
+33 2 433.7900 865.5644 863.9843 0.3070561 21.143938 3 0.19135924 3 3 14 13 MSSNAQVK trypsin-full-digest YBL030C -T
+33 2 433.7900 865.5644 864.9566 0.67410392 11.694733 7 0.089997508 4 2 12 13 NIQHPEK trypsin-full-digest YDL223C KN
+33 2 433.7900 865.5644 868.0435 0.77937192 10.029391 8 0.060927331 5 2 12 13 AYVQFLK trypsin-full-digest YKL127W KE
+33 3 433.7900 1298.3466 1295.5011 0 142.93625 1 0.74851775 1 11 44 5 TSFFQALGVPTK trypsin-full-digest YLR340W KI
+33 3 433.7900 1298.3466 1300.4741 1.1231706 11.750471 5 -0.092195369 2 3 40 5 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+33 3 433.7900 1298.3466 1298.5687 1.2744842 56.905846 2 -0.20545629 3 6 40 5 LNNPAIALMWR trypsin-full-digest YHR183W KG
+33 3 433.7900 1298.3466 1299.4120 1.2848094 14.490228 4 -0.21318488 4 4 36 5 FEELCADLFR trypsin-full-digest YLL024C RS
+33 3 433.7900 1298.3466 1299.4670 1.4924383 46.446587 3 -0.36859885 5 7 40 5 MPYTLSDAHHK trypsin-full-digest YLR058C -L
+34 2 750.9200 1499.8243 1500.4829 0 35.232906 1 0.51629972 1 4 22 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+34 2 750.9200 1499.8243 1500.7172 0.51376176 11.712827 3 0.25104466 2 2 24 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+34 2 750.9200 1499.8243 1497.7600 0.79214215 14.823524 2 0.10731694 3 3 24 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+35 1 709.0700 708.0622 708.7692 0 14.558948 3 0.26784292 1 2 10 8 DFQTAK trypsin-full-digest YMR309C KD
+35 1 709.0700 708.0622 709.8869 0.36011532 11.018554 4 0.17138858 2 2 10 8 SIHILK trypsin-full-digest YMR242C RV
+35 1 709.0700 708.0622 710.8309 0.46457091 52.933228 1 0.14341089 3 3 10 8 AFAQFK trypsin-full-digest YJR069C KE
+35 1 709.0700 708.0622 710.7880 0.66859102 16.86434 2 0.088765554 4 2 12 8 HIDAGAK trypsin-full-digest YGR192C KK
+35 1 709.0700 708.0622 707.7845 0.86462736 2.7231455 5 0.036258604 5 1 10 8 FESAVR trypsin-full-digest YOR168W RK
+36 2 427.3800 852.7444 853.0293 0 107.2902 1 0.787049 1 6 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+36 2 427.3800 852.7444 852.0445 0.28271866 70.995552 2 0.56453556 2 5 14 13 HASLILAK trypsin-full-digest YMR235C KA
+36 2 427.3800 852.7444 852.8194 0.68353808 50.631237 3 0.24907105 3 3 12 13 DSCTENK trypsin-full-digest YNL166C KE
+36 2 427.3800 852.7444 855.0451 0.69871479 31.401226 4 0.23712622 4 4 14 13 LLGPQLSK trypsin-full-digest YGL135W RA
+36 2 427.3800 852.7444 852.0011 0.70649135 10.25797 8 0.2310057 5 2 14 13 LPLNPNGK trypsin-full-digest YBR115C KV
+37 2 652.3400 1302.6644 1301.4161 0 613.67346 1 2.9785695 1 18 22 8 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+37 2 652.3400 1302.6644 1301.4161 0.77743554 51.197414 3 0.66292375 2 6 22 8 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+37 2 652.3400 1302.6644 1303.4968 0.8709349 69.481659 2 0.3844294 3 8 22 8 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+37 2 652.3400 1302.6644 1304.4626 0.90986937 19.165369 5 0.26846039 4 5 22 8 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+37 2 652.3400 1302.6644 1300.4741 0.92362046 8.7759972 6 0.22750174 5 3 20 8 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+38 3 1032.3900 3094.1465 3095.2366 0 1161.2994 1 4.266221 1 34 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+38 3 1032.3900 3094.1465 3095.4709 0.91375649 57.854763 2 0.36793384 2 12 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+39 2 613.1300 1224.2444 1223.4375 0 19.768681 2 0.47953755 1 3 20 5 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+39 2 613.1300 1224.2444 1222.3203 0.55245852 38.796162 1 0.21461295 2 5 22 5 GGEGEVSVFVSR trypsin-full-digest YDR037W KV
+39 2 613.1300 1224.2444 1221.2867 0.68277049 5.8917556 5 0.15212347 3 2 22 5 TTTPAATSEQSK trypsin-full-digest YDL223C KV
+39 2 613.1300 1224.2444 1223.2670 0.94518626 8.5665131 4 0.026285237 4 2 18 5 YYGGNEHIDR trypsin-full-digest YLR058C RM
+39 2 613.1300 1224.2444 1224.3788 1.0179251 15.589462 3 -0.0085957637 5 3 18 5 LAFLENQDFK trypsin-full-digest YBR115C RL
+40 2 636.3700 1270.7244 1270.4917 0 35.940578 2 0.80229896 1 4 22 6 SGLIVEIQGVQK trypsin-full-digest YDR093W KE
+40 2 636.3700 1270.7244 1273.4087 0.023744045 95.220009 1 0.78324914 2 6 20 6 TVLDLEVNNTR trypsin-full-digest YDR093W RT
+40 2 636.3700 1270.7244 1272.5227 0.83309722 23.839369 3 0.13390592 3 4 22 6 MSVEPVVVIDGK trypsin-full-digest YIL133C -G
+40 2 636.3700 1270.7244 1271.5254 0.85973752 0.86187017 6 0.11253244 4 1 20 6 KPQVYPALLSR trypsin-full-digest YLR371W KV
+40 2 636.3700 1270.7244 1272.3778 1.3148003 14.258236 4 -0.25256389 5 4 22 6 VTAVVESPEGER trypsin-full-digest YGL008C KI
+41 2 1003.8400 2005.6644 2006.3051 0 419.7645 1 3.8897491 1 16 34 3 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+41 2 1003.8400 2005.6644 2004.0973 0.74423027 39.264839 2 0.99488002 2 5 36 3 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+41 2 1003.8400 2005.6644 2005.2764 1.0753206 9.034647 3 -0.29297847 3 4 34 3 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+42 3 1032.2600 3093.7566 3095.2366 0 1344.3297 1 4.2084866 1 36 108 3 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+42 3 1032.2600 3093.7566 3095.4709 1.0023168 51.772331 2 -0.0097504091 2 11 112 3 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+42 3 1032.2600 3093.7566 3090.7644 1.1557556 13.163209 3 -0.65549535 3 6 112 3 NIVPVIMAGIIAIYGLVVSVLVCYSLGQK trypsin-full-digest YEL027W KQ
+43 1 713.0700 712.0622 710.7880 0 35.014496 3 0.36360914 1 4 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+43 1 713.0700 712.0622 714.7765 0.043656271 37.214542 2 0.34773532 2 4 12 9 SGPTPTR trypsin-full-digest YDL223C KS
+43 1 713.0700 712.0622 713.7887 0.12476196 39.507935 1 0.31824455 3 4 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+43 1 713.0700 712.0622 710.8309 1.0670638 12.245291 4 -0.024385018 4 2 10 9 AFAQFK trypsin-full-digest YJR069C KE
+43 1 713.0700 712.0622 714.8626 1.256899 9.9744434 5 -0.093410835 5 2 10 9 ALPTWK trypsin-full-digest YMR235C KD
+44 2 1002.5200 2003.0244 2000.2000 0 4.9326487 2 0.64485914 1 3 28 4 FESIIHEFDPWFNYR trypsin-full-digest YGL022W KA
+44 2 1002.5200 2003.0244 2005.2764 0.12105732 35.548817 1 0.56679422 2 6 34 4 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+44 2 1002.5200 2003.0244 2000.1700 0.99633354 3.1540933 3 0.0023643672 3 2 34 4 ESDTGLAPSHLWDIMGDR trypsin-full-digest YKL145W KQ
+44 2 1002.5200 2003.0244 2004.0973 1.272543 2.1951361 4 -0.17575185 4 2 36 4 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+45 2 419.3200 836.6244 837.9280 0 120.29333 1 0.93879902 1 8 12 10 ETSNFIK trypsin-full-digest YBR118W KK
+45 2 419.3200 836.6244 839.0054 0.21616718 73.09761 2 0.73586148 2 6 14 10 IAGLNPVR trypsin-full-digest YPL106C RI
+45 2 419.3200 836.6244 835.9554 0.55938864 40.067127 4 0.41364554 3 5 12 10 FDNLLSK trypsin-full-digest YDL198C R-
+45 2 419.3200 836.6244 835.0110 0.65359831 45.420536 3 0.32520157 4 4 12 10 EYILGLK trypsin-full-digest YDL198C KD
+45 2 419.3200 836.6244 835.9554 0.72016436 31.306742 5 0.26270941 5 5 14 10 IGDYAGIK trypsin-full-digest YMR303C KW
+46 2 613.8100 1225.6044 1224.3788 0 7.4563694 3 0.28366849 1 2 18 4 LAFLENQDFK trypsin-full-digest YBR115C RL
+46 2 613.8100 1225.6044 1223.4375 0.78064227 9.3816624 2 0.06222488 2 2 20 4 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+46 2 613.8100 1225.6044 1227.4233 0.89254183 12.353053 1 0.030482505 3 2 18 4 IEVLEQELVR trypsin-full-digest YGR086C KA
+46 2 613.8100 1225.6044 1223.2670 1.9748561 3.6607263 4 -0.27653596 4 1 18 4 YYGGNEHIDR trypsin-full-digest YLR058C RM
+47 2 731.7700 1461.5244 1462.7675 0 977.83374 1 2.9550073 1 16 24 5 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+47 2 731.7700 1461.5244 1460.6036 0.76668084 39.054245 4 0.68945986 2 5 22 5 EEPDLENLLFNK trypsin-full-digest YHR183W RF
+47 2 731.7700 1461.5244 1459.6195 0.77189511 53.278816 3 0.67405158 3 6 26 5 SQVDEIVLVGGSTR trypsin-full-digest YLL024C KI
+47 2 731.7700 1461.5244 1460.4707 0.88700467 20.282669 5 0.333902 4 3 24 5 ELGDAYVSSDEEF trypsin-full-digest YLR249W K-
+47 2 731.7700 1461.5244 1463.5709 0.93729258 89.043457 2 0.18530098 5 7 24 5 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+48 2 692.1400 1382.2644 1382.4467 0 1650.222 1 3.2511344 1 19 24 7 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+48 2 692.1400 1382.2644 1379.3623 0.91646332 111.14242 2 0.27158907 2 7 24 7 FDDGAGGDNEVQR trypsin-full-digest YKL145W RT
+48 2 692.1400 1382.2644 1381.6099 0.94984984 56.814457 3 0.16304493 3 5 22 7 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+48 2 692.1400 1382.2644 1381.5258 1.0133696 15.170854 4 -0.043466073 4 3 22 7 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+48 2 692.1400 1382.2644 1379.5791 1.0143504 13.739942 5 -0.046654966 5 3 24 7 LIVTAHSSSHSIK trypsin-full-digest YLR371W RY
+49 2 652.2200 1302.4243 1301.4161 0 1331.3566 1 2.9836347 1 19 22 9 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+49 2 652.2200 1302.4243 1301.4161 0.47995821 476.32742 2 1.5516148 2 13 22 9 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+49 2 652.2200 1302.4243 1300.4741 0.68522078 147.28616 3 0.93918622 3 8 20 9 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+49 2 652.2200 1302.4243 1303.4968 0.76649767 98.610008 4 0.69668561 4 7 22 9 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+49 2 652.2200 1302.4243 1304.4626 0.83955383 96.138992 5 0.47871277 5 7 22 9 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+50 2 651.2900 1300.5643 1301.4161 0 1851.6044 1 4.5879292 1 20 22 10 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+50 2 651.2900 1300.5643 1301.4161 0.68850791 133.35484 2 1.4291036 2 8 22 10 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+50 2 651.2900 1300.5643 1303.4968 0.83599889 122.15955 3 0.75242537 3 7 22 10 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+50 2 651.2900 1300.5643 1298.5687 0.91140366 20.537592 6 0.40647364 4 3 20 10 LNNPAIALMWR trypsin-full-digest YHR183W KG
+50 2 651.2900 1300.5643 1300.4741 0.93134964 60.500343 4 0.31496304 5 5 20 10 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+51 2 498.7000 995.3844 996.0446 0 619.99927 1 2.5252917 1 13 18 14 NGFQTGSASK trypsin-full-digest YLR185W KA
+51 2 498.7000 995.3844 993.0570 0.73925728 16.682711 7 0.65845144 2 3 14 14 GEINCCLK trypsin-full-digest YOR267C RQ
+51 2 498.7000 995.3844 998.1502 0.76451415 156.03938 2 0.59467053 3 8 20 14 IAAVGAANGVR trypsin-full-digest YKL127W KK
+51 2 498.7000 995.3844 998.1038 0.81507969 33.531857 5 0.46697778 4 4 16 14 SSIQLGEHK trypsin-full-digest YLR371W KK
+51 2 498.7000 995.3844 993.2323 0.85587269 60.745483 3 0.36396354 5 5 14 14 VSILMFQR trypsin-full-digest YPL266W RE
+52 2 501.1300 1000.2444 999.1753 0 142.79124 1 1.1606123 1 8 16 10 EALGELVIR trypsin-full-digest YPL215W KA
+52 2 501.1300 1000.2444 998.1502 0.34597751 99.963516 2 0.75906658 2 7 20 10 IAAVGAANGVR trypsin-full-digest YKL127W KK
+52 2 501.1300 1000.2444 1003.0769 0.72584987 20.871323 6 0.31818202 3 3 16 10 NLDGETNLK trypsin-full-digest YDR093W KV
+52 2 501.1300 1000.2444 1003.1383 0.7358076 44.979645 4 0.30662498 4 5 18 10 AVNTGMEPGK trypsin-full-digest YLR340W RT
+52 2 501.1300 1000.2444 1000.1217 0.74814993 32.278728 5 0.29230028 5 4 12 10 EAYYWLR trypsin-full-digest YGL022W RM
+52 3 501.1300 1500.3666 1500.7172 0 43.558441 1 0.55699539 1 8 48 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+52 3 501.1300 1500.3666 1500.4829 1.2666898 20.81834 2 -0.14854498 2 6 44 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+52 3 501.1300 1500.3666 1497.7600 2.3426661 5.7192822 3 -0.74785888 3 3 48 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+53 2 745.7500 1489.4844 1489.7319 0 2781.0261 1 5.3343987 1 21 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+53 2 745.7500 1489.4844 1486.6195 0.76325125 235.51993 2 1.2629123 2 10 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+53 2 745.7500 1489.4844 1490.6510 0.9047128 25.391062 4 0.50830007 3 3 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+53 2 745.7500 1489.4844 1488.7063 0.95565957 74.514969 3 0.23652941 4 5 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+54 3 410.2000 1227.5765 1227.4233 0 56.159355 1 0.036128547 1 6 36 2 IEVLEQELVR trypsin-full-digest YGR086C KA
+54 3 410.2000 1227.5765 1229.3525 5.2370372 44.455582 2 -0.153078 2 7 40 2 EILGTDEPTVR trypsin-full-digest YKL127W KT
+55 2 475.8100 949.6044 949.0466 0 26.808455 2 0.71967018 1 4 14 9 MSQQDNVK trypsin-full-digest YDR037W -A
+55 2 475.8100 949.6044 950.1027 0.18550882 35.054756 1 0.58616501 2 5 14 9 SFLESVIR trypsin-full-digest YBR009C KD
+55 2 475.8100 949.6044 950.0160 0.27314121 11.84093 6 0.52309859 3 3 14 9 QTNPESFK trypsin-full-digest YDL198C RG
+55 2 475.8100 949.6044 951.0929 0.44186732 13.180162 5 0.40167144 4 3 14 9 EHAPWALK trypsin-full-digest YGL009C RD
+55 2 475.8100 949.6044 949.1149 0.47345805 13.361526 4 0.37893653 5 3 14 9 IFENVSIK trypsin-full-digest YDR205W KA
+56 2 902.9600 1803.9044 1801.9713 0 271.61176 1 1.4312 1 12 32 2 AEAESLVAEAQLSNITR trypsin-full-digest YGR086C RS
+56 2 902.9600 1803.9044 1805.0215 0.91516519 30.447412 2 0.12141556 2 5 32 2 LSAIESLAGVEILCSDK trypsin-full-digest YGL008C KT
+57 2 564.6800 1127.3444 1126.2928 0 1.6282531 8 0.38786855 1 1 18 9 GDVVMIYSSR trypsin-full-digest YBR115C RG
+57 2 564.6800 1127.3444 1129.2966 0.69543523 16.327734 3 0.1181311 2 4 18 9 NVVAVEMDPR trypsin-full-digest YPL266W KM
+57 2 564.6800 1127.3444 1126.2004 0.80020344 2.7844698 7 0.077494793 3 1 18 9 CTINGVSYGR trypsin-full-digest YDR093W KA
+57 2 564.6800 1127.3444 1125.2004 0.85385883 19.824213 2 0.056683555 4 3 20 9 YESATASALVN trypsin-full-digest YDR064W K-
+57 2 564.6800 1127.3444 1126.2340 0.9029569 32.730118 1 0.037639961 5 3 16 9 DEGLFNLYR trypsin-full-digest YDL198C RG
+58 2 565.6500 1129.2844 1130.2659 0 10.387362 3 0.17425571 1 2 18 6 NSPWVVDSVK trypsin-full-digest YOR168W KN
+58 2 565.6500 1129.2844 1129.2966 0.032992441 7.5589361 6 0.16850659 2 2 18 6 NVVAVEMDPR trypsin-full-digest YPL266W KM
+58 2 565.6500 1129.2844 1131.1674 0.27751508 33.858917 1 0.12589712 3 4 20 6 IDQASGAAQDR trypsin-full-digest YLR371W RH
+58 2 565.6500 1129.2844 1126.2928 1.4995954 21.486506 2 -0.087057345 4 3 18 6 GDVVMIYSSR trypsin-full-digest YBR115C RG
+58 2 565.6500 1129.2844 1129.3646 2.1613607 8.9149437 5 -0.20237374 5 2 18 6 GITIDIALWK trypsin-full-digest YBR118W RF
+59 2 474.3000 946.5844 945.0836 0 163.22826 1 0.79811859 1 6 14 7 LQTIIDSR trypsin-full-digest YMR309C RG
+59 2 474.3000 946.5844 946.0281 0.48343256 26.635284 6 0.41228208 2 4 16 7 LSVATADNR trypsin-full-digest YLR249W KH
+59 2 474.3000 946.5844 949.0466 0.51973206 79.889168 3 0.38331077 3 6 14 7 MSQQDNVK trypsin-full-digest YDR037W -A
+59 2 474.3000 946.5844 949.1149 0.74977499 81.326645 2 0.19970922 4 4 14 7 IFENVSIK trypsin-full-digest YDR205W KA
+59 2 474.3000 946.5844 945.0836 0.7771157 41.841644 4 0.1778881 5 5 20 7 LLGSGAGGSVK trypsin-full-digest YOR267C KV
+59 3 474.3000 1419.8765 1417.4955 0 122.20961 1 0.76713252 1 13 56 7 ADTGIAVEGATDAAR trypsin-full-digest YGL008C KS
+59 3 474.3000 1419.8765 1419.5200 0.60215867 52.378551 3 0.30519703 2 9 44 7 GEDELWCVINGK trypsin-full-digest YMR073C KV
+59 3 474.3000 1419.8765 1420.7550 0.64994532 79.130165 2 0.26853833 3 9 48 7 GVDLMVCVMGVLK trypsin-full-digest YBR115C RA
+59 3 474.3000 1419.8765 1420.5975 0.78942293 27.125801 5 0.16154051 4 7 44 7 LLARPGDSLYCR trypsin-full-digest YPL266W RL
+59 3 474.3000 1419.8765 1422.5168 0.95424658 50.471569 4 0.035098951 5 7 44 7 NFHNAIDEFSTK trypsin-full-digest YDR093W KE
+60 1 713.3600 712.3522 710.7880 0 24.40822 1 0.43409193 1 4 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+60 1 713.3600 712.3522 713.7887 0.54279155 22.626112 3 0.1984705 2 3 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+60 1 713.3600 712.3522 713.7881 0.66906232 1.9599029 6 0.14365739 3 1 12 9 TLYGFGG trypsin-full-digest YBR009C R-
+60 1 713.3600 712.3522 714.8626 0.7312721 13.145251 4 0.1166526 4 2 10 9 ALPTWK trypsin-full-digest YMR235C KD
+60 1 713.3600 712.3522 714.7765 1.0561372 24.213102 2 -0.024368707 5 4 12 9 SGPTPTR trypsin-full-digest YDL223C KS
+61 2 1004.4300 2006.8444 2006.3051 0 871.86584 1 3.8326077 1 18 34 4 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+61 2 1004.4300 2006.8444 2004.0973 0.74373084 43.846146 3 0.98217922 2 5 36 4 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+61 2 1004.4300 2006.8444 2009.1975 1.0181385 50.501587 2 -0.069518089 3 6 38 4 YDSPVSSPITSASELGSIAK trypsin-full-digest YNL166C KL
+61 2 1004.4300 2006.8444 2005.2764 1.057922 4.156528 4 -0.22199231 4 2 34 4 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+62 2 745.8600 1489.7043 1489.7319 0 2761.3391 1 5.301578 1 21 24 3 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+62 2 745.8600 1489.7043 1490.6510 0.86824602 44.483547 3 0.69850397 2 4 24 3 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+62 2 745.8600 1489.7043 1488.7063 0.96409976 82.697823 2 0.19032791 3 5 24 3 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+63 2 444.4100 886.8044 886.9603 0 26.139324 4 0.71276307 1 3 14 8 DLDRPGSK trypsin-full-digest YOR063W RF
+63 2 444.4100 886.8044 886.9292 0.39397162 26.822899 3 0.43195465 2 3 12 8 SHTLCNR trypsin-full-digest YLR185W KC
+63 2 444.4100 886.8044 887.0439 0.68880337 42.980015 1 0.22180946 3 3 14 8 ELQSLLGK trypsin-full-digest YCR012W KD
+63 2 444.4100 886.8044 886.0563 0.75538975 41.696362 2 0.17434917 4 4 14 8 ALLDEVVK trypsin-full-digest YCR012W KS
+63 2 444.4100 886.8044 887.0092 0.8485781 12.152888 5 0.10792796 5 2 12 8 RPTNPFR trypsin-full-digest YNL166C RV
+64 2 676.1000 1350.1843 1348.5188 0 29.814545 1 0.20261776 1 4 22 2 LVETLPSSYPSR trypsin-full-digest YBR115C KE
+64 2 676.1000 1350.1843 1351.3583 2.6623373 0 2 -0.33681905 2 0 20 2 DETCESNPFPR trypsin-full-digest YLR298C RL
+64 3 676.1000 2025.2765 2027.1876 0 24.818066 1 0.08459115 1 7 80 1 NVIAETGAGQHGVATATACAK trypsin-full-digest YGL026C KF
+65 2 452.8500 903.6844 904.0949 0 97.185295 4 0.74056631 1 5 14 20 HAFMGTLK trypsin-full-digest YOR063W KK
+65 2 452.8500 903.6844 904.9293 0.022225995 153.16431 1 0.72410649 2 7 14 20 EQPESTSK trypsin-full-digest YDL223C KN
+65 2 452.8500 903.6844 904.8859 0.29299486 40.426414 9 0.52358419 3 4 14 20 ESTPDNDK trypsin-full-digest YOR267C KE
+65 2 452.8500 903.6844 903.0921 0.32120171 101.14278 3 0.50269514 4 6 14 20 NLALLFGR trypsin-full-digest YLR371W RS
+65 2 452.8500 903.6844 905.1050 0.45861647 20.786068 15 0.4009304 5 3 16 20 IALIAGYGK trypsin-full-digest YGR086C KA
+66 2 427.3800 852.7444 853.0293 0 86.936096 2 0.80033225 1 5 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+66 2 427.3800 852.7444 855.0049 0.097246684 152.10268 1 0.72250259 2 7 16 13 SALVPGGVR trypsin-full-digest YLR058C KI
+66 2 427.3800 852.7444 851.9758 0.47781974 63.129513 3 0.4179177 3 5 14 13 SSMGPAFR trypsin-full-digest YGL135W KL
+66 2 427.3800 852.7444 852.8194 0.61674178 31.039164 4 0.30673394 4 3 12 13 DSCTENK trypsin-full-digest YNL166C KE
+66 2 427.3800 852.7444 852.0011 0.80157036 15.659703 9 0.15880965 5 3 14 13 LPLNPNGK trypsin-full-digest YBR115C KV
+67 2 692.1500 1382.2844 1382.4467 0 1821.1417 1 4.1942277 1 19 24 7 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+67 2 692.1500 1382.2844 1381.5258 0.82534504 46.728306 3 0.73254275 2 5 22 7 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+67 2 692.1500 1382.2844 1381.6099 0.88650858 119.8332 2 0.47600889 3 6 22 7 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+67 2 692.1500 1382.2844 1379.5791 0.92010963 43.565853 4 0.33507845 4 5 24 7 LIVTAHSSSHSIK trypsin-full-digest YLR371W RY
+67 2 692.1500 1382.2844 1379.3623 0.940844 29.001404 5 0.24811386 5 4 24 7 FDDGAGGDNEVQR trypsin-full-digest YKL145W RT
+68 2 468.8000 935.5844 935.0446 0 49.533195 4 0.74895662 1 6 14 11 LNLEGDFK trypsin-full-digest YGL245W KK
+68 2 468.8000 935.5844 933.9707 0.16079384 12.465908 7 0.62852901 2 4 16 11 NTISEAGDK trypsin-full-digest YLL024C KL
+68 2 468.8000 935.5844 935.1315 0.23179226 71.465187 2 0.57535428 3 5 16 11 VLPGPEVPK trypsin-full-digest YHR183W KD
+68 2 468.8000 935.5844 935.8565 0.28700686 98.048073 1 0.53400093 4 6 14 11 EDDSNNDK trypsin-full-digest YOR267C KE
+68 2 468.8000 935.5844 937.0202 0.62856978 36.394066 6 0.27818513 5 4 16 11 SDGVAGLYR trypsin-full-digest YBL030C KG
+68 3 468.8000 1403.3765 1404.5829 0 40.724213 2 0.37462369 1 9 44 6 TTLHYALSELEK trypsin-full-digest YDR399W RD
+68 3 468.8000 1403.3765 1404.4968 0.58936948 13.110674 6 0.15383191 2 7 56 6 VASANATAAESDVAK trypsin-full-digest YIL133C KQ
+68 3 468.8000 1403.3765 1405.7032 0.81445163 74.083321 1 0.069510803 3 11 48 6 GFLPSVVGIVVYR trypsin-full-digest YBL030C RG
+68 3 468.8000 1403.3765 1402.6282 1.1776992 21.763506 3 -0.066570319 4 8 44 6 MTSGYYLGELLR trypsin-full-digest YFR053C KL
+68 3 468.8000 1403.3765 1405.4899 1.3059314 15.813335 4 -0.11460918 5 6 44 6 STSTVNLNNHYR trypsin-full-digest YOR267C KA
+69 2 652.4800 1302.9443 1301.4161 0 866.42224 1 3.2185082 1 16 22 8 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+69 2 652.4800 1302.9443 1301.4161 0.61322856 165.8327 2 1.2448272 2 8 22 8 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+69 2 652.4800 1302.9443 1303.4968 0.75579822 75.887726 4 0.7859655 3 6 22 8 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+69 2 652.4800 1302.9443 1300.4741 0.77344012 113.19061 3 0.72918487 4 7 20 8 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+69 2 652.4800 1302.9443 1304.4626 0.87005603 46.928429 5 0.4182258 5 5 22 8 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+70 2 691.9500 1381.8844 1382.4467 0 1932.3346 1 3.9032106 1 19 24 7 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+70 2 691.9500 1381.8844 1381.5258 0.84123105 49.488419 4 0.61970872 2 5 22 7 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+70 2 691.9500 1381.8844 1379.3623 0.87033457 72.380486 3 0.5061115 3 6 24 7 FDDGAGGDNEVQR trypsin-full-digest YKL145W RT
+70 2 691.9500 1381.8844 1381.6099 0.89363277 82.036919 2 0.41517377 4 5 22 7 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+70 2 691.9500 1381.8844 1380.6042 0.98013854 8.8494978 6 0.077523351 5 2 22 7 EVVELPLLSPER trypsin-full-digest YKL145W RF
+71 2 488.7600 975.5044 974.1251 0 51.582912 1 0.57350701 1 5 16 10 STSANILLR trypsin-full-digest YDR205W KL
+71 2 488.7600 975.5044 974.0044 0.23152198 34.17643 2 0.44072753 2 4 14 10 DQPGLCER trypsin-full-digest YDR037W RF
+71 2 488.7600 975.5044 974.0121 0.52275521 6.3304238 6 0.27370325 3 2 12 10 HHHNHHR trypsin-full-digest YDL223C KH
+71 2 488.7600 975.5044 978.1595 0.53639543 6.1636882 7 0.26588047 4 2 16 10 HTAIVNPVK trypsin-full-digest YGL245W RI
+71 2 488.7600 975.5044 975.0636 0.64310586 7.7996826 5 0.20468129 5 2 16 10 DISTPDLSK trypsin-full-digest YDR093W KV
+72 2 651.6300 1301.2444 1301.4161 0 1339.0245 1 3.3731258 1 18 22 10 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+72 2 651.6300 1301.2444 1301.4161 0.61750263 258.82028 2 1.2902117 2 9 22 10 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+72 2 651.6300 1301.2444 1303.4968 0.82103974 53.011913 3 0.60365552 3 5 22 10 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+72 2 651.6300 1301.2444 1298.5687 0.86949509 32.90501 4 0.44020939 4 4 20 10 LNNPAIALMWR trypsin-full-digest YHR183W KG
+72 2 651.6300 1301.2444 1300.4741 0.89867258 29.368866 6 0.3417902 5 3 20 10 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+73 2 452.8500 903.6844 902.0586 0 56.347805 2 1.0837035 1 6 16 20 QGVTSLGIK trypsin-full-digest YML092C KA
+73 2 452.8500 903.6844 906.0465 0.21322978 68.521774 1 0.85262567 2 5 14 20 FDIGDLVK trypsin-full-digest YLR298C RA
+73 2 452.8500 903.6844 904.0338 0.41111323 23.418583 9 0.63817865 3 3 14 20 VSHTVSFK trypsin-full-digest YOR168W KS
+73 2 452.8500 903.6844 902.0587 0.5519315 24.958044 8 0.48557344 4 4 16 20 VIAVTNGTK trypsin-full-digest YGL026C KT
+73 2 452.8500 903.6844 904.8859 0.60063833 11.533216 15 0.43278965 5 3 14 20 ESTPDNDK trypsin-full-digest YOR267C KE
+73 3 452.8500 1355.5265 1354.3092 0 97.742645 1 0.66088116 1 10 48 7 GDDEANGATSFDR trypsin-full-digest YOR063W KT
+73 3 452.8500 1355.5265 1355.5164 0.41827905 96.809456 2 0.38444841 2 10 44 7 YQVTVIDAPGHR trypsin-full-digest YBR118W KD
+73 3 452.8500 1355.5265 1355.6616 0.59096551 21.397329 7 0.27032319 3 5 44 7 GMLNVQLLVVNR trypsin-full-digest YBR115C KN
+73 3 452.8500 1355.5265 1357.6157 0.76384509 52.985188 3 0.15607032 4 9 48 7 APIVAYAELIAAR trypsin-full-digest YGL245W KI
+73 3 452.8500 1355.5265 1354.4875 0.84334892 43.882256 4 0.10352775 5 7 40 7 GEYHFFQGITR trypsin-full-digest YJR069C RG
+74 2 427.3800 852.7444 853.0293 0 46.593933 3 0.44586661 1 4 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+74 2 427.3800 852.7444 854.0171 0.19086304 46.874577 2 0.36076716 2 4 14 13 THILSGVK trypsin-full-digest YDR093W RN
+74 2 427.3800 852.7444 849.9823 0.44673637 43.607098 5 0.24668178 3 4 12 13 IADQYLK trypsin-full-digest YPL215W RD
+74 2 427.3800 852.7444 852.0445 0.4754456 8.7929144 11 0.23388129 4 2 14 13 HASLILAK trypsin-full-digest YMR235C KA
+74 2 427.3800 852.7444 852.8194 0.49826011 39.332458 6 0.22370906 5 3 12 13 DSCTENK trypsin-full-digest YNL166C KE
+75 2 877.2700 1752.5244 1752.8573 0 1072.6307 1 3.9823563 1 16 26 4 LVSWYDNEYGYSTR trypsin-full-digest YGR192C KV
+75 2 877.2700 1752.5244 1753.9385 1.020926 7.8260818 2 -0.083334833 2 3 30 4 ACIIFFDEIDAVGGAR trypsin-full-digest YKL145W KF
+75 2 877.2700 1752.5244 1750.8798 1.100632 4.3475466 3 -0.4007521 3 2 30 4 AEETIAWLDSNTTATK trypsin-full-digest YLL024C KE
+75 2 877.2700 1752.5244 1754.9578 1.1276983 0 4 -0.50854033 4 0 34 4 ISHVSTGGGASLELLEGK trypsin-full-digest YCR012W KE
+76 2 731.8100 1461.6044 1462.7675 0 1339.4905 1 3.6146004 1 19 24 5 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+76 2 731.8100 1461.6044 1463.5709 0.89022428 15.232876 4 0.3967953 2 4 24 5 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+76 2 731.8100 1461.6044 1460.6036 0.90547442 10.096539 5 0.34167209 3 3 22 5 EEPDLENLLFNK trypsin-full-digest YHR183W RF
+76 2 731.8100 1461.6044 1460.4707 0.94390142 21.407425 2 0.2027739 4 4 24 5 ELGDAYVSSDEEF trypsin-full-digest YLR249W K-
+76 2 731.8100 1461.6044 1459.6195 0.97492385 21.211966 3 0.090640165 5 5 26 5 SQVDEIVLVGGSTR trypsin-full-digest YLL024C KI
+77 2 745.4300 1488.8444 1489.7319 0 2646.4438 1 4.6354041 1 21 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+77 2 745.4300 1488.8444 1486.6195 0.80580199 209.53319 2 0.9001863 2 9 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+77 2 745.4300 1488.8444 1490.6510 0.8935802 27.22241 4 0.49329877 3 3 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+77 2 745.4300 1488.8444 1488.7063 0.9329536 57.869457 3 0.31078729 4 4 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+78 2 452.2200 902.4244 902.0586 0 102.61301 1 0.80108744 1 7 16 19 QGVTSLGIK trypsin-full-digest YML092C KA
+78 2 452.2200 902.4244 904.9293 0.10703871 74.167198 2 0.71534008 2 5 14 19 EQPESTSK trypsin-full-digest YDL223C KN
+78 2 452.2200 902.4244 903.0513 0.43047881 35.246094 5 0.45623627 3 4 12 19 QFWLGPR trypsin-full-digest YBR115C RD
+78 2 452.2200 902.4244 903.9957 0.504062 42.685417 4 0.39728969 4 4 14 19 GWGWTAAR trypsin-full-digest YDL198C RN
+78 2 452.2200 902.4244 901.9256 0.5203054 7.4105458 15 0.38427731 5 2 14 19 APLEDDDK trypsin-full-digest YKL145W KK
+78 3 452.2200 1353.6365 1354.4875 0 109.16689 2 0.85549891 1 10 40 7 GEYHFFQGITR trypsin-full-digest YJR069C RG
+78 3 452.2200 1353.6365 1355.6616 0.046028499 77.322945 4 0.81612158 2 9 44 7 GMLNVQLLVVNR trypsin-full-digest YBR115C KN
+78 3 452.2200 1353.6365 1354.3092 0.4786047 101.63564 3 0.44605312 3 10 48 7 GDDEANGATSFDR trypsin-full-digest YOR063W KT
+78 3 452.2200 1353.6365 1355.5164 0.55555004 147.19391 1 0.38022646 4 11 44 7 YQVTVIDAPGHR trypsin-full-digest YBR118W KD
+78 3 452.2200 1353.6365 1355.4419 0.86263269 69.608704 5 0.11751757 5 8 48 7 FDSGTSGSQNMPK trypsin-full-digest YDL223C KA
+79 2 559.1000 1116.1843 1119.1559 0 22.954494 2 0.23699306 1 3 16 11 YHIEEEGSR trypsin-full-digest YCR012W RK
+79 2 559.1000 1116.1843 1118.3104 0.074480131 12.163911 5 0.21934178 2 3 16 11 INMIEELEK trypsin-full-digest YDR037W RV
+79 2 559.1000 1116.1843 1113.3398 0.39199558 8.6371117 6 0.14409283 3 3 18 11 AIMVNFGYAK trypsin-full-digest YOR168W KY
+79 2 559.1000 1116.1843 1113.1975 0.57595927 14.989534 4 0.10049471 4 4 16 11 DYFGAHTFR trypsin-full-digest YHR183W RV
+79 2 559.1000 1116.1843 1117.3536 0.65604508 35.847515 1 0.081514932 5 6 18 11 FLDGQIALLK trypsin-full-digest YBL076C KK
+80 2 509.2700 1016.5244 1017.1068 0 150.40614 1 0.90325707 1 6 16 9 ITSGQELNR trypsin-full-digest YDL198C KV
+80 2 509.2700 1016.5244 1017.1035 0.1405158 98.749428 2 0.77633518 2 5 16 9 VSSAEYYAK trypsin-full-digest YIL133C KK
+80 2 509.2700 1016.5244 1015.1717 0.84938502 54.884029 3 0.13604406 3 4 16 9 LDAELVLDK trypsin-full-digest YNL166C KF
+80 2 509.2700 1016.5244 1017.2080 0.85867649 17.96553 6 0.12765144 4 2 16 9 MTAFYSGIK trypsin-full-digest YMR309C RV
+80 2 509.2700 1016.5244 1018.0887 1.0889183 2.9468262 8 -0.080316156 5 1 14 9 LEEIETER trypsin-full-digest YMR235C KL
+81 2 427.3800 852.7444 853.0293 0 40.234848 3 0.71672249 1 3 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+81 2 427.3800 852.7444 854.0171 0.1037989 48.62289 2 0.64232749 2 4 14 13 THILSGVK trypsin-full-digest YDR093W RN
+81 2 427.3800 852.7444 852.0445 0.55270237 26.911837 6 0.32058826 3 3 14 13 HASLILAK trypsin-full-digest YMR235C KA
+81 2 427.3800 852.7444 851.9758 0.58951396 66.419243 1 0.29420456 4 5 14 13 SSMGPAFR trypsin-full-digest YGL135W KL
+81 2 427.3800 852.7444 851.8712 0.75772524 33.243809 4 0.17364377 5 4 12 13 FQTGEDR trypsin-full-digest YLR249W RE
+82 2 452.8500 903.6844 904.8859 0 64.193161 2 0.5262 1 4 14 20 ESTPDNDK trypsin-full-digest YOR267C KE
+82 2 452.8500 903.6844 906.0465 0.11277704 56.972046 3 0.46685672 2 4 14 20 FDIGDLVK trypsin-full-digest YLR298C RA
+82 2 452.8500 903.6844 904.9293 0.2270361 47.524639 5 0.4067336 3 4 14 20 EQPESTSK trypsin-full-digest YDL223C KN
+82 2 452.8500 903.6844 903.0002 0.42635316 51.255814 4 0.30185297 4 4 16 20 DTGVVDAVK trypsin-full-digest YNL166C KV
+82 2 452.8500 903.6844 904.0338 0.52230549 64.921379 1 0.25136286 5 4 14 20 VSHTVSFK trypsin-full-digest YOR168W KS
+82 3 452.8500 1355.5265 1355.5164 0 156.55568 2 0.72244394 1 10 44 7 YQVTVIDAPGHR trypsin-full-digest YBR118W KD
+82 3 452.8500 1355.5265 1355.4419 0.25582105 104.23301 4 0.53762758 2 10 48 7 FDSGTSGSQNMPK trypsin-full-digest YDL223C KA
+82 3 452.8500 1355.5265 1354.3928 0.72055531 159.81966 1 0.20188312 3 11 48 7 SGDAETAAYDNIK trypsin-full-digest YDL223C KN
+82 3 452.8500 1355.5265 1355.6616 0.78724837 51.907604 6 0.15370114 4 6 44 7 GMLNVQLLVVNR trypsin-full-digest YBR115C KN
+82 3 452.8500 1355.5265 1357.6157 1.0172542 42.36615 7 -0.012465239 5 7 48 7 APIVAYAELIAAR trypsin-full-digest YGL245W KI
+83 2 468.8000 935.5844 937.0202 0 165.04073 1 0.70322478 1 8 16 11 SDGVAGLYR trypsin-full-digest YBL030C KG
+83 2 468.8000 935.5844 937.0635 0.051904984 157.04977 2 0.66672391 2 7 14 11 LTSQGIYR trypsin-full-digest YGR157W KY
+83 2 468.8000 935.5844 935.1315 0.23450169 68.503082 4 0.53831738 3 5 16 11 VLPGPEVPK trypsin-full-digest YHR183W KD
+83 2 468.8000 935.5844 935.0446 0.30850619 18.517334 6 0.48627558 4 3 14 11 LNLEGDFK trypsin-full-digest YGL245W KK
+83 2 468.8000 935.5844 935.8565 0.42743704 51.483372 5 0.40264046 5 4 14 11 EDDSNNDK trypsin-full-digest YOR267C KE
+83 3 468.8000 1403.3765 1404.4968 0 43.463505 3 0.39917707 1 11 56 6 VASANATAAESDVAK trypsin-full-digest YIL133C KQ
+83 3 468.8000 1403.3765 1404.5829 0.13736853 77.41394 1 0.34434271 2 10 44 6 TTLHYALSELEK trypsin-full-digest YDR399W RD
+83 3 468.8000 1403.3765 1405.7032 0.552109 64.443207 2 0.17878783 3 9 48 6 GFLPSVVGIVVYR trypsin-full-digest YBL030C RG
+83 3 468.8000 1403.3765 1405.4899 1.5814054 3.3649597 6 -0.23208369 4 2 44 6 STSTVNLNNHYR trypsin-full-digest YOR267C KA
+83 3 468.8000 1403.3765 1402.6282 1.6719476 5.7472043 5 -0.26822606 5 4 44 6 MTSGYYLGELLR trypsin-full-digest YFR053C KL
+84 2 440.0600 878.1044 877.0109 0 18.001448 6 0.8047384 1 4 14 12 QGIYGLAR trypsin-full-digest YKL127W KS
+84 2 440.0600 878.1044 877.0080 0.18432704 45.319706 2 0.65640336 2 5 14 12 LSTSVGWK trypsin-full-digest YIL133C KY
+84 2 440.0600 878.1044 876.0233 0.21106918 59.926601 1 0.63488293 3 6 14 12 FVVGLGER trypsin-full-digest YKL145W KV
+84 2 440.0600 878.1044 875.8907 0.38777286 23.468019 5 0.4926827 4 4 12 12 LEEQDSR trypsin-full-digest YMR145C KR
+84 2 440.0600 878.1044 877.0135 0.43924966 8.4855242 9 0.45125732 5 2 12 12 NFGVWVR trypsin-full-digest YMR242C KY
+85 3 497.6200 1489.8365 1489.7319 0 2629.9929 1 5.015099 1 28 48 3 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+85 3 497.6200 1489.8365 1488.7063 0.84448564 590.96753 2 0.77991986 2 17 48 3 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+85 3 497.6200 1489.8365 1490.6510 0.92268771 84.568672 3 0.3877289 3 9 48 3 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+86 1 713.0700 712.0622 713.7887 0 42.898697 1 0.25811729 1 4 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+86 1 713.0700 712.0622 710.7880 0.43596756 26.317953 2 0.14558652 2 3 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+86 1 713.0700 712.0622 713.7881 0.89537442 14.902379 3 0.027005678 3 2 12 9 TLYGFGG trypsin-full-digest YBR009C R-
+86 1 713.0700 712.0622 714.7765 1.1662105 13.06544 4 -0.042901821 4 2 12 9 SGPTPTR trypsin-full-digest YDL223C KS
+86 1 713.0700 712.0622 709.8033 1.3344504 6.7109046 5 -0.086327426 5 2 14 9 AHGGVAAK trypsin-full-digest YCR034W RV
+87 2 501.1300 1000.2444 998.1502 0 82.180992 1 0.94085401 1 6 20 10 IAAVGAANGVR trypsin-full-digest YKL127W KK
+87 2 501.1300 1000.2444 999.1753 0.0071040629 52.168655 3 0.93417013 2 5 16 10 EALGELVIR trypsin-full-digest YPL215W KA
+87 2 501.1300 1000.2444 1003.0769 0.31822187 32.207912 4 0.64145368 3 4 16 10 NLDGETNLK trypsin-full-digest YDR093W KV
+87 2 501.1300 1000.2444 1003.1383 0.40787295 56.638897 2 0.55710512 4 6 18 10 AVNTGMEPGK trypsin-full-digest YLR340W RT
+87 2 501.1300 1000.2444 998.1038 0.58649296 12.313833 6 0.38904974 5 3 16 10 SSIQLGEHK trypsin-full-digest YLR371W KK
+87 3 501.1300 1500.3666 1500.7172 0 41.45351 1 0.32945254 1 8 48 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+87 3 501.1300 1500.3666 1497.7600 1.226549 22.535898 2 -0.074637152 2 6 48 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+87 3 501.1300 1500.3666 1500.4829 1.4662495 19.797424 3 -0.15360707 3 6 44 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+88 2 419.3200 836.6244 835.8872 0 24.406082 2 0.40368167 1 3 12 10 SDNVMDR trypsin-full-digest YBL076C KW
+88 2 419.3200 836.6244 834.0013 0.31547526 12.321632 4 0.27633008 2 2 12 10 LSMSQLR trypsin-full-digest YOR267C KS
+88 2 419.3200 836.6244 839.0054 0.49235049 17.52681 3 0.2049288 3 3 14 10 IAGLNPVR trypsin-full-digest YPL106C RI
+88 2 419.3200 836.6244 835.0110 0.76761371 2.3227963 9 0.093810096 4 1 12 10 EYILGLK trypsin-full-digest YDL198C KD
+88 2 419.3200 836.6244 837.9280 0.8460986 7.1517234 5 0.062127165 5 2 12 10 ETSNFIK trypsin-full-digest YBR118W KK
+89 2 452.8500 903.6844 906.0465 0 67.909523 1 0.66419196 1 5 14 20 FDIGDLVK trypsin-full-digest YLR298C RA
+89 2 452.8500 903.6844 904.8859 0.11163299 46.654369 2 0.59004623 2 5 14 20 ESTPDNDK trypsin-full-digest YOR267C KE
+89 2 452.8500 903.6844 903.0513 0.32041824 4.8063245 13 0.45137274 3 2 12 20 QFWLGPR trypsin-full-digest YBR115C RD
+89 2 452.8500 903.6844 900.9867 0.48289984 21.544519 4 0.34345376 4 3 12 20 ITADYYR trypsin-full-digest YLR298C RN
+89 2 452.8500 903.6844 905.0593 0.5430572 1.1933155 18 0.30349773 5 1 16 20 VSSTSLALK trypsin-full-digest YLR371W RR
+89 3 452.8500 1355.5265 1355.4419 0 115.35501 2 1.0529802 1 13 48 7 FDSGTSGSQNMPK trypsin-full-digest YDL223C KA
+89 3 452.8500 1355.5265 1354.3092 0.6454857 152.35396 1 0.37329653 2 12 48 7 GDDEANGATSFDR trypsin-full-digest YOR063W KT
+89 3 452.8500 1355.5265 1357.6157 0.64984179 32.56052 6 0.36870968 3 8 48 7 APIVAYAELIAAR trypsin-full-digest YGL245W KI
+89 3 452.8500 1355.5265 1355.6616 0.69778049 44.920116 4 0.31823114 4 7 44 7 GMLNVQLLVVNR trypsin-full-digest YBR115C KN
+89 3 452.8500 1355.5265 1354.3928 0.86221355 78.549049 3 0.14508639 5 11 48 7 SGDAETAAYDNIK trypsin-full-digest YDL223C KN
+90 3 1032.0000 3092.9766 3095.2366 0 1014.6406 1 4.1437883 1 32 108 3 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+90 3 1032.0000 3092.9766 3095.4709 0.99053985 48.36216 2 0.039200895 2 12 112 3 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+90 3 1032.0000 3092.9766 3090.7644 1.2211008 8.0220041 3 -0.91619474 3 5 112 3 NIVPVIMAGIIAIYGLVVSVLVCYSLGQK trypsin-full-digest YEL027W KQ
+91 2 466.0900 930.1644 932.2044 0 65.519272 2 0.60412568 1 5 14 9 MIAPMIEK trypsin-full-digest YLR043C KF
+91 2 466.0900 930.1644 933.0876 0.026813155 100.87474 1 0.58792716 2 6 14 9 MSIPETQK trypsin-full-digest YMR303C -A
+91 2 466.0900 930.1644 930.0287 0.048423041 58.461544 3 0.57487208 3 4 14 9 QVSDIVNR trypsin-full-digest YGR157W RI
+91 2 466.0900 930.1644 931.0996 0.40841615 30.83877 5 0.357391 4 4 14 9 LWVLTGDK trypsin-full-digest YDR093W KV
+91 2 466.0900 930.1644 930.0690 0.71705782 42.043987 4 0.17093264 5 4 14 9 IETGELIR trypsin-full-digest YLR371W KC
+92 3 497.2800 1488.8165 1489.7319 0 1872.1616 1 3.8966787 1 24 48 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+92 3 497.2800 1488.8165 1486.6195 0.83217859 344.51291 2 0.65394616 2 14 52 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+92 3 497.2800 1488.8165 1488.7063 0.84458709 281.42068 3 0.60559422 3 13 48 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+92 3 497.2800 1488.8165 1490.6510 1.0214745 92.455688 4 -0.083679095 4 9 48 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+93 2 693.0300 1384.0444 1382.4467 0 1282.8864 1 3.071521 1 18 24 5 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+93 2 693.0300 1384.0444 1381.5258 0.82522219 24.710701 3 0.53683364 2 4 22 5 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+93 2 693.0300 1384.0444 1381.6099 0.92968917 132.91029 2 0.21596114 3 7 22 5 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+93 2 693.0300 1384.0444 1386.6718 1.0372562 2.1949697 5 -0.11443344 4 1 20 5 LAEMIPQFFYK trypsin-full-digest YDR093W RN
+93 2 693.0300 1384.0444 1383.6108 1.0673972 2.2312288 4 -0.20701215 5 1 26 5 NVIVSGIVLAADGR trypsin-full-digest YBL076C KK
+94 3 669.4400 2005.2965 2006.3051 0 676.56519 1 2.6910779 1 27 68 3 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+94 3 669.4400 2005.2965 2004.0973 0.97163469 106.12769 2 0.076333262 2 14 72 3 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+94 3 669.4400 2005.2965 2005.2764 1.1398195 27.866337 3 -0.37626526 3 8 68 3 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+95 2 1004.4600 2006.9044 2006.3051 0 723.72211 1 3.9027524 1 16 34 4 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+95 2 1004.4600 2006.9044 2004.0973 0.82395792 26.607611 3 0.68704855 2 4 36 4 EANPSTQVPQSDTFPNGSK trypsin-full-digest YMR145C RR
+95 2 1004.4600 2006.9044 2009.1975 0.9481867 26.953934 2 0.2022146 3 4 38 4 YDSPVSSPITSASELGSIAK trypsin-full-digest YNL166C KL
+95 2 1004.4600 2006.9044 2005.2764 0.99055701 8.0184507 4 0.036853641 4 3 34 4 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+96 2 652.2400 1302.4644 1301.4161 0 1587.1769 1 4.1044731 1 18 22 9 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+96 2 652.2400 1302.4644 1301.4161 0.77718401 146.15948 2 0.9145422 2 7 22 9 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+96 2 652.2400 1302.4644 1303.4968 0.78656965 136.04576 3 0.87601912 3 7 22 9 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+96 2 652.2400 1302.4644 1301.4192 0.8966037 43.772213 5 0.42438722 4 4 22 9 DALPSVTSEQVR trypsin-full-digest YBL076C KE
+96 2 652.2400 1302.4644 1304.4626 0.9150939 87.347191 4 0.34849483 5 6 22 9 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+97 2 433.7800 865.5444 863.9689 0 22.758293 3 0.22999756 1 2 12 13 EYQVIGR trypsin-full-digest YMR242C KR
+97 2 433.7800 865.5444 865.1040 0.27651593 141.54544 1 0.16639957 2 5 10 13 FLWMIR trypsin-full-digest YGL022W KI
+97 2 433.7800 865.5444 862.9965 1.1270387 31.535526 2 -0.029218594 3 3 14 13 IMDTAGQK trypsin-full-digest YHR183W KG
+97 2 433.7800 865.5444 867.9752 1.3190436 0 8 -0.073379271 4 0 12 13 MANFETR trypsin-full-digest YNL166C KR
+97 2 433.7800 865.5444 863.9843 1.572087 18.824604 5 -0.13157864 5 3 14 13 MSSNAQVK trypsin-full-digest YBL030C -T
+97 3 433.7800 1298.3165 1295.5011 0 108.83713 1 0.50911599 1 9 44 5 TSFFQALGVPTK trypsin-full-digest YLR340W KI
+97 3 433.7800 1298.3165 1300.4741 0.5583092 77.047203 3 0.22487184 2 8 40 5 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+97 3 433.7800 1298.3165 1299.4670 0.79660463 95.325806 2 0.10355183 3 9 40 5 MPYTLSDAHHK trypsin-full-digest YLR058C -L
+97 3 433.7800 1298.3165 1298.5687 1.2789003 34.471161 5 -0.1419926 4 5 40 5 LNNPAIALMWR trypsin-full-digest YHR183W KG
+97 3 433.7800 1298.3165 1299.4120 1.4781585 36.938969 4 -0.24343814 5 5 36 5 FEELCADLFR trypsin-full-digest YLL024C RS
+98 2 751.2800 1500.5444 1500.4829 0 85.739204 1 0.73663002 1 6 22 3 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+98 2 751.2800 1500.5444 1497.7600 0.39315757 57.672653 2 0.44701836 2 6 24 3 LHHAFFVGDILTK trypsin-full-digest YBR115C KR
+98 2 751.2800 1500.5444 1500.7172 1.3417306 5.9268188 3 -0.25172904 3 2 24 3 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+99 3 581.9500 1742.8265 1740.0070 0 95.88134 1 0.48460686 1 11 56 3 MNSLVTQYAAPLFER trypsin-full-digest YCR034W -Y
+99 3 581.9500 1742.8265 1742.9492 0.37074959 43.33564 2 0.30493906 2 7 56 3 SLLNIDPHSSDYLIR trypsin-full-digest YMR309C KL
+99 3 581.9500 1742.8265 1742.9031 1.6881881 9.5394077 3 -0.33350065 3 4 56 3 ESLVEVNFADLYTSR trypsin-full-digest YMR235C RL
+100 1 763.1100 762.1022 764.9664 0 10.836562 7 0.33078977 1 2 12 15 LVLVHGK trypsin-full-digest YDR093W RW
+100 1 763.1100 762.1022 759.8577 0.046465401 32.205807 1 0.3154195 2 4 14 15 SGDAALVK trypsin-full-digest YBR118W KF
+100 1 763.1100 762.1022 762.9196 0.28373277 20.508097 2 0.23693387 3 3 12 15 MAAELTK trypsin-full-digest YPL266W RR
+100 1 763.1100 762.1022 761.8761 0.46104947 18.759415 4 0.17827933 4 3 10 15 DPVIYR trypsin-full-digest YGL245W RC
+100 1 763.1100 762.1022 764.8363 0.46744531 19.572428 3 0.17616364 5 3 12 15 YGADALR trypsin-full-digest YBL076C KL
+101 1 833.2400 832.2322 829.9922 0 25.544271 2 0.28301004 1 3 14 16 DIVSAVVK trypsin-full-digest YMR303C KA
+101 1 833.2400 832.2322 834.0013 0.083209559 14.410157 3 0.2594609 2 2 12 16 LSMSQLR trypsin-full-digest YOR267C KS
+101 1 833.2400 832.2322 832.9573 0.3484197 67.488708 1 0.18440376 3 3 12 16 NAPAWFK trypsin-full-digest YDR064W RL
+101 1 833.2400 832.2322 835.0112 0.46711424 2.5795839 10 0.15081201 4 1 12 16 TIFVVEK trypsin-full-digest YMR309C KG
+101 1 833.2400 832.2322 834.9862 0.69176388 4.319622 8 0.087233908 5 1 16 16 AAATAAMTK trypsin-full-digest YLR249W KA
+102 2 733.2200 1464.4243 1462.7675 0 963.87823 1 3.3292608 1 16 24 3 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+102 2 733.2200 1464.4243 1463.5709 0.91493738 1.7641164 3 0.28319573 2 1 24 3 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+102 2 733.2200 1464.4243 1466.6692 0.93777496 36.194633 2 0.20716341 3 4 22 3 DFMVEQELLNTK trypsin-full-digest YFR053C KD
+103 2 559.1000 1116.1843 1119.1559 0 27.676226 1 0.44975054 1 3 16 11 YHIEEEGSR trypsin-full-digest YCR012W RK
+103 2 559.1000 1116.1843 1114.1895 0.19610925 9.8223457 3 0.3615503 2 3 16 11 TLQPNPECR trypsin-full-digest YDR093W RF
+103 2 559.1000 1116.1843 1116.1615 0.39587018 7.9366827 4 0.27170771 3 3 16 11 YDGAFDCLR trypsin-full-digest YBL030C KK
+103 2 559.1000 1116.1843 1113.1975 0.65997499 0.809264 11 0.15292643 4 1 16 11 DYFGAHTFR trypsin-full-digest YHR183W RV
+103 2 559.1000 1116.1843 1115.2114 0.77206689 17.480232 2 0.10251305 5 4 18 11 DVSNSKPNVR trypsin-full-digest YMR073C RF
+104 2 565.2200 1128.4243 1129.2966 0 8.6711378 3 0.40850091 1 2 18 7 NVVAVEMDPR trypsin-full-digest YPL266W KM
+104 2 565.2200 1128.4243 1126.2340 0.37231663 18.984291 1 0.25640923 2 2 16 7 DEGLFNLYR trypsin-full-digest YDL198C RG
+104 2 565.2200 1128.4243 1126.2928 0.73227251 7.3460369 4 0.10936692 3 2 18 7 GDVVMIYSSR trypsin-full-digest YBR115C RG
+104 2 565.2200 1128.4243 1131.1674 1.013297 15.935033 2 -0.0054318211 4 3 20 7 IDQASGAAQDR trypsin-full-digest YLR371W RH
+104 2 565.2200 1128.4243 1126.2004 1.2105 3.8605995 5 -0.085989423 5 1 18 7 CTINGVSYGR trypsin-full-digest YDR093W KA
+105 2 483.1200 964.2244 964.0862 0 29.478136 2 0.52027655 1 4 14 9 SDTPLLYR trypsin-full-digest YBL076C RS
+105 2 483.1200 964.2244 965.1637 0.12127268 45.200874 1 0.45718122 2 4 14 9 VLVHTQIR trypsin-full-digest YOR063W RK
+105 2 483.1200 964.2244 967.0465 0.58198601 15.500867 4 0.21748286 3 3 16 9 GADSVIYSR trypsin-full-digest YDR093W KL
+105 2 483.1200 964.2244 962.1570 0.77023834 26.160965 3 0.1195396 4 3 14 9 LFTLEAIR trypsin-full-digest YOR168W RR
+105 2 483.1200 964.2244 962.1136 0.78001142 1.991576 5 0.1144549 5 1 14 9 LALIDDFR trypsin-full-digest YGL022W KE
+106 1 713.0700 712.0622 713.7887 0 19.851704 2 0.24297184 1 3 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+106 1 713.0700 712.0622 710.7880 0.56537306 9.3046618 4 0.10560211 2 2 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+106 1 713.0700 712.0622 714.8626 0.81795621 2.3578839 9 0.044231515 3 1 10 9 ALPTWK trypsin-full-digest YMR235C KD
+106 1 713.0700 712.0622 710.8309 0.96226132 9.7281923 3 0.0091694407 4 2 10 9 AFAQFK trypsin-full-digest YJR069C KE
+106 1 713.0700 712.0622 709.8033 1.3992343 6.9487085 5 -0.097002678 5 2 14 9 AHGGVAAK trypsin-full-digest YCR034W RV
+107 2 433.7800 865.5444 866.0430 0 2.096514 11 0.18164477 1 1 12 13 NDFIMVK trypsin-full-digest YOR063W KG
+107 2 433.7800 865.5444 863.9689 0.0033280628 54.479156 1 0.18104024 2 3 12 13 EYQVIGR trypsin-full-digest YMR242C KR
+107 2 433.7800 865.5444 864.9566 0.31438479 3.6916726 8 0.12453841 3 1 12 13 NIQHPEK trypsin-full-digest YDL223C KN
+107 2 433.7800 865.5444 864.0271 0.50945479 18.027445 5 0.089104973 4 2 12 13 LAEWMSK trypsin-full-digest YBR115C RY
+107 2 433.7800 865.5444 867.8272 0.59848398 17.266714 6 0.072933286 5 2 12 13 DSDDNFR trypsin-full-digest YOR267C RL
+107 3 433.7800 1298.3165 1295.5011 0 217.9725 1 0.61248285 1 10 44 5 TSFFQALGVPTK trypsin-full-digest YLR340W KI
+107 3 433.7800 1298.3165 1299.4670 0.57715613 143.61385 2 0.25898463 2 9 40 5 MPYTLSDAHHK trypsin-full-digest YLR058C -L
+107 3 433.7800 1298.3165 1298.5687 1.2572666 93.581177 3 -0.15757143 3 7 40 5 LNNPAIALMWR trypsin-full-digest YHR183W KG
+107 3 433.7800 1298.3165 1299.4120 1.3784283 34.675423 4 -0.23178086 4 5 36 5 FEELCADLFR trypsin-full-digest YLL024C RS
+107 3 433.7800 1298.3165 1300.4741 1.4784603 26.163458 5 -0.29304871 5 4 40 5 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+108 3 1032.5000 3094.4766 3095.2366 0 612.73865 1 3.6182745 1 28 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+108 3 1032.5000 3094.4766 3095.4709 0.90336043 41.487244 2 0.34966859 2 10 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+109 2 419.3200 836.6244 835.8872 0 24.110601 5 0.3558453 1 3 12 10 SDNVMDR trypsin-full-digest YBL076C KW
+109 2 419.3200 836.6244 839.0054 0.1598686 21.904999 6 0.29895681 2 3 14 10 IAGLNPVR trypsin-full-digest YPL106C RI
+109 2 419.3200 836.6244 835.0110 0.52057219 15.567754 8 0.17060213 3 3 12 10 EYILGLK trypsin-full-digest YDL198C KD
+109 2 419.3200 836.6244 835.9554 0.6000371 95.850708 1 0.14232492 4 6 14 10 IGDYAGIK trypsin-full-digest YMR303C KW
+109 2 419.3200 836.6244 837.9280 0.63456231 5.9988446 9 0.13003929 5 2 12 10 ETSNFIK trypsin-full-digest YBR118W KK
+110 2 613.1900 1224.3644 1222.3203 0 20.85313 1 0.51401627 1 3 22 4 GGEGEVSVFVSR trypsin-full-digest YDR037W KV
+110 2 613.1900 1224.3644 1223.4375 0.0089263823 11.477989 3 0.50942796 2 2 20 4 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+110 2 613.1900 1224.3644 1223.2670 0.44400001 14.988181 2 0.28579304 3 2 18 4 YYGGNEHIDR trypsin-full-digest YLR058C RM
+110 2 613.1900 1224.3644 1224.3788 0.87815511 8.9747524 4 0.062630266 4 2 18 4 LAFLENQDFK trypsin-full-digest YBR115C RL
+111 3 1033.0200 3096.0366 3095.2366 0 934.97644 1 4.0064011 1 31 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+111 3 1033.0200 3096.0366 3095.4709 0.9004131 97.407951 2 0.39898497 2 13 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+112 2 403.3000 804.5844 803.8675 0 66.118599 2 0.9786734 1 5 12 20 ELDTAQK trypsin-full-digest YGR192C KH
+112 2 403.3000 804.5844 803.9288 0.26627362 49.190113 6 0.71807849 2 5 14 20 GSMADVPK trypsin-full-digest YFR053C KE
+112 2 403.3000 804.5844 804.8577 0.52704316 56.694237 3 0.46287027 3 5 10 20 EWNQTK trypsin-full-digest YDR093W KF
+112 2 403.3000 804.5844 801.9383 0.61698544 10.482521 12 0.37484616 4 3 14 20 LSPGITSK trypsin-full-digest YGL009C KD
+112 2 403.3000 804.5844 804.8957 0.67115271 76.747498 1 0.32183412 5 6 12 20 ESVTEIK trypsin-full-digest YGR157W KA
+112 3 403.3000 1206.8765 1204.3109 0 33.421028 1 0.73118997 1 6 40 2 VNGDAHVISHR trypsin-full-digest YGR157W RA
+112 3 403.3000 1206.8765 1207.4535 0.65048796 28.29888 2 0.25555971 2 6 36 2 DTLKPMAIYR trypsin-full-digest YLR371W RV
+113 2 751.4200 1500.8243 1500.4829 0 2.2083549 1 0.20484404 1 2 22 2 YLPNGDCECCGR trypsin-full-digest YBR115C RA
+113 2 751.4200 1500.8243 1500.7172 1.3362254 0.41176486 2 -0.068873771 2 1 24 2 AALLNQYFAQAYK trypsin-full-digest YGL245W KG
+114 3 670.5500 2008.6265 2006.3051 0 431.85522 1 2.2389128 1 24 68 2 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+114 3 670.5500 2008.6265 2009.1975 0.7732603 74.17244 2 0.50765038 2 14 76 2 YDSPVSSPITSASELGSIAK trypsin-full-digest YNL166C KL
+115 2 452.8500 903.6844 905.0214 0 68.137947 2 0.39396563 1 4 12 20 HHEELLK trypsin-full-digest YOR267C RE
+115 2 452.8500 903.6844 904.9293 0.15361577 75.46859 1 0.33344629 2 5 14 20 EQPESTSK trypsin-full-digest YDL223C KN
+115 2 452.8500 903.6844 903.0513 0.26712555 40.726894 6 0.28872734 3 4 12 20 QFWLGPR trypsin-full-digest YBR115C RD
+115 2 452.8500 903.6844 905.1050 0.30531314 38.380623 7 0.27368274 4 4 16 20 IALIAGYGK trypsin-full-digest YGR086C KA
+115 2 452.8500 903.6844 903.0921 0.33805606 49.166584 4 0.26078317 5 5 14 20 NLALLFGR trypsin-full-digest YLR371W RS
+116 2 613.3100 1224.6044 1224.3788 0 30.347525 2 0.61062574 1 4 18 5 LAFLENQDFK trypsin-full-digest YBR115C RL
+116 2 613.3100 1224.6044 1222.3203 0.40603259 55.583378 1 0.36269179 2 5 22 5 GGEGEVSVFVSR trypsin-full-digest YDR037W KV
+116 2 613.3100 1224.6044 1223.4375 0.463314 28.741871 3 0.32771429 3 3 20 5 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+116 2 613.3100 1224.6044 1223.2670 1.3308802 4.6025863 4 -0.20204397 4 1 18 5 YYGGNEHIDR trypsin-full-digest YLR058C RM
+116 2 613.3100 1224.6044 1227.4233 1.5334202 3.0746751 5 -0.32572013 5 1 18 5 IEVLEQELVR trypsin-full-digest YGR086C KA
+117 2 652.5200 1303.0244 1301.4161 0 1256.421 1 3.6139576 1 18 22 8 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+117 2 652.5200 1303.0244 1301.4161 0.77656871 141.89146 2 0.80747122 2 7 22 8 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+117 2 652.5200 1303.0244 1300.4741 0.85818648 125.72668 3 0.51250803 3 8 20 8 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+117 2 652.5200 1303.0244 1304.4626 0.90605557 53.969692 5 0.3395111 4 5 22 8 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+117 2 652.5200 1303.0244 1303.4968 0.91972971 114.00854 4 0.29009345 5 7 22 8 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+118 3 1031.9399 3092.7964 3095.2366 0 2070.8057 1 4.5130448 1 42 108 3 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+118 3 1031.9399 3092.7964 3095.4709 0.9686414 41.307964 2 0.14152278 2 10 112 3 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+118 3 1031.9399 3092.7964 3090.7644 1.0997559 28.020123 3 -0.45020282 3 9 112 3 NIVPVIMAGIIAIYGLVVSVLVCYSLGQK trypsin-full-digest YEL027W KQ
+119 2 651.7700 1301.5244 1301.4161 0 1300.1331 1 3.780313 1 17 22 11 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+119 2 651.7700 1301.5244 1301.4161 0.71379524 221.25522 2 1.0819436 2 9 22 11 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+119 2 651.7700 1301.5244 1298.5687 0.81658727 125.39308 4 0.69335759 3 7 20 11 LNNPAIALMWR trypsin-full-digest YHR183W KG
+119 2 651.7700 1301.5244 1303.4968 0.84427452 163.24036 3 0.58869106 4 8 22 11 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+119 2 651.7700 1301.5244 1304.4626 0.85154969 104.09963 5 0.56118876 5 7 22 11 IPGTFEPDTLSK trypsin-full-digest YDL223C KS
+120 2 409.2100 816.4044 818.8417 0 124.02093 1 0.57712847 1 5 12 9 QSNDSLR trypsin-full-digest YOR267C KS
+120 2 409.2100 816.4044 815.9681 0.20467918 48.632717 3 0.45900229 2 3 12 9 SLNLTLR trypsin-full-digest YOR136W RK
+120 2 409.2100 816.4044 814.8504 0.22414759 34.387234 4 0.44776651 3 3 12 9 APELDDR trypsin-full-digest YBR115C KN
+120 2 409.2100 816.4044 816.9555 0.3102152 25.83992 6 0.39809445 4 2 12 9 HLSSVFK trypsin-full-digest YPL266W KF
+120 2 409.2100 816.4044 818.9838 0.33361226 99.746979 2 0.38459134 5 4 12 9 LEEAMVK trypsin-full-digest YMR309C KL
+121 2 651.5800 1301.1444 1301.4161 0 1479.4915 1 4.3240523 1 18 22 10 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+121 2 651.5800 1301.1444 1303.4968 0.78806555 74.371384 3 0.91641569 2 5 22 10 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+121 2 651.5800 1301.1444 1300.4741 0.86330932 74.331306 4 0.5910576 3 5 20 10 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+121 2 651.5800 1301.1444 1301.4161 0.86501253 103.94946 2 0.58369279 4 6 22 10 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+121 2 651.5800 1301.1444 1301.4192 0.88314486 54.668568 5 0.50528789 5 5 22 10 DALPSVTSEQVR trypsin-full-digest YBL076C KE
+122 1 760.2200 759.2122 759.8577 0 70.539841 1 0.42828295 1 5 14 13 SGDAALVK trypsin-full-digest YBR118W KF
+122 1 760.2200 759.2122 758.7892 0.059807912 19.467524 5 0.40266824 2 3 12 13 GSSQQPR trypsin-full-digest YEL027W RL
+122 1 760.2200 759.2122 756.8137 0.21858351 17.001827 6 0.33466735 3 3 12 13 SHSEGLK trypsin-full-digest YMR235C KV
+122 1 760.2200 759.2122 758.8753 0.24966337 23.554132 4 0.32135639 4 3 10 13 IGWDLR trypsin-full-digest YGL026C KF
+122 1 760.2200 759.2122 759.8577 0.46435907 69.700447 2 0.22940588 5 5 12 13 NSTIPTK trypsin-full-digest YLL024C RK
+123 2 565.0300 1128.0444 1129.2966 0 15.687304 2 0.33831081 1 3 18 7 NVVAVEMDPR trypsin-full-digest YPL266W KM
+123 2 565.0300 1128.0444 1125.2004 0.22678033 19.670055 1 0.26158857 2 4 20 7 YESATASALVN trypsin-full-digest YDR064W K-
+123 2 565.0300 1128.0444 1130.2659 0.40167227 10.035781 4 0.20242074 3 2 18 7 NSPWVVDSVK trypsin-full-digest YOR168W KN
+123 2 565.0300 1128.0444 1126.2340 0.41678071 10.784776 3 0.19730939 4 2 16 7 DEGLFNLYR trypsin-full-digest YDL198C RG
+123 2 565.0300 1128.0444 1126.2004 1.3182964 10.035781 4 -0.10768311 5 2 18 7 CTINGVSYGR trypsin-full-digest YDR093W KA
+124 2 495.0600 988.1044 987.0771 0 147.71281 1 1.242798 1 7 16 3 YSFLEGGSK trypsin-full-digest YGL009C KL
+124 2 495.0600 988.1044 989.0935 0.68469864 6.1323128 3 0.39185587 2 2 16 3 SLEASVIDR trypsin-full-digest YBR115C KN
+124 2 495.0600 988.1044 988.1950 0.79839063 12.011983 2 0.25055972 3 3 18 3 TPLPPAPAPK trypsin-full-digest YBL030C KK
+125 1 805.0000 803.9922 804.8957 0 67.403206 1 0.68201995 1 4 12 20 ESVTEIK trypsin-full-digest YGR157W KA
+125 1 805.0000 803.9922 802.9286 0.3362076 46.575958 2 0.45271966 2 4 12 20 THAIFSK trypsin-full-digest YGR157W KI
+125 1 805.0000 803.9922 804.8956 0.49661425 22.291025 6 0.34331912 3 2 12 20 ESTIDIK trypsin-full-digest YOR267C KI
+125 1 805.0000 803.9922 804.8577 0.50674599 32.34922 4 0.33640909 4 3 10 20 EWNQTK trypsin-full-digest YDR093W KF
+125 1 805.0000 803.9922 803.8675 0.57547224 26.311508 5 0.28953642 5 3 12 20 ELDTAQK trypsin-full-digest YGR192C KH
+126 2 745.2600 1488.5044 1489.7319 0 573.63257 1 3.4199548 1 14 24 5 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+126 2 745.2600 1488.5044 1486.6195 0.79367924 34.449203 4 0.70560771 2 5 26 5 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+126 2 745.2600 1488.5044 1488.7063 0.84733301 35.298698 3 0.52211416 3 4 24 5 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+126 2 745.2600 1488.5044 1485.6539 0.94492072 53.523678 2 0.18836875 4 5 22 5 QEAIYEVYITEK trypsin-full-digest YLR371W RN
+126 2 745.2600 1488.5044 1490.6510 0.97745997 6.6915894 5 0.077085875 5 2 24 5 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+127 2 474.7400 947.4644 947.0990 0 49.968937 1 0.57516605 1 4 14 8 LTWLADTK trypsin-full-digest YGL245W KD
+127 2 474.7400 947.4644 949.1149 0.36377129 24.094387 5 0.36593714 2 4 14 8 IFENVSIK trypsin-full-digest YDR205W KA
+127 2 474.7400 947.4644 945.0836 0.50043005 19.564295 6 0.28733566 3 3 14 8 LQTIIDSR trypsin-full-digest YMR309C RG
+127 2 474.7400 947.4644 945.0836 0.73157567 26.662403 4 0.15438858 4 4 20 8 LLGSGAGGSVK trypsin-full-digest YOR267C KV
+127 2 474.7400 947.4644 950.1027 0.78049624 49.048164 2 0.12625112 5 5 14 8 SFLESVIR trypsin-full-digest YBR009C KD
+128 1 711.0700 710.0622 709.8869 0 12.085135 3 0.16219591 1 2 10 9 SIHILK trypsin-full-digest YMR242C RV
+128 1 711.0700 710.0622 710.7880 0.71393204 8.2783346 4 0.046399057 2 2 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+128 1 711.0700 710.0622 710.8309 0.72429669 23.710316 1 0.044717953 3 3 10 9 AFAQFK trypsin-full-digest YJR069C KE
+128 1 711.0700 710.0622 712.8472 0.97089922 19.031324 2 0.0047200308 4 3 12 9 TPGGILR trypsin-full-digest YER056C-A KA
+128 1 711.0700 710.0622 708.8125 1.0198404 2.5368099 6 -0.0032180157 5 1 10 9 FSLQSK trypsin-full-digest YMR145C RS
+129 2 523.2900 1044.5643 1045.1577 0 46.084091 1 0.65602416 1 4 16 6 ELEELTGVR trypsin-full-digest YBL076C KN
+129 2 523.2900 1044.5643 1044.1908 0.96237737 15.760937 4 0.024681358 2 3 16 6 QTHSMAELK trypsin-full-digest YOR267C KR
+129 2 523.2900 1044.5643 1045.2443 1.032151 5.7093325 5 -0.021091802 3 2 18 6 LNITGTVLSK trypsin-full-digest YOR168W RR
+129 2 523.2900 1044.5643 1047.2213 1.041258 3.3512132 6 -0.027066199 4 1 12 6 YWYFLQK trypsin-full-digest YMR242C RL
+129 2 523.2900 1044.5643 1046.2346 1.1082737 16.434448 3 -0.071030214 5 3 16 6 YKPGEAILR trypsin-full-digest YOR168W KM
+130 2 733.0300 1464.0444 1462.7675 0 1393.9764 1 3.6638756 1 19 24 3 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+130 2 733.0300 1464.0444 1463.5709 0.95259821 6.5836983 3 0.17367421 2 3 24 3 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+130 2 733.0300 1464.0444 1466.6692 0.96637368 7.5720978 2 0.12320261 3 2 22 3 DFMVEQELLNTK trypsin-full-digest YFR053C KD
+131 2 745.8500 1489.6843 1489.7319 0 2819.5974 1 5.3028259 1 21 24 3 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+131 2 745.8500 1489.6843 1488.7063 0.8833434 85.206764 2 0.61860967 2 5 24 3 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+131 2 745.8500 1489.6843 1490.6510 0.90654737 26.993124 3 0.49556294 3 3 24 3 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+132 2 474.7400 947.4644 945.0836 0 54.108074 1 0.59248811 1 4 14 8 LQTIIDSR trypsin-full-digest YMR309C RG
+132 2 474.7400 947.4644 947.0990 0.13254599 25.854864 6 0.51395619 2 3 14 8 LTWLADTK trypsin-full-digest YGL245W KD
+132 2 474.7400 947.4644 950.1027 0.17679264 34.256989 3 0.48774058 3 4 14 8 SFLESVIR trypsin-full-digest YBR009C KD
+132 2 474.7400 947.4644 949.0466 0.2716538 48.32312 2 0.43153647 4 4 14 8 MSQQDNVK trypsin-full-digest YDR037W -A
+132 2 474.7400 947.4644 946.0281 0.31869599 26.415321 5 0.40366453 5 4 16 8 LSVATADNR trypsin-full-digest YLR249W KH
+133 2 483.1200 964.2244 965.1637 0 66.851875 1 0.60504568 1 6 14 9 VLVHTQIR trypsin-full-digest YOR063W RK
+133 2 483.1200 964.2244 962.1136 0.27866718 28.080624 3 0.43643931 2 4 14 9 LALIDDFR trypsin-full-digest YGL022W KE
+133 2 483.1200 964.2244 962.1570 0.71846265 42.350151 2 0.17034295 3 5 14 9 LFTLEAIR trypsin-full-digest YOR168W RR
+133 2 483.1200 964.2244 967.0465 0.89122903 6.9606466 4 0.065811396 4 2 16 9 GADSVIYSR trypsin-full-digest YDR093W KL
+133 2 483.1200 964.2244 966.0991 1.1542394 4.0717926 6 -0.093321867 5 2 14 9 DLTEFLTK trypsin-full-digest YGR157W KV
+134 2 457.5500 913.0844 914.1131 0 103.68198 1 1.1871964 1 7 16 11 QTVAVGVIK trypsin-full-digest YBR118W RS
+134 2 457.5500 913.0844 915.0573 0.51189619 31.804583 4 0.5794751 2 4 16 11 QGQAAIISK trypsin-full-digest YLR371W KT
+134 2 457.5500 913.0844 914.1532 0.54558873 37.778015 3 0.53947538 3 4 14 11 SIILLIDK trypsin-full-digest YLR371W KK
+134 2 457.5500 913.0844 914.0292 0.57700694 22.956854 5 0.50217581 4 3 14 11 QNNIAVQK trypsin-full-digest YMR309C KR
+134 2 457.5500 913.0844 914.0289 0.78891629 38.178898 2 0.2505978 5 4 14 11 AFHVTPDK trypsin-full-digest YLR058C KW
+135 2 1004.9900 2007.9644 2006.3051 0 933.36005 1 4.2101994 1 19 34 3 SGVGICATCVLRPDLLFK trypsin-full-digest YEL027W KN
+135 2 1004.9900 2007.9644 2009.1975 1.0327803 34.554996 2 -0.13801165 2 5 38 3 YDSPVSSPITSASELGSIAK trypsin-full-digest YNL166C KL
+135 2 1004.9900 2007.9644 2005.2764 1.0644609 3.5093601 3 -0.27139318 3 2 34 3 IPDIENSVNMVPVDHVAR trypsin-full-digest YBR115C KV
+136 1 717.0700 716.0622 716.7893 0 33.504017 6 0.72184199 1 4 12 16 EAAELGK trypsin-full-digest YBR118W KG
+136 1 717.0700 716.0622 714.7765 0.10004064 114.26469 1 0.64962846 2 6 12 16 SGPTPTR trypsin-full-digest YDL223C KS
+136 1 717.0700 716.0622 717.8204 0.1884166 23.559481 8 0.58583498 3 3 10 16 SLEITR trypsin-full-digest YLR371W KD
+136 1 717.0700 716.0622 718.7643 0.38262898 39.344013 5 0.44564432 4 4 10 16 GAEWEK trypsin-full-digest YGL009C KA
+136 1 717.0700 716.0622 713.7887 0.49265304 44.671604 4 0.36622435 5 4 12 16 NPAVGEK trypsin-full-digest YGL245W KK
+137 3 497.2900 1488.8466 1489.7319 0 1202.3578 1 3.5980604 1 22 48 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+137 3 497.2900 1488.8466 1488.7063 0.81239575 238.33492 2 0.67501152 2 13 48 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+137 3 497.2900 1488.8466 1490.6510 0.91495377 106.84063 3 0.30600145 3 10 48 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+137 3 497.2900 1488.8466 1486.6195 0.96376705 104.79422 4 0.13036823 4 9 52 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+138 1 719.0600 718.0522 716.8506 0 52.676434 1 0.83089995 1 4 12 13 DVMPAGK trypsin-full-digest YBR115C KG
+138 1 719.0600 718.0522 717.8204 0.24423222 27.570053 4 0.62796742 2 3 10 13 SLEITR trypsin-full-digest YLR371W KD
+138 1 719.0600 718.0522 718.8077 0.44881228 42.191254 2 0.45798185 3 3 10 13 FDNVPK trypsin-full-digest YGL009C KR
+138 1 719.0600 718.0522 717.8817 0.54288805 30.408899 3 0.37981433 4 3 10 13 QSKPMK trypsin-full-digest YDR093W RD
+138 1 719.0600 718.0522 718.7643 0.58580309 26.714539 5 0.34415618 5 2 10 13 GAEWEK trypsin-full-digest YGL009C KA
+139 3 1032.0900 3093.2463 3095.2366 0 1460.1478 1 3.9592109 1 39 108 3 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+139 3 1032.0900 3093.2463 3095.4709 0.89455146 39.019924 2 0.41749313 2 11 112 3 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+139 3 1032.0900 3093.2463 3090.7644 1.1534919 13.67534 3 -0.60770655 3 6 112 3 NIVPVIMAGIIAIYGLVVSVLVCYSLGQK trypsin-full-digest YEL027W KQ
+140 1 717.0600 716.0522 716.7893 0 31.130041 3 0.59465551 1 4 12 16 EAAELGK trypsin-full-digest YBR118W KG
+140 1 717.0600 716.0522 716.7460 0.0037337129 23.396549 6 0.59243524 2 3 10 16 KPDDDK trypsin-full-digest YKL145W KI
+140 1 717.0600 716.0522 714.7765 0.42896518 40.463547 2 0.339569 3 4 12 16 SGPTPTR trypsin-full-digest YDL223C KS
+140 1 717.0600 716.0522 718.8077 0.43547797 48.258392 1 0.33569613 4 4 10 16 FDNVPK trypsin-full-digest YGL009C KR
+140 1 717.0600 716.0522 717.8817 0.44567406 29.726236 4 0.32963297 5 3 10 16 QSKPMK trypsin-full-digest YDR093W RD
+141 3 497.2900 1488.8466 1489.7319 0 1504.3676 1 4.4072876 1 24 48 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+141 3 497.2900 1488.8466 1486.6195 0.81095272 174.72479 3 0.83318573 2 12 52 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+141 3 497.2900 1488.8466 1488.7063 0.8131507 369.57693 2 0.82349861 3 15 48 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+141 3 497.2900 1488.8466 1490.6510 0.96138328 67.817703 4 0.17019501 4 8 48 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+142 1 715.0700 714.0622 716.7893 0 72.108284 1 0.72181535 1 5 12 12 EAAELGK trypsin-full-digest YBR118W KG
+142 1 715.0700 714.0622 713.7887 0.55028677 11.598034 6 0.32460991 2 2 12 12 NPAVGEK trypsin-full-digest YGL245W KK
+142 1 715.0700 714.0622 714.7765 0.71276796 21.419298 3 0.20732848 3 3 12 12 SGPTPTR trypsin-full-digest YDL223C KS
+142 1 715.0700 714.0622 716.8506 0.7541483 8.9955482 8 0.17745954 4 2 12 12 DVMPAGK trypsin-full-digest YBR115C KG
+142 1 715.0700 714.0622 715.9341 0.7584759 12.551558 4 0.17433582 5 2 10 12 LLPFVK trypsin-full-digest YLR340W KG
+143 2 452.8500 903.6844 906.0465 0 200.59422 1 0.94311553 1 8 14 20 FDIGDLVK trypsin-full-digest YLR298C RA
+143 2 452.8500 903.6844 905.0214 0.28600335 74.133629 3 0.67338133 2 5 12 20 HHEELLK trypsin-full-digest YOR267C RE
+143 2 452.8500 903.6844 904.0949 0.36352864 52.860504 6 0.60026604 3 5 14 20 HAFMGTLK trypsin-full-digest YOR063W KK
+143 2 452.8500 903.6844 904.0338 0.41108957 83.931282 2 0.55541056 4 6 14 20 VSHTVSFK trypsin-full-digest YOR168W KS
+143 2 452.8500 903.6844 904.9293 0.41509125 34.957909 12 0.55163652 5 4 14 20 EQPESTSK trypsin-full-digest YDL223C KN
+144 3 497.2900 1488.8466 1489.7319 0 1053.226 1 3.5541759 1 21 48 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+144 3 497.2900 1488.8466 1488.7063 0.86864299 272.68655 2 0.46686584 2 13 48 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
+144 3 497.2900 1488.8466 1486.6195 1.0075978 137.61798 3 -0.027004087 3 11 52 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+144 3 497.2900 1488.8466 1490.6510 1.0094203 64.820557 4 -0.033481151 4 7 48 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+145 1 717.0600 716.0522 714.7765 0 58.588223 1 0.90983647 1 5 12 16 SGPTPTR trypsin-full-digest YDL223C KS
+145 1 717.0600 716.0522 715.9341 0.44376087 41.323978 3 0.50608665 2 4 10 16 LLPFVK trypsin-full-digest YLR340W KG
+145 1 717.0600 716.0522 716.7893 0.48714566 22.007057 7 0.46661359 3 3 12 16 EAAELGK trypsin-full-digest YBR118W KG
+145 1 717.0600 716.0522 713.7887 0.49324587 33.729961 4 0.46106339 4 4 12 16 NPAVGEK trypsin-full-digest YGL245W KK
+145 1 717.0600 716.0522 717.8204 0.53495586 9.8458958 9 0.42311412 5 2 10 16 SLEITR trypsin-full-digest YLR371W KD
+146 2 692.6800 1383.3444 1382.4467 0 2011.0013 1 3.8734953 1 19 24 5 TASEFDSAIAQDK trypsin-full-digest YLR043C KL
+146 2 692.6800 1383.3444 1381.6099 0.68104291 337.00198 2 1.2354789 2 10 22 5 LAMFLTDSNTIR trypsin-full-digest YDR037W RE
+146 2 692.6800 1383.3444 1381.5258 0.88333881 9.5191793 3 0.45188648 3 2 22 5 MSESNAHFSFPK trypsin-full-digest YBL076C -E
+146 2 692.6800 1383.3444 1380.6042 1.0289 3.3277209 5 -0.11194392 4 1 22 5 EVVELPLLSPER trypsin-full-digest YKL145W RF
+146 2 692.6800 1383.3444 1383.6108 1.1577057 7.8270969 4 -0.61087209 5 2 26 5 NVIVSGIVLAADGR trypsin-full-digest YBL076C KK
+147 2 614.5800 1227.1444 1227.4233 0 7.4682322 1 0.01874348 1 2 18 3 IEVLEQELVR trypsin-full-digest YGR086C KA
+147 2 614.5800 1227.1444 1224.3788 3.5171313 1.7642522 3 -0.0471798 2 1 18 3 LAFLENQDFK trypsin-full-digest YBR115C RL
+147 2 614.5800 1227.1444 1229.3525 6.4989333 4.1427054 2 -0.10306915 3 2 20 3 EILGTDEPTVR trypsin-full-digest YKL127W KT
+148 1 713.0700 712.0622 713.7887 0 24.496252 4 0.33537182 1 3 12 9 NPAVGEK trypsin-full-digest YGL245W KK
+148 1 713.0700 712.0622 713.7881 0.33931932 46.403988 3 0.22157368 2 4 12 9 TLYGFGG trypsin-full-digest YBR009C R-
+148 1 713.0700 712.0622 710.7880 0.54243892 48.601635 2 0.1534531 3 4 12 9 HIDAGAK trypsin-full-digest YGR192C KK
+148 1 713.0700 712.0622 712.8472 0.59844357 11.41906 5 0.1346707 4 3 12 9 TPGGILR trypsin-full-digest YER056C-A KA
+148 1 713.0700 712.0622 710.8309 0.78597832 59.82716 1 0.071776837 5 4 10 9 AFAQFK trypsin-full-digest YJR069C KE
+149 2 733.7700 1465.5244 1462.7675 0 1203.868 1 3.1824079 1 18 24 3 NEVSAMPTLLLFK trypsin-full-digest YLR043C KN
+149 2 733.7700 1465.5244 1466.6692 0.92764938 7.8815074 2 0.23024926 2 2 22 3 DFMVEQELLNTK trypsin-full-digest YFR053C KD
+149 2 733.7700 1465.5244 1463.5709 0.96620041 1.0003113 3 0.10756414 3 1 24 3 TCVVETPTLNSDK trypsin-full-digest YBR115C RS
+150 1 832.2400 831.2322 834.0013 0 12.4148 2 0.15348957 1 2 12 12 LSMSQLR trypsin-full-digest YOR267C KS
+150 1 832.2400 831.2322 832.9573 0.33006737 31.373159 1 0.10282768 2 2 12 12 NAPAWFK trypsin-full-digest YDR064W RL
+150 1 832.2400 831.2322 832.9578 0.37659156 10.274959 3 0.095686696 3 2 14 12 VAINGFGR trypsin-full-digest YGR192C RI
+150 1 832.2400 831.2322 830.9366 0.58833861 3.6209517 5 0.063185729 4 1 12 12 VTDVIER trypsin-full-digest YDR093W KE
+150 1 832.2400 831.2322 829.9922 1.1218611 2.9467273 6 -0.018704401 5 1 14 12 DIVSAVVK trypsin-full-digest YMR303C KA
+151 2 651.6200 1301.2244 1301.4161 0 1202.2273 1 4.0469213 1 17 22 10 LDVDELGDVAQK trypsin-full-digest YLR043C KN
+151 2 651.6200 1301.2244 1301.4192 0.77860552 43.713001 5 0.89596611 2 5 22 10 DALPSVTSEQVR trypsin-full-digest YBL076C KE
+151 2 651.6200 1301.2244 1301.4161 0.77958488 94.108009 3 0.89200252 3 6 22 10 ETAQDSPELLAK trypsin-full-digest YPL215W KS
+151 2 651.6200 1301.2244 1303.4968 0.78279489 228.81261 2 0.87901193 4 9 22 10 LAVCGIAAICQK trypsin-full-digest YFR053C RR
+151 2 651.6200 1301.2244 1300.4741 0.85280436 85.688034 4 0.59568912 5 6 20 10 ISEGIWPEEIK trypsin-full-digest YGL022W RE
+152 2 531.2200 1060.4243 1059.2889 0 26.479269 2 0.6205802 1 3 16 8 MNLQELLAK trypsin-full-digest YDR205W -V
+152 2 531.2200 1060.4243 1060.2126 0.056052148 86.054985 1 0.58579534 2 5 18 8 GTIEIVSDVK trypsin-full-digest YLR340W RV
+152 2 531.2200 1060.4243 1060.1289 0.84516138 11.819891 7 0.096089773 3 2 16 8 EISDAQEIR trypsin-full-digest YMR145C KL
+152 2 531.2200 1060.4243 1058.1594 0.8702845 24.158962 4 0.080498867 4 3 18 8 DQKPGTSGLR trypsin-full-digest YKL127W KK
+152 2 531.2200 1060.4243 1062.1960 1.003428 7.30264 8 -0.0021273475 5 2 16 8 FANWIANAR trypsin-full-digest YBL076C RD
+153 2 613.7900 1225.5643 1224.3788 0 5.6870127 2 0.16703272 1 2 18 4 LAFLENQDFK trypsin-full-digest YBR115C RL
+153 2 613.7900 1225.5643 1223.4375 1.2733541 7.349463 1 -0.045659065 2 2 20 4 LIDFGSAVVFR trypsin-full-digest YOR267C KY
+153 2 613.7900 1225.5643 1223.2670 2.1510031 2.7957928 4 -0.19225518 3 1 18 4 YYGGNEHIDR trypsin-full-digest YLR058C RM
+153 2 613.7900 1225.5643 1227.4233 2.5895705 4.6158304 3 -0.26551029 4 2 18 4 IEVLEQELVR trypsin-full-digest YGR086C KA
+154 1 717.0600 716.0522 716.8506 0 215.65358 1 0.59496731 1 6 12 16 DVMPAGK trypsin-full-digest YBR115C KG
+154 1 717.0600 716.0522 716.7460 0.072602049 154.65167 2 0.55177146 2 5 10 16 KPDDDK trypsin-full-digest YKL145W KI
+154 1 717.0600 716.0522 716.7893 0.41614333 80.299057 4 0.34737563 3 4 12 16 EAAELGK trypsin-full-digest YBR118W KG
+154 1 717.0600 716.0522 715.9341 0.48545897 47.664581 7 0.30613509 4 3 10 16 LLPFVK trypsin-full-digest YLR340W KG
+154 1 717.0600 716.0522 717.8817 0.5674172 68.329742 6 0.25737262 5 3 10 16 QSKPMK trypsin-full-digest YDR093W RD
+155 2 419.3200 836.6244 835.8872 0 69.90876 1 0.78055704 1 5 12 10 SDNVMDR trypsin-full-digest YBL076C KW
+155 2 419.3200 836.6244 835.9554 0.60037106 41.898266 2 0.31193319 2 4 14 10 IGDYAGIK trypsin-full-digest YMR303C KW
+155 2 419.3200 836.6244 834.8437 0.75223875 8.1968241 7 0.19339177 3 2 12 10 YDSTHGR trypsin-full-digest YGR192C KY
+155 2 419.3200 836.6244 839.0054 0.80877531 7.8815541 8 0.14926179 4 2 14 10 IAGLNPVR trypsin-full-digest YPL106C RI
+155 2 419.3200 836.6244 834.0013 0.8121413 29.737709 3 0.14663443 5 3 12 10 LSMSQLR trypsin-full-digest YOR267C KS
+156 3 1032.4399 3094.2964 3095.2366 0 1813.374 1 5.0189385 1 42 108 2 ELESAAYDHAEPVQPEDAPQDIANDELK trypsin-full-digest YGL009C KD
+156 3 1032.4399 3094.2964 3095.4709 0.96011585 39.488911 2 0.20017597 2 10 112 2 YPFEDGVTMAHGIVGSDPYLAPEVITSTK trypsin-full-digest YOR267C RS
+157 2 509.3200 1016.6244 1017.1068 0 158.00694 1 1.1119214 1 7 16 9 ITSGQELNR trypsin-full-digest YDL198C KV
+157 2 509.3200 1016.6244 1017.1035 0.43675607 28.964193 3 0.62628299 2 3 16 9 VSSAEYYAK trypsin-full-digest YIL133C KK
+157 2 509.3200 1016.6244 1018.1962 0.61605942 23.395197 4 0.42691177 3 3 16 9 MQSVIDLGR trypsin-full-digest YBL076C RN
+157 2 509.3200 1016.6244 1018.0887 0.80515426 42.167759 2 0.21665314 4 3 14 9 LEEIETER trypsin-full-digest YMR235C KL
+157 2 509.3200 1016.6244 1018.1529 0.98998845 10.166105 8 0.011132082 5 2 16 9 VALNGEEMR trypsin-full-digest YDR093W KR
+158 2 427.3800 852.7444 852.0445 0 280.23941 1 1.6478953 1 8 14 13 HASLILAK trypsin-full-digest YMR235C KA
+158 2 427.3800 852.7444 852.8194 0.72617084 44.829403 4 0.45124179 2 4 12 13 DSCTENK trypsin-full-digest YNL166C KE
+158 2 427.3800 852.7444 849.9823 0.72882479 92.955452 2 0.44686839 3 5 12 13 IADQYLK trypsin-full-digest YPL215W RD
+158 2 427.3800 852.7444 853.0293 0.75062484 38.825851 5 0.41094413 4 4 16 13 GPLATPIGK trypsin-full-digest YOR136W KG
+158 2 427.3800 852.7444 852.0011 0.82441694 10.621344 11 0.28934249 5 2 14 13 LPLNPNGK trypsin-full-digest YBR115C KV
+159 2 745.7500 1489.4844 1489.7319 0 1736.3658 1 4.2195272 1 18 24 4 NFLETVELQVGLK trypsin-full-digest YGL135W RN
+159 2 745.7500 1489.4844 1486.6195 0.81333941 176.23169 2 0.78761947 2 8 26 4 SPMPQNNTLGGENK trypsin-full-digest YNL166C KL
+159 2 745.7500 1489.4844 1490.6510 0.92798012 23.23929 4 0.30388993 3 3 24 4 ESVMEHNFGDVVK trypsin-full-digest YOR168W KN
+159 2 745.7500 1489.4844 1488.7063 0.95878029 29.159029 3 0.17392777 4 3 24 4 FHVSISNPEFLAK trypsin-full-digest YDR037W KY
diff --git a/doc/user/example-files/small-yeast.fasta b/doc/user/example-files/small-yeast.fasta
new file mode 100644
index 0000000..2d25ef0
--- /dev/null
+++ b/doc/user/example-files/small-yeast.fasta
@@ -0,0 +1,165 @@
+>YBL030C PET9 SGDID:S000000126, Chr II from 164000-163044, reverse complement, Verified ORF, "Major ADP/ATP carrier of the mitochondrial inner membrane, exchanges cytosolic ADP for mitochondrially synthesized ATP; required for viability in many common lab strains carrying a mutation in the polymorphic SAL1 gene"
+MSSNAQVKTPLPPAPAPKKESNFLIDFLMGGVSAAVAKTAASPIERVKLLIQNQDEMLKQGTLDRKYAGILDCFKRTATQEGVISFWRGNTANVIRYFPTQALNFAFKDKIKAMFGFKKEEGYAKWFAGNLASGGAAGALSLLFVYSLDYARTRLAADSKSSKKGGARQFNGLIDVYKKTLKSDGVAGLYRGFLPSVVGIVVYRGLYFGMYDSLKPLLLTGSLEGSFLASFLLGWVVTTGASTCSYPLDTVRRRMMMTSGQAVKYDGAFDCLRKIVAAEGVGSLFKGCGANILRGVAGAGVISMYDQLQMILFGKKFK
+
+>YBL076C ILS1 SGDID:S000000172, Chr II from 84259-81041, reverse complement, Verified ORF, "Cytoplasmic isoleucine-tRNA synthetase, target of the G1-specific inhibitor reveromycin A"
+MSESNAHFSFPKEEEKVLSLWDEIDAFHTSLELTKDKPEFSFFDGPPFATGTPHYGHILASTIKDIVPRYATMTGHHVERRFGWDTHGVPIEHIIDKKLGITGKDDVFKYGLENYNNECRSIVMTYASDWRKTIGRLGRWIDFDNDYKTMYPSFMESTWWAFKQLHEKGQVYRGFKVMPYSTGLTTPLSNFEAQQNYKDVNDPAVTIGFNVIGQEKTQLVAWTTTPWTLPSNLSLCVNADFEYVKIYDETRDRYFILLESLIKTLYKKPKNEKYKIVEKIKGSDLVGLKYEPLFPYFAEQFHETAFRVISDDYVTSDSGTGIVHNAPAFGEEDNAACLKNGVISEDSVLPNAIDDLGRFTKDVPDFEGVYVKDADKLIIKYLTNTGNLLLASQIRHSYPFCWRSDTPLLYRSVPAWFVRVKNIVPQMLDSVMKSHWVPNTIKEKRFANWIANARDWNVSRNRYWGTPIPLWVSDDFEEVVCVGSIKELEELT [...]
+
+>YBR009C HHF1 SGDID:S000000213, Chr II from 255682-255371, reverse complement, Verified ORF, "One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity"
+MSGRGKGGKGLGKGGAKRHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYGFGG
+
+>YBR115C LYS2 SGDID:S000000319, Chr II from 473920-469742, reverse complement, Verified ORF, "Alpha aminoadipate reductase, catalyzes the reduction of alpha-aminoadipate to alpha-aminoadipate 6-semialdehyde, which is the fifth step in biosynthesis of lysine; activation requires posttranslational phosphopantetheinylation by Lys5p"
+MTNEKVWIEKLDNPTLSVLPHDFLRPQQEPYTKQATYSLQLPQLDVPHDSFSNKYAVALSVWAALIYRVTGDDDIVLYIANNKILRFNIQPTWSFNELYSTINNELNKLNSIEANFSFDELAEKIQSCQDLERTPQLFRLAFLENQDFKLDEFKHHLVDFALNLDTSNNAHVLNLIYNSLLYSNERVTIVADQFTQYLTAALSDPSNCITKISLITASSKDSLPDPTKNLGWCDFVGCIHDIFQDNAEAFPERTCVVETPTLNSDKSRSFTYRDINRTSNIVAHYLIKTGIKRGDVVMIYSSRGVDLMVCVMGVLKAGATFSVIDPAYPPARQTIYLGVAKPRGLIVIRAAGQLDQLVEDYINDELEIVSRINSIAIQENGTIEGGKLDNGEDVLAPYDHYKDTRTGVVVGPDSNPTLSFTSGSEGIPKGVLGRHFSLAYYFNWMSKRFNLTENDKFTMLSGIAHDPIQRDMFTPLFLGAQLYVPTQDDIGT [...]
+
+>YBR118W TEF2 SGDID:S000000322, Chr II from 477665-479041, Verified ORF, "Translational elongation factor EF-1 alpha; also encoded by TEF1; functions in the binding reaction of aminoacyl-tRNA (AA-tRNA) to ribosomes"
+MGKEKSHINVVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAELGKGSFKYAWVLDKLKAERERGITIDIALWKFETPKYQVTVIDAPGHRDFIKNMITGTSQADCAILIIAGGVGEFEAGISKDGQTREHALLAFTLGVRQLIVAVNKMDSVKWDESRFQEIVKETSNFIKKVGYNPKTVPFVPISGWNGDNMIEATTNAPWYKGWEKETKAGVVKGKTLLEAIDAIEQPSRPTDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFAPAGVTTEVKSVEMHHEQLEQGVPGDNVGFNVKNVSVKEIRRGNVCGDAKNDPPKGCASFNATVIVLNHPGQISAGYSPVLDCHTAHIACRFDELLEKNDRRSGKKLEDHPKFLKSGDAALVKFVPSKPMCVEAFSEYPPLGRFAVRDMRQTVAVGVIKSVDKTEKAAKVTKAAQKAAKK
+
+>YCR012W PGK1 SGDID:S000000605, Chr III from 137744-138994, Verified ORF, "3-phosphoglycerate kinase, catalyzes transfer of high-energy phosphoryl groups from the acyl phosphate of 1,3-bisphosphoglycerate to ADP to produce ATP; key enzyme in glycolysis and gluconeogenesis"
+MSLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVLEHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVGPEVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHELSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALENPTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEIGDSIFDKAGAEIVPKLMEKAKAKGVEVVLPVDFIIADAFSADANTKTVTDKEGIPAGWQGLDNGPESRKLFAATVAKAKTIVWNGPPGVFEFEKFAAGTKALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELLEGKELPGVAFLSEKK
+
+>YCR034W FEN1 SGDID:S000000630, Chr III from 190588-191631, Verified ORF, "Fatty acid elongase, involved in sphingolipid biosynthesis; acts on fatty acids of up to 24 carbons in length; mutations have regulatory effects on 1,3-beta-glucan synthase, vacuolar ATPase, and the secretory pathway"
+MNSLVTQYAAPLFERYPQLHDYLPTLERPFFNISLWEHFDDVVTRVTNGRFVPSEFQFIAGELPLSTLPPVLYAITAYYVIIFGGRFLLSKSKPFKLNGLFQLHNLVLTSLSLTLLLLMVEQLVPIIVQHGLYFAICNIGAWTQPLVTLYYMNYIVKFIEFIDTFFLVLKHKKLTFLHTYHHGATALLCYTQLMGTTSISWVPISLNLGVHVVMYWYYFLAARGIRVWWKEWVTRFQIIQFVLDIGFIYFAVYQKAVHLYFPILPHCGDCVGSTTATFAGCAIISSYLVLFISFYINVYKRKGTKTSRVVKRAHGGVAAKVNEYVNVDLKNVPTPSPSPKPQHRRKR
+
+>YDL198C GGC1 SGDID:S000002357, Chr IV from 104552-103650, reverse complement, Verified ORF, "Mitochondrial GTP/GDP transporter, essential for mitochondrial genome maintenance; has a role in mitochondrial iron transport; member of the mitochondrial carrier family"
+MPHTDKKQSGLARLLGSASAGIMEIAVFHPVDTISKRLMSNHTKITSGQELNRVIFRDHFSEPLGKRLFTLFPGLGYAASYKVLQRVYKYGGQPFANEFLNKHYKKDFDNLFGEKTGKAMRSAAAGSLIGIGEIVLLPLDVLKIKRQTNPESFKGRGFIKILRDEGLFNLYRGWGWTAARNAPGSFALFGGNAFAKEYILGLKDYSQATWSQNFISSIVGACSSLIVSAPLDVIKTRIQNRNFDNPESGLRIVKNTLKNEGVTAFFKGLTPKLLTTGPKLVFSFALAQSLIPRFDNLLSK
+
+>YDL223C HBT1 SGDID:S000002382, Chr IV from 60406-57266, reverse complement, Verified ORF, "Substrate of the Hub1p ubiquitin-like protein that localizes to the shmoo tip (mating projection); mutants are defective for mating projection formation, thereby implicating Hbt1p in polarized cell morphogenesis"
+MNMNESISKDGQGEEEQNNFSFGGKPGSYDSNSDSAQRKKSFSTTKPTEYNLPKEQPESTSKNLETKAKNILLPWRKKHNKDSETPHEDTEADANRRANVTSDVNPVSADTKSSSGPNATITTHGYSYVKTTTPAATSEQSKVKTSPPTSHEHSNIKASPTAHRHSKGDAGHPSIATTHNHSTSKAATSPVTHTHGHSSATTSPVTHTHGHASVKTTSPTNTHEHSKANTGPSATATTHGHINVKTTHPVSHGHSGSSTGPKSTAAAQDHSSTKTNPSVTHGHTSVKDNSSATKGYSNTDSNSDRDVIPGSFRGMTGTDVNPVDPSVYTSTGPKSNVSSGMNAVDPSVYTDTSSKSADRRKYSGNTATGPPQDTIKEIAQNVKMDESEQTGLKNDQVSGSDAIQQQTMEPEPKAAVGTSGFVSQQPSYHDSNKNIQHPEKNKVDNKNISERAAEKFNIERDDILESADDYQQKNIKSKTDSNWGPIEYSSSA [...]
+
+>YDR037W KRS1 SGDID:S000002444, Chr IV from 525437-527212, Verified ORF, "Lysyl-tRNA synthetase; also identified as a negative regulator of general control of amino acid biosynthesis "
+MSQQDNVKAAAEGVANLHLDEATGEMVSKSELKKRIKQRQVEAKKAAKKAAAQPKPASKKKTDLFADLDPSQYFETRSRQIQELRKTHEPNPYPHKFHVSISNPEFLAKYAHLKKGETLPEEKVSIAGRIHAKRESGSKLKFYVLHGDGVEVQLMSQLQDYCDPDSYEKDHDLLKRGDIVGVEGYVGRTQPKKGGEGEVSVFVSRVQLLTPCLHMLPADHFGFKDQETRYRKRYLDLIMNKDARNRFITRSEIIRYIRRFLDQRKFIEVETPMMNVIAGGATAKPFITHHNDLDMDMYMRIAPELFLKQLVVGGLDRVYEIGRQFRNEGIDMTHNPEFTTCEFYQAYADVYDLMDMTELMFSEMVKEITGSYIIKYHPDPADPAKELELNFSRPWKRINMIEELEKVFNVKFPSGDQLHTAETGEFLKKILVDNKLECPPPLTNARMLDKLVGELEDTCINPTFIFGHPQMMSPLAKYSRDQPGLCERFEVF [...]
+
+>YDR064W RPS13 SGDID:S000002471, Chr IV from 579456-579476,580016-580450, Verified ORF, "Protein component of the small (40S) ribosomal subunit; has similarity to E. coli S15 and rat S13 ribosomal proteins"
+MGRMHSAGKGISSSAIPYSRNAPAWFKLSSESVIEQIVKYARKGLTPSQIGVLLRDAHGVTQARVITGNKIMRILKSNGLAPEIPEDLYYLIKKAVSVRKHLERNRKDKDAKFRLILIESRIHRLARYYRTVAVLPPNWKYESATASALVN
+
+>YDR093W DNF2 SGDID:S000002500, Chr IV from 631279-636117, Verified ORF, "Aminophospholipid translocase (flippase) that localizes primarily to the plasma membrane; contributes to endocytosis, protein transport and cell polarity; type 4 P-type ATPase"
+MSSPSKPTSPFVDDIEHESGSASNGLSSMSPFDDSFQFEKPSSAHGNIEVAKTGGSVLKRQSKPMKDISTPDLSKVTFDGIDDYSNDNDINDDDELNGKKTEIHEHENEVDDDLHSFQATPMPNTGGFEDVELDNNEGSNNDSQADHKLKRVRFGTRRNKSGRIDINRSKTLKWAKKNFHNAIDEFSTKEDSLENSALQNRSDELRTVYYNLPLPEDMLDEDGLPLAVYPRNKIRTTKYTPLTFFPKNILFQFHNFANIYFLILLILGAFQIFGVTNPGFASVPLIVIVIITAIKDGIEDSRRTVLDLEVNNTRTHILSGVKNENVAVDNVSLWRRFKKANTRALIKIFEYFSENLTAAGREKKLQKKREELRRKRNSRSFGPRGSLDSIGSYRMSADFGRPSLDYENLNQTMSQANRYNDGENLVDRTLQPNPECRFAKDYWKNVKVGDIVRVHNNDEIPADMILLSTSDVDGACYVETKNLDGETNLKVR [...]
+
+>YDR205W MSC2 SGDID:S000002613, Chr IV from 859343-861517, Verified ORF, "Member of the cation diffusion facilitator family, localizes to the endoplasmic reticulum and nucleus; mutations affect the cellular distribution of zinc and also confer defects in meiotic recombination between homologous chromatids"
+MNLQELLAKVPLLLSYPTIILSSNLIVPSHNDLISRAASTSAAEYADEKLIFFSTDHAIRLIFLPTFVASSFNLFAHYFNFINYSSRRKYYVLFTAIYFLSILTAIFHPIQSTCITLLIIKLLTTADESSPKIALNFKTILKTFVPFITLTLVILRWDPSFDASSGDVNKISTSLAAYALLILTLRYASPLILSTLSSSIGVVSKDTSVAQHSISRNKRFPLILVLPIFSFVLLYLMTIVNKTYNIQLLMVFVFFGCLSIFFLSLKDLFTEDGNQKKGGQEDEYCRMFDIKYMISYLWLTRFTILLTGIMAIVVHFLSFNEITSSIKTDLLSLLFVVVAEYVSSFSNKQPDSHSHNHAHHHSHLTDSLPLENESMFKQMALNKDTRSIFSFLLLNTAFMFVQLLYSFRSKSLGLLSDSLHMALDCTSLLLGLIAGVLTKKPASDKFPFGLNYLGTLAGFTNGVLLLGIVCGIFVEAIERIFNPIHLHATNEL [...]
+
+>YDR399W HPT1 SGDID:S000002807, Chr IV from 1270060-1270725, Verified ORF, "Dimeric hypoxanthine-guanine phosphoribosyltransferase, catalyzes the formation of both inosine monophosphate and guanosine monophosphate; mutations in the human homolog HPRT1 can cause Lesch-Nyhan syndrome and Kelley-Seegmiller syndrome"
+MSANDKQYISYNNVHQLCQVSAERIKNFKPDLIIAIGGGGFIPARILRTFLKEPGVPTIRIFAIILSLYEDLNSVGSEVEEVGVKVSRTQWIDYEQCKLDLVGKNVLIVDEVDDTRTTLHYALSELEKDAAEQAKAKGIDTEKSPEMKTNFGIFVLHDKQKPKKADLPAEMLNDKNRYFAAKTVPDKWYAYPWESTDIVFHTRMAIEQGNDIFIPEQEHKQ
+
+>YEL027W CUP5 SGDID:S000000753, Chr V from 100769-101251, Verified ORF, "Proteolipid subunit of the vacuolar H(+)-ATPase V0 sector (subunit c; dicyclohexylcarbodiimide binding subunit); required for vacuolar acidification and important for copper and iron metal ion homeostasis"
+MTELCPVYAPFFGAIGCASAIIFTSLGAAYGTAKSGVGICATCVLRPDLLFKNIVPVIMAGIIAIYGLVVSVLVCYSLGQKQALYTGFIQLGAGLSVGLSGLAAGFAIGIVGDAGVRGSSQQPRLFVGMILILIFAEVLGLYGLIVALLLNSRATQDVVC
+
+>YER056C-A RPL34A SGDID:S000002135, Chr V from 270183-270147,269749-269421, reverse complement, Verified ORF, "Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl34Bp and has similarity to rat L34 ribosomal protein"
+MAQRVTFRRRNPYNTRSNKIKVVKTPGGILRAQHVKKLATRPKCGDCGSALQGISTLRPRQYATVSKTHKTVSRAYGGSRCANCVKERIIRAFLIEEQKIVKKVVKEQTEAAKKSEKKAKK
+
+>YFR053C HXK1 SGDID:S000001949, Chr VI from 255036-253579, reverse complement, Verified ORF, "Hexokinase isoenzyme 1, a cytosolic protein that catalyzes phosphorylation of glucose during glucose metabolism; expression is highest during growth on non-glucose carbon sources; glucose-induced repression involves the hexokinase Hxk2p"
+MVHLGPKKPQARKGSMADVPKELMDEIHQLEDMFTVDSETLRKVVKHFIDELNKGLTKKGGNIPMIPGWVMEFPTGKESGNYLAIDLGGTNLRVVLVKLSGNHTFDTTQSKYKLPHDMRTTKHQEELWSFIADSLKDFMVEQELLNTKDTLPLGFTFSYPASQNKINEGILQRWTKGFDIPNVEGHDVVPLLQNEISKRELPIEIVALINDTVGTLIASYYTDPETKMGVIFGTGVNGAFYDVVSDIEKLEGKLADDIPSNSPMAINCEYGSFDNEHLVLPRTKYDVAVDEQSPRPGQQAFEKMTSGYYLGELLRLVLLELNEKGLMLKDQDLSKLKQPYIMDTSYPARIEDDPFENLEDTDDIFQKDFGVKTTLPERKLIRRLCELIGTRAARLAVCGIAAICQKRGYKTGHIAADGSVYNKYPGFKEAAAKGLRDIYGWTGDASKDPITIVPAEDGSGAGAAVIAALSEKRIAEGKSLGIIGA
+
+>YGL008C PMA1 SGDID:S000002976, Chr VII from 482671-479915, reverse complement, Verified ORF, "Plasma membrane H+-ATPase, pumps protons out of the cell; major regulator of cytoplasmic pH and plasma membrane potential; part of the P2 subgroup of cation-transporting ATPases"
+MTDTSSSSSSSSASSVSAHQPTQEKPAKTYDDAASESSDDDDIDALIEELQSNHGVDDEDSDNDGPVAAGEARPVPEEYLQTDPSYGLTSDEVLKRRKKYGLNQMADEKESLVVKFVMFFVGPIQFVMEAAAILAAGLSDWVDFGVICGLLMLNAGVGFVQEFQAGSIVDELKKTLANTAVVIRDGQLVEIPANEVVPGDILQLEDGTVIPTDGRIVTEDCFLQIDQSAITGESLAVDKHYGDQTFSSSTVKRGEGFMVVTATGDNTFVGRAAALVNKAAGGQGHFTEVLNGIGIILLVLVIATLLLVWTACFYRTNGIVRILRYTLGITIIGVPVGLPAVVTTTMAVGAAYLAKKQAIVQKLSAIESLAGVEILCSDKTGTLTKNKLSLHEPYTVEGVSPDDLMLTACLAASRKKKGLDAIDKAFLKSLKQYPKAKDALTKYKVLEFHPFDPVSKKVTAVVESPEGERIVCVKGAPLFVLKTVEEDHPIPE [...]
+>YGL009C LEU1 SGDID:S000002977, Chr VII from 478657-476318, reverse complement, Verified ORF, "Isopropylmalate isomerase, catalyzes the second step in the leucine biosynthesis pathway"
+MVYTPSKGPRTLYDKVFDAHVVHQDENGSFLLYIDRHLVHEVTSPQAFEGLENAGRKVRRVDCTLATVDHNIPTESRKNFKSLDTFIKQTDSRLQVKTLENNVKQFGVPYFGMSDARQGIVHTIGPEEGFTLPGTTVVCGDSHTSTHGAFGSLAFGIGTSEVEHVLATQTIIQAKSKNMRITVNGKLSPGITSKDLILYIIGLIGTAGGTGCVIEFAGEAIEALSMEARMSMCNMAIEAGARAGMIKPDETTFQYTKGRPLAPKGAEWEKAVAYWKTLKTDEGAKFDHEINIEAVDVIPTITWGTSPQDALPITGSVPDPKNVTDPIKKSGMERALAYMGLEPNTPLKSIKVDKVFIGSCTNGRIEDLRSAAAVVRGQKLASNIKLAMVVPGSGLVKKQAEAEGLDKIFQEAGFEWREAGCSICLGMNPDILDAYERCASTSNRNFEGRQGALSRTHLMSPAMAAAAGIAGHFVDIREFEYKDQDQSSPKVE [...]
+
+>YGL022W STT3 SGDID:S000002990, Chr VII from 452409-454565, Verified ORF, "Subunit of the oligosaccharyltransferase complex of the ER lumen, which catalyzes asparagine-linked glycosylation of newly synthesized proteins; forms a subcomplex with Ost3p and Ost4p and is directly involved in catalysis"
+MGSDRSCVLSVFQTILKLVIFVAIFGAAISSRLFAVIKFESIIHEFDPWFNYRATKYLVNNSFYKFLNWFDDRTWYPLGRVTGGTLYPGLMTTSAFIWHALRNWLGLPIDIRNVCVLFAPLFSGVTAWATYEFTKEIKDASAGLLAAGFIAIVPGYISRSVAGSYDNEAIAITLLMVTFMFWIKAQKTGSIMHATCAALFYFYMVSAWGGYVFITNLIPLHVFLLILMGRYSSKLYSAYTTWYAIGTVASMQIPFVGFLPIRSNDHMAALGVFGLIQIVAFGDFVKGQISTAKFKVIMMVSLFLILVLGVVGLSALTYMGLIAPWTGRFYSLWDTNYAKIHIPIIASVSEHQPVSWPAFFFDTHFLIWLFPAGVFLLFLDLKDEHVFVIAYSVLCSYFAGVMVRLMLTLTPVICVSAAVALSKIFDIYLDFKTSDRKYAIKPAALLAKLIVSGSFIFYLYLFVFHSTWVTRTAYSSPSVVLPSQTPDGKLAL [...]
+
+>YGL026C TRP5 SGDID:S000002994, Chr VII from 448540-446417, reverse complement, Verified ORF, "Tryptophan synthase involved in tryptophan biosynthesis, regulated by the general control system of amino acid biosynthesis"
+MSEQLRQTFANAKKENRNALVTFMTAGYPTVKDTVPILKGFQDGGVDIIELGMPFSDPIADGPTIQLSNTVALQNGVTLPQTLEMVSQARNEGVTVPIILMGYYNPILNYGEERFIQDAAKAGANGFIIVDLPPEEALKVRNYINDNGLSLIPLVAPSTTDERLELLSHIADSFVYVVSRMGTTGVQSSVASDLDELISRVRKYTKDTPLAVGFGVSTREHFQSVGSVADGVVIGSKIVTLCGDAPEGKRYDVAKEYVQGILNGAKHKVLSKDEFFAFQKESLKSANVKKEILDEFDENHKHPIRFGDFGGQYVPEALHACLRELEKGFDEAVADPTFWEDFKSLYSYIGRPSSLHKAERLTEHCQGAQIWLKREDLNHTGSHKINNALAQVLLAKRLGKKNVIAETGAGQHGVATATACAKFGLTCTVFMGAEDVRRQALNVFRMRILGAKVIAVTNGTKTLRDATSEAFRFWVTNLKTTYYVVGSAIGPH [...]
+
+>YGL135W RPL1B SGDID:S000003103, Chr VII from 254646-255299, Verified ORF, "N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl1Ap and has similarity to E. coli L1 and rat L10a ribosomal proteins; rpl1a rpl1b double null mutation is lethal"
+MSKITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPRPNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQVPRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLVNQILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRLY
+
+>YGL245W GUS1 SGDID:S000003214, Chr VII from 39023-41149, Verified ORF, "Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm"
+MPSTLTINGKAPIVAYAELIAARIVNALAPNSIAIKLVDDKKAPAAKLDDATEDVFNKITSKFAAIFDNGDKEQVAKWVNLAQKELVIKNFAKLSQSLETLDSQLNLRTFILGGLKYSAADVACWGALRSNGMCGSIIKNKVDVNVSRWYTLLEMDPIFGEAHDFLSKSLLELKKSANVGKKKETHKANFEIDLPDAKMGEVVTRFPPEPSGYLHIGHAKAALLNQYFAQAYKGKLIIRFDDTNPSKEKEEFQDSILEDLDLLGIKGDRITYSSDYFQEMYDYCVQMIKDGKAYCDDTPTEKMREERMDGVASARRDRSVEENLRIFTEEMKNGTEEGLKNCVRAKIDYKALNKTLRDPVIYRCNLTPHHRTGSTWKIYPTYDFCVPIVDAIEGVTHALRTIEYRDRNAQYDWMLQALRLRKVHIWDFARINFVRTLLSKRKLQWMVDKDLVGNWDDPRFPTVRGVRRRGMTVEGLRNFVLSQGPSRNVINL [...]
+
+>YGR086C PIL1 SGDID:S000003318, Chr VII from 650621-649602, reverse complement, Verified ORF, "Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Lsp1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways"
+MHRTYSLRNSRAPTASQLQNPPPPPSTTKGRFFGKGGLAYSFRRSAAGAFGPELSRKLSQLVKIEKNVLRSMELTANERRDAAKQLSIWGLENDDDVSDITDKLGVLIYEVSELDDQFIDRYDQYRLTLKSIRDIEGSVQPSRDRKDKITDKIAYLKYKDPQSPKIEVLEQELVRAEAESLVAEAQLSNITRSKLRAAFNYQFDSIIEHSEKIALIAGYGKALLELLDDSPVTPGETRPAYDGYEASKQIIIDAESALNEWTLDSAQVKPTLSFKQDYEDFEPEEGEEEEEEDGQGRWSEDEQEDGQIEEPEQEEEGAVEEHEQVGHQQSESLPQQTTA
+
+>YGR157W CHO2 SGDID:S000003389, Chr VII from 802445-805054, Verified ORF, "Phosphatidylethanolamine methyltransferase (PEMT), catalyzes the first step in the conversion of phosphatidylethanolamine to phosphatidylcholine during the methylation pathway of phosphatidylcholine biosynthesis"
+MSSCKTTLSEMVGSVTKDRGTINVEARTRSSNVTFKPPVTHDMVRSLFDPTLKKSLLEKCIALAIISNFFICYWVFQRFGLQFTKYFFLVQYLFWRIAYNLGIGLVLHYQSHYETLTNCAKTHAIFSKIPQNKDANSNFSTNSNSFSEKFWNFIRKFCQYEIRSKMPKEYDLFAYPEEINVWLIFRQFVDLILMQDFVTYIIYVYLSIPYSWVQIFNWRSLLGVILILFNIWVKLDAHRVVKDYAWYWGDFFFLEESELIFDGVFNISPHPMYSIGYLGYYGLSLICNDYKVLLVSVFGHYSQFLFLKYVENPHIERTYGDGTDSDSQMNSRIDDLISKENYDYSRPLINMGLSFNNFNKLRFTDYFTIGTVAALMLGTIMNARFINLNYLFITVFVTKLVSWLFISTILYKQSQSKWFTRLFLENGYTQVYSYEQWQFIYNYYLVLTYTLMIIHTGLQIWSNFSNINNSQLIFGLILVALQTWCDKETRLA [...]
+
+>YGR192C TDH3 SGDID:S000003424, Chr VII from 883815-882817, reverse complement, Verified ORF, "Glyceraldehyde-3-phosphate dehydrogenase, isozyme 3, involved in glycolysis and gluconeogenesis; tetramer that catalyzes the reaction of glyceraldehyde-3-phosphate to 1,3 bis-phosphoglycerate; detected in the cytoplasm and cell-wall "
+MVRVAINGFGRIGRLVMRIALSRPNVEVVALNDPFITNDYAAYMFKYDSTHGRYAGEVSHDDKHIIVDGKKIATYQERDPANLPWGSSNVDIAIDSTGVFKELDTAQKHIDAGAKKVVITAPSSTAPMFVMGVNEEKYTSDLKIVSNASCTTNCLAPLAKVINDAFGIEEGLMTTVHSLTATQKTVDGPSHKDWRGGRTASGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTVDVSVVDLTVKLNKETTYDEIKKVVKAAAEGKLKGVLGYTEDAVVSSDFLGDSHSSIFDASAGIQLSPKFVKLVSWYDNEYGYSTRVVDLVEHVAKA
+
+>YHR021C RPS27B SGDID:S000001063, Chr VIII from 148662-148660,148109-147864, reverse complement, Verified ORF, "Protein component of the small (40S) ribosomal subunit; nearly identical to Rps27Ap and has similarity to rat S27 ribosomal protein"
+MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCSTVLCTPTGGKAKLSEGTSFRRK
+
+>YHR183W GND1 SGDID:S000001226, Chr VIII from 470960-472429, Verified ORF, "6-phosphogluconate dehydrogenase (decarboxylating), catalyzes an NADPH regenerating reaction in the pentose phosphate pathway; required for growth on D-glucono-delta-lactone and adaptation to oxidative stress"
+MSADFGLIGLAVMGQNLILNAADHGFTVCAYNRTQSKVDHFLANEAKGKSIIGATSIEDFISKLKRPRKVMLLVKAGAPVDALINQIVPLLEKGDIIIDGGNSHFPDSNRRYEELKKKGILFVGSGVSGGEEGARYGPSLMPGGSEEAWPHIKNIFQSISAKSDGEPCCEWVGPAGAGHYVKMVHNGIEYGDMQLICEAYDIMKRLGGFTDKEISDVFAKWNNGVLDSFLVEITRDILKFDDVDGKPLVEKIMDTAGQKGTGKWTAINALDLGMPVTLIGEAVFARCLSALKNERIRASKVLPGPEVPKDAVKDREQFVDDLEQALYASKIISYAQGFMLIREAAATYGWKLNNPAIALMWRGGCIIRSVFLGQITKAYREEPDLENLLFNKFFADAVTKAQSGWRKSIALATTYGIPTPAFSTALSFYDGYRSERLPANLLQAQRDYFGAHTFRVLPECASDNLPVDKDIHINWTGHGGNVSSSTYQA
+
+>YIL133C RPL16A SGDID:S000001395, Chr IX from 99416-99386,99095-98527, reverse complement, Verified ORF, "N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p"
+MSVEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRKATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVVPQALRVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVASANATAAESDVAKQLAALGY
+
+>YJR069C HAM1 SGDID:S000003830, Chr X from 569392-568799, reverse complement, Verified ORF, "Protein of unknown function that is involved in DNA repair; mutant is sensitive to the base analog, 6-N-hydroxylaminopurine, while gene disruption does not increase the rate of spontaneous mutagenesis"
+MSNNEIVFVTGNANKLKEVQSILTQEVDNNNKTIHLINEALDLEELQDTDLNAIALAKGKQAVAALGKGKPVFVEDTALRFDEFNGLPGAYIKWFLKSMGLEKIVKMLEPFENKNAEAVTTICFADSRGEYHFFQGITRGKIVPSRGPTTFGWDSIFEPFDSHGLTYAEMSKDAKNAISHRGKAFAQFKEYLYQNDF
+
+>YKL127W PGM1 SGDID:S000001610, Chr XI from 203185-204897, Verified ORF, "Phosphoglucomutase, minor isoform; catalyzes the conversion from glucose-1-phosphate to glucose-6-phosphate, which is a key step in hexose metabolism"
+MSLLIDSVPTVAYKDQKPGTSGLRKKTKVFMDEPHYTENFIQATMQSIPNGSEGTTLVVGGDGRFYNDVIMNKIAAVGAANGVRKLVIGQGGLLSTPAASHIIRTYEEKCTGGGIILTASHNPGGPENDLGIKYNLPNGGPAPESVTNAIWEASKKLTHYKIIKNFPKLNLNKLGKNQKYGPLLVDIIDPAKAYVQFLKEIFDFDLIKSFLAKQRKDKGWKLLFDSLNGITGPYGKAIFVDEFGLPAEEVLQNWHPLPDFGGLHPDPNLTYARTLVDRVDREKIAFGAASDGDGDRNMIYGYGPAFVSPGDSVAIIAEYAPEIPYFAKQGIYGLARSFPTSSAIDRVAAKKGLRCYEVPTGWKFFCALFDAKKLSICGEESFGTGSNHIREKDGLWAIIAWLNILAIYHRRNPEKEASIKTIQDEFWNEYGRTFFTRYDYEHIECEQAEKVVALLSEFVSRPNVCGSHFPADESLTVIDCGDFSYRDLDGSI [...]
+
+>YKL145W RPT1 SGDID:S000001628, Chr XI from 174218-175621, Verified ORF, "One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; required for optimal CDC20 transcription; interacts with Rpn12p and the E3 ubiquitin-protein ligase Ubr1p"
+MPPKEDWEKYKAPLEDDDKKPDDDKIVPLTEGDIQVLKSYGAAPYAAKLKQTENDLKDIEARIKEKAGVKESDTGLAPSHLWDIMGDRQRLGEEHPLQVARCTKIIKGNGESDETTTDNNNSGNSNSNSNQQSTDADEDDEDAKYVINLKQIAKFVVGLGERVSPTDIEEGMRVGVDRSKYNIELPLPPRIDPSVTMMTVEEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDPRGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRARRKVATEKDFLKAVDKVISGYKKFSSTSRYMQYN
+>YKL145W-A YKL145W-A SGDID:S000028841, Chr XI from 174963-175055, Dubious ORF, "Dubious open reading frame, unlikely to encode a protein; completely overlaps the verified essential gene RPT1; identified by expression profiling and mass spectrometry"
+MGHLVLVRHYVLVLLLIELMQLLLGSLGLS
+
+>YLL024C SSA2 SGDID:S000003947, Chr XII from 97484-95565, reverse complement, Verified ORF, "ATP binding protein involved in protein folding and vacuolar import of proteins; member of heat shock protein 70 (HSP70) family; associated with the chaperonin-containing T-complex; present in the cytoplasm, vacuolar membrane and cell wall"
+MSKAVGIDLGTTYSCVAHFSNDRVDIIANDQGNRTTPSFVGFTDTERLIGDAAKNQAAMNPANTVFDAKRLIGRNFNDPEVQGDMKHFPFKLIDVDGKPQIQVEFKGETKNFTPEQISSMVLGKMKETAESYLGAKVNDAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKGKEEHVLIFDLGGGTFDVSLLSIEDGIFEVKATAGDTHLGGEDFDNRLVNHFIQEFKRKNKKDLSTNQRALRRLRTACERAKRTLSSSAQTSVEIDSLFEGIDFYTSITRARFEELCADLFRSTLDPVEKVLRDAKLDKSQVDEIVLVGGSTRIPKVQKLVTDYFNGKEPNRSINPDEAVAYGAAVQAAILTGDESSKTQDLLLLDVAPLSLGIETAGGVMTKLIPRNSTIPTKKSEVFSTYADNQPGVLIQVFEGERAKTKDNNLLGKFELSGIPPAPRGVPQIEVTFDVDSNGILNVSAVEKGT [...]
+
+>YLR043C TRX1 SGDID:S000004033, Chr XII from 232014-231703, reverse complement, Verified ORF, "Cytoplasmic thioredoxin isoenzyme of the thioredoxin system which protects cells against both oxidative and reductive stress, forms LMA1 complex with Pbi2p, acts as a cofactor for Tsa1p, required for ER-Golgi transport and vacuole inheritance"
+MVTQFKTASEFDSAIAQDKLVVVDFYATWCGPCKMIAPMIEKFSEQYPQADFYKLDVDELGDVAQKNEVSAMPTLLLFKNGKEVAKVVGANPAAIKQAIAANA
+
+>YLR058C SHM2 SGDID:S000004048, Chr XII from 259402-257993, reverse complement, Verified ORF, "Cytosolic serine hydroxymethyltransferase, involved in one-carbon metabolism"
+MPYTLSDAHHKLITSHLVDTDPEVDSIIKDEIERQKHSIDLIASENFTSTSVFDALGTPLSNKYSEGYPGARYYGGNEHIDRMEILCQQRALKAFHVTPDKWGVNVQTLSGSPANLQVYQAIMKPHERLMGLYLPDGGHLSHGYATENRKISAVSTYFESFPYRVNPETGIIDYDTLEKNAILYRPKVLVAGTSAYCRLIDYKRMREIADKCGAYLMVDMAHISGLIAAGVIPSPFEYADIVTTTTHKSLRGPRGAMIFFRRGVRSINPKTGKEVLYDLENPINFSVFPGHQGGPHNHTIAALATALKQAATPEFKEYQTQVLKNAKALESEFKNLGYRLVSNGTDSHMVLVSLREKGVDGARVEYICEKINIALNKNSIPGDKSALVPGGVRIGAPAMTTRGMGEEDFHRIVQYINKAVEFAQQVQQSLPKDACRLKDFKAKVDEGSDVLNTWKKEIYDWAGEYPLAV
+
+>YLR185W RPL37A SGDID:S000004175, Chr XII from 522665-522671,523031-523290, Verified ORF, "Protein component of the large (60S) ribosomal subunit, has similarity to Rpl37Bp and to rat L37 ribosomal protein"
+MGKGTPSFGKRHNKSHTLCNRCGRRSFHVQKKTCSSCGYPAAKTRSYNWGAKAKRRHTTGTGRMRYLKHVSRRFKNGFQTGSASKASA
+
+>YLR249W YEF3 SGDID:S000004239, Chr XII from 636782-639916, Verified ORF, "Translational elongation factor, stimulates the binding of aminoacyl-tRNA (AA-tRNA) to ribosomes by releasing EF-1 alpha from the ribosomal complex; contains two ABC cassettes; binds and hydrolyses ATP"
+MSDSQQSIKVLEELFQKLSVATADNRHEIASEVASFLNGNIIEHDVPEHFFGELAKGIKDKKTAANAMQAVAHIANQSNLSPSVEPYIVQLVPAICTNAGNKDKEIQSVASETLISIVNAVNPVAIKALLPHLTNAIVETNKWQEKIAILAAISAMVDAAKDQVALRMPELIPVLSETMWDTKKEVKAAATAAMTKATETVDNKDIERFIPSLIQCIADPTEVPETVHLLGATTFVAEVTPATLSIMVPLLSRGLNERETGIKRKSAVIIDNMCKLVEDPQVIAPFLGKLLPGLKSNFATIADPEAREVTLRALKTLRRVGNVGEDDAIPEVSHAGDVSTTLQVVNELLKDETVAPRFKIVVEYIAAIGADLIDERIIDQQAWFTHITPYMTIFLHEKKAKDILDEFRKRAVDNIPVGPNFDDEEDEGEDLCNCEFSLAYGAKILLNKTQLRLKRARRYGICGPNGCGKSTLMRAIANGQVDGFPTQEECRT [...]
+
+>YLR298C YHC1 SGDID:S000004289, Chr XII from 725418-724723, reverse complement, Verified ORF, "Component of the U1 snRNP complex required for pre-mRNA splicing; putative ortholog of human U1C protein, which is involved in formation of a complex between U1 snRNP and the pre-mRNA 5' splice site"
+MTRYYCEYCHSYLTHDTLSVRKSHLVGKNHLRITADYYRNKARDIINKHNHKRRHIGKRGRKERENSSQNETLKVTCLSNKEKRHIMHVKKMNQKELAQTSIDTLKLLYDGSPGYSKVFVDANRFDIGDLVKASKLPQRANEKSAHHSFKQTSRSRDETCESNPFPRLNNPKKLEPPKILSQWSNTIPKTSIFYSVDILQTTIKESKKRMHSDGIRKPSSANGYKRRRYGN
+
+>YLR340W RPP0 SGDID:S000004332, Chr XII from 805887-806825, Verified ORF, "Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302"
+MGGIREKKAEYFAKLREYLEEYKSLFVVGVDNVSSQQMHEVRKELRGRAVVLMGKNTMVRRAIRGFLSDLPDFEKLLPFVKGNVGFVFTNEPLTEIKNVIVSNRVAAPARAGAVAPEDIWVRAVNTGMEPGKTSFFQALGVPTKIARGTIEIVSDVKVVDAGNKVGQSEASLLNLLNISPFTFGLTVVQVYDNGQVFPSSILDITDEELVSHFVSAVSTIASISLAIGYPTLPSVGHTLINNYKDLLAVAIAASYHYPEIEDLVDRIENPEKYAAAAPAATSAASGDAAPAEEAAAEEEEESDDDMGFGLFD
+
+>YLR371W ROM2 SGDID:S000004363, Chr XII from 862713-866783, Verified ORF, "GDP/GTP exchange protein (GEP) for Rho1p and Rho2p; mutations are synthetically lethal with mutations in rom1, which also encodes a GEP"
+MSETNVDSLGDRNDIYSQIFGVERRPDSFATFDSDSHGDISSQLLPNRIENIQNLNVLLSEDIANDIIIAKQRRRSGVEAAIDDSDIPNNEMKGKSSNYILSQQTNIKEVPDTQSLSSADNTPVSSPKKARDATSSHPIVHAKSMSHIYSTSNSASRQAKHYNDHPLPPMSPRNEVYQKNKSTTAFVPKRKPSLPQLALAGLKKQSSFSTGSASTTPTQARKSPLQGFGFFSRPSSKDLHEQHQHHQHIQHNNINNHNNNNTNNNGAHYQVGSSNSNYPQHSHSISSRSMSLNSSTLKNIASSFQSKTSNSRKATQKYDITSNPFSDPHHHHHHHHSSNSHSSLNNVHGSGNSSSVMGSSSNIGLGLKTRVSSTSLALKRYTSVSGTSLSSPRRSSMTPLSASRPVMSASSKKPQVYPALLSRVATKFKSSIQLGEHKKDGLVYRDAFTGQQAVDVICAIIRTSDRNLALLFGRSLDAQKLFHDVVYEHRLR [...]
+
+>YML092C PRE8 SGDID:S000004557, Chr XIII from 86739-85987, reverse complement, Verified ORF, "20S proteasome beta-type subunit"
+MTDRYSFSLTTFSPSGKLGQIDYALTAVKQGVTSLGIKATNGVVIATEKKSSSPLAMSETLSKVSLLTPDIGAVYSGMGPDYRVLVDKSRKVAHTSYKRIYGEYPPTKLLVSEVAKIMQEATQSGGVRPFGVSLLIAGHDEFNGFSLYQVDPSGSYFPWKATAIGKGSVAAKTFLEKRWNDELELEDAIHIALLTLKESVEGEFNGDTIELAIIGDENPDLLGYTGIPTDKGPRFRKLTSQEINDRLEAL
+
+>YMR073C YMR073C SGDID:S000004677, Chr XIII from 412872-412267, reverse complement, Uncharacterized ORF, "Putative protein of unknown function; proposed to be involved in resistance to carboplatin and cisplatin; shares similarity to a human cytochrome oxidoreductase"
+MSSDGMNRDVSNSKPNVRFAAPQRLSVAHPAISSPLHMPMSKSSRKPLVRTKIRLDPGHSALDWHSLTSNPANYYTKFVSLQLIQDLLDDPVFQKDNFKFSPSQLKNQLLVQKIPLYKIMPPLRINRKIVKKHCKGEDELWCVINGKVYDISSYLKFHPGGTDILIKHRNSDDLITYFNKYHQWVNYEKLLQVCFIGVVCE
+
+>YMR145C NDE1 SGDID:S000004753, Chr XIII from 556474-554792, reverse complement, Verified ORF, "Mitochondrial external NADH dehydrogenase, catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2p are involved in providing the cytosolic NADH to the mitochondrial respiratory chain"
+MIRQSLMKTVWANSSRFSLQSKSGLVKYAKNRSFHAARNLLEDKKVILQKVAPTTGVVAKQSFFKRTGKFTLKALLYSALAGTAYVSYSLYREANPSTQVPQSDTFPNGSKRKTLVILGSGWGSVSLLKNLDTTLYNVVVVSPRNYFLFTPLLPSTPVGTIELKSIVEPVRTIARRSHGEVHYYEAEAYDVDPENKTIKVKSSAKNNDYDLDLKYDYLVVGVGAQPNTFGTPGVYEYSSFLKEISDAQEIRLKIMSSIEKAASLSPKDPERARLLSFVVVGGGPTGVEFAAELRDYVDQDLRKWMPELSKEIKVTLVEALPNILNMFDKYLVDYAQDLFKEEKIDLRLKTMVKKVDATTITAKTGDGDIENIPYGVLVWATGNAPREVSKNLMTKLEEQDSRRGLLIDNKLQLLGAKGSIFAIGDCTFHPGLFPTAQVAHQEGEYLAQYFKKAYKIDQLNWKMTHAKDDSEVARLKNQIVKTQSQIEDFKYN [...]
+
+>YMR235C RNA1 SGDID:S000004848, Chr XIII from 742734-741511, reverse complement, Verified ORF, "GTPase activating protein (GAP) for Gsp1p, involved in nuclear transport"
+MATLHFVPQHEEEQVYSISGKALKLTTSDDIKPYLEELAALKTCTKLDLSGNTIGTEASEALAKCIAENTQVRESLVEVNFADLYTSRLVDEVVDSLKFLLPVLLKCPHLEIVNLSDNAFGLRTIELLEDYIAHAVNIKHLILSNNGMGPFAGERIGKALFHLAQNKKAASKPFLETFICGRNRLENGSAVYLALGLKSHSEGLKVVKLYQNGIRPKGVATLIHYGLQYLKNLEILDLQDNTFTKHASLILAKALPTWKDSLFELNLNDCLLKTAGSDEVFKVFTEVKFPNLHVLKFEYNEMAQETIEVSFLPAMEKGNLPELEKLEINGNRLDEDSDALDLLQSKFDDLEVDDFEEVDSEDEEGEDEEDEDEDEKLEEIETERLEKELLEVQVDDLAERLAETEIK
+
+>YMR242C RPL20A SGDID:S000004855, Chr XIII from 754196-754178,753741-753224, reverse complement, Verified ORF, "Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Bp and has similarity to rat L18a ribosomal protein"
+MPQKWKMAHFKEYQVIGRRLPTESVPEPKLFRMRIFASNEVIAKSRYWYFLQKLHKVKKASGEIVSINQINEAHPTKVKNFGVWVRYDSRSGTHNMYKEIRDVSRVAAVETLYQDMAARHRARFRSIHILKVAEIEKTADVKRQYVKQFLTKDLKFPLPHRVQKSTKTFSYKRPSTFY
+
+>YMR303C ADH2 SGDID:S000004918, Chr XIII from 874336-873290, reverse complement, Verified ORF, "Glucose-repressible alcohol dehydrogenase II, catalyzes the conversion of ethanol to acetaldehyde; involved in the production of certain carboxylate esters; regulated by ADR1"
+MSIPETQKAIIFYESNGKLEHKDIPVPKPKPNELLINVKYSGVCHTDLHAWHGDWPLPTKLPLVGGHEGAGVVVGMGENVKGWKIGDYAGIKWLNGSCMACEYCELGNESNCPHADLSGYTHDGSFQEYATADAVQAAHIPQGTDLAEVAPILCAGITVYKALKSANLRAGHWAAISGAAGGLGSLAVQYAKAMGYRVLGIDGGPGKEELFTSLGGEVFIDFTKEKDIVSAVVKATNGGAHGIINVSVSEAAIEASTRYCRANGTVVLVGLPAGAKCSSDVFNHVVKSISIVGSYVGNRADTREALDFFARGLVKSPIKVVGLSSLPEIYEKMEKGQIAGRYVVDTSK
+
+>YMR309C NIP1 SGDID:S000004926, Chr XIII from 895425-892987, reverse complement, Verified ORF, "Subunit of the eukaryotic translation initiation factor 3 (eIF3), involved in the assembly of preinitiation complex and start codon selection"
+MSRFFSSNYEYDVASSSSEEDLLSSSEEDLLSSSSSESELDQESDDSFFNESESESEADVDSDDSDAKPYGPDWFKKSEFRKQGGGSNKFLKSSNYDSSDEESDEEDGKKVVKSAKEKLLDEMQDVYNKISQAENSDDWLTISNEFDLISRLLVRAQQQNWGTPNIFIKVVAQVEDAVNNTQQADLKNKAVARAYNTTKQRVKKVSRENEDSMAKFRNDPESFDKEPTADLDISANGFTISSSQGNDQAVQEDFFTRLQTIIDSRGKKTVNQQSLISTLEELLTVAEKPYEFIMAYLTLIPSRFDASANLSYQPIDQWKSSFNDISKLLSILDQTIDTYQVNEFADPIDFIEDEPKEDSDGVKRILGSIFSFVERLDDEFMKSLLNIDPHSSDYLIRLRDEQSIYNLILRTQLYFEATLKDEHDLERALTRPFVKRLDHIYYKSENLIKIMETAAWNIIPAQFKSKFTSKDQLDSADYVDNLIDGLSTILSK [...]
+
+>YNL166C BNI5 SGDID:S000005110, Chr XIV from 323567-322221, reverse complement, Verified ORF, "Protein involved in organization of septins at the mother-bud neck, may interact directly with the Cdc11p septin, localizes to bud neck in a septin-dependent manner"
+MGLDQDKIKKRLSQIEIDINQMNQMIDENLQLVEPAEDEAVEDNVKDTGVVDAVKVAETALFSGNDGADSNPGDSAQVEEHKTAQVHIPTENEANKSTDDPSQLSVTQPFIAKEQITHTAIAIGDSYNSFVANSAGNEKAKDSCTENKEDGTVNIDQNRGEADVEIIENNDDEWEDEKSDVEEGRVDKGTEENSEIESFKSPMPQNNTLGGENKLDAELVLDKFSSANKDLDIQPQTIVVGGDNEYNHESSRLADQTPHDDNSENCPNRSGGSTPLDSQTKIFIPKKNSKEDGTNINHFNSDGDGQKKMANFETRRPTNPFRVISVSSNSNSRNGSRKSSLNKYDSPVSSPITSASELGSIAKLEKRHDYLSMKCIKLQKEIDYLNKMNAQGSLSMEDGKRLHRAVVKLQEYLDKKTKEKYEVGVLLSRHLRKQIDRGENGQFWIGTK
+
+>YOR063W RPL3 SGDID:S000005589, Chr XV from 444688-445851, Verified ORF, "Protein component of the large (60S) ribosomal subunit, has similarity to E. coli L3 and rat L3 ribosomal proteins; involved in the replication and maintenance of killer double stranded RNA virus"
+MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLDRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKNWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEIQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRKTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRTKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDTASKFGKGRFQTPAEKHAFMGTLKKDL
+
+>YOR136W IDH2 SGDID:S000005662, Chr XV from 580251-581360, Verified ORF, "Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of isocitrate to alpha-ketoglutarate in the TCA cycle"
+MLRNTFFRNTSRRFLATVKQPSIGRYTGKPNPSTGKYTVSFIEGDGIGPEISKSVKKIFSAANVPIEWESCDVSPIFVNGLTTIPDPAVQSITKNLVALKGPLATPIGKGHRSLNLTLRKTFGLFANVRPAKSIEGFKTTYENVDLVLIRENTEGEYSGIEHIVCPGVVQSIKLITRDASERVIRYAFEYARAIGRPRVIVVHKSTIQRLADGLFVNVAKELSKEYPDLTLETELIDNSVLKVVTNPSAYTDAVSVCPNLYGDILSDLNSGLSAGSLGLTPSANIGHKISIFEAVHGSAPDIAGQDKANPTALLLSSVMMLNHMGLTNHADQIQNAVLSTIASGPENRTGDLAGTATTSSFTEAVIKRL
+
+>YOR168W GLN4 SGDID:S000005694, Chr XV from 649304-651733, Verified ORF, "Glutamine tRNA synthetase, monomeric class I tRNA synthetase that catalyzes the specific glutaminylation of tRNA(Glu); N-terminal domain proposed to be involved in enzyme-tRNA interactions"
+MSSVEELTQLFSQVGFEDKKVKEIVKNKKVSDSLYKLIKETPSDYQWNKSTRALVHNLASFVKGTDLPKSELIVNGIINGDLKTSLQVDAAFKYVKANGEASTKMGMNENSGVGIEITEDQVRNYVMQYIQENKERILTERYKLVPGIFADVKNLKELKWADPRSFKPIIDQEVLKLLGPKDERDLIKKKTKNNEKKKTNSAKKSSDNSASSGPKRTMFNEGFLGDLHKVGENPQAYPELMKEHLEVTGGKVRTRFPPEPNGYLHIGHSKAIMVNFGYAKYHNGTCYLRFDDTNPEKEAPEYFESIKRMVSWLGFKPWKITYSSDYFDELYRLAEVLIKNGKAYVCHCTAEEIKRGRGIKEDGTPGGERYACKHRDQSIEQNLQEFRDMRDGKYKPGEAILRMKQDLNSPSPQMWDLIAYRVLNAPHPRTGTKWRIYPTYDFTHCLVDSMENITHSLCTTEFYLSRESYEWLCDQVHVFRPAQREYGRLNIT [...]
+
+>YOR267C HRK1 SGDID:S000005793, Chr XV from 824866-822587, reverse complement, Verified ORF, "Protein kinase implicated in activation of the plasma membrane H(+)-ATPase Pma1p in response to glucose metabolism; plays a role in ion homeostasis"
+MPNLLSRNPFHGHHNDHHHDRENSSNNPPQLIRSSKSFLNFIGRKQSNDSLRSEKSTDSMKSTTTTTNYTTTNLNNNTHSHSNATSISTNNYNNNYETNHHHNISHGLHDYTSPASPKQTHSMAELKRFFRPSVNKKLSMSQLRSKKHSTHSPPPSKSTSTVNLNNHYRAQHPHGFTDHYAHTQSAIPPSTDSILSLSNNINIYHDDCILAQKYGKLGKLLGSGAGGSVKVLVRPTDGATFAVKEFRPRKPNESVKEYAKKCTAEFCIGSTLHHPNVIETVDVFSDSKQNKYYEVMEYCPIDFFAVVMTGKMSRGEINCCLKQLTEGVKYLHSMGLAHRDLKLDNCVMTSQGILKLIDFGSAVVFRYPFEDGVTMAHGIVGSDPYLAPEVITSTKSYDPQCVDIWSIGIIYCCMVLKRFPWKAPRDSDDNFRLYCMPDDIEHDYVESARHHEELLKERKEKRQRFLNHSDCSAINQQQPAHESNLKTVQNQV [...]
+
+>YPL106C SSE1 SGDID:S000006027, Chr XVI from 352272-350191, reverse complement, Verified ORF, "ATPase that is a component of the heat shock protein Hsp90 chaperone complex; binds unfolded proteins; member of the heat shock protein 70 (HSP70) family; localized to the cytoplasm"
+MSTPFGLDLGNNNSVLAVARNRGIDIVVNEVSNRSTPSVVGFGPKNRYLGETGKNKQTSNIKNTVANLKRIIGLDYHHPDFEQESKHFTSKLVELDDKKTGAEVRFAGEKHVFSATQLAAMFIDKVKDTVKQDTKANITDVCIAVPPWYTEEQRYNIADAARIAGLNPVRIVNDVTAAGVSYGIFKTDLPEGEEKPRIVAFVDIGHSSYTCSIMAFKKGQLKVLGTACDKHFGGRDFDLAITEHFADEFKTKYKIDIRENPKAYNRILTAAEKLKKVLSANTNAPFSVESVMNDVDVSSQLSREELEELVKPLLERVTEPVTKALAQAKLSAEEVDFVEIIGGTTRIPTLKQSISEAFGKPLSTTLNQDEAIAKGAAFICAIHSPTLRVRPFKFEDIHPYSVSYSWDKQVEDEDHMEVFPAGSSFPSTKLITLNRTGDFSMAASYTDITQLPPNTPEQIANWEITGVQLPEGQDSVPVKLKLRCDPSGLHTI [...]
+
+>YPL215W CBP3 SGDID:S000006136, Chr XVI from 147415-148422, Verified ORF, "Mitochondrial protein required for assembly of ubiquinol cytochrome-c reductase complex (cytochrome bc1 complex); interacts with Cbp4p and function is partially redundant with that of Cbp4p"
+MMSVNRFTSGRLPVFLRKSPFYYSRAYLHQTCVFKQNKETAQDSPELLAKSSHLNSKPLDVSNKAPVKTAQNKIPLAHSKYESSKYELPKWKEALGELVIRAFHLDMDRVRAGPVAGSYYYKICKEQGLQYEDEPLSETAKYFYEDLKLPRTFSQWFQITVLHEWILFVRMRAMPFKYGRNYQQKLVDRTFSDIELRLFEEMKVNSGRIADQYLKDFNTQLRGAIFAYDEGFATDDGTLATAVWRNLFGGRKNIDMVHLESVVRYIYSQLYVLSRLSDREFATGKFKFVPPGVKVEKLTPKQEEELKAKTIAKYEALDKDPKTLPSERSRLSYTN
+
+>YPL266W DIM1 SGDID:S000006187, Chr XVI from 39121-40077, Verified ORF, "Essential 18S rRNA dimethylase, responsible for conserved m6(2)Am6(2)A dimethylation in 3'-terminal loop of 18 S rRNA, part of 90S and 40S pre-particles in nucleolus, involved in pre-ribosomal RNA processing"
+MGKAAKKKYSGATSSKQVSAEKHLSSVFKFNTDLGQHILKNPLVAQGIVDKAQIRPSDVVLEVGPGTGNLTVRILEQAKNVVAVEMDPRMAAELTKRVRGTPVEKKLEIMLGDFMKTELPYFDICISNTPYQISSPLVFKLINQPRPPRVSILMFQREFALRLLARPGDSLYCRLSANVQMWANVTHIMKVGKNNFRPPPQVESSVVRLEIKNPRPQVDYNEWDGLLRIVFVRKNRTISAGFKSTTVMDILEKNYKTFLAMNNEMVDDTKGSMHDVVKEKIDTVLKETDLGDKRAGKCDQNDFLRLLYAFHQVGIHFS
diff --git a/doc/user/example-files/target.sqt b/doc/user/example-files/target.sqt
new file mode 100644
index 0000000..3c4e472
--- /dev/null
+++ b/doc/user/example-files/target.sqt
@@ -0,0 +1,33 @@
+H SQTGenerator Crux
+H SQTGeneratorVersion 1.0
+H Comment Crux was written by...
+H Comment ref...
+H StartTime Tue Dec 2 15:22:50 2008
+H EndTime
+H Database test_crux_index/test-binary-fasta
+H DBSeqLength ?
+H DBLocusCount 4
+H PrecursorMasses average
+H FragmentMasses mono
+H Alg-PreMasTol 3.0
+H Alg-FragMassTol 0.50
+H Alg-XCorrMode 0
+H Comment preliminary algorithm sp
+H Comment final algorithm xcorr
+H StaticMod C=160.139
+H Alg-DisplayTop 5
+H EnzymeSpec tryptic
+H Line fields: S, scan number, scan number,charge, 0, precursor m/z, 0, 0, number of matches
+H Line fields: M, rank by xcorr score, rank by sp score, peptide mass, deltaCn, xcorr score, sp score, number ions matched, total ions compared, sequence
+S 14 14 2 0.00 server 500.41 0.00 0.00 1
+M 1 1 1001.15 0.00 0.29 98.43 6 14 K.FHLELSQK.D U
+L gi|6381999|ref|NP_009311.2|
+S 14 14 3 0.00 server 500.41 0.00 0.00 1
+M 1 1 1495.81 0.00 -0.09 55.08 8 44 R.VMFTTFYMITNK.Y U
+L gi|6382000|ref|NP_009314.2|
+S 15 15 2 0.00 server 488.82 0.00 0.00 1
+M 1 1 973.09 0.00 -0.10 0.00 0 16 K.SGATAYIYK.A U
+L gi|6381999|ref|NP_009311.2|
+S 15 15 3 0.00 server 488.82 0.00 0.00 1
+M 1 1 1464.81 0.00 0.13 15.58 5 44 K.QYLLLNIAYLLK.L U
+L gi|6381999|ref|NP_009311.2|
diff --git a/doc/user/extract-columns.html b/doc/user/extract-columns.html
new file mode 100644
index 0000000..0d799f5
--- /dev/null
+++ b/doc/user/extract-columns.html
@@ -0,0 +1,131 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>extract-columns</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>extract-columns</h1>
+<h2>Usage:</h2>
+<p><code>crux extract-columns [options] <tsv file> <column names></code></p>
+<h2>Description:</h2>
+<p>Given a tab-delimited file and a comma-delimited list of column names, extract the requested columns.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tsv file</code> – A tab-delimited file, with column headers in the first row. Use "-" to read from standard input.</li>
+ <li><code>column names</code> – A comma-delimited list of column names.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – the requested columns in tab-delimited format. The columns are printed in the same order that they appear in the input column list.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--delimiter <string></code> – Specify the input and output delimiter to use when processing the delimited file. The argument can be either a single character or the keyword 'tab.' Default = <code>tab</code>.</li>
+ <li class="nobullet"><code>--header T|F</code> – Print the header line of the file, in addition to the columns that match. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/extract-rows.html b/doc/user/extract-rows.html
new file mode 100644
index 0000000..033c1f9
--- /dev/null
+++ b/doc/user/extract-rows.html
@@ -0,0 +1,134 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>extract-rows</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>extract-rows</h1>
+<h2>Usage:</h2>
+<p><code>crux extract-rows [options] <tsv file> <column name> <column value></code></p>
+<h2>Description:</h2>
+Given a tab-delimited file, a column name and a column cell value, extract the rows that have the matching values for that column.
+<h2>Input:</h2>
+<ul>
+ <li><code>tsv file</code> – A tab-delimited file, with column headers in the first row. Use "-" to read from standard input.</li>
+ <li><code>column name</code> – A column name.</li>
+ <li><code>column value</code> – A cell value for a column.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – the rows for which the value observed in the specified column of the input file match the <column value> given on the command line.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--delimiter <string></code> – Specify the input and output delimiter to use when processing the delimited file. The argument can be either a single character or the keyword 'tab.' Default = <code>tab</code>.</li>
+ <li class="nobullet"><code>--header T|F</code> – Print the header line of the file, in addition to the columns that match. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--comparison eq|gt|gte|lt|lte|neq</code> – Specify the operator that is used to compare an entry in the specified column to the value given on the command line. Legal values are as follows:<ul><li>eq – The two values are equal</li><li>lt – The file value is less than the argument value</li><li>lte – The file value is less than or equal to the argument value</li><li>gt – The file value is greater than the argument value</li><li>gt [...]
+ <li class="nobullet"><code>--column-type int|real|string</code> – Specifies the data type of the column, either an integer (int), a floating point number (real), or a string. Default = <code>string</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/faq.html b/doc/user/faq.html
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--- /dev/null
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@@ -0,0 +1,638 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux FAQs</title>
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+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Crux Frequently Asked Questions</h2>
+
+ <ol>
+
+ <li>
+ <b>What is the difference between Tide and Comet?</b></li>
+
+ <p>
+ The differences are as follows:
+ <ul>
+ <li>
+ Tide converts your FASTA file to an index (either as part
+ of <code>tide-search</code> or by using <code>tide-index</code>),
+ whereas Comet does searching directly from the FASTA file. The
+ indexing step allows Tide to pre-compute many parts of the search
+ procedure, thereby making the search faster.
+ <li>
+ Comet is multi-threaded, whereas Tide runs on a single thread. On
+ multi-threaded CPUs, this feature can offset the speed difference
+ between Comet and Tide.</li>
+ <li>
+ For each match, Comet reports the <i>total</i> number of candidate
+ peptides, whereas Tide reports the number of <i>distinct</i> candidate
+ peptides.</li>
+ <li>
+ Comet provides an option to report an E-value in addition to the raw
+ XCorr score, whereas Tide provides an option to report a p-value. The
+ methods for computing these two statistical confidence measures are
+ quite different.</li>
+ <li>
+ Some options are available only in Comet (various options related to
+ different types of theoretical fragment ions, max_fragment_charge,
+ nucleotide_reading_frame, etc.) whereas others are only available in
+ Tide (e.g., keep-terminal-aminos).</li>
+ </ul></p>
+
+ <p>
+ Overall, for a given set of spectra, the XCorr scores computed by
+ Comet and by Tide should be quite similar to one another, assuming
+ that the various search parameters are set similarly between the two
+ algorithms. Below is a table summarizing the correspondence between
+ the two sets of parameters. The specified values will yield nearly
+ identical XCorr scores from the two search engines.</p>
+
+ <table border="1">
+ <tr>
+ <td>
+ <b>Tide parameter</b></td>
+ <td>
+ <b>Tide value</b></td>
+ <td>
+ <b>Comet parameter</b></td>
+ <td>
+ <b>Comet value</b></td>
+ </tr>
+
+ <tr>
+ <td>
+ enzyme</td>
+ <td>
+ trypsin</td>
+ <td>
+ search_enzyme_number</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ digestion</td>
+ <td>
+ full-digest</td>
+ <td>
+ num_enzyme_termini</td>
+ <td>
+ 2</td>
+ </tr>
+
+ <tr>
+ <td>
+ missed-cleavages</td>
+ <td>
+ 0</td>
+ <td>
+ allowed_missed_cleavage</td>
+ <td>
+ 0</td>
+ </tr>
+
+ <tr>
+ <td>
+ min-peaks</td>
+ <td>
+ 10</td>
+ <td>
+ minimum_peaks</td>
+ <td>
+ 10</td>
+ </tr>
+
+ <tr>
+ <td>
+ precursor-window</td>
+ <td>
+ 3</td>
+ <td>
+ peptide_mass_tolerance</td>
+ <td>
+ 3</td>
+ </tr>
+
+ <tr>
+ <td>
+ precursor-window-type</td>
+ <td>
+ mass</td>
+ <td>
+ peptide_mass_units</td>
+ <td>
+ 0</td>
+ </tr>
+
+ <tr>
+ <td>
+ fragment-mass</td>
+ <td>
+ mono</td>
+ <td>
+ mass_type_fragment</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ decoy-format</td>
+ <td>
+ peptide-reverse</td>
+ <td>
+ N/A</td>
+ <td>
+ </td>
+ </tr>
+
+ <tr>
+ <td>
+ keep-terminal-aminos</td>
+ <td>
+ C</td>
+ <td>
+ N/A</td>
+ <td>
+ </td>
+ </tr>
+
+ <tr>
+ <td>
+ concat</td>
+ <td>
+ T</td>
+ <td>
+ decoy_search</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ top-match</td>
+ <td>
+ 5</td>
+ <td>
+ num_results, num_output_lines</td>
+ <td>
+ 6, 5</td>
+ </tr>
+
+ <tr>
+ <td>
+ remove-precursor-peak</td>
+ <td>
+ T</td>
+ <td>
+ remove_precursor_peak</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ remove-precursor-tolerance</td>
+ <td>
+ 15</td>
+ <td>
+ remove_precursor_tolerance</td>
+ <td>
+ 15</td>
+ </tr>
+
+ <tr>
+ <td>
+ use-flanking-peaks</td>
+ <td>
+ F</td>
+ <td>
+ theoretical_fragment_ions</td>
+ <td>
+ 1</td>
+ </tr>
+
+ <tr>
+ <td>
+ use-neutral-loss-peaks</td>
+ <td>
+ F</td>
+ <td>
+ use_NL_ions</td>
+ <td>
+ F</td>
+ </tr>
+
+ <tr>
+ <td>
+ mz-bin-width</td>
+ <td>
+ 1.0005079</td>
+ <td>
+ fragment_bin_tol</td>
+ <td>
+ 1.0005079</td>
+ </tr>
+
+ <tr>
+ <td>
+ mz-bin-offset</td>
+ <td>
+ 0.4</td>
+ <td>
+ fragment_bin_offset</td>
+ <td>
+ 0.4</td>
+ </tr>
+
+ <tr>
+ <td>
+ min-mass, max-mass</td>
+ <td>
+ 200, 7200</td>
+ <td>
+ digest_mass_range</td>
+ <td>
+ 200 7200</td>
+ </tr>
+
+ <tr>
+ <td>
+ N/A</td>
+ <td>
+ </td>
+ <td>
+ max_fragment_charge</td>
+ <td>
+ 2</td>
+ </tr>
+
+ </table>
+
+ <p>
+ Here is a scatter plot of XCorr scores from a search run with the
+ parameters listed above:</p>
+
+ <img src="images/stored-xcorr.png">
+
+
+ <li>
+ <b>What operating systems does Crux work with?</b></li>
+
+ <p>
+ Crux is written in C++, so in principle it should work on virtually
+ any modern operating system. We provide pre-compiled binaries for
+ Linux, MacOS and Windows.</p>
+
+ <li>
+ <b>How does Crux compute the masses of peptides and peptide
+ fragments?</b></li>
+
+ <p>
+ <ul>
+
+ <li>
+ Each amino acid can be characterized either by its monoisotopic mass,
+ which is the mass of the most abundant isotopic form of that amino acid,
+ or the average mass, which is a weighted average of the masses of all
+ the isotopic forms. By default, Crux uses average mass to calculate
+ peptide masses, though this behavior can be controlled by the
+ <code>isotopic-mass</code> option to <code>tide-index</code> and the
+ <code>mass_type_parent</code> option to <code>comet</code>. For
+ fragments, <code>tide-search</code> always uses the monoisotopic mass,
+ whereas <code>comet</code> allows selection
+ via <code>mass_type_fragment</code>.</li>
+
+ <li>
+ The neutral mass of a peptide is not the sum of the masses of its
+ amino acids. The N-terminus and C-terminus of the peptide together
+ contribute an additional water molecule, whose mass is either
+ 18.010564684 Da (monoisotopic) or 18.0153 Da (average).</li>
+ <li>
+ A charged peptide has an additional approximately 1 Da mass for each
+ charge, corresponding to the mass of a hydrogen atom. The exact mass
+ to be added depends on whether we are using the monoisotopic mass
+ (1.007825035) or average mass (1.00794).</li>
+
+ <li>When a peptide fragments, each b-ion will have a mass equal to
+ the sum of its amino acids plus one hydrogen for each charge on the
+ fragment, while each y-ion will have a mass equal to the sum of its
+ amino acids plus water plus one hydrogen for each charge on the
+ fragment.</li>
+
+ <li>
+ By default, both Tide and Comet add a static modification of
+ 57.021464 Da to all cysteines. This is because in most protein
+ preparation protocols the peptides are alkylated with iodoacetamide,
+ resulting in carbamidomethylation of cysteine. The alkylation step
+ prevents the reformation of disulfide bonds. Other alykylation
+ reagents may be used, in which case the appropriate mass shift can be
+ specified with the <code>C=[mass]</code> option
+ to <code>tide-index</code> or the <code>add_C_cysteine</code> option
+ to <code>comet</code>.</li>
+
+ </ul>
+ </p>
+
+ <li>
+ <b>How does Crux assign fragment masses to bins prior to computing
+ the XCorr score?</b>
+ </li>
+
+ <p>The XCorr score is essentially a dot product between a preprocessed
+ form of the observed spectrum and the theoretical spectrum derived
+ from the candidate peptide. In order to compute this dot product, the
+ masses of the fragments in both spectra are assigned to discrete mass
+ bins. This can be viewed as a form of rounding, but with more control
+ over the discrete masses. Two parameters, <code>mz-bin-width</code> and
+ <code>mz-bin-offset</code>, control the size and location of the bins,
+ and are used to convert fragment masses according to this formula:</p>
+
+ <p align=center>binned mass = floor( ( original mass / <code>bin-width</code> ) + 1.0 - <code>bin-offset</code> )</p>
+
+ <p>
+ The default values <code>bin-width</code>=1.0005079
+ and <code>bin-offset</code>=0.40 are suitable for most low-resolution
+ datasets.
+ </p>
+
+ <li>
+ <b>How does Crux estimate the possible charge states of the peptides when the
+ information is not provided within the spectra file?</b>
+ </li>
+
+ <p>
+ Crux calculates the ratio of two values: (1) the sum of the
+ intensities from the peaks in the fragmentation spectrum whose m/z is
+ greater than the precursor m/z versus (2) the sum of the peaks whose
+ m/z is smaller than the precursor. If this ratio is greater than or
+ equal to a calculated threshold based upon the location of the
+ precursor m/z and the max m/z in the spectrum, Crux then assigns both
+ +2 and +3 as possible charge states to the spectrum. Otherwise, Crux
+ assigns +1 as the charge state. The algorithm is based upon the
+ observation that fragmentation spectra collected from +1 peptides
+ should have no peaks above the precursor m/z. In contrast, a peptide
+ of charge state greater than +1 can generate fragment ions of lower
+ charge whose m/z is greater than the precursor m/z, thus indicating a
+ multiply charged precursor.</p>
+
+ <p>
+ Note that, in addition, <code>comet</code> includes
+ a <code>precursor_charge</code> parameter. If the first number in
+ this parameter is set to 0, i.e., <code>precursor_charge = 0 0</code>,
+ then the charge state rule above is applied. However, if a user
+ specifies a precursor charge range, i.e., <code>precursor_charge = 1
+ 5</code>, then Comet will search every spectrum through this range of
+ assumed charge states for every spectrum whose precursor charge
+ is unknown.</p>
+
+ <li>
+ <b>How does Crux create peptides from the given set of proteins in the
+ database?</b></li>
+
+ <p>
+ The options <code>enzyme</code> (for <code>tide-index</code>)
+ and <code>search_enzyme_number</code> (for <code>comet</code>) define
+ the enzymatic cleavage rules. When <code>enzyme=no-enzyme</code>
+ or <code>search_enzyme_number=0</code>, then any subsequence of a
+ protein may be considered as a candidate peptide. For other values of
+ these parameters, the residues at the termini of the protein
+ subsequence must follow specific rules. For example, trypsin requires
+ that the preceeding residue must be an R or K and the following
+ residue may not be a P.</p>
+
+ <p>
+ When <code>digestion=full-digest</code> (for <code>tide-index</code>)
+ or <code>num_enzyme_termini=2</code> (for <code>comet</code>), then
+ these rules must be true at both ends of the peptide. When it
+ is <code>digestion=partial-digest</code>
+ or <code>num_enzyme_termini=1</code>, then the rules must be true at
+ at least one of the ends. The <code>missed-cleavages</code>
+ and <code>allowed_missed_cleavages</code> parameters control the
+ maximum number of cleavage sites that may lie within the peptide
+ sequence.</p>
+
+ <p>
+ Note that if <code>enzyme=no-enzyme</code>
+ or <code>search_enzyme_number=0</code>, then
+ the <code>digestion</code>, <code>num_enzyme_termini</code>, <code>missed-cleavages</code>
+ and <code>allowed_missed_cleaveages</code> parameters are not used.</p>
+
+
+ <li>
+ <b>How does Crux select candidate peptides from the database?</b></li>
+
+ <p>
+ The Crux search tools (<code>tide-index</code> and <code>comet</code>)
+ select candidate peptides for each spectrum based on its precursor
+ singly charged mass (m+h) or the mass-to-charge (m/z) and an assumed
+ charge state (specified in the input file). If the m+h and charge is
+ provided in the input file (e.g., from the Z lines of an MS2 file),
+ then the precursor mass is calculated from the m+h minus the mass of a
+ proton. Otherwise, the precursor mass is calculated from the precursor
+ m/z and an assumed charge. A mass window is defined in one of three
+ ways based on the
+ <code>precursor-window-type</code> and <code>precursor-window</code>
+ options.</p>
+
+ <ul>
+ <li>
+ If the <code>precursor-window-type</code> is set to <code>mz</code>,
+ then the window is calculated as spectrum precursor m/z ±
+ <code>precursor-window</code> and the resulting range is converted
+ to mass using the charge state with the formula:<br>
+ Mass=m/z * charge - MASS_PROTON * charge, where MASS_PROTON=1.00727646677
+ </li>
+
+ <li>
+ If the <code>precursor-window-type</code> is set to <code>mass</code>, then
+ the window is defined as the precursor mass ±
+ <code>precursor-window</code>.
+ </li>
+
+ <li>
+ If the <code>precursor-window-type</code> is set to <code>ppm</code>
+ (parts per million), then the window spans from the precursor mass /
+ (1.0 + window * 1e-6) to precursor mass / (1.0 - window * 1e-6).</li>
+ </ul>
+
+ <p>
+ Candidate peptides are those whose mass falls within the defined
+ window. The peptide mass is computed as the sum of the average amino
+ acid masses plus 18 Da for the terminal OH group. Candidate peptides
+ can also be constrained by minimum and maximum allowed length. </p>
+
+ <li>
+ <b>How can I search my ITRAQ data?</b></li>
+
+ <p>
+ ITRAQ and other tagged seaches can be done by using terninal
+ modifications. For example, if your tag has a mass of 304.199040, add
+ these lines to your parameter file:
+ <pre>
+nmod=304.199040:-1
+cmod=304.199040:-1
+ </pre>
+ <p>
+ Crux will then generate peptides with this modification (+304.199904)
+ on the n-terminus, the c-terminus and on both termini. The -1 in the
+ option means to add the modification regardless of where the peptide
+ terminus lies relative to the rest of the protein.
+
+ <li>
+ <b>What happens if I decrease the size of the precursor window during
+ searching?</b></li>
+
+ <p>
+ Reducing the precursor mass tolerance has two main benefits. One is
+ reduced search time, and the other is improved statistical power to
+ detect matches. With a smaller window, fewer candidates are tested
+ against a spectrum. As a result, the statistical confidence measure
+ calculated after multiple testing correction will be more significant.
+ Of course, the flipside is that if you make the precursor window too
+ small, then you may end up throwing out correct identifications.
+ Control over the size of the window is provided by the using
+ the <code>precursor-window</code> and
+ <code>precursor-window-type</code> options.</p>
+
+ <li>
+ <b>How can I run many jobs in parallel?</b>
+
+
+ <p>
+ In combination with GNU parallel, parallelization of Crux can be
+ achieved rather painlessly. For example, to run tide-search on a set
+ of spectrum files, you can just get your spectra files into a filelist:</p>
+
+ <pre>
+find . -name "*.mzXML" > file.list
+ </pre>
+
+ <p>
+ Then, with a bit of bash magic, run parallel as follows (assuming
+ there are 100 files in file.list):</p>
+
+ <pre>
+parallel --xapply crux tide-search <options> --fileroot {1} {2} database.db ::: $(seq 1 100) ::: $(cat file.list)
+ </pre>
+
+ <p>
+ <i>Thanks to Ben Temperton for this answer.</i></p>
+
+ <li>
+ <b>How can I contribute to Crux?</b></li>
+
+ <p>
+ Patches implementing new features can be emailed to the development
+ team at crux-support at uw.edu for review and inclusion in subsequent
+ releases of Crux.</p>
+
+ <li>
+ <b>Where does the name "Crux" come from?</b></li>
+
+ <p>
+ Thin air. The name is not an acronym or a reference to anything in
+ particular.</p>
+
+ </ol>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/file-formats/barista-xml-format.html b/doc/user/file-formats/barista-xml-format.html
new file mode 100644
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+++ b/doc/user/file-formats/barista-xml-format.html
@@ -0,0 +1,249 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+ <img src="../images/crux-logo.png" id="logo"></a>
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+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>barista.xml </h2>
+ <p>
+ The barista.xml is an XML files that used to record four main
+ parts:
+ </p>
+ <pre>
+< proteins > ... < /proteins >
+< subset_proteins > ... < /subset_proteins >
+< peptides > ... < /peptides >
+< psms > ... < /psms >
+ </pre>
+ <p>
+ <ol>
+ <li>
+ <b>Proteins:</b>contains the ranked list of groups of indistinguishable
+ target proteins. Each protein entry includes the following fields:
+ <ol>
+ <li>
+ <b>protein group:</b> a number that identifies a group. </li>
+ <li>
+ <b>q-value: </b>The minimal protein-level false discovery rate at which this
+ protein is deemed significant. This q-value is computed based on the
+ ranking of the proteins induced by the Barista score.</li>
+ <li>
+ <b>score:</b> The score assigned to the proteins by Barista. Higher values
+ correspond to more confident identifications.</code>
+ <li>
+ <b>protein_ids:</b> proteins in the protein group. </li>
+ <li>
+ <b>alternative_peptide_id: </b>peptides are considered indistinguishable if
+ they have identical amino acid sequences or they differ only by I/L or
+ T/S in the same position in the peptide. If the peptides shared by the
+ group are not identical, they are listed immediately after the
+ proteins they belong to. </li>
+ <li><b>
+ peptide_ids:</b> belong to each of the proteins in the
+ group.</li>
+ </ol>
+
+ <br>
+ For example, suppose that
+ <dl>
+ <dd> <b> protein_a </b> has peptide <b> KLEAEVEALKK </b>       // 'L' in second position </dd>
+ <dd> and peptide <b> VLGAK </b> </dd>
+ <dd> <b> protein_b </b> has peptide <b> KIEAEVEALKK </b>       // 'I' in second position
+ <dd> and peptide <b> VLGAK </b> </dd>
+ </dl>
+
+ <br>
+ Then the xml entry could look like this <br />
+ <pre>
+< proteins >
+< q_value > 0 < /q_value >
+< score > 8.9 > < /score >
+< protein_group group_id="1" >
+< protein_ids >
+< protein_id > protein_a < /protein_id >
+< alternative_peptide_id > KLEAEVEALKK < /alternative_peptide_id >
+< protein_id > protein_b < /protein_id >
+< alternative_peptide_id > KIEAEVEALKK < /alternative_peptide_id >
+< /protein_ids >
+< peptide_ids >
+< peptide_id > VLGAK < /peptide_id >
+< /peptide_ids >
+< /protein_group >
+< /proteins >
+ </pre>
+ </li>
+ </p>
+ <li>
+ <p>
+ <b>Subset proteins</b> contains groups of indistinguishable proteins, which
+ constitute a subset of some group in the proteins section in
+ terms of the peptides identified in these proteins. Each entry includes
+ <ol>
+ <li>
+ group id and parent group id: the identifier of the group and the
+ identifier of the protein group which has the superset of the peptide
+ set belonging the current group
+ </li>
+ <li>
+ protein_ids : proteins that belong to the group
+ </li>
+ <li>
+ peptide_ids: peptides that belong to the proteins in the group.
+ </li>
+ </ol>
+ </li>
+ </p>
+ <li>
+ <p>
+ <b>Peptides</b> contains a ranked list of target peptides. Each peptide entry
+ includes:
+ <ol>
+ <li>
+ peptide: Peptide amino acid sequence.
+ <li>
+ q-value: The minimal peptide-level false discovery rate at which this
+ peptide is deemed significant. This q-value is computed based on the
+ ranking of the peptides induced by the Barista score.</li>
+ <li>
+ score: The score assigned to the peptide by Barista. Higher values
+ correspond to more confident identifications.</li>
+ <li>
+ main_psm_id: The PSM identifier based on which the peptide received
+ its score. A peptide score is the maximum over all the PSMs that
+ contain this peptide. </li>
+ <li>
+ psm_ids: The identifiers of all the PMS that contain this peptide .</li>
+ <li>
+ protein_ids: All the proteins that contain this peptide and were
+ infered based on some PSMs from the database search. </li>
+ </ol>
+
+ </li>
+ </p>
+ <li>
+ <p>
+ <b>PSMs</b> contains ranked list of target peptide-spectrum matches. The
+ following columns are included:
+ <ol>
+ <li>
+ psm_id: PSM identifier. </li>
+ <li>
+ q-value: The minimal PSM-level false discovery rate at which this PSM
+ is deemed significant. This q-value is computed based on the ranking
+ of the PSMs induced by the Barista score.</li>
+ <li>
+ score: The score assigned to the PSM by Barista. Higher values
+ correspond to more confident identifications.</code>
+ <li>
+ scan: the scan number</li>
+ <li>
+ charge: the inferred charge state</li>
+ <li>
+ precursor_mass: precrusor mass as recorded during the MS1 scan </li>
+ <li>
+ peptide: the peptide sequence</li>
+ <li>
+ filename: name of the file in which the PSM appears</li>
+ </ol>
+ </p>
+ </ol>
+ </li>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/file-formats/fasta-format.html b/doc/user/file-formats/fasta-format.html
new file mode 100644
index 0000000..13cb395
--- /dev/null
+++ b/doc/user/file-formats/fasta-format.html
@@ -0,0 +1,169 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <H2>FASTA file format</H2>
+
+ <p>
+ Crux searches protein sequence databases given in FASTA format. The
+ format is very simple. Every entry consists of a sequence identifier
+ (ID), an optional comment (COMMENT), and a sequence (SEQUENCE). The
+ format looks like this:
+ </p>
+
+ <pre>
+>ID COMMENT
+SEQUENCE
+ </pre>
+
+ <p>
+ The special character ">" marks the beginning of a new sequence.
+ The ">" character is followed immediately by the sequence
+ identifier. The rest of that line is occupied by the optional
+ comment. Subsequent lines contain the sequence itself.
+ </p>
+
+ <p>Some rules about representing sequences:</p>
+
+ <ul style="padding:0; font-size:14px;">
+
+ <li>
+ A single protein sequence can span multiple lines. The > character
+ occurring at the beginning of the line indicates the end of the
+ sequence.</li>
+
+ <li>
+ Case doesn't matter. Crux Suite converts everything to uppercase.</li>
+
+ <li>
+ White space (spaces and newlines) within the sequence are
+ ignored.</li>
+
+ <li>
+ Characters should be from the amino acid alphabet, which contains
+ twenty characters for amino acids ("ACDEFGHIKLMNPQRSTVWY") and is
+ augmented by four more ambiguous characters ("BUXZ"):</li>
+
+ <pre>
+A alanine P proline
+B aspartate or asparagine Q glutamine
+C cystine R arginine
+D aspartate S serine
+E glutamate T threonine
+F phenylalanine U any
+G glycine V valine
+H histidine W tryptophan
+I isoleucine Y tyrosine
+K lysine Z glutamate or glutamine
+L leucine X any
+M methionine
+N asparagine
+ </pre>
+
+ </ul>
+
+ <p>
+ <a href="sample.fasta">Here</a> is an example of three sequences in
+ FASTA format.</p>
+
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/file-formats/features.html b/doc/user/file-formats/features.html
new file mode 100644
index 0000000..eb81b6a
--- /dev/null
+++ b/doc/user/file-formats/features.html
@@ -0,0 +1,398 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <div id="content">
+ <h2>Features used by percolator and q-ranker</h2>
+
+ <p>
+ Following is a list of the features used by the <span class="code">crux
+ percolator</span> and <span class="code">crux q-ranker</span> commands to represent
+ each peptide-spectrum match (PSM).</p>
+
+
+ <table border="1" align="center" id="featurestable">
+ <tr>
+ <!--table header-->
+ <th>Number</th>
+ <th>Name</th>
+ <th>Type</th>
+ <th>Description</th>
+ <th>Percolator</th>
+ <th>q-ranker</th>
+ <th>barista</th>
+ </tr>
+ <!--tr backgoud(grey)"#DEDEDE"-->
+ <!--check mark : "✓" or "✔, not supported use: -->
+
+ <tr bgcolor="#DEDEDE" >
+ <td>1</td>
+ <td><code>lnrSp</code></td>
+ <td>Float</td>
+ <td>The natural logarithm of the rank of the match
+ based on the Sp score</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr>
+ <td>2</td>
+ <td><code>deltLCn</code></td>
+ <td>Float</td>
+ <td>The difference between this PSM's XCorr and the
+ XCorr of the <i>last-ranked</i> PSM for this spectrum, divided by
+ this PSM's XCorr or 1, whichever is larger.</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE" >
+ <td>3</td>
+ <td><code>deltCn</code></td>
+ <td>Float</td>
+ <td>The difference between this PSM's XCorr and the
+ XCorr of the <i>next-ranked</i> PSM for this spectrum, divided by
+ this PSM's XCorr or 1, whichever is larger.
+ Note that this definition differs from that of the
+ standard delta Cn reported by SEQUEST<sup>®</sup>.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>4</td>
+ <td><code>Xcorr / XCorr Score</code></td>
+ <td>Float</td>
+ <td>The SEQUEST cross-correlation score</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>5</td>
+ <td><code>Sp / Sp score</code></td>
+ <td>Float</td>
+ <td>The preliminary SEQUEST score.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>6</td>
+ <td><code>IonFrac</code></td>
+ <td>Float</td>
+ <td>The fraction of b and y ions theoretical ions matched to the spectrum</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>7</td>
+ <td><code>Mass</code></td>
+ <td>Float</td>
+ <td>The observed mass [M+H]<sup>+</sup></td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>8</td>
+ <td><code>PepLen</code></td>
+ <td>Integer</td>
+ <td>The length of the matched peptide, in residues</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>9-11</td>
+ <td><code>Charge[n]</code></td>
+ <td>Boolean</td>
+ <td>Is this a 1+/2+/3+ charged spectrum?</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>12</td>
+ <td><code>enzN</code></td>
+ <td>Boolean</td>
+ <td>Is the peptide preceded by an enzymatic (tryptic) site?</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>13</td>
+ <td><code>enzC</code></td>
+ <td>Boolean</td>
+ <td>Does the peptide have an enzymatic (tryptic) C-terminus?</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>14</td>
+ <td><code>enzInt</code></td>
+ <td>Integer</td>
+ <td>Number of missed internal enzymatic (tryptic) sites</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>15</td>
+ <td><code>lnNumSP</code></td>
+ <td>Float</td>
+ <td>The natural logarithm of the number of database
+ peptides within the specified precursor range</td>
+ <td>✓</td>
+ <td></td>
+ <td></td>
+ </tr>
+
+ <tr>
+ <td>16</td>
+ <td><code>dM</code></td>
+ <td>Float</td>
+ <td>The difference between the calculated and observed mass</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>17</td>
+ <td><code>absdM</code></td>
+ <td>Float</td>
+ <td>The absolute value of the difference between the calculated and observed mass</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>18</td>
+ <td><code>label</code></td>
+ <td>Boolean</td>
+ <td>Is this decoy or target?</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+
+ <tr bgcolor="#DEDEDE">
+ <td>19</td>
+ <td><code>xcorr rank</code></td>
+ <td>Integer</td>
+ <td>The rank of this PSM when sorted by xcorr</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>20</td>
+ <td><code>Sp rank</code></td>
+ <td>Integer</td>
+ <td>The rank of this PSM when sorted by sp score.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE" >
+ <td>21</td>
+ <td><code>missed cleavage</code></td>
+ <td>Boolean</td>
+ <td>Does the peptide contain one or more missed cleavage sites?</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>22</td>
+ <td><code>number of sequence comparisons</code></td>
+ <td>Integer</td>
+ <td>The number of sequence comparisons</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>23</td>
+ <td><code>delta mass</code></td>
+ <td>Float</td>
+ <td>Difference between measured and calculated mass</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr-->
+
+ <tr>
+ <td>24</td>
+ <td><code>abs(delta mass)</code></td>
+ <td>Float</td>
+ <td>Absolute value of delta mass</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>25</td>
+ <td><code>b ions</code></td>
+ <td>Float</td>
+ <td>The XCorr from the theoretical b-ions.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>26</td>
+ <td><code>y ions</code></td>
+ <td>Float</td>
+ <td>The XCorr from the theoretical y-ions.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>27</td>
+ <td><code>flanking</code></td>
+ <td>Float</td>
+ <td>The XCorr from the flanking peaks</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td><b>Total</b></td>
+ <td> </td>
+ <td> </td>
+ <td></td>
+ <td><b>17</td>
+ <td><b>20</td>
+ <td><b>20</b></td>
+ </tr>
+ </table>
+ </div>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/file-formats/ms2-format.html b/doc/user/file-formats/ms2-format.html
new file mode 100644
index 0000000..a5d385a
--- /dev/null
+++ b/doc/user/file-formats/ms2-format.html
@@ -0,0 +1,283 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>MS2 file format</h2>
+ <p>
+ The MS2 file format is used to record MS/MS spectra.
+ A full description of the MS2 file format may be found in:
+ <cite>
+ McDonald,W.H. et al.
+ MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage
+ of shotgun proteomic spectra and identifications. Rapid Commun. Mass Spectrom.
+ <b>18</b>, 2162-2168 (2004).
+ </cite>
+ </p>
+ <p>
+ An MS2 file consists of a header followed by one or more sets of scan data.
+ The header and scan data are broken into records, one record per line.
+ The fields within a record are separated by white space.
+ The header records list information applicable to all the scans in the file.
+ Each scan begins with a few records describing the parameters for that scan.
+ This is followed by pairs of m/z and intensity values, one pair per line.
+ </p>
+ <p>
+ A sample MS2 file may be found <a href="../example-files/demo.ms2">here</a>.
+ </p>
+ <h3>Header details</h3>
+ <p>
+ Each line in the header must begin with an <code>H</code>.
+ This is followed by a field label, and then a field value,
+ all separated by white space.
+ The field label must be one of the labels listed below,
+ while the field value can be an aribrary string.
+ A typical header is shown below.
+ </p>
+ <pre>
+H CreationDate 2/14/2007 6:19:18 PM
+H Extractor MakeMS2
+H ExtractorVersion 1.0
+H Comments MakeMS2 written by Michael J. MacCoss, 2004
+H ExtractorOptions MS2/MS1
+ </pre>
+ <p>
+ The following field labels must appear in the header:
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Required header field labels</caption>
+ <thead>
+ <tr>
+ <th>Field Label</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>CreationDate</td><td>The date and time when the file was created</td>
+ </tr>
+ <tr>
+ <td>Extractor</td><td>The name of the software used to create the MS2 file</td>
+ </tr>
+ <tr>
+ <td>ExtractorVersion</td><td>The version number of the Extractor software</td>
+ </tr>
+ <tr>
+ <td>ExtractorOptions</td><td>The options used in running the extractor software</td>
+ </tr>
+ </tbody>
+ </table>
+ <p>
+ The following field labels are optional, and may appear in the header:
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Optional header field labels</caption>
+ <thead>
+ <tr>
+ <th>Field Label</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>IAnalyzer</td>
+ <td>Name of software used to conduct charge-state independent analysis of the spectra</td>
+ </tr>
+ <tr>
+ <td>IAnalyzerVersion</td>
+ <td>The version number of the IAnalyzer software</td>
+ </tr>
+ <tr>
+ <td>IAnalyzerOptions</td>
+ <td>The options used in running the IAnalyzer software</td>
+ </tr>
+ <tr>
+ <td>DAnalyzer</td>
+ <td>Name of software used to conduct charge-state dependent analysis of the spectra</td>
+ </tr>
+ <tr>
+ <td>DAnalyzerVersion</td>
+ <td>The version number of the DAnalyzer software</td>
+ </tr>
+ <tr>
+ <td>DAnalyzerOptions</td>
+ <td>The options used in running the DAnalyzer software</td>
+ </tr>
+ <tr>
+ <td>SortedBy</td>
+ <td>Name of field use to sort spectra<td>
+ </tr>
+ <tr>
+ <td>InstrumentType</td>
+ <td>The type of mass analyzer used<td>
+ </tr>
+ <tr>
+ <td>Comment</td>
+ <td>Remarks. Multiple comment lines are allowed<td>
+ </tr>
+ <tr>
+ <td>InstrumentSN</td>
+ <td>Serial number of the mass spectrometer used<td>
+ </tr>
+ </tbody>
+ </table>
+ <h3>Scan details</h3>
+ <p>
+ Each scan begins with a few records listing the parameters describing the spectrum.
+ These lines must begin with S, I, Z, or D.
+ The records are followed by pairs of m/z and intensity values, one pair per line.
+ A fragment of a typical scan is shown below.
+ </p>
+ <pre>
+S 10 10 636.34
+Z 2 1271.67
+187.4 12.5
+193.1 19.5
+194.3 13.7
+198.3 29.8
+199.1 12.2
+ </pre>
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Record types for scans</caption>
+ <thead>
+ <tr>
+ <th>Symbol</th>
+ <th>Description</th>
+ <th>Generic form</th>
+ <th>Required</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>S</td>
+ <td>scan</td>
+ <td><code>S [first scan] [second scan] [pre m/z]</code></td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>I</td>
+ <td>Charge independent analysis</td>
+ <td><code>I [field label] [field value]</code></td>
+ <td>no</td>
+ </tr>
+ <tr>
+ <td>Z</td>
+ <td>Charge</td>
+ <td><code>I [charge] [mass]</code></td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>D</td>
+ <td>Charge dependent analysis</td>
+ <td><code>I [field label] [field value]</code></td>
+ <td>no</td>
+ </tr>
+ <tr>
+ <td>[data]</td>
+ <td>m/z intensity paris</td>
+ <td><code>[m/z] [intensity]</code></td>
+ <td>yes</td>
+ </tr>
+ </tbody>
+ </table>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/file-formats/parameter-file.html b/doc/user/file-formats/parameter-file.html
new file mode 100644
index 0000000..6c4fe1d
--- /dev/null
+++ b/doc/user/file-formats/parameter-file.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Crux parameter files</h2>
+
+ <b>Description:</b>
+ <p>A file containing parameters and their arguments passed to a crux
+ program to control various aspects of execution. Every command-line
+ option and many additional options can be read from a parameter
+ file. If an option is specified in a file and on the command line,
+ the command line value will be used.
+ </p>
+
+ <b>Usage:</b>
+ <p><span class="code"><program name> --parameter-file <file name> [<argument>+]</span></p>
+
+ <b>Format:</b>
+ <p>The parameter file can contain parameter lines, comment lines and
+ blank lines. Parameter lines are name-value pairs separated by an
+ equal sign, '=' with no spaces in between. Comment lines must begin
+ with '#'. Blank lines should contain no spaces or tabs before the newline.
+ </p>
+
+ <p>
+ <a href="../commands/default.params">Here</a> is a sample parameter file
+ containing the default values for every parameter/option available to
+ all crux programs.</p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/file-formats/sample.fasta b/doc/user/file-formats/sample.fasta
new file mode 100644
index 0000000..1f51f20
--- /dev/null
+++ b/doc/user/file-formats/sample.fasta
@@ -0,0 +1,17 @@
+>ICYA_MANSE
+GDIFYPGYCPDVKPVNDFDLSAFAGAWHEIAKLPLENENQGKCTIAEYKY
+DGKKASVYNSFVSNGVKEYMEGDLEIAPDAKYTKQGKYVMTFKFGQRVVN
+LVPWVLATDYKNYAINYNCDYHPDKKAHSIHAWILSKSKVLEGNTKEVVD
+NVLKTFSHLIDASKFISNDFSEAACQYSTTYSLTGPDRH
+
+>LACB_BOVIN
+MKCLLLALALTCGAQALIVTQTMKGLDIQKVAGTWYSLAMAASDISLLDA
+QSAPLRVYVEELKPTPEGDLEILLQKWENGECAQKKIIAEKTKIPAVFKI
+DALNENKVLVLDTDYKKYLLFCMENSAEPEQSLACQCLVRTPEVDDEALE
+KFDKALKALPMHIRLSFNPTQLEEQCHI
+
+>BBP_PIEBR
+NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPE
+GKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFN
+VLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLI
+GSPVVDSQKLVYSDFSEAACKVN
diff --git a/doc/user/file-formats/sqt-format.html b/doc/user/file-formats/sqt-format.html
new file mode 100644
index 0000000..1540f6d
--- /dev/null
+++ b/doc/user/file-formats/sqt-format.html
@@ -0,0 +1,329 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
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+
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+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>SQT file format</h2>
+ <p>
+ The SQT file format is used to record the matches between MS/MS spectra
+ and a sequence database.
+ A full description of the SQT file format may be found in:</p>
+
+ McDonald, W.H. et al.
+ <a href="http://onlinelibrary.wiley.com/doi/10.1002/rcm.1603/abstract">"MS1, MS2, and SQT-three unified, compact, and easily parsed file formats for the storage
+ of shotgun proteomic spectra and identifications."</a> <i>Rapid
+ Communications in Mass Spectrometry.</i> <b>18</b>, 2162-2168 (2004).
+ </blockquote>
+
+ <p>
+ An SQT file consists of a header followed by one or more spectrum matches.
+ The header and match data are broken into records, one record per line.
+ Fields within a record are separated by white space.
+ </p>
+ <p>
+ A sample SQT file may be found <a href="../example-files/target.sqt">here</a>.
+ </p>
+
+ <h3>Header details</h3>
+ <p>
+ Each line in the header must begin with an <code>H</code>.
+ This is followed by a field label, and then a field value,
+ all separated by white space.
+ The field label must be one of the labels listed below,
+ while the field value can be an aribrary string.
+ A typical header is shown below.
+ </p>
+ <pre>
+H SQTGenerator Crux
+H SQTGeneratorVersion 1.0
+H Comment Crux was written by...
+H Comment ref...
+H StartTime Tue Dec 2 15:22:50 2008
+H EndTime
+H Database test_crux_index/test-binary-fasta
+H DBSeqLength ?
+H DBLocusCount 4
+H PrecursorMasses average
+H FragmentMasses mono
+H Alg-PreMasTol 3.0
+H Alg-FragMassTol 0.50
+H Alg-XCorrMode 0
+H Comment preliminary algorithm sp
+H Comment final algorithm xcorr
+H StaticMod C=160.139
+H Alg-DisplayTop 5
+H EnzymeSpec tryptic
+ </pre>
+ <p>
+ The following field labels must appear in the header:
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Required header field labels</caption>
+ <thead>
+ <tr>
+ <th>Field Label</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>SQTGenerator</td><td>The name of the software used to create the SQT file</td>
+ </tr>
+ <tr>
+ <td>SQTGeneratorVersion</td><td>The version number of the SQTGenerator software</td>
+ </tr>
+ <tr>
+ <td>Database</td><td>Path to sequence database used to generate the SQT file</td>
+ </tr>
+ <tr>
+ <td>FragmentMasses</td>
+ <td>Were average or mono-istopic residue masses used to predict the fragment ion mass</td>
+ </tr>
+ <tr>
+ <td>PrecursorMasses</td>
+ <td>Were average or mono-istopic residue masses used to predict the precursor ion mass</td>
+ </tr>
+ <tr>
+ <td>StartTime</td><td>Time when SQT file was created</td>
+ </tr>
+ <tr>
+ <td>StaticMod</td>
+ <td>Non-standard amino-acid masses used in identification
+ (repeat this record if there are multiple non-standard masses)</td>
+ </tr>
+ <tr>
+ <td>DynamicMod</td>
+ <td>List of dynamic modifications used in identification</td>
+ </tr>
+ </tbody>
+ </table>
+ <p>
+ The following field labels are optional, and may appear in the header:
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Optional header field labels</caption>
+ <thead>
+ <tr>
+ <th>Field Label</th>
+ <th>Description</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>Comment</td>
+ <td>Remarks. Multiple comment lines are allowed<td>
+ </tr>
+ <tr>
+ <td>DBSeqLength</td>
+ <td>Number of aminio acids in sequence database</td>
+ </tr>
+ <tr>
+ <td>DBLocusCount</td>
+ <td>Number of proteins in sequence database</td>
+ </tr>
+ <tr>
+ <td>DBMD5Sum</td>
+ <td>MD5 checksum of sequence database</td>
+ </tr>
+ <tr>
+ <td>SortedBy</td>
+ <td>Name of field use to sort spectra<td>
+ </tr>
+ <tr>
+ <td>Alg-</td>
+ <td>Field names begining with Alg- are algorithm specific<td>
+ </tr>
+ <tr>
+ <td>*</td>
+ <td>Other field names are allowed, but may not contain white-space<td>
+ </tr>
+ </tbody>
+ </table>
+
+ <h3>Match details</h3>
+ <p>
+ Each spectrum match begins with a spectrum (S) record,
+ each S record is followed by one or more match (M) records,
+ and each M record is followed by one or more Locus (L) records.
+ The S record contains the scan number and other details for the spectum,
+ the M records contains the highest scoring peptide matches for the parent spectrum,
+ and the L records give the names of proteins containing the parent match peptide.
+ </p>
+ <pre>
+S 45894 45894 2 1 maccoss007 2038.59 9199.5 147.1 153628
+M 1 27 2040.244 0.0000 1.5881 245.6 11 34 V.YKCAADKQDATVVELTNL.T U
+L YCR102C
+M 2 68 2038.265 0.0116 1.5698 208.4 11 36 S.TQSGIVAEQALLHSLNENL.S U
+L YGR080W
+M 3 34 2039.247 0.1582 1.3369 239.3 11 36 I.NEKTSPALVIPTPDAENEI.S U
+L YLR035C
+M 4 322 2040.365 0.1699 1.3183 160.0 9 36 I.LKESKSVQPGKAIPDIIES.P U
+L YJL126W
+M 5 74 2039.453 0.2288 1.2248 203.6 10 32 D.MISVDLKTPLVIFKCHH.G U
+L YAL002W
+M 65 1 2041.246 0.4179 0.9245 370.2 13 32 S.CCGLSLPGLHDLLRHYE.E U
+L YLR403W
+S 45904 45904 3 1 maccoss007 2834.54 10103.7 246.4 152668
+M 1 237 2833.059 0.0000 1.9175 273.1 20 108 N.NSGSDTVDPLAGLNNLRNSIKSAGNGME.N U
+L YDR505C
+M 2 223 2834.278 0.1390 1.6510 274.8 18 96 G.HLSRISNIDDILISMRMDAFDSLIG.Y U
+L YLR247C
+M 3 52 2835.100 0.1503 1.6292 324.1 20 96 S.KSTTEPIQLNNKHDLHLGQELTEST.V U
+L YDR098C-B
+L YDR365W-B
+L YER138C
+L YGR027W-B
+ </pre>
+ </p>
+ <table style="text-align: left;">
+ <caption style="text-align: left;">Record types for scans</caption>
+ <thead>
+ <tr>
+ <th>Symbol</th>
+ <th>Description</th>
+ <th>Generic form</th>
+ <th>Required</th>
+ </tr>
+ </thead>
+ <tbody>
+ <tr>
+ <td>S</td>
+ <td>Spectrum</td>
+ <td><code>S [low scan] [high scan] [charge] [process time]
+ <br />
+ [server] [experimental neutral mass] [total ion intensity] [lowest Sp] [# of seq. matched]
+ </code></td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>M</td>
+ <td>Match</td>
+ <td><code>M [rank by Xcorr] [rank by Sp] [calculated mass]
+ <br />
+ [DeltaCN] [Xcorr] [Sp] [matched ions] [expected ions] [sequence matched]
+ <br />
+ [validation status U = unknown, Y = yes, N = no, M = Maybe]
+ </code></td>
+ <td>yes</td>
+ </tr>
+ <tr>
+ <td>L</td>
+ <td>Locus</td>
+ <td><code>L [locus name] [description if available]</code></td>
+ <td>yes</td>
+ </tr>
+ </tbody>
+ </table>
+
+ <h3>Differences between Crux's SQT format and the published
+ version</h3>
+
+ <ul>
+ <li>
+ Relative to the original specification of SQT, Crux expects an
+ additional field [total ion intensity] in the "S" lines.</li>
+ <li>
+ In the original specification, the FragmentMasses and PrecursorMasses
+ header lines used the values "AVG" or "MONO", but Crux uses "average"
+ and "mono".</li>
+ </ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/file-formats/txt-format.html b/doc/user/file-formats/txt-format.html
new file mode 100644
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--- /dev/null
+++ b/doc/user/file-formats/txt-format.html
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+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Tab-delimited File Format</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
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+ menu.slideToggle();
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+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
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+ }
+ });
+ });
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+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Tab-delimited file format</h2>
+ <p>
+ Various programs in Crux report their output and read inputs in tab-delimited text format. Each such file consists of a single line containing the tab-separated names of fields, followed by one or more lines giving the corresponding field values.
+ </p>
+ <table border="1" id="tabformat">
+ <!-- table headers-->
+ <tr>
+ <th rowspan="2">Name</th>
+ <th rowspan="2">Description</th>
+ <th rowspan="2">comet</th>
+ <th rowspan="2">tide</th>
+ <th rowspan="2">cascade-search</th>
+ <th rowspan="2">search-for-xlinks</th>
+ <th rowspan="2">search-for-xlinks (new)</th>
+ <th colspan="4">barista</th>
+ <th rowspan="2">q-ranker</th>
+ <th colspan="3">percolator</th>
+ <th rowspan="2">spectral-counts</th>
+ </tr>
+
+ <tr>
+ <!--barista-->
+ <th>PSM</th>
+ <th>peptides</th>
+ <th>proteins</th>
+ <th>sub-proteins</th>
+ <!--percolator-->
+ <th>PSM</th>
+ <th>peptides</th>
+ <th>proteins</th>
+ </tr>
+
+ <!--"✓"= "✓" or "✔"-->
+ <!--"✕"= "✕" or "✖"-->
+ <!--"–"=–-->
+
+ <tr bgcolor="#DEDEDE">
+ <td>file</td>
+ <td>The name of the file containing the scan.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>fileidx</td>
+ <td>The integer index of the file containing the scan.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>scan</td>
+ <td>The identifying number of each scan.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>charge</td>
+ <td>The charge state for this spectrum in this PSM.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>spectrum precursor m/z</td>
+ <td>The observed m/z of the spectrum precursor ion.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>spectrum neutral mass</td>
+ <td>The computed mass of the spectrum precursor at the given charge state. This is equal to the precursor m/z minus the mass of a proton (1.00727646677 Da), all multiplied by the charge.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>peptide mass</td>
+ <td>The mass of the peptide sequence, computed as the sum of the the amino acid masses plus the mass of water (18.010564684 Da or 18.0153 Da, depending on whether we are using monoisotopic or average mass).</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>delta_cn</td>
+ <td>The normalized difference in XCorr for this PSM
+ relative to the next ranked PSM for the same spectrum
+ and charge. The denominator for normalization is the
+ minimum of the current XCorr and 1.0.
+ If <code>exact-p-value=T</code>, then the difference
+ is computed between -log(p-value) rather than XCorr,
+ and no normalization is applied.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>delta_lcn</td>
+ <td>Similar to delta_cn, except that the difference
+ is computed with respect to the lowest reported XCorr
+ score for a given spectrum and charge state.</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>sp score</td>
+ <td>The SEQUEST-type preliminary score.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>sp rank</td>
+ <td>The rank of this PSM when sorted by Sp score. Note that,
+ in <code>tide-search</code>, the Sp score is only computed for PSMs
+ that are reported to the user. Hence, the rank of the Sp score
+ will be in the range from 1 to <i>n</i>, where the value
+ of <i>n</i> is determined by the <code>--top-match</code> parameter.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>xcorr score</td>
+ <td>The SEQUEST-type cross correlation score.
+ This column only appears when <code>exact-p-value=F</code>.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>exact p-value</td>
+ <td>The p-value computed as described in
+ <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">"Computing Exact p-values
+ for a Cross-correlation Shotgun Proteomics Score Function"</a>.
+ This column only appears when <code>exact-p-value=T</code>.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>refactored xcorr</td>
+ <td>A discretized version of XCorr, used to compute the p-value.
+ This column only appears when <code>exact-p-value=T</code>.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>xcorr rank</td>
+ <td>The rank of this PSM when sorted by xcorr.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>p-value</td>
+ <td>The p-value computed from the estimated Weibull parameters of the score distribution for this spectrum.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>percolator score</td>
+ <td>The discriminant score assigned by percolator.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>percolator q-value</td>
+ <td>The q-value assigned by percolator.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>percolator PEP</td>
+ <td>The posterior error probability assigned by percolator.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>q-ranker score</td>
+ <td>The discriminant score assigned by q-ranker.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>q-ranker q-value</td>
+ <td>The q-value assigned by q-ranker.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>q-ranker PEP</td>
+ <td>The posterior error probability estimated from the q-ranker score</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>barista score</td>
+ <td>The discriminant score assigned by barista.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>barista q-value</td>
+ <td>The q-value assigned by barista.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>barista PEP</td>
+ <td>The PEP assigned by barista</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>b/y ions matched</td>
+ <td>The number of b-ions and y-ions in the peptide that have a corresponding peak in the spectrum.</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>b/y ions total</td>
+ <td>The total number of b- and y-ions predicted for this peptide.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>total matches/spectrum</td>
+ <td>The number of candidate peptides in the database found for this
+ spectrum, including duplicates. Note that this is always the number of target candidate
+ peptides, even if the PSM involves a decoy peptide.</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>distinct matches/spectrum</td>
+ <td>The number of unique candidate peptides in the database found for this
+ spectrum. Note that this is always the number of target candidate
+ peptides, even if the PSM involves a decoy peptide.</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+
+ <tr>
+ <td>sequence</td>
+ <td>The peptide sequence, not including any modifications.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>modified sequence</td>
+ <td>The peptide sequence, with modifications included.</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>modifications</td>
+ <!-- This description needs to be expanded considerably. -->
+ <td>Variable modifications applied to the sequence.</td>
+ <td></td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>cleavage type</td>
+ <td>The cleavage rules for generating this peptide based on the user-specified enzyme specificity.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>protein id</td>
+ <td>A comma-separated list of proteins in which this peptide
+ appears. Optionally, the protein name may be followed by a number in parentheses giving the start position of the peptide in the protein.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>flanking aa</td>
+ <td>The amino acids that precede and follow this
+ peptide in the parent protein ID. If the peptide
+ occurs in more than one protein, then this column
+ will contain a comma-separated list of pairs of amino
+ acids.</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>original target sequence</td>
+ <td>The unmodified target sequence. For a target PSM,
+ the value in this column will be identical to the
+ value in the "sequence" column. For a decoy PSM,
+ this column will contain the corresponding target
+ sequence.</td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>RAW</td>
+ <td>The raw (unnormalized) count of spectra per peptide</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>SIN</td>
+ <td>A protein quantification score</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>NSAF</td>
+ <td>The normalized spectral abundace factor</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td>dNSAF</td>
+ <td>The distributed normalized spectral abundace factor</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>EMPAI</td>
+ <td>The exponentially modified protein abundance index</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr>
+ <td> parsimony rank</td>
+ <td>The protein rank based on its spectral-counts score.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>psm_id</td>
+ <td>PSM identifier.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>protein group number</td>
+ <td>Protein group index</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>peptides-scan.charge</td>
+ <td>Peptides belonging to each protein in the group, with scan and charge (for example, EAMPK-001285.2)</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>proteins</td>
+ <td>Proteins in the protein group. Each protein can be followed by peptides in parenthesis, if they belong only to this particular protein in the group. Since peptides are considered indistinguishable if they have identical amino acid sequences or they differ only by I/L or T/S in the same position in the peptide, the peptides shared by the group may not all be identical.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>parent group numbers</td>
+ <td>The numbers of the protein groups in the barista.target.proteins.txt that are supersets of this group in terms of peptides.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>peptide mass mono</td>
+ <td>Monoisotopic peptide mass</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>peptide mass average</td>
+ <td>Average peptide mass</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>mass error(ppm)</td>
+ <td>The mass error (in ppm) between the observed precursor mass and the
+ cross-link peptide product</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>protein id(loc)</td>
+ <td>List of protein IDs that give rise to the first and second peptide in the
+ cross-link peptide product. (loc) indicates the location of the
+ peptide in the protein. The ";" separates the protein ids from the
+ first and second peptide.</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>protein id(loc) 1</td>
+ <td>List of protein IDs that give rise to the first peptide in the
+ cross-link peptide product. (loc) indicates the location of the
+ peptide in the protein</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>protein id(loc) 2</td>
+ <td>List of protein IDs that give rise to the second peptide in the
+ cross-link peptide product. (loc) indicates the location of the
+ peptide in the protein</td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>by total</td>
+ <td>Total number of b-y ions in product</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>by observable (0-1200)</td>
+ <td>Total number of b and y ions observable in the 0-1200 m/z range</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>by observable bin (0-1200)</td>
+ <td>Total number of b and y ions observable in the 0-1200 m/z range
+ using 1 Da bins</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>by observable (0-max)</td>
+ <td>Total number of b and y ions observable in the entire m/z range</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>by observable bin (0-max)</td>
+ <td>Total number of b and y ions observable in the entire m/z range
+ using 1 Da bins</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>by observed bin</td>
+ <td>Total number of b-y ions observed in spectrum</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>ion current total</td>
+ <td>Total ion current for spectrum</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr bgcolor="#DEDEDE">
+ <td>ion current observed</td>
+ <td>Total ion current observed for matching b-y ions</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>ions observable bin (0-1200)</td>
+ <td>Total ions observable (b, y, flanks, and neutral losses) within 0-1200 m/z range</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>✓</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ </table>
+<!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/fileformats.html b/doc/user/fileformats.html
new file mode 100644
index 0000000..51aaf71
--- /dev/null
+++ b/doc/user/fileformats.html
@@ -0,0 +1,387 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux File Formats</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <div id="content">
+ <h2>File formats</h2>
+
+ <table id="fileFormatsTable">
+ <tr>
+ <td> </td>
+ <td>bullseye</td>
+ <td>tide-index</td>
+ <td>tide-search</td>
+ <td>comet</td>
+ <td>percolator</td>
+ <td>q-ranker</td>
+ <td>barista</td>
+ <td>search-for-xlinks</td>
+ <td>spectral-counts</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/ms2-format.html">MS1</a>
+ </td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/ms2-format.html">MS2</a>
+ (<a href="example-files/demo.ms2">sample</a>) / CMS2
+ </td>
+ <td>in/out</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://www.matrixscience.com/help/data_file_help.html">MGF</a>
+ </td>
+ <td>in/out</td>
+ <td> </td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://www.psidev.info/mzml_1_0_0">mzML</a>,
+ <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML">mzXML</a>
+ </td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ Thermo .raw files
+ (Windows only)
+ </td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://proteowizard.sourceforge.net/formats.shtml">Other
+ proprietary vendor formats</a> (Windows only)
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/fasta-format.html">FASTA</a>
+ (<a href="file-formats/sample.fasta">sample</a>)
+ </td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>in</td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ database index
+ </td>
+ <td> </td>
+ <td>out</td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/txt-format.html">Tab-delimited text</a>
+ (<a href="example-files/search.target.txt">sample</a>)
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td>out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>out</td>
+ <td>in/out</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">
+ pepXML</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td>out</td>
+ <td>in/out</td>
+ <td>out</td>
+ <td>out</td>
+ <td> </td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="https://github.com/percolator/percolator/wiki/Interface">PIN</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td> </td>
+ <td>in</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="https://github.com/percolator/percolator/wiki/Interface">POUT</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="http://www.psidev.info/mzidentml">mzIdentML</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td>out</td>
+ <td>out</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/sqt-format.html">SQT</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td>out</td>
+ <td>in</td>
+ <td>in</td>
+ <td>in</td>
+ <td> </td>
+ <td>in</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/features.html">Feature file</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>in/out</td>
+ <td>out</td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/barista-xml-format.html">Barista XML</a>
+ </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td> </td>
+ <td>out</td>
+ <td> </td>
+ <td> </td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="file-formats/parameter-file.html">Crux parameters</a>
+ (<a href="example-files/default.params">sample</a>)
+ </td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ <td>in/out</td>
+ </tr>
+
+ </table>
+ </div>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/generate-peptides.html b/doc/user/generate-peptides.html
new file mode 100644
index 0000000..dc0ec41
--- /dev/null
+++ b/doc/user/generate-peptides.html
@@ -0,0 +1,166 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>generate-peptides</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>generate-peptides</h1>
+<h2>Usage:</h2>
+<p><code>crux generate-peptides [options] <protein fasta file></code></p>
+<h2>Description:</h2>
+<p>This command takes as input a protein FASTA file and outputs the corresponding list of peptides, as well as a matched list of decoy peptides and decoy proteins. Decoys are generated either by reversing or shuffling the non-terminal amino acids of each peptide. The program will shuffle each peptide multiple times to attempt to ensure that there is no overlap between the target and decoy peptides. For homopolymers, this is not possible. In this case, the occurrence of these target/decoy [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>protein fasta file</code> – The name of the file in FASTA format from which to retrieve proteins.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>generate-peptides.target.txt</code> – A text file containing the target peptides, one per line. Each line has three tab-delimited columns, containing the peptide sequence, the m+h mass of the unmodified peptide, and a comma-delimited list of protein IDs in which the peptide occurs.</li>
+ <li><code>generate-peptides.decoy.txt</code> – A text file containing the decoy peptides, one per line. Each line has three tab-delimited columns, containing the peptide sequence, the m+h mass of the unmodified peptide, and a comma-delimited list of protein IDs in which the peptide occurs. There is a one-to-one correspondence between targets and decoys.</li>
+ <li><code>generate-peptides.proteins.decoy.txt</code> – a FASTA format file containing decoy proteins, in which all of the peptides have been replaced with their shuffled or reversed counterparts. Note that this file will only be created if the enzyme specificity is "full-digest" and no missed cleavages are allowed.</li>
+ <li><code>generate-peptides.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>generate-peptides.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Peptide properties</h3>
+<ul>
+ <li class="nobullet"><code>--min-mass <float></code> – The minimum mass (in Da) of peptides to consider. Default = <code>200</code>.</li>
+ <li class="nobullet"><code>--max-mass <float></code> – The maximum mass (in Da) of peptides to consider. Default = <code>7200</code>.</li>
+ <li class="nobullet"><code>--min-length <integer></code> – The minimum length of peptides to consider. Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--max-length <integer></code> – The maximum length of peptides to consider. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--isotopic-mass average|mono</code> – Specify the type of isotopic masses to use when calculating the peptide mass. Default = <code>mono</code>.</li>
+ <li class="nobullet"><code>--clip-nterm-methionine T|F</code> – When set to T, for each protein that begins with methionine, tide-index will put two copies of the leading peptide into the index, with and without the N-terminal methionine. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Decoy database generation</h3>
+<ul>
+ <li class="nobullet"><code>--seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--decoy-format none|shuffle|peptide-reverse|protein-reverse</code> – Include a decoy version of every peptide by shuffling or reversing the target sequence or protein. In shuffle or peptide-reverse mode, each peptide is either reversed or shuffled, leaving the N-terminal and C-terminal amino acids in place. Note that peptides appear multiple times in the target database are only shuffled once. In peptide-reverse mode, palindromic peptides are shuffled. [...]
+ <li class="nobullet"><code>--keep-terminal-aminos N|C|NC|none</code> – When creating decoy peptides using decoy-format=shuffle or decoy-format=peptide-reverse, this option specifies whether the N-terminal and C-terminal amino acids are kept in place or allowed to be shuffled or reversed. For a target peptide "EAMPK" with decoy-format=peptide-reverse, setting keep-terminal-aminos to "NC" will yield "EPMAK"; setting it to "C" will yield "PMAEK"; setting it to "N" will yield "EKPMA" [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+ <li class="nobullet"><code>--custom-enzyme <string></code> – Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. If the residues are required for digestion, they are in square brackets, '[' and ']'. If the re [...]
+ <li class="nobullet"><code>--digestion full-digest|partial-digest|non-specific-digest</code> – Specify whether every peptide in the database must have two enzymatic termini (full-digest) or if peptides with only one enzymatic terminus are also included (partial-digest). Default = <code>full-digest</code>.</li>
+ <li class="nobullet"><code>--missed-cleavages <integer></code> – Maximum number of missed cleavages per peptide to allow in enzymatic digestion. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/get-ms2-spectrum.html b/doc/user/get-ms2-spectrum.html
new file mode 100644
index 0000000..a42c4a8
--- /dev/null
+++ b/doc/user/get-ms2-spectrum.html
@@ -0,0 +1,143 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>get-ms2-spectrum</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>get-ms2-spectrum</h1>
+<h2>Usage:</h2>
+<p><code>crux get-ms2-spectrum [options] <ms2 file></code></p>
+<h2>Description:</h2>
+<p>Extract one or more MS-MS spectra from an MS2 file by scan number. Optionally output summary statistics for each spectrum.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – the requested spectrum or spectra in MS2 format.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>get-ms2-spectrum options</h3>
+<ul>
+ <li class="nobullet"><code>--stats T|F</code> – Rather than the spectrum, output summary statistics to standard output. Each statistic is placed on a separate line, in the format <name>:<value> (e.g. "TIC:1000.0").<br>The following statistics are reported for the entire spectrum:<ul><li>Precursor m/z</li><li>Total Ion Current</li><li>Base Peak Intensity</li><li>Number of peaks</li><li>Minimum m/z</li><li>Maximum m/z</li></ul>In addition, for each possible spectrum charge state, t [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/glossary.html b/doc/user/glossary.html
new file mode 100644
index 0000000..998f042
--- /dev/null
+++ b/doc/user/glossary.html
@@ -0,0 +1,165 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux glossary</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Crux glossary</h2>
+
+ <h3>Mass spectrometry terminology</h3>
+
+ <ul>
+
+ <li><b>c-term peptide</b>: The last peptide in the protein,
+ occurring at the c-terminal end of the protein.</li>
+
+ <li><b>decoy peptide</b>: A shuffled, reversed or randomly
+ generated peptide sequence. Matches to decoy peptides are used
+ for two purposes: to estimate statistical confidence measures
+ such as the false discovery rate, and to train machine learning
+ methods to recognize correctly identified spectra.</li>
+
+ <li><b>modification</b>: A chemical modification of a single amino
+ acid, typically corresponding to the addition of a molecular
+ group to the amino acid side chain.</li>
+
+ <li><b>n-term peptide</b>: The first peptide in the protein,
+ occurring at the n-terminal end of the protein.</li>
+
+ <li><b>peptide</b>: A subsequence of a protein.</li>
+
+ <li><b>peptide-spectrum match (PSM)</b>: An observed spectrum
+ paired with a peptide sequence, along with a score quantifying
+ the quality of the match.</li>
+
+ <li><b>static modification</b>: A chemical modification of a
+ single amino that is expected to occur on every instance of that
+ amino acid. A common example is carbamidomethylation of
+ cysteine, which adds 57.02146 Da to the mass of every
+ cysteine.</li>
+
+ <li><b>target peptide</b>: A real peptide, usually drawn from a
+ protein database.</li>
+
+ <li><b>trypsin</b>: An enzyme used to cleave a protein into
+ peptides.</li>
+
+ <li><b>variable modification</b>: A chemical modification of a
+ single amino that is expected to occur on some instances of that
+ amino acid but not others. A common example is phosphorylation
+ of serine, threonine or tyrosine, which adds a mass of 79.966331
+ Da to each of those amino acids.</li>
+
+ </ul>
+
+ <h3>Analysis terminology</h3>
+
+ <ul>
+
+ <li><b>false discovery rate (FDR)</b>: Estimated proportion of
+ incorrectly identifications among a set of PSMs, peptides or
+ proteins.</li>
+
+ <li><b>support vector machine (SVM)</b>: A machine learning method
+ that learns to classify data objects into two groups.</li>
+
+ </ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/hardklor.html b/doc/user/hardklor.html
new file mode 100644
index 0000000..fc8f219
--- /dev/null
+++ b/doc/user/hardklor.html
@@ -0,0 +1,168 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>hardklor</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>hardklor</h1>
+<h2>Usage:</h2>
+<p><code>crux hardklor [options] <spectra></code></p>
+<h2>Description:</h2>
+<p>Hardklör analyzes high-resolution mass spectra, identifying protein or peptide isotope distributions and determining the corresponding monoisotopic masses and charge states. The algorithm aims to identify persistence peptide isotope distribution (PPIDs), i.e., isotope distributions that recur over multiple scans. Hardklör is specifically designed to handle overlapping isotope distributions in a single spectrum. A detailed description of the Hardklör algorithm is given i [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>spectra</code> – The name of a file from which to parse high-resolution spectra. The file may be in MS1 (.ms1), binary MS1 (.bms1), compressed MS1 (.cms1), or mzXML (.mzXML) format.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>hardklor.mono.txt</code> – a tab-delimited text file containing one line for each isotope distribution. The columns appear in the following order:<ol><li><strong>scan</strong>: The scan number assigned to this spectrum in the input file.</li><li><strong>retention time</strong>: The time (in seconds) at which the spectrum was collected.</li><li><strong>mass</strong>: The uncharged monoisotopic mass of the protein or peptide.</li><li><strong>charge</strong>: The inferred [...]
+ <li><code>hardklor.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>hardklor.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>hardklor options</h3>
+<ul>
+ <li class="nobullet"><code>--hardklor-algorithm basic|version1|version2</code> – Determines which spectral feature detection algorithm to use. Different results are possible with each algorithm, and there are pros and cons to each. There are three algorithms to choose from:<ul><li>basic – Performs unoptimized deconvolution and is provided for legacy purposes only.</li><li>version1 – Uses the optimizations developed during the 1.0+ series. It is very accurate, but has [...]
+ <li class="nobullet"><code>--averagine-mod <string></code> – Defines alternative averagine models in the analysis that incorporate additional atoms and/or isotopic enrichments. Modifications are represented as text strings. Inclusion of additional atoms in the model is done using by entering an atomic formula, such as: PO2 or Cl. Inclusion of isotopic enrichment to the model is done by specifying the percent enrichment (as a decimal) followed by the atom being enriched and [...]
+ <li class="nobullet"><code>--boxcar-averaging <integer></code> – Boxcar averaging is a sliding window that averages n adjacent spectra prior to feature detection. Averaging generally improves the signal-to-noise ratio of features in the spectra, as well as improving the shape of isotopic envelopes. However, averaging will also change the observed peak intensities. Averaging with too wide a window will increase the occurrence of overlapping features and broaden the chromatog [...]
+ <li class="nobullet"><code>--boxcar-filter <integer></code> – This parameter is only functional when boxcar-averaging is used. The filter will remove any peaks not seen in n scans in the boxcar window. The effect is to reduce peak accumulation due to noise and reduce chromatographic broadening of peaks. Caution should be used as over-filtering can occur. The suggested number of scans to set for filtering should be equal to or less than the boxcar-averaging window size. A va [...]
+ <li class="nobullet"><code>--boxcar-filter-ppm <float></code> – This parameter is only functional when boxcar-filter is used. The value specifies the mass tolerance in ppm for declaring a peak the same prior to filtering across all scans in the boxcar window. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--centroided T|F</code> – Indicates whether the data contain profile or centroided peaks. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--cdm B|F|P|Q|S</code> – Choose the charge state determination method. There are five methods to choose from:<ul><li>B – Basic method, assume all charge states are possible.</li><li>F – Fast Fourier transform.</li><li>P – Patterson algorithm.</li><li>Q – QuickCharge method, uses inverse peak distances.</li><li>S – Senko method, or combined Fast Fourier Transform and Patterson algorithm.</li></ul> Default = <code>Q</code>.</li>
+ <li class="nobullet"><code>--min-charge <integer></code> – Specifies the minimum charge state to allow when finding spectral features. It is best to set this value to the lowest assumed charge state to be present. If set higher than actual charge states that are present, those features will not be identified or incorrectly assigned a different charge state and mass. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--max-charge <integer></code> – Specifies the maximum charge state to allow when finding spectral features. It is best to set this value to a practical number (i.e. do not set it to 20 when doing a tryptic shotgun analysis). If set higher than actual charge states that are present, the algorithm will perform significantly slower without any improvement in results. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--corr <float></code> – Sets the correlation threshold (cosine similarity) for accepting each predicted feature. Default = <code>0.85</code>.</li>
+ <li class="nobullet"><code>--depth <integer></code> – Sets the depth of combinatorial analysis. For a given set of peaks in a spectrum, search for up to this number of combined peptides that explain the observed peaks. The analysis stops before depth is reached if the current number of deconvolved features explains the observed peaks with a correlation score above the threshold defined with the correlation parameter. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--distribution-area T|F</code> – When reporting each feature, report abundance as the sum of all isotope peaks. The value reported is the estimate of the correct peak heights based on the averagine model scaled to the observed peak heights. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--hardklor-data-file <string></code> – Specifies an ASCII text file that defines symbols for the periodic table. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--instrument fticr|orbitrap|tof|qit</code> – Indicates the type of instrument used to collect data. This parameter, combined with the resolution parameter, define how spectra will be centroided (if you provide profile spectra) and the accuracy when aligning observed peaks to the models. Default = <code>fticr</code>.</li>
+ <li class="nobullet"><code>--isotope-data-file <string></code> – Specifies an ASCII text file that can be read to override the natural isotope abundances for all elements. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--max-features <integer></code> – Specifies the maximum number of models to build for a set of peaks being analyzed. Regardless of the setting, the number of models will never exceed the number of peaks in the current set. However, as many of the low abundance peaks are noise or tail ends of distributions, defining models for them is detrimental to the analysis. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--mzxml-filter <integer></code> – Filters the spectra prior to analysis for the requested MS/MS level. For example, if the data contain MS and MS/MS spectra, setting mzxml-filter = 1 will analyze only the MS scan events. Setting mzxml-filter = 2 will analyze only the MS/MS scan events. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--mz-max <float></code> – Constrains the search in each spectrum to signals below this value in Thomsons. Setting to 0 disables this feature. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--mz-min <float></code> – Constrains the search in each spectrum to signals above this value in Thomsons. Setting to 0 disables this feature. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--mz-window <float></code> – Only used when algorithm = version1. Defines the maximum window size in Thomsons to analyze when deconvolving peaks in a spectrum into features. Default = <code>4</code>.</li>
+ <li class="nobullet"><code>--resolution <float></code> – Specifies the resolution of the instrument at 400 m/z for the data being analyzed. Default = <code>100000</code>.</li>
+ <li class="nobullet"><code>--scan-range-max <integer></code> – Used to restrict analysis to spectra with scan numbers below this parameter value. A value of 0 disables this feature. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--scan-range-min <integer></code> – Used to restrict analysis to spectra with scan numbers above this parameter value. A value of 0 disables this feature. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--sensitivity <integer></code> – Set the sensitivity level. There are four levels: 0 (low), 1 (moderate), 2 (high), and 3 (max). Increasing the sensitivity will increase computation time, but will also yield more isotope distributions. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--signal-to-noise <float></code> – Filters spectra to remove peaks below this signal-to-noise ratio prior to finding features. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--smooth <integer></code> – Uses Savitzky-Golay smoothing on profile peak data prior to centroiding the spectra. This parameter is recommended for low resolution spectra only. Smoothing data causes peak depression and broadening. Only use odd numbers for the degree of smoothing (as it defines a window centered on each data point). Higher values will produce smoother peaks, but with greater depression and broadening. Setting this parameter to 0 dis [...]
+ <li class="nobullet"><code>--sn-window <float></code> – Set the signal-to-noise window length (in m/z). Because noise may be non-uniform across a spectrum, this value adjusts the segment size considered when calculating a signal-over-noise ratio. Default = <code>250</code>.</li>
+ <li class="nobullet"><code>--static-sn T|F</code> – Applies the lowest noise threshold of any sn_window across the entire mass range for a spectrum. Setting this parameter to 0 turns off this feature, and different noise thresholds will be used for each local mass window in a spectrum. Default = <code>true</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
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+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
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+<title>Crux tandem mass spectrometry analysis software</title>
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+ <div id="schematic">
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+ <map name="commands-files" id="schematic_map">
+ <area shape="rect" coords="253,135,349,169" alt="tide-index" href="commands/tide-index.html">
+ <area shape="rect" coords="260,247,342,278" alt="bullseye" href="commands/bullseye.html">
+ <area shape="rect" coords="510,100,612,132" alt="tide-search" href="commands/tide-search.html">
+ <area shape="rect" coords="528,191,595,222" alt="comet" href="commands/comet.html">
+ <area shape="rect" coords="512,281,613,335" alt="search-for-xlinks" href="commands/search-for-xlinks.html">
+ <area shape="rect" coords="776,100,873,132" alt="percolator" href="commands/percolator.html">
+ <area shape="rect" coords="791,160,861,192" alt="barista" href="commands/barista.html">
+ <area shape="rect" coords="783,222,866,252" alt="q-ranker" href="commands/q-ranker.html">
+ <area shape="rect" coords="784,281,867,334" alt="spectral-counts" href="commands/spectral-counts.html">
+ </map>
+ <img src="images/crux-logo.png" style="width:200px; float:left; padding:10px;">
+ <p>The Crux mass spectrometry analysis toolkit is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. The toolkit includes several search engines for both standard and cross-linked database search, as well as a variety of pre- and post-processing engines for assigning high-resolution precursor masses to spectra, assigning statistical confidence estimates to spectra, peptides and proteins, and [...]
+ <br />
+ <span class="indentcitation">Christopher Y. Park, Aaron A. Klammer, Lukas Käll, Michael
+ J. MacCoss and William Stafford
+ Noble. <a href="http://noble.gs.washington.edu/papers/park2008rapid.html">"Rapid
+ and accurate peptide identification from tandem mass spectra."</a>
+ <i>Journal of Proteome Research.</i> 7(7):3022-3027, 2008.</li></span>
+ <br /><br />
+
+ For a more up-to-date description of Crux, please read:<br />
+
+ <span class="indentcitation">Sean McIlwain, Kaipo Tamura, Attila Kertesz-Farkas,
+ Charles E. Grant, Benjamin Diament, Barbara Frewen, J. Jeffry
+ Howbert, Michael R. Hoopmann, Lukas Käll, Jimmy K. Eng, Michael
+ J. MacCoss and William Stafford
+ Noble. <a href="http://pubs.acs.org/doi/abs/10.1021/pr500741y">"Crux:
+ rapid open source protein tandem mass spectrometry
+ analysis."</a> <i>Journal of Proteome Research.</i>
+ 13(10):4488-4491, 2014.</span>
+ </p>
+ </div>
+
+
+ <br />
+ <p/>
+ Crux is provided as a single executable that supports the following
+ commands:</p>
+ <table id="commandstable">
+
+ <tr>
+ <td colspan="2"><b>Primary commands</b></td>
+ </tr>
+
+ <tr>
+ <td><a href="commands/bullseye.html">bullseye</a></td>
+ <td>Assign high resolution precursor m/z values to MS/MS data using the Hardklör algorithm.
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/tide-index.html">tide-index</a></td>
+ <td>
+ Create an index of all peptides in a fasta file, for use in subsequent
+ calls to <code>tide-search</code>.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/tide-search.html">tide-search</a></td>
+ <td>
+ Search a collection of spectra against a sequence database, provided
+ either as a FASTA file or an index, returning a collection of
+ peptide-spectrum matches (PSMs). This is a fast search engine, but it
+ runs most quickly if provided with a peptide index built
+ with <code>tide-index</code>.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/cascade-search.html">cascade-search</a></td>
+ <td>
+ An iterative procedure for incorporating information about peptide
+ groups into the database search and confidence estimation
+ procedure.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/comet.html">comet</a></td>
+ <td>
+ Search a collection of spectra against a sequence database, returning
+ a collection of PSMs. This search engine runs directly on a protein
+ database in FASTA format.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/percolator.html">percolator</a></td>
+ <td>
+ Re-rank and assign confidence estimates to a collection of PSMs using
+ the Percolator algorithm. Optionally, also produce protein rankings
+ using the Fido algorithm.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/q-ranker.html">q-ranker</a></td>
+ <td>
+ Re-rank a collection of PSMs using the Q-ranker algorithm.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/barista.html">barista</a></td>
+ <td>
+ Rank PSMs, peptides and proteins, assigning a confidence measure to each
+ identification.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/search-for-xlinks.html">search-for-xlinks</a></td>
+ <td>
+ Search a collection of spectra against a sequence database, finding
+ cross-linked peptide matches.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/spectral-counts.html">spectral-counts</a></td>
+ <td>
+ Quantify peptides or proteins using one of three spectral counting
+ methods.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/pipeline.html">pipeline</a></td>
+ <td>
+ Given one or more sets of tandem mass spectra as well as a protein
+ database, this command runs a series of Crux tools and reports all of
+ the results in a single output directory.
+ </td></tr>
+
+ <tr>
+ <td colspan="2"><b>Utilities</b></td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/assign-confidence.html">assign-confidence</a></td>
+ <td>
+ Assign statistical confidence measures to each PSM in a given set.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/generate-peptides.html">generate-peptides</a></td>
+ <td>
+ Extract from a given set of protein sequences a list of target and
+ decoy peptides fitting the specified criteria.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/get-ms2-spectrum.html">get-ms2-spectrum</a></td>
+ <td>
+ Extract one or more fragmentation spectra, specified by scan number, from
+ an <code>MS2</code> file.</td>
+ </tr>
+
+ <tr>
+ <td><a href="commands/hardklor.html">hardklör</a></td>
+ <td>Identify isotopic distributions from high-resolution mass spectra.</td>
+ </tr>
+
+ <tr>
+ <td><a href="commands/make-pin.html">make-pin</a></td>
+ <td>Given a set of search results files, generate a pin file for input to
+ <code>crux percolator</code></td>
+ </tr>
+
+ <tr>
+ <td><a href="commands/param-medic.html">param-medic</a></td>
+ <td>Examine the spectra in a file to estimate the best precursor
+ and fragment error tolerances for database search.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/predict-peptide-ions.html">predict-peptide-ions</a></td>
+ <td>
+ Given a peptide and a charge state, predict the m/z values of the
+ resulting fragment ions.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/print-processed-spectra.html">print-processed-spectra</a></td>
+ <td>
+ Process spectra as for scoring xcorr and print the results to a file.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/psm-convert.html">psm-convert</a></td>
+ <td>
+ Convert a file containing peptide-spectrum matches (PSMs) from one
+ format to another.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/subtract-index.html">subtract-index</a></td>
+ <td>Subtract one index file from another, assuming both were generated
+ by tide-index.</td></tr>
+
+ <tr>
+ <td>
+ <a href="commands/xlink-assign-ions.html">xlink-assign-ions</a></td>
+ <td>Given a spectrum and a pair of cross-linked peptides, assign theoretical
+ ion type labels to peaks in the observed spectrum.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/xlink-score-spectrum.html">xlink-score-spectrum</a></td>
+ <td>Takes a defined cross-linked peptide, a spectra file, and a scan number,
+ and will calculate the XCorr score a number of different ways.</td>
+ </tr>
+
+ <tr>
+ <td>
+ version</td>
+ <td>
+ Print the Crux version number to standard output, then exit.</td>
+ </tr>
+
+ <tr>
+ <td colspan="2"><b>Utilities for processing tab-delimited text files</b>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/extract-columns.html">extract-columns</a></td>
+ <td>Print specified columns from a tab-delimited file.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/extract-rows.html">extract-rows</a></td>
+ <td>Print specified rows from a tab-delimited file.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/stat-column.html">stat-column</a></td>
+ <td>Collect summary statistics from a column in a tab-delimited file.</td>
+ </tr>
+
+ <tr>
+ <td>
+ <a href="commands/sort-by-column.html">sort-by-column</a></td>
+ <td>Sort a tab-delimited file by a column.</td>
+ </tr>
+
+ </table>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/make-pin.html b/doc/user/make-pin.html
new file mode 100644
index 0000000..dbf3496
--- /dev/null
+++ b/doc/user/make-pin.html
@@ -0,0 +1,139 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>make-pin</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>make-pin</h1>
+<h2>Usage:</h2>
+<p><code>crux make-pin [options] <target input></code></p>
+<h2>Description:</h2>
+<p>Make-pin is a utility program that combines a collection of target and decoy peptide-spectrum matches (PSMs) into a single file in pin format, according to <a href="https://github.com/percolator/percolator/wiki/Interface">this format</a>. The resulting file can be provided as input to <code><a href="percolator.html">crux percolator</a></code>.</p><p><code>make-pin</code> requires as input two sets of PSMs, one set derived from matching observed spectra against real ("target" [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>target input</code> – One or more files, each containing a collection of peptide-spectrum matches (PSMs) in <a href="../file-formats/txt-format.html">tab-delimited text</a>, <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">PepXML</a>, or <a href="http://www.psidev.info/mzidentml">mzIdentML</a> format. In tab-delimited text format, only the specified score column is required. However if --estimation-method is tdc, then the columns "scan" and [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>make-pin.pin</code> – a tab-delimited file containing the input target and decoy PSMs in pin format. This file can be changed to an absolute path (see --output-file option).</li>
+ <li><code>make-pin.params.txt</code> – a file containing the name and value of all parameters for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>make-pin.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--output-file <string></code> – Path where pin file will be written instead of make-pin.pin. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/mstoolkit.html b/doc/user/mstoolkit.html
new file mode 100644
index 0000000..06696e6
--- /dev/null
+++ b/doc/user/mstoolkit.html
@@ -0,0 +1,129 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>MSToolKit</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>MSToolkit</h2>
+ <p>
+ MSToolkit is a library for handling mass spectrometry data in various file
+ formats. Crux is capable of using MSToolkit to parse spectrum files. The
+ ProteoWizard parser is used by default, but the MSToolkit parser can be used by
+ commands that support the <span class="code">spectrum-parser</span> parameter.
+ </p>
+ <p>
+ The following is a list of spectrum file formats supported by MSToolkit.
+ </p>
+ <ul>
+ <li>MS1/CMS1/BMS1</li>
+ <li><a href="file-formats/ms2-format.html">MS2</a>/CMS2/BMS2</li>
+ <li>ZS</li>
+ <li>UZS</li>
+ <li>MSMAT</li>
+ <li>RAW</li>
+ <li><a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:mzXML">MZXML[.GZ]</a></li>
+ <li>MZ5</li>
+ <li><a href="http://www.psidev.info/mzml_1_0_0">MZML[.GZ]</a></li>
+ <li><a href="http://www.matrixscience.com/help/data_file_help.html">MGF</a> (Mascot Generic Format)</li>
+ <li>SQLITE3</li>
+ <li>PSM</li>
+ </ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/param-medic.html b/doc/user/param-medic.html
new file mode 100644
index 0000000..894cd35
--- /dev/null
+++ b/doc/user/param-medic.html
@@ -0,0 +1,146 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>param-medic</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>param-medic</h1>
+<h2>Usage:</h2>
+<p><code>crux param-medic [options] <spectrum-file>+</code></p>
+<h2>Description:</h2>
+<p>Examine the spectra in a file to estimate the best precursor and fragment error tolerances for database search.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>spectrum-file+</code> – File from which to parse fragmentation spectra.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – the estimated parameter values for precursor mass tolerance (in ppm) and fragment bin size (in Th), as well as the standard deviations of the estimated error distributions for precursor and fragment masses.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/param-table.html b/doc/user/param-table.html
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+++ b/doc/user/param-table.html
@@ -0,0 +1,678 @@
+<!DOCTYPE HTML>
+<html><head><meta charset="UTF-8">
+<title>Crux parameters</title>
+<link href="../crux.css" rel="styleSheet" type="text/css"></head>
+<body><h1>Crux parameters</h1>
+<table border="1" align="center">
+<tr><td> </td><td>assign-confidence</td><td>barista</td><td>cascade-search</td><td>comet</td><td>create-docs</td><td>bullseye</td><td>hardklor</td><td>extract-columns</td><td>extract-rows</td><td>generate-peptides</td><td>get-ms2-spectrum</td><td>make-pin</td><td>param-medic</td><td>percolator</td><td>pipeline</td><td>predict-peptide-ions</td><td>print-processed-spectra</td><td>psm-convert</td><td>q-ranker</td><td>read-tide-index</td><td>search-for-xlinks</td><td>sort-by-column</td> [...]
+<tr bgcolor="#DEDEDE">
+<td>estimation-method</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>decoy-prefix</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>score</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>sidak</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>verbosity</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> [...]
+<tr>
+<td>parameter-file</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>overwrite</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td></tr>
+<tr>
+<td>output-dir</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>list-of-files</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>combine-charge-states</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>combine-modified-peptides</td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>fileroot</td><td>✓</td><td>✓</td><td>✓</td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>enzyme</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>separate-searches</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>pepxml-output</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr>
+<td>txt-output</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>skip-cleanup</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>re-run</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>use-spec-features</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>feature-file-out</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>optimization</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>spectrum-parser</td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>q-value-threshold</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>precursor-window</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>auto-precursor-window</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr>
+<td>precursor-window-type</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>spectrum-min-mz</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr>
+<td>spectrum-max-mz</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>min-peaks</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr>
+<td>spectrum-charge</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>scan-number</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr>
+<td>store-spectra</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>store-index</td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td></tr>
+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<td>variable_mod03</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<td>variable_mod04</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
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+<td>variable_mod05</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>variable_mod06</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>variable_mod07</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>variable_mod08</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>variable_mod09</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>max_variable_mods_in_peptide</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>require_variable_mod</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_Cterm_peptide</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_Nterm_peptide</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_Cterm_protein</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_Nterm_protein</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_A_alanine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_B_user_amino_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_C_cysteine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_D_aspartic_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_E_glutamic_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_F_phenylalanine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_G_glycine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_H_histidine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_I_isoleucine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_J_user_amino_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_K_lysine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_L_leucine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_M_methionine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_N_asparagine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_O_ornithine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_P_proline</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_Q_glutamine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_R_arginine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_S_serine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_T_threonine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_U_selenocysteine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_V_valine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_W_tryptophan</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_X_user_amino_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>add_Y_tyrosine</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>add_Z_user_amino_acid</td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>max-persist</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>exact-match</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>exact-tolerance</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>persist-tolerance</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>gap-tolerance</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>scan-tolerance</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>bullseye-max-mass</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>bullseye-min-mass</td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
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+<tr>
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+<tr bgcolor="#DEDEDE">
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+<tr bgcolor="#DEDEDE">
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+<td>N</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>P</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>Q</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>R</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>S</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>T</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>V</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>W</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>Y</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>ascending</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>parsimony</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>threshold</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>threshold-type</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>input-ms2</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>unique-mapping</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>quant-level</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>measure</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>custom-threshold-name</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>custom-threshold-min</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>mzid-use-pass-threshold</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>precision</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td><td>✓</td><td> </td></tr>
+<tr>
+<td>peptide-list</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>mods-spec</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>cterm-peptide-mods-spec</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>nterm-peptide-mods-spec</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>min-mods</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>allow-dups</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr>
+<td>temp-dir</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td><td> </td><td> </td><td> </td></tr>
+<tr bgcolor="#DEDEDE">
+<td>xlink-score-method</td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td> </td><td>✓</td></tr>
+</table></body></html>
diff --git a/doc/user/percolator.html b/doc/user/percolator.html
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+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>percolator</h1>
+<h2>Usage:</h2>
+<p><code>crux percolator [options] <peptide-spectrum matches></code></p>
+<h2>Description:</h2>
+<p>Percolator is a semi-supervised learning algorithm that dynamically learns to separate target from decoy peptide-spectrum matches (PSMs). The algorithm is described in this article:</p><blockquote> Lukas Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and Michael J. MacCoss. <a href="http://noble.gs.washington.edu/papers/kall2007semi-supervised.html">"Semi-supervised learning for peptide identification from shotgun proteomics datasets."</a> <em>Nature Metho [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>peptide-spectrum matches</code> – A collection of target and decoy peptide-spectrum matches (PSMs). Input may be in one of five formats: PIN, SQT, pepXML, <a href="../file-formats/txt-format.html">Crux tab-delimited text</a>, or a list of files (when list-of-files=T). Note that if the input is provided as SQT, pepXML, or Crux tab-delimited text, then a PIN file will be generated in the output directory prior to execution.Crux determines the format of the input file by e [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>percolator.target.proteins.txt</code> – a tab-delimited file containing the target protein matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.proteins.txt</code> – a tab-delimited file containing the decoy protein matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.target.peptides.txt</code> – a tab-delimited file containing the target peptide matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.peptides.txt</code> – a tab-delimited file containing the decoy peptide matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.target.psms.txt</code> – a tab-delimited file containing the target PSMs. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.psms.txt</code> – a tab-delimited file containing the decoy PSMs. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.params.txt</code> – a file containing the name and value of all parameters for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>percolator.pep.xml</code> – a file containing the PSMs in <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">pepXML format</a>. This file can be used as input to some of the tools in the <a href="http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP">Transproteomic Pipeline</a>.</li>
+ <li><code>percolator.mzid</code> – a file containing the protein, peptide, and spectrum matches in <a href="http://www.psidev.info/mzidentml">mzIdentML format</a>.</li>
+ <li><code>percolator.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Protein inference options</h3>
+<ul>
+ <li class="nobullet"><code>--picked-protein <string></code> – Use the picked protein-level FDR to infer protein probabilities, provide the fasta file as the argument to this flag. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--protein-enzyme no_enzyme|elastase|pepsin|proteinasek|thermolysin|trypsinp|chymotrypsin|lys-n|lys-c|arg-c|asp-n|glu-c|trypsin</code> – Type of enzyme Default = <code>trypsin</code>.</li>
+ <li class="nobullet"><code>--protein-report-fragments T|F</code> – By default, if the peptides associated with protein A are a proper subset of the peptides associated with protein B, then protein A is eliminated and all the peptides are considered as evidence for protein B. Note that this filtering is done based on the complete set of peptides in the database, not based on the identified peptides in the search results. Alternatively, if this option is set and if all of the ident [...]
+ <li class="nobullet"><code>--protein-report-duplicates T|F</code> – If multiple database proteins contain exactly the same set of peptides, then Percolator will randomly discard all but one of the proteins. If this option is set, then the IDs of these duplicated proteins will be reported as a comma-separated list. Not available for Fido. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fido options</h3>
+<ul>
+ <li class="nobullet"><code>--protein T|F</code> – Use the Fido algorithm to infer protein probabilities. Must be true to use any of the Fido options. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fido-alpha <float></code> – Specify the probability with which a present protein emits an associated peptide. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-beta <float></code> – Specify the probability of the creation of a peptide from noise. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-gamma <float></code> – Specify the prior probability that a protein is present in the sample. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-empirical-protein-q T|F</code> – Estimate empirical p-values and q-values for proteins using target-decoy analysis. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fido-gridsearch-depth <integer></code> – Set depth of the grid search for alpha, beta and gamma estimation. The values considered, for each possible value of the --fido-gridsearch-depth parameter, are as follows:<ul><li>0: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36, 0.5}; beta = {0.0, 0.01, 0.15, 0.025, 0.035, 0.05, 0.1}; gamma = {0.1, 0.25, 0.5, 0.75}.</li><li>1: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36}; beta = {0.0, 0.01, 0.15, 0.025, 0.0 [...]
+ <li class="nobullet"><code>--fido-gridsearch-mse-threshold <float></code> – Q-value threshold that will be used in the computation of the MSE and ROC AUC score in the grid search. Default = <code>0.05</code>.</li>
+ <li class="nobullet"><code>--fido-fast-gridsearch <float></code> – Apply the specified threshold to PSM, peptide and protein probabilities to obtain a faster estimate of the alpha, beta and gamma parameters. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-protein-truncation-threshold <float></code> – To speed up inference, proteins for which none of the associated peptides has a probability exceeding the specified threshold will be assigned probability = 0. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--fido-no-split-large-components T|F</code> – Do not approximate the posterior distribution by allowing large graph components to be split into subgraphs. The splitting is done by duplicating peptides with low probabilities. Splitting continues until the number of possible configurations of each subgraph is below 2^18 Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>General options</h3>
+<ul>
+ <li class="nobullet"><code>--only-psms T|F</code> – Do not remove redundant peptides; keep all PSMs and exclude peptide level probability. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--tdc T|F</code> – Use target-decoy competition to assign q-values and PEPs. When set to F, the mix-max method, which estimates the proportion pi0 of incorrect target PSMs, is used instead. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--search-input auto|separate|concatenated</code> – Specify the type of target-decoy search. Using 'auto', percolator attempts to detect the search type automatically. Using 'separate' specifies two searches: one against target and one against decoy protein db. Using 'concatenated' specifies a single search on concatenated target-decoy protein db. Default = <code>auto</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>SVM training options</h3>
+<ul>
+ <li class="nobullet"><code>--subset-max-train <integer></code> – Only train Percolator on a subset of PSMs, and use the resulting score vector to evaluate the other PSMs. Recommended when analyzing huge numbers (>1 million) of PSMs. When set to 0, all PSMs are used for training as normal. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--c-pos <float></code> – Penalty for mistakes made on positive examples. If this value is set to 0, then it is set via cross validation over the values {0.1, 1, 10}, selecting the value that yields the largest number of PSMs identified at the q-value threshold set via the --test-fdr parameter. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--c-neg <float></code> – Penalty for mistake made on negative examples. If not specified, then this value is set by cross validation over {0.1, 1, 10}. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--train-fdr <float></code> – False discovery rate threshold to define positive examples in training. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--test-fdr <float></code> – False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--maxiter <integer></code> – Maximum number of iterations for training. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--quick-validation T|F</code> – Quicker execution by reduced internal cross-validation. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--test-each-iteration T|F</code> – Measure performance on test set each iteration. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--percolator-seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>SVM feature input options</h3>
+<ul>
+ <li class="nobullet"><code>--output-weights T|F</code> – Output final weights to a file named "percolator.weights.txt". Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--init-weights <string></code> – Read initial weights from the given file (one per line). Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--default-direction <string></code> – In its initial round of training, Percolator uses one feature to induce a ranking of PSMs. By default, Percolator will select the feature that produces the largest set of target PSMs at a specified FDR threshold (cf. --train-fdr). This option allows the user to specify which feature is used for the initial ranking, using the name as a string from <a href="../file-formats/features.html">this table</a>. The name [...]
+ <li class="nobullet"><code>--unitnorm T|F</code> – Use unit normalization (i.e., linearly rescale each PSM's feature vector to have a Euclidean length of 1), instead of standard deviation normalization. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--override T|F</code> – By default, Percolator will examine the learned weights for each feature, and if the weight appears to be problematic, then percolator will discard the learned weights and instead employ a previously trained, static score vector. This switch allows this error checking to be overriden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--klammer T|F</code> – Use retention time features calculated as in "Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions" by Klammer AA, Yi X, MacCoss MJ and Noble WS. (<em>Analytical Chemistry</em>. 2007 Aug 15;79(16):6111-8.). Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--pout-output T|F</code> – Output a Percolator <a href="https://github.com/percolator/percolator/blob/master/src/xml/percolator_out.xsd">pout.xml</a> format results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mzid-output T|F</code> – Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-out T|F</code> – Output the computed features in <a href="../file-formats/features.html">tab-delimited text format</a>. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--feature-file-in T|F</code> – When set to T, interpret the input file as a PIN file. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-xml-output T|F</code> – Include decoys (PSMs, peptides, and/or proteins) in the XML output. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
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+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
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+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
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+</html>
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+<title>pipeline</title>
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+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>pipeline</h1>
+<h2>Usage:</h2>
+<p><code>crux pipeline [options] <mass spectra>+ <peptide source></code></p>
+<h2>Description:</h2>
+<p>Given one or more sets of tandem mass spectra as well as a protein database, this command runs a series of Crux tools and reports all of the results in a single output directory. There are three steps in the pipeline:</p><ol><li><a href="bullseye.html">Bullseye</a> to assign high-resolution precursor m/z values to MS/MS data. This step is optional.</li><li>Database searching using either <a href="tide-search.html">Tide-search</a> or <a href="comet.html">Comet</a>. The database can be [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>mass spectra+</code> – The name of the file(s) from which to parse the fragmentation spectra, in any of the <a href="http://proteowizard.sourceforge.net/tools.shtml">file formats supported by ProteoWizard</a>. Alteratively, with Tide-search, these files may be binary spectrum files produced by a previous run of <code>crux tide-search</code> using the <code>store-spectra</code> parameter.</li>
+ <li><code>peptide source</code> – Either the name of a file in fasta format from which to retrieve proteins and peptides or an index created by a previous run of <code>crux tide-index</code> (for Tide searching).</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>bullseye.pid.<format></code> – a file containing the fragmentation spectra for which accurate masses were successfully inferred. Unless otherwise specified (with the --spectrum-format option), the output file format is ".ms2". Note that if the output format is ".ms2," then a single spectrum may have multiple "Z" lines, each indicating a charge state and accurate mass. In addition, Bullseye inserts an "I" line (for charge-dependent analysis) corresponding to each "Z" lin [...]
+ <li><code>bullseye.no-pid.<format></code> – a file containing the fragmentation spectra for which accurate masses were not inferred.</li>
+ <li><code>hardklor.mono.txt</code> – a tab-delimited text file containing one line for each isotope distribution, as described <a href="hardklor.html">here</a>.</li>
+ <li><code>bullseye.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>bullseye.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+ <li><code>tide-search.target.txt</code> – a tab-delimited text file containing the target PSMs. See <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>tide-search.decoy.txt</code> – a tab-delimited text file containing the decoy PSMs. This file will only be created if the index was created with decoys.</li>
+ <li><code>tide-search.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other Crux programs.</li>
+ <li><code>tide-search.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+ <li><code>comet.target.txt</code> – a tab-delimited text file containing the target PSMs. See <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>comet.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>comet.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+ <li><code>percolator.target.proteins.txt</code> – a tab-delimited file containing the target protein matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.proteins.txt</code> – a tab-delimited file containing the decoy protein matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.target.peptides.txt</code> – a tab-delimited file containing the target peptide matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.peptides.txt</code> – a tab-delimited file containing the decoy peptide matches. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.target.psms.txt</code> – a tab-delimited file containing the target PSMs. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.decoy.psms.txt</code> – a tab-delimited file containing the decoy PSMs. See <a href="../file-formats/txt-format.html">here</a> for a list of the fields.</li>
+ <li><code>percolator.params.txt</code> – a file containing the name and value of all parameters for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>percolator.pep.xml</code> – a file containing the PSMs in <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">pepXML format</a>. This file can be used as input to some of the tools in the <a href="http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP">Transproteomic Pipeline</a>.</li>
+ <li><code>percolator.mzid</code> – a file containing the protein, peptide, and spectrum matches in <a href="http://www.psidev.info/mzidentml">mzIdentML format</a>.</li>
+ <li><code>percolator.log.txt</code> – a log file containing a copy of all messages that were printed to standard error.</li>
+ <li><code>assign-confidence.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> that contains the targets, sorted by score. The file will contain one new column, named "<method> q-value", where <method> is either "tdc" or "mix-max".</li>
+ <li><code>assign-confidence.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>assign-confidence.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>pipeline options</h3>
+<ul>
+ <li class="nobullet"><code>--bullseye T|F</code> – Run the Bullseye algorithm on the given MS data, using it to assign high-resolution precursor values to the MS/MS data. If a spectrum file ends with .ms2 or .cms2, matching .ms1/.cms1 files will be used as the MS1 file. Otherwise, it is assumed that the spectrum file contains both MS1 and MS2 scans. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--search-engine comet|tide-search</code> – Specify which search engine to use. Default = <code>tide-search</code>.</li>
+ <li class="nobullet"><code>--post-processor percolator|assign-confidence|none</code> – Specify which post-processor to apply to the search results. Default = <code>percolator</code>.</li>
+ <li class="nobullet"><code>--estimation-method mix-max|tdc|peptide-level</code> – Specify the method used to estimate q-values. The mix-max procedure or target-decoy competition apply to PSMs. The peptide-level option eliminates any PSM for which there exists a better scoring PSM involving the same peptide, and then uses decoys to assign confidence estimates. Default = <code>tdc</code>.</li>
+ <li class="nobullet"><code>--score <string></code> – Specify the column (for tab-delimited input) or tag (for XML input) used as input to the q-value estimation procedure. If this parameter is unspecified, then the program searches for "xcorr score", "evalue" (comet), "exact p-value" score fields in this order in the input file. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--sidak T|F</code> – Adjust the score using the Sidak adjustment and reports them in a new column in the output file. Note that this adjustment only makes sense if the given scores are p-values, and that it requires the presence of the "distinct matches/spectrum" feature for each PSM. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-charge-states T|F</code> – Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--combine-modified-peptides T|F</code> – Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Identifying PPIDs in MS1 spectra</h3>
+<ul>
+ <li class="nobullet"><code>--max-persist <float></code> – Ignore PPIDs that persist for longer than this length of time in the MS1 spectra. The unit of time is whatever unit is used in your data file (usually minutes). These PPIDs are considered contaminants. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--persist-tolerance <float></code> – Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--gap-tolerance <integer></code> – Allowed gap size when checking for PPIDs across consecutive MS1 scans. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--scan-tolerance <integer></code> – Total number of MS1 scans over which a PPID must be observed to be considered real. Gaps in persistence are allowed by setting --gap-tolerance. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--bullseye-max-mass <float></code> – Only consider PPIDs below this maximum mass in daltons. Default = <code>8000</code>.</li>
+ <li class="nobullet"><code>--bullseye-min-mass <float></code> – Only consider PPIDs above this minimum mass in daltons. Default = <code>600</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Matching PPIDs to MS2 spectra</h3>
+<ul>
+ <li class="nobullet"><code>--exact-match T|F</code> – When true, require an exact match (as defined by --exact-tolerance) between the center of the precursor isolation window in the MS2 scan and the base isotopic peak of the PPID. If this option is set to false and no exact match is observed, then attempt to match using a wider m/z tolerance. This wider tolerance is calculated using the PPID's monoisotopic mass and charge (the higher the charge, the smaller the window). Default = [...]
+ <li class="nobullet"><code>--exact-tolerance <float></code> – Set the tolerance (+/-ppm) for --exact-match. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--retention-tolerance <float></code> – Set the tolerance (+/-units) around the retention time over which a PPID can be matches to the MS2 spectrum. The unit of time is whatever unit is used in your data file (usually minutes). Default = <code>0.5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Precursor selection</h3>
+<ul>
+ <li class="nobullet"><code>--precursor-window <float></code> – Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto-precursor-window false|warn|fail</code> – Automatically estimate optimal value for the precursor-window parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> – Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not avail [...]
+ <li class="nobullet"><code>--max-precursor-charge <integer></code> – The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-min-mz <float></code> – The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum-max-mz <float></code> – The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
+ <li class="nobullet"><code>--min-peaks <integer></code> – The minimum number of peaks a spectrum must have for it to be searched. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--spectrum-charge 1|2|3|all</code> – The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge state will be searched. Default = <code>all</code>.</li>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--compute-sp T|F</code> – Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spe [...]
+ <li class="nobullet"><code>--remove-precursor-peak T|F</code> – If true, all peaks around the precursor m/z will be removed, within a range specified by the --remove-precursor-tolerance option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--exact-p-value T|F</code> – Enable the calculation of exact p-values for the XCorr score as described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this article</a>. Calculation of p-values increases the running time but increases the number of identifications at a fixed confidence threshold. The p-values will be reported in a new column with header "exact p-value", and the "xcorr score" column will be replaced with a "refactored xcorr" colu [...]
+ <li class="nobullet"><code>--use-neutral-loss-peaks T|F</code> – Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+ <li class="nobullet"><code>--auto-mz-bin-width false|warn|fail</code> – Automatically estimate optimal value for the mz-bin-width parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-offset <float></code> – In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--peptide-centric-search T|F</code> – Carries out a peptide-centric search. For each peptide the top-scoring spectra are reported, in contrast to the standard spectrum-centric search where the top-scoring peptides are reported. Note that in this case the "xcorr rank" column will contain the rank of the given spectrum with respect to the given candidate peptide, rather than vice versa (which is the default). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--isotope-error <string></code> – List of positive, non-zero integers. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--skip-preprocessing T|F</code> – Skip preprocessing steps on spectra. Default = F. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Protein inference options</h3>
+<ul>
+ <li class="nobullet"><code>--picked-protein <string></code> – Use the picked protein-level FDR to infer protein probabilities, provide the fasta file as the argument to this flag. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--protein-enzyme no_enzyme|elastase|pepsin|proteinasek|thermolysin|trypsinp|chymotrypsin|lys-n|lys-c|arg-c|asp-n|glu-c|trypsin</code> – Type of enzyme Default = <code>trypsin</code>.</li>
+ <li class="nobullet"><code>--protein-report-fragments T|F</code> – By default, if the peptides associated with protein A are a proper subset of the peptides associated with protein B, then protein A is eliminated and all the peptides are considered as evidence for protein B. Note that this filtering is done based on the complete set of peptides in the database, not based on the identified peptides in the search results. Alternatively, if this option is set and if all of the ident [...]
+ <li class="nobullet"><code>--protein-report-duplicates T|F</code> – If multiple database proteins contain exactly the same set of peptides, then Percolator will randomly discard all but one of the proteins. If this option is set, then the IDs of these duplicated proteins will be reported as a comma-separated list. Not available for Fido. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fido options</h3>
+<ul>
+ <li class="nobullet"><code>--protein T|F</code> – Use the Fido algorithm to infer protein probabilities. Must be true to use any of the Fido options. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fido-alpha <float></code> – Specify the probability with which a present protein emits an associated peptide. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-beta <float></code> – Specify the probability of the creation of a peptide from noise. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-gamma <float></code> – Specify the prior probability that a protein is present in the sample. Set by grid search (see --fido-gridsearch-depth parameter) if not specified. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-empirical-protein-q T|F</code> – Estimate empirical p-values and q-values for proteins using target-decoy analysis. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fido-gridsearch-depth <integer></code> – Set depth of the grid search for alpha, beta and gamma estimation. The values considered, for each possible value of the --fido-gridsearch-depth parameter, are as follows:<ul><li>0: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36, 0.5}; beta = {0.0, 0.01, 0.15, 0.025, 0.035, 0.05, 0.1}; gamma = {0.1, 0.25, 0.5, 0.75}.</li><li>1: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36}; beta = {0.0, 0.01, 0.15, 0.025, 0.0 [...]
+ <li class="nobullet"><code>--fido-gridsearch-mse-threshold <float></code> – Q-value threshold that will be used in the computation of the MSE and ROC AUC score in the grid search. Default = <code>0.05</code>.</li>
+ <li class="nobullet"><code>--fido-fast-gridsearch <float></code> – Apply the specified threshold to PSM, peptide and protein probabilities to obtain a faster estimate of the alpha, beta and gamma parameters. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--fido-protein-truncation-threshold <float></code> – To speed up inference, proteins for which none of the associated peptides has a probability exceeding the specified threshold will be assigned probability = 0. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--fido-no-split-large-components T|F</code> – Do not approximate the posterior distribution by allowing large graph components to be split into subgraphs. The splitting is done by duplicating peptides with low probabilities. Splitting continues until the number of possible configurations of each subgraph is below 2^18 Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Database</h3>
+<ul>
+ <li class="nobullet"><code>--decoy_search <integer></code> – 0=no, 1=concatenated search, 2=separate search. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>CPU threads</h3>
+<ul>
+ <li class="nobullet"><code>--num-threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--num_threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Masses</h3>
+<ul>
+ <li class="nobullet"><code>--peptide_mass_tolerance <float></code> – Controls the mass tolerance value. The mass tolerance is set at +/- the specified number i.e. an entered value of "1.0" applies a -1.0 to +1.0 tolerance. The units of the mass tolerance is controlled by the parameter "peptide_mass_units". Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto_peptide_mass_tolerance false|warn|fail</code> – Automatically estimate optimal value for the peptide_mass_tolerancel parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--peptide_mass_units <integer></code> – 0=amu, 1=mmu, 2=ppm. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--mass_type_parent <integer></code> – 0=average masses, 1=monoisotopic masses. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--mass_type_fragment <integer></code> – 0=average masses, 1=monoisotopic masses. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--precursor_tolerance_type <integer></code> – 0=singly charged peptide mass, 1=precursor m/z. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--isotope_error <integer></code> – 0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8 labeling). Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search enzyme</h3>
+<ul>
+ <li class="nobullet"><code>--search_enzyme_number <integer></code> – Specify a search enzyme from the end of the parameter file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--num_enzyme_termini <integer></code> – valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--allowed_missed_cleavage <integer></code> – Maximum value is 5; for enzyme search. Default = <code>2</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fragment ions</h3>
+<ul>
+ <li class="nobullet"><code>--fragment_bin_tol <float></code> – Binning to use on fragment ions. Default = <code>1.000507</code>.</li>
+ <li class="nobullet"><code>--fragment_bin_offset <float></code> – Offset position to start the binning (0.0 to 1.0). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--auto_fragment_bin_tol false|warn|fail</code> – Automatically estimate optimal value for the fragment_bin_tol parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--theoretical_fragment_ions <integer></code> – 0=default peak shape, 1=M peak only. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_A_ions <integer></code> – Controls whether or not A-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_B_ions <integer></code> – Controls whether or not B-ions are considered in the search (0 - no, 1 - yes). Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_C_ions <integer></code> – Controls whether or not C-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_X_ions <integer></code> – Controls whether or not X-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_Y_ions <integer></code> – Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes). Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--use_Z_ions <integer></code> – Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--use_NL_ions <integer></code> – 0=no, 1= yes to consider NH3/H2O neutral loss peak. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>mzXML/mzML parameters</h3>
+<ul>
+ <li class="nobullet"><code>--scan_range <string></code> – Start and scan scan range to search; 0 as first entry ignores parameter. Default = <code>0 0</code>.</li>
+ <li class="nobullet"><code>--precursor_charge <string></code> – Precursor charge range to analyze; does not override mzXML charge; 0 as first entry ignores parameter. Default = <code>0 0</code>.</li>
+ <li class="nobullet"><code>--override_charge <integer></code> – Specifies the whether to override existing precursor charge state information when present in the files with the charge range specified by the "precursor_charge" parameter. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--ms_level <integer></code> – MS level to analyze, valid are levels 2 or 3. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--activation_method ALL|CID|ECD|ETD|PQD|HCD|IRMPD</code> – Specifies which scan types are searched. Default = <code>ALL</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Miscellaneous parameters</h3>
+<ul>
+ <li class="nobullet"><code>--digest_mass_range <string></code> – MH+ peptide mass range to analyze. Default = <code>600.0 5000.0</code>.</li>
+ <li class="nobullet"><code>--num_results <integer></code> – Number of search hits to store internally. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--skip_researching <integer></code> – For '.out' file output only, 0=search everything again, 1=don't search if .out exists. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--max_fragment_charge <integer></code> – Set maximum fragment charge state to analyze (allowed max 5). Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--max_precursor_charge <integer></code> – Set maximum precursor charge state to analyze (allowed max 9). Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--nucleotide_reading_frame <integer></code> – 0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--clip_nterm_methionine <integer></code> – 0=leave sequences as-is; 1=also consider sequence w/o N-term methionine. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum_batch_size <integer></code> – Maximum number of spectra to search at a time; 0 to search the entire scan range in one loop. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--decoy_prefix <string></code> – Specifies the prefix of the protein names that indicates a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--output_suffix <string></code> – Specifies the suffix string that is appended to the base output name for the pep.xml, pin.xml, txt and sqt output files. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--mass_offsets <string></code> – Specifies one or more mass offsets to apply. This value(s) are effectively subtracted from each precursor mass such that peptides that are smaller than the precursor mass by the offset value can still be matched to the respective spectrum. Default = <code><empty></code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Spectral processing</h3>
+<ul>
+ <li class="nobullet"><code>--minimum_peaks <integer></code> – Minimum number of peaks in spectrum to search. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--minimum_intensity <float></code> – Minimum intensity value to read in. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--remove_precursor_peak <integer></code> – 0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--remove_precursor_tolerance <float></code> – +- Da tolerance for precursor removal. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--clear_mz_range <string></code> – For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range. Default = <code>0.0 0.0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Variable modifications</h3>
+<ul>
+ <li class="nobullet"><code>--variable_mod01 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod02 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod03 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod04 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod05 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod06 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod07 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod08 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--variable_mod09 <string></code> – Up to 9 variable modifications are supported; format: "<mass> <residues> <0=variable/1=binary> <max mods per a peptide>" e.g. 79.966331 STY 0 3. Default = <code>0.0 null 0 4 -1 0 0</code>.</li>
+ <li class="nobullet"><code>--max_variable_mods_in_peptide <integer></code> – Specifies the total/maximum number of residues that can be modified in a peptide. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--require_variable_mod <integer></code> – Controls whether the analyzed peptides must contain at least one variable modification. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Static modifications</h3>
+<ul>
+ <li class="nobullet"><code>--add_Cterm_peptide <float></code> – Specifiy a static modification to the c-terminus of all peptides. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Nterm_peptide <float></code> – Specify a static modification to the n-terminus of all peptides. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Cterm_protein <float></code> – Specify a static modification to the c-terminal peptide of each protein. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Nterm_protein <float></code> – Specify a static modification to the n-terminal peptide of each protein. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_A_alanine <float></code> – Specify a static modification to the residue A. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_B_user_amino_acid <float></code> – Specify a static modification to the residue B. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_C_cysteine <float></code> – Specify a static modification to the residue C. Default = <code>57.021464</code>.</li>
+ <li class="nobullet"><code>--add_D_aspartic_acid <float></code> – Specify a static modification to the residue D. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_E_glutamic_acid <float></code> – Specify a static modification to the residue E. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_F_phenylalanine <float></code> – Specify a static modification to the residue F. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_G_glycine <float></code> – Specify a static modification to the residue G. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_H_histidine <float></code> – Specify a static modification to the residue H. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_I_isoleucine <float></code> – Specify a static modification to the residue I. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_J_user_amino_acid <float></code> – Specify a static modification to the residue J. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_K_lysine <float></code> – Specify a static modification to the residue K. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_L_leucine <float></code> – Specify a static modification to the residue L. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_M_methionine <float></code> – Specify a static modification to the residue M. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_N_asparagine <float></code> – Specify a static modification to the residue N. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_O_ornithine <float></code> – Specify a static modification to the residue O. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_P_proline <float></code> – Specify a static modification to the residue P. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Q_glutamine <float></code> – Specify a static modification to the residue Q. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_R_arginine <float></code> – Specify a static modification to the residue R. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_S_serine <float></code> – Specify a static modification to the residue S. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_T_threonine <float></code> – Specify a static modification to the residue T. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_U_selenocysteine <float></code> – Specify a static modification to the residue U. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_V_valine <float></code> – Specify a static modification to the residue V. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_W_tryptophan <float></code> – Specify a static modification to the residue W. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_X_user_amino_acid <float></code> – Specify a static modification to the residue X. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Y_tyrosine <float></code> – Specify a static modification to the residue Y. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--add_Z_user_amino_acid <float></code> – Specify a static modification to the residue Z. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>General options</h3>
+<ul>
+ <li class="nobullet"><code>--only-psms T|F</code> – Do not remove redundant peptides; keep all PSMs and exclude peptide level probability. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--tdc T|F</code> – Use target-decoy competition to assign q-values and PEPs. When set to F, the mix-max method, which estimates the proportion pi0 of incorrect target PSMs, is used instead. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--search-input auto|separate|concatenated</code> – Specify the type of target-decoy search. Using 'auto', percolator attempts to detect the search type automatically. Using 'separate' specifies two searches: one against target and one against decoy protein db. Using 'concatenated' specifies a single search on concatenated target-decoy protein db. Default = <code>auto</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>SVM training options</h3>
+<ul>
+ <li class="nobullet"><code>--subset-max-train <integer></code> – Only train Percolator on a subset of PSMs, and use the resulting score vector to evaluate the other PSMs. Recommended when analyzing huge numbers (>1 million) of PSMs. When set to 0, all PSMs are used for training as normal. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--c-pos <float></code> – Penalty for mistakes made on positive examples. If this value is set to 0, then it is set via cross validation over the values {0.1, 1, 10}, selecting the value that yields the largest number of PSMs identified at the q-value threshold set via the --test-fdr parameter. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--c-neg <float></code> – Penalty for mistake made on negative examples. If not specified, then this value is set by cross validation over {0.1, 1, 10}. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--train-fdr <float></code> – False discovery rate threshold to define positive examples in training. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--test-fdr <float></code> – False discovery rate threshold used in selecting hyperparameters during internal cross-validation and for reporting the final results. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--maxiter <integer></code> – Maximum number of iterations for training. Default = <code>10</code>.</li>
+ <li class="nobullet"><code>--quick-validation T|F</code> – Quicker execution by reduced internal cross-validation. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--test-each-iteration T|F</code> – Measure performance on test set each iteration. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--percolator-seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>SVM feature input options</h3>
+<ul>
+ <li class="nobullet"><code>--output-weights T|F</code> – Output final weights to a file named "percolator.weights.txt". Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--init-weights <string></code> – Read initial weights from the given file (one per line). Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--default-direction <string></code> – In its initial round of training, Percolator uses one feature to induce a ranking of PSMs. By default, Percolator will select the feature that produces the largest set of target PSMs at a specified FDR threshold (cf. --train-fdr). This option allows the user to specify which feature is used for the initial ranking, using the name as a string from <a href="../file-formats/features.html">this table</a>. The name [...]
+ <li class="nobullet"><code>--unitnorm T|F</code> – Use unit normalization (i.e., linearly rescale each PSM's feature vector to have a Euclidean length of 1), instead of standard deviation normalization. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--override T|F</code> – By default, Percolator will examine the learned weights for each feature, and if the weight appears to be problematic, then percolator will discard the learned weights and instead employ a previously trained, static score vector. This switch allows this error checking to be overriden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--klammer T|F</code> – Use retention time features calculated as in "Improving tandem mass spectrum identification using peptide retention time prediction across diverse chromatography conditions" by Klammer AA, Yi X, MacCoss MJ and Noble WS. (<em>Analytical Chemistry</em>. 2007 Aug 15;79(16):6111-8.). Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--spectrum-format |ms2|bms2|cms2|mgf</code> – The format to write the output spectra to. If empty, the spectra will be output in the same format as the MS2 input. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--store-spectra <string></code> – Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir). This option is not valid if multiple input spectrum files are given. Default = <code><e [...]
+ <li class="nobullet"><code>--store-index <string></code> – When providing a FASTA file as the index, the generated binary index will be stored at the given path. This option has no effect if a binary index is provided as the index. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--concat T|F</code> – When set to T, target and decoy search results are reported in a single file, and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--print-search-progress <integer></code> – Show search progress by printing every n spectra searched. Set to 0 to show no search progress. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--sqt-output T|F</code> – Outputs an SQT results file to the output directory. Note that if sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mzid-output T|F</code> – Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pin-output T|F</code> – Output a Percolator input (PIN) file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--file-column T|F</code> – Include the file column in tab-delimited output. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--output_sqtfile <integer></code> – 0=no, 1=yes write sqt file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--output_txtfile <integer></code> – 0=no, 1=yes write tab-delimited text file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--output_pepxmlfile <integer></code> – 0=no, 1=yes write pep.xml file. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--output_percolatorfile <integer></code> – 0=no, 1=yes write percolator file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--output_outfiles <integer></code> – 0=no, 1=yes write .out files. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--print_expect_score <integer></code> – 0=no, 1=yes to replace Sp with expect in out & sqt. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--num_output_lines <integer></code> – num peptide results to show. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--show_fragment_ions <integer></code> – 0=no, 1=yes for out files only. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--sample_enzyme_number <integer></code> – Sample enzyme which is possibly different than the one applied to the search. Used to calculate NTT & NMC in pepXML output. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--pout-output T|F</code> – Output a Percolator <a href="https://github.com/percolator/percolator/blob/master/src/xml/percolator_out.xsd">pout.xml</a> format results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-out T|F</code> – Output the computed features in <a href="../file-formats/features.html">tab-delimited text format</a>. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-in T|F</code> – When set to T, interpret the input file as a PIN file. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-xml-output T|F</code> – Include decoys (PSMs, peptides, and/or proteins) in the XML output. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
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+ <div id="centerfooter">
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+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/predict-peptide-ions.html b/doc/user/predict-peptide-ions.html
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+++ b/doc/user/predict-peptide-ions.html
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+<!DOCTYPE html>
+<html>
+<head>
+<title>predict-peptide-ions</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>predict-peptide-ions</h1>
+<h2>Usage:</h2>
+<p><code>crux predict-peptide-ions [options] <peptide sequence> <charge state></code></p>
+<h2>Description:</h2>
+<p>Given a peptide and a charge state, predict the corresponding fragment ions according to the provided options.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>peptide sequence</code> – The peptide sequence.</li>
+ <li><code>charge state</code> – The charge state of the peptide.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – a series of lines, describing how the ions were predicted. <blockquote style="font-family: monospace;"># PEPTIDE: <peptide sequence><br># CHARGE: <peptide charge></blockquote>The program then prints a one-line header that labels the tab-delimited columns, followed by one line per ion:<blockquote style="font-family: monospace;">m/z mass charge ion-series peptide-bond-index nh3 h2o isotope flank</blockquo [...]
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>predict-peptide-ions options</h3>
+<ul>
+ <li class="nobullet"><code>--primary-ions a|b|y|by|bya</code> – Predict the specified primary ion series. 'a' indicates a-ions only, 'b' indicates b-ions only, 'y' indicates y-ions only, 'by' indicates both b and y, 'bya' indicates b, y, and a. Default = <code>by</code>.</li>
+ <li class="nobullet"><code>--precursor-ions T|F</code> – Predict the precursor ions, and all associated ions (neutral losses, multiple charge states) consistent with the other specified options. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--isotope <integer></code> – Predict the given number of isotope peaks (0|1|2). Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--flanking T|F</code> – Predict flanking peaks for b- and y ions. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--nh3 <integer></code> – Include among the predicted peaks b/y ions with up to n losses of nh3. For example, for --nh3 2, predict a peak for each b- and y-ion with the loss of one nh3 group and predict a second peak for each b- and y-ion with the loss of two nh3 groups. These peaks will have 1 and 2, respectively, in the NH3 column of the output. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--h2o <integer></code> – Include in the predicted peaks, b/y ions with the loss of 1 to n water molecules. See --nh3 for an example. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--max-ion-charge <string></code> – Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state of the peptide ("peptide"). If the max-ion-charge is greater than the charge state of the peptide, then the maximum is the peptide charge. Default = <code>peptide</code>.</li>
+ <li class="nobullet"><code>--fragment-mass average|mono</code> – Specify which isotopes to use in calculating fragment ion mass. Default = <code>mono</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
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+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
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+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/print-processed-spectra.html b/doc/user/print-processed-spectra.html
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--- /dev/null
+++ b/doc/user/print-processed-spectra.html
@@ -0,0 +1,141 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>print-processed-spectra</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
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+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>print-processed-spectra</h1>
+<h2>Usage:</h2>
+<p><code>crux print-processed-spectra [options] <ms2 file> <output file></code></p>
+<h2>Description:</h2>
+<p>Pre-process each spectrum in a given file in preparation for computing XCorr. The pre-processing steps are described in detail in this paper:</p><blockquote>J. K. Eng, B. Fischer, J. Grossman and M. J. MacCoss. <a href="http://pubs.acs.org/doi/abs/10.1021/pr800420s">"A fast SEQUEST cross correlation algorithm process the peaks as for computing."</a> <em>Journal of Proteome Research</em>. 7(10):4598-4602, 2008.</blockquote><p>The output of this program is equivalent to the sp [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+ <li><code>output file</code> – File where spectrum will be written.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>output file</code> – The name of the file in which the processed spectra will be printed in MS2 format.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>print-processed-spectra options</h3>
+<ul>
+ <li class="nobullet"><code>--stop-after remove-precursor|square-root|remove-grass|ten-bin|xcorr</code> – Stop after the specified pre-processing step. Default = <code>xcorr</code>.</li>
+ <li class="nobullet"><code>--output-units mz|bin</code> – Specify the output units for processed spectra. Default = <code>bin</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/psm-convert.html b/doc/user/psm-convert.html
new file mode 100644
index 0000000..296d0d6
--- /dev/null
+++ b/doc/user/psm-convert.html
@@ -0,0 +1,142 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>psm-convert</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
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+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>psm-convert</h1>
+<h2>Usage:</h2>
+<p><code>crux psm-convert [options] <input PSM file> <output format></code></p>
+<h2>Description:</h2>
+Reads in a file containing peptide-spectrum matches (PSMs) in one of the variety of supported formats and outputs the same PSMs in a different format
+<h2>Input:</h2>
+<ul>
+ <li><code>input PSM file</code> – The name of a PSM file in tab-delimited text, SQT, pepXML or mzIdentML format</li>
+ <li><code>output format</code> – The desired format of the output file. Legal values are tsv, html, sqt, pin, pepxml, mzidentml.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>psm-convert.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>psm-convert.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>psm-convert options</h3>
+<ul>
+ <li class="nobullet"><code>--input-format auto|tsv|sqt|pepxml|mzidentml</code> – Legal values are auto, tsv, sqt, pepxml or mzidentml format. Default = <code>auto</code>.</li>
+ <li class="nobullet"><code>--distinct-matches T|F</code> – Whether matches/ion are distinct (as opposed to total). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--protein-database <string></code> – The name of the file in FASTA format. Default = <code><empty></code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/q-ranker.html b/doc/user/q-ranker.html
new file mode 100644
index 0000000..0a4abc2
--- /dev/null
+++ b/doc/user/q-ranker.html
@@ -0,0 +1,160 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>q-ranker</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>q-ranker</h1>
+<h2>Usage:</h2>
+<p><code>crux q-ranker [options] <fragmentation spectra> <search results></code></p>
+<h2>Description:</h2>
+<p>Q-ranker dynamically learns to separate target from decoy PSMs. The algorithm is described in this article:</p><blockquote>Marina Spivak, Jason Weston, Leon Bottou and William Stafford Noble. <a href="http://noble.gs.washington.edu/papers/spivak2009improvements.html">"Direct <em>q</em> value optimization methods for peptide identification from shotgun proteomics data sets."</a> <em>Journal of Proteome Research</em>. 8(7):3737-3745, 2009.</blockquote><p>For more on q-values a [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>fragmentation spectra</code> – The fragmentation spectra must be provided in <a href="../file-formats/ms2-format.html">MS2</a>, mzXML, or MGF format.</li>
+ <li><code>search results</code> – Search results in the <a href="../file-formats/txt-format.html">tab-delimited text format</a> produced by Crux or in <a href="../file-formats/sqt-format.html">SQT format</a>. Like the spectra, the search results can be provided as a single file, a list of files or a directory of files. Note, however, that the input mode for spectra and for search results must be the same; i.e., if you provide a list of files for the spectra, then you must also pr [...]
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>qranker.target.pep.xml</code> – An xml file containing ranked list of target peptide-spectrum matches. Thefollowing entries are included: scan, charge, psm_id, q-value, score, precursor_mass, peptide, filename.</li>
+ <li><code>qranker.decoy.pep.xml</code> – An xml file containing ranked list of decoy peptide-spectrum matches.</li>
+ <li><code>qranker.target.psm.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text format</a> containing a ranked list of target peptide-spectrum matches with the associated Q-ranker scores and q-values.</li>
+ <li><code>qranker.decoy.psm.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text format</a> containing a ranked list of decoy peptide-spectrum matches with the associated Q-ranker scores and q-values.</li>
+ <li><code>qranker.log.txt</code> – a file where the program reports its progress.</li>
+ <li><code>qranker.params.txt</code> – a file with the values of all the options given to the current run.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>q-ranker options</h3>
+<ul>
+ <li class="nobullet"><code>--separate-searches <string></code> – If the target and decoy searches were run separately, rather than using a concatenated database, then the program will assume that the database search results provided as a required argument are from the target database search. This option then allows the user to specify the location of the decoy search results. Like the required arguments, these search results can be provided as a single file, a list of files [...]
+ <li class="nobullet"><code>--skip-cleanup T|F</code> – Analysis begins with a pre-processsing step that creates a set of lookup tables which are then used during training. Normally, these lookup tables are deleted at the end of the analysis, but setting this option to T prevents the deletion of these tables. Subsequently, analyses can be repeated more efficiently by specifying the --re-run option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--re-run <string></code> – Re-run a previous analysis using a previously computed set of lookup tables. For this option to work, the --skip-cleanup option must have been set to true when the program was run the first time. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--use-spec-features T|F</code> – Use an enriched feature set, including separate features for each ion type. Default = <code>true</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--feature-file-out T|F</code> – Output the computed features in <a href="../file-formats/features.html">tab-delimited text format</a>. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/read-tide-index.html b/doc/user/read-tide-index.html
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--- /dev/null
+++ b/doc/user/read-tide-index.html
@@ -0,0 +1,128 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>read-tide-index</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
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+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>read-tide-index</h1>
+<h2>Usage:</h2>
+<p><code>crux read-tide-index [options] <tide database></code></p>
+<h2>Description:</h2>
+Reads an index generated by tide-index and outputs information about the peptides it contains.
+<h2>Input:</h2>
+<ul>
+ <li><code>tide database</code> – Either a FASTA file or a directory containing a database index created by a previous run of crux tide-index.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>read-tide-index.peptides.txt</code> – a tab-delimited file containing two columns with headers: the peptide, and a semicolon-delimited list of IDs of the proteins that peptide occurs in.</li>
+ <li><code>read-tide-index.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>read-tide-index.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<p>This command does not support any optional parameters.</p>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/release-notes.html b/doc/user/release-notes.html
new file mode 100644
index 0000000..750d3d5
--- /dev/null
+++ b/doc/user/release-notes.html
@@ -0,0 +1,1849 @@
+<html>
+<head>
+<title>Release notes for Crux</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
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+
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+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <blockquote>
+ <h2>Release notes for Crux</h2>
+
+<h3>Version 3.1</h3> January 10, 2017
+
+<h4>Major changes</h4>
+
+<ul>
+
+ <li>8 Nov 2016: Updated Percolator to use the latest version on GitHub.</li>
+ <li>31 Oct 2016: Added param-medic options to Comet and Tide</li>
+ <li>11 Oct 2016: Added the param-medic command.</li>
+ <li>07 Sept 2016: Added isotope-error parameter to Tide.</li>
+ <li>30 Aug 2016: Updated Percolator to version 3.00.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+ <li>
+ 9 Jan 2017: Added search-input option to Percolator.</li>
+
+ <li>
+ 29 Dec 2016: Allow assign-confidence to rank by Percolator score.</li>
+
+ <li>
+ 1 Nov 2016: Added tdc and subset-max-train options to Percolator.</li>
+
+ <li>
+ 20 Sept 2016: Percolator changed to use a modified version of its
+ native output.</li>
+
+ <li>
+ 30 Nov 2016: Added +1 to the numerator of the FDR estimation when
+ carrying out target-decoy competition. This correction was
+ proposed by Barber and
+ Candes, <a href="https://arxiv.org/abs/1404.5609"><i>Annals of
+ Statistics</i></a>, 2015, as well as by He et al.,
+ <a href="http://arxiv.org/abs/1501.00537"</a>arXiv:1501.00537</a>,
+ 2015.</li>
+
+ <li>
+ 8 Aug 2016: Fixed incorrect default value for the cpos parameter
+ to percolator.</li>
+
+ <li>Many other minor bug fixes and enhancements.</li>
+
+</ul>
+
+<hr/>
+
+<h3>Version 3.0</h3> August 1, 2016
+
+<h4>Major changes</h4>
+
+<ul>
+
+<li>
+The <code>tide-search</code> command now supports threading. See the
+<code>num-threads</code> parameter for details.</li>
+
+<li>
+Added the <code>pipeline</a> command to run a series of commands, and
+the <code>cascade-search</code> to run searches across a series of
+databases.</li>
+
+<li>
+Renamed the command <code>calibrate-scores</code>
+to <code>assign-confidence</code> and completely revamped its
+functionality.</li>
+
+<li>
+The <code>search-for-xlinks</code> command offers parameters to
+control categories of
+candidates: <code>xlink-include-inter</code>, <code>xlink-include-intra</code>,
+and
+<code>xlink-include-inter-intra</code>.</li>
+
+<li>
+Added the <code>peptide-centric-search</code> option to tide-search.</li>
+
+<li>
+Compiling the Mac OS version now requires OS X Yosemite. It can be built
+from source using the Clang compilers distributed with the latest version of
+XCode.</li>
+
+<li>
+32-bit and 64-bit Windows versions are now available, built using Visual Studio 2013.</li>
+
+<li>
+Updated Percolator to version 2.10.</li>
+
+<li>
+Updated Hardklor to version 2.30.</li>
+
+<li>
+Updated Comet to version 2016.01 rev. 1.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The Windows version of Crux can be built with support for vendor specific file
+formats disabled.</li>
+
+<li>
+Added the <code>temp-dir</code> option
+to <code>tide-index</code>.</li>
+
+<li>
+The utilities <code>create-docs</code>, <code>subtract-index</code>,
+and <code>psm-convert</code> were added to Crux.</li>
+
+<li>The <code>generate-peptides</code> application has been revamped.</li>
+
+<li>Fixed a bug in <code>barista</code> that occurred when the number of
+peptides exceeded the number of PSMs.</li>
+
+<li>Precursor mass selection is fixed in <code>tide-search</code> when units
+are m/z.</li>
+
+<li><code>hardklor</code> and <code>bullseye</code> now use standard logging.</li>
+
+<li>Version number added to log files. Additionally, the version numbers of
+<code>percolator</code>, <code>comet</code>, and <code>boost</code> are shown
+in the output of the <code>version</code> command.</li>
+
+<li>
+Short usage message is displayed on error (the full usage message is still
+displayed when a command is entered with no arguments).</li>
+
+<li>
+<code>feature-in-file</code> parameter added to <code>percolator</code>.</li>
+
+<li>
+The <code>seed</code> parameter for <code>percolator</code> has been renamed
+to <code>percolator-seed</code>.</li>
+
+<li>
+<code>comet</code> exits with return code 1 on failure, rather than 0.</li>
+
+<li>
+Default value for <code>use_sparse_matrix</code> changed to <code>1</code>.</li>
+
+<li>
+Default value for <code>use-neutral-loss-peaks<code> changed to <code>true</code>.</li>
+
+<li>
+<code>xlink-score-method</code> parameter added to <code>xlink-score-spectrum</code>.</li>
+
+<li>
+deltaLCn column added to <code>tide-search</code> tab-delimited output.</li>
+
+<li>
+Bug fixed in reporting flanking amino acids in <code>PostProcessProtein.cpp</code>.</li>
+
+<li>
+<code>Mix-max</code> procedure is updated to handle ties among target and decoy scores.</li>
+
+<li>
+Default value of <code>use-neutral-loss-peaks</code> changed to <code>true</code></li>
+
+<li>
+<code>Exact p-value</code> calculation takes into account the flanking and neutral loss peaks. </li>
+
+<li>
+A bug was fixed in the naming of the Percolator input (.pin) file that
+is produced by Comet when the <code>output_percolatorfile</code>
+option is turned on. Previously, the file was named "comet.tsv"; now
+it is "comet.target.pin."</li>
+
+<li>
+<code>Assign-confidence</code> can take multiple input files.
+</li>
+
+<li>
+The <code>comet</code> command can take multiple input files.
+</li>
+
+<li>
+The <code>sidak</code> option has been added
+to <code>assign-confidence</code> to perform a Sidak adjustment.
+</li>
+
+<li>
+The <code>peptide-level</code> option has been added
+to <code>assign-confidence</code>.
+</li>
+
+<li>
+The refactored XCorr score has been re-scaled (by dividing by 20) to
+put it into a range that is comparable to that of the original XCorr score.</li>
+
+<li>
+The default value of <code>mz-bin-offset</code> has been changed from
+0.68 to 0.40.</li>
+
+<li>
+The <code>percolator</code> command outputs the <code>pout</code> XML format
+again (controlled by the <code>pout-output</code> parameter).</li>
+
+<li>
+The <code>percolator</code> command can output its native output by using the
+<code>original-output</code> parameter.</li>
+
+<li>
+Fixed a bug in <code>tide-search</code> causing it to fail when
+<code>remove-precursor-peak</code> removed all peaks in a spectrum.</li>
+
+<li>
+The <code>max-precursor-charge</code> parameter
+for <code>tide-search</code> has been introduced.</li>
+
+<li>
+Fixed a bug in candidate peptide selection when m/z tolerance is
+used.</li>
+
+<li>
+Added the <code>read-tide-index</code> command, which reads an index produced
+by <code>tide-index</code> and prints a list of peptides it contains.</li>
+
+<li>
+Added the <code>stop-after</code> option to print-processed-spectra, which
+controls the point at which to stop preprocessing.</li>
+
+<li>
+The <code>tide-search</code> command now accepts multiple spectrum input files.
+</li>
+
+<li>
+Added the <code>use-z-line</code> option to specify whether precursor
+information is taken from the S or Z line when parsing MS2 files using
+ProteoWizard.</li>
+
+<li>
+Added missing options to the <code>percolator</code> command.</li>
+
+<li>
+The <code>tide-search</code> command may now accept a FASTA database in
+place of the index, in which case <code>tide-index</code> will be run prior to
+the search. The <code>store-index</code> option allows the generated index
+to be saved.</li>
+
+<li>
+The <code>assign-confidence</code> command will automatically detect
+score type if the <code>score</code> parameter is not specified, searching for
+xcorr, e-value, or exact p-values.</li>
+
+<li>
+The <code>cascade-search</code> will report the source index database of the
+peptide for all identified PSMs.</li>
+
+<li>
+The <code>top-match</code> parameter has been removed from
+<code>cascade-search</code>.</li>
+
+<li>
+<code>Assign-confidence</code> has got new options: "combine-modified-peptide"
+and "combine-charge-states".</li>
+
+<li>
+<code>Assign-confidence</code> now supports top-match>1 in peptide-level filtering
+mode.</li>
+
+<li>
+<code>Assign-confidence</code> can use smoothed-p-value scores for PSM ranking.</li>
+
+<li>
+<code>Assign-confidence</code> now does not carry out target-decoy competition in
+peptide-level filtering mode.</li>
+
+<li>
+Added the <code>xlink-assign-ions</code> and <code>xlink-score-spectrum
+</code> commands.</li>
+
+<li>
+Rearranged estimation methods in <code>assign-confidence</code>.</li>
+
+<li>
+Added top-match option for <code>estimation-method=peptide-level</code>
+case in <code>assign-confidence</code>.</li>
+
+<li>
+Modified assign-confidence so that ties during target-decoy
+competition are broken randomly.</li>
+
+<li>
+Changed the Percolator output feature "file" to contain the name of
+ the file containing the spectrum (if available), rather than the
+ name of the file containing the PSM.</li>
+
+<li>
+Added to <code>search-for-xlinks</code>, <code>xlink-assign-ions</code>
+ and <code>xlink-score-spectrum</code> parameters of the form
+ "use-a-ion" for a, b, c, x, y, and z-ions.</li>
+
+<li>Various other minor bug/leak fixes and performance enhancements.</li>
+
+<li>Added the <code>allow-dups</code> option to tide-index.</li>
+
+</ul>
+
+<hr></hr>
+
+
+<h3>Version 2.1</h3> October 8, 2014
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+The <code>tide-search</code> command now supports calculation of exact
+p-values via dynamic programming, as described
+in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this
+article</a>. The p-value calculation is controlled with
+the <code>exact-p-value</code> parameter.</li>
+
+<li>
+<code>search-for-xlinks</code> now supports variable modifications and
+larger protein databases. This new code is disabled by default, but
+can be turned on by setting the
+parameter <code>use-old-xlink=F</code>.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The default value of <code>mz_bin_offset</code> has been changed to 0.40 from 0.68.</li>
+
+<li>
+The <code>centroided</code> parameter for the <code>hardklor</code> command is
+now implemented.</li>
+
+<li>
+The <code>spectrum-format</code> parameter for the <code>bullseye</code> command
+works properly.</li>
+
+<li>
+The <code>tide-search</code> command now uses information from the Z line rather
+than the S line when reading spectrum files in the MS2 file format.</li>
+
+<li>
+The <code>tide-search</code> command now accepts the
+<code>spectrum-parser</code> parameter.</li>
+
+<li>
+The <code>protein-database</code> parameter
+to <code>spectral-counts</code> now only accepts fasta files. Parsing
+of a protein index is no longer supported.</li>
+
+<li>
+A bug was fixed in the <code>spectral-counts</code> command that prevented
+<code>tide-search</code> output files from being parsed correctly.</li>
+
+<li>
+The <code>default-direction</code> parameter now takes a string value of the feature
+name rather than an integer.
+</li>
+
+<li>
+The parameters <code>mz-bin-width</code> and <code>mz-bin-offset</code> have been added
+to <code>tide-search</code>.</li>
+
+<li>
+Percolator output now includes, for each PSM, the name of the file
+in which the spectrum resides.
+</li>
+
+<li>
+The parameters <code>clip-nterm-methionine</code>, <code>keep-terminal-aminos</code>, and <code>min-mods</code> have been added to <code>tide-index</code>.
+</li>
+
+<li>
+The parameters <code>use-flanking-peaks</code>
+and <code>use-neutral-loss-peaks</code> have been added to
+<code>tide-search</code>.</li>
+
+<li>
+The calculation of XCorr was simplified in Tide. In the new version,
+<code>tide-index</code> only generates peptides and sorts them,
+leaving the generation of theoretical peaks to be done entirely on the
+fly by <code>tide-search</code>.</li>
+
+<li>
+The <code>tide-search</code> command now prints search progress reports both to
+the screen and to the log file. The interval at which progress is printed can
+be controlled using the <code>print-search-progress</code> parameter.</li>
+
+<li>
+The <code>calibrate-scores</code> command now outputs files with the stem
+"calibrate-scores" rather than "qvalue."</li>
+
+<li>
+The <code>use-flanking-peaks</code> parameter now has a default value of
+false.</li>
+
+<li>
+The Comet search engine was updated to version 2014011.</li>
+
+<li>
+The MSToolkit parser was updated to the latest version (r73).</li>
+
+<li>
+The <code>version</code> command now outputs the revision number.</code>
+
+<li>
+Various improvements in performance and error handling were implemented.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 2.0</h3> June 6, 2014
+<h4>Major enhancements</h4>
+<ul>
+
+<li>
+Two new search engines are now included in Crux: Comet and Tide. The
+old search engine, search-for-matches, has been retired.</li>
+
+<li>Percolator has been updated to version 2.07.</li>
+
+<li>
+Crux now compiles in native Windows, rather than requiring
+Cygwin. Consequently, Crux running under Windows can parse vendor
+proprietary formats using the appropriate Proteowizard libraries.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The "enyzme" parameters "lysc", "lysn", "arg_c", "glue_c", and
+"pepsin_a" were renamed to "lys-c", "lys-n", "arg-c", "glue-c", and
+"pepsin-a".</li>
+
+<li>
+Percolator outputs decoy files in addition to target files.</li>
+
+<li>
+Percolator tab-delimited peptides output now contain a posterior error
+probability (PEP) column.</li>
+
+<li>
+The Percolator tab-delimited peptide output has been corrected to show
+the PSM with the best score, rather than the worst.</li>
+
+<li>
+The Percolator tab-delimited PSMs output "matches/spectrum" value has
+been corrected.</li>
+
+<li>
+A new utility command, <code>make-pin</code>, is provided to create
+input files for use by Percolator.</li>
+
+<li>
+The <code>spectrum-min-mass</code> and <code>spectrum-max-mass</code>
+options have been renamed to <code>spectrum-min-mz</code> and
+<code>spectrum-max-mz</code>, respectively.</li>
+
+<li>
+A <code>spectrum-parser</code> option was added to <code>q-ranker</code> and
+<code>barista</code>.</li>
+
+<li>
+A bug was fixed in <code>q-ranker</code> and <code>barista</code> when
+reading peptides with modifications.</li>
+
+<li>
+Fixed the <code>q-ranker</code> tab delimited output so that, for a
+given peptide, flanking amino acids are reported for each protein that
+contains that peptide, rather than only reporting one set of flanking
+amino acids.</li>
+
+<li>
+A bug was fixed in <code>percolator</code>, wherein the first and last
+two characters were being truncated from peptide sequences when the
+input was missing the flanking amino acids or when the charge state
+was not indicated in the PSM IDs.</li>
+
+<li>
+The crux spectrum parser has been removed.</li>
+
+<li>
+Q-ranker now outputs decoy files.</li>
+
+<li>
+The Boost.Random library is now being used for random number
+generation.</li>
+
+<li>
+<code>calibrate-scores</code> no longer requires a protein input.</li>
+
+<li>
+<code>calibrate-scores</code> now only takes the top match per
+spectrum and charge.</li>
+
+<li>
+<code>get-ms2-spectrum</code> now prints z-lines with Bullseye
+files.</li>
+
+<li>
+Various performance and error handling improvements.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.40</h3> May 22, 2013
+<h4>Major enchancements</h4>
+<ul>
+
+<li>
+Crux Percolator was updated from version 1.05 to the latest release,
+version 2.04.</li>
+
+</ul>
+<h4>Minor changes</h4>
+<ul>
+
+<li>
+<p>The formula that is used to convert fragment m/z values from real
+numbers into integers was modified. Previously, the conversion was<br>
+<pre>
+ floor( (x / mz-bin-size) + 0.5 + mz-bin-offset )
+</pre>
+<br>The new conversion formula is <br>
+<pre>
+ floor( (x / mz-bin-size) + 1.0 - mz-bin-offset )
+</pre>
+<br>The default values of the two parameters (mz-bin-size and
+mz-bin-offset) have not changed. The allowed range of the
+mz-bin-offset parameter was previously [-1,1], but has been changed to
+[0,1].</p>
+
+<p>
+To understand the motivation for the changed formula, note that the
+mz-bin-offset parameter controls the location of bin edges, relative
+to integer masses on the mass scale. In general, mz-bin-offset should
+be chosen so that bin edges fall between the expected clusters of
+fragment masses. For fragments with 1+ charge, masses will cluster
+near integer values (after dividing by mz-bin-width), and the ideal
+value of mz-bin-offset would be 0.5. For mixtures of fragments with
+1+ and 2+ charges, masses will cluster near integer and half-integer
+values, so mz-bin-offset near 0.25 or 0.75 would produce bin edges
+that best avoid the clusters of fragment masses. The old conversion
+formula did not correctly locate bin edges, given a chosen
+mz-bin-offset. The new conversion formula produces a proper
+translation of mz-bin-offset into bin edge locations.</p></li>
+
+<li>
+The <code>seed</code> parameter is now available to control the
+seeding of random number generator. The default value is 1.
+<code>seed</code> is available as a parameter from all applications.
+It can be set as a command line option for
+<code>crux search-for-matches</code>
+and
+<code>crux percolator</code>.
+</li>
+
+<li>
+The default value of the <code>decoys</code> parameter for <code>crux
+search-for-matches</code> was incorrectly documented. The default is
+actually <code>peptide-shuffle</code>, but the documentation said the
+default was <code>protein-shuffle</code>. The documentation has been
+corrected.</li>
+
+<li>
+The incorrectly labeled column header <code>xcorr rank</code> in barista and
+q-ranker feature files has been corrected to <code>xcorr score</code>.
+</li>
+
+<li>
+The q-ranker output file <code>qranker_output.xml</code> has been renamed to
+<code>qranker.xml</code>.
+</li>
+
+<li>
+The deltaCn computation has been modified to be consistent with
+Percolator. Rather than using
+<br /><pre>
+ deltaCn<sub>i</sub> = (xcorr<sub>1</sub> - xcorr<sub>i+1</sub>) / xcorr<sub>1</sub>
+</pre><br />
+it is now computed using<br />
+<pre>
+ deltaCn<sub>i</sub> = (xcorr<sub>i</sub> - xcorr<sub>i+1</sub>) / max(xcorr<sub>i</sub>, 1.0)
+</pre><br />
+</li>
+
+<li>
+Percolator now accepts inputs in SQT, PepXML, and tab-delimited formats in addition to
+the PinXML format.
+</li>
+
+<li>
+Flags were added to several commands allowing the user to control
+whether various results files are created in the output directory:
+<ul>
+ <li><code>--sqt-output <T|F></code> (search-for-matches)</li>
+ <li><code>--mzid-output <T|F></code> (search-for-matches, percolator)</li>
+ <li><code>--pinxml-output <T|F></code> (search-for-matches)</li>
+ <li><code>--pepxml-output <T|F></code> (search-for-matches, q-ranker, barista, percolator)</li>
+ <li><code>--txt-output <T|F></code> (search-for-matches, q-ranker, barista, percolator)</li>
+</ul>
+By default, all of these flags are set to false except <code>txt-output</code>.
+</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.39</h3> October 6, 2012
+
+<h4>Major enchancements</h4>
+
+<ul>
+
+<li>
+Crux is now released under an Apache license for all users.
+</li>
+
+
+<li>
+Parsing MS/MS spectra is now supported using <a href="http://proteowizard.sourceforge.net/">Proteowizard</a> (v. 3.0.3950).
+This allows Crux to
+handle MS/MS spectra in mzML (1.0 and 1.1), mzXML, MGF, MS2 and CMS2
+formats.
+Use <code>spectrum-parser=pwiz</code> to enable Proteowizard parsing.</li>
+<li>
+Crux now uses <code>cmake</code> for the build process rather than
+<code>autoconf</code>/<code>automake</code>.
+</li>
+</ul>
+<h3>Minor changes</h3>
+<ul>
+
+<li>
+The Tide database search software is no longer distributed as part of Crux because its license is not compatible with the new Crux license.
+</li>
+
+<li>
+Support for PIN XML output was added to <code>crux
+search-for-matches</code>.
+</li>
+<li>
+Fixed a bug in <code>crux create-index</code> on Windows and Cygin
+that caused the program to fail with the message:
+<br /><pre>
+WARNING: Cannot rename directory
+FATAL: Failed to create index
+</pre>
+</li>
+<li>
+The parameter <code>protein database</code> is now an option rather than a required argument for <code>crux spectral-counts</code>.
+</li>
+<li>
+mzIdentML file support has been added for <code>crux spectral-counts</code>.
+</li>
+<li>
+PepXML file support has been fixed for <code>crux spectral-counts</code> .
+</li>
+<li>
+Fixed bug in packedNorm() that sometimes generated incorrect values for the posterior error probability.
+</li>
+<li>
+Fixed bug in <code>crux create-index</code> on Windows and Cygwin that caused it to fail on Windows and Cygin.
+</li>
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.38</h3> July 20, 2012
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+Hardklor and Bullseye, tools for analyzing high-resolution precursor
+spectra, are now incorporated into Crux.</li>
+
+<li>
+Barista has been modified extensively so that it more closely
+resembles the other tools in Crux:</li>
+
+<ul>
+<li>
+Barista and Q-ranker accept search results in tab-delimited format, in addition to
+SQT format.</li>
+<li>
+Barista now reports posterior error probabilities, in addition to
+q-values, for PSMs, peptides and proteins.</li>
+<li>
+Barista's pep.xml output has been updated to be compatible with the
+TransProteomic Pipeline (TPP).</li>
+</ul>
+
+<li>
+The <code>sequest-search</code> command has been removed. The
+functionality of this command is still available using options for
+the <code>search-for-matches</code> command (see
+the <a href="faq.html">frequently asked questions list</a> for
+details).</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+<code>crux predict-peptide-ions</code> calculates the mass shift
+resulting from the nh3 or h2o neutral loss correctly. Previously, a
+neutral loss resulted in an addition of mass rather than subtraction.
+</li>
+
+<li>
+<code>crux predict-peptide-ions</code> reports ion-type as
+'b','y','a', or 'p' rather than a number (i.e. 0, 1, 2, 3).</li>
+
+<li>
+<code>crux predict-peptide-ions</code> now only allows one type of
+neutral loss modification per ion. Previously, multiple different
+types of neutral loss could be applied simultaneously to a single
+ion.</li>
+
+<li>
+The <code>neutral-losses</code> option was removed from <code>crux
+predict-peptide-ions</code>, due to its redundancy with the supported
+the <code>--nh3</code> and <code>--h2o</code> options.</li>
+
+<li>
+<code>crux predict-peptide-ions</code> supports 'bya' in the
+<code>--primary-ions</code> parameter, which will generate
+the a-ion series in addition to the 'b' and 'y' ions.</li>
+
+<li>
+The spectrum parsing is updated so that peaks with zero intensity are
+ignored.</li>
+
+<li>
+<code>crux spectral-counts</code> now has an option to compute the raw
+spectral count.</li>
+
+<li>
+<code>crux spectral-counts</code> now has an option to compute dNSAF
+values.</li>
+
+<li>
+A bug in <code>crux spectral-counts</code> was fixed so that it now
+properly normalizes the NSAF value.</li>
+
+<li>
+Multiple missed cleavages are now handled by <code>crux
+search-for-xlinks</code> using the missed-cleavages parameter.
+Previously, this was unsupported.</li>
+
+<li>
+Ambiguous amino acids are handled differently. 'J' is interpreted to
+indicate 'I' or 'L'. Peptides containing B, Z, and X are no longer be
+allowed, and a warning is issued when these amino acid codes are
+encountered.</li>
+
+<li>
+The stand-alone <code>crux-predict-peptide-ions</code>
+and <code>crux-generate-peptides</code> applications have been integrated
+into the main <code>crux</code> application.</li>
+
+<li>
+A bug has been fixed that affected the intensity adjustment of
+observed spectra when the bin width was set much larger or smaller
+than 1.</li>
+
+<li>
+Beginning with version 1.37, q-ranker erroneously included decoy PSMs
+along with target PSMs in the q-ranker.target.psms.txt file. All PSMs
+were sorted by q-ranker score so the targets and decoys were mixed
+together with no accompanying labels. This bug has been fixed so that
+Q-ranker once again returns only target PSMs.</li>
+
+<li>
+The search option <code>display-summed-masses</code> has been replaced by
+<code>mod-mass-format</code>. With this option, there is a new format
+for reporting modificiations: the mass in the square braces is that of the
+preceeding amino acid plus the modification mass. This format is compliant
+with TPP pep.xml output.</li>
+
+<li>
+Modifications are reported differently in the pep.xml header to be
+compliant with the TPP.</li>
+
+<li>
+The command <code>crux compute-q-values</code> now reports posterior
+error probabilities in addition to q-values. Consequently, the
+command was renamed <code>crux calibrate-scores</code>.</li>
+
+<li>
+Crux now provides an explicit error message when an incorrectly
+formatted MS2 file is parsed. Previously, crux simply reported that
+no spectra were found.</li>
+
+<li>
+Several additional scores were added to the <code>q-ranker</code>
+pep.xml files.</li>
+
+<li>Fixed the build procedure to work on both Lion and pre-Lion versions of OS X.</li>
+
+<li>Fixed a bug in the normalization of the observed spectra.
+Previously, after the 10-bin normalization of intensities, peaks with
+heights below 5% of the maximum were not being removed.</li>
+
+<li>
+When a fragmentation spectra file is read, the assumed
+peptide charge state information can be missing for the scans.
+In cases where this information has not been provided,
+Crux will now estimate the possible charge states.
+</li>
+
+<li>
+The feature files for Q-ranker and Barista now contain a header
+describing each feature.
+</li>
+
+<li>
+Q-ranker and Barista now output all of the fields provided in the
+input search files.
+</li>
+
+</ul>
+
+<hr></hr>
+
+
+<h3>Version 1.37</h3> December 22, 2011
+
+<h4>Major enhancements</h4>
+
+<ul>
+<li>
+Added <code>crux barista</code>, a tool for inferring protein
+identifications.</li>
+
+<li>
+Reimplemented <code>crux q-ranker</code> with new outputs and
+command-line syntax.</li>
+
+<li>
+Percolator and compute-q-values now compute and report posterior error
+probabilities, in addition to q-values.</li>
+
+<li>
+<code>crux create-index</code> now generates and store decoy
+peptides in the index. Decoys can still be generated on-the-fly when
+searching .fasta files.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+A pair of options, <code>cterm-fixed</code>
+and <code>nterm-fixed</code>, allow fixed terminal peptide
+modifications, i.e., a mass shift applied to every peptide on either or
+both termini.</li>
+
+<li>
+A bug in the spectrum processing code was fixed, which was erroneously
+eliminating a few of the highest m/z fragment peaks. Xcorrs have
+changed slightly as a result.</li>
+
+<li>
+Simplified the <code>--mz-bin-width</code> and
+</code>--mz-offset</code> parameters so that <code>--xcorr-var-bin</code>
+is no longer needed.</li>
+
+<li>
+Indexes now store information about any static mods used when they
+were created.</li>
+
+<li>
+In the tab-delimited output files the 'matches/spectrum' column gives
+the number of target peptides compared to the spectrum and the decoy
+file has an additional column, 'decoy matches/spectrum' that gives the
+number of decoy peptides compared to the spectrum. These two numbers
+may differ when decoys are not generated on-the-fly.</li>
+<li>
+The header lines of Barista and QRanker include all of the columns
+in the search results.</li>
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.36</h3> August 4, 2011
+
+<h4>Tide changes</h4>
+
+<ul>
+
+<li>
+Added support for user-specifiable variable and static amino acid
+modifications.</li>
+
+<li>
+Tide's version of XCorr has been modified so that it is always
+identical to those of a recent version SEQUEST<sup>®</sup>.</li>
+
+<li>
+Added support for user-specifiable maximum number of missed enzyme
+cleavage points.</li>
+
+<li>
+Tide now performs basic charge state inference when this information
+is missing from the spectrum input files.</li>
+
+<li>
+User-specifiable output formatting, using new
+the <code>tide-results</code> utility, including
+ <ul>
+ <li>Text format with user-specifiable fields.
+ <li>SQT format.
+ <li>PepXML format.
+ <li>Choose whether to display all proteins in which each peptide occurs or
+just one representative.
+ </ul>
+
+<li>
+Note that new file formats are created
+by <code>tide-index</code>. Index files created by previous versions
+of Tide should not be used with the new version.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+<li>
+Q-ranker now reports q-values instead of false discovery rates.</li>
+
+<li>
+Corrected several errors in the pep.xml output, related to reporting
+the spectrum filename, charge, and neutral mass.</li>
+
+<li>
+Changed the <code>missed-cleavages</code> option to allow specifying
+the maximum number of missed cleavages in a peptide rather than
+specifying none/any.</li>
+
+<li>
+Fixed a bug that did not print the spectrum file name correctly in the
+pep.xml files.</li>
+
+<li>
+Improved the error message produced by <code>crux
+spectral-counts</code> when the input PSM file does not contain the
+required q-values.</li>
+
+<li>
+Previously, Crux's theoretical spectrum includes two flanking peaks
+around each b- and y-ion. The new
+Boolean flag <code>use-flanking-peaks</code>, allows these to be
+either on or off. Flanking peaks are by default in
+<code>crux sequest-search</code> but are not used by default
+in <code>crux search-for-matches</code>.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.35</h3> March 23, 2011
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+Added the <code>crux spectral-counts</code> command for estimating
+protein quantification.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The spectrum neutral mass is now calculated from the m+h value
+provided by the Z-lines of an MS2 file. Also, multiple z-lines of a
+spectrum that have the same charge are now supported. With these
+changes, <code>crux search-for-matches</code> and <code>crux
+sequest-search</code> can now take advantage of accurate precursor
+masses in MS2 files generated by Bullseye (Hsieh et al. <i>J. Proteome
+Res.</i> 9(2):1138-43, 2010).</li>
+
+<li>
+Made the <code>pep.xml</code> file header produced by Crux compatible
+with the Transproteomic Pipeline.</li>
+
+<li>
+Introduced several changes to improve performance on MacOS X.</li>
+
+<li>
+Added an <code>nterm</code> option to the link argument of <code>crux
+search-for-xlinks</code>.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.34</h3> December 22, 2010
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The default value of the "pi-zero" parameter has been changed from 0.9
+to 1.0.</li>
+
+<li>
+A new option <code>--peptide-list</code> has been added to <code>crux
+create-index</code>. When set to T, this option causes an ASCII
+file of peptides to be included in the output directory. Each line
+of the file lists the peptide sequence and its neutral mass.</li>
+
+<li>
+The default bin offset was returned to 0.68. It had erroneously been
+changed to 0 in version 1.33.</li>
+
+<li>
+A new option <code>--compute-sp</code> has been added to <code>crux
+search-for-matches</code>. When set to true, all candidate peptides
+will be scored by Sp in addition to xcorr. This option is recommended
+for generating input to <code>percolator</code>
+or <code>q-ranker</code>.</li>
+
+<li>
+Added <code>max-ion-charge</code> parameter to designate the maximum
+charge for theoretical ions in <code>crux search-for-xlinks</code> and
+<code>crux xlink-assign-ions</code>.
+
+<li>
+Modifications may optionally indicate if they prevent cleavage or
+prevent cross linking.
+
+<li>
+Results are printed to .pep.xml files in addition to .txt files.
+
+<li>
+Added a <code>mass-precision</code> option which sets how many digits
+are written for all mass and m/z values in .txt, .sqt, and .ms2 files.
+
+<li>
+The columns printed to the .txt files now vary with the
+<code>crux</code> command being run and the settings so that unused
+columns are not printed.
+
+<li>
+Fixed a bug that limited what files were used as input for post-search
+commands (e.g. <code>crux percolator</code>) based on fileroot. Now
+files with different fileroots can be analyzed together.
+
+<li>
+Fixed a bug that caused searches using fasta files to search peptides
+multiple times if they appeared in a file multiple times.
+
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.33</h3> July 7, 2010
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+The command line syntax
+for <code>compute-q-values</code>, <code>percolator</code>
+and <code>q-ranker</code> was modified to allow the programs to read
+from and write to separate directories.</li>
+
+<li>
+A bug in q-ranker and percolator was fixed. This bug was introduced
+several versions ago, and it led to erroneously many PSMs receiving
+very small q-values. The problem relates to the scaling of the delta
+Cn feature, and the fix is a temporary stopgap: we remove the feature
+entirely. The next version should have the corrected feature in
+place.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+A new option <code>--min-peaks</code> has been added to set a filter
+for the minimum number of peaks a spectrum must have in order for it
+to be searched. The default minimum is 20 peaks.</li>
+
+<li>
+The hardcoded limit for the number of proteins allowed in a database
+has been removed.</li>
+
+<li>
+The hardcoded limit for the number of spectra and the number of
+peaks/spectrum has been removed.</li>
+
+<li>
+A new option <code>--xcorr-var-bin</code> has been added to toggle the
+new binning of the m/z axis. The default bin offset was returned back
+to 0, but the default bin width is still 1.000508. (<i>Note: this
+erroneous change was subsequently reverted in version 1.34</i>.)
+</li>
+
+<li>
+The option <code>--max-ion-charge</code> now places a limit on the
+maximum charge state of the ions generated for the xcorr theoretical
+spectra for <code>crux search-for-xlinks</code>. This change is also
+supported by <code>xlink-assign-ions</code>.
+
+<li>
+The option <code>--no-xval</code> was added to q-ranker, allowing
+faster execution by skipping the internal cross-validation to select
+hyperparameters.</li>
+
+<li>
+The precision of modification masses written to the .txt files now matches
+the maximum precision given in the parameter file.
+
+<li>
+Sub-options <code>prevents cleavage</code> and
+<code>prevents cross-link</code> have been added to variable modifications
+and support has been provided for the <code>"prevents cleavage"</code>
+sub-option.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.32</h3> July 6, 2010
+
+<h4>Major enhancement</h4>
+
+<ul>
+
+<li>
+Version 1.32 includes changes only to Tide. A new binary is introduced
+— a modified version of ProteoWizard's <b>msconvert</b> program
+— that is capable of converting spectrum data from a wide range
+of file formats into Tide-readable <i>.spectrumrecords</i> input
+files.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+<b>tide-import-spectra</b> is removed from the distribution. Although
+it was faster than msconvert, it was specific to ms2 files, whereas
+msconvert now works with any ProteoWizard-supported file format.</li>
+
+<li>
+A standalone utility for reading binary <i>.spectrumrecords</i> files
+is introduced, called <b>read-spectrumrecords</b>. This program is
+useful, for example, for visually checking the output of msconvert.</li>
+
+<li>
+Demo input files <b>worm-06-10000.spectrumrecords</b>
+and <b>yeast-02-10000.spectrumrecords</b> now replace their
+counterparts worm-06-10000.ms2 and yeast-02-10000.ms2. With the
+introduction of Tide-compatible msconvert, ms2 files are in no way
+special to Tide anymore. Any ProteoWizard-supported file format can be
+converted to the <i>.spectrumrecords</i> format for use with
+Tide. Starting with data files in Tide's spectrumrecords format
+eliminates the conversion step in the Tide search demo.</li>
+
+<li>
+The old demo scripts worm-demo.sh and yeast-demo.sh have each been
+replaced by a pair of new scripts that demonstrate the indexing and
+searching steps separately. This is in order to highlight the two-step
+process and the fact that indexing needs to be done just once for each
+fasta file, whereafter the index may be reused indefinitely to perform
+searches.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.31</h3> June 2, 2010
+
+<h4>Major enhancements</h4>
+
+<ul>
+
+<li>
+This version of Crux is released with a demo version of a new search
+engine, Tide. Tide is an independent
+reimplementation of the SEQUEST<sup>®</sup> algorithm. The
+immediate ancestor of Tide is the Crux <code>search-for-matches</code>
+command, but Tide has been completely re-engineered to achieve a
+thousandfold improvement in speed while exactly replicating Crux XCorr
+scores. Currently, Tide is not fully integrated with Crux, and is
+available only in binary executable format.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+<li>
+Two options have been added to <code>crux search-for-matches</code>
+(<code>--mz-bin-width</code> and <code>--mz-bin-offset</code>) to
+allow control of the binning of the m/z axis.</li>
+
+<li>
+The <code>ion-tolerance</code> option was removed from the search
+tools.</li>
+
+<li>
+The default location of the left edge of the first bin along the m/z
+axis is 0.68, rather than 0.0. This change makes bin edges less
+likely to fall near fragment peak locations. The default bin width
+has also changed from 1.001141 to 1.000508</li>
+
+<li>
+The log file now includes information about the date and time that the
+command was issued, the name of the computer on which the command was
+run, and the elapsed wall clock time at the end of the run.</li>
+
+<li>
+The command line option <code>--version T</code> has been replaced
+with a command <code>crux version</code> that prints the version
+number to standard output and then exits.</li>
+
+<li>
+The header for the feature file produced optionally by
+<code>crux percolator</code> and <code>crux q-ranker</code> now includes names
+for the first two columns, scan number and label (i.e. target or decoy peptide).
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.30</h3> May 5, 2010
+
+<h4>Major enhancements</h4>
+
+<ul>
+<li>
+A new command, <code>xlink-search</code>, has been added. This command
+searches a collection of spectra against a sequence database, finding
+cross-linked peptide matches. The algorithm was described in the
+following article:</li>
+
+<blockquote>
+Sean McIlwain, Paul Draghicescu, Pragya Singh, David R. Goodlett and
+William Stafford
+Noble. <a href="http://noble.gs.washington.edu/proj/xhhc/">"Detecting
+cross-linked peptides by searching against a database of cross-linked
+peptide pairs."</a> <i>Journal of Proteome Research</i>. 2010.
+</blockquote>
+
+<li>
+A new search command, <code>sequest-search</code>, was added. The
+original command, <code>search-for-matches</code>, behaves as before
+except that no .sqt files are printed and no Sp scoring is performed.
+The new <code>sequest-search</code> emulates SEQUEST<sup>®</sup>
+searching. It first scores all candidate peptides with the Sp score,
+then ranks and filters the results by that score, scoring the
+remaining candidates with xcorr. Results are printed to .txt and .sqt
+files.</li>
+
+<li>
+The .mzXML file format is now supported for crux search-for-matches
+and crux sequest-search when the <code>--use-mstoolkit</code> option
+is set to TRUE.</li>
+
+<li>
+The .csm output files from <code>search-for-matches</code> are no
+longer produced and post-search operations take .txt files as input.
+</li>
+
+</ul>
+
+<h4>
+Minor changes</h4>
+
+<ul>
+
+<li>
+Replaced <code>mass-window</code> parameter with <code>
+precursor-window</code> and added <code>precursor-window-type</code>
+for selecting windows of type mass, m/z, or ppm.
+</li>
+
+<li>
+The <code>feature-file</code> option is now true/false instead of
+taking a file name. The file is named '<fileroot>.<qranker|
+percolator>.features.txt'. A header with the column names was
+added to the file.</li>
+
+<li>
+The new option, <code>--scan-number</code>, performs a search on a
+specified subset of the spectra in the given file.</li>
+
+<li>
+When only one decoy file is produced, the name is now 'decoy.txt'
+instead of 'decoy-1.txt'
+
+<li>
+In the .txt files, protein names are now followed by the start index
+of the peptide.
+
+<li>
+Modified sequences are reported differently in the .txt files.
+Instead of modifications being represented by symbols (*,@,#, etc.)
+they are indicated with the mass shift of the modification within
+square brackets. As before, the modification information follows the
+residue that is modified. If multiple modifications appear on one
+residue, the masses may either be summed together or printed
+separately in a comma separated list. This behavior is controlled by
+the <code>--display-summed-mod-masses</code> option.</li>
+
+<li>
+The modified decoy sequences are generated differently. Before, all
+modified peptides were generated and each one was shuffled to create a
+decoy peptide. Now a peptide is shuffled once for each peptide_mod
+and all modifications are applied to that same shuffled peptide.</li>
+
+<li>
+The 'percolator rank' column is now based on percolator scores instead
+of percolator q-values. For cases where two PSMs have different
+percolator scores but the same q-value, the ranks will reflect the
+score differences.</li>
+
+<li>
+The Weibull parameters used for computing p-values are now printed to
+the .txt files.</li>
+
+<li>
+The reporting of DeltaCn has changed. For PSMs of rank i, deltaCn
+used to computed be as deltaCn_i = (xcorr_0 - xcorr_i) / xcorr_0.
+Thus, deltaCn for the top-ranked PSM was always 0. Now deltaCn_i =
+(xcorr_0 - xcorr_i+1) / xcorr_0. This change only
+affects <code>search-for-matches</code>,
+not <code>sequest-search</code>. It also means that
+<code>q-ranker</code> and <code>percolator</code> use the correct
+DeltaCn values.
+</li>
+
+<li>
+A new command, <code>print-processed-spectra</code>, performs
+XCorr-style pre-processing on all spectra in a given file.</li>
+
+<li>
+A small bug was fixed, in which even if the user requested average
+mass, the search programs still used monoisotopic mass in the
+calculation of XCorr and Sp.</li>
+
+<li>
+Protein fasta files are now parsed protein-by-protein so that parsing
+large files does not use excessive amounts of memory.</li>
+
+<li>
+A limit was removed on how many peptides a protein can produce.</li>
+
+<li>
+Crux is now built with g++ instead of gcc.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.22</h3> September 16, 2009
+
+<h4>
+Major enhancements</h4>
+
+<ul>
+
+<li>
+Crux is now distributed in two versions, a full version that is
+covered by the same type of license as before (free to non-profit
+users, and via a licensing fee to commercial users), as well as a
+stripped-down version that is released under an open source license.
+The stripped-down version does not include the database search
+functionality but does include all of the post-processing tools. We
+are unable to release the entire Crux package under an open source
+license due to intellectual property issues. Both versions of Crux
+are available via the Crux web
+page: <a href="http://noble.gs.washington.edu/proj/crux/">http://noble.gs.washington.edu/proj/crux/</a>.</li>
+
+<li>
+A new tool, q-ranker, is available for estimating peptide-spectrum
+match q-values. This tool was described in the following article:
+
+<blockquote>
+Marina Spivak, Jason Weston, Leon Bottou, Lukas Käll and William
+Stafford Noble. "Improvements to the Percolator algorithm for peptide
+identification from shotgun proteomics data sets." <i>Journal of
+Proteome Research.</i></blockquote></li>
+
+<li>
+Version 1.05 of <code>percolator</code> has now been integrated into
+the Crux source tree. A separate installation
+of <code>percolator</code> is no longer needed for basic
+<code>percolator</code> functionality. Note, however,
+that <code>percolator</code> remains under active development. You
+may therefore wish to install the current, stand-alone version
+of <code>percolator</code> and run it separately to take advantage of
+new features.</li>
+
+</ul>
+
+<h4>Minor changes</h4>
+
+<ul>
+
+<li>
+The internal normalization of the observed spectra has been modifed to
+drop those peaks whose intensity is less than 1/20 of the maximum
+intensity in the spectrum. This brings the xcorr score
+for <code>crux</code> into closer agreement with the xcorr score
+for SEQUEST<sup>®</sup>.</li>
+
+<li>
+Compute-q-values now generates three different q-values (1) from
+p-values using an analytical null model, (2) from decoys and xcorr
+using an empirical null model, or (3) from decoys and p-values using
+an empirical null model. All three types of q-values are computed
+when p-values and decoys are present in the search results.</li>
+
+<li>
+A parameter file is now automatically written to the output
+directory.</li>
+
+<li>
+A log file recording messages sent to stderr has been added for
+<code>search-for-matches</code>, <code>compute-q-values</code>,
+and <code>percolator</code>.</li>
+
+<li>
+The <code>--use-mz-window</code> parameter is now available for
+<code>search-for-matches</code>. When enabled, peptides must be
+within +/- 'm/z-window' of the spectrum m/z. The m/z-window value is
+taken from <code>mass-window</code>.</li>
+
+<li>
+A numerical bug in the Weibull p-value calculation was fixed, which
+had previously caused occasional erroneous NaNs to be output.</li>
+
+<li>
+The Weibull estimated p-values generated
+by <code>search-for-matches</code> are now returned as p-values
+instead of as -log(p-value). The corresponding q-values returned from
+<code>compute-q-values</code> are also now returned without the -log
+transform.</li>
+
+<li>
+The <code>--precision</code> option has been changed to control the
+total number of significant digits printed instead of the number of
+digits after the decimal point. The default precision has changed
+from 6 to 8.</li>
+
+<li>
+The parameters estimated for the Weibull distribution (used for
+computing p-values) now use the xcorrs from all PSMs for a spectrum
+instead of a random selection of 500.</li>
+
+<li>
+The estimation of Weibull distribution parameters requires a minimum
+number of scored PSMs. In the previous version, spectra with fewer
+PSMs than the minimum were not given a p-value. Crux will now
+generate extra decoys until there are enough scores.</li>
+
+<li>
+The p-values for decoy PSMs are now generated from the same Weibull
+distribution parameters as are used for the targets of the same
+spectrum.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.21</h3> May 14, 2009
+
+<ul>
+
+<li>
+The output for <code>search-for-matches</code>,
+<code>compute-q-values</code>, and <code>percolator</code>
+has been revised extensively.
+<code>crux</code> will now create a directory, and all output files
+will be created in that directory.
+By default the directory will be named <code>crux-output</code>,
+but this can be changed using the new <code>output-dir</code> option.
+<br>
+The output files for <code>search-for-matches</code> will be:
+<ul>
+<li><code>search.target.csm</code></li>
+<li><code>search.decoy-?.csm</code></li>
+<li><code>search.target.sqt</code></li>
+<li><code>search.target.txt</code></li>
+</ul>
+The output files for <code>compute-q-values</code> will be:
+<ul>
+<li><code>qvalues.target.sqt</code></li>
+<li><code>qvalues.target.txt</code></li>
+</ul>
+The output files for <code>percolator</code> will be:
+<ul>
+<li><code>percolator.target.sqt</code></li>
+<li><code>percolator.target.txt</code></li>
+</ul>
+</li>
+<li>
+The <code>fileroot</code> option has been added.
+This option is used to specify a string which will be added as a prefix
+to all output files.
+</li>
+<li>
+The option <code>cleavages</code> was replaced with two
+options, <code>enzyme</code> which specifies the name of an enzyme
+(e.g.trypsin) and <code>digestion</code> which indicates
+the degree of specificity, partial or full digest. The full list of
+available enzymes is in the html docs and in the usage statement.
+See also <code>custom-enzyme</code> below.
+
+<li>
+The option <code>custom-enzyme</code> allows users to define arbitrary
+digestion rules. This overrides the <code>enzyme</code> option.
+Syntax for the custom digestion rule is the same the syntax used by
+X!Tandem and is described in the html docs.
+
+<li>
+The number of PSMs per spectrum printed to the output files is now
+controlled by one option, <code>top-match</code>. This
+makes <code>max-sqt-result</code> obsolete.
+
+<li>
+It is now possible to control how many decoy sequences are generated
+and in which file(s) they are returned. There is a new
+option, <code>num-decoys-per-target</code>, which can be used to
+generate more than one shuffled peptide per spectrum. This
+replaces <code>number-decoy-set</code>.
+
+<li>
+A new option, <code>decoy-location</code> has been introduced. The
+three possible values are 'target-file' where all PSMs (target and
+decoys) are sorted together for each spectrum and returned in one
+file, 'one-decoy-file' where target PSMs are printed to one file and
+all decoys are printed to another, and 'separate-decoy-files' where
+there are as many decoy files as there are decoys per target.
+
+<li>
+Protein names for decoy matches are now prepended with 'rand_' in the
+SQT files as in
+'L rand_Y45678'.
+
+<li>
+The option <code>unique-peptides</code> only applies
+to <code>crux-generate-matches</code>. Each peptide is stored in the
+index exactly once with references to all protein sources. Searches with
+fasta files print each peptide only once.
+
+<li>
+The precision of the masses and scores printed to the sqt and text
+files can now be specified by the user. The default precision changed
+from 2 to 6.</li>
+
+<li>
+Search progress is now reported by printing every 10th spectrum that is
+searched. The verbosity can be adjusted with the parameter
+<code>print-search-progress</code>.
+
+<li>
+Decoy (shuffled) sequences now keep the first and last residue the
+same as the target sequence that was shuffled to produce it. This is
+a reversion to previous behavior.
+
+<li>
+It is now possible to skip the Sp score and score all PSMs with xcorr.
+The default procedure is still to score all peptides for one spectrum
+with Sp, rank by Sp, and eliminate all but the best-ranking PSMs (by
+default, the top 500). The remaining PSMs are scored by xcorr,
+re-ranked by xcorr and the top results returned. By setting
+max-rank-preliminary=0, the Sp scoring is skipped and xcorr is
+computed for all PSMs.</li>
+
+<li>
+A new parameter <code>reverse-sequence</code> can be used to generate
+decoy peptides by reversing them rather than shuffling. The first and
+last residues are left unmoved. If the sequence is a palindrome ,
+then a decoy will be generated by shuffling and a note to that effect
+will be printed at the DETAILED INFO level of output (verbosity =
+40).</li>
+
+<li>
+P-values are now computed for decoy peptides.</li>
+
+<li>
+The algorithm used to calculated the xcorr score has been modified so
+that xcorr score will be in better agreement with scores generated by
+SEQUEST<sup>®</sup>.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.20</h3> January 6, 2009
+
+<ul>
+
+<li>
+Generating peptides and searching with up to eleven different dynamic
+modifications is now possible. New options associated with this
+feature are mod, cmod, nmod, max-mods, max-aas-modified.
+
+<li>
+The format of the .csm files has changed and files written by older
+versions of crux are not readable with crux version 1.2.
+
+<li>
+When the option <code>cleavages</code> is set to <code>all</code>,
+peptide generation ignores all tryptic cleavage sites, effectively setting
+the <code>missed-cleavages</code> option to <code>TRUE</code>
+regardless of user settings.
+
+<li>
+When one spectrum has identical xcorr scores for different sequences,
+the rank of all those matches will be the same. Matches with the next
+highest score will rank one below.
+
+<li>
+The options for setting the preliminary and primary score type have
+been removed and are fixed as Sp and xcorr, respectively. A new
+option, <code>compute-p-values=<T | F></code>, was added to
+control p-value computation.
+
+<li>
+The SQT file contains the spectrum calculated mass instead of observed
+mass/charge on the S line.
+
+<li>
+There is now a test for confirming that the file downloaded from the
+crux website was not corrupted. See installation instructions for
+details.
+
+<li>
+Calculating a p-value requires a minimum of 40 matches. Spectra with
+fewer than 40 matches will have p-value scores returned as NaN and a
+warning will be printed at the DETAILED_INFO level (40) of verbosity.
+
+<li>
+Fixed error in generating neutral-loss peaks created as part of the
+theoretical spectrum.
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.02</h3> December 1, 2008
+
+<ul>
+
+<li>
+Three programs, <code>crux-create-index</code>,
+<code>crux-search-for-matches</code>,
+and <code>crux-analyze-matches</code>, were merged into one program
+named
+<code>crux</code>.</li>
+
+<li>
+Percolator is now truly optional as all Crux programs will build
+without it.</li>
+
+<li>
+Fragment masses can now be calculated as average or mono-isotopic.
+This is controlled by the <code>fragment-mass</code> option in the
+parameter file.</li>
+
+<li>
+The name of the score-type option that calculates p-values was changed
+from xcorr-logp to xcorr-pvalue.</li>
+
+<li>
+SQT files have two new lines in the header which describe the
+arrangement of values in the results.</li>
+
+<li>
+HTML documentation was updated to reflect the above changes.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.01</h3>
+
+<p>October 15, 2008</p>
+
+<ul>
+
+<li>
+A bug limiting the length of the name of an index file was fixed.</li>
+
+<li>
+Modifications were made so that Crux will build with version
+1.05 of Percolator. This is the only supported version of
+Percolator.</li>
+
+<li>
+Memory leaks in <code>crux-search-for-matches</code> were patched.</li>
+
+<li>
+The <code>--version</code> option was added.</li>
+
+</ul>
+
+<hr></hr>
+
+<h3>Version 1.0</h3>
+
+<p>March 4, 2008</p>
+
+<blockquote>
+Initial release
+</blockquote>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
+
diff --git a/doc/user/runall b/doc/user/runall
new file mode 100755
index 0000000..94d37db
--- /dev/null
+++ b/doc/user/runall
@@ -0,0 +1,28 @@
+#!/bin/bash -x
+
+# These three options make it harder to for some part of a script to
+# fail without you recognizing it. nounset means that references to an
+# unset variable result in an error. This means that you can no longer
+# do stuff like this if VAR is potentially unset, because "$VAR" returns
+# an error rather than "":
+#
+# if [ "$VAR" ]; then
+#
+# fi
+#
+# To explicitly indicate that you are OK with the variable potentially
+# being empty you can instead use ${VAR:-}.
+
+# To avoid errexit for a single command, use "|| true", e.g.,
+# diff foo foobar || true
+
+set -o nounset
+set -o pipefail
+set -o errexit
+set -o xtrace
+
+CRUX=../../src/crux
+for command in `$CRUX create-docs list`; do
+ $CRUX create-docs $command > $command.html
+done
+$CRUX create-docs default-params > default.params
diff --git a/doc/user/search-for-xlinks.html b/doc/user/search-for-xlinks.html
new file mode 100644
index 0000000..0af3430
--- /dev/null
+++ b/doc/user/search-for-xlinks.html
@@ -0,0 +1,256 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>search-for-xlinks</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>search-for-xlinks</h1>
+<h2>Usage:</h2>
+<p><code>crux search-for-xlinks [options] <ms2 file> <protein fasta file> <link sites> <link mass></code></p>
+<h2>Description:</h2>
+<p>This command compares a set of spectra to cross-linked peptides derived from a protein database in FASTA format. For each spectrum, the program generates a list of candidate molecules, including linear peptides, dead-end products, self-loop products and cross-linked products, with masses that lie within a specified range of the spectrum's precursor mass. These candidate molecules are ranked using XCorr, and the XCorr scores are assigned statistical confidence estimates using an empiri [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+ <li><code>protein fasta file</code> – The name of the file in FASTA format from which to retrieve proteins.</li>
+ <li><code>link sites</code> – A comma delimited list of the amino acids to allow cross-links with. For example, "A:K,A:D" means that the cross linker can attach A to K or A to D. Cross-links involving the N-terminus of a protein can be specified as a link site by using "nterm". For example, "nterm:K" means that a cross-link can attach a protein's N-terminus to a lysine.</li>
+ <li><code>link mass</code> – The mass modification of the linker when attached to a peptide.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>search-for-xlinks.target.txt</code> – a tab-delimited text file containing the peptide-spectrum matches (PSMs). See the <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>search-for-xlinks.decoy.txt</code> – a tab-delimited text file containing the decoy PSMs. See the <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>search-for-xlinks.qvalues.txt</code> – a tab-delimited text file containing the top ranked PSMs with calculated q-values. See the <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>search-for-xlinks.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>search-for-xlinks.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>search-for-xlinks options</h3>
+<ul>
+ <li class="nobullet"><code>--require-xlink-candidate T|F</code> – If there is no cross-link candidate found, then don't bother looking for linear, self-loop, and dead-link candidates. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--xlink-top-n <integer></code> – Top-n open-mod peptides to consider in the second pass, value of 0 will search all candiates. Default = <code>250</code>.</li>
+ <li class="nobullet"><code>--cmod <string></code> – Specify a variable modification to apply to C-terminus of peptides. <mass change>:<max distance from protein c-term (-1 for no max)>. Note that this parameter only takes effect when specified in the parameter file. Default = <code>NO MODS</code>.</li>
+ <li class="nobullet"><code>--nmod <string></code> – Specify a variable modification to apply to N-terminus of peptides. <mass change>:<max distance from protein n-term (-1 for no max)> Note that this parameter only takes effect when specified in the parameter file. Default = <code>NO MODS</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Peptide properties</h3>
+<ul>
+ <li class="nobullet"><code>--min-mass <float></code> – The minimum mass (in Da) of peptides to consider. Default = <code>200</code>.</li>
+ <li class="nobullet"><code>--max-mass <float></code> – The maximum mass (in Da) of peptides to consider. Default = <code>7200</code>.</li>
+ <li class="nobullet"><code>--min-length <integer></code> – The minimum length of peptides to consider. Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--max-length <integer></code> – The maximum length of peptides to consider. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--isotopic-mass average|mono</code> – Specify the type of isotopic masses to use when calculating the peptide mass. Default = <code>mono</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Amino acid modifications</h3>
+<ul>
+ <li class="nobullet"><code>--mod <string></code> – Consider modifications on any amino acid in aa list with at most max-per-peptide in one peptide. The parameter takes the form <mass change>:<aa list>:<max per peptide>:<prevents cleavage>:<prevents cross-link>. This parameter may be included with different values multiple times so long as the total number of mod, cmod, and nmod parameters does not exceed 11. The "prevents cleavage" and "prevent [...]
+ <li class="nobullet"><code>--max-mods <integer></code> – The maximum number of modifications that can be applied to a single peptide. Default = <code>255</code>.</li>
+ <li class="nobullet"><code>--A <float></code> – Change the mass of all amino acids 'A' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--C <float></code> – Change the mass of all amino acids 'C' by the given amount. Default = <code>57.021464</code>.</li>
+ <li class="nobullet"><code>--D <float></code> – Change the mass of all amino acids 'D' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--E <float></code> – Change the mass of all amino acids 'E' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--F <float></code> – Change the mass of all amino acids 'F' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--G <float></code> – Change the mass of all amino acids 'G' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--H <float></code> – Change the mass of all amino acids 'H' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--I <float></code> – Change the mass of all amino acids 'I' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--K <float></code> – Change the mass of all amino acids 'K' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--L <float></code> – Change the mass of all amino acids 'L' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--M <float></code> – Change the mass of all amino acids 'M' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--N <float></code> – Change the mass of all amino acids 'N' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--P <float></code> – Change the mass of all amino acids 'P' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--Q <float></code> – Change the mass of all amino acids 'Q' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--R <float></code> – Change the mass of all amino acids 'R' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--S <float></code> – Change the mass of all amino acids 'S' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--T <float></code> – Change the mass of all amino acids 'T' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--V <float></code> – Change the mass of all amino acids 'V' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--W <float></code> – Change the mass of all amino acids 'W' by the given amount. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--Y <float></code> – Change the mass of all amino acids 'Y' by the given amount. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Decoy database generation</h3>
+<ul>
+ <li class="nobullet"><code>--seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+ <li class="nobullet"><code>--custom-enzyme <string></code> – Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. If the residues are required for digestion, they are in square brackets, '[' and ']'. If the re [...]
+ <li class="nobullet"><code>--digestion full-digest|partial-digest|non-specific-digest</code> – Specify whether every peptide in the database must have two enzymatic termini (full-digest) or if peptides with only one enzymatic terminus are also included (partial-digest). Default = <code>full-digest</code>.</li>
+ <li class="nobullet"><code>--missed-cleavages <integer></code> – Maximum number of missed cleavages per peptide to allow in enzymatic digestion. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Precursor selection</h3>
+<ul>
+ <li class="nobullet"><code>--precursor-window <float></code> – Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> – Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not avail [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-min-mz <float></code> – The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum-max-mz <float></code> – The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
+ <li class="nobullet"><code>--spectrum-charge 1|2|3|all</code> – The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge state will be searched. Default = <code>all</code>.</li>
+ <li class="nobullet"><code>--compute-sp T|F</code> – Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spe [...]
+ <li class="nobullet"><code>--precursor-window-weibull <float></code> – Search decoy peptides within +/- precursor-window-weibull of the precursor mass. The resulting scores are used only for fitting the Weibull distribution Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type-weibull mass|mz|ppm</code> – Window type to use in conjunction with the precursor-window-weibull parameter. Default = <code>mass</code>.</li>
+ <li class="nobullet"><code>--min-weibull-points <integer></code> – Keep shuffling and collecting XCorr scores until the minimum number of points for weibull fitting (using targets and decoys) is achieved. Default = <code>4000</code>.</li>
+ <li class="nobullet"><code>--max-ion-charge <string></code> – Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state of the peptide ("peptide"). If the max-ion-charge is greater than the charge state of the peptide, then the maximum is the peptide charge. Default = <code>peptide</code>.</li>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+ <li class="nobullet"><code>--mz-bin-offset <float></code> – In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--mod-mass-format mod-only|total|separate</code> – Specify how sequence modifications are reported in various output files. Each modification is reported as a number enclosed in square braces following the modified residue; however, the number may correspond to one of three different masses: (1) 'mod-only' reports the value of the mass shift induced by the modification; (2) 'total' reports the mass of the residue with the modification (residue mass plus [...]
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fragment-mass average|mono</code> – Specify which isotopes to use in calculating fragment ion mass. Default = <code>mono</code>.</li>
+ <li class="nobullet"><code>--isotope-windows <string></code> – Provides a list of isotopic windows to search. For example, -1,0,1 will search in three disjoint windows: (1) precursor_mass - neutron_mass +/- window, (2) precursor_mass +/- window, and (3) precursor_mass + neutron_mass +/- window. The window size is defined from the precursor-window and precursor-window-type parameters. This option is only available when use-old-xlink=F. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--compute-p-values T|F</code> – Estimate the parameters of the score distribution for each spectrum by fitting to a Weibull distribution, and compute a p-value for each xlink product. This option is only available when use-old-xlink=F. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fragment ion parameters</h3>
+<ul>
+ <li class="nobullet"><code>--use-a-ions T|F</code> – Consider a-ions in the search? Note that an a-ion is equivalent to a neutral loss of CO from the b-ion. Peak height is 10 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-b-ions T|F</code> – Consider b-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-c-ions T|F</code> – Consider c-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-x-ions T|F</code> – Consider x-ions in the search? Peak height is 10 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-y-ions T|F</code> – Consider y-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-z-ions T|F</code> – Consider z-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Cross-linking parameters</h3>
+<ul>
+ <li class="nobullet"><code>--use-old-xlink T|F</code> – Use the old version of xlink-searching algorithm. When false, a new version of the code is run. The new version supports variable modifications and can handle more complex databases. This new code is still in development and should be considered a beta release. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-linears T|F</code> – Include linear peptides in the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-deadends T|F</code> – Include dead-end peptides in the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-selfloops T|F</code> – Include self-loop peptides in the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-inter T|F</code> – Include inter-protein cross-link candidates within the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-intra T|F</code> – Include intra-protein cross-link candiates within the search. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-include-inter-intra T|F</code> – Include crosslink candidates that are both inter and intra. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--xlink-prevents-cleavage <string></code> – List of amino acids for which the cross-linker can prevent cleavage. This option is only available when use-old-xlink=F. Default = <code>K</code>.</li>
+ <li class="nobullet"><code>--max-xlink-mods <integer></code> – Specify the maximum number of modifications allowed on a crosslinked peptide. This option is only available when use-old-xlink=F. Default = <code>255</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/sort-by-column.html b/doc/user/sort-by-column.html
new file mode 100644
index 0000000..81fc8f2
--- /dev/null
+++ b/doc/user/sort-by-column.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>sort-by-column</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>sort-by-column</h1>
+<h2>Usage:</h2>
+<p><code>crux sort-by-column [options] <tsv file> <column name></code></p>
+<h2>Description:</h2>
+<p>Sort the rows of a tab-delimited file according to the values in a specified column.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tsv file</code> – A tab-delimited file, with column headers in the first row. Use "-" to read from standard input.</li>
+ <li><code>column name</code> – A column name.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – a copy of the given file, with rows sorted according to the values in the specified column.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--delimiter <string></code> – Specify the input and output delimiter to use when processing the delimited file. The argument can be either a single character or the keyword 'tab.' Default = <code>tab</code>.</li>
+ <li class="nobullet"><code>--header T|F</code> – Print the header line of the file, in addition to the columns that match. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--column-type int|real|string</code> – Specifies the data type of the column, either an integer (int), a floating point number (real), or a string. Default = <code>string</code>.</li>
+ <li class="nobullet"><code>--ascending T|F</code> – Sort in ascending (T) or descending (F) order. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/spectral-counts.html b/doc/user/spectral-counts.html
new file mode 100644
index 0000000..f95b686
--- /dev/null
+++ b/doc/user/spectral-counts.html
@@ -0,0 +1,152 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>spectral-counts</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>spectral-counts</h1>
+<h2>Usage:</h2>
+<p><code>crux spectral-counts [options] <input PSMs></code></p>
+<h2>Description:</h2>
+<p>Given a collection of scored PSMs, produce a list of proteins or peptides ranked by a quantification score. Spectral-counts supports four types of quantification: Normalized Spectral Abundance Factor (NSAF), Distributed Normalized Spectral Abundance (dNSAF), Normalized Spectral Index (SI<sub>N</sub>) and Exponentially Modified Protein Abundance Index (emPAI). The NSAF method is from <a href="http://www.ncbi.nlm.nih.gov/pubmed/17138671">Paoletti et al. (2006)</a>. The SI<sub>N</sub> me [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>input PSMs</code> – A PSM file in either tab delimited text format (as produced by percolator, q-ranker, or barista) or pepXML format.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>spectral-counts.target.txt</code> – a tab-delimited text file containing the protein IDs and their corresponding scores, in sorted order.</li>
+ <li><code>spectral-counts.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other Crux programs.</li>
+ <li><code>spectral-counts.log.txt</code> – All messages written to standard error.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>spectral-counts options</h3>
+<ul>
+ <li class="nobullet"><code>--parsimony none|simple|greedy</code> – Perform a parsimony analysis on the proteins, and report a "parsimony rank" column in the output file. This column contains integers indicating the protein's rank in a list sorted by spectral counts. If the parsimony analysis results in two proteins being merged, then their parsimony rank is the same. In such a case, the rank is assigned based on the largest spectral count of any protein in the merged meta-protein [...]
+ <li class="nobullet"><code>--threshold <float></code> – Only consider PSMs with a threshold value. By default, q-values are thresholded using a specified threshold value. This behavior can be changed using the --custom-threshold and --threshold-min parameters. Default = <code>0.01</code>.</li>
+ <li class="nobullet"><code>--threshold-type none|qvalue|custom</code> – Determines what type of threshold to use when filtering matches. none : read all matches, qvalue : use calculated q-value from percolator or q-ranker, custom : use --custom-threshold-name and --custom-threshold-min parameters. Default = <code>qvalue</code>.</li>
+ <li class="nobullet"><code>--input-ms2 <string></code> – MS2 file corresponding to the psm file. Required to measure the SIN. Ignored for NSAF, dNSAF and EMPAI. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--unique-mapping T|F</code> – Ignore peptides that map to multiple proteins. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--quant-level protein|peptide</code> – Quantification at protein or peptide level. Default = <code>protein</code>.</li>
+ <li class="nobullet"><code>--measure RAW|NSAF|dNSAF|SIN|EMPAI</code> – Type of analysis to make on the match results: (RAW|NSAF|dNSAF|SIN|EMPAI). With exception of the RAW metric, the database of sequences need to be provided using --protein-database. Default = <code>NSAF</code>.</li>
+ <li class="nobullet"><code>--custom-threshold-name <string></code> – Specify which field to apply the threshold to. The direction of the threshold (<= or >=) is governed by --custom-threshold-min. By default, the threshold applies to the q-value, specified by "percolator q-value", "q-ranker q-value", "decoy q-value (xcorr)", or "barista q-value". Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--custom-threshold-min T|F</code> – When selecting matches with a custom threshold, custom-threshold-min determines whether to filter matches with custom-threshold-name values that are greater-than or equal (F) or less-than or equal (T) than the threshold. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--mzid-use-pass-threshold T|F</code> – Use mzid's passThreshold attribute to filter matches. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--protein-database <string></code> – The name of the file in FASTA format. Default = <code><empty></code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/stat-column.html b/doc/user/stat-column.html
new file mode 100644
index 0000000..71d8dc9
--- /dev/null
+++ b/doc/user/stat-column.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>stat-column</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>stat-column</h1>
+<h2>Usage:</h2>
+<p><code>crux stat-column [options] <tsv file> <column name></code></p>
+<h2>Description:</h2>
+<p>Given a tab-delimited file, collect summary statistics on the values within a specified column. The specified column must contain numeric values.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tsv file</code> – A tab-delimited file, with column headers in the first row. Use "-" to read from standard input.</li>
+ <li><code>column name</code> – A column name.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – The program prints to standard output the following statistics for the specified column: number of rows, minimum, maximum, sum, average, and median of the data values.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--delimiter <string></code> – Specify the input and output delimiter to use when processing the delimited file. The argument can be either a single character or the keyword 'tab.' Default = <code>tab</code>.</li>
+ <li class="nobullet"><code>--header T|F</code> – Print the header line of the file, in addition to the columns that match. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--precision <integer></code> – Set the precision for scores written to sqt and text files. Default = <code>8</code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/styles.css b/doc/user/styles.css
new file mode 100644
index 0000000..6eb6d2b
--- /dev/null
+++ b/doc/user/styles.css
@@ -0,0 +1,570 @@
+ at import url(https://fonts.googleapis.com/css?family=Roboto:400,300,600);
+
+* {
+ margin: 0;
+}
+a {
+ border: none;
+ text-decoration: none;
+}
+html {
+ font-size: 100%; /* 1 */
+ -webkit-text-size-adjust: 100%; /* 2 */
+ -ms-text-size-adjust: 100%; /* 2 */
+}
+
+body {
+ background-color: #ece8e5;
+ margin: 0;
+ padding: 0;
+
+}
+
+/*Sticky Footer*/
+html, body {
+ height: 100%;
+ font-family: Arial,Verdana,sans-serif;
+ font-size:14px;
+}
+
+table {
+ border-collapse: collapse;
+}
+table > thead, th{
+ border: 1px solid #000;
+ padding:5px;
+ background: #4d87a2;
+ color:#f3f3f7;
+ font-weight: 400;
+ font-family: 'Roboto', sans-serif;
+}
+caption
+{ font-weight: 400;
+ font-family: 'Roboto', sans-serif;
+ padding-left:10px;
+}
+table tr:nth-child(even) {
+ background: #f3f3f7;
+}
+
+.code {
+ background:#F8F8FF;
+ border:black dashed 1px;
+ padding:1px;
+ font:monospace;
+ padding-left:3px;
+ padding-right:3px;
+ padding-bottom:0px;
+ display: inline-block; /* box only as wide as content */
+}
+code {
+ font-family: monospace;
+}
+.page-wrap {
+ min-height: 100%;
+ margin-bottom: -180px; /* equal to footer height */
+ width:100%;
+}
+.page-wrap:after {
+ content: "";
+ display: block;
+}
+pre {
+ white-space: pre-wrap; /* Since CSS 2.1 */
+ white-space: -moz-pre-wrap; /* Mozilla, since 1999 */
+ white-space: -pre-wrap; /* Opera 4-6 */
+ white-space: -o-pre-wrap; /* Opera 7 */
+ word-wrap: break-word; /* Internet Explorer 5.5+ */
+ padding: 10px;
+ background: #eee;
+ border-radius: 5px;
+ overflow-x: auto;
+ background: #f3f3f7;
+ border: 1px solid #dedee3;
+ margin-bottom: 22px;
+ font-family: monospace;
+ font-size: 12px;
+ overflow-x: auto;
+ white-space: pre-wrap;
+ padding-bottom:0px;
+ display: inline-block;
+ padding-right:20px;
+}
+/* Content STYLES */
+#content {
+ background-color: #FFF;
+ min-height: calc(100vh - 280px);
+ width:80%;
+ margin:auto;
+ min-width:320px;
+ overflow: break-word;
+ padding:10px;
+ padding-bottom:20px;
+}
+#content p {
+ font-size:14px;
+ padding-top:5px;
+ padding-bottom:5px;
+}
+#content h2 {
+ font-size:30px;
+ color:#034463;
+ font-size: 30px;
+ font-weight: 600;
+ line-height: 30px;
+ margin: 5px;
+ text-align: center;
+ font-family: 'Roboto', sans-serif;
+}
+#content h3 {
+ font-size:20px;
+ padding:5px;
+ padding-top:15px;
+ padding-bottom:2px;
+ font-weight:400;
+ font-family: 'Roboto', sans-serif;
+}
+#content h4 {
+ font-size:16px;
+ padding:2px;
+ padding-left:5px;
+}
+#content a {
+ color: #2188b8;
+}
+#content a:hover {
+ color: #AA2244;
+}
+#content ul > li {
+
+}
+.nobullet {
+ list-style-type: none;
+}
+/*END content STYLES*/
+#centerfooter {
+ display: inline-block;
+}
+.site-footer, .page-wrap:after {
+ height: 180px;
+ text-align: center;
+}
+.site-footer {
+ background: #FFF;
+ color: #076FA2;
+ font-size:12px !important;
+ padding-top:30px;
+ /*margin-top:20px;*/
+ border-top: 2px solid #69B2D5;
+ font-family:Arial,Verdana,sans-serif !important;
+}
+.site-footer a{
+ color: #076FA2;
+ text-decoration: none;
+}
+.site-footer a:hover{
+ color: #2682AF;
+ text-decoration: none;
+}
+.site-footer h3 {
+ color:#034463;
+ font-size:16px;
+ line-height:22px;
+ border-bottom: 2px solid #B3DAED;
+ width:200px;
+}
+.site-footer img {
+ float:left;
+ padding-right:6px;
+}
+.footerimportantlinks {
+ float:left;
+ margin-left:50px;
+ height:100px;
+ text-align: left;
+}
+.footerimportantlinks ul{
+ float:left;
+ list-style-type: none;
+ margin-left:-40px;
+ margin-top:4px;
+ -moz-column-count: 2;
+ -moz-column-gap: 10px;
+ -webkit-column-count: 2;
+ -webkit-column-gap: 10px;
+ column-count: 2;
+ column-gap: 10px;
+
+}
+.footerimportantlinks li{
+ margin-top:5px;
+ width:150px;
+}
+.tutoriallinks {
+ margin-left:50px;
+}
+.tutoriallinks ul {
+ -moz-column-count: 1;
+ -moz-column-gap: 10px;
+ -webkit-column-count: 1;
+ -webkit-column-gap: 10px;
+ column-count: 1;
+ column-gap: 10px;
+}
+.tutoriallinks li {
+ width:300px;
+}
+#footertext {
+ float:left;
+ margin-top:20px;
+ padding-top:5px;
+ margin-left:20px;
+ height:100px;
+ width:300px;
+ border-top: 2px solid #B3DAED;
+}
+#footertext p {
+ text-align: center;
+ font-size:11px;
+}
+#footertext a {
+ color: #05577F;
+ text-decoration: underline;
+}
+/*******************/
+/* Responsive Menu */
+nav {
+ height: 100px;
+ overflow: show;
+ width: 100%;
+ background: #FFF;
+ font-size: 13pt;
+ font-weight: bold;
+ position: relative;
+ border-bottom: 2px solid #69B2D5;
+ min-width:300px;
+}
+
+#navitems a {
+ display: inline-block;
+ text-align: center;
+ text-decoration: none;
+ line-height: 40px;
+ padding-left:10px;
+ padding-right:10px;
+ color:#4f8bac;
+ /*text-shadow: 1px 1px 0px #283744;*/
+}
+
+nav header {
+ display: none;
+
+}
+
+nav ul {
+ padding: 0;
+ width:100%;
+ /*margin-left:370px;*/
+ float:left;
+ padding-left: 20px;
+ /*margin: 0 auto; /* CENTER MENU */
+ width: 400px;
+ height: 40px;
+ margin-top:60px;
+ background: #FFF;
+}
+nav li {
+ display: inline;
+ float: left;
+}
+
+#logo{
+ float:left;
+ height:100px;
+ margin-left:10%;
+}
+
+nav li a {
+ border-right: 1px solid #4199C4;
+ box-sizing:border-box;
+ -moz-box-sizing:border-box;
+ -webkit-box-sizing:border-box;
+}
+
+nav li:last-child a {
+ border-right: 0;
+}
+#navitems a:hover, #navitems a:active {
+ background-color: #B3DAED;
+}
+
+ at media screen and (max-width: 1124px) {
+ .page-wrap {
+ min-height: 100%;
+ margin-bottom: -250px; /* equal to footer height */
+ }
+ .site-footer, .page-wrap:after {
+ height: 250px;
+ }
+ #footertext {
+ padding-top:40px;
+ border:none;
+ margin-top:20px;
+ display: inline;
+ width:90%;
+ padding-left: 20px;
+ padding-right:20px;
+ text-align: center;
+ }
+}
+/*Styles for 780px (footer changes)*/
+ at media screen and (max-width: 780px) {
+ table {
+ margin:0;
+ }
+ #content {
+ width:100%;
+ }
+ body {
+ background-color: #FFF;
+ }
+ nav {
+ height: 140px;
+ }
+
+ nav ul {
+ width: 100%;
+ display: block;
+ height: auto;
+ margin-top:0px;
+ }
+
+ .footerimportantlinks {
+ margin-left:50px;
+ margin-top:10px;
+ }
+ .page-wrap {
+ min-height: 100%;
+ margin-bottom: -300px; /* equal to footer height */
+ }
+ .site-footer, .page-wrap:after {
+ height: 300px;
+ }
+}
+ at media screen and (max-width: 730px) {
+ .page-wrap {
+ min-height: 100%;
+ margin-bottom: -380px; /* equal to footer height */
+ }
+ .site-footer, .page-wrap:after {
+ height: 380px;
+ }
+}
+/*Styles for screen 600px and lower*/
+ at media screen and (max-width: 600px) {
+ nav {
+ height: 182px;
+ }
+
+ nav ul {
+ width: 100%;
+ display: block;
+ height: auto;
+ }
+ nav li {
+ width: 50%;
+ float: left;
+ position: relative;
+ }
+ nav li a {
+ border: none;
+ }
+ #navitems a {
+ text-align: left;
+ width: 100%;
+ text-indent: 25px;
+ background: #FFF;
+ }
+}
+
+/*Styles for screen 515px and lower*/
+ at media only screen and (max-width : 515px) {
+ #logo {
+ height: 33px;
+ padding-top:0px;
+ }
+
+ nav {
+ border-bottom: 0;
+ width: 100%;
+ height: 33px;
+ padding: 7px 0 0 0;
+
+ }
+ nav ul {
+ display: none;
+ height: auto;
+ padding: 0 0 0 0;
+ clear: both;
+ background: #2188b8;
+
+ }
+ .btn {
+ width: 24px;
+ height: 22px;
+ background: #034463;
+ float: left;
+ cursor: pointer;
+ margin: 0 10px 0 10px;
+ padding: 3px 0px 0 6px;
+ -webkit-border-radius: 2px;
+ -moz-border-radius: 2px;
+ border-radius: 2px;
+ background:url('images/hamburger-menu.png') no-repeat center;
+ }
+
+ .btn .icon {
+ display: block;
+ width: 18px;
+ height: 2px;
+ margin-top: 3px;
+ background-color: #034463;
+ -webkit-border-radius: 1px;
+ -moz-border-radius: 1px;
+ border-radius: 1px;
+ -webkit-box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25);
+ -moz-box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25);
+ box-shadow: 0 1px 0 rgba(0, 0, 0, 0.25);
+}
+
+
+
+
+}
+
+/*Smartphone*/
+ at media only screen and (max-width : 320px) {
+ nav li {
+ display: block;
+ float: none;
+ width: 100%;
+ }
+ nav li a {
+ border-bottom: 1px solid #787878;
+ }
+}
+
+/*index.html*/
+/***********/
+blockquote {
+ font-family:monospace;
+}
+.indentcitation {
+ border-left:4px solid #034463;
+ padding: 0px 10px;
+ -webkit-box-decoration-break: clone;
+ box-decoration-break: clone;
+ break-word:none;
+ background-color:#f9f9f9;
+}
+#schematic img {
+ width:calc(100% + 20px);
+ margin-left:-10px;
+ margin-top:-10px;
+}
+#schematic p {
+ font-size:14px;
+ margin:0;
+ padding:0;
+ width: calc(100%-10px);
+ padding:10px;
+}
+#commandstable {
+ font-family:monospace;
+ font-size:15px;
+}
+
+#commandstable b {
+ font-size:17px;
+ font-family: Arial;
+ line-height: 40px;
+ vertical-align: text-bottom;
+}
+#commandstable td {
+ padding:5px;
+ border:none;
+}
+#commandstable td:nth-child(even) {
+ padding-left:10px;
+ font-family: Arial;
+}
+/* fileformats.html */
+#fileFormatsTable {
+ border-collapse: collapse;
+ margin-left:auto;
+ margin-right: auto;
+ padding:0;
+}
+#fileFormatsTable tr:nth-child(even) {
+ background: #DEDEDE;
+}
+#fileFormatsTable th, td {
+ padding-top:5px;
+ padding-bottom: 5px;
+ padding-left:3px;
+ border: 1px solid #000;
+}
+
+/* features.html */
+#featurestable {
+ text-align: left;
+ font-size:14px;
+}
+
+#featurestable td{
+ padding-left:3px;
+}
+
+/*txt-format.html*/
+#tabformat td {
+ padding:3px;
+ font-size:14px;
+}
+
+/*search.html*/
+.searchtable td {
+ padding:2px 4px 2px 4px;
+ border:1px solid #000;
+ font-size:12px;
+ word-wrap: break-word;
+}
+
+/*STYLES FOR ALL AUTOGENERATED CONTENT*/
+.autogenerated h1 {
+ font-size:30px;
+ color:#034463;
+ font-size: 30px;
+ font-weight: 600;
+ line-height: 30px;
+ margin: 5px;
+ text-align: center;
+ font-family: 'Roboto', sans-serif;
+}
+.autogenerated h2, h3, h4 {
+ color: #000 !important;
+ font-size:16px !important;
+ margin:2px !important;
+ text-align: left !important;
+ line-height: 16px !important;
+ font-weight:600 !important;
+}
+.autogenerated h2 {
+ margin-top:10px !important;
+}
+.autogenerated h3 {
+ font-size:14px !important;
+ padding:0px !important;
+}
+.autogenerated ul {
+ padding-left:20px;
+}
\ No newline at end of file
diff --git a/doc/user/subtract-index.html b/doc/user/subtract-index.html
new file mode 100644
index 0000000..8a925b0
--- /dev/null
+++ b/doc/user/subtract-index.html
@@ -0,0 +1,138 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>subtract-index</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>subtract-index</h1>
+<h2>Usage:</h2>
+<p><code>crux subtract-index [options] <tide index 1> <tide index 2> <output index></code></p>
+<h2>Description:</h2>
+<p>This command takes two peptide indices, created by the tide-index command, and subtracts the second index from the first. The result is an output index that contains peptides that appear in the first index but not the second.</p>
+<h2>Input:</h2>
+<ul>
+ <li><code>tide index 1</code> – A peptide index produced using tide-index</li>
+ <li><code>tide index 2</code> – A second peptide index, to be subtracted from the first index.</li>
+ <li><code>output index</code> – A new peptide index containing all peptides that occur in thefirst index but not the second.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>subtract-index.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> containing the target peptides.</li>
+ <li><code>subtract-index.decoy.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> containing the decoy peptides.</li>
+ <li><code>subtract-index.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
+ <li><code>subtract-index.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--peptide-list T|F</code> – Create in the output directory a text file listing of all the peptides in the database, along with their neutral masses, one per line. If decoys are generated, then a second file will be created containing the decoy peptides. Decoys that also appear in the target database are marked with an asterisk in a third column. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/template.html b/doc/user/template.html
new file mode 100644
index 0000000..6ba71fa
--- /dev/null
+++ b/doc/user/template.html
@@ -0,0 +1,105 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Template</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="download.html">Download</a></li>
+ <li><a href="fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="faq.html">Crux FAQ</a></li>
+ <li><a href="glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="tutorials/install.html">Installation</a></li>
+ <li><a href="tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/tide-index.html b/doc/user/tide-index.html
new file mode 100644
index 0000000..770cc21
--- /dev/null
+++ b/doc/user/tide-index.html
@@ -0,0 +1,177 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>tide-index</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>tide-index</h1>
+<h2>Usage:</h2>
+<p><code>crux tide-index [options] <protein fasta file> <index name></code></p>
+<h2>Description:</h2>
+<p>Tide is a tool for identifying peptides from tandem mass spectra. It is an independent reimplementation of the SEQUEST<sup>®</sup> algorithm, which assigns peptides to spectra by comparing the observed spectra to a catalog of theoretical spectra derived from a database of known proteins. Tide's primary advantage is its speed. Our published paper provides more detail on how Tide works. If you use Tide in your research, please cite:</p><blockquote>Benjamin J. Diament and William Sta [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>protein fasta file</code> – The name of the file in FASTA format from which to retrieve proteins.</li>
+ <li><code>index name</code> – The desired name of the binary index.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>index</code> – A binary index, using the name specified on the command line.</li>
+ <li><code>tide-index.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
+ <li><code>tide-index.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Peptide properties</h3>
+<ul>
+ <li class="nobullet"><code>--max-length <integer></code> – The maximum length of peptides to consider. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--max-mass <float></code> – The maximum mass (in Da) of peptides to consider. Default = <code>7200</code>.</li>
+ <li class="nobullet"><code>--min-length <integer></code> – The minimum length of peptides to consider. Default = <code>6</code>.</li>
+ <li class="nobullet"><code>--min-mass <float></code> – The minimum mass (in Da) of peptides to consider. Default = <code>200</code>.</li>
+ <li class="nobullet"><code>--isotopic-mass average|mono</code> – Specify the type of isotopic masses to use when calculating the peptide mass. Default = <code>mono</code>.</li>
+ <li class="nobullet"><code>--clip-nterm-methionine T|F</code> – When set to T, for each protein that begins with methionine, tide-index will put two copies of the leading peptide into the index, with and without the N-terminal methionine. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Amino acid modifications</h3>
+<ul>
+ <li class="nobullet"><code>--mods-spec <string></code> – The general form of a modification specification has three components, as exemplified by <span style="color: red;">1</span><span style="color: green;">STY</span>+<span style="color: blue">79.966331</span>.<br>The three components are: [<span style="color: red;">max_per_peptide</span>]<span style="color: green;">residues</span>[+/-]<span style-"color: blue;">mass_change</span><br>In the example, <span style="color: red [...]
+ <li class="nobullet"><code>--cterm-peptide-mods-spec <string></code> – Specify peptide c-terminal modifications. See nterm-peptide-mods-spec for syntax. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--nterm-peptide-mods-spec <string></code> – Specify peptide n-terminal modifications. Like --mods-spec, this specification has three components, but with a slightly different syntax. The <span style="color: red;">max_per_peptide</span> can be either "1", in which case it defines a variable terminal modification, or missing, in which case the modification is static. The <span style="color: green;">residues</span> field indicates which amino acids a [...]
+ <li class="nobullet"><code>--max-mods <integer></code> – The maximum number of modifications that can be applied to a single peptide. Default = <code>255</code>.</li>
+ <li class="nobullet"><code>--min-mods <integer></code> – The minimum number of modifications that can be applied to a single peptide. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Decoy database generation</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-format none|shuffle|peptide-reverse|protein-reverse</code> – Include a decoy version of every peptide by shuffling or reversing the target sequence or protein. In shuffle or peptide-reverse mode, each peptide is either reversed or shuffled, leaving the N-terminal and C-terminal amino acids in place. Note that peptides appear multiple times in the target database are only shuffled once. In peptide-reverse mode, palindromic peptides are shuffled. [...]
+ <li class="nobullet"><code>--keep-terminal-aminos N|C|NC|none</code> – When creating decoy peptides using decoy-format=shuffle or decoy-format=peptide-reverse, this option specifies whether the N-terminal and C-terminal amino acids are kept in place or allowed to be shuffled or reversed. For a target peptide "EAMPK" with decoy-format=peptide-reverse, setting keep-terminal-aminos to "NC" will yield "EPMAK"; setting it to "C" will yield "PMAEK"; setting it to "N" will yield "EKPMA" [...]
+ <li class="nobullet"><code>--seed <string></code> – When given a unsigned integer value seeds the random number generator with that value. When given the string "time" seeds the random number generator with the system time. Default = <code>1</code>.</li>
+ <li class="nobullet"><code>--allow-dups T|F</code> – Prevent duplicate peptides between the target and decoy databases. When set to "F", the program keeps all target and previously generated decoy peptides in memory. A shuffled decoy will be re-shuffled multiple times to avoid duplication. If a non-duplicated peptide cannot be generated, the decoy is skipped entirely. When set to "T", every decoy is added to the database without checking for duplication. This option reduces the m [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Enzymatic digestion</h3>
+<ul>
+ <li class="nobullet"><code>--enzyme no-enzyme|trypsin|trypsin/p|chymotrypsin|elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|elastase-trypsin-chymotrypsin|custom-enzyme</code> – Specify the enzyme used to digest the proteins in silico. Available enzymes (with the corresponding digestion rules indicated in parentheses) include no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin [...]
+ <li class="nobullet"><code>--custom-enzyme <string></code> – Specify rules for in silico digestion of protein sequences. Overrides the enzyme option. Two lists of residues are given enclosed in square brackets or curly braces and separated by a |. The first list contains residues required/prohibited before the cleavage site and the second list is residues after the cleavage site. If the residues are required for digestion, they are in square brackets, '[' and ']'. If the re [...]
+ <li class="nobullet"><code>--digestion full-digest|partial-digest|non-specific-digest</code> – Specify whether every peptide in the database must have two enzymatic termini (full-digest) or if peptides with only one enzymatic terminus are also included (partial-digest). Default = <code>full-digest</code>.</li>
+ <li class="nobullet"><code>--missed-cleavages <integer></code> – Maximum number of missed cleavages per peptide to allow in enzymatic digestion. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--peptide-list T|F</code> – Create in the output directory a text file listing of all the peptides in the database, along with their neutral masses, one per line. If decoys are generated, then a second file will be created containing the decoy peptides. Decoys that also appear in the target database are marked with an asterisk in a third column. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--temp-dir <string></code> – The name of the directory where temporary files will be created. If this parameter is blank, then the system temporary directory will be used Default = <code><empty></code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/tide-search.html b/doc/user/tide-search.html
new file mode 100644
index 0000000..d973456
--- /dev/null
+++ b/doc/user/tide-search.html
@@ -0,0 +1,204 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>tide-search</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>tide-search</h1>
+<h2>Usage:</h2>
+<p><code>crux tide-search [options] <tide spectra file>+ <tide database></code></p>
+<h2>Description:</h2>
+<p>Tide is a tool for identifying peptides from tandem mass spectra. It is an independent reimplementation of the SEQUEST<sup>®</sup> algorithm, which assigns peptides to spectra by comparing the observed spectra to a catalog of theoretical spectra derived from a database of known proteins. Tide's primary advantage is its speed. Our published paper provides more detail on how Tide works. If you use Tide in your research, please cite:</p><blockquote>Benjamin J. Diament and William Sta [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>tide spectra file+</code> – The name of one or more files from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard. Alternatively, the argument may be one or more binary spectrum files produced by a previous run of crux tide-search using the store-spectra parameter.</li>
+ <li><code>tide database</code> – Either a FASTA file or a directory containing a database index created by a previous run of crux tide-index.</li>
+</ul>
+<h2>Output:</h2>
+<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
+<ul>
+ <li><code>tide-search.target.txt</code> – a tab-delimited text file containing the target PSMs. See <a href="../file-formats/txt-format.html">txt file format</a> for a list of the fields.</li>
+ <li><code>tide-search.decoy.txt</code> – a tab-delimited text file containing the decoy PSMs. This file will only be created if the index was created with decoys.</li>
+ <li><code>tide-search.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other Crux programs.</li>
+ <li><code>tide-search.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Precursor selection</h3>
+<ul>
+ <li class="nobullet"><code>--precursor-window <float></code> – Tolerance used for matching peptides to spectra. Peptides must be within +/- 'precursor-window' of the spectrum value. The precursor window units depend upon precursor-window-type. Default = <code>3</code>.</li>
+ <li class="nobullet"><code>--auto-precursor-window false|warn|fail</code> – Automatically estimate optimal value for the precursor-window parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--precursor-window-type mass|mz|ppm</code> – Specify the units for the window that is used to select peptides around the precursor mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-window option, and candidate peptides must fall within this window. For the mass window-type, the spectrum precursor m+h value is converted to mass, and the window is defined as that mass +/- precursor-window. If the m+h value is not avail [...]
+ <li class="nobullet"><code>--max-precursor-charge <integer></code> – The maximum charge state of a spectra to consider in search. Default = <code>5</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--spectrum-min-mz <float></code> – The lowest spectrum m/z to search in the ms2 file. Default = <code>0</code>.</li>
+ <li class="nobullet"><code>--spectrum-max-mz <float></code> – The highest spectrum m/z to search in the ms2 file. Default = <code>1e+09</code>.</li>
+ <li class="nobullet"><code>--min-peaks <integer></code> – The minimum number of peaks a spectrum must have for it to be searched. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--spectrum-charge 1|2|3|all</code> – The spectrum charges to search. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge state will be searched. Default = <code>all</code>.</li>
+ <li class="nobullet"><code>--scan-number <string></code> – A single scan number or a range of numbers to be searched. Range should be specified as 'first-last' which will include scans 'first' and 'last'. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--compute-sp T|F</code> – Compute the preliminary score Sp for all candidate peptides. Report this score in the output, along with the corresponding rank, the number of matched ions and the total number of ions. This option is recommended if results are to be analyzed by Percolator or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Note that the Sp computation requires re-processing each observed spe [...]
+ <li class="nobullet"><code>--remove-precursor-peak T|F</code> – If true, all peaks around the precursor m/z will be removed, within a range specified by the --remove-precursor-tolerance option. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--remove-precursor-tolerance <float></code> – This parameter specifies the tolerance (in Th) around each precursor m/z that is removed when the --remove-precursor-peak option is invoked. Default = <code>1.5</code>.</li>
+ <li class="nobullet"><code>--exact-p-value T|F</code> – Enable the calculation of exact p-values for the XCorr score as described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/24895379">this article</a>. Calculation of p-values increases the running time but increases the number of identifications at a fixed confidence threshold. The p-values will be reported in a new column with header "exact p-value", and the "xcorr score" column will be replaced with a "refactored xcorr" colu [...]
+ <li class="nobullet"><code>--use-neutral-loss-peaks T|F</code> – Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+ <li class="nobullet"><code>--auto-mz-bin-width false|warn|fail</code> – Automatically estimate optimal value for the mz-bin-width parameter from the spectra themselves. false=no estimation, warn=try to estimate but use the default value in case of failure, fail=try to estimate and quit in case of failure. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mz-bin-offset <float></code> – In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). Default = <code>0.4</code>.</li>
+ <li class="nobullet"><code>--peptide-centric-search T|F</code> – Carries out a peptide-centric search. For each peptide the top-scoring spectra are reported, in contrast to the standard spectrum-centric search where the top-scoring peptides are reported. Note that in this case the "xcorr rank" column will contain the rank of the given spectrum with respect to the given candidate peptide, rather than vice versa (which is the default). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--isotope-error <string></code> – List of positive, non-zero integers. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--skip-preprocessing T|F</code> – Skip preprocessing steps on spectra. Default = F. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>CPU threads</h3>
+<ul>
+ <li class="nobullet"><code>--num-threads <integer></code> – 0=poll CPU to set num threads; else specify num threads directly. Default = <code>0</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>param-medic options</h3>
+<ul>
+ <li class="nobullet"><code>--pm-min-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>400</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-mz <float></code> – Minimum precursor m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-frag-mz <float></code> – Minimum fragment m/z value to use in measurement error estimation. Default = <code>150</code>.</li>
+ <li class="nobullet"><code>--pm-max-frag-mz <float></code> – Maximum fragment m/z value to use in measurement error estimation. Default = <code>1800</code>.</li>
+ <li class="nobullet"><code>--pm-min-scan-frag-peaks <integer></code> – Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation. Default = <code>40</code>.</li>
+ <li class="nobullet"><code>--pm-max-precursor-delta-ppm <float></code> – Maximum ppm distance between precursor m/z values to consider two scans potentially generated by the same peptide for measurement error estimation. Default = <code>50</code>.</li>
+ <li class="nobullet"><code>--pm-charge <integer></code> – Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this should be the most frequently occurring charge state in the given data. Default = <code>2</code>.</li>
+ <li class="nobullet"><code>--pm-top-n-frag-peaks <integer></code> – Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--pm-pair-top-n-frag-peaks <integer></code> – Number of fragment peaks per spectrum pair to be used in fragment error estimation. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--pm-min-common-frag-peaks <integer></code> – Number of the most-intense peaks that two spectra must share in order to potentially be generated by the same peptide, for measurement error estimation. Default = <code>20</code>.</li>
+ <li class="nobullet"><code>--pm-max-scan-separation <integer></code> – Maximum number of scans two spectra can be separated by in order to be considered potentially generated by the same peptide, for measurement error estimation. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--pm-min-peak-pairs <integer></code> – Minimum number of peak pairs (for precursor or fragment) that must be successfully paired in order to attempt to estimate measurement error distribution. Default = <code>100</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--top-match <integer></code> – Specify the number of matches to report for each spectrum. Default = <code>5</code>.</li>
+ <li class="nobullet"><code>--store-spectra <string></code> – Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir). This option is not valid if multiple input spectrum files are given. Default = <code><e [...]
+ <li class="nobullet"><code>--store-index <string></code> – When providing a FASTA file as the index, the generated binary index will be stored at the given path. This option has no effect if a binary index is provided as the index. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--concat T|F</code> – When set to T, target and decoy search results are reported in a single file, and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--print-search-progress <integer></code> – Show search progress by printing every n spectra searched. Set to 0 to show no search progress. Default = <code>1000</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--use-z-line T|F</code> – Specify whether, when parsing an MS2 spectrum file, Crux obtains the precursor mass information from the "S" line or the "Z" line. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--txt-output T|F</code> – Output a tab-delimited results file to the output directory. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--sqt-output T|F</code> – Outputs an SQT results file to the output directory. Note that if sqt-output is enabled, then compute-sp is automatically enabled and cannot be overridden. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pepxml-output T|F</code> – Output a pepXML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--mzid-output T|F</code> – Output an mzIdentML results file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--pin-output T|F</code> – Output a Percolator input (PIN) file to the output directory. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--file-column T|F</code> – Include the file column in tab-delimited output. Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
+ <li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
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+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
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+<!DOCTYPE html>
+<html>
+<head>
+<title>Customization and search options</title>
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+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Customization and search options</h2>
+
+ <p><span class="prog">Crux</span> allows the user the flexibility to
+ change many of the search and analysis parameters. Attributes like
+ the output format and which peptides are selected from the protein
+ database are controlled through numerous options. This page
+ starts with some general information about options and then describe
+ the use of some key <span class="prog">crux</span> options.
+ </p>
+
+ <a name="intro"></a>
+ <h3>Introduction to options</h3>
+
+ <p>
+ A <span class="prog">crux</span> command is made up of four parts:
+ executable name, command, options, and required arguments. Let's use
+ a <span class="prog">crux tide-search</span> command as an example.
+ Here is the general form.</p>
+
+ <div class="code"><code>
+ $ crux tide-search [options] <mass spectra> <peptide index>
+ </code>
+ </div>
+
+ <p>
+ In this case, the command is <span class="prog">tide-search</span>.
+ This is followed by zero or more optional arguments. Finally, the
+ required arguments, listed above inside angle brackets, include the
+ name of the file containing the spectra to be identified and the name
+ of a peptide index produced previously by
+ the <span class="prog">tide-index</span> command.</p>
+
+ <p>
+ All of the available options are described for each command on
+ the <a href="../index.html">documentation</a> pages. You can also get a
+ list of available options by running a command with no arguments.
+ For example, the command</p>
+
+ <div class="code"><code>
+ $ crux tide-search</code>
+ </div>
+
+ <p>
+ will produce output that looks like this:</p>
+
+ <pre>
+bash-3.2$ ~/proj/crux/trunk/src/c/crux tide-search
+FATAL: Error in command line. Error # 5
+The required argument <tide spectra file> is missing.
+
+USAGE:
+
+ crux tide-search [options] <tide spectra file> <tide database index>
+
+REQUIRED ARGUMENTS:
+
+ <tide spectra file> The name of the file from which to parse the fragmentation spectra, in any of the file formats supported by ProteoWizard. Alternatively, the argument may be a binary spectrum file produced by a previous run of crux tide-search using the store-spectra parameter.
+ <tide database index> A directory containing a database index created by a previous run of crux tide-index.
+
+OPTIONAL ARGUMENTS:
+
+ [--precursor-window <double>]
+ Search peptides within +/- 'precursor-window' of the spectrum mass.
+ Definition of precursor window depends upon precursor-window-type.
+ Default=3.0.
+ [--precursor-window-type <string>]
+ Window type to use for selecting candidate peptides.
+ <string>=mass|mz|ppm. Default=mass.
+ [--spectrum-min-mz <double>]
+ The lowest spectrum m/z to search. Default=0.0.
+ [--spectrum-max-mz <double>]
+ The highest spectrum m/z to search. Default=no maximum.
+ [--min-peaks <int>]
+ The minimum number of peaks a spectrum must have for it to be
+ searched. Default=20.
+...
+ </pre>
+
+ <p>The first three lines are telling you that you forgot the required
+ arguments and are reminding you what they are. The following lines
+ list all the options (only five of which are shown
+ above). <span class="prog">Crux</span> options all begin with two
+ dashes followed by the option name. The name is followed by a space
+ and the appropriate argument. This example increases the verbosity to
+ 40:
+ </p>
+
+ <div class="code"><code>
+ $ crux tide-search --verbosity 40 sample.ms2 yeast.fasta</code>
+ </div>
+
+ <a name="file"></a>
+ <h3>Specifying options via a parameter file</h3>
+
+ <p>
+ The second option listed
+ above, <span class="out">--parameter-file</span>, is available for all
+ Crux commands. The parameter file allows multiple options to be
+ specified in a file. All of the command line options can be put in a
+ parameter file, but the format is slightly different. In the
+ parameter file, the two leading dashes are removed from the option
+ name, and the option name and value must be separated by an equal sign
+ instead of a space:
+ </p>
+ <div class=code><code>
+ <option name>=<argument></code>
+ </div>
+
+ <p>
+ The above example, in which we changed the verbosity, would look like this
+ in a parameter file:</p>
+
+ <div class="code"><code>
+ verbosity=40
+ </code>
+ </div>
+
+ <p>
+ The parameter file allows only one option per line. Lines beginning
+ with "#" are considered comments and are ignored. A sample parameter
+ file can be found <a href="../file-formats/parameter-file.html">here</a>. Command
+ line and parameter file options may be used separately or together.
+ If an option is specified in both places, then value on the command
+ line will be used.
+ </p>
+
+ <p>
+ During execution of any Crux command, a parameter file containing the
+ name and value of all the options for the current operation
+ will be automatically be saved in the output directory. Note that not
+ all parameters in the file may have been used in the operation. The
+ parameter file will be named
+ <code><command>.params.txt</code>,
+ where <code><tag></code> is the name of the command that was
+ executed.</p>
+
+ <a name="shared"></a>
+ <h3>Shared options</h3>
+
+ <p>
+ In addition to <code>--parameter-file</code>, Crux includes several
+ other options that are shared across all, or nearly all, Crux commands.
+ </p>
+
+ <ul>
+ <li>
+ <code>--output-dir <filename></code> –
+ The name of the directory where output files will be created.
+ Default = crux-output.</li>
+
+ <li>
+ <code>--fileroot <string></code> –
+ The <code>fileroot</code> string will be added as a prefix to all
+ output file names. Default = none.</li>
+
+ <li>
+ <code>--overwrite <T|F></code> – By default, if Crux
+ detects that the output file it is about to produce already exists,
+ then Crux will exit with an error. This option allows Crux to
+ overwrite existing files.</li>
+
+ <li>
+ <code>--verbosity <0-100></code> – Specify the verbosity
+ of the current command. Each level prints the following messages,
+ including all those at lower verbosity levels: 0-fatal errors,
+ 10-non-fatal errors, 20-warnings, 30-information on the progress of
+ execution, 40-more progress information, 50-debug info, 60-detailed
+ debug info. Default = 30.</li>
+
+ <li>
+ In addition, many Crux commands include various options of the form
+ <code>--<format>-output</code>. These options take Boolean
+ arguments (specified as "T" or "F") and indicate whether output files
+ in the specified format should be produced. For example, in addition
+ to tab-delimited text format, <code>tide-search</code> can produce
+ output in PepXML, MZid, SQT and PINxml formats.</li>
+
+ </ul>
+
+ <a name="index"></a>
+ <h3>Changing the indexing and searching parameters</h3>
+
+ <p>
+ Various options to <span class="prog">tide-index</span> control how
+ the proteins in the database are converted to peptides. These options
+ fall into several categories, allowing specification of peptide
+ properties such as minimum and maximum length, enzymatic digestion
+ rules, decoy database generation and specification of various static
+ and variable modifications. These options are fully
+ documented <a href="../commands/tide-index.html">here</a>. Similarly,
+ the <code><a href="../commands/tide-search.html">tide-search</a></code>
+ documentation describes options for selecting which spectra to score,
+ the rules for selecting candidate peptides for a given spectrum, and
+ for deciding what kinds of scores to report.</p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/tutorials/gettingstarted.html b/doc/user/tutorials/gettingstarted.html
new file mode 100644
index 0000000..023bacb
--- /dev/null
+++ b/doc/user/tutorials/gettingstarted.html
@@ -0,0 +1,218 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Getting started with Crux</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Getting started with Crux</h2>
+
+ <p> This page will talk about setting up your environment and choosing
+ your input files. Be sure to have completed the software <a
+ href="install.html">installation</a> first.
+ </p>
+
+ <a name="env"></a>
+ <h3>Your environment</h3>
+ <p>For this tutorial, we'll assume you are working in a Linux/Unix
+ type shell (<a href="http://www.cygwin.com/">cygwin</a> is a good
+ choice for Windows users) and already know some basic
+ commands for changing directories, listing files, and other simple
+ tasks. To successfully run the sample commands, you'll need to work from
+ a directory for which you have write permission. Anywhere
+ in your home directory should work. Create a new directory and
+ navigate to it.</p>
+ <div class=code><code>
+ $ mkdir crux-demo<br>
+ $ cd crux-demo</code>
+ </div>
+ <p>
+ We will refer to this directory, <code>'crux-demo'</code>, as the
+ <em>working directory</em>.</p>
+ <p>Next, make sure that the computer knows where to look for the
+ <span class=prog>crux</span> programs. Try this command. </p>
+ <div class=code><code>
+ $ which crux</code>
+ </div>
+ <p>
+ If it returns a single line with a path ending in <span
+ class=out>crux</span>, then you are set. If not,
+ review the <a href="install.html#path">installation instructions</a> on setting your
+ <span class=code>$PATH</span> environment variable.
+
+ </p>
+
+ <a name=ms2></a>
+ <h3>Input file: mass spectra</h3>
+ <p>Included in the <span class=prog>crux</span> distribution in the
+ <span class=file>doc/example-files</span> directory are some
+ sample files containing mass spectra. We will use the <a
+ href="../example-files/demo.ms2">demo.ms2</a> for this tutorial. Locate the
+ file and copy it to the current working directory.
+ </p>
+ <p>The beginning of the file looks like this.
+ </p>
+ <pre>
+H CreationDate 2/14/2007 6:19:18 PM
+H Extractor MakeMS2
+H ExtractorVersion 1.0
+H Comments MakeMS2 written by Michael J. MacCoss, 2004
+H ExtractorOptions MS2/MS1
+S 10 10 636.34
+Z 2 1271.67
+187.4 12.5
+193.1 19.5
+194.3 13.7
+ </pre>
+ <div class=note><em>NOTE: There are two kinds of optional lines which
+ may be included for each spectrum. Lines beginning with </em><span
+ class=file>I</span><em> are contain information independent of the
+ charge state. Following a </em> <span class=file>Z</span><em> line may
+ be one beginning with </em><span class=file>D</span><em> containing
+ information specific to the above charge state. </em>
+ </div>
+
+ <p>
+ The first lines beginning with <span class=file>H</span> are the
+ header lines and contain information about the program that generated
+ the file, the date it was created, and so on. The line starting with
+ <span class=file>S</span> begins the information about the first
+ spectrum. Following the <span class=file>S</span> is the scan number
+ (twice) and the m/z of the precursor ion. The lines beginning with
+ <span class=file>Z</span> list the possible charge states of the
+ spectrum (in this case 2) and the mass of the peptide at that
+ charge state. Following the <span class=file>Z</span> lines is the
+ list of peaks for the spectrum. The subsequent spectra in the file
+ repeat this pattern of <span class=file>S</span> line, <span
+ class=file>Z</span> line(s), and peak list. <span
+ class=file>demo.ms2</span> contains 150 spectra.
+ </p>
+
+ <a name="fasta"></a>
+ <h3>Input file: protein database (fasta file)</h3>
+ <p>The second input file you will need is a protein database.
+ This file is in fasta format and contains
+ a list of proteins you expect to find in your sample and their
+ sequences. A sample fasta file is also comes with the distribution in
+ <span class=file>doc/example-files</span>. We will use <a
+ href="../example-files/small-yeast.fasta">small-yeast.fasta</a>. Copy it to your
+ current working directory.
+ </p>
+
+ <p>The beginning of the file looks like this.
+ </p>
+
+ <pre>
+>YBL030C PET9 SGDID:S000000126, Chr II from 164000-163044, reverse complement, Verified ORF, "Major ADP/ATP carrier of the mitochondrial inner membrane, exchanges cytosolic ADP for mitochondrially synthesized ATP; required for viability in many common lab strains carrying a mutation in the polymorphic SAL1 gene"
+MSSNAQVKTPLPPAPAPKKESNFLIDFLMGGVSAAVAKTAASPIERVKLLIQNQDEML
+KQGTLDRKYAGILDCFKRTATQEGVISFWRGNTANVIRYFPTQALNFAFKDKIKAMFG
+FKKEEGYAKWFAGNLASGGAAGALSLLFVYSLDYARTRLAADSKSSKKGGARQFNGLI
+DVYKKTLKSDGVAGLYRGFLPSVVGIVVYRGLYFGMYDSLKPLLLTGSLEGSFLASFL
+LGWVVTTGASTCSYPLDTVRRRMMMTSGQAVKYDGAFDCLRKIVAAEGVGSLFKGCGA
+NILRGVAGAGVISMYDQLQMILFGKKFK
+ </pre>
+
+ <p>Lines beginning with <span class=file>></span> give the name of
+ a protein. The first word is the protein name followed by an optional
+ description of any length. The following lines contain the protein
+ sequence. Proteins may or may not be separated by blank lines.
+ <span class=file>small-yeast.fasta</span> contains 56 proteins.
+ </p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/tutorials/install.html b/doc/user/tutorials/install.html
new file mode 100644
index 0000000..3468902
--- /dev/null
+++ b/doc/user/tutorials/install.html
@@ -0,0 +1,805 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Crux Installation Instructions</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
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+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <div id="main">
+ <h2>Crux Installation Instructions</h2>
+
+ <p/>
+ This page will walk you through the steps of
+ installing <span class=prog>crux<span/> on your computer.
+ Seperate sections describe the installation for
+ <a href="#LINUX">Linux</a>,
+ <a href="#OSX">OS X</a>,
+ and
+ <a href="#WINDOWS">Windows</a>.
+ You have the choice of installing precompiled binaries or building
+ Crux from the source code.
+ The compiled binaries offer the easiest installation option.
+
+ <a name="LINUX"></a>
+ <h3>Linux</h3>
+ <b>Note:</b> when typing the commands shown in these instructions
+ do not type the
+ leading <code>$</code> before each command; it indicates the
+ prompt. These instructions will refer to your home directory as
+ <code>$HOME</code>. You can type <code>$HOME</code> in the commands
+ or you can use the fully qualified path to your home directory which
+ may be something like <code>/home/yourname/</code>. Note that you can
+ find out the location of your home directory by logging in and
+ typing <code>pwd</code> or <code>echo $HOME</code>.
+ <h3>Installing Pre-compiled Crux Binaries on Linux</h3>
+ <ul>
+ <li><b>Download the files</b>
+ <p/>
+ <span class=prog>Crux</span> is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license</a>.
+ On the download page click on the link "Linux [architecture]
+ Build (zipped)" to download them to your computer.
+ If your computer is running a 32-bit version of Linux select the
+ i686 version.
+ If your computer is running a 64-bit version of Linux select the
+ x86_64 version.
+ If a window pops
+ up, select the "Save" button.
+ To check that the file was
+ transfered correctly, run this command
+
+ <div class=code><code>
+ $ md5sum <i>[downloaded file]</i></code>
+ </div>
+ <p/>
+ and compare the output to the "MD5 checksum" link next to the file you
+ downloaded.
+ <p/>
+ </li>
+
+ <li><b>Unpack and install the files</b>
+ <p/>
+ The file you downloaded
+ should be named something like
+ <span class=file>crux-x.xx-XXXX-GNU-Linux.zip</span>
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ and
+ <span class=file>XXXX</span> is either i686 or x86_64.
+ Move this file
+ to a convenient location and unpack the file with this command.
+
+ <div class=code><code>
+ $ unzip crux-x.xx-XXXX-GNU-Linux.zip</code>
+ </div>
+ <p/>
+ You should now have a new directory,
+ <span class=file>crux-x.xx-XXXX-GNU-Linux</span>,
+ with two subdirectories <span class=file>bin</span>, and <span
+ class=file>doc</span>. The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> directory. You may want to move
+ these files somewhere
+ more convenient for you, but otherwise, that completes the
+ installation! Skip ahead to
+ <a href="#linux_path">Setting the PATH on Linux and OS X</a>
+ for notes on how to run the executables.
+ </ul>
+ <h3>Building Crux From Source on Linux</h3>
+ <ul>
+ <li><b>Prerequisites</b>
+ <p/>
+ To build Crux from source on Linux you must have installed the
+ following software:
+ <ul>
+ <li><code>gcc</code></li>
+ <li><code>g++</code></li>
+ <li><code>cmake</code></li>
+ <li><code>make</code></li>
+ <li><code>svn</code></li>
+ <li><code>wget</code> (must support SSL)</li>
+ </ul>
+ <p/>
+ Building <span class=prog>crux</span> also requires the
+ <a href="http://proteowizard.sourceforge.net"><span class=prog>Proteowizard</span></a>
+ and
+ <a href="http://per-colator.com"><span class=prog>Percolator</span></a>
+ libraries.
+ These will automatically be copied from the <span class=prog>Proteowizard</span>
+ and <span class=prog>Percolator</span>
+ repositories and statically linked into <span class=prog>crux</span>.
+
+ <li><b>Download the files</b>
+ <p/>
+ The <span class=prog>Crux</span> source is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license></a>.
+ On the download page click on the link "Source (tarred, gzipped)",
+ and choose save to disk if prompted.
+ To check that the file was
+ transfered correctly, run this command
+
+ <div class=code><code>
+ $ md5sum <i>[downloaded file]</i></code>
+ </div>
+ <p/>
+ and compare the output to the "MD5 checksum" link next to the file you
+ selected on the Crux download page.
+ <p/>
+ The file you downloaded should be named something like
+ <span class=file>crux-x.xx.source.tar.gz</span>,
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ <li><b>Unpack the files</b>
+ <p/>
+ Move the downloaded file to a
+ convenient location and unpack it with this command.
+
+ <div class=code>
+ $ tar -zxvf crux-x.xx.Source.tar.gz
+ </div>
+ A new directory named <span class=file>crux-x.xx.Source</span> will be
+ created and a long list of files will stream by as they are being put
+ into the new directory.
+ <p/>
+ </li>
+
+ <li><b>Configure the build</b>
+ <p/>
+ Move into the <span class=file>crux-x.xx.Source</span>
+ directory from step 1.
+ Run the command
+ <div class=code><code>
+ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+ </code>
+ </div>
+ <p/>
+ where <span class=file><install directory></span> is
+ the location where you wish to install the <span class=prog>crux</span> programs.
+ If you want <span class=prog>crux</span> to go in <span class=file>$HOME/bin</span>,
+ then <span class=file><install directory></span> would be <span class=file>$HOME</span>.
+ The installation process will automatically put the programs in a directory called
+ <span class=file>bin</span>.
+ <p/>
+ Note, this configuration will build with optimizations turned on,
+ and will not include debug symbols.
+ To build with optimizations turned off,
+ and debug symbols included,
+ use the command:
+ <div class=code><code>
+ cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+ </code>
+ </div>
+ </li>
+ <p/>
+ <li><b>Build and install</b>
+ <p/>
+ To complete the process, run these two commands.</li>
+ <div class=code><code>
+ $ make<br>
+ $ make install
+ </code>
+ </div>
+ <p/>
+ The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> subdirectory
+ of the
+ <span class=file><install directory></span>
+ That completes the installation! Skip ahead to
+ <a href="#linux_path">Setting the PATH on Linux and OS X</a>
+ for notes on how to run the executables.
+ </ul>
+ <a name="OSX"></a>
+ <h3>OS X</h3>
+ <span class=prog>Crux</span> requires OS X Yosemite or later.
+ <p/>
+ <b>Note:</b>
+ when typing the commands shown in these instructions do not type the
+ leading <code>$</code> before each command; it indicates the
+ prompt. These instructions will refer to your home directory as
+ <code>$HOME</code>. You can type <code>$HOME</code> in the commands
+ or you can use the fully qualified path to your home directory which
+ may be something like <code>/home/yourname/</code>. Note that you can
+ find out the location of your home directory by logging in and
+ typing <code>pwd</code> or <code>echo $HOME</code>.
+ <p/>
+ To install and use <code>crux</code> on OS X
+ you'll need to be familiar with the <span class=code>Terminal</span>
+ application.
+ <h3>Installing Pre-compiled Crux Binaries on OS X</h3>
+ <ul>
+ <li><b>Download the files</b>
+ <p/>
+ <span class=prog>Crux</span> is freely
+ available for download under an
+ <a href=""http://www.apache.org/licenses/LICENSE-2.0>Apache 2.0 license</a>.
+ On the download page click on the link "OS X x86_64 Build (zipped)"
+ to download them to your computer.
+ If a window pops
+ up, select the "Save" button.
+ To check that the file was
+ transfered correctly, run this command
+
+ <div class=code><code>
+ $ md5 <i>[downloaded file]</i></code>
+ </div>
+ <p/>
+ and compare the output to the "MD5 checksum" link next to the file you
+ downloaded.
+ <p/>
+ </li>
+
+ <li><b>Unpack and install the files</b>
+ <p/>
+ The file you downloaded
+ should be named something like
+ <span class=file>crux-x.xx.Darwin.x86_64.zip</span>
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ Move this file
+ to a convenient location and unpack the file with this command.
+
+ <div class=code><code>
+ $ unzip crux-x.xx.Darwin.x86_64.zip</code>
+ </div>
+ <p/>
+ You should now have a new directory,
+ <span class=file>crux-x.xx.Darwin.x86_64</span>,
+ with two subdirectories <span class=file>bin</span>, and <span
+ class=file>doc</span>. The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> directory. You may want to move
+ these files somewhere
+ more convenient for you, but otherwise, that completes the
+ installation! Skip ahead to
+ <a href="#linux_path">Setting the PATH on Linux and OS X</a>
+ for notes on how to run the executables.
+ </ul>
+ <h3>Building Crux From Source on OS X</h3>
+ <ul>
+ <li><b>Prerequisites</b>
+ <p/>
+ To build Crux from source on OS X you must have installed the
+ following software:
+ <ul>
+ <li><code>OS X Yosemite or later</code></li>
+ <li><code>XCode 6.3.1 or later</code></li>
+ <li><code>XCode Command Line Tools</code></li>
+ <li><code>cmake</code></li>
+ <li><code>make</code></li>
+ <li><code>svn</code></li>
+ <li><code>wget</code> (must support SSL)</li>
+ <li><code>gnutar</code> (Apple's version of tar is incompatible with GNU's
+ version of tar)</li>
+ </ul>
+ <p/>
+ Building <span class=prog>crux</span> also requires the
+ <a href="http://proteowizard.sourceforge.net"><span class=prog>Proteowizard</span></a>
+ and
+ <a href="http://per-colator.com"><span class=prog>Percolator</span></a>
+ libraries.
+ These will automatically be copied from the <span class=prog>Proteowizard</span>
+ and <span class=prog>Percolator</span>
+ repositories and statically linked into <span class=prog>crux</span>.
+ <p />
+ Building <span class=prog>Crux</span> on OS X requires a current version of
+ <span class=prog>XCode</span>, and the XCode command line tools.
+ Earlier versions of <span class=prog>Crux</span>
+ had to be built using the GCC compilers.
+ which are no supported by Apple.
+ If you have the both the GCC and Apple compilers installed, you'll need to
+ adjust the <span class=prog>PATH</span> environment variable so that the
+ Apple compilers are found first.
+ Alternatively, you can specify which compilers should be used by setting
+ the <span class=prog>CC</span>, and <span class=prog>CXX</span>.
+ For example,
+ <div class=code>
+ <code>
+ export CC=/usr/bin/gcc
+ <br />
+ export CXX=/usr/bin/g++
+ </code>
+ </div>
+ <p/>
+ The programs
+ <span class=prog>cmake</span>,
+ <span class=prog>svn</span>,
+ and
+ <span class=prog>wget</span>,
+ can be installed from
+ <a href="https://www.macports.org">MacPorts</a>
+ or
+ <a href="http://brew.sh">Homebrew</a>.
+ Note that you must install the <span class=prog>ssl</span> variant of
+ <span class=prog>wget</span>:
+ <div class=code>
+ <code>
+ $ sudo port install wget +ssl
+ </code>
+ </div>
+ <p/>
+ <li><b>Download the files</b>
+ <p/>
+ The <span class=prog>Crux</span> source is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license></a>.
+ On the download page click on the link "Source (tarred, gzipped)",
+ and choose save to disk if prompted.
+ To check that the file was
+ transfered correctly, run this command
+
+ <div class=code><code>
+ $ md5sum <i>[downloaded file]</i></code>
+ </div>
+ <p/>
+ and compare the output to the "MD5 checksum" link next to the file you
+ selected on the Crux download page.
+ <p/>
+ The file you downloaded should be named something like
+ <span class=file>crux-x.xx.source.tar.gz</span>,
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ <li><b>Unpack the files</b>
+ <p/>
+ Move the downloaded file to a
+ convenient location and unpack it with this command.
+
+ <div class=code>
+ $ tar -zxvf crux-x.xx.Source.tar.gz
+ </div>
+ A new directory named <span class=file>crux-x.xx.Source</span> will be
+ created and a long list of files will stream by as they are being put
+ into the new directory.
+ <p/>
+ </li>
+
+ <li><b>Configure the build</b>
+ <p/>
+ Move into the <span class=file>crux-x.xx.Source</span>
+ directory from step 1.
+ Run the command
+ <div class=code><code>
+ cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+ </code>
+ </div>
+ <p/>
+ where <span class=file><install directory></span> is
+ the location where you wish to install the <span class=prog>crux</span> programs.
+ If you want <span class=prog>crux</span> to go in <span class=file>$HOME/bin</span>,
+ then <span class=file><install directory></span> would be <span class=file>$HOME</span>.
+ The installation process will automatically put the programs in a directory called
+ <span class=file>bin</span>.
+ <p/>
+ Note, this configuration will build with optimizations turned on,
+ and will not include debug symbols.
+ To build with optimizations turned off,
+ and debug symbols included,
+ use the command:
+ <div class=code><code>
+ cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX:PATH=<install directory> .
+ </code>
+ </div>
+ </li>
+ <p/>
+ <li><b>Build and install</b>
+ <p/>
+ To complete the process, run these two commands.</li>
+ <div class=code><code>
+ $ make<br>
+ $ make install
+ </code>
+ </div>
+ <p/>
+ The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> subdirectory
+ of the
+ <span class=file><install directory></span>
+ That completes the installation! Skip ahead to
+ <a href="#linux_path">Setting the PATH on Linux and OS X</a>
+ for notes on how to run the executables.
+ </ul>
+
+ <a name="linux_path"></a>
+ <h3>Setting the PATH on Linux and OS X</h3>
+ <ul>
+ <li>
+ <p/>
+ On Linux and OS X systems you can always run any of the programs by specifying its full
+ path. For example,</p>
+
+ <div class=code><code>
+ $ <em><install directory></em>/bin/crux comet</code>
+ </div>
+
+ <p>In this final step of the installation, we'll set things up so that
+ you can also run any of the programs by just typing its name. This is
+ done with an environment variable called <span
+ class=code>$PATH</span>. <span class=code>$PATH</span> is a list of
+ places that the computer looks for executable programs. Find out what
+ is in the current list with this command:
+
+ <div class=code><code>
+ $ echo $PATH</code><br>
+ </div>
+ <p>The value returned might look something like this:
+ <code>
+ /usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/games
+ </code>
+ <p>The first directory in this colon-separated list, <span
+ class=out>/usr/local/bin</span>, is the first place the computer looks
+ for a program. If it doesn't find the program there it tries <span
+ class=out>/usr/bin</span> and so on down the list. You can either
+ move the crux executable files into one of these directories already
+ in your PATH, or you can add <span
+ class=code><em><install directory></em></span> to PATH with this
+ command. (Remember to replace the word <em><install directory></em> with the
+ actual location of your installation)</p>
+
+ <div class=code><code>
+ $ export PATH=$PATH:<install directory>/bin</code>
+ </div>
+
+ <p>Try '<span class=code>echo $PATH</span>' again to see that the
+ change was made. <em><install directory>/bin</em> should be at the end of the
+ list. Now you can
+ run the <span class=prog>crux</span> programs by just typing their
+ names. Try this.</p>
+
+ <div class=code><code>
+ $ crux comet</code>
+ </div>
+
+ <p>The change to <span class=code>$PATH</span> is only temporary. As
+ soon as you close the window, the change will disappear. In order to
+ make the change every time you log on, add the line <span
+ class=code>export PATH=$PATH:<install directory>/bin</span> to the file <span
+ class=out>.bashrc</span> located in your home directory. You will
+ have to log on again for the change to take effect.
+ </ul>
+ <a name="WINDOWS"></a>
+ <h3>Windows</h3>
+ <h3>Installing Pre-compiled Crux Binaries on Windows</h3>
+
+ <ul>
+ <li><b>Prerequisites</b>
+ <p/>
+ To run Crux with support for vendor specific file formats
+ on Windows you must have installed the following software:
+ <ul>
+ <li>
+ <a href="https://thermo.flexnetoperations.com/control/thmo/login">
+ <code>Thermo MSFileReader</code></a>
+ </li>
+ <li>
+ <a href="https://www.microsoft.com/en-us/download/details.aspx?id=40784">
+ <code>Visual C++ 2013 Runtime Libraries</code></a>
+ </li>
+ </ul>
+ <p/>
+ <li><b>Download the files</b>
+ <p/>
+ <span class=prog>Crux</span> is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license</a>.
+ On the download page click on the link "Windows x86
+ Build (zipped)" to download them to your computer.
+ If a window pops up, select the "Save" button.
+ </li>
+ <li><b>Unpack and install the files</b>
+ <p/>
+ Browse to the downloaded file in Windows Explorer.
+ Right click on the file and choose "Expand All ...".
+ You should now have a new directory,
+ <span class=file>crux-x.xx</span>,
+ with two subdirectories <span class=file>bin</span>, and <span
+ class=file>doc</span>. The <span class=prog>crux</span> programs are
+ in the <span class=file>bin</span> directory. You may want to move
+ these files somewhere
+ more convenient for you, but otherwise, that completes the
+ installation! Skip ahead to
+ <a href="#windows_path">Setting the PATH on Windows</a>
+ for notes on how to run the executables.
+ </ul>
+
+ <h3>Building Crux From Source on Windows</h3>
+ <ul>
+ <li><b>Prerequisites</b>
+ <p/>
+ To build Crux from source on Windows you must have installed the
+ following software:
+ <ul>
+ <li><code>
+ <a
+ href="http://www.visualstudio.com/downloads/download-visual-studio-vs#DownloadFamilies_4">Microsoft
+ Visual C++ 2013</a></code></li>
+ <li><a href="http://www.cmake.org/cmake/resources/software.html"><code>CMake</code></a></li>
+ <li><a href="http://sourceforge.net/projects/win32svn/"><code>SVN</code></a></li>
+ <li><a href="http://getgnuwin32.sourceforge.net"><code>wget</code> (must support SSL)</a></li>
+ <li><a
+ href="https://thermo.flexnetoperations.com/control/thmo/login">
+ <code>Thermo MSFileReader</code></a> (This may be omitted if support for
+ vendor specific file formats is disabled.)</li>
+ </ul>
+ <p/>
+ <b>Other verions of Visual Studio will not be able to build Crux!</b>
+ You must have Visual Studio 2013.
+ Visual Studio 2013 Express for Windows Desktop does work.
+ <p/>
+ <span class=code>wget</span> is available as part of the GnuWin32 package.
+ The easiest way to install this is via the
+ <a href="http://getgnuwin32.sourceforge.net"><code>GetGnuWin32</code></a>
+ package manager.
+ <span class=code>wget</span> must support SSL, so install the optional
+ packages provided by
+ <a href="http://getgnuwin32.sourceforge.net"><code>GetGnuWin32</code></a> .
+ <p/>
+ <span class=code>wget</span> and
+ <span class=code>svn</span> must be included in the execution PATH
+ for your system.
+ See the section <i>Setting the PATH on Windows</i> for more information.
+ <p/>
+ <li><b>Download the file</b>
+ <p/>
+ The <span class=prog>Crux</span> source is freely
+ available for download under an
+ <a href="http://www.apache.org/licenses/LICENSE-2.0">Apache 2.0 license></a>.
+ On the download page click on the link "Source (zipped)",
+ and choose save to disk if prompted.
+ <p/>
+ The file you downloaded should be named something like
+ <span class=file>crux-x.xx.Source.zip</span>,
+ where <span class=file>x.xx</span>
+ is replaced with the most current release version.
+ <p />
+ <li><b>Unpack the files</b>
+ <p />
+ Unpack the downloaded file using Windows Explorer.
+ Right click on the file icon and click on "Extract All ...".
+ A new directory named <span class=file>crux-x.xx.Source</span> will be
+ created containing the source code and documentation for Crux.
+ <p/>
+ <b>Note</b> Windows has a fixed maximum path length of 270 characters.
+ The Crux build creates several levels of directories so it
+ is very easy to exceed this limit.
+ This will cause the build to fail.
+ To avoid this problem we recommend keeping the Crux source and build trees
+ very near the disk root (typically
+ <span class=code>C:\</span>
+
+ </li>
+ <li>
+ <p/>
+ <b>Open the command line development environment.</b>
+ <p/>
+ Under the "Start" button
+ open the "Visual Studio 2013" folder, then open the "Visual Studio Tools"
+ folder, and double-click on "Developer Command Prompt for VS2013".
+ This will launch a
+ <span class=file>cmd</span> shell configured to use the
+ Microsoft development tools.
+ </li>
+ <li><b>Configure</b>
+ <p/>
+ In the <span class=file>cmd</span> shell you just opened,
+ move into the <span class=file>crux-x.xx.Source</span>
+ directory from step 1.
+ Run the command
+ <div class=code><code>
+ cmake -DCMAKE_INSTALL_PREFIX:PATH=<install directory> -G "Visual Studio
+ 12 Win64" .
+ </code>
+ </div>
+ <p/>
+ where <span class=file><install directory></span> is
+ the location where you wish to install the <span class=prog>crux</span> programs.
+ Note that, somewhat confusingly, Visual Studio 2013 is version 12.
+ <p/>
+ If you wish to disable support for vendor specific file formats,
+ use this command instead
+ <p/>
+ <div class=code><code>
+ cmake
+ -DCMAKE_INSTALL_PREFIX:PATH=<install directory> -DINCLUDE_VENDOR_LIBRARIES=FALSE -G "Visual Studio 12 Win64" .
+ </code>
+ </div>
+ <p/>
+ <li><b>Build and install</b>
+ <p/>
+ To complete the process run the commands</li>
+ <div class=code><code>
+ cmake --build . --config Release --target ALL_BUILD
+ <br/>
+ cmake --build . --config Release --target INSTALL
+ </code>
+ <p/>
+ Once you've run the configuration step
+ you can also build and debug Crux from within the Visual Studio IDE.
+ CMake will generate a file named
+ <span class=file>crux.sln</span>.
+ Open this file in Visual Studio.
+ You can select the build configuration: Release or Debug
+ in the combo box under the menu bar.
+ <p/>
+ <b>Note</b> The Crux build will not automatically generate
+ debugging symbols even if you've selected the Debug configuration.
+ Right click on the Crux folder in the "Solution Explorer" and
+ select "Properties" from the pop-up menu.
+ In the "Properties" page select the "Debugging" item under the "Linker"
+ properties. Set "Generate Debug Info" to "Yes".
+ <p/>
+ Changes made to the Visual Studio solution and project files will be lost
+ the next time CMake regenerates the project.
+ </div>
+ <p/>
+
+ </ul>
+ </ul>
+
+ <a name="windows_path"></a>
+ <h3>Setting the PATH on Windows</h3>
+ <ul>
+ <li>
+ On Windows systems you can always run any of the programs by specifying its full
+ path. For example,</p>
+
+ <div class=code><code>
+ C:\ <em><install directory></em>\bin\crux comet</code>
+ </div>
+
+ <p>In this final step of the installation, we'll set things up so that
+ you can also run any of the programs by just typing its name. This is
+ done with an environment variable called <span
+ class=code>PATH</span>. <span class=code>PATH</span> is a list of
+ directoires that the computer looks for executable programs. Find out what
+ is in the current list with this command:
+ <p/>
+ <div class=code><code>
+ C:\ echo %PATH%</code><br>
+ </div>
+ <p/>
+ <p>The value returned might look something like this:
+ <p/>
+ <div class=code><code>
+ <code>
+ C:\Windows;C:\Windows\system32;c:\Program Files\Microsoft Visual
+ Studio 10.0\Common7\IDE\;c:\Program Files\Microsoft
+ Visual Studio 10.0\VC\BIN;C:\Program Files\Common Files\Microsoft Shared\
+ Windows Live;C:\Windows\System32\Wbem;C:\Windows\S
+ ystem32\WindowsPowerShell\v1.0\;c:\Program files\Notepad++;C:\Program Files\Tort
+ oiseSVN\bin;C:\Program Files\Windows Live\Shared;C:\Program Files\CMake 2.8\bin;
+ C:\Program Files\PuTTY;C:\Program Files\Subversion\bin;C:\GnuWin32\bin;
+ </code>
+ </div>
+ <p>The first directory in this semicolon-separated list, <span
+ class=out>C:\Windows</span>, is the first place the computer looks
+ for a program. If it doesn't find the program there it tries <span
+ class=out>C:\WIndows\system32</span> and so on down the list. You can either
+ move the crux executable files into one of these directories already
+ in your PATH, or you can add <span
+ class=code><em><install directory></em></span> to PATH with this
+ command. (Remember to replace the word <em><install directory></em> with the
+ actual location of your installation)</p>
+ <div class=code><code>
+ set PATH=%PATH%;<install directory>\bin;</code><br>
+ </div>
+ <p>The change to <span class=code>PATH</span> is only temporary.
+ To make a permanent change to the path follow the following steps:
+ <ol>
+ <li>Open the "Control Panel".</li>
+ <li>Click on "System and Security".</li>
+ <li>Click on "Advanced System Settings" in the list on the left
+ (you may be asked to give an administrative password).
+ <li>
+ You'll presented with a dialog box titled "System Properties".
+ Click on the button labeled "Environment Variables".
+ <li>
+ You'll be presented with a new dialog box containing two list boxes: one for user
+ environment variables, and one for system environment variables.
+ Select the
+ <span class=code>PATH</span>
+ variable in the system variables list, and click on the "Edit ..." button.
+ <li>
+ Add the full path to the directory containing the Crux executables to the
+ list of directories. Remember that each
+ <span class=code>PATH</span>
+ entry should end with a semi-colon.
+ </ol>
+
+ </div>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/tutorials/search.html b/doc/user/tutorials/search.html
new file mode 100644
index 0000000..2788a27
--- /dev/null
+++ b/doc/user/tutorials/search.html
@@ -0,0 +1,422 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Running a Simple Search Using Tide and Percolator</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Running a Simple Search Using Tide and Percolator</h2>
+
+ <p>
+ Now that you have your environment <a href="gettingstarted.html">set
+ up</a> and the two input files in your working directory, you can
+ conduct the search. The search process compares each spectrum
+ in <span class=file>demo.ms2</span> to peptides (subsequences of the
+ proteins) in fasta files provided in a
+ dirctory, <span class=file>yeast-index/</span>. Peptides whose
+ precursor mass is close to that of the observed spectrum are scored
+ against that spectrum, and the top scores are reported in the output.
+ To conduct the search, we first create a peptide index
+ using <code>tide-index</code> and then execute the search
+ using <code>tide-search</code>.</p>
+
+ <ol>
+ <li>
+ <div class=code>
+ <code>$ crux tide-index small-yeast.fasta yeast-index </code>
+ </div>
+
+ <p>
+ While generating the peptide index, you will see output like this:</p>
+
+ <pre>
+INFO: CPU: pyrrolysine.gs.washington.edu
+INFO: Crux version: 2.1
+INFO: Fri Feb 5 11:24:02 PST 2016
+COMMAND LINE: ./crux tide-index small-yeast.fasta yeast-index
+INFO: Running tide-index...
+INFO: Writing results to output directory 'yeast-index'.
+INFO: Reading small-yeast.fasta and computing unmodified peptides...
+INFO: Writing decoy fasta...
+INFO: Reading proteins
+INFO: Precomputing theoretical spectra...
+INFO: Elapsed time: 0.0973 s
+INFO: Finished crux tide-index.
+INFO: Return Code:0
+ </pre>
+
+ <p>
+ This command produces the peptide index in <code>yeast-index</code>
+ and also produces a directory <code>crux-output</code> containing
+ the following files:
+ <ol>
+
+ <li>
+ tide-index.decoy.fasta – a set of decoy proteins, derived from
+ the proteins in the input set,</li>
+
+ <li>
+ tide-search.params.txt – a record of all the parameters used in
+ the search, and</li>
+
+ <li>tide-search.log.txt – a log file containing a copy of all
+ the messages printed to the screen during the search.</li>
+ </ol>
+
+ <p>
+ Now you can run this command:</p></li>
+
+ <div class=code>
+ <li><code>$ crux tide-search --compute-sp T demo.ms2 yeast-index</code>
+ </div>
+
+ <p>While the search is running, you will see output like this:</p>
+
+ <pre>
+INFO: CPU: pyrrolysine.gs.washington.edu
+INFO: Crux version: 2.1
+INFO: Fri Feb 5 11:24:23 PST 2016
+COMMAND LINE: ./crux tide-search --compute-sp T demo.ms2 yeast-index
+INFO: Running tide-search...
+INFO: Reading index yeast-index
+INFO: Converting demo.ms2 to spectrumrecords format
+INFO: Reading spectra file crux-output/demo.ms2.spectrumrecords.tmp
+INFO: Sorting spectra
+INFO: Running search
+INFO: Time per spectrum-charge combination: 0.002318 s.
+INFO: Average number of candidates per spectrum-charge combination: 15.204820
+INFO: Elapsed time: 0.389 s
+INFO: Finished crux tide-search.
+INFO: Return Code:0
+ </pre>
+
+ <p>
+ The <span class=file>crux-output</span> directory now contains four new files
+ containing the search results:
+
+ <ol>
+
+ <li>
+ tide-search.target.txt – search results
+ in <a href="../file-formats/txt-format.html">tab-delimited format</a>.</li>
+
+ <li>
+ tide-search.decoy.txt – search results from a decoy database
+ in <a href="../file-formats/txt-format.html">tab-delimited format</a>.</li>
+
+ <li>
+ tide-search.params.txt – a record of all the parameters used in
+ the search.</li>
+
+ <li>tide-search.log.txt – a log file containing a copy of all
+ the messages printed to the screen during the search.</li>
+ </ol>
+
+ </p>
+ </li>
+
+ <p>
+ Note that the peptide-spectrum matches (PSMs) in the
+ tide-search.target.txt are sorted by the precursor m/z value
+ associated with the spectrum. If you want to see which PSMs got the
+ highest XCorr scores, you can do so like this:</p>
+
+ <div class=code>
+ <li><code>$ crux sort-by-column --column-type real --ascending T crux-output/tide-search.target.txt "xcorr score" > crux-output/tide-search.target.sort.txt</code>
+ </div>
+
+ <p>
+ The first lines of the resulting sorted output file should look like this:</p>
+
+ <table class="searchtable">
+ <td><b>file</b></td><td><b>scan</b></td><td><b>charge</b></td><td><b>spectrum precursor m/z</b></td><td><b>spectrum neutral mass</b></td><td><b>peptide mass</b></td><td><b>delta_cn</b></td><td><b>sp score</b></td><td><b>sp rank</b></td><td><b>xcorr score</b></td><td><b>xcorr rank</b></td><td><b>b/y ions matched</b></td><td><b>b/y ions total</b></td><td><b>distinct matches/spectrum</b></td><td><b>sequence</b></td><td><b>cleavage type</b></td><td><b>protein id</b></td><td><b>flanking aa< [...]
+ <tr>
+ <td>demo.ms2</td><td>85</td><td>3</td><td>497.618</td><td>1489.83</td><td>1488.82</td><td>0.936932</td><td>2430.56</td><td>1</td><td>5.20757</td><td>1</td><td>27</td><td>48</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W(27)</td><td>RN</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>118</td><td>3</td><td>1031.94</td><td>3092.8</td><td>3093.41</td><td>0.949698</td><td>2383.16</td><td>1</td><td>4.76204</td><td>1</td><td>44</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>156</td><td>3</td><td>1032.44</td><td>3094.3</td><td>3093.41</td><td>0.938358</td><td>1929.77</td><td>1</td><td>4.7476</td><td>1</td><td>43</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>18</td><td>3</td><td>1032.4</td><td>3094.18</td><td>3093.41</td><td>0.902056</td><td>1732.23</td><td>1</td><td>4.48933</td><td>1</td><td>40</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>11</td><td>2</td><td>745.269</td><td>1488.52</td><td>1488.82</td><td>0.822851</td><td>2816.6</td><td>1</td><td>4.44855</td><td>1</td><td>21</td><td>24</td><td>4</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W(27)</td><td>RN</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>53</td><td>2</td><td>745.749</td><td>1489.48</td><td>1488.82</td><td>0.935648</td><td>2797.78</td><td>1</td><td>4.39828</td><td>1</td><td>21</td><td>24</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W(27)</td><td>RN</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>38</td><td>3</td><td>1032.39</td><td>3094.15</td><td>3093.41</td><td>0.975741</td><td>1460.28</td><td>1</td><td>4.39627</td><td>1</td><td>37</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>42</td><td>3</td><td>1032.26</td><td>3093.76</td><td>3093.41</td><td>1.0216</td><td>1509.47</td><td>1</td><td>4.35676</td><td>1</td><td>38</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>111</td><td>3</td><td>1033.02</td><td>3096.04</td><td>3093.41</td><td>0.952727</td><td>1366.71</td><td>1</td><td>4.3498</td><td>1</td><td>36</td><td>108</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C(500)</td><td>KD</td></tr>
+ <tr>
+ <td>demo.ms2</td><td>62</td><td>2</td><td>745.859</td><td>1489.7</td><td>1488.82</td><td>0.913711</td><td>2766.65</td><td>1</td><td>4.34057</td><td>1</td><td>21</td><td>24</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W(27)</td><td>RN</td></tr>
+ </table>
+
+
+ <p>
+ The final step is to post-process the search results using Percolator.
+ Each spectrum has been compared to many peptides and we would like to
+ return only the best match for each spectrum. We also expect that
+ some fraction of the spectra will not be identifiable as peptides (due
+ to chemical noise, multiple peptides co-eluting, poor fragmentation,
+ etc.). The analysis step filters out those spectra and ranks the
+ matches by quality.
+ </p></li>
+
+ <li>
+ <div class=code><code>
+ $ crux percolator crux-output/tide-search.target.txt</code>
+ </div>
+
+ <p>While the analysis is running, you will see output like this
+ </p>
+
+ <pre>
+INFO: CPU: pyrrolysine.gs.washington.edu
+INFO: Crux version: 2.1
+INFO: Fri Feb 5 11:25:51 PST 2016
+COMMAND LINE: ./crux percolator crux-output/tide-search.target.txt
+INFO: Reading file crux-output/tide-search.target.txt
+INFO: Running make-pin
+INFO: Parsing crux-output/tide-search.target.txt
+INFO: Parsing crux-output/tide-search.decoy.txt
+INFO: There are 690 target matches and 690 decoys
+INFO: Finished make-pin.
+INFO: Percolator version 2.09, Build Date Sep 22 2015 14:29:11
+INFO: Copyright (c) 2006-9 University of Washington. All rights reserved.
+INFO: Written by Lukas Käll (lukall at u.washington.edu) in the
+INFO: Department of Genome Sciences at the University of Washington.
+INFO: Issued command:
+INFO: percolator -r crux-output/percolator.target.peptides.txt -v 2 -P decoy_ --seed 1 -p 0.01 -n 0 --trainFDR 0.01 --testFDR 0.01 --maxiter 10 -s crux-output/make-pin.pin
+INFO: Started Fri Feb 5 11:25:52 2016
+INFO: on pyrrolysine.gs.washington.edu
+INFO: Hyperparameters selectionFdr=0.01, Cpos=0.01, Cneg=0, maxNiter=10
+INFO: Reading Tab delimited input from datafile crux-output/make-pin.pin
+INFO: Features:
+INFO: lnrSp deltCn XCorr Sp IonFrac PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM
+INFO: Train/test set contains 690 positives and 690 negatives, size ratio=1 and pi0=1
+INFO: selecting cneg by cross validation
+INFO: Selected feature number 4 as initial search direction, could separate 39 positives in that direction
+INFO: Selected feature number 3 as initial search direction, could separate 38 positives in that direction
+INFO: Selected feature number 3 as initial search direction, could separate 30 positives in that direction
+INFO: Estimating 53 over q=0.01 in initial direction
+INFO: Reading in data and feature calculation took 0.03 cpu seconds or 0 seconds wall time
+INFO: ---Training with Cpos=0.01, Cneg selected by cross validation, fdr=0.01
+INFO: Iteration 1 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 2 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 3 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 4 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 5 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 6 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 7 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 8 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 9 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Iteration 10 : After the iteration step, 53 target PSMs with q<0.01 were estimated by cross validation
+INFO: Obtained weights (only showing weights of first cross validation set)
+INFO: # first line contains normalized weights, second line the raw weights
+INFO: lnrSp deltCn XCorr Sp IonFrac PepLen Charge1 Charge2 Charge3 enzN enzC enzInt lnNumSP dM absdM m0
+INFO: 0.0352 0.0014 0.1465 0.2956 -0.0130 0.0224 0.0051 -0.0025 -0.0020 0.0000 0.0000 -0.0001 -0.0049 -0.0055 0.0169 -0.9248
+INFO: 0.0580 0.0069 0.2096 0.0010 -0.0922 0.0052 0.0136 -0.0052 -0.0053 0.0000 0.0000 -0.0006 -0.0077 -0.0059 0.0300 -1.1931
+INFO: After all training done, 56 target PSMs with q<0.0100 were found when measuring on the test set
+INFO: Found 56 target PSMs scoring over 1.0000% FDR level on testset
+INFO: Merging results from 3 datasets
+INFO: Target Decoy Competition yielded 116 target PSMs and 50 decoy PSMs
+INFO: Tossing out "redundant" PSMs keeping only the best scoring PSM for each unique peptide.
+INFO: Calibrating statistics - calculating q values
+INFO: Merged list gives 9 peptides over q=0.0100
+INFO: Calibrating statistics - calculating Posterior error probabilities (PEPs)
+INFO: Processing took 0.67 cpu seconds or 0 seconds wall time
+INFO: Elapsed time: 0.933 s
+INFO: Finished crux percolator.
+INFO: Return Code:0
+ </pre>
+
+ <p>
+ The <span class=file>crux-output</span> directory will now contain
+ eight new files:</p>
+ <ol>
+
+ <li>
+ percolator.target.psms.txt – a list of peptide-spectrum matches
+ (PSMs), ranked by quality,</li>
+
+ <li>
+ percolator.target.peptides.txt – a list of peptides, ranked by
+ quality,</li>
+
+ <li>
+ percolator.decoy.psms.txt – a ranked list of decoy PSMs, </li>
+
+ <li>
+ percolator.decoy.peptides.txt – a ranked list of decoy peptides,</li>
+
+ <li>
+ percolator.pout.xml – a single XML output file containing all of
+ the Percolator results,</li>
+
+ <li>
+ make-pin.pin.xml: an intermediate XML format file that is used by
+ Percolator.</li>
+
+ <li>
+ percolator.params.txt – parameter file, and</li>
+
+ <li>
+ percolator.log.txt – log file.</li>
+
+ </ol>
+ </p>
+
+ <p>
+ As before, you might want to sort the Percolator output files, this
+ time by the "percolator score" column:</p>
+
+
+ <li>
+ <div class=code><code>
+ $ crux sort-by-column --column-type real --ascending T crux-output/percolator.target.psms.txt "percolator score" > crux-output/percolator.target.psms.sort.txt
+ </code>
+ </div>
+
+ <p>
+ The beginning of the resulting percolator.target.psms.sort.txt file will look like
+ this:</p>
+
+ <table class="searchtable">
+ <td><b>file</b></td><td><b>file_idx</b></td><td><b>scan</b></td><td><b>charge</b></td><td><b>spectrum precursor m/z</b></td><td><b>spectrum neutral mass</b></td><td><b>peptide mass</b></td><td><b>percolator score</b></td><td><b>percolator rank</b></td><td><b>percolator q-value</b></td><td><b>total matches/spectrum</b></td><td><b>sequence</b></td><td><b>cleavage type</b></td><td><b>protein id</b></td><td><b>flanking aa</b></td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>118</td><td>3</td><td>1031.9407</td><td>3092.8000</td><td>3095.2366</td><td>8.6190662</td><td>1</td><td>0</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C</td><td>KD</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>26</td><td>2</td><td>692.3773</td><td>1382.7400</td><td>1382.4467</td><td>7.0481362</td><td>2</td><td>0</td><td>6</td><td>TASEFDSAIAQDK</td><td>trypsin-full-digest</td><td>YLR043C</td><td>KL</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>53</td><td>2</td><td>745.7473</td><td>1489.4800</td><td>1489.7318</td><td>6.7469611</td><td>3</td><td>0</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W</td><td>RN</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>62</td><td>2</td><td>745.8572</td><td>1489.7000</td><td>1489.7318</td><td>6.6489625</td><td>4</td><td>0</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W</td><td>RN</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>146</td><td>2</td><td>692.6772</td><td>1383.3400</td><td>1382.4467</td><td>6.6027999</td><td>5</td><td>0</td><td>5</td><td>TASEFDSAIAQDK</td><td>trypsin-full-digest</td><td>YLR043C</td><td>KL</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>131</td><td>2</td><td>745.8473</td><td>1489.6801</td><td>1489.7318</td><td>6.5627294</td><td>6</td><td>0</td><td>3</td><td>NFLETVELQVGLK</td><td>trypsin-full-digest</td><td>YGL135W</td><td>RN</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>50</td><td>2</td><td>651.2873</td><td>1300.5601</td><td>1301.4160</td><td>6.3757763</td><td>7</td><td>0</td><td>10</td><td>LDVDELGDVAQK</td><td>trypsin-full-digest</td><td>YLR043C</td><td>KN</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>42</td><td>3</td><td>1032.2606</td><td>3093.7600</td><td>3095.2366</td><td>5.8047724</td><td>8</td><td>0</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C</td><td>KD</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>90</td><td>3</td><td>1032.0006</td><td>3092.9800</td><td>3095.2366</td><td>5.4775882</td><td>9</td><td>0</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C</td><td>KD</td></tr>
+ <tr>
+ <td>crux-output/tide-search.target.txt</td><td>1</td><td>111</td><td>3</td><td>1033.0206</td><td>3096.0400</td><td>3095.2366</td><td>5.4364419</td><td>10</td><td>0</td><td>2</td><td>ELESAAYDHAEPVQPEDAPQDIANDELK</td><td>trypsin-full-digest</td><td>YGL009C</td><td>KD</td></tr>
+ </table>
+
+ <p>
+ In this output, the PSMs are ranked by "percolator score," with higher
+ scores indicating a higher quality match. The associated statistical
+ confidence estimate is reported as a "percolator q-value," interpreted
+ as the minimal false discovery rate threshold at which this match is
+ deemed significant. In the list above, all of the matches have
+ q-values of 0, meaning that they are highly significant.
+ The meanings of the remaining columns are
+ described <a href="../file-formats/txt-format.html">here</a>. Note that when you run
+ Percolator on your own computer, the results may be somewhat
+ different than the ones reported here. This is because Percolator
+ involves randomly subdividing the data in a cross-validation scheme
+ (described in detail
+ <a href="http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-S16-S3">here</a>.)</p>
+ </li>
+ </ol>
+ <!-- END CONTENT -->
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+ <div class="footerimportantlinks tutoriallinks">
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+ </ul>
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+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
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+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
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+
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diff --git a/doc/user/tutorials/spectralcounts.html b/doc/user/tutorials/spectralcounts.html
new file mode 100644
index 0000000..4e5be1c
--- /dev/null
+++ b/doc/user/tutorials/spectralcounts.html
@@ -0,0 +1,182 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>Using spectral-counts</title>
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+ </ul>
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+ <div id="content">
+ <!-- START CONTENT -->
+ <h2>Using spectral-counts</h2>
+
+ <p>
+ After you have run a <a href="search.html">search</a> and
+ assigned confidence to your identified PSMs, you can now calculate
+ relative quantification values for the proteins by running the
+ command:<br>
+
+ <div class=code>
+ <code>$ crux spectral-counts --protein-database small-yeast.fasta ./crux-output/percolator.target.psms.txt</code>
+ </div>
+ <br>
+ Alternatively, you can use the pepXML output by q-ranker using the command:<br>
+ <br>
+ <div class=code>
+ <code>$ crux spectral-counts --protein-database small-yeast.fasta ./crux-output/percolator.target.psms.txt</code>
+ </div>
+
+ <p>While the command is running, you will see output like this
+ </p>
+
+ <pre>
+INFO: Beginning spectral-counts.
+INFO: Total proteins found: 56
+INFO: Number of matches passed the threshold 116
+ </pre>
+
+ <p>When the command is finished, it will print</p>
+ <pre>
+INFO: Finished crux spectral-counts.
+ </pre>
+
+ <p>
+ Within the <code>crux-output</code> directory, there will be three new files:
+ <li>spectral-counts.target.txt – tab-delimited file of the <code>spectral-counts</code> results</li>
+ <li>spectral-counts.params.txt – the parameters used for running <code>spectral-counts</code></li>
+ <li>spectral-counts.log.txt – the log output of <code>spectral-counts</code></li>
+ </p>
+
+ <p>The spectral-counts.target.txt file will look something like:<br>
+ <pre>
+protein id NSAF
+YLR043C 0.61643416
+YGL135W 0.17810018
+YEL027W 0.10352074
+YGL009C 0.035437137
+YLR185W 0.031369921
+YJR069C 0.014012959
+YGR192C 0.0083149187
+YMR235C 0.0067826854
+YBR118W 0.0060274079
+ </pre>
+
+ <p>
+ In this output, the first field is the identifier and the second field
+ is the spectral-counting measure (NSAF, dNSAF, SIN, or EMPAI) result
+ for each protein. To select which measure is computed, see the
+ <a href="../commands/spectral-counts.html">crux spectral-counts</a> documentation.</p>
+
+
+ <h3>Using peptideprophet probability from pepXML</h3>
+ <p><code>crux spectral-counts</code> also supports using the Peptide Prophet probability provided in the pepXML file. Use the command:<br>
+ <br>
+ <div class=code>
+ <code>$ crux spectral-counts --protein-database small-yeast.fasta --threshold-type custom --custom-threshold-name peptideprophet --threshold 0.9 --custom-threshold-min F target.pep.xml</code>
+ </div>
+ This code will filter out matches whose Peptide Prophet probability is < 0.9 and calculate NSAF for the proteins of the remaining PSMs.<br>
+
+ <h3>Using mzIdentML files with spectral-counts</h3>
+ <p><code>crux spectral-counts</code> also supports mzIdentML as input. For example, </p>
+ <div class="code">
+ $ crux spectral-counts --measure RAW file.mzid
+ </div>
+ <p>
+ If the protein sequences are not provided in the mzIdentML file, then you will have to provide
+ a database using the <span class="code">protein-database</span> parameter for the NSAF, dNSAF, EMPAI, and SIN metrics.
+ </p>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="install.html">Installation</a></li>
+ <li><a href="gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="customizedsearch.html">Customization and search options</a></li>
+ <li><a href="spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+
+</body>
+
+</html>
diff --git a/doc/user/xlink-assign-ions.html b/doc/user/xlink-assign-ions.html
new file mode 100644
index 0000000..84897bb
--- /dev/null
+++ b/doc/user/xlink-assign-ions.html
@@ -0,0 +1,145 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>xlink-assign-ions</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>xlink-assign-ions</h1>
+<h2>Usage:</h2>
+<p><code>crux xlink-assign-ions [options] <peptide A> <peptide B> <pos A> <pos B> <link mass> <charge state> <scan number> <ms2 file></code></p>
+<h2>Description:</h2>
+Given a spectrum and a pair of cross-linked peptides, assign theoretical ion type labels to peaks in the observed spectrum.
+<h2>Input:</h2>
+<ul>
+ <li><code>peptide A</code> – The sequence of peptide A.</li>
+ <li><code>peptide B</code> – The sequence of peptide B.</li>
+ <li><code>pos A</code> – Position of cross-link on peptide A</li>
+ <li><code>pos B</code> – Position of cross-link on peptide B</li>
+ <li><code>link mass</code> – The mass modification of the linker when attached to a peptide.</li>
+ <li><code>charge state</code> – The charge state of the peptide.</li>
+ <li><code>scan number</code> – Scan number identifying the spectrum.</li>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – tab-delimited text in which each row is a peak in the observed spectrum, and the columns are <ol><li>The m/z value.</li><li>The observed intensity.</li><li>The matched intensity.</li><li>The calculated m/z value of the theoretical peak.</li><li>The mass associated with the observed peak.</li><li>The mass difference (in ppm) between the observed and theoretical peaks.</li><li>The ion type, specified as b or y, followed by the charge state in parentheses.< [...]
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--fragment-mass average|mono</code> – Specify which isotopes to use in calculating fragment ion mass. Default = <code>mono</code>.</li>
+ <li class="nobullet"><code>--max-ion-charge <string></code> – Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state of the peptide ("peptide"). If the max-ion-charge is greater than the charge state of the peptide, then the maximum is the peptide charge. Default = <code>peptide</code>.</li>
+ <li class="nobullet"><code>--mz-bin-width <float></code> – Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. Default = <code>1.00 [...]
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+ <li class="nobullet"><code>--spectrum-parser pwiz|mstoolkit</code> – Specify the parser to use for reading in MS/MS spectra. The default, ProteoWizard parser can read the MS/MS file formats listed <a href="http://proteowizard.sourceforge.net/formats.shtml">here</a>. The alternative is <a href="../mstoolkit.html">MSToolkit parser</a>. If the ProteoWizard parser fails to read your files properly, you may want to try the MSToolkit parser instead. Default = <code>pwiz</code>.</li>
+ <li class="nobullet"><code>--precision <integer></code> – Set the precision for scores written to sqt and text files. Default = <code>8</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/doc/user/xlink-score-spectrum.html b/doc/user/xlink-score-spectrum.html
new file mode 100644
index 0000000..be37984
--- /dev/null
+++ b/doc/user/xlink-score-spectrum.html
@@ -0,0 +1,158 @@
+<!DOCTYPE html>
+<html>
+<head>
+<title>xlink-score-spectrum</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0" />
+<link rel="stylesheet" type="text/css" href="../styles.css">
+<script type="text/javascript"
+ src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/javascript">
+ MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});
+</script>
+<script type="text/javascript">
+ var _gaq = _gaq || [];
+ _gaq.push(['_setAccount', 'UA-26136956-1']);
+ _gaq.push(['_trackPageview']);
+ (function() {
+ var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+ ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+</script>
+<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+<script type="text/javascript">
+ // Main Menu
+ $( document ).ready(function() {
+ var pull = $('.btn');
+ menu = $('nav ul');
+ menuHeight = menu.height();
+ $(pull).on('click', function(e) {
+ e.preventDefault();
+ menu.slideToggle();
+ });
+ $(window).resize(function(){
+ var w = $(window).width();
+ if(w > 320 && menu.is(':hidden')) {
+ menu.removeAttr('style');
+ }
+ });
+ });
+</script>
+</head>
+<body>
+ <div class="page-wrap">
+ <nav>
+ <div class="btn">
+ </div>
+ <img src="../images/crux-logo.png" id="logo"></a>
+ <ul id="navitems">
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../download.html">Download</a></li>
+ <li><a href="../fileformats.html">File Formats</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Contact</a></li> <!--Link to google support board-->
+ </ul>
+ </nav>
+ <div id="content" class="autogenerated">
+ <!-- START CONTENT -->
+<h1>xlink-score-spectrum</h1>
+<h2>Usage:</h2>
+<p><code>crux xlink-score-spectrum [options] <peptide A> <peptide B> <pos A> <pos B> <link mass> <charge state> <scan number> <ms2 file></code></p>
+<h2>Description:</h2>
+Given a cross-linked peptide and a spectrum calculate the corresponding XCorr score a number of different ways, depending upon the xlink-score-method parameter:<ul><li>composite – compute a combined XCorr score</li><li>modification - score the two peptides separately, treating the second peptide as a variable modification on the first peptide</li><li>concatenated - score as the concatenation of the two peptides. Note that this mode gives four scores, corresponding to the two relat [...]
+<h2>Input:</h2>
+<ul>
+ <li><code>peptide A</code> – The sequence of peptide A.</li>
+ <li><code>peptide B</code> – The sequence of peptide B.</li>
+ <li><code>pos A</code> – Position of cross-link on peptide A</li>
+ <li><code>pos B</code> – Position of cross-link on peptide B</li>
+ <li><code>link mass</code> – The mass modification of the linker when attached to a peptide.</li>
+ <li><code>charge state</code> – The charge state of the peptide.</li>
+ <li><code>scan number</code> – Scan number identifying the spectrum.</li>
+ <li><code>ms2 file</code> – File containing spectra to be searched.</li>
+</ul>
+<h2>Output:</h2>
+<ul>
+ <li><code>stdout</code> – XCorr score(s) in descending order</li>
+</ul>
+<h2>Options:</h2>
+<ul style="list-style-type: none;">
+<li class="nobullet">
+<h3>xlink-score-spectrum options</h3>
+<ul>
+ <li class="nobullet"><code>--xlink-score-method composite|modification|concatenated</code> – Score method for xlink {composite, modification, concatenated}. Default = <code>composite</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Search parameters</h3>
+<ul>
+ <li class="nobullet"><code>--use-flanking-peaks T|F</code> – Include flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Fragment ion parameters</h3>
+<ul>
+ <li class="nobullet"><code>--use-a-ions T|F</code> – Consider a-ions in the search? Note that an a-ion is equivalent to a neutral loss of CO from the b-ion. Peak height is 10 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-b-ions T|F</code> – Consider b-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-c-ions T|F</code> – Consider c-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-x-ions T|F</code> – Consider x-ions in the search? Peak height is 10 (in arbitrary units). Default = <code>false</code>.</li>
+ <li class="nobullet"><code>--use-y-ions T|F</code> – Consider y-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>true</code>.</li>
+ <li class="nobullet"><code>--use-z-ions T|F</code> – Consider z-ions in the search? Peak height is 50 (in arbitrary units). Default = <code>false</code>.</li>
+</ul>
+</li>
+<li class="nobullet">
+<h3>Input and output</h3>
+<ul>
+ <li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
+</ul>
+</li>
+
+</ul>
+ <!-- END CONTENT -->
+ </div>
+ </div>
+<footer class="site-footer">
+ <div id="centerfooter">
+ <div class="footerimportantlinks">
+ <img src="../images/linkicon.png" style="width:16px; height:16px"><h3>Important links</h3>
+ <ul>
+ <li><a href="../faq.html">Crux FAQ</a></li>
+ <li><a href="../glossary.html">Glossary of terminology</a></li>
+ <li><a href="http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ">Google Scholar profile</a></li>
+ <li><a href="https://github.com/crux-toolkit/crux-toolkit">GitHub</a></li>
+ <li><a href="../release-notes.html">Release Notes</a></li>
+ <li><a href="https://mailman1.u.washington.edu/mailman/listinfo/crux-users" title="Receive announcements of new versions">Join the mailing list</a></li>
+ <li><a href="http://www.apache.org/licenses/LICENSE-2.0">Apache license</a></li>
+ <li><a href="http://groups.google.com/group/crux-users">Support Board</a></li>
+ </ul>
+ </div>
+ <div class="footerimportantlinks tutoriallinks">
+ <img src="../images/tutorialicon.png" style="height:16px"><h3>Tutorials</h3>
+ <ul>
+ <li><a href="../tutorials/install.html">Installation</a></li>
+ <li><a href="../tutorials/gettingstarted.html">Getting started with Crux</a></li>
+ <li><a href="../tutorials/search.html">Running a simple search using Tide and Percolator</a></li>
+ <li><a href="../tutorials/customizedsearch.html">Customization and search options</a></li>
+ <li><a href="../tutorials/spectralcounts.html">Using spectral-counts</a></li>
+ </ul>
+ </div>
+ <div id="footertext">
+ <p>
+ The original version of Crux was written by Chris Park and Aaron Klammer
+ under the supervision
+ of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
+ MacCoss</a>
+ and <a href="http://noble.gs.washington.edu/~noble">Prof. William
+ Stafford Noble</a> in the Department of Genome Sciences at the
+ University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>.
+ <br />The complete list of contributors
+ can be found <a href="../contributors.html">here</a>.
+ <br />
+ <br />
+ Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> award P41 GM103533.
+ </p>
+ </div>
+ </div>
+</footer>
+</body>
+</html>
\ No newline at end of file
diff --git a/ext/CMakeLists.txt b/ext/CMakeLists.txt
new file mode 100644
index 0000000..8954251
--- /dev/null
+++ b/ext/CMakeLists.txt
@@ -0,0 +1,342 @@
+include(ExternalProject)
+
+INCLUDE_DIRECTORIES(BEFORE SYSTEM ${CMAKE_CURRENT_BINARY_DIR}/include)
+
+if (UNIX)
+ SET(ENV{BOOSTROOT} ${CMAKE_CURRENT_BINARY_DIR})
+ SET(ENV{LIBPATH} ${CMAKE_CURRENT_BINARY_DIR}/lib:$ENV{LIBPATH})
+ SET(ENV{LD_LIBRARY_PATH} ${CMAKE_CURRENT_BINARY_DIR}/lib:$ENV{LD_LIBRARY_PATH})
+ SET(ENV{PATH} ${CMAKE_CURRENT_BINARY_DIR}/bin:$ENV{PATH})
+ SET(CPP_ARGS "-I${CMAKE_CURRENT_BINARY_DIR}/include")
+ SET(LD_ARGS "-L${CMAKE_CURRENT_BINARY_DIR}/lib")
+endif (UNIX)
+SET(ENV{CMAKE_PREFIX_PATH} ${CMAKE_CURRENT_BINARY_DIR})
+SET(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_BINARY_DIR})
+SET(USE_LATEST_PWIZ ON CACHE BOOL "Use lastest version of ProteoWizard")
+
+if (WIN32 AND NOT CYGWIN)
+ # If windows build we need to select 32/64 bit platform
+ if (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ SET(MSBUILD_PLATFORM "x64")
+ else (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ SET(MSBUILD_PLATFORM "Win32")
+ endif (CMAKE_GENERATOR MATCHES "^.*Win64$")
+
+ # On Windows we should build vendor libraries by default
+ if (NOT DEFINED INCLUDE_VENDOR_LIBRARIES)
+ set(INCLUDE_VENDOR_LIBRARIES TRUE)
+ endif (NOT DEFINED INCLUDE_VENDOR_LIBRARIES)
+ if (INCLUDE_VENDOR_LIBRARIES)
+ message(STATUS "Including vendor libraries.")
+ else (INCLUDE_VENDOR_LIBRARIES)
+ message(STATUS "Not including vendor libraries.")
+ endif (INCLUDE_VENDOR_LIBRARIES)
+endif (WIN32 AND NOT CYGWIN)
+
+# Download and build a partial distribution of the pwiz source
+# from the ProteoWizard TeamCity repository.
+if (WIN32 AND NOT CYGWIN)
+ ExternalProject_Add(
+ ProteoWizard
+ URL http://noble.gs.washington.edu/crux-downloads/pwiz-src-3_0_10273.tar.bz2
+ DOWNLOAD_DIR ${CMAKE_CURRENT_BINARY_DIR}/downloads
+ PREFIX ${CMAKE_CURRENT_BINARY_DIR}/build
+ CONFIGURE_COMMAND ""
+ BUILD_COMMAND
+ ${CMAKE_COMMAND}
+ -DMSBUILD_PLATFORM=${MSBUILD_PLATFORM}
+ -DBUILD_TYPE:STRING=${CMAKE_CFG_INTDIR}
+ -DPREFIX:PATH=${CMAKE_CURRENT_BINARY_DIR}
+ -DWORKING_DIR:PATH=${CMAKE_CURRENT_BINARY_DIR}/build/src/ProteoWizard
+ -DINCLUDE_VENDOR_LIBRARIES:BOOLEAN=${INCLUDE_VENDOR_LIBRARIES}
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/build_pwiz.cmake
+ INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory
+ ${CMAKE_CURRENT_SOURCE_DIR}/patches/boost ${CMAKE_CURRENT_BINARY_DIR}/include/boost
+ BUILD_IN_SOURCE 1
+ )
+ # On Windows we have to do some extra house keeping
+ ExternalProject_Add_Step(
+ ProteoWizard
+ windows_post_install
+ COMMAND
+ ${CMAKE_COMMAND}
+ -DBUILD_TYPE:STRING=${CMAKE_CFG_INTDIR}
+ -DPREFIX:PATH=${CMAKE_CURRENT_BINARY_DIR}
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/post_install_pwiz.cmake
+ DEPENDEES install
+ )
+else (WIN32 AND NOT CYGWIN)
+ ExternalProject_Add(
+ ProteoWizard
+ URL http://noble.gs.washington.edu/crux-downloads/pwiz-src-3_0_10273.tar.bz2
+ DOWNLOAD_DIR ${CMAKE_CURRENT_BINARY_DIR}/downloads
+ PREFIX ${CMAKE_CURRENT_BINARY_DIR}/build
+ CONFIGURE_COMMAND ""
+ BUILD_COMMAND
+ ${CMAKE_COMMAND}
+ -DBUILD_TYPE:STRING=${CMAKE_CFG_INTDIR}
+ -DPREFIX:PATH=${CMAKE_CURRENT_BINARY_DIR}
+ -DWORKING_DIR:PATH=${CMAKE_CURRENT_BINARY_DIR}/build/src/ProteoWizard
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/build_pwiz.cmake
+ INSTALL_COMMAND
+ ${CMAKE_CURRENT_SOURCE_DIR}/create_links.sh
+ --prefix=${CMAKE_CURRENT_BINARY_DIR}
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${CMAKE_CURRENT_SOURCE_DIR}/patches/boost/asio.hpp
+ ${CMAKE_CURRENT_BINARY_DIR}/include/boost
+ COMMAND ${CMAKE_COMMAND} -E copy_directory
+ ${CMAKE_CURRENT_SOURCE_DIR}/patches/boost/asio
+ ${CMAKE_CURRENT_BINARY_DIR}/include/boost/asio
+ COMMAND ${CMAKE_COMMAND} -E copy_directory
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/ProteoWizard/libraries/boost_aux/boost/utility
+ ${CMAKE_CURRENT_BINARY_DIR}/include/boost/utility
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/ProteoWizard/libraries/boost_1_56_0/boost/date_time/gregorian_calendar.ipp
+ ${CMAKE_CURRENT_BINARY_DIR}/include/boost/date_time
+ BUILD_IN_SOURCE 1
+ )
+endif (WIN32 AND NOT CYGWIN)
+
+ExternalProject_Add(
+ percolator
+ GIT_REPOSITORY https://github.com/percolator/percolator.git
+ GIT_TAG "6f20e6b"
+ PREFIX ${CMAKE_CURRENT_BINARY_DIR}/build
+ CMAKE_ARGS -DCMAKE_VERBOSE_MAKEFILE=ON
+ -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}
+ -DCMAKE_PREFIX_PATH=${CMAKE_CURRENT_BINARY_DIR}
+ -DCMAKE_BUILD_TYPE=${CMAKE_CFG_INTDIR}
+ -DCRUX=${CMAKE_CURRENT_SOURCE_DIR}/..
+ -DEXT_BINARY_DIR=${CMAKE_CURRENT_BINARY_DIR}/include
+ INSTALL_COMMAND ""
+)
+
+if (UNIX)
+ ExternalProject_Add(
+ protobuf-2.5.0
+ PREFIX ${CMAKE_CURRENT_BINARY_DIR}/build
+ DOWNLOAD_COMMAND
+ ${CMAKE_COMMAND}
+ -DDOWNLOAD_DIR:PATH=${CMAKE_CURRENT_BINARY_DIR}/downloads
+ -DWORKING_DIR:PATH=${CMAKE_CURRENT_BINARY_DIR}/build/src
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/download_pbuffers.cmake
+ CONFIGURE_COMMAND
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/protobuf-2.5.0/configure
+ --prefix=${CMAKE_CURRENT_BINARY_DIR}
+ --enable-shared=no
+ BUILD_COMMAND make
+ INSTALL_COMMAND make install
+ BUILD_IN_SOURCE 1
+ )
+elseif (WIN32 AND NOT CYGWIN)
+ # Update Microsoft VS project files and build ProtocolBuffers using MSBuild
+ ExternalProject_Add(
+ protobuf-2.5.0
+ PREFIX ${CMAKE_CURRENT_BINARY_DIR}/build
+ DOWNLOAD_COMMAND
+ ${CMAKE_COMMAND}
+ -DDOWNLOAD_DIR:PATH=${CMAKE_CURRENT_BINARY_DIR}/downloads
+ -DWORKING_DIR:PATH=${CMAKE_CURRENT_BINARY_DIR}/build/src
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/download_pbuffers.cmake
+ PATCH_COMMAND ${CMAKE_COMMAND} -E copy_directory
+ ${CMAKE_CURRENT_SOURCE_DIR}/patches/protobuf/vsprojects/
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/protobuf-2.5.0/vsprojects/ &&
+ ${CMAKE_COMMAND} -E copy_directory
+ ${CMAKE_CURRENT_SOURCE_DIR}/patches/protobuf/src/
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/protobuf-2.5.0/src/
+ CONFIGURE_COMMAND ""
+ BUILD_COMMAND msbuild
+ /p:Configuration=${CMAKE_CFG_INTDIR}
+ /p:Platform=${MSBUILD_PLATFORM}
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/protobuf-2.5.0/vsprojects/libprotobuf.vcxproj &&
+ msbuild
+ /p:Configuration=${CMAKE_CFG_INTDIR}
+ /p:Platform=${MSBUILD_PLATFORM}
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/protobuf-2.5.0/vsprojects/libprotoc.vcxproj &&
+ msbuild
+ /p:Configuration=${CMAKE_CFG_INTDIR}
+ /p:Platform=${MSBUILD_PLATFORM}
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/protobuf-2.5.0/vsprojects/protoc.vcxproj
+ INSTALL_COMMAND ""
+ BUILD_IN_SOURCE 1
+ )
+ ExternalProject_Add_Step(
+ protobuf-2.5.0
+ copy_binaries
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/protobuf-2.5.0/vsprojects/${MSBUILD_PLATFORM}/${CMAKE_CFG_INTDIR}/protoc.exe
+ ${CMAKE_CURRENT_BINARY_DIR}/bin/protoc.exe
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/protobuf-2.5.0/vsprojects/${MSBUILD_PLATFORM}/${CMAKE_CFG_INTDIR}/libprotobuf.lib
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/protobuf.lib
+ DEPENDEES install
+ )
+endif (UNIX)
+
+ExternalProject_Add(
+ gflags-2.1.2
+ DOWNLOAD_COMMAND
+ ${CMAKE_COMMAND}
+ -DDOWNLOAD_DIR:PATH=${CMAKE_CURRENT_BINARY_DIR}/downloads
+ -DWORKING_DIR:PATH=${CMAKE_CURRENT_BINARY_DIR}/build/src
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/download_gflags.cmake
+ PREFIX ${CMAKE_CURRENT_BINARY_DIR}/build
+ CMAKE_ARGS -DCMAKE_VERBOSE_MAKEFILE=ON
+ -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}
+ -DCMAKE_PREFIX_PATH=${CMAKE_CURRENT_BINARY_DIR}
+ -DCMAKE_BUILD_TYPE=${CMAKE_CFG_INTDIR}
+ PATCH_COMMAND ""
+)
+
+if (UNIX)
+ # Get Comet source from SVN and buld using it's own makefile
+ ExternalProject_Add(
+ comet
+ SVN_REPOSITORY svn://svn.code.sf.net/p/comet-ms/code/tags/release_2016011/
+ PREFIX ${CMAKE_CURRENT_BINARY_DIR}/build
+ UPDATE_COMMAND ""
+ CONFIGURE_COMMAND ""
+ PATCH_COMMAND cp
+ ${CMAKE_CURRENT_SOURCE_DIR}/patches/comet/CometSearch/CometSearchManager.cpp
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/
+ BUILD_COMMAND make -C MSToolkit
+ COMMAND make -C CometSearch CXXFLAGS=-DCRUX
+ INSTALL_COMMAND ""
+ BUILD_IN_SOURCE 1
+ )
+ # Copy the Comet and MSToolkit include files and libraries to
+ # the desired directories.
+ add_custom_command(
+ TARGET comet
+ POST_BUILD
+ COMMAND
+ [ -d ${CMAKE_CURRENT_BINARY_DIR}/include/MSToolkit ] ||
+ mkdir ${CMAKE_CURRENT_BINARY_DIR}/include/MSToolkit
+ COMMAND
+ cp -p
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/MSToolkit/include/*
+ ${CMAKE_CURRENT_BINARY_DIR}/include/MSToolkit
+ COMMAND
+ cp -p
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/MSToolkit/libmstoolkitlite.a
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/libcometsearch.a
+ ${CMAKE_CURRENT_BINARY_DIR}/lib
+ COMMAND
+ [ -d ${CMAKE_CURRENT_BINARY_DIR}/include/CometSearch ] ||
+ mkdir ${CMAKE_CURRENT_BINARY_DIR}/include/CometSearch
+ COMMAND
+ cp -p
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/Common.h
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/CometData.h
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/CometSearch.h
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/CometSearchManager.h
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/CometPreprocess.h
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/ThreadPool.h
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/Threading.h
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/OSSpecificThreading.h
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/CometSearch/CometInterfaces.h
+ ${CMAKE_CURRENT_BINARY_DIR}/include/CometSearch
+ )
+elseif (WIN32 AND NOT CYGWIN)
+ set(LIBPATH "${CMAKE_CURRENT_BINARY_DIR}/lib;")
+ ExternalProject_Add(
+ comet
+ SVN_REPOSITORY http://svn.code.sf.net/p/comet-ms/code/tags/release_2016011/
+ PREFIX ${CMAKE_CURRENT_BINARY_DIR}/build
+ UPDATE_COMMAND ""
+ # Copy the Comet and MSToolkit include files and libraries to
+ # the desired directories.
+ CONFIGURE_COMMAND
+ ${CMAKE_COMMAND} -E copy_directory
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/MSToolkit/include
+ ${CMAKE_CURRENT_BINARY_DIR}/include/MSToolkit/
+ PATCH_COMMAND
+ ${CMAKE_COMMAND}
+ -DSOURCE_DIR:STRING=${CMAKE_CURRENT_SOURCE_DIR}
+ -DBINARY_DIR:STRING=${CMAKE_CURRENT_BINARY_DIR}
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/patch-comet.cmake
+ BUILD_COMMAND
+ ${CMAKE_COMMAND}
+ -DLIBPATH:STRING="${LIBPATH}"
+ -DMSBUILD_ARGS:STRING=/p:Configuration=${CMAKE_CFG_INTDIR}
+ -DMSBUILD_PLATFORM=${MSBUILD_PLATFORM}
+ -DPROJ_FILE:STRING=comet.sln
+ -P ${CMAKE_CURRENT_SOURCE_DIR}/build-comet.cmake
+ INSTALL_COMMAND ""
+ BUILD_IN_SOURCE 1
+ )
+ ExternalProject_Add_Step(
+ comet
+ copy_comet_library
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/${MSBUILD_PLATFORM}/${CMAKE_CFG_INTDIR}/CometSearch.lib
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/CometSearch.lib
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/comet/${MSBUILD_PLATFORM}/${CMAKE_CFG_INTDIR}/MSToolkitLite.lib
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/MSToolkitLite.lib
+ DEPENDEES install
+ )
+endif (UNIX)
+
+
+# On Windows we have to include the vendor libraries in the package
+if (WIN32 AND NOT CYGWIN)
+ if (INCLUDE_VENDOR_LIBRARIES)
+ if (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ set(
+ vendor_binaries
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/agtsampleinforw.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/baf2sql_c.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/BaseCommon.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/BaseDataAccess.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/BaseError.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/BaseTof.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Compression.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Data.AnalystDataProvider.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Data.CommonInterfaces.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Data.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Data.WiffReader.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.InternalRawXYProcessing.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Muni.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.RawXYProcessing.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.StructuredStorage.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Utility.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/fileio_x64.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/fregistry_x64.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/MassSpecDataReader.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/MIDAC.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/MSFileReader.XRawfile2.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/ProteoWizard/pwiz_aux/msrc/utility/vendor_api/Waters/vc12_x64/cdt.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/ProteoWizard/pwiz_aux/msrc/utility/vendor_api/Waters/vc12_x64/MassLynxRaw.dll
+ )
+ else (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ set(
+ vendor_binaries
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/agtsampleinforw.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/baf2sql_c.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/BaseCommon.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/BaseDataAccess.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/BaseError.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/BaseTof.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Compression.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Data.AnalystDataProvider.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Data.CommonInterfaces.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Data.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Data.WiffReader.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.InternalRawXYProcessing.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Muni.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.RawXYProcessing.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.StructuredStorage.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/Clearcore2.Utility.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/fileio.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/fregistry.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/MassSpecDataReader.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/MIDAC.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/lib/MSFileReader.XRawfile2.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/ProteoWizard/pwiz_aux/msrc/utility/vendor_api/Waters/vc12_x86/cdt.dll
+ ${CMAKE_CURRENT_BINARY_DIR}/build/src/ProteoWizard/pwiz_aux/msrc/utility/vendor_api/Waters/vc12_x86/MassLynxRaw.dll
+ )
+ endif (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ install (FILES ${vendor_binaries} DESTINATION bin)
+ endif (INCLUDE_VENDOR_LIBRARIES)
+endif (WIN32 AND NOT CYGWIN)
diff --git a/ext/Makefile b/ext/Makefile
new file mode 100644
index 0000000..bf31446
--- /dev/null
+++ b/ext/Makefile
@@ -0,0 +1,267 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+# A target that is always out of date.
+cmake_force:
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
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+
+# The CMake executable.
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+
+# The command to remove a file.
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+
+# Escaping for special characters.
+EQUALS = =
+
+# The program to use to edit the cache.
+CMAKE_EDIT_COMMAND = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+#=============================================================================
+# Targets provided globally by CMake.
+
+# Special rule for the target edit_cache
+edit_cache:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake cache editor..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : edit_cache
+
+# Special rule for the target edit_cache
+edit_cache/fast: edit_cache
+.PHONY : edit_cache/fast
+
+# Special rule for the target install
+install: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -P cmake_install.cmake
+.PHONY : install
+
+# Special rule for the target install
+install/fast: preinstall/fast
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -P cmake_install.cmake
+.PHONY : install/fast
+
+# Special rule for the target install/local
+install/local: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local
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+# Special rule for the target install/local
+install/local/fast: install/local
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+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
+.PHONY : install/strip
+
+# Special rule for the target install/strip
+install/strip/fast: install/strip
+.PHONY : install/strip/fast
+
+# Special rule for the target list_install_components
+list_install_components:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
+.PHONY : list_install_components
+
+# Special rule for the target list_install_components
+list_install_components/fast: list_install_components
+.PHONY : list_install_components/fast
+
+# Special rule for the target package
+package: preinstall
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Run CPack packaging tool..."
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cpack --config ./CPackConfig.cmake
+.PHONY : package
+
+# Special rule for the target package
+package/fast: package
+.PHONY : package/fast
+
+# Special rule for the target package_source
+package_source:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Run CPack packaging tool for source..."
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cpack --config ./CPackSourceConfig.cmake /data/TeamCity/buildAgent/work/779d99b0241b2175/CPackSourceConfig.cmake
+.PHONY : package_source
+
+# Special rule for the target package_source
+package_source/fast: package_source
+.PHONY : package_source/fast
+
+# Special rule for the target rebuild_cache
+rebuild_cache:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake to regenerate build system..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : rebuild_cache
+
+# Special rule for the target rebuild_cache
+rebuild_cache/fast: rebuild_cache
+.PHONY : rebuild_cache/fast
+
+# The main all target
+all: cmake_check_build_system
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -E cmake_progress_start /data/TeamCity/buildAgent/work/779d99b0241b2175/CMakeFiles /data/TeamCity/buildAgent/work/779d99b0241b2175/ext/CMakeFiles/progress.marks
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/all
+ $(CMAKE_COMMAND) -E cmake_progress_start /data/TeamCity/buildAgent/work/779d99b0241b2175/CMakeFiles 0
+.PHONY : all
+
+# The main clean target
+clean:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/clean
+.PHONY : clean
+
+# The main clean target
+clean/fast: clean
+.PHONY : clean/fast
+
+# Prepare targets for installation.
+preinstall: all
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/preinstall
+.PHONY : preinstall
+
+# Prepare targets for installation.
+preinstall/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/preinstall
+.PHONY : preinstall/fast
+
+# clear depends
+depend:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
+.PHONY : depend
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+# Convenience name for target.
+ext/CMakeFiles/ProteoWizard.dir/rule:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/CMakeFiles/ProteoWizard.dir/rule
+.PHONY : ext/CMakeFiles/ProteoWizard.dir/rule
+
+# Convenience name for target.
+ProteoWizard: ext/CMakeFiles/ProteoWizard.dir/rule
+.PHONY : ProteoWizard
+
+# fast build rule for target.
+ProteoWizard/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f ext/CMakeFiles/ProteoWizard.dir/build.make ext/CMakeFiles/ProteoWizard.dir/build
+.PHONY : ProteoWizard/fast
+
+# Convenience name for target.
+ext/CMakeFiles/comet.dir/rule:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/CMakeFiles/comet.dir/rule
+.PHONY : ext/CMakeFiles/comet.dir/rule
+
+# Convenience name for target.
+comet: ext/CMakeFiles/comet.dir/rule
+.PHONY : comet
+
+# fast build rule for target.
+comet/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f ext/CMakeFiles/comet.dir/build.make ext/CMakeFiles/comet.dir/build
+.PHONY : comet/fast
+
+# Convenience name for target.
+ext/CMakeFiles/gflags-2.1.2.dir/rule:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/CMakeFiles/gflags-2.1.2.dir/rule
+.PHONY : ext/CMakeFiles/gflags-2.1.2.dir/rule
+
+# Convenience name for target.
+gflags-2.1.2: ext/CMakeFiles/gflags-2.1.2.dir/rule
+.PHONY : gflags-2.1.2
+
+# fast build rule for target.
+gflags-2.1.2/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f ext/CMakeFiles/gflags-2.1.2.dir/build.make ext/CMakeFiles/gflags-2.1.2.dir/build
+.PHONY : gflags-2.1.2/fast
+
+# Convenience name for target.
+ext/CMakeFiles/percolator.dir/rule:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/CMakeFiles/percolator.dir/rule
+.PHONY : ext/CMakeFiles/percolator.dir/rule
+
+# Convenience name for target.
+percolator: ext/CMakeFiles/percolator.dir/rule
+.PHONY : percolator
+
+# fast build rule for target.
+percolator/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f ext/CMakeFiles/percolator.dir/build.make ext/CMakeFiles/percolator.dir/build
+.PHONY : percolator/fast
+
+# Convenience name for target.
+ext/CMakeFiles/protobuf-2.5.0.dir/rule:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 ext/CMakeFiles/protobuf-2.5.0.dir/rule
+.PHONY : ext/CMakeFiles/protobuf-2.5.0.dir/rule
+
+# Convenience name for target.
+protobuf-2.5.0: ext/CMakeFiles/protobuf-2.5.0.dir/rule
+.PHONY : protobuf-2.5.0
+
+# fast build rule for target.
+protobuf-2.5.0/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f ext/CMakeFiles/protobuf-2.5.0.dir/build.make ext/CMakeFiles/protobuf-2.5.0.dir/build
+.PHONY : protobuf-2.5.0/fast
+
+# Help Target
+help:
+ @echo "The following are some of the valid targets for this Makefile:"
+ @echo "... all (the default if no target is provided)"
+ @echo "... clean"
+ @echo "... depend"
+ @echo "... ProteoWizard"
+ @echo "... comet"
+ @echo "... edit_cache"
+ @echo "... gflags-2.1.2"
+ @echo "... install"
+ @echo "... install/local"
+ @echo "... install/strip"
+ @echo "... list_install_components"
+ @echo "... package"
+ @echo "... package_source"
+ @echo "... percolator"
+ @echo "... protobuf-2.5.0"
+ @echo "... rebuild_cache"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+
diff --git a/ext/build-comet.cmake b/ext/build-comet.cmake
new file mode 100644
index 0000000..0b0ed78
--- /dev/null
+++ b/ext/build-comet.cmake
@@ -0,0 +1,10 @@
+message(LIB="$ENV{LIB}")
+message(LIBPATH="$ENV{LIBPATH}")
+message(MSBUILD_ARGS=${MSBUILD_ARGS})
+message(PROJ_FILE=${PROJ_FILE})
+set(ENV{LIBPATH} "$ENV{LIBPATH};${LIBPATH}")
+set(ENV{LIB} "$ENV{LIB};${LIBPATH}")
+message(LIB="$ENV{LIB}")
+message(LIBPATH="$ENV{LIBPATH}")
+message(MSBUILD_PLATFORM="${MSBUILD_PLATFORM}")
+execute_process(COMMAND msbuild /p:platform=${MSBUILD_PLATFORM} /p:useenv=true ${MSBUILD_ARGS} ${PROJ_FILE})
diff --git a/ext/build_pwiz.cmake b/ext/build_pwiz.cmake
new file mode 100644
index 0000000..c8e077e
--- /dev/null
+++ b/ext/build_pwiz.cmake
@@ -0,0 +1,77 @@
+# This is a CMake script for building ProteoWizard.
+# We construct the command line for building ProteoWizard
+# based upond the platform (UNIX or Windows) and the build
+# type (Release or Debug)
+
+# This script expects two variables to be passed on the command line:
+# BUILD_TYPE, the building configuration: Release or Debug
+# PREFIX, the location to store binaries from the build.
+# WORKING_DIR, the location where the expanded source files can be found
+
+# This macro checks download status codes for errors
+macro (check_status status_code)
+ if (${status_code} EQUAL 0)
+ message(STATUS "Built ProteoWizard.")
+ else ()
+ message(
+ FATAL_ERROR
+ "ProteoWizard build failed"
+ )
+ endif (${status_code} EQUAL 0)
+endmacro (check_status)
+
+# Set up arguments needed for ProteoWizard build.
+# quickbuild.sh is the script provided by ProteoWizard on UNIX
+# and quickbuild.bat is the corresponding script on Windows
+set(pwiz_build_args ${pwiz_build_args} --prefix=${PREFIX})
+
+# Get number of processors
+if (EXISTS "/proc/cpuinfo")
+ file(STRINGS "/proc/cpuinfo" procs REGEX "^processor.: [0-9]+$")
+ list(LENGTH procs PROCESSOR_COUNT)
+elseif (APPLE)
+ find_program(cmd_sys_pro "sysctl")
+ if (cmd_sys_pro)
+ execute_process(COMMAND ${cmd_sys_pro} -n hw.ncpu OUTPUT_VARIABLE info)
+ set(PROCESSOR_COUNT "${info}")
+ endif()
+elseif (WIN32)
+ set(PROCESSOR_COUNT "$ENV{NUMBER_OF_PROCESSORS}")
+endif()
+if (PROCESSOR_COUNT)
+ message("ProteoWizard build will use ${PROCESSOR_COUNT} threads")
+ set(pwiz_build_args ${pwiz_build_args} -j${PROCESSOR_COUNT})
+endif()
+
+if (WIN32 AND NOT CYGWIN)
+ set(pwiz_build "pwiz_tools\\build-apps.bat")
+ if (MSBUILD_PLATFORM STREQUAL "x64")
+ set(pwiz_build_args ${pwiz_build_args} 64)
+ elseif (MSBUILD_PLATFORM STREQUAL "Win32")
+ set(pwiz_build_args ${pwiz_build_args} 32)
+ else (MSBUILD_PLATFORM STREQUAL "Win32")
+ message(FATAL_ERROR "${MSBUILD_PLATFORM}: Windows build architecture unknown.")
+ endif (MSBUILD_PLATFORM STREQUAL "x64")
+ set(pwiz_build_args ${pwiz_build_args} --layout=versioned)
+ set(pwiz_build_args ${pwiz_build_args} --link=static)
+ set(pwiz_build_args ${pwiz_build_args} toolset=msvc-12.0)
+ set(pwiz_build_args ${pwiz_build_args} --i-agree-to-the-vendor-licenses)
+ set(pwiz_build_args ${pwiz_build_args} --without-mz5)
+else()
+ set(pwiz_build ./quickbuild.sh)
+ set(pwiz_build_args ${pwiz_build_args} --without-binary-msdata)
+ set(pwiz_build_args ${pwiz_build_args} --layout=system)
+ set(pwiz_build_args ${pwiz_build_args} runtime-link=shared)
+endif (WIN32 AND NOT CYGWIN)
+
+if (${BUILD_TYPE} MATCHES "Debug")
+ set(pwiz_build_args ${pwiz_build_args} variant=debug)
+endif (${BUILD_TYPE} MATCHES "Debug")
+
+set(pwiz_build_args ${pwiz_build_args} libraries)
+
+execute_process(
+ COMMAND ${pwiz_build} ${pwiz_build_args}
+ RESULT_VARIABLE status
+)
+check_status(status)
diff --git a/ext/cmake_install.cmake b/ext/cmake_install.cmake
new file mode 100644
index 0000000..2ad1b4d
--- /dev/null
+++ b/ext/cmake_install.cmake
@@ -0,0 +1,34 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/ext
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/data/TeamCity/buildAgent/work/779d99b0241b2175/ext")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
diff --git a/ext/create_links.sh b/ext/create_links.sh
new file mode 100755
index 0000000..b0c509a
--- /dev/null
+++ b/ext/create_links.sh
@@ -0,0 +1,44 @@
+#!/bin/bash
+#
+# script for creating symbolic links to the boost libraries (for LINUX)
+#
+
+echo "CREATING GENERICALLY NAMED SYMBOLIC LINKS TO LIBRARIES"
+
+install_path=.
+for arg in $*; do
+ echo "arg:$arg"
+ if [[ $arg = --prefix=* ]]; then
+ echo "parsing $arg"
+ install_path=`echo "$arg" | cut -d"=" -f2`
+ fi
+
+done
+
+echo "path:$install_path"
+
+
+
+cd $install_path/lib
+
+ln -s -f libboost_chrono*-mt.a libboost_chrono.a
+ln -s -f libboost_date_time-*-mt.a libboost_date_time-mt-s.a
+ln -s -f libboost_date_time-*-mt.a libboost_date_time.a
+ln -s -f libboost_iostreams-*-mt.a libboost_iostreams-mt-s.a
+ln -s -f libboost_iostreams-*-mt.a libboost_iostreams.a
+ln -s -f libboost_serialization-*-mt.a libboost_serialization-mt-s.a
+ln -s -f libboost_serialization-*-mt.a libboost_serialization.a
+ln -s -f libboost_thread-*-mt.a libboost_thread-mt-s.a
+ln -s -f libboost_thread-*-mt.a libboost_thread.a
+ln -s -f libgd-*-mt-2_1.a libgd-mt-s-2_1.a
+ln -s -f libgd-*-mt-2_1.a libgd.a
+[ -f libzlib.a ] &&
+ { ln -s -f libzlib.a libz-mt-s-1_2.a; ln -s -f libzlib.a libz.a; } ||
+ { ln -s -f libz-*-mt-1_2.a libz-mt-s-1_2.a; ln -s -f libz-*-mt-1_2.a libz.a; }
+ln -s -f libboost_filesystem-*-mt.a libboost_filesystem-mt-s.a
+ln -s -f libboost_filesystem-*-mt.a libboost_filesystem.a
+ln -s -f libboost_system-*-mt.a libboost_system-mt-s.a
+ln -s -f libboost_system-*-mt.a libboost_system.a
+ln -s -f libfreetype-*-mt-2_4.a libfreetype-mt-s-2_4.a
+ln -s -f libfreetype-*-mt-2_4.a libfreetype.a
+
diff --git a/ext/download-pwiz-tarball.sh b/ext/download-pwiz-tarball.sh
new file mode 100755
index 0000000..a55054a
--- /dev/null
+++ b/ext/download-pwiz-tarball.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# This script downloads the source tarball for the most recent successful build of
+# ProteoWizard including dependencies (build type = bt81)
+
+set -e
+set -o pipefail
+
+build_id=$(wget --no-check-certificate -q -O -\
+ https://teamcity.labkey.org:/app/rest/buildTypes/id:bt81/builds\?status=SUCCESS\&count=1\&guest=1)
+build_id=$(echo $build_id| sed 's/^.*build id=.\([0-9]*\).*/\1/')
+echo "build_id=" $build_id
+version=$(wget --no-check-certificate -q -O -\
+ https://teamcity.labkey.org/repository/download/bt81/$build_id:id/VERSION?guest=1)
+version=$(echo $version|sed 's/\./_/g')
+echo "version = " $version
+wget --no-check-certificate \
+ https://teamcity.labkey.org:/guestAuth/repository/download/bt81/.lastSuccessful/pwiz-src-$version.tar.bz2
diff --git a/ext/download_gflags.cmake b/ext/download_gflags.cmake
new file mode 100644
index 0000000..334682b
--- /dev/null
+++ b/ext/download_gflags.cmake
@@ -0,0 +1,66 @@
+# This is a CMake script for downloading the partial source distribution of
+# Google gflags from its GitHub repository.
+#
+# We have to use 'wget' for downloading because the GitHub site uses
+# HTTPS rather than HTTP. HTTPS is not directly supported by the standard
+# build of CMake.
+#
+# This script expects two variables to be passed on the command line:
+# DOWNLOAD_DIR, the location to store the downloaded tar ball.
+# WORKING_DIR, the location where the expanded source files
+
+# This macro checks download status codes for errors
+macro (check_status download_name status_code error_message)
+ if (${status_code} EQUAL 0)
+ message(STATUS "Downloaded ${download_name}.")
+ else (${status_code} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to download ${download_name} "
+ "\nError message: ${error_message}."
+ "\nDownload of Google gflags failed."
+ )
+ endif (${status_code} EQUAL 0)
+endmacro (check_status)
+
+# 'wget' has to be available
+find_program(wget "wget")
+if (${wget} STREQUAL "wget-NOTFOUND")
+ message(
+ FATAL_ERROR
+ "The program 'wget' was not found.\n"
+ "'wget' is required in order to download Google gflags."
+ )
+endif (${wget} STREQUAL "wget-NOTFOUND")
+# 'tar' has to be available
+find_program(tar "tar")
+if (${tar} STREQUAL "tar-NOTFOUND")
+ message(
+ FATAL_ERROR
+ "The program 'tar' was not found.\n"
+ "'tar' is required in order to download Google gflags."
+ )
+endif (${tar} STREQUAL "tar-NOTFOUND")
+
+set(download_url "https://codeload.github.com/gflags/gflags/tar.gz/v2.1.2")
+set(filename "gflags-2.1.2.tar.gz")
+execute_process(
+ COMMAND ${wget} --no-check-certificate -nv -O ${DOWNLOAD_DIR}/${filename} "${download_url}"
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+check_status("Google gflags distribution" status ${error_message})
+
+# Expand the tar file into the working directory
+# COMMAND ${tar} --strip-components=1 -xf ${DOWNLOAD_DIR}/${filename}
+execute_process(
+ COMMAND ${CMAKE_COMMAND} -E tar xf ${DOWNLOAD_DIR}/${filename}
+ RESULT_VARIABLE status
+ WORKING_DIRECTORY ${WORKING_DIR}
+)
+if (${status} EQUAL 0)
+ message(STATUS "Generated Google gflags source files.")
+else (${status} EQUAL 0)
+ message(FATAL_ERROR "Unable to generate Google gflags source files.")
+endif (${status} EQUAL 0)
diff --git a/ext/download_pbuffers.cmake b/ext/download_pbuffers.cmake
new file mode 100644
index 0000000..6d14ce9
--- /dev/null
+++ b/ext/download_pbuffers.cmake
@@ -0,0 +1,65 @@
+# This is a CMake script for downloading the partial source distribution of
+# Google Protocol Buffers from its GitHub repository.
+#
+# We have to use 'wget' for downloading because the GitHub site uses
+# HTTPS rather than HTTP. HTTPS is not directly supported by the standard
+# build of CMake.
+#
+# This script expects two variables to be passed on the command line:
+# DOWNLOAD_DIR, the location to store the downloaded tar ball.
+# WORKING_DIR, the location where the expanded source files
+
+# This macro checks download status codes for errors
+macro (check_status download_name status_code error_message)
+ if (${status_code} EQUAL 0)
+ message(STATUS "Downloaded ${download_name}.")
+ else (${status_code} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to download ${download_name} "
+ "\nError message: ${error_message}."
+ "\nDownload of Google Protocol Buffers failed."
+ )
+ endif (${status_code} EQUAL 0)
+endmacro (check_status)
+
+# 'wget' has to be available
+find_program(wget "wget")
+if (${wget} STREQUAL "wget-NOTFOUND")
+ message(
+ FATAL_ERROR
+ "The program 'wget' was not found.\n"
+ "'wget' is required in order to download Google Protocol Buffers."
+ )
+endif (${wget} STREQUAL "wget-NOTFOUND")
+# 'tar' has to be available
+find_program(tar "tar")
+if (${tar} STREQUAL "tar-NOTFOUND")
+ message(
+ FATAL_ERROR
+ "The program 'tar' was not found.\n"
+ "'tar' is required in order to download Google Protocol Buffers."
+ )
+endif (${tar} STREQUAL "tar-NOTFOUND")
+
+set(download_url "https://github.com/google/protobuf/releases/download/v2.5.0/protobuf-2.5.0.tar.bz2")
+set(filename "protobuf-2.5.0.tar.bz2")
+execute_process(
+ COMMAND ${wget} --no-check-certificate -nv -O ${DOWNLOAD_DIR}/${filename} "${download_url}"
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+check_status("Google Protocol Buffers distribution" status ${error_message})
+
+# Expand the tar file into the working directory
+execute_process(
+ COMMAND ${CMAKE_COMMAND} -E tar xf ${DOWNLOAD_DIR}/${filename}
+ RESULT_VARIABLE status
+ WORKING_DIRECTORY ${WORKING_DIR}
+)
+if (${status} EQUAL 0)
+ message(STATUS "Generated Google Protocol Buffers source files.")
+else (${status} EQUAL 0)
+ message(FATAL_ERROR "Unable to generate Google Protocol Buffers source files.")
+endif (${status} EQUAL 0)
diff --git a/ext/download_pwiz.cmake b/ext/download_pwiz.cmake
new file mode 100644
index 0000000..907c4ab
--- /dev/null
+++ b/ext/download_pwiz.cmake
@@ -0,0 +1,103 @@
+# This is a CMake script for downloading the partial source distribution of
+# Proteowizard from its Team City repository.
+#
+# We have to use 'wget' for downloading because the Proteowizard site uses
+# HTTPS rather than HTTP. HTTPS is not directly supported by the standard
+# build of CMake.
+#
+# To get the URL for the distribution tarball we have to find the build id,
+# then use the build id to look up the Proteowizard version number.
+# Once we have the version number we can build the URL for downloading the distribution.
+
+# This script expects two variables to be passed on the command line:
+# DOWNLOAD_DIR, the location to store the downloaded tar ball.
+# WORKING_DIR, the location where the expanded source files
+
+# This macro checks download status codes for errors
+macro (check_status download_name status_code error_message)
+ if (${status_code} EQUAL 0)
+ message(STATUS "Downloaded ${download_name}.")
+ else (${status_code} EQUAL 0)
+ message(
+ FATAL_ERROR
+ "Unable to download ${download_name} "
+ "\nError message: ${error_message}."
+ "\nDownload of Proteowizard failed."
+ )
+ endif (${status_code} EQUAL 0)
+endmacro (check_status)
+
+# 'wget' has to be available
+find_program(wget "wget")
+if (${wget} STREQUAL "wget-NOTFOUND")
+ message(
+ FATAL_ERROR
+ "The program 'wget' was not found.\n"
+ "'wget' is required in order to download ProteoWizard."
+ )
+endif (${wget} STREQUAL "wget-NOTFOUND")
+
+# Team City performs several different builds. We want the one
+# for Pwiz source without Skyline but with vendor library suppport.
+set(build_type "bt81")
+
+set(
+ build_info_url
+ https://teamcity.labkey.org:/app/rest/buildTypes/id:${build_type}/builds?status=SUCCESS&count=1&guest=1
+)
+execute_process(
+ COMMAND ${wget} --no-check-certificate -nv -O build.info.txt "${build_info_url}"
+ RESULT_VARIABLE status
+ OUTPUT_VARIABLE build_info
+ ERROR_VARIABLE error_message
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+check_status("build info" status ${error_message})
+file (STRINGS "build.info.txt" build_info)
+
+# Using the build id download the version string
+string(REGEX REPLACE "^.*build id=\"([0-9]+)\".*$" "\\1" build_id "${build_info}")
+set(
+ build_info_url https://teamcity.labkey.org/repository/download/${build_type}/${build_id}:id/VERSION?guest=1
+)
+execute_process(
+ COMMAND ${wget} --no-check-certificate -nv -O version.info.txt "${build_info_url}"
+ RESULT_VARIABLE status
+ OUTPUT_VARIABLE version_info
+ ERROR_VARIABLE error_message
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+check_status("version string" status ${error_message})
+file (STRINGS "version.info.txt" version_info)
+
+# Use the version string to build the URL
+set(
+ base_download_url
+ "https://teamcity.labkey.org:/guestAuth/repository/download/${build_type}/.lastSuccessful/"
+)
+string(REGEX REPLACE "^([0-9]+) ([0-9]+) ([0-9]+).*$" "\\1_\\2_\\3" version_id "${version_info}")
+set(filename pwiz-src-${version_id}.tar.bz2)
+set(
+ download_url
+ "${base_download_url}${filename}"
+)
+# Using the version string download the file
+execute_process(
+ COMMAND ${wget} --no-check-certificate -nv -O ${DOWNLOAD_DIR}/${filename} "${download_url}"
+ RESULT_VARIABLE status
+ ERROR_VARIABLE error_message
+ OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+check_status("Proteowizard distribution" status ${error_message})
+
+# Expand the tar file into the working directory
+execute_process(
+ COMMAND ${CMAKE_COMMAND} -E tar xf ${DOWNLOAD_DIR}/${filename}
+ RESULT_VARIABLE status
+ WORKING_DIRECTORY ${WORKING_DIR}
+)
+if (${status} EQUAL 0)
+ message(STATUS "Generated ProteoWizard source files.")
+else (${status} EQUAL 0)
+ message(FATAL_ERROR "Unable to generate ProteoWizard source files.")
+endif (${status} EQUAL 0)
diff --git a/ext/fdstream.hpp b/ext/fdstream.hpp
new file mode 100644
index 0000000..585e03d
--- /dev/null
+++ b/ext/fdstream.hpp
@@ -0,0 +1,184 @@
+/* The following code declares classes to read from and write to
+ * file descriptore or file handles.
+ *
+ * See
+ * http://www.josuttis.com/cppcode
+ * for details and the latest version.
+ *
+ * - open:
+ * - integrating BUFSIZ on some systems?
+ * - optimized reading of multiple characters
+ * - stream for reading AND writing
+ * - i18n
+ *
+ * (C) Copyright Nicolai M. Josuttis 2001.
+ * Permission to copy, use, modify, sell and distribute this software
+ * is granted provided this copyright notice appears in all copies.
+ * This software is provided "as is" without express or implied
+ * warranty, and with no claim as to its suitability for any purpose.
+ *
+ * Version: Jul 28, 2002
+ * History:
+ * Jul 28, 2002: bugfix memcpy() => memmove()
+ * fdinbuf::underflow(): cast for return statements
+ * Aug 05, 2001: first public version
+ */
+#ifndef BOOST_FDSTREAM_HPP
+#define BOOST_FDSTREAM_HPP
+
+#include <istream>
+#include <ostream>
+#include <streambuf>
+// for EOF:
+#include <cstdio>
+// for memmove():
+#include <cstring>
+
+
+// low-level read and write functions
+#ifdef _MSC_VER
+# include <io.h>
+#else
+# include <unistd.h>
+//extern "C" {
+// int write (int fd, const char* buf, int num);
+// int read (int fd, char* buf, int num);
+//}
+#endif
+
+
+// BEGIN namespace BOOST
+namespace boost {
+
+
+/************************************************************
+ * fdostream
+ * - a stream that writes on a file descriptor
+ ************************************************************/
+
+
+class fdoutbuf : public std::streambuf {
+ protected:
+ int fd; // file descriptor
+ public:
+ // constructor
+ fdoutbuf (int _fd) : fd(_fd) {
+ }
+ protected:
+ // write one character
+ virtual int_type overflow (int_type c) {
+ if (c != EOF) {
+ char z = c;
+ if (write (fd, &z, 1) != 1) {
+ return EOF;
+ }
+ }
+ return c;
+ }
+ // write multiple characters
+ virtual
+ std::streamsize xsputn (const char* s,
+ std::streamsize num) {
+ return write(fd,s,num);
+ }
+};
+
+class fdostream : public std::ostream {
+ protected:
+ fdoutbuf buf;
+ public:
+ fdostream (int fd) : std::ostream(0), buf(fd) {
+ rdbuf(&buf);
+ }
+};
+
+
+/************************************************************
+ * fdistream
+ * - a stream that reads on a file descriptor
+ ************************************************************/
+
+class fdinbuf : public std::streambuf {
+ protected:
+ int fd; // file descriptor
+ protected:
+ /* data buffer:
+ * - at most, pbSize characters in putback area plus
+ * - at most, bufSize characters in ordinary read buffer
+ */
+ static const int pbSize = 4; // size of putback area
+ static const int bufSize = 1024; // size of the data buffer
+ char buffer[bufSize+pbSize]; // data buffer
+
+ public:
+ /* constructor
+ * - initialize file descriptor
+ * - initialize empty data buffer
+ * - no putback area
+ * => force underflow()
+ */
+ fdinbuf (int _fd) : fd(_fd) {
+ setg (buffer+pbSize, // beginning of putback area
+ buffer+pbSize, // read position
+ buffer+pbSize); // end position
+ }
+
+ protected:
+ // insert new characters into the buffer
+ virtual int_type underflow () {
+#ifndef _MSC_VER
+ using std::memmove;
+#endif
+
+ // is read position before end of buffer?
+ if (gptr() < egptr()) {
+ return traits_type::to_int_type(*gptr());
+ }
+
+ /* process size of putback area
+ * - use number of characters read
+ * - but at most size of putback area
+ */
+ int numPutback;
+ numPutback = gptr() - eback();
+ if (numPutback > pbSize) {
+ numPutback = pbSize;
+ }
+
+ /* copy up to pbSize characters previously read into
+ * the putback area
+ */
+ memmove (buffer+(pbSize-numPutback), gptr()-numPutback,
+ numPutback);
+
+ // read at most bufSize new characters
+ int num;
+ num = read (fd, buffer+pbSize, bufSize);
+ if (num <= 0) {
+ // ERROR or EOF
+ return EOF;
+ }
+
+ // reset buffer pointers
+ setg (buffer+(pbSize-numPutback), // beginning of putback area
+ buffer+pbSize, // read position
+ buffer+pbSize+num); // end of buffer
+
+ // return next character
+ return traits_type::to_int_type(*gptr());
+ }
+};
+
+class fdistream : public std::istream {
+ protected:
+ fdinbuf buf;
+ public:
+ fdistream (int fd) : std::istream(0), buf(fd) {
+ rdbuf(&buf);
+ }
+};
+
+
+} // END namespace boost
+
+#endif /*BOOST_FDSTREAM_HPP*/
diff --git a/ext/patch-comet.cmake b/ext/patch-comet.cmake
new file mode 100644
index 0000000..ec63c0c
--- /dev/null
+++ b/ext/patch-comet.cmake
@@ -0,0 +1,73 @@
+# This is a CMake script for patching Comet on Windows for use in the Crux
+# build.
+
+# This script expects two variables to be passed on the command line:
+# SOURCE_DIR, the path to the directory containing the patch source.
+# BINARY_DIR, the path to the directory containing the patch destination.
+
+# This macro checks download status codes for errors
+macro (check_status status_code)
+ if (${status_code} EQUAL 0)
+ message(STATUS "Patched Comet.")
+ else ()
+ message(
+ FATAL_ERROR
+ "Comet patch failed"
+ )
+ endif (${status_code} EQUAL 0)
+endmacro (check_status)
+
+# This macro checks download status codes for errors
+if (WIN32 AND NOT CYGWIN)
+ message(${SOURCE_DIR}/patches/comet/Comet.sln)
+ message(${BINARY_DIR}/build/src/comet/Comet.sln)
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${SOURCE_DIR}/patches/comet/Comet.sln
+ ${BINARY_DIR}/build/src/comet/Comet.sln
+ RESULT_VARIABLE status
+ )
+ message(${SOURCE_DIR}/patches/comet/Comet.vcxproj)
+ message(${BINARY_DIR}/build/src/comet/Comet.vcxproj)
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${SOURCE_DIR}/patches/comet/Comet.vcxproj
+ ${BINARY_DIR}/build/src/comet/Comet.vcxproj
+ RESULT_VARIABLE status
+ )
+ message(${SOURCE_DIR}/patches/comet/CometSearch/CometSearch.vcxproj)
+ message(${BINARY_DIR}/build/src/comet/CometSearch/CometSearch.vcxproj)
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${SOURCE_DIR}/patches/comet/CometSearch/CometSearch.vcxproj
+ ${BINARY_DIR}/build/src/comet/CometSearch/CometSearch.vcxproj
+ RESULT_VARIABLE status
+ )
+ message(${SOURCE_DIR}/patches/comet/MSToolkit/MSToolkitLite.vcxproj)
+ message(${BINARY_DIR}/build/src/comet/MSToolkit/MSToolkitLite.vcxproj)
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${SOURCE_DIR}/patches/comet/MSToolkit/MSToolkitLite.vcxproj
+ ${BINARY_DIR}/build/src/comet/MSToolkit/MSToolkitLite.vcxproj
+ RESULT_VARIABLE status
+ )
+ check_status(status)
+ message(${SOURCE_DIR}/patches/comet/MSToolkit/RAWReader.cpp)
+ message(${BINARY_DIR}/build/src/comet/MSToolkit/src/MSToolkit/RAWReader.cpp)
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${SOURCE_DIR}/patches/comet/MSToolkit/RAWReader.cpp
+ ${BINARY_DIR}/build/src/comet/MSToolkit/src/MSToolkit/RAWReader.cpp
+ RESULT_VARIABLE status
+ )
+ check_status(status)
+ message(${SOURCE_DIR}/patches/comet/CometSearch/CometSearchManager.cpp)
+ message(${BINARY_DIR}/build/src/comet/CometSearch/CometSearchManager.cpp)
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${SOURCE_DIR}/patches/comet/CometSearch/CometSearchManager.cpp
+ ${BINARY_DIR}/build/src/comet/CometSearch/CometSearchManager.cpp
+ RESULT_VARIABLE status
+ )
+ check_status(status)
+endif (WIN32 AND NOT CYGWIN)
diff --git a/ext/patches/XSD/mac_xdr_fix/xdr-stream-extraction.hxx b/ext/patches/XSD/mac_xdr_fix/xdr-stream-extraction.hxx
new file mode 100644
index 0000000..0e4b8f7
--- /dev/null
+++ b/ext/patches/XSD/mac_xdr_fix/xdr-stream-extraction.hxx
@@ -0,0 +1,308 @@
+// file : xsd/cxx/tree/xdr-stream-extraction.hxx
+// author : Boris Kolpackov <boris at codesynthesis.com>
+// copyright : Copyright (c) 2005-2011 Code Synthesis Tools CC
+// license : GNU GPL v2 + exceptions; see accompanying LICENSE file
+
+#ifndef XSD_CXX_TREE_XDR_STREAM_EXTRACTION_HXX
+#define XSD_CXX_TREE_XDR_STREAM_EXTRACTION_HXX
+
+#include <rpc/types.h>
+#include <rpc/xdr.h>
+
+// Of course BSD has to be different and name its functions u_intXX
+// instead of uintXX. Plus it does not have XX == 8.
+//
+#if defined(__APPLE__) || defined(__FreeBSD__) || defined(__NetBSD__)
+# if !defined(XSD_CXX_TREE_ASSUME_SUN_XDR) && !defined(xdr_int8_t)
+# define xdr_int8_t(x, y) xdr_char(x, reinterpret_cast<char*> (y))
+# define xdr_uint8_t(x, y) xdr_u_char(x, reinterpret_cast<unsigned char*> (y))
+# define xdr_uint16_t xdr_u_int16_t
+# define xdr_uint32_t xdr_u_int32_t
+# define xdr_uint64_t xdr_u_int64_t
+# endif
+#endif
+
+#include <string>
+
+#include <xsd/cxx/tree/buffer.hxx>
+#include <xsd/cxx/tree/istream.hxx>
+#include <xsd/cxx/tree/xdr-stream-common.hxx>
+
+namespace xsd
+{
+ namespace cxx
+ {
+ namespace tree
+ {
+ struct xdr_stream_extraction: xdr_stream_operation
+ {
+ virtual const char*
+ what () const throw ()
+ {
+ return "XDR stream extraction operation failed";
+ }
+ };
+
+
+ // as_size
+ //
+#ifdef XSD_CXX_TREE_USE_64_BIT_SIZE
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_size<T>& x)
+ {
+ uint64_t v;
+
+ if (!xdr_uint64_t (&s.impl (), &v) || v > ~(T (0)))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+#else
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_size<T>& x)
+ {
+ uint32_t v;
+
+ if (!xdr_uint32_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+#endif
+
+
+ // 8-bit
+ //
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_int8<T>& x)
+ {
+ int8_t v;
+
+ if (!xdr_int8_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_uint8<T>& x)
+ {
+ uint8_t v;
+
+ if (!xdr_uint8_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+
+ // 16-bit
+ //
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_int16<T>& x)
+ {
+ int16_t v;
+
+ if (!xdr_int16_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_uint16<T>& x)
+ {
+ uint16_t v;
+
+ if (!xdr_uint16_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+
+ // 32-bit
+ //
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_int32<T>& x)
+ {
+ int32_t v;
+
+ if (!xdr_int32_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_uint32<T>& x)
+ {
+ uint32_t v;
+
+ if (!xdr_uint32_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+
+ // 64-bit
+ //
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_int64<T>& x)
+ {
+ int64_t v;
+
+ if (!xdr_int64_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_uint64<T>& x)
+ {
+ uint64_t v;
+
+ if (!xdr_uint64_t (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+
+ // Boolean
+ //
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_bool<T>& x)
+ {
+ bool_t v;
+
+ if (!xdr_bool (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+
+ // Floating-point
+ //
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_float32<T>& x)
+ {
+ float v;
+
+ if (!xdr_float (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+ template <typename T>
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, istream<XDR>::as_float64<T>& x)
+ {
+ double v;
+
+ if (!xdr_double (&s.impl (), &v))
+ throw xdr_stream_extraction ();
+
+ x.x_ = static_cast<T> (v);
+
+ return s;
+ }
+
+ // Extraction of std::basic_string.
+ //
+
+ inline istream<XDR>&
+ operator>> (istream<XDR>& s, std::basic_string<char>& x)
+ {
+ unsigned int n;
+
+ if (!xdr_u_int (&s.impl (), &n))
+ throw xdr_stream_extraction ();
+
+ // Dangerous but fast.
+ //
+ x.clear ();
+
+ if (n != 0)
+ {
+ x.resize (n);
+ char* p (const_cast<char*> (x.c_str ()));
+
+ if (!xdr_opaque (&s.impl (), p, n))
+ throw xdr_stream_extraction ();
+ }
+
+ return s;
+ }
+
+ // Wide strings are not supported by XDR.
+ //
+ // inline istream<XDR>&
+ // operator>> (istream<XDR>& s, std::basic_string<wchar_t>& x)
+ // {
+ // }
+
+
+ // Extraction of a binary buffer.
+ //
+ template <typename C>
+ istream<XDR>&
+ operator>> (istream<XDR>& s, buffer<C>& x)
+ {
+ unsigned int n;
+
+ if (!xdr_u_int (&s.impl (), &n))
+ throw xdr_stream_extraction ();
+
+ x.size (n);
+
+ if (!xdr_opaque (&s.impl (), x.data (), n))
+ throw xdr_stream_extraction ();
+
+ return s;
+ }
+ }
+ }
+}
+
+#endif // XSD_CXX_TREE_XDR_STREAM_EXTRACTION_HXX
diff --git a/ext/patches/XSD/mac_xdr_fix/xdr-stream-insertion.hxx b/ext/patches/XSD/mac_xdr_fix/xdr-stream-insertion.hxx
new file mode 100644
index 0000000..b81deb5
--- /dev/null
+++ b/ext/patches/XSD/mac_xdr_fix/xdr-stream-insertion.hxx
@@ -0,0 +1,277 @@
+// file : xsd/cxx/tree/xdr-stream-insertion.hxx
+// author : Boris Kolpackov <boris at codesynthesis.com>
+// copyright : Copyright (c) 2005-2011 Code Synthesis Tools CC
+// license : GNU GPL v2 + exceptions; see accompanying LICENSE file
+
+#ifndef XSD_CXX_TREE_XDR_STREAM_INSERTION_HXX
+#define XSD_CXX_TREE_XDR_STREAM_INSERTION_HXX
+
+#include <rpc/types.h>
+// In Cygwin these types seem not to have been defined.
+typedef unsigned char u_char;
+typedef unsigned short u_short;
+typedef unsigned int u_int;
+typedef unsigned long u_long;
+#include <rpc/xdr.h>
+
+// Of course BSD has to be different and name its functions u_intXX
+// instead of uintXX. Plus it does not have XX == 8.
+//
+#if defined(__APPLE__) || defined(__FreeBSD__) || defined(__NetBSD__)
+# if !defined(XSD_CXX_TREE_ASSUME_SUN_XDR) && !defined(xdr_int8_t)
+# define xdr_int8_t(x, y) xdr_char(x, reinterpret_cast<char*> (y))
+# define xdr_uint8_t(x, y) xdr_u_char(x, reinterpret_cast<unsigned char*> (y))
+# define xdr_uint16_t xdr_u_int16_t
+# define xdr_uint32_t xdr_u_int32_t
+# define xdr_uint64_t xdr_u_int64_t
+# endif
+#endif
+
+#include <string>
+
+#include <xsd/cxx/tree/buffer.hxx>
+#include <xsd/cxx/tree/ostream.hxx>
+#include <xsd/cxx/tree/xdr-stream-common.hxx>
+
+namespace xsd
+{
+ namespace cxx
+ {
+ namespace tree
+ {
+ struct xdr_stream_insertion: xdr_stream_operation
+ {
+ virtual const char*
+ what () const throw ()
+ {
+ return "XDR stream insertion operation failed";
+ }
+ };
+
+ // as_size
+ //
+#ifdef XSD_CXX_TREE_USE_64_BIT_SIZE
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_size<T> x)
+ {
+ uint64_t v (static_cast<uint64_t> (x.x_));
+
+ if (!xdr_uint64_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+#else
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_size<T> x)
+ {
+ uint32_t v (static_cast<uint32_t> (x.x_));
+
+ if (x.x_ > ~(uint32_t (0)) || !xdr_uint32_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+#endif
+
+
+ // 8-bit
+ //
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_int8<T> x)
+ {
+ int8_t v (static_cast<int8_t> (x.x_));
+
+ if (!xdr_int8_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_uint8<T> x)
+ {
+ uint8_t v (static_cast<uint8_t> (x.x_));
+
+ if (!xdr_uint8_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+
+ // 16-bit
+ //
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_int16<T> x)
+ {
+ int16_t v (static_cast<int16_t> (x.x_));
+
+ if (!xdr_int16_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_uint16<T> x)
+ {
+ uint16_t v (static_cast<uint16_t> (x.x_));
+
+ if (!xdr_uint16_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+
+ // 32-bit
+ //
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_int32<T> x)
+ {
+ int32_t v (static_cast<int32_t> (x.x_));
+
+ if (!xdr_int32_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_uint32<T> x)
+ {
+ uint32_t v (static_cast<uint32_t> (x.x_));
+
+ if (!xdr_uint32_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+
+ // 64-bit
+ //
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_int64<T> x)
+ {
+ int64_t v (static_cast<int64_t> (x.x_));
+
+ if (!xdr_int64_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_uint64<T> x)
+ {
+ uint64_t v (static_cast<uint64_t> (x.x_));
+
+ if (!xdr_uint64_t (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+
+ // Boolean
+ //
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_bool<T> x)
+ {
+ bool_t v (static_cast<bool_t> (x.x_));
+
+ if (!xdr_bool (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+
+ // Floating-point
+ //
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_float32<T> x)
+ {
+ float v (static_cast<float> (x.x_));
+
+ if (!xdr_float (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+ template <typename T>
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, ostream<XDR>::as_float64<T> x)
+ {
+ double v (static_cast<double> (x.x_));
+
+ if (!xdr_double (&s.impl (), &v))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+ // Insertion of std::basic_string.
+ //
+
+ inline ostream<XDR>&
+ operator<< (ostream<XDR>& s, const std::basic_string<char>& x)
+ {
+ // XDR strings are hard-wired with a 32 bit (unsigned int) length.
+ //
+ char* p (const_cast<char*> (x.c_str ()));
+ unsigned int n (static_cast<unsigned int> (x.length ()));
+
+ if (x.length () > ~((unsigned int) 0) ||
+ !xdr_u_int (&s.impl (), &n) ||
+ !xdr_opaque (&s.impl (), p, n))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+
+ // Wide strings are not supported by XDR.
+ //
+ // inline ostream<XDR>&
+ // operator<< (ostream<XDR>& s, const std::basic_string<wchar_t>& x)
+ // {
+ // }
+
+
+ // Insertion of a binary buffer.
+ //
+ template <typename C>
+ ostream<XDR>&
+ operator<< (ostream<XDR>& s, const buffer<C>& x)
+ {
+ // It is not possible to write an array with a 64-bit size.
+ //
+ unsigned int n (static_cast<unsigned int> (x.size ()));
+
+ if (x.size () > ~((unsigned int) 0) ||
+ !xdr_u_int (&s.impl (), &n) ||
+ !xdr_opaque (&s.impl (), const_cast<char*> (x.data ()), n))
+ throw xdr_stream_insertion ();
+
+ return s;
+ }
+ }
+ }
+}
+
+#endif // XSD_CXX_TREE_XDR_STREAM_INSERTION_HXX
diff --git a/ext/patches/boost/asio.hpp b/ext/patches/boost/asio.hpp
new file mode 100644
index 0000000..871fcbe
--- /dev/null
+++ b/ext/patches/boost/asio.hpp
@@ -0,0 +1,121 @@
+//
+// asio.hpp
+// ~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+// See www.boost.org/libs/asio for documentation.
+//
+
+#ifndef BOOST_ASIO_HPP
+#define BOOST_ASIO_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_datagram_socket.hpp>
+#include <boost/asio/basic_deadline_timer.hpp>
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/basic_raw_socket.hpp>
+#include <boost/asio/basic_seq_packet_socket.hpp>
+#include <boost/asio/basic_serial_port.hpp>
+#include <boost/asio/basic_signal_set.hpp>
+#include <boost/asio/basic_socket_acceptor.hpp>
+#include <boost/asio/basic_socket_iostream.hpp>
+#include <boost/asio/basic_socket_streambuf.hpp>
+#include <boost/asio/basic_stream_socket.hpp>
+#include <boost/asio/basic_streambuf.hpp>
+#include <boost/asio/basic_waitable_timer.hpp>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/buffered_read_stream_fwd.hpp>
+#include <boost/asio/buffered_read_stream.hpp>
+#include <boost/asio/buffered_stream_fwd.hpp>
+#include <boost/asio/buffered_stream.hpp>
+#include <boost/asio/buffered_write_stream_fwd.hpp>
+#include <boost/asio/buffered_write_stream.hpp>
+#include <boost/asio/buffers_iterator.hpp>
+#include <boost/asio/completion_condition.hpp>
+#include <boost/asio/connect.hpp>
+#include <boost/asio/coroutine.hpp>
+#include <boost/asio/datagram_socket_service.hpp>
+#include <boost/asio/deadline_timer_service.hpp>
+#include <boost/asio/deadline_timer.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/generic/basic_endpoint.hpp>
+#include <boost/asio/generic/datagram_protocol.hpp>
+#include <boost/asio/generic/raw_protocol.hpp>
+#include <boost/asio/generic/seq_packet_protocol.hpp>
+#include <boost/asio/generic/stream_protocol.hpp>
+#include <boost/asio/handler_alloc_hook.hpp>
+#include <boost/asio/handler_continuation_hook.hpp>
+#include <boost/asio/handler_invoke_hook.hpp>
+#include <boost/asio/handler_type.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ip/address.hpp>
+#include <boost/asio/ip/address_v4.hpp>
+#include <boost/asio/ip/address_v6.hpp>
+#include <boost/asio/ip/basic_endpoint.hpp>
+#include <boost/asio/ip/basic_resolver.hpp>
+#include <boost/asio/ip/basic_resolver_entry.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+#include <boost/asio/ip/host_name.hpp>
+#include <boost/asio/ip/icmp.hpp>
+#include <boost/asio/ip/multicast.hpp>
+#include <boost/asio/ip/resolver_query_base.hpp>
+#include <boost/asio/ip/resolver_service.hpp>
+#include <boost/asio/ip/tcp.hpp>
+#include <boost/asio/ip/udp.hpp>
+#include <boost/asio/ip/unicast.hpp>
+#include <boost/asio/ip/v6_only.hpp>
+#include <boost/asio/is_read_buffered.hpp>
+#include <boost/asio/is_write_buffered.hpp>
+#include <boost/asio/local/basic_endpoint.hpp>
+#include <boost/asio/local/connect_pair.hpp>
+#include <boost/asio/local/datagram_protocol.hpp>
+#include <boost/asio/local/stream_protocol.hpp>
+#include <boost/asio/placeholders.hpp>
+#include <boost/asio/posix/basic_descriptor.hpp>
+#include <boost/asio/posix/basic_stream_descriptor.hpp>
+#include <boost/asio/posix/descriptor_base.hpp>
+#include <boost/asio/posix/stream_descriptor.hpp>
+#include <boost/asio/posix/stream_descriptor_service.hpp>
+#include <boost/asio/raw_socket_service.hpp>
+#include <boost/asio/read.hpp>
+#include <boost/asio/read_at.hpp>
+#include <boost/asio/read_until.hpp>
+#include <boost/asio/seq_packet_socket_service.hpp>
+#include <boost/asio/serial_port.hpp>
+#include <boost/asio/serial_port_base.hpp>
+#include <boost/asio/serial_port_service.hpp>
+#include <boost/asio/signal_set.hpp>
+#include <boost/asio/signal_set_service.hpp>
+#include <boost/asio/socket_acceptor_service.hpp>
+#include <boost/asio/socket_base.hpp>
+#include <boost/asio/strand.hpp>
+#include <boost/asio/stream_socket_service.hpp>
+#include <boost/asio/streambuf.hpp>
+#include <boost/asio/time_traits.hpp>
+#include <boost/asio/version.hpp>
+#include <boost/asio/wait_traits.hpp>
+#include <boost/asio/waitable_timer_service.hpp>
+#include <boost/asio/windows/basic_handle.hpp>
+#include <boost/asio/windows/basic_object_handle.hpp>
+#include <boost/asio/windows/basic_random_access_handle.hpp>
+#include <boost/asio/windows/basic_stream_handle.hpp>
+#include <boost/asio/windows/object_handle.hpp>
+#include <boost/asio/windows/object_handle_service.hpp>
+#include <boost/asio/windows/overlapped_ptr.hpp>
+#include <boost/asio/windows/random_access_handle.hpp>
+#include <boost/asio/windows/random_access_handle_service.hpp>
+#include <boost/asio/windows/stream_handle.hpp>
+#include <boost/asio/windows/stream_handle_service.hpp>
+#include <boost/asio/write.hpp>
+#include <boost/asio/write_at.hpp>
+
+#endif // BOOST_ASIO_HPP
diff --git a/ext/patches/boost/asio/async_result.hpp b/ext/patches/boost/asio/async_result.hpp
new file mode 100644
index 0000000..4f09b9a
--- /dev/null
+++ b/ext/patches/boost/asio/async_result.hpp
@@ -0,0 +1,96 @@
+//
+// async_result.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_ASYNC_RESULT_HPP
+#define BOOST_ASIO_ASYNC_RESULT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/handler_type.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// An interface for customising the behaviour of an initiating function.
+/**
+ * This template may be specialised for user-defined handler types.
+ */
+template <typename Handler>
+class async_result
+{
+public:
+ /// The return type of the initiating function.
+ typedef void type;
+
+ /// Construct an async result from a given handler.
+ /**
+ * When using a specalised async_result, the constructor has an opportunity
+ * to initialise some state associated with the handler, which is then
+ * returned from the initiating function.
+ */
+ explicit async_result(Handler&)
+ {
+ }
+
+ /// Obtain the value to be returned from the initiating function.
+ type get()
+ {
+ }
+};
+
+namespace detail {
+
+// Helper template to deduce the true type of a handler, capture a local copy
+// of the handler, and then create an async_result for the handler.
+template <typename Handler, typename Signature>
+struct async_result_init
+{
+ explicit async_result_init(BOOST_ASIO_MOVE_ARG(Handler) orig_handler)
+ : handler(BOOST_ASIO_MOVE_CAST(Handler)(orig_handler)),
+ result(handler)
+ {
+ }
+
+ typename handler_type<Handler, Signature>::type handler;
+ async_result<typename handler_type<Handler, Signature>::type> result;
+};
+
+template <typename Handler, typename Signature>
+struct async_result_type_helper
+{
+ typedef typename async_result<
+ typename handler_type<Handler, Signature>::type
+ >::type type;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(GENERATING_DOCUMENTATION)
+# define BOOST_ASIO_INITFN_RESULT_TYPE(h, sig) \
+ void_or_deduced
+#elif defined(_MSC_VER) && (_MSC_VER < 1500)
+# define BOOST_ASIO_INITFN_RESULT_TYPE(h, sig) \
+ typename ::boost::asio::detail::async_result_type_helper<h, sig>::type
+#else
+# define BOOST_ASIO_INITFN_RESULT_TYPE(h, sig) \
+ typename ::boost::asio::async_result< \
+ typename ::boost::asio::handler_type<h, sig>::type>::type
+#endif
+
+#endif // BOOST_ASIO_ASYNC_RESULT_HPP
diff --git a/ext/patches/boost/asio/basic_datagram_socket.hpp b/ext/patches/boost/asio/basic_datagram_socket.hpp
new file mode 100644
index 0000000..196b45e
--- /dev/null
+++ b/ext/patches/boost/asio/basic_datagram_socket.hpp
@@ -0,0 +1,951 @@
+//
+// basic_datagram_socket.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_DATAGRAM_SOCKET_HPP
+#define BOOST_ASIO_BASIC_DATAGRAM_SOCKET_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/datagram_socket_service.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides datagram-oriented socket functionality.
+/**
+ * The basic_datagram_socket class template provides asynchronous and blocking
+ * datagram-oriented socket functionality.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename Protocol,
+ typename DatagramSocketService = datagram_socket_service<Protocol> >
+class basic_datagram_socket
+ : public basic_socket<Protocol, DatagramSocketService>
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// socket.
+ typedef typename DatagramSocketService::native_handle_type native_type;
+
+ /// The native representation of a socket.
+ typedef typename DatagramSocketService::native_handle_type native_handle_type;
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ /// Construct a basic_datagram_socket without opening it.
+ /**
+ * This constructor creates a datagram socket without opening it. The open()
+ * function must be called before data can be sent or received on the socket.
+ *
+ * @param io_service The io_service object that the datagram socket will use
+ * to dispatch handlers for any asynchronous operations performed on the
+ * socket.
+ */
+ explicit basic_datagram_socket(boost::asio::io_service& io_service)
+ : basic_socket<Protocol, DatagramSocketService>(io_service)
+ {
+ }
+
+ /// Construct and open a basic_datagram_socket.
+ /**
+ * This constructor creates and opens a datagram socket.
+ *
+ * @param io_service The io_service object that the datagram socket will use
+ * to dispatch handlers for any asynchronous operations performed on the
+ * socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_datagram_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol)
+ : basic_socket<Protocol, DatagramSocketService>(io_service, protocol)
+ {
+ }
+
+ /// Construct a basic_datagram_socket, opening it and binding it to the given
+ /// local endpoint.
+ /**
+ * This constructor creates a datagram socket and automatically opens it bound
+ * to the specified endpoint on the local machine. The protocol used is the
+ * protocol associated with the given endpoint.
+ *
+ * @param io_service The io_service object that the datagram socket will use
+ * to dispatch handlers for any asynchronous operations performed on the
+ * socket.
+ *
+ * @param endpoint An endpoint on the local machine to which the datagram
+ * socket will be bound.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_datagram_socket(boost::asio::io_service& io_service,
+ const endpoint_type& endpoint)
+ : basic_socket<Protocol, DatagramSocketService>(io_service, endpoint)
+ {
+ }
+
+ /// Construct a basic_datagram_socket on an existing native socket.
+ /**
+ * This constructor creates a datagram socket object to hold an existing
+ * native socket.
+ *
+ * @param io_service The io_service object that the datagram socket will use
+ * to dispatch handlers for any asynchronous operations performed on the
+ * socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @param native_socket The new underlying socket implementation.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_datagram_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol, const native_handle_type& native_socket)
+ : basic_socket<Protocol, DatagramSocketService>(
+ io_service, protocol, native_socket)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_datagram_socket from another.
+ /**
+ * This constructor moves a datagram socket from one object to another.
+ *
+ * @param other The other basic_datagram_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_datagram_socket(io_service&) constructor.
+ */
+ basic_datagram_socket(basic_datagram_socket&& other)
+ : basic_socket<Protocol, DatagramSocketService>(
+ BOOST_ASIO_MOVE_CAST(basic_datagram_socket)(other))
+ {
+ }
+
+ /// Move-assign a basic_datagram_socket from another.
+ /**
+ * This assignment operator moves a datagram socket from one object to
+ * another.
+ *
+ * @param other The other basic_datagram_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_datagram_socket(io_service&) constructor.
+ */
+ basic_datagram_socket& operator=(basic_datagram_socket&& other)
+ {
+ basic_socket<Protocol, DatagramSocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_datagram_socket)(other));
+ return *this;
+ }
+
+ /// Move-construct a basic_datagram_socket from a socket of another protocol
+ /// type.
+ /**
+ * This constructor moves a datagram socket from one object to another.
+ *
+ * @param other The other basic_datagram_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_datagram_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename DatagramSocketService1>
+ basic_datagram_socket(
+ basic_datagram_socket<Protocol1, DatagramSocketService1>&& other,
+ typename enable_if<is_convertible<Protocol1, Protocol>::value>::type* = 0)
+ : basic_socket<Protocol, DatagramSocketService>(
+ BOOST_ASIO_MOVE_CAST2(basic_datagram_socket<
+ Protocol1, DatagramSocketService1>)(other))
+ {
+ }
+
+ /// Move-assign a basic_datagram_socket from a socket of another protocol
+ /// type.
+ /**
+ * This assignment operator moves a datagram socket from one object to
+ * another.
+ *
+ * @param other The other basic_datagram_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_datagram_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename DatagramSocketService1>
+ typename enable_if<is_convertible<Protocol1, Protocol>::value,
+ basic_datagram_socket>::type& operator=(
+ basic_datagram_socket<Protocol1, DatagramSocketService1>&& other)
+ {
+ basic_socket<Protocol, DatagramSocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST2(basic_datagram_socket<
+ Protocol1, DatagramSocketService1>)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Send some data on a connected socket.
+ /**
+ * This function is used to send data on the datagram socket. The function
+ * call will block until the data has been sent successfully or an error
+ * occurs.
+ *
+ * @param buffers One ore more data buffers to be sent on the socket.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The send operation can only be used with a connected socket. Use
+ * the send_to function to send data on an unconnected datagram socket.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code socket.send(boost::asio::buffer(data, size)); @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send(
+ this->get_implementation(), buffers, 0, ec);
+ boost::asio::detail::throw_error(ec, "send");
+ return s;
+ }
+
+ /// Send some data on a connected socket.
+ /**
+ * This function is used to send data on the datagram socket. The function
+ * call will block until the data has been sent successfully or an error
+ * occurs.
+ *
+ * @param buffers One ore more data buffers to be sent on the socket.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The send operation can only be used with a connected socket. Use
+ * the send_to function to send data on an unconnected datagram socket.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send(
+ this->get_implementation(), buffers, flags, ec);
+ boost::asio::detail::throw_error(ec, "send");
+ return s;
+ }
+
+ /// Send some data on a connected socket.
+ /**
+ * This function is used to send data on the datagram socket. The function
+ * call will block until the data has been sent successfully or an error
+ * occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @note The send operation can only be used with a connected socket. Use
+ * the send_to function to send data on an unconnected datagram socket.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return this->get_service().send(
+ this->get_implementation(), buffers, flags, ec);
+ }
+
+ /// Start an asynchronous send on a connected socket.
+ /**
+ * This function is used to asynchronously send data on the datagram socket.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent on the socket. Although
+ * the buffers object may be copied as necessary, ownership of the underlying
+ * memory blocks is retained by the caller, which must guarantee that they
+ * remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The async_send operation can only be used with a connected socket.
+ * Use the async_send_to function to send data on an unconnected datagram
+ * socket.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.async_send(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send(this->get_implementation(),
+ buffers, 0, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Start an asynchronous send on a connected socket.
+ /**
+ * This function is used to asynchronously send data on the datagram socket.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent on the socket. Although
+ * the buffers object may be copied as necessary, ownership of the underlying
+ * memory blocks is retained by the caller, which must guarantee that they
+ * remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The async_send operation can only be used with a connected socket.
+ * Use the async_send_to function to send data on an unconnected datagram
+ * socket.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send(this->get_implementation(),
+ buffers, flags, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Send a datagram to the specified endpoint.
+ /**
+ * This function is used to send a datagram to the specified remote endpoint.
+ * The function call will block until the data has been sent successfully or
+ * an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * boost::asio::ip::udp::endpoint destination(
+ * boost::asio::ip::address::from_string("1.2.3.4"), 12345);
+ * socket.send_to(boost::asio::buffer(data, size), destination);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send_to(
+ this->get_implementation(), buffers, destination, 0, ec);
+ boost::asio::detail::throw_error(ec, "send_to");
+ return s;
+ }
+
+ /// Send a datagram to the specified endpoint.
+ /**
+ * This function is used to send a datagram to the specified remote endpoint.
+ * The function call will block until the data has been sent successfully or
+ * an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send_to(
+ this->get_implementation(), buffers, destination, flags, ec);
+ boost::asio::detail::throw_error(ec, "send_to");
+ return s;
+ }
+
+ /// Send a datagram to the specified endpoint.
+ /**
+ * This function is used to send a datagram to the specified remote endpoint.
+ * The function call will block until the data has been sent successfully or
+ * an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes sent.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().send_to(this->get_implementation(),
+ buffers, destination, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ /**
+ * This function is used to asynchronously send a datagram to the specified
+ * remote endpoint. The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ * Copies will be made of the endpoint as required.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * boost::asio::ip::udp::endpoint destination(
+ * boost::asio::ip::address::from_string("1.2.3.4"), 12345);
+ * socket.async_send_to(
+ * boost::asio::buffer(data, size), destination, handler);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send_to(
+ this->get_implementation(), buffers, destination, 0,
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Start an asynchronous send.
+ /**
+ * This function is used to asynchronously send a datagram to the specified
+ * remote endpoint. The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ * Copies will be made of the endpoint as required.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send_to(
+ this->get_implementation(), buffers, destination, flags,
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Receive some data on a connected socket.
+ /**
+ * This function is used to receive data on the datagram socket. The function
+ * call will block until data has been received successfully or an error
+ * occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The receive operation can only be used with a connected socket. Use
+ * the receive_from function to receive data on an unconnected datagram
+ * socket.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code socket.receive(boost::asio::buffer(data, size)); @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, 0, ec);
+ boost::asio::detail::throw_error(ec, "receive");
+ return s;
+ }
+
+ /// Receive some data on a connected socket.
+ /**
+ * This function is used to receive data on the datagram socket. The function
+ * call will block until data has been received successfully or an error
+ * occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The receive operation can only be used with a connected socket. Use
+ * the receive_from function to receive data on an unconnected datagram
+ * socket.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, flags, ec);
+ boost::asio::detail::throw_error(ec, "receive");
+ return s;
+ }
+
+ /// Receive some data on a connected socket.
+ /**
+ * This function is used to receive data on the datagram socket. The function
+ * call will block until data has been received successfully or an error
+ * occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes received.
+ *
+ * @note The receive operation can only be used with a connected socket. Use
+ * the receive_from function to receive data on an unconnected datagram
+ * socket.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return this->get_service().receive(
+ this->get_implementation(), buffers, flags, ec);
+ }
+
+ /// Start an asynchronous receive on a connected socket.
+ /**
+ * This function is used to asynchronously receive data from the datagram
+ * socket. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The async_receive operation can only be used with a connected socket.
+ * Use the async_receive_from function to receive data on an unconnected
+ * datagram socket.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.async_receive(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(this->get_implementation(),
+ buffers, 0, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Start an asynchronous receive on a connected socket.
+ /**
+ * This function is used to asynchronously receive data from the datagram
+ * socket. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The async_receive operation can only be used with a connected socket.
+ * Use the async_receive_from function to receive data on an unconnected
+ * datagram socket.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(this->get_implementation(),
+ buffers, flags, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Receive a datagram with the endpoint of the sender.
+ /**
+ * This function is used to receive a datagram. The function call will block
+ * until data has been received successfully or an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the datagram.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * boost::asio::ip::udp::endpoint sender_endpoint;
+ * socket.receive_from(
+ * boost::asio::buffer(data, size), sender_endpoint);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive_from(
+ this->get_implementation(), buffers, sender_endpoint, 0, ec);
+ boost::asio::detail::throw_error(ec, "receive_from");
+ return s;
+ }
+
+ /// Receive a datagram with the endpoint of the sender.
+ /**
+ * This function is used to receive a datagram. The function call will block
+ * until data has been received successfully or an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the datagram.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint, socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive_from(
+ this->get_implementation(), buffers, sender_endpoint, flags, ec);
+ boost::asio::detail::throw_error(ec, "receive_from");
+ return s;
+ }
+
+ /// Receive a datagram with the endpoint of the sender.
+ /**
+ * This function is used to receive a datagram. The function call will block
+ * until data has been received successfully or an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the datagram.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes received.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint, socket_base::message_flags flags,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().receive_from(this->get_implementation(),
+ buffers, sender_endpoint, flags, ec);
+ }
+
+ /// Start an asynchronous receive.
+ /**
+ * This function is used to asynchronously receive a datagram. The function
+ * call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the datagram. Ownership of the sender_endpoint object
+ * is retained by the caller, which must guarantee that it is valid until the
+ * handler is called.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code socket.async_receive_from(
+ * boost::asio::buffer(data, size), sender_endpoint, handler); @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive_from(
+ this->get_implementation(), buffers, sender_endpoint, 0,
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Start an asynchronous receive.
+ /**
+ * This function is used to asynchronously receive a datagram. The function
+ * call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the datagram. Ownership of the sender_endpoint object
+ * is retained by the caller, which must guarantee that it is valid until the
+ * handler is called.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint, socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive_from(
+ this->get_implementation(), buffers, sender_endpoint, flags,
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_DATAGRAM_SOCKET_HPP
diff --git a/ext/patches/boost/asio/basic_deadline_timer.hpp b/ext/patches/boost/asio/basic_deadline_timer.hpp
new file mode 100644
index 0000000..ed61719
--- /dev/null
+++ b/ext/patches/boost/asio/basic_deadline_timer.hpp
@@ -0,0 +1,520 @@
+//
+// basic_deadline_timer.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_DEADLINE_TIMER_HPP
+#define BOOST_ASIO_BASIC_DEADLINE_TIMER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/deadline_timer_service.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides waitable timer functionality.
+/**
+ * The basic_deadline_timer class template provides the ability to perform a
+ * blocking or asynchronous wait for a timer to expire.
+ *
+ * A deadline timer is always in one of two states: "expired" or "not expired".
+ * If the wait() or async_wait() function is called on an expired timer, the
+ * wait operation will complete immediately.
+ *
+ * Most applications will use the boost::asio::deadline_timer typedef.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Examples
+ * Performing a blocking wait:
+ * @code
+ * // Construct a timer without setting an expiry time.
+ * boost::asio::deadline_timer timer(io_service);
+ *
+ * // Set an expiry time relative to now.
+ * timer.expires_from_now(boost::posix_time::seconds(5));
+ *
+ * // Wait for the timer to expire.
+ * timer.wait();
+ * @endcode
+ *
+ * @par
+ * Performing an asynchronous wait:
+ * @code
+ * void handler(const boost::system::error_code& error)
+ * {
+ * if (!error)
+ * {
+ * // Timer expired.
+ * }
+ * }
+ *
+ * ...
+ *
+ * // Construct a timer with an absolute expiry time.
+ * boost::asio::deadline_timer timer(io_service,
+ * boost::posix_time::time_from_string("2005-12-07 23:59:59.000"));
+ *
+ * // Start an asynchronous wait.
+ * timer.async_wait(handler);
+ * @endcode
+ *
+ * @par Changing an active deadline_timer's expiry time
+ *
+ * Changing the expiry time of a timer while there are pending asynchronous
+ * waits causes those wait operations to be cancelled. To ensure that the action
+ * associated with the timer is performed only once, use something like this:
+ * used:
+ *
+ * @code
+ * void on_some_event()
+ * {
+ * if (my_timer.expires_from_now(seconds(5)) > 0)
+ * {
+ * // We managed to cancel the timer. Start new asynchronous wait.
+ * my_timer.async_wait(on_timeout);
+ * }
+ * else
+ * {
+ * // Too late, timer has already expired!
+ * }
+ * }
+ *
+ * void on_timeout(const boost::system::error_code& e)
+ * {
+ * if (e != boost::asio::error::operation_aborted)
+ * {
+ * // Timer was not cancelled, take necessary action.
+ * }
+ * }
+ * @endcode
+ *
+ * @li The boost::asio::basic_deadline_timer::expires_from_now() function
+ * cancels any pending asynchronous waits, and returns the number of
+ * asynchronous waits that were cancelled. If it returns 0 then you were too
+ * late and the wait handler has already been executed, or will soon be
+ * executed. If it returns 1 then the wait handler was successfully cancelled.
+ *
+ * @li If a wait handler is cancelled, the boost::system::error_code passed to
+ * it contains the value boost::asio::error::operation_aborted.
+ */
+template <typename Time,
+ typename TimeTraits = boost::asio::time_traits<Time>,
+ typename TimerService = deadline_timer_service<Time, TimeTraits> >
+class basic_deadline_timer
+ : public basic_io_object<TimerService>
+{
+public:
+ /// The time traits type.
+ typedef TimeTraits traits_type;
+
+ /// The time type.
+ typedef typename traits_type::time_type time_type;
+
+ /// The duration type.
+ typedef typename traits_type::duration_type duration_type;
+
+ /// Constructor.
+ /**
+ * This constructor creates a timer without setting an expiry time. The
+ * expires_at() or expires_from_now() functions must be called to set an
+ * expiry time before the timer can be waited on.
+ *
+ * @param io_service The io_service object that the timer will use to dispatch
+ * handlers for any asynchronous operations performed on the timer.
+ */
+ explicit basic_deadline_timer(boost::asio::io_service& io_service)
+ : basic_io_object<TimerService>(io_service)
+ {
+ }
+
+ /// Constructor to set a particular expiry time as an absolute time.
+ /**
+ * This constructor creates a timer and sets the expiry time.
+ *
+ * @param io_service The io_service object that the timer will use to dispatch
+ * handlers for any asynchronous operations performed on the timer.
+ *
+ * @param expiry_time The expiry time to be used for the timer, expressed
+ * as an absolute time.
+ */
+ basic_deadline_timer(boost::asio::io_service& io_service,
+ const time_type& expiry_time)
+ : basic_io_object<TimerService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->service.expires_at(this->implementation, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_at");
+ }
+
+ /// Constructor to set a particular expiry time relative to now.
+ /**
+ * This constructor creates a timer and sets the expiry time.
+ *
+ * @param io_service The io_service object that the timer will use to dispatch
+ * handlers for any asynchronous operations performed on the timer.
+ *
+ * @param expiry_time The expiry time to be used for the timer, relative to
+ * now.
+ */
+ basic_deadline_timer(boost::asio::io_service& io_service,
+ const duration_type& expiry_time)
+ : basic_io_object<TimerService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->service.expires_from_now(this->implementation, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_from_now");
+ }
+
+ /// Cancel any asynchronous operations that are waiting on the timer.
+ /**
+ * This function forces the completion of any pending asynchronous wait
+ * operations against the timer. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * Cancelling the timer does not change the expiry time.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If the timer has already expired when cancel() is called, then the
+ * handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t cancel()
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->service.cancel(this->implementation, ec);
+ boost::asio::detail::throw_error(ec, "cancel");
+ return s;
+ }
+
+ /// Cancel any asynchronous operations that are waiting on the timer.
+ /**
+ * This function forces the completion of any pending asynchronous wait
+ * operations against the timer. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * Cancelling the timer does not change the expiry time.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @note If the timer has already expired when cancel() is called, then the
+ * handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t cancel(boost::system::error_code& ec)
+ {
+ return this->service.cancel(this->implementation, ec);
+ }
+
+ /// Cancels one asynchronous operation that is waiting on the timer.
+ /**
+ * This function forces the completion of one pending asynchronous wait
+ * operation against the timer. Handlers are cancelled in FIFO order. The
+ * handler for the cancelled operation will be invoked with the
+ * boost::asio::error::operation_aborted error code.
+ *
+ * Cancelling the timer does not change the expiry time.
+ *
+ * @return The number of asynchronous operations that were cancelled. That is,
+ * either 0 or 1.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If the timer has already expired when cancel_one() is called, then
+ * the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t cancel_one()
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->service.cancel_one(this->implementation, ec);
+ boost::asio::detail::throw_error(ec, "cancel_one");
+ return s;
+ }
+
+ /// Cancels one asynchronous operation that is waiting on the timer.
+ /**
+ * This function forces the completion of one pending asynchronous wait
+ * operation against the timer. Handlers are cancelled in FIFO order. The
+ * handler for the cancelled operation will be invoked with the
+ * boost::asio::error::operation_aborted error code.
+ *
+ * Cancelling the timer does not change the expiry time.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of asynchronous operations that were cancelled. That is,
+ * either 0 or 1.
+ *
+ * @note If the timer has already expired when cancel_one() is called, then
+ * the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t cancel_one(boost::system::error_code& ec)
+ {
+ return this->service.cancel_one(this->implementation, ec);
+ }
+
+ /// Get the timer's expiry time as an absolute time.
+ /**
+ * This function may be used to obtain the timer's current expiry time.
+ * Whether the timer has expired or not does not affect this value.
+ */
+ time_type expires_at() const
+ {
+ return this->service.expires_at(this->implementation);
+ }
+
+ /// Set the timer's expiry time as an absolute time.
+ /**
+ * This function sets the expiry time. Any pending asynchronous wait
+ * operations will be cancelled. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If the timer has already expired when expires_at() is called, then
+ * the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t expires_at(const time_type& expiry_time)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->service.expires_at(
+ this->implementation, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_at");
+ return s;
+ }
+
+ /// Set the timer's expiry time as an absolute time.
+ /**
+ * This function sets the expiry time. Any pending asynchronous wait
+ * operations will be cancelled. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @note If the timer has already expired when expires_at() is called, then
+ * the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t expires_at(const time_type& expiry_time,
+ boost::system::error_code& ec)
+ {
+ return this->service.expires_at(this->implementation, expiry_time, ec);
+ }
+
+ /// Get the timer's expiry time relative to now.
+ /**
+ * This function may be used to obtain the timer's current expiry time.
+ * Whether the timer has expired or not does not affect this value.
+ */
+ duration_type expires_from_now() const
+ {
+ return this->service.expires_from_now(this->implementation);
+ }
+
+ /// Set the timer's expiry time relative to now.
+ /**
+ * This function sets the expiry time. Any pending asynchronous wait
+ * operations will be cancelled. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If the timer has already expired when expires_from_now() is called,
+ * then the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t expires_from_now(const duration_type& expiry_time)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->service.expires_from_now(
+ this->implementation, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_from_now");
+ return s;
+ }
+
+ /// Set the timer's expiry time relative to now.
+ /**
+ * This function sets the expiry time. Any pending asynchronous wait
+ * operations will be cancelled. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @note If the timer has already expired when expires_from_now() is called,
+ * then the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t expires_from_now(const duration_type& expiry_time,
+ boost::system::error_code& ec)
+ {
+ return this->service.expires_from_now(
+ this->implementation, expiry_time, ec);
+ }
+
+ /// Perform a blocking wait on the timer.
+ /**
+ * This function is used to wait for the timer to expire. This function
+ * blocks and does not return until the timer has expired.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void wait()
+ {
+ boost::system::error_code ec;
+ this->service.wait(this->implementation, ec);
+ boost::asio::detail::throw_error(ec, "wait");
+ }
+
+ /// Perform a blocking wait on the timer.
+ /**
+ * This function is used to wait for the timer to expire. This function
+ * blocks and does not return until the timer has expired.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ void wait(boost::system::error_code& ec)
+ {
+ this->service.wait(this->implementation, ec);
+ }
+
+ /// Start an asynchronous wait on the timer.
+ /**
+ * This function may be used to initiate an asynchronous wait against the
+ * timer. It always returns immediately.
+ *
+ * For each call to async_wait(), the supplied handler will be called exactly
+ * once. The handler will be called when:
+ *
+ * @li The timer has expired.
+ *
+ * @li The timer was cancelled, in which case the handler is passed the error
+ * code boost::asio::error::operation_aborted.
+ *
+ * @param handler The handler to be called when the timer expires. Copies
+ * will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename WaitHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WaitHandler,
+ void (boost::system::error_code))
+ async_wait(BOOST_ASIO_MOVE_ARG(WaitHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WaitHandler.
+ BOOST_ASIO_WAIT_HANDLER_CHECK(WaitHandler, handler) type_check;
+
+ return this->service.async_wait(this->implementation,
+ BOOST_ASIO_MOVE_CAST(WaitHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_BASIC_DEADLINE_TIMER_HPP
diff --git a/ext/patches/boost/asio/basic_io_object.hpp b/ext/patches/boost/asio/basic_io_object.hpp
new file mode 100644
index 0000000..0ac4426
--- /dev/null
+++ b/ext/patches/boost/asio/basic_io_object.hpp
@@ -0,0 +1,242 @@
+//
+// basic_io_object.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_IO_OBJECT_HPP
+#define BOOST_ASIO_BASIC_IO_OBJECT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+namespace detail
+{
+ // Type trait used to determine whether a service supports move.
+ template <typename IoObjectService>
+ class service_has_move
+ {
+ private:
+ typedef IoObjectService service_type;
+ typedef typename service_type::implementation_type implementation_type;
+
+ template <typename T, typename U>
+ static auto eval(T* t, U* u) -> decltype(t->move_construct(*u, *u), char());
+ static char (&eval(...))[2];
+
+ public:
+ static const bool value =
+ sizeof(service_has_move::eval(
+ static_cast<service_type*>(0),
+ static_cast<implementation_type*>(0))) == 1;
+ };
+}
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+/// Base class for all I/O objects.
+/**
+ * @note All I/O objects are non-copyable. However, when using C++0x, certain
+ * I/O objects do support move construction and move assignment.
+ */
+#if !defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+template <typename IoObjectService>
+#else
+template <typename IoObjectService,
+ bool Movable = detail::service_has_move<IoObjectService>::value>
+#endif
+class basic_io_object
+{
+public:
+ /// The type of the service that will be used to provide I/O operations.
+ typedef IoObjectService service_type;
+
+ /// The underlying implementation type of I/O object.
+ typedef typename service_type::implementation_type implementation_type;
+
+ /// Get the io_service associated with the object.
+ /**
+ * This function may be used to obtain the io_service object that the I/O
+ * object uses to dispatch handlers for asynchronous operations.
+ *
+ * @return A reference to the io_service object that the I/O object will use
+ * to dispatch handlers. Ownership is not transferred to the caller.
+ */
+ boost::asio::io_service& get_io_service()
+ {
+ return service.get_io_service();
+ }
+
+protected:
+ /// Construct a basic_io_object.
+ /**
+ * Performs:
+ * @code get_service().construct(get_implementation()); @endcode
+ */
+ explicit basic_io_object(boost::asio::io_service& io_service)
+ : service(boost::asio::use_service<IoObjectService>(io_service))
+ {
+ service.construct(implementation);
+ }
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_io_object.
+ /**
+ * Performs:
+ * @code get_service().move_construct(
+ * get_implementation(), other.get_implementation()); @endcode
+ *
+ * @note Available only for services that support movability,
+ */
+ basic_io_object(basic_io_object&& other);
+
+ /// Move-assign a basic_io_object.
+ /**
+ * Performs:
+ * @code get_service().move_assign(get_implementation(),
+ * other.get_service(), other.get_implementation()); @endcode
+ *
+ * @note Available only for services that support movability,
+ */
+ basic_io_object& operator=(basic_io_object&& other);
+#endif // defined(GENERATING_DOCUMENTATION)
+
+ /// Protected destructor to prevent deletion through this type.
+ /**
+ * Performs:
+ * @code get_service().destroy(get_implementation()); @endcode
+ */
+ ~basic_io_object()
+ {
+ service.destroy(implementation);
+ }
+
+ /// Get the service associated with the I/O object.
+ service_type& get_service()
+ {
+ return service;
+ }
+
+ /// Get the service associated with the I/O object.
+ const service_type& get_service() const
+ {
+ return service;
+ }
+
+ /// (Deprecated: Use get_service().) The service associated with the I/O
+ /// object.
+ /**
+ * @note Available only for services that do not support movability.
+ */
+ service_type& service;
+
+ /// Get the underlying implementation of the I/O object.
+ implementation_type& get_implementation()
+ {
+ return implementation;
+ }
+
+ /// Get the underlying implementation of the I/O object.
+ const implementation_type& get_implementation() const
+ {
+ return implementation;
+ }
+
+ /// (Deprecated: Use get_implementation().) The underlying implementation of
+ /// the I/O object.
+ implementation_type implementation;
+
+private:
+ basic_io_object(const basic_io_object&);
+ basic_io_object& operator=(const basic_io_object&);
+};
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+// Specialisation for movable objects.
+template <typename IoObjectService>
+class basic_io_object<IoObjectService, true>
+{
+public:
+ typedef IoObjectService service_type;
+ typedef typename service_type::implementation_type implementation_type;
+
+ boost::asio::io_service& get_io_service()
+ {
+ return service_->get_io_service();
+ }
+
+protected:
+ explicit basic_io_object(boost::asio::io_service& io_service)
+ : service_(&boost::asio::use_service<IoObjectService>(io_service))
+ {
+ service_->construct(implementation);
+ }
+
+ basic_io_object(basic_io_object&& other)
+ : service_(&other.get_service())
+ {
+ service_->move_construct(implementation, other.implementation);
+ }
+
+ ~basic_io_object()
+ {
+ service_->destroy(implementation);
+ }
+
+ basic_io_object& operator=(basic_io_object&& other)
+ {
+ service_->move_assign(implementation,
+ *other.service_, other.implementation);
+ service_ = other.service_;
+ return *this;
+ }
+
+ service_type& get_service()
+ {
+ return *service_;
+ }
+
+ const service_type& get_service() const
+ {
+ return *service_;
+ }
+
+ implementation_type& get_implementation()
+ {
+ return implementation;
+ }
+
+ const implementation_type& get_implementation() const
+ {
+ return implementation;
+ }
+
+ implementation_type implementation;
+
+private:
+ basic_io_object(const basic_io_object&);
+ void operator=(const basic_io_object&);
+
+ IoObjectService* service_;
+};
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_IO_OBJECT_HPP
diff --git a/ext/patches/boost/asio/basic_raw_socket.hpp b/ext/patches/boost/asio/basic_raw_socket.hpp
new file mode 100644
index 0000000..d24c58c
--- /dev/null
+++ b/ext/patches/boost/asio/basic_raw_socket.hpp
@@ -0,0 +1,942 @@
+//
+// basic_raw_socket.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_RAW_SOCKET_HPP
+#define BOOST_ASIO_BASIC_RAW_SOCKET_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/raw_socket_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides raw-oriented socket functionality.
+/**
+ * The basic_raw_socket class template provides asynchronous and blocking
+ * raw-oriented socket functionality.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename Protocol,
+ typename RawSocketService = raw_socket_service<Protocol> >
+class basic_raw_socket
+ : public basic_socket<Protocol, RawSocketService>
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// socket.
+ typedef typename RawSocketService::native_handle_type native_type;
+
+ /// The native representation of a socket.
+ typedef typename RawSocketService::native_handle_type native_handle_type;
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ /// Construct a basic_raw_socket without opening it.
+ /**
+ * This constructor creates a raw socket without opening it. The open()
+ * function must be called before data can be sent or received on the socket.
+ *
+ * @param io_service The io_service object that the raw socket will use
+ * to dispatch handlers for any asynchronous operations performed on the
+ * socket.
+ */
+ explicit basic_raw_socket(boost::asio::io_service& io_service)
+ : basic_socket<Protocol, RawSocketService>(io_service)
+ {
+ }
+
+ /// Construct and open a basic_raw_socket.
+ /**
+ * This constructor creates and opens a raw socket.
+ *
+ * @param io_service The io_service object that the raw socket will use
+ * to dispatch handlers for any asynchronous operations performed on the
+ * socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_raw_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol)
+ : basic_socket<Protocol, RawSocketService>(io_service, protocol)
+ {
+ }
+
+ /// Construct a basic_raw_socket, opening it and binding it to the given
+ /// local endpoint.
+ /**
+ * This constructor creates a raw socket and automatically opens it bound
+ * to the specified endpoint on the local machine. The protocol used is the
+ * protocol associated with the given endpoint.
+ *
+ * @param io_service The io_service object that the raw socket will use
+ * to dispatch handlers for any asynchronous operations performed on the
+ * socket.
+ *
+ * @param endpoint An endpoint on the local machine to which the raw
+ * socket will be bound.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_raw_socket(boost::asio::io_service& io_service,
+ const endpoint_type& endpoint)
+ : basic_socket<Protocol, RawSocketService>(io_service, endpoint)
+ {
+ }
+
+ /// Construct a basic_raw_socket on an existing native socket.
+ /**
+ * This constructor creates a raw socket object to hold an existing
+ * native socket.
+ *
+ * @param io_service The io_service object that the raw socket will use
+ * to dispatch handlers for any asynchronous operations performed on the
+ * socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @param native_socket The new underlying socket implementation.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_raw_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol, const native_handle_type& native_socket)
+ : basic_socket<Protocol, RawSocketService>(
+ io_service, protocol, native_socket)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_raw_socket from another.
+ /**
+ * This constructor moves a raw socket from one object to another.
+ *
+ * @param other The other basic_raw_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_raw_socket(io_service&) constructor.
+ */
+ basic_raw_socket(basic_raw_socket&& other)
+ : basic_socket<Protocol, RawSocketService>(
+ BOOST_ASIO_MOVE_CAST(basic_raw_socket)(other))
+ {
+ }
+
+ /// Move-assign a basic_raw_socket from another.
+ /**
+ * This assignment operator moves a raw socket from one object to another.
+ *
+ * @param other The other basic_raw_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_raw_socket(io_service&) constructor.
+ */
+ basic_raw_socket& operator=(basic_raw_socket&& other)
+ {
+ basic_socket<Protocol, RawSocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_raw_socket)(other));
+ return *this;
+ }
+
+ /// Move-construct a basic_raw_socket from a socket of another protocol type.
+ /**
+ * This constructor moves a raw socket from one object to another.
+ *
+ * @param other The other basic_raw_socket object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_raw_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename RawSocketService1>
+ basic_raw_socket(basic_raw_socket<Protocol1, RawSocketService1>&& other,
+ typename enable_if<is_convertible<Protocol1, Protocol>::value>::type* = 0)
+ : basic_socket<Protocol, RawSocketService>(
+ BOOST_ASIO_MOVE_CAST2(basic_raw_socket<
+ Protocol1, RawSocketService1>)(other))
+ {
+ }
+
+ /// Move-assign a basic_raw_socket from a socket of another protocol type.
+ /**
+ * This assignment operator moves a raw socket from one object to another.
+ *
+ * @param other The other basic_raw_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_raw_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename RawSocketService1>
+ typename enable_if<is_convertible<Protocol1, Protocol>::value,
+ basic_raw_socket>::type& operator=(
+ basic_raw_socket<Protocol1, RawSocketService1>&& other)
+ {
+ basic_socket<Protocol, RawSocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST2(basic_raw_socket<
+ Protocol1, RawSocketService1>)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Send some data on a connected socket.
+ /**
+ * This function is used to send data on the raw socket. The function call
+ * will block until the data has been sent successfully or an error occurs.
+ *
+ * @param buffers One ore more data buffers to be sent on the socket.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The send operation can only be used with a connected socket. Use
+ * the send_to function to send data on an unconnected raw socket.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code socket.send(boost::asio::buffer(data, size)); @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send(
+ this->get_implementation(), buffers, 0, ec);
+ boost::asio::detail::throw_error(ec, "send");
+ return s;
+ }
+
+ /// Send some data on a connected socket.
+ /**
+ * This function is used to send data on the raw socket. The function call
+ * will block until the data has been sent successfully or an error occurs.
+ *
+ * @param buffers One ore more data buffers to be sent on the socket.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The send operation can only be used with a connected socket. Use
+ * the send_to function to send data on an unconnected raw socket.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send(
+ this->get_implementation(), buffers, flags, ec);
+ boost::asio::detail::throw_error(ec, "send");
+ return s;
+ }
+
+ /// Send some data on a connected socket.
+ /**
+ * This function is used to send data on the raw socket. The function call
+ * will block until the data has been sent successfully or an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @note The send operation can only be used with a connected socket. Use
+ * the send_to function to send data on an unconnected raw socket.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return this->get_service().send(
+ this->get_implementation(), buffers, flags, ec);
+ }
+
+ /// Start an asynchronous send on a connected socket.
+ /**
+ * This function is used to send data on the raw socket. The function call
+ * will block until the data has been sent successfully or an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket. Although
+ * the buffers object may be copied as necessary, ownership of the underlying
+ * memory blocks is retained by the caller, which must guarantee that they
+ * remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The async_send operation can only be used with a connected socket.
+ * Use the async_send_to function to send data on an unconnected raw
+ * socket.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.async_send(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send(this->get_implementation(),
+ buffers, 0, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Start an asynchronous send on a connected socket.
+ /**
+ * This function is used to send data on the raw socket. The function call
+ * will block until the data has been sent successfully or an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket. Although
+ * the buffers object may be copied as necessary, ownership of the underlying
+ * memory blocks is retained by the caller, which must guarantee that they
+ * remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The async_send operation can only be used with a connected socket.
+ * Use the async_send_to function to send data on an unconnected raw
+ * socket.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send(this->get_implementation(),
+ buffers, flags, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Send raw data to the specified endpoint.
+ /**
+ * This function is used to send raw data to the specified remote endpoint.
+ * The function call will block until the data has been sent successfully or
+ * an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * boost::asio::ip::udp::endpoint destination(
+ * boost::asio::ip::address::from_string("1.2.3.4"), 12345);
+ * socket.send_to(boost::asio::buffer(data, size), destination);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send_to(
+ this->get_implementation(), buffers, destination, 0, ec);
+ boost::asio::detail::throw_error(ec, "send_to");
+ return s;
+ }
+
+ /// Send raw data to the specified endpoint.
+ /**
+ * This function is used to send raw data to the specified remote endpoint.
+ * The function call will block until the data has been sent successfully or
+ * an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send_to(
+ this->get_implementation(), buffers, destination, flags, ec);
+ boost::asio::detail::throw_error(ec, "send_to");
+ return s;
+ }
+
+ /// Send raw data to the specified endpoint.
+ /**
+ * This function is used to send raw data to the specified remote endpoint.
+ * The function call will block until the data has been sent successfully or
+ * an error occurs.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes sent.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().send_to(this->get_implementation(),
+ buffers, destination, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ /**
+ * This function is used to asynchronously send raw data to the specified
+ * remote endpoint. The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ * Copies will be made of the endpoint as required.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * boost::asio::ip::udp::endpoint destination(
+ * boost::asio::ip::address::from_string("1.2.3.4"), 12345);
+ * socket.async_send_to(
+ * boost::asio::buffer(data, size), destination, handler);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send_to(this->get_implementation(),
+ buffers, destination, 0, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Start an asynchronous send.
+ /**
+ * This function is used to asynchronously send raw data to the specified
+ * remote endpoint. The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent to the remote endpoint.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param destination The remote endpoint to which the data will be sent.
+ * Copies will be made of the endpoint as required.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send_to(const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send_to(
+ this->get_implementation(), buffers, destination, flags,
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Receive some data on a connected socket.
+ /**
+ * This function is used to receive data on the raw socket. The function
+ * call will block until data has been received successfully or an error
+ * occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The receive operation can only be used with a connected socket. Use
+ * the receive_from function to receive data on an unconnected raw
+ * socket.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code socket.receive(boost::asio::buffer(data, size)); @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, 0, ec);
+ boost::asio::detail::throw_error(ec, "receive");
+ return s;
+ }
+
+ /// Receive some data on a connected socket.
+ /**
+ * This function is used to receive data on the raw socket. The function
+ * call will block until data has been received successfully or an error
+ * occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The receive operation can only be used with a connected socket. Use
+ * the receive_from function to receive data on an unconnected raw
+ * socket.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, flags, ec);
+ boost::asio::detail::throw_error(ec, "receive");
+ return s;
+ }
+
+ /// Receive some data on a connected socket.
+ /**
+ * This function is used to receive data on the raw socket. The function
+ * call will block until data has been received successfully or an error
+ * occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes received.
+ *
+ * @note The receive operation can only be used with a connected socket. Use
+ * the receive_from function to receive data on an unconnected raw
+ * socket.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return this->get_service().receive(
+ this->get_implementation(), buffers, flags, ec);
+ }
+
+ /// Start an asynchronous receive on a connected socket.
+ /**
+ * This function is used to asynchronously receive data from the raw
+ * socket. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The async_receive operation can only be used with a connected socket.
+ * Use the async_receive_from function to receive data on an unconnected
+ * raw socket.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.async_receive(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(this->get_implementation(),
+ buffers, 0, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Start an asynchronous receive on a connected socket.
+ /**
+ * This function is used to asynchronously receive data from the raw
+ * socket. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The async_receive operation can only be used with a connected socket.
+ * Use the async_receive_from function to receive data on an unconnected
+ * raw socket.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(this->get_implementation(),
+ buffers, flags, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Receive raw data with the endpoint of the sender.
+ /**
+ * This function is used to receive raw data. The function call will block
+ * until data has been received successfully or an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the data.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * boost::asio::ip::udp::endpoint sender_endpoint;
+ * socket.receive_from(
+ * boost::asio::buffer(data, size), sender_endpoint);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive_from(
+ this->get_implementation(), buffers, sender_endpoint, 0, ec);
+ boost::asio::detail::throw_error(ec, "receive_from");
+ return s;
+ }
+
+ /// Receive raw data with the endpoint of the sender.
+ /**
+ * This function is used to receive raw data. The function call will block
+ * until data has been received successfully or an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the data.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint, socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive_from(
+ this->get_implementation(), buffers, sender_endpoint, flags, ec);
+ boost::asio::detail::throw_error(ec, "receive_from");
+ return s;
+ }
+
+ /// Receive raw data with the endpoint of the sender.
+ /**
+ * This function is used to receive raw data. The function call will block
+ * until data has been received successfully or an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the data.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes received.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint, socket_base::message_flags flags,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().receive_from(this->get_implementation(),
+ buffers, sender_endpoint, flags, ec);
+ }
+
+ /// Start an asynchronous receive.
+ /**
+ * This function is used to asynchronously receive raw data. The function
+ * call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the data. Ownership of the sender_endpoint object
+ * is retained by the caller, which must guarantee that it is valid until the
+ * handler is called.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code socket.async_receive_from(
+ * boost::asio::buffer(data, size), 0, sender_endpoint, handler); @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive_from(
+ this->get_implementation(), buffers, sender_endpoint, 0,
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Start an asynchronous receive.
+ /**
+ * This function is used to asynchronously receive raw data. The function
+ * call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param sender_endpoint An endpoint object that receives the endpoint of
+ * the remote sender of the data. Ownership of the sender_endpoint object
+ * is retained by the caller, which must guarantee that it is valid until the
+ * handler is called.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive_from(const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint, socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive_from(
+ this->get_implementation(), buffers, sender_endpoint, flags,
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_RAW_SOCKET_HPP
diff --git a/ext/patches/boost/asio/basic_seq_packet_socket.hpp b/ext/patches/boost/asio/basic_seq_packet_socket.hpp
new file mode 100644
index 0000000..92a5026
--- /dev/null
+++ b/ext/patches/boost/asio/basic_seq_packet_socket.hpp
@@ -0,0 +1,567 @@
+//
+// basic_seq_packet_socket.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_SEQ_PACKET_SOCKET_HPP
+#define BOOST_ASIO_BASIC_SEQ_PACKET_SOCKET_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/seq_packet_socket_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides sequenced packet socket functionality.
+/**
+ * The basic_seq_packet_socket class template provides asynchronous and blocking
+ * sequenced packet socket functionality.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename Protocol,
+ typename SeqPacketSocketService = seq_packet_socket_service<Protocol> >
+class basic_seq_packet_socket
+ : public basic_socket<Protocol, SeqPacketSocketService>
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// socket.
+ typedef typename SeqPacketSocketService::native_handle_type native_type;
+
+ /// The native representation of a socket.
+ typedef typename SeqPacketSocketService::native_handle_type
+ native_handle_type;
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ /// Construct a basic_seq_packet_socket without opening it.
+ /**
+ * This constructor creates a sequenced packet socket without opening it. The
+ * socket needs to be opened and then connected or accepted before data can
+ * be sent or received on it.
+ *
+ * @param io_service The io_service object that the sequenced packet socket
+ * will use to dispatch handlers for any asynchronous operations performed on
+ * the socket.
+ */
+ explicit basic_seq_packet_socket(boost::asio::io_service& io_service)
+ : basic_socket<Protocol, SeqPacketSocketService>(io_service)
+ {
+ }
+
+ /// Construct and open a basic_seq_packet_socket.
+ /**
+ * This constructor creates and opens a sequenced_packet socket. The socket
+ * needs to be connected or accepted before data can be sent or received on
+ * it.
+ *
+ * @param io_service The io_service object that the sequenced packet socket
+ * will use to dispatch handlers for any asynchronous operations performed on
+ * the socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_seq_packet_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol)
+ : basic_socket<Protocol, SeqPacketSocketService>(io_service, protocol)
+ {
+ }
+
+ /// Construct a basic_seq_packet_socket, opening it and binding it to the
+ /// given local endpoint.
+ /**
+ * This constructor creates a sequenced packet socket and automatically opens
+ * it bound to the specified endpoint on the local machine. The protocol used
+ * is the protocol associated with the given endpoint.
+ *
+ * @param io_service The io_service object that the sequenced packet socket
+ * will use to dispatch handlers for any asynchronous operations performed on
+ * the socket.
+ *
+ * @param endpoint An endpoint on the local machine to which the sequenced
+ * packet socket will be bound.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_seq_packet_socket(boost::asio::io_service& io_service,
+ const endpoint_type& endpoint)
+ : basic_socket<Protocol, SeqPacketSocketService>(io_service, endpoint)
+ {
+ }
+
+ /// Construct a basic_seq_packet_socket on an existing native socket.
+ /**
+ * This constructor creates a sequenced packet socket object to hold an
+ * existing native socket.
+ *
+ * @param io_service The io_service object that the sequenced packet socket
+ * will use to dispatch handlers for any asynchronous operations performed on
+ * the socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @param native_socket The new underlying socket implementation.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_seq_packet_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol, const native_handle_type& native_socket)
+ : basic_socket<Protocol, SeqPacketSocketService>(
+ io_service, protocol, native_socket)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_seq_packet_socket from another.
+ /**
+ * This constructor moves a sequenced packet socket from one object to
+ * another.
+ *
+ * @param other The other basic_seq_packet_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_seq_packet_socket(io_service&) constructor.
+ */
+ basic_seq_packet_socket(basic_seq_packet_socket&& other)
+ : basic_socket<Protocol, SeqPacketSocketService>(
+ BOOST_ASIO_MOVE_CAST(basic_seq_packet_socket)(other))
+ {
+ }
+
+ /// Move-assign a basic_seq_packet_socket from another.
+ /**
+ * This assignment operator moves a sequenced packet socket from one object to
+ * another.
+ *
+ * @param other The other basic_seq_packet_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_seq_packet_socket(io_service&) constructor.
+ */
+ basic_seq_packet_socket& operator=(basic_seq_packet_socket&& other)
+ {
+ basic_socket<Protocol, SeqPacketSocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_seq_packet_socket)(other));
+ return *this;
+ }
+
+ /// Move-construct a basic_seq_packet_socket from a socket of another protocol
+ /// type.
+ /**
+ * This constructor moves a sequenced packet socket from one object to
+ * another.
+ *
+ * @param other The other basic_seq_packet_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_seq_packet_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename SeqPacketSocketService1>
+ basic_seq_packet_socket(
+ basic_seq_packet_socket<Protocol1, SeqPacketSocketService1>&& other,
+ typename enable_if<is_convertible<Protocol1, Protocol>::value>::type* = 0)
+ : basic_socket<Protocol, SeqPacketSocketService>(
+ BOOST_ASIO_MOVE_CAST2(basic_seq_packet_socket<
+ Protocol1, SeqPacketSocketService1>)(other))
+ {
+ }
+
+ /// Move-assign a basic_seq_packet_socket from a socket of another protocol
+ /// type.
+ /**
+ * This assignment operator moves a sequenced packet socket from one object to
+ * another.
+ *
+ * @param other The other basic_seq_packet_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_seq_packet_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename SeqPacketSocketService1>
+ typename enable_if<is_convertible<Protocol1, Protocol>::value,
+ basic_seq_packet_socket>::type& operator=(
+ basic_seq_packet_socket<Protocol1, SeqPacketSocketService1>&& other)
+ {
+ basic_socket<Protocol, SeqPacketSocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST2(basic_seq_packet_socket<
+ Protocol1, SeqPacketSocketService1>)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Send some data on the socket.
+ /**
+ * This function is used to send data on the sequenced packet socket. The
+ * function call will block until the data has been sent successfully, or an
+ * until error occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.send(boost::asio::buffer(data, size), 0);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send(
+ this->get_implementation(), buffers, flags, ec);
+ boost::asio::detail::throw_error(ec, "send");
+ return s;
+ }
+
+ /// Send some data on the socket.
+ /**
+ * This function is used to send data on the sequenced packet socket. The
+ * function call will block the data has been sent successfully, or an until
+ * error occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes sent. Returns 0 if an error occurred.
+ *
+ * @note The send operation may not transmit all of the data to the peer.
+ * Consider using the @ref write function if you need to ensure that all data
+ * is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return this->get_service().send(
+ this->get_implementation(), buffers, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ /**
+ * This function is used to asynchronously send data on the sequenced packet
+ * socket. The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent on the socket. Although
+ * the buffers object may be copied as necessary, ownership of the underlying
+ * memory blocks is retained by the caller, which must guarantee that they
+ * remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.async_send(boost::asio::buffer(data, size), 0, handler);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send(this->get_implementation(),
+ buffers, flags, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Receive some data on the socket.
+ /**
+ * This function is used to receive data on the sequenced packet socket. The
+ * function call will block until data has been received successfully, or
+ * until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param out_flags After the receive call completes, contains flags
+ * associated with the received data. For example, if the
+ * socket_base::message_end_of_record bit is set then the received data marks
+ * the end of a record.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.receive(boost::asio::buffer(data, size), out_flags);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags& out_flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, 0, out_flags, ec);
+ boost::asio::detail::throw_error(ec, "receive");
+ return s;
+ }
+
+ /// Receive some data on the socket.
+ /**
+ * This function is used to receive data on the sequenced packet socket. The
+ * function call will block until data has been received successfully, or
+ * until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param in_flags Flags specifying how the receive call is to be made.
+ *
+ * @param out_flags After the receive call completes, contains flags
+ * associated with the received data. For example, if the
+ * socket_base::message_end_of_record bit is set then the received data marks
+ * the end of a record.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The receive operation may not receive all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.receive(boost::asio::buffer(data, size), 0, out_flags);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, in_flags, out_flags, ec);
+ boost::asio::detail::throw_error(ec, "receive");
+ return s;
+ }
+
+ /// Receive some data on a connected socket.
+ /**
+ * This function is used to receive data on the sequenced packet socket. The
+ * function call will block until data has been received successfully, or
+ * until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param in_flags Flags specifying how the receive call is to be made.
+ *
+ * @param out_flags After the receive call completes, contains flags
+ * associated with the received data. For example, if the
+ * socket_base::message_end_of_record bit is set then the received data marks
+ * the end of a record.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes received. Returns 0 if an error occurred.
+ *
+ * @note The receive operation may not receive all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, boost::system::error_code& ec)
+ {
+ return this->get_service().receive(this->get_implementation(),
+ buffers, in_flags, out_flags, ec);
+ }
+
+ /// Start an asynchronous receive.
+ /**
+ * This function is used to asynchronously receive data from the sequenced
+ * packet socket. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param out_flags Once the asynchronous operation completes, contains flags
+ * associated with the received data. For example, if the
+ * socket_base::message_end_of_record bit is set then the received data marks
+ * the end of a record. The caller must guarantee that the referenced
+ * variable remains valid until the handler is called.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.async_receive(boost::asio::buffer(data, size), out_flags, handler);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags& out_flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(
+ this->get_implementation(), buffers, 0, out_flags,
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Start an asynchronous receive.
+ /**
+ * This function is used to asynchronously receive data from the sequenced
+ * data socket. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param in_flags Flags specifying how the receive call is to be made.
+ *
+ * @param out_flags Once the asynchronous operation completes, contains flags
+ * associated with the received data. For example, if the
+ * socket_base::message_end_of_record bit is set then the received data marks
+ * the end of a record. The caller must guarantee that the referenced
+ * variable remains valid until the handler is called.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.async_receive(
+ * boost::asio::buffer(data, size),
+ * 0, out_flags, handler);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(
+ this->get_implementation(), buffers, in_flags, out_flags,
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_SEQ_PACKET_SOCKET_HPP
diff --git a/ext/patches/boost/asio/basic_serial_port.hpp b/ext/patches/boost/asio/basic_serial_port.hpp
new file mode 100644
index 0000000..b7278e0
--- /dev/null
+++ b/ext/patches/boost/asio/basic_serial_port.hpp
@@ -0,0 +1,697 @@
+//
+// basic_serial_port.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_SERIAL_PORT_HPP
+#define BOOST_ASIO_BASIC_SERIAL_PORT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_SERIAL_PORT) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <string>
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/serial_port_base.hpp>
+#include <boost/asio/serial_port_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides serial port functionality.
+/**
+ * The basic_serial_port class template provides functionality that is common
+ * to all serial ports.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename SerialPortService = serial_port_service>
+class basic_serial_port
+ : public basic_io_object<SerialPortService>,
+ public serial_port_base
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// serial port.
+ typedef typename SerialPortService::native_handle_type native_type;
+
+ /// The native representation of a serial port.
+ typedef typename SerialPortService::native_handle_type native_handle_type;
+
+ /// A basic_serial_port is always the lowest layer.
+ typedef basic_serial_port<SerialPortService> lowest_layer_type;
+
+ /// Construct a basic_serial_port without opening it.
+ /**
+ * This constructor creates a serial port without opening it.
+ *
+ * @param io_service The io_service object that the serial port will use to
+ * dispatch handlers for any asynchronous operations performed on the port.
+ */
+ explicit basic_serial_port(boost::asio::io_service& io_service)
+ : basic_io_object<SerialPortService>(io_service)
+ {
+ }
+
+ /// Construct and open a basic_serial_port.
+ /**
+ * This constructor creates and opens a serial port for the specified device
+ * name.
+ *
+ * @param io_service The io_service object that the serial port will use to
+ * dispatch handlers for any asynchronous operations performed on the port.
+ *
+ * @param device The platform-specific device name for this serial
+ * port.
+ */
+ explicit basic_serial_port(boost::asio::io_service& io_service,
+ const char* device)
+ : basic_io_object<SerialPortService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().open(this->get_implementation(), device, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ }
+
+ /// Construct and open a basic_serial_port.
+ /**
+ * This constructor creates and opens a serial port for the specified device
+ * name.
+ *
+ * @param io_service The io_service object that the serial port will use to
+ * dispatch handlers for any asynchronous operations performed on the port.
+ *
+ * @param device The platform-specific device name for this serial
+ * port.
+ */
+ explicit basic_serial_port(boost::asio::io_service& io_service,
+ const std::string& device)
+ : basic_io_object<SerialPortService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().open(this->get_implementation(), device, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ }
+
+ /// Construct a basic_serial_port on an existing native serial port.
+ /**
+ * This constructor creates a serial port object to hold an existing native
+ * serial port.
+ *
+ * @param io_service The io_service object that the serial port will use to
+ * dispatch handlers for any asynchronous operations performed on the port.
+ *
+ * @param native_serial_port A native serial port.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_serial_port(boost::asio::io_service& io_service,
+ const native_handle_type& native_serial_port)
+ : basic_io_object<SerialPortService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(),
+ native_serial_port, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_serial_port from another.
+ /**
+ * This constructor moves a serial port from one object to another.
+ *
+ * @param other The other basic_serial_port object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_serial_port(io_service&) constructor.
+ */
+ basic_serial_port(basic_serial_port&& other)
+ : basic_io_object<SerialPortService>(
+ BOOST_ASIO_MOVE_CAST(basic_serial_port)(other))
+ {
+ }
+
+ /// Move-assign a basic_serial_port from another.
+ /**
+ * This assignment operator moves a serial port from one object to another.
+ *
+ * @param other The other basic_serial_port object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_serial_port(io_service&) constructor.
+ */
+ basic_serial_port& operator=(basic_serial_port&& other)
+ {
+ basic_io_object<SerialPortService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_serial_port)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Get a reference to the lowest layer.
+ /**
+ * This function returns a reference to the lowest layer in a stack of
+ * layers. Since a basic_serial_port cannot contain any further layers, it
+ * simply returns a reference to itself.
+ *
+ * @return A reference to the lowest layer in the stack of layers. Ownership
+ * is not transferred to the caller.
+ */
+ lowest_layer_type& lowest_layer()
+ {
+ return *this;
+ }
+
+ /// Get a const reference to the lowest layer.
+ /**
+ * This function returns a const reference to the lowest layer in a stack of
+ * layers. Since a basic_serial_port cannot contain any further layers, it
+ * simply returns a reference to itself.
+ *
+ * @return A const reference to the lowest layer in the stack of layers.
+ * Ownership is not transferred to the caller.
+ */
+ const lowest_layer_type& lowest_layer() const
+ {
+ return *this;
+ }
+
+ /// Open the serial port using the specified device name.
+ /**
+ * This function opens the serial port for the specified device name.
+ *
+ * @param device The platform-specific device name.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void open(const std::string& device)
+ {
+ boost::system::error_code ec;
+ this->get_service().open(this->get_implementation(), device, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ }
+
+ /// Open the serial port using the specified device name.
+ /**
+ * This function opens the serial port using the given platform-specific
+ * device name.
+ *
+ * @param device The platform-specific device name.
+ *
+ * @param ec Set the indicate what error occurred, if any.
+ */
+ boost::system::error_code open(const std::string& device,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().open(this->get_implementation(), device, ec);
+ }
+
+ /// Assign an existing native serial port to the serial port.
+ /*
+ * This function opens the serial port to hold an existing native serial port.
+ *
+ * @param native_serial_port A native serial port.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void assign(const native_handle_type& native_serial_port)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(),
+ native_serial_port, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+ /// Assign an existing native serial port to the serial port.
+ /*
+ * This function opens the serial port to hold an existing native serial port.
+ *
+ * @param native_serial_port A native serial port.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code assign(const native_handle_type& native_serial_port,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().assign(this->get_implementation(),
+ native_serial_port, ec);
+ }
+
+ /// Determine whether the serial port is open.
+ bool is_open() const
+ {
+ return this->get_service().is_open(this->get_implementation());
+ }
+
+ /// Close the serial port.
+ /**
+ * This function is used to close the serial port. Any asynchronous read or
+ * write operations will be cancelled immediately, and will complete with the
+ * boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void close()
+ {
+ boost::system::error_code ec;
+ this->get_service().close(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "close");
+ }
+
+ /// Close the serial port.
+ /**
+ * This function is used to close the serial port. Any asynchronous read or
+ * write operations will be cancelled immediately, and will complete with the
+ * boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code close(boost::system::error_code& ec)
+ {
+ return this->get_service().close(this->get_implementation(), ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native serial port
+ /// representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * serial port. This is intended to allow access to native serial port
+ * functionality that is not otherwise provided.
+ */
+ native_type native()
+ {
+ return this->get_service().native_handle(this->get_implementation());
+ }
+
+ /// Get the native serial port representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * serial port. This is intended to allow access to native serial port
+ * functionality that is not otherwise provided.
+ */
+ native_handle_type native_handle()
+ {
+ return this->get_service().native_handle(this->get_implementation());
+ }
+
+ /// Cancel all asynchronous operations associated with the serial port.
+ /**
+ * This function causes all outstanding asynchronous read or write operations
+ * to finish immediately, and the handlers for cancelled operations will be
+ * passed the boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void cancel()
+ {
+ boost::system::error_code ec;
+ this->get_service().cancel(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "cancel");
+ }
+
+ /// Cancel all asynchronous operations associated with the serial port.
+ /**
+ * This function causes all outstanding asynchronous read or write operations
+ * to finish immediately, and the handlers for cancelled operations will be
+ * passed the boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code cancel(boost::system::error_code& ec)
+ {
+ return this->get_service().cancel(this->get_implementation(), ec);
+ }
+
+ /// Send a break sequence to the serial port.
+ /**
+ * This function causes a break sequence of platform-specific duration to be
+ * sent out the serial port.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void send_break()
+ {
+ boost::system::error_code ec;
+ this->get_service().send_break(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "send_break");
+ }
+
+ /// Send a break sequence to the serial port.
+ /**
+ * This function causes a break sequence of platform-specific duration to be
+ * sent out the serial port.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code send_break(boost::system::error_code& ec)
+ {
+ return this->get_service().send_break(this->get_implementation(), ec);
+ }
+
+ /// Set an option on the serial port.
+ /**
+ * This function is used to set an option on the serial port.
+ *
+ * @param option The option value to be set on the serial port.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa SettableSerialPortOption @n
+ * boost::asio::serial_port_base::baud_rate @n
+ * boost::asio::serial_port_base::flow_control @n
+ * boost::asio::serial_port_base::parity @n
+ * boost::asio::serial_port_base::stop_bits @n
+ * boost::asio::serial_port_base::character_size
+ */
+ template <typename SettableSerialPortOption>
+ void set_option(const SettableSerialPortOption& option)
+ {
+ boost::system::error_code ec;
+ this->get_service().set_option(this->get_implementation(), option, ec);
+ boost::asio::detail::throw_error(ec, "set_option");
+ }
+
+ /// Set an option on the serial port.
+ /**
+ * This function is used to set an option on the serial port.
+ *
+ * @param option The option value to be set on the serial port.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @sa SettableSerialPortOption @n
+ * boost::asio::serial_port_base::baud_rate @n
+ * boost::asio::serial_port_base::flow_control @n
+ * boost::asio::serial_port_base::parity @n
+ * boost::asio::serial_port_base::stop_bits @n
+ * boost::asio::serial_port_base::character_size
+ */
+ template <typename SettableSerialPortOption>
+ boost::system::error_code set_option(const SettableSerialPortOption& option,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().set_option(
+ this->get_implementation(), option, ec);
+ }
+
+ /// Get an option from the serial port.
+ /**
+ * This function is used to get the current value of an option on the serial
+ * port.
+ *
+ * @param option The option value to be obtained from the serial port.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa GettableSerialPortOption @n
+ * boost::asio::serial_port_base::baud_rate @n
+ * boost::asio::serial_port_base::flow_control @n
+ * boost::asio::serial_port_base::parity @n
+ * boost::asio::serial_port_base::stop_bits @n
+ * boost::asio::serial_port_base::character_size
+ */
+ template <typename GettableSerialPortOption>
+ void get_option(GettableSerialPortOption& option)
+ {
+ boost::system::error_code ec;
+ this->get_service().get_option(this->get_implementation(), option, ec);
+ boost::asio::detail::throw_error(ec, "get_option");
+ }
+
+ /// Get an option from the serial port.
+ /**
+ * This function is used to get the current value of an option on the serial
+ * port.
+ *
+ * @param option The option value to be obtained from the serial port.
+ *
+ * @param ec Set to indicate what error occured, if any.
+ *
+ * @sa GettableSerialPortOption @n
+ * boost::asio::serial_port_base::baud_rate @n
+ * boost::asio::serial_port_base::flow_control @n
+ * boost::asio::serial_port_base::parity @n
+ * boost::asio::serial_port_base::stop_bits @n
+ * boost::asio::serial_port_base::character_size
+ */
+ template <typename GettableSerialPortOption>
+ boost::system::error_code get_option(GettableSerialPortOption& option,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().get_option(
+ this->get_implementation(), option, ec);
+ }
+
+ /// Write some data to the serial port.
+ /**
+ * This function is used to write data to the serial port. The function call
+ * will block until one or more bytes of the data has been written
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more data buffers to be written to the serial port.
+ *
+ * @returns The number of bytes written.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * serial_port.write_some(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().write_some(
+ this->get_implementation(), buffers, ec);
+ boost::asio::detail::throw_error(ec, "write_some");
+ return s;
+ }
+
+ /// Write some data to the serial port.
+ /**
+ * This function is used to write data to the serial port. The function call
+ * will block until one or more bytes of the data has been written
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more data buffers to be written to the serial port.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. Returns 0 if an error occurred.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().write_some(
+ this->get_implementation(), buffers, ec);
+ }
+
+ /// Start an asynchronous write.
+ /**
+ * This function is used to asynchronously write data to the serial port.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be written to the serial port.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes written.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The write operation may not transmit all of the data to the peer.
+ * Consider using the @ref async_write function if you need to ensure that all
+ * data is written before the asynchronous operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * serial_port.async_write_some(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_write_some(this->get_implementation(),
+ buffers, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Read some data from the serial port.
+ /**
+ * This function is used to read data from the serial port. The function
+ * call will block until one or more bytes of data has been read successfully,
+ * or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @returns The number of bytes read.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * serial_port.read_some(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().read_some(
+ this->get_implementation(), buffers, ec);
+ boost::asio::detail::throw_error(ec, "read_some");
+ return s;
+ }
+
+ /// Read some data from the serial port.
+ /**
+ * This function is used to read data from the serial port. The function
+ * call will block until one or more bytes of data has been read successfully,
+ * or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. Returns 0 if an error occurred.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().read_some(
+ this->get_implementation(), buffers, ec);
+ }
+
+ /// Start an asynchronous read.
+ /**
+ * This function is used to asynchronously read data from the serial port.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes read.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The read operation may not read all of the requested number of bytes.
+ * Consider using the @ref async_read function if you need to ensure that the
+ * requested amount of data is read before the asynchronous operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * serial_port.async_read_some(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_read_some(this->get_implementation(),
+ buffers, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_SERIAL_PORT)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_BASIC_SERIAL_PORT_HPP
diff --git a/ext/patches/boost/asio/basic_signal_set.hpp b/ext/patches/boost/asio/basic_signal_set.hpp
new file mode 100644
index 0000000..2b0656d
--- /dev/null
+++ b/ext/patches/boost/asio/basic_signal_set.hpp
@@ -0,0 +1,386 @@
+//
+// basic_signal_set.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_SIGNAL_SET_HPP
+#define BOOST_ASIO_BASIC_SIGNAL_SET_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/signal_set_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides signal functionality.
+/**
+ * The basic_signal_set class template provides the ability to perform an
+ * asynchronous wait for one or more signals to occur.
+ *
+ * Most applications will use the boost::asio::signal_set typedef.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Example
+ * Performing an asynchronous wait:
+ * @code
+ * void handler(
+ * const boost::system::error_code& error,
+ * int signal_number)
+ * {
+ * if (!error)
+ * {
+ * // A signal occurred.
+ * }
+ * }
+ *
+ * ...
+ *
+ * // Construct a signal set registered for process termination.
+ * boost::asio::signal_set signals(io_service, SIGINT, SIGTERM);
+ *
+ * // Start an asynchronous wait for one of the signals to occur.
+ * signals.async_wait(handler);
+ * @endcode
+ *
+ * @par Queueing of signal notifications
+ *
+ * If a signal is registered with a signal_set, and the signal occurs when
+ * there are no waiting handlers, then the signal notification is queued. The
+ * next async_wait operation on that signal_set will dequeue the notification.
+ * If multiple notifications are queued, subsequent async_wait operations
+ * dequeue them one at a time. Signal notifications are dequeued in order of
+ * ascending signal number.
+ *
+ * If a signal number is removed from a signal_set (using the @c remove or @c
+ * erase member functions) then any queued notifications for that signal are
+ * discarded.
+ *
+ * @par Multiple registration of signals
+ *
+ * The same signal number may be registered with different signal_set objects.
+ * When the signal occurs, one handler is called for each signal_set object.
+ *
+ * Note that multiple registration only works for signals that are registered
+ * using Asio. The application must not also register a signal handler using
+ * functions such as @c signal() or @c sigaction().
+ *
+ * @par Signal masking on POSIX platforms
+ *
+ * POSIX allows signals to be blocked using functions such as @c sigprocmask()
+ * and @c pthread_sigmask(). For signals to be delivered, programs must ensure
+ * that any signals registered using signal_set objects are unblocked in at
+ * least one thread.
+ */
+template <typename SignalSetService = signal_set_service>
+class basic_signal_set
+ : public basic_io_object<SignalSetService>
+{
+public:
+ /// Construct a signal set without adding any signals.
+ /**
+ * This constructor creates a signal set without registering for any signals.
+ *
+ * @param io_service The io_service object that the signal set will use to
+ * dispatch handlers for any asynchronous operations performed on the set.
+ */
+ explicit basic_signal_set(boost::asio::io_service& io_service)
+ : basic_io_object<SignalSetService>(io_service)
+ {
+ }
+
+ /// Construct a signal set and add one signal.
+ /**
+ * This constructor creates a signal set and registers for one signal.
+ *
+ * @param io_service The io_service object that the signal set will use to
+ * dispatch handlers for any asynchronous operations performed on the set.
+ *
+ * @param signal_number_1 The signal number to be added.
+ *
+ * @note This constructor is equivalent to performing:
+ * @code boost::asio::signal_set signals(io_service);
+ * signals.add(signal_number_1); @endcode
+ */
+ basic_signal_set(boost::asio::io_service& io_service, int signal_number_1)
+ : basic_io_object<SignalSetService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->service.add(this->implementation, signal_number_1, ec);
+ boost::asio::detail::throw_error(ec, "add");
+ }
+
+ /// Construct a signal set and add two signals.
+ /**
+ * This constructor creates a signal set and registers for two signals.
+ *
+ * @param io_service The io_service object that the signal set will use to
+ * dispatch handlers for any asynchronous operations performed on the set.
+ *
+ * @param signal_number_1 The first signal number to be added.
+ *
+ * @param signal_number_2 The second signal number to be added.
+ *
+ * @note This constructor is equivalent to performing:
+ * @code boost::asio::signal_set signals(io_service);
+ * signals.add(signal_number_1);
+ * signals.add(signal_number_2); @endcode
+ */
+ basic_signal_set(boost::asio::io_service& io_service, int signal_number_1,
+ int signal_number_2)
+ : basic_io_object<SignalSetService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->service.add(this->implementation, signal_number_1, ec);
+ boost::asio::detail::throw_error(ec, "add");
+ this->service.add(this->implementation, signal_number_2, ec);
+ boost::asio::detail::throw_error(ec, "add");
+ }
+
+ /// Construct a signal set and add three signals.
+ /**
+ * This constructor creates a signal set and registers for three signals.
+ *
+ * @param io_service The io_service object that the signal set will use to
+ * dispatch handlers for any asynchronous operations performed on the set.
+ *
+ * @param signal_number_1 The first signal number to be added.
+ *
+ * @param signal_number_2 The second signal number to be added.
+ *
+ * @param signal_number_3 The third signal number to be added.
+ *
+ * @note This constructor is equivalent to performing:
+ * @code boost::asio::signal_set signals(io_service);
+ * signals.add(signal_number_1);
+ * signals.add(signal_number_2);
+ * signals.add(signal_number_3); @endcode
+ */
+ basic_signal_set(boost::asio::io_service& io_service, int signal_number_1,
+ int signal_number_2, int signal_number_3)
+ : basic_io_object<SignalSetService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->service.add(this->implementation, signal_number_1, ec);
+ boost::asio::detail::throw_error(ec, "add");
+ this->service.add(this->implementation, signal_number_2, ec);
+ boost::asio::detail::throw_error(ec, "add");
+ this->service.add(this->implementation, signal_number_3, ec);
+ boost::asio::detail::throw_error(ec, "add");
+ }
+
+ /// Add a signal to a signal_set.
+ /**
+ * This function adds the specified signal to the set. It has no effect if the
+ * signal is already in the set.
+ *
+ * @param signal_number The signal to be added to the set.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void add(int signal_number)
+ {
+ boost::system::error_code ec;
+ this->service.add(this->implementation, signal_number, ec);
+ boost::asio::detail::throw_error(ec, "add");
+ }
+
+ /// Add a signal to a signal_set.
+ /**
+ * This function adds the specified signal to the set. It has no effect if the
+ * signal is already in the set.
+ *
+ * @param signal_number The signal to be added to the set.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code add(int signal_number,
+ boost::system::error_code& ec)
+ {
+ return this->service.add(this->implementation, signal_number, ec);
+ }
+
+ /// Remove a signal from a signal_set.
+ /**
+ * This function removes the specified signal from the set. It has no effect
+ * if the signal is not in the set.
+ *
+ * @param signal_number The signal to be removed from the set.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Removes any notifications that have been queued for the specified
+ * signal number.
+ */
+ void remove(int signal_number)
+ {
+ boost::system::error_code ec;
+ this->service.remove(this->implementation, signal_number, ec);
+ boost::asio::detail::throw_error(ec, "remove");
+ }
+
+ /// Remove a signal from a signal_set.
+ /**
+ * This function removes the specified signal from the set. It has no effect
+ * if the signal is not in the set.
+ *
+ * @param signal_number The signal to be removed from the set.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Removes any notifications that have been queued for the specified
+ * signal number.
+ */
+ boost::system::error_code remove(int signal_number,
+ boost::system::error_code& ec)
+ {
+ return this->service.remove(this->implementation, signal_number, ec);
+ }
+
+ /// Remove all signals from a signal_set.
+ /**
+ * This function removes all signals from the set. It has no effect if the set
+ * is already empty.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Removes all queued notifications.
+ */
+ void clear()
+ {
+ boost::system::error_code ec;
+ this->service.clear(this->implementation, ec);
+ boost::asio::detail::throw_error(ec, "clear");
+ }
+
+ /// Remove all signals from a signal_set.
+ /**
+ * This function removes all signals from the set. It has no effect if the set
+ * is already empty.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Removes all queued notifications.
+ */
+ boost::system::error_code clear(boost::system::error_code& ec)
+ {
+ return this->service.clear(this->implementation, ec);
+ }
+
+ /// Cancel all operations associated with the signal set.
+ /**
+ * This function forces the completion of any pending asynchronous wait
+ * operations against the signal set. The handler for each cancelled
+ * operation will be invoked with the boost::asio::error::operation_aborted
+ * error code.
+ *
+ * Cancellation does not alter the set of registered signals.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If a registered signal occurred before cancel() is called, then the
+ * handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ void cancel()
+ {
+ boost::system::error_code ec;
+ this->service.cancel(this->implementation, ec);
+ boost::asio::detail::throw_error(ec, "cancel");
+ }
+
+ /// Cancel all operations associated with the signal set.
+ /**
+ * This function forces the completion of any pending asynchronous wait
+ * operations against the signal set. The handler for each cancelled
+ * operation will be invoked with the boost::asio::error::operation_aborted
+ * error code.
+ *
+ * Cancellation does not alter the set of registered signals.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note If a registered signal occurred before cancel() is called, then the
+ * handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ boost::system::error_code cancel(boost::system::error_code& ec)
+ {
+ return this->service.cancel(this->implementation, ec);
+ }
+
+ /// Start an asynchronous operation to wait for a signal to be delivered.
+ /**
+ * This function may be used to initiate an asynchronous wait against the
+ * signal set. It always returns immediately.
+ *
+ * For each call to async_wait(), the supplied handler will be called exactly
+ * once. The handler will be called when:
+ *
+ * @li One of the registered signals in the signal set occurs; or
+ *
+ * @li The signal set was cancelled, in which case the handler is passed the
+ * error code boost::asio::error::operation_aborted.
+ *
+ * @param handler The handler to be called when the signal occurs. Copies
+ * will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * int signal_number // Indicates which signal occurred.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename SignalHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(SignalHandler,
+ void (boost::system::error_code, int))
+ async_wait(BOOST_ASIO_MOVE_ARG(SignalHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a SignalHandler.
+ BOOST_ASIO_SIGNAL_HANDLER_CHECK(SignalHandler, handler) type_check;
+
+ return this->service.async_wait(this->implementation,
+ BOOST_ASIO_MOVE_CAST(SignalHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_SIGNAL_SET_HPP
diff --git a/ext/patches/boost/asio/basic_socket.hpp b/ext/patches/boost/asio/basic_socket.hpp
new file mode 100644
index 0000000..a65ca47
--- /dev/null
+++ b/ext/patches/boost/asio/basic_socket.hpp
@@ -0,0 +1,1520 @@
+//
+// basic_socket.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_SOCKET_HPP
+#define BOOST_ASIO_BASIC_SOCKET_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/socket_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides socket functionality.
+/**
+ * The basic_socket class template provides functionality that is common to both
+ * stream-oriented and datagram-oriented sockets.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename Protocol, typename SocketService>
+class basic_socket
+ : public basic_io_object<SocketService>,
+ public socket_base
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// socket.
+ typedef typename SocketService::native_handle_type native_type;
+
+ /// The native representation of a socket.
+ typedef typename SocketService::native_handle_type native_handle_type;
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ /// A basic_socket is always the lowest layer.
+ typedef basic_socket<Protocol, SocketService> lowest_layer_type;
+
+ /// Construct a basic_socket without opening it.
+ /**
+ * This constructor creates a socket without opening it.
+ *
+ * @param io_service The io_service object that the socket will use to
+ * dispatch handlers for any asynchronous operations performed on the socket.
+ */
+ explicit basic_socket(boost::asio::io_service& io_service)
+ : basic_io_object<SocketService>(io_service)
+ {
+ }
+
+ /// Construct and open a basic_socket.
+ /**
+ * This constructor creates and opens a socket.
+ *
+ * @param io_service The io_service object that the socket will use to
+ * dispatch handlers for any asynchronous operations performed on the socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol)
+ : basic_io_object<SocketService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().open(this->get_implementation(), protocol, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ }
+
+ /// Construct a basic_socket, opening it and binding it to the given local
+ /// endpoint.
+ /**
+ * This constructor creates a socket and automatically opens it bound to the
+ * specified endpoint on the local machine. The protocol used is the protocol
+ * associated with the given endpoint.
+ *
+ * @param io_service The io_service object that the socket will use to
+ * dispatch handlers for any asynchronous operations performed on the socket.
+ *
+ * @param endpoint An endpoint on the local machine to which the socket will
+ * be bound.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_socket(boost::asio::io_service& io_service,
+ const endpoint_type& endpoint)
+ : basic_io_object<SocketService>(io_service)
+ {
+ boost::system::error_code ec;
+ const protocol_type protocol = endpoint.protocol();
+ this->get_service().open(this->get_implementation(), protocol, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ this->get_service().bind(this->get_implementation(), endpoint, ec);
+ boost::asio::detail::throw_error(ec, "bind");
+ }
+
+ /// Construct a basic_socket on an existing native socket.
+ /**
+ * This constructor creates a socket object to hold an existing native socket.
+ *
+ * @param io_service The io_service object that the socket will use to
+ * dispatch handlers for any asynchronous operations performed on the socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @param native_socket A native socket.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol, const native_handle_type& native_socket)
+ : basic_io_object<SocketService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(),
+ protocol, native_socket, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_socket from another.
+ /**
+ * This constructor moves a socket from one object to another.
+ *
+ * @param other The other basic_socket object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_socket(io_service&) constructor.
+ */
+ basic_socket(basic_socket&& other)
+ : basic_io_object<SocketService>(
+ BOOST_ASIO_MOVE_CAST(basic_socket)(other))
+ {
+ }
+
+ /// Move-assign a basic_socket from another.
+ /**
+ * This assignment operator moves a socket from one object to another.
+ *
+ * @param other The other basic_socket object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_socket(io_service&) constructor.
+ */
+ basic_socket& operator=(basic_socket&& other)
+ {
+ basic_io_object<SocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_socket)(other));
+ return *this;
+ }
+
+ // All sockets have access to each other's implementations.
+ template <typename Protocol1, typename SocketService1>
+ friend class basic_socket;
+
+ /// Move-construct a basic_socket from a socket of another protocol type.
+ /**
+ * This constructor moves a socket from one object to another.
+ *
+ * @param other The other basic_socket object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename SocketService1>
+ basic_socket(basic_socket<Protocol1, SocketService1>&& other,
+ typename enable_if<is_convertible<Protocol1, Protocol>::value>::type* = 0)
+ : basic_io_object<SocketService>(other.get_io_service())
+ {
+ this->get_service().template converting_move_construct<Protocol1>(
+ this->get_implementation(), other.get_implementation());
+ }
+
+ /// Move-assign a basic_socket from a socket of another protocol type.
+ /**
+ * This assignment operator moves a socket from one object to another.
+ *
+ * @param other The other basic_socket object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename SocketService1>
+ typename enable_if<is_convertible<Protocol1, Protocol>::value,
+ basic_socket>::type& operator=(
+ basic_socket<Protocol1, SocketService1>&& other)
+ {
+ basic_socket tmp(BOOST_ASIO_MOVE_CAST2(basic_socket<
+ Protocol1, SocketService1>)(other));
+ basic_io_object<SocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_socket)(tmp));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Get a reference to the lowest layer.
+ /**
+ * This function returns a reference to the lowest layer in a stack of
+ * layers. Since a basic_socket cannot contain any further layers, it simply
+ * returns a reference to itself.
+ *
+ * @return A reference to the lowest layer in the stack of layers. Ownership
+ * is not transferred to the caller.
+ */
+ lowest_layer_type& lowest_layer()
+ {
+ return *this;
+ }
+
+ /// Get a const reference to the lowest layer.
+ /**
+ * This function returns a const reference to the lowest layer in a stack of
+ * layers. Since a basic_socket cannot contain any further layers, it simply
+ * returns a reference to itself.
+ *
+ * @return A const reference to the lowest layer in the stack of layers.
+ * Ownership is not transferred to the caller.
+ */
+ const lowest_layer_type& lowest_layer() const
+ {
+ return *this;
+ }
+
+ /// Open the socket using the specified protocol.
+ /**
+ * This function opens the socket so that it will use the specified protocol.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * socket.open(boost::asio::ip::tcp::v4());
+ * @endcode
+ */
+ void open(const protocol_type& protocol = protocol_type())
+ {
+ boost::system::error_code ec;
+ this->get_service().open(this->get_implementation(), protocol, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ }
+
+ /// Open the socket using the specified protocol.
+ /**
+ * This function opens the socket so that it will use the specified protocol.
+ *
+ * @param protocol An object specifying which protocol is to be used.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * boost::system::error_code ec;
+ * socket.open(boost::asio::ip::tcp::v4(), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ boost::system::error_code open(const protocol_type& protocol,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().open(this->get_implementation(), protocol, ec);
+ }
+
+ /// Assign an existing native socket to the socket.
+ /*
+ * This function opens the socket to hold an existing native socket.
+ *
+ * @param protocol An object specifying which protocol is to be used.
+ *
+ * @param native_socket A native socket.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void assign(const protocol_type& protocol,
+ const native_handle_type& native_socket)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(),
+ protocol, native_socket, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+ /// Assign an existing native socket to the socket.
+ /*
+ * This function opens the socket to hold an existing native socket.
+ *
+ * @param protocol An object specifying which protocol is to be used.
+ *
+ * @param native_socket A native socket.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code assign(const protocol_type& protocol,
+ const native_handle_type& native_socket, boost::system::error_code& ec)
+ {
+ return this->get_service().assign(this->get_implementation(),
+ protocol, native_socket, ec);
+ }
+
+ /// Determine whether the socket is open.
+ bool is_open() const
+ {
+ return this->get_service().is_open(this->get_implementation());
+ }
+
+ /// Close the socket.
+ /**
+ * This function is used to close the socket. Any asynchronous send, receive
+ * or connect operations will be cancelled immediately, and will complete
+ * with the boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure. Note that, even if
+ * the function indicates an error, the underlying descriptor is closed.
+ *
+ * @note For portable behaviour with respect to graceful closure of a
+ * connected socket, call shutdown() before closing the socket.
+ */
+ void close()
+ {
+ boost::system::error_code ec;
+ this->get_service().close(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "close");
+ }
+
+ /// Close the socket.
+ /**
+ * This function is used to close the socket. Any asynchronous send, receive
+ * or connect operations will be cancelled immediately, and will complete
+ * with the boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any. Note that, even if
+ * the function indicates an error, the underlying descriptor is closed.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::system::error_code ec;
+ * socket.close(ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ *
+ * @note For portable behaviour with respect to graceful closure of a
+ * connected socket, call shutdown() before closing the socket.
+ */
+ boost::system::error_code close(boost::system::error_code& ec)
+ {
+ return this->get_service().close(this->get_implementation(), ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native socket representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * socket. This is intended to allow access to native socket functionality
+ * that is not otherwise provided.
+ */
+ native_type native()
+ {
+ return this->get_service().native_handle(this->get_implementation());
+ }
+
+ /// Get the native socket representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * socket. This is intended to allow access to native socket functionality
+ * that is not otherwise provided.
+ */
+ native_handle_type native_handle()
+ {
+ return this->get_service().native_handle(this->get_implementation());
+ }
+
+ /// Cancel all asynchronous operations associated with the socket.
+ /**
+ * This function causes all outstanding asynchronous connect, send and receive
+ * operations to finish immediately, and the handlers for cancelled operations
+ * will be passed the boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls to cancel() will always fail with
+ * boost::asio::error::operation_not_supported when run on Windows XP, Windows
+ * Server 2003, and earlier versions of Windows, unless
+ * BOOST_ASIO_ENABLE_CANCELIO is defined. However, the CancelIo function has
+ * two issues that should be considered before enabling its use:
+ *
+ * @li It will only cancel asynchronous operations that were initiated in the
+ * current thread.
+ *
+ * @li It can appear to complete without error, but the request to cancel the
+ * unfinished operations may be silently ignored by the operating system.
+ * Whether it works or not seems to depend on the drivers that are installed.
+ *
+ * For portable cancellation, consider using one of the following
+ * alternatives:
+ *
+ * @li Disable asio's I/O completion port backend by defining
+ * BOOST_ASIO_DISABLE_IOCP.
+ *
+ * @li Use the close() function to simultaneously cancel the outstanding
+ * operations and close the socket.
+ *
+ * When running on Windows Vista, Windows Server 2008, and later, the
+ * CancelIoEx function is always used. This function does not have the
+ * problems described above.
+ */
+#if defined(BOOST_ASIO_MSVC) && (BOOST_ASIO_MSVC >= 1400) \
+ && (!defined(_WIN32_WINNT) || _WIN32_WINNT < 0x0600) \
+ && !defined(BOOST_ASIO_ENABLE_CANCELIO)
+ __declspec(deprecated("By default, this function always fails with "
+ "operation_not_supported when used on Windows XP, Windows Server 2003, "
+ "or earlier. Consult documentation for details."))
+#endif
+ void cancel()
+ {
+ boost::system::error_code ec;
+ this->get_service().cancel(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "cancel");
+ }
+
+ /// Cancel all asynchronous operations associated with the socket.
+ /**
+ * This function causes all outstanding asynchronous connect, send and receive
+ * operations to finish immediately, and the handlers for cancelled operations
+ * will be passed the boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls to cancel() will always fail with
+ * boost::asio::error::operation_not_supported when run on Windows XP, Windows
+ * Server 2003, and earlier versions of Windows, unless
+ * BOOST_ASIO_ENABLE_CANCELIO is defined. However, the CancelIo function has
+ * two issues that should be considered before enabling its use:
+ *
+ * @li It will only cancel asynchronous operations that were initiated in the
+ * current thread.
+ *
+ * @li It can appear to complete without error, but the request to cancel the
+ * unfinished operations may be silently ignored by the operating system.
+ * Whether it works or not seems to depend on the drivers that are installed.
+ *
+ * For portable cancellation, consider using one of the following
+ * alternatives:
+ *
+ * @li Disable asio's I/O completion port backend by defining
+ * BOOST_ASIO_DISABLE_IOCP.
+ *
+ * @li Use the close() function to simultaneously cancel the outstanding
+ * operations and close the socket.
+ *
+ * When running on Windows Vista, Windows Server 2008, and later, the
+ * CancelIoEx function is always used. This function does not have the
+ * problems described above.
+ */
+#if defined(BOOST_ASIO_MSVC) && (BOOST_ASIO_MSVC >= 1400) \
+ && (!defined(_WIN32_WINNT) || _WIN32_WINNT < 0x0600) \
+ && !defined(BOOST_ASIO_ENABLE_CANCELIO)
+ __declspec(deprecated("By default, this function always fails with "
+ "operation_not_supported when used on Windows XP, Windows Server 2003, "
+ "or earlier. Consult documentation for details."))
+#endif
+ boost::system::error_code cancel(boost::system::error_code& ec)
+ {
+ return this->get_service().cancel(this->get_implementation(), ec);
+ }
+
+ /// Determine whether the socket is at the out-of-band data mark.
+ /**
+ * This function is used to check whether the socket input is currently
+ * positioned at the out-of-band data mark.
+ *
+ * @return A bool indicating whether the socket is at the out-of-band data
+ * mark.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ bool at_mark() const
+ {
+ boost::system::error_code ec;
+ bool b = this->get_service().at_mark(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "at_mark");
+ return b;
+ }
+
+ /// Determine whether the socket is at the out-of-band data mark.
+ /**
+ * This function is used to check whether the socket input is currently
+ * positioned at the out-of-band data mark.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return A bool indicating whether the socket is at the out-of-band data
+ * mark.
+ */
+ bool at_mark(boost::system::error_code& ec) const
+ {
+ return this->get_service().at_mark(this->get_implementation(), ec);
+ }
+
+ /// Determine the number of bytes available for reading.
+ /**
+ * This function is used to determine the number of bytes that may be read
+ * without blocking.
+ *
+ * @return The number of bytes that may be read without blocking, or 0 if an
+ * error occurs.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ std::size_t available() const
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().available(
+ this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "available");
+ return s;
+ }
+
+ /// Determine the number of bytes available for reading.
+ /**
+ * This function is used to determine the number of bytes that may be read
+ * without blocking.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of bytes that may be read without blocking, or 0 if an
+ * error occurs.
+ */
+ std::size_t available(boost::system::error_code& ec) const
+ {
+ return this->get_service().available(this->get_implementation(), ec);
+ }
+
+ /// Bind the socket to the given local endpoint.
+ /**
+ * This function binds the socket to the specified endpoint on the local
+ * machine.
+ *
+ * @param endpoint An endpoint on the local machine to which the socket will
+ * be bound.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * socket.open(boost::asio::ip::tcp::v4());
+ * socket.bind(boost::asio::ip::tcp::endpoint(
+ * boost::asio::ip::tcp::v4(), 12345));
+ * @endcode
+ */
+ void bind(const endpoint_type& endpoint)
+ {
+ boost::system::error_code ec;
+ this->get_service().bind(this->get_implementation(), endpoint, ec);
+ boost::asio::detail::throw_error(ec, "bind");
+ }
+
+ /// Bind the socket to the given local endpoint.
+ /**
+ * This function binds the socket to the specified endpoint on the local
+ * machine.
+ *
+ * @param endpoint An endpoint on the local machine to which the socket will
+ * be bound.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * socket.open(boost::asio::ip::tcp::v4());
+ * boost::system::error_code ec;
+ * socket.bind(boost::asio::ip::tcp::endpoint(
+ * boost::asio::ip::tcp::v4(), 12345), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ boost::system::error_code bind(const endpoint_type& endpoint,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().bind(this->get_implementation(), endpoint, ec);
+ }
+
+ /// Connect the socket to the specified endpoint.
+ /**
+ * This function is used to connect a socket to the specified remote endpoint.
+ * The function call will block until the connection is successfully made or
+ * an error occurs.
+ *
+ * The socket is automatically opened if it is not already open. If the
+ * connect fails, and the socket was automatically opened, the socket is
+ * not returned to the closed state.
+ *
+ * @param peer_endpoint The remote endpoint to which the socket will be
+ * connected.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * boost::asio::ip::tcp::endpoint endpoint(
+ * boost::asio::ip::address::from_string("1.2.3.4"), 12345);
+ * socket.connect(endpoint);
+ * @endcode
+ */
+ void connect(const endpoint_type& peer_endpoint)
+ {
+ boost::system::error_code ec;
+ if (!is_open())
+ {
+ this->get_service().open(this->get_implementation(),
+ peer_endpoint.protocol(), ec);
+ boost::asio::detail::throw_error(ec, "connect");
+ }
+ this->get_service().connect(this->get_implementation(), peer_endpoint, ec);
+ boost::asio::detail::throw_error(ec, "connect");
+ }
+
+ /// Connect the socket to the specified endpoint.
+ /**
+ * This function is used to connect a socket to the specified remote endpoint.
+ * The function call will block until the connection is successfully made or
+ * an error occurs.
+ *
+ * The socket is automatically opened if it is not already open. If the
+ * connect fails, and the socket was automatically opened, the socket is
+ * not returned to the closed state.
+ *
+ * @param peer_endpoint The remote endpoint to which the socket will be
+ * connected.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * boost::asio::ip::tcp::endpoint endpoint(
+ * boost::asio::ip::address::from_string("1.2.3.4"), 12345);
+ * boost::system::error_code ec;
+ * socket.connect(endpoint, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ boost::system::error_code connect(const endpoint_type& peer_endpoint,
+ boost::system::error_code& ec)
+ {
+ if (!is_open())
+ {
+ if (this->get_service().open(this->get_implementation(),
+ peer_endpoint.protocol(), ec))
+ {
+ return ec;
+ }
+ }
+
+ return this->get_service().connect(
+ this->get_implementation(), peer_endpoint, ec);
+ }
+
+ /// Start an asynchronous connect.
+ /**
+ * This function is used to asynchronously connect a socket to the specified
+ * remote endpoint. The function call always returns immediately.
+ *
+ * The socket is automatically opened if it is not already open. If the
+ * connect fails, and the socket was automatically opened, the socket is
+ * not returned to the closed state.
+ *
+ * @param peer_endpoint The remote endpoint to which the socket will be
+ * connected. Copies will be made of the endpoint object as required.
+ *
+ * @param handler The handler to be called when the connection operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * @code
+ * void connect_handler(const boost::system::error_code& error)
+ * {
+ * if (!error)
+ * {
+ * // Connect succeeded.
+ * }
+ * }
+ *
+ * ...
+ *
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * boost::asio::ip::tcp::endpoint endpoint(
+ * boost::asio::ip::address::from_string("1.2.3.4"), 12345);
+ * socket.async_connect(endpoint, connect_handler);
+ * @endcode
+ */
+ template <typename ConnectHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ConnectHandler,
+ void (boost::system::error_code))
+ async_connect(const endpoint_type& peer_endpoint,
+ BOOST_ASIO_MOVE_ARG(ConnectHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ConnectHandler.
+ BOOST_ASIO_CONNECT_HANDLER_CHECK(ConnectHandler, handler) type_check;
+
+ if (!is_open())
+ {
+ boost::system::error_code ec;
+ const protocol_type protocol = peer_endpoint.protocol();
+ if (this->get_service().open(this->get_implementation(), protocol, ec))
+ {
+ detail::async_result_init<
+ ConnectHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(ConnectHandler)(handler));
+
+ this->get_io_service().post(
+ boost::asio::detail::bind_handler(
+ BOOST_ASIO_MOVE_CAST(BOOST_ASIO_HANDLER_TYPE(
+ ConnectHandler, void (boost::system::error_code)))(
+ init.handler), ec));
+
+ return init.result.get();
+ }
+ }
+
+ return this->get_service().async_connect(this->get_implementation(),
+ peer_endpoint, BOOST_ASIO_MOVE_CAST(ConnectHandler)(handler));
+ }
+
+ /// Set an option on the socket.
+ /**
+ * This function is used to set an option on the socket.
+ *
+ * @param option The new option value to be set on the socket.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa SettableSocketOption @n
+ * boost::asio::socket_base::broadcast @n
+ * boost::asio::socket_base::do_not_route @n
+ * boost::asio::socket_base::keep_alive @n
+ * boost::asio::socket_base::linger @n
+ * boost::asio::socket_base::receive_buffer_size @n
+ * boost::asio::socket_base::receive_low_watermark @n
+ * boost::asio::socket_base::reuse_address @n
+ * boost::asio::socket_base::send_buffer_size @n
+ * boost::asio::socket_base::send_low_watermark @n
+ * boost::asio::ip::multicast::join_group @n
+ * boost::asio::ip::multicast::leave_group @n
+ * boost::asio::ip::multicast::enable_loopback @n
+ * boost::asio::ip::multicast::outbound_interface @n
+ * boost::asio::ip::multicast::hops @n
+ * boost::asio::ip::tcp::no_delay
+ *
+ * @par Example
+ * Setting the IPPROTO_TCP/TCP_NODELAY option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::no_delay option(true);
+ * socket.set_option(option);
+ * @endcode
+ */
+ template <typename SettableSocketOption>
+ void set_option(const SettableSocketOption& option)
+ {
+ boost::system::error_code ec;
+ this->get_service().set_option(this->get_implementation(), option, ec);
+ boost::asio::detail::throw_error(ec, "set_option");
+ }
+
+ /// Set an option on the socket.
+ /**
+ * This function is used to set an option on the socket.
+ *
+ * @param option The new option value to be set on the socket.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @sa SettableSocketOption @n
+ * boost::asio::socket_base::broadcast @n
+ * boost::asio::socket_base::do_not_route @n
+ * boost::asio::socket_base::keep_alive @n
+ * boost::asio::socket_base::linger @n
+ * boost::asio::socket_base::receive_buffer_size @n
+ * boost::asio::socket_base::receive_low_watermark @n
+ * boost::asio::socket_base::reuse_address @n
+ * boost::asio::socket_base::send_buffer_size @n
+ * boost::asio::socket_base::send_low_watermark @n
+ * boost::asio::ip::multicast::join_group @n
+ * boost::asio::ip::multicast::leave_group @n
+ * boost::asio::ip::multicast::enable_loopback @n
+ * boost::asio::ip::multicast::outbound_interface @n
+ * boost::asio::ip::multicast::hops @n
+ * boost::asio::ip::tcp::no_delay
+ *
+ * @par Example
+ * Setting the IPPROTO_TCP/TCP_NODELAY option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::no_delay option(true);
+ * boost::system::error_code ec;
+ * socket.set_option(option, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ template <typename SettableSocketOption>
+ boost::system::error_code set_option(const SettableSocketOption& option,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().set_option(
+ this->get_implementation(), option, ec);
+ }
+
+ /// Get an option from the socket.
+ /**
+ * This function is used to get the current value of an option on the socket.
+ *
+ * @param option The option value to be obtained from the socket.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa GettableSocketOption @n
+ * boost::asio::socket_base::broadcast @n
+ * boost::asio::socket_base::do_not_route @n
+ * boost::asio::socket_base::keep_alive @n
+ * boost::asio::socket_base::linger @n
+ * boost::asio::socket_base::receive_buffer_size @n
+ * boost::asio::socket_base::receive_low_watermark @n
+ * boost::asio::socket_base::reuse_address @n
+ * boost::asio::socket_base::send_buffer_size @n
+ * boost::asio::socket_base::send_low_watermark @n
+ * boost::asio::ip::multicast::join_group @n
+ * boost::asio::ip::multicast::leave_group @n
+ * boost::asio::ip::multicast::enable_loopback @n
+ * boost::asio::ip::multicast::outbound_interface @n
+ * boost::asio::ip::multicast::hops @n
+ * boost::asio::ip::tcp::no_delay
+ *
+ * @par Example
+ * Getting the value of the SOL_SOCKET/SO_KEEPALIVE option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::socket::keep_alive option;
+ * socket.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ */
+ template <typename GettableSocketOption>
+ void get_option(GettableSocketOption& option) const
+ {
+ boost::system::error_code ec;
+ this->get_service().get_option(this->get_implementation(), option, ec);
+ boost::asio::detail::throw_error(ec, "get_option");
+ }
+
+ /// Get an option from the socket.
+ /**
+ * This function is used to get the current value of an option on the socket.
+ *
+ * @param option The option value to be obtained from the socket.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @sa GettableSocketOption @n
+ * boost::asio::socket_base::broadcast @n
+ * boost::asio::socket_base::do_not_route @n
+ * boost::asio::socket_base::keep_alive @n
+ * boost::asio::socket_base::linger @n
+ * boost::asio::socket_base::receive_buffer_size @n
+ * boost::asio::socket_base::receive_low_watermark @n
+ * boost::asio::socket_base::reuse_address @n
+ * boost::asio::socket_base::send_buffer_size @n
+ * boost::asio::socket_base::send_low_watermark @n
+ * boost::asio::ip::multicast::join_group @n
+ * boost::asio::ip::multicast::leave_group @n
+ * boost::asio::ip::multicast::enable_loopback @n
+ * boost::asio::ip::multicast::outbound_interface @n
+ * boost::asio::ip::multicast::hops @n
+ * boost::asio::ip::tcp::no_delay
+ *
+ * @par Example
+ * Getting the value of the SOL_SOCKET/SO_KEEPALIVE option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::socket::keep_alive option;
+ * boost::system::error_code ec;
+ * socket.get_option(option, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * bool is_set = option.value();
+ * @endcode
+ */
+ template <typename GettableSocketOption>
+ boost::system::error_code get_option(GettableSocketOption& option,
+ boost::system::error_code& ec) const
+ {
+ return this->get_service().get_option(
+ this->get_implementation(), option, ec);
+ }
+
+ /// Perform an IO control command on the socket.
+ /**
+ * This function is used to execute an IO control command on the socket.
+ *
+ * @param command The IO control command to be performed on the socket.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa IoControlCommand @n
+ * boost::asio::socket_base::bytes_readable @n
+ * boost::asio::socket_base::non_blocking_io
+ *
+ * @par Example
+ * Getting the number of bytes ready to read:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::socket::bytes_readable command;
+ * socket.io_control(command);
+ * std::size_t bytes_readable = command.get();
+ * @endcode
+ */
+ template <typename IoControlCommand>
+ void io_control(IoControlCommand& command)
+ {
+ boost::system::error_code ec;
+ this->get_service().io_control(this->get_implementation(), command, ec);
+ boost::asio::detail::throw_error(ec, "io_control");
+ }
+
+ /// Perform an IO control command on the socket.
+ /**
+ * This function is used to execute an IO control command on the socket.
+ *
+ * @param command The IO control command to be performed on the socket.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @sa IoControlCommand @n
+ * boost::asio::socket_base::bytes_readable @n
+ * boost::asio::socket_base::non_blocking_io
+ *
+ * @par Example
+ * Getting the number of bytes ready to read:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::socket::bytes_readable command;
+ * boost::system::error_code ec;
+ * socket.io_control(command, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * std::size_t bytes_readable = command.get();
+ * @endcode
+ */
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(IoControlCommand& command,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().io_control(
+ this->get_implementation(), command, ec);
+ }
+
+ /// Gets the non-blocking mode of the socket.
+ /**
+ * @returns @c true if the socket's synchronous operations will fail with
+ * boost::asio::error::would_block if they are unable to perform the requested
+ * operation immediately. If @c false, synchronous operations will block
+ * until complete.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ bool non_blocking() const
+ {
+ return this->get_service().non_blocking(this->get_implementation());
+ }
+
+ /// Sets the non-blocking mode of the socket.
+ /**
+ * @param mode If @c true, the socket's synchronous operations will fail with
+ * boost::asio::error::would_block if they are unable to perform the requested
+ * operation immediately. If @c false, synchronous operations will block
+ * until complete.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ void non_blocking(bool mode)
+ {
+ boost::system::error_code ec;
+ this->get_service().non_blocking(this->get_implementation(), mode, ec);
+ boost::asio::detail::throw_error(ec, "non_blocking");
+ }
+
+ /// Sets the non-blocking mode of the socket.
+ /**
+ * @param mode If @c true, the socket's synchronous operations will fail with
+ * boost::asio::error::would_block if they are unable to perform the requested
+ * operation immediately. If @c false, synchronous operations will block
+ * until complete.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ boost::system::error_code non_blocking(
+ bool mode, boost::system::error_code& ec)
+ {
+ return this->get_service().non_blocking(
+ this->get_implementation(), mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native socket implementation.
+ /**
+ * This function is used to retrieve the non-blocking mode of the underlying
+ * native socket. This mode has no effect on the behaviour of the socket
+ * object's synchronous operations.
+ *
+ * @returns @c true if the underlying socket is in non-blocking mode and
+ * direct system calls may fail with boost::asio::error::would_block (or the
+ * equivalent system error).
+ *
+ * @note The current non-blocking mode is cached by the socket object.
+ * Consequently, the return value may be incorrect if the non-blocking mode
+ * was set directly on the native socket.
+ *
+ * @par Example
+ * This function is intended to allow the encapsulation of arbitrary
+ * non-blocking system calls as asynchronous operations, in a way that is
+ * transparent to the user of the socket object. The following example
+ * illustrates how Linux's @c sendfile system call might be encapsulated:
+ * @code template <typename Handler>
+ * struct sendfile_op
+ * {
+ * tcp::socket& sock_;
+ * int fd_;
+ * Handler handler_;
+ * off_t offset_;
+ * std::size_t total_bytes_transferred_;
+ *
+ * // Function call operator meeting WriteHandler requirements.
+ * // Used as the handler for the async_write_some operation.
+ * void operator()(boost::system::error_code ec, std::size_t)
+ * {
+ * // Put the underlying socket into non-blocking mode.
+ * if (!ec)
+ * if (!sock_.native_non_blocking())
+ * sock_.native_non_blocking(true, ec);
+ *
+ * if (!ec)
+ * {
+ * for (;;)
+ * {
+ * // Try the system call.
+ * errno = 0;
+ * int n = ::sendfile(sock_.native_handle(), fd_, &offset_, 65536);
+ * ec = boost::system::error_code(n < 0 ? errno : 0,
+ * boost::asio::error::get_system_category());
+ * total_bytes_transferred_ += ec ? 0 : n;
+ *
+ * // Retry operation immediately if interrupted by signal.
+ * if (ec == boost::asio::error::interrupted)
+ * continue;
+ *
+ * // Check if we need to run the operation again.
+ * if (ec == boost::asio::error::would_block
+ * || ec == boost::asio::error::try_again)
+ * {
+ * // We have to wait for the socket to become ready again.
+ * sock_.async_write_some(boost::asio::null_buffers(), *this);
+ * return;
+ * }
+ *
+ * if (ec || n == 0)
+ * {
+ * // An error occurred, or we have reached the end of the file.
+ * // Either way we must exit the loop so we can call the handler.
+ * break;
+ * }
+ *
+ * // Loop around to try calling sendfile again.
+ * }
+ * }
+ *
+ * // Pass result back to user's handler.
+ * handler_(ec, total_bytes_transferred_);
+ * }
+ * };
+ *
+ * template <typename Handler>
+ * void async_sendfile(tcp::socket& sock, int fd, Handler h)
+ * {
+ * sendfile_op<Handler> op = { sock, fd, h, 0, 0 };
+ * sock.async_write_some(boost::asio::null_buffers(), op);
+ * } @endcode
+ */
+ bool native_non_blocking() const
+ {
+ return this->get_service().native_non_blocking(this->get_implementation());
+ }
+
+ /// Sets the non-blocking mode of the native socket implementation.
+ /**
+ * This function is used to modify the non-blocking mode of the underlying
+ * native socket. It has no effect on the behaviour of the socket object's
+ * synchronous operations.
+ *
+ * @param mode If @c true, the underlying socket is put into non-blocking
+ * mode and direct system calls may fail with boost::asio::error::would_block
+ * (or the equivalent system error).
+ *
+ * @throws boost::system::system_error Thrown on failure. If the @c mode is
+ * @c false, but the current value of @c non_blocking() is @c true, this
+ * function fails with boost::asio::error::invalid_argument, as the
+ * combination does not make sense.
+ *
+ * @par Example
+ * This function is intended to allow the encapsulation of arbitrary
+ * non-blocking system calls as asynchronous operations, in a way that is
+ * transparent to the user of the socket object. The following example
+ * illustrates how Linux's @c sendfile system call might be encapsulated:
+ * @code template <typename Handler>
+ * struct sendfile_op
+ * {
+ * tcp::socket& sock_;
+ * int fd_;
+ * Handler handler_;
+ * off_t offset_;
+ * std::size_t total_bytes_transferred_;
+ *
+ * // Function call operator meeting WriteHandler requirements.
+ * // Used as the handler for the async_write_some operation.
+ * void operator()(boost::system::error_code ec, std::size_t)
+ * {
+ * // Put the underlying socket into non-blocking mode.
+ * if (!ec)
+ * if (!sock_.native_non_blocking())
+ * sock_.native_non_blocking(true, ec);
+ *
+ * if (!ec)
+ * {
+ * for (;;)
+ * {
+ * // Try the system call.
+ * errno = 0;
+ * int n = ::sendfile(sock_.native_handle(), fd_, &offset_, 65536);
+ * ec = boost::system::error_code(n < 0 ? errno : 0,
+ * boost::asio::error::get_system_category());
+ * total_bytes_transferred_ += ec ? 0 : n;
+ *
+ * // Retry operation immediately if interrupted by signal.
+ * if (ec == boost::asio::error::interrupted)
+ * continue;
+ *
+ * // Check if we need to run the operation again.
+ * if (ec == boost::asio::error::would_block
+ * || ec == boost::asio::error::try_again)
+ * {
+ * // We have to wait for the socket to become ready again.
+ * sock_.async_write_some(boost::asio::null_buffers(), *this);
+ * return;
+ * }
+ *
+ * if (ec || n == 0)
+ * {
+ * // An error occurred, or we have reached the end of the file.
+ * // Either way we must exit the loop so we can call the handler.
+ * break;
+ * }
+ *
+ * // Loop around to try calling sendfile again.
+ * }
+ * }
+ *
+ * // Pass result back to user's handler.
+ * handler_(ec, total_bytes_transferred_);
+ * }
+ * };
+ *
+ * template <typename Handler>
+ * void async_sendfile(tcp::socket& sock, int fd, Handler h)
+ * {
+ * sendfile_op<Handler> op = { sock, fd, h, 0, 0 };
+ * sock.async_write_some(boost::asio::null_buffers(), op);
+ * } @endcode
+ */
+ void native_non_blocking(bool mode)
+ {
+ boost::system::error_code ec;
+ this->get_service().native_non_blocking(
+ this->get_implementation(), mode, ec);
+ boost::asio::detail::throw_error(ec, "native_non_blocking");
+ }
+
+ /// Sets the non-blocking mode of the native socket implementation.
+ /**
+ * This function is used to modify the non-blocking mode of the underlying
+ * native socket. It has no effect on the behaviour of the socket object's
+ * synchronous operations.
+ *
+ * @param mode If @c true, the underlying socket is put into non-blocking
+ * mode and direct system calls may fail with boost::asio::error::would_block
+ * (or the equivalent system error).
+ *
+ * @param ec Set to indicate what error occurred, if any. If the @c mode is
+ * @c false, but the current value of @c non_blocking() is @c true, this
+ * function fails with boost::asio::error::invalid_argument, as the
+ * combination does not make sense.
+ *
+ * @par Example
+ * This function is intended to allow the encapsulation of arbitrary
+ * non-blocking system calls as asynchronous operations, in a way that is
+ * transparent to the user of the socket object. The following example
+ * illustrates how Linux's @c sendfile system call might be encapsulated:
+ * @code template <typename Handler>
+ * struct sendfile_op
+ * {
+ * tcp::socket& sock_;
+ * int fd_;
+ * Handler handler_;
+ * off_t offset_;
+ * std::size_t total_bytes_transferred_;
+ *
+ * // Function call operator meeting WriteHandler requirements.
+ * // Used as the handler for the async_write_some operation.
+ * void operator()(boost::system::error_code ec, std::size_t)
+ * {
+ * // Put the underlying socket into non-blocking mode.
+ * if (!ec)
+ * if (!sock_.native_non_blocking())
+ * sock_.native_non_blocking(true, ec);
+ *
+ * if (!ec)
+ * {
+ * for (;;)
+ * {
+ * // Try the system call.
+ * errno = 0;
+ * int n = ::sendfile(sock_.native_handle(), fd_, &offset_, 65536);
+ * ec = boost::system::error_code(n < 0 ? errno : 0,
+ * boost::asio::error::get_system_category());
+ * total_bytes_transferred_ += ec ? 0 : n;
+ *
+ * // Retry operation immediately if interrupted by signal.
+ * if (ec == boost::asio::error::interrupted)
+ * continue;
+ *
+ * // Check if we need to run the operation again.
+ * if (ec == boost::asio::error::would_block
+ * || ec == boost::asio::error::try_again)
+ * {
+ * // We have to wait for the socket to become ready again.
+ * sock_.async_write_some(boost::asio::null_buffers(), *this);
+ * return;
+ * }
+ *
+ * if (ec || n == 0)
+ * {
+ * // An error occurred, or we have reached the end of the file.
+ * // Either way we must exit the loop so we can call the handler.
+ * break;
+ * }
+ *
+ * // Loop around to try calling sendfile again.
+ * }
+ * }
+ *
+ * // Pass result back to user's handler.
+ * handler_(ec, total_bytes_transferred_);
+ * }
+ * };
+ *
+ * template <typename Handler>
+ * void async_sendfile(tcp::socket& sock, int fd, Handler h)
+ * {
+ * sendfile_op<Handler> op = { sock, fd, h, 0, 0 };
+ * sock.async_write_some(boost::asio::null_buffers(), op);
+ * } @endcode
+ */
+ boost::system::error_code native_non_blocking(
+ bool mode, boost::system::error_code& ec)
+ {
+ return this->get_service().native_non_blocking(
+ this->get_implementation(), mode, ec);
+ }
+
+ /// Get the local endpoint of the socket.
+ /**
+ * This function is used to obtain the locally bound endpoint of the socket.
+ *
+ * @returns An object that represents the local endpoint of the socket.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::endpoint endpoint = socket.local_endpoint();
+ * @endcode
+ */
+ endpoint_type local_endpoint() const
+ {
+ boost::system::error_code ec;
+ endpoint_type ep = this->get_service().local_endpoint(
+ this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "local_endpoint");
+ return ep;
+ }
+
+ /// Get the local endpoint of the socket.
+ /**
+ * This function is used to obtain the locally bound endpoint of the socket.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns An object that represents the local endpoint of the socket.
+ * Returns a default-constructed endpoint object if an error occurred.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::system::error_code ec;
+ * boost::asio::ip::tcp::endpoint endpoint = socket.local_endpoint(ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ endpoint_type local_endpoint(boost::system::error_code& ec) const
+ {
+ return this->get_service().local_endpoint(this->get_implementation(), ec);
+ }
+
+ /// Get the remote endpoint of the socket.
+ /**
+ * This function is used to obtain the remote endpoint of the socket.
+ *
+ * @returns An object that represents the remote endpoint of the socket.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::endpoint endpoint = socket.remote_endpoint();
+ * @endcode
+ */
+ endpoint_type remote_endpoint() const
+ {
+ boost::system::error_code ec;
+ endpoint_type ep = this->get_service().remote_endpoint(
+ this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "remote_endpoint");
+ return ep;
+ }
+
+ /// Get the remote endpoint of the socket.
+ /**
+ * This function is used to obtain the remote endpoint of the socket.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns An object that represents the remote endpoint of the socket.
+ * Returns a default-constructed endpoint object if an error occurred.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::system::error_code ec;
+ * boost::asio::ip::tcp::endpoint endpoint = socket.remote_endpoint(ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ endpoint_type remote_endpoint(boost::system::error_code& ec) const
+ {
+ return this->get_service().remote_endpoint(this->get_implementation(), ec);
+ }
+
+ /// Disable sends or receives on the socket.
+ /**
+ * This function is used to disable send operations, receive operations, or
+ * both.
+ *
+ * @param what Determines what types of operation will no longer be allowed.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * Shutting down the send side of the socket:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * socket.shutdown(boost::asio::ip::tcp::socket::shutdown_send);
+ * @endcode
+ */
+ void shutdown(shutdown_type what)
+ {
+ boost::system::error_code ec;
+ this->get_service().shutdown(this->get_implementation(), what, ec);
+ boost::asio::detail::throw_error(ec, "shutdown");
+ }
+
+ /// Disable sends or receives on the socket.
+ /**
+ * This function is used to disable send operations, receive operations, or
+ * both.
+ *
+ * @param what Determines what types of operation will no longer be allowed.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * Shutting down the send side of the socket:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::system::error_code ec;
+ * socket.shutdown(boost::asio::ip::tcp::socket::shutdown_send, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ boost::system::error_code shutdown(shutdown_type what,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().shutdown(this->get_implementation(), what, ec);
+ }
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~basic_socket()
+ {
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_SOCKET_HPP
diff --git a/ext/patches/boost/asio/basic_socket_acceptor.hpp b/ext/patches/boost/asio/basic_socket_acceptor.hpp
new file mode 100644
index 0000000..624f36c
--- /dev/null
+++ b/ext/patches/boost/asio/basic_socket_acceptor.hpp
@@ -0,0 +1,1138 @@
+//
+// basic_socket_acceptor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_SOCKET_ACCEPTOR_HPP
+#define BOOST_ASIO_BASIC_SOCKET_ACCEPTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/socket_acceptor_service.hpp>
+#include <boost/asio/socket_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides the ability to accept new connections.
+/**
+ * The basic_socket_acceptor class template is used for accepting new socket
+ * connections.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Example
+ * Opening a socket acceptor with the SO_REUSEADDR option enabled:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * boost::asio::ip::tcp::endpoint endpoint(boost::asio::ip::tcp::v4(), port);
+ * acceptor.open(endpoint.protocol());
+ * acceptor.set_option(boost::asio::ip::tcp::acceptor::reuse_address(true));
+ * acceptor.bind(endpoint);
+ * acceptor.listen();
+ * @endcode
+ */
+template <typename Protocol,
+ typename SocketAcceptorService = socket_acceptor_service<Protocol> >
+class basic_socket_acceptor
+ : public basic_io_object<SocketAcceptorService>,
+ public socket_base
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of an
+ /// acceptor.
+ typedef typename SocketAcceptorService::native_handle_type native_type;
+
+ /// The native representation of an acceptor.
+ typedef typename SocketAcceptorService::native_handle_type native_handle_type;
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ /// Construct an acceptor without opening it.
+ /**
+ * This constructor creates an acceptor without opening it to listen for new
+ * connections. The open() function must be called before the acceptor can
+ * accept new socket connections.
+ *
+ * @param io_service The io_service object that the acceptor will use to
+ * dispatch handlers for any asynchronous operations performed on the
+ * acceptor.
+ */
+ explicit basic_socket_acceptor(boost::asio::io_service& io_service)
+ : basic_io_object<SocketAcceptorService>(io_service)
+ {
+ }
+
+ /// Construct an open acceptor.
+ /**
+ * This constructor creates an acceptor and automatically opens it.
+ *
+ * @param io_service The io_service object that the acceptor will use to
+ * dispatch handlers for any asynchronous operations performed on the
+ * acceptor.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_socket_acceptor(boost::asio::io_service& io_service,
+ const protocol_type& protocol)
+ : basic_io_object<SocketAcceptorService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().open(this->get_implementation(), protocol, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ }
+
+ /// Construct an acceptor opened on the given endpoint.
+ /**
+ * This constructor creates an acceptor and automatically opens it to listen
+ * for new connections on the specified endpoint.
+ *
+ * @param io_service The io_service object that the acceptor will use to
+ * dispatch handlers for any asynchronous operations performed on the
+ * acceptor.
+ *
+ * @param endpoint An endpoint on the local machine on which the acceptor
+ * will listen for new connections.
+ *
+ * @param reuse_addr Whether the constructor should set the socket option
+ * socket_base::reuse_address.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note This constructor is equivalent to the following code:
+ * @code
+ * basic_socket_acceptor<Protocol> acceptor(io_service);
+ * acceptor.open(endpoint.protocol());
+ * if (reuse_addr)
+ * acceptor.set_option(socket_base::reuse_address(true));
+ * acceptor.bind(endpoint);
+ * acceptor.listen(listen_backlog);
+ * @endcode
+ */
+ basic_socket_acceptor(boost::asio::io_service& io_service,
+ const endpoint_type& endpoint, bool reuse_addr = true)
+ : basic_io_object<SocketAcceptorService>(io_service)
+ {
+ boost::system::error_code ec;
+ const protocol_type protocol = endpoint.protocol();
+ this->get_service().open(this->get_implementation(), protocol, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ if (reuse_addr)
+ {
+ this->get_service().set_option(this->get_implementation(),
+ socket_base::reuse_address(true), ec);
+ boost::asio::detail::throw_error(ec, "set_option");
+ }
+ this->get_service().bind(this->get_implementation(), endpoint, ec);
+ boost::asio::detail::throw_error(ec, "bind");
+ this->get_service().listen(this->get_implementation(),
+ socket_base::max_connections, ec);
+ boost::asio::detail::throw_error(ec, "listen");
+ }
+
+ /// Construct a basic_socket_acceptor on an existing native acceptor.
+ /**
+ * This constructor creates an acceptor object to hold an existing native
+ * acceptor.
+ *
+ * @param io_service The io_service object that the acceptor will use to
+ * dispatch handlers for any asynchronous operations performed on the
+ * acceptor.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @param native_acceptor A native acceptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_socket_acceptor(boost::asio::io_service& io_service,
+ const protocol_type& protocol, const native_handle_type& native_acceptor)
+ : basic_io_object<SocketAcceptorService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(),
+ protocol, native_acceptor, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_socket_acceptor from another.
+ /**
+ * This constructor moves an acceptor from one object to another.
+ *
+ * @param other The other basic_socket_acceptor object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_socket_acceptor(io_service&) constructor.
+ */
+ basic_socket_acceptor(basic_socket_acceptor&& other)
+ : basic_io_object<SocketAcceptorService>(
+ BOOST_ASIO_MOVE_CAST(basic_socket_acceptor)(other))
+ {
+ }
+
+ /// Move-assign a basic_socket_acceptor from another.
+ /**
+ * This assignment operator moves an acceptor from one object to another.
+ *
+ * @param other The other basic_socket_acceptor object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_socket_acceptor(io_service&) constructor.
+ */
+ basic_socket_acceptor& operator=(basic_socket_acceptor&& other)
+ {
+ basic_io_object<SocketAcceptorService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_socket_acceptor)(other));
+ return *this;
+ }
+
+ // All socket acceptors have access to each other's implementations.
+ template <typename Protocol1, typename SocketAcceptorService1>
+ friend class basic_socket_acceptor;
+
+ /// Move-construct a basic_socket_acceptor from an acceptor of another
+ /// protocol type.
+ /**
+ * This constructor moves an acceptor from one object to another.
+ *
+ * @param other The other basic_socket_acceptor object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename SocketAcceptorService1>
+ basic_socket_acceptor(
+ basic_socket_acceptor<Protocol1, SocketAcceptorService1>&& other,
+ typename enable_if<is_convertible<Protocol1, Protocol>::value>::type* = 0)
+ : basic_io_object<SocketAcceptorService>(other.get_io_service())
+ {
+ this->get_service().template converting_move_construct<Protocol1>(
+ this->get_implementation(), other.get_implementation());
+ }
+
+ /// Move-assign a basic_socket_acceptor from an acceptor of another protocol
+ /// type.
+ /**
+ * This assignment operator moves an acceptor from one object to another.
+ *
+ * @param other The other basic_socket_acceptor object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename SocketAcceptorService1>
+ typename enable_if<is_convertible<Protocol1, Protocol>::value,
+ basic_socket_acceptor>::type& operator=(
+ basic_socket_acceptor<Protocol1, SocketAcceptorService1>&& other)
+ {
+ basic_socket_acceptor tmp(BOOST_ASIO_MOVE_CAST2(basic_socket_acceptor<
+ Protocol1, SocketAcceptorService1>)(other));
+ basic_io_object<SocketAcceptorService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_socket_acceptor)(tmp));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Open the acceptor using the specified protocol.
+ /**
+ * This function opens the socket acceptor so that it will use the specified
+ * protocol.
+ *
+ * @param protocol An object specifying which protocol is to be used.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * acceptor.open(boost::asio::ip::tcp::v4());
+ * @endcode
+ */
+ void open(const protocol_type& protocol = protocol_type())
+ {
+ boost::system::error_code ec;
+ this->get_service().open(this->get_implementation(), protocol, ec);
+ boost::asio::detail::throw_error(ec, "open");
+ }
+
+ /// Open the acceptor using the specified protocol.
+ /**
+ * This function opens the socket acceptor so that it will use the specified
+ * protocol.
+ *
+ * @param protocol An object specifying which protocol is to be used.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * boost::system::error_code ec;
+ * acceptor.open(boost::asio::ip::tcp::v4(), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ boost::system::error_code open(const protocol_type& protocol,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().open(this->get_implementation(), protocol, ec);
+ }
+
+ /// Assigns an existing native acceptor to the acceptor.
+ /*
+ * This function opens the acceptor to hold an existing native acceptor.
+ *
+ * @param protocol An object specifying which protocol is to be used.
+ *
+ * @param native_acceptor A native acceptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void assign(const protocol_type& protocol,
+ const native_handle_type& native_acceptor)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(),
+ protocol, native_acceptor, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+ /// Assigns an existing native acceptor to the acceptor.
+ /*
+ * This function opens the acceptor to hold an existing native acceptor.
+ *
+ * @param protocol An object specifying which protocol is to be used.
+ *
+ * @param native_acceptor A native acceptor.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code assign(const protocol_type& protocol,
+ const native_handle_type& native_acceptor, boost::system::error_code& ec)
+ {
+ return this->get_service().assign(this->get_implementation(),
+ protocol, native_acceptor, ec);
+ }
+
+ /// Determine whether the acceptor is open.
+ bool is_open() const
+ {
+ return this->get_service().is_open(this->get_implementation());
+ }
+
+ /// Bind the acceptor to the given local endpoint.
+ /**
+ * This function binds the socket acceptor to the specified endpoint on the
+ * local machine.
+ *
+ * @param endpoint An endpoint on the local machine to which the socket
+ * acceptor will be bound.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * boost::asio::ip::tcp::endpoint endpoint(boost::asio::ip::tcp::v4(), 12345);
+ * acceptor.open(endpoint.protocol());
+ * acceptor.bind(endpoint);
+ * @endcode
+ */
+ void bind(const endpoint_type& endpoint)
+ {
+ boost::system::error_code ec;
+ this->get_service().bind(this->get_implementation(), endpoint, ec);
+ boost::asio::detail::throw_error(ec, "bind");
+ }
+
+ /// Bind the acceptor to the given local endpoint.
+ /**
+ * This function binds the socket acceptor to the specified endpoint on the
+ * local machine.
+ *
+ * @param endpoint An endpoint on the local machine to which the socket
+ * acceptor will be bound.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * boost::asio::ip::tcp::endpoint endpoint(boost::asio::ip::tcp::v4(), 12345);
+ * acceptor.open(endpoint.protocol());
+ * boost::system::error_code ec;
+ * acceptor.bind(endpoint, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ boost::system::error_code bind(const endpoint_type& endpoint,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().bind(this->get_implementation(), endpoint, ec);
+ }
+
+ /// Place the acceptor into the state where it will listen for new
+ /// connections.
+ /**
+ * This function puts the socket acceptor into the state where it may accept
+ * new connections.
+ *
+ * @param backlog The maximum length of the queue of pending connections.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void listen(int backlog = socket_base::max_connections)
+ {
+ boost::system::error_code ec;
+ this->get_service().listen(this->get_implementation(), backlog, ec);
+ boost::asio::detail::throw_error(ec, "listen");
+ }
+
+ /// Place the acceptor into the state where it will listen for new
+ /// connections.
+ /**
+ * This function puts the socket acceptor into the state where it may accept
+ * new connections.
+ *
+ * @param backlog The maximum length of the queue of pending connections.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::system::error_code ec;
+ * acceptor.listen(boost::asio::socket_base::max_connections, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ boost::system::error_code listen(int backlog, boost::system::error_code& ec)
+ {
+ return this->get_service().listen(this->get_implementation(), backlog, ec);
+ }
+
+ /// Close the acceptor.
+ /**
+ * This function is used to close the acceptor. Any asynchronous accept
+ * operations will be cancelled immediately.
+ *
+ * A subsequent call to open() is required before the acceptor can again be
+ * used to again perform socket accept operations.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void close()
+ {
+ boost::system::error_code ec;
+ this->get_service().close(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "close");
+ }
+
+ /// Close the acceptor.
+ /**
+ * This function is used to close the acceptor. Any asynchronous accept
+ * operations will be cancelled immediately.
+ *
+ * A subsequent call to open() is required before the acceptor can again be
+ * used to again perform socket accept operations.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::system::error_code ec;
+ * acceptor.close(ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ boost::system::error_code close(boost::system::error_code& ec)
+ {
+ return this->get_service().close(this->get_implementation(), ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native acceptor representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * acceptor. This is intended to allow access to native acceptor functionality
+ * that is not otherwise provided.
+ */
+ native_type native()
+ {
+ return this->get_service().native_handle(this->get_implementation());
+ }
+
+ /// Get the native acceptor representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * acceptor. This is intended to allow access to native acceptor functionality
+ * that is not otherwise provided.
+ */
+ native_handle_type native_handle()
+ {
+ return this->get_service().native_handle(this->get_implementation());
+ }
+
+ /// Cancel all asynchronous operations associated with the acceptor.
+ /**
+ * This function causes all outstanding asynchronous connect, send and receive
+ * operations to finish immediately, and the handlers for cancelled operations
+ * will be passed the boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void cancel()
+ {
+ boost::system::error_code ec;
+ this->get_service().cancel(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "cancel");
+ }
+
+ /// Cancel all asynchronous operations associated with the acceptor.
+ /**
+ * This function causes all outstanding asynchronous connect, send and receive
+ * operations to finish immediately, and the handlers for cancelled operations
+ * will be passed the boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code cancel(boost::system::error_code& ec)
+ {
+ return this->get_service().cancel(this->get_implementation(), ec);
+ }
+
+ /// Set an option on the acceptor.
+ /**
+ * This function is used to set an option on the acceptor.
+ *
+ * @param option The new option value to be set on the acceptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa SettableSocketOption @n
+ * boost::asio::socket_base::reuse_address
+ * boost::asio::socket_base::enable_connection_aborted
+ *
+ * @par Example
+ * Setting the SOL_SOCKET/SO_REUSEADDR option:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::acceptor::reuse_address option(true);
+ * acceptor.set_option(option);
+ * @endcode
+ */
+ template <typename SettableSocketOption>
+ void set_option(const SettableSocketOption& option)
+ {
+ boost::system::error_code ec;
+ this->get_service().set_option(this->get_implementation(), option, ec);
+ boost::asio::detail::throw_error(ec, "set_option");
+ }
+
+ /// Set an option on the acceptor.
+ /**
+ * This function is used to set an option on the acceptor.
+ *
+ * @param option The new option value to be set on the acceptor.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @sa SettableSocketOption @n
+ * boost::asio::socket_base::reuse_address
+ * boost::asio::socket_base::enable_connection_aborted
+ *
+ * @par Example
+ * Setting the SOL_SOCKET/SO_REUSEADDR option:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::acceptor::reuse_address option(true);
+ * boost::system::error_code ec;
+ * acceptor.set_option(option, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ template <typename SettableSocketOption>
+ boost::system::error_code set_option(const SettableSocketOption& option,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().set_option(
+ this->get_implementation(), option, ec);
+ }
+
+ /// Get an option from the acceptor.
+ /**
+ * This function is used to get the current value of an option on the
+ * acceptor.
+ *
+ * @param option The option value to be obtained from the acceptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa GettableSocketOption @n
+ * boost::asio::socket_base::reuse_address
+ *
+ * @par Example
+ * Getting the value of the SOL_SOCKET/SO_REUSEADDR option:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::acceptor::reuse_address option;
+ * acceptor.get_option(option);
+ * bool is_set = option.get();
+ * @endcode
+ */
+ template <typename GettableSocketOption>
+ void get_option(GettableSocketOption& option)
+ {
+ boost::system::error_code ec;
+ this->get_service().get_option(this->get_implementation(), option, ec);
+ boost::asio::detail::throw_error(ec, "get_option");
+ }
+
+ /// Get an option from the acceptor.
+ /**
+ * This function is used to get the current value of an option on the
+ * acceptor.
+ *
+ * @param option The option value to be obtained from the acceptor.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @sa GettableSocketOption @n
+ * boost::asio::socket_base::reuse_address
+ *
+ * @par Example
+ * Getting the value of the SOL_SOCKET/SO_REUSEADDR option:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::acceptor::reuse_address option;
+ * boost::system::error_code ec;
+ * acceptor.get_option(option, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * bool is_set = option.get();
+ * @endcode
+ */
+ template <typename GettableSocketOption>
+ boost::system::error_code get_option(GettableSocketOption& option,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().get_option(
+ this->get_implementation(), option, ec);
+ }
+
+ /// Perform an IO control command on the acceptor.
+ /**
+ * This function is used to execute an IO control command on the acceptor.
+ *
+ * @param command The IO control command to be performed on the acceptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa IoControlCommand @n
+ * boost::asio::socket_base::non_blocking_io
+ *
+ * @par Example
+ * Getting the number of bytes ready to read:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::acceptor::non_blocking_io command(true);
+ * socket.io_control(command);
+ * @endcode
+ */
+ template <typename IoControlCommand>
+ void io_control(IoControlCommand& command)
+ {
+ boost::system::error_code ec;
+ this->get_service().io_control(this->get_implementation(), command, ec);
+ boost::asio::detail::throw_error(ec, "io_control");
+ }
+
+ /// Perform an IO control command on the acceptor.
+ /**
+ * This function is used to execute an IO control command on the acceptor.
+ *
+ * @param command The IO control command to be performed on the acceptor.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @sa IoControlCommand @n
+ * boost::asio::socket_base::non_blocking_io
+ *
+ * @par Example
+ * Getting the number of bytes ready to read:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::acceptor::non_blocking_io command(true);
+ * boost::system::error_code ec;
+ * socket.io_control(command, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(IoControlCommand& command,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().io_control(
+ this->get_implementation(), command, ec);
+ }
+
+ /// Gets the non-blocking mode of the acceptor.
+ /**
+ * @returns @c true if the acceptor's synchronous operations will fail with
+ * boost::asio::error::would_block if they are unable to perform the requested
+ * operation immediately. If @c false, synchronous operations will block
+ * until complete.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ bool non_blocking() const
+ {
+ return this->get_service().non_blocking(this->get_implementation());
+ }
+
+ /// Sets the non-blocking mode of the acceptor.
+ /**
+ * @param mode If @c true, the acceptor's synchronous operations will fail
+ * with boost::asio::error::would_block if they are unable to perform the
+ * requested operation immediately. If @c false, synchronous operations will
+ * block until complete.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ void non_blocking(bool mode)
+ {
+ boost::system::error_code ec;
+ this->get_service().non_blocking(this->get_implementation(), mode, ec);
+ boost::asio::detail::throw_error(ec, "non_blocking");
+ }
+
+ /// Sets the non-blocking mode of the acceptor.
+ /**
+ * @param mode If @c true, the acceptor's synchronous operations will fail
+ * with boost::asio::error::would_block if they are unable to perform the
+ * requested operation immediately. If @c false, synchronous operations will
+ * block until complete.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ boost::system::error_code non_blocking(
+ bool mode, boost::system::error_code& ec)
+ {
+ return this->get_service().non_blocking(
+ this->get_implementation(), mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native acceptor implementation.
+ /**
+ * This function is used to retrieve the non-blocking mode of the underlying
+ * native acceptor. This mode has no effect on the behaviour of the acceptor
+ * object's synchronous operations.
+ *
+ * @returns @c true if the underlying acceptor is in non-blocking mode and
+ * direct system calls may fail with boost::asio::error::would_block (or the
+ * equivalent system error).
+ *
+ * @note The current non-blocking mode is cached by the acceptor object.
+ * Consequently, the return value may be incorrect if the non-blocking mode
+ * was set directly on the native acceptor.
+ */
+ bool native_non_blocking() const
+ {
+ return this->get_service().native_non_blocking(this->get_implementation());
+ }
+
+ /// Sets the non-blocking mode of the native acceptor implementation.
+ /**
+ * This function is used to modify the non-blocking mode of the underlying
+ * native acceptor. It has no effect on the behaviour of the acceptor object's
+ * synchronous operations.
+ *
+ * @param mode If @c true, the underlying acceptor is put into non-blocking
+ * mode and direct system calls may fail with boost::asio::error::would_block
+ * (or the equivalent system error).
+ *
+ * @throws boost::system::system_error Thrown on failure. If the @c mode is
+ * @c false, but the current value of @c non_blocking() is @c true, this
+ * function fails with boost::asio::error::invalid_argument, as the
+ * combination does not make sense.
+ */
+ void native_non_blocking(bool mode)
+ {
+ boost::system::error_code ec;
+ this->get_service().native_non_blocking(
+ this->get_implementation(), mode, ec);
+ boost::asio::detail::throw_error(ec, "native_non_blocking");
+ }
+
+ /// Sets the non-blocking mode of the native acceptor implementation.
+ /**
+ * This function is used to modify the non-blocking mode of the underlying
+ * native acceptor. It has no effect on the behaviour of the acceptor object's
+ * synchronous operations.
+ *
+ * @param mode If @c true, the underlying acceptor is put into non-blocking
+ * mode and direct system calls may fail with boost::asio::error::would_block
+ * (or the equivalent system error).
+ *
+ * @param ec Set to indicate what error occurred, if any. If the @c mode is
+ * @c false, but the current value of @c non_blocking() is @c true, this
+ * function fails with boost::asio::error::invalid_argument, as the
+ * combination does not make sense.
+ */
+ boost::system::error_code native_non_blocking(
+ bool mode, boost::system::error_code& ec)
+ {
+ return this->get_service().native_non_blocking(
+ this->get_implementation(), mode, ec);
+ }
+
+ /// Get the local endpoint of the acceptor.
+ /**
+ * This function is used to obtain the locally bound endpoint of the acceptor.
+ *
+ * @returns An object that represents the local endpoint of the acceptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::endpoint endpoint = acceptor.local_endpoint();
+ * @endcode
+ */
+ endpoint_type local_endpoint() const
+ {
+ boost::system::error_code ec;
+ endpoint_type ep = this->get_service().local_endpoint(
+ this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "local_endpoint");
+ return ep;
+ }
+
+ /// Get the local endpoint of the acceptor.
+ /**
+ * This function is used to obtain the locally bound endpoint of the acceptor.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns An object that represents the local endpoint of the acceptor.
+ * Returns a default-constructed endpoint object if an error occurred and the
+ * error handler did not throw an exception.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::system::error_code ec;
+ * boost::asio::ip::tcp::endpoint endpoint = acceptor.local_endpoint(ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ endpoint_type local_endpoint(boost::system::error_code& ec) const
+ {
+ return this->get_service().local_endpoint(this->get_implementation(), ec);
+ }
+
+ /// Accept a new connection.
+ /**
+ * This function is used to accept a new connection from a peer into the
+ * given socket. The function call will block until a new connection has been
+ * accepted successfully or an error occurs.
+ *
+ * @param peer The socket into which the new connection will be accepted.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * acceptor.accept(socket);
+ * @endcode
+ */
+ template <typename Protocol1, typename SocketService>
+ void accept(basic_socket<Protocol1, SocketService>& peer,
+ typename enable_if<is_convertible<Protocol, Protocol1>::value>::type* = 0)
+ {
+ boost::system::error_code ec;
+ this->get_service().accept(this->get_implementation(),
+ peer, static_cast<endpoint_type*>(0), ec);
+ boost::asio::detail::throw_error(ec, "accept");
+ }
+
+ /// Accept a new connection.
+ /**
+ * This function is used to accept a new connection from a peer into the
+ * given socket. The function call will block until a new connection has been
+ * accepted successfully or an error occurs.
+ *
+ * @param peer The socket into which the new connection will be accepted.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::soocket socket(io_service);
+ * boost::system::error_code ec;
+ * acceptor.accept(socket, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ template <typename Protocol1, typename SocketService>
+ boost::system::error_code accept(
+ basic_socket<Protocol1, SocketService>& peer,
+ boost::system::error_code& ec,
+ typename enable_if<is_convertible<Protocol, Protocol1>::value>::type* = 0)
+ {
+ return this->get_service().accept(this->get_implementation(),
+ peer, static_cast<endpoint_type*>(0), ec);
+ }
+
+ /// Start an asynchronous accept.
+ /**
+ * This function is used to asynchronously accept a new connection into a
+ * socket. The function call always returns immediately.
+ *
+ * @param peer The socket into which the new connection will be accepted.
+ * Ownership of the peer object is retained by the caller, which must
+ * guarantee that it is valid until the handler is called.
+ *
+ * @param handler The handler to be called when the accept operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * @code
+ * void accept_handler(const boost::system::error_code& error)
+ * {
+ * if (!error)
+ * {
+ * // Accept succeeded.
+ * }
+ * }
+ *
+ * ...
+ *
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * acceptor.async_accept(socket, accept_handler);
+ * @endcode
+ */
+ template <typename Protocol1, typename SocketService, typename AcceptHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(AcceptHandler,
+ void (boost::system::error_code))
+ async_accept(basic_socket<Protocol1, SocketService>& peer,
+ BOOST_ASIO_MOVE_ARG(AcceptHandler) handler,
+ typename enable_if<is_convertible<Protocol, Protocol1>::value>::type* = 0)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a AcceptHandler.
+ BOOST_ASIO_ACCEPT_HANDLER_CHECK(AcceptHandler, handler) type_check;
+
+ return this->get_service().async_accept(this->get_implementation(),
+ peer, static_cast<endpoint_type*>(0),
+ BOOST_ASIO_MOVE_CAST(AcceptHandler)(handler));
+ }
+
+ /// Accept a new connection and obtain the endpoint of the peer
+ /**
+ * This function is used to accept a new connection from a peer into the
+ * given socket, and additionally provide the endpoint of the remote peer.
+ * The function call will block until a new connection has been accepted
+ * successfully or an error occurs.
+ *
+ * @param peer The socket into which the new connection will be accepted.
+ *
+ * @param peer_endpoint An endpoint object which will receive the endpoint of
+ * the remote peer.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * boost::asio::ip::tcp::endpoint endpoint;
+ * acceptor.accept(socket, endpoint);
+ * @endcode
+ */
+ template <typename SocketService>
+ void accept(basic_socket<protocol_type, SocketService>& peer,
+ endpoint_type& peer_endpoint)
+ {
+ boost::system::error_code ec;
+ this->get_service().accept(this->get_implementation(),
+ peer, &peer_endpoint, ec);
+ boost::asio::detail::throw_error(ec, "accept");
+ }
+
+ /// Accept a new connection and obtain the endpoint of the peer
+ /**
+ * This function is used to accept a new connection from a peer into the
+ * given socket, and additionally provide the endpoint of the remote peer.
+ * The function call will block until a new connection has been accepted
+ * successfully or an error occurs.
+ *
+ * @param peer The socket into which the new connection will be accepted.
+ *
+ * @param peer_endpoint An endpoint object which will receive the endpoint of
+ * the remote peer.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * boost::asio::ip::tcp::endpoint endpoint;
+ * boost::system::error_code ec;
+ * acceptor.accept(socket, endpoint, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * @endcode
+ */
+ template <typename SocketService>
+ boost::system::error_code accept(
+ basic_socket<protocol_type, SocketService>& peer,
+ endpoint_type& peer_endpoint, boost::system::error_code& ec)
+ {
+ return this->get_service().accept(
+ this->get_implementation(), peer, &peer_endpoint, ec);
+ }
+
+ /// Start an asynchronous accept.
+ /**
+ * This function is used to asynchronously accept a new connection into a
+ * socket, and additionally obtain the endpoint of the remote peer. The
+ * function call always returns immediately.
+ *
+ * @param peer The socket into which the new connection will be accepted.
+ * Ownership of the peer object is retained by the caller, which must
+ * guarantee that it is valid until the handler is called.
+ *
+ * @param peer_endpoint An endpoint object into which the endpoint of the
+ * remote peer will be written. Ownership of the peer_endpoint object is
+ * retained by the caller, which must guarantee that it is valid until the
+ * handler is called.
+ *
+ * @param handler The handler to be called when the accept operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename SocketService, typename AcceptHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(AcceptHandler,
+ void (boost::system::error_code))
+ async_accept(basic_socket<protocol_type, SocketService>& peer,
+ endpoint_type& peer_endpoint, BOOST_ASIO_MOVE_ARG(AcceptHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a AcceptHandler.
+ BOOST_ASIO_ACCEPT_HANDLER_CHECK(AcceptHandler, handler) type_check;
+
+ return this->get_service().async_accept(this->get_implementation(), peer,
+ &peer_endpoint, BOOST_ASIO_MOVE_CAST(AcceptHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_SOCKET_ACCEPTOR_HPP
diff --git a/ext/patches/boost/asio/basic_socket_iostream.hpp b/ext/patches/boost/asio/basic_socket_iostream.hpp
new file mode 100644
index 0000000..e36cb82
--- /dev/null
+++ b/ext/patches/boost/asio/basic_socket_iostream.hpp
@@ -0,0 +1,288 @@
+//
+// basic_socket_iostream.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_SOCKET_IOSTREAM_HPP
+#define BOOST_ASIO_BASIC_SOCKET_IOSTREAM_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <istream>
+#include <ostream>
+#include <boost/asio/basic_socket_streambuf.hpp>
+#include <boost/asio/stream_socket_service.hpp>
+
+#if !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+# include <boost/asio/detail/variadic_templates.hpp>
+
+// A macro that should expand to:
+// template <typename T1, ..., typename Tn>
+// explicit basic_socket_iostream(T1 x1, ..., Tn xn)
+// : std::basic_iostream<char>(
+// &this->detail::socket_iostream_base<
+// Protocol, StreamSocketService, Time,
+// TimeTraits, TimerService>::streambuf_)
+// {
+// if (rdbuf()->connect(x1, ..., xn) == 0)
+// this->setstate(std::ios_base::failbit);
+// }
+// This macro should only persist within this file.
+
+# define BOOST_ASIO_PRIVATE_CTR_DEF(n) \
+ template <BOOST_ASIO_VARIADIC_TPARAMS(n)> \
+ explicit basic_socket_iostream(BOOST_ASIO_VARIADIC_PARAMS(n)) \
+ : std::basic_iostream<char>( \
+ &this->detail::socket_iostream_base< \
+ Protocol, StreamSocketService, Time, \
+ TimeTraits, TimerService>::streambuf_) \
+ { \
+ this->setf(std::ios_base::unitbuf); \
+ if (rdbuf()->connect(BOOST_ASIO_VARIADIC_ARGS(n)) == 0) \
+ this->setstate(std::ios_base::failbit); \
+ } \
+ /**/
+
+// A macro that should expand to:
+// template <typename T1, ..., typename Tn>
+// void connect(T1 x1, ..., Tn xn)
+// {
+// if (rdbuf()->connect(x1, ..., xn) == 0)
+// this->setstate(std::ios_base::failbit);
+// }
+// This macro should only persist within this file.
+
+# define BOOST_ASIO_PRIVATE_CONNECT_DEF(n) \
+ template <BOOST_ASIO_VARIADIC_TPARAMS(n)> \
+ void connect(BOOST_ASIO_VARIADIC_PARAMS(n)) \
+ { \
+ if (rdbuf()->connect(BOOST_ASIO_VARIADIC_ARGS(n)) == 0) \
+ this->setstate(std::ios_base::failbit); \
+ } \
+ /**/
+
+#endif // !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// A separate base class is used to ensure that the streambuf is initialised
+// prior to the basic_socket_iostream's basic_iostream base class.
+template <typename Protocol, typename StreamSocketService,
+ typename Time, typename TimeTraits, typename TimerService>
+class socket_iostream_base
+{
+protected:
+ basic_socket_streambuf<Protocol, StreamSocketService,
+ Time, TimeTraits, TimerService> streambuf_;
+};
+
+}
+
+/// Iostream interface for a socket.
+template <typename Protocol,
+ typename StreamSocketService = stream_socket_service<Protocol>,
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME) \
+ || defined(GENERATING_DOCUMENTATION)
+ typename Time = boost::posix_time::ptime,
+ typename TimeTraits = boost::asio::time_traits<Time>,
+ typename TimerService = deadline_timer_service<Time, TimeTraits> >
+#else
+ typename Time = steady_timer::clock_type,
+ typename TimeTraits = steady_timer::traits_type,
+ typename TimerService = steady_timer::service_type>
+#endif
+class basic_socket_iostream
+ : private detail::socket_iostream_base<Protocol,
+ StreamSocketService, Time, TimeTraits, TimerService>,
+ public std::basic_iostream<char>
+{
+private:
+ // These typedefs are intended keep this class's implementation independent
+ // of whether it's using Boost.DateTime, Boost.Chrono or std::chrono.
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ typedef TimeTraits traits_helper;
+#else
+ typedef detail::chrono_time_traits<Time, TimeTraits> traits_helper;
+#endif
+
+public:
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// The time type.
+ typedef typename TimeTraits::time_type time_type;
+
+ /// The duration type.
+ typedef typename TimeTraits::duration_type duration_type;
+#else
+ typedef typename traits_helper::time_type time_type;
+ typedef typename traits_helper::duration_type duration_type;
+#endif
+
+ /// Construct a basic_socket_iostream without establishing a connection.
+ basic_socket_iostream()
+ : std::basic_iostream<char>(
+ &this->detail::socket_iostream_base<
+ Protocol, StreamSocketService, Time,
+ TimeTraits, TimerService>::streambuf_)
+ {
+ this->setf(std::ios_base::unitbuf);
+ }
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// Establish a connection to an endpoint corresponding to a resolver query.
+ /**
+ * This constructor automatically establishes a connection based on the
+ * supplied resolver query parameters. The arguments are used to construct
+ * a resolver query object.
+ */
+ template <typename T1, ..., typename TN>
+ explicit basic_socket_iostream(T1 t1, ..., TN tn);
+#elif defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+ template <typename... T>
+ explicit basic_socket_iostream(T... x)
+ : std::basic_iostream<char>(
+ &this->detail::socket_iostream_base<
+ Protocol, StreamSocketService, Time,
+ TimeTraits, TimerService>::streambuf_)
+ {
+ this->setf(std::ios_base::unitbuf);
+ if (rdbuf()->connect(x...) == 0)
+ this->setstate(std::ios_base::failbit);
+ }
+#else
+ BOOST_ASIO_VARIADIC_GENERATE(BOOST_ASIO_PRIVATE_CTR_DEF)
+#endif
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// Establish a connection to an endpoint corresponding to a resolver query.
+ /**
+ * This function automatically establishes a connection based on the supplied
+ * resolver query parameters. The arguments are used to construct a resolver
+ * query object.
+ */
+ template <typename T1, ..., typename TN>
+ void connect(T1 t1, ..., TN tn);
+#elif defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+ template <typename... T>
+ void connect(T... x)
+ {
+ if (rdbuf()->connect(x...) == 0)
+ this->setstate(std::ios_base::failbit);
+ }
+#else
+ BOOST_ASIO_VARIADIC_GENERATE(BOOST_ASIO_PRIVATE_CONNECT_DEF)
+#endif
+
+ /// Close the connection.
+ void close()
+ {
+ if (rdbuf()->close() == 0)
+ this->setstate(std::ios_base::failbit);
+ }
+
+ /// Return a pointer to the underlying streambuf.
+ basic_socket_streambuf<Protocol, StreamSocketService,
+ Time, TimeTraits, TimerService>* rdbuf() const
+ {
+ return const_cast<basic_socket_streambuf<Protocol, StreamSocketService,
+ Time, TimeTraits, TimerService>*>(
+ &this->detail::socket_iostream_base<
+ Protocol, StreamSocketService, Time,
+ TimeTraits, TimerService>::streambuf_);
+ }
+
+ /// Get the last error associated with the stream.
+ /**
+ * @return An \c error_code corresponding to the last error from the stream.
+ *
+ * @par Example
+ * To print the error associated with a failure to establish a connection:
+ * @code tcp::iostream s("www.boost.org", "http");
+ * if (!s)
+ * {
+ * std::cout << "Error: " << s.error().message() << std::endl;
+ * } @endcode
+ */
+ const boost::system::error_code& error() const
+ {
+ return rdbuf()->puberror();
+ }
+
+ /// Get the stream's expiry time as an absolute time.
+ /**
+ * @return An absolute time value representing the stream's expiry time.
+ */
+ time_type expires_at() const
+ {
+ return rdbuf()->expires_at();
+ }
+
+ /// Set the stream's expiry time as an absolute time.
+ /**
+ * This function sets the expiry time associated with the stream. Stream
+ * operations performed after this time (where the operations cannot be
+ * completed using the internal buffers) will fail with the error
+ * boost::asio::error::operation_aborted.
+ *
+ * @param expiry_time The expiry time to be used for the stream.
+ */
+ void expires_at(const time_type& expiry_time)
+ {
+ rdbuf()->expires_at(expiry_time);
+ }
+
+ /// Get the timer's expiry time relative to now.
+ /**
+ * @return A relative time value representing the stream's expiry time.
+ */
+ duration_type expires_from_now() const
+ {
+ return rdbuf()->expires_from_now();
+ }
+
+ /// Set the stream's expiry time relative to now.
+ /**
+ * This function sets the expiry time associated with the stream. Stream
+ * operations performed after this time (where the operations cannot be
+ * completed using the internal buffers) will fail with the error
+ * boost::asio::error::operation_aborted.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ */
+ void expires_from_now(const duration_type& expiry_time)
+ {
+ rdbuf()->expires_from_now(expiry_time);
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+# undef BOOST_ASIO_PRIVATE_CTR_DEF
+# undef BOOST_ASIO_PRIVATE_CONNECT_DEF
+#endif // !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_BASIC_SOCKET_IOSTREAM_HPP
diff --git a/ext/patches/boost/asio/basic_socket_streambuf.hpp b/ext/patches/boost/asio/basic_socket_streambuf.hpp
new file mode 100644
index 0000000..7ab62be
--- /dev/null
+++ b/ext/patches/boost/asio/basic_socket_streambuf.hpp
@@ -0,0 +1,569 @@
+//
+// basic_socket_streambuf.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_SOCKET_STREAMBUF_HPP
+#define BOOST_ASIO_BASIC_SOCKET_STREAMBUF_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <streambuf>
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/deadline_timer_service.hpp>
+#include <boost/asio/detail/array.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/stream_socket_service.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+# include <boost/asio/deadline_timer.hpp>
+#else
+# include <boost/asio/steady_timer.hpp>
+#endif
+
+#if !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+# include <boost/asio/detail/variadic_templates.hpp>
+
+// A macro that should expand to:
+// template <typename T1, ..., typename Tn>
+// basic_socket_streambuf<Protocol, StreamSocketService,
+// Time, TimeTraits, TimerService>* connect(
+// T1 x1, ..., Tn xn)
+// {
+// init_buffers();
+// this->basic_socket<Protocol, StreamSocketService>::close(ec_);
+// typedef typename Protocol::resolver resolver_type;
+// typedef typename resolver_type::query resolver_query;
+// resolver_query query(x1, ..., xn);
+// resolve_and_connect(query);
+// return !ec_ ? this : 0;
+// }
+// This macro should only persist within this file.
+
+# define BOOST_ASIO_PRIVATE_CONNECT_DEF(n) \
+ template <BOOST_ASIO_VARIADIC_TPARAMS(n)> \
+ basic_socket_streambuf<Protocol, StreamSocketService, \
+ Time, TimeTraits, TimerService>* connect(BOOST_ASIO_VARIADIC_PARAMS(n)) \
+ { \
+ init_buffers(); \
+ this->basic_socket<Protocol, StreamSocketService>::close(ec_); \
+ typedef typename Protocol::resolver resolver_type; \
+ typedef typename resolver_type::query resolver_query; \
+ resolver_query query(BOOST_ASIO_VARIADIC_ARGS(n)); \
+ resolve_and_connect(query); \
+ return !ec_ ? this : 0; \
+ } \
+ /**/
+
+#endif // !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// A separate base class is used to ensure that the io_service is initialised
+// prior to the basic_socket_streambuf's basic_socket base class.
+class socket_streambuf_base
+{
+protected:
+ io_service io_service_;
+};
+
+} // namespace detail
+
+/// Iostream streambuf for a socket.
+template <typename Protocol,
+ typename StreamSocketService = stream_socket_service<Protocol>,
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME) \
+ || defined(GENERATING_DOCUMENTATION)
+ typename Time = boost::posix_time::ptime,
+ typename TimeTraits = boost::asio::time_traits<Time>,
+ typename TimerService = deadline_timer_service<Time, TimeTraits> >
+#else
+ typename Time = steady_timer::clock_type,
+ typename TimeTraits = steady_timer::traits_type,
+ typename TimerService = steady_timer::service_type>
+#endif
+class basic_socket_streambuf
+ : public std::streambuf,
+ private detail::socket_streambuf_base,
+ public basic_socket<Protocol, StreamSocketService>
+{
+private:
+ // These typedefs are intended keep this class's implementation independent
+ // of whether it's using Boost.DateTime, Boost.Chrono or std::chrono.
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ typedef TimeTraits traits_helper;
+#else
+ typedef detail::chrono_time_traits<Time, TimeTraits> traits_helper;
+#endif
+
+public:
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// The time type.
+ typedef typename TimeTraits::time_type time_type;
+
+ /// The duration type.
+ typedef typename TimeTraits::duration_type duration_type;
+#else
+ typedef typename traits_helper::time_type time_type;
+ typedef typename traits_helper::duration_type duration_type;
+#endif
+
+ /// Construct a basic_socket_streambuf without establishing a connection.
+ basic_socket_streambuf()
+ : basic_socket<Protocol, StreamSocketService>(
+ this->detail::socket_streambuf_base::io_service_),
+ unbuffered_(false),
+ timer_service_(0),
+ timer_state_(no_timer)
+ {
+ init_buffers();
+ }
+
+ /// Destructor flushes buffered data.
+ virtual ~basic_socket_streambuf()
+ {
+ if (pptr() != pbase())
+ overflow(traits_type::eof());
+
+ destroy_timer();
+ }
+
+ /// Establish a connection.
+ /**
+ * This function establishes a connection to the specified endpoint.
+ *
+ * @return \c this if a connection was successfully established, a null
+ * pointer otherwise.
+ */
+ basic_socket_streambuf<Protocol, StreamSocketService,
+ Time, TimeTraits, TimerService>* connect(
+ const endpoint_type& endpoint)
+ {
+ init_buffers();
+
+ this->basic_socket<Protocol, StreamSocketService>::close(ec_);
+
+ if (timer_state_ == timer_has_expired)
+ {
+ ec_ = boost::asio::error::operation_aborted;
+ return 0;
+ }
+
+ io_handler handler = { this };
+ this->basic_socket<Protocol, StreamSocketService>::async_connect(
+ endpoint, handler);
+
+ ec_ = boost::asio::error::would_block;
+ this->get_service().get_io_service().reset();
+ do this->get_service().get_io_service().run_one();
+ while (ec_ == boost::asio::error::would_block);
+
+ return !ec_ ? this : 0;
+ }
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// Establish a connection.
+ /**
+ * This function automatically establishes a connection based on the supplied
+ * resolver query parameters. The arguments are used to construct a resolver
+ * query object.
+ *
+ * @return \c this if a connection was successfully established, a null
+ * pointer otherwise.
+ */
+ template <typename T1, ..., typename TN>
+ basic_socket_streambuf<Protocol, StreamSocketService>* connect(
+ T1 t1, ..., TN tn);
+#elif defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+ template <typename... T>
+ basic_socket_streambuf<Protocol, StreamSocketService,
+ Time, TimeTraits, TimerService>* connect(T... x)
+ {
+ init_buffers();
+ this->basic_socket<Protocol, StreamSocketService>::close(ec_);
+ typedef typename Protocol::resolver resolver_type;
+ typedef typename resolver_type::query resolver_query;
+ resolver_query query(x...);
+ resolve_and_connect(query);
+ return !ec_ ? this : 0;
+ }
+#else
+ BOOST_ASIO_VARIADIC_GENERATE(BOOST_ASIO_PRIVATE_CONNECT_DEF)
+#endif
+
+ /// Close the connection.
+ /**
+ * @return \c this if a connection was successfully established, a null
+ * pointer otherwise.
+ */
+ basic_socket_streambuf<Protocol, StreamSocketService,
+ Time, TimeTraits, TimerService>* close()
+ {
+ sync();
+ this->basic_socket<Protocol, StreamSocketService>::close(ec_);
+ if (!ec_)
+ init_buffers();
+ return !ec_ ? this : 0;
+ }
+
+ /// Get the last error associated with the stream buffer.
+ /**
+ * @return An \c error_code corresponding to the last error from the stream
+ * buffer.
+ */
+ const boost::system::error_code& puberror() const
+ {
+ return error();
+ }
+
+ /// Get the stream buffer's expiry time as an absolute time.
+ /**
+ * @return An absolute time value representing the stream buffer's expiry
+ * time.
+ */
+ time_type expires_at() const
+ {
+ return timer_service_
+ ? timer_service_->expires_at(timer_implementation_)
+ : time_type();
+ }
+
+ /// Set the stream buffer's expiry time as an absolute time.
+ /**
+ * This function sets the expiry time associated with the stream. Stream
+ * operations performed after this time (where the operations cannot be
+ * completed using the internal buffers) will fail with the error
+ * boost::asio::error::operation_aborted.
+ *
+ * @param expiry_time The expiry time to be used for the stream.
+ */
+ void expires_at(const time_type& expiry_time)
+ {
+ construct_timer();
+
+ boost::system::error_code ec;
+ timer_service_->expires_at(timer_implementation_, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_at");
+
+ start_timer();
+ }
+
+ /// Get the stream buffer's expiry time relative to now.
+ /**
+ * @return A relative time value representing the stream buffer's expiry time.
+ */
+ duration_type expires_from_now() const
+ {
+ return traits_helper::subtract(expires_at(), traits_helper::now());
+ }
+
+ /// Set the stream buffer's expiry time relative to now.
+ /**
+ * This function sets the expiry time associated with the stream. Stream
+ * operations performed after this time (where the operations cannot be
+ * completed using the internal buffers) will fail with the error
+ * boost::asio::error::operation_aborted.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ */
+ void expires_from_now(const duration_type& expiry_time)
+ {
+ construct_timer();
+
+ boost::system::error_code ec;
+ timer_service_->expires_from_now(timer_implementation_, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_from_now");
+
+ start_timer();
+ }
+
+protected:
+ int_type underflow()
+ {
+ if (gptr() == egptr())
+ {
+ if (timer_state_ == timer_has_expired)
+ {
+ ec_ = boost::asio::error::operation_aborted;
+ return traits_type::eof();
+ }
+
+ io_handler handler = { this };
+ this->get_service().async_receive(this->get_implementation(),
+ boost::asio::buffer(boost::asio::buffer(get_buffer_) + putback_max),
+ 0, handler);
+
+ ec_ = boost::asio::error::would_block;
+ this->get_service().get_io_service().reset();
+ do this->get_service().get_io_service().run_one();
+ while (ec_ == boost::asio::error::would_block);
+ if (ec_)
+ return traits_type::eof();
+
+ setg(&get_buffer_[0], &get_buffer_[0] + putback_max,
+ &get_buffer_[0] + putback_max + bytes_transferred_);
+ return traits_type::to_int_type(*gptr());
+ }
+ else
+ {
+ return traits_type::eof();
+ }
+ }
+
+ int_type overflow(int_type c)
+ {
+ if (unbuffered_)
+ {
+ if (traits_type::eq_int_type(c, traits_type::eof()))
+ {
+ // Nothing to do.
+ return traits_type::not_eof(c);
+ }
+ else
+ {
+ if (timer_state_ == timer_has_expired)
+ {
+ ec_ = boost::asio::error::operation_aborted;
+ return traits_type::eof();
+ }
+
+ // Send the single character immediately.
+ char_type ch = traits_type::to_char_type(c);
+ io_handler handler = { this };
+ this->get_service().async_send(this->get_implementation(),
+ boost::asio::buffer(&ch, sizeof(char_type)), 0, handler);
+
+ ec_ = boost::asio::error::would_block;
+ this->get_service().get_io_service().reset();
+ do this->get_service().get_io_service().run_one();
+ while (ec_ == boost::asio::error::would_block);
+ if (ec_)
+ return traits_type::eof();
+
+ return c;
+ }
+ }
+ else
+ {
+ // Send all data in the output buffer.
+ boost::asio::const_buffer buffer =
+ boost::asio::buffer(pbase(), pptr() - pbase());
+ while (boost::asio::buffer_size(buffer) > 0)
+ {
+ if (timer_state_ == timer_has_expired)
+ {
+ ec_ = boost::asio::error::operation_aborted;
+ return traits_type::eof();
+ }
+
+ io_handler handler = { this };
+ this->get_service().async_send(this->get_implementation(),
+ boost::asio::buffer(buffer), 0, handler);
+
+ ec_ = boost::asio::error::would_block;
+ this->get_service().get_io_service().reset();
+ do this->get_service().get_io_service().run_one();
+ while (ec_ == boost::asio::error::would_block);
+ if (ec_)
+ return traits_type::eof();
+
+ buffer = buffer + bytes_transferred_;
+ }
+ setp(&put_buffer_[0], &put_buffer_[0] + put_buffer_.size());
+
+ // If the new character is eof then our work here is done.
+ if (traits_type::eq_int_type(c, traits_type::eof()))
+ return traits_type::not_eof(c);
+
+ // Add the new character to the output buffer.
+ *pptr() = traits_type::to_char_type(c);
+ pbump(1);
+ return c;
+ }
+ }
+
+ int sync()
+ {
+ return overflow(traits_type::eof());
+ }
+
+ std::streambuf* setbuf(char_type* s, std::streamsize n)
+ {
+ if (pptr() == pbase() && s == 0 && n == 0)
+ {
+ unbuffered_ = true;
+ setp(0, 0);
+ return this;
+ }
+
+ return 0;
+ }
+
+ /// Get the last error associated with the stream buffer.
+ /**
+ * @return An \c error_code corresponding to the last error from the stream
+ * buffer.
+ */
+ virtual const boost::system::error_code& error() const
+ {
+ return ec_;
+ }
+
+private:
+ void init_buffers()
+ {
+ setg(&get_buffer_[0],
+ &get_buffer_[0] + putback_max,
+ &get_buffer_[0] + putback_max);
+ if (unbuffered_)
+ setp(0, 0);
+ else
+ setp(&put_buffer_[0], &put_buffer_[0] + put_buffer_.size());
+ }
+
+ template <typename ResolverQuery>
+ void resolve_and_connect(const ResolverQuery& query)
+ {
+ typedef typename Protocol::resolver resolver_type;
+ typedef typename resolver_type::iterator iterator_type;
+ resolver_type resolver(detail::socket_streambuf_base::io_service_);
+ iterator_type i = resolver.resolve(query, ec_);
+ if (!ec_)
+ {
+ iterator_type end;
+ ec_ = boost::asio::error::host_not_found;
+ while (ec_ && i != end)
+ {
+ this->basic_socket<Protocol, StreamSocketService>::close(ec_);
+
+ if (timer_state_ == timer_has_expired)
+ {
+ ec_ = boost::asio::error::operation_aborted;
+ return;
+ }
+
+ io_handler handler = { this };
+ this->basic_socket<Protocol, StreamSocketService>::async_connect(
+ *i, handler);
+
+ ec_ = boost::asio::error::would_block;
+ this->get_service().get_io_service().reset();
+ do this->get_service().get_io_service().run_one();
+ while (ec_ == boost::asio::error::would_block);
+
+ ++i;
+ }
+ }
+ }
+
+ struct io_handler;
+ friend struct io_handler;
+ struct io_handler
+ {
+ basic_socket_streambuf* this_;
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred = 0)
+ {
+ this_->ec_ = ec;
+ this_->bytes_transferred_ = bytes_transferred;
+ }
+ };
+
+ struct timer_handler;
+ friend struct timer_handler;
+ struct timer_handler
+ {
+ basic_socket_streambuf* this_;
+
+ void operator()(const boost::system::error_code&)
+ {
+ time_type now = traits_helper::now();
+
+ time_type expiry_time = this_->timer_service_->expires_at(
+ this_->timer_implementation_);
+
+ if (traits_helper::less_than(now, expiry_time))
+ {
+ this_->timer_state_ = timer_is_pending;
+ this_->timer_service_->async_wait(this_->timer_implementation_, *this);
+ }
+ else
+ {
+ this_->timer_state_ = timer_has_expired;
+ boost::system::error_code ec;
+ this_->basic_socket<Protocol, StreamSocketService>::close(ec);
+ }
+ }
+ };
+
+ void construct_timer()
+ {
+ if (timer_service_ == 0)
+ {
+ TimerService& timer_service = use_service<TimerService>(
+ detail::socket_streambuf_base::io_service_);
+ timer_service.construct(timer_implementation_);
+ timer_service_ = &timer_service;
+ }
+ }
+
+ void destroy_timer()
+ {
+ if (timer_service_)
+ timer_service_->destroy(timer_implementation_);
+ }
+
+ void start_timer()
+ {
+ if (timer_state_ != timer_is_pending)
+ {
+ timer_handler handler = { this };
+ handler(boost::system::error_code());
+ }
+ }
+
+ enum { putback_max = 8 };
+ enum { buffer_size = 512 };
+ boost::asio::detail::array<char, buffer_size> get_buffer_;
+ boost::asio::detail::array<char, buffer_size> put_buffer_;
+ bool unbuffered_;
+ boost::system::error_code ec_;
+ std::size_t bytes_transferred_;
+ TimerService* timer_service_;
+ typename TimerService::implementation_type timer_implementation_;
+ enum state { no_timer, timer_is_pending, timer_has_expired } timer_state_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+# undef BOOST_ASIO_PRIVATE_CONNECT_DEF
+#endif // !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_BASIC_SOCKET_STREAMBUF_HPP
diff --git a/ext/patches/boost/asio/basic_stream_socket.hpp b/ext/patches/boost/asio/basic_stream_socket.hpp
new file mode 100644
index 0000000..ed31554
--- /dev/null
+++ b/ext/patches/boost/asio/basic_stream_socket.hpp
@@ -0,0 +1,854 @@
+//
+// basic_stream_socket.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_STREAM_SOCKET_HPP
+#define BOOST_ASIO_BASIC_STREAM_SOCKET_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/stream_socket_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides stream-oriented socket functionality.
+/**
+ * The basic_stream_socket class template provides asynchronous and blocking
+ * stream-oriented socket functionality.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * AsyncReadStream, AsyncWriteStream, Stream, SyncReadStream, SyncWriteStream.
+ */
+template <typename Protocol,
+ typename StreamSocketService = stream_socket_service<Protocol> >
+class basic_stream_socket
+ : public basic_socket<Protocol, StreamSocketService>
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// socket.
+ typedef typename StreamSocketService::native_handle_type native_type;
+
+ /// The native representation of a socket.
+ typedef typename StreamSocketService::native_handle_type native_handle_type;
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ /// Construct a basic_stream_socket without opening it.
+ /**
+ * This constructor creates a stream socket without opening it. The socket
+ * needs to be opened and then connected or accepted before data can be sent
+ * or received on it.
+ *
+ * @param io_service The io_service object that the stream socket will use to
+ * dispatch handlers for any asynchronous operations performed on the socket.
+ */
+ explicit basic_stream_socket(boost::asio::io_service& io_service)
+ : basic_socket<Protocol, StreamSocketService>(io_service)
+ {
+ }
+
+ /// Construct and open a basic_stream_socket.
+ /**
+ * This constructor creates and opens a stream socket. The socket needs to be
+ * connected or accepted before data can be sent or received on it.
+ *
+ * @param io_service The io_service object that the stream socket will use to
+ * dispatch handlers for any asynchronous operations performed on the socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_stream_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol)
+ : basic_socket<Protocol, StreamSocketService>(io_service, protocol)
+ {
+ }
+
+ /// Construct a basic_stream_socket, opening it and binding it to the given
+ /// local endpoint.
+ /**
+ * This constructor creates a stream socket and automatically opens it bound
+ * to the specified endpoint on the local machine. The protocol used is the
+ * protocol associated with the given endpoint.
+ *
+ * @param io_service The io_service object that the stream socket will use to
+ * dispatch handlers for any asynchronous operations performed on the socket.
+ *
+ * @param endpoint An endpoint on the local machine to which the stream
+ * socket will be bound.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_stream_socket(boost::asio::io_service& io_service,
+ const endpoint_type& endpoint)
+ : basic_socket<Protocol, StreamSocketService>(io_service, endpoint)
+ {
+ }
+
+ /// Construct a basic_stream_socket on an existing native socket.
+ /**
+ * This constructor creates a stream socket object to hold an existing native
+ * socket.
+ *
+ * @param io_service The io_service object that the stream socket will use to
+ * dispatch handlers for any asynchronous operations performed on the socket.
+ *
+ * @param protocol An object specifying protocol parameters to be used.
+ *
+ * @param native_socket The new underlying socket implementation.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_stream_socket(boost::asio::io_service& io_service,
+ const protocol_type& protocol, const native_handle_type& native_socket)
+ : basic_socket<Protocol, StreamSocketService>(
+ io_service, protocol, native_socket)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_stream_socket from another.
+ /**
+ * This constructor moves a stream socket from one object to another.
+ *
+ * @param other The other basic_stream_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_stream_socket(io_service&) constructor.
+ */
+ basic_stream_socket(basic_stream_socket&& other)
+ : basic_socket<Protocol, StreamSocketService>(
+ BOOST_ASIO_MOVE_CAST(basic_stream_socket)(other))
+ {
+ }
+
+ /// Move-assign a basic_stream_socket from another.
+ /**
+ * This assignment operator moves a stream socket from one object to another.
+ *
+ * @param other The other basic_stream_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_stream_socket(io_service&) constructor.
+ */
+ basic_stream_socket& operator=(basic_stream_socket&& other)
+ {
+ basic_socket<Protocol, StreamSocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_stream_socket)(other));
+ return *this;
+ }
+
+ /// Move-construct a basic_stream_socket from a socket of another protocol
+ /// type.
+ /**
+ * This constructor moves a stream socket from one object to another.
+ *
+ * @param other The other basic_stream_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_stream_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename StreamSocketService1>
+ basic_stream_socket(
+ basic_stream_socket<Protocol1, StreamSocketService1>&& other,
+ typename enable_if<is_convertible<Protocol1, Protocol>::value>::type* = 0)
+ : basic_socket<Protocol, StreamSocketService>(
+ BOOST_ASIO_MOVE_CAST2(basic_stream_socket<
+ Protocol1, StreamSocketService1>)(other))
+ {
+ }
+
+ /// Move-assign a basic_stream_socket from a socket of another protocol type.
+ /**
+ * This assignment operator moves a stream socket from one object to another.
+ *
+ * @param other The other basic_stream_socket object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_stream_socket(io_service&) constructor.
+ */
+ template <typename Protocol1, typename StreamSocketService1>
+ typename enable_if<is_convertible<Protocol1, Protocol>::value,
+ basic_stream_socket>::type& operator=(
+ basic_stream_socket<Protocol1, StreamSocketService1>&& other)
+ {
+ basic_socket<Protocol, StreamSocketService>::operator=(
+ BOOST_ASIO_MOVE_CAST2(basic_stream_socket<
+ Protocol1, StreamSocketService1>)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Send some data on the socket.
+ /**
+ * This function is used to send data on the stream socket. The function
+ * call will block until one or more bytes of the data has been sent
+ * successfully, or an until error occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The send operation may not transmit all of the data to the peer.
+ * Consider using the @ref write function if you need to ensure that all data
+ * is written before the blocking operation completes.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.send(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send(
+ this->get_implementation(), buffers, 0, ec);
+ boost::asio::detail::throw_error(ec, "send");
+ return s;
+ }
+
+ /// Send some data on the socket.
+ /**
+ * This function is used to send data on the stream socket. The function
+ * call will block until one or more bytes of the data has been sent
+ * successfully, or an until error occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @returns The number of bytes sent.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The send operation may not transmit all of the data to the peer.
+ * Consider using the @ref write function if you need to ensure that all data
+ * is written before the blocking operation completes.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.send(boost::asio::buffer(data, size), 0);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send(
+ this->get_implementation(), buffers, flags, ec);
+ boost::asio::detail::throw_error(ec, "send");
+ return s;
+ }
+
+ /// Send some data on the socket.
+ /**
+ * This function is used to send data on the stream socket. The function
+ * call will block until one or more bytes of the data has been sent
+ * successfully, or an until error occurs.
+ *
+ * @param buffers One or more data buffers to be sent on the socket.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes sent. Returns 0 if an error occurred.
+ *
+ * @note The send operation may not transmit all of the data to the peer.
+ * Consider using the @ref write function if you need to ensure that all data
+ * is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return this->get_service().send(
+ this->get_implementation(), buffers, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ /**
+ * This function is used to asynchronously send data on the stream socket.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent on the socket. Although
+ * the buffers object may be copied as necessary, ownership of the underlying
+ * memory blocks is retained by the caller, which must guarantee that they
+ * remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The send operation may not transmit all of the data to the peer.
+ * Consider using the @ref async_write function if you need to ensure that all
+ * data is written before the asynchronous operation completes.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.async_send(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send(
+ this->get_implementation(), buffers, 0,
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Start an asynchronous send.
+ /**
+ * This function is used to asynchronously send data on the stream socket.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be sent on the socket. Although
+ * the buffers object may be copied as necessary, ownership of the underlying
+ * memory blocks is retained by the caller, which must guarantee that they
+ * remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the send call is to be made.
+ *
+ * @param handler The handler to be called when the send operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes sent.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The send operation may not transmit all of the data to the peer.
+ * Consider using the @ref async_write function if you need to ensure that all
+ * data is written before the asynchronous operation completes.
+ *
+ * @par Example
+ * To send a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.async_send(boost::asio::buffer(data, size), 0, handler);
+ * @endcode
+ * See the @ref buffer documentation for information on sending multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(const ConstBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send(
+ this->get_implementation(), buffers, flags,
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Receive some data on the socket.
+ /**
+ * This function is used to receive data on the stream socket. The function
+ * call will block until one or more bytes of data has been received
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The receive operation may not receive all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.receive(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, 0, ec);
+ boost::asio::detail::throw_error(ec, "receive");
+ return s;
+ }
+
+ /// Receive some data on the socket.
+ /**
+ * This function is used to receive data on the stream socket. The function
+ * call will block until one or more bytes of data has been received
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @returns The number of bytes received.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The receive operation may not receive all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.receive(boost::asio::buffer(data, size), 0);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, flags, ec);
+ boost::asio::detail::throw_error(ec, "receive");
+ return s;
+ }
+
+ /// Receive some data on a connected socket.
+ /**
+ * This function is used to receive data on the stream socket. The function
+ * call will block until one or more bytes of data has been received
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes received. Returns 0 if an error occurred.
+ *
+ * @note The receive operation may not receive all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return this->get_service().receive(
+ this->get_implementation(), buffers, flags, ec);
+ }
+
+ /// Start an asynchronous receive.
+ /**
+ * This function is used to asynchronously receive data from the stream
+ * socket. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The receive operation may not receive all of the requested number of
+ * bytes. Consider using the @ref async_read function if you need to ensure
+ * that the requested amount of data is received before the asynchronous
+ * operation completes.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.async_receive(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(this->get_implementation(),
+ buffers, 0, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Start an asynchronous receive.
+ /**
+ * This function is used to asynchronously receive data from the stream
+ * socket. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be received.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param flags Flags specifying how the receive call is to be made.
+ *
+ * @param handler The handler to be called when the receive operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes received.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The receive operation may not receive all of the requested number of
+ * bytes. Consider using the @ref async_read function if you need to ensure
+ * that the requested amount of data is received before the asynchronous
+ * operation completes.
+ *
+ * @par Example
+ * To receive into a single data buffer use the @ref buffer function as
+ * follows:
+ * @code
+ * socket.async_receive(boost::asio::buffer(data, size), 0, handler);
+ * @endcode
+ * See the @ref buffer documentation for information on receiving into
+ * multiple buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(const MutableBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(this->get_implementation(),
+ buffers, flags, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Write some data to the socket.
+ /**
+ * This function is used to write data to the stream socket. The function call
+ * will block until one or more bytes of the data has been written
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more data buffers to be written to the socket.
+ *
+ * @returns The number of bytes written.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.write_some(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().send(
+ this->get_implementation(), buffers, 0, ec);
+ boost::asio::detail::throw_error(ec, "write_some");
+ return s;
+ }
+
+ /// Write some data to the socket.
+ /**
+ * This function is used to write data to the stream socket. The function call
+ * will block until one or more bytes of the data has been written
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more data buffers to be written to the socket.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. Returns 0 if an error occurred.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().send(this->get_implementation(), buffers, 0, ec);
+ }
+
+ /// Start an asynchronous write.
+ /**
+ * This function is used to asynchronously write data to the stream socket.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be written to the socket.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes written.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The write operation may not transmit all of the data to the peer.
+ * Consider using the @ref async_write function if you need to ensure that all
+ * data is written before the asynchronous operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.async_write_some(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_send(this->get_implementation(),
+ buffers, 0, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Read some data from the socket.
+ /**
+ * This function is used to read data from the stream socket. The function
+ * call will block until one or more bytes of data has been read successfully,
+ * or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @returns The number of bytes read.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.read_some(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().receive(
+ this->get_implementation(), buffers, 0, ec);
+ boost::asio::detail::throw_error(ec, "read_some");
+ return s;
+ }
+
+ /// Read some data from the socket.
+ /**
+ * This function is used to read data from the stream socket. The function
+ * call will block until one or more bytes of data has been read successfully,
+ * or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. Returns 0 if an error occurred.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().receive(
+ this->get_implementation(), buffers, 0, ec);
+ }
+
+ /// Start an asynchronous read.
+ /**
+ * This function is used to asynchronously read data from the stream socket.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes read.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The read operation may not read all of the requested number of bytes.
+ * Consider using the @ref async_read function if you need to ensure that the
+ * requested amount of data is read before the asynchronous operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * socket.async_read_some(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_receive(this->get_implementation(),
+ buffers, 0, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_STREAM_SOCKET_HPP
diff --git a/ext/patches/boost/asio/basic_streambuf.hpp b/ext/patches/boost/asio/basic_streambuf.hpp
new file mode 100644
index 0000000..4251398
--- /dev/null
+++ b/ext/patches/boost/asio/basic_streambuf.hpp
@@ -0,0 +1,371 @@
+//
+// basic_streambuf.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_STREAMBUF_HPP
+#define BOOST_ASIO_BASIC_STREAMBUF_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <algorithm>
+#include <cstring>
+#include <stdexcept>
+#include <streambuf>
+#include <vector>
+#include <boost/asio/basic_streambuf_fwd.hpp>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Automatically resizable buffer class based on std::streambuf.
+/**
+ * The @c basic_streambuf class is derived from @c std::streambuf to associate
+ * the streambuf's input and output sequences with one or more character
+ * arrays. These character arrays are internal to the @c basic_streambuf
+ * object, but direct access to the array elements is provided to permit them
+ * to be used efficiently with I/O operations. Characters written to the output
+ * sequence of a @c basic_streambuf object are appended to the input sequence
+ * of the same object.
+ *
+ * The @c basic_streambuf class's public interface is intended to permit the
+ * following implementation strategies:
+ *
+ * @li A single contiguous character array, which is reallocated as necessary
+ * to accommodate changes in the size of the character sequence. This is the
+ * implementation approach currently used in Asio.
+ *
+ * @li A sequence of one or more character arrays, where each array is of the
+ * same size. Additional character array objects are appended to the sequence
+ * to accommodate changes in the size of the character sequence.
+ *
+ * @li A sequence of one or more character arrays of varying sizes. Additional
+ * character array objects are appended to the sequence to accommodate changes
+ * in the size of the character sequence.
+ *
+ * The constructor for basic_streambuf accepts a @c size_t argument specifying
+ * the maximum of the sum of the sizes of the input sequence and output
+ * sequence. During the lifetime of the @c basic_streambuf object, the following
+ * invariant holds:
+ * @code size() <= max_size()@endcode
+ * Any member function that would, if successful, cause the invariant to be
+ * violated shall throw an exception of class @c std::length_error.
+ *
+ * The constructor for @c basic_streambuf takes an Allocator argument. A copy
+ * of this argument is used for any memory allocation performed, by the
+ * constructor and by all member functions, during the lifetime of each @c
+ * basic_streambuf object.
+ *
+ * @par Examples
+ * Writing directly from an streambuf to a socket:
+ * @code
+ * boost::asio::streambuf b;
+ * std::ostream os(&b);
+ * os << "Hello, World!\n";
+ *
+ * // try sending some data in input sequence
+ * size_t n = sock.send(b.data());
+ *
+ * b.consume(n); // sent data is removed from input sequence
+ * @endcode
+ *
+ * Reading from a socket directly into a streambuf:
+ * @code
+ * boost::asio::streambuf b;
+ *
+ * // reserve 512 bytes in output sequence
+ * boost::asio::streambuf::mutable_buffers_type bufs = b.prepare(512);
+ *
+ * size_t n = sock.receive(bufs);
+ *
+ * // received data is "committed" from output sequence to input sequence
+ * b.commit(n);
+ *
+ * std::istream is(&b);
+ * std::string s;
+ * is >> s;
+ * @endcode
+ */
+#if defined(GENERATING_DOCUMENTATION)
+template <typename Allocator = std::allocator<char> >
+#else
+template <typename Allocator>
+#endif
+class basic_streambuf
+ : public std::streambuf,
+ private noncopyable
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The type used to represent the input sequence as a list of buffers.
+ typedef implementation_defined const_buffers_type;
+
+ /// The type used to represent the output sequence as a list of buffers.
+ typedef implementation_defined mutable_buffers_type;
+#else
+ typedef boost::asio::const_buffers_1 const_buffers_type;
+ typedef boost::asio::mutable_buffers_1 mutable_buffers_type;
+#endif
+
+ /// Construct a basic_streambuf object.
+ /**
+ * Constructs a streambuf with the specified maximum size. The initial size
+ * of the streambuf's input sequence is 0.
+ */
+ explicit basic_streambuf(
+ std::size_t maximum_size = (std::numeric_limits<std::size_t>::max)(),
+ const Allocator& allocator = Allocator())
+ : max_size_(maximum_size),
+ buffer_(allocator)
+ {
+ std::size_t pend = (std::min<std::size_t>)(max_size_, buffer_delta);
+ buffer_.resize((std::max<std::size_t>)(pend, 1));
+ setg(&buffer_[0], &buffer_[0], &buffer_[0]);
+ setp(&buffer_[0], &buffer_[0] + pend);
+ }
+
+ /// Get the size of the input sequence.
+ /**
+ * @returns The size of the input sequence. The value is equal to that
+ * calculated for @c s in the following code:
+ * @code
+ * size_t s = 0;
+ * const_buffers_type bufs = data();
+ * const_buffers_type::const_iterator i = bufs.begin();
+ * while (i != bufs.end())
+ * {
+ * const_buffer buf(*i++);
+ * s += buffer_size(buf);
+ * }
+ * @endcode
+ */
+ std::size_t size() const
+ {
+ return pptr() - gptr();
+ }
+
+ /// Get the maximum size of the basic_streambuf.
+ /**
+ * @returns The allowed maximum of the sum of the sizes of the input sequence
+ * and output sequence.
+ */
+ std::size_t max_size() const
+ {
+ return max_size_;
+ }
+
+ /// Get a list of buffers that represents the input sequence.
+ /**
+ * @returns An object of type @c const_buffers_type that satisfies
+ * ConstBufferSequence requirements, representing all character arrays in the
+ * input sequence.
+ *
+ * @note The returned object is invalidated by any @c basic_streambuf member
+ * function that modifies the input sequence or output sequence.
+ */
+ const_buffers_type data() const
+ {
+ return boost::asio::buffer(boost::asio::const_buffer(gptr(),
+ (pptr() - gptr()) * sizeof(char_type)));
+ }
+
+ /// Get a list of buffers that represents the output sequence, with the given
+ /// size.
+ /**
+ * Ensures that the output sequence can accommodate @c n characters,
+ * reallocating character array objects as necessary.
+ *
+ * @returns An object of type @c mutable_buffers_type that satisfies
+ * MutableBufferSequence requirements, representing character array objects
+ * at the start of the output sequence such that the sum of the buffer sizes
+ * is @c n.
+ *
+ * @throws std::length_error If <tt>size() + n > max_size()</tt>.
+ *
+ * @note The returned object is invalidated by any @c basic_streambuf member
+ * function that modifies the input sequence or output sequence.
+ */
+ mutable_buffers_type prepare(std::size_t n)
+ {
+ reserve(n);
+ return boost::asio::buffer(boost::asio::mutable_buffer(
+ pptr(), n * sizeof(char_type)));
+ }
+
+ /// Move characters from the output sequence to the input sequence.
+ /**
+ * Appends @c n characters from the start of the output sequence to the input
+ * sequence. The beginning of the output sequence is advanced by @c n
+ * characters.
+ *
+ * Requires a preceding call <tt>prepare(x)</tt> where <tt>x >= n</tt>, and
+ * no intervening operations that modify the input or output sequence.
+ *
+ * @note If @c n is greater than the size of the output sequence, the entire
+ * output sequence is moved to the input sequence and no error is issued.
+ */
+ void commit(std::size_t n)
+ {
+ if (pptr() + n > epptr())
+ n = epptr() - pptr();
+ pbump(static_cast<int>(n));
+ setg(eback(), gptr(), pptr());
+ }
+
+ /// Remove characters from the input sequence.
+ /**
+ * Removes @c n characters from the beginning of the input sequence.
+ *
+ * @note If @c n is greater than the size of the input sequence, the entire
+ * input sequence is consumed and no error is issued.
+ */
+ void consume(std::size_t n)
+ {
+ if (egptr() < pptr())
+ setg(&buffer_[0], gptr(), pptr());
+ if (gptr() + n > pptr())
+ n = pptr() - gptr();
+ gbump(static_cast<int>(n));
+ }
+
+protected:
+ enum { buffer_delta = 128 };
+
+ /// Override std::streambuf behaviour.
+ /**
+ * Behaves according to the specification of @c std::streambuf::underflow().
+ */
+ int_type underflow()
+ {
+ if (gptr() < pptr())
+ {
+ setg(&buffer_[0], gptr(), pptr());
+ return traits_type::to_int_type(*gptr());
+ }
+ else
+ {
+ return traits_type::eof();
+ }
+ }
+
+ /// Override std::streambuf behaviour.
+ /**
+ * Behaves according to the specification of @c std::streambuf::overflow(),
+ * with the specialisation that @c std::length_error is thrown if appending
+ * the character to the input sequence would require the condition
+ * <tt>size() > max_size()</tt> to be true.
+ */
+ int_type overflow(int_type c)
+ {
+ if (!traits_type::eq_int_type(c, traits_type::eof()))
+ {
+ if (pptr() == epptr())
+ {
+ std::size_t buffer_size = pptr() - gptr();
+ if (buffer_size < max_size_ && max_size_ - buffer_size < buffer_delta)
+ {
+ reserve(max_size_ - buffer_size);
+ }
+ else
+ {
+ reserve(buffer_delta);
+ }
+ }
+
+ *pptr() = traits_type::to_char_type(c);
+ pbump(1);
+ return c;
+ }
+
+ return traits_type::not_eof(c);
+ }
+
+ void reserve(std::size_t n)
+ {
+ // Get current stream positions as offsets.
+ std::size_t gnext = gptr() - &buffer_[0];
+ std::size_t pnext = pptr() - &buffer_[0];
+ std::size_t pend = epptr() - &buffer_[0];
+
+ // Check if there is already enough space in the put area.
+ if (n <= pend - pnext)
+ {
+ return;
+ }
+
+ // Shift existing contents of get area to start of buffer.
+ if (gnext > 0)
+ {
+ pnext -= gnext;
+ std::memmove(&buffer_[0], &buffer_[0] + gnext, pnext);
+ }
+
+ // Ensure buffer is large enough to hold at least the specified size.
+ if (n > pend - pnext)
+ {
+ if (n <= max_size_ && pnext <= max_size_ - n)
+ {
+ pend = pnext + n;
+ buffer_.resize((std::max<std::size_t>)(pend, 1));
+ }
+ else
+ {
+ std::length_error ex("boost::asio::streambuf too long");
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+
+ // Update stream positions.
+ setg(&buffer_[0], &buffer_[0], &buffer_[0] + pnext);
+ setp(&buffer_[0] + pnext, &buffer_[0] + pend);
+ }
+
+private:
+ std::size_t max_size_;
+ std::vector<char_type, Allocator> buffer_;
+
+ // Helper function to get the preferred size for reading data.
+ friend std::size_t read_size_helper(
+ basic_streambuf& sb, std::size_t max_size)
+ {
+ return std::min<std::size_t>(
+ std::max<std::size_t>(512, sb.buffer_.capacity() - sb.size()),
+ std::min<std::size_t>(max_size, sb.max_size() - sb.size()));
+ }
+};
+
+// Helper function to get the preferred size for reading data. Used for any
+// user-provided specialisations of basic_streambuf.
+template <typename Allocator>
+inline std::size_t read_size_helper(
+ basic_streambuf<Allocator>& sb, std::size_t max_size)
+{
+ return std::min<std::size_t>(512,
+ std::min<std::size_t>(max_size, sb.max_size() - sb.size()));
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_BASIC_STREAMBUF_HPP
diff --git a/ext/patches/boost/asio/basic_streambuf_fwd.hpp b/ext/patches/boost/asio/basic_streambuf_fwd.hpp
new file mode 100644
index 0000000..1b50079
--- /dev/null
+++ b/ext/patches/boost/asio/basic_streambuf_fwd.hpp
@@ -0,0 +1,35 @@
+//
+// basic_streambuf_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_STREAMBUF_FWD_HPP
+#define BOOST_ASIO_BASIC_STREAMBUF_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <memory>
+
+namespace boost {
+namespace asio {
+
+template <typename Allocator = std::allocator<char> >
+class basic_streambuf;
+
+} // namespace asio
+} // namespace boost
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_BASIC_STREAMBUF_FWD_HPP
diff --git a/ext/patches/boost/asio/basic_waitable_timer.hpp b/ext/patches/boost/asio/basic_waitable_timer.hpp
new file mode 100644
index 0000000..2f4f4bc
--- /dev/null
+++ b/ext/patches/boost/asio/basic_waitable_timer.hpp
@@ -0,0 +1,521 @@
+//
+// basic_waitable_timer.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BASIC_WAITABLE_TIMER_HPP
+#define BOOST_ASIO_BASIC_WAITABLE_TIMER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/wait_traits.hpp>
+#include <boost/asio/waitable_timer_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides waitable timer functionality.
+/**
+ * The basic_waitable_timer class template provides the ability to perform a
+ * blocking or asynchronous wait for a timer to expire.
+ *
+ * A waitable timer is always in one of two states: "expired" or "not expired".
+ * If the wait() or async_wait() function is called on an expired timer, the
+ * wait operation will complete immediately.
+ *
+ * Most applications will use one of the boost::asio::steady_timer,
+ * boost::asio::system_timer or boost::asio::high_resolution_timer typedefs.
+ *
+ * @note This waitable timer functionality is for use with the C++11 standard
+ * library's @c <chrono> facility, or with the Boost.Chrono library.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Examples
+ * Performing a blocking wait (C++11):
+ * @code
+ * // Construct a timer without setting an expiry time.
+ * boost::asio::steady_timer timer(io_service);
+ *
+ * // Set an expiry time relative to now.
+ * timer.expires_from_now(std::chrono::seconds(5));
+ *
+ * // Wait for the timer to expire.
+ * timer.wait();
+ * @endcode
+ *
+ * @par
+ * Performing an asynchronous wait (C++11):
+ * @code
+ * void handler(const boost::system::error_code& error)
+ * {
+ * if (!error)
+ * {
+ * // Timer expired.
+ * }
+ * }
+ *
+ * ...
+ *
+ * // Construct a timer with an absolute expiry time.
+ * boost::asio::steady_timer timer(io_service,
+ * std::chrono::steady_clock::now() + std::chrono::seconds(60));
+ *
+ * // Start an asynchronous wait.
+ * timer.async_wait(handler);
+ * @endcode
+ *
+ * @par Changing an active waitable timer's expiry time
+ *
+ * Changing the expiry time of a timer while there are pending asynchronous
+ * waits causes those wait operations to be cancelled. To ensure that the action
+ * associated with the timer is performed only once, use something like this:
+ * used:
+ *
+ * @code
+ * void on_some_event()
+ * {
+ * if (my_timer.expires_from_now(seconds(5)) > 0)
+ * {
+ * // We managed to cancel the timer. Start new asynchronous wait.
+ * my_timer.async_wait(on_timeout);
+ * }
+ * else
+ * {
+ * // Too late, timer has already expired!
+ * }
+ * }
+ *
+ * void on_timeout(const boost::system::error_code& e)
+ * {
+ * if (e != boost::asio::error::operation_aborted)
+ * {
+ * // Timer was not cancelled, take necessary action.
+ * }
+ * }
+ * @endcode
+ *
+ * @li The boost::asio::basic_waitable_timer::expires_from_now() function
+ * cancels any pending asynchronous waits, and returns the number of
+ * asynchronous waits that were cancelled. If it returns 0 then you were too
+ * late and the wait handler has already been executed, or will soon be
+ * executed. If it returns 1 then the wait handler was successfully cancelled.
+ *
+ * @li If a wait handler is cancelled, the boost::system::error_code passed to
+ * it contains the value boost::asio::error::operation_aborted.
+ */
+template <typename Clock,
+ typename WaitTraits = boost::asio::wait_traits<Clock>,
+ typename WaitableTimerService = waitable_timer_service<Clock, WaitTraits> >
+class basic_waitable_timer
+ : public basic_io_object<WaitableTimerService>
+{
+public:
+ /// The clock type.
+ typedef Clock clock_type;
+
+ /// The duration type of the clock.
+ typedef typename clock_type::duration duration;
+
+ /// The time point type of the clock.
+ typedef typename clock_type::time_point time_point;
+
+ /// The wait traits type.
+ typedef WaitTraits traits_type;
+
+ /// Constructor.
+ /**
+ * This constructor creates a timer without setting an expiry time. The
+ * expires_at() or expires_from_now() functions must be called to set an
+ * expiry time before the timer can be waited on.
+ *
+ * @param io_service The io_service object that the timer will use to dispatch
+ * handlers for any asynchronous operations performed on the timer.
+ */
+ explicit basic_waitable_timer(boost::asio::io_service& io_service)
+ : basic_io_object<WaitableTimerService>(io_service)
+ {
+ }
+
+ /// Constructor to set a particular expiry time as an absolute time.
+ /**
+ * This constructor creates a timer and sets the expiry time.
+ *
+ * @param io_service The io_service object that the timer will use to dispatch
+ * handlers for any asynchronous operations performed on the timer.
+ *
+ * @param expiry_time The expiry time to be used for the timer, expressed
+ * as an absolute time.
+ */
+ basic_waitable_timer(boost::asio::io_service& io_service,
+ const time_point& expiry_time)
+ : basic_io_object<WaitableTimerService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->service.expires_at(this->implementation, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_at");
+ }
+
+ /// Constructor to set a particular expiry time relative to now.
+ /**
+ * This constructor creates a timer and sets the expiry time.
+ *
+ * @param io_service The io_service object that the timer will use to dispatch
+ * handlers for any asynchronous operations performed on the timer.
+ *
+ * @param expiry_time The expiry time to be used for the timer, relative to
+ * now.
+ */
+ basic_waitable_timer(boost::asio::io_service& io_service,
+ const duration& expiry_time)
+ : basic_io_object<WaitableTimerService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->service.expires_from_now(this->implementation, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_from_now");
+ }
+
+ /// Cancel any asynchronous operations that are waiting on the timer.
+ /**
+ * This function forces the completion of any pending asynchronous wait
+ * operations against the timer. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * Cancelling the timer does not change the expiry time.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If the timer has already expired when cancel() is called, then the
+ * handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t cancel()
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->service.cancel(this->implementation, ec);
+ boost::asio::detail::throw_error(ec, "cancel");
+ return s;
+ }
+
+ /// Cancel any asynchronous operations that are waiting on the timer.
+ /**
+ * This function forces the completion of any pending asynchronous wait
+ * operations against the timer. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * Cancelling the timer does not change the expiry time.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @note If the timer has already expired when cancel() is called, then the
+ * handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t cancel(boost::system::error_code& ec)
+ {
+ return this->service.cancel(this->implementation, ec);
+ }
+
+ /// Cancels one asynchronous operation that is waiting on the timer.
+ /**
+ * This function forces the completion of one pending asynchronous wait
+ * operation against the timer. Handlers are cancelled in FIFO order. The
+ * handler for the cancelled operation will be invoked with the
+ * boost::asio::error::operation_aborted error code.
+ *
+ * Cancelling the timer does not change the expiry time.
+ *
+ * @return The number of asynchronous operations that were cancelled. That is,
+ * either 0 or 1.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If the timer has already expired when cancel_one() is called, then
+ * the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t cancel_one()
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->service.cancel_one(this->implementation, ec);
+ boost::asio::detail::throw_error(ec, "cancel_one");
+ return s;
+ }
+
+ /// Cancels one asynchronous operation that is waiting on the timer.
+ /**
+ * This function forces the completion of one pending asynchronous wait
+ * operation against the timer. Handlers are cancelled in FIFO order. The
+ * handler for the cancelled operation will be invoked with the
+ * boost::asio::error::operation_aborted error code.
+ *
+ * Cancelling the timer does not change the expiry time.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of asynchronous operations that were cancelled. That is,
+ * either 0 or 1.
+ *
+ * @note If the timer has already expired when cancel_one() is called, then
+ * the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t cancel_one(boost::system::error_code& ec)
+ {
+ return this->service.cancel_one(this->implementation, ec);
+ }
+
+ /// Get the timer's expiry time as an absolute time.
+ /**
+ * This function may be used to obtain the timer's current expiry time.
+ * Whether the timer has expired or not does not affect this value.
+ */
+ time_point expires_at() const
+ {
+ return this->service.expires_at(this->implementation);
+ }
+
+ /// Set the timer's expiry time as an absolute time.
+ /**
+ * This function sets the expiry time. Any pending asynchronous wait
+ * operations will be cancelled. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If the timer has already expired when expires_at() is called, then
+ * the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t expires_at(const time_point& expiry_time)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->service.expires_at(
+ this->implementation, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_at");
+ return s;
+ }
+
+ /// Set the timer's expiry time as an absolute time.
+ /**
+ * This function sets the expiry time. Any pending asynchronous wait
+ * operations will be cancelled. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @note If the timer has already expired when expires_at() is called, then
+ * the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t expires_at(const time_point& expiry_time,
+ boost::system::error_code& ec)
+ {
+ return this->service.expires_at(this->implementation, expiry_time, ec);
+ }
+
+ /// Get the timer's expiry time relative to now.
+ /**
+ * This function may be used to obtain the timer's current expiry time.
+ * Whether the timer has expired or not does not affect this value.
+ */
+ duration expires_from_now() const
+ {
+ return this->service.expires_from_now(this->implementation);
+ }
+
+ /// Set the timer's expiry time relative to now.
+ /**
+ * This function sets the expiry time. Any pending asynchronous wait
+ * operations will be cancelled. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note If the timer has already expired when expires_from_now() is called,
+ * then the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t expires_from_now(const duration& expiry_time)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->service.expires_from_now(
+ this->implementation, expiry_time, ec);
+ boost::asio::detail::throw_error(ec, "expires_from_now");
+ return s;
+ }
+
+ /// Set the timer's expiry time relative to now.
+ /**
+ * This function sets the expiry time. Any pending asynchronous wait
+ * operations will be cancelled. The handler for each cancelled operation will
+ * be invoked with the boost::asio::error::operation_aborted error code.
+ *
+ * @param expiry_time The expiry time to be used for the timer.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of asynchronous operations that were cancelled.
+ *
+ * @note If the timer has already expired when expires_from_now() is called,
+ * then the handlers for asynchronous wait operations will:
+ *
+ * @li have already been invoked; or
+ *
+ * @li have been queued for invocation in the near future.
+ *
+ * These handlers can no longer be cancelled, and therefore are passed an
+ * error code that indicates the successful completion of the wait operation.
+ */
+ std::size_t expires_from_now(const duration& expiry_time,
+ boost::system::error_code& ec)
+ {
+ return this->service.expires_from_now(
+ this->implementation, expiry_time, ec);
+ }
+
+ /// Perform a blocking wait on the timer.
+ /**
+ * This function is used to wait for the timer to expire. This function
+ * blocks and does not return until the timer has expired.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void wait()
+ {
+ boost::system::error_code ec;
+ this->service.wait(this->implementation, ec);
+ boost::asio::detail::throw_error(ec, "wait");
+ }
+
+ /// Perform a blocking wait on the timer.
+ /**
+ * This function is used to wait for the timer to expire. This function
+ * blocks and does not return until the timer has expired.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ void wait(boost::system::error_code& ec)
+ {
+ this->service.wait(this->implementation, ec);
+ }
+
+ /// Start an asynchronous wait on the timer.
+ /**
+ * This function may be used to initiate an asynchronous wait against the
+ * timer. It always returns immediately.
+ *
+ * For each call to async_wait(), the supplied handler will be called exactly
+ * once. The handler will be called when:
+ *
+ * @li The timer has expired.
+ *
+ * @li The timer was cancelled, in which case the handler is passed the error
+ * code boost::asio::error::operation_aborted.
+ *
+ * @param handler The handler to be called when the timer expires. Copies
+ * will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename WaitHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WaitHandler,
+ void (boost::system::error_code))
+ async_wait(BOOST_ASIO_MOVE_ARG(WaitHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WaitHandler.
+ BOOST_ASIO_WAIT_HANDLER_CHECK(WaitHandler, handler) type_check;
+
+ return this->service.async_wait(this->implementation,
+ BOOST_ASIO_MOVE_CAST(WaitHandler)(handler));
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BASIC_WAITABLE_TIMER_HPP
diff --git a/ext/patches/boost/asio/buffer.hpp b/ext/patches/boost/asio/buffer.hpp
new file mode 100644
index 0000000..c2b1249
--- /dev/null
+++ b/ext/patches/boost/asio/buffer.hpp
@@ -0,0 +1,2241 @@
+//
+// buffer.hpp
+// ~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BUFFER_HPP
+#define BOOST_ASIO_BUFFER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <cstring>
+#include <string>
+#include <vector>
+#include <boost/asio/detail/array_fwd.hpp>
+
+#if defined(BOOST_ASIO_MSVC)
+# if defined(_HAS_ITERATOR_DEBUGGING) && (_HAS_ITERATOR_DEBUGGING != 0)
+# if !defined(BOOST_ASIO_DISABLE_BUFFER_DEBUGGING)
+# define BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+# endif // !defined(BOOST_ASIO_DISABLE_BUFFER_DEBUGGING)
+# endif // defined(_HAS_ITERATOR_DEBUGGING)
+#endif // defined(BOOST_ASIO_MSVC)
+
+#if defined(__GNUC__)
+# if defined(_GLIBCXX_DEBUG)
+# if !defined(BOOST_ASIO_DISABLE_BUFFER_DEBUGGING)
+# define BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+# endif // !defined(BOOST_ASIO_DISABLE_BUFFER_DEBUGGING)
+# endif // defined(_GLIBCXX_DEBUG)
+#endif // defined(__GNUC__)
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+# include <boost/asio/detail/function.hpp>
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+
+#if defined(BOOST_ASIO_HAS_BOOST_WORKAROUND)
+# include <boost/detail/workaround.hpp>
+# if BOOST_WORKAROUND(__BORLANDC__, BOOST_TESTED_AT(0x582)) \
+ || BOOST_WORKAROUND(__SUNPRO_CC, BOOST_TESTED_AT(0x590))
+# define BOOST_ASIO_ENABLE_ARRAY_BUFFER_WORKAROUND
+# endif // BOOST_WORKAROUND(__BORLANDC__, BOOST_TESTED_AT(0x582))
+ // || BOOST_WORKAROUND(__SUNPRO_CC, BOOST_TESTED_AT(0x590))
+#endif // defined(BOOST_ASIO_HAS_BOOST_WORKAROUND)
+
+#if defined(BOOST_ASIO_ENABLE_ARRAY_BUFFER_WORKAROUND)
+# include <boost/asio/detail/type_traits.hpp>
+#endif // defined(BOOST_ASIO_ENABLE_ARRAY_BUFFER_WORKAROUND)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+class mutable_buffer;
+class const_buffer;
+
+namespace detail {
+void* buffer_cast_helper(const mutable_buffer&);
+const void* buffer_cast_helper(const const_buffer&);
+std::size_t buffer_size_helper(const mutable_buffer&);
+std::size_t buffer_size_helper(const const_buffer&);
+} // namespace detail
+
+/// Holds a buffer that can be modified.
+/**
+ * The mutable_buffer class provides a safe representation of a buffer that can
+ * be modified. It does not own the underlying data, and so is cheap to copy or
+ * assign.
+ *
+ * @par Accessing Buffer Contents
+ *
+ * The contents of a buffer may be accessed using the @ref buffer_size
+ * and @ref buffer_cast functions:
+ *
+ * @code boost::asio::mutable_buffer b1 = ...;
+ * std::size_t s1 = boost::asio::buffer_size(b1);
+ * unsigned char* p1 = boost::asio::buffer_cast<unsigned char*>(b1);
+ * @endcode
+ *
+ * The boost::asio::buffer_cast function permits violations of type safety, so
+ * uses of it in application code should be carefully considered.
+ */
+class mutable_buffer
+{
+public:
+ /// Construct an empty buffer.
+ mutable_buffer()
+ : data_(0),
+ size_(0)
+ {
+ }
+
+ /// Construct a buffer to represent a given memory range.
+ mutable_buffer(void* data, std::size_t size)
+ : data_(data),
+ size_(size)
+ {
+ }
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ mutable_buffer(void* data, std::size_t size,
+ boost::asio::detail::function<void()> debug_check)
+ : data_(data),
+ size_(size),
+ debug_check_(debug_check)
+ {
+ }
+
+ const boost::asio::detail::function<void()>& get_debug_check() const
+ {
+ return debug_check_;
+ }
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+
+private:
+ friend void* boost::asio::detail::buffer_cast_helper(
+ const mutable_buffer& b);
+ friend std::size_t boost::asio::detail::buffer_size_helper(
+ const mutable_buffer& b);
+
+ void* data_;
+ std::size_t size_;
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ boost::asio::detail::function<void()> debug_check_;
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+};
+
+namespace detail {
+
+inline void* buffer_cast_helper(const mutable_buffer& b)
+{
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ if (b.size_ && b.debug_check_)
+ b.debug_check_();
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ return b.data_;
+}
+
+inline std::size_t buffer_size_helper(const mutable_buffer& b)
+{
+ return b.size_;
+}
+
+} // namespace detail
+
+/// Adapts a single modifiable buffer so that it meets the requirements of the
+/// MutableBufferSequence concept.
+class mutable_buffers_1
+ : public mutable_buffer
+{
+public:
+ /// The type for each element in the list of buffers.
+ typedef mutable_buffer value_type;
+
+ /// A random-access iterator type that may be used to read elements.
+ typedef const mutable_buffer* const_iterator;
+
+ /// Construct to represent a given memory range.
+ mutable_buffers_1(void* data, std::size_t size)
+ : mutable_buffer(data, size)
+ {
+ }
+
+ /// Construct to represent a single modifiable buffer.
+ explicit mutable_buffers_1(const mutable_buffer& b)
+ : mutable_buffer(b)
+ {
+ }
+
+ /// Get a random-access iterator to the first element.
+ const_iterator begin() const
+ {
+ return this;
+ }
+
+ /// Get a random-access iterator for one past the last element.
+ const_iterator end() const
+ {
+ return begin() + 1;
+ }
+};
+
+/// Holds a buffer that cannot be modified.
+/**
+ * The const_buffer class provides a safe representation of a buffer that cannot
+ * be modified. It does not own the underlying data, and so is cheap to copy or
+ * assign.
+ *
+ * @par Accessing Buffer Contents
+ *
+ * The contents of a buffer may be accessed using the @ref buffer_size
+ * and @ref buffer_cast functions:
+ *
+ * @code boost::asio::const_buffer b1 = ...;
+ * std::size_t s1 = boost::asio::buffer_size(b1);
+ * const unsigned char* p1 = boost::asio::buffer_cast<const unsigned char*>(b1);
+ * @endcode
+ *
+ * The boost::asio::buffer_cast function permits violations of type safety, so
+ * uses of it in application code should be carefully considered.
+ */
+class const_buffer
+{
+public:
+ /// Construct an empty buffer.
+ const_buffer()
+ : data_(0),
+ size_(0)
+ {
+ }
+
+ /// Construct a buffer to represent a given memory range.
+ const_buffer(const void* data, std::size_t size)
+ : data_(data),
+ size_(size)
+ {
+ }
+
+ /// Construct a non-modifiable buffer from a modifiable one.
+ const_buffer(const mutable_buffer& b)
+ : data_(boost::asio::detail::buffer_cast_helper(b)),
+ size_(boost::asio::detail::buffer_size_helper(b))
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , debug_check_(b.get_debug_check())
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ {
+ }
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ const_buffer(const void* data, std::size_t size,
+ boost::asio::detail::function<void()> debug_check)
+ : data_(data),
+ size_(size),
+ debug_check_(debug_check)
+ {
+ }
+
+ const boost::asio::detail::function<void()>& get_debug_check() const
+ {
+ return debug_check_;
+ }
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+
+private:
+ friend const void* boost::asio::detail::buffer_cast_helper(
+ const const_buffer& b);
+ friend std::size_t boost::asio::detail::buffer_size_helper(
+ const const_buffer& b);
+
+ const void* data_;
+ std::size_t size_;
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ boost::asio::detail::function<void()> debug_check_;
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+};
+
+namespace detail {
+
+inline const void* buffer_cast_helper(const const_buffer& b)
+{
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ if (b.size_ && b.debug_check_)
+ b.debug_check_();
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ return b.data_;
+}
+
+inline std::size_t buffer_size_helper(const const_buffer& b)
+{
+ return b.size_;
+}
+
+} // namespace detail
+
+/// Adapts a single non-modifiable buffer so that it meets the requirements of
+/// the ConstBufferSequence concept.
+class const_buffers_1
+ : public const_buffer
+{
+public:
+ /// The type for each element in the list of buffers.
+ typedef const_buffer value_type;
+
+ /// A random-access iterator type that may be used to read elements.
+ typedef const const_buffer* const_iterator;
+
+ /// Construct to represent a given memory range.
+ const_buffers_1(const void* data, std::size_t size)
+ : const_buffer(data, size)
+ {
+ }
+
+ /// Construct to represent a single non-modifiable buffer.
+ explicit const_buffers_1(const const_buffer& b)
+ : const_buffer(b)
+ {
+ }
+
+ /// Get a random-access iterator to the first element.
+ const_iterator begin() const
+ {
+ return this;
+ }
+
+ /// Get a random-access iterator for one past the last element.
+ const_iterator end() const
+ {
+ return begin() + 1;
+ }
+};
+
+/// An implementation of both the ConstBufferSequence and MutableBufferSequence
+/// concepts to represent a null buffer sequence.
+class null_buffers
+{
+public:
+ /// The type for each element in the list of buffers.
+ typedef mutable_buffer value_type;
+
+ /// A random-access iterator type that may be used to read elements.
+ typedef const mutable_buffer* const_iterator;
+
+ /// Get a random-access iterator to the first element.
+ const_iterator begin() const
+ {
+ return &buf_;
+ }
+
+ /// Get a random-access iterator for one past the last element.
+ const_iterator end() const
+ {
+ return &buf_;
+ }
+
+private:
+ mutable_buffer buf_;
+};
+
+/** @defgroup buffer_size boost::asio::buffer_size
+ *
+ * @brief The boost::asio::buffer_size function determines the total number of
+ * bytes in a buffer or buffer sequence.
+ */
+/*@{*/
+
+/// Get the number of bytes in a modifiable buffer.
+inline std::size_t buffer_size(const mutable_buffer& b)
+{
+ return detail::buffer_size_helper(b);
+}
+
+/// Get the number of bytes in a modifiable buffer.
+inline std::size_t buffer_size(const mutable_buffers_1& b)
+{
+ return detail::buffer_size_helper(b);
+}
+
+/// Get the number of bytes in a non-modifiable buffer.
+inline std::size_t buffer_size(const const_buffer& b)
+{
+ return detail::buffer_size_helper(b);
+}
+
+/// Get the number of bytes in a non-modifiable buffer.
+inline std::size_t buffer_size(const const_buffers_1& b)
+{
+ return detail::buffer_size_helper(b);
+}
+
+/// Get the total number of bytes in a buffer sequence.
+/**
+ * The @c BufferSequence template parameter may meet either of the @c
+ * ConstBufferSequence or @c MutableBufferSequence type requirements.
+ */
+template <typename BufferSequence>
+inline std::size_t buffer_size(const BufferSequence& b)
+{
+ std::size_t total_buffer_size = 0;
+
+ typename BufferSequence::const_iterator iter = b.begin();
+ typename BufferSequence::const_iterator end = b.end();
+ for (; iter != end; ++iter)
+ total_buffer_size += detail::buffer_size_helper(*iter);
+
+ return total_buffer_size;
+}
+
+/*@}*/
+
+/** @defgroup buffer_cast boost::asio::buffer_cast
+ *
+ * @brief The boost::asio::buffer_cast function is used to obtain a pointer to
+ * the underlying memory region associated with a buffer.
+ *
+ * @par Examples:
+ *
+ * To access the memory of a non-modifiable buffer, use:
+ * @code boost::asio::const_buffer b1 = ...;
+ * const unsigned char* p1 = boost::asio::buffer_cast<const unsigned char*>(b1);
+ * @endcode
+ *
+ * To access the memory of a modifiable buffer, use:
+ * @code boost::asio::mutable_buffer b2 = ...;
+ * unsigned char* p2 = boost::asio::buffer_cast<unsigned char*>(b2);
+ * @endcode
+ *
+ * The boost::asio::buffer_cast function permits violations of type safety, so
+ * uses of it in application code should be carefully considered.
+ */
+/*@{*/
+
+/// Cast a non-modifiable buffer to a specified pointer to POD type.
+template <typename PointerToPodType>
+inline PointerToPodType buffer_cast(const mutable_buffer& b)
+{
+ return static_cast<PointerToPodType>(detail::buffer_cast_helper(b));
+}
+
+/// Cast a non-modifiable buffer to a specified pointer to POD type.
+template <typename PointerToPodType>
+inline PointerToPodType buffer_cast(const const_buffer& b)
+{
+ return static_cast<PointerToPodType>(detail::buffer_cast_helper(b));
+}
+
+/*@}*/
+
+/// Create a new modifiable buffer that is offset from the start of another.
+/**
+ * @relates mutable_buffer
+ */
+inline mutable_buffer operator+(const mutable_buffer& b, std::size_t start)
+{
+ if (start > buffer_size(b))
+ return mutable_buffer();
+ char* new_data = buffer_cast<char*>(b) + start;
+ std::size_t new_size = buffer_size(b) - start;
+ return mutable_buffer(new_data, new_size
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , b.get_debug_check()
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ );
+}
+
+/// Create a new modifiable buffer that is offset from the start of another.
+/**
+ * @relates mutable_buffer
+ */
+inline mutable_buffer operator+(std::size_t start, const mutable_buffer& b)
+{
+ if (start > buffer_size(b))
+ return mutable_buffer();
+ char* new_data = buffer_cast<char*>(b) + start;
+ std::size_t new_size = buffer_size(b) - start;
+ return mutable_buffer(new_data, new_size
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , b.get_debug_check()
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ );
+}
+
+/// Create a new non-modifiable buffer that is offset from the start of another.
+/**
+ * @relates const_buffer
+ */
+inline const_buffer operator+(const const_buffer& b, std::size_t start)
+{
+ if (start > buffer_size(b))
+ return const_buffer();
+ const char* new_data = buffer_cast<const char*>(b) + start;
+ std::size_t new_size = buffer_size(b) - start;
+ return const_buffer(new_data, new_size
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , b.get_debug_check()
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ );
+}
+
+/// Create a new non-modifiable buffer that is offset from the start of another.
+/**
+ * @relates const_buffer
+ */
+inline const_buffer operator+(std::size_t start, const const_buffer& b)
+{
+ if (start > buffer_size(b))
+ return const_buffer();
+ const char* new_data = buffer_cast<const char*>(b) + start;
+ std::size_t new_size = buffer_size(b) - start;
+ return const_buffer(new_data, new_size
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , b.get_debug_check()
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ );
+}
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+namespace detail {
+
+template <typename Iterator>
+class buffer_debug_check
+{
+public:
+ buffer_debug_check(Iterator iter)
+ : iter_(iter)
+ {
+ }
+
+ ~buffer_debug_check()
+ {
+#if defined(BOOST_ASIO_MSVC) && (BOOST_ASIO_MSVC == 1400)
+ // MSVC 8's string iterator checking may crash in a std::string::iterator
+ // object's destructor when the iterator points to an already-destroyed
+ // std::string object, unless the iterator is cleared first.
+ iter_ = Iterator();
+#endif // defined(BOOST_ASIO_MSVC) && (BOOST_ASIO_MSVC == 1400)
+ }
+
+ void operator()()
+ {
+ *iter_;
+ }
+
+private:
+ Iterator iter_;
+};
+
+} // namespace detail
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+
+/** @defgroup buffer boost::asio::buffer
+ *
+ * @brief The boost::asio::buffer function is used to create a buffer object to
+ * represent raw memory, an array of POD elements, a vector of POD elements,
+ * or a std::string.
+ *
+ * A buffer object represents a contiguous region of memory as a 2-tuple
+ * consisting of a pointer and size in bytes. A tuple of the form <tt>{void*,
+ * size_t}</tt> specifies a mutable (modifiable) region of memory. Similarly, a
+ * tuple of the form <tt>{const void*, size_t}</tt> specifies a const
+ * (non-modifiable) region of memory. These two forms correspond to the classes
+ * mutable_buffer and const_buffer, respectively. To mirror C++'s conversion
+ * rules, a mutable_buffer is implicitly convertible to a const_buffer, and the
+ * opposite conversion is not permitted.
+ *
+ * The simplest use case involves reading or writing a single buffer of a
+ * specified size:
+ *
+ * @code sock.send(boost::asio::buffer(data, size)); @endcode
+ *
+ * In the above example, the return value of boost::asio::buffer meets the
+ * requirements of the ConstBufferSequence concept so that it may be directly
+ * passed to the socket's write function. A buffer created for modifiable
+ * memory also meets the requirements of the MutableBufferSequence concept.
+ *
+ * An individual buffer may be created from a builtin array, std::vector,
+ * std::array or boost::array of POD elements. This helps prevent buffer
+ * overruns by automatically determining the size of the buffer:
+ *
+ * @code char d1[128];
+ * size_t bytes_transferred = sock.receive(boost::asio::buffer(d1));
+ *
+ * std::vector<char> d2(128);
+ * bytes_transferred = sock.receive(boost::asio::buffer(d2));
+ *
+ * std::array<char, 128> d3;
+ * bytes_transferred = sock.receive(boost::asio::buffer(d3));
+ *
+ * boost::array<char, 128> d4;
+ * bytes_transferred = sock.receive(boost::asio::buffer(d4)); @endcode
+ *
+ * In all three cases above, the buffers created are exactly 128 bytes long.
+ * Note that a vector is @e never automatically resized when creating or using
+ * a buffer. The buffer size is determined using the vector's <tt>size()</tt>
+ * member function, and not its capacity.
+ *
+ * @par Accessing Buffer Contents
+ *
+ * The contents of a buffer may be accessed using the @ref buffer_size and
+ * @ref buffer_cast functions:
+ *
+ * @code boost::asio::mutable_buffer b1 = ...;
+ * std::size_t s1 = boost::asio::buffer_size(b1);
+ * unsigned char* p1 = boost::asio::buffer_cast<unsigned char*>(b1);
+ *
+ * boost::asio::const_buffer b2 = ...;
+ * std::size_t s2 = boost::asio::buffer_size(b2);
+ * const void* p2 = boost::asio::buffer_cast<const void*>(b2); @endcode
+ *
+ * The boost::asio::buffer_cast function permits violations of type safety, so
+ * uses of it in application code should be carefully considered.
+ *
+ * For convenience, the @ref buffer_size function also works on buffer
+ * sequences (that is, types meeting the ConstBufferSequence or
+ * MutableBufferSequence type requirements). In this case, the function returns
+ * the total size of all buffers in the sequence.
+ *
+ * @par Buffer Copying
+ *
+ * The @ref buffer_copy function may be used to copy raw bytes between
+ * individual buffers and buffer sequences.
+ *
+ * In particular, when used with the @ref buffer_size, the @ref buffer_copy
+ * function can be used to linearise a sequence of buffers. For example:
+ *
+ * @code vector<const_buffer> buffers = ...;
+ *
+ * vector<unsigned char> data(boost::asio::buffer_size(buffers));
+ * boost::asio::buffer_copy(boost::asio::buffer(data), buffers); @endcode
+ *
+ * Note that @ref buffer_copy is implemented in terms of @c memcpy, and
+ * consequently it cannot be used to copy between overlapping memory regions.
+ *
+ * @par Buffer Invalidation
+ *
+ * A buffer object does not have any ownership of the memory it refers to. It
+ * is the responsibility of the application to ensure the memory region remains
+ * valid until it is no longer required for an I/O operation. When the memory
+ * is no longer available, the buffer is said to have been invalidated.
+ *
+ * For the boost::asio::buffer overloads that accept an argument of type
+ * std::vector, the buffer objects returned are invalidated by any vector
+ * operation that also invalidates all references, pointers and iterators
+ * referring to the elements in the sequence (C++ Std, 23.2.4)
+ *
+ * For the boost::asio::buffer overloads that accept an argument of type
+ * std::basic_string, the buffer objects returned are invalidated according to
+ * the rules defined for invalidation of references, pointers and iterators
+ * referring to elements of the sequence (C++ Std, 21.3).
+ *
+ * @par Buffer Arithmetic
+ *
+ * Buffer objects may be manipulated using simple arithmetic in a safe way
+ * which helps prevent buffer overruns. Consider an array initialised as
+ * follows:
+ *
+ * @code boost::array<char, 6> a = { 'a', 'b', 'c', 'd', 'e' }; @endcode
+ *
+ * A buffer object @c b1 created using:
+ *
+ * @code b1 = boost::asio::buffer(a); @endcode
+ *
+ * represents the entire array, <tt>{ 'a', 'b', 'c', 'd', 'e' }</tt>. An
+ * optional second argument to the boost::asio::buffer function may be used to
+ * limit the size, in bytes, of the buffer:
+ *
+ * @code b2 = boost::asio::buffer(a, 3); @endcode
+ *
+ * such that @c b2 represents the data <tt>{ 'a', 'b', 'c' }</tt>. Even if the
+ * size argument exceeds the actual size of the array, the size of the buffer
+ * object created will be limited to the array size.
+ *
+ * An offset may be applied to an existing buffer to create a new one:
+ *
+ * @code b3 = b1 + 2; @endcode
+ *
+ * where @c b3 will set to represent <tt>{ 'c', 'd', 'e' }</tt>. If the offset
+ * exceeds the size of the existing buffer, the newly created buffer will be
+ * empty.
+ *
+ * Both an offset and size may be specified to create a buffer that corresponds
+ * to a specific range of bytes within an existing buffer:
+ *
+ * @code b4 = boost::asio::buffer(b1 + 1, 3); @endcode
+ *
+ * so that @c b4 will refer to the bytes <tt>{ 'b', 'c', 'd' }</tt>.
+ *
+ * @par Buffers and Scatter-Gather I/O
+ *
+ * To read or write using multiple buffers (i.e. scatter-gather I/O), multiple
+ * buffer objects may be assigned into a container that supports the
+ * MutableBufferSequence (for read) or ConstBufferSequence (for write) concepts:
+ *
+ * @code
+ * char d1[128];
+ * std::vector<char> d2(128);
+ * boost::array<char, 128> d3;
+ *
+ * boost::array<mutable_buffer, 3> bufs1 = {
+ * boost::asio::buffer(d1),
+ * boost::asio::buffer(d2),
+ * boost::asio::buffer(d3) };
+ * bytes_transferred = sock.receive(bufs1);
+ *
+ * std::vector<const_buffer> bufs2;
+ * bufs2.push_back(boost::asio::buffer(d1));
+ * bufs2.push_back(boost::asio::buffer(d2));
+ * bufs2.push_back(boost::asio::buffer(d3));
+ * bytes_transferred = sock.send(bufs2); @endcode
+ */
+/*@{*/
+
+/// Create a new modifiable buffer from an existing buffer.
+/**
+ * @returns <tt>mutable_buffers_1(b)</tt>.
+ */
+inline mutable_buffers_1 buffer(const mutable_buffer& b)
+{
+ return mutable_buffers_1(b);
+}
+
+/// Create a new modifiable buffer from an existing buffer.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * buffer_cast<void*>(b),
+ * min(buffer_size(b), max_size_in_bytes)); @endcode
+ */
+inline mutable_buffers_1 buffer(const mutable_buffer& b,
+ std::size_t max_size_in_bytes)
+{
+ return mutable_buffers_1(
+ mutable_buffer(buffer_cast<void*>(b),
+ buffer_size(b) < max_size_in_bytes
+ ? buffer_size(b) : max_size_in_bytes
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , b.get_debug_check()
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ ));
+}
+
+/// Create a new non-modifiable buffer from an existing buffer.
+/**
+ * @returns <tt>const_buffers_1(b)</tt>.
+ */
+inline const_buffers_1 buffer(const const_buffer& b)
+{
+ return const_buffers_1(b);
+}
+
+/// Create a new non-modifiable buffer from an existing buffer.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * buffer_cast<const void*>(b),
+ * min(buffer_size(b), max_size_in_bytes)); @endcode
+ */
+inline const_buffers_1 buffer(const const_buffer& b,
+ std::size_t max_size_in_bytes)
+{
+ return const_buffers_1(
+ const_buffer(buffer_cast<const void*>(b),
+ buffer_size(b) < max_size_in_bytes
+ ? buffer_size(b) : max_size_in_bytes
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , b.get_debug_check()
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ ));
+}
+
+/// Create a new modifiable buffer that represents the given memory range.
+/**
+ * @returns <tt>mutable_buffers_1(data, size_in_bytes)</tt>.
+ */
+inline mutable_buffers_1 buffer(void* data, std::size_t size_in_bytes)
+{
+ return mutable_buffers_1(mutable_buffer(data, size_in_bytes));
+}
+
+/// Create a new non-modifiable buffer that represents the given memory range.
+/**
+ * @returns <tt>const_buffers_1(data, size_in_bytes)</tt>.
+ */
+inline const_buffers_1 buffer(const void* data,
+ std::size_t size_in_bytes)
+{
+ return const_buffers_1(const_buffer(data, size_in_bytes));
+}
+
+/// Create a new modifiable buffer that represents the given POD array.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * static_cast<void*>(data),
+ * N * sizeof(PodType)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline mutable_buffers_1 buffer(PodType (&data)[N])
+{
+ return mutable_buffers_1(mutable_buffer(data, N * sizeof(PodType)));
+}
+
+/// Create a new modifiable buffer that represents the given POD array.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * static_cast<void*>(data),
+ * min(N * sizeof(PodType), max_size_in_bytes)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline mutable_buffers_1 buffer(PodType (&data)[N],
+ std::size_t max_size_in_bytes)
+{
+ return mutable_buffers_1(
+ mutable_buffer(data,
+ N * sizeof(PodType) < max_size_in_bytes
+ ? N * sizeof(PodType) : max_size_in_bytes));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * static_cast<const void*>(data),
+ * N * sizeof(PodType)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(const PodType (&data)[N])
+{
+ return const_buffers_1(const_buffer(data, N * sizeof(PodType)));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * static_cast<const void*>(data),
+ * min(N * sizeof(PodType), max_size_in_bytes)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(const PodType (&data)[N],
+ std::size_t max_size_in_bytes)
+{
+ return const_buffers_1(
+ const_buffer(data,
+ N * sizeof(PodType) < max_size_in_bytes
+ ? N * sizeof(PodType) : max_size_in_bytes));
+}
+
+#if defined(BOOST_ASIO_ENABLE_ARRAY_BUFFER_WORKAROUND)
+
+// Borland C++ and Sun Studio think the overloads:
+//
+// unspecified buffer(boost::array<PodType, N>& array ...);
+//
+// and
+//
+// unspecified buffer(boost::array<const PodType, N>& array ...);
+//
+// are ambiguous. This will be worked around by using a buffer_types traits
+// class that contains typedefs for the appropriate buffer and container
+// classes, based on whether PodType is const or non-const.
+
+namespace detail {
+
+template <bool IsConst>
+struct buffer_types_base;
+
+template <>
+struct buffer_types_base<false>
+{
+ typedef mutable_buffer buffer_type;
+ typedef mutable_buffers_1 container_type;
+};
+
+template <>
+struct buffer_types_base<true>
+{
+ typedef const_buffer buffer_type;
+ typedef const_buffers_1 container_type;
+};
+
+template <typename PodType>
+struct buffer_types
+ : public buffer_types_base<is_const<PodType>::value>
+{
+};
+
+} // namespace detail
+
+template <typename PodType, std::size_t N>
+inline typename detail::buffer_types<PodType>::container_type
+buffer(boost::array<PodType, N>& data)
+{
+ typedef typename boost::asio::detail::buffer_types<PodType>::buffer_type
+ buffer_type;
+ typedef typename boost::asio::detail::buffer_types<PodType>::container_type
+ container_type;
+ return container_type(
+ buffer_type(data.c_array(), data.size() * sizeof(PodType)));
+}
+
+template <typename PodType, std::size_t N>
+inline typename detail::buffer_types<PodType>::container_type
+buffer(boost::array<PodType, N>& data, std::size_t max_size_in_bytes)
+{
+ typedef typename boost::asio::detail::buffer_types<PodType>::buffer_type
+ buffer_type;
+ typedef typename boost::asio::detail::buffer_types<PodType>::container_type
+ container_type;
+ return container_type(
+ buffer_type(data.c_array(),
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes));
+}
+
+#else // defined(BOOST_ASIO_ENABLE_ARRAY_BUFFER_WORKAROUND)
+
+/// Create a new modifiable buffer that represents the given POD array.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * data.data(),
+ * data.size() * sizeof(PodType)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline mutable_buffers_1 buffer(boost::array<PodType, N>& data)
+{
+ return mutable_buffers_1(
+ mutable_buffer(data.c_array(), data.size() * sizeof(PodType)));
+}
+
+/// Create a new modifiable buffer that represents the given POD array.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * data.data(),
+ * min(data.size() * sizeof(PodType), max_size_in_bytes)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline mutable_buffers_1 buffer(boost::array<PodType, N>& data,
+ std::size_t max_size_in_bytes)
+{
+ return mutable_buffers_1(
+ mutable_buffer(data.c_array(),
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * data.size() * sizeof(PodType)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(boost::array<const PodType, N>& data)
+{
+ return const_buffers_1(
+ const_buffer(data.data(), data.size() * sizeof(PodType)));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * min(data.size() * sizeof(PodType), max_size_in_bytes)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(boost::array<const PodType, N>& data,
+ std::size_t max_size_in_bytes)
+{
+ return const_buffers_1(
+ const_buffer(data.data(),
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes));
+}
+
+#endif // defined(BOOST_ASIO_ENABLE_ARRAY_BUFFER_WORKAROUND)
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * data.size() * sizeof(PodType)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(const boost::array<PodType, N>& data)
+{
+ return const_buffers_1(
+ const_buffer(data.data(), data.size() * sizeof(PodType)));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * min(data.size() * sizeof(PodType), max_size_in_bytes)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(const boost::array<PodType, N>& data,
+ std::size_t max_size_in_bytes)
+{
+ return const_buffers_1(
+ const_buffer(data.data(),
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes));
+}
+
+#if defined(BOOST_ASIO_HAS_STD_ARRAY) || defined(GENERATING_DOCUMENTATION)
+
+/// Create a new modifiable buffer that represents the given POD array.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * data.data(),
+ * data.size() * sizeof(PodType)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline mutable_buffers_1 buffer(std::array<PodType, N>& data)
+{
+ return mutable_buffers_1(
+ mutable_buffer(data.data(), data.size() * sizeof(PodType)));
+}
+
+/// Create a new modifiable buffer that represents the given POD array.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * data.data(),
+ * min(data.size() * sizeof(PodType), max_size_in_bytes)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline mutable_buffers_1 buffer(std::array<PodType, N>& data,
+ std::size_t max_size_in_bytes)
+{
+ return mutable_buffers_1(
+ mutable_buffer(data.data(),
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * data.size() * sizeof(PodType)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(std::array<const PodType, N>& data)
+{
+ return const_buffers_1(
+ const_buffer(data.data(), data.size() * sizeof(PodType)));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * min(data.size() * sizeof(PodType), max_size_in_bytes)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(std::array<const PodType, N>& data,
+ std::size_t max_size_in_bytes)
+{
+ return const_buffers_1(
+ const_buffer(data.data(),
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * data.size() * sizeof(PodType)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(const std::array<PodType, N>& data)
+{
+ return const_buffers_1(
+ const_buffer(data.data(), data.size() * sizeof(PodType)));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD array.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * min(data.size() * sizeof(PodType), max_size_in_bytes)); @endcode
+ */
+template <typename PodType, std::size_t N>
+inline const_buffers_1 buffer(const std::array<PodType, N>& data,
+ std::size_t max_size_in_bytes)
+{
+ return const_buffers_1(
+ const_buffer(data.data(),
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes));
+}
+
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY) || defined(GENERATING_DOCUMENTATION)
+
+/// Create a new modifiable buffer that represents the given POD vector.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * data.size() ? &data[0] : 0,
+ * data.size() * sizeof(PodType)); @endcode
+ *
+ * @note The buffer is invalidated by any vector operation that would also
+ * invalidate iterators.
+ */
+template <typename PodType, typename Allocator>
+inline mutable_buffers_1 buffer(std::vector<PodType, Allocator>& data)
+{
+ return mutable_buffers_1(
+ mutable_buffer(data.size() ? &data[0] : 0, data.size() * sizeof(PodType)
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , detail::buffer_debug_check<
+ typename std::vector<PodType, Allocator>::iterator
+ >(data.begin())
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ ));
+}
+
+/// Create a new modifiable buffer that represents the given POD vector.
+/**
+ * @returns A mutable_buffers_1 value equivalent to:
+ * @code mutable_buffers_1(
+ * data.size() ? &data[0] : 0,
+ * min(data.size() * sizeof(PodType), max_size_in_bytes)); @endcode
+ *
+ * @note The buffer is invalidated by any vector operation that would also
+ * invalidate iterators.
+ */
+template <typename PodType, typename Allocator>
+inline mutable_buffers_1 buffer(std::vector<PodType, Allocator>& data,
+ std::size_t max_size_in_bytes)
+{
+ return mutable_buffers_1(
+ mutable_buffer(data.size() ? &data[0] : 0,
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , detail::buffer_debug_check<
+ typename std::vector<PodType, Allocator>::iterator
+ >(data.begin())
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ ));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD vector.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.size() ? &data[0] : 0,
+ * data.size() * sizeof(PodType)); @endcode
+ *
+ * @note The buffer is invalidated by any vector operation that would also
+ * invalidate iterators.
+ */
+template <typename PodType, typename Allocator>
+inline const_buffers_1 buffer(
+ const std::vector<PodType, Allocator>& data)
+{
+ return const_buffers_1(
+ const_buffer(data.size() ? &data[0] : 0, data.size() * sizeof(PodType)
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , detail::buffer_debug_check<
+ typename std::vector<PodType, Allocator>::const_iterator
+ >(data.begin())
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ ));
+}
+
+/// Create a new non-modifiable buffer that represents the given POD vector.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.size() ? &data[0] : 0,
+ * min(data.size() * sizeof(PodType), max_size_in_bytes)); @endcode
+ *
+ * @note The buffer is invalidated by any vector operation that would also
+ * invalidate iterators.
+ */
+template <typename PodType, typename Allocator>
+inline const_buffers_1 buffer(
+ const std::vector<PodType, Allocator>& data, std::size_t max_size_in_bytes)
+{
+ return const_buffers_1(
+ const_buffer(data.size() ? &data[0] : 0,
+ data.size() * sizeof(PodType) < max_size_in_bytes
+ ? data.size() * sizeof(PodType) : max_size_in_bytes
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , detail::buffer_debug_check<
+ typename std::vector<PodType, Allocator>::const_iterator
+ >(data.begin())
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ ));
+}
+
+/// Create a new non-modifiable buffer that represents the given string.
+/**
+ * @returns <tt>const_buffers_1(data.data(), data.size() * sizeof(Elem))</tt>.
+ *
+ * @note The buffer is invalidated by any non-const operation called on the
+ * given string object.
+ */
+template <typename Elem, typename Traits, typename Allocator>
+inline const_buffers_1 buffer(
+ const std::basic_string<Elem, Traits, Allocator>& data)
+{
+ return const_buffers_1(const_buffer(data.data(), data.size() * sizeof(Elem)
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , detail::buffer_debug_check<
+ typename std::basic_string<Elem, Traits, Allocator>::const_iterator
+ >(data.begin())
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ ));
+}
+
+/// Create a new non-modifiable buffer that represents the given string.
+/**
+ * @returns A const_buffers_1 value equivalent to:
+ * @code const_buffers_1(
+ * data.data(),
+ * min(data.size() * sizeof(Elem), max_size_in_bytes)); @endcode
+ *
+ * @note The buffer is invalidated by any non-const operation called on the
+ * given string object.
+ */
+template <typename Elem, typename Traits, typename Allocator>
+inline const_buffers_1 buffer(
+ const std::basic_string<Elem, Traits, Allocator>& data,
+ std::size_t max_size_in_bytes)
+{
+ return const_buffers_1(
+ const_buffer(data.data(),
+ data.size() * sizeof(Elem) < max_size_in_bytes
+ ? data.size() * sizeof(Elem) : max_size_in_bytes
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ , detail::buffer_debug_check<
+ typename std::basic_string<Elem, Traits, Allocator>::const_iterator
+ >(data.begin())
+#endif // BOOST_ASIO_ENABLE_BUFFER_DEBUGGING
+ ));
+}
+
+/*@}*/
+
+/** @defgroup buffer_copy boost::asio::buffer_copy
+ *
+ * @brief The boost::asio::buffer_copy function is used to copy bytes from a
+ * source buffer (or buffer sequence) to a target buffer (or buffer sequence).
+ *
+ * The @c buffer_copy function is available in two forms:
+ *
+ * @li A 2-argument form: @c buffer_copy(target, source)
+ *
+ * @li A 3-argument form: @c buffer_copy(target, source, max_bytes_to_copy)
+
+ * Both forms return the number of bytes actually copied. The number of bytes
+ * copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c If specified, @c max_bytes_to_copy.
+ *
+ * This prevents buffer overflow, regardless of the buffer sizes used in the
+ * copy operation.
+ *
+ * Note that @ref buffer_copy is implemented in terms of @c memcpy, and
+ * consequently it cannot be used to copy between overlapping memory regions.
+ */
+/*@{*/
+
+/// Copies bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const const_buffer& source)
+{
+ using namespace std; // For memcpy.
+ std::size_t target_size = buffer_size(target);
+ std::size_t source_size = buffer_size(source);
+ std::size_t n = target_size < source_size ? target_size : source_size;
+ memcpy(buffer_cast<void*>(target), buffer_cast<const void*>(source), n);
+ return n;
+}
+
+/// Copies bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const const_buffers_1& source)
+{
+ return buffer_copy(target, static_cast<const const_buffer&>(source));
+}
+
+/// Copies bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const mutable_buffer& source)
+{
+ return buffer_copy(target, const_buffer(source));
+}
+
+/// Copies bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const mutable_buffers_1& source)
+{
+ return buffer_copy(target, const_buffer(source));
+}
+
+/// Copies bytes from a source buffer sequence to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer sequence representing the memory
+ * regions from which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename ConstBufferSequence>
+std::size_t buffer_copy(const mutable_buffer& target,
+ const ConstBufferSequence& source)
+{
+ std::size_t total_bytes_copied = 0;
+
+ typename ConstBufferSequence::const_iterator source_iter = source.begin();
+ typename ConstBufferSequence::const_iterator source_end = source.end();
+
+ for (mutable_buffer target_buffer(target);
+ buffer_size(target_buffer) && source_iter != source_end; ++source_iter)
+ {
+ const_buffer source_buffer(*source_iter);
+ std::size_t bytes_copied = buffer_copy(target_buffer, source_buffer);
+ total_bytes_copied += bytes_copied;
+ target_buffer = target_buffer + bytes_copied;
+ }
+
+ return total_bytes_copied;
+}
+
+/// Copies bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const const_buffer& source)
+{
+ return buffer_copy(static_cast<const mutable_buffer&>(target), source);
+}
+
+/// Copies bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const const_buffers_1& source)
+{
+ return buffer_copy(static_cast<const mutable_buffer&>(target),
+ static_cast<const const_buffer&>(source));
+}
+
+/// Copies bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const mutable_buffer& source)
+{
+ return buffer_copy(static_cast<const mutable_buffer&>(target),
+ const_buffer(source));
+}
+
+/// Copies bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const mutable_buffers_1& source)
+{
+ return buffer_copy(static_cast<const mutable_buffer&>(target),
+ const_buffer(source));
+}
+
+/// Copies bytes from a source buffer sequence to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer sequence representing the memory
+ * regions from which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename ConstBufferSequence>
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const ConstBufferSequence& source)
+{
+ return buffer_copy(static_cast<const mutable_buffer&>(target), source);
+}
+
+/// Copies bytes from a source buffer to a target buffer sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence>
+std::size_t buffer_copy(const MutableBufferSequence& target,
+ const const_buffer& source)
+{
+ std::size_t total_bytes_copied = 0;
+
+ typename MutableBufferSequence::const_iterator target_iter = target.begin();
+ typename MutableBufferSequence::const_iterator target_end = target.end();
+
+ for (const_buffer source_buffer(source);
+ buffer_size(source_buffer) && target_iter != target_end; ++target_iter)
+ {
+ mutable_buffer target_buffer(*target_iter);
+ std::size_t bytes_copied = buffer_copy(target_buffer, source_buffer);
+ total_bytes_copied += bytes_copied;
+ source_buffer = source_buffer + bytes_copied;
+ }
+
+ return total_bytes_copied;
+}
+
+/// Copies bytes from a source buffer to a target buffer sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence>
+inline std::size_t buffer_copy(const MutableBufferSequence& target,
+ const const_buffers_1& source)
+{
+ return buffer_copy(target, static_cast<const const_buffer&>(source));
+}
+
+/// Copies bytes from a source buffer to a target buffer sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence>
+inline std::size_t buffer_copy(const MutableBufferSequence& target,
+ const mutable_buffer& source)
+{
+ return buffer_copy(target, const_buffer(source));
+}
+
+/// Copies bytes from a source buffer to a target buffer sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence>
+inline std::size_t buffer_copy(const MutableBufferSequence& target,
+ const mutable_buffers_1& source)
+{
+ return buffer_copy(target, const_buffer(source));
+}
+
+/// Copies bytes from a source buffer sequence to a target buffer sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer sequence representing the memory
+ * regions from which the bytes will be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence, typename ConstBufferSequence>
+std::size_t buffer_copy(const MutableBufferSequence& target,
+ const ConstBufferSequence& source)
+{
+ std::size_t total_bytes_copied = 0;
+
+ typename MutableBufferSequence::const_iterator target_iter = target.begin();
+ typename MutableBufferSequence::const_iterator target_end = target.end();
+ std::size_t target_buffer_offset = 0;
+
+ typename ConstBufferSequence::const_iterator source_iter = source.begin();
+ typename ConstBufferSequence::const_iterator source_end = source.end();
+ std::size_t source_buffer_offset = 0;
+
+ while (target_iter != target_end && source_iter != source_end)
+ {
+ mutable_buffer target_buffer =
+ mutable_buffer(*target_iter) + target_buffer_offset;
+
+ const_buffer source_buffer =
+ const_buffer(*source_iter) + source_buffer_offset;
+
+ std::size_t bytes_copied = buffer_copy(target_buffer, source_buffer);
+ total_bytes_copied += bytes_copied;
+
+ if (bytes_copied == buffer_size(target_buffer))
+ {
+ ++target_iter;
+ target_buffer_offset = 0;
+ }
+ else
+ target_buffer_offset += bytes_copied;
+
+ if (bytes_copied == buffer_size(source_buffer))
+ {
+ ++source_iter;
+ source_buffer_offset = 0;
+ }
+ else
+ source_buffer_offset += bytes_copied;
+ }
+
+ return total_bytes_copied;
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const const_buffer& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const const_buffers_1& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const mutable_buffer& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const mutable_buffers_1& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer sequence to a target
+/// buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer sequence representing the memory
+ * regions from which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename ConstBufferSequence>
+inline std::size_t buffer_copy(const mutable_buffer& target,
+ const ConstBufferSequence& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const const_buffer& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const const_buffers_1& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const mutable_buffer& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const mutable_buffers_1& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer sequence to a target
+/// buffer.
+/**
+ * @param target A modifiable buffer representing the memory region to which
+ * the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer sequence representing the memory
+ * regions from which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename ConstBufferSequence>
+inline std::size_t buffer_copy(const mutable_buffers_1& target,
+ const ConstBufferSequence& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(buffer(target, max_bytes_to_copy), source);
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer
+/// sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence>
+inline std::size_t buffer_copy(const MutableBufferSequence& target,
+ const const_buffer& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(target, buffer(source, max_bytes_to_copy));
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer
+/// sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer representing the memory region from
+ * which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence>
+inline std::size_t buffer_copy(const MutableBufferSequence& target,
+ const const_buffers_1& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(target, buffer(source, max_bytes_to_copy));
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer
+/// sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence>
+inline std::size_t buffer_copy(const MutableBufferSequence& target,
+ const mutable_buffer& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(target, buffer(source, max_bytes_to_copy));
+}
+
+/// Copies a limited number of bytes from a source buffer to a target buffer
+/// sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A modifiable buffer representing the memory region from which
+ * the bytes will be copied. The contents of the source buffer will not be
+ * modified.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence>
+inline std::size_t buffer_copy(const MutableBufferSequence& target,
+ const mutable_buffers_1& source, std::size_t max_bytes_to_copy)
+{
+ return buffer_copy(target, buffer(source, max_bytes_to_copy));
+}
+
+/// Copies a limited number of bytes from a source buffer sequence to a target
+/// buffer sequence.
+/**
+ * @param target A modifiable buffer sequence representing the memory regions to
+ * which the bytes will be copied.
+ *
+ * @param source A non-modifiable buffer sequence representing the memory
+ * regions from which the bytes will be copied.
+ *
+ * @param max_bytes_to_copy The maximum number of bytes to be copied.
+ *
+ * @returns The number of bytes copied.
+ *
+ * @note The number of bytes copied is the lesser of:
+ *
+ * @li @c buffer_size(target)
+ *
+ * @li @c buffer_size(source)
+ *
+ * @li @c max_bytes_to_copy
+ *
+ * This function is implemented in terms of @c memcpy, and consequently it
+ * cannot be used to copy between overlapping memory regions.
+ */
+template <typename MutableBufferSequence, typename ConstBufferSequence>
+std::size_t buffer_copy(const MutableBufferSequence& target,
+ const ConstBufferSequence& source, std::size_t max_bytes_to_copy)
+{
+ std::size_t total_bytes_copied = 0;
+
+ typename MutableBufferSequence::const_iterator target_iter = target.begin();
+ typename MutableBufferSequence::const_iterator target_end = target.end();
+ std::size_t target_buffer_offset = 0;
+
+ typename ConstBufferSequence::const_iterator source_iter = source.begin();
+ typename ConstBufferSequence::const_iterator source_end = source.end();
+ std::size_t source_buffer_offset = 0;
+
+ while (total_bytes_copied != max_bytes_to_copy
+ && target_iter != target_end && source_iter != source_end)
+ {
+ mutable_buffer target_buffer =
+ mutable_buffer(*target_iter) + target_buffer_offset;
+
+ const_buffer source_buffer =
+ const_buffer(*source_iter) + source_buffer_offset;
+
+ std::size_t bytes_copied = buffer_copy(target_buffer,
+ source_buffer, max_bytes_to_copy - total_bytes_copied);
+ total_bytes_copied += bytes_copied;
+
+ if (bytes_copied == buffer_size(target_buffer))
+ {
+ ++target_iter;
+ target_buffer_offset = 0;
+ }
+ else
+ target_buffer_offset += bytes_copied;
+
+ if (bytes_copied == buffer_size(source_buffer))
+ {
+ ++source_iter;
+ source_buffer_offset = 0;
+ }
+ else
+ source_buffer_offset += bytes_copied;
+ }
+
+ return total_bytes_copied;
+}
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BUFFER_HPP
diff --git a/ext/patches/boost/asio/buffered_read_stream.hpp b/ext/patches/boost/asio/buffered_read_stream.hpp
new file mode 100644
index 0000000..d8c92f7
--- /dev/null
+++ b/ext/patches/boost/asio/buffered_read_stream.hpp
@@ -0,0 +1,246 @@
+//
+// buffered_read_stream.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BUFFERED_READ_STREAM_HPP
+#define BOOST_ASIO_BUFFERED_READ_STREAM_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/buffered_read_stream_fwd.hpp>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_resize_guard.hpp>
+#include <boost/asio/detail/buffered_stream_storage.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Adds buffering to the read-related operations of a stream.
+/**
+ * The buffered_read_stream class template can be used to add buffering to the
+ * synchronous and asynchronous read operations of a stream.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * AsyncReadStream, AsyncWriteStream, Stream, SyncReadStream, SyncWriteStream.
+ */
+template <typename Stream>
+class buffered_read_stream
+ : private noncopyable
+{
+public:
+ /// The type of the next layer.
+ typedef typename remove_reference<Stream>::type next_layer_type;
+
+ /// The type of the lowest layer.
+ typedef typename next_layer_type::lowest_layer_type lowest_layer_type;
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// The default buffer size.
+ static const std::size_t default_buffer_size = implementation_defined;
+#else
+ BOOST_ASIO_STATIC_CONSTANT(std::size_t, default_buffer_size = 1024);
+#endif
+
+ /// Construct, passing the specified argument to initialise the next layer.
+ template <typename Arg>
+ explicit buffered_read_stream(Arg& a)
+ : next_layer_(a),
+ storage_(default_buffer_size)
+ {
+ }
+
+ /// Construct, passing the specified argument to initialise the next layer.
+ template <typename Arg>
+ buffered_read_stream(Arg& a, std::size_t buffer_size)
+ : next_layer_(a),
+ storage_(buffer_size)
+ {
+ }
+
+ /// Get a reference to the next layer.
+ next_layer_type& next_layer()
+ {
+ return next_layer_;
+ }
+
+ /// Get a reference to the lowest layer.
+ lowest_layer_type& lowest_layer()
+ {
+ return next_layer_.lowest_layer();
+ }
+
+ /// Get a const reference to the lowest layer.
+ const lowest_layer_type& lowest_layer() const
+ {
+ return next_layer_.lowest_layer();
+ }
+
+ /// Get the io_service associated with the object.
+ boost::asio::io_service& get_io_service()
+ {
+ return next_layer_.get_io_service();
+ }
+
+ /// Close the stream.
+ void close()
+ {
+ next_layer_.close();
+ }
+
+ /// Close the stream.
+ boost::system::error_code close(boost::system::error_code& ec)
+ {
+ return next_layer_.close(ec);
+ }
+
+ /// Write the given data to the stream. Returns the number of bytes written.
+ /// Throws an exception on failure.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers)
+ {
+ return next_layer_.write_some(buffers);
+ }
+
+ /// Write the given data to the stream. Returns the number of bytes written,
+ /// or 0 if an error occurred.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return next_layer_.write_some(buffers, ec);
+ }
+
+ /// Start an asynchronous write. The data being written must be valid for the
+ /// lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ next_layer_.async_write_some(buffers,
+ BOOST_ASIO_MOVE_CAST(BOOST_ASIO_HANDLER_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t)))(init.handler));
+
+ return init.result.get();
+ }
+
+ /// Fill the buffer with some data. Returns the number of bytes placed in the
+ /// buffer as a result of the operation. Throws an exception on failure.
+ std::size_t fill();
+
+ /// Fill the buffer with some data. Returns the number of bytes placed in the
+ /// buffer as a result of the operation, or 0 if an error occurred.
+ std::size_t fill(boost::system::error_code& ec);
+
+ /// Start an asynchronous fill.
+ template <typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_fill(BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+ /// Read some data from the stream. Returns the number of bytes read. Throws
+ /// an exception on failure.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers);
+
+ /// Read some data from the stream. Returns the number of bytes read or 0 if
+ /// an error occurred.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec);
+
+ /// Start an asynchronous read. The buffer into which the data will be read
+ /// must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+ /// Peek at the incoming data on the stream. Returns the number of bytes read.
+ /// Throws an exception on failure.
+ template <typename MutableBufferSequence>
+ std::size_t peek(const MutableBufferSequence& buffers);
+
+ /// Peek at the incoming data on the stream. Returns the number of bytes read,
+ /// or 0 if an error occurred.
+ template <typename MutableBufferSequence>
+ std::size_t peek(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec);
+
+ /// Determine the amount of data that may be read without blocking.
+ std::size_t in_avail()
+ {
+ return storage_.size();
+ }
+
+ /// Determine the amount of data that may be read without blocking.
+ std::size_t in_avail(boost::system::error_code& ec)
+ {
+ ec = boost::system::error_code();
+ return storage_.size();
+ }
+
+private:
+ /// Copy data out of the internal buffer to the specified target buffer.
+ /// Returns the number of bytes copied.
+ template <typename MutableBufferSequence>
+ std::size_t copy(const MutableBufferSequence& buffers)
+ {
+ std::size_t bytes_copied = boost::asio::buffer_copy(
+ buffers, storage_.data(), storage_.size());
+ storage_.consume(bytes_copied);
+ return bytes_copied;
+ }
+
+ /// Copy data from the internal buffer to the specified target buffer, without
+ /// removing the data from the internal buffer. Returns the number of bytes
+ /// copied.
+ template <typename MutableBufferSequence>
+ std::size_t peek_copy(const MutableBufferSequence& buffers)
+ {
+ return boost::asio::buffer_copy(buffers, storage_.data(), storage_.size());
+ }
+
+ /// The next layer.
+ Stream next_layer_;
+
+ // The data in the buffer.
+ detail::buffered_stream_storage storage_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/buffered_read_stream.hpp>
+
+#endif // BOOST_ASIO_BUFFERED_READ_STREAM_HPP
diff --git a/ext/patches/boost/asio/buffered_read_stream_fwd.hpp b/ext/patches/boost/asio/buffered_read_stream_fwd.hpp
new file mode 100644
index 0000000..9cf88df
--- /dev/null
+++ b/ext/patches/boost/asio/buffered_read_stream_fwd.hpp
@@ -0,0 +1,27 @@
+//
+// buffered_read_stream_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BUFFERED_READ_STREAM_FWD_HPP
+#define BOOST_ASIO_BUFFERED_READ_STREAM_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+namespace boost {
+namespace asio {
+
+template <typename Stream>
+class buffered_read_stream;
+
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_BUFFERED_READ_STREAM_FWD_HPP
diff --git a/ext/patches/boost/asio/buffered_stream.hpp b/ext/patches/boost/asio/buffered_stream.hpp
new file mode 100644
index 0000000..46040d0
--- /dev/null
+++ b/ext/patches/boost/asio/buffered_stream.hpp
@@ -0,0 +1,260 @@
+//
+// buffered_stream.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BUFFERED_STREAM_HPP
+#define BOOST_ASIO_BUFFERED_STREAM_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/buffered_read_stream.hpp>
+#include <boost/asio/buffered_write_stream.hpp>
+#include <boost/asio/buffered_stream_fwd.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Adds buffering to the read- and write-related operations of a stream.
+/**
+ * The buffered_stream class template can be used to add buffering to the
+ * synchronous and asynchronous read and write operations of a stream.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * AsyncReadStream, AsyncWriteStream, Stream, SyncReadStream, SyncWriteStream.
+ */
+template <typename Stream>
+class buffered_stream
+ : private noncopyable
+{
+public:
+ /// The type of the next layer.
+ typedef typename remove_reference<Stream>::type next_layer_type;
+
+ /// The type of the lowest layer.
+ typedef typename next_layer_type::lowest_layer_type lowest_layer_type;
+
+ /// Construct, passing the specified argument to initialise the next layer.
+ template <typename Arg>
+ explicit buffered_stream(Arg& a)
+ : inner_stream_impl_(a),
+ stream_impl_(inner_stream_impl_)
+ {
+ }
+
+ /// Construct, passing the specified argument to initialise the next layer.
+ template <typename Arg>
+ explicit buffered_stream(Arg& a, std::size_t read_buffer_size,
+ std::size_t write_buffer_size)
+ : inner_stream_impl_(a, write_buffer_size),
+ stream_impl_(inner_stream_impl_, read_buffer_size)
+ {
+ }
+
+ /// Get a reference to the next layer.
+ next_layer_type& next_layer()
+ {
+ return stream_impl_.next_layer().next_layer();
+ }
+
+ /// Get a reference to the lowest layer.
+ lowest_layer_type& lowest_layer()
+ {
+ return stream_impl_.lowest_layer();
+ }
+
+ /// Get a const reference to the lowest layer.
+ const lowest_layer_type& lowest_layer() const
+ {
+ return stream_impl_.lowest_layer();
+ }
+
+ /// Get the io_service associated with the object.
+ boost::asio::io_service& get_io_service()
+ {
+ return stream_impl_.get_io_service();
+ }
+
+ /// Close the stream.
+ void close()
+ {
+ stream_impl_.close();
+ }
+
+ /// Close the stream.
+ boost::system::error_code close(boost::system::error_code& ec)
+ {
+ return stream_impl_.close(ec);
+ }
+
+ /// Flush all data from the buffer to the next layer. Returns the number of
+ /// bytes written to the next layer on the last write operation. Throws an
+ /// exception on failure.
+ std::size_t flush()
+ {
+ return stream_impl_.next_layer().flush();
+ }
+
+ /// Flush all data from the buffer to the next layer. Returns the number of
+ /// bytes written to the next layer on the last write operation, or 0 if an
+ /// error occurred.
+ std::size_t flush(boost::system::error_code& ec)
+ {
+ return stream_impl_.next_layer().flush(ec);
+ }
+
+ /// Start an asynchronous flush.
+ template <typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_flush(BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ return stream_impl_.next_layer().async_flush(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Write the given data to the stream. Returns the number of bytes written.
+ /// Throws an exception on failure.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers)
+ {
+ return stream_impl_.write_some(buffers);
+ }
+
+ /// Write the given data to the stream. Returns the number of bytes written,
+ /// or 0 if an error occurred.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return stream_impl_.write_some(buffers, ec);
+ }
+
+ /// Start an asynchronous write. The data being written must be valid for the
+ /// lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ return stream_impl_.async_write_some(buffers,
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Fill the buffer with some data. Returns the number of bytes placed in the
+ /// buffer as a result of the operation. Throws an exception on failure.
+ std::size_t fill()
+ {
+ return stream_impl_.fill();
+ }
+
+ /// Fill the buffer with some data. Returns the number of bytes placed in the
+ /// buffer as a result of the operation, or 0 if an error occurred.
+ std::size_t fill(boost::system::error_code& ec)
+ {
+ return stream_impl_.fill(ec);
+ }
+
+ /// Start an asynchronous fill.
+ template <typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_fill(BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ return stream_impl_.async_fill(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Read some data from the stream. Returns the number of bytes read. Throws
+ /// an exception on failure.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers)
+ {
+ return stream_impl_.read_some(buffers);
+ }
+
+ /// Read some data from the stream. Returns the number of bytes read or 0 if
+ /// an error occurred.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return stream_impl_.read_some(buffers, ec);
+ }
+
+ /// Start an asynchronous read. The buffer into which the data will be read
+ /// must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ return stream_impl_.async_read_some(buffers,
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+
+ /// Peek at the incoming data on the stream. Returns the number of bytes read.
+ /// Throws an exception on failure.
+ template <typename MutableBufferSequence>
+ std::size_t peek(const MutableBufferSequence& buffers)
+ {
+ return stream_impl_.peek(buffers);
+ }
+
+ /// Peek at the incoming data on the stream. Returns the number of bytes read,
+ /// or 0 if an error occurred.
+ template <typename MutableBufferSequence>
+ std::size_t peek(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return stream_impl_.peek(buffers, ec);
+ }
+
+ /// Determine the amount of data that may be read without blocking.
+ std::size_t in_avail()
+ {
+ return stream_impl_.in_avail();
+ }
+
+ /// Determine the amount of data that may be read without blocking.
+ std::size_t in_avail(boost::system::error_code& ec)
+ {
+ return stream_impl_.in_avail(ec);
+ }
+
+private:
+ // The buffered write stream.
+ typedef buffered_write_stream<Stream> write_stream_type;
+ write_stream_type inner_stream_impl_;
+
+ // The buffered read stream.
+ typedef buffered_read_stream<write_stream_type&> read_stream_type;
+ read_stream_type stream_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BUFFERED_STREAM_HPP
diff --git a/ext/patches/boost/asio/buffered_stream_fwd.hpp b/ext/patches/boost/asio/buffered_stream_fwd.hpp
new file mode 100644
index 0000000..6b8269d
--- /dev/null
+++ b/ext/patches/boost/asio/buffered_stream_fwd.hpp
@@ -0,0 +1,27 @@
+//
+// buffered_stream_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BUFFERED_STREAM_FWD_HPP
+#define BOOST_ASIO_BUFFERED_STREAM_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+namespace boost {
+namespace asio {
+
+template <typename Stream>
+class buffered_stream;
+
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_BUFFERED_STREAM_FWD_HPP
diff --git a/ext/patches/boost/asio/buffered_write_stream.hpp b/ext/patches/boost/asio/buffered_write_stream.hpp
new file mode 100644
index 0000000..1a45c24
--- /dev/null
+++ b/ext/patches/boost/asio/buffered_write_stream.hpp
@@ -0,0 +1,238 @@
+//
+// buffered_write_stream.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BUFFERED_WRITE_STREAM_HPP
+#define BOOST_ASIO_BUFFERED_WRITE_STREAM_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/buffered_write_stream_fwd.hpp>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/completion_condition.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffered_stream_storage.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/write.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Adds buffering to the write-related operations of a stream.
+/**
+ * The buffered_write_stream class template can be used to add buffering to the
+ * synchronous and asynchronous write operations of a stream.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * AsyncReadStream, AsyncWriteStream, Stream, SyncReadStream, SyncWriteStream.
+ */
+template <typename Stream>
+class buffered_write_stream
+ : private noncopyable
+{
+public:
+ /// The type of the next layer.
+ typedef typename remove_reference<Stream>::type next_layer_type;
+
+ /// The type of the lowest layer.
+ typedef typename next_layer_type::lowest_layer_type lowest_layer_type;
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// The default buffer size.
+ static const std::size_t default_buffer_size = implementation_defined;
+#else
+ BOOST_ASIO_STATIC_CONSTANT(std::size_t, default_buffer_size = 1024);
+#endif
+
+ /// Construct, passing the specified argument to initialise the next layer.
+ template <typename Arg>
+ explicit buffered_write_stream(Arg& a)
+ : next_layer_(a),
+ storage_(default_buffer_size)
+ {
+ }
+
+ /// Construct, passing the specified argument to initialise the next layer.
+ template <typename Arg>
+ buffered_write_stream(Arg& a, std::size_t buffer_size)
+ : next_layer_(a),
+ storage_(buffer_size)
+ {
+ }
+
+ /// Get a reference to the next layer.
+ next_layer_type& next_layer()
+ {
+ return next_layer_;
+ }
+
+ /// Get a reference to the lowest layer.
+ lowest_layer_type& lowest_layer()
+ {
+ return next_layer_.lowest_layer();
+ }
+
+ /// Get a const reference to the lowest layer.
+ const lowest_layer_type& lowest_layer() const
+ {
+ return next_layer_.lowest_layer();
+ }
+
+ /// Get the io_service associated with the object.
+ boost::asio::io_service& get_io_service()
+ {
+ return next_layer_.get_io_service();
+ }
+
+ /// Close the stream.
+ void close()
+ {
+ next_layer_.close();
+ }
+
+ /// Close the stream.
+ boost::system::error_code close(boost::system::error_code& ec)
+ {
+ return next_layer_.close(ec);
+ }
+
+ /// Flush all data from the buffer to the next layer. Returns the number of
+ /// bytes written to the next layer on the last write operation. Throws an
+ /// exception on failure.
+ std::size_t flush();
+
+ /// Flush all data from the buffer to the next layer. Returns the number of
+ /// bytes written to the next layer on the last write operation, or 0 if an
+ /// error occurred.
+ std::size_t flush(boost::system::error_code& ec);
+
+ /// Start an asynchronous flush.
+ template <typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_flush(BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+ /// Write the given data to the stream. Returns the number of bytes written.
+ /// Throws an exception on failure.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers);
+
+ /// Write the given data to the stream. Returns the number of bytes written,
+ /// or 0 if an error occurred and the error handler did not throw.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec);
+
+ /// Start an asynchronous write. The data being written must be valid for the
+ /// lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+ /// Read some data from the stream. Returns the number of bytes read. Throws
+ /// an exception on failure.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers)
+ {
+ return next_layer_.read_some(buffers);
+ }
+
+ /// Read some data from the stream. Returns the number of bytes read or 0 if
+ /// an error occurred.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return next_layer_.read_some(buffers, ec);
+ }
+
+ /// Start an asynchronous read. The buffer into which the data will be read
+ /// must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ next_layer_.async_read_some(buffers,
+ BOOST_ASIO_MOVE_CAST(BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t)))(init.handler));
+
+ return init.result.get();
+ }
+
+ /// Peek at the incoming data on the stream. Returns the number of bytes read.
+ /// Throws an exception on failure.
+ template <typename MutableBufferSequence>
+ std::size_t peek(const MutableBufferSequence& buffers)
+ {
+ return next_layer_.peek(buffers);
+ }
+
+ /// Peek at the incoming data on the stream. Returns the number of bytes read,
+ /// or 0 if an error occurred.
+ template <typename MutableBufferSequence>
+ std::size_t peek(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return next_layer_.peek(buffers, ec);
+ }
+
+ /// Determine the amount of data that may be read without blocking.
+ std::size_t in_avail()
+ {
+ return next_layer_.in_avail();
+ }
+
+ /// Determine the amount of data that may be read without blocking.
+ std::size_t in_avail(boost::system::error_code& ec)
+ {
+ return next_layer_.in_avail(ec);
+ }
+
+private:
+ /// Copy data into the internal buffer from the specified source buffer.
+ /// Returns the number of bytes copied.
+ template <typename ConstBufferSequence>
+ std::size_t copy(const ConstBufferSequence& buffers);
+
+ /// The next layer.
+ Stream next_layer_;
+
+ // The data in the buffer.
+ detail::buffered_stream_storage storage_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/buffered_write_stream.hpp>
+
+#endif // BOOST_ASIO_BUFFERED_WRITE_STREAM_HPP
diff --git a/ext/patches/boost/asio/buffered_write_stream_fwd.hpp b/ext/patches/boost/asio/buffered_write_stream_fwd.hpp
new file mode 100644
index 0000000..8a0990f
--- /dev/null
+++ b/ext/patches/boost/asio/buffered_write_stream_fwd.hpp
@@ -0,0 +1,27 @@
+//
+// buffered_write_stream_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BUFFERED_WRITE_STREAM_FWD_HPP
+#define BOOST_ASIO_BUFFERED_WRITE_STREAM_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+namespace boost {
+namespace asio {
+
+template <typename Stream>
+class buffered_write_stream;
+
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_BUFFERED_WRITE_STREAM_FWD_HPP
diff --git a/ext/patches/boost/asio/buffers_iterator.hpp b/ext/patches/boost/asio/buffers_iterator.hpp
new file mode 100644
index 0000000..f8bc332
--- /dev/null
+++ b/ext/patches/boost/asio/buffers_iterator.hpp
@@ -0,0 +1,483 @@
+//
+// buffers_iterator.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_BUFFERS_ITERATOR_HPP
+#define BOOST_ASIO_BUFFERS_ITERATOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <iterator>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+namespace detail
+{
+ template <bool IsMutable>
+ struct buffers_iterator_types_helper;
+
+ template <>
+ struct buffers_iterator_types_helper<false>
+ {
+ typedef const_buffer buffer_type;
+ template <typename ByteType>
+ struct byte_type
+ {
+ typedef typename add_const<ByteType>::type type;
+ };
+ };
+
+ template <>
+ struct buffers_iterator_types_helper<true>
+ {
+ typedef mutable_buffer buffer_type;
+ template <typename ByteType>
+ struct byte_type
+ {
+ typedef ByteType type;
+ };
+ };
+
+ template <typename BufferSequence, typename ByteType>
+ struct buffers_iterator_types
+ {
+ enum
+ {
+ is_mutable = is_convertible<
+ typename BufferSequence::value_type,
+ mutable_buffer>::value
+ };
+ typedef buffers_iterator_types_helper<is_mutable> helper;
+ typedef typename helper::buffer_type buffer_type;
+ typedef typename helper::template byte_type<ByteType>::type byte_type;
+ };
+}
+
+/// A random access iterator over the bytes in a buffer sequence.
+template <typename BufferSequence, typename ByteType = char>
+class buffers_iterator
+{
+private:
+ typedef typename detail::buffers_iterator_types<
+ BufferSequence, ByteType>::buffer_type buffer_type;
+
+public:
+ /// The type used for the distance between two iterators.
+ typedef std::ptrdiff_t difference_type;
+
+ /// The type of the value pointed to by the iterator.
+ typedef ByteType value_type;
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// The type of the result of applying operator->() to the iterator.
+ /**
+ * If the buffer sequence stores buffer objects that are convertible to
+ * mutable_buffer, this is a pointer to a non-const ByteType. Otherwise, a
+ * pointer to a const ByteType.
+ */
+ typedef const_or_non_const_ByteType* pointer;
+#else // defined(GENERATING_DOCUMENTATION)
+ typedef typename detail::buffers_iterator_types<
+ BufferSequence, ByteType>::byte_type* pointer;
+#endif // defined(GENERATING_DOCUMENTATION)
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// The type of the result of applying operator*() to the iterator.
+ /**
+ * If the buffer sequence stores buffer objects that are convertible to
+ * mutable_buffer, this is a reference to a non-const ByteType. Otherwise, a
+ * reference to a const ByteType.
+ */
+ typedef const_or_non_const_ByteType& reference;
+#else // defined(GENERATING_DOCUMENTATION)
+ typedef typename detail::buffers_iterator_types<
+ BufferSequence, ByteType>::byte_type& reference;
+#endif // defined(GENERATING_DOCUMENTATION)
+
+ /// The iterator category.
+ typedef std::random_access_iterator_tag iterator_category;
+
+ /// Default constructor. Creates an iterator in an undefined state.
+ buffers_iterator()
+ : current_buffer_(),
+ current_buffer_position_(0),
+ begin_(),
+ current_(),
+ end_(),
+ position_(0)
+ {
+ }
+
+ /// Construct an iterator representing the beginning of the buffers' data.
+ static buffers_iterator begin(const BufferSequence& buffers)
+#if defined(__GNUC__) && (__GNUC__ == 4) && (__GNUC_MINOR__ == 3)
+ __attribute__ ((__noinline__))
+#endif // defined(__GNUC__) && (__GNUC__ == 4) && (__GNUC_MINOR__ == 3)
+ {
+ buffers_iterator new_iter;
+ new_iter.begin_ = buffers.begin();
+ new_iter.current_ = buffers.begin();
+ new_iter.end_ = buffers.end();
+ while (new_iter.current_ != new_iter.end_)
+ {
+ new_iter.current_buffer_ = *new_iter.current_;
+ if (boost::asio::buffer_size(new_iter.current_buffer_) > 0)
+ break;
+ ++new_iter.current_;
+ }
+ return new_iter;
+ }
+
+ /// Construct an iterator representing the end of the buffers' data.
+ static buffers_iterator end(const BufferSequence& buffers)
+#if defined(__GNUC__) && (__GNUC__ == 4) && (__GNUC_MINOR__ == 3)
+ __attribute__ ((__noinline__))
+#endif // defined(__GNUC__) && (__GNUC__ == 4) && (__GNUC_MINOR__ == 3)
+ {
+ buffers_iterator new_iter;
+ new_iter.begin_ = buffers.begin();
+ new_iter.current_ = buffers.begin();
+ new_iter.end_ = buffers.end();
+ while (new_iter.current_ != new_iter.end_)
+ {
+ buffer_type buffer = *new_iter.current_;
+ new_iter.position_ += boost::asio::buffer_size(buffer);
+ ++new_iter.current_;
+ }
+ return new_iter;
+ }
+
+ /// Dereference an iterator.
+ reference operator*() const
+ {
+ return dereference();
+ }
+
+ /// Dereference an iterator.
+ pointer operator->() const
+ {
+ return &dereference();
+ }
+
+ /// Access an individual element.
+ reference operator[](std::ptrdiff_t difference) const
+ {
+ buffers_iterator tmp(*this);
+ tmp.advance(difference);
+ return *tmp;
+ }
+
+ /// Increment operator (prefix).
+ buffers_iterator& operator++()
+ {
+ increment();
+ return *this;
+ }
+
+ /// Increment operator (postfix).
+ buffers_iterator operator++(int)
+ {
+ buffers_iterator tmp(*this);
+ ++*this;
+ return tmp;
+ }
+
+ /// Decrement operator (prefix).
+ buffers_iterator& operator--()
+ {
+ decrement();
+ return *this;
+ }
+
+ /// Decrement operator (postfix).
+ buffers_iterator operator--(int)
+ {
+ buffers_iterator tmp(*this);
+ --*this;
+ return tmp;
+ }
+
+ /// Addition operator.
+ buffers_iterator& operator+=(std::ptrdiff_t difference)
+ {
+ advance(difference);
+ return *this;
+ }
+
+ /// Subtraction operator.
+ buffers_iterator& operator-=(std::ptrdiff_t difference)
+ {
+ advance(-difference);
+ return *this;
+ }
+
+ /// Addition operator.
+ friend buffers_iterator operator+(const buffers_iterator& iter,
+ std::ptrdiff_t difference)
+ {
+ buffers_iterator tmp(iter);
+ tmp.advance(difference);
+ return tmp;
+ }
+
+ /// Addition operator.
+ friend buffers_iterator operator+(std::ptrdiff_t difference,
+ const buffers_iterator& iter)
+ {
+ buffers_iterator tmp(iter);
+ tmp.advance(difference);
+ return tmp;
+ }
+
+ /// Subtraction operator.
+ friend buffers_iterator operator-(const buffers_iterator& iter,
+ std::ptrdiff_t difference)
+ {
+ buffers_iterator tmp(iter);
+ tmp.advance(-difference);
+ return tmp;
+ }
+
+ /// Subtraction operator.
+ friend std::ptrdiff_t operator-(const buffers_iterator& a,
+ const buffers_iterator& b)
+ {
+ return b.distance_to(a);
+ }
+
+ /// Test two iterators for equality.
+ friend bool operator==(const buffers_iterator& a, const buffers_iterator& b)
+ {
+ return a.equal(b);
+ }
+
+ /// Test two iterators for inequality.
+ friend bool operator!=(const buffers_iterator& a, const buffers_iterator& b)
+ {
+ return !a.equal(b);
+ }
+
+ /// Compare two iterators.
+ friend bool operator<(const buffers_iterator& a, const buffers_iterator& b)
+ {
+ return a.distance_to(b) > 0;
+ }
+
+ /// Compare two iterators.
+ friend bool operator<=(const buffers_iterator& a, const buffers_iterator& b)
+ {
+ return !(b < a);
+ }
+
+ /// Compare two iterators.
+ friend bool operator>(const buffers_iterator& a, const buffers_iterator& b)
+ {
+ return b < a;
+ }
+
+ /// Compare two iterators.
+ friend bool operator>=(const buffers_iterator& a, const buffers_iterator& b)
+ {
+ return !(a < b);
+ }
+
+private:
+ // Dereference the iterator.
+ reference dereference() const
+ {
+ return buffer_cast<pointer>(current_buffer_)[current_buffer_position_];
+ }
+
+ // Compare two iterators for equality.
+ bool equal(const buffers_iterator& other) const
+ {
+ return position_ == other.position_;
+ }
+
+ // Increment the iterator.
+ void increment()
+ {
+ BOOST_ASIO_ASSERT(current_ != end_ && "iterator out of bounds");
+ ++position_;
+
+ // Check if the increment can be satisfied by the current buffer.
+ ++current_buffer_position_;
+ if (current_buffer_position_ != boost::asio::buffer_size(current_buffer_))
+ return;
+
+ // Find the next non-empty buffer.
+ ++current_;
+ current_buffer_position_ = 0;
+ while (current_ != end_)
+ {
+ current_buffer_ = *current_;
+ if (boost::asio::buffer_size(current_buffer_) > 0)
+ return;
+ ++current_;
+ }
+ }
+
+ // Decrement the iterator.
+ void decrement()
+ {
+ BOOST_ASIO_ASSERT(position_ > 0 && "iterator out of bounds");
+ --position_;
+
+ // Check if the decrement can be satisfied by the current buffer.
+ if (current_buffer_position_ != 0)
+ {
+ --current_buffer_position_;
+ return;
+ }
+
+ // Find the previous non-empty buffer.
+ typename BufferSequence::const_iterator iter = current_;
+ while (iter != begin_)
+ {
+ --iter;
+ buffer_type buffer = *iter;
+ std::size_t buffer_size = boost::asio::buffer_size(buffer);
+ if (buffer_size > 0)
+ {
+ current_ = iter;
+ current_buffer_ = buffer;
+ current_buffer_position_ = buffer_size - 1;
+ return;
+ }
+ }
+ }
+
+ // Advance the iterator by the specified distance.
+ void advance(std::ptrdiff_t n)
+ {
+ if (n > 0)
+ {
+ BOOST_ASIO_ASSERT(current_ != end_ && "iterator out of bounds");
+ for (;;)
+ {
+ std::ptrdiff_t current_buffer_balance
+ = boost::asio::buffer_size(current_buffer_)
+ - current_buffer_position_;
+
+ // Check if the advance can be satisfied by the current buffer.
+ if (current_buffer_balance > n)
+ {
+ position_ += n;
+ current_buffer_position_ += n;
+ return;
+ }
+
+ // Update position.
+ n -= current_buffer_balance;
+ position_ += current_buffer_balance;
+
+ // Move to next buffer. If it is empty then it will be skipped on the
+ // next iteration of this loop.
+ if (++current_ == end_)
+ {
+ BOOST_ASIO_ASSERT(n == 0 && "iterator out of bounds");
+ current_buffer_ = buffer_type();
+ current_buffer_position_ = 0;
+ return;
+ }
+ current_buffer_ = *current_;
+ current_buffer_position_ = 0;
+ }
+ }
+ else if (n < 0)
+ {
+ std::size_t abs_n = -n;
+ BOOST_ASIO_ASSERT(position_ >= abs_n && "iterator out of bounds");
+ for (;;)
+ {
+ // Check if the advance can be satisfied by the current buffer.
+ if (current_buffer_position_ >= abs_n)
+ {
+ position_ -= abs_n;
+ current_buffer_position_ -= abs_n;
+ return;
+ }
+
+ // Update position.
+ abs_n -= current_buffer_position_;
+ position_ -= current_buffer_position_;
+
+ // Check if we've reached the beginning of the buffers.
+ if (current_ == begin_)
+ {
+ BOOST_ASIO_ASSERT(abs_n == 0 && "iterator out of bounds");
+ current_buffer_position_ = 0;
+ return;
+ }
+
+ // Find the previous non-empty buffer.
+ typename BufferSequence::const_iterator iter = current_;
+ while (iter != begin_)
+ {
+ --iter;
+ buffer_type buffer = *iter;
+ std::size_t buffer_size = boost::asio::buffer_size(buffer);
+ if (buffer_size > 0)
+ {
+ current_ = iter;
+ current_buffer_ = buffer;
+ current_buffer_position_ = buffer_size;
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ // Determine the distance between two iterators.
+ std::ptrdiff_t distance_to(const buffers_iterator& other) const
+ {
+ return other.position_ - position_;
+ }
+
+ buffer_type current_buffer_;
+ std::size_t current_buffer_position_;
+ typename BufferSequence::const_iterator begin_;
+ typename BufferSequence::const_iterator current_;
+ typename BufferSequence::const_iterator end_;
+ std::size_t position_;
+};
+
+/// Construct an iterator representing the beginning of the buffers' data.
+template <typename BufferSequence>
+inline buffers_iterator<BufferSequence> buffers_begin(
+ const BufferSequence& buffers)
+{
+ return buffers_iterator<BufferSequence>::begin(buffers);
+}
+
+/// Construct an iterator representing the end of the buffers' data.
+template <typename BufferSequence>
+inline buffers_iterator<BufferSequence> buffers_end(
+ const BufferSequence& buffers)
+{
+ return buffers_iterator<BufferSequence>::end(buffers);
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_BUFFERS_ITERATOR_HPP
diff --git a/ext/patches/boost/asio/completion_condition.hpp b/ext/patches/boost/asio/completion_condition.hpp
new file mode 100644
index 0000000..41e89b3
--- /dev/null
+++ b/ext/patches/boost/asio/completion_condition.hpp
@@ -0,0 +1,220 @@
+//
+// completion_condition.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_COMPLETION_CONDITION_HPP
+#define BOOST_ASIO_COMPLETION_CONDITION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+namespace detail {
+
+// The default maximum number of bytes to transfer in a single operation.
+enum default_max_transfer_size_t { default_max_transfer_size = 65536 };
+
+// Adapt result of old-style completion conditions (which had a bool result
+// where true indicated that the operation was complete).
+inline std::size_t adapt_completion_condition_result(bool result)
+{
+ return result ? 0 : default_max_transfer_size;
+}
+
+// Adapt result of current completion conditions (which have a size_t result
+// where 0 means the operation is complete, and otherwise the result is the
+// maximum number of bytes to transfer on the next underlying operation).
+inline std::size_t adapt_completion_condition_result(std::size_t result)
+{
+ return result;
+}
+
+class transfer_all_t
+{
+public:
+ typedef std::size_t result_type;
+
+ template <typename Error>
+ std::size_t operator()(const Error& err, std::size_t)
+ {
+ return !!err ? 0 : default_max_transfer_size;
+ }
+};
+
+class transfer_at_least_t
+{
+public:
+ typedef std::size_t result_type;
+
+ explicit transfer_at_least_t(std::size_t minimum)
+ : minimum_(minimum)
+ {
+ }
+
+ template <typename Error>
+ std::size_t operator()(const Error& err, std::size_t bytes_transferred)
+ {
+ return (!!err || bytes_transferred >= minimum_)
+ ? 0 : default_max_transfer_size;
+ }
+
+private:
+ std::size_t minimum_;
+};
+
+class transfer_exactly_t
+{
+public:
+ typedef std::size_t result_type;
+
+ explicit transfer_exactly_t(std::size_t size)
+ : size_(size)
+ {
+ }
+
+ template <typename Error>
+ std::size_t operator()(const Error& err, std::size_t bytes_transferred)
+ {
+ return (!!err || bytes_transferred >= size_) ? 0 :
+ (size_ - bytes_transferred < default_max_transfer_size
+ ? size_ - bytes_transferred : std::size_t(default_max_transfer_size));
+ }
+
+private:
+ std::size_t size_;
+};
+
+} // namespace detail
+
+/**
+ * @defgroup completion_condition Completion Condition Function Objects
+ *
+ * Function objects used for determining when a read or write operation should
+ * complete.
+ */
+/*@{*/
+
+/// Return a completion condition function object that indicates that a read or
+/// write operation should continue until all of the data has been transferred,
+/// or until an error occurs.
+/**
+ * This function is used to create an object, of unspecified type, that meets
+ * CompletionCondition requirements.
+ *
+ * @par Example
+ * Reading until a buffer is full:
+ * @code
+ * boost::array<char, 128> buf;
+ * boost::system::error_code ec;
+ * std::size_t n = boost::asio::read(
+ * sock, boost::asio::buffer(buf),
+ * boost::asio::transfer_all(), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * else
+ * {
+ * // n == 128
+ * }
+ * @endcode
+ */
+#if defined(GENERATING_DOCUMENTATION)
+unspecified transfer_all();
+#else
+inline detail::transfer_all_t transfer_all()
+{
+ return detail::transfer_all_t();
+}
+#endif
+
+/// Return a completion condition function object that indicates that a read or
+/// write operation should continue until a minimum number of bytes has been
+/// transferred, or until an error occurs.
+/**
+ * This function is used to create an object, of unspecified type, that meets
+ * CompletionCondition requirements.
+ *
+ * @par Example
+ * Reading until a buffer is full or contains at least 64 bytes:
+ * @code
+ * boost::array<char, 128> buf;
+ * boost::system::error_code ec;
+ * std::size_t n = boost::asio::read(
+ * sock, boost::asio::buffer(buf),
+ * boost::asio::transfer_at_least(64), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * else
+ * {
+ * // n >= 64 && n <= 128
+ * }
+ * @endcode
+ */
+#if defined(GENERATING_DOCUMENTATION)
+unspecified transfer_at_least(std::size_t minimum);
+#else
+inline detail::transfer_at_least_t transfer_at_least(std::size_t minimum)
+{
+ return detail::transfer_at_least_t(minimum);
+}
+#endif
+
+/// Return a completion condition function object that indicates that a read or
+/// write operation should continue until an exact number of bytes has been
+/// transferred, or until an error occurs.
+/**
+ * This function is used to create an object, of unspecified type, that meets
+ * CompletionCondition requirements.
+ *
+ * @par Example
+ * Reading until a buffer is full or contains exactly 64 bytes:
+ * @code
+ * boost::array<char, 128> buf;
+ * boost::system::error_code ec;
+ * std::size_t n = boost::asio::read(
+ * sock, boost::asio::buffer(buf),
+ * boost::asio::transfer_exactly(64), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * else
+ * {
+ * // n == 64
+ * }
+ * @endcode
+ */
+#if defined(GENERATING_DOCUMENTATION)
+unspecified transfer_exactly(std::size_t size);
+#else
+inline detail::transfer_exactly_t transfer_exactly(std::size_t size)
+{
+ return detail::transfer_exactly_t(size);
+}
+#endif
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_COMPLETION_CONDITION_HPP
diff --git a/ext/patches/boost/asio/connect.hpp b/ext/patches/boost/asio/connect.hpp
new file mode 100644
index 0000000..6f793fe
--- /dev/null
+++ b/ext/patches/boost/asio/connect.hpp
@@ -0,0 +1,825 @@
+//
+// connect.hpp
+// ~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_CONNECT_HPP
+#define BOOST_ASIO_CONNECT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/**
+ * @defgroup connect boost::asio::connect
+ *
+ * @brief Establishes a socket connection by trying each endpoint in a sequence.
+ */
+/*@{*/
+
+/// Establishes a socket connection by trying each endpoint in a sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c connect member
+ * function, once for each endpoint in the sequence, until a connection is
+ * successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @returns On success, an iterator denoting the successfully connected
+ * endpoint. Otherwise, the end iterator.
+ *
+ * @throws boost::system::system_error Thrown on failure. If the sequence is
+ * empty, the associated @c error_code is boost::asio::error::not_found.
+ * Otherwise, contains the error from the last connection attempt.
+ *
+ * @note This overload assumes that a default constructed object of type @c
+ * Iterator represents the end of the sequence. This is a valid assumption for
+ * iterator types such as @c boost::asio::ip::tcp::resolver::iterator.
+ *
+ * @par Example
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::socket s(io_service);
+ * boost::asio::connect(s, r.resolve(q)); @endcode
+ */
+template <typename Protocol, typename SocketService, typename Iterator>
+Iterator connect(basic_socket<Protocol, SocketService>& s, Iterator begin);
+
+/// Establishes a socket connection by trying each endpoint in a sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c connect member
+ * function, once for each endpoint in the sequence, until a connection is
+ * successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param ec Set to indicate what error occurred, if any. If the sequence is
+ * empty, set to boost::asio::error::not_found. Otherwise, contains the error
+ * from the last connection attempt.
+ *
+ * @returns On success, an iterator denoting the successfully connected
+ * endpoint. Otherwise, the end iterator.
+ *
+ * @note This overload assumes that a default constructed object of type @c
+ * Iterator represents the end of the sequence. This is a valid assumption for
+ * iterator types such as @c boost::asio::ip::tcp::resolver::iterator.
+ *
+ * @par Example
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::socket s(io_service);
+ * boost::system::error_code ec;
+ * boost::asio::connect(s, r.resolve(q), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * } @endcode
+ */
+template <typename Protocol, typename SocketService, typename Iterator>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, boost::system::error_code& ec);
+
+/// Establishes a socket connection by trying each endpoint in a sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c connect member
+ * function, once for each endpoint in the sequence, until a connection is
+ * successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param end An iterator pointing to the end of a sequence of endpoints.
+ *
+ * @returns On success, an iterator denoting the successfully connected
+ * endpoint. Otherwise, the end iterator.
+ *
+ * @throws boost::system::system_error Thrown on failure. If the sequence is
+ * empty, the associated @c error_code is boost::asio::error::not_found.
+ * Otherwise, contains the error from the last connection attempt.
+ *
+ * @par Example
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::resolver::iterator i = r.resolve(q), end;
+ * tcp::socket s(io_service);
+ * boost::asio::connect(s, i, end); @endcode
+ */
+template <typename Protocol, typename SocketService, typename Iterator>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end);
+
+/// Establishes a socket connection by trying each endpoint in a sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c connect member
+ * function, once for each endpoint in the sequence, until a connection is
+ * successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param end An iterator pointing to the end of a sequence of endpoints.
+ *
+ * @param ec Set to indicate what error occurred, if any. If the sequence is
+ * empty, set to boost::asio::error::not_found. Otherwise, contains the error
+ * from the last connection attempt.
+ *
+ * @returns On success, an iterator denoting the successfully connected
+ * endpoint. Otherwise, the end iterator.
+ *
+ * @par Example
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::resolver::iterator i = r.resolve(q), end;
+ * tcp::socket s(io_service);
+ * boost::system::error_code ec;
+ * boost::asio::connect(s, i, end, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * } @endcode
+ */
+template <typename Protocol, typename SocketService, typename Iterator>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end, boost::system::error_code& ec);
+
+/// Establishes a socket connection by trying each endpoint in a sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c connect member
+ * function, once for each endpoint in the sequence, until a connection is
+ * successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param connect_condition A function object that is called prior to each
+ * connection attempt. The signature of the function object must be:
+ * @code Iterator connect_condition(
+ * const boost::system::error_code& ec,
+ * Iterator next); @endcode
+ * The @c ec parameter contains the result from the most recent connect
+ * operation. Before the first connection attempt, @c ec is always set to
+ * indicate success. The @c next parameter is an iterator pointing to the next
+ * endpoint to be tried. The function object should return the next iterator,
+ * but is permitted to return a different iterator so that endpoints may be
+ * skipped. The implementation guarantees that the function object will never
+ * be called with the end iterator.
+ *
+ * @returns On success, an iterator denoting the successfully connected
+ * endpoint. Otherwise, the end iterator.
+ *
+ * @throws boost::system::system_error Thrown on failure. If the sequence is
+ * empty, the associated @c error_code is boost::asio::error::not_found.
+ * Otherwise, contains the error from the last connection attempt.
+ *
+ * @note This overload assumes that a default constructed object of type @c
+ * Iterator represents the end of the sequence. This is a valid assumption for
+ * iterator types such as @c boost::asio::ip::tcp::resolver::iterator.
+ *
+ * @par Example
+ * The following connect condition function object can be used to output
+ * information about the individual connection attempts:
+ * @code struct my_connect_condition
+ * {
+ * template <typename Iterator>
+ * Iterator operator()(
+ * const boost::system::error_code& ec,
+ * Iterator next)
+ * {
+ * if (ec) std::cout << "Error: " << ec.message() << std::endl;
+ * std::cout << "Trying: " << next->endpoint() << std::endl;
+ * return next;
+ * }
+ * }; @endcode
+ * It would be used with the boost::asio::connect function as follows:
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::socket s(io_service);
+ * tcp::resolver::iterator i = boost::asio::connect(
+ * s, r.resolve(q), my_connect_condition());
+ * std::cout << "Connected to: " << i->endpoint() << std::endl; @endcode
+ */
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ConnectCondition>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, ConnectCondition connect_condition);
+
+/// Establishes a socket connection by trying each endpoint in a sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c connect member
+ * function, once for each endpoint in the sequence, until a connection is
+ * successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param connect_condition A function object that is called prior to each
+ * connection attempt. The signature of the function object must be:
+ * @code Iterator connect_condition(
+ * const boost::system::error_code& ec,
+ * Iterator next); @endcode
+ * The @c ec parameter contains the result from the most recent connect
+ * operation. Before the first connection attempt, @c ec is always set to
+ * indicate success. The @c next parameter is an iterator pointing to the next
+ * endpoint to be tried. The function object should return the next iterator,
+ * but is permitted to return a different iterator so that endpoints may be
+ * skipped. The implementation guarantees that the function object will never
+ * be called with the end iterator.
+ *
+ * @param ec Set to indicate what error occurred, if any. If the sequence is
+ * empty, set to boost::asio::error::not_found. Otherwise, contains the error
+ * from the last connection attempt.
+ *
+ * @returns On success, an iterator denoting the successfully connected
+ * endpoint. Otherwise, the end iterator.
+ *
+ * @note This overload assumes that a default constructed object of type @c
+ * Iterator represents the end of the sequence. This is a valid assumption for
+ * iterator types such as @c boost::asio::ip::tcp::resolver::iterator.
+ *
+ * @par Example
+ * The following connect condition function object can be used to output
+ * information about the individual connection attempts:
+ * @code struct my_connect_condition
+ * {
+ * template <typename Iterator>
+ * Iterator operator()(
+ * const boost::system::error_code& ec,
+ * Iterator next)
+ * {
+ * if (ec) std::cout << "Error: " << ec.message() << std::endl;
+ * std::cout << "Trying: " << next->endpoint() << std::endl;
+ * return next;
+ * }
+ * }; @endcode
+ * It would be used with the boost::asio::connect function as follows:
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::socket s(io_service);
+ * boost::system::error_code ec;
+ * tcp::resolver::iterator i = boost::asio::connect(
+ * s, r.resolve(q), my_connect_condition(), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * else
+ * {
+ * std::cout << "Connected to: " << i->endpoint() << std::endl;
+ * } @endcode
+ */
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ConnectCondition>
+Iterator connect(basic_socket<Protocol, SocketService>& s, Iterator begin,
+ ConnectCondition connect_condition, boost::system::error_code& ec);
+
+/// Establishes a socket connection by trying each endpoint in a sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c connect member
+ * function, once for each endpoint in the sequence, until a connection is
+ * successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param end An iterator pointing to the end of a sequence of endpoints.
+ *
+ * @param connect_condition A function object that is called prior to each
+ * connection attempt. The signature of the function object must be:
+ * @code Iterator connect_condition(
+ * const boost::system::error_code& ec,
+ * Iterator next); @endcode
+ * The @c ec parameter contains the result from the most recent connect
+ * operation. Before the first connection attempt, @c ec is always set to
+ * indicate success. The @c next parameter is an iterator pointing to the next
+ * endpoint to be tried. The function object should return the next iterator,
+ * but is permitted to return a different iterator so that endpoints may be
+ * skipped. The implementation guarantees that the function object will never
+ * be called with the end iterator.
+ *
+ * @returns On success, an iterator denoting the successfully connected
+ * endpoint. Otherwise, the end iterator.
+ *
+ * @throws boost::system::system_error Thrown on failure. If the sequence is
+ * empty, the associated @c error_code is boost::asio::error::not_found.
+ * Otherwise, contains the error from the last connection attempt.
+ *
+ * @par Example
+ * The following connect condition function object can be used to output
+ * information about the individual connection attempts:
+ * @code struct my_connect_condition
+ * {
+ * template <typename Iterator>
+ * Iterator operator()(
+ * const boost::system::error_code& ec,
+ * Iterator next)
+ * {
+ * if (ec) std::cout << "Error: " << ec.message() << std::endl;
+ * std::cout << "Trying: " << next->endpoint() << std::endl;
+ * return next;
+ * }
+ * }; @endcode
+ * It would be used with the boost::asio::connect function as follows:
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::resolver::iterator i = r.resolve(q), end;
+ * tcp::socket s(io_service);
+ * i = boost::asio::connect(s, i, end, my_connect_condition());
+ * std::cout << "Connected to: " << i->endpoint() << std::endl; @endcode
+ */
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ConnectCondition>
+Iterator connect(basic_socket<Protocol, SocketService>& s, Iterator begin,
+ Iterator end, ConnectCondition connect_condition);
+
+/// Establishes a socket connection by trying each endpoint in a sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c connect member
+ * function, once for each endpoint in the sequence, until a connection is
+ * successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param end An iterator pointing to the end of a sequence of endpoints.
+ *
+ * @param connect_condition A function object that is called prior to each
+ * connection attempt. The signature of the function object must be:
+ * @code Iterator connect_condition(
+ * const boost::system::error_code& ec,
+ * Iterator next); @endcode
+ * The @c ec parameter contains the result from the most recent connect
+ * operation. Before the first connection attempt, @c ec is always set to
+ * indicate success. The @c next parameter is an iterator pointing to the next
+ * endpoint to be tried. The function object should return the next iterator,
+ * but is permitted to return a different iterator so that endpoints may be
+ * skipped. The implementation guarantees that the function object will never
+ * be called with the end iterator.
+ *
+ * @param ec Set to indicate what error occurred, if any. If the sequence is
+ * empty, set to boost::asio::error::not_found. Otherwise, contains the error
+ * from the last connection attempt.
+ *
+ * @returns On success, an iterator denoting the successfully connected
+ * endpoint. Otherwise, the end iterator.
+ *
+ * @par Example
+ * The following connect condition function object can be used to output
+ * information about the individual connection attempts:
+ * @code struct my_connect_condition
+ * {
+ * template <typename Iterator>
+ * Iterator operator()(
+ * const boost::system::error_code& ec,
+ * Iterator next)
+ * {
+ * if (ec) std::cout << "Error: " << ec.message() << std::endl;
+ * std::cout << "Trying: " << next->endpoint() << std::endl;
+ * return next;
+ * }
+ * }; @endcode
+ * It would be used with the boost::asio::connect function as follows:
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::resolver::iterator i = r.resolve(q), end;
+ * tcp::socket s(io_service);
+ * boost::system::error_code ec;
+ * i = boost::asio::connect(s, i, end, my_connect_condition(), ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * else
+ * {
+ * std::cout << "Connected to: " << i->endpoint() << std::endl;
+ * } @endcode
+ */
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ConnectCondition>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end, ConnectCondition connect_condition,
+ boost::system::error_code& ec);
+
+/*@}*/
+
+/**
+ * @defgroup async_connect boost::asio::async_connect
+ *
+ * @brief Asynchronously establishes a socket connection by trying each
+ * endpoint in a sequence.
+ */
+/*@{*/
+
+/// Asynchronously establishes a socket connection by trying each endpoint in a
+/// sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c async_connect
+ * member function, once for each endpoint in the sequence, until a connection
+ * is successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param handler The handler to be called when the connect operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * // Result of operation. if the sequence is empty, set to
+ * // boost::asio::error::not_found. Otherwise, contains the
+ * // error from the last connection attempt.
+ * const boost::system::error_code& error,
+ *
+ * // On success, an iterator denoting the successfully
+ * // connected endpoint. Otherwise, the end iterator.
+ * Iterator iterator
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note This overload assumes that a default constructed object of type @c
+ * Iterator represents the end of the sequence. This is a valid assumption for
+ * iterator types such as @c boost::asio::ip::tcp::resolver::iterator.
+ *
+ * @par Example
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::socket s(io_service);
+ *
+ * // ...
+ *
+ * r.async_resolve(q, resolve_handler);
+ *
+ * // ...
+ *
+ * void resolve_handler(
+ * const boost::system::error_code& ec,
+ * tcp::resolver::iterator i)
+ * {
+ * if (!ec)
+ * {
+ * boost::asio::async_connect(s, i, connect_handler);
+ * }
+ * }
+ *
+ * // ...
+ *
+ * void connect_handler(
+ * const boost::system::error_code& ec,
+ * tcp::resolver::iterator i)
+ * {
+ * // ...
+ * } @endcode
+ */
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ComposedConnectHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ComposedConnectHandler,
+ void (boost::system::error_code, Iterator))
+async_connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, BOOST_ASIO_MOVE_ARG(ComposedConnectHandler) handler);
+
+/// Asynchronously establishes a socket connection by trying each endpoint in a
+/// sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c async_connect
+ * member function, once for each endpoint in the sequence, until a connection
+ * is successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param end An iterator pointing to the end of a sequence of endpoints.
+ *
+ * @param handler The handler to be called when the connect operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * // Result of operation. if the sequence is empty, set to
+ * // boost::asio::error::not_found. Otherwise, contains the
+ * // error from the last connection attempt.
+ * const boost::system::error_code& error,
+ *
+ * // On success, an iterator denoting the successfully
+ * // connected endpoint. Otherwise, the end iterator.
+ * Iterator iterator
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::socket s(io_service);
+ *
+ * // ...
+ *
+ * r.async_resolve(q, resolve_handler);
+ *
+ * // ...
+ *
+ * void resolve_handler(
+ * const boost::system::error_code& ec,
+ * tcp::resolver::iterator i)
+ * {
+ * if (!ec)
+ * {
+ * tcp::resolver::iterator end;
+ * boost::asio::async_connect(s, i, end, connect_handler);
+ * }
+ * }
+ *
+ * // ...
+ *
+ * void connect_handler(
+ * const boost::system::error_code& ec,
+ * tcp::resolver::iterator i)
+ * {
+ * // ...
+ * } @endcode
+ */
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ComposedConnectHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ComposedConnectHandler,
+ void (boost::system::error_code, Iterator))
+async_connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end,
+ BOOST_ASIO_MOVE_ARG(ComposedConnectHandler) handler);
+
+/// Asynchronously establishes a socket connection by trying each endpoint in a
+/// sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c async_connect
+ * member function, once for each endpoint in the sequence, until a connection
+ * is successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param connect_condition A function object that is called prior to each
+ * connection attempt. The signature of the function object must be:
+ * @code Iterator connect_condition(
+ * const boost::system::error_code& ec,
+ * Iterator next); @endcode
+ * The @c ec parameter contains the result from the most recent connect
+ * operation. Before the first connection attempt, @c ec is always set to
+ * indicate success. The @c next parameter is an iterator pointing to the next
+ * endpoint to be tried. The function object should return the next iterator,
+ * but is permitted to return a different iterator so that endpoints may be
+ * skipped. The implementation guarantees that the function object will never
+ * be called with the end iterator.
+ *
+ * @param handler The handler to be called when the connect operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * // Result of operation. if the sequence is empty, set to
+ * // boost::asio::error::not_found. Otherwise, contains the
+ * // error from the last connection attempt.
+ * const boost::system::error_code& error,
+ *
+ * // On success, an iterator denoting the successfully
+ * // connected endpoint. Otherwise, the end iterator.
+ * Iterator iterator
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note This overload assumes that a default constructed object of type @c
+ * Iterator represents the end of the sequence. This is a valid assumption for
+ * iterator types such as @c boost::asio::ip::tcp::resolver::iterator.
+ *
+ * @par Example
+ * The following connect condition function object can be used to output
+ * information about the individual connection attempts:
+ * @code struct my_connect_condition
+ * {
+ * template <typename Iterator>
+ * Iterator operator()(
+ * const boost::system::error_code& ec,
+ * Iterator next)
+ * {
+ * if (ec) std::cout << "Error: " << ec.message() << std::endl;
+ * std::cout << "Trying: " << next->endpoint() << std::endl;
+ * return next;
+ * }
+ * }; @endcode
+ * It would be used with the boost::asio::connect function as follows:
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::socket s(io_service);
+ *
+ * // ...
+ *
+ * r.async_resolve(q, resolve_handler);
+ *
+ * // ...
+ *
+ * void resolve_handler(
+ * const boost::system::error_code& ec,
+ * tcp::resolver::iterator i)
+ * {
+ * if (!ec)
+ * {
+ * boost::asio::async_connect(s, i,
+ * my_connect_condition(),
+ * connect_handler);
+ * }
+ * }
+ *
+ * // ...
+ *
+ * void connect_handler(
+ * const boost::system::error_code& ec,
+ * tcp::resolver::iterator i)
+ * {
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * else
+ * {
+ * std::cout << "Connected to: " << i->endpoint() << std::endl;
+ * }
+ * } @endcode
+ */
+template <typename Protocol, typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ComposedConnectHandler,
+ void (boost::system::error_code, Iterator))
+async_connect(basic_socket<Protocol, SocketService>& s, Iterator begin,
+ ConnectCondition connect_condition,
+ BOOST_ASIO_MOVE_ARG(ComposedConnectHandler) handler);
+
+/// Asynchronously establishes a socket connection by trying each endpoint in a
+/// sequence.
+/**
+ * This function attempts to connect a socket to one of a sequence of
+ * endpoints. It does this by repeated calls to the socket's @c async_connect
+ * member function, once for each endpoint in the sequence, until a connection
+ * is successfully established.
+ *
+ * @param s The socket to be connected. If the socket is already open, it will
+ * be closed.
+ *
+ * @param begin An iterator pointing to the start of a sequence of endpoints.
+ *
+ * @param end An iterator pointing to the end of a sequence of endpoints.
+ *
+ * @param connect_condition A function object that is called prior to each
+ * connection attempt. The signature of the function object must be:
+ * @code Iterator connect_condition(
+ * const boost::system::error_code& ec,
+ * Iterator next); @endcode
+ * The @c ec parameter contains the result from the most recent connect
+ * operation. Before the first connection attempt, @c ec is always set to
+ * indicate success. The @c next parameter is an iterator pointing to the next
+ * endpoint to be tried. The function object should return the next iterator,
+ * but is permitted to return a different iterator so that endpoints may be
+ * skipped. The implementation guarantees that the function object will never
+ * be called with the end iterator.
+ *
+ * @param handler The handler to be called when the connect operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * // Result of operation. if the sequence is empty, set to
+ * // boost::asio::error::not_found. Otherwise, contains the
+ * // error from the last connection attempt.
+ * const boost::system::error_code& error,
+ *
+ * // On success, an iterator denoting the successfully
+ * // connected endpoint. Otherwise, the end iterator.
+ * Iterator iterator
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * The following connect condition function object can be used to output
+ * information about the individual connection attempts:
+ * @code struct my_connect_condition
+ * {
+ * template <typename Iterator>
+ * Iterator operator()(
+ * const boost::system::error_code& ec,
+ * Iterator next)
+ * {
+ * if (ec) std::cout << "Error: " << ec.message() << std::endl;
+ * std::cout << "Trying: " << next->endpoint() << std::endl;
+ * return next;
+ * }
+ * }; @endcode
+ * It would be used with the boost::asio::connect function as follows:
+ * @code tcp::resolver r(io_service);
+ * tcp::resolver::query q("host", "service");
+ * tcp::socket s(io_service);
+ *
+ * // ...
+ *
+ * r.async_resolve(q, resolve_handler);
+ *
+ * // ...
+ *
+ * void resolve_handler(
+ * const boost::system::error_code& ec,
+ * tcp::resolver::iterator i)
+ * {
+ * if (!ec)
+ * {
+ * tcp::resolver::iterator end;
+ * boost::asio::async_connect(s, i, end,
+ * my_connect_condition(),
+ * connect_handler);
+ * }
+ * }
+ *
+ * // ...
+ *
+ * void connect_handler(
+ * const boost::system::error_code& ec,
+ * tcp::resolver::iterator i)
+ * {
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * else
+ * {
+ * std::cout << "Connected to: " << i->endpoint() << std::endl;
+ * }
+ * } @endcode
+ */
+template <typename Protocol, typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ComposedConnectHandler,
+ void (boost::system::error_code, Iterator))
+async_connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end, ConnectCondition connect_condition,
+ BOOST_ASIO_MOVE_ARG(ComposedConnectHandler) handler);
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/connect.hpp>
+
+#endif
diff --git a/ext/patches/boost/asio/coroutine.hpp b/ext/patches/boost/asio/coroutine.hpp
new file mode 100644
index 0000000..3f803b8
--- /dev/null
+++ b/ext/patches/boost/asio/coroutine.hpp
@@ -0,0 +1,330 @@
+//
+// coroutine.hpp
+// ~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_COROUTINE_HPP
+#define BOOST_ASIO_COROUTINE_HPP
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class coroutine_ref;
+
+} // namespace detail
+
+/// Provides support for implementing stackless coroutines.
+/**
+ * The @c coroutine class may be used to implement stackless coroutines. The
+ * class itself is used to store the current state of the coroutine.
+ *
+ * Coroutines are copy-constructible and assignable, and the space overhead is
+ * a single int. They can be used as a base class:
+ *
+ * @code class session : coroutine
+ * {
+ * ...
+ * }; @endcode
+ *
+ * or as a data member:
+ *
+ * @code class session
+ * {
+ * ...
+ * coroutine coro_;
+ * }; @endcode
+ *
+ * or even bound in as a function argument using lambdas or @c bind(). The
+ * important thing is that as the application maintains a copy of the object
+ * for as long as the coroutine must be kept alive.
+ *
+ * @par Pseudo-keywords
+ *
+ * A coroutine is used in conjunction with certain "pseudo-keywords", which
+ * are implemented as macros. These macros are defined by a header file:
+ *
+ * @code #include <boost/asio/yield.hpp>@endcode
+ *
+ * and may conversely be undefined as follows:
+ *
+ * @code #include <boost/asio/unyield.hpp>@endcode
+ *
+ * <b>reenter</b>
+ *
+ * The @c reenter macro is used to define the body of a coroutine. It takes a
+ * single argument: a pointer or reference to a coroutine object. For example,
+ * if the base class is a coroutine object you may write:
+ *
+ * @code reenter (this)
+ * {
+ * ... coroutine body ...
+ * } @endcode
+ *
+ * and if a data member or other variable you can write:
+ *
+ * @code reenter (coro_)
+ * {
+ * ... coroutine body ...
+ * } @endcode
+ *
+ * When @c reenter is executed at runtime, control jumps to the location of the
+ * last @c yield or @c fork.
+ *
+ * The coroutine body may also be a single statement, such as:
+ *
+ * @code reenter (this) for (;;)
+ * {
+ * ...
+ * } @endcode
+ *
+ * @b Limitation: The @c reenter macro is implemented using a switch. This
+ * means that you must take care when using local variables within the
+ * coroutine body. The local variable is not allowed in a position where
+ * reentering the coroutine could bypass the variable definition.
+ *
+ * <b>yield <em>statement</em></b>
+ *
+ * This form of the @c yield keyword is often used with asynchronous operations:
+ *
+ * @code yield socket_->async_read_some(buffer(*buffer_), *this); @endcode
+ *
+ * This divides into four logical steps:
+ *
+ * @li @c yield saves the current state of the coroutine.
+ * @li The statement initiates the asynchronous operation.
+ * @li The resume point is defined immediately following the statement.
+ * @li Control is transferred to the end of the coroutine body.
+ *
+ * When the asynchronous operation completes, the function object is invoked
+ * and @c reenter causes control to transfer to the resume point. It is
+ * important to remember to carry the coroutine state forward with the
+ * asynchronous operation. In the above snippet, the current class is a
+ * function object object with a coroutine object as base class or data member.
+ *
+ * The statement may also be a compound statement, and this permits us to
+ * define local variables with limited scope:
+ *
+ * @code yield
+ * {
+ * mutable_buffers_1 b = buffer(*buffer_);
+ * socket_->async_read_some(b, *this);
+ * } @endcode
+ *
+ * <b>yield return <em>expression</em> ;</b>
+ *
+ * This form of @c yield is often used in generators or coroutine-based parsers.
+ * For example, the function object:
+ *
+ * @code struct interleave : coroutine
+ * {
+ * istream& is1;
+ * istream& is2;
+ * char operator()(char c)
+ * {
+ * reenter (this) for (;;)
+ * {
+ * yield return is1.get();
+ * yield return is2.get();
+ * }
+ * }
+ * }; @endcode
+ *
+ * defines a trivial coroutine that interleaves the characters from two input
+ * streams.
+ *
+ * This type of @c yield divides into three logical steps:
+ *
+ * @li @c yield saves the current state of the coroutine.
+ * @li The resume point is defined immediately following the semicolon.
+ * @li The value of the expression is returned from the function.
+ *
+ * <b>yield ;</b>
+ *
+ * This form of @c yield is equivalent to the following steps:
+ *
+ * @li @c yield saves the current state of the coroutine.
+ * @li The resume point is defined immediately following the semicolon.
+ * @li Control is transferred to the end of the coroutine body.
+ *
+ * This form might be applied when coroutines are used for cooperative
+ * threading and scheduling is explicitly managed. For example:
+ *
+ * @code struct task : coroutine
+ * {
+ * ...
+ * void operator()()
+ * {
+ * reenter (this)
+ * {
+ * while (... not finished ...)
+ * {
+ * ... do something ...
+ * yield;
+ * ... do some more ...
+ * yield;
+ * }
+ * }
+ * }
+ * ...
+ * };
+ * ...
+ * task t1, t2;
+ * for (;;)
+ * {
+ * t1();
+ * t2();
+ * } @endcode
+ *
+ * <b>yield break ;</b>
+ *
+ * The final form of @c yield is used to explicitly terminate the coroutine.
+ * This form is comprised of two steps:
+ *
+ * @li @c yield sets the coroutine state to indicate termination.
+ * @li Control is transferred to the end of the coroutine body.
+ *
+ * Once terminated, calls to is_complete() return true and the coroutine cannot
+ * be reentered.
+ *
+ * Note that a coroutine may also be implicitly terminated if the coroutine
+ * body is exited without a yield, e.g. by return, throw or by running to the
+ * end of the body.
+ *
+ * <b>fork <em>statement</em></b>
+ *
+ * The @c fork pseudo-keyword is used when "forking" a coroutine, i.e. splitting
+ * it into two (or more) copies. One use of @c fork is in a server, where a new
+ * coroutine is created to handle each client connection:
+ *
+ * @code reenter (this)
+ * {
+ * do
+ * {
+ * socket_.reset(new tcp::socket(io_service_));
+ * yield acceptor->async_accept(*socket_, *this);
+ * fork server(*this)();
+ * } while (is_parent());
+ * ... client-specific handling follows ...
+ * } @endcode
+ *
+ * The logical steps involved in a @c fork are:
+ *
+ * @li @c fork saves the current state of the coroutine.
+ * @li The statement creates a copy of the coroutine and either executes it
+ * immediately or schedules it for later execution.
+ * @li The resume point is defined immediately following the semicolon.
+ * @li For the "parent", control immediately continues from the next line.
+ *
+ * The functions is_parent() and is_child() can be used to differentiate
+ * between parent and child. You would use these functions to alter subsequent
+ * control flow.
+ *
+ * Note that @c fork doesn't do the actual forking by itself. It is the
+ * application's responsibility to create a clone of the coroutine and call it.
+ * The clone can be called immediately, as above, or scheduled for delayed
+ * execution using something like io_service::post().
+ *
+ * @par Alternate macro names
+ *
+ * If preferred, an application can use macro names that follow a more typical
+ * naming convention, rather than the pseudo-keywords. These are:
+ *
+ * @li @c BOOST_ASIO_CORO_REENTER instead of @c reenter
+ * @li @c BOOST_ASIO_CORO_YIELD instead of @c yield
+ * @li @c BOOST_ASIO_CORO_FORK instead of @c fork
+ */
+class coroutine
+{
+public:
+ /// Constructs a coroutine in its initial state.
+ coroutine() : value_(0) {}
+
+ /// Returns true if the coroutine is the child of a fork.
+ bool is_child() const { return value_ < 0; }
+
+ /// Returns true if the coroutine is the parent of a fork.
+ bool is_parent() const { return !is_child(); }
+
+ /// Returns true if the coroutine has reached its terminal state.
+ bool is_complete() const { return value_ == -1; }
+
+private:
+ friend class detail::coroutine_ref;
+ int value_;
+};
+
+
+namespace detail {
+
+class coroutine_ref
+{
+public:
+ coroutine_ref(coroutine& c) : value_(c.value_), modified_(false) {}
+ coroutine_ref(coroutine* c) : value_(c->value_), modified_(false) {}
+ ~coroutine_ref() { if (!modified_) value_ = -1; }
+ operator int() const { return value_; }
+ int& operator=(int v) { modified_ = true; return value_ = v; }
+private:
+ void operator=(const coroutine_ref&);
+ int& value_;
+ bool modified_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#define BOOST_ASIO_CORO_REENTER(c) \
+ switch (::boost::asio::detail::coroutine_ref _coro_value = c) \
+ case -1: if (_coro_value) \
+ { \
+ goto terminate_coroutine; \
+ terminate_coroutine: \
+ _coro_value = -1; \
+ goto bail_out_of_coroutine; \
+ bail_out_of_coroutine: \
+ break; \
+ } \
+ else case 0:
+
+#define BOOST_ASIO_CORO_YIELD_IMPL(n) \
+ for (_coro_value = (n);;) \
+ if (_coro_value == 0) \
+ { \
+ case (n): ; \
+ break; \
+ } \
+ else \
+ switch (_coro_value ? 0 : 1) \
+ for (;;) \
+ case -1: if (_coro_value) \
+ goto terminate_coroutine; \
+ else for (;;) \
+ case 1: if (_coro_value) \
+ goto bail_out_of_coroutine; \
+ else case 0:
+
+#define BOOST_ASIO_CORO_FORK_IMPL(n) \
+ for (_coro_value = -(n);; _coro_value = (n)) \
+ if (_coro_value == (n)) \
+ { \
+ case -(n): ; \
+ break; \
+ } \
+ else
+
+#if defined(_MSC_VER)
+# define BOOST_ASIO_CORO_YIELD BOOST_ASIO_CORO_YIELD_IMPL(__COUNTER__ + 1)
+# define BOOST_ASIO_CORO_FORK BOOST_ASIO_CORO_FORK_IMPL(__COUNTER__ + 1)
+#else // defined(_MSC_VER)
+# define BOOST_ASIO_CORO_YIELD BOOST_ASIO_CORO_YIELD_IMPL(__LINE__)
+# define BOOST_ASIO_CORO_FORK BOOST_ASIO_CORO_FORK_IMPL(__LINE__)
+#endif // defined(_MSC_VER)
+
+#endif // BOOST_ASIO_COROUTINE_HPP
diff --git a/ext/patches/boost/asio/datagram_socket_service.hpp b/ext/patches/boost/asio/datagram_socket_service.hpp
new file mode 100644
index 0000000..63f7b25
--- /dev/null
+++ b/ext/patches/boost/asio/datagram_socket_service.hpp
@@ -0,0 +1,434 @@
+//
+// datagram_socket_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DATAGRAM_SOCKET_SERVICE_HPP
+#define BOOST_ASIO_DATAGRAM_SOCKET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/null_socket_service.hpp>
+#elif defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_socket_service.hpp>
+#else
+# include <boost/asio/detail/reactive_socket_service.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a datagram socket.
+template <typename Protocol>
+class datagram_socket_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<datagram_socket_service<Protocol> >
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+private:
+ // The type of the platform-specific implementation.
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ typedef detail::null_socket_service<Protocol> service_impl_type;
+#elif defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::win_iocp_socket_service<Protocol> service_impl_type;
+#else
+ typedef detail::reactive_socket_service<Protocol> service_impl_type;
+#endif
+
+public:
+ /// The type of a datagram socket.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef typename service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native socket type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native socket type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new datagram socket service for the specified io_service.
+ explicit datagram_socket_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ datagram_socket_service<Protocol> >(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new datagram socket implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new datagram socket implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another datagram socket implementation.
+ void move_assign(implementation_type& impl,
+ datagram_socket_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+
+ /// Move-construct a new datagram socket implementation from another protocol
+ /// type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type& impl,
+ typename datagram_socket_service<
+ Protocol1>::implementation_type& other_impl,
+ typename enable_if<is_convertible<
+ Protocol1, Protocol>::value>::type* = 0)
+ {
+ service_impl_.template converting_move_construct<Protocol1>(
+ impl, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a datagram socket implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ // Open a new datagram socket implementation.
+ boost::system::error_code open(implementation_type& impl,
+ const protocol_type& protocol, boost::system::error_code& ec)
+ {
+ if (protocol.type() == BOOST_ASIO_OS_DEF(SOCK_DGRAM))
+ service_impl_.open(impl, protocol, ec);
+ else
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ /// Assign an existing native socket to a datagram socket.
+ boost::system::error_code assign(implementation_type& impl,
+ const protocol_type& protocol, const native_handle_type& native_socket,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, protocol, native_socket, ec);
+ }
+
+ /// Determine whether the socket is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close a datagram socket implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native socket implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native socket implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the socket.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Determine whether the socket is at the out-of-band data mark.
+ bool at_mark(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.at_mark(impl, ec);
+ }
+
+ /// Determine the number of bytes available for reading.
+ std::size_t available(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.available(impl, ec);
+ }
+
+ // Bind the datagram socket to the specified local endpoint.
+ boost::system::error_code bind(implementation_type& impl,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.bind(impl, endpoint, ec);
+ }
+
+ /// Connect the datagram socket to the specified endpoint.
+ boost::system::error_code connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.connect(impl, peer_endpoint, ec);
+ }
+
+ /// Start an asynchronous connect.
+ template <typename ConnectHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ConnectHandler,
+ void (boost::system::error_code))
+ async_connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint,
+ BOOST_ASIO_MOVE_ARG(ConnectHandler) handler)
+ {
+ detail::async_result_init<
+ ConnectHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(ConnectHandler)(handler));
+
+ service_impl_.async_connect(impl, peer_endpoint, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Set a socket option.
+ template <typename SettableSocketOption>
+ boost::system::error_code set_option(implementation_type& impl,
+ const SettableSocketOption& option, boost::system::error_code& ec)
+ {
+ return service_impl_.set_option(impl, option, ec);
+ }
+
+ /// Get a socket option.
+ template <typename GettableSocketOption>
+ boost::system::error_code get_option(const implementation_type& impl,
+ GettableSocketOption& option, boost::system::error_code& ec) const
+ {
+ return service_impl_.get_option(impl, option, ec);
+ }
+
+ /// Perform an IO control command on the socket.
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(implementation_type& impl,
+ IoControlCommand& command, boost::system::error_code& ec)
+ {
+ return service_impl_.io_control(impl, command, ec);
+ }
+
+ /// Gets the non-blocking mode of the socket.
+ bool non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the socket.
+ boost::system::error_code non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.non_blocking(impl, mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native socket implementation.
+ bool native_non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.native_non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the native socket implementation.
+ boost::system::error_code native_non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.native_non_blocking(impl, mode, ec);
+ }
+
+ /// Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.local_endpoint(impl, ec);
+ }
+
+ /// Get the remote endpoint.
+ endpoint_type remote_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.remote_endpoint(impl, ec);
+ }
+
+ /// Disable sends or receives on the socket.
+ boost::system::error_code shutdown(implementation_type& impl,
+ socket_base::shutdown_type what, boost::system::error_code& ec)
+ {
+ return service_impl_.shutdown(impl, what, ec);
+ }
+
+ /// Send the given data to the peer.
+ template <typename ConstBufferSequence>
+ std::size_t send(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.send(impl, buffers, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(implementation_type& impl, const ConstBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_send(impl, buffers, flags, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Send a datagram to the specified endpoint.
+ template <typename ConstBufferSequence>
+ std::size_t send_to(implementation_type& impl,
+ const ConstBufferSequence& buffers, const endpoint_type& destination,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.send_to(impl, buffers, destination, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send_to(implementation_type& impl,
+ const ConstBufferSequence& buffers, const endpoint_type& destination,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_send_to(impl, buffers,
+ destination, flags, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Receive some data from the peer.
+ template <typename MutableBufferSequence>
+ std::size_t receive(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.receive(impl, buffers, flags, ec);
+ }
+
+ /// Start an asynchronous receive.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_receive(impl, buffers, flags, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Receive a datagram with the endpoint of the sender.
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(implementation_type& impl,
+ const MutableBufferSequence& buffers, endpoint_type& sender_endpoint,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.receive_from(impl, buffers, sender_endpoint, flags,
+ ec);
+ }
+
+ /// Start an asynchronous receive that will get the endpoint of the sender.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive_from(implementation_type& impl,
+ const MutableBufferSequence& buffers, endpoint_type& sender_endpoint,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_receive_from(impl, buffers,
+ sender_endpoint, flags, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DATAGRAM_SOCKET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/deadline_timer.hpp b/ext/patches/boost/asio/deadline_timer.hpp
new file mode 100644
index 0000000..ffbee73
--- /dev/null
+++ b/ext/patches/boost/asio/deadline_timer.hpp
@@ -0,0 +1,42 @@
+//
+// deadline_timer.hpp
+// ~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DEADLINE_TIMER_HPP
+#define BOOST_ASIO_DEADLINE_TIMER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/detail/socket_types.hpp> // Must come before posix_time.
+#include <boost/asio/basic_deadline_timer.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+#include <boost/date_time/posix_time/posix_time_types.hpp>
+#include <boost/asio/detail/pop_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Typedef for the typical usage of timer. Uses a UTC clock.
+typedef basic_deadline_timer<boost::posix_time::ptime> deadline_timer;
+
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_DEADLINE_TIMER_HPP
diff --git a/ext/patches/boost/asio/deadline_timer_service.hpp b/ext/patches/boost/asio/deadline_timer_service.hpp
new file mode 100644
index 0000000..8d9f972
--- /dev/null
+++ b/ext/patches/boost/asio/deadline_timer_service.hpp
@@ -0,0 +1,173 @@
+//
+// deadline_timer_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DEADLINE_TIMER_SERVICE_HPP
+#define BOOST_ASIO_DEADLINE_TIMER_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/deadline_timer_service.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/time_traits.hpp>
+#include <boost/asio/detail/timer_queue_ptime.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a timer.
+template <typename TimeType,
+ typename TimeTraits = boost::asio::time_traits<TimeType> >
+class deadline_timer_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<
+ deadline_timer_service<TimeType, TimeTraits> >
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The time traits type.
+ typedef TimeTraits traits_type;
+
+ /// The time type.
+ typedef typename traits_type::time_type time_type;
+
+ /// The duration type.
+ typedef typename traits_type::duration_type duration_type;
+
+private:
+ // The type of the platform-specific implementation.
+ typedef detail::deadline_timer_service<traits_type> service_impl_type;
+
+public:
+ /// The implementation type of the deadline timer.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef typename service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// Construct a new timer service for the specified io_service.
+ explicit deadline_timer_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ deadline_timer_service<TimeType, TimeTraits> >(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new timer implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+ /// Destroy a timer implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Cancel any asynchronous wait operations associated with the timer.
+ std::size_t cancel(implementation_type& impl, boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Cancels one asynchronous wait operation associated with the timer.
+ std::size_t cancel_one(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel_one(impl, ec);
+ }
+
+ /// Get the expiry time for the timer as an absolute time.
+ time_type expires_at(const implementation_type& impl) const
+ {
+ return service_impl_.expires_at(impl);
+ }
+
+ /// Set the expiry time for the timer as an absolute time.
+ std::size_t expires_at(implementation_type& impl,
+ const time_type& expiry_time, boost::system::error_code& ec)
+ {
+ return service_impl_.expires_at(impl, expiry_time, ec);
+ }
+
+ /// Get the expiry time for the timer relative to now.
+ duration_type expires_from_now(const implementation_type& impl) const
+ {
+ return service_impl_.expires_from_now(impl);
+ }
+
+ /// Set the expiry time for the timer relative to now.
+ std::size_t expires_from_now(implementation_type& impl,
+ const duration_type& expiry_time, boost::system::error_code& ec)
+ {
+ return service_impl_.expires_from_now(impl, expiry_time, ec);
+ }
+
+ // Perform a blocking wait on the timer.
+ void wait(implementation_type& impl, boost::system::error_code& ec)
+ {
+ service_impl_.wait(impl, ec);
+ }
+
+ // Start an asynchronous wait on the timer.
+ template <typename WaitHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WaitHandler,
+ void (boost::system::error_code))
+ async_wait(implementation_type& impl,
+ BOOST_ASIO_MOVE_ARG(WaitHandler) handler)
+ {
+ detail::async_result_init<
+ WaitHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(WaitHandler)(handler));
+
+ service_impl_.async_wait(impl, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_DEADLINE_TIMER_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/addressof.hpp b/ext/patches/boost/asio/detail/addressof.hpp
new file mode 100644
index 0000000..269b9b6
--- /dev/null
+++ b/ext/patches/boost/asio/detail/addressof.hpp
@@ -0,0 +1,40 @@
+//
+// detail/addressof.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_ADDRESSOF_HPP
+#define BOOST_ASIO_DETAIL_ADDRESSOF_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_ADDRESSOF)
+# include <memory>
+#else // defined(BOOST_ASIO_HAS_STD_ADDRESSOF)
+# include <boost/utility/addressof.hpp>
+#endif // defined(BOOST_ASIO_HAS_STD_ADDRESSOF)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_HAS_STD_ADDRESSOF)
+using std::addressof;
+#else // defined(BOOST_ASIO_HAS_STD_ADDRESSOF)
+using boost::addressof;
+#endif // defined(BOOST_ASIO_HAS_STD_ADDRESSOF)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_ADDRESSOF_HPP
diff --git a/ext/patches/boost/asio/detail/array.hpp b/ext/patches/boost/asio/detail/array.hpp
new file mode 100644
index 0000000..c921731
--- /dev/null
+++ b/ext/patches/boost/asio/detail/array.hpp
@@ -0,0 +1,40 @@
+//
+// detail/array.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_ARRAY_HPP
+#define BOOST_ASIO_DETAIL_ARRAY_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+# include <array>
+#else // defined(BOOST_ASIO_HAS_STD_ARRAY)
+# include <boost/array.hpp>
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+using std::array;
+#else // defined(BOOST_ASIO_HAS_STD_ARRAY)
+using boost::array;
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_ARRAY_HPP
diff --git a/ext/patches/boost/asio/detail/array_fwd.hpp b/ext/patches/boost/asio/detail/array_fwd.hpp
new file mode 100644
index 0000000..496685a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/array_fwd.hpp
@@ -0,0 +1,34 @@
+//
+// detail/array_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_ARRAY_FWD_HPP
+#define BOOST_ASIO_DETAIL_ARRAY_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+namespace boost {
+
+template<class T, std::size_t N>
+class array;
+
+} // namespace boost
+
+// Standard library components can't be forward declared, so we'll have to
+// include the array header. Fortunately, it's fairly lightweight and doesn't
+// add significantly to the compile time.
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+# include <array>
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+#endif // BOOST_ASIO_DETAIL_ARRAY_FWD_HPP
diff --git a/ext/patches/boost/asio/detail/assert.hpp b/ext/patches/boost/asio/detail/assert.hpp
new file mode 100644
index 0000000..c9c8305
--- /dev/null
+++ b/ext/patches/boost/asio/detail/assert.hpp
@@ -0,0 +1,32 @@
+//
+// detail/assert.hpp
+// ~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_ASSERT_HPP
+#define BOOST_ASIO_DETAIL_ASSERT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_ASSERT)
+# include <boost/assert.hpp>
+#else // defined(BOOST_ASIO_HAS_BOOST_ASSERT)
+# include <cassert>
+#endif // defined(BOOST_ASIO_HAS_BOOST_ASSERT)
+
+#if defined(BOOST_ASIO_HAS_BOOST_ASSERT)
+# define BOOST_ASIO_ASSERT(expr) BOOST_ASSERT(expr)
+#else // defined(BOOST_ASIO_HAS_BOOST_ASSERT)
+# define BOOST_ASIO_ASSERT(expr) assert(expr)
+#endif // defined(BOOST_ASIO_HAS_BOOST_ASSERT)
+
+#endif // BOOST_ASIO_DETAIL_ASSERT_HPP
diff --git a/ext/patches/boost/asio/detail/atomic_count.hpp b/ext/patches/boost/asio/detail/atomic_count.hpp
new file mode 100644
index 0000000..63069a1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/atomic_count.hpp
@@ -0,0 +1,47 @@
+//
+// detail/atomic_count.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_ATOMIC_COUNT_HPP
+#define BOOST_ASIO_DETAIL_ATOMIC_COUNT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+// Nothing to include.
+#elif defined(BOOST_ASIO_HAS_STD_ATOMIC)
+# include <atomic>
+#else // defined(BOOST_ASIO_HAS_STD_ATOMIC)
+# include <boost/detail/atomic_count.hpp>
+#endif // defined(BOOST_ASIO_HAS_STD_ATOMIC)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+typedef long atomic_count;
+inline void increment(atomic_count& a, long b) { a += b; }
+#elif defined(BOOST_ASIO_HAS_STD_ATOMIC)
+typedef std::atomic<long> atomic_count;
+inline void increment(atomic_count& a, long b) { a += b; }
+#else // defined(BOOST_ASIO_HAS_STD_ATOMIC)
+typedef boost::detail::atomic_count atomic_count;
+inline void increment(atomic_count& a, long b) { while (b > 0) ++a, --b; }
+#endif // defined(BOOST_ASIO_HAS_STD_ATOMIC)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_ATOMIC_COUNT_HPP
diff --git a/ext/patches/boost/asio/detail/base_from_completion_cond.hpp b/ext/patches/boost/asio/detail/base_from_completion_cond.hpp
new file mode 100644
index 0000000..e175045
--- /dev/null
+++ b/ext/patches/boost/asio/detail/base_from_completion_cond.hpp
@@ -0,0 +1,70 @@
+//
+// detail/base_from_completion_cond.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_BASE_FROM_COMPLETION_COND_HPP
+#define BOOST_ASIO_DETAIL_BASE_FROM_COMPLETION_COND_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/completion_condition.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename CompletionCondition>
+class base_from_completion_cond
+{
+protected:
+ explicit base_from_completion_cond(CompletionCondition completion_condition)
+ : completion_condition_(completion_condition)
+ {
+ }
+
+ std::size_t check_for_completion(
+ const boost::system::error_code& ec,
+ std::size_t total_transferred)
+ {
+ return detail::adapt_completion_condition_result(
+ completion_condition_(ec, total_transferred));
+ }
+
+private:
+ CompletionCondition completion_condition_;
+};
+
+template <>
+class base_from_completion_cond<transfer_all_t>
+{
+protected:
+ explicit base_from_completion_cond(transfer_all_t)
+ {
+ }
+
+ static std::size_t check_for_completion(
+ const boost::system::error_code& ec,
+ std::size_t total_transferred)
+ {
+ return transfer_all_t()(ec, total_transferred);
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_BASE_FROM_COMPLETION_COND_HPP
diff --git a/ext/patches/boost/asio/detail/bind_handler.hpp b/ext/patches/boost/asio/detail/bind_handler.hpp
new file mode 100644
index 0000000..4fea5a7
--- /dev/null
+++ b/ext/patches/boost/asio/detail/bind_handler.hpp
@@ -0,0 +1,491 @@
+//
+// detail/bind_handler.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_BIND_HANDLER_HPP
+#define BOOST_ASIO_DETAIL_BIND_HANDLER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler, typename Arg1>
+class binder1
+{
+public:
+ binder1(const Handler& handler, const Arg1& arg1)
+ : handler_(handler),
+ arg1_(arg1)
+ {
+ }
+
+ binder1(Handler& handler, const Arg1& arg1)
+ : handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler)),
+ arg1_(arg1)
+ {
+ }
+
+ void operator()()
+ {
+ handler_(static_cast<const Arg1&>(arg1_));
+ }
+
+ void operator()() const
+ {
+ handler_(arg1_);
+ }
+
+//private:
+ Handler handler_;
+ Arg1 arg1_;
+};
+
+template <typename Handler, typename Arg1>
+inline void* asio_handler_allocate(std::size_t size,
+ binder1<Handler, Arg1>* this_handler)
+{
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1>
+inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ binder1<Handler, Arg1>* this_handler)
+{
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1>
+inline bool asio_handler_is_continuation(
+ binder1<Handler, Arg1>* this_handler)
+{
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1>
+inline void asio_handler_invoke(Function& function,
+ binder1<Handler, Arg1>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1>
+inline void asio_handler_invoke(const Function& function,
+ binder1<Handler, Arg1>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1>
+inline binder1<Handler, Arg1> bind_handler(Handler handler,
+ const Arg1& arg1)
+{
+ return binder1<Handler, Arg1>(handler, arg1);
+}
+
+template <typename Handler, typename Arg1, typename Arg2>
+class binder2
+{
+public:
+ binder2(const Handler& handler, const Arg1& arg1, const Arg2& arg2)
+ : handler_(handler),
+ arg1_(arg1),
+ arg2_(arg2)
+ {
+ }
+
+ binder2(Handler& handler, const Arg1& arg1, const Arg2& arg2)
+ : handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler)),
+ arg1_(arg1),
+ arg2_(arg2)
+ {
+ }
+
+ void operator()()
+ {
+ handler_(static_cast<const Arg1&>(arg1_),
+ static_cast<const Arg2&>(arg2_));
+ }
+
+ void operator()() const
+ {
+ handler_(arg1_, arg2_);
+ }
+
+//private:
+ Handler handler_;
+ Arg1 arg1_;
+ Arg2 arg2_;
+};
+
+template <typename Handler, typename Arg1, typename Arg2>
+inline void* asio_handler_allocate(std::size_t size,
+ binder2<Handler, Arg1, Arg2>* this_handler)
+{
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2>
+inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ binder2<Handler, Arg1, Arg2>* this_handler)
+{
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2>
+inline bool asio_handler_is_continuation(
+ binder2<Handler, Arg1, Arg2>* this_handler)
+{
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1, typename Arg2>
+inline void asio_handler_invoke(Function& function,
+ binder2<Handler, Arg1, Arg2>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1, typename Arg2>
+inline void asio_handler_invoke(const Function& function,
+ binder2<Handler, Arg1, Arg2>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2>
+inline binder2<Handler, Arg1, Arg2> bind_handler(Handler handler,
+ const Arg1& arg1, const Arg2& arg2)
+{
+ return binder2<Handler, Arg1, Arg2>(handler, arg1, arg2);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3>
+class binder3
+{
+public:
+ binder3(const Handler& handler, const Arg1& arg1, const Arg2& arg2,
+ const Arg3& arg3)
+ : handler_(handler),
+ arg1_(arg1),
+ arg2_(arg2),
+ arg3_(arg3)
+ {
+ }
+
+ binder3(Handler& handler, const Arg1& arg1, const Arg2& arg2,
+ const Arg3& arg3)
+ : handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler)),
+ arg1_(arg1),
+ arg2_(arg2),
+ arg3_(arg3)
+ {
+ }
+
+ void operator()()
+ {
+ handler_(static_cast<const Arg1&>(arg1_),
+ static_cast<const Arg2&>(arg2_),
+ static_cast<const Arg3&>(arg3_));
+ }
+
+ void operator()() const
+ {
+ handler_(arg1_, arg2_, arg3_);
+ }
+
+//private:
+ Handler handler_;
+ Arg1 arg1_;
+ Arg2 arg2_;
+ Arg3 arg3_;
+};
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3>
+inline void* asio_handler_allocate(std::size_t size,
+ binder3<Handler, Arg1, Arg2, Arg3>* this_handler)
+{
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3>
+inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ binder3<Handler, Arg1, Arg2, Arg3>* this_handler)
+{
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3>
+inline bool asio_handler_is_continuation(
+ binder3<Handler, Arg1, Arg2, Arg3>* this_handler)
+{
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1, typename Arg2,
+ typename Arg3>
+inline void asio_handler_invoke(Function& function,
+ binder3<Handler, Arg1, Arg2, Arg3>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1, typename Arg2,
+ typename Arg3>
+inline void asio_handler_invoke(const Function& function,
+ binder3<Handler, Arg1, Arg2, Arg3>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3>
+inline binder3<Handler, Arg1, Arg2, Arg3> bind_handler(Handler handler,
+ const Arg1& arg1, const Arg2& arg2, const Arg3& arg3)
+{
+ return binder3<Handler, Arg1, Arg2, Arg3>(handler, arg1, arg2, arg3);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4>
+class binder4
+{
+public:
+ binder4(const Handler& handler, const Arg1& arg1, const Arg2& arg2,
+ const Arg3& arg3, const Arg4& arg4)
+ : handler_(handler),
+ arg1_(arg1),
+ arg2_(arg2),
+ arg3_(arg3),
+ arg4_(arg4)
+ {
+ }
+
+ binder4(Handler& handler, const Arg1& arg1, const Arg2& arg2,
+ const Arg3& arg3, const Arg4& arg4)
+ : handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler)),
+ arg1_(arg1),
+ arg2_(arg2),
+ arg3_(arg3),
+ arg4_(arg4)
+ {
+ }
+
+ void operator()()
+ {
+ handler_(static_cast<const Arg1&>(arg1_),
+ static_cast<const Arg2&>(arg2_),
+ static_cast<const Arg3&>(arg3_),
+ static_cast<const Arg4&>(arg4_));
+ }
+
+ void operator()() const
+ {
+ handler_(arg1_, arg2_, arg3_, arg4_);
+ }
+
+//private:
+ Handler handler_;
+ Arg1 arg1_;
+ Arg2 arg2_;
+ Arg3 arg3_;
+ Arg4 arg4_;
+};
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4>
+inline void* asio_handler_allocate(std::size_t size,
+ binder4<Handler, Arg1, Arg2, Arg3, Arg4>* this_handler)
+{
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4>
+inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ binder4<Handler, Arg1, Arg2, Arg3, Arg4>* this_handler)
+{
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4>
+inline bool asio_handler_is_continuation(
+ binder4<Handler, Arg1, Arg2, Arg3, Arg4>* this_handler)
+{
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1, typename Arg2,
+ typename Arg3, typename Arg4>
+inline void asio_handler_invoke(Function& function,
+ binder4<Handler, Arg1, Arg2, Arg3, Arg4>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1, typename Arg2,
+ typename Arg3, typename Arg4>
+inline void asio_handler_invoke(const Function& function,
+ binder4<Handler, Arg1, Arg2, Arg3, Arg4>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4>
+inline binder4<Handler, Arg1, Arg2, Arg3, Arg4> bind_handler(
+ Handler handler, const Arg1& arg1, const Arg2& arg2,
+ const Arg3& arg3, const Arg4& arg4)
+{
+ return binder4<Handler, Arg1, Arg2, Arg3, Arg4>(handler, arg1, arg2, arg3,
+ arg4);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4, typename Arg5>
+class binder5
+{
+public:
+ binder5(const Handler& handler, const Arg1& arg1, const Arg2& arg2,
+ const Arg3& arg3, const Arg4& arg4, const Arg5& arg5)
+ : handler_(handler),
+ arg1_(arg1),
+ arg2_(arg2),
+ arg3_(arg3),
+ arg4_(arg4),
+ arg5_(arg5)
+ {
+ }
+
+ binder5(Handler& handler, const Arg1& arg1, const Arg2& arg2,
+ const Arg3& arg3, const Arg4& arg4, const Arg5& arg5)
+ : handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler)),
+ arg1_(arg1),
+ arg2_(arg2),
+ arg3_(arg3),
+ arg4_(arg4),
+ arg5_(arg5)
+ {
+ }
+
+ void operator()()
+ {
+ handler_(static_cast<const Arg1&>(arg1_),
+ static_cast<const Arg2&>(arg2_),
+ static_cast<const Arg3&>(arg3_),
+ static_cast<const Arg4&>(arg4_),
+ static_cast<const Arg5&>(arg5_));
+ }
+
+ void operator()() const
+ {
+ handler_(arg1_, arg2_, arg3_, arg4_, arg5_);
+ }
+
+//private:
+ Handler handler_;
+ Arg1 arg1_;
+ Arg2 arg2_;
+ Arg3 arg3_;
+ Arg4 arg4_;
+ Arg5 arg5_;
+};
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4, typename Arg5>
+inline void* asio_handler_allocate(std::size_t size,
+ binder5<Handler, Arg1, Arg2, Arg3, Arg4, Arg5>* this_handler)
+{
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4, typename Arg5>
+inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ binder5<Handler, Arg1, Arg2, Arg3, Arg4, Arg5>* this_handler)
+{
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4, typename Arg5>
+inline bool asio_handler_is_continuation(
+ binder5<Handler, Arg1, Arg2, Arg3, Arg4, Arg5>* this_handler)
+{
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1, typename Arg2,
+ typename Arg3, typename Arg4, typename Arg5>
+inline void asio_handler_invoke(Function& function,
+ binder5<Handler, Arg1, Arg2, Arg3, Arg4, Arg5>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Function, typename Handler, typename Arg1, typename Arg2,
+ typename Arg3, typename Arg4, typename Arg5>
+inline void asio_handler_invoke(const Function& function,
+ binder5<Handler, Arg1, Arg2, Arg3, Arg4, Arg5>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Handler, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4, typename Arg5>
+inline binder5<Handler, Arg1, Arg2, Arg3, Arg4, Arg5> bind_handler(
+ Handler handler, const Arg1& arg1, const Arg2& arg2,
+ const Arg3& arg3, const Arg4& arg4, const Arg5& arg5)
+{
+ return binder5<Handler, Arg1, Arg2, Arg3, Arg4, Arg5>(handler, arg1, arg2,
+ arg3, arg4, arg5);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_BIND_HANDLER_HPP
diff --git a/ext/patches/boost/asio/detail/buffer_resize_guard.hpp b/ext/patches/boost/asio/detail/buffer_resize_guard.hpp
new file mode 100644
index 0000000..daa033c
--- /dev/null
+++ b/ext/patches/boost/asio/detail/buffer_resize_guard.hpp
@@ -0,0 +1,68 @@
+//
+// detail/buffer_resize_guard.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_BUFFER_RESIZE_GUARD_HPP
+#define BOOST_ASIO_DETAIL_BUFFER_RESIZE_GUARD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/limits.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Helper class to manage buffer resizing in an exception safe way.
+template <typename Buffer>
+class buffer_resize_guard
+{
+public:
+ // Constructor.
+ buffer_resize_guard(Buffer& buffer)
+ : buffer_(buffer),
+ old_size_(buffer.size())
+ {
+ }
+
+ // Destructor rolls back the buffer resize unless commit was called.
+ ~buffer_resize_guard()
+ {
+ if (old_size_ != (std::numeric_limits<size_t>::max)())
+ {
+ buffer_.resize(old_size_);
+ }
+ }
+
+ // Commit the resize transaction.
+ void commit()
+ {
+ old_size_ = (std::numeric_limits<size_t>::max)();
+ }
+
+private:
+ // The buffer being managed.
+ Buffer& buffer_;
+
+ // The size of the buffer at the time the guard was constructed.
+ size_t old_size_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_BUFFER_RESIZE_GUARD_HPP
diff --git a/ext/patches/boost/asio/detail/buffer_sequence_adapter.hpp b/ext/patches/boost/asio/detail/buffer_sequence_adapter.hpp
new file mode 100644
index 0000000..2a0cbde
--- /dev/null
+++ b/ext/patches/boost/asio/detail/buffer_sequence_adapter.hpp
@@ -0,0 +1,385 @@
+//
+// detail/buffer_sequence_adapter.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_BUFFER_SEQUENCE_ADAPTER_HPP
+#define BOOST_ASIO_DETAIL_BUFFER_SEQUENCE_ADAPTER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/detail/array_fwd.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class buffer_sequence_adapter_base
+{
+protected:
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // The maximum number of buffers to support in a single operation.
+ enum { max_buffers = 1 };
+
+ typedef Windows::Storage::Streams::IBuffer^ native_buffer_type;
+
+ BOOST_ASIO_DECL static void init_native_buffer(
+ native_buffer_type& buf,
+ const boost::asio::mutable_buffer& buffer);
+
+ BOOST_ASIO_DECL static void init_native_buffer(
+ native_buffer_type& buf,
+ const boost::asio::const_buffer& buffer);
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // The maximum number of buffers to support in a single operation.
+ enum { max_buffers = 64 < max_iov_len ? 64 : max_iov_len };
+
+ typedef WSABUF native_buffer_type;
+
+ static void init_native_buffer(WSABUF& buf,
+ const boost::asio::mutable_buffer& buffer)
+ {
+ buf.buf = boost::asio::buffer_cast<char*>(buffer);
+ buf.len = static_cast<ULONG>(boost::asio::buffer_size(buffer));
+ }
+
+ static void init_native_buffer(WSABUF& buf,
+ const boost::asio::const_buffer& buffer)
+ {
+ buf.buf = const_cast<char*>(boost::asio::buffer_cast<const char*>(buffer));
+ buf.len = static_cast<ULONG>(boost::asio::buffer_size(buffer));
+ }
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // The maximum number of buffers to support in a single operation.
+ enum { max_buffers = 64 < max_iov_len ? 64 : max_iov_len };
+
+ typedef iovec native_buffer_type;
+
+ static void init_iov_base(void*& base, void* addr)
+ {
+ base = addr;
+ }
+
+ template <typename T>
+ static void init_iov_base(T& base, void* addr)
+ {
+ base = static_cast<T>(addr);
+ }
+
+ static void init_native_buffer(iovec& iov,
+ const boost::asio::mutable_buffer& buffer)
+ {
+ init_iov_base(iov.iov_base, boost::asio::buffer_cast<void*>(buffer));
+ iov.iov_len = boost::asio::buffer_size(buffer);
+ }
+
+ static void init_native_buffer(iovec& iov,
+ const boost::asio::const_buffer& buffer)
+ {
+ init_iov_base(iov.iov_base, const_cast<void*>(
+ boost::asio::buffer_cast<const void*>(buffer)));
+ iov.iov_len = boost::asio::buffer_size(buffer);
+ }
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+};
+
+// Helper class to translate buffers into the native buffer representation.
+template <typename Buffer, typename Buffers>
+class buffer_sequence_adapter
+ : buffer_sequence_adapter_base
+{
+public:
+ explicit buffer_sequence_adapter(const Buffers& buffer_sequence)
+ : count_(0), total_buffer_size_(0)
+ {
+ typename Buffers::const_iterator iter = buffer_sequence.begin();
+ typename Buffers::const_iterator end = buffer_sequence.end();
+ for (; iter != end && count_ < max_buffers; ++iter, ++count_)
+ {
+ Buffer buffer(*iter);
+ init_native_buffer(buffers_[count_], buffer);
+ total_buffer_size_ += boost::asio::buffer_size(buffer);
+ }
+ }
+
+ native_buffer_type* buffers()
+ {
+ return buffers_;
+ }
+
+ std::size_t count() const
+ {
+ return count_;
+ }
+
+ bool all_empty() const
+ {
+ return total_buffer_size_ == 0;
+ }
+
+ static bool all_empty(const Buffers& buffer_sequence)
+ {
+ typename Buffers::const_iterator iter = buffer_sequence.begin();
+ typename Buffers::const_iterator end = buffer_sequence.end();
+ std::size_t i = 0;
+ for (; iter != end && i < max_buffers; ++iter, ++i)
+ if (boost::asio::buffer_size(Buffer(*iter)) > 0)
+ return false;
+ return true;
+ }
+
+ static void validate(const Buffers& buffer_sequence)
+ {
+ typename Buffers::const_iterator iter = buffer_sequence.begin();
+ typename Buffers::const_iterator end = buffer_sequence.end();
+ for (; iter != end; ++iter)
+ {
+ Buffer buffer(*iter);
+ boost::asio::buffer_cast<const void*>(buffer);
+ }
+ }
+
+ static Buffer first(const Buffers& buffer_sequence)
+ {
+ typename Buffers::const_iterator iter = buffer_sequence.begin();
+ typename Buffers::const_iterator end = buffer_sequence.end();
+ for (; iter != end; ++iter)
+ {
+ Buffer buffer(*iter);
+ if (boost::asio::buffer_size(buffer) != 0)
+ return buffer;
+ }
+ return Buffer();
+ }
+
+private:
+ native_buffer_type buffers_[max_buffers];
+ std::size_t count_;
+ std::size_t total_buffer_size_;
+};
+
+template <typename Buffer>
+class buffer_sequence_adapter<Buffer, boost::asio::mutable_buffers_1>
+ : buffer_sequence_adapter_base
+{
+public:
+ explicit buffer_sequence_adapter(
+ const boost::asio::mutable_buffers_1& buffer_sequence)
+ {
+ init_native_buffer(buffer_, Buffer(buffer_sequence));
+ total_buffer_size_ = boost::asio::buffer_size(buffer_sequence);
+ }
+
+ native_buffer_type* buffers()
+ {
+ return &buffer_;
+ }
+
+ std::size_t count() const
+ {
+ return 1;
+ }
+
+ bool all_empty() const
+ {
+ return total_buffer_size_ == 0;
+ }
+
+ static bool all_empty(const boost::asio::mutable_buffers_1& buffer_sequence)
+ {
+ return boost::asio::buffer_size(buffer_sequence) == 0;
+ }
+
+ static void validate(const boost::asio::mutable_buffers_1& buffer_sequence)
+ {
+ boost::asio::buffer_cast<const void*>(buffer_sequence);
+ }
+
+ static Buffer first(const boost::asio::mutable_buffers_1& buffer_sequence)
+ {
+ return Buffer(buffer_sequence);
+ }
+
+private:
+ native_buffer_type buffer_;
+ std::size_t total_buffer_size_;
+};
+
+template <typename Buffer>
+class buffer_sequence_adapter<Buffer, boost::asio::const_buffers_1>
+ : buffer_sequence_adapter_base
+{
+public:
+ explicit buffer_sequence_adapter(
+ const boost::asio::const_buffers_1& buffer_sequence)
+ {
+ init_native_buffer(buffer_, Buffer(buffer_sequence));
+ total_buffer_size_ = boost::asio::buffer_size(buffer_sequence);
+ }
+
+ native_buffer_type* buffers()
+ {
+ return &buffer_;
+ }
+
+ std::size_t count() const
+ {
+ return 1;
+ }
+
+ bool all_empty() const
+ {
+ return total_buffer_size_ == 0;
+ }
+
+ static bool all_empty(const boost::asio::const_buffers_1& buffer_sequence)
+ {
+ return boost::asio::buffer_size(buffer_sequence) == 0;
+ }
+
+ static void validate(const boost::asio::const_buffers_1& buffer_sequence)
+ {
+ boost::asio::buffer_cast<const void*>(buffer_sequence);
+ }
+
+ static Buffer first(const boost::asio::const_buffers_1& buffer_sequence)
+ {
+ return Buffer(buffer_sequence);
+ }
+
+private:
+ native_buffer_type buffer_;
+ std::size_t total_buffer_size_;
+};
+
+template <typename Buffer, typename Elem>
+class buffer_sequence_adapter<Buffer, boost::array<Elem, 2> >
+ : buffer_sequence_adapter_base
+{
+public:
+ explicit buffer_sequence_adapter(
+ const boost::array<Elem, 2>& buffer_sequence)
+ {
+ init_native_buffer(buffers_[0], Buffer(buffer_sequence[0]));
+ init_native_buffer(buffers_[1], Buffer(buffer_sequence[1]));
+ total_buffer_size_ = boost::asio::buffer_size(buffer_sequence[0])
+ + boost::asio::buffer_size(buffer_sequence[1]);
+ }
+
+ native_buffer_type* buffers()
+ {
+ return buffers_;
+ }
+
+ std::size_t count() const
+ {
+ return 2;
+ }
+
+ bool all_empty() const
+ {
+ return total_buffer_size_ == 0;
+ }
+
+ static bool all_empty(const boost::array<Elem, 2>& buffer_sequence)
+ {
+ return boost::asio::buffer_size(buffer_sequence[0]) == 0
+ && boost::asio::buffer_size(buffer_sequence[1]) == 0;
+ }
+
+ static void validate(const boost::array<Elem, 2>& buffer_sequence)
+ {
+ boost::asio::buffer_cast<const void*>(buffer_sequence[0]);
+ boost::asio::buffer_cast<const void*>(buffer_sequence[1]);
+ }
+
+ static Buffer first(const boost::array<Elem, 2>& buffer_sequence)
+ {
+ return Buffer(boost::asio::buffer_size(buffer_sequence[0]) != 0
+ ? buffer_sequence[0] : buffer_sequence[1]);
+ }
+
+private:
+ native_buffer_type buffers_[2];
+ std::size_t total_buffer_size_;
+};
+
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+template <typename Buffer, typename Elem>
+class buffer_sequence_adapter<Buffer, std::array<Elem, 2> >
+ : buffer_sequence_adapter_base
+{
+public:
+ explicit buffer_sequence_adapter(
+ const std::array<Elem, 2>& buffer_sequence)
+ {
+ init_native_buffer(buffers_[0], Buffer(buffer_sequence[0]));
+ init_native_buffer(buffers_[1], Buffer(buffer_sequence[1]));
+ total_buffer_size_ = boost::asio::buffer_size(buffer_sequence[0])
+ + boost::asio::buffer_size(buffer_sequence[1]);
+ }
+
+ native_buffer_type* buffers()
+ {
+ return buffers_;
+ }
+
+ std::size_t count() const
+ {
+ return 2;
+ }
+
+ bool all_empty() const
+ {
+ return total_buffer_size_ == 0;
+ }
+
+ static bool all_empty(const std::array<Elem, 2>& buffer_sequence)
+ {
+ return boost::asio::buffer_size(buffer_sequence[0]) == 0
+ && boost::asio::buffer_size(buffer_sequence[1]) == 0;
+ }
+
+ static void validate(const std::array<Elem, 2>& buffer_sequence)
+ {
+ boost::asio::buffer_cast<const void*>(buffer_sequence[0]);
+ boost::asio::buffer_cast<const void*>(buffer_sequence[1]);
+ }
+
+ static Buffer first(const std::array<Elem, 2>& buffer_sequence)
+ {
+ return Buffer(boost::asio::buffer_size(buffer_sequence[0]) != 0
+ ? buffer_sequence[0] : buffer_sequence[1]);
+ }
+
+private:
+ native_buffer_type buffers_[2];
+ std::size_t total_buffer_size_;
+};
+
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/buffer_sequence_adapter.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_BUFFER_SEQUENCE_ADAPTER_HPP
diff --git a/ext/patches/boost/asio/detail/buffered_stream_storage.hpp b/ext/patches/boost/asio/detail/buffered_stream_storage.hpp
new file mode 100644
index 0000000..f0a4b93
--- /dev/null
+++ b/ext/patches/boost/asio/detail/buffered_stream_storage.hpp
@@ -0,0 +1,128 @@
+//
+// detail/buffered_stream_storage.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_BUFFERED_STREAM_STORAGE_HPP
+#define BOOST_ASIO_DETAIL_BUFFERED_STREAM_STORAGE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/detail/assert.hpp>
+#include <cstddef>
+#include <cstring>
+#include <vector>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class buffered_stream_storage
+{
+public:
+ // The type of the bytes stored in the buffer.
+ typedef unsigned char byte_type;
+
+ // The type used for offsets into the buffer.
+ typedef std::size_t size_type;
+
+ // Constructor.
+ explicit buffered_stream_storage(std::size_t buffer_capacity)
+ : begin_offset_(0),
+ end_offset_(0),
+ buffer_(buffer_capacity)
+ {
+ }
+
+ /// Clear the buffer.
+ void clear()
+ {
+ begin_offset_ = 0;
+ end_offset_ = 0;
+ }
+
+ // Return a pointer to the beginning of the unread data.
+ mutable_buffer data()
+ {
+ return boost::asio::buffer(buffer_) + begin_offset_;
+ }
+
+ // Return a pointer to the beginning of the unread data.
+ const_buffer data() const
+ {
+ return boost::asio::buffer(buffer_) + begin_offset_;
+ }
+
+ // Is there no unread data in the buffer.
+ bool empty() const
+ {
+ return begin_offset_ == end_offset_;
+ }
+
+ // Return the amount of unread data the is in the buffer.
+ size_type size() const
+ {
+ return end_offset_ - begin_offset_;
+ }
+
+ // Resize the buffer to the specified length.
+ void resize(size_type length)
+ {
+ BOOST_ASIO_ASSERT(length <= capacity());
+ if (begin_offset_ + length <= capacity())
+ {
+ end_offset_ = begin_offset_ + length;
+ }
+ else
+ {
+ using namespace std; // For memmove.
+ memmove(&buffer_[0], &buffer_[0] + begin_offset_, size());
+ end_offset_ = length;
+ begin_offset_ = 0;
+ }
+ }
+
+ // Return the maximum size for data in the buffer.
+ size_type capacity() const
+ {
+ return buffer_.size();
+ }
+
+ // Consume multiple bytes from the beginning of the buffer.
+ void consume(size_type count)
+ {
+ BOOST_ASIO_ASSERT(begin_offset_ + count <= end_offset_);
+ begin_offset_ += count;
+ if (empty())
+ clear();
+ }
+
+private:
+ // The offset to the beginning of the unread data.
+ size_type begin_offset_;
+
+ // The offset to the end of the unread data.
+ size_type end_offset_;
+
+ // The data in the buffer.
+ std::vector<byte_type> buffer_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_BUFFERED_STREAM_STORAGE_HPP
diff --git a/ext/patches/boost/asio/detail/call_stack.hpp b/ext/patches/boost/asio/detail/call_stack.hpp
new file mode 100644
index 0000000..82ebd4f
--- /dev/null
+++ b/ext/patches/boost/asio/detail/call_stack.hpp
@@ -0,0 +1,127 @@
+//
+// detail/call_stack.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_CALL_STACK_HPP
+#define BOOST_ASIO_DETAIL_CALL_STACK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/tss_ptr.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Helper class to determine whether or not the current thread is inside an
+// invocation of io_service::run() for a specified io_service object.
+template <typename Key, typename Value = unsigned char>
+class call_stack
+{
+public:
+ // Context class automatically pushes the key/value pair on to the stack.
+ class context
+ : private noncopyable
+ {
+ public:
+ // Push the key on to the stack.
+ explicit context(Key* k)
+ : key_(k),
+ next_(call_stack<Key, Value>::top_)
+ {
+ value_ = reinterpret_cast<unsigned char*>(this);
+ call_stack<Key, Value>::top_ = this;
+ }
+
+ // Push the key/value pair on to the stack.
+ context(Key* k, Value& v)
+ : key_(k),
+ value_(&v),
+ next_(call_stack<Key, Value>::top_)
+ {
+ call_stack<Key, Value>::top_ = this;
+ }
+
+ // Pop the key/value pair from the stack.
+ ~context()
+ {
+ call_stack<Key, Value>::top_ = next_;
+ }
+
+ // Find the next context with the same key.
+ Value* next_by_key() const
+ {
+ context* elem = next_;
+ while (elem)
+ {
+ if (elem->key_ == key_)
+ return elem->value_;
+ elem = elem->next_;
+ }
+ return 0;
+ }
+
+ private:
+ friend class call_stack<Key, Value>;
+
+ // The key associated with the context.
+ Key* key_;
+
+ // The value associated with the context.
+ Value* value_;
+
+ // The next element in the stack.
+ context* next_;
+ };
+
+ friend class context;
+
+ // Determine whether the specified owner is on the stack. Returns address of
+ // key if present, 0 otherwise.
+ static Value* contains(Key* k)
+ {
+ context* elem = top_;
+ while (elem)
+ {
+ if (elem->key_ == k)
+ return elem->value_;
+ elem = elem->next_;
+ }
+ return 0;
+ }
+
+ // Obtain the value at the top of the stack.
+ static Value* top()
+ {
+ context* elem = top_;
+ return elem ? elem->value_ : 0;
+ }
+
+private:
+ // The top of the stack of calls for the current thread.
+ static tss_ptr<context> top_;
+};
+
+template <typename Key, typename Value>
+tss_ptr<typename call_stack<Key, Value>::context>
+call_stack<Key, Value>::top_;
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_CALL_STACK_HPP
diff --git a/ext/patches/boost/asio/detail/chrono_time_traits.hpp b/ext/patches/boost/asio/detail/chrono_time_traits.hpp
new file mode 100644
index 0000000..72d4478
--- /dev/null
+++ b/ext/patches/boost/asio/detail/chrono_time_traits.hpp
@@ -0,0 +1,192 @@
+//
+// detail/chrono_time_traits.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_CHRONO_TIME_TRAITS_HPP
+#define BOOST_ASIO_DETAIL_CHRONO_TIME_TRAITS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/cstdint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Helper template to compute the greatest common divisor.
+template <int64_t v1, int64_t v2>
+struct gcd { enum { value = gcd<v2, v1 % v2>::value }; };
+
+template <int64_t v1>
+struct gcd<v1, 0> { enum { value = v1 }; };
+
+// Adapts std::chrono clocks for use with a deadline timer.
+template <typename Clock, typename WaitTraits>
+struct chrono_time_traits
+{
+ // The clock type.
+ typedef Clock clock_type;
+
+ // The duration type of the clock.
+ typedef typename clock_type::duration duration_type;
+
+ // The time point type of the clock.
+ typedef typename clock_type::time_point time_type;
+
+ // The period of the clock.
+ typedef typename duration_type::period period_type;
+
+ // Get the current time.
+ static time_type now()
+ {
+ return clock_type::now();
+ }
+
+ // Add a duration to a time.
+ static time_type add(const time_type& t, const duration_type& d)
+ {
+ const time_type epoch;
+ if (t >= epoch)
+ {
+ if ((time_type::max)() - t < d)
+ return (time_type::max)();
+ }
+ else // t < epoch
+ {
+ if (-(t - (time_type::min)()) > d)
+ return (time_type::min)();
+ }
+
+ return t + d;
+ }
+
+ // Subtract one time from another.
+ static duration_type subtract(const time_type& t1, const time_type& t2)
+ {
+ const time_type epoch;
+ if (t1 >= epoch)
+ {
+ if (t2 >= epoch)
+ {
+ return t1 - t2;
+ }
+ else if (t2 == (time_type::min)())
+ {
+ return (duration_type::max)();
+ }
+ else if ((time_type::max)() - t1 < epoch - t2)
+ {
+ return (duration_type::max)();
+ }
+ else
+ {
+ return t1 - t2;
+ }
+ }
+ else // t1 < epoch
+ {
+ if (t2 < epoch)
+ {
+ return t1 - t2;
+ }
+ else if (t1 == (time_type::min)())
+ {
+ return (duration_type::min)();
+ }
+ else if ((time_type::max)() - t2 < epoch - t1)
+ {
+ return (duration_type::min)();
+ }
+ else
+ {
+ return -(t2 - t1);
+ }
+ }
+ }
+
+ // Test whether one time is less than another.
+ static bool less_than(const time_type& t1, const time_type& t2)
+ {
+ return t1 < t2;
+ }
+
+ // Implement just enough of the posix_time::time_duration interface to supply
+ // what the timer_queue requires.
+ class posix_time_duration
+ {
+ public:
+ explicit posix_time_duration(const duration_type& d)
+ : d_(d)
+ {
+ }
+
+ int64_t ticks() const
+ {
+ return d_.count();
+ }
+
+ int64_t total_seconds() const
+ {
+ return duration_cast<1, 1>();
+ }
+
+ int64_t total_milliseconds() const
+ {
+ return duration_cast<1, 1000>();
+ }
+
+ int64_t total_microseconds() const
+ {
+ return duration_cast<1, 1000000>();
+ }
+
+ private:
+ template <int64_t Num, int64_t Den>
+ int64_t duration_cast() const
+ {
+ const int64_t num1 = period_type::num / gcd<period_type::num, Num>::value;
+ const int64_t num2 = Num / gcd<period_type::num, Num>::value;
+
+ const int64_t den1 = period_type::den / gcd<period_type::den, Den>::value;
+ const int64_t den2 = Den / gcd<period_type::den, Den>::value;
+
+ const int64_t num = num1 * den2;
+ const int64_t den = num2 * den1;
+
+ if (num == 1 && den == 1)
+ return ticks();
+ else if (num != 1 && den == 1)
+ return ticks() * num;
+ else if (num == 1 && period_type::den != 1)
+ return ticks() / den;
+ else
+ return ticks() * num / den;
+ }
+
+ duration_type d_;
+ };
+
+ // Convert to POSIX duration type.
+ static posix_time_duration to_posix_duration(const duration_type& d)
+ {
+ return posix_time_duration(WaitTraits::to_wait_duration(d));
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_CHRONO_TIME_TRAITS_HPP
diff --git a/ext/patches/boost/asio/detail/completion_handler.hpp b/ext/patches/boost/asio/detail/completion_handler.hpp
new file mode 100644
index 0000000..4e68380
--- /dev/null
+++ b/ext/patches/boost/asio/detail/completion_handler.hpp
@@ -0,0 +1,83 @@
+//
+// detail/completion_handler.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_COMPLETION_HANDLER_HPP
+#define BOOST_ASIO_DETAIL_COMPLETION_HANDLER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+class completion_handler : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(completion_handler);
+
+ completion_handler(Handler& h)
+ : operation(&completion_handler::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(h))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ completion_handler* h(static_cast<completion_handler*>(base));
+ ptr p = { boost::asio::detail::addressof(h->handler_), h, h };
+
+ BOOST_ASIO_HANDLER_COMPLETION((h));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ Handler handler(BOOST_ASIO_MOVE_CAST(Handler)(h->handler_));
+ p.h = boost::asio::detail::addressof(handler);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN(());
+ boost_asio_handler_invoke_helpers::invoke(handler, handler);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_COMPLETION_HANDLER_HPP
diff --git a/ext/patches/boost/asio/detail/config.hpp b/ext/patches/boost/asio/detail/config.hpp
new file mode 100644
index 0000000..fc90ee5
--- /dev/null
+++ b/ext/patches/boost/asio/detail/config.hpp
@@ -0,0 +1,906 @@
+//
+// detail/config.hpp
+// ~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_CONFIG_HPP
+#define BOOST_ASIO_DETAIL_CONFIG_HPP
+
+#if defined(BOOST_ASIO_STANDALONE)
+# define BOOST_ASIO_DISABLE_BOOST_ARRAY 1
+# define BOOST_ASIO_DISABLE_BOOST_ASSERT 1
+# define BOOST_ASIO_DISABLE_BOOST_BIND 1
+# define BOOST_ASIO_DISABLE_BOOST_CHRONO 1
+# define BOOST_ASIO_DISABLE_BOOST_DATE_TIME 1
+# define BOOST_ASIO_DISABLE_BOOST_LIMITS 1
+# define BOOST_ASIO_DISABLE_BOOST_REGEX 1
+# define BOOST_ASIO_DISABLE_BOOST_STATIC_CONSTANT 1
+# define BOOST_ASIO_DISABLE_BOOST_THROW_EXCEPTION 1
+# define BOOST_ASIO_DISABLE_BOOST_WORKAROUND 1
+#else // defined(BOOST_ASIO_STANDALONE)
+# include <boost/config.hpp>
+# include <boost/version.hpp>
+# define BOOST_ASIO_HAS_BOOST_CONFIG 1
+#endif // defined(BOOST_ASIO_STANDALONE)
+
+// Default to a header-only implementation. The user must specifically request
+// separate compilation by defining either BOOST_ASIO_SEPARATE_COMPILATION or
+// BOOST_ASIO_DYN_LINK (as a DLL/shared library implies separate compilation).
+#if !defined(BOOST_ASIO_HEADER_ONLY)
+# if !defined(BOOST_ASIO_SEPARATE_COMPILATION)
+# if !defined(BOOST_ASIO_DYN_LINK)
+# define BOOST_ASIO_HEADER_ONLY 1
+# endif // !defined(BOOST_ASIO_DYN_LINK)
+# endif // !defined(BOOST_ASIO_SEPARATE_COMPILATION)
+#endif // !defined(BOOST_ASIO_HEADER_ONLY)
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# define BOOST_ASIO_DECL inline
+#else // defined(BOOST_ASIO_HEADER_ONLY)
+# if defined(_MSC_VER) || defined(__BORLANDC__) || defined(__CODEGEARC__)
+// We need to import/export our code only if the user has specifically asked
+// for it by defining BOOST_ASIO_DYN_LINK.
+# if defined(BOOST_ASIO_DYN_LINK)
+// Export if this is our own source, otherwise import.
+# if defined(BOOST_ASIO_SOURCE)
+# define BOOST_ASIO_DECL __declspec(dllexport)
+# else // defined(BOOST_ASIO_SOURCE)
+# define BOOST_ASIO_DECL __declspec(dllimport)
+# endif // defined(BOOST_ASIO_SOURCE)
+# endif // defined(BOOST_ASIO_DYN_LINK)
+# endif // defined(_MSC_VER) || defined(__BORLANDC__) || defined(__CODEGEARC__)
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+// If BOOST_ASIO_DECL isn't defined yet define it now.
+#if !defined(BOOST_ASIO_DECL)
+# define BOOST_ASIO_DECL
+#endif // !defined(BOOST_ASIO_DECL)
+
+// Microsoft Visual C++ detection.
+#if !defined(BOOST_ASIO_MSVC)
+# if defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_MSVC)
+# define BOOST_ASIO_MSVC BOOST_MSVC
+# elif defined(_MSC_VER) && !defined(__MWERKS__) && !defined(__EDG_VERSION__)
+# define BOOST_ASIO_MSVC _MSC_VER
+# endif // defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_MSVC)
+#endif // defined(BOOST_ASIO_MSVC)
+
+// Clang / libc++ detection.
+#if defined(__clang__)
+# if (__cplusplus >= 201103)
+# if __has_include(<__config>)
+# include <__config>
+# if defined(_LIBCPP_VERSION)
+# define BOOST_ASIO_HAS_CLANG_LIBCXX 1
+# endif // defined(_LIBCPP_VERSION)
+# endif // __has_include(<__config>)
+# endif // (__cplusplus >= 201103)
+#endif // defined(__clang__)
+
+// Support move construction and assignment on compilers known to allow it.
+#if !defined(BOOST_ASIO_HAS_MOVE)
+# if !defined(BOOST_ASIO_DISABLE_MOVE)
+# if defined(__clang__)
+# if __has_feature(__cxx_rvalue_references__)
+# define BOOST_ASIO_HAS_MOVE 1
+# endif // __has_feature(__cxx_rvalue_references__)
+# endif // defined(__clang__)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_MOVE 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_MOVE 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_MOVE)
+#endif // !defined(BOOST_ASIO_HAS_MOVE)
+
+// If BOOST_ASIO_MOVE_CAST isn't defined, and move support is available, define
+// BOOST_ASIO_MOVE_ARG and BOOST_ASIO_MOVE_CAST to take advantage of rvalue
+// references and perfect forwarding.
+#if defined(BOOST_ASIO_HAS_MOVE) && !defined(BOOST_ASIO_MOVE_CAST)
+# define BOOST_ASIO_MOVE_ARG(type) type&&
+# define BOOST_ASIO_MOVE_CAST(type) static_cast<type&&>
+# define BOOST_ASIO_MOVE_CAST2(type1, type2) static_cast<type1, type2&&>
+#endif // defined(BOOST_ASIO_HAS_MOVE) && !defined(BOOST_ASIO_MOVE_CAST)
+
+// If BOOST_ASIO_MOVE_CAST still isn't defined, default to a C++03-compatible
+// implementation. Note that older g++ and MSVC versions don't like it when you
+// pass a non-member function through a const reference, so for most compilers
+// we'll play it safe and stick with the old approach of passing the handler by
+// value.
+#if !defined(BOOST_ASIO_MOVE_CAST)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 1)) || (__GNUC__ > 4)
+# define BOOST_ASIO_MOVE_ARG(type) const type&
+# else // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 1)) || (__GNUC__ > 4)
+# define BOOST_ASIO_MOVE_ARG(type) type
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 1)) || (__GNUC__ > 4)
+# elif defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1400)
+# define BOOST_ASIO_MOVE_ARG(type) const type&
+# else // (_MSC_VER >= 1400)
+# define BOOST_ASIO_MOVE_ARG(type) type
+# endif // (_MSC_VER >= 1400)
+# else
+# define BOOST_ASIO_MOVE_ARG(type) type
+# endif
+# define BOOST_ASIO_MOVE_CAST(type) static_cast<const type&>
+# define BOOST_ASIO_MOVE_CAST2(type1, type2) static_cast<const type1, type2&>
+#endif // !defined(BOOST_ASIO_MOVE_CAST)
+
+// Support variadic templates on compilers known to allow it.
+#if !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+# if !defined(BOOST_ASIO_DISABLE_VARIADIC_TEMPLATES)
+# if defined(__clang__)
+# if __has_feature(__cxx_variadic_templates__)
+# define BOOST_ASIO_HAS_VARIADIC_TEMPLATES 1
+# endif // __has_feature(__cxx_variadic_templates__)
+# endif // defined(__clang__)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_VARIADIC_TEMPLATES 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# endif // !defined(BOOST_ASIO_DISABLE_VARIADIC_TEMPLATES)
+#endif // !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+// Support constexpr on compilers known to allow it.
+#if !defined(BOOST_ASIO_HAS_CONSTEXPR)
+# if !defined(BOOST_ASIO_DISABLE_CONSTEXPR)
+# if defined(__clang__)
+# if __has_feature(__cxx_constexpr__)
+# define BOOST_ASIO_HAS_CONSTEXPR 1
+# endif // __has_feature(__cxx_constexr__)
+# endif // defined(__clang__)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 6)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_CONSTEXPR 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 6)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# endif // !defined(BOOST_ASIO_DISABLE_CONSTEXPR)
+#endif // !defined(BOOST_ASIO_HAS_CONSTEXPR)
+#if !defined(BOOST_ASIO_CONSTEXPR)
+# if defined(BOOST_ASIO_HAS_CONSTEXPR)
+# define BOOST_ASIO_CONSTEXPR constexpr
+# else // defined(BOOST_ASIO_HAS_CONSTEXPR)
+# define BOOST_ASIO_CONSTEXPR
+# endif // defined(BOOST_ASIO_HAS_CONSTEXPR)
+#endif // !defined(BOOST_ASIO_CONSTEXPR)
+
+// Standard library support for system errors.
+# if !defined(BOOST_ASIO_DISABLE_STD_SYSTEM_ERROR)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_SYSTEM_ERROR 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 6)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_SYSTEM_ERROR 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 6)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_STD_SYSTEM_ERROR 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_SYSTEM_ERROR)
+
+// Compliant C++11 compilers put noexcept specifiers on error_category members.
+#if !defined(BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT)
+# if (BOOST_VERSION >= 105300)
+# define BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT BOOST_NOEXCEPT
+# elif defined(__clang__)
+# if __has_feature(__cxx_noexcept__)
+# define BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT noexcept(true)
+# endif // __has_feature(__cxx_noexcept__)
+# elif defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT noexcept(true)
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if !defined(BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT)
+# define BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT
+# endif // !defined(BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT)
+#endif // !defined(BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT)
+
+// Standard library support for arrays.
+#if !defined(BOOST_ASIO_HAS_STD_ARRAY)
+# if !defined(BOOST_ASIO_DISABLE_STD_ARRAY)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_ARRAY 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_ARRAY 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1600)
+# define BOOST_ASIO_HAS_STD_ARRAY 1
+# endif // (_MSC_VER >= 1600)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_ARRAY)
+#endif // !defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+// Standard library support for shared_ptr and weak_ptr.
+#if !defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+# if !defined(BOOST_ASIO_DISABLE_STD_SHARED_PTR)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_SHARED_PTR 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_SHARED_PTR 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1600)
+# define BOOST_ASIO_HAS_STD_SHARED_PTR 1
+# endif // (_MSC_VER >= 1600)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_SHARED_PTR)
+#endif // !defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+
+// Standard library support for atomic operations.
+#if !defined(BOOST_ASIO_HAS_STD_ATOMIC)
+# if !defined(BOOST_ASIO_DISABLE_STD_ATOMIC)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_ATOMIC 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_ATOMIC 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_STD_ATOMIC 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_ATOMIC)
+#endif // !defined(BOOST_ASIO_HAS_STD_ATOMIC)
+
+// Standard library support for chrono. Some standard libraries (such as the
+// libstdc++ shipped with gcc 4.6) provide monotonic_clock as per early C++0x
+// drafts, rather than the eventually standardised name of steady_clock.
+#if !defined(BOOST_ASIO_HAS_STD_CHRONO)
+# if !defined(BOOST_ASIO_DISABLE_STD_CHRONO)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_CHRONO 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 6)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_CHRONO 1
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ == 6))
+# define BOOST_ASIO_HAS_STD_CHRONO_MONOTONIC_CLOCK 1
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ == 6))
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 6)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_STD_CHRONO 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_CHRONO)
+#endif // !defined(BOOST_ASIO_HAS_STD_CHRONO)
+
+// Boost support for chrono.
+#if !defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_CHRONO)
+# if (BOOST_VERSION >= 104700)
+# define BOOST_ASIO_HAS_BOOST_CHRONO 1
+# endif // (BOOST_VERSION >= 104700)
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_CHRONO)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+
+// Boost support for the DateTime library.
+#if !defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_DATE_TIME)
+# define BOOST_ASIO_HAS_BOOST_DATE_TIME 1
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_DATE_TIME)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+
+// Standard library support for addressof.
+#if !defined(BOOST_ASIO_HAS_STD_ADDRESSOF)
+# if !defined(BOOST_ASIO_DISABLE_STD_ADDRESSOF)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_ADDRESSOF 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_ADDRESSOF 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_STD_ADDRESSOF 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_ADDRESSOF)
+#endif // !defined(BOOST_ASIO_HAS_STD_ADDRESSOF)
+
+// Standard library support for the function class.
+#if !defined(BOOST_ASIO_HAS_STD_FUNCTION)
+# if !defined(BOOST_ASIO_DISABLE_STD_FUNCTION)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_FUNCTION 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_FUNCTION 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_STD_FUNCTION 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_FUNCTION)
+#endif // !defined(BOOST_ASIO_HAS_STD_FUNCTION)
+
+// Standard library support for type traits.
+#if !defined(BOOST_ASIO_HAS_STD_TYPE_TRAITS)
+# if !defined(BOOST_ASIO_DISABLE_STD_TYPE_TRAITS)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_TYPE_TRAITS 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_TYPE_TRAITS 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_STD_TYPE_TRAITS 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_TYPE_TRAITS)
+#endif // !defined(BOOST_ASIO_HAS_STD_TYPE_TRAITS)
+
+// Standard library support for the cstdint header.
+#if !defined(BOOST_ASIO_HAS_CSTDINT)
+# if !defined(BOOST_ASIO_DISABLE_CSTDINT)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_CSTDINT 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_CSTDINT 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_CSTDINT 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_CSTDINT)
+#endif // !defined(BOOST_ASIO_HAS_CSTDINT)
+
+// Standard library support for the thread class.
+#if !defined(BOOST_ASIO_HAS_STD_THREAD)
+# if !defined(BOOST_ASIO_DISABLE_STD_THREAD)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_THREAD 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_THREAD 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_STD_THREAD 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_THREAD)
+#endif // !defined(BOOST_ASIO_HAS_STD_THREAD)
+
+// Standard library support for the mutex and condition variable classes.
+#if !defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+# if !defined(BOOST_ASIO_DISABLE_STD_MUTEX_AND_CONDVAR)
+# if defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# define BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR 1
+# endif // defined(BOOST_ASIO_HAS_CLANG_LIBCXX)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 7)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR 1
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC)
+# endif // !defined(BOOST_ASIO_DISABLE_STD_MUTEX_AND_CONDVAR)
+#endif // !defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+
+// WinRT target.
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# if defined(__cplusplus_winrt)
+# include <winapifamily.h>
+# if WINAPI_FAMILY_ONE_PARTITION(WINAPI_FAMILY, WINAPI_PARTITION_APP)
+# define BOOST_ASIO_WINDOWS_RUNTIME 1
+# endif // WINAPI_FAMILY_ONE_PARTITION(WINAPI_FAMILY, WINAPI_PARTITION_APP)
+# endif // defined(__cplusplus_winrt)
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+// Windows target. Excludes WinRT.
+#if !defined(BOOST_ASIO_WINDOWS)
+# if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# if defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_WINDOWS)
+# define BOOST_ASIO_WINDOWS 1
+# elif defined(WIN32) || defined(_WIN32) || defined(__WIN32__)
+# define BOOST_ASIO_WINDOWS 1
+# endif // defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_WINDOWS)
+# endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+#endif // !defined(BOOST_ASIO_WINDOWS)
+
+// Windows: target OS version.
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if !defined(_WIN32_WINNT) && !defined(_WIN32_WINDOWS)
+# if defined(_MSC_VER) || defined(__BORLANDC__)
+# pragma message( \
+ "Please define _WIN32_WINNT or _WIN32_WINDOWS appropriately. For example:\n"\
+ "- add -D_WIN32_WINNT=0x0501 to the compiler command line; or\n"\
+ "- add _WIN32_WINNT=0x0501 to your project's Preprocessor Definitions.\n"\
+ "Assuming _WIN32_WINNT=0x0501 (i.e. Windows XP target).")
+# else // defined(_MSC_VER) || defined(__BORLANDC__)
+# warning Please define _WIN32_WINNT or _WIN32_WINDOWS appropriately.
+# warning For example, add -D_WIN32_WINNT=0x0501 to the compiler command line.
+# warning Assuming _WIN32_WINNT=0x0501 (i.e. Windows XP target).
+# endif // defined(_MSC_VER) || defined(__BORLANDC__)
+# define _WIN32_WINNT 0x0501
+# endif // !defined(_WIN32_WINNT) && !defined(_WIN32_WINDOWS)
+# if defined(_MSC_VER)
+# if defined(_WIN32) && !defined(WIN32)
+# if !defined(_WINSOCK2API_)
+# define WIN32 // Needed for correct types in winsock2.h
+# else // !defined(_WINSOCK2API_)
+# error Please define the macro WIN32 in your compiler options
+# endif // !defined(_WINSOCK2API_)
+# endif // defined(_WIN32) && !defined(WIN32)
+# endif // defined(_MSC_VER)
+# if defined(__BORLANDC__)
+# if defined(__WIN32__) && !defined(WIN32)
+# if !defined(_WINSOCK2API_)
+# define WIN32 // Needed for correct types in winsock2.h
+# else // !defined(_WINSOCK2API_)
+# error Please define the macro WIN32 in your compiler options
+# endif // !defined(_WINSOCK2API_)
+# endif // defined(__WIN32__) && !defined(WIN32)
+# endif // defined(__BORLANDC__)
+# if defined(__CYGWIN__)
+# if !defined(__USE_W32_SOCKETS)
+# error You must add -D__USE_W32_SOCKETS to your compiler options.
+# endif // !defined(__USE_W32_SOCKETS)
+# endif // defined(__CYGWIN__)
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+// Windows: minimise header inclusion.
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if !defined(BOOST_ASIO_NO_WIN32_LEAN_AND_MEAN)
+# if !defined(WIN32_LEAN_AND_MEAN)
+# define WIN32_LEAN_AND_MEAN
+# endif // !defined(WIN32_LEAN_AND_MEAN)
+# endif // !defined(BOOST_ASIO_NO_WIN32_LEAN_AND_MEAN)
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+// Windows: suppress definition of "min" and "max" macros.
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if !defined(BOOST_ASIO_NO_NOMINMAX)
+# if !defined(NOMINMAX)
+# define NOMINMAX 1
+# endif // !defined(NOMINMAX)
+# endif // !defined(BOOST_ASIO_NO_NOMINMAX)
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+// Windows: IO Completion Ports.
+#if !defined(BOOST_ASIO_HAS_IOCP)
+# if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if defined(_WIN32_WINNT) && (_WIN32_WINNT >= 0x0400)
+# if !defined(UNDER_CE)
+# if !defined(BOOST_ASIO_DISABLE_IOCP)
+# define BOOST_ASIO_HAS_IOCP 1
+# endif // !defined(BOOST_ASIO_DISABLE_IOCP)
+# endif // !defined(UNDER_CE)
+# endif // defined(_WIN32_WINNT) && (_WIN32_WINNT >= 0x0400)
+# endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+#endif // !defined(BOOST_ASIO_HAS_IOCP)
+
+// Linux: epoll, eventfd and timerfd.
+#if defined(__linux__)
+# include <linux/version.h>
+# if !defined(BOOST_ASIO_HAS_EPOLL)
+# if !defined(BOOST_ASIO_DISABLE_EPOLL)
+# if LINUX_VERSION_CODE >= KERNEL_VERSION(2,5,45)
+# define BOOST_ASIO_HAS_EPOLL 1
+# endif // LINUX_VERSION_CODE >= KERNEL_VERSION(2,5,45)
+# endif // !defined(BOOST_ASIO_DISABLE_EPOLL)
+# endif // !defined(BOOST_ASIO_HAS_EPOLL)
+# if !defined(BOOST_ASIO_HAS_EVENTFD)
+# if !defined(BOOST_ASIO_DISABLE_EVENTFD)
+# if LINUX_VERSION_CODE >= KERNEL_VERSION(2,6,22)
+# define BOOST_ASIO_HAS_EVENTFD 1
+# endif // LINUX_VERSION_CODE >= KERNEL_VERSION(2,6,22)
+# endif // !defined(BOOST_ASIO_DISABLE_EVENTFD)
+# endif // !defined(BOOST_ASIO_HAS_EVENTFD)
+# if !defined(BOOST_ASIO_HAS_TIMERFD)
+# if defined(BOOST_ASIO_HAS_EPOLL)
+# if (__GLIBC__ > 2) || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 8)
+# define BOOST_ASIO_HAS_TIMERFD 1
+# endif // (__GLIBC__ > 2) || (__GLIBC__ == 2 && __GLIBC_MINOR__ >= 8)
+# endif // defined(BOOST_ASIO_HAS_EPOLL)
+# endif // !defined(BOOST_ASIO_HAS_TIMERFD)
+#endif // defined(__linux__)
+
+// Mac OS X, FreeBSD, NetBSD, OpenBSD: kqueue.
+#if (defined(__MACH__) && defined(__APPLE__)) \
+ || defined(__FreeBSD__) \
+ || defined(__NetBSD__) \
+ || defined(__OpenBSD__)
+# if !defined(BOOST_ASIO_HAS_KQUEUE)
+# if !defined(BOOST_ASIO_DISABLE_KQUEUE)
+# define BOOST_ASIO_HAS_KQUEUE 1
+# endif // !defined(BOOST_ASIO_DISABLE_KQUEUE)
+# endif // !defined(BOOST_ASIO_HAS_KQUEUE)
+#endif // (defined(__MACH__) && defined(__APPLE__))
+ // || defined(__FreeBSD__)
+ // || defined(__NetBSD__)
+ // || defined(__OpenBSD__)
+
+// Solaris: /dev/poll.
+#if defined(__sun)
+# if !defined(BOOST_ASIO_HAS_DEV_POLL)
+# if !defined(BOOST_ASIO_DISABLE_DEV_POLL)
+# define BOOST_ASIO_HAS_DEV_POLL 1
+# endif // !defined(BOOST_ASIO_DISABLE_DEV_POLL)
+# endif // !defined(BOOST_ASIO_HAS_DEV_POLL)
+#endif // defined(__sun)
+
+// Serial ports.
+#if !defined(BOOST_ASIO_HAS_SERIAL_PORT)
+# if defined(BOOST_ASIO_HAS_IOCP) \
+ || !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+# if !defined(__SYMBIAN32__)
+# if !defined(BOOST_ASIO_DISABLE_SERIAL_PORT)
+# define BOOST_ASIO_HAS_SERIAL_PORT 1
+# endif // !defined(BOOST_ASIO_DISABLE_SERIAL_PORT)
+# endif // !defined(__SYMBIAN32__)
+# endif // defined(BOOST_ASIO_HAS_IOCP)
+ // || !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+#endif // !defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+// Windows: stream handles.
+#if !defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE)
+# if !defined(BOOST_ASIO_DISABLE_WINDOWS_STREAM_HANDLE)
+# if defined(BOOST_ASIO_HAS_IOCP)
+# define BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE 1
+# endif // defined(BOOST_ASIO_HAS_IOCP)
+# endif // !defined(BOOST_ASIO_DISABLE_WINDOWS_STREAM_HANDLE)
+#endif // !defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE)
+
+// Windows: random access handles.
+#if !defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE)
+# if !defined(BOOST_ASIO_DISABLE_WINDOWS_RANDOM_ACCESS_HANDLE)
+# if defined(BOOST_ASIO_HAS_IOCP)
+# define BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE 1
+# endif // defined(BOOST_ASIO_HAS_IOCP)
+# endif // !defined(BOOST_ASIO_DISABLE_WINDOWS_RANDOM_ACCESS_HANDLE)
+#endif // !defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE)
+
+// Windows: object handles.
+#if !defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+# if !defined(BOOST_ASIO_DISABLE_WINDOWS_OBJECT_HANDLE)
+# if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if !defined(UNDER_CE)
+# define BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE 1
+# endif // !defined(UNDER_CE)
+# endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# endif // !defined(BOOST_ASIO_DISABLE_WINDOWS_OBJECT_HANDLE)
+#endif // !defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+
+// Windows: OVERLAPPED wrapper.
+#if !defined(BOOST_ASIO_HAS_WINDOWS_OVERLAPPED_PTR)
+# if !defined(BOOST_ASIO_DISABLE_WINDOWS_OVERLAPPED_PTR)
+# if defined(BOOST_ASIO_HAS_IOCP)
+# define BOOST_ASIO_HAS_WINDOWS_OVERLAPPED_PTR 1
+# endif // defined(BOOST_ASIO_HAS_IOCP)
+# endif // !defined(BOOST_ASIO_DISABLE_WINDOWS_OVERLAPPED_PTR)
+#endif // !defined(BOOST_ASIO_HAS_WINDOWS_OVERLAPPED_PTR)
+
+// POSIX: stream-oriented file descriptors.
+#if !defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR)
+# if !defined(BOOST_ASIO_DISABLE_POSIX_STREAM_DESCRIPTOR)
+# if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+# define BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR 1
+# endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+# endif // !defined(BOOST_ASIO_DISABLE_POSIX_STREAM_DESCRIPTOR)
+#endif // !defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR)
+
+// UNIX domain sockets.
+#if !defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+# if !defined(BOOST_ASIO_DISABLE_LOCAL_SOCKETS)
+# if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+# define BOOST_ASIO_HAS_LOCAL_SOCKETS 1
+# endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+# endif // !defined(BOOST_ASIO_DISABLE_LOCAL_SOCKETS)
+#endif // !defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+
+// Can use sigaction() instead of signal().
+#if !defined(BOOST_ASIO_HAS_SIGACTION)
+# if !defined(BOOST_ASIO_DISABLE_SIGACTION)
+# if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+# define BOOST_ASIO_HAS_SIGACTION 1
+# endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+# endif // !defined(BOOST_ASIO_DISABLE_SIGACTION)
+#endif // !defined(BOOST_ASIO_HAS_SIGACTION)
+
+// Can use signal().
+#if !defined(BOOST_ASIO_HAS_SIGNAL)
+# if !defined(BOOST_ASIO_DISABLE_SIGNAL)
+# if !defined(UNDER_CE)
+# define BOOST_ASIO_HAS_SIGNAL 1
+# endif // !defined(UNDER_CE)
+# endif // !defined(BOOST_ASIO_DISABLE_SIGNAL)
+#endif // !defined(BOOST_ASIO_HAS_SIGNAL)
+
+// Can use getaddrinfo() and getnameinfo().
+#if !defined(BOOST_ASIO_HAS_GETADDRINFO)
+# if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if defined(_WIN32_WINNT) && (_WIN32_WINNT >= 0x0501)
+# define BOOST_ASIO_HAS_GETADDRINFO 1
+# elif defined(UNDER_CE)
+# define BOOST_ASIO_HAS_GETADDRINFO 1
+# endif // defined(UNDER_CE)
+# elif !(defined(__MACH__) && defined(__APPLE__))
+# define BOOST_ASIO_HAS_GETADDRINFO 1
+# endif // !(defined(__MACH__) && defined(__APPLE__))
+#endif // !defined(BOOST_ASIO_HAS_GETADDRINFO)
+
+// Whether standard iostreams are disabled.
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+# if defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_NO_IOSTREAM)
+# define BOOST_ASIO_NO_IOSTREAM 1
+# endif // !defined(BOOST_NO_IOSTREAM)
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+// Whether exception handling is disabled.
+#if !defined(BOOST_ASIO_NO_EXCEPTIONS)
+# if defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_NO_EXCEPTIONS)
+# define BOOST_ASIO_NO_EXCEPTIONS 1
+# endif // !defined(BOOST_NO_EXCEPTIONS)
+#endif // !defined(BOOST_ASIO_NO_EXCEPTIONS)
+
+// Whether the typeid operator is supported.
+#if !defined(BOOST_ASIO_NO_TYPEID)
+# if defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_NO_TYPEID)
+# define BOOST_ASIO_NO_TYPEID 1
+# endif // !defined(BOOST_NO_TYPEID)
+#endif // !defined(BOOST_ASIO_NO_TYPEID)
+
+// On POSIX (and POSIX-like) platforms we need to include unistd.h in order to
+// get access to the various platform feature macros, e.g. to be able to test
+// for threads support.
+#if !defined(BOOST_ASIO_HAS_UNISTD_H)
+# if !defined(BOOST_ASIO_HAS_BOOST_CONFIG)
+# if defined(unix) \
+ || defined(__unix) \
+ || defined(_XOPEN_SOURCE) \
+ || defined(_POSIX_SOURCE) \
+ || (defined(__MACH__) && defined(__APPLE__)) \
+ || defined(__FreeBSD__) \
+ || defined(__NetBSD__) \
+ || defined(__OpenBSD__) \
+ || defined(__linux__)
+# define BOOST_ASIO_HAS_UNISTD_H 1
+# endif
+# endif // !defined(BOOST_ASIO_HAS_BOOST_CONFIG)
+#endif // !defined(BOOST_ASIO_HAS_UNISTD_H)
+#if defined(BOOST_ASIO_HAS_UNISTD_H)
+# include <unistd.h>
+#endif // defined(BOOST_ASIO_HAS_UNISTD_H)
+
+// Threads.
+#if !defined(BOOST_ASIO_HAS_THREADS)
+# if !defined(BOOST_ASIO_DISABLE_THREADS)
+# if defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_HAS_THREADS)
+# define BOOST_ASIO_HAS_THREADS 1
+# elif defined(_MSC_VER) && defined(_MT)
+# define BOOST_ASIO_HAS_THREADS 1
+# elif defined(__BORLANDC__) && defined(__MT__)
+# define BOOST_ASIO_HAS_THREADS 1
+# elif defined(_POSIX_THREADS)
+# define BOOST_ASIO_HAS_THREADS 1
+# endif // defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_HAS_THREADS)
+# endif // !defined(BOOST_ASIO_DISABLE_THREADS)
+#endif // !defined(BOOST_ASIO_HAS_THREADS)
+
+// POSIX threads.
+#if !defined(BOOST_ASIO_HAS_PTHREADS)
+# if defined(BOOST_ASIO_HAS_THREADS)
+# if defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_HAS_PTHREADS)
+# define BOOST_ASIO_HAS_PTHREADS 1
+# elif defined(_POSIX_THREADS)
+# define BOOST_ASIO_HAS_PTHREADS 1
+# endif // defined(BOOST_ASIO_HAS_BOOST_CONFIG) && defined(BOOST_HAS_PTHREADS)
+# endif // defined(BOOST_ASIO_HAS_THREADS)
+#endif // !defined(BOOST_ASIO_HAS_PTHREADS)
+
+// Helper to prevent macro expansion.
+#define BOOST_ASIO_PREVENT_MACRO_SUBSTITUTION
+
+// Helper to define in-class constants.
+#if !defined(BOOST_ASIO_STATIC_CONSTANT)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_STATIC_CONSTANT)
+# define BOOST_ASIO_STATIC_CONSTANT(type, assignment) \
+ BOOST_STATIC_CONSTANT(type, assignment)
+# else // !defined(BOOST_ASIO_DISABLE_BOOST_STATIC_CONSTANT)
+# define BOOST_ASIO_STATIC_CONSTANT(type, assignment) \
+ static const type assignment
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_STATIC_CONSTANT)
+#endif // !defined(BOOST_ASIO_STATIC_CONSTANT)
+
+// Boost array library.
+#if !defined(BOOST_ASIO_HAS_BOOST_ARRAY)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_ARRAY)
+# define BOOST_ASIO_HAS_BOOST_ARRAY 1
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_ARRAY)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_ARRAY)
+
+// Boost assert macro.
+#if !defined(BOOST_ASIO_HAS_BOOST_ASSERT)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_ASSERT)
+# define BOOST_ASIO_HAS_BOOST_ASSERT 1
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_ASSERT)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_ASSERT)
+
+// Boost limits header.
+#if !defined(BOOST_ASIO_HAS_BOOST_LIMITS)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_LIMITS)
+# define BOOST_ASIO_HAS_BOOST_LIMITS 1
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_LIMITS)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_LIMITS)
+
+// Boost throw_exception function.
+#if !defined(BOOST_ASIO_HAS_BOOST_THROW_EXCEPTION)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_THROW_EXCEPTION)
+# define BOOST_ASIO_HAS_BOOST_THROW_EXCEPTION 1
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_THROW_EXCEPTION)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_THROW_EXCEPTION)
+
+// Boost regex library.
+#if !defined(BOOST_ASIO_HAS_BOOST_REGEX)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_REGEX)
+# define BOOST_ASIO_HAS_BOOST_REGEX 1
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_REGEX)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_REGEX)
+
+// Boost bind function.
+#if !defined(BOOST_ASIO_HAS_BOOST_BIND)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_BIND)
+# define BOOST_ASIO_HAS_BOOST_BIND 1
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_BIND)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_BIND)
+
+// Boost's BOOST_WORKAROUND macro.
+#if !defined(BOOST_ASIO_HAS_BOOST_WORKAROUND)
+# if !defined(BOOST_ASIO_DISABLE_BOOST_WORKAROUND)
+# define BOOST_ASIO_HAS_BOOST_WORKAROUND 1
+# endif // !defined(BOOST_ASIO_DISABLE_BOOST_WORKAROUND)
+#endif // !defined(BOOST_ASIO_HAS_BOOST_WORKAROUND)
+
+// Microsoft Visual C++'s secure C runtime library.
+#if !defined(BOOST_ASIO_HAS_SECURE_RTL)
+# if !defined(BOOST_ASIO_DISABLE_SECURE_RTL)
+# if defined(BOOST_ASIO_MSVC) \
+ && (BOOST_ASIO_MSVC >= 1400) \
+ && !defined(UNDER_CE)
+# define BOOST_ASIO_HAS_SECURE_RTL 1
+# endif // defined(BOOST_ASIO_MSVC)
+ // && (BOOST_ASIO_MSVC >= 1400)
+ // && !defined(UNDER_CE)
+# endif // !defined(BOOST_ASIO_DISABLE_SECURE_RTL)
+#endif // !defined(BOOST_ASIO_HAS_SECURE_RTL)
+
+// Handler hooking. Disabled for ancient Borland C++ and gcc compilers.
+#if !defined(BOOST_ASIO_HAS_HANDLER_HOOKS)
+# if !defined(BOOST_ASIO_DISABLE_HANDLER_HOOKS)
+# if defined(__GNUC__)
+# if (__GNUC__ >= 3)
+# define BOOST_ASIO_HAS_HANDLER_HOOKS 1
+# endif // (__GNUC__ >= 3)
+# elif !defined(__BORLANDC__)
+# define BOOST_ASIO_HAS_HANDLER_HOOKS 1
+# endif // !defined(__BORLANDC__)
+# endif // !defined(BOOST_ASIO_DISABLE_HANDLER_HOOKS)
+#endif // !defined(BOOST_ASIO_HAS_HANDLER_HOOKS)
+
+// Support for the __thread keyword extension.
+#if !defined(BOOST_ASIO_DISABLE_THREAD_KEYWORD_EXTENSION)
+# if defined(__linux__)
+# if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
+# if ((__GNUC__ == 3) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 3)
+# if !defined(__INTEL_COMPILER) && !defined(__ICL)
+# define BOOST_ASIO_HAS_THREAD_KEYWORD_EXTENSION 1
+# define BOOST_ASIO_THREAD_KEYWORD __thread
+# elif defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 1100)
+# define BOOST_ASIO_HAS_THREAD_KEYWORD_EXTENSION 1
+# endif // defined(__INTEL_COMPILER) && (__INTEL_COMPILER >= 1100)
+# endif // ((__GNUC__ == 3) && (__GNUC_MINOR__ >= 3)) || (__GNUC__ > 3)
+# endif // defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
+# endif // defined(__linux__)
+# if defined(BOOST_ASIO_MSVC) && defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# if (_MSC_VER >= 1700)
+# define BOOST_ASIO_HAS_THREAD_KEYWORD_EXTENSION 1
+# define BOOST_ASIO_THREAD_KEYWORD __declspec(thread)
+# endif // (_MSC_VER >= 1700)
+# endif // defined(BOOST_ASIO_MSVC) && defined(BOOST_ASIO_WINDOWS_RUNTIME)
+#endif // !defined(BOOST_ASIO_DISABLE_THREAD_KEYWORD_EXTENSION)
+#if !defined(BOOST_ASIO_THREAD_KEYWORD)
+# define BOOST_ASIO_THREAD_KEYWORD __thread
+#endif // !defined(BOOST_ASIO_THREAD_KEYWORD)
+
+// Support for POSIX ssize_t typedef.
+#if !defined(BOOST_ASIO_DISABLE_SSIZE_T)
+# if defined(__linux__) \
+ || (defined(__MACH__) && defined(__APPLE__))
+# define BOOST_ASIO_HAS_SSIZE_T 1
+# endif // defined(__linux__)
+ // || (defined(__MACH__) && defined(__APPLE__))
+#endif // !defined(BOOST_ASIO_DISABLE_SSIZE_T)
+
+#endif // BOOST_ASIO_DETAIL_CONFIG_HPP
diff --git a/ext/patches/boost/asio/detail/consuming_buffers.hpp b/ext/patches/boost/asio/detail/consuming_buffers.hpp
new file mode 100644
index 0000000..ad40d44
--- /dev/null
+++ b/ext/patches/boost/asio/detail/consuming_buffers.hpp
@@ -0,0 +1,294 @@
+//
+// detail/consuming_buffers.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_CONSUMING_BUFFERS_HPP
+#define BOOST_ASIO_DETAIL_CONSUMING_BUFFERS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <iterator>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/detail/limits.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// A proxy iterator for a sub-range in a list of buffers.
+template <typename Buffer, typename Buffer_Iterator>
+class consuming_buffers_iterator
+{
+public:
+ /// The type used for the distance between two iterators.
+ typedef std::ptrdiff_t difference_type;
+
+ /// The type of the value pointed to by the iterator.
+ typedef Buffer value_type;
+
+ /// The type of the result of applying operator->() to the iterator.
+ typedef const Buffer* pointer;
+
+ /// The type of the result of applying operator*() to the iterator.
+ typedef const Buffer& reference;
+
+ /// The iterator category.
+ typedef std::forward_iterator_tag iterator_category;
+
+ // Default constructor creates an end iterator.
+ consuming_buffers_iterator()
+ : at_end_(true)
+ {
+ }
+
+ // Construct with a buffer for the first entry and an iterator
+ // range for the remaining entries.
+ consuming_buffers_iterator(bool at_end, const Buffer& first,
+ Buffer_Iterator begin_remainder, Buffer_Iterator end_remainder,
+ std::size_t max_size)
+ : at_end_(max_size > 0 ? at_end : true),
+ first_(buffer(first, max_size)),
+ begin_remainder_(begin_remainder),
+ end_remainder_(end_remainder),
+ offset_(0),
+ max_size_(max_size)
+ {
+ }
+
+ // Dereference an iterator.
+ const Buffer& operator*() const
+ {
+ return dereference();
+ }
+
+ // Dereference an iterator.
+ const Buffer* operator->() const
+ {
+ return &dereference();
+ }
+
+ // Increment operator (prefix).
+ consuming_buffers_iterator& operator++()
+ {
+ increment();
+ return *this;
+ }
+
+ // Increment operator (postfix).
+ consuming_buffers_iterator operator++(int)
+ {
+ consuming_buffers_iterator tmp(*this);
+ ++*this;
+ return tmp;
+ }
+
+ // Test two iterators for equality.
+ friend bool operator==(const consuming_buffers_iterator& a,
+ const consuming_buffers_iterator& b)
+ {
+ return a.equal(b);
+ }
+
+ // Test two iterators for inequality.
+ friend bool operator!=(const consuming_buffers_iterator& a,
+ const consuming_buffers_iterator& b)
+ {
+ return !a.equal(b);
+ }
+
+private:
+ void increment()
+ {
+ if (!at_end_)
+ {
+ if (begin_remainder_ == end_remainder_
+ || offset_ + buffer_size(first_) >= max_size_)
+ {
+ at_end_ = true;
+ }
+ else
+ {
+ offset_ += buffer_size(first_);
+ first_ = buffer(*begin_remainder_++, max_size_ - offset_);
+ }
+ }
+ }
+
+ bool equal(const consuming_buffers_iterator& other) const
+ {
+ if (at_end_ && other.at_end_)
+ return true;
+ return !at_end_ && !other.at_end_
+ && buffer_cast<const void*>(first_)
+ == buffer_cast<const void*>(other.first_)
+ && buffer_size(first_) == buffer_size(other.first_)
+ && begin_remainder_ == other.begin_remainder_
+ && end_remainder_ == other.end_remainder_;
+ }
+
+ const Buffer& dereference() const
+ {
+ return first_;
+ }
+
+ bool at_end_;
+ Buffer first_;
+ Buffer_Iterator begin_remainder_;
+ Buffer_Iterator end_remainder_;
+ std::size_t offset_;
+ std::size_t max_size_;
+};
+
+// A proxy for a sub-range in a list of buffers.
+template <typename Buffer, typename Buffers>
+class consuming_buffers
+{
+public:
+ // The type for each element in the list of buffers.
+ typedef Buffer value_type;
+
+ // A forward-only iterator type that may be used to read elements.
+ typedef consuming_buffers_iterator<Buffer, typename Buffers::const_iterator>
+ const_iterator;
+
+ // Construct to represent the entire list of buffers.
+ consuming_buffers(const Buffers& buffers)
+ : buffers_(buffers),
+ at_end_(buffers_.begin() == buffers_.end()),
+ begin_remainder_(buffers_.begin()),
+ max_size_((std::numeric_limits<std::size_t>::max)())
+ {
+ if (!at_end_)
+ {
+ first_ = *buffers_.begin();
+ ++begin_remainder_;
+ }
+ }
+
+ // Copy constructor.
+ consuming_buffers(const consuming_buffers& other)
+ : buffers_(other.buffers_),
+ at_end_(other.at_end_),
+ first_(other.first_),
+ begin_remainder_(buffers_.begin()),
+ max_size_(other.max_size_)
+ {
+ typename Buffers::const_iterator first = other.buffers_.begin();
+ typename Buffers::const_iterator second = other.begin_remainder_;
+ std::advance(begin_remainder_, std::distance(first, second));
+ }
+
+ // Assignment operator.
+ consuming_buffers& operator=(const consuming_buffers& other)
+ {
+ buffers_ = other.buffers_;
+ at_end_ = other.at_end_;
+ first_ = other.first_;
+ begin_remainder_ = buffers_.begin();
+ typename Buffers::const_iterator first = other.buffers_.begin();
+ typename Buffers::const_iterator second = other.begin_remainder_;
+ std::advance(begin_remainder_, std::distance(first, second));
+ max_size_ = other.max_size_;
+ return *this;
+ }
+
+ // Get a forward-only iterator to the first element.
+ const_iterator begin() const
+ {
+ return const_iterator(at_end_, first_,
+ begin_remainder_, buffers_.end(), max_size_);
+ }
+
+ // Get a forward-only iterator for one past the last element.
+ const_iterator end() const
+ {
+ return const_iterator();
+ }
+
+ // Set the maximum size for a single transfer.
+ void prepare(std::size_t max_size)
+ {
+ max_size_ = max_size;
+ }
+
+ // Consume the specified number of bytes from the buffers.
+ void consume(std::size_t size)
+ {
+ // Remove buffers from the start until the specified size is reached.
+ while (size > 0 && !at_end_)
+ {
+ if (buffer_size(first_) <= size)
+ {
+ size -= buffer_size(first_);
+ if (begin_remainder_ == buffers_.end())
+ at_end_ = true;
+ else
+ first_ = *begin_remainder_++;
+ }
+ else
+ {
+ first_ = first_ + size;
+ size = 0;
+ }
+ }
+
+ // Remove any more empty buffers at the start.
+ while (!at_end_ && buffer_size(first_) == 0)
+ {
+ if (begin_remainder_ == buffers_.end())
+ at_end_ = true;
+ else
+ first_ = *begin_remainder_++;
+ }
+ }
+
+private:
+ Buffers buffers_;
+ bool at_end_;
+ Buffer first_;
+ typename Buffers::const_iterator begin_remainder_;
+ std::size_t max_size_;
+};
+
+// Specialisation for null_buffers to ensure that the null_buffers type is
+// always passed through to the underlying read or write operation.
+template <typename Buffer>
+class consuming_buffers<Buffer, boost::asio::null_buffers>
+ : public boost::asio::null_buffers
+{
+public:
+ consuming_buffers(const boost::asio::null_buffers&)
+ {
+ // No-op.
+ }
+
+ void prepare(std::size_t)
+ {
+ // No-op.
+ }
+
+ void consume(std::size_t)
+ {
+ // No-op.
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_CONSUMING_BUFFERS_HPP
diff --git a/ext/patches/boost/asio/detail/cstdint.hpp b/ext/patches/boost/asio/detail/cstdint.hpp
new file mode 100644
index 0000000..7d4855a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/cstdint.hpp
@@ -0,0 +1,48 @@
+//
+// detail/cstdint.hpp
+// ~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_CSTDINT_HPP
+#define BOOST_ASIO_DETAIL_CSTDINT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_CSTDINT)
+# include <cstdint>
+#else // defined(BOOST_ASIO_HAS_CSTDINT)
+# include <boost/cstdint.hpp>
+#endif // defined(BOOST_ASIO_HAS_CSTDINT)
+
+namespace boost {
+namespace asio {
+
+#if defined(BOOST_ASIO_HAS_CSTDINT)
+using std::int16_t;
+using std::uint16_t;
+using std::int32_t;
+using std::uint32_t;
+using std::int64_t;
+using std::uint64_t;
+#else // defined(BOOST_ASIO_HAS_CSTDINT)
+using boost::int16_t;
+using boost::uint16_t;
+using boost::int32_t;
+using boost::uint32_t;
+using boost::int64_t;
+using boost::uint64_t;
+#endif // defined(BOOST_ASIO_HAS_CSTDINT)
+
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_CSTDINT_HPP
diff --git a/ext/patches/boost/asio/detail/date_time_fwd.hpp b/ext/patches/boost/asio/detail/date_time_fwd.hpp
new file mode 100644
index 0000000..8d6d07b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/date_time_fwd.hpp
@@ -0,0 +1,34 @@
+//
+// detail/date_time_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_DATE_TIME_FWD_HPP
+#define BOOST_ASIO_DETAIL_DATE_TIME_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+namespace boost {
+namespace date_time {
+
+template<class T, class TimeSystem>
+class base_time;
+
+} // namespace date_time
+namespace posix_time {
+
+class ptime;
+
+} // namespace posix_time
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_DATE_TIME_FWD_HPP
diff --git a/ext/patches/boost/asio/detail/deadline_timer_service.hpp b/ext/patches/boost/asio/detail/deadline_timer_service.hpp
new file mode 100644
index 0000000..7002c47
--- /dev/null
+++ b/ext/patches/boost/asio/detail/deadline_timer_service.hpp
@@ -0,0 +1,229 @@
+//
+// detail/deadline_timer_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_DEADLINE_TIMER_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_DEADLINE_TIMER_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/timer_queue.hpp>
+#include <boost/asio/detail/timer_scheduler.hpp>
+#include <boost/asio/detail/wait_handler.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <chrono>
+# include <thread>
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Time_Traits>
+class deadline_timer_service
+{
+public:
+ // The time type.
+ typedef typename Time_Traits::time_type time_type;
+
+ // The duration type.
+ typedef typename Time_Traits::duration_type duration_type;
+
+ // The implementation type of the timer. This type is dependent on the
+ // underlying implementation of the timer service.
+ struct implementation_type
+ : private boost::asio::detail::noncopyable
+ {
+ time_type expiry;
+ bool might_have_pending_waits;
+ typename timer_queue<Time_Traits>::per_timer_data timer_data;
+ };
+
+ // Constructor.
+ deadline_timer_service(boost::asio::io_service& io_service)
+ : scheduler_(boost::asio::use_service<timer_scheduler>(io_service))
+ {
+ scheduler_.init_task();
+ scheduler_.add_timer_queue(timer_queue_);
+ }
+
+ // Destructor.
+ ~deadline_timer_service()
+ {
+ scheduler_.remove_timer_queue(timer_queue_);
+ }
+
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ }
+
+ // Construct a new timer implementation.
+ void construct(implementation_type& impl)
+ {
+ impl.expiry = time_type();
+ impl.might_have_pending_waits = false;
+ }
+
+ // Destroy a timer implementation.
+ void destroy(implementation_type& impl)
+ {
+ boost::system::error_code ec;
+ cancel(impl, ec);
+ }
+
+ // Cancel any asynchronous wait operations associated with the timer.
+ std::size_t cancel(implementation_type& impl, boost::system::error_code& ec)
+ {
+ if (!impl.might_have_pending_waits)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ BOOST_ASIO_HANDLER_OPERATION(("deadline_timer", &impl, "cancel"));
+
+ std::size_t count = scheduler_.cancel_timer(timer_queue_, impl.timer_data);
+ impl.might_have_pending_waits = false;
+ ec = boost::system::error_code();
+ return count;
+ }
+
+ // Cancels one asynchronous wait operation associated with the timer.
+ std::size_t cancel_one(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ if (!impl.might_have_pending_waits)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ BOOST_ASIO_HANDLER_OPERATION(("deadline_timer", &impl, "cancel_one"));
+
+ std::size_t count = scheduler_.cancel_timer(
+ timer_queue_, impl.timer_data, 1);
+ if (count == 0)
+ impl.might_have_pending_waits = false;
+ ec = boost::system::error_code();
+ return count;
+ }
+
+ // Get the expiry time for the timer as an absolute time.
+ time_type expires_at(const implementation_type& impl) const
+ {
+ return impl.expiry;
+ }
+
+ // Set the expiry time for the timer as an absolute time.
+ std::size_t expires_at(implementation_type& impl,
+ const time_type& expiry_time, boost::system::error_code& ec)
+ {
+ std::size_t count = cancel(impl, ec);
+ impl.expiry = expiry_time;
+ ec = boost::system::error_code();
+ return count;
+ }
+
+ // Get the expiry time for the timer relative to now.
+ duration_type expires_from_now(const implementation_type& impl) const
+ {
+ return Time_Traits::subtract(expires_at(impl), Time_Traits::now());
+ }
+
+ // Set the expiry time for the timer relative to now.
+ std::size_t expires_from_now(implementation_type& impl,
+ const duration_type& expiry_time, boost::system::error_code& ec)
+ {
+ return expires_at(impl,
+ Time_Traits::add(Time_Traits::now(), expiry_time), ec);
+ }
+
+ // Perform a blocking wait on the timer.
+ void wait(implementation_type& impl, boost::system::error_code& ec)
+ {
+ time_type now = Time_Traits::now();
+ ec = boost::system::error_code();
+ while (Time_Traits::less_than(now, impl.expiry) && !ec)
+ {
+ this->do_wait(Time_Traits::to_posix_duration(
+ Time_Traits::subtract(impl.expiry, now)), ec);
+ now = Time_Traits::now();
+ }
+ }
+
+ // Start an asynchronous wait on the timer.
+ template <typename Handler>
+ void async_wait(implementation_type& impl, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef wait_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ impl.might_have_pending_waits = true;
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "deadline_timer", &impl, "async_wait"));
+
+ scheduler_.schedule_timer(timer_queue_, impl.expiry, impl.timer_data, p.p);
+ p.v = p.p = 0;
+ }
+
+private:
+ // Helper function to wait given a duration type. The duration type should
+ // either be of type boost::posix_time::time_duration, or implement the
+ // required subset of its interface.
+ template <typename Duration>
+ void do_wait(const Duration& timeout, boost::system::error_code& ec)
+ {
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ std::this_thread::sleep_for(
+ std::chrono::seconds(timeout.total_seconds())
+ + std::chrono::microseconds(timeout.total_microseconds()));
+ ec = boost::system::error_code();
+#else // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ ::timeval tv;
+ tv.tv_sec = timeout.total_seconds();
+ tv.tv_usec = timeout.total_microseconds() % 1000000;
+ socket_ops::select(0, 0, 0, 0, &tv, ec);
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ }
+
+ // The queue of timers.
+ timer_queue<Time_Traits> timer_queue_;
+
+ // The object that schedules and executes timers. Usually a reactor.
+ timer_scheduler& scheduler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_DEADLINE_TIMER_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/dependent_type.hpp b/ext/patches/boost/asio/detail/dependent_type.hpp
new file mode 100644
index 0000000..255c8fe
--- /dev/null
+++ b/ext/patches/boost/asio/detail/dependent_type.hpp
@@ -0,0 +1,38 @@
+//
+// detail/dependent_type.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_DEPENDENT_TYPE_HPP
+#define BOOST_ASIO_DETAIL_DEPENDENT_TYPE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename DependsOn, typename T>
+struct dependent_type
+{
+ typedef T type;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_DEPENDENT_TYPE_HPP
diff --git a/ext/patches/boost/asio/detail/descriptor_ops.hpp b/ext/patches/boost/asio/detail/descriptor_ops.hpp
new file mode 100644
index 0000000..515c661
--- /dev/null
+++ b/ext/patches/boost/asio/detail/descriptor_ops.hpp
@@ -0,0 +1,119 @@
+//
+// detail/descriptor_ops.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_DESCRIPTOR_OPS_HPP
+#define BOOST_ASIO_DETAIL_DESCRIPTOR_OPS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+
+#include <cstddef>
+#include <boost/system/error_code.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+namespace descriptor_ops {
+
+// Descriptor state bits.
+enum
+{
+ // The user wants a non-blocking descriptor.
+ user_set_non_blocking = 1,
+
+ // The descriptor has been set non-blocking.
+ internal_non_blocking = 2,
+
+ // Helper "state" used to determine whether the descriptor is non-blocking.
+ non_blocking = user_set_non_blocking | internal_non_blocking,
+
+ // The descriptor may have been dup()-ed.
+ possible_dup = 4
+};
+
+typedef unsigned char state_type;
+
+template <typename ReturnType>
+inline ReturnType error_wrapper(ReturnType return_value,
+ boost::system::error_code& ec)
+{
+ ec = boost::system::error_code(errno,
+ boost::asio::error::get_system_category());
+ return return_value;
+}
+
+BOOST_ASIO_DECL int open(const char* path, int flags,
+ boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int close(int d, state_type& state,
+ boost::system::error_code& ec);
+
+BOOST_ASIO_DECL bool set_user_non_blocking(int d,
+ state_type& state, bool value, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL bool set_internal_non_blocking(int d,
+ state_type& state, bool value, boost::system::error_code& ec);
+
+typedef iovec buf;
+
+BOOST_ASIO_DECL std::size_t sync_read(int d, state_type state, buf* bufs,
+ std::size_t count, bool all_empty, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL bool non_blocking_read(int d, buf* bufs, std::size_t count,
+ boost::system::error_code& ec, std::size_t& bytes_transferred);
+
+BOOST_ASIO_DECL std::size_t sync_write(int d, state_type state,
+ const buf* bufs, std::size_t count, bool all_empty,
+ boost::system::error_code& ec);
+
+BOOST_ASIO_DECL bool non_blocking_write(int d,
+ const buf* bufs, std::size_t count,
+ boost::system::error_code& ec, std::size_t& bytes_transferred);
+
+BOOST_ASIO_DECL int ioctl(int d, state_type& state, long cmd,
+ ioctl_arg_type* arg, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int fcntl(int d, int cmd, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int fcntl(int d, int cmd,
+ long arg, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int poll_read(int d,
+ state_type state, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int poll_write(int d,
+ state_type state, boost::system::error_code& ec);
+
+} // namespace descriptor_ops
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/descriptor_ops.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_DESCRIPTOR_OPS_HPP
diff --git a/ext/patches/boost/asio/detail/descriptor_read_op.hpp b/ext/patches/boost/asio/detail/descriptor_read_op.hpp
new file mode 100644
index 0000000..d2bb5e3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/descriptor_read_op.hpp
@@ -0,0 +1,121 @@
+//
+// detail/descriptor_read_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_DESCRIPTOR_READ_OP_HPP
+#define BOOST_ASIO_DETAIL_DESCRIPTOR_READ_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/descriptor_ops.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence>
+class descriptor_read_op_base : public reactor_op
+{
+public:
+ descriptor_read_op_base(int descriptor,
+ const MutableBufferSequence& buffers, func_type complete_func)
+ : reactor_op(&descriptor_read_op_base::do_perform, complete_func),
+ descriptor_(descriptor),
+ buffers_(buffers)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ descriptor_read_op_base* o(static_cast<descriptor_read_op_base*>(base));
+
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(o->buffers_);
+
+ return descriptor_ops::non_blocking_read(o->descriptor_,
+ bufs.buffers(), bufs.count(), o->ec_, o->bytes_transferred_);
+ }
+
+private:
+ int descriptor_;
+ MutableBufferSequence buffers_;
+};
+
+template <typename MutableBufferSequence, typename Handler>
+class descriptor_read_op
+ : public descriptor_read_op_base<MutableBufferSequence>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(descriptor_read_op);
+
+ descriptor_read_op(int descriptor,
+ const MutableBufferSequence& buffers, Handler& handler)
+ : descriptor_read_op_base<MutableBufferSequence>(
+ descriptor, buffers, &descriptor_read_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ descriptor_read_op* o(static_cast<descriptor_read_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->bytes_transferred_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_DESCRIPTOR_READ_OP_HPP
diff --git a/ext/patches/boost/asio/detail/descriptor_write_op.hpp b/ext/patches/boost/asio/detail/descriptor_write_op.hpp
new file mode 100644
index 0000000..1691d75
--- /dev/null
+++ b/ext/patches/boost/asio/detail/descriptor_write_op.hpp
@@ -0,0 +1,121 @@
+//
+// detail/descriptor_write_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_DESCRIPTOR_WRITE_OP_HPP
+#define BOOST_ASIO_DETAIL_DESCRIPTOR_WRITE_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/descriptor_ops.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename ConstBufferSequence>
+class descriptor_write_op_base : public reactor_op
+{
+public:
+ descriptor_write_op_base(int descriptor,
+ const ConstBufferSequence& buffers, func_type complete_func)
+ : reactor_op(&descriptor_write_op_base::do_perform, complete_func),
+ descriptor_(descriptor),
+ buffers_(buffers)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ descriptor_write_op_base* o(static_cast<descriptor_write_op_base*>(base));
+
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(o->buffers_);
+
+ return descriptor_ops::non_blocking_write(o->descriptor_,
+ bufs.buffers(), bufs.count(), o->ec_, o->bytes_transferred_);
+ }
+
+private:
+ int descriptor_;
+ ConstBufferSequence buffers_;
+};
+
+template <typename ConstBufferSequence, typename Handler>
+class descriptor_write_op
+ : public descriptor_write_op_base<ConstBufferSequence>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(descriptor_write_op);
+
+ descriptor_write_op(int descriptor,
+ const ConstBufferSequence& buffers, Handler& handler)
+ : descriptor_write_op_base<ConstBufferSequence>(
+ descriptor, buffers, &descriptor_write_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ descriptor_write_op* o(static_cast<descriptor_write_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->bytes_transferred_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_DESCRIPTOR_WRITE_OP_HPP
diff --git a/ext/patches/boost/asio/detail/dev_poll_reactor.hpp b/ext/patches/boost/asio/detail/dev_poll_reactor.hpp
new file mode 100644
index 0000000..e8ff2d1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/dev_poll_reactor.hpp
@@ -0,0 +1,212 @@
+//
+// detail/dev_poll_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_DEV_POLL_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_DEV_POLL_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_DEV_POLL)
+
+#include <cstddef>
+#include <vector>
+#include <sys/devpoll.h>
+#include <boost/asio/detail/hash_map.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/reactor_op_queue.hpp>
+#include <boost/asio/detail/select_interrupter.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/timer_queue_base.hpp>
+#include <boost/asio/detail/timer_queue_set.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class dev_poll_reactor
+ : public boost::asio::detail::service_base<dev_poll_reactor>
+{
+public:
+ enum op_types { read_op = 0, write_op = 1,
+ connect_op = 1, except_op = 2, max_ops = 3 };
+
+ // Per-descriptor data.
+ struct per_descriptor_data
+ {
+ };
+
+ // Constructor.
+ BOOST_ASIO_DECL dev_poll_reactor(boost::asio::io_service& io_service);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~dev_poll_reactor();
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Recreate internal descriptors following a fork.
+ BOOST_ASIO_DECL void fork_service(
+ boost::asio::io_service::fork_event fork_ev);
+
+ // Initialise the task.
+ BOOST_ASIO_DECL void init_task();
+
+ // Register a socket with the reactor. Returns 0 on success, system error
+ // code on failure.
+ BOOST_ASIO_DECL int register_descriptor(socket_type, per_descriptor_data&);
+
+ // Register a descriptor with an associated single operation. Returns 0 on
+ // success, system error code on failure.
+ BOOST_ASIO_DECL int register_internal_descriptor(
+ int op_type, socket_type descriptor,
+ per_descriptor_data& descriptor_data, reactor_op* op);
+
+ // Move descriptor registration from one descriptor_data object to another.
+ BOOST_ASIO_DECL void move_descriptor(socket_type descriptor,
+ per_descriptor_data& target_descriptor_data,
+ per_descriptor_data& source_descriptor_data);
+
+ // Post a reactor operation for immediate completion.
+ void post_immediate_completion(reactor_op* op, bool is_continuation)
+ {
+ io_service_.post_immediate_completion(op, is_continuation);
+ }
+
+ // Start a new operation. The reactor operation will be performed when the
+ // given descriptor is flagged as ready, or an error has occurred.
+ BOOST_ASIO_DECL void start_op(int op_type, socket_type descriptor,
+ per_descriptor_data&, reactor_op* op,
+ bool is_continuation, bool allow_speculative);
+
+ // Cancel all operations associated with the given descriptor. The
+ // handlers associated with the descriptor will be invoked with the
+ // operation_aborted error.
+ BOOST_ASIO_DECL void cancel_ops(socket_type descriptor, per_descriptor_data&);
+
+ // Cancel any operations that are running against the descriptor and remove
+ // its registration from the reactor.
+ BOOST_ASIO_DECL void deregister_descriptor(socket_type descriptor,
+ per_descriptor_data&, bool closing);
+
+ // Cancel any operations that are running against the descriptor and remove
+ // its registration from the reactor.
+ BOOST_ASIO_DECL void deregister_internal_descriptor(
+ socket_type descriptor, per_descriptor_data&);
+
+ // Add a new timer queue to the reactor.
+ template <typename Time_Traits>
+ void add_timer_queue(timer_queue<Time_Traits>& queue);
+
+ // Remove a timer queue from the reactor.
+ template <typename Time_Traits>
+ void remove_timer_queue(timer_queue<Time_Traits>& queue);
+
+ // Schedule a new operation in the given timer queue to expire at the
+ // specified absolute time.
+ template <typename Time_Traits>
+ void schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op);
+
+ // Cancel the timer operations associated with the given token. Returns the
+ // number of operations that have been posted or dispatched.
+ template <typename Time_Traits>
+ std::size_t cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled = (std::numeric_limits<std::size_t>::max)());
+
+ // Run /dev/poll once until interrupted or events are ready to be dispatched.
+ BOOST_ASIO_DECL void run(bool block, op_queue<operation>& ops);
+
+ // Interrupt the select loop.
+ BOOST_ASIO_DECL void interrupt();
+
+private:
+ // Create the /dev/poll file descriptor. Throws an exception if the descriptor
+ // cannot be created.
+ BOOST_ASIO_DECL static int do_dev_poll_create();
+
+ // Helper function to add a new timer queue.
+ BOOST_ASIO_DECL void do_add_timer_queue(timer_queue_base& queue);
+
+ // Helper function to remove a timer queue.
+ BOOST_ASIO_DECL void do_remove_timer_queue(timer_queue_base& queue);
+
+ // Get the timeout value for the /dev/poll DP_POLL operation. The timeout
+ // value is returned as a number of milliseconds. A return value of -1
+ // indicates that the poll should block indefinitely.
+ BOOST_ASIO_DECL int get_timeout();
+
+ // Cancel all operations associated with the given descriptor. The do_cancel
+ // function of the handler objects will be invoked. This function does not
+ // acquire the dev_poll_reactor's mutex.
+ BOOST_ASIO_DECL void cancel_ops_unlocked(socket_type descriptor,
+ const boost::system::error_code& ec);
+
+ // Helper class used to reregister descriptors after a fork.
+ class fork_helper;
+ friend class fork_helper;
+
+ // Add a pending event entry for the given descriptor.
+ BOOST_ASIO_DECL ::pollfd& add_pending_event_change(int descriptor);
+
+ // The io_service implementation used to post completions.
+ io_service_impl& io_service_;
+
+ // Mutex to protect access to internal data.
+ boost::asio::detail::mutex mutex_;
+
+ // The /dev/poll file descriptor.
+ int dev_poll_fd_;
+
+ // Vector of /dev/poll events waiting to be written to the descriptor.
+ std::vector< ::pollfd> pending_event_changes_;
+
+ // Hash map to associate a descriptor with a pending event change index.
+ hash_map<int, std::size_t> pending_event_change_index_;
+
+ // The interrupter is used to break a blocking DP_POLL operation.
+ select_interrupter interrupter_;
+
+ // The queues of read, write and except operations.
+ reactor_op_queue<socket_type> op_queue_[max_ops];
+
+ // The timer queues.
+ timer_queue_set timer_queues_;
+
+ // Whether the service has been shut down.
+ bool shutdown_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/dev_poll_reactor.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/dev_poll_reactor.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_DEV_POLL)
+
+#endif // BOOST_ASIO_DETAIL_DEV_POLL_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/epoll_reactor.hpp b/ext/patches/boost/asio/detail/epoll_reactor.hpp
new file mode 100644
index 0000000..c8b86fb
--- /dev/null
+++ b/ext/patches/boost/asio/detail/epoll_reactor.hpp
@@ -0,0 +1,244 @@
+//
+// detail/epoll_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_EPOLL_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_EPOLL_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_EPOLL)
+
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/atomic_count.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/object_pool.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/select_interrupter.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/timer_queue_base.hpp>
+#include <boost/asio/detail/timer_queue_set.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class epoll_reactor
+ : public boost::asio::detail::service_base<epoll_reactor>
+{
+public:
+ enum op_types { read_op = 0, write_op = 1,
+ connect_op = 1, except_op = 2, max_ops = 3 };
+
+ // Per-descriptor queues.
+ class descriptor_state : operation
+ {
+ friend class epoll_reactor;
+ friend class object_pool_access;
+
+ descriptor_state* next_;
+ descriptor_state* prev_;
+
+ mutex mutex_;
+ epoll_reactor* reactor_;
+ int descriptor_;
+ uint32_t registered_events_;
+ op_queue<reactor_op> op_queue_[max_ops];
+ bool shutdown_;
+
+ BOOST_ASIO_DECL descriptor_state();
+ void set_ready_events(uint32_t events) { task_result_ = events; }
+ BOOST_ASIO_DECL operation* perform_io(uint32_t events);
+ BOOST_ASIO_DECL static void do_complete(
+ io_service_impl* owner, operation* base,
+ const boost::system::error_code& ec, std::size_t bytes_transferred);
+ };
+
+ // Per-descriptor data.
+ typedef descriptor_state* per_descriptor_data;
+
+ // Constructor.
+ BOOST_ASIO_DECL epoll_reactor(boost::asio::io_service& io_service);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~epoll_reactor();
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Recreate internal descriptors following a fork.
+ BOOST_ASIO_DECL void fork_service(
+ boost::asio::io_service::fork_event fork_ev);
+
+ // Initialise the task.
+ BOOST_ASIO_DECL void init_task();
+
+ // Register a socket with the reactor. Returns 0 on success, system error
+ // code on failure.
+ BOOST_ASIO_DECL int register_descriptor(socket_type descriptor,
+ per_descriptor_data& descriptor_data);
+
+ // Register a descriptor with an associated single operation. Returns 0 on
+ // success, system error code on failure.
+ BOOST_ASIO_DECL int register_internal_descriptor(
+ int op_type, socket_type descriptor,
+ per_descriptor_data& descriptor_data, reactor_op* op);
+
+ // Move descriptor registration from one descriptor_data object to another.
+ BOOST_ASIO_DECL void move_descriptor(socket_type descriptor,
+ per_descriptor_data& target_descriptor_data,
+ per_descriptor_data& source_descriptor_data);
+
+ // Post a reactor operation for immediate completion.
+ void post_immediate_completion(reactor_op* op, bool is_continuation)
+ {
+ io_service_.post_immediate_completion(op, is_continuation);
+ }
+
+ // Start a new operation. The reactor operation will be performed when the
+ // given descriptor is flagged as ready, or an error has occurred.
+ BOOST_ASIO_DECL void start_op(int op_type, socket_type descriptor,
+ per_descriptor_data& descriptor_data, reactor_op* op,
+ bool is_continuation, bool allow_speculative);
+
+ // Cancel all operations associated with the given descriptor. The
+ // handlers associated with the descriptor will be invoked with the
+ // operation_aborted error.
+ BOOST_ASIO_DECL void cancel_ops(socket_type descriptor,
+ per_descriptor_data& descriptor_data);
+
+ // Cancel any operations that are running against the descriptor and remove
+ // its registration from the reactor.
+ BOOST_ASIO_DECL void deregister_descriptor(socket_type descriptor,
+ per_descriptor_data& descriptor_data, bool closing);
+
+ // Remote the descriptor's registration from the reactor.
+ BOOST_ASIO_DECL void deregister_internal_descriptor(
+ socket_type descriptor, per_descriptor_data& descriptor_data);
+
+ // Add a new timer queue to the reactor.
+ template <typename Time_Traits>
+ void add_timer_queue(timer_queue<Time_Traits>& timer_queue);
+
+ // Remove a timer queue from the reactor.
+ template <typename Time_Traits>
+ void remove_timer_queue(timer_queue<Time_Traits>& timer_queue);
+
+ // Schedule a new operation in the given timer queue to expire at the
+ // specified absolute time.
+ template <typename Time_Traits>
+ void schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op);
+
+ // Cancel the timer operations associated with the given token. Returns the
+ // number of operations that have been posted or dispatched.
+ template <typename Time_Traits>
+ std::size_t cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled = (std::numeric_limits<std::size_t>::max)());
+
+ // Run epoll once until interrupted or events are ready to be dispatched.
+ BOOST_ASIO_DECL void run(bool block, op_queue<operation>& ops);
+
+ // Interrupt the select loop.
+ BOOST_ASIO_DECL void interrupt();
+
+private:
+ // The hint to pass to epoll_create to size its data structures.
+ enum { epoll_size = 20000 };
+
+ // Create the epoll file descriptor. Throws an exception if the descriptor
+ // cannot be created.
+ BOOST_ASIO_DECL static int do_epoll_create();
+
+ // Create the timerfd file descriptor. Does not throw.
+ BOOST_ASIO_DECL static int do_timerfd_create();
+
+ // Allocate a new descriptor state object.
+ BOOST_ASIO_DECL descriptor_state* allocate_descriptor_state();
+
+ // Free an existing descriptor state object.
+ BOOST_ASIO_DECL void free_descriptor_state(descriptor_state* s);
+
+ // Helper function to add a new timer queue.
+ BOOST_ASIO_DECL void do_add_timer_queue(timer_queue_base& queue);
+
+ // Helper function to remove a timer queue.
+ BOOST_ASIO_DECL void do_remove_timer_queue(timer_queue_base& queue);
+
+ // Called to recalculate and update the timeout.
+ BOOST_ASIO_DECL void update_timeout();
+
+ // Get the timeout value for the epoll_wait call. The timeout value is
+ // returned as a number of milliseconds. A return value of -1 indicates
+ // that epoll_wait should block indefinitely.
+ BOOST_ASIO_DECL int get_timeout();
+
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+ // Get the timeout value for the timer descriptor. The return value is the
+ // flag argument to be used when calling timerfd_settime.
+ BOOST_ASIO_DECL int get_timeout(itimerspec& ts);
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+
+ // The io_service implementation used to post completions.
+ io_service_impl& io_service_;
+
+ // Mutex to protect access to internal data.
+ mutex mutex_;
+
+ // The interrupter is used to break a blocking epoll_wait call.
+ select_interrupter interrupter_;
+
+ // The epoll file descriptor.
+ int epoll_fd_;
+
+ // The timer file descriptor.
+ int timer_fd_;
+
+ // The timer queues.
+ timer_queue_set timer_queues_;
+
+ // Whether the service has been shut down.
+ bool shutdown_;
+
+ // Mutex to protect access to the registered descriptors.
+ mutex registered_descriptors_mutex_;
+
+ // Keep track of all registered descriptors.
+ object_pool<descriptor_state> registered_descriptors_;
+
+ // Helper class to do post-perform_io cleanup.
+ struct perform_io_cleanup_on_block_exit;
+ friend struct perform_io_cleanup_on_block_exit;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/epoll_reactor.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/epoll_reactor.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_EPOLL)
+
+#endif // BOOST_ASIO_DETAIL_EPOLL_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/event.hpp b/ext/patches/boost/asio/detail/event.hpp
new file mode 100644
index 0000000..013bb88
--- /dev/null
+++ b/ext/patches/boost/asio/detail/event.hpp
@@ -0,0 +1,50 @@
+//
+// detail/event.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_EVENT_HPP
+#define BOOST_ASIO_DETAIL_EVENT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+# include <boost/asio/detail/null_event.hpp>
+#elif defined(BOOST_ASIO_WINDOWS)
+# include <boost/asio/detail/win_event.hpp>
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+# include <boost/asio/detail/posix_event.hpp>
+#elif defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+# include <boost/asio/detail/std_event.hpp>
+#else
+# error Only Windows, POSIX and std::condition_variable are supported!
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+typedef null_event event;
+#elif defined(BOOST_ASIO_WINDOWS)
+typedef win_event event;
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+typedef posix_event event;
+#elif defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+typedef std_event event;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_EVENT_HPP
diff --git a/ext/patches/boost/asio/detail/eventfd_select_interrupter.hpp b/ext/patches/boost/asio/detail/eventfd_select_interrupter.hpp
new file mode 100644
index 0000000..5e67b34
--- /dev/null
+++ b/ext/patches/boost/asio/detail/eventfd_select_interrupter.hpp
@@ -0,0 +1,85 @@
+//
+// detail/eventfd_select_interrupter.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Roelof Naude (roelof.naude at gmail dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_EVENTFD_SELECT_INTERRUPTER_HPP
+#define BOOST_ASIO_DETAIL_EVENTFD_SELECT_INTERRUPTER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_EVENTFD)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class eventfd_select_interrupter
+{
+public:
+ // Constructor.
+ BOOST_ASIO_DECL eventfd_select_interrupter();
+
+ // Destructor.
+ BOOST_ASIO_DECL ~eventfd_select_interrupter();
+
+ // Recreate the interrupter's descriptors. Used after a fork.
+ BOOST_ASIO_DECL void recreate();
+
+ // Interrupt the select call.
+ BOOST_ASIO_DECL void interrupt();
+
+ // Reset the select interrupt. Returns true if the call was interrupted.
+ BOOST_ASIO_DECL bool reset();
+
+ // Get the read descriptor to be passed to select.
+ int read_descriptor() const
+ {
+ return read_descriptor_;
+ }
+
+private:
+ // Open the descriptors. Throws on error.
+ BOOST_ASIO_DECL void open_descriptors();
+
+ // Close the descriptors.
+ BOOST_ASIO_DECL void close_descriptors();
+
+ // The read end of a connection used to interrupt the select call. This file
+ // descriptor is passed to select such that when it is time to stop, a single
+ // 64bit value will be written on the other end of the connection and this
+ // descriptor will become readable.
+ int read_descriptor_;
+
+ // The write end of a connection used to interrupt the select call. A single
+ // 64bit non-zero value may be written to this to wake up the select which is
+ // waiting for the other end to become readable. This descriptor will only
+ // differ from the read descriptor when a pipe is used.
+ int write_descriptor_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/eventfd_select_interrupter.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_EVENTFD)
+
+#endif // BOOST_ASIO_DETAIL_EVENTFD_SELECT_INTERRUPTER_HPP
diff --git a/ext/patches/boost/asio/detail/fd_set_adapter.hpp b/ext/patches/boost/asio/detail/fd_set_adapter.hpp
new file mode 100644
index 0000000..14a7e37
--- /dev/null
+++ b/ext/patches/boost/asio/detail/fd_set_adapter.hpp
@@ -0,0 +1,41 @@
+//
+// detail/fd_set_adapter.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_FD_SET_ADAPTER_HPP
+#define BOOST_ASIO_DETAIL_FD_SET_ADAPTER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/posix_fd_set_adapter.hpp>
+#include <boost/asio/detail/win_fd_set_adapter.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+typedef win_fd_set_adapter fd_set_adapter;
+#else
+typedef posix_fd_set_adapter fd_set_adapter;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_FD_SET_ADAPTER_HPP
diff --git a/ext/patches/boost/asio/detail/fenced_block.hpp b/ext/patches/boost/asio/detail/fenced_block.hpp
new file mode 100644
index 0000000..af5a337
--- /dev/null
+++ b/ext/patches/boost/asio/detail/fenced_block.hpp
@@ -0,0 +1,78 @@
+//
+// detail/fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS) \
+ || defined(BOOST_ASIO_DISABLE_FENCED_BLOCK)
+# include <boost/asio/detail/null_fenced_block.hpp>
+#elif defined(__MACH__) && defined(__APPLE__)
+# include <boost/asio/detail/macos_fenced_block.hpp>
+#elif defined(__sun)
+# include <boost/asio/detail/solaris_fenced_block.hpp>
+#elif defined(__GNUC__) && defined(__arm__) \
+ && !defined(__GCC_HAVE_SYNC_COMPARE_AND_SWAP_4)
+# include <boost/asio/detail/gcc_arm_fenced_block.hpp>
+#elif defined(__GNUC__) && (defined(__hppa) || defined(__hppa__))
+# include <boost/asio/detail/gcc_hppa_fenced_block.hpp>
+#elif defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
+# include <boost/asio/detail/gcc_x86_fenced_block.hpp>
+#elif defined(__GNUC__) \
+ && ((__GNUC__ == 4 && __GNUC_MINOR__ >= 1) || (__GNUC__ > 4)) \
+ && !defined(__INTEL_COMPILER) && !defined(__ICL) \
+ && !defined(__ICC) && !defined(__ECC) && !defined(__PATHSCALE__)
+# include <boost/asio/detail/gcc_sync_fenced_block.hpp>
+#elif defined(BOOST_ASIO_WINDOWS) && !defined(UNDER_CE)
+# include <boost/asio/detail/win_fenced_block.hpp>
+#else
+# include <boost/asio/detail/null_fenced_block.hpp>
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if !defined(BOOST_ASIO_HAS_THREADS) \
+ || defined(BOOST_ASIO_DISABLE_FENCED_BLOCK)
+typedef null_fenced_block fenced_block;
+#elif defined(__MACH__) && defined(__APPLE__)
+typedef macos_fenced_block fenced_block;
+#elif defined(__sun)
+typedef solaris_fenced_block fenced_block;
+#elif defined(__GNUC__) && defined(__arm__) \
+ && !defined(__GCC_HAVE_SYNC_COMPARE_AND_SWAP_4)
+typedef gcc_arm_fenced_block fenced_block;
+#elif defined(__GNUC__) && (defined(__hppa) || defined(__hppa__))
+typedef gcc_hppa_fenced_block fenced_block;
+#elif defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
+typedef gcc_x86_fenced_block fenced_block;
+#elif defined(__GNUC__) \
+ && ((__GNUC__ == 4 && __GNUC_MINOR__ >= 1) || (__GNUC__ > 4)) \
+ && !defined(__INTEL_COMPILER) && !defined(__ICL) \
+ && !defined(__ICC) && !defined(__ECC) && !defined(__PATHSCALE__)
+typedef gcc_sync_fenced_block fenced_block;
+#elif defined(BOOST_ASIO_WINDOWS) && !defined(UNDER_CE)
+typedef win_fenced_block fenced_block;
+#else
+typedef null_fenced_block fenced_block;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/function.hpp b/ext/patches/boost/asio/detail/function.hpp
new file mode 100644
index 0000000..b17edd3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/function.hpp
@@ -0,0 +1,40 @@
+//
+// detail/function.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_FUNCTION_HPP
+#define BOOST_ASIO_DETAIL_FUNCTION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_FUNCTION)
+# include <functional>
+#else // defined(BOOST_ASIO_HAS_STD_FUNCTION)
+# include <boost/function.hpp>
+#endif // defined(BOOST_ASIO_HAS_STD_FUNCTION)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_HAS_STD_FUNCTION)
+using std::function;
+#else // defined(BOOST_ASIO_HAS_STD_FUNCTION)
+using boost::function;
+#endif // defined(BOOST_ASIO_HAS_STD_FUNCTION)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_FUNCTION_HPP
diff --git a/ext/patches/boost/asio/detail/gcc_arm_fenced_block.hpp b/ext/patches/boost/asio/detail/gcc_arm_fenced_block.hpp
new file mode 100644
index 0000000..8017eb1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/gcc_arm_fenced_block.hpp
@@ -0,0 +1,91 @@
+//
+// detail/gcc_arm_fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_GCC_ARM_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_GCC_ARM_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(__GNUC__) && defined(__arm__)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class gcc_arm_fenced_block
+ : private noncopyable
+{
+public:
+ enum half_t { half };
+ enum full_t { full };
+
+ // Constructor for a half fenced block.
+ explicit gcc_arm_fenced_block(half_t)
+ {
+ }
+
+ // Constructor for a full fenced block.
+ explicit gcc_arm_fenced_block(full_t)
+ {
+ barrier();
+ }
+
+ // Destructor.
+ ~gcc_arm_fenced_block()
+ {
+ barrier();
+ }
+
+private:
+ static void barrier()
+ {
+#if defined(__ARM_ARCH_4__) \
+ || defined(__ARM_ARCH_4T__) \
+ || defined(__ARM_ARCH_5__) \
+ || defined(__ARM_ARCH_5E__) \
+ || defined(__ARM_ARCH_5T__) \
+ || defined(__ARM_ARCH_5TE__) \
+ || defined(__ARM_ARCH_5TEJ__) \
+ || defined(__ARM_ARCH_6__) \
+ || defined(__ARM_ARCH_6J__) \
+ || defined(__ARM_ARCH_6K__) \
+ || defined(__ARM_ARCH_6Z__) \
+ || defined(__ARM_ARCH_6ZK__) \
+ || defined(__ARM_ARCH_6T2__)
+# if defined(__thumb__)
+ // This is just a placeholder and almost certainly not sufficient.
+ __asm__ __volatile__ ("" : : : "memory");
+# else // defined(__thumb__)
+ int a = 0, b = 0;
+ __asm__ __volatile__ ("swp %0, %1, [%2]"
+ : "=&r"(a) : "r"(1), "r"(&b) : "memory", "cc");
+# endif // defined(__thumb__)
+#else
+ // ARMv7 and later.
+ __asm__ __volatile__ ("dmb" : : : "memory");
+#endif
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(__GNUC__) && defined(__arm__)
+
+#endif // BOOST_ASIO_DETAIL_GCC_ARM_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/gcc_hppa_fenced_block.hpp b/ext/patches/boost/asio/detail/gcc_hppa_fenced_block.hpp
new file mode 100644
index 0000000..ebe10e1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/gcc_hppa_fenced_block.hpp
@@ -0,0 +1,68 @@
+//
+// detail/gcc_hppa_fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_GCC_HPPA_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_GCC_HPPA_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(__GNUC__) && (defined(__hppa) || defined(__hppa__))
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class gcc_hppa_fenced_block
+ : private noncopyable
+{
+public:
+ enum half_t { half };
+ enum full_t { full };
+
+ // Constructor for a half fenced block.
+ explicit gcc_hppa_fenced_block(half_t)
+ {
+ }
+
+ // Constructor for a full fenced block.
+ explicit gcc_hppa_fenced_block(full_t)
+ {
+ barrier();
+ }
+
+ // Destructor.
+ ~gcc_hppa_fenced_block()
+ {
+ barrier();
+ }
+
+private:
+ static void barrier()
+ {
+ // This is just a placeholder and almost certainly not sufficient.
+ __asm__ __volatile__ ("" : : : "memory");
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(__GNUC__) && (defined(__hppa) || defined(__hppa__))
+
+#endif // BOOST_ASIO_DETAIL_GCC_HPPA_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/gcc_sync_fenced_block.hpp b/ext/patches/boost/asio/detail/gcc_sync_fenced_block.hpp
new file mode 100644
index 0000000..ff968ef
--- /dev/null
+++ b/ext/patches/boost/asio/detail/gcc_sync_fenced_block.hpp
@@ -0,0 +1,65 @@
+//
+// detail/gcc_sync_fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_GCC_SYNC_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_GCC_SYNC_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(__GNUC__) \
+ && ((__GNUC__ == 4 && __GNUC_MINOR__ >= 1) || (__GNUC__ > 4)) \
+ && !defined(__INTEL_COMPILER) && !defined(__ICL) \
+ && !defined(__ICC) && !defined(__ECC) && !defined(__PATHSCALE__)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class gcc_sync_fenced_block
+ : private noncopyable
+{
+public:
+ enum half_or_full_t { half, full };
+
+ // Constructor.
+ explicit gcc_sync_fenced_block(half_or_full_t)
+ : value_(0)
+ {
+ __sync_lock_test_and_set(&value_, 1);
+ }
+
+ // Destructor.
+ ~gcc_sync_fenced_block()
+ {
+ __sync_lock_release(&value_);
+ }
+
+private:
+ int value_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(__GNUC__)
+ // && ((__GNUC__ == 4 && __GNUC_MINOR__ >= 1) || (__GNUC__ > 4))
+ // && !defined(__INTEL_COMPILER) && !defined(__ICL)
+ // && !defined(__ICC) && !defined(__ECC) && !defined(__PATHSCALE__)
+
+#endif // BOOST_ASIO_DETAIL_GCC_SYNC_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/gcc_x86_fenced_block.hpp b/ext/patches/boost/asio/detail/gcc_x86_fenced_block.hpp
new file mode 100644
index 0000000..b0f4639
--- /dev/null
+++ b/ext/patches/boost/asio/detail/gcc_x86_fenced_block.hpp
@@ -0,0 +1,99 @@
+//
+// detail/gcc_x86_fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_GCC_X86_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_GCC_X86_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class gcc_x86_fenced_block
+ : private noncopyable
+{
+public:
+ enum half_t { half };
+ enum full_t { full };
+
+ // Constructor for a half fenced block.
+ explicit gcc_x86_fenced_block(half_t)
+ {
+ }
+
+ // Constructor for a full fenced block.
+ explicit gcc_x86_fenced_block(full_t)
+ {
+ lbarrier();
+ }
+
+ // Destructor.
+ ~gcc_x86_fenced_block()
+ {
+ sbarrier();
+ }
+
+private:
+ static int barrier()
+ {
+ int r = 0, m = 1;
+ __asm__ __volatile__ (
+ "xchgl %0, %1" :
+ "=r"(r), "=m"(m) :
+ "0"(1), "m"(m) :
+ "memory", "cc");
+ return r;
+ }
+
+ static void lbarrier()
+ {
+#if defined(__SSE2__)
+# if (__GNUC__ >= 4) && !defined(__INTEL_COMPILER) && !defined(__ICL)
+ __builtin_ia32_lfence();
+# else // (__GNUC__ >= 4) && !defined(__INTEL_COMPILER) && !defined(__ICL)
+ __asm__ __volatile__ ("lfence" ::: "memory");
+# endif // (__GNUC__ >= 4) && !defined(__INTEL_COMPILER) && !defined(__ICL)
+#else // defined(__SSE2__)
+ barrier();
+#endif // defined(__SSE2__)
+ }
+
+ static void sbarrier()
+ {
+#if defined(__SSE2__)
+# if (__GNUC__ >= 4) && !defined(__INTEL_COMPILER) && !defined(__ICL)
+ __builtin_ia32_sfence();
+# else // (__GNUC__ >= 4) && !defined(__INTEL_COMPILER) && !defined(__ICL)
+ __asm__ __volatile__ ("sfence" ::: "memory");
+# endif // (__GNUC__ >= 4) && !defined(__INTEL_COMPILER) && !defined(__ICL)
+#else // defined(__SSE2__)
+ barrier();
+#endif // defined(__SSE2__)
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(__GNUC__) && (defined(__i386__) || defined(__x86_64__))
+
+#endif // BOOST_ASIO_DETAIL_GCC_X86_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/handler_alloc_helpers.hpp b/ext/patches/boost/asio/detail/handler_alloc_helpers.hpp
new file mode 100644
index 0000000..9620f9b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/handler_alloc_helpers.hpp
@@ -0,0 +1,82 @@
+//
+// detail/handler_alloc_helpers.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_HANDLER_ALLOC_HELPERS_HPP
+#define BOOST_ASIO_DETAIL_HANDLER_ALLOC_HELPERS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/handler_alloc_hook.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+// Calls to asio_handler_allocate and asio_handler_deallocate must be made from
+// a namespace that does not contain any overloads of these functions. The
+// boost_asio_handler_alloc_helpers namespace is defined here for that purpose.
+namespace boost_asio_handler_alloc_helpers {
+
+template <typename Handler>
+inline void* allocate(std::size_t s, Handler& h)
+{
+#if !defined(BOOST_ASIO_HAS_HANDLER_HOOKS)
+ return ::operator new(s);
+#else
+ using boost::asio::asio_handler_allocate;
+ return asio_handler_allocate(s, boost::asio::detail::addressof(h));
+#endif
+}
+
+template <typename Handler>
+inline void deallocate(void* p, std::size_t s, Handler& h)
+{
+#if !defined(BOOST_ASIO_HAS_HANDLER_HOOKS)
+ ::operator delete(p);
+#else
+ using boost::asio::asio_handler_deallocate;
+ asio_handler_deallocate(p, s, boost::asio::detail::addressof(h));
+#endif
+}
+
+} // namespace boost_asio_handler_alloc_helpers
+
+#define BOOST_ASIO_DEFINE_HANDLER_PTR(op) \
+ struct ptr \
+ { \
+ Handler* h; \
+ void* v; \
+ op* p; \
+ ~ptr() \
+ { \
+ reset(); \
+ } \
+ void reset() \
+ { \
+ if (p) \
+ { \
+ p->~op(); \
+ p = 0; \
+ } \
+ if (v) \
+ { \
+ boost_asio_handler_alloc_helpers::deallocate(v, sizeof(op), *h); \
+ v = 0; \
+ } \
+ } \
+ } \
+ /**/
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_HANDLER_ALLOC_HELPERS_HPP
diff --git a/ext/patches/boost/asio/detail/handler_cont_helpers.hpp b/ext/patches/boost/asio/detail/handler_cont_helpers.hpp
new file mode 100644
index 0000000..29ea02d
--- /dev/null
+++ b/ext/patches/boost/asio/detail/handler_cont_helpers.hpp
@@ -0,0 +1,45 @@
+//
+// detail/handler_cont_helpers.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_HANDLER_CONT_HELPERS_HPP
+#define BOOST_ASIO_DETAIL_HANDLER_CONT_HELPERS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/handler_continuation_hook.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+// Calls to asio_handler_is_continuation must be made from a namespace that
+// does not contain overloads of this function. This namespace is defined here
+// for that purpose.
+namespace boost_asio_handler_cont_helpers {
+
+template <typename Context>
+inline bool is_continuation(Context& context)
+{
+#if !defined(BOOST_ASIO_HAS_HANDLER_HOOKS)
+ return false;
+#else
+ using boost::asio::asio_handler_is_continuation;
+ return asio_handler_is_continuation(
+ boost::asio::detail::addressof(context));
+#endif
+}
+
+} // namespace boost_asio_handler_cont_helpers
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_HANDLER_CONT_HELPERS_HPP
diff --git a/ext/patches/boost/asio/detail/handler_invoke_helpers.hpp b/ext/patches/boost/asio/detail/handler_invoke_helpers.hpp
new file mode 100644
index 0000000..956f93f
--- /dev/null
+++ b/ext/patches/boost/asio/detail/handler_invoke_helpers.hpp
@@ -0,0 +1,57 @@
+//
+// detail/handler_invoke_helpers.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_HANDLER_INVOKE_HELPERS_HPP
+#define BOOST_ASIO_DETAIL_HANDLER_INVOKE_HELPERS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/handler_invoke_hook.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+// Calls to asio_handler_invoke must be made from a namespace that does not
+// contain overloads of this function. The boost_asio_handler_invoke_helpers
+// namespace is defined here for that purpose.
+namespace boost_asio_handler_invoke_helpers {
+
+template <typename Function, typename Context>
+inline void invoke(Function& function, Context& context)
+{
+#if !defined(BOOST_ASIO_HAS_HANDLER_HOOKS)
+ Function tmp(function);
+ tmp();
+#else
+ using boost::asio::asio_handler_invoke;
+ asio_handler_invoke(function, boost::asio::detail::addressof(context));
+#endif
+}
+
+template <typename Function, typename Context>
+inline void invoke(const Function& function, Context& context)
+{
+#if !defined(BOOST_ASIO_HAS_HANDLER_HOOKS)
+ Function tmp(function);
+ tmp();
+#else
+ using boost::asio::asio_handler_invoke;
+ asio_handler_invoke(function, boost::asio::detail::addressof(context));
+#endif
+}
+
+} // namespace boost_asio_handler_invoke_helpers
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_HANDLER_INVOKE_HELPERS_HPP
diff --git a/ext/patches/boost/asio/detail/handler_tracking.hpp b/ext/patches/boost/asio/detail/handler_tracking.hpp
new file mode 100644
index 0000000..c6e9ac4
--- /dev/null
+++ b/ext/patches/boost/asio/detail/handler_tracking.hpp
@@ -0,0 +1,161 @@
+//
+// detail/handler_tracking.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_HANDLER_TRACKING_HPP
+#define BOOST_ASIO_DETAIL_HANDLER_TRACKING_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_ENABLE_HANDLER_TRACKING)
+# include <boost/system/error_code.hpp>
+# include <boost/asio/detail/cstdint.hpp>
+# include <boost/asio/detail/static_mutex.hpp>
+# include <boost/asio/detail/tss_ptr.hpp>
+#endif // defined(BOOST_ASIO_ENABLE_HANDLER_TRACKING)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_ENABLE_HANDLER_TRACKING)
+
+class handler_tracking
+{
+public:
+ class completion;
+
+ // Base class for objects containing tracked handlers.
+ class tracked_handler
+ {
+ private:
+ // Only the handler_tracking class will have access to the id.
+ friend class handler_tracking;
+ friend class completion;
+ uint64_t id_;
+
+ protected:
+ // Constructor initialises with no id.
+ tracked_handler() : id_(0) {}
+
+ // Prevent deletion through this type.
+ ~tracked_handler() {}
+ };
+
+ // Initialise the tracking system.
+ BOOST_ASIO_DECL static void init();
+
+ // Record the creation of a tracked handler.
+ BOOST_ASIO_DECL static void creation(tracked_handler* h,
+ const char* object_type, void* object, const char* op_name);
+
+ class completion
+ {
+ public:
+ // Constructor records that handler is to be invoked with no arguments.
+ BOOST_ASIO_DECL explicit completion(tracked_handler* h);
+
+ // Destructor records only when an exception is thrown from the handler, or
+ // if the memory is being freed without the handler having been invoked.
+ BOOST_ASIO_DECL ~completion();
+
+ // Records that handler is to be invoked with no arguments.
+ BOOST_ASIO_DECL void invocation_begin();
+
+ // Records that handler is to be invoked with one arguments.
+ BOOST_ASIO_DECL void invocation_begin(const boost::system::error_code& ec);
+
+ // Constructor records that handler is to be invoked with two arguments.
+ BOOST_ASIO_DECL void invocation_begin(
+ const boost::system::error_code& ec, std::size_t bytes_transferred);
+
+ // Constructor records that handler is to be invoked with two arguments.
+ BOOST_ASIO_DECL void invocation_begin(
+ const boost::system::error_code& ec, int signal_number);
+
+ // Constructor records that handler is to be invoked with two arguments.
+ BOOST_ASIO_DECL void invocation_begin(
+ const boost::system::error_code& ec, const char* arg);
+
+ // Record that handler invocation has ended.
+ BOOST_ASIO_DECL void invocation_end();
+
+ private:
+ friend class handler_tracking;
+ uint64_t id_;
+ bool invoked_;
+ completion* next_;
+ };
+
+ // Record an operation that affects pending handlers.
+ BOOST_ASIO_DECL static void operation(const char* object_type,
+ void* object, const char* op_name);
+
+ // Write a line of output.
+ BOOST_ASIO_DECL static void write_line(const char* format, ...);
+
+private:
+ struct tracking_state;
+ BOOST_ASIO_DECL static tracking_state* get_state();
+};
+
+# define BOOST_ASIO_INHERIT_TRACKED_HANDLER \
+ : public boost::asio::detail::handler_tracking::tracked_handler
+
+# define BOOST_ASIO_ALSO_INHERIT_TRACKED_HANDLER \
+ , public boost::asio::detail::handler_tracking::tracked_handler
+
+# define BOOST_ASIO_HANDLER_TRACKING_INIT \
+ boost::asio::detail::handler_tracking::init()
+
+# define BOOST_ASIO_HANDLER_CREATION(args) \
+ boost::asio::detail::handler_tracking::creation args
+
+# define BOOST_ASIO_HANDLER_COMPLETION(args) \
+ boost::asio::detail::handler_tracking::completion tracked_completion args
+
+# define BOOST_ASIO_HANDLER_INVOCATION_BEGIN(args) \
+ tracked_completion.invocation_begin args
+
+# define BOOST_ASIO_HANDLER_INVOCATION_END \
+ tracked_completion.invocation_end()
+
+# define BOOST_ASIO_HANDLER_OPERATION(args) \
+ boost::asio::detail::handler_tracking::operation args
+
+#else // defined(BOOST_ASIO_ENABLE_HANDLER_TRACKING)
+
+# define BOOST_ASIO_INHERIT_TRACKED_HANDLER
+# define BOOST_ASIO_ALSO_INHERIT_TRACKED_HANDLER
+# define BOOST_ASIO_HANDLER_TRACKING_INIT (void)0
+# define BOOST_ASIO_HANDLER_CREATION(args) (void)0
+# define BOOST_ASIO_HANDLER_COMPLETION(args) (void)0
+# define BOOST_ASIO_HANDLER_INVOCATION_BEGIN(args) (void)0
+# define BOOST_ASIO_HANDLER_INVOCATION_END (void)0
+# define BOOST_ASIO_HANDLER_OPERATION(args) (void)0
+
+#endif // defined(BOOST_ASIO_ENABLE_HANDLER_TRACKING)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/handler_tracking.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_HANDLER_TRACKING_HPP
diff --git a/ext/patches/boost/asio/detail/handler_type_requirements.hpp b/ext/patches/boost/asio/detail/handler_type_requirements.hpp
new file mode 100644
index 0000000..406889a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/handler_type_requirements.hpp
@@ -0,0 +1,490 @@
+//
+// detail/handler_type_requirements.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_HANDLER_TYPE_REQUIREMENTS_HPP
+#define BOOST_ASIO_DETAIL_HANDLER_TYPE_REQUIREMENTS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+// Older versions of gcc have difficulty compiling the sizeof expressions where
+// we test the handler type requirements. We'll disable checking of handler type
+// requirements for those compilers, but otherwise enable it by default.
+#if !defined(BOOST_ASIO_DISABLE_HANDLER_TYPE_REQUIREMENTS)
+# if !defined(__GNUC__) || (__GNUC__ >= 4)
+# define BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS 1
+# endif // !defined(__GNUC__) || (__GNUC__ >= 4)
+#endif // !defined(BOOST_ASIO_DISABLE_HANDLER_TYPE_REQUIREMENTS)
+
+// With C++0x we can use a combination of enhanced SFINAE and static_assert to
+// generate better template error messages. As this technique is not yet widely
+// portable, we'll only enable it for tested compilers.
+#if !defined(BOOST_ASIO_DISABLE_HANDLER_TYPE_REQUIREMENTS_ASSERT)
+# if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# if defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS_ASSERT 1
+# endif // defined(__GXX_EXPERIMENTAL_CXX0X__)
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 5)) || (__GNUC__ > 4)
+# endif // defined(__GNUC__)
+# if defined(BOOST_ASIO_MSVC)
+# if (_MSC_VER >= 1600)
+# define BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS_ASSERT 1
+# endif // (_MSC_VER >= 1600)
+# endif // defined(BOOST_ASIO_MSVC)
+# if defined(__clang__)
+# if __has_feature(__cxx_static_assert__)
+# define BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS_ASSERT 1
+# endif // __has_feature(cxx_static_assert)
+# endif // defined(__clang__)
+#endif // !defined(BOOST_ASIO_DISABLE_HANDLER_TYPE_REQUIREMENTS)
+
+#if defined(BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS)
+# include <boost/asio/handler_type.hpp>
+#endif // defined(BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS)
+
+// Newer gcc needs special treatment to suppress unused typedef warnings.
+#if defined(__GNUC__)
+# if ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 8)) || (__GNUC__ > 4)
+# define BOOST_ASIO_UNUSED_TYPEDEF __attribute__((__unused__))
+# endif // ((__GNUC__ == 4) && (__GNUC_MINOR__ >= 8)) || (__GNUC__ > 4)
+#endif // defined(__GNUC__)
+#if !defined(BOOST_ASIO_UNUSED_TYPEDEF)
+# define BOOST_ASIO_UNUSED_TYPEDEF
+#endif // !defined(BOOST_ASIO_UNUSED_TYPEDEF)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS)
+
+# if defined(BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS_ASSERT)
+
+template <typename Handler>
+auto zero_arg_handler_test(Handler h, void*)
+ -> decltype(
+ sizeof(Handler(static_cast<const Handler&>(h))),
+ ((h)()),
+ char(0));
+
+template <typename Handler>
+char (&zero_arg_handler_test(Handler, ...))[2];
+
+template <typename Handler, typename Arg1>
+auto one_arg_handler_test(Handler h, Arg1* a1)
+ -> decltype(
+ sizeof(Handler(static_cast<const Handler&>(h))),
+ ((h)(*a1)),
+ char(0));
+
+template <typename Handler>
+char (&one_arg_handler_test(Handler h, ...))[2];
+
+template <typename Handler, typename Arg1, typename Arg2>
+auto two_arg_handler_test(Handler h, Arg1* a1, Arg2* a2)
+ -> decltype(
+ sizeof(Handler(static_cast<const Handler&>(h))),
+ ((h)(*a1, *a2)),
+ char(0));
+
+template <typename Handler>
+char (&two_arg_handler_test(Handler, ...))[2];
+
+# define BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT(expr, msg) \
+ static_assert(expr, msg);
+
+# else // defined(BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS_ASSERT)
+
+# define BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT(expr, msg)
+
+# endif // defined(BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS_ASSERT)
+
+template <typename T> T& lvref();
+template <typename T> T& lvref(T);
+template <typename T> const T& clvref();
+template <typename T> const T& clvref(T);
+template <typename T> char argbyv(T);
+
+template <int>
+struct handler_type_requirements
+{
+};
+
+#define BOOST_ASIO_COMPLETION_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void()) asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::zero_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), 0)) == 1, \
+ "CompletionHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()(), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_READ_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code, std::size_t)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::two_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0), \
+ static_cast<const std::size_t*>(0))) == 1, \
+ "ReadHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>(), \
+ boost::asio::detail::lvref<const std::size_t>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+
+#define BOOST_ASIO_WRITE_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code, std::size_t)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::two_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0), \
+ static_cast<const std::size_t*>(0))) == 1, \
+ "WriteHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>(), \
+ boost::asio::detail::lvref<const std::size_t>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_ACCEPT_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::one_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0))) == 1, \
+ "AcceptHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_CONNECT_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::one_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0))) == 1, \
+ "ConnectHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_COMPOSED_CONNECT_HANDLER_CHECK( \
+ handler_type, handler, iter_type) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code, iter_type)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::two_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0), \
+ static_cast<const iter_type*>(0))) == 1, \
+ "ComposedConnectHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>(), \
+ boost::asio::detail::lvref<const iter_type>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_RESOLVE_HANDLER_CHECK( \
+ handler_type, handler, iter_type) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code, iter_type)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::two_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0), \
+ static_cast<const iter_type*>(0))) == 1, \
+ "ResolveHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>(), \
+ boost::asio::detail::lvref<const iter_type>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_WAIT_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::one_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0))) == 1, \
+ "WaitHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_SIGNAL_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code, int)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::two_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0), \
+ static_cast<const int*>(0))) == 1, \
+ "SignalHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>(), \
+ boost::asio::detail::lvref<const int>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_HANDSHAKE_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::one_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0))) == 1, \
+ "HandshakeHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_BUFFERED_HANDSHAKE_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code, std::size_t)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::two_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0), \
+ static_cast<const std::size_t*>(0))) == 1, \
+ "BufferedHandshakeHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>(), \
+ boost::asio::detail::lvref<const std::size_t>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_SHUTDOWN_HANDLER_CHECK( \
+ handler_type, handler) \
+ \
+ typedef BOOST_ASIO_HANDLER_TYPE(handler_type, \
+ void(boost::system::error_code)) \
+ asio_true_handler_type; \
+ \
+ BOOST_ASIO_HANDLER_TYPE_REQUIREMENTS_ASSERT( \
+ sizeof(boost::asio::detail::one_arg_handler_test( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>(), \
+ static_cast<const boost::system::error_code*>(0))) == 1, \
+ "ShutdownHandler type requirements not met") \
+ \
+ typedef boost::asio::detail::handler_type_requirements< \
+ sizeof( \
+ boost::asio::detail::argbyv( \
+ boost::asio::detail::clvref< \
+ asio_true_handler_type>())) + \
+ sizeof( \
+ boost::asio::detail::lvref< \
+ asio_true_handler_type>()( \
+ boost::asio::detail::lvref<const boost::system::error_code>()), \
+ char(0))> BOOST_ASIO_UNUSED_TYPEDEF
+
+#else // !defined(BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS)
+
+#define BOOST_ASIO_COMPLETION_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_READ_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_WRITE_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_ACCEPT_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_CONNECT_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_COMPOSED_CONNECT_HANDLER_CHECK( \
+ handler_type, handler, iter_type) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_RESOLVE_HANDLER_CHECK( \
+ handler_type, handler, iter_type) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_WAIT_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_SIGNAL_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_HANDSHAKE_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_BUFFERED_HANDSHAKE_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#define BOOST_ASIO_SHUTDOWN_HANDLER_CHECK( \
+ handler_type, handler) \
+ typedef int BOOST_ASIO_UNUSED_TYPEDEF
+
+#endif // !defined(BOOST_ASIO_ENABLE_HANDLER_TYPE_REQUIREMENTS)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_HANDLER_TYPE_REQUIREMENTS_HPP
diff --git a/ext/patches/boost/asio/detail/hash_map.hpp b/ext/patches/boost/asio/detail/hash_map.hpp
new file mode 100644
index 0000000..cfd7704
--- /dev/null
+++ b/ext/patches/boost/asio/detail/hash_map.hpp
@@ -0,0 +1,333 @@
+//
+// detail/hash_map.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_HASH_MAP_HPP
+#define BOOST_ASIO_DETAIL_HASH_MAP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <list>
+#include <utility>
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# include <boost/asio/detail/socket_types.hpp>
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+inline std::size_t calculate_hash_value(int i)
+{
+ return static_cast<std::size_t>(i);
+}
+
+inline std::size_t calculate_hash_value(void* p)
+{
+ return reinterpret_cast<std::size_t>(p)
+ + (reinterpret_cast<std::size_t>(p) >> 3);
+}
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+inline std::size_t calculate_hash_value(SOCKET s)
+{
+ return static_cast<std::size_t>(s);
+}
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+// Note: assumes K and V are POD types.
+template <typename K, typename V>
+class hash_map
+ : private noncopyable
+{
+public:
+ // The type of a value in the map.
+ typedef std::pair<K, V> value_type;
+
+ // The type of a non-const iterator over the hash map.
+ typedef typename std::list<value_type>::iterator iterator;
+
+ // The type of a const iterator over the hash map.
+ typedef typename std::list<value_type>::const_iterator const_iterator;
+
+ // Constructor.
+ hash_map()
+ : size_(0),
+ buckets_(0),
+ num_buckets_(0)
+ {
+ }
+
+ // Destructor.
+ ~hash_map()
+ {
+ delete[] buckets_;
+ }
+
+ // Get an iterator for the beginning of the map.
+ iterator begin()
+ {
+ return values_.begin();
+ }
+
+ // Get an iterator for the beginning of the map.
+ const_iterator begin() const
+ {
+ return values_.begin();
+ }
+
+ // Get an iterator for the end of the map.
+ iterator end()
+ {
+ return values_.end();
+ }
+
+ // Get an iterator for the end of the map.
+ const_iterator end() const
+ {
+ return values_.end();
+ }
+
+ // Check whether the map is empty.
+ bool empty() const
+ {
+ return values_.empty();
+ }
+
+ // Find an entry in the map.
+ iterator find(const K& k)
+ {
+ if (num_buckets_)
+ {
+ size_t bucket = calculate_hash_value(k) % num_buckets_;
+ iterator it = buckets_[bucket].first;
+ if (it == values_.end())
+ return values_.end();
+ iterator end_it = buckets_[bucket].last;
+ ++end_it;
+ while (it != end_it)
+ {
+ if (it->first == k)
+ return it;
+ ++it;
+ }
+ }
+ return values_.end();
+ }
+
+ // Find an entry in the map.
+ const_iterator find(const K& k) const
+ {
+ if (num_buckets_)
+ {
+ size_t bucket = calculate_hash_value(k) % num_buckets_;
+ const_iterator it = buckets_[bucket].first;
+ if (it == values_.end())
+ return it;
+ const_iterator end_it = buckets_[bucket].last;
+ ++end_it;
+ while (it != end_it)
+ {
+ if (it->first == k)
+ return it;
+ ++it;
+ }
+ }
+ return values_.end();
+ }
+
+ // Insert a new entry into the map.
+ std::pair<iterator, bool> insert(const value_type& v)
+ {
+ if (size_ + 1 >= num_buckets_)
+ rehash(hash_size(size_ + 1));
+ size_t bucket = calculate_hash_value(v.first) % num_buckets_;
+ iterator it = buckets_[bucket].first;
+ if (it == values_.end())
+ {
+ buckets_[bucket].first = buckets_[bucket].last =
+ values_insert(values_.end(), v);
+ ++size_;
+ return std::pair<iterator, bool>(buckets_[bucket].last, true);
+ }
+ iterator end_it = buckets_[bucket].last;
+ ++end_it;
+ while (it != end_it)
+ {
+ if (it->first == v.first)
+ return std::pair<iterator, bool>(it, false);
+ ++it;
+ }
+ buckets_[bucket].last = values_insert(end_it, v);
+ ++size_;
+ return std::pair<iterator, bool>(buckets_[bucket].last, true);
+ }
+
+ // Erase an entry from the map.
+ void erase(iterator it)
+ {
+ BOOST_ASIO_ASSERT(it != values_.end());
+ BOOST_ASIO_ASSERT(num_buckets_ != 0);
+
+ size_t bucket = calculate_hash_value(it->first) % num_buckets_;
+ bool is_first = (it == buckets_[bucket].first);
+ bool is_last = (it == buckets_[bucket].last);
+ if (is_first && is_last)
+ buckets_[bucket].first = buckets_[bucket].last = values_.end();
+ else if (is_first)
+ ++buckets_[bucket].first;
+ else if (is_last)
+ --buckets_[bucket].last;
+
+ values_erase(it);
+ --size_;
+ }
+
+ // Erase a key from the map.
+ void erase(const K& k)
+ {
+ iterator it = find(k);
+ if (it != values_.end())
+ erase(it);
+ }
+
+ // Remove all entries from the map.
+ void clear()
+ {
+ // Clear the values.
+ values_.clear();
+ size_ = 0;
+
+ // Initialise all buckets to empty.
+ iterator end_it = values_.end();
+ for (size_t i = 0; i < num_buckets_; ++i)
+ buckets_[i].first = buckets_[i].last = end_it;
+ }
+
+private:
+ // Calculate the hash size for the specified number of elements.
+ static std::size_t hash_size(std::size_t num_elems)
+ {
+ static std::size_t sizes[] =
+ {
+#if defined(BOOST_ASIO_HASH_MAP_BUCKETS)
+ BOOST_ASIO_HASH_MAP_BUCKETS
+#else // BOOST_ASIO_HASH_MAP_BUCKETS
+ 3, 13, 23, 53, 97, 193, 389, 769, 1543, 3079, 6151, 12289, 24593,
+ 49157, 98317, 196613, 393241, 786433, 1572869, 3145739, 6291469,
+ 12582917, 25165843
+#endif // BOOST_ASIO_HASH_MAP_BUCKETS
+ };
+ const std::size_t nth_size = sizeof(sizes) / sizeof(std::size_t) - 1;
+ for (std::size_t i = 0; i < nth_size; ++i)
+ if (num_elems < sizes[i])
+ return sizes[i];
+ return sizes[nth_size];
+ }
+
+ // Re-initialise the hash from the values already contained in the list.
+ void rehash(std::size_t num_buckets)
+ {
+ if (num_buckets == num_buckets_)
+ return;
+ num_buckets_ = num_buckets;
+ BOOST_ASIO_ASSERT(num_buckets_ != 0);
+
+ iterator end_iter = values_.end();
+
+ // Update number of buckets and initialise all buckets to empty.
+ bucket_type* tmp = new bucket_type[num_buckets_];
+ delete[] buckets_;
+ buckets_ = tmp;
+ for (std::size_t i = 0; i < num_buckets_; ++i)
+ buckets_[i].first = buckets_[i].last = end_iter;
+
+ // Put all values back into the hash.
+ iterator iter = values_.begin();
+ while (iter != end_iter)
+ {
+ std::size_t bucket = calculate_hash_value(iter->first) % num_buckets_;
+ if (buckets_[bucket].last == end_iter)
+ {
+ buckets_[bucket].first = buckets_[bucket].last = iter++;
+ }
+ else if (++buckets_[bucket].last == iter)
+ {
+ ++iter;
+ }
+ else
+ {
+ values_.splice(buckets_[bucket].last, values_, iter++);
+ --buckets_[bucket].last;
+ }
+ }
+ }
+
+ // Insert an element into the values list by splicing from the spares list,
+ // if a spare is available, and otherwise by inserting a new element.
+ iterator values_insert(iterator it, const value_type& v)
+ {
+ if (spares_.empty())
+ {
+ return values_.insert(it, v);
+ }
+ else
+ {
+ spares_.front() = v;
+ values_.splice(it, spares_, spares_.begin());
+ return --it;
+ }
+ }
+
+ // Erase an element from the values list by splicing it to the spares list.
+ void values_erase(iterator it)
+ {
+ *it = value_type();
+ spares_.splice(spares_.begin(), values_, it);
+ }
+
+ // The number of elements in the hash.
+ std::size_t size_;
+
+ // The list of all values in the hash map.
+ std::list<value_type> values_;
+
+ // The list of spare nodes waiting to be recycled. Assumes that POD types only
+ // are stored in the hash map.
+ std::list<value_type> spares_;
+
+ // The type for a bucket in the hash table.
+ struct bucket_type
+ {
+ iterator first;
+ iterator last;
+ };
+
+ // The buckets in the hash.
+ bucket_type* buckets_;
+
+ // The number of buckets in the hash.
+ std::size_t num_buckets_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_HASH_MAP_HPP
diff --git a/ext/patches/boost/asio/detail/impl/buffer_sequence_adapter.ipp b/ext/patches/boost/asio/detail/impl/buffer_sequence_adapter.ipp
new file mode 100644
index 0000000..8c8c08c
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/buffer_sequence_adapter.ipp
@@ -0,0 +1,120 @@
+//
+// detail/impl/buffer_sequence_adapter.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_BUFFER_SEQUENCE_ADAPTER_IPP
+#define BOOST_ASIO_DETAIL_IMPL_BUFFER_SEQUENCE_ADAPTER_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <robuffer.h>
+#include <windows.storage.streams.h>
+#include <wrl/implements.h>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class winrt_buffer_impl :
+ public Microsoft::WRL::RuntimeClass<
+ Microsoft::WRL::RuntimeClassFlags<
+ Microsoft::WRL::RuntimeClassType::WinRtClassicComMix>,
+ ABI::Windows::Storage::Streams::IBuffer,
+ Windows::Storage::Streams::IBufferByteAccess>
+{
+public:
+ explicit winrt_buffer_impl(const boost::asio::const_buffer& b)
+ {
+ bytes_ = const_cast<byte*>(boost::asio::buffer_cast<const byte*>(b));
+ length_ = boost::asio::buffer_size(b);
+ capacity_ = boost::asio::buffer_size(b);
+ }
+
+ explicit winrt_buffer_impl(const boost::asio::mutable_buffer& b)
+ {
+ bytes_ = const_cast<byte*>(boost::asio::buffer_cast<const byte*>(b));
+ length_ = 0;
+ capacity_ = boost::asio::buffer_size(b);
+ }
+
+ ~winrt_buffer_impl()
+ {
+ }
+
+ STDMETHODIMP Buffer(byte** value)
+ {
+ *value = bytes_;
+ return S_OK;
+ }
+
+ STDMETHODIMP get_Capacity(UINT32* value)
+ {
+ *value = capacity_;
+ return S_OK;
+ }
+
+ STDMETHODIMP get_Length(UINT32 *value)
+ {
+ *value = length_;
+ return S_OK;
+ }
+
+ STDMETHODIMP put_Length(UINT32 value)
+ {
+ if (value > capacity_)
+ return E_INVALIDARG;
+ length_ = value;
+ return S_OK;
+ }
+
+private:
+ byte* bytes_;
+ UINT32 length_;
+ UINT32 capacity_;
+};
+
+void buffer_sequence_adapter_base::init_native_buffer(
+ buffer_sequence_adapter_base::native_buffer_type& buf,
+ const boost::asio::mutable_buffer& buffer)
+{
+ std::memset(&buf, 0, sizeof(native_buffer_type));
+ Microsoft::WRL::ComPtr<IInspectable> insp
+ = Microsoft::WRL::Make<winrt_buffer_impl>(buffer);
+ buf = reinterpret_cast<Windows::Storage::Streams::IBuffer^>(insp.Get());
+}
+
+void buffer_sequence_adapter_base::init_native_buffer(
+ buffer_sequence_adapter_base::native_buffer_type& buf,
+ const boost::asio::const_buffer& buffer)
+{
+ std::memset(&buf, 0, sizeof(native_buffer_type));
+ Microsoft::WRL::ComPtr<IInspectable> insp
+ = Microsoft::WRL::Make<winrt_buffer_impl>(buffer);
+ Platform::Object^ buf_obj = reinterpret_cast<Platform::Object^>(insp.Get());
+ buf = reinterpret_cast<Windows::Storage::Streams::IBuffer^>(insp.Get());
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_BUFFER_SEQUENCE_ADAPTER_IPP
diff --git a/ext/patches/boost/asio/detail/impl/descriptor_ops.ipp b/ext/patches/boost/asio/detail/impl/descriptor_ops.ipp
new file mode 100644
index 0000000..84c93e3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/descriptor_ops.ipp
@@ -0,0 +1,453 @@
+//
+// detail/impl/descriptor_ops.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_DESCRIPTOR_OPS_IPP
+#define BOOST_ASIO_DETAIL_IMPL_DESCRIPTOR_OPS_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cerrno>
+#include <boost/asio/detail/descriptor_ops.hpp>
+#include <boost/asio/error.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+namespace descriptor_ops {
+
+int open(const char* path, int flags, boost::system::error_code& ec)
+{
+ errno = 0;
+ int result = error_wrapper(::open(path, flags), ec);
+ if (result >= 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+int close(int d, state_type& state, boost::system::error_code& ec)
+{
+ int result = 0;
+ if (d != -1)
+ {
+ errno = 0;
+ result = error_wrapper(::close(d), ec);
+
+ if (result != 0
+ && (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again))
+ {
+ // According to UNIX Network Programming Vol. 1, it is possible for
+ // close() to fail with EWOULDBLOCK under certain circumstances. What
+ // isn't clear is the state of the descriptor after this error. The one
+ // current OS where this behaviour is seen, Windows, says that the socket
+ // remains open. Therefore we'll put the descriptor back into blocking
+ // mode and have another attempt at closing it.
+#if defined(__SYMBIAN32__)
+ int flags = ::fcntl(d, F_GETFL, 0);
+ if (flags >= 0)
+ ::fcntl(d, F_SETFL, flags & ~O_NONBLOCK);
+#else // defined(__SYMBIAN32__)
+ ioctl_arg_type arg = 0;
+ ::ioctl(d, FIONBIO, &arg);
+#endif // defined(__SYMBIAN32__)
+ state &= ~non_blocking;
+
+ errno = 0;
+ result = error_wrapper(::close(d), ec);
+ }
+ }
+
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+bool set_user_non_blocking(int d, state_type& state,
+ bool value, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return false;
+ }
+
+ errno = 0;
+#if defined(__SYMBIAN32__)
+ int result = error_wrapper(::fcntl(d, F_GETFL, 0), ec);
+ if (result >= 0)
+ {
+ errno = 0;
+ int flag = (value ? (result | O_NONBLOCK) : (result & ~O_NONBLOCK));
+ result = error_wrapper(::fcntl(d, F_SETFL, flag), ec);
+ }
+#else // defined(__SYMBIAN32__)
+ ioctl_arg_type arg = (value ? 1 : 0);
+ int result = error_wrapper(::ioctl(d, FIONBIO, &arg), ec);
+#endif // defined(__SYMBIAN32__)
+
+ if (result >= 0)
+ {
+ ec = boost::system::error_code();
+ if (value)
+ state |= user_set_non_blocking;
+ else
+ {
+ // Clearing the user-set non-blocking mode always overrides any
+ // internally-set non-blocking flag. Any subsequent asynchronous
+ // operations will need to re-enable non-blocking I/O.
+ state &= ~(user_set_non_blocking | internal_non_blocking);
+ }
+ return true;
+ }
+
+ return false;
+}
+
+bool set_internal_non_blocking(int d, state_type& state,
+ bool value, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return false;
+ }
+
+ if (!value && (state & user_set_non_blocking))
+ {
+ // It does not make sense to clear the internal non-blocking flag if the
+ // user still wants non-blocking behaviour. Return an error and let the
+ // caller figure out whether to update the user-set non-blocking flag.
+ ec = boost::asio::error::invalid_argument;
+ return false;
+ }
+
+ errno = 0;
+#if defined(__SYMBIAN32__)
+ int result = error_wrapper(::fcntl(d, F_GETFL, 0), ec);
+ if (result >= 0)
+ {
+ errno = 0;
+ int flag = (value ? (result | O_NONBLOCK) : (result & ~O_NONBLOCK));
+ result = error_wrapper(::fcntl(d, F_SETFL, flag), ec);
+ }
+#else // defined(__SYMBIAN32__)
+ ioctl_arg_type arg = (value ? 1 : 0);
+ int result = error_wrapper(::ioctl(d, FIONBIO, &arg), ec);
+#endif // defined(__SYMBIAN32__)
+
+ if (result >= 0)
+ {
+ ec = boost::system::error_code();
+ if (value)
+ state |= internal_non_blocking;
+ else
+ state &= ~internal_non_blocking;
+ return true;
+ }
+
+ return false;
+}
+
+std::size_t sync_read(int d, state_type state, buf* bufs,
+ std::size_t count, bool all_empty, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // A request to read 0 bytes on a stream is a no-op.
+ if (all_empty)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ // Read some data.
+ for (;;)
+ {
+ // Try to complete the operation without blocking.
+ errno = 0;
+ signed_size_type bytes = error_wrapper(::readv(
+ d, bufs, static_cast<int>(count)), ec);
+
+ // Check if operation succeeded.
+ if (bytes > 0)
+ return bytes;
+
+ // Check for EOF.
+ if (bytes == 0)
+ {
+ ec = boost::asio::error::eof;
+ return 0;
+ }
+
+ // Operation failed.
+ if ((state & user_set_non_blocking)
+ || (ec != boost::asio::error::would_block
+ && ec != boost::asio::error::try_again))
+ return 0;
+
+ // Wait for descriptor to become ready.
+ if (descriptor_ops::poll_read(d, 0, ec) < 0)
+ return 0;
+ }
+}
+
+bool non_blocking_read(int d, buf* bufs, std::size_t count,
+ boost::system::error_code& ec, std::size_t& bytes_transferred)
+{
+ for (;;)
+ {
+ // Read some data.
+ errno = 0;
+ signed_size_type bytes = error_wrapper(::readv(
+ d, bufs, static_cast<int>(count)), ec);
+
+ // Check for end of stream.
+ if (bytes == 0)
+ {
+ ec = boost::asio::error::eof;
+ return true;
+ }
+
+ // Retry operation if interrupted by signal.
+ if (ec == boost::asio::error::interrupted)
+ continue;
+
+ // Check if we need to run the operation again.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ return false;
+
+ // Operation is complete.
+ if (bytes > 0)
+ {
+ ec = boost::system::error_code();
+ bytes_transferred = bytes;
+ }
+ else
+ bytes_transferred = 0;
+
+ return true;
+ }
+}
+
+std::size_t sync_write(int d, state_type state, const buf* bufs,
+ std::size_t count, bool all_empty, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // A request to write 0 bytes on a stream is a no-op.
+ if (all_empty)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ // Write some data.
+ for (;;)
+ {
+ // Try to complete the operation without blocking.
+ errno = 0;
+ signed_size_type bytes = error_wrapper(::writev(
+ d, bufs, static_cast<int>(count)), ec);
+
+ // Check if operation succeeded.
+ if (bytes > 0)
+ return bytes;
+
+ // Operation failed.
+ if ((state & user_set_non_blocking)
+ || (ec != boost::asio::error::would_block
+ && ec != boost::asio::error::try_again))
+ return 0;
+
+ // Wait for descriptor to become ready.
+ if (descriptor_ops::poll_write(d, 0, ec) < 0)
+ return 0;
+ }
+}
+
+bool non_blocking_write(int d, const buf* bufs, std::size_t count,
+ boost::system::error_code& ec, std::size_t& bytes_transferred)
+{
+ for (;;)
+ {
+ // Write some data.
+ errno = 0;
+ signed_size_type bytes = error_wrapper(::writev(
+ d, bufs, static_cast<int>(count)), ec);
+
+ // Retry operation if interrupted by signal.
+ if (ec == boost::asio::error::interrupted)
+ continue;
+
+ // Check if we need to run the operation again.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ return false;
+
+ // Operation is complete.
+ if (bytes >= 0)
+ {
+ ec = boost::system::error_code();
+ bytes_transferred = bytes;
+ }
+ else
+ bytes_transferred = 0;
+
+ return true;
+ }
+}
+
+int ioctl(int d, state_type& state, long cmd,
+ ioctl_arg_type* arg, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return -1;
+ }
+
+ errno = 0;
+ int result = error_wrapper(::ioctl(d, cmd, arg), ec);
+
+ if (result >= 0)
+ {
+ ec = boost::system::error_code();
+
+ // When updating the non-blocking mode we always perform the ioctl syscall,
+ // even if the flags would otherwise indicate that the descriptor is
+ // already in the correct state. This ensures that the underlying
+ // descriptor is put into the state that has been requested by the user. If
+ // the ioctl syscall was successful then we need to update the flags to
+ // match.
+ if (cmd == static_cast<long>(FIONBIO))
+ {
+ if (*arg)
+ {
+ state |= user_set_non_blocking;
+ }
+ else
+ {
+ // Clearing the non-blocking mode always overrides any internally-set
+ // non-blocking flag. Any subsequent asynchronous operations will need
+ // to re-enable non-blocking I/O.
+ state &= ~(user_set_non_blocking | internal_non_blocking);
+ }
+ }
+ }
+
+ return result;
+}
+
+int fcntl(int d, int cmd, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return -1;
+ }
+
+ errno = 0;
+ int result = error_wrapper(::fcntl(d, cmd), ec);
+ if (result != -1)
+ ec = boost::system::error_code();
+ return result;
+}
+
+int fcntl(int d, int cmd, long arg, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return -1;
+ }
+
+ errno = 0;
+ int result = error_wrapper(::fcntl(d, cmd, arg), ec);
+ if (result != -1)
+ ec = boost::system::error_code();
+ return result;
+}
+
+int poll_read(int d, state_type state, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return -1;
+ }
+
+ pollfd fds;
+ fds.fd = d;
+ fds.events = POLLIN;
+ fds.revents = 0;
+ int timeout = (state & user_set_non_blocking) ? 0 : -1;
+ errno = 0;
+ int result = error_wrapper(::poll(&fds, 1, timeout), ec);
+ if (result == 0)
+ ec = (state & user_set_non_blocking)
+ ? boost::asio::error::would_block : boost::system::error_code();
+ else if (result > 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+int poll_write(int d, state_type state, boost::system::error_code& ec)
+{
+ if (d == -1)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return -1;
+ }
+
+ pollfd fds;
+ fds.fd = d;
+ fds.events = POLLOUT;
+ fds.revents = 0;
+ int timeout = (state & user_set_non_blocking) ? 0 : -1;
+ errno = 0;
+ int result = error_wrapper(::poll(&fds, 1, timeout), ec);
+ if (result == 0)
+ ec = (state & user_set_non_blocking)
+ ? boost::asio::error::would_block : boost::system::error_code();
+ else if (result > 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+} // namespace descriptor_ops
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_DESCRIPTOR_OPS_IPP
diff --git a/ext/patches/boost/asio/detail/impl/dev_poll_reactor.hpp b/ext/patches/boost/asio/detail/impl/dev_poll_reactor.hpp
new file mode 100644
index 0000000..5be3037
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/dev_poll_reactor.hpp
@@ -0,0 +1,80 @@
+//
+// detail/impl/dev_poll_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_DEV_POLL_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_IMPL_DEV_POLL_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_DEV_POLL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Time_Traits>
+void dev_poll_reactor::add_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_add_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void dev_poll_reactor::remove_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_remove_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void dev_poll_reactor::schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ if (shutdown_)
+ {
+ io_service_.post_immediate_completion(op, false);
+ return;
+ }
+
+ bool earliest = queue.enqueue_timer(time, timer, op);
+ io_service_.work_started();
+ if (earliest)
+ interrupter_.interrupt();
+}
+
+template <typename Time_Traits>
+std::size_t dev_poll_reactor::cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ op_queue<operation> ops;
+ std::size_t n = queue.cancel_timer(timer, ops, max_cancelled);
+ lock.unlock();
+ io_service_.post_deferred_completions(ops);
+ return n;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_DEV_POLL)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_DEV_POLL_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/impl/dev_poll_reactor.ipp b/ext/patches/boost/asio/detail/impl/dev_poll_reactor.ipp
new file mode 100644
index 0000000..399c591
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/dev_poll_reactor.ipp
@@ -0,0 +1,447 @@
+//
+// detail/impl/dev_poll_reactor.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_DEV_POLL_REACTOR_IPP
+#define BOOST_ASIO_DETAIL_IMPL_DEV_POLL_REACTOR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_DEV_POLL)
+
+#include <boost/asio/detail/dev_poll_reactor.hpp>
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+dev_poll_reactor::dev_poll_reactor(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<dev_poll_reactor>(io_service),
+ io_service_(use_service<io_service_impl>(io_service)),
+ mutex_(),
+ dev_poll_fd_(do_dev_poll_create()),
+ interrupter_(),
+ shutdown_(false)
+{
+ // Add the interrupter's descriptor to /dev/poll.
+ ::pollfd ev = { 0, 0, 0 };
+ ev.fd = interrupter_.read_descriptor();
+ ev.events = POLLIN | POLLERR;
+ ev.revents = 0;
+ ::write(dev_poll_fd_, &ev, sizeof(ev));
+}
+
+dev_poll_reactor::~dev_poll_reactor()
+{
+ shutdown_service();
+ ::close(dev_poll_fd_);
+}
+
+void dev_poll_reactor::shutdown_service()
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ shutdown_ = true;
+ lock.unlock();
+
+ op_queue<operation> ops;
+
+ for (int i = 0; i < max_ops; ++i)
+ op_queue_[i].get_all_operations(ops);
+
+ timer_queues_.get_all_timers(ops);
+
+ io_service_.abandon_operations(ops);
+}
+
+// Helper class to re-register all descriptors with /dev/poll.
+class dev_poll_reactor::fork_helper
+{
+public:
+ fork_helper(dev_poll_reactor* reactor, short events)
+ : reactor_(reactor), events_(events)
+ {
+ }
+
+ bool set(int descriptor)
+ {
+ ::pollfd& ev = reactor_->add_pending_event_change(descriptor);
+ ev.events = events_;
+ return true;
+ }
+
+private:
+ dev_poll_reactor* reactor_;
+ short events_;
+};
+
+void dev_poll_reactor::fork_service(boost::asio::io_service::fork_event fork_ev)
+{
+ if (fork_ev == boost::asio::io_service::fork_child)
+ {
+ detail::mutex::scoped_lock lock(mutex_);
+
+ if (dev_poll_fd_ != -1)
+ ::close(dev_poll_fd_);
+ dev_poll_fd_ = -1;
+ dev_poll_fd_ = do_dev_poll_create();
+
+ interrupter_.recreate();
+
+ // Add the interrupter's descriptor to /dev/poll.
+ ::pollfd ev = { 0, 0, 0 };
+ ev.fd = interrupter_.read_descriptor();
+ ev.events = POLLIN | POLLERR;
+ ev.revents = 0;
+ ::write(dev_poll_fd_, &ev, sizeof(ev));
+
+ // Re-register all descriptors with /dev/poll. The changes will be written
+ // to the /dev/poll descriptor the next time the reactor is run.
+ op_queue<operation> ops;
+ fork_helper read_op_helper(this, POLLERR | POLLHUP | POLLIN);
+ op_queue_[read_op].get_descriptors(read_op_helper, ops);
+ fork_helper write_op_helper(this, POLLERR | POLLHUP | POLLOUT);
+ op_queue_[write_op].get_descriptors(write_op_helper, ops);
+ fork_helper except_op_helper(this, POLLERR | POLLHUP | POLLPRI);
+ op_queue_[except_op].get_descriptors(except_op_helper, ops);
+ interrupter_.interrupt();
+
+ // The ops op_queue will always be empty because the fork_helper's set()
+ // member function never returns false.
+ BOOST_ASIO_ASSERT(ops.empty());
+ }
+}
+
+void dev_poll_reactor::init_task()
+{
+ io_service_.init_task();
+}
+
+int dev_poll_reactor::register_descriptor(socket_type, per_descriptor_data&)
+{
+ return 0;
+}
+
+int dev_poll_reactor::register_internal_descriptor(int op_type,
+ socket_type descriptor, per_descriptor_data&, reactor_op* op)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ op_queue_[op_type].enqueue_operation(descriptor, op);
+ ::pollfd& ev = add_pending_event_change(descriptor);
+ ev.events = POLLERR | POLLHUP;
+ switch (op_type)
+ {
+ case read_op: ev.events |= POLLIN; break;
+ case write_op: ev.events |= POLLOUT; break;
+ case except_op: ev.events |= POLLPRI; break;
+ default: break;
+ }
+ interrupter_.interrupt();
+
+ return 0;
+}
+
+void dev_poll_reactor::move_descriptor(socket_type,
+ dev_poll_reactor::per_descriptor_data&,
+ dev_poll_reactor::per_descriptor_data&)
+{
+}
+
+void dev_poll_reactor::start_op(int op_type, socket_type descriptor,
+ dev_poll_reactor::per_descriptor_data&, reactor_op* op,
+ bool is_continuation, bool allow_speculative)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ if (shutdown_)
+ {
+ post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ if (allow_speculative)
+ {
+ if (op_type != read_op || !op_queue_[except_op].has_operation(descriptor))
+ {
+ if (!op_queue_[op_type].has_operation(descriptor))
+ {
+ if (op->perform())
+ {
+ lock.unlock();
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+ }
+ }
+ }
+
+ bool first = op_queue_[op_type].enqueue_operation(descriptor, op);
+ io_service_.work_started();
+ if (first)
+ {
+ ::pollfd& ev = add_pending_event_change(descriptor);
+ ev.events = POLLERR | POLLHUP;
+ if (op_type == read_op
+ || op_queue_[read_op].has_operation(descriptor))
+ ev.events |= POLLIN;
+ if (op_type == write_op
+ || op_queue_[write_op].has_operation(descriptor))
+ ev.events |= POLLOUT;
+ if (op_type == except_op
+ || op_queue_[except_op].has_operation(descriptor))
+ ev.events |= POLLPRI;
+ interrupter_.interrupt();
+ }
+}
+
+void dev_poll_reactor::cancel_ops(socket_type descriptor,
+ dev_poll_reactor::per_descriptor_data&)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ cancel_ops_unlocked(descriptor, boost::asio::error::operation_aborted);
+}
+
+void dev_poll_reactor::deregister_descriptor(socket_type descriptor,
+ dev_poll_reactor::per_descriptor_data&, bool)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ // Remove the descriptor from /dev/poll.
+ ::pollfd& ev = add_pending_event_change(descriptor);
+ ev.events = POLLREMOVE;
+ interrupter_.interrupt();
+
+ // Cancel any outstanding operations associated with the descriptor.
+ cancel_ops_unlocked(descriptor, boost::asio::error::operation_aborted);
+}
+
+void dev_poll_reactor::deregister_internal_descriptor(
+ socket_type descriptor, dev_poll_reactor::per_descriptor_data&)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ // Remove the descriptor from /dev/poll. Since this function is only called
+ // during a fork, we can apply the change immediately.
+ ::pollfd ev = { 0, 0, 0 };
+ ev.fd = descriptor;
+ ev.events = POLLREMOVE;
+ ev.revents = 0;
+ ::write(dev_poll_fd_, &ev, sizeof(ev));
+
+ // Destroy all operations associated with the descriptor.
+ op_queue<operation> ops;
+ boost::system::error_code ec;
+ for (int i = 0; i < max_ops; ++i)
+ op_queue_[i].cancel_operations(descriptor, ops, ec);
+}
+
+void dev_poll_reactor::run(bool block, op_queue<operation>& ops)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ // We can return immediately if there's no work to do and the reactor is
+ // not supposed to block.
+ if (!block && op_queue_[read_op].empty() && op_queue_[write_op].empty()
+ && op_queue_[except_op].empty() && timer_queues_.all_empty())
+ return;
+
+ // Write the pending event registration changes to the /dev/poll descriptor.
+ std::size_t events_size = sizeof(::pollfd) * pending_event_changes_.size();
+ if (events_size > 0)
+ {
+ errno = 0;
+ int result = ::write(dev_poll_fd_,
+ &pending_event_changes_[0], events_size);
+ if (result != static_cast<int>(events_size))
+ {
+ boost::system::error_code ec = boost::system::error_code(
+ errno, boost::asio::error::get_system_category());
+ for (std::size_t i = 0; i < pending_event_changes_.size(); ++i)
+ {
+ int descriptor = pending_event_changes_[i].fd;
+ for (int j = 0; j < max_ops; ++j)
+ op_queue_[j].cancel_operations(descriptor, ops, ec);
+ }
+ }
+ pending_event_changes_.clear();
+ pending_event_change_index_.clear();
+ }
+
+ int timeout = block ? get_timeout() : 0;
+ lock.unlock();
+
+ // Block on the /dev/poll descriptor.
+ ::pollfd events[128] = { { 0, 0, 0 } };
+ ::dvpoll dp = { 0, 0, 0 };
+ dp.dp_fds = events;
+ dp.dp_nfds = 128;
+ dp.dp_timeout = timeout;
+ int num_events = ::ioctl(dev_poll_fd_, DP_POLL, &dp);
+
+ lock.lock();
+
+ // Dispatch the waiting events.
+ for (int i = 0; i < num_events; ++i)
+ {
+ int descriptor = events[i].fd;
+ if (descriptor == interrupter_.read_descriptor())
+ {
+ interrupter_.reset();
+ }
+ else
+ {
+ bool more_reads = false;
+ bool more_writes = false;
+ bool more_except = false;
+
+ // Exception operations must be processed first to ensure that any
+ // out-of-band data is read before normal data.
+ if (events[i].events & (POLLPRI | POLLERR | POLLHUP))
+ more_except =
+ op_queue_[except_op].perform_operations(descriptor, ops);
+ else
+ more_except = op_queue_[except_op].has_operation(descriptor);
+
+ if (events[i].events & (POLLIN | POLLERR | POLLHUP))
+ more_reads = op_queue_[read_op].perform_operations(descriptor, ops);
+ else
+ more_reads = op_queue_[read_op].has_operation(descriptor);
+
+ if (events[i].events & (POLLOUT | POLLERR | POLLHUP))
+ more_writes = op_queue_[write_op].perform_operations(descriptor, ops);
+ else
+ more_writes = op_queue_[write_op].has_operation(descriptor);
+
+ if ((events[i].events & (POLLERR | POLLHUP)) != 0
+ && !more_except && !more_reads && !more_writes)
+ {
+ // If we have an event and no operations associated with the
+ // descriptor then we need to delete the descriptor from /dev/poll.
+ // The poll operation can produce POLLHUP or POLLERR events when there
+ // is no operation pending, so if we do not remove the descriptor we
+ // can end up in a tight polling loop.
+ ::pollfd ev = { 0, 0, 0 };
+ ev.fd = descriptor;
+ ev.events = POLLREMOVE;
+ ev.revents = 0;
+ ::write(dev_poll_fd_, &ev, sizeof(ev));
+ }
+ else
+ {
+ ::pollfd ev = { 0, 0, 0 };
+ ev.fd = descriptor;
+ ev.events = POLLERR | POLLHUP;
+ if (more_reads)
+ ev.events |= POLLIN;
+ if (more_writes)
+ ev.events |= POLLOUT;
+ if (more_except)
+ ev.events |= POLLPRI;
+ ev.revents = 0;
+ int result = ::write(dev_poll_fd_, &ev, sizeof(ev));
+ if (result != sizeof(ev))
+ {
+ boost::system::error_code ec(errno,
+ boost::asio::error::get_system_category());
+ for (int j = 0; j < max_ops; ++j)
+ op_queue_[j].cancel_operations(descriptor, ops, ec);
+ }
+ }
+ }
+ }
+ timer_queues_.get_ready_timers(ops);
+}
+
+void dev_poll_reactor::interrupt()
+{
+ interrupter_.interrupt();
+}
+
+int dev_poll_reactor::do_dev_poll_create()
+{
+ int fd = ::open("/dev/poll", O_RDWR);
+ if (fd == -1)
+ {
+ boost::system::error_code ec(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "/dev/poll");
+ }
+ return fd;
+}
+
+void dev_poll_reactor::do_add_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.insert(&queue);
+}
+
+void dev_poll_reactor::do_remove_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.erase(&queue);
+}
+
+int dev_poll_reactor::get_timeout()
+{
+ // By default we will wait no longer than 5 minutes. This will ensure that
+ // any changes to the system clock are detected after no longer than this.
+ return timer_queues_.wait_duration_msec(5 * 60 * 1000);
+}
+
+void dev_poll_reactor::cancel_ops_unlocked(socket_type descriptor,
+ const boost::system::error_code& ec)
+{
+ bool need_interrupt = false;
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ need_interrupt = op_queue_[i].cancel_operations(
+ descriptor, ops, ec) || need_interrupt;
+ io_service_.post_deferred_completions(ops);
+ if (need_interrupt)
+ interrupter_.interrupt();
+}
+
+::pollfd& dev_poll_reactor::add_pending_event_change(int descriptor)
+{
+ hash_map<int, std::size_t>::iterator iter
+ = pending_event_change_index_.find(descriptor);
+ if (iter == pending_event_change_index_.end())
+ {
+ std::size_t index = pending_event_changes_.size();
+ pending_event_changes_.reserve(pending_event_changes_.size() + 1);
+ pending_event_change_index_.insert(std::make_pair(descriptor, index));
+ pending_event_changes_.push_back(::pollfd());
+ pending_event_changes_[index].fd = descriptor;
+ pending_event_changes_[index].revents = 0;
+ return pending_event_changes_[index];
+ }
+ else
+ {
+ return pending_event_changes_[iter->second];
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_DEV_POLL)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_DEV_POLL_REACTOR_IPP
diff --git a/ext/patches/boost/asio/detail/impl/epoll_reactor.hpp b/ext/patches/boost/asio/detail/impl/epoll_reactor.hpp
new file mode 100644
index 0000000..a05b547
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/epoll_reactor.hpp
@@ -0,0 +1,78 @@
+//
+// detail/impl/epoll_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_EPOLL_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_IMPL_EPOLL_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#if defined(BOOST_ASIO_HAS_EPOLL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Time_Traits>
+void epoll_reactor::add_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_add_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void epoll_reactor::remove_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_remove_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void epoll_reactor::schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op)
+{
+ mutex::scoped_lock lock(mutex_);
+
+ if (shutdown_)
+ {
+ io_service_.post_immediate_completion(op, false);
+ return;
+ }
+
+ bool earliest = queue.enqueue_timer(time, timer, op);
+ io_service_.work_started();
+ if (earliest)
+ update_timeout();
+}
+
+template <typename Time_Traits>
+std::size_t epoll_reactor::cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled)
+{
+ mutex::scoped_lock lock(mutex_);
+ op_queue<operation> ops;
+ std::size_t n = queue.cancel_timer(timer, ops, max_cancelled);
+ lock.unlock();
+ io_service_.post_deferred_completions(ops);
+ return n;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_EPOLL)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_EPOLL_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/impl/epoll_reactor.ipp b/ext/patches/boost/asio/detail/impl/epoll_reactor.ipp
new file mode 100644
index 0000000..0a2a273
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/epoll_reactor.ipp
@@ -0,0 +1,664 @@
+//
+// detail/impl/epoll_reactor.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_EPOLL_REACTOR_IPP
+#define BOOST_ASIO_DETAIL_IMPL_EPOLL_REACTOR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_EPOLL)
+
+#include <cstddef>
+#include <sys/epoll.h>
+#include <boost/asio/detail/epoll_reactor.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+# include <sys/timerfd.h>
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+epoll_reactor::epoll_reactor(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<epoll_reactor>(io_service),
+ io_service_(use_service<io_service_impl>(io_service)),
+ mutex_(),
+ interrupter_(),
+ epoll_fd_(do_epoll_create()),
+ timer_fd_(do_timerfd_create()),
+ shutdown_(false)
+{
+ // Add the interrupter's descriptor to epoll.
+ epoll_event ev = { 0, { 0 } };
+ ev.events = EPOLLIN | EPOLLERR | EPOLLET;
+ ev.data.ptr = &interrupter_;
+ epoll_ctl(epoll_fd_, EPOLL_CTL_ADD, interrupter_.read_descriptor(), &ev);
+ interrupter_.interrupt();
+
+ // Add the timer descriptor to epoll.
+ if (timer_fd_ != -1)
+ {
+ ev.events = EPOLLIN | EPOLLERR;
+ ev.data.ptr = &timer_fd_;
+ epoll_ctl(epoll_fd_, EPOLL_CTL_ADD, timer_fd_, &ev);
+ }
+}
+
+epoll_reactor::~epoll_reactor()
+{
+ if (epoll_fd_ != -1)
+ close(epoll_fd_);
+ if (timer_fd_ != -1)
+ close(timer_fd_);
+}
+
+void epoll_reactor::shutdown_service()
+{
+ mutex::scoped_lock lock(mutex_);
+ shutdown_ = true;
+ lock.unlock();
+
+ op_queue<operation> ops;
+
+ while (descriptor_state* state = registered_descriptors_.first())
+ {
+ for (int i = 0; i < max_ops; ++i)
+ ops.push(state->op_queue_[i]);
+ state->shutdown_ = true;
+ registered_descriptors_.free(state);
+ }
+
+ timer_queues_.get_all_timers(ops);
+
+ io_service_.abandon_operations(ops);
+}
+
+void epoll_reactor::fork_service(boost::asio::io_service::fork_event fork_ev)
+{
+ if (fork_ev == boost::asio::io_service::fork_child)
+ {
+ if (epoll_fd_ != -1)
+ ::close(epoll_fd_);
+ epoll_fd_ = -1;
+ epoll_fd_ = do_epoll_create();
+
+ if (timer_fd_ != -1)
+ ::close(timer_fd_);
+ timer_fd_ = -1;
+ timer_fd_ = do_timerfd_create();
+
+ interrupter_.recreate();
+
+ // Add the interrupter's descriptor to epoll.
+ epoll_event ev = { 0, { 0 } };
+ ev.events = EPOLLIN | EPOLLERR | EPOLLET;
+ ev.data.ptr = &interrupter_;
+ epoll_ctl(epoll_fd_, EPOLL_CTL_ADD, interrupter_.read_descriptor(), &ev);
+ interrupter_.interrupt();
+
+ // Add the timer descriptor to epoll.
+ if (timer_fd_ != -1)
+ {
+ ev.events = EPOLLIN | EPOLLERR;
+ ev.data.ptr = &timer_fd_;
+ epoll_ctl(epoll_fd_, EPOLL_CTL_ADD, timer_fd_, &ev);
+ }
+
+ update_timeout();
+
+ // Re-register all descriptors with epoll.
+ mutex::scoped_lock descriptors_lock(registered_descriptors_mutex_);
+ for (descriptor_state* state = registered_descriptors_.first();
+ state != 0; state = state->next_)
+ {
+ ev.events = state->registered_events_;
+ ev.data.ptr = state;
+ int result = epoll_ctl(epoll_fd_, EPOLL_CTL_ADD, state->descriptor_, &ev);
+ if (result != 0)
+ {
+ boost::system::error_code ec(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "epoll re-registration");
+ }
+ }
+ }
+}
+
+void epoll_reactor::init_task()
+{
+ io_service_.init_task();
+}
+
+int epoll_reactor::register_descriptor(socket_type descriptor,
+ epoll_reactor::per_descriptor_data& descriptor_data)
+{
+ descriptor_data = allocate_descriptor_state();
+
+ {
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ descriptor_data->reactor_ = this;
+ descriptor_data->descriptor_ = descriptor;
+ descriptor_data->shutdown_ = false;
+ }
+
+ epoll_event ev = { 0, { 0 } };
+ ev.events = EPOLLIN | EPOLLERR | EPOLLHUP | EPOLLPRI | EPOLLET;
+ descriptor_data->registered_events_ = ev.events;
+ ev.data.ptr = descriptor_data;
+ int result = epoll_ctl(epoll_fd_, EPOLL_CTL_ADD, descriptor, &ev);
+ if (result != 0)
+ return errno;
+
+ return 0;
+}
+
+int epoll_reactor::register_internal_descriptor(
+ int op_type, socket_type descriptor,
+ epoll_reactor::per_descriptor_data& descriptor_data, reactor_op* op)
+{
+ descriptor_data = allocate_descriptor_state();
+
+ {
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ descriptor_data->reactor_ = this;
+ descriptor_data->descriptor_ = descriptor;
+ descriptor_data->shutdown_ = false;
+ descriptor_data->op_queue_[op_type].push(op);
+ }
+
+ epoll_event ev = { 0, { 0 } };
+ ev.events = EPOLLIN | EPOLLERR | EPOLLHUP | EPOLLPRI | EPOLLET;
+ descriptor_data->registered_events_ = ev.events;
+ ev.data.ptr = descriptor_data;
+ int result = epoll_ctl(epoll_fd_, EPOLL_CTL_ADD, descriptor, &ev);
+ if (result != 0)
+ return errno;
+
+ return 0;
+}
+
+void epoll_reactor::move_descriptor(socket_type,
+ epoll_reactor::per_descriptor_data& target_descriptor_data,
+ epoll_reactor::per_descriptor_data& source_descriptor_data)
+{
+ target_descriptor_data = source_descriptor_data;
+ source_descriptor_data = 0;
+}
+
+void epoll_reactor::start_op(int op_type, socket_type descriptor,
+ epoll_reactor::per_descriptor_data& descriptor_data, reactor_op* op,
+ bool is_continuation, bool allow_speculative)
+{
+ if (!descriptor_data)
+ {
+ op->ec_ = boost::asio::error::bad_descriptor;
+ post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ if (descriptor_data->shutdown_)
+ {
+ post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ if (descriptor_data->op_queue_[op_type].empty())
+ {
+ if (allow_speculative
+ && (op_type != read_op
+ || descriptor_data->op_queue_[except_op].empty()))
+ {
+ if (op->perform())
+ {
+ descriptor_lock.unlock();
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ if (op_type == write_op)
+ {
+ if ((descriptor_data->registered_events_ & EPOLLOUT) == 0)
+ {
+ epoll_event ev = { 0, { 0 } };
+ ev.events = descriptor_data->registered_events_ | EPOLLOUT;
+ ev.data.ptr = descriptor_data;
+ if (epoll_ctl(epoll_fd_, EPOLL_CTL_MOD, descriptor, &ev) == 0)
+ {
+ descriptor_data->registered_events_ |= ev.events;
+ }
+ else
+ {
+ op->ec_ = boost::system::error_code(errno,
+ boost::asio::error::get_system_category());
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+ }
+ }
+ }
+ else
+ {
+ if (op_type == write_op)
+ {
+ descriptor_data->registered_events_ |= EPOLLOUT;
+ }
+
+ epoll_event ev = { 0, { 0 } };
+ ev.events = descriptor_data->registered_events_;
+ ev.data.ptr = descriptor_data;
+ epoll_ctl(epoll_fd_, EPOLL_CTL_MOD, descriptor, &ev);
+ }
+ }
+
+ descriptor_data->op_queue_[op_type].push(op);
+ io_service_.work_started();
+}
+
+void epoll_reactor::cancel_ops(socket_type,
+ epoll_reactor::per_descriptor_data& descriptor_data)
+{
+ if (!descriptor_data)
+ return;
+
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ {
+ while (reactor_op* op = descriptor_data->op_queue_[i].front())
+ {
+ op->ec_ = boost::asio::error::operation_aborted;
+ descriptor_data->op_queue_[i].pop();
+ ops.push(op);
+ }
+ }
+
+ descriptor_lock.unlock();
+
+ io_service_.post_deferred_completions(ops);
+}
+
+void epoll_reactor::deregister_descriptor(socket_type descriptor,
+ epoll_reactor::per_descriptor_data& descriptor_data, bool closing)
+{
+ if (!descriptor_data)
+ return;
+
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ if (!descriptor_data->shutdown_)
+ {
+ if (closing)
+ {
+ // The descriptor will be automatically removed from the epoll set when
+ // it is closed.
+ }
+ else
+ {
+ epoll_event ev = { 0, { 0 } };
+ epoll_ctl(epoll_fd_, EPOLL_CTL_DEL, descriptor, &ev);
+ }
+
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ {
+ while (reactor_op* op = descriptor_data->op_queue_[i].front())
+ {
+ op->ec_ = boost::asio::error::operation_aborted;
+ descriptor_data->op_queue_[i].pop();
+ ops.push(op);
+ }
+ }
+
+ descriptor_data->descriptor_ = -1;
+ descriptor_data->shutdown_ = true;
+
+ descriptor_lock.unlock();
+
+ free_descriptor_state(descriptor_data);
+ descriptor_data = 0;
+
+ io_service_.post_deferred_completions(ops);
+ }
+}
+
+void epoll_reactor::deregister_internal_descriptor(socket_type descriptor,
+ epoll_reactor::per_descriptor_data& descriptor_data)
+{
+ if (!descriptor_data)
+ return;
+
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ if (!descriptor_data->shutdown_)
+ {
+ epoll_event ev = { 0, { 0 } };
+ epoll_ctl(epoll_fd_, EPOLL_CTL_DEL, descriptor, &ev);
+
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ ops.push(descriptor_data->op_queue_[i]);
+
+ descriptor_data->descriptor_ = -1;
+ descriptor_data->shutdown_ = true;
+
+ descriptor_lock.unlock();
+
+ free_descriptor_state(descriptor_data);
+ descriptor_data = 0;
+ }
+}
+
+void epoll_reactor::run(bool block, op_queue<operation>& ops)
+{
+ // This code relies on the fact that the task_io_service queues the reactor
+ // task behind all descriptor operations generated by this function. This
+ // means, that by the time we reach this point, any previously returned
+ // descriptor operations have already been dequeued. Therefore it is now safe
+ // for us to reuse and return them for the task_io_service to queue again.
+
+ // Calculate a timeout only if timerfd is not used.
+ int timeout;
+ if (timer_fd_ != -1)
+ timeout = block ? -1 : 0;
+ else
+ {
+ mutex::scoped_lock lock(mutex_);
+ timeout = block ? get_timeout() : 0;
+ }
+
+ // Block on the epoll descriptor.
+ epoll_event events[128];
+ int num_events = epoll_wait(epoll_fd_, events, 128, timeout);
+
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+ bool check_timers = (timer_fd_ == -1);
+#else // defined(BOOST_ASIO_HAS_TIMERFD)
+ bool check_timers = true;
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+
+ // Dispatch the waiting events.
+ for (int i = 0; i < num_events; ++i)
+ {
+ void* ptr = events[i].data.ptr;
+ if (ptr == &interrupter_)
+ {
+ // No need to reset the interrupter since we're leaving the descriptor
+ // in a ready-to-read state and relying on edge-triggered notifications
+ // to make it so that we only get woken up when the descriptor's epoll
+ // registration is updated.
+
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+ if (timer_fd_ == -1)
+ check_timers = true;
+#else // defined(BOOST_ASIO_HAS_TIMERFD)
+ check_timers = true;
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+ }
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+ else if (ptr == &timer_fd_)
+ {
+ check_timers = true;
+ }
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+ else
+ {
+ // The descriptor operation doesn't count as work in and of itself, so we
+ // don't call work_started() here. This still allows the io_service to
+ // stop if the only remaining operations are descriptor operations.
+ descriptor_state* descriptor_data = static_cast<descriptor_state*>(ptr);
+ descriptor_data->set_ready_events(events[i].events);
+ ops.push(descriptor_data);
+ }
+ }
+
+ if (check_timers)
+ {
+ mutex::scoped_lock common_lock(mutex_);
+ timer_queues_.get_ready_timers(ops);
+
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+ if (timer_fd_ != -1)
+ {
+ itimerspec new_timeout;
+ itimerspec old_timeout;
+ int flags = get_timeout(new_timeout);
+ timerfd_settime(timer_fd_, flags, &new_timeout, &old_timeout);
+ }
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+ }
+}
+
+void epoll_reactor::interrupt()
+{
+ epoll_event ev = { 0, { 0 } };
+ ev.events = EPOLLIN | EPOLLERR | EPOLLET;
+ ev.data.ptr = &interrupter_;
+ epoll_ctl(epoll_fd_, EPOLL_CTL_MOD, interrupter_.read_descriptor(), &ev);
+}
+
+int epoll_reactor::do_epoll_create()
+{
+#if defined(EPOLL_CLOEXEC)
+ int fd = epoll_create1(EPOLL_CLOEXEC);
+#else // defined(EPOLL_CLOEXEC)
+ int fd = -1;
+ errno = EINVAL;
+#endif // defined(EPOLL_CLOEXEC)
+
+ if (fd == -1 && (errno == EINVAL || errno == ENOSYS))
+ {
+ fd = epoll_create(epoll_size);
+ if (fd != -1)
+ ::fcntl(fd, F_SETFD, FD_CLOEXEC);
+ }
+
+ if (fd == -1)
+ {
+ boost::system::error_code ec(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "epoll");
+ }
+
+ return fd;
+}
+
+int epoll_reactor::do_timerfd_create()
+{
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+# if defined(TFD_CLOEXEC)
+ int fd = timerfd_create(CLOCK_MONOTONIC, TFD_CLOEXEC);
+# else // defined(TFD_CLOEXEC)
+ int fd = -1;
+ errno = EINVAL;
+# endif // defined(TFD_CLOEXEC)
+
+ if (fd == -1 && errno == EINVAL)
+ {
+ fd = timerfd_create(CLOCK_MONOTONIC, 0);
+ if (fd != -1)
+ ::fcntl(fd, F_SETFD, FD_CLOEXEC);
+ }
+
+ return fd;
+#else // defined(BOOST_ASIO_HAS_TIMERFD)
+ return -1;
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+}
+
+epoll_reactor::descriptor_state* epoll_reactor::allocate_descriptor_state()
+{
+ mutex::scoped_lock descriptors_lock(registered_descriptors_mutex_);
+ return registered_descriptors_.alloc();
+}
+
+void epoll_reactor::free_descriptor_state(epoll_reactor::descriptor_state* s)
+{
+ mutex::scoped_lock descriptors_lock(registered_descriptors_mutex_);
+ registered_descriptors_.free(s);
+}
+
+void epoll_reactor::do_add_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.insert(&queue);
+}
+
+void epoll_reactor::do_remove_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.erase(&queue);
+}
+
+void epoll_reactor::update_timeout()
+{
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+ if (timer_fd_ != -1)
+ {
+ itimerspec new_timeout;
+ itimerspec old_timeout;
+ int flags = get_timeout(new_timeout);
+ timerfd_settime(timer_fd_, flags, &new_timeout, &old_timeout);
+ return;
+ }
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+ interrupt();
+}
+
+int epoll_reactor::get_timeout()
+{
+ // By default we will wait no longer than 5 minutes. This will ensure that
+ // any changes to the system clock are detected after no longer than this.
+ return timer_queues_.wait_duration_msec(5 * 60 * 1000);
+}
+
+#if defined(BOOST_ASIO_HAS_TIMERFD)
+int epoll_reactor::get_timeout(itimerspec& ts)
+{
+ ts.it_interval.tv_sec = 0;
+ ts.it_interval.tv_nsec = 0;
+
+ long usec = timer_queues_.wait_duration_usec(5 * 60 * 1000 * 1000);
+ ts.it_value.tv_sec = usec / 1000000;
+ ts.it_value.tv_nsec = usec ? (usec % 1000000) * 1000 : 1;
+
+ return usec ? 0 : TFD_TIMER_ABSTIME;
+}
+#endif // defined(BOOST_ASIO_HAS_TIMERFD)
+
+struct epoll_reactor::perform_io_cleanup_on_block_exit
+{
+ explicit perform_io_cleanup_on_block_exit(epoll_reactor* r)
+ : reactor_(r), first_op_(0)
+ {
+ }
+
+ ~perform_io_cleanup_on_block_exit()
+ {
+ if (first_op_)
+ {
+ // Post the remaining completed operations for invocation.
+ if (!ops_.empty())
+ reactor_->io_service_.post_deferred_completions(ops_);
+
+ // A user-initiated operation has completed, but there's no need to
+ // explicitly call work_finished() here. Instead, we'll take advantage of
+ // the fact that the task_io_service will call work_finished() once we
+ // return.
+ }
+ else
+ {
+ // No user-initiated operations have completed, so we need to compensate
+ // for the work_finished() call that the task_io_service will make once
+ // this operation returns.
+ reactor_->io_service_.work_started();
+ }
+ }
+
+ epoll_reactor* reactor_;
+ op_queue<operation> ops_;
+ operation* first_op_;
+};
+
+epoll_reactor::descriptor_state::descriptor_state()
+ : operation(&epoll_reactor::descriptor_state::do_complete)
+{
+}
+
+operation* epoll_reactor::descriptor_state::perform_io(uint32_t events)
+{
+ mutex_.lock();
+ perform_io_cleanup_on_block_exit io_cleanup(reactor_);
+ mutex::scoped_lock descriptor_lock(mutex_, mutex::scoped_lock::adopt_lock);
+
+ // Exception operations must be processed first to ensure that any
+ // out-of-band data is read before normal data.
+ static const int flag[max_ops] = { EPOLLIN, EPOLLOUT, EPOLLPRI };
+ for (int j = max_ops - 1; j >= 0; --j)
+ {
+ if (events & (flag[j] | EPOLLERR | EPOLLHUP))
+ {
+ while (reactor_op* op = op_queue_[j].front())
+ {
+ if (op->perform())
+ {
+ op_queue_[j].pop();
+ io_cleanup.ops_.push(op);
+ }
+ else
+ break;
+ }
+ }
+ }
+
+ // The first operation will be returned for completion now. The others will
+ // be posted for later by the io_cleanup object's destructor.
+ io_cleanup.first_op_ = io_cleanup.ops_.front();
+ io_cleanup.ops_.pop();
+ return io_cleanup.first_op_;
+}
+
+void epoll_reactor::descriptor_state::do_complete(
+ io_service_impl* owner, operation* base,
+ const boost::system::error_code& ec, std::size_t bytes_transferred)
+{
+ if (owner)
+ {
+ descriptor_state* descriptor_data = static_cast<descriptor_state*>(base);
+ uint32_t events = static_cast<uint32_t>(bytes_transferred);
+ if (operation* op = descriptor_data->perform_io(events))
+ {
+ op->complete(*owner, ec, 0);
+ }
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_EPOLL)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_EPOLL_REACTOR_IPP
diff --git a/ext/patches/boost/asio/detail/impl/eventfd_select_interrupter.ipp b/ext/patches/boost/asio/detail/impl/eventfd_select_interrupter.ipp
new file mode 100644
index 0000000..fef1c0a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/eventfd_select_interrupter.ipp
@@ -0,0 +1,167 @@
+//
+// detail/impl/eventfd_select_interrupter.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Roelof Naude (roelof.naude at gmail dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_EVENTFD_SELECT_INTERRUPTER_IPP
+#define BOOST_ASIO_DETAIL_IMPL_EVENTFD_SELECT_INTERRUPTER_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_EVENTFD)
+
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <fcntl.h>
+#if __GLIBC__ == 2 && __GLIBC_MINOR__ < 8
+# include <asm/unistd.h>
+#else // __GLIBC__ == 2 && __GLIBC_MINOR__ < 8
+# include <sys/eventfd.h>
+#endif // __GLIBC__ == 2 && __GLIBC_MINOR__ < 8
+#include <boost/asio/detail/cstdint.hpp>
+#include <boost/asio/detail/eventfd_select_interrupter.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+eventfd_select_interrupter::eventfd_select_interrupter()
+{
+ open_descriptors();
+}
+
+void eventfd_select_interrupter::open_descriptors()
+{
+#if __GLIBC__ == 2 && __GLIBC_MINOR__ < 8
+ write_descriptor_ = read_descriptor_ = syscall(__NR_eventfd, 0);
+ if (read_descriptor_ != -1)
+ {
+ ::fcntl(read_descriptor_, F_SETFL, O_NONBLOCK);
+ ::fcntl(read_descriptor_, F_SETFD, FD_CLOEXEC);
+ }
+#else // __GLIBC__ == 2 && __GLIBC_MINOR__ < 8
+# if defined(EFD_CLOEXEC) && defined(EFD_NONBLOCK)
+ write_descriptor_ = read_descriptor_ =
+ ::eventfd(0, EFD_CLOEXEC | EFD_NONBLOCK);
+# else // defined(EFD_CLOEXEC) && defined(EFD_NONBLOCK)
+ errno = EINVAL;
+ write_descriptor_ = read_descriptor_ = -1;
+# endif // defined(EFD_CLOEXEC) && defined(EFD_NONBLOCK)
+ if (read_descriptor_ == -1 && errno == EINVAL)
+ {
+ write_descriptor_ = read_descriptor_ = ::eventfd(0, 0);
+ if (read_descriptor_ != -1)
+ {
+ ::fcntl(read_descriptor_, F_SETFL, O_NONBLOCK);
+ ::fcntl(read_descriptor_, F_SETFD, FD_CLOEXEC);
+ }
+ }
+#endif // __GLIBC__ == 2 && __GLIBC_MINOR__ < 8
+
+ if (read_descriptor_ == -1)
+ {
+ int pipe_fds[2];
+ if (pipe(pipe_fds) == 0)
+ {
+ read_descriptor_ = pipe_fds[0];
+ ::fcntl(read_descriptor_, F_SETFL, O_NONBLOCK);
+ ::fcntl(read_descriptor_, F_SETFD, FD_CLOEXEC);
+ write_descriptor_ = pipe_fds[1];
+ ::fcntl(write_descriptor_, F_SETFL, O_NONBLOCK);
+ ::fcntl(write_descriptor_, F_SETFD, FD_CLOEXEC);
+ }
+ else
+ {
+ boost::system::error_code ec(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "eventfd_select_interrupter");
+ }
+ }
+}
+
+eventfd_select_interrupter::~eventfd_select_interrupter()
+{
+ close_descriptors();
+}
+
+void eventfd_select_interrupter::close_descriptors()
+{
+ if (write_descriptor_ != -1 && write_descriptor_ != read_descriptor_)
+ ::close(write_descriptor_);
+ if (read_descriptor_ != -1)
+ ::close(read_descriptor_);
+}
+
+void eventfd_select_interrupter::recreate()
+{
+ close_descriptors();
+
+ write_descriptor_ = -1;
+ read_descriptor_ = -1;
+
+ open_descriptors();
+}
+
+void eventfd_select_interrupter::interrupt()
+{
+ uint64_t counter(1UL);
+ int result = ::write(write_descriptor_, &counter, sizeof(uint64_t));
+ (void)result;
+}
+
+bool eventfd_select_interrupter::reset()
+{
+ if (write_descriptor_ == read_descriptor_)
+ {
+ for (;;)
+ {
+ // Only perform one read. The kernel maintains an atomic counter.
+ uint64_t counter(0);
+ errno = 0;
+ int bytes_read = ::read(read_descriptor_, &counter, sizeof(uint64_t));
+ if (bytes_read < 0 && errno == EINTR)
+ continue;
+ bool was_interrupted = (bytes_read > 0);
+ return was_interrupted;
+ }
+ }
+ else
+ {
+ for (;;)
+ {
+ // Clear all data from the pipe.
+ char data[1024];
+ int bytes_read = ::read(read_descriptor_, data, sizeof(data));
+ if (bytes_read < 0 && errno == EINTR)
+ continue;
+ bool was_interrupted = (bytes_read > 0);
+ while (bytes_read == sizeof(data))
+ bytes_read = ::read(read_descriptor_, data, sizeof(data));
+ return was_interrupted;
+ }
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_EVENTFD)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_EVENTFD_SELECT_INTERRUPTER_IPP
diff --git a/ext/patches/boost/asio/detail/impl/handler_tracking.ipp b/ext/patches/boost/asio/detail/impl/handler_tracking.ipp
new file mode 100644
index 0000000..56e874a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/handler_tracking.ipp
@@ -0,0 +1,307 @@
+//
+// detail/impl/handler_tracking.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_HANDLER_TRACKING_IPP
+#define BOOST_ASIO_DETAIL_IMPL_HANDLER_TRACKING_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_ENABLE_HANDLER_TRACKING)
+
+#include <cstdarg>
+#include <cstdio>
+#include <boost/asio/detail/handler_tracking.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+# include <boost/asio/time_traits.hpp>
+#else // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+# if defined(BOOST_ASIO_HAS_STD_CHRONO)
+# include <chrono>
+# elif defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+# include <boost/chrono/system_clocks.hpp>
+# endif
+# include <boost/asio/detail/chrono_time_traits.hpp>
+# include <boost/asio/wait_traits.hpp>
+#endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+
+#if !defined(BOOST_ASIO_WINDOWS)
+# include <unistd.h>
+#endif // !defined(BOOST_ASIO_WINDOWS)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct handler_tracking_timestamp
+{
+ uint64_t seconds;
+ uint64_t microseconds;
+
+ handler_tracking_timestamp()
+ {
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ boost::posix_time::ptime epoch(boost::gregorian::date(1970, 1, 1));
+ boost::posix_time::time_duration now =
+ boost::posix_time::microsec_clock::universal_time() - epoch;
+#elif defined(BOOST_ASIO_HAS_STD_CHRONO)
+ typedef chrono_time_traits<std::chrono::system_clock,
+ boost::asio::wait_traits<std::chrono::system_clock> > traits_helper;
+ traits_helper::posix_time_duration now(
+ std::chrono::system_clock::now().time_since_epoch());
+#elif defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+ typedef chrono_time_traits<boost::chrono::system_clock,
+ boost::asio::wait_traits<boost::chrono::system_clock> > traits_helper;
+ traits_helper::posix_time_duration now(
+ boost::chrono::system_clock::now().time_since_epoch());
+#endif
+ seconds = static_cast<uint64_t>(now.total_seconds());
+ microseconds = static_cast<uint64_t>(now.total_microseconds() % 1000000);
+ }
+};
+
+struct handler_tracking::tracking_state
+{
+ static_mutex mutex_;
+ uint64_t next_id_;
+ tss_ptr<completion>* current_completion_;
+};
+
+handler_tracking::tracking_state* handler_tracking::get_state()
+{
+ static tracking_state state = { BOOST_ASIO_STATIC_MUTEX_INIT, 1, 0 };
+ return &state;
+}
+
+void handler_tracking::init()
+{
+ static tracking_state* state = get_state();
+
+ state->mutex_.init();
+
+ static_mutex::scoped_lock lock(state->mutex_);
+ if (state->current_completion_ == 0)
+ state->current_completion_ = new tss_ptr<completion>;
+}
+
+void handler_tracking::creation(handler_tracking::tracked_handler* h,
+ const char* object_type, void* object, const char* op_name)
+{
+ static tracking_state* state = get_state();
+
+ static_mutex::scoped_lock lock(state->mutex_);
+ h->id_ = state->next_id_++;
+ lock.unlock();
+
+ handler_tracking_timestamp timestamp;
+
+ uint64_t current_id = 0;
+ if (completion* current_completion = *state->current_completion_)
+ current_id = current_completion->id_;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|%I64u*%I64u|%.20s@%p.%.50s\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|%llu*%llu|%.20s@%p.%.50s\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds,
+ current_id, h->id_, object_type, object, op_name);
+}
+
+handler_tracking::completion::completion(handler_tracking::tracked_handler* h)
+ : id_(h->id_),
+ invoked_(false),
+ next_(*get_state()->current_completion_)
+{
+ *get_state()->current_completion_ = this;
+}
+
+handler_tracking::completion::~completion()
+{
+ if (id_)
+ {
+ handler_tracking_timestamp timestamp;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|%c%I64u|\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|%c%llu|\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds,
+ invoked_ ? '!' : '~', id_);
+ }
+
+ *get_state()->current_completion_ = next_;
+}
+
+void handler_tracking::completion::invocation_begin()
+{
+ handler_tracking_timestamp timestamp;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|>%I64u|\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|>%llu|\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds, id_);
+
+ invoked_ = true;
+}
+
+void handler_tracking::completion::invocation_begin(
+ const boost::system::error_code& ec)
+{
+ handler_tracking_timestamp timestamp;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|>%I64u|ec=%.20s:%d\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|>%llu|ec=%.20s:%d\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds,
+ id_, ec.category().name(), ec.value());
+
+ invoked_ = true;
+}
+
+void handler_tracking::completion::invocation_begin(
+ const boost::system::error_code& ec, std::size_t bytes_transferred)
+{
+ handler_tracking_timestamp timestamp;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|>%I64u|ec=%.20s:%d,bytes_transferred=%I64u\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|>%llu|ec=%.20s:%d,bytes_transferred=%llu\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds,
+ id_, ec.category().name(), ec.value(),
+ static_cast<uint64_t>(bytes_transferred));
+
+ invoked_ = true;
+}
+
+void handler_tracking::completion::invocation_begin(
+ const boost::system::error_code& ec, int signal_number)
+{
+ handler_tracking_timestamp timestamp;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|>%I64u|ec=%.20s:%d,signal_number=%d\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|>%llu|ec=%.20s:%d,signal_number=%d\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds,
+ id_, ec.category().name(), ec.value(), signal_number);
+
+ invoked_ = true;
+}
+
+void handler_tracking::completion::invocation_begin(
+ const boost::system::error_code& ec, const char* arg)
+{
+ handler_tracking_timestamp timestamp;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|>%I64u|ec=%.20s:%d,%.50s\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|>%llu|ec=%.20s:%d,%.50s\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds,
+ id_, ec.category().name(), ec.value(), arg);
+
+ invoked_ = true;
+}
+
+void handler_tracking::completion::invocation_end()
+{
+ if (id_)
+ {
+ handler_tracking_timestamp timestamp;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|<%I64u|\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|<%llu|\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds, id_);
+
+ id_ = 0;
+ }
+}
+
+void handler_tracking::operation(const char* object_type,
+ void* object, const char* op_name)
+{
+ static tracking_state* state = get_state();
+
+ handler_tracking_timestamp timestamp;
+
+ unsigned long long current_id = 0;
+ if (completion* current_completion = *state->current_completion_)
+ current_id = current_completion->id_;
+
+ write_line(
+#if defined(BOOST_ASIO_WINDOWS)
+ "@asio|%I64u.%06I64u|%I64u|%.20s@%p.%.50s\n",
+#else // defined(BOOST_ASIO_WINDOWS)
+ "@asio|%llu.%06llu|%llu|%.20s@%p.%.50s\n",
+#endif // defined(BOOST_ASIO_WINDOWS)
+ timestamp.seconds, timestamp.microseconds,
+ current_id, object_type, object, op_name);
+}
+
+void handler_tracking::write_line(const char* format, ...)
+{
+ using namespace std; // For sprintf (or equivalent).
+
+ va_list args;
+ va_start(args, format);
+
+ char line[256] = "";
+#if defined(BOOST_ASIO_HAS_SECURE_RTL)
+ int length = vsprintf_s(line, sizeof(line), format, args);
+#else // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ int length = vsprintf(line, format, args);
+#endif // defined(BOOST_ASIO_HAS_SECURE_RTL)
+
+ va_end(args);
+
+#if defined(BOOST_ASIO_WINDOWS)
+ HANDLE stderr_handle = ::GetStdHandle(STD_ERROR_HANDLE);
+ DWORD bytes_written = 0;
+ ::WriteFile(stderr_handle, line, length, &bytes_written, 0);
+#else // defined(BOOST_ASIO_WINDOWS)
+ ::write(STDERR_FILENO, line, length);
+#endif // defined(BOOST_ASIO_WINDOWS)
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_ENABLE_HANDLER_TRACKING)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_HANDLER_TRACKING_IPP
diff --git a/ext/patches/boost/asio/detail/impl/kqueue_reactor.hpp b/ext/patches/boost/asio/detail/impl/kqueue_reactor.hpp
new file mode 100644
index 0000000..de090d1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/kqueue_reactor.hpp
@@ -0,0 +1,82 @@
+//
+// detail/impl/kqueue_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2005 Stefan Arentz (stefan at soze dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_KQUEUE_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_IMPL_KQUEUE_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_KQUEUE)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Time_Traits>
+void kqueue_reactor::add_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_add_timer_queue(queue);
+}
+
+// Remove a timer queue from the reactor.
+template <typename Time_Traits>
+void kqueue_reactor::remove_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_remove_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void kqueue_reactor::schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ if (shutdown_)
+ {
+ io_service_.post_immediate_completion(op, false);
+ return;
+ }
+
+ bool earliest = queue.enqueue_timer(time, timer, op);
+ io_service_.work_started();
+ if (earliest)
+ interrupt();
+}
+
+template <typename Time_Traits>
+std::size_t kqueue_reactor::cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ op_queue<operation> ops;
+ std::size_t n = queue.cancel_timer(timer, ops, max_cancelled);
+ lock.unlock();
+ io_service_.post_deferred_completions(ops);
+ return n;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_KQUEUE)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_KQUEUE_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/impl/kqueue_reactor.ipp b/ext/patches/boost/asio/detail/impl/kqueue_reactor.ipp
new file mode 100644
index 0000000..e1212f7
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/kqueue_reactor.ipp
@@ -0,0 +1,465 @@
+//
+// detail/impl/kqueue_reactor.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2005 Stefan Arentz (stefan at soze dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_KQUEUE_REACTOR_IPP
+#define BOOST_ASIO_DETAIL_IMPL_KQUEUE_REACTOR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_KQUEUE)
+
+#include <boost/asio/detail/kqueue_reactor.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+#if defined(__NetBSD__)
+# define BOOST_ASIO_KQUEUE_EV_SET(ev, ident, filt, flags, fflags, data, udata) \
+ EV_SET(ev, ident, filt, flags, fflags, data, \
+ reinterpret_cast<intptr_t>(static_cast<void*>(udata)))
+#else
+# define BOOST_ASIO_KQUEUE_EV_SET(ev, ident, filt, flags, fflags, data, udata) \
+ EV_SET(ev, ident, filt, flags, fflags, data, udata)
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+kqueue_reactor::kqueue_reactor(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<kqueue_reactor>(io_service),
+ io_service_(use_service<io_service_impl>(io_service)),
+ mutex_(),
+ kqueue_fd_(do_kqueue_create()),
+ interrupter_(),
+ shutdown_(false)
+{
+ struct kevent event;
+ BOOST_ASIO_KQUEUE_EV_SET(&event, interrupter_.read_descriptor(),
+ EVFILT_READ, EV_ADD, 0, 0, &interrupter_);
+ if (::kevent(kqueue_fd_, &event, 1, 0, 0, 0) == -1)
+ {
+ boost::system::error_code error(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(error);
+ }
+}
+
+kqueue_reactor::~kqueue_reactor()
+{
+ close(kqueue_fd_);
+}
+
+void kqueue_reactor::shutdown_service()
+{
+ mutex::scoped_lock lock(mutex_);
+ shutdown_ = true;
+ lock.unlock();
+
+ op_queue<operation> ops;
+
+ while (descriptor_state* state = registered_descriptors_.first())
+ {
+ for (int i = 0; i < max_ops; ++i)
+ ops.push(state->op_queue_[i]);
+ state->shutdown_ = true;
+ registered_descriptors_.free(state);
+ }
+
+ timer_queues_.get_all_timers(ops);
+
+ io_service_.abandon_operations(ops);
+}
+
+void kqueue_reactor::fork_service(boost::asio::io_service::fork_event fork_ev)
+{
+ if (fork_ev == boost::asio::io_service::fork_child)
+ {
+ // The kqueue descriptor is automatically closed in the child.
+ kqueue_fd_ = -1;
+ kqueue_fd_ = do_kqueue_create();
+
+ interrupter_.recreate();
+
+ struct kevent event;
+ BOOST_ASIO_KQUEUE_EV_SET(&event, interrupter_.read_descriptor(),
+ EVFILT_READ, EV_ADD, 0, 0, &interrupter_);
+ if (::kevent(kqueue_fd_, &event, 1, 0, 0, 0) == -1)
+ {
+ boost::system::error_code error(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(error);
+ }
+
+ // Re-register all descriptors with kqueue.
+ mutex::scoped_lock descriptors_lock(registered_descriptors_mutex_);
+ for (descriptor_state* state = registered_descriptors_.first();
+ state != 0; state = state->next_)
+ {
+ struct kevent events[2];
+ BOOST_ASIO_KQUEUE_EV_SET(&events[0], state->descriptor_,
+ EVFILT_READ, EV_ADD | EV_CLEAR, 0, 0, state);
+ BOOST_ASIO_KQUEUE_EV_SET(&events[1], state->descriptor_,
+ EVFILT_WRITE, EV_ADD | EV_CLEAR, 0, 0, state);
+ if (::kevent(kqueue_fd_, events, 2, 0, 0, 0) == -1)
+ {
+ boost::system::error_code error(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(error);
+ }
+ }
+ }
+}
+
+void kqueue_reactor::init_task()
+{
+ io_service_.init_task();
+}
+
+int kqueue_reactor::register_descriptor(socket_type descriptor,
+ kqueue_reactor::per_descriptor_data& descriptor_data)
+{
+ descriptor_data = allocate_descriptor_state();
+
+ mutex::scoped_lock lock(descriptor_data->mutex_);
+
+ descriptor_data->descriptor_ = descriptor;
+ descriptor_data->shutdown_ = false;
+
+ struct kevent events[2];
+ BOOST_ASIO_KQUEUE_EV_SET(&events[0], descriptor, EVFILT_READ,
+ EV_ADD | EV_CLEAR, 0, 0, descriptor_data);
+ BOOST_ASIO_KQUEUE_EV_SET(&events[1], descriptor, EVFILT_WRITE,
+ EV_ADD | EV_CLEAR, 0, 0, descriptor_data);
+ if (::kevent(kqueue_fd_, events, 2, 0, 0, 0) == -1)
+ return errno;
+
+ return 0;
+}
+
+int kqueue_reactor::register_internal_descriptor(
+ int op_type, socket_type descriptor,
+ kqueue_reactor::per_descriptor_data& descriptor_data, reactor_op* op)
+{
+ descriptor_data = allocate_descriptor_state();
+
+ mutex::scoped_lock lock(descriptor_data->mutex_);
+
+ descriptor_data->descriptor_ = descriptor;
+ descriptor_data->shutdown_ = false;
+ descriptor_data->op_queue_[op_type].push(op);
+
+ struct kevent events[2];
+ BOOST_ASIO_KQUEUE_EV_SET(&events[0], descriptor, EVFILT_READ,
+ EV_ADD | EV_CLEAR, 0, 0, descriptor_data);
+ BOOST_ASIO_KQUEUE_EV_SET(&events[1], descriptor, EVFILT_WRITE,
+ EV_ADD | EV_CLEAR, 0, 0, descriptor_data);
+ if (::kevent(kqueue_fd_, events, 2, 0, 0, 0) == -1)
+ return errno;
+
+ return 0;
+}
+
+void kqueue_reactor::move_descriptor(socket_type,
+ kqueue_reactor::per_descriptor_data& target_descriptor_data,
+ kqueue_reactor::per_descriptor_data& source_descriptor_data)
+{
+ target_descriptor_data = source_descriptor_data;
+ source_descriptor_data = 0;
+}
+
+void kqueue_reactor::start_op(int op_type, socket_type descriptor,
+ kqueue_reactor::per_descriptor_data& descriptor_data, reactor_op* op,
+ bool is_continuation, bool allow_speculative)
+{
+ if (!descriptor_data)
+ {
+ op->ec_ = boost::asio::error::bad_descriptor;
+ post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ if (descriptor_data->shutdown_)
+ {
+ post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ bool first = descriptor_data->op_queue_[op_type].empty();
+ if (first)
+ {
+ if (allow_speculative
+ && (op_type != read_op
+ || descriptor_data->op_queue_[except_op].empty()))
+ {
+ if (op->perform())
+ {
+ descriptor_lock.unlock();
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+ }
+ else
+ {
+ struct kevent events[2];
+ BOOST_ASIO_KQUEUE_EV_SET(&events[0], descriptor, EVFILT_READ,
+ EV_ADD | EV_CLEAR, 0, 0, descriptor_data);
+ BOOST_ASIO_KQUEUE_EV_SET(&events[1], descriptor, EVFILT_WRITE,
+ EV_ADD | EV_CLEAR, 0, 0, descriptor_data);
+ ::kevent(kqueue_fd_, events, 2, 0, 0, 0);
+ }
+ }
+
+ descriptor_data->op_queue_[op_type].push(op);
+ io_service_.work_started();
+}
+
+void kqueue_reactor::cancel_ops(socket_type,
+ kqueue_reactor::per_descriptor_data& descriptor_data)
+{
+ if (!descriptor_data)
+ return;
+
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ {
+ while (reactor_op* op = descriptor_data->op_queue_[i].front())
+ {
+ op->ec_ = boost::asio::error::operation_aborted;
+ descriptor_data->op_queue_[i].pop();
+ ops.push(op);
+ }
+ }
+
+ descriptor_lock.unlock();
+
+ io_service_.post_deferred_completions(ops);
+}
+
+void kqueue_reactor::deregister_descriptor(socket_type descriptor,
+ kqueue_reactor::per_descriptor_data& descriptor_data, bool closing)
+{
+ if (!descriptor_data)
+ return;
+
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ if (!descriptor_data->shutdown_)
+ {
+ if (closing)
+ {
+ // The descriptor will be automatically removed from the kqueue when it
+ // is closed.
+ }
+ else
+ {
+ struct kevent events[2];
+ BOOST_ASIO_KQUEUE_EV_SET(&events[0], descriptor,
+ EVFILT_READ, EV_DELETE, 0, 0, 0);
+ BOOST_ASIO_KQUEUE_EV_SET(&events[1], descriptor,
+ EVFILT_WRITE, EV_DELETE, 0, 0, 0);
+ ::kevent(kqueue_fd_, events, 2, 0, 0, 0);
+ }
+
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ {
+ while (reactor_op* op = descriptor_data->op_queue_[i].front())
+ {
+ op->ec_ = boost::asio::error::operation_aborted;
+ descriptor_data->op_queue_[i].pop();
+ ops.push(op);
+ }
+ }
+
+ descriptor_data->descriptor_ = -1;
+ descriptor_data->shutdown_ = true;
+
+ descriptor_lock.unlock();
+
+ free_descriptor_state(descriptor_data);
+ descriptor_data = 0;
+
+ io_service_.post_deferred_completions(ops);
+ }
+}
+
+void kqueue_reactor::deregister_internal_descriptor(socket_type descriptor,
+ kqueue_reactor::per_descriptor_data& descriptor_data)
+{
+ if (!descriptor_data)
+ return;
+
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ if (!descriptor_data->shutdown_)
+ {
+ struct kevent events[2];
+ BOOST_ASIO_KQUEUE_EV_SET(&events[0], descriptor,
+ EVFILT_READ, EV_DELETE, 0, 0, 0);
+ BOOST_ASIO_KQUEUE_EV_SET(&events[1], descriptor,
+ EVFILT_WRITE, EV_DELETE, 0, 0, 0);
+ ::kevent(kqueue_fd_, events, 2, 0, 0, 0);
+
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ ops.push(descriptor_data->op_queue_[i]);
+
+ descriptor_data->descriptor_ = -1;
+ descriptor_data->shutdown_ = true;
+
+ descriptor_lock.unlock();
+
+ free_descriptor_state(descriptor_data);
+ descriptor_data = 0;
+ }
+}
+
+void kqueue_reactor::run(bool block, op_queue<operation>& ops)
+{
+ mutex::scoped_lock lock(mutex_);
+
+ // Determine how long to block while waiting for events.
+ timespec timeout_buf = { 0, 0 };
+ timespec* timeout = block ? get_timeout(timeout_buf) : &timeout_buf;
+
+ lock.unlock();
+
+ // Block on the kqueue descriptor.
+ struct kevent events[128];
+ int num_events = kevent(kqueue_fd_, 0, 0, events, 128, timeout);
+
+ // Dispatch the waiting events.
+ for (int i = 0; i < num_events; ++i)
+ {
+ void* ptr = reinterpret_cast<void*>(events[i].udata);
+ if (ptr == &interrupter_)
+ {
+ interrupter_.reset();
+ }
+ else
+ {
+ descriptor_state* descriptor_data = static_cast<descriptor_state*>(ptr);
+ mutex::scoped_lock descriptor_lock(descriptor_data->mutex_);
+
+ // Exception operations must be processed first to ensure that any
+ // out-of-band data is read before normal data.
+#if defined(__NetBSD__)
+ static const unsigned int filter[max_ops] =
+#else
+ static const int filter[max_ops] =
+#endif
+ { EVFILT_READ, EVFILT_WRITE, EVFILT_READ };
+ for (int j = max_ops - 1; j >= 0; --j)
+ {
+ if (events[i].filter == filter[j])
+ {
+ if (j != except_op || events[i].flags & EV_OOBAND)
+ {
+ while (reactor_op* op = descriptor_data->op_queue_[j].front())
+ {
+ if (events[i].flags & EV_ERROR)
+ {
+ op->ec_ = boost::system::error_code(
+ static_cast<int>(events[i].data),
+ boost::asio::error::get_system_category());
+ descriptor_data->op_queue_[j].pop();
+ ops.push(op);
+ }
+ if (op->perform())
+ {
+ descriptor_data->op_queue_[j].pop();
+ ops.push(op);
+ }
+ else
+ break;
+ }
+ }
+ }
+ }
+ }
+ }
+
+ lock.lock();
+ timer_queues_.get_ready_timers(ops);
+}
+
+void kqueue_reactor::interrupt()
+{
+ interrupter_.interrupt();
+}
+
+int kqueue_reactor::do_kqueue_create()
+{
+ int fd = ::kqueue();
+ if (fd == -1)
+ {
+ boost::system::error_code ec(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "kqueue");
+ }
+ return fd;
+}
+
+kqueue_reactor::descriptor_state* kqueue_reactor::allocate_descriptor_state()
+{
+ mutex::scoped_lock descriptors_lock(registered_descriptors_mutex_);
+ return registered_descriptors_.alloc();
+}
+
+void kqueue_reactor::free_descriptor_state(kqueue_reactor::descriptor_state* s)
+{
+ mutex::scoped_lock descriptors_lock(registered_descriptors_mutex_);
+ registered_descriptors_.free(s);
+}
+
+void kqueue_reactor::do_add_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.insert(&queue);
+}
+
+void kqueue_reactor::do_remove_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.erase(&queue);
+}
+
+timespec* kqueue_reactor::get_timeout(timespec& ts)
+{
+ // By default we will wait no longer than 5 minutes. This will ensure that
+ // any changes to the system clock are detected after no longer than this.
+ long usec = timer_queues_.wait_duration_usec(5 * 60 * 1000 * 1000);
+ ts.tv_sec = usec / 1000000;
+ ts.tv_nsec = (usec % 1000000) * 1000;
+ return &ts;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#undef BOOST_ASIO_KQUEUE_EV_SET
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_KQUEUE)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_KQUEUE_REACTOR_IPP
diff --git a/ext/patches/boost/asio/detail/impl/pipe_select_interrupter.ipp b/ext/patches/boost/asio/detail/impl/pipe_select_interrupter.ipp
new file mode 100644
index 0000000..309e45f
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/pipe_select_interrupter.ipp
@@ -0,0 +1,126 @@
+//
+// detail/impl/pipe_select_interrupter.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_PIPE_SELECT_INTERRUPTER_IPP
+#define BOOST_ASIO_DETAIL_IMPL_PIPE_SELECT_INTERRUPTER_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+#if !defined(BOOST_ASIO_WINDOWS)
+#if !defined(__CYGWIN__)
+#if !defined(__SYMBIAN32__)
+#if !defined(BOOST_ASIO_HAS_EVENTFD)
+
+#include <fcntl.h>
+#include <sys/stat.h>
+#include <sys/types.h>
+#include <unistd.h>
+#include <boost/asio/detail/pipe_select_interrupter.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+pipe_select_interrupter::pipe_select_interrupter()
+{
+ open_descriptors();
+}
+
+void pipe_select_interrupter::open_descriptors()
+{
+ int pipe_fds[2];
+ if (pipe(pipe_fds) == 0)
+ {
+ read_descriptor_ = pipe_fds[0];
+ ::fcntl(read_descriptor_, F_SETFL, O_NONBLOCK);
+ write_descriptor_ = pipe_fds[1];
+ ::fcntl(write_descriptor_, F_SETFL, O_NONBLOCK);
+
+#if defined(FD_CLOEXEC)
+ ::fcntl(read_descriptor_, F_SETFD, FD_CLOEXEC);
+ ::fcntl(write_descriptor_, F_SETFD, FD_CLOEXEC);
+#endif // defined(FD_CLOEXEC)
+ }
+ else
+ {
+ boost::system::error_code ec(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "pipe_select_interrupter");
+ }
+}
+
+pipe_select_interrupter::~pipe_select_interrupter()
+{
+ close_descriptors();
+}
+
+void pipe_select_interrupter::close_descriptors()
+{
+ if (read_descriptor_ != -1)
+ ::close(read_descriptor_);
+ if (write_descriptor_ != -1)
+ ::close(write_descriptor_);
+}
+
+void pipe_select_interrupter::recreate()
+{
+ close_descriptors();
+
+ write_descriptor_ = -1;
+ read_descriptor_ = -1;
+
+ open_descriptors();
+}
+
+void pipe_select_interrupter::interrupt()
+{
+ char byte = 0;
+ signed_size_type result = ::write(write_descriptor_, &byte, 1);
+ (void)result;
+}
+
+bool pipe_select_interrupter::reset()
+{
+ for (;;)
+ {
+ char data[1024];
+ signed_size_type bytes_read = ::read(read_descriptor_, data, sizeof(data));
+ if (bytes_read < 0 && errno == EINTR)
+ continue;
+ bool was_interrupted = (bytes_read > 0);
+ while (bytes_read == sizeof(data))
+ bytes_read = ::read(read_descriptor_, data, sizeof(data));
+ return was_interrupted;
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_EVENTFD)
+#endif // !defined(__SYMBIAN32__)
+#endif // !defined(__CYGWIN__)
+#endif // !defined(BOOST_ASIO_WINDOWS)
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_PIPE_SELECT_INTERRUPTER_IPP
diff --git a/ext/patches/boost/asio/detail/impl/posix_event.ipp b/ext/patches/boost/asio/detail/impl/posix_event.ipp
new file mode 100644
index 0000000..bb2a3d2
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/posix_event.ipp
@@ -0,0 +1,49 @@
+//
+// detail/impl/posix_event.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_POSIX_EVENT_IPP
+#define BOOST_ASIO_DETAIL_IMPL_POSIX_EVENT_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <boost/asio/detail/posix_event.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+posix_event::posix_event()
+ : state_(0)
+{
+ int error = ::pthread_cond_init(&cond_, 0);
+ boost::system::error_code ec(error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "event");
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_POSIX_EVENT_IPP
diff --git a/ext/patches/boost/asio/detail/impl/posix_mutex.ipp b/ext/patches/boost/asio/detail/impl/posix_mutex.ipp
new file mode 100644
index 0000000..7cc3b6f
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/posix_mutex.ipp
@@ -0,0 +1,48 @@
+//
+// detail/impl/posix_mutex.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_POSIX_MUTEX_IPP
+#define BOOST_ASIO_DETAIL_IMPL_POSIX_MUTEX_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <boost/asio/detail/posix_mutex.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+posix_mutex::posix_mutex()
+{
+ int error = ::pthread_mutex_init(&mutex_, 0);
+ boost::system::error_code ec(error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "mutex");
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_POSIX_MUTEX_IPP
diff --git a/ext/patches/boost/asio/detail/impl/posix_thread.ipp b/ext/patches/boost/asio/detail/impl/posix_thread.ipp
new file mode 100644
index 0000000..386dc77
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/posix_thread.ipp
@@ -0,0 +1,76 @@
+//
+// detail/impl/posix_thread.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_POSIX_THREAD_IPP
+#define BOOST_ASIO_DETAIL_IMPL_POSIX_THREAD_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <boost/asio/detail/posix_thread.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+posix_thread::~posix_thread()
+{
+ if (!joined_)
+ ::pthread_detach(thread_);
+}
+
+void posix_thread::join()
+{
+ if (!joined_)
+ {
+ ::pthread_join(thread_, 0);
+ joined_ = true;
+ }
+}
+
+void posix_thread::start_thread(func_base* arg)
+{
+ int error = ::pthread_create(&thread_, 0,
+ boost_asio_detail_posix_thread_function, arg);
+ if (error != 0)
+ {
+ delete arg;
+ boost::system::error_code ec(error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "thread");
+ }
+}
+
+void* boost_asio_detail_posix_thread_function(void* arg)
+{
+ posix_thread::auto_func_base_ptr func = {
+ static_cast<posix_thread::func_base*>(arg) };
+ func.ptr->run();
+ return 0;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_POSIX_THREAD_IPP
diff --git a/ext/patches/boost/asio/detail/impl/posix_tss_ptr.ipp b/ext/patches/boost/asio/detail/impl/posix_tss_ptr.ipp
new file mode 100644
index 0000000..3d83cff
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/posix_tss_ptr.ipp
@@ -0,0 +1,48 @@
+//
+// detail/impl/posix_tss_ptr.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_POSIX_TSS_PTR_IPP
+#define BOOST_ASIO_DETAIL_IMPL_POSIX_TSS_PTR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <boost/asio/detail/posix_tss_ptr.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+void posix_tss_ptr_create(pthread_key_t& key)
+{
+ int error = ::pthread_key_create(&key, 0);
+ boost::system::error_code ec(error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "tss");
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_POSIX_TSS_PTR_IPP
diff --git a/ext/patches/boost/asio/detail/impl/reactive_descriptor_service.ipp b/ext/patches/boost/asio/detail/impl/reactive_descriptor_service.ipp
new file mode 100644
index 0000000..d046b93
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/reactive_descriptor_service.ipp
@@ -0,0 +1,210 @@
+//
+// detail/impl/reactive_descriptor_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_REACTIVE_DESCRIPTOR_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_REACTIVE_DESCRIPTOR_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+
+#include <boost/asio/error.hpp>
+#include <boost/asio/detail/reactive_descriptor_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+reactive_descriptor_service::reactive_descriptor_service(
+ boost::asio::io_service& io_service)
+ : reactor_(boost::asio::use_service<reactor>(io_service))
+{
+ reactor_.init_task();
+}
+
+void reactive_descriptor_service::shutdown_service()
+{
+}
+
+void reactive_descriptor_service::construct(
+ reactive_descriptor_service::implementation_type& impl)
+{
+ impl.descriptor_ = -1;
+ impl.state_ = 0;
+}
+
+void reactive_descriptor_service::move_construct(
+ reactive_descriptor_service::implementation_type& impl,
+ reactive_descriptor_service::implementation_type& other_impl)
+{
+ impl.descriptor_ = other_impl.descriptor_;
+ other_impl.descriptor_ = -1;
+
+ impl.state_ = other_impl.state_;
+ other_impl.state_ = 0;
+
+ reactor_.move_descriptor(impl.descriptor_,
+ impl.reactor_data_, other_impl.reactor_data_);
+}
+
+void reactive_descriptor_service::move_assign(
+ reactive_descriptor_service::implementation_type& impl,
+ reactive_descriptor_service& other_service,
+ reactive_descriptor_service::implementation_type& other_impl)
+{
+ destroy(impl);
+
+ impl.descriptor_ = other_impl.descriptor_;
+ other_impl.descriptor_ = -1;
+
+ impl.state_ = other_impl.state_;
+ other_impl.state_ = 0;
+
+ other_service.reactor_.move_descriptor(impl.descriptor_,
+ impl.reactor_data_, other_impl.reactor_data_);
+}
+
+void reactive_descriptor_service::destroy(
+ reactive_descriptor_service::implementation_type& impl)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("descriptor", &impl, "close"));
+
+ reactor_.deregister_descriptor(impl.descriptor_, impl.reactor_data_,
+ (impl.state_ & descriptor_ops::possible_dup) == 0);
+ }
+
+ boost::system::error_code ignored_ec;
+ descriptor_ops::close(impl.descriptor_, impl.state_, ignored_ec);
+}
+
+boost::system::error_code reactive_descriptor_service::assign(
+ reactive_descriptor_service::implementation_type& impl,
+ const native_handle_type& native_descriptor, boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ if (int err = reactor_.register_descriptor(
+ native_descriptor, impl.reactor_data_))
+ {
+ ec = boost::system::error_code(err,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ impl.descriptor_ = native_descriptor;
+ impl.state_ = descriptor_ops::possible_dup;
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code reactive_descriptor_service::close(
+ reactive_descriptor_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("descriptor", &impl, "close"));
+
+ reactor_.deregister_descriptor(impl.descriptor_, impl.reactor_data_,
+ (impl.state_ & descriptor_ops::possible_dup) == 0);
+ }
+
+ descriptor_ops::close(impl.descriptor_, impl.state_, ec);
+
+ // The descriptor is closed by the OS even if close() returns an error.
+ //
+ // (Actually, POSIX says the state of the descriptor is unspecified. On
+ // Linux the descriptor is apparently closed anyway; e.g. see
+ // http://lkml.org/lkml/2005/9/10/129
+ // We'll just have to assume that other OSes follow the same behaviour.)
+ construct(impl);
+
+ return ec;
+}
+
+reactive_descriptor_service::native_handle_type
+reactive_descriptor_service::release(
+ reactive_descriptor_service::implementation_type& impl)
+{
+ native_handle_type descriptor = impl.descriptor_;
+
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("descriptor", &impl, "release"));
+
+ reactor_.deregister_descriptor(impl.descriptor_, impl.reactor_data_, false);
+ construct(impl);
+ }
+
+ return descriptor;
+}
+
+boost::system::error_code reactive_descriptor_service::cancel(
+ reactive_descriptor_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return ec;
+ }
+
+ BOOST_ASIO_HANDLER_OPERATION(("descriptor", &impl, "cancel"));
+
+ reactor_.cancel_ops(impl.descriptor_, impl.reactor_data_);
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void reactive_descriptor_service::start_op(
+ reactive_descriptor_service::implementation_type& impl,
+ int op_type, reactor_op* op, bool is_continuation,
+ bool is_non_blocking, bool noop)
+{
+ if (!noop)
+ {
+ if ((impl.state_ & descriptor_ops::non_blocking) ||
+ descriptor_ops::set_internal_non_blocking(
+ impl.descriptor_, impl.state_, true, op->ec_))
+ {
+ reactor_.start_op(op_type, impl.descriptor_,
+ impl.reactor_data_, op, is_continuation, is_non_blocking);
+ return;
+ }
+ }
+
+ reactor_.post_immediate_completion(op, is_continuation);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_REACTIVE_DESCRIPTOR_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/reactive_serial_port_service.ipp b/ext/patches/boost/asio/detail/impl/reactive_serial_port_service.ipp
new file mode 100644
index 0000000..d8ddae5
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/reactive_serial_port_service.ipp
@@ -0,0 +1,153 @@
+//
+// detail/impl/reactive_serial_port_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_REACTIVE_SERIAL_PORT_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_REACTIVE_SERIAL_PORT_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_SERIAL_PORT)
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#include <cstring>
+#include <boost/asio/detail/reactive_serial_port_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+reactive_serial_port_service::reactive_serial_port_service(
+ boost::asio::io_service& io_service)
+ : descriptor_service_(io_service)
+{
+}
+
+void reactive_serial_port_service::shutdown_service()
+{
+ descriptor_service_.shutdown_service();
+}
+
+boost::system::error_code reactive_serial_port_service::open(
+ reactive_serial_port_service::implementation_type& impl,
+ const std::string& device, boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ descriptor_ops::state_type state = 0;
+ int fd = descriptor_ops::open(device.c_str(),
+ O_RDWR | O_NONBLOCK | O_NOCTTY, ec);
+ if (fd < 0)
+ return ec;
+
+ int s = descriptor_ops::fcntl(fd, F_GETFL, ec);
+ if (s >= 0)
+ s = descriptor_ops::fcntl(fd, F_SETFL, s | O_NONBLOCK, ec);
+ if (s < 0)
+ {
+ boost::system::error_code ignored_ec;
+ descriptor_ops::close(fd, state, ignored_ec);
+ return ec;
+ }
+
+ // Set up default serial port options.
+ termios ios;
+ errno = 0;
+ s = descriptor_ops::error_wrapper(::tcgetattr(fd, &ios), ec);
+ if (s >= 0)
+ {
+#if defined(_BSD_SOURCE)
+ ::cfmakeraw(&ios);
+#else
+ ios.c_iflag &= ~(IGNBRK | BRKINT | PARMRK
+ | ISTRIP | INLCR | IGNCR | ICRNL | IXON);
+ ios.c_oflag &= ~OPOST;
+ ios.c_lflag &= ~(ECHO | ECHONL | ICANON | ISIG | IEXTEN);
+ ios.c_cflag &= ~(CSIZE | PARENB);
+ ios.c_cflag |= CS8;
+#endif
+ ios.c_iflag |= IGNPAR;
+ ios.c_cflag |= CREAD | CLOCAL;
+ errno = 0;
+ s = descriptor_ops::error_wrapper(::tcsetattr(fd, TCSANOW, &ios), ec);
+ }
+ if (s < 0)
+ {
+ boost::system::error_code ignored_ec;
+ descriptor_ops::close(fd, state, ignored_ec);
+ return ec;
+ }
+
+ // We're done. Take ownership of the serial port descriptor.
+ if (descriptor_service_.assign(impl, fd, ec))
+ {
+ boost::system::error_code ignored_ec;
+ descriptor_ops::close(fd, state, ignored_ec);
+ }
+
+ return ec;
+}
+
+boost::system::error_code reactive_serial_port_service::do_set_option(
+ reactive_serial_port_service::implementation_type& impl,
+ reactive_serial_port_service::store_function_type store,
+ const void* option, boost::system::error_code& ec)
+{
+ termios ios;
+ errno = 0;
+ descriptor_ops::error_wrapper(::tcgetattr(
+ descriptor_service_.native_handle(impl), &ios), ec);
+ if (ec)
+ return ec;
+
+ if (store(option, ios, ec))
+ return ec;
+
+ errno = 0;
+ descriptor_ops::error_wrapper(::tcsetattr(
+ descriptor_service_.native_handle(impl), TCSANOW, &ios), ec);
+ return ec;
+}
+
+boost::system::error_code reactive_serial_port_service::do_get_option(
+ const reactive_serial_port_service::implementation_type& impl,
+ reactive_serial_port_service::load_function_type load,
+ void* option, boost::system::error_code& ec) const
+{
+ termios ios;
+ errno = 0;
+ descriptor_ops::error_wrapper(::tcgetattr(
+ descriptor_service_.native_handle(impl), &ios), ec);
+ if (ec)
+ return ec;
+
+ return load(option, ios, ec);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+#endif // defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_REACTIVE_SERIAL_PORT_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/reactive_socket_service_base.ipp b/ext/patches/boost/asio/detail/impl/reactive_socket_service_base.ipp
new file mode 100644
index 0000000..c53fc88
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/reactive_socket_service_base.ipp
@@ -0,0 +1,269 @@
+//
+// detail/reactive_socket_service_base.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_REACTIVE_SOCKET_SERVICE_BASE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_REACTIVE_SOCKET_SERVICE_BASE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_IOCP) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/reactive_socket_service_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+reactive_socket_service_base::reactive_socket_service_base(
+ boost::asio::io_service& io_service)
+ : reactor_(use_service<reactor>(io_service))
+{
+ reactor_.init_task();
+}
+
+void reactive_socket_service_base::shutdown_service()
+{
+}
+
+void reactive_socket_service_base::construct(
+ reactive_socket_service_base::base_implementation_type& impl)
+{
+ impl.socket_ = invalid_socket;
+ impl.state_ = 0;
+}
+
+void reactive_socket_service_base::base_move_construct(
+ reactive_socket_service_base::base_implementation_type& impl,
+ reactive_socket_service_base::base_implementation_type& other_impl)
+{
+ impl.socket_ = other_impl.socket_;
+ other_impl.socket_ = invalid_socket;
+
+ impl.state_ = other_impl.state_;
+ other_impl.state_ = 0;
+
+ reactor_.move_descriptor(impl.socket_,
+ impl.reactor_data_, other_impl.reactor_data_);
+}
+
+void reactive_socket_service_base::base_move_assign(
+ reactive_socket_service_base::base_implementation_type& impl,
+ reactive_socket_service_base& other_service,
+ reactive_socket_service_base::base_implementation_type& other_impl)
+{
+ destroy(impl);
+
+ impl.socket_ = other_impl.socket_;
+ other_impl.socket_ = invalid_socket;
+
+ impl.state_ = other_impl.state_;
+ other_impl.state_ = 0;
+
+ other_service.reactor_.move_descriptor(impl.socket_,
+ impl.reactor_data_, other_impl.reactor_data_);
+}
+
+void reactive_socket_service_base::destroy(
+ reactive_socket_service_base::base_implementation_type& impl)
+{
+ if (impl.socket_ != invalid_socket)
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("socket", &impl, "close"));
+
+ reactor_.deregister_descriptor(impl.socket_, impl.reactor_data_,
+ (impl.state_ & socket_ops::possible_dup) == 0);
+
+ boost::system::error_code ignored_ec;
+ socket_ops::close(impl.socket_, impl.state_, true, ignored_ec);
+ }
+}
+
+boost::system::error_code reactive_socket_service_base::close(
+ reactive_socket_service_base::base_implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("socket", &impl, "close"));
+
+ reactor_.deregister_descriptor(impl.socket_, impl.reactor_data_,
+ (impl.state_ & socket_ops::possible_dup) == 0);
+ }
+
+ socket_ops::close(impl.socket_, impl.state_, false, ec);
+
+ // The descriptor is closed by the OS even if close() returns an error.
+ //
+ // (Actually, POSIX says the state of the descriptor is unspecified. On
+ // Linux the descriptor is apparently closed anyway; e.g. see
+ // http://lkml.org/lkml/2005/9/10/129
+ // We'll just have to assume that other OSes follow the same behaviour. The
+ // known exception is when Windows's closesocket() function fails with
+ // WSAEWOULDBLOCK, but this case is handled inside socket_ops::close().
+ construct(impl);
+
+ return ec;
+}
+
+boost::system::error_code reactive_socket_service_base::cancel(
+ reactive_socket_service_base::base_implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return ec;
+ }
+
+ BOOST_ASIO_HANDLER_OPERATION(("socket", &impl, "cancel"));
+
+ reactor_.cancel_ops(impl.socket_, impl.reactor_data_);
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code reactive_socket_service_base::do_open(
+ reactive_socket_service_base::base_implementation_type& impl,
+ int af, int type, int protocol, boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ socket_holder sock(socket_ops::socket(af, type, protocol, ec));
+ if (sock.get() == invalid_socket)
+ return ec;
+
+ if (int err = reactor_.register_descriptor(sock.get(), impl.reactor_data_))
+ {
+ ec = boost::system::error_code(err,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ impl.socket_ = sock.release();
+ switch (type)
+ {
+ case SOCK_STREAM: impl.state_ = socket_ops::stream_oriented; break;
+ case SOCK_DGRAM: impl.state_ = socket_ops::datagram_oriented; break;
+ default: impl.state_ = 0; break;
+ }
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code reactive_socket_service_base::do_assign(
+ reactive_socket_service_base::base_implementation_type& impl, int type,
+ const reactive_socket_service_base::native_handle_type& native_socket,
+ boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ if (int err = reactor_.register_descriptor(
+ native_socket, impl.reactor_data_))
+ {
+ ec = boost::system::error_code(err,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ impl.socket_ = native_socket;
+ switch (type)
+ {
+ case SOCK_STREAM: impl.state_ = socket_ops::stream_oriented; break;
+ case SOCK_DGRAM: impl.state_ = socket_ops::datagram_oriented; break;
+ default: impl.state_ = 0; break;
+ }
+ impl.state_ |= socket_ops::possible_dup;
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void reactive_socket_service_base::start_op(
+ reactive_socket_service_base::base_implementation_type& impl,
+ int op_type, reactor_op* op, bool is_continuation,
+ bool is_non_blocking, bool noop)
+{
+ if (!noop)
+ {
+ if ((impl.state_ & socket_ops::non_blocking)
+ || socket_ops::set_internal_non_blocking(
+ impl.socket_, impl.state_, true, op->ec_))
+ {
+ reactor_.start_op(op_type, impl.socket_,
+ impl.reactor_data_, op, is_continuation, is_non_blocking);
+ return;
+ }
+ }
+
+ reactor_.post_immediate_completion(op, is_continuation);
+}
+
+void reactive_socket_service_base::start_accept_op(
+ reactive_socket_service_base::base_implementation_type& impl,
+ reactor_op* op, bool is_continuation, bool peer_is_open)
+{
+ if (!peer_is_open)
+ start_op(impl, reactor::read_op, op, true, is_continuation, false);
+ else
+ {
+ op->ec_ = boost::asio::error::already_open;
+ reactor_.post_immediate_completion(op, is_continuation);
+ }
+}
+
+void reactive_socket_service_base::start_connect_op(
+ reactive_socket_service_base::base_implementation_type& impl,
+ reactor_op* op, bool is_continuation,
+ const socket_addr_type* addr, size_t addrlen)
+{
+ if ((impl.state_ & socket_ops::non_blocking)
+ || socket_ops::set_internal_non_blocking(
+ impl.socket_, impl.state_, true, op->ec_))
+ {
+ if (socket_ops::connect(impl.socket_, addr, addrlen, op->ec_) != 0)
+ {
+ if (op->ec_ == boost::asio::error::in_progress
+ || op->ec_ == boost::asio::error::would_block)
+ {
+ op->ec_ = boost::system::error_code();
+ reactor_.start_op(reactor::connect_op, impl.socket_,
+ impl.reactor_data_, op, is_continuation, false);
+ return;
+ }
+ }
+ }
+
+ reactor_.post_immediate_completion(op, is_continuation);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_IOCP)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_REACTIVE_SOCKET_SERVICE_BASE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/resolver_service_base.ipp b/ext/patches/boost/asio/detail/impl/resolver_service_base.ipp
new file mode 100644
index 0000000..bffc4fb
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/resolver_service_base.ipp
@@ -0,0 +1,132 @@
+//
+// detail/impl/resolver_service_base.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_RESOLVER_SERVICE_BASE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_RESOLVER_SERVICE_BASE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/resolver_service_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class resolver_service_base::work_io_service_runner
+{
+public:
+ work_io_service_runner(boost::asio::io_service& io_service)
+ : io_service_(io_service) {}
+ void operator()() { io_service_.run(); }
+private:
+ boost::asio::io_service& io_service_;
+};
+
+resolver_service_base::resolver_service_base(
+ boost::asio::io_service& io_service)
+ : io_service_impl_(boost::asio::use_service<io_service_impl>(io_service)),
+ work_io_service_(new boost::asio::io_service),
+ work_io_service_impl_(boost::asio::use_service<
+ io_service_impl>(*work_io_service_)),
+ work_(new boost::asio::io_service::work(*work_io_service_)),
+ work_thread_(0)
+{
+}
+
+resolver_service_base::~resolver_service_base()
+{
+ shutdown_service();
+}
+
+void resolver_service_base::shutdown_service()
+{
+ work_.reset();
+ if (work_io_service_.get())
+ {
+ work_io_service_->stop();
+ if (work_thread_.get())
+ {
+ work_thread_->join();
+ work_thread_.reset();
+ }
+ work_io_service_.reset();
+ }
+}
+
+void resolver_service_base::fork_service(
+ boost::asio::io_service::fork_event fork_ev)
+{
+ if (work_thread_.get())
+ {
+ if (fork_ev == boost::asio::io_service::fork_prepare)
+ {
+ work_io_service_->stop();
+ work_thread_->join();
+ }
+ else
+ {
+ work_io_service_->reset();
+ work_thread_.reset(new boost::asio::detail::thread(
+ work_io_service_runner(*work_io_service_)));
+ }
+ }
+}
+
+void resolver_service_base::construct(
+ resolver_service_base::implementation_type& impl)
+{
+ impl.reset(static_cast<void*>(0), socket_ops::noop_deleter());
+}
+
+void resolver_service_base::destroy(
+ resolver_service_base::implementation_type& impl)
+{
+ BOOST_ASIO_HANDLER_OPERATION(("resolver", &impl, "cancel"));
+
+ impl.reset();
+}
+
+void resolver_service_base::cancel(
+ resolver_service_base::implementation_type& impl)
+{
+ BOOST_ASIO_HANDLER_OPERATION(("resolver", &impl, "cancel"));
+
+ impl.reset(static_cast<void*>(0), socket_ops::noop_deleter());
+}
+
+void resolver_service_base::start_resolve_op(operation* op)
+{
+ start_work_thread();
+ io_service_impl_.work_started();
+ work_io_service_impl_.post_immediate_completion(op, false);
+}
+
+void resolver_service_base::start_work_thread()
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ if (!work_thread_.get())
+ {
+ work_thread_.reset(new boost::asio::detail::thread(
+ work_io_service_runner(*work_io_service_)));
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_RESOLVER_SERVICE_BASE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/select_reactor.hpp b/ext/patches/boost/asio/detail/impl/select_reactor.hpp
new file mode 100644
index 0000000..8b7ac76
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/select_reactor.hpp
@@ -0,0 +1,89 @@
+//
+// detail/impl/select_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_SELECT_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_IMPL_SELECT_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP) \
+ || (!defined(BOOST_ASIO_HAS_DEV_POLL) \
+ && !defined(BOOST_ASIO_HAS_EPOLL) \
+ && !defined(BOOST_ASIO_HAS_KQUEUE) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME))
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Time_Traits>
+void select_reactor::add_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_add_timer_queue(queue);
+}
+
+// Remove a timer queue from the reactor.
+template <typename Time_Traits>
+void select_reactor::remove_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_remove_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void select_reactor::schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ if (shutdown_)
+ {
+ io_service_.post_immediate_completion(op, false);
+ return;
+ }
+
+ bool earliest = queue.enqueue_timer(time, timer, op);
+ io_service_.work_started();
+ if (earliest)
+ interrupter_.interrupt();
+}
+
+template <typename Time_Traits>
+std::size_t select_reactor::cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ op_queue<operation> ops;
+ std::size_t n = queue.cancel_timer(timer, ops, max_cancelled);
+ lock.unlock();
+ io_service_.post_deferred_completions(ops);
+ return n;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+ // || (!defined(BOOST_ASIO_HAS_DEV_POLL)
+ // && !defined(BOOST_ASIO_HAS_EPOLL)
+ // && !defined(BOOST_ASIO_HAS_KQUEUE)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME))
+
+#endif // BOOST_ASIO_DETAIL_IMPL_SELECT_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/impl/select_reactor.ipp b/ext/patches/boost/asio/detail/impl/select_reactor.ipp
new file mode 100644
index 0000000..fda191a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/select_reactor.ipp
@@ -0,0 +1,315 @@
+//
+// detail/impl/select_reactor.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_SELECT_REACTOR_IPP
+#define BOOST_ASIO_DETAIL_IMPL_SELECT_REACTOR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP) \
+ || (!defined(BOOST_ASIO_HAS_DEV_POLL) \
+ && !defined(BOOST_ASIO_HAS_EPOLL) \
+ && !defined(BOOST_ASIO_HAS_KQUEUE) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME))
+
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/fd_set_adapter.hpp>
+#include <boost/asio/detail/select_reactor.hpp>
+#include <boost/asio/detail/signal_blocker.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+select_reactor::select_reactor(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<select_reactor>(io_service),
+ io_service_(use_service<io_service_impl>(io_service)),
+ mutex_(),
+ interrupter_(),
+#if defined(BOOST_ASIO_HAS_IOCP)
+ stop_thread_(false),
+ thread_(0),
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+ shutdown_(false)
+{
+#if defined(BOOST_ASIO_HAS_IOCP)
+ boost::asio::detail::signal_blocker sb;
+ thread_ = new boost::asio::detail::thread(
+ bind_handler(&select_reactor::call_run_thread, this));
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+}
+
+select_reactor::~select_reactor()
+{
+ shutdown_service();
+}
+
+void select_reactor::shutdown_service()
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ shutdown_ = true;
+#if defined(BOOST_ASIO_HAS_IOCP)
+ stop_thread_ = true;
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+ lock.unlock();
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+ if (thread_)
+ {
+ interrupter_.interrupt();
+ thread_->join();
+ delete thread_;
+ thread_ = 0;
+ }
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+ op_queue<operation> ops;
+
+ for (int i = 0; i < max_ops; ++i)
+ op_queue_[i].get_all_operations(ops);
+
+ timer_queues_.get_all_timers(ops);
+
+ io_service_.abandon_operations(ops);
+}
+
+void select_reactor::fork_service(boost::asio::io_service::fork_event fork_ev)
+{
+ if (fork_ev == boost::asio::io_service::fork_child)
+ interrupter_.recreate();
+}
+
+void select_reactor::init_task()
+{
+ io_service_.init_task();
+}
+
+int select_reactor::register_descriptor(socket_type,
+ select_reactor::per_descriptor_data&)
+{
+ return 0;
+}
+
+int select_reactor::register_internal_descriptor(
+ int op_type, socket_type descriptor,
+ select_reactor::per_descriptor_data&, reactor_op* op)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ op_queue_[op_type].enqueue_operation(descriptor, op);
+ interrupter_.interrupt();
+
+ return 0;
+}
+
+void select_reactor::move_descriptor(socket_type,
+ select_reactor::per_descriptor_data&,
+ select_reactor::per_descriptor_data&)
+{
+}
+
+void select_reactor::start_op(int op_type, socket_type descriptor,
+ select_reactor::per_descriptor_data&, reactor_op* op,
+ bool is_continuation, bool)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ if (shutdown_)
+ {
+ post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ bool first = op_queue_[op_type].enqueue_operation(descriptor, op);
+ io_service_.work_started();
+ if (first)
+ interrupter_.interrupt();
+}
+
+void select_reactor::cancel_ops(socket_type descriptor,
+ select_reactor::per_descriptor_data&)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ cancel_ops_unlocked(descriptor, boost::asio::error::operation_aborted);
+}
+
+void select_reactor::deregister_descriptor(socket_type descriptor,
+ select_reactor::per_descriptor_data&, bool)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ cancel_ops_unlocked(descriptor, boost::asio::error::operation_aborted);
+}
+
+void select_reactor::deregister_internal_descriptor(
+ socket_type descriptor, select_reactor::per_descriptor_data&)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ op_queue_[i].cancel_operations(descriptor, ops);
+}
+
+void select_reactor::run(bool block, op_queue<operation>& ops)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+ // Check if the thread is supposed to stop.
+ if (stop_thread_)
+ return;
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+ // Set up the descriptor sets.
+ for (int i = 0; i < max_select_ops; ++i)
+ fd_sets_[i].reset();
+ fd_sets_[read_op].set(interrupter_.read_descriptor());
+ socket_type max_fd = 0;
+ bool have_work_to_do = !timer_queues_.all_empty();
+ for (int i = 0; i < max_select_ops; ++i)
+ {
+ have_work_to_do = have_work_to_do || !op_queue_[i].empty();
+ fd_sets_[i].set(op_queue_[i], ops);
+ if (fd_sets_[i].max_descriptor() > max_fd)
+ max_fd = fd_sets_[i].max_descriptor();
+ }
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // Connection operations on Windows use both except and write fd_sets.
+ have_work_to_do = have_work_to_do || !op_queue_[connect_op].empty();
+ fd_sets_[write_op].set(op_queue_[connect_op], ops);
+ if (fd_sets_[write_op].max_descriptor() > max_fd)
+ max_fd = fd_sets_[write_op].max_descriptor();
+ fd_sets_[except_op].set(op_queue_[connect_op], ops);
+ if (fd_sets_[except_op].max_descriptor() > max_fd)
+ max_fd = fd_sets_[except_op].max_descriptor();
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+ // We can return immediately if there's no work to do and the reactor is
+ // not supposed to block.
+ if (!block && !have_work_to_do)
+ return;
+
+ // Determine how long to block while waiting for events.
+ timeval tv_buf = { 0, 0 };
+ timeval* tv = block ? get_timeout(tv_buf) : &tv_buf;
+
+ lock.unlock();
+
+ // Block on the select call until descriptors become ready.
+ boost::system::error_code ec;
+ int retval = socket_ops::select(static_cast<int>(max_fd + 1),
+ fd_sets_[read_op], fd_sets_[write_op], fd_sets_[except_op], tv, ec);
+
+ // Reset the interrupter.
+ if (retval > 0 && fd_sets_[read_op].is_set(interrupter_.read_descriptor()))
+ {
+ interrupter_.reset();
+ --retval;
+ }
+
+ lock.lock();
+
+ // Dispatch all ready operations.
+ if (retval > 0)
+ {
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // Connection operations on Windows use both except and write fd_sets.
+ fd_sets_[except_op].perform(op_queue_[connect_op], ops);
+ fd_sets_[write_op].perform(op_queue_[connect_op], ops);
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+ // Exception operations must be processed first to ensure that any
+ // out-of-band data is read before normal data.
+ for (int i = max_select_ops - 1; i >= 0; --i)
+ fd_sets_[i].perform(op_queue_[i], ops);
+ }
+ timer_queues_.get_ready_timers(ops);
+}
+
+void select_reactor::interrupt()
+{
+ interrupter_.interrupt();
+}
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+void select_reactor::run_thread()
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ while (!stop_thread_)
+ {
+ lock.unlock();
+ op_queue<operation> ops;
+ run(true, ops);
+ io_service_.post_deferred_completions(ops);
+ lock.lock();
+ }
+}
+
+void select_reactor::call_run_thread(select_reactor* reactor)
+{
+ reactor->run_thread();
+}
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+void select_reactor::do_add_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.insert(&queue);
+}
+
+void select_reactor::do_remove_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.erase(&queue);
+}
+
+timeval* select_reactor::get_timeout(timeval& tv)
+{
+ // By default we will wait no longer than 5 minutes. This will ensure that
+ // any changes to the system clock are detected after no longer than this.
+ long usec = timer_queues_.wait_duration_usec(5 * 60 * 1000 * 1000);
+ tv.tv_sec = usec / 1000000;
+ tv.tv_usec = usec % 1000000;
+ return &tv;
+}
+
+void select_reactor::cancel_ops_unlocked(socket_type descriptor,
+ const boost::system::error_code& ec)
+{
+ bool need_interrupt = false;
+ op_queue<operation> ops;
+ for (int i = 0; i < max_ops; ++i)
+ need_interrupt = op_queue_[i].cancel_operations(
+ descriptor, ops, ec) || need_interrupt;
+ io_service_.post_deferred_completions(ops);
+ if (need_interrupt)
+ interrupter_.interrupt();
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+ // || (!defined(BOOST_ASIO_HAS_DEV_POLL)
+ // && !defined(BOOST_ASIO_HAS_EPOLL)
+ // && !defined(BOOST_ASIO_HAS_KQUEUE))
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME))
+
+#endif // BOOST_ASIO_DETAIL_IMPL_SELECT_REACTOR_IPP
diff --git a/ext/patches/boost/asio/detail/impl/service_registry.hpp b/ext/patches/boost/asio/detail/impl/service_registry.hpp
new file mode 100644
index 0000000..71e23bb
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/service_registry.hpp
@@ -0,0 +1,90 @@
+//
+// detail/impl/service_registry.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_SERVICE_REGISTRY_HPP
+#define BOOST_ASIO_DETAIL_IMPL_SERVICE_REGISTRY_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Service, typename Arg>
+service_registry::service_registry(
+ boost::asio::io_service& o, Service*, Arg arg)
+ : owner_(o),
+ first_service_(new Service(o, arg))
+{
+ boost::asio::io_service::service::key key;
+ init_key(key, Service::id);
+ first_service_->key_ = key;
+ first_service_->next_ = 0;
+}
+
+template <typename Service>
+Service& service_registry::first_service()
+{
+ return *static_cast<Service*>(first_service_);
+}
+
+template <typename Service>
+Service& service_registry::use_service()
+{
+ boost::asio::io_service::service::key key;
+ init_key(key, Service::id);
+ factory_type factory = &service_registry::create<Service>;
+ return *static_cast<Service*>(do_use_service(key, factory));
+}
+
+template <typename Service>
+void service_registry::add_service(Service* new_service)
+{
+ boost::asio::io_service::service::key key;
+ init_key(key, Service::id);
+ return do_add_service(key, new_service);
+}
+
+template <typename Service>
+bool service_registry::has_service() const
+{
+ boost::asio::io_service::service::key key;
+ init_key(key, Service::id);
+ return do_has_service(key);
+}
+
+#if !defined(BOOST_ASIO_NO_TYPEID)
+template <typename Service>
+void service_registry::init_key(boost::asio::io_service::service::key& key,
+ const boost::asio::detail::service_id<Service>& /*id*/)
+{
+ key.type_info_ = &typeid(typeid_wrapper<Service>);
+ key.id_ = 0;
+}
+#endif // !defined(BOOST_ASIO_NO_TYPEID)
+
+template <typename Service>
+boost::asio::io_service::service* service_registry::create(
+ boost::asio::io_service& owner)
+{
+ return new Service(owner);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_SERVICE_REGISTRY_HPP
diff --git a/ext/patches/boost/asio/detail/impl/service_registry.ipp b/ext/patches/boost/asio/detail/impl/service_registry.ipp
new file mode 100644
index 0000000..46f9045
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/service_registry.ipp
@@ -0,0 +1,190 @@
+//
+// detail/impl/service_registry.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_SERVICE_REGISTRY_IPP
+#define BOOST_ASIO_DETAIL_IMPL_SERVICE_REGISTRY_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <vector>
+#include <boost/asio/detail/service_registry.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+service_registry::~service_registry()
+{
+ // Shutdown all services. This must be done in a separate loop before the
+ // services are destroyed since the destructors of user-defined handler
+ // objects may try to access other service objects.
+ boost::asio::io_service::service* service = first_service_;
+ while (service)
+ {
+ service->shutdown_service();
+ service = service->next_;
+ }
+
+ // Destroy all services.
+ while (first_service_)
+ {
+ boost::asio::io_service::service* next_service = first_service_->next_;
+ destroy(first_service_);
+ first_service_ = next_service;
+ }
+}
+
+void service_registry::notify_fork(boost::asio::io_service::fork_event fork_ev)
+{
+ // Make a copy of all of the services while holding the lock. We don't want
+ // to hold the lock while calling into each service, as it may try to call
+ // back into this class.
+ std::vector<boost::asio::io_service::service*> services;
+ {
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ boost::asio::io_service::service* service = first_service_;
+ while (service)
+ {
+ services.push_back(service);
+ service = service->next_;
+ }
+ }
+
+ // If processing the fork_prepare event, we want to go in reverse order of
+ // service registration, which happens to be the existing order of the
+ // services in the vector. For the other events we want to go in the other
+ // direction.
+ std::size_t num_services = services.size();
+ if (fork_ev == boost::asio::io_service::fork_prepare)
+ for (std::size_t i = 0; i < num_services; ++i)
+ services[i]->fork_service(fork_ev);
+ else
+ for (std::size_t i = num_services; i > 0; --i)
+ services[i - 1]->fork_service(fork_ev);
+}
+
+void service_registry::init_key(boost::asio::io_service::service::key& key,
+ const boost::asio::io_service::id& id)
+{
+ key.type_info_ = 0;
+ key.id_ = &id;
+}
+
+bool service_registry::keys_match(
+ const boost::asio::io_service::service::key& key1,
+ const boost::asio::io_service::service::key& key2)
+{
+ if (key1.id_ && key2.id_)
+ if (key1.id_ == key2.id_)
+ return true;
+ if (key1.type_info_ && key2.type_info_)
+ if (*key1.type_info_ == *key2.type_info_)
+ return true;
+ return false;
+}
+
+void service_registry::destroy(boost::asio::io_service::service* service)
+{
+ delete service;
+}
+
+boost::asio::io_service::service* service_registry::do_use_service(
+ const boost::asio::io_service::service::key& key,
+ factory_type factory)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ // First see if there is an existing service object with the given key.
+ boost::asio::io_service::service* service = first_service_;
+ while (service)
+ {
+ if (keys_match(service->key_, key))
+ return service;
+ service = service->next_;
+ }
+
+ // Create a new service object. The service registry's mutex is not locked
+ // at this time to allow for nested calls into this function from the new
+ // service's constructor.
+ lock.unlock();
+ auto_service_ptr new_service = { factory(owner_) };
+ new_service.ptr_->key_ = key;
+ lock.lock();
+
+ // Check that nobody else created another service object of the same type
+ // while the lock was released.
+ service = first_service_;
+ while (service)
+ {
+ if (keys_match(service->key_, key))
+ return service;
+ service = service->next_;
+ }
+
+ // Service was successfully initialised, pass ownership to registry.
+ new_service.ptr_->next_ = first_service_;
+ first_service_ = new_service.ptr_;
+ new_service.ptr_ = 0;
+ return first_service_;
+}
+
+void service_registry::do_add_service(
+ const boost::asio::io_service::service::key& key,
+ boost::asio::io_service::service* new_service)
+{
+ if (&owner_ != &new_service->get_io_service())
+ boost::asio::detail::throw_exception(invalid_service_owner());
+
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ // Check if there is an existing service object with the given key.
+ boost::asio::io_service::service* service = first_service_;
+ while (service)
+ {
+ if (keys_match(service->key_, key))
+ boost::asio::detail::throw_exception(service_already_exists());
+ service = service->next_;
+ }
+
+ // Take ownership of the service object.
+ new_service->key_ = key;
+ new_service->next_ = first_service_;
+ first_service_ = new_service;
+}
+
+bool service_registry::do_has_service(
+ const boost::asio::io_service::service::key& key) const
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ boost::asio::io_service::service* service = first_service_;
+ while (service)
+ {
+ if (keys_match(service->key_, key))
+ return true;
+ service = service->next_;
+ }
+
+ return false;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_SERVICE_REGISTRY_IPP
diff --git a/ext/patches/boost/asio/detail/impl/signal_set_service.ipp b/ext/patches/boost/asio/detail/impl/signal_set_service.ipp
new file mode 100644
index 0000000..b1a7aa1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/signal_set_service.ipp
@@ -0,0 +1,649 @@
+//
+// detail/impl/signal_set_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_SIGNAL_SET_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_SIGNAL_SET_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <cstring>
+#include <boost/asio/detail/reactor.hpp>
+#include <boost/asio/detail/signal_blocker.hpp>
+#include <boost/asio/detail/signal_set_service.hpp>
+#include <boost/asio/detail/static_mutex.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct signal_state
+{
+ // Mutex used for protecting global state.
+ static_mutex mutex_;
+
+ // The read end of the pipe used for signal notifications.
+ int read_descriptor_;
+
+ // The write end of the pipe used for signal notifications.
+ int write_descriptor_;
+
+ // Whether the signal state has been prepared for a fork.
+ bool fork_prepared_;
+
+ // The head of a linked list of all signal_set_service instances.
+ class signal_set_service* service_list_;
+
+ // A count of the number of objects that are registered for each signal.
+ std::size_t registration_count_[max_signal_number];
+};
+
+signal_state* get_signal_state()
+{
+ static signal_state state = {
+ BOOST_ASIO_STATIC_MUTEX_INIT, -1, -1, false, 0, { 0 } };
+ return &state;
+}
+
+void boost_asio_signal_handler(int signal_number)
+{
+#if defined(BOOST_ASIO_WINDOWS) \
+ || defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ || defined(__CYGWIN__)
+ signal_set_service::deliver_signal(signal_number);
+#else // defined(BOOST_ASIO_WINDOWS)
+ // || defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // || defined(__CYGWIN__)
+ int saved_errno = errno;
+ signal_state* state = get_signal_state();
+ signed_size_type result = ::write(state->write_descriptor_,
+ &signal_number, sizeof(signal_number));
+ (void)result;
+ errno = saved_errno;
+#endif // defined(BOOST_ASIO_WINDOWS)
+ // || defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // || defined(__CYGWIN__)
+
+#if defined(BOOST_ASIO_HAS_SIGNAL) && !defined(BOOST_ASIO_HAS_SIGACTION)
+ ::signal(signal_number, boost_asio_signal_handler);
+#endif // defined(BOOST_ASIO_HAS_SIGNAL) && !defined(BOOST_ASIO_HAS_SIGACTION)
+}
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+class signal_set_service::pipe_read_op : public reactor_op
+{
+public:
+ pipe_read_op()
+ : reactor_op(&pipe_read_op::do_perform, pipe_read_op::do_complete)
+ {
+ }
+
+ static bool do_perform(reactor_op*)
+ {
+ signal_state* state = get_signal_state();
+
+ int fd = state->read_descriptor_;
+ int signal_number = 0;
+ while (::read(fd, &signal_number, sizeof(int)) == sizeof(int))
+ if (signal_number >= 0 && signal_number < max_signal_number)
+ signal_set_service::deliver_signal(signal_number);
+
+ return false;
+ }
+
+ static void do_complete(io_service_impl* /*owner*/, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ pipe_read_op* o(static_cast<pipe_read_op*>(base));
+ delete o;
+ }
+};
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+
+signal_set_service::signal_set_service(
+ boost::asio::io_service& io_service)
+ : io_service_(boost::asio::use_service<io_service_impl>(io_service)),
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+ reactor_(boost::asio::use_service<reactor>(io_service)),
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+ next_(0),
+ prev_(0)
+{
+ get_signal_state()->mutex_.init();
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+ reactor_.init_task();
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+
+ for (int i = 0; i < max_signal_number; ++i)
+ registrations_[i] = 0;
+
+ add_service(this);
+}
+
+signal_set_service::~signal_set_service()
+{
+ remove_service(this);
+}
+
+void signal_set_service::shutdown_service()
+{
+ remove_service(this);
+
+ op_queue<operation> ops;
+
+ for (int i = 0; i < max_signal_number; ++i)
+ {
+ registration* reg = registrations_[i];
+ while (reg)
+ {
+ ops.push(*reg->queue_);
+ reg = reg->next_in_table_;
+ }
+ }
+
+ io_service_.abandon_operations(ops);
+}
+
+void signal_set_service::fork_service(
+ boost::asio::io_service::fork_event fork_ev)
+{
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+ switch (fork_ev)
+ {
+ case boost::asio::io_service::fork_prepare:
+ {
+ int read_descriptor = state->read_descriptor_;
+ state->fork_prepared_ = true;
+ lock.unlock();
+ reactor_.deregister_internal_descriptor(read_descriptor, reactor_data_);
+ }
+ break;
+ case boost::asio::io_service::fork_parent:
+ if (state->fork_prepared_)
+ {
+ int read_descriptor = state->read_descriptor_;
+ state->fork_prepared_ = false;
+ lock.unlock();
+ reactor_.register_internal_descriptor(reactor::read_op,
+ read_descriptor, reactor_data_, new pipe_read_op);
+ }
+ break;
+ case boost::asio::io_service::fork_child:
+ if (state->fork_prepared_)
+ {
+ boost::asio::detail::signal_blocker blocker;
+ close_descriptors();
+ open_descriptors();
+ int read_descriptor = state->read_descriptor_;
+ state->fork_prepared_ = false;
+ lock.unlock();
+ reactor_.register_internal_descriptor(reactor::read_op,
+ read_descriptor, reactor_data_, new pipe_read_op);
+ }
+ break;
+ default:
+ break;
+ }
+#else // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+ (void)fork_ev;
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+}
+
+void signal_set_service::construct(
+ signal_set_service::implementation_type& impl)
+{
+ impl.signals_ = 0;
+}
+
+void signal_set_service::destroy(
+ signal_set_service::implementation_type& impl)
+{
+ boost::system::error_code ignored_ec;
+ clear(impl, ignored_ec);
+ cancel(impl, ignored_ec);
+}
+
+boost::system::error_code signal_set_service::add(
+ signal_set_service::implementation_type& impl,
+ int signal_number, boost::system::error_code& ec)
+{
+ // Check that the signal number is valid.
+ if (signal_number < 0 || signal_number >= max_signal_number)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+ // Find the appropriate place to insert the registration.
+ registration** insertion_point = &impl.signals_;
+ registration* next = impl.signals_;
+ while (next && next->signal_number_ < signal_number)
+ {
+ insertion_point = &next->next_in_set_;
+ next = next->next_in_set_;
+ }
+
+ // Only do something if the signal is not already registered.
+ if (next == 0 || next->signal_number_ != signal_number)
+ {
+ registration* new_registration = new registration;
+
+#if defined(BOOST_ASIO_HAS_SIGNAL) || defined(BOOST_ASIO_HAS_SIGACTION)
+ // Register for the signal if we're the first.
+ if (state->registration_count_[signal_number] == 0)
+ {
+# if defined(BOOST_ASIO_HAS_SIGACTION)
+ using namespace std; // For memset.
+ struct sigaction sa;
+ memset(&sa, 0, sizeof(sa));
+ sa.sa_handler = boost_asio_signal_handler;
+ sigfillset(&sa.sa_mask);
+ if (::sigaction(signal_number, &sa, 0) == -1)
+# else // defined(BOOST_ASIO_HAS_SIGACTION)
+ if (::signal(signal_number, boost_asio_signal_handler) == SIG_ERR)
+# endif // defined(BOOST_ASIO_HAS_SIGACTION)
+ {
+# if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ec = boost::asio::error::invalid_argument;
+# else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ec = boost::system::error_code(errno,
+ boost::asio::error::get_system_category());
+# endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ delete new_registration;
+ return ec;
+ }
+ }
+#endif // defined(BOOST_ASIO_HAS_SIGNAL) || defined(BOOST_ASIO_HAS_SIGACTION)
+
+ // Record the new registration in the set.
+ new_registration->signal_number_ = signal_number;
+ new_registration->queue_ = &impl.queue_;
+ new_registration->next_in_set_ = next;
+ *insertion_point = new_registration;
+
+ // Insert registration into the registration table.
+ new_registration->next_in_table_ = registrations_[signal_number];
+ if (registrations_[signal_number])
+ registrations_[signal_number]->prev_in_table_ = new_registration;
+ registrations_[signal_number] = new_registration;
+
+ ++state->registration_count_[signal_number];
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code signal_set_service::remove(
+ signal_set_service::implementation_type& impl,
+ int signal_number, boost::system::error_code& ec)
+{
+ // Check that the signal number is valid.
+ if (signal_number < 0 || signal_number >= max_signal_number)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+ // Find the signal number in the list of registrations.
+ registration** deletion_point = &impl.signals_;
+ registration* reg = impl.signals_;
+ while (reg && reg->signal_number_ < signal_number)
+ {
+ deletion_point = ®->next_in_set_;
+ reg = reg->next_in_set_;
+ }
+
+ if (reg != 0 && reg->signal_number_ == signal_number)
+ {
+#if defined(BOOST_ASIO_HAS_SIGNAL) || defined(BOOST_ASIO_HAS_SIGACTION)
+ // Set signal handler back to the default if we're the last.
+ if (state->registration_count_[signal_number] == 1)
+ {
+# if defined(BOOST_ASIO_HAS_SIGACTION)
+ using namespace std; // For memset.
+ struct sigaction sa;
+ memset(&sa, 0, sizeof(sa));
+ sa.sa_handler = SIG_DFL;
+ if (::sigaction(signal_number, &sa, 0) == -1)
+# else // defined(BOOST_ASIO_HAS_SIGACTION)
+ if (::signal(signal_number, SIG_DFL) == SIG_ERR)
+# endif // defined(BOOST_ASIO_HAS_SIGACTION)
+ {
+# if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ec = boost::asio::error::invalid_argument;
+# else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ec = boost::system::error_code(errno,
+ boost::asio::error::get_system_category());
+# endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ return ec;
+ }
+ }
+#endif // defined(BOOST_ASIO_HAS_SIGNAL) || defined(BOOST_ASIO_HAS_SIGACTION)
+
+ // Remove the registration from the set.
+ *deletion_point = reg->next_in_set_;
+
+ // Remove the registration from the registration table.
+ if (registrations_[signal_number] == reg)
+ registrations_[signal_number] = reg->next_in_table_;
+ if (reg->prev_in_table_)
+ reg->prev_in_table_->next_in_table_ = reg->next_in_table_;
+ if (reg->next_in_table_)
+ reg->next_in_table_->prev_in_table_ = reg->prev_in_table_;
+
+ --state->registration_count_[signal_number];
+
+ delete reg;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code signal_set_service::clear(
+ signal_set_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+ while (registration* reg = impl.signals_)
+ {
+#if defined(BOOST_ASIO_HAS_SIGNAL) || defined(BOOST_ASIO_HAS_SIGACTION)
+ // Set signal handler back to the default if we're the last.
+ if (state->registration_count_[reg->signal_number_] == 1)
+ {
+# if defined(BOOST_ASIO_HAS_SIGACTION)
+ using namespace std; // For memset.
+ struct sigaction sa;
+ memset(&sa, 0, sizeof(sa));
+ sa.sa_handler = SIG_DFL;
+ if (::sigaction(reg->signal_number_, &sa, 0) == -1)
+# else // defined(BOOST_ASIO_HAS_SIGACTION)
+ if (::signal(reg->signal_number_, SIG_DFL) == SIG_ERR)
+# endif // defined(BOOST_ASIO_HAS_SIGACTION)
+ {
+# if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ec = boost::asio::error::invalid_argument;
+# else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ec = boost::system::error_code(errno,
+ boost::asio::error::get_system_category());
+# endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ return ec;
+ }
+ }
+#endif // defined(BOOST_ASIO_HAS_SIGNAL) || defined(BOOST_ASIO_HAS_SIGACTION)
+
+ // Remove the registration from the registration table.
+ if (registrations_[reg->signal_number_] == reg)
+ registrations_[reg->signal_number_] = reg->next_in_table_;
+ if (reg->prev_in_table_)
+ reg->prev_in_table_->next_in_table_ = reg->next_in_table_;
+ if (reg->next_in_table_)
+ reg->next_in_table_->prev_in_table_ = reg->prev_in_table_;
+
+ --state->registration_count_[reg->signal_number_];
+
+ impl.signals_ = reg->next_in_set_;
+ delete reg;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code signal_set_service::cancel(
+ signal_set_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ BOOST_ASIO_HANDLER_OPERATION(("signal_set", &impl, "cancel"));
+
+ op_queue<operation> ops;
+ {
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+ while (signal_op* op = impl.queue_.front())
+ {
+ op->ec_ = boost::asio::error::operation_aborted;
+ impl.queue_.pop();
+ ops.push(op);
+ }
+ }
+
+ io_service_.post_deferred_completions(ops);
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void signal_set_service::deliver_signal(int signal_number)
+{
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+ signal_set_service* service = state->service_list_;
+ while (service)
+ {
+ op_queue<operation> ops;
+
+ registration* reg = service->registrations_[signal_number];
+ while (reg)
+ {
+ if (reg->queue_->empty())
+ {
+ ++reg->undelivered_;
+ }
+ else
+ {
+ while (signal_op* op = reg->queue_->front())
+ {
+ op->signal_number_ = signal_number;
+ reg->queue_->pop();
+ ops.push(op);
+ }
+ }
+
+ reg = reg->next_in_table_;
+ }
+
+ service->io_service_.post_deferred_completions(ops);
+
+ service = service->next_;
+ }
+}
+
+void signal_set_service::add_service(signal_set_service* service)
+{
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+ // If this is the first service to be created, open a new pipe.
+ if (state->service_list_ == 0)
+ open_descriptors();
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+ // Insert service into linked list of all services.
+ service->next_ = state->service_list_;
+ service->prev_ = 0;
+ if (state->service_list_)
+ state->service_list_->prev_ = service;
+ state->service_list_ = service;
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+ // Register for pipe readiness notifications.
+ int read_descriptor = state->read_descriptor_;
+ lock.unlock();
+ service->reactor_.register_internal_descriptor(reactor::read_op,
+ read_descriptor, service->reactor_data_, new pipe_read_op);
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+}
+
+void signal_set_service::remove_service(signal_set_service* service)
+{
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+ if (service->next_ || service->prev_ || state->service_list_ == service)
+ {
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+ // Disable the pipe readiness notifications.
+ int read_descriptor = state->read_descriptor_;
+ lock.unlock();
+ service->reactor_.deregister_descriptor(
+ read_descriptor, service->reactor_data_, false);
+ lock.lock();
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+
+ // Remove service from linked list of all services.
+ if (state->service_list_ == service)
+ state->service_list_ = service->next_;
+ if (service->prev_)
+ service->prev_->next_ = service->next_;
+ if (service->next_)
+ service->next_->prev_= service->prev_;
+ service->next_ = 0;
+ service->prev_ = 0;
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+ // If this is the last service to be removed, close the pipe.
+ if (state->service_list_ == 0)
+ close_descriptors();
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+ }
+}
+
+void signal_set_service::open_descriptors()
+{
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+ signal_state* state = get_signal_state();
+
+ int pipe_fds[2];
+ if (::pipe(pipe_fds) == 0)
+ {
+ state->read_descriptor_ = pipe_fds[0];
+ ::fcntl(state->read_descriptor_, F_SETFL, O_NONBLOCK);
+
+ state->write_descriptor_ = pipe_fds[1];
+ ::fcntl(state->write_descriptor_, F_SETFL, O_NONBLOCK);
+
+#if defined(FD_CLOEXEC)
+ ::fcntl(state->read_descriptor_, F_SETFD, FD_CLOEXEC);
+ ::fcntl(state->write_descriptor_, F_SETFD, FD_CLOEXEC);
+#endif // defined(FD_CLOEXEC)
+ }
+ else
+ {
+ boost::system::error_code ec(errno,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "signal_set_service pipe");
+ }
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+}
+
+void signal_set_service::close_descriptors()
+{
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+ signal_state* state = get_signal_state();
+
+ if (state->read_descriptor_ != -1)
+ ::close(state->read_descriptor_);
+ state->read_descriptor_ = -1;
+
+ if (state->write_descriptor_ != -1)
+ ::close(state->write_descriptor_);
+ state->write_descriptor_ = -1;
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+}
+
+void signal_set_service::start_wait_op(
+ signal_set_service::implementation_type& impl, signal_op* op)
+{
+ io_service_.work_started();
+
+ signal_state* state = get_signal_state();
+ static_mutex::scoped_lock lock(state->mutex_);
+
+ registration* reg = impl.signals_;
+ while (reg)
+ {
+ if (reg->undelivered_ > 0)
+ {
+ --reg->undelivered_;
+ op->signal_number_ = reg->signal_number_;
+ io_service_.post_deferred_completion(op);
+ return;
+ }
+
+ reg = reg->next_in_set_;
+ }
+
+ impl.queue_.push(op);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_SIGNAL_SET_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/socket_ops.ipp b/ext/patches/boost/asio/detail/impl/socket_ops.ipp
new file mode 100644
index 0000000..307e747
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/socket_ops.ipp
@@ -0,0 +1,3395 @@
+//
+// detail/impl/socket_ops.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SOCKET_OPS_IPP
+#define BOOST_ASIO_DETAIL_SOCKET_OPS_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <cctype>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <cerrno>
+#include <new>
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/error.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <codecvt>
+# include <locale>
+# include <string>
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__) \
+ || defined(__MACH__) && defined(__APPLE__)
+# if defined(BOOST_ASIO_HAS_PTHREADS)
+# include <pthread.h>
+# endif // defined(BOOST_ASIO_HAS_PTHREADS)
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // || defined(__MACH__) && defined(__APPLE__)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+namespace socket_ops {
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+struct msghdr { int msg_namelen; };
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#if defined(__hpux)
+// HP-UX doesn't declare these functions extern "C", so they are declared again
+// here to avoid linker errors about undefined symbols.
+extern "C" char* if_indextoname(unsigned int, char*);
+extern "C" unsigned int if_nametoindex(const char*);
+#endif // defined(__hpux)
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+inline void clear_last_error()
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ WSASetLastError(0);
+#else
+ errno = 0;
+#endif
+}
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+template <typename ReturnType>
+inline ReturnType error_wrapper(ReturnType return_value,
+ boost::system::error_code& ec)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ec = boost::system::error_code(WSAGetLastError(),
+ boost::asio::error::get_system_category());
+#else
+ ec = boost::system::error_code(errno,
+ boost::asio::error::get_system_category());
+#endif
+ return return_value;
+}
+
+template <typename SockLenType>
+inline socket_type call_accept(SockLenType msghdr::*,
+ socket_type s, socket_addr_type* addr, std::size_t* addrlen)
+{
+ SockLenType tmp_addrlen = addrlen ? (SockLenType)*addrlen : 0;
+ socket_type result = ::accept(s, addr, addrlen ? &tmp_addrlen : 0);
+ if (addrlen)
+ *addrlen = (std::size_t)tmp_addrlen;
+ return result;
+}
+
+socket_type accept(socket_type s, socket_addr_type* addr,
+ std::size_t* addrlen, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return invalid_socket;
+ }
+
+ clear_last_error();
+
+ socket_type new_s = error_wrapper(call_accept(
+ &msghdr::msg_namelen, s, addr, addrlen), ec);
+ if (new_s == invalid_socket)
+ return new_s;
+
+#if defined(__MACH__) && defined(__APPLE__) || defined(__FreeBSD__)
+ int optval = 1;
+ int result = error_wrapper(::setsockopt(new_s,
+ SOL_SOCKET, SO_NOSIGPIPE, &optval, sizeof(optval)), ec);
+ if (result != 0)
+ {
+ ::close(new_s);
+ return invalid_socket;
+ }
+#endif
+
+ ec = boost::system::error_code();
+ return new_s;
+}
+
+socket_type sync_accept(socket_type s, state_type state,
+ socket_addr_type* addr, std::size_t* addrlen, boost::system::error_code& ec)
+{
+ // Accept a socket.
+ for (;;)
+ {
+ // Try to complete the operation without blocking.
+ socket_type new_socket = socket_ops::accept(s, addr, addrlen, ec);
+
+ // Check if operation succeeded.
+ if (new_socket != invalid_socket)
+ return new_socket;
+
+ // Operation failed.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ {
+ if (state & user_set_non_blocking)
+ return invalid_socket;
+ // Fall through to retry operation.
+ }
+ else if (ec == boost::asio::error::connection_aborted)
+ {
+ if (state & enable_connection_aborted)
+ return invalid_socket;
+ // Fall through to retry operation.
+ }
+#if defined(EPROTO)
+ else if (ec.value() == EPROTO)
+ {
+ if (state & enable_connection_aborted)
+ return invalid_socket;
+ // Fall through to retry operation.
+ }
+#endif // defined(EPROTO)
+ else
+ return invalid_socket;
+
+ // Wait for socket to become ready.
+ if (socket_ops::poll_read(s, 0, ec) < 0)
+ return invalid_socket;
+ }
+}
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+void complete_iocp_accept(socket_type s,
+ void* output_buffer, DWORD address_length,
+ socket_addr_type* addr, std::size_t* addrlen,
+ socket_type new_socket, boost::system::error_code& ec)
+{
+ // Map non-portable errors to their portable counterparts.
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ ec = boost::asio::error::connection_aborted;
+
+ if (!ec)
+ {
+ // Get the address of the peer.
+ if (addr && addrlen)
+ {
+ LPSOCKADDR local_addr = 0;
+ int local_addr_length = 0;
+ LPSOCKADDR remote_addr = 0;
+ int remote_addr_length = 0;
+ GetAcceptExSockaddrs(output_buffer, 0, address_length,
+ address_length, &local_addr, &local_addr_length,
+ &remote_addr, &remote_addr_length);
+ if (static_cast<std::size_t>(remote_addr_length) > *addrlen)
+ {
+ ec = boost::asio::error::invalid_argument;
+ }
+ else
+ {
+ using namespace std; // For memcpy.
+ memcpy(addr, remote_addr, remote_addr_length);
+ *addrlen = static_cast<std::size_t>(remote_addr_length);
+ }
+ }
+
+ // Need to set the SO_UPDATE_ACCEPT_CONTEXT option so that getsockname
+ // and getpeername will work on the accepted socket.
+ SOCKET update_ctx_param = s;
+ socket_ops::state_type state = 0;
+ socket_ops::setsockopt(new_socket, state,
+ SOL_SOCKET, SO_UPDATE_ACCEPT_CONTEXT,
+ &update_ctx_param, sizeof(SOCKET), ec);
+ }
+}
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+bool non_blocking_accept(socket_type s,
+ state_type state, socket_addr_type* addr, std::size_t* addrlen,
+ boost::system::error_code& ec, socket_type& new_socket)
+{
+ for (;;)
+ {
+ // Accept the waiting connection.
+ new_socket = socket_ops::accept(s, addr, addrlen, ec);
+
+ // Check if operation succeeded.
+ if (new_socket != invalid_socket)
+ return true;
+
+ // Retry operation if interrupted by signal.
+ if (ec == boost::asio::error::interrupted)
+ continue;
+
+ // Operation failed.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ {
+ if (state & user_set_non_blocking)
+ return true;
+ // Fall through to retry operation.
+ }
+ else if (ec == boost::asio::error::connection_aborted)
+ {
+ if (state & enable_connection_aborted)
+ return true;
+ // Fall through to retry operation.
+ }
+#if defined(EPROTO)
+ else if (ec.value() == EPROTO)
+ {
+ if (state & enable_connection_aborted)
+ return true;
+ // Fall through to retry operation.
+ }
+#endif // defined(EPROTO)
+ else
+ return true;
+
+ return false;
+ }
+}
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+template <typename SockLenType>
+inline int call_bind(SockLenType msghdr::*,
+ socket_type s, const socket_addr_type* addr, std::size_t addrlen)
+{
+ return ::bind(s, addr, (SockLenType)addrlen);
+}
+
+int bind(socket_type s, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+ clear_last_error();
+ int result = error_wrapper(call_bind(
+ &msghdr::msg_namelen, s, addr, addrlen), ec);
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+int close(socket_type s, state_type& state,
+ bool destruction, boost::system::error_code& ec)
+{
+ int result = 0;
+ if (s != invalid_socket)
+ {
+ // We don't want the destructor to block, so set the socket to linger in
+ // the background. If the user doesn't like this behaviour then they need
+ // to explicitly close the socket.
+ if (destruction && (state & user_set_linger))
+ {
+ ::linger opt;
+ opt.l_onoff = 0;
+ opt.l_linger = 0;
+ boost::system::error_code ignored_ec;
+ socket_ops::setsockopt(s, state, SOL_SOCKET,
+ SO_LINGER, &opt, sizeof(opt), ignored_ec);
+ }
+
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ result = error_wrapper(::closesocket(s), ec);
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ result = error_wrapper(::close(s), ec);
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+ if (result != 0
+ && (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again))
+ {
+ // According to UNIX Network Programming Vol. 1, it is possible for
+ // close() to fail with EWOULDBLOCK under certain circumstances. What
+ // isn't clear is the state of the descriptor after this error. The one
+ // current OS where this behaviour is seen, Windows, says that the socket
+ // remains open. Therefore we'll put the descriptor back into blocking
+ // mode and have another attempt at closing it.
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ioctl_arg_type arg = 0;
+ ::ioctlsocket(s, FIONBIO, &arg);
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if defined(__SYMBIAN32__)
+ int flags = ::fcntl(s, F_GETFL, 0);
+ if (flags >= 0)
+ ::fcntl(s, F_SETFL, flags & ~O_NONBLOCK);
+# else // defined(__SYMBIAN32__)
+ ioctl_arg_type arg = 0;
+ ::ioctl(s, FIONBIO, &arg);
+# endif // defined(__SYMBIAN32__)
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ state &= ~non_blocking;
+
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ result = error_wrapper(::closesocket(s), ec);
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ result = error_wrapper(::close(s), ec);
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ }
+ }
+
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+bool set_user_non_blocking(socket_type s,
+ state_type& state, bool value, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return false;
+ }
+
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ioctl_arg_type arg = (value ? 1 : 0);
+ int result = error_wrapper(::ioctlsocket(s, FIONBIO, &arg), ec);
+#elif defined(__SYMBIAN32__)
+ int result = error_wrapper(::fcntl(s, F_GETFL, 0), ec);
+ if (result >= 0)
+ {
+ clear_last_error();
+ int flag = (value ? (result | O_NONBLOCK) : (result & ~O_NONBLOCK));
+ result = error_wrapper(::fcntl(s, F_SETFL, flag), ec);
+ }
+#else
+ ioctl_arg_type arg = (value ? 1 : 0);
+ int result = error_wrapper(::ioctl(s, FIONBIO, &arg), ec);
+#endif
+
+ if (result >= 0)
+ {
+ ec = boost::system::error_code();
+ if (value)
+ state |= user_set_non_blocking;
+ else
+ {
+ // Clearing the user-set non-blocking mode always overrides any
+ // internally-set non-blocking flag. Any subsequent asynchronous
+ // operations will need to re-enable non-blocking I/O.
+ state &= ~(user_set_non_blocking | internal_non_blocking);
+ }
+ return true;
+ }
+
+ return false;
+}
+
+bool set_internal_non_blocking(socket_type s,
+ state_type& state, bool value, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return false;
+ }
+
+ if (!value && (state & user_set_non_blocking))
+ {
+ // It does not make sense to clear the internal non-blocking flag if the
+ // user still wants non-blocking behaviour. Return an error and let the
+ // caller figure out whether to update the user-set non-blocking flag.
+ ec = boost::asio::error::invalid_argument;
+ return false;
+ }
+
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ ioctl_arg_type arg = (value ? 1 : 0);
+ int result = error_wrapper(::ioctlsocket(s, FIONBIO, &arg), ec);
+#elif defined(__SYMBIAN32__)
+ int result = error_wrapper(::fcntl(s, F_GETFL, 0), ec);
+ if (result >= 0)
+ {
+ clear_last_error();
+ int flag = (value ? (result | O_NONBLOCK) : (result & ~O_NONBLOCK));
+ result = error_wrapper(::fcntl(s, F_SETFL, flag), ec);
+ }
+#else
+ ioctl_arg_type arg = (value ? 1 : 0);
+ int result = error_wrapper(::ioctl(s, FIONBIO, &arg), ec);
+#endif
+
+ if (result >= 0)
+ {
+ ec = boost::system::error_code();
+ if (value)
+ state |= internal_non_blocking;
+ else
+ state &= ~internal_non_blocking;
+ return true;
+ }
+
+ return false;
+}
+
+int shutdown(socket_type s, int what, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+ clear_last_error();
+ int result = error_wrapper(::shutdown(s, what), ec);
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+template <typename SockLenType>
+inline int call_connect(SockLenType msghdr::*,
+ socket_type s, const socket_addr_type* addr, std::size_t addrlen)
+{
+ return ::connect(s, addr, (SockLenType)addrlen);
+}
+
+int connect(socket_type s, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+ clear_last_error();
+ int result = error_wrapper(call_connect(
+ &msghdr::msg_namelen, s, addr, addrlen), ec);
+ if (result == 0)
+ ec = boost::system::error_code();
+#if defined(__linux__)
+ else if (ec == boost::asio::error::try_again)
+ ec = boost::asio::error::no_buffer_space;
+#endif // defined(__linux__)
+ return result;
+}
+
+void sync_connect(socket_type s, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec)
+{
+ // Perform the connect operation.
+ socket_ops::connect(s, addr, addrlen, ec);
+ if (ec != boost::asio::error::in_progress
+ && ec != boost::asio::error::would_block)
+ {
+ // The connect operation finished immediately.
+ return;
+ }
+
+ // Wait for socket to become ready.
+ if (socket_ops::poll_connect(s, ec) < 0)
+ return;
+
+ // Get the error code from the connect operation.
+ int connect_error = 0;
+ size_t connect_error_len = sizeof(connect_error);
+ if (socket_ops::getsockopt(s, 0, SOL_SOCKET, SO_ERROR,
+ &connect_error, &connect_error_len, ec) == socket_error_retval)
+ return;
+
+ // Return the result of the connect operation.
+ ec = boost::system::error_code(connect_error,
+ boost::asio::error::get_system_category());
+}
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+void complete_iocp_connect(socket_type s, boost::system::error_code& ec)
+{
+ if (!ec)
+ {
+ // Need to set the SO_UPDATE_CONNECT_CONTEXT option so that getsockname
+ // and getpeername will work on the connected socket.
+ socket_ops::state_type state = 0;
+ const int so_update_connect_context = 0x7010;
+ socket_ops::setsockopt(s, state, SOL_SOCKET,
+ so_update_connect_context, 0, 0, ec);
+ }
+}
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+bool non_blocking_connect(socket_type s, boost::system::error_code& ec)
+{
+ // Check if the connect operation has finished. This is required since we may
+ // get spurious readiness notifications from the reactor.
+#if defined(BOOST_ASIO_WINDOWS) \
+ || defined(__CYGWIN__) \
+ || defined(__SYMBIAN32__)
+ fd_set write_fds;
+ FD_ZERO(&write_fds);
+ FD_SET(s, &write_fds);
+ fd_set except_fds;
+ FD_ZERO(&except_fds);
+ FD_SET(s, &except_fds);
+ timeval zero_timeout;
+ zero_timeout.tv_sec = 0;
+ zero_timeout.tv_usec = 0;
+ int ready = ::select(s + 1, 0, &write_fds, &except_fds, &zero_timeout);
+#else // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+ pollfd fds;
+ fds.fd = s;
+ fds.events = POLLOUT;
+ fds.revents = 0;
+ int ready = ::poll(&fds, 1, 0);
+#endif // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+ if (ready == 0)
+ {
+ // The asynchronous connect operation is still in progress.
+ return false;
+ }
+
+ // Get the error code from the connect operation.
+ int connect_error = 0;
+ size_t connect_error_len = sizeof(connect_error);
+ if (socket_ops::getsockopt(s, 0, SOL_SOCKET, SO_ERROR,
+ &connect_error, &connect_error_len, ec) == 0)
+ {
+ if (connect_error)
+ {
+ ec = boost::system::error_code(connect_error,
+ boost::asio::error::get_system_category());
+ }
+ else
+ ec = boost::system::error_code();
+ }
+
+ return true;
+}
+
+int socketpair(int af, int type, int protocol,
+ socket_type sv[2], boost::system::error_code& ec)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ (void)(af);
+ (void)(type);
+ (void)(protocol);
+ (void)(sv);
+ ec = boost::asio::error::operation_not_supported;
+ return socket_error_retval;
+#else
+ clear_last_error();
+ int result = error_wrapper(::socketpair(af, type, protocol, sv), ec);
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+#endif
+}
+
+bool sockatmark(socket_type s, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return false;
+ }
+
+#if defined(SIOCATMARK)
+ ioctl_arg_type value = 0;
+# if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ int result = error_wrapper(::ioctlsocket(s, SIOCATMARK, &value), ec);
+# else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ int result = error_wrapper(::ioctl(s, SIOCATMARK, &value), ec);
+# endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ if (result == 0)
+ ec = boost::system::error_code();
+# if defined(ENOTTY)
+ if (ec.value() == ENOTTY)
+ ec = boost::asio::error::not_socket;
+# endif // defined(ENOTTY)
+#else // defined(SIOCATMARK)
+ int value = error_wrapper(::sockatmark(s), ec);
+ if (value != -1)
+ ec = boost::system::error_code();
+#endif // defined(SIOCATMARK)
+
+ return ec ? false : value != 0;
+}
+
+size_t available(socket_type s, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ ioctl_arg_type value = 0;
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ int result = error_wrapper(::ioctlsocket(s, FIONREAD, &value), ec);
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ int result = error_wrapper(::ioctl(s, FIONREAD, &value), ec);
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ if (result == 0)
+ ec = boost::system::error_code();
+#if defined(ENOTTY)
+ if (ec.value() == ENOTTY)
+ ec = boost::asio::error::not_socket;
+#endif // defined(ENOTTY)
+
+ return ec ? static_cast<size_t>(0) : static_cast<size_t>(value);
+}
+
+int listen(socket_type s, int backlog, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+ clear_last_error();
+ int result = error_wrapper(::listen(s, backlog), ec);
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+inline void init_buf_iov_base(void*& base, void* addr)
+{
+ base = addr;
+}
+
+template <typename T>
+inline void init_buf_iov_base(T& base, void* addr)
+{
+ base = static_cast<T>(addr);
+}
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+typedef WSABUF buf;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+typedef iovec buf;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+void init_buf(buf& b, void* data, size_t size)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ b.buf = static_cast<char*>(data);
+ b.len = static_cast<u_long>(size);
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ init_buf_iov_base(b.iov_base, data);
+ b.iov_len = size;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+void init_buf(buf& b, const void* data, size_t size)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ b.buf = static_cast<char*>(const_cast<void*>(data));
+ b.len = static_cast<u_long>(size);
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ init_buf_iov_base(b.iov_base, const_cast<void*>(data));
+ b.iov_len = size;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+inline void init_msghdr_msg_name(void*& name, socket_addr_type* addr)
+{
+ name = addr;
+}
+
+inline void init_msghdr_msg_name(void*& name, const socket_addr_type* addr)
+{
+ name = const_cast<socket_addr_type*>(addr);
+}
+
+template <typename T>
+inline void init_msghdr_msg_name(T& name, socket_addr_type* addr)
+{
+ name = reinterpret_cast<T>(addr);
+}
+
+template <typename T>
+inline void init_msghdr_msg_name(T& name, const socket_addr_type* addr)
+{
+ name = reinterpret_cast<T>(const_cast<socket_addr_type*>(addr));
+}
+
+signed_size_type recv(socket_type s, buf* bufs, size_t count,
+ int flags, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // Receive some data.
+ DWORD recv_buf_count = static_cast<DWORD>(count);
+ DWORD bytes_transferred = 0;
+ DWORD recv_flags = flags;
+ int result = error_wrapper(::WSARecv(s, bufs,
+ recv_buf_count, &bytes_transferred, &recv_flags, 0, 0), ec);
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ ec = boost::asio::error::connection_reset;
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ ec = boost::asio::error::connection_refused;
+ if (result != 0)
+ return socket_error_retval;
+ ec = boost::system::error_code();
+ return bytes_transferred;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ msghdr msg = msghdr();
+ msg.msg_iov = bufs;
+ msg.msg_iovlen = static_cast<int>(count);
+ signed_size_type result = error_wrapper(::recvmsg(s, &msg, flags), ec);
+ if (result >= 0)
+ ec = boost::system::error_code();
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+size_t sync_recv(socket_type s, state_type state, buf* bufs,
+ size_t count, int flags, bool all_empty, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // A request to read 0 bytes on a stream is a no-op.
+ if (all_empty && (state & stream_oriented))
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ // Read some data.
+ for (;;)
+ {
+ // Try to complete the operation without blocking.
+ signed_size_type bytes = socket_ops::recv(s, bufs, count, flags, ec);
+
+ // Check if operation succeeded.
+ if (bytes > 0)
+ return bytes;
+
+ // Check for EOF.
+ if ((state & stream_oriented) && bytes == 0)
+ {
+ ec = boost::asio::error::eof;
+ return 0;
+ }
+
+ // Operation failed.
+ if ((state & user_set_non_blocking)
+ || (ec != boost::asio::error::would_block
+ && ec != boost::asio::error::try_again))
+ return 0;
+
+ // Wait for socket to become ready.
+ if (socket_ops::poll_read(s, 0, ec) < 0)
+ return 0;
+ }
+}
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+void complete_iocp_recv(state_type state,
+ const weak_cancel_token_type& cancel_token, bool all_empty,
+ boost::system::error_code& ec, size_t bytes_transferred)
+{
+ // Map non-portable errors to their portable counterparts.
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ {
+ if (cancel_token.expired())
+ ec = boost::asio::error::operation_aborted;
+ else
+ ec = boost::asio::error::connection_reset;
+ }
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ {
+ ec = boost::asio::error::connection_refused;
+ }
+
+ // Check for connection closed.
+ else if (!ec && bytes_transferred == 0
+ && (state & stream_oriented) != 0
+ && !all_empty)
+ {
+ ec = boost::asio::error::eof;
+ }
+}
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+bool non_blocking_recv(socket_type s,
+ buf* bufs, size_t count, int flags, bool is_stream,
+ boost::system::error_code& ec, size_t& bytes_transferred)
+{
+ for (;;)
+ {
+ // Read some data.
+ signed_size_type bytes = socket_ops::recv(s, bufs, count, flags, ec);
+
+ // Check for end of stream.
+ if (is_stream && bytes == 0)
+ {
+ ec = boost::asio::error::eof;
+ return true;
+ }
+
+ // Retry operation if interrupted by signal.
+ if (ec == boost::asio::error::interrupted)
+ continue;
+
+ // Check if we need to run the operation again.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ return false;
+
+ // Operation is complete.
+ if (bytes >= 0)
+ {
+ ec = boost::system::error_code();
+ bytes_transferred = bytes;
+ }
+ else
+ bytes_transferred = 0;
+
+ return true;
+ }
+}
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+signed_size_type recvfrom(socket_type s, buf* bufs, size_t count,
+ int flags, socket_addr_type* addr, std::size_t* addrlen,
+ boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // Receive some data.
+ DWORD recv_buf_count = static_cast<DWORD>(count);
+ DWORD bytes_transferred = 0;
+ DWORD recv_flags = flags;
+ int tmp_addrlen = (int)*addrlen;
+ int result = error_wrapper(::WSARecvFrom(s, bufs, recv_buf_count,
+ &bytes_transferred, &recv_flags, addr, &tmp_addrlen, 0, 0), ec);
+ *addrlen = (std::size_t)tmp_addrlen;
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ ec = boost::asio::error::connection_reset;
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ ec = boost::asio::error::connection_refused;
+ if (result != 0)
+ return socket_error_retval;
+ ec = boost::system::error_code();
+ return bytes_transferred;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ msghdr msg = msghdr();
+ init_msghdr_msg_name(msg.msg_name, addr);
+ msg.msg_namelen = static_cast<int>(*addrlen);
+ msg.msg_iov = bufs;
+ msg.msg_iovlen = static_cast<int>(count);
+ signed_size_type result = error_wrapper(::recvmsg(s, &msg, flags), ec);
+ *addrlen = msg.msg_namelen;
+ if (result >= 0)
+ ec = boost::system::error_code();
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+size_t sync_recvfrom(socket_type s, state_type state, buf* bufs,
+ size_t count, int flags, socket_addr_type* addr,
+ std::size_t* addrlen, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // Read some data.
+ for (;;)
+ {
+ // Try to complete the operation without blocking.
+ signed_size_type bytes = socket_ops::recvfrom(
+ s, bufs, count, flags, addr, addrlen, ec);
+
+ // Check if operation succeeded.
+ if (bytes >= 0)
+ return bytes;
+
+ // Operation failed.
+ if ((state & user_set_non_blocking)
+ || (ec != boost::asio::error::would_block
+ && ec != boost::asio::error::try_again))
+ return 0;
+
+ // Wait for socket to become ready.
+ if (socket_ops::poll_read(s, 0, ec) < 0)
+ return 0;
+ }
+}
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+void complete_iocp_recvfrom(
+ const weak_cancel_token_type& cancel_token,
+ boost::system::error_code& ec)
+{
+ // Map non-portable errors to their portable counterparts.
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ {
+ if (cancel_token.expired())
+ ec = boost::asio::error::operation_aborted;
+ else
+ ec = boost::asio::error::connection_reset;
+ }
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ {
+ ec = boost::asio::error::connection_refused;
+ }
+}
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+bool non_blocking_recvfrom(socket_type s,
+ buf* bufs, size_t count, int flags,
+ socket_addr_type* addr, std::size_t* addrlen,
+ boost::system::error_code& ec, size_t& bytes_transferred)
+{
+ for (;;)
+ {
+ // Read some data.
+ signed_size_type bytes = socket_ops::recvfrom(
+ s, bufs, count, flags, addr, addrlen, ec);
+
+ // Retry operation if interrupted by signal.
+ if (ec == boost::asio::error::interrupted)
+ continue;
+
+ // Check if we need to run the operation again.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ return false;
+
+ // Operation is complete.
+ if (bytes >= 0)
+ {
+ ec = boost::system::error_code();
+ bytes_transferred = bytes;
+ }
+ else
+ bytes_transferred = 0;
+
+ return true;
+ }
+}
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+signed_size_type recvmsg(socket_type s, buf* bufs, size_t count,
+ int in_flags, int& out_flags, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ out_flags = 0;
+ return socket_ops::recv(s, bufs, count, in_flags, ec);
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ msghdr msg = msghdr();
+ msg.msg_iov = bufs;
+ msg.msg_iovlen = static_cast<int>(count);
+ signed_size_type result = error_wrapper(::recvmsg(s, &msg, in_flags), ec);
+ if (result >= 0)
+ {
+ ec = boost::system::error_code();
+ out_flags = msg.msg_flags;
+ }
+ else
+ out_flags = 0;
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+size_t sync_recvmsg(socket_type s, state_type state,
+ buf* bufs, size_t count, int in_flags, int& out_flags,
+ boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // Read some data.
+ for (;;)
+ {
+ // Try to complete the operation without blocking.
+ signed_size_type bytes = socket_ops::recvmsg(
+ s, bufs, count, in_flags, out_flags, ec);
+
+ // Check if operation succeeded.
+ if (bytes >= 0)
+ return bytes;
+
+ // Operation failed.
+ if ((state & user_set_non_blocking)
+ || (ec != boost::asio::error::would_block
+ && ec != boost::asio::error::try_again))
+ return 0;
+
+ // Wait for socket to become ready.
+ if (socket_ops::poll_read(s, 0, ec) < 0)
+ return 0;
+ }
+}
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+void complete_iocp_recvmsg(
+ const weak_cancel_token_type& cancel_token,
+ boost::system::error_code& ec)
+{
+ // Map non-portable errors to their portable counterparts.
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ {
+ if (cancel_token.expired())
+ ec = boost::asio::error::operation_aborted;
+ else
+ ec = boost::asio::error::connection_reset;
+ }
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ {
+ ec = boost::asio::error::connection_refused;
+ }
+}
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+bool non_blocking_recvmsg(socket_type s,
+ buf* bufs, size_t count, int in_flags, int& out_flags,
+ boost::system::error_code& ec, size_t& bytes_transferred)
+{
+ for (;;)
+ {
+ // Read some data.
+ signed_size_type bytes = socket_ops::recvmsg(
+ s, bufs, count, in_flags, out_flags, ec);
+
+ // Retry operation if interrupted by signal.
+ if (ec == boost::asio::error::interrupted)
+ continue;
+
+ // Check if we need to run the operation again.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ return false;
+
+ // Operation is complete.
+ if (bytes >= 0)
+ {
+ ec = boost::system::error_code();
+ bytes_transferred = bytes;
+ }
+ else
+ bytes_transferred = 0;
+
+ return true;
+ }
+}
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+signed_size_type send(socket_type s, const buf* bufs, size_t count,
+ int flags, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // Send the data.
+ DWORD send_buf_count = static_cast<DWORD>(count);
+ DWORD bytes_transferred = 0;
+ DWORD send_flags = flags;
+ int result = error_wrapper(::WSASend(s, const_cast<buf*>(bufs),
+ send_buf_count, &bytes_transferred, send_flags, 0, 0), ec);
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ ec = boost::asio::error::connection_reset;
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ ec = boost::asio::error::connection_refused;
+ if (result != 0)
+ return socket_error_retval;
+ ec = boost::system::error_code();
+ return bytes_transferred;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ msghdr msg = msghdr();
+ msg.msg_iov = const_cast<buf*>(bufs);
+ msg.msg_iovlen = static_cast<int>(count);
+#if defined(__linux__)
+ flags |= MSG_NOSIGNAL;
+#endif // defined(__linux__)
+ signed_size_type result = error_wrapper(::sendmsg(s, &msg, flags), ec);
+ if (result >= 0)
+ ec = boost::system::error_code();
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+size_t sync_send(socket_type s, state_type state, const buf* bufs,
+ size_t count, int flags, bool all_empty, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // A request to write 0 bytes to a stream is a no-op.
+ if (all_empty && (state & stream_oriented))
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ // Read some data.
+ for (;;)
+ {
+ // Try to complete the operation without blocking.
+ signed_size_type bytes = socket_ops::send(s, bufs, count, flags, ec);
+
+ // Check if operation succeeded.
+ if (bytes >= 0)
+ return bytes;
+
+ // Operation failed.
+ if ((state & user_set_non_blocking)
+ || (ec != boost::asio::error::would_block
+ && ec != boost::asio::error::try_again))
+ return 0;
+
+ // Wait for socket to become ready.
+ if (socket_ops::poll_write(s, 0, ec) < 0)
+ return 0;
+ }
+}
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+void complete_iocp_send(
+ const weak_cancel_token_type& cancel_token,
+ boost::system::error_code& ec)
+{
+ // Map non-portable errors to their portable counterparts.
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ {
+ if (cancel_token.expired())
+ ec = boost::asio::error::operation_aborted;
+ else
+ ec = boost::asio::error::connection_reset;
+ }
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ {
+ ec = boost::asio::error::connection_refused;
+ }
+}
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+bool non_blocking_send(socket_type s,
+ const buf* bufs, size_t count, int flags,
+ boost::system::error_code& ec, size_t& bytes_transferred)
+{
+ for (;;)
+ {
+ // Write some data.
+ signed_size_type bytes = socket_ops::send(s, bufs, count, flags, ec);
+
+ // Retry operation if interrupted by signal.
+ if (ec == boost::asio::error::interrupted)
+ continue;
+
+ // Check if we need to run the operation again.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ return false;
+
+ // Operation is complete.
+ if (bytes >= 0)
+ {
+ ec = boost::system::error_code();
+ bytes_transferred = bytes;
+ }
+ else
+ bytes_transferred = 0;
+
+ return true;
+ }
+}
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+signed_size_type sendto(socket_type s, const buf* bufs, size_t count,
+ int flags, const socket_addr_type* addr, std::size_t addrlen,
+ boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ // Send the data.
+ DWORD send_buf_count = static_cast<DWORD>(count);
+ DWORD bytes_transferred = 0;
+ int result = error_wrapper(::WSASendTo(s, const_cast<buf*>(bufs),
+ send_buf_count, &bytes_transferred, flags, addr,
+ static_cast<int>(addrlen), 0, 0), ec);
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ ec = boost::asio::error::connection_reset;
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ ec = boost::asio::error::connection_refused;
+ if (result != 0)
+ return socket_error_retval;
+ ec = boost::system::error_code();
+ return bytes_transferred;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ msghdr msg = msghdr();
+ init_msghdr_msg_name(msg.msg_name, addr);
+ msg.msg_namelen = static_cast<int>(addrlen);
+ msg.msg_iov = const_cast<buf*>(bufs);
+ msg.msg_iovlen = static_cast<int>(count);
+#if defined(__linux__)
+ flags |= MSG_NOSIGNAL;
+#endif // defined(__linux__)
+ signed_size_type result = error_wrapper(::sendmsg(s, &msg, flags), ec);
+ if (result >= 0)
+ ec = boost::system::error_code();
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+size_t sync_sendto(socket_type s, state_type state, const buf* bufs,
+ size_t count, int flags, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // Write some data.
+ for (;;)
+ {
+ // Try to complete the operation without blocking.
+ signed_size_type bytes = socket_ops::sendto(
+ s, bufs, count, flags, addr, addrlen, ec);
+
+ // Check if operation succeeded.
+ if (bytes >= 0)
+ return bytes;
+
+ // Operation failed.
+ if ((state & user_set_non_blocking)
+ || (ec != boost::asio::error::would_block
+ && ec != boost::asio::error::try_again))
+ return 0;
+
+ // Wait for socket to become ready.
+ if (socket_ops::poll_write(s, 0, ec) < 0)
+ return 0;
+ }
+}
+
+#if !defined(BOOST_ASIO_HAS_IOCP)
+
+bool non_blocking_sendto(socket_type s,
+ const buf* bufs, size_t count, int flags,
+ const socket_addr_type* addr, std::size_t addrlen,
+ boost::system::error_code& ec, size_t& bytes_transferred)
+{
+ for (;;)
+ {
+ // Write some data.
+ signed_size_type bytes = socket_ops::sendto(
+ s, bufs, count, flags, addr, addrlen, ec);
+
+ // Retry operation if interrupted by signal.
+ if (ec == boost::asio::error::interrupted)
+ continue;
+
+ // Check if we need to run the operation again.
+ if (ec == boost::asio::error::would_block
+ || ec == boost::asio::error::try_again)
+ return false;
+
+ // Operation is complete.
+ if (bytes >= 0)
+ {
+ ec = boost::system::error_code();
+ bytes_transferred = bytes;
+ }
+ else
+ bytes_transferred = 0;
+
+ return true;
+ }
+}
+
+#endif // !defined(BOOST_ASIO_HAS_IOCP)
+
+socket_type socket(int af, int type, int protocol,
+ boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ socket_type s = error_wrapper(::WSASocket(af, type, protocol, 0, 0,
+ WSA_FLAG_OVERLAPPED), ec);
+ if (s == invalid_socket)
+ return s;
+
+ if (af == BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ // Try to enable the POSIX default behaviour of having IPV6_V6ONLY set to
+ // false. This will only succeed on Windows Vista and later versions of
+ // Windows, where a dual-stack IPv4/v6 implementation is available.
+ DWORD optval = 0;
+ ::setsockopt(s, IPPROTO_IPV6, IPV6_V6ONLY,
+ reinterpret_cast<const char*>(&optval), sizeof(optval));
+ }
+
+ ec = boost::system::error_code();
+
+ return s;
+#elif defined(__MACH__) && defined(__APPLE__) || defined(__FreeBSD__)
+ socket_type s = error_wrapper(::socket(af, type, protocol), ec);
+ if (s == invalid_socket)
+ return s;
+
+ int optval = 1;
+ int result = error_wrapper(::setsockopt(s,
+ SOL_SOCKET, SO_NOSIGPIPE, &optval, sizeof(optval)), ec);
+ if (result != 0)
+ {
+ ::close(s);
+ return invalid_socket;
+ }
+
+ return s;
+#else
+ int s = error_wrapper(::socket(af, type, protocol), ec);
+ if (s >= 0)
+ ec = boost::system::error_code();
+ return s;
+#endif
+}
+
+template <typename SockLenType>
+inline int call_setsockopt(SockLenType msghdr::*,
+ socket_type s, int level, int optname,
+ const void* optval, std::size_t optlen)
+{
+ return ::setsockopt(s, level, optname,
+ (const char*)optval, (SockLenType)optlen);
+}
+
+int setsockopt(socket_type s, state_type& state, int level, int optname,
+ const void* optval, std::size_t optlen, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+ if (level == custom_socket_option_level && optname == always_fail_option)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return socket_error_retval;
+ }
+
+ if (level == custom_socket_option_level
+ && optname == enable_connection_aborted_option)
+ {
+ if (optlen != sizeof(int))
+ {
+ ec = boost::asio::error::invalid_argument;
+ return socket_error_retval;
+ }
+
+ if (*static_cast<const int*>(optval))
+ state |= enable_connection_aborted;
+ else
+ state &= ~enable_connection_aborted;
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ if (level == SOL_SOCKET && optname == SO_LINGER)
+ state |= user_set_linger;
+
+#if defined(__BORLANDC__)
+ // Mysteriously, using the getsockopt and setsockopt functions directly with
+ // Borland C++ results in incorrect values being set and read. The bug can be
+ // worked around by using function addresses resolved with GetProcAddress.
+ if (HMODULE winsock_module = ::GetModuleHandleA("ws2_32"))
+ {
+ typedef int (WSAAPI *sso_t)(SOCKET, int, int, const char*, int);
+ if (sso_t sso = (sso_t)::GetProcAddress(winsock_module, "setsockopt"))
+ {
+ clear_last_error();
+ return error_wrapper(sso(s, level, optname,
+ reinterpret_cast<const char*>(optval),
+ static_cast<int>(optlen)), ec);
+ }
+ }
+ ec = boost::asio::error::fault;
+ return socket_error_retval;
+#else // defined(__BORLANDC__)
+ clear_last_error();
+ int result = error_wrapper(call_setsockopt(&msghdr::msg_namelen,
+ s, level, optname, optval, optlen), ec);
+ if (result == 0)
+ {
+ ec = boost::system::error_code();
+
+#if defined(__MACH__) && defined(__APPLE__) \
+ || defined(__NetBSD__) || defined(__FreeBSD__) || defined(__OpenBSD__)
+ // To implement portable behaviour for SO_REUSEADDR with UDP sockets we
+ // need to also set SO_REUSEPORT on BSD-based platforms.
+ if ((state & datagram_oriented)
+ && level == SOL_SOCKET && optname == SO_REUSEADDR)
+ {
+ call_setsockopt(&msghdr::msg_namelen, s,
+ SOL_SOCKET, SO_REUSEPORT, optval, optlen);
+ }
+#endif
+ }
+
+ return result;
+#endif // defined(__BORLANDC__)
+}
+
+template <typename SockLenType>
+inline int call_getsockopt(SockLenType msghdr::*,
+ socket_type s, int level, int optname,
+ void* optval, std::size_t* optlen)
+{
+ SockLenType tmp_optlen = (SockLenType)*optlen;
+ int result = ::getsockopt(s, level, optname, (char*)optval, &tmp_optlen);
+ *optlen = (std::size_t)tmp_optlen;
+ return result;
+}
+
+int getsockopt(socket_type s, state_type state, int level, int optname,
+ void* optval, size_t* optlen, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+ if (level == custom_socket_option_level && optname == always_fail_option)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return socket_error_retval;
+ }
+
+ if (level == custom_socket_option_level
+ && optname == enable_connection_aborted_option)
+ {
+ if (*optlen != sizeof(int))
+ {
+ ec = boost::asio::error::invalid_argument;
+ return socket_error_retval;
+ }
+
+ *static_cast<int*>(optval) = (state & enable_connection_aborted) ? 1 : 0;
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+#if defined(__BORLANDC__)
+ // Mysteriously, using the getsockopt and setsockopt functions directly with
+ // Borland C++ results in incorrect values being set and read. The bug can be
+ // worked around by using function addresses resolved with GetProcAddress.
+ if (HMODULE winsock_module = ::GetModuleHandleA("ws2_32"))
+ {
+ typedef int (WSAAPI *gso_t)(SOCKET, int, int, char*, int*);
+ if (gso_t gso = (gso_t)::GetProcAddress(winsock_module, "getsockopt"))
+ {
+ clear_last_error();
+ int tmp_optlen = static_cast<int>(*optlen);
+ int result = error_wrapper(gso(s, level, optname,
+ reinterpret_cast<char*>(optval), &tmp_optlen), ec);
+ *optlen = static_cast<size_t>(tmp_optlen);
+ if (result != 0 && level == IPPROTO_IPV6 && optname == IPV6_V6ONLY
+ && ec.value() == WSAENOPROTOOPT && *optlen == sizeof(DWORD))
+ {
+ // Dual-stack IPv4/v6 sockets, and the IPV6_V6ONLY socket option, are
+ // only supported on Windows Vista and later. To simplify program logic
+ // we will fake success of getting this option and specify that the
+ // value is non-zero (i.e. true). This corresponds to the behavior of
+ // IPv6 sockets on Windows platforms pre-Vista.
+ *static_cast<DWORD*>(optval) = 1;
+ ec = boost::system::error_code();
+ }
+ return result;
+ }
+ }
+ ec = boost::asio::error::fault;
+ return socket_error_retval;
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ clear_last_error();
+ int result = error_wrapper(call_getsockopt(&msghdr::msg_namelen,
+ s, level, optname, optval, optlen), ec);
+ if (result != 0 && level == IPPROTO_IPV6 && optname == IPV6_V6ONLY
+ && ec.value() == WSAENOPROTOOPT && *optlen == sizeof(DWORD))
+ {
+ // Dual-stack IPv4/v6 sockets, and the IPV6_V6ONLY socket option, are only
+ // supported on Windows Vista and later. To simplify program logic we will
+ // fake success of getting this option and specify that the value is
+ // non-zero (i.e. true). This corresponds to the behavior of IPv6 sockets
+ // on Windows platforms pre-Vista.
+ *static_cast<DWORD*>(optval) = 1;
+ ec = boost::system::error_code();
+ }
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ clear_last_error();
+ int result = error_wrapper(call_getsockopt(&msghdr::msg_namelen,
+ s, level, optname, optval, optlen), ec);
+#if defined(__linux__)
+ if (result == 0 && level == SOL_SOCKET && *optlen == sizeof(int)
+ && (optname == SO_SNDBUF || optname == SO_RCVBUF))
+ {
+ // On Linux, setting SO_SNDBUF or SO_RCVBUF to N actually causes the kernel
+ // to set the buffer size to N*2. Linux puts additional stuff into the
+ // buffers so that only about half is actually available to the application.
+ // The retrieved value is divided by 2 here to make it appear as though the
+ // correct value has been set.
+ *static_cast<int*>(optval) /= 2;
+ }
+#endif // defined(__linux__)
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+template <typename SockLenType>
+inline int call_getpeername(SockLenType msghdr::*,
+ socket_type s, socket_addr_type* addr, std::size_t* addrlen)
+{
+ SockLenType tmp_addrlen = (SockLenType)*addrlen;
+ int result = ::getpeername(s, addr, &tmp_addrlen);
+ *addrlen = (std::size_t)tmp_addrlen;
+ return result;
+}
+
+int getpeername(socket_type s, socket_addr_type* addr,
+ std::size_t* addrlen, bool cached, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ if (cached)
+ {
+ // Check if socket is still connected.
+ DWORD connect_time = 0;
+ size_t connect_time_len = sizeof(connect_time);
+ if (socket_ops::getsockopt(s, 0, SOL_SOCKET, SO_CONNECT_TIME,
+ &connect_time, &connect_time_len, ec) == socket_error_retval)
+ {
+ return socket_error_retval;
+ }
+ if (connect_time == 0xFFFFFFFF)
+ {
+ ec = boost::asio::error::not_connected;
+ return socket_error_retval;
+ }
+
+ // The cached value is still valid.
+ ec = boost::system::error_code();
+ return 0;
+ }
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ (void)cached;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+ clear_last_error();
+ int result = error_wrapper(call_getpeername(
+ &msghdr::msg_namelen, s, addr, addrlen), ec);
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+template <typename SockLenType>
+inline int call_getsockname(SockLenType msghdr::*,
+ socket_type s, socket_addr_type* addr, std::size_t* addrlen)
+{
+ SockLenType tmp_addrlen = (SockLenType)*addrlen;
+ int result = ::getsockname(s, addr, &tmp_addrlen);
+ *addrlen = (std::size_t)tmp_addrlen;
+ return result;
+}
+
+int getsockname(socket_type s, socket_addr_type* addr,
+ std::size_t* addrlen, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+ clear_last_error();
+ int result = error_wrapper(call_getsockname(
+ &msghdr::msg_namelen, s, addr, addrlen), ec);
+ if (result == 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+int ioctl(socket_type s, state_type& state, int cmd,
+ ioctl_arg_type* arg, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ int result = error_wrapper(::ioctlsocket(s, cmd, arg), ec);
+#elif defined(__MACH__) && defined(__APPLE__) \
+ || defined(__NetBSD__) || defined(__FreeBSD__) || defined(__OpenBSD__)
+ int result = error_wrapper(::ioctl(s,
+ static_cast<unsigned int>(cmd), arg), ec);
+#else
+ int result = error_wrapper(::ioctl(s, cmd, arg), ec);
+#endif
+ if (result >= 0)
+ {
+ ec = boost::system::error_code();
+
+ // When updating the non-blocking mode we always perform the ioctl syscall,
+ // even if the flags would otherwise indicate that the socket is already in
+ // the correct state. This ensures that the underlying socket is put into
+ // the state that has been requested by the user. If the ioctl syscall was
+ // successful then we need to update the flags to match.
+ if (cmd == static_cast<int>(FIONBIO))
+ {
+ if (*arg)
+ {
+ state |= user_set_non_blocking;
+ }
+ else
+ {
+ // Clearing the non-blocking mode always overrides any internally-set
+ // non-blocking flag. Any subsequent asynchronous operations will need
+ // to re-enable non-blocking I/O.
+ state &= ~(user_set_non_blocking | internal_non_blocking);
+ }
+ }
+ }
+
+ return result;
+}
+
+int select(int nfds, fd_set* readfds, fd_set* writefds,
+ fd_set* exceptfds, timeval* timeout, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ if (!readfds && !writefds && !exceptfds && timeout)
+ {
+ DWORD milliseconds = timeout->tv_sec * 1000 + timeout->tv_usec / 1000;
+ if (milliseconds == 0)
+ milliseconds = 1; // Force context switch.
+ ::Sleep(milliseconds);
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ // The select() call allows timeout values measured in microseconds, but the
+ // system clock (as wrapped by boost::posix_time::microsec_clock) typically
+ // has a resolution of 10 milliseconds. This can lead to a spinning select
+ // reactor, meaning increased CPU usage, when waiting for the earliest
+ // scheduled timeout if it's less than 10 milliseconds away. To avoid a tight
+ // spin we'll use a minimum timeout of 1 millisecond.
+ if (timeout && timeout->tv_sec == 0
+ && timeout->tv_usec > 0 && timeout->tv_usec < 1000)
+ timeout->tv_usec = 1000;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#if defined(__hpux) && defined(__SELECT)
+ timespec ts;
+ ts.tv_sec = timeout ? timeout->tv_sec : 0;
+ ts.tv_nsec = timeout ? timeout->tv_usec * 1000 : 0;
+ return error_wrapper(::pselect(nfds, readfds,
+ writefds, exceptfds, timeout ? &ts : 0, 0), ec);
+#else
+ int result = error_wrapper(::select(nfds, readfds,
+ writefds, exceptfds, timeout), ec);
+ if (result >= 0)
+ ec = boost::system::error_code();
+ return result;
+#endif
+}
+
+int poll_read(socket_type s, state_type state, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+#if defined(BOOST_ASIO_WINDOWS) \
+ || defined(__CYGWIN__) \
+ || defined(__SYMBIAN32__)
+ fd_set fds;
+ FD_ZERO(&fds);
+ FD_SET(s, &fds);
+ timeval zero_timeout;
+ zero_timeout.tv_sec = 0;
+ zero_timeout.tv_usec = 0;
+ timeval* timeout = (state & user_set_non_blocking) ? &zero_timeout : 0;
+ clear_last_error();
+ int result = error_wrapper(::select(s + 1, &fds, 0, 0, timeout), ec);
+#else // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+ pollfd fds;
+ fds.fd = s;
+ fds.events = POLLIN;
+ fds.revents = 0;
+ int timeout = (state & user_set_non_blocking) ? 0 : -1;
+ clear_last_error();
+ int result = error_wrapper(::poll(&fds, 1, timeout), ec);
+#endif // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+ if (result == 0)
+ ec = (state & user_set_non_blocking)
+ ? boost::asio::error::would_block : boost::system::error_code();
+ else if (result > 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+int poll_write(socket_type s, state_type state, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+#if defined(BOOST_ASIO_WINDOWS) \
+ || defined(__CYGWIN__) \
+ || defined(__SYMBIAN32__)
+ fd_set fds;
+ FD_ZERO(&fds);
+ FD_SET(s, &fds);
+ timeval zero_timeout;
+ zero_timeout.tv_sec = 0;
+ zero_timeout.tv_usec = 0;
+ timeval* timeout = (state & user_set_non_blocking) ? &zero_timeout : 0;
+ clear_last_error();
+ int result = error_wrapper(::select(s + 1, 0, &fds, 0, timeout), ec);
+#else // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+ pollfd fds;
+ fds.fd = s;
+ fds.events = POLLOUT;
+ fds.revents = 0;
+ int timeout = (state & user_set_non_blocking) ? 0 : -1;
+ clear_last_error();
+ int result = error_wrapper(::poll(&fds, 1, timeout), ec);
+#endif // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+ if (result == 0)
+ ec = (state & user_set_non_blocking)
+ ? boost::asio::error::would_block : boost::system::error_code();
+ else if (result > 0)
+ ec = boost::system::error_code();
+ return result;
+}
+
+int poll_connect(socket_type s, boost::system::error_code& ec)
+{
+ if (s == invalid_socket)
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return socket_error_retval;
+ }
+
+#if defined(BOOST_ASIO_WINDOWS) \
+ || defined(__CYGWIN__) \
+ || defined(__SYMBIAN32__)
+ fd_set write_fds;
+ FD_ZERO(&write_fds);
+ FD_SET(s, &write_fds);
+ fd_set except_fds;
+ FD_ZERO(&except_fds);
+ FD_SET(s, &except_fds);
+ clear_last_error();
+ int result = error_wrapper(::select(
+ s + 1, 0, &write_fds, &except_fds, 0), ec);
+ if (result >= 0)
+ ec = boost::system::error_code();
+ return result;
+#else // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+ pollfd fds;
+ fds.fd = s;
+ fds.events = POLLOUT;
+ fds.revents = 0;
+ clear_last_error();
+ int result = error_wrapper(::poll(&fds, 1, -1), ec);
+ if (result >= 0)
+ ec = boost::system::error_code();
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+}
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+const char* inet_ntop(int af, const void* src, char* dest, size_t length,
+ unsigned long scope_id, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ using namespace std; // For sprintf.
+ const unsigned char* bytes = static_cast<const unsigned char*>(src);
+ if (af == BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ sprintf_s(dest, length, "%u.%u.%u.%u",
+ bytes[0], bytes[1], bytes[2], bytes[3]);
+ return dest;
+ }
+ else if (af == BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ size_t n = 0, b = 0, z = 0;
+ while (n < length && b < 16)
+ {
+ if (bytes[b] == 0 && bytes[b + 1] == 0 && z == 0)
+ {
+ do b += 2; while (b < 16 && bytes[b] == 0 && bytes[b + 1] == 0);
+ n += sprintf_s(dest + n, length - n, ":%s", b < 16 ? "" : ":"), ++z;
+ }
+ else
+ {
+ n += sprintf_s(dest + n, length - n, "%s%x", b ? ":" : "",
+ (static_cast<u_long_type>(bytes[b]) << 8) | bytes[b + 1]);
+ b += 2;
+ }
+ }
+ if (scope_id)
+ n += sprintf_s(dest + n, length - n, "%%%lu", scope_id);
+ return dest;
+ }
+ else
+ {
+ ec = boost::asio::error::address_family_not_supported;
+ return 0;
+ }
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ using namespace std; // For memcpy.
+
+ if (af != BOOST_ASIO_OS_DEF(AF_INET) && af != BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ ec = boost::asio::error::address_family_not_supported;
+ return 0;
+ }
+
+ union
+ {
+ socket_addr_type base;
+ sockaddr_storage_type storage;
+ sockaddr_in4_type v4;
+ sockaddr_in6_type v6;
+ } address;
+ DWORD address_length;
+ if (af == BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ address_length = sizeof(sockaddr_in4_type);
+ address.v4.sin_family = BOOST_ASIO_OS_DEF(AF_INET);
+ address.v4.sin_port = 0;
+ memcpy(&address.v4.sin_addr, src, sizeof(in4_addr_type));
+ }
+ else // AF_INET6
+ {
+ address_length = sizeof(sockaddr_in6_type);
+ address.v6.sin6_family = BOOST_ASIO_OS_DEF(AF_INET6);
+ address.v6.sin6_port = 0;
+ address.v6.sin6_flowinfo = 0;
+ address.v6.sin6_scope_id = scope_id;
+ memcpy(&address.v6.sin6_addr, src, sizeof(in6_addr_type));
+ }
+
+ DWORD string_length = static_cast<DWORD>(length);
+#if defined(BOOST_NO_ANSI_APIS) || (defined(_MSC_VER) && (_MSC_VER >= 1800))
+ LPWSTR string_buffer = (LPWSTR)_alloca(length * sizeof(WCHAR));
+ int result = error_wrapper(::WSAAddressToStringW(&address.base,
+ address_length, 0, string_buffer, &string_length), ec);
+ ::WideCharToMultiByte(CP_ACP, 0, string_buffer, -1, dest, length, 0, 0);
+#else
+ int result = error_wrapper(::WSAAddressToStringA(
+ &address.base, address_length, 0, dest, &string_length), ec);
+#endif
+
+ // Windows may set error code on success.
+ if (result != socket_error_retval)
+ ec = boost::system::error_code();
+
+ // Windows may not set an error code on failure.
+ else if (result == socket_error_retval && !ec)
+ ec = boost::asio::error::invalid_argument;
+
+ return result == socket_error_retval ? 0 : dest;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ const char* result = error_wrapper(::inet_ntop(
+ af, src, dest, static_cast<int>(length)), ec);
+ if (result == 0 && !ec)
+ ec = boost::asio::error::invalid_argument;
+ if (result != 0 && af == BOOST_ASIO_OS_DEF(AF_INET6) && scope_id != 0)
+ {
+ using namespace std; // For strcat and sprintf.
+ char if_name[IF_NAMESIZE + 1] = "%";
+ const in6_addr_type* ipv6_address = static_cast<const in6_addr_type*>(src);
+ bool is_link_local = ((ipv6_address->s6_addr[0] == 0xfe)
+ && ((ipv6_address->s6_addr[1] & 0xc0) == 0x80));
+ bool is_multicast_link_local = ((ipv6_address->s6_addr[0] == 0xff)
+ && ((ipv6_address->s6_addr[1] & 0x0f) == 0x02));
+ if ((!is_link_local && !is_multicast_link_local)
+ || if_indextoname(static_cast<unsigned>(scope_id), if_name + 1) == 0)
+ sprintf(if_name + 1, "%lu", scope_id);
+ strcat(dest, if_name);
+ }
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+int inet_pton(int af, const char* src, void* dest,
+ unsigned long* scope_id, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ using namespace std; // For sscanf.
+ unsigned char* bytes = static_cast<unsigned char*>(dest);
+ if (af == BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ unsigned int b0, b1, b2, b3;
+ if (sscanf_s(src, "%u.%u.%u.%u", &b0, &b1, &b2, &b3) != 4)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return -1;
+ }
+ if (b0 > 255 || b1 > 255 || b2 > 255 || b3 > 255)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return -1;
+ }
+ bytes[0] = static_cast<unsigned char>(b0);
+ bytes[1] = static_cast<unsigned char>(b1);
+ bytes[2] = static_cast<unsigned char>(b2);
+ bytes[3] = static_cast<unsigned char>(b3);
+ ec = boost::system::error_code();
+ return 1;
+ }
+ else if (af == BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ unsigned char* bytes = static_cast<unsigned char*>(dest);
+ std::memset(bytes, 0, 16);
+ unsigned char back_bytes[16] = { 0 };
+ int num_front_bytes = 0, num_back_bytes = 0;
+ const char* p = src;
+
+ enum { fword, fcolon, bword, scope, done } state = fword;
+ unsigned long current_word = 0;
+ while (state != done)
+ {
+ if (current_word > 0xFFFF)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return -1;
+ }
+
+ switch (state)
+ {
+ case fword:
+ if (*p >= '0' && *p <= '9')
+ current_word = current_word * 16 + *p++ - '0';
+ else if (*p >= 'a' && *p <= 'f')
+ current_word = current_word * 16 + *p++ - 'a' + 10;
+ else if (*p >= 'A' && *p <= 'F')
+ current_word = current_word * 16 + *p++ - 'A' + 10;
+ else
+ {
+ if (num_front_bytes == 16)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return -1;
+ }
+
+ bytes[num_front_bytes++] = (current_word >> 8) & 0xFF;
+ bytes[num_front_bytes++] = current_word & 0xFF;
+ current_word = 0;
+
+ if (*p == ':')
+ state = fcolon, ++p;
+ else if (*p == '%')
+ state = scope, ++p;
+ else if (*p == 0)
+ state = done;
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ return -1;
+ }
+ }
+ break;
+
+ case fcolon:
+ if (*p == ':')
+ state = bword, ++p;
+ else
+ state = fword;
+ break;
+
+ case bword:
+ if (*p >= '0' && *p <= '9')
+ current_word = current_word * 16 + *p++ - '0';
+ else if (*p >= 'a' && *p <= 'f')
+ current_word = current_word * 16 + *p++ - 'a' + 10;
+ else if (*p >= 'A' && *p <= 'F')
+ current_word = current_word * 16 + *p++ - 'A' + 10;
+ else
+ {
+ if (num_front_bytes + num_back_bytes == 16)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return -1;
+ }
+
+ back_bytes[num_back_bytes++] = (current_word >> 8) & 0xFF;
+ back_bytes[num_back_bytes++] = current_word & 0xFF;
+ current_word = 0;
+
+ if (*p == ':')
+ state = bword, ++p;
+ else if (*p == '%')
+ state = scope, ++p;
+ else if (*p == 0)
+ state = done;
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ return -1;
+ }
+ }
+ break;
+
+ case scope:
+ if (*p >= '0' && *p <= '9')
+ current_word = current_word * 10 + *p++ - '0';
+ else if (*p == 0)
+ *scope_id = current_word, state = done;
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ return -1;
+ }
+ break;
+
+ default:
+ break;
+ }
+ }
+
+ for (int i = 0; i < num_back_bytes; ++i)
+ bytes[16 - num_back_bytes + i] = back_bytes[i];
+
+ ec = boost::system::error_code();
+ return 1;
+ }
+ else
+ {
+ ec = boost::asio::error::address_family_not_supported;
+ return -1;
+ }
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ using namespace std; // For memcpy and strcmp.
+
+ if (af != BOOST_ASIO_OS_DEF(AF_INET) && af != BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ ec = boost::asio::error::address_family_not_supported;
+ return -1;
+ }
+
+ union
+ {
+ socket_addr_type base;
+ sockaddr_storage_type storage;
+ sockaddr_in4_type v4;
+ sockaddr_in6_type v6;
+ } address;
+ int address_length = sizeof(sockaddr_storage_type);
+#if defined(BOOST_NO_ANSI_APIS) || (defined(_MSC_VER) && (_MSC_VER >= 1800))
+ int num_wide_chars = strlen(src) + 1;
+ LPWSTR wide_buffer = (LPWSTR)_alloca(num_wide_chars * sizeof(WCHAR));
+ ::MultiByteToWideChar(CP_ACP, 0, src, -1, wide_buffer, num_wide_chars);
+ int result = error_wrapper(::WSAStringToAddressW(
+ wide_buffer, af, 0, &address.base, &address_length), ec);
+#else
+ int result = error_wrapper(::WSAStringToAddressA(
+ const_cast<char*>(src), af, 0, &address.base, &address_length), ec);
+#endif
+
+ if (af == BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ if (result != socket_error_retval)
+ {
+ memcpy(dest, &address.v4.sin_addr, sizeof(in4_addr_type));
+ ec = boost::system::error_code();
+ }
+ else if (strcmp(src, "255.255.255.255") == 0)
+ {
+ static_cast<in4_addr_type*>(dest)->s_addr = INADDR_NONE;
+ ec = boost::system::error_code();
+ }
+ }
+ else // AF_INET6
+ {
+ if (result != socket_error_retval)
+ {
+ memcpy(dest, &address.v6.sin6_addr, sizeof(in6_addr_type));
+ if (scope_id)
+ *scope_id = address.v6.sin6_scope_id;
+ ec = boost::system::error_code();
+ }
+ }
+
+ // Windows may not set an error code on failure.
+ if (result == socket_error_retval && !ec)
+ ec = boost::asio::error::invalid_argument;
+
+ if (result != socket_error_retval)
+ ec = boost::system::error_code();
+
+ return result == socket_error_retval ? -1 : 1;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ int result = error_wrapper(::inet_pton(af, src, dest), ec);
+ if (result <= 0 && !ec)
+ ec = boost::asio::error::invalid_argument;
+ if (result > 0 && af == BOOST_ASIO_OS_DEF(AF_INET6) && scope_id)
+ {
+ using namespace std; // For strchr and atoi.
+ *scope_id = 0;
+ if (const char* if_name = strchr(src, '%'))
+ {
+ in6_addr_type* ipv6_address = static_cast<in6_addr_type*>(dest);
+ bool is_link_local = ((ipv6_address->s6_addr[0] == 0xfe)
+ && ((ipv6_address->s6_addr[1] & 0xc0) == 0x80));
+ bool is_multicast_link_local = ((ipv6_address->s6_addr[0] == 0xff)
+ && ((ipv6_address->s6_addr[1] & 0x0f) == 0x02));
+ if (is_link_local || is_multicast_link_local)
+ *scope_id = if_nametoindex(if_name + 1);
+ if (*scope_id == 0)
+ *scope_id = atoi(if_name + 1);
+ }
+ }
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+}
+
+int gethostname(char* name, int namelen, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ try
+ {
+ using namespace Windows::Foundation::Collections;
+ using namespace Windows::Networking;
+ using namespace Windows::Networking::Connectivity;
+ IVectorView<HostName^>^ hostnames = NetworkInformation::GetHostNames();
+ for (unsigned i = 0; i < hostnames->Size; ++i)
+ {
+ HostName^ hostname = hostnames->GetAt(i);
+ if (hostname->Type == HostNameType::DomainName)
+ {
+ std::wstring_convert<std::codecvt_utf8<wchar_t>> converter;
+ std::string raw_name = converter.to_bytes(hostname->RawName->Data());
+ if (namelen > 0 && raw_name.size() < static_cast<std::size_t>(namelen))
+ {
+ strcpy_s(name, namelen, raw_name.c_str());
+ return 0;
+ }
+ }
+ }
+ return -1;
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ return -1;
+ }
+#else // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ int result = error_wrapper(::gethostname(name, namelen), ec);
+# if defined(BOOST_ASIO_WINDOWS)
+ if (result == 0)
+ ec = boost::system::error_code();
+# endif // defined(BOOST_ASIO_WINDOWS)
+ return result;
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+}
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#if !defined(BOOST_ASIO_HAS_GETADDRINFO)
+
+// The following functions are only needed for emulation of getaddrinfo and
+// getnameinfo.
+
+inline boost::system::error_code translate_netdb_error(int error)
+{
+ switch (error)
+ {
+ case 0:
+ return boost::system::error_code();
+ case HOST_NOT_FOUND:
+ return boost::asio::error::host_not_found;
+ case TRY_AGAIN:
+ return boost::asio::error::host_not_found_try_again;
+ case NO_RECOVERY:
+ return boost::asio::error::no_recovery;
+ case NO_DATA:
+ return boost::asio::error::no_data;
+ default:
+ BOOST_ASIO_ASSERT(false);
+ return boost::asio::error::invalid_argument;
+ }
+}
+
+inline hostent* gethostbyaddr(const char* addr, int length, int af,
+ hostent* result, char* buffer, int buflength, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ (void)(buffer);
+ (void)(buflength);
+ hostent* retval = error_wrapper(::gethostbyaddr(addr, length, af), ec);
+ if (!retval)
+ return 0;
+ ec = boost::system::error_code();
+ *result = *retval;
+ return retval;
+#elif defined(__sun) || defined(__QNX__)
+ int error = 0;
+ hostent* retval = error_wrapper(::gethostbyaddr_r(addr, length, af, result,
+ buffer, buflength, &error), ec);
+ if (error)
+ ec = translate_netdb_error(error);
+ return retval;
+#elif defined(__MACH__) && defined(__APPLE__)
+ (void)(buffer);
+ (void)(buflength);
+ int error = 0;
+ hostent* retval = error_wrapper(::getipnodebyaddr(
+ addr, length, af, &error), ec);
+ if (error)
+ ec = translate_netdb_error(error);
+ if (!retval)
+ return 0;
+ *result = *retval;
+ return retval;
+#else
+ hostent* retval = 0;
+ int error = 0;
+ error_wrapper(::gethostbyaddr_r(addr, length, af, result, buffer,
+ buflength, &retval, &error), ec);
+ if (error)
+ ec = translate_netdb_error(error);
+ return retval;
+#endif
+}
+
+inline hostent* gethostbyname(const char* name, int af, struct hostent* result,
+ char* buffer, int buflength, int ai_flags, boost::system::error_code& ec)
+{
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ (void)(buffer);
+ (void)(buflength);
+ (void)(ai_flags);
+ if (af != BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ ec = boost::asio::error::address_family_not_supported;
+ return 0;
+ }
+ hostent* retval = error_wrapper(::gethostbyname(name), ec);
+ if (!retval)
+ return 0;
+ ec = boost::system::error_code();
+ *result = *retval;
+ return result;
+#elif defined(__sun) || defined(__QNX__)
+ (void)(ai_flags);
+ if (af != BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ ec = boost::asio::error::address_family_not_supported;
+ return 0;
+ }
+ int error = 0;
+ hostent* retval = error_wrapper(::gethostbyname_r(name, result, buffer,
+ buflength, &error), ec);
+ if (error)
+ ec = translate_netdb_error(error);
+ return retval;
+#elif defined(__MACH__) && defined(__APPLE__)
+ (void)(buffer);
+ (void)(buflength);
+ int error = 0;
+ hostent* retval = error_wrapper(::getipnodebyname(
+ name, af, ai_flags, &error), ec);
+ if (error)
+ ec = translate_netdb_error(error);
+ if (!retval)
+ return 0;
+ *result = *retval;
+ return retval;
+#else
+ (void)(ai_flags);
+ if (af != BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ ec = boost::asio::error::address_family_not_supported;
+ return 0;
+ }
+ hostent* retval = 0;
+ int error = 0;
+ error_wrapper(::gethostbyname_r(name, result,
+ buffer, buflength, &retval, &error), ec);
+ if (error)
+ ec = translate_netdb_error(error);
+ return retval;
+#endif
+}
+
+inline void freehostent(hostent* h)
+{
+#if defined(__MACH__) && defined(__APPLE__)
+ if (h)
+ ::freehostent(h);
+#else
+ (void)(h);
+#endif
+}
+
+// Emulation of getaddrinfo based on implementation in:
+// Stevens, W. R., UNIX Network Programming Vol. 1, 2nd Ed., Prentice-Hall 1998.
+
+struct gai_search
+{
+ const char* host;
+ int family;
+};
+
+inline int gai_nsearch(const char* host,
+ const addrinfo_type* hints, gai_search (&search)[2])
+{
+ int search_count = 0;
+ if (host == 0 || host[0] == '\0')
+ {
+ if (hints->ai_flags & AI_PASSIVE)
+ {
+ // No host and AI_PASSIVE implies wildcard bind.
+ switch (hints->ai_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ search[search_count].host = "0.0.0.0";
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET);
+ ++search_count;
+ break;
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ search[search_count].host = "0::0";
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET6);
+ ++search_count;
+ break;
+ case BOOST_ASIO_OS_DEF(AF_UNSPEC):
+ search[search_count].host = "0::0";
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET6);
+ ++search_count;
+ search[search_count].host = "0.0.0.0";
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET);
+ ++search_count;
+ break;
+ default:
+ break;
+ }
+ }
+ else
+ {
+ // No host and not AI_PASSIVE means connect to local host.
+ switch (hints->ai_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ search[search_count].host = "localhost";
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET);
+ ++search_count;
+ break;
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ search[search_count].host = "localhost";
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET6);
+ ++search_count;
+ break;
+ case BOOST_ASIO_OS_DEF(AF_UNSPEC):
+ search[search_count].host = "localhost";
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET6);
+ ++search_count;
+ search[search_count].host = "localhost";
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET);
+ ++search_count;
+ break;
+ default:
+ break;
+ }
+ }
+ }
+ else
+ {
+ // Host is specified.
+ switch (hints->ai_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ search[search_count].host = host;
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET);
+ ++search_count;
+ break;
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ search[search_count].host = host;
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET6);
+ ++search_count;
+ break;
+ case BOOST_ASIO_OS_DEF(AF_UNSPEC):
+ search[search_count].host = host;
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET6);
+ ++search_count;
+ search[search_count].host = host;
+ search[search_count].family = BOOST_ASIO_OS_DEF(AF_INET);
+ ++search_count;
+ break;
+ default:
+ break;
+ }
+ }
+ return search_count;
+}
+
+template <typename T>
+inline T* gai_alloc(std::size_t size = sizeof(T))
+{
+ using namespace std;
+ T* p = static_cast<T*>(::operator new(size, std::nothrow));
+ if (p)
+ memset(p, 0, size);
+ return p;
+}
+
+inline void gai_free(void* p)
+{
+ ::operator delete(p);
+}
+
+inline void gai_strcpy(char* target, const char* source, std::size_t max_size)
+{
+ using namespace std;
+#if defined(BOOST_ASIO_HAS_SECURE_RTL)
+ strcpy_s(target, max_size, source);
+#else // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ *target = 0;
+ strncat(target, source, max_size);
+#endif // defined(BOOST_ASIO_HAS_SECURE_RTL)
+}
+
+enum { gai_clone_flag = 1 << 30 };
+
+inline int gai_aistruct(addrinfo_type*** next, const addrinfo_type* hints,
+ const void* addr, int family)
+{
+ using namespace std;
+
+ addrinfo_type* ai = gai_alloc<addrinfo_type>();
+ if (ai == 0)
+ return EAI_MEMORY;
+
+ ai->ai_next = 0;
+ **next = ai;
+ *next = &ai->ai_next;
+
+ ai->ai_canonname = 0;
+ ai->ai_socktype = hints->ai_socktype;
+ if (ai->ai_socktype == 0)
+ ai->ai_flags |= gai_clone_flag;
+ ai->ai_protocol = hints->ai_protocol;
+ ai->ai_family = family;
+
+ switch (ai->ai_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ {
+ sockaddr_in4_type* sinptr = gai_alloc<sockaddr_in4_type>();
+ if (sinptr == 0)
+ return EAI_MEMORY;
+ sinptr->sin_family = BOOST_ASIO_OS_DEF(AF_INET);
+ memcpy(&sinptr->sin_addr, addr, sizeof(in4_addr_type));
+ ai->ai_addr = reinterpret_cast<sockaddr*>(sinptr);
+ ai->ai_addrlen = sizeof(sockaddr_in4_type);
+ break;
+ }
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ {
+ sockaddr_in6_type* sin6ptr = gai_alloc<sockaddr_in6_type>();
+ if (sin6ptr == 0)
+ return EAI_MEMORY;
+ sin6ptr->sin6_family = BOOST_ASIO_OS_DEF(AF_INET6);
+ memcpy(&sin6ptr->sin6_addr, addr, sizeof(in6_addr_type));
+ ai->ai_addr = reinterpret_cast<sockaddr*>(sin6ptr);
+ ai->ai_addrlen = sizeof(sockaddr_in6_type);
+ break;
+ }
+ default:
+ break;
+ }
+
+ return 0;
+}
+
+inline addrinfo_type* gai_clone(addrinfo_type* ai)
+{
+ using namespace std;
+
+ addrinfo_type* new_ai = gai_alloc<addrinfo_type>();
+ if (new_ai == 0)
+ return new_ai;
+
+ new_ai->ai_next = ai->ai_next;
+ ai->ai_next = new_ai;
+
+ new_ai->ai_flags = 0;
+ new_ai->ai_family = ai->ai_family;
+ new_ai->ai_socktype = ai->ai_socktype;
+ new_ai->ai_protocol = ai->ai_protocol;
+ new_ai->ai_canonname = 0;
+ new_ai->ai_addrlen = ai->ai_addrlen;
+ new_ai->ai_addr = gai_alloc<sockaddr>(ai->ai_addrlen);
+ memcpy(new_ai->ai_addr, ai->ai_addr, ai->ai_addrlen);
+
+ return new_ai;
+}
+
+inline int gai_port(addrinfo_type* aihead, int port, int socktype)
+{
+ int num_found = 0;
+
+ for (addrinfo_type* ai = aihead; ai; ai = ai->ai_next)
+ {
+ if (ai->ai_flags & gai_clone_flag)
+ {
+ if (ai->ai_socktype != 0)
+ {
+ ai = gai_clone(ai);
+ if (ai == 0)
+ return -1;
+ // ai now points to newly cloned entry.
+ }
+ }
+ else if (ai->ai_socktype != socktype)
+ {
+ // Ignore if mismatch on socket type.
+ continue;
+ }
+
+ ai->ai_socktype = socktype;
+
+ switch (ai->ai_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ {
+ sockaddr_in4_type* sinptr =
+ reinterpret_cast<sockaddr_in4_type*>(ai->ai_addr);
+ sinptr->sin_port = port;
+ ++num_found;
+ break;
+ }
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ {
+ sockaddr_in6_type* sin6ptr =
+ reinterpret_cast<sockaddr_in6_type*>(ai->ai_addr);
+ sin6ptr->sin6_port = port;
+ ++num_found;
+ break;
+ }
+ default:
+ break;
+ }
+ }
+
+ return num_found;
+}
+
+inline int gai_serv(addrinfo_type* aihead,
+ const addrinfo_type* hints, const char* serv)
+{
+ using namespace std;
+
+ int num_found = 0;
+
+ if (
+#if defined(AI_NUMERICSERV)
+ (hints->ai_flags & AI_NUMERICSERV) ||
+#endif
+ isdigit(static_cast<unsigned char>(serv[0])))
+ {
+ int port = htons(atoi(serv));
+ if (hints->ai_socktype)
+ {
+ // Caller specifies socket type.
+ int rc = gai_port(aihead, port, hints->ai_socktype);
+ if (rc < 0)
+ return EAI_MEMORY;
+ num_found += rc;
+ }
+ else
+ {
+ // Caller does not specify socket type.
+ int rc = gai_port(aihead, port, SOCK_STREAM);
+ if (rc < 0)
+ return EAI_MEMORY;
+ num_found += rc;
+ rc = gai_port(aihead, port, SOCK_DGRAM);
+ if (rc < 0)
+ return EAI_MEMORY;
+ num_found += rc;
+ }
+ }
+ else
+ {
+ // Try service name with TCP first, then UDP.
+ if (hints->ai_socktype == 0 || hints->ai_socktype == SOCK_STREAM)
+ {
+ servent* sptr = getservbyname(serv, "tcp");
+ if (sptr != 0)
+ {
+ int rc = gai_port(aihead, sptr->s_port, SOCK_STREAM);
+ if (rc < 0)
+ return EAI_MEMORY;
+ num_found += rc;
+ }
+ }
+ if (hints->ai_socktype == 0 || hints->ai_socktype == SOCK_DGRAM)
+ {
+ servent* sptr = getservbyname(serv, "udp");
+ if (sptr != 0)
+ {
+ int rc = gai_port(aihead, sptr->s_port, SOCK_DGRAM);
+ if (rc < 0)
+ return EAI_MEMORY;
+ num_found += rc;
+ }
+ }
+ }
+
+ if (num_found == 0)
+ {
+ if (hints->ai_socktype == 0)
+ {
+ // All calls to getservbyname() failed.
+ return EAI_NONAME;
+ }
+ else
+ {
+ // Service not supported for socket type.
+ return EAI_SERVICE;
+ }
+ }
+
+ return 0;
+}
+
+inline int gai_echeck(const char* host, const char* service,
+ int flags, int family, int socktype, int protocol)
+{
+ (void)(flags);
+ (void)(protocol);
+
+ // Host or service must be specified.
+ if (host == 0 || host[0] == '\0')
+ if (service == 0 || service[0] == '\0')
+ return EAI_NONAME;
+
+ // Check combination of family and socket type.
+ switch (family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_UNSPEC):
+ break;
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ if (service != 0 && service[0] != '\0')
+ if (socktype != 0 && socktype != SOCK_STREAM && socktype != SOCK_DGRAM)
+ return EAI_SOCKTYPE;
+ break;
+ default:
+ return EAI_FAMILY;
+ }
+
+ return 0;
+}
+
+inline void freeaddrinfo_emulation(addrinfo_type* aihead)
+{
+ addrinfo_type* ai = aihead;
+ while (ai)
+ {
+ gai_free(ai->ai_addr);
+ gai_free(ai->ai_canonname);
+ addrinfo_type* ainext = ai->ai_next;
+ gai_free(ai);
+ ai = ainext;
+ }
+}
+
+inline int getaddrinfo_emulation(const char* host, const char* service,
+ const addrinfo_type* hintsp, addrinfo_type** result)
+{
+ // Set up linked list of addrinfo structures.
+ addrinfo_type* aihead = 0;
+ addrinfo_type** ainext = &aihead;
+ char* canon = 0;
+
+ // Supply default hints if not specified by caller.
+ addrinfo_type hints = addrinfo_type();
+ hints.ai_family = BOOST_ASIO_OS_DEF(AF_UNSPEC);
+ if (hintsp)
+ hints = *hintsp;
+
+ // If the resolution is not specifically for AF_INET6, remove the AI_V4MAPPED
+ // and AI_ALL flags.
+#if defined(AI_V4MAPPED)
+ if (hints.ai_family != BOOST_ASIO_OS_DEF(AF_INET6))
+ hints.ai_flags &= ~AI_V4MAPPED;
+#endif
+#if defined(AI_ALL)
+ if (hints.ai_family != BOOST_ASIO_OS_DEF(AF_INET6))
+ hints.ai_flags &= ~AI_ALL;
+#endif
+
+ // Basic error checking.
+ int rc = gai_echeck(host, service, hints.ai_flags, hints.ai_family,
+ hints.ai_socktype, hints.ai_protocol);
+ if (rc != 0)
+ {
+ freeaddrinfo_emulation(aihead);
+ return rc;
+ }
+
+ gai_search search[2];
+ int search_count = gai_nsearch(host, &hints, search);
+ for (gai_search* sptr = search; sptr < search + search_count; ++sptr)
+ {
+ // Check for IPv4 dotted decimal string.
+ in4_addr_type inaddr;
+ boost::system::error_code ec;
+ if (socket_ops::inet_pton(BOOST_ASIO_OS_DEF(AF_INET),
+ sptr->host, &inaddr, 0, ec) == 1)
+ {
+ if (hints.ai_family != BOOST_ASIO_OS_DEF(AF_UNSPEC)
+ && hints.ai_family != BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ freeaddrinfo_emulation(aihead);
+ gai_free(canon);
+ return EAI_FAMILY;
+ }
+ if (sptr->family == BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ rc = gai_aistruct(&ainext, &hints, &inaddr, BOOST_ASIO_OS_DEF(AF_INET));
+ if (rc != 0)
+ {
+ freeaddrinfo_emulation(aihead);
+ gai_free(canon);
+ return rc;
+ }
+ }
+ continue;
+ }
+
+ // Check for IPv6 hex string.
+ in6_addr_type in6addr;
+ if (socket_ops::inet_pton(BOOST_ASIO_OS_DEF(AF_INET6),
+ sptr->host, &in6addr, 0, ec) == 1)
+ {
+ if (hints.ai_family != BOOST_ASIO_OS_DEF(AF_UNSPEC)
+ && hints.ai_family != BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ freeaddrinfo_emulation(aihead);
+ gai_free(canon);
+ return EAI_FAMILY;
+ }
+ if (sptr->family == BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ rc = gai_aistruct(&ainext, &hints, &in6addr,
+ BOOST_ASIO_OS_DEF(AF_INET6));
+ if (rc != 0)
+ {
+ freeaddrinfo_emulation(aihead);
+ gai_free(canon);
+ return rc;
+ }
+ }
+ continue;
+ }
+
+ // Look up hostname.
+ hostent hent;
+ char hbuf[8192] = "";
+ hostent* hptr = socket_ops::gethostbyname(sptr->host,
+ sptr->family, &hent, hbuf, sizeof(hbuf), hints.ai_flags, ec);
+ if (hptr == 0)
+ {
+ if (search_count == 2)
+ {
+ // Failure is OK if there are multiple searches.
+ continue;
+ }
+ freeaddrinfo_emulation(aihead);
+ gai_free(canon);
+ if (ec == boost::asio::error::host_not_found)
+ return EAI_NONAME;
+ if (ec == boost::asio::error::host_not_found_try_again)
+ return EAI_AGAIN;
+ if (ec == boost::asio::error::no_recovery)
+ return EAI_FAIL;
+ if (ec == boost::asio::error::no_data)
+ return EAI_NONAME;
+ return EAI_NONAME;
+ }
+
+ // Check for address family mismatch if one was specified.
+ if (hints.ai_family != BOOST_ASIO_OS_DEF(AF_UNSPEC)
+ && hints.ai_family != hptr->h_addrtype)
+ {
+ freeaddrinfo_emulation(aihead);
+ gai_free(canon);
+ socket_ops::freehostent(hptr);
+ return EAI_FAMILY;
+ }
+
+ // Save canonical name first time.
+ if (host != 0 && host[0] != '\0' && hptr->h_name && hptr->h_name[0]
+ && (hints.ai_flags & AI_CANONNAME) && canon == 0)
+ {
+ std::size_t canon_len = strlen(hptr->h_name) + 1;
+ canon = gai_alloc<char>(canon_len);
+ if (canon == 0)
+ {
+ freeaddrinfo_emulation(aihead);
+ socket_ops::freehostent(hptr);
+ return EAI_MEMORY;
+ }
+ gai_strcpy(canon, hptr->h_name, canon_len);
+ }
+
+ // Create an addrinfo structure for each returned address.
+ for (char** ap = hptr->h_addr_list; *ap; ++ap)
+ {
+ rc = gai_aistruct(&ainext, &hints, *ap, hptr->h_addrtype);
+ if (rc != 0)
+ {
+ freeaddrinfo_emulation(aihead);
+ gai_free(canon);
+ socket_ops::freehostent(hptr);
+ return EAI_FAMILY;
+ }
+ }
+
+ socket_ops::freehostent(hptr);
+ }
+
+ // Check if we found anything.
+ if (aihead == 0)
+ {
+ gai_free(canon);
+ return EAI_NONAME;
+ }
+
+ // Return canonical name in first entry.
+ if (host != 0 && host[0] != '\0' && (hints.ai_flags & AI_CANONNAME))
+ {
+ if (canon)
+ {
+ aihead->ai_canonname = canon;
+ canon = 0;
+ }
+ else
+ {
+ std::size_t canonname_len = strlen(search[0].host) + 1;
+ aihead->ai_canonname = gai_alloc<char>(canonname_len);
+ if (aihead->ai_canonname == 0)
+ {
+ freeaddrinfo_emulation(aihead);
+ return EAI_MEMORY;
+ }
+ gai_strcpy(aihead->ai_canonname, search[0].host, canonname_len);
+ }
+ }
+ gai_free(canon);
+
+ // Process the service name.
+ if (service != 0 && service[0] != '\0')
+ {
+ rc = gai_serv(aihead, &hints, service);
+ if (rc != 0)
+ {
+ freeaddrinfo_emulation(aihead);
+ return rc;
+ }
+ }
+
+ // Return result to caller.
+ *result = aihead;
+ return 0;
+}
+
+inline boost::system::error_code getnameinfo_emulation(
+ const socket_addr_type* sa, std::size_t salen, char* host,
+ std::size_t hostlen, char* serv, std::size_t servlen, int flags,
+ boost::system::error_code& ec)
+{
+ using namespace std;
+
+ const char* addr;
+ size_t addr_len;
+ unsigned short port;
+ switch (sa->sa_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ if (salen != sizeof(sockaddr_in4_type))
+ {
+ return ec = boost::asio::error::invalid_argument;
+ }
+ addr = reinterpret_cast<const char*>(
+ &reinterpret_cast<const sockaddr_in4_type*>(sa)->sin_addr);
+ addr_len = sizeof(in4_addr_type);
+ port = reinterpret_cast<const sockaddr_in4_type*>(sa)->sin_port;
+ break;
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ if (salen != sizeof(sockaddr_in6_type))
+ {
+ return ec = boost::asio::error::invalid_argument;
+ }
+ addr = reinterpret_cast<const char*>(
+ &reinterpret_cast<const sockaddr_in6_type*>(sa)->sin6_addr);
+ addr_len = sizeof(in6_addr_type);
+ port = reinterpret_cast<const sockaddr_in6_type*>(sa)->sin6_port;
+ break;
+ default:
+ return ec = boost::asio::error::address_family_not_supported;
+ }
+
+ if (host && hostlen > 0)
+ {
+ if (flags & NI_NUMERICHOST)
+ {
+ if (socket_ops::inet_ntop(sa->sa_family, addr, host, hostlen, 0, ec) == 0)
+ {
+ return ec;
+ }
+ }
+ else
+ {
+ hostent hent;
+ char hbuf[8192] = "";
+ hostent* hptr = socket_ops::gethostbyaddr(addr,
+ static_cast<int>(addr_len), sa->sa_family,
+ &hent, hbuf, sizeof(hbuf), ec);
+ if (hptr && hptr->h_name && hptr->h_name[0] != '\0')
+ {
+ if (flags & NI_NOFQDN)
+ {
+ char* dot = strchr(hptr->h_name, '.');
+ if (dot)
+ {
+ *dot = 0;
+ }
+ }
+ gai_strcpy(host, hptr->h_name, hostlen);
+ socket_ops::freehostent(hptr);
+ }
+ else
+ {
+ socket_ops::freehostent(hptr);
+ if (flags & NI_NAMEREQD)
+ {
+ return ec = boost::asio::error::host_not_found;
+ }
+ if (socket_ops::inet_ntop(sa->sa_family,
+ addr, host, hostlen, 0, ec) == 0)
+ {
+ return ec;
+ }
+ }
+ }
+ }
+
+ if (serv && servlen > 0)
+ {
+ if (flags & NI_NUMERICSERV)
+ {
+ if (servlen < 6)
+ {
+ return ec = boost::asio::error::no_buffer_space;
+ }
+#if defined(BOOST_ASIO_HAS_SECURE_RTL)
+ sprintf_s(serv, servlen, "%u", ntohs(port));
+#else // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ sprintf(serv, "%u", ntohs(port));
+#endif // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ }
+ else
+ {
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+ static ::pthread_mutex_t mutex = PTHREAD_MUTEX_INITIALIZER;
+ ::pthread_mutex_lock(&mutex);
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+ servent* sptr = ::getservbyport(port, (flags & NI_DGRAM) ? "udp" : 0);
+ if (sptr && sptr->s_name && sptr->s_name[0] != '\0')
+ {
+ gai_strcpy(serv, sptr->s_name, servlen);
+ }
+ else
+ {
+ if (servlen < 6)
+ {
+ return ec = boost::asio::error::no_buffer_space;
+ }
+#if defined(BOOST_ASIO_HAS_SECURE_RTL)
+ sprintf_s(serv, servlen, "%u", ntohs(port));
+#else // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ sprintf(serv, "%u", ntohs(port));
+#endif // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ }
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+ ::pthread_mutex_unlock(&mutex);
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+ }
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+#endif // !defined(BOOST_ASIO_HAS_GETADDRINFO)
+
+inline boost::system::error_code translate_addrinfo_error(int error)
+{
+ switch (error)
+ {
+ case 0:
+ return boost::system::error_code();
+ case EAI_AGAIN:
+ return boost::asio::error::host_not_found_try_again;
+ case EAI_BADFLAGS:
+ return boost::asio::error::invalid_argument;
+ case EAI_FAIL:
+ return boost::asio::error::no_recovery;
+ case EAI_FAMILY:
+ return boost::asio::error::address_family_not_supported;
+ case EAI_MEMORY:
+ return boost::asio::error::no_memory;
+ case EAI_NONAME:
+#if defined(EAI_ADDRFAMILY)
+ case EAI_ADDRFAMILY:
+#endif
+#if defined(EAI_NODATA) && (EAI_NODATA != EAI_NONAME)
+ case EAI_NODATA:
+#endif
+ return boost::asio::error::host_not_found;
+ case EAI_SERVICE:
+ return boost::asio::error::service_not_found;
+ case EAI_SOCKTYPE:
+ return boost::asio::error::socket_type_not_supported;
+ default: // Possibly the non-portable EAI_SYSTEM.
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ return boost::system::error_code(
+ WSAGetLastError(), boost::asio::error::get_system_category());
+#else
+ return boost::system::error_code(
+ errno, boost::asio::error::get_system_category());
+#endif
+ }
+}
+
+boost::system::error_code getaddrinfo(const char* host,
+ const char* service, const addrinfo_type& hints,
+ addrinfo_type** result, boost::system::error_code& ec)
+{
+ host = (host && *host) ? host : 0;
+ service = (service && *service) ? service : 0;
+ clear_last_error();
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if defined(BOOST_ASIO_HAS_GETADDRINFO)
+ // Building for Windows XP, Windows Server 2003, or later.
+ int error = ::getaddrinfo(host, service, &hints, result);
+ return ec = translate_addrinfo_error(error);
+# else
+ // Building for Windows 2000 or earlier.
+ typedef int (WSAAPI *gai_t)(const char*,
+ const char*, const addrinfo_type*, addrinfo_type**);
+ if (HMODULE winsock_module = ::GetModuleHandleA("ws2_32"))
+ {
+ if (gai_t gai = (gai_t)::GetProcAddress(winsock_module, "getaddrinfo"))
+ {
+ int error = gai(host, service, &hints, result);
+ return ec = translate_addrinfo_error(error);
+ }
+ }
+ int error = getaddrinfo_emulation(host, service, &hints, result);
+ return ec = translate_addrinfo_error(error);
+# endif
+#elif !defined(BOOST_ASIO_HAS_GETADDRINFO)
+ int error = getaddrinfo_emulation(host, service, &hints, result);
+ return ec = translate_addrinfo_error(error);
+#else
+ int error = ::getaddrinfo(host, service, &hints, result);
+ return ec = translate_addrinfo_error(error);
+#endif
+}
+
+boost::system::error_code background_getaddrinfo(
+ const weak_cancel_token_type& cancel_token, const char* host,
+ const char* service, const addrinfo_type& hints,
+ addrinfo_type** result, boost::system::error_code& ec)
+{
+ if (cancel_token.expired())
+ ec = boost::asio::error::operation_aborted;
+ else
+ socket_ops::getaddrinfo(host, service, hints, result, ec);
+ return ec;
+}
+
+void freeaddrinfo(addrinfo_type* ai)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if defined(BOOST_ASIO_HAS_GETADDRINFO)
+ // Building for Windows XP, Windows Server 2003, or later.
+ ::freeaddrinfo(ai);
+# else
+ // Building for Windows 2000 or earlier.
+ typedef int (WSAAPI *fai_t)(addrinfo_type*);
+ if (HMODULE winsock_module = ::GetModuleHandleA("ws2_32"))
+ {
+ if (fai_t fai = (fai_t)::GetProcAddress(winsock_module, "freeaddrinfo"))
+ {
+ fai(ai);
+ return;
+ }
+ }
+ freeaddrinfo_emulation(ai);
+# endif
+#elif !defined(BOOST_ASIO_HAS_GETADDRINFO)
+ freeaddrinfo_emulation(ai);
+#else
+ ::freeaddrinfo(ai);
+#endif
+}
+
+boost::system::error_code getnameinfo(const socket_addr_type* addr,
+ std::size_t addrlen, char* host, std::size_t hostlen,
+ char* serv, std::size_t servlen, int flags, boost::system::error_code& ec)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if defined(BOOST_ASIO_HAS_GETADDRINFO)
+ // Building for Windows XP, Windows Server 2003, or later.
+ clear_last_error();
+ int error = ::getnameinfo(addr, static_cast<socklen_t>(addrlen),
+ host, static_cast<DWORD>(hostlen),
+ serv, static_cast<DWORD>(servlen), flags);
+ return ec = translate_addrinfo_error(error);
+# else
+ // Building for Windows 2000 or earlier.
+ typedef int (WSAAPI *gni_t)(const socket_addr_type*,
+ int, char*, DWORD, char*, DWORD, int);
+ if (HMODULE winsock_module = ::GetModuleHandleA("ws2_32"))
+ {
+ if (gni_t gni = (gni_t)::GetProcAddress(winsock_module, "getnameinfo"))
+ {
+ clear_last_error();
+ int error = gni(addr, static_cast<int>(addrlen),
+ host, static_cast<DWORD>(hostlen),
+ serv, static_cast<DWORD>(servlen), flags);
+ return ec = translate_addrinfo_error(error);
+ }
+ }
+ clear_last_error();
+ return getnameinfo_emulation(addr, addrlen,
+ host, hostlen, serv, servlen, flags, ec);
+# endif
+#elif !defined(BOOST_ASIO_HAS_GETADDRINFO)
+ using namespace std; // For memcpy.
+ sockaddr_storage_type tmp_addr;
+ memcpy(&tmp_addr, addr, addrlen);
+ tmp_addr.ss_len = addrlen;
+ addr = reinterpret_cast<socket_addr_type*>(&tmp_addr);
+ clear_last_error();
+ return getnameinfo_emulation(addr, addrlen,
+ host, hostlen, serv, servlen, flags, ec);
+#else
+ clear_last_error();
+ int error = ::getnameinfo(addr, addrlen, host, hostlen, serv, servlen, flags);
+ return ec = translate_addrinfo_error(error);
+#endif
+}
+
+boost::system::error_code sync_getnameinfo(
+ const socket_addr_type* addr, std::size_t addrlen,
+ char* host, std::size_t hostlen, char* serv,
+ std::size_t servlen, int sock_type, boost::system::error_code& ec)
+{
+ // First try resolving with the service name. If that fails try resolving
+ // but allow the service to be returned as a number.
+ int flags = (sock_type == SOCK_DGRAM) ? NI_DGRAM : 0;
+ socket_ops::getnameinfo(addr, addrlen, host,
+ hostlen, serv, servlen, flags, ec);
+ if (ec)
+ {
+ socket_ops::getnameinfo(addr, addrlen, host, hostlen,
+ serv, servlen, flags | NI_NUMERICSERV, ec);
+ }
+
+ return ec;
+}
+
+boost::system::error_code background_getnameinfo(
+ const weak_cancel_token_type& cancel_token,
+ const socket_addr_type* addr, std::size_t addrlen,
+ char* host, std::size_t hostlen, char* serv,
+ std::size_t servlen, int sock_type, boost::system::error_code& ec)
+{
+ if (cancel_token.expired())
+ {
+ ec = boost::asio::error::operation_aborted;
+ }
+ else
+ {
+ // First try resolving with the service name. If that fails try resolving
+ // but allow the service to be returned as a number.
+ int flags = (sock_type == SOCK_DGRAM) ? NI_DGRAM : 0;
+ socket_ops::getnameinfo(addr, addrlen, host,
+ hostlen, serv, servlen, flags, ec);
+ if (ec)
+ {
+ socket_ops::getnameinfo(addr, addrlen, host, hostlen,
+ serv, servlen, flags | NI_NUMERICSERV, ec);
+ }
+ }
+
+ return ec;
+}
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+u_long_type network_to_host_long(u_long_type value)
+{
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ unsigned char* value_p = reinterpret_cast<unsigned char*>(&value);
+ u_long_type result = (static_cast<u_long_type>(value_p[0]) << 24)
+ | (static_cast<u_long_type>(value_p[1]) << 16)
+ | (static_cast<u_long_type>(value_p[2]) << 8)
+ | static_cast<u_long_type>(value_p[3]);
+ return result;
+#else // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ return ntohl(value);
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+}
+
+u_long_type host_to_network_long(u_long_type value)
+{
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ u_long_type result;
+ unsigned char* result_p = reinterpret_cast<unsigned char*>(&result);
+ result_p[0] = static_cast<unsigned char>((value >> 24) & 0xFF);
+ result_p[1] = static_cast<unsigned char>((value >> 16) & 0xFF);
+ result_p[2] = static_cast<unsigned char>((value >> 8) & 0xFF);
+ result_p[3] = static_cast<unsigned char>(value & 0xFF);
+ return result;
+#else // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ return htonl(value);
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+}
+
+u_short_type network_to_host_short(u_short_type value)
+{
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ unsigned char* value_p = reinterpret_cast<unsigned char*>(&value);
+ u_short_type result = (static_cast<u_long_type>(value_p[0]) << 8)
+ | static_cast<u_long_type>(value_p[1]);
+ return result;
+#else // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ return ntohs(value);
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+}
+
+u_short_type host_to_network_short(u_short_type value)
+{
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ u_long_type result;
+ unsigned char* result_p = reinterpret_cast<unsigned char*>(&result);
+ result_p[0] = static_cast<unsigned char>((value >> 8) & 0xFF);
+ result_p[1] = static_cast<unsigned char>(value & 0xFF);
+ return result;
+#else // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ return htons(value);
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+}
+
+} // namespace socket_ops
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_SOCKET_OPS_IPP
diff --git a/ext/patches/boost/asio/detail/impl/socket_select_interrupter.ipp b/ext/patches/boost/asio/detail/impl/socket_select_interrupter.ipp
new file mode 100644
index 0000000..4ea71c7
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/socket_select_interrupter.ipp
@@ -0,0 +1,177 @@
+//
+// detail/impl/socket_select_interrupter.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_SOCKET_SELECT_INTERRUPTER_IPP
+#define BOOST_ASIO_DETAIL_IMPL_SOCKET_SELECT_INTERRUPTER_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#if defined(BOOST_ASIO_WINDOWS) \
+ || defined(__CYGWIN__) \
+ || defined(__SYMBIAN32__)
+
+#include <cstdlib>
+#include <boost/asio/detail/socket_holder.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_select_interrupter.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+socket_select_interrupter::socket_select_interrupter()
+{
+ open_descriptors();
+}
+
+void socket_select_interrupter::open_descriptors()
+{
+ boost::system::error_code ec;
+ socket_holder acceptor(socket_ops::socket(
+ AF_INET, SOCK_STREAM, IPPROTO_TCP, ec));
+ if (acceptor.get() == invalid_socket)
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ int opt = 1;
+ socket_ops::state_type acceptor_state = 0;
+ socket_ops::setsockopt(acceptor.get(), acceptor_state,
+ SOL_SOCKET, SO_REUSEADDR, &opt, sizeof(opt), ec);
+
+ using namespace std; // For memset.
+ sockaddr_in4_type addr;
+ std::size_t addr_len = sizeof(addr);
+ memset(&addr, 0, sizeof(addr));
+ addr.sin_family = AF_INET;
+ addr.sin_addr.s_addr = socket_ops::host_to_network_long(INADDR_LOOPBACK);
+ addr.sin_port = 0;
+ if (socket_ops::bind(acceptor.get(), (const socket_addr_type*)&addr,
+ addr_len, ec) == socket_error_retval)
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ if (socket_ops::getsockname(acceptor.get(), (socket_addr_type*)&addr,
+ &addr_len, ec) == socket_error_retval)
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ // Some broken firewalls on Windows will intermittently cause getsockname to
+ // return 0.0.0.0 when the socket is actually bound to 127.0.0.1. We
+ // explicitly specify the target address here to work around this problem.
+ addr.sin_addr.s_addr = socket_ops::host_to_network_long(INADDR_LOOPBACK);
+
+ if (socket_ops::listen(acceptor.get(),
+ SOMAXCONN, ec) == socket_error_retval)
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ socket_holder client(socket_ops::socket(
+ AF_INET, SOCK_STREAM, IPPROTO_TCP, ec));
+ if (client.get() == invalid_socket)
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ if (socket_ops::connect(client.get(), (const socket_addr_type*)&addr,
+ addr_len, ec) == socket_error_retval)
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ socket_holder server(socket_ops::accept(acceptor.get(), 0, 0, ec));
+ if (server.get() == invalid_socket)
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ ioctl_arg_type non_blocking = 1;
+ socket_ops::state_type client_state = 0;
+ if (socket_ops::ioctl(client.get(), client_state,
+ FIONBIO, &non_blocking, ec))
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ opt = 1;
+ socket_ops::setsockopt(client.get(), client_state,
+ IPPROTO_TCP, TCP_NODELAY, &opt, sizeof(opt), ec);
+
+ non_blocking = 1;
+ socket_ops::state_type server_state = 0;
+ if (socket_ops::ioctl(server.get(), server_state,
+ FIONBIO, &non_blocking, ec))
+ boost::asio::detail::throw_error(ec, "socket_select_interrupter");
+
+ opt = 1;
+ socket_ops::setsockopt(server.get(), server_state,
+ IPPROTO_TCP, TCP_NODELAY, &opt, sizeof(opt), ec);
+
+ read_descriptor_ = server.release();
+ write_descriptor_ = client.release();
+}
+
+socket_select_interrupter::~socket_select_interrupter()
+{
+ close_descriptors();
+}
+
+void socket_select_interrupter::close_descriptors()
+{
+ boost::system::error_code ec;
+ socket_ops::state_type state = socket_ops::internal_non_blocking;
+ if (read_descriptor_ != invalid_socket)
+ socket_ops::close(read_descriptor_, state, true, ec);
+ if (write_descriptor_ != invalid_socket)
+ socket_ops::close(write_descriptor_, state, true, ec);
+}
+
+void socket_select_interrupter::recreate()
+{
+ close_descriptors();
+
+ write_descriptor_ = invalid_socket;
+ read_descriptor_ = invalid_socket;
+
+ open_descriptors();
+}
+
+void socket_select_interrupter::interrupt()
+{
+ char byte = 0;
+ socket_ops::buf b;
+ socket_ops::init_buf(b, &byte, 1);
+ boost::system::error_code ec;
+ socket_ops::send(write_descriptor_, &b, 1, 0, ec);
+}
+
+bool socket_select_interrupter::reset()
+{
+ char data[1024];
+ socket_ops::buf b;
+ socket_ops::init_buf(b, data, sizeof(data));
+ boost::system::error_code ec;
+ int bytes_read = socket_ops::recv(read_descriptor_, &b, 1, 0, ec);
+ bool was_interrupted = (bytes_read > 0);
+ while (bytes_read == sizeof(data))
+ bytes_read = socket_ops::recv(read_descriptor_, &b, 1, 0, ec);
+ return was_interrupted;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_SOCKET_SELECT_INTERRUPTER_IPP
diff --git a/ext/patches/boost/asio/detail/impl/strand_service.hpp b/ext/patches/boost/asio/detail/impl/strand_service.hpp
new file mode 100644
index 0000000..6e15042
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/strand_service.hpp
@@ -0,0 +1,120 @@
+//
+// detail/impl/strand_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_STRAND_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_IMPL_STRAND_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/call_stack.hpp>
+#include <boost/asio/detail/completion_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+inline strand_service::strand_impl::strand_impl()
+ : operation(&strand_service::do_complete),
+ locked_(false)
+{
+}
+
+struct strand_service::on_dispatch_exit
+{
+ io_service_impl* io_service_;
+ strand_impl* impl_;
+
+ ~on_dispatch_exit()
+ {
+ impl_->mutex_.lock();
+ impl_->ready_queue_.push(impl_->waiting_queue_);
+ bool more_handlers = impl_->locked_ = !impl_->ready_queue_.empty();
+ impl_->mutex_.unlock();
+
+ if (more_handlers)
+ io_service_->post_immediate_completion(impl_, false);
+ }
+};
+
+template <typename Handler>
+void strand_service::dispatch(strand_service::implementation_type& impl,
+ Handler& handler)
+{
+ // If we are already in the strand then the handler can run immediately.
+ if (call_stack<strand_impl>::contains(impl))
+ {
+ fenced_block b(fenced_block::full);
+ boost_asio_handler_invoke_helpers::invoke(handler, handler);
+ return;
+ }
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef completion_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "strand", impl, "dispatch"));
+
+ bool dispatch_immediately = do_dispatch(impl, p.p);
+ operation* o = p.p;
+ p.v = p.p = 0;
+
+ if (dispatch_immediately)
+ {
+ // Indicate that this strand is executing on the current thread.
+ call_stack<strand_impl>::context ctx(impl);
+
+ // Ensure the next handler, if any, is scheduled on block exit.
+ on_dispatch_exit on_exit = { &io_service_, impl };
+ (void)on_exit;
+
+ completion_handler<Handler>::do_complete(
+ &io_service_, o, boost::system::error_code(), 0);
+ }
+}
+
+// Request the io_service to invoke the given handler and return immediately.
+template <typename Handler>
+void strand_service::post(strand_service::implementation_type& impl,
+ Handler& handler)
+{
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef completion_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "strand", impl, "post"));
+
+ do_post(impl, p.p, is_continuation);
+ p.v = p.p = 0;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_STRAND_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/impl/strand_service.ipp b/ext/patches/boost/asio/detail/impl/strand_service.ipp
new file mode 100644
index 0000000..cd80e70
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/strand_service.ipp
@@ -0,0 +1,178 @@
+//
+// detail/impl/strand_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_STRAND_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_STRAND_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/call_stack.hpp>
+#include <boost/asio/detail/strand_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct strand_service::on_do_complete_exit
+{
+ io_service_impl* owner_;
+ strand_impl* impl_;
+
+ ~on_do_complete_exit()
+ {
+ impl_->mutex_.lock();
+ impl_->ready_queue_.push(impl_->waiting_queue_);
+ bool more_handlers = impl_->locked_ = !impl_->ready_queue_.empty();
+ impl_->mutex_.unlock();
+
+ if (more_handlers)
+ owner_->post_immediate_completion(impl_, true);
+ }
+};
+
+strand_service::strand_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<strand_service>(io_service),
+ io_service_(boost::asio::use_service<io_service_impl>(io_service)),
+ mutex_(),
+ salt_(0)
+{
+}
+
+void strand_service::shutdown_service()
+{
+ op_queue<operation> ops;
+
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ for (std::size_t i = 0; i < num_implementations; ++i)
+ {
+ if (strand_impl* impl = implementations_[i].get())
+ {
+ ops.push(impl->waiting_queue_);
+ ops.push(impl->ready_queue_);
+ }
+ }
+}
+
+void strand_service::construct(strand_service::implementation_type& impl)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ std::size_t salt = salt_++;
+#if defined(BOOST_ASIO_ENABLE_SEQUENTIAL_STRAND_ALLOCATION)
+ std::size_t index = salt;
+#else // defined(BOOST_ASIO_ENABLE_SEQUENTIAL_STRAND_ALLOCATION)
+ std::size_t index = reinterpret_cast<std::size_t>(&impl);
+ index += (reinterpret_cast<std::size_t>(&impl) >> 3);
+ index ^= salt + 0x9e3779b9 + (index << 6) + (index >> 2);
+#endif // defined(BOOST_ASIO_ENABLE_SEQUENTIAL_STRAND_ALLOCATION)
+ index = index % num_implementations;
+
+ if (!implementations_[index].get())
+ implementations_[index].reset(new strand_impl);
+ impl = implementations_[index].get();
+}
+
+bool strand_service::running_in_this_thread(
+ const implementation_type& impl) const
+{
+ return call_stack<strand_impl>::contains(impl) != 0;
+}
+
+bool strand_service::do_dispatch(implementation_type& impl, operation* op)
+{
+ // If we are running inside the io_service, and no other handler already
+ // holds the strand lock, then the handler can run immediately.
+ bool can_dispatch = io_service_.can_dispatch();
+ impl->mutex_.lock();
+ if (can_dispatch && !impl->locked_)
+ {
+ // Immediate invocation is allowed.
+ impl->locked_ = true;
+ impl->mutex_.unlock();
+ return true;
+ }
+
+ if (impl->locked_)
+ {
+ // Some other handler already holds the strand lock. Enqueue for later.
+ impl->waiting_queue_.push(op);
+ impl->mutex_.unlock();
+ }
+ else
+ {
+ // The handler is acquiring the strand lock and so is responsible for
+ // scheduling the strand.
+ impl->locked_ = true;
+ impl->mutex_.unlock();
+ impl->ready_queue_.push(op);
+ io_service_.post_immediate_completion(impl, false);
+ }
+
+ return false;
+}
+
+void strand_service::do_post(implementation_type& impl,
+ operation* op, bool is_continuation)
+{
+ impl->mutex_.lock();
+ if (impl->locked_)
+ {
+ // Some other handler already holds the strand lock. Enqueue for later.
+ impl->waiting_queue_.push(op);
+ impl->mutex_.unlock();
+ }
+ else
+ {
+ // The handler is acquiring the strand lock and so is responsible for
+ // scheduling the strand.
+ impl->locked_ = true;
+ impl->mutex_.unlock();
+ impl->ready_queue_.push(op);
+ io_service_.post_immediate_completion(impl, is_continuation);
+ }
+}
+
+void strand_service::do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& ec, std::size_t /*bytes_transferred*/)
+{
+ if (owner)
+ {
+ strand_impl* impl = static_cast<strand_impl*>(base);
+
+ // Indicate that this strand is executing on the current thread.
+ call_stack<strand_impl>::context ctx(impl);
+
+ // Ensure the next handler, if any, is scheduled on block exit.
+ on_do_complete_exit on_exit = { owner, impl };
+ (void)on_exit;
+
+ // Run all ready handlers. No lock is required since the ready queue is
+ // accessed only within the strand.
+ while (operation* o = impl->ready_queue_.front())
+ {
+ impl->ready_queue_.pop();
+ o->complete(*owner, ec, 0);
+ }
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_STRAND_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/task_io_service.hpp b/ext/patches/boost/asio/detail/impl/task_io_service.hpp
new file mode 100644
index 0000000..9ad3da3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/task_io_service.hpp
@@ -0,0 +1,80 @@
+//
+// detail/impl/task_io_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_TASK_IO_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_IMPL_TASK_IO_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/completion_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+void task_io_service::dispatch(Handler& handler)
+{
+ if (thread_call_stack::contains(this))
+ {
+ fenced_block b(fenced_block::full);
+ boost_asio_handler_invoke_helpers::invoke(handler, handler);
+ }
+ else
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef completion_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "io_service", this, "dispatch"));
+
+ do_dispatch(p.p);
+ p.v = p.p = 0;
+ }
+}
+
+template <typename Handler>
+void task_io_service::post(Handler& handler)
+{
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef completion_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "io_service", this, "post"));
+
+ post_immediate_completion(p.p, is_continuation);
+ p.v = p.p = 0;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_TASK_IO_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/impl/task_io_service.ipp b/ext/patches/boost/asio/detail/impl/task_io_service.ipp
new file mode 100644
index 0000000..2190937
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/task_io_service.ipp
@@ -0,0 +1,476 @@
+//
+// detail/impl/task_io_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_TASK_IO_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_TASK_IO_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/event.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/reactor.hpp>
+#include <boost/asio/detail/task_io_service.hpp>
+#include <boost/asio/detail/task_io_service_thread_info.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct task_io_service::task_cleanup
+{
+ ~task_cleanup()
+ {
+ if (this_thread_->private_outstanding_work > 0)
+ {
+ boost::asio::detail::increment(
+ task_io_service_->outstanding_work_,
+ this_thread_->private_outstanding_work);
+ }
+ this_thread_->private_outstanding_work = 0;
+
+ // Enqueue the completed operations and reinsert the task at the end of
+ // the operation queue.
+ lock_->lock();
+ task_io_service_->task_interrupted_ = true;
+ task_io_service_->op_queue_.push(this_thread_->private_op_queue);
+ task_io_service_->op_queue_.push(&task_io_service_->task_operation_);
+ }
+
+ task_io_service* task_io_service_;
+ mutex::scoped_lock* lock_;
+ thread_info* this_thread_;
+};
+
+struct task_io_service::work_cleanup
+{
+ ~work_cleanup()
+ {
+ if (this_thread_->private_outstanding_work > 1)
+ {
+ boost::asio::detail::increment(
+ task_io_service_->outstanding_work_,
+ this_thread_->private_outstanding_work - 1);
+ }
+ else if (this_thread_->private_outstanding_work < 1)
+ {
+ task_io_service_->work_finished();
+ }
+ this_thread_->private_outstanding_work = 0;
+
+#if defined(BOOST_ASIO_HAS_THREADS)
+ if (!this_thread_->private_op_queue.empty())
+ {
+ lock_->lock();
+ task_io_service_->op_queue_.push(this_thread_->private_op_queue);
+ }
+#endif // defined(BOOST_ASIO_HAS_THREADS)
+ }
+
+ task_io_service* task_io_service_;
+ mutex::scoped_lock* lock_;
+ thread_info* this_thread_;
+};
+
+task_io_service::task_io_service(
+ boost::asio::io_service& io_service, std::size_t concurrency_hint)
+ : boost::asio::detail::service_base<task_io_service>(io_service),
+ one_thread_(concurrency_hint == 1),
+ mutex_(),
+ task_(0),
+ task_interrupted_(true),
+ outstanding_work_(0),
+ stopped_(false),
+ shutdown_(false)
+{
+ BOOST_ASIO_HANDLER_TRACKING_INIT;
+}
+
+void task_io_service::shutdown_service()
+{
+ mutex::scoped_lock lock(mutex_);
+ shutdown_ = true;
+ lock.unlock();
+
+ // Destroy handler objects.
+ while (!op_queue_.empty())
+ {
+ operation* o = op_queue_.front();
+ op_queue_.pop();
+ if (o != &task_operation_)
+ o->destroy();
+ }
+
+ // Reset to initial state.
+ task_ = 0;
+}
+
+void task_io_service::init_task()
+{
+ mutex::scoped_lock lock(mutex_);
+ if (!shutdown_ && !task_)
+ {
+ task_ = &use_service<reactor>(this->get_io_service());
+ op_queue_.push(&task_operation_);
+ wake_one_thread_and_unlock(lock);
+ }
+}
+
+std::size_t task_io_service::run(boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ if (outstanding_work_ == 0)
+ {
+ stop();
+ return 0;
+ }
+
+ thread_info this_thread;
+ this_thread.private_outstanding_work = 0;
+ thread_call_stack::context ctx(this, this_thread);
+
+ mutex::scoped_lock lock(mutex_);
+
+ std::size_t n = 0;
+ for (; do_run_one(lock, this_thread, ec); lock.lock())
+ if (n != (std::numeric_limits<std::size_t>::max)())
+ ++n;
+ return n;
+}
+
+std::size_t task_io_service::run_one(boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ if (outstanding_work_ == 0)
+ {
+ stop();
+ return 0;
+ }
+
+ thread_info this_thread;
+ this_thread.private_outstanding_work = 0;
+ thread_call_stack::context ctx(this, this_thread);
+
+ mutex::scoped_lock lock(mutex_);
+
+ return do_run_one(lock, this_thread, ec);
+}
+
+std::size_t task_io_service::poll(boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ if (outstanding_work_ == 0)
+ {
+ stop();
+ return 0;
+ }
+
+ thread_info this_thread;
+ this_thread.private_outstanding_work = 0;
+ thread_call_stack::context ctx(this, this_thread);
+
+ mutex::scoped_lock lock(mutex_);
+
+#if defined(BOOST_ASIO_HAS_THREADS)
+ // We want to support nested calls to poll() and poll_one(), so any handlers
+ // that are already on a thread-private queue need to be put on to the main
+ // queue now.
+ if (one_thread_)
+ if (thread_info* outer_thread_info = ctx.next_by_key())
+ op_queue_.push(outer_thread_info->private_op_queue);
+#endif // defined(BOOST_ASIO_HAS_THREADS)
+
+ std::size_t n = 0;
+ for (; do_poll_one(lock, this_thread, ec); lock.lock())
+ if (n != (std::numeric_limits<std::size_t>::max)())
+ ++n;
+ return n;
+}
+
+std::size_t task_io_service::poll_one(boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ if (outstanding_work_ == 0)
+ {
+ stop();
+ return 0;
+ }
+
+ thread_info this_thread;
+ this_thread.private_outstanding_work = 0;
+ thread_call_stack::context ctx(this, this_thread);
+
+ mutex::scoped_lock lock(mutex_);
+
+#if defined(BOOST_ASIO_HAS_THREADS)
+ // We want to support nested calls to poll() and poll_one(), so any handlers
+ // that are already on a thread-private queue need to be put on to the main
+ // queue now.
+ if (one_thread_)
+ if (thread_info* outer_thread_info = ctx.next_by_key())
+ op_queue_.push(outer_thread_info->private_op_queue);
+#endif // defined(BOOST_ASIO_HAS_THREADS)
+
+ return do_poll_one(lock, this_thread, ec);
+}
+
+void task_io_service::stop()
+{
+ mutex::scoped_lock lock(mutex_);
+ stop_all_threads(lock);
+}
+
+bool task_io_service::stopped() const
+{
+ mutex::scoped_lock lock(mutex_);
+ return stopped_;
+}
+
+void task_io_service::reset()
+{
+ mutex::scoped_lock lock(mutex_);
+ stopped_ = false;
+}
+
+void task_io_service::post_immediate_completion(
+ task_io_service::operation* op, bool is_continuation)
+{
+#if defined(BOOST_ASIO_HAS_THREADS)
+ if (one_thread_ || is_continuation)
+ {
+ if (thread_info* this_thread = thread_call_stack::contains(this))
+ {
+ ++this_thread->private_outstanding_work;
+ this_thread->private_op_queue.push(op);
+ return;
+ }
+ }
+#else // defined(BOOST_ASIO_HAS_THREADS)
+ (void)is_continuation;
+#endif // defined(BOOST_ASIO_HAS_THREADS)
+
+ work_started();
+ mutex::scoped_lock lock(mutex_);
+ op_queue_.push(op);
+ wake_one_thread_and_unlock(lock);
+}
+
+void task_io_service::post_deferred_completion(task_io_service::operation* op)
+{
+#if defined(BOOST_ASIO_HAS_THREADS)
+ if (one_thread_)
+ {
+ if (thread_info* this_thread = thread_call_stack::contains(this))
+ {
+ this_thread->private_op_queue.push(op);
+ return;
+ }
+ }
+#endif // defined(BOOST_ASIO_HAS_THREADS)
+
+ mutex::scoped_lock lock(mutex_);
+ op_queue_.push(op);
+ wake_one_thread_and_unlock(lock);
+}
+
+void task_io_service::post_deferred_completions(
+ op_queue<task_io_service::operation>& ops)
+{
+ if (!ops.empty())
+ {
+#if defined(BOOST_ASIO_HAS_THREADS)
+ if (one_thread_)
+ {
+ if (thread_info* this_thread = thread_call_stack::contains(this))
+ {
+ this_thread->private_op_queue.push(ops);
+ return;
+ }
+ }
+#endif // defined(BOOST_ASIO_HAS_THREADS)
+
+ mutex::scoped_lock lock(mutex_);
+ op_queue_.push(ops);
+ wake_one_thread_and_unlock(lock);
+ }
+}
+
+void task_io_service::do_dispatch(
+ task_io_service::operation* op)
+{
+ work_started();
+ mutex::scoped_lock lock(mutex_);
+ op_queue_.push(op);
+ wake_one_thread_and_unlock(lock);
+}
+
+void task_io_service::abandon_operations(
+ op_queue<task_io_service::operation>& ops)
+{
+ op_queue<task_io_service::operation> ops2;
+ ops2.push(ops);
+}
+
+std::size_t task_io_service::do_run_one(mutex::scoped_lock& lock,
+ task_io_service::thread_info& this_thread,
+ const boost::system::error_code& ec)
+{
+ while (!stopped_)
+ {
+ if (!op_queue_.empty())
+ {
+ // Prepare to execute first handler from queue.
+ operation* o = op_queue_.front();
+ op_queue_.pop();
+ bool more_handlers = (!op_queue_.empty());
+
+ if (o == &task_operation_)
+ {
+ task_interrupted_ = more_handlers;
+
+ if (more_handlers && !one_thread_)
+ wakeup_event_.unlock_and_signal_one(lock);
+ else
+ lock.unlock();
+
+ task_cleanup on_exit = { this, &lock, &this_thread };
+ (void)on_exit;
+
+ // Run the task. May throw an exception. Only block if the operation
+ // queue is empty and we're not polling, otherwise we want to return
+ // as soon as possible.
+ task_->run(!more_handlers, this_thread.private_op_queue);
+ }
+ else
+ {
+ std::size_t task_result = o->task_result_;
+
+ if (more_handlers && !one_thread_)
+ wake_one_thread_and_unlock(lock);
+ else
+ lock.unlock();
+
+ // Ensure the count of outstanding work is decremented on block exit.
+ work_cleanup on_exit = { this, &lock, &this_thread };
+ (void)on_exit;
+
+ // Complete the operation. May throw an exception. Deletes the object.
+ o->complete(*this, ec, task_result);
+
+ return 1;
+ }
+ }
+ else
+ {
+ wakeup_event_.clear(lock);
+ wakeup_event_.wait(lock);
+ }
+ }
+
+ return 0;
+}
+
+std::size_t task_io_service::do_poll_one(mutex::scoped_lock& lock,
+ task_io_service::thread_info& this_thread,
+ const boost::system::error_code& ec)
+{
+ if (stopped_)
+ return 0;
+
+ operation* o = op_queue_.front();
+ if (o == &task_operation_)
+ {
+ op_queue_.pop();
+ lock.unlock();
+
+ {
+ task_cleanup c = { this, &lock, &this_thread };
+ (void)c;
+
+ // Run the task. May throw an exception. Only block if the operation
+ // queue is empty and we're not polling, otherwise we want to return
+ // as soon as possible.
+ task_->run(false, this_thread.private_op_queue);
+ }
+
+ o = op_queue_.front();
+ if (o == &task_operation_)
+ {
+ wakeup_event_.maybe_unlock_and_signal_one(lock);
+ return 0;
+ }
+ }
+
+ if (o == 0)
+ return 0;
+
+ op_queue_.pop();
+ bool more_handlers = (!op_queue_.empty());
+
+ std::size_t task_result = o->task_result_;
+
+ if (more_handlers && !one_thread_)
+ wake_one_thread_and_unlock(lock);
+ else
+ lock.unlock();
+
+ // Ensure the count of outstanding work is decremented on block exit.
+ work_cleanup on_exit = { this, &lock, &this_thread };
+ (void)on_exit;
+
+ // Complete the operation. May throw an exception. Deletes the object.
+ o->complete(*this, ec, task_result);
+
+ return 1;
+}
+
+void task_io_service::stop_all_threads(
+ mutex::scoped_lock& lock)
+{
+ stopped_ = true;
+ wakeup_event_.signal_all(lock);
+
+ if (!task_interrupted_ && task_)
+ {
+ task_interrupted_ = true;
+ task_->interrupt();
+ }
+}
+
+void task_io_service::wake_one_thread_and_unlock(
+ mutex::scoped_lock& lock)
+{
+ if (!wakeup_event_.maybe_unlock_and_signal_one(lock))
+ {
+ if (!task_interrupted_ && task_)
+ {
+ task_interrupted_ = true;
+ task_->interrupt();
+ }
+ lock.unlock();
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_TASK_IO_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/throw_error.ipp b/ext/patches/boost/asio/detail/impl/throw_error.ipp
new file mode 100644
index 0000000..8c27912
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/throw_error.ipp
@@ -0,0 +1,47 @@
+//
+// detail/impl/throw_error.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_THROW_ERROR_IPP
+#define BOOST_ASIO_DETAIL_IMPL_THROW_ERROR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/system/system_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+void do_throw_error(const boost::system::error_code& err)
+{
+ boost::system::system_error e(err);
+ boost::asio::detail::throw_exception(e);
+}
+
+void do_throw_error(const boost::system::error_code& err, const char* location)
+{
+ boost::system::system_error e(err, location);
+ boost::asio::detail::throw_exception(e);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_THROW_ERROR_IPP
diff --git a/ext/patches/boost/asio/detail/impl/timer_queue_ptime.ipp b/ext/patches/boost/asio/detail/impl/timer_queue_ptime.ipp
new file mode 100644
index 0000000..31184d8
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/timer_queue_ptime.ipp
@@ -0,0 +1,86 @@
+//
+// detail/impl/timer_queue_ptime.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_TIMER_QUEUE_PTIME_IPP
+#define BOOST_ASIO_DETAIL_IMPL_TIMER_QUEUE_PTIME_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/timer_queue_ptime.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+timer_queue<time_traits<boost::posix_time::ptime> >::timer_queue()
+{
+}
+
+timer_queue<time_traits<boost::posix_time::ptime> >::~timer_queue()
+{
+}
+
+bool timer_queue<time_traits<boost::posix_time::ptime> >::enqueue_timer(
+ const time_type& time, per_timer_data& timer, wait_op* op)
+{
+ return impl_.enqueue_timer(time, timer, op);
+}
+
+bool timer_queue<time_traits<boost::posix_time::ptime> >::empty() const
+{
+ return impl_.empty();
+}
+
+long timer_queue<time_traits<boost::posix_time::ptime> >::wait_duration_msec(
+ long max_duration) const
+{
+ return impl_.wait_duration_msec(max_duration);
+}
+
+long timer_queue<time_traits<boost::posix_time::ptime> >::wait_duration_usec(
+ long max_duration) const
+{
+ return impl_.wait_duration_usec(max_duration);
+}
+
+void timer_queue<time_traits<boost::posix_time::ptime> >::get_ready_timers(
+ op_queue<operation>& ops)
+{
+ impl_.get_ready_timers(ops);
+}
+
+void timer_queue<time_traits<boost::posix_time::ptime> >::get_all_timers(
+ op_queue<operation>& ops)
+{
+ impl_.get_all_timers(ops);
+}
+
+std::size_t timer_queue<time_traits<boost::posix_time::ptime> >::cancel_timer(
+ per_timer_data& timer, op_queue<operation>& ops, std::size_t max_cancelled)
+{
+ return impl_.cancel_timer(timer, ops, max_cancelled);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_TIMER_QUEUE_PTIME_IPP
diff --git a/ext/patches/boost/asio/detail/impl/timer_queue_set.ipp b/ext/patches/boost/asio/detail/impl/timer_queue_set.ipp
new file mode 100644
index 0000000..49ee860
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/timer_queue_set.ipp
@@ -0,0 +1,103 @@
+//
+// detail/impl/timer_queue_set.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_TIMER_QUEUE_SET_IPP
+#define BOOST_ASIO_DETAIL_IMPL_TIMER_QUEUE_SET_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/timer_queue_set.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+timer_queue_set::timer_queue_set()
+ : first_(0)
+{
+}
+
+void timer_queue_set::insert(timer_queue_base* q)
+{
+ q->next_ = first_;
+ first_ = q;
+}
+
+void timer_queue_set::erase(timer_queue_base* q)
+{
+ if (first_)
+ {
+ if (q == first_)
+ {
+ first_ = q->next_;
+ q->next_ = 0;
+ return;
+ }
+
+ for (timer_queue_base* p = first_; p->next_; p = p->next_)
+ {
+ if (p->next_ == q)
+ {
+ p->next_ = q->next_;
+ q->next_ = 0;
+ return;
+ }
+ }
+ }
+}
+
+bool timer_queue_set::all_empty() const
+{
+ for (timer_queue_base* p = first_; p; p = p->next_)
+ if (!p->empty())
+ return false;
+ return true;
+}
+
+long timer_queue_set::wait_duration_msec(long max_duration) const
+{
+ long min_duration = max_duration;
+ for (timer_queue_base* p = first_; p; p = p->next_)
+ min_duration = p->wait_duration_msec(min_duration);
+ return min_duration;
+}
+
+long timer_queue_set::wait_duration_usec(long max_duration) const
+{
+ long min_duration = max_duration;
+ for (timer_queue_base* p = first_; p; p = p->next_)
+ min_duration = p->wait_duration_usec(min_duration);
+ return min_duration;
+}
+
+void timer_queue_set::get_ready_timers(op_queue<operation>& ops)
+{
+ for (timer_queue_base* p = first_; p; p = p->next_)
+ p->get_ready_timers(ops);
+}
+
+void timer_queue_set::get_all_timers(op_queue<operation>& ops)
+{
+ for (timer_queue_base* p = first_; p; p = p->next_)
+ p->get_all_timers(ops);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IMPL_TIMER_QUEUE_SET_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_event.ipp b/ext/patches/boost/asio/detail/impl/win_event.ipp
new file mode 100644
index 0000000..5863a1b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_event.ipp
@@ -0,0 +1,69 @@
+//
+// detail/win_event.ipp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_EVENT_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_EVENT_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS)
+
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/win_event.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+win_event::win_event()
+ : state_(0)
+{
+ events_[0] = ::CreateEvent(0, true, false, 0);
+ if (!events_[0])
+ {
+ DWORD last_error = ::GetLastError();
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "event");
+ }
+
+ events_[1] = ::CreateEvent(0, false, false, 0);
+ if (!events_[1])
+ {
+ DWORD last_error = ::GetLastError();
+ ::CloseHandle(events_[0]);
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "event");
+ }
+}
+
+win_event::~win_event()
+{
+ ::CloseHandle(events_[0]);
+ ::CloseHandle(events_[1]);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_EVENT_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_iocp_handle_service.ipp b/ext/patches/boost/asio/detail/impl/win_iocp_handle_service.ipp
new file mode 100644
index 0000000..2c9fc16
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_iocp_handle_service.ipp
@@ -0,0 +1,527 @@
+//
+// detail/impl/win_iocp_handle_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_HANDLE_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_HANDLE_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/win_iocp_handle_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_iocp_handle_service::overlapped_wrapper
+ : public OVERLAPPED
+{
+public:
+ explicit overlapped_wrapper(boost::system::error_code& ec)
+ {
+ Internal = 0;
+ InternalHigh = 0;
+ Offset = 0;
+ OffsetHigh = 0;
+
+ // Create a non-signalled manual-reset event, for GetOverlappedResult.
+ hEvent = ::CreateEvent(0, TRUE, FALSE, 0);
+ if (hEvent)
+ {
+ // As documented in GetQueuedCompletionStatus, setting the low order
+ // bit of this event prevents our synchronous writes from being treated
+ // as completion port events.
+ DWORD_PTR tmp = reinterpret_cast<DWORD_PTR>(hEvent);
+ hEvent = reinterpret_cast<HANDLE>(tmp | 1);
+ }
+ else
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ }
+
+ ~overlapped_wrapper()
+ {
+ if (hEvent)
+ {
+ ::CloseHandle(hEvent);
+ }
+ }
+};
+
+win_iocp_handle_service::win_iocp_handle_service(
+ boost::asio::io_service& io_service)
+ : iocp_service_(boost::asio::use_service<win_iocp_io_service>(io_service)),
+ mutex_(),
+ impl_list_(0)
+{
+}
+
+void win_iocp_handle_service::shutdown_service()
+{
+ // Close all implementations, causing all operations to complete.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ implementation_type* impl = impl_list_;
+ while (impl)
+ {
+ close_for_destruction(*impl);
+ impl = impl->next_;
+ }
+}
+
+void win_iocp_handle_service::construct(
+ win_iocp_handle_service::implementation_type& impl)
+{
+ impl.handle_ = INVALID_HANDLE_VALUE;
+ impl.safe_cancellation_thread_id_ = 0;
+
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ impl.next_ = impl_list_;
+ impl.prev_ = 0;
+ if (impl_list_)
+ impl_list_->prev_ = &impl;
+ impl_list_ = &impl;
+}
+
+void win_iocp_handle_service::move_construct(
+ win_iocp_handle_service::implementation_type& impl,
+ win_iocp_handle_service::implementation_type& other_impl)
+{
+ impl.handle_ = other_impl.handle_;
+ other_impl.handle_ = INVALID_HANDLE_VALUE;
+
+ impl.safe_cancellation_thread_id_ = other_impl.safe_cancellation_thread_id_;
+ other_impl.safe_cancellation_thread_id_ = 0;
+
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ impl.next_ = impl_list_;
+ impl.prev_ = 0;
+ if (impl_list_)
+ impl_list_->prev_ = &impl;
+ impl_list_ = &impl;
+}
+
+void win_iocp_handle_service::move_assign(
+ win_iocp_handle_service::implementation_type& impl,
+ win_iocp_handle_service& other_service,
+ win_iocp_handle_service::implementation_type& other_impl)
+{
+ close_for_destruction(impl);
+
+ if (this != &other_service)
+ {
+ // Remove implementation from linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ if (impl_list_ == &impl)
+ impl_list_ = impl.next_;
+ if (impl.prev_)
+ impl.prev_->next_ = impl.next_;
+ if (impl.next_)
+ impl.next_->prev_= impl.prev_;
+ impl.next_ = 0;
+ impl.prev_ = 0;
+ }
+
+ impl.handle_ = other_impl.handle_;
+ other_impl.handle_ = INVALID_HANDLE_VALUE;
+
+ impl.safe_cancellation_thread_id_ = other_impl.safe_cancellation_thread_id_;
+ other_impl.safe_cancellation_thread_id_ = 0;
+
+ if (this != &other_service)
+ {
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(other_service.mutex_);
+ impl.next_ = other_service.impl_list_;
+ impl.prev_ = 0;
+ if (other_service.impl_list_)
+ other_service.impl_list_->prev_ = &impl;
+ other_service.impl_list_ = &impl;
+ }
+}
+
+void win_iocp_handle_service::destroy(
+ win_iocp_handle_service::implementation_type& impl)
+{
+ close_for_destruction(impl);
+
+ // Remove implementation from linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ if (impl_list_ == &impl)
+ impl_list_ = impl.next_;
+ if (impl.prev_)
+ impl.prev_->next_ = impl.next_;
+ if (impl.next_)
+ impl.next_->prev_= impl.prev_;
+ impl.next_ = 0;
+ impl.prev_ = 0;
+}
+
+boost::system::error_code win_iocp_handle_service::assign(
+ win_iocp_handle_service::implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ if (iocp_service_.register_handle(handle, ec))
+ return ec;
+
+ impl.handle_ = handle;
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code win_iocp_handle_service::close(
+ win_iocp_handle_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("handle", &impl, "close"));
+
+ if (!::CloseHandle(impl.handle_))
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ }
+
+ impl.handle_ = INVALID_HANDLE_VALUE;
+ impl.safe_cancellation_thread_id_ = 0;
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ }
+
+ return ec;
+}
+
+boost::system::error_code win_iocp_handle_service::cancel(
+ win_iocp_handle_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return ec;
+ }
+
+ BOOST_ASIO_HANDLER_OPERATION(("handle", &impl, "cancel"));
+
+ if (FARPROC cancel_io_ex_ptr = ::GetProcAddress(
+ ::GetModuleHandleA("KERNEL32"), "CancelIoEx"))
+ {
+ // The version of Windows supports cancellation from any thread.
+ typedef BOOL (WINAPI* cancel_io_ex_t)(HANDLE, LPOVERLAPPED);
+ cancel_io_ex_t cancel_io_ex = (cancel_io_ex_t)cancel_io_ex_ptr;
+ if (!cancel_io_ex(impl.handle_, 0))
+ {
+ DWORD last_error = ::GetLastError();
+ if (last_error == ERROR_NOT_FOUND)
+ {
+ // ERROR_NOT_FOUND means that there were no operations to be
+ // cancelled. We swallow this error to match the behaviour on other
+ // platforms.
+ ec = boost::system::error_code();
+ }
+ else
+ {
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ }
+ }
+ else if (impl.safe_cancellation_thread_id_ == 0)
+ {
+ // No operations have been started, so there's nothing to cancel.
+ ec = boost::system::error_code();
+ }
+ else if (impl.safe_cancellation_thread_id_ == ::GetCurrentThreadId())
+ {
+ // Asynchronous operations have been started from the current thread only,
+ // so it is safe to try to cancel them using CancelIo.
+ if (!::CancelIo(impl.handle_))
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ }
+ }
+ else
+ {
+ // Asynchronous operations have been started from more than one thread,
+ // so cancellation is not safe.
+ ec = boost::asio::error::operation_not_supported;
+ }
+
+ return ec;
+}
+
+size_t win_iocp_handle_service::do_write(
+ win_iocp_handle_service::implementation_type& impl, uint64_t offset,
+ const boost::asio::const_buffer& buffer, boost::system::error_code& ec)
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // A request to write 0 bytes on a handle is a no-op.
+ if (boost::asio::buffer_size(buffer) == 0)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ overlapped_wrapper overlapped(ec);
+ if (ec)
+ {
+ return 0;
+ }
+
+ // Write the data.
+ overlapped.Offset = offset & 0xFFFFFFFF;
+ overlapped.OffsetHigh = (offset >> 32) & 0xFFFFFFFF;
+ BOOL ok = ::WriteFile(impl.handle_,
+ boost::asio::buffer_cast<LPCVOID>(buffer),
+ static_cast<DWORD>(boost::asio::buffer_size(buffer)), 0, &overlapped);
+ if (!ok)
+ {
+ DWORD last_error = ::GetLastError();
+ if (last_error != ERROR_IO_PENDING)
+ {
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return 0;
+ }
+ }
+
+ // Wait for the operation to complete.
+ DWORD bytes_transferred = 0;
+ ok = ::GetOverlappedResult(impl.handle_,
+ &overlapped, &bytes_transferred, TRUE);
+ if (!ok)
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return 0;
+ }
+
+ ec = boost::system::error_code();
+ return bytes_transferred;
+}
+
+void win_iocp_handle_service::start_write_op(
+ win_iocp_handle_service::implementation_type& impl, uint64_t offset,
+ const boost::asio::const_buffer& buffer, operation* op)
+{
+ update_cancellation_thread_id(impl);
+ iocp_service_.work_started();
+
+ if (!is_open(impl))
+ {
+ iocp_service_.on_completion(op, boost::asio::error::bad_descriptor);
+ }
+ else if (boost::asio::buffer_size(buffer) == 0)
+ {
+ // A request to write 0 bytes on a handle is a no-op.
+ iocp_service_.on_completion(op);
+ }
+ else
+ {
+ DWORD bytes_transferred = 0;
+ op->Offset = offset & 0xFFFFFFFF;
+ op->OffsetHigh = (offset >> 32) & 0xFFFFFFFF;
+ BOOL ok = ::WriteFile(impl.handle_,
+ boost::asio::buffer_cast<LPCVOID>(buffer),
+ static_cast<DWORD>(boost::asio::buffer_size(buffer)),
+ &bytes_transferred, op);
+ DWORD last_error = ::GetLastError();
+ if (!ok && last_error != ERROR_IO_PENDING
+ && last_error != ERROR_MORE_DATA)
+ {
+ iocp_service_.on_completion(op, last_error, bytes_transferred);
+ }
+ else
+ {
+ iocp_service_.on_pending(op);
+ }
+ }
+}
+
+size_t win_iocp_handle_service::do_read(
+ win_iocp_handle_service::implementation_type& impl, uint64_t offset,
+ const boost::asio::mutable_buffer& buffer, boost::system::error_code& ec)
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ // A request to read 0 bytes on a stream handle is a no-op.
+ if (boost::asio::buffer_size(buffer) == 0)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ overlapped_wrapper overlapped(ec);
+ if (ec)
+ {
+ return 0;
+ }
+
+ // Read some data.
+ overlapped.Offset = offset & 0xFFFFFFFF;
+ overlapped.OffsetHigh = (offset >> 32) & 0xFFFFFFFF;
+ BOOL ok = ::ReadFile(impl.handle_,
+ boost::asio::buffer_cast<LPVOID>(buffer),
+ static_cast<DWORD>(boost::asio::buffer_size(buffer)), 0, &overlapped);
+ if (!ok)
+ {
+ DWORD last_error = ::GetLastError();
+ if (last_error != ERROR_IO_PENDING && last_error != ERROR_MORE_DATA)
+ {
+ if (last_error == ERROR_HANDLE_EOF)
+ {
+ ec = boost::asio::error::eof;
+ }
+ else
+ {
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ return 0;
+ }
+ }
+
+ // Wait for the operation to complete.
+ DWORD bytes_transferred = 0;
+ ok = ::GetOverlappedResult(impl.handle_,
+ &overlapped, &bytes_transferred, TRUE);
+ if (!ok)
+ {
+ DWORD last_error = ::GetLastError();
+ if (last_error == ERROR_HANDLE_EOF)
+ {
+ ec = boost::asio::error::eof;
+ }
+ else
+ {
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ return (last_error == ERROR_MORE_DATA) ? bytes_transferred : 0;
+ }
+
+ ec = boost::system::error_code();
+ return bytes_transferred;
+}
+
+void win_iocp_handle_service::start_read_op(
+ win_iocp_handle_service::implementation_type& impl, uint64_t offset,
+ const boost::asio::mutable_buffer& buffer, operation* op)
+{
+ update_cancellation_thread_id(impl);
+ iocp_service_.work_started();
+
+ if (!is_open(impl))
+ {
+ iocp_service_.on_completion(op, boost::asio::error::bad_descriptor);
+ }
+ else if (boost::asio::buffer_size(buffer) == 0)
+ {
+ // A request to read 0 bytes on a handle is a no-op.
+ iocp_service_.on_completion(op);
+ }
+ else
+ {
+ DWORD bytes_transferred = 0;
+ op->Offset = offset & 0xFFFFFFFF;
+ op->OffsetHigh = (offset >> 32) & 0xFFFFFFFF;
+ BOOL ok = ::ReadFile(impl.handle_,
+ boost::asio::buffer_cast<LPVOID>(buffer),
+ static_cast<DWORD>(boost::asio::buffer_size(buffer)),
+ &bytes_transferred, op);
+ DWORD last_error = ::GetLastError();
+ if (!ok && last_error != ERROR_IO_PENDING
+ && last_error != ERROR_MORE_DATA)
+ {
+ iocp_service_.on_completion(op, last_error, bytes_transferred);
+ }
+ else
+ {
+ iocp_service_.on_pending(op);
+ }
+ }
+}
+
+void win_iocp_handle_service::update_cancellation_thread_id(
+ win_iocp_handle_service::implementation_type& impl)
+{
+ if (impl.safe_cancellation_thread_id_ == 0)
+ impl.safe_cancellation_thread_id_ = ::GetCurrentThreadId();
+ else if (impl.safe_cancellation_thread_id_ != ::GetCurrentThreadId())
+ impl.safe_cancellation_thread_id_ = ~DWORD(0);
+}
+
+void win_iocp_handle_service::close_for_destruction(implementation_type& impl)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("handle", &impl, "close"));
+
+ ::CloseHandle(impl.handle_);
+ impl.handle_ = INVALID_HANDLE_VALUE;
+ impl.safe_cancellation_thread_id_ = 0;
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_HANDLE_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_iocp_io_service.hpp b/ext/patches/boost/asio/detail/impl/win_iocp_io_service.hpp
new file mode 100644
index 0000000..3933d0a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_iocp_io_service.hpp
@@ -0,0 +1,132 @@
+//
+// detail/impl/win_iocp_io_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_IO_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_IO_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/completion_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+void win_iocp_io_service::dispatch(Handler& handler)
+{
+ if (thread_call_stack::contains(this))
+ {
+ fenced_block b(fenced_block::full);
+ boost_asio_handler_invoke_helpers::invoke(handler, handler);
+ }
+ else
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef completion_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "io_service", this, "dispatch"));
+
+ post_immediate_completion(p.p, false);
+ p.v = p.p = 0;
+ }
+}
+
+template <typename Handler>
+void win_iocp_io_service::post(Handler& handler)
+{
+ // Allocate and construct an operation to wrap the handler.
+ typedef completion_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "io_service", this, "post"));
+
+ post_immediate_completion(p.p, false);
+ p.v = p.p = 0;
+}
+
+template <typename Time_Traits>
+void win_iocp_io_service::add_timer_queue(
+ timer_queue<Time_Traits>& queue)
+{
+ do_add_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void win_iocp_io_service::remove_timer_queue(
+ timer_queue<Time_Traits>& queue)
+{
+ do_remove_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void win_iocp_io_service::schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op)
+{
+ // If the service has been shut down we silently discard the timer.
+ if (::InterlockedExchangeAdd(&shutdown_, 0) != 0)
+ {
+ post_immediate_completion(op, false);
+ return;
+ }
+
+ mutex::scoped_lock lock(dispatch_mutex_);
+
+ bool earliest = queue.enqueue_timer(time, timer, op);
+ work_started();
+ if (earliest)
+ update_timeout();
+}
+
+template <typename Time_Traits>
+std::size_t win_iocp_io_service::cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled)
+{
+ // If the service has been shut down we silently ignore the cancellation.
+ if (::InterlockedExchangeAdd(&shutdown_, 0) != 0)
+ return 0;
+
+ mutex::scoped_lock lock(dispatch_mutex_);
+ op_queue<win_iocp_operation> ops;
+ std::size_t n = queue.cancel_timer(timer, ops, max_cancelled);
+ post_deferred_completions(ops);
+ return n;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_IO_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/impl/win_iocp_io_service.ipp b/ext/patches/boost/asio/detail/impl/win_iocp_io_service.ipp
new file mode 100644
index 0000000..2050c13
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_iocp_io_service.ipp
@@ -0,0 +1,540 @@
+//
+// detail/impl/win_iocp_io_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_IO_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_IO_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/cstdint.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/win_iocp_io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct win_iocp_io_service::work_finished_on_block_exit
+{
+ ~work_finished_on_block_exit()
+ {
+ io_service_->work_finished();
+ }
+
+ win_iocp_io_service* io_service_;
+};
+
+struct win_iocp_io_service::timer_thread_function
+{
+ void operator()()
+ {
+ while (::InterlockedExchangeAdd(&io_service_->shutdown_, 0) == 0)
+ {
+ if (::WaitForSingleObject(io_service_->waitable_timer_.handle,
+ INFINITE) == WAIT_OBJECT_0)
+ {
+ ::InterlockedExchange(&io_service_->dispatch_required_, 1);
+ ::PostQueuedCompletionStatus(io_service_->iocp_.handle,
+ 0, wake_for_dispatch, 0);
+ }
+ }
+ }
+
+ win_iocp_io_service* io_service_;
+};
+
+win_iocp_io_service::win_iocp_io_service(
+ boost::asio::io_service& io_service, size_t concurrency_hint)
+ : boost::asio::detail::service_base<win_iocp_io_service>(io_service),
+ iocp_(),
+ outstanding_work_(0),
+ stopped_(0),
+ stop_event_posted_(0),
+ shutdown_(0),
+ gqcs_timeout_(get_gqcs_timeout()),
+ dispatch_required_(0)
+{
+ BOOST_ASIO_HANDLER_TRACKING_INIT;
+
+ iocp_.handle = ::CreateIoCompletionPort(INVALID_HANDLE_VALUE, 0, 0,
+ static_cast<DWORD>(concurrency_hint < DWORD(~0)
+ ? concurrency_hint : DWORD(~0)));
+ if (!iocp_.handle)
+ {
+ DWORD last_error = ::GetLastError();
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "iocp");
+ }
+}
+
+void win_iocp_io_service::shutdown_service()
+{
+ ::InterlockedExchange(&shutdown_, 1);
+
+ if (timer_thread_.get())
+ {
+ LARGE_INTEGER timeout;
+ timeout.QuadPart = 1;
+ ::SetWaitableTimer(waitable_timer_.handle, &timeout, 1, 0, 0, FALSE);
+ }
+
+ while (::InterlockedExchangeAdd(&outstanding_work_, 0) > 0)
+ {
+ op_queue<win_iocp_operation> ops;
+ timer_queues_.get_all_timers(ops);
+ ops.push(completed_ops_);
+ if (!ops.empty())
+ {
+ while (win_iocp_operation* op = ops.front())
+ {
+ ops.pop();
+ ::InterlockedDecrement(&outstanding_work_);
+ op->destroy();
+ }
+ }
+ else
+ {
+ DWORD bytes_transferred = 0;
+ dword_ptr_t completion_key = 0;
+ LPOVERLAPPED overlapped = 0;
+ ::GetQueuedCompletionStatus(iocp_.handle, &bytes_transferred,
+ &completion_key, &overlapped, gqcs_timeout_);
+ if (overlapped)
+ {
+ ::InterlockedDecrement(&outstanding_work_);
+ static_cast<win_iocp_operation*>(overlapped)->destroy();
+ }
+ }
+ }
+
+ if (timer_thread_.get())
+ timer_thread_->join();
+}
+
+boost::system::error_code win_iocp_io_service::register_handle(
+ HANDLE handle, boost::system::error_code& ec)
+{
+ if (::CreateIoCompletionPort(handle, iocp_.handle, 0, 0) == 0)
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ }
+ return ec;
+}
+
+size_t win_iocp_io_service::run(boost::system::error_code& ec)
+{
+ if (::InterlockedExchangeAdd(&outstanding_work_, 0) == 0)
+ {
+ stop();
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ win_iocp_thread_info this_thread;
+ thread_call_stack::context ctx(this, this_thread);
+
+ size_t n = 0;
+ while (do_one(true, ec))
+ if (n != (std::numeric_limits<size_t>::max)())
+ ++n;
+ return n;
+}
+
+size_t win_iocp_io_service::run_one(boost::system::error_code& ec)
+{
+ if (::InterlockedExchangeAdd(&outstanding_work_, 0) == 0)
+ {
+ stop();
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ win_iocp_thread_info this_thread;
+ thread_call_stack::context ctx(this, this_thread);
+
+ return do_one(true, ec);
+}
+
+size_t win_iocp_io_service::poll(boost::system::error_code& ec)
+{
+ if (::InterlockedExchangeAdd(&outstanding_work_, 0) == 0)
+ {
+ stop();
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ win_iocp_thread_info this_thread;
+ thread_call_stack::context ctx(this, this_thread);
+
+ size_t n = 0;
+ while (do_one(false, ec))
+ if (n != (std::numeric_limits<size_t>::max)())
+ ++n;
+ return n;
+}
+
+size_t win_iocp_io_service::poll_one(boost::system::error_code& ec)
+{
+ if (::InterlockedExchangeAdd(&outstanding_work_, 0) == 0)
+ {
+ stop();
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ win_iocp_thread_info this_thread;
+ thread_call_stack::context ctx(this, this_thread);
+
+ return do_one(false, ec);
+}
+
+void win_iocp_io_service::stop()
+{
+ if (::InterlockedExchange(&stopped_, 1) == 0)
+ {
+ if (::InterlockedExchange(&stop_event_posted_, 1) == 0)
+ {
+ if (!::PostQueuedCompletionStatus(iocp_.handle, 0, 0, 0))
+ {
+ DWORD last_error = ::GetLastError();
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "pqcs");
+ }
+ }
+ }
+}
+
+void win_iocp_io_service::post_deferred_completion(win_iocp_operation* op)
+{
+ // Flag the operation as ready.
+ op->ready_ = 1;
+
+ // Enqueue the operation on the I/O completion port.
+ if (!::PostQueuedCompletionStatus(iocp_.handle, 0, 0, op))
+ {
+ // Out of resources. Put on completed queue instead.
+ mutex::scoped_lock lock(dispatch_mutex_);
+ completed_ops_.push(op);
+ ::InterlockedExchange(&dispatch_required_, 1);
+ }
+}
+
+void win_iocp_io_service::post_deferred_completions(
+ op_queue<win_iocp_operation>& ops)
+{
+ while (win_iocp_operation* op = ops.front())
+ {
+ ops.pop();
+
+ // Flag the operation as ready.
+ op->ready_ = 1;
+
+ // Enqueue the operation on the I/O completion port.
+ if (!::PostQueuedCompletionStatus(iocp_.handle, 0, 0, op))
+ {
+ // Out of resources. Put on completed queue instead.
+ mutex::scoped_lock lock(dispatch_mutex_);
+ completed_ops_.push(op);
+ completed_ops_.push(ops);
+ ::InterlockedExchange(&dispatch_required_, 1);
+ }
+ }
+}
+
+void win_iocp_io_service::abandon_operations(
+ op_queue<win_iocp_operation>& ops)
+{
+ while (win_iocp_operation* op = ops.front())
+ {
+ ops.pop();
+ ::InterlockedDecrement(&outstanding_work_);
+ op->destroy();
+ }
+}
+
+void win_iocp_io_service::on_pending(win_iocp_operation* op)
+{
+ if (::InterlockedCompareExchange(&op->ready_, 1, 0) == 1)
+ {
+ // Enqueue the operation on the I/O completion port.
+ if (!::PostQueuedCompletionStatus(iocp_.handle,
+ 0, overlapped_contains_result, op))
+ {
+ // Out of resources. Put on completed queue instead.
+ mutex::scoped_lock lock(dispatch_mutex_);
+ completed_ops_.push(op);
+ ::InterlockedExchange(&dispatch_required_, 1);
+ }
+ }
+}
+
+void win_iocp_io_service::on_completion(win_iocp_operation* op,
+ DWORD last_error, DWORD bytes_transferred)
+{
+ // Flag that the operation is ready for invocation.
+ op->ready_ = 1;
+
+ // Store results in the OVERLAPPED structure.
+ op->Internal = reinterpret_cast<ulong_ptr_t>(
+ &boost::asio::error::get_system_category());
+ op->Offset = last_error;
+ op->OffsetHigh = bytes_transferred;
+
+ // Enqueue the operation on the I/O completion port.
+ if (!::PostQueuedCompletionStatus(iocp_.handle,
+ 0, overlapped_contains_result, op))
+ {
+ // Out of resources. Put on completed queue instead.
+ mutex::scoped_lock lock(dispatch_mutex_);
+ completed_ops_.push(op);
+ ::InterlockedExchange(&dispatch_required_, 1);
+ }
+}
+
+void win_iocp_io_service::on_completion(win_iocp_operation* op,
+ const boost::system::error_code& ec, DWORD bytes_transferred)
+{
+ // Flag that the operation is ready for invocation.
+ op->ready_ = 1;
+
+ // Store results in the OVERLAPPED structure.
+ op->Internal = reinterpret_cast<ulong_ptr_t>(&ec.category());
+ op->Offset = ec.value();
+ op->OffsetHigh = bytes_transferred;
+
+ // Enqueue the operation on the I/O completion port.
+ if (!::PostQueuedCompletionStatus(iocp_.handle,
+ 0, overlapped_contains_result, op))
+ {
+ // Out of resources. Put on completed queue instead.
+ mutex::scoped_lock lock(dispatch_mutex_);
+ completed_ops_.push(op);
+ ::InterlockedExchange(&dispatch_required_, 1);
+ }
+}
+
+size_t win_iocp_io_service::do_one(bool block, boost::system::error_code& ec)
+{
+ for (;;)
+ {
+ // Try to acquire responsibility for dispatching timers and completed ops.
+ if (::InterlockedCompareExchange(&dispatch_required_, 0, 1) == 1)
+ {
+ mutex::scoped_lock lock(dispatch_mutex_);
+
+ // Dispatch pending timers and operations.
+ op_queue<win_iocp_operation> ops;
+ ops.push(completed_ops_);
+ timer_queues_.get_ready_timers(ops);
+ post_deferred_completions(ops);
+ update_timeout();
+ }
+
+ // Get the next operation from the queue.
+ DWORD bytes_transferred = 0;
+ dword_ptr_t completion_key = 0;
+ LPOVERLAPPED overlapped = 0;
+ ::SetLastError(0);
+ BOOL ok = ::GetQueuedCompletionStatus(iocp_.handle, &bytes_transferred,
+ &completion_key, &overlapped, block ? gqcs_timeout_ : 0);
+ DWORD last_error = ::GetLastError();
+
+ if (overlapped)
+ {
+ win_iocp_operation* op = static_cast<win_iocp_operation*>(overlapped);
+ boost::system::error_code result_ec(last_error,
+ boost::asio::error::get_system_category());
+
+ // We may have been passed the last_error and bytes_transferred in the
+ // OVERLAPPED structure itself.
+ if (completion_key == overlapped_contains_result)
+ {
+ result_ec = boost::system::error_code(static_cast<int>(op->Offset),
+ *reinterpret_cast<boost::system::error_category*>(op->Internal));
+ bytes_transferred = op->OffsetHigh;
+ }
+
+ // Otherwise ensure any result has been saved into the OVERLAPPED
+ // structure.
+ else
+ {
+ op->Internal = reinterpret_cast<ulong_ptr_t>(&result_ec.category());
+ op->Offset = result_ec.value();
+ op->OffsetHigh = bytes_transferred;
+ }
+
+ // Dispatch the operation only if ready. The operation may not be ready
+ // if the initiating function (e.g. a call to WSARecv) has not yet
+ // returned. This is because the initiating function still wants access
+ // to the operation's OVERLAPPED structure.
+ if (::InterlockedCompareExchange(&op->ready_, 1, 0) == 1)
+ {
+ // Ensure the count of outstanding work is decremented on block exit.
+ work_finished_on_block_exit on_exit = { this };
+ (void)on_exit;
+
+ op->complete(*this, result_ec, bytes_transferred);
+ ec = boost::system::error_code();
+ return 1;
+ }
+ }
+ else if (!ok)
+ {
+ if (last_error != WAIT_TIMEOUT)
+ {
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return 0;
+ }
+
+ // If we're not polling we need to keep going until we get a real handler.
+ if (block)
+ continue;
+
+ ec = boost::system::error_code();
+ return 0;
+ }
+ else if (completion_key == wake_for_dispatch)
+ {
+ // We have been woken up to try to acquire responsibility for dispatching
+ // timers and completed operations.
+ }
+ else
+ {
+ // Indicate that there is no longer an in-flight stop event.
+ ::InterlockedExchange(&stop_event_posted_, 0);
+
+ // The stopped_ flag is always checked to ensure that any leftover
+ // stop events from a previous run invocation are ignored.
+ if (::InterlockedExchangeAdd(&stopped_, 0) != 0)
+ {
+ // Wake up next thread that is blocked on GetQueuedCompletionStatus.
+ if (::InterlockedExchange(&stop_event_posted_, 1) == 0)
+ {
+ if (!::PostQueuedCompletionStatus(iocp_.handle, 0, 0, 0))
+ {
+ last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return 0;
+ }
+ }
+
+ ec = boost::system::error_code();
+ return 0;
+ }
+ }
+ }
+}
+
+DWORD win_iocp_io_service::get_gqcs_timeout()
+{
+ OSVERSIONINFOEX osvi;
+ ZeroMemory(&osvi, sizeof(osvi));
+ osvi.dwOSVersionInfoSize = sizeof(osvi);
+ osvi.dwMajorVersion = 6ul;
+
+ const uint64_t condition_mask = ::VerSetConditionMask(
+ 0, VER_MAJORVERSION, VER_GREATER_EQUAL);
+
+ if (!!::VerifyVersionInfo(&osvi, VER_MAJORVERSION, condition_mask))
+ return INFINITE;
+
+ return default_gqcs_timeout;
+}
+
+void win_iocp_io_service::do_add_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(dispatch_mutex_);
+
+ timer_queues_.insert(&queue);
+
+ if (!waitable_timer_.handle)
+ {
+ waitable_timer_.handle = ::CreateWaitableTimer(0, FALSE, 0);
+ if (waitable_timer_.handle == 0)
+ {
+ DWORD last_error = ::GetLastError();
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "timer");
+ }
+
+ LARGE_INTEGER timeout;
+ timeout.QuadPart = -max_timeout_usec;
+ timeout.QuadPart *= 10;
+ ::SetWaitableTimer(waitable_timer_.handle,
+ &timeout, max_timeout_msec, 0, 0, FALSE);
+ }
+
+ if (!timer_thread_.get())
+ {
+ timer_thread_function thread_function = { this };
+ timer_thread_.reset(new thread(thread_function, 65536));
+ }
+}
+
+void win_iocp_io_service::do_remove_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(dispatch_mutex_);
+
+ timer_queues_.erase(&queue);
+}
+
+void win_iocp_io_service::update_timeout()
+{
+ if (timer_thread_.get())
+ {
+ // There's no point updating the waitable timer if the new timeout period
+ // exceeds the maximum timeout. In that case, we might as well wait for the
+ // existing period of the timer to expire.
+ long timeout_usec = timer_queues_.wait_duration_usec(max_timeout_usec);
+ if (timeout_usec < max_timeout_usec)
+ {
+ LARGE_INTEGER timeout;
+ timeout.QuadPart = -timeout_usec;
+ timeout.QuadPart *= 10;
+ ::SetWaitableTimer(waitable_timer_.handle,
+ &timeout, max_timeout_msec, 0, 0, FALSE);
+ }
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_IO_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_iocp_serial_port_service.ipp b/ext/patches/boost/asio/detail/impl/win_iocp_serial_port_service.ipp
new file mode 100644
index 0000000..7a8e649
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_iocp_serial_port_service.ipp
@@ -0,0 +1,182 @@
+//
+// detail/impl/win_iocp_serial_port_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_SERIAL_PORT_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_SERIAL_PORT_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP) && defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+#include <cstring>
+#include <boost/asio/detail/win_iocp_serial_port_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+win_iocp_serial_port_service::win_iocp_serial_port_service(
+ boost::asio::io_service& io_service)
+ : handle_service_(io_service)
+{
+}
+
+void win_iocp_serial_port_service::shutdown_service()
+{
+}
+
+boost::system::error_code win_iocp_serial_port_service::open(
+ win_iocp_serial_port_service::implementation_type& impl,
+ const std::string& device, boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ // For convenience, add a leading \\.\ sequence if not already present.
+ std::string name = (device[0] == '\\') ? device : "\\\\.\\" + device;
+
+ // Open a handle to the serial port.
+ ::HANDLE handle = ::CreateFileA(name.c_str(),
+ GENERIC_READ | GENERIC_WRITE, 0, 0,
+ OPEN_EXISTING, FILE_FLAG_OVERLAPPED, 0);
+ if (handle == INVALID_HANDLE_VALUE)
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ // Determine the initial serial port parameters.
+ using namespace std; // For memset.
+ ::DCB dcb;
+ memset(&dcb, 0, sizeof(DCB));
+ dcb.DCBlength = sizeof(DCB);
+ if (!::GetCommState(handle, &dcb))
+ {
+ DWORD last_error = ::GetLastError();
+ ::CloseHandle(handle);
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ // Set some default serial port parameters. This implementation does not
+ // support changing these, so they might as well be in a known state.
+ dcb.fBinary = TRUE; // Win32 only supports binary mode.
+ dcb.fDsrSensitivity = FALSE;
+ dcb.fNull = FALSE; // Do not ignore NULL characters.
+ dcb.fAbortOnError = FALSE; // Ignore serial framing errors.
+ if (!::SetCommState(handle, &dcb))
+ {
+ DWORD last_error = ::GetLastError();
+ ::CloseHandle(handle);
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ // Set up timeouts so that the serial port will behave similarly to a
+ // network socket. Reads wait for at least one byte, then return with
+ // whatever they have. Writes return once everything is out the door.
+ ::COMMTIMEOUTS timeouts;
+ timeouts.ReadIntervalTimeout = 1;
+ timeouts.ReadTotalTimeoutMultiplier = 0;
+ timeouts.ReadTotalTimeoutConstant = 0;
+ timeouts.WriteTotalTimeoutMultiplier = 0;
+ timeouts.WriteTotalTimeoutConstant = 0;
+ if (!::SetCommTimeouts(handle, &timeouts))
+ {
+ DWORD last_error = ::GetLastError();
+ ::CloseHandle(handle);
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ // We're done. Take ownership of the serial port handle.
+ if (handle_service_.assign(impl, handle, ec))
+ ::CloseHandle(handle);
+ return ec;
+}
+
+boost::system::error_code win_iocp_serial_port_service::do_set_option(
+ win_iocp_serial_port_service::implementation_type& impl,
+ win_iocp_serial_port_service::store_function_type store,
+ const void* option, boost::system::error_code& ec)
+{
+ using namespace std; // For memcpy.
+
+ ::DCB dcb;
+ memset(&dcb, 0, sizeof(DCB));
+ dcb.DCBlength = sizeof(DCB);
+ if (!::GetCommState(handle_service_.native_handle(impl), &dcb))
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ if (store(option, dcb, ec))
+ return ec;
+
+ if (!::SetCommState(handle_service_.native_handle(impl), &dcb))
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code win_iocp_serial_port_service::do_get_option(
+ const win_iocp_serial_port_service::implementation_type& impl,
+ win_iocp_serial_port_service::load_function_type load,
+ void* option, boost::system::error_code& ec) const
+{
+ using namespace std; // For memset.
+
+ ::DCB dcb;
+ memset(&dcb, 0, sizeof(DCB));
+ dcb.DCBlength = sizeof(DCB);
+ if (!::GetCommState(handle_service_.native_handle(impl), &dcb))
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ return ec;
+ }
+
+ return load(option, dcb, ec);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP) && defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_SERIAL_PORT_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_iocp_socket_service_base.ipp b/ext/patches/boost/asio/detail/impl/win_iocp_socket_service_base.ipp
new file mode 100644
index 0000000..99a90dc
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_iocp_socket_service_base.ipp
@@ -0,0 +1,730 @@
+//
+// detail/impl/win_iocp_socket_service_base.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_SOCKET_SERVICE_BASE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_SOCKET_SERVICE_BASE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/win_iocp_socket_service_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+win_iocp_socket_service_base::win_iocp_socket_service_base(
+ boost::asio::io_service& io_service)
+ : io_service_(io_service),
+ iocp_service_(use_service<win_iocp_io_service>(io_service)),
+ reactor_(0),
+ connect_ex_(0),
+ mutex_(),
+ impl_list_(0)
+{
+}
+
+void win_iocp_socket_service_base::shutdown_service()
+{
+ // Close all implementations, causing all operations to complete.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ base_implementation_type* impl = impl_list_;
+ while (impl)
+ {
+ boost::system::error_code ignored_ec;
+ close_for_destruction(*impl);
+ impl = impl->next_;
+ }
+}
+
+void win_iocp_socket_service_base::construct(
+ win_iocp_socket_service_base::base_implementation_type& impl)
+{
+ impl.socket_ = invalid_socket;
+ impl.state_ = 0;
+ impl.cancel_token_.reset();
+#if defined(BOOST_ASIO_ENABLE_CANCELIO)
+ impl.safe_cancellation_thread_id_ = 0;
+#endif // defined(BOOST_ASIO_ENABLE_CANCELIO)
+
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ impl.next_ = impl_list_;
+ impl.prev_ = 0;
+ if (impl_list_)
+ impl_list_->prev_ = &impl;
+ impl_list_ = &impl;
+}
+
+void win_iocp_socket_service_base::base_move_construct(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ win_iocp_socket_service_base::base_implementation_type& other_impl)
+{
+ impl.socket_ = other_impl.socket_;
+ other_impl.socket_ = invalid_socket;
+
+ impl.state_ = other_impl.state_;
+ other_impl.state_ = 0;
+
+ impl.cancel_token_ = other_impl.cancel_token_;
+ other_impl.cancel_token_.reset();
+
+#if defined(BOOST_ASIO_ENABLE_CANCELIO)
+ impl.safe_cancellation_thread_id_ = other_impl.safe_cancellation_thread_id_;
+ other_impl.safe_cancellation_thread_id_ = 0;
+#endif // defined(BOOST_ASIO_ENABLE_CANCELIO)
+
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ impl.next_ = impl_list_;
+ impl.prev_ = 0;
+ if (impl_list_)
+ impl_list_->prev_ = &impl;
+ impl_list_ = &impl;
+}
+
+void win_iocp_socket_service_base::base_move_assign(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ win_iocp_socket_service_base& other_service,
+ win_iocp_socket_service_base::base_implementation_type& other_impl)
+{
+ close_for_destruction(impl);
+
+ if (this != &other_service)
+ {
+ // Remove implementation from linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ if (impl_list_ == &impl)
+ impl_list_ = impl.next_;
+ if (impl.prev_)
+ impl.prev_->next_ = impl.next_;
+ if (impl.next_)
+ impl.next_->prev_= impl.prev_;
+ impl.next_ = 0;
+ impl.prev_ = 0;
+ }
+
+ impl.socket_ = other_impl.socket_;
+ other_impl.socket_ = invalid_socket;
+
+ impl.state_ = other_impl.state_;
+ other_impl.state_ = 0;
+
+ impl.cancel_token_ = other_impl.cancel_token_;
+ other_impl.cancel_token_.reset();
+
+#if defined(BOOST_ASIO_ENABLE_CANCELIO)
+ impl.safe_cancellation_thread_id_ = other_impl.safe_cancellation_thread_id_;
+ other_impl.safe_cancellation_thread_id_ = 0;
+#endif // defined(BOOST_ASIO_ENABLE_CANCELIO)
+
+ if (this != &other_service)
+ {
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(other_service.mutex_);
+ impl.next_ = other_service.impl_list_;
+ impl.prev_ = 0;
+ if (other_service.impl_list_)
+ other_service.impl_list_->prev_ = &impl;
+ other_service.impl_list_ = &impl;
+ }
+}
+
+void win_iocp_socket_service_base::destroy(
+ win_iocp_socket_service_base::base_implementation_type& impl)
+{
+ close_for_destruction(impl);
+
+ // Remove implementation from linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ if (impl_list_ == &impl)
+ impl_list_ = impl.next_;
+ if (impl.prev_)
+ impl.prev_->next_ = impl.next_;
+ if (impl.next_)
+ impl.next_->prev_= impl.prev_;
+ impl.next_ = 0;
+ impl.prev_ = 0;
+}
+
+boost::system::error_code win_iocp_socket_service_base::close(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("socket", &impl, "close"));
+
+ // Check if the reactor was created, in which case we need to close the
+ // socket on the reactor as well to cancel any operations that might be
+ // running there.
+ reactor* r = static_cast<reactor*>(
+ interlocked_compare_exchange_pointer(
+ reinterpret_cast<void**>(&reactor_), 0, 0));
+ if (r)
+ r->deregister_descriptor(impl.socket_, impl.reactor_data_, true);
+ }
+
+ socket_ops::close(impl.socket_, impl.state_, false, ec);
+
+ impl.socket_ = invalid_socket;
+ impl.state_ = 0;
+ impl.cancel_token_.reset();
+#if defined(BOOST_ASIO_ENABLE_CANCELIO)
+ impl.safe_cancellation_thread_id_ = 0;
+#endif // defined(BOOST_ASIO_ENABLE_CANCELIO)
+
+ return ec;
+}
+
+boost::system::error_code win_iocp_socket_service_base::cancel(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return ec;
+ }
+
+ BOOST_ASIO_HANDLER_OPERATION(("socket", &impl, "cancel"));
+
+ if (FARPROC cancel_io_ex_ptr = ::GetProcAddress(
+ ::GetModuleHandleA("KERNEL32"), "CancelIoEx"))
+ {
+ // The version of Windows supports cancellation from any thread.
+ typedef BOOL (WINAPI* cancel_io_ex_t)(HANDLE, LPOVERLAPPED);
+ cancel_io_ex_t cancel_io_ex = (cancel_io_ex_t)cancel_io_ex_ptr;
+ socket_type sock = impl.socket_;
+ HANDLE sock_as_handle = reinterpret_cast<HANDLE>(sock);
+ if (!cancel_io_ex(sock_as_handle, 0))
+ {
+ DWORD last_error = ::GetLastError();
+ if (last_error == ERROR_NOT_FOUND)
+ {
+ // ERROR_NOT_FOUND means that there were no operations to be
+ // cancelled. We swallow this error to match the behaviour on other
+ // platforms.
+ ec = boost::system::error_code();
+ }
+ else
+ {
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ }
+ }
+#if defined(BOOST_ASIO_ENABLE_CANCELIO)
+ else if (impl.safe_cancellation_thread_id_ == 0)
+ {
+ // No operations have been started, so there's nothing to cancel.
+ ec = boost::system::error_code();
+ }
+ else if (impl.safe_cancellation_thread_id_ == ::GetCurrentThreadId())
+ {
+ // Asynchronous operations have been started from the current thread only,
+ // so it is safe to try to cancel them using CancelIo.
+ socket_type sock = impl.socket_;
+ HANDLE sock_as_handle = reinterpret_cast<HANDLE>(sock);
+ if (!::CancelIo(sock_as_handle))
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ }
+ }
+ else
+ {
+ // Asynchronous operations have been started from more than one thread,
+ // so cancellation is not safe.
+ ec = boost::asio::error::operation_not_supported;
+ }
+#else // defined(BOOST_ASIO_ENABLE_CANCELIO)
+ else
+ {
+ // Cancellation is not supported as CancelIo may not be used.
+ ec = boost::asio::error::operation_not_supported;
+ }
+#endif // defined(BOOST_ASIO_ENABLE_CANCELIO)
+
+ // Cancel any operations started via the reactor.
+ if (!ec)
+ {
+ reactor* r = static_cast<reactor*>(
+ interlocked_compare_exchange_pointer(
+ reinterpret_cast<void**>(&reactor_), 0, 0));
+ if (r)
+ r->cancel_ops(impl.socket_, impl.reactor_data_);
+ }
+
+ return ec;
+}
+
+boost::system::error_code win_iocp_socket_service_base::do_open(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ int family, int type, int protocol, boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ socket_holder sock(socket_ops::socket(family, type, protocol, ec));
+ if (sock.get() == invalid_socket)
+ return ec;
+
+ HANDLE sock_as_handle = reinterpret_cast<HANDLE>(sock.get());
+ if (iocp_service_.register_handle(sock_as_handle, ec))
+ return ec;
+
+ impl.socket_ = sock.release();
+ switch (type)
+ {
+ case SOCK_STREAM: impl.state_ = socket_ops::stream_oriented; break;
+ case SOCK_DGRAM: impl.state_ = socket_ops::datagram_oriented; break;
+ default: impl.state_ = 0; break;
+ }
+ impl.cancel_token_.reset(static_cast<void*>(0), socket_ops::noop_deleter());
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code win_iocp_socket_service_base::do_assign(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ int type, socket_type native_socket, boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ HANDLE sock_as_handle = reinterpret_cast<HANDLE>(native_socket);
+ if (iocp_service_.register_handle(sock_as_handle, ec))
+ return ec;
+
+ impl.socket_ = native_socket;
+ switch (type)
+ {
+ case SOCK_STREAM: impl.state_ = socket_ops::stream_oriented; break;
+ case SOCK_DGRAM: impl.state_ = socket_ops::datagram_oriented; break;
+ default: impl.state_ = 0; break;
+ }
+ impl.cancel_token_.reset(static_cast<void*>(0), socket_ops::noop_deleter());
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void win_iocp_socket_service_base::start_send_op(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ WSABUF* buffers, std::size_t buffer_count,
+ socket_base::message_flags flags, bool noop, operation* op)
+{
+ update_cancellation_thread_id(impl);
+ iocp_service_.work_started();
+
+ if (noop)
+ iocp_service_.on_completion(op);
+ else if (!is_open(impl))
+ iocp_service_.on_completion(op, boost::asio::error::bad_descriptor);
+ else
+ {
+ DWORD bytes_transferred = 0;
+ int result = ::WSASend(impl.socket_, buffers,
+ static_cast<DWORD>(buffer_count), &bytes_transferred, flags, op, 0);
+ DWORD last_error = ::WSAGetLastError();
+ if (last_error == ERROR_PORT_UNREACHABLE)
+ last_error = WSAECONNREFUSED;
+ if (result != 0 && last_error != WSA_IO_PENDING)
+ iocp_service_.on_completion(op, last_error, bytes_transferred);
+ else
+ iocp_service_.on_pending(op);
+ }
+}
+
+void win_iocp_socket_service_base::start_send_to_op(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ WSABUF* buffers, std::size_t buffer_count,
+ const socket_addr_type* addr, int addrlen,
+ socket_base::message_flags flags, operation* op)
+{
+ update_cancellation_thread_id(impl);
+ iocp_service_.work_started();
+
+ if (!is_open(impl))
+ iocp_service_.on_completion(op, boost::asio::error::bad_descriptor);
+ else
+ {
+ DWORD bytes_transferred = 0;
+ int result = ::WSASendTo(impl.socket_, buffers,
+ static_cast<DWORD>(buffer_count),
+ &bytes_transferred, flags, addr, addrlen, op, 0);
+ DWORD last_error = ::WSAGetLastError();
+ if (last_error == ERROR_PORT_UNREACHABLE)
+ last_error = WSAECONNREFUSED;
+ if (result != 0 && last_error != WSA_IO_PENDING)
+ iocp_service_.on_completion(op, last_error, bytes_transferred);
+ else
+ iocp_service_.on_pending(op);
+ }
+}
+
+void win_iocp_socket_service_base::start_receive_op(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ WSABUF* buffers, std::size_t buffer_count,
+ socket_base::message_flags flags, bool noop, operation* op)
+{
+ update_cancellation_thread_id(impl);
+ iocp_service_.work_started();
+
+ if (noop)
+ iocp_service_.on_completion(op);
+ else if (!is_open(impl))
+ iocp_service_.on_completion(op, boost::asio::error::bad_descriptor);
+ else
+ {
+ DWORD bytes_transferred = 0;
+ DWORD recv_flags = flags;
+ int result = ::WSARecv(impl.socket_, buffers,
+ static_cast<DWORD>(buffer_count),
+ &bytes_transferred, &recv_flags, op, 0);
+ DWORD last_error = ::WSAGetLastError();
+ if (last_error == ERROR_NETNAME_DELETED)
+ last_error = WSAECONNRESET;
+ else if (last_error == ERROR_PORT_UNREACHABLE)
+ last_error = WSAECONNREFUSED;
+ if (result != 0 && last_error != WSA_IO_PENDING)
+ iocp_service_.on_completion(op, last_error, bytes_transferred);
+ else
+ iocp_service_.on_pending(op);
+ }
+}
+
+void win_iocp_socket_service_base::start_null_buffers_receive_op(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ socket_base::message_flags flags, reactor_op* op)
+{
+ if ((impl.state_ & socket_ops::stream_oriented) != 0)
+ {
+ // For stream sockets on Windows, we may issue a 0-byte overlapped
+ // WSARecv to wait until there is data available on the socket.
+ ::WSABUF buf = { 0, 0 };
+ start_receive_op(impl, &buf, 1, flags, false, op);
+ }
+ else
+ {
+ start_reactor_op(impl,
+ (flags & socket_base::message_out_of_band)
+ ? reactor::except_op : reactor::read_op,
+ op);
+ }
+}
+
+void win_iocp_socket_service_base::start_receive_from_op(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ WSABUF* buffers, std::size_t buffer_count, socket_addr_type* addr,
+ socket_base::message_flags flags, int* addrlen, operation* op)
+{
+ update_cancellation_thread_id(impl);
+ iocp_service_.work_started();
+
+ if (!is_open(impl))
+ iocp_service_.on_completion(op, boost::asio::error::bad_descriptor);
+ else
+ {
+ DWORD bytes_transferred = 0;
+ DWORD recv_flags = flags;
+ int result = ::WSARecvFrom(impl.socket_, buffers,
+ static_cast<DWORD>(buffer_count),
+ &bytes_transferred, &recv_flags, addr, addrlen, op, 0);
+ DWORD last_error = ::WSAGetLastError();
+ if (last_error == ERROR_PORT_UNREACHABLE)
+ last_error = WSAECONNREFUSED;
+ if (result != 0 && last_error != WSA_IO_PENDING)
+ iocp_service_.on_completion(op, last_error, bytes_transferred);
+ else
+ iocp_service_.on_pending(op);
+ }
+}
+
+void win_iocp_socket_service_base::start_accept_op(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ bool peer_is_open, socket_holder& new_socket, int family, int type,
+ int protocol, void* output_buffer, DWORD address_length, operation* op)
+{
+ update_cancellation_thread_id(impl);
+ iocp_service_.work_started();
+
+ if (!is_open(impl))
+ iocp_service_.on_completion(op, boost::asio::error::bad_descriptor);
+ else if (peer_is_open)
+ iocp_service_.on_completion(op, boost::asio::error::already_open);
+ else
+ {
+ boost::system::error_code ec;
+ new_socket.reset(socket_ops::socket(family, type, protocol, ec));
+ if (new_socket.get() == invalid_socket)
+ iocp_service_.on_completion(op, ec);
+ else
+ {
+ DWORD bytes_read = 0;
+ BOOL result = ::AcceptEx(impl.socket_, new_socket.get(), output_buffer,
+ 0, address_length, address_length, &bytes_read, op);
+ DWORD last_error = ::WSAGetLastError();
+ if (!result && last_error != WSA_IO_PENDING)
+ iocp_service_.on_completion(op, last_error);
+ else
+ iocp_service_.on_pending(op);
+ }
+ }
+}
+
+void win_iocp_socket_service_base::restart_accept_op(
+ socket_type s, socket_holder& new_socket, int family, int type,
+ int protocol, void* output_buffer, DWORD address_length, operation* op)
+{
+ new_socket.reset();
+ iocp_service_.work_started();
+
+ boost::system::error_code ec;
+ new_socket.reset(socket_ops::socket(family, type, protocol, ec));
+ if (new_socket.get() == invalid_socket)
+ iocp_service_.on_completion(op, ec);
+ else
+ {
+ DWORD bytes_read = 0;
+ BOOL result = ::AcceptEx(s, new_socket.get(), output_buffer,
+ 0, address_length, address_length, &bytes_read, op);
+ DWORD last_error = ::WSAGetLastError();
+ if (!result && last_error != WSA_IO_PENDING)
+ iocp_service_.on_completion(op, last_error);
+ else
+ iocp_service_.on_pending(op);
+ }
+}
+
+void win_iocp_socket_service_base::start_reactor_op(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ int op_type, reactor_op* op)
+{
+ reactor& r = get_reactor();
+ update_cancellation_thread_id(impl);
+
+ if (is_open(impl))
+ {
+ r.start_op(op_type, impl.socket_, impl.reactor_data_, op, false, false);
+ return;
+ }
+ else
+ op->ec_ = boost::asio::error::bad_descriptor;
+
+ iocp_service_.post_immediate_completion(op, false);
+}
+
+void win_iocp_socket_service_base::start_connect_op(
+ win_iocp_socket_service_base::base_implementation_type& impl,
+ int family, int type, const socket_addr_type* addr,
+ std::size_t addrlen, win_iocp_socket_connect_op_base* op)
+{
+ // If ConnectEx is available, use that.
+ if (family == BOOST_ASIO_OS_DEF(AF_INET)
+ || family == BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ if (connect_ex_fn connect_ex = get_connect_ex(impl, type))
+ {
+ union address_union
+ {
+ socket_addr_type base;
+ sockaddr_in4_type v4;
+ sockaddr_in6_type v6;
+ } a;
+
+ using namespace std; // For memset.
+ memset(&a, 0, sizeof(a));
+ a.base.sa_family = family;
+
+ socket_ops::bind(impl.socket_, &a.base,
+ family == BOOST_ASIO_OS_DEF(AF_INET)
+ ? sizeof(a.v4) : sizeof(a.v6), op->ec_);
+ if (op->ec_ && op->ec_ != boost::asio::error::invalid_argument)
+ {
+ iocp_service_.post_immediate_completion(op, false);
+ return;
+ }
+
+ op->connect_ex_ = true;
+ update_cancellation_thread_id(impl);
+ iocp_service_.work_started();
+
+ BOOL result = connect_ex(impl.socket_,
+ addr, static_cast<int>(addrlen), 0, 0, 0, op);
+ DWORD last_error = ::WSAGetLastError();
+ if (!result && last_error != WSA_IO_PENDING)
+ iocp_service_.on_completion(op, last_error);
+ else
+ iocp_service_.on_pending(op);
+ return;
+ }
+ }
+
+ // Otherwise, fall back to a reactor-based implementation.
+ reactor& r = get_reactor();
+ update_cancellation_thread_id(impl);
+
+ if ((impl.state_ & socket_ops::non_blocking) != 0
+ || socket_ops::set_internal_non_blocking(
+ impl.socket_, impl.state_, true, op->ec_))
+ {
+ if (socket_ops::connect(impl.socket_, addr, addrlen, op->ec_) != 0)
+ {
+ if (op->ec_ == boost::asio::error::in_progress
+ || op->ec_ == boost::asio::error::would_block)
+ {
+ op->ec_ = boost::system::error_code();
+ r.start_op(reactor::connect_op, impl.socket_,
+ impl.reactor_data_, op, false, false);
+ return;
+ }
+ }
+ }
+
+ r.post_immediate_completion(op, false);
+}
+
+void win_iocp_socket_service_base::close_for_destruction(
+ win_iocp_socket_service_base::base_implementation_type& impl)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("socket", &impl, "close"));
+
+ // Check if the reactor was created, in which case we need to close the
+ // socket on the reactor as well to cancel any operations that might be
+ // running there.
+ reactor* r = static_cast<reactor*>(
+ interlocked_compare_exchange_pointer(
+ reinterpret_cast<void**>(&reactor_), 0, 0));
+ if (r)
+ r->deregister_descriptor(impl.socket_, impl.reactor_data_, true);
+ }
+
+ boost::system::error_code ignored_ec;
+ socket_ops::close(impl.socket_, impl.state_, true, ignored_ec);
+ impl.socket_ = invalid_socket;
+ impl.state_ = 0;
+ impl.cancel_token_.reset();
+#if defined(BOOST_ASIO_ENABLE_CANCELIO)
+ impl.safe_cancellation_thread_id_ = 0;
+#endif // defined(BOOST_ASIO_ENABLE_CANCELIO)
+}
+
+void win_iocp_socket_service_base::update_cancellation_thread_id(
+ win_iocp_socket_service_base::base_implementation_type& impl)
+{
+#if defined(BOOST_ASIO_ENABLE_CANCELIO)
+ if (impl.safe_cancellation_thread_id_ == 0)
+ impl.safe_cancellation_thread_id_ = ::GetCurrentThreadId();
+ else if (impl.safe_cancellation_thread_id_ != ::GetCurrentThreadId())
+ impl.safe_cancellation_thread_id_ = ~DWORD(0);
+#else // defined(BOOST_ASIO_ENABLE_CANCELIO)
+ (void)impl;
+#endif // defined(BOOST_ASIO_ENABLE_CANCELIO)
+}
+
+reactor& win_iocp_socket_service_base::get_reactor()
+{
+ reactor* r = static_cast<reactor*>(
+ interlocked_compare_exchange_pointer(
+ reinterpret_cast<void**>(&reactor_), 0, 0));
+ if (!r)
+ {
+ r = &(use_service<reactor>(io_service_));
+ interlocked_exchange_pointer(reinterpret_cast<void**>(&reactor_), r);
+ }
+ return *r;
+}
+
+win_iocp_socket_service_base::connect_ex_fn
+win_iocp_socket_service_base::get_connect_ex(
+ win_iocp_socket_service_base::base_implementation_type& impl, int type)
+{
+ if (type != BOOST_ASIO_OS_DEF(SOCK_STREAM)
+ && type != BOOST_ASIO_OS_DEF(SOCK_SEQPACKET))
+ return 0;
+
+ void* ptr = interlocked_compare_exchange_pointer(&connect_ex_, 0, 0);
+ if (!ptr)
+ {
+ GUID guid = { 0x25a207b9, 0xddf3, 0x4660,
+ { 0x8e, 0xe9, 0x76, 0xe5, 0x8c, 0x74, 0x06, 0x3e } };
+
+ DWORD bytes = 0;
+ if (::WSAIoctl(impl.socket_, SIO_GET_EXTENSION_FUNCTION_POINTER,
+ &guid, sizeof(guid), &ptr, sizeof(ptr), &bytes, 0, 0) != 0)
+ {
+ // Set connect_ex_ to a special value to indicate that ConnectEx is
+ // unavailable. That way we won't bother trying to look it up again.
+ ptr = this;
+ }
+
+ interlocked_exchange_pointer(&connect_ex_, ptr);
+ }
+
+ return reinterpret_cast<connect_ex_fn>(ptr == this ? 0 : ptr);
+}
+
+void* win_iocp_socket_service_base::interlocked_compare_exchange_pointer(
+ void** dest, void* exch, void* cmp)
+{
+#if defined(_M_IX86)
+ return reinterpret_cast<void*>(InterlockedCompareExchange(
+ reinterpret_cast<PLONG>(dest), reinterpret_cast<LONG>(exch),
+ reinterpret_cast<LONG>(cmp)));
+#else
+ return InterlockedCompareExchangePointer(dest, exch, cmp);
+#endif
+}
+
+void* win_iocp_socket_service_base::interlocked_exchange_pointer(
+ void** dest, void* val)
+{
+#if defined(_M_IX86)
+ return reinterpret_cast<void*>(InterlockedExchange(
+ reinterpret_cast<PLONG>(dest), reinterpret_cast<LONG>(val)));
+#else
+ return InterlockedExchangePointer(dest, val);
+#endif
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_IOCP_SOCKET_SERVICE_BASE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_mutex.ipp b/ext/patches/boost/asio/detail/impl/win_mutex.ipp
new file mode 100644
index 0000000..8661030
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_mutex.ipp
@@ -0,0 +1,80 @@
+//
+// detail/impl/win_mutex.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_MUTEX_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_MUTEX_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS)
+
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/win_mutex.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+win_mutex::win_mutex()
+{
+ int error = do_init();
+ boost::system::error_code ec(error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "mutex");
+}
+
+int win_mutex::do_init()
+{
+#if defined(__MINGW32__)
+ // Not sure if MinGW supports structured exception handling, so for now
+ // we'll just call the Windows API and hope.
+# if defined(UNDER_CE)
+ ::InitializeCriticalSection(&crit_section_);
+# else
+ if (!::InitializeCriticalSectionAndSpinCount(&crit_section_, 0x80000000))
+ return ::GetLastError();
+# endif
+ return 0;
+#else
+ __try
+ {
+# if defined(UNDER_CE)
+ ::InitializeCriticalSection(&crit_section_);
+# else
+ if (!::InitializeCriticalSectionAndSpinCount(&crit_section_, 0x80000000))
+ return ::GetLastError();
+# endif
+ }
+ __except(GetExceptionCode() == STATUS_NO_MEMORY
+ ? EXCEPTION_EXECUTE_HANDLER : EXCEPTION_CONTINUE_SEARCH)
+ {
+ return ERROR_OUTOFMEMORY;
+ }
+
+ return 0;
+#endif
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_MUTEX_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_object_handle_service.ipp b/ext/patches/boost/asio/detail/impl/win_object_handle_service.ipp
new file mode 100644
index 0000000..938371d
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_object_handle_service.ipp
@@ -0,0 +1,446 @@
+//
+// detail/impl/win_object_handle_service.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2011 Boris Schaeling (boris at highscore.de)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_OBJECT_HANDLE_SERVICE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_OBJECT_HANDLE_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+
+#include <boost/asio/detail/win_object_handle_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+win_object_handle_service::win_object_handle_service(
+ boost::asio::io_service& io_service)
+ : io_service_(boost::asio::use_service<io_service_impl>(io_service)),
+ mutex_(),
+ impl_list_(0),
+ shutdown_(false)
+{
+}
+
+void win_object_handle_service::shutdown_service()
+{
+ mutex::scoped_lock lock(mutex_);
+
+ // Setting this flag to true prevents new objects from being registered, and
+ // new asynchronous wait operations from being started. We only need to worry
+ // about cleaning up the operations that are currently in progress.
+ shutdown_ = true;
+
+ op_queue<operation> ops;
+ for (implementation_type* impl = impl_list_; impl; impl = impl->next_)
+ ops.push(impl->op_queue_);
+
+ lock.unlock();
+
+ io_service_.abandon_operations(ops);
+}
+
+void win_object_handle_service::construct(
+ win_object_handle_service::implementation_type& impl)
+{
+ impl.handle_ = INVALID_HANDLE_VALUE;
+ impl.wait_handle_ = INVALID_HANDLE_VALUE;
+ impl.owner_ = this;
+
+ // Insert implementation into linked list of all implementations.
+ mutex::scoped_lock lock(mutex_);
+ if (!shutdown_)
+ {
+ impl.next_ = impl_list_;
+ impl.prev_ = 0;
+ if (impl_list_)
+ impl_list_->prev_ = &impl;
+ impl_list_ = &impl;
+ }
+}
+
+void win_object_handle_service::move_construct(
+ win_object_handle_service::implementation_type& impl,
+ win_object_handle_service::implementation_type& other_impl)
+{
+ mutex::scoped_lock lock(mutex_);
+
+ // Insert implementation into linked list of all implementations.
+ if (!shutdown_)
+ {
+ impl.next_ = impl_list_;
+ impl.prev_ = 0;
+ if (impl_list_)
+ impl_list_->prev_ = &impl;
+ impl_list_ = &impl;
+ }
+
+ impl.handle_ = other_impl.handle_;
+ other_impl.handle_ = INVALID_HANDLE_VALUE;
+ impl.wait_handle_ = other_impl.wait_handle_;
+ other_impl.wait_handle_ = INVALID_HANDLE_VALUE;
+ impl.op_queue_.push(other_impl.op_queue_);
+ impl.owner_ = this;
+
+ // We must not hold the lock while calling UnregisterWaitEx. This is because
+ // the registered callback function might be invoked while we are waiting for
+ // UnregisterWaitEx to complete.
+ lock.unlock();
+
+ if (impl.wait_handle_ != INVALID_HANDLE_VALUE)
+ ::UnregisterWaitEx(impl.wait_handle_, INVALID_HANDLE_VALUE);
+
+ if (!impl.op_queue_.empty())
+ register_wait_callback(impl, lock);
+}
+
+void win_object_handle_service::move_assign(
+ win_object_handle_service::implementation_type& impl,
+ win_object_handle_service& other_service,
+ win_object_handle_service::implementation_type& other_impl)
+{
+ boost::system::error_code ignored_ec;
+ close(impl, ignored_ec);
+
+ mutex::scoped_lock lock(mutex_);
+
+ if (this != &other_service)
+ {
+ // Remove implementation from linked list of all implementations.
+ if (impl_list_ == &impl)
+ impl_list_ = impl.next_;
+ if (impl.prev_)
+ impl.prev_->next_ = impl.next_;
+ if (impl.next_)
+ impl.next_->prev_= impl.prev_;
+ impl.next_ = 0;
+ impl.prev_ = 0;
+ }
+
+ impl.handle_ = other_impl.handle_;
+ other_impl.handle_ = INVALID_HANDLE_VALUE;
+ impl.wait_handle_ = other_impl.wait_handle_;
+ other_impl.wait_handle_ = INVALID_HANDLE_VALUE;
+ impl.op_queue_.push(other_impl.op_queue_);
+ impl.owner_ = this;
+
+ if (this != &other_service)
+ {
+ // Insert implementation into linked list of all implementations.
+ impl.next_ = other_service.impl_list_;
+ impl.prev_ = 0;
+ if (other_service.impl_list_)
+ other_service.impl_list_->prev_ = &impl;
+ other_service.impl_list_ = &impl;
+ }
+
+ // We must not hold the lock while calling UnregisterWaitEx. This is because
+ // the registered callback function might be invoked while we are waiting for
+ // UnregisterWaitEx to complete.
+ lock.unlock();
+
+ if (impl.wait_handle_ != INVALID_HANDLE_VALUE)
+ ::UnregisterWaitEx(impl.wait_handle_, INVALID_HANDLE_VALUE);
+
+ if (!impl.op_queue_.empty())
+ register_wait_callback(impl, lock);
+}
+
+void win_object_handle_service::destroy(
+ win_object_handle_service::implementation_type& impl)
+{
+ mutex::scoped_lock lock(mutex_);
+
+ // Remove implementation from linked list of all implementations.
+ if (impl_list_ == &impl)
+ impl_list_ = impl.next_;
+ if (impl.prev_)
+ impl.prev_->next_ = impl.next_;
+ if (impl.next_)
+ impl.next_->prev_= impl.prev_;
+ impl.next_ = 0;
+ impl.prev_ = 0;
+
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("object_handle", &impl, "close"));
+
+ HANDLE wait_handle = impl.wait_handle_;
+ impl.wait_handle_ = INVALID_HANDLE_VALUE;
+
+ op_queue<operation> ops;
+ while (wait_op* op = impl.op_queue_.front())
+ {
+ op->ec_ = boost::asio::error::operation_aborted;
+ impl.op_queue_.pop();
+ ops.push(op);
+ }
+
+ // We must not hold the lock while calling UnregisterWaitEx. This is
+ // because the registered callback function might be invoked while we are
+ // waiting for UnregisterWaitEx to complete.
+ lock.unlock();
+
+ if (wait_handle != INVALID_HANDLE_VALUE)
+ ::UnregisterWaitEx(wait_handle, INVALID_HANDLE_VALUE);
+
+ ::CloseHandle(impl.handle_);
+ impl.handle_ = INVALID_HANDLE_VALUE;
+
+ io_service_.post_deferred_completions(ops);
+ }
+}
+
+boost::system::error_code win_object_handle_service::assign(
+ win_object_handle_service::implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ impl.handle_ = handle;
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code win_object_handle_service::close(
+ win_object_handle_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("object_handle", &impl, "close"));
+
+ mutex::scoped_lock lock(mutex_);
+
+ HANDLE wait_handle = impl.wait_handle_;
+ impl.wait_handle_ = INVALID_HANDLE_VALUE;
+
+ op_queue<operation> completed_ops;
+ while (wait_op* op = impl.op_queue_.front())
+ {
+ impl.op_queue_.pop();
+ op->ec_ = boost::asio::error::operation_aborted;
+ completed_ops.push(op);
+ }
+
+ // We must not hold the lock while calling UnregisterWaitEx. This is
+ // because the registered callback function might be invoked while we are
+ // waiting for UnregisterWaitEx to complete.
+ lock.unlock();
+
+ if (wait_handle != INVALID_HANDLE_VALUE)
+ ::UnregisterWaitEx(wait_handle, INVALID_HANDLE_VALUE);
+
+ if (::CloseHandle(impl.handle_))
+ {
+ impl.handle_ = INVALID_HANDLE_VALUE;
+ ec = boost::system::error_code();
+ }
+ else
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ }
+
+ io_service_.post_deferred_completions(completed_ops);
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ }
+
+ return ec;
+}
+
+boost::system::error_code win_object_handle_service::cancel(
+ win_object_handle_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (is_open(impl))
+ {
+ BOOST_ASIO_HANDLER_OPERATION(("object_handle", &impl, "cancel"));
+
+ mutex::scoped_lock lock(mutex_);
+
+ HANDLE wait_handle = impl.wait_handle_;
+ impl.wait_handle_ = INVALID_HANDLE_VALUE;
+
+ op_queue<operation> completed_ops;
+ while (wait_op* op = impl.op_queue_.front())
+ {
+ op->ec_ = boost::asio::error::operation_aborted;
+ impl.op_queue_.pop();
+ completed_ops.push(op);
+ }
+
+ // We must not hold the lock while calling UnregisterWaitEx. This is
+ // because the registered callback function might be invoked while we are
+ // waiting for UnregisterWaitEx to complete.
+ lock.unlock();
+
+ if (wait_handle != INVALID_HANDLE_VALUE)
+ ::UnregisterWaitEx(wait_handle, INVALID_HANDLE_VALUE);
+
+ ec = boost::system::error_code();
+
+ io_service_.post_deferred_completions(completed_ops);
+ }
+ else
+ {
+ ec = boost::asio::error::bad_descriptor;
+ }
+
+ return ec;
+}
+
+void win_object_handle_service::wait(
+ win_object_handle_service::implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ switch (::WaitForSingleObject(impl.handle_, INFINITE))
+ {
+ case WAIT_FAILED:
+ {
+ DWORD last_error = ::GetLastError();
+ ec = boost::system::error_code(last_error,
+ boost::asio::error::get_system_category());
+ break;
+ }
+ case WAIT_OBJECT_0:
+ case WAIT_ABANDONED:
+ default:
+ ec = boost::system::error_code();
+ break;
+ }
+}
+
+void win_object_handle_service::start_wait_op(
+ win_object_handle_service::implementation_type& impl, wait_op* op)
+{
+ io_service_.work_started();
+
+ if (is_open(impl))
+ {
+ mutex::scoped_lock lock(mutex_);
+
+ if (!shutdown_)
+ {
+ impl.op_queue_.push(op);
+
+ // Only the first operation to be queued gets to register a wait callback.
+ // Subsequent operations have to wait for the first to finish.
+ if (impl.op_queue_.front() == op)
+ register_wait_callback(impl, lock);
+ }
+ else
+ {
+ lock.unlock();
+ io_service_.post_deferred_completion(op);
+ }
+ }
+ else
+ {
+ op->ec_ = boost::asio::error::bad_descriptor;
+ io_service_.post_deferred_completion(op);
+ }
+}
+
+void win_object_handle_service::register_wait_callback(
+ win_object_handle_service::implementation_type& impl,
+ mutex::scoped_lock& lock)
+{
+ lock.lock();
+
+ if (!RegisterWaitForSingleObject(&impl.wait_handle_,
+ impl.handle_, &win_object_handle_service::wait_callback,
+ &impl, INFINITE, WT_EXECUTEONLYONCE))
+ {
+ DWORD last_error = ::GetLastError();
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+
+ op_queue<operation> completed_ops;
+ while (wait_op* op = impl.op_queue_.front())
+ {
+ op->ec_ = ec;
+ impl.op_queue_.pop();
+ completed_ops.push(op);
+ }
+
+ lock.unlock();
+ io_service_.post_deferred_completions(completed_ops);
+ }
+}
+
+void win_object_handle_service::wait_callback(PVOID param, BOOLEAN)
+{
+ implementation_type* impl = static_cast<implementation_type*>(param);
+ mutex::scoped_lock lock(impl->owner_->mutex_);
+
+ if (impl->wait_handle_ != INVALID_HANDLE_VALUE)
+ {
+ ::UnregisterWaitEx(impl->wait_handle_, NULL);
+ impl->wait_handle_ = INVALID_HANDLE_VALUE;
+ }
+
+ if (wait_op* op = impl->op_queue_.front())
+ {
+ op_queue<operation> completed_ops;
+
+ op->ec_ = boost::system::error_code();
+ impl->op_queue_.pop();
+ completed_ops.push(op);
+
+ if (!impl->op_queue_.empty())
+ {
+ if (!RegisterWaitForSingleObject(&impl->wait_handle_,
+ impl->handle_, &win_object_handle_service::wait_callback,
+ param, INFINITE, WT_EXECUTEONLYONCE))
+ {
+ DWORD last_error = ::GetLastError();
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+
+ while ((op = impl->op_queue_.front()) != 0)
+ {
+ op->ec_ = ec;
+ impl->op_queue_.pop();
+ completed_ops.push(op);
+ }
+ }
+ }
+
+ lock.unlock();
+ impl->owner_->io_service_.post_deferred_completions(completed_ops);
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_OBJECT_HANDLE_SERVICE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_static_mutex.ipp b/ext/patches/boost/asio/detail/impl/win_static_mutex.ipp
new file mode 100644
index 0000000..3d9a484
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_static_mutex.ipp
@@ -0,0 +1,120 @@
+//
+// detail/impl/win_static_mutex.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_STATIC_MUTEX_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_STATIC_MUTEX_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS)
+
+#include <cstdio>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/win_static_mutex.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+void win_static_mutex::init()
+{
+ int error = do_init();
+ boost::system::error_code ec(error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "static_mutex");
+}
+
+int win_static_mutex::do_init()
+{
+ using namespace std; // For sprintf.
+ wchar_t mutex_name[128];
+#if defined(BOOST_ASIO_HAS_SECURE_RTL)
+ swprintf_s(
+#else // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ _snwprintf(
+#endif // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ mutex_name, 128, L"asio-58CCDC44-6264-4842-90C2-F3C545CB8AA7-%u-%p",
+ static_cast<unsigned int>(::GetCurrentProcessId()), this);
+
+ HANDLE mutex = ::CreateMutexW(0, TRUE, mutex_name);
+ DWORD last_error = ::GetLastError();
+ if (mutex == 0)
+ return ::GetLastError();
+
+ if (last_error == ERROR_ALREADY_EXISTS)
+ ::WaitForSingleObject(mutex, INFINITE);
+
+ if (initialised_)
+ {
+ ::ReleaseMutex(mutex);
+ ::CloseHandle(mutex);
+ return 0;
+ }
+
+#if defined(__MINGW32__)
+ // Not sure if MinGW supports structured exception handling, so for now
+ // we'll just call the Windows API and hope.
+# if defined(UNDER_CE)
+ ::InitializeCriticalSection(&crit_section_);
+# else
+ if (!::InitializeCriticalSectionAndSpinCount(&crit_section_, 0x80000000))
+ {
+ last_error = ::GetLastError();
+ ::ReleaseMutex(mutex);
+ ::CloseHandle(mutex);
+ return last_error;
+ }
+# endif
+#else
+ __try
+ {
+# if defined(UNDER_CE)
+ ::InitializeCriticalSection(&crit_section_);
+# else
+ if (!::InitializeCriticalSectionAndSpinCount(&crit_section_, 0x80000000))
+ {
+ last_error = ::GetLastError();
+ ::ReleaseMutex(mutex);
+ ::CloseHandle(mutex);
+ return last_error;
+ }
+# endif
+ }
+ __except(GetExceptionCode() == STATUS_NO_MEMORY
+ ? EXCEPTION_EXECUTE_HANDLER : EXCEPTION_CONTINUE_SEARCH)
+ {
+ ::ReleaseMutex(mutex);
+ ::CloseHandle(mutex);
+ return ERROR_OUTOFMEMORY;
+ }
+#endif
+
+ initialised_ = true;
+ ::ReleaseMutex(mutex);
+ ::CloseHandle(mutex);
+ return 0;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_STATIC_MUTEX_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_thread.ipp b/ext/patches/boost/asio/detail/impl/win_thread.ipp
new file mode 100644
index 0000000..26d0ad9
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_thread.ipp
@@ -0,0 +1,141 @@
+//
+// detail/impl/win_thread.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_THREAD_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_THREAD_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) && !defined(UNDER_CE)
+
+#include <process.h>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/win_thread.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+win_thread::~win_thread()
+{
+ ::CloseHandle(thread_);
+
+ // The exit_event_ handle is deliberately allowed to leak here since it
+ // is an error for the owner of an internal thread not to join() it.
+}
+
+void win_thread::join()
+{
+ HANDLE handles[2] = { exit_event_, thread_ };
+ ::WaitForMultipleObjects(2, handles, FALSE, INFINITE);
+ ::CloseHandle(exit_event_);
+ if (terminate_threads())
+ {
+ ::TerminateThread(thread_, 0);
+ }
+ else
+ {
+ ::QueueUserAPC(apc_function, thread_, 0);
+ ::WaitForSingleObject(thread_, INFINITE);
+ }
+}
+
+void win_thread::start_thread(func_base* arg, unsigned int stack_size)
+{
+ ::HANDLE entry_event = 0;
+ arg->entry_event_ = entry_event = ::CreateEvent(0, true, false, 0);
+ if (!entry_event)
+ {
+ DWORD last_error = ::GetLastError();
+ delete arg;
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "thread.entry_event");
+ }
+
+ arg->exit_event_ = exit_event_ = ::CreateEvent(0, true, false, 0);
+ if (!exit_event_)
+ {
+ DWORD last_error = ::GetLastError();
+ delete arg;
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "thread.exit_event");
+ }
+
+ unsigned int thread_id = 0;
+ thread_ = reinterpret_cast<HANDLE>(::_beginthreadex(0,
+ stack_size, win_thread_function, arg, 0, &thread_id));
+ if (!thread_)
+ {
+ DWORD last_error = ::GetLastError();
+ delete arg;
+ if (entry_event)
+ ::CloseHandle(entry_event);
+ if (exit_event_)
+ ::CloseHandle(exit_event_);
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "thread");
+ }
+
+ if (entry_event)
+ {
+ ::WaitForSingleObject(entry_event, INFINITE);
+ ::CloseHandle(entry_event);
+ }
+}
+
+unsigned int __stdcall win_thread_function(void* arg)
+{
+ win_thread::auto_func_base_ptr func = {
+ static_cast<win_thread::func_base*>(arg) };
+
+ ::SetEvent(func.ptr->entry_event_);
+
+ func.ptr->run();
+
+ // Signal that the thread has finished its work, but rather than returning go
+ // to sleep to put the thread into a well known state. If the thread is being
+ // joined during global object destruction then it may be killed using
+ // TerminateThread (to avoid a deadlock in DllMain). Otherwise, the SleepEx
+ // call will be interrupted using QueueUserAPC and the thread will shut down
+ // cleanly.
+ HANDLE exit_event = func.ptr->exit_event_;
+ delete func.ptr;
+ func.ptr = 0;
+ ::SetEvent(exit_event);
+ ::SleepEx(INFINITE, TRUE);
+
+ return 0;
+}
+
+#if defined(WINVER) && (WINVER < 0x0500)
+void __stdcall apc_function(ULONG) {}
+#else
+void __stdcall apc_function(ULONG_PTR) {}
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS) && !defined(UNDER_CE)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_THREAD_IPP
diff --git a/ext/patches/boost/asio/detail/impl/win_tss_ptr.ipp b/ext/patches/boost/asio/detail/impl/win_tss_ptr.ipp
new file mode 100644
index 0000000..4b3bc38
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/win_tss_ptr.ipp
@@ -0,0 +1,59 @@
+//
+// detail/impl/win_tss_ptr.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WIN_TSS_PTR_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WIN_TSS_PTR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS)
+
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/win_tss_ptr.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+DWORD win_tss_ptr_create()
+{
+#if defined(UNDER_CE)
+ enum { out_of_indexes = 0xFFFFFFFF };
+#else
+ enum { out_of_indexes = TLS_OUT_OF_INDEXES };
+#endif
+
+ DWORD tss_key = ::TlsAlloc();
+ if (tss_key == out_of_indexes)
+ {
+ DWORD last_error = ::GetLastError();
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "tss");
+ }
+ return tss_key;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WIN_TSS_PTR_IPP
diff --git a/ext/patches/boost/asio/detail/impl/winrt_ssocket_service_base.ipp b/ext/patches/boost/asio/detail/impl/winrt_ssocket_service_base.ipp
new file mode 100644
index 0000000..ae896d4
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/winrt_ssocket_service_base.ipp
@@ -0,0 +1,614 @@
+//
+// detail/impl/winrt_ssocket_service_base.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WINRT_SSOCKET_SERVICE_BASE_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WINRT_SSOCKET_SERVICE_BASE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <cstring>
+#include <boost/asio/detail/winrt_ssocket_service_base.hpp>
+#include <boost/asio/detail/winrt_async_op.hpp>
+#include <boost/asio/detail/winrt_utils.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+winrt_ssocket_service_base::winrt_ssocket_service_base(
+ boost::asio::io_service& io_service)
+ : io_service_(use_service<io_service_impl>(io_service)),
+ async_manager_(use_service<winrt_async_manager>(io_service)),
+ mutex_(),
+ impl_list_(0)
+{
+}
+
+void winrt_ssocket_service_base::shutdown_service()
+{
+ // Close all implementations, causing all operations to complete.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ base_implementation_type* impl = impl_list_;
+ while (impl)
+ {
+ boost::system::error_code ignored_ec;
+ close(*impl, ignored_ec);
+ impl = impl->next_;
+ }
+}
+
+void winrt_ssocket_service_base::construct(
+ winrt_ssocket_service_base::base_implementation_type& impl)
+{
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ impl.next_ = impl_list_;
+ impl.prev_ = 0;
+ if (impl_list_)
+ impl_list_->prev_ = &impl;
+ impl_list_ = &impl;
+}
+
+void winrt_ssocket_service_base::base_move_construct(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ winrt_ssocket_service_base::base_implementation_type& other_impl)
+{
+ impl.socket_ = other_impl.socket_;
+ other_impl.socket_ = nullptr;
+
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ impl.next_ = impl_list_;
+ impl.prev_ = 0;
+ if (impl_list_)
+ impl_list_->prev_ = &impl;
+ impl_list_ = &impl;
+}
+
+void winrt_ssocket_service_base::base_move_assign(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ winrt_ssocket_service_base& other_service,
+ winrt_ssocket_service_base::base_implementation_type& other_impl)
+{
+ boost::system::error_code ignored_ec;
+ close(impl, ignored_ec);
+
+ if (this != &other_service)
+ {
+ // Remove implementation from linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ if (impl_list_ == &impl)
+ impl_list_ = impl.next_;
+ if (impl.prev_)
+ impl.prev_->next_ = impl.next_;
+ if (impl.next_)
+ impl.next_->prev_= impl.prev_;
+ impl.next_ = 0;
+ impl.prev_ = 0;
+ }
+
+ impl.socket_ = other_impl.socket_;
+ other_impl.socket_ = nullptr;
+
+ if (this != &other_service)
+ {
+ // Insert implementation into linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(other_service.mutex_);
+ impl.next_ = other_service.impl_list_;
+ impl.prev_ = 0;
+ if (other_service.impl_list_)
+ other_service.impl_list_->prev_ = &impl;
+ other_service.impl_list_ = &impl;
+ }
+}
+
+void winrt_ssocket_service_base::destroy(
+ winrt_ssocket_service_base::base_implementation_type& impl)
+{
+ boost::system::error_code ignored_ec;
+ close(impl, ignored_ec);
+
+ // Remove implementation from linked list of all implementations.
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ if (impl_list_ == &impl)
+ impl_list_ = impl.next_;
+ if (impl.prev_)
+ impl.prev_->next_ = impl.next_;
+ if (impl.next_)
+ impl.next_->prev_= impl.prev_;
+ impl.next_ = 0;
+ impl.prev_ = 0;
+}
+
+boost::system::error_code winrt_ssocket_service_base::close(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ boost::system::error_code& ec)
+{
+ if (impl.socket_)
+ {
+ delete impl.socket_;
+ impl.socket_ = nullptr;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+std::size_t winrt_ssocket_service_base::do_get_endpoint(
+ const base_implementation_type& impl, bool local,
+ void* addr, std::size_t addr_len, boost::system::error_code& ec) const
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return addr_len;
+ }
+
+ try
+ {
+ std::string addr_string = winrt_utils::string(local
+ ? impl.socket_->Information->LocalAddress->CanonicalName
+ : impl.socket_->Information->RemoteAddress->CanonicalName);
+ unsigned short port = winrt_utils::integer(local
+ ? impl.socket_->Information->LocalPort
+ : impl.socket_->Information->RemotePort);
+ unsigned long scope = 0;
+
+ switch (reinterpret_cast<const socket_addr_type*>(addr)->sa_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ if (addr_len < sizeof(sockaddr_in4_type))
+ {
+ ec = boost::asio::error::invalid_argument;
+ return addr_len;
+ }
+ else
+ {
+ socket_ops::inet_pton(BOOST_ASIO_OS_DEF(AF_INET), addr_string.c_str(),
+ &reinterpret_cast<sockaddr_in4_type*>(addr)->sin_addr, &scope, ec);
+ reinterpret_cast<sockaddr_in4_type*>(addr)->sin_port
+ = socket_ops::host_to_network_short(port);
+ ec = boost::system::error_code();
+ return sizeof(sockaddr_in4_type);
+ }
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ if (addr_len < sizeof(sockaddr_in6_type))
+ {
+ ec = boost::asio::error::invalid_argument;
+ return addr_len;
+ }
+ else
+ {
+ socket_ops::inet_pton(BOOST_ASIO_OS_DEF(AF_INET6), addr_string.c_str(),
+ &reinterpret_cast<sockaddr_in6_type*>(addr)->sin6_addr, &scope, ec);
+ reinterpret_cast<sockaddr_in6_type*>(addr)->sin6_port
+ = socket_ops::host_to_network_short(port);
+ ec = boost::system::error_code();
+ return sizeof(sockaddr_in6_type);
+ }
+ default:
+ ec = boost::asio::error::address_family_not_supported;
+ return addr_len;
+ }
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ return addr_len;
+ }
+}
+
+boost::system::error_code winrt_ssocket_service_base::do_set_option(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ int level, int optname, const void* optval,
+ std::size_t optlen, boost::system::error_code& ec)
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return ec;
+ }
+
+ try
+ {
+ if (level == BOOST_ASIO_OS_DEF(SOL_SOCKET)
+ && optname == BOOST_ASIO_OS_DEF(SO_KEEPALIVE))
+ {
+ if (optlen == sizeof(int))
+ {
+ int value = 0;
+ std::memcpy(&value, optval, optlen);
+ impl.socket_->Control->KeepAlive = !!value;
+ ec = boost::system::error_code();
+ }
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ }
+ }
+ else if (level == BOOST_ASIO_OS_DEF(IPPROTO_TCP)
+ && optname == BOOST_ASIO_OS_DEF(TCP_NODELAY))
+ {
+ if (optlen == sizeof(int))
+ {
+ int value = 0;
+ std::memcpy(&value, optval, optlen);
+ impl.socket_->Control->NoDelay = !!value;
+ ec = boost::system::error_code();
+ }
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ }
+ }
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ }
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ }
+
+ return ec;
+}
+
+void winrt_ssocket_service_base::do_get_option(
+ const winrt_ssocket_service_base::base_implementation_type& impl,
+ int level, int optname, void* optval,
+ std::size_t* optlen, boost::system::error_code& ec) const
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return;
+ }
+
+ try
+ {
+ if (level == BOOST_ASIO_OS_DEF(SOL_SOCKET)
+ && optname == BOOST_ASIO_OS_DEF(SO_KEEPALIVE))
+ {
+ if (*optlen >= sizeof(int))
+ {
+ int value = impl.socket_->Control->KeepAlive ? 1 : 0;
+ std::memcpy(optval, &value, sizeof(int));
+ *optlen = sizeof(int);
+ ec = boost::system::error_code();
+ }
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ }
+ }
+ else if (level == BOOST_ASIO_OS_DEF(IPPROTO_TCP)
+ && optname == BOOST_ASIO_OS_DEF(TCP_NODELAY))
+ {
+ if (*optlen >= sizeof(int))
+ {
+ int value = impl.socket_->Control->NoDelay ? 1 : 0;
+ std::memcpy(optval, &value, sizeof(int));
+ *optlen = sizeof(int);
+ ec = boost::system::error_code();
+ }
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ }
+ }
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ }
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ }
+}
+
+boost::system::error_code winrt_ssocket_service_base::do_connect(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ const void* addr, boost::system::error_code& ec)
+{
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return ec;
+ }
+
+ char addr_string[max_addr_v6_str_len];
+ unsigned short port;
+ switch (reinterpret_cast<const socket_addr_type*>(addr)->sa_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ socket_ops::inet_ntop(BOOST_ASIO_OS_DEF(AF_INET),
+ &reinterpret_cast<const sockaddr_in4_type*>(addr)->sin_addr,
+ addr_string, sizeof(addr_string), 0, ec);
+ port = socket_ops::network_to_host_short(
+ reinterpret_cast<const sockaddr_in4_type*>(addr)->sin_port);
+ break;
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ socket_ops::inet_ntop(BOOST_ASIO_OS_DEF(AF_INET6),
+ &reinterpret_cast<const sockaddr_in6_type*>(addr)->sin6_addr,
+ addr_string, sizeof(addr_string), 0, ec);
+ port = socket_ops::network_to_host_short(
+ reinterpret_cast<const sockaddr_in6_type*>(addr)->sin6_port);
+ break;
+ default:
+ ec = boost::asio::error::address_family_not_supported;
+ return ec;
+ }
+
+ if (!ec) try
+ {
+ async_manager_.sync(impl.socket_->ConnectAsync(
+ ref new Windows::Networking::HostName(
+ winrt_utils::string(addr_string)),
+ winrt_utils::string(port)), ec);
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ }
+
+ return ec;
+}
+
+void winrt_ssocket_service_base::start_connect_op(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ const void* addr, winrt_async_op<void>* op, bool is_continuation)
+{
+ if (!is_open(impl))
+ {
+ op->ec_ = boost::asio::error::bad_descriptor;
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ char addr_string[max_addr_v6_str_len];
+ unsigned short port = 0;
+ switch (reinterpret_cast<const socket_addr_type*>(addr)->sa_family)
+ {
+ case BOOST_ASIO_OS_DEF(AF_INET):
+ socket_ops::inet_ntop(BOOST_ASIO_OS_DEF(AF_INET),
+ &reinterpret_cast<const sockaddr_in4_type*>(addr)->sin_addr,
+ addr_string, sizeof(addr_string), 0, op->ec_);
+ port = socket_ops::network_to_host_short(
+ reinterpret_cast<const sockaddr_in4_type*>(addr)->sin_port);
+ break;
+ case BOOST_ASIO_OS_DEF(AF_INET6):
+ socket_ops::inet_ntop(BOOST_ASIO_OS_DEF(AF_INET6),
+ &reinterpret_cast<const sockaddr_in6_type*>(addr)->sin6_addr,
+ addr_string, sizeof(addr_string), 0, op->ec_);
+ port = socket_ops::network_to_host_short(
+ reinterpret_cast<const sockaddr_in6_type*>(addr)->sin6_port);
+ break;
+ default:
+ op->ec_ = boost::asio::error::address_family_not_supported;
+ break;
+ }
+
+ if (op->ec_)
+ {
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ try
+ {
+ async_manager_.async(impl.socket_->ConnectAsync(
+ ref new Windows::Networking::HostName(
+ winrt_utils::string(addr_string)),
+ winrt_utils::string(port)), op);
+ }
+ catch (Platform::Exception^ e)
+ {
+ op->ec_ = boost::system::error_code(
+ e->HResult, boost::system::system_category());
+ io_service_.post_immediate_completion(op, is_continuation);
+ }
+}
+
+std::size_t winrt_ssocket_service_base::do_send(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ const boost::asio::const_buffer& data,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+{
+ if (flags)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ try
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ boost::asio::const_buffers_1> bufs(boost::asio::buffer(data));
+
+ if (bufs.all_empty())
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ return async_manager_.sync(
+ impl.socket_->OutputStream->WriteAsync(bufs.buffers()[0]), ec);
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ return 0;
+ }
+}
+
+void winrt_ssocket_service_base::start_send_op(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ const boost::asio::const_buffer& data, socket_base::message_flags flags,
+ winrt_async_op<unsigned int>* op, bool is_continuation)
+{
+ if (flags)
+ {
+ op->ec_ = boost::asio::error::operation_not_supported;
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ if (!is_open(impl))
+ {
+ op->ec_ = boost::asio::error::bad_descriptor;
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ try
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ boost::asio::const_buffers_1> bufs(boost::asio::buffer(data));
+
+ if (bufs.all_empty())
+ {
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ async_manager_.async(
+ impl.socket_->OutputStream->WriteAsync(bufs.buffers()[0]), op);
+ }
+ catch (Platform::Exception^ e)
+ {
+ op->ec_ = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ io_service_.post_immediate_completion(op, is_continuation);
+ }
+}
+
+std::size_t winrt_ssocket_service_base::do_receive(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ const boost::asio::mutable_buffer& data,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+{
+ if (flags)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ if (!is_open(impl))
+ {
+ ec = boost::asio::error::bad_descriptor;
+ return 0;
+ }
+
+ try
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ boost::asio::mutable_buffers_1> bufs(boost::asio::buffer(data));
+
+ if (bufs.all_empty())
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ async_manager_.sync(
+ impl.socket_->InputStream->ReadAsync(
+ bufs.buffers()[0], bufs.buffers()[0]->Capacity,
+ Windows::Storage::Streams::InputStreamOptions::Partial), ec);
+
+ std::size_t bytes_transferred = bufs.buffers()[0]->Length;
+ if (bytes_transferred == 0 && !ec)
+ {
+ ec = boost::asio::error::eof;
+ }
+
+ return bytes_transferred;
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ return 0;
+ }
+}
+
+void winrt_ssocket_service_base::start_receive_op(
+ winrt_ssocket_service_base::base_implementation_type& impl,
+ const boost::asio::mutable_buffer& data, socket_base::message_flags flags,
+ winrt_async_op<Windows::Storage::Streams::IBuffer^>* op,
+ bool is_continuation)
+{
+ if (flags)
+ {
+ op->ec_ = boost::asio::error::operation_not_supported;
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ if (!is_open(impl))
+ {
+ op->ec_ = boost::asio::error::bad_descriptor;
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ try
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ boost::asio::mutable_buffers_1> bufs(boost::asio::buffer(data));
+
+ if (bufs.all_empty())
+ {
+ io_service_.post_immediate_completion(op, is_continuation);
+ return;
+ }
+
+ async_manager_.async(
+ impl.socket_->InputStream->ReadAsync(
+ bufs.buffers()[0], bufs.buffers()[0]->Capacity,
+ Windows::Storage::Streams::InputStreamOptions::Partial), op);
+ }
+ catch (Platform::Exception^ e)
+ {
+ op->ec_ = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ io_service_.post_immediate_completion(op, is_continuation);
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WINRT_SSOCKET_SERVICE_BASE_IPP
diff --git a/ext/patches/boost/asio/detail/impl/winrt_timer_scheduler.hpp b/ext/patches/boost/asio/detail/impl/winrt_timer_scheduler.hpp
new file mode 100644
index 0000000..594a744
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/winrt_timer_scheduler.hpp
@@ -0,0 +1,81 @@
+//
+// detail/impl/winrt_timer_scheduler.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WINRT_TIMER_SCHEDULER_HPP
+#define BOOST_ASIO_DETAIL_IMPL_WINRT_TIMER_SCHEDULER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Time_Traits>
+void winrt_timer_scheduler::add_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_add_timer_queue(queue);
+}
+
+// Remove a timer queue from the reactor.
+template <typename Time_Traits>
+void winrt_timer_scheduler::remove_timer_queue(timer_queue<Time_Traits>& queue)
+{
+ do_remove_timer_queue(queue);
+}
+
+template <typename Time_Traits>
+void winrt_timer_scheduler::schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+
+ if (shutdown_)
+ {
+ io_service_.post_immediate_completion(op, false);
+ return;
+ }
+
+ bool earliest = queue.enqueue_timer(time, timer, op);
+ io_service_.work_started();
+ if (earliest)
+ event_.signal(lock);
+}
+
+template <typename Time_Traits>
+std::size_t winrt_timer_scheduler::cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled)
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ op_queue<operation> ops;
+ std::size_t n = queue.cancel_timer(timer, ops, max_cancelled);
+ lock.unlock();
+ io_service_.post_deferred_completions(ops);
+ return n;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WINRT_TIMER_SCHEDULER_HPP
diff --git a/ext/patches/boost/asio/detail/impl/winrt_timer_scheduler.ipp b/ext/patches/boost/asio/detail/impl/winrt_timer_scheduler.ipp
new file mode 100644
index 0000000..d3cb2ac
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/winrt_timer_scheduler.ipp
@@ -0,0 +1,124 @@
+//
+// detail/impl/winrt_timer_scheduler.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WINRT_TIMER_SCHEDULER_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WINRT_TIMER_SCHEDULER_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/winrt_timer_scheduler.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+winrt_timer_scheduler::winrt_timer_scheduler(
+ boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<winrt_timer_scheduler>(io_service),
+ io_service_(use_service<io_service_impl>(io_service)),
+ mutex_(),
+ event_(),
+ timer_queues_(),
+ thread_(0),
+ stop_thread_(false),
+ shutdown_(false)
+{
+ thread_ = new boost::asio::detail::thread(
+ bind_handler(&winrt_timer_scheduler::call_run_thread, this));
+}
+
+winrt_timer_scheduler::~winrt_timer_scheduler()
+{
+ shutdown_service();
+}
+
+void winrt_timer_scheduler::shutdown_service()
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ shutdown_ = true;
+ stop_thread_ = true;
+ event_.signal(lock);
+ lock.unlock();
+
+ if (thread_)
+ {
+ thread_->join();
+ delete thread_;
+ thread_ = 0;
+ }
+
+ op_queue<operation> ops;
+ timer_queues_.get_all_timers(ops);
+ io_service_.abandon_operations(ops);
+}
+
+void winrt_timer_scheduler::fork_service(boost::asio::io_service::fork_event)
+{
+}
+
+void winrt_timer_scheduler::init_task()
+{
+}
+
+void winrt_timer_scheduler::run_thread()
+{
+ boost::asio::detail::mutex::scoped_lock lock(mutex_);
+ while (!stop_thread_)
+ {
+ const long max_wait_duration = 5 * 60 * 1000000;
+ long wait_duration = timer_queues_.wait_duration_usec(max_wait_duration);
+ event_.wait_for_usec(lock, wait_duration);
+ event_.clear(lock);
+ op_queue<operation> ops;
+ timer_queues_.get_ready_timers(ops);
+ if (!ops.empty())
+ {
+ lock.unlock();
+ io_service_.post_deferred_completions(ops);
+ lock.lock();
+ }
+ }
+}
+
+void winrt_timer_scheduler::call_run_thread(winrt_timer_scheduler* scheduler)
+{
+ scheduler->run_thread();
+}
+
+void winrt_timer_scheduler::do_add_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.insert(&queue);
+}
+
+void winrt_timer_scheduler::do_remove_timer_queue(timer_queue_base& queue)
+{
+ mutex::scoped_lock lock(mutex_);
+ timer_queues_.erase(&queue);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WINRT_TIMER_SCHEDULER_IPP
diff --git a/ext/patches/boost/asio/detail/impl/winsock_init.ipp b/ext/patches/boost/asio/detail/impl/winsock_init.ipp
new file mode 100644
index 0000000..158addd
--- /dev/null
+++ b/ext/patches/boost/asio/detail/impl/winsock_init.ipp
@@ -0,0 +1,84 @@
+//
+// detail/impl/winsock_init.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IMPL_WINSOCK_INIT_IPP
+#define BOOST_ASIO_DETAIL_IMPL_WINSOCK_INIT_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/winsock_init.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+void winsock_init_base::startup(data& d,
+ unsigned char major, unsigned char minor)
+{
+ if (::InterlockedIncrement(&d.init_count_) == 1)
+ {
+ WSADATA wsa_data;
+ long result = ::WSAStartup(MAKEWORD(major, minor), &wsa_data);
+ ::InterlockedExchange(&d.result_, result);
+ }
+}
+
+void winsock_init_base::manual_startup(data& d)
+{
+ if (::InterlockedIncrement(&d.init_count_) == 1)
+ {
+ ::InterlockedExchange(&d.result_, 0);
+ }
+}
+
+void winsock_init_base::cleanup(data& d)
+{
+ if (::InterlockedDecrement(&d.init_count_) == 0)
+ {
+ ::WSACleanup();
+ }
+}
+
+void winsock_init_base::manual_cleanup(data& d)
+{
+ ::InterlockedDecrement(&d.init_count_);
+}
+
+void winsock_init_base::throw_on_error(data& d)
+{
+ long result = ::InterlockedExchangeAdd(&d.result_, 0);
+ if (result != 0)
+ {
+ boost::system::error_code ec(result,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "winsock");
+ }
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_IMPL_WINSOCK_INIT_IPP
diff --git a/ext/patches/boost/asio/detail/io_control.hpp b/ext/patches/boost/asio/detail/io_control.hpp
new file mode 100644
index 0000000..e342899
--- /dev/null
+++ b/ext/patches/boost/asio/detail/io_control.hpp
@@ -0,0 +1,136 @@
+//
+// detail/io_control.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_IO_CONTROL_HPP
+#define BOOST_ASIO_DETAIL_IO_CONTROL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+namespace io_control {
+
+// IO control command for non-blocking I/O.
+class non_blocking_io
+{
+public:
+ // Default constructor.
+ non_blocking_io()
+ : value_(0)
+ {
+ }
+
+ // Construct with a specific command value.
+ non_blocking_io(bool value)
+ : value_(value ? 1 : 0)
+ {
+ }
+
+ // Get the name of the IO control command.
+ int name() const
+ {
+ return static_cast<int>(BOOST_ASIO_OS_DEF(FIONBIO));
+ }
+
+ // Set the value of the I/O control command.
+ void set(bool value)
+ {
+ value_ = value ? 1 : 0;
+ }
+
+ // Get the current value of the I/O control command.
+ bool get() const
+ {
+ return value_ != 0;
+ }
+
+ // Get the address of the command data.
+ detail::ioctl_arg_type* data()
+ {
+ return &value_;
+ }
+
+ // Get the address of the command data.
+ const detail::ioctl_arg_type* data() const
+ {
+ return &value_;
+ }
+
+private:
+ detail::ioctl_arg_type value_;
+};
+
+// I/O control command for getting number of bytes available.
+class bytes_readable
+{
+public:
+ // Default constructor.
+ bytes_readable()
+ : value_(0)
+ {
+ }
+
+ // Construct with a specific command value.
+ bytes_readable(std::size_t value)
+ : value_(static_cast<detail::ioctl_arg_type>(value))
+ {
+ }
+
+ // Get the name of the IO control command.
+ int name() const
+ {
+ return static_cast<int>(BOOST_ASIO_OS_DEF(FIONREAD));
+ }
+
+ // Set the value of the I/O control command.
+ void set(std::size_t value)
+ {
+ value_ = static_cast<detail::ioctl_arg_type>(value);
+ }
+
+ // Get the current value of the I/O control command.
+ std::size_t get() const
+ {
+ return static_cast<std::size_t>(value_);
+ }
+
+ // Get the address of the command data.
+ detail::ioctl_arg_type* data()
+ {
+ return &value_;
+ }
+
+ // Get the address of the command data.
+ const detail::ioctl_arg_type* data() const
+ {
+ return &value_;
+ }
+
+private:
+ detail::ioctl_arg_type value_;
+};
+
+} // namespace io_control
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_IO_CONTROL_HPP
diff --git a/ext/patches/boost/asio/detail/keyword_tss_ptr.hpp b/ext/patches/boost/asio/detail/keyword_tss_ptr.hpp
new file mode 100644
index 0000000..d192ed2
--- /dev/null
+++ b/ext/patches/boost/asio/detail/keyword_tss_ptr.hpp
@@ -0,0 +1,72 @@
+//
+// detail/keyword_tss_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_KEYWORD_TSS_PTR_HPP
+#define BOOST_ASIO_DETAIL_KEYWORD_TSS_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_THREAD_KEYWORD_EXTENSION)
+
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename T>
+class keyword_tss_ptr
+ : private noncopyable
+{
+public:
+ // Constructor.
+ keyword_tss_ptr()
+ {
+ }
+
+ // Destructor.
+ ~keyword_tss_ptr()
+ {
+ }
+
+ // Get the value.
+ operator T*() const
+ {
+ return value_;
+ }
+
+ // Set the value.
+ void operator=(T* value)
+ {
+ value_ = value;
+ }
+
+private:
+ static BOOST_ASIO_THREAD_KEYWORD T* value_;
+};
+
+template <typename T>
+BOOST_ASIO_THREAD_KEYWORD T* keyword_tss_ptr<T>::value_;
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_THREAD_KEYWORD_EXTENSION)
+
+#endif // BOOST_ASIO_DETAIL_KEYWORD_TSS_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/kqueue_reactor.hpp b/ext/patches/boost/asio/detail/kqueue_reactor.hpp
new file mode 100644
index 0000000..080f9d4
--- /dev/null
+++ b/ext/patches/boost/asio/detail/kqueue_reactor.hpp
@@ -0,0 +1,221 @@
+//
+// detail/kqueue_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2005 Stefan Arentz (stefan at soze dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_KQUEUE_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_KQUEUE_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_KQUEUE)
+
+#include <cstddef>
+#include <sys/types.h>
+#include <sys/event.h>
+#include <sys/time.h>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/object_pool.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/select_interrupter.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/timer_queue_base.hpp>
+#include <boost/asio/detail/timer_queue_set.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+// Older versions of Mac OS X may not define EV_OOBAND.
+#if !defined(EV_OOBAND)
+# define EV_OOBAND EV_FLAG1
+#endif // !defined(EV_OOBAND)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class kqueue_reactor
+ : public boost::asio::detail::service_base<kqueue_reactor>
+{
+public:
+ enum op_types { read_op = 0, write_op = 1,
+ connect_op = 1, except_op = 2, max_ops = 3 };
+
+ // Per-descriptor queues.
+ struct descriptor_state
+ {
+ friend class kqueue_reactor;
+ friend class object_pool_access;
+
+ descriptor_state* next_;
+ descriptor_state* prev_;
+
+ mutex mutex_;
+ int descriptor_;
+ op_queue<reactor_op> op_queue_[max_ops];
+ bool shutdown_;
+ };
+
+ // Per-descriptor data.
+ typedef descriptor_state* per_descriptor_data;
+
+ // Constructor.
+ BOOST_ASIO_DECL kqueue_reactor(boost::asio::io_service& io_service);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~kqueue_reactor();
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Recreate internal descriptors following a fork.
+ BOOST_ASIO_DECL void fork_service(
+ boost::asio::io_service::fork_event fork_ev);
+
+ // Initialise the task.
+ BOOST_ASIO_DECL void init_task();
+
+ // Register a socket with the reactor. Returns 0 on success, system error
+ // code on failure.
+ BOOST_ASIO_DECL int register_descriptor(socket_type descriptor,
+ per_descriptor_data& descriptor_data);
+
+ // Register a descriptor with an associated single operation. Returns 0 on
+ // success, system error code on failure.
+ BOOST_ASIO_DECL int register_internal_descriptor(
+ int op_type, socket_type descriptor,
+ per_descriptor_data& descriptor_data, reactor_op* op);
+
+ // Move descriptor registration from one descriptor_data object to another.
+ BOOST_ASIO_DECL void move_descriptor(socket_type descriptor,
+ per_descriptor_data& target_descriptor_data,
+ per_descriptor_data& source_descriptor_data);
+
+ // Post a reactor operation for immediate completion.
+ void post_immediate_completion(reactor_op* op, bool is_continuation)
+ {
+ io_service_.post_immediate_completion(op, is_continuation);
+ }
+
+ // Start a new operation. The reactor operation will be performed when the
+ // given descriptor is flagged as ready, or an error has occurred.
+ BOOST_ASIO_DECL void start_op(int op_type, socket_type descriptor,
+ per_descriptor_data& descriptor_data, reactor_op* op,
+ bool is_continuation, bool allow_speculative);
+
+ // Cancel all operations associated with the given descriptor. The
+ // handlers associated with the descriptor will be invoked with the
+ // operation_aborted error.
+ BOOST_ASIO_DECL void cancel_ops(socket_type descriptor,
+ per_descriptor_data& descriptor_data);
+
+ // Cancel any operations that are running against the descriptor and remove
+ // its registration from the reactor.
+ BOOST_ASIO_DECL void deregister_descriptor(socket_type descriptor,
+ per_descriptor_data& descriptor_data, bool closing);
+
+ // Remote the descriptor's registration from the reactor.
+ BOOST_ASIO_DECL void deregister_internal_descriptor(
+ socket_type descriptor, per_descriptor_data& descriptor_data);
+
+ // Add a new timer queue to the reactor.
+ template <typename Time_Traits>
+ void add_timer_queue(timer_queue<Time_Traits>& queue);
+
+ // Remove a timer queue from the reactor.
+ template <typename Time_Traits>
+ void remove_timer_queue(timer_queue<Time_Traits>& queue);
+
+ // Schedule a new operation in the given timer queue to expire at the
+ // specified absolute time.
+ template <typename Time_Traits>
+ void schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op);
+
+ // Cancel the timer operations associated with the given token. Returns the
+ // number of operations that have been posted or dispatched.
+ template <typename Time_Traits>
+ std::size_t cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled = (std::numeric_limits<std::size_t>::max)());
+
+ // Run the kqueue loop.
+ BOOST_ASIO_DECL void run(bool block, op_queue<operation>& ops);
+
+ // Interrupt the kqueue loop.
+ BOOST_ASIO_DECL void interrupt();
+
+private:
+ // Create the kqueue file descriptor. Throws an exception if the descriptor
+ // cannot be created.
+ BOOST_ASIO_DECL static int do_kqueue_create();
+
+ // Allocate a new descriptor state object.
+ BOOST_ASIO_DECL descriptor_state* allocate_descriptor_state();
+
+ // Free an existing descriptor state object.
+ BOOST_ASIO_DECL void free_descriptor_state(descriptor_state* s);
+
+ // Helper function to add a new timer queue.
+ BOOST_ASIO_DECL void do_add_timer_queue(timer_queue_base& queue);
+
+ // Helper function to remove a timer queue.
+ BOOST_ASIO_DECL void do_remove_timer_queue(timer_queue_base& queue);
+
+ // Get the timeout value for the kevent call.
+ BOOST_ASIO_DECL timespec* get_timeout(timespec& ts);
+
+ // The io_service implementation used to post completions.
+ io_service_impl& io_service_;
+
+ // Mutex to protect access to internal data.
+ mutex mutex_;
+
+ // The kqueue file descriptor.
+ int kqueue_fd_;
+
+ // The interrupter is used to break a blocking kevent call.
+ select_interrupter interrupter_;
+
+ // The timer queues.
+ timer_queue_set timer_queues_;
+
+ // Whether the service has been shut down.
+ bool shutdown_;
+
+ // Mutex to protect access to the registered descriptors.
+ mutex registered_descriptors_mutex_;
+
+ // Keep track of all registered descriptors.
+ object_pool<descriptor_state> registered_descriptors_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/kqueue_reactor.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/kqueue_reactor.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_KQUEUE)
+
+#endif // BOOST_ASIO_DETAIL_KQUEUE_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/limits.hpp b/ext/patches/boost/asio/detail/limits.hpp
new file mode 100644
index 0000000..4dfdc4a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/limits.hpp
@@ -0,0 +1,26 @@
+//
+// detail/limits.hpp
+// ~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2011 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_LIMITS_HPP
+#define BOOST_ASIO_DETAIL_LIMITS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_LIMITS)
+# include <boost/limits.hpp>
+#else // defined(BOOST_ASIO_HAS_BOOST_LIMITS)
+# include <limits>
+#endif // defined(BOOST_ASIO_HAS_BOOST_LIMITS)
+
+#endif // BOOST_ASIO_DETAIL_LIMITS_HPP
diff --git a/ext/patches/boost/asio/detail/local_free_on_block_exit.hpp b/ext/patches/boost/asio/detail/local_free_on_block_exit.hpp
new file mode 100644
index 0000000..332d2a3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/local_free_on_block_exit.hpp
@@ -0,0 +1,59 @@
+//
+// detail/local_free_on_block_exit.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_LOCAL_FREE_ON_BLOCK_EXIT_HPP
+#define BOOST_ASIO_DETAIL_LOCAL_FREE_ON_BLOCK_EXIT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class local_free_on_block_exit
+ : private noncopyable
+{
+public:
+ // Constructor blocks all signals for the calling thread.
+ explicit local_free_on_block_exit(void* p)
+ : p_(p)
+ {
+ }
+
+ // Destructor restores the previous signal mask.
+ ~local_free_on_block_exit()
+ {
+ ::LocalFree(p_);
+ }
+
+private:
+ void* p_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_LOCAL_FREE_ON_BLOCK_EXIT_HPP
diff --git a/ext/patches/boost/asio/detail/macos_fenced_block.hpp b/ext/patches/boost/asio/detail/macos_fenced_block.hpp
new file mode 100644
index 0000000..d36ea55
--- /dev/null
+++ b/ext/patches/boost/asio/detail/macos_fenced_block.hpp
@@ -0,0 +1,63 @@
+//
+// detail/macos_fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_MACOS_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_MACOS_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(__MACH__) && defined(__APPLE__)
+
+#include <libkern/OSAtomic.h>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class macos_fenced_block
+ : private noncopyable
+{
+public:
+ enum half_t { half };
+ enum full_t { full };
+
+ // Constructor for a half fenced block.
+ explicit macos_fenced_block(half_t)
+ {
+ }
+
+ // Constructor for a full fenced block.
+ explicit macos_fenced_block(full_t)
+ {
+ OSMemoryBarrier();
+ }
+
+ // Destructor.
+ ~macos_fenced_block()
+ {
+ OSMemoryBarrier();
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(__MACH__) && defined(__APPLE__)
+
+#endif // BOOST_ASIO_DETAIL_MACOS_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/mutex.hpp b/ext/patches/boost/asio/detail/mutex.hpp
new file mode 100644
index 0000000..2456417
--- /dev/null
+++ b/ext/patches/boost/asio/detail/mutex.hpp
@@ -0,0 +1,50 @@
+//
+// detail/mutex.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+# include <boost/asio/detail/null_mutex.hpp>
+#elif defined(BOOST_ASIO_WINDOWS)
+# include <boost/asio/detail/win_mutex.hpp>
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+# include <boost/asio/detail/posix_mutex.hpp>
+#elif defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+# include <boost/asio/detail/std_mutex.hpp>
+#else
+# error Only Windows, POSIX and std::mutex are supported!
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+typedef null_mutex mutex;
+#elif defined(BOOST_ASIO_WINDOWS)
+typedef win_mutex mutex;
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+typedef posix_mutex mutex;
+#elif defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+typedef std_mutex mutex;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/noncopyable.hpp b/ext/patches/boost/asio/detail/noncopyable.hpp
new file mode 100644
index 0000000..666779c
--- /dev/null
+++ b/ext/patches/boost/asio/detail/noncopyable.hpp
@@ -0,0 +1,45 @@
+//
+// detail/noncopyable.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NONCOPYABLE_HPP
+#define BOOST_ASIO_DETAIL_NONCOPYABLE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class noncopyable
+{
+protected:
+ noncopyable() {}
+ ~noncopyable() {}
+private:
+ noncopyable(const noncopyable&);
+ const noncopyable& operator=(const noncopyable&);
+};
+
+} // namespace detail
+
+using boost::asio::detail::noncopyable;
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_NONCOPYABLE_HPP
diff --git a/ext/patches/boost/asio/detail/null_event.hpp b/ext/patches/boost/asio/detail/null_event.hpp
new file mode 100644
index 0000000..a94c86f
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_event.hpp
@@ -0,0 +1,90 @@
+//
+// detail/null_event.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_EVENT_HPP
+#define BOOST_ASIO_DETAIL_NULL_EVENT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class null_event
+ : private noncopyable
+{
+public:
+ // Constructor.
+ null_event()
+ {
+ }
+
+ // Destructor.
+ ~null_event()
+ {
+ }
+
+ // Signal the event. (Retained for backward compatibility.)
+ template <typename Lock>
+ void signal(Lock&)
+ {
+ }
+
+ // Signal all waiters.
+ template <typename Lock>
+ void signal_all(Lock&)
+ {
+ }
+
+ // Unlock the mutex and signal one waiter.
+ template <typename Lock>
+ void unlock_and_signal_one(Lock&)
+ {
+ }
+
+ // If there's a waiter, unlock the mutex and signal it.
+ template <typename Lock>
+ bool maybe_unlock_and_signal_one(Lock&)
+ {
+ return false;
+ }
+
+ // Reset the event.
+ template <typename Lock>
+ void clear(Lock&)
+ {
+ }
+
+ // Wait for the event to become signalled.
+ template <typename Lock>
+ void wait(Lock&)
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_THREADS)
+
+#endif // BOOST_ASIO_DETAIL_NULL_EVENT_HPP
diff --git a/ext/patches/boost/asio/detail/null_fenced_block.hpp b/ext/patches/boost/asio/detail/null_fenced_block.hpp
new file mode 100644
index 0000000..29cb778
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_fenced_block.hpp
@@ -0,0 +1,47 @@
+//
+// detail/null_fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_NULL_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class null_fenced_block
+ : private noncopyable
+{
+public:
+ enum half_or_full_t { half, full };
+
+ // Constructor.
+ explicit null_fenced_block(half_or_full_t)
+ {
+ }
+
+ // Destructor.
+ ~null_fenced_block()
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_NULL_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/null_mutex.hpp b/ext/patches/boost/asio/detail/null_mutex.hpp
new file mode 100644
index 0000000..a401387
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_mutex.hpp
@@ -0,0 +1,66 @@
+//
+// detail/null_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_NULL_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/scoped_lock.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class null_mutex
+ : private noncopyable
+{
+public:
+ typedef boost::asio::detail::scoped_lock<null_mutex> scoped_lock;
+
+ // Constructor.
+ null_mutex()
+ {
+ }
+
+ // Destructor.
+ ~null_mutex()
+ {
+ }
+
+ // Lock the mutex.
+ void lock()
+ {
+ }
+
+ // Unlock the mutex.
+ void unlock()
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_THREADS)
+
+#endif // BOOST_ASIO_DETAIL_NULL_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/null_reactor.hpp b/ext/patches/boost/asio/detail/null_reactor.hpp
new file mode 100644
index 0000000..3ae8973
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_reactor.hpp
@@ -0,0 +1,69 @@
+//
+// detail/null_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_NULL_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class null_reactor
+ : public boost::asio::detail::service_base<null_reactor>
+{
+public:
+ // Constructor.
+ null_reactor(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<null_reactor>(io_service)
+ {
+ }
+
+ // Destructor.
+ ~null_reactor()
+ {
+ }
+
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ }
+
+ // No-op because should never be called.
+ void run(bool /*block*/, op_queue<operation>& /*ops*/)
+ {
+ }
+
+ // No-op.
+ void interrupt()
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_NULL_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/null_signal_blocker.hpp b/ext/patches/boost/asio/detail/null_signal_blocker.hpp
new file mode 100644
index 0000000..d67bf23
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_signal_blocker.hpp
@@ -0,0 +1,71 @@
+//
+// detail/null_signal_blocker.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_SIGNAL_BLOCKER_HPP
+#define BOOST_ASIO_DETAIL_NULL_SIGNAL_BLOCKER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS) \
+ || defined(BOOST_ASIO_WINDOWS) \
+ || defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ || defined(__CYGWIN__) \
+ || defined(__SYMBIAN32__)
+
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class null_signal_blocker
+ : private noncopyable
+{
+public:
+ // Constructor blocks all signals for the calling thread.
+ null_signal_blocker()
+ {
+ }
+
+ // Destructor restores the previous signal mask.
+ ~null_signal_blocker()
+ {
+ }
+
+ // Block all signals for the calling thread.
+ void block()
+ {
+ }
+
+ // Restore the previous signal mask.
+ void unblock()
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_THREADS)
+ // || defined(BOOST_ASIO_WINDOWS)
+ // || defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+
+#endif // BOOST_ASIO_DETAIL_NULL_SIGNAL_BLOCKER_HPP
diff --git a/ext/patches/boost/asio/detail/null_socket_service.hpp b/ext/patches/boost/asio/detail/null_socket_service.hpp
new file mode 100644
index 0000000..e5bc002
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_socket_service.hpp
@@ -0,0 +1,499 @@
+//
+// detail/null_socket_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_SOCKET_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_NULL_SOCKET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/socket_base.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol>
+class null_socket_service
+{
+public:
+ // The protocol type.
+ typedef Protocol protocol_type;
+
+ // The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ // The native type of a socket.
+ typedef int native_handle_type;
+
+ // The implementation type of the socket.
+ struct implementation_type
+ {
+ };
+
+ // Constructor.
+ null_socket_service(boost::asio::io_service& io_service)
+ : io_service_(io_service)
+ {
+ }
+
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ }
+
+ // Construct a new socket implementation.
+ void construct(implementation_type&)
+ {
+ }
+
+ // Move-construct a new socket implementation.
+ void move_construct(implementation_type&, implementation_type&)
+ {
+ }
+
+ // Move-assign from another socket implementation.
+ void move_assign(implementation_type&,
+ null_socket_service&, implementation_type&)
+ {
+ }
+
+ // Move-construct a new socket implementation from another protocol type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type&,
+ typename null_socket_service<Protocol1>::implementation_type&)
+ {
+ }
+
+ // Destroy a socket implementation.
+ void destroy(implementation_type&)
+ {
+ }
+
+ // Open a new socket implementation.
+ boost::system::error_code open(implementation_type&,
+ const protocol_type&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Assign a native socket to a socket implementation.
+ boost::system::error_code assign(implementation_type&, const protocol_type&,
+ const native_handle_type&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Determine whether the socket is open.
+ bool is_open(const implementation_type&) const
+ {
+ return false;
+ }
+
+ // Destroy a socket implementation.
+ boost::system::error_code close(implementation_type&,
+ boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Get the native socket representation.
+ native_handle_type native_handle(implementation_type&)
+ {
+ return 0;
+ }
+
+ // Cancel all operations associated with the socket.
+ boost::system::error_code cancel(implementation_type&,
+ boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Determine whether the socket is at the out-of-band data mark.
+ bool at_mark(const implementation_type&,
+ boost::system::error_code& ec) const
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return false;
+ }
+
+ // Determine the number of bytes available for reading.
+ std::size_t available(const implementation_type&,
+ boost::system::error_code& ec) const
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Place the socket into the state where it will listen for new connections.
+ boost::system::error_code listen(implementation_type&,
+ int, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Perform an IO control command on the socket.
+ template <typename IO_Control_Command>
+ boost::system::error_code io_control(implementation_type&,
+ IO_Control_Command&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the socket.
+ bool non_blocking(const implementation_type&) const
+ {
+ return false;
+ }
+
+ // Sets the non-blocking mode of the socket.
+ boost::system::error_code non_blocking(implementation_type&,
+ bool, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the native socket implementation.
+ bool native_non_blocking(const implementation_type&) const
+ {
+ return false;
+ }
+
+ // Sets the non-blocking mode of the native socket implementation.
+ boost::system::error_code native_non_blocking(implementation_type&,
+ bool, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Disable sends or receives on the socket.
+ boost::system::error_code shutdown(implementation_type&,
+ socket_base::shutdown_type, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Bind the socket to the specified local endpoint.
+ boost::system::error_code bind(implementation_type&,
+ const endpoint_type&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Set a socket option.
+ template <typename Option>
+ boost::system::error_code set_option(implementation_type&,
+ const Option&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Set a socket option.
+ template <typename Option>
+ boost::system::error_code get_option(const implementation_type&,
+ Option&, boost::system::error_code& ec) const
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type&,
+ boost::system::error_code& ec) const
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return endpoint_type();
+ }
+
+ // Get the remote endpoint.
+ endpoint_type remote_endpoint(const implementation_type&,
+ boost::system::error_code& ec) const
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return endpoint_type();
+ }
+
+ // Send the given data to the peer.
+ template <typename ConstBufferSequence>
+ std::size_t send(implementation_type&, const ConstBufferSequence&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Wait until data can be sent without blocking.
+ std::size_t send(implementation_type&, const null_buffers&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Start an asynchronous send. The data being sent must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_send(implementation_type&, const ConstBufferSequence&,
+ socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Start an asynchronous wait until data can be sent without blocking.
+ template <typename Handler>
+ void async_send(implementation_type&, const null_buffers&,
+ socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Receive some data from the peer. Returns the number of bytes received.
+ template <typename MutableBufferSequence>
+ std::size_t receive(implementation_type&, const MutableBufferSequence&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Wait until data can be received without blocking.
+ std::size_t receive(implementation_type&, const null_buffers&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received
+ // must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive(implementation_type&, const MutableBufferSequence&,
+ socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive(implementation_type&, const null_buffers&,
+ socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Receive some data with associated flags. Returns the number of bytes
+ // received.
+ template <typename MutableBufferSequence>
+ std::size_t receive_with_flags(implementation_type&,
+ const MutableBufferSequence&, socket_base::message_flags,
+ socket_base::message_flags&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Wait until data can be received without blocking.
+ std::size_t receive_with_flags(implementation_type&,
+ const null_buffers&, socket_base::message_flags,
+ socket_base::message_flags&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received
+ // must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive_with_flags(implementation_type&,
+ const MutableBufferSequence&, socket_base::message_flags,
+ socket_base::message_flags&, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive_with_flags(implementation_type&,
+ const null_buffers&, socket_base::message_flags,
+ socket_base::message_flags&, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Send a datagram to the specified endpoint. Returns the number of bytes
+ // sent.
+ template <typename ConstBufferSequence>
+ std::size_t send_to(implementation_type&, const ConstBufferSequence&,
+ const endpoint_type&, socket_base::message_flags,
+ boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Wait until data can be sent without blocking.
+ std::size_t send_to(implementation_type&, const null_buffers&,
+ const endpoint_type&, socket_base::message_flags,
+ boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Start an asynchronous send. The data being sent must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_send_to(implementation_type&, const ConstBufferSequence&,
+ const endpoint_type&, socket_base::message_flags,
+ Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Start an asynchronous wait until data can be sent without blocking.
+ template <typename Handler>
+ void async_send_to(implementation_type&, const null_buffers&,
+ const endpoint_type&, socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Receive a datagram with the endpoint of the sender. Returns the number of
+ // bytes received.
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(implementation_type&, const MutableBufferSequence&,
+ endpoint_type&, socket_base::message_flags,
+ boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Wait until data can be received without blocking.
+ std::size_t receive_from(implementation_type&, const null_buffers&,
+ endpoint_type&, socket_base::message_flags,
+ boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received and
+ // the sender_endpoint object must both be valid for the lifetime of the
+ // asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive_from(implementation_type&,
+ const MutableBufferSequence&, endpoint_type&,
+ socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive_from(implementation_type&,
+ const null_buffers&, endpoint_type&,
+ socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.post(detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Accept a new connection.
+ template <typename Socket>
+ boost::system::error_code accept(implementation_type&,
+ Socket&, endpoint_type*, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Start an asynchronous accept. The peer and peer_endpoint objects
+ // must be valid until the accept's handler is invoked.
+ template <typename Socket, typename Handler>
+ void async_accept(implementation_type&, Socket&,
+ endpoint_type*, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ io_service_.post(detail::bind_handler(handler, ec));
+ }
+
+ // Connect the socket to the specified endpoint.
+ boost::system::error_code connect(implementation_type&,
+ const endpoint_type&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Start an asynchronous connect.
+ template <typename Handler>
+ void async_connect(implementation_type&,
+ const endpoint_type&, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ io_service_.post(detail::bind_handler(handler, ec));
+ }
+
+private:
+ boost::asio::io_service& io_service_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_NULL_SOCKET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/null_static_mutex.hpp b/ext/patches/boost/asio/detail/null_static_mutex.hpp
new file mode 100644
index 0000000..0019d22
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_static_mutex.hpp
@@ -0,0 +1,62 @@
+//
+// detail/null_static_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_STATIC_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_NULL_STATIC_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+
+#include <boost/asio/detail/scoped_lock.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct null_static_mutex
+{
+ typedef boost::asio::detail::scoped_lock<null_static_mutex> scoped_lock;
+
+ // Initialise the mutex.
+ void init()
+ {
+ }
+
+ // Lock the mutex.
+ void lock()
+ {
+ }
+
+ // Unlock the mutex.
+ void unlock()
+ {
+ }
+
+ int unused_;
+};
+
+#define BOOST_ASIO_NULL_STATIC_MUTEX_INIT { 0 }
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_THREADS)
+
+#endif // BOOST_ASIO_DETAIL_NULL_STATIC_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/null_thread.hpp b/ext/patches/boost/asio/detail/null_thread.hpp
new file mode 100644
index 0000000..fe9fb01
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_thread.hpp
@@ -0,0 +1,63 @@
+//
+// detail/null_thread.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_THREAD_HPP
+#define BOOST_ASIO_DETAIL_NULL_THREAD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class null_thread
+ : private noncopyable
+{
+public:
+ // Constructor.
+ template <typename Function>
+ null_thread(Function, unsigned int = 0)
+ {
+ boost::asio::detail::throw_error(
+ boost::asio::error::operation_not_supported, "thread");
+ }
+
+ // Destructor.
+ ~null_thread()
+ {
+ }
+
+ // Wait for the thread to exit.
+ void join()
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_THREADS)
+
+#endif // BOOST_ASIO_DETAIL_NULL_THREAD_HPP
diff --git a/ext/patches/boost/asio/detail/null_tss_ptr.hpp b/ext/patches/boost/asio/detail/null_tss_ptr.hpp
new file mode 100644
index 0000000..2cfcbd1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/null_tss_ptr.hpp
@@ -0,0 +1,70 @@
+//
+// detail/null_tss_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_NULL_TSS_PTR_HPP
+#define BOOST_ASIO_DETAIL_NULL_TSS_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename T>
+class null_tss_ptr
+ : private noncopyable
+{
+public:
+ // Constructor.
+ null_tss_ptr()
+ : value_(0)
+ {
+ }
+
+ // Destructor.
+ ~null_tss_ptr()
+ {
+ }
+
+ // Get the value.
+ operator T*() const
+ {
+ return value_;
+ }
+
+ // Set the value.
+ void operator=(T* value)
+ {
+ value_ = value;
+ }
+
+private:
+ T* value_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_THREADS)
+
+#endif // BOOST_ASIO_DETAIL_NULL_TSS_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/object_pool.hpp b/ext/patches/boost/asio/detail/object_pool.hpp
new file mode 100644
index 0000000..1b8f94d
--- /dev/null
+++ b/ext/patches/boost/asio/detail/object_pool.hpp
@@ -0,0 +1,148 @@
+//
+// detail/object_pool.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_OBJECT_POOL_HPP
+#define BOOST_ASIO_DETAIL_OBJECT_POOL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Object>
+class object_pool;
+
+class object_pool_access
+{
+public:
+ template <typename Object>
+ static Object* create()
+ {
+ return new Object;
+ }
+
+ template <typename Object>
+ static void destroy(Object* o)
+ {
+ delete o;
+ }
+
+ template <typename Object>
+ static Object*& next(Object* o)
+ {
+ return o->next_;
+ }
+
+ template <typename Object>
+ static Object*& prev(Object* o)
+ {
+ return o->prev_;
+ }
+};
+
+template <typename Object>
+class object_pool
+ : private noncopyable
+{
+public:
+ // Constructor.
+ object_pool()
+ : live_list_(0),
+ free_list_(0)
+ {
+ }
+
+ // Destructor destroys all objects.
+ ~object_pool()
+ {
+ destroy_list(live_list_);
+ destroy_list(free_list_);
+ }
+
+ // Get the object at the start of the live list.
+ Object* first()
+ {
+ return live_list_;
+ }
+
+ // Allocate a new object.
+ Object* alloc()
+ {
+ Object* o = free_list_;
+ if (o)
+ free_list_ = object_pool_access::next(free_list_);
+ else
+ o = object_pool_access::create<Object>();
+
+ object_pool_access::next(o) = live_list_;
+ object_pool_access::prev(o) = 0;
+ if (live_list_)
+ object_pool_access::prev(live_list_) = o;
+ live_list_ = o;
+
+ return o;
+ }
+
+ // Free an object. Moves it to the free list. No destructors are run.
+ void free(Object* o)
+ {
+ if (live_list_ == o)
+ live_list_ = object_pool_access::next(o);
+
+ if (object_pool_access::prev(o))
+ {
+ object_pool_access::next(object_pool_access::prev(o))
+ = object_pool_access::next(o);
+ }
+
+ if (object_pool_access::next(o))
+ {
+ object_pool_access::prev(object_pool_access::next(o))
+ = object_pool_access::prev(o);
+ }
+
+ object_pool_access::next(o) = free_list_;
+ object_pool_access::prev(o) = 0;
+ free_list_ = o;
+ }
+
+private:
+ // Helper function to destroy all elements in a list.
+ void destroy_list(Object* list)
+ {
+ while (list)
+ {
+ Object* o = list;
+ list = object_pool_access::next(o);
+ object_pool_access::destroy(o);
+ }
+ }
+
+ // The list of live objects.
+ Object* live_list_;
+
+ // The free list.
+ Object* free_list_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_OBJECT_POOL_HPP
diff --git a/ext/patches/boost/asio/detail/old_win_sdk_compat.hpp b/ext/patches/boost/asio/detail/old_win_sdk_compat.hpp
new file mode 100644
index 0000000..8ee6457
--- /dev/null
+++ b/ext/patches/boost/asio/detail/old_win_sdk_compat.hpp
@@ -0,0 +1,216 @@
+//
+// detail/old_win_sdk_compat.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_OLD_WIN_SDK_COMPAT_HPP
+#define BOOST_ASIO_DETAIL_OLD_WIN_SDK_COMPAT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+// Guess whether we are building against on old Platform SDK.
+#if !defined(IN6ADDR_ANY_INIT)
+#define BOOST_ASIO_HAS_OLD_WIN_SDK 1
+#endif // !defined(IN6ADDR_ANY_INIT)
+
+#if defined(BOOST_ASIO_HAS_OLD_WIN_SDK)
+
+// Emulation of types that are missing from old Platform SDKs.
+//
+// N.B. this emulation is also used if building for a Windows 2000 target with
+// a recent (i.e. Vista or later) SDK, as the SDK does not provide IPv6 support
+// in that case.
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+enum
+{
+ sockaddr_storage_maxsize = 128, // Maximum size.
+ sockaddr_storage_alignsize = (sizeof(__int64)), // Desired alignment.
+ sockaddr_storage_pad1size = (sockaddr_storage_alignsize - sizeof(short)),
+ sockaddr_storage_pad2size = (sockaddr_storage_maxsize -
+ (sizeof(short) + sockaddr_storage_pad1size + sockaddr_storage_alignsize))
+};
+
+struct sockaddr_storage_emulation
+{
+ short ss_family;
+ char __ss_pad1[sockaddr_storage_pad1size];
+ __int64 __ss_align;
+ char __ss_pad2[sockaddr_storage_pad2size];
+};
+
+struct in6_addr_emulation
+{
+ union
+ {
+ u_char Byte[16];
+ u_short Word[8];
+ } u;
+};
+
+#if !defined(s6_addr)
+# define _S6_un u
+# define _S6_u8 Byte
+# define s6_addr _S6_un._S6_u8
+#endif // !defined(s6_addr)
+
+struct sockaddr_in6_emulation
+{
+ short sin6_family;
+ u_short sin6_port;
+ u_long sin6_flowinfo;
+ in6_addr_emulation sin6_addr;
+ u_long sin6_scope_id;
+};
+
+struct ipv6_mreq_emulation
+{
+ in6_addr_emulation ipv6mr_multiaddr;
+ unsigned int ipv6mr_interface;
+};
+
+struct addrinfo_emulation
+{
+ int ai_flags;
+ int ai_family;
+ int ai_socktype;
+ int ai_protocol;
+ size_t ai_addrlen;
+ char* ai_canonname;
+ sockaddr* ai_addr;
+ addrinfo_emulation* ai_next;
+};
+
+#if !defined(AI_PASSIVE)
+# define AI_PASSIVE 0x1
+#endif
+
+#if !defined(AI_CANONNAME)
+# define AI_CANONNAME 0x2
+#endif
+
+#if !defined(AI_NUMERICHOST)
+# define AI_NUMERICHOST 0x4
+#endif
+
+#if !defined(EAI_AGAIN)
+# define EAI_AGAIN WSATRY_AGAIN
+#endif
+
+#if !defined(EAI_BADFLAGS)
+# define EAI_BADFLAGS WSAEINVAL
+#endif
+
+#if !defined(EAI_FAIL)
+# define EAI_FAIL WSANO_RECOVERY
+#endif
+
+#if !defined(EAI_FAMILY)
+# define EAI_FAMILY WSAEAFNOSUPPORT
+#endif
+
+#if !defined(EAI_MEMORY)
+# define EAI_MEMORY WSA_NOT_ENOUGH_MEMORY
+#endif
+
+#if !defined(EAI_NODATA)
+# define EAI_NODATA WSANO_DATA
+#endif
+
+#if !defined(EAI_NONAME)
+# define EAI_NONAME WSAHOST_NOT_FOUND
+#endif
+
+#if !defined(EAI_SERVICE)
+# define EAI_SERVICE WSATYPE_NOT_FOUND
+#endif
+
+#if !defined(EAI_SOCKTYPE)
+# define EAI_SOCKTYPE WSAESOCKTNOSUPPORT
+#endif
+
+#if !defined(NI_NOFQDN)
+# define NI_NOFQDN 0x01
+#endif
+
+#if !defined(NI_NUMERICHOST)
+# define NI_NUMERICHOST 0x02
+#endif
+
+#if !defined(NI_NAMEREQD)
+# define NI_NAMEREQD 0x04
+#endif
+
+#if !defined(NI_NUMERICSERV)
+# define NI_NUMERICSERV 0x08
+#endif
+
+#if !defined(NI_DGRAM)
+# define NI_DGRAM 0x10
+#endif
+
+#if !defined(IPPROTO_IPV6)
+# define IPPROTO_IPV6 41
+#endif
+
+#if !defined(IPV6_UNICAST_HOPS)
+# define IPV6_UNICAST_HOPS 4
+#endif
+
+#if !defined(IPV6_MULTICAST_IF)
+# define IPV6_MULTICAST_IF 9
+#endif
+
+#if !defined(IPV6_MULTICAST_HOPS)
+# define IPV6_MULTICAST_HOPS 10
+#endif
+
+#if !defined(IPV6_MULTICAST_LOOP)
+# define IPV6_MULTICAST_LOOP 11
+#endif
+
+#if !defined(IPV6_JOIN_GROUP)
+# define IPV6_JOIN_GROUP 12
+#endif
+
+#if !defined(IPV6_LEAVE_GROUP)
+# define IPV6_LEAVE_GROUP 13
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_OLD_WIN_SDK)
+
+// Even newer Platform SDKs that support IPv6 may not define IPV6_V6ONLY.
+#if !defined(IPV6_V6ONLY)
+# define IPV6_V6ONLY 27
+#endif
+
+// Some SDKs (e.g. Windows CE) don't define IPPROTO_ICMPV6.
+#if !defined(IPPROTO_ICMPV6)
+# define IPPROTO_ICMPV6 58
+#endif
+
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_OLD_WIN_SDK_COMPAT_HPP
diff --git a/ext/patches/boost/asio/detail/op_queue.hpp b/ext/patches/boost/asio/detail/op_queue.hpp
new file mode 100644
index 0000000..ac17b14
--- /dev/null
+++ b/ext/patches/boost/asio/detail/op_queue.hpp
@@ -0,0 +1,158 @@
+//
+// detail/op_queue.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_OP_QUEUE_HPP
+#define BOOST_ASIO_DETAIL_OP_QUEUE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Operation>
+class op_queue;
+
+class op_queue_access
+{
+public:
+ template <typename Operation>
+ static Operation* next(Operation* o)
+ {
+ return static_cast<Operation*>(o->next_);
+ }
+
+ template <typename Operation1, typename Operation2>
+ static void next(Operation1*& o1, Operation2* o2)
+ {
+ o1->next_ = o2;
+ }
+
+ template <typename Operation>
+ static void destroy(Operation* o)
+ {
+ o->destroy();
+ }
+
+ template <typename Operation>
+ static Operation*& front(op_queue<Operation>& q)
+ {
+ return q.front_;
+ }
+
+ template <typename Operation>
+ static Operation*& back(op_queue<Operation>& q)
+ {
+ return q.back_;
+ }
+};
+
+template <typename Operation>
+class op_queue
+ : private noncopyable
+{
+public:
+ // Constructor.
+ op_queue()
+ : front_(0),
+ back_(0)
+ {
+ }
+
+ // Destructor destroys all operations.
+ ~op_queue()
+ {
+ while (Operation* op = front_)
+ {
+ pop();
+ op_queue_access::destroy(op);
+ }
+ }
+
+ // Get the operation at the front of the queue.
+ Operation* front()
+ {
+ return front_;
+ }
+
+ // Pop an operation from the front of the queue.
+ void pop()
+ {
+ if (front_)
+ {
+ Operation* tmp = front_;
+ front_ = op_queue_access::next(front_);
+ if (front_ == 0)
+ back_ = 0;
+ op_queue_access::next(tmp, static_cast<Operation*>(0));
+ }
+ }
+
+ // Push an operation on to the back of the queue.
+ void push(Operation* h)
+ {
+ op_queue_access::next(h, static_cast<Operation*>(0));
+ if (back_)
+ {
+ op_queue_access::next(back_, h);
+ back_ = h;
+ }
+ else
+ {
+ front_ = back_ = h;
+ }
+ }
+
+ // Push all operations from another queue on to the back of the queue. The
+ // source queue may contain operations of a derived type.
+ template <typename OtherOperation>
+ void push(op_queue<OtherOperation>& q)
+ {
+ if (Operation* other_front = op_queue_access::front(q))
+ {
+ if (back_)
+ op_queue_access::next(back_, other_front);
+ else
+ front_ = other_front;
+ back_ = op_queue_access::back(q);
+ op_queue_access::front(q) = 0;
+ op_queue_access::back(q) = 0;
+ }
+ }
+
+ // Whether the queue is empty.
+ bool empty() const
+ {
+ return front_ == 0;
+ }
+
+private:
+ friend class op_queue_access;
+
+ // The front of the queue.
+ Operation* front_;
+
+ // The back of the queue.
+ Operation* back_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_OP_QUEUE_HPP
diff --git a/ext/patches/boost/asio/detail/operation.hpp b/ext/patches/boost/asio/detail/operation.hpp
new file mode 100644
index 0000000..91b3392
--- /dev/null
+++ b/ext/patches/boost/asio/detail/operation.hpp
@@ -0,0 +1,40 @@
+//
+// detail/operation.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_OPERATION_HPP
+#define BOOST_ASIO_DETAIL_OPERATION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_operation.hpp>
+#else
+# include <boost/asio/detail/task_io_service_operation.hpp>
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+typedef win_iocp_operation operation;
+#else
+typedef task_io_service_operation operation;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_OPERATION_HPP
diff --git a/ext/patches/boost/asio/detail/pipe_select_interrupter.hpp b/ext/patches/boost/asio/detail/pipe_select_interrupter.hpp
new file mode 100644
index 0000000..dacab28
--- /dev/null
+++ b/ext/patches/boost/asio/detail/pipe_select_interrupter.hpp
@@ -0,0 +1,91 @@
+//
+// detail/pipe_select_interrupter.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_PIPE_SELECT_INTERRUPTER_HPP
+#define BOOST_ASIO_DETAIL_PIPE_SELECT_INTERRUPTER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS)
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+#if !defined(__CYGWIN__)
+#if !defined(__SYMBIAN32__)
+#if !defined(BOOST_ASIO_HAS_EVENTFD)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class pipe_select_interrupter
+{
+public:
+ // Constructor.
+ BOOST_ASIO_DECL pipe_select_interrupter();
+
+ // Destructor.
+ BOOST_ASIO_DECL ~pipe_select_interrupter();
+
+ // Recreate the interrupter's descriptors. Used after a fork.
+ BOOST_ASIO_DECL void recreate();
+
+ // Interrupt the select call.
+ BOOST_ASIO_DECL void interrupt();
+
+ // Reset the select interrupt. Returns true if the call was interrupted.
+ BOOST_ASIO_DECL bool reset();
+
+ // Get the read descriptor to be passed to select.
+ int read_descriptor() const
+ {
+ return read_descriptor_;
+ }
+
+private:
+ // Open the descriptors. Throws on error.
+ BOOST_ASIO_DECL void open_descriptors();
+
+ // Close the descriptors.
+ BOOST_ASIO_DECL void close_descriptors();
+
+ // The read end of a connection used to interrupt the select call. This file
+ // descriptor is passed to select such that when it is time to stop, a single
+ // byte will be written on the other end of the connection and this
+ // descriptor will become readable.
+ int read_descriptor_;
+
+ // The write end of a connection used to interrupt the select call. A single
+ // byte may be written to this to wake up the select which is waiting for the
+ // other end to become readable.
+ int write_descriptor_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/pipe_select_interrupter.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // !defined(BOOST_ASIO_HAS_EVENTFD)
+#endif // !defined(__SYMBIAN32__)
+#endif // !defined(__CYGWIN__)
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+#endif // !defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_PIPE_SELECT_INTERRUPTER_HPP
diff --git a/ext/patches/boost/asio/detail/pop_options.hpp b/ext/patches/boost/asio/detail/pop_options.hpp
new file mode 100644
index 0000000..8ff4797
--- /dev/null
+++ b/ext/patches/boost/asio/detail/pop_options.hpp
@@ -0,0 +1,105 @@
+//
+// detail/pop_options.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+// No header guard
+
+#if defined(__COMO__)
+
+// Comeau C++
+
+#elif defined(__DMC__)
+
+// Digital Mars C++
+
+#elif defined(__INTEL_COMPILER) || defined(__ICL) \
+ || defined(__ICC) || defined(__ECC)
+
+// Intel C++
+
+#elif defined(__GNUC__)
+
+// GNU C++
+
+# if defined(__MINGW32__) || defined(__CYGWIN__)
+# pragma pack (pop)
+# endif
+
+# if defined(__OBJC__)
+# if !defined(__APPLE_CC__) || (__APPLE_CC__ <= 1)
+# if defined(BOOST_ASIO_OBJC_WORKAROUND)
+# undef Protocol
+# undef id
+# undef BOOST_ASIO_OBJC_WORKAROUND
+# endif
+# endif
+# endif
+
+#elif defined(__KCC)
+
+// Kai C++
+
+#elif defined(__sgi)
+
+// SGI MIPSpro C++
+
+#elif defined(__DECCXX)
+
+// Compaq Tru64 Unix cxx
+
+#elif defined(__ghs)
+
+// Greenhills C++
+
+#elif defined(__BORLANDC__)
+
+// Borland C++
+
+# pragma option pop
+# pragma nopushoptwarn
+# pragma nopackwarning
+
+#elif defined(__MWERKS__)
+
+// Metrowerks CodeWarrior
+
+#elif defined(__SUNPRO_CC)
+
+// Sun Workshop Compiler C++
+
+#elif defined(__HP_aCC)
+
+// HP aCC
+
+#elif defined(__MRC__) || defined(__SC__)
+
+// MPW MrCpp or SCpp
+
+#elif defined(__IBMCPP__)
+
+// IBM Visual Age
+
+#elif defined(_MSC_VER)
+
+// Microsoft Visual C++
+//
+// Must remain the last #elif since some other vendors (Metrowerks, for example)
+// also #define _MSC_VER
+
+# pragma warning (pop)
+# pragma pack (pop)
+
+# if defined(__cplusplus_cli) || defined(__cplusplus_winrt)
+# if defined(BOOST_ASIO_CLR_WORKAROUND)
+# undef generic
+# undef BOOST_ASIO_CLR_WORKAROUND
+# endif
+# endif
+
+#endif
diff --git a/ext/patches/boost/asio/detail/posix_event.hpp b/ext/patches/boost/asio/detail/posix_event.hpp
new file mode 100644
index 0000000..febfca2
--- /dev/null
+++ b/ext/patches/boost/asio/detail/posix_event.hpp
@@ -0,0 +1,128 @@
+//
+// detail/posix_event.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_POSIX_EVENT_HPP
+#define BOOST_ASIO_DETAIL_POSIX_EVENT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <pthread.h>
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class posix_event
+ : private noncopyable
+{
+public:
+ // Constructor.
+ BOOST_ASIO_DECL posix_event();
+
+ // Destructor.
+ ~posix_event()
+ {
+ ::pthread_cond_destroy(&cond_);
+ }
+
+ // Signal the event. (Retained for backward compatibility.)
+ template <typename Lock>
+ void signal(Lock& lock)
+ {
+ this->signal_all(lock);
+ }
+
+ // Signal all waiters.
+ template <typename Lock>
+ void signal_all(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ (void)lock;
+ state_ |= 1;
+ ::pthread_cond_broadcast(&cond_); // Ignore EINVAL.
+ }
+
+ // Unlock the mutex and signal one waiter.
+ template <typename Lock>
+ void unlock_and_signal_one(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ state_ |= 1;
+ bool have_waiters = (state_ > 1);
+ lock.unlock();
+ if (have_waiters)
+ ::pthread_cond_signal(&cond_); // Ignore EINVAL.
+ }
+
+ // If there's a waiter, unlock the mutex and signal it.
+ template <typename Lock>
+ bool maybe_unlock_and_signal_one(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ state_ |= 1;
+ if (state_ > 1)
+ {
+ lock.unlock();
+ ::pthread_cond_signal(&cond_); // Ignore EINVAL.
+ return true;
+ }
+ return false;
+ }
+
+ // Reset the event.
+ template <typename Lock>
+ void clear(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ (void)lock;
+ state_ &= ~std::size_t(1);
+ }
+
+ // Wait for the event to become signalled.
+ template <typename Lock>
+ void wait(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ while ((state_ & 1) == 0)
+ {
+ state_ += 2;
+ ::pthread_cond_wait(&cond_, &lock.mutex().mutex_); // Ignore EINVAL.
+ state_ -= 2;
+ }
+ }
+
+private:
+ ::pthread_cond_t cond_;
+ std::size_t state_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/posix_event.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_POSIX_EVENT_HPP
diff --git a/ext/patches/boost/asio/detail/posix_fd_set_adapter.hpp b/ext/patches/boost/asio/detail/posix_fd_set_adapter.hpp
new file mode 100644
index 0000000..bf8ddc4
--- /dev/null
+++ b/ext/patches/boost/asio/detail/posix_fd_set_adapter.hpp
@@ -0,0 +1,120 @@
+//
+// detail/posix_fd_set_adapter.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_POSIX_FD_SET_ADAPTER_HPP
+#define BOOST_ASIO_DETAIL_POSIX_FD_SET_ADAPTER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(__CYGWIN__) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <cstring>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/reactor_op_queue.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Adapts the FD_SET type to meet the Descriptor_Set concept's requirements.
+class posix_fd_set_adapter : noncopyable
+{
+public:
+ posix_fd_set_adapter()
+ : max_descriptor_(invalid_socket)
+ {
+ using namespace std; // Needed for memset on Solaris.
+ FD_ZERO(&fd_set_);
+ }
+
+ void reset()
+ {
+ using namespace std; // Needed for memset on Solaris.
+ FD_ZERO(&fd_set_);
+ }
+
+ bool set(socket_type descriptor)
+ {
+ if (descriptor < (socket_type)FD_SETSIZE)
+ {
+ if (max_descriptor_ == invalid_socket || descriptor > max_descriptor_)
+ max_descriptor_ = descriptor;
+ FD_SET(descriptor, &fd_set_);
+ return true;
+ }
+ return false;
+ }
+
+ void set(reactor_op_queue<socket_type>& operations, op_queue<operation>& ops)
+ {
+ reactor_op_queue<socket_type>::iterator i = operations.begin();
+ while (i != operations.end())
+ {
+ reactor_op_queue<socket_type>::iterator op_iter = i++;
+ if (!set(op_iter->first))
+ {
+ boost::system::error_code ec(error::fd_set_failure);
+ operations.cancel_operations(op_iter, ops, ec);
+ }
+ }
+ }
+
+ bool is_set(socket_type descriptor) const
+ {
+ return FD_ISSET(descriptor, &fd_set_) != 0;
+ }
+
+ operator fd_set*()
+ {
+ return &fd_set_;
+ }
+
+ socket_type max_descriptor() const
+ {
+ return max_descriptor_;
+ }
+
+ void perform(reactor_op_queue<socket_type>& operations,
+ op_queue<operation>& ops) const
+ {
+ reactor_op_queue<socket_type>::iterator i = operations.begin();
+ while (i != operations.end())
+ {
+ reactor_op_queue<socket_type>::iterator op_iter = i++;
+ if (is_set(op_iter->first))
+ operations.perform_operations(op_iter, ops);
+ }
+ }
+
+private:
+ mutable fd_set fd_set_;
+ socket_type max_descriptor_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(__CYGWIN__)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_POSIX_FD_SET_ADAPTER_HPP
diff --git a/ext/patches/boost/asio/detail/posix_mutex.hpp b/ext/patches/boost/asio/detail/posix_mutex.hpp
new file mode 100644
index 0000000..8160c54
--- /dev/null
+++ b/ext/patches/boost/asio/detail/posix_mutex.hpp
@@ -0,0 +1,78 @@
+//
+// detail/posix_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_POSIX_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_POSIX_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <pthread.h>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/scoped_lock.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class posix_event;
+
+class posix_mutex
+ : private noncopyable
+{
+public:
+ typedef boost::asio::detail::scoped_lock<posix_mutex> scoped_lock;
+
+ // Constructor.
+ BOOST_ASIO_DECL posix_mutex();
+
+ // Destructor.
+ ~posix_mutex()
+ {
+ ::pthread_mutex_destroy(&mutex_); // Ignore EBUSY.
+ }
+
+ // Lock the mutex.
+ void lock()
+ {
+ (void)::pthread_mutex_lock(&mutex_); // Ignore EINVAL.
+ }
+
+ // Unlock the mutex.
+ void unlock()
+ {
+ (void)::pthread_mutex_unlock(&mutex_); // Ignore EINVAL.
+ }
+
+private:
+ friend class posix_event;
+ ::pthread_mutex_t mutex_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/posix_mutex.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_POSIX_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/posix_signal_blocker.hpp b/ext/patches/boost/asio/detail/posix_signal_blocker.hpp
new file mode 100644
index 0000000..b564c68
--- /dev/null
+++ b/ext/patches/boost/asio/detail/posix_signal_blocker.hpp
@@ -0,0 +1,87 @@
+//
+// detail/posix_signal_blocker.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_POSIX_SIGNAL_BLOCKER_HPP
+#define BOOST_ASIO_DETAIL_POSIX_SIGNAL_BLOCKER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <csignal>
+#include <pthread.h>
+#include <signal.h>
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class posix_signal_blocker
+ : private noncopyable
+{
+public:
+ // Constructor blocks all signals for the calling thread.
+ posix_signal_blocker()
+ : blocked_(false)
+ {
+ sigset_t new_mask;
+ sigfillset(&new_mask);
+ blocked_ = (pthread_sigmask(SIG_BLOCK, &new_mask, &old_mask_) == 0);
+ }
+
+ // Destructor restores the previous signal mask.
+ ~posix_signal_blocker()
+ {
+ if (blocked_)
+ pthread_sigmask(SIG_SETMASK, &old_mask_, 0);
+ }
+
+ // Block all signals for the calling thread.
+ void block()
+ {
+ if (!blocked_)
+ {
+ sigset_t new_mask;
+ sigfillset(&new_mask);
+ blocked_ = (pthread_sigmask(SIG_BLOCK, &new_mask, &old_mask_) == 0);
+ }
+ }
+
+ // Restore the previous signal mask.
+ void unblock()
+ {
+ if (blocked_)
+ blocked_ = (pthread_sigmask(SIG_SETMASK, &old_mask_, 0) != 0);
+ }
+
+private:
+ // Have signals been blocked.
+ bool blocked_;
+
+ // The previous signal mask.
+ sigset_t old_mask_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_POSIX_SIGNAL_BLOCKER_HPP
diff --git a/ext/patches/boost/asio/detail/posix_static_mutex.hpp b/ext/patches/boost/asio/detail/posix_static_mutex.hpp
new file mode 100644
index 0000000..f702a45
--- /dev/null
+++ b/ext/patches/boost/asio/detail/posix_static_mutex.hpp
@@ -0,0 +1,66 @@
+//
+// detail/posix_static_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_POSIX_STATIC_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_POSIX_STATIC_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <pthread.h>
+#include <boost/asio/detail/scoped_lock.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct posix_static_mutex
+{
+ typedef boost::asio::detail::scoped_lock<posix_static_mutex> scoped_lock;
+
+ // Initialise the mutex.
+ void init()
+ {
+ // Nothing to do.
+ }
+
+ // Lock the mutex.
+ void lock()
+ {
+ (void)::pthread_mutex_lock(&mutex_); // Ignore EINVAL.
+ }
+
+ // Unlock the mutex.
+ void unlock()
+ {
+ (void)::pthread_mutex_unlock(&mutex_); // Ignore EINVAL.
+ }
+
+ ::pthread_mutex_t mutex_;
+};
+
+#define BOOST_ASIO_POSIX_STATIC_MUTEX_INIT { PTHREAD_MUTEX_INITIALIZER }
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_POSIX_STATIC_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/posix_thread.hpp b/ext/patches/boost/asio/detail/posix_thread.hpp
new file mode 100644
index 0000000..8d2257b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/posix_thread.hpp
@@ -0,0 +1,107 @@
+//
+// detail/posix_thread.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_POSIX_THREAD_HPP
+#define BOOST_ASIO_DETAIL_POSIX_THREAD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <pthread.h>
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+extern "C"
+{
+ BOOST_ASIO_DECL void* boost_asio_detail_posix_thread_function(void* arg);
+}
+
+class posix_thread
+ : private noncopyable
+{
+public:
+ // Constructor.
+ template <typename Function>
+ posix_thread(Function f, unsigned int = 0)
+ : joined_(false)
+ {
+ start_thread(new func<Function>(f));
+ }
+
+ // Destructor.
+ BOOST_ASIO_DECL ~posix_thread();
+
+ // Wait for the thread to exit.
+ BOOST_ASIO_DECL void join();
+
+private:
+ friend void* boost_asio_detail_posix_thread_function(void* arg);
+
+ class func_base
+ {
+ public:
+ virtual ~func_base() {}
+ virtual void run() = 0;
+ };
+
+ struct auto_func_base_ptr
+ {
+ func_base* ptr;
+ ~auto_func_base_ptr() { delete ptr; }
+ };
+
+ template <typename Function>
+ class func
+ : public func_base
+ {
+ public:
+ func(Function f)
+ : f_(f)
+ {
+ }
+
+ virtual void run()
+ {
+ f_();
+ }
+
+ private:
+ Function f_;
+ };
+
+ BOOST_ASIO_DECL void start_thread(func_base* arg);
+
+ ::pthread_t thread_;
+ bool joined_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/posix_thread.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_POSIX_THREAD_HPP
diff --git a/ext/patches/boost/asio/detail/posix_tss_ptr.hpp b/ext/patches/boost/asio/detail/posix_tss_ptr.hpp
new file mode 100644
index 0000000..516bf2c
--- /dev/null
+++ b/ext/patches/boost/asio/detail/posix_tss_ptr.hpp
@@ -0,0 +1,81 @@
+//
+// detail/posix_tss_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_POSIX_TSS_PTR_HPP
+#define BOOST_ASIO_DETAIL_POSIX_TSS_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_PTHREADS)
+
+#include <pthread.h>
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Helper function to create thread-specific storage.
+BOOST_ASIO_DECL void posix_tss_ptr_create(pthread_key_t& key);
+
+template <typename T>
+class posix_tss_ptr
+ : private noncopyable
+{
+public:
+ // Constructor.
+ posix_tss_ptr()
+ {
+ posix_tss_ptr_create(tss_key_);
+ }
+
+ // Destructor.
+ ~posix_tss_ptr()
+ {
+ ::pthread_key_delete(tss_key_);
+ }
+
+ // Get the value.
+ operator T*() const
+ {
+ return static_cast<T*>(::pthread_getspecific(tss_key_));
+ }
+
+ // Set the value.
+ void operator=(T* value)
+ {
+ ::pthread_setspecific(tss_key_, value);
+ }
+
+private:
+ // Thread-specific storage to allow unlocked access to determine whether a
+ // thread is a member of the pool.
+ pthread_key_t tss_key_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/posix_tss_ptr.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_PTHREADS)
+
+#endif // BOOST_ASIO_DETAIL_POSIX_TSS_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/push_options.hpp b/ext/patches/boost/asio/detail/push_options.hpp
new file mode 100644
index 0000000..8725afa
--- /dev/null
+++ b/ext/patches/boost/asio/detail/push_options.hpp
@@ -0,0 +1,138 @@
+//
+// detail/push_options.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+// No header guard
+
+#if defined(__COMO__)
+
+// Comeau C++
+
+#elif defined(__DMC__)
+
+// Digital Mars C++
+
+#elif defined(__INTEL_COMPILER) || defined(__ICL) \
+ || defined(__ICC) || defined(__ECC)
+
+// Intel C++
+
+#elif defined(__GNUC__)
+
+// GNU C++
+
+# if defined(__MINGW32__) || defined(__CYGWIN__)
+# pragma pack (push, 8)
+# endif
+
+# if defined(__OBJC__)
+# if !defined(__APPLE_CC__) || (__APPLE_CC__ <= 1)
+# if !defined(BOOST_ASIO_DISABLE_OBJC_WORKAROUND)
+# if !defined(Protocol) && !defined(id)
+# define Protocol cpp_Protocol
+# define id cpp_id
+# define BOOST_ASIO_OBJC_WORKAROUND
+# endif
+# endif
+# endif
+# endif
+
+#elif defined(__KCC)
+
+// Kai C++
+
+#elif defined(__sgi)
+
+// SGI MIPSpro C++
+
+#elif defined(__DECCXX)
+
+// Compaq Tru64 Unix cxx
+
+#elif defined(__ghs)
+
+// Greenhills C++
+
+#elif defined(__BORLANDC__)
+
+// Borland C++
+
+# pragma option push -a8 -b -Ve- -Vx- -w-inl -vi-
+# pragma nopushoptwarn
+# pragma nopackwarning
+# if !defined(__MT__)
+# error Multithreaded RTL must be selected.
+# endif // !defined(__MT__)
+
+#elif defined(__MWERKS__)
+
+// Metrowerks CodeWarrior
+
+#elif defined(__SUNPRO_CC)
+
+// Sun Workshop Compiler C++
+
+#elif defined(__HP_aCC)
+
+// HP aCC
+
+#elif defined(__MRC__) || defined(__SC__)
+
+// MPW MrCpp or SCpp
+
+#elif defined(__IBMCPP__)
+
+// IBM Visual Age
+
+#elif defined(_MSC_VER)
+
+// Microsoft Visual C++
+//
+// Must remain the last #elif since some other vendors (Metrowerks, for example)
+// also #define _MSC_VER
+
+# pragma warning (disable:4103)
+# pragma warning (push)
+# pragma warning (disable:4127)
+# pragma warning (disable:4180)
+# pragma warning (disable:4244)
+# pragma warning (disable:4355)
+# pragma warning (disable:4510)
+# pragma warning (disable:4512)
+# pragma warning (disable:4610)
+# pragma warning (disable:4675)
+# if defined(_M_IX86) && defined(_Wp64)
+// The /Wp64 option is broken. If you want to check 64 bit portability, use a
+// 64 bit compiler!
+# pragma warning (disable:4311)
+# pragma warning (disable:4312)
+# endif // defined(_M_IX86) && defined(_Wp64)
+# pragma pack (push, 8)
+// Note that if the /Og optimisation flag is enabled with MSVC6, the compiler
+// has a tendency to incorrectly optimise away some calls to member template
+// functions, even though those functions contain code that should not be
+// optimised away! Therefore we will always disable this optimisation option
+// for the MSVC6 compiler.
+# if (_MSC_VER < 1300)
+# pragma optimize ("g", off)
+# endif
+# if !defined(_MT)
+# error Multithreaded RTL must be selected.
+# endif // !defined(_MT)
+
+# if defined(__cplusplus_cli) || defined(__cplusplus_winrt)
+# if !defined(BOOST_ASIO_DISABLE_CLR_WORKAROUND)
+# if !defined(generic)
+# define generic cpp_generic
+# define BOOST_ASIO_CLR_WORKAROUND
+# endif
+# endif
+# endif
+
+#endif
diff --git a/ext/patches/boost/asio/detail/reactive_descriptor_service.hpp b/ext/patches/boost/asio/detail/reactive_descriptor_service.hpp
new file mode 100644
index 0000000..2c2e828
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_descriptor_service.hpp
@@ -0,0 +1,324 @@
+//
+// detail/reactive_descriptor_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_DESCRIPTOR_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_DESCRIPTOR_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/descriptor_ops.hpp>
+#include <boost/asio/detail/descriptor_read_op.hpp>
+#include <boost/asio/detail/descriptor_write_op.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/reactive_null_buffers_op.hpp>
+#include <boost/asio/detail/reactor.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class reactive_descriptor_service
+{
+public:
+ // The native type of a descriptor.
+ typedef int native_handle_type;
+
+ // The implementation type of the descriptor.
+ class implementation_type
+ : private boost::asio::detail::noncopyable
+ {
+ public:
+ // Default constructor.
+ implementation_type()
+ : descriptor_(-1),
+ state_(0)
+ {
+ }
+
+ private:
+ // Only this service will have access to the internal values.
+ friend class reactive_descriptor_service;
+
+ // The native descriptor representation.
+ int descriptor_;
+
+ // The current state of the descriptor.
+ descriptor_ops::state_type state_;
+
+ // Per-descriptor data used by the reactor.
+ reactor::per_descriptor_data reactor_data_;
+ };
+
+ // Constructor.
+ BOOST_ASIO_DECL reactive_descriptor_service(
+ boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new descriptor implementation.
+ BOOST_ASIO_DECL void construct(implementation_type& impl);
+
+ // Move-construct a new descriptor implementation.
+ BOOST_ASIO_DECL void move_construct(implementation_type& impl,
+ implementation_type& other_impl);
+
+ // Move-assign from another descriptor implementation.
+ BOOST_ASIO_DECL void move_assign(implementation_type& impl,
+ reactive_descriptor_service& other_service,
+ implementation_type& other_impl);
+
+ // Destroy a descriptor implementation.
+ BOOST_ASIO_DECL void destroy(implementation_type& impl);
+
+ // Assign a native descriptor to a descriptor implementation.
+ BOOST_ASIO_DECL boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& native_descriptor,
+ boost::system::error_code& ec);
+
+ // Determine whether the descriptor is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return impl.descriptor_ != -1;
+ }
+
+ // Destroy a descriptor implementation.
+ BOOST_ASIO_DECL boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ // Get the native descriptor representation.
+ native_handle_type native_handle(const implementation_type& impl) const
+ {
+ return impl.descriptor_;
+ }
+
+ // Release ownership of the native descriptor representation.
+ BOOST_ASIO_DECL native_handle_type release(implementation_type& impl);
+
+ // Cancel all operations associated with the descriptor.
+ BOOST_ASIO_DECL boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ // Perform an IO control command on the descriptor.
+ template <typename IO_Control_Command>
+ boost::system::error_code io_control(implementation_type& impl,
+ IO_Control_Command& command, boost::system::error_code& ec)
+ {
+ descriptor_ops::ioctl(impl.descriptor_, impl.state_,
+ command.name(), static_cast<ioctl_arg_type*>(command.data()), ec);
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the descriptor.
+ bool non_blocking(const implementation_type& impl) const
+ {
+ return (impl.state_ & descriptor_ops::user_set_non_blocking) != 0;
+ }
+
+ // Sets the non-blocking mode of the descriptor.
+ boost::system::error_code non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ descriptor_ops::set_user_non_blocking(
+ impl.descriptor_, impl.state_, mode, ec);
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the native descriptor implementation.
+ bool native_non_blocking(const implementation_type& impl) const
+ {
+ return (impl.state_ & descriptor_ops::internal_non_blocking) != 0;
+ }
+
+ // Sets the non-blocking mode of the native descriptor implementation.
+ boost::system::error_code native_non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ descriptor_ops::set_internal_non_blocking(
+ impl.descriptor_, impl.state_, mode, ec);
+ return ec;
+ }
+
+ // Write some data to the descriptor.
+ template <typename ConstBufferSequence>
+ size_t write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(buffers);
+
+ return descriptor_ops::sync_write(impl.descriptor_, impl.state_,
+ bufs.buffers(), bufs.count(), bufs.all_empty(), ec);
+ }
+
+ // Wait until data can be written without blocking.
+ size_t write_some(implementation_type& impl,
+ const null_buffers&, boost::system::error_code& ec)
+ {
+ // Wait for descriptor to become ready.
+ descriptor_ops::poll_write(impl.descriptor_, impl.state_, ec);
+
+ return 0;
+ }
+
+ // Start an asynchronous write. The data being sent must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef descriptor_write_op<ConstBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.descriptor_, buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "descriptor", &impl, "async_write_some"));
+
+ start_op(impl, reactor::write_op, p.p, is_continuation, true,
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::all_empty(buffers));
+ p.v = p.p = 0;
+ }
+
+ // Start an asynchronous wait until data can be written without blocking.
+ template <typename Handler>
+ void async_write_some(implementation_type& impl,
+ const null_buffers&, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "descriptor",
+ &impl, "async_write_some(null_buffers)"));
+
+ start_op(impl, reactor::write_op, p.p, is_continuation, false, false);
+ p.v = p.p = 0;
+ }
+
+ // Read some data from the stream. Returns the number of bytes read.
+ template <typename MutableBufferSequence>
+ size_t read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ return descriptor_ops::sync_read(impl.descriptor_, impl.state_,
+ bufs.buffers(), bufs.count(), bufs.all_empty(), ec);
+ }
+
+ // Wait until data can be read without blocking.
+ size_t read_some(implementation_type& impl,
+ const null_buffers&, boost::system::error_code& ec)
+ {
+ // Wait for descriptor to become ready.
+ descriptor_ops::poll_read(impl.descriptor_, impl.state_, ec);
+
+ return 0;
+ }
+
+ // Start an asynchronous read. The buffer for the data being read must be
+ // valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef descriptor_read_op<MutableBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.descriptor_, buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "descriptor", &impl, "async_read_some"));
+
+ start_op(impl, reactor::read_op, p.p, is_continuation, true,
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::all_empty(buffers));
+ p.v = p.p = 0;
+ }
+
+ // Wait until data can be read without blocking.
+ template <typename Handler>
+ void async_read_some(implementation_type& impl,
+ const null_buffers&, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "descriptor",
+ &impl, "async_read_some(null_buffers)"));
+
+ start_op(impl, reactor::read_op, p.p, is_continuation, false, false);
+ p.v = p.p = 0;
+ }
+
+private:
+ // Start the asynchronous operation.
+ BOOST_ASIO_DECL void start_op(implementation_type& impl, int op_type,
+ reactor_op* op, bool is_continuation, bool is_non_blocking, bool noop);
+
+ // The selector that performs event demultiplexing for the service.
+ reactor& reactor_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/reactive_descriptor_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_DESCRIPTOR_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_null_buffers_op.hpp b/ext/patches/boost/asio/detail/reactive_null_buffers_op.hpp
new file mode 100644
index 0000000..8834fdd
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_null_buffers_op.hpp
@@ -0,0 +1,90 @@
+//
+// detail/reactive_null_buffers_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_NULL_BUFFERS_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_NULL_BUFFERS_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+class reactive_null_buffers_op : public reactor_op
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(reactive_null_buffers_op);
+
+ reactive_null_buffers_op(Handler& handler)
+ : reactor_op(&reactive_null_buffers_op::do_perform,
+ &reactive_null_buffers_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static bool do_perform(reactor_op*)
+ {
+ return true;
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ reactive_null_buffers_op* o(static_cast<reactive_null_buffers_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->bytes_transferred_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_NULL_BUFFERS_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_serial_port_service.hpp b/ext/patches/boost/asio/detail/reactive_serial_port_service.hpp
new file mode 100644
index 0000000..d4c68f1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_serial_port_service.hpp
@@ -0,0 +1,236 @@
+//
+// detail/reactive_serial_port_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SERIAL_PORT_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SERIAL_PORT_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_SERIAL_PORT)
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#include <string>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/serial_port_base.hpp>
+#include <boost/asio/detail/descriptor_ops.hpp>
+#include <boost/asio/detail/reactive_descriptor_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Extend reactive_descriptor_service to provide serial port support.
+class reactive_serial_port_service
+{
+public:
+ // The native type of a serial port.
+ typedef reactive_descriptor_service::native_handle_type native_handle_type;
+
+ // The implementation type of the serial port.
+ typedef reactive_descriptor_service::implementation_type implementation_type;
+
+ BOOST_ASIO_DECL reactive_serial_port_service(
+ boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new serial port implementation.
+ void construct(implementation_type& impl)
+ {
+ descriptor_service_.construct(impl);
+ }
+
+ // Move-construct a new serial port implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ descriptor_service_.move_construct(impl, other_impl);
+ }
+
+ // Move-assign from another serial port implementation.
+ void move_assign(implementation_type& impl,
+ reactive_serial_port_service& other_service,
+ implementation_type& other_impl)
+ {
+ descriptor_service_.move_assign(impl,
+ other_service.descriptor_service_, other_impl);
+ }
+
+ // Destroy a serial port implementation.
+ void destroy(implementation_type& impl)
+ {
+ descriptor_service_.destroy(impl);
+ }
+
+ // Open the serial port using the specified device name.
+ BOOST_ASIO_DECL boost::system::error_code open(implementation_type& impl,
+ const std::string& device, boost::system::error_code& ec);
+
+ // Assign a native descriptor to a serial port implementation.
+ boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& native_descriptor,
+ boost::system::error_code& ec)
+ {
+ return descriptor_service_.assign(impl, native_descriptor, ec);
+ }
+
+ // Determine whether the serial port is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return descriptor_service_.is_open(impl);
+ }
+
+ // Destroy a serial port implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return descriptor_service_.close(impl, ec);
+ }
+
+ // Get the native serial port representation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return descriptor_service_.native_handle(impl);
+ }
+
+ // Cancel all operations associated with the serial port.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return descriptor_service_.cancel(impl, ec);
+ }
+
+ // Set an option on the serial port.
+ template <typename SettableSerialPortOption>
+ boost::system::error_code set_option(implementation_type& impl,
+ const SettableSerialPortOption& option, boost::system::error_code& ec)
+ {
+ return do_set_option(impl,
+ &reactive_serial_port_service::store_option<SettableSerialPortOption>,
+ &option, ec);
+ }
+
+ // Get an option from the serial port.
+ template <typename GettableSerialPortOption>
+ boost::system::error_code get_option(const implementation_type& impl,
+ GettableSerialPortOption& option, boost::system::error_code& ec) const
+ {
+ return do_get_option(impl,
+ &reactive_serial_port_service::load_option<GettableSerialPortOption>,
+ &option, ec);
+ }
+
+ // Send a break sequence to the serial port.
+ boost::system::error_code send_break(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ errno = 0;
+ descriptor_ops::error_wrapper(::tcsendbreak(
+ descriptor_service_.native_handle(impl), 0), ec);
+ return ec;
+ }
+
+ // Write the given data. Returns the number of bytes sent.
+ template <typename ConstBufferSequence>
+ size_t write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return descriptor_service_.write_some(impl, buffers, ec);
+ }
+
+ // Start an asynchronous write. The data being written must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, Handler& handler)
+ {
+ descriptor_service_.async_write_some(impl, buffers, handler);
+ }
+
+ // Read some data. Returns the number of bytes received.
+ template <typename MutableBufferSequence>
+ size_t read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return descriptor_service_.read_some(impl, buffers, ec);
+ }
+
+ // Start an asynchronous read. The buffer for the data being received must be
+ // valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, Handler& handler)
+ {
+ descriptor_service_.async_read_some(impl, buffers, handler);
+ }
+
+private:
+ // Function pointer type for storing a serial port option.
+ typedef boost::system::error_code (*store_function_type)(
+ const void*, termios&, boost::system::error_code&);
+
+ // Helper function template to store a serial port option.
+ template <typename SettableSerialPortOption>
+ static boost::system::error_code store_option(const void* option,
+ termios& storage, boost::system::error_code& ec)
+ {
+ return static_cast<const SettableSerialPortOption*>(option)->store(
+ storage, ec);
+ }
+
+ // Helper function to set a serial port option.
+ BOOST_ASIO_DECL boost::system::error_code do_set_option(
+ implementation_type& impl, store_function_type store,
+ const void* option, boost::system::error_code& ec);
+
+ // Function pointer type for loading a serial port option.
+ typedef boost::system::error_code (*load_function_type)(
+ void*, const termios&, boost::system::error_code&);
+
+ // Helper function template to load a serial port option.
+ template <typename GettableSerialPortOption>
+ static boost::system::error_code load_option(void* option,
+ const termios& storage, boost::system::error_code& ec)
+ {
+ return static_cast<GettableSerialPortOption*>(option)->load(storage, ec);
+ }
+
+ // Helper function to get a serial port option.
+ BOOST_ASIO_DECL boost::system::error_code do_get_option(
+ const implementation_type& impl, load_function_type load,
+ void* option, boost::system::error_code& ec) const;
+
+ // The implementation used for initiating asynchronous operations.
+ reactive_descriptor_service descriptor_service_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/reactive_serial_port_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+#endif // defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SERIAL_PORT_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_accept_op.hpp b/ext/patches/boost/asio/detail/reactive_socket_accept_op.hpp
new file mode 100644
index 0000000..71661b8
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_accept_op.hpp
@@ -0,0 +1,138 @@
+//
+// detail/reactive_socket_accept_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_ACCEPT_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_ACCEPT_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_holder.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Socket, typename Protocol>
+class reactive_socket_accept_op_base : public reactor_op
+{
+public:
+ reactive_socket_accept_op_base(socket_type socket,
+ socket_ops::state_type state, Socket& peer, const Protocol& protocol,
+ typename Protocol::endpoint* peer_endpoint, func_type complete_func)
+ : reactor_op(&reactive_socket_accept_op_base::do_perform, complete_func),
+ socket_(socket),
+ state_(state),
+ peer_(peer),
+ protocol_(protocol),
+ peer_endpoint_(peer_endpoint)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ reactive_socket_accept_op_base* o(
+ static_cast<reactive_socket_accept_op_base*>(base));
+
+ std::size_t addrlen = o->peer_endpoint_ ? o->peer_endpoint_->capacity() : 0;
+ socket_type new_socket = invalid_socket;
+ bool result = socket_ops::non_blocking_accept(o->socket_,
+ o->state_, o->peer_endpoint_ ? o->peer_endpoint_->data() : 0,
+ o->peer_endpoint_ ? &addrlen : 0, o->ec_, new_socket);
+
+ // On success, assign new connection to peer socket object.
+ if (new_socket != invalid_socket)
+ {
+ socket_holder new_socket_holder(new_socket);
+ if (o->peer_endpoint_)
+ o->peer_endpoint_->resize(addrlen);
+ if (!o->peer_.assign(o->protocol_, new_socket, o->ec_))
+ new_socket_holder.release();
+ }
+
+ return result;
+ }
+
+private:
+ socket_type socket_;
+ socket_ops::state_type state_;
+ Socket& peer_;
+ Protocol protocol_;
+ typename Protocol::endpoint* peer_endpoint_;
+};
+
+template <typename Socket, typename Protocol, typename Handler>
+class reactive_socket_accept_op :
+ public reactive_socket_accept_op_base<Socket, Protocol>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(reactive_socket_accept_op);
+
+ reactive_socket_accept_op(socket_type socket,
+ socket_ops::state_type state, Socket& peer, const Protocol& protocol,
+ typename Protocol::endpoint* peer_endpoint, Handler& handler)
+ : reactive_socket_accept_op_base<Socket, Protocol>(socket, state, peer,
+ protocol, peer_endpoint, &reactive_socket_accept_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ reactive_socket_accept_op* o(static_cast<reactive_socket_accept_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder1<Handler, boost::system::error_code>
+ handler(o->handler_, o->ec_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_ACCEPT_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_connect_op.hpp b/ext/patches/boost/asio/detail/reactive_socket_connect_op.hpp
new file mode 100644
index 0000000..b247ce4
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_connect_op.hpp
@@ -0,0 +1,108 @@
+//
+// detail/reactive_socket_connect_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_CONNECT_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_CONNECT_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class reactive_socket_connect_op_base : public reactor_op
+{
+public:
+ reactive_socket_connect_op_base(socket_type socket, func_type complete_func)
+ : reactor_op(&reactive_socket_connect_op_base::do_perform, complete_func),
+ socket_(socket)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ reactive_socket_connect_op_base* o(
+ static_cast<reactive_socket_connect_op_base*>(base));
+
+ return socket_ops::non_blocking_connect(o->socket_, o->ec_);
+ }
+
+private:
+ socket_type socket_;
+};
+
+template <typename Handler>
+class reactive_socket_connect_op : public reactive_socket_connect_op_base
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(reactive_socket_connect_op);
+
+ reactive_socket_connect_op(socket_type socket, Handler& handler)
+ : reactive_socket_connect_op_base(socket,
+ &reactive_socket_connect_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ reactive_socket_connect_op* o
+ (static_cast<reactive_socket_connect_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder1<Handler, boost::system::error_code>
+ handler(o->handler_, o->ec_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_CONNECT_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_recv_op.hpp b/ext/patches/boost/asio/detail/reactive_socket_recv_op.hpp
new file mode 100644
index 0000000..24ff66a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_recv_op.hpp
@@ -0,0 +1,125 @@
+//
+// detail/reactive_socket_recv_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECV_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECV_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence>
+class reactive_socket_recv_op_base : public reactor_op
+{
+public:
+ reactive_socket_recv_op_base(socket_type socket,
+ socket_ops::state_type state, const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, func_type complete_func)
+ : reactor_op(&reactive_socket_recv_op_base::do_perform, complete_func),
+ socket_(socket),
+ state_(state),
+ buffers_(buffers),
+ flags_(flags)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ reactive_socket_recv_op_base* o(
+ static_cast<reactive_socket_recv_op_base*>(base));
+
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(o->buffers_);
+
+ return socket_ops::non_blocking_recv(o->socket_,
+ bufs.buffers(), bufs.count(), o->flags_,
+ (o->state_ & socket_ops::stream_oriented) != 0,
+ o->ec_, o->bytes_transferred_);
+ }
+
+private:
+ socket_type socket_;
+ socket_ops::state_type state_;
+ MutableBufferSequence buffers_;
+ socket_base::message_flags flags_;
+};
+
+template <typename MutableBufferSequence, typename Handler>
+class reactive_socket_recv_op :
+ public reactive_socket_recv_op_base<MutableBufferSequence>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(reactive_socket_recv_op);
+
+ reactive_socket_recv_op(socket_type socket,
+ socket_ops::state_type state, const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, Handler& handler)
+ : reactive_socket_recv_op_base<MutableBufferSequence>(socket, state,
+ buffers, flags, &reactive_socket_recv_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ reactive_socket_recv_op* o(static_cast<reactive_socket_recv_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->bytes_transferred_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECV_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_recvfrom_op.hpp b/ext/patches/boost/asio/detail/reactive_socket_recvfrom_op.hpp
new file mode 100644
index 0000000..fe7253b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_recvfrom_op.hpp
@@ -0,0 +1,135 @@
+//
+// detail/reactive_socket_recvfrom_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECVFROM_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECVFROM_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence, typename Endpoint>
+class reactive_socket_recvfrom_op_base : public reactor_op
+{
+public:
+ reactive_socket_recvfrom_op_base(socket_type socket, int protocol_type,
+ const MutableBufferSequence& buffers, Endpoint& endpoint,
+ socket_base::message_flags flags, func_type complete_func)
+ : reactor_op(&reactive_socket_recvfrom_op_base::do_perform, complete_func),
+ socket_(socket),
+ protocol_type_(protocol_type),
+ buffers_(buffers),
+ sender_endpoint_(endpoint),
+ flags_(flags)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ reactive_socket_recvfrom_op_base* o(
+ static_cast<reactive_socket_recvfrom_op_base*>(base));
+
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(o->buffers_);
+
+ std::size_t addr_len = o->sender_endpoint_.capacity();
+ bool result = socket_ops::non_blocking_recvfrom(o->socket_,
+ bufs.buffers(), bufs.count(), o->flags_,
+ o->sender_endpoint_.data(), &addr_len,
+ o->ec_, o->bytes_transferred_);
+
+ if (result && !o->ec_)
+ o->sender_endpoint_.resize(addr_len);
+
+ return result;
+ }
+
+private:
+ socket_type socket_;
+ int protocol_type_;
+ MutableBufferSequence buffers_;
+ Endpoint& sender_endpoint_;
+ socket_base::message_flags flags_;
+};
+
+template <typename MutableBufferSequence, typename Endpoint, typename Handler>
+class reactive_socket_recvfrom_op :
+ public reactive_socket_recvfrom_op_base<MutableBufferSequence, Endpoint>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(reactive_socket_recvfrom_op);
+
+ reactive_socket_recvfrom_op(socket_type socket, int protocol_type,
+ const MutableBufferSequence& buffers, Endpoint& endpoint,
+ socket_base::message_flags flags, Handler& handler)
+ : reactive_socket_recvfrom_op_base<MutableBufferSequence, Endpoint>(
+ socket, protocol_type, buffers, endpoint, flags,
+ &reactive_socket_recvfrom_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ reactive_socket_recvfrom_op* o(
+ static_cast<reactive_socket_recvfrom_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->bytes_transferred_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECVFROM_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_recvmsg_op.hpp b/ext/patches/boost/asio/detail/reactive_socket_recvmsg_op.hpp
new file mode 100644
index 0000000..75ba4e3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_recvmsg_op.hpp
@@ -0,0 +1,127 @@
+//
+// detail/reactive_socket_recvmsg_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECVMSG_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECVMSG_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/socket_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence>
+class reactive_socket_recvmsg_op_base : public reactor_op
+{
+public:
+ reactive_socket_recvmsg_op_base(socket_type socket,
+ const MutableBufferSequence& buffers, socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, func_type complete_func)
+ : reactor_op(&reactive_socket_recvmsg_op_base::do_perform, complete_func),
+ socket_(socket),
+ buffers_(buffers),
+ in_flags_(in_flags),
+ out_flags_(out_flags)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ reactive_socket_recvmsg_op_base* o(
+ static_cast<reactive_socket_recvmsg_op_base*>(base));
+
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(o->buffers_);
+
+ return socket_ops::non_blocking_recvmsg(o->socket_,
+ bufs.buffers(), bufs.count(),
+ o->in_flags_, o->out_flags_,
+ o->ec_, o->bytes_transferred_);
+ }
+
+private:
+ socket_type socket_;
+ MutableBufferSequence buffers_;
+ socket_base::message_flags in_flags_;
+ socket_base::message_flags& out_flags_;
+};
+
+template <typename MutableBufferSequence, typename Handler>
+class reactive_socket_recvmsg_op :
+ public reactive_socket_recvmsg_op_base<MutableBufferSequence>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(reactive_socket_recvmsg_op);
+
+ reactive_socket_recvmsg_op(socket_type socket,
+ const MutableBufferSequence& buffers, socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, Handler& handler)
+ : reactive_socket_recvmsg_op_base<MutableBufferSequence>(socket, buffers,
+ in_flags, out_flags, &reactive_socket_recvmsg_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ reactive_socket_recvmsg_op* o(
+ static_cast<reactive_socket_recvmsg_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->bytes_transferred_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_RECVMSG_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_send_op.hpp b/ext/patches/boost/asio/detail/reactive_socket_send_op.hpp
new file mode 100644
index 0000000..3940cb1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_send_op.hpp
@@ -0,0 +1,122 @@
+//
+// detail/reactive_socket_send_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SEND_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SEND_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename ConstBufferSequence>
+class reactive_socket_send_op_base : public reactor_op
+{
+public:
+ reactive_socket_send_op_base(socket_type socket,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, func_type complete_func)
+ : reactor_op(&reactive_socket_send_op_base::do_perform, complete_func),
+ socket_(socket),
+ buffers_(buffers),
+ flags_(flags)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ reactive_socket_send_op_base* o(
+ static_cast<reactive_socket_send_op_base*>(base));
+
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(o->buffers_);
+
+ return socket_ops::non_blocking_send(o->socket_,
+ bufs.buffers(), bufs.count(), o->flags_,
+ o->ec_, o->bytes_transferred_);
+ }
+
+private:
+ socket_type socket_;
+ ConstBufferSequence buffers_;
+ socket_base::message_flags flags_;
+};
+
+template <typename ConstBufferSequence, typename Handler>
+class reactive_socket_send_op :
+ public reactive_socket_send_op_base<ConstBufferSequence>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(reactive_socket_send_op);
+
+ reactive_socket_send_op(socket_type socket,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, Handler& handler)
+ : reactive_socket_send_op_base<ConstBufferSequence>(socket,
+ buffers, flags, &reactive_socket_send_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ reactive_socket_send_op* o(static_cast<reactive_socket_send_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->bytes_transferred_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SEND_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_sendto_op.hpp b/ext/patches/boost/asio/detail/reactive_socket_sendto_op.hpp
new file mode 100644
index 0000000..df85def
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_sendto_op.hpp
@@ -0,0 +1,125 @@
+//
+// detail/reactive_socket_sendto_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SENDTO_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SENDTO_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename ConstBufferSequence, typename Endpoint>
+class reactive_socket_sendto_op_base : public reactor_op
+{
+public:
+ reactive_socket_sendto_op_base(socket_type socket,
+ const ConstBufferSequence& buffers, const Endpoint& endpoint,
+ socket_base::message_flags flags, func_type complete_func)
+ : reactor_op(&reactive_socket_sendto_op_base::do_perform, complete_func),
+ socket_(socket),
+ buffers_(buffers),
+ destination_(endpoint),
+ flags_(flags)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ reactive_socket_sendto_op_base* o(
+ static_cast<reactive_socket_sendto_op_base*>(base));
+
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(o->buffers_);
+
+ return socket_ops::non_blocking_sendto(o->socket_,
+ bufs.buffers(), bufs.count(), o->flags_,
+ o->destination_.data(), o->destination_.size(),
+ o->ec_, o->bytes_transferred_);
+ }
+
+private:
+ socket_type socket_;
+ ConstBufferSequence buffers_;
+ Endpoint destination_;
+ socket_base::message_flags flags_;
+};
+
+template <typename ConstBufferSequence, typename Endpoint, typename Handler>
+class reactive_socket_sendto_op :
+ public reactive_socket_sendto_op_base<ConstBufferSequence, Endpoint>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(reactive_socket_sendto_op);
+
+ reactive_socket_sendto_op(socket_type socket,
+ const ConstBufferSequence& buffers, const Endpoint& endpoint,
+ socket_base::message_flags flags, Handler& handler)
+ : reactive_socket_sendto_op_base<ConstBufferSequence, Endpoint>(socket,
+ buffers, endpoint, flags, &reactive_socket_sendto_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ reactive_socket_sendto_op* o(static_cast<reactive_socket_sendto_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->bytes_transferred_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SENDTO_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_service.hpp b/ext/patches/boost/asio/detail/reactive_socket_service.hpp
new file mode 100644
index 0000000..68ad22a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_service.hpp
@@ -0,0 +1,459 @@
+//
+// detail/reactive_socket_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/socket_base.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/reactive_null_buffers_op.hpp>
+#include <boost/asio/detail/reactive_socket_accept_op.hpp>
+#include <boost/asio/detail/reactive_socket_connect_op.hpp>
+#include <boost/asio/detail/reactive_socket_recvfrom_op.hpp>
+#include <boost/asio/detail/reactive_socket_sendto_op.hpp>
+#include <boost/asio/detail/reactive_socket_service_base.hpp>
+#include <boost/asio/detail/reactor.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_holder.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol>
+class reactive_socket_service :
+ public reactive_socket_service_base
+{
+public:
+ // The protocol type.
+ typedef Protocol protocol_type;
+
+ // The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ // The native type of a socket.
+ typedef socket_type native_handle_type;
+
+ // The implementation type of the socket.
+ struct implementation_type :
+ reactive_socket_service_base::base_implementation_type
+ {
+ // Default constructor.
+ implementation_type()
+ : protocol_(endpoint_type().protocol())
+ {
+ }
+
+ // The protocol associated with the socket.
+ protocol_type protocol_;
+ };
+
+ // Constructor.
+ reactive_socket_service(boost::asio::io_service& io_service)
+ : reactive_socket_service_base(io_service)
+ {
+ }
+
+ // Move-construct a new socket implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ this->base_move_construct(impl, other_impl);
+
+ impl.protocol_ = other_impl.protocol_;
+ other_impl.protocol_ = endpoint_type().protocol();
+ }
+
+ // Move-assign from another socket implementation.
+ void move_assign(implementation_type& impl,
+ reactive_socket_service_base& other_service,
+ implementation_type& other_impl)
+ {
+ this->base_move_assign(impl, other_service, other_impl);
+
+ impl.protocol_ = other_impl.protocol_;
+ other_impl.protocol_ = endpoint_type().protocol();
+ }
+
+ // Move-construct a new socket implementation from another protocol type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type& impl,
+ typename reactive_socket_service<
+ Protocol1>::implementation_type& other_impl)
+ {
+ this->base_move_construct(impl, other_impl);
+
+ impl.protocol_ = protocol_type(other_impl.protocol_);
+ other_impl.protocol_ = typename Protocol1::endpoint().protocol();
+ }
+
+ // Open a new socket implementation.
+ boost::system::error_code open(implementation_type& impl,
+ const protocol_type& protocol, boost::system::error_code& ec)
+ {
+ if (!do_open(impl, protocol.family(),
+ protocol.type(), protocol.protocol(), ec))
+ impl.protocol_ = protocol;
+ return ec;
+ }
+
+ // Assign a native socket to a socket implementation.
+ boost::system::error_code assign(implementation_type& impl,
+ const protocol_type& protocol, const native_handle_type& native_socket,
+ boost::system::error_code& ec)
+ {
+ if (!do_assign(impl, protocol.type(), native_socket, ec))
+ impl.protocol_ = protocol;
+ return ec;
+ }
+
+ // Get the native socket representation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return impl.socket_;
+ }
+
+ // Bind the socket to the specified local endpoint.
+ boost::system::error_code bind(implementation_type& impl,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ socket_ops::bind(impl.socket_, endpoint.data(), endpoint.size(), ec);
+ return ec;
+ }
+
+ // Set a socket option.
+ template <typename Option>
+ boost::system::error_code set_option(implementation_type& impl,
+ const Option& option, boost::system::error_code& ec)
+ {
+ socket_ops::setsockopt(impl.socket_, impl.state_,
+ option.level(impl.protocol_), option.name(impl.protocol_),
+ option.data(impl.protocol_), option.size(impl.protocol_), ec);
+ return ec;
+ }
+
+ // Set a socket option.
+ template <typename Option>
+ boost::system::error_code get_option(const implementation_type& impl,
+ Option& option, boost::system::error_code& ec) const
+ {
+ std::size_t size = option.size(impl.protocol_);
+ socket_ops::getsockopt(impl.socket_, impl.state_,
+ option.level(impl.protocol_), option.name(impl.protocol_),
+ option.data(impl.protocol_), &size, ec);
+ if (!ec)
+ option.resize(impl.protocol_, size);
+ return ec;
+ }
+
+ // Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ endpoint_type endpoint;
+ std::size_t addr_len = endpoint.capacity();
+ if (socket_ops::getsockname(impl.socket_, endpoint.data(), &addr_len, ec))
+ return endpoint_type();
+ endpoint.resize(addr_len);
+ return endpoint;
+ }
+
+ // Get the remote endpoint.
+ endpoint_type remote_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ endpoint_type endpoint;
+ std::size_t addr_len = endpoint.capacity();
+ if (socket_ops::getpeername(impl.socket_,
+ endpoint.data(), &addr_len, false, ec))
+ return endpoint_type();
+ endpoint.resize(addr_len);
+ return endpoint;
+ }
+
+ // Send a datagram to the specified endpoint. Returns the number of bytes
+ // sent.
+ template <typename ConstBufferSequence>
+ size_t send_to(implementation_type& impl, const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags,
+ boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(buffers);
+
+ return socket_ops::sync_sendto(impl.socket_, impl.state_,
+ bufs.buffers(), bufs.count(), flags,
+ destination.data(), destination.size(), ec);
+ }
+
+ // Wait until data can be sent without blocking.
+ size_t send_to(implementation_type& impl, const null_buffers&,
+ const endpoint_type&, socket_base::message_flags,
+ boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_write(impl.socket_, impl.state_, ec);
+
+ return 0;
+ }
+
+ // Start an asynchronous send. The data being sent must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_send_to(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags,
+ Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_socket_sendto_op<ConstBufferSequence,
+ endpoint_type, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.socket_, buffers, destination, flags, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_send_to"));
+
+ start_op(impl, reactor::write_op, p.p, is_continuation, true, false);
+ p.v = p.p = 0;
+ }
+
+ // Start an asynchronous wait until data can be sent without blocking.
+ template <typename Handler>
+ void async_send_to(implementation_type& impl, const null_buffers&,
+ const endpoint_type&, socket_base::message_flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_send_to(null_buffers)"));
+
+ start_op(impl, reactor::write_op, p.p, is_continuation, false, false);
+ p.v = p.p = 0;
+ }
+
+ // Receive a datagram with the endpoint of the sender. Returns the number of
+ // bytes received.
+ template <typename MutableBufferSequence>
+ size_t receive_from(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint, socket_base::message_flags flags,
+ boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ std::size_t addr_len = sender_endpoint.capacity();
+ std::size_t bytes_recvd = socket_ops::sync_recvfrom(
+ impl.socket_, impl.state_, bufs.buffers(), bufs.count(),
+ flags, sender_endpoint.data(), &addr_len, ec);
+
+ if (!ec)
+ sender_endpoint.resize(addr_len);
+
+ return bytes_recvd;
+ }
+
+ // Wait until data can be received without blocking.
+ size_t receive_from(implementation_type& impl, const null_buffers&,
+ endpoint_type& sender_endpoint, socket_base::message_flags,
+ boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_read(impl.socket_, impl.state_, ec);
+
+ // Reset endpoint since it can be given no sensible value at this time.
+ sender_endpoint = endpoint_type();
+
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received and
+ // the sender_endpoint object must both be valid for the lifetime of the
+ // asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive_from(implementation_type& impl,
+ const MutableBufferSequence& buffers, endpoint_type& sender_endpoint,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_socket_recvfrom_op<MutableBufferSequence,
+ endpoint_type, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ int protocol = impl.protocol_.type();
+ p.p = new (p.v) op(impl.socket_, protocol,
+ buffers, sender_endpoint, flags, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_receive_from"));
+
+ start_op(impl,
+ (flags & socket_base::message_out_of_band)
+ ? reactor::except_op : reactor::read_op,
+ p.p, is_continuation, true, false);
+ p.v = p.p = 0;
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive_from(implementation_type& impl,
+ const null_buffers&, endpoint_type& sender_endpoint,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_receive_from(null_buffers)"));
+
+ // Reset endpoint since it can be given no sensible value at this time.
+ sender_endpoint = endpoint_type();
+
+ start_op(impl,
+ (flags & socket_base::message_out_of_band)
+ ? reactor::except_op : reactor::read_op,
+ p.p, is_continuation, false, false);
+ p.v = p.p = 0;
+ }
+
+ // Accept a new connection.
+ template <typename Socket>
+ boost::system::error_code accept(implementation_type& impl,
+ Socket& peer, endpoint_type* peer_endpoint, boost::system::error_code& ec)
+ {
+ // We cannot accept a socket that is already open.
+ if (peer.is_open())
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ std::size_t addr_len = peer_endpoint ? peer_endpoint->capacity() : 0;
+ socket_holder new_socket(socket_ops::sync_accept(impl.socket_,
+ impl.state_, peer_endpoint ? peer_endpoint->data() : 0,
+ peer_endpoint ? &addr_len : 0, ec));
+
+ // On success, assign new connection to peer socket object.
+ if (new_socket.get() != invalid_socket)
+ {
+ if (peer_endpoint)
+ peer_endpoint->resize(addr_len);
+ if (!peer.assign(impl.protocol_, new_socket.get(), ec))
+ new_socket.release();
+ }
+
+ return ec;
+ }
+
+ // Start an asynchronous accept. The peer and peer_endpoint objects
+ // must be valid until the accept's handler is invoked.
+ template <typename Socket, typename Handler>
+ void async_accept(implementation_type& impl, Socket& peer,
+ endpoint_type* peer_endpoint, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_socket_accept_op<Socket, Protocol, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.socket_, impl.state_, peer,
+ impl.protocol_, peer_endpoint, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_accept"));
+
+ start_accept_op(impl, p.p, is_continuation, peer.is_open());
+ p.v = p.p = 0;
+ }
+
+ // Connect the socket to the specified endpoint.
+ boost::system::error_code connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, boost::system::error_code& ec)
+ {
+ socket_ops::sync_connect(impl.socket_,
+ peer_endpoint.data(), peer_endpoint.size(), ec);
+ return ec;
+ }
+
+ // Start an asynchronous connect.
+ template <typename Handler>
+ void async_connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_socket_connect_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.socket_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_connect"));
+
+ start_connect_op(impl, p.p, is_continuation,
+ peer_endpoint.data(), peer_endpoint.size());
+ p.v = p.p = 0;
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/reactive_socket_service_base.hpp b/ext/patches/boost/asio/detail/reactive_socket_service_base.hpp
new file mode 100644
index 0000000..9e880ac
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactive_socket_service_base.hpp
@@ -0,0 +1,452 @@
+//
+// detail/reactive_socket_service_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SERVICE_BASE_HPP
+#define BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SERVICE_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_IOCP) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/socket_base.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/reactive_null_buffers_op.hpp>
+#include <boost/asio/detail/reactive_socket_recv_op.hpp>
+#include <boost/asio/detail/reactive_socket_recvmsg_op.hpp>
+#include <boost/asio/detail/reactive_socket_send_op.hpp>
+#include <boost/asio/detail/reactor.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_holder.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class reactive_socket_service_base
+{
+public:
+ // The native type of a socket.
+ typedef socket_type native_handle_type;
+
+ // The implementation type of the socket.
+ struct base_implementation_type
+ {
+ // The native socket representation.
+ socket_type socket_;
+
+ // The current state of the socket.
+ socket_ops::state_type state_;
+
+ // Per-descriptor data used by the reactor.
+ reactor::per_descriptor_data reactor_data_;
+ };
+
+ // Constructor.
+ BOOST_ASIO_DECL reactive_socket_service_base(
+ boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new socket implementation.
+ BOOST_ASIO_DECL void construct(base_implementation_type& impl);
+
+ // Move-construct a new socket implementation.
+ BOOST_ASIO_DECL void base_move_construct(base_implementation_type& impl,
+ base_implementation_type& other_impl);
+
+ // Move-assign from another socket implementation.
+ BOOST_ASIO_DECL void base_move_assign(base_implementation_type& impl,
+ reactive_socket_service_base& other_service,
+ base_implementation_type& other_impl);
+
+ // Destroy a socket implementation.
+ BOOST_ASIO_DECL void destroy(base_implementation_type& impl);
+
+ // Determine whether the socket is open.
+ bool is_open(const base_implementation_type& impl) const
+ {
+ return impl.socket_ != invalid_socket;
+ }
+
+ // Destroy a socket implementation.
+ BOOST_ASIO_DECL boost::system::error_code close(
+ base_implementation_type& impl, boost::system::error_code& ec);
+
+ // Get the native socket representation.
+ native_handle_type native_handle(base_implementation_type& impl)
+ {
+ return impl.socket_;
+ }
+
+ // Cancel all operations associated with the socket.
+ BOOST_ASIO_DECL boost::system::error_code cancel(
+ base_implementation_type& impl, boost::system::error_code& ec);
+
+ // Determine whether the socket is at the out-of-band data mark.
+ bool at_mark(const base_implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return socket_ops::sockatmark(impl.socket_, ec);
+ }
+
+ // Determine the number of bytes available for reading.
+ std::size_t available(const base_implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return socket_ops::available(impl.socket_, ec);
+ }
+
+ // Place the socket into the state where it will listen for new connections.
+ boost::system::error_code listen(base_implementation_type& impl,
+ int backlog, boost::system::error_code& ec)
+ {
+ socket_ops::listen(impl.socket_, backlog, ec);
+ return ec;
+ }
+
+ // Perform an IO control command on the socket.
+ template <typename IO_Control_Command>
+ boost::system::error_code io_control(base_implementation_type& impl,
+ IO_Control_Command& command, boost::system::error_code& ec)
+ {
+ socket_ops::ioctl(impl.socket_, impl.state_, command.name(),
+ static_cast<ioctl_arg_type*>(command.data()), ec);
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the socket.
+ bool non_blocking(const base_implementation_type& impl) const
+ {
+ return (impl.state_ & socket_ops::user_set_non_blocking) != 0;
+ }
+
+ // Sets the non-blocking mode of the socket.
+ boost::system::error_code non_blocking(base_implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ socket_ops::set_user_non_blocking(impl.socket_, impl.state_, mode, ec);
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the native socket implementation.
+ bool native_non_blocking(const base_implementation_type& impl) const
+ {
+ return (impl.state_ & socket_ops::internal_non_blocking) != 0;
+ }
+
+ // Sets the non-blocking mode of the native socket implementation.
+ boost::system::error_code native_non_blocking(base_implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ socket_ops::set_internal_non_blocking(impl.socket_, impl.state_, mode, ec);
+ return ec;
+ }
+
+ // Disable sends or receives on the socket.
+ boost::system::error_code shutdown(base_implementation_type& impl,
+ socket_base::shutdown_type what, boost::system::error_code& ec)
+ {
+ socket_ops::shutdown(impl.socket_, what, ec);
+ return ec;
+ }
+
+ // Send the given data to the peer.
+ template <typename ConstBufferSequence>
+ size_t send(base_implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(buffers);
+
+ return socket_ops::sync_send(impl.socket_, impl.state_,
+ bufs.buffers(), bufs.count(), flags, bufs.all_empty(), ec);
+ }
+
+ // Wait until data can be sent without blocking.
+ size_t send(base_implementation_type& impl, const null_buffers&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_write(impl.socket_, impl.state_, ec);
+
+ return 0;
+ }
+
+ // Start an asynchronous send. The data being sent must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_send(base_implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_socket_send_op<ConstBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.socket_, buffers, flags, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_send"));
+
+ start_op(impl, reactor::write_op, p.p, is_continuation, true,
+ ((impl.state_ & socket_ops::stream_oriented)
+ && buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::all_empty(buffers)));
+ p.v = p.p = 0;
+ }
+
+ // Start an asynchronous wait until data can be sent without blocking.
+ template <typename Handler>
+ void async_send(base_implementation_type& impl, const null_buffers&,
+ socket_base::message_flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_send(null_buffers)"));
+
+ start_op(impl, reactor::write_op, p.p, is_continuation, false, false);
+ p.v = p.p = 0;
+ }
+
+ // Receive some data from the peer. Returns the number of bytes received.
+ template <typename MutableBufferSequence>
+ size_t receive(base_implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ return socket_ops::sync_recv(impl.socket_, impl.state_,
+ bufs.buffers(), bufs.count(), flags, bufs.all_empty(), ec);
+ }
+
+ // Wait until data can be received without blocking.
+ size_t receive(base_implementation_type& impl, const null_buffers&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_read(impl.socket_, impl.state_, ec);
+
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received
+ // must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive(base_implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_socket_recv_op<MutableBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.socket_, impl.state_, buffers, flags, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_receive"));
+
+ start_op(impl,
+ (flags & socket_base::message_out_of_band)
+ ? reactor::except_op : reactor::read_op,
+ p.p, is_continuation,
+ (flags & socket_base::message_out_of_band) == 0,
+ ((impl.state_ & socket_ops::stream_oriented)
+ && buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::all_empty(buffers)));
+ p.v = p.p = 0;
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive(base_implementation_type& impl, const null_buffers&,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_receive(null_buffers)"));
+
+ start_op(impl,
+ (flags & socket_base::message_out_of_band)
+ ? reactor::except_op : reactor::read_op,
+ p.p, is_continuation, false, false);
+ p.v = p.p = 0;
+ }
+
+ // Receive some data with associated flags. Returns the number of bytes
+ // received.
+ template <typename MutableBufferSequence>
+ size_t receive_with_flags(base_implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ return socket_ops::sync_recvmsg(impl.socket_, impl.state_,
+ bufs.buffers(), bufs.count(), in_flags, out_flags, ec);
+ }
+
+ // Wait until data can be received without blocking.
+ size_t receive_with_flags(base_implementation_type& impl,
+ const null_buffers&, socket_base::message_flags,
+ socket_base::message_flags& out_flags, boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_read(impl.socket_, impl.state_, ec);
+
+ // Clear out_flags, since we cannot give it any other sensible value when
+ // performing a null_buffers operation.
+ out_flags = 0;
+
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received
+ // must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive_with_flags(base_implementation_type& impl,
+ const MutableBufferSequence& buffers, socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_socket_recvmsg_op<MutableBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.socket_, buffers, in_flags, out_flags, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_receive_with_flags"));
+
+ start_op(impl,
+ (in_flags & socket_base::message_out_of_band)
+ ? reactor::except_op : reactor::read_op,
+ p.p, is_continuation,
+ (in_flags & socket_base::message_out_of_band) == 0, false);
+ p.v = p.p = 0;
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive_with_flags(base_implementation_type& impl,
+ const null_buffers&, socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef reactive_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl,
+ "async_receive_with_flags(null_buffers)"));
+
+ // Clear out_flags, since we cannot give it any other sensible value when
+ // performing a null_buffers operation.
+ out_flags = 0;
+
+ start_op(impl,
+ (in_flags & socket_base::message_out_of_band)
+ ? reactor::except_op : reactor::read_op,
+ p.p, is_continuation, false, false);
+ p.v = p.p = 0;
+ }
+
+protected:
+ // Open a new socket implementation.
+ BOOST_ASIO_DECL boost::system::error_code do_open(
+ base_implementation_type& impl, int af,
+ int type, int protocol, boost::system::error_code& ec);
+
+ // Assign a native socket to a socket implementation.
+ BOOST_ASIO_DECL boost::system::error_code do_assign(
+ base_implementation_type& impl, int type,
+ const native_handle_type& native_socket, boost::system::error_code& ec);
+
+ // Start the asynchronous read or write operation.
+ BOOST_ASIO_DECL void start_op(base_implementation_type& impl, int op_type,
+ reactor_op* op, bool is_continuation, bool is_non_blocking, bool noop);
+
+ // Start the asynchronous accept operation.
+ BOOST_ASIO_DECL void start_accept_op(base_implementation_type& impl,
+ reactor_op* op, bool is_continuation, bool peer_is_open);
+
+ // Start the asynchronous connect operation.
+ BOOST_ASIO_DECL void start_connect_op(base_implementation_type& impl,
+ reactor_op* op, bool is_continuation,
+ const socket_addr_type* addr, size_t addrlen);
+
+ // The selector that performs event demultiplexing for the service.
+ reactor& reactor_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/reactive_socket_service_base.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // !defined(BOOST_ASIO_HAS_IOCP)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_REACTIVE_SOCKET_SERVICE_BASE_HPP
diff --git a/ext/patches/boost/asio/detail/reactor.hpp b/ext/patches/boost/asio/detail/reactor.hpp
new file mode 100644
index 0000000..f5918e3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactor.hpp
@@ -0,0 +1,32 @@
+//
+// detail/reactor.hpp
+// ~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/reactor_fwd.hpp>
+
+#if defined(BOOST_ASIO_HAS_EPOLL)
+# include <boost/asio/detail/epoll_reactor.hpp>
+#elif defined(BOOST_ASIO_HAS_KQUEUE)
+# include <boost/asio/detail/kqueue_reactor.hpp>
+#elif defined(BOOST_ASIO_HAS_DEV_POLL)
+# include <boost/asio/detail/dev_poll_reactor.hpp>
+#elif defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/null_reactor.hpp>
+#else
+# include <boost/asio/detail/select_reactor.hpp>
+#endif
+
+#endif // BOOST_ASIO_DETAIL_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/reactor_fwd.hpp b/ext/patches/boost/asio/detail/reactor_fwd.hpp
new file mode 100644
index 0000000..75f2911
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactor_fwd.hpp
@@ -0,0 +1,42 @@
+//
+// detail/reactor_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTOR_FWD_HPP
+#define BOOST_ASIO_DETAIL_REACTOR_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+typedef class null_reactor reactor;
+#elif defined(BOOST_ASIO_HAS_IOCP)
+typedef class select_reactor reactor;
+#elif defined(BOOST_ASIO_HAS_EPOLL)
+typedef class epoll_reactor reactor;
+#elif defined(BOOST_ASIO_HAS_KQUEUE)
+typedef class kqueue_reactor reactor;
+#elif defined(BOOST_ASIO_HAS_DEV_POLL)
+typedef class dev_poll_reactor reactor;
+#else
+typedef class select_reactor reactor;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_REACTOR_FWD_HPP
diff --git a/ext/patches/boost/asio/detail/reactor_op.hpp b/ext/patches/boost/asio/detail/reactor_op.hpp
new file mode 100644
index 0000000..fab7143
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactor_op.hpp
@@ -0,0 +1,63 @@
+//
+// detail/reactor_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTOR_OP_HPP
+#define BOOST_ASIO_DETAIL_REACTOR_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class reactor_op
+ : public operation
+{
+public:
+ // The error code to be passed to the completion handler.
+ boost::system::error_code ec_;
+
+ // The number of bytes transferred, to be passed to the completion handler.
+ std::size_t bytes_transferred_;
+
+ // Perform the operation. Returns true if it is finished.
+ bool perform()
+ {
+ return perform_func_(this);
+ }
+
+protected:
+ typedef bool (*perform_func_type)(reactor_op*);
+
+ reactor_op(perform_func_type perform_func, func_type complete_func)
+ : operation(complete_func),
+ bytes_transferred_(0),
+ perform_func_(perform_func)
+ {
+ }
+
+private:
+ perform_func_type perform_func_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTOR_OP_HPP
diff --git a/ext/patches/boost/asio/detail/reactor_op_queue.hpp b/ext/patches/boost/asio/detail/reactor_op_queue.hpp
new file mode 100644
index 0000000..f13365b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/reactor_op_queue.hpp
@@ -0,0 +1,170 @@
+//
+// detail/reactor_op_queue.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REACTOR_OP_QUEUE_HPP
+#define BOOST_ASIO_DETAIL_REACTOR_OP_QUEUE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/hash_map.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Descriptor>
+class reactor_op_queue
+ : private noncopyable
+{
+public:
+ typedef Descriptor key_type;
+
+ struct mapped_type : op_queue<reactor_op>
+ {
+ mapped_type() {}
+ mapped_type(const mapped_type&) {}
+ void operator=(const mapped_type&) {}
+ };
+
+ typedef typename hash_map<key_type, mapped_type>::value_type value_type;
+ typedef typename hash_map<key_type, mapped_type>::iterator iterator;
+
+ // Constructor.
+ reactor_op_queue()
+ : operations_()
+ {
+ }
+
+ // Obtain iterators to all registered descriptors.
+ iterator begin() { return operations_.begin(); }
+ iterator end() { return operations_.end(); }
+
+ // Add a new operation to the queue. Returns true if this is the only
+ // operation for the given descriptor, in which case the reactor's event
+ // demultiplexing function call may need to be interrupted and restarted.
+ bool enqueue_operation(Descriptor descriptor, reactor_op* op)
+ {
+ std::pair<iterator, bool> entry =
+ operations_.insert(value_type(descriptor, mapped_type()));
+ entry.first->second.push(op);
+ return entry.second;
+ }
+
+ // Cancel all operations associated with the descriptor identified by the
+ // supplied iterator. Any operations pending for the descriptor will be
+ // cancelled. Returns true if any operations were cancelled, in which case
+ // the reactor's event demultiplexing function may need to be interrupted and
+ // restarted.
+ bool cancel_operations(iterator i, op_queue<operation>& ops,
+ const boost::system::error_code& ec =
+ boost::asio::error::operation_aborted)
+ {
+ if (i != operations_.end())
+ {
+ while (reactor_op* op = i->second.front())
+ {
+ op->ec_ = ec;
+ i->second.pop();
+ ops.push(op);
+ }
+ operations_.erase(i);
+ return true;
+ }
+
+ return false;
+ }
+
+ // Cancel all operations associated with the descriptor. Any operations
+ // pending for the descriptor will be cancelled. Returns true if any
+ // operations were cancelled, in which case the reactor's event
+ // demultiplexing function may need to be interrupted and restarted.
+ bool cancel_operations(Descriptor descriptor, op_queue<operation>& ops,
+ const boost::system::error_code& ec =
+ boost::asio::error::operation_aborted)
+ {
+ return this->cancel_operations(operations_.find(descriptor), ops, ec);
+ }
+
+ // Whether there are no operations in the queue.
+ bool empty() const
+ {
+ return operations_.empty();
+ }
+
+ // Determine whether there are any operations associated with the descriptor.
+ bool has_operation(Descriptor descriptor) const
+ {
+ return operations_.find(descriptor) != operations_.end();
+ }
+
+ // Perform the operations corresponding to the descriptor identified by the
+ // supplied iterator. Returns true if there are still unfinished operations
+ // queued for the descriptor.
+ bool perform_operations(iterator i, op_queue<operation>& ops)
+ {
+ if (i != operations_.end())
+ {
+ while (reactor_op* op = i->second.front())
+ {
+ if (op->perform())
+ {
+ i->second.pop();
+ ops.push(op);
+ }
+ else
+ {
+ return true;
+ }
+ }
+ operations_.erase(i);
+ }
+ return false;
+ }
+
+ // Perform the operations corresponding to the descriptor. Returns true if
+ // there are still unfinished operations queued for the descriptor.
+ bool perform_operations(Descriptor descriptor, op_queue<operation>& ops)
+ {
+ return this->perform_operations(operations_.find(descriptor), ops);
+ }
+
+ // Get all operations owned by the queue.
+ void get_all_operations(op_queue<operation>& ops)
+ {
+ iterator i = operations_.begin();
+ while (i != operations_.end())
+ {
+ iterator op_iter = i++;
+ ops.push(op_iter->second);
+ operations_.erase(op_iter);
+ }
+ }
+
+private:
+ // The operations that are currently executing asynchronously.
+ hash_map<key_type, mapped_type> operations_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_REACTOR_OP_QUEUE_HPP
diff --git a/ext/patches/boost/asio/detail/regex_fwd.hpp b/ext/patches/boost/asio/detail/regex_fwd.hpp
new file mode 100644
index 0000000..a36c727
--- /dev/null
+++ b/ext/patches/boost/asio/detail/regex_fwd.hpp
@@ -0,0 +1,35 @@
+//
+// detail/regex_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_REGEX_FWD_HPP
+#define BOOST_ASIO_DETAIL_REGEX_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#if defined(BOOST_ASIO_HAS_BOOST_REGEX)
+
+#include <boost/regex_fwd.hpp>
+#include <boost/regex/v4/match_flags.hpp>
+
+namespace boost {
+
+template <class BidiIterator>
+struct sub_match;
+
+template <class BidiIterator, class Allocator>
+class match_results;
+
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_REGEX)
+
+#endif // BOOST_ASIO_DETAIL_REGEX_FWD_HPP
diff --git a/ext/patches/boost/asio/detail/resolve_endpoint_op.hpp b/ext/patches/boost/asio/detail/resolve_endpoint_op.hpp
new file mode 100644
index 0000000..f167696
--- /dev/null
+++ b/ext/patches/boost/asio/detail/resolve_endpoint_op.hpp
@@ -0,0 +1,123 @@
+//
+// detail/resolve_endpoint_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_RESOLVER_ENDPOINT_OP_HPP
+#define BOOST_ASIO_DETAIL_RESOLVER_ENDPOINT_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol, typename Handler>
+class resolve_endpoint_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(resolve_endpoint_op);
+
+ typedef typename Protocol::endpoint endpoint_type;
+ typedef boost::asio::ip::basic_resolver_iterator<Protocol> iterator_type;
+
+ resolve_endpoint_op(socket_ops::weak_cancel_token_type cancel_token,
+ const endpoint_type& endpoint, io_service_impl& ios, Handler& handler)
+ : operation(&resolve_endpoint_op::do_complete),
+ cancel_token_(cancel_token),
+ endpoint_(endpoint),
+ io_service_impl_(ios),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the operation object.
+ resolve_endpoint_op* o(static_cast<resolve_endpoint_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ if (owner && owner != &o->io_service_impl_)
+ {
+ // The operation is being run on the worker io_service. Time to perform
+ // the resolver operation.
+
+ // Perform the blocking endpoint resolution operation.
+ char host_name[NI_MAXHOST];
+ char service_name[NI_MAXSERV];
+ socket_ops::background_getnameinfo(o->cancel_token_, o->endpoint_.data(),
+ o->endpoint_.size(), host_name, NI_MAXHOST, service_name, NI_MAXSERV,
+ o->endpoint_.protocol().type(), o->ec_);
+ o->iter_ = iterator_type::create(o->endpoint_, host_name, service_name);
+
+ // Pass operation back to main io_service for completion.
+ o->io_service_impl_.post_deferred_completion(o);
+ p.v = p.p = 0;
+ }
+ else
+ {
+ // The operation has been returned to the main io_service. The completion
+ // handler is ready to be delivered.
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated
+ // before the upcall is made. Even if we're not about to make an upcall,
+ // a sub-object of the handler may be the true owner of the memory
+ // associated with the handler. Consequently, a local copy of the handler
+ // is required to ensure that any owning sub-object remains valid until
+ // after we have deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, iterator_type>
+ handler(o->handler_, o->ec_, o->iter_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, "..."));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+ }
+
+private:
+ socket_ops::weak_cancel_token_type cancel_token_;
+ endpoint_type endpoint_;
+ io_service_impl& io_service_impl_;
+ Handler handler_;
+ boost::system::error_code ec_;
+ iterator_type iter_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_RESOLVER_ENDPOINT_OP_HPP
diff --git a/ext/patches/boost/asio/detail/resolve_op.hpp b/ext/patches/boost/asio/detail/resolve_op.hpp
new file mode 100644
index 0000000..33a897e
--- /dev/null
+++ b/ext/patches/boost/asio/detail/resolve_op.hpp
@@ -0,0 +1,133 @@
+//
+// detail/resolve_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_RESOLVE_OP_HPP
+#define BOOST_ASIO_DETAIL_RESOLVE_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol, typename Handler>
+class resolve_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(resolve_op);
+
+ typedef boost::asio::ip::basic_resolver_query<Protocol> query_type;
+ typedef boost::asio::ip::basic_resolver_iterator<Protocol> iterator_type;
+
+ resolve_op(socket_ops::weak_cancel_token_type cancel_token,
+ const query_type& query, io_service_impl& ios, Handler& handler)
+ : operation(&resolve_op::do_complete),
+ cancel_token_(cancel_token),
+ query_(query),
+ io_service_impl_(ios),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler)),
+ addrinfo_(0)
+ {
+ }
+
+ ~resolve_op()
+ {
+ if (addrinfo_)
+ socket_ops::freeaddrinfo(addrinfo_);
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the operation object.
+ resolve_op* o(static_cast<resolve_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ if (owner && owner != &o->io_service_impl_)
+ {
+ // The operation is being run on the worker io_service. Time to perform
+ // the resolver operation.
+
+ // Perform the blocking host resolution operation.
+ socket_ops::background_getaddrinfo(o->cancel_token_,
+ o->query_.host_name().c_str(), o->query_.service_name().c_str(),
+ o->query_.hints(), &o->addrinfo_, o->ec_);
+
+ // Pass operation back to main io_service for completion.
+ o->io_service_impl_.post_deferred_completion(o);
+ p.v = p.p = 0;
+ }
+ else
+ {
+ // The operation has been returned to the main io_service. The completion
+ // handler is ready to be delivered.
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated
+ // before the upcall is made. Even if we're not about to make an upcall,
+ // a sub-object of the handler may be the true owner of the memory
+ // associated with the handler. Consequently, a local copy of the handler
+ // is required to ensure that any owning sub-object remains valid until
+ // after we have deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, iterator_type>
+ handler(o->handler_, o->ec_, iterator_type());
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ if (o->addrinfo_)
+ {
+ handler.arg2_ = iterator_type::create(o->addrinfo_,
+ o->query_.host_name(), o->query_.service_name());
+ }
+ p.reset();
+
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, "..."));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+ }
+
+private:
+ socket_ops::weak_cancel_token_type cancel_token_;
+ query_type query_;
+ io_service_impl& io_service_impl_;
+ Handler handler_;
+ boost::system::error_code ec_;
+ boost::asio::detail::addrinfo_type* addrinfo_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_RESOLVE_OP_HPP
diff --git a/ext/patches/boost/asio/detail/resolver_service.hpp b/ext/patches/boost/asio/detail/resolver_service.hpp
new file mode 100644
index 0000000..8e33d31
--- /dev/null
+++ b/ext/patches/boost/asio/detail/resolver_service.hpp
@@ -0,0 +1,131 @@
+//
+// detail/resolver_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_RESOLVER_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_RESOLVER_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/resolve_endpoint_op.hpp>
+#include <boost/asio/detail/resolve_op.hpp>
+#include <boost/asio/detail/resolver_service_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol>
+class resolver_service : public resolver_service_base
+{
+public:
+ // The implementation type of the resolver. A cancellation token is used to
+ // indicate to the background thread that the operation has been cancelled.
+ typedef socket_ops::shared_cancel_token_type implementation_type;
+
+ // The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ // The query type.
+ typedef boost::asio::ip::basic_resolver_query<Protocol> query_type;
+
+ // The iterator type.
+ typedef boost::asio::ip::basic_resolver_iterator<Protocol> iterator_type;
+
+ // Constructor.
+ resolver_service(boost::asio::io_service& io_service)
+ : resolver_service_base(io_service)
+ {
+ }
+
+ // Resolve a query to a list of entries.
+ iterator_type resolve(implementation_type&, const query_type& query,
+ boost::system::error_code& ec)
+ {
+ boost::asio::detail::addrinfo_type* address_info = 0;
+
+ socket_ops::getaddrinfo(query.host_name().c_str(),
+ query.service_name().c_str(), query.hints(), &address_info, ec);
+ auto_addrinfo auto_address_info(address_info);
+
+ return ec ? iterator_type() : iterator_type::create(
+ address_info, query.host_name(), query.service_name());
+ }
+
+ // Asynchronously resolve a query to a list of entries.
+ template <typename Handler>
+ void async_resolve(implementation_type& impl,
+ const query_type& query, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef resolve_op<Protocol, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl, query, io_service_impl_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "resolver", &impl, "async_resolve"));
+
+ start_resolve_op(p.p);
+ p.v = p.p = 0;
+ }
+
+ // Resolve an endpoint to a list of entries.
+ iterator_type resolve(implementation_type&,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ char host_name[NI_MAXHOST];
+ char service_name[NI_MAXSERV];
+ socket_ops::sync_getnameinfo(endpoint.data(), endpoint.size(),
+ host_name, NI_MAXHOST, service_name, NI_MAXSERV,
+ endpoint.protocol().type(), ec);
+
+ return ec ? iterator_type() : iterator_type::create(
+ endpoint, host_name, service_name);
+ }
+
+ // Asynchronously resolve an endpoint to a list of entries.
+ template <typename Handler>
+ void async_resolve(implementation_type& impl,
+ const endpoint_type& endpoint, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef resolve_endpoint_op<Protocol, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl, endpoint, io_service_impl_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "resolver", &impl, "async_resolve"));
+
+ start_resolve_op(p.p);
+ p.v = p.p = 0;
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_RESOLVER_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/resolver_service_base.hpp b/ext/patches/boost/asio/detail/resolver_service_base.hpp
new file mode 100644
index 0000000..9e4d458
--- /dev/null
+++ b/ext/patches/boost/asio/detail/resolver_service_base.hpp
@@ -0,0 +1,131 @@
+//
+// detail/resolver_service_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_RESOLVER_SERVICE_BASE_HPP
+#define BOOST_ASIO_DETAIL_RESOLVER_SERVICE_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/scoped_ptr.hpp>
+#include <boost/asio/detail/thread.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class resolver_service_base
+{
+public:
+ // The implementation type of the resolver. A cancellation token is used to
+ // indicate to the background thread that the operation has been cancelled.
+ typedef socket_ops::shared_cancel_token_type implementation_type;
+
+ // Constructor.
+ BOOST_ASIO_DECL resolver_service_base(boost::asio::io_service& io_service);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~resolver_service_base();
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Perform any fork-related housekeeping.
+ BOOST_ASIO_DECL void fork_service(
+ boost::asio::io_service::fork_event fork_ev);
+
+ // Construct a new resolver implementation.
+ BOOST_ASIO_DECL void construct(implementation_type& impl);
+
+ // Destroy a resolver implementation.
+ BOOST_ASIO_DECL void destroy(implementation_type&);
+
+ // Cancel pending asynchronous operations.
+ BOOST_ASIO_DECL void cancel(implementation_type& impl);
+
+protected:
+ // Helper function to start an asynchronous resolve operation.
+ BOOST_ASIO_DECL void start_resolve_op(operation* op);
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // Helper class to perform exception-safe cleanup of addrinfo objects.
+ class auto_addrinfo
+ : private boost::asio::detail::noncopyable
+ {
+ public:
+ explicit auto_addrinfo(boost::asio::detail::addrinfo_type* ai)
+ : ai_(ai)
+ {
+ }
+
+ ~auto_addrinfo()
+ {
+ if (ai_)
+ socket_ops::freeaddrinfo(ai_);
+ }
+
+ operator boost::asio::detail::addrinfo_type*()
+ {
+ return ai_;
+ }
+
+ private:
+ boost::asio::detail::addrinfo_type* ai_;
+ };
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+ // Helper class to run the work io_service in a thread.
+ class work_io_service_runner;
+
+ // Start the work thread if it's not already running.
+ BOOST_ASIO_DECL void start_work_thread();
+
+ // The io_service implementation used to post completions.
+ io_service_impl& io_service_impl_;
+
+private:
+ // Mutex to protect access to internal data.
+ boost::asio::detail::mutex mutex_;
+
+ // Private io_service used for performing asynchronous host resolution.
+ boost::asio::detail::scoped_ptr<boost::asio::io_service> work_io_service_;
+
+ // The work io_service implementation used to post completions.
+ io_service_impl& work_io_service_impl_;
+
+ // Work for the private io_service to perform.
+ boost::asio::detail::scoped_ptr<boost::asio::io_service::work> work_;
+
+ // Thread used for running the work io_service's run loop.
+ boost::asio::detail::scoped_ptr<boost::asio::detail::thread> work_thread_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/resolver_service_base.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_RESOLVER_SERVICE_BASE_HPP
diff --git a/ext/patches/boost/asio/detail/scoped_lock.hpp b/ext/patches/boost/asio/detail/scoped_lock.hpp
new file mode 100644
index 0000000..1f1a72c
--- /dev/null
+++ b/ext/patches/boost/asio/detail/scoped_lock.hpp
@@ -0,0 +1,103 @@
+//
+// detail/scoped_lock.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SCOPED_LOCK_HPP
+#define BOOST_ASIO_DETAIL_SCOPED_LOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Helper class to lock and unlock a mutex automatically.
+template <typename Mutex>
+class scoped_lock
+ : private noncopyable
+{
+public:
+ // Tag type used to distinguish constructors.
+ enum adopt_lock_t { adopt_lock };
+
+ // Constructor adopts a lock that is already held.
+ scoped_lock(Mutex& m, adopt_lock_t)
+ : mutex_(m),
+ locked_(true)
+ {
+ }
+
+ // Constructor acquires the lock.
+ explicit scoped_lock(Mutex& m)
+ : mutex_(m)
+ {
+ mutex_.lock();
+ locked_ = true;
+ }
+
+ // Destructor releases the lock.
+ ~scoped_lock()
+ {
+ if (locked_)
+ mutex_.unlock();
+ }
+
+ // Explicitly acquire the lock.
+ void lock()
+ {
+ if (!locked_)
+ {
+ mutex_.lock();
+ locked_ = true;
+ }
+ }
+
+ // Explicitly release the lock.
+ void unlock()
+ {
+ if (locked_)
+ {
+ mutex_.unlock();
+ locked_ = false;
+ }
+ }
+
+ // Test whether the lock is held.
+ bool locked() const
+ {
+ return locked_;
+ }
+
+ // Get the underlying mutex.
+ Mutex& mutex()
+ {
+ return mutex_;
+ }
+
+private:
+ // The underlying mutex.
+ Mutex& mutex_;
+
+ // Whether the mutex is currently locked or unlocked.
+ bool locked_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_SCOPED_LOCK_HPP
diff --git a/ext/patches/boost/asio/detail/scoped_ptr.hpp b/ext/patches/boost/asio/detail/scoped_ptr.hpp
new file mode 100644
index 0000000..73ebcf7
--- /dev/null
+++ b/ext/patches/boost/asio/detail/scoped_ptr.hpp
@@ -0,0 +1,81 @@
+//
+// detail/scoped_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SCOPED_PTR_HPP
+#define BOOST_ASIO_DETAIL_SCOPED_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename T>
+class scoped_ptr
+{
+public:
+ // Constructor.
+ explicit scoped_ptr(T* p = 0)
+ : p_(p)
+ {
+ }
+
+ // Destructor.
+ ~scoped_ptr()
+ {
+ delete p_;
+ }
+
+ // Access.
+ T* get()
+ {
+ return p_;
+ }
+
+ // Access.
+ T* operator->()
+ {
+ return p_;
+ }
+
+ // Dereference.
+ T& operator*()
+ {
+ return *p_;
+ }
+
+ // Reset pointer.
+ void reset(T* p = 0)
+ {
+ delete p_;
+ p_ = p;
+ }
+
+private:
+ // Disallow copying and assignment.
+ scoped_ptr(const scoped_ptr&);
+ scoped_ptr& operator=(const scoped_ptr&);
+
+ T* p_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_SCOPED_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/select_interrupter.hpp b/ext/patches/boost/asio/detail/select_interrupter.hpp
new file mode 100644
index 0000000..869fd65
--- /dev/null
+++ b/ext/patches/boost/asio/detail/select_interrupter.hpp
@@ -0,0 +1,48 @@
+//
+// detail/select_interrupter.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SELECT_INTERRUPTER_HPP
+#define BOOST_ASIO_DETAIL_SELECT_INTERRUPTER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__) || defined(__SYMBIAN32__)
+# include <boost/asio/detail/socket_select_interrupter.hpp>
+#elif defined(BOOST_ASIO_HAS_EVENTFD)
+# include <boost/asio/detail/eventfd_select_interrupter.hpp>
+#else
+# include <boost/asio/detail/pipe_select_interrupter.hpp>
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__) || defined(__SYMBIAN32__)
+typedef socket_select_interrupter select_interrupter;
+#elif defined(BOOST_ASIO_HAS_EVENTFD)
+typedef eventfd_select_interrupter select_interrupter;
+#else
+typedef pipe_select_interrupter select_interrupter;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_SELECT_INTERRUPTER_HPP
diff --git a/ext/patches/boost/asio/detail/select_reactor.hpp b/ext/patches/boost/asio/detail/select_reactor.hpp
new file mode 100644
index 0000000..3d9aab2
--- /dev/null
+++ b/ext/patches/boost/asio/detail/select_reactor.hpp
@@ -0,0 +1,221 @@
+//
+// detail/select_reactor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SELECT_REACTOR_HPP
+#define BOOST_ASIO_DETAIL_SELECT_REACTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP) \
+ || (!defined(BOOST_ASIO_HAS_DEV_POLL) \
+ && !defined(BOOST_ASIO_HAS_EPOLL) \
+ && !defined(BOOST_ASIO_HAS_KQUEUE) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME))
+
+#include <cstddef>
+#include <boost/asio/detail/fd_set_adapter.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/reactor_op_queue.hpp>
+#include <boost/asio/detail/select_interrupter.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/timer_queue_base.hpp>
+#include <boost/asio/detail/timer_queue_set.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+#include <boost/asio/io_service.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/thread.hpp>
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class select_reactor
+ : public boost::asio::detail::service_base<select_reactor>
+{
+public:
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ enum op_types { read_op = 0, write_op = 1, except_op = 2,
+ max_select_ops = 3, connect_op = 3, max_ops = 4 };
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ enum op_types { read_op = 0, write_op = 1, except_op = 2,
+ max_select_ops = 3, connect_op = 1, max_ops = 3 };
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+ // Per-descriptor data.
+ struct per_descriptor_data
+ {
+ };
+
+ // Constructor.
+ BOOST_ASIO_DECL select_reactor(boost::asio::io_service& io_service);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~select_reactor();
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Recreate internal descriptors following a fork.
+ BOOST_ASIO_DECL void fork_service(
+ boost::asio::io_service::fork_event fork_ev);
+
+ // Initialise the task, but only if the reactor is not in its own thread.
+ BOOST_ASIO_DECL void init_task();
+
+ // Register a socket with the reactor. Returns 0 on success, system error
+ // code on failure.
+ BOOST_ASIO_DECL int register_descriptor(socket_type, per_descriptor_data&);
+
+ // Register a descriptor with an associated single operation. Returns 0 on
+ // success, system error code on failure.
+ BOOST_ASIO_DECL int register_internal_descriptor(
+ int op_type, socket_type descriptor,
+ per_descriptor_data& descriptor_data, reactor_op* op);
+
+ // Post a reactor operation for immediate completion.
+ void post_immediate_completion(reactor_op* op, bool is_continuation)
+ {
+ io_service_.post_immediate_completion(op, is_continuation);
+ }
+
+ // Start a new operation. The reactor operation will be performed when the
+ // given descriptor is flagged as ready, or an error has occurred.
+ BOOST_ASIO_DECL void start_op(int op_type, socket_type descriptor,
+ per_descriptor_data&, reactor_op* op, bool is_continuation, bool);
+
+ // Cancel all operations associated with the given descriptor. The
+ // handlers associated with the descriptor will be invoked with the
+ // operation_aborted error.
+ BOOST_ASIO_DECL void cancel_ops(socket_type descriptor, per_descriptor_data&);
+
+ // Cancel any operations that are running against the descriptor and remove
+ // its registration from the reactor.
+ BOOST_ASIO_DECL void deregister_descriptor(socket_type descriptor,
+ per_descriptor_data&, bool closing);
+
+ // Remote the descriptor's registration from the reactor.
+ BOOST_ASIO_DECL void deregister_internal_descriptor(
+ socket_type descriptor, per_descriptor_data& descriptor_data);
+
+ // Move descriptor registration from one descriptor_data object to another.
+ BOOST_ASIO_DECL void move_descriptor(socket_type descriptor,
+ per_descriptor_data& target_descriptor_data,
+ per_descriptor_data& source_descriptor_data);
+
+ // Add a new timer queue to the reactor.
+ template <typename Time_Traits>
+ void add_timer_queue(timer_queue<Time_Traits>& queue);
+
+ // Remove a timer queue from the reactor.
+ template <typename Time_Traits>
+ void remove_timer_queue(timer_queue<Time_Traits>& queue);
+
+ // Schedule a new operation in the given timer queue to expire at the
+ // specified absolute time.
+ template <typename Time_Traits>
+ void schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op);
+
+ // Cancel the timer operations associated with the given token. Returns the
+ // number of operations that have been posted or dispatched.
+ template <typename Time_Traits>
+ std::size_t cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled = (std::numeric_limits<std::size_t>::max)());
+
+ // Run select once until interrupted or events are ready to be dispatched.
+ BOOST_ASIO_DECL void run(bool block, op_queue<operation>& ops);
+
+ // Interrupt the select loop.
+ BOOST_ASIO_DECL void interrupt();
+
+private:
+#if defined(BOOST_ASIO_HAS_IOCP)
+ // Run the select loop in the thread.
+ BOOST_ASIO_DECL void run_thread();
+
+ // Entry point for the select loop thread.
+ BOOST_ASIO_DECL static void call_run_thread(select_reactor* reactor);
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+ // Helper function to add a new timer queue.
+ BOOST_ASIO_DECL void do_add_timer_queue(timer_queue_base& queue);
+
+ // Helper function to remove a timer queue.
+ BOOST_ASIO_DECL void do_remove_timer_queue(timer_queue_base& queue);
+
+ // Get the timeout value for the select call.
+ BOOST_ASIO_DECL timeval* get_timeout(timeval& tv);
+
+ // Cancel all operations associated with the given descriptor. This function
+ // does not acquire the select_reactor's mutex.
+ BOOST_ASIO_DECL void cancel_ops_unlocked(socket_type descriptor,
+ const boost::system::error_code& ec);
+
+ // The io_service implementation used to post completions.
+ io_service_impl& io_service_;
+
+ // Mutex to protect access to internal data.
+ boost::asio::detail::mutex mutex_;
+
+ // The interrupter is used to break a blocking select call.
+ select_interrupter interrupter_;
+
+ // The queues of read, write and except operations.
+ reactor_op_queue<socket_type> op_queue_[max_ops];
+
+ // The file descriptor sets to be passed to the select system call.
+ fd_set_adapter fd_sets_[max_select_ops];
+
+ // The timer queues.
+ timer_queue_set timer_queues_;
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+ // Does the reactor loop thread need to stop.
+ bool stop_thread_;
+
+ // The thread that is running the reactor loop.
+ boost::asio::detail::thread* thread_;
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+ // Whether the service has been shut down.
+ bool shutdown_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/select_reactor.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/select_reactor.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+ // || (!defined(BOOST_ASIO_HAS_DEV_POLL)
+ // && !defined(BOOST_ASIO_HAS_EPOLL)
+ // && !defined(BOOST_ASIO_HAS_KQUEUE)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME))
+
+#endif // BOOST_ASIO_DETAIL_SELECT_REACTOR_HPP
diff --git a/ext/patches/boost/asio/detail/service_registry.hpp b/ext/patches/boost/asio/detail/service_registry.hpp
new file mode 100644
index 0000000..2a3fda5
--- /dev/null
+++ b/ext/patches/boost/asio/detail/service_registry.hpp
@@ -0,0 +1,158 @@
+//
+// detail/service_registry.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SERVICE_REGISTRY_HPP
+#define BOOST_ASIO_DETAIL_SERVICE_REGISTRY_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <typeinfo>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(__GNUC__)
+# if (__GNUC__ == 4 && __GNUC_MINOR__ >= 1) || (__GNUC__ > 4)
+# pragma GCC visibility push (default)
+# endif // (__GNUC__ == 4 && __GNUC_MINOR__ >= 1) || (__GNUC__ > 4)
+#endif // defined(__GNUC__)
+
+template <typename T>
+class typeid_wrapper {};
+
+#if defined(__GNUC__)
+# if (__GNUC__ == 4 && __GNUC_MINOR__ >= 1) || (__GNUC__ > 4)
+# pragma GCC visibility pop
+# endif // (__GNUC__ == 4 && __GNUC_MINOR__ >= 1) || (__GNUC__ > 4)
+#endif // defined(__GNUC__)
+
+class service_registry
+ : private noncopyable
+{
+public:
+ // Constructor. Adds the initial service.
+ template <typename Service, typename Arg>
+ service_registry(boost::asio::io_service& o,
+ Service* initial_service, Arg arg);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~service_registry();
+
+ // Notify all services of a fork event.
+ BOOST_ASIO_DECL void notify_fork(boost::asio::io_service::fork_event fork_ev);
+
+ // Get the first service object cast to the specified type. Called during
+ // io_service construction and so performs no locking or type checking.
+ template <typename Service>
+ Service& first_service();
+
+ // Get the service object corresponding to the specified service type. Will
+ // create a new service object automatically if no such object already
+ // exists. Ownership of the service object is not transferred to the caller.
+ template <typename Service>
+ Service& use_service();
+
+ // Add a service object. Throws on error, in which case ownership of the
+ // object is retained by the caller.
+ template <typename Service>
+ void add_service(Service* new_service);
+
+ // Check whether a service object of the specified type already exists.
+ template <typename Service>
+ bool has_service() const;
+
+private:
+ // Initialise a service's key based on its id.
+ BOOST_ASIO_DECL static void init_key(
+ boost::asio::io_service::service::key& key,
+ const boost::asio::io_service::id& id);
+
+#if !defined(BOOST_ASIO_NO_TYPEID)
+ // Initialise a service's key based on its id.
+ template <typename Service>
+ static void init_key(boost::asio::io_service::service::key& key,
+ const boost::asio::detail::service_id<Service>& /*id*/);
+#endif // !defined(BOOST_ASIO_NO_TYPEID)
+
+ // Check if a service matches the given id.
+ BOOST_ASIO_DECL static bool keys_match(
+ const boost::asio::io_service::service::key& key1,
+ const boost::asio::io_service::service::key& key2);
+
+ // The type of a factory function used for creating a service instance.
+ typedef boost::asio::io_service::service*
+ (*factory_type)(boost::asio::io_service&);
+
+ // Factory function for creating a service instance.
+ template <typename Service>
+ static boost::asio::io_service::service* create(
+ boost::asio::io_service& owner);
+
+ // Destroy a service instance.
+ BOOST_ASIO_DECL static void destroy(
+ boost::asio::io_service::service* service);
+
+ // Helper class to manage service pointers.
+ struct auto_service_ptr;
+ friend struct auto_service_ptr;
+ struct auto_service_ptr
+ {
+ boost::asio::io_service::service* ptr_;
+ ~auto_service_ptr() { destroy(ptr_); }
+ };
+
+ // Get the service object corresponding to the specified service key. Will
+ // create a new service object automatically if no such object already
+ // exists. Ownership of the service object is not transferred to the caller.
+ BOOST_ASIO_DECL boost::asio::io_service::service* do_use_service(
+ const boost::asio::io_service::service::key& key,
+ factory_type factory);
+
+ // Add a service object. Throws on error, in which case ownership of the
+ // object is retained by the caller.
+ BOOST_ASIO_DECL void do_add_service(
+ const boost::asio::io_service::service::key& key,
+ boost::asio::io_service::service* new_service);
+
+ // Check whether a service object with the specified key already exists.
+ BOOST_ASIO_DECL bool do_has_service(
+ const boost::asio::io_service::service::key& key) const;
+
+ // Mutex to protect access to internal data.
+ mutable boost::asio::detail::mutex mutex_;
+
+ // The owner of this service registry and the services it contains.
+ boost::asio::io_service& owner_;
+
+ // The first service in the list of contained services.
+ boost::asio::io_service::service* first_service_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/service_registry.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/service_registry.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_SERVICE_REGISTRY_HPP
diff --git a/ext/patches/boost/asio/detail/shared_ptr.hpp b/ext/patches/boost/asio/detail/shared_ptr.hpp
new file mode 100644
index 0000000..c1182fd
--- /dev/null
+++ b/ext/patches/boost/asio/detail/shared_ptr.hpp
@@ -0,0 +1,40 @@
+//
+// detail/shared_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SHARED_PTR_HPP
+#define BOOST_ASIO_DETAIL_SHARED_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+# include <memory>
+#else // defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+# include <boost/shared_ptr.hpp>
+#endif // defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+using std::shared_ptr;
+#else // defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+using boost::shared_ptr;
+#endif // defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_SHARED_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/signal_blocker.hpp b/ext/patches/boost/asio/detail/signal_blocker.hpp
new file mode 100644
index 0000000..4b883b0
--- /dev/null
+++ b/ext/patches/boost/asio/detail/signal_blocker.hpp
@@ -0,0 +1,46 @@
+//
+// detail/signal_blocker.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SIGNAL_BLOCKER_HPP
+#define BOOST_ASIO_DETAIL_SIGNAL_BLOCKER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS) || defined(BOOST_ASIO_WINDOWS) \
+ || defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ || defined(__CYGWIN__) || defined(__SYMBIAN32__)
+# include <boost/asio/detail/null_signal_blocker.hpp>
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+# include <boost/asio/detail/posix_signal_blocker.hpp>
+#else
+# error Only Windows and POSIX are supported!
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if !defined(BOOST_ASIO_HAS_THREADS) || defined(BOOST_ASIO_WINDOWS) \
+ || defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ || defined(__CYGWIN__) || defined(__SYMBIAN32__)
+typedef null_signal_blocker signal_blocker;
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+typedef posix_signal_blocker signal_blocker;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_SIGNAL_BLOCKER_HPP
diff --git a/ext/patches/boost/asio/detail/signal_handler.hpp b/ext/patches/boost/asio/detail/signal_handler.hpp
new file mode 100644
index 0000000..2fdf08c
--- /dev/null
+++ b/ext/patches/boost/asio/detail/signal_handler.hpp
@@ -0,0 +1,84 @@
+//
+// detail/signal_handler.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SIGNAL_HANDLER_HPP
+#define BOOST_ASIO_DETAIL_SIGNAL_HANDLER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/signal_op.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+class signal_handler : public signal_op
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(signal_handler);
+
+ signal_handler(Handler& h)
+ : signal_op(&signal_handler::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(h))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ signal_handler* h(static_cast<signal_handler*>(base));
+ ptr p = { boost::asio::detail::addressof(h->handler_), h, h };
+
+ BOOST_ASIO_HANDLER_COMPLETION((h));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, int>
+ handler(h->handler_, h->ec_, h->signal_number_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_SIGNAL_HANDLER_HPP
diff --git a/ext/patches/boost/asio/detail/signal_init.hpp b/ext/patches/boost/asio/detail/signal_init.hpp
new file mode 100644
index 0000000..461c83c
--- /dev/null
+++ b/ext/patches/boost/asio/detail/signal_init.hpp
@@ -0,0 +1,49 @@
+//
+// detail/signal_init.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SIGNAL_INIT_HPP
+#define BOOST_ASIO_DETAIL_SIGNAL_INIT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#include <csignal>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <int Signal = SIGPIPE>
+class signal_init
+{
+public:
+ // Constructor.
+ signal_init()
+ {
+ std::signal(Signal, SIG_IGN);
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_SIGNAL_INIT_HPP
diff --git a/ext/patches/boost/asio/detail/signal_op.hpp b/ext/patches/boost/asio/detail/signal_op.hpp
new file mode 100644
index 0000000..730b629
--- /dev/null
+++ b/ext/patches/boost/asio/detail/signal_op.hpp
@@ -0,0 +1,51 @@
+//
+// detail/signal_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SIGNAL_OP_HPP
+#define BOOST_ASIO_DETAIL_SIGNAL_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class signal_op
+ : public operation
+{
+public:
+ // The error code to be passed to the completion handler.
+ boost::system::error_code ec_;
+
+ // The signal number to be passed to the completion handler.
+ int signal_number_;
+
+protected:
+ signal_op(func_type func)
+ : operation(func),
+ signal_number_(0)
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_SIGNAL_OP_HPP
diff --git a/ext/patches/boost/asio/detail/signal_set_service.hpp b/ext/patches/boost/asio/detail/signal_set_service.hpp
new file mode 100644
index 0000000..05271f1
--- /dev/null
+++ b/ext/patches/boost/asio/detail/signal_set_service.hpp
@@ -0,0 +1,218 @@
+//
+// detail/signal_set_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SIGNAL_SET_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_SIGNAL_SET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <cstddef>
+#include <signal.h>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/signal_handler.hpp>
+#include <boost/asio/detail/signal_op.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+# include <boost/asio/detail/reactor.hpp>
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(NSIG) && (NSIG > 0)
+enum { max_signal_number = NSIG };
+#else
+enum { max_signal_number = 128 };
+#endif
+
+extern BOOST_ASIO_DECL struct signal_state* get_signal_state();
+
+extern "C" BOOST_ASIO_DECL void boost_asio_signal_handler(int signal_number);
+
+class signal_set_service
+{
+public:
+ // Type used for tracking an individual signal registration.
+ class registration
+ {
+ public:
+ // Default constructor.
+ registration()
+ : signal_number_(0),
+ queue_(0),
+ undelivered_(0),
+ next_in_table_(0),
+ prev_in_table_(0),
+ next_in_set_(0)
+ {
+ }
+
+ private:
+ // Only this service will have access to the internal values.
+ friend class signal_set_service;
+
+ // The signal number that is registered.
+ int signal_number_;
+
+ // The waiting signal handlers.
+ op_queue<signal_op>* queue_;
+
+ // The number of undelivered signals.
+ std::size_t undelivered_;
+
+ // Pointers to adjacent registrations in the registrations_ table.
+ registration* next_in_table_;
+ registration* prev_in_table_;
+
+ // Link to next registration in the signal set.
+ registration* next_in_set_;
+ };
+
+ // The implementation type of the signal_set.
+ class implementation_type
+ {
+ public:
+ // Default constructor.
+ implementation_type()
+ : signals_(0)
+ {
+ }
+
+ private:
+ // Only this service will have access to the internal values.
+ friend class signal_set_service;
+
+ // The pending signal handlers.
+ op_queue<signal_op> queue_;
+
+ // Linked list of registered signals.
+ registration* signals_;
+ };
+
+ // Constructor.
+ BOOST_ASIO_DECL signal_set_service(boost::asio::io_service& io_service);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~signal_set_service();
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Perform fork-related housekeeping.
+ BOOST_ASIO_DECL void fork_service(
+ boost::asio::io_service::fork_event fork_ev);
+
+ // Construct a new signal_set implementation.
+ BOOST_ASIO_DECL void construct(implementation_type& impl);
+
+ // Destroy a signal_set implementation.
+ BOOST_ASIO_DECL void destroy(implementation_type& impl);
+
+ // Add a signal to a signal_set.
+ BOOST_ASIO_DECL boost::system::error_code add(implementation_type& impl,
+ int signal_number, boost::system::error_code& ec);
+
+ // Remove a signal to a signal_set.
+ BOOST_ASIO_DECL boost::system::error_code remove(implementation_type& impl,
+ int signal_number, boost::system::error_code& ec);
+
+ // Remove all signals from a signal_set.
+ BOOST_ASIO_DECL boost::system::error_code clear(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ // Cancel all operations associated with the signal set.
+ BOOST_ASIO_DECL boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ // Start an asynchronous operation to wait for a signal to be delivered.
+ template <typename Handler>
+ void async_wait(implementation_type& impl, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef signal_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "signal_set", &impl, "async_wait"));
+
+ start_wait_op(impl, p.p);
+ p.v = p.p = 0;
+ }
+
+ // Deliver notification that a particular signal occurred.
+ BOOST_ASIO_DECL static void deliver_signal(int signal_number);
+
+private:
+ // Helper function to add a service to the global signal state.
+ BOOST_ASIO_DECL static void add_service(signal_set_service* service);
+
+ // Helper function to remove a service from the global signal state.
+ BOOST_ASIO_DECL static void remove_service(signal_set_service* service);
+
+ // Helper function to create the pipe descriptors.
+ BOOST_ASIO_DECL static void open_descriptors();
+
+ // Helper function to close the pipe descriptors.
+ BOOST_ASIO_DECL static void close_descriptors();
+
+ // Helper function to start a wait operation.
+ BOOST_ASIO_DECL void start_wait_op(implementation_type& impl, signal_op* op);
+
+ // The io_service instance used for dispatching handlers.
+ io_service_impl& io_service_;
+
+#if !defined(BOOST_ASIO_WINDOWS) \
+ && !defined(BOOST_ASIO_WINDOWS_RUNTIME) \
+ && !defined(__CYGWIN__)
+ // The type used for registering for pipe reactor notifications.
+ class pipe_read_op;
+
+ // The reactor used for waiting for pipe readiness.
+ reactor& reactor_;
+
+ // The per-descriptor reactor data used for the pipe.
+ reactor::per_descriptor_data reactor_data_;
+#endif // !defined(BOOST_ASIO_WINDOWS)
+ // && !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ // && !defined(__CYGWIN__)
+
+ // A mapping from signal number to the registered signal sets.
+ registration* registrations_[max_signal_number];
+
+ // Pointers to adjacent services in linked list.
+ signal_set_service* next_;
+ signal_set_service* prev_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/signal_set_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_SIGNAL_SET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/socket_holder.hpp b/ext/patches/boost/asio/detail/socket_holder.hpp
new file mode 100644
index 0000000..49183b0
--- /dev/null
+++ b/ext/patches/boost/asio/detail/socket_holder.hpp
@@ -0,0 +1,100 @@
+//
+// detail/socket_holder.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SOCKET_HOLDER_HPP
+#define BOOST_ASIO_DETAIL_SOCKET_HOLDER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Implement the resource acquisition is initialisation idiom for sockets.
+class socket_holder
+ : private noncopyable
+{
+public:
+ // Construct as an uninitialised socket.
+ socket_holder()
+ : socket_(invalid_socket)
+ {
+ }
+
+ // Construct to take ownership of the specified socket.
+ explicit socket_holder(socket_type s)
+ : socket_(s)
+ {
+ }
+
+ // Destructor.
+ ~socket_holder()
+ {
+ if (socket_ != invalid_socket)
+ {
+ boost::system::error_code ec;
+ socket_ops::state_type state = 0;
+ socket_ops::close(socket_, state, true, ec);
+ }
+ }
+
+ // Get the underlying socket.
+ socket_type get() const
+ {
+ return socket_;
+ }
+
+ // Reset to an uninitialised socket.
+ void reset()
+ {
+ if (socket_ != invalid_socket)
+ {
+ boost::system::error_code ec;
+ socket_ops::state_type state = 0;
+ socket_ops::close(socket_, state, true, ec);
+ socket_ = invalid_socket;
+ }
+ }
+
+ // Reset to take ownership of the specified socket.
+ void reset(socket_type s)
+ {
+ reset();
+ socket_ = s;
+ }
+
+ // Release ownership of the socket.
+ socket_type release()
+ {
+ socket_type tmp = socket_;
+ socket_ = invalid_socket;
+ return tmp;
+ }
+
+private:
+ // The underlying socket.
+ socket_type socket_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_SOCKET_HOLDER_HPP
diff --git a/ext/patches/boost/asio/detail/socket_ops.hpp b/ext/patches/boost/asio/detail/socket_ops.hpp
new file mode 100644
index 0000000..b66f768
--- /dev/null
+++ b/ext/patches/boost/asio/detail/socket_ops.hpp
@@ -0,0 +1,336 @@
+//
+// detail/socket_ops.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SOCKET_OPS_HPP
+#define BOOST_ASIO_DETAIL_SOCKET_OPS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/system/error_code.hpp>
+#include <boost/asio/detail/shared_ptr.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/weak_ptr.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+namespace socket_ops {
+
+// Socket state bits.
+enum
+{
+ // The user wants a non-blocking socket.
+ user_set_non_blocking = 1,
+
+ // The socket has been set non-blocking.
+ internal_non_blocking = 2,
+
+ // Helper "state" used to determine whether the socket is non-blocking.
+ non_blocking = user_set_non_blocking | internal_non_blocking,
+
+ // User wants connection_aborted errors, which are disabled by default.
+ enable_connection_aborted = 4,
+
+ // The user set the linger option. Needs to be checked when closing.
+ user_set_linger = 8,
+
+ // The socket is stream-oriented.
+ stream_oriented = 16,
+
+ // The socket is datagram-oriented.
+ datagram_oriented = 32,
+
+ // The socket may have been dup()-ed.
+ possible_dup = 64
+};
+
+typedef unsigned char state_type;
+
+struct noop_deleter { void operator()(void*) {} };
+typedef shared_ptr<void> shared_cancel_token_type;
+typedef weak_ptr<void> weak_cancel_token_type;
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+BOOST_ASIO_DECL socket_type accept(socket_type s, socket_addr_type* addr,
+ std::size_t* addrlen, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL socket_type sync_accept(socket_type s,
+ state_type state, socket_addr_type* addr,
+ std::size_t* addrlen, boost::system::error_code& ec);
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL void complete_iocp_accept(socket_type s,
+ void* output_buffer, DWORD address_length,
+ socket_addr_type* addr, std::size_t* addrlen,
+ socket_type new_socket, boost::system::error_code& ec);
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL bool non_blocking_accept(socket_type s,
+ state_type state, socket_addr_type* addr, std::size_t* addrlen,
+ boost::system::error_code& ec, socket_type& new_socket);
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL int bind(socket_type s, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int close(socket_type s, state_type& state,
+ bool destruction, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL bool set_user_non_blocking(socket_type s,
+ state_type& state, bool value, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL bool set_internal_non_blocking(socket_type s,
+ state_type& state, bool value, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int shutdown(socket_type s,
+ int what, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int connect(socket_type s, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL void sync_connect(socket_type s, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec);
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL void complete_iocp_connect(socket_type s,
+ boost::system::error_code& ec);
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL bool non_blocking_connect(socket_type s,
+ boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int socketpair(int af, int type, int protocol,
+ socket_type sv[2], boost::system::error_code& ec);
+
+BOOST_ASIO_DECL bool sockatmark(socket_type s, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL size_t available(socket_type s, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int listen(socket_type s,
+ int backlog, boost::system::error_code& ec);
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+typedef WSABUF buf;
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+typedef iovec buf;
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+BOOST_ASIO_DECL void init_buf(buf& b, void* data, size_t size);
+
+BOOST_ASIO_DECL void init_buf(buf& b, const void* data, size_t size);
+
+BOOST_ASIO_DECL signed_size_type recv(socket_type s, buf* bufs,
+ size_t count, int flags, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL size_t sync_recv(socket_type s, state_type state, buf* bufs,
+ size_t count, int flags, bool all_empty, boost::system::error_code& ec);
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL void complete_iocp_recv(state_type state,
+ const weak_cancel_token_type& cancel_token, bool all_empty,
+ boost::system::error_code& ec, size_t bytes_transferred);
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL bool non_blocking_recv(socket_type s,
+ buf* bufs, size_t count, int flags, bool is_stream,
+ boost::system::error_code& ec, size_t& bytes_transferred);
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL signed_size_type recvfrom(socket_type s, buf* bufs,
+ size_t count, int flags, socket_addr_type* addr,
+ std::size_t* addrlen, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL size_t sync_recvfrom(socket_type s, state_type state,
+ buf* bufs, size_t count, int flags, socket_addr_type* addr,
+ std::size_t* addrlen, boost::system::error_code& ec);
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL void complete_iocp_recvfrom(
+ const weak_cancel_token_type& cancel_token,
+ boost::system::error_code& ec);
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL bool non_blocking_recvfrom(socket_type s,
+ buf* bufs, size_t count, int flags,
+ socket_addr_type* addr, std::size_t* addrlen,
+ boost::system::error_code& ec, size_t& bytes_transferred);
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL signed_size_type recvmsg(socket_type s, buf* bufs,
+ size_t count, int in_flags, int& out_flags,
+ boost::system::error_code& ec);
+
+BOOST_ASIO_DECL size_t sync_recvmsg(socket_type s, state_type state,
+ buf* bufs, size_t count, int in_flags, int& out_flags,
+ boost::system::error_code& ec);
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL void complete_iocp_recvmsg(
+ const weak_cancel_token_type& cancel_token,
+ boost::system::error_code& ec);
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL bool non_blocking_recvmsg(socket_type s,
+ buf* bufs, size_t count, int in_flags, int& out_flags,
+ boost::system::error_code& ec, size_t& bytes_transferred);
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL signed_size_type send(socket_type s, const buf* bufs,
+ size_t count, int flags, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL size_t sync_send(socket_type s, state_type state,
+ const buf* bufs, size_t count, int flags,
+ bool all_empty, boost::system::error_code& ec);
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL void complete_iocp_send(
+ const weak_cancel_token_type& cancel_token,
+ boost::system::error_code& ec);
+
+#else // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL bool non_blocking_send(socket_type s,
+ const buf* bufs, size_t count, int flags,
+ boost::system::error_code& ec, size_t& bytes_transferred);
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL signed_size_type sendto(socket_type s, const buf* bufs,
+ size_t count, int flags, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL size_t sync_sendto(socket_type s, state_type state,
+ const buf* bufs, size_t count, int flags, const socket_addr_type* addr,
+ std::size_t addrlen, boost::system::error_code& ec);
+
+#if !defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL bool non_blocking_sendto(socket_type s,
+ const buf* bufs, size_t count, int flags,
+ const socket_addr_type* addr, std::size_t addrlen,
+ boost::system::error_code& ec, size_t& bytes_transferred);
+
+#endif // !defined(BOOST_ASIO_HAS_IOCP)
+
+BOOST_ASIO_DECL socket_type socket(int af, int type, int protocol,
+ boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int setsockopt(socket_type s, state_type& state,
+ int level, int optname, const void* optval,
+ std::size_t optlen, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int getsockopt(socket_type s, state_type state,
+ int level, int optname, void* optval,
+ size_t* optlen, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int getpeername(socket_type s, socket_addr_type* addr,
+ std::size_t* addrlen, bool cached, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int getsockname(socket_type s, socket_addr_type* addr,
+ std::size_t* addrlen, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int ioctl(socket_type s, state_type& state,
+ int cmd, ioctl_arg_type* arg, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int select(int nfds, fd_set* readfds, fd_set* writefds,
+ fd_set* exceptfds, timeval* timeout, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int poll_read(socket_type s,
+ state_type state, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int poll_write(socket_type s,
+ state_type state, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int poll_connect(socket_type s, boost::system::error_code& ec);
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+BOOST_ASIO_DECL const char* inet_ntop(int af, const void* src, char* dest,
+ size_t length, unsigned long scope_id, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int inet_pton(int af, const char* src, void* dest,
+ unsigned long* scope_id, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL int gethostname(char* name,
+ int namelen, boost::system::error_code& ec);
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+BOOST_ASIO_DECL boost::system::error_code getaddrinfo(const char* host,
+ const char* service, const addrinfo_type& hints,
+ addrinfo_type** result, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL boost::system::error_code background_getaddrinfo(
+ const weak_cancel_token_type& cancel_token, const char* host,
+ const char* service, const addrinfo_type& hints,
+ addrinfo_type** result, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL void freeaddrinfo(addrinfo_type* ai);
+
+BOOST_ASIO_DECL boost::system::error_code getnameinfo(
+ const socket_addr_type* addr, std::size_t addrlen,
+ char* host, std::size_t hostlen, char* serv,
+ std::size_t servlen, int flags, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL boost::system::error_code sync_getnameinfo(
+ const socket_addr_type* addr, std::size_t addrlen,
+ char* host, std::size_t hostlen, char* serv,
+ std::size_t servlen, int sock_type, boost::system::error_code& ec);
+
+BOOST_ASIO_DECL boost::system::error_code background_getnameinfo(
+ const weak_cancel_token_type& cancel_token,
+ const socket_addr_type* addr, std::size_t addrlen,
+ char* host, std::size_t hostlen, char* serv,
+ std::size_t servlen, int sock_type, boost::system::error_code& ec);
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+BOOST_ASIO_DECL u_long_type network_to_host_long(u_long_type value);
+
+BOOST_ASIO_DECL u_long_type host_to_network_long(u_long_type value);
+
+BOOST_ASIO_DECL u_short_type network_to_host_short(u_short_type value);
+
+BOOST_ASIO_DECL u_short_type host_to_network_short(u_short_type value);
+
+} // namespace socket_ops
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/socket_ops.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_SOCKET_OPS_HPP
diff --git a/ext/patches/boost/asio/detail/socket_option.hpp b/ext/patches/boost/asio/detail/socket_option.hpp
new file mode 100644
index 0000000..3c0f760
--- /dev/null
+++ b/ext/patches/boost/asio/detail/socket_option.hpp
@@ -0,0 +1,318 @@
+//
+// detail/socket_option.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SOCKET_OPTION_HPP
+#define BOOST_ASIO_DETAIL_SOCKET_OPTION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <stdexcept>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+namespace socket_option {
+
+// Helper template for implementing boolean-based options.
+template <int Level, int Name>
+class boolean
+{
+public:
+ // Default constructor.
+ boolean()
+ : value_(0)
+ {
+ }
+
+ // Construct with a specific option value.
+ explicit boolean(bool v)
+ : value_(v ? 1 : 0)
+ {
+ }
+
+ // Set the current value of the boolean.
+ boolean& operator=(bool v)
+ {
+ value_ = v ? 1 : 0;
+ return *this;
+ }
+
+ // Get the current value of the boolean.
+ bool value() const
+ {
+ return !!value_;
+ }
+
+ // Convert to bool.
+ operator bool() const
+ {
+ return !!value_;
+ }
+
+ // Test for false.
+ bool operator!() const
+ {
+ return !value_;
+ }
+
+ // Get the level of the socket option.
+ template <typename Protocol>
+ int level(const Protocol&) const
+ {
+ return Level;
+ }
+
+ // Get the name of the socket option.
+ template <typename Protocol>
+ int name(const Protocol&) const
+ {
+ return Name;
+ }
+
+ // Get the address of the boolean data.
+ template <typename Protocol>
+ int* data(const Protocol&)
+ {
+ return &value_;
+ }
+
+ // Get the address of the boolean data.
+ template <typename Protocol>
+ const int* data(const Protocol&) const
+ {
+ return &value_;
+ }
+
+ // Get the size of the boolean data.
+ template <typename Protocol>
+ std::size_t size(const Protocol&) const
+ {
+ return sizeof(value_);
+ }
+
+ // Set the size of the boolean data.
+ template <typename Protocol>
+ void resize(const Protocol&, std::size_t s)
+ {
+ // On some platforms (e.g. Windows Vista), the getsockopt function will
+ // return the size of a boolean socket option as one byte, even though a
+ // four byte integer was passed in.
+ switch (s)
+ {
+ case sizeof(char):
+ value_ = *reinterpret_cast<char*>(&value_) ? 1 : 0;
+ break;
+ case sizeof(value_):
+ break;
+ default:
+ {
+ std::length_error ex("boolean socket option resize");
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+ }
+
+private:
+ int value_;
+};
+
+// Helper template for implementing integer options.
+template <int Level, int Name>
+class integer
+{
+public:
+ // Default constructor.
+ integer()
+ : value_(0)
+ {
+ }
+
+ // Construct with a specific option value.
+ explicit integer(int v)
+ : value_(v)
+ {
+ }
+
+ // Set the value of the int option.
+ integer& operator=(int v)
+ {
+ value_ = v;
+ return *this;
+ }
+
+ // Get the current value of the int option.
+ int value() const
+ {
+ return value_;
+ }
+
+ // Get the level of the socket option.
+ template <typename Protocol>
+ int level(const Protocol&) const
+ {
+ return Level;
+ }
+
+ // Get the name of the socket option.
+ template <typename Protocol>
+ int name(const Protocol&) const
+ {
+ return Name;
+ }
+
+ // Get the address of the int data.
+ template <typename Protocol>
+ int* data(const Protocol&)
+ {
+ return &value_;
+ }
+
+ // Get the address of the int data.
+ template <typename Protocol>
+ const int* data(const Protocol&) const
+ {
+ return &value_;
+ }
+
+ // Get the size of the int data.
+ template <typename Protocol>
+ std::size_t size(const Protocol&) const
+ {
+ return sizeof(value_);
+ }
+
+ // Set the size of the int data.
+ template <typename Protocol>
+ void resize(const Protocol&, std::size_t s)
+ {
+ if (s != sizeof(value_))
+ {
+ std::length_error ex("integer socket option resize");
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+
+private:
+ int value_;
+};
+
+// Helper template for implementing linger options.
+template <int Level, int Name>
+class linger
+{
+public:
+ // Default constructor.
+ linger()
+ {
+ value_.l_onoff = 0;
+ value_.l_linger = 0;
+ }
+
+ // Construct with specific option values.
+ linger(bool e, int t)
+ {
+ enabled(e);
+ timeout BOOST_ASIO_PREVENT_MACRO_SUBSTITUTION(t);
+ }
+
+ // Set the value for whether linger is enabled.
+ void enabled(bool value)
+ {
+ value_.l_onoff = value ? 1 : 0;
+ }
+
+ // Get the value for whether linger is enabled.
+ bool enabled() const
+ {
+ return value_.l_onoff != 0;
+ }
+
+ // Set the value for the linger timeout.
+ void timeout BOOST_ASIO_PREVENT_MACRO_SUBSTITUTION(int value)
+ {
+#if defined(WIN32)
+ value_.l_linger = static_cast<u_short>(value);
+#else
+ value_.l_linger = value;
+#endif
+ }
+
+ // Get the value for the linger timeout.
+ int timeout BOOST_ASIO_PREVENT_MACRO_SUBSTITUTION() const
+ {
+ return static_cast<int>(value_.l_linger);
+ }
+
+ // Get the level of the socket option.
+ template <typename Protocol>
+ int level(const Protocol&) const
+ {
+ return Level;
+ }
+
+ // Get the name of the socket option.
+ template <typename Protocol>
+ int name(const Protocol&) const
+ {
+ return Name;
+ }
+
+ // Get the address of the linger data.
+ template <typename Protocol>
+ detail::linger_type* data(const Protocol&)
+ {
+ return &value_;
+ }
+
+ // Get the address of the linger data.
+ template <typename Protocol>
+ const detail::linger_type* data(const Protocol&) const
+ {
+ return &value_;
+ }
+
+ // Get the size of the linger data.
+ template <typename Protocol>
+ std::size_t size(const Protocol&) const
+ {
+ return sizeof(value_);
+ }
+
+ // Set the size of the int data.
+ template <typename Protocol>
+ void resize(const Protocol&, std::size_t s)
+ {
+ if (s != sizeof(value_))
+ {
+ std::length_error ex("linger socket option resize");
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+
+private:
+ detail::linger_type value_;
+};
+
+} // namespace socket_option
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_SOCKET_OPTION_HPP
diff --git a/ext/patches/boost/asio/detail/socket_select_interrupter.hpp b/ext/patches/boost/asio/detail/socket_select_interrupter.hpp
new file mode 100644
index 0000000..a0e5663
--- /dev/null
+++ b/ext/patches/boost/asio/detail/socket_select_interrupter.hpp
@@ -0,0 +1,93 @@
+//
+// detail/socket_select_interrupter.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SOCKET_SELECT_INTERRUPTER_HPP
+#define BOOST_ASIO_DETAIL_SOCKET_SELECT_INTERRUPTER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#if defined(BOOST_ASIO_WINDOWS) \
+ || defined(__CYGWIN__) \
+ || defined(__SYMBIAN32__)
+
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class socket_select_interrupter
+{
+public:
+ // Constructor.
+ BOOST_ASIO_DECL socket_select_interrupter();
+
+ // Destructor.
+ BOOST_ASIO_DECL ~socket_select_interrupter();
+
+ // Recreate the interrupter's descriptors. Used after a fork.
+ BOOST_ASIO_DECL void recreate();
+
+ // Interrupt the select call.
+ BOOST_ASIO_DECL void interrupt();
+
+ // Reset the select interrupt. Returns true if the call was interrupted.
+ BOOST_ASIO_DECL bool reset();
+
+ // Get the read descriptor to be passed to select.
+ socket_type read_descriptor() const
+ {
+ return read_descriptor_;
+ }
+
+private:
+ // Open the descriptors. Throws on error.
+ BOOST_ASIO_DECL void open_descriptors();
+
+ // Close the descriptors.
+ BOOST_ASIO_DECL void close_descriptors();
+
+ // The read end of a connection used to interrupt the select call. This file
+ // descriptor is passed to select such that when it is time to stop, a single
+ // byte will be written on the other end of the connection and this
+ // descriptor will become readable.
+ socket_type read_descriptor_;
+
+ // The write end of a connection used to interrupt the select call. A single
+ // byte may be written to this to wake up the select which is waiting for the
+ // other end to become readable.
+ socket_type write_descriptor_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/socket_select_interrupter.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+ // || defined(__CYGWIN__)
+ // || defined(__SYMBIAN32__)
+
+#endif // !defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_SOCKET_SELECT_INTERRUPTER_HPP
diff --git a/ext/patches/boost/asio/detail/socket_types.hpp b/ext/patches/boost/asio/detail/socket_types.hpp
new file mode 100644
index 0000000..5318c99
--- /dev/null
+++ b/ext/patches/boost/asio/detail/socket_types.hpp
@@ -0,0 +1,406 @@
+//
+// detail/socket_types.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SOCKET_TYPES_HPP
+#define BOOST_ASIO_DETAIL_SOCKET_TYPES_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+// Empty.
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# if defined(_WINSOCKAPI_) && !defined(_WINSOCK2API_)
+# error WinSock.h has already been included
+# endif // defined(_WINSOCKAPI_) && !defined(_WINSOCK2API_)
+# if defined(__BORLANDC__)
+# include <stdlib.h> // Needed for __errno
+# if !defined(_WSPIAPI_H_)
+# define _WSPIAPI_H_
+# define BOOST_ASIO_WSPIAPI_H_DEFINED
+# endif // !defined(_WSPIAPI_H_)
+# endif // defined(__BORLANDC__)
+# if defined(WINAPI_FAMILY)
+# if ((WINAPI_FAMILY & WINAPI_PARTITION_DESKTOP) != 0)
+# include <windows.h>
+# endif // ((WINAPI_FAMILY & WINAPI_PARTITION_DESKTOP) != 0)
+# endif // defined(WINAPI_FAMILY)
+# include <winsock2.h>
+# include <ws2tcpip.h>
+# include <mswsock.h>
+# if defined(BOOST_ASIO_WSPIAPI_H_DEFINED)
+# undef _WSPIAPI_H_
+# undef BOOST_ASIO_WSPIAPI_H_DEFINED
+# endif // defined(BOOST_ASIO_WSPIAPI_H_DEFINED)
+# if !defined(BOOST_ASIO_NO_DEFAULT_LINKED_LIBS)
+# if defined(UNDER_CE)
+# pragma comment(lib, "ws2.lib")
+# elif defined(_MSC_VER) || defined(__BORLANDC__)
+# pragma comment(lib, "ws2_32.lib")
+# pragma comment(lib, "mswsock.lib")
+# endif // defined(_MSC_VER) || defined(__BORLANDC__)
+# endif // !defined(BOOST_ASIO_NO_DEFAULT_LINKED_LIBS)
+# include <boost/asio/detail/old_win_sdk_compat.hpp>
+#else
+# include <sys/ioctl.h>
+# if !defined(__SYMBIAN32__)
+# include <sys/poll.h>
+# endif
+# include <sys/types.h>
+# include <sys/stat.h>
+# include <fcntl.h>
+# if defined(__hpux)
+# include <sys/time.h>
+# endif
+# if !defined(__hpux) || defined(__SELECT)
+# include <sys/select.h>
+# endif
+# include <sys/socket.h>
+# include <sys/uio.h>
+# include <sys/un.h>
+# include <netinet/in.h>
+# if !defined(__SYMBIAN32__)
+# include <netinet/tcp.h>
+# endif
+# include <arpa/inet.h>
+# include <netdb.h>
+# include <net/if.h>
+# include <limits.h>
+# if defined(__sun)
+# include <sys/filio.h>
+# include <sys/sockio.h>
+# endif
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+const int max_addr_v4_str_len = 256;
+const int max_addr_v6_str_len = 256;
+typedef unsigned __int32 u_long_type;
+typedef unsigned __int16 u_short_type;
+struct in4_addr_type { u_long_type s_addr; };
+struct in4_mreq_type { in4_addr_type imr_multiaddr, imr_interface; };
+struct in6_addr_type { unsigned char s6_addr[16]; };
+struct in6_mreq_type { in6_addr_type ipv6mr_multiaddr;
+ unsigned long ipv6mr_interface; };
+struct socket_addr_type { int sa_family; };
+struct sockaddr_in4_type { int sin_family;
+ in4_addr_type sin_addr; u_short_type sin_port; };
+struct sockaddr_in6_type { int sin6_family;
+ in6_addr_type sin6_addr; u_short_type sin6_port;
+ u_long_type sin6_flowinfo; u_long_type sin6_scope_id; };
+struct sockaddr_storage_type { int ss_family;
+ unsigned char ss_bytes[128 - sizeof(int)]; };
+struct addrinfo_type { int ai_flags;
+ int ai_family, ai_socktype, ai_protocol;
+ int ai_addrlen; const void* ai_addr;
+ const char* ai_canonname; addrinfo_type* ai_next; };
+struct linger_type { u_short_type l_onoff, l_linger; };
+typedef u_long_type ioctl_arg_type;
+typedef int signed_size_type;
+# define BOOST_ASIO_OS_DEF(c) BOOST_ASIO_OS_DEF_##c
+# define BOOST_ASIO_OS_DEF_AF_UNSPEC 0
+# define BOOST_ASIO_OS_DEF_AF_INET 2
+# define BOOST_ASIO_OS_DEF_AF_INET6 23
+# define BOOST_ASIO_OS_DEF_SOCK_STREAM 1
+# define BOOST_ASIO_OS_DEF_SOCK_DGRAM 2
+# define BOOST_ASIO_OS_DEF_SOCK_RAW 3
+# define BOOST_ASIO_OS_DEF_SOCK_SEQPACKET 5
+# define BOOST_ASIO_OS_DEF_IPPROTO_IP 0
+# define BOOST_ASIO_OS_DEF_IPPROTO_IPV6 41
+# define BOOST_ASIO_OS_DEF_IPPROTO_TCP 6
+# define BOOST_ASIO_OS_DEF_IPPROTO_UDP 17
+# define BOOST_ASIO_OS_DEF_IPPROTO_ICMP 1
+# define BOOST_ASIO_OS_DEF_IPPROTO_ICMPV6 58
+# define BOOST_ASIO_OS_DEF_FIONBIO 1
+# define BOOST_ASIO_OS_DEF_FIONREAD 2
+# define BOOST_ASIO_OS_DEF_INADDR_ANY 0
+# define BOOST_ASIO_OS_DEF_MSG_OOB 0x1
+# define BOOST_ASIO_OS_DEF_MSG_PEEK 0x2
+# define BOOST_ASIO_OS_DEF_MSG_DONTROUTE 0x4
+# define BOOST_ASIO_OS_DEF_MSG_EOR 0 // Not supported.
+# define BOOST_ASIO_OS_DEF_SHUT_RD 0x0
+# define BOOST_ASIO_OS_DEF_SHUT_WR 0x1
+# define BOOST_ASIO_OS_DEF_SHUT_RDWR 0x2
+# define BOOST_ASIO_OS_DEF_SOMAXCONN 0x7fffffff
+# define BOOST_ASIO_OS_DEF_SOL_SOCKET 0xffff
+# define BOOST_ASIO_OS_DEF_SO_BROADCAST 0x20
+# define BOOST_ASIO_OS_DEF_SO_DEBUG 0x1
+# define BOOST_ASIO_OS_DEF_SO_DONTROUTE 0x10
+# define BOOST_ASIO_OS_DEF_SO_KEEPALIVE 0x8
+# define BOOST_ASIO_OS_DEF_SO_LINGER 0x80
+# define BOOST_ASIO_OS_DEF_SO_SNDBUF 0x1001
+# define BOOST_ASIO_OS_DEF_SO_RCVBUF 0x1002
+# define BOOST_ASIO_OS_DEF_SO_SNDLOWAT 0x1003
+# define BOOST_ASIO_OS_DEF_SO_RCVLOWAT 0x1004
+# define BOOST_ASIO_OS_DEF_SO_REUSEADDR 0x4
+# define BOOST_ASIO_OS_DEF_TCP_NODELAY 0x1
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_IF 2
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_TTL 3
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_LOOP 4
+# define BOOST_ASIO_OS_DEF_IP_ADD_MEMBERSHIP 5
+# define BOOST_ASIO_OS_DEF_IP_DROP_MEMBERSHIP 6
+# define BOOST_ASIO_OS_DEF_IP_TTL 7
+# define BOOST_ASIO_OS_DEF_IPV6_UNICAST_HOPS 4
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_IF 9
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_HOPS 10
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_LOOP 11
+# define BOOST_ASIO_OS_DEF_IPV6_JOIN_GROUP 12
+# define BOOST_ASIO_OS_DEF_IPV6_LEAVE_GROUP 13
+# define BOOST_ASIO_OS_DEF_AI_CANONNAME 0x2
+# define BOOST_ASIO_OS_DEF_AI_PASSIVE 0x1
+# define BOOST_ASIO_OS_DEF_AI_NUMERICHOST 0x4
+# define BOOST_ASIO_OS_DEF_AI_NUMERICSERV 0x8
+# define BOOST_ASIO_OS_DEF_AI_V4MAPPED 0x800
+# define BOOST_ASIO_OS_DEF_AI_ALL 0x100
+# define BOOST_ASIO_OS_DEF_AI_ADDRCONFIG 0x400
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+typedef SOCKET socket_type;
+const SOCKET invalid_socket = INVALID_SOCKET;
+const int socket_error_retval = SOCKET_ERROR;
+const int max_addr_v4_str_len = 256;
+const int max_addr_v6_str_len = 256;
+typedef sockaddr socket_addr_type;
+typedef in_addr in4_addr_type;
+typedef ip_mreq in4_mreq_type;
+typedef sockaddr_in sockaddr_in4_type;
+# if defined(BOOST_ASIO_HAS_OLD_WIN_SDK)
+typedef in6_addr_emulation in6_addr_type;
+typedef ipv6_mreq_emulation in6_mreq_type;
+typedef sockaddr_in6_emulation sockaddr_in6_type;
+typedef sockaddr_storage_emulation sockaddr_storage_type;
+typedef addrinfo_emulation addrinfo_type;
+# else
+typedef in6_addr in6_addr_type;
+typedef ipv6_mreq in6_mreq_type;
+typedef sockaddr_in6 sockaddr_in6_type;
+typedef sockaddr_storage sockaddr_storage_type;
+typedef addrinfo addrinfo_type;
+# endif
+typedef ::linger linger_type;
+typedef unsigned long ioctl_arg_type;
+typedef u_long u_long_type;
+typedef u_short u_short_type;
+typedef int signed_size_type;
+# define BOOST_ASIO_OS_DEF(c) BOOST_ASIO_OS_DEF_##c
+# define BOOST_ASIO_OS_DEF_AF_UNSPEC AF_UNSPEC
+# define BOOST_ASIO_OS_DEF_AF_INET AF_INET
+# define BOOST_ASIO_OS_DEF_AF_INET6 AF_INET6
+# define BOOST_ASIO_OS_DEF_SOCK_STREAM SOCK_STREAM
+# define BOOST_ASIO_OS_DEF_SOCK_DGRAM SOCK_DGRAM
+# define BOOST_ASIO_OS_DEF_SOCK_RAW SOCK_RAW
+# define BOOST_ASIO_OS_DEF_SOCK_SEQPACKET SOCK_SEQPACKET
+# define BOOST_ASIO_OS_DEF_IPPROTO_IP IPPROTO_IP
+# define BOOST_ASIO_OS_DEF_IPPROTO_IPV6 IPPROTO_IPV6
+# define BOOST_ASIO_OS_DEF_IPPROTO_TCP IPPROTO_TCP
+# define BOOST_ASIO_OS_DEF_IPPROTO_UDP IPPROTO_UDP
+# define BOOST_ASIO_OS_DEF_IPPROTO_ICMP IPPROTO_ICMP
+# define BOOST_ASIO_OS_DEF_IPPROTO_ICMPV6 IPPROTO_ICMPV6
+# define BOOST_ASIO_OS_DEF_FIONBIO FIONBIO
+# define BOOST_ASIO_OS_DEF_FIONREAD FIONREAD
+# define BOOST_ASIO_OS_DEF_INADDR_ANY INADDR_ANY
+# define BOOST_ASIO_OS_DEF_MSG_OOB MSG_OOB
+# define BOOST_ASIO_OS_DEF_MSG_PEEK MSG_PEEK
+# define BOOST_ASIO_OS_DEF_MSG_DONTROUTE MSG_DONTROUTE
+# define BOOST_ASIO_OS_DEF_MSG_EOR 0 // Not supported on Windows.
+# define BOOST_ASIO_OS_DEF_SHUT_RD SD_RECEIVE
+# define BOOST_ASIO_OS_DEF_SHUT_WR SD_SEND
+# define BOOST_ASIO_OS_DEF_SHUT_RDWR SD_BOTH
+# define BOOST_ASIO_OS_DEF_SOMAXCONN SOMAXCONN
+# define BOOST_ASIO_OS_DEF_SOL_SOCKET SOL_SOCKET
+# define BOOST_ASIO_OS_DEF_SO_BROADCAST SO_BROADCAST
+# define BOOST_ASIO_OS_DEF_SO_DEBUG SO_DEBUG
+# define BOOST_ASIO_OS_DEF_SO_DONTROUTE SO_DONTROUTE
+# define BOOST_ASIO_OS_DEF_SO_KEEPALIVE SO_KEEPALIVE
+# define BOOST_ASIO_OS_DEF_SO_LINGER SO_LINGER
+# define BOOST_ASIO_OS_DEF_SO_SNDBUF SO_SNDBUF
+# define BOOST_ASIO_OS_DEF_SO_RCVBUF SO_RCVBUF
+# define BOOST_ASIO_OS_DEF_SO_SNDLOWAT SO_SNDLOWAT
+# define BOOST_ASIO_OS_DEF_SO_RCVLOWAT SO_RCVLOWAT
+# define BOOST_ASIO_OS_DEF_SO_REUSEADDR SO_REUSEADDR
+# define BOOST_ASIO_OS_DEF_TCP_NODELAY TCP_NODELAY
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_IF IP_MULTICAST_IF
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_TTL IP_MULTICAST_TTL
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_LOOP IP_MULTICAST_LOOP
+# define BOOST_ASIO_OS_DEF_IP_ADD_MEMBERSHIP IP_ADD_MEMBERSHIP
+# define BOOST_ASIO_OS_DEF_IP_DROP_MEMBERSHIP IP_DROP_MEMBERSHIP
+# define BOOST_ASIO_OS_DEF_IP_TTL IP_TTL
+# define BOOST_ASIO_OS_DEF_IPV6_UNICAST_HOPS IPV6_UNICAST_HOPS
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_IF IPV6_MULTICAST_IF
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_HOPS IPV6_MULTICAST_HOPS
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_LOOP IPV6_MULTICAST_LOOP
+# define BOOST_ASIO_OS_DEF_IPV6_JOIN_GROUP IPV6_JOIN_GROUP
+# define BOOST_ASIO_OS_DEF_IPV6_LEAVE_GROUP IPV6_LEAVE_GROUP
+# define BOOST_ASIO_OS_DEF_AI_CANONNAME AI_CANONNAME
+# define BOOST_ASIO_OS_DEF_AI_PASSIVE AI_PASSIVE
+# define BOOST_ASIO_OS_DEF_AI_NUMERICHOST AI_NUMERICHOST
+# if defined(AI_NUMERICSERV)
+# define BOOST_ASIO_OS_DEF_AI_NUMERICSERV AI_NUMERICSERV
+# else
+# define BOOST_ASIO_OS_DEF_AI_NUMERICSERV 0
+# endif
+# if defined(AI_V4MAPPED)
+# define BOOST_ASIO_OS_DEF_AI_V4MAPPED AI_V4MAPPED
+# else
+# define BOOST_ASIO_OS_DEF_AI_V4MAPPED 0
+# endif
+# if defined(AI_ALL)
+# define BOOST_ASIO_OS_DEF_AI_ALL AI_ALL
+# else
+# define BOOST_ASIO_OS_DEF_AI_ALL 0
+# endif
+# if defined(AI_ADDRCONFIG)
+# define BOOST_ASIO_OS_DEF_AI_ADDRCONFIG AI_ADDRCONFIG
+# else
+# define BOOST_ASIO_OS_DEF_AI_ADDRCONFIG 0
+# endif
+# if defined (_WIN32_WINNT)
+const int max_iov_len = 64;
+# else
+const int max_iov_len = 16;
+# endif
+#else
+typedef int socket_type;
+const int invalid_socket = -1;
+const int socket_error_retval = -1;
+const int max_addr_v4_str_len = INET_ADDRSTRLEN;
+#if defined(INET6_ADDRSTRLEN)
+const int max_addr_v6_str_len = INET6_ADDRSTRLEN + 1 + IF_NAMESIZE;
+#else // defined(INET6_ADDRSTRLEN)
+const int max_addr_v6_str_len = 256;
+#endif // defined(INET6_ADDRSTRLEN)
+typedef sockaddr socket_addr_type;
+typedef in_addr in4_addr_type;
+# if defined(__hpux)
+// HP-UX doesn't provide ip_mreq when _XOPEN_SOURCE_EXTENDED is defined.
+struct in4_mreq_type
+{
+ struct in_addr imr_multiaddr;
+ struct in_addr imr_interface;
+};
+# else
+typedef ip_mreq in4_mreq_type;
+# endif
+typedef sockaddr_in sockaddr_in4_type;
+typedef in6_addr in6_addr_type;
+typedef ipv6_mreq in6_mreq_type;
+typedef sockaddr_in6 sockaddr_in6_type;
+typedef sockaddr_storage sockaddr_storage_type;
+typedef sockaddr_un sockaddr_un_type;
+typedef addrinfo addrinfo_type;
+typedef ::linger linger_type;
+typedef int ioctl_arg_type;
+typedef uint32_t u_long_type;
+typedef uint16_t u_short_type;
+#if defined(BOOST_ASIO_HAS_SSIZE_T)
+typedef ssize_t signed_size_type;
+#else // defined(BOOST_ASIO_HAS_SSIZE_T)
+typedef int signed_size_type;
+#endif // defined(BOOST_ASIO_HAS_SSIZE_T)
+# define BOOST_ASIO_OS_DEF(c) BOOST_ASIO_OS_DEF_##c
+# define BOOST_ASIO_OS_DEF_AF_UNSPEC AF_UNSPEC
+# define BOOST_ASIO_OS_DEF_AF_INET AF_INET
+# define BOOST_ASIO_OS_DEF_AF_INET6 AF_INET6
+# define BOOST_ASIO_OS_DEF_SOCK_STREAM SOCK_STREAM
+# define BOOST_ASIO_OS_DEF_SOCK_DGRAM SOCK_DGRAM
+# define BOOST_ASIO_OS_DEF_SOCK_RAW SOCK_RAW
+# define BOOST_ASIO_OS_DEF_SOCK_SEQPACKET SOCK_SEQPACKET
+# define BOOST_ASIO_OS_DEF_IPPROTO_IP IPPROTO_IP
+# define BOOST_ASIO_OS_DEF_IPPROTO_IPV6 IPPROTO_IPV6
+# define BOOST_ASIO_OS_DEF_IPPROTO_TCP IPPROTO_TCP
+# define BOOST_ASIO_OS_DEF_IPPROTO_UDP IPPROTO_UDP
+# define BOOST_ASIO_OS_DEF_IPPROTO_ICMP IPPROTO_ICMP
+# define BOOST_ASIO_OS_DEF_IPPROTO_ICMPV6 IPPROTO_ICMPV6
+# define BOOST_ASIO_OS_DEF_FIONBIO FIONBIO
+# define BOOST_ASIO_OS_DEF_FIONREAD FIONREAD
+# define BOOST_ASIO_OS_DEF_INADDR_ANY INADDR_ANY
+# define BOOST_ASIO_OS_DEF_MSG_OOB MSG_OOB
+# define BOOST_ASIO_OS_DEF_MSG_PEEK MSG_PEEK
+# define BOOST_ASIO_OS_DEF_MSG_DONTROUTE MSG_DONTROUTE
+# define BOOST_ASIO_OS_DEF_MSG_EOR MSG_EOR
+# define BOOST_ASIO_OS_DEF_SHUT_RD SHUT_RD
+# define BOOST_ASIO_OS_DEF_SHUT_WR SHUT_WR
+# define BOOST_ASIO_OS_DEF_SHUT_RDWR SHUT_RDWR
+# define BOOST_ASIO_OS_DEF_SOMAXCONN SOMAXCONN
+# define BOOST_ASIO_OS_DEF_SOL_SOCKET SOL_SOCKET
+# define BOOST_ASIO_OS_DEF_SO_BROADCAST SO_BROADCAST
+# define BOOST_ASIO_OS_DEF_SO_DEBUG SO_DEBUG
+# define BOOST_ASIO_OS_DEF_SO_DONTROUTE SO_DONTROUTE
+# define BOOST_ASIO_OS_DEF_SO_KEEPALIVE SO_KEEPALIVE
+# define BOOST_ASIO_OS_DEF_SO_LINGER SO_LINGER
+# define BOOST_ASIO_OS_DEF_SO_SNDBUF SO_SNDBUF
+# define BOOST_ASIO_OS_DEF_SO_RCVBUF SO_RCVBUF
+# define BOOST_ASIO_OS_DEF_SO_SNDLOWAT SO_SNDLOWAT
+# define BOOST_ASIO_OS_DEF_SO_RCVLOWAT SO_RCVLOWAT
+# define BOOST_ASIO_OS_DEF_SO_REUSEADDR SO_REUSEADDR
+# define BOOST_ASIO_OS_DEF_TCP_NODELAY TCP_NODELAY
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_IF IP_MULTICAST_IF
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_TTL IP_MULTICAST_TTL
+# define BOOST_ASIO_OS_DEF_IP_MULTICAST_LOOP IP_MULTICAST_LOOP
+# define BOOST_ASIO_OS_DEF_IP_ADD_MEMBERSHIP IP_ADD_MEMBERSHIP
+# define BOOST_ASIO_OS_DEF_IP_DROP_MEMBERSHIP IP_DROP_MEMBERSHIP
+# define BOOST_ASIO_OS_DEF_IP_TTL IP_TTL
+# define BOOST_ASIO_OS_DEF_IPV6_UNICAST_HOPS IPV6_UNICAST_HOPS
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_IF IPV6_MULTICAST_IF
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_HOPS IPV6_MULTICAST_HOPS
+# define BOOST_ASIO_OS_DEF_IPV6_MULTICAST_LOOP IPV6_MULTICAST_LOOP
+# define BOOST_ASIO_OS_DEF_IPV6_JOIN_GROUP IPV6_JOIN_GROUP
+# define BOOST_ASIO_OS_DEF_IPV6_LEAVE_GROUP IPV6_LEAVE_GROUP
+# define BOOST_ASIO_OS_DEF_AI_CANONNAME AI_CANONNAME
+# define BOOST_ASIO_OS_DEF_AI_PASSIVE AI_PASSIVE
+# define BOOST_ASIO_OS_DEF_AI_NUMERICHOST AI_NUMERICHOST
+# if defined(AI_NUMERICSERV)
+# define BOOST_ASIO_OS_DEF_AI_NUMERICSERV AI_NUMERICSERV
+# else
+# define BOOST_ASIO_OS_DEF_AI_NUMERICSERV 0
+# endif
+// Note: QNX Neutrino 6.3 defines AI_V4MAPPED, AI_ALL and AI_ADDRCONFIG but
+// does not implement them. Therefore they are specifically excluded here.
+# if defined(AI_V4MAPPED) && !defined(__QNXNTO__)
+# define BOOST_ASIO_OS_DEF_AI_V4MAPPED AI_V4MAPPED
+# else
+# define BOOST_ASIO_OS_DEF_AI_V4MAPPED 0
+# endif
+# if defined(AI_ALL) && !defined(__QNXNTO__)
+# define BOOST_ASIO_OS_DEF_AI_ALL AI_ALL
+# else
+# define BOOST_ASIO_OS_DEF_AI_ALL 0
+# endif
+# if defined(AI_ADDRCONFIG) && !defined(__QNXNTO__)
+# define BOOST_ASIO_OS_DEF_AI_ADDRCONFIG AI_ADDRCONFIG
+# else
+# define BOOST_ASIO_OS_DEF_AI_ADDRCONFIG 0
+# endif
+# if defined(IOV_MAX)
+const int max_iov_len = IOV_MAX;
+# else
+// POSIX platforms are not required to define IOV_MAX.
+const int max_iov_len = 16;
+# endif
+#endif
+const int custom_socket_option_level = 0xA5100000;
+const int enable_connection_aborted_option = 1;
+const int always_fail_option = 2;
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_SOCKET_TYPES_HPP
diff --git a/ext/patches/boost/asio/detail/solaris_fenced_block.hpp b/ext/patches/boost/asio/detail/solaris_fenced_block.hpp
new file mode 100644
index 0000000..89a850f
--- /dev/null
+++ b/ext/patches/boost/asio/detail/solaris_fenced_block.hpp
@@ -0,0 +1,63 @@
+//
+// detail/solaris_fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_SOLARIS_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_SOLARIS_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(__sun)
+
+#include <atomic.h>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class solaris_fenced_block
+ : private noncopyable
+{
+public:
+ enum half_t { half };
+ enum full_t { full };
+
+ // Constructor for a half fenced block.
+ explicit solaris_fenced_block(half_t)
+ {
+ }
+
+ // Constructor for a full fenced block.
+ explicit solaris_fenced_block(full_t)
+ {
+ membar_consumer();
+ }
+
+ // Destructor.
+ ~solaris_fenced_block()
+ {
+ membar_producer();
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(__sun)
+
+#endif // BOOST_ASIO_DETAIL_SOLARIS_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/static_mutex.hpp b/ext/patches/boost/asio/detail/static_mutex.hpp
new file mode 100644
index 0000000..3bbd198
--- /dev/null
+++ b/ext/patches/boost/asio/detail/static_mutex.hpp
@@ -0,0 +1,54 @@
+//
+// detail/static_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_STATIC_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_STATIC_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+# include <boost/asio/detail/null_static_mutex.hpp>
+#elif defined(BOOST_ASIO_WINDOWS)
+# include <boost/asio/detail/win_static_mutex.hpp>
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+# include <boost/asio/detail/posix_static_mutex.hpp>
+#elif defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+# include <boost/asio/detail/std_static_mutex.hpp>
+#else
+# error Only Windows and POSIX are supported!
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+typedef null_static_mutex static_mutex;
+# define BOOST_ASIO_STATIC_MUTEX_INIT BOOST_ASIO_NULL_STATIC_MUTEX_INIT
+#elif defined(BOOST_ASIO_WINDOWS)
+typedef win_static_mutex static_mutex;
+# define BOOST_ASIO_STATIC_MUTEX_INIT BOOST_ASIO_WIN_STATIC_MUTEX_INIT
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+typedef posix_static_mutex static_mutex;
+# define BOOST_ASIO_STATIC_MUTEX_INIT BOOST_ASIO_POSIX_STATIC_MUTEX_INIT
+#elif defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+typedef std_static_mutex static_mutex;
+# define BOOST_ASIO_STATIC_MUTEX_INIT BOOST_ASIO_STD_STATIC_MUTEX_INIT
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_STATIC_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/std_event.hpp b/ext/patches/boost/asio/detail/std_event.hpp
new file mode 100644
index 0000000..4b622af
--- /dev/null
+++ b/ext/patches/boost/asio/detail/std_event.hpp
@@ -0,0 +1,178 @@
+//
+// detail/std_event.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_STD_EVENT_HPP
+#define BOOST_ASIO_DETAIL_STD_EVENT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+
+#include <chrono>
+#include <condition_variable>
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class std_event
+ : private noncopyable
+{
+public:
+ // Constructor.
+ std_event()
+ : state_(0)
+ {
+ }
+
+ // Destructor.
+ ~std_event()
+ {
+ }
+
+ // Signal the event. (Retained for backward compatibility.)
+ template <typename Lock>
+ void signal(Lock& lock)
+ {
+ this->signal_all(lock);
+ }
+
+ // Signal all waiters.
+ template <typename Lock>
+ void signal_all(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ (void)lock;
+ state_ |= 1;
+ cond_.notify_all();
+ }
+
+ // Unlock the mutex and signal one waiter.
+ template <typename Lock>
+ void unlock_and_signal_one(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ state_ |= 1;
+ bool have_waiters = (state_ > 1);
+ lock.unlock();
+ if (have_waiters)
+ cond_.notify_one();
+ }
+
+ // If there's a waiter, unlock the mutex and signal it.
+ template <typename Lock>
+ bool maybe_unlock_and_signal_one(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ state_ |= 1;
+ if (state_ > 1)
+ {
+ lock.unlock();
+ cond_.notify_one();
+ return true;
+ }
+ return false;
+ }
+
+ // Reset the event.
+ template <typename Lock>
+ void clear(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ (void)lock;
+ state_ &= ~std::size_t(1);
+ }
+
+ // Wait for the event to become signalled.
+ template <typename Lock>
+ void wait(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ unique_lock_adapter u_lock(lock);
+ while ((state_ & 1) == 0)
+ {
+ waiter w(state_);
+ cond_.wait(u_lock.unique_lock_);
+ }
+ }
+
+ // Timed wait for the event to become signalled.
+ template <typename Lock>
+ bool wait_for_usec(Lock& lock, long usec)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ unique_lock_adapter u_lock(lock);
+ if ((state_ & 1) == 0)
+ {
+ waiter w(state_);
+ cond_.wait_for(u_lock.unique_lock_, std::chrono::microseconds(usec));
+ }
+ return (state_ & 1) != 0;
+ }
+
+private:
+ // Helper class to temporarily adapt a scoped_lock into a unique_lock so that
+ // it can be passed to std::condition_variable::wait().
+ struct unique_lock_adapter
+ {
+ template <typename Lock>
+ explicit unique_lock_adapter(Lock& lock)
+ : unique_lock_(lock.mutex().mutex_, std::adopt_lock)
+ {
+ }
+
+ ~unique_lock_adapter()
+ {
+ unique_lock_.release();
+ }
+
+ std::unique_lock<std::mutex> unique_lock_;
+ };
+
+ // Helper to increment and decrement the state to track outstanding waiters.
+ class waiter
+ {
+ public:
+ explicit waiter(std::size_t& state)
+ : state_(state)
+ {
+ state_ += 2;
+ }
+
+ ~waiter()
+ {
+ state_ -= 2;
+ }
+
+ private:
+ std::size_t& state_;
+ };
+
+ std::condition_variable cond_;
+ std::size_t state_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+
+#endif // BOOST_ASIO_DETAIL_STD_EVENT_HPP
diff --git a/ext/patches/boost/asio/detail/std_mutex.hpp b/ext/patches/boost/asio/detail/std_mutex.hpp
new file mode 100644
index 0000000..e806aa0
--- /dev/null
+++ b/ext/patches/boost/asio/detail/std_mutex.hpp
@@ -0,0 +1,75 @@
+//
+// detail/std_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_STD_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_STD_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+
+#include <mutex>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/scoped_lock.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class std_event;
+
+class std_mutex
+ : private noncopyable
+{
+public:
+ typedef boost::asio::detail::scoped_lock<std_mutex> scoped_lock;
+
+ // Constructor.
+ std_mutex()
+ {
+ }
+
+ // Destructor.
+ ~std_mutex()
+ {
+ }
+
+ // Lock the mutex.
+ void lock()
+ {
+ mutex_.lock();
+ }
+
+ // Unlock the mutex.
+ void unlock()
+ {
+ mutex_.unlock();
+ }
+
+private:
+ friend class std_event;
+ std::mutex mutex_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+
+#endif // BOOST_ASIO_DETAIL_STD_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/std_static_mutex.hpp b/ext/patches/boost/asio/detail/std_static_mutex.hpp
new file mode 100644
index 0000000..5c4d654
--- /dev/null
+++ b/ext/patches/boost/asio/detail/std_static_mutex.hpp
@@ -0,0 +1,83 @@
+//
+// detail/std_static_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_STD_STATIC_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_STD_STATIC_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+
+#include <mutex>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/scoped_lock.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class std_event;
+
+class std_static_mutex
+ : private noncopyable
+{
+public:
+ typedef boost::asio::detail::scoped_lock<std_static_mutex> scoped_lock;
+
+ // Constructor.
+ std_static_mutex(int)
+ {
+ }
+
+ // Destructor.
+ ~std_static_mutex()
+ {
+ }
+
+ // Initialise the mutex.
+ void init()
+ {
+ // Nothing to do.
+ }
+
+ // Lock the mutex.
+ void lock()
+ {
+ mutex_.lock();
+ }
+
+ // Unlock the mutex.
+ void unlock()
+ {
+ mutex_.unlock();
+ }
+
+private:
+ friend class std_event;
+ std::mutex mutex_;
+};
+
+#define BOOST_ASIO_STD_STATIC_MUTEX_INIT 0
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_STD_MUTEX_AND_CONDVAR)
+
+#endif // BOOST_ASIO_DETAIL_STD_STATIC_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/std_thread.hpp b/ext/patches/boost/asio/detail/std_thread.hpp
new file mode 100644
index 0000000..61587e2
--- /dev/null
+++ b/ext/patches/boost/asio/detail/std_thread.hpp
@@ -0,0 +1,67 @@
+//
+// detail/std_thread.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_STD_THREAD_HPP
+#define BOOST_ASIO_DETAIL_STD_THREAD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_THREAD)
+
+#include <thread>
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class std_thread
+ : private noncopyable
+{
+public:
+ // Constructor.
+ template <typename Function>
+ std_thread(Function f, unsigned int = 0)
+ : thread_(f)
+ {
+ }
+
+ // Destructor.
+ ~std_thread()
+ {
+ join();
+ }
+
+ // Wait for the thread to exit.
+ void join()
+ {
+ if (thread_.joinable())
+ thread_.join();
+ }
+
+private:
+ std::thread thread_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_STD_THREAD)
+
+#endif // BOOST_ASIO_DETAIL_STD_THREAD_HPP
diff --git a/ext/patches/boost/asio/detail/strand_service.hpp b/ext/patches/boost/asio/detail/strand_service.hpp
new file mode 100644
index 0000000..d3046bb
--- /dev/null
+++ b/ext/patches/boost/asio/detail/strand_service.hpp
@@ -0,0 +1,144 @@
+//
+// detail/strand_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_STRAND_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_STRAND_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/scoped_ptr.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Default service implementation for a strand.
+class strand_service
+ : public boost::asio::detail::service_base<strand_service>
+{
+private:
+ // Helper class to re-post the strand on exit.
+ struct on_do_complete_exit;
+
+ // Helper class to re-post the strand on exit.
+ struct on_dispatch_exit;
+
+public:
+
+ // The underlying implementation of a strand.
+ class strand_impl
+ : public operation
+ {
+ public:
+ strand_impl();
+
+ private:
+ // Only this service will have access to the internal values.
+ friend class strand_service;
+ friend struct on_do_complete_exit;
+ friend struct on_dispatch_exit;
+
+ // Mutex to protect access to internal data.
+ boost::asio::detail::mutex mutex_;
+
+ // Indicates whether the strand is currently "locked" by a handler. This
+ // means that there is a handler upcall in progress, or that the strand
+ // itself has been scheduled in order to invoke some pending handlers.
+ bool locked_;
+
+ // The handlers that are waiting on the strand but should not be run until
+ // after the next time the strand is scheduled. This queue must only be
+ // modified while the mutex is locked.
+ op_queue<operation> waiting_queue_;
+
+ // The handlers that are ready to be run. Logically speaking, these are the
+ // handlers that hold the strand's lock. The ready queue is only modified
+ // from within the strand and so may be accessed without locking the mutex.
+ op_queue<operation> ready_queue_;
+ };
+
+ typedef strand_impl* implementation_type;
+
+ // Construct a new strand service for the specified io_service.
+ BOOST_ASIO_DECL explicit strand_service(boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new strand implementation.
+ BOOST_ASIO_DECL void construct(implementation_type& impl);
+
+ // Request the io_service to invoke the given handler.
+ template <typename Handler>
+ void dispatch(implementation_type& impl, Handler& handler);
+
+ // Request the io_service to invoke the given handler and return immediately.
+ template <typename Handler>
+ void post(implementation_type& impl, Handler& handler);
+
+ // Determine whether the strand is running in the current thread.
+ BOOST_ASIO_DECL bool running_in_this_thread(
+ const implementation_type& impl) const;
+
+private:
+ // Helper function to dispatch a handler. Returns true if the handler should
+ // be dispatched immediately.
+ BOOST_ASIO_DECL bool do_dispatch(implementation_type& impl, operation* op);
+
+ // Helper fiunction to post a handler.
+ BOOST_ASIO_DECL void do_post(implementation_type& impl,
+ operation* op, bool is_continuation);
+
+ BOOST_ASIO_DECL static void do_complete(io_service_impl* owner,
+ operation* base, const boost::system::error_code& ec,
+ std::size_t bytes_transferred);
+
+ // The io_service implementation used to post completions.
+ io_service_impl& io_service_;
+
+ // Mutex to protect access to the array of implementations.
+ boost::asio::detail::mutex mutex_;
+
+ // Number of implementations shared between all strand objects.
+#if defined(BOOST_ASIO_STRAND_IMPLEMENTATIONS)
+ enum { num_implementations = BOOST_ASIO_STRAND_IMPLEMENTATIONS };
+#else // defined(BOOST_ASIO_STRAND_IMPLEMENTATIONS)
+ enum { num_implementations = 193 };
+#endif // defined(BOOST_ASIO_STRAND_IMPLEMENTATIONS)
+
+ // Pool of implementations.
+ scoped_ptr<strand_impl> implementations_[num_implementations];
+
+ // Extra value used when hashing to prevent recycled memory locations from
+ // getting the same strand implementation.
+ std::size_t salt_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/strand_service.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/strand_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_STRAND_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/task_io_service.hpp b/ext/patches/boost/asio/detail/task_io_service.hpp
new file mode 100644
index 0000000..42b4c40
--- /dev/null
+++ b/ext/patches/boost/asio/detail/task_io_service.hpp
@@ -0,0 +1,203 @@
+//
+// detail/task_io_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TASK_IO_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_TASK_IO_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/system/error_code.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/atomic_count.hpp>
+#include <boost/asio/detail/call_stack.hpp>
+#include <boost/asio/detail/event.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/reactor_fwd.hpp>
+#include <boost/asio/detail/task_io_service_operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct task_io_service_thread_info;
+
+class task_io_service
+ : public boost::asio::detail::service_base<task_io_service>
+{
+public:
+ typedef task_io_service_operation operation;
+
+ // Constructor. Specifies the number of concurrent threads that are likely to
+ // run the io_service. If set to 1 certain optimisation are performed.
+ BOOST_ASIO_DECL task_io_service(boost::asio::io_service& io_service,
+ std::size_t concurrency_hint = 0);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Initialise the task, if required.
+ BOOST_ASIO_DECL void init_task();
+
+ // Run the event loop until interrupted or no more work.
+ BOOST_ASIO_DECL std::size_t run(boost::system::error_code& ec);
+
+ // Run until interrupted or one operation is performed.
+ BOOST_ASIO_DECL std::size_t run_one(boost::system::error_code& ec);
+
+ // Poll for operations without blocking.
+ BOOST_ASIO_DECL std::size_t poll(boost::system::error_code& ec);
+
+ // Poll for one operation without blocking.
+ BOOST_ASIO_DECL std::size_t poll_one(boost::system::error_code& ec);
+
+ // Interrupt the event processing loop.
+ BOOST_ASIO_DECL void stop();
+
+ // Determine whether the io_service is stopped.
+ BOOST_ASIO_DECL bool stopped() const;
+
+ // Reset in preparation for a subsequent run invocation.
+ BOOST_ASIO_DECL void reset();
+
+ // Notify that some work has started.
+ void work_started()
+ {
+ ++outstanding_work_;
+ }
+
+ // Notify that some work has finished.
+ void work_finished()
+ {
+ if (--outstanding_work_ == 0)
+ stop();
+ }
+
+ // Return whether a handler can be dispatched immediately.
+ bool can_dispatch()
+ {
+ return thread_call_stack::contains(this) != 0;
+ }
+
+ // Request invocation of the given handler.
+ template <typename Handler>
+ void dispatch(Handler& handler);
+
+ // Request invocation of the given handler and return immediately.
+ template <typename Handler>
+ void post(Handler& handler);
+
+ // Request invocation of the given operation and return immediately. Assumes
+ // that work_started() has not yet been called for the operation.
+ BOOST_ASIO_DECL void post_immediate_completion(
+ operation* op, bool is_continuation);
+
+ // Request invocation of the given operation and return immediately. Assumes
+ // that work_started() was previously called for the operation.
+ BOOST_ASIO_DECL void post_deferred_completion(operation* op);
+
+ // Request invocation of the given operations and return immediately. Assumes
+ // that work_started() was previously called for each operation.
+ BOOST_ASIO_DECL void post_deferred_completions(op_queue<operation>& ops);
+
+ // Process unfinished operations as part of a shutdown_service operation.
+ // Assumes that work_started() was previously called for the operations.
+ BOOST_ASIO_DECL void abandon_operations(op_queue<operation>& ops);
+
+private:
+ // Structure containing thread-specific data.
+ typedef task_io_service_thread_info thread_info;
+
+ // Enqueue the given operation following a failed attempt to dispatch the
+ // operation for immediate invocation.
+ BOOST_ASIO_DECL void do_dispatch(operation* op);
+
+ // Run at most one operation. May block.
+ BOOST_ASIO_DECL std::size_t do_run_one(mutex::scoped_lock& lock,
+ thread_info& this_thread, const boost::system::error_code& ec);
+
+ // Poll for at most one operation.
+ BOOST_ASIO_DECL std::size_t do_poll_one(mutex::scoped_lock& lock,
+ thread_info& this_thread, const boost::system::error_code& ec);
+
+ // Stop the task and all idle threads.
+ BOOST_ASIO_DECL void stop_all_threads(mutex::scoped_lock& lock);
+
+ // Wake a single idle thread, or the task, and always unlock the mutex.
+ BOOST_ASIO_DECL void wake_one_thread_and_unlock(
+ mutex::scoped_lock& lock);
+
+ // Helper class to perform task-related operations on block exit.
+ struct task_cleanup;
+ friend struct task_cleanup;
+
+ // Helper class to call work-related operations on block exit.
+ struct work_cleanup;
+ friend struct work_cleanup;
+
+ // Whether to optimise for single-threaded use cases.
+ const bool one_thread_;
+
+ // Mutex to protect access to internal data.
+ mutable mutex mutex_;
+
+ // Event to wake up blocked threads.
+ event wakeup_event_;
+
+ // The task to be run by this service.
+ reactor* task_;
+
+ // Operation object to represent the position of the task in the queue.
+ struct task_operation : operation
+ {
+ task_operation() : operation(0) {}
+ } task_operation_;
+
+ // Whether the task has been interrupted.
+ bool task_interrupted_;
+
+ // The count of unfinished work.
+ atomic_count outstanding_work_;
+
+ // The queue of handlers that are ready to be delivered.
+ op_queue<operation> op_queue_;
+
+ // Flag to indicate that the dispatcher has been stopped.
+ bool stopped_;
+
+ // Flag to indicate that the dispatcher has been shut down.
+ bool shutdown_;
+
+ // Per-thread call stack to track the state of each thread in the io_service.
+ typedef call_stack<task_io_service, thread_info> thread_call_stack;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/task_io_service.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/task_io_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // !defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_TASK_IO_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/task_io_service_operation.hpp b/ext/patches/boost/asio/detail/task_io_service_operation.hpp
new file mode 100644
index 0000000..f04dff0
--- /dev/null
+++ b/ext/patches/boost/asio/detail/task_io_service_operation.hpp
@@ -0,0 +1,78 @@
+//
+// detail/task_io_service_operation.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TASK_IO_SERVICE_OPERATION_HPP
+#define BOOST_ASIO_DETAIL_TASK_IO_SERVICE_OPERATION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/system/error_code.hpp>
+#include <boost/asio/detail/handler_tracking.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class task_io_service;
+
+// Base class for all operations. A function pointer is used instead of virtual
+// functions to avoid the associated overhead.
+class task_io_service_operation BOOST_ASIO_INHERIT_TRACKED_HANDLER
+{
+public:
+ void complete(task_io_service& owner,
+ const boost::system::error_code& ec, std::size_t bytes_transferred)
+ {
+ func_(&owner, this, ec, bytes_transferred);
+ }
+
+ void destroy()
+ {
+ func_(0, this, boost::system::error_code(), 0);
+ }
+
+protected:
+ typedef void (*func_type)(task_io_service*,
+ task_io_service_operation*,
+ const boost::system::error_code&, std::size_t);
+
+ task_io_service_operation(func_type func)
+ : next_(0),
+ func_(func),
+ task_result_(0)
+ {
+ }
+
+ // Prevents deletion through this type.
+ ~task_io_service_operation()
+ {
+ }
+
+private:
+ friend class op_queue_access;
+ task_io_service_operation* next_;
+ func_type func_;
+protected:
+ friend class task_io_service;
+ unsigned int task_result_; // Passed into bytes transferred.
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_TASK_IO_SERVICE_OPERATION_HPP
diff --git a/ext/patches/boost/asio/detail/task_io_service_thread_info.hpp b/ext/patches/boost/asio/detail/task_io_service_thread_info.hpp
new file mode 100644
index 0000000..ff59fbe
--- /dev/null
+++ b/ext/patches/boost/asio/detail/task_io_service_thread_info.hpp
@@ -0,0 +1,42 @@
+//
+// detail/task_io_service_thread_info.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TASK_IO_SERVICE_THREAD_INFO_HPP
+#define BOOST_ASIO_DETAIL_TASK_IO_SERVICE_THREAD_INFO_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/thread_info_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class task_io_service;
+class task_io_service_operation;
+
+struct task_io_service_thread_info : public thread_info_base
+{
+ op_queue<task_io_service_operation> private_op_queue;
+ long private_outstanding_work;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_TASK_IO_SERVICE_THREAD_INFO_HPP
diff --git a/ext/patches/boost/asio/detail/thread.hpp b/ext/patches/boost/asio/detail/thread.hpp
new file mode 100644
index 0000000..df4df6b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/thread.hpp
@@ -0,0 +1,58 @@
+//
+// detail/thread.hpp
+// ~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_THREAD_HPP
+#define BOOST_ASIO_DETAIL_THREAD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+# include <boost/asio/detail/null_thread.hpp>
+#elif defined(BOOST_ASIO_WINDOWS)
+# if defined(UNDER_CE)
+# include <boost/asio/detail/wince_thread.hpp>
+# else
+# include <boost/asio/detail/win_thread.hpp>
+# endif
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+# include <boost/asio/detail/posix_thread.hpp>
+#elif defined(BOOST_ASIO_HAS_STD_THREAD)
+# include <boost/asio/detail/std_thread.hpp>
+#else
+# error Only Windows, POSIX and std::thread are supported!
+#endif
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+typedef null_thread thread;
+#elif defined(BOOST_ASIO_WINDOWS)
+# if defined(UNDER_CE)
+typedef wince_thread thread;
+# else
+typedef win_thread thread;
+# endif
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+typedef posix_thread thread;
+#elif defined(BOOST_ASIO_HAS_STD_THREAD)
+typedef std_thread thread;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_THREAD_HPP
diff --git a/ext/patches/boost/asio/detail/thread_info_base.hpp b/ext/patches/boost/asio/detail/thread_info_base.hpp
new file mode 100644
index 0000000..558d749
--- /dev/null
+++ b/ext/patches/boost/asio/detail/thread_info_base.hpp
@@ -0,0 +1,93 @@
+//
+// detail/thread_info_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_THREAD_INFO_BASE_HPP
+#define BOOST_ASIO_DETAIL_THREAD_INFO_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <climits>
+#include <cstddef>
+#include <boost/asio/detail/noncopyable.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class thread_info_base
+ : private noncopyable
+{
+public:
+ thread_info_base()
+ : reusable_memory_(0)
+ {
+ }
+
+ ~thread_info_base()
+ {
+ if (reusable_memory_)
+ ::operator delete(reusable_memory_);
+ }
+
+ static void* allocate(thread_info_base* this_thread, std::size_t size)
+ {
+ if (this_thread && this_thread->reusable_memory_)
+ {
+ void* const pointer = this_thread->reusable_memory_;
+ this_thread->reusable_memory_ = 0;
+
+ unsigned char* const mem = static_cast<unsigned char*>(pointer);
+ if (static_cast<std::size_t>(mem[0]) >= size)
+ {
+ mem[size] = mem[0];
+ return pointer;
+ }
+
+ ::operator delete(pointer);
+ }
+
+ void* const pointer = ::operator new(size + 1);
+ unsigned char* const mem = static_cast<unsigned char*>(pointer);
+ mem[size] = (size <= UCHAR_MAX) ? static_cast<unsigned char>(size) : 0;
+ return pointer;
+ }
+
+ static void deallocate(thread_info_base* this_thread,
+ void* pointer, std::size_t size)
+ {
+ if (size <= UCHAR_MAX)
+ {
+ if (this_thread && this_thread->reusable_memory_ == 0)
+ {
+ unsigned char* const mem = static_cast<unsigned char*>(pointer);
+ mem[0] = mem[size];
+ this_thread->reusable_memory_ = pointer;
+ return;
+ }
+ }
+
+ ::operator delete(pointer);
+ }
+
+private:
+ void* reusable_memory_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_THREAD_INFO_BASE_HPP
diff --git a/ext/patches/boost/asio/detail/throw_error.hpp b/ext/patches/boost/asio/detail/throw_error.hpp
new file mode 100644
index 0000000..9cd37d7
--- /dev/null
+++ b/ext/patches/boost/asio/detail/throw_error.hpp
@@ -0,0 +1,55 @@
+//
+// detail/throw_error.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_THROW_ERROR_HPP
+#define BOOST_ASIO_DETAIL_THROW_ERROR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/system/error_code.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+BOOST_ASIO_DECL void do_throw_error(const boost::system::error_code& err);
+
+BOOST_ASIO_DECL void do_throw_error(const boost::system::error_code& err,
+ const char* location);
+
+inline void throw_error(const boost::system::error_code& err)
+{
+ if (err)
+ do_throw_error(err);
+}
+
+inline void throw_error(const boost::system::error_code& err,
+ const char* location)
+{
+ if (err)
+ do_throw_error(err, location);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/throw_error.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_THROW_ERROR_HPP
diff --git a/ext/patches/boost/asio/detail/throw_exception.hpp b/ext/patches/boost/asio/detail/throw_exception.hpp
new file mode 100644
index 0000000..92e97e3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/throw_exception.hpp
@@ -0,0 +1,53 @@
+//
+// detail/throw_exception.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_THROW_EXCEPTION_HPP
+#define BOOST_ASIO_DETAIL_THROW_EXCEPTION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_THROW_EXCEPTION)
+# include <boost/throw_exception.hpp>
+#endif // defined(BOOST_ASIO_BOOST_THROW_EXCEPTION)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_HAS_BOOST_THROW_EXCEPTION)
+using boost::throw_exception;
+#else // defined(BOOST_ASIO_HAS_BOOST_THROW_EXCEPTION)
+
+// Declare the throw_exception function for all targets.
+template <typename Exception>
+void throw_exception(const Exception& e);
+
+// Only define the throw_exception function when exceptions are enabled.
+// Otherwise, it is up to the application to provide a definition of this
+// function.
+# if !defined(BOOST_ASIO_NO_EXCEPTIONS)
+template <typename Exception>
+void throw_exception(const Exception& e)
+{
+ throw e;
+}
+# endif // !defined(BOOST_ASIO_NO_EXCEPTIONS)
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_THROW_EXCEPTION)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_THROW_EXCEPTION_HPP
diff --git a/ext/patches/boost/asio/detail/timer_queue.hpp b/ext/patches/boost/asio/detail/timer_queue.hpp
new file mode 100644
index 0000000..249a434
--- /dev/null
+++ b/ext/patches/boost/asio/detail/timer_queue.hpp
@@ -0,0 +1,334 @@
+//
+// detail/timer_queue.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TIMER_QUEUE_HPP
+#define BOOST_ASIO_DETAIL_TIMER_QUEUE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <vector>
+#include <boost/asio/detail/cstdint.hpp>
+#include <boost/asio/detail/date_time_fwd.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/timer_queue_base.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Time_Traits>
+class timer_queue
+ : public timer_queue_base
+{
+public:
+ // The time type.
+ typedef typename Time_Traits::time_type time_type;
+
+ // The duration type.
+ typedef typename Time_Traits::duration_type duration_type;
+
+ // Per-timer data.
+ class per_timer_data
+ {
+ public:
+ per_timer_data() : next_(0), prev_(0) {}
+
+ private:
+ friend class timer_queue;
+
+ // The operations waiting on the timer.
+ op_queue<wait_op> op_queue_;
+
+ // The index of the timer in the heap.
+ std::size_t heap_index_;
+
+ // Pointers to adjacent timers in a linked list.
+ per_timer_data* next_;
+ per_timer_data* prev_;
+ };
+
+ // Constructor.
+ timer_queue()
+ : timers_(),
+ heap_()
+ {
+ }
+
+ // Add a new timer to the queue. Returns true if this is the timer that is
+ // earliest in the queue, in which case the reactor's event demultiplexing
+ // function call may need to be interrupted and restarted.
+ bool enqueue_timer(const time_type& time, per_timer_data& timer, wait_op* op)
+ {
+ // Enqueue the timer object.
+ if (timer.prev_ == 0 && &timer != timers_)
+ {
+ if (this->is_positive_infinity(time))
+ {
+ // No heap entry is required for timers that never expire.
+ timer.heap_index_ = (std::numeric_limits<std::size_t>::max)();
+ }
+ else
+ {
+ // Put the new timer at the correct position in the heap. This is done
+ // first since push_back() can throw due to allocation failure.
+ timer.heap_index_ = heap_.size();
+ heap_entry entry = { time, &timer };
+ heap_.push_back(entry);
+ up_heap(heap_.size() - 1);
+ }
+
+ // Insert the new timer into the linked list of active timers.
+ timer.next_ = timers_;
+ timer.prev_ = 0;
+ if (timers_)
+ timers_->prev_ = &timer;
+ timers_ = &timer;
+ }
+
+ // Enqueue the individual timer operation.
+ timer.op_queue_.push(op);
+
+ // Interrupt reactor only if newly added timer is first to expire.
+ return timer.heap_index_ == 0 && timer.op_queue_.front() == op;
+ }
+
+ // Whether there are no timers in the queue.
+ virtual bool empty() const
+ {
+ return timers_ == 0;
+ }
+
+ // Get the time for the timer that is earliest in the queue.
+ virtual long wait_duration_msec(long max_duration) const
+ {
+ if (heap_.empty())
+ return max_duration;
+
+ return this->to_msec(
+ Time_Traits::to_posix_duration(
+ Time_Traits::subtract(heap_[0].time_, Time_Traits::now())),
+ max_duration);
+ }
+
+ // Get the time for the timer that is earliest in the queue.
+ virtual long wait_duration_usec(long max_duration) const
+ {
+ if (heap_.empty())
+ return max_duration;
+
+ return this->to_usec(
+ Time_Traits::to_posix_duration(
+ Time_Traits::subtract(heap_[0].time_, Time_Traits::now())),
+ max_duration);
+ }
+
+ // Dequeue all timers not later than the current time.
+ virtual void get_ready_timers(op_queue<operation>& ops)
+ {
+ if (!heap_.empty())
+ {
+ const time_type now = Time_Traits::now();
+ while (!heap_.empty() && !Time_Traits::less_than(now, heap_[0].time_))
+ {
+ per_timer_data* timer = heap_[0].timer_;
+ ops.push(timer->op_queue_);
+ remove_timer(*timer);
+ }
+ }
+ }
+
+ // Dequeue all timers.
+ virtual void get_all_timers(op_queue<operation>& ops)
+ {
+ while (timers_)
+ {
+ per_timer_data* timer = timers_;
+ timers_ = timers_->next_;
+ ops.push(timer->op_queue_);
+ timer->next_ = 0;
+ timer->prev_ = 0;
+ }
+
+ heap_.clear();
+ }
+
+ // Cancel and dequeue operations for the given timer.
+ std::size_t cancel_timer(per_timer_data& timer, op_queue<operation>& ops,
+ std::size_t max_cancelled = (std::numeric_limits<std::size_t>::max)())
+ {
+ std::size_t num_cancelled = 0;
+ if (timer.prev_ != 0 || &timer == timers_)
+ {
+ while (wait_op* op = (num_cancelled != max_cancelled)
+ ? timer.op_queue_.front() : 0)
+ {
+ op->ec_ = boost::asio::error::operation_aborted;
+ timer.op_queue_.pop();
+ ops.push(op);
+ ++num_cancelled;
+ }
+ if (timer.op_queue_.empty())
+ remove_timer(timer);
+ }
+ return num_cancelled;
+ }
+
+private:
+ // Move the item at the given index up the heap to its correct position.
+ void up_heap(std::size_t index)
+ {
+ std::size_t parent = (index - 1) / 2;
+ while (index > 0
+ && Time_Traits::less_than(heap_[index].time_, heap_[parent].time_))
+ {
+ swap_heap(index, parent);
+ index = parent;
+ parent = (index - 1) / 2;
+ }
+ }
+
+ // Move the item at the given index down the heap to its correct position.
+ void down_heap(std::size_t index)
+ {
+ std::size_t child = index * 2 + 1;
+ while (child < heap_.size())
+ {
+ std::size_t min_child = (child + 1 == heap_.size()
+ || Time_Traits::less_than(
+ heap_[child].time_, heap_[child + 1].time_))
+ ? child : child + 1;
+ if (Time_Traits::less_than(heap_[index].time_, heap_[min_child].time_))
+ break;
+ swap_heap(index, min_child);
+ index = min_child;
+ child = index * 2 + 1;
+ }
+ }
+
+ // Swap two entries in the heap.
+ void swap_heap(std::size_t index1, std::size_t index2)
+ {
+ heap_entry tmp = heap_[index1];
+ heap_[index1] = heap_[index2];
+ heap_[index2] = tmp;
+ heap_[index1].timer_->heap_index_ = index1;
+ heap_[index2].timer_->heap_index_ = index2;
+ }
+
+ // Remove a timer from the heap and list of timers.
+ void remove_timer(per_timer_data& timer)
+ {
+ // Remove the timer from the heap.
+ std::size_t index = timer.heap_index_;
+ if (!heap_.empty() && index < heap_.size())
+ {
+ if (index == heap_.size() - 1)
+ {
+ heap_.pop_back();
+ }
+ else
+ {
+ swap_heap(index, heap_.size() - 1);
+ heap_.pop_back();
+ std::size_t parent = (index - 1) / 2;
+ if (index > 0 && Time_Traits::less_than(
+ heap_[index].time_, heap_[parent].time_))
+ up_heap(index);
+ else
+ down_heap(index);
+ }
+ }
+
+ // Remove the timer from the linked list of active timers.
+ if (timers_ == &timer)
+ timers_ = timer.next_;
+ if (timer.prev_)
+ timer.prev_->next_ = timer.next_;
+ if (timer.next_)
+ timer.next_->prev_= timer.prev_;
+ timer.next_ = 0;
+ timer.prev_ = 0;
+ }
+
+ // Determine if the specified absolute time is positive infinity.
+ template <typename Time_Type>
+ static bool is_positive_infinity(const Time_Type&)
+ {
+ return false;
+ }
+
+ // Determine if the specified absolute time is positive infinity.
+ template <typename T, typename TimeSystem>
+ static bool is_positive_infinity(
+ const boost::date_time::base_time<T, TimeSystem>& time)
+ {
+ return time.is_pos_infinity();
+ }
+
+ // Helper function to convert a duration into milliseconds.
+ template <typename Duration>
+ long to_msec(const Duration& d, long max_duration) const
+ {
+ if (d.ticks() <= 0)
+ return 0;
+ int64_t msec = d.total_milliseconds();
+ if (msec == 0)
+ return 1;
+ if (msec > max_duration)
+ return max_duration;
+ return static_cast<long>(msec);
+ }
+
+ // Helper function to convert a duration into microseconds.
+ template <typename Duration>
+ long to_usec(const Duration& d, long max_duration) const
+ {
+ if (d.ticks() <= 0)
+ return 0;
+ int64_t usec = d.total_microseconds();
+ if (usec == 0)
+ return 1;
+ if (usec > max_duration)
+ return max_duration;
+ return static_cast<long>(usec);
+ }
+
+ // The head of a linked list of all active timers.
+ per_timer_data* timers_;
+
+ struct heap_entry
+ {
+ // The time when the timer should fire.
+ time_type time_;
+
+ // The associated timer with enqueued operations.
+ per_timer_data* timer_;
+ };
+
+ // The heap of timers, with the earliest timer at the front.
+ std::vector<heap_entry> heap_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_TIMER_QUEUE_HPP
diff --git a/ext/patches/boost/asio/detail/timer_queue_base.hpp b/ext/patches/boost/asio/detail/timer_queue_base.hpp
new file mode 100644
index 0000000..f397027
--- /dev/null
+++ b/ext/patches/boost/asio/detail/timer_queue_base.hpp
@@ -0,0 +1,70 @@
+//
+// detail/timer_queue_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TIMER_QUEUE_BASE_HPP
+#define BOOST_ASIO_DETAIL_TIMER_QUEUE_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class timer_queue_base
+ : private noncopyable
+{
+public:
+ // Constructor.
+ timer_queue_base() : next_(0) {}
+
+ // Destructor.
+ virtual ~timer_queue_base() {}
+
+ // Whether there are no timers in the queue.
+ virtual bool empty() const = 0;
+
+ // Get the time to wait until the next timer.
+ virtual long wait_duration_msec(long max_duration) const = 0;
+
+ // Get the time to wait until the next timer.
+ virtual long wait_duration_usec(long max_duration) const = 0;
+
+ // Dequeue all ready timers.
+ virtual void get_ready_timers(op_queue<operation>& ops) = 0;
+
+ // Dequeue all timers.
+ virtual void get_all_timers(op_queue<operation>& ops) = 0;
+
+private:
+ friend class timer_queue_set;
+
+ // Next timer queue in the set.
+ timer_queue_base* next_;
+};
+
+template <typename Time_Traits>
+class timer_queue;
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_TIMER_QUEUE_BASE_HPP
diff --git a/ext/patches/boost/asio/detail/timer_queue_ptime.hpp b/ext/patches/boost/asio/detail/timer_queue_ptime.hpp
new file mode 100644
index 0000000..3eaf095
--- /dev/null
+++ b/ext/patches/boost/asio/detail/timer_queue_ptime.hpp
@@ -0,0 +1,95 @@
+//
+// detail/timer_queue_ptime.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TIMER_QUEUE_PTIME_HPP
+#define BOOST_ASIO_DETAIL_TIMER_QUEUE_PTIME_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/time_traits.hpp>
+#include <boost/asio/detail/timer_queue.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct forwarding_posix_time_traits : time_traits<boost::posix_time::ptime> {};
+
+// Template specialisation for the commonly used instantation.
+template <>
+class timer_queue<time_traits<boost::posix_time::ptime> >
+ : public timer_queue_base
+{
+public:
+ // The time type.
+ typedef boost::posix_time::ptime time_type;
+
+ // The duration type.
+ typedef boost::posix_time::time_duration duration_type;
+
+ // Per-timer data.
+ typedef timer_queue<forwarding_posix_time_traits>::per_timer_data
+ per_timer_data;
+
+ // Constructor.
+ BOOST_ASIO_DECL timer_queue();
+
+ // Destructor.
+ BOOST_ASIO_DECL virtual ~timer_queue();
+
+ // Add a new timer to the queue. Returns true if this is the timer that is
+ // earliest in the queue, in which case the reactor's event demultiplexing
+ // function call may need to be interrupted and restarted.
+ BOOST_ASIO_DECL bool enqueue_timer(const time_type& time,
+ per_timer_data& timer, wait_op* op);
+
+ // Whether there are no timers in the queue.
+ BOOST_ASIO_DECL virtual bool empty() const;
+
+ // Get the time for the timer that is earliest in the queue.
+ BOOST_ASIO_DECL virtual long wait_duration_msec(long max_duration) const;
+
+ // Get the time for the timer that is earliest in the queue.
+ BOOST_ASIO_DECL virtual long wait_duration_usec(long max_duration) const;
+
+ // Dequeue all timers not later than the current time.
+ BOOST_ASIO_DECL virtual void get_ready_timers(op_queue<operation>& ops);
+
+ // Dequeue all timers.
+ BOOST_ASIO_DECL virtual void get_all_timers(op_queue<operation>& ops);
+
+ // Cancel and dequeue operations for the given timer.
+ BOOST_ASIO_DECL std::size_t cancel_timer(
+ per_timer_data& timer, op_queue<operation>& ops,
+ std::size_t max_cancelled = (std::numeric_limits<std::size_t>::max)());
+
+private:
+ timer_queue<forwarding_posix_time_traits> impl_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/timer_queue_ptime.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_TIMER_QUEUE_PTIME_HPP
diff --git a/ext/patches/boost/asio/detail/timer_queue_set.hpp b/ext/patches/boost/asio/detail/timer_queue_set.hpp
new file mode 100644
index 0000000..fb8edd0
--- /dev/null
+++ b/ext/patches/boost/asio/detail/timer_queue_set.hpp
@@ -0,0 +1,68 @@
+//
+// detail/timer_queue_set.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TIMER_QUEUE_SET_HPP
+#define BOOST_ASIO_DETAIL_TIMER_QUEUE_SET_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/timer_queue_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class timer_queue_set
+{
+public:
+ // Constructor.
+ BOOST_ASIO_DECL timer_queue_set();
+
+ // Add a timer queue to the set.
+ BOOST_ASIO_DECL void insert(timer_queue_base* q);
+
+ // Remove a timer queue from the set.
+ BOOST_ASIO_DECL void erase(timer_queue_base* q);
+
+ // Determine whether all queues are empty.
+ BOOST_ASIO_DECL bool all_empty() const;
+
+ // Get the wait duration in milliseconds.
+ BOOST_ASIO_DECL long wait_duration_msec(long max_duration) const;
+
+ // Get the wait duration in microseconds.
+ BOOST_ASIO_DECL long wait_duration_usec(long max_duration) const;
+
+ // Dequeue all ready timers.
+ BOOST_ASIO_DECL void get_ready_timers(op_queue<operation>& ops);
+
+ // Dequeue all timers.
+ BOOST_ASIO_DECL void get_all_timers(op_queue<operation>& ops);
+
+private:
+ timer_queue_base* first_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/timer_queue_set.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_DETAIL_TIMER_QUEUE_SET_HPP
diff --git a/ext/patches/boost/asio/detail/timer_scheduler.hpp b/ext/patches/boost/asio/detail/timer_scheduler.hpp
new file mode 100644
index 0000000..1eb6b82
--- /dev/null
+++ b/ext/patches/boost/asio/detail/timer_scheduler.hpp
@@ -0,0 +1,35 @@
+//
+// detail/timer_scheduler.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TIMER_SCHEDULER_HPP
+#define BOOST_ASIO_DETAIL_TIMER_SCHEDULER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/timer_scheduler_fwd.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/winrt_timer_scheduler.hpp>
+#elif defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_io_service.hpp>
+#elif defined(BOOST_ASIO_HAS_EPOLL)
+# include <boost/asio/detail/epoll_reactor.hpp>
+#elif defined(BOOST_ASIO_HAS_KQUEUE)
+# include <boost/asio/detail/kqueue_reactor.hpp>
+#elif defined(BOOST_ASIO_HAS_DEV_POLL)
+# include <boost/asio/detail/dev_poll_reactor.hpp>
+#else
+# include <boost/asio/detail/select_reactor.hpp>
+#endif
+
+#endif // BOOST_ASIO_DETAIL_TIMER_SCHEDULER_HPP
diff --git a/ext/patches/boost/asio/detail/timer_scheduler_fwd.hpp b/ext/patches/boost/asio/detail/timer_scheduler_fwd.hpp
new file mode 100644
index 0000000..e5aa34d
--- /dev/null
+++ b/ext/patches/boost/asio/detail/timer_scheduler_fwd.hpp
@@ -0,0 +1,42 @@
+//
+// detail/timer_scheduler_fwd.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TIMER_SCHEDULER_FWD_HPP
+#define BOOST_ASIO_DETAIL_TIMER_SCHEDULER_FWD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+typedef class winrt_timer_scheduler timer_scheduler;
+#elif defined(BOOST_ASIO_HAS_IOCP)
+typedef class win_iocp_io_service timer_scheduler;
+#elif defined(BOOST_ASIO_HAS_EPOLL)
+typedef class epoll_reactor timer_scheduler;
+#elif defined(BOOST_ASIO_HAS_KQUEUE)
+typedef class kqueue_reactor timer_scheduler;
+#elif defined(BOOST_ASIO_HAS_DEV_POLL)
+typedef class dev_poll_reactor timer_scheduler;
+#else
+typedef class select_reactor timer_scheduler;
+#endif
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_TIMER_SCHEDULER_FWD_HPP
diff --git a/ext/patches/boost/asio/detail/tss_ptr.hpp b/ext/patches/boost/asio/detail/tss_ptr.hpp
new file mode 100644
index 0000000..9258fb8
--- /dev/null
+++ b/ext/patches/boost/asio/detail/tss_ptr.hpp
@@ -0,0 +1,71 @@
+//
+// detail/tss_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TSS_PTR_HPP
+#define BOOST_ASIO_DETAIL_TSS_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_THREADS)
+# include <boost/asio/detail/null_tss_ptr.hpp>
+#elif defined(BOOST_ASIO_HAS_THREAD_KEYWORD_EXTENSION)
+# include <boost/asio/detail/keyword_tss_ptr.hpp>
+#elif defined(BOOST_ASIO_WINDOWS)
+# include <boost/asio/detail/win_tss_ptr.hpp>
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+# include <boost/asio/detail/posix_tss_ptr.hpp>
+#else
+# error Only Windows and POSIX are supported!
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename T>
+class tss_ptr
+#if !defined(BOOST_ASIO_HAS_THREADS)
+ : public null_tss_ptr<T>
+#elif defined(BOOST_ASIO_HAS_THREAD_KEYWORD_EXTENSION)
+ : public keyword_tss_ptr<T>
+#elif defined(BOOST_ASIO_WINDOWS)
+ : public win_tss_ptr<T>
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+ : public posix_tss_ptr<T>
+#endif
+{
+public:
+ void operator=(T* value)
+ {
+#if !defined(BOOST_ASIO_HAS_THREADS)
+ null_tss_ptr<T>::operator=(value);
+#elif defined(BOOST_ASIO_HAS_THREAD_KEYWORD_EXTENSION)
+ keyword_tss_ptr<T>::operator=(value);
+#elif defined(BOOST_ASIO_WINDOWS)
+ win_tss_ptr<T>::operator=(value);
+#elif defined(BOOST_ASIO_HAS_PTHREADS)
+ posix_tss_ptr<T>::operator=(value);
+#endif
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_TSS_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/type_traits.hpp b/ext/patches/boost/asio/detail/type_traits.hpp
new file mode 100644
index 0000000..5dab201
--- /dev/null
+++ b/ext/patches/boost/asio/detail/type_traits.hpp
@@ -0,0 +1,60 @@
+//
+// detail/type_traits.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_TYPE_TRAITS_HPP
+#define BOOST_ASIO_DETAIL_TYPE_TRAITS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_TYPE_TRAITS)
+# include <type_traits>
+#else // defined(BOOST_ASIO_HAS_TYPE_TRAITS)
+# include <boost/type_traits/add_const.hpp>
+# include <boost/type_traits/is_const.hpp>
+# include <boost/type_traits/is_convertible.hpp>
+# include <boost/type_traits/is_function.hpp>
+# include <boost/type_traits/is_same.hpp>
+# include <boost/type_traits/remove_pointer.hpp>
+# include <boost/type_traits/remove_reference.hpp>
+# include <boost/utility/enable_if.hpp>
+#endif // defined(BOOST_ASIO_HAS_TYPE_TRAITS)
+
+namespace boost {
+namespace asio {
+
+#if defined(BOOST_ASIO_HAS_STD_TYPE_TRAITS)
+using std::add_const;
+using std::enable_if;
+using std::is_const;
+using std::is_convertible;
+using std::is_function;
+using std::is_same;
+using std::remove_pointer;
+using std::remove_reference;
+#else // defined(BOOST_ASIO_HAS_STD_TYPE_TRAITS)
+using boost::add_const;
+template <bool Condition, typename Type = void>
+struct enable_if : boost::enable_if_c<Condition, Type> {};
+using boost::is_const;
+using boost::is_convertible;
+using boost::is_function;
+using boost::is_same;
+using boost::remove_pointer;
+using boost::remove_reference;
+#endif // defined(BOOST_ASIO_HAS_STD_TYPE_TRAITS)
+
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_TYPE_TRAITS_HPP
diff --git a/ext/patches/boost/asio/detail/variadic_templates.hpp b/ext/patches/boost/asio/detail/variadic_templates.hpp
new file mode 100644
index 0000000..0530289
--- /dev/null
+++ b/ext/patches/boost/asio/detail/variadic_templates.hpp
@@ -0,0 +1,63 @@
+//
+// detail/variadic_templates.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_VARIADIC_TEMPLATES_HPP
+#define BOOST_ASIO_DETAIL_VARIADIC_TEMPLATES_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+# define BOOST_ASIO_VARIADIC_TPARAMS(n) BOOST_ASIO_VARIADIC_TPARAMS_##n
+
+# define BOOST_ASIO_VARIADIC_TPARAMS_1 \
+ typename T1
+# define BOOST_ASIO_VARIADIC_TPARAMS_2 \
+ typename T1, typename T2
+# define BOOST_ASIO_VARIADIC_TPARAMS_3 \
+ typename T1, typename T2, typename T3
+# define BOOST_ASIO_VARIADIC_TPARAMS_4 \
+ typename T1, typename T2, typename T3, typename T4
+# define BOOST_ASIO_VARIADIC_TPARAMS_5 \
+ typename T1, typename T2, typename T3, typename T4, typename T5
+
+# define BOOST_ASIO_VARIADIC_TARGS(n) BOOST_ASIO_VARIADIC_TARGS_##n
+
+# define BOOST_ASIO_VARIADIC_TARGS_1 x1
+# define BOOST_ASIO_VARIADIC_TARGS_2 x1, x2
+# define BOOST_ASIO_VARIADIC_TARGS_3 x1, x2, x3
+# define BOOST_ASIO_VARIADIC_TARGS_4 x1, x2, x3, x4
+# define BOOST_ASIO_VARIADIC_TARGS_5 x1, x2, x3, x4, x5
+
+# define BOOST_ASIO_VARIADIC_PARAMS(n) BOOST_ASIO_VARIADIC_PARAMS_##n
+
+# define BOOST_ASIO_VARIADIC_PARAMS_1 T1 x1
+# define BOOST_ASIO_VARIADIC_PARAMS_2 T1 x1, T2 x2
+# define BOOST_ASIO_VARIADIC_PARAMS_3 T1 x1, T2 x2, T3 x3
+# define BOOST_ASIO_VARIADIC_PARAMS_4 T1 x1, T2 x2, T3 x3, T4 x4
+# define BOOST_ASIO_VARIADIC_PARAMS_5 T1 x1, T2 x2, T3 x3, T4 x4, T5 x5
+
+# define BOOST_ASIO_VARIADIC_ARGS(n) BOOST_ASIO_VARIADIC_ARGS_##n
+
+# define BOOST_ASIO_VARIADIC_ARGS_1 x1
+# define BOOST_ASIO_VARIADIC_ARGS_2 x1, x2
+# define BOOST_ASIO_VARIADIC_ARGS_3 x1, x2, x3
+# define BOOST_ASIO_VARIADIC_ARGS_4 x1, x2, x3, x4
+# define BOOST_ASIO_VARIADIC_ARGS_5 x1, x2, x3, x4, x5
+
+# define BOOST_ASIO_VARIADIC_GENERATE(m) m(1) m(2) m(3) m(4) m(5)
+
+#endif // !defined(BOOST_ASIO_HAS_VARIADIC_TEMPLATES)
+
+#endif // BOOST_ASIO_DETAIL_VARIADIC_TEMPLATES_HPP
diff --git a/ext/patches/boost/asio/detail/wait_handler.hpp b/ext/patches/boost/asio/detail/wait_handler.hpp
new file mode 100644
index 0000000..3f722a0
--- /dev/null
+++ b/ext/patches/boost/asio/detail/wait_handler.hpp
@@ -0,0 +1,85 @@
+//
+// detail/wait_handler.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WAIT_HANDLER_HPP
+#define BOOST_ASIO_DETAIL_WAIT_HANDLER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+class wait_handler : public wait_op
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(wait_handler);
+
+ wait_handler(Handler& h)
+ : wait_op(&wait_handler::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(h))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& /*ec*/,
+ std::size_t /*bytes_transferred*/)
+ {
+ // Take ownership of the handler object.
+ wait_handler* h(static_cast<wait_handler*>(base));
+ ptr p = { boost::asio::detail::addressof(h->handler_), h, h };
+
+ BOOST_ASIO_HANDLER_COMPLETION((h));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder1<Handler, boost::system::error_code>
+ handler(h->handler_, h->ec_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_WAIT_HANDLER_HPP
diff --git a/ext/patches/boost/asio/detail/wait_op.hpp b/ext/patches/boost/asio/detail/wait_op.hpp
new file mode 100644
index 0000000..927f2e4
--- /dev/null
+++ b/ext/patches/boost/asio/detail/wait_op.hpp
@@ -0,0 +1,47 @@
+//
+// detail/wait_op.hpp
+// ~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WAIT_OP_HPP
+#define BOOST_ASIO_DETAIL_WAIT_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class wait_op
+ : public operation
+{
+public:
+ // The error code to be passed to the completion handler.
+ boost::system::error_code ec_;
+
+protected:
+ wait_op(func_type func)
+ : operation(func)
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_WAIT_OP_HPP
diff --git a/ext/patches/boost/asio/detail/weak_ptr.hpp b/ext/patches/boost/asio/detail/weak_ptr.hpp
new file mode 100644
index 0000000..52ade1f
--- /dev/null
+++ b/ext/patches/boost/asio/detail/weak_ptr.hpp
@@ -0,0 +1,40 @@
+//
+// detail/weak_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WEAK_PTR_HPP
+#define BOOST_ASIO_DETAIL_WEAK_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+# include <memory>
+#else // defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+# include <boost/weak_ptr.hpp>
+#endif // defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+#if defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+using std::weak_ptr;
+#else // defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+using boost::weak_ptr;
+#endif // defined(BOOST_ASIO_HAS_STD_SHARED_PTR)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_DETAIL_WEAK_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/win_event.hpp b/ext/patches/boost/asio/detail/win_event.hpp
new file mode 100644
index 0000000..6afdca3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_event.hpp
@@ -0,0 +1,128 @@
+//
+// detail/win_event.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_EVENT_HPP
+#define BOOST_ASIO_DETAIL_WIN_EVENT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS)
+
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_event
+ : private noncopyable
+{
+public:
+ // Constructor.
+ BOOST_ASIO_DECL win_event();
+
+ // Destructor.
+ BOOST_ASIO_DECL ~win_event();
+
+ // Signal the event. (Retained for backward compatibility.)
+ template <typename Lock>
+ void signal(Lock& lock)
+ {
+ this->signal_all(lock);
+ }
+
+ // Signal all waiters.
+ template <typename Lock>
+ void signal_all(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ (void)lock;
+ state_ |= 1;
+ ::SetEvent(events_[0]);
+ }
+
+ // Unlock the mutex and signal one waiter.
+ template <typename Lock>
+ void unlock_and_signal_one(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ state_ |= 1;
+ bool have_waiters = (state_ > 1);
+ lock.unlock();
+ if (have_waiters)
+ ::SetEvent(events_[1]);
+ }
+
+ // If there's a waiter, unlock the mutex and signal it.
+ template <typename Lock>
+ bool maybe_unlock_and_signal_one(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ state_ |= 1;
+ if (state_ > 1)
+ {
+ lock.unlock();
+ ::SetEvent(events_[1]);
+ return true;
+ }
+ return false;
+ }
+
+ // Reset the event.
+ template <typename Lock>
+ void clear(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ (void)lock;
+ ::ResetEvent(events_[0]);
+ state_ &= ~std::size_t(1);
+ }
+
+ // Wait for the event to become signalled.
+ template <typename Lock>
+ void wait(Lock& lock)
+ {
+ BOOST_ASIO_ASSERT(lock.locked());
+ while ((state_ & 1) == 0)
+ {
+ state_ += 2;
+ lock.unlock();
+ ::WaitForMultipleObjects(2, events_, false, INFINITE);
+ lock.lock();
+ state_ -= 2;
+ }
+ }
+
+private:
+ HANDLE events_[2];
+ std::size_t state_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_event.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_WIN_EVENT_HPP
diff --git a/ext/patches/boost/asio/detail/win_fd_set_adapter.hpp b/ext/patches/boost/asio/detail/win_fd_set_adapter.hpp
new file mode 100644
index 0000000..b14d11a
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_fd_set_adapter.hpp
@@ -0,0 +1,151 @@
+//
+// detail/win_fd_set_adapter.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_FD_SET_ADAPTER_HPP
+#define BOOST_ASIO_DETAIL_WIN_FD_SET_ADAPTER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/reactor_op_queue.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Adapts the FD_SET type to meet the Descriptor_Set concept's requirements.
+class win_fd_set_adapter : noncopyable
+{
+public:
+ enum { default_fd_set_size = 1024 };
+
+ win_fd_set_adapter()
+ : capacity_(default_fd_set_size),
+ max_descriptor_(invalid_socket)
+ {
+ fd_set_ = static_cast<win_fd_set*>(::operator new(
+ sizeof(win_fd_set) - sizeof(SOCKET)
+ + sizeof(SOCKET) * (capacity_)));
+ fd_set_->fd_count = 0;
+ }
+
+ ~win_fd_set_adapter()
+ {
+ ::operator delete(fd_set_);
+ }
+
+ void reset()
+ {
+ fd_set_->fd_count = 0;
+ max_descriptor_ = invalid_socket;
+ }
+
+ bool set(socket_type descriptor)
+ {
+ for (u_int i = 0; i < fd_set_->fd_count; ++i)
+ if (fd_set_->fd_array[i] == descriptor)
+ return true;
+
+ reserve(fd_set_->fd_count + 1);
+ fd_set_->fd_array[fd_set_->fd_count++] = descriptor;
+ return true;
+ }
+
+ void set(reactor_op_queue<socket_type>& operations, op_queue<operation>&)
+ {
+ reactor_op_queue<socket_type>::iterator i = operations.begin();
+ while (i != operations.end())
+ {
+ reactor_op_queue<socket_type>::iterator op_iter = i++;
+ reserve(fd_set_->fd_count + 1);
+ fd_set_->fd_array[fd_set_->fd_count++] = op_iter->first;
+ }
+ }
+
+ bool is_set(socket_type descriptor) const
+ {
+ return !!__WSAFDIsSet(descriptor,
+ const_cast<fd_set*>(reinterpret_cast<const fd_set*>(fd_set_)));
+ }
+
+ operator fd_set*()
+ {
+ return reinterpret_cast<fd_set*>(fd_set_);
+ }
+
+ socket_type max_descriptor() const
+ {
+ return max_descriptor_;
+ }
+
+ void perform(reactor_op_queue<socket_type>& operations,
+ op_queue<operation>& ops) const
+ {
+ for (u_int i = 0; i < fd_set_->fd_count; ++i)
+ operations.perform_operations(fd_set_->fd_array[i], ops);
+ }
+
+private:
+ // This structure is defined to be compatible with the Windows API fd_set
+ // structure, but without being dependent on the value of FD_SETSIZE. We use
+ // the "struct hack" to allow the number of descriptors to be varied at
+ // runtime.
+ struct win_fd_set
+ {
+ u_int fd_count;
+ SOCKET fd_array[1];
+ };
+
+ // Increase the fd_set_ capacity to at least the specified number of elements.
+ void reserve(u_int n)
+ {
+ if (n <= capacity_)
+ return;
+
+ u_int new_capacity = capacity_ + capacity_ / 2;
+ if (new_capacity < n)
+ new_capacity = n;
+
+ win_fd_set* new_fd_set = static_cast<win_fd_set*>(::operator new(
+ sizeof(win_fd_set) - sizeof(SOCKET)
+ + sizeof(SOCKET) * (new_capacity)));
+
+ new_fd_set->fd_count = fd_set_->fd_count;
+ for (u_int i = 0; i < fd_set_->fd_count; ++i)
+ new_fd_set->fd_array[i] = fd_set_->fd_array[i];
+
+ ::operator delete(fd_set_);
+ fd_set_ = new_fd_set;
+ capacity_ = new_capacity;
+ }
+
+ win_fd_set* fd_set_;
+ u_int capacity_;
+ socket_type max_descriptor_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_WIN_FD_SET_ADAPTER_HPP
diff --git a/ext/patches/boost/asio/detail/win_fenced_block.hpp b/ext/patches/boost/asio/detail/win_fenced_block.hpp
new file mode 100644
index 0000000..8fb0eaf
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_fenced_block.hpp
@@ -0,0 +1,91 @@
+//
+// detail/win_fenced_block.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_FENCED_BLOCK_HPP
+#define BOOST_ASIO_DETAIL_WIN_FENCED_BLOCK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) && !defined(UNDER_CE)
+
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_fenced_block
+ : private noncopyable
+{
+public:
+ enum half_t { half };
+ enum full_t { full };
+
+ // Constructor for a half fenced block.
+ explicit win_fenced_block(half_t)
+ {
+ }
+
+ // Constructor for a full fenced block.
+ explicit win_fenced_block(full_t)
+ {
+#if defined(__BORLANDC__)
+ LONG barrier = 0;
+ ::InterlockedExchange(&barrier, 1);
+#elif defined(BOOST_ASIO_MSVC) \
+ && ((BOOST_ASIO_MSVC < 1400) || !defined(MemoryBarrier))
+# if defined(_M_IX86)
+# pragma warning(push)
+# pragma warning(disable:4793)
+ LONG barrier;
+ __asm { xchg barrier, eax }
+# pragma warning(pop)
+# endif // defined(_M_IX86)
+#else
+ MemoryBarrier();
+#endif
+ }
+
+ // Destructor.
+ ~win_fenced_block()
+ {
+#if defined(__BORLANDC__)
+ LONG barrier = 0;
+ ::InterlockedExchange(&barrier, 1);
+#elif defined(BOOST_ASIO_MSVC) \
+ && ((BOOST_ASIO_MSVC < 1400) || !defined(MemoryBarrier))
+# if defined(_M_IX86)
+# pragma warning(push)
+# pragma warning(disable:4793)
+ LONG barrier;
+ __asm { xchg barrier, eax }
+# pragma warning(pop)
+# endif // defined(_M_IX86)
+#else
+ MemoryBarrier();
+#endif
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS) && !defined(UNDER_CE)
+
+#endif // BOOST_ASIO_DETAIL_WIN_FENCED_BLOCK_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_handle_read_op.hpp b/ext/patches/boost/asio/detail/win_iocp_handle_read_op.hpp
new file mode 100644
index 0000000..68aac67
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_handle_read_op.hpp
@@ -0,0 +1,111 @@
+//
+// detail/win_iocp_handle_read_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_READ_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_READ_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/error.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence, typename Handler>
+class win_iocp_handle_read_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_handle_read_op);
+
+ win_iocp_handle_read_op(
+ const MutableBufferSequence& buffers, Handler& handler)
+ : operation(&win_iocp_handle_read_op::do_complete),
+ buffers_(buffers),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& result_ec,
+ std::size_t bytes_transferred)
+ {
+ boost::system::error_code ec(result_ec);
+
+ // Take ownership of the operation object.
+ win_iocp_handle_read_op* o(static_cast<win_iocp_handle_read_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ if (owner)
+ {
+ // Check whether buffers are still valid.
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::validate(o->buffers_);
+ }
+#endif // defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+
+ // Map non-portable errors to their portable counterparts.
+ if (ec.value() == ERROR_HANDLE_EOF)
+ ec = boost::asio::error::eof;
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, ec, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ MutableBufferSequence buffers_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_READ_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_handle_service.hpp b/ext/patches/boost/asio/detail/win_iocp_handle_service.hpp
new file mode 100644
index 0000000..288aeb6
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_handle_service.hpp
@@ -0,0 +1,324 @@
+//
+// detail/win_iocp_handle_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/cstdint.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/win_iocp_handle_read_op.hpp>
+#include <boost/asio/detail/win_iocp_handle_write_op.hpp>
+#include <boost/asio/detail/win_iocp_io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_iocp_handle_service
+{
+public:
+ // The native type of a stream handle.
+ typedef HANDLE native_handle_type;
+
+ // The implementation type of the stream handle.
+ class implementation_type
+ {
+ public:
+ // Default constructor.
+ implementation_type()
+ : handle_(INVALID_HANDLE_VALUE),
+ safe_cancellation_thread_id_(0),
+ next_(0),
+ prev_(0)
+ {
+ }
+
+ private:
+ // Only this service will have access to the internal values.
+ friend class win_iocp_handle_service;
+
+ // The native stream handle representation.
+ native_handle_type handle_;
+
+ // The ID of the thread from which it is safe to cancel asynchronous
+ // operations. 0 means no asynchronous operations have been started yet.
+ // ~0 means asynchronous operations have been started from more than one
+ // thread, and cancellation is not supported for the handle.
+ DWORD safe_cancellation_thread_id_;
+
+ // Pointers to adjacent handle implementations in linked list.
+ implementation_type* next_;
+ implementation_type* prev_;
+ };
+
+ BOOST_ASIO_DECL win_iocp_handle_service(boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new handle implementation.
+ BOOST_ASIO_DECL void construct(implementation_type& impl);
+
+ // Move-construct a new handle implementation.
+ BOOST_ASIO_DECL void move_construct(implementation_type& impl,
+ implementation_type& other_impl);
+
+ // Move-assign from another handle implementation.
+ BOOST_ASIO_DECL void move_assign(implementation_type& impl,
+ win_iocp_handle_service& other_service,
+ implementation_type& other_impl);
+
+ // Destroy a handle implementation.
+ BOOST_ASIO_DECL void destroy(implementation_type& impl);
+
+ // Assign a native handle to a handle implementation.
+ BOOST_ASIO_DECL boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec);
+
+ // Determine whether the handle is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return impl.handle_ != INVALID_HANDLE_VALUE;
+ }
+
+ // Destroy a handle implementation.
+ BOOST_ASIO_DECL boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ // Get the native handle representation.
+ native_handle_type native_handle(const implementation_type& impl) const
+ {
+ return impl.handle_;
+ }
+
+ // Cancel all operations associated with the handle.
+ BOOST_ASIO_DECL boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ // Write the given data. Returns the number of bytes written.
+ template <typename ConstBufferSequence>
+ size_t write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return write_some_at(impl, 0, buffers, ec);
+ }
+
+ // Write the given data at the specified offset. Returns the number of bytes
+ // written.
+ template <typename ConstBufferSequence>
+ size_t write_some_at(implementation_type& impl, uint64_t offset,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ boost::asio::const_buffer buffer =
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::first(buffers);
+
+ return do_write(impl, offset, buffer, ec);
+ }
+
+ // Start an asynchronous write. The data being written must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_handle_write_op<ConstBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "handle", &impl, "async_write_some"));
+
+ start_write_op(impl, 0,
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::first(buffers), p.p);
+ p.v = p.p = 0;
+ }
+
+ // Start an asynchronous write at a specified offset. The data being written
+ // must be valid for the lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_write_some_at(implementation_type& impl, uint64_t offset,
+ const ConstBufferSequence& buffers, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_handle_write_op<ConstBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "handle", &impl, "async_write_some_at"));
+
+ start_write_op(impl, offset,
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::first(buffers), p.p);
+ p.v = p.p = 0;
+ }
+
+ // Read some data. Returns the number of bytes received.
+ template <typename MutableBufferSequence>
+ size_t read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return read_some_at(impl, 0, buffers, ec);
+ }
+
+ // Read some data at a specified offset. Returns the number of bytes received.
+ template <typename MutableBufferSequence>
+ size_t read_some_at(implementation_type& impl, uint64_t offset,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ boost::asio::mutable_buffer buffer =
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::first(buffers);
+
+ return do_read(impl, offset, buffer, ec);
+ }
+
+ // Start an asynchronous read. The buffer for the data being received must be
+ // valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_handle_read_op<MutableBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "handle", &impl, "async_read_some"));
+
+ start_read_op(impl, 0,
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::first(buffers), p.p);
+ p.v = p.p = 0;
+ }
+
+ // Start an asynchronous read at a specified offset. The buffer for the data
+ // being received must be valid for the lifetime of the asynchronous
+ // operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_read_some_at(implementation_type& impl, uint64_t offset,
+ const MutableBufferSequence& buffers, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_handle_read_op<MutableBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "handle", &impl, "async_read_some_at"));
+
+ start_read_op(impl, offset,
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::first(buffers), p.p);
+ p.v = p.p = 0;
+ }
+
+private:
+ // Prevent the use of the null_buffers type with this service.
+ size_t write_some(implementation_type& impl,
+ const null_buffers& buffers, boost::system::error_code& ec);
+ size_t write_some_at(implementation_type& impl, uint64_t offset,
+ const null_buffers& buffers, boost::system::error_code& ec);
+ template <typename Handler>
+ void async_write_some(implementation_type& impl,
+ const null_buffers& buffers, Handler& handler);
+ template <typename Handler>
+ void async_write_some_at(implementation_type& impl, uint64_t offset,
+ const null_buffers& buffers, Handler& handler);
+ size_t read_some(implementation_type& impl,
+ const null_buffers& buffers, boost::system::error_code& ec);
+ size_t read_some_at(implementation_type& impl, uint64_t offset,
+ const null_buffers& buffers, boost::system::error_code& ec);
+ template <typename Handler>
+ void async_read_some(implementation_type& impl,
+ const null_buffers& buffers, Handler& handler);
+ template <typename Handler>
+ void async_read_some_at(implementation_type& impl, uint64_t offset,
+ const null_buffers& buffers, Handler& handler);
+
+ // Helper class for waiting for synchronous operations to complete.
+ class overlapped_wrapper;
+
+ // Helper function to perform a synchronous write operation.
+ BOOST_ASIO_DECL size_t do_write(implementation_type& impl,
+ uint64_t offset, const boost::asio::const_buffer& buffer,
+ boost::system::error_code& ec);
+
+ // Helper function to start a write operation.
+ BOOST_ASIO_DECL void start_write_op(implementation_type& impl,
+ uint64_t offset, const boost::asio::const_buffer& buffer,
+ operation* op);
+
+ // Helper function to perform a synchronous write operation.
+ BOOST_ASIO_DECL size_t do_read(implementation_type& impl,
+ uint64_t offset, const boost::asio::mutable_buffer& buffer,
+ boost::system::error_code& ec);
+
+ // Helper function to start a read operation.
+ BOOST_ASIO_DECL void start_read_op(implementation_type& impl,
+ uint64_t offset, const boost::asio::mutable_buffer& buffer,
+ operation* op);
+
+ // Update the ID of the thread from which cancellation is safe.
+ BOOST_ASIO_DECL void update_cancellation_thread_id(implementation_type& impl);
+
+ // Helper function to close a handle when the associated object is being
+ // destroyed.
+ BOOST_ASIO_DECL void close_for_destruction(implementation_type& impl);
+
+ // The IOCP service used for running asynchronous operations and dispatching
+ // handlers.
+ win_iocp_io_service& iocp_service_;
+
+ // Mutex to protect access to the linked list of implementations.
+ mutex mutex_;
+
+ // The head of a linked list of all implementations.
+ implementation_type* impl_list_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_iocp_handle_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_handle_write_op.hpp b/ext/patches/boost/asio/detail/win_iocp_handle_write_op.hpp
new file mode 100644
index 0000000..738c2f3
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_handle_write_op.hpp
@@ -0,0 +1,103 @@
+//
+// detail/win_iocp_handle_write_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_WRITE_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_WRITE_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/error.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename ConstBufferSequence, typename Handler>
+class win_iocp_handle_write_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_handle_write_op);
+
+ win_iocp_handle_write_op(const ConstBufferSequence& buffers, Handler& handler)
+ : operation(&win_iocp_handle_write_op::do_complete),
+ buffers_(buffers),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& ec, std::size_t bytes_transferred)
+ {
+ // Take ownership of the operation object.
+ win_iocp_handle_write_op* o(static_cast<win_iocp_handle_write_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ if (owner)
+ {
+ // Check whether buffers are still valid.
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::validate(o->buffers_);
+ }
+#endif // defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, ec, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ ConstBufferSequence buffers_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_HANDLE_WRITE_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_io_service.hpp b/ext/patches/boost/asio/detail/win_iocp_io_service.hpp
new file mode 100644
index 0000000..04678ed
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_io_service.hpp
@@ -0,0 +1,317 @@
+//
+// detail/win_iocp_io_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_IO_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_IO_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/call_stack.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/scoped_ptr.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/thread.hpp>
+#include <boost/asio/detail/timer_queue_base.hpp>
+#include <boost/asio/detail/timer_queue_set.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+#include <boost/asio/detail/win_iocp_operation.hpp>
+#include <boost/asio/detail/win_iocp_thread_info.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class wait_op;
+
+class win_iocp_io_service
+ : public boost::asio::detail::service_base<win_iocp_io_service>
+{
+public:
+
+ // Constructor. Specifies a concurrency hint that is passed through to the
+ // underlying I/O completion port.
+ BOOST_ASIO_DECL win_iocp_io_service(boost::asio::io_service& io_service,
+ size_t concurrency_hint = 0);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Initialise the task. Nothing to do here.
+ void init_task()
+ {
+ }
+
+ // Register a handle with the IO completion port.
+ BOOST_ASIO_DECL boost::system::error_code register_handle(
+ HANDLE handle, boost::system::error_code& ec);
+
+ // Run the event loop until stopped or no more work.
+ BOOST_ASIO_DECL size_t run(boost::system::error_code& ec);
+
+ // Run until stopped or one operation is performed.
+ BOOST_ASIO_DECL size_t run_one(boost::system::error_code& ec);
+
+ // Poll for operations without blocking.
+ BOOST_ASIO_DECL size_t poll(boost::system::error_code& ec);
+
+ // Poll for one operation without blocking.
+ BOOST_ASIO_DECL size_t poll_one(boost::system::error_code& ec);
+
+ // Stop the event processing loop.
+ BOOST_ASIO_DECL void stop();
+
+ // Determine whether the io_service is stopped.
+ bool stopped() const
+ {
+ return ::InterlockedExchangeAdd(&stopped_, 0) != 0;
+ }
+
+ // Reset in preparation for a subsequent run invocation.
+ void reset()
+ {
+ ::InterlockedExchange(&stopped_, 0);
+ }
+
+ // Notify that some work has started.
+ void work_started()
+ {
+ ::InterlockedIncrement(&outstanding_work_);
+ }
+
+ // Notify that some work has finished.
+ void work_finished()
+ {
+ if (::InterlockedDecrement(&outstanding_work_) == 0)
+ stop();
+ }
+
+ // Return whether a handler can be dispatched immediately.
+ bool can_dispatch()
+ {
+ return thread_call_stack::contains(this) != 0;
+ }
+
+ // Request invocation of the given handler.
+ template <typename Handler>
+ void dispatch(Handler& handler);
+
+ // Request invocation of the given handler and return immediately.
+ template <typename Handler>
+ void post(Handler& handler);
+
+ // Request invocation of the given operation and return immediately. Assumes
+ // that work_started() has not yet been called for the operation.
+ void post_immediate_completion(win_iocp_operation* op, bool)
+ {
+ work_started();
+ post_deferred_completion(op);
+ }
+
+ // Request invocation of the given operation and return immediately. Assumes
+ // that work_started() was previously called for the operation.
+ BOOST_ASIO_DECL void post_deferred_completion(win_iocp_operation* op);
+
+ // Request invocation of the given operation and return immediately. Assumes
+ // that work_started() was previously called for the operations.
+ BOOST_ASIO_DECL void post_deferred_completions(
+ op_queue<win_iocp_operation>& ops);
+
+ // Request invocation of the given operation using the thread-private queue
+ // and return immediately. Assumes that work_started() has not yet been
+ // called for the operation.
+ void post_private_immediate_completion(win_iocp_operation* op)
+ {
+ post_immediate_completion(op, false);
+ }
+
+ // Request invocation of the given operation using the thread-private queue
+ // and return immediately. Assumes that work_started() was previously called
+ // for the operation.
+ void post_private_deferred_completion(win_iocp_operation* op)
+ {
+ post_deferred_completion(op);
+ }
+
+ // Process unfinished operations as part of a shutdown_service operation.
+ // Assumes that work_started() was previously called for the operations.
+ BOOST_ASIO_DECL void abandon_operations(op_queue<operation>& ops);
+
+ // Called after starting an overlapped I/O operation that did not complete
+ // immediately. The caller must have already called work_started() prior to
+ // starting the operation.
+ BOOST_ASIO_DECL void on_pending(win_iocp_operation* op);
+
+ // Called after starting an overlapped I/O operation that completed
+ // immediately. The caller must have already called work_started() prior to
+ // starting the operation.
+ BOOST_ASIO_DECL void on_completion(win_iocp_operation* op,
+ DWORD last_error = 0, DWORD bytes_transferred = 0);
+
+ // Called after starting an overlapped I/O operation that completed
+ // immediately. The caller must have already called work_started() prior to
+ // starting the operation.
+ BOOST_ASIO_DECL void on_completion(win_iocp_operation* op,
+ const boost::system::error_code& ec, DWORD bytes_transferred = 0);
+
+ // Add a new timer queue to the service.
+ template <typename Time_Traits>
+ void add_timer_queue(timer_queue<Time_Traits>& timer_queue);
+
+ // Remove a timer queue from the service.
+ template <typename Time_Traits>
+ void remove_timer_queue(timer_queue<Time_Traits>& timer_queue);
+
+ // Schedule a new operation in the given timer queue to expire at the
+ // specified absolute time.
+ template <typename Time_Traits>
+ void schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op);
+
+ // Cancel the timer associated with the given token. Returns the number of
+ // handlers that have been posted or dispatched.
+ template <typename Time_Traits>
+ std::size_t cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled = (std::numeric_limits<std::size_t>::max)());
+
+private:
+#if defined(WINVER) && (WINVER < 0x0500)
+ typedef DWORD dword_ptr_t;
+ typedef ULONG ulong_ptr_t;
+#else // defined(WINVER) && (WINVER < 0x0500)
+ typedef DWORD_PTR dword_ptr_t;
+ typedef ULONG_PTR ulong_ptr_t;
+#endif // defined(WINVER) && (WINVER < 0x0500)
+
+ // Dequeues at most one operation from the I/O completion port, and then
+ // executes it. Returns the number of operations that were dequeued (i.e.
+ // either 0 or 1).
+ BOOST_ASIO_DECL size_t do_one(bool block, boost::system::error_code& ec);
+
+ // Helper to calculate the GetQueuedCompletionStatus timeout.
+ BOOST_ASIO_DECL static DWORD get_gqcs_timeout();
+
+ // Helper function to add a new timer queue.
+ BOOST_ASIO_DECL void do_add_timer_queue(timer_queue_base& queue);
+
+ // Helper function to remove a timer queue.
+ BOOST_ASIO_DECL void do_remove_timer_queue(timer_queue_base& queue);
+
+ // Called to recalculate and update the timeout.
+ BOOST_ASIO_DECL void update_timeout();
+
+ // Helper class to call work_finished() on block exit.
+ struct work_finished_on_block_exit;
+
+ // Helper class for managing a HANDLE.
+ struct auto_handle
+ {
+ HANDLE handle;
+ auto_handle() : handle(0) {}
+ ~auto_handle() { if (handle) ::CloseHandle(handle); }
+ };
+
+ // The IO completion port used for queueing operations.
+ auto_handle iocp_;
+
+ // The count of unfinished work.
+ long outstanding_work_;
+
+ // Flag to indicate whether the event loop has been stopped.
+ mutable long stopped_;
+
+ // Flag to indicate whether there is an in-flight stop event. Every event
+ // posted using PostQueuedCompletionStatus consumes non-paged pool, so to
+ // avoid exhausting this resouce we limit the number of outstanding events.
+ long stop_event_posted_;
+
+ // Flag to indicate whether the service has been shut down.
+ long shutdown_;
+
+ enum
+ {
+ // Timeout to use with GetQueuedCompletionStatus on older versions of
+ // Windows. Some versions of windows have a "bug" where a call to
+ // GetQueuedCompletionStatus can appear stuck even though there are events
+ // waiting on the queue. Using a timeout helps to work around the issue.
+ default_gqcs_timeout = 500,
+
+ // Maximum waitable timer timeout, in milliseconds.
+ max_timeout_msec = 5 * 60 * 1000,
+
+ // Maximum waitable timer timeout, in microseconds.
+ max_timeout_usec = max_timeout_msec * 1000,
+
+ // Completion key value used to wake up a thread to dispatch timers or
+ // completed operations.
+ wake_for_dispatch = 1,
+
+ // Completion key value to indicate that an operation has posted with the
+ // original last_error and bytes_transferred values stored in the fields of
+ // the OVERLAPPED structure.
+ overlapped_contains_result = 2
+ };
+
+ // Timeout to use with GetQueuedCompletionStatus.
+ const DWORD gqcs_timeout_;
+
+ // Function object for processing timeouts in a background thread.
+ struct timer_thread_function;
+ friend struct timer_thread_function;
+
+ // Background thread used for processing timeouts.
+ scoped_ptr<thread> timer_thread_;
+
+ // A waitable timer object used for waiting for timeouts.
+ auto_handle waitable_timer_;
+
+ // Non-zero if timers or completed operations need to be dispatched.
+ long dispatch_required_;
+
+ // Mutex for protecting access to the timer queues and completed operations.
+ mutex dispatch_mutex_;
+
+ // The timer queues.
+ timer_queue_set timer_queues_;
+
+ // The operations that are ready to dispatch.
+ op_queue<win_iocp_operation> completed_ops_;
+
+ // Per-thread call stack to track the state of each thread in the io_service.
+ typedef call_stack<win_iocp_io_service,
+ win_iocp_thread_info> thread_call_stack;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/win_iocp_io_service.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_iocp_io_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_IO_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_null_buffers_op.hpp b/ext/patches/boost/asio/detail/win_iocp_null_buffers_op.hpp
new file mode 100644
index 0000000..6ec7f63
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_null_buffers_op.hpp
@@ -0,0 +1,121 @@
+//
+// detail/win_iocp_null_buffers_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_NULL_BUFFERS_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_NULL_BUFFERS_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+class win_iocp_null_buffers_op : public reactor_op
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_null_buffers_op);
+
+ win_iocp_null_buffers_op(socket_ops::weak_cancel_token_type cancel_token,
+ Handler& handler)
+ : reactor_op(&win_iocp_null_buffers_op::do_perform,
+ &win_iocp_null_buffers_op::do_complete),
+ cancel_token_(cancel_token),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static bool do_perform(reactor_op*)
+ {
+ return true;
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& result_ec,
+ std::size_t bytes_transferred)
+ {
+ boost::system::error_code ec(result_ec);
+
+ // Take ownership of the operation object.
+ win_iocp_null_buffers_op* o(static_cast<win_iocp_null_buffers_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // The reactor may have stored a result in the operation object.
+ if (o->ec_)
+ ec = o->ec_;
+
+ // Map non-portable errors to their portable counterparts.
+ if (ec.value() == ERROR_NETNAME_DELETED)
+ {
+ if (o->cancel_token_.expired())
+ ec = boost::asio::error::operation_aborted;
+ else
+ ec = boost::asio::error::connection_reset;
+ }
+ else if (ec.value() == ERROR_PORT_UNREACHABLE)
+ {
+ ec = boost::asio::error::connection_refused;
+ }
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, ec, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ socket_ops::weak_cancel_token_type cancel_token_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_NULL_BUFFERS_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_operation.hpp b/ext/patches/boost/asio/detail/win_iocp_operation.hpp
new file mode 100644
index 0000000..3a0a759
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_operation.hpp
@@ -0,0 +1,97 @@
+//
+// detail/win_iocp_operation.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_OPERATION_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_OPERATION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/handler_tracking.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/system/error_code.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_iocp_io_service;
+
+// Base class for all operations. A function pointer is used instead of virtual
+// functions to avoid the associated overhead.
+class win_iocp_operation
+ : public OVERLAPPED
+ BOOST_ASIO_ALSO_INHERIT_TRACKED_HANDLER
+{
+public:
+ void complete(win_iocp_io_service& owner,
+ const boost::system::error_code& ec,
+ std::size_t bytes_transferred)
+ {
+ func_(&owner, this, ec, bytes_transferred);
+ }
+
+ void destroy()
+ {
+ func_(0, this, boost::system::error_code(), 0);
+ }
+
+protected:
+ typedef void (*func_type)(
+ win_iocp_io_service*, win_iocp_operation*,
+ const boost::system::error_code&, std::size_t);
+
+ win_iocp_operation(func_type func)
+ : next_(0),
+ func_(func)
+ {
+ reset();
+ }
+
+ // Prevents deletion through this type.
+ ~win_iocp_operation()
+ {
+ }
+
+ void reset()
+ {
+ Internal = 0;
+ InternalHigh = 0;
+ Offset = 0;
+ OffsetHigh = 0;
+ hEvent = 0;
+ ready_ = 0;
+ }
+
+private:
+ friend class op_queue_access;
+ friend class win_iocp_io_service;
+ win_iocp_operation* next_;
+ func_type func_;
+ long ready_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_OPERATION_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_overlapped_op.hpp b/ext/patches/boost/asio/detail/win_iocp_overlapped_op.hpp
new file mode 100644
index 0000000..0e0db76
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_overlapped_op.hpp
@@ -0,0 +1,90 @@
+//
+// detail/win_iocp_overlapped_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_OVERLAPPED_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_OVERLAPPED_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/error.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+class win_iocp_overlapped_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_overlapped_op);
+
+ win_iocp_overlapped_op(Handler& handler)
+ : operation(&win_iocp_overlapped_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& ec, std::size_t bytes_transferred)
+ {
+ // Take ownership of the operation object.
+ win_iocp_overlapped_op* o(static_cast<win_iocp_overlapped_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, ec, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_OVERLAPPED_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_overlapped_ptr.hpp b/ext/patches/boost/asio/detail/win_iocp_overlapped_ptr.hpp
new file mode 100644
index 0000000..b467db5
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_overlapped_ptr.hpp
@@ -0,0 +1,146 @@
+//
+// detail/win_iocp_overlapped_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_OVERLAPPED_PTR_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_OVERLAPPED_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/win_iocp_overlapped_op.hpp>
+#include <boost/asio/detail/win_iocp_io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Wraps a handler to create an OVERLAPPED object for use with overlapped I/O.
+class win_iocp_overlapped_ptr
+ : private noncopyable
+{
+public:
+ // Construct an empty win_iocp_overlapped_ptr.
+ win_iocp_overlapped_ptr()
+ : ptr_(0),
+ iocp_service_(0)
+ {
+ }
+
+ // Construct an win_iocp_overlapped_ptr to contain the specified handler.
+ template <typename Handler>
+ explicit win_iocp_overlapped_ptr(
+ boost::asio::io_service& io_service, BOOST_ASIO_MOVE_ARG(Handler) handler)
+ : ptr_(0),
+ iocp_service_(0)
+ {
+ this->reset(io_service, BOOST_ASIO_MOVE_CAST(Handler)(handler));
+ }
+
+ // Destructor automatically frees the OVERLAPPED object unless released.
+ ~win_iocp_overlapped_ptr()
+ {
+ reset();
+ }
+
+ // Reset to empty.
+ void reset()
+ {
+ if (ptr_)
+ {
+ ptr_->destroy();
+ ptr_ = 0;
+ iocp_service_->work_finished();
+ iocp_service_ = 0;
+ }
+ }
+
+ // Reset to contain the specified handler, freeing any current OVERLAPPED
+ // object.
+ template <typename Handler>
+ void reset(boost::asio::io_service& io_service, Handler handler)
+ {
+ typedef win_iocp_overlapped_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "io_service",
+ &io_service.impl_, "overlapped"));
+
+ io_service.impl_.work_started();
+ reset();
+ ptr_ = p.p;
+ p.v = p.p = 0;
+ iocp_service_ = &io_service.impl_;
+ }
+
+ // Get the contained OVERLAPPED object.
+ OVERLAPPED* get()
+ {
+ return ptr_;
+ }
+
+ // Get the contained OVERLAPPED object.
+ const OVERLAPPED* get() const
+ {
+ return ptr_;
+ }
+
+ // Release ownership of the OVERLAPPED object.
+ OVERLAPPED* release()
+ {
+ if (ptr_)
+ iocp_service_->on_pending(ptr_);
+
+ OVERLAPPED* tmp = ptr_;
+ ptr_ = 0;
+ iocp_service_ = 0;
+ return tmp;
+ }
+
+ // Post completion notification for overlapped operation. Releases ownership.
+ void complete(const boost::system::error_code& ec,
+ std::size_t bytes_transferred)
+ {
+ if (ptr_)
+ {
+ iocp_service_->on_completion(ptr_, ec,
+ static_cast<DWORD>(bytes_transferred));
+ ptr_ = 0;
+ iocp_service_ = 0;
+ }
+ }
+
+private:
+ win_iocp_operation* ptr_;
+ win_iocp_io_service* iocp_service_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_OVERLAPPED_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_serial_port_service.hpp b/ext/patches/boost/asio/detail/win_iocp_serial_port_service.hpp
new file mode 100644
index 0000000..5e348c2
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_serial_port_service.hpp
@@ -0,0 +1,230 @@
+//
+// detail/win_iocp_serial_port_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SERIAL_PORT_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SERIAL_PORT_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP) && defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+#include <string>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/win_iocp_handle_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Extend win_iocp_handle_service to provide serial port support.
+class win_iocp_serial_port_service
+{
+public:
+ // The native type of a serial port.
+ typedef win_iocp_handle_service::native_handle_type native_handle_type;
+
+ // The implementation type of the serial port.
+ typedef win_iocp_handle_service::implementation_type implementation_type;
+
+ // Constructor.
+ BOOST_ASIO_DECL win_iocp_serial_port_service(
+ boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new serial port implementation.
+ void construct(implementation_type& impl)
+ {
+ handle_service_.construct(impl);
+ }
+
+ // Move-construct a new serial port implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ handle_service_.move_construct(impl, other_impl);
+ }
+
+ // Move-assign from another serial port implementation.
+ void move_assign(implementation_type& impl,
+ win_iocp_serial_port_service& other_service,
+ implementation_type& other_impl)
+ {
+ handle_service_.move_assign(impl,
+ other_service.handle_service_, other_impl);
+ }
+
+ // Destroy a serial port implementation.
+ void destroy(implementation_type& impl)
+ {
+ handle_service_.destroy(impl);
+ }
+
+ // Open the serial port using the specified device name.
+ BOOST_ASIO_DECL boost::system::error_code open(implementation_type& impl,
+ const std::string& device, boost::system::error_code& ec);
+
+ // Assign a native handle to a serial port implementation.
+ boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec)
+ {
+ return handle_service_.assign(impl, handle, ec);
+ }
+
+ // Determine whether the serial port is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return handle_service_.is_open(impl);
+ }
+
+ // Destroy a serial port implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return handle_service_.close(impl, ec);
+ }
+
+ // Get the native serial port representation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return handle_service_.native_handle(impl);
+ }
+
+ // Cancel all operations associated with the handle.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return handle_service_.cancel(impl, ec);
+ }
+
+ // Set an option on the serial port.
+ template <typename SettableSerialPortOption>
+ boost::system::error_code set_option(implementation_type& impl,
+ const SettableSerialPortOption& option, boost::system::error_code& ec)
+ {
+ return do_set_option(impl,
+ &win_iocp_serial_port_service::store_option<SettableSerialPortOption>,
+ &option, ec);
+ }
+
+ // Get an option from the serial port.
+ template <typename GettableSerialPortOption>
+ boost::system::error_code get_option(const implementation_type& impl,
+ GettableSerialPortOption& option, boost::system::error_code& ec) const
+ {
+ return do_get_option(impl,
+ &win_iocp_serial_port_service::load_option<GettableSerialPortOption>,
+ &option, ec);
+ }
+
+ // Send a break sequence to the serial port.
+ boost::system::error_code send_break(implementation_type&,
+ boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Write the given data. Returns the number of bytes sent.
+ template <typename ConstBufferSequence>
+ size_t write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return handle_service_.write_some(impl, buffers, ec);
+ }
+
+ // Start an asynchronous write. The data being written must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, Handler& handler)
+ {
+ handle_service_.async_write_some(impl, buffers, handler);
+ }
+
+ // Read some data. Returns the number of bytes received.
+ template <typename MutableBufferSequence>
+ size_t read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return handle_service_.read_some(impl, buffers, ec);
+ }
+
+ // Start an asynchronous read. The buffer for the data being received must be
+ // valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, Handler& handler)
+ {
+ handle_service_.async_read_some(impl, buffers, handler);
+ }
+
+private:
+ // Function pointer type for storing a serial port option.
+ typedef boost::system::error_code (*store_function_type)(
+ const void*, ::DCB&, boost::system::error_code&);
+
+ // Helper function template to store a serial port option.
+ template <typename SettableSerialPortOption>
+ static boost::system::error_code store_option(const void* option,
+ ::DCB& storage, boost::system::error_code& ec)
+ {
+ return static_cast<const SettableSerialPortOption*>(option)->store(
+ storage, ec);
+ }
+
+ // Helper function to set a serial port option.
+ BOOST_ASIO_DECL boost::system::error_code do_set_option(
+ implementation_type& impl, store_function_type store,
+ const void* option, boost::system::error_code& ec);
+
+ // Function pointer type for loading a serial port option.
+ typedef boost::system::error_code (*load_function_type)(
+ void*, const ::DCB&, boost::system::error_code&);
+
+ // Helper function template to load a serial port option.
+ template <typename GettableSerialPortOption>
+ static boost::system::error_code load_option(void* option,
+ const ::DCB& storage, boost::system::error_code& ec)
+ {
+ return static_cast<GettableSerialPortOption*>(option)->load(storage, ec);
+ }
+
+ // Helper function to get a serial port option.
+ BOOST_ASIO_DECL boost::system::error_code do_get_option(
+ const implementation_type& impl, load_function_type load,
+ void* option, boost::system::error_code& ec) const;
+
+ // The implementation used for initiating asynchronous operations.
+ win_iocp_handle_service handle_service_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_iocp_serial_port_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_IOCP) && defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SERIAL_PORT_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_socket_accept_op.hpp b/ext/patches/boost/asio/detail/win_iocp_socket_accept_op.hpp
new file mode 100644
index 0000000..a860c52
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_socket_accept_op.hpp
@@ -0,0 +1,167 @@
+//
+// detail/win_iocp_socket_accept_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_ACCEPT_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_ACCEPT_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/win_iocp_socket_service_base.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Socket, typename Protocol, typename Handler>
+class win_iocp_socket_accept_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_socket_accept_op);
+
+ win_iocp_socket_accept_op(win_iocp_socket_service_base& socket_service,
+ socket_type socket, Socket& peer, const Protocol& protocol,
+ typename Protocol::endpoint* peer_endpoint,
+ bool enable_connection_aborted, Handler& handler)
+ : operation(&win_iocp_socket_accept_op::do_complete),
+ socket_service_(socket_service),
+ socket_(socket),
+ peer_(peer),
+ protocol_(protocol),
+ peer_endpoint_(peer_endpoint),
+ enable_connection_aborted_(enable_connection_aborted),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ socket_holder& new_socket()
+ {
+ return new_socket_;
+ }
+
+ void* output_buffer()
+ {
+ return output_buffer_;
+ }
+
+ DWORD address_length()
+ {
+ return sizeof(sockaddr_storage_type) + 16;
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& result_ec,
+ std::size_t /*bytes_transferred*/)
+ {
+ boost::system::error_code ec(result_ec);
+
+ // Take ownership of the operation object.
+ win_iocp_socket_accept_op* o(static_cast<win_iocp_socket_accept_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ if (owner)
+ {
+ typename Protocol::endpoint peer_endpoint;
+ std::size_t addr_len = peer_endpoint.capacity();
+ socket_ops::complete_iocp_accept(o->socket_,
+ o->output_buffer(), o->address_length(),
+ peer_endpoint.data(), &addr_len,
+ o->new_socket_.get(), ec);
+
+ // Restart the accept operation if we got the connection_aborted error
+ // and the enable_connection_aborted socket option is not set.
+ if (ec == boost::asio::error::connection_aborted
+ && !o->enable_connection_aborted_)
+ {
+ o->reset();
+ o->socket_service_.restart_accept_op(o->socket_,
+ o->new_socket_, o->protocol_.family(),
+ o->protocol_.type(), o->protocol_.protocol(),
+ o->output_buffer(), o->address_length(), o);
+ p.v = p.p = 0;
+ return;
+ }
+
+ // If the socket was successfully accepted, transfer ownership of the
+ // socket to the peer object.
+ if (!ec)
+ {
+ o->peer_.assign(o->protocol_,
+ typename Socket::native_handle_type(
+ o->new_socket_.get(), peer_endpoint), ec);
+ if (!ec)
+ o->new_socket_.release();
+ }
+
+ // Pass endpoint back to caller.
+ if (o->peer_endpoint_)
+ *o->peer_endpoint_ = peer_endpoint;
+ }
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder1<Handler, boost::system::error_code>
+ handler(o->handler_, ec);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ win_iocp_socket_service_base& socket_service_;
+ socket_type socket_;
+ socket_holder new_socket_;
+ Socket& peer_;
+ Protocol protocol_;
+ typename Protocol::endpoint* peer_endpoint_;
+ unsigned char output_buffer_[(sizeof(sockaddr_storage_type) + 16) * 2];
+ bool enable_connection_aborted_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_ACCEPT_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_socket_connect_op.hpp b/ext/patches/boost/asio/detail/win_iocp_socket_connect_op.hpp
new file mode 100644
index 0000000..fc78da0
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_socket_connect_op.hpp
@@ -0,0 +1,126 @@
+//
+// detail/win_iocp_socket_connect_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_CONNECT_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_CONNECT_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_iocp_socket_connect_op_base : public reactor_op
+{
+public:
+ win_iocp_socket_connect_op_base(socket_type socket, func_type complete_func)
+ : reactor_op(&win_iocp_socket_connect_op_base::do_perform, complete_func),
+ socket_(socket),
+ connect_ex_(false)
+ {
+ }
+
+ static bool do_perform(reactor_op* base)
+ {
+ win_iocp_socket_connect_op_base* o(
+ static_cast<win_iocp_socket_connect_op_base*>(base));
+
+ return socket_ops::non_blocking_connect(o->socket_, o->ec_);
+ }
+
+ socket_type socket_;
+ bool connect_ex_;
+};
+
+template <typename Handler>
+class win_iocp_socket_connect_op : public win_iocp_socket_connect_op_base
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_socket_connect_op);
+
+ win_iocp_socket_connect_op(socket_type socket, Handler& handler)
+ : win_iocp_socket_connect_op_base(socket,
+ &win_iocp_socket_connect_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& result_ec,
+ std::size_t /*bytes_transferred*/)
+ {
+ boost::system::error_code ec(result_ec);
+
+ // Take ownership of the operation object.
+ win_iocp_socket_connect_op* o(
+ static_cast<win_iocp_socket_connect_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ if (owner)
+ {
+ if (o->connect_ex_)
+ socket_ops::complete_iocp_connect(o->socket_, ec);
+ else
+ ec = o->ec_;
+ }
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder1<Handler, boost::system::error_code>
+ handler(o->handler_, ec);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_CONNECT_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_socket_recv_op.hpp b/ext/patches/boost/asio/detail/win_iocp_socket_recv_op.hpp
new file mode 100644
index 0000000..035dc4b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_socket_recv_op.hpp
@@ -0,0 +1,117 @@
+//
+// detail/win_iocp_socket_recv_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECV_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECV_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence, typename Handler>
+class win_iocp_socket_recv_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_socket_recv_op);
+
+ win_iocp_socket_recv_op(socket_ops::state_type state,
+ socket_ops::weak_cancel_token_type cancel_token,
+ const MutableBufferSequence& buffers, Handler& handler)
+ : operation(&win_iocp_socket_recv_op::do_complete),
+ state_(state),
+ cancel_token_(cancel_token),
+ buffers_(buffers),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& result_ec,
+ std::size_t bytes_transferred)
+ {
+ boost::system::error_code ec(result_ec);
+
+ // Take ownership of the operation object.
+ win_iocp_socket_recv_op* o(static_cast<win_iocp_socket_recv_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ // Check whether buffers are still valid.
+ if (owner)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::validate(o->buffers_);
+ }
+#endif // defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+
+ socket_ops::complete_iocp_recv(o->state_, o->cancel_token_,
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::all_empty(o->buffers_),
+ ec, bytes_transferred);
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, ec, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ socket_ops::state_type state_;
+ socket_ops::weak_cancel_token_type cancel_token_;
+ MutableBufferSequence buffers_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECV_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_socket_recvfrom_op.hpp b/ext/patches/boost/asio/detail/win_iocp_socket_recvfrom_op.hpp
new file mode 100644
index 0000000..35c4033
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_socket_recvfrom_op.hpp
@@ -0,0 +1,125 @@
+//
+// detail/win_iocp_socket_recvfrom_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECVFROM_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECVFROM_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence, typename Endpoint, typename Handler>
+class win_iocp_socket_recvfrom_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_socket_recvfrom_op);
+
+ win_iocp_socket_recvfrom_op(Endpoint& endpoint,
+ socket_ops::weak_cancel_token_type cancel_token,
+ const MutableBufferSequence& buffers, Handler& handler)
+ : operation(&win_iocp_socket_recvfrom_op::do_complete),
+ endpoint_(endpoint),
+ endpoint_size_(static_cast<int>(endpoint.capacity())),
+ cancel_token_(cancel_token),
+ buffers_(buffers),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ int& endpoint_size()
+ {
+ return endpoint_size_;
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& result_ec,
+ std::size_t bytes_transferred)
+ {
+ boost::system::error_code ec(result_ec);
+
+ // Take ownership of the operation object.
+ win_iocp_socket_recvfrom_op* o(
+ static_cast<win_iocp_socket_recvfrom_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ // Check whether buffers are still valid.
+ if (owner)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::validate(o->buffers_);
+ }
+#endif // defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+
+ socket_ops::complete_iocp_recvfrom(o->cancel_token_, ec);
+
+ // Record the size of the endpoint returned by the operation.
+ o->endpoint_.resize(o->endpoint_size_);
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, ec, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Endpoint& endpoint_;
+ int endpoint_size_;
+ socket_ops::weak_cancel_token_type cancel_token_;
+ MutableBufferSequence buffers_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECVFROM_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_socket_recvmsg_op.hpp b/ext/patches/boost/asio/detail/win_iocp_socket_recvmsg_op.hpp
new file mode 100644
index 0000000..1e895ce
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_socket_recvmsg_op.hpp
@@ -0,0 +1,118 @@
+//
+// detail/win_iocp_socket_recvmsg_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECVMSG_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECVMSG_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/socket_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence, typename Handler>
+class win_iocp_socket_recvmsg_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_socket_recvmsg_op);
+
+ win_iocp_socket_recvmsg_op(
+ socket_ops::weak_cancel_token_type cancel_token,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags& out_flags, Handler& handler)
+ : operation(&win_iocp_socket_recvmsg_op::do_complete),
+ cancel_token_(cancel_token),
+ buffers_(buffers),
+ out_flags_(out_flags),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& result_ec,
+ std::size_t bytes_transferred)
+ {
+ boost::system::error_code ec(result_ec);
+
+ // Take ownership of the operation object.
+ win_iocp_socket_recvmsg_op* o(
+ static_cast<win_iocp_socket_recvmsg_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ // Check whether buffers are still valid.
+ if (owner)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::validate(o->buffers_);
+ }
+#endif // defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+
+ socket_ops::complete_iocp_recvmsg(o->cancel_token_, ec);
+ o->out_flags_ = 0;
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, ec, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ socket_ops::weak_cancel_token_type cancel_token_;
+ MutableBufferSequence buffers_;
+ socket_base::message_flags& out_flags_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_RECVMSG_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_socket_send_op.hpp b/ext/patches/boost/asio/detail/win_iocp_socket_send_op.hpp
new file mode 100644
index 0000000..844d28b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_socket_send_op.hpp
@@ -0,0 +1,111 @@
+//
+// detail/win_iocp_socket_send_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SEND_OP_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SEND_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename ConstBufferSequence, typename Handler>
+class win_iocp_socket_send_op : public operation
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(win_iocp_socket_send_op);
+
+ win_iocp_socket_send_op(socket_ops::weak_cancel_token_type cancel_token,
+ const ConstBufferSequence& buffers, Handler& handler)
+ : operation(&win_iocp_socket_send_op::do_complete),
+ cancel_token_(cancel_token),
+ buffers_(buffers),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code& result_ec,
+ std::size_t bytes_transferred)
+ {
+ boost::system::error_code ec(result_ec);
+
+ // Take ownership of the operation object.
+ win_iocp_socket_send_op* o(static_cast<win_iocp_socket_send_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ // Check whether buffers are still valid.
+ if (owner)
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::validate(o->buffers_);
+ }
+#endif // defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+
+ socket_ops::complete_iocp_send(o->cancel_token_, ec);
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, ec, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ socket_ops::weak_cancel_token_type cancel_token_;
+ ConstBufferSequence buffers_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SEND_OP_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_socket_service.hpp b/ext/patches/boost/asio/detail/win_iocp_socket_service.hpp
new file mode 100644
index 0000000..4594adc
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_socket_service.hpp
@@ -0,0 +1,527 @@
+//
+// detail/win_iocp_socket_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <cstring>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/socket_base.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/reactor.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_holder.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/win_iocp_io_service.hpp>
+#include <boost/asio/detail/win_iocp_null_buffers_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_accept_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_connect_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_recvfrom_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_send_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_service_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol>
+class win_iocp_socket_service : public win_iocp_socket_service_base
+{
+public:
+ // The protocol type.
+ typedef Protocol protocol_type;
+
+ // The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ // The native type of a socket.
+ class native_handle_type
+ {
+ public:
+ native_handle_type(socket_type s)
+ : socket_(s),
+ have_remote_endpoint_(false)
+ {
+ }
+
+ native_handle_type(socket_type s, const endpoint_type& ep)
+ : socket_(s),
+ have_remote_endpoint_(true),
+ remote_endpoint_(ep)
+ {
+ }
+
+ void operator=(socket_type s)
+ {
+ socket_ = s;
+ have_remote_endpoint_ = false;
+ remote_endpoint_ = endpoint_type();
+ }
+
+ operator socket_type() const
+ {
+ return socket_;
+ }
+
+ bool have_remote_endpoint() const
+ {
+ return have_remote_endpoint_;
+ }
+
+ endpoint_type remote_endpoint() const
+ {
+ return remote_endpoint_;
+ }
+
+ private:
+ socket_type socket_;
+ bool have_remote_endpoint_;
+ endpoint_type remote_endpoint_;
+ };
+
+ // The implementation type of the socket.
+ struct implementation_type :
+ win_iocp_socket_service_base::base_implementation_type
+ {
+ // Default constructor.
+ implementation_type()
+ : protocol_(endpoint_type().protocol()),
+ have_remote_endpoint_(false),
+ remote_endpoint_()
+ {
+ }
+
+ // The protocol associated with the socket.
+ protocol_type protocol_;
+
+ // Whether we have a cached remote endpoint.
+ bool have_remote_endpoint_;
+
+ // A cached remote endpoint.
+ endpoint_type remote_endpoint_;
+ };
+
+ // Constructor.
+ win_iocp_socket_service(boost::asio::io_service& io_service)
+ : win_iocp_socket_service_base(io_service)
+ {
+ }
+
+ // Move-construct a new socket implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ this->base_move_construct(impl, other_impl);
+
+ impl.protocol_ = other_impl.protocol_;
+ other_impl.protocol_ = endpoint_type().protocol();
+
+ impl.have_remote_endpoint_ = other_impl.have_remote_endpoint_;
+ other_impl.have_remote_endpoint_ = false;
+
+ impl.remote_endpoint_ = other_impl.remote_endpoint_;
+ other_impl.remote_endpoint_ = endpoint_type();
+ }
+
+ // Move-assign from another socket implementation.
+ void move_assign(implementation_type& impl,
+ win_iocp_socket_service_base& other_service,
+ implementation_type& other_impl)
+ {
+ this->base_move_assign(impl, other_service, other_impl);
+
+ impl.protocol_ = other_impl.protocol_;
+ other_impl.protocol_ = endpoint_type().protocol();
+
+ impl.have_remote_endpoint_ = other_impl.have_remote_endpoint_;
+ other_impl.have_remote_endpoint_ = false;
+
+ impl.remote_endpoint_ = other_impl.remote_endpoint_;
+ other_impl.remote_endpoint_ = endpoint_type();
+ }
+
+ // Move-construct a new socket implementation from another protocol type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type& impl,
+ typename win_iocp_socket_service<
+ Protocol1>::implementation_type& other_impl)
+ {
+ this->base_move_construct(impl, other_impl);
+
+ impl.protocol_ = protocol_type(other_impl.protocol_);
+ other_impl.protocol_ = typename Protocol1::endpoint().protocol();
+
+ impl.have_remote_endpoint_ = other_impl.have_remote_endpoint_;
+ other_impl.have_remote_endpoint_ = false;
+
+ impl.remote_endpoint_ = other_impl.remote_endpoint_;
+ other_impl.remote_endpoint_ = typename Protocol1::endpoint();
+ }
+
+ // Open a new socket implementation.
+ boost::system::error_code open(implementation_type& impl,
+ const protocol_type& protocol, boost::system::error_code& ec)
+ {
+ if (!do_open(impl, protocol.family(),
+ protocol.type(), protocol.protocol(), ec))
+ {
+ impl.protocol_ = protocol;
+ impl.have_remote_endpoint_ = false;
+ impl.remote_endpoint_ = endpoint_type();
+ }
+ return ec;
+ }
+
+ // Assign a native socket to a socket implementation.
+ boost::system::error_code assign(implementation_type& impl,
+ const protocol_type& protocol, const native_handle_type& native_socket,
+ boost::system::error_code& ec)
+ {
+ if (!do_assign(impl, protocol.type(), native_socket, ec))
+ {
+ impl.protocol_ = protocol;
+ impl.have_remote_endpoint_ = native_socket.have_remote_endpoint();
+ impl.remote_endpoint_ = native_socket.remote_endpoint();
+ }
+ return ec;
+ }
+
+ // Get the native socket representation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ if (impl.have_remote_endpoint_)
+ return native_handle_type(impl.socket_, impl.remote_endpoint_);
+ return native_handle_type(impl.socket_);
+ }
+
+ // Bind the socket to the specified local endpoint.
+ boost::system::error_code bind(implementation_type& impl,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ socket_ops::bind(impl.socket_, endpoint.data(), endpoint.size(), ec);
+ return ec;
+ }
+
+ // Set a socket option.
+ template <typename Option>
+ boost::system::error_code set_option(implementation_type& impl,
+ const Option& option, boost::system::error_code& ec)
+ {
+ socket_ops::setsockopt(impl.socket_, impl.state_,
+ option.level(impl.protocol_), option.name(impl.protocol_),
+ option.data(impl.protocol_), option.size(impl.protocol_), ec);
+ return ec;
+ }
+
+ // Set a socket option.
+ template <typename Option>
+ boost::system::error_code get_option(const implementation_type& impl,
+ Option& option, boost::system::error_code& ec) const
+ {
+ std::size_t size = option.size(impl.protocol_);
+ socket_ops::getsockopt(impl.socket_, impl.state_,
+ option.level(impl.protocol_), option.name(impl.protocol_),
+ option.data(impl.protocol_), &size, ec);
+ if (!ec)
+ option.resize(impl.protocol_, size);
+ return ec;
+ }
+
+ // Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ endpoint_type endpoint;
+ std::size_t addr_len = endpoint.capacity();
+ if (socket_ops::getsockname(impl.socket_, endpoint.data(), &addr_len, ec))
+ return endpoint_type();
+ endpoint.resize(addr_len);
+ return endpoint;
+ }
+
+ // Get the remote endpoint.
+ endpoint_type remote_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ endpoint_type endpoint = impl.remote_endpoint_;
+ std::size_t addr_len = endpoint.capacity();
+ if (socket_ops::getpeername(impl.socket_, endpoint.data(),
+ &addr_len, impl.have_remote_endpoint_, ec))
+ return endpoint_type();
+ endpoint.resize(addr_len);
+ return endpoint;
+ }
+
+ // Send a datagram to the specified endpoint. Returns the number of bytes
+ // sent.
+ template <typename ConstBufferSequence>
+ size_t send_to(implementation_type& impl, const ConstBufferSequence& buffers,
+ const endpoint_type& destination, socket_base::message_flags flags,
+ boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(buffers);
+
+ return socket_ops::sync_sendto(impl.socket_, impl.state_,
+ bufs.buffers(), bufs.count(), flags,
+ destination.data(), destination.size(), ec);
+ }
+
+ // Wait until data can be sent without blocking.
+ size_t send_to(implementation_type& impl, const null_buffers&,
+ const endpoint_type&, socket_base::message_flags,
+ boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_write(impl.socket_, impl.state_, ec);
+
+ return 0;
+ }
+
+ // Start an asynchronous send. The data being sent must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_send_to(implementation_type& impl,
+ const ConstBufferSequence& buffers, const endpoint_type& destination,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_socket_send_op<ConstBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.cancel_token_, buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_send_to"));
+
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(buffers);
+
+ start_send_to_op(impl, bufs.buffers(), bufs.count(),
+ destination.data(), static_cast<int>(destination.size()),
+ flags, p.p);
+ p.v = p.p = 0;
+ }
+
+ // Start an asynchronous wait until data can be sent without blocking.
+ template <typename Handler>
+ void async_send_to(implementation_type& impl, const null_buffers&,
+ const endpoint_type&, socket_base::message_flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.cancel_token_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_send_to(null_buffers)"));
+
+ start_reactor_op(impl, reactor::write_op, p.p);
+ p.v = p.p = 0;
+ }
+
+ // Receive a datagram with the endpoint of the sender. Returns the number of
+ // bytes received.
+ template <typename MutableBufferSequence>
+ size_t receive_from(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ endpoint_type& sender_endpoint, socket_base::message_flags flags,
+ boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ std::size_t addr_len = sender_endpoint.capacity();
+ std::size_t bytes_recvd = socket_ops::sync_recvfrom(
+ impl.socket_, impl.state_, bufs.buffers(), bufs.count(),
+ flags, sender_endpoint.data(), &addr_len, ec);
+
+ if (!ec)
+ sender_endpoint.resize(addr_len);
+
+ return bytes_recvd;
+ }
+
+ // Wait until data can be received without blocking.
+ size_t receive_from(implementation_type& impl,
+ const null_buffers&, endpoint_type& sender_endpoint,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_read(impl.socket_, impl.state_, ec);
+
+ // Reset endpoint since it can be given no sensible value at this time.
+ sender_endpoint = endpoint_type();
+
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received and
+ // the sender_endpoint object must both be valid for the lifetime of the
+ // asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive_from(implementation_type& impl,
+ const MutableBufferSequence& buffers, endpoint_type& sender_endp,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_socket_recvfrom_op<
+ MutableBufferSequence, endpoint_type, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(sender_endp, impl.cancel_token_, buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_receive_from"));
+
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ start_receive_from_op(impl, bufs.buffers(), bufs.count(),
+ sender_endp.data(), flags, &p.p->endpoint_size(), p.p);
+ p.v = p.p = 0;
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive_from(implementation_type& impl,
+ const null_buffers&, endpoint_type& sender_endpoint,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.cancel_token_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl,
+ "async_receive_from(null_buffers)"));
+
+ // Reset endpoint since it can be given no sensible value at this time.
+ sender_endpoint = endpoint_type();
+
+ start_null_buffers_receive_op(impl, flags, p.p);
+ p.v = p.p = 0;
+ }
+
+ // Accept a new connection.
+ template <typename Socket>
+ boost::system::error_code accept(implementation_type& impl, Socket& peer,
+ endpoint_type* peer_endpoint, boost::system::error_code& ec)
+ {
+ // We cannot accept a socket that is already open.
+ if (peer.is_open())
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ std::size_t addr_len = peer_endpoint ? peer_endpoint->capacity() : 0;
+ socket_holder new_socket(socket_ops::sync_accept(impl.socket_,
+ impl.state_, peer_endpoint ? peer_endpoint->data() : 0,
+ peer_endpoint ? &addr_len : 0, ec));
+
+ // On success, assign new connection to peer socket object.
+ if (new_socket.get() != invalid_socket)
+ {
+ if (peer_endpoint)
+ peer_endpoint->resize(addr_len);
+ if (!peer.assign(impl.protocol_, new_socket.get(), ec))
+ new_socket.release();
+ }
+
+ return ec;
+ }
+
+ // Start an asynchronous accept. The peer and peer_endpoint objects
+ // must be valid until the accept's handler is invoked.
+ template <typename Socket, typename Handler>
+ void async_accept(implementation_type& impl, Socket& peer,
+ endpoint_type* peer_endpoint, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_socket_accept_op<Socket, protocol_type, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ bool enable_connection_aborted =
+ (impl.state_ & socket_ops::enable_connection_aborted) != 0;
+ p.p = new (p.v) op(*this, impl.socket_, peer, impl.protocol_,
+ peer_endpoint, enable_connection_aborted, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_accept"));
+
+ start_accept_op(impl, peer.is_open(), p.p->new_socket(),
+ impl.protocol_.family(), impl.protocol_.type(),
+ impl.protocol_.protocol(), p.p->output_buffer(),
+ p.p->address_length(), p.p);
+ p.v = p.p = 0;
+ }
+
+ // Connect the socket to the specified endpoint.
+ boost::system::error_code connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, boost::system::error_code& ec)
+ {
+ socket_ops::sync_connect(impl.socket_,
+ peer_endpoint.data(), peer_endpoint.size(), ec);
+ return ec;
+ }
+
+ // Start an asynchronous connect.
+ template <typename Handler>
+ void async_connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_socket_connect_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.socket_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_connect"));
+
+ start_connect_op(impl, impl.protocol_.family(), impl.protocol_.type(),
+ peer_endpoint.data(), static_cast<int>(peer_endpoint.size()), p.p);
+ p.v = p.p = 0;
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_socket_service_base.hpp b/ext/patches/boost/asio/detail/win_iocp_socket_service_base.hpp
new file mode 100644
index 0000000..f0fa055
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_socket_service_base.hpp
@@ -0,0 +1,526 @@
+//
+// detail/win_iocp_socket_service_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SERVICE_BASE_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SERVICE_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/socket_base.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/operation.hpp>
+#include <boost/asio/detail/reactor.hpp>
+#include <boost/asio/detail/reactor_op.hpp>
+#include <boost/asio/detail/socket_holder.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/win_iocp_io_service.hpp>
+#include <boost/asio/detail/win_iocp_null_buffers_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_connect_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_send_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_recv_op.hpp>
+#include <boost/asio/detail/win_iocp_socket_recvmsg_op.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_iocp_socket_service_base
+{
+public:
+ // The implementation type of the socket.
+ struct base_implementation_type
+ {
+ // The native socket representation.
+ socket_type socket_;
+
+ // The current state of the socket.
+ socket_ops::state_type state_;
+
+ // We use a shared pointer as a cancellation token here to work around the
+ // broken Windows support for cancellation. MSDN says that when you call
+ // closesocket any outstanding WSARecv or WSASend operations will complete
+ // with the error ERROR_OPERATION_ABORTED. In practice they complete with
+ // ERROR_NETNAME_DELETED, which means you can't tell the difference between
+ // a local cancellation and the socket being hard-closed by the peer.
+ socket_ops::shared_cancel_token_type cancel_token_;
+
+ // Per-descriptor data used by the reactor.
+ reactor::per_descriptor_data reactor_data_;
+
+#if defined(BOOST_ASIO_ENABLE_CANCELIO)
+ // The ID of the thread from which it is safe to cancel asynchronous
+ // operations. 0 means no asynchronous operations have been started yet.
+ // ~0 means asynchronous operations have been started from more than one
+ // thread, and cancellation is not supported for the socket.
+ DWORD safe_cancellation_thread_id_;
+#endif // defined(BOOST_ASIO_ENABLE_CANCELIO)
+
+ // Pointers to adjacent socket implementations in linked list.
+ base_implementation_type* next_;
+ base_implementation_type* prev_;
+ };
+
+ // Constructor.
+ BOOST_ASIO_DECL win_iocp_socket_service_base(
+ boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new socket implementation.
+ BOOST_ASIO_DECL void construct(base_implementation_type& impl);
+
+ // Move-construct a new socket implementation.
+ BOOST_ASIO_DECL void base_move_construct(base_implementation_type& impl,
+ base_implementation_type& other_impl);
+
+ // Move-assign from another socket implementation.
+ BOOST_ASIO_DECL void base_move_assign(base_implementation_type& impl,
+ win_iocp_socket_service_base& other_service,
+ base_implementation_type& other_impl);
+
+ // Destroy a socket implementation.
+ BOOST_ASIO_DECL void destroy(base_implementation_type& impl);
+
+ // Determine whether the socket is open.
+ bool is_open(const base_implementation_type& impl) const
+ {
+ return impl.socket_ != invalid_socket;
+ }
+
+ // Destroy a socket implementation.
+ BOOST_ASIO_DECL boost::system::error_code close(
+ base_implementation_type& impl, boost::system::error_code& ec);
+
+ // Cancel all operations associated with the socket.
+ BOOST_ASIO_DECL boost::system::error_code cancel(
+ base_implementation_type& impl, boost::system::error_code& ec);
+
+ // Determine whether the socket is at the out-of-band data mark.
+ bool at_mark(const base_implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return socket_ops::sockatmark(impl.socket_, ec);
+ }
+
+ // Determine the number of bytes available for reading.
+ std::size_t available(const base_implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return socket_ops::available(impl.socket_, ec);
+ }
+
+ // Place the socket into the state where it will listen for new connections.
+ boost::system::error_code listen(base_implementation_type& impl,
+ int backlog, boost::system::error_code& ec)
+ {
+ socket_ops::listen(impl.socket_, backlog, ec);
+ return ec;
+ }
+
+ // Perform an IO control command on the socket.
+ template <typename IO_Control_Command>
+ boost::system::error_code io_control(base_implementation_type& impl,
+ IO_Control_Command& command, boost::system::error_code& ec)
+ {
+ socket_ops::ioctl(impl.socket_, impl.state_, command.name(),
+ static_cast<ioctl_arg_type*>(command.data()), ec);
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the socket.
+ bool non_blocking(const base_implementation_type& impl) const
+ {
+ return (impl.state_ & socket_ops::user_set_non_blocking) != 0;
+ }
+
+ // Sets the non-blocking mode of the socket.
+ boost::system::error_code non_blocking(base_implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ socket_ops::set_user_non_blocking(impl.socket_, impl.state_, mode, ec);
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the native socket implementation.
+ bool native_non_blocking(const base_implementation_type& impl) const
+ {
+ return (impl.state_ & socket_ops::internal_non_blocking) != 0;
+ }
+
+ // Sets the non-blocking mode of the native socket implementation.
+ boost::system::error_code native_non_blocking(base_implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ socket_ops::set_internal_non_blocking(impl.socket_, impl.state_, mode, ec);
+ return ec;
+ }
+
+ // Disable sends or receives on the socket.
+ boost::system::error_code shutdown(base_implementation_type& impl,
+ socket_base::shutdown_type what, boost::system::error_code& ec)
+ {
+ socket_ops::shutdown(impl.socket_, what, ec);
+ return ec;
+ }
+
+ // Send the given data to the peer. Returns the number of bytes sent.
+ template <typename ConstBufferSequence>
+ size_t send(base_implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(buffers);
+
+ return socket_ops::sync_send(impl.socket_, impl.state_,
+ bufs.buffers(), bufs.count(), flags, bufs.all_empty(), ec);
+ }
+
+ // Wait until data can be sent without blocking.
+ size_t send(base_implementation_type& impl, const null_buffers&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_write(impl.socket_, impl.state_, ec);
+
+ return 0;
+ }
+
+ // Start an asynchronous send. The data being sent must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_send(base_implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_socket_send_op<ConstBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.cancel_token_, buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_send"));
+
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence> bufs(buffers);
+
+ start_send_op(impl, bufs.buffers(), bufs.count(), flags,
+ (impl.state_ & socket_ops::stream_oriented) != 0 && bufs.all_empty(),
+ p.p);
+ p.v = p.p = 0;
+ }
+
+ // Start an asynchronous wait until data can be sent without blocking.
+ template <typename Handler>
+ void async_send(base_implementation_type& impl, const null_buffers&,
+ socket_base::message_flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.cancel_token_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_send(null_buffers)"));
+
+ start_reactor_op(impl, reactor::write_op, p.p);
+ p.v = p.p = 0;
+ }
+
+ // Receive some data from the peer. Returns the number of bytes received.
+ template <typename MutableBufferSequence>
+ size_t receive(base_implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ return socket_ops::sync_recv(impl.socket_, impl.state_,
+ bufs.buffers(), bufs.count(), flags, bufs.all_empty(), ec);
+ }
+
+ // Wait until data can be received without blocking.
+ size_t receive(base_implementation_type& impl, const null_buffers&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_read(impl.socket_, impl.state_, ec);
+
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received
+ // must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive(base_implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_socket_recv_op<MutableBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.state_, impl.cancel_token_, buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_receive"));
+
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ start_receive_op(impl, bufs.buffers(), bufs.count(), flags,
+ (impl.state_ & socket_ops::stream_oriented) != 0 && bufs.all_empty(),
+ p.p);
+ p.v = p.p = 0;
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive(base_implementation_type& impl, const null_buffers&,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.cancel_token_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_receive(null_buffers)"));
+
+ start_null_buffers_receive_op(impl, flags, p.p);
+ p.v = p.p = 0;
+ }
+
+ // Receive some data with associated flags. Returns the number of bytes
+ // received.
+ template <typename MutableBufferSequence>
+ size_t receive_with_flags(base_implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, boost::system::error_code& ec)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ return socket_ops::sync_recvmsg(impl.socket_, impl.state_,
+ bufs.buffers(), bufs.count(), in_flags, out_flags, ec);
+ }
+
+ // Wait until data can be received without blocking.
+ size_t receive_with_flags(base_implementation_type& impl,
+ const null_buffers&, socket_base::message_flags,
+ socket_base::message_flags& out_flags, boost::system::error_code& ec)
+ {
+ // Wait for socket to become ready.
+ socket_ops::poll_read(impl.socket_, impl.state_, ec);
+
+ // Clear out_flags, since we cannot give it any other sensible value when
+ // performing a null_buffers operation.
+ out_flags = 0;
+
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received
+ // must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive_with_flags(base_implementation_type& impl,
+ const MutableBufferSequence& buffers, socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_socket_recvmsg_op<MutableBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.cancel_token_, buffers, out_flags, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket",
+ &impl, "async_receive_with_flags"));
+
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence> bufs(buffers);
+
+ start_receive_op(impl, bufs.buffers(), bufs.count(), in_flags, false, p.p);
+ p.v = p.p = 0;
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive_with_flags(base_implementation_type& impl,
+ const null_buffers&, socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef win_iocp_null_buffers_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(impl.cancel_token_, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl,
+ "async_receive_with_flags(null_buffers)"));
+
+ // Reset out_flags since it can be given no sensible value at this time.
+ out_flags = 0;
+
+ start_null_buffers_receive_op(impl, in_flags, p.p);
+ p.v = p.p = 0;
+ }
+
+ // Helper function to restart an asynchronous accept operation.
+ BOOST_ASIO_DECL void restart_accept_op(socket_type s,
+ socket_holder& new_socket, int family, int type, int protocol,
+ void* output_buffer, DWORD address_length, operation* op);
+
+protected:
+ // Open a new socket implementation.
+ BOOST_ASIO_DECL boost::system::error_code do_open(
+ base_implementation_type& impl, int family, int type,
+ int protocol, boost::system::error_code& ec);
+
+ // Assign a native socket to a socket implementation.
+ BOOST_ASIO_DECL boost::system::error_code do_assign(
+ base_implementation_type& impl, int type,
+ socket_type native_socket, boost::system::error_code& ec);
+
+ // Helper function to start an asynchronous send operation.
+ BOOST_ASIO_DECL void start_send_op(base_implementation_type& impl,
+ WSABUF* buffers, std::size_t buffer_count,
+ socket_base::message_flags flags, bool noop, operation* op);
+
+ // Helper function to start an asynchronous send_to operation.
+ BOOST_ASIO_DECL void start_send_to_op(base_implementation_type& impl,
+ WSABUF* buffers, std::size_t buffer_count,
+ const socket_addr_type* addr, int addrlen,
+ socket_base::message_flags flags, operation* op);
+
+ // Helper function to start an asynchronous receive operation.
+ BOOST_ASIO_DECL void start_receive_op(base_implementation_type& impl,
+ WSABUF* buffers, std::size_t buffer_count,
+ socket_base::message_flags flags, bool noop, operation* op);
+
+ // Helper function to start an asynchronous null_buffers receive operation.
+ BOOST_ASIO_DECL void start_null_buffers_receive_op(
+ base_implementation_type& impl,
+ socket_base::message_flags flags, reactor_op* op);
+
+ // Helper function to start an asynchronous receive_from operation.
+ BOOST_ASIO_DECL void start_receive_from_op(base_implementation_type& impl,
+ WSABUF* buffers, std::size_t buffer_count, socket_addr_type* addr,
+ socket_base::message_flags flags, int* addrlen, operation* op);
+
+ // Helper function to start an asynchronous accept operation.
+ BOOST_ASIO_DECL void start_accept_op(base_implementation_type& impl,
+ bool peer_is_open, socket_holder& new_socket, int family, int type,
+ int protocol, void* output_buffer, DWORD address_length, operation* op);
+
+ // Start an asynchronous read or write operation using the reactor.
+ BOOST_ASIO_DECL void start_reactor_op(base_implementation_type& impl,
+ int op_type, reactor_op* op);
+
+ // Start the asynchronous connect operation using the reactor.
+ BOOST_ASIO_DECL void start_connect_op(base_implementation_type& impl,
+ int family, int type, const socket_addr_type* remote_addr,
+ std::size_t remote_addrlen, win_iocp_socket_connect_op_base* op);
+
+ // Helper function to close a socket when the associated object is being
+ // destroyed.
+ BOOST_ASIO_DECL void close_for_destruction(base_implementation_type& impl);
+
+ // Update the ID of the thread from which cancellation is safe.
+ BOOST_ASIO_DECL void update_cancellation_thread_id(
+ base_implementation_type& impl);
+
+ // Helper function to get the reactor. If no reactor has been created yet, a
+ // new one is obtained from the io_service and a pointer to it is cached in
+ // this service.
+ BOOST_ASIO_DECL reactor& get_reactor();
+
+ // The type of a ConnectEx function pointer, as old SDKs may not provide it.
+ typedef BOOL (PASCAL *connect_ex_fn)(SOCKET,
+ const socket_addr_type*, int, void*, DWORD, DWORD*, OVERLAPPED*);
+
+ // Helper function to get the ConnectEx pointer. If no ConnectEx pointer has
+ // been obtained yet, one is obtained using WSAIoctl and the pointer is
+ // cached. Returns a null pointer if ConnectEx is not available.
+ BOOST_ASIO_DECL connect_ex_fn get_connect_ex(
+ base_implementation_type& impl, int type);
+
+ // Helper function to emulate InterlockedCompareExchangePointer functionality
+ // for:
+ // - very old Platform SDKs; and
+ // - platform SDKs where MSVC's /Wp64 option causes spurious warnings.
+ BOOST_ASIO_DECL void* interlocked_compare_exchange_pointer(
+ void** dest, void* exch, void* cmp);
+
+ // Helper function to emulate InterlockedExchangePointer functionality for:
+ // - very old Platform SDKs; and
+ // - platform SDKs where MSVC's /Wp64 option causes spurious warnings.
+ BOOST_ASIO_DECL void* interlocked_exchange_pointer(void** dest, void* val);
+
+ // The io_service used to obtain the reactor, if required.
+ boost::asio::io_service& io_service_;
+
+ // The IOCP service used for running asynchronous operations and dispatching
+ // handlers.
+ win_iocp_io_service& iocp_service_;
+
+ // The reactor used for performing connect operations. This object is created
+ // only if needed.
+ reactor* reactor_;
+
+ // Pointer to ConnectEx implementation.
+ void* connect_ex_;
+
+ // Mutex to protect access to the linked list of implementations.
+ boost::asio::detail::mutex mutex_;
+
+ // The head of a linked list of all implementations.
+ base_implementation_type* impl_list_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_iocp_socket_service_base.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_SOCKET_SERVICE_BASE_HPP
diff --git a/ext/patches/boost/asio/detail/win_iocp_thread_info.hpp b/ext/patches/boost/asio/detail/win_iocp_thread_info.hpp
new file mode 100644
index 0000000..de58a54
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_iocp_thread_info.hpp
@@ -0,0 +1,36 @@
+//
+// detail/win_iocp_thread_info.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_IOCP_THREAD_INFO_HPP
+#define BOOST_ASIO_DETAIL_WIN_IOCP_THREAD_INFO_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/thread_info_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct win_iocp_thread_info : public thread_info_base
+{
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_WIN_IOCP_THREAD_INFO_HPP
diff --git a/ext/patches/boost/asio/detail/win_mutex.hpp b/ext/patches/boost/asio/detail/win_mutex.hpp
new file mode 100644
index 0000000..5dc2028
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_mutex.hpp
@@ -0,0 +1,80 @@
+//
+// detail/win_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_WIN_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS)
+
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/scoped_lock.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_mutex
+ : private noncopyable
+{
+public:
+ typedef boost::asio::detail::scoped_lock<win_mutex> scoped_lock;
+
+ // Constructor.
+ BOOST_ASIO_DECL win_mutex();
+
+ // Destructor.
+ ~win_mutex()
+ {
+ ::DeleteCriticalSection(&crit_section_);
+ }
+
+ // Lock the mutex.
+ void lock()
+ {
+ ::EnterCriticalSection(&crit_section_);
+ }
+
+ // Unlock the mutex.
+ void unlock()
+ {
+ ::LeaveCriticalSection(&crit_section_);
+ }
+
+private:
+ // Initialisation must be performed in a separate function to the constructor
+ // since the compiler does not support the use of structured exceptions and
+ // C++ exceptions in the same function.
+ BOOST_ASIO_DECL int do_init();
+
+ ::CRITICAL_SECTION crit_section_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_mutex.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_WIN_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/win_object_handle_service.hpp b/ext/patches/boost/asio/detail/win_object_handle_service.hpp
new file mode 100644
index 0000000..ed91a7f
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_object_handle_service.hpp
@@ -0,0 +1,185 @@
+//
+// detail/win_object_handle_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2011 Boris Schaeling (boris at highscore.de)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_OBJECT_HANDLE_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_WIN_OBJECT_HANDLE_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/wait_handler.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class win_object_handle_service
+{
+public:
+ // The native type of an object handle.
+ typedef HANDLE native_handle_type;
+
+ // The implementation type of the object handle.
+ class implementation_type
+ {
+ public:
+ // Default constructor.
+ implementation_type()
+ : handle_(INVALID_HANDLE_VALUE),
+ wait_handle_(INVALID_HANDLE_VALUE),
+ owner_(0),
+ next_(0),
+ prev_(0)
+ {
+ }
+
+ private:
+ // Only this service will have access to the internal values.
+ friend class win_object_handle_service;
+
+ // The native object handle representation. May be accessed or modified
+ // without locking the mutex.
+ native_handle_type handle_;
+
+ // The handle used to unregister the wait operation. The mutex must be
+ // locked when accessing or modifying this member.
+ HANDLE wait_handle_;
+
+ // The operations waiting on the object handle. If there is a registered
+ // wait then the mutex must be locked when accessing or modifying this
+ // member
+ op_queue<wait_op> op_queue_;
+
+ // The service instance that owns the object handle implementation.
+ win_object_handle_service* owner_;
+
+ // Pointers to adjacent handle implementations in linked list. The mutex
+ // must be locked when accessing or modifying these members.
+ implementation_type* next_;
+ implementation_type* prev_;
+ };
+
+ // Constructor.
+ BOOST_ASIO_DECL win_object_handle_service(
+ boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new handle implementation.
+ BOOST_ASIO_DECL void construct(implementation_type& impl);
+
+ // Move-construct a new handle implementation.
+ BOOST_ASIO_DECL void move_construct(implementation_type& impl,
+ implementation_type& other_impl);
+
+ // Move-assign from another handle implementation.
+ BOOST_ASIO_DECL void move_assign(implementation_type& impl,
+ win_object_handle_service& other_service,
+ implementation_type& other_impl);
+
+ // Destroy a handle implementation.
+ BOOST_ASIO_DECL void destroy(implementation_type& impl);
+
+ // Assign a native handle to a handle implementation.
+ BOOST_ASIO_DECL boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec);
+
+ // Determine whether the handle is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return impl.handle_ != INVALID_HANDLE_VALUE && impl.handle_ != 0;
+ }
+
+ // Destroy a handle implementation.
+ BOOST_ASIO_DECL boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ // Get the native handle representation.
+ native_handle_type native_handle(const implementation_type& impl) const
+ {
+ return impl.handle_;
+ }
+
+ // Cancel all operations associated with the handle.
+ BOOST_ASIO_DECL boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ // Perform a synchronous wait for the object to enter a signalled state.
+ BOOST_ASIO_DECL void wait(implementation_type& impl,
+ boost::system::error_code& ec);
+
+ /// Start an asynchronous wait.
+ template <typename Handler>
+ void async_wait(implementation_type& impl, Handler& handler)
+ {
+ // Allocate and construct an operation to wrap the handler.
+ typedef wait_handler<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "object_handle", &impl, "async_wait"));
+
+ start_wait_op(impl, p.p);
+ p.v = p.p = 0;
+ }
+
+private:
+ // Helper function to start an asynchronous wait operation.
+ BOOST_ASIO_DECL void start_wait_op(implementation_type& impl, wait_op* op);
+
+ // Helper function to register a wait operation.
+ BOOST_ASIO_DECL void register_wait_callback(
+ implementation_type& impl, mutex::scoped_lock& lock);
+
+ // Callback function invoked when the registered wait completes.
+ static BOOST_ASIO_DECL VOID CALLBACK wait_callback(
+ PVOID param, BOOLEAN timeout);
+
+ // The io_service implementation used to post completions.
+ io_service_impl& io_service_;
+
+ // Mutex to protect access to internal state.
+ mutex mutex_;
+
+ // The head of a linked list of all implementations.
+ implementation_type* impl_list_;
+
+ // Flag to indicate that the dispatcher has been shut down.
+ bool shutdown_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_object_handle_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+
+#endif // BOOST_ASIO_DETAIL_WIN_OBJECT_HANDLE_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/win_static_mutex.hpp b/ext/patches/boost/asio/detail/win_static_mutex.hpp
new file mode 100644
index 0000000..1baf27d
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_static_mutex.hpp
@@ -0,0 +1,76 @@
+//
+// detail/win_static_mutex.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_STATIC_MUTEX_HPP
+#define BOOST_ASIO_DETAIL_WIN_STATIC_MUTEX_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS)
+
+#include <boost/asio/detail/scoped_lock.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct win_static_mutex
+{
+ typedef boost::asio::detail::scoped_lock<win_static_mutex> scoped_lock;
+
+ // Initialise the mutex.
+ BOOST_ASIO_DECL void init();
+
+ // Initialisation must be performed in a separate function to the "public"
+ // init() function since the compiler does not support the use of structured
+ // exceptions and C++ exceptions in the same function.
+ BOOST_ASIO_DECL int do_init();
+
+ // Lock the mutex.
+ void lock()
+ {
+ ::EnterCriticalSection(&crit_section_);
+ }
+
+ // Unlock the mutex.
+ void unlock()
+ {
+ ::LeaveCriticalSection(&crit_section_);
+ }
+
+ bool initialised_;
+ ::CRITICAL_SECTION crit_section_;
+};
+
+#if defined(UNDER_CE)
+# define BOOST_ASIO_WIN_STATIC_MUTEX_INIT { false, { 0, 0, 0, 0, 0 } }
+#else // defined(UNDER_CE)
+# define BOOST_ASIO_WIN_STATIC_MUTEX_INIT { false, { 0, 0, 0, 0, 0, 0 } }
+#endif // defined(UNDER_CE)
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_static_mutex.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_WIN_STATIC_MUTEX_HPP
diff --git a/ext/patches/boost/asio/detail/win_thread.hpp b/ext/patches/boost/asio/detail/win_thread.hpp
new file mode 100644
index 0000000..a5f2414
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_thread.hpp
@@ -0,0 +1,141 @@
+//
+// detail/win_thread.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_THREAD_HPP
+#define BOOST_ASIO_DETAIL_WIN_THREAD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) && !defined(UNDER_CE)
+
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+BOOST_ASIO_DECL unsigned int __stdcall win_thread_function(void* arg);
+
+#if defined(WINVER) && (WINVER < 0x0500)
+BOOST_ASIO_DECL void __stdcall apc_function(ULONG data);
+#else
+BOOST_ASIO_DECL void __stdcall apc_function(ULONG_PTR data);
+#endif
+
+template <typename T>
+class win_thread_base
+{
+public:
+ static bool terminate_threads()
+ {
+ return ::InterlockedExchangeAdd(&terminate_threads_, 0) != 0;
+ }
+
+ static void set_terminate_threads(bool b)
+ {
+ ::InterlockedExchange(&terminate_threads_, b ? 1 : 0);
+ }
+
+private:
+ static long terminate_threads_;
+};
+
+template <typename T>
+long win_thread_base<T>::terminate_threads_ = 0;
+
+class win_thread
+ : private noncopyable,
+ public win_thread_base<win_thread>
+{
+public:
+ // Constructor.
+ template <typename Function>
+ win_thread(Function f, unsigned int stack_size = 0)
+ : thread_(0),
+ exit_event_(0)
+ {
+ start_thread(new func<Function>(f), stack_size);
+ }
+
+ // Destructor.
+ BOOST_ASIO_DECL ~win_thread();
+
+ // Wait for the thread to exit.
+ BOOST_ASIO_DECL void join();
+
+private:
+ friend BOOST_ASIO_DECL unsigned int __stdcall win_thread_function(void* arg);
+
+#if defined(WINVER) && (WINVER < 0x0500)
+ friend BOOST_ASIO_DECL void __stdcall apc_function(ULONG);
+#else
+ friend BOOST_ASIO_DECL void __stdcall apc_function(ULONG_PTR);
+#endif
+
+ class func_base
+ {
+ public:
+ virtual ~func_base() {}
+ virtual void run() = 0;
+ ::HANDLE entry_event_;
+ ::HANDLE exit_event_;
+ };
+
+ struct auto_func_base_ptr
+ {
+ func_base* ptr;
+ ~auto_func_base_ptr() { delete ptr; }
+ };
+
+ template <typename Function>
+ class func
+ : public func_base
+ {
+ public:
+ func(Function f)
+ : f_(f)
+ {
+ }
+
+ virtual void run()
+ {
+ f_();
+ }
+
+ private:
+ Function f_;
+ };
+
+ BOOST_ASIO_DECL void start_thread(func_base* arg, unsigned int stack_size);
+
+ ::HANDLE thread_;
+ ::HANDLE exit_event_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_thread.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS) && !defined(UNDER_CE)
+
+#endif // BOOST_ASIO_DETAIL_WIN_THREAD_HPP
diff --git a/ext/patches/boost/asio/detail/win_tss_ptr.hpp b/ext/patches/boost/asio/detail/win_tss_ptr.hpp
new file mode 100644
index 0000000..c96aa8d
--- /dev/null
+++ b/ext/patches/boost/asio/detail/win_tss_ptr.hpp
@@ -0,0 +1,81 @@
+//
+// detail/win_tss_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WIN_TSS_PTR_HPP
+#define BOOST_ASIO_DETAIL_WIN_TSS_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS)
+
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+// Helper function to create thread-specific storage.
+BOOST_ASIO_DECL DWORD win_tss_ptr_create();
+
+template <typename T>
+class win_tss_ptr
+ : private noncopyable
+{
+public:
+ // Constructor.
+ win_tss_ptr()
+ : tss_key_(win_tss_ptr_create())
+ {
+ }
+
+ // Destructor.
+ ~win_tss_ptr()
+ {
+ ::TlsFree(tss_key_);
+ }
+
+ // Get the value.
+ operator T*() const
+ {
+ return static_cast<T*>(::TlsGetValue(tss_key_));
+ }
+
+ // Set the value.
+ void operator=(T* value)
+ {
+ ::TlsSetValue(tss_key_, value);
+ }
+
+private:
+ // Thread-specific storage to allow unlocked access to determine whether a
+ // thread is a member of the pool.
+ DWORD tss_key_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/win_tss_ptr.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS)
+
+#endif // BOOST_ASIO_DETAIL_WIN_TSS_PTR_HPP
diff --git a/ext/patches/boost/asio/detail/wince_thread.hpp b/ext/patches/boost/asio/detail/wince_thread.hpp
new file mode 100644
index 0000000..f1dbaed
--- /dev/null
+++ b/ext/patches/boost/asio/detail/wince_thread.hpp
@@ -0,0 +1,118 @@
+//
+// detail/wince_thread.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINCE_THREAD_HPP
+#define BOOST_ASIO_DETAIL_WINCE_THREAD_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) && defined(UNDER_CE)
+
+#include <memory>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+DWORD WINAPI wince_thread_function(LPVOID arg);
+
+class wince_thread
+ : private noncopyable
+{
+public:
+ // Constructor.
+ template <typename Function>
+ wince_thread(Function f, unsigned int = 0)
+ {
+ std::auto_ptr<func_base> arg(new func<Function>(f));
+ DWORD thread_id = 0;
+ thread_ = ::CreateThread(0, 0, wince_thread_function,
+ arg.get(), 0, &thread_id);
+ if (!thread_)
+ {
+ DWORD last_error = ::GetLastError();
+ boost::system::error_code ec(last_error,
+ boost::asio::error::get_system_category());
+ boost::asio::detail::throw_error(ec, "thread");
+ }
+ arg.release();
+ }
+
+ // Destructor.
+ ~wince_thread()
+ {
+ ::CloseHandle(thread_);
+ }
+
+ // Wait for the thread to exit.
+ void join()
+ {
+ ::WaitForSingleObject(thread_, INFINITE);
+ }
+
+private:
+ friend DWORD WINAPI wince_thread_function(LPVOID arg);
+
+ class func_base
+ {
+ public:
+ virtual ~func_base() {}
+ virtual void run() = 0;
+ };
+
+ template <typename Function>
+ class func
+ : public func_base
+ {
+ public:
+ func(Function f)
+ : f_(f)
+ {
+ }
+
+ virtual void run()
+ {
+ f_();
+ }
+
+ private:
+ Function f_;
+ };
+
+ ::HANDLE thread_;
+};
+
+inline DWORD WINAPI wince_thread_function(LPVOID arg)
+{
+ std::auto_ptr<wince_thread::func_base> func(
+ static_cast<wince_thread::func_base*>(arg));
+ func->run();
+ return 0;
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS) && defined(UNDER_CE)
+
+#endif // BOOST_ASIO_DETAIL_WINCE_THREAD_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_async_manager.hpp b/ext/patches/boost/asio/detail/winrt_async_manager.hpp
new file mode 100644
index 0000000..754b8e0
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_async_manager.hpp
@@ -0,0 +1,296 @@
+//
+// detail/winrt_async_manager.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_ASYNC_MANAGER_HPP
+#define BOOST_ASIO_DETAIL_WINRT_ASYNC_MANAGER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <future>
+#include <boost/asio/detail/atomic_count.hpp>
+#include <boost/asio/detail/winrt_async_op.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class winrt_async_manager
+ : public boost::asio::detail::service_base<winrt_async_manager>
+{
+public:
+ // Constructor.
+ winrt_async_manager(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<winrt_async_manager>(io_service),
+ io_service_(use_service<io_service_impl>(io_service)),
+ outstanding_ops_(1)
+ {
+ }
+
+ // Destructor.
+ ~winrt_async_manager()
+ {
+ }
+
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ if (--outstanding_ops_ > 0)
+ {
+ // Block until last operation is complete.
+ std::future<void> f = promise_.get_future();
+ f.wait();
+ }
+ }
+
+ void sync(Windows::Foundation::IAsyncAction^ action,
+ boost::system::error_code& ec)
+ {
+ using namespace Windows::Foundation;
+ using Windows::Foundation::AsyncStatus;
+
+ auto promise = std::make_shared<std::promise<boost::system::error_code>>();
+ auto future = promise->get_future();
+
+ action->Completed = ref new AsyncActionCompletedHandler(
+ [promise](IAsyncAction^ action, AsyncStatus status)
+ {
+ switch (status)
+ {
+ case AsyncStatus::Canceled:
+ promise->set_value(boost::asio::error::operation_aborted);
+ break;
+ case AsyncStatus::Error:
+ case AsyncStatus::Completed:
+ default:
+ boost::system::error_code ec(
+ action->ErrorCode.Value,
+ boost::system::system_category());
+ promise->set_value(ec);
+ break;
+ }
+ });
+
+ ec = future.get();
+ }
+
+ template <typename TResult>
+ TResult sync(Windows::Foundation::IAsyncOperation<TResult>^ operation,
+ boost::system::error_code& ec)
+ {
+ using namespace Windows::Foundation;
+ using Windows::Foundation::AsyncStatus;
+
+ auto promise = std::make_shared<std::promise<boost::system::error_code>>();
+ auto future = promise->get_future();
+
+ operation->Completed = ref new AsyncOperationCompletedHandler<TResult>(
+ [promise](IAsyncOperation<TResult>^ operation, AsyncStatus status)
+ {
+ switch (status)
+ {
+ case AsyncStatus::Canceled:
+ promise->set_value(boost::asio::error::operation_aborted);
+ break;
+ case AsyncStatus::Error:
+ case AsyncStatus::Completed:
+ default:
+ boost::system::error_code ec(
+ operation->ErrorCode.Value,
+ boost::system::system_category());
+ promise->set_value(ec);
+ break;
+ }
+ });
+
+ ec = future.get();
+ return operation->GetResults();
+ }
+
+ template <typename TResult, typename TProgress>
+ TResult sync(
+ Windows::Foundation::IAsyncOperationWithProgress<
+ TResult, TProgress>^ operation,
+ boost::system::error_code& ec)
+ {
+ using namespace Windows::Foundation;
+ using Windows::Foundation::AsyncStatus;
+
+ auto promise = std::make_shared<std::promise<boost::system::error_code>>();
+ auto future = promise->get_future();
+
+ operation->Completed
+ = ref new AsyncOperationWithProgressCompletedHandler<TResult, TProgress>(
+ [promise](IAsyncOperationWithProgress<TResult, TProgress>^ operation,
+ AsyncStatus status)
+ {
+ switch (status)
+ {
+ case AsyncStatus::Canceled:
+ promise->set_value(boost::asio::error::operation_aborted);
+ break;
+ case AsyncStatus::Started:
+ break;
+ case AsyncStatus::Error:
+ case AsyncStatus::Completed:
+ default:
+ boost::system::error_code ec(
+ operation->ErrorCode.Value,
+ boost::system::system_category());
+ promise->set_value(ec);
+ break;
+ }
+ });
+
+ ec = future.get();
+ return operation->GetResults();
+ }
+
+ void async(Windows::Foundation::IAsyncAction^ action,
+ winrt_async_op<void>* handler)
+ {
+ using namespace Windows::Foundation;
+ using Windows::Foundation::AsyncStatus;
+
+ auto on_completed = ref new AsyncActionCompletedHandler(
+ [this, handler](IAsyncAction^ action, AsyncStatus status)
+ {
+ switch (status)
+ {
+ case AsyncStatus::Canceled:
+ handler->ec_ = boost::asio::error::operation_aborted;
+ break;
+ case AsyncStatus::Started:
+ return;
+ case AsyncStatus::Completed:
+ case AsyncStatus::Error:
+ default:
+ handler->ec_ = boost::system::error_code(
+ action->ErrorCode.Value,
+ boost::system::system_category());
+ break;
+ }
+ io_service_.post_deferred_completion(handler);
+ if (--outstanding_ops_ == 0)
+ promise_.set_value();
+ });
+
+ io_service_.work_started();
+ ++outstanding_ops_;
+ action->Completed = on_completed;
+ }
+
+ template <typename TResult>
+ void async(Windows::Foundation::IAsyncOperation<TResult>^ operation,
+ winrt_async_op<TResult>* handler)
+ {
+ using namespace Windows::Foundation;
+ using Windows::Foundation::AsyncStatus;
+
+ auto on_completed = ref new AsyncOperationCompletedHandler<TResult>(
+ [this, handler](IAsyncOperation<TResult>^ operation, AsyncStatus status)
+ {
+ switch (status)
+ {
+ case AsyncStatus::Canceled:
+ handler->ec_ = boost::asio::error::operation_aborted;
+ break;
+ case AsyncStatus::Started:
+ return;
+ case AsyncStatus::Completed:
+ handler->result_ = operation->GetResults();
+ // Fall through.
+ case AsyncStatus::Error:
+ default:
+ handler->ec_ = boost::system::error_code(
+ operation->ErrorCode.Value,
+ boost::system::system_category());
+ break;
+ }
+ io_service_.post_deferred_completion(handler);
+ if (--outstanding_ops_ == 0)
+ promise_.set_value();
+ });
+
+ io_service_.work_started();
+ ++outstanding_ops_;
+ operation->Completed = on_completed;
+ }
+
+ template <typename TResult, typename TProgress>
+ void async(
+ Windows::Foundation::IAsyncOperationWithProgress<
+ TResult, TProgress>^ operation,
+ winrt_async_op<TResult>* handler)
+ {
+ using namespace Windows::Foundation;
+ using Windows::Foundation::AsyncStatus;
+
+ auto on_completed
+ = ref new AsyncOperationWithProgressCompletedHandler<TResult, TProgress>(
+ [this, handler](IAsyncOperationWithProgress<
+ TResult, TProgress>^ operation, AsyncStatus status)
+ {
+ switch (status)
+ {
+ case AsyncStatus::Canceled:
+ handler->ec_ = boost::asio::error::operation_aborted;
+ break;
+ case AsyncStatus::Started:
+ return;
+ case AsyncStatus::Completed:
+ handler->result_ = operation->GetResults();
+ // Fall through.
+ case AsyncStatus::Error:
+ default:
+ handler->ec_ = boost::system::error_code(
+ operation->ErrorCode.Value,
+ boost::system::system_category());
+ break;
+ }
+ io_service_.post_deferred_completion(handler);
+ if (--outstanding_ops_ == 0)
+ promise_.set_value();
+ });
+
+ io_service_.work_started();
+ ++outstanding_ops_;
+ operation->Completed = on_completed;
+ }
+
+private:
+ // The io_service implementation used to post completed handlers.
+ io_service_impl& io_service_;
+
+ // Count of outstanding operations.
+ atomic_count outstanding_ops_;
+
+ // Used to keep wait for outstanding operations to complete.
+ std::promise<void> promise_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_ASYNC_MANAGER_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_async_op.hpp b/ext/patches/boost/asio/detail/winrt_async_op.hpp
new file mode 100644
index 0000000..80f809b
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_async_op.hpp
@@ -0,0 +1,67 @@
+//
+// detail/winrt_async_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_ASYNC_OP_HPP
+#define BOOST_ASIO_DETAIL_WINRT_ASYNC_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/operation.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename TResult>
+class winrt_async_op
+ : public operation
+{
+public:
+ // The error code to be passed to the completion handler.
+ boost::system::error_code ec_;
+
+ // The result of the operation, to be passed to the completion handler.
+ TResult result_;
+
+protected:
+ winrt_async_op(func_type complete_func)
+ : operation(complete_func),
+ result_()
+ {
+ }
+};
+
+template <>
+class winrt_async_op<void>
+ : public operation
+{
+public:
+ // The error code to be passed to the completion handler.
+ boost::system::error_code ec_;
+
+protected:
+ winrt_async_op(func_type complete_func)
+ : operation(complete_func)
+ {
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_WINRT_ASYNC_OP_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_resolve_op.hpp b/ext/patches/boost/asio/detail/winrt_resolve_op.hpp
new file mode 100644
index 0000000..5825483
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_resolve_op.hpp
@@ -0,0 +1,119 @@
+//
+// detail/winrt_resolve_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_RESOLVE_OP_HPP
+#define BOOST_ASIO_DETAIL_WINRT_RESOLVE_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/winrt_async_op.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol, typename Handler>
+class winrt_resolve_op :
+ public winrt_async_op<
+ Windows::Foundation::Collections::IVectorView<
+ Windows::Networking::EndpointPair^>^>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(winrt_resolve_op);
+
+ typedef typename Protocol::endpoint endpoint_type;
+ typedef boost::asio::ip::basic_resolver_query<Protocol> query_type;
+ typedef boost::asio::ip::basic_resolver_iterator<Protocol> iterator_type;
+
+ winrt_resolve_op(const query_type& query, Handler& handler)
+ : winrt_async_op<
+ Windows::Foundation::Collections::IVectorView<
+ Windows::Networking::EndpointPair^>^>(
+ &winrt_resolve_op::do_complete),
+ query_(query),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code&, std::size_t)
+ {
+ // Take ownership of the operation object.
+ winrt_resolve_op* o(static_cast<winrt_resolve_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ iterator_type iterator = iterator_type();
+ if (!o->ec_)
+ {
+ try
+ {
+ iterator = iterator_type::create(
+ o->result_, o->query_.hints(),
+ o->query_.host_name(), o->query_.service_name());
+ }
+ catch (Platform::Exception^ e)
+ {
+ o->ec_ = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ }
+ }
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, iterator_type>
+ handler(o->handler_, o->ec_, iterator);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ query_type query_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_RESOLVE_OP_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_resolver_service.hpp b/ext/patches/boost/asio/detail/winrt_resolver_service.hpp
new file mode 100644
index 0000000..8f5fd43
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_resolver_service.hpp
@@ -0,0 +1,185 @@
+//
+// detail/winrt_resolver_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_RESOLVER_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_WINRT_RESOLVER_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/winrt_async_manager.hpp>
+#include <boost/asio/detail/winrt_resolve_op.hpp>
+#include <boost/asio/detail/winrt_utils.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol>
+class winrt_resolver_service
+{
+public:
+ // The implementation type of the resolver. A cancellation token is used to
+ // indicate to the asynchronous operation that the operation has been
+ // cancelled.
+ typedef socket_ops::shared_cancel_token_type implementation_type;
+
+ // The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ // The query type.
+ typedef boost::asio::ip::basic_resolver_query<Protocol> query_type;
+
+ // The iterator type.
+ typedef boost::asio::ip::basic_resolver_iterator<Protocol> iterator_type;
+
+ // Constructor.
+ winrt_resolver_service(boost::asio::io_service& io_service)
+ : io_service_(use_service<io_service_impl>(io_service)),
+ async_manager_(use_service<winrt_async_manager>(io_service))
+ {
+ }
+
+ // Destructor.
+ ~winrt_resolver_service()
+ {
+ }
+
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ }
+
+ // Perform any fork-related housekeeping.
+ void fork_service(boost::asio::io_service::fork_event)
+ {
+ }
+
+ // Construct a new resolver implementation.
+ void construct(implementation_type&)
+ {
+ }
+
+ // Destroy a resolver implementation.
+ void destroy(implementation_type&)
+ {
+ }
+
+ // Cancel pending asynchronous operations.
+ void cancel(implementation_type&)
+ {
+ }
+
+ // Resolve a query to a list of entries.
+ iterator_type resolve(implementation_type&,
+ const query_type& query, boost::system::error_code& ec)
+ {
+ try
+ {
+ using namespace Windows::Networking::Sockets;
+ auto endpoint_pairs = async_manager_.sync(
+ DatagramSocket::GetEndpointPairsAsync(
+ winrt_utils::host_name(query.host_name()),
+ winrt_utils::string(query.service_name())), ec);
+
+ if (ec)
+ return iterator_type();
+
+ return iterator_type::create(
+ endpoint_pairs, query.hints(),
+ query.host_name(), query.service_name());
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ return iterator_type();
+ }
+ }
+
+ // Asynchronously resolve a query to a list of entries.
+ template <typename Handler>
+ void async_resolve(implementation_type&,
+ const query_type& query, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef winrt_resolve_op<Protocol, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(query, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "resolver", &impl, "async_resolve"));
+
+ try
+ {
+ using namespace Windows::Networking::Sockets;
+ async_manager_.async(DatagramSocket::GetEndpointPairsAsync(
+ winrt_utils::host_name(query.host_name()),
+ winrt_utils::string(query.service_name())), p.p);
+ p.v = p.p = 0;
+ }
+ catch (Platform::Exception^ e)
+ {
+ p.p->ec_ = boost::system::error_code(
+ e->HResult, boost::system::system_category());
+ io_service_.post_immediate_completion(p.p, is_continuation);
+ p.v = p.p = 0;
+ }
+ }
+
+ // Resolve an endpoint to a list of entries.
+ iterator_type resolve(implementation_type&,
+ const endpoint_type&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return iterator_type();
+ }
+
+ // Asynchronously resolve an endpoint to a list of entries.
+ template <typename Handler>
+ void async_resolve(implementation_type&,
+ const endpoint_type&, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const iterator_type iterator;
+ io_service_.get_io_service().post(
+ detail::bind_handler(handler, ec, iterator));
+ }
+
+private:
+ io_service_impl& io_service_;
+ winrt_async_manager& async_manager_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_RESOLVER_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_socket_connect_op.hpp b/ext/patches/boost/asio/detail/winrt_socket_connect_op.hpp
new file mode 100644
index 0000000..2d94c0d
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_socket_connect_op.hpp
@@ -0,0 +1,92 @@
+//
+// detail/winrt_socket_connect_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_SOCKET_CONNECT_OP_HPP
+#define BOOST_ASIO_DETAIL_WINRT_SOCKET_CONNECT_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/winrt_async_op.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Handler>
+class winrt_socket_connect_op :
+ public winrt_async_op<void>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(winrt_socket_connect_op);
+
+ winrt_socket_connect_op(Handler& handler)
+ : winrt_async_op<void>(&winrt_socket_connect_op::do_complete),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code&, std::size_t)
+ {
+ // Take ownership of the operation object.
+ winrt_socket_connect_op* o(static_cast<winrt_socket_connect_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder1<Handler, boost::system::error_code>
+ handler(o->handler_, o->ec_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_SOCKET_CONNECT_OP_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_socket_recv_op.hpp b/ext/patches/boost/asio/detail/winrt_socket_recv_op.hpp
new file mode 100644
index 0000000..1ad91de
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_socket_recv_op.hpp
@@ -0,0 +1,112 @@
+//
+// detail/winrt_socket_recv_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_SOCKET_RECV_OP_HPP
+#define BOOST_ASIO_DETAIL_WINRT_SOCKET_RECV_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/winrt_async_op.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename MutableBufferSequence, typename Handler>
+class winrt_socket_recv_op :
+ public winrt_async_op<Windows::Storage::Streams::IBuffer^>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(winrt_socket_recv_op);
+
+ winrt_socket_recv_op(const MutableBufferSequence& buffers, Handler& handler)
+ : winrt_async_op<Windows::Storage::Streams::IBuffer^>(
+ &winrt_socket_recv_op::do_complete),
+ buffers_(buffers),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code&, std::size_t)
+ {
+ // Take ownership of the operation object.
+ winrt_socket_recv_op* o(static_cast<winrt_socket_recv_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ // Check whether buffers are still valid.
+ if (owner)
+ {
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::validate(o->buffers_);
+ }
+#endif // defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+
+ std::size_t bytes_transferred = o->result_ ? o->result_->Length : 0;
+ if (bytes_transferred == 0 && !o->ec_ &&
+ !buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::all_empty(o->buffers_))
+ {
+ o->ec_ = boost::asio::error::eof;
+ }
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, bytes_transferred);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ MutableBufferSequence buffers_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_SOCKET_RECV_OP_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_socket_send_op.hpp b/ext/patches/boost/asio/detail/winrt_socket_send_op.hpp
new file mode 100644
index 0000000..d098f09
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_socket_send_op.hpp
@@ -0,0 +1,103 @@
+//
+// detail/winrt_socket_send_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_SOCKET_SEND_OP_HPP
+#define BOOST_ASIO_DETAIL_WINRT_SOCKET_SEND_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/fenced_block.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/winrt_async_op.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename ConstBufferSequence, typename Handler>
+class winrt_socket_send_op :
+ public winrt_async_op<unsigned int>
+{
+public:
+ BOOST_ASIO_DEFINE_HANDLER_PTR(winrt_socket_send_op);
+
+ winrt_socket_send_op(const ConstBufferSequence& buffers, Handler& handler)
+ : winrt_async_op<unsigned int>(&winrt_socket_send_op::do_complete),
+ buffers_(buffers),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ static void do_complete(io_service_impl* owner, operation* base,
+ const boost::system::error_code&, std::size_t)
+ {
+ // Take ownership of the operation object.
+ winrt_socket_send_op* o(static_cast<winrt_socket_send_op*>(base));
+ ptr p = { boost::asio::detail::addressof(o->handler_), o, o };
+
+ BOOST_ASIO_HANDLER_COMPLETION((o));
+
+#if defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+ // Check whether buffers are still valid.
+ if (owner)
+ {
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::validate(o->buffers_);
+ }
+#endif // defined(BOOST_ASIO_ENABLE_BUFFER_DEBUGGING)
+
+ // Make a copy of the handler so that the memory can be deallocated before
+ // the upcall is made. Even if we're not about to make an upcall, a
+ // sub-object of the handler may be the true owner of the memory associated
+ // with the handler. Consequently, a local copy of the handler is required
+ // to ensure that any owning sub-object remains valid until after we have
+ // deallocated the memory here.
+ detail::binder2<Handler, boost::system::error_code, std::size_t>
+ handler(o->handler_, o->ec_, o->result_);
+ p.h = boost::asio::detail::addressof(handler.handler_);
+ p.reset();
+
+ // Make the upcall if required.
+ if (owner)
+ {
+ fenced_block b(fenced_block::half);
+ BOOST_ASIO_HANDLER_INVOCATION_BEGIN((handler.arg1_, handler.arg2_));
+ boost_asio_handler_invoke_helpers::invoke(handler, handler.handler_);
+ BOOST_ASIO_HANDLER_INVOCATION_END;
+ }
+ }
+
+private:
+ ConstBufferSequence buffers_;
+ Handler handler_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_SOCKET_SEND_OP_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_ssocket_service.hpp b/ext/patches/boost/asio/detail/winrt_ssocket_service.hpp
new file mode 100644
index 0000000..8886515
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_ssocket_service.hpp
@@ -0,0 +1,234 @@
+//
+// detail/winrt_ssocket_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_SSOCKET_SERVICE_HPP
+#define BOOST_ASIO_DETAIL_WINRT_SSOCKET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/winrt_socket_connect_op.hpp>
+#include <boost/asio/detail/winrt_ssocket_service_base.hpp>
+#include <boost/asio/detail/winrt_utils.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+template <typename Protocol>
+class winrt_ssocket_service :
+ public winrt_ssocket_service_base
+{
+public:
+ // The protocol type.
+ typedef Protocol protocol_type;
+
+ // The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+ // The native type of a socket.
+ typedef Windows::Networking::Sockets::StreamSocket^ native_handle_type;
+
+ // The implementation type of the socket.
+ struct implementation_type : base_implementation_type
+ {
+ // Default constructor.
+ implementation_type()
+ : base_implementation_type(),
+ protocol_(endpoint_type().protocol())
+ {
+ }
+
+ // The protocol associated with the socket.
+ protocol_type protocol_;
+ };
+
+ // Constructor.
+ winrt_ssocket_service(boost::asio::io_service& io_service)
+ : winrt_ssocket_service_base(io_service)
+ {
+ }
+
+ // Move-construct a new socket implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ this->base_move_construct(impl, other_impl);
+
+ impl.protocol_ = other_impl.protocol_;
+ other_impl.protocol_ = endpoint_type().protocol();
+ }
+
+ // Move-assign from another socket implementation.
+ void move_assign(implementation_type& impl,
+ winrt_ssocket_service& other_service,
+ implementation_type& other_impl)
+ {
+ this->base_move_assign(impl, other_service, other_impl);
+
+ impl.protocol_ = other_impl.protocol_;
+ other_impl.protocol_ = endpoint_type().protocol();
+ }
+
+ // Move-construct a new socket implementation from another protocol type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type& impl,
+ typename winrt_ssocket_service<
+ Protocol1>::implementation_type& other_impl)
+ {
+ this->base_move_construct(impl, other_impl);
+
+ impl.protocol_ = protocol_type(other_impl.protocol_);
+ other_impl.protocol_ = typename Protocol1::endpoint().protocol();
+ }
+
+ // Open a new socket implementation.
+ boost::system::error_code open(implementation_type& impl,
+ const protocol_type& protocol, boost::system::error_code& ec)
+ {
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ try
+ {
+ impl.socket_ = ref new Windows::Networking::Sockets::StreamSocket;
+ impl.protocol_ = protocol;
+ ec = boost::system::error_code();
+ }
+ catch (Platform::Exception^ e)
+ {
+ ec = boost::system::error_code(e->HResult,
+ boost::system::system_category());
+ }
+
+ return ec;
+ }
+
+ // Assign a native socket to a socket implementation.
+ boost::system::error_code assign(implementation_type& impl,
+ const protocol_type& protocol, const native_handle_type& native_socket,
+ boost::system::error_code& ec)
+ {
+ if (is_open(impl))
+ {
+ ec = boost::asio::error::already_open;
+ return ec;
+ }
+
+ impl.socket_ = native_socket;
+ impl.protocol_ = protocol;
+ ec = boost::system::error_code();
+
+ return ec;
+ }
+
+ // Bind the socket to the specified local endpoint.
+ boost::system::error_code bind(implementation_type&,
+ const endpoint_type&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ endpoint_type endpoint;
+ endpoint.resize(do_get_endpoint(impl, true,
+ endpoint.data(), endpoint.size(), ec));
+ return endpoint;
+ }
+
+ // Get the remote endpoint.
+ endpoint_type remote_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ endpoint_type endpoint;
+ endpoint.resize(do_get_endpoint(impl, false,
+ endpoint.data(), endpoint.size(), ec));
+ return endpoint;
+ }
+
+ // Set a socket option.
+ template <typename Option>
+ boost::system::error_code set_option(implementation_type& impl,
+ const Option& option, boost::system::error_code& ec)
+ {
+ return do_set_option(impl, option.level(impl.protocol_),
+ option.name(impl.protocol_), option.data(impl.protocol_),
+ option.size(impl.protocol_), ec);
+ }
+
+ // Get a socket option.
+ template <typename Option>
+ boost::system::error_code get_option(const implementation_type& impl,
+ Option& option, boost::system::error_code& ec) const
+ {
+ std::size_t size = option.size(impl.protocol_);
+ do_get_option(impl, option.level(impl.protocol_),
+ option.name(impl.protocol_),
+ option.data(impl.protocol_), &size, ec);
+ if (!ec)
+ option.resize(impl.protocol_, size);
+ return ec;
+ }
+
+ // Connect the socket to the specified endpoint.
+ boost::system::error_code connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, boost::system::error_code& ec)
+ {
+ return do_connect(impl, peer_endpoint.data(), ec);
+ }
+
+ // Start an asynchronous connect.
+ template <typename Handler>
+ void async_connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef winrt_socket_connect_op<Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_connect"));
+
+ start_connect_op(impl, peer_endpoint.data(), p.p, is_continuation);
+ p.v = p.p = 0;
+ }
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_SSOCKET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_ssocket_service_base.hpp b/ext/patches/boost/asio/detail/winrt_ssocket_service_base.hpp
new file mode 100644
index 0000000..7181884
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_ssocket_service_base.hpp
@@ -0,0 +1,357 @@
+//
+// detail/winrt_ssocket_service_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_SSOCKET_SERVICE_BASE_HPP
+#define BOOST_ASIO_DETAIL_WINRT_SSOCKET_SERVICE_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/socket_base.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/winrt_async_manager.hpp>
+#include <boost/asio/detail/winrt_socket_recv_op.hpp>
+#include <boost/asio/detail/winrt_socket_send_op.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class winrt_ssocket_service_base
+{
+public:
+ // The native type of a socket.
+ typedef Windows::Networking::Sockets::StreamSocket^ native_handle_type;
+
+ // The implementation type of the socket.
+ struct base_implementation_type
+ {
+ // Default constructor.
+ base_implementation_type()
+ : socket_(nullptr),
+ next_(0),
+ prev_(0)
+ {
+ }
+
+ // The underlying native socket.
+ native_handle_type socket_;
+
+ // Pointers to adjacent socket implementations in linked list.
+ base_implementation_type* next_;
+ base_implementation_type* prev_;
+ };
+
+ // Constructor.
+ BOOST_ASIO_DECL winrt_ssocket_service_base(
+ boost::asio::io_service& io_service);
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Construct a new socket implementation.
+ BOOST_ASIO_DECL void construct(base_implementation_type&);
+
+ // Move-construct a new socket implementation.
+ BOOST_ASIO_DECL void base_move_construct(base_implementation_type& impl,
+ base_implementation_type& other_impl);
+
+ // Move-assign from another socket implementation.
+ BOOST_ASIO_DECL void base_move_assign(base_implementation_type& impl,
+ winrt_ssocket_service_base& other_service,
+ base_implementation_type& other_impl);
+
+ // Destroy a socket implementation.
+ BOOST_ASIO_DECL void destroy(base_implementation_type& impl);
+
+ // Determine whether the socket is open.
+ bool is_open(const base_implementation_type& impl) const
+ {
+ return impl.socket_ != nullptr;
+ }
+
+ // Destroy a socket implementation.
+ BOOST_ASIO_DECL boost::system::error_code close(
+ base_implementation_type& impl, boost::system::error_code& ec);
+
+ // Get the native socket representation.
+ native_handle_type native_handle(base_implementation_type& impl)
+ {
+ return impl.socket_;
+ }
+
+ // Cancel all operations associated with the socket.
+ boost::system::error_code cancel(base_implementation_type&,
+ boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Determine whether the socket is at the out-of-band data mark.
+ bool at_mark(const base_implementation_type&,
+ boost::system::error_code& ec) const
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return false;
+ }
+
+ // Determine the number of bytes available for reading.
+ std::size_t available(const base_implementation_type&,
+ boost::system::error_code& ec) const
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Perform an IO control command on the socket.
+ template <typename IO_Control_Command>
+ boost::system::error_code io_control(base_implementation_type&,
+ IO_Control_Command&, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the socket.
+ bool non_blocking(const base_implementation_type&) const
+ {
+ return false;
+ }
+
+ // Sets the non-blocking mode of the socket.
+ boost::system::error_code non_blocking(base_implementation_type&,
+ bool, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Gets the non-blocking mode of the native socket implementation.
+ bool native_non_blocking(const base_implementation_type&) const
+ {
+ return false;
+ }
+
+ // Sets the non-blocking mode of the native socket implementation.
+ boost::system::error_code native_non_blocking(base_implementation_type&,
+ bool, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Disable sends or receives on the socket.
+ boost::system::error_code shutdown(base_implementation_type&,
+ socket_base::shutdown_type, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+
+ // Send the given data to the peer.
+ template <typename ConstBufferSequence>
+ std::size_t send(base_implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return do_send(impl,
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::first(buffers), flags, ec);
+ }
+
+ // Wait until data can be sent without blocking.
+ std::size_t send(base_implementation_type&, const null_buffers&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Start an asynchronous send. The data being sent must be valid for the
+ // lifetime of the asynchronous operation.
+ template <typename ConstBufferSequence, typename Handler>
+ void async_send(base_implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef winrt_socket_send_op<ConstBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_send"));
+
+ start_send_op(impl,
+ buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::first(buffers),
+ flags, p.p, is_continuation);
+ p.v = p.p = 0;
+ }
+
+ // Start an asynchronous wait until data can be sent without blocking.
+ template <typename Handler>
+ void async_send(base_implementation_type&, const null_buffers&,
+ socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.get_io_service().post(
+ detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+ // Receive some data from the peer. Returns the number of bytes received.
+ template <typename MutableBufferSequence>
+ std::size_t receive(base_implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return do_receive(impl,
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::first(buffers), flags, ec);
+ }
+
+ // Wait until data can be received without blocking.
+ std::size_t receive(base_implementation_type&, const null_buffers&,
+ socket_base::message_flags, boost::system::error_code& ec)
+ {
+ ec = boost::asio::error::operation_not_supported;
+ return 0;
+ }
+
+ // Start an asynchronous receive. The buffer for the data being received
+ // must be valid for the lifetime of the asynchronous operation.
+ template <typename MutableBufferSequence, typename Handler>
+ void async_receive(base_implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, Handler& handler)
+ {
+ bool is_continuation =
+ boost_asio_handler_cont_helpers::is_continuation(handler);
+
+ // Allocate and construct an operation to wrap the handler.
+ typedef winrt_socket_recv_op<MutableBufferSequence, Handler> op;
+ typename op::ptr p = { boost::asio::detail::addressof(handler),
+ boost_asio_handler_alloc_helpers::allocate(
+ sizeof(op), handler), 0 };
+ p.p = new (p.v) op(buffers, handler);
+
+ BOOST_ASIO_HANDLER_CREATION((p.p, "socket", &impl, "async_receive"));
+
+ start_receive_op(impl,
+ buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::first(buffers),
+ flags, p.p, is_continuation);
+ p.v = p.p = 0;
+ }
+
+ // Wait until data can be received without blocking.
+ template <typename Handler>
+ void async_receive(base_implementation_type&, const null_buffers&,
+ socket_base::message_flags, Handler& handler)
+ {
+ boost::system::error_code ec = boost::asio::error::operation_not_supported;
+ const std::size_t bytes_transferred = 0;
+ io_service_.get_io_service().post(
+ detail::bind_handler(handler, ec, bytes_transferred));
+ }
+
+protected:
+ // Helper function to obtain endpoints associated with the connection.
+ BOOST_ASIO_DECL std::size_t do_get_endpoint(
+ const base_implementation_type& impl, bool local,
+ void* addr, std::size_t addr_len, boost::system::error_code& ec) const;
+
+ // Helper function to set a socket option.
+ BOOST_ASIO_DECL boost::system::error_code do_set_option(
+ base_implementation_type& impl,
+ int level, int optname, const void* optval,
+ std::size_t optlen, boost::system::error_code& ec);
+
+ // Helper function to get a socket option.
+ BOOST_ASIO_DECL void do_get_option(
+ const base_implementation_type& impl,
+ int level, int optname, void* optval,
+ std::size_t* optlen, boost::system::error_code& ec) const;
+
+ // Helper function to perform a synchronous connect.
+ BOOST_ASIO_DECL boost::system::error_code do_connect(
+ base_implementation_type& impl,
+ const void* addr, boost::system::error_code& ec);
+
+ // Helper function to start an asynchronous connect.
+ BOOST_ASIO_DECL void start_connect_op(
+ base_implementation_type& impl, const void* addr,
+ winrt_async_op<void>* op, bool is_continuation);
+
+ // Helper function to perform a synchronous send.
+ BOOST_ASIO_DECL std::size_t do_send(
+ base_implementation_type& impl, const boost::asio::const_buffer& data,
+ socket_base::message_flags flags, boost::system::error_code& ec);
+
+ // Helper function to start an asynchronous send.
+ BOOST_ASIO_DECL void start_send_op(base_implementation_type& impl,
+ const boost::asio::const_buffer& data, socket_base::message_flags flags,
+ winrt_async_op<unsigned int>* op, bool is_continuation);
+
+ // Helper function to perform a synchronous receive.
+ BOOST_ASIO_DECL std::size_t do_receive(
+ base_implementation_type& impl, const boost::asio::mutable_buffer& data,
+ socket_base::message_flags flags, boost::system::error_code& ec);
+
+ // Helper function to start an asynchronous receive.
+ BOOST_ASIO_DECL void start_receive_op(base_implementation_type& impl,
+ const boost::asio::mutable_buffer& data, socket_base::message_flags flags,
+ winrt_async_op<Windows::Storage::Streams::IBuffer^>* op,
+ bool is_continuation);
+
+ // The io_service implementation used for delivering completions.
+ io_service_impl& io_service_;
+
+ // The manager that keeps track of outstanding operations.
+ winrt_async_manager& async_manager_;
+
+ // Mutex to protect access to the linked list of implementations.
+ boost::asio::detail::mutex mutex_;
+
+ // The head of a linked list of all implementations.
+ base_implementation_type* impl_list_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/winrt_ssocket_service_base.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_SSOCKET_SERVICE_BASE_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_timer_scheduler.hpp b/ext/patches/boost/asio/detail/winrt_timer_scheduler.hpp
new file mode 100644
index 0000000..7925794
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_timer_scheduler.hpp
@@ -0,0 +1,133 @@
+//
+// detail/winrt_timer_scheduler.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_TIMER_SCHEDULER_HPP
+#define BOOST_ASIO_DETAIL_WINRT_TIMER_SCHEDULER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <cstddef>
+#include <boost/asio/detail/event.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/op_queue.hpp>
+#include <boost/asio/detail/thread.hpp>
+#include <boost/asio/detail/timer_queue_base.hpp>
+#include <boost/asio/detail/timer_queue_set.hpp>
+#include <boost/asio/detail/wait_op.hpp>
+#include <boost/asio/io_service.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/thread.hpp>
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class winrt_timer_scheduler
+ : public boost::asio::detail::service_base<winrt_timer_scheduler>
+{
+public:
+ // Constructor.
+ BOOST_ASIO_DECL winrt_timer_scheduler(boost::asio::io_service& io_service);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~winrt_timer_scheduler();
+
+ // Destroy all user-defined handler objects owned by the service.
+ BOOST_ASIO_DECL void shutdown_service();
+
+ // Recreate internal descriptors following a fork.
+ BOOST_ASIO_DECL void fork_service(
+ boost::asio::io_service::fork_event fork_ev);
+
+ // Initialise the task. No effect as this class uses its own thread.
+ BOOST_ASIO_DECL void init_task();
+
+ // Add a new timer queue to the reactor.
+ template <typename Time_Traits>
+ void add_timer_queue(timer_queue<Time_Traits>& queue);
+
+ // Remove a timer queue from the reactor.
+ template <typename Time_Traits>
+ void remove_timer_queue(timer_queue<Time_Traits>& queue);
+
+ // Schedule a new operation in the given timer queue to expire at the
+ // specified absolute time.
+ template <typename Time_Traits>
+ void schedule_timer(timer_queue<Time_Traits>& queue,
+ const typename Time_Traits::time_type& time,
+ typename timer_queue<Time_Traits>::per_timer_data& timer, wait_op* op);
+
+ // Cancel the timer operations associated with the given token. Returns the
+ // number of operations that have been posted or dispatched.
+ template <typename Time_Traits>
+ std::size_t cancel_timer(timer_queue<Time_Traits>& queue,
+ typename timer_queue<Time_Traits>::per_timer_data& timer,
+ std::size_t max_cancelled = (std::numeric_limits<std::size_t>::max)());
+
+private:
+ // Run the select loop in the thread.
+ BOOST_ASIO_DECL void run_thread();
+
+ // Entry point for the select loop thread.
+ BOOST_ASIO_DECL static void call_run_thread(winrt_timer_scheduler* reactor);
+
+ // Helper function to add a new timer queue.
+ BOOST_ASIO_DECL void do_add_timer_queue(timer_queue_base& queue);
+
+ // Helper function to remove a timer queue.
+ BOOST_ASIO_DECL void do_remove_timer_queue(timer_queue_base& queue);
+
+ // The io_service implementation used to post completions.
+ io_service_impl& io_service_;
+
+ // Mutex used to protect internal variables.
+ boost::asio::detail::mutex mutex_;
+
+ // Event used to wake up background thread.
+ boost::asio::detail::event event_;
+
+ // The timer queues.
+ timer_queue_set timer_queues_;
+
+ // The background thread that is waiting for timers to expire.
+ boost::asio::detail::thread* thread_;
+
+ // Does the background thread need to stop.
+ bool stop_thread_;
+
+ // Whether the service has been shut down.
+ bool shutdown_;
+};
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/impl/winrt_timer_scheduler.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/winrt_timer_scheduler.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_TIMER_SCHEDULER_HPP
diff --git a/ext/patches/boost/asio/detail/winrt_utils.hpp b/ext/patches/boost/asio/detail/winrt_utils.hpp
new file mode 100644
index 0000000..ff2a068
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winrt_utils.hpp
@@ -0,0 +1,108 @@
+//
+// detail/winrt_utils.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINRT_UTILS_HPP
+#define BOOST_ASIO_DETAIL_WINRT_UTILS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <codecvt>
+#include <cstdlib>
+#include <future>
+#include <locale>
+#include <memory>
+#include <robuffer.h>
+#include <windows.storage.streams.h>
+#include <wrl/implements.h>
+#include <boost/asio/buffer.hpp>
+#include <boost/system/error_code.hpp>
+#include <boost/asio/detail/addressof.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+namespace winrt_utils {
+
+inline Platform::String^ string(const char* from)
+{
+ std::wstring tmp(from, from + std::strlen(from));
+ return ref new Platform::String(tmp.c_str());
+}
+
+inline Platform::String^ string(const std::string& from)
+{
+ std::wstring tmp(from.begin(), from.end());
+ return ref new Platform::String(tmp.c_str());
+}
+
+inline std::string string(Platform::String^ from)
+{
+ std::wstring_convert<std::codecvt_utf8<wchar_t>> converter;
+ return converter.to_bytes(from->Data());
+}
+
+inline Platform::String^ string(unsigned short from)
+{
+ return string(std::to_string(from));
+}
+
+template <typename T>
+inline Platform::String^ string(const T& from)
+{
+ return string(from.to_string());
+}
+
+inline int integer(Platform::String^ from)
+{
+ return _wtoi(from->Data());
+}
+
+template <typename T>
+inline Windows::Networking::HostName^ host_name(const T& from)
+{
+ return ref new Windows::Networking::HostName((string)(from));
+}
+
+template <typename ConstBufferSequence>
+inline Windows::Storage::Streams::IBuffer^ buffer_dup(
+ const ConstBufferSequence& buffers)
+{
+ using Microsoft::WRL::ComPtr;
+ std::size_t size = boost::asio::buffer_size(buffers);
+ auto b = ref new Windows::Storage::Streams::Buffer(size);
+ ComPtr<IInspectable> insp = reinterpret_cast<IInspectable*>(b);
+ ComPtr<Windows::Storage::Streams::IBufferByteAccess> bacc;
+ insp.As(&bacc);
+ byte* bytes = nullptr;
+ bacc->Buffer(&bytes);
+ boost::asio::buffer_copy(boost::asio::buffer(bytes, size), buffers);
+ b->Length = size;
+ return b;
+}
+
+} // namespace winrt_utils
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#endif // BOOST_ASIO_DETAIL_WINRT_UTILS_HPP
diff --git a/ext/patches/boost/asio/detail/winsock_init.hpp b/ext/patches/boost/asio/detail/winsock_init.hpp
new file mode 100644
index 0000000..5b18fee
--- /dev/null
+++ b/ext/patches/boost/asio/detail/winsock_init.hpp
@@ -0,0 +1,130 @@
+//
+// detail/winsock_init.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WINSOCK_INIT_HPP
+#define BOOST_ASIO_DETAIL_WINSOCK_INIT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+class winsock_init_base
+{
+protected:
+ // Structure to track result of initialisation and number of uses. POD is used
+ // to ensure that the values are zero-initialised prior to any code being run.
+ struct data
+ {
+ long init_count_;
+ long result_;
+ };
+
+ BOOST_ASIO_DECL static void startup(data& d,
+ unsigned char major, unsigned char minor);
+
+ BOOST_ASIO_DECL static void manual_startup(data& d);
+
+ BOOST_ASIO_DECL static void cleanup(data& d);
+
+ BOOST_ASIO_DECL static void manual_cleanup(data& d);
+
+ BOOST_ASIO_DECL static void throw_on_error(data& d);
+};
+
+template <int Major = 2, int Minor = 0>
+class winsock_init : private winsock_init_base
+{
+public:
+ winsock_init(bool allow_throw = true)
+ {
+ startup(data_, Major, Minor);
+ if (allow_throw)
+ throw_on_error(data_);
+ }
+
+ winsock_init(const winsock_init&)
+ {
+ startup(data_, Major, Minor);
+ throw_on_error(data_);
+ }
+
+ ~winsock_init()
+ {
+ cleanup(data_);
+ }
+
+ // This class may be used to indicate that user code will manage Winsock
+ // initialisation and cleanup. This may be required in the case of a DLL, for
+ // example, where it is not safe to initialise Winsock from global object
+ // constructors.
+ //
+ // To prevent asio from initialising Winsock, the object must be constructed
+ // before any Asio's own global objects. With MSVC, this may be accomplished
+ // by adding the following code to the DLL:
+ //
+ // #pragma warning(push)
+ // #pragma warning(disable:4073)
+ // #pragma init_seg(lib)
+ // boost::asio::detail::winsock_init<>::manual manual_winsock_init;
+ // #pragma warning(pop)
+ class manual
+ {
+ public:
+ manual()
+ {
+ manual_startup(data_);
+ }
+
+ manual(const manual&)
+ {
+ manual_startup(data_);
+ }
+
+ ~manual()
+ {
+ manual_cleanup(data_);
+ }
+ };
+
+private:
+ friend class manual;
+ static data data_;
+};
+
+template <int Major, int Minor>
+winsock_init_base::data winsock_init<Major, Minor>::data_;
+
+// Static variable to ensure that winsock is initialised before main, and
+// therefore before any other threads can get started.
+static const winsock_init<>& winsock_init_instance = winsock_init<>(false);
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/detail/impl/winsock_init.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+
+#endif // BOOST_ASIO_DETAIL_WINSOCK_INIT_HPP
diff --git a/ext/patches/boost/asio/detail/wrapped_handler.hpp b/ext/patches/boost/asio/detail/wrapped_handler.hpp
new file mode 100644
index 0000000..eb8eb51
--- /dev/null
+++ b/ext/patches/boost/asio/detail/wrapped_handler.hpp
@@ -0,0 +1,293 @@
+//
+// detail/wrapped_handler.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_DETAIL_WRAPPED_HANDLER_HPP
+#define BOOST_ASIO_DETAIL_WRAPPED_HANDLER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+struct is_continuation_delegated
+{
+ template <typename Dispatcher, typename Handler>
+ bool operator()(Dispatcher&, Handler& handler) const
+ {
+ return boost_asio_handler_cont_helpers::is_continuation(handler);
+ }
+};
+
+struct is_continuation_if_running
+{
+ template <typename Dispatcher, typename Handler>
+ bool operator()(Dispatcher& dispatcher, Handler&) const
+ {
+ return dispatcher.running_in_this_thread();
+ }
+};
+
+template <typename Dispatcher, typename Handler,
+ typename IsContinuation = is_continuation_delegated>
+class wrapped_handler
+{
+public:
+ typedef void result_type;
+
+ wrapped_handler(Dispatcher dispatcher, Handler& handler)
+ : dispatcher_(dispatcher),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ wrapped_handler(const wrapped_handler& other)
+ : dispatcher_(other.dispatcher_),
+ handler_(other.handler_)
+ {
+ }
+
+ wrapped_handler(wrapped_handler&& other)
+ : dispatcher_(other.dispatcher_),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()()
+ {
+ dispatcher_.dispatch(BOOST_ASIO_MOVE_CAST(Handler)(handler_));
+ }
+
+ void operator()() const
+ {
+ dispatcher_.dispatch(handler_);
+ }
+
+ template <typename Arg1>
+ void operator()(const Arg1& arg1)
+ {
+ dispatcher_.dispatch(detail::bind_handler(handler_, arg1));
+ }
+
+ template <typename Arg1>
+ void operator()(const Arg1& arg1) const
+ {
+ dispatcher_.dispatch(detail::bind_handler(handler_, arg1));
+ }
+
+ template <typename Arg1, typename Arg2>
+ void operator()(const Arg1& arg1, const Arg2& arg2)
+ {
+ dispatcher_.dispatch(detail::bind_handler(handler_, arg1, arg2));
+ }
+
+ template <typename Arg1, typename Arg2>
+ void operator()(const Arg1& arg1, const Arg2& arg2) const
+ {
+ dispatcher_.dispatch(detail::bind_handler(handler_, arg1, arg2));
+ }
+
+ template <typename Arg1, typename Arg2, typename Arg3>
+ void operator()(const Arg1& arg1, const Arg2& arg2, const Arg3& arg3)
+ {
+ dispatcher_.dispatch(detail::bind_handler(handler_, arg1, arg2, arg3));
+ }
+
+ template <typename Arg1, typename Arg2, typename Arg3>
+ void operator()(const Arg1& arg1, const Arg2& arg2, const Arg3& arg3) const
+ {
+ dispatcher_.dispatch(detail::bind_handler(handler_, arg1, arg2, arg3));
+ }
+
+ template <typename Arg1, typename Arg2, typename Arg3, typename Arg4>
+ void operator()(const Arg1& arg1, const Arg2& arg2, const Arg3& arg3,
+ const Arg4& arg4)
+ {
+ dispatcher_.dispatch(
+ detail::bind_handler(handler_, arg1, arg2, arg3, arg4));
+ }
+
+ template <typename Arg1, typename Arg2, typename Arg3, typename Arg4>
+ void operator()(const Arg1& arg1, const Arg2& arg2, const Arg3& arg3,
+ const Arg4& arg4) const
+ {
+ dispatcher_.dispatch(
+ detail::bind_handler(handler_, arg1, arg2, arg3, arg4));
+ }
+
+ template <typename Arg1, typename Arg2, typename Arg3, typename Arg4,
+ typename Arg5>
+ void operator()(const Arg1& arg1, const Arg2& arg2, const Arg3& arg3,
+ const Arg4& arg4, const Arg5& arg5)
+ {
+ dispatcher_.dispatch(
+ detail::bind_handler(handler_, arg1, arg2, arg3, arg4, arg5));
+ }
+
+ template <typename Arg1, typename Arg2, typename Arg3, typename Arg4,
+ typename Arg5>
+ void operator()(const Arg1& arg1, const Arg2& arg2, const Arg3& arg3,
+ const Arg4& arg4, const Arg5& arg5) const
+ {
+ dispatcher_.dispatch(
+ detail::bind_handler(handler_, arg1, arg2, arg3, arg4, arg5));
+ }
+
+//private:
+ Dispatcher dispatcher_;
+ Handler handler_;
+};
+
+template <typename Handler, typename Context>
+class rewrapped_handler
+{
+public:
+ explicit rewrapped_handler(Handler& handler, const Context& context)
+ : context_(context),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ explicit rewrapped_handler(const Handler& handler, const Context& context)
+ : context_(context),
+ handler_(handler)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ rewrapped_handler(const rewrapped_handler& other)
+ : context_(other.context_),
+ handler_(other.handler_)
+ {
+ }
+
+ rewrapped_handler(rewrapped_handler&& other)
+ : context_(BOOST_ASIO_MOVE_CAST(Context)(other.context_)),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()()
+ {
+ handler_();
+ }
+
+ void operator()() const
+ {
+ handler_();
+ }
+
+//private:
+ Context context_;
+ Handler handler_;
+};
+
+template <typename Dispatcher, typename Handler, typename IsContinuation>
+inline void* asio_handler_allocate(std::size_t size,
+ wrapped_handler<Dispatcher, Handler, IsContinuation>* this_handler)
+{
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+}
+
+template <typename Dispatcher, typename Handler, typename IsContinuation>
+inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ wrapped_handler<Dispatcher, Handler, IsContinuation>* this_handler)
+{
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+}
+
+template <typename Dispatcher, typename Handler, typename IsContinuation>
+inline bool asio_handler_is_continuation(
+ wrapped_handler<Dispatcher, Handler, IsContinuation>* this_handler)
+{
+ return IsContinuation()(this_handler->dispatcher_, this_handler->handler_);
+}
+
+template <typename Function, typename Dispatcher,
+ typename Handler, typename IsContinuation>
+inline void asio_handler_invoke(Function& function,
+ wrapped_handler<Dispatcher, Handler, IsContinuation>* this_handler)
+{
+ this_handler->dispatcher_.dispatch(
+ rewrapped_handler<Function, Handler>(
+ function, this_handler->handler_));
+}
+
+template <typename Function, typename Dispatcher,
+ typename Handler, typename IsContinuation>
+inline void asio_handler_invoke(const Function& function,
+ wrapped_handler<Dispatcher, Handler, IsContinuation>* this_handler)
+{
+ this_handler->dispatcher_.dispatch(
+ rewrapped_handler<Function, Handler>(
+ function, this_handler->handler_));
+}
+
+template <typename Handler, typename Context>
+inline void* asio_handler_allocate(std::size_t size,
+ rewrapped_handler<Handler, Context>* this_handler)
+{
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->context_);
+}
+
+template <typename Handler, typename Context>
+inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ rewrapped_handler<Handler, Context>* this_handler)
+{
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->context_);
+}
+
+template <typename Dispatcher, typename Context>
+inline bool asio_handler_is_continuation(
+ rewrapped_handler<Dispatcher, Context>* this_handler)
+{
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->context_);
+}
+
+template <typename Function, typename Handler, typename Context>
+inline void asio_handler_invoke(Function& function,
+ rewrapped_handler<Handler, Context>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->context_);
+}
+
+template <typename Function, typename Handler, typename Context>
+inline void asio_handler_invoke(const Function& function,
+ rewrapped_handler<Handler, Context>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->context_);
+}
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_DETAIL_WRAPPED_HANDLER_HPP
diff --git a/ext/patches/boost/asio/error.hpp b/ext/patches/boost/asio/error.hpp
new file mode 100644
index 0000000..30bb197
--- /dev/null
+++ b/ext/patches/boost/asio/error.hpp
@@ -0,0 +1,336 @@
+//
+// error.hpp
+// ~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_ERROR_HPP
+#define BOOST_ASIO_ERROR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/cerrno.hpp>
+#include <boost/system/error_code.hpp>
+#include <boost/system/system_error.hpp>
+#if defined(BOOST_ASIO_WINDOWS) \
+ || defined(__CYGWIN__) \
+ || defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <winerror.h>
+#else
+# include <cerrno>
+# include <netdb.h>
+#endif
+
+#if defined(GENERATING_DOCUMENTATION)
+/// INTERNAL ONLY.
+# define BOOST_ASIO_NATIVE_ERROR(e) implementation_defined
+/// INTERNAL ONLY.
+# define BOOST_ASIO_SOCKET_ERROR(e) implementation_defined
+/// INTERNAL ONLY.
+# define BOOST_ASIO_NETDB_ERROR(e) implementation_defined
+/// INTERNAL ONLY.
+# define BOOST_ASIO_GETADDRINFO_ERROR(e) implementation_defined
+/// INTERNAL ONLY.
+# define BOOST_ASIO_WIN_OR_POSIX(e_win, e_posix) implementation_defined
+#elif defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# define BOOST_ASIO_NATIVE_ERROR(e) __HRESULT_FROM_WIN32(e)
+# define BOOST_ASIO_SOCKET_ERROR(e) __HRESULT_FROM_WIN32(WSA ## e)
+# define BOOST_ASIO_NETDB_ERROR(e) __HRESULT_FROM_WIN32(WSA ## e)
+# define BOOST_ASIO_GETADDRINFO_ERROR(e) __HRESULT_FROM_WIN32(WSA ## e)
+# define BOOST_ASIO_WIN_OR_POSIX(e_win, e_posix) e_win
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# define BOOST_ASIO_NATIVE_ERROR(e) e
+# define BOOST_ASIO_SOCKET_ERROR(e) WSA ## e
+# define BOOST_ASIO_NETDB_ERROR(e) WSA ## e
+# define BOOST_ASIO_GETADDRINFO_ERROR(e) WSA ## e
+# define BOOST_ASIO_WIN_OR_POSIX(e_win, e_posix) e_win
+#else
+# define BOOST_ASIO_NATIVE_ERROR(e) e
+# define BOOST_ASIO_SOCKET_ERROR(e) e
+# define BOOST_ASIO_NETDB_ERROR(e) e
+# define BOOST_ASIO_GETADDRINFO_ERROR(e) e
+# define BOOST_ASIO_WIN_OR_POSIX(e_win, e_posix) e_posix
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace error {
+
+enum basic_errors
+{
+ /// Permission denied.
+ access_denied = BOOST_ASIO_SOCKET_ERROR(EACCES),
+
+ /// Address family not supported by protocol.
+ address_family_not_supported = BOOST_ASIO_SOCKET_ERROR(EAFNOSUPPORT),
+
+ /// Address already in use.
+ address_in_use = BOOST_ASIO_SOCKET_ERROR(EADDRINUSE),
+
+ /// Transport endpoint is already connected.
+ already_connected = BOOST_ASIO_SOCKET_ERROR(EISCONN),
+
+ /// Operation already in progress.
+ already_started = BOOST_ASIO_SOCKET_ERROR(EALREADY),
+
+ /// Broken pipe.
+ broken_pipe = BOOST_ASIO_WIN_OR_POSIX(
+ BOOST_ASIO_NATIVE_ERROR(ERROR_BROKEN_PIPE),
+ BOOST_ASIO_NATIVE_ERROR(EPIPE)),
+
+ /// A connection has been aborted.
+ connection_aborted = BOOST_ASIO_SOCKET_ERROR(ECONNABORTED),
+
+ /// Connection refused.
+ connection_refused = BOOST_ASIO_SOCKET_ERROR(ECONNREFUSED),
+
+ /// Connection reset by peer.
+ connection_reset = BOOST_ASIO_SOCKET_ERROR(ECONNRESET),
+
+ /// Bad file descriptor.
+ bad_descriptor = BOOST_ASIO_SOCKET_ERROR(EBADF),
+
+ /// Bad address.
+ fault = BOOST_ASIO_SOCKET_ERROR(EFAULT),
+
+ /// No route to host.
+ host_unreachable = BOOST_ASIO_SOCKET_ERROR(EHOSTUNREACH),
+
+ /// Operation now in progress.
+ in_progress = BOOST_ASIO_SOCKET_ERROR(EINPROGRESS),
+
+ /// Interrupted system call.
+ interrupted = BOOST_ASIO_SOCKET_ERROR(EINTR),
+
+ /// Invalid argument.
+ invalid_argument = BOOST_ASIO_SOCKET_ERROR(EINVAL),
+
+ /// Message too long.
+ message_size = BOOST_ASIO_SOCKET_ERROR(EMSGSIZE),
+
+ /// The name was too long.
+ name_too_long = BOOST_ASIO_SOCKET_ERROR(ENAMETOOLONG),
+
+ /// Network is down.
+ network_down = BOOST_ASIO_SOCKET_ERROR(ENETDOWN),
+
+ /// Network dropped connection on reset.
+ network_reset = BOOST_ASIO_SOCKET_ERROR(ENETRESET),
+
+ /// Network is unreachable.
+ network_unreachable = BOOST_ASIO_SOCKET_ERROR(ENETUNREACH),
+
+ /// Too many open files.
+ no_descriptors = BOOST_ASIO_SOCKET_ERROR(EMFILE),
+
+ /// No buffer space available.
+ no_buffer_space = BOOST_ASIO_SOCKET_ERROR(ENOBUFS),
+
+ /// Cannot allocate memory.
+ no_memory = BOOST_ASIO_WIN_OR_POSIX(
+ BOOST_ASIO_NATIVE_ERROR(ERROR_OUTOFMEMORY),
+ BOOST_ASIO_NATIVE_ERROR(ENOMEM)),
+
+ /// Operation not permitted.
+ no_permission = BOOST_ASIO_WIN_OR_POSIX(
+ BOOST_ASIO_NATIVE_ERROR(ERROR_ACCESS_DENIED),
+ BOOST_ASIO_NATIVE_ERROR(EPERM)),
+
+ /// Protocol not available.
+ no_protocol_option = BOOST_ASIO_SOCKET_ERROR(ENOPROTOOPT),
+
+ /// Transport endpoint is not connected.
+ not_connected = BOOST_ASIO_SOCKET_ERROR(ENOTCONN),
+
+ /// Socket operation on non-socket.
+ not_socket = BOOST_ASIO_SOCKET_ERROR(ENOTSOCK),
+
+ /// Operation cancelled.
+ operation_aborted = BOOST_ASIO_WIN_OR_POSIX(
+ BOOST_ASIO_NATIVE_ERROR(ERROR_OPERATION_ABORTED),
+ BOOST_ASIO_NATIVE_ERROR(ECANCELED)),
+
+ /// Operation not supported.
+ operation_not_supported = BOOST_ASIO_SOCKET_ERROR(EOPNOTSUPP),
+
+ /// Cannot send after transport endpoint shutdown.
+ shut_down = BOOST_ASIO_SOCKET_ERROR(ESHUTDOWN),
+
+ /// Connection timed out.
+ timed_out = BOOST_ASIO_SOCKET_ERROR(ETIMEDOUT),
+
+ /// Resource temporarily unavailable.
+ try_again = BOOST_ASIO_WIN_OR_POSIX(
+ BOOST_ASIO_NATIVE_ERROR(ERROR_RETRY),
+ BOOST_ASIO_NATIVE_ERROR(EAGAIN)),
+
+ /// The socket is marked non-blocking and the requested operation would block.
+ would_block = BOOST_ASIO_SOCKET_ERROR(EWOULDBLOCK)
+};
+
+enum netdb_errors
+{
+ /// Host not found (authoritative).
+ host_not_found = BOOST_ASIO_NETDB_ERROR(HOST_NOT_FOUND),
+
+ /// Host not found (non-authoritative).
+ host_not_found_try_again = BOOST_ASIO_NETDB_ERROR(TRY_AGAIN),
+
+ /// The query is valid but does not have associated address data.
+ no_data = BOOST_ASIO_NETDB_ERROR(NO_DATA),
+
+ /// A non-recoverable error occurred.
+ no_recovery = BOOST_ASIO_NETDB_ERROR(NO_RECOVERY)
+};
+
+enum addrinfo_errors
+{
+ /// The service is not supported for the given socket type.
+ service_not_found = BOOST_ASIO_WIN_OR_POSIX(
+ BOOST_ASIO_NATIVE_ERROR(WSATYPE_NOT_FOUND),
+ BOOST_ASIO_GETADDRINFO_ERROR(EAI_SERVICE)),
+
+ /// The socket type is not supported.
+ socket_type_not_supported = BOOST_ASIO_WIN_OR_POSIX(
+ BOOST_ASIO_NATIVE_ERROR(WSAESOCKTNOSUPPORT),
+ BOOST_ASIO_GETADDRINFO_ERROR(EAI_SOCKTYPE))
+};
+
+enum misc_errors
+{
+ /// Already open.
+ already_open = 1,
+
+ /// End of file or stream.
+ eof,
+
+ /// Element not found.
+ not_found,
+
+ /// The descriptor cannot fit into the select system call's fd_set.
+ fd_set_failure
+};
+
+inline const boost::system::error_category& get_system_category()
+{
+ return boost::system::system_category();
+}
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+extern BOOST_ASIO_DECL
+const boost::system::error_category& get_netdb_category();
+
+extern BOOST_ASIO_DECL
+const boost::system::error_category& get_addrinfo_category();
+
+#else // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+inline const boost::system::error_category& get_netdb_category()
+{
+ return get_system_category();
+}
+
+inline const boost::system::error_category& get_addrinfo_category()
+{
+ return get_system_category();
+}
+
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+extern BOOST_ASIO_DECL
+const boost::system::error_category& get_misc_category();
+
+static const boost::system::error_category& system_category
+ = boost::asio::error::get_system_category();
+static const boost::system::error_category& netdb_category
+ = boost::asio::error::get_netdb_category();
+static const boost::system::error_category& addrinfo_category
+ = boost::asio::error::get_addrinfo_category();
+static const boost::system::error_category& misc_category
+ = boost::asio::error::get_misc_category();
+
+} // namespace error
+} // namespace asio
+} // namespace boost
+
+namespace boost {
+namespace system {
+
+template<> struct is_error_code_enum<boost::asio::error::basic_errors>
+{
+ static const bool value = true;
+};
+
+template<> struct is_error_code_enum<boost::asio::error::netdb_errors>
+{
+ static const bool value = true;
+};
+
+template<> struct is_error_code_enum<boost::asio::error::addrinfo_errors>
+{
+ static const bool value = true;
+};
+
+template<> struct is_error_code_enum<boost::asio::error::misc_errors>
+{
+ static const bool value = true;
+};
+
+} // namespace system
+} // namespace boost
+
+namespace boost {
+namespace asio {
+namespace error {
+
+inline boost::system::error_code make_error_code(basic_errors e)
+{
+ return boost::system::error_code(
+ static_cast<int>(e), get_system_category());
+}
+
+inline boost::system::error_code make_error_code(netdb_errors e)
+{
+ return boost::system::error_code(
+ static_cast<int>(e), get_netdb_category());
+}
+
+inline boost::system::error_code make_error_code(addrinfo_errors e)
+{
+ return boost::system::error_code(
+ static_cast<int>(e), get_addrinfo_category());
+}
+
+inline boost::system::error_code make_error_code(misc_errors e)
+{
+ return boost::system::error_code(
+ static_cast<int>(e), get_misc_category());
+}
+
+} // namespace error
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#undef BOOST_ASIO_NATIVE_ERROR
+#undef BOOST_ASIO_SOCKET_ERROR
+#undef BOOST_ASIO_NETDB_ERROR
+#undef BOOST_ASIO_GETADDRINFO_ERROR
+#undef BOOST_ASIO_WIN_OR_POSIX
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/impl/error.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_ERROR_HPP
diff --git a/ext/patches/boost/asio/generic/basic_endpoint.hpp b/ext/patches/boost/asio/generic/basic_endpoint.hpp
new file mode 100644
index 0000000..f946c33
--- /dev/null
+++ b/ext/patches/boost/asio/generic/basic_endpoint.hpp
@@ -0,0 +1,195 @@
+//
+// generic/basic_endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_GENERIC_BASIC_ENDPOINT_HPP
+#define BOOST_ASIO_GENERIC_BASIC_ENDPOINT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/generic/detail/endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace generic {
+
+/// Describes an endpoint for any socket type.
+/**
+ * The boost::asio::generic::basic_endpoint class template describes an endpoint
+ * that may be associated with any socket type.
+ *
+ * @note The socket types sockaddr type must be able to fit into a
+ * @c sockaddr_storage structure.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * Endpoint.
+ */
+template <typename Protocol>
+class basic_endpoint
+{
+public:
+ /// The protocol type associated with the endpoint.
+ typedef Protocol protocol_type;
+
+ /// The type of the endpoint structure. This type is dependent on the
+ /// underlying implementation of the socket layer.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined data_type;
+#else
+ typedef boost::asio::detail::socket_addr_type data_type;
+#endif
+
+ /// Default constructor.
+ basic_endpoint()
+ {
+ }
+
+ /// Construct an endpoint from the specified socket address.
+ basic_endpoint(const void* socket_address,
+ std::size_t socket_address_size, int socket_protocol = 0)
+ : impl_(socket_address, socket_address_size, socket_protocol)
+ {
+ }
+
+ /// Construct an endpoint from the specific endpoint type.
+ template <typename Endpoint>
+ basic_endpoint(const Endpoint& endpoint)
+ : impl_(endpoint.data(), endpoint.size(), endpoint.protocol().protocol())
+ {
+ }
+
+ /// Copy constructor.
+ basic_endpoint(const basic_endpoint& other)
+ : impl_(other.impl_)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move constructor.
+ basic_endpoint(basic_endpoint&& other)
+ : impl_(other.impl_)
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// Assign from another endpoint.
+ basic_endpoint& operator=(const basic_endpoint& other)
+ {
+ impl_ = other.impl_;
+ return *this;
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move-assign from another endpoint.
+ basic_endpoint& operator=(basic_endpoint&& other)
+ {
+ impl_ = other.impl_;
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// The protocol associated with the endpoint.
+ protocol_type protocol() const
+ {
+ return protocol_type(impl_.family(), impl_.protocol());
+ }
+
+ /// Get the underlying endpoint in the native type.
+ data_type* data()
+ {
+ return impl_.data();
+ }
+
+ /// Get the underlying endpoint in the native type.
+ const data_type* data() const
+ {
+ return impl_.data();
+ }
+
+ /// Get the underlying size of the endpoint in the native type.
+ std::size_t size() const
+ {
+ return impl_.size();
+ }
+
+ /// Set the underlying size of the endpoint in the native type.
+ void resize(std::size_t new_size)
+ {
+ impl_.resize(new_size);
+ }
+
+ /// Get the capacity of the endpoint in the native type.
+ std::size_t capacity() const
+ {
+ return impl_.capacity();
+ }
+
+ /// Compare two endpoints for equality.
+ friend bool operator==(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return e1.impl_ == e2.impl_;
+ }
+
+ /// Compare two endpoints for inequality.
+ friend bool operator!=(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return !(e1.impl_ == e2.impl_);
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator<(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return e1.impl_ < e2.impl_;
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator>(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return e2.impl_ < e1.impl_;
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator<=(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return !(e2 < e1);
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator>=(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return !(e1 < e2);
+ }
+
+private:
+ // The underlying generic endpoint.
+ boost::asio::generic::detail::endpoint impl_;
+};
+
+} // namespace generic
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_GENERIC_BASIC_ENDPOINT_HPP
diff --git a/ext/patches/boost/asio/generic/datagram_protocol.hpp b/ext/patches/boost/asio/generic/datagram_protocol.hpp
new file mode 100644
index 0000000..85159f2
--- /dev/null
+++ b/ext/patches/boost/asio/generic/datagram_protocol.hpp
@@ -0,0 +1,125 @@
+//
+// generic/datagram_protocol.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_GENERIC_DATAGRAM_PROTOCOL_HPP
+#define BOOST_ASIO_GENERIC_DATAGRAM_PROTOCOL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <typeinfo>
+#include <boost/asio/basic_datagram_socket.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/generic/basic_endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace generic {
+
+/// Encapsulates the flags needed for a generic datagram-oriented socket.
+/**
+ * The boost::asio::generic::datagram_protocol class contains flags necessary
+ * for datagram-oriented sockets of any address family and protocol.
+ *
+ * @par Examples
+ * Constructing using a native address family and socket protocol:
+ * @code datagram_protocol p(AF_INET, IPPROTO_UDP); @endcode
+ * Constructing from a specific protocol type:
+ * @code datagram_protocol p(boost::asio::ip::udp::v4()); @endcode
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol.
+ */
+class datagram_protocol
+{
+public:
+ /// Construct a protocol object for a specific address family and protocol.
+ datagram_protocol(int address_family, int socket_protocol)
+ : family_(address_family),
+ protocol_(socket_protocol)
+ {
+ }
+
+ /// Construct a generic protocol object from a specific protocol.
+ /**
+ * @throws @c bad_cast Thrown if the source protocol is not datagram-oriented.
+ */
+ template <typename Protocol>
+ datagram_protocol(const Protocol& source_protocol)
+ : family_(source_protocol.family()),
+ protocol_(source_protocol.protocol())
+ {
+ if (source_protocol.type() != type())
+ {
+ std::bad_cast ex;
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return BOOST_ASIO_OS_DEF(SOCK_DGRAM);
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return protocol_;
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return family_;
+ }
+
+ /// Compare two protocols for equality.
+ friend bool operator==(const datagram_protocol& p1,
+ const datagram_protocol& p2)
+ {
+ return p1.family_ == p2.family_ && p1.protocol_ == p2.protocol_;
+ }
+
+ /// Compare two protocols for inequality.
+ friend bool operator!=(const datagram_protocol& p1,
+ const datagram_protocol& p2)
+ {
+ return !(p1 == p2);
+ }
+
+ /// The type of an endpoint.
+ typedef basic_endpoint<datagram_protocol> endpoint;
+
+ /// The generic socket type.
+ typedef basic_datagram_socket<datagram_protocol> socket;
+
+private:
+ int family_;
+ int protocol_;
+};
+
+} // namespace generic
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_GENERIC_DATAGRAM_PROTOCOL_HPP
diff --git a/ext/patches/boost/asio/generic/detail/endpoint.hpp b/ext/patches/boost/asio/generic/detail/endpoint.hpp
new file mode 100644
index 0000000..d156ed4
--- /dev/null
+++ b/ext/patches/boost/asio/generic/detail/endpoint.hpp
@@ -0,0 +1,135 @@
+//
+// generic/detail/endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_GENERIC_DETAIL_ENDPOINT_HPP
+#define BOOST_ASIO_GENERIC_DETAIL_ENDPOINT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <cstddef>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace generic {
+namespace detail {
+
+// Helper class for implementing a generic socket endpoint.
+class endpoint
+{
+public:
+ // Default constructor.
+ BOOST_ASIO_DECL endpoint();
+
+ // Construct an endpoint from the specified raw bytes.
+ BOOST_ASIO_DECL endpoint(const void* sock_addr,
+ std::size_t sock_addr_size, int sock_protocol);
+
+ // Copy constructor.
+ endpoint(const endpoint& other)
+ : data_(other.data_),
+ size_(other.size_),
+ protocol_(other.protocol_)
+ {
+ }
+
+ // Assign from another endpoint.
+ endpoint& operator=(const endpoint& other)
+ {
+ data_ = other.data_;
+ size_ = other.size_;
+ protocol_ = other.protocol_;
+ return *this;
+ }
+
+ // Get the address family associated with the endpoint.
+ int family() const
+ {
+ return data_.base.sa_family;
+ }
+
+ // Get the socket protocol associated with the endpoint.
+ int protocol() const
+ {
+ return protocol_;
+ }
+
+ // Get the underlying endpoint in the native type.
+ boost::asio::detail::socket_addr_type* data()
+ {
+ return &data_.base;
+ }
+
+ // Get the underlying endpoint in the native type.
+ const boost::asio::detail::socket_addr_type* data() const
+ {
+ return &data_.base;
+ }
+
+ // Get the underlying size of the endpoint in the native type.
+ std::size_t size() const
+ {
+ return size_;
+ }
+
+ // Set the underlying size of the endpoint in the native type.
+ BOOST_ASIO_DECL void resize(std::size_t size);
+
+ // Get the capacity of the endpoint in the native type.
+ std::size_t capacity() const
+ {
+ return sizeof(boost::asio::detail::sockaddr_storage_type);
+ }
+
+ // Compare two endpoints for equality.
+ BOOST_ASIO_DECL friend bool operator==(
+ const endpoint& e1, const endpoint& e2);
+
+ // Compare endpoints for ordering.
+ BOOST_ASIO_DECL friend bool operator<(
+ const endpoint& e1, const endpoint& e2);
+
+private:
+ // The underlying socket address.
+ union data_union
+ {
+ boost::asio::detail::socket_addr_type base;
+ boost::asio::detail::sockaddr_storage_type generic;
+ } data_;
+
+ // The length of the socket address stored in the endpoint.
+ std::size_t size_;
+
+ // The socket protocol associated with the endpoint.
+ int protocol_;
+
+ // Initialise with a specified memory.
+ BOOST_ASIO_DECL void init(const void* sock_addr,
+ std::size_t sock_addr_size, int sock_protocol);
+};
+
+} // namespace detail
+} // namespace generic
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/generic/detail/impl/endpoint.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_GENERIC_DETAIL_ENDPOINT_HPP
diff --git a/ext/patches/boost/asio/generic/detail/impl/endpoint.ipp b/ext/patches/boost/asio/generic/detail/impl/endpoint.ipp
new file mode 100644
index 0000000..a8b09ae
--- /dev/null
+++ b/ext/patches/boost/asio/generic/detail/impl/endpoint.ipp
@@ -0,0 +1,111 @@
+//
+// generic/detail/impl/endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_GENERIC_DETAIL_IMPL_ENDPOINT_IPP
+#define BOOST_ASIO_GENERIC_DETAIL_IMPL_ENDPOINT_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <cstring>
+#include <typeinfo>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/generic/detail/endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace generic {
+namespace detail {
+
+endpoint::endpoint()
+{
+ init(0, 0, 0);
+}
+
+endpoint::endpoint(const void* sock_addr,
+ std::size_t sock_addr_size, int sock_protocol)
+{
+ init(sock_addr, sock_addr_size, sock_protocol);
+}
+
+void endpoint::resize(std::size_t new_size)
+{
+ if (new_size > sizeof(boost::asio::detail::sockaddr_storage_type))
+ {
+ boost::system::error_code ec(boost::asio::error::invalid_argument);
+ boost::asio::detail::throw_error(ec);
+ }
+ else
+ {
+ size_ = new_size;
+ protocol_ = 0;
+ }
+}
+
+bool operator==(const endpoint& e1, const endpoint& e2)
+{
+ using namespace std; // For memcmp.
+ return e1.size() == e2.size() && memcmp(e1.data(), e2.data(), e1.size()) == 0;
+}
+
+bool operator<(const endpoint& e1, const endpoint& e2)
+{
+ if (e1.protocol() < e2.protocol())
+ return true;
+
+ if (e1.protocol() > e2.protocol())
+ return false;
+
+ using namespace std; // For memcmp.
+ std::size_t compare_size = e1.size() < e2.size() ? e1.size() : e2.size();
+ int compare_result = memcmp(e1.data(), e2.data(), compare_size);
+
+ if (compare_result < 0)
+ return true;
+
+ if (compare_result > 0)
+ return false;
+
+ return e1.size() < e2.size();
+}
+
+void endpoint::init(const void* sock_addr,
+ std::size_t sock_addr_size, int sock_protocol)
+{
+ if (sock_addr_size > sizeof(boost::asio::detail::sockaddr_storage_type))
+ {
+ boost::system::error_code ec(boost::asio::error::invalid_argument);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ using namespace std; // For memset and memcpy.
+ memset(&data_.generic, 0, sizeof(boost::asio::detail::sockaddr_storage_type));
+ memcpy(&data_.generic, sock_addr, sock_addr_size);
+
+ size_ = sock_addr_size;
+ protocol_ = sock_protocol;
+}
+
+} // namespace detail
+} // namespace generic
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_GENERIC_DETAIL_IMPL_ENDPOINT_IPP
diff --git a/ext/patches/boost/asio/generic/raw_protocol.hpp b/ext/patches/boost/asio/generic/raw_protocol.hpp
new file mode 100644
index 0000000..a955297
--- /dev/null
+++ b/ext/patches/boost/asio/generic/raw_protocol.hpp
@@ -0,0 +1,123 @@
+//
+// generic/raw_protocol.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_GENERIC_RAW_PROTOCOL_HPP
+#define BOOST_ASIO_GENERIC_RAW_PROTOCOL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <typeinfo>
+#include <boost/asio/basic_raw_socket.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/generic/basic_endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace generic {
+
+/// Encapsulates the flags needed for a generic raw socket.
+/**
+ * The boost::asio::generic::raw_protocol class contains flags necessary for
+ * raw sockets of any address family and protocol.
+ *
+ * @par Examples
+ * Constructing using a native address family and socket protocol:
+ * @code raw_protocol p(AF_INET, IPPROTO_ICMP); @endcode
+ * Constructing from a specific protocol type:
+ * @code raw_protocol p(boost::asio::ip::icmp::v4()); @endcode
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol.
+ */
+class raw_protocol
+{
+public:
+ /// Construct a protocol object for a specific address family and protocol.
+ raw_protocol(int address_family, int socket_protocol)
+ : family_(address_family),
+ protocol_(socket_protocol)
+ {
+ }
+
+ /// Construct a generic protocol object from a specific protocol.
+ /**
+ * @throws @c bad_cast Thrown if the source protocol is not raw-oriented.
+ */
+ template <typename Protocol>
+ raw_protocol(const Protocol& source_protocol)
+ : family_(source_protocol.family()),
+ protocol_(source_protocol.protocol())
+ {
+ if (source_protocol.type() != type())
+ {
+ std::bad_cast ex;
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return BOOST_ASIO_OS_DEF(SOCK_RAW);
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return protocol_;
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return family_;
+ }
+
+ /// Compare two protocols for equality.
+ friend bool operator==(const raw_protocol& p1, const raw_protocol& p2)
+ {
+ return p1.family_ == p2.family_ && p1.protocol_ == p2.protocol_;
+ }
+
+ /// Compare two protocols for inequality.
+ friend bool operator!=(const raw_protocol& p1, const raw_protocol& p2)
+ {
+ return !(p1 == p2);
+ }
+
+ /// The type of an endpoint.
+ typedef basic_endpoint<raw_protocol> endpoint;
+
+ /// The generic socket type.
+ typedef basic_raw_socket<raw_protocol> socket;
+
+private:
+ int family_;
+ int protocol_;
+};
+
+} // namespace generic
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_GENERIC_RAW_PROTOCOL_HPP
diff --git a/ext/patches/boost/asio/generic/seq_packet_protocol.hpp b/ext/patches/boost/asio/generic/seq_packet_protocol.hpp
new file mode 100644
index 0000000..cb15c98
--- /dev/null
+++ b/ext/patches/boost/asio/generic/seq_packet_protocol.hpp
@@ -0,0 +1,124 @@
+//
+// generic/seq_packet_protocol.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_GENERIC_SEQ_PACKET_PROTOCOL_HPP
+#define BOOST_ASIO_GENERIC_SEQ_PACKET_PROTOCOL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <typeinfo>
+#include <boost/asio/basic_seq_packet_socket.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/generic/basic_endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace generic {
+
+/// Encapsulates the flags needed for a generic sequenced packet socket.
+/**
+ * The boost::asio::generic::seq_packet_protocol class contains flags necessary
+ * for seq_packet-oriented sockets of any address family and protocol.
+ *
+ * @par Examples
+ * Constructing using a native address family and socket protocol:
+ * @code seq_packet_protocol p(AF_INET, IPPROTO_SCTP); @endcode
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol.
+ */
+class seq_packet_protocol
+{
+public:
+ /// Construct a protocol object for a specific address family and protocol.
+ seq_packet_protocol(int address_family, int socket_protocol)
+ : family_(address_family),
+ protocol_(socket_protocol)
+ {
+ }
+
+ /// Construct a generic protocol object from a specific protocol.
+ /**
+ * @throws @c bad_cast Thrown if the source protocol is not based around
+ * sequenced packets.
+ */
+ template <typename Protocol>
+ seq_packet_protocol(const Protocol& source_protocol)
+ : family_(source_protocol.family()),
+ protocol_(source_protocol.protocol())
+ {
+ if (source_protocol.type() != type())
+ {
+ std::bad_cast ex;
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return BOOST_ASIO_OS_DEF(SOCK_SEQPACKET);
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return protocol_;
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return family_;
+ }
+
+ /// Compare two protocols for equality.
+ friend bool operator==(const seq_packet_protocol& p1,
+ const seq_packet_protocol& p2)
+ {
+ return p1.family_ == p2.family_ && p1.protocol_ == p2.protocol_;
+ }
+
+ /// Compare two protocols for inequality.
+ friend bool operator!=(const seq_packet_protocol& p1,
+ const seq_packet_protocol& p2)
+ {
+ return !(p1 == p2);
+ }
+
+ /// The type of an endpoint.
+ typedef basic_endpoint<seq_packet_protocol> endpoint;
+
+ /// The generic socket type.
+ typedef basic_seq_packet_socket<seq_packet_protocol> socket;
+
+private:
+ int family_;
+ int protocol_;
+};
+
+} // namespace generic
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_GENERIC_SEQ_PACKET_PROTOCOL_HPP
diff --git a/ext/patches/boost/asio/generic/stream_protocol.hpp b/ext/patches/boost/asio/generic/stream_protocol.hpp
new file mode 100644
index 0000000..e895b1d
--- /dev/null
+++ b/ext/patches/boost/asio/generic/stream_protocol.hpp
@@ -0,0 +1,129 @@
+//
+// generic/stream_protocol.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_GENERIC_STREAM_PROTOCOL_HPP
+#define BOOST_ASIO_GENERIC_STREAM_PROTOCOL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <typeinfo>
+#include <boost/asio/basic_socket_iostream.hpp>
+#include <boost/asio/basic_stream_socket.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/generic/basic_endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace generic {
+
+/// Encapsulates the flags needed for a generic stream-oriented socket.
+/**
+ * The boost::asio::generic::stream_protocol class contains flags necessary for
+ * stream-oriented sockets of any address family and protocol.
+ *
+ * @par Examples
+ * Constructing using a native address family and socket protocol:
+ * @code stream_protocol p(AF_INET, IPPROTO_TCP); @endcode
+ * Constructing from a specific protocol type:
+ * @code stream_protocol p(boost::asio::ip::tcp::v4()); @endcode
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol.
+ */
+class stream_protocol
+{
+public:
+ /// Construct a protocol object for a specific address family and protocol.
+ stream_protocol(int address_family, int socket_protocol)
+ : family_(address_family),
+ protocol_(socket_protocol)
+ {
+ }
+
+ /// Construct a generic protocol object from a specific protocol.
+ /**
+ * @throws @c bad_cast Thrown if the source protocol is not stream-oriented.
+ */
+ template <typename Protocol>
+ stream_protocol(const Protocol& source_protocol)
+ : family_(source_protocol.family()),
+ protocol_(source_protocol.protocol())
+ {
+ if (source_protocol.type() != type())
+ {
+ std::bad_cast ex;
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return BOOST_ASIO_OS_DEF(SOCK_STREAM);
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return protocol_;
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return family_;
+ }
+
+ /// Compare two protocols for equality.
+ friend bool operator==(const stream_protocol& p1, const stream_protocol& p2)
+ {
+ return p1.family_ == p2.family_ && p1.protocol_ == p2.protocol_;
+ }
+
+ /// Compare two protocols for inequality.
+ friend bool operator!=(const stream_protocol& p1, const stream_protocol& p2)
+ {
+ return !(p1 == p2);
+ }
+
+ /// The type of an endpoint.
+ typedef basic_endpoint<stream_protocol> endpoint;
+
+ /// The generic socket type.
+ typedef basic_stream_socket<stream_protocol> socket;
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+ /// The generic socket iostream type.
+ typedef basic_socket_iostream<stream_protocol> iostream;
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+private:
+ int family_;
+ int protocol_;
+};
+
+} // namespace generic
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_GENERIC_STREAM_PROTOCOL_HPP
diff --git a/ext/patches/boost/asio/handler_alloc_hook.hpp b/ext/patches/boost/asio/handler_alloc_hook.hpp
new file mode 100644
index 0000000..f1d3125
--- /dev/null
+++ b/ext/patches/boost/asio/handler_alloc_hook.hpp
@@ -0,0 +1,83 @@
+//
+// handler_alloc_hook.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_HANDLER_ALLOC_HOOK_HPP
+#define BOOST_ASIO_HANDLER_ALLOC_HOOK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default allocation function for handlers.
+/**
+ * Asynchronous operations may need to allocate temporary objects. Since
+ * asynchronous operations have a handler function object, these temporary
+ * objects can be said to be associated with the handler.
+ *
+ * Implement asio_handler_allocate and asio_handler_deallocate for your own
+ * handlers to provide custom allocation for these temporary objects.
+ *
+ * The default implementation of these allocation hooks uses <tt>::operator
+ * new</tt> and <tt>::operator delete</tt>.
+ *
+ * @note All temporary objects associated with a handler will be deallocated
+ * before the upcall to the handler is performed. This allows the same memory to
+ * be reused for a subsequent asynchronous operation initiated by the handler.
+ *
+ * @par Example
+ * @code
+ * class my_handler;
+ *
+ * void* asio_handler_allocate(std::size_t size, my_handler* context)
+ * {
+ * return ::operator new(size);
+ * }
+ *
+ * void asio_handler_deallocate(void* pointer, std::size_t size,
+ * my_handler* context)
+ * {
+ * ::operator delete(pointer);
+ * }
+ * @endcode
+ */
+BOOST_ASIO_DECL void* asio_handler_allocate(
+ std::size_t size, ...);
+
+/// Default deallocation function for handlers.
+/**
+ * Implement asio_handler_allocate and asio_handler_deallocate for your own
+ * handlers to provide custom allocation for the associated temporary objects.
+ *
+ * The default implementation of these allocation hooks uses <tt>::operator
+ * new</tt> and <tt>::operator delete</tt>.
+ *
+ * @sa asio_handler_allocate.
+ */
+BOOST_ASIO_DECL void asio_handler_deallocate(
+ void* pointer, std::size_t size, ...);
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/impl/handler_alloc_hook.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_HANDLER_ALLOC_HOOK_HPP
diff --git a/ext/patches/boost/asio/handler_continuation_hook.hpp b/ext/patches/boost/asio/handler_continuation_hook.hpp
new file mode 100644
index 0000000..763af3f
--- /dev/null
+++ b/ext/patches/boost/asio/handler_continuation_hook.hpp
@@ -0,0 +1,56 @@
+//
+// handler_continuation_hook.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_HANDLER_CONTINUATION_HOOK_HPP
+#define BOOST_ASIO_HANDLER_CONTINUATION_HOOK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default continuation function for handlers.
+/**
+ * Asynchronous operations may represent a continuation of the asynchronous
+ * control flow associated with the current handler. The implementation can use
+ * this knowledge to optimise scheduling of the handler.
+ *
+ * Implement asio_handler_is_continuation for your own handlers to indicate
+ * when a handler represents a continuation.
+ *
+ * The default implementation of the continuation hook returns <tt>false</tt>.
+ *
+ * @par Example
+ * @code
+ * class my_handler;
+ *
+ * bool asio_handler_is_continuation(my_handler* context)
+ * {
+ * return true;
+ * }
+ * @endcode
+ */
+inline bool asio_handler_is_continuation(...)
+{
+ return false;
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_HANDLER_CONTINUATION_HOOK_HPP
diff --git a/ext/patches/boost/asio/handler_invoke_hook.hpp b/ext/patches/boost/asio/handler_invoke_hook.hpp
new file mode 100644
index 0000000..d4f7987
--- /dev/null
+++ b/ext/patches/boost/asio/handler_invoke_hook.hpp
@@ -0,0 +1,87 @@
+//
+// handler_invoke_hook.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_HANDLER_INVOKE_HOOK_HPP
+#define BOOST_ASIO_HANDLER_INVOKE_HOOK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/** @defgroup asio_handler_invoke boost::asio::asio_handler_invoke
+ *
+ * @brief Default invoke function for handlers.
+ *
+ * Completion handlers for asynchronous operations are invoked by the
+ * io_service associated with the corresponding object (e.g. a socket or
+ * deadline_timer). Certain guarantees are made on when the handler may be
+ * invoked, in particular that a handler can only be invoked from a thread that
+ * is currently calling @c run() on the corresponding io_service object.
+ * Handlers may subsequently be invoked through other objects (such as
+ * io_service::strand objects) that provide additional guarantees.
+ *
+ * When asynchronous operations are composed from other asynchronous
+ * operations, all intermediate handlers should be invoked using the same
+ * method as the final handler. This is required to ensure that user-defined
+ * objects are not accessed in a way that may violate the guarantees. This
+ * hooking function ensures that the invoked method used for the final handler
+ * is accessible at each intermediate step.
+ *
+ * Implement asio_handler_invoke for your own handlers to specify a custom
+ * invocation strategy.
+ *
+ * This default implementation invokes the function object like so:
+ * @code function(); @endcode
+ * If necessary, the default implementation makes a copy of the function object
+ * so that the non-const operator() can be used.
+ *
+ * @par Example
+ * @code
+ * class my_handler;
+ *
+ * template <typename Function>
+ * void asio_handler_invoke(Function function, my_handler* context)
+ * {
+ * context->strand_.dispatch(function);
+ * }
+ * @endcode
+ */
+/*@{*/
+
+/// Default handler invocation hook used for non-const function objects.
+template <typename Function>
+inline void asio_handler_invoke(Function& function, ...)
+{
+ function();
+}
+
+/// Default handler invocation hook used for const function objects.
+template <typename Function>
+inline void asio_handler_invoke(const Function& function, ...)
+{
+ Function tmp(function);
+ tmp();
+}
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_HANDLER_INVOKE_HOOK_HPP
diff --git a/ext/patches/boost/asio/handler_type.hpp b/ext/patches/boost/asio/handler_type.hpp
new file mode 100644
index 0000000..f09d634
--- /dev/null
+++ b/ext/patches/boost/asio/handler_type.hpp
@@ -0,0 +1,114 @@
+//
+// handler_type.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_HANDLER_TYPE_HPP
+#define BOOST_ASIO_HANDLER_TYPE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default handler type traits provided for all handlers.
+/**
+ * The handler_type traits class is used for determining the concrete handler
+ * type to be used for an asynchronous operation. It allows the handler type to
+ * be determined at the point where the specific completion handler signature
+ * is known.
+ *
+ * This template may be specialised for user-defined handler types.
+ */
+template <typename Handler, typename Signature>
+struct handler_type
+{
+ /// The handler type for the specific signature.
+ typedef Handler type;
+};
+
+#if !defined(GENERATING_DOCUMENTATION)
+
+template <typename Handler, typename Signature>
+struct handler_type<const Handler, Signature>
+ : handler_type<Handler, Signature> {};
+
+template <typename Handler, typename Signature>
+struct handler_type<volatile Handler, Signature>
+ : handler_type<Handler, Signature> {};
+
+template <typename Handler, typename Signature>
+struct handler_type<const volatile Handler, Signature>
+ : handler_type<Handler, Signature> {};
+
+template <typename Handler, typename Signature>
+struct handler_type<const Handler&, Signature>
+ : handler_type<Handler, Signature> {};
+
+template <typename Handler, typename Signature>
+struct handler_type<volatile Handler&, Signature>
+ : handler_type<Handler, Signature> {};
+
+template <typename Handler, typename Signature>
+struct handler_type<const volatile Handler&, Signature>
+ : handler_type<Handler, Signature> {};
+
+template <typename Handler, typename Signature>
+struct handler_type<Handler&, Signature>
+ : handler_type<Handler, Signature> {};
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+template <typename Handler, typename Signature>
+struct handler_type<Handler&&, Signature>
+ : handler_type<Handler, Signature> {};
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+template <typename ReturnType, typename Signature>
+struct handler_type<ReturnType(), Signature>
+ : handler_type<ReturnType(*)(), Signature> {};
+
+template <typename ReturnType, typename Arg1, typename Signature>
+struct handler_type<ReturnType(Arg1), Signature>
+ : handler_type<ReturnType(*)(Arg1), Signature> {};
+
+template <typename ReturnType, typename Arg1, typename Arg2, typename Signature>
+struct handler_type<ReturnType(Arg1, Arg2), Signature>
+ : handler_type<ReturnType(*)(Arg1, Arg2), Signature> {};
+
+template <typename ReturnType, typename Arg1, typename Arg2, typename Arg3,
+ typename Signature>
+struct handler_type<ReturnType(Arg1, Arg2, Arg3), Signature>
+ : handler_type<ReturnType(*)(Arg1, Arg2, Arg3), Signature> {};
+
+template <typename ReturnType, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4, typename Signature>
+struct handler_type<ReturnType(Arg1, Arg2, Arg3, Arg4), Signature>
+ : handler_type<ReturnType(*)(Arg1, Arg2, Arg3, Arg4), Signature> {};
+
+template <typename ReturnType, typename Arg1, typename Arg2, typename Arg3,
+ typename Arg4, typename Arg5, typename Signature>
+struct handler_type<ReturnType(Arg1, Arg2, Arg3, Arg4, Arg5), Signature>
+ : handler_type<ReturnType(*)(Arg1, Arg2, Arg3, Arg4, Arg5), Signature> {};
+
+#endif // !defined(GENERATING_DOCUMENTATION)
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#define BOOST_ASIO_HANDLER_TYPE(h, sig) \
+ typename handler_type<h, sig>::type
+
+#endif // BOOST_ASIO_HANDLER_TYPE_HPP
diff --git a/ext/patches/boost/asio/high_resolution_timer.hpp b/ext/patches/boost/asio/high_resolution_timer.hpp
new file mode 100644
index 0000000..ac55ede
--- /dev/null
+++ b/ext/patches/boost/asio/high_resolution_timer.hpp
@@ -0,0 +1,65 @@
+//
+// high_resolution_timer.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_HIGH_RESOLUTION_TIMER_HPP
+#define BOOST_ASIO_HIGH_RESOLUTION_TIMER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_CHRONO) \
+ || defined(BOOST_ASIO_HAS_BOOST_CHRONO) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#if defined(BOOST_ASIO_HAS_STD_CHRONO)
+# include <chrono>
+#elif defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+# include <boost/chrono/system_clocks.hpp>
+#endif
+
+#include <boost/asio/basic_waitable_timer.hpp>
+
+namespace boost {
+namespace asio {
+
+#if defined(GENERATING_DOCUMENTATION)
+/// Typedef for a timer based on the high resolution clock.
+/**
+ * This typedef uses the C++11 @c <chrono> standard library facility, if
+ * available. Otherwise, it may use the Boost.Chrono library. To explicitly
+ * utilise Boost.Chrono, use the basic_waitable_timer template directly:
+ * @code
+ * typedef basic_waitable_timer<boost::chrono::high_resolution_clock> timer;
+ * @endcode
+ */
+typedef basic_waitable_timer<
+ chrono::high_resolution_clock>
+ high_resolution_timer;
+#elif defined(BOOST_ASIO_HAS_STD_CHRONO)
+typedef basic_waitable_timer<
+ std::chrono::high_resolution_clock>
+ high_resolution_timer;
+#elif defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+typedef basic_waitable_timer<
+ boost::chrono::high_resolution_clock>
+ high_resolution_timer;
+#endif
+
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_STD_CHRONO)
+ // || defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_HIGH_RESOLUTION_TIMER_HPP
diff --git a/ext/patches/boost/asio/impl/buffered_read_stream.hpp b/ext/patches/boost/asio/impl/buffered_read_stream.hpp
new file mode 100644
index 0000000..2685f1d
--- /dev/null
+++ b/ext/patches/boost/asio/impl/buffered_read_stream.hpp
@@ -0,0 +1,360 @@
+//
+// impl/buffered_read_stream.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_BUFFERED_READ_STREAM_HPP
+#define BOOST_ASIO_IMPL_BUFFERED_READ_STREAM_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename Stream>
+std::size_t buffered_read_stream<Stream>::fill()
+{
+ detail::buffer_resize_guard<detail::buffered_stream_storage>
+ resize_guard(storage_);
+ std::size_t previous_size = storage_.size();
+ storage_.resize(storage_.capacity());
+ storage_.resize(previous_size + next_layer_.read_some(buffer(
+ storage_.data() + previous_size,
+ storage_.size() - previous_size)));
+ resize_guard.commit();
+ return storage_.size() - previous_size;
+}
+
+template <typename Stream>
+std::size_t buffered_read_stream<Stream>::fill(boost::system::error_code& ec)
+{
+ detail::buffer_resize_guard<detail::buffered_stream_storage>
+ resize_guard(storage_);
+ std::size_t previous_size = storage_.size();
+ storage_.resize(storage_.capacity());
+ storage_.resize(previous_size + next_layer_.read_some(buffer(
+ storage_.data() + previous_size,
+ storage_.size() - previous_size),
+ ec));
+ resize_guard.commit();
+ return storage_.size() - previous_size;
+}
+
+namespace detail
+{
+ template <typename ReadHandler>
+ class buffered_fill_handler
+ {
+ public:
+ buffered_fill_handler(detail::buffered_stream_storage& storage,
+ std::size_t previous_size, ReadHandler& handler)
+ : storage_(storage),
+ previous_size_(previous_size),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ buffered_fill_handler(const buffered_fill_handler& other)
+ : storage_(other.storage_),
+ previous_size_(other.previous_size_),
+ handler_(other.handler_)
+ {
+ }
+
+ buffered_fill_handler(buffered_fill_handler&& other)
+ : storage_(other.storage_),
+ previous_size_(other.previous_size_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ const std::size_t bytes_transferred)
+ {
+ storage_.resize(previous_size_ + bytes_transferred);
+ handler_(ec, bytes_transferred);
+ }
+
+ //private:
+ detail::buffered_stream_storage& storage_;
+ std::size_t previous_size_;
+ ReadHandler handler_;
+ };
+
+ template <typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ buffered_fill_handler<ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ buffered_fill_handler<ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ buffered_fill_handler<ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ buffered_fill_handler<ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ buffered_fill_handler<ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename Stream>
+template <typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+buffered_read_stream<Stream>::async_fill(
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ std::size_t previous_size = storage_.size();
+ storage_.resize(storage_.capacity());
+ next_layer_.async_read_some(
+ buffer(
+ storage_.data() + previous_size,
+ storage_.size() - previous_size),
+ detail::buffered_fill_handler<BOOST_ASIO_HANDLER_TYPE(
+ ReadHandler, void (boost::system::error_code, std::size_t))>(
+ storage_, previous_size, init.handler));
+
+ return init.result.get();
+}
+
+template <typename Stream>
+template <typename MutableBufferSequence>
+std::size_t buffered_read_stream<Stream>::read_some(
+ const MutableBufferSequence& buffers)
+{
+ if (boost::asio::buffer_size(buffers) == 0)
+ return 0;
+
+ if (storage_.empty())
+ this->fill();
+
+ return this->copy(buffers);
+}
+
+template <typename Stream>
+template <typename MutableBufferSequence>
+std::size_t buffered_read_stream<Stream>::read_some(
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+
+ if (boost::asio::buffer_size(buffers) == 0)
+ return 0;
+
+ if (storage_.empty() && !this->fill(ec))
+ return 0;
+
+ return this->copy(buffers);
+}
+
+namespace detail
+{
+ template <typename MutableBufferSequence, typename ReadHandler>
+ class buffered_read_some_handler
+ {
+ public:
+ buffered_read_some_handler(detail::buffered_stream_storage& storage,
+ const MutableBufferSequence& buffers, ReadHandler& handler)
+ : storage_(storage),
+ buffers_(buffers),
+ handler_(handler)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ buffered_read_some_handler(const buffered_read_some_handler& other)
+ : storage_(other.storage_),
+ buffers_(other.buffers_),
+ handler_(other.handler_)
+ {
+ }
+
+ buffered_read_some_handler(buffered_read_some_handler&& other)
+ : storage_(other.storage_),
+ buffers_(other.buffers_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec, std::size_t)
+ {
+ if (ec || storage_.empty())
+ {
+ const std::size_t length = 0;
+ handler_(ec, length);
+ }
+ else
+ {
+ const std::size_t bytes_copied = boost::asio::buffer_copy(
+ buffers_, storage_.data(), storage_.size());
+ storage_.consume(bytes_copied);
+ handler_(ec, bytes_copied);
+ }
+ }
+
+ //private:
+ detail::buffered_stream_storage& storage_;
+ MutableBufferSequence buffers_;
+ ReadHandler handler_;
+ };
+
+ template <typename MutableBufferSequence, typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ buffered_read_some_handler<
+ MutableBufferSequence, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename MutableBufferSequence, typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ buffered_read_some_handler<
+ MutableBufferSequence, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename MutableBufferSequence, typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ buffered_read_some_handler<
+ MutableBufferSequence, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename MutableBufferSequence,
+ typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ buffered_read_some_handler<
+ MutableBufferSequence, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename MutableBufferSequence,
+ typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ buffered_read_some_handler<
+ MutableBufferSequence, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename Stream>
+template <typename MutableBufferSequence, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+buffered_read_stream<Stream>::async_read_some(
+ const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ if (boost::asio::buffer_size(buffers) == 0 || !storage_.empty())
+ {
+ next_layer_.async_read_some(boost::asio::mutable_buffers_1(0, 0),
+ detail::buffered_read_some_handler<
+ MutableBufferSequence, BOOST_ASIO_HANDLER_TYPE(
+ ReadHandler, void (boost::system::error_code, std::size_t))>(
+ storage_, buffers, init.handler));
+ }
+ else
+ {
+ this->async_fill(detail::buffered_read_some_handler<
+ MutableBufferSequence, BOOST_ASIO_HANDLER_TYPE(
+ ReadHandler, void (boost::system::error_code, std::size_t))>(
+ storage_, buffers, init.handler));
+ }
+
+ return init.result.get();
+}
+
+template <typename Stream>
+template <typename MutableBufferSequence>
+std::size_t buffered_read_stream<Stream>::peek(
+ const MutableBufferSequence& buffers)
+{
+ if (storage_.empty())
+ this->fill();
+ return this->peek_copy(buffers);
+}
+
+template <typename Stream>
+template <typename MutableBufferSequence>
+std::size_t buffered_read_stream<Stream>::peek(
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ if (storage_.empty() && !this->fill(ec))
+ return 0;
+ return this->peek_copy(buffers);
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_BUFFERED_READ_STREAM_HPP
diff --git a/ext/patches/boost/asio/impl/buffered_write_stream.hpp b/ext/patches/boost/asio/impl/buffered_write_stream.hpp
new file mode 100644
index 0000000..6bbfe7f
--- /dev/null
+++ b/ext/patches/boost/asio/impl/buffered_write_stream.hpp
@@ -0,0 +1,340 @@
+//
+// impl/buffered_write_stream.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_BUFFERED_WRITE_STREAM_HPP
+#define BOOST_ASIO_IMPL_BUFFERED_WRITE_STREAM_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename Stream>
+std::size_t buffered_write_stream<Stream>::flush()
+{
+ std::size_t bytes_written = write(next_layer_,
+ buffer(storage_.data(), storage_.size()));
+ storage_.consume(bytes_written);
+ return bytes_written;
+}
+
+template <typename Stream>
+std::size_t buffered_write_stream<Stream>::flush(boost::system::error_code& ec)
+{
+ std::size_t bytes_written = write(next_layer_,
+ buffer(storage_.data(), storage_.size()),
+ transfer_all(), ec);
+ storage_.consume(bytes_written);
+ return bytes_written;
+}
+
+namespace detail
+{
+ template <typename WriteHandler>
+ class buffered_flush_handler
+ {
+ public:
+ buffered_flush_handler(detail::buffered_stream_storage& storage,
+ WriteHandler& handler)
+ : storage_(storage),
+ handler_(handler)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ buffered_flush_handler(const buffered_flush_handler& other)
+ : storage_(other.storage_),
+ handler_(other.handler_)
+ {
+ }
+
+ buffered_flush_handler(buffered_flush_handler&& other)
+ : storage_(other.storage_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ const std::size_t bytes_written)
+ {
+ storage_.consume(bytes_written);
+ handler_(ec, bytes_written);
+ }
+
+ //private:
+ detail::buffered_stream_storage& storage_;
+ WriteHandler handler_;
+ };
+
+ template <typename WriteHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ buffered_flush_handler<WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename WriteHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ buffered_flush_handler<WriteHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename WriteHandler>
+ inline bool asio_handler_is_continuation(
+ buffered_flush_handler<WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename WriteHandler>
+ inline void asio_handler_invoke(Function& function,
+ buffered_flush_handler<WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename WriteHandler>
+ inline void asio_handler_invoke(const Function& function,
+ buffered_flush_handler<WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+}
+
+template <typename Stream>
+template <typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+buffered_write_stream<Stream>::async_flush(
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ async_write(next_layer_, buffer(storage_.data(), storage_.size()),
+ detail::buffered_flush_handler<BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ storage_, init.handler));
+
+ return init.result.get();
+}
+
+template <typename Stream>
+template <typename ConstBufferSequence>
+std::size_t buffered_write_stream<Stream>::write_some(
+ const ConstBufferSequence& buffers)
+{
+ if (boost::asio::buffer_size(buffers) == 0)
+ return 0;
+
+ if (storage_.size() == storage_.capacity())
+ this->flush();
+
+ return this->copy(buffers);
+}
+
+template <typename Stream>
+template <typename ConstBufferSequence>
+std::size_t buffered_write_stream<Stream>::write_some(
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+
+ if (boost::asio::buffer_size(buffers) == 0)
+ return 0;
+
+ if (storage_.size() == storage_.capacity() && !flush(ec))
+ return 0;
+
+ return this->copy(buffers);
+}
+
+namespace detail
+{
+ template <typename ConstBufferSequence, typename WriteHandler>
+ class buffered_write_some_handler
+ {
+ public:
+ buffered_write_some_handler(detail::buffered_stream_storage& storage,
+ const ConstBufferSequence& buffers, WriteHandler& handler)
+ : storage_(storage),
+ buffers_(buffers),
+ handler_(handler)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ buffered_write_some_handler(const buffered_write_some_handler& other)
+ : storage_(other.storage_),
+ buffers_(other.buffers_),
+ handler_(other.handler_)
+ {
+ }
+
+ buffered_write_some_handler(buffered_write_some_handler&& other)
+ : storage_(other.storage_),
+ buffers_(other.buffers_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec, std::size_t)
+ {
+ if (ec)
+ {
+ const std::size_t length = 0;
+ handler_(ec, length);
+ }
+ else
+ {
+ std::size_t orig_size = storage_.size();
+ std::size_t space_avail = storage_.capacity() - orig_size;
+ std::size_t bytes_avail = boost::asio::buffer_size(buffers_);
+ std::size_t length = bytes_avail < space_avail
+ ? bytes_avail : space_avail;
+ storage_.resize(orig_size + length);
+ const std::size_t bytes_copied = boost::asio::buffer_copy(
+ storage_.data() + orig_size, buffers_, length);
+ handler_(ec, bytes_copied);
+ }
+ }
+
+ //private:
+ detail::buffered_stream_storage& storage_;
+ ConstBufferSequence buffers_;
+ WriteHandler handler_;
+ };
+
+ template <typename ConstBufferSequence, typename WriteHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ buffered_write_some_handler<
+ ConstBufferSequence, WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename ConstBufferSequence, typename WriteHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ buffered_write_some_handler<
+ ConstBufferSequence, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename ConstBufferSequence, typename WriteHandler>
+ inline bool asio_handler_is_continuation(
+ buffered_write_some_handler<
+ ConstBufferSequence, WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename ConstBufferSequence,
+ typename WriteHandler>
+ inline void asio_handler_invoke(Function& function,
+ buffered_write_some_handler<
+ ConstBufferSequence, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename ConstBufferSequence,
+ typename WriteHandler>
+ inline void asio_handler_invoke(const Function& function,
+ buffered_write_some_handler<
+ ConstBufferSequence, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename Stream>
+template <typename ConstBufferSequence, typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+buffered_write_stream<Stream>::async_write_some(
+ const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ if (boost::asio::buffer_size(buffers) == 0
+ || storage_.size() < storage_.capacity())
+ {
+ next_layer_.async_write_some(boost::asio::const_buffers_1(0, 0),
+ detail::buffered_write_some_handler<
+ ConstBufferSequence, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ storage_, buffers, init.handler));
+ }
+ else
+ {
+ this->async_flush(detail::buffered_write_some_handler<
+ ConstBufferSequence, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ storage_, buffers, init.handler));
+ }
+
+ return init.result.get();
+}
+
+template <typename Stream>
+template <typename ConstBufferSequence>
+std::size_t buffered_write_stream<Stream>::copy(
+ const ConstBufferSequence& buffers)
+{
+ std::size_t orig_size = storage_.size();
+ std::size_t space_avail = storage_.capacity() - orig_size;
+ std::size_t bytes_avail = boost::asio::buffer_size(buffers);
+ std::size_t length = bytes_avail < space_avail ? bytes_avail : space_avail;
+ storage_.resize(orig_size + length);
+ return boost::asio::buffer_copy(
+ storage_.data() + orig_size, buffers, length);
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_BUFFERED_WRITE_STREAM_HPP
diff --git a/ext/patches/boost/asio/impl/connect.hpp b/ext/patches/boost/asio/impl/connect.hpp
new file mode 100644
index 0000000..5f059bb
--- /dev/null
+++ b/ext/patches/boost/asio/impl/connect.hpp
@@ -0,0 +1,430 @@
+//
+// impl/connect.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_CONNECT_HPP
+#define BOOST_ASIO_IMPL_CONNECT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/consuming_buffers.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+namespace detail
+{
+ struct default_connect_condition
+ {
+ template <typename Iterator>
+ Iterator operator()(const boost::system::error_code&, Iterator next)
+ {
+ return next;
+ }
+ };
+}
+
+template <typename Protocol, typename SocketService, typename Iterator>
+Iterator connect(basic_socket<Protocol, SocketService>& s, Iterator begin)
+{
+ boost::system::error_code ec;
+ Iterator result = connect(s, begin, ec);
+ boost::asio::detail::throw_error(ec, "connect");
+ return result;
+}
+
+template <typename Protocol, typename SocketService, typename Iterator>
+inline Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, boost::system::error_code& ec)
+{
+ return connect(s, begin, Iterator(), detail::default_connect_condition(), ec);
+}
+
+template <typename Protocol, typename SocketService, typename Iterator>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end)
+{
+ boost::system::error_code ec;
+ Iterator result = connect(s, begin, end, ec);
+ boost::asio::detail::throw_error(ec, "connect");
+ return result;
+}
+
+template <typename Protocol, typename SocketService, typename Iterator>
+inline Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end, boost::system::error_code& ec)
+{
+ return connect(s, begin, end, detail::default_connect_condition(), ec);
+}
+
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ConnectCondition>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, ConnectCondition connect_condition)
+{
+ boost::system::error_code ec;
+ Iterator result = connect(s, begin, connect_condition, ec);
+ boost::asio::detail::throw_error(ec, "connect");
+ return result;
+}
+
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ConnectCondition>
+inline Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, ConnectCondition connect_condition,
+ boost::system::error_code& ec)
+{
+ return connect(s, begin, Iterator(), connect_condition, ec);
+}
+
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ConnectCondition>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end, ConnectCondition connect_condition)
+{
+ boost::system::error_code ec;
+ Iterator result = connect(s, begin, end, connect_condition, ec);
+ boost::asio::detail::throw_error(ec, "connect");
+ return result;
+}
+
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ConnectCondition>
+Iterator connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end, ConnectCondition connect_condition,
+ boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+
+ for (Iterator iter = begin; iter != end; ++iter)
+ {
+ iter = connect_condition(ec, iter);
+ if (iter != end)
+ {
+ s.close(ec);
+ s.connect(*iter, ec);
+ if (!ec)
+ return iter;
+ }
+ }
+
+ if (!ec)
+ ec = boost::asio::error::not_found;
+
+ return end;
+}
+
+namespace detail
+{
+ // Enable the empty base class optimisation for the connect condition.
+ template <typename ConnectCondition>
+ class base_from_connect_condition
+ {
+ protected:
+ explicit base_from_connect_condition(
+ const ConnectCondition& connect_condition)
+ : connect_condition_(connect_condition)
+ {
+ }
+
+ template <typename Iterator>
+ void check_condition(const boost::system::error_code& ec,
+ Iterator& iter, Iterator& end)
+ {
+ if (iter != end)
+ iter = connect_condition_(ec, static_cast<const Iterator&>(iter));
+ }
+
+ private:
+ ConnectCondition connect_condition_;
+ };
+
+ // The default_connect_condition implementation is essentially a no-op. This
+ // template specialisation lets us eliminate all costs associated with it.
+ template <>
+ class base_from_connect_condition<default_connect_condition>
+ {
+ protected:
+ explicit base_from_connect_condition(const default_connect_condition&)
+ {
+ }
+
+ template <typename Iterator>
+ void check_condition(const boost::system::error_code&, Iterator&, Iterator&)
+ {
+ }
+ };
+
+ template <typename Protocol, typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+ class connect_op : base_from_connect_condition<ConnectCondition>
+ {
+ public:
+ connect_op(basic_socket<Protocol, SocketService>& sock,
+ const Iterator& begin, const Iterator& end,
+ const ConnectCondition& connect_condition,
+ ComposedConnectHandler& handler)
+ : base_from_connect_condition<ConnectCondition>(connect_condition),
+ socket_(sock),
+ iter_(begin),
+ end_(end),
+ start_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ComposedConnectHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ connect_op(const connect_op& other)
+ : base_from_connect_condition<ConnectCondition>(other),
+ socket_(other.socket_),
+ iter_(other.iter_),
+ end_(other.end_),
+ start_(other.start_),
+ handler_(other.handler_)
+ {
+ }
+
+ connect_op(connect_op&& other)
+ : base_from_connect_condition<ConnectCondition>(other),
+ socket_(other.socket_),
+ iter_(other.iter_),
+ end_(other.end_),
+ start_(other.start_),
+ handler_(BOOST_ASIO_MOVE_CAST(ComposedConnectHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(boost::system::error_code ec, int start = 0)
+ {
+ switch (start_ = start)
+ {
+ case 1:
+ for (;;)
+ {
+ this->check_condition(ec, iter_, end_);
+
+ if (iter_ != end_)
+ {
+ socket_.close(ec);
+ socket_.async_connect(*iter_,
+ BOOST_ASIO_MOVE_CAST(connect_op)(*this));
+ return;
+ }
+
+ if (start)
+ {
+ ec = boost::asio::error::not_found;
+ socket_.get_io_service().post(detail::bind_handler(*this, ec));
+ return;
+ }
+
+ default:
+
+ if (iter_ == end_)
+ break;
+
+ if (!socket_.is_open())
+ {
+ ec = boost::asio::error::operation_aborted;
+ break;
+ }
+
+ if (!ec)
+ break;
+
+ ++iter_;
+ }
+
+ handler_(static_cast<const boost::system::error_code&>(ec),
+ static_cast<const Iterator&>(iter_));
+ }
+ }
+
+ //private:
+ basic_socket<Protocol, SocketService>& socket_;
+ Iterator iter_;
+ Iterator end_;
+ int start_;
+ ComposedConnectHandler handler_;
+ };
+
+ template <typename Protocol, typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ connect_op<Protocol, SocketService, Iterator,
+ ConnectCondition, ComposedConnectHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename Protocol, typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ connect_op<Protocol, SocketService, Iterator,
+ ConnectCondition, ComposedConnectHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename Protocol, typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+ inline bool asio_handler_is_continuation(
+ connect_op<Protocol, SocketService, Iterator,
+ ConnectCondition, ComposedConnectHandler>* this_handler)
+ {
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename Protocol,
+ typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+ inline void asio_handler_invoke(Function& function,
+ connect_op<Protocol, SocketService, Iterator,
+ ConnectCondition, ComposedConnectHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename Protocol,
+ typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+ inline void asio_handler_invoke(const Function& function,
+ connect_op<Protocol, SocketService, Iterator,
+ ConnectCondition, ComposedConnectHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ComposedConnectHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ComposedConnectHandler,
+ void (boost::system::error_code, Iterator))
+async_connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, BOOST_ASIO_MOVE_ARG(ComposedConnectHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ComposedConnectHandler.
+ BOOST_ASIO_COMPOSED_CONNECT_HANDLER_CHECK(
+ ComposedConnectHandler, handler, Iterator) type_check;
+
+ detail::async_result_init<ComposedConnectHandler,
+ void (boost::system::error_code, Iterator)> init(
+ BOOST_ASIO_MOVE_CAST(ComposedConnectHandler)(handler));
+
+ detail::connect_op<Protocol, SocketService, Iterator,
+ detail::default_connect_condition, BOOST_ASIO_HANDLER_TYPE(
+ ComposedConnectHandler, void (boost::system::error_code, Iterator))>(s,
+ begin, Iterator(), detail::default_connect_condition(), init.handler)(
+ boost::system::error_code(), 1);
+
+ return init.result.get();
+}
+
+template <typename Protocol, typename SocketService,
+ typename Iterator, typename ComposedConnectHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ComposedConnectHandler,
+ void (boost::system::error_code, Iterator))
+async_connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end,
+ BOOST_ASIO_MOVE_ARG(ComposedConnectHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ComposedConnectHandler.
+ BOOST_ASIO_COMPOSED_CONNECT_HANDLER_CHECK(
+ ComposedConnectHandler, handler, Iterator) type_check;
+
+ detail::async_result_init<ComposedConnectHandler,
+ void (boost::system::error_code, Iterator)> init(
+ BOOST_ASIO_MOVE_CAST(ComposedConnectHandler)(handler));
+
+ detail::connect_op<Protocol, SocketService, Iterator,
+ detail::default_connect_condition, BOOST_ASIO_HANDLER_TYPE(
+ ComposedConnectHandler, void (boost::system::error_code, Iterator))>(s,
+ begin, end, detail::default_connect_condition(), init.handler)(
+ boost::system::error_code(), 1);
+
+ return init.result.get();
+}
+
+template <typename Protocol, typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ComposedConnectHandler,
+ void (boost::system::error_code, Iterator))
+async_connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, ConnectCondition connect_condition,
+ BOOST_ASIO_MOVE_ARG(ComposedConnectHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ComposedConnectHandler.
+ BOOST_ASIO_COMPOSED_CONNECT_HANDLER_CHECK(
+ ComposedConnectHandler, handler, Iterator) type_check;
+
+ detail::async_result_init<ComposedConnectHandler,
+ void (boost::system::error_code, Iterator)> init(
+ BOOST_ASIO_MOVE_CAST(ComposedConnectHandler)(handler));
+
+ detail::connect_op<Protocol, SocketService, Iterator,
+ ConnectCondition, BOOST_ASIO_HANDLER_TYPE(
+ ComposedConnectHandler, void (boost::system::error_code, Iterator))>(s,
+ begin, Iterator(), connect_condition, init.handler)(
+ boost::system::error_code(), 1);
+
+ return init.result.get();
+}
+
+template <typename Protocol, typename SocketService, typename Iterator,
+ typename ConnectCondition, typename ComposedConnectHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ComposedConnectHandler,
+ void (boost::system::error_code, Iterator))
+async_connect(basic_socket<Protocol, SocketService>& s,
+ Iterator begin, Iterator end, ConnectCondition connect_condition,
+ BOOST_ASIO_MOVE_ARG(ComposedConnectHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ComposedConnectHandler.
+ BOOST_ASIO_COMPOSED_CONNECT_HANDLER_CHECK(
+ ComposedConnectHandler, handler, Iterator) type_check;
+
+ detail::async_result_init<ComposedConnectHandler,
+ void (boost::system::error_code, Iterator)> init(
+ BOOST_ASIO_MOVE_CAST(ComposedConnectHandler)(handler));
+
+ detail::connect_op<Protocol, SocketService, Iterator,
+ ConnectCondition, BOOST_ASIO_HANDLER_TYPE(
+ ComposedConnectHandler, void (boost::system::error_code, Iterator))>(s,
+ begin, end, connect_condition, init.handler)(
+ boost::system::error_code(), 1);
+
+ return init.result.get();
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_CONNECT_HPP
diff --git a/ext/patches/boost/asio/impl/error.ipp b/ext/patches/boost/asio/impl/error.ipp
new file mode 100644
index 0000000..9b020d9
--- /dev/null
+++ b/ext/patches/boost/asio/impl/error.ipp
@@ -0,0 +1,130 @@
+//
+// impl/error.ipp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_ERROR_IPP
+#define BOOST_ASIO_IMPL_ERROR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace error {
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+namespace detail {
+
+class netdb_category : public boost::system::error_category
+{
+public:
+ const char* name() const BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT
+ {
+ return "asio.netdb";
+ }
+
+ std::string message(int value) const
+ {
+ if (value == error::host_not_found)
+ return "Host not found (authoritative)";
+ if (value == error::host_not_found_try_again)
+ return "Host not found (non-authoritative), try again later";
+ if (value == error::no_data)
+ return "The query is valid, but it does not have associated data";
+ if (value == error::no_recovery)
+ return "A non-recoverable error occurred during database lookup";
+ return "asio.netdb error";
+ }
+};
+
+} // namespace detail
+
+const boost::system::error_category& get_netdb_category()
+{
+ static detail::netdb_category instance;
+ return instance;
+}
+
+namespace detail {
+
+class addrinfo_category : public boost::system::error_category
+{
+public:
+ const char* name() const BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT
+ {
+ return "asio.addrinfo";
+ }
+
+ std::string message(int value) const
+ {
+ if (value == error::service_not_found)
+ return "Service not found";
+ if (value == error::socket_type_not_supported)
+ return "Socket type not supported";
+ return "asio.addrinfo error";
+ }
+};
+
+} // namespace detail
+
+const boost::system::error_category& get_addrinfo_category()
+{
+ static detail::addrinfo_category instance;
+ return instance;
+}
+
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+namespace detail {
+
+class misc_category : public boost::system::error_category
+{
+public:
+ const char* name() const BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT
+ {
+ return "asio.misc";
+ }
+
+ std::string message(int value) const
+ {
+ if (value == error::already_open)
+ return "Already open";
+ if (value == error::eof)
+ return "End of file";
+ if (value == error::not_found)
+ return "Element not found";
+ if (value == error::fd_set_failure)
+ return "The descriptor does not fit into the select call's fd_set";
+ return "asio.misc error";
+ }
+};
+
+} // namespace detail
+
+const boost::system::error_category& get_misc_category()
+{
+ static detail::misc_category instance;
+ return instance;
+}
+
+} // namespace error
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_ERROR_IPP
diff --git a/ext/patches/boost/asio/impl/handler_alloc_hook.ipp b/ext/patches/boost/asio/impl/handler_alloc_hook.ipp
new file mode 100644
index 0000000..def2406
--- /dev/null
+++ b/ext/patches/boost/asio/impl/handler_alloc_hook.ipp
@@ -0,0 +1,79 @@
+//
+// impl/handler_alloc_hook.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_HANDLER_ALLOC_HOOK_IPP
+#define BOOST_ASIO_IMPL_HANDLER_ALLOC_HOOK_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/call_stack.hpp>
+#include <boost/asio/handler_alloc_hook.hpp>
+
+#if !defined(BOOST_ASIO_DISABLE_SMALL_BLOCK_RECYCLING)
+# if defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_thread_info.hpp>
+# else // defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/task_io_service_thread_info.hpp>
+# endif // defined(BOOST_ASIO_HAS_IOCP)
+#endif // !defined(BOOST_ASIO_DISABLE_SMALL_BLOCK_RECYCLING)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+namespace detail { class win_iocp_io_service; }
+#endif // defined(BOOST_ASIO_HAS_IOCP)
+
+void* asio_handler_allocate(std::size_t size, ...)
+{
+#if !defined(BOOST_ASIO_DISABLE_SMALL_BLOCK_RECYCLING)
+# if defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::win_iocp_io_service io_service_impl;
+ typedef detail::win_iocp_thread_info thread_info;
+# else // defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::task_io_service io_service_impl;
+ typedef detail::task_io_service_thread_info thread_info;
+# endif // defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::call_stack<io_service_impl, thread_info> call_stack;
+ return thread_info::allocate(call_stack::top(), size);
+#else // !defined(BOOST_ASIO_DISABLE_SMALL_BLOCK_RECYCLING)
+ return ::operator new(size);
+#endif // !defined(BOOST_ASIO_DISABLE_SMALL_BLOCK_RECYCLING)
+}
+
+void asio_handler_deallocate(void* pointer, std::size_t size, ...)
+{
+#if !defined(BOOST_ASIO_DISABLE_SMALL_BLOCK_RECYCLING)
+# if defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::win_iocp_io_service io_service_impl;
+ typedef detail::win_iocp_thread_info thread_info;
+# else // defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::task_io_service io_service_impl;
+ typedef detail::task_io_service_thread_info thread_info;
+# endif // defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::call_stack<io_service_impl, thread_info> call_stack;
+ thread_info::deallocate(call_stack::top(), pointer, size);
+#else // !defined(BOOST_ASIO_DISABLE_SMALL_BLOCK_RECYCLING)
+ (void)size;
+ ::operator delete(pointer);
+#endif // !defined(BOOST_ASIO_DISABLE_SMALL_BLOCK_RECYCLING)
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_HANDLER_ALLOC_HOOK_IPP
diff --git a/ext/patches/boost/asio/impl/io_service.hpp b/ext/patches/boost/asio/impl/io_service.hpp
new file mode 100644
index 0000000..bc87820
--- /dev/null
+++ b/ext/patches/boost/asio/impl/io_service.hpp
@@ -0,0 +1,156 @@
+//
+// impl/io_service.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_IO_SERVICE_HPP
+#define BOOST_ASIO_IMPL_IO_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/service_registry.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename Service>
+inline Service& use_service(io_service& ios)
+{
+ // Check that Service meets the necessary type requirements.
+ (void)static_cast<io_service::service*>(static_cast<Service*>(0));
+ (void)static_cast<const io_service::id*>(&Service::id);
+
+ return ios.service_registry_->template use_service<Service>();
+}
+
+template <>
+inline detail::io_service_impl& use_service<detail::io_service_impl>(
+ io_service& ios)
+{
+ return ios.impl_;
+}
+
+template <typename Service>
+inline void add_service(io_service& ios, Service* svc)
+{
+ // Check that Service meets the necessary type requirements.
+ (void)static_cast<io_service::service*>(static_cast<Service*>(0));
+ (void)static_cast<const io_service::id*>(&Service::id);
+
+ ios.service_registry_->template add_service<Service>(svc);
+}
+
+template <typename Service>
+inline bool has_service(io_service& ios)
+{
+ // Check that Service meets the necessary type requirements.
+ (void)static_cast<io_service::service*>(static_cast<Service*>(0));
+ (void)static_cast<const io_service::id*>(&Service::id);
+
+ return ios.service_registry_->template has_service<Service>();
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_io_service.hpp>
+#else
+# include <boost/asio/detail/task_io_service.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename CompletionHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(CompletionHandler, void ())
+io_service::dispatch(BOOST_ASIO_MOVE_ARG(CompletionHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a CompletionHandler.
+ BOOST_ASIO_COMPLETION_HANDLER_CHECK(CompletionHandler, handler) type_check;
+
+ detail::async_result_init<
+ CompletionHandler, void ()> init(
+ BOOST_ASIO_MOVE_CAST(CompletionHandler)(handler));
+
+ impl_.dispatch(init.handler);
+
+ return init.result.get();
+}
+
+template <typename CompletionHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(CompletionHandler, void ())
+io_service::post(BOOST_ASIO_MOVE_ARG(CompletionHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a CompletionHandler.
+ BOOST_ASIO_COMPLETION_HANDLER_CHECK(CompletionHandler, handler) type_check;
+
+ detail::async_result_init<
+ CompletionHandler, void ()> init(
+ BOOST_ASIO_MOVE_CAST(CompletionHandler)(handler));
+
+ impl_.post(init.handler);
+
+ return init.result.get();
+}
+
+template <typename Handler>
+#if defined(GENERATING_DOCUMENTATION)
+unspecified
+#else
+inline detail::wrapped_handler<io_service&, Handler>
+#endif
+io_service::wrap(Handler handler)
+{
+ return detail::wrapped_handler<io_service&, Handler>(*this, handler);
+}
+
+inline io_service::work::work(boost::asio::io_service& io_service)
+ : io_service_impl_(io_service.impl_)
+{
+ io_service_impl_.work_started();
+}
+
+inline io_service::work::work(const work& other)
+ : io_service_impl_(other.io_service_impl_)
+{
+ io_service_impl_.work_started();
+}
+
+inline io_service::work::~work()
+{
+ io_service_impl_.work_finished();
+}
+
+inline boost::asio::io_service& io_service::work::get_io_service()
+{
+ return io_service_impl_.get_io_service();
+}
+
+inline boost::asio::io_service& io_service::service::get_io_service()
+{
+ return owner_;
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_IO_SERVICE_HPP
diff --git a/ext/patches/boost/asio/impl/io_service.ipp b/ext/patches/boost/asio/impl/io_service.ipp
new file mode 100644
index 0000000..814d031
--- /dev/null
+++ b/ext/patches/boost/asio/impl/io_service.ipp
@@ -0,0 +1,157 @@
+//
+// impl/io_service.ipp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_IO_SERVICE_IPP
+#define BOOST_ASIO_IMPL_IO_SERVICE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/scoped_ptr.hpp>
+#include <boost/asio/detail/service_registry.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+
+#if defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_io_service.hpp>
+#else
+# include <boost/asio/detail/task_io_service.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+io_service::io_service()
+ : service_registry_(new boost::asio::detail::service_registry(
+ *this, static_cast<impl_type*>(0),
+ (std::numeric_limits<std::size_t>::max)())),
+ impl_(service_registry_->first_service<impl_type>())
+{
+}
+
+io_service::io_service(std::size_t concurrency_hint)
+ : service_registry_(new boost::asio::detail::service_registry(
+ *this, static_cast<impl_type*>(0), concurrency_hint)),
+ impl_(service_registry_->first_service<impl_type>())
+{
+}
+
+io_service::~io_service()
+{
+ delete service_registry_;
+}
+
+std::size_t io_service::run()
+{
+ boost::system::error_code ec;
+ std::size_t s = impl_.run(ec);
+ boost::asio::detail::throw_error(ec);
+ return s;
+}
+
+std::size_t io_service::run(boost::system::error_code& ec)
+{
+ return impl_.run(ec);
+}
+
+std::size_t io_service::run_one()
+{
+ boost::system::error_code ec;
+ std::size_t s = impl_.run_one(ec);
+ boost::asio::detail::throw_error(ec);
+ return s;
+}
+
+std::size_t io_service::run_one(boost::system::error_code& ec)
+{
+ return impl_.run_one(ec);
+}
+
+std::size_t io_service::poll()
+{
+ boost::system::error_code ec;
+ std::size_t s = impl_.poll(ec);
+ boost::asio::detail::throw_error(ec);
+ return s;
+}
+
+std::size_t io_service::poll(boost::system::error_code& ec)
+{
+ return impl_.poll(ec);
+}
+
+std::size_t io_service::poll_one()
+{
+ boost::system::error_code ec;
+ std::size_t s = impl_.poll_one(ec);
+ boost::asio::detail::throw_error(ec);
+ return s;
+}
+
+std::size_t io_service::poll_one(boost::system::error_code& ec)
+{
+ return impl_.poll_one(ec);
+}
+
+void io_service::stop()
+{
+ impl_.stop();
+}
+
+bool io_service::stopped() const
+{
+ return impl_.stopped();
+}
+
+void io_service::reset()
+{
+ impl_.reset();
+}
+
+void io_service::notify_fork(boost::asio::io_service::fork_event event)
+{
+ service_registry_->notify_fork(event);
+}
+
+io_service::service::service(boost::asio::io_service& owner)
+ : owner_(owner),
+ next_(0)
+{
+}
+
+io_service::service::~service()
+{
+}
+
+void io_service::service::fork_service(boost::asio::io_service::fork_event)
+{
+}
+
+service_already_exists::service_already_exists()
+ : std::logic_error("Service already exists.")
+{
+}
+
+invalid_service_owner::invalid_service_owner()
+ : std::logic_error("Invalid service owner.")
+{
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_IO_SERVICE_IPP
diff --git a/ext/patches/boost/asio/impl/read.hpp b/ext/patches/boost/asio/impl/read.hpp
new file mode 100644
index 0000000..b740028
--- /dev/null
+++ b/ext/patches/boost/asio/impl/read.hpp
@@ -0,0 +1,755 @@
+//
+// impl/read.hpp
+// ~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_READ_HPP
+#define BOOST_ASIO_IMPL_READ_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <algorithm>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/completion_condition.hpp>
+#include <boost/asio/detail/array_fwd.hpp>
+#include <boost/asio/detail/base_from_completion_cond.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/consuming_buffers.hpp>
+#include <boost/asio/detail/dependent_type.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename SyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition>
+std::size_t read(SyncReadStream& s, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ boost::asio::detail::consuming_buffers<
+ mutable_buffer, MutableBufferSequence> tmp(buffers);
+ std::size_t total_transferred = 0;
+ tmp.prepare(detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred)));
+ while (tmp.begin() != tmp.end())
+ {
+ std::size_t bytes_transferred = s.read_some(tmp, ec);
+ tmp.consume(bytes_transferred);
+ total_transferred += bytes_transferred;
+ tmp.prepare(detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred)));
+ }
+ return total_transferred;
+}
+
+template <typename SyncReadStream, typename MutableBufferSequence>
+inline std::size_t read(SyncReadStream& s, const MutableBufferSequence& buffers)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read(s, buffers, transfer_all(), ec);
+ boost::asio::detail::throw_error(ec, "read");
+ return bytes_transferred;
+}
+
+template <typename SyncReadStream, typename MutableBufferSequence>
+inline std::size_t read(SyncReadStream& s, const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+{
+ return read(s, buffers, transfer_all(), ec);
+}
+
+template <typename SyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition>
+inline std::size_t read(SyncReadStream& s, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read(s, buffers, completion_condition, ec);
+ boost::asio::detail::throw_error(ec, "read");
+ return bytes_transferred;
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+template <typename SyncReadStream, typename Allocator,
+ typename CompletionCondition>
+std::size_t read(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ std::size_t total_transferred = 0;
+ std::size_t max_size = detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred));
+ std::size_t bytes_available = read_size_helper(b, max_size);
+ while (bytes_available > 0)
+ {
+ std::size_t bytes_transferred = s.read_some(b.prepare(bytes_available), ec);
+ b.commit(bytes_transferred);
+ total_transferred += bytes_transferred;
+ max_size = detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred));
+ bytes_available = read_size_helper(b, max_size);
+ }
+ return total_transferred;
+}
+
+template <typename SyncReadStream, typename Allocator>
+inline std::size_t read(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read(s, b, transfer_all(), ec);
+ boost::asio::detail::throw_error(ec, "read");
+ return bytes_transferred;
+}
+
+template <typename SyncReadStream, typename Allocator>
+inline std::size_t read(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ boost::system::error_code& ec)
+{
+ return read(s, b, transfer_all(), ec);
+}
+
+template <typename SyncReadStream, typename Allocator,
+ typename CompletionCondition>
+inline std::size_t read(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read(s, b, completion_condition, ec);
+ boost::asio::detail::throw_error(ec, "read");
+ return bytes_transferred;
+}
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+namespace detail
+{
+ template <typename AsyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition, typename ReadHandler>
+ class read_op
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_op(AsyncReadStream& stream, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_op(const read_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_op(read_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ switch (start_ = start)
+ {
+ case 1:
+ buffers_.prepare(this->check_for_completion(ec, total_transferred_));
+ for (;;)
+ {
+ stream_.async_read_some(buffers_,
+ BOOST_ASIO_MOVE_CAST(read_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ buffers_.consume(bytes_transferred);
+ buffers_.prepare(this->check_for_completion(ec, total_transferred_));
+ if ((!ec && bytes_transferred == 0)
+ || buffers_.begin() == buffers_.end())
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ boost::asio::detail::consuming_buffers<
+ mutable_buffer, MutableBufferSequence> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncReadStream,
+ typename CompletionCondition, typename ReadHandler>
+ class read_op<AsyncReadStream, boost::asio::mutable_buffers_1,
+ CompletionCondition, ReadHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_op(AsyncReadStream& stream,
+ const boost::asio::mutable_buffers_1& buffers,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffer_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_op(const read_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_op(read_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ stream_.async_read_some(
+ boost::asio::buffer(buffer_ + total_transferred_, n),
+ BOOST_ASIO_MOVE_CAST(read_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == boost::asio::buffer_size(buffer_))
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ boost::asio::mutable_buffer buffer_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncReadStream, typename Elem,
+ typename CompletionCondition, typename ReadHandler>
+ class read_op<AsyncReadStream, boost::array<Elem, 2>,
+ CompletionCondition, ReadHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_op(AsyncReadStream& stream, const boost::array<Elem, 2>& buffers,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_op(const read_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_op(read_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ typename boost::asio::detail::dependent_type<Elem,
+ boost::array<boost::asio::mutable_buffer, 2> >::type bufs = {{
+ boost::asio::mutable_buffer(buffers_[0]),
+ boost::asio::mutable_buffer(buffers_[1]) }};
+ std::size_t buffer_size0 = boost::asio::buffer_size(bufs[0]);
+ std::size_t buffer_size1 = boost::asio::buffer_size(bufs[1]);
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ bufs[0] = boost::asio::buffer(bufs[0] + total_transferred_, n);
+ bufs[1] = boost::asio::buffer(
+ bufs[1] + (total_transferred_ < buffer_size0
+ ? 0 : total_transferred_ - buffer_size0),
+ n - boost::asio::buffer_size(bufs[0]));
+ stream_.async_read_some(bufs, BOOST_ASIO_MOVE_CAST(read_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == buffer_size0 + buffer_size1)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ boost::array<Elem, 2> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+ template <typename AsyncReadStream, typename Elem,
+ typename CompletionCondition, typename ReadHandler>
+ class read_op<AsyncReadStream, std::array<Elem, 2>,
+ CompletionCondition, ReadHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_op(AsyncReadStream& stream, const std::array<Elem, 2>& buffers,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_op(const read_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_op(read_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ typename boost::asio::detail::dependent_type<Elem,
+ std::array<boost::asio::mutable_buffer, 2> >::type bufs = {{
+ boost::asio::mutable_buffer(buffers_[0]),
+ boost::asio::mutable_buffer(buffers_[1]) }};
+ std::size_t buffer_size0 = boost::asio::buffer_size(bufs[0]);
+ std::size_t buffer_size1 = boost::asio::buffer_size(bufs[1]);
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ bufs[0] = boost::asio::buffer(bufs[0] + total_transferred_, n);
+ bufs[1] = boost::asio::buffer(
+ bufs[1] + (total_transferred_ < buffer_size0
+ ? 0 : total_transferred_ - buffer_size0),
+ n - boost::asio::buffer_size(bufs[0]));
+ stream_.async_read_some(bufs, BOOST_ASIO_MOVE_CAST(read_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == buffer_size0 + buffer_size1)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ std::array<Elem, 2> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+ template <typename AsyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition, typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ read_op<AsyncReadStream, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition, typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ read_op<AsyncReadStream, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition, typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ read_op<AsyncReadStream, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ read_op<AsyncReadStream, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ read_op<AsyncReadStream, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition, typename ReadHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read(AsyncReadStream& s, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_op<AsyncReadStream, MutableBufferSequence,
+ CompletionCondition, BOOST_ASIO_HANDLER_TYPE(
+ ReadHandler, void (boost::system::error_code, std::size_t))>(
+ s, buffers, completion_condition, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+template <typename AsyncReadStream, typename MutableBufferSequence,
+ typename ReadHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read(AsyncReadStream& s, const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_op<AsyncReadStream, MutableBufferSequence,
+ detail::transfer_all_t, BOOST_ASIO_HANDLER_TYPE(
+ ReadHandler, void (boost::system::error_code, std::size_t))>(
+ s, buffers, transfer_all(), init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+namespace detail
+{
+ template <typename AsyncReadStream, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+ class read_streambuf_op
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_streambuf_op(AsyncReadStream& stream,
+ basic_streambuf<Allocator>& streambuf,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ streambuf_(streambuf),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_streambuf_op(const read_streambuf_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_streambuf_op(read_streambuf_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ std::size_t max_size, bytes_available;
+ switch (start_ = start)
+ {
+ case 1:
+ max_size = this->check_for_completion(ec, total_transferred_);
+ bytes_available = read_size_helper(streambuf_, max_size);
+ for (;;)
+ {
+ stream_.async_read_some(streambuf_.prepare(bytes_available),
+ BOOST_ASIO_MOVE_CAST(read_streambuf_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ streambuf_.commit(bytes_transferred);
+ max_size = this->check_for_completion(ec, total_transferred_);
+ bytes_available = read_size_helper(streambuf_, max_size);
+ if ((!ec && bytes_transferred == 0) || bytes_available == 0)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ boost::asio::basic_streambuf<Allocator>& streambuf_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ read_streambuf_op<AsyncReadStream, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ read_streambuf_op<AsyncReadStream, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ read_streambuf_op<AsyncReadStream, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream,
+ typename Allocator, typename CompletionCondition, typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ read_streambuf_op<AsyncReadStream, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream,
+ typename Allocator, typename CompletionCondition, typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ read_streambuf_op<AsyncReadStream, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncReadStream, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_streambuf_op<AsyncReadStream, Allocator,
+ CompletionCondition, BOOST_ASIO_HANDLER_TYPE(
+ ReadHandler, void (boost::system::error_code, std::size_t))>(
+ s, b, completion_condition, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_streambuf_op<AsyncReadStream, Allocator,
+ detail::transfer_all_t, BOOST_ASIO_HANDLER_TYPE(
+ ReadHandler, void (boost::system::error_code, std::size_t))>(
+ s, b, transfer_all(), init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_READ_HPP
diff --git a/ext/patches/boost/asio/impl/read_at.hpp b/ext/patches/boost/asio/impl/read_at.hpp
new file mode 100644
index 0000000..03fcf18
--- /dev/null
+++ b/ext/patches/boost/asio/impl/read_at.hpp
@@ -0,0 +1,812 @@
+//
+// impl/read_at.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_READ_AT_HPP
+#define BOOST_ASIO_IMPL_READ_AT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <algorithm>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/completion_condition.hpp>
+#include <boost/asio/detail/array_fwd.hpp>
+#include <boost/asio/detail/base_from_completion_cond.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/consuming_buffers.hpp>
+#include <boost/asio/detail/dependent_type.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename SyncRandomAccessReadDevice, typename MutableBufferSequence,
+ typename CompletionCondition>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ boost::asio::detail::consuming_buffers<
+ mutable_buffer, MutableBufferSequence> tmp(buffers);
+ std::size_t total_transferred = 0;
+ tmp.prepare(detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred)));
+ while (tmp.begin() != tmp.end())
+ {
+ std::size_t bytes_transferred = d.read_some_at(
+ offset + total_transferred, tmp, ec);
+ tmp.consume(bytes_transferred);
+ total_transferred += bytes_transferred;
+ tmp.prepare(detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred)));
+ }
+ return total_transferred;
+}
+
+template <typename SyncRandomAccessReadDevice, typename MutableBufferSequence>
+inline std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read_at(
+ d, offset, buffers, transfer_all(), ec);
+ boost::asio::detail::throw_error(ec, "read_at");
+ return bytes_transferred;
+}
+
+template <typename SyncRandomAccessReadDevice, typename MutableBufferSequence>
+inline std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+{
+ return read_at(d, offset, buffers, transfer_all(), ec);
+}
+
+template <typename SyncRandomAccessReadDevice, typename MutableBufferSequence,
+ typename CompletionCondition>
+inline std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read_at(
+ d, offset, buffers, completion_condition, ec);
+ boost::asio::detail::throw_error(ec, "read_at");
+ return bytes_transferred;
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+template <typename SyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ std::size_t total_transferred = 0;
+ std::size_t max_size = detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred));
+ std::size_t bytes_available = read_size_helper(b, max_size);
+ while (bytes_available > 0)
+ {
+ std::size_t bytes_transferred = d.read_some_at(
+ offset + total_transferred, b.prepare(bytes_available), ec);
+ b.commit(bytes_transferred);
+ total_transferred += bytes_transferred;
+ max_size = detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred));
+ bytes_available = read_size_helper(b, max_size);
+ }
+ return total_transferred;
+}
+
+template <typename SyncRandomAccessReadDevice, typename Allocator>
+inline std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read_at(
+ d, offset, b, transfer_all(), ec);
+ boost::asio::detail::throw_error(ec, "read_at");
+ return bytes_transferred;
+}
+
+template <typename SyncRandomAccessReadDevice, typename Allocator>
+inline std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ boost::system::error_code& ec)
+{
+ return read_at(d, offset, b, transfer_all(), ec);
+}
+
+template <typename SyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition>
+inline std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read_at(
+ d, offset, b, completion_condition, ec);
+ boost::asio::detail::throw_error(ec, "read_at");
+ return bytes_transferred;
+}
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+namespace detail
+{
+ template <typename AsyncRandomAccessReadDevice,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ class read_at_op
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_at_op(AsyncRandomAccessReadDevice& device,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_at_op(const read_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_at_op(read_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ switch (start_ = start)
+ {
+ case 1:
+ buffers_.prepare(this->check_for_completion(ec, total_transferred_));
+ for (;;)
+ {
+ device_.async_read_some_at(offset_ + total_transferred_,
+ buffers_, BOOST_ASIO_MOVE_CAST(read_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ buffers_.consume(bytes_transferred);
+ buffers_.prepare(this->check_for_completion(ec, total_transferred_));
+ if ((!ec && bytes_transferred == 0)
+ || buffers_.begin() == buffers_.end())
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessReadDevice& device_;
+ uint64_t offset_;
+ boost::asio::detail::consuming_buffers<
+ mutable_buffer, MutableBufferSequence> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncRandomAccessReadDevice,
+ typename CompletionCondition, typename ReadHandler>
+ class read_at_op<AsyncRandomAccessReadDevice,
+ boost::asio::mutable_buffers_1, CompletionCondition, ReadHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_at_op(AsyncRandomAccessReadDevice& device,
+ uint64_t offset, const boost::asio::mutable_buffers_1& buffers,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffer_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_at_op(const read_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_at_op(read_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ device_.async_read_some_at(offset_ + total_transferred_,
+ boost::asio::buffer(buffer_ + total_transferred_, n),
+ BOOST_ASIO_MOVE_CAST(read_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == boost::asio::buffer_size(buffer_))
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessReadDevice& device_;
+ uint64_t offset_;
+ boost::asio::mutable_buffer buffer_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncRandomAccessReadDevice, typename Elem,
+ typename CompletionCondition, typename ReadHandler>
+ class read_at_op<AsyncRandomAccessReadDevice, boost::array<Elem, 2>,
+ CompletionCondition, ReadHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_at_op(AsyncRandomAccessReadDevice& device,
+ uint64_t offset, const boost::array<Elem, 2>& buffers,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_at_op(const read_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_at_op(read_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ typename boost::asio::detail::dependent_type<Elem,
+ boost::array<boost::asio::mutable_buffer, 2> >::type bufs = {{
+ boost::asio::mutable_buffer(buffers_[0]),
+ boost::asio::mutable_buffer(buffers_[1]) }};
+ std::size_t buffer_size0 = boost::asio::buffer_size(bufs[0]);
+ std::size_t buffer_size1 = boost::asio::buffer_size(bufs[1]);
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ bufs[0] = boost::asio::buffer(bufs[0] + total_transferred_, n);
+ bufs[1] = boost::asio::buffer(
+ bufs[1] + (total_transferred_ < buffer_size0
+ ? 0 : total_transferred_ - buffer_size0),
+ n - boost::asio::buffer_size(bufs[0]));
+ device_.async_read_some_at(offset_ + total_transferred_,
+ bufs, BOOST_ASIO_MOVE_CAST(read_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == buffer_size0 + buffer_size1)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessReadDevice& device_;
+ uint64_t offset_;
+ boost::array<Elem, 2> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+ template <typename AsyncRandomAccessReadDevice, typename Elem,
+ typename CompletionCondition, typename ReadHandler>
+ class read_at_op<AsyncRandomAccessReadDevice, std::array<Elem, 2>,
+ CompletionCondition, ReadHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_at_op(AsyncRandomAccessReadDevice& device,
+ uint64_t offset, const std::array<Elem, 2>& buffers,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_at_op(const read_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_at_op(read_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ typename boost::asio::detail::dependent_type<Elem,
+ std::array<boost::asio::mutable_buffer, 2> >::type bufs = {{
+ boost::asio::mutable_buffer(buffers_[0]),
+ boost::asio::mutable_buffer(buffers_[1]) }};
+ std::size_t buffer_size0 = boost::asio::buffer_size(bufs[0]);
+ std::size_t buffer_size1 = boost::asio::buffer_size(bufs[1]);
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ bufs[0] = boost::asio::buffer(bufs[0] + total_transferred_, n);
+ bufs[1] = boost::asio::buffer(
+ bufs[1] + (total_transferred_ < buffer_size0
+ ? 0 : total_transferred_ - buffer_size0),
+ n - boost::asio::buffer_size(bufs[0]));
+ device_.async_read_some_at(offset_ + total_transferred_,
+ bufs, BOOST_ASIO_MOVE_CAST(read_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == buffer_size0 + buffer_size1)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessReadDevice& device_;
+ uint64_t offset_;
+ std::array<Elem, 2> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+ template <typename AsyncRandomAccessReadDevice,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ read_at_op<AsyncRandomAccessReadDevice, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncRandomAccessReadDevice,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ read_at_op<AsyncRandomAccessReadDevice, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncRandomAccessReadDevice,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ read_at_op<AsyncRandomAccessReadDevice, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncRandomAccessReadDevice,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ read_at_op<AsyncRandomAccessReadDevice, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncRandomAccessReadDevice,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ read_at_op<AsyncRandomAccessReadDevice, MutableBufferSequence,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename AsyncRandomAccessReadDevice,
+ typename MutableBufferSequence, typename CompletionCondition,
+ typename ReadHandler>
+ inline read_at_op<AsyncRandomAccessReadDevice,
+ MutableBufferSequence, CompletionCondition, ReadHandler>
+ make_read_at_op(AsyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition, ReadHandler handler)
+ {
+ return read_at_op<AsyncRandomAccessReadDevice,
+ MutableBufferSequence, CompletionCondition, ReadHandler>(
+ d, offset, buffers, completion_condition, handler);
+ }
+} // namespace detail
+
+template <typename AsyncRandomAccessReadDevice, typename MutableBufferSequence,
+ typename CompletionCondition, typename ReadHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_at(AsyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_at_op<AsyncRandomAccessReadDevice, MutableBufferSequence,
+ CompletionCondition, BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))>(
+ d, offset, buffers, completion_condition, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+template <typename AsyncRandomAccessReadDevice, typename MutableBufferSequence,
+ typename ReadHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_at(AsyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_at_op<AsyncRandomAccessReadDevice, MutableBufferSequence,
+ detail::transfer_all_t, BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))>(
+ d, offset, buffers, transfer_all(), init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+namespace detail
+{
+ template <typename AsyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+ class read_at_streambuf_op
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ read_at_streambuf_op(AsyncRandomAccessReadDevice& device,
+ uint64_t offset, basic_streambuf<Allocator>& streambuf,
+ CompletionCondition completion_condition, ReadHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ streambuf_(streambuf),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_at_streambuf_op(const read_at_streambuf_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ streambuf_(other.streambuf_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_at_streambuf_op(read_at_streambuf_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ streambuf_(other.streambuf_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ std::size_t max_size, bytes_available;
+ switch (start_ = start)
+ {
+ case 1:
+ max_size = this->check_for_completion(ec, total_transferred_);
+ bytes_available = read_size_helper(streambuf_, max_size);
+ for (;;)
+ {
+ device_.async_read_some_at(offset_ + total_transferred_,
+ streambuf_.prepare(bytes_available),
+ BOOST_ASIO_MOVE_CAST(read_at_streambuf_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ streambuf_.commit(bytes_transferred);
+ max_size = this->check_for_completion(ec, total_transferred_);
+ bytes_available = read_size_helper(streambuf_, max_size);
+ if ((!ec && bytes_transferred == 0) || bytes_available == 0)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessReadDevice& device_;
+ uint64_t offset_;
+ boost::asio::basic_streambuf<Allocator>& streambuf_;
+ int start_;
+ std::size_t total_transferred_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ read_at_streambuf_op<AsyncRandomAccessReadDevice, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ read_at_streambuf_op<AsyncRandomAccessReadDevice, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ read_at_streambuf_op<AsyncRandomAccessReadDevice, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncRandomAccessReadDevice,
+ typename Allocator, typename CompletionCondition, typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ read_at_streambuf_op<AsyncRandomAccessReadDevice, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncRandomAccessReadDevice,
+ typename Allocator, typename CompletionCondition, typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ read_at_streambuf_op<AsyncRandomAccessReadDevice, Allocator,
+ CompletionCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_at(AsyncRandomAccessReadDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_at_streambuf_op<AsyncRandomAccessReadDevice, Allocator,
+ CompletionCondition, BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))>(
+ d, offset, b, completion_condition, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+template <typename AsyncRandomAccessReadDevice, typename Allocator,
+ typename ReadHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_at(AsyncRandomAccessReadDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_at_streambuf_op<AsyncRandomAccessReadDevice, Allocator,
+ detail::transfer_all_t, BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))>(
+ d, offset, b, transfer_all(), init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_READ_AT_HPP
diff --git a/ext/patches/boost/asio/impl/read_until.hpp b/ext/patches/boost/asio/impl/read_until.hpp
new file mode 100644
index 0000000..3bf7b77
--- /dev/null
+++ b/ext/patches/boost/asio/impl/read_until.hpp
@@ -0,0 +1,1149 @@
+//
+// impl/read_until.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_READ_UNTIL_HPP
+#define BOOST_ASIO_IMPL_READ_UNTIL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <algorithm>
+#include <string>
+#include <vector>
+#include <utility>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/buffers_iterator.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/limits.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename SyncReadStream, typename Allocator>
+inline std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, char delim)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read_until(s, b, delim, ec);
+ boost::asio::detail::throw_error(ec, "read_until");
+ return bytes_transferred;
+}
+
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, char delim,
+ boost::system::error_code& ec)
+{
+ std::size_t search_position = 0;
+ for (;;)
+ {
+ // Determine the range of the data to be searched.
+ typedef typename boost::asio::basic_streambuf<
+ Allocator>::const_buffers_type const_buffers_type;
+ typedef boost::asio::buffers_iterator<const_buffers_type> iterator;
+ const_buffers_type buffers = b.data();
+ iterator begin = iterator::begin(buffers);
+ iterator start_pos = begin + search_position;
+ iterator end = iterator::end(buffers);
+
+ // Look for a match.
+ iterator iter = std::find(start_pos, end, delim);
+ if (iter != end)
+ {
+ // Found a match. We're done.
+ ec = boost::system::error_code();
+ return iter - begin + 1;
+ }
+ else
+ {
+ // No match. Next search can start with the new data.
+ search_position = end - begin;
+ }
+
+ // Check if buffer is full.
+ if (b.size() == b.max_size())
+ {
+ ec = error::not_found;
+ return 0;
+ }
+
+ // Need more data.
+ std::size_t bytes_to_read = read_size_helper(b, 65536);
+ b.commit(s.read_some(b.prepare(bytes_to_read), ec));
+ if (ec)
+ return 0;
+ }
+}
+
+template <typename SyncReadStream, typename Allocator>
+inline std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const std::string& delim)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read_until(s, b, delim, ec);
+ boost::asio::detail::throw_error(ec, "read_until");
+ return bytes_transferred;
+}
+
+namespace detail
+{
+ // Algorithm that finds a subsequence of equal values in a sequence. Returns
+ // (iterator,true) if a full match was found, in which case the iterator
+ // points to the beginning of the match. Returns (iterator,false) if a
+ // partial match was found at the end of the first sequence, in which case
+ // the iterator points to the beginning of the partial match. Returns
+ // (last1,false) if no full or partial match was found.
+ template <typename Iterator1, typename Iterator2>
+ std::pair<Iterator1, bool> partial_search(
+ Iterator1 first1, Iterator1 last1, Iterator2 first2, Iterator2 last2)
+ {
+ for (Iterator1 iter1 = first1; iter1 != last1; ++iter1)
+ {
+ Iterator1 test_iter1 = iter1;
+ Iterator2 test_iter2 = first2;
+ for (;; ++test_iter1, ++test_iter2)
+ {
+ if (test_iter2 == last2)
+ return std::make_pair(iter1, true);
+ if (test_iter1 == last1)
+ {
+ if (test_iter2 != first2)
+ return std::make_pair(iter1, false);
+ else
+ break;
+ }
+ if (*test_iter1 != *test_iter2)
+ break;
+ }
+ }
+ return std::make_pair(last1, false);
+ }
+} // namespace detail
+
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const std::string& delim,
+ boost::system::error_code& ec)
+{
+ std::size_t search_position = 0;
+ for (;;)
+ {
+ // Determine the range of the data to be searched.
+ typedef typename boost::asio::basic_streambuf<
+ Allocator>::const_buffers_type const_buffers_type;
+ typedef boost::asio::buffers_iterator<const_buffers_type> iterator;
+ const_buffers_type buffers = b.data();
+ iterator begin = iterator::begin(buffers);
+ iterator start_pos = begin + search_position;
+ iterator end = iterator::end(buffers);
+
+ // Look for a match.
+ std::pair<iterator, bool> result = detail::partial_search(
+ start_pos, end, delim.begin(), delim.end());
+ if (result.first != end)
+ {
+ if (result.second)
+ {
+ // Full match. We're done.
+ ec = boost::system::error_code();
+ return result.first - begin + delim.length();
+ }
+ else
+ {
+ // Partial match. Next search needs to start from beginning of match.
+ search_position = result.first - begin;
+ }
+ }
+ else
+ {
+ // No match. Next search can start with the new data.
+ search_position = end - begin;
+ }
+
+ // Check if buffer is full.
+ if (b.size() == b.max_size())
+ {
+ ec = error::not_found;
+ return 0;
+ }
+
+ // Need more data.
+ std::size_t bytes_to_read = read_size_helper(b, 65536);
+ b.commit(s.read_some(b.prepare(bytes_to_read), ec));
+ if (ec)
+ return 0;
+ }
+}
+
+#if defined(BOOST_ASIO_HAS_BOOST_REGEX)
+
+template <typename SyncReadStream, typename Allocator>
+inline std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const boost::regex& expr)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read_until(s, b, expr, ec);
+ boost::asio::detail::throw_error(ec, "read_until");
+ return bytes_transferred;
+}
+
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const boost::regex& expr,
+ boost::system::error_code& ec)
+{
+ std::size_t search_position = 0;
+ for (;;)
+ {
+ // Determine the range of the data to be searched.
+ typedef typename boost::asio::basic_streambuf<
+ Allocator>::const_buffers_type const_buffers_type;
+ typedef boost::asio::buffers_iterator<const_buffers_type> iterator;
+ const_buffers_type buffers = b.data();
+ iterator begin = iterator::begin(buffers);
+ iterator start_pos = begin + search_position;
+ iterator end = iterator::end(buffers);
+
+ // Look for a match.
+ boost::match_results<iterator,
+ typename std::vector<boost::sub_match<iterator> >::allocator_type>
+ match_results;
+ if (regex_search(start_pos, end, match_results, expr,
+ boost::match_default | boost::match_partial))
+ {
+ if (match_results[0].matched)
+ {
+ // Full match. We're done.
+ ec = boost::system::error_code();
+ return match_results[0].second - begin;
+ }
+ else
+ {
+ // Partial match. Next search needs to start from beginning of match.
+ search_position = match_results[0].first - begin;
+ }
+ }
+ else
+ {
+ // No match. Next search can start with the new data.
+ search_position = end - begin;
+ }
+
+ // Check if buffer is full.
+ if (b.size() == b.max_size())
+ {
+ ec = error::not_found;
+ return 0;
+ }
+
+ // Need more data.
+ std::size_t bytes_to_read = read_size_helper(b, 65536);
+ b.commit(s.read_some(b.prepare(bytes_to_read), ec));
+ if (ec)
+ return 0;
+ }
+}
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_REGEX)
+
+template <typename SyncReadStream, typename Allocator, typename MatchCondition>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ MatchCondition match_condition, boost::system::error_code& ec,
+ typename enable_if<is_match_condition<MatchCondition>::value>::type*)
+{
+ std::size_t search_position = 0;
+ for (;;)
+ {
+ // Determine the range of the data to be searched.
+ typedef typename boost::asio::basic_streambuf<
+ Allocator>::const_buffers_type const_buffers_type;
+ typedef boost::asio::buffers_iterator<const_buffers_type> iterator;
+ const_buffers_type buffers = b.data();
+ iterator begin = iterator::begin(buffers);
+ iterator start_pos = begin + search_position;
+ iterator end = iterator::end(buffers);
+
+ // Look for a match.
+ std::pair<iterator, bool> result = match_condition(start_pos, end);
+ if (result.second)
+ {
+ // Full match. We're done.
+ ec = boost::system::error_code();
+ return result.first - begin;
+ }
+ else if (result.first != end)
+ {
+ // Partial match. Next search needs to start from beginning of match.
+ search_position = result.first - begin;
+ }
+ else
+ {
+ // No match. Next search can start with the new data.
+ search_position = end - begin;
+ }
+
+ // Check if buffer is full.
+ if (b.size() == b.max_size())
+ {
+ ec = error::not_found;
+ return 0;
+ }
+
+ // Need more data.
+ std::size_t bytes_to_read = read_size_helper(b, 65536);
+ b.commit(s.read_some(b.prepare(bytes_to_read), ec));
+ if (ec)
+ return 0;
+ }
+}
+
+template <typename SyncReadStream, typename Allocator, typename MatchCondition>
+inline std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, MatchCondition match_condition,
+ typename enable_if<is_match_condition<MatchCondition>::value>::type*)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = read_until(s, b, match_condition, ec);
+ boost::asio::detail::throw_error(ec, "read_until");
+ return bytes_transferred;
+}
+
+namespace detail
+{
+ template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+ class read_until_delim_op
+ {
+ public:
+ read_until_delim_op(AsyncReadStream& stream,
+ boost::asio::basic_streambuf<Allocator>& streambuf,
+ char delim, ReadHandler& handler)
+ : stream_(stream),
+ streambuf_(streambuf),
+ delim_(delim),
+ start_(0),
+ search_position_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_until_delim_op(const read_until_delim_op& other)
+ : stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ delim_(other.delim_),
+ start_(other.start_),
+ search_position_(other.search_position_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_until_delim_op(read_until_delim_op&& other)
+ : stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ delim_(other.delim_),
+ start_(other.start_),
+ search_position_(other.search_position_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ const std::size_t not_found = (std::numeric_limits<std::size_t>::max)();
+ std::size_t bytes_to_read;
+ switch (start_ = start)
+ {
+ case 1:
+ for (;;)
+ {
+ {
+ // Determine the range of the data to be searched.
+ typedef typename boost::asio::basic_streambuf<
+ Allocator>::const_buffers_type const_buffers_type;
+ typedef boost::asio::buffers_iterator<const_buffers_type> iterator;
+ const_buffers_type buffers = streambuf_.data();
+ iterator begin = iterator::begin(buffers);
+ iterator start_pos = begin + search_position_;
+ iterator end = iterator::end(buffers);
+
+ // Look for a match.
+ iterator iter = std::find(start_pos, end, delim_);
+ if (iter != end)
+ {
+ // Found a match. We're done.
+ search_position_ = iter - begin + 1;
+ bytes_to_read = 0;
+ }
+
+ // No match yet. Check if buffer is full.
+ else if (streambuf_.size() == streambuf_.max_size())
+ {
+ search_position_ = not_found;
+ bytes_to_read = 0;
+ }
+
+ // Need to read some more data.
+ else
+ {
+ // Next search can start with the new data.
+ search_position_ = end - begin;
+ bytes_to_read = read_size_helper(streambuf_, 65536);
+ }
+ }
+
+ // Check if we're done.
+ if (!start && bytes_to_read == 0)
+ break;
+
+ // Start a new asynchronous read operation to obtain more data.
+ stream_.async_read_some(streambuf_.prepare(bytes_to_read),
+ BOOST_ASIO_MOVE_CAST(read_until_delim_op)(*this));
+ return; default:
+ streambuf_.commit(bytes_transferred);
+ if (ec || bytes_transferred == 0)
+ break;
+ }
+
+ const boost::system::error_code result_ec =
+ (search_position_ == not_found)
+ ? error::not_found : ec;
+
+ const std::size_t result_n =
+ (ec || search_position_ == not_found)
+ ? 0 : search_position_;
+
+ handler_(result_ec, result_n);
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ boost::asio::basic_streambuf<Allocator>& streambuf_;
+ char delim_;
+ int start_;
+ std::size_t search_position_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ read_until_delim_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ read_until_delim_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ read_until_delim_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream, typename Allocator,
+ typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ read_until_delim_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream, typename Allocator,
+ typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ read_until_delim_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_until(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, char delim,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_until_delim_op<AsyncReadStream,
+ Allocator, BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))>(
+ s, b, delim, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+namespace detail
+{
+ template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+ class read_until_delim_string_op
+ {
+ public:
+ read_until_delim_string_op(AsyncReadStream& stream,
+ boost::asio::basic_streambuf<Allocator>& streambuf,
+ const std::string& delim, ReadHandler& handler)
+ : stream_(stream),
+ streambuf_(streambuf),
+ delim_(delim),
+ start_(0),
+ search_position_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_until_delim_string_op(const read_until_delim_string_op& other)
+ : stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ delim_(other.delim_),
+ start_(other.start_),
+ search_position_(other.search_position_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_until_delim_string_op(read_until_delim_string_op&& other)
+ : stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ delim_(BOOST_ASIO_MOVE_CAST(std::string)(other.delim_)),
+ start_(other.start_),
+ search_position_(other.search_position_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ const std::size_t not_found = (std::numeric_limits<std::size_t>::max)();
+ std::size_t bytes_to_read;
+ switch (start_ = start)
+ {
+ case 1:
+ for (;;)
+ {
+ {
+ // Determine the range of the data to be searched.
+ typedef typename boost::asio::basic_streambuf<
+ Allocator>::const_buffers_type const_buffers_type;
+ typedef boost::asio::buffers_iterator<const_buffers_type> iterator;
+ const_buffers_type buffers = streambuf_.data();
+ iterator begin = iterator::begin(buffers);
+ iterator start_pos = begin + search_position_;
+ iterator end = iterator::end(buffers);
+
+ // Look for a match.
+ std::pair<iterator, bool> result = detail::partial_search(
+ start_pos, end, delim_.begin(), delim_.end());
+ if (result.first != end && result.second)
+ {
+ // Full match. We're done.
+ search_position_ = result.first - begin + delim_.length();
+ bytes_to_read = 0;
+ }
+
+ // No match yet. Check if buffer is full.
+ else if (streambuf_.size() == streambuf_.max_size())
+ {
+ search_position_ = not_found;
+ bytes_to_read = 0;
+ }
+
+ // Need to read some more data.
+ else
+ {
+ if (result.first != end)
+ {
+ // Partial match. Next search needs to start from beginning of
+ // match.
+ search_position_ = result.first - begin;
+ }
+ else
+ {
+ // Next search can start with the new data.
+ search_position_ = end - begin;
+ }
+
+ bytes_to_read = read_size_helper(streambuf_, 65536);
+ }
+ }
+
+ // Check if we're done.
+ if (!start && bytes_to_read == 0)
+ break;
+
+ // Start a new asynchronous read operation to obtain more data.
+ stream_.async_read_some(streambuf_.prepare(bytes_to_read),
+ BOOST_ASIO_MOVE_CAST(read_until_delim_string_op)(*this));
+ return; default:
+ streambuf_.commit(bytes_transferred);
+ if (ec || bytes_transferred == 0)
+ break;
+ }
+
+ const boost::system::error_code result_ec =
+ (search_position_ == not_found)
+ ? error::not_found : ec;
+
+ const std::size_t result_n =
+ (ec || search_position_ == not_found)
+ ? 0 : search_position_;
+
+ handler_(result_ec, result_n);
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ boost::asio::basic_streambuf<Allocator>& streambuf_;
+ std::string delim_;
+ int start_;
+ std::size_t search_position_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ read_until_delim_string_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ read_until_delim_string_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ read_until_delim_string_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream,
+ typename Allocator, typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ read_until_delim_string_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream,
+ typename Allocator, typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ read_until_delim_string_op<AsyncReadStream,
+ Allocator, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_until(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const std::string& delim,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_until_delim_string_op<AsyncReadStream,
+ Allocator, BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))>(
+ s, b, delim, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+#if defined(BOOST_ASIO_HAS_BOOST_REGEX)
+
+namespace detail
+{
+ template <typename AsyncReadStream, typename Allocator,
+ typename RegEx, typename ReadHandler>
+ class read_until_expr_op
+ {
+ public:
+ read_until_expr_op(AsyncReadStream& stream,
+ boost::asio::basic_streambuf<Allocator>& streambuf,
+ const boost::regex& expr, ReadHandler& handler)
+ : stream_(stream),
+ streambuf_(streambuf),
+ expr_(expr),
+ start_(0),
+ search_position_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_until_expr_op(const read_until_expr_op& other)
+ : stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ expr_(other.expr_),
+ start_(other.start_),
+ search_position_(other.search_position_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_until_expr_op(read_until_expr_op&& other)
+ : stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ expr_(other.expr_),
+ start_(other.start_),
+ search_position_(other.search_position_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ const std::size_t not_found = (std::numeric_limits<std::size_t>::max)();
+ std::size_t bytes_to_read;
+ switch (start_ = start)
+ {
+ case 1:
+ for (;;)
+ {
+ {
+ // Determine the range of the data to be searched.
+ typedef typename boost::asio::basic_streambuf<
+ Allocator>::const_buffers_type const_buffers_type;
+ typedef boost::asio::buffers_iterator<const_buffers_type> iterator;
+ const_buffers_type buffers = streambuf_.data();
+ iterator begin = iterator::begin(buffers);
+ iterator start_pos = begin + search_position_;
+ iterator end = iterator::end(buffers);
+
+ // Look for a match.
+ boost::match_results<iterator,
+ typename std::vector<boost::sub_match<iterator> >::allocator_type>
+ match_results;
+ bool match = regex_search(start_pos, end, match_results, expr_,
+ boost::match_default | boost::match_partial);
+ if (match && match_results[0].matched)
+ {
+ // Full match. We're done.
+ search_position_ = match_results[0].second - begin;
+ bytes_to_read = 0;
+ }
+
+ // No match yet. Check if buffer is full.
+ else if (streambuf_.size() == streambuf_.max_size())
+ {
+ search_position_ = not_found;
+ bytes_to_read = 0;
+ }
+
+ // Need to read some more data.
+ else
+ {
+ if (match)
+ {
+ // Partial match. Next search needs to start from beginning of
+ // match.
+ search_position_ = match_results[0].first - begin;
+ }
+ else
+ {
+ // Next search can start with the new data.
+ search_position_ = end - begin;
+ }
+
+ bytes_to_read = read_size_helper(streambuf_, 65536);
+ }
+ }
+
+ // Check if we're done.
+ if (!start && bytes_to_read == 0)
+ break;
+
+ // Start a new asynchronous read operation to obtain more data.
+ stream_.async_read_some(streambuf_.prepare(bytes_to_read),
+ BOOST_ASIO_MOVE_CAST(read_until_expr_op)(*this));
+ return; default:
+ streambuf_.commit(bytes_transferred);
+ if (ec || bytes_transferred == 0)
+ break;
+ }
+
+ const boost::system::error_code result_ec =
+ (search_position_ == not_found)
+ ? error::not_found : ec;
+
+ const std::size_t result_n =
+ (ec || search_position_ == not_found)
+ ? 0 : search_position_;
+
+ handler_(result_ec, result_n);
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ boost::asio::basic_streambuf<Allocator>& streambuf_;
+ RegEx expr_;
+ int start_;
+ std::size_t search_position_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename RegEx, typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ read_until_expr_op<AsyncReadStream,
+ Allocator, RegEx, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename RegEx, typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ read_until_expr_op<AsyncReadStream,
+ Allocator, RegEx, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename RegEx, typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ read_until_expr_op<AsyncReadStream,
+ Allocator, RegEx, ReadHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream, typename Allocator,
+ typename RegEx, typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ read_until_expr_op<AsyncReadStream,
+ Allocator, RegEx, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream, typename Allocator,
+ typename RegEx, typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ read_until_expr_op<AsyncReadStream,
+ Allocator, RegEx, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_until(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const boost::regex& expr,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_until_expr_op<AsyncReadStream, Allocator,
+ boost::regex, BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))>(
+ s, b, expr, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_REGEX)
+
+namespace detail
+{
+ template <typename AsyncReadStream, typename Allocator,
+ typename MatchCondition, typename ReadHandler>
+ class read_until_match_op
+ {
+ public:
+ read_until_match_op(AsyncReadStream& stream,
+ boost::asio::basic_streambuf<Allocator>& streambuf,
+ MatchCondition match_condition, ReadHandler& handler)
+ : stream_(stream),
+ streambuf_(streambuf),
+ match_condition_(match_condition),
+ start_(0),
+ search_position_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ read_until_match_op(const read_until_match_op& other)
+ : stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ match_condition_(other.match_condition_),
+ start_(other.start_),
+ search_position_(other.search_position_),
+ handler_(other.handler_)
+ {
+ }
+
+ read_until_match_op(read_until_match_op&& other)
+ : stream_(other.stream_),
+ streambuf_(other.streambuf_),
+ match_condition_(other.match_condition_),
+ start_(other.start_),
+ search_position_(other.search_position_),
+ handler_(BOOST_ASIO_MOVE_CAST(ReadHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ const std::size_t not_found = (std::numeric_limits<std::size_t>::max)();
+ std::size_t bytes_to_read;
+ switch (start_ = start)
+ {
+ case 1:
+ for (;;)
+ {
+ {
+ // Determine the range of the data to be searched.
+ typedef typename boost::asio::basic_streambuf<
+ Allocator>::const_buffers_type const_buffers_type;
+ typedef boost::asio::buffers_iterator<const_buffers_type> iterator;
+ const_buffers_type buffers = streambuf_.data();
+ iterator begin = iterator::begin(buffers);
+ iterator start_pos = begin + search_position_;
+ iterator end = iterator::end(buffers);
+
+ // Look for a match.
+ std::pair<iterator, bool> result = match_condition_(start_pos, end);
+ if (result.second)
+ {
+ // Full match. We're done.
+ search_position_ = result.first - begin;
+ bytes_to_read = 0;
+ }
+
+ // No match yet. Check if buffer is full.
+ else if (streambuf_.size() == streambuf_.max_size())
+ {
+ search_position_ = not_found;
+ bytes_to_read = 0;
+ }
+
+ // Need to read some more data.
+ else
+ {
+ if (result.first != end)
+ {
+ // Partial match. Next search needs to start from beginning of
+ // match.
+ search_position_ = result.first - begin;
+ }
+ else
+ {
+ // Next search can start with the new data.
+ search_position_ = end - begin;
+ }
+
+ bytes_to_read = read_size_helper(streambuf_, 65536);
+ }
+ }
+
+ // Check if we're done.
+ if (!start && bytes_to_read == 0)
+ break;
+
+ // Start a new asynchronous read operation to obtain more data.
+ stream_.async_read_some(streambuf_.prepare(bytes_to_read),
+ BOOST_ASIO_MOVE_CAST(read_until_match_op)(*this));
+ return; default:
+ streambuf_.commit(bytes_transferred);
+ if (ec || bytes_transferred == 0)
+ break;
+ }
+
+ const boost::system::error_code result_ec =
+ (search_position_ == not_found)
+ ? error::not_found : ec;
+
+ const std::size_t result_n =
+ (ec || search_position_ == not_found)
+ ? 0 : search_position_;
+
+ handler_(result_ec, result_n);
+ }
+ }
+
+ //private:
+ AsyncReadStream& stream_;
+ boost::asio::basic_streambuf<Allocator>& streambuf_;
+ MatchCondition match_condition_;
+ int start_;
+ std::size_t search_position_;
+ ReadHandler handler_;
+ };
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename MatchCondition, typename ReadHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ read_until_match_op<AsyncReadStream,
+ Allocator, MatchCondition, ReadHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename MatchCondition, typename ReadHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ read_until_match_op<AsyncReadStream,
+ Allocator, MatchCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncReadStream, typename Allocator,
+ typename MatchCondition, typename ReadHandler>
+ inline bool asio_handler_is_continuation(
+ read_until_match_op<AsyncReadStream,
+ Allocator, MatchCondition, ReadHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream, typename Allocator,
+ typename MatchCondition, typename ReadHandler>
+ inline void asio_handler_invoke(Function& function,
+ read_until_match_op<AsyncReadStream,
+ Allocator, MatchCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncReadStream, typename Allocator,
+ typename MatchCondition, typename ReadHandler>
+ inline void asio_handler_invoke(const Function& function,
+ read_until_match_op<AsyncReadStream,
+ Allocator, MatchCondition, ReadHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncReadStream, typename Allocator,
+ typename MatchCondition, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_until(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ MatchCondition match_condition, BOOST_ASIO_MOVE_ARG(ReadHandler) handler,
+ typename enable_if<is_match_condition<MatchCondition>::value>::type*)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::read_until_match_op<AsyncReadStream, Allocator,
+ MatchCondition, BOOST_ASIO_HANDLER_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))>(
+ s, b, match_condition, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_READ_UNTIL_HPP
diff --git a/ext/patches/boost/asio/impl/serial_port_base.hpp b/ext/patches/boost/asio/impl/serial_port_base.hpp
new file mode 100644
index 0000000..1fc7cb9
--- /dev/null
+++ b/ext/patches/boost/asio/impl/serial_port_base.hpp
@@ -0,0 +1,61 @@
+//
+// impl/serial_port_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_SERIAL_PORT_BASE_HPP
+#define BOOST_ASIO_IMPL_SERIAL_PORT_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+inline serial_port_base::baud_rate::baud_rate(unsigned int rate)
+ : value_(rate)
+{
+}
+
+inline unsigned int serial_port_base::baud_rate::value() const
+{
+ return value_;
+}
+
+inline serial_port_base::flow_control::type
+serial_port_base::flow_control::value() const
+{
+ return value_;
+}
+
+inline serial_port_base::parity::type serial_port_base::parity::value() const
+{
+ return value_;
+}
+
+inline serial_port_base::stop_bits::type
+serial_port_base::stop_bits::value() const
+{
+ return value_;
+}
+
+inline unsigned int serial_port_base::character_size::value() const
+{
+ return value_;
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_SERIAL_PORT_BASE_HPP
diff --git a/ext/patches/boost/asio/impl/serial_port_base.ipp b/ext/patches/boost/asio/impl/serial_port_base.ipp
new file mode 100644
index 0000000..c30601f
--- /dev/null
+++ b/ext/patches/boost/asio/impl/serial_port_base.ipp
@@ -0,0 +1,556 @@
+//
+// impl/serial_port_base.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_SERIAL_PORT_BASE_IPP
+#define BOOST_ASIO_IMPL_SERIAL_PORT_BASE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+#include <stdexcept>
+#include <boost/asio/error.hpp>
+#include <boost/asio/serial_port_base.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+
+#if defined(GENERATING_DOCUMENTATION)
+# define BOOST_ASIO_OPTION_STORAGE implementation_defined
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# define BOOST_ASIO_OPTION_STORAGE DCB
+#else
+# define BOOST_ASIO_OPTION_STORAGE termios
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+boost::system::error_code serial_port_base::baud_rate::store(
+ BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec) const
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ storage.BaudRate = value_;
+#else
+ speed_t baud;
+ switch (value_)
+ {
+ // Do POSIX-specified rates first.
+ case 0: baud = B0; break;
+ case 50: baud = B50; break;
+ case 75: baud = B75; break;
+ case 110: baud = B110; break;
+ case 134: baud = B134; break;
+ case 150: baud = B150; break;
+ case 200: baud = B200; break;
+ case 300: baud = B300; break;
+ case 600: baud = B600; break;
+ case 1200: baud = B1200; break;
+ case 1800: baud = B1800; break;
+ case 2400: baud = B2400; break;
+ case 4800: baud = B4800; break;
+ case 9600: baud = B9600; break;
+ case 19200: baud = B19200; break;
+ case 38400: baud = B38400; break;
+ // And now the extended ones conditionally.
+# ifdef B7200
+ case 7200: baud = B7200; break;
+# endif
+# ifdef B14400
+ case 14400: baud = B14400; break;
+# endif
+# ifdef B57600
+ case 57600: baud = B57600; break;
+# endif
+# ifdef B115200
+ case 115200: baud = B115200; break;
+# endif
+# ifdef B230400
+ case 230400: baud = B230400; break;
+# endif
+# ifdef B460800
+ case 460800: baud = B460800; break;
+# endif
+# ifdef B500000
+ case 500000: baud = B500000; break;
+# endif
+# ifdef B576000
+ case 576000: baud = B576000; break;
+# endif
+# ifdef B921600
+ case 921600: baud = B921600; break;
+# endif
+# ifdef B1000000
+ case 1000000: baud = B1000000; break;
+# endif
+# ifdef B1152000
+ case 1152000: baud = B1152000; break;
+# endif
+# ifdef B2000000
+ case 2000000: baud = B2000000; break;
+# endif
+# ifdef B3000000
+ case 3000000: baud = B3000000; break;
+# endif
+# ifdef B3500000
+ case 3500000: baud = B3500000; break;
+# endif
+# ifdef B4000000
+ case 4000000: baud = B4000000; break;
+# endif
+ default:
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+# if defined(_BSD_SOURCE)
+ ::cfsetspeed(&storage, baud);
+# else
+ ::cfsetispeed(&storage, baud);
+ ::cfsetospeed(&storage, baud);
+# endif
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code serial_port_base::baud_rate::load(
+ const BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ value_ = storage.BaudRate;
+#else
+ speed_t baud = ::cfgetospeed(&storage);
+ switch (baud)
+ {
+ // First do those specified by POSIX.
+ case B0: value_ = 0; break;
+ case B50: value_ = 50; break;
+ case B75: value_ = 75; break;
+ case B110: value_ = 110; break;
+ case B134: value_ = 134; break;
+ case B150: value_ = 150; break;
+ case B200: value_ = 200; break;
+ case B300: value_ = 300; break;
+ case B600: value_ = 600; break;
+ case B1200: value_ = 1200; break;
+ case B1800: value_ = 1800; break;
+ case B2400: value_ = 2400; break;
+ case B4800: value_ = 4800; break;
+ case B9600: value_ = 9600; break;
+ case B19200: value_ = 19200; break;
+ case B38400: value_ = 38400; break;
+ // Now conditionally handle a bunch of extended rates.
+# ifdef B7200
+ case B7200: value_ = 7200; break;
+# endif
+# ifdef B14400
+ case B14400: value_ = 14400; break;
+# endif
+# ifdef B57600
+ case B57600: value_ = 57600; break;
+# endif
+# ifdef B115200
+ case B115200: value_ = 115200; break;
+# endif
+# ifdef B230400
+ case B230400: value_ = 230400; break;
+# endif
+# ifdef B460800
+ case B460800: value_ = 460800; break;
+# endif
+# ifdef B500000
+ case B500000: value_ = 500000; break;
+# endif
+# ifdef B576000
+ case B576000: value_ = 576000; break;
+# endif
+# ifdef B921600
+ case B921600: value_ = 921600; break;
+# endif
+# ifdef B1000000
+ case B1000000: value_ = 1000000; break;
+# endif
+# ifdef B1152000
+ case B1152000: value_ = 1152000; break;
+# endif
+# ifdef B2000000
+ case B2000000: value_ = 2000000; break;
+# endif
+# ifdef B3000000
+ case B3000000: value_ = 3000000; break;
+# endif
+# ifdef B3500000
+ case B3500000: value_ = 3500000; break;
+# endif
+# ifdef B4000000
+ case B4000000: value_ = 4000000; break;
+# endif
+ default:
+ value_ = 0;
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+serial_port_base::flow_control::flow_control(
+ serial_port_base::flow_control::type t)
+ : value_(t)
+{
+ if (t != none && t != software && t != hardware)
+ {
+ std::out_of_range ex("invalid flow_control value");
+ boost::asio::detail::throw_exception(ex);
+ }
+}
+
+boost::system::error_code serial_port_base::flow_control::store(
+ BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec) const
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ storage.fOutxCtsFlow = FALSE;
+ storage.fOutxDsrFlow = FALSE;
+ storage.fTXContinueOnXoff = TRUE;
+ storage.fDtrControl = DTR_CONTROL_ENABLE;
+ storage.fDsrSensitivity = FALSE;
+ storage.fOutX = FALSE;
+ storage.fInX = FALSE;
+ storage.fRtsControl = RTS_CONTROL_ENABLE;
+ switch (value_)
+ {
+ case none:
+ break;
+ case software:
+ storage.fOutX = TRUE;
+ storage.fInX = TRUE;
+ break;
+ case hardware:
+ storage.fOutxCtsFlow = TRUE;
+ storage.fRtsControl = RTS_CONTROL_HANDSHAKE;
+ break;
+ default:
+ break;
+ }
+#else
+ switch (value_)
+ {
+ case none:
+ storage.c_iflag &= ~(IXOFF | IXON);
+# if defined(_BSD_SOURCE)
+ storage.c_cflag &= ~CRTSCTS;
+# elif defined(__QNXNTO__)
+ storage.c_cflag &= ~(IHFLOW | OHFLOW);
+# endif
+ break;
+ case software:
+ storage.c_iflag |= IXOFF | IXON;
+# if defined(_BSD_SOURCE)
+ storage.c_cflag &= ~CRTSCTS;
+# elif defined(__QNXNTO__)
+ storage.c_cflag &= ~(IHFLOW | OHFLOW);
+# endif
+ break;
+ case hardware:
+# if defined(_BSD_SOURCE)
+ storage.c_iflag &= ~(IXOFF | IXON);
+ storage.c_cflag |= CRTSCTS;
+ break;
+# elif defined(__QNXNTO__)
+ storage.c_iflag &= ~(IXOFF | IXON);
+ storage.c_cflag |= (IHFLOW | OHFLOW);
+ break;
+# else
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+# endif
+ default:
+ break;
+ }
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code serial_port_base::flow_control::load(
+ const BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ if (storage.fOutX && storage.fInX)
+ {
+ value_ = software;
+ }
+ else if (storage.fOutxCtsFlow && storage.fRtsControl == RTS_CONTROL_HANDSHAKE)
+ {
+ value_ = hardware;
+ }
+ else
+ {
+ value_ = none;
+ }
+#else
+ if (storage.c_iflag & (IXOFF | IXON))
+ {
+ value_ = software;
+ }
+# if defined(_BSD_SOURCE)
+ else if (storage.c_cflag & CRTSCTS)
+ {
+ value_ = hardware;
+ }
+# elif defined(__QNXNTO__)
+ else if (storage.c_cflag & IHFLOW && storage.c_cflag & OHFLOW)
+ {
+ value_ = hardware;
+ }
+# endif
+ else
+ {
+ value_ = none;
+ }
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+serial_port_base::parity::parity(serial_port_base::parity::type t)
+ : value_(t)
+{
+ if (t != none && t != odd && t != even)
+ {
+ std::out_of_range ex("invalid parity value");
+ boost::asio::detail::throw_exception(ex);
+ }
+}
+
+boost::system::error_code serial_port_base::parity::store(
+ BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec) const
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ switch (value_)
+ {
+ case none:
+ storage.fParity = FALSE;
+ storage.Parity = NOPARITY;
+ break;
+ case odd:
+ storage.fParity = TRUE;
+ storage.Parity = ODDPARITY;
+ break;
+ case even:
+ storage.fParity = TRUE;
+ storage.Parity = EVENPARITY;
+ break;
+ default:
+ break;
+ }
+#else
+ switch (value_)
+ {
+ case none:
+ storage.c_iflag |= IGNPAR;
+ storage.c_cflag &= ~(PARENB | PARODD);
+ break;
+ case even:
+ storage.c_iflag &= ~(IGNPAR | PARMRK);
+ storage.c_iflag |= INPCK;
+ storage.c_cflag |= PARENB;
+ storage.c_cflag &= ~PARODD;
+ break;
+ case odd:
+ storage.c_iflag &= ~(IGNPAR | PARMRK);
+ storage.c_iflag |= INPCK;
+ storage.c_cflag |= (PARENB | PARODD);
+ break;
+ default:
+ break;
+ }
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code serial_port_base::parity::load(
+ const BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ if (storage.Parity == EVENPARITY)
+ {
+ value_ = even;
+ }
+ else if (storage.Parity == ODDPARITY)
+ {
+ value_ = odd;
+ }
+ else
+ {
+ value_ = none;
+ }
+#else
+ if (storage.c_cflag & PARENB)
+ {
+ if (storage.c_cflag & PARODD)
+ {
+ value_ = odd;
+ }
+ else
+ {
+ value_ = even;
+ }
+ }
+ else
+ {
+ value_ = none;
+ }
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+serial_port_base::stop_bits::stop_bits(
+ serial_port_base::stop_bits::type t)
+ : value_(t)
+{
+ if (t != one && t != onepointfive && t != two)
+ {
+ std::out_of_range ex("invalid stop_bits value");
+ boost::asio::detail::throw_exception(ex);
+ }
+}
+
+boost::system::error_code serial_port_base::stop_bits::store(
+ BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec) const
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ switch (value_)
+ {
+ case one:
+ storage.StopBits = ONESTOPBIT;
+ break;
+ case onepointfive:
+ storage.StopBits = ONE5STOPBITS;
+ break;
+ case two:
+ storage.StopBits = TWOSTOPBITS;
+ break;
+ default:
+ break;
+ }
+#else
+ switch (value_)
+ {
+ case one:
+ storage.c_cflag &= ~CSTOPB;
+ break;
+ case two:
+ storage.c_cflag |= CSTOPB;
+ break;
+ default:
+ ec = boost::asio::error::operation_not_supported;
+ return ec;
+ }
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code serial_port_base::stop_bits::load(
+ const BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ if (storage.StopBits == ONESTOPBIT)
+ {
+ value_ = one;
+ }
+ else if (storage.StopBits == ONE5STOPBITS)
+ {
+ value_ = onepointfive;
+ }
+ else if (storage.StopBits == TWOSTOPBITS)
+ {
+ value_ = two;
+ }
+ else
+ {
+ value_ = one;
+ }
+#else
+ value_ = (storage.c_cflag & CSTOPB) ? two : one;
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+serial_port_base::character_size::character_size(unsigned int t)
+ : value_(t)
+{
+ if (t < 5 || t > 8)
+ {
+ std::out_of_range ex("invalid character_size value");
+ boost::asio::detail::throw_exception(ex);
+ }
+}
+
+boost::system::error_code serial_port_base::character_size::store(
+ BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec) const
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ storage.ByteSize = value_;
+#else
+ storage.c_cflag &= ~CSIZE;
+ switch (value_)
+ {
+ case 5: storage.c_cflag |= CS5; break;
+ case 6: storage.c_cflag |= CS6; break;
+ case 7: storage.c_cflag |= CS7; break;
+ case 8: storage.c_cflag |= CS8; break;
+ default: break;
+ }
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code serial_port_base::character_size::load(
+ const BOOST_ASIO_OPTION_STORAGE& storage, boost::system::error_code& ec)
+{
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ value_ = storage.ByteSize;
+#else
+ if ((storage.c_cflag & CSIZE) == CS5) { value_ = 5; }
+ else if ((storage.c_cflag & CSIZE) == CS6) { value_ = 6; }
+ else if ((storage.c_cflag & CSIZE) == CS7) { value_ = 7; }
+ else if ((storage.c_cflag & CSIZE) == CS8) { value_ = 8; }
+ else
+ {
+ // Hmmm, use 8 for now.
+ value_ = 8;
+ }
+#endif
+ ec = boost::system::error_code();
+ return ec;
+}
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#undef BOOST_ASIO_OPTION_STORAGE
+
+#endif // defined(BOOST_ASIO_HAS_SERIAL_PORT)
+
+#endif // BOOST_ASIO_IMPL_SERIAL_PORT_BASE_IPP
diff --git a/ext/patches/boost/asio/impl/spawn.hpp b/ext/patches/boost/asio/impl/spawn.hpp
new file mode 100644
index 0000000..dc3647d
--- /dev/null
+++ b/ext/patches/boost/asio/impl/spawn.hpp
@@ -0,0 +1,338 @@
+//
+// impl/spawn.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_SPAWN_HPP
+#define BOOST_ASIO_IMPL_SPAWN_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/shared_ptr.hpp>
+#include <boost/asio/handler_type.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+ template <typename Handler, typename T>
+ class coro_handler
+ {
+ public:
+ coro_handler(basic_yield_context<Handler> ctx)
+ : coro_(ctx.coro_.lock()),
+ ca_(ctx.ca_),
+ handler_(ctx.handler_),
+ ec_(ctx.ec_),
+ value_(0)
+ {
+ }
+
+ void operator()(T value)
+ {
+ *ec_ = boost::system::error_code();
+ *value_ = value;
+ (*coro_)();
+ }
+
+ void operator()(boost::system::error_code ec, T value)
+ {
+ *ec_ = ec;
+ *value_ = value;
+ (*coro_)();
+ }
+
+ //private:
+ shared_ptr<typename basic_yield_context<Handler>::callee_type> coro_;
+ typename basic_yield_context<Handler>::caller_type& ca_;
+ Handler& handler_;
+ boost::system::error_code* ec_;
+ T* value_;
+ };
+
+ template <typename Handler>
+ class coro_handler<Handler, void>
+ {
+ public:
+ coro_handler(basic_yield_context<Handler> ctx)
+ : coro_(ctx.coro_.lock()),
+ ca_(ctx.ca_),
+ handler_(ctx.handler_),
+ ec_(ctx.ec_)
+ {
+ }
+
+ void operator()()
+ {
+ *ec_ = boost::system::error_code();
+ (*coro_)();
+ }
+
+ void operator()(boost::system::error_code ec)
+ {
+ *ec_ = ec;
+ (*coro_)();
+ }
+
+ //private:
+ shared_ptr<typename basic_yield_context<Handler>::callee_type> coro_;
+ typename basic_yield_context<Handler>::caller_type& ca_;
+ Handler& handler_;
+ boost::system::error_code* ec_;
+ };
+
+ template <typename Handler, typename T>
+ inline void* asio_handler_allocate(std::size_t size,
+ coro_handler<Handler, T>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename Handler, typename T>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ coro_handler<Handler, T>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename Handler, typename T>
+ inline bool asio_handler_is_continuation(coro_handler<Handler, T>*)
+ {
+ return true;
+ }
+
+ template <typename Function, typename Handler, typename T>
+ inline void asio_handler_invoke(Function& function,
+ coro_handler<Handler, T>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename Handler, typename T>
+ inline void asio_handler_invoke(const Function& function,
+ coro_handler<Handler, T>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+} // namespace detail
+
+#if !defined(GENERATING_DOCUMENTATION)
+
+template <typename Handler, typename ReturnType>
+struct handler_type<basic_yield_context<Handler>, ReturnType()>
+{
+ typedef detail::coro_handler<Handler, void> type;
+};
+
+template <typename Handler, typename ReturnType, typename Arg1>
+struct handler_type<basic_yield_context<Handler>, ReturnType(Arg1)>
+{
+ typedef detail::coro_handler<Handler, Arg1> type;
+};
+
+template <typename Handler, typename ReturnType>
+struct handler_type<basic_yield_context<Handler>,
+ ReturnType(boost::system::error_code)>
+{
+ typedef detail::coro_handler<Handler, void> type;
+};
+
+template <typename Handler, typename ReturnType, typename Arg2>
+struct handler_type<basic_yield_context<Handler>,
+ ReturnType(boost::system::error_code, Arg2)>
+{
+ typedef detail::coro_handler<Handler, Arg2> type;
+};
+
+template <typename Handler, typename T>
+class async_result<detail::coro_handler<Handler, T> >
+{
+public:
+ typedef T type;
+
+ explicit async_result(detail::coro_handler<Handler, T>& h)
+ : handler_(h),
+ ca_(h.ca_)
+ {
+ out_ec_ = h.ec_;
+ if (!out_ec_) h.ec_ = &ec_;
+ h.value_ = &value_;
+ }
+
+ type get()
+ {
+ handler_.coro_.reset(); // Must not hold shared_ptr to coro while suspended.
+ ca_();
+ if (!out_ec_ && ec_) throw boost::system::system_error(ec_);
+ return value_;
+ }
+
+private:
+ detail::coro_handler<Handler, T>& handler_;
+ typename basic_yield_context<Handler>::caller_type& ca_;
+ boost::system::error_code* out_ec_;
+ boost::system::error_code ec_;
+ type value_;
+};
+
+template <typename Handler>
+class async_result<detail::coro_handler<Handler, void> >
+{
+public:
+ typedef void type;
+
+ explicit async_result(detail::coro_handler<Handler, void>& h)
+ : handler_(h),
+ ca_(h.ca_)
+ {
+ out_ec_ = h.ec_;
+ if (!out_ec_) h.ec_ = &ec_;
+ }
+
+ void get()
+ {
+ handler_.coro_.reset(); // Must not hold shared_ptr to coro while suspended.
+ ca_();
+ if (!out_ec_ && ec_) throw boost::system::system_error(ec_);
+ }
+
+private:
+ detail::coro_handler<Handler, void>& handler_;
+ typename basic_yield_context<Handler>::caller_type& ca_;
+ boost::system::error_code* out_ec_;
+ boost::system::error_code ec_;
+};
+
+namespace detail {
+
+ template <typename Handler, typename Function>
+ struct spawn_data : private noncopyable
+ {
+ spawn_data(BOOST_ASIO_MOVE_ARG(Handler) handler,
+ bool call_handler, BOOST_ASIO_MOVE_ARG(Function) function)
+ : handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler)),
+ call_handler_(call_handler),
+ function_(BOOST_ASIO_MOVE_CAST(Function)(function))
+ {
+ }
+
+ weak_ptr<typename basic_yield_context<Handler>::callee_type> coro_;
+ Handler handler_;
+ bool call_handler_;
+ Function function_;
+ };
+
+ template <typename Handler, typename Function>
+ struct coro_entry_point
+ {
+ void operator()(typename basic_yield_context<Handler>::caller_type& ca)
+ {
+ shared_ptr<spawn_data<Handler, Function> > data(data_);
+#if !defined(BOOST_COROUTINES_UNIDIRECT) && !defined(BOOST_COROUTINES_V2)
+ ca(); // Yield until coroutine pointer has been initialised.
+#endif // !defined(BOOST_COROUTINES_UNIDIRECT) && !defined(BOOST_COROUTINES_V2)
+ const basic_yield_context<Handler> yield(
+ data->coro_, ca, data->handler_);
+ (data->function_)(yield);
+ if (data->call_handler_)
+ (data->handler_)();
+ }
+
+ shared_ptr<spawn_data<Handler, Function> > data_;
+ };
+
+ template <typename Handler, typename Function>
+ struct spawn_helper
+ {
+ void operator()()
+ {
+ typedef typename basic_yield_context<Handler>::callee_type callee_type;
+ coro_entry_point<Handler, Function> entry_point = { data_ };
+ shared_ptr<callee_type> coro(new callee_type(entry_point, attributes_));
+ data_->coro_ = coro;
+ (*coro)();
+ }
+
+ shared_ptr<spawn_data<Handler, Function> > data_;
+ boost::coroutines::attributes attributes_;
+ };
+
+ inline void default_spawn_handler() {}
+
+} // namespace detail
+
+template <typename Handler, typename Function>
+void spawn(BOOST_ASIO_MOVE_ARG(Handler) handler,
+ BOOST_ASIO_MOVE_ARG(Function) function,
+ const boost::coroutines::attributes& attributes)
+{
+ detail::spawn_helper<Handler, Function> helper;
+ helper.data_.reset(
+ new detail::spawn_data<Handler, Function>(
+ BOOST_ASIO_MOVE_CAST(Handler)(handler), true,
+ BOOST_ASIO_MOVE_CAST(Function)(function)));
+ helper.attributes_ = attributes;
+ boost_asio_handler_invoke_helpers::invoke(helper, helper.data_->handler_);
+}
+
+template <typename Handler, typename Function>
+void spawn(basic_yield_context<Handler> ctx,
+ BOOST_ASIO_MOVE_ARG(Function) function,
+ const boost::coroutines::attributes& attributes)
+{
+ Handler handler(ctx.handler_); // Explicit copy that might be moved from.
+ detail::spawn_helper<Handler, Function> helper;
+ helper.data_.reset(
+ new detail::spawn_data<Handler, Function>(
+ BOOST_ASIO_MOVE_CAST(Handler)(handler), false,
+ BOOST_ASIO_MOVE_CAST(Function)(function)));
+ helper.attributes_ = attributes;
+ boost_asio_handler_invoke_helpers::invoke(helper, helper.data_->handler_);
+}
+
+template <typename Function>
+void spawn(boost::asio::io_service::strand strand,
+ BOOST_ASIO_MOVE_ARG(Function) function,
+ const boost::coroutines::attributes& attributes)
+{
+ boost::asio::spawn(strand.wrap(&detail::default_spawn_handler),
+ BOOST_ASIO_MOVE_CAST(Function)(function), attributes);
+}
+
+template <typename Function>
+void spawn(boost::asio::io_service& io_service,
+ BOOST_ASIO_MOVE_ARG(Function) function,
+ const boost::coroutines::attributes& attributes)
+{
+ boost::asio::spawn(boost::asio::io_service::strand(io_service),
+ BOOST_ASIO_MOVE_CAST(Function)(function), attributes);
+}
+
+#endif // !defined(GENERATING_DOCUMENTATION)
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_SPAWN_HPP
diff --git a/ext/patches/boost/asio/impl/src.cpp b/ext/patches/boost/asio/impl/src.cpp
new file mode 100644
index 0000000..c326ae8
--- /dev/null
+++ b/ext/patches/boost/asio/impl/src.cpp
@@ -0,0 +1,25 @@
+//
+// impl/src.cpp
+// ~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#if defined(_MSC_VER) \
+ || defined(__BORLANDC__) \
+ || defined(__DMC__)
+# pragma message ( \
+ "This file is deprecated. " \
+ "Please #include <boost/asio/impl/src.hpp> instead.")
+#elif defined(__GNUC__) \
+ || defined(__HP_aCC) \
+ || defined(__SUNPRO_CC) \
+ || defined(__IBMCPP__)
+# warning "This file is deprecated."
+# warning "Please #include <boost/asio/impl/src.hpp> instead."
+#endif
+
+#include <boost/asio/impl/src.hpp>
diff --git a/ext/patches/boost/asio/impl/src.hpp b/ext/patches/boost/asio/impl/src.hpp
new file mode 100644
index 0000000..dda5766
--- /dev/null
+++ b/ext/patches/boost/asio/impl/src.hpp
@@ -0,0 +1,73 @@
+//
+// impl/src.hpp
+// ~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_SRC_HPP
+#define BOOST_ASIO_IMPL_SRC_HPP
+
+#define BOOST_ASIO_SOURCE
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# error Do not compile Asio library source with BOOST_ASIO_HEADER_ONLY defined
+#endif
+
+#include <boost/asio/impl/error.ipp>
+#include <boost/asio/impl/handler_alloc_hook.ipp>
+#include <boost/asio/impl/io_service.ipp>
+#include <boost/asio/impl/serial_port_base.ipp>
+#include <boost/asio/detail/impl/buffer_sequence_adapter.ipp>
+#include <boost/asio/detail/impl/descriptor_ops.ipp>
+#include <boost/asio/detail/impl/dev_poll_reactor.ipp>
+#include <boost/asio/detail/impl/epoll_reactor.ipp>
+#include <boost/asio/detail/impl/eventfd_select_interrupter.ipp>
+#include <boost/asio/detail/impl/handler_tracking.ipp>
+#include <boost/asio/detail/impl/kqueue_reactor.ipp>
+#include <boost/asio/detail/impl/pipe_select_interrupter.ipp>
+#include <boost/asio/detail/impl/posix_event.ipp>
+#include <boost/asio/detail/impl/posix_mutex.ipp>
+#include <boost/asio/detail/impl/posix_thread.ipp>
+#include <boost/asio/detail/impl/posix_tss_ptr.ipp>
+#include <boost/asio/detail/impl/reactive_descriptor_service.ipp>
+#include <boost/asio/detail/impl/reactive_serial_port_service.ipp>
+#include <boost/asio/detail/impl/reactive_socket_service_base.ipp>
+#include <boost/asio/detail/impl/resolver_service_base.ipp>
+#include <boost/asio/detail/impl/select_reactor.ipp>
+#include <boost/asio/detail/impl/service_registry.ipp>
+#include <boost/asio/detail/impl/signal_set_service.ipp>
+#include <boost/asio/detail/impl/socket_ops.ipp>
+#include <boost/asio/detail/impl/socket_select_interrupter.ipp>
+#include <boost/asio/detail/impl/strand_service.ipp>
+#include <boost/asio/detail/impl/task_io_service.ipp>
+#include <boost/asio/detail/impl/throw_error.ipp>
+#include <boost/asio/detail/impl/timer_queue_ptime.ipp>
+#include <boost/asio/detail/impl/timer_queue_set.ipp>
+#include <boost/asio/detail/impl/win_iocp_handle_service.ipp>
+#include <boost/asio/detail/impl/win_iocp_io_service.ipp>
+#include <boost/asio/detail/impl/win_iocp_serial_port_service.ipp>
+#include <boost/asio/detail/impl/win_iocp_socket_service_base.ipp>
+#include <boost/asio/detail/impl/win_event.ipp>
+#include <boost/asio/detail/impl/win_mutex.ipp>
+#include <boost/asio/detail/impl/win_object_handle_service.ipp>
+#include <boost/asio/detail/impl/win_static_mutex.ipp>
+#include <boost/asio/detail/impl/win_thread.ipp>
+#include <boost/asio/detail/impl/win_tss_ptr.ipp>
+#include <boost/asio/detail/impl/winrt_ssocket_service_base.ipp>
+#include <boost/asio/detail/impl/winrt_timer_scheduler.ipp>
+#include <boost/asio/detail/impl/winsock_init.ipp>
+#include <boost/asio/generic/detail/impl/endpoint.ipp>
+#include <boost/asio/ip/impl/address.ipp>
+#include <boost/asio/ip/impl/address_v4.ipp>
+#include <boost/asio/ip/impl/address_v6.ipp>
+#include <boost/asio/ip/impl/host_name.ipp>
+#include <boost/asio/ip/detail/impl/endpoint.ipp>
+#include <boost/asio/local/detail/impl/endpoint.ipp>
+
+#endif // BOOST_ASIO_IMPL_SRC_HPP
diff --git a/ext/patches/boost/asio/impl/use_future.hpp b/ext/patches/boost/asio/impl/use_future.hpp
new file mode 100644
index 0000000..02368a7
--- /dev/null
+++ b/ext/patches/boost/asio/impl/use_future.hpp
@@ -0,0 +1,174 @@
+//
+// impl/use_future.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_USE_FUTURE_HPP
+#define BOOST_ASIO_IMPL_USE_FUTURE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <future>
+#include <boost/asio/async_result.hpp>
+#include <boost/system/error_code.hpp>
+#include <boost/asio/handler_type.hpp>
+#include <boost/system/system_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace detail {
+
+ // Completion handler to adapt a promise as a completion handler.
+ template <typename T>
+ class promise_handler
+ {
+ public:
+ // Construct from use_future special value.
+ template <typename Allocator>
+ promise_handler(use_future_t<Allocator> uf)
+ : promise_(std::allocate_shared<std::promise<T> >(
+ uf.get_allocator(), std::allocator_arg, uf.get_allocator()))
+ {
+ }
+
+ void operator()(T t)
+ {
+ promise_->set_value(t);
+ }
+
+ void operator()(const boost::system::error_code& ec, T t)
+ {
+ if (ec)
+ promise_->set_exception(
+ std::make_exception_ptr(
+ boost::system::system_error(ec)));
+ else
+ promise_->set_value(t);
+ }
+
+ //private:
+ std::shared_ptr<std::promise<T> > promise_;
+ };
+
+ // Completion handler to adapt a void promise as a completion handler.
+ template <>
+ class promise_handler<void>
+ {
+ public:
+ // Construct from use_future special value. Used during rebinding.
+ template <typename Allocator>
+ promise_handler(use_future_t<Allocator> uf)
+ : promise_(std::allocate_shared<std::promise<void> >(
+ uf.get_allocator(), std::allocator_arg, uf.get_allocator()))
+ {
+ }
+
+ void operator()()
+ {
+ promise_->set_value();
+ }
+
+ void operator()(const boost::system::error_code& ec)
+ {
+ if (ec)
+ promise_->set_exception(
+ std::make_exception_ptr(
+ boost::system::system_error(ec)));
+ else
+ promise_->set_value();
+ }
+
+ //private:
+ std::shared_ptr<std::promise<void> > promise_;
+ };
+
+ // Ensure any exceptions thrown from the handler are propagated back to the
+ // caller via the future.
+ template <typename Function, typename T>
+ void asio_handler_invoke(Function f, promise_handler<T>* h)
+ {
+ std::shared_ptr<std::promise<T> > p(h->promise_);
+ try
+ {
+ f();
+ }
+ catch (...)
+ {
+ p->set_exception(std::current_exception());
+ }
+ }
+
+} // namespace detail
+
+#if !defined(GENERATING_DOCUMENTATION)
+
+// Handler traits specialisation for promise_handler.
+template <typename T>
+class async_result<detail::promise_handler<T> >
+{
+public:
+ // The initiating function will return a future.
+ typedef std::future<T> type;
+
+ // Constructor creates a new promise for the async operation, and obtains the
+ // corresponding future.
+ explicit async_result(detail::promise_handler<T>& h)
+ {
+ value_ = h.promise_->get_future();
+ }
+
+ // Obtain the future to be returned from the initiating function.
+ type get() { return std::move(value_); }
+
+private:
+ type value_;
+};
+
+// Handler type specialisation for use_future.
+template <typename Allocator, typename ReturnType>
+struct handler_type<use_future_t<Allocator>, ReturnType()>
+{
+ typedef detail::promise_handler<void> type;
+};
+
+// Handler type specialisation for use_future.
+template <typename Allocator, typename ReturnType, typename Arg1>
+struct handler_type<use_future_t<Allocator>, ReturnType(Arg1)>
+{
+ typedef detail::promise_handler<Arg1> type;
+};
+
+// Handler type specialisation for use_future.
+template <typename Allocator, typename ReturnType>
+struct handler_type<use_future_t<Allocator>,
+ ReturnType(boost::system::error_code)>
+{
+ typedef detail::promise_handler<void> type;
+};
+
+// Handler type specialisation for use_future.
+template <typename Allocator, typename ReturnType, typename Arg2>
+struct handler_type<use_future_t<Allocator>,
+ ReturnType(boost::system::error_code, Arg2)>
+{
+ typedef detail::promise_handler<Arg2> type;
+};
+
+#endif // !defined(GENERATING_DOCUMENTATION)
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_USE_FUTURE_HPP
diff --git a/ext/patches/boost/asio/impl/write.hpp b/ext/patches/boost/asio/impl/write.hpp
new file mode 100644
index 0000000..5ef8b41
--- /dev/null
+++ b/ext/patches/boost/asio/impl/write.hpp
@@ -0,0 +1,767 @@
+//
+// impl/write.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_WRITE_HPP
+#define BOOST_ASIO_IMPL_WRITE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/completion_condition.hpp>
+#include <boost/asio/detail/array_fwd.hpp>
+#include <boost/asio/detail/base_from_completion_cond.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/consuming_buffers.hpp>
+#include <boost/asio/detail/dependent_type.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename SyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition>
+std::size_t write(SyncWriteStream& s, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ boost::asio::detail::consuming_buffers<
+ const_buffer, ConstBufferSequence> tmp(buffers);
+ std::size_t total_transferred = 0;
+ tmp.prepare(detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred)));
+ while (tmp.begin() != tmp.end())
+ {
+ std::size_t bytes_transferred = s.write_some(tmp, ec);
+ tmp.consume(bytes_transferred);
+ total_transferred += bytes_transferred;
+ tmp.prepare(detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred)));
+ }
+ return total_transferred;
+}
+
+template <typename SyncWriteStream, typename ConstBufferSequence>
+inline std::size_t write(SyncWriteStream& s, const ConstBufferSequence& buffers)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = write(s, buffers, transfer_all(), ec);
+ boost::asio::detail::throw_error(ec, "write");
+ return bytes_transferred;
+}
+
+template <typename SyncWriteStream, typename ConstBufferSequence>
+inline std::size_t write(SyncWriteStream& s, const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+{
+ return write(s, buffers, transfer_all(), ec);
+}
+
+template <typename SyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition>
+inline std::size_t write(SyncWriteStream& s, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = write(s, buffers, completion_condition, ec);
+ boost::asio::detail::throw_error(ec, "write");
+ return bytes_transferred;
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+template <typename SyncWriteStream, typename Allocator,
+ typename CompletionCondition>
+std::size_t write(SyncWriteStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition, boost::system::error_code& ec)
+{
+ std::size_t bytes_transferred = write(s, b.data(), completion_condition, ec);
+ b.consume(bytes_transferred);
+ return bytes_transferred;
+}
+
+template <typename SyncWriteStream, typename Allocator>
+inline std::size_t write(SyncWriteStream& s,
+ boost::asio::basic_streambuf<Allocator>& b)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = write(s, b, transfer_all(), ec);
+ boost::asio::detail::throw_error(ec, "write");
+ return bytes_transferred;
+}
+
+template <typename SyncWriteStream, typename Allocator>
+inline std::size_t write(SyncWriteStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ boost::system::error_code& ec)
+{
+ return write(s, b, transfer_all(), ec);
+}
+
+template <typename SyncWriteStream, typename Allocator,
+ typename CompletionCondition>
+inline std::size_t write(SyncWriteStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = write(s, b, completion_condition, ec);
+ boost::asio::detail::throw_error(ec, "write");
+ return bytes_transferred;
+}
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+namespace detail
+{
+ template <typename AsyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ class write_op
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_op(AsyncWriteStream& stream, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition, WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_op(const write_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_op(write_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ switch (start_ = start)
+ {
+ case 1:
+ buffers_.prepare(this->check_for_completion(ec, total_transferred_));
+ for (;;)
+ {
+ stream_.async_write_some(buffers_,
+ BOOST_ASIO_MOVE_CAST(write_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ buffers_.consume(bytes_transferred);
+ buffers_.prepare(this->check_for_completion(ec, total_transferred_));
+ if ((!ec && bytes_transferred == 0)
+ || buffers_.begin() == buffers_.end())
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncWriteStream& stream_;
+ boost::asio::detail::consuming_buffers<
+ const_buffer, ConstBufferSequence> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+ template <typename AsyncWriteStream,
+ typename CompletionCondition, typename WriteHandler>
+ class write_op<AsyncWriteStream, boost::asio::mutable_buffers_1,
+ CompletionCondition, WriteHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_op(AsyncWriteStream& stream,
+ const boost::asio::mutable_buffers_1& buffers,
+ CompletionCondition completion_condition,
+ WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffer_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_op(const write_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_op(write_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ stream_.async_write_some(
+ boost::asio::buffer(buffer_ + total_transferred_, n),
+ BOOST_ASIO_MOVE_CAST(write_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == boost::asio::buffer_size(buffer_))
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncWriteStream& stream_;
+ boost::asio::mutable_buffer buffer_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+ template <typename AsyncWriteStream,
+ typename CompletionCondition, typename WriteHandler>
+ class write_op<AsyncWriteStream, boost::asio::const_buffers_1,
+ CompletionCondition, WriteHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_op(AsyncWriteStream& stream,
+ const boost::asio::const_buffers_1& buffers,
+ CompletionCondition completion_condition,
+ WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffer_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_op(const write_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_op(write_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ stream_.async_write_some(
+ boost::asio::buffer(buffer_ + total_transferred_, n),
+ BOOST_ASIO_MOVE_CAST(write_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == boost::asio::buffer_size(buffer_))
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncWriteStream& stream_;
+ boost::asio::const_buffer buffer_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+ template <typename AsyncWriteStream, typename Elem,
+ typename CompletionCondition, typename WriteHandler>
+ class write_op<AsyncWriteStream, boost::array<Elem, 2>,
+ CompletionCondition, WriteHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_op(AsyncWriteStream& stream, const boost::array<Elem, 2>& buffers,
+ CompletionCondition completion_condition, WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_op(const write_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_op(write_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ typename boost::asio::detail::dependent_type<Elem,
+ boost::array<boost::asio::const_buffer, 2> >::type bufs = {{
+ boost::asio::const_buffer(buffers_[0]),
+ boost::asio::const_buffer(buffers_[1]) }};
+ std::size_t buffer_size0 = boost::asio::buffer_size(bufs[0]);
+ std::size_t buffer_size1 = boost::asio::buffer_size(bufs[1]);
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ bufs[0] = boost::asio::buffer(bufs[0] + total_transferred_, n);
+ bufs[1] = boost::asio::buffer(
+ bufs[1] + (total_transferred_ < buffer_size0
+ ? 0 : total_transferred_ - buffer_size0),
+ n - boost::asio::buffer_size(bufs[0]));
+ stream_.async_write_some(bufs, BOOST_ASIO_MOVE_CAST(write_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == buffer_size0 + buffer_size1)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncWriteStream& stream_;
+ boost::array<Elem, 2> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+ template <typename AsyncWriteStream, typename Elem,
+ typename CompletionCondition, typename WriteHandler>
+ class write_op<AsyncWriteStream, std::array<Elem, 2>,
+ CompletionCondition, WriteHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_op(AsyncWriteStream& stream, const std::array<Elem, 2>& buffers,
+ CompletionCondition completion_condition, WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ stream_(stream),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_op(const write_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_op(write_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ stream_(other.stream_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ typename boost::asio::detail::dependent_type<Elem,
+ std::array<boost::asio::const_buffer, 2> >::type bufs = {{
+ boost::asio::const_buffer(buffers_[0]),
+ boost::asio::const_buffer(buffers_[1]) }};
+ std::size_t buffer_size0 = boost::asio::buffer_size(bufs[0]);
+ std::size_t buffer_size1 = boost::asio::buffer_size(bufs[1]);
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ bufs[0] = boost::asio::buffer(bufs[0] + total_transferred_, n);
+ bufs[1] = boost::asio::buffer(
+ bufs[1] + (total_transferred_ < buffer_size0
+ ? 0 : total_transferred_ - buffer_size0),
+ n - boost::asio::buffer_size(bufs[0]));
+ stream_.async_write_some(bufs, BOOST_ASIO_MOVE_CAST(write_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == buffer_size0 + buffer_size1)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncWriteStream& stream_;
+ std::array<Elem, 2> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+ template <typename AsyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ write_op<AsyncWriteStream, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ write_op<AsyncWriteStream, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ inline bool asio_handler_is_continuation(
+ write_op<AsyncWriteStream, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncWriteStream,
+ typename ConstBufferSequence, typename CompletionCondition,
+ typename WriteHandler>
+ inline void asio_handler_invoke(Function& function,
+ write_op<AsyncWriteStream, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncWriteStream,
+ typename ConstBufferSequence, typename CompletionCondition,
+ typename WriteHandler>
+ inline void asio_handler_invoke(const Function& function,
+ write_op<AsyncWriteStream, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write(AsyncWriteStream& s, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ detail::write_op<AsyncWriteStream, ConstBufferSequence,
+ CompletionCondition, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ s, buffers, completion_condition, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+template <typename AsyncWriteStream, typename ConstBufferSequence,
+ typename WriteHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write(AsyncWriteStream& s, const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ detail::write_op<AsyncWriteStream, ConstBufferSequence,
+ detail::transfer_all_t, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ s, buffers, transfer_all(), init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+namespace detail
+{
+ template <typename Allocator, typename WriteHandler>
+ class write_streambuf_handler
+ {
+ public:
+ write_streambuf_handler(boost::asio::basic_streambuf<Allocator>& streambuf,
+ WriteHandler& handler)
+ : streambuf_(streambuf),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_streambuf_handler(const write_streambuf_handler& other)
+ : streambuf_(other.streambuf_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_streambuf_handler(write_streambuf_handler&& other)
+ : streambuf_(other.streambuf_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ const std::size_t bytes_transferred)
+ {
+ streambuf_.consume(bytes_transferred);
+ handler_(ec, bytes_transferred);
+ }
+
+ //private:
+ boost::asio::basic_streambuf<Allocator>& streambuf_;
+ WriteHandler handler_;
+ };
+
+ template <typename Allocator, typename WriteHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ write_streambuf_handler<Allocator, WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename Allocator, typename WriteHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ write_streambuf_handler<Allocator, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename Allocator, typename WriteHandler>
+ inline bool asio_handler_is_continuation(
+ write_streambuf_handler<Allocator, WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename Allocator, typename WriteHandler>
+ inline void asio_handler_invoke(Function& function,
+ write_streambuf_handler<Allocator, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename Allocator, typename WriteHandler>
+ inline void asio_handler_invoke(const Function& function,
+ write_streambuf_handler<Allocator, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+} // namespace detail
+
+template <typename AsyncWriteStream, typename Allocator,
+ typename CompletionCondition, typename WriteHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write(AsyncWriteStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ async_write(s, b.data(), completion_condition,
+ detail::write_streambuf_handler<Allocator, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ b, init.handler));
+
+ return init.result.get();
+}
+
+template <typename AsyncWriteStream, typename Allocator, typename WriteHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write(AsyncWriteStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ async_write(s, b.data(), transfer_all(),
+ detail::write_streambuf_handler<Allocator, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ b, init.handler));
+
+ return init.result.get();
+}
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_WRITE_HPP
diff --git a/ext/patches/boost/asio/impl/write_at.hpp b/ext/patches/boost/asio/impl/write_at.hpp
new file mode 100644
index 0000000..c4013c8
--- /dev/null
+++ b/ext/patches/boost/asio/impl/write_at.hpp
@@ -0,0 +1,827 @@
+//
+// impl/write_at.hpp
+// ~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IMPL_WRITE_AT_HPP
+#define BOOST_ASIO_IMPL_WRITE_AT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/completion_condition.hpp>
+#include <boost/asio/detail/array_fwd.hpp>
+#include <boost/asio/detail/base_from_completion_cond.hpp>
+#include <boost/asio/detail/bind_handler.hpp>
+#include <boost/asio/detail/consuming_buffers.hpp>
+#include <boost/asio/detail/dependent_type.hpp>
+#include <boost/asio/detail/handler_alloc_helpers.hpp>
+#include <boost/asio/detail/handler_cont_helpers.hpp>
+#include <boost/asio/detail/handler_invoke_helpers.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+template <typename SyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition>
+std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition, boost::system::error_code& ec)
+{
+ ec = boost::system::error_code();
+ boost::asio::detail::consuming_buffers<
+ const_buffer, ConstBufferSequence> tmp(buffers);
+ std::size_t total_transferred = 0;
+ tmp.prepare(detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred)));
+ while (tmp.begin() != tmp.end())
+ {
+ std::size_t bytes_transferred = d.write_some_at(
+ offset + total_transferred, tmp, ec);
+ tmp.consume(bytes_transferred);
+ total_transferred += bytes_transferred;
+ tmp.prepare(detail::adapt_completion_condition_result(
+ completion_condition(ec, total_transferred)));
+ }
+ return total_transferred;
+}
+
+template <typename SyncRandomAccessWriteDevice, typename ConstBufferSequence>
+inline std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = write_at(
+ d, offset, buffers, transfer_all(), ec);
+ boost::asio::detail::throw_error(ec, "write_at");
+ return bytes_transferred;
+}
+
+template <typename SyncRandomAccessWriteDevice, typename ConstBufferSequence>
+inline std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+{
+ return write_at(d, offset, buffers, transfer_all(), ec);
+}
+
+template <typename SyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition>
+inline std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = write_at(
+ d, offset, buffers, completion_condition, ec);
+ boost::asio::detail::throw_error(ec, "write_at");
+ return bytes_transferred;
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+template <typename SyncRandomAccessWriteDevice, typename Allocator,
+ typename CompletionCondition>
+std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition, boost::system::error_code& ec)
+{
+ std::size_t bytes_transferred = write_at(
+ d, offset, b.data(), completion_condition, ec);
+ b.consume(bytes_transferred);
+ return bytes_transferred;
+}
+
+template <typename SyncRandomAccessWriteDevice, typename Allocator>
+inline std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = write_at(d, offset, b, transfer_all(), ec);
+ boost::asio::detail::throw_error(ec, "write_at");
+ return bytes_transferred;
+}
+
+template <typename SyncRandomAccessWriteDevice, typename Allocator>
+inline std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ boost::system::error_code& ec)
+{
+ return write_at(d, offset, b, transfer_all(), ec);
+}
+
+template <typename SyncRandomAccessWriteDevice, typename Allocator,
+ typename CompletionCondition>
+inline std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition)
+{
+ boost::system::error_code ec;
+ std::size_t bytes_transferred = write_at(
+ d, offset, b, completion_condition, ec);
+ boost::asio::detail::throw_error(ec, "write_at");
+ return bytes_transferred;
+}
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+namespace detail
+{
+ template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ class write_at_op
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_at_op(AsyncRandomAccessWriteDevice& device,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition, WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_at_op(const write_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_at_op(write_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ switch (start_ = start)
+ {
+ case 1:
+ buffers_.prepare(this->check_for_completion(ec, total_transferred_));
+ for (;;)
+ {
+ device_.async_write_some_at(
+ offset_ + total_transferred_, buffers_,
+ BOOST_ASIO_MOVE_CAST(write_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ buffers_.consume(bytes_transferred);
+ buffers_.prepare(this->check_for_completion(ec, total_transferred_));
+ if ((!ec && bytes_transferred == 0)
+ || buffers_.begin() == buffers_.end())
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessWriteDevice& device_;
+ uint64_t offset_;
+ boost::asio::detail::consuming_buffers<
+ const_buffer, ConstBufferSequence> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+ template <typename AsyncRandomAccessWriteDevice,
+ typename CompletionCondition, typename WriteHandler>
+ class write_at_op<AsyncRandomAccessWriteDevice,
+ boost::asio::mutable_buffers_1, CompletionCondition, WriteHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_at_op(AsyncRandomAccessWriteDevice& device,
+ uint64_t offset, const boost::asio::mutable_buffers_1& buffers,
+ CompletionCondition completion_condition,
+ WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffer_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_at_op(const write_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_at_op(write_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ device_.async_write_some_at(offset_ + total_transferred_,
+ boost::asio::buffer(buffer_ + total_transferred_, n),
+ BOOST_ASIO_MOVE_CAST(write_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == boost::asio::buffer_size(buffer_))
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessWriteDevice& device_;
+ uint64_t offset_;
+ boost::asio::mutable_buffer buffer_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+ template <typename AsyncRandomAccessWriteDevice,
+ typename CompletionCondition, typename WriteHandler>
+ class write_at_op<AsyncRandomAccessWriteDevice, boost::asio::const_buffers_1,
+ CompletionCondition, WriteHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_at_op(AsyncRandomAccessWriteDevice& device,
+ uint64_t offset, const boost::asio::const_buffers_1& buffers,
+ CompletionCondition completion_condition,
+ WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffer_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_at_op(const write_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_at_op(write_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffer_(other.buffer_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ device_.async_write_some_at(offset_ + total_transferred_,
+ boost::asio::buffer(buffer_ + total_transferred_, n),
+ BOOST_ASIO_MOVE_CAST(write_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == boost::asio::buffer_size(buffer_))
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessWriteDevice& device_;
+ uint64_t offset_;
+ boost::asio::const_buffer buffer_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+ template <typename AsyncRandomAccessWriteDevice, typename Elem,
+ typename CompletionCondition, typename WriteHandler>
+ class write_at_op<AsyncRandomAccessWriteDevice, boost::array<Elem, 2>,
+ CompletionCondition, WriteHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_at_op(AsyncRandomAccessWriteDevice& device,
+ uint64_t offset, const boost::array<Elem, 2>& buffers,
+ CompletionCondition completion_condition, WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_at_op(const write_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_at_op(write_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ typename boost::asio::detail::dependent_type<Elem,
+ boost::array<boost::asio::const_buffer, 2> >::type bufs = {{
+ boost::asio::const_buffer(buffers_[0]),
+ boost::asio::const_buffer(buffers_[1]) }};
+ std::size_t buffer_size0 = boost::asio::buffer_size(bufs[0]);
+ std::size_t buffer_size1 = boost::asio::buffer_size(bufs[1]);
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ bufs[0] = boost::asio::buffer(bufs[0] + total_transferred_, n);
+ bufs[1] = boost::asio::buffer(
+ bufs[1] + (total_transferred_ < buffer_size0
+ ? 0 : total_transferred_ - buffer_size0),
+ n - boost::asio::buffer_size(bufs[0]));
+ device_.async_write_some_at(offset_ + total_transferred_,
+ bufs, BOOST_ASIO_MOVE_CAST(write_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == buffer_size0 + buffer_size1)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessWriteDevice& device_;
+ uint64_t offset_;
+ boost::array<Elem, 2> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+ template <typename AsyncRandomAccessWriteDevice, typename Elem,
+ typename CompletionCondition, typename WriteHandler>
+ class write_at_op<AsyncRandomAccessWriteDevice, std::array<Elem, 2>,
+ CompletionCondition, WriteHandler>
+ : detail::base_from_completion_cond<CompletionCondition>
+ {
+ public:
+ write_at_op(AsyncRandomAccessWriteDevice& device,
+ uint64_t offset, const std::array<Elem, 2>& buffers,
+ CompletionCondition completion_condition, WriteHandler& handler)
+ : detail::base_from_completion_cond<
+ CompletionCondition>(completion_condition),
+ device_(device),
+ offset_(offset),
+ buffers_(buffers),
+ start_(0),
+ total_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_at_op(const write_at_op& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_at_op(write_at_op&& other)
+ : detail::base_from_completion_cond<CompletionCondition>(other),
+ device_(other.device_),
+ offset_(other.offset_),
+ buffers_(other.buffers_),
+ start_(other.start_),
+ total_transferred_(other.total_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ std::size_t bytes_transferred, int start = 0)
+ {
+ typename boost::asio::detail::dependent_type<Elem,
+ std::array<boost::asio::const_buffer, 2> >::type bufs = {{
+ boost::asio::const_buffer(buffers_[0]),
+ boost::asio::const_buffer(buffers_[1]) }};
+ std::size_t buffer_size0 = boost::asio::buffer_size(bufs[0]);
+ std::size_t buffer_size1 = boost::asio::buffer_size(bufs[1]);
+ std::size_t n = 0;
+ switch (start_ = start)
+ {
+ case 1:
+ n = this->check_for_completion(ec, total_transferred_);
+ for (;;)
+ {
+ bufs[0] = boost::asio::buffer(bufs[0] + total_transferred_, n);
+ bufs[1] = boost::asio::buffer(
+ bufs[1] + (total_transferred_ < buffer_size0
+ ? 0 : total_transferred_ - buffer_size0),
+ n - boost::asio::buffer_size(bufs[0]));
+ device_.async_write_some_at(offset_ + total_transferred_,
+ bufs, BOOST_ASIO_MOVE_CAST(write_at_op)(*this));
+ return; default:
+ total_transferred_ += bytes_transferred;
+ if ((!ec && bytes_transferred == 0)
+ || (n = this->check_for_completion(ec, total_transferred_)) == 0
+ || total_transferred_ == buffer_size0 + buffer_size1)
+ break;
+ }
+
+ handler_(ec, static_cast<const std::size_t&>(total_transferred_));
+ }
+ }
+
+ //private:
+ AsyncRandomAccessWriteDevice& device_;
+ uint64_t offset_;
+ std::array<Elem, 2> buffers_;
+ int start_;
+ std::size_t total_transferred_;
+ WriteHandler handler_;
+ };
+
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+
+ template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ write_at_op<AsyncRandomAccessWriteDevice, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ write_at_op<AsyncRandomAccessWriteDevice, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ inline bool asio_handler_is_continuation(
+ write_at_op<AsyncRandomAccessWriteDevice, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncRandomAccessWriteDevice,
+ typename ConstBufferSequence, typename CompletionCondition,
+ typename WriteHandler>
+ inline void asio_handler_invoke(Function& function,
+ write_at_op<AsyncRandomAccessWriteDevice, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename AsyncRandomAccessWriteDevice,
+ typename ConstBufferSequence, typename CompletionCondition,
+ typename WriteHandler>
+ inline void asio_handler_invoke(const Function& function,
+ write_at_op<AsyncRandomAccessWriteDevice, ConstBufferSequence,
+ CompletionCondition, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+ inline write_at_op<AsyncRandomAccessWriteDevice,
+ ConstBufferSequence, CompletionCondition, WriteHandler>
+ make_write_at_op(AsyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition, WriteHandler handler)
+ {
+ return write_at_op<AsyncRandomAccessWriteDevice,
+ ConstBufferSequence, CompletionCondition, WriteHandler>(
+ d, offset, buffers, completion_condition, handler);
+ }
+} // namespace detail
+
+template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write_at(AsyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ detail::write_at_op<AsyncRandomAccessWriteDevice, ConstBufferSequence,
+ CompletionCondition, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ d, offset, buffers, completion_condition, init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename WriteHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write_at(AsyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ detail::write_at_op<AsyncRandomAccessWriteDevice, ConstBufferSequence,
+ detail::transfer_all_t, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ d, offset, buffers, transfer_all(), init.handler)(
+ boost::system::error_code(), 0, 1);
+
+ return init.result.get();
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+namespace detail
+{
+ template <typename Allocator, typename WriteHandler>
+ class write_at_streambuf_op
+ {
+ public:
+ write_at_streambuf_op(
+ boost::asio::basic_streambuf<Allocator>& streambuf,
+ WriteHandler& handler)
+ : streambuf_(streambuf),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ write_at_streambuf_op(const write_at_streambuf_op& other)
+ : streambuf_(other.streambuf_),
+ handler_(other.handler_)
+ {
+ }
+
+ write_at_streambuf_op(write_at_streambuf_op&& other)
+ : streambuf_(other.streambuf_),
+ handler_(BOOST_ASIO_MOVE_CAST(WriteHandler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(const boost::system::error_code& ec,
+ const std::size_t bytes_transferred)
+ {
+ streambuf_.consume(bytes_transferred);
+ handler_(ec, bytes_transferred);
+ }
+
+ //private:
+ boost::asio::basic_streambuf<Allocator>& streambuf_;
+ WriteHandler handler_;
+ };
+
+ template <typename Allocator, typename WriteHandler>
+ inline void* asio_handler_allocate(std::size_t size,
+ write_at_streambuf_op<Allocator, WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+ }
+
+ template <typename Allocator, typename WriteHandler>
+ inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ write_at_streambuf_op<Allocator, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+ }
+
+ template <typename Allocator, typename WriteHandler>
+ inline bool asio_handler_is_continuation(
+ write_at_streambuf_op<Allocator, WriteHandler>* this_handler)
+ {
+ return boost_asio_handler_cont_helpers::is_continuation(
+ this_handler->handler_);
+ }
+
+ template <typename Function, typename Allocator, typename WriteHandler>
+ inline void asio_handler_invoke(Function& function,
+ write_at_streambuf_op<Allocator, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Function, typename Allocator, typename WriteHandler>
+ inline void asio_handler_invoke(const Function& function,
+ write_at_streambuf_op<Allocator, WriteHandler>* this_handler)
+ {
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+ }
+
+ template <typename Allocator, typename WriteHandler>
+ inline write_at_streambuf_op<Allocator, WriteHandler>
+ make_write_at_streambuf_op(
+ boost::asio::basic_streambuf<Allocator>& b, WriteHandler handler)
+ {
+ return write_at_streambuf_op<Allocator, WriteHandler>(b, handler);
+ }
+} // namespace detail
+
+template <typename AsyncRandomAccessWriteDevice, typename Allocator,
+ typename CompletionCondition, typename WriteHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write_at(AsyncRandomAccessWriteDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ async_write_at(d, offset, b.data(), completion_condition,
+ detail::write_at_streambuf_op<Allocator, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ b, init.handler));
+
+ return init.result.get();
+}
+
+template <typename AsyncRandomAccessWriteDevice, typename Allocator,
+ typename WriteHandler>
+inline BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write_at(AsyncRandomAccessWriteDevice& d,
+ uint64_t offset, boost::asio::basic_streambuf<Allocator>& b,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+{
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ async_write_at(d, offset, b.data(), transfer_all(),
+ detail::write_at_streambuf_op<Allocator, BOOST_ASIO_HANDLER_TYPE(
+ WriteHandler, void (boost::system::error_code, std::size_t))>(
+ b, init.handler));
+
+ return init.result.get();
+}
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IMPL_WRITE_AT_HPP
diff --git a/ext/patches/boost/asio/io_service.hpp b/ext/patches/boost/asio/io_service.hpp
new file mode 100644
index 0000000..483612c
--- /dev/null
+++ b/ext/patches/boost/asio/io_service.hpp
@@ -0,0 +1,772 @@
+//
+// io_service.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IO_SERVICE_HPP
+#define BOOST_ASIO_IO_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <stdexcept>
+#include <typeinfo>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/wrapped_handler.hpp>
+#include <boost/system/error_code.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# include <boost/asio/detail/winsock_init.hpp>
+#elif defined(__sun) || defined(__QNX__) || defined(__hpux) || defined(_AIX) \
+ || defined(__osf__)
+# include <boost/asio/detail/signal_init.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+class io_service;
+template <typename Service> Service& use_service(io_service& ios);
+template <typename Service> void add_service(io_service& ios, Service* svc);
+template <typename Service> bool has_service(io_service& ios);
+
+namespace detail {
+#if defined(BOOST_ASIO_HAS_IOCP)
+ typedef class win_iocp_io_service io_service_impl;
+ class win_iocp_overlapped_ptr;
+#else
+ typedef class task_io_service io_service_impl;
+#endif
+ class service_registry;
+} // namespace detail
+
+/// Provides core I/O functionality.
+/**
+ * The io_service class provides the core I/O functionality for users of the
+ * asynchronous I/O objects, including:
+ *
+ * @li boost::asio::ip::tcp::socket
+ * @li boost::asio::ip::tcp::acceptor
+ * @li boost::asio::ip::udp::socket
+ * @li boost::asio::deadline_timer.
+ *
+ * The io_service class also includes facilities intended for developers of
+ * custom asynchronous services.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe, with the specific exceptions of the reset() and
+ * notify_fork() functions. Calling reset() while there are unfinished run(),
+ * run_one(), poll() or poll_one() calls results in undefined behaviour. The
+ * notify_fork() function should not be called while any io_service function,
+ * or any function on an I/O object that is associated with the io_service, is
+ * being called in another thread.
+ *
+ * @par Concepts:
+ * Dispatcher.
+ *
+ * @par Synchronous and asynchronous operations
+ *
+ * Synchronous operations on I/O objects implicitly run the io_service object
+ * for an individual operation. The io_service functions run(), run_one(),
+ * poll() or poll_one() must be called for the io_service to perform
+ * asynchronous operations on behalf of a C++ program. Notification that an
+ * asynchronous operation has completed is delivered by invocation of the
+ * associated handler. Handlers are invoked only by a thread that is currently
+ * calling any overload of run(), run_one(), poll() or poll_one() for the
+ * io_service.
+ *
+ * @par Effect of exceptions thrown from handlers
+ *
+ * If an exception is thrown from a handler, the exception is allowed to
+ * propagate through the throwing thread's invocation of run(), run_one(),
+ * poll() or poll_one(). No other threads that are calling any of these
+ * functions are affected. It is then the responsibility of the application to
+ * catch the exception.
+ *
+ * After the exception has been caught, the run(), run_one(), poll() or
+ * poll_one() call may be restarted @em without the need for an intervening
+ * call to reset(). This allows the thread to rejoin the io_service object's
+ * thread pool without impacting any other threads in the pool.
+ *
+ * For example:
+ *
+ * @code
+ * boost::asio::io_service io_service;
+ * ...
+ * for (;;)
+ * {
+ * try
+ * {
+ * io_service.run();
+ * break; // run() exited normally
+ * }
+ * catch (my_exception& e)
+ * {
+ * // Deal with exception as appropriate.
+ * }
+ * }
+ * @endcode
+ *
+ * @par Stopping the io_service from running out of work
+ *
+ * Some applications may need to prevent an io_service object's run() call from
+ * returning when there is no more work to do. For example, the io_service may
+ * be being run in a background thread that is launched prior to the
+ * application's asynchronous operations. The run() call may be kept running by
+ * creating an object of type boost::asio::io_service::work:
+ *
+ * @code boost::asio::io_service io_service;
+ * boost::asio::io_service::work work(io_service);
+ * ... @endcode
+ *
+ * To effect a shutdown, the application will then need to call the io_service
+ * object's stop() member function. This will cause the io_service run() call
+ * to return as soon as possible, abandoning unfinished operations and without
+ * permitting ready handlers to be dispatched.
+ *
+ * Alternatively, if the application requires that all operations and handlers
+ * be allowed to finish normally, the work object may be explicitly destroyed.
+ *
+ * @code boost::asio::io_service io_service;
+ * auto_ptr<boost::asio::io_service::work> work(
+ * new boost::asio::io_service::work(io_service));
+ * ...
+ * work.reset(); // Allow run() to exit. @endcode
+ *
+ * @par The io_service class and I/O services
+ *
+ * Class io_service implements an extensible, type-safe, polymorphic set of I/O
+ * services, indexed by service type. An object of class io_service must be
+ * initialised before I/O objects such as sockets, resolvers and timers can be
+ * used. These I/O objects are distinguished by having constructors that accept
+ * an @c io_service& parameter.
+ *
+ * I/O services exist to manage the logical interface to the operating system on
+ * behalf of the I/O objects. In particular, there are resources that are shared
+ * across a class of I/O objects. For example, timers may be implemented in
+ * terms of a single timer queue. The I/O services manage these shared
+ * resources.
+ *
+ * Access to the services of an io_service is via three function templates,
+ * use_service(), add_service() and has_service().
+ *
+ * In a call to @c use_service<Service>(), the type argument chooses a service,
+ * making available all members of the named type. If @c Service is not present
+ * in an io_service, an object of type @c Service is created and added to the
+ * io_service. A C++ program can check if an io_service implements a
+ * particular service with the function template @c has_service<Service>().
+ *
+ * Service objects may be explicitly added to an io_service using the function
+ * template @c add_service<Service>(). If the @c Service is already present, the
+ * service_already_exists exception is thrown. If the owner of the service is
+ * not the same object as the io_service parameter, the invalid_service_owner
+ * exception is thrown.
+ *
+ * Once a service reference is obtained from an io_service object by calling
+ * use_service(), that reference remains usable as long as the owning io_service
+ * object exists.
+ *
+ * All I/O service implementations have io_service::service as a public base
+ * class. Custom I/O services may be implemented by deriving from this class and
+ * then added to an io_service using the facilities described above.
+ */
+class io_service
+ : private noncopyable
+{
+private:
+ typedef detail::io_service_impl impl_type;
+#if defined(BOOST_ASIO_HAS_IOCP)
+ friend class detail::win_iocp_overlapped_ptr;
+#endif
+
+public:
+ class work;
+ friend class work;
+
+ class id;
+
+ class service;
+
+ class strand;
+
+ /// Constructor.
+ BOOST_ASIO_DECL io_service();
+
+ /// Constructor.
+ /**
+ * Construct with a hint about the required level of concurrency.
+ *
+ * @param concurrency_hint A suggestion to the implementation on how many
+ * threads it should allow to run simultaneously.
+ */
+ BOOST_ASIO_DECL explicit io_service(std::size_t concurrency_hint);
+
+ /// Destructor.
+ /**
+ * On destruction, the io_service performs the following sequence of
+ * operations:
+ *
+ * @li For each service object @c svc in the io_service set, in reverse order
+ * of the beginning of service object lifetime, performs
+ * @c svc->shutdown_service().
+ *
+ * @li Uninvoked handler objects that were scheduled for deferred invocation
+ * on the io_service, or any associated strand, are destroyed.
+ *
+ * @li For each service object @c svc in the io_service set, in reverse order
+ * of the beginning of service object lifetime, performs
+ * <tt>delete static_cast<io_service::service*>(svc)</tt>.
+ *
+ * @note The destruction sequence described above permits programs to
+ * simplify their resource management by using @c shared_ptr<>. Where an
+ * object's lifetime is tied to the lifetime of a connection (or some other
+ * sequence of asynchronous operations), a @c shared_ptr to the object would
+ * be bound into the handlers for all asynchronous operations associated with
+ * it. This works as follows:
+ *
+ * @li When a single connection ends, all associated asynchronous operations
+ * complete. The corresponding handler objects are destroyed, and all
+ * @c shared_ptr references to the objects are destroyed.
+ *
+ * @li To shut down the whole program, the io_service function stop() is
+ * called to terminate any run() calls as soon as possible. The io_service
+ * destructor defined above destroys all handlers, causing all @c shared_ptr
+ * references to all connection objects to be destroyed.
+ */
+ BOOST_ASIO_DECL ~io_service();
+
+ /// Run the io_service object's event processing loop.
+ /**
+ * The run() function blocks until all work has finished and there are no
+ * more handlers to be dispatched, or until the io_service has been stopped.
+ *
+ * Multiple threads may call the run() function to set up a pool of threads
+ * from which the io_service may execute handlers. All threads that are
+ * waiting in the pool are equivalent and the io_service may choose any one
+ * of them to invoke a handler.
+ *
+ * A normal exit from the run() function implies that the io_service object
+ * is stopped (the stopped() function returns @c true). Subsequent calls to
+ * run(), run_one(), poll() or poll_one() will return immediately unless there
+ * is a prior call to reset().
+ *
+ * @return The number of handlers that were executed.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The run() function must not be called from a thread that is currently
+ * calling one of run(), run_one(), poll() or poll_one() on the same
+ * io_service object.
+ *
+ * The poll() function may also be used to dispatch ready handlers, but
+ * without blocking.
+ */
+ BOOST_ASIO_DECL std::size_t run();
+
+ /// Run the io_service object's event processing loop.
+ /**
+ * The run() function blocks until all work has finished and there are no
+ * more handlers to be dispatched, or until the io_service has been stopped.
+ *
+ * Multiple threads may call the run() function to set up a pool of threads
+ * from which the io_service may execute handlers. All threads that are
+ * waiting in the pool are equivalent and the io_service may choose any one
+ * of them to invoke a handler.
+ *
+ * A normal exit from the run() function implies that the io_service object
+ * is stopped (the stopped() function returns @c true). Subsequent calls to
+ * run(), run_one(), poll() or poll_one() will return immediately unless there
+ * is a prior call to reset().
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of handlers that were executed.
+ *
+ * @note The run() function must not be called from a thread that is currently
+ * calling one of run(), run_one(), poll() or poll_one() on the same
+ * io_service object.
+ *
+ * The poll() function may also be used to dispatch ready handlers, but
+ * without blocking.
+ */
+ BOOST_ASIO_DECL std::size_t run(boost::system::error_code& ec);
+
+ /// Run the io_service object's event processing loop to execute at most one
+ /// handler.
+ /**
+ * The run_one() function blocks until one handler has been dispatched, or
+ * until the io_service has been stopped.
+ *
+ * @return The number of handlers that were executed. A zero return value
+ * implies that the io_service object is stopped (the stopped() function
+ * returns @c true). Subsequent calls to run(), run_one(), poll() or
+ * poll_one() will return immediately unless there is a prior call to
+ * reset().
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ BOOST_ASIO_DECL std::size_t run_one();
+
+ /// Run the io_service object's event processing loop to execute at most one
+ /// handler.
+ /**
+ * The run_one() function blocks until one handler has been dispatched, or
+ * until the io_service has been stopped.
+ *
+ * @return The number of handlers that were executed. A zero return value
+ * implies that the io_service object is stopped (the stopped() function
+ * returns @c true). Subsequent calls to run(), run_one(), poll() or
+ * poll_one() will return immediately unless there is a prior call to
+ * reset().
+ *
+ * @return The number of handlers that were executed.
+ */
+ BOOST_ASIO_DECL std::size_t run_one(boost::system::error_code& ec);
+
+ /// Run the io_service object's event processing loop to execute ready
+ /// handlers.
+ /**
+ * The poll() function runs handlers that are ready to run, without blocking,
+ * until the io_service has been stopped or there are no more ready handlers.
+ *
+ * @return The number of handlers that were executed.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ BOOST_ASIO_DECL std::size_t poll();
+
+ /// Run the io_service object's event processing loop to execute ready
+ /// handlers.
+ /**
+ * The poll() function runs handlers that are ready to run, without blocking,
+ * until the io_service has been stopped or there are no more ready handlers.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of handlers that were executed.
+ */
+ BOOST_ASIO_DECL std::size_t poll(boost::system::error_code& ec);
+
+ /// Run the io_service object's event processing loop to execute one ready
+ /// handler.
+ /**
+ * The poll_one() function runs at most one handler that is ready to run,
+ * without blocking.
+ *
+ * @return The number of handlers that were executed.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ BOOST_ASIO_DECL std::size_t poll_one();
+
+ /// Run the io_service object's event processing loop to execute one ready
+ /// handler.
+ /**
+ * The poll_one() function runs at most one handler that is ready to run,
+ * without blocking.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @return The number of handlers that were executed.
+ */
+ BOOST_ASIO_DECL std::size_t poll_one(boost::system::error_code& ec);
+
+ /// Stop the io_service object's event processing loop.
+ /**
+ * This function does not block, but instead simply signals the io_service to
+ * stop. All invocations of its run() or run_one() member functions should
+ * return as soon as possible. Subsequent calls to run(), run_one(), poll()
+ * or poll_one() will return immediately until reset() is called.
+ */
+ BOOST_ASIO_DECL void stop();
+
+ /// Determine whether the io_service object has been stopped.
+ /**
+ * This function is used to determine whether an io_service object has been
+ * stopped, either through an explicit call to stop(), or due to running out
+ * of work. When an io_service object is stopped, calls to run(), run_one(),
+ * poll() or poll_one() will return immediately without invoking any
+ * handlers.
+ *
+ * @return @c true if the io_service object is stopped, otherwise @c false.
+ */
+ BOOST_ASIO_DECL bool stopped() const;
+
+ /// Reset the io_service in preparation for a subsequent run() invocation.
+ /**
+ * This function must be called prior to any second or later set of
+ * invocations of the run(), run_one(), poll() or poll_one() functions when a
+ * previous invocation of these functions returned due to the io_service
+ * being stopped or running out of work. After a call to reset(), the
+ * io_service object's stopped() function will return @c false.
+ *
+ * This function must not be called while there are any unfinished calls to
+ * the run(), run_one(), poll() or poll_one() functions.
+ */
+ BOOST_ASIO_DECL void reset();
+
+ /// Request the io_service to invoke the given handler.
+ /**
+ * This function is used to ask the io_service to execute the given handler.
+ *
+ * The io_service guarantees that the handler will only be called in a thread
+ * in which the run(), run_one(), poll() or poll_one() member functions is
+ * currently being invoked. The handler may be executed inside this function
+ * if the guarantee can be met.
+ *
+ * @param handler The handler to be called. The io_service will make
+ * a copy of the handler object as required. The function signature of the
+ * handler must be: @code void handler(); @endcode
+ *
+ * @note This function throws an exception only if:
+ *
+ * @li the handler's @c asio_handler_allocate function; or
+ *
+ * @li the handler's copy constructor
+ *
+ * throws an exception.
+ */
+ template <typename CompletionHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(CompletionHandler, void ())
+ dispatch(BOOST_ASIO_MOVE_ARG(CompletionHandler) handler);
+
+ /// Request the io_service to invoke the given handler and return immediately.
+ /**
+ * This function is used to ask the io_service to execute the given handler,
+ * but without allowing the io_service to call the handler from inside this
+ * function.
+ *
+ * The io_service guarantees that the handler will only be called in a thread
+ * in which the run(), run_one(), poll() or poll_one() member functions is
+ * currently being invoked.
+ *
+ * @param handler The handler to be called. The io_service will make
+ * a copy of the handler object as required. The function signature of the
+ * handler must be: @code void handler(); @endcode
+ *
+ * @note This function throws an exception only if:
+ *
+ * @li the handler's @c asio_handler_allocate function; or
+ *
+ * @li the handler's copy constructor
+ *
+ * throws an exception.
+ */
+ template <typename CompletionHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(CompletionHandler, void ())
+ post(BOOST_ASIO_MOVE_ARG(CompletionHandler) handler);
+
+ /// Create a new handler that automatically dispatches the wrapped handler
+ /// on the io_service.
+ /**
+ * This function is used to create a new handler function object that, when
+ * invoked, will automatically pass the wrapped handler to the io_service
+ * object's dispatch function.
+ *
+ * @param handler The handler to be wrapped. The io_service will make a copy
+ * of the handler object as required. The function signature of the handler
+ * must be: @code void handler(A1 a1, ... An an); @endcode
+ *
+ * @return A function object that, when invoked, passes the wrapped handler to
+ * the io_service object's dispatch function. Given a function object with the
+ * signature:
+ * @code R f(A1 a1, ... An an); @endcode
+ * If this function object is passed to the wrap function like so:
+ * @code io_service.wrap(f); @endcode
+ * then the return value is a function object with the signature
+ * @code void g(A1 a1, ... An an); @endcode
+ * that, when invoked, executes code equivalent to:
+ * @code io_service.dispatch(boost::bind(f, a1, ... an)); @endcode
+ */
+ template <typename Handler>
+#if defined(GENERATING_DOCUMENTATION)
+ unspecified
+#else
+ detail::wrapped_handler<io_service&, Handler>
+#endif
+ wrap(Handler handler);
+
+ /// Fork-related event notifications.
+ enum fork_event
+ {
+ /// Notify the io_service that the process is about to fork.
+ fork_prepare,
+
+ /// Notify the io_service that the process has forked and is the parent.
+ fork_parent,
+
+ /// Notify the io_service that the process has forked and is the child.
+ fork_child
+ };
+
+ /// Notify the io_service of a fork-related event.
+ /**
+ * This function is used to inform the io_service that the process is about
+ * to fork, or has just forked. This allows the io_service, and the services
+ * it contains, to perform any necessary housekeeping to ensure correct
+ * operation following a fork.
+ *
+ * This function must not be called while any other io_service function, or
+ * any function on an I/O object associated with the io_service, is being
+ * called in another thread. It is, however, safe to call this function from
+ * within a completion handler, provided no other thread is accessing the
+ * io_service.
+ *
+ * @param event A fork-related event.
+ *
+ * @throws boost::system::system_error Thrown on failure. If the notification
+ * fails the io_service object should no longer be used and should be
+ * destroyed.
+ *
+ * @par Example
+ * The following code illustrates how to incorporate the notify_fork()
+ * function:
+ * @code my_io_service.notify_fork(boost::asio::io_service::fork_prepare);
+ * if (fork() == 0)
+ * {
+ * // This is the child process.
+ * my_io_service.notify_fork(boost::asio::io_service::fork_child);
+ * }
+ * else
+ * {
+ * // This is the parent process.
+ * my_io_service.notify_fork(boost::asio::io_service::fork_parent);
+ * } @endcode
+ *
+ * @note For each service object @c svc in the io_service set, performs
+ * <tt>svc->fork_service();</tt>. When processing the fork_prepare event,
+ * services are visited in reverse order of the beginning of service object
+ * lifetime. Otherwise, services are visited in order of the beginning of
+ * service object lifetime.
+ */
+ BOOST_ASIO_DECL void notify_fork(boost::asio::io_service::fork_event event);
+
+ /// Obtain the service object corresponding to the given type.
+ /**
+ * This function is used to locate a service object that corresponds to
+ * the given service type. If there is no existing implementation of the
+ * service, then the io_service will create a new instance of the service.
+ *
+ * @param ios The io_service object that owns the service.
+ *
+ * @return The service interface implementing the specified service type.
+ * Ownership of the service interface is not transferred to the caller.
+ */
+ template <typename Service>
+ friend Service& use_service(io_service& ios);
+
+ /// Add a service object to the io_service.
+ /**
+ * This function is used to add a service to the io_service.
+ *
+ * @param ios The io_service object that owns the service.
+ *
+ * @param svc The service object. On success, ownership of the service object
+ * is transferred to the io_service. When the io_service object is destroyed,
+ * it will destroy the service object by performing:
+ * @code delete static_cast<io_service::service*>(svc) @endcode
+ *
+ * @throws boost::asio::service_already_exists Thrown if a service of the
+ * given type is already present in the io_service.
+ *
+ * @throws boost::asio::invalid_service_owner Thrown if the service's owning
+ * io_service is not the io_service object specified by the ios parameter.
+ */
+ template <typename Service>
+ friend void add_service(io_service& ios, Service* svc);
+
+ /// Determine if an io_service contains a specified service type.
+ /**
+ * This function is used to determine whether the io_service contains a
+ * service object corresponding to the given service type.
+ *
+ * @param ios The io_service object that owns the service.
+ *
+ * @return A boolean indicating whether the io_service contains the service.
+ */
+ template <typename Service>
+ friend bool has_service(io_service& ios);
+
+private:
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ detail::winsock_init<> init_;
+#elif defined(__sun) || defined(__QNX__) || defined(__hpux) || defined(_AIX) \
+ || defined(__osf__)
+ detail::signal_init<> init_;
+#endif
+
+ // The service registry.
+ boost::asio::detail::service_registry* service_registry_;
+
+ // The implementation.
+ impl_type& impl_;
+};
+
+/// Class to inform the io_service when it has work to do.
+/**
+ * The work class is used to inform the io_service when work starts and
+ * finishes. This ensures that the io_service object's run() function will not
+ * exit while work is underway, and that it does exit when there is no
+ * unfinished work remaining.
+ *
+ * The work class is copy-constructible so that it may be used as a data member
+ * in a handler class. It is not assignable.
+ */
+class io_service::work
+{
+public:
+ /// Constructor notifies the io_service that work is starting.
+ /**
+ * The constructor is used to inform the io_service that some work has begun.
+ * This ensures that the io_service object's run() function will not exit
+ * while the work is underway.
+ */
+ explicit work(boost::asio::io_service& io_service);
+
+ /// Copy constructor notifies the io_service that work is starting.
+ /**
+ * The constructor is used to inform the io_service that some work has begun.
+ * This ensures that the io_service object's run() function will not exit
+ * while the work is underway.
+ */
+ work(const work& other);
+
+ /// Destructor notifies the io_service that the work is complete.
+ /**
+ * The destructor is used to inform the io_service that some work has
+ * finished. Once the count of unfinished work reaches zero, the io_service
+ * object's run() function is permitted to exit.
+ */
+ ~work();
+
+ /// Get the io_service associated with the work.
+ boost::asio::io_service& get_io_service();
+
+private:
+ // Prevent assignment.
+ void operator=(const work& other);
+
+ // The io_service implementation.
+ detail::io_service_impl& io_service_impl_;
+};
+
+/// Class used to uniquely identify a service.
+class io_service::id
+ : private noncopyable
+{
+public:
+ /// Constructor.
+ id() {}
+};
+
+/// Base class for all io_service services.
+class io_service::service
+ : private noncopyable
+{
+public:
+ /// Get the io_service object that owns the service.
+ boost::asio::io_service& get_io_service();
+
+protected:
+ /// Constructor.
+ /**
+ * @param owner The io_service object that owns the service.
+ */
+ BOOST_ASIO_DECL service(boost::asio::io_service& owner);
+
+ /// Destructor.
+ BOOST_ASIO_DECL virtual ~service();
+
+private:
+ /// Destroy all user-defined handler objects owned by the service.
+ virtual void shutdown_service() = 0;
+
+ /// Handle notification of a fork-related event to perform any necessary
+ /// housekeeping.
+ /**
+ * This function is not a pure virtual so that services only have to
+ * implement it if necessary. The default implementation does nothing.
+ */
+ BOOST_ASIO_DECL virtual void fork_service(
+ boost::asio::io_service::fork_event event);
+
+ friend class boost::asio::detail::service_registry;
+ struct key
+ {
+ key() : type_info_(0), id_(0) {}
+ const std::type_info* type_info_;
+ const boost::asio::io_service::id* id_;
+ } key_;
+
+ boost::asio::io_service& owner_;
+ service* next_;
+};
+
+/// Exception thrown when trying to add a duplicate service to an io_service.
+class service_already_exists
+ : public std::logic_error
+{
+public:
+ BOOST_ASIO_DECL service_already_exists();
+};
+
+/// Exception thrown when trying to add a service object to an io_service where
+/// the service has a different owner.
+class invalid_service_owner
+ : public std::logic_error
+{
+public:
+ BOOST_ASIO_DECL invalid_service_owner();
+};
+
+namespace detail {
+
+// Special derived service id type to keep classes header-file only.
+template <typename Type>
+class service_id
+ : public boost::asio::io_service::id
+{
+};
+
+// Special service base class to keep classes header-file only.
+template <typename Type>
+class service_base
+ : public boost::asio::io_service::service
+{
+public:
+ static boost::asio::detail::service_id<Type> id;
+
+ // Constructor.
+ service_base(boost::asio::io_service& io_service)
+ : boost::asio::io_service::service(io_service)
+ {
+ }
+};
+
+template <typename Type>
+boost::asio::detail::service_id<Type> service_base<Type>::id;
+
+} // namespace detail
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/io_service.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/impl/io_service.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_IO_SERVICE_HPP
diff --git a/ext/patches/boost/asio/ip/address.hpp b/ext/patches/boost/asio/ip/address.hpp
new file mode 100644
index 0000000..a04c7f0
--- /dev/null
+++ b/ext/patches/boost/asio/ip/address.hpp
@@ -0,0 +1,202 @@
+//
+// ip/address.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_ADDRESS_HPP
+#define BOOST_ASIO_IP_ADDRESS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/system/error_code.hpp>
+#include <boost/asio/ip/address_v4.hpp>
+#include <boost/asio/ip/address_v6.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+# include <iosfwd>
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Implements version-independent IP addresses.
+/**
+ * The boost::asio::ip::address class provides the ability to use either IP
+ * version 4 or version 6 addresses.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+class address
+{
+public:
+ /// Default constructor.
+ BOOST_ASIO_DECL address();
+
+ /// Construct an address from an IPv4 address.
+ BOOST_ASIO_DECL address(const boost::asio::ip::address_v4& ipv4_address);
+
+ /// Construct an address from an IPv6 address.
+ BOOST_ASIO_DECL address(const boost::asio::ip::address_v6& ipv6_address);
+
+ /// Copy constructor.
+ BOOST_ASIO_DECL address(const address& other);
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move constructor.
+ BOOST_ASIO_DECL address(address&& other);
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// Assign from another address.
+ BOOST_ASIO_DECL address& operator=(const address& other);
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move-assign from another address.
+ BOOST_ASIO_DECL address& operator=(address&& other);
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// Assign from an IPv4 address.
+ BOOST_ASIO_DECL address& operator=(
+ const boost::asio::ip::address_v4& ipv4_address);
+
+ /// Assign from an IPv6 address.
+ BOOST_ASIO_DECL address& operator=(
+ const boost::asio::ip::address_v6& ipv6_address);
+
+ /// Get whether the address is an IP version 4 address.
+ bool is_v4() const
+ {
+ return type_ == ipv4;
+ }
+
+ /// Get whether the address is an IP version 6 address.
+ bool is_v6() const
+ {
+ return type_ == ipv6;
+ }
+
+ /// Get the address as an IP version 4 address.
+ BOOST_ASIO_DECL boost::asio::ip::address_v4 to_v4() const;
+
+ /// Get the address as an IP version 6 address.
+ BOOST_ASIO_DECL boost::asio::ip::address_v6 to_v6() const;
+
+ /// Get the address as a string in dotted decimal format.
+ BOOST_ASIO_DECL std::string to_string() const;
+
+ /// Get the address as a string in dotted decimal format.
+ BOOST_ASIO_DECL std::string to_string(boost::system::error_code& ec) const;
+
+ /// Create an address from an IPv4 address string in dotted decimal form,
+ /// or from an IPv6 address in hexadecimal notation.
+ BOOST_ASIO_DECL static address from_string(const char* str);
+
+ /// Create an address from an IPv4 address string in dotted decimal form,
+ /// or from an IPv6 address in hexadecimal notation.
+ BOOST_ASIO_DECL static address from_string(
+ const char* str, boost::system::error_code& ec);
+
+ /// Create an address from an IPv4 address string in dotted decimal form,
+ /// or from an IPv6 address in hexadecimal notation.
+ BOOST_ASIO_DECL static address from_string(const std::string& str);
+
+ /// Create an address from an IPv4 address string in dotted decimal form,
+ /// or from an IPv6 address in hexadecimal notation.
+ BOOST_ASIO_DECL static address from_string(
+ const std::string& str, boost::system::error_code& ec);
+
+ /// Determine whether the address is a loopback address.
+ BOOST_ASIO_DECL bool is_loopback() const;
+
+ /// Determine whether the address is unspecified.
+ BOOST_ASIO_DECL bool is_unspecified() const;
+
+ /// Determine whether the address is a multicast address.
+ BOOST_ASIO_DECL bool is_multicast() const;
+
+ /// Compare two addresses for equality.
+ BOOST_ASIO_DECL friend bool operator==(const address& a1, const address& a2);
+
+ /// Compare two addresses for inequality.
+ friend bool operator!=(const address& a1, const address& a2)
+ {
+ return !(a1 == a2);
+ }
+
+ /// Compare addresses for ordering.
+ BOOST_ASIO_DECL friend bool operator<(const address& a1, const address& a2);
+
+ /// Compare addresses for ordering.
+ friend bool operator>(const address& a1, const address& a2)
+ {
+ return a2 < a1;
+ }
+
+ /// Compare addresses for ordering.
+ friend bool operator<=(const address& a1, const address& a2)
+ {
+ return !(a2 < a1);
+ }
+
+ /// Compare addresses for ordering.
+ friend bool operator>=(const address& a1, const address& a2)
+ {
+ return !(a1 < a2);
+ }
+
+private:
+ // The type of the address.
+ enum { ipv4, ipv6 } type_;
+
+ // The underlying IPv4 address.
+ boost::asio::ip::address_v4 ipv4_address_;
+
+ // The underlying IPv6 address.
+ boost::asio::ip::address_v6 ipv6_address_;
+};
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Output an address as a string.
+/**
+ * Used to output a human-readable string for a specified address.
+ *
+ * @param os The output stream to which the string will be written.
+ *
+ * @param addr The address to be written.
+ *
+ * @return The output stream.
+ *
+ * @relates boost::asio::ip::address
+ */
+template <typename Elem, typename Traits>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os, const address& addr);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/ip/impl/address.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ip/impl/address.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_IP_ADDRESS_HPP
diff --git a/ext/patches/boost/asio/ip/address_v4.hpp b/ext/patches/boost/asio/ip/address_v4.hpp
new file mode 100644
index 0000000..d1761da
--- /dev/null
+++ b/ext/patches/boost/asio/ip/address_v4.hpp
@@ -0,0 +1,243 @@
+//
+// ip/address_v4.hpp
+// ~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_ADDRESS_V4_HPP
+#define BOOST_ASIO_IP_ADDRESS_V4_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/asio/detail/array.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/winsock_init.hpp>
+#include <boost/system/error_code.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+# include <iosfwd>
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Implements IP version 4 style addresses.
+/**
+ * The boost::asio::ip::address_v4 class provides the ability to use and
+ * manipulate IP version 4 addresses.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+class address_v4
+{
+public:
+ /// The type used to represent an address as an array of bytes.
+ /**
+ * @note This type is defined in terms of the C++0x template @c std::array
+ * when it is available. Otherwise, it uses @c boost:array.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef array<unsigned char, 4> bytes_type;
+#else
+ typedef boost::asio::detail::array<unsigned char, 4> bytes_type;
+#endif
+
+ /// Default constructor.
+ address_v4()
+ {
+ addr_.s_addr = 0;
+ }
+
+ /// Construct an address from raw bytes.
+ BOOST_ASIO_DECL explicit address_v4(const bytes_type& bytes);
+
+ /// Construct an address from a unsigned long in host byte order.
+ BOOST_ASIO_DECL explicit address_v4(unsigned long addr);
+
+ /// Copy constructor.
+ address_v4(const address_v4& other)
+ : addr_(other.addr_)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move constructor.
+ address_v4(address_v4&& other)
+ : addr_(other.addr_)
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// Assign from another address.
+ address_v4& operator=(const address_v4& other)
+ {
+ addr_ = other.addr_;
+ return *this;
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move-assign from another address.
+ address_v4& operator=(address_v4&& other)
+ {
+ addr_ = other.addr_;
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// Get the address in bytes, in network byte order.
+ BOOST_ASIO_DECL bytes_type to_bytes() const;
+
+ /// Get the address as an unsigned long in host byte order
+ BOOST_ASIO_DECL unsigned long to_ulong() const;
+
+ /// Get the address as a string in dotted decimal format.
+ BOOST_ASIO_DECL std::string to_string() const;
+
+ /// Get the address as a string in dotted decimal format.
+ BOOST_ASIO_DECL std::string to_string(boost::system::error_code& ec) const;
+
+ /// Create an address from an IP address string in dotted decimal form.
+ BOOST_ASIO_DECL static address_v4 from_string(const char* str);
+
+ /// Create an address from an IP address string in dotted decimal form.
+ BOOST_ASIO_DECL static address_v4 from_string(
+ const char* str, boost::system::error_code& ec);
+
+ /// Create an address from an IP address string in dotted decimal form.
+ BOOST_ASIO_DECL static address_v4 from_string(const std::string& str);
+
+ /// Create an address from an IP address string in dotted decimal form.
+ BOOST_ASIO_DECL static address_v4 from_string(
+ const std::string& str, boost::system::error_code& ec);
+
+ /// Determine whether the address is a loopback address.
+ BOOST_ASIO_DECL bool is_loopback() const;
+
+ /// Determine whether the address is unspecified.
+ BOOST_ASIO_DECL bool is_unspecified() const;
+
+ /// Determine whether the address is a class A address.
+ BOOST_ASIO_DECL bool is_class_a() const;
+
+ /// Determine whether the address is a class B address.
+ BOOST_ASIO_DECL bool is_class_b() const;
+
+ /// Determine whether the address is a class C address.
+ BOOST_ASIO_DECL bool is_class_c() const;
+
+ /// Determine whether the address is a multicast address.
+ BOOST_ASIO_DECL bool is_multicast() const;
+
+ /// Compare two addresses for equality.
+ friend bool operator==(const address_v4& a1, const address_v4& a2)
+ {
+ return a1.addr_.s_addr == a2.addr_.s_addr;
+ }
+
+ /// Compare two addresses for inequality.
+ friend bool operator!=(const address_v4& a1, const address_v4& a2)
+ {
+ return a1.addr_.s_addr != a2.addr_.s_addr;
+ }
+
+ /// Compare addresses for ordering.
+ friend bool operator<(const address_v4& a1, const address_v4& a2)
+ {
+ return a1.to_ulong() < a2.to_ulong();
+ }
+
+ /// Compare addresses for ordering.
+ friend bool operator>(const address_v4& a1, const address_v4& a2)
+ {
+ return a1.to_ulong() > a2.to_ulong();
+ }
+
+ /// Compare addresses for ordering.
+ friend bool operator<=(const address_v4& a1, const address_v4& a2)
+ {
+ return a1.to_ulong() <= a2.to_ulong();
+ }
+
+ /// Compare addresses for ordering.
+ friend bool operator>=(const address_v4& a1, const address_v4& a2)
+ {
+ return a1.to_ulong() >= a2.to_ulong();
+ }
+
+ /// Obtain an address object that represents any address.
+ static address_v4 any()
+ {
+ return address_v4();
+ }
+
+ /// Obtain an address object that represents the loopback address.
+ static address_v4 loopback()
+ {
+ return address_v4(0x7F000001);
+ }
+
+ /// Obtain an address object that represents the broadcast address.
+ static address_v4 broadcast()
+ {
+ return address_v4(0xFFFFFFFF);
+ }
+
+ /// Obtain an address object that represents the broadcast address that
+ /// corresponds to the specified address and netmask.
+ BOOST_ASIO_DECL static address_v4 broadcast(
+ const address_v4& addr, const address_v4& mask);
+
+ /// Obtain the netmask that corresponds to the address, based on its address
+ /// class.
+ BOOST_ASIO_DECL static address_v4 netmask(const address_v4& addr);
+
+private:
+ // The underlying IPv4 address.
+ boost::asio::detail::in4_addr_type addr_;
+};
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Output an address as a string.
+/**
+ * Used to output a human-readable string for a specified address.
+ *
+ * @param os The output stream to which the string will be written.
+ *
+ * @param addr The address to be written.
+ *
+ * @return The output stream.
+ *
+ * @relates boost::asio::ip::address_v4
+ */
+template <typename Elem, typename Traits>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os, const address_v4& addr);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/ip/impl/address_v4.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ip/impl/address_v4.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_IP_ADDRESS_V4_HPP
diff --git a/ext/patches/boost/asio/ip/address_v6.hpp b/ext/patches/boost/asio/ip/address_v6.hpp
new file mode 100644
index 0000000..a60b6d3
--- /dev/null
+++ b/ext/patches/boost/asio/ip/address_v6.hpp
@@ -0,0 +1,248 @@
+//
+// ip/address_v6.hpp
+// ~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_ADDRESS_V6_HPP
+#define BOOST_ASIO_IP_ADDRESS_V6_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/asio/detail/array.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/winsock_init.hpp>
+#include <boost/system/error_code.hpp>
+#include <boost/asio/ip/address_v4.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+# include <iosfwd>
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Implements IP version 6 style addresses.
+/**
+ * The boost::asio::ip::address_v6 class provides the ability to use and
+ * manipulate IP version 6 addresses.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+class address_v6
+{
+public:
+ /// The type used to represent an address as an array of bytes.
+ /**
+ * @note This type is defined in terms of the C++0x template @c std::array
+ * when it is available. Otherwise, it uses @c boost:array.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef array<unsigned char, 16> bytes_type;
+#else
+ typedef boost::asio::detail::array<unsigned char, 16> bytes_type;
+#endif
+
+ /// Default constructor.
+ BOOST_ASIO_DECL address_v6();
+
+ /// Construct an address from raw bytes and scope ID.
+ BOOST_ASIO_DECL explicit address_v6(const bytes_type& bytes,
+ unsigned long scope_id = 0);
+
+ /// Copy constructor.
+ BOOST_ASIO_DECL address_v6(const address_v6& other);
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move constructor.
+ BOOST_ASIO_DECL address_v6(address_v6&& other);
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// Assign from another address.
+ BOOST_ASIO_DECL address_v6& operator=(const address_v6& other);
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move-assign from another address.
+ BOOST_ASIO_DECL address_v6& operator=(address_v6&& other);
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// The scope ID of the address.
+ /**
+ * Returns the scope ID associated with the IPv6 address.
+ */
+ unsigned long scope_id() const
+ {
+ return scope_id_;
+ }
+
+ /// The scope ID of the address.
+ /**
+ * Modifies the scope ID associated with the IPv6 address.
+ */
+ void scope_id(unsigned long id)
+ {
+ scope_id_ = id;
+ }
+
+ /// Get the address in bytes, in network byte order.
+ BOOST_ASIO_DECL bytes_type to_bytes() const;
+
+ /// Get the address as a string.
+ BOOST_ASIO_DECL std::string to_string() const;
+
+ /// Get the address as a string.
+ BOOST_ASIO_DECL std::string to_string(boost::system::error_code& ec) const;
+
+ /// Create an address from an IP address string.
+ BOOST_ASIO_DECL static address_v6 from_string(const char* str);
+
+ /// Create an address from an IP address string.
+ BOOST_ASIO_DECL static address_v6 from_string(
+ const char* str, boost::system::error_code& ec);
+
+ /// Create an address from an IP address string.
+ BOOST_ASIO_DECL static address_v6 from_string(const std::string& str);
+
+ /// Create an address from an IP address string.
+ BOOST_ASIO_DECL static address_v6 from_string(
+ const std::string& str, boost::system::error_code& ec);
+
+ /// Converts an IPv4-mapped or IPv4-compatible address to an IPv4 address.
+ BOOST_ASIO_DECL address_v4 to_v4() const;
+
+ /// Determine whether the address is a loopback address.
+ BOOST_ASIO_DECL bool is_loopback() const;
+
+ /// Determine whether the address is unspecified.
+ BOOST_ASIO_DECL bool is_unspecified() const;
+
+ /// Determine whether the address is link local.
+ BOOST_ASIO_DECL bool is_link_local() const;
+
+ /// Determine whether the address is site local.
+ BOOST_ASIO_DECL bool is_site_local() const;
+
+ /// Determine whether the address is a mapped IPv4 address.
+ BOOST_ASIO_DECL bool is_v4_mapped() const;
+
+ /// Determine whether the address is an IPv4-compatible address.
+ BOOST_ASIO_DECL bool is_v4_compatible() const;
+
+ /// Determine whether the address is a multicast address.
+ BOOST_ASIO_DECL bool is_multicast() const;
+
+ /// Determine whether the address is a global multicast address.
+ BOOST_ASIO_DECL bool is_multicast_global() const;
+
+ /// Determine whether the address is a link-local multicast address.
+ BOOST_ASIO_DECL bool is_multicast_link_local() const;
+
+ /// Determine whether the address is a node-local multicast address.
+ BOOST_ASIO_DECL bool is_multicast_node_local() const;
+
+ /// Determine whether the address is a org-local multicast address.
+ BOOST_ASIO_DECL bool is_multicast_org_local() const;
+
+ /// Determine whether the address is a site-local multicast address.
+ BOOST_ASIO_DECL bool is_multicast_site_local() const;
+
+ /// Compare two addresses for equality.
+ BOOST_ASIO_DECL friend bool operator==(
+ const address_v6& a1, const address_v6& a2);
+
+ /// Compare two addresses for inequality.
+ friend bool operator!=(const address_v6& a1, const address_v6& a2)
+ {
+ return !(a1 == a2);
+ }
+
+ /// Compare addresses for ordering.
+ BOOST_ASIO_DECL friend bool operator<(
+ const address_v6& a1, const address_v6& a2);
+
+ /// Compare addresses for ordering.
+ friend bool operator>(const address_v6& a1, const address_v6& a2)
+ {
+ return a2 < a1;
+ }
+
+ /// Compare addresses for ordering.
+ friend bool operator<=(const address_v6& a1, const address_v6& a2)
+ {
+ return !(a2 < a1);
+ }
+
+ /// Compare addresses for ordering.
+ friend bool operator>=(const address_v6& a1, const address_v6& a2)
+ {
+ return !(a1 < a2);
+ }
+
+ /// Obtain an address object that represents any address.
+ static address_v6 any()
+ {
+ return address_v6();
+ }
+
+ /// Obtain an address object that represents the loopback address.
+ BOOST_ASIO_DECL static address_v6 loopback();
+
+ /// Create an IPv4-mapped IPv6 address.
+ BOOST_ASIO_DECL static address_v6 v4_mapped(const address_v4& addr);
+
+ /// Create an IPv4-compatible IPv6 address.
+ BOOST_ASIO_DECL static address_v6 v4_compatible(const address_v4& addr);
+
+private:
+ // The underlying IPv6 address.
+ boost::asio::detail::in6_addr_type addr_;
+
+ // The scope ID associated with the address.
+ unsigned long scope_id_;
+};
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Output an address as a string.
+/**
+ * Used to output a human-readable string for a specified address.
+ *
+ * @param os The output stream to which the string will be written.
+ *
+ * @param addr The address to be written.
+ *
+ * @return The output stream.
+ *
+ * @relates boost::asio::ip::address_v6
+ */
+template <typename Elem, typename Traits>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os, const address_v6& addr);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/ip/impl/address_v6.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ip/impl/address_v6.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_IP_ADDRESS_V6_HPP
diff --git a/ext/patches/boost/asio/ip/basic_endpoint.hpp b/ext/patches/boost/asio/ip/basic_endpoint.hpp
new file mode 100644
index 0000000..84b43a2
--- /dev/null
+++ b/ext/patches/boost/asio/ip/basic_endpoint.hpp
@@ -0,0 +1,265 @@
+//
+// ip/basic_endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_BASIC_ENDPOINT_HPP
+#define BOOST_ASIO_IP_BASIC_ENDPOINT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/ip/address.hpp>
+#include <boost/asio/ip/detail/endpoint.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+# include <iosfwd>
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Describes an endpoint for a version-independent IP socket.
+/**
+ * The boost::asio::ip::basic_endpoint class template describes an endpoint that
+ * may be associated with a particular socket.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * Endpoint.
+ */
+template <typename InternetProtocol>
+class basic_endpoint
+{
+public:
+ /// The protocol type associated with the endpoint.
+ typedef InternetProtocol protocol_type;
+
+ /// The type of the endpoint structure. This type is dependent on the
+ /// underlying implementation of the socket layer.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined data_type;
+#else
+ typedef boost::asio::detail::socket_addr_type data_type;
+#endif
+
+ /// Default constructor.
+ basic_endpoint()
+ : impl_()
+ {
+ }
+
+ /// Construct an endpoint using a port number, specified in the host's byte
+ /// order. The IP address will be the any address (i.e. INADDR_ANY or
+ /// in6addr_any). This constructor would typically be used for accepting new
+ /// connections.
+ /**
+ * @par Examples
+ * To initialise an IPv4 TCP endpoint for port 1234, use:
+ * @code
+ * boost::asio::ip::tcp::endpoint ep(boost::asio::ip::tcp::v4(), 1234);
+ * @endcode
+ *
+ * To specify an IPv6 UDP endpoint for port 9876, use:
+ * @code
+ * boost::asio::ip::udp::endpoint ep(boost::asio::ip::udp::v6(), 9876);
+ * @endcode
+ */
+ basic_endpoint(const InternetProtocol& internet_protocol,
+ unsigned short port_num)
+ : impl_(internet_protocol.family(), port_num)
+ {
+ }
+
+ /// Construct an endpoint using a port number and an IP address. This
+ /// constructor may be used for accepting connections on a specific interface
+ /// or for making a connection to a remote endpoint.
+ basic_endpoint(const boost::asio::ip::address& addr, unsigned short port_num)
+ : impl_(addr, port_num)
+ {
+ }
+
+ /// Copy constructor.
+ basic_endpoint(const basic_endpoint& other)
+ : impl_(other.impl_)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move constructor.
+ basic_endpoint(basic_endpoint&& other)
+ : impl_(other.impl_)
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// Assign from another endpoint.
+ basic_endpoint& operator=(const basic_endpoint& other)
+ {
+ impl_ = other.impl_;
+ return *this;
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move-assign from another endpoint.
+ basic_endpoint& operator=(basic_endpoint&& other)
+ {
+ impl_ = other.impl_;
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// The protocol associated with the endpoint.
+ protocol_type protocol() const
+ {
+ if (impl_.is_v4())
+ return InternetProtocol::v4();
+ return InternetProtocol::v6();
+ }
+
+ /// Get the underlying endpoint in the native type.
+ data_type* data()
+ {
+ return impl_.data();
+ }
+
+ /// Get the underlying endpoint in the native type.
+ const data_type* data() const
+ {
+ return impl_.data();
+ }
+
+ /// Get the underlying size of the endpoint in the native type.
+ std::size_t size() const
+ {
+ return impl_.size();
+ }
+
+ /// Set the underlying size of the endpoint in the native type.
+ void resize(std::size_t new_size)
+ {
+ impl_.resize(new_size);
+ }
+
+ /// Get the capacity of the endpoint in the native type.
+ std::size_t capacity() const
+ {
+ return impl_.capacity();
+ }
+
+ /// Get the port associated with the endpoint. The port number is always in
+ /// the host's byte order.
+ unsigned short port() const
+ {
+ return impl_.port();
+ }
+
+ /// Set the port associated with the endpoint. The port number is always in
+ /// the host's byte order.
+ void port(unsigned short port_num)
+ {
+ impl_.port(port_num);
+ }
+
+ /// Get the IP address associated with the endpoint.
+ boost::asio::ip::address address() const
+ {
+ return impl_.address();
+ }
+
+ /// Set the IP address associated with the endpoint.
+ void address(const boost::asio::ip::address& addr)
+ {
+ impl_.address(addr);
+ }
+
+ /// Compare two endpoints for equality.
+ friend bool operator==(const basic_endpoint<InternetProtocol>& e1,
+ const basic_endpoint<InternetProtocol>& e2)
+ {
+ return e1.impl_ == e2.impl_;
+ }
+
+ /// Compare two endpoints for inequality.
+ friend bool operator!=(const basic_endpoint<InternetProtocol>& e1,
+ const basic_endpoint<InternetProtocol>& e2)
+ {
+ return !(e1 == e2);
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator<(const basic_endpoint<InternetProtocol>& e1,
+ const basic_endpoint<InternetProtocol>& e2)
+ {
+ return e1.impl_ < e2.impl_;
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator>(const basic_endpoint<InternetProtocol>& e1,
+ const basic_endpoint<InternetProtocol>& e2)
+ {
+ return e2.impl_ < e1.impl_;
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator<=(const basic_endpoint<InternetProtocol>& e1,
+ const basic_endpoint<InternetProtocol>& e2)
+ {
+ return !(e2 < e1);
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator>=(const basic_endpoint<InternetProtocol>& e1,
+ const basic_endpoint<InternetProtocol>& e2)
+ {
+ return !(e1 < e2);
+ }
+
+private:
+ // The underlying IP endpoint.
+ boost::asio::ip::detail::endpoint impl_;
+};
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Output an endpoint as a string.
+/**
+ * Used to output a human-readable string for a specified endpoint.
+ *
+ * @param os The output stream to which the string will be written.
+ *
+ * @param endpoint The endpoint to be written.
+ *
+ * @return The output stream.
+ *
+ * @relates boost::asio::ip::basic_endpoint
+ */
+template <typename Elem, typename Traits, typename InternetProtocol>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os,
+ const basic_endpoint<InternetProtocol>& endpoint);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/ip/impl/basic_endpoint.hpp>
+
+#endif // BOOST_ASIO_IP_BASIC_ENDPOINT_HPP
diff --git a/ext/patches/boost/asio/ip/basic_resolver.hpp b/ext/patches/boost/asio/ip/basic_resolver.hpp
new file mode 100644
index 0000000..395696f
--- /dev/null
+++ b/ext/patches/boost/asio/ip/basic_resolver.hpp
@@ -0,0 +1,270 @@
+//
+// ip/basic_resolver.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_BASIC_RESOLVER_HPP
+#define BOOST_ASIO_IP_BASIC_RESOLVER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+#include <boost/asio/ip/resolver_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Provides endpoint resolution functionality.
+/**
+ * The basic_resolver class template provides the ability to resolve a query
+ * to a list of endpoints.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename InternetProtocol,
+ typename ResolverService = resolver_service<InternetProtocol> >
+class basic_resolver
+ : public basic_io_object<ResolverService>
+{
+public:
+ /// The protocol type.
+ typedef InternetProtocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename InternetProtocol::endpoint endpoint_type;
+
+ /// The query type.
+ typedef basic_resolver_query<InternetProtocol> query;
+
+ /// The iterator type.
+ typedef basic_resolver_iterator<InternetProtocol> iterator;
+
+ /// Constructor.
+ /**
+ * This constructor creates a basic_resolver.
+ *
+ * @param io_service The io_service object that the resolver will use to
+ * dispatch handlers for any asynchronous operations performed on the timer.
+ */
+ explicit basic_resolver(boost::asio::io_service& io_service)
+ : basic_io_object<ResolverService>(io_service)
+ {
+ }
+
+ /// Cancel any asynchronous operations that are waiting on the resolver.
+ /**
+ * This function forces the completion of any pending asynchronous
+ * operations on the host resolver. The handler for each cancelled operation
+ * will be invoked with the boost::asio::error::operation_aborted error code.
+ */
+ void cancel()
+ {
+ return this->service.cancel(this->implementation);
+ }
+
+ /// Perform forward resolution of a query to a list of entries.
+ /**
+ * This function is used to resolve a query into a list of endpoint entries.
+ *
+ * @param q A query object that determines what endpoints will be returned.
+ *
+ * @returns A forward-only iterator that can be used to traverse the list
+ * of endpoint entries.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note A default constructed iterator represents the end of the list.
+ *
+ * A successful call to this function is guaranteed to return at least one
+ * entry.
+ */
+ iterator resolve(const query& q)
+ {
+ boost::system::error_code ec;
+ iterator i = this->service.resolve(this->implementation, q, ec);
+ boost::asio::detail::throw_error(ec, "resolve");
+ return i;
+ }
+
+ /// Perform forward resolution of a query to a list of entries.
+ /**
+ * This function is used to resolve a query into a list of endpoint entries.
+ *
+ * @param q A query object that determines what endpoints will be returned.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns A forward-only iterator that can be used to traverse the list
+ * of endpoint entries. Returns a default constructed iterator if an error
+ * occurs.
+ *
+ * @note A default constructed iterator represents the end of the list.
+ *
+ * A successful call to this function is guaranteed to return at least one
+ * entry.
+ */
+ iterator resolve(const query& q, boost::system::error_code& ec)
+ {
+ return this->service.resolve(this->implementation, q, ec);
+ }
+
+ /// Asynchronously perform forward resolution of a query to a list of entries.
+ /**
+ * This function is used to asynchronously resolve a query into a list of
+ * endpoint entries.
+ *
+ * @param q A query object that determines what endpoints will be returned.
+ *
+ * @param handler The handler to be called when the resolve operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * resolver::iterator iterator // Forward-only iterator that can
+ * // be used to traverse the list
+ * // of endpoint entries.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note A default constructed iterator represents the end of the list.
+ *
+ * A successful resolve operation is guaranteed to pass at least one entry to
+ * the handler.
+ */
+ template <typename ResolveHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ResolveHandler,
+ void (boost::system::error_code, iterator))
+ async_resolve(const query& q,
+ BOOST_ASIO_MOVE_ARG(ResolveHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ResolveHandler.
+ BOOST_ASIO_RESOLVE_HANDLER_CHECK(
+ ResolveHandler, handler, iterator) type_check;
+
+ return this->service.async_resolve(this->implementation, q,
+ BOOST_ASIO_MOVE_CAST(ResolveHandler)(handler));
+ }
+
+ /// Perform reverse resolution of an endpoint to a list of entries.
+ /**
+ * This function is used to resolve an endpoint into a list of endpoint
+ * entries.
+ *
+ * @param e An endpoint object that determines what endpoints will be
+ * returned.
+ *
+ * @returns A forward-only iterator that can be used to traverse the list
+ * of endpoint entries.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note A default constructed iterator represents the end of the list.
+ *
+ * A successful call to this function is guaranteed to return at least one
+ * entry.
+ */
+ iterator resolve(const endpoint_type& e)
+ {
+ boost::system::error_code ec;
+ iterator i = this->service.resolve(this->implementation, e, ec);
+ boost::asio::detail::throw_error(ec, "resolve");
+ return i;
+ }
+
+ /// Perform reverse resolution of an endpoint to a list of entries.
+ /**
+ * This function is used to resolve an endpoint into a list of endpoint
+ * entries.
+ *
+ * @param e An endpoint object that determines what endpoints will be
+ * returned.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns A forward-only iterator that can be used to traverse the list
+ * of endpoint entries. Returns a default constructed iterator if an error
+ * occurs.
+ *
+ * @note A default constructed iterator represents the end of the list.
+ *
+ * A successful call to this function is guaranteed to return at least one
+ * entry.
+ */
+ iterator resolve(const endpoint_type& e, boost::system::error_code& ec)
+ {
+ return this->service.resolve(this->implementation, e, ec);
+ }
+
+ /// Asynchronously perform reverse resolution of an endpoint to a list of
+ /// entries.
+ /**
+ * This function is used to asynchronously resolve an endpoint into a list of
+ * endpoint entries.
+ *
+ * @param e An endpoint object that determines what endpoints will be
+ * returned.
+ *
+ * @param handler The handler to be called when the resolve operation
+ * completes. Copies will be made of the handler as required. The function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * resolver::iterator iterator // Forward-only iterator that can
+ * // be used to traverse the list
+ * // of endpoint entries.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note A default constructed iterator represents the end of the list.
+ *
+ * A successful resolve operation is guaranteed to pass at least one entry to
+ * the handler.
+ */
+ template <typename ResolveHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ResolveHandler,
+ void (boost::system::error_code, iterator))
+ async_resolve(const endpoint_type& e,
+ BOOST_ASIO_MOVE_ARG(ResolveHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ResolveHandler.
+ BOOST_ASIO_RESOLVE_HANDLER_CHECK(
+ ResolveHandler, handler, iterator) type_check;
+
+ return this->service.async_resolve(this->implementation, e,
+ BOOST_ASIO_MOVE_CAST(ResolveHandler)(handler));
+ }
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_BASIC_RESOLVER_HPP
diff --git a/ext/patches/boost/asio/ip/basic_resolver_entry.hpp b/ext/patches/boost/asio/ip/basic_resolver_entry.hpp
new file mode 100644
index 0000000..b25e4e4
--- /dev/null
+++ b/ext/patches/boost/asio/ip/basic_resolver_entry.hpp
@@ -0,0 +1,96 @@
+//
+// ip/basic_resolver_entry.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_BASIC_RESOLVER_ENTRY_HPP
+#define BOOST_ASIO_IP_BASIC_RESOLVER_ENTRY_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// An entry produced by a resolver.
+/**
+ * The boost::asio::ip::basic_resolver_entry class template describes an entry
+ * as returned by a resolver.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename InternetProtocol>
+class basic_resolver_entry
+{
+public:
+ /// The protocol type associated with the endpoint entry.
+ typedef InternetProtocol protocol_type;
+
+ /// The endpoint type associated with the endpoint entry.
+ typedef typename InternetProtocol::endpoint endpoint_type;
+
+ /// Default constructor.
+ basic_resolver_entry()
+ {
+ }
+
+ /// Construct with specified endpoint, host name and service name.
+ basic_resolver_entry(const endpoint_type& ep,
+ const std::string& host, const std::string& service)
+ : endpoint_(ep),
+ host_name_(host),
+ service_name_(service)
+ {
+ }
+
+ /// Get the endpoint associated with the entry.
+ endpoint_type endpoint() const
+ {
+ return endpoint_;
+ }
+
+ /// Convert to the endpoint associated with the entry.
+ operator endpoint_type() const
+ {
+ return endpoint_;
+ }
+
+ /// Get the host name associated with the entry.
+ std::string host_name() const
+ {
+ return host_name_;
+ }
+
+ /// Get the service name associated with the entry.
+ std::string service_name() const
+ {
+ return service_name_;
+ }
+
+private:
+ endpoint_type endpoint_;
+ std::string host_name_;
+ std::string service_name_;
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_BASIC_RESOLVER_ENTRY_HPP
diff --git a/ext/patches/boost/asio/ip/basic_resolver_iterator.hpp b/ext/patches/boost/asio/ip/basic_resolver_iterator.hpp
new file mode 100644
index 0000000..ab14527
--- /dev/null
+++ b/ext/patches/boost/asio/ip/basic_resolver_iterator.hpp
@@ -0,0 +1,262 @@
+//
+// ip/basic_resolver_iterator.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_BASIC_RESOLVER_ITERATOR_HPP
+#define BOOST_ASIO_IP_BASIC_RESOLVER_ITERATOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <cstring>
+#include <iterator>
+#include <string>
+#include <vector>
+#include <boost/asio/detail/shared_ptr.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/ip/basic_resolver_entry.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/winrt_utils.hpp>
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// An iterator over the entries produced by a resolver.
+/**
+ * The boost::asio::ip::basic_resolver_iterator class template is used to define
+ * iterators over the results returned by a resolver.
+ *
+ * The iterator's value_type, obtained when the iterator is dereferenced, is:
+ * @code const basic_resolver_entry<InternetProtocol> @endcode
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename InternetProtocol>
+class basic_resolver_iterator
+{
+public:
+ /// The type used for the distance between two iterators.
+ typedef std::ptrdiff_t difference_type;
+
+ /// The type of the value pointed to by the iterator.
+ typedef basic_resolver_entry<InternetProtocol> value_type;
+
+ /// The type of the result of applying operator->() to the iterator.
+ typedef const basic_resolver_entry<InternetProtocol>* pointer;
+
+ /// The type of the result of applying operator*() to the iterator.
+ typedef const basic_resolver_entry<InternetProtocol>& reference;
+
+ /// The iterator category.
+ typedef std::forward_iterator_tag iterator_category;
+
+ /// Default constructor creates an end iterator.
+ basic_resolver_iterator()
+ : index_(0)
+ {
+ }
+
+ /// Create an iterator from an addrinfo list returned by getaddrinfo.
+ static basic_resolver_iterator create(
+ boost::asio::detail::addrinfo_type* address_info,
+ const std::string& host_name, const std::string& service_name)
+ {
+ basic_resolver_iterator iter;
+ if (!address_info)
+ return iter;
+
+ std::string actual_host_name = host_name;
+ if (address_info->ai_canonname)
+ actual_host_name = address_info->ai_canonname;
+
+ iter.values_.reset(new values_type);
+
+ while (address_info)
+ {
+ if (address_info->ai_family == BOOST_ASIO_OS_DEF(AF_INET)
+ || address_info->ai_family == BOOST_ASIO_OS_DEF(AF_INET6))
+ {
+ using namespace std; // For memcpy.
+ typename InternetProtocol::endpoint endpoint;
+ endpoint.resize(static_cast<std::size_t>(address_info->ai_addrlen));
+ memcpy(endpoint.data(), address_info->ai_addr,
+ address_info->ai_addrlen);
+ iter.values_->push_back(
+ basic_resolver_entry<InternetProtocol>(endpoint,
+ actual_host_name, service_name));
+ }
+ address_info = address_info->ai_next;
+ }
+
+ return iter;
+ }
+
+ /// Create an iterator from an endpoint, host name and service name.
+ static basic_resolver_iterator create(
+ const typename InternetProtocol::endpoint& endpoint,
+ const std::string& host_name, const std::string& service_name)
+ {
+ basic_resolver_iterator iter;
+ iter.values_.reset(new values_type);
+ iter.values_->push_back(
+ basic_resolver_entry<InternetProtocol>(
+ endpoint, host_name, service_name));
+ return iter;
+ }
+
+ /// Create an iterator from a sequence of endpoints, host and service name.
+ template <typename EndpointIterator>
+ static basic_resolver_iterator create(
+ EndpointIterator begin, EndpointIterator end,
+ const std::string& host_name, const std::string& service_name)
+ {
+ basic_resolver_iterator iter;
+ if (begin != end)
+ {
+ iter.values_.reset(new values_type);
+ for (EndpointIterator ep_iter = begin; ep_iter != end; ++ep_iter)
+ {
+ iter.values_->push_back(
+ basic_resolver_entry<InternetProtocol>(
+ *ep_iter, host_name, service_name));
+ }
+ }
+ return iter;
+ }
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ /// Create an iterator from a Windows Runtime list of EndpointPair objects.
+ static basic_resolver_iterator create(
+ Windows::Foundation::Collections::IVectorView<
+ Windows::Networking::EndpointPair^>^ endpoints,
+ const boost::asio::detail::addrinfo_type& hints,
+ const std::string& host_name, const std::string& service_name)
+ {
+ basic_resolver_iterator iter;
+ if (endpoints->Size)
+ {
+ iter.values_.reset(new values_type);
+ for (unsigned int i = 0; i < endpoints->Size; ++i)
+ {
+ auto pair = endpoints->GetAt(i);
+
+ if (hints.ai_family == BOOST_ASIO_OS_DEF(AF_INET)
+ && pair->RemoteHostName->Type
+ != Windows::Networking::HostNameType::Ipv4)
+ continue;
+
+ if (hints.ai_family == BOOST_ASIO_OS_DEF(AF_INET6)
+ && pair->RemoteHostName->Type
+ != Windows::Networking::HostNameType::Ipv6)
+ continue;
+
+ iter.values_->push_back(
+ basic_resolver_entry<InternetProtocol>(
+ typename InternetProtocol::endpoint(
+ ip::address::from_string(
+ boost::asio::detail::winrt_utils::string(
+ pair->RemoteHostName->CanonicalName)),
+ boost::asio::detail::winrt_utils::integer(
+ pair->RemoteServiceName)),
+ host_name, service_name));
+ }
+ }
+ return iter;
+ }
+#endif // defined(BOOST_ASIO_WINDOWS_RUNTIME)
+
+ /// Dereference an iterator.
+ const basic_resolver_entry<InternetProtocol>& operator*() const
+ {
+ return dereference();
+ }
+
+ /// Dereference an iterator.
+ const basic_resolver_entry<InternetProtocol>* operator->() const
+ {
+ return &dereference();
+ }
+
+ /// Increment operator (prefix).
+ basic_resolver_iterator& operator++()
+ {
+ increment();
+ return *this;
+ }
+
+ /// Increment operator (postfix).
+ basic_resolver_iterator operator++(int)
+ {
+ basic_resolver_iterator tmp(*this);
+ ++*this;
+ return tmp;
+ }
+
+ /// Test two iterators for equality.
+ friend bool operator==(const basic_resolver_iterator& a,
+ const basic_resolver_iterator& b)
+ {
+ return a.equal(b);
+ }
+
+ /// Test two iterators for inequality.
+ friend bool operator!=(const basic_resolver_iterator& a,
+ const basic_resolver_iterator& b)
+ {
+ return !a.equal(b);
+ }
+
+private:
+ void increment()
+ {
+ if (++index_ == values_->size())
+ {
+ // Reset state to match a default constructed end iterator.
+ values_.reset();
+ index_ = 0;
+ }
+ }
+
+ bool equal(const basic_resolver_iterator& other) const
+ {
+ if (!values_ && !other.values_)
+ return true;
+ if (values_ != other.values_)
+ return false;
+ return index_ == other.index_;
+ }
+
+ const basic_resolver_entry<InternetProtocol>& dereference() const
+ {
+ return (*values_)[index_];
+ }
+
+ typedef std::vector<basic_resolver_entry<InternetProtocol> > values_type;
+ boost::asio::detail::shared_ptr<values_type> values_;
+ std::size_t index_;
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_BASIC_RESOLVER_ITERATOR_HPP
diff --git a/ext/patches/boost/asio/ip/basic_resolver_query.hpp b/ext/patches/boost/asio/ip/basic_resolver_query.hpp
new file mode 100644
index 0000000..47cbe86
--- /dev/null
+++ b/ext/patches/boost/asio/ip/basic_resolver_query.hpp
@@ -0,0 +1,246 @@
+//
+// ip/basic_resolver_query.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_BASIC_RESOLVER_QUERY_HPP
+#define BOOST_ASIO_IP_BASIC_RESOLVER_QUERY_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/ip/resolver_query_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// An query to be passed to a resolver.
+/**
+ * The boost::asio::ip::basic_resolver_query class template describes a query
+ * that can be passed to a resolver.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename InternetProtocol>
+class basic_resolver_query
+ : public resolver_query_base
+{
+public:
+ /// The protocol type associated with the endpoint query.
+ typedef InternetProtocol protocol_type;
+
+ /// Construct with specified service name for any protocol.
+ /**
+ * This constructor is typically used to perform name resolution for local
+ * service binding.
+ *
+ * @param service A string identifying the requested service. This may be a
+ * descriptive name or a numeric string corresponding to a port number.
+ *
+ * @param resolve_flags A set of flags that determine how name resolution
+ * should be performed. The default flags are suitable for local service
+ * binding.
+ *
+ * @note On POSIX systems, service names are typically defined in the file
+ * <tt>/etc/services</tt>. On Windows, service names may be found in the file
+ * <tt>c:\\windows\\system32\\drivers\\etc\\services</tt>. Operating systems
+ * may use additional locations when resolving service names.
+ */
+ basic_resolver_query(const std::string& service,
+ resolver_query_base::flags resolve_flags = passive | address_configured)
+ : hints_(),
+ host_name_(),
+ service_name_(service)
+ {
+ typename InternetProtocol::endpoint endpoint;
+ hints_.ai_flags = static_cast<int>(resolve_flags);
+ hints_.ai_family = PF_UNSPEC;
+ hints_.ai_socktype = endpoint.protocol().type();
+ hints_.ai_protocol = endpoint.protocol().protocol();
+ hints_.ai_addrlen = 0;
+ hints_.ai_canonname = 0;
+ hints_.ai_addr = 0;
+ hints_.ai_next = 0;
+ }
+
+ /// Construct with specified service name for a given protocol.
+ /**
+ * This constructor is typically used to perform name resolution for local
+ * service binding with a specific protocol version.
+ *
+ * @param protocol A protocol object, normally representing either the IPv4 or
+ * IPv6 version of an internet protocol.
+ *
+ * @param service A string identifying the requested service. This may be a
+ * descriptive name or a numeric string corresponding to a port number.
+ *
+ * @param resolve_flags A set of flags that determine how name resolution
+ * should be performed. The default flags are suitable for local service
+ * binding.
+ *
+ * @note On POSIX systems, service names are typically defined in the file
+ * <tt>/etc/services</tt>. On Windows, service names may be found in the file
+ * <tt>c:\\windows\\system32\\drivers\\etc\\services</tt>. Operating systems
+ * may use additional locations when resolving service names.
+ */
+ basic_resolver_query(const protocol_type& protocol,
+ const std::string& service,
+ resolver_query_base::flags resolve_flags = passive | address_configured)
+ : hints_(),
+ host_name_(),
+ service_name_(service)
+ {
+ hints_.ai_flags = static_cast<int>(resolve_flags);
+ hints_.ai_family = protocol.family();
+ hints_.ai_socktype = protocol.type();
+ hints_.ai_protocol = protocol.protocol();
+ hints_.ai_addrlen = 0;
+ hints_.ai_canonname = 0;
+ hints_.ai_addr = 0;
+ hints_.ai_next = 0;
+ }
+
+ /// Construct with specified host name and service name for any protocol.
+ /**
+ * This constructor is typically used to perform name resolution for
+ * communication with remote hosts.
+ *
+ * @param host A string identifying a location. May be a descriptive name or
+ * a numeric address string. If an empty string and the passive flag has been
+ * specified, the resolved endpoints are suitable for local service binding.
+ * If an empty string and passive is not specified, the resolved endpoints
+ * will use the loopback address.
+ *
+ * @param service A string identifying the requested service. This may be a
+ * descriptive name or a numeric string corresponding to a port number. May
+ * be an empty string, in which case all resolved endpoints will have a port
+ * number of 0.
+ *
+ * @param resolve_flags A set of flags that determine how name resolution
+ * should be performed. The default flags are suitable for communication with
+ * remote hosts.
+ *
+ * @note On POSIX systems, host names may be locally defined in the file
+ * <tt>/etc/hosts</tt>. On Windows, host names may be defined in the file
+ * <tt>c:\\windows\\system32\\drivers\\etc\\hosts</tt>. Remote host name
+ * resolution is performed using DNS. Operating systems may use additional
+ * locations when resolving host names (such as NETBIOS names on Windows).
+ *
+ * On POSIX systems, service names are typically defined in the file
+ * <tt>/etc/services</tt>. On Windows, service names may be found in the file
+ * <tt>c:\\windows\\system32\\drivers\\etc\\services</tt>. Operating systems
+ * may use additional locations when resolving service names.
+ */
+ basic_resolver_query(const std::string& host, const std::string& service,
+ resolver_query_base::flags resolve_flags = address_configured)
+ : hints_(),
+ host_name_(host),
+ service_name_(service)
+ {
+ typename InternetProtocol::endpoint endpoint;
+ hints_.ai_flags = static_cast<int>(resolve_flags);
+ hints_.ai_family = BOOST_ASIO_OS_DEF(AF_UNSPEC);
+ hints_.ai_socktype = endpoint.protocol().type();
+ hints_.ai_protocol = endpoint.protocol().protocol();
+ hints_.ai_addrlen = 0;
+ hints_.ai_canonname = 0;
+ hints_.ai_addr = 0;
+ hints_.ai_next = 0;
+ }
+
+ /// Construct with specified host name and service name for a given protocol.
+ /**
+ * This constructor is typically used to perform name resolution for
+ * communication with remote hosts.
+ *
+ * @param protocol A protocol object, normally representing either the IPv4 or
+ * IPv6 version of an internet protocol.
+ *
+ * @param host A string identifying a location. May be a descriptive name or
+ * a numeric address string. If an empty string and the passive flag has been
+ * specified, the resolved endpoints are suitable for local service binding.
+ * If an empty string and passive is not specified, the resolved endpoints
+ * will use the loopback address.
+ *
+ * @param service A string identifying the requested service. This may be a
+ * descriptive name or a numeric string corresponding to a port number. May
+ * be an empty string, in which case all resolved endpoints will have a port
+ * number of 0.
+ *
+ * @param resolve_flags A set of flags that determine how name resolution
+ * should be performed. The default flags are suitable for communication with
+ * remote hosts.
+ *
+ * @note On POSIX systems, host names may be locally defined in the file
+ * <tt>/etc/hosts</tt>. On Windows, host names may be defined in the file
+ * <tt>c:\\windows\\system32\\drivers\\etc\\hosts</tt>. Remote host name
+ * resolution is performed using DNS. Operating systems may use additional
+ * locations when resolving host names (such as NETBIOS names on Windows).
+ *
+ * On POSIX systems, service names are typically defined in the file
+ * <tt>/etc/services</tt>. On Windows, service names may be found in the file
+ * <tt>c:\\windows\\system32\\drivers\\etc\\services</tt>. Operating systems
+ * may use additional locations when resolving service names.
+ */
+ basic_resolver_query(const protocol_type& protocol,
+ const std::string& host, const std::string& service,
+ resolver_query_base::flags resolve_flags = address_configured)
+ : hints_(),
+ host_name_(host),
+ service_name_(service)
+ {
+ hints_.ai_flags = static_cast<int>(resolve_flags);
+ hints_.ai_family = protocol.family();
+ hints_.ai_socktype = protocol.type();
+ hints_.ai_protocol = protocol.protocol();
+ hints_.ai_addrlen = 0;
+ hints_.ai_canonname = 0;
+ hints_.ai_addr = 0;
+ hints_.ai_next = 0;
+ }
+
+ /// Get the hints associated with the query.
+ const boost::asio::detail::addrinfo_type& hints() const
+ {
+ return hints_;
+ }
+
+ /// Get the host name associated with the query.
+ std::string host_name() const
+ {
+ return host_name_;
+ }
+
+ /// Get the service name associated with the query.
+ std::string service_name() const
+ {
+ return service_name_;
+ }
+
+private:
+ boost::asio::detail::addrinfo_type hints_;
+ std::string host_name_;
+ std::string service_name_;
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_BASIC_RESOLVER_QUERY_HPP
diff --git a/ext/patches/boost/asio/ip/detail/endpoint.hpp b/ext/patches/boost/asio/ip/detail/endpoint.hpp
new file mode 100644
index 0000000..184f4b9
--- /dev/null
+++ b/ext/patches/boost/asio/ip/detail/endpoint.hpp
@@ -0,0 +1,141 @@
+//
+// ip/detail/endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_DETAIL_ENDPOINT_HPP
+#define BOOST_ASIO_IP_DETAIL_ENDPOINT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/winsock_init.hpp>
+#include <boost/system/error_code.hpp>
+#include <boost/asio/ip/address.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+namespace detail {
+
+// Helper class for implementating an IP endpoint.
+class endpoint
+{
+public:
+ // Default constructor.
+ BOOST_ASIO_DECL endpoint();
+
+ // Construct an endpoint using a family and port number.
+ BOOST_ASIO_DECL endpoint(int family, unsigned short port_num);
+
+ // Construct an endpoint using an address and port number.
+ BOOST_ASIO_DECL endpoint(const boost::asio::ip::address& addr,
+ unsigned short port_num);
+
+ // Copy constructor.
+ endpoint(const endpoint& other)
+ : data_(other.data_)
+ {
+ }
+
+ // Assign from another endpoint.
+ endpoint& operator=(const endpoint& other)
+ {
+ data_ = other.data_;
+ return *this;
+ }
+
+ // Get the underlying endpoint in the native type.
+ boost::asio::detail::socket_addr_type* data()
+ {
+ return &data_.base;
+ }
+
+ // Get the underlying endpoint in the native type.
+ const boost::asio::detail::socket_addr_type* data() const
+ {
+ return &data_.base;
+ }
+
+ // Get the underlying size of the endpoint in the native type.
+ std::size_t size() const
+ {
+ if (is_v4())
+ return sizeof(boost::asio::detail::sockaddr_in4_type);
+ else
+ return sizeof(boost::asio::detail::sockaddr_in6_type);
+ }
+
+ // Set the underlying size of the endpoint in the native type.
+ BOOST_ASIO_DECL void resize(std::size_t new_size);
+
+ // Get the capacity of the endpoint in the native type.
+ std::size_t capacity() const
+ {
+ return sizeof(data_);
+ }
+
+ // Get the port associated with the endpoint.
+ BOOST_ASIO_DECL unsigned short port() const;
+
+ // Set the port associated with the endpoint.
+ BOOST_ASIO_DECL void port(unsigned short port_num);
+
+ // Get the IP address associated with the endpoint.
+ BOOST_ASIO_DECL boost::asio::ip::address address() const;
+
+ // Set the IP address associated with the endpoint.
+ BOOST_ASIO_DECL void address(const boost::asio::ip::address& addr);
+
+ // Compare two endpoints for equality.
+ BOOST_ASIO_DECL friend bool operator==(
+ const endpoint& e1, const endpoint& e2);
+
+ // Compare endpoints for ordering.
+ BOOST_ASIO_DECL friend bool operator<(
+ const endpoint& e1, const endpoint& e2);
+
+ // Determine whether the endpoint is IPv4.
+ bool is_v4() const
+ {
+ return data_.base.sa_family == BOOST_ASIO_OS_DEF(AF_INET);
+ }
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+ // Convert to a string.
+ BOOST_ASIO_DECL std::string to_string(boost::system::error_code& ec) const;
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+private:
+ // The underlying IP socket address.
+ union data_union
+ {
+ boost::asio::detail::socket_addr_type base;
+ boost::asio::detail::sockaddr_in4_type v4;
+ boost::asio::detail::sockaddr_in6_type v6;
+ } data_;
+};
+
+} // namespace detail
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ip/detail/impl/endpoint.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_IP_DETAIL_ENDPOINT_HPP
diff --git a/ext/patches/boost/asio/ip/detail/impl/endpoint.ipp b/ext/patches/boost/asio/ip/detail/impl/endpoint.ipp
new file mode 100644
index 0000000..5921695
--- /dev/null
+++ b/ext/patches/boost/asio/ip/detail/impl/endpoint.ipp
@@ -0,0 +1,206 @@
+//
+// ip/detail/impl/endpoint.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_DETAIL_IMPL_ENDPOINT_IPP
+#define BOOST_ASIO_IP_DETAIL_IMPL_ENDPOINT_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstring>
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+# include <sstream>
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/ip/detail/endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+namespace detail {
+
+endpoint::endpoint()
+ : data_()
+{
+ data_.v4.sin_family = BOOST_ASIO_OS_DEF(AF_INET);
+ data_.v4.sin_port = 0;
+ data_.v4.sin_addr.s_addr = BOOST_ASIO_OS_DEF(INADDR_ANY);
+}
+
+endpoint::endpoint(int family, unsigned short port_num)
+ : data_()
+{
+ using namespace std; // For memcpy.
+ if (family == BOOST_ASIO_OS_DEF(AF_INET))
+ {
+ data_.v4.sin_family = BOOST_ASIO_OS_DEF(AF_INET);
+ data_.v4.sin_port =
+ boost::asio::detail::socket_ops::host_to_network_short(port_num);
+ data_.v4.sin_addr.s_addr = BOOST_ASIO_OS_DEF(INADDR_ANY);
+ }
+ else
+ {
+ data_.v6.sin6_family = BOOST_ASIO_OS_DEF(AF_INET6);
+ data_.v6.sin6_port =
+ boost::asio::detail::socket_ops::host_to_network_short(port_num);
+ data_.v6.sin6_flowinfo = 0;
+ data_.v6.sin6_addr.s6_addr[0] = 0; data_.v6.sin6_addr.s6_addr[1] = 0;
+ data_.v6.sin6_addr.s6_addr[2] = 0, data_.v6.sin6_addr.s6_addr[3] = 0;
+ data_.v6.sin6_addr.s6_addr[4] = 0, data_.v6.sin6_addr.s6_addr[5] = 0;
+ data_.v6.sin6_addr.s6_addr[6] = 0, data_.v6.sin6_addr.s6_addr[7] = 0;
+ data_.v6.sin6_addr.s6_addr[8] = 0, data_.v6.sin6_addr.s6_addr[9] = 0;
+ data_.v6.sin6_addr.s6_addr[10] = 0, data_.v6.sin6_addr.s6_addr[11] = 0;
+ data_.v6.sin6_addr.s6_addr[12] = 0, data_.v6.sin6_addr.s6_addr[13] = 0;
+ data_.v6.sin6_addr.s6_addr[14] = 0, data_.v6.sin6_addr.s6_addr[15] = 0;
+ data_.v6.sin6_scope_id = 0;
+ }
+}
+
+endpoint::endpoint(const boost::asio::ip::address& addr,
+ unsigned short port_num)
+ : data_()
+{
+ using namespace std; // For memcpy.
+ if (addr.is_v4())
+ {
+ data_.v4.sin_family = BOOST_ASIO_OS_DEF(AF_INET);
+ data_.v4.sin_port =
+ boost::asio::detail::socket_ops::host_to_network_short(port_num);
+ data_.v4.sin_addr.s_addr =
+ boost::asio::detail::socket_ops::host_to_network_long(
+ static_cast<boost::asio::detail::u_long_type>(
+ addr.to_v4().to_ulong()));
+ }
+ else
+ {
+ data_.v6.sin6_family = BOOST_ASIO_OS_DEF(AF_INET6);
+ data_.v6.sin6_port =
+ boost::asio::detail::socket_ops::host_to_network_short(port_num);
+ data_.v6.sin6_flowinfo = 0;
+ boost::asio::ip::address_v6 v6_addr = addr.to_v6();
+ boost::asio::ip::address_v6::bytes_type bytes = v6_addr.to_bytes();
+ memcpy(data_.v6.sin6_addr.s6_addr, bytes.data(), 16);
+ data_.v6.sin6_scope_id =
+ static_cast<boost::asio::detail::u_long_type>(
+ v6_addr.scope_id());
+ }
+}
+
+void endpoint::resize(std::size_t new_size)
+{
+ if (new_size > sizeof(boost::asio::detail::sockaddr_storage_type))
+ {
+ boost::system::error_code ec(boost::asio::error::invalid_argument);
+ boost::asio::detail::throw_error(ec);
+ }
+}
+
+unsigned short endpoint::port() const
+{
+ if (is_v4())
+ {
+ return boost::asio::detail::socket_ops::network_to_host_short(
+ data_.v4.sin_port);
+ }
+ else
+ {
+ return boost::asio::detail::socket_ops::network_to_host_short(
+ data_.v6.sin6_port);
+ }
+}
+
+void endpoint::port(unsigned short port_num)
+{
+ if (is_v4())
+ {
+ data_.v4.sin_port
+ = boost::asio::detail::socket_ops::host_to_network_short(port_num);
+ }
+ else
+ {
+ data_.v6.sin6_port
+ = boost::asio::detail::socket_ops::host_to_network_short(port_num);
+ }
+}
+
+boost::asio::ip::address endpoint::address() const
+{
+ using namespace std; // For memcpy.
+ if (is_v4())
+ {
+ return boost::asio::ip::address_v4(
+ boost::asio::detail::socket_ops::network_to_host_long(
+ data_.v4.sin_addr.s_addr));
+ }
+ else
+ {
+ boost::asio::ip::address_v6::bytes_type bytes;
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+ memcpy(bytes.data(), data_.v6.sin6_addr.s6_addr, 16);
+#else // defined(BOOST_ASIO_HAS_STD_ARRAY)
+ memcpy(bytes.elems, data_.v6.sin6_addr.s6_addr, 16);
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+ return boost::asio::ip::address_v6(bytes, data_.v6.sin6_scope_id);
+ }
+}
+
+void endpoint::address(const boost::asio::ip::address& addr)
+{
+ endpoint tmp_endpoint(addr, port());
+ data_ = tmp_endpoint.data_;
+}
+
+bool operator==(const endpoint& e1, const endpoint& e2)
+{
+ return e1.address() == e2.address() && e1.port() == e2.port();
+}
+
+bool operator<(const endpoint& e1, const endpoint& e2)
+{
+ if (e1.address() < e2.address())
+ return true;
+ if (e1.address() != e2.address())
+ return false;
+ return e1.port() < e2.port();
+}
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+std::string endpoint::to_string(boost::system::error_code& ec) const
+{
+ std::string a = address().to_string(ec);
+ if (ec)
+ return std::string();
+
+ std::ostringstream tmp_os;
+ tmp_os.imbue(std::locale::classic());
+ if (is_v4())
+ tmp_os << a;
+ else
+ tmp_os << '[' << a << ']';
+ tmp_os << ':' << port();
+
+ return tmp_os.str();
+}
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+} // namespace detail
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_DETAIL_IMPL_ENDPOINT_IPP
diff --git a/ext/patches/boost/asio/ip/detail/socket_option.hpp b/ext/patches/boost/asio/ip/detail/socket_option.hpp
new file mode 100644
index 0000000..c8e14e2
--- /dev/null
+++ b/ext/patches/boost/asio/ip/detail/socket_option.hpp
@@ -0,0 +1,571 @@
+//
+// detail/socket_option.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_DETAIL_SOCKET_OPTION_HPP
+#define BOOST_ASIO_IP_DETAIL_SOCKET_OPTION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <cstring>
+#include <stdexcept>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/ip/address.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+namespace detail {
+namespace socket_option {
+
+// Helper template for implementing multicast enable loopback options.
+template <int IPv4_Level, int IPv4_Name, int IPv6_Level, int IPv6_Name>
+class multicast_enable_loopback
+{
+public:
+#if defined(__sun) || defined(__osf__)
+ typedef unsigned char ipv4_value_type;
+ typedef unsigned char ipv6_value_type;
+#elif defined(_AIX) || defined(__hpux) || defined(__QNXNTO__)
+ typedef unsigned char ipv4_value_type;
+ typedef unsigned int ipv6_value_type;
+#else
+ typedef int ipv4_value_type;
+ typedef int ipv6_value_type;
+#endif
+
+ // Default constructor.
+ multicast_enable_loopback()
+ : ipv4_value_(0),
+ ipv6_value_(0)
+ {
+ }
+
+ // Construct with a specific option value.
+ explicit multicast_enable_loopback(bool v)
+ : ipv4_value_(v ? 1 : 0),
+ ipv6_value_(v ? 1 : 0)
+ {
+ }
+
+ // Set the value of the boolean.
+ multicast_enable_loopback& operator=(bool v)
+ {
+ ipv4_value_ = v ? 1 : 0;
+ ipv6_value_ = v ? 1 : 0;
+ return *this;
+ }
+
+ // Get the current value of the boolean.
+ bool value() const
+ {
+ return !!ipv4_value_;
+ }
+
+ // Convert to bool.
+ operator bool() const
+ {
+ return !!ipv4_value_;
+ }
+
+ // Test for false.
+ bool operator!() const
+ {
+ return !ipv4_value_;
+ }
+
+ // Get the level of the socket option.
+ template <typename Protocol>
+ int level(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Level;
+ return IPv4_Level;
+ }
+
+ // Get the name of the socket option.
+ template <typename Protocol>
+ int name(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Name;
+ return IPv4_Name;
+ }
+
+ // Get the address of the boolean data.
+ template <typename Protocol>
+ void* data(const Protocol& protocol)
+ {
+ if (protocol.family() == PF_INET6)
+ return &ipv6_value_;
+ return &ipv4_value_;
+ }
+
+ // Get the address of the boolean data.
+ template <typename Protocol>
+ const void* data(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return &ipv6_value_;
+ return &ipv4_value_;
+ }
+
+ // Get the size of the boolean data.
+ template <typename Protocol>
+ std::size_t size(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return sizeof(ipv6_value_);
+ return sizeof(ipv4_value_);
+ }
+
+ // Set the size of the boolean data.
+ template <typename Protocol>
+ void resize(const Protocol& protocol, std::size_t s)
+ {
+ if (protocol.family() == PF_INET6)
+ {
+ if (s != sizeof(ipv6_value_))
+ {
+ std::length_error ex("multicast_enable_loopback socket option resize");
+ boost::asio::detail::throw_exception(ex);
+ }
+ ipv4_value_ = ipv6_value_ ? 1 : 0;
+ }
+ else
+ {
+ if (s != sizeof(ipv4_value_))
+ {
+ std::length_error ex("multicast_enable_loopback socket option resize");
+ boost::asio::detail::throw_exception(ex);
+ }
+ ipv6_value_ = ipv4_value_ ? 1 : 0;
+ }
+ }
+
+private:
+ ipv4_value_type ipv4_value_;
+ ipv6_value_type ipv6_value_;
+};
+
+// Helper template for implementing unicast hops options.
+template <int IPv4_Level, int IPv4_Name, int IPv6_Level, int IPv6_Name>
+class unicast_hops
+{
+public:
+ // Default constructor.
+ unicast_hops()
+ : value_(0)
+ {
+ }
+
+ // Construct with a specific option value.
+ explicit unicast_hops(int v)
+ : value_(v)
+ {
+ }
+
+ // Set the value of the option.
+ unicast_hops& operator=(int v)
+ {
+ value_ = v;
+ return *this;
+ }
+
+ // Get the current value of the option.
+ int value() const
+ {
+ return value_;
+ }
+
+ // Get the level of the socket option.
+ template <typename Protocol>
+ int level(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Level;
+ return IPv4_Level;
+ }
+
+ // Get the name of the socket option.
+ template <typename Protocol>
+ int name(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Name;
+ return IPv4_Name;
+ }
+
+ // Get the address of the data.
+ template <typename Protocol>
+ int* data(const Protocol&)
+ {
+ return &value_;
+ }
+
+ // Get the address of the data.
+ template <typename Protocol>
+ const int* data(const Protocol&) const
+ {
+ return &value_;
+ }
+
+ // Get the size of the data.
+ template <typename Protocol>
+ std::size_t size(const Protocol&) const
+ {
+ return sizeof(value_);
+ }
+
+ // Set the size of the data.
+ template <typename Protocol>
+ void resize(const Protocol&, std::size_t s)
+ {
+ if (s != sizeof(value_))
+ {
+ std::length_error ex("unicast hops socket option resize");
+ boost::asio::detail::throw_exception(ex);
+ }
+#if defined(__hpux)
+ if (value_ < 0)
+ value_ = value_ & 0xFF;
+#endif
+ }
+
+private:
+ int value_;
+};
+
+// Helper template for implementing multicast hops options.
+template <int IPv4_Level, int IPv4_Name, int IPv6_Level, int IPv6_Name>
+class multicast_hops
+{
+public:
+#if defined(BOOST_ASIO_WINDOWS) && defined(UNDER_CE)
+ typedef int ipv4_value_type;
+#else
+ typedef unsigned char ipv4_value_type;
+#endif
+ typedef int ipv6_value_type;
+
+ // Default constructor.
+ multicast_hops()
+ : ipv4_value_(0),
+ ipv6_value_(0)
+ {
+ }
+
+ // Construct with a specific option value.
+ explicit multicast_hops(int v)
+ {
+ if (v < 0 || v > 255)
+ {
+ std::out_of_range ex("multicast hops value out of range");
+ boost::asio::detail::throw_exception(ex);
+ }
+ ipv4_value_ = (ipv4_value_type)v;
+ ipv6_value_ = v;
+ }
+
+ // Set the value of the option.
+ multicast_hops& operator=(int v)
+ {
+ if (v < 0 || v > 255)
+ {
+ std::out_of_range ex("multicast hops value out of range");
+ boost::asio::detail::throw_exception(ex);
+ }
+ ipv4_value_ = (ipv4_value_type)v;
+ ipv6_value_ = v;
+ return *this;
+ }
+
+ // Get the current value of the option.
+ int value() const
+ {
+ return ipv6_value_;
+ }
+
+ // Get the level of the socket option.
+ template <typename Protocol>
+ int level(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Level;
+ return IPv4_Level;
+ }
+
+ // Get the name of the socket option.
+ template <typename Protocol>
+ int name(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Name;
+ return IPv4_Name;
+ }
+
+ // Get the address of the data.
+ template <typename Protocol>
+ void* data(const Protocol& protocol)
+ {
+ if (protocol.family() == PF_INET6)
+ return &ipv6_value_;
+ return &ipv4_value_;
+ }
+
+ // Get the address of the data.
+ template <typename Protocol>
+ const void* data(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return &ipv6_value_;
+ return &ipv4_value_;
+ }
+
+ // Get the size of the data.
+ template <typename Protocol>
+ std::size_t size(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return sizeof(ipv6_value_);
+ return sizeof(ipv4_value_);
+ }
+
+ // Set the size of the data.
+ template <typename Protocol>
+ void resize(const Protocol& protocol, std::size_t s)
+ {
+ if (protocol.family() == PF_INET6)
+ {
+ if (s != sizeof(ipv6_value_))
+ {
+ std::length_error ex("multicast hops socket option resize");
+ boost::asio::detail::throw_exception(ex);
+ }
+ if (ipv6_value_ < 0)
+ ipv4_value_ = 0;
+ else if (ipv6_value_ > 255)
+ ipv4_value_ = 255;
+ else
+ ipv4_value_ = (ipv4_value_type)ipv6_value_;
+ }
+ else
+ {
+ if (s != sizeof(ipv4_value_))
+ {
+ std::length_error ex("multicast hops socket option resize");
+ boost::asio::detail::throw_exception(ex);
+ }
+ ipv6_value_ = ipv4_value_;
+ }
+ }
+
+private:
+ ipv4_value_type ipv4_value_;
+ ipv6_value_type ipv6_value_;
+};
+
+// Helper template for implementing ip_mreq-based options.
+template <int IPv4_Level, int IPv4_Name, int IPv6_Level, int IPv6_Name>
+class multicast_request
+{
+public:
+ // Default constructor.
+ multicast_request()
+ : ipv4_value_(), // Zero-initialisation gives the "any" address.
+ ipv6_value_() // Zero-initialisation gives the "any" address.
+ {
+ }
+
+ // Construct with multicast address only.
+ explicit multicast_request(const boost::asio::ip::address& multicast_address)
+ : ipv4_value_(), // Zero-initialisation gives the "any" address.
+ ipv6_value_() // Zero-initialisation gives the "any" address.
+ {
+ if (multicast_address.is_v6())
+ {
+ using namespace std; // For memcpy.
+ boost::asio::ip::address_v6 ipv6_address = multicast_address.to_v6();
+ boost::asio::ip::address_v6::bytes_type bytes = ipv6_address.to_bytes();
+ memcpy(ipv6_value_.ipv6mr_multiaddr.s6_addr, bytes.data(), 16);
+ ipv6_value_.ipv6mr_interface = ipv6_address.scope_id();
+ }
+ else
+ {
+ ipv4_value_.imr_multiaddr.s_addr =
+ boost::asio::detail::socket_ops::host_to_network_long(
+ multicast_address.to_v4().to_ulong());
+ ipv4_value_.imr_interface.s_addr =
+ boost::asio::detail::socket_ops::host_to_network_long(
+ boost::asio::ip::address_v4::any().to_ulong());
+ }
+ }
+
+ // Construct with multicast address and IPv4 address specifying an interface.
+ explicit multicast_request(
+ const boost::asio::ip::address_v4& multicast_address,
+ const boost::asio::ip::address_v4& network_interface
+ = boost::asio::ip::address_v4::any())
+ : ipv6_value_() // Zero-initialisation gives the "any" address.
+ {
+ ipv4_value_.imr_multiaddr.s_addr =
+ boost::asio::detail::socket_ops::host_to_network_long(
+ multicast_address.to_ulong());
+ ipv4_value_.imr_interface.s_addr =
+ boost::asio::detail::socket_ops::host_to_network_long(
+ network_interface.to_ulong());
+ }
+
+ // Construct with multicast address and IPv6 network interface index.
+ explicit multicast_request(
+ const boost::asio::ip::address_v6& multicast_address,
+ unsigned long network_interface = 0)
+ : ipv4_value_() // Zero-initialisation gives the "any" address.
+ {
+ using namespace std; // For memcpy.
+ boost::asio::ip::address_v6::bytes_type bytes =
+ multicast_address.to_bytes();
+ memcpy(ipv6_value_.ipv6mr_multiaddr.s6_addr, bytes.data(), 16);
+ if (network_interface)
+ ipv6_value_.ipv6mr_interface = network_interface;
+ else
+ ipv6_value_.ipv6mr_interface = multicast_address.scope_id();
+ }
+
+ // Get the level of the socket option.
+ template <typename Protocol>
+ int level(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Level;
+ return IPv4_Level;
+ }
+
+ // Get the name of the socket option.
+ template <typename Protocol>
+ int name(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Name;
+ return IPv4_Name;
+ }
+
+ // Get the address of the option data.
+ template <typename Protocol>
+ const void* data(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return &ipv6_value_;
+ return &ipv4_value_;
+ }
+
+ // Get the size of the option data.
+ template <typename Protocol>
+ std::size_t size(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return sizeof(ipv6_value_);
+ return sizeof(ipv4_value_);
+ }
+
+private:
+ boost::asio::detail::in4_mreq_type ipv4_value_;
+ boost::asio::detail::in6_mreq_type ipv6_value_;
+};
+
+// Helper template for implementing options that specify a network interface.
+template <int IPv4_Level, int IPv4_Name, int IPv6_Level, int IPv6_Name>
+class network_interface
+{
+public:
+ // Default constructor.
+ network_interface()
+ {
+ ipv4_value_.s_addr =
+ boost::asio::detail::socket_ops::host_to_network_long(
+ boost::asio::ip::address_v4::any().to_ulong());
+ ipv6_value_ = 0;
+ }
+
+ // Construct with IPv4 interface.
+ explicit network_interface(const boost::asio::ip::address_v4& ipv4_interface)
+ {
+ ipv4_value_.s_addr =
+ boost::asio::detail::socket_ops::host_to_network_long(
+ ipv4_interface.to_ulong());
+ ipv6_value_ = 0;
+ }
+
+ // Construct with IPv6 interface.
+ explicit network_interface(unsigned int ipv6_interface)
+ {
+ ipv4_value_.s_addr =
+ boost::asio::detail::socket_ops::host_to_network_long(
+ boost::asio::ip::address_v4::any().to_ulong());
+ ipv6_value_ = ipv6_interface;
+ }
+
+ // Get the level of the socket option.
+ template <typename Protocol>
+ int level(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Level;
+ return IPv4_Level;
+ }
+
+ // Get the name of the socket option.
+ template <typename Protocol>
+ int name(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return IPv6_Name;
+ return IPv4_Name;
+ }
+
+ // Get the address of the option data.
+ template <typename Protocol>
+ const void* data(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return &ipv6_value_;
+ return &ipv4_value_;
+ }
+
+ // Get the size of the option data.
+ template <typename Protocol>
+ std::size_t size(const Protocol& protocol) const
+ {
+ if (protocol.family() == PF_INET6)
+ return sizeof(ipv6_value_);
+ return sizeof(ipv4_value_);
+ }
+
+private:
+ boost::asio::detail::in4_addr_type ipv4_value_;
+ unsigned int ipv6_value_;
+};
+
+} // namespace socket_option
+} // namespace detail
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_DETAIL_SOCKET_OPTION_HPP
diff --git a/ext/patches/boost/asio/ip/host_name.hpp b/ext/patches/boost/asio/ip/host_name.hpp
new file mode 100644
index 0000000..fd040cf
--- /dev/null
+++ b/ext/patches/boost/asio/ip/host_name.hpp
@@ -0,0 +1,44 @@
+//
+// ip/host_name.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_HOST_NAME_HPP
+#define BOOST_ASIO_IP_HOST_NAME_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/system/error_code.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Get the current host name.
+BOOST_ASIO_DECL std::string host_name();
+
+/// Get the current host name.
+BOOST_ASIO_DECL std::string host_name(boost::system::error_code& ec);
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ip/impl/host_name.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_IP_HOST_NAME_HPP
diff --git a/ext/patches/boost/asio/ip/icmp.hpp b/ext/patches/boost/asio/ip/icmp.hpp
new file mode 100644
index 0000000..573227c
--- /dev/null
+++ b/ext/patches/boost/asio/ip/icmp.hpp
@@ -0,0 +1,117 @@
+//
+// ip/icmp.hpp
+// ~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_ICMP_HPP
+#define BOOST_ASIO_IP_ICMP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/basic_raw_socket.hpp>
+#include <boost/asio/ip/basic_endpoint.hpp>
+#include <boost/asio/ip/basic_resolver.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Encapsulates the flags needed for ICMP.
+/**
+ * The boost::asio::ip::icmp class contains flags necessary for ICMP sockets.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol, InternetProtocol.
+ */
+class icmp
+{
+public:
+ /// The type of a ICMP endpoint.
+ typedef basic_endpoint<icmp> endpoint;
+
+ /// Construct to represent the IPv4 ICMP protocol.
+ static icmp v4()
+ {
+ return icmp(BOOST_ASIO_OS_DEF(IPPROTO_ICMP),
+ BOOST_ASIO_OS_DEF(AF_INET));
+ }
+
+ /// Construct to represent the IPv6 ICMP protocol.
+ static icmp v6()
+ {
+ return icmp(BOOST_ASIO_OS_DEF(IPPROTO_ICMPV6),
+ BOOST_ASIO_OS_DEF(AF_INET6));
+ }
+
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return BOOST_ASIO_OS_DEF(SOCK_RAW);
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return protocol_;
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return family_;
+ }
+
+ /// The ICMP socket type.
+ typedef basic_raw_socket<icmp> socket;
+
+ /// The ICMP resolver type.
+ typedef basic_resolver<icmp> resolver;
+
+ /// Compare two protocols for equality.
+ friend bool operator==(const icmp& p1, const icmp& p2)
+ {
+ return p1.protocol_ == p2.protocol_ && p1.family_ == p2.family_;
+ }
+
+ /// Compare two protocols for inequality.
+ friend bool operator!=(const icmp& p1, const icmp& p2)
+ {
+ return p1.protocol_ != p2.protocol_ || p1.family_ != p2.family_;
+ }
+
+private:
+ // Construct with a specific family.
+ explicit icmp(int protocol_id, int protocol_family)
+ : protocol_(protocol_id),
+ family_(protocol_family)
+ {
+ }
+
+ int protocol_;
+ int family_;
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_ICMP_HPP
diff --git a/ext/patches/boost/asio/ip/impl/address.hpp b/ext/patches/boost/asio/ip/impl/address.hpp
new file mode 100644
index 0000000..e7a4892
--- /dev/null
+++ b/ext/patches/boost/asio/ip/impl/address.hpp
@@ -0,0 +1,55 @@
+//
+// ip/impl/address.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_IMPL_ADDRESS_HPP
+#define BOOST_ASIO_IP_IMPL_ADDRESS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/throw_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+template <typename Elem, typename Traits>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os, const address& addr)
+{
+ boost::system::error_code ec;
+ std::string s = addr.to_string(ec);
+ if (ec)
+ {
+ if (os.exceptions() & std::basic_ostream<Elem, Traits>::failbit)
+ boost::asio::detail::throw_error(ec);
+ else
+ os.setstate(std::basic_ostream<Elem, Traits>::failbit);
+ }
+ else
+ for (std::string::iterator i = s.begin(); i != s.end(); ++i)
+ os << os.widen(*i);
+ return os;
+}
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_IP_IMPL_ADDRESS_HPP
diff --git a/ext/patches/boost/asio/ip/impl/address.ipp b/ext/patches/boost/asio/ip/impl/address.ipp
new file mode 100644
index 0000000..e11cb45
--- /dev/null
+++ b/ext/patches/boost/asio/ip/impl/address.ipp
@@ -0,0 +1,228 @@
+//
+// ip/impl/address.ipp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_IMPL_ADDRESS_IPP
+#define BOOST_ASIO_IP_IMPL_ADDRESS_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <typeinfo>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/ip/address.hpp>
+#include <boost/system/system_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+address::address()
+ : type_(ipv4),
+ ipv4_address_(),
+ ipv6_address_()
+{
+}
+
+address::address(const boost::asio::ip::address_v4& ipv4_address)
+ : type_(ipv4),
+ ipv4_address_(ipv4_address),
+ ipv6_address_()
+{
+}
+
+address::address(const boost::asio::ip::address_v6& ipv6_address)
+ : type_(ipv6),
+ ipv4_address_(),
+ ipv6_address_(ipv6_address)
+{
+}
+
+address::address(const address& other)
+ : type_(other.type_),
+ ipv4_address_(other.ipv4_address_),
+ ipv6_address_(other.ipv6_address_)
+{
+}
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+address::address(address&& other)
+ : type_(other.type_),
+ ipv4_address_(other.ipv4_address_),
+ ipv6_address_(other.ipv6_address_)
+{
+}
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+address& address::operator=(const address& other)
+{
+ type_ = other.type_;
+ ipv4_address_ = other.ipv4_address_;
+ ipv6_address_ = other.ipv6_address_;
+ return *this;
+}
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+address& address::operator=(address&& other)
+{
+ type_ = other.type_;
+ ipv4_address_ = other.ipv4_address_;
+ ipv6_address_ = other.ipv6_address_;
+ return *this;
+}
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+address& address::operator=(const boost::asio::ip::address_v4& ipv4_address)
+{
+ type_ = ipv4;
+ ipv4_address_ = ipv4_address;
+ ipv6_address_ = boost::asio::ip::address_v6();
+ return *this;
+}
+
+address& address::operator=(const boost::asio::ip::address_v6& ipv6_address)
+{
+ type_ = ipv6;
+ ipv4_address_ = boost::asio::ip::address_v4();
+ ipv6_address_ = ipv6_address;
+ return *this;
+}
+
+boost::asio::ip::address_v4 address::to_v4() const
+{
+ if (type_ != ipv4)
+ {
+ std::bad_cast ex;
+ boost::asio::detail::throw_exception(ex);
+ }
+ return ipv4_address_;
+}
+
+boost::asio::ip::address_v6 address::to_v6() const
+{
+ if (type_ != ipv6)
+ {
+ std::bad_cast ex;
+ boost::asio::detail::throw_exception(ex);
+ }
+ return ipv6_address_;
+}
+
+std::string address::to_string() const
+{
+ if (type_ == ipv6)
+ return ipv6_address_.to_string();
+ return ipv4_address_.to_string();
+}
+
+std::string address::to_string(boost::system::error_code& ec) const
+{
+ if (type_ == ipv6)
+ return ipv6_address_.to_string(ec);
+ return ipv4_address_.to_string(ec);
+}
+
+address address::from_string(const char* str)
+{
+ boost::system::error_code ec;
+ address addr = from_string(str, ec);
+ boost::asio::detail::throw_error(ec);
+ return addr;
+}
+
+address address::from_string(const char* str, boost::system::error_code& ec)
+{
+ boost::asio::ip::address_v6 ipv6_address =
+ boost::asio::ip::address_v6::from_string(str, ec);
+ if (!ec)
+ {
+ address tmp;
+ tmp.type_ = ipv6;
+ tmp.ipv6_address_ = ipv6_address;
+ return tmp;
+ }
+
+ boost::asio::ip::address_v4 ipv4_address =
+ boost::asio::ip::address_v4::from_string(str, ec);
+ if (!ec)
+ {
+ address tmp;
+ tmp.type_ = ipv4;
+ tmp.ipv4_address_ = ipv4_address;
+ return tmp;
+ }
+
+ return address();
+}
+
+address address::from_string(const std::string& str)
+{
+ return from_string(str.c_str());
+}
+
+address address::from_string(const std::string& str,
+ boost::system::error_code& ec)
+{
+ return from_string(str.c_str(), ec);
+}
+
+bool address::is_loopback() const
+{
+ return (type_ == ipv4)
+ ? ipv4_address_.is_loopback()
+ : ipv6_address_.is_loopback();
+}
+
+bool address::is_unspecified() const
+{
+ return (type_ == ipv4)
+ ? ipv4_address_.is_unspecified()
+ : ipv6_address_.is_unspecified();
+}
+
+bool address::is_multicast() const
+{
+ return (type_ == ipv4)
+ ? ipv4_address_.is_multicast()
+ : ipv6_address_.is_multicast();
+}
+
+bool operator==(const address& a1, const address& a2)
+{
+ if (a1.type_ != a2.type_)
+ return false;
+ if (a1.type_ == address::ipv6)
+ return a1.ipv6_address_ == a2.ipv6_address_;
+ return a1.ipv4_address_ == a2.ipv4_address_;
+}
+
+bool operator<(const address& a1, const address& a2)
+{
+ if (a1.type_ < a2.type_)
+ return true;
+ if (a1.type_ > a2.type_)
+ return false;
+ if (a1.type_ == address::ipv6)
+ return a1.ipv6_address_ < a2.ipv6_address_;
+ return a1.ipv4_address_ < a2.ipv4_address_;
+}
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_IMPL_ADDRESS_IPP
diff --git a/ext/patches/boost/asio/ip/impl/address_v4.hpp b/ext/patches/boost/asio/ip/impl/address_v4.hpp
new file mode 100644
index 0000000..13df75a
--- /dev/null
+++ b/ext/patches/boost/asio/ip/impl/address_v4.hpp
@@ -0,0 +1,55 @@
+//
+// ip/impl/address_v4.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_IMPL_ADDRESS_V4_HPP
+#define BOOST_ASIO_IP_IMPL_ADDRESS_V4_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/throw_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+template <typename Elem, typename Traits>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os, const address_v4& addr)
+{
+ boost::system::error_code ec;
+ std::string s = addr.to_string(ec);
+ if (ec)
+ {
+ if (os.exceptions() & std::basic_ostream<Elem, Traits>::failbit)
+ boost::asio::detail::throw_error(ec);
+ else
+ os.setstate(std::basic_ostream<Elem, Traits>::failbit);
+ }
+ else
+ for (std::string::iterator i = s.begin(); i != s.end(); ++i)
+ os << os.widen(*i);
+ return os;
+}
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_IP_IMPL_ADDRESS_V4_HPP
diff --git a/ext/patches/boost/asio/ip/impl/address_v4.ipp b/ext/patches/boost/asio/ip/impl/address_v4.ipp
new file mode 100644
index 0000000..2dd4bcc
--- /dev/null
+++ b/ext/patches/boost/asio/ip/impl/address_v4.ipp
@@ -0,0 +1,180 @@
+//
+// ip/impl/address_v4.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_IMPL_ADDRESS_V4_IPP
+#define BOOST_ASIO_IP_IMPL_ADDRESS_V4_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <climits>
+#include <stdexcept>
+#include <boost/asio/error.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/ip/address_v4.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+address_v4::address_v4(const address_v4::bytes_type& bytes)
+{
+#if UCHAR_MAX > 0xFF
+ if (bytes[0] > 0xFF || bytes[1] > 0xFF
+ || bytes[2] > 0xFF || bytes[3] > 0xFF)
+ {
+ std::out_of_range ex("address_v4 from bytes_type");
+ boost::asio::detail::throw_exception(ex);
+ }
+#endif // UCHAR_MAX > 0xFF
+
+ using namespace std; // For memcpy.
+ memcpy(&addr_.s_addr, bytes.data(), 4);
+}
+
+address_v4::address_v4(unsigned long addr)
+{
+#if ULONG_MAX > 0xFFFFFFFF
+ if (addr > 0xFFFFFFFF)
+ {
+ std::out_of_range ex("address_v4 from unsigned long");
+ boost::asio::detail::throw_exception(ex);
+ }
+#endif // ULONG_MAX > 0xFFFFFFFF
+
+ addr_.s_addr = boost::asio::detail::socket_ops::host_to_network_long(
+ static_cast<boost::asio::detail::u_long_type>(addr));
+}
+
+address_v4::bytes_type address_v4::to_bytes() const
+{
+ using namespace std; // For memcpy.
+ bytes_type bytes;
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+ memcpy(bytes.data(), &addr_.s_addr, 4);
+#else // defined(BOOST_ASIO_HAS_STD_ARRAY)
+ memcpy(bytes.elems, &addr_.s_addr, 4);
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+ return bytes;
+}
+
+unsigned long address_v4::to_ulong() const
+{
+ return boost::asio::detail::socket_ops::network_to_host_long(addr_.s_addr);
+}
+
+std::string address_v4::to_string() const
+{
+ boost::system::error_code ec;
+ std::string addr = to_string(ec);
+ boost::asio::detail::throw_error(ec);
+ return addr;
+}
+
+std::string address_v4::to_string(boost::system::error_code& ec) const
+{
+ char addr_str[boost::asio::detail::max_addr_v4_str_len];
+ const char* addr =
+ boost::asio::detail::socket_ops::inet_ntop(
+ BOOST_ASIO_OS_DEF(AF_INET), &addr_, addr_str,
+ boost::asio::detail::max_addr_v4_str_len, 0, ec);
+ if (addr == 0)
+ return std::string();
+ return addr;
+}
+
+address_v4 address_v4::from_string(const char* str)
+{
+ boost::system::error_code ec;
+ address_v4 addr = from_string(str, ec);
+ boost::asio::detail::throw_error(ec);
+ return addr;
+}
+
+address_v4 address_v4::from_string(
+ const char* str, boost::system::error_code& ec)
+{
+ address_v4 tmp;
+ if (boost::asio::detail::socket_ops::inet_pton(
+ BOOST_ASIO_OS_DEF(AF_INET), str, &tmp.addr_, 0, ec) <= 0)
+ return address_v4();
+ return tmp;
+}
+
+address_v4 address_v4::from_string(const std::string& str)
+{
+ return from_string(str.c_str());
+}
+
+address_v4 address_v4::from_string(
+ const std::string& str, boost::system::error_code& ec)
+{
+ return from_string(str.c_str(), ec);
+}
+
+bool address_v4::is_loopback() const
+{
+ return (to_ulong() & 0xFF000000) == 0x7F000000;
+}
+
+bool address_v4::is_unspecified() const
+{
+ return to_ulong() == 0;
+}
+
+bool address_v4::is_class_a() const
+{
+ return (to_ulong() & 0x80000000) == 0;
+}
+
+bool address_v4::is_class_b() const
+{
+ return (to_ulong() & 0xC0000000) == 0x80000000;
+}
+
+bool address_v4::is_class_c() const
+{
+ return (to_ulong() & 0xE0000000) == 0xC0000000;
+}
+
+bool address_v4::is_multicast() const
+{
+ return (to_ulong() & 0xF0000000) == 0xE0000000;
+}
+
+address_v4 address_v4::broadcast(const address_v4& addr, const address_v4& mask)
+{
+ return address_v4(addr.to_ulong() | (mask.to_ulong() ^ 0xFFFFFFFF));
+}
+
+address_v4 address_v4::netmask(const address_v4& addr)
+{
+ if (addr.is_class_a())
+ return address_v4(0xFF000000);
+ if (addr.is_class_b())
+ return address_v4(0xFFFF0000);
+ if (addr.is_class_c())
+ return address_v4(0xFFFFFF00);
+ return address_v4(0xFFFFFFFF);
+}
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_IMPL_ADDRESS_V4_IPP
diff --git a/ext/patches/boost/asio/ip/impl/address_v6.hpp b/ext/patches/boost/asio/ip/impl/address_v6.hpp
new file mode 100644
index 0000000..e192094
--- /dev/null
+++ b/ext/patches/boost/asio/ip/impl/address_v6.hpp
@@ -0,0 +1,55 @@
+//
+// ip/impl/address_v6.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_IMPL_ADDRESS_V6_HPP
+#define BOOST_ASIO_IP_IMPL_ADDRESS_V6_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/throw_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+template <typename Elem, typename Traits>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os, const address_v6& addr)
+{
+ boost::system::error_code ec;
+ std::string s = addr.to_string(ec);
+ if (ec)
+ {
+ if (os.exceptions() & std::basic_ostream<Elem, Traits>::failbit)
+ boost::asio::detail::throw_error(ec);
+ else
+ os.setstate(std::basic_ostream<Elem, Traits>::failbit);
+ }
+ else
+ for (std::string::iterator i = s.begin(); i != s.end(); ++i)
+ os << os.widen(*i);
+ return os;
+}
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_IP_IMPL_ADDRESS_V6_HPP
diff --git a/ext/patches/boost/asio/ip/impl/address_v6.ipp b/ext/patches/boost/asio/ip/impl/address_v6.ipp
new file mode 100644
index 0000000..0aeedd3
--- /dev/null
+++ b/ext/patches/boost/asio/ip/impl/address_v6.ipp
@@ -0,0 +1,300 @@
+//
+// ip/impl/address_v6.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_IMPL_ADDRESS_V6_IPP
+#define BOOST_ASIO_IP_IMPL_ADDRESS_V6_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstring>
+#include <stdexcept>
+#include <typeinfo>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/throw_exception.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/ip/address_v6.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+address_v6::address_v6()
+ : addr_(),
+ scope_id_(0)
+{
+}
+
+address_v6::address_v6(const address_v6::bytes_type& bytes,
+ unsigned long scope)
+ : scope_id_(scope)
+{
+#if UCHAR_MAX > 0xFF
+ for (std::size_t i = 0; i < bytes.size(); ++i)
+ {
+ if (bytes[i] > 0xFF)
+ {
+ std::out_of_range ex("address_v6 from bytes_type");
+ boost::asio::detail::throw_exception(ex);
+ }
+ }
+#endif // UCHAR_MAX > 0xFF
+
+ using namespace std; // For memcpy.
+ memcpy(addr_.s6_addr, bytes.data(), 16);
+}
+
+address_v6::address_v6(const address_v6& other)
+ : addr_(other.addr_),
+ scope_id_(other.scope_id_)
+{
+}
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+address_v6::address_v6(address_v6&& other)
+ : addr_(other.addr_),
+ scope_id_(other.scope_id_)
+{
+}
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+address_v6& address_v6::operator=(const address_v6& other)
+{
+ addr_ = other.addr_;
+ scope_id_ = other.scope_id_;
+ return *this;
+}
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+address_v6& address_v6::operator=(address_v6&& other)
+{
+ addr_ = other.addr_;
+ scope_id_ = other.scope_id_;
+ return *this;
+}
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+address_v6::bytes_type address_v6::to_bytes() const
+{
+ using namespace std; // For memcpy.
+ bytes_type bytes;
+#if defined(BOOST_ASIO_HAS_STD_ARRAY)
+ memcpy(bytes.data(), addr_.s6_addr, 16);
+#else // defined(BOOST_ASIO_HAS_STD_ARRAY)
+ memcpy(bytes.elems, addr_.s6_addr, 16);
+#endif // defined(BOOST_ASIO_HAS_STD_ARRAY)
+ return bytes;
+}
+
+std::string address_v6::to_string() const
+{
+ boost::system::error_code ec;
+ std::string addr = to_string(ec);
+ boost::asio::detail::throw_error(ec);
+ return addr;
+}
+
+std::string address_v6::to_string(boost::system::error_code& ec) const
+{
+ char addr_str[boost::asio::detail::max_addr_v6_str_len];
+ const char* addr =
+ boost::asio::detail::socket_ops::inet_ntop(
+ BOOST_ASIO_OS_DEF(AF_INET6), &addr_, addr_str,
+ boost::asio::detail::max_addr_v6_str_len, scope_id_, ec);
+ if (addr == 0)
+ return std::string();
+ return addr;
+}
+
+address_v6 address_v6::from_string(const char* str)
+{
+ boost::system::error_code ec;
+ address_v6 addr = from_string(str, ec);
+ boost::asio::detail::throw_error(ec);
+ return addr;
+}
+
+address_v6 address_v6::from_string(
+ const char* str, boost::system::error_code& ec)
+{
+ address_v6 tmp;
+ if (boost::asio::detail::socket_ops::inet_pton(
+ BOOST_ASIO_OS_DEF(AF_INET6), str, &tmp.addr_, &tmp.scope_id_, ec) <= 0)
+ return address_v6();
+ return tmp;
+}
+
+address_v6 address_v6::from_string(const std::string& str)
+{
+ return from_string(str.c_str());
+}
+
+address_v6 address_v6::from_string(
+ const std::string& str, boost::system::error_code& ec)
+{
+ return from_string(str.c_str(), ec);
+}
+
+address_v4 address_v6::to_v4() const
+{
+ if (!is_v4_mapped() && !is_v4_compatible())
+ {
+ std::bad_cast ex;
+ boost::asio::detail::throw_exception(ex);
+ }
+
+ address_v4::bytes_type v4_bytes = { { addr_.s6_addr[12],
+ addr_.s6_addr[13], addr_.s6_addr[14], addr_.s6_addr[15] } };
+ return address_v4(v4_bytes);
+}
+
+bool address_v6::is_loopback() const
+{
+ return ((addr_.s6_addr[0] == 0) && (addr_.s6_addr[1] == 0)
+ && (addr_.s6_addr[2] == 0) && (addr_.s6_addr[3] == 0)
+ && (addr_.s6_addr[4] == 0) && (addr_.s6_addr[5] == 0)
+ && (addr_.s6_addr[6] == 0) && (addr_.s6_addr[7] == 0)
+ && (addr_.s6_addr[8] == 0) && (addr_.s6_addr[9] == 0)
+ && (addr_.s6_addr[10] == 0) && (addr_.s6_addr[11] == 0)
+ && (addr_.s6_addr[12] == 0) && (addr_.s6_addr[13] == 0)
+ && (addr_.s6_addr[14] == 0) && (addr_.s6_addr[15] == 1));
+}
+
+bool address_v6::is_unspecified() const
+{
+ return ((addr_.s6_addr[0] == 0) && (addr_.s6_addr[1] == 0)
+ && (addr_.s6_addr[2] == 0) && (addr_.s6_addr[3] == 0)
+ && (addr_.s6_addr[4] == 0) && (addr_.s6_addr[5] == 0)
+ && (addr_.s6_addr[6] == 0) && (addr_.s6_addr[7] == 0)
+ && (addr_.s6_addr[8] == 0) && (addr_.s6_addr[9] == 0)
+ && (addr_.s6_addr[10] == 0) && (addr_.s6_addr[11] == 0)
+ && (addr_.s6_addr[12] == 0) && (addr_.s6_addr[13] == 0)
+ && (addr_.s6_addr[14] == 0) && (addr_.s6_addr[15] == 0));
+}
+
+bool address_v6::is_link_local() const
+{
+ return ((addr_.s6_addr[0] == 0xfe) && ((addr_.s6_addr[1] & 0xc0) == 0x80));
+}
+
+bool address_v6::is_site_local() const
+{
+ return ((addr_.s6_addr[0] == 0xfe) && ((addr_.s6_addr[1] & 0xc0) == 0xc0));
+}
+
+bool address_v6::is_v4_mapped() const
+{
+ return ((addr_.s6_addr[0] == 0) && (addr_.s6_addr[1] == 0)
+ && (addr_.s6_addr[2] == 0) && (addr_.s6_addr[3] == 0)
+ && (addr_.s6_addr[4] == 0) && (addr_.s6_addr[5] == 0)
+ && (addr_.s6_addr[6] == 0) && (addr_.s6_addr[7] == 0)
+ && (addr_.s6_addr[8] == 0) && (addr_.s6_addr[9] == 0)
+ && (addr_.s6_addr[10] == 0xff) && (addr_.s6_addr[11] == 0xff));
+}
+
+bool address_v6::is_v4_compatible() const
+{
+ return ((addr_.s6_addr[0] == 0) && (addr_.s6_addr[1] == 0)
+ && (addr_.s6_addr[2] == 0) && (addr_.s6_addr[3] == 0)
+ && (addr_.s6_addr[4] == 0) && (addr_.s6_addr[5] == 0)
+ && (addr_.s6_addr[6] == 0) && (addr_.s6_addr[7] == 0)
+ && (addr_.s6_addr[8] == 0) && (addr_.s6_addr[9] == 0)
+ && (addr_.s6_addr[10] == 0) && (addr_.s6_addr[11] == 0)
+ && !((addr_.s6_addr[12] == 0)
+ && (addr_.s6_addr[13] == 0)
+ && (addr_.s6_addr[14] == 0)
+ && ((addr_.s6_addr[15] == 0) || (addr_.s6_addr[15] == 1))));
+}
+
+bool address_v6::is_multicast() const
+{
+ return (addr_.s6_addr[0] == 0xff);
+}
+
+bool address_v6::is_multicast_global() const
+{
+ return ((addr_.s6_addr[0] == 0xff) && ((addr_.s6_addr[1] & 0x0f) == 0x0e));
+}
+
+bool address_v6::is_multicast_link_local() const
+{
+ return ((addr_.s6_addr[0] == 0xff) && ((addr_.s6_addr[1] & 0x0f) == 0x02));
+}
+
+bool address_v6::is_multicast_node_local() const
+{
+ return ((addr_.s6_addr[0] == 0xff) && ((addr_.s6_addr[1] & 0x0f) == 0x01));
+}
+
+bool address_v6::is_multicast_org_local() const
+{
+ return ((addr_.s6_addr[0] == 0xff) && ((addr_.s6_addr[1] & 0x0f) == 0x08));
+}
+
+bool address_v6::is_multicast_site_local() const
+{
+ return ((addr_.s6_addr[0] == 0xff) && ((addr_.s6_addr[1] & 0x0f) == 0x05));
+}
+
+bool operator==(const address_v6& a1, const address_v6& a2)
+{
+ using namespace std; // For memcmp.
+ return memcmp(&a1.addr_, &a2.addr_,
+ sizeof(boost::asio::detail::in6_addr_type)) == 0
+ && a1.scope_id_ == a2.scope_id_;
+}
+
+bool operator<(const address_v6& a1, const address_v6& a2)
+{
+ using namespace std; // For memcmp.
+ int memcmp_result = memcmp(&a1.addr_, &a2.addr_,
+ sizeof(boost::asio::detail::in6_addr_type));
+ if (memcmp_result < 0)
+ return true;
+ if (memcmp_result > 0)
+ return false;
+ return a1.scope_id_ < a2.scope_id_;
+}
+
+address_v6 address_v6::loopback()
+{
+ address_v6 tmp;
+ tmp.addr_.s6_addr[15] = 1;
+ return tmp;
+}
+
+address_v6 address_v6::v4_mapped(const address_v4& addr)
+{
+ address_v4::bytes_type v4_bytes = addr.to_bytes();
+ bytes_type v6_bytes = { { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0xFF, 0xFF,
+ v4_bytes[0], v4_bytes[1], v4_bytes[2], v4_bytes[3] } };
+ return address_v6(v6_bytes);
+}
+
+address_v6 address_v6::v4_compatible(const address_v4& addr)
+{
+ address_v4::bytes_type v4_bytes = addr.to_bytes();
+ bytes_type v6_bytes = { { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+ v4_bytes[0], v4_bytes[1], v4_bytes[2], v4_bytes[3] } };
+ return address_v6(v6_bytes);
+}
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_IMPL_ADDRESS_V6_IPP
diff --git a/ext/patches/boost/asio/ip/impl/basic_endpoint.hpp b/ext/patches/boost/asio/ip/impl/basic_endpoint.hpp
new file mode 100644
index 0000000..075d68f
--- /dev/null
+++ b/ext/patches/boost/asio/ip/impl/basic_endpoint.hpp
@@ -0,0 +1,57 @@
+//
+// ip/impl/basic_endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_IMPL_BASIC_ENDPOINT_HPP
+#define BOOST_ASIO_IP_IMPL_BASIC_ENDPOINT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/throw_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+template <typename Elem, typename Traits, typename InternetProtocol>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os,
+ const basic_endpoint<InternetProtocol>& endpoint)
+{
+ boost::asio::ip::detail::endpoint tmp_ep(endpoint.address(), endpoint.port());
+ boost::system::error_code ec;
+ std::string s = tmp_ep.to_string(ec);
+ if (ec)
+ {
+ if (os.exceptions() & std::basic_ostream<Elem, Traits>::failbit)
+ boost::asio::detail::throw_error(ec);
+ else
+ os.setstate(std::basic_ostream<Elem, Traits>::failbit);
+ }
+ else
+ for (std::string::iterator i = s.begin(); i != s.end(); ++i)
+ os << os.widen(*i);
+ return os;
+}
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_IP_IMPL_BASIC_ENDPOINT_HPP
diff --git a/ext/patches/boost/asio/ip/impl/host_name.ipp b/ext/patches/boost/asio/ip/impl/host_name.ipp
new file mode 100644
index 0000000..8edf89d
--- /dev/null
+++ b/ext/patches/boost/asio/ip/impl/host_name.ipp
@@ -0,0 +1,56 @@
+//
+// ip/impl/host_name.ipp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_IMPL_HOST_NAME_IPP
+#define BOOST_ASIO_IP_IMPL_HOST_NAME_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/winsock_init.hpp>
+#include <boost/asio/ip/host_name.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+std::string host_name()
+{
+ char name[1024];
+ boost::system::error_code ec;
+ if (boost::asio::detail::socket_ops::gethostname(name, sizeof(name), ec) != 0)
+ {
+ boost::asio::detail::throw_error(ec);
+ return std::string();
+ }
+ return std::string(name);
+}
+
+std::string host_name(boost::system::error_code& ec)
+{
+ char name[1024];
+ if (boost::asio::detail::socket_ops::gethostname(name, sizeof(name), ec) != 0)
+ return std::string();
+ return std::string(name);
+}
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_IMPL_HOST_NAME_IPP
diff --git a/ext/patches/boost/asio/ip/multicast.hpp b/ext/patches/boost/asio/ip/multicast.hpp
new file mode 100644
index 0000000..a822c66
--- /dev/null
+++ b/ext/patches/boost/asio/ip/multicast.hpp
@@ -0,0 +1,193 @@
+//
+// ip/multicast.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_MULTICAST_HPP
+#define BOOST_ASIO_IP_MULTICAST_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/ip/detail/socket_option.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+namespace multicast {
+
+/// Socket option to join a multicast group on a specified interface.
+/**
+ * Implements the IPPROTO_IP/IP_ADD_MEMBERSHIP socket option.
+ *
+ * @par Examples
+ * Setting the option to join a multicast group:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::address multicast_address =
+ * boost::asio::ip::address::from_string("225.0.0.1");
+ * boost::asio::ip::multicast::join_group option(multicast_address);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par Concepts:
+ * SettableSocketOption.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+typedef implementation_defined join_group;
+#else
+typedef boost::asio::ip::detail::socket_option::multicast_request<
+ BOOST_ASIO_OS_DEF(IPPROTO_IP),
+ BOOST_ASIO_OS_DEF(IP_ADD_MEMBERSHIP),
+ BOOST_ASIO_OS_DEF(IPPROTO_IPV6),
+ BOOST_ASIO_OS_DEF(IPV6_JOIN_GROUP)> join_group;
+#endif
+
+/// Socket option to leave a multicast group on a specified interface.
+/**
+ * Implements the IPPROTO_IP/IP_DROP_MEMBERSHIP socket option.
+ *
+ * @par Examples
+ * Setting the option to leave a multicast group:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::address multicast_address =
+ * boost::asio::ip::address::from_string("225.0.0.1");
+ * boost::asio::ip::multicast::leave_group option(multicast_address);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par Concepts:
+ * SettableSocketOption.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+typedef implementation_defined leave_group;
+#else
+typedef boost::asio::ip::detail::socket_option::multicast_request<
+ BOOST_ASIO_OS_DEF(IPPROTO_IP),
+ BOOST_ASIO_OS_DEF(IP_DROP_MEMBERSHIP),
+ BOOST_ASIO_OS_DEF(IPPROTO_IPV6),
+ BOOST_ASIO_OS_DEF(IPV6_LEAVE_GROUP)> leave_group;
+#endif
+
+/// Socket option for local interface to use for outgoing multicast packets.
+/**
+ * Implements the IPPROTO_IP/IP_MULTICAST_IF socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::address_v4 local_interface =
+ * boost::asio::ip::address_v4::from_string("1.2.3.4");
+ * boost::asio::ip::multicast::outbound_interface option(local_interface);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par Concepts:
+ * SettableSocketOption.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+typedef implementation_defined outbound_interface;
+#else
+typedef boost::asio::ip::detail::socket_option::network_interface<
+ BOOST_ASIO_OS_DEF(IPPROTO_IP),
+ BOOST_ASIO_OS_DEF(IP_MULTICAST_IF),
+ BOOST_ASIO_OS_DEF(IPPROTO_IPV6),
+ BOOST_ASIO_OS_DEF(IPV6_MULTICAST_IF)> outbound_interface;
+#endif
+
+/// Socket option for time-to-live associated with outgoing multicast packets.
+/**
+ * Implements the IPPROTO_IP/IP_MULTICAST_TTL socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::multicast::hops option(4);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::multicast::hops option;
+ * socket.get_option(option);
+ * int ttl = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * GettableSocketOption, SettableSocketOption.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+typedef implementation_defined hops;
+#else
+typedef boost::asio::ip::detail::socket_option::multicast_hops<
+ BOOST_ASIO_OS_DEF(IPPROTO_IP),
+ BOOST_ASIO_OS_DEF(IP_MULTICAST_TTL),
+ BOOST_ASIO_OS_DEF(IPPROTO_IPV6),
+ BOOST_ASIO_OS_DEF(IPV6_MULTICAST_HOPS)> hops;
+#endif
+
+/// Socket option determining whether outgoing multicast packets will be
+/// received on the same socket if it is a member of the multicast group.
+/**
+ * Implements the IPPROTO_IP/IP_MULTICAST_LOOP socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::multicast::enable_loopback option(true);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::multicast::enable_loopback option;
+ * socket.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * GettableSocketOption, SettableSocketOption.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+typedef implementation_defined enable_loopback;
+#else
+typedef boost::asio::ip::detail::socket_option::multicast_enable_loopback<
+ BOOST_ASIO_OS_DEF(IPPROTO_IP),
+ BOOST_ASIO_OS_DEF(IP_MULTICAST_LOOP),
+ BOOST_ASIO_OS_DEF(IPPROTO_IPV6),
+ BOOST_ASIO_OS_DEF(IPV6_MULTICAST_LOOP)> enable_loopback;
+#endif
+
+} // namespace multicast
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_MULTICAST_HPP
diff --git a/ext/patches/boost/asio/ip/resolver_query_base.hpp b/ext/patches/boost/asio/ip/resolver_query_base.hpp
new file mode 100644
index 0000000..506d129
--- /dev/null
+++ b/ext/patches/boost/asio/ip/resolver_query_base.hpp
@@ -0,0 +1,132 @@
+//
+// ip/resolver_query_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_RESOLVER_QUERY_BASE_HPP
+#define BOOST_ASIO_IP_RESOLVER_QUERY_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// The resolver_query_base class is used as a base for the
+/// basic_resolver_query class templates to provide a common place to define
+/// the flag constants.
+class resolver_query_base
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// A bitmask type (C++ Std [lib.bitmask.types]).
+ typedef unspecified flags;
+
+ /// Determine the canonical name of the host specified in the query.
+ static const flags canonical_name = implementation_defined;
+
+ /// Indicate that returned endpoint is intended for use as a locally bound
+ /// socket endpoint.
+ static const flags passive = implementation_defined;
+
+ /// Host name should be treated as a numeric string defining an IPv4 or IPv6
+ /// address and no name resolution should be attempted.
+ static const flags numeric_host = implementation_defined;
+
+ /// Service name should be treated as a numeric string defining a port number
+ /// and no name resolution should be attempted.
+ static const flags numeric_service = implementation_defined;
+
+ /// If the query protocol family is specified as IPv6, return IPv4-mapped
+ /// IPv6 addresses on finding no IPv6 addresses.
+ static const flags v4_mapped = implementation_defined;
+
+ /// If used with v4_mapped, return all matching IPv6 and IPv4 addresses.
+ static const flags all_matching = implementation_defined;
+
+ /// Only return IPv4 addresses if a non-loopback IPv4 address is configured
+ /// for the system. Only return IPv6 addresses if a non-loopback IPv6 address
+ /// is configured for the system.
+ static const flags address_configured = implementation_defined;
+#else
+ enum flags
+ {
+ canonical_name = BOOST_ASIO_OS_DEF(AI_CANONNAME),
+ passive = BOOST_ASIO_OS_DEF(AI_PASSIVE),
+ numeric_host = BOOST_ASIO_OS_DEF(AI_NUMERICHOST),
+ numeric_service = BOOST_ASIO_OS_DEF(AI_NUMERICSERV),
+ v4_mapped = BOOST_ASIO_OS_DEF(AI_V4MAPPED),
+ all_matching = BOOST_ASIO_OS_DEF(AI_ALL),
+ address_configured = BOOST_ASIO_OS_DEF(AI_ADDRCONFIG)
+ };
+
+ // Implement bitmask operations as shown in C++ Std [lib.bitmask.types].
+
+ friend flags operator&(flags x, flags y)
+ {
+ return static_cast<flags>(
+ static_cast<unsigned int>(x) & static_cast<unsigned int>(y));
+ }
+
+ friend flags operator|(flags x, flags y)
+ {
+ return static_cast<flags>(
+ static_cast<unsigned int>(x) | static_cast<unsigned int>(y));
+ }
+
+ friend flags operator^(flags x, flags y)
+ {
+ return static_cast<flags>(
+ static_cast<unsigned int>(x) ^ static_cast<unsigned int>(y));
+ }
+
+ friend flags operator~(flags x)
+ {
+ return static_cast<flags>(~static_cast<unsigned int>(x));
+ }
+
+ friend flags& operator&=(flags& x, flags y)
+ {
+ x = x & y;
+ return x;
+ }
+
+ friend flags& operator|=(flags& x, flags y)
+ {
+ x = x | y;
+ return x;
+ }
+
+ friend flags& operator^=(flags& x, flags y)
+ {
+ x = x ^ y;
+ return x;
+ }
+#endif
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~resolver_query_base()
+ {
+ }
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_RESOLVER_QUERY_BASE_HPP
diff --git a/ext/patches/boost/asio/ip/resolver_service.hpp b/ext/patches/boost/asio/ip/resolver_service.hpp
new file mode 100644
index 0000000..8f41091
--- /dev/null
+++ b/ext/patches/boost/asio/ip/resolver_service.hpp
@@ -0,0 +1,178 @@
+//
+// ip/resolver_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_RESOLVER_SERVICE_HPP
+#define BOOST_ASIO_IP_RESOLVER_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/async_result.hpp>
+#include <boost/system/error_code.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/winrt_resolver_service.hpp>
+#else
+# include <boost/asio/detail/resolver_service.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Default service implementation for a resolver.
+template <typename InternetProtocol>
+class resolver_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<
+ resolver_service<InternetProtocol> >
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The protocol type.
+ typedef InternetProtocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename InternetProtocol::endpoint endpoint_type;
+
+ /// The query type.
+ typedef basic_resolver_query<InternetProtocol> query_type;
+
+ /// The iterator type.
+ typedef basic_resolver_iterator<InternetProtocol> iterator_type;
+
+private:
+ // The type of the platform-specific implementation.
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ typedef boost::asio::detail::winrt_resolver_service<InternetProtocol>
+ service_impl_type;
+#else
+ typedef boost::asio::detail::resolver_service<InternetProtocol>
+ service_impl_type;
+#endif
+
+public:
+ /// The type of a resolver implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef typename service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// Construct a new resolver service for the specified io_service.
+ explicit resolver_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ resolver_service<InternetProtocol> >(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new resolver implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+ /// Destroy a resolver implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Cancel pending asynchronous operations.
+ void cancel(implementation_type& impl)
+ {
+ service_impl_.cancel(impl);
+ }
+
+ /// Resolve a query to a list of entries.
+ iterator_type resolve(implementation_type& impl, const query_type& query,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.resolve(impl, query, ec);
+ }
+
+ /// Asynchronously resolve a query to a list of entries.
+ template <typename ResolveHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ResolveHandler,
+ void (boost::system::error_code, iterator_type))
+ async_resolve(implementation_type& impl, const query_type& query,
+ BOOST_ASIO_MOVE_ARG(ResolveHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ ResolveHandler, void (boost::system::error_code, iterator_type)> init(
+ BOOST_ASIO_MOVE_CAST(ResolveHandler)(handler));
+
+ service_impl_.async_resolve(impl, query, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Resolve an endpoint to a list of entries.
+ iterator_type resolve(implementation_type& impl,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.resolve(impl, endpoint, ec);
+ }
+
+ /// Asynchronously resolve an endpoint to a list of entries.
+ template <typename ResolveHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ResolveHandler,
+ void (boost::system::error_code, iterator_type))
+ async_resolve(implementation_type& impl, const endpoint_type& endpoint,
+ BOOST_ASIO_MOVE_ARG(ResolveHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ ResolveHandler, void (boost::system::error_code, iterator_type)> init(
+ BOOST_ASIO_MOVE_CAST(ResolveHandler)(handler));
+
+ service_impl_.async_resolve(impl, endpoint, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // Perform any fork-related housekeeping.
+ void fork_service(boost::asio::io_service::fork_event event)
+ {
+ service_impl_.fork_service(event);
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_RESOLVER_SERVICE_HPP
diff --git a/ext/patches/boost/asio/ip/tcp.hpp b/ext/patches/boost/asio/ip/tcp.hpp
new file mode 100644
index 0000000..98892fc
--- /dev/null
+++ b/ext/patches/boost/asio/ip/tcp.hpp
@@ -0,0 +1,157 @@
+//
+// ip/tcp.hpp
+// ~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_TCP_HPP
+#define BOOST_ASIO_IP_TCP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/basic_socket_acceptor.hpp>
+#include <boost/asio/basic_socket_iostream.hpp>
+#include <boost/asio/basic_stream_socket.hpp>
+#include <boost/asio/detail/socket_option.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/ip/basic_endpoint.hpp>
+#include <boost/asio/ip/basic_resolver.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Encapsulates the flags needed for TCP.
+/**
+ * The boost::asio::ip::tcp class contains flags necessary for TCP sockets.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol, InternetProtocol.
+ */
+class tcp
+{
+public:
+ /// The type of a TCP endpoint.
+ typedef basic_endpoint<tcp> endpoint;
+
+ /// Construct to represent the IPv4 TCP protocol.
+ static tcp v4()
+ {
+ return tcp(BOOST_ASIO_OS_DEF(AF_INET));
+ }
+
+ /// Construct to represent the IPv6 TCP protocol.
+ static tcp v6()
+ {
+ return tcp(BOOST_ASIO_OS_DEF(AF_INET6));
+ }
+
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return BOOST_ASIO_OS_DEF(SOCK_STREAM);
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return BOOST_ASIO_OS_DEF(IPPROTO_TCP);
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return family_;
+ }
+
+ /// The TCP socket type.
+ typedef basic_stream_socket<tcp> socket;
+
+ /// The TCP acceptor type.
+ typedef basic_socket_acceptor<tcp> acceptor;
+
+ /// The TCP resolver type.
+ typedef basic_resolver<tcp> resolver;
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+ /// The TCP iostream type.
+ typedef basic_socket_iostream<tcp> iostream;
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+ /// Socket option for disabling the Nagle algorithm.
+ /**
+ * Implements the IPPROTO_TCP/TCP_NODELAY socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::no_delay option(true);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::tcp::no_delay option;
+ * socket.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Boolean_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined no_delay;
+#else
+ typedef boost::asio::detail::socket_option::boolean<
+ BOOST_ASIO_OS_DEF(IPPROTO_TCP), BOOST_ASIO_OS_DEF(TCP_NODELAY)> no_delay;
+#endif
+
+ /// Compare two protocols for equality.
+ friend bool operator==(const tcp& p1, const tcp& p2)
+ {
+ return p1.family_ == p2.family_;
+ }
+
+ /// Compare two protocols for inequality.
+ friend bool operator!=(const tcp& p1, const tcp& p2)
+ {
+ return p1.family_ != p2.family_;
+ }
+
+private:
+ // Construct with a specific family.
+ explicit tcp(int protocol_family)
+ : family_(protocol_family)
+ {
+ }
+
+ int family_;
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_TCP_HPP
diff --git a/ext/patches/boost/asio/ip/udp.hpp b/ext/patches/boost/asio/ip/udp.hpp
new file mode 100644
index 0000000..59e50d3
--- /dev/null
+++ b/ext/patches/boost/asio/ip/udp.hpp
@@ -0,0 +1,113 @@
+//
+// ip/udp.hpp
+// ~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_UDP_HPP
+#define BOOST_ASIO_IP_UDP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/basic_datagram_socket.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/ip/basic_endpoint.hpp>
+#include <boost/asio/ip/basic_resolver.hpp>
+#include <boost/asio/ip/basic_resolver_iterator.hpp>
+#include <boost/asio/ip/basic_resolver_query.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Encapsulates the flags needed for UDP.
+/**
+ * The boost::asio::ip::udp class contains flags necessary for UDP sockets.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol, InternetProtocol.
+ */
+class udp
+{
+public:
+ /// The type of a UDP endpoint.
+ typedef basic_endpoint<udp> endpoint;
+
+ /// Construct to represent the IPv4 UDP protocol.
+ static udp v4()
+ {
+ return udp(BOOST_ASIO_OS_DEF(AF_INET));
+ }
+
+ /// Construct to represent the IPv6 UDP protocol.
+ static udp v6()
+ {
+ return udp(BOOST_ASIO_OS_DEF(AF_INET6));
+ }
+
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return BOOST_ASIO_OS_DEF(SOCK_DGRAM);
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return BOOST_ASIO_OS_DEF(IPPROTO_UDP);
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return family_;
+ }
+
+ /// The UDP socket type.
+ typedef basic_datagram_socket<udp> socket;
+
+ /// The UDP resolver type.
+ typedef basic_resolver<udp> resolver;
+
+ /// Compare two protocols for equality.
+ friend bool operator==(const udp& p1, const udp& p2)
+ {
+ return p1.family_ == p2.family_;
+ }
+
+ /// Compare two protocols for inequality.
+ friend bool operator!=(const udp& p1, const udp& p2)
+ {
+ return p1.family_ != p2.family_;
+ }
+
+private:
+ // Construct with a specific family.
+ explicit udp(int protocol_family)
+ : family_(protocol_family)
+ {
+ }
+
+ int family_;
+};
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_UDP_HPP
diff --git a/ext/patches/boost/asio/ip/unicast.hpp b/ext/patches/boost/asio/ip/unicast.hpp
new file mode 100644
index 0000000..dd1d1aa
--- /dev/null
+++ b/ext/patches/boost/asio/ip/unicast.hpp
@@ -0,0 +1,72 @@
+//
+// ip/unicast.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_UNICAST_HPP
+#define BOOST_ASIO_IP_UNICAST_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/ip/detail/socket_option.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+namespace unicast {
+
+/// Socket option for time-to-live associated with outgoing unicast packets.
+/**
+ * Implements the IPPROTO_IP/IP_UNICAST_TTL socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::unicast::hops option(4);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::unicast::hops option;
+ * socket.get_option(option);
+ * int ttl = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * GettableSocketOption, SettableSocketOption.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+typedef implementation_defined hops;
+#else
+typedef boost::asio::ip::detail::socket_option::unicast_hops<
+ BOOST_ASIO_OS_DEF(IPPROTO_IP),
+ BOOST_ASIO_OS_DEF(IP_TTL),
+ BOOST_ASIO_OS_DEF(IPPROTO_IPV6),
+ BOOST_ASIO_OS_DEF(IPV6_UNICAST_HOPS)> hops;
+#endif
+
+} // namespace unicast
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_UNICAST_HPP
diff --git a/ext/patches/boost/asio/ip/v6_only.hpp b/ext/patches/boost/asio/ip/v6_only.hpp
new file mode 100644
index 0000000..0ab2445
--- /dev/null
+++ b/ext/patches/boost/asio/ip/v6_only.hpp
@@ -0,0 +1,71 @@
+//
+// ip/v6_only.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IP_V6_ONLY_HPP
+#define BOOST_ASIO_IP_V6_ONLY_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/socket_option.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ip {
+
+/// Socket option for determining whether an IPv6 socket supports IPv6
+/// communication only.
+/**
+ * Implements the IPPROTO_IPV6/IP_V6ONLY socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::v6_only option(true);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::ip::v6_only option;
+ * socket.get_option(option);
+ * bool v6_only = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * GettableSocketOption, SettableSocketOption.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+typedef implementation_defined v6_only;
+#elif defined(IPV6_V6ONLY)
+typedef boost::asio::detail::socket_option::boolean<
+ IPPROTO_IPV6, IPV6_V6ONLY> v6_only;
+#else
+typedef boost::asio::detail::socket_option::boolean<
+ boost::asio::detail::custom_socket_option_level,
+ boost::asio::detail::always_fail_option> v6_only;
+#endif
+
+} // namespace ip
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IP_V6_ONLY_HPP
diff --git a/ext/patches/boost/asio/is_read_buffered.hpp b/ext/patches/boost/asio/is_read_buffered.hpp
new file mode 100644
index 0000000..e0bd320
--- /dev/null
+++ b/ext/patches/boost/asio/is_read_buffered.hpp
@@ -0,0 +1,61 @@
+//
+// is_read_buffered.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IS_READ_BUFFERED_HPP
+#define BOOST_ASIO_IS_READ_BUFFERED_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/buffered_read_stream_fwd.hpp>
+#include <boost/asio/buffered_stream_fwd.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+namespace detail {
+
+template <typename Stream>
+char is_read_buffered_helper(buffered_stream<Stream>* s);
+
+template <typename Stream>
+char is_read_buffered_helper(buffered_read_stream<Stream>* s);
+
+struct is_read_buffered_big_type { char data[10]; };
+is_read_buffered_big_type is_read_buffered_helper(...);
+
+} // namespace detail
+
+/// The is_read_buffered class is a traits class that may be used to determine
+/// whether a stream type supports buffering of read data.
+template <typename Stream>
+class is_read_buffered
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The value member is true only if the Stream type supports buffering of
+ /// read data.
+ static const bool value;
+#else
+ BOOST_ASIO_STATIC_CONSTANT(bool,
+ value = sizeof(detail::is_read_buffered_helper((Stream*)0)) == 1);
+#endif
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IS_READ_BUFFERED_HPP
diff --git a/ext/patches/boost/asio/is_write_buffered.hpp b/ext/patches/boost/asio/is_write_buffered.hpp
new file mode 100644
index 0000000..6aae628
--- /dev/null
+++ b/ext/patches/boost/asio/is_write_buffered.hpp
@@ -0,0 +1,61 @@
+//
+// is_write_buffered.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_IS_WRITE_BUFFERED_HPP
+#define BOOST_ASIO_IS_WRITE_BUFFERED_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/buffered_stream_fwd.hpp>
+#include <boost/asio/buffered_write_stream_fwd.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+namespace detail {
+
+template <typename Stream>
+char is_write_buffered_helper(buffered_stream<Stream>* s);
+
+template <typename Stream>
+char is_write_buffered_helper(buffered_write_stream<Stream>* s);
+
+struct is_write_buffered_big_type { char data[10]; };
+is_write_buffered_big_type is_write_buffered_helper(...);
+
+} // namespace detail
+
+/// The is_write_buffered class is a traits class that may be used to determine
+/// whether a stream type supports buffering of written data.
+template <typename Stream>
+class is_write_buffered
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The value member is true only if the Stream type supports buffering of
+ /// written data.
+ static const bool value;
+#else
+ BOOST_ASIO_STATIC_CONSTANT(bool,
+ value = sizeof(detail::is_write_buffered_helper((Stream*)0)) == 1);
+#endif
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_IS_WRITE_BUFFERED_HPP
diff --git a/ext/patches/boost/asio/local/basic_endpoint.hpp b/ext/patches/boost/asio/local/basic_endpoint.hpp
new file mode 100644
index 0000000..66a06a2
--- /dev/null
+++ b/ext/patches/boost/asio/local/basic_endpoint.hpp
@@ -0,0 +1,241 @@
+//
+// local/basic_endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Derived from a public domain implementation written by Daniel Casimiro.
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_LOCAL_BASIC_ENDPOINT_HPP
+#define BOOST_ASIO_LOCAL_BASIC_ENDPOINT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_LOCAL_SOCKETS) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/local/detail/endpoint.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+# include <iosfwd>
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace local {
+
+/// Describes an endpoint for a UNIX socket.
+/**
+ * The boost::asio::local::basic_endpoint class template describes an endpoint
+ * that may be associated with a particular UNIX socket.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * Endpoint.
+ */
+template <typename Protocol>
+class basic_endpoint
+{
+public:
+ /// The protocol type associated with the endpoint.
+ typedef Protocol protocol_type;
+
+ /// The type of the endpoint structure. This type is dependent on the
+ /// underlying implementation of the socket layer.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined data_type;
+#else
+ typedef boost::asio::detail::socket_addr_type data_type;
+#endif
+
+ /// Default constructor.
+ basic_endpoint()
+ {
+ }
+
+ /// Construct an endpoint using the specified path name.
+ basic_endpoint(const char* path_name)
+ : impl_(path_name)
+ {
+ }
+
+ /// Construct an endpoint using the specified path name.
+ basic_endpoint(const std::string& path_name)
+ : impl_(path_name)
+ {
+ }
+
+ /// Copy constructor.
+ basic_endpoint(const basic_endpoint& other)
+ : impl_(other.impl_)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move constructor.
+ basic_endpoint(basic_endpoint&& other)
+ : impl_(other.impl_)
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// Assign from another endpoint.
+ basic_endpoint& operator=(const basic_endpoint& other)
+ {
+ impl_ = other.impl_;
+ return *this;
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ /// Move-assign from another endpoint.
+ basic_endpoint& operator=(basic_endpoint&& other)
+ {
+ impl_ = other.impl_;
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ /// The protocol associated with the endpoint.
+ protocol_type protocol() const
+ {
+ return protocol_type();
+ }
+
+ /// Get the underlying endpoint in the native type.
+ data_type* data()
+ {
+ return impl_.data();
+ }
+
+ /// Get the underlying endpoint in the native type.
+ const data_type* data() const
+ {
+ return impl_.data();
+ }
+
+ /// Get the underlying size of the endpoint in the native type.
+ std::size_t size() const
+ {
+ return impl_.size();
+ }
+
+ /// Set the underlying size of the endpoint in the native type.
+ void resize(std::size_t new_size)
+ {
+ impl_.resize(new_size);
+ }
+
+ /// Get the capacity of the endpoint in the native type.
+ std::size_t capacity() const
+ {
+ return impl_.capacity();
+ }
+
+ /// Get the path associated with the endpoint.
+ std::string path() const
+ {
+ return impl_.path();
+ }
+
+ /// Set the path associated with the endpoint.
+ void path(const char* p)
+ {
+ impl_.path(p);
+ }
+
+ /// Set the path associated with the endpoint.
+ void path(const std::string& p)
+ {
+ impl_.path(p);
+ }
+
+ /// Compare two endpoints for equality.
+ friend bool operator==(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return e1.impl_ == e2.impl_;
+ }
+
+ /// Compare two endpoints for inequality.
+ friend bool operator!=(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return !(e1.impl_ == e2.impl_);
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator<(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return e1.impl_ < e2.impl_;
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator>(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return e2.impl_ < e1.impl_;
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator<=(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return !(e2 < e1);
+ }
+
+ /// Compare endpoints for ordering.
+ friend bool operator>=(const basic_endpoint<Protocol>& e1,
+ const basic_endpoint<Protocol>& e2)
+ {
+ return !(e1 < e2);
+ }
+
+private:
+ // The underlying UNIX domain endpoint.
+ boost::asio::local::detail::endpoint impl_;
+};
+
+/// Output an endpoint as a string.
+/**
+ * Used to output a human-readable string for a specified endpoint.
+ *
+ * @param os The output stream to which the string will be written.
+ *
+ * @param endpoint The endpoint to be written.
+ *
+ * @return The output stream.
+ *
+ * @relates boost::asio::local::basic_endpoint
+ */
+template <typename Elem, typename Traits, typename Protocol>
+std::basic_ostream<Elem, Traits>& operator<<(
+ std::basic_ostream<Elem, Traits>& os,
+ const basic_endpoint<Protocol>& endpoint)
+{
+ os << endpoint.path();
+ return os;
+}
+
+} // namespace local
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_LOCAL_BASIC_ENDPOINT_HPP
diff --git a/ext/patches/boost/asio/local/connect_pair.hpp b/ext/patches/boost/asio/local/connect_pair.hpp
new file mode 100644
index 0000000..2d4c46a
--- /dev/null
+++ b/ext/patches/boost/asio/local/connect_pair.hpp
@@ -0,0 +1,106 @@
+//
+// local/connect_pair.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_LOCAL_CONNECT_PAIR_HPP
+#define BOOST_ASIO_LOCAL_CONNECT_PAIR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_LOCAL_SOCKETS) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/local/basic_endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace local {
+
+/// Create a pair of connected sockets.
+template <typename Protocol, typename SocketService1, typename SocketService2>
+void connect_pair(
+ basic_socket<Protocol, SocketService1>& socket1,
+ basic_socket<Protocol, SocketService2>& socket2);
+
+/// Create a pair of connected sockets.
+template <typename Protocol, typename SocketService1, typename SocketService2>
+boost::system::error_code connect_pair(
+ basic_socket<Protocol, SocketService1>& socket1,
+ basic_socket<Protocol, SocketService2>& socket2,
+ boost::system::error_code& ec);
+
+template <typename Protocol, typename SocketService1, typename SocketService2>
+inline void connect_pair(
+ basic_socket<Protocol, SocketService1>& socket1,
+ basic_socket<Protocol, SocketService2>& socket2)
+{
+ boost::system::error_code ec;
+ connect_pair(socket1, socket2, ec);
+ boost::asio::detail::throw_error(ec, "connect_pair");
+}
+
+template <typename Protocol, typename SocketService1, typename SocketService2>
+inline boost::system::error_code connect_pair(
+ basic_socket<Protocol, SocketService1>& socket1,
+ basic_socket<Protocol, SocketService2>& socket2,
+ boost::system::error_code& ec)
+{
+ // Check that this function is only being used with a UNIX domain socket.
+ boost::asio::local::basic_endpoint<Protocol>* tmp
+ = static_cast<typename Protocol::endpoint*>(0);
+ (void)tmp;
+
+ Protocol protocol;
+ boost::asio::detail::socket_type sv[2];
+ if (boost::asio::detail::socket_ops::socketpair(protocol.family(),
+ protocol.type(), protocol.protocol(), sv, ec)
+ == boost::asio::detail::socket_error_retval)
+ return ec;
+
+ if (socket1.assign(protocol, sv[0], ec))
+ {
+ boost::system::error_code temp_ec;
+ boost::asio::detail::socket_ops::state_type state[2] = { 0, 0 };
+ boost::asio::detail::socket_ops::close(sv[0], state[0], true, temp_ec);
+ boost::asio::detail::socket_ops::close(sv[1], state[1], true, temp_ec);
+ return ec;
+ }
+
+ if (socket2.assign(protocol, sv[1], ec))
+ {
+ boost::system::error_code temp_ec;
+ socket1.close(temp_ec);
+ boost::asio::detail::socket_ops::state_type state = 0;
+ boost::asio::detail::socket_ops::close(sv[1], state, true, temp_ec);
+ return ec;
+ }
+
+ return ec;
+}
+
+} // namespace local
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_LOCAL_CONNECT_PAIR_HPP
diff --git a/ext/patches/boost/asio/local/datagram_protocol.hpp b/ext/patches/boost/asio/local/datagram_protocol.hpp
new file mode 100644
index 0000000..6621170
--- /dev/null
+++ b/ext/patches/boost/asio/local/datagram_protocol.hpp
@@ -0,0 +1,82 @@
+//
+// local/datagram_protocol.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_LOCAL_DATAGRAM_PROTOCOL_HPP
+#define BOOST_ASIO_LOCAL_DATAGRAM_PROTOCOL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_LOCAL_SOCKETS) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/basic_datagram_socket.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/local/basic_endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace local {
+
+/// Encapsulates the flags needed for datagram-oriented UNIX sockets.
+/**
+ * The boost::asio::local::datagram_protocol class contains flags necessary for
+ * datagram-oriented UNIX domain sockets.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol.
+ */
+class datagram_protocol
+{
+public:
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return SOCK_DGRAM;
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return 0;
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return AF_UNIX;
+ }
+
+ /// The type of a UNIX domain endpoint.
+ typedef basic_endpoint<datagram_protocol> endpoint;
+
+ /// The UNIX domain socket type.
+ typedef basic_datagram_socket<datagram_protocol> socket;
+};
+
+} // namespace local
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_LOCAL_DATAGRAM_PROTOCOL_HPP
diff --git a/ext/patches/boost/asio/local/detail/endpoint.hpp b/ext/patches/boost/asio/local/detail/endpoint.hpp
new file mode 100644
index 0000000..1ca3aea
--- /dev/null
+++ b/ext/patches/boost/asio/local/detail/endpoint.hpp
@@ -0,0 +1,135 @@
+//
+// local/detail/endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Derived from a public domain implementation written by Daniel Casimiro.
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_LOCAL_DETAIL_ENDPOINT_HPP
+#define BOOST_ASIO_LOCAL_DETAIL_ENDPOINT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+
+#include <cstddef>
+#include <string>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace local {
+namespace detail {
+
+// Helper class for implementing a UNIX domain endpoint.
+class endpoint
+{
+public:
+ // Default constructor.
+ BOOST_ASIO_DECL endpoint();
+
+ // Construct an endpoint using the specified path name.
+ BOOST_ASIO_DECL endpoint(const char* path_name);
+
+ // Construct an endpoint using the specified path name.
+ BOOST_ASIO_DECL endpoint(const std::string& path_name);
+
+ // Copy constructor.
+ endpoint(const endpoint& other)
+ : data_(other.data_),
+ path_length_(other.path_length_)
+ {
+ }
+
+ // Assign from another endpoint.
+ endpoint& operator=(const endpoint& other)
+ {
+ data_ = other.data_;
+ path_length_ = other.path_length_;
+ return *this;
+ }
+
+ // Get the underlying endpoint in the native type.
+ boost::asio::detail::socket_addr_type* data()
+ {
+ return &data_.base;
+ }
+
+ // Get the underlying endpoint in the native type.
+ const boost::asio::detail::socket_addr_type* data() const
+ {
+ return &data_.base;
+ }
+
+ // Get the underlying size of the endpoint in the native type.
+ std::size_t size() const
+ {
+ return path_length_
+ + offsetof(boost::asio::detail::sockaddr_un_type, sun_path);
+ }
+
+ // Set the underlying size of the endpoint in the native type.
+ BOOST_ASIO_DECL void resize(std::size_t size);
+
+ // Get the capacity of the endpoint in the native type.
+ std::size_t capacity() const
+ {
+ return sizeof(boost::asio::detail::sockaddr_un_type);
+ }
+
+ // Get the path associated with the endpoint.
+ BOOST_ASIO_DECL std::string path() const;
+
+ // Set the path associated with the endpoint.
+ BOOST_ASIO_DECL void path(const char* p);
+
+ // Set the path associated with the endpoint.
+ BOOST_ASIO_DECL void path(const std::string& p);
+
+ // Compare two endpoints for equality.
+ BOOST_ASIO_DECL friend bool operator==(
+ const endpoint& e1, const endpoint& e2);
+
+ // Compare endpoints for ordering.
+ BOOST_ASIO_DECL friend bool operator<(
+ const endpoint& e1, const endpoint& e2);
+
+private:
+ // The underlying UNIX socket address.
+ union data_union
+ {
+ boost::asio::detail::socket_addr_type base;
+ boost::asio::detail::sockaddr_un_type local;
+ } data_;
+
+ // The length of the path associated with the endpoint.
+ std::size_t path_length_;
+
+ // Initialise with a specified path.
+ BOOST_ASIO_DECL void init(const char* path, std::size_t path_length);
+};
+
+} // namespace detail
+} // namespace local
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/local/detail/impl/endpoint.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+
+#endif // BOOST_ASIO_LOCAL_DETAIL_ENDPOINT_HPP
diff --git a/ext/patches/boost/asio/local/detail/impl/endpoint.ipp b/ext/patches/boost/asio/local/detail/impl/endpoint.ipp
new file mode 100644
index 0000000..4ba18a1
--- /dev/null
+++ b/ext/patches/boost/asio/local/detail/impl/endpoint.ipp
@@ -0,0 +1,130 @@
+//
+// local/detail/impl/endpoint.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Derived from a public domain implementation written by Daniel Casimiro.
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_LOCAL_DETAIL_IMPL_ENDPOINT_IPP
+#define BOOST_ASIO_LOCAL_DETAIL_IMPL_ENDPOINT_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+
+#include <cstring>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/local/detail/endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace local {
+namespace detail {
+
+endpoint::endpoint()
+{
+ init("", 0);
+}
+
+endpoint::endpoint(const char* path_name)
+{
+ using namespace std; // For strlen.
+ init(path_name, strlen(path_name));
+}
+
+endpoint::endpoint(const std::string& path_name)
+{
+ init(path_name.data(), path_name.length());
+}
+
+void endpoint::resize(std::size_t new_size)
+{
+ if (new_size > sizeof(boost::asio::detail::sockaddr_un_type))
+ {
+ boost::system::error_code ec(boost::asio::error::invalid_argument);
+ boost::asio::detail::throw_error(ec);
+ }
+ else if (new_size == 0)
+ {
+ path_length_ = 0;
+ }
+ else
+ {
+ path_length_ = new_size
+ - offsetof(boost::asio::detail::sockaddr_un_type, sun_path);
+
+ // The path returned by the operating system may be NUL-terminated.
+ if (path_length_ > 0 && data_.local.sun_path[path_length_ - 1] == 0)
+ --path_length_;
+ }
+}
+
+std::string endpoint::path() const
+{
+ return std::string(data_.local.sun_path, path_length_);
+}
+
+void endpoint::path(const char* p)
+{
+ using namespace std; // For strlen.
+ init(p, strlen(p));
+}
+
+void endpoint::path(const std::string& p)
+{
+ init(p.data(), p.length());
+}
+
+bool operator==(const endpoint& e1, const endpoint& e2)
+{
+ return e1.path() == e2.path();
+}
+
+bool operator<(const endpoint& e1, const endpoint& e2)
+{
+ return e1.path() < e2.path();
+}
+
+void endpoint::init(const char* path_name, std::size_t path_length)
+{
+ if (path_length > sizeof(data_.local.sun_path) - 1)
+ {
+ // The buffer is not large enough to store this address.
+ boost::system::error_code ec(boost::asio::error::name_too_long);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ using namespace std; // For memcpy.
+ data_.local = boost::asio::detail::sockaddr_un_type();
+ data_.local.sun_family = AF_UNIX;
+ memcpy(data_.local.sun_path, path_name, path_length);
+ path_length_ = path_length;
+
+ // NUL-terminate normal path names. Names that start with a NUL are in the
+ // UNIX domain protocol's "abstract namespace" and are not NUL-terminated.
+ if (path_length > 0 && data_.local.sun_path[0] == 0)
+ data_.local.sun_path[path_length] = 0;
+}
+
+} // namespace detail
+} // namespace local
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+
+#endif // BOOST_ASIO_LOCAL_DETAIL_IMPL_ENDPOINT_IPP
diff --git a/ext/patches/boost/asio/local/stream_protocol.hpp b/ext/patches/boost/asio/local/stream_protocol.hpp
new file mode 100644
index 0000000..bdf23c3
--- /dev/null
+++ b/ext/patches/boost/asio/local/stream_protocol.hpp
@@ -0,0 +1,92 @@
+//
+// local/stream_protocol.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_LOCAL_STREAM_PROTOCOL_HPP
+#define BOOST_ASIO_LOCAL_STREAM_PROTOCOL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_LOCAL_SOCKETS) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/basic_socket_acceptor.hpp>
+#include <boost/asio/basic_socket_iostream.hpp>
+#include <boost/asio/basic_stream_socket.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/asio/local/basic_endpoint.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace local {
+
+/// Encapsulates the flags needed for stream-oriented UNIX sockets.
+/**
+ * The boost::asio::local::stream_protocol class contains flags necessary for
+ * stream-oriented UNIX domain sockets.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Protocol.
+ */
+class stream_protocol
+{
+public:
+ /// Obtain an identifier for the type of the protocol.
+ int type() const
+ {
+ return SOCK_STREAM;
+ }
+
+ /// Obtain an identifier for the protocol.
+ int protocol() const
+ {
+ return 0;
+ }
+
+ /// Obtain an identifier for the protocol family.
+ int family() const
+ {
+ return AF_UNIX;
+ }
+
+ /// The type of a UNIX domain endpoint.
+ typedef basic_endpoint<stream_protocol> endpoint;
+
+ /// The UNIX domain socket type.
+ typedef basic_stream_socket<stream_protocol> socket;
+
+ /// The UNIX domain acceptor type.
+ typedef basic_socket_acceptor<stream_protocol> acceptor;
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+ /// The UNIX domain iostream type.
+ typedef basic_socket_iostream<stream_protocol> iostream;
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+};
+
+} // namespace local
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_LOCAL_SOCKETS)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_LOCAL_STREAM_PROTOCOL_HPP
diff --git a/ext/patches/boost/asio/placeholders.hpp b/ext/patches/boost/asio/placeholders.hpp
new file mode 100644
index 0000000..f042a53
--- /dev/null
+++ b/ext/patches/boost/asio/placeholders.hpp
@@ -0,0 +1,125 @@
+//
+// placeholders.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_PLACEHOLDERS_HPP
+#define BOOST_ASIO_PLACEHOLDERS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_BOOST_BIND)
+# include <boost/bind/arg.hpp>
+#endif // defined(BOOST_ASIO_HAS_BOOST_BIND)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace placeholders {
+
+#if defined(GENERATING_DOCUMENTATION)
+
+/// An argument placeholder, for use with boost::bind(), that corresponds to
+/// the error argument of a handler for any of the asynchronous functions.
+unspecified error;
+
+/// An argument placeholder, for use with boost::bind(), that corresponds to
+/// the bytes_transferred argument of a handler for asynchronous functions such
+/// as boost::asio::basic_stream_socket::async_write_some or
+/// boost::asio::async_write.
+unspecified bytes_transferred;
+
+/// An argument placeholder, for use with boost::bind(), that corresponds to
+/// the iterator argument of a handler for asynchronous functions such as
+/// boost::asio::basic_resolver::async_resolve.
+unspecified iterator;
+
+/// An argument placeholder, for use with boost::bind(), that corresponds to
+/// the signal_number argument of a handler for asynchronous functions such as
+/// boost::asio::signal_set::async_wait.
+unspecified signal_number;
+
+#elif defined(BOOST_ASIO_HAS_BOOST_BIND)
+# if defined(__BORLANDC__) || defined(__GNUC__)
+
+inline boost::arg<1> error()
+{
+ return boost::arg<1>();
+}
+
+inline boost::arg<2> bytes_transferred()
+{
+ return boost::arg<2>();
+}
+
+inline boost::arg<2> iterator()
+{
+ return boost::arg<2>();
+}
+
+inline boost::arg<2> signal_number()
+{
+ return boost::arg<2>();
+}
+
+# else
+
+namespace detail
+{
+ template <int Number>
+ struct placeholder
+ {
+ static boost::arg<Number>& get()
+ {
+ static boost::arg<Number> result;
+ return result;
+ }
+ };
+}
+
+# if defined(BOOST_ASIO_MSVC) && (BOOST_ASIO_MSVC < 1400)
+
+static boost::arg<1>& error
+ = boost::asio::placeholders::detail::placeholder<1>::get();
+static boost::arg<2>& bytes_transferred
+ = boost::asio::placeholders::detail::placeholder<2>::get();
+static boost::arg<2>& iterator
+ = boost::asio::placeholders::detail::placeholder<2>::get();
+static boost::arg<2>& signal_number
+ = boost::asio::placeholders::detail::placeholder<2>::get();
+
+# else
+
+namespace
+{
+ boost::arg<1>& error
+ = boost::asio::placeholders::detail::placeholder<1>::get();
+ boost::arg<2>& bytes_transferred
+ = boost::asio::placeholders::detail::placeholder<2>::get();
+ boost::arg<2>& iterator
+ = boost::asio::placeholders::detail::placeholder<2>::get();
+ boost::arg<2>& signal_number
+ = boost::asio::placeholders::detail::placeholder<2>::get();
+} // namespace
+
+# endif
+# endif
+#endif
+
+} // namespace placeholders
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_PLACEHOLDERS_HPP
diff --git a/ext/patches/boost/asio/posix/basic_descriptor.hpp b/ext/patches/boost/asio/posix/basic_descriptor.hpp
new file mode 100644
index 0000000..d958999
--- /dev/null
+++ b/ext/patches/boost/asio/posix/basic_descriptor.hpp
@@ -0,0 +1,492 @@
+//
+// posix/basic_descriptor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_POSIX_BASIC_DESCRIPTOR_HPP
+#define BOOST_ASIO_POSIX_BASIC_DESCRIPTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/posix/descriptor_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace posix {
+
+/// Provides POSIX descriptor functionality.
+/**
+ * The posix::basic_descriptor class template provides the ability to wrap a
+ * POSIX descriptor.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename DescriptorService>
+class basic_descriptor
+ : public basic_io_object<DescriptorService>,
+ public descriptor_base
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// descriptor.
+ typedef typename DescriptorService::native_handle_type native_type;
+
+ /// The native representation of a descriptor.
+ typedef typename DescriptorService::native_handle_type native_handle_type;
+
+ /// A basic_descriptor is always the lowest layer.
+ typedef basic_descriptor<DescriptorService> lowest_layer_type;
+
+ /// Construct a basic_descriptor without opening it.
+ /**
+ * This constructor creates a descriptor without opening it.
+ *
+ * @param io_service The io_service object that the descriptor will use to
+ * dispatch handlers for any asynchronous operations performed on the
+ * descriptor.
+ */
+ explicit basic_descriptor(boost::asio::io_service& io_service)
+ : basic_io_object<DescriptorService>(io_service)
+ {
+ }
+
+ /// Construct a basic_descriptor on an existing native descriptor.
+ /**
+ * This constructor creates a descriptor object to hold an existing native
+ * descriptor.
+ *
+ * @param io_service The io_service object that the descriptor will use to
+ * dispatch handlers for any asynchronous operations performed on the
+ * descriptor.
+ *
+ * @param native_descriptor A native descriptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_descriptor(boost::asio::io_service& io_service,
+ const native_handle_type& native_descriptor)
+ : basic_io_object<DescriptorService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(),
+ native_descriptor, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_descriptor from another.
+ /**
+ * This constructor moves a descriptor from one object to another.
+ *
+ * @param other The other basic_descriptor object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_descriptor(io_service&) constructor.
+ */
+ basic_descriptor(basic_descriptor&& other)
+ : basic_io_object<DescriptorService>(
+ BOOST_ASIO_MOVE_CAST(basic_descriptor)(other))
+ {
+ }
+
+ /// Move-assign a basic_descriptor from another.
+ /**
+ * This assignment operator moves a descriptor from one object to another.
+ *
+ * @param other The other basic_descriptor object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_descriptor(io_service&) constructor.
+ */
+ basic_descriptor& operator=(basic_descriptor&& other)
+ {
+ basic_io_object<DescriptorService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_descriptor)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Get a reference to the lowest layer.
+ /**
+ * This function returns a reference to the lowest layer in a stack of
+ * layers. Since a basic_descriptor cannot contain any further layers, it
+ * simply returns a reference to itself.
+ *
+ * @return A reference to the lowest layer in the stack of layers. Ownership
+ * is not transferred to the caller.
+ */
+ lowest_layer_type& lowest_layer()
+ {
+ return *this;
+ }
+
+ /// Get a const reference to the lowest layer.
+ /**
+ * This function returns a const reference to the lowest layer in a stack of
+ * layers. Since a basic_descriptor cannot contain any further layers, it
+ * simply returns a reference to itself.
+ *
+ * @return A const reference to the lowest layer in the stack of layers.
+ * Ownership is not transferred to the caller.
+ */
+ const lowest_layer_type& lowest_layer() const
+ {
+ return *this;
+ }
+
+ /// Assign an existing native descriptor to the descriptor.
+ /*
+ * This function opens the descriptor to hold an existing native descriptor.
+ *
+ * @param native_descriptor A native descriptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void assign(const native_handle_type& native_descriptor)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(),
+ native_descriptor, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+ /// Assign an existing native descriptor to the descriptor.
+ /*
+ * This function opens the descriptor to hold an existing native descriptor.
+ *
+ * @param native_descriptor A native descriptor.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code assign(const native_handle_type& native_descriptor,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().assign(
+ this->get_implementation(), native_descriptor, ec);
+ }
+
+ /// Determine whether the descriptor is open.
+ bool is_open() const
+ {
+ return this->get_service().is_open(this->implementation);
+ }
+
+ /// Close the descriptor.
+ /**
+ * This function is used to close the descriptor. Any asynchronous read or
+ * write operations will be cancelled immediately, and will complete with the
+ * boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure. Note that, even if
+ * the function indicates an error, the underlying descriptor is closed.
+ */
+ void close()
+ {
+ boost::system::error_code ec;
+ this->get_service().close(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "close");
+ }
+
+ /// Close the descriptor.
+ /**
+ * This function is used to close the descriptor. Any asynchronous read or
+ * write operations will be cancelled immediately, and will complete with the
+ * boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any. Note that, even if
+ * the function indicates an error, the underlying descriptor is closed.
+ */
+ boost::system::error_code close(boost::system::error_code& ec)
+ {
+ return this->get_service().close(this->get_implementation(), ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native descriptor
+ /// representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * descriptor. This is intended to allow access to native descriptor
+ * functionality that is not otherwise provided.
+ */
+ native_type native()
+ {
+ return this->get_service().native_handle(this->implementation);
+ }
+
+ /// Get the native descriptor representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * descriptor. This is intended to allow access to native descriptor
+ * functionality that is not otherwise provided.
+ */
+ native_handle_type native_handle()
+ {
+ return this->get_service().native_handle(this->implementation);
+ }
+
+ /// Release ownership of the native descriptor implementation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * descriptor. After calling this function, @c is_open() returns false. The
+ * caller is responsible for closing the descriptor.
+ *
+ * All outstanding asynchronous read or write operations will finish
+ * immediately, and the handlers for cancelled operations will be passed the
+ * boost::asio::error::operation_aborted error.
+ */
+ native_handle_type release()
+ {
+ return this->get_service().release(this->implementation);
+ }
+
+ /// Cancel all asynchronous operations associated with the descriptor.
+ /**
+ * This function causes all outstanding asynchronous read or write operations
+ * to finish immediately, and the handlers for cancelled operations will be
+ * passed the boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void cancel()
+ {
+ boost::system::error_code ec;
+ this->get_service().cancel(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "cancel");
+ }
+
+ /// Cancel all asynchronous operations associated with the descriptor.
+ /**
+ * This function causes all outstanding asynchronous read or write operations
+ * to finish immediately, and the handlers for cancelled operations will be
+ * passed the boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code cancel(boost::system::error_code& ec)
+ {
+ return this->get_service().cancel(this->get_implementation(), ec);
+ }
+
+ /// Perform an IO control command on the descriptor.
+ /**
+ * This function is used to execute an IO control command on the descriptor.
+ *
+ * @param command The IO control command to be performed on the descriptor.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @sa IoControlCommand @n
+ * boost::asio::posix::descriptor_base::bytes_readable @n
+ * boost::asio::posix::descriptor_base::non_blocking_io
+ *
+ * @par Example
+ * Getting the number of bytes ready to read:
+ * @code
+ * boost::asio::posix::stream_descriptor descriptor(io_service);
+ * ...
+ * boost::asio::posix::stream_descriptor::bytes_readable command;
+ * descriptor.io_control(command);
+ * std::size_t bytes_readable = command.get();
+ * @endcode
+ */
+ template <typename IoControlCommand>
+ void io_control(IoControlCommand& command)
+ {
+ boost::system::error_code ec;
+ this->get_service().io_control(this->get_implementation(), command, ec);
+ boost::asio::detail::throw_error(ec, "io_control");
+ }
+
+ /// Perform an IO control command on the descriptor.
+ /**
+ * This function is used to execute an IO control command on the descriptor.
+ *
+ * @param command The IO control command to be performed on the descriptor.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @sa IoControlCommand @n
+ * boost::asio::posix::descriptor_base::bytes_readable @n
+ * boost::asio::posix::descriptor_base::non_blocking_io
+ *
+ * @par Example
+ * Getting the number of bytes ready to read:
+ * @code
+ * boost::asio::posix::stream_descriptor descriptor(io_service);
+ * ...
+ * boost::asio::posix::stream_descriptor::bytes_readable command;
+ * boost::system::error_code ec;
+ * descriptor.io_control(command, ec);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * std::size_t bytes_readable = command.get();
+ * @endcode
+ */
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(IoControlCommand& command,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().io_control(
+ this->get_implementation(), command, ec);
+ }
+
+ /// Gets the non-blocking mode of the descriptor.
+ /**
+ * @returns @c true if the descriptor's synchronous operations will fail with
+ * boost::asio::error::would_block if they are unable to perform the requested
+ * operation immediately. If @c false, synchronous operations will block
+ * until complete.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ bool non_blocking() const
+ {
+ return this->get_service().non_blocking(this->implementation);
+ }
+
+ /// Sets the non-blocking mode of the descriptor.
+ /**
+ * @param mode If @c true, the descriptor's synchronous operations will fail
+ * with boost::asio::error::would_block if they are unable to perform the
+ * requested operation immediately. If @c false, synchronous operations will
+ * block until complete.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ void non_blocking(bool mode)
+ {
+ boost::system::error_code ec;
+ this->get_service().non_blocking(this->get_implementation(), mode, ec);
+ boost::asio::detail::throw_error(ec, "non_blocking");
+ }
+
+ /// Sets the non-blocking mode of the descriptor.
+ /**
+ * @param mode If @c true, the descriptor's synchronous operations will fail
+ * with boost::asio::error::would_block if they are unable to perform the
+ * requested operation immediately. If @c false, synchronous operations will
+ * block until complete.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note The non-blocking mode has no effect on the behaviour of asynchronous
+ * operations. Asynchronous operations will never fail with the error
+ * boost::asio::error::would_block.
+ */
+ boost::system::error_code non_blocking(
+ bool mode, boost::system::error_code& ec)
+ {
+ return this->get_service().non_blocking(
+ this->get_implementation(), mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native descriptor implementation.
+ /**
+ * This function is used to retrieve the non-blocking mode of the underlying
+ * native descriptor. This mode has no effect on the behaviour of the
+ * descriptor object's synchronous operations.
+ *
+ * @returns @c true if the underlying descriptor is in non-blocking mode and
+ * direct system calls may fail with boost::asio::error::would_block (or the
+ * equivalent system error).
+ *
+ * @note The current non-blocking mode is cached by the descriptor object.
+ * Consequently, the return value may be incorrect if the non-blocking mode
+ * was set directly on the native descriptor.
+ */
+ bool native_non_blocking() const
+ {
+ return this->get_service().native_non_blocking(this->implementation);
+ }
+
+ /// Sets the non-blocking mode of the native descriptor implementation.
+ /**
+ * This function is used to modify the non-blocking mode of the underlying
+ * native descriptor. It has no effect on the behaviour of the descriptor
+ * object's synchronous operations.
+ *
+ * @param mode If @c true, the underlying descriptor is put into non-blocking
+ * mode and direct system calls may fail with boost::asio::error::would_block
+ * (or the equivalent system error).
+ *
+ * @throws boost::system::system_error Thrown on failure. If the @c mode is
+ * @c false, but the current value of @c non_blocking() is @c true, this
+ * function fails with boost::asio::error::invalid_argument, as the
+ * combination does not make sense.
+ */
+ void native_non_blocking(bool mode)
+ {
+ boost::system::error_code ec;
+ this->get_service().native_non_blocking(
+ this->get_implementation(), mode, ec);
+ boost::asio::detail::throw_error(ec, "native_non_blocking");
+ }
+
+ /// Sets the non-blocking mode of the native descriptor implementation.
+ /**
+ * This function is used to modify the non-blocking mode of the underlying
+ * native descriptor. It has no effect on the behaviour of the descriptor
+ * object's synchronous operations.
+ *
+ * @param mode If @c true, the underlying descriptor is put into non-blocking
+ * mode and direct system calls may fail with boost::asio::error::would_block
+ * (or the equivalent system error).
+ *
+ * @param ec Set to indicate what error occurred, if any. If the @c mode is
+ * @c false, but the current value of @c non_blocking() is @c true, this
+ * function fails with boost::asio::error::invalid_argument, as the
+ * combination does not make sense.
+ */
+ boost::system::error_code native_non_blocking(
+ bool mode, boost::system::error_code& ec)
+ {
+ return this->get_service().native_non_blocking(
+ this->get_implementation(), mode, ec);
+ }
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~basic_descriptor()
+ {
+ }
+};
+
+} // namespace posix
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_POSIX_BASIC_DESCRIPTOR_HPP
diff --git a/ext/patches/boost/asio/posix/basic_stream_descriptor.hpp b/ext/patches/boost/asio/posix/basic_stream_descriptor.hpp
new file mode 100644
index 0000000..952567f
--- /dev/null
+++ b/ext/patches/boost/asio/posix/basic_stream_descriptor.hpp
@@ -0,0 +1,364 @@
+//
+// posix/basic_stream_descriptor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_POSIX_BASIC_STREAM_DESCRIPTOR_HPP
+#define BOOST_ASIO_POSIX_BASIC_STREAM_DESCRIPTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/posix/basic_descriptor.hpp>
+#include <boost/asio/posix/stream_descriptor_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace posix {
+
+/// Provides stream-oriented descriptor functionality.
+/**
+ * The posix::basic_stream_descriptor class template provides asynchronous and
+ * blocking stream-oriented descriptor functionality.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * AsyncReadStream, AsyncWriteStream, Stream, SyncReadStream, SyncWriteStream.
+ */
+template <typename StreamDescriptorService = stream_descriptor_service>
+class basic_stream_descriptor
+ : public basic_descriptor<StreamDescriptorService>
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// descriptor.
+ typedef typename StreamDescriptorService::native_handle_type native_type;
+
+ /// The native representation of a descriptor.
+ typedef typename StreamDescriptorService::native_handle_type
+ native_handle_type;
+
+ /// Construct a basic_stream_descriptor without opening it.
+ /**
+ * This constructor creates a stream descriptor without opening it. The
+ * descriptor needs to be opened and then connected or accepted before data
+ * can be sent or received on it.
+ *
+ * @param io_service The io_service object that the stream descriptor will
+ * use to dispatch handlers for any asynchronous operations performed on the
+ * descriptor.
+ */
+ explicit basic_stream_descriptor(boost::asio::io_service& io_service)
+ : basic_descriptor<StreamDescriptorService>(io_service)
+ {
+ }
+
+ /// Construct a basic_stream_descriptor on an existing native descriptor.
+ /**
+ * This constructor creates a stream descriptor object to hold an existing
+ * native descriptor.
+ *
+ * @param io_service The io_service object that the stream descriptor will
+ * use to dispatch handlers for any asynchronous operations performed on the
+ * descriptor.
+ *
+ * @param native_descriptor The new underlying descriptor implementation.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_stream_descriptor(boost::asio::io_service& io_service,
+ const native_handle_type& native_descriptor)
+ : basic_descriptor<StreamDescriptorService>(io_service, native_descriptor)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_stream_descriptor from another.
+ /**
+ * This constructor moves a stream descriptor from one object to another.
+ *
+ * @param other The other basic_stream_descriptor object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_stream_descriptor(io_service&) constructor.
+ */
+ basic_stream_descriptor(basic_stream_descriptor&& other)
+ : basic_descriptor<StreamDescriptorService>(
+ BOOST_ASIO_MOVE_CAST(basic_stream_descriptor)(other))
+ {
+ }
+
+ /// Move-assign a basic_stream_descriptor from another.
+ /**
+ * This assignment operator moves a stream descriptor from one object to
+ * another.
+ *
+ * @param other The other basic_stream_descriptor object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_stream_descriptor(io_service&) constructor.
+ */
+ basic_stream_descriptor& operator=(basic_stream_descriptor&& other)
+ {
+ basic_descriptor<StreamDescriptorService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_stream_descriptor)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Write some data to the descriptor.
+ /**
+ * This function is used to write data to the stream descriptor. The function
+ * call will block until one or more bytes of the data has been written
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more data buffers to be written to the descriptor.
+ *
+ * @returns The number of bytes written.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * descriptor.write_some(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().write_some(
+ this->get_implementation(), buffers, ec);
+ boost::asio::detail::throw_error(ec, "write_some");
+ return s;
+ }
+
+ /// Write some data to the descriptor.
+ /**
+ * This function is used to write data to the stream descriptor. The function
+ * call will block until one or more bytes of the data has been written
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more data buffers to be written to the descriptor.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. Returns 0 if an error occurred.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().write_some(
+ this->get_implementation(), buffers, ec);
+ }
+
+ /// Start an asynchronous write.
+ /**
+ * This function is used to asynchronously write data to the stream
+ * descriptor. The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be written to the descriptor.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes written.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The write operation may not transmit all of the data to the peer.
+ * Consider using the @ref async_write function if you need to ensure that all
+ * data is written before the asynchronous operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * descriptor.async_write_some(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_write_some(this->get_implementation(),
+ buffers, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Read some data from the descriptor.
+ /**
+ * This function is used to read data from the stream descriptor. The function
+ * call will block until one or more bytes of data has been read successfully,
+ * or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @returns The number of bytes read.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * descriptor.read_some(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().read_some(
+ this->get_implementation(), buffers, ec);
+ boost::asio::detail::throw_error(ec, "read_some");
+ return s;
+ }
+
+ /// Read some data from the descriptor.
+ /**
+ * This function is used to read data from the stream descriptor. The function
+ * call will block until one or more bytes of data has been read successfully,
+ * or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. Returns 0 if an error occurred.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().read_some(
+ this->get_implementation(), buffers, ec);
+ }
+
+ /// Start an asynchronous read.
+ /**
+ * This function is used to asynchronously read data from the stream
+ * descriptor. The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes read.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The read operation may not read all of the requested number of bytes.
+ * Consider using the @ref async_read function if you need to ensure that the
+ * requested amount of data is read before the asynchronous operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * descriptor.async_read_some(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_read_some(this->get_implementation(),
+ buffers, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+};
+
+} // namespace posix
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_POSIX_BASIC_STREAM_DESCRIPTOR_HPP
diff --git a/ext/patches/boost/asio/posix/descriptor_base.hpp b/ext/patches/boost/asio/posix/descriptor_base.hpp
new file mode 100644
index 0000000..884ea5d
--- /dev/null
+++ b/ext/patches/boost/asio/posix/descriptor_base.hpp
@@ -0,0 +1,99 @@
+//
+// posix/descriptor_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_POSIX_DESCRIPTOR_BASE_HPP
+#define BOOST_ASIO_POSIX_DESCRIPTOR_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/detail/io_control.hpp>
+#include <boost/asio/detail/socket_option.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace posix {
+
+/// The descriptor_base class is used as a base for the basic_stream_descriptor
+/// class template so that we have a common place to define the associated
+/// IO control commands.
+class descriptor_base
+{
+public:
+ /// (Deprecated: Use non_blocking().) IO control command to set the blocking
+ /// mode of the descriptor.
+ /**
+ * Implements the FIONBIO IO control command.
+ *
+ * @par Example
+ * @code
+ * boost::asio::posix::stream_descriptor descriptor(io_service);
+ * ...
+ * boost::asio::descriptor_base::non_blocking_io command(true);
+ * descriptor.io_control(command);
+ * @endcode
+ *
+ * @par Concepts:
+ * IoControlCommand.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined non_blocking_io;
+#else
+ typedef boost::asio::detail::io_control::non_blocking_io non_blocking_io;
+#endif
+
+ /// IO control command to get the amount of data that can be read without
+ /// blocking.
+ /**
+ * Implements the FIONREAD IO control command.
+ *
+ * @par Example
+ * @code
+ * boost::asio::posix::stream_descriptor descriptor(io_service);
+ * ...
+ * boost::asio::descriptor_base::bytes_readable command(true);
+ * descriptor.io_control(command);
+ * std::size_t bytes_readable = command.get();
+ * @endcode
+ *
+ * @par Concepts:
+ * IoControlCommand.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined bytes_readable;
+#else
+ typedef boost::asio::detail::io_control::bytes_readable bytes_readable;
+#endif
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~descriptor_base()
+ {
+ }
+};
+
+} // namespace posix
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_POSIX_DESCRIPTOR_BASE_HPP
diff --git a/ext/patches/boost/asio/posix/stream_descriptor.hpp b/ext/patches/boost/asio/posix/stream_descriptor.hpp
new file mode 100644
index 0000000..76a449c
--- /dev/null
+++ b/ext/patches/boost/asio/posix/stream_descriptor.hpp
@@ -0,0 +1,39 @@
+//
+// posix/stream_descriptor.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_POSIX_STREAM_DESCRIPTOR_HPP
+#define BOOST_ASIO_POSIX_STREAM_DESCRIPTOR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/posix/basic_stream_descriptor.hpp>
+
+namespace boost {
+namespace asio {
+namespace posix {
+
+/// Typedef for the typical usage of a stream-oriented descriptor.
+typedef basic_stream_descriptor<> stream_descriptor;
+
+} // namespace posix
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_POSIX_STREAM_DESCRIPTOR_HPP
diff --git a/ext/patches/boost/asio/posix/stream_descriptor_service.hpp b/ext/patches/boost/asio/posix/stream_descriptor_service.hpp
new file mode 100644
index 0000000..2c6aa88
--- /dev/null
+++ b/ext/patches/boost/asio/posix/stream_descriptor_service.hpp
@@ -0,0 +1,262 @@
+//
+// posix/stream_descriptor_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_POSIX_STREAM_DESCRIPTOR_SERVICE_HPP
+#define BOOST_ASIO_POSIX_STREAM_DESCRIPTOR_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/detail/reactive_descriptor_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace posix {
+
+/// Default service implementation for a stream descriptor.
+class stream_descriptor_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<stream_descriptor_service>
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+private:
+ // The type of the platform-specific implementation.
+ typedef detail::reactive_descriptor_service service_impl_type;
+
+public:
+ /// The type of a stream descriptor implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native descriptor type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native descriptor type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new stream descriptor service for the specified io_service.
+ explicit stream_descriptor_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<stream_descriptor_service>(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new stream descriptor implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new stream descriptor implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another stream descriptor implementation.
+ void move_assign(implementation_type& impl,
+ stream_descriptor_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a stream descriptor implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Assign an existing native descriptor to a stream descriptor.
+ boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& native_descriptor,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, native_descriptor, ec);
+ }
+
+ /// Determine whether the descriptor is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close a stream descriptor implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native descriptor
+ /// implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native descriptor implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Release ownership of the native descriptor implementation.
+ native_handle_type release(implementation_type& impl)
+ {
+ return service_impl_.release(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the descriptor.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Perform an IO control command on the descriptor.
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(implementation_type& impl,
+ IoControlCommand& command, boost::system::error_code& ec)
+ {
+ return service_impl_.io_control(impl, command, ec);
+ }
+
+ /// Gets the non-blocking mode of the descriptor.
+ bool non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the descriptor.
+ boost::system::error_code non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.non_blocking(impl, mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native descriptor implementation.
+ bool native_non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.native_non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the native descriptor implementation.
+ boost::system::error_code native_non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.native_non_blocking(impl, mode, ec);
+ }
+
+ /// Write the given data to the stream.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.write_some(impl, buffers, ec);
+ }
+
+ /// Start an asynchronous write.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_write_some(impl, buffers, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Read some data from the stream.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.read_some(impl, buffers, ec);
+ }
+
+ /// Start an asynchronous read.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_read_some(impl, buffers, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace posix
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_POSIX_STREAM_DESCRIPTOR)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_POSIX_STREAM_DESCRIPTOR_SERVICE_HPP
diff --git a/ext/patches/boost/asio/raw_socket_service.hpp b/ext/patches/boost/asio/raw_socket_service.hpp
new file mode 100644
index 0000000..7a67105
--- /dev/null
+++ b/ext/patches/boost/asio/raw_socket_service.hpp
@@ -0,0 +1,434 @@
+//
+// raw_socket_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_RAW_SOCKET_SERVICE_HPP
+#define BOOST_ASIO_RAW_SOCKET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/null_socket_service.hpp>
+#elif defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_socket_service.hpp>
+#else
+# include <boost/asio/detail/reactive_socket_service.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a raw socket.
+template <typename Protocol>
+class raw_socket_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<raw_socket_service<Protocol> >
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+private:
+ // The type of the platform-specific implementation.
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ typedef detail::null_socket_service<Protocol> service_impl_type;
+#elif defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::win_iocp_socket_service<Protocol> service_impl_type;
+#else
+ typedef detail::reactive_socket_service<Protocol> service_impl_type;
+#endif
+
+public:
+ /// The type of a raw socket.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef typename service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native socket type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native socket type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new raw socket service for the specified io_service.
+ explicit raw_socket_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ raw_socket_service<Protocol> >(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new raw socket implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new raw socket implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another raw socket implementation.
+ void move_assign(implementation_type& impl,
+ raw_socket_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+
+ /// Move-construct a new raw socket implementation from another protocol
+ /// type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type& impl,
+ typename raw_socket_service<
+ Protocol1>::implementation_type& other_impl,
+ typename enable_if<is_convertible<
+ Protocol1, Protocol>::value>::type* = 0)
+ {
+ service_impl_.template converting_move_construct<Protocol1>(
+ impl, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a raw socket implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ // Open a new raw socket implementation.
+ boost::system::error_code open(implementation_type& impl,
+ const protocol_type& protocol, boost::system::error_code& ec)
+ {
+ if (protocol.type() == BOOST_ASIO_OS_DEF(SOCK_RAW))
+ service_impl_.open(impl, protocol, ec);
+ else
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ /// Assign an existing native socket to a raw socket.
+ boost::system::error_code assign(implementation_type& impl,
+ const protocol_type& protocol, const native_handle_type& native_socket,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, protocol, native_socket, ec);
+ }
+
+ /// Determine whether the socket is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close a raw socket implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native socket implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native socket implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the socket.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Determine whether the socket is at the out-of-band data mark.
+ bool at_mark(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.at_mark(impl, ec);
+ }
+
+ /// Determine the number of bytes available for reading.
+ std::size_t available(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.available(impl, ec);
+ }
+
+ // Bind the raw socket to the specified local endpoint.
+ boost::system::error_code bind(implementation_type& impl,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.bind(impl, endpoint, ec);
+ }
+
+ /// Connect the raw socket to the specified endpoint.
+ boost::system::error_code connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.connect(impl, peer_endpoint, ec);
+ }
+
+ /// Start an asynchronous connect.
+ template <typename ConnectHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ConnectHandler,
+ void (boost::system::error_code))
+ async_connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint,
+ BOOST_ASIO_MOVE_ARG(ConnectHandler) handler)
+ {
+ detail::async_result_init<
+ ConnectHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(ConnectHandler)(handler));
+
+ service_impl_.async_connect(impl, peer_endpoint, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Set a socket option.
+ template <typename SettableSocketOption>
+ boost::system::error_code set_option(implementation_type& impl,
+ const SettableSocketOption& option, boost::system::error_code& ec)
+ {
+ return service_impl_.set_option(impl, option, ec);
+ }
+
+ /// Get a socket option.
+ template <typename GettableSocketOption>
+ boost::system::error_code get_option(const implementation_type& impl,
+ GettableSocketOption& option, boost::system::error_code& ec) const
+ {
+ return service_impl_.get_option(impl, option, ec);
+ }
+
+ /// Perform an IO control command on the socket.
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(implementation_type& impl,
+ IoControlCommand& command, boost::system::error_code& ec)
+ {
+ return service_impl_.io_control(impl, command, ec);
+ }
+
+ /// Gets the non-blocking mode of the socket.
+ bool non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the socket.
+ boost::system::error_code non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.non_blocking(impl, mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native socket implementation.
+ bool native_non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.native_non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the native socket implementation.
+ boost::system::error_code native_non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.native_non_blocking(impl, mode, ec);
+ }
+
+ /// Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.local_endpoint(impl, ec);
+ }
+
+ /// Get the remote endpoint.
+ endpoint_type remote_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.remote_endpoint(impl, ec);
+ }
+
+ /// Disable sends or receives on the socket.
+ boost::system::error_code shutdown(implementation_type& impl,
+ socket_base::shutdown_type what, boost::system::error_code& ec)
+ {
+ return service_impl_.shutdown(impl, what, ec);
+ }
+
+ /// Send the given data to the peer.
+ template <typename ConstBufferSequence>
+ std::size_t send(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.send(impl, buffers, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(implementation_type& impl, const ConstBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_send(impl, buffers, flags, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Send raw data to the specified endpoint.
+ template <typename ConstBufferSequence>
+ std::size_t send_to(implementation_type& impl,
+ const ConstBufferSequence& buffers, const endpoint_type& destination,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.send_to(impl, buffers, destination, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send_to(implementation_type& impl,
+ const ConstBufferSequence& buffers, const endpoint_type& destination,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_send_to(impl, buffers,
+ destination, flags, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Receive some data from the peer.
+ template <typename MutableBufferSequence>
+ std::size_t receive(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.receive(impl, buffers, flags, ec);
+ }
+
+ /// Start an asynchronous receive.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_receive(impl, buffers, flags, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Receive raw data with the endpoint of the sender.
+ template <typename MutableBufferSequence>
+ std::size_t receive_from(implementation_type& impl,
+ const MutableBufferSequence& buffers, endpoint_type& sender_endpoint,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.receive_from(impl, buffers, sender_endpoint, flags,
+ ec);
+ }
+
+ /// Start an asynchronous receive that will get the endpoint of the sender.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive_from(implementation_type& impl,
+ const MutableBufferSequence& buffers, endpoint_type& sender_endpoint,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_receive_from(impl, buffers,
+ sender_endpoint, flags, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_RAW_SOCKET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/read.hpp b/ext/patches/boost/asio/read.hpp
new file mode 100644
index 0000000..987781d
--- /dev/null
+++ b/ext/patches/boost/asio/read.hpp
@@ -0,0 +1,633 @@
+//
+// read.hpp
+// ~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_READ_HPP
+#define BOOST_ASIO_READ_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_streambuf_fwd.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/**
+ * @defgroup read boost::asio::read
+ *
+ * @brief Attempt to read a certain amount of data from a stream before
+ * returning.
+ */
+/*@{*/
+
+/// Attempt to read a certain amount of data from a stream before returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * stream. The call will block until one of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * stream.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::read(s, boost::asio::buffer(data, size)); @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::read(
+ * s, buffers,
+ * boost::asio::transfer_all()); @endcode
+ */
+template <typename SyncReadStream, typename MutableBufferSequence>
+std::size_t read(SyncReadStream& s, const MutableBufferSequence& buffers);
+
+/// Attempt to read a certain amount of data from a stream before returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * stream. The call will block until one of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * stream.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::read(s, boost::asio::buffer(data, size), ec); @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::read(
+ * s, buffers,
+ * boost::asio::transfer_all(), ec); @endcode
+ */
+template <typename SyncReadStream, typename MutableBufferSequence>
+std::size_t read(SyncReadStream& s, const MutableBufferSequence& buffers,
+ boost::system::error_code& ec);
+
+/// Attempt to read a certain amount of data from a stream before returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * stream. The call will block until one of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * stream.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest read_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the stream's read_some function.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::read(s, boost::asio::buffer(data, size),
+ * boost::asio::transfer_at_least(32)); @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename SyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition>
+std::size_t read(SyncReadStream& s, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition);
+
+/// Attempt to read a certain amount of data from a stream before returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * stream. The call will block until one of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * stream.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest read_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the stream's read_some function.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. If an error occurs, returns the total
+ * number of bytes successfully transferred prior to the error.
+ */
+template <typename SyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition>
+std::size_t read(SyncReadStream& s, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition, boost::system::error_code& ec);
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Attempt to read a certain amount of data from a stream before returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * stream. The call will block until one of the following conditions is true:
+ *
+ * @li The supplied buffer is full (that is, it has reached maximum size).
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b The basic_streambuf object into which the data will be read.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::read(
+ * s, b,
+ * boost::asio::transfer_all()); @endcode
+ */
+template <typename SyncReadStream, typename Allocator>
+std::size_t read(SyncReadStream& s, basic_streambuf<Allocator>& b);
+
+/// Attempt to read a certain amount of data from a stream before returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * stream. The call will block until one of the following conditions is true:
+ *
+ * @li The supplied buffer is full (that is, it has reached maximum size).
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b The basic_streambuf object into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::read(
+ * s, b,
+ * boost::asio::transfer_all(), ec); @endcode
+ */
+template <typename SyncReadStream, typename Allocator>
+std::size_t read(SyncReadStream& s, basic_streambuf<Allocator>& b,
+ boost::system::error_code& ec);
+
+/// Attempt to read a certain amount of data from a stream before returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * stream. The call will block until one of the following conditions is true:
+ *
+ * @li The supplied buffer is full (that is, it has reached maximum size).
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b The basic_streambuf object into which the data will be read.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest read_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the stream's read_some function.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+template <typename SyncReadStream, typename Allocator,
+ typename CompletionCondition>
+std::size_t read(SyncReadStream& s, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition);
+
+/// Attempt to read a certain amount of data from a stream before returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * stream. The call will block until one of the following conditions is true:
+ *
+ * @li The supplied buffer is full (that is, it has reached maximum size).
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b The basic_streambuf object into which the data will be read.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest read_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the stream's read_some function.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. If an error occurs, returns the total
+ * number of bytes successfully transferred prior to the error.
+ */
+template <typename SyncReadStream, typename Allocator,
+ typename CompletionCondition>
+std::size_t read(SyncReadStream& s, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition, boost::system::error_code& ec);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/*@}*/
+/**
+ * @defgroup async_read boost::asio::async_read
+ *
+ * @brief Start an asynchronous operation to read a certain amount of data from
+ * a stream.
+ */
+/*@{*/
+
+/// Start an asynchronous operation to read a certain amount of data from a
+/// stream.
+/**
+ * This function is used to asynchronously read a certain number of bytes of
+ * data from a stream. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions is
+ * true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_read_some function, and is known as a <em>composed operation</em>. The
+ * program must ensure that the stream performs no other read operations (such
+ * as async_read, the stream's async_read_some function, or any other composed
+ * operations that perform reads) until this operation completes.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the AsyncReadStream concept.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * stream. Although the buffers object may be copied as necessary, ownership of
+ * the underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ *
+ * std::size_t bytes_transferred // Number of bytes copied into the
+ * // buffers. If an error occurred,
+ * // this will be the number of
+ * // bytes successfully transferred
+ * // prior to the error.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * boost::asio::async_read(s, boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::async_read(
+ * s, buffers,
+ * boost::asio::transfer_all(),
+ * handler); @endcode
+ */
+template <typename AsyncReadStream, typename MutableBufferSequence,
+ typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read(AsyncReadStream& s, const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+/// Start an asynchronous operation to read a certain amount of data from a
+/// stream.
+/**
+ * This function is used to asynchronously read a certain number of bytes of
+ * data from a stream. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions is
+ * true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the AsyncReadStream concept.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * stream. Although the buffers object may be copied as necessary, ownership of
+ * the underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest async_read_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the stream's async_read_some function.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ *
+ * std::size_t bytes_transferred // Number of bytes copied into the
+ * // buffers. If an error occurred,
+ * // this will be the number of
+ * // bytes successfully transferred
+ * // prior to the error.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::async_read(s,
+ * boost::asio::buffer(data, size),
+ * boost::asio::transfer_at_least(32),
+ * handler); @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename AsyncReadStream, typename MutableBufferSequence,
+ typename CompletionCondition, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read(AsyncReadStream& s, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Start an asynchronous operation to read a certain amount of data from a
+/// stream.
+/**
+ * This function is used to asynchronously read a certain number of bytes of
+ * data from a stream. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions is
+ * true:
+ *
+ * @li The supplied buffer is full (that is, it has reached maximum size).
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_read_some function, and is known as a <em>composed operation</em>. The
+ * program must ensure that the stream performs no other read operations (such
+ * as async_read, the stream's async_read_some function, or any other composed
+ * operations that perform reads) until this operation completes.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the AsyncReadStream concept.
+ *
+ * @param b A basic_streambuf object into which the data will be read. Ownership
+ * of the streambuf is retained by the caller, which must guarantee that it
+ * remains valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ *
+ * std::size_t bytes_transferred // Number of bytes copied into the
+ * // buffers. If an error occurred,
+ * // this will be the number of
+ * // bytes successfully transferred
+ * // prior to the error.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::async_read(
+ * s, b,
+ * boost::asio::transfer_all(),
+ * handler); @endcode
+ */
+template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read(AsyncReadStream& s, basic_streambuf<Allocator>& b,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+/// Start an asynchronous operation to read a certain amount of data from a
+/// stream.
+/**
+ * This function is used to asynchronously read a certain number of bytes of
+ * data from a stream. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions is
+ * true:
+ *
+ * @li The supplied buffer is full (that is, it has reached maximum size).
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_read_some function, and is known as a <em>composed operation</em>. The
+ * program must ensure that the stream performs no other read operations (such
+ * as async_read, the stream's async_read_some function, or any other composed
+ * operations that perform reads) until this operation completes.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the AsyncReadStream concept.
+ *
+ * @param b A basic_streambuf object into which the data will be read. Ownership
+ * of the streambuf is retained by the caller, which must guarantee that it
+ * remains valid until the handler is called.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest async_read_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the stream's async_read_some function.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ *
+ * std::size_t bytes_transferred // Number of bytes copied into the
+ * // buffers. If an error occurred,
+ * // this will be the number of
+ * // bytes successfully transferred
+ * // prior to the error.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+template <typename AsyncReadStream, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read(AsyncReadStream& s, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/read.hpp>
+
+#endif // BOOST_ASIO_READ_HPP
diff --git a/ext/patches/boost/asio/read_at.hpp b/ext/patches/boost/asio/read_at.hpp
new file mode 100644
index 0000000..a1ae28a
--- /dev/null
+++ b/ext/patches/boost/asio/read_at.hpp
@@ -0,0 +1,666 @@
+//
+// read_at.hpp
+// ~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_READ_AT_HPP
+#define BOOST_ASIO_READ_AT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_streambuf_fwd.hpp>
+#include <boost/asio/detail/cstdint.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/**
+ * @defgroup read_at boost::asio::read_at
+ *
+ * @brief Attempt to read a certain amount of data at the specified offset
+ * before returning.
+ */
+/*@{*/
+
+/// Attempt to read a certain amount of data at the specified offset before
+/// returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * random access device at the specified offset. The call will block until one
+ * of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the SyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * device.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::read_at(d, 42, boost::asio::buffer(data, size)); @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::read_at(
+ * d, 42, buffers,
+ * boost::asio::transfer_all()); @endcode
+ */
+template <typename SyncRandomAccessReadDevice, typename MutableBufferSequence>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers);
+
+/// Attempt to read a certain amount of data at the specified offset before
+/// returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * random access device at the specified offset. The call will block until one
+ * of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the SyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * device.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::read_at(d, 42,
+ * boost::asio::buffer(data, size), ec); @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::read_at(
+ * d, 42, buffers,
+ * boost::asio::transfer_all(), ec); @endcode
+ */
+template <typename SyncRandomAccessReadDevice, typename MutableBufferSequence>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ boost::system::error_code& ec);
+
+/// Attempt to read a certain amount of data at the specified offset before
+/// returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * random access device at the specified offset. The call will block until one
+ * of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the SyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * device.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest read_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the device's read_some_at function.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::read_at(d, 42, boost::asio::buffer(data, size),
+ * boost::asio::transfer_at_least(32)); @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename SyncRandomAccessReadDevice, typename MutableBufferSequence,
+ typename CompletionCondition>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition);
+
+/// Attempt to read a certain amount of data at the specified offset before
+/// returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * random access device at the specified offset. The call will block until one
+ * of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the SyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * device.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest read_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the device's read_some_at function.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. If an error occurs, returns the total
+ * number of bytes successfully transferred prior to the error.
+ */
+template <typename SyncRandomAccessReadDevice, typename MutableBufferSequence,
+ typename CompletionCondition>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition, boost::system::error_code& ec);
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Attempt to read a certain amount of data at the specified offset before
+/// returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * random access device at the specified offset. The call will block until one
+ * of the following conditions is true:
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the SyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param b The basic_streambuf object into which the data will be read.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::read_at(
+ * d, 42, b,
+ * boost::asio::transfer_all()); @endcode
+ */
+template <typename SyncRandomAccessReadDevice, typename Allocator>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, basic_streambuf<Allocator>& b);
+
+/// Attempt to read a certain amount of data at the specified offset before
+/// returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * random access device at the specified offset. The call will block until one
+ * of the following conditions is true:
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the SyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param b The basic_streambuf object into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::read_at(
+ * d, 42, b,
+ * boost::asio::transfer_all(), ec); @endcode
+ */
+template <typename SyncRandomAccessReadDevice, typename Allocator>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, basic_streambuf<Allocator>& b,
+ boost::system::error_code& ec);
+
+/// Attempt to read a certain amount of data at the specified offset before
+/// returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * random access device at the specified offset. The call will block until one
+ * of the following conditions is true:
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the SyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param b The basic_streambuf object into which the data will be read.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest read_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the device's read_some_at function.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+template <typename SyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition);
+
+/// Attempt to read a certain amount of data at the specified offset before
+/// returning.
+/**
+ * This function is used to read a certain number of bytes of data from a
+ * random access device at the specified offset. The call will block until one
+ * of the following conditions is true:
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the SyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param b The basic_streambuf object into which the data will be read.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest read_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the device's read_some_at function.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. If an error occurs, returns the total
+ * number of bytes successfully transferred prior to the error.
+ */
+template <typename SyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition>
+std::size_t read_at(SyncRandomAccessReadDevice& d,
+ uint64_t offset, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition, boost::system::error_code& ec);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/*@}*/
+/**
+ * @defgroup async_read_at boost::asio::async_read_at
+ *
+ * @brief Start an asynchronous operation to read a certain amount of data at
+ * the specified offset.
+ */
+/*@{*/
+
+/// Start an asynchronous operation to read a certain amount of data at the
+/// specified offset.
+/**
+ * This function is used to asynchronously read a certain number of bytes of
+ * data from a random access device at the specified offset. The function call
+ * always returns immediately. The asynchronous operation will continue until
+ * one of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * async_read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the AsyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * device. Although the buffers object may be copied as necessary, ownership of
+ * the underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes copied into the buffers. If an error
+ * // occurred, this will be the number of bytes successfully
+ * // transferred prior to the error.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * boost::asio::async_read_at(d, 42, boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::async_read_at(
+ * d, 42, buffers,
+ * boost::asio::transfer_all(),
+ * handler); @endcode
+ */
+template <typename AsyncRandomAccessReadDevice, typename MutableBufferSequence,
+ typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_at(AsyncRandomAccessReadDevice& d, uint64_t offset,
+ const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+/// Start an asynchronous operation to read a certain amount of data at the
+/// specified offset.
+/**
+ * This function is used to asynchronously read a certain number of bytes of
+ * data from a random access device at the specified offset. The function call
+ * always returns immediately. The asynchronous operation will continue until
+ * one of the following conditions is true:
+ *
+ * @li The supplied buffers are full. That is, the bytes transferred is equal to
+ * the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the AsyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read. The sum
+ * of the buffer sizes indicates the maximum number of bytes to read from the
+ * device. Although the buffers object may be copied as necessary, ownership of
+ * the underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest async_read_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the device's async_read_some_at function.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes copied into the buffers. If an error
+ * // occurred, this will be the number of bytes successfully
+ * // transferred prior to the error.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::async_read_at(d, 42,
+ * boost::asio::buffer(data, size),
+ * boost::asio::transfer_at_least(32),
+ * handler); @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename AsyncRandomAccessReadDevice, typename MutableBufferSequence,
+ typename CompletionCondition, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_at(AsyncRandomAccessReadDevice& d,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Start an asynchronous operation to read a certain amount of data at the
+/// specified offset.
+/**
+ * This function is used to asynchronously read a certain number of bytes of
+ * data from a random access device at the specified offset. The function call
+ * always returns immediately. The asynchronous operation will continue until
+ * one of the following conditions is true:
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * async_read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the AsyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param b A basic_streambuf object into which the data will be read. Ownership
+ * of the streambuf is retained by the caller, which must guarantee that it
+ * remains valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes copied into the buffers. If an error
+ * // occurred, this will be the number of bytes successfully
+ * // transferred prior to the error.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::async_read_at(
+ * d, 42, b,
+ * boost::asio::transfer_all(),
+ * handler); @endcode
+ */
+template <typename AsyncRandomAccessReadDevice, typename Allocator,
+ typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_at(AsyncRandomAccessReadDevice& d, uint64_t offset,
+ basic_streambuf<Allocator>& b, BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+/// Start an asynchronous operation to read a certain amount of data at the
+/// specified offset.
+/**
+ * This function is used to asynchronously read a certain number of bytes of
+ * data from a random access device at the specified offset. The function call
+ * always returns immediately. The asynchronous operation will continue until
+ * one of the following conditions is true:
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * async_read_some_at function.
+ *
+ * @param d The device from which the data is to be read. The type must support
+ * the AsyncRandomAccessReadDevice concept.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param b A basic_streambuf object into which the data will be read. Ownership
+ * of the streambuf is retained by the caller, which must guarantee that it
+ * remains valid until the handler is called.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the read operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest async_read_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the read operation is complete. A non-zero
+ * return value indicates the maximum number of bytes to be read on the next
+ * call to the device's async_read_some_at function.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes copied into the buffers. If an error
+ * // occurred, this will be the number of bytes successfully
+ * // transferred prior to the error.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+template <typename AsyncRandomAccessReadDevice, typename Allocator,
+ typename CompletionCondition, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_at(AsyncRandomAccessReadDevice& d,
+ uint64_t offset, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/read_at.hpp>
+
+#endif // BOOST_ASIO_READ_AT_HPP
diff --git a/ext/patches/boost/asio/read_until.hpp b/ext/patches/boost/asio/read_until.hpp
new file mode 100644
index 0000000..8978910
--- /dev/null
+++ b/ext/patches/boost/asio/read_until.hpp
@@ -0,0 +1,925 @@
+//
+// read_until.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_READ_UNTIL_HPP
+#define BOOST_ASIO_READ_UNTIL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <cstddef>
+#include <string>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_streambuf.hpp>
+#include <boost/asio/detail/regex_fwd.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+namespace detail
+{
+ char (&has_result_type_helper(...))[2];
+
+ template <typename T>
+ char has_result_type_helper(T*, typename T::result_type* = 0);
+
+ template <typename T>
+ struct has_result_type
+ {
+ enum { value = (sizeof((has_result_type_helper)((T*)(0))) == 1) };
+ };
+} // namespace detail
+
+/// Type trait used to determine whether a type can be used as a match condition
+/// function with read_until and async_read_until.
+template <typename T>
+struct is_match_condition
+{
+#if defined(GENERATING_DOCUMENTATION)
+ /// The value member is true if the type may be used as a match condition.
+ static const bool value;
+#else
+ enum
+ {
+ value = boost::asio::is_function<
+ typename boost::asio::remove_pointer<T>::type>::value
+ || detail::has_result_type<T>::value
+ };
+#endif
+};
+
+/**
+ * @defgroup read_until boost::asio::read_until
+ *
+ * @brief Read data into a streambuf until it contains a delimiter, matches a
+ * regular expression, or a function object indicates a match.
+ */
+/*@{*/
+
+/// Read data into a streambuf until it contains a specified delimiter.
+/**
+ * This function is used to read data into the specified streambuf until the
+ * streambuf's get area contains the specified delimiter. The call will block
+ * until one of the following conditions is true:
+ *
+ * @li The get area of the streambuf contains the specified delimiter.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function. If the streambuf's get area already contains the
+ * delimiter, the function returns immediately.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param delim The delimiter character.
+ *
+ * @returns The number of bytes in the streambuf's get area up to and including
+ * the delimiter.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note After a successful read_until operation, the streambuf may contain
+ * additional data beyond the delimiter. An application will typically leave
+ * that data in the streambuf for a subsequent read_until operation to examine.
+ *
+ * @par Example
+ * To read data into a streambuf until a newline is encountered:
+ * @code boost::asio::streambuf b;
+ * boost::asio::read_until(s, b, '\n');
+ * std::istream is(&b);
+ * std::string line;
+ * std::getline(is, line); @endcode
+ * After the @c read_until operation completes successfully, the buffer @c b
+ * contains the delimiter:
+ * @code { 'a', 'b', ..., 'c', '\n', 'd', 'e', ... } @endcode
+ * The call to @c std::getline then extracts the data up to and including the
+ * delimiter, so that the string @c line contains:
+ * @code { 'a', 'b', ..., 'c', '\n' } @endcode
+ * The remaining data is left in the buffer @c b as follows:
+ * @code { 'd', 'e', ... } @endcode
+ * This data may be the start of a new line, to be extracted by a subsequent
+ * @c read_until operation.
+ */
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, char delim);
+
+/// Read data into a streambuf until it contains a specified delimiter.
+/**
+ * This function is used to read data into the specified streambuf until the
+ * streambuf's get area contains the specified delimiter. The call will block
+ * until one of the following conditions is true:
+ *
+ * @li The get area of the streambuf contains the specified delimiter.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function. If the streambuf's get area already contains the
+ * delimiter, the function returns immediately.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param delim The delimiter character.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes in the streambuf's get area up to and including
+ * the delimiter. Returns 0 if an error occurred.
+ *
+ * @note After a successful read_until operation, the streambuf may contain
+ * additional data beyond the delimiter. An application will typically leave
+ * that data in the streambuf for a subsequent read_until operation to examine.
+ */
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, char delim,
+ boost::system::error_code& ec);
+
+/// Read data into a streambuf until it contains a specified delimiter.
+/**
+ * This function is used to read data into the specified streambuf until the
+ * streambuf's get area contains the specified delimiter. The call will block
+ * until one of the following conditions is true:
+ *
+ * @li The get area of the streambuf contains the specified delimiter.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function. If the streambuf's get area already contains the
+ * delimiter, the function returns immediately.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param delim The delimiter string.
+ *
+ * @returns The number of bytes in the streambuf's get area up to and including
+ * the delimiter.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note After a successful read_until operation, the streambuf may contain
+ * additional data beyond the delimiter. An application will typically leave
+ * that data in the streambuf for a subsequent read_until operation to examine.
+ *
+ * @par Example
+ * To read data into a streambuf until a newline is encountered:
+ * @code boost::asio::streambuf b;
+ * boost::asio::read_until(s, b, "\r\n");
+ * std::istream is(&b);
+ * std::string line;
+ * std::getline(is, line); @endcode
+ * After the @c read_until operation completes successfully, the buffer @c b
+ * contains the delimiter:
+ * @code { 'a', 'b', ..., 'c', '\r', '\n', 'd', 'e', ... } @endcode
+ * The call to @c std::getline then extracts the data up to and including the
+ * delimiter, so that the string @c line contains:
+ * @code { 'a', 'b', ..., 'c', '\r', '\n' } @endcode
+ * The remaining data is left in the buffer @c b as follows:
+ * @code { 'd', 'e', ... } @endcode
+ * This data may be the start of a new line, to be extracted by a subsequent
+ * @c read_until operation.
+ */
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const std::string& delim);
+
+/// Read data into a streambuf until it contains a specified delimiter.
+/**
+ * This function is used to read data into the specified streambuf until the
+ * streambuf's get area contains the specified delimiter. The call will block
+ * until one of the following conditions is true:
+ *
+ * @li The get area of the streambuf contains the specified delimiter.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function. If the streambuf's get area already contains the
+ * delimiter, the function returns immediately.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param delim The delimiter string.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes in the streambuf's get area up to and including
+ * the delimiter. Returns 0 if an error occurred.
+ *
+ * @note After a successful read_until operation, the streambuf may contain
+ * additional data beyond the delimiter. An application will typically leave
+ * that data in the streambuf for a subsequent read_until operation to examine.
+ */
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const std::string& delim,
+ boost::system::error_code& ec);
+
+#if defined(BOOST_ASIO_HAS_BOOST_REGEX) \
+ || defined(GENERATING_DOCUMENTATION)
+
+/// Read data into a streambuf until some part of the data it contains matches
+/// a regular expression.
+/**
+ * This function is used to read data into the specified streambuf until the
+ * streambuf's get area contains some data that matches a regular expression.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li A substring of the streambuf's get area matches the regular expression.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function. If the streambuf's get area already contains data that
+ * matches the regular expression, the function returns immediately.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param expr The regular expression.
+ *
+ * @returns The number of bytes in the streambuf's get area up to and including
+ * the substring that matches the regular expression.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note After a successful read_until operation, the streambuf may contain
+ * additional data beyond that which matched the regular expression. An
+ * application will typically leave that data in the streambuf for a subsequent
+ * read_until operation to examine.
+ *
+ * @par Example
+ * To read data into a streambuf until a CR-LF sequence is encountered:
+ * @code boost::asio::streambuf b;
+ * boost::asio::read_until(s, b, boost::regex("\r\n"));
+ * std::istream is(&b);
+ * std::string line;
+ * std::getline(is, line); @endcode
+ * After the @c read_until operation completes successfully, the buffer @c b
+ * contains the data which matched the regular expression:
+ * @code { 'a', 'b', ..., 'c', '\r', '\n', 'd', 'e', ... } @endcode
+ * The call to @c std::getline then extracts the data up to and including the
+ * match, so that the string @c line contains:
+ * @code { 'a', 'b', ..., 'c', '\r', '\n' } @endcode
+ * The remaining data is left in the buffer @c b as follows:
+ * @code { 'd', 'e', ... } @endcode
+ * This data may be the start of a new line, to be extracted by a subsequent
+ * @c read_until operation.
+ */
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const boost::regex& expr);
+
+/// Read data into a streambuf until some part of the data it contains matches
+/// a regular expression.
+/**
+ * This function is used to read data into the specified streambuf until the
+ * streambuf's get area contains some data that matches a regular expression.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li A substring of the streambuf's get area matches the regular expression.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function. If the streambuf's get area already contains data that
+ * matches the regular expression, the function returns immediately.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param expr The regular expression.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes in the streambuf's get area up to and including
+ * the substring that matches the regular expression. Returns 0 if an error
+ * occurred.
+ *
+ * @note After a successful read_until operation, the streambuf may contain
+ * additional data beyond that which matched the regular expression. An
+ * application will typically leave that data in the streambuf for a subsequent
+ * read_until operation to examine.
+ */
+template <typename SyncReadStream, typename Allocator>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const boost::regex& expr,
+ boost::system::error_code& ec);
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_REGEX)
+ // || defined(GENERATING_DOCUMENTATION)
+
+/// Read data into a streambuf until a function object indicates a match.
+/**
+ * This function is used to read data into the specified streambuf until a
+ * user-defined match condition function object, when applied to the data
+ * contained in the streambuf, indicates a successful match. The call will
+ * block until one of the following conditions is true:
+ *
+ * @li The match condition function object returns a std::pair where the second
+ * element evaluates to true.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function. If the match condition function object already indicates
+ * a match, the function returns immediately.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param match_condition The function object to be called to determine whether
+ * a match exists. The signature of the function object must be:
+ * @code pair<iterator, bool> match_condition(iterator begin, iterator end);
+ * @endcode
+ * where @c iterator represents the type:
+ * @code buffers_iterator<basic_streambuf<Allocator>::const_buffers_type>
+ * @endcode
+ * The iterator parameters @c begin and @c end define the range of bytes to be
+ * scanned to determine whether there is a match. The @c first member of the
+ * return value is an iterator marking one-past-the-end of the bytes that have
+ * been consumed by the match function. This iterator is used to calculate the
+ * @c begin parameter for any subsequent invocation of the match condition. The
+ * @c second member of the return value is true if a match has been found, false
+ * otherwise.
+ *
+ * @returns The number of bytes in the streambuf's get area that have been fully
+ * consumed by the match function.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note After a successful read_until operation, the streambuf may contain
+ * additional data beyond that which matched the function object. An application
+ * will typically leave that data in the streambuf for a subsequent
+ *
+ * @note The default implementation of the @c is_match_condition type trait
+ * evaluates to true for function pointers and function objects with a
+ * @c result_type typedef. It must be specialised for other user-defined
+ * function objects.
+ *
+ * @par Examples
+ * To read data into a streambuf until whitespace is encountered:
+ * @code typedef boost::asio::buffers_iterator<
+ * boost::asio::streambuf::const_buffers_type> iterator;
+ *
+ * std::pair<iterator, bool>
+ * match_whitespace(iterator begin, iterator end)
+ * {
+ * iterator i = begin;
+ * while (i != end)
+ * if (std::isspace(*i++))
+ * return std::make_pair(i, true);
+ * return std::make_pair(i, false);
+ * }
+ * ...
+ * boost::asio::streambuf b;
+ * boost::asio::read_until(s, b, match_whitespace);
+ * @endcode
+ *
+ * To read data into a streambuf until a matching character is found:
+ * @code class match_char
+ * {
+ * public:
+ * explicit match_char(char c) : c_(c) {}
+ *
+ * template <typename Iterator>
+ * std::pair<Iterator, bool> operator()(
+ * Iterator begin, Iterator end) const
+ * {
+ * Iterator i = begin;
+ * while (i != end)
+ * if (c_ == *i++)
+ * return std::make_pair(i, true);
+ * return std::make_pair(i, false);
+ * }
+ *
+ * private:
+ * char c_;
+ * };
+ *
+ * namespace asio {
+ * template <> struct is_match_condition<match_char>
+ * : public boost::true_type {};
+ * } // namespace asio
+ * ...
+ * boost::asio::streambuf b;
+ * boost::asio::read_until(s, b, match_char('a'));
+ * @endcode
+ */
+template <typename SyncReadStream, typename Allocator, typename MatchCondition>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, MatchCondition match_condition,
+ typename enable_if<is_match_condition<MatchCondition>::value>::type* = 0);
+
+/// Read data into a streambuf until a function object indicates a match.
+/**
+ * This function is used to read data into the specified streambuf until a
+ * user-defined match condition function object, when applied to the data
+ * contained in the streambuf, indicates a successful match. The call will
+ * block until one of the following conditions is true:
+ *
+ * @li The match condition function object returns a std::pair where the second
+ * element evaluates to true.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * read_some function. If the match condition function object already indicates
+ * a match, the function returns immediately.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the SyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param match_condition The function object to be called to determine whether
+ * a match exists. The signature of the function object must be:
+ * @code pair<iterator, bool> match_condition(iterator begin, iterator end);
+ * @endcode
+ * where @c iterator represents the type:
+ * @code buffers_iterator<basic_streambuf<Allocator>::const_buffers_type>
+ * @endcode
+ * The iterator parameters @c begin and @c end define the range of bytes to be
+ * scanned to determine whether there is a match. The @c first member of the
+ * return value is an iterator marking one-past-the-end of the bytes that have
+ * been consumed by the match function. This iterator is used to calculate the
+ * @c begin parameter for any subsequent invocation of the match condition. The
+ * @c second member of the return value is true if a match has been found, false
+ * otherwise.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes in the streambuf's get area that have been fully
+ * consumed by the match function. Returns 0 if an error occurred.
+ *
+ * @note After a successful read_until operation, the streambuf may contain
+ * additional data beyond that which matched the function object. An application
+ * will typically leave that data in the streambuf for a subsequent
+ *
+ * @note The default implementation of the @c is_match_condition type trait
+ * evaluates to true for function pointers and function objects with a
+ * @c result_type typedef. It must be specialised for other user-defined
+ * function objects.
+ */
+template <typename SyncReadStream, typename Allocator, typename MatchCondition>
+std::size_t read_until(SyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ MatchCondition match_condition, boost::system::error_code& ec,
+ typename enable_if<is_match_condition<MatchCondition>::value>::type* = 0);
+
+/*@}*/
+/**
+ * @defgroup async_read_until boost::asio::async_read_until
+ *
+ * @brief Start an asynchronous operation to read data into a streambuf until it
+ * contains a delimiter, matches a regular expression, or a function object
+ * indicates a match.
+ */
+/*@{*/
+
+/// Start an asynchronous operation to read data into a streambuf until it
+/// contains a specified delimiter.
+/**
+ * This function is used to asynchronously read data into the specified
+ * streambuf until the streambuf's get area contains the specified delimiter.
+ * The function call always returns immediately. The asynchronous operation
+ * will continue until one of the following conditions is true:
+ *
+ * @li The get area of the streambuf contains the specified delimiter.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_read_some function, and is known as a <em>composed operation</em>. If
+ * the streambuf's get area already contains the delimiter, this asynchronous
+ * operation completes immediately. The program must ensure that the stream
+ * performs no other read operations (such as async_read, async_read_until, the
+ * stream's async_read_some function, or any other composed operations that
+ * perform reads) until this operation completes.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the AsyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read. Ownership of
+ * the streambuf is retained by the caller, which must guarantee that it remains
+ * valid until the handler is called.
+ *
+ * @param delim The delimiter character.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // The number of bytes in the streambuf's get
+ * // area up to and including the delimiter.
+ * // 0 if an error occurred.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note After a successful async_read_until operation, the streambuf may
+ * contain additional data beyond the delimiter. An application will typically
+ * leave that data in the streambuf for a subsequent async_read_until operation
+ * to examine.
+ *
+ * @par Example
+ * To asynchronously read data into a streambuf until a newline is encountered:
+ * @code boost::asio::streambuf b;
+ * ...
+ * void handler(const boost::system::error_code& e, std::size_t size)
+ * {
+ * if (!e)
+ * {
+ * std::istream is(&b);
+ * std::string line;
+ * std::getline(is, line);
+ * ...
+ * }
+ * }
+ * ...
+ * boost::asio::async_read_until(s, b, '\n', handler); @endcode
+ * After the @c async_read_until operation completes successfully, the buffer
+ * @c b contains the delimiter:
+ * @code { 'a', 'b', ..., 'c', '\n', 'd', 'e', ... } @endcode
+ * The call to @c std::getline then extracts the data up to and including the
+ * delimiter, so that the string @c line contains:
+ * @code { 'a', 'b', ..., 'c', '\n' } @endcode
+ * The remaining data is left in the buffer @c b as follows:
+ * @code { 'd', 'e', ... } @endcode
+ * This data may be the start of a new line, to be extracted by a subsequent
+ * @c async_read_until operation.
+ */
+template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_until(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ char delim, BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+/// Start an asynchronous operation to read data into a streambuf until it
+/// contains a specified delimiter.
+/**
+ * This function is used to asynchronously read data into the specified
+ * streambuf until the streambuf's get area contains the specified delimiter.
+ * The function call always returns immediately. The asynchronous operation
+ * will continue until one of the following conditions is true:
+ *
+ * @li The get area of the streambuf contains the specified delimiter.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_read_some function, and is known as a <em>composed operation</em>. If
+ * the streambuf's get area already contains the delimiter, this asynchronous
+ * operation completes immediately. The program must ensure that the stream
+ * performs no other read operations (such as async_read, async_read_until, the
+ * stream's async_read_some function, or any other composed operations that
+ * perform reads) until this operation completes.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the AsyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read. Ownership of
+ * the streambuf is retained by the caller, which must guarantee that it remains
+ * valid until the handler is called.
+ *
+ * @param delim The delimiter string.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // The number of bytes in the streambuf's get
+ * // area up to and including the delimiter.
+ * // 0 if an error occurred.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note After a successful async_read_until operation, the streambuf may
+ * contain additional data beyond the delimiter. An application will typically
+ * leave that data in the streambuf for a subsequent async_read_until operation
+ * to examine.
+ *
+ * @par Example
+ * To asynchronously read data into a streambuf until a newline is encountered:
+ * @code boost::asio::streambuf b;
+ * ...
+ * void handler(const boost::system::error_code& e, std::size_t size)
+ * {
+ * if (!e)
+ * {
+ * std::istream is(&b);
+ * std::string line;
+ * std::getline(is, line);
+ * ...
+ * }
+ * }
+ * ...
+ * boost::asio::async_read_until(s, b, "\r\n", handler); @endcode
+ * After the @c async_read_until operation completes successfully, the buffer
+ * @c b contains the delimiter:
+ * @code { 'a', 'b', ..., 'c', '\r', '\n', 'd', 'e', ... } @endcode
+ * The call to @c std::getline then extracts the data up to and including the
+ * delimiter, so that the string @c line contains:
+ * @code { 'a', 'b', ..., 'c', '\r', '\n' } @endcode
+ * The remaining data is left in the buffer @c b as follows:
+ * @code { 'd', 'e', ... } @endcode
+ * This data may be the start of a new line, to be extracted by a subsequent
+ * @c async_read_until operation.
+ */
+template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_until(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const std::string& delim,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+#if defined(BOOST_ASIO_HAS_BOOST_REGEX) \
+ || defined(GENERATING_DOCUMENTATION)
+
+/// Start an asynchronous operation to read data into a streambuf until some
+/// part of its data matches a regular expression.
+/**
+ * This function is used to asynchronously read data into the specified
+ * streambuf until the streambuf's get area contains some data that matches a
+ * regular expression. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions
+ * is true:
+ *
+ * @li A substring of the streambuf's get area matches the regular expression.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_read_some function, and is known as a <em>composed operation</em>. If
+ * the streambuf's get area already contains data that matches the regular
+ * expression, this asynchronous operation completes immediately. The program
+ * must ensure that the stream performs no other read operations (such as
+ * async_read, async_read_until, the stream's async_read_some function, or any
+ * other composed operations that perform reads) until this operation
+ * completes.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the AsyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read. Ownership of
+ * the streambuf is retained by the caller, which must guarantee that it remains
+ * valid until the handler is called.
+ *
+ * @param expr The regular expression.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // The number of bytes in the streambuf's get
+ * // area up to and including the substring
+ * // that matches the regular. expression.
+ * // 0 if an error occurred.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note After a successful async_read_until operation, the streambuf may
+ * contain additional data beyond that which matched the regular expression. An
+ * application will typically leave that data in the streambuf for a subsequent
+ * async_read_until operation to examine.
+ *
+ * @par Example
+ * To asynchronously read data into a streambuf until a CR-LF sequence is
+ * encountered:
+ * @code boost::asio::streambuf b;
+ * ...
+ * void handler(const boost::system::error_code& e, std::size_t size)
+ * {
+ * if (!e)
+ * {
+ * std::istream is(&b);
+ * std::string line;
+ * std::getline(is, line);
+ * ...
+ * }
+ * }
+ * ...
+ * boost::asio::async_read_until(s, b, boost::regex("\r\n"), handler); @endcode
+ * After the @c async_read_until operation completes successfully, the buffer
+ * @c b contains the data which matched the regular expression:
+ * @code { 'a', 'b', ..., 'c', '\r', '\n', 'd', 'e', ... } @endcode
+ * The call to @c std::getline then extracts the data up to and including the
+ * match, so that the string @c line contains:
+ * @code { 'a', 'b', ..., 'c', '\r', '\n' } @endcode
+ * The remaining data is left in the buffer @c b as follows:
+ * @code { 'd', 'e', ... } @endcode
+ * This data may be the start of a new line, to be extracted by a subsequent
+ * @c async_read_until operation.
+ */
+template <typename AsyncReadStream, typename Allocator, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_until(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b, const boost::regex& expr,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler);
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_REGEX)
+ // || defined(GENERATING_DOCUMENTATION)
+
+/// Start an asynchronous operation to read data into a streambuf until a
+/// function object indicates a match.
+/**
+ * This function is used to asynchronously read data into the specified
+ * streambuf until a user-defined match condition function object, when applied
+ * to the data contained in the streambuf, indicates a successful match. The
+ * function call always returns immediately. The asynchronous operation will
+ * continue until one of the following conditions is true:
+ *
+ * @li The match condition function object returns a std::pair where the second
+ * element evaluates to true.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_read_some function, and is known as a <em>composed operation</em>. If
+ * the match condition function object already indicates a match, this
+ * asynchronous operation completes immediately. The program must ensure that
+ * the stream performs no other read operations (such as async_read,
+ * async_read_until, the stream's async_read_some function, or any other
+ * composed operations that perform reads) until this operation completes.
+ *
+ * @param s The stream from which the data is to be read. The type must support
+ * the AsyncReadStream concept.
+ *
+ * @param b A streambuf object into which the data will be read.
+ *
+ * @param match_condition The function object to be called to determine whether
+ * a match exists. The signature of the function object must be:
+ * @code pair<iterator, bool> match_condition(iterator begin, iterator end);
+ * @endcode
+ * where @c iterator represents the type:
+ * @code buffers_iterator<basic_streambuf<Allocator>::const_buffers_type>
+ * @endcode
+ * The iterator parameters @c begin and @c end define the range of bytes to be
+ * scanned to determine whether there is a match. The @c first member of the
+ * return value is an iterator marking one-past-the-end of the bytes that have
+ * been consumed by the match function. This iterator is used to calculate the
+ * @c begin parameter for any subsequent invocation of the match condition. The
+ * @c second member of the return value is true if a match has been found, false
+ * otherwise.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // The number of bytes in the streambuf's get
+ * // area that have been fully consumed by the
+ * // match function. O if an error occurred.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note After a successful async_read_until operation, the streambuf may
+ * contain additional data beyond that which matched the function object. An
+ * application will typically leave that data in the streambuf for a subsequent
+ * async_read_until operation to examine.
+ *
+ * @note The default implementation of the @c is_match_condition type trait
+ * evaluates to true for function pointers and function objects with a
+ * @c result_type typedef. It must be specialised for other user-defined
+ * function objects.
+ *
+ * @par Examples
+ * To asynchronously read data into a streambuf until whitespace is encountered:
+ * @code typedef boost::asio::buffers_iterator<
+ * boost::asio::streambuf::const_buffers_type> iterator;
+ *
+ * std::pair<iterator, bool>
+ * match_whitespace(iterator begin, iterator end)
+ * {
+ * iterator i = begin;
+ * while (i != end)
+ * if (std::isspace(*i++))
+ * return std::make_pair(i, true);
+ * return std::make_pair(i, false);
+ * }
+ * ...
+ * void handler(const boost::system::error_code& e, std::size_t size);
+ * ...
+ * boost::asio::streambuf b;
+ * boost::asio::async_read_until(s, b, match_whitespace, handler);
+ * @endcode
+ *
+ * To asynchronously read data into a streambuf until a matching character is
+ * found:
+ * @code class match_char
+ * {
+ * public:
+ * explicit match_char(char c) : c_(c) {}
+ *
+ * template <typename Iterator>
+ * std::pair<Iterator, bool> operator()(
+ * Iterator begin, Iterator end) const
+ * {
+ * Iterator i = begin;
+ * while (i != end)
+ * if (c_ == *i++)
+ * return std::make_pair(i, true);
+ * return std::make_pair(i, false);
+ * }
+ *
+ * private:
+ * char c_;
+ * };
+ *
+ * namespace asio {
+ * template <> struct is_match_condition<match_char>
+ * : public boost::true_type {};
+ * } // namespace asio
+ * ...
+ * void handler(const boost::system::error_code& e, std::size_t size);
+ * ...
+ * boost::asio::streambuf b;
+ * boost::asio::async_read_until(s, b, match_char('a'), handler);
+ * @endcode
+ */
+template <typename AsyncReadStream, typename Allocator,
+ typename MatchCondition, typename ReadHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+async_read_until(AsyncReadStream& s,
+ boost::asio::basic_streambuf<Allocator>& b,
+ MatchCondition match_condition, BOOST_ASIO_MOVE_ARG(ReadHandler) handler,
+ typename enable_if<is_match_condition<MatchCondition>::value>::type* = 0);
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/read_until.hpp>
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_READ_UNTIL_HPP
diff --git a/ext/patches/boost/asio/seq_packet_socket_service.hpp b/ext/patches/boost/asio/seq_packet_socket_service.hpp
new file mode 100644
index 0000000..b47ab53
--- /dev/null
+++ b/ext/patches/boost/asio/seq_packet_socket_service.hpp
@@ -0,0 +1,382 @@
+//
+// seq_packet_socket_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SEQ_PACKET_SOCKET_SERVICE_HPP
+#define BOOST_ASIO_SEQ_PACKET_SOCKET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/null_socket_service.hpp>
+#elif defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_socket_service.hpp>
+#else
+# include <boost/asio/detail/reactive_socket_service.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a sequenced packet socket.
+template <typename Protocol>
+class seq_packet_socket_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<
+ seq_packet_socket_service<Protocol> >
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+private:
+ // The type of the platform-specific implementation.
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ typedef detail::null_socket_service<Protocol> service_impl_type;
+#elif defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::win_iocp_socket_service<Protocol> service_impl_type;
+#else
+ typedef detail::reactive_socket_service<Protocol> service_impl_type;
+#endif
+
+public:
+ /// The type of a sequenced packet socket implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef typename service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native socket type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native socket type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new sequenced packet socket service for the specified
+ /// io_service.
+ explicit seq_packet_socket_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ seq_packet_socket_service<Protocol> >(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new sequenced packet socket implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new sequenced packet socket implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another sequenced packet socket implementation.
+ void move_assign(implementation_type& impl,
+ seq_packet_socket_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+
+ /// Move-construct a new sequenced packet socket implementation from another
+ /// protocol type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type& impl,
+ typename seq_packet_socket_service<
+ Protocol1>::implementation_type& other_impl,
+ typename enable_if<is_convertible<
+ Protocol1, Protocol>::value>::type* = 0)
+ {
+ service_impl_.template converting_move_construct<Protocol1>(
+ impl, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a sequenced packet socket implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Open a sequenced packet socket.
+ boost::system::error_code open(implementation_type& impl,
+ const protocol_type& protocol, boost::system::error_code& ec)
+ {
+ if (protocol.type() == BOOST_ASIO_OS_DEF(SOCK_SEQPACKET))
+ service_impl_.open(impl, protocol, ec);
+ else
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ /// Assign an existing native socket to a sequenced packet socket.
+ boost::system::error_code assign(implementation_type& impl,
+ const protocol_type& protocol, const native_handle_type& native_socket,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, protocol, native_socket, ec);
+ }
+
+ /// Determine whether the socket is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close a sequenced packet socket implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native socket implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native socket implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the socket.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Determine whether the socket is at the out-of-band data mark.
+ bool at_mark(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.at_mark(impl, ec);
+ }
+
+ /// Determine the number of bytes available for reading.
+ std::size_t available(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.available(impl, ec);
+ }
+
+ /// Bind the sequenced packet socket to the specified local endpoint.
+ boost::system::error_code bind(implementation_type& impl,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.bind(impl, endpoint, ec);
+ }
+
+ /// Connect the sequenced packet socket to the specified endpoint.
+ boost::system::error_code connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.connect(impl, peer_endpoint, ec);
+ }
+
+ /// Start an asynchronous connect.
+ template <typename ConnectHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ConnectHandler,
+ void (boost::system::error_code))
+ async_connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint,
+ BOOST_ASIO_MOVE_ARG(ConnectHandler) handler)
+ {
+ detail::async_result_init<
+ ConnectHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(ConnectHandler)(handler));
+
+ service_impl_.async_connect(impl, peer_endpoint, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Set a socket option.
+ template <typename SettableSocketOption>
+ boost::system::error_code set_option(implementation_type& impl,
+ const SettableSocketOption& option, boost::system::error_code& ec)
+ {
+ return service_impl_.set_option(impl, option, ec);
+ }
+
+ /// Get a socket option.
+ template <typename GettableSocketOption>
+ boost::system::error_code get_option(const implementation_type& impl,
+ GettableSocketOption& option, boost::system::error_code& ec) const
+ {
+ return service_impl_.get_option(impl, option, ec);
+ }
+
+ /// Perform an IO control command on the socket.
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(implementation_type& impl,
+ IoControlCommand& command, boost::system::error_code& ec)
+ {
+ return service_impl_.io_control(impl, command, ec);
+ }
+
+ /// Gets the non-blocking mode of the socket.
+ bool non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the socket.
+ boost::system::error_code non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.non_blocking(impl, mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native socket implementation.
+ bool native_non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.native_non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the native socket implementation.
+ boost::system::error_code native_non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.native_non_blocking(impl, mode, ec);
+ }
+
+ /// Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.local_endpoint(impl, ec);
+ }
+
+ /// Get the remote endpoint.
+ endpoint_type remote_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.remote_endpoint(impl, ec);
+ }
+
+ /// Disable sends or receives on the socket.
+ boost::system::error_code shutdown(implementation_type& impl,
+ socket_base::shutdown_type what, boost::system::error_code& ec)
+ {
+ return service_impl_.shutdown(impl, what, ec);
+ }
+
+ /// Send the given data to the peer.
+ template <typename ConstBufferSequence>
+ std::size_t send(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.send(impl, buffers, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_send(impl, buffers, flags, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Receive some data from the peer.
+ template <typename MutableBufferSequence>
+ std::size_t receive(implementation_type& impl,
+ const MutableBufferSequence& buffers, socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags, boost::system::error_code& ec)
+ {
+ return service_impl_.receive_with_flags(impl,
+ buffers, in_flags, out_flags, ec);
+ }
+
+ /// Start an asynchronous receive.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(implementation_type& impl,
+ const MutableBufferSequence& buffers, socket_base::message_flags in_flags,
+ socket_base::message_flags& out_flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_receive_with_flags(impl,
+ buffers, in_flags, out_flags, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SEQ_PACKET_SOCKET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/serial_port.hpp b/ext/patches/boost/asio/serial_port.hpp
new file mode 100644
index 0000000..e114f5a
--- /dev/null
+++ b/ext/patches/boost/asio/serial_port.hpp
@@ -0,0 +1,38 @@
+//
+// serial_port.hpp
+// ~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SERIAL_PORT_HPP
+#define BOOST_ASIO_SERIAL_PORT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_SERIAL_PORT) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/basic_serial_port.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Typedef for the typical usage of a serial port.
+typedef basic_serial_port<> serial_port;
+
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_SERIAL_PORT)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_SERIAL_PORT_HPP
diff --git a/ext/patches/boost/asio/serial_port_base.hpp b/ext/patches/boost/asio/serial_port_base.hpp
new file mode 100644
index 0000000..df7679e
--- /dev/null
+++ b/ext/patches/boost/asio/serial_port_base.hpp
@@ -0,0 +1,169 @@
+//
+// serial_port_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2008 Rep Invariant Systems, Inc. (info at repinvariant.com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SERIAL_PORT_BASE_HPP
+#define BOOST_ASIO_SERIAL_PORT_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_SERIAL_PORT) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+# include <termios.h>
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#include <boost/asio/detail/socket_types.hpp>
+#include <boost/system/error_code.hpp>
+
+#if defined(GENERATING_DOCUMENTATION)
+# define BOOST_ASIO_OPTION_STORAGE implementation_defined
+#elif defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+# define BOOST_ASIO_OPTION_STORAGE DCB
+#else
+# define BOOST_ASIO_OPTION_STORAGE termios
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// The serial_port_base class is used as a base for the basic_serial_port class
+/// template so that we have a common place to define the serial port options.
+class serial_port_base
+{
+public:
+ /// Serial port option to permit changing the baud rate.
+ /**
+ * Implements changing the baud rate for a given serial port.
+ */
+ class baud_rate
+ {
+ public:
+ explicit baud_rate(unsigned int rate = 0);
+ unsigned int value() const;
+ BOOST_ASIO_DECL boost::system::error_code store(
+ BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec) const;
+ BOOST_ASIO_DECL boost::system::error_code load(
+ const BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec);
+ private:
+ unsigned int value_;
+ };
+
+ /// Serial port option to permit changing the flow control.
+ /**
+ * Implements changing the flow control for a given serial port.
+ */
+ class flow_control
+ {
+ public:
+ enum type { none, software, hardware };
+ BOOST_ASIO_DECL explicit flow_control(type t = none);
+ type value() const;
+ BOOST_ASIO_DECL boost::system::error_code store(
+ BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec) const;
+ BOOST_ASIO_DECL boost::system::error_code load(
+ const BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec);
+ private:
+ type value_;
+ };
+
+ /// Serial port option to permit changing the parity.
+ /**
+ * Implements changing the parity for a given serial port.
+ */
+ class parity
+ {
+ public:
+ enum type { none, odd, even };
+ BOOST_ASIO_DECL explicit parity(type t = none);
+ type value() const;
+ BOOST_ASIO_DECL boost::system::error_code store(
+ BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec) const;
+ BOOST_ASIO_DECL boost::system::error_code load(
+ const BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec);
+ private:
+ type value_;
+ };
+
+ /// Serial port option to permit changing the number of stop bits.
+ /**
+ * Implements changing the number of stop bits for a given serial port.
+ */
+ class stop_bits
+ {
+ public:
+ enum type { one, onepointfive, two };
+ BOOST_ASIO_DECL explicit stop_bits(type t = one);
+ type value() const;
+ BOOST_ASIO_DECL boost::system::error_code store(
+ BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec) const;
+ BOOST_ASIO_DECL boost::system::error_code load(
+ const BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec);
+ private:
+ type value_;
+ };
+
+ /// Serial port option to permit changing the character size.
+ /**
+ * Implements changing the character size for a given serial port.
+ */
+ class character_size
+ {
+ public:
+ BOOST_ASIO_DECL explicit character_size(unsigned int t = 8);
+ unsigned int value() const;
+ BOOST_ASIO_DECL boost::system::error_code store(
+ BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec) const;
+ BOOST_ASIO_DECL boost::system::error_code load(
+ const BOOST_ASIO_OPTION_STORAGE& storage,
+ boost::system::error_code& ec);
+ private:
+ unsigned int value_;
+ };
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~serial_port_base()
+ {
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#undef BOOST_ASIO_OPTION_STORAGE
+
+#include <boost/asio/impl/serial_port_base.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/impl/serial_port_base.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // defined(BOOST_ASIO_HAS_SERIAL_PORT)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_SERIAL_PORT_BASE_HPP
diff --git a/ext/patches/boost/asio/serial_port_service.hpp b/ext/patches/boost/asio/serial_port_service.hpp
new file mode 100644
index 0000000..4f53da8
--- /dev/null
+++ b/ext/patches/boost/asio/serial_port_service.hpp
@@ -0,0 +1,255 @@
+//
+// serial_port_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SERIAL_PORT_SERVICE_HPP
+#define BOOST_ASIO_SERIAL_PORT_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_SERIAL_PORT) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <string>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/reactive_serial_port_service.hpp>
+#include <boost/asio/detail/win_iocp_serial_port_service.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/serial_port_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a serial port.
+class serial_port_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<serial_port_service>
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+private:
+ // The type of the platform-specific implementation.
+#if defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::win_iocp_serial_port_service service_impl_type;
+#else
+ typedef detail::reactive_serial_port_service service_impl_type;
+#endif
+
+public:
+ /// The type of a serial port implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native handle type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native handle type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new serial port service for the specified io_service.
+ explicit serial_port_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<serial_port_service>(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new serial port implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new serial port implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another serial port implementation.
+ void move_assign(implementation_type& impl,
+ serial_port_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a serial port implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Open a serial port.
+ boost::system::error_code open(implementation_type& impl,
+ const std::string& device, boost::system::error_code& ec)
+ {
+ return service_impl_.open(impl, device, ec);
+ }
+
+ /// Assign an existing native handle to a serial port.
+ boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, handle, ec);
+ }
+
+ /// Determine whether the handle is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close a serial port implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native handle implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native handle implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the handle.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Set a serial port option.
+ template <typename SettableSerialPortOption>
+ boost::system::error_code set_option(implementation_type& impl,
+ const SettableSerialPortOption& option, boost::system::error_code& ec)
+ {
+ return service_impl_.set_option(impl, option, ec);
+ }
+
+ /// Get a serial port option.
+ template <typename GettableSerialPortOption>
+ boost::system::error_code get_option(const implementation_type& impl,
+ GettableSerialPortOption& option, boost::system::error_code& ec) const
+ {
+ return service_impl_.get_option(impl, option, ec);
+ }
+
+ /// Send a break sequence to the serial port.
+ boost::system::error_code send_break(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.send_break(impl, ec);
+ }
+
+ /// Write the given data to the stream.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.write_some(impl, buffers, ec);
+ }
+
+ /// Start an asynchronous write.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_write_some(impl, buffers, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Read some data from the stream.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.read_some(impl, buffers, ec);
+ }
+
+ /// Start an asynchronous read.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_read_some(impl, buffers, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_SERIAL_PORT)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_SERIAL_PORT_SERVICE_HPP
diff --git a/ext/patches/boost/asio/signal_set.hpp b/ext/patches/boost/asio/signal_set.hpp
new file mode 100644
index 0000000..44d4dfa
--- /dev/null
+++ b/ext/patches/boost/asio/signal_set.hpp
@@ -0,0 +1,30 @@
+//
+// signal_set.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SIGNAL_SET_HPP
+#define BOOST_ASIO_SIGNAL_SET_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/basic_signal_set.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Typedef for the typical usage of a signal set.
+typedef basic_signal_set<> signal_set;
+
+} // namespace asio
+} // namespace boost
+
+#endif // BOOST_ASIO_SIGNAL_SET_HPP
diff --git a/ext/patches/boost/asio/signal_set_service.hpp b/ext/patches/boost/asio/signal_set_service.hpp
new file mode 100644
index 0000000..92b334c
--- /dev/null
+++ b/ext/patches/boost/asio/signal_set_service.hpp
@@ -0,0 +1,136 @@
+//
+// signal_set_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SIGNAL_SET_SERVICE_HPP
+#define BOOST_ASIO_SIGNAL_SET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/signal_set_service.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a signal set.
+class signal_set_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<signal_set_service>
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+public:
+ /// The type of a signal set implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef detail::signal_set_service::implementation_type implementation_type;
+#endif
+
+ /// Construct a new signal set service for the specified io_service.
+ explicit signal_set_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<signal_set_service>(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new signal set implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+ /// Destroy a signal set implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Add a signal to a signal_set.
+ boost::system::error_code add(implementation_type& impl,
+ int signal_number, boost::system::error_code& ec)
+ {
+ return service_impl_.add(impl, signal_number, ec);
+ }
+
+ /// Remove a signal to a signal_set.
+ boost::system::error_code remove(implementation_type& impl,
+ int signal_number, boost::system::error_code& ec)
+ {
+ return service_impl_.remove(impl, signal_number, ec);
+ }
+
+ /// Remove all signals from a signal_set.
+ boost::system::error_code clear(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.clear(impl, ec);
+ }
+
+ /// Cancel all operations associated with the signal set.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ // Start an asynchronous operation to wait for a signal to be delivered.
+ template <typename SignalHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(SignalHandler,
+ void (boost::system::error_code, int))
+ async_wait(implementation_type& impl,
+ BOOST_ASIO_MOVE_ARG(SignalHandler) handler)
+ {
+ detail::async_result_init<
+ SignalHandler, void (boost::system::error_code, int)> init(
+ BOOST_ASIO_MOVE_CAST(SignalHandler)(handler));
+
+ service_impl_.async_wait(impl, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // Perform any fork-related housekeeping.
+ void fork_service(boost::asio::io_service::fork_event event)
+ {
+ service_impl_.fork_service(event);
+ }
+
+ // The platform-specific implementation.
+ detail::signal_set_service service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SIGNAL_SET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/socket_acceptor_service.hpp b/ext/patches/boost/asio/socket_acceptor_service.hpp
new file mode 100644
index 0000000..87ea518
--- /dev/null
+++ b/ext/patches/boost/asio/socket_acceptor_service.hpp
@@ -0,0 +1,304 @@
+//
+// socket_acceptor_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SOCKET_ACCEPTOR_SERVICE_HPP
+#define BOOST_ASIO_SOCKET_ACCEPTOR_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/basic_socket.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/null_socket_service.hpp>
+#elif defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_socket_service.hpp>
+#else
+# include <boost/asio/detail/reactive_socket_service.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a socket acceptor.
+template <typename Protocol>
+class socket_acceptor_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<socket_acceptor_service<Protocol> >
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename protocol_type::endpoint endpoint_type;
+
+private:
+ // The type of the platform-specific implementation.
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ typedef detail::null_socket_service<Protocol> service_impl_type;
+#elif defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::win_iocp_socket_service<Protocol> service_impl_type;
+#else
+ typedef detail::reactive_socket_service<Protocol> service_impl_type;
+#endif
+
+public:
+ /// The native type of the socket acceptor.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef typename service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native acceptor type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native acceptor type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new socket acceptor service for the specified io_service.
+ explicit socket_acceptor_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ socket_acceptor_service<Protocol> >(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new socket acceptor implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new socket acceptor implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another socket acceptor implementation.
+ void move_assign(implementation_type& impl,
+ socket_acceptor_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+
+ /// Move-construct a new socket acceptor implementation from another protocol
+ /// type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type& impl,
+ typename socket_acceptor_service<
+ Protocol1>::implementation_type& other_impl,
+ typename enable_if<is_convertible<
+ Protocol1, Protocol>::value>::type* = 0)
+ {
+ service_impl_.template converting_move_construct<Protocol1>(
+ impl, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a socket acceptor implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Open a new socket acceptor implementation.
+ boost::system::error_code open(implementation_type& impl,
+ const protocol_type& protocol, boost::system::error_code& ec)
+ {
+ return service_impl_.open(impl, protocol, ec);
+ }
+
+ /// Assign an existing native acceptor to a socket acceptor.
+ boost::system::error_code assign(implementation_type& impl,
+ const protocol_type& protocol, const native_handle_type& native_acceptor,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, protocol, native_acceptor, ec);
+ }
+
+ /// Determine whether the acceptor is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the acceptor.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Bind the socket acceptor to the specified local endpoint.
+ boost::system::error_code bind(implementation_type& impl,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.bind(impl, endpoint, ec);
+ }
+
+ /// Place the socket acceptor into the state where it will listen for new
+ /// connections.
+ boost::system::error_code listen(implementation_type& impl, int backlog,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.listen(impl, backlog, ec);
+ }
+
+ /// Close a socket acceptor implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native acceptor implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native acceptor implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Set a socket option.
+ template <typename SettableSocketOption>
+ boost::system::error_code set_option(implementation_type& impl,
+ const SettableSocketOption& option, boost::system::error_code& ec)
+ {
+ return service_impl_.set_option(impl, option, ec);
+ }
+
+ /// Get a socket option.
+ template <typename GettableSocketOption>
+ boost::system::error_code get_option(const implementation_type& impl,
+ GettableSocketOption& option, boost::system::error_code& ec) const
+ {
+ return service_impl_.get_option(impl, option, ec);
+ }
+
+ /// Perform an IO control command on the socket.
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(implementation_type& impl,
+ IoControlCommand& command, boost::system::error_code& ec)
+ {
+ return service_impl_.io_control(impl, command, ec);
+ }
+
+ /// Gets the non-blocking mode of the acceptor.
+ bool non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the acceptor.
+ boost::system::error_code non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.non_blocking(impl, mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native acceptor implementation.
+ bool native_non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.native_non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the native acceptor implementation.
+ boost::system::error_code native_non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.native_non_blocking(impl, mode, ec);
+ }
+
+ /// Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.local_endpoint(impl, ec);
+ }
+
+ /// Accept a new connection.
+ template <typename Protocol1, typename SocketService>
+ boost::system::error_code accept(implementation_type& impl,
+ basic_socket<Protocol1, SocketService>& peer,
+ endpoint_type* peer_endpoint, boost::system::error_code& ec,
+ typename enable_if<is_convertible<Protocol, Protocol1>::value>::type* = 0)
+ {
+ return service_impl_.accept(impl, peer, peer_endpoint, ec);
+ }
+
+ /// Start an asynchronous accept.
+ template <typename Protocol1, typename SocketService, typename AcceptHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(AcceptHandler,
+ void (boost::system::error_code))
+ async_accept(implementation_type& impl,
+ basic_socket<Protocol1, SocketService>& peer,
+ endpoint_type* peer_endpoint,
+ BOOST_ASIO_MOVE_ARG(AcceptHandler) handler,
+ typename enable_if<is_convertible<Protocol, Protocol1>::value>::type* = 0)
+ {
+ detail::async_result_init<
+ AcceptHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(AcceptHandler)(handler));
+
+ service_impl_.async_accept(impl, peer, peer_endpoint, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SOCKET_ACCEPTOR_SERVICE_HPP
diff --git a/ext/patches/boost/asio/socket_base.hpp b/ext/patches/boost/asio/socket_base.hpp
new file mode 100644
index 0000000..3191d13
--- /dev/null
+++ b/ext/patches/boost/asio/socket_base.hpp
@@ -0,0 +1,522 @@
+//
+// socket_base.hpp
+// ~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SOCKET_BASE_HPP
+#define BOOST_ASIO_SOCKET_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/detail/io_control.hpp>
+#include <boost/asio/detail/socket_option.hpp>
+#include <boost/asio/detail/socket_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// The socket_base class is used as a base for the basic_stream_socket and
+/// basic_datagram_socket class templates so that we have a common place to
+/// define the shutdown_type and enum.
+class socket_base
+{
+public:
+ /// Different ways a socket may be shutdown.
+ enum shutdown_type
+ {
+#if defined(GENERATING_DOCUMENTATION)
+ /// Shutdown the receive side of the socket.
+ shutdown_receive = implementation_defined,
+
+ /// Shutdown the send side of the socket.
+ shutdown_send = implementation_defined,
+
+ /// Shutdown both send and receive on the socket.
+ shutdown_both = implementation_defined
+#else
+ shutdown_receive = BOOST_ASIO_OS_DEF(SHUT_RD),
+ shutdown_send = BOOST_ASIO_OS_DEF(SHUT_WR),
+ shutdown_both = BOOST_ASIO_OS_DEF(SHUT_RDWR)
+#endif
+ };
+
+ /// Bitmask type for flags that can be passed to send and receive operations.
+ typedef int message_flags;
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// Peek at incoming data without removing it from the input queue.
+ static const int message_peek = implementation_defined;
+
+ /// Process out-of-band data.
+ static const int message_out_of_band = implementation_defined;
+
+ /// Specify that the data should not be subject to routing.
+ static const int message_do_not_route = implementation_defined;
+
+ /// Specifies that the data marks the end of a record.
+ static const int message_end_of_record = implementation_defined;
+#else
+ BOOST_ASIO_STATIC_CONSTANT(int,
+ message_peek = BOOST_ASIO_OS_DEF(MSG_PEEK));
+ BOOST_ASIO_STATIC_CONSTANT(int,
+ message_out_of_band = BOOST_ASIO_OS_DEF(MSG_OOB));
+ BOOST_ASIO_STATIC_CONSTANT(int,
+ message_do_not_route = BOOST_ASIO_OS_DEF(MSG_DONTROUTE));
+ BOOST_ASIO_STATIC_CONSTANT(int,
+ message_end_of_record = BOOST_ASIO_OS_DEF(MSG_EOR));
+#endif
+
+ /// Socket option to permit sending of broadcast messages.
+ /**
+ * Implements the SOL_SOCKET/SO_BROADCAST socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::broadcast option(true);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::broadcast option;
+ * socket.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Boolean_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined broadcast;
+#else
+ typedef boost::asio::detail::socket_option::boolean<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_BROADCAST)>
+ broadcast;
+#endif
+
+ /// Socket option to enable socket-level debugging.
+ /**
+ * Implements the SOL_SOCKET/SO_DEBUG socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::debug option(true);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::debug option;
+ * socket.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Boolean_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined debug;
+#else
+ typedef boost::asio::detail::socket_option::boolean<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_DEBUG)> debug;
+#endif
+
+ /// Socket option to prevent routing, use local interfaces only.
+ /**
+ * Implements the SOL_SOCKET/SO_DONTROUTE socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::do_not_route option(true);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::udp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::do_not_route option;
+ * socket.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Boolean_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined do_not_route;
+#else
+ typedef boost::asio::detail::socket_option::boolean<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_DONTROUTE)>
+ do_not_route;
+#endif
+
+ /// Socket option to send keep-alives.
+ /**
+ * Implements the SOL_SOCKET/SO_KEEPALIVE socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::keep_alive option(true);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::keep_alive option;
+ * socket.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Boolean_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined keep_alive;
+#else
+ typedef boost::asio::detail::socket_option::boolean<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_KEEPALIVE)> keep_alive;
+#endif
+
+ /// Socket option for the send buffer size of a socket.
+ /**
+ * Implements the SOL_SOCKET/SO_SNDBUF socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::send_buffer_size option(8192);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::send_buffer_size option;
+ * socket.get_option(option);
+ * int size = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Integer_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined send_buffer_size;
+#else
+ typedef boost::asio::detail::socket_option::integer<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_SNDBUF)>
+ send_buffer_size;
+#endif
+
+ /// Socket option for the send low watermark.
+ /**
+ * Implements the SOL_SOCKET/SO_SNDLOWAT socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::send_low_watermark option(1024);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::send_low_watermark option;
+ * socket.get_option(option);
+ * int size = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Integer_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined send_low_watermark;
+#else
+ typedef boost::asio::detail::socket_option::integer<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_SNDLOWAT)>
+ send_low_watermark;
+#endif
+
+ /// Socket option for the receive buffer size of a socket.
+ /**
+ * Implements the SOL_SOCKET/SO_RCVBUF socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::receive_buffer_size option(8192);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::receive_buffer_size option;
+ * socket.get_option(option);
+ * int size = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Integer_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined receive_buffer_size;
+#else
+ typedef boost::asio::detail::socket_option::integer<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_RCVBUF)>
+ receive_buffer_size;
+#endif
+
+ /// Socket option for the receive low watermark.
+ /**
+ * Implements the SOL_SOCKET/SO_RCVLOWAT socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::receive_low_watermark option(1024);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::receive_low_watermark option;
+ * socket.get_option(option);
+ * int size = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Integer_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined receive_low_watermark;
+#else
+ typedef boost::asio::detail::socket_option::integer<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_RCVLOWAT)>
+ receive_low_watermark;
+#endif
+
+ /// Socket option to allow the socket to be bound to an address that is
+ /// already in use.
+ /**
+ * Implements the SOL_SOCKET/SO_REUSEADDR socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::socket_base::reuse_address option(true);
+ * acceptor.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::socket_base::reuse_address option;
+ * acceptor.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Boolean_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined reuse_address;
+#else
+ typedef boost::asio::detail::socket_option::boolean<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_REUSEADDR)>
+ reuse_address;
+#endif
+
+ /// Socket option to specify whether the socket lingers on close if unsent
+ /// data is present.
+ /**
+ * Implements the SOL_SOCKET/SO_LINGER socket option.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::linger option(true, 30);
+ * socket.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::linger option;
+ * socket.get_option(option);
+ * bool is_set = option.enabled();
+ * unsigned short timeout = option.timeout();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Linger_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined linger;
+#else
+ typedef boost::asio::detail::socket_option::linger<
+ BOOST_ASIO_OS_DEF(SOL_SOCKET), BOOST_ASIO_OS_DEF(SO_LINGER)>
+ linger;
+#endif
+
+ /// Socket option to report aborted connections on accept.
+ /**
+ * Implements a custom socket option that determines whether or not an accept
+ * operation is permitted to fail with boost::asio::error::connection_aborted.
+ * By default the option is false.
+ *
+ * @par Examples
+ * Setting the option:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::socket_base::enable_connection_aborted option(true);
+ * acceptor.set_option(option);
+ * @endcode
+ *
+ * @par
+ * Getting the current option value:
+ * @code
+ * boost::asio::ip::tcp::acceptor acceptor(io_service);
+ * ...
+ * boost::asio::socket_base::enable_connection_aborted option;
+ * acceptor.get_option(option);
+ * bool is_set = option.value();
+ * @endcode
+ *
+ * @par Concepts:
+ * Socket_Option, Boolean_Socket_Option.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined enable_connection_aborted;
+#else
+ typedef boost::asio::detail::socket_option::boolean<
+ boost::asio::detail::custom_socket_option_level,
+ boost::asio::detail::enable_connection_aborted_option>
+ enable_connection_aborted;
+#endif
+
+ /// (Deprecated: Use non_blocking().) IO control command to
+ /// set the blocking mode of the socket.
+ /**
+ * Implements the FIONBIO IO control command.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::non_blocking_io command(true);
+ * socket.io_control(command);
+ * @endcode
+ *
+ * @par Concepts:
+ * IO_Control_Command, Boolean_IO_Control_Command.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined non_blocking_io;
+#else
+ typedef boost::asio::detail::io_control::non_blocking_io non_blocking_io;
+#endif
+
+ /// IO control command to get the amount of data that can be read without
+ /// blocking.
+ /**
+ * Implements the FIONREAD IO control command.
+ *
+ * @par Example
+ * @code
+ * boost::asio::ip::tcp::socket socket(io_service);
+ * ...
+ * boost::asio::socket_base::bytes_readable command(true);
+ * socket.io_control(command);
+ * std::size_t bytes_readable = command.get();
+ * @endcode
+ *
+ * @par Concepts:
+ * IO_Control_Command, Size_IO_Control_Command.
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined bytes_readable;
+#else
+ typedef boost::asio::detail::io_control::bytes_readable bytes_readable;
+#endif
+
+ /// The maximum length of the queue of pending incoming connections.
+#if defined(GENERATING_DOCUMENTATION)
+ static const int max_connections = implementation_defined;
+#else
+ BOOST_ASIO_STATIC_CONSTANT(int, max_connections
+ = BOOST_ASIO_OS_DEF(SOMAXCONN));
+#endif
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~socket_base()
+ {
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SOCKET_BASE_HPP
diff --git a/ext/patches/boost/asio/spawn.hpp b/ext/patches/boost/asio/spawn.hpp
new file mode 100644
index 0000000..4f1c086
--- /dev/null
+++ b/ext/patches/boost/asio/spawn.hpp
@@ -0,0 +1,267 @@
+//
+// spawn.hpp
+// ~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SPAWN_HPP
+#define BOOST_ASIO_SPAWN_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/coroutine/all.hpp>
+#include <boost/asio/detail/weak_ptr.hpp>
+#include <boost/asio/detail/wrapped_handler.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/strand.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Context object the represents the currently executing coroutine.
+/**
+ * The basic_yield_context class is used to represent the currently executing
+ * stackful coroutine. A basic_yield_context may be passed as a handler to an
+ * asynchronous operation. For example:
+ *
+ * @code template <typename Handler>
+ * void my_coroutine(basic_yield_context<Handler> yield)
+ * {
+ * ...
+ * std::size_t n = my_socket.async_read_some(buffer, yield);
+ * ...
+ * } @endcode
+ *
+ * The initiating function (async_read_some in the above example) suspends the
+ * current coroutine. The coroutine is resumed when the asynchronous operation
+ * completes, and the result of the operation is returned.
+ */
+template <typename Handler>
+class basic_yield_context
+{
+public:
+ /// The coroutine callee type, used by the implementation.
+ /**
+ * When using Boost.Coroutine v1, this type is:
+ * @code typename coroutine<void()> @endcode
+ * When using Boost.Coroutine v2 (unidirectional coroutines), this type is:
+ * @code push_coroutine<void> @endcode
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined callee_type;
+#elif defined(BOOST_COROUTINES_UNIDIRECT) || defined(BOOST_COROUTINES_V2)
+ typedef boost::coroutines::push_coroutine<void> callee_type;
+#else
+ typedef boost::coroutines::coroutine<void()> callee_type;
+#endif
+
+ /// The coroutine caller type, used by the implementation.
+ /**
+ * When using Boost.Coroutine v1, this type is:
+ * @code typename coroutine<void()>::caller_type @endcode
+ * When using Boost.Coroutine v2 (unidirectional coroutines), this type is:
+ * @code pull_coroutine<void> @endcode
+ */
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined caller_type;
+#elif defined(BOOST_COROUTINES_UNIDIRECT) || defined(BOOST_COROUTINES_V2)
+ typedef boost::coroutines::pull_coroutine<void> caller_type;
+#else
+ typedef boost::coroutines::coroutine<void()>::caller_type caller_type;
+#endif
+
+ /// Construct a yield context to represent the specified coroutine.
+ /**
+ * Most applications do not need to use this constructor. Instead, the
+ * spawn() function passes a yield context as an argument to the coroutine
+ * function.
+ */
+ basic_yield_context(
+ const detail::weak_ptr<callee_type>& coro,
+ caller_type& ca, Handler& handler)
+ : coro_(coro),
+ ca_(ca),
+ handler_(handler),
+ ec_(0)
+ {
+ }
+
+ /// Return a yield context that sets the specified error_code.
+ /**
+ * By default, when a yield context is used with an asynchronous operation, a
+ * non-success error_code is converted to system_error and thrown. This
+ * operator may be used to specify an error_code object that should instead be
+ * set with the asynchronous operation's result. For example:
+ *
+ * @code template <typename Handler>
+ * void my_coroutine(basic_yield_context<Handler> yield)
+ * {
+ * ...
+ * std::size_t n = my_socket.async_read_some(buffer, yield[ec]);
+ * if (ec)
+ * {
+ * // An error occurred.
+ * }
+ * ...
+ * } @endcode
+ */
+ basic_yield_context operator[](boost::system::error_code& ec) const
+ {
+ basic_yield_context tmp(*this);
+ tmp.ec_ = &ec;
+ return tmp;
+ }
+
+#if defined(GENERATING_DOCUMENTATION)
+private:
+#endif // defined(GENERATING_DOCUMENTATION)
+ detail::weak_ptr<callee_type> coro_;
+ caller_type& ca_;
+ Handler& handler_;
+ boost::system::error_code* ec_;
+};
+
+#if defined(GENERATING_DOCUMENTATION)
+/// Context object that represents the currently executing coroutine.
+typedef basic_yield_context<unspecified> yield_context;
+#else // defined(GENERATING_DOCUMENTATION)
+typedef basic_yield_context<
+ detail::wrapped_handler<
+ io_service::strand, void(*)(),
+ detail::is_continuation_if_running> > yield_context;
+#endif // defined(GENERATING_DOCUMENTATION)
+
+/**
+ * @defgroup spawn boost::asio::spawn
+ *
+ * @brief Start a new stackful coroutine.
+ *
+ * The spawn() function is a high-level wrapper over the Boost.Coroutine
+ * library. This function enables programs to implement asynchronous logic in a
+ * synchronous manner, as illustrated by the following example:
+ *
+ * @code boost::asio::spawn(my_strand, do_echo);
+ *
+ * // ...
+ *
+ * void do_echo(boost::asio::yield_context yield)
+ * {
+ * try
+ * {
+ * char data[128];
+ * for (;;)
+ * {
+ * std::size_t length =
+ * my_socket.async_read_some(
+ * boost::asio::buffer(data), yield);
+ *
+ * boost::asio::async_write(my_socket,
+ * boost::asio::buffer(data, length), yield);
+ * }
+ * }
+ * catch (std::exception& e)
+ * {
+ * // ...
+ * }
+ * } @endcode
+ */
+/*@{*/
+
+/// Start a new stackful coroutine, calling the specified handler when it
+/// completes.
+/**
+ * This function is used to launch a new coroutine.
+ *
+ * @param handler A handler to be called when the coroutine exits. More
+ * importantly, the handler provides an execution context (via the the handler
+ * invocation hook) for the coroutine. The handler must have the signature:
+ * @code void handler(); @endcode
+ *
+ * @param function The coroutine function. The function must have the signature:
+ * @code void function(basic_yield_context<Handler> yield); @endcode
+ *
+ * @param attributes Boost.Coroutine attributes used to customise the coroutine.
+ */
+template <typename Handler, typename Function>
+void spawn(BOOST_ASIO_MOVE_ARG(Handler) handler,
+ BOOST_ASIO_MOVE_ARG(Function) function,
+ const boost::coroutines::attributes& attributes
+ = boost::coroutines::attributes());
+
+/// Start a new stackful coroutine, inheriting the execution context of another.
+/**
+ * This function is used to launch a new coroutine.
+ *
+ * @param ctx Identifies the current coroutine as a parent of the new
+ * coroutine. This specifies that the new coroutine should inherit the
+ * execution context of the parent. For example, if the parent coroutine is
+ * executing in a particular strand, then the new coroutine will execute in the
+ * same strand.
+ *
+ * @param function The coroutine function. The function must have the signature:
+ * @code void function(basic_yield_context<Handler> yield); @endcode
+ *
+ * @param attributes Boost.Coroutine attributes used to customise the coroutine.
+ */
+template <typename Handler, typename Function>
+void spawn(basic_yield_context<Handler> ctx,
+ BOOST_ASIO_MOVE_ARG(Function) function,
+ const boost::coroutines::attributes& attributes
+ = boost::coroutines::attributes());
+
+/// Start a new stackful coroutine that executes in the context of a strand.
+/**
+ * This function is used to launch a new coroutine.
+ *
+ * @param strand Identifies a strand. By starting multiple coroutines on the
+ * same strand, the implementation ensures that none of those coroutines can
+ * execute simultaneously.
+ *
+ * @param function The coroutine function. The function must have the signature:
+ * @code void function(yield_context yield); @endcode
+ *
+ * @param attributes Boost.Coroutine attributes used to customise the coroutine.
+ */
+template <typename Function>
+void spawn(boost::asio::io_service::strand strand,
+ BOOST_ASIO_MOVE_ARG(Function) function,
+ const boost::coroutines::attributes& attributes
+ = boost::coroutines::attributes());
+
+/// Start a new stackful coroutine that executes on a given io_service.
+/**
+ * This function is used to launch a new coroutine.
+ *
+ * @param io_service Identifies the io_service that will run the coroutine. The
+ * new coroutine is implicitly given its own strand within this io_service.
+ *
+ * @param function The coroutine function. The function must have the signature:
+ * @code void function(yield_context yield); @endcode
+ *
+ * @param attributes Boost.Coroutine attributes used to customise the coroutine.
+ */
+template <typename Function>
+void spawn(boost::asio::io_service& io_service,
+ BOOST_ASIO_MOVE_ARG(Function) function,
+ const boost::coroutines::attributes& attributes
+ = boost::coroutines::attributes());
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/spawn.hpp>
+
+#endif // BOOST_ASIO_SPAWN_HPP
diff --git a/ext/patches/boost/asio/ssl.hpp b/ext/patches/boost/asio/ssl.hpp
new file mode 100644
index 0000000..9c09a0a
--- /dev/null
+++ b/ext/patches/boost/asio/ssl.hpp
@@ -0,0 +1,30 @@
+//
+// ssl.hpp
+// ~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_HPP
+#define BOOST_ASIO_SSL_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/ssl/basic_context.hpp>
+#include <boost/asio/ssl/context.hpp>
+#include <boost/asio/ssl/context_base.hpp>
+#include <boost/asio/ssl/context_service.hpp>
+#include <boost/asio/ssl/error.hpp>
+#include <boost/asio/ssl/rfc2818_verification.hpp>
+#include <boost/asio/ssl/stream.hpp>
+#include <boost/asio/ssl/stream_base.hpp>
+#include <boost/asio/ssl/stream_service.hpp>
+#include <boost/asio/ssl/verify_context.hpp>
+#include <boost/asio/ssl/verify_mode.hpp>
+
+#endif // BOOST_ASIO_SSL_HPP
diff --git a/ext/patches/boost/asio/ssl/basic_context.hpp b/ext/patches/boost/asio/ssl/basic_context.hpp
new file mode 100644
index 0000000..7f58e53
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/basic_context.hpp
@@ -0,0 +1,42 @@
+//
+// ssl/basic_context.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_BASIC_CONTEXT_HPP
+#define BOOST_ASIO_SSL_BASIC_CONTEXT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/old/basic_context.hpp>
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+using boost::asio::ssl::old::basic_context;
+
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_BASIC_CONTEXT_HPP
diff --git a/ext/patches/boost/asio/ssl/context.hpp b/ext/patches/boost/asio/ssl/context.hpp
new file mode 100644
index 0000000..4390c00
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/context.hpp
@@ -0,0 +1,789 @@
+//
+// ssl/context.hpp
+// ~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_CONTEXT_HPP
+#define BOOST_ASIO_SSL_CONTEXT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/basic_context.hpp>
+# include <boost/asio/ssl/context_service.hpp>
+#else // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <string>
+# include <boost/asio/buffer.hpp>
+# include <boost/asio/io_service.hpp>
+# include <boost/asio/ssl/context_base.hpp>
+# include <boost/asio/ssl/detail/openssl_types.hpp>
+# include <boost/asio/ssl/detail/openssl_init.hpp>
+# include <boost/asio/ssl/detail/password_callback.hpp>
+# include <boost/asio/ssl/detail/verify_callback.hpp>
+# include <boost/asio/ssl/verify_mode.hpp>
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+/// Typedef for the typical usage of context.
+typedef basic_context<context_service> context;
+
+#else // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+class context
+ : public context_base,
+ private noncopyable
+{
+public:
+ /// The native handle type of the SSL context.
+ typedef SSL_CTX* native_handle_type;
+
+ /// (Deprecated: Use native_handle_type.) The native type of the SSL context.
+ typedef SSL_CTX* impl_type;
+
+ /// Constructor.
+ BOOST_ASIO_DECL explicit context(method m);
+
+ /// Deprecated constructor taking a reference to an io_service object.
+ BOOST_ASIO_DECL context(boost::asio::io_service&, method m);
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a context from another.
+ /**
+ * This constructor moves an SSL context from one object to another.
+ *
+ * @param other The other context object from which the move will occur.
+ *
+ * @note Following the move, the following operations only are valid for the
+ * moved-from object:
+ * @li Destruction.
+ * @li As a target for move-assignment.
+ */
+ BOOST_ASIO_DECL context(context&& other);
+
+ /// Move-assign a context from another.
+ /**
+ * This assignment operator moves an SSL context from one object to another.
+ *
+ * @param other The other context object from which the move will occur.
+ *
+ * @note Following the move, the following operations only are valid for the
+ * moved-from object:
+ * @li Destruction.
+ * @li As a target for move-assignment.
+ */
+ BOOST_ASIO_DECL context& operator=(context&& other);
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destructor.
+ BOOST_ASIO_DECL ~context();
+
+ /// Get the underlying implementation in the native type.
+ /**
+ * This function may be used to obtain the underlying implementation of the
+ * context. This is intended to allow access to context functionality that is
+ * not otherwise provided.
+ */
+ BOOST_ASIO_DECL native_handle_type native_handle();
+
+ /// (Deprecated: Use native_handle().) Get the underlying implementation in
+ /// the native type.
+ /**
+ * This function may be used to obtain the underlying implementation of the
+ * context. This is intended to allow access to context functionality that is
+ * not otherwise provided.
+ */
+ BOOST_ASIO_DECL impl_type impl();
+
+ /// Clear options on the context.
+ /**
+ * This function may be used to configure the SSL options used by the context.
+ *
+ * @param o A bitmask of options. The available option values are defined in
+ * the context_base class. The specified options, if currently enabled on the
+ * context, are cleared.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_clear_options.
+ */
+ BOOST_ASIO_DECL void clear_options(options o);
+
+ /// Clear options on the context.
+ /**
+ * This function may be used to configure the SSL options used by the context.
+ *
+ * @param o A bitmask of options. The available option values are defined in
+ * the context_base class. The specified options, if currently enabled on the
+ * context, are cleared.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_clear_options.
+ */
+ BOOST_ASIO_DECL boost::system::error_code clear_options(options o,
+ boost::system::error_code& ec);
+
+ /// Set options on the context.
+ /**
+ * This function may be used to configure the SSL options used by the context.
+ *
+ * @param o A bitmask of options. The available option values are defined in
+ * the context_base class. The options are bitwise-ored with any existing
+ * value for the options.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_set_options.
+ */
+ BOOST_ASIO_DECL void set_options(options o);
+
+ /// Set options on the context.
+ /**
+ * This function may be used to configure the SSL options used by the context.
+ *
+ * @param o A bitmask of options. The available option values are defined in
+ * the context_base class. The options are bitwise-ored with any existing
+ * value for the options.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_set_options.
+ */
+ BOOST_ASIO_DECL boost::system::error_code set_options(options o,
+ boost::system::error_code& ec);
+
+ /// Set the peer verification mode.
+ /**
+ * This function may be used to configure the peer verification mode used by
+ * the context.
+ *
+ * @param v A bitmask of peer verification modes. See @ref verify_mode for
+ * available values.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_set_verify.
+ */
+ BOOST_ASIO_DECL void set_verify_mode(verify_mode v);
+
+ /// Set the peer verification mode.
+ /**
+ * This function may be used to configure the peer verification mode used by
+ * the context.
+ *
+ * @param v A bitmask of peer verification modes. See @ref verify_mode for
+ * available values.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_set_verify.
+ */
+ BOOST_ASIO_DECL boost::system::error_code set_verify_mode(
+ verify_mode v, boost::system::error_code& ec);
+
+ /// Set the peer verification depth.
+ /**
+ * This function may be used to configure the maximum verification depth
+ * allowed by the context.
+ *
+ * @param depth Maximum depth for the certificate chain verification that
+ * shall be allowed.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_set_verify_depth.
+ */
+ BOOST_ASIO_DECL void set_verify_depth(int depth);
+
+ /// Set the peer verification depth.
+ /**
+ * This function may be used to configure the maximum verification depth
+ * allowed by the context.
+ *
+ * @param depth Maximum depth for the certificate chain verification that
+ * shall be allowed.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_set_verify_depth.
+ */
+ BOOST_ASIO_DECL boost::system::error_code set_verify_depth(
+ int depth, boost::system::error_code& ec);
+
+ /// Set the callback used to verify peer certificates.
+ /**
+ * This function is used to specify a callback function that will be called
+ * by the implementation when it needs to verify a peer certificate.
+ *
+ * @param callback The function object to be used for verifying a certificate.
+ * The function signature of the handler must be:
+ * @code bool verify_callback(
+ * bool preverified, // True if the certificate passed pre-verification.
+ * verify_context& ctx // The peer certificate and other context.
+ * ); @endcode
+ * The return value of the callback is true if the certificate has passed
+ * verification, false otherwise.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_set_verify.
+ */
+ template <typename VerifyCallback>
+ void set_verify_callback(VerifyCallback callback);
+
+ /// Set the callback used to verify peer certificates.
+ /**
+ * This function is used to specify a callback function that will be called
+ * by the implementation when it needs to verify a peer certificate.
+ *
+ * @param callback The function object to be used for verifying a certificate.
+ * The function signature of the handler must be:
+ * @code bool verify_callback(
+ * bool preverified, // True if the certificate passed pre-verification.
+ * verify_context& ctx // The peer certificate and other context.
+ * ); @endcode
+ * The return value of the callback is true if the certificate has passed
+ * verification, false otherwise.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_set_verify.
+ */
+ template <typename VerifyCallback>
+ boost::system::error_code set_verify_callback(VerifyCallback callback,
+ boost::system::error_code& ec);
+
+ /// Load a certification authority file for performing verification.
+ /**
+ * This function is used to load one or more trusted certification authorities
+ * from a file.
+ *
+ * @param filename The name of a file containing certification authority
+ * certificates in PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_load_verify_locations.
+ */
+ BOOST_ASIO_DECL void load_verify_file(const std::string& filename);
+
+ /// Load a certification authority file for performing verification.
+ /**
+ * This function is used to load the certificates for one or more trusted
+ * certification authorities from a file.
+ *
+ * @param filename The name of a file containing certification authority
+ * certificates in PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_load_verify_locations.
+ */
+ BOOST_ASIO_DECL boost::system::error_code load_verify_file(
+ const std::string& filename, boost::system::error_code& ec);
+
+ /// Add certification authority for performing verification.
+ /**
+ * This function is used to add one trusted certification authority
+ * from a memory buffer.
+ *
+ * @param ca The buffer containing the certification authority certificate.
+ * The certificate must use the PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_get_cert_store and @c X509_STORE_add_cert.
+ */
+ BOOST_ASIO_DECL void add_certificate_authority(const const_buffer& ca);
+
+ /// Add certification authority for performing verification.
+ /**
+ * This function is used to add one trusted certification authority
+ * from a memory buffer.
+ *
+ * @param ca The buffer containing the certification authority certificate.
+ * The certificate must use the PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_get_cert_store and @c X509_STORE_add_cert.
+ */
+ BOOST_ASIO_DECL boost::system::error_code add_certificate_authority(
+ const const_buffer& ca, boost::system::error_code& ec);
+
+ /// Configures the context to use the default directories for finding
+ /// certification authority certificates.
+ /**
+ * This function specifies that the context should use the default,
+ * system-dependent directories for locating certification authority
+ * certificates.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_set_default_verify_paths.
+ */
+ BOOST_ASIO_DECL void set_default_verify_paths();
+
+ /// Configures the context to use the default directories for finding
+ /// certification authority certificates.
+ /**
+ * This function specifies that the context should use the default,
+ * system-dependent directories for locating certification authority
+ * certificates.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_set_default_verify_paths.
+ */
+ BOOST_ASIO_DECL boost::system::error_code set_default_verify_paths(
+ boost::system::error_code& ec);
+
+ /// Add a directory containing certificate authority files to be used for
+ /// performing verification.
+ /**
+ * This function is used to specify the name of a directory containing
+ * certification authority certificates. Each file in the directory must
+ * contain a single certificate. The files must be named using the subject
+ * name's hash and an extension of ".0".
+ *
+ * @param path The name of a directory containing the certificates.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_load_verify_locations.
+ */
+ BOOST_ASIO_DECL void add_verify_path(const std::string& path);
+
+ /// Add a directory containing certificate authority files to be used for
+ /// performing verification.
+ /**
+ * This function is used to specify the name of a directory containing
+ * certification authority certificates. Each file in the directory must
+ * contain a single certificate. The files must be named using the subject
+ * name's hash and an extension of ".0".
+ *
+ * @param path The name of a directory containing the certificates.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_load_verify_locations.
+ */
+ BOOST_ASIO_DECL boost::system::error_code add_verify_path(
+ const std::string& path, boost::system::error_code& ec);
+
+ /// Use a certificate from a memory buffer.
+ /**
+ * This function is used to load a certificate into the context from a buffer.
+ *
+ * @param certificate The buffer containing the certificate.
+ *
+ * @param format The certificate format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_use_certificate or SSL_CTX_use_certificate_ASN1.
+ */
+ BOOST_ASIO_DECL void use_certificate(
+ const const_buffer& certificate, file_format format);
+
+ /// Use a certificate from a memory buffer.
+ /**
+ * This function is used to load a certificate into the context from a buffer.
+ *
+ * @param certificate The buffer containing the certificate.
+ *
+ * @param format The certificate format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_use_certificate or SSL_CTX_use_certificate_ASN1.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_certificate(
+ const const_buffer& certificate, file_format format,
+ boost::system::error_code& ec);
+
+ /// Use a certificate from a file.
+ /**
+ * This function is used to load a certificate into the context from a file.
+ *
+ * @param filename The name of the file containing the certificate.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_use_certificate_file.
+ */
+ BOOST_ASIO_DECL void use_certificate_file(
+ const std::string& filename, file_format format);
+
+ /// Use a certificate from a file.
+ /**
+ * This function is used to load a certificate into the context from a file.
+ *
+ * @param filename The name of the file containing the certificate.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_use_certificate_file.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_certificate_file(
+ const std::string& filename, file_format format,
+ boost::system::error_code& ec);
+
+ /// Use a certificate chain from a memory buffer.
+ /**
+ * This function is used to load a certificate chain into the context from a
+ * buffer.
+ *
+ * @param chain The buffer containing the certificate chain. The certificate
+ * chain must use the PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_use_certificate and SSL_CTX_add_extra_chain_cert.
+ */
+ BOOST_ASIO_DECL void use_certificate_chain(const const_buffer& chain);
+
+ /// Use a certificate chain from a memory buffer.
+ /**
+ * This function is used to load a certificate chain into the context from a
+ * buffer.
+ *
+ * @param chain The buffer containing the certificate chain. The certificate
+ * chain must use the PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_use_certificate and SSL_CTX_add_extra_chain_cert.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_certificate_chain(
+ const const_buffer& chain, boost::system::error_code& ec);
+
+ /// Use a certificate chain from a file.
+ /**
+ * This function is used to load a certificate chain into the context from a
+ * file.
+ *
+ * @param filename The name of the file containing the certificate. The file
+ * must use the PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_use_certificate_chain_file.
+ */
+ BOOST_ASIO_DECL void use_certificate_chain_file(const std::string& filename);
+
+ /// Use a certificate chain from a file.
+ /**
+ * This function is used to load a certificate chain into the context from a
+ * file.
+ *
+ * @param filename The name of the file containing the certificate. The file
+ * must use the PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_use_certificate_chain_file.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_certificate_chain_file(
+ const std::string& filename, boost::system::error_code& ec);
+
+ /// Use a private key from a memory buffer.
+ /**
+ * This function is used to load a private key into the context from a buffer.
+ *
+ * @param private_key The buffer containing the private key.
+ *
+ * @param format The private key format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_use_PrivateKey or SSL_CTX_use_PrivateKey_ASN1.
+ */
+ BOOST_ASIO_DECL void use_private_key(
+ const const_buffer& private_key, file_format format);
+
+ /// Use a private key from a memory buffer.
+ /**
+ * This function is used to load a private key into the context from a buffer.
+ *
+ * @param private_key The buffer containing the private key.
+ *
+ * @param format The private key format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_use_PrivateKey or SSL_CTX_use_PrivateKey_ASN1.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_private_key(
+ const const_buffer& private_key, file_format format,
+ boost::system::error_code& ec);
+
+ /// Use a private key from a file.
+ /**
+ * This function is used to load a private key into the context from a file.
+ *
+ * @param filename The name of the file containing the private key.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_use_PrivateKey_file.
+ */
+ BOOST_ASIO_DECL void use_private_key_file(
+ const std::string& filename, file_format format);
+
+ /// Use a private key from a file.
+ /**
+ * This function is used to load a private key into the context from a file.
+ *
+ * @param filename The name of the file containing the private key.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_use_PrivateKey_file.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_private_key_file(
+ const std::string& filename, file_format format,
+ boost::system::error_code& ec);
+
+ /// Use an RSA private key from a memory buffer.
+ /**
+ * This function is used to load an RSA private key into the context from a
+ * buffer.
+ *
+ * @param private_key The buffer containing the RSA private key.
+ *
+ * @param format The private key format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_use_RSAPrivateKey or SSL_CTX_use_RSAPrivateKey_ASN1.
+ */
+ BOOST_ASIO_DECL void use_rsa_private_key(
+ const const_buffer& private_key, file_format format);
+
+ /// Use an RSA private key from a memory buffer.
+ /**
+ * This function is used to load an RSA private key into the context from a
+ * buffer.
+ *
+ * @param private_key The buffer containing the RSA private key.
+ *
+ * @param format The private key format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_use_RSAPrivateKey or SSL_CTX_use_RSAPrivateKey_ASN1.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_rsa_private_key(
+ const const_buffer& private_key, file_format format,
+ boost::system::error_code& ec);
+
+ /// Use an RSA private key from a file.
+ /**
+ * This function is used to load an RSA private key into the context from a
+ * file.
+ *
+ * @param filename The name of the file containing the RSA private key.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_use_RSAPrivateKey_file.
+ */
+ BOOST_ASIO_DECL void use_rsa_private_key_file(
+ const std::string& filename, file_format format);
+
+ /// Use an RSA private key from a file.
+ /**
+ * This function is used to load an RSA private key into the context from a
+ * file.
+ *
+ * @param filename The name of the file containing the RSA private key.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_use_RSAPrivateKey_file.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_rsa_private_key_file(
+ const std::string& filename, file_format format,
+ boost::system::error_code& ec);
+
+ /// Use the specified memory buffer to obtain the temporary Diffie-Hellman
+ /// parameters.
+ /**
+ * This function is used to load Diffie-Hellman parameters into the context
+ * from a buffer.
+ *
+ * @param dh The memory buffer containing the Diffie-Hellman parameters. The
+ * buffer must use the PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_set_tmp_dh.
+ */
+ BOOST_ASIO_DECL void use_tmp_dh(const const_buffer& dh);
+
+ /// Use the specified memory buffer to obtain the temporary Diffie-Hellman
+ /// parameters.
+ /**
+ * This function is used to load Diffie-Hellman parameters into the context
+ * from a buffer.
+ *
+ * @param dh The memory buffer containing the Diffie-Hellman parameters. The
+ * buffer must use the PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_set_tmp_dh.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_tmp_dh(
+ const const_buffer& dh, boost::system::error_code& ec);
+
+ /// Use the specified file to obtain the temporary Diffie-Hellman parameters.
+ /**
+ * This function is used to load Diffie-Hellman parameters into the context
+ * from a file.
+ *
+ * @param filename The name of the file containing the Diffie-Hellman
+ * parameters. The file must use the PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_set_tmp_dh.
+ */
+ BOOST_ASIO_DECL void use_tmp_dh_file(const std::string& filename);
+
+ /// Use the specified file to obtain the temporary Diffie-Hellman parameters.
+ /**
+ * This function is used to load Diffie-Hellman parameters into the context
+ * from a file.
+ *
+ * @param filename The name of the file containing the Diffie-Hellman
+ * parameters. The file must use the PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_set_tmp_dh.
+ */
+ BOOST_ASIO_DECL boost::system::error_code use_tmp_dh_file(
+ const std::string& filename, boost::system::error_code& ec);
+
+ /// Set the password callback.
+ /**
+ * This function is used to specify a callback function to obtain password
+ * information about an encrypted key in PEM format.
+ *
+ * @param callback The function object to be used for obtaining the password.
+ * The function signature of the handler must be:
+ * @code std::string password_callback(
+ * std::size_t max_length, // The maximum size for a password.
+ * password_purpose purpose // Whether password is for reading or writing.
+ * ); @endcode
+ * The return value of the callback is a string containing the password.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_CTX_set_default_passwd_cb.
+ */
+ template <typename PasswordCallback>
+ void set_password_callback(PasswordCallback callback);
+
+ /// Set the password callback.
+ /**
+ * This function is used to specify a callback function to obtain password
+ * information about an encrypted key in PEM format.
+ *
+ * @param callback The function object to be used for obtaining the password.
+ * The function signature of the handler must be:
+ * @code std::string password_callback(
+ * std::size_t max_length, // The maximum size for a password.
+ * password_purpose purpose // Whether password is for reading or writing.
+ * ); @endcode
+ * The return value of the callback is a string containing the password.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_CTX_set_default_passwd_cb.
+ */
+ template <typename PasswordCallback>
+ boost::system::error_code set_password_callback(PasswordCallback callback,
+ boost::system::error_code& ec);
+
+private:
+ struct bio_cleanup;
+ struct x509_cleanup;
+ struct evp_pkey_cleanup;
+ struct rsa_cleanup;
+ struct dh_cleanup;
+
+ // Helper function used to set a peer certificate verification callback.
+ BOOST_ASIO_DECL boost::system::error_code do_set_verify_callback(
+ detail::verify_callback_base* callback, boost::system::error_code& ec);
+
+ // Callback used when the SSL implementation wants to verify a certificate.
+ BOOST_ASIO_DECL static int verify_callback_function(
+ int preverified, X509_STORE_CTX* ctx);
+
+ // Helper function used to set a password callback.
+ BOOST_ASIO_DECL boost::system::error_code do_set_password_callback(
+ detail::password_callback_base* callback, boost::system::error_code& ec);
+
+ // Callback used when the SSL implementation wants a password.
+ BOOST_ASIO_DECL static int password_callback_function(
+ char* buf, int size, int purpose, void* data);
+
+ // Helper function to set the temporary Diffie-Hellman parameters from a BIO.
+ BOOST_ASIO_DECL boost::system::error_code do_use_tmp_dh(
+ BIO* bio, boost::system::error_code& ec);
+
+ // Helper function to make a BIO from a memory buffer.
+ BOOST_ASIO_DECL BIO* make_buffer_bio(const const_buffer& b);
+
+ // The underlying native implementation.
+ native_handle_type handle_;
+
+ // Ensure openssl is initialised.
+ boost::asio::ssl::detail::openssl_init<> init_;
+};
+
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/ssl/impl/context.hpp>
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ssl/impl/context.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_SSL_CONTEXT_HPP
diff --git a/ext/patches/boost/asio/ssl/context_base.hpp b/ext/patches/boost/asio/ssl/context_base.hpp
new file mode 100644
index 0000000..6c0d03a
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/context_base.hpp
@@ -0,0 +1,169 @@
+//
+// ssl/context_base.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_CONTEXT_BASE_HPP
+#define BOOST_ASIO_SSL_CONTEXT_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/ssl/detail/openssl_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+/// The context_base class is used as a base for the basic_context class
+/// template so that we have a common place to define various enums.
+class context_base
+{
+public:
+ /// Different methods supported by a context.
+ enum method
+ {
+ /// Generic SSL version 2.
+ sslv2,
+
+ /// SSL version 2 client.
+ sslv2_client,
+
+ /// SSL version 2 server.
+ sslv2_server,
+
+ /// Generic SSL version 3.
+ sslv3,
+
+ /// SSL version 3 client.
+ sslv3_client,
+
+ /// SSL version 3 server.
+ sslv3_server,
+
+ /// Generic TLS version 1.
+ tlsv1,
+
+ /// TLS version 1 client.
+ tlsv1_client,
+
+ /// TLS version 1 server.
+ tlsv1_server,
+
+ /// Generic SSL/TLS.
+ sslv23,
+
+ /// SSL/TLS client.
+ sslv23_client,
+
+ /// SSL/TLS server.
+ sslv23_server,
+
+ /// Generic TLS version 1.1.
+ tlsv11,
+
+ /// TLS version 1.1 client.
+ tlsv11_client,
+
+ /// TLS version 1.1 server.
+ tlsv11_server,
+
+ /// Generic TLS version 1.2.
+ tlsv12,
+
+ /// TLS version 1.2 client.
+ tlsv12_client,
+
+ /// TLS version 1.2 server.
+ tlsv12_server
+ };
+
+ /// Bitmask type for SSL options.
+ typedef long options;
+
+#if defined(GENERATING_DOCUMENTATION)
+ /// Implement various bug workarounds.
+ static const long default_workarounds = implementation_defined;
+
+ /// Always create a new key when using tmp_dh parameters.
+ static const long single_dh_use = implementation_defined;
+
+ /// Disable SSL v2.
+ static const long no_sslv2 = implementation_defined;
+
+ /// Disable SSL v3.
+ static const long no_sslv3 = implementation_defined;
+
+ /// Disable TLS v1.
+ static const long no_tlsv1 = implementation_defined;
+
+ /// Disable compression. Compression is disabled by default.
+ static const long no_compression = implementation_defined;
+#else
+ BOOST_ASIO_STATIC_CONSTANT(long, default_workarounds = SSL_OP_ALL);
+ BOOST_ASIO_STATIC_CONSTANT(long, single_dh_use = SSL_OP_SINGLE_DH_USE);
+ BOOST_ASIO_STATIC_CONSTANT(long, no_sslv2 = SSL_OP_NO_SSLv2);
+ BOOST_ASIO_STATIC_CONSTANT(long, no_sslv3 = SSL_OP_NO_SSLv3);
+ BOOST_ASIO_STATIC_CONSTANT(long, no_tlsv1 = SSL_OP_NO_TLSv1);
+# if defined(SSL_OP_NO_COMPRESSION)
+ BOOST_ASIO_STATIC_CONSTANT(long, no_compression = SSL_OP_NO_COMPRESSION);
+# else // defined(SSL_OP_NO_COMPRESSION)
+ BOOST_ASIO_STATIC_CONSTANT(long, no_compression = 0x20000L);
+# endif // defined(SSL_OP_NO_COMPRESSION)
+#endif
+
+ /// File format types.
+ enum file_format
+ {
+ /// ASN.1 file.
+ asn1,
+
+ /// PEM file.
+ pem
+ };
+
+#if !defined(GENERATING_DOCUMENTATION)
+ // The following types and constants are preserved for backward compatibility.
+ // New programs should use the equivalents of the same names that are defined
+ // in the boost::asio::ssl namespace.
+ typedef int verify_mode;
+ BOOST_ASIO_STATIC_CONSTANT(int, verify_none = SSL_VERIFY_NONE);
+ BOOST_ASIO_STATIC_CONSTANT(int, verify_peer = SSL_VERIFY_PEER);
+ BOOST_ASIO_STATIC_CONSTANT(int,
+ verify_fail_if_no_peer_cert = SSL_VERIFY_FAIL_IF_NO_PEER_CERT);
+ BOOST_ASIO_STATIC_CONSTANT(int, verify_client_once = SSL_VERIFY_CLIENT_ONCE);
+#endif
+
+ /// Purpose of PEM password.
+ enum password_purpose
+ {
+ /// The password is needed for reading/decryption.
+ for_reading,
+
+ /// The password is needed for writing/encryption.
+ for_writing
+ };
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~context_base()
+ {
+ }
+};
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_CONTEXT_BASE_HPP
diff --git a/ext/patches/boost/asio/ssl/context_service.hpp b/ext/patches/boost/asio/ssl/context_service.hpp
new file mode 100644
index 0000000..0df119c
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/context_service.hpp
@@ -0,0 +1,42 @@
+//
+// ssl/context_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_CONTEXT_SERVICE_HPP
+#define BOOST_ASIO_SSL_CONTEXT_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/old/context_service.hpp>
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+using boost::asio::ssl::old::context_service;
+
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_CONTEXT_SERVICE_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/buffered_handshake_op.hpp b/ext/patches/boost/asio/ssl/detail/buffered_handshake_op.hpp
new file mode 100644
index 0000000..ce98311
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/buffered_handshake_op.hpp
@@ -0,0 +1,112 @@
+//
+// ssl/detail/buffered_handshake_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_BUFFERED_HANDSHAKE_OP_HPP
+#define BOOST_ASIO_SSL_DETAIL_BUFFERED_HANDSHAKE_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/detail/engine.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+template <typename ConstBufferSequence>
+class buffered_handshake_op
+{
+public:
+ buffered_handshake_op(stream_base::handshake_type type,
+ const ConstBufferSequence& buffers)
+ : type_(type),
+ buffers_(buffers),
+ total_buffer_size_(boost::asio::buffer_size(buffers_))
+ {
+ }
+
+ engine::want operator()(engine& eng,
+ boost::system::error_code& ec,
+ std::size_t& bytes_transferred) const
+ {
+ typename ConstBufferSequence::const_iterator iter = buffers_.begin();
+ typename ConstBufferSequence::const_iterator end = buffers_.end();
+ std::size_t accumulated_size = 0;
+
+ for (;;)
+ {
+ engine::want want = eng.handshake(type_, ec);
+ if (want != engine::want_input_and_retry
+ || bytes_transferred == total_buffer_size_)
+ return want;
+
+ // Find the next buffer piece to be fed to the engine.
+ while (iter != end)
+ {
+ const_buffer buffer(*iter);
+
+ // Skip over any buffers which have already been consumed by the engine.
+ if (bytes_transferred >= accumulated_size + buffer_size(buffer))
+ {
+ accumulated_size += buffer_size(buffer);
+ ++iter;
+ continue;
+ }
+
+ // The current buffer may have been partially consumed by the engine on
+ // a previous iteration. If so, adjust the buffer to point to the
+ // unused portion.
+ if (bytes_transferred > accumulated_size)
+ buffer = buffer + (bytes_transferred - accumulated_size);
+
+ // Pass the buffer to the engine, and update the bytes transferred to
+ // reflect the total number of bytes consumed so far.
+ bytes_transferred += buffer_size(buffer);
+ buffer = eng.put_input(buffer);
+ bytes_transferred -= buffer_size(buffer);
+ break;
+ }
+ }
+ }
+
+ template <typename Handler>
+ void call_handler(Handler& handler,
+ const boost::system::error_code& ec,
+ const std::size_t& bytes_transferred) const
+ {
+ handler(ec, bytes_transferred);
+ }
+
+private:
+ stream_base::handshake_type type_;
+ ConstBufferSequence buffers_;
+ std::size_t total_buffer_size_;
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_BUFFERED_HANDSHAKE_OP_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/engine.hpp b/ext/patches/boost/asio/ssl/detail/engine.hpp
new file mode 100644
index 0000000..6964d3d
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/engine.hpp
@@ -0,0 +1,166 @@
+//
+// ssl/detail/engine.hpp
+// ~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_ENGINE_HPP
+#define BOOST_ASIO_SSL_DETAIL_ENGINE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/buffer.hpp>
+# include <boost/asio/detail/static_mutex.hpp>
+# include <boost/asio/ssl/detail/openssl_types.hpp>
+# include <boost/asio/ssl/detail/verify_callback.hpp>
+# include <boost/asio/ssl/stream_base.hpp>
+# include <boost/asio/ssl/verify_mode.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+class engine
+{
+public:
+ enum want
+ {
+ // Returned by functions to indicate that the engine wants input. The input
+ // buffer should be updated to point to the data. The engine then needs to
+ // be called again to retry the operation.
+ want_input_and_retry = -2,
+
+ // Returned by functions to indicate that the engine wants to write output.
+ // The output buffer points to the data to be written. The engine then
+ // needs to be called again to retry the operation.
+ want_output_and_retry = -1,
+
+ // Returned by functions to indicate that the engine doesn't need input or
+ // output.
+ want_nothing = 0,
+
+ // Returned by functions to indicate that the engine wants to write output.
+ // The output buffer points to the data to be written. After that the
+ // operation is complete, and the engine does not need to be called again.
+ want_output = 1
+ };
+
+ // Construct a new engine for the specified context.
+ BOOST_ASIO_DECL explicit engine(SSL_CTX* context);
+
+ // Destructor.
+ BOOST_ASIO_DECL ~engine();
+
+ // Get the underlying implementation in the native type.
+ BOOST_ASIO_DECL SSL* native_handle();
+
+ // Set the peer verification mode.
+ BOOST_ASIO_DECL boost::system::error_code set_verify_mode(
+ verify_mode v, boost::system::error_code& ec);
+
+ // Set the peer verification depth.
+ BOOST_ASIO_DECL boost::system::error_code set_verify_depth(
+ int depth, boost::system::error_code& ec);
+
+ // Set a peer certificate verification callback.
+ BOOST_ASIO_DECL boost::system::error_code set_verify_callback(
+ verify_callback_base* callback, boost::system::error_code& ec);
+
+ // Perform an SSL handshake using either SSL_connect (client-side) or
+ // SSL_accept (server-side).
+ BOOST_ASIO_DECL want handshake(
+ stream_base::handshake_type type, boost::system::error_code& ec);
+
+ // Perform a graceful shutdown of the SSL session.
+ BOOST_ASIO_DECL want shutdown(boost::system::error_code& ec);
+
+ // Write bytes to the SSL session.
+ BOOST_ASIO_DECL want write(const boost::asio::const_buffer& data,
+ boost::system::error_code& ec, std::size_t& bytes_transferred);
+
+ // Read bytes from the SSL session.
+ BOOST_ASIO_DECL want read(const boost::asio::mutable_buffer& data,
+ boost::system::error_code& ec, std::size_t& bytes_transferred);
+
+ // Get output data to be written to the transport.
+ BOOST_ASIO_DECL boost::asio::mutable_buffers_1 get_output(
+ const boost::asio::mutable_buffer& data);
+
+ // Put input data that was read from the transport.
+ BOOST_ASIO_DECL boost::asio::const_buffer put_input(
+ const boost::asio::const_buffer& data);
+
+ // Map an error::eof code returned by the underlying transport according to
+ // the type and state of the SSL session. Returns a const reference to the
+ // error code object, suitable for passing to a completion handler.
+ BOOST_ASIO_DECL const boost::system::error_code& map_error_code(
+ boost::system::error_code& ec) const;
+
+private:
+ // Disallow copying and assignment.
+ engine(const engine&);
+ engine& operator=(const engine&);
+
+ // Callback used when the SSL implementation wants to verify a certificate.
+ BOOST_ASIO_DECL static int verify_callback_function(
+ int preverified, X509_STORE_CTX* ctx);
+
+ // The SSL_accept function may not be thread safe. This mutex is used to
+ // protect all calls to the SSL_accept function.
+ BOOST_ASIO_DECL static boost::asio::detail::static_mutex& accept_mutex();
+
+ // Perform one operation. Returns >= 0 on success or error, want_read if the
+ // operation needs more input, or want_write if it needs to write some output
+ // before the operation can complete.
+ BOOST_ASIO_DECL want perform(int (engine::* op)(void*, std::size_t),
+ void* data, std::size_t length, boost::system::error_code& ec,
+ std::size_t* bytes_transferred);
+
+ // Adapt the SSL_accept function to the signature needed for perform().
+ BOOST_ASIO_DECL int do_accept(void*, std::size_t);
+
+ // Adapt the SSL_connect function to the signature needed for perform().
+ BOOST_ASIO_DECL int do_connect(void*, std::size_t);
+
+ // Adapt the SSL_shutdown function to the signature needed for perform().
+ BOOST_ASIO_DECL int do_shutdown(void*, std::size_t);
+
+ // Adapt the SSL_read function to the signature needed for perform().
+ BOOST_ASIO_DECL int do_read(void* data, std::size_t length);
+
+ // Adapt the SSL_write function to the signature needed for perform().
+ BOOST_ASIO_DECL int do_write(void* data, std::size_t length);
+
+ SSL* ssl_;
+ BIO* ext_bio_;
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ssl/detail/impl/engine.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_SSL_DETAIL_ENGINE_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/handshake_op.hpp b/ext/patches/boost/asio/ssl/detail/handshake_op.hpp
new file mode 100644
index 0000000..a962f42
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/handshake_op.hpp
@@ -0,0 +1,70 @@
+//
+// ssl/detail/handshake_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_HANDSHAKE_OP_HPP
+#define BOOST_ASIO_SSL_DETAIL_HANDSHAKE_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/detail/engine.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+class handshake_op
+{
+public:
+ handshake_op(stream_base::handshake_type type)
+ : type_(type)
+ {
+ }
+
+ engine::want operator()(engine& eng,
+ boost::system::error_code& ec,
+ std::size_t& bytes_transferred) const
+ {
+ bytes_transferred = 0;
+ return eng.handshake(type_, ec);
+ }
+
+ template <typename Handler>
+ void call_handler(Handler& handler,
+ const boost::system::error_code& ec,
+ const std::size_t&) const
+ {
+ handler(ec);
+ }
+
+private:
+ stream_base::handshake_type type_;
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_HANDSHAKE_OP_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/impl/engine.ipp b/ext/patches/boost/asio/ssl/detail/impl/engine.ipp
new file mode 100644
index 0000000..8587a66
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/impl/engine.ipp
@@ -0,0 +1,328 @@
+//
+// ssl/detail/impl/engine.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_IMPL_ENGINE_IPP
+#define BOOST_ASIO_SSL_DETAIL_IMPL_ENGINE_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/detail/throw_error.hpp>
+# include <boost/asio/error.hpp>
+# include <boost/asio/ssl/detail/engine.hpp>
+# include <boost/asio/ssl/error.hpp>
+# include <boost/asio/ssl/verify_context.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+engine::engine(SSL_CTX* context)
+ : ssl_(::SSL_new(context))
+{
+ if (!ssl_)
+ {
+ boost::system::error_code ec(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ boost::asio::detail::throw_error(ec, "engine");
+ }
+
+ accept_mutex().init();
+
+ ::SSL_set_mode(ssl_, SSL_MODE_ENABLE_PARTIAL_WRITE);
+ ::SSL_set_mode(ssl_, SSL_MODE_ACCEPT_MOVING_WRITE_BUFFER);
+#if defined(SSL_MODE_RELEASE_BUFFERS)
+ ::SSL_set_mode(ssl_, SSL_MODE_RELEASE_BUFFERS);
+#endif // defined(SSL_MODE_RELEASE_BUFFERS)
+
+ ::BIO* int_bio = 0;
+ ::BIO_new_bio_pair(&int_bio, 0, &ext_bio_, 0);
+ ::SSL_set_bio(ssl_, int_bio, int_bio);
+}
+
+engine::~engine()
+{
+ if (SSL_get_app_data(ssl_))
+ {
+ delete static_cast<verify_callback_base*>(SSL_get_app_data(ssl_));
+ SSL_set_app_data(ssl_, 0);
+ }
+
+ ::BIO_free(ext_bio_);
+ ::SSL_free(ssl_);
+}
+
+SSL* engine::native_handle()
+{
+ return ssl_;
+}
+
+boost::system::error_code engine::set_verify_mode(
+ verify_mode v, boost::system::error_code& ec)
+{
+ ::SSL_set_verify(ssl_, v, ::SSL_get_verify_callback(ssl_));
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code engine::set_verify_depth(
+ int depth, boost::system::error_code& ec)
+{
+ ::SSL_set_verify_depth(ssl_, depth);
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+boost::system::error_code engine::set_verify_callback(
+ verify_callback_base* callback, boost::system::error_code& ec)
+{
+ if (SSL_get_app_data(ssl_))
+ delete static_cast<verify_callback_base*>(SSL_get_app_data(ssl_));
+
+ SSL_set_app_data(ssl_, callback);
+
+ ::SSL_set_verify(ssl_, ::SSL_get_verify_mode(ssl_),
+ &engine::verify_callback_function);
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+int engine::verify_callback_function(int preverified, X509_STORE_CTX* ctx)
+{
+ if (ctx)
+ {
+ if (SSL* ssl = static_cast<SSL*>(
+ ::X509_STORE_CTX_get_ex_data(
+ ctx, ::SSL_get_ex_data_X509_STORE_CTX_idx())))
+ {
+ if (SSL_get_app_data(ssl))
+ {
+ verify_callback_base* callback =
+ static_cast<verify_callback_base*>(
+ SSL_get_app_data(ssl));
+
+ verify_context verify_ctx(ctx);
+ return callback->call(preverified != 0, verify_ctx) ? 1 : 0;
+ }
+ }
+ }
+
+ return 0;
+}
+
+engine::want engine::handshake(
+ stream_base::handshake_type type, boost::system::error_code& ec)
+{
+ return perform((type == boost::asio::ssl::stream_base::client)
+ ? &engine::do_connect : &engine::do_accept, 0, 0, ec, 0);
+}
+
+engine::want engine::shutdown(boost::system::error_code& ec)
+{
+ return perform(&engine::do_shutdown, 0, 0, ec, 0);
+}
+
+engine::want engine::write(const boost::asio::const_buffer& data,
+ boost::system::error_code& ec, std::size_t& bytes_transferred)
+{
+ if (boost::asio::buffer_size(data) == 0)
+ {
+ ec = boost::system::error_code();
+ return engine::want_nothing;
+ }
+
+ return perform(&engine::do_write,
+ const_cast<void*>(boost::asio::buffer_cast<const void*>(data)),
+ boost::asio::buffer_size(data), ec, &bytes_transferred);
+}
+
+engine::want engine::read(const boost::asio::mutable_buffer& data,
+ boost::system::error_code& ec, std::size_t& bytes_transferred)
+{
+ if (boost::asio::buffer_size(data) == 0)
+ {
+ ec = boost::system::error_code();
+ return engine::want_nothing;
+ }
+
+ return perform(&engine::do_read,
+ boost::asio::buffer_cast<void*>(data),
+ boost::asio::buffer_size(data), ec, &bytes_transferred);
+}
+
+boost::asio::mutable_buffers_1 engine::get_output(
+ const boost::asio::mutable_buffer& data)
+{
+ int length = ::BIO_read(ext_bio_,
+ boost::asio::buffer_cast<void*>(data),
+ static_cast<int>(boost::asio::buffer_size(data)));
+
+ return boost::asio::buffer(data,
+ length > 0 ? static_cast<std::size_t>(length) : 0);
+}
+
+boost::asio::const_buffer engine::put_input(
+ const boost::asio::const_buffer& data)
+{
+ int length = ::BIO_write(ext_bio_,
+ boost::asio::buffer_cast<const void*>(data),
+ static_cast<int>(boost::asio::buffer_size(data)));
+
+ return boost::asio::buffer(data +
+ (length > 0 ? static_cast<std::size_t>(length) : 0));
+}
+
+const boost::system::error_code& engine::map_error_code(
+ boost::system::error_code& ec) const
+{
+ // We only want to map the error::eof code.
+ if (ec != boost::asio::error::eof)
+ return ec;
+
+ // If there's data yet to be read, it's an error.
+ if (BIO_wpending(ext_bio_))
+ {
+ ec = boost::system::error_code(
+ ERR_PACK(ERR_LIB_SSL, 0, SSL_R_SHORT_READ),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ // SSL v2 doesn't provide a protocol-level shutdown, so an eof on the
+ // underlying transport is passed through.
+ if (ssl_ && ssl_->version == SSL2_VERSION)
+ return ec;
+
+ // Otherwise, the peer should have negotiated a proper shutdown.
+ if ((::SSL_get_shutdown(ssl_) & SSL_RECEIVED_SHUTDOWN) == 0)
+ {
+ ec = boost::system::error_code(
+ ERR_PACK(ERR_LIB_SSL, 0, SSL_R_SHORT_READ),
+ boost::asio::error::get_ssl_category());
+ }
+
+ return ec;
+}
+
+boost::asio::detail::static_mutex& engine::accept_mutex()
+{
+ static boost::asio::detail::static_mutex mutex = BOOST_ASIO_STATIC_MUTEX_INIT;
+ return mutex;
+}
+
+engine::want engine::perform(int (engine::* op)(void*, std::size_t),
+ void* data, std::size_t length, boost::system::error_code& ec,
+ std::size_t* bytes_transferred)
+{
+ std::size_t pending_output_before = ::BIO_ctrl_pending(ext_bio_);
+ int result = (this->*op)(data, length);
+ int ssl_error = ::SSL_get_error(ssl_, result);
+ int sys_error = static_cast<int>(::ERR_get_error());
+ std::size_t pending_output_after = ::BIO_ctrl_pending(ext_bio_);
+
+ if (ssl_error == SSL_ERROR_SSL)
+ {
+ ec = boost::system::error_code(sys_error,
+ boost::asio::error::get_ssl_category());
+ return want_nothing;
+ }
+
+ if (ssl_error == SSL_ERROR_SYSCALL)
+ {
+ ec = boost::system::error_code(sys_error,
+ boost::asio::error::get_system_category());
+ return want_nothing;
+ }
+
+ if (result > 0 && bytes_transferred)
+ *bytes_transferred = static_cast<std::size_t>(result);
+
+ if (ssl_error == SSL_ERROR_WANT_WRITE)
+ {
+ ec = boost::system::error_code();
+ return want_output_and_retry;
+ }
+ else if (pending_output_after > pending_output_before)
+ {
+ ec = boost::system::error_code();
+ return result > 0 ? want_output : want_output_and_retry;
+ }
+ else if (ssl_error == SSL_ERROR_WANT_READ)
+ {
+ ec = boost::system::error_code();
+ return want_input_and_retry;
+ }
+ else if (::SSL_get_shutdown(ssl_) & SSL_RECEIVED_SHUTDOWN)
+ {
+ ec = boost::asio::error::eof;
+ return want_nothing;
+ }
+ else
+ {
+ ec = boost::system::error_code();
+ return want_nothing;
+ }
+}
+
+int engine::do_accept(void*, std::size_t)
+{
+ boost::asio::detail::static_mutex::scoped_lock lock(accept_mutex());
+ return ::SSL_accept(ssl_);
+}
+
+int engine::do_connect(void*, std::size_t)
+{
+ return ::SSL_connect(ssl_);
+}
+
+int engine::do_shutdown(void*, std::size_t)
+{
+ int result = ::SSL_shutdown(ssl_);
+ if (result == 0)
+ result = ::SSL_shutdown(ssl_);
+ return result;
+}
+
+int engine::do_read(void* data, std::size_t length)
+{
+ return ::SSL_read(ssl_, data,
+ length < INT_MAX ? static_cast<int>(length) : INT_MAX);
+}
+
+int engine::do_write(void* data, std::size_t length)
+{
+ return ::SSL_write(ssl_, data,
+ length < INT_MAX ? static_cast<int>(length) : INT_MAX);
+}
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_IMPL_ENGINE_IPP
diff --git a/ext/patches/boost/asio/ssl/detail/impl/openssl_init.ipp b/ext/patches/boost/asio/ssl/detail/impl/openssl_init.ipp
new file mode 100644
index 0000000..906bb5f
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/impl/openssl_init.ipp
@@ -0,0 +1,147 @@
+//
+// ssl/detail/impl/openssl_init.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_IMPL_OPENSSL_INIT_IPP
+#define BOOST_ASIO_SSL_DETAIL_IMPL_OPENSSL_INIT_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <vector>
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/mutex.hpp>
+#include <boost/asio/detail/tss_ptr.hpp>
+#include <boost/asio/ssl/detail/openssl_init.hpp>
+#include <boost/asio/ssl/detail/openssl_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+class openssl_init_base::do_init
+{
+public:
+ do_init()
+ {
+ ::SSL_library_init();
+ ::SSL_load_error_strings();
+ ::OpenSSL_add_all_algorithms();
+
+ mutexes_.resize(::CRYPTO_num_locks());
+ for (size_t i = 0; i < mutexes_.size(); ++i)
+ mutexes_[i].reset(new boost::asio::detail::mutex);
+ ::CRYPTO_set_locking_callback(&do_init::openssl_locking_func);
+ ::CRYPTO_set_id_callback(&do_init::openssl_id_func);
+
+#if !defined(SSL_OP_NO_COMPRESSION) \
+ && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ null_compression_methods_ = sk_SSL_COMP_new_null();
+#endif // !defined(SSL_OP_NO_COMPRESSION)
+ // && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ }
+
+ ~do_init()
+ {
+#if !defined(SSL_OP_NO_COMPRESSION) \
+ && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ sk_SSL_COMP_free(null_compression_methods_);
+#endif // !defined(SSL_OP_NO_COMPRESSION)
+ // && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+
+ ::CRYPTO_set_id_callback(0);
+ ::CRYPTO_set_locking_callback(0);
+ ::ERR_free_strings();
+ ::ERR_remove_state(0);
+ ::EVP_cleanup();
+ ::CRYPTO_cleanup_all_ex_data();
+ ::CONF_modules_unload(1);
+#if !defined(OPENSSL_NO_ENGINE)
+ ::ENGINE_cleanup();
+#endif // !defined(OPENSSL_NO_ENGINE)
+ }
+
+#if !defined(SSL_OP_NO_COMPRESSION) \
+ && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ STACK_OF(SSL_COMP)* get_null_compression_methods() const
+ {
+ return null_compression_methods_;
+ }
+#endif // !defined(SSL_OP_NO_COMPRESSION)
+ // && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+
+private:
+ static unsigned long openssl_id_func()
+ {
+#if defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ return ::GetCurrentThreadId();
+#else // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ void* id = instance()->thread_id_;
+ if (id == 0)
+ instance()->thread_id_ = id = &id; // Ugh.
+ BOOST_ASIO_ASSERT(sizeof(unsigned long) >= sizeof(void*));
+ return reinterpret_cast<unsigned long>(id);
+#endif // defined(BOOST_ASIO_WINDOWS) || defined(__CYGWIN__)
+ }
+
+ static void openssl_locking_func(int mode, int n,
+ const char* /*file*/, int /*line*/)
+ {
+ if (mode & CRYPTO_LOCK)
+ instance()->mutexes_[n]->lock();
+ else
+ instance()->mutexes_[n]->unlock();
+ }
+
+ // Mutexes to be used in locking callbacks.
+ std::vector<boost::asio::detail::shared_ptr<
+ boost::asio::detail::mutex> > mutexes_;
+
+#if !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+ // The thread identifiers to be used by openssl.
+ boost::asio::detail::tss_ptr<void> thread_id_;
+#endif // !defined(BOOST_ASIO_WINDOWS) && !defined(__CYGWIN__)
+
+#if !defined(SSL_OP_NO_COMPRESSION) \
+ && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ STACK_OF(SSL_COMP)* null_compression_methods_;
+#endif // !defined(SSL_OP_NO_COMPRESSION)
+ // && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+};
+
+boost::asio::detail::shared_ptr<openssl_init_base::do_init>
+openssl_init_base::instance()
+{
+ static boost::asio::detail::shared_ptr<do_init> init(new do_init);
+ return init;
+}
+
+#if !defined(SSL_OP_NO_COMPRESSION) \
+ && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+STACK_OF(SSL_COMP)* openssl_init_base::get_null_compression_methods()
+{
+ return instance()->get_null_compression_methods();
+}
+#endif // !defined(SSL_OP_NO_COMPRESSION)
+ // && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_IMPL_OPENSSL_INIT_IPP
diff --git a/ext/patches/boost/asio/ssl/detail/io.hpp b/ext/patches/boost/asio/ssl/detail/io.hpp
new file mode 100644
index 0000000..38bf160
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/io.hpp
@@ -0,0 +1,349 @@
+//
+// ssl/detail/io.hpp
+// ~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_IO_HPP
+#define BOOST_ASIO_SSL_DETAIL_IO_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/detail/engine.hpp>
+# include <boost/asio/ssl/detail/stream_core.hpp>
+# include <boost/asio/write.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+template <typename Stream, typename Operation>
+std::size_t io(Stream& next_layer, stream_core& core,
+ const Operation& op, boost::system::error_code& ec)
+{
+ std::size_t bytes_transferred = 0;
+ do switch (op(core.engine_, ec, bytes_transferred))
+ {
+ case engine::want_input_and_retry:
+
+ // If the input buffer is empty then we need to read some more data from
+ // the underlying transport.
+ if (boost::asio::buffer_size(core.input_) == 0)
+ core.input_ = boost::asio::buffer(core.input_buffer_,
+ next_layer.read_some(core.input_buffer_, ec));
+
+ // Pass the new input data to the engine.
+ core.input_ = core.engine_.put_input(core.input_);
+
+ // Try the operation again.
+ continue;
+
+ case engine::want_output_and_retry:
+
+ // Get output data from the engine and write it to the underlying
+ // transport.
+ boost::asio::write(next_layer,
+ core.engine_.get_output(core.output_buffer_), ec);
+
+ // Try the operation again.
+ continue;
+
+ case engine::want_output:
+
+ // Get output data from the engine and write it to the underlying
+ // transport.
+ boost::asio::write(next_layer,
+ core.engine_.get_output(core.output_buffer_), ec);
+
+ // Operation is complete. Return result to caller.
+ core.engine_.map_error_code(ec);
+ return bytes_transferred;
+
+ default:
+
+ // Operation is complete. Return result to caller.
+ core.engine_.map_error_code(ec);
+ return bytes_transferred;
+
+ } while (!ec);
+
+ // Operation failed. Return result to caller.
+ core.engine_.map_error_code(ec);
+ return 0;
+}
+
+template <typename Stream, typename Operation, typename Handler>
+class io_op
+{
+public:
+ io_op(Stream& next_layer, stream_core& core,
+ const Operation& op, Handler& handler)
+ : next_layer_(next_layer),
+ core_(core),
+ op_(op),
+ start_(0),
+ want_(engine::want_nothing),
+ bytes_transferred_(0),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE)
+ io_op(const io_op& other)
+ : next_layer_(other.next_layer_),
+ core_(other.core_),
+ op_(other.op_),
+ start_(other.start_),
+ want_(other.want_),
+ ec_(other.ec_),
+ bytes_transferred_(other.bytes_transferred_),
+ handler_(other.handler_)
+ {
+ }
+
+ io_op(io_op&& other)
+ : next_layer_(other.next_layer_),
+ core_(other.core_),
+ op_(other.op_),
+ start_(other.start_),
+ want_(other.want_),
+ ec_(other.ec_),
+ bytes_transferred_(other.bytes_transferred_),
+ handler_(BOOST_ASIO_MOVE_CAST(Handler)(other.handler_))
+ {
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE)
+
+ void operator()(boost::system::error_code ec,
+ std::size_t bytes_transferred = ~std::size_t(0), int start = 0)
+ {
+ switch (start_ = start)
+ {
+ case 1: // Called after at least one async operation.
+ do
+ {
+ switch (want_ = op_(core_.engine_, ec_, bytes_transferred_))
+ {
+ case engine::want_input_and_retry:
+
+ // If the input buffer already has data in it we can pass it to the
+ // engine and then retry the operation immediately.
+ if (boost::asio::buffer_size(core_.input_) != 0)
+ {
+ core_.input_ = core_.engine_.put_input(core_.input_);
+ continue;
+ }
+
+ // The engine wants more data to be read from input. However, we
+ // cannot allow more than one read operation at a time on the
+ // underlying transport. The pending_read_ timer's expiry is set to
+ // pos_infin if a read is in progress, and neg_infin otherwise.
+ if (core_.pending_read_.expires_at() == core_.neg_infin())
+ {
+ // Prevent other read operations from being started.
+ core_.pending_read_.expires_at(core_.pos_infin());
+
+ // Start reading some data from the underlying transport.
+ next_layer_.async_read_some(
+ boost::asio::buffer(core_.input_buffer_),
+ BOOST_ASIO_MOVE_CAST(io_op)(*this));
+ }
+ else
+ {
+ // Wait until the current read operation completes.
+ core_.pending_read_.async_wait(BOOST_ASIO_MOVE_CAST(io_op)(*this));
+ }
+
+ // Yield control until asynchronous operation completes. Control
+ // resumes at the "default:" label below.
+ return;
+
+ case engine::want_output_and_retry:
+ case engine::want_output:
+
+ // The engine wants some data to be written to the output. However, we
+ // cannot allow more than one write operation at a time on the
+ // underlying transport. The pending_write_ timer's expiry is set to
+ // pos_infin if a write is in progress, and neg_infin otherwise.
+ if (core_.pending_write_.expires_at() == core_.neg_infin())
+ {
+ // Prevent other write operations from being started.
+ core_.pending_write_.expires_at(core_.pos_infin());
+
+ // Start writing all the data to the underlying transport.
+ boost::asio::async_write(next_layer_,
+ core_.engine_.get_output(core_.output_buffer_),
+ BOOST_ASIO_MOVE_CAST(io_op)(*this));
+ }
+ else
+ {
+ // Wait until the current write operation completes.
+ core_.pending_write_.async_wait(BOOST_ASIO_MOVE_CAST(io_op)(*this));
+ }
+
+ // Yield control until asynchronous operation completes. Control
+ // resumes at the "default:" label below.
+ return;
+
+ default:
+
+ // The SSL operation is done and we can invoke the handler, but we
+ // have to keep in mind that this function might be being called from
+ // the async operation's initiating function. In this case we're not
+ // allowed to call the handler directly. Instead, issue a zero-sized
+ // read so the handler runs "as-if" posted using io_service::post().
+ if (start)
+ {
+ next_layer_.async_read_some(
+ boost::asio::buffer(core_.input_buffer_, 0),
+ BOOST_ASIO_MOVE_CAST(io_op)(*this));
+
+ // Yield control until asynchronous operation completes. Control
+ // resumes at the "default:" label below.
+ return;
+ }
+ else
+ {
+ // Continue on to run handler directly.
+ break;
+ }
+ }
+
+ default:
+ if (bytes_transferred != ~std::size_t(0) && !ec_)
+ ec_ = ec;
+
+ switch (want_)
+ {
+ case engine::want_input_and_retry:
+
+ // Add received data to the engine's input.
+ core_.input_ = boost::asio::buffer(
+ core_.input_buffer_, bytes_transferred);
+ core_.input_ = core_.engine_.put_input(core_.input_);
+
+ // Release any waiting read operations.
+ core_.pending_read_.expires_at(core_.neg_infin());
+
+ // Try the operation again.
+ continue;
+
+ case engine::want_output_and_retry:
+
+ // Release any waiting write operations.
+ core_.pending_write_.expires_at(core_.neg_infin());
+
+ // Try the operation again.
+ continue;
+
+ case engine::want_output:
+
+ // Release any waiting write operations.
+ core_.pending_write_.expires_at(core_.neg_infin());
+
+ // Fall through to call handler.
+
+ default:
+
+ // Pass the result to the handler.
+ op_.call_handler(handler_,
+ core_.engine_.map_error_code(ec_),
+ ec_ ? 0 : bytes_transferred_);
+
+ // Our work here is done.
+ return;
+ }
+ } while (!ec_);
+
+ // Operation failed. Pass the result to the handler.
+ op_.call_handler(handler_, core_.engine_.map_error_code(ec_), 0);
+ }
+ }
+
+//private:
+ Stream& next_layer_;
+ stream_core& core_;
+ Operation op_;
+ int start_;
+ engine::want want_;
+ boost::system::error_code ec_;
+ std::size_t bytes_transferred_;
+ Handler handler_;
+};
+
+template <typename Stream, typename Operation, typename Handler>
+inline void* asio_handler_allocate(std::size_t size,
+ io_op<Stream, Operation, Handler>* this_handler)
+{
+ return boost_asio_handler_alloc_helpers::allocate(
+ size, this_handler->handler_);
+}
+
+template <typename Stream, typename Operation, typename Handler>
+inline void asio_handler_deallocate(void* pointer, std::size_t size,
+ io_op<Stream, Operation, Handler>* this_handler)
+{
+ boost_asio_handler_alloc_helpers::deallocate(
+ pointer, size, this_handler->handler_);
+}
+
+template <typename Stream, typename Operation, typename Handler>
+inline bool asio_handler_is_continuation(
+ io_op<Stream, Operation, Handler>* this_handler)
+{
+ return this_handler->start_ == 0 ? true
+ : boost_asio_handler_cont_helpers::is_continuation(this_handler->handler_);
+}
+
+template <typename Function, typename Stream,
+ typename Operation, typename Handler>
+inline void asio_handler_invoke(Function& function,
+ io_op<Stream, Operation, Handler>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Function, typename Stream,
+ typename Operation, typename Handler>
+inline void asio_handler_invoke(const Function& function,
+ io_op<Stream, Operation, Handler>* this_handler)
+{
+ boost_asio_handler_invoke_helpers::invoke(
+ function, this_handler->handler_);
+}
+
+template <typename Stream, typename Operation, typename Handler>
+inline void async_io(Stream& next_layer, stream_core& core,
+ const Operation& op, Handler& handler)
+{
+ io_op<Stream, Operation, Handler>(
+ next_layer, core, op, handler)(
+ boost::system::error_code(), 0, 1);
+}
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_IO_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/openssl_init.hpp b/ext/patches/boost/asio/ssl/detail/openssl_init.hpp
new file mode 100644
index 0000000..90782da
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/openssl_init.hpp
@@ -0,0 +1,103 @@
+//
+// ssl/detail/openssl_init.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_OPENSSL_INIT_HPP
+#define BOOST_ASIO_SSL_DETAIL_OPENSSL_INIT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstring>
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/shared_ptr.hpp>
+#include <boost/asio/ssl/detail/openssl_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+class openssl_init_base
+ : private noncopyable
+{
+protected:
+ // Class that performs the actual initialisation.
+ class do_init;
+
+ // Helper function to manage a do_init singleton. The static instance of the
+ // openssl_init object ensures that this function is always called before
+ // main, and therefore before any other threads can get started. The do_init
+ // instance must be static in this function to ensure that it gets
+ // initialised before any other global objects try to use it.
+ BOOST_ASIO_DECL static boost::asio::detail::shared_ptr<do_init> instance();
+
+#if !defined(SSL_OP_NO_COMPRESSION) \
+ && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ // Get an empty stack of compression methods, to be used when disabling
+ // compression.
+ BOOST_ASIO_DECL static STACK_OF(SSL_COMP)* get_null_compression_methods();
+#endif // !defined(SSL_OP_NO_COMPRESSION)
+ // && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+};
+
+template <bool Do_Init = true>
+class openssl_init : private openssl_init_base
+{
+public:
+ // Constructor.
+ openssl_init()
+ : ref_(instance())
+ {
+ using namespace std; // For memmove.
+
+ // Ensure openssl_init::instance_ is linked in.
+ openssl_init* tmp = &instance_;
+ memmove(&tmp, &tmp, sizeof(openssl_init*));
+ }
+
+ // Destructor.
+ ~openssl_init()
+ {
+ }
+
+#if !defined(SSL_OP_NO_COMPRESSION) \
+ && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ using openssl_init_base::get_null_compression_methods;
+#endif // !defined(SSL_OP_NO_COMPRESSION)
+ // && (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+
+private:
+ // Instance to force initialisation of openssl at global scope.
+ static openssl_init instance_;
+
+ // Reference to singleton do_init object to ensure that openssl does not get
+ // cleaned up until the last user has finished with it.
+ boost::asio::detail::shared_ptr<do_init> ref_;
+};
+
+template <bool Do_Init>
+openssl_init<Do_Init> openssl_init<Do_Init>::instance_;
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ssl/detail/impl/openssl_init.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_SSL_DETAIL_OPENSSL_INIT_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/openssl_types.hpp b/ext/patches/boost/asio/ssl/detail/openssl_types.hpp
new file mode 100644
index 0000000..2c80f4b
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/openssl_types.hpp
@@ -0,0 +1,28 @@
+//
+// ssl/detail/openssl_types.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_OPENSSL_TYPES_HPP
+#define BOOST_ASIO_SSL_DETAIL_OPENSSL_TYPES_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <openssl/conf.h>
+#include <openssl/ssl.h>
+#if !defined(OPENSSL_NO_ENGINE)
+# include <openssl/engine.h>
+#endif // !defined(OPENSSL_NO_ENGINE)
+#include <openssl/err.h>
+#include <openssl/x509v3.h>
+#include <boost/asio/detail/socket_types.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_OPENSSL_TYPES_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/password_callback.hpp b/ext/patches/boost/asio/ssl/detail/password_callback.hpp
new file mode 100644
index 0000000..2f570b2
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/password_callback.hpp
@@ -0,0 +1,74 @@
+//
+// ssl/detail/password_callback.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_PASSWORD_CALLBACK_HPP
+#define BOOST_ASIO_SSL_DETAIL_PASSWORD_CALLBACK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <cstddef>
+# include <string>
+# include <boost/asio/ssl/context_base.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+class password_callback_base
+{
+public:
+ virtual ~password_callback_base()
+ {
+ }
+
+ virtual std::string call(std::size_t size,
+ context_base::password_purpose purpose) = 0;
+};
+
+template <typename PasswordCallback>
+class password_callback : public password_callback_base
+{
+public:
+ explicit password_callback(PasswordCallback callback)
+ : callback_(callback)
+ {
+ }
+
+ virtual std::string call(std::size_t size,
+ context_base::password_purpose purpose)
+ {
+ return callback_(size, purpose);
+ }
+
+private:
+ PasswordCallback callback_;
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_PASSWORD_CALLBACK_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/read_op.hpp b/ext/patches/boost/asio/ssl/detail/read_op.hpp
new file mode 100644
index 0000000..6f6a687
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/read_op.hpp
@@ -0,0 +1,75 @@
+//
+// ssl/detail/read_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_READ_OP_HPP
+#define BOOST_ASIO_SSL_DETAIL_READ_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/detail/buffer_sequence_adapter.hpp>
+# include <boost/asio/ssl/detail/engine.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+template <typename MutableBufferSequence>
+class read_op
+{
+public:
+ read_op(const MutableBufferSequence& buffers)
+ : buffers_(buffers)
+ {
+ }
+
+ engine::want operator()(engine& eng,
+ boost::system::error_code& ec,
+ std::size_t& bytes_transferred) const
+ {
+ boost::asio::mutable_buffer buffer =
+ boost::asio::detail::buffer_sequence_adapter<boost::asio::mutable_buffer,
+ MutableBufferSequence>::first(buffers_);
+
+ return eng.read(buffer, ec, bytes_transferred);
+ }
+
+ template <typename Handler>
+ void call_handler(Handler& handler,
+ const boost::system::error_code& ec,
+ const std::size_t& bytes_transferred) const
+ {
+ handler(ec, bytes_transferred);
+ }
+
+private:
+ MutableBufferSequence buffers_;
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_READ_OP_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/shutdown_op.hpp b/ext/patches/boost/asio/ssl/detail/shutdown_op.hpp
new file mode 100644
index 0000000..0af1c34
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/shutdown_op.hpp
@@ -0,0 +1,62 @@
+//
+// ssl/detail/shutdown_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_SHUTDOWN_OP_HPP
+#define BOOST_ASIO_SSL_DETAIL_SHUTDOWN_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/detail/engine.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+class shutdown_op
+{
+public:
+ engine::want operator()(engine& eng,
+ boost::system::error_code& ec,
+ std::size_t& bytes_transferred) const
+ {
+ bytes_transferred = 0;
+ return eng.shutdown(ec);
+ }
+
+ template <typename Handler>
+ void call_handler(Handler& handler,
+ const boost::system::error_code& ec,
+ const std::size_t&) const
+ {
+ handler(ec);
+ }
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_SHUTDOWN_OP_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/stream_core.hpp b/ext/patches/boost/asio/ssl/detail/stream_core.hpp
new file mode 100644
index 0000000..1fcb150
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/stream_core.hpp
@@ -0,0 +1,128 @@
+//
+// ssl/detail/stream_core.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_STREAM_CORE_HPP
+#define BOOST_ASIO_SSL_DETAIL_STREAM_CORE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+# include <boost/asio/deadline_timer.hpp>
+# else // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+# include <boost/asio/steady_timer.hpp>
+# endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+# include <boost/asio/ssl/detail/engine.hpp>
+# include <boost/asio/buffer.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+struct stream_core
+{
+ // According to the OpenSSL documentation, this is the buffer size that is
+ // sufficient to hold the largest possible TLS record.
+ enum { max_tls_record_size = 17 * 1024 };
+
+ stream_core(SSL_CTX* context, boost::asio::io_service& io_service)
+ : engine_(context),
+ pending_read_(io_service),
+ pending_write_(io_service),
+ output_buffer_space_(max_tls_record_size),
+ output_buffer_(boost::asio::buffer(output_buffer_space_)),
+ input_buffer_space_(max_tls_record_size),
+ input_buffer_(boost::asio::buffer(input_buffer_space_))
+ {
+ pending_read_.expires_at(neg_infin());
+ pending_write_.expires_at(neg_infin());
+ }
+
+ ~stream_core()
+ {
+ }
+
+ // The SSL engine.
+ engine engine_;
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ // Timer used for storing queued read operations.
+ boost::asio::deadline_timer pending_read_;
+
+ // Timer used for storing queued write operations.
+ boost::asio::deadline_timer pending_write_;
+
+ // Helper function for obtaining a time value that always fires.
+ static boost::asio::deadline_timer::time_type neg_infin()
+ {
+ return boost::posix_time::neg_infin;
+ }
+
+ // Helper function for obtaining a time value that never fires.
+ static boost::asio::deadline_timer::time_type pos_infin()
+ {
+ return boost::posix_time::pos_infin;
+ }
+#else // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ // Timer used for storing queued read operations.
+ boost::asio::steady_timer pending_read_;
+
+ // Timer used for storing queued write operations.
+ boost::asio::steady_timer pending_write_;
+
+ // Helper function for obtaining a time value that always fires.
+ static boost::asio::steady_timer::time_point neg_infin()
+ {
+ return (boost::asio::steady_timer::time_point::min)();
+ }
+
+ // Helper function for obtaining a time value that never fires.
+ static boost::asio::steady_timer::time_point pos_infin()
+ {
+ return (boost::asio::steady_timer::time_point::max)();
+ }
+#endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+
+ // Buffer space used to prepare output intended for the transport.
+ std::vector<unsigned char> output_buffer_space_;
+
+ // A buffer that may be used to prepare output intended for the transport.
+ const boost::asio::mutable_buffers_1 output_buffer_;
+
+ // Buffer space used to read input intended for the engine.
+ std::vector<unsigned char> input_buffer_space_;
+
+ // A buffer that may be used to read input intended for the engine.
+ const boost::asio::mutable_buffers_1 input_buffer_;
+
+ // The buffer pointing to the engine's unconsumed input.
+ boost::asio::const_buffer input_;
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_STREAM_CORE_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/verify_callback.hpp b/ext/patches/boost/asio/ssl/detail/verify_callback.hpp
new file mode 100644
index 0000000..68c669c
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/verify_callback.hpp
@@ -0,0 +1,70 @@
+//
+// ssl/detail/verify_callback.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_VERIFY_CALLBACK_HPP
+#define BOOST_ASIO_SSL_DETAIL_VERIFY_CALLBACK_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/verify_context.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+class verify_callback_base
+{
+public:
+ virtual ~verify_callback_base()
+ {
+ }
+
+ virtual bool call(bool preverified, verify_context& ctx) = 0;
+};
+
+template <typename VerifyCallback>
+class verify_callback : public verify_callback_base
+{
+public:
+ explicit verify_callback(VerifyCallback callback)
+ : callback_(callback)
+ {
+ }
+
+ virtual bool call(bool preverified, verify_context& ctx)
+ {
+ return callback_(preverified, ctx);
+ }
+
+private:
+ VerifyCallback callback_;
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_VERIFY_CALLBACK_HPP
diff --git a/ext/patches/boost/asio/ssl/detail/write_op.hpp b/ext/patches/boost/asio/ssl/detail/write_op.hpp
new file mode 100644
index 0000000..e748901
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/detail/write_op.hpp
@@ -0,0 +1,75 @@
+//
+// ssl/detail/write_op.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_DETAIL_WRITE_OP_HPP
+#define BOOST_ASIO_SSL_DETAIL_WRITE_OP_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/detail/buffer_sequence_adapter.hpp>
+# include <boost/asio/ssl/detail/engine.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace detail {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+template <typename ConstBufferSequence>
+class write_op
+{
+public:
+ write_op(const ConstBufferSequence& buffers)
+ : buffers_(buffers)
+ {
+ }
+
+ engine::want operator()(engine& eng,
+ boost::system::error_code& ec,
+ std::size_t& bytes_transferred) const
+ {
+ boost::asio::const_buffer buffer =
+ boost::asio::detail::buffer_sequence_adapter<boost::asio::const_buffer,
+ ConstBufferSequence>::first(buffers_);
+
+ return eng.write(buffer, ec, bytes_transferred);
+ }
+
+ template <typename Handler>
+ void call_handler(Handler& handler,
+ const boost::system::error_code& ec,
+ const std::size_t& bytes_transferred) const
+ {
+ handler(ec, bytes_transferred);
+ }
+
+private:
+ ConstBufferSequence buffers_;
+};
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace detail
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_DETAIL_WRITE_OP_HPP
diff --git a/ext/patches/boost/asio/ssl/error.hpp b/ext/patches/boost/asio/ssl/error.hpp
new file mode 100644
index 0000000..dae24de
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/error.hpp
@@ -0,0 +1,72 @@
+//
+// ssl/error.hpp
+// ~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_ERROR_HPP
+#define BOOST_ASIO_SSL_ERROR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/system/error_code.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace error {
+
+enum ssl_errors
+{
+};
+
+extern BOOST_ASIO_DECL
+const boost::system::error_category& get_ssl_category();
+
+static const boost::system::error_category& ssl_category
+ = boost::asio::error::get_ssl_category();
+
+} // namespace error
+} // namespace asio
+} // namespace boost
+
+namespace boost {
+namespace system {
+
+template<> struct is_error_code_enum<boost::asio::error::ssl_errors>
+{
+ static const bool value = true;
+};
+
+} // namespace system
+} // namespace boost
+
+namespace boost {
+namespace asio {
+namespace error {
+
+inline boost::system::error_code make_error_code(ssl_errors e)
+{
+ return boost::system::error_code(
+ static_cast<int>(e), get_ssl_category());
+}
+
+} // namespace error
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ssl/impl/error.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_SSL_ERROR_HPP
diff --git a/ext/patches/boost/asio/ssl/impl/context.hpp b/ext/patches/boost/asio/ssl/impl/context.hpp
new file mode 100644
index 0000000..1bfdc4f
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/impl/context.hpp
@@ -0,0 +1,73 @@
+//
+// ssl/impl/context.hpp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_IMPL_CONTEXT_HPP
+#define BOOST_ASIO_SSL_IMPL_CONTEXT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/detail/throw_error.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+template <typename VerifyCallback>
+void context::set_verify_callback(VerifyCallback callback)
+{
+ boost::system::error_code ec;
+ this->set_verify_callback(callback, ec);
+ boost::asio::detail::throw_error(ec, "set_verify_callback");
+}
+
+template <typename VerifyCallback>
+boost::system::error_code context::set_verify_callback(
+ VerifyCallback callback, boost::system::error_code& ec)
+{
+ return do_set_verify_callback(
+ new detail::verify_callback<VerifyCallback>(callback), ec);
+}
+
+template <typename PasswordCallback>
+void context::set_password_callback(PasswordCallback callback)
+{
+ boost::system::error_code ec;
+ this->set_password_callback(callback, ec);
+ boost::asio::detail::throw_error(ec, "set_password_callback");
+}
+
+template <typename PasswordCallback>
+boost::system::error_code context::set_password_callback(
+ PasswordCallback callback, boost::system::error_code& ec)
+{
+ return do_set_password_callback(
+ new detail::password_callback<PasswordCallback>(callback), ec);
+}
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_IMPL_CONTEXT_HPP
diff --git a/ext/patches/boost/asio/ssl/impl/context.ipp b/ext/patches/boost/asio/ssl/impl/context.ipp
new file mode 100644
index 0000000..07c6b0a
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/impl/context.ipp
@@ -0,0 +1,952 @@
+//
+// ssl/impl/context.ipp
+// ~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_IMPL_CONTEXT_IPP
+#define BOOST_ASIO_SSL_IMPL_CONTEXT_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <cstring>
+# include <boost/asio/detail/throw_error.hpp>
+# include <boost/asio/error.hpp>
+# include <boost/asio/ssl/context.hpp>
+# include <boost/asio/ssl/error.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+struct context::bio_cleanup
+{
+ BIO* p;
+ ~bio_cleanup() { if (p) ::BIO_free(p); }
+};
+
+struct context::x509_cleanup
+{
+ X509* p;
+ ~x509_cleanup() { if (p) ::X509_free(p); }
+};
+
+struct context::evp_pkey_cleanup
+{
+ EVP_PKEY* p;
+ ~evp_pkey_cleanup() { if (p) ::EVP_PKEY_free(p); }
+};
+
+struct context::rsa_cleanup
+{
+ RSA* p;
+ ~rsa_cleanup() { if (p) ::RSA_free(p); }
+};
+
+struct context::dh_cleanup
+{
+ DH* p;
+ ~dh_cleanup() { if (p) ::DH_free(p); }
+};
+
+context::context(context::method m)
+ : handle_(0)
+{
+ switch (m)
+ {
+#if defined(OPENSSL_NO_SSL2)
+ case context::sslv2:
+ case context::sslv2_client:
+ case context::sslv2_server:
+ boost::asio::detail::throw_error(
+ boost::asio::error::invalid_argument, "context");
+ break;
+#else // defined(OPENSSL_NO_SSL2)
+ case context::sslv2:
+ handle_ = ::SSL_CTX_new(::SSLv2_method());
+ break;
+ case context::sslv2_client:
+ handle_ = ::SSL_CTX_new(::SSLv2_client_method());
+ break;
+ case context::sslv2_server:
+ handle_ = ::SSL_CTX_new(::SSLv2_server_method());
+ break;
+#endif // defined(OPENSSL_NO_SSL2)
+ case context::sslv3:
+ handle_ = ::SSL_CTX_new(::SSLv3_method());
+ break;
+ case context::sslv3_client:
+ handle_ = ::SSL_CTX_new(::SSLv3_client_method());
+ break;
+ case context::sslv3_server:
+ handle_ = ::SSL_CTX_new(::SSLv3_server_method());
+ break;
+ case context::tlsv1:
+ handle_ = ::SSL_CTX_new(::TLSv1_method());
+ break;
+ case context::tlsv1_client:
+ handle_ = ::SSL_CTX_new(::TLSv1_client_method());
+ break;
+ case context::tlsv1_server:
+ handle_ = ::SSL_CTX_new(::TLSv1_server_method());
+ break;
+ case context::sslv23:
+ handle_ = ::SSL_CTX_new(::SSLv23_method());
+ break;
+ case context::sslv23_client:
+ handle_ = ::SSL_CTX_new(::SSLv23_client_method());
+ break;
+ case context::sslv23_server:
+ handle_ = ::SSL_CTX_new(::SSLv23_server_method());
+ break;
+#if defined(SSL_TXT_TLSV1_1)
+ case context::tlsv11:
+ handle_ = ::SSL_CTX_new(::TLSv1_1_method());
+ break;
+ case context::tlsv11_client:
+ handle_ = ::SSL_CTX_new(::TLSv1_1_client_method());
+ break;
+ case context::tlsv11_server:
+ handle_ = ::SSL_CTX_new(::TLSv1_1_server_method());
+ break;
+#else // defined(SSL_TXT_TLSV1_1)
+ case context::tlsv11:
+ case context::tlsv11_client:
+ case context::tlsv11_server:
+ boost::asio::detail::throw_error(
+ boost::asio::error::invalid_argument, "context");
+ break;
+#endif // defined(SSL_TXT_TLSV1_1)
+#if defined(SSL_TXT_TLSV1_2)
+ case context::tlsv12:
+ handle_ = ::SSL_CTX_new(::TLSv1_2_method());
+ break;
+ case context::tlsv12_client:
+ handle_ = ::SSL_CTX_new(::TLSv1_2_client_method());
+ break;
+ case context::tlsv12_server:
+ handle_ = ::SSL_CTX_new(::TLSv1_2_server_method());
+ break;
+#else // defined(SSL_TXT_TLSV1_2)
+ case context::tlsv12:
+ case context::tlsv12_client:
+ case context::tlsv12_server:
+ boost::asio::detail::throw_error(
+ boost::asio::error::invalid_argument, "context");
+ break;
+#endif // defined(SSL_TXT_TLSV1_2)
+ default:
+ handle_ = ::SSL_CTX_new(0);
+ break;
+ }
+
+ if (handle_ == 0)
+ {
+ boost::system::error_code ec(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ boost::asio::detail::throw_error(ec, "context");
+ }
+
+ set_options(no_compression);
+}
+
+context::context(boost::asio::io_service&, context::method m)
+ : handle_(0)
+{
+ context tmp(m);
+ handle_ = tmp.handle_;
+ tmp.handle_ = 0;
+}
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+context::context(context&& other)
+{
+ handle_ = other.handle_;
+ other.handle_ = 0;
+}
+
+context& context::operator=(context&& other)
+{
+ context tmp(BOOST_ASIO_MOVE_CAST(context)(*this));
+ handle_ = other.handle_;
+ other.handle_ = 0;
+ return *this;
+}
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+context::~context()
+{
+ if (handle_)
+ {
+ if (handle_->default_passwd_callback_userdata)
+ {
+ detail::password_callback_base* callback =
+ static_cast<detail::password_callback_base*>(
+ handle_->default_passwd_callback_userdata);
+ delete callback;
+ handle_->default_passwd_callback_userdata = 0;
+ }
+
+ if (SSL_CTX_get_app_data(handle_))
+ {
+ detail::verify_callback_base* callback =
+ static_cast<detail::verify_callback_base*>(
+ SSL_CTX_get_app_data(handle_));
+ delete callback;
+ SSL_CTX_set_app_data(handle_, 0);
+ }
+
+ ::SSL_CTX_free(handle_);
+ }
+}
+
+context::native_handle_type context::native_handle()
+{
+ return handle_;
+}
+
+context::impl_type context::impl()
+{
+ return handle_;
+}
+
+void context::clear_options(context::options o)
+{
+ boost::system::error_code ec;
+ clear_options(o, ec);
+ boost::asio::detail::throw_error(ec, "clear_options");
+}
+
+boost::system::error_code context::clear_options(
+ context::options o, boost::system::error_code& ec)
+{
+#if (OPENSSL_VERSION_NUMBER >= 0x009080DFL) \
+ && (OPENSSL_VERSION_NUMBER != 0x00909000L)
+# if !defined(SSL_OP_NO_COMPRESSION)
+ if ((o & context::no_compression) != 0)
+ {
+# if (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ handle_->comp_methods = SSL_COMP_get_compression_methods();
+# endif // (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ o ^= context::no_compression;
+ }
+# endif // !defined(SSL_OP_NO_COMPRESSION)
+
+ ::SSL_CTX_clear_options(handle_, o);
+
+ ec = boost::system::error_code();
+#else // (OPENSSL_VERSION_NUMBER >= 0x009080DFL)
+ // && (OPENSSL_VERSION_NUMBER != 0x00909000L)
+ (void)o;
+ ec = boost::asio::error::operation_not_supported;
+#endif // (OPENSSL_VERSION_NUMBER >= 0x009080DFL)
+ // && (OPENSSL_VERSION_NUMBER != 0x00909000L)
+ return ec;
+}
+
+void context::set_options(context::options o)
+{
+ boost::system::error_code ec;
+ set_options(o, ec);
+ boost::asio::detail::throw_error(ec, "set_options");
+}
+
+boost::system::error_code context::set_options(
+ context::options o, boost::system::error_code& ec)
+{
+#if !defined(SSL_OP_NO_COMPRESSION)
+ if ((o & context::no_compression) != 0)
+ {
+#if (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ handle_->comp_methods =
+ boost::asio::ssl::detail::openssl_init<>::get_null_compression_methods();
+#endif // (OPENSSL_VERSION_NUMBER >= 0x00908000L)
+ o ^= context::no_compression;
+ }
+#endif // !defined(SSL_OP_NO_COMPRESSION)
+
+ ::SSL_CTX_set_options(handle_, o);
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::set_verify_mode(verify_mode v)
+{
+ boost::system::error_code ec;
+ set_verify_mode(v, ec);
+ boost::asio::detail::throw_error(ec, "set_verify_mode");
+}
+
+boost::system::error_code context::set_verify_mode(
+ verify_mode v, boost::system::error_code& ec)
+{
+ ::SSL_CTX_set_verify(handle_, v, ::SSL_CTX_get_verify_callback(handle_));
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::set_verify_depth(int depth)
+{
+ boost::system::error_code ec;
+ set_verify_depth(depth, ec);
+ boost::asio::detail::throw_error(ec, "set_verify_depth");
+}
+
+boost::system::error_code context::set_verify_depth(
+ int depth, boost::system::error_code& ec)
+{
+ ::SSL_CTX_set_verify_depth(handle_, depth);
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::load_verify_file(const std::string& filename)
+{
+ boost::system::error_code ec;
+ load_verify_file(filename, ec);
+ boost::asio::detail::throw_error(ec, "load_verify_file");
+}
+
+boost::system::error_code context::load_verify_file(
+ const std::string& filename, boost::system::error_code& ec)
+{
+ if (::SSL_CTX_load_verify_locations(handle_, filename.c_str(), 0) != 1)
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::add_certificate_authority(const const_buffer& ca)
+{
+ boost::system::error_code ec;
+ add_certificate_authority(ca, ec);
+ boost::asio::detail::throw_error(ec, "add_certificate_authority");
+}
+
+boost::system::error_code context::add_certificate_authority(
+ const const_buffer& ca, boost::system::error_code& ec)
+{
+ ::ERR_clear_error();
+
+ bio_cleanup bio = { make_buffer_bio(ca) };
+ if (bio.p)
+ {
+ x509_cleanup cert = { ::PEM_read_bio_X509(bio.p, 0, 0, 0) };
+ if (cert.p)
+ {
+ if (X509_STORE* store = ::SSL_CTX_get_cert_store(handle_))
+ {
+ if (::X509_STORE_add_cert(store, cert.p) == 1)
+ {
+ ec = boost::system::error_code();
+ return ec;
+ }
+ }
+ }
+ }
+
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+}
+
+void context::set_default_verify_paths()
+{
+ boost::system::error_code ec;
+ set_default_verify_paths(ec);
+ boost::asio::detail::throw_error(ec, "set_default_verify_paths");
+}
+
+boost::system::error_code context::set_default_verify_paths(
+ boost::system::error_code& ec)
+{
+ if (::SSL_CTX_set_default_verify_paths(handle_) != 1)
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::add_verify_path(const std::string& path)
+{
+ boost::system::error_code ec;
+ add_verify_path(path, ec);
+ boost::asio::detail::throw_error(ec, "add_verify_path");
+}
+
+boost::system::error_code context::add_verify_path(
+ const std::string& path, boost::system::error_code& ec)
+{
+ if (::SSL_CTX_load_verify_locations(handle_, 0, path.c_str()) != 1)
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::use_certificate(
+ const const_buffer& certificate, file_format format)
+{
+ boost::system::error_code ec;
+ use_certificate(certificate, format, ec);
+ boost::asio::detail::throw_error(ec, "use_certificate");
+}
+
+boost::system::error_code context::use_certificate(
+ const const_buffer& certificate, file_format format,
+ boost::system::error_code& ec)
+{
+ ::ERR_clear_error();
+
+ if (format == context_base::asn1)
+ {
+ if (::SSL_CTX_use_certificate_ASN1(handle_,
+ static_cast<int>(buffer_size(certificate)),
+ buffer_cast<const unsigned char*>(certificate)) == 1)
+ {
+ ec = boost::system::error_code();
+ return ec;
+ }
+ }
+ else if (format == context_base::pem)
+ {
+ bio_cleanup bio = { make_buffer_bio(certificate) };
+ if (bio.p)
+ {
+ x509_cleanup cert = { ::PEM_read_bio_X509(bio.p, 0, 0, 0) };
+ if (cert.p)
+ {
+ if (::SSL_CTX_use_certificate(handle_, cert.p) == 1)
+ {
+ ec = boost::system::error_code();
+ return ec;
+ }
+ }
+ }
+ }
+ else
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+}
+
+void context::use_certificate_file(
+ const std::string& filename, file_format format)
+{
+ boost::system::error_code ec;
+ use_certificate_file(filename, format, ec);
+ boost::asio::detail::throw_error(ec, "use_certificate_file");
+}
+
+boost::system::error_code context::use_certificate_file(
+ const std::string& filename, file_format format,
+ boost::system::error_code& ec)
+{
+ int file_type;
+ switch (format)
+ {
+ case context_base::asn1:
+ file_type = SSL_FILETYPE_ASN1;
+ break;
+ case context_base::pem:
+ file_type = SSL_FILETYPE_PEM;
+ break;
+ default:
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+ }
+
+ if (::SSL_CTX_use_certificate_file(handle_, filename.c_str(), file_type) != 1)
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::use_certificate_chain(const const_buffer& chain)
+{
+ boost::system::error_code ec;
+ use_certificate_chain(chain, ec);
+ boost::asio::detail::throw_error(ec, "use_certificate_chain");
+}
+
+boost::system::error_code context::use_certificate_chain(
+ const const_buffer& chain, boost::system::error_code& ec)
+{
+ ::ERR_clear_error();
+
+ bio_cleanup bio = { make_buffer_bio(chain) };
+ if (bio.p)
+ {
+ x509_cleanup cert = {
+ ::PEM_read_bio_X509_AUX(bio.p, 0,
+ handle_->default_passwd_callback,
+ handle_->default_passwd_callback_userdata) };
+ if (!cert.p)
+ {
+ ec = boost::system::error_code(ERR_R_PEM_LIB,
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ int result = ::SSL_CTX_use_certificate(handle_, cert.p);
+ if (result == 0 || ::ERR_peek_error() != 0)
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ if (handle_->extra_certs)
+ {
+ ::sk_X509_pop_free(handle_->extra_certs, X509_free);
+ handle_->extra_certs = 0;
+ }
+
+ while (X509* cacert = ::PEM_read_bio_X509(bio.p, 0,
+ handle_->default_passwd_callback,
+ handle_->default_passwd_callback_userdata))
+ {
+ if (!::SSL_CTX_add_extra_chain_cert(handle_, cacert))
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+ }
+
+ result = ::ERR_peek_last_error();
+ if ((ERR_GET_LIB(result) == ERR_LIB_PEM)
+ && (ERR_GET_REASON(result) == PEM_R_NO_START_LINE))
+ {
+ ::ERR_clear_error();
+ ec = boost::system::error_code();
+ return ec;
+ }
+ }
+
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+}
+
+void context::use_certificate_chain_file(const std::string& filename)
+{
+ boost::system::error_code ec;
+ use_certificate_chain_file(filename, ec);
+ boost::asio::detail::throw_error(ec, "use_certificate_chain_file");
+}
+
+boost::system::error_code context::use_certificate_chain_file(
+ const std::string& filename, boost::system::error_code& ec)
+{
+ if (::SSL_CTX_use_certificate_chain_file(handle_, filename.c_str()) != 1)
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::use_private_key(
+ const const_buffer& private_key, context::file_format format)
+{
+ boost::system::error_code ec;
+ use_private_key(private_key, format, ec);
+ boost::asio::detail::throw_error(ec, "use_private_key");
+}
+
+boost::system::error_code context::use_private_key(
+ const const_buffer& private_key, context::file_format format,
+ boost::system::error_code& ec)
+{
+ ::ERR_clear_error();
+
+ bio_cleanup bio = { make_buffer_bio(private_key) };
+ if (bio.p)
+ {
+ evp_pkey_cleanup evp_private_key = { 0 };
+ switch (format)
+ {
+ case context_base::asn1:
+ evp_private_key.p = ::d2i_PrivateKey_bio(bio.p, 0);
+ break;
+ case context_base::pem:
+ evp_private_key.p = ::PEM_read_bio_PrivateKey(bio.p, 0, 0, 0);
+ break;
+ default:
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+ }
+
+ if (evp_private_key.p)
+ {
+ if (::SSL_CTX_use_PrivateKey(handle_, evp_private_key.p) == 1)
+ {
+ ec = boost::system::error_code();
+ return ec;
+ }
+ }
+ }
+
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+}
+
+void context::use_private_key_file(
+ const std::string& filename, context::file_format format)
+{
+ boost::system::error_code ec;
+ use_private_key_file(filename, format, ec);
+ boost::asio::detail::throw_error(ec, "use_private_key_file");
+}
+
+void context::use_rsa_private_key(
+ const const_buffer& private_key, context::file_format format)
+{
+ boost::system::error_code ec;
+ use_rsa_private_key(private_key, format, ec);
+ boost::asio::detail::throw_error(ec, "use_rsa_private_key");
+}
+
+boost::system::error_code context::use_rsa_private_key(
+ const const_buffer& private_key, context::file_format format,
+ boost::system::error_code& ec)
+{
+ ::ERR_clear_error();
+
+ bio_cleanup bio = { make_buffer_bio(private_key) };
+ if (bio.p)
+ {
+ rsa_cleanup rsa_private_key = { 0 };
+ switch (format)
+ {
+ case context_base::asn1:
+ rsa_private_key.p = ::d2i_RSAPrivateKey_bio(bio.p, 0);
+ break;
+ case context_base::pem:
+ rsa_private_key.p = ::PEM_read_bio_RSAPrivateKey(bio.p, 0, 0, 0);
+ break;
+ default:
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+ }
+
+ if (rsa_private_key.p)
+ {
+ if (::SSL_CTX_use_RSAPrivateKey(handle_, rsa_private_key.p) == 1)
+ {
+ ec = boost::system::error_code();
+ return ec;
+ }
+ }
+ }
+
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+}
+
+boost::system::error_code context::use_private_key_file(
+ const std::string& filename, context::file_format format,
+ boost::system::error_code& ec)
+{
+ int file_type;
+ switch (format)
+ {
+ case context_base::asn1:
+ file_type = SSL_FILETYPE_ASN1;
+ break;
+ case context_base::pem:
+ file_type = SSL_FILETYPE_PEM;
+ break;
+ default:
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+ }
+
+ if (::SSL_CTX_use_PrivateKey_file(handle_, filename.c_str(), file_type) != 1)
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::use_rsa_private_key_file(
+ const std::string& filename, context::file_format format)
+{
+ boost::system::error_code ec;
+ use_rsa_private_key_file(filename, format, ec);
+ boost::asio::detail::throw_error(ec, "use_rsa_private_key_file");
+}
+
+boost::system::error_code context::use_rsa_private_key_file(
+ const std::string& filename, context::file_format format,
+ boost::system::error_code& ec)
+{
+ int file_type;
+ switch (format)
+ {
+ case context_base::asn1:
+ file_type = SSL_FILETYPE_ASN1;
+ break;
+ case context_base::pem:
+ file_type = SSL_FILETYPE_PEM;
+ break;
+ default:
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+ }
+
+ if (::SSL_CTX_use_RSAPrivateKey_file(
+ handle_, filename.c_str(), file_type) != 1)
+ {
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+void context::use_tmp_dh(const const_buffer& dh)
+{
+ boost::system::error_code ec;
+ use_tmp_dh(dh, ec);
+ boost::asio::detail::throw_error(ec, "use_tmp_dh");
+}
+
+boost::system::error_code context::use_tmp_dh(
+ const const_buffer& dh, boost::system::error_code& ec)
+{
+ bio_cleanup bio = { make_buffer_bio(dh) };
+ if (bio.p)
+ {
+ return do_use_tmp_dh(bio.p, ec);
+ }
+
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+}
+
+void context::use_tmp_dh_file(const std::string& filename)
+{
+ boost::system::error_code ec;
+ use_tmp_dh_file(filename, ec);
+ boost::asio::detail::throw_error(ec, "use_tmp_dh_file");
+}
+
+boost::system::error_code context::use_tmp_dh_file(
+ const std::string& filename, boost::system::error_code& ec)
+{
+ bio_cleanup bio = { ::BIO_new_file(filename.c_str(), "r") };
+ if (bio.p)
+ {
+ return do_use_tmp_dh(bio.p, ec);
+ }
+
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+}
+
+boost::system::error_code context::do_use_tmp_dh(
+ BIO* bio, boost::system::error_code& ec)
+{
+ ::ERR_clear_error();
+
+ dh_cleanup dh = { ::PEM_read_bio_DHparams(bio, 0, 0, 0) };
+ if (dh.p)
+ {
+ if (::SSL_CTX_set_tmp_dh(handle_, dh.p) == 1)
+ {
+ ec = boost::system::error_code();
+ return ec;
+ }
+ }
+
+ ec = boost::system::error_code(
+ static_cast<int>(::ERR_get_error()),
+ boost::asio::error::get_ssl_category());
+ return ec;
+}
+
+boost::system::error_code context::do_set_verify_callback(
+ detail::verify_callback_base* callback, boost::system::error_code& ec)
+{
+ if (SSL_CTX_get_app_data(handle_))
+ {
+ delete static_cast<detail::verify_callback_base*>(
+ SSL_CTX_get_app_data(handle_));
+ }
+
+ SSL_CTX_set_app_data(handle_, callback);
+
+ ::SSL_CTX_set_verify(handle_,
+ ::SSL_CTX_get_verify_mode(handle_),
+ &context::verify_callback_function);
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+int context::verify_callback_function(int preverified, X509_STORE_CTX* ctx)
+{
+ if (ctx)
+ {
+ if (SSL* ssl = static_cast<SSL*>(
+ ::X509_STORE_CTX_get_ex_data(
+ ctx, ::SSL_get_ex_data_X509_STORE_CTX_idx())))
+ {
+ if (SSL_CTX* handle = ::SSL_get_SSL_CTX(ssl))
+ {
+ if (SSL_CTX_get_app_data(handle))
+ {
+ detail::verify_callback_base* callback =
+ static_cast<detail::verify_callback_base*>(
+ SSL_CTX_get_app_data(handle));
+
+ verify_context verify_ctx(ctx);
+ return callback->call(preverified != 0, verify_ctx) ? 1 : 0;
+ }
+ }
+ }
+ }
+
+ return 0;
+}
+
+boost::system::error_code context::do_set_password_callback(
+ detail::password_callback_base* callback, boost::system::error_code& ec)
+{
+ if (handle_->default_passwd_callback_userdata)
+ delete static_cast<detail::password_callback_base*>(
+ handle_->default_passwd_callback_userdata);
+
+ handle_->default_passwd_callback_userdata = callback;
+
+ SSL_CTX_set_default_passwd_cb(handle_, &context::password_callback_function);
+
+ ec = boost::system::error_code();
+ return ec;
+}
+
+int context::password_callback_function(
+ char* buf, int size, int purpose, void* data)
+{
+ using namespace std; // For strncat and strlen.
+
+ if (data)
+ {
+ detail::password_callback_base* callback =
+ static_cast<detail::password_callback_base*>(data);
+
+ std::string passwd = callback->call(static_cast<std::size_t>(size),
+ purpose ? context_base::for_writing : context_base::for_reading);
+
+#if defined(BOOST_ASIO_HAS_SECURE_RTL)
+ strcpy_s(buf, size, passwd.c_str());
+#else // defined(BOOST_ASIO_HAS_SECURE_RTL)
+ *buf = '\0';
+ strncat(buf, passwd.c_str(), size);
+#endif // defined(BOOST_ASIO_HAS_SECURE_RTL)
+
+ return static_cast<int>(strlen(buf));
+ }
+
+ return 0;
+}
+
+BIO* context::make_buffer_bio(const const_buffer& b)
+{
+ return ::BIO_new_mem_buf(
+ const_cast<void*>(buffer_cast<const void*>(b)),
+ static_cast<int>(buffer_size(b)));
+}
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_IMPL_CONTEXT_IPP
diff --git a/ext/patches/boost/asio/ssl/impl/error.ipp b/ext/patches/boost/asio/ssl/impl/error.ipp
new file mode 100644
index 0000000..c85c9ed
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/impl/error.ipp
@@ -0,0 +1,59 @@
+//
+// ssl/impl/error.ipp
+// ~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_IMPL_ERROR_IPP
+#define BOOST_ASIO_SSL_IMPL_ERROR_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/ssl/error.hpp>
+#include <boost/asio/ssl/detail/openssl_init.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace error {
+
+namespace detail {
+
+class ssl_category : public boost::system::error_category
+{
+public:
+ const char* name() const BOOST_ASIO_ERROR_CATEGORY_NOEXCEPT
+ {
+ return "asio.ssl";
+ }
+
+ std::string message(int value) const
+ {
+ const char* s = ::ERR_reason_error_string(value);
+ return s ? s : "asio.ssl error";
+ }
+};
+
+} // namespace detail
+
+const boost::system::error_category& get_ssl_category()
+{
+ static detail::ssl_category instance;
+ return instance;
+}
+
+} // namespace error
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_IMPL_ERROR_IPP
diff --git a/ext/patches/boost/asio/ssl/impl/rfc2818_verification.ipp b/ext/patches/boost/asio/ssl/impl/rfc2818_verification.ipp
new file mode 100644
index 0000000..e036204
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/impl/rfc2818_verification.ipp
@@ -0,0 +1,168 @@
+//
+// ssl/impl/rfc2818_verification.ipp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_IMPL_RFC2818_VERIFICATION_IPP
+#define BOOST_ASIO_SSL_IMPL_RFC2818_VERIFICATION_IPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <cctype>
+# include <cstring>
+# include <boost/asio/ip/address.hpp>
+# include <boost/asio/ssl/rfc2818_verification.hpp>
+# include <boost/asio/ssl/detail/openssl_types.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+bool rfc2818_verification::operator()(
+ bool preverified, verify_context& ctx) const
+{
+ using namespace std; // For memcmp.
+
+ // Don't bother looking at certificates that have failed pre-verification.
+ if (!preverified)
+ return false;
+
+ // We're only interested in checking the certificate at the end of the chain.
+ int depth = X509_STORE_CTX_get_error_depth(ctx.native_handle());
+ if (depth > 0)
+ return true;
+
+ // Try converting the host name to an address. If it is an address then we
+ // need to look for an IP address in the certificate rather than a host name.
+ boost::system::error_code ec;
+ ip::address address = ip::address::from_string(host_, ec);
+ bool is_address = !ec;
+
+ X509* cert = X509_STORE_CTX_get_current_cert(ctx.native_handle());
+
+ // Go through the alternate names in the certificate looking for matching DNS
+ // or IP address entries.
+ GENERAL_NAMES* gens = static_cast<GENERAL_NAMES*>(
+ X509_get_ext_d2i(cert, NID_subject_alt_name, 0, 0));
+ for (int i = 0; i < sk_GENERAL_NAME_num(gens); ++i)
+ {
+ GENERAL_NAME* gen = sk_GENERAL_NAME_value(gens, i);
+ if (gen->type == GEN_DNS && !is_address)
+ {
+ ASN1_IA5STRING* domain = gen->d.dNSName;
+ if (domain->type == V_ASN1_IA5STRING && domain->data && domain->length)
+ {
+ const char* pattern = reinterpret_cast<const char*>(domain->data);
+ std::size_t pattern_length = domain->length;
+ if (match_pattern(pattern, pattern_length, host_.c_str()))
+ {
+ GENERAL_NAMES_free(gens);
+ return true;
+ }
+ }
+ }
+ else if (gen->type == GEN_IPADD && is_address)
+ {
+ ASN1_OCTET_STRING* ip_address = gen->d.iPAddress;
+ if (ip_address->type == V_ASN1_OCTET_STRING && ip_address->data)
+ {
+ if (address.is_v4() && ip_address->length == 4)
+ {
+ ip::address_v4::bytes_type bytes = address.to_v4().to_bytes();
+ if (memcmp(bytes.data(), ip_address->data, 4) == 0)
+ {
+ GENERAL_NAMES_free(gens);
+ return true;
+ }
+ }
+ else if (address.is_v6() && ip_address->length == 16)
+ {
+ ip::address_v6::bytes_type bytes = address.to_v6().to_bytes();
+ if (memcmp(bytes.data(), ip_address->data, 16) == 0)
+ {
+ GENERAL_NAMES_free(gens);
+ return true;
+ }
+ }
+ }
+ }
+ }
+ GENERAL_NAMES_free(gens);
+
+ // No match in the alternate names, so try the common names. We should only
+ // use the "most specific" common name, which is the last one in the list.
+ X509_NAME* name = X509_get_subject_name(cert);
+ int i = -1;
+ ASN1_STRING* common_name = 0;
+ while ((i = X509_NAME_get_index_by_NID(name, NID_commonName, i)) >= 0)
+ {
+ X509_NAME_ENTRY* name_entry = X509_NAME_get_entry(name, i);
+ common_name = X509_NAME_ENTRY_get_data(name_entry);
+ }
+ if (common_name && common_name->data && common_name->length)
+ {
+ const char* pattern = reinterpret_cast<const char*>(common_name->data);
+ std::size_t pattern_length = common_name->length;
+ if (match_pattern(pattern, pattern_length, host_.c_str()))
+ return true;
+ }
+
+ return false;
+}
+
+bool rfc2818_verification::match_pattern(const char* pattern,
+ std::size_t pattern_length, const char* host)
+{
+ using namespace std; // For tolower.
+
+ const char* p = pattern;
+ const char* p_end = p + pattern_length;
+ const char* h = host;
+
+ while (p != p_end && *h)
+ {
+ if (*p == '*')
+ {
+ ++p;
+ while (*h && *h != '.')
+ if (match_pattern(p, p_end - p, h++))
+ return true;
+ }
+ else if (tolower(*p) == tolower(*h))
+ {
+ ++p;
+ ++h;
+ }
+ else
+ {
+ return false;
+ }
+ }
+
+ return p == p_end && !*h;
+}
+
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_IMPL_RFC2818_VERIFICATION_IPP
diff --git a/ext/patches/boost/asio/ssl/impl/src.hpp b/ext/patches/boost/asio/ssl/impl/src.hpp
new file mode 100644
index 0000000..175e3d6
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/impl/src.hpp
@@ -0,0 +1,28 @@
+//
+// impl/ssl/src.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_IMPL_SRC_HPP
+#define BOOST_ASIO_SSL_IMPL_SRC_HPP
+
+#define BOOST_ASIO_SOURCE
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# error Do not compile Asio library source with BOOST_ASIO_HEADER_ONLY defined
+#endif
+
+#include <boost/asio/ssl/impl/context.ipp>
+#include <boost/asio/ssl/impl/error.ipp>
+#include <boost/asio/ssl/detail/impl/engine.ipp>
+#include <boost/asio/ssl/detail/impl/openssl_init.ipp>
+#include <boost/asio/ssl/impl/rfc2818_verification.ipp>
+
+#endif // BOOST_ASIO_SSL_IMPL_SRC_HPP
diff --git a/ext/patches/boost/asio/ssl/old/basic_context.hpp b/ext/patches/boost/asio/ssl/old/basic_context.hpp
new file mode 100644
index 0000000..f2c54a1
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/old/basic_context.hpp
@@ -0,0 +1,436 @@
+//
+// ssl/old/basic_context.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_OLD_BASIC_CONTEXT_HPP
+#define BOOST_ASIO_SSL_OLD_BASIC_CONTEXT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/noncopyable.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ssl/context_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace old {
+
+/// SSL context.
+template <typename Service>
+class basic_context
+ : public context_base,
+ private boost::noncopyable
+{
+public:
+ /// The type of the service that will be used to provide context operations.
+ typedef Service service_type;
+
+ /// The native implementation type of the SSL context.
+ typedef typename service_type::impl_type impl_type;
+
+ /// Constructor.
+ basic_context(boost::asio::io_service& io_service, method m)
+ : service_(boost::asio::use_service<Service>(io_service)),
+ impl_(service_.null())
+ {
+ service_.create(impl_, m);
+ }
+
+ /// Destructor.
+ ~basic_context()
+ {
+ service_.destroy(impl_);
+ }
+
+ /// Get the underlying implementation in the native type.
+ /**
+ * This function may be used to obtain the underlying implementation of the
+ * context. This is intended to allow access to context functionality that is
+ * not otherwise provided.
+ */
+ impl_type impl()
+ {
+ return impl_;
+ }
+
+ /// Set options on the context.
+ /**
+ * This function may be used to configure the SSL options used by the context.
+ *
+ * @param o A bitmask of options. The available option values are defined in
+ * the context_base class. The options are bitwise-ored with any existing
+ * value for the options.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void set_options(options o)
+ {
+ boost::system::error_code ec;
+ service_.set_options(impl_, o, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Set options on the context.
+ /**
+ * This function may be used to configure the SSL options used by the context.
+ *
+ * @param o A bitmask of options. The available option values are defined in
+ * the context_base class. The options are bitwise-ored with any existing
+ * value for the options.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code set_options(options o,
+ boost::system::error_code& ec)
+ {
+ return service_.set_options(impl_, o, ec);
+ }
+
+ /// Set the peer verification mode.
+ /**
+ * This function may be used to configure the peer verification mode used by
+ * the context.
+ *
+ * @param v A bitmask of peer verification modes. The available verify_mode
+ * values are defined in the context_base class.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void set_verify_mode(verify_mode v)
+ {
+ boost::system::error_code ec;
+ service_.set_verify_mode(impl_, v, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Set the peer verification mode.
+ /**
+ * This function may be used to configure the peer verification mode used by
+ * the context.
+ *
+ * @param v A bitmask of peer verification modes. The available verify_mode
+ * values are defined in the context_base class.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code set_verify_mode(verify_mode v,
+ boost::system::error_code& ec)
+ {
+ return service_.set_verify_mode(impl_, v, ec);
+ }
+
+ /// Load a certification authority file for performing verification.
+ /**
+ * This function is used to load one or more trusted certification authorities
+ * from a file.
+ *
+ * @param filename The name of a file containing certification authority
+ * certificates in PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void load_verify_file(const std::string& filename)
+ {
+ boost::system::error_code ec;
+ service_.load_verify_file(impl_, filename, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Load a certification authority file for performing verification.
+ /**
+ * This function is used to load the certificates for one or more trusted
+ * certification authorities from a file.
+ *
+ * @param filename The name of a file containing certification authority
+ * certificates in PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code load_verify_file(const std::string& filename,
+ boost::system::error_code& ec)
+ {
+ return service_.load_verify_file(impl_, filename, ec);
+ }
+
+ /// Add a directory containing certificate authority files to be used for
+ /// performing verification.
+ /**
+ * This function is used to specify the name of a directory containing
+ * certification authority certificates. Each file in the directory must
+ * contain a single certificate. The files must be named using the subject
+ * name's hash and an extension of ".0".
+ *
+ * @param path The name of a directory containing the certificates.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void add_verify_path(const std::string& path)
+ {
+ boost::system::error_code ec;
+ service_.add_verify_path(impl_, path, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Add a directory containing certificate authority files to be used for
+ /// performing verification.
+ /**
+ * This function is used to specify the name of a directory containing
+ * certification authority certificates. Each file in the directory must
+ * contain a single certificate. The files must be named using the subject
+ * name's hash and an extension of ".0".
+ *
+ * @param path The name of a directory containing the certificates.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code add_verify_path(const std::string& path,
+ boost::system::error_code& ec)
+ {
+ return service_.add_verify_path(impl_, path, ec);
+ }
+
+ /// Use a certificate from a file.
+ /**
+ * This function is used to load a certificate into the context from a file.
+ *
+ * @param filename The name of the file containing the certificate.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void use_certificate_file(const std::string& filename, file_format format)
+ {
+ boost::system::error_code ec;
+ service_.use_certificate_file(impl_, filename, format, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Use a certificate from a file.
+ /**
+ * This function is used to load a certificate into the context from a file.
+ *
+ * @param filename The name of the file containing the certificate.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code use_certificate_file(const std::string& filename,
+ file_format format, boost::system::error_code& ec)
+ {
+ return service_.use_certificate_file(impl_, filename, format, ec);
+ }
+
+ /// Use a certificate chain from a file.
+ /**
+ * This function is used to load a certificate chain into the context from a
+ * file.
+ *
+ * @param filename The name of the file containing the certificate. The file
+ * must use the PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void use_certificate_chain_file(const std::string& filename)
+ {
+ boost::system::error_code ec;
+ service_.use_certificate_chain_file(impl_, filename, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Use a certificate chain from a file.
+ /**
+ * This function is used to load a certificate chain into the context from a
+ * file.
+ *
+ * @param filename The name of the file containing the certificate. The file
+ * must use the PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code use_certificate_chain_file(
+ const std::string& filename, boost::system::error_code& ec)
+ {
+ return service_.use_certificate_chain_file(impl_, filename, ec);
+ }
+
+ /// Use a private key from a file.
+ /**
+ * This function is used to load a private key into the context from a file.
+ *
+ * @param filename The name of the file containing the private key.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void use_private_key_file(const std::string& filename, file_format format)
+ {
+ boost::system::error_code ec;
+ service_.use_private_key_file(impl_, filename, format, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Use a private key from a file.
+ /**
+ * This function is used to load a private key into the context from a file.
+ *
+ * @param filename The name of the file containing the private key.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code use_private_key_file(const std::string& filename,
+ file_format format, boost::system::error_code& ec)
+ {
+ return service_.use_private_key_file(impl_, filename, format, ec);
+ }
+
+ /// Use an RSA private key from a file.
+ /**
+ * This function is used to load an RSA private key into the context from a
+ * file.
+ *
+ * @param filename The name of the file containing the RSA private key.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void use_rsa_private_key_file(const std::string& filename, file_format format)
+ {
+ boost::system::error_code ec;
+ service_.use_rsa_private_key_file(impl_, filename, format, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Use an RSA private key from a file.
+ /**
+ * This function is used to load an RSA private key into the context from a
+ * file.
+ *
+ * @param filename The name of the file containing the RSA private key.
+ *
+ * @param format The file format (ASN.1 or PEM).
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code use_rsa_private_key_file(
+ const std::string& filename, file_format format,
+ boost::system::error_code& ec)
+ {
+ return service_.use_rsa_private_key_file(impl_, filename, format, ec);
+ }
+
+ /// Use the specified file to obtain the temporary Diffie-Hellman parameters.
+ /**
+ * This function is used to load Diffie-Hellman parameters into the context
+ * from a file.
+ *
+ * @param filename The name of the file containing the Diffie-Hellman
+ * parameters. The file must use the PEM format.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void use_tmp_dh_file(const std::string& filename)
+ {
+ boost::system::error_code ec;
+ service_.use_tmp_dh_file(impl_, filename, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Use the specified file to obtain the temporary Diffie-Hellman parameters.
+ /**
+ * This function is used to load Diffie-Hellman parameters into the context
+ * from a file.
+ *
+ * @param filename The name of the file containing the Diffie-Hellman
+ * parameters. The file must use the PEM format.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code use_tmp_dh_file(const std::string& filename,
+ boost::system::error_code& ec)
+ {
+ return service_.use_tmp_dh_file(impl_, filename, ec);
+ }
+
+ /// Set the password callback.
+ /**
+ * This function is used to specify a callback function to obtain password
+ * information about an encrypted key in PEM format.
+ *
+ * @param callback The function object to be used for obtaining the password.
+ * The function signature of the handler must be:
+ * @code std::string password_callback(
+ * std::size_t max_length, // The maximum size for a password.
+ * password_purpose purpose // Whether password is for reading or writing.
+ * ); @endcode
+ * The return value of the callback is a string containing the password.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ template <typename PasswordCallback>
+ void set_password_callback(PasswordCallback callback)
+ {
+ boost::system::error_code ec;
+ service_.set_password_callback(impl_, callback, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Set the password callback.
+ /**
+ * This function is used to specify a callback function to obtain password
+ * information about an encrypted key in PEM format.
+ *
+ * @param callback The function object to be used for obtaining the password.
+ * The function signature of the handler must be:
+ * @code std::string password_callback(
+ * std::size_t max_length, // The maximum size for a password.
+ * password_purpose purpose // Whether password is for reading or writing.
+ * ); @endcode
+ * The return value of the callback is a string containing the password.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ template <typename PasswordCallback>
+ boost::system::error_code set_password_callback(PasswordCallback callback,
+ boost::system::error_code& ec)
+ {
+ return service_.set_password_callback(impl_, callback, ec);
+ }
+
+private:
+ /// The backend service implementation.
+ service_type& service_;
+
+ /// The underlying native implementation.
+ impl_type impl_;
+};
+
+} // namespace old
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_OLD_BASIC_CONTEXT_HPP
diff --git a/ext/patches/boost/asio/ssl/old/context_service.hpp b/ext/patches/boost/asio/ssl/old/context_service.hpp
new file mode 100644
index 0000000..1915792
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/old/context_service.hpp
@@ -0,0 +1,176 @@
+//
+// ssl/old/context_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_OLD_CONTEXT_SERVICE_HPP
+#define BOOST_ASIO_SSL_OLD_CONTEXT_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <string>
+#include <boost/noncopyable.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ssl/context_base.hpp>
+#include <boost/asio/ssl/old/detail/openssl_context_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace old {
+
+/// Default service implementation for a context.
+class context_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<context_service>
+#endif
+{
+private:
+ // The type of the platform-specific implementation.
+ typedef old::detail::openssl_context_service service_impl_type;
+
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The type of the context.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined impl_type;
+#else
+ typedef service_impl_type::impl_type impl_type;
+#endif
+
+ /// Constructor.
+ explicit context_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<context_service>(io_service),
+ service_impl_(boost::asio::use_service<service_impl_type>(io_service))
+ {
+ }
+
+ /// Return a null context implementation.
+ impl_type null() const
+ {
+ return service_impl_.null();
+ }
+
+ /// Create a new context implementation.
+ void create(impl_type& impl, context_base::method m)
+ {
+ service_impl_.create(impl, m);
+ }
+
+ /// Destroy a context implementation.
+ void destroy(impl_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Set options on the context.
+ boost::system::error_code set_options(impl_type& impl,
+ context_base::options o, boost::system::error_code& ec)
+ {
+ return service_impl_.set_options(impl, o, ec);
+ }
+
+ /// Set peer verification mode.
+ boost::system::error_code set_verify_mode(impl_type& impl,
+ context_base::verify_mode v, boost::system::error_code& ec)
+ {
+ return service_impl_.set_verify_mode(impl, v, ec);
+ }
+
+ /// Load a certification authority file for performing verification.
+ boost::system::error_code load_verify_file(impl_type& impl,
+ const std::string& filename, boost::system::error_code& ec)
+ {
+ return service_impl_.load_verify_file(impl, filename, ec);
+ }
+
+ /// Add a directory containing certification authority files to be used for
+ /// performing verification.
+ boost::system::error_code add_verify_path(impl_type& impl,
+ const std::string& path, boost::system::error_code& ec)
+ {
+ return service_impl_.add_verify_path(impl, path, ec);
+ }
+
+ /// Use a certificate from a file.
+ boost::system::error_code use_certificate_file(impl_type& impl,
+ const std::string& filename, context_base::file_format format,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.use_certificate_file(impl, filename, format, ec);
+ }
+
+ /// Use a certificate chain from a file.
+ boost::system::error_code use_certificate_chain_file(impl_type& impl,
+ const std::string& filename, boost::system::error_code& ec)
+ {
+ return service_impl_.use_certificate_chain_file(impl, filename, ec);
+ }
+
+ /// Use a private key from a file.
+ boost::system::error_code use_private_key_file(impl_type& impl,
+ const std::string& filename, context_base::file_format format,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.use_private_key_file(impl, filename, format, ec);
+ }
+
+ /// Use an RSA private key from a file.
+ boost::system::error_code use_rsa_private_key_file(impl_type& impl,
+ const std::string& filename, context_base::file_format format,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.use_rsa_private_key_file(impl, filename, format, ec);
+ }
+
+ /// Use the specified file to obtain the temporary Diffie-Hellman parameters.
+ boost::system::error_code use_tmp_dh_file(impl_type& impl,
+ const std::string& filename, boost::system::error_code& ec)
+ {
+ return service_impl_.use_tmp_dh_file(impl, filename, ec);
+ }
+
+ /// Set the password callback.
+ template <typename PasswordCallback>
+ boost::system::error_code set_password_callback(impl_type& impl,
+ PasswordCallback callback, boost::system::error_code& ec)
+ {
+ return service_impl_.set_password_callback(impl, callback, ec);
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ }
+
+ // The service that provides the platform-specific implementation.
+ service_impl_type& service_impl_;
+};
+
+} // namespace old
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_OLD_CONTEXT_SERVICE_HPP
diff --git a/ext/patches/boost/asio/ssl/old/detail/openssl_context_service.hpp b/ext/patches/boost/asio/ssl/old/detail/openssl_context_service.hpp
new file mode 100644
index 0000000..0f3ddbb
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/old/detail/openssl_context_service.hpp
@@ -0,0 +1,388 @@
+//
+// ssl/old/detail/openssl_context_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_CONTEXT_SERVICE_HPP
+#define BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_CONTEXT_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstring>
+#include <string>
+#include <boost/function.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ssl/context_base.hpp>
+#include <boost/asio/ssl/detail/openssl_init.hpp>
+#include <boost/asio/ssl/detail/openssl_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace old {
+namespace detail {
+
+class openssl_context_service
+ : public boost::asio::detail::service_base<openssl_context_service>
+{
+public:
+ // The native type of the context.
+ typedef ::SSL_CTX* impl_type;
+
+ // The type for the password callback function object.
+ typedef boost::function<std::string(std::size_t,
+ context_base::password_purpose)> password_callback_type;
+
+ // Constructor.
+ openssl_context_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<openssl_context_service>(io_service)
+ {
+ }
+
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ }
+
+ // Return a null context implementation.
+ static impl_type null()
+ {
+ return 0;
+ }
+
+ // Create a new context implementation.
+ void create(impl_type& impl, context_base::method m)
+ {
+ switch (m)
+ {
+#if defined(OPENSSL_NO_SSL2)
+ case context_base::sslv2:
+ case context_base::sslv2_client:
+ case context_base::sslv2_server:
+ boost::asio::detail::throw_error(boost::asio::error::invalid_argument);
+ break;
+#else // defined(OPENSSL_NO_SSL2)
+ case context_base::sslv2:
+ impl = ::SSL_CTX_new(::SSLv2_method());
+ break;
+ case context_base::sslv2_client:
+ impl = ::SSL_CTX_new(::SSLv2_client_method());
+ break;
+ case context_base::sslv2_server:
+ impl = ::SSL_CTX_new(::SSLv2_server_method());
+ break;
+#endif // defined(OPENSSL_NO_SSL2)
+ case context_base::sslv3:
+ impl = ::SSL_CTX_new(::SSLv3_method());
+ break;
+ case context_base::sslv3_client:
+ impl = ::SSL_CTX_new(::SSLv3_client_method());
+ break;
+ case context_base::sslv3_server:
+ impl = ::SSL_CTX_new(::SSLv3_server_method());
+ break;
+ case context_base::tlsv1:
+ impl = ::SSL_CTX_new(::TLSv1_method());
+ break;
+ case context_base::tlsv1_client:
+ impl = ::SSL_CTX_new(::TLSv1_client_method());
+ break;
+ case context_base::tlsv1_server:
+ impl = ::SSL_CTX_new(::TLSv1_server_method());
+ break;
+ case context_base::sslv23:
+ impl = ::SSL_CTX_new(::SSLv23_method());
+ break;
+ case context_base::sslv23_client:
+ impl = ::SSL_CTX_new(::SSLv23_client_method());
+ break;
+ case context_base::sslv23_server:
+ impl = ::SSL_CTX_new(::SSLv23_server_method());
+ break;
+ default:
+ impl = ::SSL_CTX_new(0);
+ break;
+ }
+ }
+
+ // Destroy a context implementation.
+ void destroy(impl_type& impl)
+ {
+ if (impl != null())
+ {
+ if (impl->default_passwd_callback_userdata)
+ {
+ password_callback_type* callback =
+ static_cast<password_callback_type*>(
+ impl->default_passwd_callback_userdata);
+ delete callback;
+ impl->default_passwd_callback_userdata = 0;
+ }
+
+ ::SSL_CTX_free(impl);
+ impl = null();
+ }
+ }
+
+ // Set options on the context.
+ boost::system::error_code set_options(impl_type& impl,
+ context_base::options o, boost::system::error_code& ec)
+ {
+ ::SSL_CTX_set_options(impl, o);
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Set peer verification mode.
+ boost::system::error_code set_verify_mode(impl_type& impl,
+ context_base::verify_mode v, boost::system::error_code& ec)
+ {
+ ::SSL_CTX_set_verify(impl, v, 0);
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Load a certification authority file for performing verification.
+ boost::system::error_code load_verify_file(impl_type& impl,
+ const std::string& filename, boost::system::error_code& ec)
+ {
+ if (::SSL_CTX_load_verify_locations(impl, filename.c_str(), 0) != 1)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Add a directory containing certification authority files to be used for
+ // performing verification.
+ boost::system::error_code add_verify_path(impl_type& impl,
+ const std::string& path, boost::system::error_code& ec)
+ {
+ if (::SSL_CTX_load_verify_locations(impl, 0, path.c_str()) != 1)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Use a certificate from a file.
+ boost::system::error_code use_certificate_file(impl_type& impl,
+ const std::string& filename, context_base::file_format format,
+ boost::system::error_code& ec)
+ {
+ int file_type;
+ switch (format)
+ {
+ case context_base::asn1:
+ file_type = SSL_FILETYPE_ASN1;
+ break;
+ case context_base::pem:
+ file_type = SSL_FILETYPE_PEM;
+ break;
+ default:
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+ }
+
+ if (::SSL_CTX_use_certificate_file(impl, filename.c_str(), file_type) != 1)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Use a certificate chain from a file.
+ boost::system::error_code use_certificate_chain_file(impl_type& impl,
+ const std::string& filename, boost::system::error_code& ec)
+ {
+ if (::SSL_CTX_use_certificate_chain_file(impl, filename.c_str()) != 1)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Use a private key from a file.
+ boost::system::error_code use_private_key_file(impl_type& impl,
+ const std::string& filename, context_base::file_format format,
+ boost::system::error_code& ec)
+ {
+ int file_type;
+ switch (format)
+ {
+ case context_base::asn1:
+ file_type = SSL_FILETYPE_ASN1;
+ break;
+ case context_base::pem:
+ file_type = SSL_FILETYPE_PEM;
+ break;
+ default:
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+ }
+
+ if (::SSL_CTX_use_PrivateKey_file(impl, filename.c_str(), file_type) != 1)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Use an RSA private key from a file.
+ boost::system::error_code use_rsa_private_key_file(impl_type& impl,
+ const std::string& filename, context_base::file_format format,
+ boost::system::error_code& ec)
+ {
+ int file_type;
+ switch (format)
+ {
+ case context_base::asn1:
+ file_type = SSL_FILETYPE_ASN1;
+ break;
+ case context_base::pem:
+ file_type = SSL_FILETYPE_PEM;
+ break;
+ default:
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+ }
+
+ if (::SSL_CTX_use_RSAPrivateKey_file(
+ impl, filename.c_str(), file_type) != 1)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Use the specified file to obtain the temporary Diffie-Hellman parameters.
+ boost::system::error_code use_tmp_dh_file(impl_type& impl,
+ const std::string& filename, boost::system::error_code& ec)
+ {
+ ::BIO* bio = ::BIO_new_file(filename.c_str(), "r");
+ if (!bio)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ::DH* dh = ::PEM_read_bio_DHparams(bio, 0, 0, 0);
+ if (!dh)
+ {
+ ::BIO_free(bio);
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ::BIO_free(bio);
+ int result = ::SSL_CTX_set_tmp_dh(impl, dh);
+ ::DH_free(dh);
+ if (result != 1)
+ {
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ static int password_callback(char* buf, int size, int purpose, void* data)
+ {
+ using namespace std; // For strncat and strlen.
+
+ if (data)
+ {
+ password_callback_type* callback =
+ static_cast<password_callback_type*>(data);
+ std::string passwd = (*callback)(static_cast<std::size_t>(size),
+ purpose ? context_base::for_writing : context_base::for_reading);
+ *buf = '\0';
+ strncat(buf, passwd.c_str(), size);
+ return strlen(buf);
+ }
+
+ return 0;
+ }
+
+ // Set the password callback.
+ template <typename Password_Callback>
+ boost::system::error_code set_password_callback(impl_type& impl,
+ Password_Callback callback, boost::system::error_code& ec)
+ {
+ // Allocate callback function object if not already present.
+ if (impl->default_passwd_callback_userdata)
+ {
+ password_callback_type* callback_function =
+ static_cast<password_callback_type*>(
+ impl->default_passwd_callback_userdata);
+ *callback_function = callback;
+ }
+ else
+ {
+ password_callback_type* callback_function =
+ new password_callback_type(callback);
+ impl->default_passwd_callback_userdata = callback_function;
+ }
+
+ // Set the password callback.
+ SSL_CTX_set_default_passwd_cb(impl,
+ &openssl_context_service::password_callback);
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+private:
+ // Ensure openssl is initialised.
+ boost::asio::ssl::detail::openssl_init<> init_;
+};
+
+} // namespace detail
+} // namespace old
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_CONTEXT_SERVICE_HPP
diff --git a/ext/patches/boost/asio/ssl/old/detail/openssl_operation.hpp b/ext/patches/boost/asio/ssl/old/detail/openssl_operation.hpp
new file mode 100644
index 0000000..3f6338c
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/old/detail/openssl_operation.hpp
@@ -0,0 +1,526 @@
+//
+// ssl/old/detail/openssl_operation.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_OPERATION_HPP
+#define BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_OPERATION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/function.hpp>
+#include <boost/bind.hpp>
+#include <boost/asio/buffer.hpp>
+#include <boost/asio/detail/assert.hpp>
+#include <boost/asio/detail/socket_ops.hpp>
+#include <boost/asio/placeholders.hpp>
+#include <boost/asio/ssl/detail/openssl_types.hpp>
+#include <boost/asio/ssl/error.hpp>
+#include <boost/asio/strand.hpp>
+#include <boost/system/system_error.hpp>
+#include <boost/asio/write.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace old {
+namespace detail {
+
+typedef boost::function<int (::SSL*)> ssl_primitive_func;
+typedef boost::function<void (const boost::system::error_code&, int)>
+ user_handler_func;
+
+// Network send_/recv buffer implementation
+//
+//
+class net_buffer
+{
+ static const int NET_BUF_SIZE = 16*1024 + 256; // SSL record size + spare
+
+ unsigned char buf_[NET_BUF_SIZE];
+ unsigned char* data_start_;
+ unsigned char* data_end_;
+
+public:
+ net_buffer()
+ {
+ data_start_ = data_end_ = buf_;
+ }
+ unsigned char* get_unused_start() { return data_end_; }
+ unsigned char* get_data_start() { return data_start_; }
+ size_t get_unused_len() { return (NET_BUF_SIZE - (data_end_ - buf_)); }
+ size_t get_data_len() { return (data_end_ - data_start_); }
+ void data_added(size_t count)
+ {
+ data_end_ += count;
+ data_end_ = data_end_ > (buf_ + NET_BUF_SIZE)?
+ (buf_ + NET_BUF_SIZE):
+ data_end_;
+ }
+ void data_removed(size_t count)
+ {
+ data_start_ += count;
+ if (data_start_ >= data_end_) reset();
+ }
+ void reset() { data_start_ = buf_; data_end_ = buf_; }
+ bool has_data() { return (data_start_ < data_end_); }
+}; // class net_buffer
+
+//
+// Operation class
+//
+//
+template <typename Stream>
+class openssl_operation
+{
+public:
+
+ // Constructor for asynchronous operations
+ openssl_operation(ssl_primitive_func primitive,
+ Stream& socket,
+ net_buffer& recv_buf,
+ SSL* session,
+ BIO* ssl_bio,
+ user_handler_func handler,
+ boost::asio::io_service::strand& strand
+ )
+ : primitive_(primitive)
+ , user_handler_(handler)
+ , strand_(&strand)
+ , recv_buf_(recv_buf)
+ , socket_(socket)
+ , ssl_bio_(ssl_bio)
+ , session_(session)
+ {
+ write_ = boost::bind(
+ &openssl_operation::do_async_write,
+ this, boost::arg<1>(), boost::arg<2>()
+ );
+ read_ = boost::bind(
+ &openssl_operation::do_async_read,
+ this
+ );
+ handler_= boost::bind(
+ &openssl_operation::async_user_handler,
+ this, boost::arg<1>(), boost::arg<2>()
+ );
+ }
+
+ // Constructor for synchronous operations
+ openssl_operation(ssl_primitive_func primitive,
+ Stream& socket,
+ net_buffer& recv_buf,
+ SSL* session,
+ BIO* ssl_bio)
+ : primitive_(primitive)
+ , strand_(0)
+ , recv_buf_(recv_buf)
+ , socket_(socket)
+ , ssl_bio_(ssl_bio)
+ , session_(session)
+ {
+ write_ = boost::bind(
+ &openssl_operation::do_sync_write,
+ this, boost::arg<1>(), boost::arg<2>()
+ );
+ read_ = boost::bind(
+ &openssl_operation::do_sync_read,
+ this
+ );
+ handler_ = boost::bind(
+ &openssl_operation::sync_user_handler,
+ this, boost::arg<1>(), boost::arg<2>()
+ );
+ }
+
+ // Start operation
+ // In case of asynchronous it returns 0, in sync mode returns success code
+ // or throws an error...
+ int start()
+ {
+ int rc = primitive_( session_ );
+
+ bool is_operation_done = (rc > 0);
+ // For connect/accept/shutdown, the operation
+ // is done, when return code is 1
+ // for write, it is done, when is retcode > 0
+ // for read, it is done when retcode > 0
+
+ int error_code = !is_operation_done ?
+ ::SSL_get_error( session_, rc ) :
+ 0;
+ int sys_error_code = ERR_get_error();
+
+ if (error_code == SSL_ERROR_SSL)
+ return handler_(boost::system::error_code(
+ sys_error_code, boost::asio::error::get_ssl_category()), rc);
+
+ bool is_read_needed = (error_code == SSL_ERROR_WANT_READ);
+ bool is_write_needed = (error_code == SSL_ERROR_WANT_WRITE ||
+ ::BIO_ctrl_pending( ssl_bio_ ));
+ bool is_shut_down_received =
+ ((::SSL_get_shutdown( session_ ) & SSL_RECEIVED_SHUTDOWN) ==
+ SSL_RECEIVED_SHUTDOWN);
+ bool is_shut_down_sent =
+ ((::SSL_get_shutdown( session_ ) & SSL_SENT_SHUTDOWN) ==
+ SSL_SENT_SHUTDOWN);
+
+ if (is_shut_down_sent && is_shut_down_received
+ && is_operation_done && !is_write_needed)
+ // SSL connection is shut down cleanly
+ return handler_(boost::system::error_code(), 1);
+
+ if (is_shut_down_received && !is_operation_done)
+ // Shutdown has been requested, while we were reading or writing...
+ // abort our action...
+ return handler_(boost::asio::error::shut_down, 0);
+
+ if (!is_operation_done && !is_read_needed && !is_write_needed
+ && !is_shut_down_sent)
+ {
+ // The operation has failed... It is not completed and does
+ // not want network communication nor does want to send shutdown out...
+ if (error_code == SSL_ERROR_SYSCALL)
+ {
+ return handler_(boost::system::error_code(
+ sys_error_code, boost::asio::error::system_category), rc);
+ }
+ else
+ {
+ return handler_(boost::system::error_code(
+ sys_error_code, boost::asio::error::get_ssl_category()), rc);
+ }
+ }
+
+ if (!is_operation_done && !is_write_needed)
+ {
+ // We may have left over data that we can pass to SSL immediately
+ if (recv_buf_.get_data_len() > 0)
+ {
+ // Pass the buffered data to SSL
+ int written = ::BIO_write
+ (
+ ssl_bio_,
+ recv_buf_.get_data_start(),
+ recv_buf_.get_data_len()
+ );
+
+ if (written > 0)
+ {
+ recv_buf_.data_removed(written);
+ }
+ else if (written < 0)
+ {
+ if (!BIO_should_retry(ssl_bio_))
+ {
+ // Some serios error with BIO....
+ return handler_(boost::asio::error::no_recovery, 0);
+ }
+ }
+
+ return start();
+ }
+ else if (is_read_needed || (is_shut_down_sent && !is_shut_down_received))
+ {
+ return read_();
+ }
+ }
+
+ // Continue with operation, flush any SSL data out to network...
+ return write_(is_operation_done, rc);
+ }
+
+// Private implementation
+private:
+ typedef boost::function<int (const boost::system::error_code&, int)>
+ int_handler_func;
+ typedef boost::function<int (bool, int)> write_func;
+ typedef boost::function<int ()> read_func;
+
+ ssl_primitive_func primitive_;
+ user_handler_func user_handler_;
+ boost::asio::io_service::strand* strand_;
+ write_func write_;
+ read_func read_;
+ int_handler_func handler_;
+
+ net_buffer send_buf_; // buffers for network IO
+
+ // The recv buffer is owned by the stream, not the operation, since there can
+ // be left over bytes after passing the data up to the application, and these
+ // bytes need to be kept around for the next read operation issued by the
+ // application.
+ net_buffer& recv_buf_;
+
+ Stream& socket_;
+ BIO* ssl_bio_;
+ SSL* session_;
+
+ //
+ int sync_user_handler(const boost::system::error_code& error, int rc)
+ {
+ if (!error)
+ return rc;
+
+ throw boost::system::system_error(error);
+ }
+
+ int async_user_handler(boost::system::error_code error, int rc)
+ {
+ if (rc < 0)
+ {
+ if (!error)
+ error = boost::asio::error::no_recovery;
+ rc = 0;
+ }
+
+ user_handler_(error, rc);
+ return 0;
+ }
+
+ // Writes bytes asynchronously from SSL to NET
+ int do_async_write(bool is_operation_done, int rc)
+ {
+ int len = ::BIO_ctrl_pending( ssl_bio_ );
+ if ( len )
+ {
+ // There is something to write into net, do it...
+ len = (int)send_buf_.get_unused_len() > len?
+ len:
+ send_buf_.get_unused_len();
+
+ if (len == 0)
+ {
+ // In case our send buffer is full, we have just to wait until
+ // previous send to complete...
+ return 0;
+ }
+
+ // Read outgoing data from bio
+ len = ::BIO_read( ssl_bio_, send_buf_.get_unused_start(), len);
+
+ if (len > 0)
+ {
+ unsigned char *data_start = send_buf_.get_unused_start();
+ send_buf_.data_added(len);
+
+ BOOST_ASIO_ASSERT(strand_);
+ boost::asio::async_write
+ (
+ socket_,
+ boost::asio::buffer(data_start, len),
+ strand_->wrap
+ (
+ boost::bind
+ (
+ &openssl_operation::async_write_handler,
+ this,
+ is_operation_done,
+ rc,
+ boost::asio::placeholders::error,
+ boost::asio::placeholders::bytes_transferred
+ )
+ )
+ );
+
+ return 0;
+ }
+ else if (!BIO_should_retry(ssl_bio_))
+ {
+ // Seems like fatal error
+ // reading from SSL BIO has failed...
+ handler_(boost::asio::error::no_recovery, 0);
+ return 0;
+ }
+ }
+
+ if (is_operation_done)
+ {
+ // Finish the operation, with success
+ handler_(boost::system::error_code(), rc);
+ return 0;
+ }
+
+ // OPeration is not done and writing to net has been made...
+ // start operation again
+ start();
+
+ return 0;
+ }
+
+ void async_write_handler(bool is_operation_done, int rc,
+ const boost::system::error_code& error, size_t bytes_sent)
+ {
+ if (!error)
+ {
+ // Remove data from send buffer
+ send_buf_.data_removed(bytes_sent);
+
+ if (is_operation_done)
+ handler_(boost::system::error_code(), rc);
+ else
+ // Since the operation was not completed, try it again...
+ start();
+ }
+ else
+ handler_(error, rc);
+ }
+
+ int do_async_read()
+ {
+ // Wait for new data
+ BOOST_ASIO_ASSERT(strand_);
+ socket_.async_read_some
+ (
+ boost::asio::buffer(recv_buf_.get_unused_start(),
+ recv_buf_.get_unused_len()),
+ strand_->wrap
+ (
+ boost::bind
+ (
+ &openssl_operation::async_read_handler,
+ this,
+ boost::asio::placeholders::error,
+ boost::asio::placeholders::bytes_transferred
+ )
+ )
+ );
+ return 0;
+ }
+
+ void async_read_handler(const boost::system::error_code& error,
+ size_t bytes_recvd)
+ {
+ if (!error)
+ {
+ recv_buf_.data_added(bytes_recvd);
+
+ // Pass the received data to SSL
+ int written = ::BIO_write
+ (
+ ssl_bio_,
+ recv_buf_.get_data_start(),
+ recv_buf_.get_data_len()
+ );
+
+ if (written > 0)
+ {
+ recv_buf_.data_removed(written);
+ }
+ else if (written < 0)
+ {
+ if (!BIO_should_retry(ssl_bio_))
+ {
+ // Some serios error with BIO....
+ handler_(boost::asio::error::no_recovery, 0);
+ return;
+ }
+ }
+
+ // and try the SSL primitive again
+ start();
+ }
+ else
+ {
+ // Error in network level...
+ // SSL can't continue either...
+ handler_(error, 0);
+ }
+ }
+
+ // Syncronous functions...
+ int do_sync_write(bool is_operation_done, int rc)
+ {
+ int len = ::BIO_ctrl_pending( ssl_bio_ );
+ if ( len )
+ {
+ // There is something to write into net, do it...
+ len = (int)send_buf_.get_unused_len() > len?
+ len:
+ send_buf_.get_unused_len();
+
+ // Read outgoing data from bio
+ len = ::BIO_read( ssl_bio_, send_buf_.get_unused_start(), len);
+
+ if (len > 0)
+ {
+ size_t sent_len = boost::asio::write(
+ socket_,
+ boost::asio::buffer(send_buf_.get_unused_start(), len)
+ );
+
+ send_buf_.data_added(len);
+ send_buf_.data_removed(sent_len);
+ }
+ else if (!BIO_should_retry(ssl_bio_))
+ {
+ // Seems like fatal error
+ // reading from SSL BIO has failed...
+ throw boost::system::system_error(boost::asio::error::no_recovery);
+ }
+ }
+
+ if (is_operation_done)
+ // Finish the operation, with success
+ return rc;
+
+ // Operation is not finished, start again.
+ return start();
+ }
+
+ int do_sync_read()
+ {
+ size_t len = socket_.read_some
+ (
+ boost::asio::buffer(recv_buf_.get_unused_start(),
+ recv_buf_.get_unused_len())
+ );
+
+ // Write data to ssl
+ recv_buf_.data_added(len);
+
+ // Pass the received data to SSL
+ int written = ::BIO_write
+ (
+ ssl_bio_,
+ recv_buf_.get_data_start(),
+ recv_buf_.get_data_len()
+ );
+
+ if (written > 0)
+ {
+ recv_buf_.data_removed(written);
+ }
+ else if (written < 0)
+ {
+ if (!BIO_should_retry(ssl_bio_))
+ {
+ // Some serios error with BIO....
+ throw boost::system::system_error(boost::asio::error::no_recovery);
+ }
+ }
+
+ // Try the operation again
+ return start();
+ }
+}; // class openssl_operation
+
+} // namespace detail
+} // namespace old
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_OPERATION_HPP
diff --git a/ext/patches/boost/asio/ssl/old/detail/openssl_stream_service.hpp b/ext/patches/boost/asio/ssl/old/detail/openssl_stream_service.hpp
new file mode 100644
index 0000000..752ea31
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/old/detail/openssl_stream_service.hpp
@@ -0,0 +1,573 @@
+//
+// ssl/old/detail/stream_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_STREAM_SERVICE_HPP
+#define BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_STREAM_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <climits>
+#include <memory>
+#include <boost/config.hpp>
+#include <boost/noncopyable.hpp>
+#include <boost/function.hpp>
+#include <boost/bind.hpp>
+#include <boost/asio/detail/buffer_sequence_adapter.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ssl/basic_context.hpp>
+#include <boost/asio/ssl/stream_base.hpp>
+#include <boost/asio/ssl/old/detail/openssl_operation.hpp>
+#include <boost/asio/ssl/detail/openssl_types.hpp>
+#include <boost/asio/strand.hpp>
+#include <boost/system/system_error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace old {
+namespace detail {
+
+class openssl_stream_service
+ : public boost::asio::detail::service_base<openssl_stream_service>
+{
+private:
+ enum { max_buffer_size = INT_MAX };
+
+ //Base handler for asyncrhonous operations
+ template <typename Stream>
+ class base_handler
+ {
+ public:
+ typedef boost::function<
+ void (const boost::system::error_code&, size_t)> func_t;
+
+ base_handler(boost::asio::io_service& io_service)
+ : op_(NULL)
+ , io_service_(io_service)
+ , work_(io_service)
+ {}
+
+ void do_func(const boost::system::error_code& error, size_t size)
+ {
+ func_(error, size);
+ }
+
+ void set_operation(openssl_operation<Stream>* op) { op_ = op; }
+ void set_func(func_t func) { func_ = func; }
+
+ ~base_handler()
+ {
+ delete op_;
+ }
+
+ private:
+ func_t func_;
+ openssl_operation<Stream>* op_;
+ boost::asio::io_service& io_service_;
+ boost::asio::io_service::work work_;
+ }; // class base_handler
+
+ // Handler for asynchronous IO (write/read) operations
+ template<typename Stream, typename Handler>
+ class io_handler
+ : public base_handler<Stream>
+ {
+ public:
+ io_handler(Handler handler, boost::asio::io_service& io_service)
+ : base_handler<Stream>(io_service)
+ , handler_(handler)
+ {
+ this->set_func(boost::bind(
+ &io_handler<Stream, Handler>::handler_impl,
+ this, boost::arg<1>(), boost::arg<2>() ));
+ }
+
+ private:
+ Handler handler_;
+ void handler_impl(const boost::system::error_code& error, size_t size)
+ {
+ std::auto_ptr<io_handler<Stream, Handler> > this_ptr(this);
+ handler_(error, size);
+ }
+ }; // class io_handler
+
+ // Handler for asyncrhonous handshake (connect, accept) functions
+ template <typename Stream, typename Handler>
+ class handshake_handler
+ : public base_handler<Stream>
+ {
+ public:
+ handshake_handler(Handler handler, boost::asio::io_service& io_service)
+ : base_handler<Stream>(io_service)
+ , handler_(handler)
+ {
+ this->set_func(boost::bind(
+ &handshake_handler<Stream, Handler>::handler_impl,
+ this, boost::arg<1>(), boost::arg<2>() ));
+ }
+
+ private:
+ Handler handler_;
+ void handler_impl(const boost::system::error_code& error, size_t)
+ {
+ std::auto_ptr<handshake_handler<Stream, Handler> > this_ptr(this);
+ handler_(error);
+ }
+
+ }; // class handshake_handler
+
+ // Handler for asyncrhonous shutdown
+ template <typename Stream, typename Handler>
+ class shutdown_handler
+ : public base_handler<Stream>
+ {
+ public:
+ shutdown_handler(Handler handler, boost::asio::io_service& io_service)
+ : base_handler<Stream>(io_service),
+ handler_(handler)
+ {
+ this->set_func(boost::bind(
+ &shutdown_handler<Stream, Handler>::handler_impl,
+ this, boost::arg<1>(), boost::arg<2>() ));
+ }
+
+ private:
+ Handler handler_;
+ void handler_impl(const boost::system::error_code& error, size_t)
+ {
+ std::auto_ptr<shutdown_handler<Stream, Handler> > this_ptr(this);
+ handler_(error);
+ }
+ }; // class shutdown_handler
+
+public:
+ // The implementation type.
+ typedef struct impl_struct
+ {
+ ::SSL* ssl;
+ ::BIO* ext_bio;
+ net_buffer recv_buf;
+ } * impl_type;
+
+ // Construct a new stream socket service for the specified io_service.
+ explicit openssl_stream_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<openssl_stream_service>(io_service),
+ strand_(io_service)
+ {
+ }
+
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ }
+
+ // Return a null stream implementation.
+ impl_type null() const
+ {
+ return 0;
+ }
+
+ // Create a new stream implementation.
+ template <typename Stream, typename Context_Service>
+ void create(impl_type& impl, Stream& /*next_layer*/,
+ basic_context<Context_Service>& context)
+ {
+ impl = new impl_struct;
+ impl->ssl = ::SSL_new(context.impl());
+ ::SSL_set_mode(impl->ssl, SSL_MODE_ENABLE_PARTIAL_WRITE);
+ ::SSL_set_mode(impl->ssl, SSL_MODE_ACCEPT_MOVING_WRITE_BUFFER);
+ ::BIO* int_bio = 0;
+ impl->ext_bio = 0;
+ ::BIO_new_bio_pair(&int_bio, 8192, &impl->ext_bio, 8192);
+ ::SSL_set_bio(impl->ssl, int_bio, int_bio);
+ }
+
+ // Destroy a stream implementation.
+ template <typename Stream>
+ void destroy(impl_type& impl, Stream& /*next_layer*/)
+ {
+ if (impl != 0)
+ {
+ ::BIO_free(impl->ext_bio);
+ ::SSL_free(impl->ssl);
+ delete impl;
+ impl = 0;
+ }
+ }
+
+ // Perform SSL handshaking.
+ template <typename Stream>
+ boost::system::error_code handshake(impl_type& impl, Stream& next_layer,
+ stream_base::handshake_type type, boost::system::error_code& ec)
+ {
+ try
+ {
+ openssl_operation<Stream> op(
+ type == stream_base::client ?
+ &ssl_wrap<mutex_type>::SSL_connect:
+ &ssl_wrap<mutex_type>::SSL_accept,
+ next_layer,
+ impl->recv_buf,
+ impl->ssl,
+ impl->ext_bio);
+ op.start();
+ }
+ catch (boost::system::system_error& e)
+ {
+ ec = e.code();
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Start an asynchronous SSL handshake.
+ template <typename Stream, typename Handler>
+ void async_handshake(impl_type& impl, Stream& next_layer,
+ stream_base::handshake_type type, Handler handler)
+ {
+ typedef handshake_handler<Stream, Handler> connect_handler;
+
+ connect_handler* local_handler =
+ new connect_handler(handler, get_io_service());
+
+ openssl_operation<Stream>* op = new openssl_operation<Stream>
+ (
+ type == stream_base::client ?
+ &ssl_wrap<mutex_type>::SSL_connect:
+ &ssl_wrap<mutex_type>::SSL_accept,
+ next_layer,
+ impl->recv_buf,
+ impl->ssl,
+ impl->ext_bio,
+ boost::bind
+ (
+ &base_handler<Stream>::do_func,
+ local_handler,
+ boost::arg<1>(),
+ boost::arg<2>()
+ ),
+ strand_
+ );
+ local_handler->set_operation(op);
+
+ strand_.post(boost::bind(&openssl_operation<Stream>::start, op));
+ }
+
+ // Shut down SSL on the stream.
+ template <typename Stream>
+ boost::system::error_code shutdown(impl_type& impl, Stream& next_layer,
+ boost::system::error_code& ec)
+ {
+ try
+ {
+ openssl_operation<Stream> op(
+ &ssl_wrap<mutex_type>::SSL_shutdown,
+ next_layer,
+ impl->recv_buf,
+ impl->ssl,
+ impl->ext_bio);
+ op.start();
+ }
+ catch (boost::system::system_error& e)
+ {
+ ec = e.code();
+ return ec;
+ }
+
+ ec = boost::system::error_code();
+ return ec;
+ }
+
+ // Asynchronously shut down SSL on the stream.
+ template <typename Stream, typename Handler>
+ void async_shutdown(impl_type& impl, Stream& next_layer, Handler handler)
+ {
+ typedef shutdown_handler<Stream, Handler> disconnect_handler;
+
+ disconnect_handler* local_handler =
+ new disconnect_handler(handler, get_io_service());
+
+ openssl_operation<Stream>* op = new openssl_operation<Stream>
+ (
+ &ssl_wrap<mutex_type>::SSL_shutdown,
+ next_layer,
+ impl->recv_buf,
+ impl->ssl,
+ impl->ext_bio,
+ boost::bind
+ (
+ &base_handler<Stream>::do_func,
+ local_handler,
+ boost::arg<1>(),
+ boost::arg<2>()
+ ),
+ strand_
+ );
+ local_handler->set_operation(op);
+
+ strand_.post(boost::bind(&openssl_operation<Stream>::start, op));
+ }
+
+ // Write some data to the stream.
+ template <typename Stream, typename Const_Buffers>
+ std::size_t write_some(impl_type& impl, Stream& next_layer,
+ const Const_Buffers& buffers, boost::system::error_code& ec)
+ {
+ size_t bytes_transferred = 0;
+ try
+ {
+ boost::asio::const_buffer buffer =
+ boost::asio::detail::buffer_sequence_adapter<
+ boost::asio::const_buffer, Const_Buffers>::first(buffers);
+
+ std::size_t buffer_size = boost::asio::buffer_size(buffer);
+ if (buffer_size > max_buffer_size)
+ buffer_size = max_buffer_size;
+ else if (buffer_size == 0)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ boost::function<int (SSL*)> send_func =
+ boost::bind(boost::type<int>(), &::SSL_write, boost::arg<1>(),
+ boost::asio::buffer_cast<const void*>(buffer),
+ static_cast<int>(buffer_size));
+ openssl_operation<Stream> op(
+ send_func,
+ next_layer,
+ impl->recv_buf,
+ impl->ssl,
+ impl->ext_bio
+ );
+ bytes_transferred = static_cast<size_t>(op.start());
+ }
+ catch (boost::system::system_error& e)
+ {
+ ec = e.code();
+ return 0;
+ }
+
+ ec = boost::system::error_code();
+ return bytes_transferred;
+ }
+
+ // Start an asynchronous write.
+ template <typename Stream, typename Const_Buffers, typename Handler>
+ void async_write_some(impl_type& impl, Stream& next_layer,
+ const Const_Buffers& buffers, Handler handler)
+ {
+ typedef io_handler<Stream, Handler> send_handler;
+
+ boost::asio::const_buffer buffer =
+ boost::asio::detail::buffer_sequence_adapter<
+ boost::asio::const_buffer, Const_Buffers>::first(buffers);
+
+ std::size_t buffer_size = boost::asio::buffer_size(buffer);
+ if (buffer_size > max_buffer_size)
+ buffer_size = max_buffer_size;
+ else if (buffer_size == 0)
+ {
+ get_io_service().post(boost::asio::detail::bind_handler(
+ handler, boost::system::error_code(), 0));
+ return;
+ }
+
+ send_handler* local_handler = new send_handler(handler, get_io_service());
+
+ boost::function<int (SSL*)> send_func =
+ boost::bind(boost::type<int>(), &::SSL_write, boost::arg<1>(),
+ boost::asio::buffer_cast<const void*>(buffer),
+ static_cast<int>(buffer_size));
+
+ openssl_operation<Stream>* op = new openssl_operation<Stream>
+ (
+ send_func,
+ next_layer,
+ impl->recv_buf,
+ impl->ssl,
+ impl->ext_bio,
+ boost::bind
+ (
+ &base_handler<Stream>::do_func,
+ local_handler,
+ boost::arg<1>(),
+ boost::arg<2>()
+ ),
+ strand_
+ );
+ local_handler->set_operation(op);
+
+ strand_.post(boost::bind(&openssl_operation<Stream>::start, op));
+ }
+
+ // Read some data from the stream.
+ template <typename Stream, typename Mutable_Buffers>
+ std::size_t read_some(impl_type& impl, Stream& next_layer,
+ const Mutable_Buffers& buffers, boost::system::error_code& ec)
+ {
+ size_t bytes_transferred = 0;
+ try
+ {
+ boost::asio::mutable_buffer buffer =
+ boost::asio::detail::buffer_sequence_adapter<
+ boost::asio::mutable_buffer, Mutable_Buffers>::first(buffers);
+
+ std::size_t buffer_size = boost::asio::buffer_size(buffer);
+ if (buffer_size > max_buffer_size)
+ buffer_size = max_buffer_size;
+ else if (buffer_size == 0)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ boost::function<int (SSL*)> recv_func =
+ boost::bind(boost::type<int>(), &::SSL_read, boost::arg<1>(),
+ boost::asio::buffer_cast<void*>(buffer),
+ static_cast<int>(buffer_size));
+ openssl_operation<Stream> op(recv_func,
+ next_layer,
+ impl->recv_buf,
+ impl->ssl,
+ impl->ext_bio
+ );
+
+ bytes_transferred = static_cast<size_t>(op.start());
+ }
+ catch (boost::system::system_error& e)
+ {
+ ec = e.code();
+ return 0;
+ }
+
+ ec = boost::system::error_code();
+ return bytes_transferred;
+ }
+
+ // Start an asynchronous read.
+ template <typename Stream, typename Mutable_Buffers, typename Handler>
+ void async_read_some(impl_type& impl, Stream& next_layer,
+ const Mutable_Buffers& buffers, Handler handler)
+ {
+ typedef io_handler<Stream, Handler> recv_handler;
+
+ boost::asio::mutable_buffer buffer =
+ boost::asio::detail::buffer_sequence_adapter<
+ boost::asio::mutable_buffer, Mutable_Buffers>::first(buffers);
+
+ std::size_t buffer_size = boost::asio::buffer_size(buffer);
+ if (buffer_size > max_buffer_size)
+ buffer_size = max_buffer_size;
+ else if (buffer_size == 0)
+ {
+ get_io_service().post(boost::asio::detail::bind_handler(
+ handler, boost::system::error_code(), 0));
+ return;
+ }
+
+ recv_handler* local_handler = new recv_handler(handler, get_io_service());
+
+ boost::function<int (SSL*)> recv_func =
+ boost::bind(boost::type<int>(), &::SSL_read, boost::arg<1>(),
+ boost::asio::buffer_cast<void*>(buffer),
+ static_cast<int>(buffer_size));
+
+ openssl_operation<Stream>* op = new openssl_operation<Stream>
+ (
+ recv_func,
+ next_layer,
+ impl->recv_buf,
+ impl->ssl,
+ impl->ext_bio,
+ boost::bind
+ (
+ &base_handler<Stream>::do_func,
+ local_handler,
+ boost::arg<1>(),
+ boost::arg<2>()
+ ),
+ strand_
+ );
+ local_handler->set_operation(op);
+
+ strand_.post(boost::bind(&openssl_operation<Stream>::start, op));
+ }
+
+ // Peek at the incoming data on the stream.
+ template <typename Stream, typename Mutable_Buffers>
+ std::size_t peek(impl_type& /*impl*/, Stream& /*next_layer*/,
+ const Mutable_Buffers& /*buffers*/, boost::system::error_code& ec)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+ // Determine the amount of data that may be read without blocking.
+ template <typename Stream>
+ std::size_t in_avail(impl_type& /*impl*/, Stream& /*next_layer*/,
+ boost::system::error_code& ec)
+ {
+ ec = boost::system::error_code();
+ return 0;
+ }
+
+private:
+ boost::asio::io_service::strand strand_;
+
+ typedef boost::asio::detail::mutex mutex_type;
+
+ template<typename Mutex>
+ struct ssl_wrap
+ {
+ static Mutex ssl_mutex_;
+
+ static int SSL_accept(SSL *ssl)
+ {
+ typename Mutex::scoped_lock lock(ssl_mutex_);
+ return ::SSL_accept(ssl);
+ }
+
+ static int SSL_connect(SSL *ssl)
+ {
+ typename Mutex::scoped_lock lock(ssl_mutex_);
+ return ::SSL_connect(ssl);
+ }
+
+ static int SSL_shutdown(SSL *ssl)
+ {
+ typename Mutex::scoped_lock lock(ssl_mutex_);
+ return ::SSL_shutdown(ssl);
+ }
+ };
+};
+
+template<typename Mutex>
+Mutex openssl_stream_service::ssl_wrap<Mutex>::ssl_mutex_;
+
+} // namespace detail
+} // namespace old
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_OLD_DETAIL_OPENSSL_STREAM_SERVICE_HPP
diff --git a/ext/patches/boost/asio/ssl/old/stream.hpp b/ext/patches/boost/asio/ssl/old/stream.hpp
new file mode 100644
index 0000000..fbba3be
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/old/stream.hpp
@@ -0,0 +1,503 @@
+//
+// ssl/old/stream.hpp
+// ~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_OLD_STREAM_HPP
+#define BOOST_ASIO_SSL_OLD_STREAM_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/noncopyable.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/ssl/basic_context.hpp>
+#include <boost/asio/ssl/stream_base.hpp>
+#include <boost/asio/ssl/stream_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace old {
+
+/// Provides stream-oriented functionality using SSL.
+/**
+ * The stream class template provides asynchronous and blocking stream-oriented
+ * functionality using SSL.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Example
+ * To use the SSL stream template with an ip::tcp::socket, you would write:
+ * @code
+ * boost::asio::io_service io_service;
+ * boost::asio::ssl::context context(io_service, boost::asio::ssl::context::sslv23);
+ * boost::asio::ssl::stream<boost::asio::ip::tcp::socket> sock(io_service, context);
+ * @endcode
+ *
+ * @par Concepts:
+ * AsyncReadStream, AsyncWriteStream, Stream, SyncRead_Stream, SyncWriteStream.
+ */
+template <typename Stream, typename Service = old::stream_service>
+class stream
+ : public stream_base,
+ private boost::noncopyable
+{
+public:
+ /// The type of the next layer.
+ typedef typename remove_reference<Stream>::type next_layer_type;
+
+ /// The type of the lowest layer.
+ typedef typename next_layer_type::lowest_layer_type lowest_layer_type;
+
+ /// The type of the service that will be used to provide stream operations.
+ typedef Service service_type;
+
+ /// The native implementation type of the stream.
+ typedef typename service_type::impl_type impl_type;
+
+ /// Construct a stream.
+ /**
+ * This constructor creates a stream and initialises the underlying stream
+ * object.
+ *
+ * @param arg The argument to be passed to initialise the underlying stream.
+ *
+ * @param context The SSL context to be used for the stream.
+ */
+ template <typename Arg, typename Context_Service>
+ explicit stream(Arg& arg, basic_context<Context_Service>& context)
+ : next_layer_(arg),
+ service_(boost::asio::use_service<Service>(next_layer_.get_io_service())),
+ impl_(service_.null())
+ {
+ service_.create(impl_, next_layer_, context);
+ }
+
+ /// Destructor.
+ ~stream()
+ {
+ service_.destroy(impl_, next_layer_);
+ }
+
+ /// Get the io_service associated with the object.
+ /**
+ * This function may be used to obtain the io_service object that the stream
+ * uses to dispatch handlers for asynchronous operations.
+ *
+ * @return A reference to the io_service object that stream will use to
+ * dispatch handlers. Ownership is not transferred to the caller.
+ */
+ boost::asio::io_service& get_io_service()
+ {
+ return next_layer_.get_io_service();
+ }
+
+ /// Get a reference to the next layer.
+ /**
+ * This function returns a reference to the next layer in a stack of stream
+ * layers.
+ *
+ * @return A reference to the next layer in the stack of stream layers.
+ * Ownership is not transferred to the caller.
+ */
+ next_layer_type& next_layer()
+ {
+ return next_layer_;
+ }
+
+ /// Get a reference to the lowest layer.
+ /**
+ * This function returns a reference to the lowest layer in a stack of
+ * stream layers.
+ *
+ * @return A reference to the lowest layer in the stack of stream layers.
+ * Ownership is not transferred to the caller.
+ */
+ lowest_layer_type& lowest_layer()
+ {
+ return next_layer_.lowest_layer();
+ }
+
+ /// Get a const reference to the lowest layer.
+ /**
+ * This function returns a const reference to the lowest layer in a stack of
+ * stream layers.
+ *
+ * @return A const reference to the lowest layer in the stack of stream
+ * layers. Ownership is not transferred to the caller.
+ */
+ const lowest_layer_type& lowest_layer() const
+ {
+ return next_layer_.lowest_layer();
+ }
+
+ /// Get the underlying implementation in the native type.
+ /**
+ * This function may be used to obtain the underlying implementation of the
+ * context. This is intended to allow access to stream functionality that is
+ * not otherwise provided.
+ */
+ impl_type impl()
+ {
+ return impl_;
+ }
+
+ /// Perform SSL handshaking.
+ /**
+ * This function is used to perform SSL handshaking on the stream. The
+ * function call will block until handshaking is complete or an error occurs.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void handshake(handshake_type type)
+ {
+ boost::system::error_code ec;
+ service_.handshake(impl_, next_layer_, type, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Perform SSL handshaking.
+ /**
+ * This function is used to perform SSL handshaking on the stream. The
+ * function call will block until handshaking is complete or an error occurs.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code handshake(handshake_type type,
+ boost::system::error_code& ec)
+ {
+ return service_.handshake(impl_, next_layer_, type, ec);
+ }
+
+ /// Start an asynchronous SSL handshake.
+ /**
+ * This function is used to asynchronously perform an SSL handshake on the
+ * stream. This function call always returns immediately.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @param handler The handler to be called when the handshake operation
+ * completes. Copies will be made of the handler as required. The equivalent
+ * function signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ */
+ template <typename HandshakeHandler>
+ void async_handshake(handshake_type type, HandshakeHandler handler)
+ {
+ service_.async_handshake(impl_, next_layer_, type, handler);
+ }
+
+ /// Shut down SSL on the stream.
+ /**
+ * This function is used to shut down SSL on the stream. The function call
+ * will block until SSL has been shut down or an error occurs.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void shutdown()
+ {
+ boost::system::error_code ec;
+ service_.shutdown(impl_, next_layer_, ec);
+ boost::asio::detail::throw_error(ec);
+ }
+
+ /// Shut down SSL on the stream.
+ /**
+ * This function is used to shut down SSL on the stream. The function call
+ * will block until SSL has been shut down or an error occurs.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code shutdown(boost::system::error_code& ec)
+ {
+ return service_.shutdown(impl_, next_layer_, ec);
+ }
+
+ /// Asynchronously shut down SSL on the stream.
+ /**
+ * This function is used to asynchronously shut down SSL on the stream. This
+ * function call always returns immediately.
+ *
+ * @param handler The handler to be called when the handshake operation
+ * completes. Copies will be made of the handler as required. The equivalent
+ * function signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ */
+ template <typename ShutdownHandler>
+ void async_shutdown(ShutdownHandler handler)
+ {
+ service_.async_shutdown(impl_, next_layer_, handler);
+ }
+
+ /// Write some data to the stream.
+ /**
+ * This function is used to write data on the stream. The function call will
+ * block until one or more bytes of data has been written successfully, or
+ * until an error occurs.
+ *
+ * @param buffers The data to be written.
+ *
+ * @returns The number of bytes written.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that all
+ * data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = service_.write_some(impl_, next_layer_, buffers, ec);
+ boost::asio::detail::throw_error(ec);
+ return s;
+ }
+
+ /// Write some data to the stream.
+ /**
+ * This function is used to write data on the stream. The function call will
+ * block until one or more bytes of data has been written successfully, or
+ * until an error occurs.
+ *
+ * @param buffers The data to be written to the stream.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. Returns 0 if an error occurred.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that all
+ * data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return service_.write_some(impl_, next_layer_, buffers, ec);
+ }
+
+ /// Start an asynchronous write.
+ /**
+ * This function is used to asynchronously write one or more bytes of data to
+ * the stream. The function call always returns immediately.
+ *
+ * @param buffers The data to be written to the stream. Although the buffers
+ * object may be copied as necessary, ownership of the underlying buffers is
+ * retained by the caller, which must guarantee that they remain valid until
+ * the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The equivalent function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes written.
+ * ); @endcode
+ *
+ * @note The async_write_some operation may not transmit all of the data to
+ * the peer. Consider using the @ref async_write function if you need to
+ * ensure that all data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ void async_write_some(const ConstBufferSequence& buffers,
+ WriteHandler handler)
+ {
+ service_.async_write_some(impl_, next_layer_, buffers, handler);
+ }
+
+ /// Read some data from the stream.
+ /**
+ * This function is used to read data from the stream. The function call will
+ * block until one or more bytes of data has been read successfully, or until
+ * an error occurs.
+ *
+ * @param buffers The buffers into which the data will be read.
+ *
+ * @returns The number of bytes read.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = service_.read_some(impl_, next_layer_, buffers, ec);
+ boost::asio::detail::throw_error(ec);
+ return s;
+ }
+
+ /// Read some data from the stream.
+ /**
+ * This function is used to read data from the stream. The function call will
+ * block until one or more bytes of data has been read successfully, or until
+ * an error occurs.
+ *
+ * @param buffers The buffers into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. Returns 0 if an error occurred.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return service_.read_some(impl_, next_layer_, buffers, ec);
+ }
+
+ /// Start an asynchronous read.
+ /**
+ * This function is used to asynchronously read one or more bytes of data from
+ * the stream. The function call always returns immediately.
+ *
+ * @param buffers The buffers into which the data will be read. Although the
+ * buffers object may be copied as necessary, ownership of the underlying
+ * buffers is retained by the caller, which must guarantee that they remain
+ * valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The equivalent function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes read.
+ * ); @endcode
+ *
+ * @note The async_read_some operation may not read all of the requested
+ * number of bytes. Consider using the @ref async_read function if you need to
+ * ensure that the requested amount of data is read before the asynchronous
+ * operation completes.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ void async_read_some(const MutableBufferSequence& buffers,
+ ReadHandler handler)
+ {
+ service_.async_read_some(impl_, next_layer_, buffers, handler);
+ }
+
+ /// Peek at the incoming data on the stream.
+ /**
+ * This function is used to peek at the incoming data on the stream, without
+ * removing it from the input queue. The function call will block until data
+ * has been read successfully or an error occurs.
+ *
+ * @param buffers The buffers into which the data will be read.
+ *
+ * @returns The number of bytes read.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t peek(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = service_.peek(impl_, next_layer_, buffers, ec);
+ boost::asio::detail::throw_error(ec);
+ return s;
+ }
+
+ /// Peek at the incoming data on the stream.
+ /**
+ * This function is used to peek at the incoming data on the stream, withoutxi
+ * removing it from the input queue. The function call will block until data
+ * has been read successfully or an error occurs.
+ *
+ * @param buffers The buffers into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. Returns 0 if an error occurred.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t peek(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return service_.peek(impl_, next_layer_, buffers, ec);
+ }
+
+ /// Determine the amount of data that may be read without blocking.
+ /**
+ * This function is used to determine the amount of data, in bytes, that may
+ * be read from the stream without blocking.
+ *
+ * @returns The number of bytes of data that can be read without blocking.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ std::size_t in_avail()
+ {
+ boost::system::error_code ec;
+ std::size_t s = service_.in_avail(impl_, next_layer_, ec);
+ boost::asio::detail::throw_error(ec);
+ return s;
+ }
+
+ /// Determine the amount of data that may be read without blocking.
+ /**
+ * This function is used to determine the amount of data, in bytes, that may
+ * be read from the stream without blocking.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes of data that can be read without blocking.
+ */
+ std::size_t in_avail(boost::system::error_code& ec)
+ {
+ return service_.in_avail(impl_, next_layer_, ec);
+ }
+
+private:
+ /// The next layer.
+ Stream next_layer_;
+
+ /// The backend service implementation.
+ service_type& service_;
+
+ /// The underlying native implementation.
+ impl_type impl_;
+};
+
+} // namespace old
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_OLD_STREAM_HPP
diff --git a/ext/patches/boost/asio/ssl/old/stream_service.hpp b/ext/patches/boost/asio/ssl/old/stream_service.hpp
new file mode 100644
index 0000000..37b9447
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/old/stream_service.hpp
@@ -0,0 +1,186 @@
+//
+// ssl/old/stream_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2005 Voipster / Indrek dot Juhani at voipster dot com
+// Copyright (c) 2005-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_OLD_STREAM_SERVICE_HPP
+#define BOOST_ASIO_SSL_OLD_STREAM_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/noncopyable.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/ssl/basic_context.hpp>
+#include <boost/asio/ssl/old/detail/openssl_stream_service.hpp>
+#include <boost/asio/ssl/stream_base.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+namespace old {
+
+/// Default service implementation for an SSL stream.
+class stream_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<stream_service>
+#endif
+{
+private:
+ // The type of the platform-specific implementation.
+ typedef old::detail::openssl_stream_service service_impl_type;
+
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The type of a stream implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined impl_type;
+#else
+ typedef service_impl_type::impl_type impl_type;
+#endif
+
+ /// Construct a new stream service for the specified io_service.
+ explicit stream_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<stream_service>(io_service),
+ service_impl_(boost::asio::use_service<service_impl_type>(io_service))
+ {
+ }
+
+ /// Return a null stream implementation.
+ impl_type null() const
+ {
+ return service_impl_.null();
+ }
+
+ /// Create a new stream implementation.
+ template <typename Stream, typename Context_Service>
+ void create(impl_type& impl, Stream& next_layer,
+ basic_context<Context_Service>& context)
+ {
+ service_impl_.create(impl, next_layer, context);
+ }
+
+ /// Destroy a stream implementation.
+ template <typename Stream>
+ void destroy(impl_type& impl, Stream& next_layer)
+ {
+ service_impl_.destroy(impl, next_layer);
+ }
+
+ /// Perform SSL handshaking.
+ template <typename Stream>
+ boost::system::error_code handshake(impl_type& impl, Stream& next_layer,
+ stream_base::handshake_type type, boost::system::error_code& ec)
+ {
+ return service_impl_.handshake(impl, next_layer, type, ec);
+ }
+
+ /// Start an asynchronous SSL handshake.
+ template <typename Stream, typename HandshakeHandler>
+ void async_handshake(impl_type& impl, Stream& next_layer,
+ stream_base::handshake_type type, HandshakeHandler handler)
+ {
+ service_impl_.async_handshake(impl, next_layer, type, handler);
+ }
+
+ /// Shut down SSL on the stream.
+ template <typename Stream>
+ boost::system::error_code shutdown(impl_type& impl, Stream& next_layer,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.shutdown(impl, next_layer, ec);
+ }
+
+ /// Asynchronously shut down SSL on the stream.
+ template <typename Stream, typename ShutdownHandler>
+ void async_shutdown(impl_type& impl, Stream& next_layer,
+ ShutdownHandler handler)
+ {
+ service_impl_.async_shutdown(impl, next_layer, handler);
+ }
+
+ /// Write some data to the stream.
+ template <typename Stream, typename ConstBufferSequence>
+ std::size_t write_some(impl_type& impl, Stream& next_layer,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.write_some(impl, next_layer, buffers, ec);
+ }
+
+ /// Start an asynchronous write.
+ template <typename Stream, typename ConstBufferSequence,
+ typename WriteHandler>
+ void async_write_some(impl_type& impl, Stream& next_layer,
+ const ConstBufferSequence& buffers, WriteHandler handler)
+ {
+ service_impl_.async_write_some(impl, next_layer, buffers, handler);
+ }
+
+ /// Read some data from the stream.
+ template <typename Stream, typename MutableBufferSequence>
+ std::size_t read_some(impl_type& impl, Stream& next_layer,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.read_some(impl, next_layer, buffers, ec);
+ }
+
+ /// Start an asynchronous read.
+ template <typename Stream, typename MutableBufferSequence,
+ typename ReadHandler>
+ void async_read_some(impl_type& impl, Stream& next_layer,
+ const MutableBufferSequence& buffers, ReadHandler handler)
+ {
+ service_impl_.async_read_some(impl, next_layer, buffers, handler);
+ }
+
+ /// Peek at the incoming data on the stream.
+ template <typename Stream, typename MutableBufferSequence>
+ std::size_t peek(impl_type& impl, Stream& next_layer,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.peek(impl, next_layer, buffers, ec);
+ }
+
+ /// Determine the amount of data that may be read without blocking.
+ template <typename Stream>
+ std::size_t in_avail(impl_type& impl, Stream& next_layer,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.in_avail(impl, next_layer, ec);
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ }
+
+ // The service that provides the platform-specific implementation.
+ service_impl_type& service_impl_;
+};
+
+} // namespace old
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_OLD_STREAM_SERVICE_HPP
diff --git a/ext/patches/boost/asio/ssl/rfc2818_verification.hpp b/ext/patches/boost/asio/ssl/rfc2818_verification.hpp
new file mode 100644
index 0000000..6f9062d
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/rfc2818_verification.hpp
@@ -0,0 +1,102 @@
+//
+// ssl/rfc2818_verification.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_RFC2818_VERIFICATION_HPP
+#define BOOST_ASIO_SSL_RFC2818_VERIFICATION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <string>
+# include <boost/asio/ssl/detail/openssl_types.hpp>
+# include <boost/asio/ssl/verify_context.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+/// Verifies a certificate against a hostname according to the rules described
+/// in RFC 2818.
+/**
+ * @par Example
+ * The following example shows how to synchronously open a secure connection to
+ * a given host name:
+ * @code
+ * using boost::asio::ip::tcp;
+ * namespace ssl = boost::asio::ssl;
+ * typedef ssl::stream<tcp::socket> ssl_socket;
+ *
+ * // Create a context that uses the default paths for finding CA certificates.
+ * ssl::context ctx(ssl::context::sslv23);
+ * ctx.set_default_verify_paths();
+ *
+ * // Open a socket and connect it to the remote host.
+ * boost::asio::io_service io_service;
+ * ssl_socket sock(io_service, ctx);
+ * tcp::resolver resolver(io_service);
+ * tcp::resolver::query query("host.name", "https");
+ * boost::asio::connect(sock.lowest_layer(), resolver.resolve(query));
+ * sock.lowest_layer().set_option(tcp::no_delay(true));
+ *
+ * // Perform SSL handshake and verify the remote host's certificate.
+ * sock.set_verify_mode(ssl::verify_peer);
+ * sock.set_verify_callback(ssl::rfc2818_verification("host.name"));
+ * sock.handshake(ssl_socket::client);
+ *
+ * // ... read and write as normal ...
+ * @endcode
+ */
+class rfc2818_verification
+{
+public:
+ /// The type of the function object's result.
+ typedef bool result_type;
+
+ /// Constructor.
+ explicit rfc2818_verification(const std::string& host)
+ : host_(host)
+ {
+ }
+
+ /// Perform certificate verification.
+ BOOST_ASIO_DECL bool operator()(bool preverified, verify_context& ctx) const;
+
+private:
+ // Helper function to check a host name against a pattern.
+ BOOST_ASIO_DECL static bool match_pattern(const char* pattern,
+ std::size_t pattern_length, const char* host);
+
+ // Helper function to check a host name against an IPv4 address
+ // The host name to be checked.
+ std::string host_;
+};
+
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#if defined(BOOST_ASIO_HEADER_ONLY)
+# include <boost/asio/ssl/impl/rfc2818_verification.ipp>
+#endif // defined(BOOST_ASIO_HEADER_ONLY)
+
+#endif // BOOST_ASIO_SSL_RFC2818_VERIFICATION_HPP
diff --git a/ext/patches/boost/asio/ssl/stream.hpp b/ext/patches/boost/asio/ssl/stream.hpp
new file mode 100644
index 0000000..e003bc4
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/stream.hpp
@@ -0,0 +1,758 @@
+//
+// ssl/stream.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_STREAM_HPP
+#define BOOST_ASIO_SSL_STREAM_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/old/stream.hpp>
+#else // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/async_result.hpp>
+# include <boost/asio/detail/buffer_sequence_adapter.hpp>
+# include <boost/asio/detail/handler_type_requirements.hpp>
+# include <boost/asio/detail/noncopyable.hpp>
+# include <boost/asio/detail/type_traits.hpp>
+# include <boost/asio/ssl/context.hpp>
+# include <boost/asio/ssl/detail/buffered_handshake_op.hpp>
+# include <boost/asio/ssl/detail/handshake_op.hpp>
+# include <boost/asio/ssl/detail/io.hpp>
+# include <boost/asio/ssl/detail/read_op.hpp>
+# include <boost/asio/ssl/detail/shutdown_op.hpp>
+# include <boost/asio/ssl/detail/stream_core.hpp>
+# include <boost/asio/ssl/detail/write_op.hpp>
+# include <boost/asio/ssl/stream_base.hpp>
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+using boost::asio::ssl::old::stream;
+
+#else // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+/// Provides stream-oriented functionality using SSL.
+/**
+ * The stream class template provides asynchronous and blocking stream-oriented
+ * functionality using SSL.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe. The application must also ensure that all
+ * asynchronous operations are performed within the same implicit or explicit
+ * strand.
+ *
+ * @par Example
+ * To use the SSL stream template with an ip::tcp::socket, you would write:
+ * @code
+ * boost::asio::io_service io_service;
+ * boost::asio::ssl::context ctx(boost::asio::ssl::context::sslv23);
+ * boost::asio::ssl::stream<asio:ip::tcp::socket> sock(io_service, ctx);
+ * @endcode
+ *
+ * @par Concepts:
+ * AsyncReadStream, AsyncWriteStream, Stream, SyncReadStream, SyncWriteStream.
+ */
+template <typename Stream>
+class stream :
+ public stream_base,
+ private noncopyable
+{
+public:
+ /// The native handle type of the SSL stream.
+ typedef SSL* native_handle_type;
+
+ /// Structure for use with deprecated impl_type.
+ struct impl_struct
+ {
+ SSL* ssl;
+ };
+
+ /// (Deprecated: Use native_handle_type.) The underlying implementation type.
+ typedef impl_struct* impl_type;
+
+ /// The type of the next layer.
+ typedef typename remove_reference<Stream>::type next_layer_type;
+
+ /// The type of the lowest layer.
+ typedef typename next_layer_type::lowest_layer_type lowest_layer_type;
+
+ /// Construct a stream.
+ /**
+ * This constructor creates a stream and initialises the underlying stream
+ * object.
+ *
+ * @param arg The argument to be passed to initialise the underlying stream.
+ *
+ * @param ctx The SSL context to be used for the stream.
+ */
+ template <typename Arg>
+ stream(Arg& arg, context& ctx)
+ : next_layer_(arg),
+ core_(ctx.native_handle(), next_layer_.lowest_layer().get_io_service())
+ {
+ backwards_compatible_impl_.ssl = core_.engine_.native_handle();
+ }
+
+ /// Destructor.
+ ~stream()
+ {
+ }
+
+ /// Get the io_service associated with the object.
+ /**
+ * This function may be used to obtain the io_service object that the stream
+ * uses to dispatch handlers for asynchronous operations.
+ *
+ * @return A reference to the io_service object that stream will use to
+ * dispatch handlers. Ownership is not transferred to the caller.
+ */
+ boost::asio::io_service& get_io_service()
+ {
+ return next_layer_.lowest_layer().get_io_service();
+ }
+
+ /// Get the underlying implementation in the native type.
+ /**
+ * This function may be used to obtain the underlying implementation of the
+ * context. This is intended to allow access to context functionality that is
+ * not otherwise provided.
+ *
+ * @par Example
+ * The native_handle() function returns a pointer of type @c SSL* that is
+ * suitable for passing to functions such as @c SSL_get_verify_result and
+ * @c SSL_get_peer_certificate:
+ * @code
+ * boost::asio::ssl::stream<asio:ip::tcp::socket> sock(io_service, ctx);
+ *
+ * // ... establish connection and perform handshake ...
+ *
+ * if (X509* cert = SSL_get_peer_certificate(sock.native_handle()))
+ * {
+ * if (SSL_get_verify_result(sock.native_handle()) == X509_V_OK)
+ * {
+ * // ...
+ * }
+ * }
+ * @endcode
+ */
+ native_handle_type native_handle()
+ {
+ return core_.engine_.native_handle();
+ }
+
+ /// (Deprecated: Use native_handle().) Get the underlying implementation in
+ /// the native type.
+ /**
+ * This function may be used to obtain the underlying implementation of the
+ * context. This is intended to allow access to stream functionality that is
+ * not otherwise provided.
+ */
+ impl_type impl()
+ {
+ return &backwards_compatible_impl_;
+ }
+
+ /// Get a reference to the next layer.
+ /**
+ * This function returns a reference to the next layer in a stack of stream
+ * layers.
+ *
+ * @return A reference to the next layer in the stack of stream layers.
+ * Ownership is not transferred to the caller.
+ */
+ const next_layer_type& next_layer() const
+ {
+ return next_layer_;
+ }
+
+ /// Get a reference to the next layer.
+ /**
+ * This function returns a reference to the next layer in a stack of stream
+ * layers.
+ *
+ * @return A reference to the next layer in the stack of stream layers.
+ * Ownership is not transferred to the caller.
+ */
+ next_layer_type& next_layer()
+ {
+ return next_layer_;
+ }
+
+ /// Get a reference to the lowest layer.
+ /**
+ * This function returns a reference to the lowest layer in a stack of
+ * stream layers.
+ *
+ * @return A reference to the lowest layer in the stack of stream layers.
+ * Ownership is not transferred to the caller.
+ */
+ lowest_layer_type& lowest_layer()
+ {
+ return next_layer_.lowest_layer();
+ }
+
+ /// Get a reference to the lowest layer.
+ /**
+ * This function returns a reference to the lowest layer in a stack of
+ * stream layers.
+ *
+ * @return A reference to the lowest layer in the stack of stream layers.
+ * Ownership is not transferred to the caller.
+ */
+ const lowest_layer_type& lowest_layer() const
+ {
+ return next_layer_.lowest_layer();
+ }
+
+ /// Set the peer verification mode.
+ /**
+ * This function may be used to configure the peer verification mode used by
+ * the stream. The new mode will override the mode inherited from the context.
+ *
+ * @param v A bitmask of peer verification modes. See @ref verify_mode for
+ * available values.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_set_verify.
+ */
+ void set_verify_mode(verify_mode v)
+ {
+ boost::system::error_code ec;
+ set_verify_mode(v, ec);
+ boost::asio::detail::throw_error(ec, "set_verify_mode");
+ }
+
+ /// Set the peer verification mode.
+ /**
+ * This function may be used to configure the peer verification mode used by
+ * the stream. The new mode will override the mode inherited from the context.
+ *
+ * @param v A bitmask of peer verification modes. See @ref verify_mode for
+ * available values.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_set_verify.
+ */
+ boost::system::error_code set_verify_mode(
+ verify_mode v, boost::system::error_code& ec)
+ {
+ return core_.engine_.set_verify_mode(v, ec);
+ }
+
+ /// Set the peer verification depth.
+ /**
+ * This function may be used to configure the maximum verification depth
+ * allowed by the stream.
+ *
+ * @param depth Maximum depth for the certificate chain verification that
+ * shall be allowed.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_set_verify_depth.
+ */
+ void set_verify_depth(int depth)
+ {
+ boost::system::error_code ec;
+ set_verify_depth(depth, ec);
+ boost::asio::detail::throw_error(ec, "set_verify_depth");
+ }
+
+ /// Set the peer verification depth.
+ /**
+ * This function may be used to configure the maximum verification depth
+ * allowed by the stream.
+ *
+ * @param depth Maximum depth for the certificate chain verification that
+ * shall be allowed.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_set_verify_depth.
+ */
+ boost::system::error_code set_verify_depth(
+ int depth, boost::system::error_code& ec)
+ {
+ return core_.engine_.set_verify_depth(depth, ec);
+ }
+
+ /// Set the callback used to verify peer certificates.
+ /**
+ * This function is used to specify a callback function that will be called
+ * by the implementation when it needs to verify a peer certificate.
+ *
+ * @param callback The function object to be used for verifying a certificate.
+ * The function signature of the handler must be:
+ * @code bool verify_callback(
+ * bool preverified, // True if the certificate passed pre-verification.
+ * verify_context& ctx // The peer certificate and other context.
+ * ); @endcode
+ * The return value of the callback is true if the certificate has passed
+ * verification, false otherwise.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note Calls @c SSL_set_verify.
+ */
+ template <typename VerifyCallback>
+ void set_verify_callback(VerifyCallback callback)
+ {
+ boost::system::error_code ec;
+ this->set_verify_callback(callback, ec);
+ boost::asio::detail::throw_error(ec, "set_verify_callback");
+ }
+
+ /// Set the callback used to verify peer certificates.
+ /**
+ * This function is used to specify a callback function that will be called
+ * by the implementation when it needs to verify a peer certificate.
+ *
+ * @param callback The function object to be used for verifying a certificate.
+ * The function signature of the handler must be:
+ * @code bool verify_callback(
+ * bool preverified, // True if the certificate passed pre-verification.
+ * verify_context& ctx // The peer certificate and other context.
+ * ); @endcode
+ * The return value of the callback is true if the certificate has passed
+ * verification, false otherwise.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @note Calls @c SSL_set_verify.
+ */
+ template <typename VerifyCallback>
+ boost::system::error_code set_verify_callback(VerifyCallback callback,
+ boost::system::error_code& ec)
+ {
+ return core_.engine_.set_verify_callback(
+ new detail::verify_callback<VerifyCallback>(callback), ec);
+ }
+
+ /// Perform SSL handshaking.
+ /**
+ * This function is used to perform SSL handshaking on the stream. The
+ * function call will block until handshaking is complete or an error occurs.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void handshake(handshake_type type)
+ {
+ boost::system::error_code ec;
+ handshake(type, ec);
+ boost::asio::detail::throw_error(ec, "handshake");
+ }
+
+ /// Perform SSL handshaking.
+ /**
+ * This function is used to perform SSL handshaking on the stream. The
+ * function call will block until handshaking is complete or an error occurs.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code handshake(handshake_type type,
+ boost::system::error_code& ec)
+ {
+ detail::io(next_layer_, core_, detail::handshake_op(type), ec);
+ return ec;
+ }
+
+ /// Perform SSL handshaking.
+ /**
+ * This function is used to perform SSL handshaking on the stream. The
+ * function call will block until handshaking is complete or an error occurs.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @param buffers The buffered data to be reused for the handshake.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ template <typename ConstBufferSequence>
+ void handshake(handshake_type type, const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ handshake(type, buffers, ec);
+ boost::asio::detail::throw_error(ec, "handshake");
+ }
+
+ /// Perform SSL handshaking.
+ /**
+ * This function is used to perform SSL handshaking on the stream. The
+ * function call will block until handshaking is complete or an error occurs.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @param buffers The buffered data to be reused for the handshake.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ template <typename ConstBufferSequence>
+ boost::system::error_code handshake(handshake_type type,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ detail::io(next_layer_, core_,
+ detail::buffered_handshake_op<ConstBufferSequence>(type, buffers), ec);
+ return ec;
+ }
+
+ /// Start an asynchronous SSL handshake.
+ /**
+ * This function is used to asynchronously perform an SSL handshake on the
+ * stream. This function call always returns immediately.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @param handler The handler to be called when the handshake operation
+ * completes. Copies will be made of the handler as required. The equivalent
+ * function signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ */
+ template <typename HandshakeHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(HandshakeHandler,
+ void (boost::system::error_code))
+ async_handshake(handshake_type type,
+ BOOST_ASIO_MOVE_ARG(HandshakeHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a HandshakeHandler.
+ BOOST_ASIO_HANDSHAKE_HANDLER_CHECK(HandshakeHandler, handler) type_check;
+
+ boost::asio::detail::async_result_init<
+ HandshakeHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(HandshakeHandler)(handler));
+
+ detail::async_io(next_layer_, core_,
+ detail::handshake_op(type), init.handler);
+
+ return init.result.get();
+ }
+
+ /// Start an asynchronous SSL handshake.
+ /**
+ * This function is used to asynchronously perform an SSL handshake on the
+ * stream. This function call always returns immediately.
+ *
+ * @param type The type of handshaking to be performed, i.e. as a client or as
+ * a server.
+ *
+ * @param buffers The buffered data to be reused for the handshake. Although
+ * the buffers object may be copied as necessary, ownership of the underlying
+ * buffers is retained by the caller, which must guarantee that they remain
+ * valid until the handler is called.
+ *
+ * @param handler The handler to be called when the handshake operation
+ * completes. Copies will be made of the handler as required. The equivalent
+ * function signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Amount of buffers used in handshake.
+ * ); @endcode
+ */
+ template <typename ConstBufferSequence, typename BufferedHandshakeHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(BufferedHandshakeHandler,
+ void (boost::system::error_code, std::size_t))
+ async_handshake(handshake_type type, const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(BufferedHandshakeHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a BufferedHandshakeHandler.
+ BOOST_ASIO_BUFFERED_HANDSHAKE_HANDLER_CHECK(
+ BufferedHandshakeHandler, handler) type_check;
+
+ boost::asio::detail::async_result_init<BufferedHandshakeHandler,
+ void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(BufferedHandshakeHandler)(handler));
+
+ detail::async_io(next_layer_, core_,
+ detail::buffered_handshake_op<ConstBufferSequence>(type, buffers),
+ init.handler);
+
+ return init.result.get();
+ }
+
+ /// Shut down SSL on the stream.
+ /**
+ * This function is used to shut down SSL on the stream. The function call
+ * will block until SSL has been shut down or an error occurs.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void shutdown()
+ {
+ boost::system::error_code ec;
+ shutdown(ec);
+ boost::asio::detail::throw_error(ec, "shutdown");
+ }
+
+ /// Shut down SSL on the stream.
+ /**
+ * This function is used to shut down SSL on the stream. The function call
+ * will block until SSL has been shut down or an error occurs.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code shutdown(boost::system::error_code& ec)
+ {
+ detail::io(next_layer_, core_, detail::shutdown_op(), ec);
+ return ec;
+ }
+
+ /// Asynchronously shut down SSL on the stream.
+ /**
+ * This function is used to asynchronously shut down SSL on the stream. This
+ * function call always returns immediately.
+ *
+ * @param handler The handler to be called when the handshake operation
+ * completes. Copies will be made of the handler as required. The equivalent
+ * function signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ */
+ template <typename ShutdownHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ShutdownHandler,
+ void (boost::system::error_code))
+ async_shutdown(BOOST_ASIO_MOVE_ARG(ShutdownHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ShutdownHandler.
+ BOOST_ASIO_SHUTDOWN_HANDLER_CHECK(ShutdownHandler, handler) type_check;
+
+ boost::asio::detail::async_result_init<
+ ShutdownHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(ShutdownHandler)(handler));
+
+ detail::async_io(next_layer_, core_, detail::shutdown_op(), init.handler);
+
+ return init.result.get();
+ }
+
+ /// Write some data to the stream.
+ /**
+ * This function is used to write data on the stream. The function call will
+ * block until one or more bytes of data has been written successfully, or
+ * until an error occurs.
+ *
+ * @param buffers The data to be written.
+ *
+ * @returns The number of bytes written.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that all
+ * data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t n = write_some(buffers, ec);
+ boost::asio::detail::throw_error(ec, "write_some");
+ return n;
+ }
+
+ /// Write some data to the stream.
+ /**
+ * This function is used to write data on the stream. The function call will
+ * block until one or more bytes of data has been written successfully, or
+ * until an error occurs.
+ *
+ * @param buffers The data to be written to the stream.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. Returns 0 if an error occurred.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that all
+ * data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return detail::io(next_layer_, core_,
+ detail::write_op<ConstBufferSequence>(buffers), ec);
+ }
+
+ /// Start an asynchronous write.
+ /**
+ * This function is used to asynchronously write one or more bytes of data to
+ * the stream. The function call always returns immediately.
+ *
+ * @param buffers The data to be written to the stream. Although the buffers
+ * object may be copied as necessary, ownership of the underlying buffers is
+ * retained by the caller, which must guarantee that they remain valid until
+ * the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The equivalent function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes written.
+ * ); @endcode
+ *
+ * @note The async_write_some operation may not transmit all of the data to
+ * the peer. Consider using the @ref async_write function if you need to
+ * ensure that all data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ boost::asio::detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ detail::async_io(next_layer_, core_,
+ detail::write_op<ConstBufferSequence>(buffers), init.handler);
+
+ return init.result.get();
+ }
+
+ /// Read some data from the stream.
+ /**
+ * This function is used to read data from the stream. The function call will
+ * block until one or more bytes of data has been read successfully, or until
+ * an error occurs.
+ *
+ * @param buffers The buffers into which the data will be read.
+ *
+ * @returns The number of bytes read.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t n = read_some(buffers, ec);
+ boost::asio::detail::throw_error(ec, "read_some");
+ return n;
+ }
+
+ /// Read some data from the stream.
+ /**
+ * This function is used to read data from the stream. The function call will
+ * block until one or more bytes of data has been read successfully, or until
+ * an error occurs.
+ *
+ * @param buffers The buffers into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. Returns 0 if an error occurred.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that the
+ * requested amount of data is read before the blocking operation completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return detail::io(next_layer_, core_,
+ detail::read_op<MutableBufferSequence>(buffers), ec);
+ }
+
+ /// Start an asynchronous read.
+ /**
+ * This function is used to asynchronously read one or more bytes of data from
+ * the stream. The function call always returns immediately.
+ *
+ * @param buffers The buffers into which the data will be read. Although the
+ * buffers object may be copied as necessary, ownership of the underlying
+ * buffers is retained by the caller, which must guarantee that they remain
+ * valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The equivalent function
+ * signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes read.
+ * ); @endcode
+ *
+ * @note The async_read_some operation may not read all of the requested
+ * number of bytes. Consider using the @ref async_read function if you need to
+ * ensure that the requested amount of data is read before the asynchronous
+ * operation completes.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ boost::asio::detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ detail::async_io(next_layer_, core_,
+ detail::read_op<MutableBufferSequence>(buffers), init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ Stream next_layer_;
+ detail::stream_core core_;
+ impl_struct backwards_compatible_impl_;
+};
+
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_STREAM_HPP
diff --git a/ext/patches/boost/asio/ssl/stream_base.hpp b/ext/patches/boost/asio/ssl/stream_base.hpp
new file mode 100644
index 0000000..38e2c71
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/stream_base.hpp
@@ -0,0 +1,54 @@
+//
+// ssl/stream_base.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_STREAM_BASE_HPP
+#define BOOST_ASIO_SSL_STREAM_BASE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+/// The stream_base class is used as a base for the boost::asio::ssl::stream
+/// class template so that we have a common place to define various enums.
+class stream_base
+{
+public:
+ /// Different handshake types.
+ enum handshake_type
+ {
+ /// Perform handshaking as a client.
+ client,
+
+ /// Perform handshaking as a server.
+ server
+ };
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~stream_base()
+ {
+ }
+};
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_STREAM_BASE_HPP
diff --git a/ext/patches/boost/asio/ssl/stream_service.hpp b/ext/patches/boost/asio/ssl/stream_service.hpp
new file mode 100644
index 0000000..27b4e9c
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/stream_service.hpp
@@ -0,0 +1,42 @@
+//
+// ssl/stream_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_STREAM_SERVICE_HPP
+#define BOOST_ASIO_SSL_STREAM_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/ssl/old/stream_service.hpp>
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+using boost::asio::ssl::old::stream_service;
+
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_STREAM_SERVICE_HPP
diff --git a/ext/patches/boost/asio/ssl/verify_context.hpp b/ext/patches/boost/asio/ssl/verify_context.hpp
new file mode 100644
index 0000000..ebf3db1
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/verify_context.hpp
@@ -0,0 +1,75 @@
+//
+// ssl/verify_context.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_VERIFY_CONTEXT_HPP
+#define BOOST_ASIO_SSL_VERIFY_CONTEXT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+# include <boost/asio/detail/noncopyable.hpp>
+# include <boost/asio/ssl/detail/openssl_types.hpp>
+#endif // !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+#if !defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+/// A simple wrapper around the X509_STORE_CTX type, used during verification of
+/// a peer certificate.
+/**
+ * @note The verify_context does not own the underlying X509_STORE_CTX object.
+ */
+class verify_context
+ : private noncopyable
+{
+public:
+ /// The native handle type of the verification context.
+ typedef X509_STORE_CTX* native_handle_type;
+
+ /// Constructor.
+ explicit verify_context(native_handle_type handle)
+ : handle_(handle)
+ {
+ }
+
+ /// Get the underlying implementation in the native type.
+ /**
+ * This function may be used to obtain the underlying implementation of the
+ * context. This is intended to allow access to context functionality that is
+ * not otherwise provided.
+ */
+ native_handle_type native_handle()
+ {
+ return handle_;
+ }
+
+private:
+ // The underlying native implementation.
+ native_handle_type handle_;
+};
+
+#endif // defined(BOOST_ASIO_ENABLE_OLD_SSL)
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_VERIFY_CONTEXT_HPP
diff --git a/ext/patches/boost/asio/ssl/verify_mode.hpp b/ext/patches/boost/asio/ssl/verify_mode.hpp
new file mode 100644
index 0000000..1b7bee3
--- /dev/null
+++ b/ext/patches/boost/asio/ssl/verify_mode.hpp
@@ -0,0 +1,65 @@
+//
+// ssl/verify_mode.hpp
+// ~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SSL_VERIFY_MODE_HPP
+#define BOOST_ASIO_SSL_VERIFY_MODE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/ssl/detail/openssl_types.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace ssl {
+
+/// Bitmask type for peer verification.
+/**
+ * Possible values are:
+ *
+ * @li @ref verify_none
+ * @li @ref verify_peer
+ * @li @ref verify_fail_if_no_peer_cert
+ * @li @ref verify_client_once
+ */
+typedef int verify_mode;
+
+#if defined(GENERATING_DOCUMENTATION)
+/// No verification.
+const int verify_none = implementation_defined;
+
+/// Verify the peer.
+const int verify_peer = implementation_defined;
+
+/// Fail verification if the peer has no certificate. Ignored unless
+/// @ref verify_peer is set.
+const int verify_fail_if_no_peer_cert = implementation_defined;
+
+/// Do not request client certificate on renegotiation. Ignored unless
+/// @ref verify_peer is set.
+const int verify_client_once = implementation_defined;
+#else
+const int verify_none = SSL_VERIFY_NONE;
+const int verify_peer = SSL_VERIFY_PEER;
+const int verify_fail_if_no_peer_cert = SSL_VERIFY_FAIL_IF_NO_PEER_CERT;
+const int verify_client_once = SSL_VERIFY_CLIENT_ONCE;
+#endif
+
+} // namespace ssl
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_SSL_VERIFY_MODE_HPP
diff --git a/ext/patches/boost/asio/steady_timer.hpp b/ext/patches/boost/asio/steady_timer.hpp
new file mode 100644
index 0000000..0303f7a
--- /dev/null
+++ b/ext/patches/boost/asio/steady_timer.hpp
@@ -0,0 +1,63 @@
+//
+// steady_timer.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_STEADY_TIMER_HPP
+#define BOOST_ASIO_STEADY_TIMER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_CHRONO) \
+ || defined(BOOST_ASIO_HAS_BOOST_CHRONO) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#if defined(BOOST_ASIO_HAS_STD_CHRONO)
+# include <chrono>
+#elif defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+# include <boost/chrono/system_clocks.hpp>
+#endif
+
+#include <boost/asio/basic_waitable_timer.hpp>
+
+namespace boost {
+namespace asio {
+
+#if defined(GENERATING_DOCUMENTATION)
+/// Typedef for a timer based on the steady clock.
+/**
+ * This typedef uses the C++11 @c <chrono> standard library facility, if
+ * available. Otherwise, it may use the Boost.Chrono library. To explicitly
+ * utilise Boost.Chrono, use the basic_waitable_timer template directly:
+ * @code
+ * typedef basic_waitable_timer<boost::chrono::steady_clock> timer;
+ * @endcode
+ */
+typedef basic_waitable_timer<chrono::steady_clock> steady_timer;
+#elif defined(BOOST_ASIO_HAS_STD_CHRONO)
+# if defined(BOOST_ASIO_HAS_STD_CHRONO_MONOTONIC_CLOCK)
+typedef basic_waitable_timer<std::chrono::monotonic_clock> steady_timer;
+# else // defined(BOOST_ASIO_HAS_STD_CHRONO_MONOTONIC_CLOCK)
+typedef basic_waitable_timer<std::chrono::steady_clock> steady_timer;
+# endif // defined(BOOST_ASIO_HAS_STD_CHRONO_MONOTONIC_CLOCK)
+#elif defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+typedef basic_waitable_timer<boost::chrono::steady_clock> steady_timer;
+#endif
+
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_STD_CHRONO)
+ // || defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_STEADY_TIMER_HPP
diff --git a/ext/patches/boost/asio/strand.hpp b/ext/patches/boost/asio/strand.hpp
new file mode 100644
index 0000000..6a25d5f
--- /dev/null
+++ b/ext/patches/boost/asio/strand.hpp
@@ -0,0 +1,253 @@
+//
+// strand.hpp
+// ~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_STRAND_HPP
+#define BOOST_ASIO_STRAND_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/strand_service.hpp>
+#include <boost/asio/detail/wrapped_handler.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Provides serialised handler execution.
+/**
+ * The io_service::strand class provides the ability to post and dispatch
+ * handlers with the guarantee that none of those handlers will execute
+ * concurrently.
+ *
+ * @par Order of handler invocation
+ * Given:
+ *
+ * @li a strand object @c s
+ *
+ * @li an object @c a meeting completion handler requirements
+ *
+ * @li an object @c a1 which is an arbitrary copy of @c a made by the
+ * implementation
+ *
+ * @li an object @c b meeting completion handler requirements
+ *
+ * @li an object @c b1 which is an arbitrary copy of @c b made by the
+ * implementation
+ *
+ * if any of the following conditions are true:
+ *
+ * @li @c s.post(a) happens-before @c s.post(b)
+ *
+ * @li @c s.post(a) happens-before @c s.dispatch(b), where the latter is
+ * performed outside the strand
+ *
+ * @li @c s.dispatch(a) happens-before @c s.post(b), where the former is
+ * performed outside the strand
+ *
+ * @li @c s.dispatch(a) happens-before @c s.dispatch(b), where both are
+ * performed outside the strand
+ *
+ * then @c asio_handler_invoke(a1, &a1) happens-before
+ * @c asio_handler_invoke(b1, &b1).
+ *
+ * Note that in the following case:
+ * @code async_op_1(..., s.wrap(a));
+ * async_op_2(..., s.wrap(b)); @endcode
+ * the completion of the first async operation will perform @c s.dispatch(a),
+ * and the second will perform @c s.dispatch(b), but the order in which those
+ * are performed is unspecified. That is, you cannot state whether one
+ * happens-before the other. Therefore none of the above conditions are met and
+ * no ordering guarantee is made.
+ *
+ * @note The implementation makes no guarantee that handlers posted or
+ * dispatched through different @c strand objects will be invoked concurrently.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Safe.
+ *
+ * @par Concepts:
+ * Dispatcher.
+ */
+class io_service::strand
+{
+public:
+ /// Constructor.
+ /**
+ * Constructs the strand.
+ *
+ * @param io_service The io_service object that the strand will use to
+ * dispatch handlers that are ready to be run.
+ */
+ explicit strand(boost::asio::io_service& io_service)
+ : service_(boost::asio::use_service<
+ boost::asio::detail::strand_service>(io_service))
+ {
+ service_.construct(impl_);
+ }
+
+ /// Destructor.
+ /**
+ * Destroys a strand.
+ *
+ * Handlers posted through the strand that have not yet been invoked will
+ * still be dispatched in a way that meets the guarantee of non-concurrency.
+ */
+ ~strand()
+ {
+ }
+
+ /// Get the io_service associated with the strand.
+ /**
+ * This function may be used to obtain the io_service object that the strand
+ * uses to dispatch handlers for asynchronous operations.
+ *
+ * @return A reference to the io_service object that the strand will use to
+ * dispatch handlers. Ownership is not transferred to the caller.
+ */
+ boost::asio::io_service& get_io_service()
+ {
+ return service_.get_io_service();
+ }
+
+ /// Request the strand to invoke the given handler.
+ /**
+ * This function is used to ask the strand to execute the given handler.
+ *
+ * The strand object guarantees that handlers posted or dispatched through
+ * the strand will not be executed concurrently. The handler may be executed
+ * inside this function if the guarantee can be met. If this function is
+ * called from within a handler that was posted or dispatched through the same
+ * strand, then the new handler will be executed immediately.
+ *
+ * The strand's guarantee is in addition to the guarantee provided by the
+ * underlying io_service. The io_service guarantees that the handler will only
+ * be called in a thread in which the io_service's run member function is
+ * currently being invoked.
+ *
+ * @param handler The handler to be called. The strand will make a copy of the
+ * handler object as required. The function signature of the handler must be:
+ * @code void handler(); @endcode
+ */
+ template <typename CompletionHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(CompletionHandler, void ())
+ dispatch(BOOST_ASIO_MOVE_ARG(CompletionHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a CompletionHandler.
+ BOOST_ASIO_COMPLETION_HANDLER_CHECK(CompletionHandler, handler) type_check;
+
+ detail::async_result_init<
+ CompletionHandler, void ()> init(
+ BOOST_ASIO_MOVE_CAST(CompletionHandler)(handler));
+
+ service_.dispatch(impl_, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Request the strand to invoke the given handler and return
+ /// immediately.
+ /**
+ * This function is used to ask the strand to execute the given handler, but
+ * without allowing the strand to call the handler from inside this function.
+ *
+ * The strand object guarantees that handlers posted or dispatched through
+ * the strand will not be executed concurrently. The strand's guarantee is in
+ * addition to the guarantee provided by the underlying io_service. The
+ * io_service guarantees that the handler will only be called in a thread in
+ * which the io_service's run member function is currently being invoked.
+ *
+ * @param handler The handler to be called. The strand will make a copy of the
+ * handler object as required. The function signature of the handler must be:
+ * @code void handler(); @endcode
+ */
+ template <typename CompletionHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(CompletionHandler, void ())
+ post(BOOST_ASIO_MOVE_ARG(CompletionHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a CompletionHandler.
+ BOOST_ASIO_COMPLETION_HANDLER_CHECK(CompletionHandler, handler) type_check;
+
+ detail::async_result_init<
+ CompletionHandler, void ()> init(
+ BOOST_ASIO_MOVE_CAST(CompletionHandler)(handler));
+
+ service_.post(impl_, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Create a new handler that automatically dispatches the wrapped handler
+ /// on the strand.
+ /**
+ * This function is used to create a new handler function object that, when
+ * invoked, will automatically pass the wrapped handler to the strand's
+ * dispatch function.
+ *
+ * @param handler The handler to be wrapped. The strand will make a copy of
+ * the handler object as required. The function signature of the handler must
+ * be: @code void handler(A1 a1, ... An an); @endcode
+ *
+ * @return A function object that, when invoked, passes the wrapped handler to
+ * the strand's dispatch function. Given a function object with the signature:
+ * @code R f(A1 a1, ... An an); @endcode
+ * If this function object is passed to the wrap function like so:
+ * @code strand.wrap(f); @endcode
+ * then the return value is a function object with the signature
+ * @code void g(A1 a1, ... An an); @endcode
+ * that, when invoked, executes code equivalent to:
+ * @code strand.dispatch(boost::bind(f, a1, ... an)); @endcode
+ */
+ template <typename Handler>
+#if defined(GENERATING_DOCUMENTATION)
+ unspecified
+#else
+ detail::wrapped_handler<strand, Handler, detail::is_continuation_if_running>
+#endif
+ wrap(Handler handler)
+ {
+ return detail::wrapped_handler<io_service::strand, Handler,
+ detail::is_continuation_if_running>(*this, handler);
+ }
+
+ /// Determine whether the strand is running in the current thread.
+ /**
+ * @return @c true if the current thread is executing a handler that was
+ * submitted to the strand using post(), dispatch() or wrap(). Otherwise
+ * returns @c false.
+ */
+ bool running_in_this_thread() const
+ {
+ return service_.running_in_this_thread(impl_);
+ }
+
+private:
+ boost::asio::detail::strand_service& service_;
+ boost::asio::detail::strand_service::implementation_type impl_;
+};
+
+/// Typedef for backwards compatibility.
+typedef boost::asio::io_service::strand strand;
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_STRAND_HPP
diff --git a/ext/patches/boost/asio/stream_socket_service.hpp b/ext/patches/boost/asio/stream_socket_service.hpp
new file mode 100644
index 0000000..ac671d2
--- /dev/null
+++ b/ext/patches/boost/asio/stream_socket_service.hpp
@@ -0,0 +1,378 @@
+//
+// stream_socket_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_STREAM_SOCKET_SERVICE_HPP
+#define BOOST_ASIO_STREAM_SOCKET_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/type_traits.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+# include <boost/asio/detail/winrt_ssocket_service.hpp>
+#elif defined(BOOST_ASIO_HAS_IOCP)
+# include <boost/asio/detail/win_iocp_socket_service.hpp>
+#else
+# include <boost/asio/detail/reactive_socket_service.hpp>
+#endif
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a stream socket.
+template <typename Protocol>
+class stream_socket_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<stream_socket_service<Protocol> >
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The protocol type.
+ typedef Protocol protocol_type;
+
+ /// The endpoint type.
+ typedef typename Protocol::endpoint endpoint_type;
+
+private:
+ // The type of the platform-specific implementation.
+#if defined(BOOST_ASIO_WINDOWS_RUNTIME)
+ typedef detail::winrt_ssocket_service<Protocol> service_impl_type;
+#elif defined(BOOST_ASIO_HAS_IOCP)
+ typedef detail::win_iocp_socket_service<Protocol> service_impl_type;
+#else
+ typedef detail::reactive_socket_service<Protocol> service_impl_type;
+#endif
+
+public:
+ /// The type of a stream socket implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef typename service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native socket type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native socket type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef typename service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new stream socket service for the specified io_service.
+ explicit stream_socket_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ stream_socket_service<Protocol> >(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new stream socket implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new stream socket implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another stream socket implementation.
+ void move_assign(implementation_type& impl,
+ stream_socket_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+
+ /// Move-construct a new stream socket implementation from another protocol
+ /// type.
+ template <typename Protocol1>
+ void converting_move_construct(implementation_type& impl,
+ typename stream_socket_service<
+ Protocol1>::implementation_type& other_impl,
+ typename enable_if<is_convertible<
+ Protocol1, Protocol>::value>::type* = 0)
+ {
+ service_impl_.template converting_move_construct<Protocol1>(
+ impl, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a stream socket implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Open a stream socket.
+ boost::system::error_code open(implementation_type& impl,
+ const protocol_type& protocol, boost::system::error_code& ec)
+ {
+ if (protocol.type() == BOOST_ASIO_OS_DEF(SOCK_STREAM))
+ service_impl_.open(impl, protocol, ec);
+ else
+ ec = boost::asio::error::invalid_argument;
+ return ec;
+ }
+
+ /// Assign an existing native socket to a stream socket.
+ boost::system::error_code assign(implementation_type& impl,
+ const protocol_type& protocol, const native_handle_type& native_socket,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, protocol, native_socket, ec);
+ }
+
+ /// Determine whether the socket is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close a stream socket implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native socket implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native socket implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the socket.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Determine whether the socket is at the out-of-band data mark.
+ bool at_mark(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.at_mark(impl, ec);
+ }
+
+ /// Determine the number of bytes available for reading.
+ std::size_t available(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.available(impl, ec);
+ }
+
+ /// Bind the stream socket to the specified local endpoint.
+ boost::system::error_code bind(implementation_type& impl,
+ const endpoint_type& endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.bind(impl, endpoint, ec);
+ }
+
+ /// Connect the stream socket to the specified endpoint.
+ boost::system::error_code connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint, boost::system::error_code& ec)
+ {
+ return service_impl_.connect(impl, peer_endpoint, ec);
+ }
+
+ /// Start an asynchronous connect.
+ template <typename ConnectHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ConnectHandler,
+ void (boost::system::error_code))
+ async_connect(implementation_type& impl,
+ const endpoint_type& peer_endpoint,
+ BOOST_ASIO_MOVE_ARG(ConnectHandler) handler)
+ {
+ detail::async_result_init<
+ ConnectHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(ConnectHandler)(handler));
+
+ service_impl_.async_connect(impl, peer_endpoint, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Set a socket option.
+ template <typename SettableSocketOption>
+ boost::system::error_code set_option(implementation_type& impl,
+ const SettableSocketOption& option, boost::system::error_code& ec)
+ {
+ return service_impl_.set_option(impl, option, ec);
+ }
+
+ /// Get a socket option.
+ template <typename GettableSocketOption>
+ boost::system::error_code get_option(const implementation_type& impl,
+ GettableSocketOption& option, boost::system::error_code& ec) const
+ {
+ return service_impl_.get_option(impl, option, ec);
+ }
+
+ /// Perform an IO control command on the socket.
+ template <typename IoControlCommand>
+ boost::system::error_code io_control(implementation_type& impl,
+ IoControlCommand& command, boost::system::error_code& ec)
+ {
+ return service_impl_.io_control(impl, command, ec);
+ }
+
+ /// Gets the non-blocking mode of the socket.
+ bool non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the socket.
+ boost::system::error_code non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.non_blocking(impl, mode, ec);
+ }
+
+ /// Gets the non-blocking mode of the native socket implementation.
+ bool native_non_blocking(const implementation_type& impl) const
+ {
+ return service_impl_.native_non_blocking(impl);
+ }
+
+ /// Sets the non-blocking mode of the native socket implementation.
+ boost::system::error_code native_non_blocking(implementation_type& impl,
+ bool mode, boost::system::error_code& ec)
+ {
+ return service_impl_.native_non_blocking(impl, mode, ec);
+ }
+
+ /// Get the local endpoint.
+ endpoint_type local_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.local_endpoint(impl, ec);
+ }
+
+ /// Get the remote endpoint.
+ endpoint_type remote_endpoint(const implementation_type& impl,
+ boost::system::error_code& ec) const
+ {
+ return service_impl_.remote_endpoint(impl, ec);
+ }
+
+ /// Disable sends or receives on the socket.
+ boost::system::error_code shutdown(implementation_type& impl,
+ socket_base::shutdown_type what, boost::system::error_code& ec)
+ {
+ return service_impl_.shutdown(impl, what, ec);
+ }
+
+ /// Send the given data to the peer.
+ template <typename ConstBufferSequence>
+ std::size_t send(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.send(impl, buffers, flags, ec);
+ }
+
+ /// Start an asynchronous send.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_send(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_send(impl, buffers, flags, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Receive some data from the peer.
+ template <typename MutableBufferSequence>
+ std::size_t receive(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags, boost::system::error_code& ec)
+ {
+ return service_impl_.receive(impl, buffers, flags, ec);
+ }
+
+ /// Start an asynchronous receive.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_receive(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ socket_base::message_flags flags,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_receive(impl, buffers, flags, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_STREAM_SOCKET_SERVICE_HPP
diff --git a/ext/patches/boost/asio/streambuf.hpp b/ext/patches/boost/asio/streambuf.hpp
new file mode 100644
index 0000000..28d2b99
--- /dev/null
+++ b/ext/patches/boost/asio/streambuf.hpp
@@ -0,0 +1,35 @@
+//
+// streambuf.hpp
+// ~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_STREAMBUF_HPP
+#define BOOST_ASIO_STREAMBUF_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#include <boost/asio/basic_streambuf.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Typedef for the typical usage of basic_streambuf.
+typedef basic_streambuf<> streambuf;
+
+} // namespace asio
+} // namespace boost
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+#endif // BOOST_ASIO_STREAMBUF_HPP
diff --git a/ext/patches/boost/asio/system_timer.hpp b/ext/patches/boost/asio/system_timer.hpp
new file mode 100644
index 0000000..86de280
--- /dev/null
+++ b/ext/patches/boost/asio/system_timer.hpp
@@ -0,0 +1,59 @@
+//
+// system_timer.hpp
+// ~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_SYSTEM_TIMER_HPP
+#define BOOST_ASIO_SYSTEM_TIMER_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_STD_CHRONO) \
+ || defined(BOOST_ASIO_HAS_BOOST_CHRONO) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#if defined(BOOST_ASIO_HAS_STD_CHRONO)
+# include <chrono>
+#elif defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+# include <boost/chrono/system_clocks.hpp>
+#endif
+
+#include <boost/asio/basic_waitable_timer.hpp>
+
+namespace boost {
+namespace asio {
+
+#if defined(GENERATING_DOCUMENTATION)
+/// Typedef for a timer based on the system clock.
+/**
+ * This typedef uses the C++11 @c <chrono> standard library facility, if
+ * available. Otherwise, it may use the Boost.Chrono library. To explicitly
+ * utilise Boost.Chrono, use the basic_waitable_timer template directly:
+ * @code
+ * typedef basic_waitable_timer<boost::chrono::system_clock> timer;
+ * @endcode
+ */
+typedef basic_waitable_timer<chrono::system_clock> system_timer;
+#elif defined(BOOST_ASIO_HAS_STD_CHRONO)
+typedef basic_waitable_timer<std::chrono::system_clock> system_timer;
+#elif defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+typedef basic_waitable_timer<boost::chrono::system_clock> system_timer;
+#endif
+
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_STD_CHRONO)
+ // || defined(BOOST_ASIO_HAS_BOOST_CHRONO)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_SYSTEM_TIMER_HPP
diff --git a/ext/patches/boost/asio/time_traits.hpp b/ext/patches/boost/asio/time_traits.hpp
new file mode 100644
index 0000000..35d1f76
--- /dev/null
+++ b/ext/patches/boost/asio/time_traits.hpp
@@ -0,0 +1,90 @@
+//
+// time_traits.hpp
+// ~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_TIME_TRAITS_HPP
+#define BOOST_ASIO_TIME_TRAITS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/socket_types.hpp> // Must come before posix_time.
+
+#if defined(BOOST_ASIO_HAS_BOOST_DATE_TIME) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/detail/push_options.hpp>
+#include <boost/date_time/posix_time/posix_time_types.hpp>
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Time traits suitable for use with the deadline timer.
+template <typename Time>
+struct time_traits;
+
+/// Time traits specialised for posix_time.
+template <>
+struct time_traits<boost::posix_time::ptime>
+{
+ /// The time type.
+ typedef boost::posix_time::ptime time_type;
+
+ /// The duration type.
+ typedef boost::posix_time::time_duration duration_type;
+
+ /// Get the current time.
+ static time_type now()
+ {
+#if defined(BOOST_DATE_TIME_HAS_HIGH_PRECISION_CLOCK)
+ return boost::posix_time::microsec_clock::universal_time();
+#else // defined(BOOST_DATE_TIME_HAS_HIGH_PRECISION_CLOCK)
+ return boost::posix_time::second_clock::universal_time();
+#endif // defined(BOOST_DATE_TIME_HAS_HIGH_PRECISION_CLOCK)
+ }
+
+ /// Add a duration to a time.
+ static time_type add(const time_type& t, const duration_type& d)
+ {
+ return t + d;
+ }
+
+ /// Subtract one time from another.
+ static duration_type subtract(const time_type& t1, const time_type& t2)
+ {
+ return t1 - t2;
+ }
+
+ /// Test whether one time is less than another.
+ static bool less_than(const time_type& t1, const time_type& t2)
+ {
+ return t1 < t2;
+ }
+
+ /// Convert to POSIX duration type.
+ static boost::posix_time::time_duration to_posix_duration(
+ const duration_type& d)
+ {
+ return d;
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_BOOST_DATE_TIME)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_TIME_TRAITS_HPP
diff --git a/ext/patches/boost/asio/unyield.hpp b/ext/patches/boost/asio/unyield.hpp
new file mode 100644
index 0000000..ad94427
--- /dev/null
+++ b/ext/patches/boost/asio/unyield.hpp
@@ -0,0 +1,21 @@
+//
+// unyield.hpp
+// ~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifdef reenter
+# undef reenter
+#endif
+
+#ifdef yield
+# undef yield
+#endif
+
+#ifdef fork
+# undef fork
+#endif
diff --git a/ext/patches/boost/asio/use_future.hpp b/ext/patches/boost/asio/use_future.hpp
new file mode 100644
index 0000000..8ac567a
--- /dev/null
+++ b/ext/patches/boost/asio/use_future.hpp
@@ -0,0 +1,94 @@
+//
+// use_future.hpp
+// ~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_USE_FUTURE_HPP
+#define BOOST_ASIO_USE_FUTURE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <memory>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Class used to specify that an asynchronous operation should return a future.
+/**
+ * The use_future_t class is used to indicate that an asynchronous operation
+ * should return a std::future object. A use_future_t object may be passed as a
+ * handler to an asynchronous operation, typically using the special value @c
+ * boost::asio::use_future. For example:
+ *
+ * @code std::future<std::size_t> my_future
+ * = my_socket.async_read_some(my_buffer, boost::asio::use_future); @endcode
+ *
+ * The initiating function (async_read_some in the above example) returns a
+ * future that will receive the result of the operation. If the operation
+ * completes with an error_code indicating failure, it is converted into a
+ * system_error and passed back to the caller via the future.
+ */
+template <typename Allocator = std::allocator<void> >
+class use_future_t
+{
+public:
+ /// The allocator type. The allocator is used when constructing the
+ /// @c std::promise object for a given asynchronous operation.
+ typedef Allocator allocator_type;
+
+ /// Construct using default-constructed allocator.
+ BOOST_ASIO_CONSTEXPR use_future_t()
+ {
+ }
+
+ /// Construct using specified allocator.
+ explicit use_future_t(const Allocator& allocator)
+ : allocator_(allocator)
+ {
+ }
+
+ /// Specify an alternate allocator.
+ template <typename OtherAllocator>
+ use_future_t<OtherAllocator> operator[](const OtherAllocator& allocator) const
+ {
+ return use_future_t<OtherAllocator>(allocator);
+ }
+
+ /// Obtain allocator.
+ allocator_type get_allocator() const
+ {
+ return allocator_;
+ }
+
+private:
+ Allocator allocator_;
+};
+
+/// A special value, similar to std::nothrow.
+/**
+ * See the documentation for boost::asio::use_future_t for a usage example.
+ */
+#if defined(BOOST_ASIO_HAS_CONSTEXPR) || defined(GENERATING_DOCUMENTATION)
+constexpr use_future_t<> use_future;
+#elif defined(BOOST_ASIO_MSVC)
+__declspec(selectany) use_future_t<> use_future;
+#endif
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/use_future.hpp>
+
+#endif // BOOST_ASIO_USE_FUTURE_HPP
diff --git a/ext/patches/boost/asio/version.hpp b/ext/patches/boost/asio/version.hpp
new file mode 100644
index 0000000..c55f192
--- /dev/null
+++ b/ext/patches/boost/asio/version.hpp
@@ -0,0 +1,23 @@
+//
+// version.hpp
+// ~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_VERSION_HPP
+#define BOOST_ASIO_VERSION_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+// BOOST_ASIO_VERSION % 100 is the sub-minor version
+// BOOST_ASIO_VERSION / 100 % 1000 is the minor version
+// BOOST_ASIO_VERSION / 100000 is the major version
+#define BOOST_ASIO_VERSION 101004 // 1.10.4
+
+#endif // BOOST_ASIO_VERSION_HPP
diff --git a/ext/patches/boost/asio/wait_traits.hpp b/ext/patches/boost/asio/wait_traits.hpp
new file mode 100644
index 0000000..5f55457
--- /dev/null
+++ b/ext/patches/boost/asio/wait_traits.hpp
@@ -0,0 +1,43 @@
+//
+// wait_traits.hpp
+// ~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WAIT_TRAITS_HPP
+#define BOOST_ASIO_WAIT_TRAITS_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Wait traits suitable for use with the basic_waitable_timer class template.
+template <typename Clock>
+struct wait_traits
+{
+ /// Convert a clock duration into a duration used for waiting.
+ /**
+ * @returns @c d.
+ */
+ static typename Clock::duration to_wait_duration(
+ const typename Clock::duration& d)
+ {
+ return d;
+ }
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_WAIT_TRAITS_HPP
diff --git a/ext/patches/boost/asio/waitable_timer_service.hpp b/ext/patches/boost/asio/waitable_timer_service.hpp
new file mode 100644
index 0000000..73317b6
--- /dev/null
+++ b/ext/patches/boost/asio/waitable_timer_service.hpp
@@ -0,0 +1,170 @@
+//
+// waitable_timer_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WAITABLE_TIMER_SERVICE_HPP
+#define BOOST_ASIO_WAITABLE_TIMER_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/chrono_time_traits.hpp>
+#include <boost/asio/detail/deadline_timer_service.hpp>
+#include <boost/asio/io_service.hpp>
+#include <boost/asio/wait_traits.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/// Default service implementation for a timer.
+template <typename Clock,
+ typename WaitTraits = boost::asio::wait_traits<Clock> >
+class waitable_timer_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<
+ waitable_timer_service<Clock, WaitTraits> >
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+ /// The clock type.
+ typedef Clock clock_type;
+
+ /// The duration type of the clock.
+ typedef typename clock_type::duration duration;
+
+ /// The time point type of the clock.
+ typedef typename clock_type::time_point time_point;
+
+ /// The wait traits type.
+ typedef WaitTraits traits_type;
+
+private:
+ // The type of the platform-specific implementation.
+ typedef detail::deadline_timer_service<
+ detail::chrono_time_traits<Clock, WaitTraits> > service_impl_type;
+
+public:
+ /// The implementation type of the waitable timer.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef typename service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// Construct a new timer service for the specified io_service.
+ explicit waitable_timer_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ waitable_timer_service<Clock, WaitTraits> >(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new timer implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+ /// Destroy a timer implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Cancel any asynchronous wait operations associated with the timer.
+ std::size_t cancel(implementation_type& impl, boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Cancels one asynchronous wait operation associated with the timer.
+ std::size_t cancel_one(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel_one(impl, ec);
+ }
+
+ /// Get the expiry time for the timer as an absolute time.
+ time_point expires_at(const implementation_type& impl) const
+ {
+ return service_impl_.expires_at(impl);
+ }
+
+ /// Set the expiry time for the timer as an absolute time.
+ std::size_t expires_at(implementation_type& impl,
+ const time_point& expiry_time, boost::system::error_code& ec)
+ {
+ return service_impl_.expires_at(impl, expiry_time, ec);
+ }
+
+ /// Get the expiry time for the timer relative to now.
+ duration expires_from_now(const implementation_type& impl) const
+ {
+ return service_impl_.expires_from_now(impl);
+ }
+
+ /// Set the expiry time for the timer relative to now.
+ std::size_t expires_from_now(implementation_type& impl,
+ const duration& expiry_time, boost::system::error_code& ec)
+ {
+ return service_impl_.expires_from_now(impl, expiry_time, ec);
+ }
+
+ // Perform a blocking wait on the timer.
+ void wait(implementation_type& impl, boost::system::error_code& ec)
+ {
+ service_impl_.wait(impl, ec);
+ }
+
+ // Start an asynchronous wait on the timer.
+ template <typename WaitHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WaitHandler,
+ void (boost::system::error_code))
+ async_wait(implementation_type& impl,
+ BOOST_ASIO_MOVE_ARG(WaitHandler) handler)
+ {
+ detail::async_result_init<
+ WaitHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(WaitHandler)(handler));
+
+ service_impl_.async_wait(impl, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // BOOST_ASIO_WAITABLE_TIMER_SERVICE_HPP
diff --git a/ext/patches/boost/asio/windows/basic_handle.hpp b/ext/patches/boost/asio/windows/basic_handle.hpp
new file mode 100644
index 0000000..f3c252e
--- /dev/null
+++ b/ext/patches/boost/asio/windows/basic_handle.hpp
@@ -0,0 +1,283 @@
+//
+// windows/basic_handle.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_BASIC_HANDLE_HPP
+#define BOOST_ASIO_WINDOWS_BASIC_HANDLE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE) \
+ || defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE) \
+ || defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/basic_io_object.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Provides Windows handle functionality.
+/**
+ * The windows::basic_handle class template provides the ability to wrap a
+ * Windows handle.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename HandleService>
+class basic_handle
+ : public basic_io_object<HandleService>
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// handle.
+ typedef typename HandleService::native_handle_type native_type;
+
+ /// The native representation of a handle.
+ typedef typename HandleService::native_handle_type native_handle_type;
+
+ /// A basic_handle is always the lowest layer.
+ typedef basic_handle<HandleService> lowest_layer_type;
+
+ /// Construct a basic_handle without opening it.
+ /**
+ * This constructor creates a handle without opening it.
+ *
+ * @param io_service The io_service object that the handle will use to
+ * dispatch handlers for any asynchronous operations performed on the handle.
+ */
+ explicit basic_handle(boost::asio::io_service& io_service)
+ : basic_io_object<HandleService>(io_service)
+ {
+ }
+
+ /// Construct a basic_handle on an existing native handle.
+ /**
+ * This constructor creates a handle object to hold an existing native handle.
+ *
+ * @param io_service The io_service object that the handle will use to
+ * dispatch handlers for any asynchronous operations performed on the handle.
+ *
+ * @param handle A native handle.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_handle(boost::asio::io_service& io_service,
+ const native_handle_type& handle)
+ : basic_io_object<HandleService>(io_service)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(), handle, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_handle from another.
+ /**
+ * This constructor moves a handle from one object to another.
+ *
+ * @param other The other basic_handle object from which the move will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_handle(io_service&) constructor.
+ */
+ basic_handle(basic_handle&& other)
+ : basic_io_object<HandleService>(
+ BOOST_ASIO_MOVE_CAST(basic_handle)(other))
+ {
+ }
+
+ /// Move-assign a basic_handle from another.
+ /**
+ * This assignment operator moves a handle from one object to another.
+ *
+ * @param other The other basic_handle object from which the move will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_handle(io_service&) constructor.
+ */
+ basic_handle& operator=(basic_handle&& other)
+ {
+ basic_io_object<HandleService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_handle)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Get a reference to the lowest layer.
+ /**
+ * This function returns a reference to the lowest layer in a stack of
+ * layers. Since a basic_handle cannot contain any further layers, it simply
+ * returns a reference to itself.
+ *
+ * @return A reference to the lowest layer in the stack of layers. Ownership
+ * is not transferred to the caller.
+ */
+ lowest_layer_type& lowest_layer()
+ {
+ return *this;
+ }
+
+ /// Get a const reference to the lowest layer.
+ /**
+ * This function returns a const reference to the lowest layer in a stack of
+ * layers. Since a basic_handle cannot contain any further layers, it simply
+ * returns a reference to itself.
+ *
+ * @return A const reference to the lowest layer in the stack of layers.
+ * Ownership is not transferred to the caller.
+ */
+ const lowest_layer_type& lowest_layer() const
+ {
+ return *this;
+ }
+
+ /// Assign an existing native handle to the handle.
+ /*
+ * This function opens the handle to hold an existing native handle.
+ *
+ * @param handle A native handle.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void assign(const native_handle_type& handle)
+ {
+ boost::system::error_code ec;
+ this->get_service().assign(this->get_implementation(), handle, ec);
+ boost::asio::detail::throw_error(ec, "assign");
+ }
+
+ /// Assign an existing native handle to the handle.
+ /*
+ * This function opens the handle to hold an existing native handle.
+ *
+ * @param handle A native handle.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code assign(const native_handle_type& handle,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().assign(this->get_implementation(), handle, ec);
+ }
+
+ /// Determine whether the handle is open.
+ bool is_open() const
+ {
+ return this->get_service().is_open(this->get_implementation());
+ }
+
+ /// Close the handle.
+ /**
+ * This function is used to close the handle. Any asynchronous read or write
+ * operations will be cancelled immediately, and will complete with the
+ * boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void close()
+ {
+ boost::system::error_code ec;
+ this->get_service().close(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "close");
+ }
+
+ /// Close the handle.
+ /**
+ * This function is used to close the handle. Any asynchronous read or write
+ * operations will be cancelled immediately, and will complete with the
+ * boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code close(boost::system::error_code& ec)
+ {
+ return this->get_service().close(this->get_implementation(), ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native handle representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * handle. This is intended to allow access to native handle functionality
+ * that is not otherwise provided.
+ */
+ native_type native()
+ {
+ return this->get_service().native_handle(this->get_implementation());
+ }
+
+ /// Get the native handle representation.
+ /**
+ * This function may be used to obtain the underlying representation of the
+ * handle. This is intended to allow access to native handle functionality
+ * that is not otherwise provided.
+ */
+ native_handle_type native_handle()
+ {
+ return this->get_service().native_handle(this->get_implementation());
+ }
+
+ /// Cancel all asynchronous operations associated with the handle.
+ /**
+ * This function causes all outstanding asynchronous read or write operations
+ * to finish immediately, and the handlers for cancelled operations will be
+ * passed the boost::asio::error::operation_aborted error.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void cancel()
+ {
+ boost::system::error_code ec;
+ this->get_service().cancel(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "cancel");
+ }
+
+ /// Cancel all asynchronous operations associated with the handle.
+ /**
+ * This function causes all outstanding asynchronous read or write operations
+ * to finish immediately, and the handlers for cancelled operations will be
+ * passed the boost::asio::error::operation_aborted error.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ boost::system::error_code cancel(boost::system::error_code& ec)
+ {
+ return this->get_service().cancel(this->get_implementation(), ec);
+ }
+
+protected:
+ /// Protected destructor to prevent deletion through this type.
+ ~basic_handle()
+ {
+ }
+};
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE)
+ // || defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE)
+ // || defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_BASIC_HANDLE_HPP
diff --git a/ext/patches/boost/asio/windows/basic_object_handle.hpp b/ext/patches/boost/asio/windows/basic_object_handle.hpp
new file mode 100644
index 0000000..44687a3
--- /dev/null
+++ b/ext/patches/boost/asio/windows/basic_object_handle.hpp
@@ -0,0 +1,180 @@
+//
+// windows/basic_object_handle.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2011 Boris Schaeling (boris at highscore.de)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_BASIC_OBJECT_HANDLE_HPP
+#define BOOST_ASIO_WINDOWS_BASIC_OBJECT_HANDLE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/windows/basic_handle.hpp>
+#include <boost/asio/windows/object_handle_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Provides object-oriented handle functionality.
+/**
+ * The windows::basic_object_handle class template provides asynchronous and
+ * blocking object-oriented handle functionality.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename ObjectHandleService = object_handle_service>
+class basic_object_handle
+ : public basic_handle<ObjectHandleService>
+{
+public:
+ /// The native representation of a handle.
+ typedef typename ObjectHandleService::native_handle_type native_handle_type;
+
+ /// Construct a basic_object_handle without opening it.
+ /**
+ * This constructor creates an object handle without opening it.
+ *
+ * @param io_service The io_service object that the object handle will use to
+ * dispatch handlers for any asynchronous operations performed on the handle.
+ */
+ explicit basic_object_handle(boost::asio::io_service& io_service)
+ : basic_handle<ObjectHandleService>(io_service)
+ {
+ }
+
+ /// Construct a basic_object_handle on an existing native handle.
+ /**
+ * This constructor creates an object handle object to hold an existing native
+ * handle.
+ *
+ * @param io_service The io_service object that the object handle will use to
+ * dispatch handlers for any asynchronous operations performed on the handle.
+ *
+ * @param native_handle The new underlying handle implementation.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_object_handle(boost::asio::io_service& io_service,
+ const native_handle_type& native_handle)
+ : basic_handle<ObjectHandleService>(io_service, native_handle)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_object_handle from another.
+ /**
+ * This constructor moves an object handle from one object to another.
+ *
+ * @param other The other basic_object_handle object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_object_handle(io_service&) constructor.
+ */
+ basic_object_handle(basic_object_handle&& other)
+ : basic_handle<ObjectHandleService>(
+ BOOST_ASIO_MOVE_CAST(basic_object_handle)(other))
+ {
+ }
+
+ /// Move-assign a basic_object_handle from another.
+ /**
+ * This assignment operator moves an object handle from one object to another.
+ *
+ * @param other The other basic_object_handle object from which the move will
+ * occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_object_handle(io_service&) constructor.
+ */
+ basic_object_handle& operator=(basic_object_handle&& other)
+ {
+ basic_handle<ObjectHandleService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_object_handle)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Perform a blocking wait on the object handle.
+ /**
+ * This function is used to wait for the object handle to be set to the
+ * signalled state. This function blocks and does not return until the object
+ * handle has been set to the signalled state.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ void wait()
+ {
+ boost::system::error_code ec;
+ this->get_service().wait(this->get_implementation(), ec);
+ boost::asio::detail::throw_error(ec, "wait");
+ }
+
+ /// Perform a blocking wait on the object handle.
+ /**
+ * This function is used to wait for the object handle to be set to the
+ * signalled state. This function blocks and does not return until the object
+ * handle has been set to the signalled state.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ */
+ void wait(boost::system::error_code& ec)
+ {
+ this->get_service().wait(this->get_implementation(), ec);
+ }
+
+ /// Start an asynchronous wait on the object handle.
+ /**
+ * This function is be used to initiate an asynchronous wait against the
+ * object handle. It always returns immediately.
+ *
+ * @param handler The handler to be called when the object handle is set to
+ * the signalled state. Copies will be made of the handler as required. The
+ * function signature of the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error // Result of operation.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+ template <typename WaitHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WaitHandler,
+ void (boost::system::error_code))
+ async_wait(BOOST_ASIO_MOVE_ARG(WaitHandler) handler)
+ {
+ return this->get_service().async_wait(this->get_implementation(),
+ BOOST_ASIO_MOVE_CAST(WaitHandler)(handler));
+ }
+};
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_BASIC_OBJECT_HANDLE_HPP
diff --git a/ext/patches/boost/asio/windows/basic_random_access_handle.hpp b/ext/patches/boost/asio/windows/basic_random_access_handle.hpp
new file mode 100644
index 0000000..77f6a5c
--- /dev/null
+++ b/ext/patches/boost/asio/windows/basic_random_access_handle.hpp
@@ -0,0 +1,378 @@
+//
+// windows/basic_random_access_handle.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_BASIC_RANDOM_ACCESS_HANDLE_HPP
+#define BOOST_ASIO_WINDOWS_BASIC_RANDOM_ACCESS_HANDLE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/windows/basic_handle.hpp>
+#include <boost/asio/windows/random_access_handle_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Provides random-access handle functionality.
+/**
+ * The windows::basic_random_access_handle class template provides asynchronous
+ * and blocking random-access handle functionality.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+template <typename RandomAccessHandleService = random_access_handle_service>
+class basic_random_access_handle
+ : public basic_handle<RandomAccessHandleService>
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// handle.
+ typedef typename RandomAccessHandleService::native_handle_type native_type;
+
+ /// The native representation of a handle.
+ typedef typename RandomAccessHandleService::native_handle_type
+ native_handle_type;
+
+ /// Construct a basic_random_access_handle without opening it.
+ /**
+ * This constructor creates a random-access handle without opening it. The
+ * handle needs to be opened before data can be written to or read from it.
+ *
+ * @param io_service The io_service object that the random-access handle will
+ * use to dispatch handlers for any asynchronous operations performed on the
+ * handle.
+ */
+ explicit basic_random_access_handle(boost::asio::io_service& io_service)
+ : basic_handle<RandomAccessHandleService>(io_service)
+ {
+ }
+
+ /// Construct a basic_random_access_handle on an existing native handle.
+ /**
+ * This constructor creates a random-access handle object to hold an existing
+ * native handle.
+ *
+ * @param io_service The io_service object that the random-access handle will
+ * use to dispatch handlers for any asynchronous operations performed on the
+ * handle.
+ *
+ * @param handle The new underlying handle implementation.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_random_access_handle(boost::asio::io_service& io_service,
+ const native_handle_type& handle)
+ : basic_handle<RandomAccessHandleService>(io_service, handle)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_random_access_handle from another.
+ /**
+ * This constructor moves a random-access handle from one object to another.
+ *
+ * @param other The other basic_random_access_handle object from which the
+ * move will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_random_access_handle(io_service&)
+ * constructor.
+ */
+ basic_random_access_handle(basic_random_access_handle&& other)
+ : basic_handle<RandomAccessHandleService>(
+ BOOST_ASIO_MOVE_CAST(basic_random_access_handle)(other))
+ {
+ }
+
+ /// Move-assign a basic_random_access_handle from another.
+ /**
+ * This assignment operator moves a random-access handle from one object to
+ * another.
+ *
+ * @param other The other basic_random_access_handle object from which the
+ * move will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_random_access_handle(io_service&)
+ * constructor.
+ */
+ basic_random_access_handle& operator=(basic_random_access_handle&& other)
+ {
+ basic_handle<RandomAccessHandleService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_random_access_handle)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Write some data to the handle at the specified offset.
+ /**
+ * This function is used to write data to the random-access handle. The
+ * function call will block until one or more bytes of the data has been
+ * written successfully, or until an error occurs.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more data buffers to be written to the handle.
+ *
+ * @returns The number of bytes written.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The write_some_at operation may not write all of the data. Consider
+ * using the @ref write_at function if you need to ensure that all data is
+ * written before the blocking operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * handle.write_some_at(42, boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some_at(uint64_t offset,
+ const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().write_some_at(
+ this->get_implementation(), offset, buffers, ec);
+ boost::asio::detail::throw_error(ec, "write_some_at");
+ return s;
+ }
+
+ /// Write some data to the handle at the specified offset.
+ /**
+ * This function is used to write data to the random-access handle. The
+ * function call will block until one or more bytes of the data has been
+ * written successfully, or until an error occurs.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more data buffers to be written to the handle.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. Returns 0 if an error occurred.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write_at function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some_at(uint64_t offset,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return this->get_service().write_some_at(
+ this->get_implementation(), offset, buffers, ec);
+ }
+
+ /// Start an asynchronous write at the specified offset.
+ /**
+ * This function is used to asynchronously write data to the random-access
+ * handle. The function call always returns immediately.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more data buffers to be written to the handle.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes written.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The write operation may not transmit all of the data to the peer.
+ * Consider using the @ref async_write_at function if you need to ensure that
+ * all data is written before the asynchronous operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * handle.async_write_some_at(42, boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some_at(uint64_t offset,
+ const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_write_some_at(this->get_implementation(),
+ offset, buffers, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Read some data from the handle at the specified offset.
+ /**
+ * This function is used to read data from the random-access handle. The
+ * function call will block until one or more bytes of data has been read
+ * successfully, or until an error occurs.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @returns The number of bytes read.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read_at function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * handle.read_some_at(42, boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some_at(uint64_t offset,
+ const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().read_some_at(
+ this->get_implementation(), offset, buffers, ec);
+ boost::asio::detail::throw_error(ec, "read_some_at");
+ return s;
+ }
+
+ /// Read some data from the handle at the specified offset.
+ /**
+ * This function is used to read data from the random-access handle. The
+ * function call will block until one or more bytes of data has been read
+ * successfully, or until an error occurs.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. Returns 0 if an error occurred.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read_at function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some_at(uint64_t offset,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return this->get_service().read_some_at(
+ this->get_implementation(), offset, buffers, ec);
+ }
+
+ /// Start an asynchronous read at the specified offset.
+ /**
+ * This function is used to asynchronously read data from the random-access
+ * handle. The function call always returns immediately.
+ *
+ * @param offset The offset at which the data will be read.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes read.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The read operation may not read all of the requested number of bytes.
+ * Consider using the @ref async_read_at function if you need to ensure that
+ * the requested amount of data is read before the asynchronous operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * handle.async_read_some_at(42, boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some_at(uint64_t offset,
+ const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_read_some_at(this->get_implementation(),
+ offset, buffers, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+};
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_BASIC_RANDOM_ACCESS_HANDLE_HPP
diff --git a/ext/patches/boost/asio/windows/basic_stream_handle.hpp b/ext/patches/boost/asio/windows/basic_stream_handle.hpp
new file mode 100644
index 0000000..fe34d9b
--- /dev/null
+++ b/ext/patches/boost/asio/windows/basic_stream_handle.hpp
@@ -0,0 +1,361 @@
+//
+// windows/basic_stream_handle.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_BASIC_STREAM_HANDLE_HPP
+#define BOOST_ASIO_WINDOWS_BASIC_STREAM_HANDLE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <boost/asio/detail/handler_type_requirements.hpp>
+#include <boost/asio/detail/throw_error.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/windows/basic_handle.hpp>
+#include <boost/asio/windows/stream_handle_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Provides stream-oriented handle functionality.
+/**
+ * The windows::basic_stream_handle class template provides asynchronous and
+ * blocking stream-oriented handle functionality.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ *
+ * @par Concepts:
+ * AsyncReadStream, AsyncWriteStream, Stream, SyncReadStream, SyncWriteStream.
+ */
+template <typename StreamHandleService = stream_handle_service>
+class basic_stream_handle
+ : public basic_handle<StreamHandleService>
+{
+public:
+ /// (Deprecated: Use native_handle_type.) The native representation of a
+ /// handle.
+ typedef typename StreamHandleService::native_handle_type native_type;
+
+ /// The native representation of a handle.
+ typedef typename StreamHandleService::native_handle_type native_handle_type;
+
+ /// Construct a basic_stream_handle without opening it.
+ /**
+ * This constructor creates a stream handle without opening it. The handle
+ * needs to be opened and then connected or accepted before data can be sent
+ * or received on it.
+ *
+ * @param io_service The io_service object that the stream handle will use to
+ * dispatch handlers for any asynchronous operations performed on the handle.
+ */
+ explicit basic_stream_handle(boost::asio::io_service& io_service)
+ : basic_handle<StreamHandleService>(io_service)
+ {
+ }
+
+ /// Construct a basic_stream_handle on an existing native handle.
+ /**
+ * This constructor creates a stream handle object to hold an existing native
+ * handle.
+ *
+ * @param io_service The io_service object that the stream handle will use to
+ * dispatch handlers for any asynchronous operations performed on the handle.
+ *
+ * @param handle The new underlying handle implementation.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+ basic_stream_handle(boost::asio::io_service& io_service,
+ const native_handle_type& handle)
+ : basic_handle<StreamHandleService>(io_service, handle)
+ {
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a basic_stream_handle from another.
+ /**
+ * This constructor moves a stream handle from one object to another.
+ *
+ * @param other The other basic_stream_handle object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_stream_handle(io_service&) constructor.
+ */
+ basic_stream_handle(basic_stream_handle&& other)
+ : basic_handle<StreamHandleService>(
+ BOOST_ASIO_MOVE_CAST(basic_stream_handle)(other))
+ {
+ }
+
+ /// Move-assign a basic_stream_handle from another.
+ /**
+ * This assignment operator moves a stream handle from one object to
+ * another.
+ *
+ * @param other The other basic_stream_handle object from which the move
+ * will occur.
+ *
+ * @note Following the move, the moved-from object is in the same state as if
+ * constructed using the @c basic_stream_handle(io_service&) constructor.
+ */
+ basic_stream_handle& operator=(basic_stream_handle&& other)
+ {
+ basic_handle<StreamHandleService>::operator=(
+ BOOST_ASIO_MOVE_CAST(basic_stream_handle)(other));
+ return *this;
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Write some data to the handle.
+ /**
+ * This function is used to write data to the stream handle. The function call
+ * will block until one or more bytes of the data has been written
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more data buffers to be written to the handle.
+ *
+ * @returns The number of bytes written.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * handle.write_some(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().write_some(
+ this->get_implementation(), buffers, ec);
+ boost::asio::detail::throw_error(ec, "write_some");
+ return s;
+ }
+
+ /// Write some data to the handle.
+ /**
+ * This function is used to write data to the stream handle. The function call
+ * will block until one or more bytes of the data has been written
+ * successfully, or until an error occurs.
+ *
+ * @param buffers One or more data buffers to be written to the handle.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. Returns 0 if an error occurred.
+ *
+ * @note The write_some operation may not transmit all of the data to the
+ * peer. Consider using the @ref write function if you need to ensure that
+ * all data is written before the blocking operation completes.
+ */
+ template <typename ConstBufferSequence>
+ std::size_t write_some(const ConstBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().write_some(
+ this->get_implementation(), buffers, ec);
+ }
+
+ /// Start an asynchronous write.
+ /**
+ * This function is used to asynchronously write data to the stream handle.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more data buffers to be written to the handle.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes written.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The write operation may not transmit all of the data to the peer.
+ * Consider using the @ref async_write function if you need to ensure that all
+ * data is written before the asynchronous operation completes.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * handle.async_write_some(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a WriteHandler.
+ BOOST_ASIO_WRITE_HANDLER_CHECK(WriteHandler, handler) type_check;
+
+ return this->get_service().async_write_some(this->get_implementation(),
+ buffers, BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+ }
+
+ /// Read some data from the handle.
+ /**
+ * This function is used to read data from the stream handle. The function
+ * call will block until one or more bytes of data has been read successfully,
+ * or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @returns The number of bytes read.
+ *
+ * @throws boost::system::system_error Thrown on failure. An error code of
+ * boost::asio::error::eof indicates that the connection was closed by the
+ * peer.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * handle.read_some(boost::asio::buffer(data, size));
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers)
+ {
+ boost::system::error_code ec;
+ std::size_t s = this->get_service().read_some(
+ this->get_implementation(), buffers, ec);
+ boost::asio::detail::throw_error(ec, "read_some");
+ return s;
+ }
+
+ /// Read some data from the handle.
+ /**
+ * This function is used to read data from the stream handle. The function
+ * call will block until one or more bytes of data has been read successfully,
+ * or until an error occurs.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes read. Returns 0 if an error occurred.
+ *
+ * @note The read_some operation may not read all of the requested number of
+ * bytes. Consider using the @ref read function if you need to ensure that
+ * the requested amount of data is read before the blocking operation
+ * completes.
+ */
+ template <typename MutableBufferSequence>
+ std::size_t read_some(const MutableBufferSequence& buffers,
+ boost::system::error_code& ec)
+ {
+ return this->get_service().read_some(
+ this->get_implementation(), buffers, ec);
+ }
+
+ /// Start an asynchronous read.
+ /**
+ * This function is used to asynchronously read data from the stream handle.
+ * The function call always returns immediately.
+ *
+ * @param buffers One or more buffers into which the data will be read.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the read operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ * std::size_t bytes_transferred // Number of bytes read.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation
+ * of the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @note The read operation may not read all of the requested number of bytes.
+ * Consider using the @ref async_read function if you need to ensure that the
+ * requested amount of data is read before the asynchronous operation
+ * completes.
+ *
+ * @par Example
+ * To read into a single data buffer use the @ref buffer function as follows:
+ * @code
+ * handle.async_read_some(boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on reading into multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ // If you get an error on the following line it means that your handler does
+ // not meet the documented type requirements for a ReadHandler.
+ BOOST_ASIO_READ_HANDLER_CHECK(ReadHandler, handler) type_check;
+
+ return this->get_service().async_read_some(this->get_implementation(),
+ buffers, BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+ }
+};
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_BASIC_STREAM_HANDLE_HPP
diff --git a/ext/patches/boost/asio/windows/object_handle.hpp b/ext/patches/boost/asio/windows/object_handle.hpp
new file mode 100644
index 0000000..4b2ea12
--- /dev/null
+++ b/ext/patches/boost/asio/windows/object_handle.hpp
@@ -0,0 +1,40 @@
+//
+// windows/object_handle.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2011 Boris Schaeling (boris at highscore.de)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_OBJECT_HANDLE_HPP
+#define BOOST_ASIO_WINDOWS_OBJECT_HANDLE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/windows/basic_object_handle.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Typedef for the typical usage of an object handle.
+typedef basic_object_handle<> object_handle;
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_OBJECT_HANDLE_HPP
diff --git a/ext/patches/boost/asio/windows/object_handle_service.hpp b/ext/patches/boost/asio/windows/object_handle_service.hpp
new file mode 100644
index 0000000..d4c6eee
--- /dev/null
+++ b/ext/patches/boost/asio/windows/object_handle_service.hpp
@@ -0,0 +1,179 @@
+//
+// windows/object_handle_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+// Copyright (c) 2011 Boris Schaeling (boris at highscore.de)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_OBJECT_HANDLE_SERVICE_HPP
+#define BOOST_ASIO_WINDOWS_OBJECT_HANDLE_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/win_object_handle_service.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Default service implementation for an object handle.
+class object_handle_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<object_handle_service>
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+private:
+ // The type of the platform-specific implementation.
+ typedef detail::win_object_handle_service service_impl_type;
+
+public:
+ /// The type of an object handle implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// The native handle type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new object handle service for the specified io_service.
+ explicit object_handle_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<object_handle_service>(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new object handle implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new object handle implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another object handle implementation.
+ void move_assign(implementation_type& impl,
+ object_handle_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy an object handle implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Assign an existing native handle to an object handle.
+ boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, handle, ec);
+ }
+
+ /// Determine whether the handle is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close an object handle implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// Get the native handle implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the handle.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ // Wait for a signaled state.
+ void wait(implementation_type& impl, boost::system::error_code& ec)
+ {
+ service_impl_.wait(impl, ec);
+ }
+
+ /// Start an asynchronous wait.
+ template <typename WaitHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WaitHandler,
+ void (boost::system::error_code))
+ async_wait(implementation_type& impl,
+ BOOST_ASIO_MOVE_ARG(WaitHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ WaitHandler, void (boost::system::error_code)> init(
+ BOOST_ASIO_MOVE_CAST(WaitHandler)(handler));
+
+ service_impl_.async_wait(impl, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_OBJECT_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_OBJECT_HANDLE_SERVICE_HPP
diff --git a/ext/patches/boost/asio/windows/overlapped_ptr.hpp b/ext/patches/boost/asio/windows/overlapped_ptr.hpp
new file mode 100644
index 0000000..66f519d
--- /dev/null
+++ b/ext/patches/boost/asio/windows/overlapped_ptr.hpp
@@ -0,0 +1,118 @@
+//
+// windows/overlapped_ptr.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_OVERLAPPED_PTR_HPP
+#define BOOST_ASIO_WINDOWS_OVERLAPPED_PTR_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_OVERLAPPED_PTR) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/detail/noncopyable.hpp>
+#include <boost/asio/detail/win_iocp_overlapped_ptr.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Wraps a handler to create an OVERLAPPED object for use with overlapped I/O.
+/**
+ * A special-purpose smart pointer used to wrap an application handler so that
+ * it can be passed as the LPOVERLAPPED argument to overlapped I/O functions.
+ *
+ * @par Thread Safety
+ * @e Distinct @e objects: Safe. at n
+ * @e Shared @e objects: Unsafe.
+ */
+class overlapped_ptr
+ : private noncopyable
+{
+public:
+ /// Construct an empty overlapped_ptr.
+ overlapped_ptr()
+ : impl_()
+ {
+ }
+
+ /// Construct an overlapped_ptr to contain the specified handler.
+ template <typename Handler>
+ explicit overlapped_ptr(boost::asio::io_service& io_service,
+ BOOST_ASIO_MOVE_ARG(Handler) handler)
+ : impl_(io_service, BOOST_ASIO_MOVE_CAST(Handler)(handler))
+ {
+ }
+
+ /// Destructor automatically frees the OVERLAPPED object unless released.
+ ~overlapped_ptr()
+ {
+ }
+
+ /// Reset to empty.
+ void reset()
+ {
+ impl_.reset();
+ }
+
+ /// Reset to contain the specified handler, freeing any current OVERLAPPED
+ /// object.
+ template <typename Handler>
+ void reset(boost::asio::io_service& io_service,
+ BOOST_ASIO_MOVE_ARG(Handler) handler)
+ {
+ impl_.reset(io_service, BOOST_ASIO_MOVE_CAST(Handler)(handler));
+ }
+
+ /// Get the contained OVERLAPPED object.
+ OVERLAPPED* get()
+ {
+ return impl_.get();
+ }
+
+ /// Get the contained OVERLAPPED object.
+ const OVERLAPPED* get() const
+ {
+ return impl_.get();
+ }
+
+ /// Release ownership of the OVERLAPPED object.
+ OVERLAPPED* release()
+ {
+ return impl_.release();
+ }
+
+ /// Post completion notification for overlapped operation. Releases ownership.
+ void complete(const boost::system::error_code& ec,
+ std::size_t bytes_transferred)
+ {
+ impl_.complete(ec, bytes_transferred);
+ }
+
+private:
+ detail::win_iocp_overlapped_ptr impl_;
+};
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_OVERLAPPED_PTR)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_OVERLAPPED_PTR_HPP
diff --git a/ext/patches/boost/asio/windows/random_access_handle.hpp b/ext/patches/boost/asio/windows/random_access_handle.hpp
new file mode 100644
index 0000000..b376fc9
--- /dev/null
+++ b/ext/patches/boost/asio/windows/random_access_handle.hpp
@@ -0,0 +1,39 @@
+//
+// windows/random_access_handle.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_RANDOM_ACCESS_HANDLE_HPP
+#define BOOST_ASIO_WINDOWS_RANDOM_ACCESS_HANDLE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/windows/basic_random_access_handle.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Typedef for the typical usage of a random-access handle.
+typedef basic_random_access_handle<> random_access_handle;
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_RANDOM_ACCESS_HANDLE_HPP
diff --git a/ext/patches/boost/asio/windows/random_access_handle_service.hpp b/ext/patches/boost/asio/windows/random_access_handle_service.hpp
new file mode 100644
index 0000000..bdb50dd
--- /dev/null
+++ b/ext/patches/boost/asio/windows/random_access_handle_service.hpp
@@ -0,0 +1,222 @@
+//
+// windows/random_access_handle_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_RANDOM_ACCESS_HANDLE_SERVICE_HPP
+#define BOOST_ASIO_WINDOWS_RANDOM_ACCESS_HANDLE_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/cstdint.hpp>
+#include <boost/asio/detail/win_iocp_handle_service.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Default service implementation for a random-access handle.
+class random_access_handle_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<random_access_handle_service>
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+private:
+ // The type of the platform-specific implementation.
+ typedef detail::win_iocp_handle_service service_impl_type;
+
+public:
+ /// The type of a random-access handle implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native handle type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native handle type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new random-access handle service for the specified io_service.
+ explicit random_access_handle_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<
+ random_access_handle_service>(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new random-access handle implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new random-access handle implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another random-access handle implementation.
+ void move_assign(implementation_type& impl,
+ random_access_handle_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a random-access handle implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Assign an existing native handle to a random-access handle.
+ boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, handle, ec);
+ }
+
+ /// Determine whether the handle is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close a random-access handle implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native handle implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native handle implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the handle.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Write the given data at the specified offset.
+ template <typename ConstBufferSequence>
+ std::size_t write_some_at(implementation_type& impl, uint64_t offset,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.write_some_at(impl, offset, buffers, ec);
+ }
+
+ /// Start an asynchronous write at the specified offset.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some_at(implementation_type& impl,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_write_some_at(impl, offset, buffers, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Read some data from the specified offset.
+ template <typename MutableBufferSequence>
+ std::size_t read_some_at(implementation_type& impl, uint64_t offset,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.read_some_at(impl, offset, buffers, ec);
+ }
+
+ /// Start an asynchronous read at the specified offset.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some_at(implementation_type& impl,
+ uint64_t offset, const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_read_some_at(impl, offset, buffers, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_RANDOM_ACCESS_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_RANDOM_ACCESS_HANDLE_SERVICE_HPP
diff --git a/ext/patches/boost/asio/windows/stream_handle.hpp b/ext/patches/boost/asio/windows/stream_handle.hpp
new file mode 100644
index 0000000..bff8ad6
--- /dev/null
+++ b/ext/patches/boost/asio/windows/stream_handle.hpp
@@ -0,0 +1,39 @@
+//
+// windows/stream_handle.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_STREAM_HANDLE_HPP
+#define BOOST_ASIO_WINDOWS_STREAM_HANDLE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <boost/asio/windows/basic_stream_handle.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Typedef for the typical usage of a stream-oriented handle.
+typedef basic_stream_handle<> stream_handle;
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_STREAM_HANDLE_HPP
diff --git a/ext/patches/boost/asio/windows/stream_handle_service.hpp b/ext/patches/boost/asio/windows/stream_handle_service.hpp
new file mode 100644
index 0000000..cd799cc
--- /dev/null
+++ b/ext/patches/boost/asio/windows/stream_handle_service.hpp
@@ -0,0 +1,220 @@
+//
+// windows/stream_handle_service.hpp
+// ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WINDOWS_STREAM_HANDLE_SERVICE_HPP
+#define BOOST_ASIO_WINDOWS_STREAM_HANDLE_SERVICE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+
+#if defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE) \
+ || defined(GENERATING_DOCUMENTATION)
+
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/detail/win_iocp_handle_service.hpp>
+#include <boost/asio/error.hpp>
+#include <boost/asio/io_service.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+namespace windows {
+
+/// Default service implementation for a stream handle.
+class stream_handle_service
+#if defined(GENERATING_DOCUMENTATION)
+ : public boost::asio::io_service::service
+#else
+ : public boost::asio::detail::service_base<stream_handle_service>
+#endif
+{
+public:
+#if defined(GENERATING_DOCUMENTATION)
+ /// The unique service identifier.
+ static boost::asio::io_service::id id;
+#endif
+
+private:
+ // The type of the platform-specific implementation.
+ typedef detail::win_iocp_handle_service service_impl_type;
+
+public:
+ /// The type of a stream handle implementation.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined implementation_type;
+#else
+ typedef service_impl_type::implementation_type implementation_type;
+#endif
+
+ /// (Deprecated: Use native_handle_type.) The native handle type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_type;
+#else
+ typedef service_impl_type::native_handle_type native_type;
+#endif
+
+ /// The native handle type.
+#if defined(GENERATING_DOCUMENTATION)
+ typedef implementation_defined native_handle_type;
+#else
+ typedef service_impl_type::native_handle_type native_handle_type;
+#endif
+
+ /// Construct a new stream handle service for the specified io_service.
+ explicit stream_handle_service(boost::asio::io_service& io_service)
+ : boost::asio::detail::service_base<stream_handle_service>(io_service),
+ service_impl_(io_service)
+ {
+ }
+
+ /// Construct a new stream handle implementation.
+ void construct(implementation_type& impl)
+ {
+ service_impl_.construct(impl);
+ }
+
+#if defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+ /// Move-construct a new stream handle implementation.
+ void move_construct(implementation_type& impl,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_construct(impl, other_impl);
+ }
+
+ /// Move-assign from another stream handle implementation.
+ void move_assign(implementation_type& impl,
+ stream_handle_service& other_service,
+ implementation_type& other_impl)
+ {
+ service_impl_.move_assign(impl, other_service.service_impl_, other_impl);
+ }
+#endif // defined(BOOST_ASIO_HAS_MOVE) || defined(GENERATING_DOCUMENTATION)
+
+ /// Destroy a stream handle implementation.
+ void destroy(implementation_type& impl)
+ {
+ service_impl_.destroy(impl);
+ }
+
+ /// Assign an existing native handle to a stream handle.
+ boost::system::error_code assign(implementation_type& impl,
+ const native_handle_type& handle, boost::system::error_code& ec)
+ {
+ return service_impl_.assign(impl, handle, ec);
+ }
+
+ /// Determine whether the handle is open.
+ bool is_open(const implementation_type& impl) const
+ {
+ return service_impl_.is_open(impl);
+ }
+
+ /// Close a stream handle implementation.
+ boost::system::error_code close(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.close(impl, ec);
+ }
+
+ /// (Deprecated: Use native_handle().) Get the native handle implementation.
+ native_type native(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Get the native handle implementation.
+ native_handle_type native_handle(implementation_type& impl)
+ {
+ return service_impl_.native_handle(impl);
+ }
+
+ /// Cancel all asynchronous operations associated with the handle.
+ boost::system::error_code cancel(implementation_type& impl,
+ boost::system::error_code& ec)
+ {
+ return service_impl_.cancel(impl, ec);
+ }
+
+ /// Write the given data to the stream.
+ template <typename ConstBufferSequence>
+ std::size_t write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.write_some(impl, buffers, ec);
+ }
+
+ /// Start an asynchronous write.
+ template <typename ConstBufferSequence, typename WriteHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+ async_write_some(implementation_type& impl,
+ const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ WriteHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(WriteHandler)(handler));
+
+ service_impl_.async_write_some(impl, buffers, init.handler);
+
+ return init.result.get();
+ }
+
+ /// Read some data from the stream.
+ template <typename MutableBufferSequence>
+ std::size_t read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers, boost::system::error_code& ec)
+ {
+ return service_impl_.read_some(impl, buffers, ec);
+ }
+
+ /// Start an asynchronous read.
+ template <typename MutableBufferSequence, typename ReadHandler>
+ BOOST_ASIO_INITFN_RESULT_TYPE(ReadHandler,
+ void (boost::system::error_code, std::size_t))
+ async_read_some(implementation_type& impl,
+ const MutableBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(ReadHandler) handler)
+ {
+ boost::asio::detail::async_result_init<
+ ReadHandler, void (boost::system::error_code, std::size_t)> init(
+ BOOST_ASIO_MOVE_CAST(ReadHandler)(handler));
+
+ service_impl_.async_read_some(impl, buffers, init.handler);
+
+ return init.result.get();
+ }
+
+private:
+ // Destroy all user-defined handler objects owned by the service.
+ void shutdown_service()
+ {
+ service_impl_.shutdown_service();
+ }
+
+ // The platform-specific implementation.
+ service_impl_type service_impl_;
+};
+
+} // namespace windows
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#endif // defined(BOOST_ASIO_HAS_WINDOWS_STREAM_HANDLE)
+ // || defined(GENERATING_DOCUMENTATION)
+
+#endif // BOOST_ASIO_WINDOWS_STREAM_HANDLE_SERVICE_HPP
diff --git a/ext/patches/boost/asio/write.hpp b/ext/patches/boost/asio/write.hpp
new file mode 100644
index 0000000..78d84d0
--- /dev/null
+++ b/ext/patches/boost/asio/write.hpp
@@ -0,0 +1,620 @@
+//
+// write.hpp
+// ~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WRITE_HPP
+#define BOOST_ASIO_WRITE_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_streambuf_fwd.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/**
+ * @defgroup write boost::asio::write
+ *
+ * @brief Write a certain amount of data to a stream before returning.
+ */
+/*@{*/
+
+/// Write all of the supplied data to a stream before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a stream.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * write_some function.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the SyncWriteStream concept.
+ *
+ * @param buffers One or more buffers containing the data to be written. The sum
+ * of the buffer sizes indicates the maximum number of bytes to write to the
+ * stream.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::write(s, boost::asio::buffer(data, size)); @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::write(
+ * s, buffers,
+ * boost::asio::transfer_all()); @endcode
+ */
+template <typename SyncWriteStream, typename ConstBufferSequence>
+std::size_t write(SyncWriteStream& s, const ConstBufferSequence& buffers);
+
+/// Write all of the supplied data to a stream before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a stream.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * write_some function.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the SyncWriteStream concept.
+ *
+ * @param buffers One or more buffers containing the data to be written. The sum
+ * of the buffer sizes indicates the maximum number of bytes to write to the
+ * stream.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::write(s, boost::asio::buffer(data, size), ec); @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::write(
+ * s, buffers,
+ * boost::asio::transfer_all(), ec); @endcode
+ */
+template <typename SyncWriteStream, typename ConstBufferSequence>
+std::size_t write(SyncWriteStream& s, const ConstBufferSequence& buffers,
+ boost::system::error_code& ec);
+
+/// Write a certain amount of data to a stream before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a stream.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * write_some function.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the SyncWriteStream concept.
+ *
+ * @param buffers One or more buffers containing the data to be written. The sum
+ * of the buffer sizes indicates the maximum number of bytes to write to the
+ * stream.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest write_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the stream's write_some function.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::write(s, boost::asio::buffer(data, size),
+ * boost::asio::transfer_at_least(32)); @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename SyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition>
+std::size_t write(SyncWriteStream& s, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition);
+
+/// Write a certain amount of data to a stream before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a stream.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * write_some function.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the SyncWriteStream concept.
+ *
+ * @param buffers One or more buffers containing the data to be written. The sum
+ * of the buffer sizes indicates the maximum number of bytes to write to the
+ * stream.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest write_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the stream's write_some function.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. If an error occurs, returns the total
+ * number of bytes successfully transferred prior to the error.
+ */
+template <typename SyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition>
+std::size_t write(SyncWriteStream& s, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition, boost::system::error_code& ec);
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Write all of the supplied data to a stream before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a stream.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * write_some function.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the SyncWriteStream concept.
+ *
+ * @param b The basic_streambuf object from which data will be written.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::write(
+ * s, b,
+ * boost::asio::transfer_all()); @endcode
+ */
+template <typename SyncWriteStream, typename Allocator>
+std::size_t write(SyncWriteStream& s, basic_streambuf<Allocator>& b);
+
+/// Write all of the supplied data to a stream before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a stream.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * write_some function.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the SyncWriteStream concept.
+ *
+ * @param b The basic_streambuf object from which data will be written.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::write(
+ * s, b,
+ * boost::asio::transfer_all(), ec); @endcode
+ */
+template <typename SyncWriteStream, typename Allocator>
+std::size_t write(SyncWriteStream& s, basic_streambuf<Allocator>& b,
+ boost::system::error_code& ec);
+
+/// Write a certain amount of data to a stream before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a stream.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * write_some function.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the SyncWriteStream concept.
+ *
+ * @param b The basic_streambuf object from which data will be written.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest write_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the stream's write_some function.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+template <typename SyncWriteStream, typename Allocator,
+ typename CompletionCondition>
+std::size_t write(SyncWriteStream& s, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition);
+
+/// Write a certain amount of data to a stream before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a stream.
+ * The call will block until one of the following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * write_some function.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the SyncWriteStream concept.
+ *
+ * @param b The basic_streambuf object from which data will be written.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest write_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the stream's write_some function.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. If an error occurs, returns the total
+ * number of bytes successfully transferred prior to the error.
+ */
+template <typename SyncWriteStream, typename Allocator,
+ typename CompletionCondition>
+std::size_t write(SyncWriteStream& s, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition, boost::system::error_code& ec);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/*@}*/
+/**
+ * @defgroup async_write boost::asio::async_write
+ *
+ * @brief Start an asynchronous operation to write a certain amount of data to a
+ * stream.
+ */
+/*@{*/
+
+/// Start an asynchronous operation to write all of the supplied data to a
+/// stream.
+/**
+ * This function is used to asynchronously write a certain number of bytes of
+ * data to a stream. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions
+ * is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_write_some function, and is known as a <em>composed operation</em>. The
+ * program must ensure that the stream performs no other write operations (such
+ * as async_write, the stream's async_write_some function, or any other composed
+ * operations that perform writes) until this operation completes.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the AsyncWriteStream concept.
+ *
+ * @param buffers One or more buffers containing the data to be written.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ *
+ * std::size_t bytes_transferred // Number of bytes written from the
+ * // buffers. If an error occurred,
+ * // this will be less than the sum
+ * // of the buffer sizes.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * boost::asio::async_write(s, boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename AsyncWriteStream, typename ConstBufferSequence,
+ typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write(AsyncWriteStream& s, const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+/// Start an asynchronous operation to write a certain amount of data to a
+/// stream.
+/**
+ * This function is used to asynchronously write a certain number of bytes of
+ * data to a stream. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions
+ * is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_write_some function, and is known as a <em>composed operation</em>. The
+ * program must ensure that the stream performs no other write operations (such
+ * as async_write, the stream's async_write_some function, or any other composed
+ * operations that perform writes) until this operation completes.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the AsyncWriteStream concept.
+ *
+ * @param buffers One or more buffers containing the data to be written.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest async_write_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the stream's async_write_some function.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ *
+ * std::size_t bytes_transferred // Number of bytes written from the
+ * // buffers. If an error occurred,
+ * // this will be less than the sum
+ * // of the buffer sizes.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::async_write(s,
+ * boost::asio::buffer(data, size),
+ * boost::asio::transfer_at_least(32),
+ * handler); @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename AsyncWriteStream, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write(AsyncWriteStream& s, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Start an asynchronous operation to write all of the supplied data to a
+/// stream.
+/**
+ * This function is used to asynchronously write a certain number of bytes of
+ * data to a stream. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions
+ * is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_write_some function, and is known as a <em>composed operation</em>. The
+ * program must ensure that the stream performs no other write operations (such
+ * as async_write, the stream's async_write_some function, or any other composed
+ * operations that perform writes) until this operation completes.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the AsyncWriteStream concept.
+ *
+ * @param b A basic_streambuf object from which data will be written. Ownership
+ * of the streambuf is retained by the caller, which must guarantee that it
+ * remains valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ *
+ * std::size_t bytes_transferred // Number of bytes written from the
+ * // buffers. If an error occurred,
+ * // this will be less than the sum
+ * // of the buffer sizes.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+template <typename AsyncWriteStream, typename Allocator, typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write(AsyncWriteStream& s, basic_streambuf<Allocator>& b,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+/// Start an asynchronous operation to write a certain amount of data to a
+/// stream.
+/**
+ * This function is used to asynchronously write a certain number of bytes of
+ * data to a stream. The function call always returns immediately. The
+ * asynchronous operation will continue until one of the following conditions
+ * is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the stream's
+ * async_write_some function, and is known as a <em>composed operation</em>. The
+ * program must ensure that the stream performs no other write operations (such
+ * as async_write, the stream's async_write_some function, or any other composed
+ * operations that perform writes) until this operation completes.
+ *
+ * @param s The stream to which the data is to be written. The type must support
+ * the AsyncWriteStream concept.
+ *
+ * @param b A basic_streambuf object from which data will be written. Ownership
+ * of the streambuf is retained by the caller, which must guarantee that it
+ * remains valid until the handler is called.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest async_write_some operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the stream's async_write_some function.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * const boost::system::error_code& error, // Result of operation.
+ *
+ * std::size_t bytes_transferred // Number of bytes written from the
+ * // buffers. If an error occurred,
+ * // this will be less than the sum
+ * // of the buffer sizes.
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+template <typename AsyncWriteStream, typename Allocator,
+ typename CompletionCondition, typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write(AsyncWriteStream& s, basic_streambuf<Allocator>& b,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/write.hpp>
+
+#endif // BOOST_ASIO_WRITE_HPP
diff --git a/ext/patches/boost/asio/write_at.hpp b/ext/patches/boost/asio/write_at.hpp
new file mode 100644
index 0000000..fa1b19c
--- /dev/null
+++ b/ext/patches/boost/asio/write_at.hpp
@@ -0,0 +1,672 @@
+//
+// write_at.hpp
+// ~~~~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#ifndef BOOST_ASIO_WRITE_AT_HPP
+#define BOOST_ASIO_WRITE_AT_HPP
+
+#if defined(_MSC_VER) && (_MSC_VER >= 1200)
+# pragma once
+#endif // defined(_MSC_VER) && (_MSC_VER >= 1200)
+
+#include <boost/asio/detail/config.hpp>
+#include <cstddef>
+#include <boost/asio/async_result.hpp>
+#include <boost/asio/basic_streambuf_fwd.hpp>
+#include <boost/asio/detail/cstdint.hpp>
+#include <boost/asio/error.hpp>
+
+#include <boost/asio/detail/push_options.hpp>
+
+namespace boost {
+namespace asio {
+
+/**
+ * @defgroup write_at boost::asio::write_at
+ *
+ * @brief Write a certain amount of data at a specified offset before returning.
+ */
+/*@{*/
+
+/// Write all of the supplied data at the specified offset before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a random
+ * access device at a specified offset. The call will block until one of the
+ * following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * write_some_at function.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the SyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more buffers containing the data to be written. The sum
+ * of the buffer sizes indicates the maximum number of bytes to write to the
+ * device.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::write_at(d, 42, boost::asio::buffer(data, size)); @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::write_at(
+ * d, offset, buffers,
+ * boost::asio::transfer_all()); @endcode
+ */
+template <typename SyncRandomAccessWriteDevice, typename ConstBufferSequence>
+std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers);
+
+/// Write all of the supplied data at the specified offset before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a random
+ * access device at a specified offset. The call will block until one of the
+ * following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * write_some_at function.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the SyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more buffers containing the data to be written. The sum
+ * of the buffer sizes indicates the maximum number of bytes to write to the
+ * device.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::write_at(d, 42,
+ * boost::asio::buffer(data, size), ec); @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::write_at(
+ * d, offset, buffers,
+ * boost::asio::transfer_all(), ec); @endcode
+ */
+template <typename SyncRandomAccessWriteDevice, typename ConstBufferSequence>
+std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ boost::system::error_code& ec);
+
+/// Write a certain amount of data at a specified offset before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a random
+ * access device at a specified offset. The call will block until one of the
+ * following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * write_some_at function.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the SyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more buffers containing the data to be written. The sum
+ * of the buffer sizes indicates the maximum number of bytes to write to the
+ * device.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest write_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the device's write_some_at function.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::write_at(d, 42, boost::asio::buffer(data, size),
+ * boost::asio::transfer_at_least(32)); @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename SyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition>
+std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition);
+
+/// Write a certain amount of data at a specified offset before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a random
+ * access device at a specified offset. The call will block until one of the
+ * following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * write_some_at function.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the SyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more buffers containing the data to be written. The sum
+ * of the buffer sizes indicates the maximum number of bytes to write to the
+ * device.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest write_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the device's write_some_at function.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. If an error occurs, returns the total
+ * number of bytes successfully transferred prior to the error.
+ */
+template <typename SyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition>
+std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition, boost::system::error_code& ec);
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Write all of the supplied data at the specified offset before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a random
+ * access device at a specified offset. The call will block until one of the
+ * following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * write_some_at function.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the SyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param b The basic_streambuf object from which data will be written.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::write_at(
+ * d, 42, b,
+ * boost::asio::transfer_all()); @endcode
+ */
+template <typename SyncRandomAccessWriteDevice, typename Allocator>
+std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, basic_streambuf<Allocator>& b);
+
+/// Write all of the supplied data at the specified offset before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a random
+ * access device at a specified offset. The call will block until one of the
+ * following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * write_some_at function.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the SyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param b The basic_streambuf object from which data will be written.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @note This overload is equivalent to calling:
+ * @code boost::asio::write_at(
+ * d, 42, b,
+ * boost::asio::transfer_all(), ec); @endcode
+ */
+template <typename SyncRandomAccessWriteDevice, typename Allocator>
+std::size_t write_at(SyncRandomAccessWriteDevice& d,
+ uint64_t offset, basic_streambuf<Allocator>& b,
+ boost::system::error_code& ec);
+
+/// Write a certain amount of data at a specified offset before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a random
+ * access device at a specified offset. The call will block until one of the
+ * following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * write_some_at function.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the SyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param b The basic_streambuf object from which data will be written.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest write_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the device's write_some_at function.
+ *
+ * @returns The number of bytes transferred.
+ *
+ * @throws boost::system::system_error Thrown on failure.
+ */
+template <typename SyncRandomAccessWriteDevice, typename Allocator,
+ typename CompletionCondition>
+std::size_t write_at(SyncRandomAccessWriteDevice& d, uint64_t offset,
+ basic_streambuf<Allocator>& b, CompletionCondition completion_condition);
+
+/// Write a certain amount of data at a specified offset before returning.
+/**
+ * This function is used to write a certain number of bytes of data to a random
+ * access device at a specified offset. The call will block until one of the
+ * following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * write_some_at function.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the SyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param b The basic_streambuf object from which data will be written.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest write_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the device's write_some_at function.
+ *
+ * @param ec Set to indicate what error occurred, if any.
+ *
+ * @returns The number of bytes written. If an error occurs, returns the total
+ * number of bytes successfully transferred prior to the error.
+ */
+template <typename SyncRandomAccessWriteDevice, typename Allocator,
+ typename CompletionCondition>
+std::size_t write_at(SyncRandomAccessWriteDevice& d, uint64_t offset,
+ basic_streambuf<Allocator>& b, CompletionCondition completion_condition,
+ boost::system::error_code& ec);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/*@}*/
+/**
+ * @defgroup async_write_at boost::asio::async_write_at
+ *
+ * @brief Start an asynchronous operation to write a certain amount of data at
+ * the specified offset.
+ */
+/*@{*/
+
+/// Start an asynchronous operation to write all of the supplied data at the
+/// specified offset.
+/**
+ * This function is used to asynchronously write a certain number of bytes of
+ * data to a random access device at a specified offset. The function call
+ * always returns immediately. The asynchronous operation will continue until
+ * one of the following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * async_write_some_at function, and is known as a <em>composed operation</em>.
+ * The program must ensure that the device performs no <em>overlapping</em>
+ * write operations (such as async_write_at, the device's async_write_some_at
+ * function, or any other composed operations that perform writes) until this
+ * operation completes. Operations are overlapping if the regions defined by
+ * their offsets, and the numbers of bytes to write, intersect.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the AsyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more buffers containing the data to be written.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of
+ * the handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes written from the buffers. If an error
+ * // occurred, this will be less than the sum of the buffer sizes.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code
+ * boost::asio::async_write_at(d, 42, boost::asio::buffer(data, size), handler);
+ * @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write_at(AsyncRandomAccessWriteDevice& d, uint64_t offset,
+ const ConstBufferSequence& buffers,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+/// Start an asynchronous operation to write a certain amount of data at the
+/// specified offset.
+/**
+ * This function is used to asynchronously write a certain number of bytes of
+ * data to a random access device at a specified offset. The function call
+ * always returns immediately. The asynchronous operation will continue until
+ * one of the following conditions is true:
+ *
+ * @li All of the data in the supplied buffers has been written. That is, the
+ * bytes transferred is equal to the sum of the buffer sizes.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * async_write_some_at function, and is known as a <em>composed operation</em>.
+ * The program must ensure that the device performs no <em>overlapping</em>
+ * write operations (such as async_write_at, the device's async_write_some_at
+ * function, or any other composed operations that perform writes) until this
+ * operation completes. Operations are overlapping if the regions defined by
+ * their offsets, and the numbers of bytes to write, intersect.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the AsyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param buffers One or more buffers containing the data to be written.
+ * Although the buffers object may be copied as necessary, ownership of the
+ * underlying memory blocks is retained by the caller, which must guarantee
+ * that they remain valid until the handler is called.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest async_write_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the device's async_write_some_at function.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes written from the buffers. If an error
+ * // occurred, this will be less than the sum of the buffer sizes.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ *
+ * @par Example
+ * To write a single data buffer use the @ref buffer function as follows:
+ * @code boost::asio::async_write_at(d, 42,
+ * boost::asio::buffer(data, size),
+ * boost::asio::transfer_at_least(32),
+ * handler); @endcode
+ * See the @ref buffer documentation for information on writing multiple
+ * buffers in one go, and how to use it with arrays, boost::array or
+ * std::vector.
+ */
+template <typename AsyncRandomAccessWriteDevice, typename ConstBufferSequence,
+ typename CompletionCondition, typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write_at(AsyncRandomAccessWriteDevice& d,
+ uint64_t offset, const ConstBufferSequence& buffers,
+ CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+#if !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/// Start an asynchronous operation to write all of the supplied data at the
+/// specified offset.
+/**
+ * This function is used to asynchronously write a certain number of bytes of
+ * data to a random access device at a specified offset. The function call
+ * always returns immediately. The asynchronous operation will continue until
+ * one of the following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li An error occurred.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * async_write_some_at function, and is known as a <em>composed operation</em>.
+ * The program must ensure that the device performs no <em>overlapping</em>
+ * write operations (such as async_write_at, the device's async_write_some_at
+ * function, or any other composed operations that perform writes) until this
+ * operation completes. Operations are overlapping if the regions defined by
+ * their offsets, and the numbers of bytes to write, intersect.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the AsyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param b A basic_streambuf object from which data will be written. Ownership
+ * of the streambuf is retained by the caller, which must guarantee that it
+ * remains valid until the handler is called.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes written from the buffers. If an error
+ * // occurred, this will be less than the sum of the buffer sizes.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+template <typename AsyncRandomAccessWriteDevice, typename Allocator,
+ typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write_at(AsyncRandomAccessWriteDevice& d, uint64_t offset,
+ basic_streambuf<Allocator>& b, BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+/// Start an asynchronous operation to write a certain amount of data at the
+/// specified offset.
+/**
+ * This function is used to asynchronously write a certain number of bytes of
+ * data to a random access device at a specified offset. The function call
+ * always returns immediately. The asynchronous operation will continue until
+ * one of the following conditions is true:
+ *
+ * @li All of the data in the supplied basic_streambuf has been written.
+ *
+ * @li The completion_condition function object returns 0.
+ *
+ * This operation is implemented in terms of zero or more calls to the device's
+ * async_write_some_at function, and is known as a <em>composed operation</em>.
+ * The program must ensure that the device performs no <em>overlapping</em>
+ * write operations (such as async_write_at, the device's async_write_some_at
+ * function, or any other composed operations that perform writes) until this
+ * operation completes. Operations are overlapping if the regions defined by
+ * their offsets, and the numbers of bytes to write, intersect.
+ *
+ * @param d The device to which the data is to be written. The type must support
+ * the AsyncRandomAccessWriteDevice concept.
+ *
+ * @param offset The offset at which the data will be written.
+ *
+ * @param b A basic_streambuf object from which data will be written. Ownership
+ * of the streambuf is retained by the caller, which must guarantee that it
+ * remains valid until the handler is called.
+ *
+ * @param completion_condition The function object to be called to determine
+ * whether the write operation is complete. The signature of the function object
+ * must be:
+ * @code std::size_t completion_condition(
+ * // Result of latest async_write_some_at operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes transferred so far.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * A return value of 0 indicates that the write operation is complete. A
+ * non-zero return value indicates the maximum number of bytes to be written on
+ * the next call to the device's async_write_some_at function.
+ *
+ * @param handler The handler to be called when the write operation completes.
+ * Copies will be made of the handler as required. The function signature of the
+ * handler must be:
+ * @code void handler(
+ * // Result of operation.
+ * const boost::system::error_code& error,
+ *
+ * // Number of bytes written from the buffers. If an error
+ * // occurred, this will be less than the sum of the buffer sizes.
+ * std::size_t bytes_transferred
+ * ); @endcode
+ * Regardless of whether the asynchronous operation completes immediately or
+ * not, the handler will not be invoked from within this function. Invocation of
+ * the handler will be performed in a manner equivalent to using
+ * boost::asio::io_service::post().
+ */
+template <typename AsyncRandomAccessWriteDevice, typename Allocator,
+ typename CompletionCondition, typename WriteHandler>
+BOOST_ASIO_INITFN_RESULT_TYPE(WriteHandler,
+ void (boost::system::error_code, std::size_t))
+async_write_at(AsyncRandomAccessWriteDevice& d, uint64_t offset,
+ basic_streambuf<Allocator>& b, CompletionCondition completion_condition,
+ BOOST_ASIO_MOVE_ARG(WriteHandler) handler);
+
+#endif // !defined(BOOST_ASIO_NO_IOSTREAM)
+
+/*@}*/
+
+} // namespace asio
+} // namespace boost
+
+#include <boost/asio/detail/pop_options.hpp>
+
+#include <boost/asio/impl/write_at.hpp>
+
+#endif // BOOST_ASIO_WRITE_AT_HPP
diff --git a/ext/patches/boost/asio/yield.hpp b/ext/patches/boost/asio/yield.hpp
new file mode 100644
index 0000000..3f10852
--- /dev/null
+++ b/ext/patches/boost/asio/yield.hpp
@@ -0,0 +1,23 @@
+//
+// yield.hpp
+// ~~~~~~~~~
+//
+// Copyright (c) 2003-2014 Christopher M. Kohlhoff (chris at kohlhoff dot com)
+//
+// Distributed under the Boost Software License, Version 1.0. (See accompanying
+// file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
+//
+
+#include "coroutine.hpp"
+
+#ifndef reenter
+# define reenter(c) BOOST_ASIO_CORO_REENTER(c)
+#endif
+
+#ifndef yield
+# define yield BOOST_ASIO_CORO_YIELD
+#endif
+
+#ifndef fork
+# define fork BOOST_ASIO_CORO_FORK
+#endif
diff --git a/ext/patches/comet/Comet.sln b/ext/patches/comet/Comet.sln
new file mode 100644
index 0000000..c0b3af0
--- /dev/null
+++ b/ext/patches/comet/Comet.sln
@@ -0,0 +1,81 @@
+
+Microsoft Visual Studio Solution File, Format Version 11.00
+# Visual Studio 2010
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "Comet", "Comet.vcxproj", "{EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}"
+ ProjectSection(ProjectDependencies) = postProject
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B} = {887C017B-8E91-4CCE-85C6-4D36D4033F1B}
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5} = {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}
+ EndProjectSection
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "MSToolkitLite", "MSToolkit\MSToolkitLite.vcxproj", "{8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}"
+EndProject
+Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "CometSearch", "CometSearch\CometSearch.vcxproj", "{887C017B-8E91-4CCE-85C6-4D36D4033F1B}"
+ ProjectSection(ProjectDependencies) = postProject
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5} = {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}
+ EndProjectSection
+EndProject
+Global
+ GlobalSection(SolutionConfigurationPlatforms) = preSolution
+ Debug|Mixed Platforms = Debug|Mixed Platforms
+ Debug|Win32 = Debug|Win32
+ Debug|x64 = Debug|x64
+ Debug|x86 = Debug|x86
+ Release|Mixed Platforms = Release|Mixed Platforms
+ Release|Win32 = Release|Win32
+ Release|x64 = Release|x64
+ Release|x86 = Release|x86
+ EndGlobalSection
+ GlobalSection(ProjectConfigurationPlatforms) = postSolution
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Debug|Mixed Platforms.ActiveCfg = Debug|x64
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Debug|Mixed Platforms.Build.0 = Debug|x64
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Debug|Win32.ActiveCfg = Debug|Win32
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Debug|Win32.Build.0 = Debug|Win32
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Debug|x64.ActiveCfg = Debug|x64
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Debug|x64.Build.0 = Debug|x64
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Debug|x86.ActiveCfg = Debug|Win32
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Debug|x86.Build.0 = Debug|Win32
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Release|Mixed Platforms.ActiveCfg = Release|x64
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Release|Mixed Platforms.Build.0 = Release|x64
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Release|Win32.ActiveCfg = Release|Win32
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Release|Win32.Build.0 = Release|Win32
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Release|x64.ActiveCfg = Release|x64
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Release|x64.Build.0 = Release|x64
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Release|x86.ActiveCfg = Release|Win32
+ {EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}.Release|x86.Build.0 = Release|Win32
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|Mixed Platforms.ActiveCfg = Debug|x64
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|Mixed Platforms.Build.0 = Debug|x64
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|Win32.ActiveCfg = Debug|Win32
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|Win32.Build.0 = Debug|Win32
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|x64.ActiveCfg = Debug|x64
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|x64.Build.0 = Debug|x64
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|x86.ActiveCfg = Debug|Win32
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Debug|x86.Build.0 = Debug|Win32
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|Mixed Platforms.ActiveCfg = Release|x64
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|Mixed Platforms.Build.0 = Release|x64
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|Win32.ActiveCfg = Release|Win32
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|Win32.Build.0 = Release|Win32
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|x64.ActiveCfg = Release|x64
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|x64.Build.0 = Release|x64
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|x86.ActiveCfg = Release|Win32
+ {8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}.Release|x86.Build.0 = Release|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Debug|Mixed Platforms.ActiveCfg = Debug|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Debug|Mixed Platforms.Build.0 = Debug|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Debug|Win32.ActiveCfg = Debug|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Debug|Win32.Build.0 = Debug|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Debug|x64.ActiveCfg = Debug|x64
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Debug|x64.Build.0 = Debug|x64
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Debug|x86.ActiveCfg = Debug|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Debug|x86.Build.0 = Debug|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Release|Mixed Platforms.ActiveCfg = Release|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Release|Mixed Platforms.Build.0 = Release|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Release|Win32.ActiveCfg = Release|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Release|Win32.Build.0 = Release|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Release|x64.ActiveCfg = Release|x64
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Release|x64.Build.0 = Release|x64
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Release|x86.ActiveCfg = Release|Win32
+ {887C017B-8E91-4CCE-85C6-4D36D4033F1B}.Release|x86.Build.0 = Release|Win32
+ EndGlobalSection
+ GlobalSection(SolutionProperties) = preSolution
+ HideSolutionNode = FALSE
+ EndGlobalSection
+EndGlobal
diff --git a/ext/patches/comet/Comet.vcxproj b/ext/patches/comet/Comet.vcxproj
new file mode 100644
index 0000000..a0a4224
--- /dev/null
+++ b/ext/patches/comet/Comet.vcxproj
@@ -0,0 +1,206 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+ <ItemGroup Label="ProjectConfigurations">
+ <ProjectConfiguration Include="Debug|Win32">
+ <Configuration>Debug</Configuration>
+ <Platform>Win32</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Debug|x64">
+ <Configuration>Debug</Configuration>
+ <Platform>x64</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Release|Win32">
+ <Configuration>Release</Configuration>
+ <Platform>Win32</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Release|x64">
+ <Configuration>Release</Configuration>
+ <Platform>x64</Platform>
+ </ProjectConfiguration>
+ </ItemGroup>
+ <PropertyGroup Label="Globals">
+ <ProjectGuid>{EC89AD31-11AD-4CE2-AA1D-FFFFF716DE33}</ProjectGuid>
+ <RootNamespace>Comet</RootNamespace>
+ </PropertyGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
+ <ConfigurationType>Application</ConfigurationType>
+ <UseDebugLibraries>true</UseDebugLibraries>
+ <CharacterSet>MultiByte</CharacterSet>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
+ <ConfigurationType>Application</ConfigurationType>
+ <UseDebugLibraries>true</UseDebugLibraries>
+ <CharacterSet>MultiByte</CharacterSet>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
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+ <UseDebugLibraries>false</UseDebugLibraries>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <CharacterSet>Unicode</CharacterSet>
+ <UseOfMfc>Static</UseOfMfc>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
+ <ConfigurationType>Application</ConfigurationType>
+ <UseDebugLibraries>false</UseDebugLibraries>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <CharacterSet>MultiByte</CharacterSet>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
+ <ImportGroup Label="ExtensionSettings">
+ </ImportGroup>
+ <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <PropertyGroup Label="UserMacros" />
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <OutDir>$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ <IntDir>$(Platform)\$(Configuration)\</IntDir>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <OutDir>$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <IntDir>$(Platform)\$(Configuration)\</IntDir>
+ <LinkIncremental>true</LinkIncremental>
+ </PropertyGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>MaxSpeed</Optimization>
+ <AdditionalIncludeDirectories>pthreads-w32\include;MSToolkit\include;CometSearch;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+ <StringPooling>true</StringPooling>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ <CompileAs>CompileAsCpp</CompileAs>
+ <ErrorReporting>Prompt</ErrorReporting>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
+ <BasicRuntimeChecks>Default</BasicRuntimeChecks>
+ <MinimalRebuild>false</MinimalRebuild>
+ </ClCompile>
+ <Link>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <AdditionalLibraryDirectories>$(SolutionDir)$(Platform)\$(Configuration)\</AdditionalLibraryDirectories>
+ <AdditionalDependencies>ws2_32.lib;setargv.obj;MSToolkitLite.lib;CometSearch.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies)</AdditionalDependencies>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>Disabled</Optimization>
+ <AdditionalIncludeDirectories>pthreads-w32\include;MSToolkit\include;CometSearch;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+ <InlineFunctionExpansion>Default</InlineFunctionExpansion>
+ <IntrinsicFunctions>false</IntrinsicFunctions>
+ <FavorSizeOrSpeed>Neither</FavorSizeOrSpeed>
+ <OmitFramePointers>false</OmitFramePointers>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <StringPooling>false</StringPooling>
+ <MinimalRebuild>true</MinimalRebuild>
+ <BasicRuntimeChecks>EnableFastChecks</BasicRuntimeChecks>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <FunctionLevelLinking>true</FunctionLevelLinking>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ <DebugInformationFormat>EditAndContinue</DebugInformationFormat>
+ </ClCompile>
+ <Link>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <AdditionalLibraryDirectories>$(SolutionDir)$(Platform)\$(Configuration)\</AdditionalLibraryDirectories>
+ <AdditionalDependencies>ws2_32.lib;setargv.obj;MSToolkitLite.lib;CometSearch.lib;kernel32.lib;user32.lib;gdi32.lib;winspool.lib;comdlg32.lib;advapi32.lib;shell32.lib;ole32.lib;oleaut32.lib;uuid.lib;odbc32.lib;odbccp32.lib;%(AdditionalDependencies)</AdditionalDependencies>
+ <OptimizeReferences>true</OptimizeReferences>
+ <LinkTimeCodeGeneration>UseLinkTimeCodeGeneration</LinkTimeCodeGeneration>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>MaxSpeed</Optimization>
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+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <AdditionalIncludeDirectories>pthreads-w32\include;MSToolkit\include;CometSearch;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+ <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <StringPooling>true</StringPooling>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ <PreprocessorDefinitions>_UNICODE;UNICODE;%(PreprocessorDefinitions);_CRT_SECURE_NO_WARNINGS</PreprocessorDefinitions>
+ </ClCompile>
+ <Link>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <EnableCOMDATFolding>
+ </EnableCOMDATFolding>
+ <OptimizeReferences>true</OptimizeReferences>
+ <AdditionalLibraryDirectories>$(SolutionDir)$(Platform)\$(Configuration)\</AdditionalLibraryDirectories>
+ <AdditionalDependencies>ws2_32.lib;setargv.obj;MSToolkitLite.lib;CometSearch.lib;%(AdditionalDependencies)</AdditionalDependencies>
+ <EntryPointSymbol>mainCRTStartup</EntryPointSymbol>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>MaxSpeed</Optimization>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <AdditionalIncludeDirectories>MSToolkit\include;CometSearch;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+ <PreprocessorDefinitions>
+ </PreprocessorDefinitions>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <StringPooling>true</StringPooling>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ </ClCompile>
+ <Link>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <EnableCOMDATFolding>
+ </EnableCOMDATFolding>
+ <OptimizeReferences>true</OptimizeReferences>
+ <AdditionalDependencies>ws2_32.lib;setargv.obj;MSToolkitLite.lib;CometSearch.lib;%(AdditionalDependencies)</AdditionalDependencies>
+ <AdditionalLibraryDirectories>$(SolutionDir)$(Platform)\$(Configuration)\</AdditionalLibraryDirectories>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemGroup>
+ <ClCompile Include="Comet.cpp" />
+ </ItemGroup>
+ <ItemGroup>
+ <ResourceCompile Include="Comet.rc" />
+ </ItemGroup>
+ <ItemGroup>
+ <None Include="icon\comet.ico" />
+ </ItemGroup>
+ <ItemGroup>
+ <ClInclude Include="resource.h" />
+ </ItemGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
+ <ImportGroup Label="ExtensionTargets">
+ </ImportGroup>
+</Project>
\ No newline at end of file
diff --git a/ext/patches/comet/CometSearch/CometSearch.vcxproj b/ext/patches/comet/CometSearch/CometSearch.vcxproj
new file mode 100644
index 0000000..71ddff9
--- /dev/null
+++ b/ext/patches/comet/CometSearch/CometSearch.vcxproj
@@ -0,0 +1,201 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+ <ItemGroup Label="ProjectConfigurations">
+ <ProjectConfiguration Include="Debug|Win32">
+ <Configuration>Debug</Configuration>
+ <Platform>Win32</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Debug|x64">
+ <Configuration>Debug</Configuration>
+ <Platform>x64</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Release|Win32">
+ <Configuration>Release</Configuration>
+ <Platform>Win32</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Release|x64">
+ <Configuration>Release</Configuration>
+ <Platform>x64</Platform>
+ </ProjectConfiguration>
+ </ItemGroup>
+ <PropertyGroup Label="Globals">
+ <ProjectGuid>{887C017B-8E91-4CCE-85C6-4D36D4033F1B}</ProjectGuid>
+ <RootNamespace>CometSearch</RootNamespace>
+ </PropertyGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
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+ <CharacterSet>MultiByte</CharacterSet>
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+ <CharacterSet>MultiByte</CharacterSet>
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+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
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+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <CharacterSet>MultiByte</CharacterSet>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
+ <ConfigurationType>StaticLibrary</ConfigurationType>
+ <UseDebugLibraries>false</UseDebugLibraries>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <CharacterSet>MultiByte</CharacterSet>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
+ <ImportGroup Label="ExtensionSettings">
+ </ImportGroup>
+ <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Label="PropertySheets" Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <PropertyGroup Label="UserMacros" />
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <OutDir>$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ <IntDir>$(Platform)\$(Configuration)\</IntDir>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+ <OutDir>$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ <IntDir>$(Platform)\$(Configuration)\</IntDir>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <OutDir>$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <IntDir>$(Platform)\$(Configuration)\</IntDir>
+ </PropertyGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>MaxSpeed</Optimization>
+ <AdditionalIncludeDirectories>..\pthreads-w32\include;..\MSToolkit\include;</AdditionalIncludeDirectories>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <StringPooling>true</StringPooling>
+ <MinimalRebuild>false</MinimalRebuild>
+ <BasicRuntimeChecks>Default</BasicRuntimeChecks>
+ <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
+ </ClCompile>
+ <Link>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>Disabled</Optimization>
+ <AdditionalIncludeDirectories>..\pthreads-w32\include;..\MSToolkit\include;</AdditionalIncludeDirectories>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ </ClCompile>
+ <Link>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>MaxSpeed</Optimization>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <AdditionalIncludeDirectories>..\pthreads-w32\include;..\MSToolkit\include;</AdditionalIncludeDirectories>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <StringPooling>true</StringPooling>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ <PreprocessorDefinitions>_MBCS;%(PreprocessorDefinitions);_CRT_SECURE_NO_WARNINGS</PreprocessorDefinitions>
+ </ClCompile>
+ <Link>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <EnableCOMDATFolding>true</EnableCOMDATFolding>
+ <OptimizeReferences>true</OptimizeReferences>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+ <ClCompile>
+ <WarningLevel>Level3</WarningLevel>
+ <Optimization>MaxSpeed</Optimization>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <AdditionalIncludeDirectories>..\MSToolkit\include;</AdditionalIncludeDirectories>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <StringPooling>true</StringPooling>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ </ClCompile>
+ <Link>
+ <GenerateDebugInformation>true</GenerateDebugInformation>
+ <EnableCOMDATFolding>true</EnableCOMDATFolding>
+ <OptimizeReferences>true</OptimizeReferences>
+ </Link>
+ </ItemDefinitionGroup>
+ <ItemGroup>
+ <ClInclude Include="CometData.h" />
+ <ClInclude Include="CometDataInternal.h" />
+ <ClInclude Include="CometDecoys.h" />
+ <ClInclude Include="CometInterfaces.h" />
+ <ClInclude Include="CometMassSpecUtils.h" />
+ <ClInclude Include="CometPostAnalysis.h" />
+ <ClInclude Include="CometPreprocess.h" />
+ <ClInclude Include="CometSearch.h" />
+ <ClInclude Include="CometSearchManager.h" />
+ <ClInclude Include="CometStatus.h" />
+ <ClInclude Include="CometWriteOut.h" />
+ <ClInclude Include="CometWritePepXML.h" />
+ <ClInclude Include="CometWritePercolator.h" />
+ <ClInclude Include="CometWriteSqt.h" />
+ <ClInclude Include="CometWriteTxt.h" />
+ <ClInclude Include="Common.h" />
+ <ClInclude Include="OSSpecificThreading.h" />
+ <ClInclude Include="Threading.h" />
+ <ClInclude Include="ThreadPool.h" />
+ </ItemGroup>
+ <ItemGroup>
+ <ClCompile Include="CometInterfaces.cpp" />
+ <ClCompile Include="CometMassSpecUtils.cpp" />
+ <ClCompile Include="CometPostAnalysis.cpp" />
+ <ClCompile Include="CometPreprocess.cpp" />
+ <ClCompile Include="CometSearch.cpp" />
+ <ClCompile Include="CometSearchManager.cpp" />
+ <ClCompile Include="CometWriteOut.cpp" />
+ <ClCompile Include="CometWritePepXML.cpp" />
+ <ClCompile Include="CometWritePercolator.cpp" />
+ <ClCompile Include="CometWriteSqt.cpp" />
+ <ClCompile Include="CometWriteTxt.cpp" />
+ <ClCompile Include="Threading.cpp" />
+ </ItemGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
+ <ImportGroup Label="ExtensionTargets">
+ </ImportGroup>
+</Project>
\ No newline at end of file
diff --git a/ext/patches/comet/CometSearch/CometSearchManager.cpp b/ext/patches/comet/CometSearch/CometSearchManager.cpp
new file mode 100644
index 0000000..e05ab8c
--- /dev/null
+++ b/ext/patches/comet/CometSearch/CometSearchManager.cpp
@@ -0,0 +1,2108 @@
+/*
+ Copyright 2013 University of Washington
+
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+*/
+
+#include "Common.h"
+#include "CometMassSpecUtils.h"
+#include "CometSearch.h"
+#include "CometPostAnalysis.h"
+#include "CometPreprocess.h"
+#include "CometWriteOut.h"
+#include "CometWriteSqt.h"
+#include "CometWriteTxt.h"
+#include "CometWritePepXML.h"
+#include "CometWritePercolator.h"
+#include "Threading.h"
+#include "ThreadPool.h"
+#include "CometDataInternal.h"
+#include "CometSearchManager.h"
+#include "CometStatus.h"
+
+#undef PERF_DEBUG
+
+std::vector<Query*> g_pvQuery;
+std::vector<InputFileInfo *> g_pvInputFiles;
+StaticParams g_staticParams;
+MassRange g_massRange;
+Mutex g_pvQueryMutex;
+Mutex g_preprocessMemoryPoolMutex;
+Mutex g_searchMemoryPoolMutex;
+CometStatus g_cometStatus;
+
+/******************************************************************************
+*
+* Static helper functions
+*
+******************************************************************************/
+static void GetHostName()
+{
+#ifdef _WIN32
+ WSADATA WSAData;
+ WSAStartup(MAKEWORD(1, 0), &WSAData);
+
+ if (gethostname(g_staticParams.szHostName, SIZE_FILE) != 0)
+ strcpy(g_staticParams.szHostName, "locahost");
+
+ WSACleanup();
+#else
+ if (gethostname(g_staticParams.szHostName, SIZE_FILE) != 0)
+ strcpy(g_staticParams.szHostName, "locahost");
+#endif
+
+ char *pStr;
+ if ((pStr = strchr(g_staticParams.szHostName, '.'))!=NULL)
+ *pStr = '\0';
+}
+
+static InputType GetInputType(const char *pszFileName)
+{
+ int iLen = strlen(pszFileName);
+
+ if (!STRCMP_IGNORE_CASE(pszFileName + iLen - 6, ".mzXML")
+ || !STRCMP_IGNORE_CASE(pszFileName + iLen - 5, ".mzML")
+ || !STRCMP_IGNORE_CASE(pszFileName + iLen - 9, ".mzXML.gz")
+ || !STRCMP_IGNORE_CASE(pszFileName + iLen - 8, ".mzML.gz"))
+
+ {
+ return InputType_MZXML;
+ }
+ else if (!STRCMP_IGNORE_CASE(pszFileName + iLen - 4, ".raw"))
+ {
+ return InputType_RAW;
+ }
+ else if (!STRCMP_IGNORE_CASE(pszFileName + iLen - 4, ".ms2")
+ || !STRCMP_IGNORE_CASE(pszFileName + iLen - 5, ".cms2"))
+ {
+ return InputType_MS2;
+ }
+ else if (!STRCMP_IGNORE_CASE(pszFileName + iLen - 4, ".mgf"))
+ {
+ return InputType_MGF;
+ }
+
+ return InputType_UNKNOWN;
+}
+
+static bool UpdateInputFile(InputFileInfo *pFileInfo)
+{
+ bool bUpdateBaseName = false;
+ char szTmpBaseName[SIZE_FILE];
+
+ // Make sure not set on command line OR more than 1 input file
+ // Need to do this check here before g_staticParams.inputFile is set to *pFileInfo
+ if (g_staticParams.inputFile.szBaseName[0] =='\0' || g_pvInputFiles.size()>1)
+ bUpdateBaseName = true;
+ else
+ strcpy(szTmpBaseName, g_staticParams.inputFile.szBaseName);
+
+ g_staticParams.inputFile = *pFileInfo;
+
+ g_staticParams.inputFile.iInputType = GetInputType(g_staticParams.inputFile.szFileName);
+
+ if (InputType_UNKNOWN == g_staticParams.inputFile.iInputType)
+ {
+ return false;
+ }
+ int iLen = strlen(g_staticParams.inputFile.szFileName);
+
+ // per request, perform quick check to validate file still exists
+ // to avoid creating stub output files in these cases.
+ FILE *fp;
+ if ( (fp=fopen(g_staticParams.inputFile.szFileName, "r"))==NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot read input file \"%s\".\n",
+ g_staticParams.inputFile.szFileName);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+ else
+ {
+ fclose(fp);
+ }
+
+#ifndef CRUX
+ if (bUpdateBaseName) // set individual basename from input file
+ {
+ char *pStr;
+
+ strcpy(g_staticParams.inputFile.szBaseName, g_staticParams.inputFile.szFileName);
+
+ if ( (pStr = strrchr(g_staticParams.inputFile.szBaseName, '.')))
+ *pStr = '\0';
+
+ if (!STRCMP_IGNORE_CASE(g_staticParams.inputFile.szFileName + iLen - 9, ".mzXML.gz")
+ || !STRCMP_IGNORE_CASE(g_staticParams.inputFile.szFileName + iLen - 8, ".mzML.gz"))
+ {
+ if ( (pStr = strrchr(g_staticParams.inputFile.szBaseName, '.')))
+ *pStr = '\0';
+ }
+ }
+ else
+ {
+ strcpy(g_staticParams.inputFile.szBaseName, szTmpBaseName); // set basename from command line
+ }
+#endif
+
+ // Create .out directory.
+ if (g_staticParams.options.bOutputOutFiles)
+ {
+#ifdef _WIN32
+ if (_mkdir(g_staticParams.inputFile.szBaseName) == -1)
+ {
+ errno_t err;
+ _get_errno(&err);
+
+ if (err != EEXIST)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n",
+ g_staticParams.inputFile.szBaseName);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+ }
+ if (g_staticParams.options.iDecoySearch == 2)
+ {
+ char szDecoyDir[SIZE_FILE];
+ sprintf(szDecoyDir, "%s_decoy", g_staticParams.inputFile.szBaseName);
+
+ if (_mkdir(szDecoyDir) == -1)
+ {
+ errno_t err;
+ _get_errno(&err);
+
+ if (err != EEXIST)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+ }
+ }
+#else
+ if ((mkdir(g_staticParams.inputFile.szBaseName, 0775) == -1) && (errno != EEXIST))
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n",
+ g_staticParams.inputFile.szBaseName);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+ if (g_staticParams.options.iDecoySearch == 2)
+ {
+ char szDecoyDir[SIZE_FILE];
+ sprintf(szDecoyDir, "%s_decoy", g_staticParams.inputFile.szBaseName);
+
+ if ((mkdir(szDecoyDir , 0775) == -1) && (errno != EEXIST))
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - could not create directory \"%s\".\n", szDecoyDir);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+ }
+#endif
+ }
+
+ return true;
+}
+
+static void SetMSLevelFilter(MSReader &mstReader)
+{
+ vector<MSSpectrumType> msLevel;
+ if (g_staticParams.options.iMSLevel == 3)
+ {
+ msLevel.push_back(MS3);
+ }
+ else
+ {
+ msLevel.push_back(MS2);
+ }
+ mstReader.setFilter(msLevel);
+}
+
+// Allocate memory for the _pResults struct for each g_pvQuery entry.
+static bool AllocateResultsMem()
+{
+ for (unsigned i=0; i<g_pvQuery.size(); i++)
+ {
+ Query* pQuery = g_pvQuery.at(i);
+
+ try
+ {
+ pQuery->_pResults = new Results[g_staticParams.options.iNumStored];
+ }
+ catch (std::bad_alloc& ba)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - new(_pResults[]). bad_alloc: %s.\n", ba.what());
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+
+ if (g_staticParams.options.iDecoySearch==2)
+ {
+ try
+ {
+ pQuery->_pDecoys = new Results[g_staticParams.options.iNumStored];
+ }
+ catch (std::bad_alloc& ba)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - new(_pDecoys[]). bad_alloc: %s.\n", ba.what());
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+ }
+
+ for (int j=0; j<g_staticParams.options.iNumStored; j++)
+ {
+ pQuery->_pResults[j].dPepMass = 0.0;
+ pQuery->_pResults[j].dExpect = 0.0;
+ pQuery->_pResults[j].fScoreSp = 0.0;
+ pQuery->_pResults[j].fXcorr = XCORR_CUTOFF;
+ pQuery->_pResults[j].iDuplicateCount = 0;
+ pQuery->_pResults[j].iLenPeptide = 0;
+ pQuery->_pResults[j].iRankSp = 0;
+ pQuery->_pResults[j].iMatchedIons = 0;
+ pQuery->_pResults[j].iTotalIons = 0;
+ pQuery->_pResults[j].szPeptide[0] = '\0';
+ pQuery->_pResults[j].szProtein[0] = '\0';
+
+ if (g_staticParams.options.iDecoySearch==2)
+ {
+ pQuery->_pDecoys[j].dPepMass = 0.0;
+ pQuery->_pDecoys[j].dExpect = 0.0;
+ pQuery->_pDecoys[j].fScoreSp = 0.0;
+ pQuery->_pDecoys[j].fXcorr = XCORR_CUTOFF;
+ pQuery->_pDecoys[j].iDuplicateCount = 0;
+ pQuery->_pDecoys[j].iLenPeptide = 0;
+ pQuery->_pDecoys[j].iRankSp = 0;
+ pQuery->_pDecoys[j].iMatchedIons = 0;
+ pQuery->_pDecoys[j].iTotalIons = 0;
+ pQuery->_pDecoys[j].szPeptide[0] = '\0';
+ pQuery->_pDecoys[j].szProtein[0] = '\0';
+ }
+ }
+ }
+
+ return true;
+}
+
+static bool compareByPeptideMass(Query const* a, Query const* b)
+{
+ return (a->_pepMassInfo.dExpPepMass < b->_pepMassInfo.dExpPepMass);
+}
+
+static bool compareByScanNumber(Query const* a, Query const* b)
+{
+ return (a->_spectrumInfoInternal.iScanNumber < b->_spectrumInfoInternal.iScanNumber);
+}
+
+static void CalcRunTime(time_t tStartTime)
+{
+ char szOutFileTimeString[512];
+ time_t tEndTime;
+ int iTmp;
+
+ time(&tEndTime);
+
+ int iElapseTime=(int)difftime(tEndTime, tStartTime);
+
+ // Print out header/search info.
+ sprintf(szOutFileTimeString, "%s,", g_staticParams.szDate);
+ if ( (iTmp = (int)(iElapseTime/3600) )>0)
+ sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " %d hr.", iTmp);
+ if ( (iTmp = (int)((iElapseTime-(int)(iElapseTime/3600)*3600)/60) )>0)
+ sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " %d min.", iTmp);
+ if ( (iTmp = (int)((iElapseTime-((int)(iElapseTime/3600))*3600)%60) )>0)
+ sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " %d sec.", iTmp);
+ if (iElapseTime == 0)
+ sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " 0 sec.");
+ sprintf(szOutFileTimeString+strlen(szOutFileTimeString), " on %s", g_staticParams.szHostName);
+
+ g_staticParams.iElapseTime = iElapseTime;
+ strncpy(g_staticParams.szOutFileTimeString, szOutFileTimeString, 256);
+ g_staticParams.szOutFileTimeString[255]='\0';
+}
+
+static void PrintParameters()
+{
+ // print parameters
+
+ char szIsotope[16];
+ char szPeak[16];
+
+ sprintf(g_staticParams.szIonSeries, "ion series ABCXYZ nl: %d%d%d%d%d%d %d",
+ g_staticParams.ionInformation.iIonVal[ION_SERIES_A],
+ g_staticParams.ionInformation.iIonVal[ION_SERIES_B],
+ g_staticParams.ionInformation.iIonVal[ION_SERIES_C],
+ g_staticParams.ionInformation.iIonVal[ION_SERIES_X],
+ g_staticParams.ionInformation.iIonVal[ION_SERIES_Y],
+ g_staticParams.ionInformation.iIonVal[ION_SERIES_Z],
+ g_staticParams.ionInformation.bUseNeutralLoss);
+
+ char szUnits[8];
+ char szDecoy[20];
+ char szReadingFrame[20];
+ char szRemovePrecursor[20];
+
+ if (g_staticParams.tolerances.iMassToleranceUnits==0)
+ strcpy(szUnits, " AMU");
+ else if (g_staticParams.tolerances.iMassToleranceUnits==1)
+ strcpy(szUnits, " MMU");
+ else
+ strcpy(szUnits, " PPM");
+
+ if (g_staticParams.options.iDecoySearch)
+ sprintf(szDecoy, " DECOY%d", g_staticParams.options.iDecoySearch);
+ else
+ szDecoy[0]=0;
+
+ if (g_staticParams.options.iRemovePrecursor)
+ sprintf(szRemovePrecursor, " REMOVEPREC%d", g_staticParams.options.iRemovePrecursor);
+ else
+ szRemovePrecursor[0]=0;
+
+ if (g_staticParams.options.iWhichReadingFrame)
+ sprintf(szReadingFrame, " FRAME%d", g_staticParams.options.iWhichReadingFrame);
+ else
+ szReadingFrame[0]=0;
+
+ szIsotope[0]='\0';
+ if (g_staticParams.tolerances.iIsotopeError==1)
+ strcpy(szIsotope, "ISOTOPE1");
+ else if (g_staticParams.tolerances.iIsotopeError==2)
+ strcpy(szIsotope, "ISOTOPE2");
+
+ szPeak[0]='\0';
+ if (g_staticParams.ionInformation.iTheoreticalFragmentIons==1)
+ strcpy(szPeak, "PEAK1");
+
+ sprintf(g_staticParams.szDisplayLine, "display top %d, %s%s%s%s%s%s%s%s",
+ g_staticParams.options.iNumPeptideOutputLines,
+ szRemovePrecursor,
+ szReadingFrame,
+ szPeak,
+ szUnits,
+ (g_staticParams.tolerances.iMassToleranceType==0?" MH+":" m/z"),
+ szIsotope,
+ szDecoy,
+ (g_staticParams.options.bClipNtermMet?" CLIPMET":"") );
+}
+
+static bool ValidateOutputFormat()
+{
+ if (!g_staticParams.options.bOutputSqtStream
+ && !g_staticParams.options.bOutputSqtFile
+ && !g_staticParams.options.bOutputTxtFile
+ && !g_staticParams.options.bOutputPepXMLFile
+ && !g_staticParams.options.bOutputPercolatorFile
+ && !g_staticParams.options.bOutputOutFiles)
+ {
+ string strError = " Please specify at least one output format.";
+
+ g_cometStatus.SetStatus(CometResult_Failed, strError);
+ string strErrorFormat = strError + "\n";
+ logerr(strErrorFormat.c_str());
+ return false;
+ }
+
+ return true;
+}
+
+static bool ValidateSequenceDatabaseFile()
+{
+ FILE *fpcheck;
+
+ // Quick sanity check to make sure sequence db file is present before spending
+ // time reading & processing spectra and then reporting this error.
+ if ((fpcheck=fopen(g_staticParams.databaseInfo.szDatabase, "r")) == NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot read database file \"%s\".\n Check that the file exists and is readable.\n",
+ g_staticParams.databaseInfo.szDatabase);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+
+ fclose(fpcheck);
+ return true;
+}
+
+static bool ValidateScanRange()
+{
+ if (g_staticParams.options.scanRange.iEnd < g_staticParams.options.scanRange.iStart && g_staticParams.options.scanRange.iEnd != 0)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - start scan is %d but end scan is %d.\n The end scan must be >= to the start scan.\n",
+ g_staticParams.options.scanRange.iStart,
+ g_staticParams.options.scanRange.iEnd);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+
+ return true;
+}
+
+/******************************************************************************
+*
+* CometSearchManager class implementation.
+*
+******************************************************************************/
+
+CometSearchManager::CometSearchManager()
+{
+ // Initialize the mutexes we'll use to protect global data.
+ Threading::CreateMutex(&g_pvQueryMutex);
+
+ // Initialize the mutex we'll use to protect the preprocess memory pool
+ Threading::CreateMutex(&g_preprocessMemoryPoolMutex);
+
+ // Initialize the mutex we'll use to protect the search memory pool
+ Threading::CreateMutex(&g_searchMemoryPoolMutex);
+
+ // Initialize the Comet version
+ SetParam("# comet_version ", comet_version, comet_version);
+}
+
+CometSearchManager::~CometSearchManager()
+{
+ // Destroy the mutex we used to protect g_pvQuery.
+ Threading::DestroyMutex(g_pvQueryMutex);
+
+ // Destroy the mutex we used to protect the preprocess memory pool
+ Threading::DestroyMutex(g_preprocessMemoryPoolMutex);
+
+ // Destroy the mutex we used to protect the search memory pool
+ Threading::DestroyMutex(g_searchMemoryPoolMutex);
+
+ // Clean up the input files vector
+ for (int i=0; i<(int)g_pvInputFiles.size(); i++)
+ {
+ delete g_pvInputFiles.at(i);
+ }
+ g_pvInputFiles.clear();
+
+ for (std::map<string, CometParam*>::iterator it = _mapStaticParams.begin(); it != _mapStaticParams.end(); ++it)
+ {
+ delete it->second;
+ }
+ _mapStaticParams.clear();
+}
+
+bool CometSearchManager::InitializeStaticParams()
+{
+ int iIntData;
+ double dDoubleData;
+ string strData;
+ IntRange intRangeData;
+ DoubleRange doubleRangeData;
+
+ if (GetParamValue("database_name", strData))
+ {
+ strcpy(g_staticParams.databaseInfo.szDatabase, strData.c_str());
+ }
+
+ if (GetParamValue("decoy_prefix", strData))
+ {
+ strcpy(g_staticParams.szDecoyPrefix, strData.c_str());
+ }
+
+ if (GetParamValue("output_suffix", strData))
+ {
+ strcpy(g_staticParams.szOutputSuffix, strData.c_str());
+ }
+
+ GetParamValue("mass_offsets", g_staticParams.vectorMassOffsets);
+
+ GetParamValue("xcorr_processing_offset", g_staticParams.iXcorrProcessingOffset);
+
+ GetParamValue("nucleotide_reading_frame", g_staticParams.options.iWhichReadingFrame);
+
+ GetParamValue("mass_type_parent", g_staticParams.massUtility.bMonoMassesParent);
+
+ GetParamValue("mass_type_fragment", g_staticParams.massUtility.bMonoMassesFragment);
+
+ GetParamValue("show_fragment_ions", g_staticParams.options.bShowFragmentIons);
+
+ GetParamValue("num_threads", g_staticParams.options.iNumThreads);
+
+ GetParamValue("clip_nterm_methionine", g_staticParams.options.bClipNtermMet);
+
+ GetParamValue("theoretical_fragment_ions", g_staticParams.ionInformation.iTheoreticalFragmentIons);
+ if ((g_staticParams.ionInformation.iTheoreticalFragmentIons < 0)
+ || (g_staticParams.ionInformation.iTheoreticalFragmentIons > 1))
+ {
+ g_staticParams.ionInformation.iTheoreticalFragmentIons = 0;
+ }
+
+ GetParamValue("use_A_ions", g_staticParams.ionInformation.iIonVal[ION_SERIES_A]);
+
+ GetParamValue("use_B_ions", g_staticParams.ionInformation.iIonVal[ION_SERIES_B]);
+
+ GetParamValue("use_C_ions", g_staticParams.ionInformation.iIonVal[ION_SERIES_C]);
+
+ GetParamValue("use_X_ions", g_staticParams.ionInformation.iIonVal[ION_SERIES_X]);
+
+ GetParamValue("use_Y_ions", g_staticParams.ionInformation.iIonVal[ION_SERIES_Y]);
+
+ GetParamValue("use_Z_ions", g_staticParams.ionInformation.iIonVal[ION_SERIES_Z]);
+
+ GetParamValue("use_NL_ions", g_staticParams.ionInformation.bUseNeutralLoss);
+
+ GetParamValue("variable_mod01", g_staticParams.variableModParameters.varModList[VMOD_1_INDEX]);
+
+ GetParamValue("variable_mod02", g_staticParams.variableModParameters.varModList[VMOD_2_INDEX]);
+
+ GetParamValue("variable_mod03", g_staticParams.variableModParameters.varModList[VMOD_3_INDEX]);
+
+ GetParamValue("variable_mod04", g_staticParams.variableModParameters.varModList[VMOD_4_INDEX]);
+
+ GetParamValue("variable_mod05", g_staticParams.variableModParameters.varModList[VMOD_5_INDEX]);
+
+ GetParamValue("variable_mod06", g_staticParams.variableModParameters.varModList[VMOD_6_INDEX]);
+
+ GetParamValue("variable_mod07", g_staticParams.variableModParameters.varModList[VMOD_7_INDEX]);
+
+ GetParamValue("variable_mod08", g_staticParams.variableModParameters.varModList[VMOD_8_INDEX]);
+
+ GetParamValue("variable_mod09", g_staticParams.variableModParameters.varModList[VMOD_9_INDEX]);
+
+ if (GetParamValue("max_variable_mods_in_peptide", iIntData))
+ {
+ if (iIntData > 0)
+ {
+ g_staticParams.variableModParameters.iMaxVarModPerPeptide = iIntData;
+ }
+ }
+
+ GetParamValue("require_variable_mod", g_staticParams.variableModParameters.bRequireVarMod);
+
+ GetParamValue("fragment_bin_tol", g_staticParams.tolerances.dFragmentBinSize);
+ if (g_staticParams.tolerances.dFragmentBinSize < 0.01)
+ {
+ g_staticParams.tolerances.dFragmentBinSize = 0.01;
+ }
+
+ GetParamValue("fragment_bin_offset", g_staticParams.tolerances.dFragmentBinStartOffset);
+
+ GetParamValue("peptide_mass_tolerance", g_staticParams.tolerances.dInputTolerance);
+
+ GetParamValue("precursor_tolerance_type", g_staticParams.tolerances.iMassToleranceType);
+ if ((g_staticParams.tolerances.iMassToleranceType < 0)
+ || (g_staticParams.tolerances.iMassToleranceType > 1))
+ {
+ g_staticParams.tolerances.iMassToleranceType = 0;
+ }
+
+ GetParamValue("peptide_mass_units", g_staticParams.tolerances.iMassToleranceUnits);
+ if ((g_staticParams.tolerances.iMassToleranceUnits < 0)
+ || (g_staticParams.tolerances.iMassToleranceUnits > 2))
+ {
+ g_staticParams.tolerances.iMassToleranceUnits = 0; // 0=amu, 1=mmu, 2=ppm
+ }
+
+ GetParamValue("isotope_error", g_staticParams.tolerances.iIsotopeError);
+ if ((g_staticParams.tolerances.iIsotopeError < 0)
+ || (g_staticParams.tolerances.iIsotopeError > 2))
+ {
+ g_staticParams.tolerances.iIsotopeError = 0;
+ }
+
+ GetParamValue("num_output_lines", g_staticParams.options.iNumPeptideOutputLines);
+
+ GetParamValue("num_results", g_staticParams.options.iNumStored);
+
+ GetParamValue("remove_precursor_peak", g_staticParams.options.iRemovePrecursor);
+
+ GetParamValue("remove_precursor_tolerance", g_staticParams.options.dRemovePrecursorTol);
+
+ if (GetParamValue("clear_mz_range", doubleRangeData))
+ {
+ if ((doubleRangeData.dEnd >= doubleRangeData.dStart) && (doubleRangeData.dStart >= 0.0))
+ {
+ g_staticParams.options.clearMzRange.dStart = doubleRangeData.dStart;
+ g_staticParams.options.clearMzRange.dEnd = doubleRangeData.dEnd;
+ }
+ }
+
+ GetParamValue("print_expect_score", g_staticParams.options.bPrintExpectScore);
+
+ GetParamValue("output_sqtstream", g_staticParams.options.bOutputSqtStream);
+
+ GetParamValue("output_sqtfile", g_staticParams.options.bOutputSqtFile);
+
+ GetParamValue("output_txtfile", g_staticParams.options.bOutputTxtFile);
+
+ GetParamValue("output_pepxmlfile", g_staticParams.options.bOutputPepXMLFile);
+
+ GetParamValue("output_percolatorfile", g_staticParams.options.bOutputPercolatorFile);
+
+ GetParamValue("output_outfiles", g_staticParams.options.bOutputOutFiles);
+
+ GetParamValue("skip_researching", g_staticParams.options.bSkipAlreadyDone);
+
+ GetParamValue("add_Cterm_peptide", g_staticParams.staticModifications.dAddCterminusPeptide);
+
+ GetParamValue("add_Nterm_peptide", g_staticParams.staticModifications.dAddNterminusPeptide);
+
+ GetParamValue("add_Cterm_protein", g_staticParams.staticModifications.dAddCterminusProtein);
+
+ GetParamValue("add_Nterm_protein", g_staticParams.staticModifications.dAddNterminusProtein);
+
+ if (GetParamValue("add_G_glycine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'G'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_A_alanine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'A'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_S_serine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'S'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_P_proline", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'P'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_V_valine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'V'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_T_threonine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'T'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_C_cysteine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'C'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_L_leucine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'L'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_I_isoleucine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'I'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_N_asparagine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'N'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_O_ornithine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'O'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_D_aspartic_acid", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'D'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_Q_glutamine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'Q'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_K_lysine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'K'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_E_glutamic_acid", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'E'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_M_methionine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'M'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_H_histidine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'H'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_F_phenylalanine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'F'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_R_arginine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'R'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_Y_tyrosine", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'Y'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_W_tryptophan", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'W'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_B_user_amino_acid", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'B'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_J_user_amino_acid", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'J'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_U_user_amino_acid", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'U'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_X_user_amino_acid", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'X'] = dDoubleData;
+ }
+
+ if (GetParamValue("add_Z_user_amino_acid", dDoubleData))
+ {
+ g_staticParams.staticModifications.pdStaticMods[(int)'Z'] = dDoubleData;
+ }
+
+ GetParamValue("num_enzyme_termini", g_staticParams.options.iEnzymeTermini);
+ if ((g_staticParams.options.iEnzymeTermini != 1)
+ && (g_staticParams.options.iEnzymeTermini != 8)
+ && (g_staticParams.options.iEnzymeTermini != 9))
+ {
+ g_staticParams.options.iEnzymeTermini = 2;
+ }
+
+ if (GetParamValue("scan_range", intRangeData))
+ {
+ if ((intRangeData.iEnd >= intRangeData.iStart) && (intRangeData.iStart > 0))
+ {
+ g_staticParams.options.scanRange.iStart = intRangeData.iStart;
+ g_staticParams.options.scanRange.iEnd = intRangeData.iEnd;
+ }
+ }
+
+ if (GetParamValue("spectrum_batch_size", iIntData))
+ {
+ if (iIntData > 0)
+ {
+ g_staticParams.options.iSpectrumBatchSize = iIntData;
+ }
+ }
+
+ iIntData = 0;
+ if (GetParamValue("minimum_peaks", iIntData))
+ {
+ if (iIntData > 0)
+ {
+ g_staticParams.options.iMinPeaks = iIntData;
+ }
+ }
+
+ if (GetParamValue("override_charge", iIntData))
+ {
+ if (iIntData > 0)
+ {
+ g_staticParams.options.bOverrideCharge = iIntData;
+ }
+ }
+
+ if (GetParamValue("precursor_charge", intRangeData))
+ {
+ if ((intRangeData.iStart > 0) && (intRangeData.iEnd >= intRangeData.iStart))
+ {
+ g_staticParams.options.iStartCharge = intRangeData.iStart;
+ g_staticParams.options.iEndCharge = intRangeData.iEnd;
+ }
+ }
+
+ iIntData = 0;
+ if (GetParamValue("max_fragment_charge", iIntData))
+ {
+ if (iIntData > MAX_FRAGMENT_CHARGE)
+ {
+ iIntData = MAX_FRAGMENT_CHARGE;
+ }
+
+ if (iIntData > 0)
+ {
+ g_staticParams.options.iMaxFragmentCharge = iIntData;
+ }
+ // else will go to default value (3)
+ }
+
+ iIntData = 0;
+ if (GetParamValue("max_precursor_charge", iIntData))
+ {
+ if (iIntData > MAX_PRECURSOR_CHARGE)
+ {
+ iIntData = MAX_PRECURSOR_CHARGE;
+ }
+
+ if (iIntData > 0)
+ {
+ g_staticParams.options.iMaxPrecursorCharge = iIntData;
+ }
+ // else will go to default value (6)
+ }
+
+ if (GetParamValue("digest_mass_range", doubleRangeData))
+ {
+ if ((doubleRangeData.dEnd >= doubleRangeData.dStart) && (doubleRangeData.dStart >= 0.0))
+ {
+ g_staticParams.options.dPeptideMassLow = doubleRangeData.dStart;
+ g_staticParams.options.dPeptideMassHigh = doubleRangeData.dEnd;
+ }
+ }
+
+ if (GetParamValue("ms_level", iIntData))
+ {
+ if (iIntData == 3)
+ {
+ g_staticParams.options.iMSLevel = 3;
+ }
+ // else will go to default value (2)
+ }
+
+ if (GetParamValue("activation_method", strData))
+ {
+ strcpy(g_staticParams.options.szActivationMethod, strData.c_str());
+ }
+
+ GetParamValue("minimum_intensity", g_staticParams.options.dMinIntensity);
+ if (g_staticParams.options.dMinIntensity < 0.0)
+ {
+ g_staticParams.options.dMinIntensity = 0.0;
+ }
+
+ GetParamValue("decoy_search", g_staticParams.options.iDecoySearch);
+ if ((g_staticParams.options.iDecoySearch < 0) || (g_staticParams.options.iDecoySearch > 2))
+ {
+ g_staticParams.options.iDecoySearch = 0;
+ }
+
+ // Set dInverseBinWidth to its inverse in order to use a multiply instead of divide in BIN macro.
+ // Safe to divide by dFragmentBinSize because of check earlier where minimum value is 0.01.
+ g_staticParams.dInverseBinWidth = 1.0 /g_staticParams.tolerances.dFragmentBinSize;
+ g_staticParams.dOneMinusBinOffset = 1.0 - g_staticParams.tolerances.dFragmentBinStartOffset;
+
+ // Set masses to either average or monoisotopic.
+ CometMassSpecUtils::AssignMass(g_staticParams.massUtility.pdAAMassParent,
+ g_staticParams.massUtility.bMonoMassesParent,
+ &g_staticParams.massUtility.dOH2parent);
+
+ CometMassSpecUtils::AssignMass(g_staticParams.massUtility.pdAAMassFragment,
+ g_staticParams.massUtility.bMonoMassesFragment,
+ &g_staticParams.massUtility.dOH2fragment);
+
+ g_staticParams.massUtility.dCO = g_staticParams.massUtility.pdAAMassFragment[(int)'c']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'o'];
+
+ g_staticParams.massUtility.dH2O = g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'o'];
+
+ g_staticParams.massUtility.dNH3 = g_staticParams.massUtility.pdAAMassFragment[(int)'n']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h'];
+
+ g_staticParams.massUtility.dNH2 = g_staticParams.massUtility.pdAAMassFragment[(int)'n']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h'];
+
+ g_staticParams.massUtility.dCOminusH2 = g_staticParams.massUtility.dCO
+ - g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ - g_staticParams.massUtility.pdAAMassFragment[(int)'h'];
+
+ GetHostName();
+
+ // If # threads not specified, poll system to get # threads to launch.
+ if (g_staticParams.options.iNumThreads <= 0)
+ {
+ int iNumCPUCores;
+#ifdef _WIN32
+ SYSTEM_INFO sysinfo;
+ GetSystemInfo( &sysinfo );
+ iNumCPUCores = sysinfo.dwNumberOfProcessors;
+
+ // if user specifies a negative # threads, subtract this from # cores
+ if (g_staticParams.options.iNumThreads < 0)
+ g_staticParams.options.iNumThreads = iNumCPUCores + g_staticParams.options.iNumThreads;
+ else
+ g_staticParams.options.iNumThreads = iNumCPUCores;
+#else
+ iNumCPUCores= sysconf( _SC_NPROCESSORS_ONLN );
+
+ if (g_staticParams.options.iNumThreads < 0)
+ g_staticParams.options.iNumThreads = iNumCPUCores + g_staticParams.options.iNumThreads;
+ else
+ g_staticParams.options.iNumThreads = iNumCPUCores;
+
+ // if set, use the environment variable NSLOTS which is defined in the qsub command
+ const char * nSlots = ::getenv("NSLOTS");
+ if (nSlots != NULL)
+ {
+ int detectedThreads = atoi(nSlots);
+ if (detectedThreads > 0)
+ {
+ g_staticParams.options.iNumThreads = detectedThreads;
+ }
+ }
+#endif
+ if (g_staticParams.options.iNumThreads < 1 || g_staticParams.options.iNumThreads > MAX_THREADS)
+ g_staticParams.options.iNumThreads = 2; // Default to 2 threads.
+ }
+
+ // Set masses to either average or monoisotopic.
+ CometMassSpecUtils::AssignMass(g_staticParams.massUtility.pdAAMassParent,
+ g_staticParams.massUtility.bMonoMassesParent,
+ &g_staticParams.massUtility.dOH2parent);
+
+ CometMassSpecUtils::AssignMass(g_staticParams.massUtility.pdAAMassFragment,
+ g_staticParams.massUtility.bMonoMassesFragment,
+ &g_staticParams.massUtility.dOH2fragment);
+
+ g_staticParams.massUtility.dCO = g_staticParams.massUtility.pdAAMassFragment[(int)'c']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'o'];
+
+ g_staticParams.massUtility.dH2O = g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'o'];
+
+ g_staticParams.massUtility.dNH3 = g_staticParams.massUtility.pdAAMassFragment[(int)'n']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h'];
+
+ g_staticParams.massUtility.dNH2 = g_staticParams.massUtility.pdAAMassFragment[(int)'n']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ + g_staticParams.massUtility.pdAAMassFragment[(int)'h'];
+
+ g_staticParams.massUtility.dCOminusH2 = g_staticParams.massUtility.dCO
+ - g_staticParams.massUtility.pdAAMassFragment[(int)'h']
+ - g_staticParams.massUtility.pdAAMassFragment[(int)'h'];
+
+ GetParamValue("[COMET_ENZYME_INFO]", g_staticParams.enzymeInformation);
+ if (!strncmp(g_staticParams.enzymeInformation.szSearchEnzymeBreakAA, "-", 1)
+ && !strncmp(g_staticParams.enzymeInformation.szSearchEnzymeNoBreakAA, "-", 1))
+ {
+ g_staticParams.options.bNoEnzymeSelected = 1;
+ }
+ else
+ {
+ g_staticParams.options.bNoEnzymeSelected = 0;
+ }
+
+ GetParamValue("allowed_missed_cleavage", g_staticParams.enzymeInformation.iAllowedMissedCleavage);
+ if (g_staticParams.enzymeInformation.iAllowedMissedCleavage < 0)
+ {
+ g_staticParams.enzymeInformation.iAllowedMissedCleavage = 0;
+ }
+
+ // Load ion series to consider, useA, useB, useY are for neutral losses.
+ g_staticParams.ionInformation.iNumIonSeriesUsed = 0;
+ for (int i=0; i<6; i++)
+ {
+ if (g_staticParams.ionInformation.iIonVal[i] > 0)
+ g_staticParams.ionInformation.piSelectedIonSeries[g_staticParams.ionInformation.iNumIonSeriesUsed++] = i;
+ }
+
+ // Variable mod search for AAs listed in szVarModChar.
+ g_staticParams.szMod[0] = '\0';
+ g_staticParams.variableModParameters.bVarModSearch = false;
+ g_staticParams.variableModParameters.bBinaryModSearch = false;
+ g_staticParams.variableModParameters.bRequireVarMod = false;
+
+ for (int i=0; i<VMODS; i++)
+ {
+ if (!isEqual(g_staticParams.variableModParameters.varModList[i].dVarModMass, 0.0)
+ && (g_staticParams.variableModParameters.varModList[i].szVarModChar[0]!='\0'))
+ {
+ sprintf(g_staticParams.szMod + strlen(g_staticParams.szMod), "(%s%c %+0.6f) ",
+ g_staticParams.variableModParameters.varModList[i].szVarModChar,
+ g_staticParams.variableModParameters.cModCode[i],
+ g_staticParams.variableModParameters.varModList[i].dVarModMass);
+
+ g_staticParams.variableModParameters.bVarModSearch = true;
+
+ if (g_staticParams.variableModParameters.varModList[i].iBinaryMod)
+ g_staticParams.variableModParameters.bBinaryModSearch = true;
+
+ if (g_staticParams.variableModParameters.varModList[i].bRequireThisMod)
+ g_staticParams.variableModParameters.bRequireVarMod = true;
+
+ }
+ }
+
+ // Do Sp scoring after search based on how many lines to print out.
+ if (g_staticParams.options.iNumStored < 1)
+ g_staticParams.options.iNumStored = 1;
+
+ if (g_staticParams.options.iNumPeptideOutputLines > g_staticParams.options.iNumStored)
+ g_staticParams.options.iNumPeptideOutputLines = g_staticParams.options.iNumStored;
+ else if (g_staticParams.options.iNumPeptideOutputLines < 1)
+ g_staticParams.options.iNumPeptideOutputLines = 1;
+
+ if (g_staticParams.peaksInformation.iNumMatchPeaks > 5)
+ g_staticParams.peaksInformation.iNumMatchPeaks = 5;
+
+ // FIX how to deal with term mod on both peptide and protein?
+ if (!isEqual(g_staticParams.staticModifications.dAddCterminusPeptide, 0.0))
+ {
+ sprintf(g_staticParams.szMod + strlen(g_staticParams.szMod), "+ct=%0.6f ",
+ g_staticParams.staticModifications.dAddCterminusPeptide);
+ }
+
+ if (!isEqual(g_staticParams.staticModifications.dAddNterminusPeptide, 0.0))
+ {
+ sprintf(g_staticParams.szMod + strlen(g_staticParams.szMod), "+nt=%0.6f ",
+ g_staticParams.staticModifications.dAddNterminusPeptide);
+ }
+
+ if (!isEqual(g_staticParams.staticModifications.dAddCterminusProtein, 0.0))
+ {
+ sprintf(g_staticParams.szMod + strlen(g_staticParams.szMod), "+ctprot=%0.6f ",
+ g_staticParams.staticModifications.dAddCterminusProtein);
+ }
+
+ if (!isEqual(g_staticParams.staticModifications.dAddNterminusProtein, 0.0))
+ {
+ sprintf(g_staticParams.szMod + strlen(g_staticParams.szMod), "+ntprot=%0.6f ",
+ g_staticParams.staticModifications.dAddNterminusProtein);
+ }
+
+ for (int i=65; i<=90; i++) // 65-90 represents upper case letters in ASCII
+ {
+ if (!isEqual(g_staticParams.staticModifications.pdStaticMods[i], 0.0))
+ {
+ sprintf(g_staticParams.szMod + strlen(g_staticParams.szMod), "%c=%0.6f ", i,
+ g_staticParams.massUtility.pdAAMassParent[i] += g_staticParams.staticModifications.pdStaticMods[i]);
+ g_staticParams.massUtility.pdAAMassFragment[i] += g_staticParams.staticModifications.pdStaticMods[i];
+ }
+ else if (i=='B' || i=='J' || i=='X' || i=='Z')
+ {
+ g_staticParams.massUtility.pdAAMassParent[i] = 999999.;
+ g_staticParams.massUtility.pdAAMassFragment[i] = 999999.;
+ }
+ }
+
+ // Print out enzyme name to g_staticParams.szMod.
+ if (!g_staticParams.options.bNoEnzymeSelected)
+ {
+ char szTmp[4];
+
+ szTmp[0]='\0';
+ if (g_staticParams.options.iEnzymeTermini != 2)
+ sprintf(szTmp, ":%d", g_staticParams.options.iEnzymeTermini);
+
+ sprintf(g_staticParams.szMod + strlen(g_staticParams.szMod), "Enzyme:%s (%d%s)",
+ g_staticParams.enzymeInformation.szSearchEnzymeName,
+ g_staticParams.enzymeInformation.iAllowedMissedCleavage,
+ szTmp);
+ }
+ else
+ {
+ sprintf(g_staticParams.szMod + strlen(g_staticParams.szMod), "Enzyme:%s",
+ g_staticParams.enzymeInformation.szSearchEnzymeName);
+ }
+
+ if (g_staticParams.tolerances.dFragmentBinStartOffset < 0.0
+ || g_staticParams.tolerances.dFragmentBinStartOffset >1.0)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - bin offset %f must between 0.0 and 1.0\n",
+ g_staticParams.tolerances.dFragmentBinStartOffset);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ return false;
+ }
+
+ if (!g_staticParams.options.bOutputOutFiles)
+ {
+ g_staticParams.options.bSkipAlreadyDone = 0;
+ }
+
+ g_staticParams.precalcMasses.dNtermProton = g_staticParams.staticModifications.dAddNterminusPeptide
+ + PROTON_MASS;
+
+ g_staticParams.precalcMasses.dCtermOH2Proton = g_staticParams.staticModifications.dAddCterminusPeptide
+ + g_staticParams.massUtility.dOH2fragment
+ + PROTON_MASS;
+
+ g_staticParams.precalcMasses.dOH2ProtonCtermNterm = g_staticParams.massUtility.dOH2parent
+ + PROTON_MASS
+ + g_staticParams.staticModifications.dAddCterminusPeptide
+ + g_staticParams.staticModifications.dAddNterminusPeptide;
+
+ return true;
+}
+
+void CometSearchManager::AddInputFiles(vector<InputFileInfo*> &pvInputFiles)
+{
+ int numInputFiles = pvInputFiles.size();
+ for (int i = 0; i < numInputFiles; i++)
+ {
+ g_pvInputFiles.push_back(pvInputFiles.at(i));
+ }
+}
+
+void CometSearchManager::SetOutputFileBaseName(const char *pszBaseName)
+{
+ strcpy(g_staticParams.inputFile.szBaseName, pszBaseName);
+}
+
+std::map<std::string, CometParam*>& CometSearchManager::GetParamsMap()
+{
+ return _mapStaticParams;
+}
+
+void CometSearchManager::SetParam(const string &name, const string &strValue, const string& value)
+{
+ CometParam *pParam = new TypedCometParam<string>(CometParamType_String, strValue, value);
+ pair<map<string, CometParam*>::iterator,bool> ret = _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ if (false == ret.second)
+ {
+ _mapStaticParams.erase(name);
+ _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ }
+}
+
+bool CometSearchManager::GetParamValue(const string &name, string& value)
+{
+ std::map<string, CometParam*>::iterator it;
+ it = _mapStaticParams.find(name);
+ if (it == _mapStaticParams.end())
+ {
+ return false;
+ }
+
+ TypedCometParam<string> *pParam = static_cast<TypedCometParam<string>*>(it->second);
+ value = pParam->GetValue();
+ return true;
+}
+
+void CometSearchManager::SetParam(const std::string &name, const string &strValue, const int &value)
+{
+ CometParam *pParam = new TypedCometParam<int>(CometParamType_Int, strValue, value);
+ pair<map<string, CometParam*>::iterator,bool> ret = _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ if (false == ret.second)
+ {
+ _mapStaticParams.erase(name);
+ _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ }
+}
+
+bool CometSearchManager::GetParamValue(const string &name, int& value)
+{
+ std::map<string, CometParam*>::iterator it;
+ it = _mapStaticParams.find(name);
+ if (it == _mapStaticParams.end())
+ {
+ return false;
+ }
+
+ TypedCometParam<int> *pParam = static_cast<TypedCometParam<int>*>(it->second);
+ value = pParam->GetValue();
+ return true;
+}
+
+void CometSearchManager::SetParam(const string &name, const string &strValue, const double &value)
+{
+ CometParam *pParam = new TypedCometParam<double>(CometParamType_Double, strValue, value);
+ pair<map<string, CometParam*>::iterator,bool> ret = _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ if (false == ret.second)
+ {
+ _mapStaticParams.erase(name);
+ _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ }
+}
+
+bool CometSearchManager::GetParamValue(const string &name, double& value)
+{
+ std::map<string, CometParam*>::iterator it;
+ it = _mapStaticParams.find(name);
+ if (it == _mapStaticParams.end())
+ {
+ return false;
+ }
+
+ TypedCometParam<double> *pParam = static_cast<TypedCometParam<double>*>(it->second);
+ value = pParam->GetValue();
+ return true;
+}
+
+void CometSearchManager::SetParam(const string &name, const string &strValue, const VarMods &value)
+{
+ CometParam *pParam = new TypedCometParam<VarMods>(CometParamType_VarMods, strValue, value);
+ pair<map<string, CometParam*>::iterator,bool> ret = _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ if (false == ret.second)
+ {
+ _mapStaticParams.erase(name);
+ _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ }
+}
+
+bool CometSearchManager::GetParamValue(const string &name, VarMods & value)
+{
+ std::map<string, CometParam*>::iterator it;
+ it = _mapStaticParams.find(name);
+ if (it == _mapStaticParams.end())
+ {
+ return false;
+ }
+
+ TypedCometParam<VarMods> *pParam = static_cast<TypedCometParam<VarMods>*>(it->second);
+ value = pParam->GetValue();
+ return true;
+}
+
+void CometSearchManager::SetParam(const string &name, const string &strValue, const DoubleRange &value)
+{
+ CometParam *pParam = new TypedCometParam<DoubleRange>(CometParamType_DoubleRange, strValue, value);
+ pair<map<string, CometParam*>::iterator,bool> ret = _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ if (false == ret.second)
+ {
+ _mapStaticParams.erase(name);
+ _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ }
+}
+
+bool CometSearchManager::GetParamValue(const string &name, DoubleRange &value)
+{
+ std::map<string, CometParam*>::iterator it;
+ it = _mapStaticParams.find(name);
+ if (it == _mapStaticParams.end())
+ {
+ return false;
+ }
+
+ TypedCometParam<DoubleRange> *pParam = static_cast<TypedCometParam<DoubleRange>*>(it->second);
+ value = pParam->GetValue();
+ return true;
+}
+
+void CometSearchManager::SetParam(const string &name, const string &strValue, const IntRange &value)
+{
+ CometParam *pParam = new TypedCometParam<IntRange>(CometParamType_IntRange, strValue, value);
+ pair<map<string, CometParam*>::iterator,bool> ret = _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ if (false == ret.second)
+ {
+ _mapStaticParams.erase(name);
+ _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ }
+}
+
+bool CometSearchManager::GetParamValue(const string &name, IntRange &value)
+{
+ std::map<string, CometParam*>::iterator it;
+ it = _mapStaticParams.find(name);
+ if (it == _mapStaticParams.end())
+ {
+ return false;
+ }
+
+ TypedCometParam<IntRange> *pParam = static_cast<TypedCometParam<IntRange>*>(it->second);
+ value = pParam->GetValue();
+ return true;
+}
+
+void CometSearchManager::SetParam(const string &name, const string &strValue, const EnzymeInfo &value)
+{
+ CometParam *pParam = new TypedCometParam<EnzymeInfo>(CometParamType_EnzymeInfo, strValue, value);
+ pair<map<string, CometParam*>::iterator,bool> ret = _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ if (false == ret.second)
+ {
+ _mapStaticParams.erase(name);
+ _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ }
+}
+
+bool CometSearchManager::GetParamValue(const string &name, EnzymeInfo &value)
+{
+ std::map<string, CometParam*>::iterator it;
+ it = _mapStaticParams.find(name);
+ if (it == _mapStaticParams.end())
+ {
+ return false;
+ }
+
+ TypedCometParam<EnzymeInfo> *pParam = static_cast<TypedCometParam<EnzymeInfo>*>(it->second);
+ value = pParam->GetValue();
+ return true;
+}
+
+void CometSearchManager::SetParam(const string &name, const string &strValue, const vector<double> &value)
+{
+ CometParam *pParam = new TypedCometParam< vector<double> >(CometParamType_DoubleVector, strValue, value);
+ pair<map<string, CometParam*>::iterator,bool> ret = _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ if (false == ret.second)
+ {
+ _mapStaticParams.erase(name);
+ _mapStaticParams.insert(std::pair<std::string, CometParam*>(name, pParam));
+ }
+}
+
+bool CometSearchManager::GetParamValue(const string &name, vector<double> &value)
+{
+ std::map<string, CometParam*>::iterator it;
+ it = _mapStaticParams.find(name);
+ if (it == _mapStaticParams.end())
+ {
+ return false;
+ }
+
+ TypedCometParam< vector<double> > *pParam = static_cast<TypedCometParam< vector<double> >*>(it->second);
+ value = pParam->GetValue();
+
+ return true;
+}
+
+bool CometSearchManager::IsSearchError()
+{
+ return g_cometStatus.IsError();
+}
+
+void CometSearchManager::GetStatusMessage(string &strStatusMsg)
+{
+ g_cometStatus.GetStatusMsg(strStatusMsg);
+}
+
+bool CometSearchManager::IsValidCometVersion(const string &version)
+{
+ // Major version number must match to current binary
+ const char *pszCometVersion = version.c_str();
+ return strstr(comet_version, pszCometVersion);
+}
+
+void CometSearchManager::CancelSearch()
+{
+ g_cometStatus.SetStatus(CometResult_Cancelled, string("Search was cancelled."));
+}
+
+bool CometSearchManager::IsCancelSearch()
+{
+ return g_cometStatus.IsCancel();
+}
+
+void CometSearchManager::ResetSearchStatus()
+{
+ g_cometStatus.ResetStatus();
+}
+
+bool CometSearchManager::DoSearch()
+{
+ char szOut[256];
+
+ if (!InitializeStaticParams())
+ {
+ return false;
+ }
+
+ PrintParameters();
+
+ if (!ValidateOutputFormat())
+ {
+ return false;
+ }
+
+ if (!ValidateSequenceDatabaseFile())
+ {
+ return false;
+ }
+
+ if (!ValidateScanRange())
+ {
+ return false;
+ }
+
+ bool bSucceeded = true;
+
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ sprintf(szOut, " Comet version \"%s\"\n\n", comet_version);
+ logout(szOut);
+ fflush(stdout);
+ }
+
+ for (int i=0; i<(int)g_pvInputFiles.size(); i++)
+ {
+ bSucceeded = UpdateInputFile(g_pvInputFiles.at(i));
+ if (!bSucceeded)
+ {
+ break;
+ }
+
+ time_t tStartTime;
+ time(&tStartTime);
+ strftime(g_staticParams.szDate, 26, "%m/%d/%Y, %I:%M:%S %p", localtime(&tStartTime));
+
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ sprintf(szOut, " Search start: %s\n", g_staticParams.szDate);
+ sprintf(szOut+strlen(szOut), " - Input file: %s\n", g_staticParams.inputFile.szFileName);
+ logout(szOut);
+ fflush(stdout);
+ }
+
+ int iFirstScan = g_staticParams.inputFile.iFirstScan; // First scan to search specified by user.
+ int iLastScan = g_staticParams.inputFile.iLastScan; // Last scan to search specified by user.
+ int iPercentStart = 0; // percentage within input file for start scan of batch
+ int iPercentEnd = 0; // percentage within input file for end scan of batch
+ int iAnalysisType = g_staticParams.inputFile.iAnalysisType; // 1=dta (retired),
+ // 2=specific scan,
+ // 3=specific scan + charge,
+ // 4=scan range,
+ // 5=entire file
+
+ // For SQT & pepXML output file, check if they can be written to before doing anything else.
+ FILE *fpout_sqt=NULL;
+ FILE *fpoutd_sqt=NULL;
+ FILE *fpout_pepxml=NULL;
+ FILE *fpoutd_pepxml=NULL;
+ FILE *fpout_percolator=NULL;
+ FILE *fpout_txt=NULL;
+ FILE *fpoutd_txt=NULL;
+
+ char szOutputSQT[SIZE_FILE];
+ char szOutputDecoySQT[SIZE_FILE];
+ char szOutputPepXML[SIZE_FILE];
+ char szOutputDecoyPepXML[SIZE_FILE];
+ char szOutputPercolator[SIZE_FILE];
+ char szOutputTxt[SIZE_FILE];
+ char szOutputDecoyTxt[SIZE_FILE];
+
+ if (g_staticParams.options.bOutputSqtFile)
+ {
+ if (iAnalysisType == AnalysisType_EntireFile)
+ {
+#ifdef CRUX
+ sprintf(szOutputSQT, "%s%s.target.sqt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+#else
+ sprintf(szOutputSQT, "%s%s.sqt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+#endif
+ }
+ else
+ {
+#ifdef CRUX
+ sprintf(szOutputSQT, "%s%s.%d-%d.target.sqt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+#else
+ sprintf(szOutputSQT, "%s%s.%d-%d.sqt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+#endif
+ }
+
+ if ((fpout_sqt = fopen(szOutputSQT, "w")) == NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputSQT);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ bSucceeded = false;
+ }
+
+ CometWriteSqt::PrintSqtHeader(fpout_sqt, *this);
+
+ if (bSucceeded && (g_staticParams.options.iDecoySearch == 2))
+ {
+ if (iAnalysisType == AnalysisType_EntireFile)
+ {
+ sprintf(szOutputDecoySQT, "%s%s.decoy.sqt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+ }
+ else
+ {
+ sprintf(szOutputDecoySQT, "%s%s.%d-%d.decoy.sqt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+ }
+
+ if ((fpoutd_sqt = fopen(szOutputDecoySQT, "w")) == NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoySQT);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ bSucceeded = false;
+ }
+
+ CometWriteSqt::PrintSqtHeader(fpoutd_sqt, *this);
+ }
+ }
+
+ if (bSucceeded && g_staticParams.options.bOutputTxtFile)
+ {
+ if (iAnalysisType == AnalysisType_EntireFile)
+ {
+#ifdef CRUX
+ sprintf(szOutputTxt, "%s%s.target.txt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+#else
+ sprintf(szOutputTxt, "%s%s.txt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+#endif
+ }
+ else
+ {
+#ifdef CRUX
+ sprintf(szOutputTxt, "%s%s.%d-%d.target.txt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+#else
+ sprintf(szOutputTxt, "%s%s.%d-%d.txt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+#endif
+ }
+
+ if ((fpout_txt = fopen(szOutputTxt, "w")) == NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputTxt);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ bSucceeded = false;
+ }
+
+ CometWriteTxt::PrintTxtHeader(fpout_txt);
+
+ if (bSucceeded && (g_staticParams.options.iDecoySearch == 2))
+ {
+ if (iAnalysisType == AnalysisType_EntireFile)
+ {
+ sprintf(szOutputDecoyTxt, "%s%s.decoy.txt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+ }
+ else
+ {
+ sprintf(szOutputDecoyTxt, "%s%s.%d-%d.decoy.txt",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+ }
+
+ if ((fpoutd_txt= fopen(szOutputDecoyTxt, "w")) == NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyTxt);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ bSucceeded = false;
+ }
+
+ CometWriteTxt::PrintTxtHeader(fpoutd_txt);
+ }
+ }
+
+ if (bSucceeded && g_staticParams.options.bOutputPepXMLFile)
+ {
+ if (iAnalysisType == AnalysisType_EntireFile)
+ {
+#ifdef CRUX
+ sprintf(szOutputPepXML, "%s%s.target.pep.xml",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+#else
+ sprintf(szOutputPepXML, "%s%s.pep.xml",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+#endif
+ }
+ else
+ {
+#ifdef CRUX
+ sprintf(szOutputPepXML, "%s%s.%d-%d.target.pep.xml",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+#else
+ sprintf(szOutputPepXML, "%s%s.%d-%d.pep.xml",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+#endif
+ }
+
+ if ((fpout_pepxml = fopen(szOutputPepXML, "w")) == NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPepXML);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ bSucceeded = false;
+ }
+
+ if (bSucceeded)
+ {
+ bSucceeded = CometWritePepXML::WritePepXMLHeader(fpout_pepxml, *this);
+ }
+
+ if (bSucceeded && (g_staticParams.options.iDecoySearch == 2))
+ {
+ if (iAnalysisType == AnalysisType_EntireFile)
+ {
+ sprintf(szOutputDecoyPepXML, "%s%s.decoy.pep.xml",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+ }
+ else
+ {
+ sprintf(szOutputDecoyPepXML, "%s%s.%d-%d.decoy.pep.xml",
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+ }
+
+ if ((fpoutd_pepxml = fopen(szOutputDecoyPepXML, "w")) == NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot write to decoy file \"%s\".\n", szOutputDecoyPepXML);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ bSucceeded = false;
+ }
+
+ if (bSucceeded)
+ {
+ bSucceeded = CometWritePepXML::WritePepXMLHeader(fpoutd_pepxml, *this);
+ }
+ }
+ }
+
+ if (bSucceeded && g_staticParams.options.bOutputPercolatorFile)
+ {
+ if (iAnalysisType == AnalysisType_EntireFile)
+ {
+#ifdef CRUX
+ sprintf(szOutputPercolator, "%s%s.target.pin",
+#else
+ sprintf(szOutputPercolator, "%s%s.pin",
+#endif
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix);
+ }
+ else
+ {
+#ifdef CRUX
+ sprintf(szOutputPercolator, "%s%s.%d-%d.target.pin",
+#else
+ sprintf(szOutputPercolator, "%s%s.%d-%d.pin",
+#endif
+ g_staticParams.inputFile.szBaseName, g_staticParams.szOutputSuffix, iFirstScan, iLastScan);
+ }
+
+ if ((fpout_percolator = fopen(szOutputPercolator, "w")) == NULL)
+ {
+ char szErrorMsg[256];
+ sprintf(szErrorMsg, " Error - cannot write to file \"%s\".\n", szOutputPercolator);
+ string strErrorMsg(szErrorMsg);
+ g_cometStatus.SetStatus(CometResult_Failed, strErrorMsg);
+ logerr(szErrorMsg);
+ bSucceeded = false;
+ }
+
+ if (bSucceeded)
+ {
+ // We need knowledge of max charge state in all searches
+ // here in order to write the featureDescription header
+
+ CometWritePercolator::WritePercolatorHeader(fpout_percolator);
+ }
+ }
+
+ if (bSucceeded)
+ {
+ //MH: Allocate memory shared by threads during spectral processing.
+ bSucceeded = CometPreprocess::AllocateMemory(g_staticParams.options.iNumThreads);
+ if (!bSucceeded)
+ {
+ break;
+ }
+
+ // Allocate memory shared by threads during search
+ bSucceeded = CometSearch::AllocateMemory(g_staticParams.options.iNumThreads);
+ if (!bSucceeded)
+ {
+ break;
+ }
+
+ // For file access using MSToolkit.
+ MSReader mstReader;
+
+ // We want to read only MS2/MS3 scans.
+ SetMSLevelFilter(mstReader);
+
+ int iTotalSpectraSearched = 0;
+
+ // We need to reset some of the static variables in-between input files
+ CometPreprocess::Reset();
+
+ int iBatchNum = 0;
+ while (!CometPreprocess::DoneProcessingAllSpectra()) // Loop through iMaxSpectraPerSearch
+ {
+ iBatchNum++;
+
+#ifdef PERF_DEBUG
+ time_t tTotalSearchStartTime;
+ time_t tTotalSearchEndTime;
+ time_t tLoadAndPreprocessSpectraStartTime;
+ time_t tLoadAndPreprocessSpectraEndTime;
+ time_t tRunSearchStartTime;
+ time_t tRunSearchEndTime;
+ time_t tPostAnalysisStartTime;
+ time_t tPostAnalysisEndTime;
+
+ char szTimeBuffer[32];
+ szTimeBuffer[0] = '\0';
+#endif
+
+ // Load and preprocess all the spectra.
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ logout(" - Load spectra:");
+
+#ifdef PERF_DEBUG
+ char szOut[128];
+ time(&tLoadAndPreprocessSpectraStartTime);
+ strftime(szTimeBuffer, 26, "%m/%d/%Y, %I:%M:%S %p", localtime(&tLoadAndPreprocessSpectraStartTime));
+ sprintf(szOut, " - Start LoadAndPreprocessSpectra: %s\n", szTimeBuffer);
+ logout(szOut);
+#endif
+
+ fflush(stdout);
+ }
+
+ g_cometStatus.SetStatusMsg(string("Loading and processing input spectra"));
+
+ // IMPORTANT: From this point onwards, because we've loaded some
+ // spectra, we MUST "goto cleanup_results" before exiting the loop,
+ // or we will create a memory leak!
+ bSucceeded = CometPreprocess::LoadAndPreprocessSpectra(mstReader,
+ iFirstScan, iLastScan, iAnalysisType,
+ g_staticParams.options.iNumThreads, // min # threads
+ g_staticParams.options.iNumThreads); // max # threads
+ if (!bSucceeded)
+ {
+ goto cleanup_results;
+ }
+
+ iPercentStart = iPercentEnd;
+ iPercentEnd = mstReader.getPercent();
+
+#ifdef PERF_DEBUG
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ char szOut[128];
+ time(&tLoadAndPreprocessSpectraEndTime);
+ strftime(szTimeBuffer, 26, "%m/%d/%Y, %I:%M:%S %p", localtime(&tLoadAndPreprocessSpectraEndTime));
+ sprintf(szOut, " - End LoadAndPreprocessSpectra: %s\n", szTimeBuffer);
+ logout(szOut);
+ int iElapsedTime=(int)difftime(tLoadAndPreprocessSpectraEndTime, tLoadAndPreprocessSpectraStartTime);
+ sprintf(szOut, " - Time spent in LoadAndPreprocessSpectra: %d seconds\n", iElapsedTime);
+ logout(szOut);
+ fflush(stdout);
+ }
+#endif
+
+ if (g_pvQuery.empty())
+ break; // no search to run
+ else
+ iTotalSpectraSearched += g_pvQuery.size();
+
+ bSucceeded = AllocateResultsMem();
+ if (!bSucceeded)
+ {
+ goto cleanup_results;
+ }
+
+ char szStatusMsg[256];
+ sprintf(szStatusMsg, " %d\n", (int)g_pvQuery.size());
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ char szOut[128];
+ sprintf(szOut, "%s", szStatusMsg);
+ logout(szOut);
+ }
+ g_cometStatus.SetStatusMsg(string(szStatusMsg));
+
+ // Sort g_pvQuery vector by dExpPepMass.
+ std::sort(g_pvQuery.begin(), g_pvQuery.end(), compareByPeptideMass);
+
+ g_massRange.dMinMass = g_pvQuery.at(0)->_pepMassInfo.dPeptideMassToleranceMinus;
+ g_massRange.dMaxMass = g_pvQuery.at(g_pvQuery.size()-1)->_pepMassInfo.dPeptideMassTolerancePlus;
+
+#ifdef PERF_DEBUG
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ char szOut[128];
+ time(&tRunSearchStartTime);
+ strftime(szTimeBuffer, 26, "%m/%d/%Y, %I:%M:%S %p", localtime(&tRunSearchStartTime));
+ sprintf(szOut, " - Start RunSearch: %s\n", szTimeBuffer);
+ logout(szOut);
+ fflush(stdout);
+
+ }
+#endif
+
+ bSucceeded = !g_cometStatus.IsError() && !g_cometStatus.IsCancel();
+ if (!bSucceeded)
+ {
+ goto cleanup_results;
+ }
+
+ g_cometStatus.SetStatusMsg(string("Running search..."));
+
+ // Now that spectra are loaded to memory and sorted, do search.
+ bSucceeded = CometSearch::RunSearch(g_staticParams.options.iNumThreads, g_staticParams.options.iNumThreads, iPercentStart, iPercentEnd);
+ if (!bSucceeded)
+ {
+ goto cleanup_results;
+ }
+
+#ifdef PERF_DEBUG
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ char szOut[128];
+ time(&tRunSearchEndTime);
+ strftime(szTimeBuffer, 26, "%m/%d/%Y, %I:%M:%S %p", localtime(&tRunSearchEndTime));
+ sprintf(szOut, " - End RunSearch: %s\n", szTimeBuffer);
+ logout(szOut);
+
+ int iElapsedTime=(int)difftime(tRunSearchEndTime, tRunSearchStartTime);
+ sprintf(szOut, " - Time spent in RunSearch: %d seconds\n", iElapsedTime);
+ logout(szOut);
+
+ time(&tPostAnalysisStartTime);
+ strftime(szTimeBuffer, 26, "%m/%d/%Y, %I:%M:%S %p", localtime(&tPostAnalysisStartTime));
+ sprintf(szOut, " - Start PostAnalysis: %s\n", szTimeBuffer);
+ logout(szOut);
+
+ fflush(stdout);
+ }
+#endif
+
+ bSucceeded = !g_cometStatus.IsError() && !g_cometStatus.IsCancel();
+ if (!bSucceeded)
+ {
+ goto cleanup_results;
+ }
+
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ logout(" - Post analysis:");
+ fflush(stdout);
+ }
+
+ g_cometStatus.SetStatusMsg(string("Performing post-search analysis ..."));
+
+ // Sort each entry by xcorr, calculate E-values, etc.
+ bSucceeded = CometPostAnalysis::PostAnalysis(g_staticParams.options.iNumThreads, g_staticParams.options.iNumThreads);
+ if (!bSucceeded)
+ {
+ goto cleanup_results;
+ }
+
+#ifdef PERF_DEBUG
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ char szOut[128];
+ time(&tPostAnalysisEndTime);
+ strftime(szTimeBuffer, 26, "%m/%d/%Y, %I:%M:%S %p", localtime(&tPostAnalysisEndTime));
+ sprintf(szOut, " - End PostAnalysis: %s\n", szTimeBuffer);
+ logout(szOut);
+ int iElapsedTime=(int)difftime(tPostAnalysisEndTime, tPostAnalysisStartTime);
+ sprintf(szOut, " - Time spent in PostAnalysis: %d seconds\n", iElapsedTime);
+ logout(szOut);
+ fflush(stdout);
+ }
+#endif
+
+ // Sort g_pvQuery vector by scan.
+ std::sort(g_pvQuery.begin(), g_pvQuery.end(), compareByScanNumber);
+
+ CalcRunTime(tStartTime);
+
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ logout(" done\n");
+ fflush(stdout);
+ }
+
+ if (g_staticParams.options.bOutputOutFiles)
+ {
+ bSucceeded = CometWriteOut::WriteOut();
+ if (!bSucceeded)
+ {
+ goto cleanup_results;
+ }
+ }
+
+ if (g_staticParams.options.bOutputPepXMLFile)
+ CometWritePepXML::WritePepXML(fpout_pepxml, fpoutd_pepxml);
+
+ if (g_staticParams.options.bOutputPercolatorFile)
+ {
+ bSucceeded = CometWritePercolator::WritePercolator(fpout_percolator);
+ if (!bSucceeded)
+ {
+ goto cleanup_results;
+ }
+ }
+
+ if (g_staticParams.options.bOutputTxtFile)
+ CometWriteTxt::WriteTxt(fpout_txt, fpoutd_txt);
+
+ //// Write SQT last as I destroy the g_staticParams.szMod string during that process
+ if (g_staticParams.options.bOutputSqtStream || g_staticParams.options.bOutputSqtFile)
+ CometWriteSqt::WriteSqt(fpout_sqt, fpoutd_sqt);
+
+ cleanup_results:
+ // Deleting each Query object in the vector calls its destructor, which
+ // frees the spectral memory (see definition for Query in CometData.h).
+ for (int i=0; i<(int)g_pvQuery.size(); i++)
+ delete g_pvQuery.at(i);
+
+ g_pvQuery.clear();
+
+ if (!bSucceeded)
+ {
+ break;
+ }
+ }
+
+ if (bSucceeded)
+ {
+ if (iTotalSpectraSearched == 0)
+ {
+ logout(" Warning - no spectra searched.\n\n");
+ }
+
+ if (!g_staticParams.options.bOutputSqtStream)
+ {
+ char szOut[128];
+#ifdef PERF_DEBUG
+ time_t tStartTimeSave = tStartTime;
+#endif
+ time(&tStartTime);
+ strftime(g_staticParams.szDate, 26, "%m/%d/%Y, %I:%M:%S %p", localtime(&tStartTime));
+ sprintf(szOut, " Search end: %s\n\n", g_staticParams.szDate);
+ logout(szOut);
+#ifdef PERF_DEBUG
+ int iElapsedTime=(int)difftime(tStartTime, tStartTimeSave);
+ sprintf(szOut, " - Total search time: %d seconds\n", iElapsedTime);
+ logout(szOut);
+#endif
+ }
+
+ if (NULL != fpout_pepxml)
+ {
+ CometWritePepXML::WritePepXMLEndTags(fpout_pepxml);
+ }
+
+ if (NULL != fpoutd_pepxml)
+ {
+ CometWritePepXML::WritePepXMLEndTags(fpoutd_pepxml);
+ }
+ }
+ }
+
+ //MH: Deallocate spectral processing memory.
+ CometPreprocess::DeallocateMemory(g_staticParams.options.iNumThreads);
+
+ // Deallocate search memory
+ CometSearch::DeallocateMemory(g_staticParams.options.iNumThreads);
+
+ if (NULL != fpout_pepxml)
+ {
+ fclose(fpout_pepxml);
+ fpout_pepxml = NULL;
+ }
+
+ if (NULL != fpoutd_pepxml)
+ {
+ fclose(fpoutd_pepxml);
+ fpoutd_pepxml = NULL;
+ }
+
+ if (NULL != fpout_percolator)
+ {
+ fclose(fpout_percolator);
+ fpout_percolator = NULL;
+ }
+
+ if (NULL != fpout_sqt)
+ {
+ fclose(fpout_sqt);
+ fpout_sqt = NULL;
+ }
+
+ if (NULL != fpoutd_sqt)
+ {
+ fclose(fpoutd_sqt);
+ fpoutd_sqt = NULL;
+ }
+
+ if (NULL != fpout_txt)
+ {
+ fclose(fpout_txt);
+ fpout_txt = NULL;
+ }
+
+ if (NULL != fpoutd_txt)
+ {
+ fclose(fpoutd_txt);
+ fpoutd_txt = NULL;
+ }
+
+ if (!bSucceeded)
+ {
+ break;
+ }
+ }
+
+ return bSucceeded;
+}
+
diff --git a/ext/patches/comet/MSToolkit/MSToolkitLite.vcxproj b/ext/patches/comet/MSToolkit/MSToolkitLite.vcxproj
new file mode 100644
index 0000000..f2a3547
--- /dev/null
+++ b/ext/patches/comet/MSToolkit/MSToolkitLite.vcxproj
@@ -0,0 +1,257 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project DefaultTargets="Build" ToolsVersion="12.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+ <ItemGroup Label="ProjectConfigurations">
+ <ProjectConfiguration Include="Debug|Win32">
+ <Configuration>Debug</Configuration>
+ <Platform>Win32</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Debug|x64">
+ <Configuration>Debug</Configuration>
+ <Platform>x64</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Release|Win32">
+ <Configuration>Release</Configuration>
+ <Platform>Win32</Platform>
+ </ProjectConfiguration>
+ <ProjectConfiguration Include="Release|x64">
+ <Configuration>Release</Configuration>
+ <Platform>x64</Platform>
+ </ProjectConfiguration>
+ </ItemGroup>
+ <PropertyGroup Label="Globals">
+ <ProjectGuid>{8093FAFA-4AA1-4E88-A83E-1B433A96AAE5}</ProjectGuid>
+ <RootNamespace>MSToolkitLite</RootNamespace>
+ <Keyword>Win32Proj</Keyword>
+ </PropertyGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.Default.props" />
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
+ <ConfigurationType>StaticLibrary</ConfigurationType>
+ <CharacterSet>Unicode</CharacterSet>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <UseOfMfc>false</UseOfMfc>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
+ <ConfigurationType>StaticLibrary</ConfigurationType>
+ <CharacterSet>Unicode</CharacterSet>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="Configuration">
+ <ConfigurationType>StaticLibrary</ConfigurationType>
+ <CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
+ <ConfigurationType>StaticLibrary</ConfigurationType>
+ <CharacterSet>Unicode</CharacterSet>
+ <PlatformToolset>v120</PlatformToolset>
+ </PropertyGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
+ <ImportGroup Label="ExtensionSettings">
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <ImportGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="PropertySheets">
+ <Import Project="$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props" Condition="exists('$(UserRootDir)\Microsoft.Cpp.$(Platform).user.props')" Label="LocalAppDataPlatform" />
+ </ImportGroup>
+ <PropertyGroup Label="UserMacros" />
+ <PropertyGroup>
+ <_ProjectFileVersion>10.0.40219.1</_ProjectFileVersion>
+ <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ <OutDir Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">$(Platform)\$(Configuration)\</IntDir>
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+ <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ <OutDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(SolutionDir)$(Platform)\$(Configuration)\</OutDir>
+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">$(Platform)\$(Configuration)\</IntDir>
+ <IntDir Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(Platform)\$(Configuration)\</IntDir>
+ </PropertyGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Debug|Win32'">
+ <ClCompile>
+ <Optimization>MaxSpeed</Optimization>
+ <AdditionalIncludeDirectories>./include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+ <PreprocessorDefinitions>WIN32;_DEBUG;_LIB;%(PreprocessorDefinitions);COMPILED_FROM_DSP;_NOSQLITE;XML_STATIC</PreprocessorDefinitions>
+ <MinimalRebuild>false</MinimalRebuild>
+ <BasicRuntimeChecks>Default</BasicRuntimeChecks>
+ <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
+ <PrecompiledHeader>
+ </PrecompiledHeader>
+ <WarningLevel>Level3</WarningLevel>
+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <StringPooling>true</StringPooling>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
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+ <BasicRuntimeChecks>Default</BasicRuntimeChecks>
+ <RuntimeLibrary>MultiThreadedDebugDLL</RuntimeLibrary>
+ <PrecompiledHeader>
+ </PrecompiledHeader>
+ <WarningLevel>Level3</WarningLevel>
+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <WholeProgramOptimization>true</WholeProgramOptimization>
+ <StringPooling>true</StringPooling>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ </ClCompile>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'">
+ <ClCompile>
+ <Optimization>MaxSpeed</Optimization>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <AdditionalIncludeDirectories>./include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+ <PreprocessorDefinitions>WIN32;NDEBUG;_LIB;_CRT_SECURE_NO_WARNINGS;COMPILED_FROM_DSP;_NOSQLITE;XML_STATIC;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <PrecompiledHeader>
+ </PrecompiledHeader>
+ <ObjectFileName>$(IntDir)MSToolkitLite\</ObjectFileName>
+ <ProgramDataBaseFileName>$(IntDir)MSToolkitLite\vc90.pdb</ProgramDataBaseFileName>
+ <XMLDocumentationFileName>$(IntDir)MSToolkitLite\</XMLDocumentationFileName>
+ <WarningLevel>Level3</WarningLevel>
+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
+ <DisableSpecificWarnings>4996;%(DisableSpecificWarnings)</DisableSpecificWarnings>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <OmitFramePointers>true</OmitFramePointers>
+ <StringPooling>true</StringPooling>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ </ClCompile>
+ </ItemDefinitionGroup>
+ <ItemDefinitionGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'">
+ <ClCompile>
+ <Optimization>MaxSpeed</Optimization>
+ <IntrinsicFunctions>true</IntrinsicFunctions>
+ <AdditionalIncludeDirectories>./include;%(AdditionalIncludeDirectories)</AdditionalIncludeDirectories>
+ <PreprocessorDefinitions>WIN32;NDEBUG;_LIB;_CRT_SECURE_NO_WARNINGS;COMPILED_FROM_DSP;_NOSQLITE;XML_STATIC;%(PreprocessorDefinitions)</PreprocessorDefinitions>
+ <RuntimeLibrary>MultiThreadedDLL</RuntimeLibrary>
+ <FunctionLevelLinking>false</FunctionLevelLinking>
+ <PrecompiledHeader>
+ </PrecompiledHeader>
+ <ObjectFileName>$(IntDir)MSToolkitLite\</ObjectFileName>
+ <ProgramDataBaseFileName>$(IntDir)MSToolkitLite\vc90.pdb</ProgramDataBaseFileName>
+ <XMLDocumentationFileName>$(IntDir)MSToolkitLite\</XMLDocumentationFileName>
+ <WarningLevel>Level3</WarningLevel>
+ <DebugInformationFormat>ProgramDatabase</DebugInformationFormat>
+ <DisableSpecificWarnings>4996;%(DisableSpecificWarnings)</DisableSpecificWarnings>
+ <InlineFunctionExpansion>AnySuitable</InlineFunctionExpansion>
+ <OmitFramePointers>true</OmitFramePointers>
+ <FavorSizeOrSpeed>Speed</FavorSizeOrSpeed>
+ <StringPooling>true</StringPooling>
+ <BufferSecurityCheck>false</BufferSecurityCheck>
+ <EnableEnhancedInstructionSet>StreamingSIMDExtensions2</EnableEnhancedInstructionSet>
+ <FloatingPointModel>Fast</FloatingPointModel>
+ <FloatingPointExceptions>false</FloatingPointExceptions>
+ </ClCompile>
+ </ItemDefinitionGroup>
+ <ItemGroup>
+ <ClCompile Include="src\expat-2.0.1\xmlparse.cpp" />
+ <ClCompile Include="src\expat-2.0.1\xmlrole.cpp" />
+ <ClCompile Include="src\expat-2.0.1\xmltok.cpp" />
+ <ClCompile Include="src\expat-2.0.1\xmltok_impl.cpp" />
+ <ClCompile Include="src\expat-2.0.1\xmltok_ns.cpp" />
+ <ClCompile Include="src\MSToolkit\MSObject.cpp" />
+ <ClCompile Include="src\MSToolkit\MSReader.cpp" />
+ <ClCompile Include="src\MSToolkit\mzMLWriter.cpp" />
+ <ClCompile Include="src\MSToolkit\RAWReader.cpp" />
+ <ClCompile Include="src\MSToolkit\Spectrum.cpp" />
+ <ClCompile Include="src\mzParser\BasicChromatogram.cpp" />
+ <ClCompile Include="src\mzParser\BasicSpectrum.cpp" />
+ <ClCompile Include="src\mzParser\Czran.cpp" />
+ <ClCompile Include="src\mzParser\MSNumpress.cpp" />
+ <ClCompile Include="src\mzParser\mzp_base64.cpp" />
+ <ClCompile Include="src\mzParser\mzParser.cpp" />
+ <ClCompile Include="src\mzParser\PWIZface.cpp" />
+ <ClCompile Include="src\mzParser\RAMPface.cpp" />
+ <ClCompile Include="src\mzParser\saxhandler.cpp" />
+ <ClCompile Include="src\mzParser\saxmzmlhandler.cpp" />
+ <ClCompile Include="src\mzParser\saxmzxmlhandler.cpp" />
+ <ClCompile Include="src\zLib-1.2.5\adler32.c" />
+ <ClCompile Include="src\zLib-1.2.5\compress.c" />
+ <ClCompile Include="src\zLib-1.2.5\crc32.c" />
+ <ClCompile Include="src\zLib-1.2.5\deflate.c" />
+ <ClCompile Include="src\zLib-1.2.5\gzclose.c" />
+ <ClCompile Include="src\zLib-1.2.5\gzlib.c" />
+ <ClCompile Include="src\zLib-1.2.5\gzread.c" />
+ <ClCompile Include="src\zLib-1.2.5\gzwrite.c" />
+ <ClCompile Include="src\zLib-1.2.5\infback.c" />
+ <ClCompile Include="src\zLib-1.2.5\inffast.c" />
+ <ClCompile Include="src\zLib-1.2.5\inflate.c" />
+ <ClCompile Include="src\zLib-1.2.5\inftrees.c" />
+ <ClCompile Include="src\zLib-1.2.5\trees.c" />
+ <ClCompile Include="src\zLib-1.2.5\uncompr.c" />
+ <ClCompile Include="src\zLib-1.2.5\zutil.c" />
+ </ItemGroup>
+ <ItemGroup>
+ <None Include="ReadMe.txt" />
+ </ItemGroup>
+ <ItemGroup>
+ <ClInclude Include="include\ascii.h" />
+ <ClInclude Include="include\asciitab.h" />
+ <ClInclude Include="include\crc32.h" />
+ <ClInclude Include="include\deflate.h" />
+ <ClInclude Include="include\expat.h" />
+ <ClInclude Include="include\expat_config.h" />
+ <ClInclude Include="include\expat_external.h" />
+ <ClInclude Include="include\gzguts.h" />
+ <ClInclude Include="include\iasciitab.h" />
+ <ClInclude Include="include\inffast.h" />
+ <ClInclude Include="include\inffixed.h" />
+ <ClInclude Include="include\inflate.h" />
+ <ClInclude Include="include\inftrees.h" />
+ <ClInclude Include="include\internal.h" />
+ <ClInclude Include="include\latin1tab.h" />
+ <ClInclude Include="include\MSObject.h" />
+ <ClInclude Include="include\MSReader.h" />
+ <ClInclude Include="include\MSToolkitTypes.h" />
+ <ClInclude Include="include\mzMLWriter.h" />
+ <ClInclude Include="include\mzParser.h" />
+ <ClInclude Include="include\nametab.h" />
+ <ClInclude Include="include\RAWReader.h" />
+ <ClInclude Include="include\Spectrum.h" />
+ <ClInclude Include="include\szlib.h" />
+ <ClInclude Include="include\trees.h" />
+ <ClInclude Include="include\utf8tab.h" />
+ <ClInclude Include="include\winconfig.h" />
+ <ClInclude Include="include\xmlrole.h" />
+ <ClInclude Include="include\xmltok.h" />
+ <ClInclude Include="include\xmltok_impl.h" />
+ <ClInclude Include="include\zconf.h" />
+ <ClInclude Include="include\zlib.h" />
+ <ClInclude Include="include\zutil.h" />
+ </ItemGroup>
+ <Import Project="$(VCTargetsPath)\Microsoft.Cpp.targets" />
+ <ImportGroup Label="ExtensionTargets">
+ </ImportGroup>
+</Project>
diff --git a/ext/patches/comet/MSToolkit/RAWReader.cpp b/ext/patches/comet/MSToolkit/RAWReader.cpp
new file mode 100644
index 0000000..17fe54f
--- /dev/null
+++ b/ext/patches/comet/MSToolkit/RAWReader.cpp
@@ -0,0 +1,672 @@
+#include "RAWReader.h"
+
+using namespace MSToolkit;
+
+// ==========================
+// Constructors & Destructors
+// ==========================
+RAWReader::RAWReader(){
+
+ CoInitialize( NULL );
+ bRaw = initRaw();
+ rawCurSpec=0;
+ rawTotSpec=0;
+ rawAvg=false;
+ rawAvgWidth=1;
+ rawAvgCutoff=1000;
+ rawFileOpen=false;
+ rawLabel=false;
+ rawUserFilterExact=true;
+ strcpy(rawCurrentFile,".");
+ strcpy(rawInstrument,"unknown");
+ strcpy(rawManufacturer,"Thermo Scientific");
+ strcpy(rawUserFilter,"");
+ msLevelFilter=NULL;
+
+}
+
+RAWReader::~RAWReader(){
+
+ if(bRaw){
+ if(rawFileOpen) m_Raw->Close();
+ m_Raw.Release();
+ m_Raw=NULL;
+ }
+ msLevelFilter=NULL;
+
+}
+
+int RAWReader::calcChargeState(double precursormz, double highmass, VARIANT* varMassList, long nArraySize) {
+// Assumes spectrum is +1 or +2. Figures out charge by
+// seeing if signal is present above the parent mass
+// indicating +2 (by taking ratio above/below precursor)
+
+ bool bFound;
+ long i, iStart;
+ double dLeftSum,dRightSum;
+ double FractionWindow;
+ double CorrectionFactor;
+
+ dLeftSum = 0.00001;
+ dRightSum = 0.00001;
+
+ DataPeak* pDataPeaks = NULL;
+ SAFEARRAY FAR* psa = varMassList->parray;
+ SafeArrayAccessData( psa, (void**)(&pDataPeaks) );
+
+//-------------
+// calc charge
+//-------------
+ bFound=false;
+ i=0;
+ while(i<nArraySize && !bFound){
+ if(pDataPeaks[i].dMass < precursormz - 20){
+ //do nothing
+ } else {
+ bFound = true;
+ iStart = i;
+ }
+ i++;
+ }
+ if(!bFound) iStart = nArraySize;
+
+ for(i=0;i<iStart;i++) dLeftSum = dLeftSum + pDataPeaks[i].dIntensity;
+
+ bFound=false;
+ i=0;
+ while(i<nArraySize && !bFound){
+ if(pDataPeaks[i].dMass < precursormz + 20){
+ //do nothing
+ } else {
+ bFound = true;
+ iStart = i;
+ }
+ i++;
+ }
+
+ if(!bFound) {
+ SafeArrayUnaccessData( psa );
+ psa = NULL;
+ pDataPeaks = NULL;
+ return 1;
+ }
+ if(iStart = 0) iStart++;
+
+ for(i=iStart;i<nArraySize;i++) dRightSum = dRightSum + pDataPeaks[i].dIntensity;
+
+ if(precursormz * 2 < highmass){
+ CorrectionFactor = 1;
+ } else {
+ FractionWindow = (precursormz * 2) - highmass;
+ CorrectionFactor = (precursormz - FractionWindow) / precursormz;
+ }
+
+ if(dLeftSum > 0 && (dRightSum / dLeftSum) < (0.2 * CorrectionFactor)){
+ SafeArrayUnaccessData( psa );
+ psa=NULL;
+ pDataPeaks=NULL;
+ return 1;
+ } else {
+ SafeArrayUnaccessData( psa );
+ psa=NULL;
+ pDataPeaks=NULL;
+ return 0; //Set charge to 0 to indicate that both +2 and +3 spectra should be created
+ }
+
+ //When all else fails, return 0
+ return 0;
+}
+
+MSSpectrumType RAWReader::evaluateFilter(long scan, char* chFilter, vector<double>& MZs, bool& bCentroid, double& cv, MSActivation& act) {
+
+ BSTR Filter = NULL;
+ char cStr[256];
+ string tStr;
+ string mzVal;
+ int stop;
+ bool bSA=false;
+
+ //For non-ATL and non-MFC conversions
+ int sl;
+
+ //Initialize raw values to default
+ MZs.clear();
+ cv=0;
+
+ m_Raw->GetFilterForScanNum(scan, &Filter);
+ sl = SysStringLen(Filter)+1;
+ WideCharToMultiByte(CP_ACP,0,Filter,-1,chFilter,sl,NULL,NULL);
+ SysFreeString(Filter);
+
+ strcpy(cStr,chFilter);
+ MSSpectrumType mst=Unspecified;
+ char* tok;
+ tok=strtok(cStr," \n");
+ while(tok!=NULL){
+
+ if(strcmp(tok,"c")==0){
+ bCentroid=true;
+ } else if(strlen(tok)>2 && tok[0]=='c' && tok[1]=='v'){
+ cv=atof(tok+3);
+ } else if(strcmp(tok,"d")==0){
+ } else if(strcmp(tok,"ESI")==0){
+ } else if(strcmp(tok,"FTMS")==0){
+ } else if(strcmp(tok,"Full")==0){
+ } else if(strcmp(tok,"ITMS")==0){
+ } else if(strcmp(tok,"lock")==0){
+ } else if(strcmp(tok,"ms")==0){
+ mst=MS1;
+ } else if(strcmp(tok,"msx")==0){
+ mst=MSX;
+ } else if(strcmp(tok,"ms2")==0){
+ if(mst!=MSX) mst=MS2;
+ } else if(strcmp(tok,"ms3")==0){
+ if(mst!=MSX) mst=MS3;
+ } else if(strcmp(tok,"NSI")==0){
+ } else if(strcmp(tok,"p")==0){
+ bCentroid=false;
+ } else if(strcmp(tok,"r")==0){ //appears in fusion data, no documentation
+ } else if(strcmp(tok,"sa")==0){
+ bSA=true;
+ } else if(strncmp(tok,"sid",3)==0){
+ } else if(strcmp(tok,"SRM")==0){
+ mst=SRM;
+ } else if(strcmp(tok,"u")==0){
+ mst=UZS;
+ } else if(strcmp(tok,"w")==0){ //wideband activation?
+ } else if(strcmp(tok,"Z")==0){
+ if(mst!=UZS) mst=ZS;
+ } else if(strcmp(tok,"+")==0){
+ } else if(strcmp(tok,"-")==0){
+ } else if(strcmp(tok,"t")==0){ //turbo scan
+ } else if(strcmp(tok,"E")==0){ //enhanced
+ } else if(strchr(tok,'@')!=NULL){
+ tStr=tok;
+ stop=tStr.find("@");
+ mzVal=tStr.substr(0,stop);
+ MZs.push_back(atof(&mzVal[0]));
+ mzVal=tStr.substr(stop+1,3);
+ if(mzVal.compare("cid")==0){
+ act=mstCID;
+ } else if(mzVal.compare("hcd")==0){
+ act=mstHCD;
+ } else if(mzVal.compare("etd")==0){
+ if(bSA) act=mstETDSA;
+ else act=mstETD;
+ } else {
+ cout << "Unknown activation method: " << &mzVal[0] << endl;
+ act=mstNA;
+ }
+
+ } else if(strchr(tok,'[')!=NULL){
+ } else {
+ cout << "Unknown token: " << tok << endl;
+ }
+
+ tok=strtok(NULL," \n");
+ }
+
+ return mst;
+
+}
+
+void RAWReader::getInstrument(char* str){
+ strcpy(str,rawInstrument);
+}
+
+long RAWReader::getLastScanNumber(){
+ return rawCurSpec;
+}
+
+void RAWReader::getManufacturer(char* str){
+ strcpy(str,rawManufacturer);
+}
+
+long RAWReader::getScanCount(){
+ return rawTotSpec;
+}
+
+bool RAWReader::getStatus(){
+ return bRaw;
+}
+
+bool RAWReader::initRaw(){
+
+ int raw=0;
+
+ IXRawfile2Ptr m_Raw2;
+ IXRawfile3Ptr m_Raw3;
+ IXRawfile4Ptr m_Raw4;
+ IXRawfile5Ptr m_Raw5;
+
+ //Example of Xcalibur/Foundation first
+ //if(FAILED(m_Raw5.CreateInstance("XRawfile.XRawfile.1"))){'
+
+ //Try MSFileReader - using ProteoWizard strategy
+ if(FAILED(m_Raw5.CreateInstance("MSFileReader.XRawfile.1"))){
+ if(FAILED(m_Raw4.CreateInstance("MSFileReader.XRawfile.1"))){
+ if(FAILED(m_Raw3.CreateInstance("MSFileReader.XRawfile.1"))){
+ if(FAILED(m_Raw2.CreateInstance("MSFileReader.XRawfile.1"))){
+ if(FAILED(m_Raw.CreateInstance("MSFileReader.XRawfile.1"))){
+ raw=0;
+ //cout << "Cannot load Thermo MSFileReader. Cannot read .RAW files." << endl;
+ } else {
+ raw=1;
+ }
+ } else {
+ m_Raw=m_Raw2;
+ raw=2;
+ }
+ } else {
+ m_Raw=m_Raw3;
+ raw=3;
+ }
+ } else {
+ m_Raw=m_Raw4;
+ raw=4;
+ }
+ } else {
+ m_Raw=m_Raw5;
+ raw=5;
+ }
+
+ if(raw>0) return true;
+ return false;
+}
+
+bool RAWReader::readRawFile(const char *c, Spectrum &s, int scNum){
+
+ //General purpose function members
+ bool bCheckNext;
+ bool bNewFile;
+
+ char chFilter[256];
+ char curFilter[256];
+
+ double dRTime;
+ double highmass=0.0;
+ double pm1;
+ double pw;
+
+ long i;
+ long j;
+ long lArraySize=0;
+
+ vector<double> MZs;
+
+ DataPeak* pDataPeaks = NULL;
+ HRESULT lRet;
+ MSSpectrumType MSn;
+ SAFEARRAY FAR* psa;
+ TCHAR pth[MAX_PATH];
+ VARIANT varMassList;
+ VARIANT varPeakFlags;
+
+ //Members for gathering averaged scans
+ int charge;
+ int sl;
+ int widthCount;
+
+ long FirstBkg1=0;
+ long FirstBkg2=0;
+ long LastBkg1=0;
+ long LastBkg2=0;
+ long lowerBound;
+ long upperBound;
+
+ BSTR rawFilter=NULL;
+ BSTR testStr;
+
+ //Additional members for Scan Information
+ bool bCentroid;
+
+ double cv; //Compensation Voltage
+ double BPI; //Base peak intensity
+ double BPM; //Base peak mass
+ double td; //temp double value
+ double TIC;
+
+ long tl; //temp long value
+ MSActivation act;
+
+ VARIANT Charge;
+ VARIANT ConversionA;
+ VARIANT ConversionB;
+ VARIANT ConversionC;
+ VARIANT ConversionD;
+ VARIANT ConversionE;
+ VARIANT ConversionI;
+ VARIANT IIT; //ion injection time
+ VARIANT MonoMZ;
+ VARIANT PrecursorInfo;
+
+ if(!bRaw) return false;
+
+ //Clear spectrum object
+ s.clear();
+
+ if(c==NULL){
+ //continue reading current file
+ if(!rawFileOpen) return false;
+ if(scNum>0) rawCurSpec=scNum;
+ else rawCurSpec++;
+ if(rawCurSpec>rawTotSpec) return false;
+ bNewFile=false;
+ } else {
+
+ //check if requested file is already open
+ if(rawFileOpen) {
+ if(strcmp(c,rawCurrentFile)==0){
+ if(scNum>0) rawCurSpec=scNum;
+ else rawCurSpec++;
+ if(rawCurSpec>rawTotSpec) return false;
+ bNewFile=false;
+ } else {
+ //new file requested, so close the existing one
+ lRet = m_Raw->Close();
+ rawFileOpen=false;
+ bNewFile=true;
+ }
+ } else {
+ bNewFile=true;
+ }
+
+ if(bNewFile){
+ MultiByteToWideChar(CP_ACP,0,c,-1,(LPWSTR)pth,MAX_PATH);
+ lRet = m_Raw->Open((LPWSTR)pth);
+ if(lRet != ERROR_SUCCESS) {
+ cerr << "Cannot open " << c << endl;
+ return false;
+ }
+ else lRet = m_Raw->SetCurrentController(0,1);
+ rawFileOpen=true;
+ m_Raw->GetNumSpectra(&rawTotSpec);
+ testStr=NULL;
+ m_Raw->GetInstModel(&testStr);
+ sl = SysStringLen(testStr)+1;
+ WideCharToMultiByte(CP_ACP,0,testStr,-1,rawInstrument,sl,NULL,NULL);
+ SysFreeString(testStr);
+ strcpy(rawCurrentFile,c);
+
+ //if scan number is requested, grab it
+ if(scNum>0) rawCurSpec=scNum;
+ else rawCurSpec=1;
+ if(rawCurSpec>rawTotSpec) return false;
+ }
+ }
+
+ //Initialize members
+ strcpy(chFilter,"");
+ strcpy(curFilter,"");
+ VariantInit(&varMassList);
+ VariantInit(&varPeakFlags);
+ VariantInit(&IIT);
+ VariantInit(&ConversionA);
+ VariantInit(&ConversionB);
+ VariantInit(&ConversionC);
+ VariantInit(&ConversionD);
+ VariantInit(&ConversionE);
+ VariantInit(&ConversionI);
+ VariantInit(&Charge);
+ VariantInit(&MonoMZ);
+ VariantInit(&PrecursorInfo);
+
+ rawPrecursorInfo preInfo;
+
+ //Rather than grab the next scan number, get the next scan based on a user-filter (if supplied).
+ //if the filter was set, make sure we pass the filter
+ while(true){
+
+ MSn = evaluateFilter(rawCurSpec, curFilter, MZs, bCentroid,cv,act);
+
+ //check for spectrum filter (string)
+ if(strlen(rawUserFilter)>0){
+ bCheckNext=false;
+ if(rawUserFilterExact) {
+ if(strcmp(curFilter,rawUserFilter)!=0) bCheckNext=true;
+ } else {
+ if(strstr(curFilter,rawUserFilter)==NULL) bCheckNext=true;
+ }
+
+ //if string doesn't match, get next scan until it does match or EOF
+ if(bCheckNext){
+ if(scNum>0) return false;
+ rawCurSpec++;
+ if(rawCurSpec>rawTotSpec) return false;
+ continue;
+ }
+ }
+
+ //check for msLevel filter
+ if(msLevelFilter->size()>0 && find(msLevelFilter->begin(), msLevelFilter->end(), MSn) == msLevelFilter->end()) {
+ if(scNum>0) return false;
+ rawCurSpec++;
+ if(rawCurSpec>rawTotSpec) return false;
+ } else {
+ break;
+ }
+ }
+
+ //Get spectrum meta data
+ //Get lump precursor info first. Note that MSX data likely has multiple precursor infos
+#ifdef _WIN64
+ BYTE* pData;
+ m_Raw->GetPrecursorInfoFromScanNum(rawCurSpec, &PrecursorInfo, &tl);
+ SafeArrayAccessData(PrecursorInfo.parray, (void**)&pData);
+ if (tl > 0){
+ //getting only first value!!! Note this does not support MSX here!!!
+ //TODO ? : rewrite MSX support to use this function? If so, how would 32-bit systems do this? This function
+ //doesn't seem to work on 32-bit MSFileReader...
+ memcpy(&preInfo, pData, sizeof(rawPrecursorInfo));
+ } else {
+ preInfo.charge=0;
+ preInfo.dIsoMZ=0;
+ preInfo.dMonoMZ=0;
+ preInfo.parScanNum=0;
+ }
+ SafeArrayUnaccessData(PrecursorInfo.parray);
+#else
+ sl=lstrlenA("Monoisotopic M/Z:");
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Monoisotopic M/Z:",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &MonoMZ);
+ SysFreeString(testStr);
+ preInfo.dMonoMZ=MonoMZ.dblVal;
+
+ sl=lstrlenA("Charge State:");
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Charge State:",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &Charge);
+ SysFreeString(testStr);
+ preInfo.charge=Charge.iVal;
+#endif
+
+ sl=lstrlenA("Ion Injection Time (ms):");
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Ion Injection Time (ms):",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &IIT);
+ SysFreeString(testStr);
+
+ sl=lstrlenA("Conversion Parameter A:");
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Conversion Parameter A:",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionA);
+ SysFreeString(testStr);
+
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Conversion Parameter B:",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionB);
+ SysFreeString(testStr);
+
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Conversion Parameter C:",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionC);
+ SysFreeString(testStr);
+
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Conversion Parameter D:",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionD);
+ SysFreeString(testStr);
+
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Conversion Parameter E:",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionE);
+ SysFreeString(testStr);
+
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"Conversion Parameter I:",sl,testStr,sl);
+ m_Raw->GetTrailerExtraValueForScanNum(rawCurSpec, testStr, &ConversionI);
+ SysFreeString(testStr);
+
+ m_Raw->GetScanHeaderInfoForScanNum(rawCurSpec, &tl, &td, &td, &td, &TIC, &BPM, &BPI, &tl, &tl, &td);
+ m_Raw->RTFromScanNum(rawCurSpec,&dRTime);
+
+ //Get the peaks
+ //Average raw files if requested by user
+ if(rawAvg){
+ widthCount=0;
+ lowerBound=0;
+ upperBound=0;
+ for(i=rawCurSpec-1;i>0;i--){
+ evaluateFilter(i, chFilter, MZs, bCentroid,cv,act);
+ if(strcmp(curFilter,chFilter)==0){
+ widthCount++;
+ if(widthCount==rawAvgWidth) {
+ lowerBound=i;
+ break;
+ }
+ }
+ }
+ if(lowerBound==0) lowerBound=rawCurSpec; //this will have "edge" effects
+
+ widthCount=0;
+ for(i=rawCurSpec+1;i<rawTotSpec;i++){
+ evaluateFilter(i, chFilter, MZs, bCentroid,cv,act);
+ if(strcmp(curFilter,chFilter)==0){
+ widthCount++;
+ if(widthCount==rawAvgWidth) {
+ upperBound=i;
+ break;
+ }
+ }
+ }
+ if(upperBound==0) upperBound=rawCurSpec; //this will have "edge" effects
+
+ m_Raw->GetFilterForScanNum(i, &rawFilter);
+ j=m_Raw->GetAverageMassList(&lowerBound, &upperBound, &FirstBkg1, &LastBkg1, &FirstBkg2, &LastBkg2,
+ rawFilter, 1, rawAvgCutoff, 0, FALSE, &pw, &varMassList, &varPeakFlags, &lArraySize );
+ SysFreeString(rawFilter);
+ rawFilter=NULL;
+
+ } else {
+
+ //Get regular spectrum data
+ sl=lstrlenA("");
+ testStr = SysAllocStringLen(NULL,sl);
+ MultiByteToWideChar(CP_ACP,0,"",sl,testStr,sl);
+ j=m_Raw->GetMassListFromScanNum(&rawCurSpec,testStr,0,0,0,FALSE,&pw,&varMassList,&varPeakFlags,&lArraySize);
+ SysFreeString(testStr);
+ }
+
+ //Handle MS2 and MS3 files differently to create Z-lines
+ if(MSn==MS2 || MSn==MS3){
+
+ //if charge state is assigned to spectrum, add Z-lines.
+ if(preInfo.charge>0){ //if(Charge.iVal>0){
+ if(preInfo.dMonoMZ>0.01) { //if(MonoMZ.dblVal>0.01) {
+ //pm1 = MonoMZ.dblVal * Charge.iVal - ((Charge.iVal-1)*1.007276466);
+ pm1 = preInfo.dMonoMZ * preInfo.charge - ((preInfo.charge - 1)*1.007276466);
+ s.setMZ(MZs[0], preInfo.dMonoMZ);
+ } else {
+ pm1 = MZs[0] * preInfo.charge - ((preInfo.charge - 1)*1.007276466);
+ s.setMZ(MZs[0]);
+ }
+ s.addZState(preInfo.charge, pm1);
+ s.setCharge(preInfo.charge);
+ } else {
+ s.setMZ(MZs[0]);
+ charge = calcChargeState(MZs[0], highmass, &varMassList, lArraySize);
+
+ //Charge greater than 0 means the charge state is known
+ if(charge>0){
+ pm1 = MZs[0]*charge - ((charge-1)*1.007276466);
+ s.addZState(charge,pm1);
+
+ //Charge of 0 means unknown charge state, therefore, compute +2 and +3 states.
+ } else {
+ pm1 = MZs[0]*2 - 1.007276466;
+ s.addZState(2,pm1);
+ pm1 = MZs[0]*3 - 2*1.007276466;
+ s.addZState(3,pm1);
+ }
+
+ }
+
+ } //endif MS2 and MS3
+
+ if(MSn==MSX){
+ for(i=0;i<(int)MZs.size();i++){
+ if(i==0) s.setMZ(MZs[i],0);
+ else s.addMZ(MZs[i],0);
+ }
+ s.setCharge(0);
+ }
+
+ //Set basic scan info
+ if(bCentroid) s.setCentroidStatus(1);
+ else s.setCentroidStatus(0);
+ s.setRawFilter(curFilter);
+ s.setActivationMethod(act);
+ s.setScanNumber((int)rawCurSpec);
+ s.setScanNumber((int)rawCurSpec,true);
+ s.setRTime((float)dRTime);
+ s.setFileType(MSn);
+ s.setBPI((float)BPI);
+ s.setBPM(BPM);
+ s.setCompensationVoltage(cv);
+ s.setConversionA(ConversionA.dblVal);
+ s.setConversionB(ConversionB.dblVal);
+ s.setConversionC(ConversionC.dblVal);
+ s.setConversionD(ConversionD.dblVal);
+ s.setConversionE(ConversionE.dblVal);
+ s.setConversionI(ConversionI.dblVal);
+ s.setTIC(TIC);
+ s.setIonInjectionTime(IIT.fltVal);
+ if(MSn==SRM) s.setMZ(MZs[0]);
+ switch(MSn){
+ case MS1: s.setMsLevel(1); break;
+ case MS2: s.setMsLevel(2); break;
+ case MS3: s.setMsLevel(3); break;
+ case MSX: s.setMsLevel(2); break;
+ default: s.setMsLevel(0); break;
+ }
+ psa = varMassList.parray;
+ SafeArrayAccessData( psa, (void**)(&pDataPeaks) );
+ for(j=0;j<lArraySize;j++) s.add(pDataPeaks[j].dMass,(float)pDataPeaks[j].dIntensity);
+ SafeArrayUnaccessData( psa );
+
+ //Clean up memory
+ VariantClear(&Charge);
+ VariantClear(&MonoMZ);
+ VariantClear(&IIT);
+ VariantClear(&ConversionA);
+ VariantClear(&ConversionB);
+ VariantClear(&ConversionC);
+ VariantClear(&ConversionD);
+ VariantClear(&ConversionE);
+ VariantClear(&ConversionI);
+ VariantClear(&varMassList);
+ VariantClear(&varPeakFlags);
+ VariantClear(&PrecursorInfo);
+
+ return true;
+
+}
+
+void RAWReader::setMSLevelFilter(vector<MSSpectrumType>* v){
+ msLevelFilter=v;
+}
+
+void RAWReader::setRawFilter(char *c){
+ strcpy(rawUserFilter,c);
+}
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new file mode 100644
index 0000000..066c9a0
--- /dev/null
+++ b/ext/patches/google-gflags/libgflags.vcxproj
@@ -0,0 +1,214 @@
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diff --git a/ext/patches/protobuf/src/google/protobuf/io/zero_copy_stream_impl_lite.cc b/ext/patches/protobuf/src/google/protobuf/io/zero_copy_stream_impl_lite.cc
new file mode 100644
index 0000000..34412fc
--- /dev/null
+++ b/ext/patches/protobuf/src/google/protobuf/io/zero_copy_stream_impl_lite.cc
@@ -0,0 +1,392 @@
+// Protocol Buffers - Google's data interchange format
+// Copyright 2008 Google Inc. All rights reserved.
+// http://code.google.com/p/protobuf/
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+// * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+// * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+// * Neither the name of Google Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+// Author: kenton at google.com (Kenton Varda)
+// Based on original Protocol Buffers design by
+// Sanjay Ghemawat, Jeff Dean, and others.
+
+#include <google/protobuf/io/zero_copy_stream_impl_lite.h>
+#include <google/protobuf/stubs/common.h>
+#include <google/protobuf/stubs/stl_util.h>
+#include <algorithm>
+
+namespace google {
+namespace protobuf {
+namespace io {
+
+namespace {
+
+// Default block size for Copying{In,Out}putStreamAdaptor.
+static const int kDefaultBlockSize = 8192;
+
+} // namespace
+
+ArrayInputStream::ArrayInputStream(const void* data, int size,
+ int block_size)
+ : data_(reinterpret_cast<const uint8*>(data)),
+ size_(size),
+ block_size_(block_size > 0 ? block_size : size),
+ position_(0),
+ last_returned_size_(0) {
+}
+
+ArrayInputStream::~ArrayInputStream() {
+}
+
+bool ArrayInputStream::Next(const void** data, int* size) {
+ if (position_ < size_) {
+ last_returned_size_ = min(block_size_, size_ - position_);
+ *data = data_ + position_;
+ *size = last_returned_size_;
+ position_ += last_returned_size_;
+ return true;
+ } else {
+ // We're at the end of the array.
+ last_returned_size_ = 0; // Don't let caller back up.
+ return false;
+ }
+}
+
+void ArrayInputStream::BackUp(int count) {
+ GOOGLE_CHECK_GT(last_returned_size_, 0)
+ << "BackUp() can only be called after a successful Next().";
+ GOOGLE_CHECK_LE(count, last_returned_size_);
+ GOOGLE_CHECK_GE(count, 0);
+ position_ -= count;
+ last_returned_size_ = 0; // Don't let caller back up further.
+}
+
+bool ArrayInputStream::Skip(int count) {
+ GOOGLE_CHECK_GE(count, 0);
+ last_returned_size_ = 0; // Don't let caller back up.
+ if (count > size_ - position_) {
+ position_ = size_;
+ return false;
+ } else {
+ position_ += count;
+ return true;
+ }
+}
+
+int64 ArrayInputStream::ByteCount() const {
+ return position_;
+}
+
+
+// ===================================================================
+
+ArrayOutputStream::ArrayOutputStream(void* data, int size, int block_size)
+ : data_(reinterpret_cast<uint8*>(data)),
+ size_(size),
+ block_size_(block_size > 0 ? block_size : size),
+ position_(0),
+ last_returned_size_(0) {
+}
+
+ArrayOutputStream::~ArrayOutputStream() {
+}
+
+bool ArrayOutputStream::Next(void** data, int* size) {
+ if (position_ < size_) {
+ last_returned_size_ = min(block_size_, size_ - position_);
+ *data = data_ + position_;
+ *size = last_returned_size_;
+ position_ += last_returned_size_;
+ return true;
+ } else {
+ // We're at the end of the array.
+ last_returned_size_ = 0; // Don't let caller back up.
+ return false;
+ }
+}
+
+void ArrayOutputStream::BackUp(int count) {
+ GOOGLE_CHECK_GT(last_returned_size_, 0)
+ << "BackUp() can only be called after a successful Next().";
+ GOOGLE_CHECK_LE(count, last_returned_size_);
+ GOOGLE_CHECK_GE(count, 0);
+ position_ -= count;
+ last_returned_size_ = 0; // Don't let caller back up further.
+}
+
+int64 ArrayOutputStream::ByteCount() const {
+ return position_;
+}
+
+// ===================================================================
+
+StringOutputStream::StringOutputStream(string* target)
+ : target_(target) {
+}
+
+StringOutputStream::~StringOutputStream() {
+}
+
+bool StringOutputStream::Next(void** data, int* size) {
+ int old_size = target_->size();
+
+ // Grow the string.
+ if (old_size < target_->capacity()) {
+ // Resize the string to match its capacity, since we can get away
+ // without a memory allocation this way.
+ STLStringResizeUninitialized(target_, target_->capacity());
+ } else {
+ // Size has reached capacity, so double the size. Also make sure
+ // that the new size is at least kMinimumSize.
+ STLStringResizeUninitialized(
+ target_,
+ max(old_size * 2,
+ kMinimumSize + 0)); // "+ 0" works around GCC4 weirdness.
+ }
+
+ *data = string_as_array(target_) + old_size;
+ *size = target_->size() - old_size;
+ return true;
+}
+
+void StringOutputStream::BackUp(int count) {
+ GOOGLE_CHECK_GE(count, 0);
+ GOOGLE_CHECK_LE(count, target_->size());
+ target_->resize(target_->size() - count);
+}
+
+int64 StringOutputStream::ByteCount() const {
+ return target_->size();
+}
+
+// ===================================================================
+
+CopyingInputStream::~CopyingInputStream() {}
+
+int CopyingInputStream::Skip(int count) {
+ char junk[4096];
+ int skipped = 0;
+ while (skipped < count) {
+ int bytes = Read(junk, min(count - skipped,
+ implicit_cast<int>(sizeof(junk))));
+ if (bytes <= 0) {
+ // EOF or read error.
+ return skipped;
+ }
+ skipped += bytes;
+ }
+ return skipped;
+}
+
+CopyingInputStreamAdaptor::CopyingInputStreamAdaptor(
+ CopyingInputStream* copying_stream, int block_size)
+ : copying_stream_(copying_stream),
+ owns_copying_stream_(false),
+ failed_(false),
+ position_(0),
+ buffer_size_(block_size > 0 ? block_size : kDefaultBlockSize),
+ buffer_used_(0),
+ backup_bytes_(0) {
+}
+
+CopyingInputStreamAdaptor::~CopyingInputStreamAdaptor() {
+ if (owns_copying_stream_) {
+ delete copying_stream_;
+ }
+}
+
+bool CopyingInputStreamAdaptor::Next(const void** data, int* size) {
+ if (failed_) {
+ // Already failed on a previous read.
+ return false;
+ }
+
+ AllocateBufferIfNeeded();
+
+ if (backup_bytes_ > 0) {
+ // We have data left over from a previous BackUp(), so just return that.
+ *data = buffer_.get() + buffer_used_ - backup_bytes_;
+ *size = backup_bytes_;
+ backup_bytes_ = 0;
+ return true;
+ }
+
+ // Read new data into the buffer.
+ buffer_used_ = copying_stream_->Read(buffer_.get(), buffer_size_);
+ if (buffer_used_ <= 0) {
+ // EOF or read error. We don't need the buffer anymore.
+ if (buffer_used_ < 0) {
+ // Read error (not EOF).
+ failed_ = true;
+ }
+ FreeBuffer();
+ return false;
+ }
+ position_ += buffer_used_;
+
+ *size = buffer_used_;
+ *data = buffer_.get();
+ return true;
+}
+
+void CopyingInputStreamAdaptor::BackUp(int count) {
+ GOOGLE_CHECK(backup_bytes_ == 0 && buffer_.get() != NULL)
+ << " BackUp() can only be called after Next().";
+ GOOGLE_CHECK_LE(count, buffer_used_)
+ << " Can't back up over more bytes than were returned by the last call"
+ " to Next().";
+ GOOGLE_CHECK_GE(count, 0)
+ << " Parameter to BackUp() can't be negative.";
+
+ backup_bytes_ = count;
+}
+
+bool CopyingInputStreamAdaptor::Skip(int count) {
+ GOOGLE_CHECK_GE(count, 0);
+
+ if (failed_) {
+ // Already failed on a previous read.
+ return false;
+ }
+
+ // First skip any bytes left over from a previous BackUp().
+ if (backup_bytes_ >= count) {
+ // We have more data left over than we're trying to skip. Just chop it.
+ backup_bytes_ -= count;
+ return true;
+ }
+
+ count -= backup_bytes_;
+ backup_bytes_ = 0;
+
+ int skipped = copying_stream_->Skip(count);
+ position_ += skipped;
+ return skipped == count;
+}
+
+int64 CopyingInputStreamAdaptor::ByteCount() const {
+ return position_ - backup_bytes_;
+}
+
+void CopyingInputStreamAdaptor::AllocateBufferIfNeeded() {
+ if (buffer_.get() == NULL) {
+ buffer_.reset(new uint8[buffer_size_]);
+ }
+}
+
+void CopyingInputStreamAdaptor::FreeBuffer() {
+ GOOGLE_CHECK_EQ(backup_bytes_, 0);
+ buffer_used_ = 0;
+ buffer_.reset();
+}
+
+// ===================================================================
+
+CopyingOutputStream::~CopyingOutputStream() {}
+
+CopyingOutputStreamAdaptor::CopyingOutputStreamAdaptor(
+ CopyingOutputStream* copying_stream, int block_size)
+ : copying_stream_(copying_stream),
+ owns_copying_stream_(false),
+ failed_(false),
+ position_(0),
+ buffer_size_(block_size > 0 ? block_size : kDefaultBlockSize),
+ buffer_used_(0) {
+}
+
+CopyingOutputStreamAdaptor::~CopyingOutputStreamAdaptor() {
+ WriteBuffer();
+ if (owns_copying_stream_) {
+ delete copying_stream_;
+ }
+}
+
+bool CopyingOutputStreamAdaptor::Flush() {
+ return WriteBuffer();
+}
+
+bool CopyingOutputStreamAdaptor::Next(void** data, int* size) {
+ if (buffer_used_ == buffer_size_) {
+ if (!WriteBuffer()) return false;
+ }
+
+ AllocateBufferIfNeeded();
+
+ *data = buffer_.get() + buffer_used_;
+ *size = buffer_size_ - buffer_used_;
+ buffer_used_ = buffer_size_;
+ return true;
+}
+
+void CopyingOutputStreamAdaptor::BackUp(int count) {
+ GOOGLE_CHECK_GE(count, 0);
+ GOOGLE_CHECK_EQ(buffer_used_, buffer_size_)
+ << " BackUp() can only be called after Next().";
+ GOOGLE_CHECK_LE(count, buffer_used_)
+ << " Can't back up over more bytes than were returned by the last call"
+ " to Next().";
+
+ buffer_used_ -= count;
+}
+
+int64 CopyingOutputStreamAdaptor::ByteCount() const {
+ return position_ + buffer_used_;
+}
+
+bool CopyingOutputStreamAdaptor::WriteBuffer() {
+ if (failed_) {
+ // Already failed on a previous write.
+ return false;
+ }
+
+ if (buffer_used_ == 0) return true;
+
+ if (copying_stream_->Write(buffer_.get(), buffer_used_)) {
+ position_ += buffer_used_;
+ buffer_used_ = 0;
+ return true;
+ } else {
+ failed_ = true;
+ FreeBuffer();
+ return false;
+ }
+}
+
+void CopyingOutputStreamAdaptor::AllocateBufferIfNeeded() {
+ if (buffer_ == NULL) {
+ buffer_.reset(new uint8[buffer_size_]);
+ }
+}
+
+void CopyingOutputStreamAdaptor::FreeBuffer() {
+ buffer_used_ = 0;
+ buffer_.reset();
+}
+
+// ===================================================================
+
+} // namespace io
+} // namespace protobuf
+} // namespace google
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new file mode 100644
index 0000000..172af61
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+ <ReferenceOutputAssembly>false</ReferenceOutputAssembly>
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\ No newline at end of file
diff --git a/ext/post_install_pwiz.cmake b/ext/post_install_pwiz.cmake
new file mode 100644
index 0000000..5bbcf00
--- /dev/null
+++ b/ext/post_install_pwiz.cmake
@@ -0,0 +1,62 @@
+# This is a CMake script for installing ProteoWizard for use in building crux.
+# We have to rename one of the boost libraries and install the Thermo RAW
+# reader DLL
+
+# This script expects two variables to be passed on the command line:
+# BUILD_TYPE, the building configuration: Release or Debug
+# PREFIX, the location to store binaries from the build.
+
+# This macro checks download status codes for errors
+macro (check_status status_code)
+ if (${status_code} EQUAL 0)
+ message(STATUS "Fixed ProteoWizard install.")
+ else ()
+ message(
+ FATAL_ERROR
+ "ProteoWizard install failed"
+ )
+ endif (${status_code} EQUAL 0)
+endmacro (check_status)
+
+if (WIN32 AND NOT CYGWIN)
+ if (${BUILD_TYPE} MATCHES "Debug")
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${PREFIX}/lib/libboost_filesystem-vc120-mt-gd.lib
+ ${PREFIX}/lib/libboost_filesystem-vc120-mt-gd-1_56.lib
+ RESULT_VARIABLE status
+ )
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${PREFIX}/lib/libboost_nowide-vc120-mt-gd.lib
+ ${PREFIX}/lib/libboost_nowide-vc120-mt-gd-1_56.lib
+ RESULT_VARIABLE status
+ )
+ else()
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${PREFIX}/lib/libboost_filesystem-vc120-mt.lib
+ ${PREFIX}/lib/libboost_filesystem-vc120-mt-1_56.lib
+ RESULT_VARIABLE status
+ )
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${PREFIX}/lib/libboost_nowide-vc120-mt.lib
+ ${PREFIX}/lib/libboost_nowide-vc120-mt-1_56.lib
+ RESULT_VARIABLE status
+ )
+ execute_process(
+ COMMAND ${CMAKE_COMMAND} -E copy
+ ${PREFIX}/lib/libboost_chrono-vc120-mt.lib
+ ${PREFIX}/lib/libboost_chrono-vc120-mt-1_56.lib
+ RESULT_VARIABLE status
+ )
+ endif (${BUILD_TYPE} MATCHES "Debug")
+ check_status(status)
+ execute_process(
+ COMMAND regsvr32
+ /s
+ ${PREFIX}/lib/MSFileReader.XRawfile2.dll
+ )
+ # Don't care about status of regsvr32 command
+endif (WIN32 AND NOT CYGWIN)
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index 0000000..d76fb2c
--- /dev/null
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diff --git a/license.txt b/license.txt
new file mode 100644
index 0000000..9176754
--- /dev/null
+++ b/license.txt
@@ -0,0 +1,12 @@
+Copyright 2007-2013 University of Washington
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
diff --git a/make-version-header.cmake b/make-version-header.cmake
new file mode 100644
index 0000000..6818ae1
--- /dev/null
+++ b/make-version-header.cmake
@@ -0,0 +1,24 @@
+if (EXISTS ${CMAKE_SOURCE_DIR}/.svn)
+ include(FindSubversion)
+
+# extract working copy information for SOURCE_DIR into MY_XXX variables
+ Subversion_WC_INFO(${SOURCE_DIR} MY)
+
+ file(WRITE crux_version.h.txt "#define CRUX_VERSION \"${CRUX_VERSION}.${MY_WC_REVISION}\"\n")
+
+# Copy the file to the final header only if the version changes
+# reduces needless rebuilds
+ execute_process(
+ COMMAND
+ ${CMAKE_COMMAND} -E copy_if_different crux_version.h.txt crux_version.h
+ )
+else (EXISTS ${CMAKE_SOURCE_DIR}/.svn)
+ file(WRITE crux_version.h.txt "#define CRUX_VERSION \"${CRUX_VERSION}\"\n")
+
+# Copy the file to the final header only if the version changes
+# reduces needless rebuilds
+ execute_process(
+ COMMAND
+ ${CMAKE_COMMAND} -E copy_if_different crux_version.h.txt crux_version.h
+ )
+endif (EXISTS ${CMAKE_SOURCE_DIR}/.svn)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 0000000..46e3091
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,445 @@
+cmake_minimum_required(VERSION 2.8.4)
+cmake_policy(VERSION 2.8.4)
+
+add_subdirectory(app/bullseye)
+add_subdirectory(app/hardklor)
+add_subdirectory(app/qranker-barista)
+add_subdirectory(app/xlink)
+add_subdirectory(app/tide)
+
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+include_directories(.)
+include_directories(app/bullseye)
+include_directories(app/hardklor)
+include_directories(app/qranker-barista)
+include_directories(app/xlink)
+include_directories(${CMAKE_SOURCE_DIR}/src/io)
+include_directories(${CMAKE_SOURCE_DIR}/ext)
+include_directories(${CMAKE_BINARY_DIR})
+include_directories(${CMAKE_BINARY_DIR}/ext)
+include_directories(${CMAKE_BINARY_DIR}/ext/include)
+include_directories(${CMAKE_BINARY_DIR}/ext/include/CometSearch)
+include_directories(${CMAKE_BINARY_DIR}/ext/include/MSToolkit)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_1_56_0)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_aux)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/percolator/src/)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/percolator/src/fido)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/percolator/src/picked_protein)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/percolator-build/src/)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/percolator-build/src/fido)
+include_directories(${CMAKE_CURRENT_BINARY_DIR}/app/tide/protoobj)
+if (WIN32 AND NOT Cygwin)
+ # Needed to put DLL containing type libraries
+ # in include path for Windows
+ include_directories(${CMAKE_BINARY_DIR}/ext/lib)
+ # Needed to include gflags/gflags.h on Windows
+ include_directories(${CMAKE_BINARY_DIR}/ext/build/src/google-gflags/src/windows)
+ # Needed to include google/protobuf on Windows
+ include_directories(${CMAKE_BINARY_DIR}/ext/build/src/protobuf-2.5.0/src)
+ SET(
+ CMAKE_EXE_LINKER_FLAGS
+ "${CMAKE_EXE_LINKER_FLAGS} /VERBOSE:LIB /NODEFAULTLIB:libboost_date_time-vc120-mt-1_56 /NODEFAULTLIB:libboost_system-vc120-mt-1_56 /NODEFAULTLIB:libboost_thread-vc120-mt-1_56"
+ )
+ SET(
+ CMAKE_EXE_LINKER_FLAGS_DEBUG
+ "${CMAKE_EXE_LINKER_FLAGS}
+ /VERBOSE:LIB /NODEFAULTLIB:libboost_chrono-vc120-mt-gd-1_56 /NODEFAULTLIB:libboost_date_time-vc120-mt-gd-1_56 /NODEFAULTLIB:libboost_system-vc120-mt-gd-1_56 /NODEFAULTLIB:libboost_thread-vc120-mt-gd-1_56"
+)
+ # Need Comet base directory for Windows
+ include_directories(${CMAKE_BINARY_DIR}/ext/build/src/comet/)
+
+ # On Windows we should build vendor libraries by default
+ if (NOT DEFINED INCLUDE_VENDOR_LIBRARIES)
+ set(INCLUDE_VENDOR_LIBRARIES TRUE)
+ endif (NOT DEFINED INCLUDE_VENDOR_LIBRARIES)
+
+endif (WIN32 AND NOT Cygwin)
+
+link_directories(.)
+link_directories(./app/bullseye)
+link_directories(./app/hardklor)
+link_directories(./app/qranker-barista)
+link_directories(./app/xlink)
+link_directories(${CMAKE_BINARY_DIR}/ext/lib)
+link_directories(${CMAKE_BINARY_DIR}/ext/build/src/percolator-build/src)
+link_directories(${CMAKE_BINARY_DIR}/ext/build/src/percolator-build/src/fido)
+link_directories(${CMAKE_BINARY_DIR}/ext/build/src/percolator-build/src/picked_protein)
+if (WIN32 AND NOT Cygwin)
+ # Needed for windows build of vendor libraries
+ if (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ link_directories(
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/pwiz_aux/msrc/utility/vendor_api/Waters/vc12_x64
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/pwiz_aux/msrc/utility/vendor_api/Bruker/x64
+ )
+ else (CMAKE_GENERATOR MATCHES "^.*Win64$")
+ link_directories(
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/pwiz_aux/msrc/utility/vendor_api/Waters/vc12_x86
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/pwiz_aux/msrc/utility/vendor_api/Bruker/x86
+ )
+ endif (CMAKE_GENERATOR MATCHES "^.*Win64$")
+endif (WIN32 AND NOT Cygwin)
+
+set (
+ crux_lib_files
+ app/SubtractIndexApplication.cpp
+ app/CascadeSearchApplication.cpp
+ app/AssignConfidenceApplication.cpp
+ util/Alphabet.cpp
+ util/AminoAcidUtil.cpp
+ util/ArgParser.cpp
+ util/CacheableMass.cpp
+ util/GlobalParams.cpp
+ io/carp.cpp
+ util/CarpStreamBuf.cpp
+ app/CometApplication.cpp
+ app/ComputeQValues.cpp
+ app/CreateDocs.cpp
+ util/crux-utils.cpp
+ model/Database.cpp
+ model/DatabaseProteinIterator.cpp
+ model/DatabasePeptideIterator.cpp
+ app/CruxApplication.cpp
+ app/CruxApplicationList.cpp
+ io/DelimitedFile.cpp
+ io/DelimitedFileReader.cpp
+ io/DelimitedFileWriter.cpp
+ app/ExtractColumns.cpp
+ app/ExtractRows.cpp
+ util/FileUtils.cpp
+ model/FilteredSpectrumChargeIterator.cpp
+ model/GeneratePeptidesIterator.cpp
+ app/GetMs2Spectrum.cpp
+ io/HTMLWriter.cpp
+ model/Ion.cpp
+ model/IonConstraint.cpp
+ model/IonFilteredIterator.cpp
+ model/IonSeries.cpp
+ util/linked_list.cpp
+ io/LineFileReader.cpp
+ util/mass.cpp
+ app/MakePinApplication.cpp
+ model/Match.cpp
+ io/MatchColumns.cpp
+ io/MatchFileReader.cpp
+ io/MatchFileWriter.cpp
+ model/MatchCollection.cpp
+ model/MatchCollectionIterator.cpp
+ io/MatchCollectionParser.cpp
+ model/MatchIterator.cpp
+ util/MathUtil.cpp
+ model/Modification.cpp
+ util/modifications.cpp
+ model/ModifiedPeptidesIterator.cpp
+ io/MSToolkitSpectrumCollection.cpp
+ io/MzIdentMLReader.cpp
+ io/MzIdentMLWriter.cpp
+ io/OutputFiles.cpp
+ parameter.cpp
+ app/ParamMedicApplication.cpp
+ util/Params.cpp
+ model/Peak.cpp
+ model/Peptide.cpp
+ model/PeptideConstraint.cpp
+ util/peptide_modifications.cpp
+ model/PeptideSrc.cpp
+ io/PepXMLReader.cpp
+ io/PepXMLWriter.cpp
+ app/PercolatorAdapter.cpp
+ app/PercolatorApplication.cpp
+ io/PinWriter.cpp
+ app/Pipeline.cpp
+ app/GeneratePeptides.cpp
+ model/PostProcessProtein.cpp
+ app/PredictPeptideIons.cpp
+ app/PrintProcessedSpectra.cpp
+ app/PrintVersion.cpp
+ model/Protein.cpp
+ model/ProteinPeptideIterator.cpp
+ model/ProteinIndex.cpp
+ model/ProteinIndexIterator.cpp
+ model/ProteinMatchCollection.cpp
+ app/PSMConvertApplication.cpp
+ io/PSMReader.cpp
+ io/PSMWriter.cpp
+ model/AbstractMatch.cpp
+ model/ProteinMatch.cpp
+ model/PeptideMatch.cpp
+ io/PMCDelimitedFileWriter.cpp
+ io/PMCPepXMLWriter.cpp
+ io/PMCSQTWriter.cpp
+ model/SpectrumMatch.cpp
+ io/PWIZSpectrumCollection.cpp
+ app/ReadSpectrumRecordsApplication.cpp
+ app/ReadTideIndex.cpp
+ app/SortColumn.cpp
+ model/Scorer.cpp
+ app/SpectralCounts.cpp
+ io/SpectrumCollection.cpp
+ io/SpectrumCollectionFactory.cpp
+ model/Spectrum.cpp
+ io/SpectrumRecordWriter.cpp
+ model/SpectrumZState.cpp
+ app/StatColumn.cpp
+ util/StringUtils.cpp
+ io/SQTReader.cpp
+ io/SQTWriter.cpp
+ app/TideIndexApplication.cpp
+ app/TideMatchSet.cpp
+ app/TideSearchApplication.cpp
+ util/utils.cpp
+)
+
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set(
+ crux_lib_files
+ ${crux_lib_files}
+ util/WinCrux.cpp
+ )
+endif (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+add_library(
+ crux-support
+ STATIC
+ ${crux_lib_files}
+)
+add_dependencies(crux-support tide-support)
+
+if (APPLE)
+ set(OPENMP_FOUND FALSE)
+else(APPLE)
+ find_package(OpenMP)
+ if (OPENMP_FOUND)
+ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+ endif(OPENMP_FOUND)
+endif(APPLE)
+
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -DDEBUG")
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELWITHDEBINFO} -DNDEBUG")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -DNDEBUG")
+
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ APPEND
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _CRT_SECURE_NO_WARNINGS
+ NOMINMAX
+ )
+else (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ APPEND
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _LARGEFILE_SOURCE
+ _LARGEFILE64_SOURCE
+ _BSD_SOURCE
+ _POSIX_C_SOURCE=199506L
+ _FILE_OFFSET_BITS=64
+ _GNU_SOURCE
+ GCC
+ CRUX
+ HAVE_EXPAT_CONFIG_H
+ )
+ if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ set_property(
+ DIRECTORY
+ APPEND
+ PROPERTY
+ COMPILE_DEFINITIONS
+ DARWIN
+ _DARWIN_C_SOURCE
+ )
+ if (${CMAKE_SYSTEM_VERSION} VERSION_LESS "12")
+ set_property(
+ DIRECTORY
+ APPEND
+ PROPERTY
+ COMPILE_DEFINITIONS
+ PRE_MOUNTAIN_LION
+ )
+ endif (${CMAKE_SYSTEM_VERSION} VERSION_LESS "12")
+ if (${CMAKE_SYSTEM_VERSION} VERSION_LESS "11")
+ set_property(
+ DIRECTORY
+ APPEND
+ PROPERTY
+ COMPILE_DEFINITIONS
+ PRE_LION
+ )
+ endif(${CMAKE_SYSTEM_VERSION} VERSION_LESS "11")
+ endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+endif (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+add_executable(crux crux-main.cpp)
+if (WIN32 AND NOT CYGWIN)
+ set_property(
+ TARGET crux
+ PROPERTY
+ COMPILE_DEFINITIONS
+ MAIN
+ GFLAGS_DLL_DECL=
+ GFLAGS_DLL_DECLARE_FLAG=
+ GFLAGS_DLL_DEFINE_FLAG=
+ )
+else (WIN32 AND NOT CYGWIN)
+ set_property(
+ TARGET
+ crux
+ PROPERTY
+ COMPILE_DEFINITIONS
+ MAIN
+ )
+endif (WIN32 AND NOT CYGWIN)
+
+if (WIN32 AND NOT CYGWIN)
+ # These definititions are needed to set the
+ # the proper calling conventions (static lib)
+ # for Boost and expat. Expat is used in the
+ # MSToolkit library.
+ add_definitions(-DBOOST_ALL_NO_LIB)
+ add_definitions(-DXML_STATIC)
+ if (INCLUDE_VENDOR_LIBRARIES)
+ add_definitions(-DINCLUDE_VENDOR_LIBRARIES)
+ endif (INCLUDE_VENDOR_LIBRARIES)
+endif (WIN32 AND NOT CYGWIN)
+
+# The rt library is not needed for OS X
+if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ set(RT_LIBRARY "")
+else(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ set(RT_LIBRARY "rt")
+endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+if (WIN32 AND NOT CYGWIN)
+ if (INCLUDE_VENDOR_LIBRARIES)
+ set (
+ PWIZ_LIBRARIES
+ libpwiz_data_identdata
+ libpwiz_data_identdata_version
+ libpwiz_data_misc
+ libpwiz_data_msdata
+ libpwiz_data_msdata_version
+ libpwiz_data_proteome
+ libpwiz_data_common
+ libpwiz_data_vendor_readers
+ libpwiz_reader_abi
+ libpwiz_reader_abi_t2d
+ libpwiz_reader_agilent
+ libpwiz_reader_shimadzu
+ libpwiz_reader_thermo
+ libpwiz_reader_waters
+ libpwiz_vendor_api_abi
+ libpwiz_vendor_api_agilent
+ libpwiz_vendor_api_shimadzu
+ libpwiz_vendor_api_thermo
+ libpwiz_utility_chemistry
+ libpwiz_utility_minimxml
+ libpwiz_utility_misc
+ libpwiz_version
+ libSHA1
+ libzlib
+ MassLynxRaw
+ cdt
+ )
+ else (INCLUDE_VENDOR_LIBRARIES)
+ set (
+ PWIZ_LIBRARIES
+ libpwiz_data_identdata
+ libpwiz_data_identdata_version
+ libpwiz_data_misc
+ libpwiz_data_msdata
+ libpwiz_data_msdata_version
+ libpwiz_data_proteome
+ libpwiz_data_common
+ libpwiz_utility_chemistry
+ libpwiz_utility_minimxml
+ libpwiz_utility_misc
+ libpwiz_version
+ libSHA1
+ libzlib
+ )
+ endif (INCLUDE_VENDOR_LIBRARIES)
+ target_link_libraries(
+ crux
+ barista
+ bullseye
+ hardklor
+ cometsearch
+ perclibrary
+ fido
+ picked_protein
+ xlink
+ gflags
+ crux-support
+ tide-support
+ mstoolkitlite
+ protobuf
+ ${PWIZ_LIBRARIES}
+ ws2_32
+ shlwapi
+ optimized libboost_system-vc120-mt
+ optimized libboost_iostreams-vc120-mt
+ optimized libboost_nowide-vc120-mt
+ optimized libboost_filesystem-vc120-mt
+ optimized libboost_thread-vc120-mt
+ optimized libboost_chrono-vc120-mt
+ debug libboost_system-vc120-mt-gd
+ debug libboost_iostreams-vc120-mt-gd
+ debug libboost_nowide-vc120-mt-gd
+ debug libboost_filesystem-vc120-mt-gd
+ debug libboost_thread-vc120-mt-gd
+ debug libboost_chrono-vc120-mt-gd
+ )
+else()
+ target_link_libraries(
+ crux
+ xlink
+ barista
+ bullseye
+ crux-support
+ tide-support
+ protobuf
+ gflags
+ cometsearch
+ dl
+ hardklor
+ m
+ ${RT_LIBRARY}
+ mstoolkitlite
+ perclibrary
+ fido
+ picked_protein
+ pwiz_data_identdata
+ pwiz_data_identdata_version
+ pwiz_data_misc
+ pwiz_data_msdata
+ pwiz_data_msdata_version
+ pwiz_data_proteome
+ pwiz_data_common
+ pwiz_utility_chemistry
+ pwiz_utility_minimxml
+ pwiz_utility_misc
+ pwiz_version
+ SHA1
+ boost_system-mt-s
+ boost_iostreams-mt-s
+ z-mt-s-1_2
+ boost_filesystem-mt-s
+ boost_thread-mt-s
+ boost_chrono
+ boost_filesystem
+ boost_system
+ pthread
+ )
+endif(WIN32 AND NOT CYGWIN)
+
+install (
+ TARGETS
+ crux
+ DESTINATION
+ bin
+)
+
diff --git a/src/Makefile b/src/Makefile
new file mode 100644
index 0000000..aad9066
--- /dev/null
+++ b/src/Makefile
@@ -0,0 +1,3111 @@
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+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
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+
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+# The top-level source directory on which CMake was run.
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+
+# The top-level build directory on which CMake was run.
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+
+#=============================================================================
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+ @echo "... util/GlobalParams.o"
+ @echo "... util/GlobalParams.i"
+ @echo "... util/GlobalParams.s"
+ @echo "... util/MathUtil.o"
+ @echo "... util/MathUtil.i"
+ @echo "... util/MathUtil.s"
+ @echo "... util/Params.o"
+ @echo "... util/Params.i"
+ @echo "... util/Params.s"
+ @echo "... util/StringUtils.o"
+ @echo "... util/StringUtils.i"
+ @echo "... util/StringUtils.s"
+ @echo "... util/crux-utils.o"
+ @echo "... util/crux-utils.i"
+ @echo "... util/crux-utils.s"
+ @echo "... util/linked_list.o"
+ @echo "... util/linked_list.i"
+ @echo "... util/linked_list.s"
+ @echo "... util/mass.o"
+ @echo "... util/mass.i"
+ @echo "... util/mass.s"
+ @echo "... util/modifications.o"
+ @echo "... util/modifications.i"
+ @echo "... util/modifications.s"
+ @echo "... util/peptide_modifications.o"
+ @echo "... util/peptide_modifications.i"
+ @echo "... util/peptide_modifications.s"
+ @echo "... util/utils.o"
+ @echo "... util/utils.i"
+ @echo "... util/utils.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+
diff --git a/src/Makefile.mzidentml b/src/Makefile.mzidentml
new file mode 100644
index 0000000..b3d6a76
--- /dev/null
+++ b/src/Makefile.mzidentml
@@ -0,0 +1,44 @@
+
+PWIZ_DIR=../external/include
+
+CC=g++
+COPTS=-I../external/include
+
+MST_LIB=-L../external/MSToolkit/ -lMSToolkit
+CRUX_LIB=-L. -lcrux-support
+
+PWIZ_LIB_FILES = \
+ -lpwiz_data_msdata \
+ -lpwiz_data_common \
+ -lpwiz_data_identdata \
+ -lpwiz_data_msdata_version \
+ -lpwiz_data_misc \
+ -lpwiz_utility_chemistry \
+ -lpwiz_utility_misc \
+ -lpwiz_utility_minimxml \
+ -lpwiz_data_common \
+ -lpwiz_data_identdata \
+ -lpwiz_data_identdata_version \
+ -lpwiz_data_proteome \
+ -lboost_system-mt-s \
+ -lboost_iostreams-mt-s \
+ -lz-mt-s-1_2 \
+ -lboost_filesystem-mt-s \
+ -lboost_regex-mt-s \
+ -lboost_thread-mt-s \
+ -lpthread
+
+PWIZ_LIB=-L../external/lib ${PWIZ_LIB_FILES}
+
+
+all:mzid
+
+
+mzid.o:mzid.cpp
+ g++ ${COPTS} -c mzid.cpp -o mzid.o
+
+mzid:mzid.o
+ g++ mzid.o ${CRUX_LIB} ${MST_LIB} ${PWIZ_LIB} -o mzid
+
+clean:
+ rm -f mzid MzIdentMLReader.o
diff --git a/src/app/AssignConfidenceApplication.cpp b/src/app/AssignConfidenceApplication.cpp
new file mode 100644
index 0000000..8f31fc3
--- /dev/null
+++ b/src/app/AssignConfidenceApplication.cpp
@@ -0,0 +1,1247 @@
+/**
+* \file AssignConfidenceApplication.h
+* AUTHOR: Attila Kertesz-Farkas
+* CREATE DATE: May 01, 2015
+****************************************************************************/
+
+#include "AssignConfidenceApplication.h"
+#include "io/MatchCollectionParser.h"
+#include "PosteriorEstimator.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+#include "boost/tuple/tuple.hpp" // This will be <tuple> once we move to C++11.
+#include "boost/tuple/tuple_comparison.hpp"
+
+#include <map>
+#include <utility>
+
+using namespace std;
+using namespace Crux;
+
+static const int MAX_PSMS = 10000000;
+// 14th decimal place
+static const double EPSILON = 0.00000000000001;
+
+#ifdef _MSC_VER
+// The Microsoft 10.0 C++ compiler has trouble resolving the proper virtual
+// function call when the STL make_pair is combined with the STL ptr_fun.
+// They promise to fix this in v11, but until then we create our own wrapper
+// for this use of make_pair. (See corresponding ifdef block in compute_PEP)
+pair<double, bool> make_pair(double db, bool b);
+// pair<double,bool> make_pair(double db, bool b) {
+// return std::pair<double,bool>(db, b);
+// }
+#endif
+
+
+/**
+* \returns a blank ComputeQValues object
+*/
+AssignConfidenceApplication::AssignConfidenceApplication():
+ spectrum_flag_(NULL), iteration_cnt_(0) {
+}
+
+/**
+* Destructor
+*/
+AssignConfidenceApplication::~AssignConfidenceApplication() {
+}
+
+/**
+ * Generate keys when building a hash on PSMs.
+ * http://stackoverflow.com/questions/98153/whats-the-best-hashing-algorithm-to-use-on-a-stl-string-when-using-hash-map/
+ */
+int stringToIndex(string myString) {
+ int returnValue = 0;
+ for(std::string::iterator it = myString.begin(); it != myString.end(); ++it) {
+ returnValue = (returnValue * 101) + (int)*it;
+ }
+ return(returnValue);
+}
+
+/**
+* main method for ComputeQValues
+*/
+
+int AssignConfidenceApplication::main(int argc, char** argv) {
+ return main(Params::GetStrings("target input"));
+}
+
+int AssignConfidenceApplication::main(const vector<string> input_files) {
+ // Prepare the output files if not in Cascade Search
+ if (spectrum_flag_ == NULL) {
+ output_ = new OutputFiles(this);
+ }
+
+ ESTIMATION_METHOD_T estimation_method;
+ string method_param = Params::GetString("estimation-method");
+ carp(CARP_INFO, "Estimation method = %s.", method_param.c_str());
+ if (method_param == "tdc") {
+ estimation_method = TDC_METHOD;
+ } else if (method_param == "mix-max") {
+ estimation_method = MIXMAX_METHOD;
+ } else if (method_param == "peptide-level") {
+ estimation_method = PEPTIDE_LEVEL_METHOD;
+ } else {
+ carp(CARP_FATAL, "The estimation method \"%s\" is not supported.", method_param.c_str());
+ }
+
+ // Perform the analysis.
+ if (input_files.size() == 0) {
+ carp(CARP_FATAL, "No input files found.");
+ }
+ if (estimation_method != PEPTIDE_LEVEL_METHOD &&
+ Params::GetBool("combine-modified-peptides")) {
+ carp(CARP_WARNING, "The \"combine-modified-peptides\" option is ignored when estimation-method is not peptide-level.");
+ }
+ bool sidak = Params::GetBool("sidak");
+
+ int top_match = 1;
+ if (estimation_method == PEPTIDE_LEVEL_METHOD) {
+ top_match = MAX_PSMS+1;
+ }
+
+ SCORER_TYPE_T score_type = INVALID_SCORER_TYPE;
+ SCORER_TYPE_T derived_score_type = INVALID_SCORER_TYPE;
+ bool ascending;
+
+ string score_param = Params::GetString("score");
+ if (!score_param.empty()) {
+ switch (get_column_idx(score_param.c_str())) {
+ case SP_SCORE_COL:
+ score_type = SP; ///< SEQUEST preliminary score
+ break;
+ case XCORR_SCORE_COL:
+ score_type = XCORR; ///< SEQUEST primary score
+ break;
+ case EVALUE_COL:
+ score_type = EVALUE; ///< Comet e-value
+ break;
+ case PVALUE_COL: ///< Search-for-xlinks p-value
+ score_type = LOGP_BONF_WEIBULL_XCORR;
+ break;
+ case PERCOLATOR_SCORE_COL:
+ score_type = PERCOLATOR_SCORE;
+ break;
+ case PERCOLATOR_QVALUE_COL:
+ score_type = PERCOLATOR_QVALUE;
+ break;
+ case PERCOLATOR_PEP_COL:
+ score_type = PERCOLATOR_PEP;
+ break;
+ case QRANKER_SCORE_COL:
+ score_type = QRANKER_SCORE;
+ break;
+ case QRANKER_QVALUE_COL:
+ score_type = QRANKER_QVALUE;
+ break;
+ case QRANKER_PEP_COL:
+ score_type = QRANKER_PEP;
+ break;
+ case BARISTA_SCORE_COL:
+ score_type = BARISTA_SCORE;
+ break;
+ case BARISTA_QVALUE_COL:
+ score_type = BARISTA_QVALUE;
+ break;
+ case EXACT_PVALUE_COL:
+ score_type = TIDE_SEARCH_EXACT_PVAL;
+ break;
+ case REFACTORED_SCORE_COL:
+ score_type = TIDE_SEARCH_REFACTORED_XCORR;
+ break;
+ case ELUTION_WINDOW_COL:
+ score_type = TIDE_SEARCH_EXACT_SMOOTHED;
+ break;
+ default:
+ carp(CARP_FATAL, "The PSM feature \"%s\" is not supported.", score_param.c_str());
+ }
+ }
+
+ if (sidak && score_type != TIDE_SEARCH_EXACT_PVAL) {
+ carp(CARP_WARNING, "Sidak adjustment may not be compatible"
+ "with score: %s", score_param.c_str());
+ }
+
+ // Create two match collections, for targets and decoys.
+ MatchCollection* decoy_matches = new MatchCollection();
+ MatchCollection* target_matches = new MatchCollection();
+
+ bool distinct_matches = false;
+ MatchCollectionParser parser;
+ std::map<string, FLOAT_T> BestPeptideScore;
+
+ for (vector<string>::const_iterator iter = input_files.begin(); iter != input_files.end(); ++iter) {
+ string target_path = *iter;
+ string decoy_path = *iter;
+
+ if (target_path.find("decoy") != string::npos) {
+ carp(CARP_FATAL, "%s appears to be a decoy file. Only target or concatenated files "
+ "should be given to assign-confidence because it automatically searches for "
+ "corresponding decoy files.", target_path.c_str());
+ }
+
+ check_target_decoy_files(target_path, decoy_path);
+
+ if (!FileUtils::Exists(target_path)) {
+ carp(CARP_FATAL, "Target file %s not found", target_path.c_str());
+ }
+
+ if (!FileUtils::Exists(decoy_path)) {
+ if (estimation_method == MIXMAX_METHOD) {
+ carp(CARP_FATAL, "Cannot find file %s.", decoy_path.c_str());
+ carp(CARP_FATAL, "Decoy file from separate target-decoy search is required "
+ "for mix-max q-value calculation");
+ }
+ carp(CARP_DEBUG, "Decoy file %s not found", decoy_path.c_str());
+ decoy_path = "";
+ }
+
+ MatchCollection* match_collection =
+ parser.create(target_path, Params::GetString("protein-database"));
+ distinct_matches = match_collection->getHasDistinctMatches();
+
+ carp(CARP_INFO, "Found %d PSMs in %s.", match_collection->getMatchTotal(),
+ target_path.c_str());
+
+ // If necessary, automatically identify the score type.
+ if (score_type == INVALID_SCORER_TYPE) {
+ vector<SCORER_TYPE_T> scoreTypes;
+ scoreTypes.push_back(XCORR);
+ scoreTypes.push_back(EVALUE);
+ scoreTypes.push_back(TIDE_SEARCH_EXACT_PVAL);
+ scoreTypes.push_back(TIDE_SEARCH_EXACT_SMOOTHED);
+ scoreTypes.push_back(LOGP_BONF_WEIBULL_XCORR);
+ scoreTypes.push_back(PERCOLATOR_SCORE);
+ for (vector<SCORER_TYPE_T>::const_iterator i = scoreTypes.begin();
+ i != scoreTypes.end();
+ i++) {
+ if (match_collection->getScoredType(*i)) {
+ score_type = *i;
+ carp(CARP_INFO, "Automatically detected score type: %s",
+ scorer_type_to_string(score_type));
+ break;
+ }
+ }
+ if (score_type == INVALID_SCORER_TYPE) {
+ carp(CARP_FATAL, "Could not detect score type. Specify the score type using the "
+ "\"score\" parameter.");
+ }
+ }
+ int direction = getDirection(score_type);
+ if (direction == -1) {
+ ascending = false;
+ } else if (direction == 1) {
+ ascending = true;
+ } else {
+ carp(CARP_FATAL, "Cannot infer sort order for score %s.",
+ scorer_type_to_string(score_type));
+ }
+ carp(CARP_INFO, "Score type=%s, sorting in %s order",
+ scorer_type_to_string(score_type),
+ ascending ? "ascending" : "descending");
+
+ if (!match_collection->getScoredType(score_type)) {
+ const char* score_str = scorer_type_to_string(score_type);
+ carp(CARP_FATAL, "The PSM feature \"%s\" was not found in file \"%s\".",
+ score_str, target_path.c_str());
+ }
+
+ // Find and keep the best score for each peptide.
+ if (estimation_method == PEPTIDE_LEVEL_METHOD) {
+ peptide_level_filtering(match_collection, &BestPeptideScore, score_type, ascending);
+ carp(CARP_INFO, "%d distinct target peptides.", BestPeptideScore.size());
+ }
+
+ target_matches->setScoredType(score_type, match_collection->getScoredType(score_type));
+ target_matches->setScoredType(EVALUE, match_collection->getScoredType(EVALUE));
+ target_matches->setScoredType(DELTA_CN, match_collection->getScoredType(DELTA_CN));
+ target_matches->setScoredType(SP, match_collection->getScoredType(SP));
+ target_matches->setScoredType(BY_IONS_MATCHED, match_collection->getScoredType(BY_IONS_MATCHED));
+ target_matches->setScoredType(BY_IONS_TOTAL, match_collection->getScoredType(BY_IONS_TOTAL));
+ target_matches->setScoredType(SIDAK_ADJUSTED, sidak);
+ decoy_matches->setScoredType(SIDAK_ADJUSTED, sidak);
+
+ // Counters just to let the user know what's up.
+ int num_target_rank_skipped = 0;
+ int num_decoy_rank_skipped = 0;
+ int num_target_peptide_skipped = 0;
+ int num_decoy_peptide_skipped = 0;
+
+ if (decoy_path != "") {
+ MatchCollection* temp_collection = parser.create(decoy_path, Params::GetString("protein-database"));
+ carp(CARP_INFO, "Found %d PSMs in %s.", temp_collection->getMatchTotal(),
+ decoy_path.c_str());
+
+ // Mark decoy matches
+ // key = (filename, scan number, charge, rank); value = index
+ std::map<boost::tuple <int, int, int, int>, int> pairidx;
+ int fileIndex;
+ int scanid;
+ int charge;
+ int rank;
+ int cnt = 0;
+ MatchIterator* temp_iter = new MatchIterator(temp_collection);
+ while (temp_iter->hasNext()) {
+ Crux::Match* decoy_match = temp_iter->next();
+ cnt++;
+
+ // Only use top-ranked matches.
+ if (decoy_match->getRank(XCORR) > top_match) {
+ num_decoy_rank_skipped++;
+ continue;
+ }
+
+ fileIndex = stringToIndex(decoy_match->getSpectrum()->getFullFilename());
+ scanid = decoy_match->getSpectrum()->getFirstScan();
+ charge = decoy_match->getCharge();
+ rank = decoy_match->getRank(XCORR);
+ boost::tuple<int, int, int, int> myTuple (fileIndex, scanid, charge, rank);
+
+ decoy_match->setNullPeptide(true);
+ switch (estimation_method) {
+ case MIXMAX_METHOD:
+ // Put match directly in the final set of decoys, because no TDC.
+ decoy_matches->addMatch(decoy_match);
+ break;
+ case TDC_METHOD:
+ case PEPTIDE_LEVEL_METHOD:
+ // If the PSM is already there, that means there was a tie
+ // for top-ranked decoys. In that case, there is no need to
+ // store a pointer to the second one.
+ if (pairidx[myTuple] == 0) {
+ pairidx[myTuple] = cnt;
+ }
+ break;
+ case NUMBER_METHOD_TYPES:
+ case INVALID_METHOD:
+ carp(CARP_FATAL, "No estimation method specified.");
+ }
+ }
+ delete temp_iter;
+
+ // Find and keep the best score for each decoy peptide.
+ if (estimation_method == PEPTIDE_LEVEL_METHOD) {
+ peptide_level_filtering(temp_collection, &BestPeptideScore, score_type, ascending);
+ carp(CARP_INFO, "%d distinct target+decoy peptides.", BestPeptideScore.size());
+ }
+
+ if (estimation_method != MIXMAX_METHOD) {
+ int decoy_idx;
+ int numCandidates;
+ int numCompetitions = 0;
+ int numLostDecoys = 0;
+ int numTies = 0;
+ MatchCollection* tdc_collection = new MatchCollection();
+ tdc_collection->setScoredType(score_type, true);
+ MatchIterator* target_iter = new MatchIterator(match_collection);
+ MatchIterator* decoy_iter = new MatchIterator(temp_collection);
+ while (target_iter->hasNext()) {
+ Crux::Match* target_match = target_iter->next();
+
+ // Only use top-ranked matches.
+ if (target_match->getRank(XCORR) > top_match) {
+ num_target_rank_skipped++;
+ continue;
+ }
+
+ // Retrieve the index of the corresponding decoy PSM.
+ Crux::Match* decoy_match;
+ fileIndex = stringToIndex(target_match->getSpectrum()->getFullFilename());
+ scanid = target_match->getSpectrum()->getFirstScan();
+ charge = target_match->getCharge();
+ rank = target_match->getRank(XCORR);
+ decoy_idx = pairidx[boost::tuple <int, int, int, int>
+ (fileIndex, scanid, charge, rank)];
+ if (decoy_idx == 0) {
+ carp(CARP_DEBUG,
+ "Failed to find decoy for file=%s scan=%d charge=%d rank=%d.",
+ target_match->getSpectrum()->getFullFilename(),
+ scanid, charge, rank);
+ numLostDecoys++;
+ }
+
+ if (estimation_method == PEPTIDE_LEVEL_METHOD) {
+ if (decoy_idx > 0) {
+ decoy_match = decoy_iter->getMatch(decoy_idx - 1);
+ numCandidates = target_match->getTargetExperimentSize() + decoy_match->getTargetExperimentSize();
+ target_match->setTargetExperimentSize(numCandidates);
+ decoy_match->setTargetExperimentSize(numCandidates);
+ tdc_collection->addMatch(target_match);
+ tdc_collection->addMatch(decoy_match);
+ } else {
+ numCandidates = target_match->getTargetExperimentSize();
+ target_match->setTargetExperimentSize(numCandidates);
+ tdc_collection->addMatch(target_match);
+ }
+ } else {
+ if (decoy_idx > 0) {
+ decoy_match = decoy_iter->getMatch(decoy_idx - 1);
+ } else {
+ tdc_collection->addMatch(target_match);
+ continue;
+ }
+ numCandidates = target_match->getTargetExperimentSize() + decoy_match->getTargetExperimentSize();
+ target_match->setTargetExperimentSize(numCandidates);
+ decoy_match->setTargetExperimentSize(numCandidates);
+
+ // This is where the target-decoy competition happens.
+ carp(CARP_DEBUG, "TDC: Comparing target (%d, +%d) with score %g to decoy (%d, +%d) with score %g.",
+ target_match->getSpectrum()->getFirstScan(),
+ target_match->getCharge(),
+ target_match->getScore(score_type),
+ decoy_match->getSpectrum()->getFirstScan(),
+ decoy_match->getCharge(),
+ decoy_match->getScore(score_type));
+
+ float score_difference = target_match->getScore(score_type) - decoy_match->getScore(score_type);
+ numCompetitions++;
+ // Randomly break ties.
+ if (fabs(score_difference) < 1e-10) {
+ numTies++;
+ score_difference += 0.5 - ((double)myrandom() / UNIFORM_INT_DISTRIBUTION_MAX);
+ }
+ if (ascending) { // smaller scores are better
+ score_difference *= -1.0;
+ }
+ if (score_difference >= 0.0) {
+ tdc_collection->addMatch(target_match);
+ } else {
+ tdc_collection->addMatch(decoy_match);
+ }
+ }
+ }
+ delete target_iter;
+ delete decoy_iter;
+ delete match_collection;
+ match_collection = tdc_collection;
+ if (numCompetitions > 0) {
+ carp(CARP_INFO, "Randomly broke %d ties in %d target-decoy competitions.",
+ numTies, numCompetitions);
+ }
+ if (numLostDecoys > 0) {
+ carp(CARP_INFO, "Failed to find %d decoys.", numLostDecoys);
+ }
+ }
+ delete temp_collection;
+ }
+
+ // Iterate, gathering matches into one or two collections.
+ MatchIterator* match_iterator =
+ new MatchIterator(match_collection, score_type, false);
+ double sidak_adjustment;
+ while (match_iterator->hasNext()) {
+ Match* match = match_iterator->next();
+ bool is_decoy = match->getNullPeptide();
+
+ // Only use top-ranked matches.
+ if (match->getRank(XCORR) > top_match) {
+ if (is_decoy) {
+ num_decoy_rank_skipped++;
+ } else {
+ num_target_rank_skipped++;
+ }
+ continue;
+ }
+
+ // Find and keep the best score for each decoy peptide.
+ if (estimation_method == PEPTIDE_LEVEL_METHOD) {
+ FLOAT_T score = match->getScore(score_type);
+ string peptideStr = getPeptideSeq(match);
+
+ FLOAT_T bestScore;
+ try {
+ bestScore = BestPeptideScore.at(peptideStr);
+ if (bestScore != score) { //not the best scoring peptide
+ if (is_decoy) {
+ num_decoy_peptide_skipped++;
+ } else {
+ num_target_peptide_skipped++;
+ }
+ continue;
+ } else {
+ BestPeptideScore.at(peptideStr) += ascending ? -1.0 : 1.0; //make sure only one best scoring peptide reported.
+ }
+ } catch (const std::out_of_range& oor) {
+ carp(CARP_DEBUG, "Error in peptide-level filtering");
+ }
+ }
+
+ // Do the Sidak correction.
+ if (sidak) {
+ if (match->getRank(XCORR) > 1) {
+ carp_once(CARP_WARNING, "Sidak correction is not defined for non-top-matches. Further warnings are not shown.");
+ }
+ sidak_adjustment = 1.0 - pow(1.0 - match->getScore(score_type), match->getTargetExperimentSize());
+ match->setScore(SIDAK_ADJUSTED, sidak_adjustment);
+ }
+
+ // Add this match to one of the collections.
+ if (is_decoy) {
+ decoy_matches->addMatch(match);
+ } else {
+ target_matches->addMatch(match);
+ }
+ Match::freeMatch(match);
+ }
+ delete match_iterator;
+ delete match_collection;
+ if (num_decoy_rank_skipped + num_target_rank_skipped > 0) {
+ carp(CARP_INFO, "Skipped %d target and %d decoy PSMs with rank > %d.",
+ num_target_rank_skipped, num_decoy_rank_skipped, top_match);
+ }
+ if (num_target_peptide_skipped + num_decoy_peptide_skipped > 0) {
+ carp(CARP_INFO, "Skipped %d target and %d decoy PSMs due to peptide-level filtering.",
+ num_target_peptide_skipped, num_decoy_peptide_skipped);
+ }
+ }
+
+ if (sidak) {
+ score_type = SIDAK_ADJUSTED;
+ }
+
+ target_matches->setScoredType(score_type, true);
+ decoy_matches->setScoredType(score_type, true);
+
+
+ // get from the input files which columns to print in the output files
+ if (iteration_cnt_ == 0) {
+ vector<bool> cols_to_print(NUMBER_MATCH_COLUMNS);
+ cols_to_print[FILE_COL] = Params::GetBool("file-column");
+ cols_to_print[SCAN_COL] = true;
+ cols_to_print[CHARGE_COL] = true;
+ cols_to_print[SPECTRUM_PRECURSOR_MZ_COL] = true;
+ cols_to_print[SPECTRUM_NEUTRAL_MASS_COL] = true;
+ cols_to_print[PEPTIDE_MASS_COL] = true;
+ cols_to_print[DELTA_CN_COL] = target_matches->getScoredType(DELTA_CN);
+ cols_to_print[SP_SCORE_COL] = target_matches->getScoredType(SP);
+ cols_to_print[SP_RANK_COL] = target_matches->getScoredType(SP);
+ cols_to_print[XCORR_SCORE_COL] = !target_matches->getScoredType(TIDE_SEARCH_EXACT_PVAL);
+ cols_to_print[XCORR_RANK_COL] = true;
+ cols_to_print[EVALUE_COL] = target_matches->getScoredType(EVALUE);
+ cols_to_print[EXACT_PVALUE_COL] = target_matches->getScoredType(TIDE_SEARCH_EXACT_PVAL);
+ cols_to_print[PVALUE_COL] = target_matches->getScoredType(LOGP_BONF_WEIBULL_XCORR);
+ cols_to_print[SIDAK_ADJUSTED_COL] = sidak;
+ if (target_matches->getScoredType(TIDE_SEARCH_EXACT_PVAL)) {
+ cols_to_print[REFACTORED_SCORE_COL] = true;
+ }
+ cols_to_print[BY_IONS_MATCHED_COL] = target_matches->getScoredType(BY_IONS_MATCHED);
+ cols_to_print[BY_IONS_TOTAL_COL] = target_matches->getScoredType(BY_IONS_TOTAL);
+
+ if (distinct_matches) {
+ cols_to_print[DISTINCT_MATCHES_SPECTRUM_COL] = true;
+ } else {
+ cols_to_print[MATCHES_SPECTRUM_COL] = true;
+ }
+ switch (estimation_method) {
+ case TDC_METHOD:
+ case PEPTIDE_LEVEL_METHOD: // FIXME: Make a peptide-level q-value column. --WSN 4 Feb 2016
+ cols_to_print[QVALUE_TDC_COL] = true;
+ break;
+ case MIXMAX_METHOD:
+ cols_to_print[QVALUE_MIXMAX_COL] = true;
+ break;
+ case NUMBER_METHOD_TYPES:
+ case INVALID_METHOD:
+ carp(CARP_FATAL, "No estimation method specified.");
+ }
+ cols_to_print[SEQUENCE_COL] = true;
+ cols_to_print[CLEAVAGE_TYPE_COL] = true;
+ cols_to_print[PROTEIN_ID_COL] = true;
+ cols_to_print[FLANKING_AA_COL] = true;
+ if (spectrum_flag_ != NULL) {
+ cols_to_print[INDEX_NAME_COL] = true;
+ }
+
+ output_->writeHeaders(cols_to_print);
+ }
+ switch (estimation_method) {
+ case TDC_METHOD:
+ case PEPTIDE_LEVEL_METHOD:
+ derived_score_type = QVALUE_TDC;
+ break;
+ case MIXMAX_METHOD:
+ derived_score_type = QVALUE_MIXMAX;
+ break;
+ case NUMBER_METHOD_TYPES:
+ case INVALID_METHOD:
+ carp(CARP_FATAL, "No estimation method specified.");
+ }
+
+ // Compute q-values.
+ FLOAT_T* target_scores = target_matches->extractScores(score_type);
+ int num_targets = target_matches->getMatchTotal();
+ FLOAT_T* decoy_scores = decoy_matches->extractScores(score_type);
+ int num_decoys = decoy_matches->getMatchTotal();
+ carp(CARP_INFO,
+ "There are %d target and %d decoy PSMs for q-value computation.",
+ num_targets, num_decoys);
+
+ FLOAT_T* qvalues = NULL;
+ switch (estimation_method) {
+ case TDC_METHOD:
+ case PEPTIDE_LEVEL_METHOD:
+ qvalues = compute_decoy_qvalues_tdc(target_scores, num_targets,
+ decoy_scores, num_decoys, ascending, 1.0);
+ break;
+ case MIXMAX_METHOD:
+ qvalues = compute_decoy_qvalues_mixmax(target_scores, num_targets,
+ decoy_scores, num_decoys,
+ ascending,
+ Params::GetDouble("pi-zero"));
+ break;
+ case NUMBER_METHOD_TYPES:
+ case INVALID_METHOD:
+ carp(CARP_FATAL, "No estimation method specified.");
+ }
+
+ unsigned int fdr1 = 0;
+ unsigned int fdr5 = 0;
+ unsigned int fdr10 = 0;
+ for (unsigned int i = 0; i < num_targets; ++i) {
+ if (qvalues[i] < 0.01) ++fdr1;
+ if (qvalues[i] < 0.05) ++fdr5;
+ if (qvalues[i] < 0.10) ++fdr10;
+ }
+ carp(CARP_INFO, "Number of PSMs at 1%% FDR = %d.", fdr1);
+ carp(CARP_INFO, "Number of PSMs at 5%% FDR = %d.", fdr5);
+ carp(CARP_INFO, "Number of PSMs at 10%% FDR = %d.", fdr10);
+
+ free(decoy_scores);
+
+ // Store p-values to q-values as a hash, and then assign them.
+ map<FLOAT_T, FLOAT_T> qvalue_hash
+ = store_arrays_as_hash(target_scores, qvalues, num_targets);
+
+ target_matches->assignQValues(&qvalue_hash, score_type, derived_score_type);
+
+ free(target_scores);
+ free(qvalues);
+
+ // Store targets by score.
+ target_matches->sort(score_type);
+ if (spectrum_flag_ == NULL) {
+ output_->writeMatches(target_matches);
+ output_->writeFooters();
+ delete output_;
+ } else {
+ accepted_psms_ = 0;
+ //print out accepted matches in Cascade Search
+ MatchCollection* accepted_matches = new MatchCollection();
+ MatchIterator* match_iterator =
+ new MatchIterator(target_matches, score_type, false);
+
+ while (match_iterator->hasNext()) {
+ Match* match = match_iterator->next();
+
+ if (match->getScore(QVALUE_TDC) > Params::GetDouble("q-value-threshold")) {
+ break;
+ }
+ spectrum_flag_->insert(make_pair(pair<string, unsigned int>(
+ match->getSpectrum()->getFullFilename(),
+ match->getSpectrum()->getFirstScan() * 10 + match->getCharge()), true));
+
+ match->setDatabaseIndexName(index_name_);
+
+ accepted_matches->addMatch(match);
+ ++accepted_psms_;
+ }
+ output_->writeMatches(accepted_matches);
+ delete accepted_matches;
+ delete match_iterator;
+ }
+ delete decoy_matches;
+ delete target_matches;
+
+ return 0;
+} // Main
+
+
+/**
+* Find the best-scoring match for each peptide in a given collection.
+* Only consider the top-ranked PSM per spectrum.
+*
+* Results are stored in the given match collection.
+*/
+void AssignConfidenceApplication::identify_best_psm_per_peptide(
+ MatchCollection* all_matches,
+ SCORER_TYPE_T score_type
+) {
+ /* Instantiate a hash table. key = peptide; value = maximal xcorr
+ for that peptide. */
+ map<string, FLOAT_T> best_score_per_peptide;
+
+ // Store in the hash the best score per peptide.
+ MatchIterator* match_iterator
+ = new MatchIterator(all_matches, score_type, false);
+ while(match_iterator->hasNext()) {
+ Match* match = match_iterator->next();
+
+ // Skip matches that are not top-ranked.
+ if (match->getRank(score_type) == 1) {
+ char *peptide = match->getModSequenceStrWithSymbols();
+ FLOAT_T this_score = match->getScore(score_type);
+
+ map<string, FLOAT_T>::iterator map_position
+ = best_score_per_peptide.find(peptide);
+
+ if (map_position == best_score_per_peptide.end()) {
+ best_score_per_peptide[peptide] = this_score;
+ } else {
+ // FIXME: Need a generic compare operator for score_type.
+ if (map_position->second < this_score) {
+ best_score_per_peptide[peptide] = this_score;
+ }
+ }
+ free(peptide);
+ }
+ }
+ delete match_iterator;
+
+
+ // Set the best_per_peptide Boolean in the match, based on the hash.
+ match_iterator = new MatchIterator(all_matches, score_type, false);
+ while(match_iterator->hasNext()) {
+ Match* match = match_iterator->next();
+
+ // Skip matches that are not top-ranked.
+ if (match->getRank(score_type) == 1) {
+ char* peptide = match->getModSequenceStrWithSymbols();
+ FLOAT_T this_score = match->getScore(score_type);
+
+ map<string, FLOAT_T>::iterator map_position
+ = best_score_per_peptide.find(peptide);
+
+ if (map_position->second == this_score) {
+ match->setBestPerPeptide();
+
+ // Prevent ties from causing two peptides to be best.
+ best_score_per_peptide[peptide] = HUGE_VAL;
+ }
+
+ free(peptide);
+ }
+ }
+ delete match_iterator;
+}
+
+
+/**
+ * The q-value is defined as the minimum FDR at which a given score is
+ * deemed significant. This function takes a list of FDRs and
+ * converts them into q-values. The FDRs should be ordered from
+ * lowest to highest, sorted according to the underlying score.
+ */
+void AssignConfidenceApplication::convert_fdr_to_qvalue(
+ FLOAT_T* qvalues, ///< Come in as FDRs, go out as q-values.
+ int num_values
+) {
+ FLOAT_T prev_fdr = qvalues[num_values - 1];
+ int idx;
+ for (idx=num_values - 2; idx >= 0; idx--) {
+ carp(CARP_DETAILED_DEBUG, "fdr[%i] = %.10f", idx, qvalues[idx]);
+ FLOAT_T this_fdr = qvalues[idx];
+ if (prev_fdr < this_fdr) {
+ qvalues[idx] = prev_fdr;
+ }
+ prev_fdr = qvalues[idx];
+ carp(CARP_DETAILED_DEBUG, "qvalue[%i] = %.10f", idx, qvalues[idx]);
+ }
+}
+
+/**
+ * Store two parallel arrays of floats in a hash table.
+ */
+map<FLOAT_T, FLOAT_T> AssignConfidenceApplication::store_arrays_as_hash(
+ FLOAT_T* keys,
+ FLOAT_T* values,
+ int num_values
+) {
+ map<FLOAT_T, FLOAT_T> return_value;
+ for (int idx=0; idx < num_values; idx++) {
+ carp(CARP_DETAILED_DEBUG, "%g maps to %g", keys[idx], values[idx]);
+ return_value[keys[idx]] = values[idx];
+ }
+ return(return_value);
+}
+
+/**
+ * \brief Compute q-values from a given set of scores, using a second
+ * set of scores as an empirical null. Sorts the incoming target
+ * scores and returns a corresponding list of q-values.
+ *
+ * This function is only exported to allow unit testing.
+ */
+FLOAT_T* AssignConfidenceApplication::compute_decoy_qvalues_tdc(
+ FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool ascending,
+ FLOAT_T pi_zero
+) {
+ if ((num_targets == 0) || (num_decoys == 0)) {
+ carp(CARP_FATAL, "Cannot compute q-values (%d targets, %d nulls).",
+ num_targets, num_decoys);
+ }
+ carp(CARP_DEBUG, "Computing decoy q-values with %d targets and %d decoys.",
+ num_targets, num_decoys);
+
+ // Sort both sets of scores.
+ if (ascending) {
+ sort(target_scores, target_scores + num_targets, Match::ScoreLess);
+ sort(decoy_scores, decoy_scores + num_decoys, Match::ScoreLess);
+ } else {
+ sort(target_scores, target_scores + num_targets, Match::ScoreGreater);
+ sort(decoy_scores, decoy_scores + num_decoys, Match::ScoreGreater);
+ }
+
+ // Compute false discovery rate for each target score.
+ FLOAT_T* qvalues = (FLOAT_T*)mycalloc(num_targets, sizeof(FLOAT_T));
+ int decoy_idx = 0;
+ for (int target_idx = 0; target_idx < num_targets; target_idx++) {
+ FLOAT_T target_score = target_scores[target_idx];
+
+ // Find the index of the first decoy score greater than this target score.
+ if (ascending) {
+ while (decoy_idx < num_decoys &&
+ Match::ScoreLess(decoy_scores[decoy_idx], target_score)) {
+ carp(CARP_DEBUG, "Decoy score %g.", decoy_scores[decoy_idx]);
+ decoy_idx++;
+ }
+ } else {
+ while (decoy_idx < num_decoys &&
+ Match::ScoreGreater(decoy_scores[decoy_idx], target_score)) {
+ carp(CARP_DEBUG, "Decoy score %g.", decoy_scores[decoy_idx]);
+ decoy_idx++;
+ }
+ }
+
+ // FDR = (#decoys + 1)/ #targets
+ FLOAT_T fdr =
+ ((FLOAT_T)(decoy_idx + 1)/ (FLOAT_T)(target_idx + 1));
+
+ if ( fdr > 1.0 ) {
+ fdr = 1.0;
+ }
+
+ carp(CARP_DEBUG, "FDR for score %g = min(1,%d/%d) = %g",
+ target_score, decoy_idx, target_idx + 1, fdr);
+
+ qvalues[target_idx] = fdr;
+ }
+
+ // Convert the FDRs into q-values.
+ convert_fdr_to_qvalue(qvalues, num_targets);
+
+ return qvalues;
+}
+
+FLOAT_T AssignConfidenceApplication::estimate_pi0(FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool ascending
+) {
+ vector<pair<double, bool> > score_labels;
+ transform(target_scores, target_scores + num_targets,
+ back_inserter(score_labels),
+ bind2nd(ptr_fun<double, bool, pair<double, bool> >(make_pair), true));
+ transform(decoy_scores, decoy_scores + num_decoys,
+ back_inserter(score_labels),
+ bind2nd(ptr_fun<double, bool, pair<double, bool> >(make_pair), false));
+
+ // sort them
+ if (ascending) {
+ sort(score_labels.begin(), score_labels.end());
+ PosteriorEstimator::setReversed(true);
+ } else {
+ sort(score_labels.begin(), score_labels.end(),
+ greater<pair<double, bool> > ());
+ }
+ // get p-values
+ vector<double> pvals;
+ PosteriorEstimator::getPValues(score_labels, pvals);
+
+ // estimate pi_zero
+ FLOAT_T pi_zero = PosteriorEstimator::estimatePi0(pvals);
+
+ carp(CARP_INFO, "Estimated pi_zero = %f", pi_zero);
+ return pi_zero;
+}
+
+/**
+ * \brief Compute q-values using mix-max procedure. This part is a
+ * reimplementation of Uri Keich's code written in R.
+ *
+ */
+FLOAT_T* AssignConfidenceApplication::compute_decoy_qvalues_mixmax(
+ FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool ascending,
+ FLOAT_T pi_zero
+) {
+ if ((num_targets == 0) || (num_decoys == 0)) {
+ carp(CARP_FATAL, "Cannot compute q-values (%d targets, %d decoys).",
+ num_targets, num_decoys);
+ }
+ if (num_targets != num_decoys) {
+ carp(CARP_WARNING, "The mix-max procedure is not well behaved when # targets (%d) != # of decoys (%d).",
+ num_targets, num_decoys);
+ }
+ //estimate pi0 from data if it is not given.
+ if (pi_zero == 1.0) {
+
+ // put all of the scores in a single vector of pairs: score, is_target
+ vector<pair<double, bool> > score_labels;
+ transform(target_scores, target_scores + num_targets,
+ back_inserter(score_labels),
+ bind2nd(ptr_fun<double, bool, pair<double, bool> >(make_pair), true));
+ transform(decoy_scores, decoy_scores + num_decoys,
+ back_inserter(score_labels),
+ bind2nd(ptr_fun<double, bool, pair<double, bool> >(make_pair), false));
+
+ // sort them
+ if (ascending) {
+ sort(score_labels.begin(), score_labels.end());
+ PosteriorEstimator::setReversed(true);
+ } else {
+ sort(score_labels.begin(), score_labels.end(),
+ greater<pair<double, bool> > ());
+ }
+ // get p-values
+ vector<double> pvals;
+ PosteriorEstimator::getPValues(score_labels, pvals);
+
+ // estimate pi_zero
+ pi_zero = PosteriorEstimator::estimatePi0(pvals);
+
+ carp(CARP_INFO, "Estimated pi_zero = %f", pi_zero);
+
+ }
+ // continue with mix-max procedure
+ for (int target_idx = 0; target_idx < num_targets; ++target_idx) {
+ carp(CARP_DEBUG, "target_scores[%d]=%lf decoy_scores[%d]=%lf",
+ target_idx, target_scores[target_idx],
+ target_idx, decoy_scores[target_idx]);
+ }
+
+ //Sort decoy and target stores
+ if (ascending) {
+ sort(target_scores, target_scores + num_targets, greater<FLOAT_T>());
+ sort(decoy_scores, decoy_scores + num_decoys, greater<FLOAT_T>());
+ } else {
+ sort(target_scores, target_scores + num_targets);
+ sort(decoy_scores, decoy_scores + num_decoys);
+ }
+
+ //histogram of the target scores.
+ double* h_w_le_z = new double[num_decoys + 1]; //histogram for N_{w<=z}
+ double* h_z_le_z = new double[num_decoys + 1]; //histogram for N_{z<=z}
+
+ int idx = 0;
+ int cnt = 0;
+ int i;
+ for (i = 0; i < num_decoys; ++i) {
+ while (idx < num_targets && ascending ?
+ decoy_scores[i] <= target_scores[idx] :
+ decoy_scores[i] >= target_scores[idx]) {
+ ++cnt;
+ ++idx;
+ }
+ h_w_le_z[i] = (double)cnt;
+ }
+ cnt = 0;
+ idx = 0;
+ for (i = 0; i < num_decoys; ++i) {
+ while (idx < num_targets && ascending ?
+ decoy_scores[i] <= decoy_scores[idx] :
+ decoy_scores[i] >= decoy_scores[idx]) {
+ ++cnt;
+ ++idx;
+ }
+ h_z_le_z[i] = (double)cnt;
+ }
+ h_w_le_z[num_decoys] = (double)(num_targets);
+ h_z_le_z[num_decoys] = (double)(num_decoys);
+
+ FLOAT_T* fdrmod = new FLOAT_T[num_targets];
+ double estPx_lt_zj = 0.0;
+ double E_f1_mod_run_tot = 0.0;
+ int j = num_decoys-1;
+ int k = num_targets-1;
+ int n_z_ge_w = 0;
+ int n_w_ge_w = 0;
+ double qvalue;
+ double cnt_z, cnt_w;
+ double prev_fdr = -1;
+
+ for (i = num_targets - 1; i >= 0; --i) {
+ while (j >= 0 && (ascending ?
+ decoy_scores[j] <= target_scores[i] :
+ decoy_scores[j] >= target_scores[i])) {
+ cnt_w = h_w_le_z[j + 1];
+ cnt_z = h_z_le_z[j + 1];
+ estPx_lt_zj = (double)(cnt_w - pi_zero*cnt_z) / ((1.0 - pi_zero)*cnt_z);
+ estPx_lt_zj = estPx_lt_zj > 1 ? 1 : estPx_lt_zj;
+ estPx_lt_zj = estPx_lt_zj < 0 ? 0 : estPx_lt_zj;
+ E_f1_mod_run_tot += estPx_lt_zj * ((1.0 - pi_zero));
+ ++n_z_ge_w;
+ --j;
+ }
+ while (k >= 0 && (ascending ?
+ target_scores[k] <= target_scores[i] :
+ target_scores[k] >= target_scores[i])) {
+ ++n_w_ge_w;
+ --k;
+ }
+ qvalue = ((double)n_z_ge_w * pi_zero + E_f1_mod_run_tot) / (double)(n_w_ge_w);
+ fdrmod[i] = qvalue > 1.0 ? 1.0 : qvalue;
+
+ //convert qvalues to fdr
+ if (prev_fdr > fdrmod[i])
+ fdrmod[i] = prev_fdr;
+
+ prev_fdr = fdrmod[i];
+ }
+ // Convert the FDRs into q-values.
+ delete[] h_w_le_z;
+ delete[] h_z_le_z;
+ return fdrmod;
+}
+
+void AssignConfidenceApplication::peptide_level_filtering(
+ MatchCollection* match_collection,
+ std::map<string, FLOAT_T>* BestPeptideScore,
+ SCORER_TYPE_T score_type,
+ bool ascending) {
+
+ MatchIterator* temp_iter = new MatchIterator(match_collection);
+
+ while (temp_iter->hasNext()) {
+ Crux::Match* match = temp_iter->next();
+ FLOAT_T score = match->getScore(score_type);
+ string peptideStr = getPeptideSeq(match);
+
+ FLOAT_T bestScore = 0.0;
+ try {
+ bestScore = BestPeptideScore->at(peptideStr);
+ } catch (const std::out_of_range& oor) {
+ BestPeptideScore->insert(std::pair<string, FLOAT_T>(peptideStr, score));
+ continue;
+ }
+ if ((ascending && bestScore > score) || (!ascending && score > bestScore)) {
+ BestPeptideScore->at(peptideStr) = score;
+ }
+ }
+ delete temp_iter;
+}
+
+string AssignConfidenceApplication::getPeptideSeq(Match* match) {
+ string peptideSeq;
+ if (Params::GetBool("combine-modified-peptides")) {
+ peptideSeq = match->getPeptide()->getSequence();
+ } else {
+ peptideSeq = match->getPeptide()->getModifiedSequenceWithMasses();
+ }
+ if (Params::GetBool("combine-charge-states")) {
+ peptideSeq += StringUtils::ToString(match->getCharge());
+ }
+ return peptideSeq;
+}
+
+map<pair<string, unsigned int>, bool>* AssignConfidenceApplication::getSpectrumFlag() {
+ return spectrum_flag_;
+}
+
+void AssignConfidenceApplication::setSpectrumFlag(map<pair<string, unsigned int>, bool>* spectrum_flag) {
+ spectrum_flag_ = spectrum_flag;
+}
+
+void AssignConfidenceApplication::setIterationCnt(unsigned int iteration_cnt) {
+ iteration_cnt_ = iteration_cnt;
+}
+
+void AssignConfidenceApplication::setOutput(OutputFiles *output) {
+ output_ = output;
+}
+
+void AssignConfidenceApplication::setIndexName(string index_name) {
+ index_name_ = index_name;
+}
+
+unsigned int AssignConfidenceApplication::getAcceptedPSMs() {
+ return accepted_psms_;
+}
+
+int AssignConfidenceApplication::getDirection(SCORER_TYPE_T scoreType) {
+ // Return -1 for higher score better, 1 for lower score better, or 0 for unknown
+ switch (scoreType) {
+ case SP:
+ case XCORR:
+ case LOGP_BONF_WEIBULL_XCORR: // negative log p-values
+ case TIDE_SEARCH_REFACTORED_XCORR:
+ case PERCOLATOR_SCORE:
+ // higher score better, ascending = false
+ return -1;
+ case EVALUE:
+ case TIDE_SEARCH_EXACT_PVAL:
+ case TIDE_SEARCH_EXACT_SMOOTHED:
+ // lower score better, ascending = true
+ return 1;
+ default:
+ carp(CARP_FATAL, "Unknown score type %s", scorer_type_to_string(scoreType));
+ // unknown score type
+ return 0;
+ }
+}
+
+/**
+* \returns the command name for ComputeQValues
+*/
+string AssignConfidenceApplication::getName() const {
+ return "assign-confidence";
+}
+
+/**
+* \returns the description for ComputeQValues
+*/
+string AssignConfidenceApplication::getDescription() const {
+ return
+ "[[nohtml:Assign two types of statistical confidence measures (q-values "
+ "and posterior error probabilities) to each PSM in a given set.]]"
+ "[[html:<p>Given target and decoy scores, estimate a q-value for each "
+ "target score. The q-value is analogous to a p-value but incorporates "
+ "false discovery rate multiple testing correction. The q-value associated "
+ "with a score threshold T is defined as the minimal false discovery rate "
+ "(FDR) at which a score of T is deemed significant. In this setting, the "
+ "q-value accounts for the fact that we are analyzing a large collection of "
+ "scores. For confidence estimation afficionados, please note that this "
+ "definition of \"q-value\" is independent of the notion of \"positive FDR\" "
+ "as defined in (Storey <em>Annals of Statistics</em> 31:2013-2015:2003).</p>"
+ "<p>To estimate FDRs, <code>assign-confidence</code> uses one of two "
+ "different procedures. Both require that the input contain both target and "
+ "decoy scores. The default, target-decoy competition (TDC) procedure is "
+ "described in this article:</p><blockquote>Josh E. Elias and Steve P. Gygi. "
+ "\"Target-decoy search strategy for increased confidence in large-scale "
+ "protein identifications by mass spectrometry.\" <em>Nature Methods</em>. "
+ "4(3):207-14, 2007.</blockquote><p>Note that <code>assign-confidence</code> "
+ "implements a variant of the protocol proposed by Elias and Gygi: rather "
+ "than reporting a list that contains both targets and decoys, <code>"
+ "assign-confidence</code> reports only the targets. The FDR estimate is "
+ "adjusted accordingly (by dividing by 2).</p><p>The alternative, <em>"
+ "mix-max</em> procedure is described in this article:</p><blockquote>Uri "
+ "Keich, Attila Kertesz-Farkas and William Stafford Noble. "
+ "<a href=\"http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00081\">"
+ "\"An improved false discovery rate estimation procedure for shotgun proteomics.\"</a> "
+ "<i>Journal of Proteome Research</i>. 14(8):3148-3161, 2015.</blockquote>"
+ "<p>Note that the mix-max procedure requires as "
+ "input calibrated scores, such as Comet E-values or p-values produced "
+ "using Tide-s <code>exact-p-value</code> option.</p>"
+ "<p>The mix-max procedure requires that scores "
+ "are reported from separate target and decoy searches. Thus, this approach "
+ "is incompatible with a search that is run using the <code>--concat T"
+ "</code> option to <code>tide-search</code> or the <code>--decoy_search 2"
+ "</code> option to <code>comet</code>. On the other hand, the TDC "
+ "procedure can take as input "
+ "searches conducted in either mode (concatenated or separate). If given "
+ "separate search results and asked to do TDC estimation, <code>"
+ "assign-confidence</code> will carry out the target-decoy competition as "
+ "part of the confidence estimation procedure.</p><p>In each case, the "
+ "estimated FDRs are converted to q-values by sorting the scores then "
+ "taking, for each score, the minimum of the current FDR and all of the FDRs "
+ "below it in the ranked list.</p><p>A primer on multiple testing correction "
+ "can be found here:</p><blockquote>William Stafford Noble. <a href=\""
+ "http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1135.html\">\"How "
+ "does multiple testing correction work?\"</a> <em>Nature Biotechnology</em>. "
+ "27(12):1135-1137, 2009.</blockquote>]]";
+}
+
+/**
+* \returns the command arguments
+*/
+vector<string> AssignConfidenceApplication::getArgs() const {
+ string arr[] = {
+ "target input+"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+* \returns the command options
+*/
+vector<string> AssignConfidenceApplication::getOptions() const {
+ string arr[] = {
+ "estimation-method",
+ "decoy-prefix",
+ "score",
+ "sidak",
+ "verbosity",
+ "parameter-file",
+ "overwrite",
+ "output-dir",
+ "list-of-files",
+ "combine-charge-states",
+ "combine-modified-peptides",
+ "fileroot"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+* \returns the command outputs
+*/
+vector< pair<string, string> > AssignConfidenceApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("assign-confidence.target.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited text file</a> that contains the "
+ "targets, sorted by score. The file will contain one new column, named "
+ "\"<method> q-value\", where <method> is either \"tdc\" or \"mix-max\"."));
+ outputs.push_back(make_pair("assign-confidence.log.txt",
+ "a log file containing a copy of all messages that were printed to stderr."));
+ outputs.push_back(make_pair("assign-confidence.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ return outputs;
+}
+
+/**
+* \returns the filestem for ComputeQValues
+*/
+string AssignConfidenceApplication::getFileStem() const {
+ return "assign-confidence";
+}
+
+COMMAND_T AssignConfidenceApplication::getCommand() const {
+ return QVALUE_COMMAND; // FIXME: Rename this. --WSN 4 Feb 2016
+}
+
+/**
+* \returns whether the application needs the output directory or not.
+*/
+bool AssignConfidenceApplication::needsOutputDirectory() const {
+ return true;
+}
+
+void AssignConfidenceApplication::processParams() {
+ if (Params::GetString("estimation-method") != "peptide-level") {
+ if (Params::GetInt("top-match") != 1 && !Params::IsDefault("top-match")) {
+ carp(CARP_WARNING, "assign-confidence can work with top-match = 1 only.");
+ }
+ Params::Set("top-match", 1);
+ }
+}
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/app/AssignConfidenceApplication.h b/src/app/AssignConfidenceApplication.h
new file mode 100644
index 0000000..d80c437
--- /dev/null
+++ b/src/app/AssignConfidenceApplication.h
@@ -0,0 +1,177 @@
+/**
+* \file AssignConfidenceApplication.h
+* AUTHOR: Attila Kertesz-Farkas
+* CREATE DATE: May 01, 2015
+****************************************************************************/
+
+#ifndef ASSIGNCONFIDENCE_H
+#define ASSIGNCONFIDENCE_H
+
+#include <stdlib.h>
+#include <stdio.h>
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "model/objects.h"
+#include "parameter.h"
+#include "model/Protein.h"
+#include "model/Spectrum.h"
+#include "io/SpectrumCollection.h"
+#include "model/Scorer.h"
+#include "model/Match.h"
+#include "model/MatchCollection.h"
+#include "io/OutputFiles.h"
+#include "model/Peptide.h"
+
+/**
+ * Legal values for the --estimation-method option.
+ */
+enum _estimation_method {
+ INVALID_METHOD,
+ MIXMAX_METHOD, ///< compute q-values using mix-max (Uri Keich)
+ TDC_METHOD, ///< compute q-values using TDC (Elias-Gygi)
+ PEPTIDE_LEVEL_METHOD,///< simple peptide-level decoy-based estimation (WOTE)
+ NUMBER_METHOD_TYPES ///< always keep this last so the value
+ /// changes as cmds are added
+};
+
+typedef enum _estimation_method ESTIMATION_METHOD_T;
+
+class AssignConfidenceApplication : public CruxApplication {
+ protected:
+ map<pair<string, unsigned int>, bool>* spectrum_flag_; // this variable is used in Cascade Search, this is an idicator
+ unsigned int iteration_cnt_;
+ OutputFiles* output_;
+ unsigned int accepted_psms_;
+ string index_name_;
+
+ public:
+ map<pair<string, unsigned int>, bool>* getSpectrumFlag();
+ void setSpectrumFlag(map<pair<string, unsigned int>, bool>* spectrum_flag);
+ void setIterationCnt(unsigned int iteration_cnt);
+ void setOutput(OutputFiles *output);
+ unsigned int getAcceptedPSMs();
+ std::string getPeptideSeq(Crux::Match* match);
+
+ /**
+ * stores the name of the index file used in an iteration in Cascade Search.
+ */
+ void setIndexName(string index_name);
+
+ /**
+ * \returns a blank ComputeQValues object
+ */
+ AssignConfidenceApplication();
+
+ /**
+ * Destructor
+ */
+ ~AssignConfidenceApplication();
+
+ /**
+ * main method for ComputeQValues
+ */
+ virtual int main(int argc, char** argv);
+
+ virtual int main(const vector<string> input_files);
+
+ static int getDirection(SCORER_TYPE_T scoreType);
+
+ /**
+ * \returns the command name for ComputeQValues
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for ComputeQValues
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns the filestem for ComputeQValues
+ */
+ virtual std::string getFileStem() const;
+
+ /**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+ virtual COMMAND_T getCommand() const;
+
+ /**
+ * \Preprocesses the program arguments before finalizing them.
+ */
+ virtual void processParams();
+
+ /**
+ * \returns whether the application needs the output directory or not.
+ */
+ virtual bool needsOutputDirectory() const;
+
+ FLOAT_T* compute_decoy_qvalues_tdc(
+ FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool reverse);
+
+ FLOAT_T* compute_qvalues_from_pvalues(
+ FLOAT_T* pvalues,
+ int num_pvals,
+ FLOAT_T pi_zero);
+
+ FLOAT_T estimate_pi0(FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool ascending);
+
+ void peptide_level_filtering(
+ MatchCollection* match_collection,
+ std::map<string, FLOAT_T>* BestPeptideScore,
+ SCORER_TYPE_T score_type,
+ bool ascending);
+
+ void identify_best_psm_per_peptide
+ (MatchCollection* all_matches,
+ SCORER_TYPE_T score_type);
+ void convert_fdr_to_qvalue
+ (FLOAT_T* qvalues, ///< Come in as FDRs, go out as q-values.
+ int num_values);
+ map<FLOAT_T, FLOAT_T> store_arrays_as_hash
+ (FLOAT_T* keys,
+ FLOAT_T* values,
+ int num_values);
+ FLOAT_T* compute_decoy_qvalues_tdc(
+ FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool forward,
+ FLOAT_T pi_zero
+ );
+ FLOAT_T* compute_decoy_qvalues_mixmax(
+ FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool ascending,
+ FLOAT_T pi_zero
+ );
+};
+
+#endif //ASSIGNCONFIDENCE_H
+
diff --git a/src/app/CascadeSearchApplication.cpp b/src/app/CascadeSearchApplication.cpp
new file mode 100644
index 0000000..e7d8697
--- /dev/null
+++ b/src/app/CascadeSearchApplication.cpp
@@ -0,0 +1,228 @@
+/**
+ * \file CascadeSearchApplication.cpp
+ * \brief Iterative PSM meta-search via Cascade protocol
+ ************************************************************/
+#include "CascadeSearchApplication.h"
+#include "io/OutputFiles.h"
+#include "AssignConfidenceApplication.h"
+#include "TideSearchApplication.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "util/FileUtils.h"
+#include "stdio.h"
+#include "boost/filesystem.hpp"
+
+using namespace std;
+
+int const CascadeSearchApplication::CASCADE_TERMINATION_CONDITION = 20;
+
+/**
+ * \returns a blank CascadeSearchApplication object
+ */
+CascadeSearchApplication::CascadeSearchApplication() {
+
+}
+
+/**
+ * Destructor
+ */
+CascadeSearchApplication::~CascadeSearchApplication() {
+}
+
+/**
+ * main method for CascadeSearchApplication
+ */
+int CascadeSearchApplication::main(int argc, char** argv) {
+ map<pair<string, unsigned int>, bool>* spectrum_flag = new map<pair<string, unsigned int>, bool>;
+
+ carp(CARP_INFO, "Running cascade-search...");
+
+ string database_string = Params::GetString("database-series");
+ vector<string> database_indeces = StringUtils::Split(database_string, ',');
+ OutputFiles* output = new OutputFiles(this);
+
+ int return_code;
+ for (unsigned int cascade_cnt = 0; cascade_cnt < database_indeces.size(); ++cascade_cnt) {
+
+ //carry out tide-search
+ TideSearchApplication TideSearchProgram;
+ TideSearchProgram.setSpectrumFlag(spectrum_flag);
+ return_code = TideSearchProgram.main(Params::GetStrings("tide spectra file"), database_indeces[cascade_cnt]);
+ if (return_code != 0) {
+ return return_code;
+ }
+
+ //pass the output from Tide-Search to Assign-Confidence
+ vector<string> bridge_file_name;
+ bridge_file_name.push_back(TideSearchProgram.getOutputFileName());
+
+ //carry out assign confidence
+ AssignConfidenceApplication AssignConfidenceProgram;
+ AssignConfidenceProgram.setSpectrumFlag(spectrum_flag);
+ AssignConfidenceProgram.setIterationCnt(cascade_cnt);
+ AssignConfidenceProgram.setOutput(output);
+ AssignConfidenceProgram.setIndexName(database_indeces[cascade_cnt]);
+
+ return_code = AssignConfidenceProgram.main(bridge_file_name);
+ if (return_code != 0) {
+ return return_code;
+ }
+ spectrum_flag = AssignConfidenceProgram.getSpectrumFlag();
+
+ //remove tide-search and assign-confidence output files.
+ string outputdir = Params::GetString("output-dir");
+ RemoveTempFiles(outputdir, TideSearchProgram.getName());
+ RemoveTempFiles(outputdir, AssignConfidenceProgram.getName());
+
+ int numAccepted = AssignConfidenceProgram.getAcceptedPSMs();
+ if (numAccepted < CASCADE_TERMINATION_CONDITION) {
+ carp(CARP_INFO,
+ "Terminating search early because only %d PSMs were accepted.",
+ numAccepted);
+ break;
+ }
+
+ }
+ delete output;
+
+ return 0;
+}
+
+/**
+ * \returns the command name for CascadeSearchApplication
+ */
+string CascadeSearchApplication::getName() const {
+ return "cascade-search";
+}
+
+/**
+ * \returns the description for CascadeSearchApplication
+ */
+string CascadeSearchApplication::getDescription() const {
+ return
+ "[[nohtml:An iterative procedure for incorporating information about "
+ "peptide groups into the database search and confidence estimation "
+ "procedure.]]"
+ "[[html:<p>Cascade-search is a general procedure for incorporating information about "
+ "peptide groups into the database search and confidence estimation procedure. Peptides "
+ "may be grouped according to, for example, their enzymatic properties (zero, one, or "
+ "two enzymatic termini) or the presence of different types of numbers of variable "
+ "modifications. The algorithm works on a series of databases, each corresponding to a "
+ "different peptide group. The database is searched in series, and after each search, any "
+ "spectrum that is identified with a user-specified confidence threshold is sequestered "
+ "from subsequent searches. The full cascade search procedure is described in this article: </p>"
+ "<blockquote>Attila Kertesz-Farkas, Uri Keich and William Stafford Noble. "
+ "<a href=\"http://pubs.acs.org/doi/abs/10.1021/pr501173s\">\"Tandem mass spectrum "
+ "identification via cascaded search.\"</a> <i>Journal of Proteome Research</i>. "
+ "14(8):3027-38, 2015. </blockquote>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> CascadeSearchApplication::getArgs() const {
+ string arr[] = {
+ "tide spectra file+",
+ "database-series"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+
+/**
+ * \returns the command options
+ */
+vector<string> CascadeSearchApplication::getOptions() const {
+
+ string arr[] = {
+ "q-value-threshold"
+ };
+ vector<string> options(arr, arr + sizeof(arr) / sizeof(string));
+ addOptionsFrom<AssignConfidenceApplication>(&options);
+ addOptionsFrom<TideSearchApplication>(&options);
+ removeOptionFrom(&options, "top-match");
+
+ return options;
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > CascadeSearchApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("cascade-search.target.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited text file</a> containing the "
+ "target PSMs accepted at a pre-defined fdr."));
+ outputs.push_back(make_pair("cascade-search.log.txt",
+ "a log file containing a copy of all messages that were printed to stderr."));
+ outputs.push_back(make_pair("cascade-search.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ return outputs;
+}
+
+/**
+ * \returns the filestem for CascadeSearchApplication
+ */
+string CascadeSearchApplication::getFileStem() const {
+ return "cascade-search";
+}
+
+COMMAND_T CascadeSearchApplication::getCommand() const {
+ return CASCADE_COMMAND;
+}
+
+/**
+ * \returns whether the application needs the output directory or not.
+ */
+bool CascadeSearchApplication::needsOutputDirectory() const {
+ return true;
+}
+
+void CascadeSearchApplication::processParams() {
+
+ if (Params::GetInt("top-match") != 1 && !Params::IsDefault("top-match")) {
+ carp(CARP_WARNING, "Cascade-Search can work with top-match = 1 only.");
+ }
+ Params::Set("top-match", 1);
+
+ if (Params::GetBool("exact-p-value")) {
+ Params::Set("score", "exact p-value");
+ }
+ if (Params::GetBool("pin-output")) {
+ carp(CARP_FATAL, "Cascade-Search cannot work with pinxml-output=T.");
+ }
+ if (Params::GetBool("pepxml-output")) {
+ carp(CARP_FATAL, "Cascade-Search cannot work with pepxml-output=T.");
+ }
+ if (Params::GetBool("mzid-output")) {
+ carp(CARP_FATAL, "Cascade-Search cannot work with mzid-output=T.");
+ }
+ if (Params::GetBool("sqt-output")) {
+ carp(CARP_FATAL, "Cascade-Search cannot work with sqt-output=T.");
+ }
+}
+
+void CascadeSearchApplication::RemoveTempFiles(const string& path, const string& prefix) {
+ boost::filesystem::directory_iterator end_itr; // Default ctor yields past-the-end
+ for (boost::filesystem::directory_iterator i(path); i != end_itr; ++i) {
+ // Skip if not a file
+ if (!boost::filesystem::is_regular_file(i->status())) {
+ continue;
+ }
+
+ string filename = i->path().filename().generic_string();
+ if (filename.compare(0, prefix.length(), prefix) == 0) {
+ FileUtils::Remove(FileUtils::Join(path, filename));
+ }
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/CascadeSearchApplication.h b/src/app/CascadeSearchApplication.h
new file mode 100644
index 0000000..847f849
--- /dev/null
+++ b/src/app/CascadeSearchApplication.h
@@ -0,0 +1,89 @@
+/**
+ * \file CascadeSearchApplication.h
+ * AUTHOR: Attila Kertesz-Farkas
+ * CREATE DATE: 30 May 2015
+ * \brief Iterative PSM meta-search via Cascade protocol
+ ***********************************************************/
+#ifndef CascadeSearchApplication_H
+#define CascadeSearchApplication_H
+
+#include "CruxApplication.h"
+
+#include <string>
+
+class CascadeSearchApplication: public CruxApplication {
+
+ public:
+
+ /**
+ * \returns a blank CascadeSearchApplication object
+ */
+ CascadeSearchApplication();
+
+ /**
+ * Destructor
+ */
+ ~CascadeSearchApplication();
+
+ /**
+ * main method for CascadeSearchApplication
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for CascadeSearchApplication
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for CascadeSearchApplication
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns the filestem for CascadeSearchApplication
+ */
+ virtual std::string getFileStem() const;
+
+ /**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+ virtual COMMAND_T getCommand() const;
+
+ /**
+ * \returns whether the application needs the output directory or not.
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual void processParams();
+ void RemoveTempFiles(const std::string& path, const std::string& prefix);
+
+
+ static const int CASCADE_TERMINATION_CONDITION;
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/CometApplication.cpp b/src/app/CometApplication.cpp
new file mode 100644
index 0000000..17ff74e
--- /dev/null
+++ b/src/app/CometApplication.cpp
@@ -0,0 +1,546 @@
+/**
+ * \file CometApplication.cpp
+ * \brief Runs comet
+ *****************************************************************************/
+#include "CometSearch/Common.h"
+#include "CometSearch/CometSearchManager.h"
+#include "util/AminoAcidUtil.h"
+#include "util/CarpStreamBuf.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "CometApplication.h"
+#include "ParamMedicApplication.h"
+#include "io/DelimitedFileWriter.h"
+#include "io/DelimitedFile.h"
+
+using namespace std;
+
+/**
+ * \returns a blank CometApplication object
+ */
+CometApplication::CometApplication() {
+}
+
+/**
+ * Destructor
+ */
+CometApplication::~CometApplication() {
+}
+
+/**
+ * main method for CometApplication
+ */
+int CometApplication::main(int argc, char** argv) {
+ return main(Params::GetStrings("input spectra"));
+}
+
+int CometApplication::main(const vector<string>& input_files) {
+ for (vector<string>::const_iterator i = input_files.begin(); i != input_files.end(); i++) {
+ if (!StringUtils::IEndsWith(*i, ".mzXML") && !StringUtils::IEndsWith(*i, ".mzML") &&
+ !StringUtils::IEndsWith(*i, ".mzXML.gz") && !StringUtils::IEndsWith(*i, ".mzML.gz") &&
+ !StringUtils::IEndsWith(*i, ".raw") && !StringUtils::IEndsWith(*i, ".mgf") &&
+ !StringUtils::IEndsWith(*i, ".ms2") && !StringUtils::IEndsWith(*i, ".cms2")) {
+ carp(CARP_FATAL, "The format of file '%s' is not supported.", i->c_str());
+ }
+ }
+
+ /* Re-route stderr to log file */
+ CarpStreamBuf buffer;
+ streambuf* old = std::cerr.rdbuf();
+ std::cerr.rdbuf(&buffer);
+
+ /* set parameters */
+ vector<InputFileInfo*> pv_input_files;
+ setCometParameters(input_files, pv_input_files);
+ searchManager_.AddInputFiles(pv_input_files);
+
+ /* Run search */
+ bool success = searchManager_.DoSearch();
+
+ /* Recover stderr */
+ std::cerr.rdbuf(old);
+
+ return success ? 0 : 1;
+}
+
+void CometApplication::setString(const string& param) {
+ searchManager_.SetParam(param, Params::GetString(param), Params::GetString(param));
+}
+
+void CometApplication::setInt(const string& param) {
+ searchManager_.SetParam(param, Params::GetString(param), Params::GetInt(param));
+}
+
+void CometApplication::setIntRange(const string& param) {
+ vector<int> tokens = StringUtils::Fields<int>(Params::GetString(param));
+ IntRange r;
+ r.iStart = tokens[0];
+ r.iEnd = tokens[1];
+ searchManager_.SetParam(param, Params::GetString(param), r);
+}
+
+void CometApplication::setDouble(const string& param) {
+ searchManager_.SetParam(param, Params::GetString(param), Params::GetDouble(param));
+}
+
+void CometApplication::setDoubleRange(const string& param) {
+ vector<double> tokens = StringUtils::Fields<double>(Params::GetString(param));
+ DoubleRange r;
+ r.dStart = tokens[0];
+ r.dEnd = tokens[1];
+ searchManager_.SetParam(param, Params::GetString(param), r);
+}
+
+void CometApplication::setDoubleVector(const string& param) {
+ vector<double> v = StringUtils::Fields<double>(Params::GetString(param));
+ searchManager_.SetParam(param, Params::GetString(param), v);
+}
+
+void CometApplication::setVarMod(const string& param) {
+ vector<string> fields = StringUtils::Fields(Params::GetString(param));
+ if (fields.empty()) {
+ return;
+ }
+ VarMods m;
+ for (size_t i = 0; i < fields.size(); i++) {
+ string field = fields[i];
+ switch (i) {
+ case 0: m.dVarModMass = StringUtils::FromString<double>(field); break;
+ case 1: strcpy(m.szVarModChar, field.c_str()); break;
+ case 2: m.iBinaryMod = StringUtils::FromString<int>(field); break;
+ case 3: m.iMaxNumVarModAAPerMod = StringUtils::FromString<int>(field); break;
+ case 4: m.iVarModTermDistance = StringUtils::FromString<int>(field); break;
+ case 5: m.iWhichTerm = StringUtils::FromString<int>(field); break;
+ case 6: m.bRequireThisMod = StringUtils::FromString<int>(field); break;
+ }
+ }
+ searchManager_.SetParam(param, Params::GetString(param), m);
+}
+
+void CometApplication::setEnzyme(
+ const string& param,
+ const string& searchParam,
+ const string& sampleParam,
+ const string& missedCleavageParam) {
+ EnzymeInfo e;
+ double temp;
+ int search = Params::GetInt(searchParam);
+ if (search >= 0 && (size_t)search < get_comet_enzyme_info_lines().size()) {
+ const char* szParamBuf = get_comet_enzyme_info_lines()[search].c_str();
+ sscanf(szParamBuf, "%lf %48s %d %20s %20s\n",
+ &temp,
+ e.szSearchEnzymeName,
+ &e.iSearchEnzymeOffSet,
+ e.szSearchEnzymeBreakAA,
+ e.szSearchEnzymeNoBreakAA);
+ } else {
+ carp(CARP_FATAL, "search_enzyme_number=%d out of range (0-%d)",
+ search, get_comet_enzyme_info_lines().size() - 1);
+ }
+
+ int sample = Params::GetInt(sampleParam);
+ if (sample >= 0 && (size_t)sample < get_comet_enzyme_info_lines().size()) {
+ const char* szParamBuf = get_comet_enzyme_info_lines()[sample].c_str();
+ sscanf(szParamBuf, "%lf %48s %d %20s %20s\n",
+ &temp,
+ e.szSampleEnzymeName,
+ &e.iSampleEnzymeOffSet,
+ e.szSampleEnzymeBreakAA,
+ e.szSampleEnzymeNoBreakAA);
+ } else {
+ carp(CARP_FATAL, "sample_enzyme_number=%d out of range (0-%d)",
+ sample, get_comet_enzyme_info_lines().size() - 1);
+ }
+ e.iAllowedMissedCleavage = Params::GetInt(missedCleavageParam);
+ searchManager_.SetParam(param, "TODO", e);
+}
+
+/**
+ * Sets the parameters for the Comet application using the crux parameters
+ */
+void CometApplication::setCometParameters(
+ const vector<string>& spec_files,
+ vector<InputFileInfo*>& pvInputFiles ///<vector of input spectra files
+ ) {
+ string scan_range_str = Params::GetString("scan_range");
+ int analysis_type = AnalysisType_EntireFile;
+ int first_scan, last_scan;
+ if (scan_range_str != "0 0") {
+ analysis_type = AnalysisType_SpecificScanRange;
+ vector<string> tokens = StringUtils::Fields(scan_range_str);
+ first_scan = StringUtils::FromString<int>(tokens[0]);
+ last_scan = StringUtils::FromString<int>(tokens[1]);
+ }
+
+ for (vector<string>::const_iterator i = spec_files.begin(); i != spec_files.end(); i++) {
+ if (!FileUtils::Exists(*i)) {
+ carp(CARP_FATAL, "Spectra File Not Found:%s", i->c_str());
+ }
+ InputFileInfo* pInputFile = new InputFileInfo();
+ strcpy(pInputFile->szFileName, i->c_str());
+ pInputFile->iAnalysisType = analysis_type;
+ if (analysis_type == AnalysisType_SpecificScanRange) {
+ pInputFile->iFirstScan = first_scan;
+ pInputFile->iLastScan = last_scan;
+ }
+ string basename = make_file_path(getFileStem());
+ if (spec_files.size() > 1) {
+ basename += "." + FileUtils::Stem(*i);
+ }
+ strcpy(pInputFile->szBaseName, basename.c_str());
+ pvInputFiles.push_back(pInputFile);
+ }
+
+ // Database
+ setString("database_name");
+ setInt("decoy_search");
+ // CPU threads
+ setInt("num_threads");
+ // Masses
+ setDouble("peptide_mass_tolerance");
+ setInt("peptide_mass_units");
+ setInt("mass_type_parent");
+ setInt("mass_type_fragment");
+ setInt("precursor_tolerance_type");
+ setInt("isotope_error");
+ // Search enzyme
+ setInt("search_enzyme_number");
+ setInt("num_enzyme_termini");
+ setInt("allowed_missed_cleavage");
+ // Fragment ions
+ setDouble("fragment_bin_tol");
+ setDouble("fragment_bin_offset");
+ setInt("theoretical_fragment_ions");
+ setInt("use_A_ions");
+ setInt("use_B_ions");
+ setInt("use_C_ions");
+ setInt("use_X_ions");
+ setInt("use_Y_ions");
+ setInt("use_Z_ions");
+ setInt("use_NL_ions");
+ // Output
+ searchManager_.SetParam("output_sqtstream", "0", 0);
+ setInt("output_sqtfile");
+ setInt("output_txtfile");
+ setInt("output_pepxmlfile");
+ setInt("output_percolatorfile");
+ setInt("output_outfiles");
+ setInt("print_expect_score");
+ setInt("num_output_lines");
+ setInt("show_fragment_ions");
+ setInt("sample_enzyme_number");
+ // mzXML/mzML parameters
+ setIntRange("scan_range");
+ setIntRange("precursor_charge");
+ setInt("override_charge");
+ setInt("ms_level");
+ setString("activation_method");
+ // Misc. parameters
+ setDoubleRange("digest_mass_range");
+ setInt("num_results");
+ setInt("skip_researching");
+ setInt("max_fragment_charge");
+ setInt("max_precursor_charge");
+ setInt("nucleotide_reading_frame");
+ setInt("clip_nterm_methionine");
+ setInt("spectrum_batch_size");
+ setString("decoy_prefix");
+ setString("output_suffix");
+ setDoubleVector("mass_offsets");
+ // Spectral processing
+ setInt("minimum_peaks");
+ setDouble("minimum_intensity");
+ setInt("remove_precursor_peak");
+ setDouble("remove_precursor_tolerance");
+ setDoubleRange("clear_mz_range");
+ // Variable modifications
+ setVarMod("variable_mod01");
+ setVarMod("variable_mod02");
+ setVarMod("variable_mod03");
+ setVarMod("variable_mod04");
+ setVarMod("variable_mod05");
+ setVarMod("variable_mod06");
+ setVarMod("variable_mod07");
+ setVarMod("variable_mod08");
+ setVarMod("variable_mod09");
+ setInt("max_variable_mods_in_peptide");
+ setInt("require_variable_mod");
+ // Static modifications
+ setDouble("add_Cterm_peptide");
+ setDouble("add_Nterm_peptide");
+ setDouble("add_Cterm_protein");
+ setDouble("add_Nterm_protein");
+ for (char c = 'A'; c <= 'Z'; c++) {
+ string aaName = AminoAcidUtil::GetName(c);
+ aaName = aaName.empty() ? "user_amino_acid" : StringUtils::Replace(aaName, " ", "_");
+ string param = "add_" + string(1, c) + "_" + aaName;
+ setDouble(param);
+ }
+
+ setEnzyme("[COMET_ENZYME_INFO]",
+ "search_enzyme_number", "sample_enzyme_number", "allowed_missed_cleavage");
+}
+
+/**
+ * \returns the command name for CometApplication
+ */
+string CometApplication::getName() const {
+ return "comet";
+}
+
+/**
+ * \returns the description for CometApplication
+ */
+string CometApplication::getDescription() const {
+ return
+ "[[nohtml:Search a collection of spectra against a sequence database, "
+ "returning a collection of PSMs. This search engine runs directly on a "
+ "protein database in FASTA format.]]"
+ "[[html:<p>This command searches a protein database with a set of spectra, "
+ "assigning peptide sequences to the observed spectra. This search engine "
+ "was developed by Jimmy Eng at the University of Washington Proteomics "
+ "Resource.</p><p>Although its history goes back two decades, the Comet "
+ "search engine was first made publicly available in August 2012 on "
+ "SourceForge. Comet is multithreaded and supports multiple input and "
+ "output formats.</p><blockquote><a href=\"http://onlinelibrary.wiley.com/"
+ "doi/10.1002/pmic.201200439/abstract\">"Comet: an open source tandem "
+ "mass spectrometry sequence database search tool."</a> Eng JK, Jahan "
+ "TA, Hoopmann MR. <em>Proteomics</em>. 2012 Nov 12. doi: "
+ "10.1002/pmic201200439</blockquote>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> CometApplication::getArgs() const {
+ string arr[] = {
+ "input spectra+",
+ "database_name"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> CometApplication::getOptions() const {
+ string arr[] = {
+ "fileroot",
+ "output-dir",
+ "overwrite",
+ "parameter-file",
+ "verbosity",
+ // Database
+ "decoy_search",
+ // CPU threads
+ "num_threads",
+ // Masses
+ "peptide_mass_tolerance",
+ "auto_peptide_mass_tolerance",
+ "peptide_mass_units",
+ "mass_type_parent",
+ "mass_type_fragment",
+ "precursor_tolerance_type",
+ "isotope_error",
+ // Search enzyme
+ "search_enzyme_number",
+ "num_enzyme_termini",
+ "allowed_missed_cleavage",
+ // Fragment ions
+ "fragment_bin_tol",
+ "fragment_bin_offset",
+ "auto_fragment_bin_tol",
+ "theoretical_fragment_ions",
+ "use_A_ions",
+ "use_B_ions",
+ "use_C_ions",
+ "use_X_ions",
+ "use_Y_ions",
+ "use_Z_ions",
+ "use_NL_ions",
+ // Output
+ "output_sqtfile",
+ "output_txtfile",
+ "output_pepxmlfile",
+ "output_percolatorfile",
+ "output_outfiles",
+ "print_expect_score",
+ "num_output_lines",
+ "show_fragment_ions",
+ "sample_enzyme_number",
+ // mzXML/mzML parameters
+ "scan_range",
+ "precursor_charge",
+ "override_charge",
+ "ms_level",
+ "activation_method",
+ // Misc. parameters
+ "digest_mass_range",
+ "num_results",
+ "skip_researching",
+ "max_fragment_charge",
+ "max_precursor_charge",
+ "nucleotide_reading_frame",
+ "clip_nterm_methionine",
+ "spectrum_batch_size",
+ "decoy_prefix",
+ "output_suffix",
+ "mass_offsets",
+ // Spectral processing
+ "minimum_peaks",
+ "minimum_intensity",
+ "remove_precursor_peak",
+ "remove_precursor_tolerance",
+ "clear_mz_range",
+ // Variable modifications
+ "variable_mod01",
+ "variable_mod02",
+ "variable_mod03",
+ "variable_mod04",
+ "variable_mod05",
+ "variable_mod06",
+ "variable_mod07",
+ "variable_mod08",
+ "variable_mod09",
+ "max_variable_mods_in_peptide",
+ "require_variable_mod",
+ // Static modifications
+ "add_Cterm_peptide",
+ "add_Nterm_peptide",
+ "add_Cterm_protein",
+ "add_Nterm_protein",
+ "add_A_alanine",
+ "add_B_user_amino_acid",
+ "add_C_cysteine",
+ "add_D_aspartic_acid",
+ "add_E_glutamic_acid",
+ "add_F_phenylalanine",
+ "add_G_glycine",
+ "add_H_histidine",
+ "add_I_isoleucine",
+ "add_J_user_amino_acid",
+ "add_K_lysine",
+ "add_L_leucine",
+ "add_M_methionine",
+ "add_N_asparagine",
+ "add_O_ornithine",
+ "add_P_proline",
+ "add_Q_glutamine",
+ "add_R_arginine",
+ "add_S_serine",
+ "add_T_threonine",
+ "add_U_selenocysteine",
+ "add_V_valine",
+ "add_W_tryptophan",
+ "add_X_user_amino_acid",
+ "add_Y_tyrosine",
+ "add_Z_user_amino_acid",
+ // param-medic
+ "pm-min-precursor-mz",
+ "pm-max-precursor-mz",
+ "pm-min-frag-mz",
+ "pm-max-frag-mz",
+ "pm-min-scan-frag-peaks",
+ "pm-max-precursor-delta-ppm",
+ "pm-charge",
+ "pm-top-n-frag-peaks",
+ "pm-pair-top-n-frag-peaks",
+ "pm-min-common-frag-peaks",
+ "pm-max-scan-separation",
+ "pm-min-peak-pairs"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > CometApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("comet.target.txt",
+ "a tab-delimited text file containing the target PSMs. See <a href=\""
+ "../file-formats/txt-format.html\">"
+ "txt file format</a> for a list of the fields."));
+ outputs.push_back(make_pair("comet.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("comet.log.txt",
+ "a log file containing a copy of all messages that were printed to "
+ "standard error."));
+ return outputs;
+}
+
+COMMAND_T CometApplication::getCommand() const {
+ return COMET_COMMAND;
+}
+
+/**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+bool CometApplication::needsOutputDirectory() const {
+ return true;
+}
+
+void CometApplication::processParams() {
+ const string varModPrefix = "variable_mod0";
+ const string varModEmptyDefault = "0.0 null 0 4 -1 0 0";
+ for (int i = 1; i <= 9; i++) {
+ string mod = varModPrefix + StringUtils::ToString(i);
+ if (Params::GetString(mod).empty()) {
+ Params::Set(mod, varModEmptyDefault);
+ }
+ }
+ // run param-medic?
+ const string autoPrecursor = Params::GetString("auto_peptide_mass_tolerance");
+ const string autoFragment = Params::GetString("auto_fragment_bin_tol");
+ if (autoPrecursor != "false" || autoFragment != "false") {
+ if (autoPrecursor != "false" && Params::GetInt("peptide_mass_units") != 2) {
+ carp(CARP_FATAL, "Automatic peptide mass tolerance detection is only supported with ppm "
+ "units. Please rerun with either auto_peptide_mass_tolerance set to 'false' "
+ "or peptide_mass_units set to '2'.");
+ }
+ ParamMedicErrorCalculator errCalc;
+ errCalc.processFiles(Params::GetStrings("input spectra"));
+ string precursorFailure, fragmentFailure;
+ double precursorSigmaPpm = 0;
+ double fragmentSigmaPpm = 0;
+ double fragmentSigmaTh = 0;
+ double precursorPredictionPpm = 0;
+ double fragmentPredictionPpm = 0;
+ double fragmentPredictionTh = 0;
+ errCalc.calcMassErrorDist(&precursorFailure, &fragmentFailure,
+ &precursorSigmaPpm, &fragmentSigmaPpm,
+ &precursorPredictionPpm, &fragmentPredictionTh);
+
+ if (autoPrecursor != "false") {
+ if (precursorFailure.empty()) {
+ carp(CARP_INFO, "precursor ppm standard deviation: %f", precursorSigmaPpm);
+ carp(CARP_INFO, "Precursor error estimate (ppm): %.2f", precursorPredictionPpm);
+ Params::Set("peptide_mass_tolerance", precursorPredictionPpm);
+ } else {
+ carp(autoPrecursor == "fail" ? CARP_FATAL : CARP_ERROR,
+ "failed to calculate precursor error: %s", precursorFailure.c_str());
+ }
+ }
+ if (autoFragment != "false") {
+ if (fragmentFailure.empty()) {
+ carp(CARP_INFO, "fragment standard deviation (ppm): %f", fragmentSigmaPpm);
+ carp(CARP_INFO, "Fragment bin size estimate (Th): %.4f", fragmentPredictionTh);
+ Params::Set("fragment_bin_tol", fragmentPredictionTh);
+ } else {
+ carp(autoFragment == "fail" ? CARP_FATAL : CARP_ERROR,
+ "failed to calculate fragment error: %s", fragmentFailure.c_str());
+ }
+ }
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/CometApplication.h b/src/app/CometApplication.h
new file mode 100644
index 0000000..647fef0
--- /dev/null
+++ b/src/app/CometApplication.h
@@ -0,0 +1,102 @@
+/**
+ * \file CruxHardklorApplication.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 4 November 2011
+ * \brief Interface for calling hardklor.
+ *****************************************************************************/
+#ifndef COMETAPPLICATION_H
+#define COMETAPPLICATION_H
+
+#include "CruxApplication.h"
+#include "CometSearch/CometSearchManager.h"
+#include <string>
+#include <fstream>
+#include <iostream>
+
+class CometApplication: public CruxApplication {
+
+ protected:
+ CometSearchManager searchManager_;
+
+ void setString(const std::string& param);
+ void setInt(const std::string& param);
+ void setIntRange(const std::string& param);
+ void setDouble(const std::string& param);
+ void setDoubleRange(const std::string& param);
+ void setDoubleVector(const std::string& param);
+ void setVarMod(const std::string& param);
+ void setEnzyme(const std::string& param,
+ const std::string& searchParam,
+ const std::string& sampleParam,
+ const std::string& missedCleavageParam);
+
+ public:
+
+ /**
+ * \returns a blank CometApplication object
+ */
+ CometApplication();
+
+ /**
+ * Destructor
+ */
+ ~CometApplication();
+
+ /**
+ * main method for CometApplication
+ */
+ virtual int main(int argc, char** argv);
+
+ int main(const std::vector<std::string>& input_files);
+
+ /**
+ * \returns the command name for CometApplication
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for CometApplication
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ virtual COMMAND_T getCommand() const;
+
+ /**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual void processParams();
+
+ /**
+ * Sets the parameters for the Comet application using the crux parameters
+ */
+ void setCometParameters(
+ const std::vector<std::string>& spec_files,
+ std::vector<InputFileInfo*>& pvInputFiles ///<vector of input spectra files
+ );
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ComputeQValues.cpp b/src/app/ComputeQValues.cpp
new file mode 100644
index 0000000..2628675
--- /dev/null
+++ b/src/app/ComputeQValues.cpp
@@ -0,0 +1,275 @@
+/**
+ * \file ComputeQValues.cpp
+ * \brief Object for calling compute-q-values
+ *****************************************************************************/
+#include "ComputeQValues.h"
+#include "io/OutputFiles.h"
+#include "util/Params.h"
+#include "PosteriorEstimator.h"
+
+
+using namespace std;
+
+#ifdef _MSC_VER
+// The Microsoft C++ compiler has trouble resolving the proper virtual
+// function call when the STL make_pair is combined with the STL ptr_fun.
+// They promise to fix this a later version, but until then we create our own wrapper
+// for this use of make_pair.
+pair<double, bool> make_pair(double db, bool b);
+#endif
+
+/**
+ * \returns a blank ComputeQValues object
+ */
+ComputeQValues::ComputeQValues() {
+
+}
+
+/**
+ * Destructor
+ */
+ComputeQValues::~ComputeQValues() {
+}
+
+/**
+ * main method for ComputeQValues
+ */
+int ComputeQValues::main(int argc, char** argv) {
+ vector<string> input_files = Params::GetStrings("target input");
+
+ if (Params::GetBool("list-of-files")) {
+ get_files_from_list(input_files[0], input_files);
+ }
+ return main(input_files);
+}
+
+int ComputeQValues::main(const vector<string>& input_files) {
+ // Prepare the output files.
+
+ return 0;
+}
+
+/**
+ * Compute posterior error probabilities (PEP) from the given target
+ * and decoy scores.
+ * \returns A newly allocated array of PEP for the target scores
+ * sorted.
+ */
+
+#ifdef _MSC_VER
+// The Microsoft 10.0 C++ compiler has trouble resolving the proper virtual
+// function call when the STL make_pair is combined with the STL ptr_fun.
+// They promise to fix this in v11, but until then we create our own wrapper
+// for this use of make_pair. (See corresponding ifdef block in compute_PEP)
+pair<double, bool> make_pair(double db, bool b) {
+ return std::pair<double, bool>(db, b);
+}
+#endif
+double* ComputeQValues::compute_PEP(double* target_scores, ///< scores for target matches
+ int num_targets, ///< size of target_scores
+ double* decoy_scores, ///< scores for decoy matches
+ int num_decoys, ///< size of decoy_scores
+ bool ascending ///< are the scores ascending or descending
+) {
+ if (target_scores == NULL || decoy_scores == NULL || num_targets == 0 || num_decoys == 0) {
+ carp(CARP_FATAL, "Cannot compute PEP without target or decoy scores.");
+ }
+// pi0 = estimate_pi0(target_scores, num_targets, decoy_scores, num_decoys, ascending);
+
+ // put all of the scores in a single vector of pairs: score, is_target
+ vector<pair<double, bool> > score_labels;
+
+ transform(target_scores, target_scores + num_targets,
+ back_inserter(score_labels),
+ bind2nd(ptr_fun<double, bool, pair<double, bool> >(make_pair), true));
+ transform(decoy_scores, decoy_scores + num_decoys,
+ back_inserter(score_labels),
+ bind2nd(ptr_fun<double, bool, pair<double, bool> >(make_pair), false));
+
+ // sort them
+ if (ascending) {
+ sort(score_labels.begin(), score_labels.end());
+ PosteriorEstimator::setReversed(true);
+ } else {
+ sort(score_labels.begin(), score_labels.end(),
+ greater<pair<double, bool> > ());
+ }
+ // get p-values
+ vector<double> pvals;
+ PosteriorEstimator::getPValues(score_labels, pvals);
+
+ // estimate pi0
+ double pi0 = PosteriorEstimator::estimatePi0(pvals);
+
+ // estimate PEPs
+ vector<double> PEP_vector;
+
+ PosteriorEstimator::estimatePEP(score_labels,
+ true, // usePi0
+ pi0, PEP_vector,
+ true); // include decoy PEPs
+
+ // now score_labels and PEPs are similarly sorted
+
+ // pull out the PEPs in the order that the scores were given
+ double* PEP_array = new double[PEP_vector.size()];
+
+ for (int target_idx = 0; target_idx < num_targets; target_idx++) {
+ // the score to return next
+ double curr_target_score = target_scores[target_idx];
+
+ // find its position in score_labels
+ vector< pair<double, bool> >::iterator found_score_pos;
+ if (ascending) {
+ found_score_pos
+ = lower_bound(score_labels.begin(), score_labels.end(),
+ make_pair(curr_target_score, true));
+ } else {
+ found_score_pos
+ = lower_bound(score_labels.begin(), score_labels.end(),
+ make_pair(curr_target_score, true),
+ greater<pair<double, bool> >());
+ }
+
+ size_t found_index = distance(score_labels.begin(), found_score_pos);
+
+ // pull out the PEP at the same position in PEP_vector
+ PEP_array[target_idx] = PEP_vector[found_index];
+ }
+
+ return PEP_array;
+}
+
+/**
+ * \returns the command name for ComputeQValues
+ */
+string ComputeQValues::getName() const {
+ return "assign-confidence";
+}
+
+/**
+ * \returns the description for ComputeQValues
+ */
+string ComputeQValues::getDescription() const {
+ return
+ "[[nohtml:Assign two types of statistical confidence measures (q-values "
+ "and posterior error probabilities) to each PSM in a given set.]]"
+ "[[html:<p>Given target and decoy scores, estimate a q-value for each "
+ "target score. The q-value is analogous to a p-value but incorporates "
+ "false discovery rate multiple testing correction. The q-value associated "
+ "with a score threshold T is defined as the minimal false discovery rate "
+ "(FDR) at which a score of T is deemed significant. In this setting, the "
+ "q-value accounts for the fact that we are analyzing a large collection of "
+ "scores. For confidence estimation afficionados, please note that this "
+ "definition of \"q-value\" is independent of the notion of \"positive FDR\" "
+ "as defined in (Storey <em>Annals of Statistics</em> 31:2013-2015:2003).</p>"
+ "<p>To estimate FDRs, <code>assign-confidence</code> uses one of two "
+ "different procedures. Both require that the input contain both target and "
+ "decoy scores. The default, target-decoy competition (TDC) procedure is "
+ "described in this article:</p><blockquote>Josh E. Elias and Steve P. Gygi. "
+ "\"Target-decoy search strategy for increased confidence in large-scale "
+ "protein identifications by mass spectrometry.\" <em>Nature Methods</em>. "
+ "4(3):207-14, 2007.</blockquote><p>Note that <code>assign-confidence</code> "
+ "implements a variant of the protocol proposed by Elias and Gygi: rather "
+ "than reporting a list that contains both targets and decoys, <code>"
+ "assign-confidence</code> reports only the targets. The FDR estimate is "
+ "adjusted accordingly (by dividing by 2).</p><p>The alternative, <em>"
+ "mix-max</em> procedure is described in this article:</p><blockquote>Uri "
+ "Keich, Attila Kertesz-Farkas and William Stafford Noble. \"An improved "
+ "false discovery rate estimation procedure for shotgun proteomics.\" "
+ "Submitted.</blockquote><p>Note that the mix-max procedure requires as "
+ "input calibrated scores, such as Comet E-values or p-values produced "
+ "using Tide-s <code>exact-p-value</code> option.</p>"
+ "<p>The mix-max procedure requires that scores "
+ "are reported from separate target and decoy searches. Thus, this approach "
+ "is incompatible with a search that is run using the <code>--concat T"
+ "</code> option to <code>tide-search</code> or the <code>--decoy_search 2"
+ "</code> option to <code>comet</code>. On the other hand, the TDC "
+ "procedure can take as input "
+ "searches conducted in either mode (concatenated or separate). If given "
+ "separate search results and asked to do TDC estimation, <code>"
+ "assign-confidence</code> will carry out the target-decoy competition as "
+ "part of the confidence estimation procedure.</p><p>In each case, the "
+ "estimated FDRs are converted to q-values by sorting the scores then "
+ "taking, for each score, the minimum of the current FDR and all of the FDRs "
+ "below it in the ranked list.</p><p>A primer on multiple testing correction "
+ "can be found here:</p><blockquote>William Stafford Noble. <a href=\""
+ "http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1135.html\">\"How "
+ "does multiple testing correction work?\"</a> <em>Nature Biotechnology</em>. "
+ "27(12):1135-1137, 2009.</blockquote>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> ComputeQValues::getArgs() const {
+ string arr[] = {
+ "target input+"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> ComputeQValues::getOptions() const {
+ string arr[] = {
+ "estimation-method",
+ "decoy-prefix",
+ "score",
+ "sidak",
+ "peptide-level",
+ "verbosity",
+ "parameter-file",
+ "overwrite",
+ "output-dir",
+ "list-of-files",
+ "fileroot"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > ComputeQValues::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("assign-confidence.target.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited text file</a> that contains the "
+ "targets, sorted by score. The file will contain one new column, named "
+ "\"<method> q-value\", where <method> is either \"tdc\" or \"mix-max\"."));
+ outputs.push_back(make_pair("assign-confidence.log.txt",
+ "a log file containing a copy of all messages that were printed to stderr."));
+ outputs.push_back(make_pair("assign-confidence.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ return outputs;
+}
+
+/**
+ * \returns the filestem for ComputeQValues
+ */
+string ComputeQValues::getFileStem() const {
+ return "assign-confidence";
+}
+
+COMMAND_T ComputeQValues::getCommand() const {
+ return QVALUE_COMMAND;
+}
+
+/**
+ * \returns whether the application needs the output directory or not.
+ */
+bool ComputeQValues::needsOutputDirectory() const {
+ return true;
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ComputeQValues.h b/src/app/ComputeQValues.h
new file mode 100644
index 0000000..ab127bf
--- /dev/null
+++ b/src/app/ComputeQValues.h
@@ -0,0 +1,98 @@
+/**
+ * \file ComputeQValues.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Object for running compute-q-values
+ *****************************************************************************/
+#ifndef ComputeQValues_H
+#define ComputeQValues_H
+
+#include "CruxApplication.h"
+
+#include <string>
+
+class ComputeQValues: public CruxApplication {
+
+ public:
+
+ /**
+ * \returns a blank ComputeQValues object
+ */
+ ComputeQValues();
+
+ /**
+ * Destructor
+ */
+ ~ComputeQValues();
+
+ /**
+ * main method for ComputeQValues
+ */
+ virtual int main(int argc, char** argv);
+
+ int main(const std::vector<std::string>& input_files);
+
+ /**
+ * Compute posterior error probabilities (PEP) from the given target
+ * and decoy scores.
+ * \returns A newly allocated array of PEP for the target scores
+ * sorted.
+ */
+ static double* compute_PEP(double* target_scores, ///< scores for target matches
+ int num_targets, ///< size of target_scores
+ double* decoy_scores, ///< scores for decoy matches
+ int num_decoys, ///< size of decoy_scores
+ bool ascending = false); ///< are the scores ascending/descending?
+
+ /**
+ * \returns the command name for ComputeQValues
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for ComputeQValues
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns the filestem for ComputeQValues
+ */
+ virtual std::string getFileStem() const;
+
+ /**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+ virtual COMMAND_T getCommand() const;
+
+ /**
+ * \returns whether the application needs the output directory or not.
+ */
+ virtual bool needsOutputDirectory() const;
+
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ComputeQValuesLegacy.h b/src/app/ComputeQValuesLegacy.h
new file mode 100644
index 0000000..fc7aa9b
--- /dev/null
+++ b/src/app/ComputeQValuesLegacy.h
@@ -0,0 +1,46 @@
+/**
+ *
+ */
+#ifndef ComputeQValuesLegacy_H
+#define ComputeQValuesLegacy_H
+
+#include "ComputeQValues.h"
+
+class ComputeQValuesLegacy : public ComputeQValues {
+
+ public:
+ /**
+ * \returns A blank ComputeQValues object.
+ */
+ ComputeQValuesLegacy() {}
+
+ /**
+ * Destructor
+ */
+ ~ComputeQValuesLegacy() {}
+
+ /**
+ * \returns The command name for ComputeQValues.
+ */
+ virtual std::string getName() const {
+ return "compute-q-values";
+ }
+ /**
+ * Exclude this application from the usage statement.
+ */
+ virtual bool hidden() const {
+ return true;
+ }
+};
+
+
+
+#endif // ComputeQValuesLegacy_H
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/CreateDocs.cpp b/src/app/CreateDocs.cpp
new file mode 100644
index 0000000..e42da09
--- /dev/null
+++ b/src/app/CreateDocs.cpp
@@ -0,0 +1,598 @@
+#include <algorithm>
+#include <cctype>
+#include <functional>
+#include <fstream>
+#include <iostream>
+
+#include "CreateDocs.h"
+#include "CruxApplicationList.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+#include "xlink/xlink_assign_ions.h"
+#include "xlink/xhhc_score_peptide_spectrum.h"
+#include "qranker-barista/Barista.h"
+#include "ComputeQValues.h"
+#include "CruxBullseyeApplication.h"
+#include "CruxHardklorApplication.h"
+#include "ExtractColumns.h"
+#include "ExtractRows.h"
+#include "GeneratePeptides.h"
+#include "GetMs2Spectrum.h"
+#include "MakePinApplication.h"
+#include "ParamMedicApplication.h"
+#include "PercolatorApplication.h"
+#include "Pipeline.h"
+#include "PredictPeptideIons.h"
+#include "PrintProcessedSpectra.h"
+#include "PSMConvertApplication.h"
+#include "qranker-barista/QRanker.h"
+#include "ReadTideIndex.h"
+#include "xlink/SearchForXLinks.h"
+#include "SortColumn.h"
+#include "SpectralCounts.h"
+#include "StatColumn.h"
+#include "TideIndexApplication.h"
+#include "TideSearchApplication.h"
+#include "CometApplication.h"
+#include "app/CascadeSearchApplication.h"
+#include "app/AssignConfidenceApplication.h"
+#include "app/SubtractIndexApplication.h"
+
+using namespace std;
+
+CreateDocs::CreateDocs() {
+}
+
+CreateDocs::~CreateDocs() {
+}
+
+int CreateDocs::main(int argc, char** argv) {
+ CruxApplicationList apps("crux");
+ apps.add(new AssignConfidenceApplication());
+ apps.add(new Barista());
+ apps.add(new CascadeSearchApplication());
+ apps.add(new CometApplication());
+ apps.add(new CreateDocs());
+ apps.add(new CruxBullseyeApplication());
+ apps.add(new CruxHardklorApplication());
+ apps.add(new ExtractColumns());
+ apps.add(new ExtractRows());
+ apps.add(new GeneratePeptides());
+ apps.add(new GetMs2Spectrum());
+ apps.add(new MakePinApplication());
+ apps.add(new ParamMedicApplication());
+ apps.add(new PercolatorApplication());
+ apps.add(new PipelineApplication());
+ apps.add(new PredictPeptideIons());
+ apps.add(new PrintProcessedSpectra());
+ apps.add(new PSMConvertApplication());
+ apps.add(new QRanker());
+ apps.add(new ReadTideIndex());
+ apps.add(new SearchForXLinks());
+ apps.add(new SortColumn());
+ apps.add(new SpectralCounts());
+ apps.add(new StatColumn());
+ apps.add(new SubtractIndexApplication());
+ apps.add(new TideIndexApplication());
+ apps.add(new TideSearchApplication());
+ apps.add(new XLinkAssignIons());
+ apps.add(new XLinkScoreSpectrum());
+
+ string targetApp = Params::GetString("tool-name");
+ if (targetApp == "list") {
+ // List the applications available for create-docs
+ for (vector<CruxApplication*>::const_iterator i = apps.begin(); i != apps.end(); i++) {
+ cout << (*i)->getName() << endl;
+ }
+ } else if (targetApp == "default-params") {
+ // Write a default parameter file
+ cout << "########################################"
+ "########################################" << endl
+ << "# Sample parameter file" << endl
+ << "#" << endl
+ << "# On each line, anything after a '#' will be ignored." << endl
+ << "# The format is:" << endl
+ << "#" << endl
+ << "# <parameter-name>=<value>" << endl
+ << "#" << endl
+ << "########################################"
+ "########################################" << endl
+ << endl;
+ Params::Write(&cout, true);
+ } else if (targetApp == "check-params") {
+ // Check for issues with parameters
+ checkParams(&apps);
+ } else if (targetApp == "param-table") {
+ // Make a table of parameters x commands.
+ makeParamTable(&apps);
+ } else {
+ CruxApplication* app = apps.find(targetApp);
+ if (app == NULL) {
+ carp(CARP_FATAL, "Invalid application '%s'", targetApp.c_str());
+ }
+ generateToolHtml(&cout, app);
+ }
+
+ return 0;
+}
+
+void CreateDocs::checkParams(const CruxApplicationList* apps) {
+ carp(CARP_INFO, "Running parameter validity checks...");
+ for (map<string, Param*>::const_iterator i = Params::BeginAll();
+ i != Params::EndAll();
+ i++) {
+ Param* param = i->second;
+ string name = param->GetName();
+ bool isArg = param->IsArgument();
+ // Check for unused if passed an application list
+ if (apps) {
+ vector<CruxApplication*> appsUsing;
+ int appArgCount = 0;
+ int appOptionCount = 0;
+ for (vector<CruxApplication*>::const_iterator j = apps->begin();
+ j != apps->end();
+ j++) {
+ vector<string> appArgs = (*j)->getArgs();
+ for (vector<string>::iterator k = appArgs.begin(); k != appArgs.end(); k++) {
+ if (StringUtils::EndsWith(*k, "+")) {
+ *k = k->substr(k->length() - 1);
+ }
+ }
+ vector<string> appOptions = (*j)->getOptions();
+ bool appArg =
+ std::find(appArgs.begin(), appArgs.end(), name) != appArgs.end();
+ bool appOption =
+ std::find(appOptions.begin(), appOptions.end(), name) != appOptions.end();
+ if (!appArg && !appOption) {
+ continue;
+ }
+ string appName = (*j)->getName();
+ appsUsing.push_back(*j);
+ if (appArg) {
+ ++appArgCount;
+ if (!isArg) {
+ carp(CARP_WARNING, "'%s' is an option, but is listed as an argument for '%s'",
+ name.c_str(), appName.c_str());
+ }
+ }
+ if (appOption) {
+ ++appOptionCount;
+ if (isArg) {
+ carp(CARP_WARNING, "'%s' is an argument, but is listed as an option for '%s'",
+ name.c_str(), appName.c_str());
+ }
+ if (!Params::IsVisible(name)) {
+ carp(CARP_WARNING, "'%s' is marked as hidden, but is listed as an option for '%s'",
+ name.c_str(), appName.c_str());
+ }
+ }
+ }
+ if (appArgCount > 0 && appOptionCount > 0) {
+ carp(CARP_WARNING, "'%s' is both an option and an argument", name.c_str());
+ }
+ if (!appsUsing.empty()) {
+ stringstream ss;
+ for (vector<CruxApplication*>::const_iterator j = appsUsing.begin();
+ j != appsUsing.end();
+ j++) {
+ if (j > appsUsing.begin()) {
+ ss << ", ";
+ }
+ ss << (*j)->getName();
+ }
+ carp(CARP_DEBUG, "'%s' is used by: %s", name.c_str(), ss.str().c_str());
+ } else {
+ carp(CARP_WARNING, "No applications are using '%s'", name.c_str());
+ }
+ }
+ }
+}
+
+void CreateDocs::makeParamTable(const CruxApplicationList* apps) {
+ carp(CARP_INFO, "Creating a table of parameters X commands.");
+ cout << "<!DOCTYPE HTML>" << endl
+ << "<html><head><meta charset=\"UTF-8\">" << endl
+ << "<title>Crux parameters</title>" << endl
+ << "<link href=\"../crux.css\" rel=\"styleSheet\" type=\"text/css\">"
+ << "</head>" << endl
+ << "<body><h1>Crux parameters</h1>" << endl
+ << "<table border=\"1\" align=\"center\">" << endl;
+
+ // Print the header row.
+ cout << "<tr><td> </td>";
+ for (vector<CruxApplication*>::const_iterator appIter = apps->begin();
+ appIter != apps->end();
+ appIter++) {
+ cout << "<td>" << (*appIter)->getName() << "</td>";
+ }
+ cout << "</tr>" << endl;
+
+ // Keep track of whether this parameter row has been printed.
+ std::map<const string, bool> isPrinted;
+
+ // Alternate background.
+ bool backgroundIsGrey = true;
+
+ /*
+ * We use a double loop to print the parameters so that we ensure
+ * that parameters are listed in order of their use by the commands.
+ */
+ for (vector<CruxApplication*>::const_iterator appIter1 = apps->begin();
+ appIter1 != apps->end();
+ appIter1++) {
+ vector<string> appOptions1 = (*appIter1)->getOptions();
+ for (vector<string>::const_iterator appOptionIter = appOptions1.begin();
+ appOptionIter != appOptions1.end();
+ appOptionIter++) {
+ if (!isPrinted[*appOptionIter] && Params::IsVisible(*appOptionIter)) {
+ isPrinted[*appOptionIter] = true;
+ if (backgroundIsGrey) {
+ cout << "<tr bgcolor=\"#DEDEDE\">" << endl;
+ } else {
+ cout << "<tr>" << endl;
+ }
+ backgroundIsGrey = !backgroundIsGrey;
+ cout << "<td>" << *appOptionIter << "</td>";
+ for (vector<CruxApplication*>::const_iterator appIter2 = apps->begin();
+ appIter2 != apps->end();
+ appIter2++) {
+
+ vector<string> appOptions = (*appIter2)->getOptions();
+ bool hasOption = std::find(appOptions.begin(), appOptions.end(),
+ *appOptionIter) != appOptions.end();
+ if (hasOption) {
+ cout << "<td>✓</td>";
+ } else {
+ cout << "<td> </td>";
+ }
+ }
+ cout << "</tr>" << endl;
+ }
+ }
+ }
+ cout << "</table></body></html>" << endl;
+
+ // Check that all parameters were printed.
+ for (vector<const Param*>::const_iterator paramIter = Params::Begin();
+ paramIter != Params::End();
+ paramIter++) {
+ string paramName = (*paramIter)->GetName();
+ if (!isPrinted[paramName] && Params::IsVisible(paramName)) {
+ carp(CARP_WARNING, "Parameter %s was not printed.", paramName.c_str());
+ }
+ }
+
+}
+
+
+void CreateDocs::generateToolHtml(
+ ostream* outStream,
+ const CruxApplication* application
+) {
+ string doc = TOOL_TEMPLATE;
+ string inputTemplate = TOOL_INPUT_TEMPLATE;
+ string outputTemplate = TOOL_OUTPUT_TEMPLATE;
+ string categoryTemplate = TOOL_OPTION_CATEGORY_TEMPLATE;
+ string optionTemplate = TOOL_OPTION_TEMPLATE;
+
+ string appName = application->getName();
+ string appDescription = application->getDescription();
+ vector<string> args = application->getArgs();
+ vector< pair<string, string> > out = application->getOutputs();
+ vector<string> opts = application->getOptions();
+
+ // Build usage and input strings
+ string usage = "crux " + appName + " [options]";
+ string inputs;
+ for (vector<string>::const_iterator i = args.begin(); i != args.end(); i++) {
+ bool multiArg = StringUtils::EndsWith(*i, "+");
+ string argName = multiArg ? i->substr(0, i->length() - 1) : *i;
+ usage += " <" + argName + ">";
+ if (multiArg) {
+ usage += "+";
+ }
+
+ if (!Params::Exists(argName)) {
+ carp(CARP_FATAL, "Invalid argument '%s' for application '%s'",
+ argName.c_str(), appName.c_str());
+ }
+ string single = inputTemplate;
+ map<string, string> replaceMap;
+ replaceMap["#NAME#"] = !multiArg ? argName : argName + "+";
+ replaceMap["#DESCRIPTION#"] = Params::ProcessHtmlDocTags(Params::GetUsage(argName), true);
+ makeReplacements(&single, replaceMap);
+ inputs += single;
+ }
+ // Build outputs introductory string
+ string outputsIntro;
+ if (application->needsOutputDirectory()) {
+ outputsIntro = "<p>The program writes files to the folder <code>" +
+ Params::GetStringDefault("output-dir") + "</code> by default. The name "
+ "of the output folder can be set by the user using the <code>--output-dir"
+ "</code> option. The following files will be created:\n";
+ }
+ // Build outputs string
+ string outputs;
+ for (vector< pair<string, string> >::const_iterator i = out.begin(); i != out.end(); i++) {
+ string single = outputTemplate;
+ map<string, string> replaceMap;
+ replaceMap["#NAME#"] = i->first;
+ replaceMap["#DESCRIPTION#"] = Params::ProcessHtmlDocTags(i->second, true);
+ makeReplacements(&single, replaceMap);
+ outputs += single;
+ }
+ // Build options string
+ string options;
+ for (int i = opts.size() - 1; i >= 0; i--) {
+ if (!Params::IsVisible(opts[i])) {
+ opts.erase(opts.begin() + i);
+ }
+ }
+ vector< pair< string, vector<string> > > categories = Params::GroupByCategory(opts);
+ for (vector< pair< string, vector<string> > >::const_iterator i = categories.begin();
+ i != categories.end();
+ i++) {
+ string categoryName = i->first;
+ if (categoryName.empty()) {
+ // Give category to all uncategorized options
+ categoryName = appName + " options";
+ }
+ string optionSubset;
+ const vector<string>& items = i->second;
+ for (vector<string>::const_iterator j = items.begin(); j != items.end(); j++) {
+ if (!Params::Exists(*j)) {
+ carp(CARP_FATAL, "Invalid option '%s' for application '%s'",
+ j->c_str(), appName.c_str());
+ }
+ string single = optionTemplate;
+ map<string, string> replaceMap;
+ replaceMap["#NAME#"] = *j;
+ replaceMap["#DESCRIPTION#"] = Params::ProcessHtmlDocTags(Params::GetUsage(*j), true);
+ string acceptedValues = Params::GetAcceptedValues(*j);
+ acceptedValues = StringUtils::Replace(acceptedValues, "<", "<");
+ acceptedValues = StringUtils::Replace(acceptedValues, ">", ">");
+ replaceMap["#VALUES#"] = acceptedValues;
+ string defaultOutput = Params::GetStringDefault(*j);
+ replaceMap["#DEFAULT#"] = !defaultOutput.empty() ? defaultOutput : "<empty>";
+ makeReplacements(&single, replaceMap);
+ optionSubset += single;
+ }
+
+ string single = categoryTemplate;
+ map<string, string> replaceMap;
+ replaceMap["#NAME#"] = categoryName;
+ replaceMap["#OPTIONS#"] = optionSubset;
+ makeReplacements(&single, replaceMap);
+ options += single;
+ }
+ if (options.empty()) {
+ options = TOOL_NO_OPTIONS_TEMPLATE;
+ }
+
+ map<string, string> replacements;
+ replacements["#NAME#"] = appName;
+ replacements["#DESCRIPTION#"] = Params::ProcessHtmlDocTags(appDescription, true);
+ replacements["#USAGE#"] = usage;
+ replacements["#INPUTS#"] = inputs;
+ replacements["#OUTPUTSINTRODUCTION#"] = outputsIntro;
+ replacements["#OUTPUTS#"] = outputs;
+ replacements["#OPTIONS#"] = options;
+ makeReplacements(&doc, replacements);
+ *outStream << doc;
+}
+
+void CreateDocs::makeReplacements(
+ string* templateStr,
+ const map<string, string>& replacements
+) {
+ const string OPEN_TAG = "<!--";
+ const string CLOSE_TAG = "-->";
+
+ size_t idx, end_idx = 0;
+ while ((idx = templateStr->find(OPEN_TAG, end_idx)) != string::npos) {
+ if (idx > templateStr->length()) {
+ break;
+ }
+ idx += OPEN_TAG.length();
+ end_idx = templateStr->find(CLOSE_TAG, idx);
+ if (end_idx == string::npos) {
+ break;
+ }
+ string comment = templateStr->substr(idx, end_idx - idx);
+ comment.erase(comment.begin(),
+ find_if(comment.begin(), comment.end(),
+ not1(ptr_fun<int, int>(isspace))));
+ comment.erase(find_if(comment.rbegin(), comment.rend(),
+ not1(ptr_fun<int, int>(isspace))).base(), comment.end());
+ map<string, string>::const_iterator iter = replacements.find(comment);
+ if (iter == replacements.end()) {
+ continue;
+ }
+ idx -= OPEN_TAG.length();
+ end_idx += CLOSE_TAG.length();
+ templateStr->replace(idx, end_idx - idx, iter->second);
+ end_idx = idx + iter->second.length();
+ }
+}
+
+string CreateDocs::getName() const {
+ return "create-docs";
+}
+
+string CreateDocs::getDescription() const {
+ return "[[html:<p>]]This command prints to standard output an HTML formatted version of the documentation for a specified Crux command.[[html:</p>]]";
+}
+
+vector<string> CreateDocs::getArgs() const {
+ string arr[] = {
+ "tool-name"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> CreateDocs::getOptions() const {
+ return vector<string>();
+}
+
+vector< pair<string, string> > CreateDocs::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "The command prints to standard output the HTML documentation for the specified Crux tool."));
+ return outputs;
+}
+
+bool CreateDocs::needsOutputDirectory() const {
+ return false;
+}
+
+bool CreateDocs::hidden() const {
+ return true;
+}
+
+const string CreateDocs::TOOL_TEMPLATE =
+ "<!DOCTYPE html>\n"
+ "<html>\n"
+ "<head>\n"
+ "<title><!-- #NAME# --></title>\n"
+ "<meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\" />\n"
+ "<link rel=\"stylesheet\" type=\"text/css\" href=\"../styles.css\">\n"
+ "<script type=\"text/javascript\"\n"
+ " src=\"http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML\">\n"
+ "</script>\n"
+ "<script type=\"text/javascript\">\n"
+ " MathJax.Hub.Config({jax: ['input/TeX','output/HTML-CSS'], displayAlign: 'left'});\n"
+ "</script>\n"
+ "<script type=\"text/javascript\">\n"
+ " var _gaq = _gaq || [];\n"
+ " _gaq.push(['_setAccount', 'UA-26136956-1']);\n"
+ " _gaq.push(['_trackPageview']);\n"
+ " (function() {\n"
+ " var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;\n"
+ " ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';\n"
+ " var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);\n"
+ " })();\n"
+ "</script>\n"
+ "<script src=\"http://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js\"></script>\n"
+ "<script type=\"text/javascript\">\n"
+ " // Main Menu\n"
+ " $( document ).ready(function() {\n"
+ " var pull = $('.btn');\n"
+ " menu = $('nav ul');\n"
+ " menuHeight = menu.height();\n"
+ " $(pull).on('click', function(e) {\n"
+ " e.preventDefault();\n"
+ " menu.slideToggle();\n"
+ " });\n"
+ " $(window).resize(function(){\n"
+ " var w = $(window).width();\n"
+ " if(w > 320 && menu.is(':hidden')) {\n"
+ " menu.removeAttr('style');\n"
+ " } \n"
+ " });\n"
+ " });\n"
+ "</script>\n"
+ "</head>\n"
+ "<body>\n"
+ " <div class=\"page-wrap\">\n"
+ " <nav>\n"
+ " <div class=\"btn\">\n"
+ " </div>\n"
+ " <img src=\"../images/crux-logo.png\" id=\"logo\"></a>\n"
+ " <ul id=\"navitems\">\n"
+ " <li><a href=\"../index.html\">Home</a></li>\n"
+ " <li><a href=\"../download.html\">Download</a></li>\n"
+ " <li><a href=\"../fileformats.html\">File Formats</a></li>\n"
+ " <li><a href=\"http://groups.google.com/group/crux-users\">Contact</a></li> <!--Link to google support board-->\n"
+ " </ul>\n"
+ " </nav>\n"
+ " <div id=\"content\" class=\"autogenerated\">\n"
+ " <!-- START CONTENT -->\n"
+ "<h1><!-- #NAME# --></h1>\n"
+ "<h2>Usage:</h2>\n"
+ "<p><code><!-- #USAGE# --></code></p>\n"
+ "<h2>Description:</h2>\n"
+ "<!-- #DESCRIPTION# -->\n"
+ "<h2>Input:</h2>\n"
+ "<ul>\n"
+ "<!-- #INPUTS# --></ul>\n"
+ "<h2>Output:</h2>\n"
+ "<!-- #OUTPUTSINTRODUCTION# -->"
+ "<ul>\n"
+ "<!-- #OUTPUTS# --></ul>\n"
+ "<h2>Options:</h2>\n"
+ "<ul style=\"list-style-type: none;\">\n"
+ "<!-- #OPTIONS# -->\n"
+ "</ul>\n"
+ " <!-- END CONTENT -->\n"
+ " </div>\n"
+ " </div>\n"
+ "<footer class=\"site-footer\">\n"
+ " <div id=\"centerfooter\">\n"
+ " <div class=\"footerimportantlinks\">\n"
+ " <img src=\"../images/linkicon.png\" style=\"width:16px; height:16px\"><h3>Important links</h3>\n"
+ " <ul>\n"
+ " <li><a href=\"../faq.html\">Crux FAQ</a></li>\n"
+ " <li><a href=\"../glossary.html\">Glossary of terminology</a></li>\n"
+ " <li><a href=\"http://scholar.google.com/citations?hl=en&user=Rw9S1HIAAAAJ\">Google Scholar profile</a></li>\n"
+ " <li><a href=\"https://github.com/crux-toolkit/crux-toolkit\">GitHub</a></li>\n"
+ " <li><a href=\"../release-notes.html\">Release Notes</a></li>\n"
+ " <li><a href=\"https://mailman1.u.washington.edu/mailman/listinfo/crux-users\" title=\"Receive announcements of new versions\">Join the mailing list</a></li>\n"
+ " <li><a href=\"http://www.apache.org/licenses/LICENSE-2.0\">Apache license</a></li>\n"
+ " <li><a href=\"http://groups.google.com/group/crux-users\">Support Board</a></li>\n"
+ " </ul>\n"
+ " </div>\n"
+ " <div class=\"footerimportantlinks tutoriallinks\">\n"
+ " <img src=\"../images/tutorialicon.png\" style=\"height:16px\"><h3>Tutorials</h3>\n"
+ " <ul>\n"
+ " <li><a href=\"../tutorials/install.html\">Installation</a></li>\n"
+ " <li><a href=\"../tutorials/gettingstarted.html\">Getting started with Crux</a></li>\n"
+ " <li><a href=\"../tutorials/search.html\">Running a simple search using Tide and Percolator</a></li>\n"
+ " <li><a href=\"../tutorials/customizedsearch.html\">Customization and search options</a></li>\n"
+ " <li><a href=\"../tutorials/spectralcounts.html\">Using spectral-counts</a></li>\n"
+ " </ul>\n"
+ " </div>\n"
+ " <div id=\"footertext\">\n"
+ " <p>\n"
+ " The original version of Crux was written by Chris Park and Aaron Klammer\n"
+ " under the supervision\n"
+ " of <a href=\"http://www.gs.washington.edu/faculty/maccoss.htm\">Prof. Michael\n"
+ " MacCoss</a>\n"
+ " and <a href=\"http://noble.gs.washington.edu/~noble\">Prof. William\n"
+ " Stafford Noble</a> in the Department of Genome Sciences at the\n"
+ " University of Washington, Seattle. Website by <a href=\"http://www.yuvalboss.com/\">Yuval Boss</a>. \n"
+ " <br />The complete list of contributors\n"
+ " can be found <a href=\"../contributors.html\">here</a>.\n"
+ " <br />\n"
+ " <br />\n"
+ " Maintenance and development of Crux is funded by the <a href=\"https://www.nih.gov/\">National Institutes of Health</a> award P41 GM103533. \n"
+ " </p>\n"
+ " </div>\n"
+ " </div>\n"
+ "</footer>\n"
+ "</body>\n"
+ "</html>";
+
+const string CreateDocs::TOOL_INPUT_TEMPLATE =
+ " <li><code><!-- #NAME# --></code> – <!-- #DESCRIPTION# --></li>\n";
+
+const string CreateDocs::TOOL_OUTPUT_TEMPLATE =
+ " <li><code><!-- #NAME# --></code> – <!-- #DESCRIPTION# --></li>\n";
+
+const string CreateDocs::TOOL_OPTION_CATEGORY_TEMPLATE =
+ "<li class=\"nobullet\">\n"
+ "<h3><!-- #NAME# --></h3>\n"
+ "<ul>\n"
+ "<!-- #OPTIONS# --></ul>\n"
+ "</li>\n";
+
+const string CreateDocs::TOOL_NO_OPTIONS_TEMPLATE =
+ "<li class=\"nobullet\">\n"
+ "<p>This command does not support any optional parameters.</p>\n"
+ "</li>\n";
+
+const string CreateDocs::TOOL_OPTION_TEMPLATE =
+ " <li class=\"nobullet\"><code>--<!-- #NAME# --> <!-- #VALUES# --></code> – "
+ "<!-- #DESCRIPTION# --> Default = <code><!-- #DEFAULT# --></code>.</li>\n";
+
diff --git a/src/app/CreateDocs.h b/src/app/CreateDocs.h
new file mode 100644
index 0000000..5974672
--- /dev/null
+++ b/src/app/CreateDocs.h
@@ -0,0 +1,52 @@
+#ifndef CREATEDOCS_H
+#define CREATEDOCS_H
+
+#include <map>
+#include <ostream>
+#include <string>
+#include <vector>
+
+#include "CruxApplicationList.h"
+
+class CreateDocs : public CruxApplication {
+ public:
+ CreateDocs();
+ virtual ~CreateDocs();
+
+ virtual int main(int argc, char** argv);
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+ virtual bool needsOutputDirectory() const;
+ virtual bool hidden() const;
+
+ protected:
+ void checkParams(const CruxApplicationList* apps = NULL);
+
+ void makeParamTable(const CruxApplicationList* apps);
+ void generateToolHtml(std::ostream* outStream, const CruxApplication* application);
+
+ void makeReplacements(
+ std::string* templateStr,
+ const std::map<std::string, std::string>& replacements
+ );
+
+ static const std::string TOOL_TEMPLATE;
+ static const std::string TOOL_INPUT_TEMPLATE;
+ static const std::string TOOL_OUTPUT_TEMPLATE;
+ static const std::string TOOL_OPTION_CATEGORY_TEMPLATE;
+ static const std::string TOOL_NO_OPTIONS_TEMPLATE;
+ static const std::string TOOL_OPTION_TEMPLATE;
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/CruxApplication.cpp b/src/app/CruxApplication.cpp
new file mode 100644
index 0000000..2190a8e
--- /dev/null
+++ b/src/app/CruxApplication.cpp
@@ -0,0 +1,245 @@
+/**
+ * \file CruxApplication.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Abstract Object for a CruxApplication
+ *****************************************************************************/
+#include "CruxApplication.h"
+#include "crux_version.h"
+#include "io/carp.h"
+#include "parameter.h"
+#include "util/ArgParser.h"
+#include "util/crux-utils.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "util/GlobalParams.h"
+#include "util/WinCrux.h"
+
+#include <iostream>
+#include <boost/thread.hpp>
+
+using namespace std;
+
+/**
+ * Frees an allocated CruxApplication
+ */
+CruxApplication::~CruxApplication() {
+}
+
+/**
+ * \returns the arguments of the application
+ */
+vector<string> CruxApplication::getArgs() const {
+ return vector<string>();
+}
+
+/**
+ * \returns the options of the application
+ */
+vector<string> CruxApplication::getOptions() const {
+ return vector<string>();
+}
+
+/**
+ * \returns the outputs of the application as name -> description
+ */
+vector< pair<string, string> > CruxApplication::getOutputs() const {
+ return vector< pair<string, string> >();
+}
+
+/**
+ * \returns the file stem of the application, default getName.
+ */
+string CruxApplication::getFileStem() const {
+ return getName();
+}
+
+/**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+COMMAND_T CruxApplication::getCommand() const {
+ return MISC_COMMAND;
+}
+
+
+bool CruxApplication::needsOutputDirectory() const {
+ return false;
+}
+
+void CruxApplication::initialize(int argc, char** argv) {
+ initializeParams(getName(), getArgs(), getOptions(), argc, argv);
+ processParams();
+ Params::Finalize();
+ GlobalParams::set();
+ if (!Params::GetBool("no-analytics")) {
+ // Post data to Google Analytics using a separate thread
+ boost::thread analytics_thread(postToAnalytics, getName());
+ }
+
+ set_verbosity_level(Params::GetInt("verbosity"));
+
+ carp(CARP_INFO, "Beginning %s.", getName().c_str());
+
+ // Set seed for random number generation
+ if (Params::GetString("seed") == "time") {
+ time_t seconds; // use current time to seed
+ time(&seconds); // Get value from sys clock and set seconds variable.
+ mysrandom((unsigned)seconds); // Convert seconds to a unsigned int
+ } else {
+ mysrandom(StringUtils::FromString<unsigned>(Params::GetString("seed")));
+ }
+
+ // Start the timer.
+ wall_clock();
+
+ // Create output directory if appliation needs it.
+ if (needsOutputDirectory()) {
+ // Create output directory
+ string output_folder = Params::GetString("output-dir");
+ if (create_output_directory(output_folder, Params::GetBool("overwrite")) == -1) {
+ carp(CARP_FATAL, "Unable to create output directory %s.", output_folder.c_str());
+ }
+
+ // Open the log file to record carp messages
+ open_log_file(getFileStem() + ".log.txt");
+
+ // Store the host name, start date and time, version number, and command line.
+ carp(CARP_INFO, "CPU: %s", hostname());
+ carp(CARP_INFO, "Crux version: %s", CRUX_VERSION);
+ carp(CARP_INFO, date_and_time());
+ log_command_line(argc, argv);
+
+ // Write the parameter file
+ string paramFile = make_file_path(getFileStem() + ".params.txt");
+ ofstream* file = FileUtils::GetWriteStream(paramFile, Params::GetBool("overwrite"));
+ if (file == NULL) {
+ throw runtime_error("Could not open " + paramFile + " for writing");
+ }
+ Params::Write(file);
+ delete file;
+ }
+}
+
+/**
+ * Should this application be kept from the usage statement?
+ */
+bool CruxApplication::hidden() const {
+ return false;
+}
+
+/**
+ * Read in all parameters from command line and parameter file
+ */
+void CruxApplication::initializeParams(
+ const string& appName,
+ const vector<string>& appArgs,
+ const vector<string>& appOptions,
+ int argc,
+ char** argv
+) {
+ initialize_parameters();
+ set_verbosity_level(Params::GetInt("verbosity"));
+
+ // Parse command line
+ ArgParser argParser;
+ try {
+ argParser.Parse(argc, argv, appArgs);
+
+ // Read parameter file if specified
+ string parameter_file = argParser.GetOption("parameter-file");
+ if (!parameter_file.empty()) {
+ parse_parameter_file(parameter_file.c_str());
+ read_mods_from_file(parameter_file.c_str());
+ }
+ // Process command line options
+ const map<string, string>& options = argParser.GetOptions();
+ for (map<string, string>::const_iterator i = options.begin(); i != options.end(); i++) {
+ try {
+ Params::Set(i->first, i->second);
+ } catch (const runtime_error& e) {
+ throw ArgParserException(e.what());
+ }
+ }
+ // Process command line arguments
+ const map< string, vector<string> >& args = argParser.GetArgs();
+ for (map< string, vector<string> >::const_iterator i = args.begin(); i != args.end(); i++) {
+ for (vector<string>::const_iterator j = i->second.begin(); j != i->second.end(); j++) {
+ try {
+ Params::AddArgValue(i->first, *j);
+ } catch (const runtime_error& e) {
+ throw ArgParserException(e.what());
+ }
+ }
+ }
+ } catch (const ArgParserException& e) {
+ carp(CARP_FATAL, "%s\n\n%s\n", e.what(),
+ getUsage(appName, appArgs, appOptions, e.ShowFullUsage()).c_str());
+ } catch (const runtime_error& e) {
+ carp(CARP_FATAL, "%s", e.what());
+ }
+}
+
+/**
+ * Process parameters after they have been set up, but before they have been
+ * finalized
+ */
+void CruxApplication::processParams() {
+}
+
+string CruxApplication::getUsage(
+ const string& appName,
+ const vector<string>& args,
+ const vector<string>& options,
+ bool full
+) {
+ vector<string> argDisplay;
+ for (vector<string>::const_iterator i = args.begin(); i != args.end(); i++) {
+ argDisplay.push_back(StringUtils::EndsWith(*i, "+") ?
+ "<" + i->substr(0, i->length() - 1) + ">+" :"<" + *i + ">");
+ }
+
+ stringstream usage;
+ usage << "USAGE:" << endl
+ << endl
+ << " crux " << appName << " [options]";
+ for (vector<string>::const_iterator i = argDisplay.begin(); i != argDisplay.end(); i++) {
+ usage << ' ' << *i;
+ }
+
+ if (full) {
+ usage << endl << endl
+ << "REQUIRED ARGUMENTS:";
+ for (vector<string>::const_iterator i = argDisplay.begin(); i != argDisplay.end(); i++) {
+ stringstream line;
+ string argName = i->substr(1, i->length() - (StringUtils::EndsWith(*i, "+") ? 3 : 2));
+ line << *i << ' ' << Params::ProcessHtmlDocTags(Params::GetUsage(argName));
+ usage << endl << endl << StringUtils::LineFormat(line.str(), 80, 2);
+ }
+ usage << endl << endl
+ << "OPTIONAL ARGUMENTS:" << endl;
+ for (vector<string>::const_iterator i = options.begin(); i != options.end(); i++) {
+ if (!Params::IsVisible(*i)) {
+ continue;
+ }
+ string defaultString = Params::GetStringDefault(*i);
+ if (defaultString.empty()) {
+ defaultString = "<empty>";
+ }
+ usage << endl
+ << " [--" << *i << " " << Params::GetAcceptedValues(*i) << "]" << endl
+ << StringUtils::LineFormat(Params::ProcessHtmlDocTags(Params::GetUsage(*i)) +
+ " Default = " + defaultString + ".", 80, 5);
+ }
+ if (options.empty()) {
+ usage << endl
+ << " This command does not support any optional parameters.";
+ }
+ } else {
+ usage << endl << endl
+ << "Run \"crux " << appName << "\" with no arguments to see a full "
+ "list of options.";
+ }
+ return usage.str();
+}
+
diff --git a/src/app/CruxApplication.h b/src/app/CruxApplication.h
new file mode 100644
index 0000000..958ca06
--- /dev/null
+++ b/src/app/CruxApplication.h
@@ -0,0 +1,159 @@
+/**
+ * \file CruxApplication.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Abstract Object for a CruxApplication
+ *****************************************************************************/
+#ifndef CRUXAPPLICATION_H
+#define CRUXAPPLICATION_H
+#include "model/objects.h"
+
+#include <algorithm>
+#include <string>
+#include <vector>
+#include <map>
+
+class CruxApplication{
+ public:
+ /**
+ * the main method for CruxApplication. Subclasses of
+ * CruxApplication define this.
+ * \returns exit code for the executed program.
+ */
+ virtual int main(int argc, char** argv) = 0;
+
+ /**
+ * \returns the name of the subclassed application
+ */
+ virtual std::string getName() const = 0;
+
+ /**
+ * \returns the description of the subclassed application
+ */
+ virtual std::string getDescription() const = 0;
+
+ /**
+ * \returns the arguments of the application
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the options of the application
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ template<typename T>
+ static void addOptionsFrom(std::vector<std::string>* optionsVector) {
+ using std::find;
+ using std::string;
+ using std::vector;
+ CruxApplication* app = new T();
+ vector<string> options = app->getOptions();
+ delete app;
+ for (vector<string>::const_iterator i = options.begin(); i != options.end(); i++) {
+ if (find(optionsVector->begin(), optionsVector->end(), *i) == optionsVector->end()) {
+ optionsVector->push_back(*i);
+ }
+ }
+ }
+
+ static void removeOptionFrom(std::vector<std::string>* optionsVector, std::string option) {
+ using std::find;
+ using std::string;
+ using std::vector;
+ vector<string>::iterator i;
+ i = find(optionsVector->begin(), optionsVector->end(), option);
+ if (i != optionsVector->end()) {
+ optionsVector->erase(i);
+ }
+ }
+
+ /**
+ * \returns the outputs of the application as <name, description>
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ template<typename T>
+ static void addOutputsFrom(
+ std::vector< std::pair<std::string, std::string> >* outputsVector) {
+ using std::pair;
+ using std::set;
+ using std::string;
+ using std::vector;
+ set<string> existing;
+ for (vector< pair<string, string> >::const_iterator i = outputsVector->begin();
+ i != outputsVector->end();
+ i++) {
+ existing.insert(i->first);
+ }
+
+ CruxApplication* app = new T();
+ vector< pair<string, string> > outputs = app->getOutputs();
+ delete app;
+ for (vector< pair<string, string> >::const_iterator i = outputs.begin();
+ i != outputs.end();
+ i++) {
+ if (existing.insert(i->first).second) {
+ outputsVector->push_back(*i);
+ }
+ }
+ }
+
+ /**
+ * \returns the file stem of the application, default getName.
+ */
+ virtual std::string getFileStem() const;
+
+ /**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+ virtual COMMAND_T getCommand() const;
+
+ /**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual void initialize(int argc, char** argv);
+
+ /**
+ * Frees an allocated CruxApplication
+ */
+ virtual ~CruxApplication();
+
+ /**
+ * Should this application be kept from the usage statement?
+ */
+ virtual bool hidden() const;
+
+ /**
+ * Read in all parameters from command line and parameter file
+ */
+ static void initializeParams(
+ const std::string& appName,
+ const std::vector<std::string>& appArgs,
+ const std::vector<std::string>& appOptions,
+ int argc,
+ char** argv
+ );
+
+ /**
+ * Process parameters after they have been set up, but before they have been
+ * finalized
+ */
+ virtual void processParams();
+
+ /**
+ * Get usage statement for the program.
+ */
+ static std::string getUsage(
+ const std::string& appName,
+ const std::vector<std::string>& args,
+ const std::vector<std::string>& options,
+ bool full
+ );
+};
+
+
+
+#endif
diff --git a/src/app/CruxApplicationList.cpp b/src/app/CruxApplicationList.cpp
new file mode 100644
index 0000000..6fa4e3e
--- /dev/null
+++ b/src/app/CruxApplicationList.cpp
@@ -0,0 +1,227 @@
+/**
+ * \file CruxApplicationList.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: December 6th, 2010
+ * \brief Maintains a list of executable applications
+ *****************************************************************************/
+#include "CruxApplicationList.h"
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+#include <iostream>
+
+using namespace std;
+
+/**
+ * Creates an application list with a listname
+ */
+CruxApplicationList::CruxApplicationList(
+ const char* list_name ///<name of the list
+) {
+ list_name_ = string(list_name);
+}
+
+
+/**
+ * Destructor for CruxApplicationList
+ */
+CruxApplicationList::~CruxApplicationList() {
+
+ for (unsigned int idx=0;idx < applications_.size();idx++) {
+ delete applications_.at(idx);
+ }
+ applications_.clear();
+
+}
+
+/**
+ * Adds an application pointer to the list of applications
+ */
+void CruxApplicationList::add(
+ CruxApplication* application ///< application to add
+ ) {
+
+ if (find(application->getName()) != NULL) {
+ carp(CARP_FATAL, "Name clash! %s", application->getName().c_str());
+ }
+
+ applications_.push_back(application);
+}
+
+/**
+ * Adds a message to be printed in the usage statement
+ */
+void CruxApplicationList::addMessage(
+ const string& message ///< message to add
+) {
+ messages_[applications_.size()] = message;
+}
+
+/**
+ * \returns an application by a name,
+ * returns NULL if not found
+ */
+CruxApplication* CruxApplicationList::find(
+ const string& appname ///<name of the application to find
+ ) {
+ return find(appname.c_str());
+}
+
+/**
+ * \returns an application by a name,
+ * returns NULL if not found
+ */
+CruxApplication* CruxApplicationList::find(
+ const char* appname ///<name of the application to find
+ ) {
+
+ CruxApplication* crux_application = NULL;
+
+ for (vector<CruxApplication*>::iterator app_iter =
+ applications_.begin();
+ app_iter != applications_.end();
+ ++app_iter) {
+ if (appname == (*app_iter) -> getName()) {
+ crux_application = *app_iter;
+ break;
+ }
+ }
+ return crux_application;
+}
+
+/**
+ * \returns an iterator pointing to the beginning of the application list
+ */
+vector<CruxApplication*>::const_iterator CruxApplicationList::begin() const {
+ return applications_.begin();
+}
+
+/**
+ * \returns an iterator pointing to the end of the application list
+ */
+vector<CruxApplication*>::const_iterator CruxApplicationList::end() const {
+ return applications_.end();
+}
+
+/**
+ * prints out the usage statement for this application list.
+ * Each applications name is printed along with its description
+ */
+void CruxApplicationList::usage() {
+
+ vector<CruxApplication*>::iterator iter;
+
+ size_t max_name_length = 0;
+
+ for (iter = applications_.begin();
+ iter != applications_.end();
+ ++iter) {
+
+ max_name_length = max(max_name_length, (*iter) -> getName().length());
+
+ }
+
+ cerr << " Usage: " << list_name_ << " <command> [options] <argument>" << endl;
+
+ for (unsigned int i = 0; i < applications_.size(); ++i) {
+ map<int, string>::const_iterator msg = messages_.find(i);
+ if (msg != messages_.end()) {
+ cerr << endl << msg->second << endl << endl;
+ }
+ if ((applications_[i])->hidden()) { // skip deprecated commands
+ continue;
+ }
+ string name = applications_[i]->getName();
+ string description = Params::ProcessHtmlDocTags(applications_[i]->getDescription());
+ int padding = max_name_length - name.length();
+
+ cerr << " " << name << " ";
+ for (int idx = 0; idx < padding; idx++) {
+ cerr << " ";
+ }
+
+ const int LINE_WIDTH = 80;
+ unsigned int max_descr_line = LINE_WIDTH - (max_name_length+4);
+
+
+ // If the description is short enough, just print.
+ if (description.length() < max_descr_line) {
+ cerr << " " << description << endl;
+ } else {
+ // Otherwise, insert EOLs.
+ vector<string> words = StringUtils::Split(description, ' ');
+
+ unsigned int word_index = 0;
+ unsigned int line_length = 0;
+
+ // Print the first line.
+ while(line_length + words[word_index].length() + 1 < max_descr_line) {
+ cerr << " ";
+ cerr << words[word_index];
+ line_length += words[word_index].length() + 1;
+ word_index++;
+ }
+
+ // Print subsequent lines.
+ while (word_index < words.size()) {
+ line_length = 0;
+ cerr << endl;
+ for (unsigned int idx =0;idx < max_name_length + 3; idx++) {
+ cerr << " ";
+ }
+ while ((word_index < words.size()) &&
+ (line_length + words[word_index].length() + 1 < max_descr_line)) {
+ cerr << " ";
+ cerr << words[word_index];
+ line_length += words[word_index].length() + 1;
+ word_index++;
+ }
+ }
+ cerr << endl;
+ }
+ }
+ cerr << endl << endl;
+ cerr << "Options and arguments are specific to each command." << endl;
+ cerr << "Type '" << list_name_ << " <command>' for details." << endl;
+
+}
+
+/**
+ * Gets the name of the list
+ */
+string CruxApplicationList::getListName() const {
+ return list_name_;
+}
+
+/**
+ * the main method for CruxApplicationList. Attempts to find
+ * an application by name from the first argument. If successful,
+ * calls that applications main method with the rest of the parameters.
+ */
+int CruxApplicationList::main(int argc, char** argv) {
+
+ if (argc < 2) {
+ usage();
+ return -1;
+ }
+
+ string appname = string(argv[1]);
+ CruxApplication* crux_application = find(appname);
+
+ if (crux_application == NULL) {
+ cerr << "Cannot find " << appname << " in available applications" << endl;
+ usage();
+ return -1;
+ }
+
+ crux_application->initialize(argc-1, argv+1);
+ int ret = crux_application->main(argc-1, argv+1);
+
+ carp(CARP_INFO, "Elapsed time: %.3g s", wall_clock() / 1e6);
+ carp(CARP_INFO, "Finished crux %s.", appname.c_str());
+ carp(CARP_INFO, "Return Code:%i", ret);
+
+ return ret;
+}
diff --git a/src/app/CruxApplicationList.h b/src/app/CruxApplicationList.h
new file mode 100644
index 0000000..c9df590
--- /dev/null
+++ b/src/app/CruxApplicationList.h
@@ -0,0 +1,103 @@
+/**
+ * \file CruxApplicationList.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Maintains a list of executable applications. Calling the main method
+ * will try to find the application by name and try to execute it if found.
+ *****************************************************************************/
+#ifndef CRUXAPPLICATIONLIST_H
+#define CRUXAPPLICATIONLIST_H
+
+#include "CruxApplication.h"
+
+#include <map>
+#include <vector>
+#include <string>
+
+
+class CruxApplicationList {
+
+ protected:
+ std::vector<CruxApplication*> applications_; ///< list of applications
+ std::map<int, std::string> messages_; ///< messages and their indexes
+ std::string list_name_; ///<Name of this list
+
+ public:
+ /**
+ * \brief Creates an application list with a listname
+ */
+ explicit CruxApplicationList(const char* list_name);
+
+
+ /**
+ * Frees an allocated CruxApplicationList
+ */
+ ~CruxApplicationList();
+
+ /**
+ * Adds an application pointer to the list of applications
+ */
+ void add(
+ CruxApplication* application ///< application to add
+ );
+
+ /**
+ * Adds a message to be printed in the usage statement
+ */
+ void addMessage(
+ const std::string& message ///< message to add
+ );
+
+ /**
+ * \returns an application by a name,
+ * returns NULL if not found
+ */
+ CruxApplication* find(
+ const std::string& appname ///< name of application to find
+ );
+
+ /**
+ * \returns an application by a name,
+ * returns NULL if not found
+ */
+ CruxApplication* find(
+ const char* appname ///< name of application to find
+ );
+
+ /**
+ * \returns an iterator pointing to the beginning of the application list
+ */
+ std::vector<CruxApplication*>::const_iterator begin() const;
+
+ /**
+ * \returns an iterator pointing to the end of the application list
+ */
+ std::vector<CruxApplication*>::const_iterator end() const;
+
+ /**
+ * prints out the usage statement for this application list.
+ * Each applications name is printed along with its description
+ */
+ void usage();
+
+ /**
+ * Gets the name of the list
+ */
+ std::string getListName() const;
+
+ /**
+ * the main method for CruxApplicationList. Attempts to find
+ * an application by name from the first argument. If successful,
+ * calls that applications main method with the rest of the parameters.
+ */
+ int main(int argc, char** argv);
+};
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/app/ExtractColumns.cpp b/src/app/ExtractColumns.cpp
new file mode 100644
index 0000000..a2fb4c3
--- /dev/null
+++ b/src/app/ExtractColumns.cpp
@@ -0,0 +1,134 @@
+/**
+ * \file ExtractColumns.cpp
+ * \brief Give a tab delimited file and a comma-separated list of column names
+ * print out a tab delimied file with only those columns
+ *****************************************************************************/
+#include "ExtractColumns.h"
+#include "util/crux-utils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+
+
+/**
+ * \returns a blank ExtractRows object
+ */
+ExtractColumns::ExtractColumns() {
+
+}
+
+/**
+ * Destructor
+ */
+ExtractColumns::~ExtractColumns() {
+}
+
+/**
+ * main method for ExtractColumns
+ */
+int ExtractColumns::main(int argc, char** argv) {
+ string delimited_filename = Params::GetString("tsv file");
+ string column_names_string = Params::GetString("column names");
+
+ char delimiter = get_delimiter_parameter("delimiter");
+
+ DelimitedFileReader delimited_file(delimited_filename, true, delimiter);
+
+ vector<string> column_name_list = StringUtils::Split(column_names_string, ',');
+
+ vector<int> column_indices;
+ for (unsigned int i = 0; i < column_name_list.size(); i++) {
+ int col_idx = delimited_file.findColumn(column_name_list[i]);
+ if (col_idx != -1) {
+ column_indices.push_back(col_idx);
+ } else {
+ carp(CARP_ERROR, "column not found:%s\n\n%s",
+ column_name_list[i].c_str(),
+ delimited_file.getAvailableColumnsString().c_str());
+ return(-1);
+ }
+ }
+
+ //print out the header if desired
+ if (Params::GetBool("header")) {
+ cout << column_name_list[0];
+ for (unsigned int col_idx = 1; col_idx < column_name_list.size(); col_idx++) {
+ cout << delimiter << column_name_list[col_idx];
+ }
+ cout << endl;
+ }
+
+ while(delimited_file.hasNext()) {
+
+ int col_idx = column_indices[0];
+ cout << delimited_file.getString(col_idx);
+ for (unsigned int col_idx_idx = 1;col_idx_idx < column_indices.size();col_idx_idx++) {
+ col_idx = column_indices[col_idx_idx];
+ cout << delimiter << delimited_file.getString(col_idx);
+ }
+ cout <<endl;
+ delimited_file.next();
+ }
+
+ return 0;
+
+}
+
+/**
+ * \returns the command name for ExtractColumns
+ */
+string ExtractColumns::getName() const {
+ return "extract-columns";
+}
+
+/**
+ * \returns the description for ExtractColumns
+ */
+string ExtractColumns::getDescription() const {
+ return
+ "[[nohtml:Print specified columns from a tab-delimited file.]]"
+ "[[html:<p>Given a tab-delimited file and a comma-delimited list of column "
+ "names, extract the requested columns.</p>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> ExtractColumns::getArgs() const {
+ string arr[] = {
+ "tsv file",
+ "column names"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> ExtractColumns::getOptions() const {
+ string arr[] = {
+ "delimiter",
+ "header",
+ "verbosity"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > ExtractColumns::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "the requested columns in tab-delimited format. The columns are printed in "
+ "the same order that they appear in the input column list."));
+ return outputs;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ExtractColumns.h b/src/app/ExtractColumns.h
new file mode 100644
index 0000000..0038b16
--- /dev/null
+++ b/src/app/ExtractColumns.h
@@ -0,0 +1,70 @@
+/**
+ * \file ExtractColumns.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Give a tab delimited file and a comma-separated list of column names
+ * print out a tab delimied file with only those columns
+ *****************************************************************************/
+#ifndef EXTRACTCOLUMNS_H
+#define EXTRACTCOLUMNS_H
+
+#include "CruxApplication.h"
+#include "io/DelimitedFileReader.h"
+
+#include <string>
+
+class ExtractColumns: public CruxApplication {
+
+ public:
+
+ /**
+ * \returns a blank ExtractRows object
+ */
+ ExtractColumns();
+
+ /**
+ * Destructor
+ */
+ ~ExtractColumns();
+
+ /**
+ * main method for ExtractColumns
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for ExtractColumns
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for ExtractColumns
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ExtractRows.cpp b/src/app/ExtractRows.cpp
new file mode 100644
index 0000000..b15b70d
--- /dev/null
+++ b/src/app/ExtractRows.cpp
@@ -0,0 +1,188 @@
+/*******************************************************************************
+ * \file ExtractRows.cpp
+ * \brief Given a tab delimited file and column name and value, print
+ * out all rows that pass the relation operator (default equals).
+ ****************************************************************************/
+
+#include "ExtractRows.h"
+
+#include <iostream>
+
+#include "io/DelimitedFileReader.h"
+#include "io/DelimitedFile.h"
+#include "io/carp.h"
+#include "parameter.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+
+/**
+ * \returns a blank ExtractRows object
+ */
+ExtractRows::ExtractRows() {
+}
+
+/**
+ * Destructor
+ */
+ExtractRows::~ExtractRows() {
+}
+
+
+/**
+ * Determines whether the a op b is true/false
+ */
+template<typename TValue>
+bool passesThreshold(
+ TValue a,
+ TValue b,
+ COMPARISON_T& comparison) {
+
+ switch (comparison) {
+ case COMPARISON_LT:
+ return a < b;
+ case COMPARISON_LTE:
+ return a <= b;
+ case COMPARISON_EQ:
+ return a == b;
+ case COMPARISON_GTE:
+ return a >= b;
+ case COMPARISON_GT:
+ return a > b;
+ case COMPARISON_NEQ:
+ return a != b;
+ case NUMBER_COMPARISONS:
+ case COMPARISON_INVALID:
+ carp(CARP_FATAL, "Invalid comparison type!");
+ return false;
+ }
+ return false;
+}
+
+/**
+ * main method for ExtractRows
+ */
+int ExtractRows::main(int argc, char** argv) {
+ /* Get parameters */
+ string delimited_filename = Params::GetString("tsv file");
+
+ string column_name = Params::GetString("column name");
+ string column_value = Params::GetString("column value");
+
+ COLTYPE_T column_type = get_column_type_parameter("column-type");
+ COMPARISON_T comparison = get_comparison_parameter("comparison");
+ char delimiter = get_delimiter_parameter("delimiter");
+
+
+ DelimitedFileReader delimited_file(delimited_filename, true, delimiter);
+ int column_idx = delimited_file.findColumn(column_name);
+
+ if (column_idx == -1) {
+ carp(CARP_FATAL, "column not found:%s\n\n:%s",
+ column_name.c_str(),
+ delimited_file.getAvailableColumnsString().c_str());
+ }
+
+ if (Params::GetBool("header")) {
+ cout << delimited_file.getHeaderString() << endl;
+ }
+
+ string column_value_str = Params::GetString("column value");
+
+ while (delimited_file.hasNext()) {
+ bool passes = false;
+ switch(column_type) {
+ case COLTYPE_INT:
+ passes = passesThreshold(
+ delimited_file.getInteger(column_idx),
+ StringUtils::FromString<int>(column_value_str),
+ comparison);
+ break;
+ case COLTYPE_REAL:
+ passes = passesThreshold(
+ delimited_file.getFloat(column_idx),
+ StringUtils::FromString<FLOAT_T>(column_value_str),
+ comparison);
+ break;
+ case COLTYPE_STRING:
+ passes = passesThreshold(
+ delimited_file.getString(column_idx),
+ column_value_str,
+ comparison);
+ break;
+ case NUMBER_COLTYPES:
+ case COLTYPE_INVALID:
+ carp(CARP_FATAL, "Unknown column type");
+ }
+
+ if (passes) {
+ cout << delimited_file.getString() << endl;
+ }
+ delimited_file.next();
+ }
+
+ return 0;
+
+}
+
+/**
+ * \returns the command name for ExtractRows
+ */
+string ExtractRows::getName() const {
+ return "extract-rows";
+}
+
+/**
+ * \returns the description for ExtractRows
+ */
+string ExtractRows::getDescription() const {
+ return
+ "[[nohtml:Print specified rows from a tab-delimited file.]]"
+ "[[html:Given a tab-delimited file, a column name and a column cell value, "
+ "extract the rows that have the matching values for that column.]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> ExtractRows::getArgs() const {
+ string arr[] = {
+ "tsv file",
+ "column name",
+ "column value"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> ExtractRows::getOptions() const {
+ string arr[] = {
+ "delimiter",
+ "header",
+ "comparison",
+ "column-type",
+ "verbosity"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > ExtractRows::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "the rows for which the value observed in the specified column of the input "
+ "file match the <column value> given on the command line."));
+ return outputs;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ExtractRows.h b/src/app/ExtractRows.h
new file mode 100644
index 0000000..6399e29
--- /dev/null
+++ b/src/app/ExtractRows.h
@@ -0,0 +1,70 @@
+/**
+ * \file ExtractRows.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Given a tab delimited file and column name and value, print
+ * out all rows that pass the relation operator (default equals).
+ *****************************************************************************/
+#ifndef EXTRACTROWS_H
+#define EXTRACTROWS_H
+
+#include "CruxApplication.h"
+
+#include <string>
+
+class ExtractRows: public CruxApplication {
+
+ public:
+
+ /**
+ * \returns a blank ExtractRows object
+ */
+ ExtractRows();
+
+ /**
+ * Destructor
+ */
+ ~ExtractRows();
+
+ /**
+ * main method for ExtractRows
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for ExtractRows
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for ExtractRows
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+};
+
+
+#endif //EXTRACTROWS_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/GeneratePeptides.cpp b/src/app/GeneratePeptides.cpp
new file mode 100644
index 0000000..7d3806f
--- /dev/null
+++ b/src/app/GeneratePeptides.cpp
@@ -0,0 +1,607 @@
+#include "GeneratePeptides.h"
+#include "parameter.h"
+#include "model/ProteinPeptideIterator.h"
+#include "util/mass.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+
+MASS_TYPE_T GeneratePeptides::massType_ = AVERAGE;
+
+GeneratePeptides::GeneratePeptides() {
+}
+
+GeneratePeptides::~GeneratePeptides() {
+}
+
+int GeneratePeptides::main(int argc, char** argv) {
+ string fastaPath = Params::GetString("protein fasta file");
+ if (!FileUtils::Exists(fastaPath)) {
+ carp(CARP_FATAL, "File does not exist: '%s'", fastaPath.c_str());
+ }
+
+ DECOY_TYPE_T decoyType = get_tide_decoy_type_parameter("decoy-format");
+ massType_ = get_mass_type_parameter("isotopic-mass");
+ bool overwrite = Params::GetBool("overwrite");
+
+ string targetsFile = make_file_path("generate-peptides.target.txt");
+ string decoysFile = make_file_path("generate-peptides.decoy.txt");
+
+ ofstream* targetPeptides = create_stream_in_path(targetsFile.c_str(), NULL, overwrite);
+ ofstream* decoyPeptides = decoyType != NO_DECOYS
+ ? create_stream_in_path(decoysFile.c_str(), NULL, overwrite)
+ : NULL;
+
+ string decoyFastaPath = canGenerateDecoyProteins()
+ ? make_file_path("generate-peptides.proteins.decoy.txt")
+ : "";
+
+ processFasta(fastaPath, targetPeptides, decoyFastaPath, decoyPeptides, decoyType);
+ return 0;
+}
+
+void GeneratePeptides::processFasta(
+ const string& fastaPath,
+ ofstream* targetList,
+ const string& decoyFastaPath,
+ ofstream* decoyList,
+ DECOY_TYPE_T decoyType
+) {
+ double minMass = Params::GetDouble("min-mass");
+ double maxMass = Params::GetDouble("max-mass");
+
+ carp(CARP_INFO, "Reading %s", fastaPath.c_str());
+ ifstream* fasta = new ifstream(fastaPath.c_str(), ifstream::in);
+
+ ofstream* decoyFasta = decoyFastaPath.empty() ? NULL
+ : create_stream_in_path(decoyFastaPath.c_str(), NULL, Params::GetBool("overwrite"));
+
+ ENZYME_T enzyme = get_enzyme_type_parameter("enzyme");
+ if (!Params::GetString("custom-enzyme").empty()) {
+ enzyme = CUSTOM_ENZYME;
+ }
+ DIGEST_T digest = get_digest_type_parameter("digestion");
+ int missed = Params::GetInt("missed-cleavages");
+ int minLen = Params::GetInt("min-length");
+ int maxLen = Params::GetInt("max-length");
+ string decoyPrefix = Params::GetString("decoy-prefix");
+ bool proteinReverse = decoyType == PROTEIN_REVERSE_DECOYS;
+ bool peptideShuffle = decoyType == PEPTIDE_SHUFFLE_DECOYS;
+ bool peptideReverse = decoyType == PEPTIDE_REVERSE_DECOYS;
+
+ set<string> targets, decoys;
+ map<const string*, const string*> targetToDecoy;
+ map< OrderedPeptide, vector<string> > peptideToProtein;
+ int proteinTotal = 0, peptideTotal = 0;
+
+ // Iterate over all proteins from this FASTA
+ while (true) {
+ string id, proteinSequence;
+ if (!getNextProtein(*fasta, &id, &proteinSequence)) {
+ break;
+ }
+ ++proteinTotal;
+ carp(CARP_DEBUG, "Read %s", id.c_str());
+
+ // Get peptides
+ vector<CleavedPeptide> peptides =
+ cleaveProtein(proteinSequence, enzyme, digest, missed, minLen, maxLen);
+ peptideTotal += peptides.size();
+
+ // Write reversed protein to decoy FASTA, if protein reverse
+ if (decoyFasta && proteinReverse) {
+ reverse(proteinSequence.begin(), proteinSequence.end());
+ *decoyFasta << '>' << decoyPrefix << id << endl
+ << proteinSequence << endl;
+ }
+
+ // Iterate over all peptides from this protein
+ for (vector<CleavedPeptide>::const_iterator i = peptides.begin();
+ i != peptides.end();
+ i++) {
+ FLOAT_T mass = i->Mass();
+ if (mass < minMass || mass > maxMass) {
+ carp(CARP_DETAILED_DEBUG, "Skipping peptide with mass %f", mass);
+ continue;
+ }
+ const string& sequence = i->Sequence();
+ pair<set<string>::iterator, bool> insert = targets.insert(sequence);
+ if (insert.second) {
+ peptideToProtein[*i] = vector<string>(1, id);
+ } else {
+ peptideToProtein[*i].push_back(id);
+ }
+ }
+ }
+ delete fasta;
+ carp(CARP_DEBUG, "Read %d proteins and %d peptides", proteinTotal, peptideTotal);
+
+ // Once we have all targets, try to generate a decoy for each one
+ if (peptideShuffle || peptideReverse) {
+ int decoyFailures = 0;
+ for (set<string>::const_iterator i = targets.begin(); i != targets.end(); i++) {
+ string decoy;
+ if (makeDecoy(*i, targets, decoys, peptideShuffle, decoy)) {
+ targetToDecoy[&*i] = &*(decoys.insert(decoy).first);
+ } else {
+ ++decoyFailures;
+ }
+ }
+ if (decoyFailures > 0) {
+ carp(CARP_WARNING, "Failed to generate decoys for %d targets", decoyFailures);
+ }
+ }
+
+ // Re-read FASTA and generate decoy FASTA
+ if (decoyFasta && (peptideShuffle || peptideReverse)) {
+ ifstream* fasta = new ifstream(fastaPath.c_str(), ifstream::in);
+ while (true) {
+ string id, proteinSequence;
+ if (!getNextProtein(*fasta, &id, &proteinSequence)) {
+ break;
+ }
+
+ *decoyFasta << '>' << decoyPrefix << id << endl;
+
+ // Get peptides
+ vector<CleavedPeptide> peptides =
+ cleaveProtein(proteinSequence, enzyme, digest, missed, 0, 1000000);
+
+ // Iterate over all peptides from this protein
+ for (vector<CleavedPeptide>::const_iterator i = peptides.begin();
+ i != peptides.end();
+ i++) {
+ const string& sequence = i->Sequence();
+ set<string>::const_iterator j = targets.find(sequence);
+ if (j != targets.end()) {
+ map<const string*, const string*>::const_iterator k = targetToDecoy.find(&*j);
+ if (k != targetToDecoy.end()) {
+ *decoyFasta << *k->second;
+ continue;
+ }
+ }
+ *decoyFasta << sequence;
+ }
+ *decoyFasta << endl;
+ }
+ delete fasta;
+ }
+
+ int precision = Params::GetInt("mass-precision");
+ for (map< OrderedPeptide, vector<string> >::const_iterator i = peptideToProtein.begin();
+ i != peptideToProtein.end();
+ i++) {
+ const string& sequence = i->first.Sequence();
+ FLOAT_T mass = i->first.Mass();
+ vector<string>::const_iterator j = i->second.begin();
+ *targetList << sequence << '\t'
+ << StringUtils::ToString(mass + MASS_PROTON, precision) << '\t'
+ << *j;
+ for (j = j + 1; j != i->second.end(); j++) {
+ string proteinId = *j;
+ *targetList << ',' << proteinId;
+ }
+ *targetList << endl;
+
+ if ((peptideShuffle || peptideReverse) && decoyList) {
+ set<string>::const_iterator target = targets.find(sequence);
+ map<const string*, const string*>::const_iterator k = targetToDecoy.find(&*target);
+ if (k != targetToDecoy.end()) {
+ j = i->second.begin();
+ *decoyList << *k->second << '\t'
+ << StringUtils::ToString(mass + MASS_PROTON, precision) << '\t'
+ << decoyPrefix << *j;
+ for (j = j + 1; j != i->second.end(); j++) {
+ *decoyList << ',' << decoyPrefix << *j;
+ }
+ *decoyList << endl;
+ }
+ }
+ }
+
+ if (decoyFasta) {
+ delete decoyFasta;
+ }
+
+ delete targetList;
+
+ if (proteinReverse && !decoyFastaPath.empty()) {
+ processFasta(decoyFastaPath, decoyList, "", NULL, NO_DECOYS);
+ } else if (decoyList) {
+ delete decoyList;
+ }
+}
+
+bool GeneratePeptides::canGenerateDecoyProteins() {
+ const string decoyFormat = Params::GetString("decoy-format");
+
+ // Can never write decoy proteins if not making decoys
+ if (decoyFormat == "none") {
+ return false;
+ }
+
+ // Can always write decoy proteins if making protein-level decoys
+ if (decoyFormat == "protein-reverse") {
+ return true;
+ }
+
+ // If making peptide-level decoys, we can only write decoy proteins if:
+ // Using an enzyme, full digestion, no missed cleavages
+ bool customEnzyme = !Params::GetString("custom-enzyme").empty();
+ bool useEnzyme = get_enzyme_type_parameter("enzyme") != NO_ENZYME;
+ bool fullDigest = get_digest_type_parameter("digestion") == FULL_DIGEST;
+ bool noMissedCleavages = Params::GetInt("missed-cleavages") == 0;
+
+ return (customEnzyme || useEnzyme) && fullDigest && noMissedCleavages;
+}
+
+/**
+ * Reads the next protein ID and corresponding sequence from the FASTA stream
+ * Returns false if no more proteins in stream
+ */
+bool GeneratePeptides::getNextProtein(
+ ifstream& fasta, ///< FASTA stream
+ string* outId, ///< string to store protein ID
+ string* outSequence ///< string to store sequence
+) {
+ outId->clear();
+ outSequence->clear();
+ if (!fasta.good()) {
+ return false;
+ }
+
+ while (fasta.good()) {
+ string line;
+ getline(fasta, line);
+ line = StringUtils::Trim(line);
+ if (outId->empty()) {
+ // Reading id
+ if (StringUtils::StartsWith(line, ">")) {
+ bool idStart = false;
+ string::const_iterator begin = line.begin() + 1;
+ string::const_iterator end = line.end();
+ for (string::const_iterator i = begin; i != line.end(); i++) {
+ bool space = isspace(*i);
+ if (!idStart && !space) {
+ begin = i;
+ idStart = true;
+ } else if (idStart && space) {
+ end = i;
+ break;
+ }
+ }
+ *outId = string(begin, end);
+ }
+ } else {
+ // Reading sequence
+ *outSequence += line;
+ if (fasta.eof() || fasta.peek() == '>') {
+ break;
+ }
+ }
+ }
+
+ if (StringUtils::EndsWith(*outSequence, "*")) {
+ // Remove the last character of the sequence if it is an asterisk
+ outSequence->erase(outSequence->length() - 1);
+ }
+
+ if (outSequence->empty()) {
+ carp(CARP_WARNING, "Found protein ID without sequence: %s", outId->c_str());
+ outId->clear();
+ return false;
+ }
+
+ if (fasta.fail()) {
+ carp(CARP_FATAL, "Error reading FASTA file");
+ }
+
+ return true;
+}
+
+/**
+ * Cleave protein sequence using specified enzyme and store results in vector
+ * Vector also contains start location of each peptide within the protein
+ */
+vector<GeneratePeptides::CleavedPeptide> GeneratePeptides::cleaveProtein(
+ const string& sequence, ///< Protein sequence to cleave
+ ENZYME_T enzyme, ///< Enzyme to use for cleavage
+ DIGEST_T digest, ///< Digestion to use for cleavage
+ int missedCleavages, ///< Maximum allowed missed cleavages
+ int minLength, //< Min length of peptides to return
+ int maxLength //< Max length of peptides to return
+) {
+ vector<CleavedPeptide> peptides;
+ // No enzyme
+ // Get all substrings min <= length <= max
+ if (enzyme == NO_ENZYME) {
+ for (int i = 0; i < sequence.length(); ++i) {
+ for (int j = minLength; i + j <= sequence.length() && j <= maxLength; ++j) {
+ peptides.push_back(CleavedPeptide(sequence.substr(i, j), i));
+ }
+ }
+ return peptides;
+ }
+
+ size_t pepStart = 0, nextPepStart = 0;
+ int cleaveSites = 0;
+ for (int i = 0; i < sequence.length(); ++i) {
+ // Determine if this is a valid cleavage position
+ bool cleavePos = i != sequence.length() - 1 &&
+ ProteinPeptideIterator::validCleavagePosition(sequence.c_str() + i, enzyme);
+ if (digest == PARTIAL_DIGEST && i != sequence.length() - 1 && !cleavePos) {
+ // Partial digestion (not last AA or cleavage position), add this peptide
+ peptides.push_back(CleavedPeptide(sequence.substr(pepStart, i + 1 - pepStart), pepStart));
+ } else if (cleavePos) {
+ // Cleavage position, add this peptide
+ peptides.push_back(CleavedPeptide(sequence.substr(pepStart, i + 1 - pepStart), pepStart));
+ if (Params::GetBool("clip-nterm-methionine") && sequence[0] == 'M' &&
+ pepStart == 0 && digest != PARTIAL_DIGEST) {
+ peptides.push_back(CleavedPeptide(
+ sequence.substr(pepStart + 1, i + 1 - pepStart - 1), pepStart + 1));
+ }
+ if (++cleaveSites == 1) {
+ // This is the first cleavage position, remember it
+ nextPepStart = i + 1;
+ }
+ if (digest == PARTIAL_DIGEST) {
+ // For partial digest, add peptides ending at this cleavage position
+ for (int j = pepStart + 1; j < nextPepStart; ++j) {
+ peptides.push_back(CleavedPeptide(sequence.substr(j, i - j + 1), j));
+ }
+ }
+ if (cleaveSites > missedCleavages) {
+ // We have missed the allowed amount of cleavages
+ // Move iterator+pepStart to the first cleavage position
+ pepStart = nextPepStart;
+ i = pepStart - 1;
+ cleaveSites = 0;
+ }
+ } else if (i == sequence.length() - 1 &&
+ cleaveSites > 0 && cleaveSites <= missedCleavages) {
+ // Last AA in sequence and we haven't missed the allowed amount yet
+ // Add this peptide and move iterator+pepStart to first cleavage position
+ peptides.push_back(CleavedPeptide(sequence.substr(pepStart), pepStart));
+ if (digest == PARTIAL_DIGEST) {
+ // For partial digest, add peptides ending at last AA
+ for (int j = pepStart + 1; j < nextPepStart; ++j) {
+ peptides.push_back(CleavedPeptide(sequence.substr(j, i - j + 1), j));
+ }
+ }
+ pepStart = nextPepStart;
+ i = pepStart - 1;
+ cleaveSites = 0;
+ }
+ }
+ // Add the last peptide
+ peptides.push_back(CleavedPeptide(sequence.substr(nextPepStart), nextPepStart));
+ if (digest == PARTIAL_DIGEST) {
+ // For partial digest, add peptides ending at last AA
+ for (int j = pepStart + 1; j < sequence.length(); ++j) {
+ peptides.push_back(CleavedPeptide(sequence.substr(j), j));
+ }
+ }
+ // Erase peptides that don't meet length requirement
+ for (vector<CleavedPeptide>::iterator i = peptides.begin(); i != peptides.end(); ) {
+ if (i->Length() < minLength || i->Length() > maxLength) {
+ i = peptides.erase(i);
+ } else {
+ ++i;
+ }
+ }
+ return peptides;
+}
+
+/**
+ * Makes a decoy from the sequence.
+ * Returns false on failure, and decoyOut will be the same as seq.
+ */
+bool GeneratePeptides::makeDecoy(
+ const string& seq, ///< sequence to make decoy from
+ const set<string>& targetSeqs, ///< targets to check against
+ const set<string>& decoySeqs, ///< decoys to check against
+ bool shuffle, ///< shuffle (if false, reverse)
+ string& decoyOut ///< string to store decoy
+) {
+ const string keepTerminal = Params::GetString("keep-terminal-aminos");
+ string decoyPre, decoyPost;
+ if (keepTerminal == "N") {
+ if (seq.length() <= 2) {
+ decoyOut = seq;
+ return false;
+ }
+ decoyPre = seq[0];
+ decoyOut = seq.substr(1);
+ } else if (keepTerminal == "C") {
+ if (seq.length() <= 2) {
+ decoyOut = seq;
+ return false;
+ }
+ decoyPost = seq[seq.length() - 1];
+ decoyOut = seq.substr(0, seq.length() - 1);
+ } else if (keepTerminal == "NC") {
+ if (seq.length() <= 3) {
+ decoyOut = seq;
+ return false;
+ }
+ decoyPre = seq[0];
+ decoyPost = seq[seq.length() - 1];
+ decoyOut = seq.substr(1, seq.length() - 2);
+ } else {
+ decoyOut = seq;
+ if (seq.length() <= 1) {
+ return false;
+ }
+ }
+
+ if (!shuffle) {
+ // Reverse
+ if (reversePeptide(decoyOut)) {
+ // Re-add n/c
+ string decoyCheck = decoyPre + decoyOut + decoyPost;
+ // Check in sets
+ if (targetSeqs.find(decoyCheck) == targetSeqs.end() &&
+ decoySeqs.find(decoyCheck) == decoySeqs.end()) {
+ decoyOut = decoyCheck;
+ return true;
+ }
+ }
+ carp(CARP_DEBUG, "Failed reversing %s, shuffling", seq.c_str());
+ }
+
+ // Shuffle
+ if (shufflePeptide(decoyOut)) {
+ // Re-add n/c
+ string decoyCheck = decoyPre + decoyOut + decoyPost;
+ // Check in sets
+ if (targetSeqs.find(decoyCheck) == targetSeqs.end() &&
+ decoySeqs.find(decoyCheck) == decoySeqs.end()) {
+ decoyOut = decoyCheck;
+ return true;
+ }
+ }
+
+ decoyOut = seq;
+ return false;
+}
+
+/**
+ * Shuffles the peptide randomly.
+ * Returns false if no different sequence was generated
+ */
+bool GeneratePeptides::shufflePeptide(
+ string& seq, ///< Peptide sequence to shuffle
+ unsigned int maxShuffleAttempts ///< Maximum number of shuffle attempts
+) {
+ switch (seq.length()) {
+ case 0:
+ case 1:
+ return false;
+ case 2: {
+ char second = seq[1];
+ seq[1] = seq[0];
+ seq[0] = second;
+ return true;
+ }
+ default:
+ string originalSeq(seq);
+ for (int i = 0; i < maxShuffleAttempts; i++) {
+ random_shuffle(seq.begin(), seq.end(), myrandom_limit);
+ if (seq != originalSeq) {
+ return true;
+ }
+ }
+ return false;
+ }
+}
+
+/**
+ * Reverses the peptide sequence.
+ * Returns false if no different sequence was generated
+ */
+bool GeneratePeptides::reversePeptide(
+ string& seq ///< Peptide sequence to reverse
+) {
+ string originalSeq(seq);
+ reverse(seq.begin(), seq.end());
+ return seq != originalSeq;
+}
+
+string GeneratePeptides::getName() const {
+ return "generate-peptides";
+}
+
+string GeneratePeptides::getDescription() const {
+ return
+ "[[nohtml:Extract from a given set of protein sequences a list of target "
+ "and decoy peptides fitting the specified criteria.]]"
+ "[[html:<p>This command takes as input a protein FASTA file and outputs "
+ "the corresponding list of peptides, as well as a matched list of decoy "
+ "peptides and decoy proteins. Decoys are generated either by reversing or "
+ "shuffling the non-terminal amino acids of each peptide. The program will "
+ "shuffle each peptide multiple times to attempt to ensure that there is no "
+ "overlap between the target and decoy peptides. For homopolymers, this is "
+ "not possible. In this case, the occurrence of these target/decoy overlaps "
+ "is recorded in the log file.</p><p>The program considers only the "
+ "standard set of 20 amino acids. Peptides containing non-amino acid "
+ "alphanumeric characters (BJOUXZ) are skipped. Non-alphanumeric characters "
+ "are ignored completely.</p>]]";
+}
+
+vector<string> GeneratePeptides::getArgs() const {
+ string arr[] = {
+ "protein fasta file"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> GeneratePeptides::getOptions() const {
+ string arr[] = {
+ "min-mass",
+ "max-mass",
+ "min-length",
+ "max-length",
+ "enzyme",
+ "custom-enzyme",
+ "digestion",
+ "missed-cleavages",
+ "isotopic-mass",
+ "seed",
+ "clip-nterm-methionine",
+ "decoy-format",
+ "decoy-prefix",
+ "keep-terminal-aminos",
+ "overwrite",
+ "fileroot",
+ "output-dir",
+ "parameter-file",
+ "verbosity"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > GeneratePeptides::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("generate-peptides.target.txt",
+ "A text file containing the target peptides, one per line. Each line has "
+ "three tab-delimited columns, containing the peptide sequence, the m+h "
+ "mass of the unmodified peptide, and a comma-delimited list of protein IDs "
+ "in which the peptide occurs."));
+ outputs.push_back(make_pair("generate-peptides.decoy.txt",
+ "A text file containing the decoy peptides, one per line. Each line has "
+ "three tab-delimited columns, containing the peptide sequence, the m+h "
+ "mass of the unmodified peptide, and a comma-delimited list of protein IDs "
+ "in which the peptide occurs. "
+ "There is a one-to-one correspondence between targets and decoys."));
+ outputs.push_back(make_pair("generate-peptides.proteins.decoy.txt",
+ "a FASTA format file containing decoy proteins, in which all of the "
+ "peptides have been replaced with their shuffled or reversed counterparts. "
+ "Note that this file will only be created if the enzyme specificity is "
+ "\"full-digest\" and no missed cleavages are allowed."));
+ outputs.push_back(make_pair("generate-peptides.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("generate-peptides.log.txt",
+ "a log file containing a copy of all messages that were printed to the "
+ "screen during execution."));
+ return outputs;
+}
+
+bool GeneratePeptides::needsOutputDirectory() const {
+ return true;
+}
+
+COMMAND_T GeneratePeptides::getCommand() const {
+ return GENERATE_PEPTIDES_COMMAND;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/GeneratePeptides.h b/src/app/GeneratePeptides.h
new file mode 100644
index 0000000..80843e2
--- /dev/null
+++ b/src/app/GeneratePeptides.h
@@ -0,0 +1,154 @@
+#ifndef GENERATE_PEPTIDES_H
+#define GENERATE_PEPTIDES_H
+
+#include <fstream>
+
+#include "CruxApplication.h"
+#include "model/Peptide.h"
+
+class GeneratePeptides : public CruxApplication {
+
+ protected:
+ static MASS_TYPE_T massType_;
+
+ public:
+
+ class OrderedPeptide {
+ public:
+ explicit OrderedPeptide(const std::string& sequence):
+ sequence_(sequence), sequencePtr_(NULL),
+ mass_(Crux::Peptide::calcSequenceMass(sequence, massType_)) {}
+ explicit OrderedPeptide(const std::string* sequence):
+ sequence_(""), sequencePtr_(sequence),
+ mass_(Crux::Peptide::calcSequenceMass(*sequence, massType_)) {}
+
+ std::string Sequence() const { return sequencePtr_ ? *sequencePtr_ : sequence_; }
+ unsigned int Length() const { return Sequence().length(); }
+ FLOAT_T Mass() const { return mass_; }
+ bool operator <(const OrderedPeptide& rhs) const { return Sequence() < rhs.Sequence(); }
+ protected:
+ std::string sequence_;
+ const std::string* sequencePtr_;
+ FLOAT_T mass_;
+ };
+
+ class CleavedPeptide : public OrderedPeptide {
+ public:
+ CleavedPeptide(const std::string& sequence, unsigned int position):
+ OrderedPeptide(sequence), position_(position) {}
+ unsigned int Position() const { return position_; }
+ private:
+ unsigned int position_;
+ };
+
+ /**
+ * Constructor
+ */
+ GeneratePeptides();
+
+ /**
+ * Destructor
+ */
+ ~GeneratePeptides();
+
+ /**
+ * Main method
+ */
+ virtual int main(int argc, char** argv);
+
+ void processFasta(
+ const std::string& fastaPath,
+ std::ofstream* targetList,
+ const std::string& decoyFastaPath,
+ std::ofstream* decoyList,
+ DECOY_TYPE_T decoyType
+ );
+
+ /**
+ * Check if we can generate decoy proteins with the current settings.
+ */
+ static bool canGenerateDecoyProteins();
+
+ /**
+ * Reads the next protein ID and corresponding sequence from the FASTA stream
+ * Returns false if no more proteins in stream
+ */
+ static bool getNextProtein(
+ std::ifstream& fasta, ///< FASTA stream
+ std::string* outId, ///< string to store protein ID
+ std::string* outSequence ///< string to store sequence
+ );
+
+ /**
+ * Cleave protein sequence using specified enzyme and store results in vector
+ * Vector also contains start location of each peptide within the protein
+ */
+ static std::vector<CleavedPeptide> cleaveProtein(
+ const std::string& sequence, ///< Protein sequence to cleave
+ ENZYME_T enzyme, ///< Enzyme to use for cleavage
+ DIGEST_T digest, ///< Digestion to use for cleavage
+ int missedCleavages, ///< Maximum allowed missed cleavages
+ int minLength, //< Min length of peptides to return
+ int maxLength //< Max length of peptides to return
+ );
+
+ /**
+ * Makes a decoy from the sequence.
+ * Returns false on failure, and decoyOut will be the same as seq.
+ */
+ static bool makeDecoy(
+ const std::string& seq, ///< sequence to make decoy from
+ const std::set<std::string>& targetSeqs, ///< targets to check against
+ const std::set<std::string>& decoySeqs, ///< decoys to check against
+ bool shuffle, ///< shuffle (if false, reverse)
+ std::string& decoyOut ///< string to store decoy
+ );
+
+ /**
+ * Shuffles the peptide sequence.
+ * Returns false if no different sequence was generated
+ */
+ static bool shufflePeptide(
+ std::string& seq, ///< Peptide sequence to shuffle
+ unsigned int maxShuffleAttempts = 6 ///< Maximum number of shuffle attempts
+ );
+
+ /**
+ * Reverses the peptide sequence.
+ * Returns false if no different sequence was generated
+ */
+ static bool reversePeptide(
+ std::string& seq ///< Peptide sequence to reverse
+ );
+
+ /**
+ * Returns the command name
+ */
+ virtual std::string getName() const;
+
+ /**
+ * Returns the command description
+ */
+ virtual std::string getDescription() const;
+
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * Returns whether the application needs the output directory or not. (default false)
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual COMMAND_T getCommand() const;
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/GetMs2Spectrum.cpp b/src/app/GetMs2Spectrum.cpp
new file mode 100644
index 0000000..1f6bf26
--- /dev/null
+++ b/src/app/GetMs2Spectrum.cpp
@@ -0,0 +1,185 @@
+/**
+ * \file GetMs2Spectrum.cpp
+ *
+ * AUTHOR: Manijeh Naser
+ * CREATE DATE: January 31, 2012
+ *
+ * DESCRIPTION:brief searches a given ms2 file for the spectrum with the given
+ * scan number.
+ */
+
+#include "GetMs2Spectrum.h"
+
+#include <math.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#include <vector>
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include "parameter.h"
+#include "io/carp.h"
+#include "model/Spectrum.h"
+#include "model/Peak.h"
+#include "io/SpectrumCollectionFactory.h"
+#include "util/Params.h"
+#include "util/WinCrux.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * \returns A blank GetMs2Spectrum object.
+ */
+GetMs2Spectrum::GetMs2Spectrum() {
+
+}
+
+/**
+ * Destructorm
+ */
+GetMs2Spectrum::~GetMs2Spectrum() {
+}
+
+/****************************************************************************
+ * MAIN
+ ****************************************************************************/
+int GetMs2Spectrum::main(int argc, char** argv) {
+ /* Get arguments */
+ int min_scan = -1;
+ int max_scan = -1;
+ string range_string = Params::GetString("scan-number");
+
+ get_range_from_string(
+ range_string,
+ min_scan,
+ max_scan);
+
+ fprintf(stderr, "Scanning from %d to %d.\n", min_scan, max_scan);
+
+ string ms2_filename = Params::GetString("ms2 file");
+ carp(CARP_DETAILED_DEBUG, "ms2_filename: %s", ms2_filename.c_str());
+
+ /* Get options */
+ bool options = Params::GetBool("stats");
+
+ /* read input file */
+ if (access(ms2_filename.c_str(), F_OK)) {
+ carp(CARP_FATAL, "Could not read from ms2 file '%s'", ms2_filename.c_str());
+ }
+ carp(CARP_DETAILED_DEBUG, "Creating spectrum collection.");
+ Crux::SpectrumCollection* collection = SpectrumCollectionFactory::create(ms2_filename);
+ collection->parse();
+ int num_found = 0;
+
+ for (SpectrumIterator iter = collection->begin(); iter != collection->end(); ++iter) {
+
+ Spectrum* spectrum = *iter;
+ carp(CARP_DETAILED_DEBUG, "spectrum number:%d", spectrum->getFirstScan());
+ if (spectrum->getFirstScan() >= min_scan && spectrum->getFirstScan() <= max_scan) {
+
+ /* Print either the spectrum or stats. */
+ if (!options) {
+ spectrum->print(stdout);
+ } else {
+ int charge_state_index = 0;
+ int charge_state_num = spectrum->getNumZStates();
+ std::vector<SpectrumZState> zstates_array = spectrum->getZStates();
+
+ printf("Scan number: %i\n", spectrum->getFirstScan());
+ printf("Precursor m/z:%.2f\n", spectrum->getPrecursorMz());
+ printf("Total Ion Current:%.2f\n", spectrum->getTotalEnergy());
+ printf("Base Peak Intensity:%.1f\n", spectrum->getMaxPeakIntensity()); // base is max
+ printf("Number of peaks:%d\n", spectrum->getNumPeaks());
+ printf("Minimum m/z:%.1f\n", spectrum->getMinPeakMz());
+ printf("Maximum m/z:%.1f\n", spectrum->getMaxPeakMz());
+
+ for (charge_state_index = 0; charge_state_index < charge_state_num; ++charge_state_index) {
+ SpectrumZState& zstate = zstates_array[charge_state_index];
+ FLOAT_T charged_mass = spectrum->getPrecursorMz() * (FLOAT_T)zstate.getCharge();
+
+ printf("Charge state:%d\n", zstate.getCharge());
+ printf("Neutral mass:%.2f\n", zstate.getNeutralMass());
+ printf("Charged mass:%.2f\n", charged_mass);
+ printf("M+H+ mass:%.2f\n", zstate.getSinglyChargedMass());
+ }
+ }
+ num_found++;
+ }
+ }
+ delete collection;
+
+ carp(CARP_INFO, "Found %d spectra.\n", num_found);
+
+ return(0);
+}
+/**
+ * \returns The command name for GetMs2SPectrum.
+ */
+string GetMs2Spectrum::getName() const {
+ return "get-ms2-spectrum";
+}
+
+/**
+ * \returns The description for GetMs2Spectrum.
+ */
+string GetMs2Spectrum::getDescription() const {
+ return
+ "[[nohtml:Extract one or more fragmentation spectra, specified by scan "
+ "number, from an MS2 file.]]"
+ "[[html:<p>Extract one or more MS-MS spectra from an MS2 file by scan "
+ "number. Optionally output summary statistics for each spectrum.</p>]]";
+}
+
+/**
+ * \returns The command arguments
+ */
+vector<string> GetMs2Spectrum::getArgs() const {
+ string arr[] = {
+ "ms2 file"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns The command options
+ */
+vector<string> GetMs2Spectrum::getOptions() const {
+ string arr[] = {
+ "scan-number",
+ "remove-precursor-tolerance",
+ "stats",
+ "verbosity",
+ "spectrum-parser",
+ "use-z-line"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns The command outputs
+ */
+vector< pair<string, string> > GetMs2Spectrum::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "the requested spectrum or spectra in MS2 format."));
+ return outputs;
+}
+
+/**
+ * \returns The enum of the application, default GET_MS2_SPECTRUM_COMMAND.
+ */
+COMMAND_T GetMs2Spectrum::getCommand() const {
+ return GET_MS2_SPECTRUM_COMMAND;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/GetMs2Spectrum.h b/src/app/GetMs2Spectrum.h
new file mode 100644
index 0000000..5885f72
--- /dev/null
+++ b/src/app/GetMs2Spectrum.h
@@ -0,0 +1,86 @@
+/**
+ * \file GetMs2Spectrum.h
+ *
+ * AUTHOR: Manijeh Naseri
+ * CREATE DATE: February 2, 2012
+ * DESCRIPTION: Main method for the generate-peptides command.
+ * Output all peptide sequences in the given fasta file
+ * that fall within all peptide constraints.
+ */
+#ifndef GETMS2SPECTRUM_H
+#define GETMS2SPECTRUM_H
+
+#include "CruxApplication.h"
+#include "util/crux-utils.h"
+#include "io/carp.h"
+#include "parameter.h"
+
+class GetMs2Spectrum: public CruxApplication {
+
+ public:
+ /**
+ * \returns A blank GetMs2Spectrum object.
+ */
+ GetMs2Spectrum();
+
+ /**
+ * Destructor
+ */
+ ~GetMs2Spectrum();
+
+ /**
+ * Main method for GetMs2Spectrum.
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns The command name for GetMs2Spectrum.
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns The description for GetMs2Spectrum.
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns The command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns The command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns The command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns The file stem of the application, default getName.
+ */
+
+ virtual COMMAND_T getCommand() const;
+
+
+ protected:
+ /**
+ * Print header lines to stdout.
+ */
+ void printHeader();
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/app/MakePinApplication.cpp b/src/app/MakePinApplication.cpp
new file mode 100644
index 0000000..51e79c9
--- /dev/null
+++ b/src/app/MakePinApplication.cpp
@@ -0,0 +1,241 @@
+/**
+ *\file MakePinApplication.cpp
+ *****************************************************************************/
+#include "MakePinApplication.h"
+#include "io/PinWriter.h"
+#include "parameter.h"
+#include "util/Params.h"
+#include "io/MatchCollectionParser.h"
+#include "io/SQTReader.h"
+#include "util/StringUtils.h"
+#include <sstream>
+#include <iomanip>
+#include <ios>
+
+using namespace std;
+
+/**
+ * \returns a blank PercolatorApplication object
+ */
+MakePinApplication::MakePinApplication() {
+}
+
+/**
+ * Destructor
+ */
+MakePinApplication::~MakePinApplication() {}
+
+/**
+ * main method for MakePinApplication
+ */
+int MakePinApplication::main(int argc, char** argv) {
+ string target_path = Params::GetString("target input");
+
+ vector<string> search_result_files;
+ get_search_result_paths(target_path, search_result_files);
+
+ return main(search_result_files);
+}
+
+/**
+ * \runs make-pin application
+ */
+int MakePinApplication::main(const vector<string>& paths) {
+ //create MatchColletion
+ MatchCollectionParser parser;
+
+ if (paths.empty()) {
+ carp(CARP_FATAL, "No search paths found!");
+ }
+
+ MatchCollection* target_collection = new MatchCollection();
+ MatchCollection* decoy_collection = new MatchCollection();
+
+ int max_charge = 0;
+ for (vector<string>::const_iterator iter = paths.begin(); iter != paths.end(); ++iter) {
+ carp(CARP_INFO, "Parsing %s", iter->c_str());
+ if (StringUtils::IEndsWith(*iter, ".sqt")) {
+ SQTReader::readSymbols(*iter);
+ }
+
+ MatchCollection* current_collection = parser.create(iter->c_str(), "");
+ if (!target_collection->getHasDistinctMatches() && current_collection->getHasDistinctMatches()) {
+ target_collection->setHasDistinctMatches(true);
+ decoy_collection->setHasDistinctMatches(true);
+ }
+ for (int scorer_idx = (int)SP; scorer_idx < (int)NUMBER_SCORER_TYPES; scorer_idx++) {
+ SCORER_TYPE_T cur_type = (SCORER_TYPE_T)scorer_idx;
+ bool scored = current_collection->getScoredType(cur_type);
+ target_collection->setScoredType(cur_type, scored);
+ decoy_collection->setScoredType(cur_type, scored);
+ }
+ MatchIterator match_iter(current_collection);
+ while (match_iter.hasNext()) {
+ Crux::Match* match = match_iter.next();
+ if (match->getNullPeptide()) {
+ decoy_collection->addMatch(match);
+ } else {
+ target_collection->addMatch(match);
+ }
+ int charge = match->getCharge();
+ if (charge > max_charge) {
+ max_charge = charge;
+ }
+ }
+ delete current_collection;
+ }
+
+ carp(CARP_INFO, "There are %d target matches and %d decoys",
+ target_collection->getMatchTotal(), decoy_collection->getMatchTotal());
+ if (target_collection->getMatchTotal() == 0) {
+ carp(CARP_FATAL, "No target matches found!");
+ } else if (decoy_collection->getMatchTotal() == 0) {
+ carp(CARP_FATAL, "No decoy matches found! Did you set 'decoy-prefix' properly?");
+ }
+
+ //prepare output file
+ string output_filename = Params::GetString("output-file");
+ if (output_filename.empty()) {
+ string fileroot = Params::GetString("fileroot");
+ if (!fileroot.empty()) {
+ fileroot += ".";
+ }
+ output_filename = fileroot + "make-pin.pin";
+ }
+ PinWriter writer;
+ writer.openFile(output_filename, Params::GetString("output-dir"),
+ Params::GetBool("overwrite"));
+
+ for (int i = 1; i <= max_charge; i++) {
+ writer.setEnabledStatus("Charge" + StringUtils::ToString(i), true);
+ }
+ writer.setEnabledStatus("deltCn", target_collection->getScoredType(DELTA_CN));
+ writer.setEnabledStatus("deltLCn", target_collection->getScoredType(DELTA_LCN));
+ bool is_sp = target_collection->getScoredType(SP);
+ writer.setEnabledStatus("lnrSp", is_sp);
+ writer.setEnabledStatus("Sp", is_sp);
+ writer.setEnabledStatus("IonFrac", is_sp);
+ bool is_refactored_xcorr = target_collection->getScoredType(TIDE_SEARCH_REFACTORED_XCORR);
+ writer.setEnabledStatus("XCorr", !is_refactored_xcorr);
+ writer.setEnabledStatus("RefactoredXCorr", is_refactored_xcorr);
+ writer.setEnabledStatus("NegLog10PValue",
+ target_collection->getScoredType(TIDE_SEARCH_EXACT_PVAL));
+ if (writer.getEnabledStatus("lnNumSP") && target_collection->getHasDistinctMatches()) {
+ writer.setEnabledStatus("lnNumSP", false);
+ writer.setEnabledStatus("lnNumDSP", true);
+ }
+
+ //write .pin file
+ writer.printHeader();
+ writer.write(target_collection, vector<MatchCollection*>(1, decoy_collection),
+ Params::GetInt("top-match"));
+
+ delete target_collection;
+ delete decoy_collection;
+
+ return 0;
+}
+
+/**
+ * \returns the command name for PercolatorApplication
+ */
+string MakePinApplication::getName() const {
+ return "make-pin";
+}
+
+/**
+ * \returns the description for PercolatorApplication
+ */
+string MakePinApplication::getDescription() const {
+ return
+ "[[nohtml:Given a set of search results files, generate a pin file for "
+ "input to crux percolator]]"
+ "[[html:<p>Make-pin is a utility program that combines a collection of "
+ "target and decoy peptide-spectrum matches (PSMs) into a single file in "
+ "pin format, according to <a href=\"https://github.com/percolator/"
+ "percolator/wiki/Interface\">this format</a>. The resulting file can be "
+ "provided as input to <code><a href=\"percolator.html\">crux percolator</a>"
+ "</code>.</p><p><code>make-pin</code> requires as input two sets of PSMs, "
+ "one set derived from matching observed spectra against real "
+ "("target") peptides and a second set derived from matching the "
+ "same spectra against "decoy" peptides. The output file contains, "
+ "for each PSM, a set of features for use by the Percolator algorithm. These "
+ "features are summarized <a href=\"../file-formats/features.html\">here</a>.</p><p>Note "
+ "that, in the stand-alone version of Percolator, the functionality provided "
+ "by <code>crux make-pin</code> is incorporated into a program called "
+ "<code>sqt2pin</code>. However, a significant difference between <code>crux "
+ "percolator</code> and the stand-alone version of the program is that "
+ "<code>crux percolator</code> does not require an explicit call to "
+ "<code>crux make-pin</code>: if input is provided to <code>crux percolator"
+ "</code> in a non-pin format, then the input will be automatically "
+ "converted to pin format.</p>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> MakePinApplication::getArgs() const {
+ string arr[] = {
+ "target input"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> MakePinApplication::getOptions() const {
+ string arr[] = {
+ "top-match",
+ "list-of-files",
+ "filestem-prefixes",
+ "decoy-prefix",
+ "fileroot",
+ "output-dir",
+ "output-file",
+ "overwrite",
+ "parameter-file",
+ "verbosity"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > MakePinApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("make-pin.pin",
+ "a tab-delimited file containing the input target and decoy PSMs in pin "
+ "format. This file can be changed to an absolute path (see --output-file "
+ "option)."));
+ outputs.push_back(make_pair("make-pin.params.txt",
+ "a file containing the name and value of all parameters for the current "
+ "operation. Not all parameters in the file may have been used in the "
+ "operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("make-pin.log.txt",
+ "a log file containing a copy of all messages that were printed to "
+ "standard error."));
+ return outputs;
+}
+
+/**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+bool MakePinApplication::needsOutputDirectory() const {
+ return true;
+}
+
+
+bool MakePinApplication:: hidden() const {
+ return false;
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/MakePinApplication.h b/src/app/MakePinApplication.h
new file mode 100644
index 0000000..8afdbb8
--- /dev/null
+++ b/src/app/MakePinApplication.h
@@ -0,0 +1,88 @@
+/**
+ * \file PercolatorApplication.h
+ * AUTHOR: Manije Naseri
+ * CREATE DATE: 4 September 2012
+ * \
+ *****************************************************************************/
+#ifndef MAKEPINAPPLICATION_H
+#define MAKEPINAPPLICATION_H
+
+#include "CruxApplication.h"
+
+#include <string>
+#include <fstream>
+#include <string>
+
+using namespace std;
+
+class MakePinApplication: public CruxApplication {
+
+ public:
+
+ /**
+ * \returns a blank MakePinApplication object
+ */
+ MakePinApplication();
+
+ /**
+ * Destructor
+ */
+ ~MakePinApplication();
+
+ /**
+ * main method for MakePinApplication
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * runs make-pin application
+ */
+ static int main(const std::vector<std::string>& paths);
+
+ /**
+ * \returns the command name for MakePinApplication
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for MakePinApplication
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+ virtual bool needsOutputDirectory() const;
+
+
+ /**
+ * hide sequest search
+ */
+
+ virtual bool hidden() const;
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/PSMConvertApplication.cpp b/src/app/PSMConvertApplication.cpp
new file mode 100644
index 0000000..c032a79
--- /dev/null
+++ b/src/app/PSMConvertApplication.cpp
@@ -0,0 +1,209 @@
+#include <cstdio>
+
+#include "io/carp.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "PSMConvertApplication.h"
+#include "model/MatchCollection.h"
+#include "model/ProteinMatchCollection.h"
+#include "io/HTMLWriter.h"
+#include "io/MatchFileReader.h"
+#include "io/MzIdentMLReader.h"
+#include "io/MzIdentMLWriter.h"
+#include "io/PepXMLReader.h"
+#include "io/PepXMLWriter.h"
+#include "io/PinWriter.h"
+#include "io/PMCDelimitedFileWriter.h"
+#include "io/PMCPepXMLWriter.h"
+#include "io/PMCSQTWriter.h"
+#include "io/PSMReader.h"
+#include "io/PSMWriter.h"
+#include "io/SQTReader.h"
+
+PSMConvertApplication::PSMConvertApplication() {
+}
+
+PSMConvertApplication::~PSMConvertApplication() {
+}
+
+void PSMConvertApplication::convertFile(string input_format, string output_format, string input_file, string output_file_base, string database_file, bool distinct_matches) {
+ Database* data;
+ if (database_file.empty()) {
+ data = new Database();
+ carp(CARP_INFO, "Database not provided, will use empty database");
+ } else {
+ data = new Database(database_file.c_str(), false);
+ carp(CARP_INFO, "Created Database using Fasta File");
+ }
+
+ bool isTabDelimited = false;
+ PSMReader* reader;
+
+ if (input_format != "auto") {
+ if (input_format == "tsv") {
+ reader = new MatchFileReader(input_file.c_str(), data);
+ isTabDelimited = true;
+ } else if (input_format == "html") {
+ carp(CARP_FATAL, "HTML format has not been implemented yet");
+ } else if (input_format == "sqt") {
+ reader = new SQTReader(input_file.c_str(), data);
+ } else if (input_format == "pin") {
+ carp(CARP_FATAL, "Pin format has not been implemented yet");
+ } else if (input_format == "pepxml") {
+ reader = new PepXMLReader(input_file.c_str(), data);
+ } else if (input_format == "mzidentml") {
+ reader = new MzIdentMLReader(input_file.c_str(), data);
+ } else if (input_format == "barista-xml") {
+ carp(CARP_FATAL, "Barista-XML format has not been implemented yet");
+ } else {
+ carp(CARP_FATAL, "Invalid Input Format, valid formats are: tsv, html, "
+ "sqt, pin, pepxml, mzidentml, barista-xml");
+ }
+ } else {
+ if (StringUtils::IEndsWith(input_file, ".txt")) {
+ reader = new MatchFileReader(input_file.c_str(), data);
+ isTabDelimited = true;
+ } else if (StringUtils::IEndsWith(input_file, ".html")) {
+ carp(CARP_FATAL, "HTML format has not been implemented yet");
+ } else if (StringUtils::IEndsWith(input_file, ".sqt")) {
+ reader = new SQTReader(input_file.c_str(), data);
+ } else if (StringUtils::IEndsWith(input_file, ".pin")) {
+ carp(CARP_FATAL, "Pin format has not been implemented yet");
+ } else if (StringUtils::IEndsWith(input_file, ".xml")) {
+ reader = new PepXMLReader(input_file.c_str(), data);
+ } else if (StringUtils::IEndsWith(input_file, ".mzid")) {
+ reader = new MzIdentMLReader(input_file.c_str(), data);
+ } else if (StringUtils::IEndsWith(input_file, ".barista.xml")) {
+ carp(CARP_FATAL, "Barista-XML format has not been implemented yet");
+ } else {
+ carp(CARP_FATAL, "Could not determine input format, "
+ "Please name your files ending with .txt, .html, .sqt, .pin, "
+ ".xml, .mzid, .barista.xml or use the --input-format option to "
+ "specify file type");
+ }
+ }
+
+ MatchCollection* collection = reader->parse();
+
+ if (!isTabDelimited) {
+ collection->setHasDistinctMatches(distinct_matches);
+ } else if (collection->getHasDistinctMatches() != distinct_matches) {
+ const char* matchType = collection->getHasDistinctMatches() ?
+ "distinct" : "not distinct";
+ carp(CARP_WARNING, "Parser has detected that matches are %s, but parameter "
+ "distinct-matches is set to %s. We will assume that matches are %s",
+ matchType, distinct_matches ? "distinct" : "not distinct",
+ matchType);
+ }
+
+ carp(CARP_INFO, "Reader has been succesfully parsed");
+
+ // What will be used when PSMWriter is finished.
+
+ PSMWriter* writer;
+ stringstream output_file_name_builder;
+ output_file_name_builder << output_file_base;
+
+ if (output_format == "tsv") {
+ output_file_name_builder << "txt";
+ writer = new PMCDelimitedFileWriter();
+ } else if (output_format == "html") {
+ output_file_name_builder << "html";
+ writer = new HTMLWriter();
+ } else if (output_format == "sqt") {
+ output_file_name_builder << "sqt";
+ writer = new PMCSQTWriter();
+ } else if (output_format == "pin") {
+ output_file_name_builder << "pin";
+ writer = new PinWriter();
+ } else if (output_format == "pepxml") {
+ output_file_name_builder << "pep.xml";
+ writer = new PMCPepXMLWriter();
+ } else if (output_format == "mzidentml") {
+ output_file_name_builder << "mzid";
+ writer = new MzIdentMLWriter();
+ } else if (output_format == "barista-xml") {
+ carp(CARP_FATAL, "Barista-XML format has not been implemented yet");
+ } else {
+ carp(CARP_FATAL, "Invalid Output Format, valid formats are: tsv, html, "
+ "sqt, pin, pepxml, mzidentml, barista-xml");
+ }
+
+ string output_file_name = make_file_path(output_file_name_builder.str());
+
+ writer->openFile(this, output_file_name, PSMWriter::PSMS);
+ writer->write(collection, database_file);
+ writer->closeFile();
+
+ // Clean Up
+ delete collection;
+ delete reader;
+ delete writer;
+
+}
+
+
+int PSMConvertApplication::main(int argc, char** argv) {
+ string database_file = Params::GetString("protein-database");
+ string input_format = Params::GetString("input-format");
+ string input_file = Params::GetString("input PSM file");
+ string output_format = Params::GetString("output format");
+ bool distinct_matches = Params::GetBool("distinct-matches");
+
+ convertFile(input_format, output_format, input_file, "psm-convert.", database_file, distinct_matches);
+
+ return 0;
+}
+
+string PSMConvertApplication::getName() const {
+ return "psm-convert";
+}
+
+string PSMConvertApplication::getDescription() const {
+ return
+ "Reads in a file containing peptide-spectrum matches "
+ "(PSMs) in one of the variety of supported formats and "
+ "outputs the same PSMs in a different format";
+}
+
+vector<string> PSMConvertApplication::getArgs() const {
+ string arr[] = {
+ "input PSM file",
+ "output format"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> PSMConvertApplication::getOptions() const {
+ string arr[] = {
+ "input-format",
+ "distinct-matches",
+ "protein-database",
+ "output-dir",
+ "overwrite",
+ "parameter-file",
+ "verbosity",
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > PSMConvertApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("psm-convert.log.txt",
+ "a log file containing a copy of all messages that were printed to stderr."));
+ outputs.push_back(make_pair("psm-convert.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ return outputs;
+}
+
+bool PSMConvertApplication::needsOutputDirectory() const {
+ return true;
+}
+
+COMMAND_T PSMConvertApplication::getCommand() const {
+ return PSM_CONVERT_COMMAND;
+}
+
diff --git a/src/app/PSMConvertApplication.h b/src/app/PSMConvertApplication.h
new file mode 100644
index 0000000..0f4766b
--- /dev/null
+++ b/src/app/PSMConvertApplication.h
@@ -0,0 +1,72 @@
+#ifndef PSMCONVERTAPPLICATION_H
+#define PSMCONVERTAPPLICATION_H
+
+#include "CruxApplication.h"
+
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+#include <gflags/gflags.h>
+#include <string>
+
+using namespace std;
+
+class PSMConvertApplication : public CruxApplication {
+
+ public:
+
+ /**
+ * Constructor
+ */
+ PSMConvertApplication();
+
+ /**
+ * Destructor
+ */
+ ~PSMConvertApplication();
+
+ /**
+ * Main method
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * Perform Convert
+ */
+ virtual void convertFile(string input_format, string output_format, string input_file, string output_file_base, string database_file, bool distinct_matches);
+
+ /**
+ * Returns the command name
+ */
+ virtual string getName() const;
+
+ /**
+ * Returns the command description
+ */
+ virtual string getDescription() const;
+
+ /**
+ * Returns the command arguments
+ */
+ virtual vector<string> getArgs() const;
+
+ /**
+ * Returns the command options
+ */
+ virtual vector<string> getOptions() const;
+
+ /**
+ * \returns the outputs of the application as <name, description>
+ */
+ virtual vector< pair<string, string> > getOutputs() const;
+
+ /**
+ * Returns whether the application needs the output directory or not. (default false)
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual COMMAND_T getCommand() const;
+
+};
+
+#endif
diff --git a/src/app/ParamMedicApplication.cpp b/src/app/ParamMedicApplication.cpp
new file mode 100644
index 0000000..ce84e72
--- /dev/null
+++ b/src/app/ParamMedicApplication.cpp
@@ -0,0 +1,658 @@
+#include "ParamMedicApplication.h"
+#include "io/carp.h"
+#include "io/SpectrumCollectionFactory.h"
+#include "parameter.h"
+#include "util/Params.h"
+
+#include <cmath>
+#include <numeric>
+
+using namespace Crux;
+using namespace std;
+
+const double SQRT_2_PI = 2.50662827463;
+
+// maximum proportion of precursor delta-masses that can be 0, otherwise we give up
+const double MAX_PROPORTION_PRECURSOR_DELTAS_ZERO = 0.5;
+
+// maximum peaks to use to fit a mixed distribution
+const int MAX_PEAKPAIRS = 100000;
+
+// multipliers to transform standard error values into algorithm parameters
+const double PRECURSOR_SIGMA_MULTIPLIER = 37.404067;
+const double FRAGMENT_SIGMA_MULTIPLIER = 0.004662;
+
+// separation between averagine peaks used for binning spectra
+const double AVERAGINE_PEAK_SEPARATION = 1.0005079;
+
+// minimum allowed values for sigma of the estimated normal
+const double MIN_SIGMA_PPM = 0.01;
+const double MIN_SIGMA_TH = 0.00001;
+
+ParamMedicApplication::ParamMedicApplication() {
+}
+
+ParamMedicApplication::~ParamMedicApplication() {
+}
+
+int ParamMedicApplication::main(int argc, char** argv) {
+ ParamMedicErrorCalculator errCalc;
+ errCalc.processFiles(Params::GetStrings("spectrum-file"));
+
+ // calculate mass error distributions
+ string precursorFailure, fragmentFailure;
+ double precursorSigmaPpm = 0;
+ double fragmentSigmaPpm = 0;
+ double fragmentSigmaTh = 0;
+ double precursorPredictionPpm = 0;
+ double fragmentPredictionPpm = 0;
+ double fragmentPredictionTh = 0;
+ errCalc.calcMassErrorDist(
+ &precursorFailure,
+ &fragmentFailure,
+ &precursorSigmaPpm,
+ &fragmentSigmaPpm,
+ &precursorPredictionPpm,
+ &fragmentPredictionTh
+ );
+
+ if (precursorFailure.empty()) {
+ carp(CARP_INFO, "precursor ppm standard deviation: %f", precursorSigmaPpm);
+ carp(CARP_INFO, "Precursor error estimate (ppm): %.2f", precursorPredictionPpm);
+ } else {
+ carp(CARP_ERROR, "failed to calculate precursor error: %s", precursorFailure.c_str());
+ }
+ if (fragmentFailure.empty()) {
+ carp(CARP_INFO, "fragment standard deviation (ppm): %f", fragmentSigmaPpm);
+ carp(CARP_INFO, "Fragment bin size estimate (Th): %.4f", fragmentPredictionTh);
+ } else {
+ carp(CARP_ERROR, "failed to calculate fragment error: %s", fragmentFailure.c_str());
+ }
+ return 0;
+}
+
+string ParamMedicApplication::getName() const {
+ return "param-medic";
+}
+
+string ParamMedicApplication::getDescription() const {
+ return
+ "[[html:<p>]]Examine the spectra in a file to estimate the best precursor "
+ "and fragment error tolerances for database search.[[html:</p>]]";
+}
+
+bool ParamMedicApplication::hidden() const {
+ return false;
+}
+
+vector<string> ParamMedicApplication::getArgs() const {
+ string arr[] = {
+ "spectrum-file+"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> ParamMedicApplication::getOptions() const {
+ string arr[] = {
+ "verbosity",
+ "spectrum-parser",
+ "pm-min-precursor-mz",
+ "pm-max-precursor-mz",
+ "pm-min-frag-mz",
+ "pm-max-frag-mz",
+ "pm-min-scan-frag-peaks",
+ "pm-max-precursor-delta-ppm",
+ "pm-charge",
+ "pm-top-n-frag-peaks",
+ "pm-pair-top-n-frag-peaks",
+ "pm-min-common-frag-peaks",
+ "pm-max-scan-separation",
+ "pm-min-peak-pairs"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > ParamMedicApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "the estimated parameter values for precursor mass tolerance (in ppm) and "
+ "fragment bin size (in Th), as well as the standard deviations of the "
+ "estimated error distributions for precursor and fragment masses."));
+ return outputs;
+}
+
+bool ParamMedicApplication::needsOutputDirectory() const {
+ return false;
+}
+
+void ParamMedicApplication::processParams() {
+ if (!Params::GetBool("use-z-line")) {
+ carp(CARP_DEBUG, "Forcing use-z-line=T");
+ Params::Set("use-z-line", true);
+ }
+ if (!Params::GetBool("pm-ignore-no-charge")) {
+ carp(CARP_DEBUG, "Forcing pm-ignore-no-charge=T");
+ Params::Set("pm-ignore-no-charge", true);
+ }
+}
+
+ParamMedicErrorCalculator::ParamMedicErrorCalculator():
+ numTotalSpectra_(0), numPassingSpectra_(0) {
+ if (!numeric_limits<double>::is_iec559) {
+ carp(CARP_FATAL, "Something went wrong.");
+ }
+ lowestPrecursorBinStartMz_ = Params::GetDouble("pm-min-precursor-mz") -
+ fmod(Params::GetDouble("pm-min-precursor-mz"), AVERAGINE_PEAK_SEPARATION / Params::GetInt("pm-charge"));
+ lowestFragmentBinStartMz_ = Params::GetDouble("pm-min-frag-mz") -
+ fmod(Params::GetDouble("pm-min-frag-mz"), AVERAGINE_PEAK_SEPARATION);
+ numPrecursorBins_ = getBinIndexPrecursor(Params::GetDouble("pm-max-precursor-mz")) + 1;
+ numFragmentBins_ = getBinIndexFragment(Params::GetDouble("pm-max-frag-mz")) + 1;
+}
+
+ParamMedicErrorCalculator::~ParamMedicErrorCalculator() {
+ for (vector< pair<const Peak*, const Peak*> >::const_iterator i = pairedFragmentPeaks_.begin();
+ i != pairedFragmentPeaks_.begin();
+ i++) {
+ delete i->first;
+ delete i->second;
+ }
+}
+
+void ParamMedicErrorCalculator::processFiles(const vector<string>& files) {
+ for (vector<string>::const_iterator i = files.begin(); i != files.end(); i++) {
+ carp(CARP_INFO, "param-medic processing input file %s...", i->c_str());
+ SpectrumCollection* collection = SpectrumCollectionFactory::create(*i);
+ collection->parse();
+ for (SpectrumIterator j = collection->begin(); j != collection->end(); j++) {
+ processSpectrum(*j);
+ }
+ delete collection;
+ clearBins();
+ }
+}
+
+void ParamMedicErrorCalculator::processSpectrum(Spectrum* spectrum) {
+ ++numTotalSpectra_;
+
+ if (spectrum->getNumPeaks() < Params::GetInt("pm-min-scan-frag-peaks")) {
+ return;
+ }
+
+ double precursorMz = getPrecursorMz(spectrum);
+ if (!(Params::GetDouble("pm-min-precursor-mz") <= precursorMz && precursorMz <= Params::GetDouble("pm-max-precursor-mz"))) {
+ return;
+ }
+
+ ++numPassingSpectra_;
+ // pull out the top fragments by intensity
+ spectrum->sortPeaks(_PEAK_INTENSITY);
+ spectrum->truncatePeaks(Params::GetInt("pm-top-n-frag-peaks"));
+
+ int precursorBinIndex = getBinIndexPrecursor(precursorMz);
+ map<int, Spectrum*>::const_iterator prevIter = spectra_.find(precursorBinIndex);
+ if (prevIter != spectra_.end()) {
+ // there was a previous spectrum in this bin; check to see if they're a pair
+ const Spectrum* prev = prevIter->second;
+ const double precursorMzPrev = getPrecursorMz(prev);
+ const double precursorMzDiffPpm = (precursorMz - precursorMzPrev) * MILLION / precursorMz;
+ // check precursor and scan count between the scans
+ if (abs(precursorMzDiffPpm) <= Params::GetDouble("pm-max-precursor-delta-ppm") &&
+ abs(spectrum->getFirstScan() - prev->getFirstScan()) <= Params::GetInt("pm-max-scan-separation")) {
+ // count the fragment peaks in common
+ vector< pair<const Peak*, const Peak*> > pairedFragments = pairFragments(prev, spectrum);
+ if (pairedFragments.size() >= Params::GetInt("pm-min-common-frag-peaks")) {
+ // we've got a pair! record everything
+ sort(pairedFragments.begin(), pairedFragments.end(), sortPairedFragments);
+ vector< pair<const Peak*, const Peak*> >::const_iterator stop =
+ pairedFragments.size() >= Params::GetInt("pm-pair-top-n-frag-peaks")
+ ? pairedFragments.begin() + Params::GetInt("pm-pair-top-n-frag-peaks")
+ : pairedFragments.end();
+ for (vector< pair<const Peak*, const Peak*> >::const_iterator i = pairedFragments.begin();
+ i != stop;
+ i++) {
+ pairedFragmentPeaks_.push_back(make_pair(
+ new Peak(i->first->getIntensity(), i->first->getLocation()),
+ new Peak(i->second->getIntensity(), i->second->getLocation())));
+ }
+ pairedPrecursorMzs_.push_back(make_pair(precursorMzPrev, precursorMz));
+ }
+ }
+ }
+ // make the new spectrum its bin's representative
+ spectra_[precursorBinIndex] = spectrum;
+}
+
+void ParamMedicErrorCalculator::clearBins() {
+ spectra_.clear();
+}
+
+void ParamMedicErrorCalculator::calcMassErrorDist(
+ string* precursorFailure,
+ string* fragmentFailure,
+ double* precursorSigmaPpm,
+ double* fragmentSigmaPpm,
+ double* precursorPredictionPpm,
+ double* fragmentPredictionTh
+) {
+ precursorFailure->clear();
+ fragmentFailure->clear();
+ carp(CARP_INFO, "Processed %d total spectra", numTotalSpectra_);
+ carp(CARP_INFO, "Processed %d qualifying spectra", numPassingSpectra_);
+ carp(CARP_INFO, "Precursor pairs: %d", pairedPrecursorMzs_.size());
+ carp(CARP_INFO, "Fragment pairs: %d", pairedFragmentPeaks_.size());
+
+ if (pairedPrecursorMzs_.size() > MAX_PEAKPAIRS) {
+ carp(CARP_DEBUG, "Using %d of %d peak pairs for precursor...",
+ MAX_PEAKPAIRS, pairedPrecursorMzs_.size());
+ random_shuffle(pairedPrecursorMzs_.begin(), pairedPrecursorMzs_.end(), myrandom_limit);
+ pairedPrecursorMzs_.resize(MAX_PEAKPAIRS);
+ }
+
+ vector<double> precursorDistancesPpm;
+ int numZeroPrecursorDeltas = 0;
+ for (vector< pair<double, double> >::const_iterator i = pairedPrecursorMzs_.begin();
+ i != pairedPrecursorMzs_.end();
+ i++) {
+ double diffTh = i->first - i->second;
+ if (diffTh == 0) {
+ ++numZeroPrecursorDeltas;
+ }
+ precursorDistancesPpm.push_back(diffTh * MILLION / i->first);
+ }
+
+ // check for conditions that would cause us to bomb out
+ if (precursorDistancesPpm.size() < Params::GetInt("pm-min-peak-pairs")) {
+ *precursorFailure =
+ "Need >= " + Params::GetString("pm-min-peak-pairs") + " peak pairs to fit mixed distribution. "
+ "Got only " + StringUtils::ToString(precursorDistancesPpm.size());
+ }
+ if (precursorFailure->empty()) {
+ double proportionPrecursorMzsZero = (double)numZeroPrecursorDeltas / pairedPrecursorMzs_.size();
+ carp(CARP_DEBUG, "proportion zero: %f", proportionPrecursorMzsZero);
+ if (proportionPrecursorMzsZero > MAX_PROPORTION_PRECURSOR_DELTAS_ZERO) {
+ *precursorFailure =
+ "Too high a proportion of precursor mass differences (" +
+ StringUtils::ToString(proportionPrecursorMzsZero) + ") are exactly 0. "
+ "Some processing has been done on this run that param-medic can't handle. "
+ "You should investigate what that processing might be.";
+ }
+ }
+
+ double precursorMuPpm2Measures = numeric_limits<double>::quiet_NaN();
+ double precursorSigmaPpm2Measures = numeric_limits<double>::quiet_NaN();
+ if (precursorFailure->empty()) {
+ estimateMuSigma(precursorDistancesPpm, MIN_SIGMA_PPM,
+ &precursorMuPpm2Measures, &precursorSigmaPpm2Measures);
+ }
+
+ if (pairedFragmentPeaks_.size() < Params::GetInt("pm-min-peak-pairs")) {
+ *fragmentFailure =
+ "Need >= " + Params::GetString("pm-min-peak-pairs") + " peak pairs to fit mixed distribution. "
+ "Got only " + StringUtils::ToString(pairedFragmentPeaks_.size());
+ }
+
+ double fragmentMuPpm2Measures = numeric_limits<double>::quiet_NaN();
+ double fragmentSigmaPpm2Measures = numeric_limits<double>::quiet_NaN();
+ if (fragmentFailure->empty()) {
+ if (pairedFragmentPeaks_.size() > MAX_PEAKPAIRS) {
+ carp(CARP_DEBUG, "Using %d of %d peak pairs for fragment...",
+ MAX_PEAKPAIRS, pairedFragmentPeaks_.size());
+ random_shuffle(pairedFragmentPeaks_.begin(), pairedFragmentPeaks_.end(), myrandom_limit);
+ pairedFragmentPeaks_.resize(MAX_PEAKPAIRS);
+ }
+ vector<double> fragmentDistancesTh;
+ vector<double> fragmentDistancesPpm;
+ for (vector< pair<const Peak*, const Peak*> >::const_iterator i = pairedFragmentPeaks_.begin();
+ i != pairedFragmentPeaks_.end();
+ i++) {
+ double diffTh = i->first->getLocation() - i->second->getLocation();
+ fragmentDistancesTh.push_back(diffTh);
+ fragmentDistancesPpm.push_back(diffTh * MILLION / i->first->getLocation());
+ }
+ // estimate the parameters of the component distributions for each of the mixed distributions
+ estimateMuSigma(fragmentDistancesPpm, MIN_SIGMA_PPM,
+ &fragmentMuPpm2Measures, &fragmentSigmaPpm2Measures);
+ }
+
+ if (!precursorFailure->empty()) {
+ carp(CARP_DEBUG, "Failed precursor! %s", precursorFailure->c_str());
+ } else {
+ carp(CARP_DEBUG, "precursor_mu_ppm_2measures: %f", precursorMuPpm2Measures);
+ carp(CARP_DEBUG, "precursor_sigma_ppm_2measures: %f", precursorSigmaPpm2Measures);
+ }
+
+ if (!fragmentFailure->empty()) {
+ carp(CARP_DEBUG, "Failed fragment! %s", fragmentFailure->c_str());
+ } else {
+ carp(CARP_DEBUG, "fragment_mu_ppm_2measures: %f", fragmentMuPpm2Measures);
+ carp(CARP_DEBUG, "fragment_sigma_ppm_2measures: %f", fragmentSigmaPpm2Measures);
+ }
+
+ // what we have now measured, in the fit Gaussians, is the distribution of the difference
+ // of two values drawn from the distribution of error values.
+ // Assuming the error values are normally distributed with mean 0 and variance s^2, the
+ // differences are normally distributed with mean 0 and variance 2*s^2:
+ // http://mathworld.wolfram.com/NormalDifferenceDistribution.html
+ // i.e., differences are normally distributed with mean=0 and sd=sqrt(2)*s
+ // hence, if differences have sd=diff_sigma, then errors have sd diff_sigma/sqrt(2)
+ //
+ // incidentally, this transformation doesn't matter one bit, practically, since we're
+ // inferring a multiplier for this value empirically. But it lets us report something
+ // with an easily-interpretable meaning as an intermediate value
+ *precursorSigmaPpm = numeric_limits<double>::quiet_NaN();
+ *precursorPredictionPpm = numeric_limits<double>::quiet_NaN();
+ if (precursorFailure->empty()) {
+ *precursorSigmaPpm = precursorSigmaPpm2Measures / sqrt(2);
+ // generate prediction by multiplying by empirically-derived value
+ *precursorPredictionPpm = PRECURSOR_SIGMA_MULTIPLIER * *precursorSigmaPpm;
+ }
+ *fragmentSigmaPpm = numeric_limits<double>::quiet_NaN();
+ *fragmentPredictionTh = numeric_limits<double>::quiet_NaN();
+ if (fragmentFailure->empty()) {
+ *fragmentSigmaPpm = fragmentSigmaPpm2Measures / sqrt(2);
+ // generate prediction by multiplying by empirically-derived value
+ *fragmentPredictionTh = FRAGMENT_SIGMA_MULTIPLIER * *fragmentSigmaPpm;
+ }
+}
+
+void ParamMedicErrorCalculator::estimateMuSigma(
+ const vector<double>& data,
+ double minSigma,
+ double* muFit,
+ double* sigmaFit
+) {
+ double dataMin = data[0];
+ double dataMax = data[0];
+ double muMixedDist = data[0];
+ for (vector<double>::const_iterator i = data.begin() + 1; i != data.end(); i++) {
+ muMixedDist += *i;
+ if (*i < dataMin) {
+ dataMin = *i;
+ }
+ if (*i > dataMax) {
+ dataMax = *i;
+ }
+ }
+ muMixedDist /= data.size();
+
+ double sigmaMixedDist = 0;
+ for (vector<double>::const_iterator i = data.begin(); i != data.end(); i++) {
+ sigmaMixedDist += pow(*i - muMixedDist, 2);
+ }
+ sigmaMixedDist = sqrt(sigmaMixedDist / data.size());
+
+ carp(CARP_DEBUG, "mixed distribution: min %f, max %f, mean %f, sd %f",
+ dataMin, dataMax, muMixedDist, sigmaMixedDist);
+
+ // model the observed distribution as a mixture of Gaussian and uniform
+ ParamMedicModel model(muMixedDist, sigmaMixedDist, minSigma, dataMin, dataMax);
+ // fit the mixture model with EM
+ double improvement = model.fit(data);
+ carp(CARP_DEBUG, "model improvement: %f", improvement);
+
+ *muFit = model.getMu();
+ *sigmaFit = model.getSigma();
+ carp(CARP_DEBUG, "fit: mean=%f, sigma=%f", *muFit, *sigmaFit);
+}
+
+int ParamMedicErrorCalculator::getBinIndexPrecursor(double mz) const {
+ return (int)((mz - lowestPrecursorBinStartMz_) / (AVERAGINE_PEAK_SEPARATION / Params::GetInt("pm-charge")));
+}
+
+int ParamMedicErrorCalculator::getBinIndexFragment(double mz) const {
+ return (int)((mz - lowestFragmentBinStartMz_) / AVERAGINE_PEAK_SEPARATION);
+}
+
+double ParamMedicErrorCalculator::getPrecursorMz(const Spectrum* spectrum) const {
+ const vector<SpectrumZState>& zStates = spectrum->getZStates();
+ for (vector<SpectrumZState>::const_iterator i = zStates.begin(); i != zStates.end(); i++) {
+ if (i->getCharge() == Params::GetInt("pm-charge")) {
+ return i->getMZ();
+ }
+ }
+ return -1;
+}
+
+vector< pair<const Peak*, const Peak*> > ParamMedicErrorCalculator::pairFragments(
+ const Spectrum* prev,
+ const Spectrum* cur
+) const {
+ map<int, const Peak*> mapPrev = binFragments(prev);
+ map<int, const Peak*> mapCur = binFragments(cur);
+ vector< pair<const Peak*, const Peak*> > pairs;
+ for (map<int, const Peak*>::const_iterator i = mapPrev.begin(); i != mapPrev.end(); i++) {
+ map<int, const Peak*>::const_iterator j = mapCur.find(i->first);
+ if (j != mapCur.end()) {
+ pairs.push_back(make_pair(i->second, j->second));
+ }
+ }
+ return pairs;
+}
+
+map<int, const Peak*> ParamMedicErrorCalculator::binFragments(const Spectrum* spectrum) const {
+ map<int, const Peak*> binFragmentMap;
+ set<int> binsToRemove;
+ for (PeakIterator i = spectrum->begin(); i != spectrum->end(); i++) {
+ FLOAT_T mz = (*i)->getLocation();
+ FLOAT_T intensity = (*i)->getIntensity();
+ if (mz < Params::GetDouble("pm-min-frag-mz")) {
+ continue;
+ }
+ int binIndex = getBinIndexFragment(mz);
+ if (binFragmentMap.find(binIndex) != binFragmentMap.end()) {
+ binsToRemove.insert(binIndex);
+ } else {
+ binFragmentMap[binIndex] = *i;
+ }
+ }
+ for (set<int>::const_iterator i = binsToRemove.begin(); i != binsToRemove.end(); i++) {
+ binFragmentMap.erase(*i);
+ }
+ return binFragmentMap;
+}
+
+bool ParamMedicErrorCalculator::sortPairedFragments(
+ const pair<const Peak*, const Peak*> x,
+ const pair<const Peak*, const Peak*> y
+) {
+ return min(x.first->getIntensity(), x.second->getIntensity()) <
+ min(y.first->getIntensity(), y.second->getIntensity());
+}
+
+ParamMedicModel::ParamMedicModel(double nMean, double nStd, double nMinStd, double uStart, double uEnd):
+ normal_(NormalDistribution(nMean, nStd, nMinStd)), uniform_(UniformDistribution(uStart, uEnd)) {
+ weights_[0] = weights_[1] = log(0.5);
+ summaries_[0] = summaries_[1] = 0;
+}
+
+ParamMedicModel::~ParamMedicModel() {
+}
+
+double ParamMedicModel::fit(const vector<double>& data) {
+ const double stopThreshold = 0.1;
+ const int maxIterations = 1e8;
+
+ double initialLogProbSum = -numeric_limits<double>::infinity();
+ double lastLogProbSum;
+ int i = 0;
+ double improvement = numeric_limits<double>::infinity();
+ while (improvement > 0.1 && i < maxIterations + 1) {
+ fromSummaries();
+ double logProbSum = summarize(data);
+
+ if (i++ == 0) {
+ initialLogProbSum = logProbSum;
+ } else {
+ improvement = logProbSum - lastLogProbSum;
+ carp(CARP_DETAILED_DEBUG, "Improvement: %f", improvement);
+ }
+ lastLogProbSum = logProbSum;
+ }
+ clearSummaries();
+ return lastLogProbSum - initialLogProbSum;
+}
+
+double ParamMedicModel::getMu() const {
+ return normal_.getMu();
+}
+
+double ParamMedicModel::getSigma() const {
+ return normal_.getSigma();
+}
+
+double ParamMedicModel::summarize(const vector<double>& x) {
+ vector<double> r;
+ r.reserve(x.size() * 2);
+ normal_.logProbability(x, &r);
+ uniform_.logProbability(x, &r);
+
+ double logProbSum = 0;
+ for (size_t i = 0; i < x.size(); i++) {
+ double total = -numeric_limits<double>::infinity();
+
+ for (size_t j = 0; j < 2; j++) {
+ r[j * x.size() + i] += weights_[j];
+ total = pairLse(total, r[j * x.size() + i]);
+ }
+
+ for (size_t j = 0; j < 2; j++) {
+ r[j * x.size() + i] = exp(r[j * x.size() + i] - total);
+ summaries_[j] += r[j * x.size() + i];
+ }
+
+ logProbSum += total;
+ }
+
+ normal_.summarize(x, &r[0]);
+ uniform_.summarize(x, &r[x.size()]);
+ return logProbSum;
+}
+
+void ParamMedicModel::fromSummaries() {
+ double sum = summaries_[0] + summaries_[1];
+ if (sum == 0) {
+ return;
+ }
+
+ summaries_[0] /= sum;
+ summaries_[1] /= sum;
+
+ normal_.fromSummaries();
+ weights_[0] = log(summaries_[0]);
+ summaries_[0] = 0;
+
+ uniform_.fromSummaries();
+ weights_[1] = log(summaries_[1]);
+ summaries_[1] = 0;
+}
+
+void ParamMedicModel::clearSummaries() {
+ summaries_[0] = summaries_[1] = 0;
+ normal_.clearSummaries();
+ uniform_.clearSummaries();
+}
+
+double ParamMedicModel::pairLse(double x, double y) {
+ const double inf = numeric_limits<double>::infinity();
+ if (x == inf || y == inf) {
+ return inf;
+ } else if (x == -inf) {
+ return y;
+ } else if (y == -inf) {
+ return x;
+ } else if (x > y) {
+ return x + log(exp(y - x) + 1);
+ }
+ return y + log(exp(x - y) + 1);
+}
+
+ParamMedicModel::NormalDistribution::NormalDistribution(double mean, double std, double minStd):
+ mu_(mean), sigma_(std), minStd_(minStd),
+ logSigmaSqrt2Pi_(-log(std * SQRT_2_PI)), twoSigmaSquared_(2 * pow(std, 2)) {
+ clearSummaries();
+}
+
+ParamMedicModel::NormalDistribution::~NormalDistribution() {
+}
+
+double ParamMedicModel::NormalDistribution::getMu() const {
+ return mu_;
+}
+
+double ParamMedicModel::NormalDistribution::getSigma() const {
+ return sigma_;
+}
+
+void ParamMedicModel::NormalDistribution::logProbability(const vector<double>& x, vector<double>* r) const {
+ for (vector<double>::const_iterator i = x.begin(); i != x.end(); i++) {
+ r->push_back(logSigmaSqrt2Pi_ - pow(*i - mu_, 2) / twoSigmaSquared_);
+ }
+}
+
+void ParamMedicModel::NormalDistribution::summarize(const vector<double>& x, double* weights) {
+ for (size_t i = 0; i < x.size(); i++) {
+ summaries_[0] += weights[i];
+ summaries_[1] += weights[i] * x[i];
+ summaries_[2] += weights[i] * pow(x[i], 2);
+ }
+}
+
+void ParamMedicModel::NormalDistribution::fromSummaries() {
+ if (summaries_[0] == 0) {
+ return;
+ }
+ mu_ = summaries_[1] / summaries_[0];
+ sigma_ = sqrt(summaries_[2] / summaries_[0] - pow(summaries_[1], 2) / pow(summaries_[0], 2));
+ if (sigma_ < minStd_) {
+ sigma_ = minStd_;
+ }
+ clearSummaries();
+ logSigmaSqrt2Pi_ = -log(sigma_ * SQRT_2_PI);
+ twoSigmaSquared_ = 2 * pow(sigma_, 2);
+}
+
+void ParamMedicModel::NormalDistribution::clearSummaries() {
+ summaries_[0] = summaries_[1] = summaries_[2] = 0;
+}
+
+ParamMedicModel::UniformDistribution::UniformDistribution(double start, double end):
+ start_(start), end_(end), logP_(-log(end - start)) {
+ clearSummaries();
+}
+
+ParamMedicModel::UniformDistribution::~UniformDistribution() {
+}
+
+void ParamMedicModel::UniformDistribution::logProbability(const vector<double>& x, vector<double>* r) const {
+ for (vector<double>::const_iterator i = x.begin(); i != x.end(); i++) {
+ r->push_back(start_ <= *i && *i <= end_ ? logP_ : -numeric_limits<double>::infinity());
+ }
+}
+
+void ParamMedicModel::UniformDistribution::summarize(const vector<double>& x, double* weights) {
+ for (size_t i = 0; i < x.size(); i++) {
+ if (weights[i] <= 0) {
+ continue;
+ }
+ double value = x[i];
+ if (value < summaries_[0]) {
+ summaries_[0] = value;
+ }
+ if (value > summaries_[1]) {
+ summaries_[1] = value;
+ }
+ }
+}
+
+void ParamMedicModel::UniformDistribution::fromSummaries() {
+ start_ = summaries_[0];
+ end_ = summaries_[1];
+ logP_ = -log(end_ - start_);
+ clearSummaries();
+}
+
+void ParamMedicModel::UniformDistribution::clearSummaries() {
+ summaries_[0] = numeric_limits<double>::infinity();
+ summaries_[1] = -numeric_limits<double>::infinity();
+}
+
diff --git a/src/app/ParamMedicApplication.h b/src/app/ParamMedicApplication.h
new file mode 100644
index 0000000..c9c2ed9
--- /dev/null
+++ b/src/app/ParamMedicApplication.h
@@ -0,0 +1,165 @@
+#ifndef PARAMMEDIC_H
+#define PARAMMEDIC_H
+
+#include "CruxApplication.h"
+#include "Spectrum.h"
+
+class ParamMedicApplication : public CruxApplication {
+ public:
+ ParamMedicApplication();
+ virtual ~ParamMedicApplication();
+ virtual int main(int argc, char** argv);
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual bool hidden() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+ virtual bool needsOutputDirectory() const;
+ virtual void processParams();
+};
+
+class ParamMedicErrorCalculator {
+ public:
+ ParamMedicErrorCalculator();
+ virtual ~ParamMedicErrorCalculator();
+
+ void processFiles(const std::vector<std::string>& files);
+ void processSpectrum(Crux::Spectrum* spectrum);
+ void clearBins();
+
+ // this is to be run after all spectra have been processed;
+ // fits the mixed model to the mixed distributions of m/z differences
+ void calcMassErrorDist(
+ std::string* precursorFailure,
+ std::string* fragmentFailure,
+ double* precursorSigmaPpm,
+ double* fragmentSigmaPpm,
+ double* precursorPredictionPpm,
+ double* fragmentPredictionTh
+ );
+
+ // estimate mu and sigma of the mixed distribution, as initial estimate for Gaussian
+ static void estimateMuSigma(
+ const std::vector<double>& data,
+ double minSigma,
+ double* muFit,
+ double* sigmaFit
+ );
+ protected:
+ int getBinIndexPrecursor(double mz) const;
+ int getBinIndexFragment(double mz) const;
+ double getPrecursorMz(const Crux::Spectrum* spectrum) const;
+
+ // given two spectra, pair up their fragments that are in the same bin
+ std::vector< std::pair<const Peak*, const Peak*> > pairFragments(
+ const Crux::Spectrum* prev,
+ const Crux::Spectrum* cur
+ ) const;
+
+ // keep only one fragment per bin; if another fragment wants to be in the bin,
+ // toss them both out - this reduces ambiguity
+ std::map<int, const Peak*> binFragments(const Crux::Spectrum* spectrum) const;
+
+ static bool sortPairedFragments(
+ const std::pair<const Peak*, const Peak*> x,
+ const std::pair<const Peak*, const Peak*> y
+ );
+
+ // count the spectra that go by
+ int numTotalSpectra_;
+ int numPassingSpectra_;
+ // number and position of bins
+ double lowestPrecursorBinStartMz_;
+ double lowestFragmentBinStartMz_;
+ int numPrecursorBins_;
+ int numFragmentBins_;
+ // map from bin index to current spectrum
+ std::map<int, Crux::Spectrum*> spectra_;
+ // the paired peak values that we'll use to estimate mass error
+ std::vector< std::pair<const Peak*, const Peak*> > pairedFragmentPeaks_;
+ std::vector< std::pair<double, double> > pairedPrecursorMzs_;
+};
+
+class ParamMedicModel {
+ public:
+ ParamMedicModel(double nMean, double nStd, double nMinStd, double uStart, double uEnd);
+ virtual ~ParamMedicModel();
+
+ // fit the model to new data using EM.
+ // this method fits the components of the model to new data using the EM method.
+ // it will iterate until either max iterations has been reached, or the stop
+ // threshold has been passed.
+ double fit(const std::vector<double>& data);
+
+ double getMu() const;
+ double getSigma() const;
+
+ // summarize a batch of data and store sufficient statistics.
+ // this will run the expectation step of EM and store sufficient statistics in
+ // the appropriate distribution objects.
+ // the summarization can be thought of as a chunk of the E step, and the
+ // fromSummaries method as the M step.
+ double summarize(const std::vector<double>& x);
+
+ // fit the model to the collected sufficient statistics.
+ // fit the parameters of the model to the sufficient statistics gathered during
+ // the summarize calls.
+ // this should return an exact update.
+ void fromSummaries();
+
+ // clear the summary statistics stored in the object
+ void clearSummaries();
+
+ // perform log-sum-exp on a pair of numbers in a log space.
+ // this is calculated as z = log( e^x + e^y ).
+ // however, this causes underflow sometimes when x or y are too negative.
+ // a simplification of this is thus z = x + log( e^(y-x) + 1 ), where x is the
+ // greater number.
+ // if either of the inputs are infinity, return infinity, and if either of the
+ // inputs are negative infinity, then simply return the other input.
+ static double pairLse(double x, double y);
+ protected:
+ class NormalDistribution {
+ public:
+ NormalDistribution(double mean, double std, double minStd);
+ virtual ~NormalDistribution();
+ double getMu() const;
+ double getSigma() const;
+ void logProbability(const std::vector<double>& x, std::vector<double>* r) const;
+ void summarize(const std::vector<double>& x, double* r);
+ void fromSummaries();
+ void clearSummaries();
+ protected:
+ double mu_;
+ double sigma_;
+ double minStd_;
+ double logSigmaSqrt2Pi_;
+ double twoSigmaSquared_;
+ double summaries_[3];
+ };
+
+ class UniformDistribution {
+ public:
+ UniformDistribution(double start, double end);
+ virtual ~UniformDistribution();
+ void logProbability(const std::vector<double>& x, std::vector<double>* r) const;
+ void summarize(const std::vector<double>& x, double* r);
+ void summarize();
+ void fromSummaries();
+ void clearSummaries();
+ protected:
+ double start_;
+ double end_;
+ double logP_;
+ double summaries_[2];
+ };
+
+ NormalDistribution normal_;
+ UniformDistribution uniform_;
+ double weights_[2];
+ double summaries_[2];
+};
+
+#endif
+
diff --git a/src/app/PercolatorAdapter.cpp b/src/app/PercolatorAdapter.cpp
new file mode 100644
index 0000000..ed75a17
--- /dev/null
+++ b/src/app/PercolatorAdapter.cpp
@@ -0,0 +1,556 @@
+/**
+ * \file PercolatorAdapter.cpp
+ * $Revision$
+ * \brief Converts Percolator result objects to Crux result objects.
+ */
+
+#include "PercolatorAdapter.h"
+#include "DataSet.h"
+#include "util/AminoAcidUtil.h"
+#include "util/StringUtils.h"
+#include "FeatureNames.h"
+
+#include <map>
+
+using namespace std;
+
+/**
+ * Constructor for PercolatorAdapter.
+ */
+PercolatorAdapter::PercolatorAdapter() : Caller() {
+ collection_ = new ProteinMatchCollection();
+ decoy_collection_ = new ProteinMatchCollection();
+}
+
+/**
+ * Destructor for PercolatorAdapter
+ */
+PercolatorAdapter::~PercolatorAdapter() {
+ // delete match collections created by this adapter
+ int collectionsDeleted = 0;
+ for (vector<MatchCollection*>::iterator iter = match_collections_made_.begin();
+ iter != match_collections_made_.end();
+ ++iter) {
+ delete *iter;
+ ++collectionsDeleted;
+ }
+ // delete proteins created by this adapter
+ int proteinsDeleted = 0;
+ for (vector<PostProcessProtein*>::iterator iter = proteins_made_.begin();
+ iter != proteins_made_.end();
+ ++iter) {
+ delete *iter;
+ ++proteinsDeleted;
+ }
+
+ deleteCollections();
+ carp(CARP_DEBUG, "PercolatorAdapter::~PercolatorAdapter - done. %d "
+ "MatchCollections deleted.", collectionsDeleted);
+}
+
+void PercolatorAdapter::deleteCollections() {
+ delete collection_;
+ delete decoy_collection_;
+ collection_ = NULL;
+ decoy_collection_ = NULL;
+}
+
+/**
+ * Adds PSM scores from Percolator objects into a ProteinMatchCollection
+ */
+void PercolatorAdapter::processPsmScores(Scores& allScores) {
+ if (collection_ == NULL || decoy_collection_ == NULL) {
+ return;
+ }
+
+ // Create new MatchCollection object that will be the converted Percolator Scores
+ MatchCollection* targets = new MatchCollection();
+ MatchCollection* decoys = new MatchCollection();
+ match_collections_made_.push_back(targets);
+ match_collections_made_.push_back(decoys);
+
+ // Find out which feature is lnNumSP and get indices of charge state features
+ bool lnNumDSP = false;
+ int lnNumSPIndex = findFeatureIndex("lnnumsp");
+ if (lnNumSPIndex == -1) {
+ if ((lnNumSPIndex = findFeatureIndex("lnnumdsp")) != -1) {
+ lnNumDSP = true;
+ }
+ }
+
+ map<int, int> chargeStates = mapChargeFeatures();
+
+ Normalizer* normalizer = Normalizer::getNormalizer();
+ double* normSub = normalizer->getSub();
+ double* normDiv = normalizer->getDiv();
+
+ // Iterate over each ScoreHolder in Scores object
+ for (vector<ScoreHolder>::iterator score_itr = allScores.begin();
+ score_itr != allScores.end();
+ score_itr++) {
+ bool is_decoy = score_itr->isDecoy();
+
+ PSMDescription* psm = score_itr->pPSM;
+
+ int psm_file_idx = -1;
+ int psm_charge;
+ parsePSMId(psm->id_, psm_file_idx, psm_charge);
+
+ // Try to look up charge state in map
+ int charge_state = -1;
+ for (map<int, int>::const_iterator i = chargeStates.begin();
+ i != chargeStates.end();
+ ++i) {
+ if (psm->features[i->first] > 0) {
+ charge_state = i->second;
+ break;
+ }
+ }
+
+ if (charge_state == -1) {
+ carp_once(CARP_WARNING, "Could not determine charge state of PSM");
+ }
+
+ Crux::Peptide* peptide = extractPeptide(psm, charge_state, is_decoy);
+ if (peptide == NULL) {
+ deleteCollections();
+ return;
+ }
+
+ SpectrumZState zState;
+ zState.setSinglyChargedMass(psm->expMass, charge_state);
+ // calcMass/expMass = singly charged mass
+ Crux::Spectrum* spectrum = new Crux::Spectrum(
+ psm->scan, psm->scan, zState.getMZ(), vector<int>(1, charge_state), "");
+
+ Crux::Match* match = new Crux::Match(peptide, spectrum, zState, is_decoy);
+ match->setScore(PERCOLATOR_SCORE, score_itr->score);
+ match->setScore(PERCOLATOR_QVALUE, score_itr->q);
+ match->setScore(PERCOLATOR_PEP, score_itr->pep);
+
+ match->setFileIndex(psm_file_idx);
+
+ // Get matches/spectrum
+ if (lnNumSPIndex < 0) {
+ match->setLnExperimentSize(-1);
+ } else {
+ double lnNumSP = unnormalize(psm, lnNumSPIndex, normDiv, normSub);
+ match->setLnExperimentSize(lnNumSP);
+ }
+
+ if (!is_decoy) {
+ targets->addMatch(match);
+ } else {
+ decoys->addMatch(match);
+ }
+ match->setPostProcess(true); // so spectra get deleted when match does
+ Crux::Match::freeMatch(match); // so match gets deleted when collection does
+ }
+
+ if (lnNumSPIndex >= 0 && lnNumDSP) {
+ targets->setHasDistinctMatches(true);
+ decoys->setHasDistinctMatches(true);
+ }
+
+ targets->setScoredType(PERCOLATOR_SCORE, true);
+ targets->setScoredType(PERCOLATOR_QVALUE, true);
+ targets->setScoredType(PERCOLATOR_PEP, true);
+ targets->populateMatchRank(PERCOLATOR_SCORE);
+
+ decoys->setScoredType(PERCOLATOR_SCORE, true);
+ decoys->setScoredType(PERCOLATOR_QVALUE, true);
+ decoys->setScoredType(PERCOLATOR_PEP, true);
+ decoys->populateMatchRank(PERCOLATOR_SCORE);
+
+ // sort by q-value
+ targets->sort(PERCOLATOR_QVALUE);
+ decoys->sort(PERCOLATOR_QVALUE);
+
+ collection_->addMatches(targets);
+ decoy_collection_->addMatches(decoys);
+}
+
+/**
+ * Adds peptide scores from Percolator objects into a ProteinMatchCollection
+ */
+void PercolatorAdapter::processPeptideScores(Scores& allScores) {
+ if (collection_ == NULL || decoy_collection_ == NULL) {
+ return;
+ }
+
+ carp(CARP_DEBUG, "Setting peptide scores");
+
+ // Iterate over each ScoreHolder in Scores object
+ for (vector<ScoreHolder>::iterator score_itr = allScores.begin();
+ score_itr != allScores.end();
+ score_itr++) {
+
+ PSMDescription* psm = score_itr->pPSM;
+ string sequence;
+ MODIFIED_AA_T* mod_seq = getModifiedAASequence(psm, sequence);
+ if (mod_seq == NULL) {
+ deleteCollections();
+ return;
+ }
+
+ // Set scores
+ PeptideMatch* peptide_match = !score_itr->isDecoy()
+ ? collection_->getPeptideMatch(mod_seq)
+ : decoy_collection_->getPeptideMatch(mod_seq);
+ free(mod_seq);
+ if (peptide_match == NULL) {
+ deleteCollections();
+ return;
+ }
+ peptide_match->setScore(PERCOLATOR_SCORE, score_itr->score);
+ peptide_match->setScore(PERCOLATOR_QVALUE, score_itr->q);
+ peptide_match->setScore(PERCOLATOR_PEP, score_itr->pep);
+ }
+}
+
+/**
+ * Adds protein scores from Percolator objects into a ProteinMatchCollection
+ */
+void PercolatorAdapter::processProteinScores(ProteinProbEstimator* protEstimator) {
+ if (collection_ == NULL || decoy_collection_ == NULL) {
+ return;
+ }
+
+ vector<ProteinMatch*> matches;
+ vector<ProteinMatch*> decoy_matches;
+ const vector<ProteinScoreHolder>& protein_scores = protEstimator->getProteins();
+
+ for (vector<ProteinScoreHolder>::const_iterator score_iter = protein_scores.begin();
+ score_iter != protein_scores.end();
+ score_iter++) {
+ // Set scores
+ ProteinMatch* protein_match;
+ if (!score_iter->isDecoy()) {
+ protein_match = collection_->getProteinMatch(score_iter->getName());
+ matches.push_back(protein_match);
+ } else {
+ protein_match = decoy_collection_->getProteinMatch(score_iter->getName());
+ decoy_matches.push_back(protein_match);
+ }
+ protein_match->setScore(PERCOLATOR_SCORE, -log(score_iter->getP()));
+ protein_match->setScore(PERCOLATOR_QVALUE, score_iter->getQ());
+ protein_match->setScore(PERCOLATOR_PEP, score_iter->getPEP());
+ }
+
+ // set percolator score ranks
+ std::sort(matches.begin(), matches.end(),
+ PercolatorAdapter::comparePercolatorScores);
+ std::sort(decoy_matches.begin(), decoy_matches.end(),
+ PercolatorAdapter::comparePercolatorScores);
+ int cur_rank = 0;
+ for (vector<ProteinMatch*>::iterator iter = matches.begin();
+ iter != matches.end();
+ ++iter) {
+ (*iter)->setRank(PERCOLATOR_SCORE, ++cur_rank);
+ }
+ cur_rank = 0;
+ for (vector<ProteinMatch*>::iterator iter = decoy_matches.begin();
+ iter != decoy_matches.end();
+ ++iter) {
+ (*iter)->setRank(PERCOLATOR_SCORE, ++cur_rank);
+ }
+}
+
+/*
+ *\returns the ProteinMatchCollection, to be called after Caller::run() is finished
+ */
+ProteinMatchCollection* PercolatorAdapter::getProteinMatchCollection() {
+ return collection_;
+}
+
+/*
+ *\returns the decoy ProteinMatchCollection, to be called after Caller::run() is finished
+ */
+ProteinMatchCollection* PercolatorAdapter::getDecoyProteinMatchCollection() {
+ return decoy_collection_;
+}
+
+bool PercolatorAdapter::parsePSMId(
+ const string& psm_id, ///< psm id to parse information from
+ int& file_idx, ///< file index of psm
+ int& charge ///< charge of psm
+) {
+ // <target|decoy>_<fileindex>_<scan>_<charge>_<rank> OR
+ // <filestem>_<scan>_<charge>_<rank>
+ vector<string> tokens = StringUtils::Split(psm_id, '_');
+ if (tokens.size() < 4) {
+ return false;
+ }
+ try {
+ if (tokens.size() == 5 && (tokens[0] == "target" || tokens[0] == "decoy")) {
+ // Parse as <target|decoy>_<fileindex>_<scan>_<charge>_<rank>
+ file_idx = StringUtils::FromString<int>(tokens[1]);
+ // tokens[2] = scan
+ charge = StringUtils::FromString<int>(tokens[3]);
+ // tokens[4] = rank
+ } else {
+ // Try to parse as <filestem>_<scan>_<charge>_<rank>
+ // tokens.back() = rank
+ tokens.pop_back();
+ charge = StringUtils::FromString<int>(tokens.back());
+ tokens.pop_back();
+ // tokens.back() = scan
+ tokens.pop_back();
+ stringstream ss;
+ for (vector<string>::const_iterator i = tokens.begin(); i != tokens.end(); i++) {
+ if (i != tokens.begin()) {
+ ss << '_' << *i;
+ } else {
+ ss << *i;
+ }
+ }
+ file_idx = Crux::Match::findFileIndex(ss.str(), true);
+ }
+ return true;
+ } catch (...) {
+ return false;
+ }
+}
+
+/**
+ * Compares two AbstractMatches by Percolator score
+ */
+bool PercolatorAdapter::comparePercolatorScores(
+ AbstractMatch* lhs, ///< first match with Percolator scores to compare
+ AbstractMatch* rhs ///< second match with Percolator scores to compare
+) {
+ if (!lhs->hasScore(PERCOLATOR_SCORE) || !rhs->hasScore(PERCOLATOR_SCORE)) {
+ carp(CARP_FATAL, "Could not compare matches by Percolator score.");
+ }
+ return lhs->getScore(PERCOLATOR_SCORE) < rhs->getScore(PERCOLATOR_SCORE);
+}
+
+/**
+* \returns a Crux peptide from the PSM
+*/
+Crux::Peptide* PercolatorAdapter::extractPeptide(
+ PSMDescription* psm, ///< psm
+ int charge_state, ///< charge state
+ bool is_decoy ///< is psm a decoy?
+) {
+ string seq;
+ MODIFIED_AA_T* mod_seq = getModifiedAASequence(psm, seq);
+ if (mod_seq == NULL) {
+ return NULL;
+ }
+
+ string full_peptide(psm->getFullPeptide());
+ carp(CARP_DEBUG, "full peptide:%s", full_peptide.c_str());
+ carp(CARP_DEBUG, "=======================");
+ string n_term = "";
+ string c_term = "";
+ if (!full_peptide.empty()) {
+ n_term += full_peptide[0];
+ c_term += full_peptide[full_peptide.length() - 1];
+ }
+
+ // add proteins
+ Crux::Peptide* peptide = NULL;
+ for (vector<string>::const_iterator i = psm->proteinIds.begin();
+ i != psm->proteinIds.end();
+ ++i) {
+ PostProcessProtein* protein = new PostProcessProtein();
+ proteins_made_.push_back(protein);
+ protein->setId(i->c_str());
+ int start_idx = protein->findStart(seq, n_term, c_term);
+ if (peptide == NULL) {
+ peptide = new Crux::Peptide(seq.length(), protein, start_idx);
+ peptide->setModifiedAASequence(mod_seq, is_decoy);
+ free(mod_seq);
+ } else {
+ peptide->addPeptideSrc(new PeptideSrc(NON_SPECIFIC_DIGEST, protein, start_idx));
+ }
+ }
+
+ return peptide;
+}
+
+/**
+ * \returns the modified and unmodified peptide sequence
+ * for the psm
+ */
+MODIFIED_AA_T* PercolatorAdapter::getModifiedAASequence(
+ PSMDescription* psm, ///< psm -in
+ string& seq ///< sequence -out
+) {
+ string perc_seq = psm->getFullPeptideSequence();
+ if (perc_seq.length() >= 5 &&
+ perc_seq[1] == '.' && perc_seq[perc_seq.length() - 2] == '.') {
+ // Trim off flanking AA if they exist
+ perc_seq = perc_seq.substr(2, perc_seq.length() - 4);
+ }
+
+ if (perc_seq.find("UNIMOD") != string::npos) {
+ // UNIMOD modifications currently not supported
+ return NULL;
+ }
+
+ MODIFIED_AA_T* mod_seq = NULL;
+ carp(CARP_DEBUG, "PercolatorAdapter::getModifiedAASequence(): seq:%s", perc_seq.c_str());
+
+ // Turn off warnings
+ int verbosity = get_verbosity_level();
+ set_verbosity_level(0);
+
+ int mod_len = convert_to_mod_aa_seq(perc_seq.c_str(), &mod_seq, MOD_MASS_ONLY);
+ seq = string(mod_len, '\0');
+ for (int i = 0; i < mod_len; i++) {
+ seq[i] = modified_aa_to_char(mod_seq[i]);
+ }
+
+ // Restore verbosity
+ set_verbosity_level(verbosity);
+
+ return mod_seq;
+}
+
+// Finds the index of the given feature name (case insensitive).
+int PercolatorAdapter::findFeatureIndex(string feature) {
+ feature = StringUtils::ToLower(feature);
+ vector<string> features = StringUtils::Split(DataSet::getFeatureNames().getFeatureNames(), '\t');
+ for (int i = 0; i < features.size(); ++i) {
+ if (StringUtils::ToLower(features[i]) == feature) {
+ return i;
+ }
+ }
+ return -1;
+}
+
+// Generate a map where the keys are feature indices and their values are the
+// charge state of that feature.
+map<int, int> PercolatorAdapter::mapChargeFeatures() {
+ map<int, int> charges;
+ vector<string> features = StringUtils::Split(DataSet::getFeatureNames().getFeatureNames(), '\t');
+ for (int i = 0; i < features.size(); ++i) {
+ if (StringUtils::StartsWith(StringUtils::ToLower(features[i]), "charge")) {
+ size_t charge = StringUtils::FromString<size_t>(features[i].substr(6));
+ charges[i] = charge;
+ }
+ }
+ return charges;
+}
+
+// Unnormalize a PSM feature to obtain its original value.
+// normDiv and normSub are optional; if they are NULL, they will be
+// automatically retrieved.
+double PercolatorAdapter::unnormalize(
+ const PSMDescription* psm,
+ int featureIndex,
+ double* normDiv,
+ double* normSub
+) {
+ if (normDiv == NULL || normSub == NULL) {
+ Normalizer* normalizer = Normalizer::getNormalizer();
+ normDiv = normalizer->getDiv();
+ normSub = normalizer->getSub();
+ }
+ return psm->features[featureIndex] * normDiv[featureIndex] + normSub[featureIndex];
+}
+
+void PercolatorAdapter::printScores(Scores* scores, int label, ostream& os) {
+ std::vector<ScoreHolder>::iterator scoreIt = scores->begin();
+
+ bool lnNumDSP = false;
+ int lnNumSPIdx = PercolatorAdapter::findFeatureIndex("lnnumsp");
+ if (lnNumSPIdx == -1) {
+ if ((lnNumSPIdx = PercolatorAdapter::findFeatureIndex("lnnumdsp")) != -1) {
+ lnNumDSP = true;
+ }
+ }
+
+ os //<< "file\t"
+ << "file_idx\t"
+ << "scan\t"
+ << "charge\t"
+ << "spectrum precursor m/z\t"
+ << "spectrum neutral mass\t"
+ << "peptide mass\t"
+ << "percolator score\t"
+ << "percolator q-value\t"
+ << "percolator PEP\t"
+ << (lnNumDSP ? "distinct matches/spectrum" : "total matches/spectrum") << '\t'
+ << "sequence\t"
+ //<< "modifications\t"
+ << "protein id\t"
+ << "flanking aa\n";
+
+ Normalizer* normalizer = Normalizer::getNormalizer();
+ double* nSub = normalizer->getSub();
+ double* nDiv = normalizer->getDiv();
+
+ for ( ; scoreIt != scores->end(); ++scoreIt) {
+ if (scoreIt->label != label) {
+ continue;
+ }
+ std::string fileIdxStr, chargeStr;
+ int charge = 0;
+ const std::string& psmId = scoreIt->pPSM->getId();
+ std::vector<std::string> idPieces = StringUtils::Split(psmId, '_');
+ if (idPieces.size() == 5) {
+ fileIdxStr = idPieces[1];
+ chargeStr = idPieces[3];
+ StringUtils::TryFromString(chargeStr, &charge);
+ }
+
+ std::string flankingStr = "XX";
+ std::string seq = scoreIt->pPSM->peptide;
+ if (seq.length() >= 5 && seq[1] == '.' && seq[seq.length() - 2] == '.') {
+ flankingStr[0] = seq[0];
+ flankingStr[1] = seq[seq.length() - 1];
+ seq = seq.substr(2, seq.length() - 4);
+ }
+
+ double neutralMass = scoreIt->pPSM->expMass - MASS_PROTON;
+ double peptideMass = MASS_H2O_MONO; // Reported as 0 if a problem occurs
+ for (size_t i = 0; i < seq.length(); i++) {
+ if (seq[i] == '[') {
+ double modMass = 0.0;
+ size_t j = seq.find(']', ++i);
+ if (j == string::npos || !StringUtils::TryFromString(seq.substr(i, j - i), &modMass)) {
+ peptideMass = 0;
+ break;
+ }
+ peptideMass += modMass;
+ i = j;
+ } else {
+ try {
+ peptideMass += AminoAcidUtil::GetMass(seq[i], true);
+ } catch (...) {
+ peptideMass = 0;
+ break;
+ }
+ }
+ }
+
+ int precision = Params::GetInt("precision");
+ int massPrecision = Params::GetInt("mass-precision");
+ os //<< "" << '\t' // file
+ << fileIdxStr << '\t'
+ << scoreIt->pPSM->scan << '\t'
+ << chargeStr << '\t'
+ << StringUtils::ToString((charge > 0 ? neutralMass/charge + MASS_PROTON : 0), massPrecision) << '\t'
+ << StringUtils::ToString(neutralMass, massPrecision) << '\t'
+ << StringUtils::ToString(peptideMass, massPrecision) << '\t'
+ << StringUtils::ToString(scoreIt->score, precision) << '\t'
+ << StringUtils::ToString(scoreIt->q, precision, false) << '\t'
+ << StringUtils::ToString(scoreIt->pep, precision, false) << '\t'
+ << (lnNumSPIdx >= 0 ? exp(PercolatorAdapter::unnormalize(scoreIt->pPSM, lnNumSPIdx, nDiv, nSub)) : 0) << '\t'
+ << seq << '\t'
+ //<< "" << '\t' // mods
+ << StringUtils::Join(scoreIt->pPSM->proteinIds, ',') << '\t'
+ << flankingStr << std::endl;
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/PercolatorAdapter.h b/src/app/PercolatorAdapter.h
new file mode 100644
index 0000000..16a23f5
--- /dev/null
+++ b/src/app/PercolatorAdapter.h
@@ -0,0 +1,140 @@
+/**
+ * \file PercolatorAdapter.h
+ * $Revision$
+ * \brief Converts Percolator result objects to Crux result objects.
+ */
+
+#ifndef PERCOLATORADAPTER_H_
+#define PERCOLATORADAPTER_H_
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <vector>
+
+#include "Caller.h"
+#include "model/MatchCollection.h"
+#include "model/PeptideMatch.h"
+#include "model/PostProcessProtein.h"
+#include "model/ProteinMatchCollection.h"
+#include "model/ProteinMatch.h"
+#include "ProteinProbEstimator.h"
+#include "model/SpectrumMatch.h"
+#include "Scores.h"
+
+/**
+ * \brief: Converts Percolator results objects to Crux results objects.
+ * Class inherits the Caller class from percolator, which runs the percolator
+ * algorithm and prints out the results.
+ * All of the collections can then be accessed via the ProteinMatchCollection object.
+ * During the execution of Caller::run(), percolator discards the psms after
+ * Calculating the peptide level statistics, hence the need to pull the data for the
+ * psms before the removal occurs.
+ */
+class PercolatorAdapter : public Caller {
+
+ public:
+
+ /**
+ * Constructor for PercolatorAdapter.
+ */
+ PercolatorAdapter();
+
+ /**
+ * Destructor for PercolatorAdapter
+ */
+ virtual ~PercolatorAdapter();
+
+ void deleteCollections();
+
+ /**
+ * Adds PSM scores from Percolator objects into a ProteinMatchCollection
+ */
+ void processPsmScores(Scores& allScores);
+
+ /**
+ * Adds peptide scores from Percolator objects into a ProteinMatchCollection
+ */
+ void processPeptideScores(Scores& allScores);
+
+ /**
+ * Adds protein scores from Percolator objects into a ProteinMatchCollection
+ */
+ void processProteinScores(ProteinProbEstimator* protEstimator);
+
+ /*
+ *\returns the ProteinMatchCollection, to be called after Caller::run() is finished
+ */
+ ProteinMatchCollection* getProteinMatchCollection();
+
+ /**
+ *\returns the decoy ProteinMatchCollection, to be called after Caller::run() is finished
+ */
+ ProteinMatchCollection* getDecoyProteinMatchCollection();
+
+ static int findFeatureIndex(std::string feature);
+ static std::map<int, int> mapChargeFeatures(); // map index of feature -> charge
+
+ static double unnormalize(
+ const PSMDescription* psm,
+ int featureIndex,
+ double* normDiv = NULL,
+ double* normSub = NULL
+ );
+
+ static void printScores(Scores* scores, int label, std::ostream& os);
+
+ protected:
+
+ ProteinMatchCollection* collection_; ///< Collection containing all of the psm, peptide, and protein results.
+ ProteinMatchCollection* decoy_collection_; ///< Decoy ProteinMatchCollection
+ std::vector<MatchCollection*> match_collections_made_; ///< MatchCollections created
+ std::vector<PostProcessProtein*> proteins_made_; ///< Proteins created
+
+ /**
+ * Given a Percolator psm_id in the form ".*_([0-9]+)_[^_]*",
+ * parse the file_idx, scan#, charge, and rank
+ * Returns true on success
+ */
+ static bool parsePSMId(
+ const std::string& psm_id, ///<psmid to parse
+ int& file_idx, ///< psm file idx
+ int& charge ///< psm charge
+ );
+
+ /**
+ * Compare two AbstractMatches by Percolator score
+ */
+ static bool comparePercolatorScores(
+ AbstractMatch* lhs, ///< first match with Percolator score to compare
+ AbstractMatch* rhs ///< second match with Percolator score to compare
+ );
+
+ /**
+ * \returns a Crux peptide from the PSM
+ */
+ Crux::Peptide* extractPeptide(
+ PSMDescription* psm, ///< psm
+ int charge_state, ///< charge state
+ bool is_decoy ///< is psm a decoy?
+ );
+
+ /**
+ * \returns the modified and unmodified peptide sequence
+ * for the psm
+ */
+ static MODIFIED_AA_T* getModifiedAASequence(
+ PSMDescription* psm, ///< psm -in
+ std::string& seq ///< sequence -out
+ );
+};
+
+#endif /* PERCOLATORADAPTER_H_ */
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/PercolatorApplication.cpp b/src/app/PercolatorApplication.cpp
new file mode 100644
index 0000000..a3e13ca
--- /dev/null
+++ b/src/app/PercolatorApplication.cpp
@@ -0,0 +1,601 @@
+/**
+ * \file PercolatorApplication.cpp
+ * \brief Runs Percolator
+ *****************************************************************************/
+#include "MakePinApplication.h"
+#include "PercolatorApplication.h"
+#include "PercolatorAdapter.h"
+#include "Caller.h"
+#include "util/Params.h"
+#include <string>
+#include <algorithm>
+#include <sstream>
+#include <iomanip>
+#include <ios>
+#include "util/CarpStreamBuf.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "io/MzIdentMLWriter.h"
+#include "model/ProteinMatchCollection.h"
+#include "io/PMCDelimitedFileWriter.h"
+#include "io/PMCPepXMLWriter.h"
+#include "io/PMCSQTWriter.h"
+
+
+using namespace std;
+
+/**
+ * \returns a blank PercolatorApplication object
+ */
+PercolatorApplication::PercolatorApplication() {
+}
+
+/**
+ * Destructor
+ */
+PercolatorApplication::~PercolatorApplication() {
+}
+
+/**
+ * main method for PercolatorApplication
+ */
+int PercolatorApplication::main(int argc, char** argv) {
+ string input_pin = Params::GetString("peptide-spectrum matches");
+ carp(CARP_INFO, "Reading file %s", input_pin.c_str());
+
+ // Check if we need to run make-pin first
+ if (!Params::GetBool("feature-file-in") &&
+ (Params::GetBool("list-of-files") ||
+ StringUtils::IEndsWith(input_pin, ".txt") ||
+ StringUtils::IEndsWith(input_pin, ".sqt") ||
+ StringUtils::IEndsWith(input_pin, ".pep.xml") ||
+ StringUtils::IEndsWith(input_pin, ".mzid"))) {
+ vector<string> result_files;
+ get_search_result_paths(input_pin, result_files);
+
+ input_pin = make_file_path("make-pin.pin");
+
+ vector<string>::const_iterator fileIter = result_files.begin();
+ if (StringUtils::IEndsWith(*fileIter, ".pin")) {
+ if (FileUtils::Exists(input_pin)) {
+ if (Params::GetBool("overwrite")) {
+ FileUtils::Remove(input_pin);
+ } else {
+ carp(CARP_FATAL, "The file '%s' already exists and cannot be overwritten. "
+ "Use --overwrite T to replace or choose a different output file name",
+ input_pin.c_str());
+ }
+ }
+ FileUtils::Copy(*fileIter, input_pin);
+ string headers;
+ fstream out(input_pin.c_str());
+ if (!out.good()) {
+ carp(CARP_FATAL, "Filestream error '%s'", input_pin.c_str());
+ }
+ getline(out, headers);
+ out.seekp(0, ios_base::end);
+ for (fileIter++; fileIter != result_files.end(); fileIter++) {
+ if (!StringUtils::IEndsWith(*fileIter, ".pin")) {
+ FileUtils::Remove(input_pin);
+ carp(CARP_FATAL, "Cannot mix .pin with non-pin files");
+ }
+ ifstream in(fileIter->c_str());
+ if (!in.good()) {
+ FileUtils::Remove(input_pin);
+ carp(CARP_FATAL, "Error opening file '%s' for reading", fileIter->c_str());
+ }
+ string inLine;
+ getline(in, inLine);
+ if (headers != inLine) {
+ FileUtils::Remove(input_pin);
+ carp(CARP_FATAL, "Headers in pin file '%s' were '%s', but expected '%s'",
+ fileIter->c_str(), inLine.c_str(), headers.c_str());
+ }
+ while (!in.eof()) {
+ getline(in, inLine);
+ out << inLine;
+ if (in.peek() != EOF) {
+ out << endl;
+ }
+ }
+ }
+ } else {
+ carp(CARP_INFO, "Converting input to pin format.");
+ if (MakePinApplication::main(result_files) != 0 || !FileUtils::Exists(input_pin)) {
+ carp(CARP_FATAL, "make-pin failed. Not running Percolator.");
+ }
+ carp(CARP_INFO, "File conversion complete.");
+ }
+ }
+ return main(input_pin);
+}
+
+/**
+ * \brief runs percolator on the input pin
+ * \returns whether percolator was successful or not
+ */
+int PercolatorApplication::main(
+ const string& input_pin ///< file path of pin to process.
+ ) {
+ /* build argument list */
+ vector<string> perc_args_vec;
+ perc_args_vec.push_back("percolator");
+
+ string output_target_peptides = make_file_path(getFileStem() + ".target.peptides.txt");
+ string output_target_psms = make_file_path(getFileStem() + ".target.psms.txt");
+ string output_target_proteins = make_file_path(getFileStem() + ".target.proteins.txt");
+ string output_decoy_peptides = make_file_path(getFileStem() + ".decoy.peptides.txt");
+ string output_decoy_psms = make_file_path(getFileStem() + ".decoy.psms.txt");
+ string output_decoy_proteins = make_file_path(getFileStem() + ".decoy.proteins.txt");
+
+ if (Params::GetBool("only-psms")) {
+ perc_args_vec.push_back("--only-psms");
+ }
+
+ // Target peptides file is written to prevent writing to stdout
+ perc_args_vec.push_back("--results-peptides");
+ perc_args_vec.push_back(output_target_peptides);
+ if (Params::GetBool("txt-output")) {
+ perc_args_vec.push_back("--decoy-results-peptides");
+ perc_args_vec.push_back(output_decoy_peptides);
+ perc_args_vec.push_back("--results-psms");
+ perc_args_vec.push_back(output_target_psms);
+ perc_args_vec.push_back("--decoy-results-psms");
+ perc_args_vec.push_back(output_decoy_psms);
+ }
+
+ //add verbosity
+ perc_args_vec.push_back("--verbose");
+ int verbosity = get_verbosity_level();
+ if (verbosity <= CARP_FATAL) {
+ perc_args_vec.push_back("0");
+ } else if (verbosity <= CARP_ERROR) {
+ perc_args_vec.push_back("1");
+ } else if (verbosity <= CARP_WARNING) {
+ perc_args_vec.push_back("1");
+ } else if (verbosity <= CARP_INFO) {
+ perc_args_vec.push_back("2");
+ } else if (verbosity <= CARP_DETAILED_INFO) {
+ perc_args_vec.push_back("3");
+ } else if (verbosity <= CARP_DEBUG) {
+ perc_args_vec.push_back("4");
+ } else if (verbosity <= CARP_DETAILED_DEBUG) {
+ perc_args_vec.push_back("5");
+ } else if (verbosity <= CARP_MAX) {
+ perc_args_vec.push_back("5");
+ }
+
+ perc_args_vec.push_back("--protein-decoy-pattern");
+ string decoy_pre = Params::GetString("decoy-prefix");
+ perc_args_vec.push_back(!decoy_pre.empty() ? decoy_pre : "random_");
+
+ string seed_parameter = Params::GetString("percolator-seed");
+ unsigned int seed_value;
+ if (seed_parameter == "time") {
+ time_t seconds; // use current time to seed
+ time(&seconds); // Get value from sys clock and set seconds variable.
+ // percolator accepts seed values 1-20000
+ seed_value = (unsigned int)seconds % 20000 + 1;
+ } else if ((seed_value = StringUtils::FromString<unsigned>(seed_parameter)) == 0) {
+ // seed 0 causes segfault in percolator
+ ++seed_value;
+ }
+ perc_args_vec.push_back("--seed");
+ perc_args_vec.push_back(StringUtils::ToString(seed_value));
+
+ if (Params::GetBool("pout-output")) {
+ perc_args_vec.push_back("--xmloutput");
+ perc_args_vec.push_back(make_file_path(getFileStem() + ".pout.xml"));
+ if (Params::GetBool("decoy-xml-output")) {
+ perc_args_vec.push_back("--decoy-xml-output");
+ }
+ }
+
+ perc_args_vec.push_back("--subset-max-train");
+ perc_args_vec.push_back(Params::GetString("subset-max-train"));
+
+ if (!Params::IsDefault("c-pos")) {
+ perc_args_vec.push_back("--Cpos");
+ perc_args_vec.push_back(Params::GetString("c-pos"));
+ }
+
+ if (!Params::IsDefault("c-neg")) {
+ perc_args_vec.push_back("--Cneg");
+ perc_args_vec.push_back(Params::GetString("c-neg"));
+ }
+
+ perc_args_vec.push_back("--trainFDR");
+ perc_args_vec.push_back(Params::GetString("train-fdr"));
+
+ perc_args_vec.push_back("--testFDR");
+ perc_args_vec.push_back(Params::GetString("test-fdr"));
+
+ perc_args_vec.push_back("--maxiter");
+ perc_args_vec.push_back(Params::GetString("maxiter"));
+
+ if (!Params::GetString("search-input").empty()) {
+ perc_args_vec.push_back("--search-input");
+ perc_args_vec.push_back(Params::GetString("search-input"));
+ }
+
+ if (Params::GetBool("quick-validation")) {
+ perc_args_vec.push_back("--quick-validation");
+ }
+
+
+ if (Params::GetBool("feature-file-out")) {
+ perc_args_vec.push_back("--tab-out");
+ perc_args_vec.push_back(make_file_path(getFileStem() + ".feature.txt"));
+ }
+
+ if (Params::GetBool("output-weights")) {
+ perc_args_vec.push_back("--weights");
+ perc_args_vec.push_back(make_file_path(getFileStem() + ".weights.txt"));
+ }
+
+ if (!Params::GetString("init-weights").empty()) {
+ perc_args_vec.push_back("--init-weights");
+ perc_args_vec.push_back(Params::GetString("init-weights"));
+ }
+
+ if (!Params::GetString("default-direction").empty()) {
+ perc_args_vec.push_back("--default-direction");
+ perc_args_vec.push_back(Params::GetString("default-direction"));
+ }
+
+ if (Params::GetBool("unitnorm")) {
+ perc_args_vec.push_back("--unitnorm");
+ }
+
+ if (Params::GetBool("test-each-iteration")) {
+ perc_args_vec.push_back("--test-each-iteration");
+ }
+
+ if (Params::GetBool("override")) {
+ perc_args_vec.push_back("--override");
+ }
+
+ if (Params::GetBool("klammer")) {
+ perc_args_vec.push_back("--klammer");
+ }
+
+ /* --doc option disabled, need retention times in pin file
+ int doc_parameter = Params::GetInt("doc");
+ if(doc_parameter >= 0) {
+ perc_args_vec.push_back("--doc");
+ perc_args_vec.push_back(to_string(doc_parameter));
+ }
+ */
+
+ // FIXME include schema as part of distribution and add option to turn on validation
+ perc_args_vec.push_back("--no-schema-validation");
+
+ if (!Params::GetString("picked-protein").empty()) {
+ perc_args_vec.push_back("--picked-protein");
+ perc_args_vec.push_back(Params::GetString("picked-protein"));
+ }
+ if (!Params::GetString("protein-enzyme").empty()) {
+ perc_args_vec.push_back("--protein-enzyme");
+ perc_args_vec.push_back(Params::GetString("protein-enzyme"));
+ }
+ if (Params::GetBool("protein-report-fragments")) {
+ perc_args_vec.push_back("--protein-report-fragments");
+ }
+ if (Params::GetBool("protein-report-duplicates")) {
+ perc_args_vec.push_back("--protein-report-duplicates");
+ }
+
+ bool set_protein = Params::GetBool("protein");
+ if (set_protein) {
+ perc_args_vec.push_back("--fido-protein");
+
+ if (Params::GetDouble("fido-alpha") > 0) {
+ perc_args_vec.push_back("--fido-alpha");
+ perc_args_vec.push_back(Params::GetString("fido-alpha"));
+ }
+ if (Params::GetDouble("fido-beta") > 0) {
+ perc_args_vec.push_back("--fido-beta");
+ perc_args_vec.push_back(Params::GetString("fido-beta"));
+ }
+ if (Params::GetDouble("fido-gamma") > 0) {
+ perc_args_vec.push_back("--fido-gamma");
+ perc_args_vec.push_back(Params::GetString("fido-gamma"));
+ }
+
+ if (Params::GetBool("fido-empirical-protein-q")) {
+ perc_args_vec.push_back("--fido-empirical-protein-q");
+ }
+
+ perc_args_vec.push_back("--fido-gridsearch-depth");
+ perc_args_vec.push_back(Params::GetString("fido-gridsearch-depth"));
+
+
+ perc_args_vec.push_back("--fido-fast-gridsearch");
+ perc_args_vec.push_back(Params::GetString("fido-fast-gridsearch"));
+
+ perc_args_vec.push_back("--fido-protein-truncation-threshold");
+ perc_args_vec.push_back(Params::GetString("fido-protein-truncation-threshold"));
+
+ if (Params::GetBool("fido-no-split-large-components")) {
+ perc_args_vec.push_back("--fido-no-split-large-components");
+ }
+
+ perc_args_vec.push_back("--fido-gridsearch-mse-threshold");
+ perc_args_vec.push_back(Params::GetString("fido-gridsearch-mse-threshold"));
+
+ // Target proteins file is written to prevent writing to stdout
+ perc_args_vec.push_back("--results-proteins");
+ perc_args_vec.push_back(output_target_proteins);
+ if (Params::GetBool("txt-output")) {
+ perc_args_vec.push_back("--decoy-results-proteins");
+ perc_args_vec.push_back(output_decoy_proteins);
+ }
+ }
+
+ if (Params::GetBool("tdc")) {
+ perc_args_vec.push_back("--post-processing-tdc");
+ } else {
+ perc_args_vec.push_back("--post-processing-mix-max");
+ }
+
+ perc_args_vec.push_back(input_pin);
+
+ /* build argv line */
+
+ string perc_cmd;
+ vector<const char*> perc_argv;
+ for (vector<string>::const_iterator i = perc_args_vec.begin();
+ i != perc_args_vec.end();
+ i++) {
+ perc_argv.push_back(i->c_str());
+ perc_cmd += " " + *i;
+ }
+
+ carp(CARP_DEBUG, "cmd:%s", perc_cmd.c_str());
+
+ /* Re-route stdeer to log file. */
+ CarpStreamBuf buffer;
+ streambuf* old = std::cerr.rdbuf();
+ std::cerr.rdbuf(&buffer);
+
+ /* Call percolatorMain */
+ PercolatorAdapter pCaller;
+ try {
+ int retVal;
+ if (pCaller.parseOptions(perc_args_vec.size(), (char**)&perc_argv.front()) &&
+ (retVal = pCaller.run()) != 1) { // Percolator return value 1 means success
+ carp(CARP_FATAL, "Error running percolator:%d", retVal);
+ }
+ } catch (const std::exception& e) {
+ /* Recover stderr */
+ std::cerr.rdbuf(old);
+ throw runtime_error(e.what());
+ }
+
+ /* Recover stderr */
+ std::cerr.rdbuf(old);
+
+ // get percolator score information into crux objects
+ ProteinMatchCollection* target_pmc = pCaller.getProteinMatchCollection();
+ ProteinMatchCollection* decoy_pmc = pCaller.getDecoyProteinMatchCollection();
+ if (target_pmc == NULL || decoy_pmc == NULL) {
+ carp(CARP_WARNING, "Failed translating Percolator objects into Crux objects");
+ }
+
+ string output_dir = Params::GetString("output-dir");
+
+ if (!Params::GetBool("txt-output")) {
+ FileUtils::Remove(output_target_peptides);
+ }
+
+ // write mzid
+ if (Params::GetBool("mzid-output")) {
+ MzIdentMLWriter mzid_writer, decoy_mzid_writer;
+ string mzid_path = make_file_path(getFileStem() + ".target.mzid");
+ mzid_writer.openFile(mzid_path, Params::GetBool("overwrite"));
+ mzid_writer.addProteinMatches(target_pmc);
+ mzid_writer.closeFile();
+ mzid_path = make_file_path(getFileStem() + ".decoy.mzid");
+ decoy_mzid_writer.openFile(mzid_path, Params::GetBool("overwrite"));
+ decoy_mzid_writer.addProteinMatches(decoy_pmc);
+ decoy_mzid_writer.closeFile();
+ }
+
+ // write pepxml
+ if (Params::GetBool("pepxml-output")) {
+ PMCPepXMLWriter pep_writer;
+ string pep_path = make_file_path(getFileStem() + ".target.pep.xml");
+ pep_writer.openFile(pep_path.c_str(), Params::GetBool("overwrite"));
+ pep_writer.write(target_pmc);
+ pep_writer.closeFile();
+ pep_path = make_file_path(getFileStem() + ".decoy.pep.xml");
+ pep_writer.openFile(pep_path.c_str(), Params::GetBool("overwrite"));
+ pep_writer.write(decoy_pmc);
+ pep_writer.closeFile();
+ }
+
+ Globals::clean();
+
+ return 0;
+}
+
+COMMAND_T PercolatorApplication::getCommand() const {
+ return PERCOLATOR_COMMAND;
+
+}
+
+/**
+ * \returns the command name for PercolatorApplication
+ */
+string PercolatorApplication::getName() const {
+ return "percolator";
+}
+
+/**
+ * \returns the description for PercolatorApplication
+ */
+string PercolatorApplication::getDescription() const {
+ return
+ "[[nohtml:Re-rank a collection of PSMs using the Percolator algorithm. "
+ "Optionally, also produce protein rankings using the Fido algorithm.]]"
+ "[[html:<p>Percolator is a semi-supervised learning algorithm that "
+ "dynamically learns to separate target from decoy peptide-spectrum matches "
+ "(PSMs). The algorithm is described in this article:</p><blockquote> Lukas "
+ "Käll, Jesse Canterbury, Jason Weston, William Stafford Noble and "
+ "Michael J. MacCoss. <a href=\"http://noble.gs.washington.edu/papers/"
+ "kall2007semi-supervised.html\">"Semi-supervised learning for peptide "
+ "identification from shotgun proteomics datasets."</a> <em>Nature "
+ "Methods</em>. 4(11):923-925, 2007.</blockquote><p>Percolator requires as "
+ "input two collections of PSMs, one set derived from matching observed "
+ "spectra against real ("target") peptides, and a second derived "
+ "from matching the same spectra against "decoy" peptides. The "
+ "output consists of ranked lists of PSMs, peptides and proteins. Peptides "
+ "and proteins are assigned two types of statistical confidence estimates: "
+ "q-values and posterior error probabilities.</p><p>The features used by "
+ "Percolator to represent each PSM are summarized <a href=\"../file-formats/features.html\">"
+ "here</a>.</p><p>Percolator also includes code from <a href=\""
+ "http://noble.gs.washington.edu/proj/fido/\">Fido</a>, whch performs "
+ "protein-level inference. The Fido algorithm is described in this article:"
+ "</p><blockquote>Oliver Serang, Michael J. MacCoss and William Stafford "
+ "Noble. <a href=\"http://pubs.acs.org/doi/abs/10.1021/pr100594k\">"
+ ""Efficient marginalization to compute protein posterior probabilities "
+ "from shotgun mass spectrometry data."</a> <em>Journal of Proteome "
+ "Research</em>. 9(10):5346-5357, 2010.</blockquote><p>Crux includes code "
+ "from <a href=\"http://per-colator.com/\">Percolator</a>. Crux Percolator "
+ "differs from the stand-alone version of Percolator in the following "
+ "respects:</p><ul><li>In addition to the native Percolator XML file "
+ "format, Crux Percolator supports additional input file formats (SQT, "
+ "PepXML, tab-delimited text) and output file formats (PepXML, mzIdentML, "
+ "tab-delimited text). To maintain consistency with the rest of the Crux "
+ "commands, Crux Percolator uses different parameter syntax than the stand-"
+ "alone version of Percolator.</li><li>Like the rest of the Crux commands, "
+ "Crux Percolator writes its files to an output directory, logs all standard "
+ "error messages to a log file, and is capable of reading parameters from a "
+ "parameter file.</li><li>Reading from XML and stdin are not supported at "
+ "this time.</li></ul>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> PercolatorApplication::getArgs() const {
+ string arr[] = {
+ "peptide-spectrum matches"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> PercolatorApplication::getOptions() const {
+ string arr[] = {
+ "fileroot",
+ "output-dir",
+ "overwrite",
+ "txt-output",
+ "pout-output",
+ "mzid-output",
+ "pepxml-output",
+ "feature-file-out",
+ "list-of-files",
+ "parameter-file",
+ "feature-file-in",
+ "picked-protein",
+ "protein-enzyme",
+ "protein-report-fragments",
+ "protein-report-duplicates",
+ "protein",
+ "decoy-xml-output",
+ "decoy-prefix",
+ "subset-max-train",
+ "c-pos",
+ "c-neg",
+ "train-fdr",
+ "test-fdr",
+ "maxiter",
+ "quick-validation",
+ "output-weights",
+ "init-weights",
+ "default-direction",
+ "unitnorm",
+ "fido-alpha",
+ "fido-beta",
+ "fido-gamma",
+ "test-each-iteration",
+ "override",
+ "percolator-seed",
+ "klammer",
+ "only-psms",
+ //"doc",
+ "fido-empirical-protein-q",
+ "fido-gridsearch-depth",
+ "fido-gridsearch-mse-threshold",
+ "fido-fast-gridsearch",
+ "fido-protein-truncation-threshold",
+ "fido-no-split-large-components",
+ "tdc",
+ "verbosity",
+ "top-match",
+ "search-input"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > PercolatorApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("percolator.target.proteins.txt",
+ "a tab-delimited file containing the target protein matches. See "
+ "<a href=\"../file-formats/txt-format.html\">here</a> for a list of the fields."));
+ outputs.push_back(make_pair("percolator.decoy.proteins.txt",
+ "a tab-delimited file containing the decoy protein matches. See "
+ "<a href=\"../file-formats/txt-format.html\">here</a> for a list of the fields."));
+ outputs.push_back(make_pair("percolator.target.peptides.txt",
+ "a tab-delimited file containing the target peptide matches. See "
+ "<a href=\"../file-formats/txt-format.html\">here</a> for a list of the fields."));
+ outputs.push_back(make_pair("percolator.decoy.peptides.txt",
+ "a tab-delimited file containing the decoy peptide matches. See "
+ "<a href=\"../file-formats/txt-format.html\">here</a> for a list of the fields."));
+ outputs.push_back(make_pair("percolator.target.psms.txt",
+ "a tab-delimited file containing the target PSMs. See "
+ "<a href=\"../file-formats/txt-format.html\">here</a> for a list of the fields."));
+ outputs.push_back(make_pair("percolator.decoy.psms.txt",
+ "a tab-delimited file containing the decoy PSMs. See "
+ "<a href=\"../file-formats/txt-format.html\">here</a> for a list of the fields."));
+ outputs.push_back(make_pair("percolator.params.txt",
+ "a file containing the name and value of all parameters for the current "
+ "operation. Not all parameters in the file may have been used in the "
+ "operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("percolator.pep.xml",
+ "a file containing the PSMs in "
+ "<a href=\"http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML\">"
+ "pepXML format</a>. This file can be used as input to some of the tools in the "
+ "<a href=\"http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP\">"
+ "Transproteomic Pipeline</a>."));
+ outputs.push_back(make_pair("percolator.mzid",
+ "a file containing the protein, peptide, and spectrum matches in <a href=\""
+ "http://www.psidev.info/mzidentml\">mzIdentML format</a>."));
+ outputs.push_back(make_pair("percolator.log.txt",
+ "a log file containing a copy of all messages that were printed to "
+ "standard error."));
+ return outputs;
+}
+
+/**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+bool PercolatorApplication::needsOutputDirectory() const {
+ return true;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/PercolatorApplication.h b/src/app/PercolatorApplication.h
new file mode 100644
index 0000000..143557c
--- /dev/null
+++ b/src/app/PercolatorApplication.h
@@ -0,0 +1,91 @@
+/**
+ * \file PercolatorApplication.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 4 November 2011
+ * \brief Interface for calling hardklor.
+ *****************************************************************************/
+#ifndef PERCOLATORAPPLICATION_H
+#define PERCOLATORAPPLICATION_H
+
+#include "CruxApplication.h"
+
+#include <string>
+#include <fstream>
+
+
+class PercolatorApplication: public CruxApplication {
+
+ protected:
+
+ //Calls the main method in Percolator Application
+ static int percolatorMain(int argc, char* argv[]);
+
+
+ public:
+
+ /**
+ * \returns a blank PercolatorApplication object
+ */
+ PercolatorApplication();
+
+ /**
+ * Destructor
+ */
+ ~PercolatorApplication();
+
+ /**
+ * main method for PercolatorApplication
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for PercolatorApplication
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for PercolatorApplication
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual COMMAND_T getCommand() const;
+
+ /**
+ * \brief runs hardklor on the input spectra
+ * \returns whether hardklor was successful or not
+ */
+ int main(
+ const std::string& input_pinxml ///< file path of spectra to process
+ );
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/Pipeline.cpp b/src/app/Pipeline.cpp
new file mode 100644
index 0000000..e554b52
--- /dev/null
+++ b/src/app/Pipeline.cpp
@@ -0,0 +1,341 @@
+#include "io/carp.h"
+#include "AssignConfidenceApplication.h"
+#include "bullseye/CruxBullseyeApplication.h"
+#include "util/FileUtils.h"
+#include "MakePinApplication.h"
+#include "PercolatorApplication.h"
+#include "Pipeline.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "TideSearchApplication.h"
+#include "CometApplication.h"
+
+using namespace std;
+
+PipelineApplication::PipelineApplication() {
+}
+
+PipelineApplication::~PipelineApplication() {
+}
+
+int PipelineApplication::main(int argc, char** argv) {
+ checkParams();
+
+ carp(CARP_INFO, "Running pipeline with the following steps:");
+ for (vector<CruxApplication*>::iterator i = apps_.begin(); i != apps_.end(); i++) {
+ carp(CARP_INFO, "--> %s", (*i)->getName().c_str());
+ }
+
+ vector<string> spectra = Params::GetStrings("mass spectra");
+ string database = Params::GetString("peptide source");
+
+ vector<string> resultsFiles;
+ while (!apps_.empty()) {
+ CruxApplication* cur = apps_.front();
+ carp(CARP_INFO, "Running %s...", cur->getName().c_str());
+ int ret;
+ switch (cur->getCommand()) {
+ case BULLSEYE_COMMAND:
+ ret = runBullseye(cur, &spectra);
+ break;
+ case COMET_COMMAND:
+ case TIDE_SEARCH_COMMAND:
+ ret = runSearch(cur, spectra, database, &resultsFiles);
+ break;
+ case QVALUE_COMMAND:
+ case PERCOLATOR_COMMAND:
+ ret = runPostProcessor(cur, resultsFiles);
+ break;
+ default:
+ carp(CARP_FATAL, "Pipeline is not set up to run command '%s'",
+ cur->getName().c_str());
+ break;
+ }
+ delete cur;
+ apps_.erase(apps_.begin());
+
+ if (ret != 0) {
+ carp(CARP_FATAL, "Error running %s", cur->getName().c_str());
+ }
+ }
+
+ return 0;
+}
+
+void PipelineApplication::checkParams() {
+ string search = Params::GetString("search-engine");
+ string postProcessor = Params::GetString("post-processor");
+ if (search == "comet") {
+ if (Params::GetInt("decoy_search") == 0 && postProcessor != "none") {
+ carp(CARP_FATAL, "Cannot perform post-processing without decoys. "
+ "Set decoy_search to 1 or 2.");
+ }
+ }
+}
+
+vector<string> PipelineApplication::getExpectedResultsFiles(
+ CruxApplication* app,
+ const vector<string>& spectra
+) {
+ string outputBase = make_file_path(app->getName());
+ if (app->getCommand() == COMET_COMMAND) {
+ if (Params::GetInt("decoy_search") < 1) {
+ carp(CARP_WARNING, "Searching without decoys (see decoy_search option)");
+ }
+
+ bool multiFile = spectra.size() > 1;
+ string outputExt;
+ if (Params::GetBool("output_txtfile")) {
+ outputExt =".txt";
+ } else if (Params::GetBool("output_pepxmlfile")) {
+ outputExt =".pep.xml";
+ } else if (Params::GetBool("output_sqtfile")) {
+ outputExt =".sqt";
+ } else if (Params::GetBool("output_percolatorfile") && !multiFile) {
+ outputExt =".pin";
+ } else {
+ carp(CARP_FATAL, "No valid Comet output options enabled");
+ }
+
+ vector<string> outputBases;
+ if (!multiFile) {
+ outputBases.push_back(outputBase);
+ } else {
+ // TODO Same file stems?
+ for (vector<string>::const_iterator i = spectra.begin(); i != spectra.end(); i++) {
+ outputBases.push_back(outputBase + "." + FileUtils::Stem(*i));
+ }
+ }
+
+ vector<string> resultsFiles;
+ for (vector<string>::const_iterator i = outputBases.begin(); i != outputBases.end(); i++) {
+ resultsFiles.push_back(*i + ".target" + outputExt);
+ if (Params::GetInt("decoy_search") == 2) {
+ resultsFiles.push_back(*i + ".decoy" + outputExt);
+ }
+ }
+ return resultsFiles;
+ }
+
+ bool concat = Params::GetBool("concat");
+ string outputExt;
+ if (Params::GetBool("txt-output")) {
+ outputExt = ".txt";
+ } else if (Params::GetBool("pepxml-output")) {
+ outputExt = ".pep.xml";
+ } else if (Params::GetBool("sqt-output")) {
+ outputExt = ".sqt";
+ } else if (Params::GetBool("mzid-output")) {
+ outputExt = ".mzid";
+ } else if (Params::GetBool("pin-output")) {
+ outputExt = ".pin";
+ } else {
+ carp(CARP_FATAL, "No valid Tide output options enabled");
+ }
+ vector<string> resultsFiles;
+ if (concat || outputExt == ".mzid" || outputExt == ".pin") {
+ resultsFiles.push_back(outputBase + outputExt);
+ } else {
+ resultsFiles.push_back(outputBase + ".target" + outputExt);
+ resultsFiles.push_back(outputBase + ".decoy" + outputExt);
+ }
+ return resultsFiles;
+}
+
+int PipelineApplication::runBullseye(CruxApplication* app, vector<string>* spectra) {
+ if (app->getCommand() != BULLSEYE_COMMAND) {
+ carp(CARP_FATAL, "Something went wrong.");
+ }
+
+ string outFormat = Params::GetString("spectrum-format");
+ if (outFormat.empty()) {
+ outFormat = "ms2";
+ }
+ for (vector<string>::iterator i = spectra->begin(); i != spectra->end(); i++) {
+ string ms1 = *i;
+ if (StringUtils::IEndsWith(ms1, ".ms2") || StringUtils::IEndsWith(ms1, ".cms2")) {
+ string ms1Check = ms1.substr(0, ms1.length() - 1) + '1';
+ if (FileUtils::Exists(ms1Check)) {
+ ms1 = ms1Check;
+ }
+ }
+ string outBase = make_file_path(app->getFileStem() + "." + FileUtils::BaseName(*i));
+ string outMatch = outBase + ".pid." + outFormat;
+ string outNoMatch = outBase + ".nopid." + outFormat;
+ int ret = ((CruxBullseyeApplication*)app)->main(ms1, *i, outMatch, outNoMatch);
+ if (ret != 0) {
+ carp(CARP_ERROR, "Error running Bullseye on '%s'", i->c_str());
+ return ret;
+ }
+ *i = outMatch;
+ }
+ return 0;
+}
+
+int PipelineApplication::runSearch(
+ CruxApplication* app,
+ const vector<string>& spectra,
+ const string& database,
+ vector<string>* resultsFiles
+) {
+ bool comet = app->getCommand() == COMET_COMMAND;
+ bool tide = app->getCommand() == TIDE_SEARCH_COMMAND;
+ if (!comet && !tide) {
+ carp(CARP_FATAL, "Something went wrong.");
+ }
+
+ carp(CARP_INFO, "Search will be run with the following files against database '%s':",
+ database.c_str());
+ for (vector<string>::const_iterator i = spectra.begin(); i != spectra.end(); i++) {
+ carp(CARP_INFO, "--> %s", i->c_str());
+ }
+
+ *resultsFiles = getExpectedResultsFiles(app, spectra);
+
+ if (comet) {
+ return ((CometApplication*)app)->main(spectra);
+ }
+ return ((TideSearchApplication*)app)->main(spectra);
+}
+
+int PipelineApplication::runPostProcessor(
+ CruxApplication* app,
+ const vector<string>& resultsFiles
+) {
+ bool assignConfidence = app->getCommand() == QVALUE_COMMAND;
+ bool percolator = app->getCommand() == PERCOLATOR_COMMAND;
+ if (!assignConfidence && !percolator) {
+ carp(CARP_FATAL, "Something went wrong.");
+ }
+
+ carp(CARP_INFO, "Post-processing will be run using the following files:");
+ for (vector<string>::const_iterator i = resultsFiles.begin(); i != resultsFiles.end(); i++) {
+ carp(CARP_INFO, "--> %s", i->c_str());
+ }
+
+ if (assignConfidence) {
+ vector<string> targetFiles;
+ for (vector<string>::const_iterator i = resultsFiles.begin(); i != resultsFiles.end(); i++) {
+ if (i->find("decoy") == string::npos) {
+ targetFiles.push_back(*i);
+ }
+ }
+ return ((AssignConfidenceApplication*)app)->main(targetFiles);
+ }
+
+ string pin;
+ if (resultsFiles.size() == 1 && StringUtils::IEndsWith(resultsFiles.front(), ".pin")) {
+ pin = resultsFiles.front();
+ } else {
+ // If passed anything but a single pin file, run make-pin
+ pin = make_file_path("make-pin.pin");
+ carp(CARP_INFO, "Running make-pin");
+ if (MakePinApplication::main(resultsFiles) != 0) {
+ carp(CARP_FATAL, "make-pin failed. Not running Percolator.");
+ }
+ carp(CARP_INFO, "Finished make-pin.");
+ }
+ return ((PercolatorApplication*)app)->main(pin);
+}
+
+string PipelineApplication::getName() const {
+ return "pipeline";
+}
+
+string PipelineApplication::getDescription() const {
+ return
+ "[[nohtml:Runs a series of Crux tools on a protein database and one or more "
+ "sets of tandem mass spectra.]]"
+ "[[html:<p>Given one or more sets of tandem mass spectra as well as a "
+ "protein database, this command runs a series of Crux tools and reports all "
+ "of the results in a single output directory. There are three steps in the "
+ "pipeline:</p><ol><li><a href=\"bullseye.html\">Bullseye</a> to assign high-"
+ "resolution precursor m/z values to MS/MS data. This step is optional.</li>"
+ "<li>Database searching using either <a href=\"tide-search.html\">"
+ "Tide-search</a> or <a href=\"comet.html\">Comet</a>. The database can be "
+ "provided as a file in FASTA format, or additionally, an index as produced "
+ "by <a href=\"tide-index.html\">tide-index</a>.</li><li>Post-processing "
+ "using either <a href=\"assign-confidence.html\">assign-confidence</a> or "
+ "<a href=\"percolator.html\">Percolator</a>.</li></ol><p>All of the command "
+ "line options associated with the individual tools in the pipeline can be "
+ "used with the <code>pipeline</code> command.</p>]]";
+}
+
+vector<string> PipelineApplication::getArgs() const {
+ string arr[] = {
+ "mass spectra+",
+ "peptide source"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> PipelineApplication::getOptions() const {
+ string arr[] = {
+ "bullseye",
+ "search-engine",
+ "post-processor"
+ };
+ vector<string> options(arr, arr + sizeof(arr) / sizeof(string));
+
+ addOptionsFrom<CruxBullseyeApplication>(&options);
+ addOptionsFrom<TideSearchApplication>(&options);
+ addOptionsFrom<CometApplication>(&options);
+ addOptionsFrom<PercolatorApplication>(&options);
+ addOptionsFrom<AssignConfidenceApplication>(&options);
+
+ return options;
+}
+
+vector< pair<string, string> > PipelineApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+
+ addOutputsFrom<CruxBullseyeApplication>(&outputs);
+ addOutputsFrom<TideSearchApplication>(&outputs);
+ addOutputsFrom<CometApplication>(&outputs);
+ addOutputsFrom<PercolatorApplication>(&outputs);
+ addOutputsFrom<AssignConfidenceApplication>(&outputs);
+
+ return outputs;
+}
+
+string PipelineApplication::getFileStem() const {
+ return getName();
+}
+
+COMMAND_T PipelineApplication::getCommand() const {
+ return PIPELINE_COMMAND;
+}
+
+bool PipelineApplication::needsOutputDirectory() const {
+ return true;
+}
+
+bool PipelineApplication::hidden() const {
+ return false;
+}
+
+void PipelineApplication::processParams() {
+ if (Params::GetBool("bullseye")) {
+ apps_.push_back(new CruxBullseyeApplication());
+ }
+
+ if (Params::GetString("search-engine") == "comet") {
+ Params::Set("database_name", Params::GetString("peptide source"));
+ apps_.push_back(new CometApplication());
+ } else {
+ Params::Set("tide database", Params::GetString("peptide source"));
+ apps_.push_back(new TideSearchApplication());
+ }
+
+ const string postProcessor = Params::GetString("post-processor");
+ if (postProcessor == "assign-confidence") {
+ apps_.push_back(new AssignConfidenceApplication());
+ } else if (postProcessor == "percolator") {
+ apps_.push_back(new PercolatorApplication());
+ }
+
+ for (vector<CruxApplication*>::iterator i = apps_.begin(); i != apps_.end(); i++) {
+ (*i)->processParams();
+ }
+}
+
diff --git a/src/app/Pipeline.h b/src/app/Pipeline.h
new file mode 100644
index 0000000..c88a647
--- /dev/null
+++ b/src/app/Pipeline.h
@@ -0,0 +1,41 @@
+#ifndef PIPELINE_H
+#define PIPELINE_H
+
+#include "CruxApplication.h"
+
+class PipelineApplication : public CruxApplication {
+ public:
+ PipelineApplication();
+ virtual ~PipelineApplication();
+
+ virtual int main(int argc, char** argv);
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+ virtual std::string getFileStem() const;
+ virtual COMMAND_T getCommand() const;
+ virtual bool needsOutputDirectory() const;
+ virtual bool hidden() const;
+ virtual void processParams();
+
+ private:
+ std::vector<CruxApplication*> apps_;
+
+ static void checkParams();
+ static std::vector<std::string> getExpectedResultsFiles(
+ CruxApplication* app,
+ const std::vector<std::string>& spectra
+ );
+ int runBullseye(CruxApplication* app,
+ std::vector<std::string>* spectra);
+ int runSearch(CruxApplication* app,
+ const std::vector<std::string>& spectra,
+ const std::string& database,
+ std::vector<std::string>* resultsFiles);
+ int runPostProcessor(CruxApplication* app,
+ const std::vector<std::string>& resultsFiles);
+};
+
+#endif
diff --git a/src/app/PredictPeptideIons.cpp b/src/app/PredictPeptideIons.cpp
new file mode 100644
index 0000000..efec446
--- /dev/null
+++ b/src/app/PredictPeptideIons.cpp
@@ -0,0 +1,226 @@
+/**
+ * \file PredictPeptideIons.cpp
+ *
+ * AUTHOR: Manijeh Naseri
+ * CREATE DATE: January 27, 2012
+ *
+ * DESCRIPTION: Main method for the predict-peptide-ions.
+ * Given a peptide sequence, and a charge state, predict
+ * the fragmentation ions.
+ */
+
+#include "PredictPeptideIons.h"
+
+#include <algorithm>
+#include <math.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "model/objects.h"
+#include "parameter.h"
+#include "model/Ion.h"
+#include "model/IonSeries.h"
+#include "model/IonConstraint.h"
+#include "model/Peptide.h"
+#include "util/Params.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * \returns A blank PredictPeptideIons object.
+ */
+PredictPeptideIons::PredictPeptideIons() {
+
+}
+
+/**
+ * Destructor
+ */
+PredictPeptideIons::~PredictPeptideIons() {
+}
+
+/**
+ * Main method for PredictPeptideIons.
+ */
+int PredictPeptideIons::main(int argc, char** argv) {
+ /* Get Arguments */
+ string peptide_sequence = Params::GetString("peptide sequence");
+ int charge_state = Params::GetInt("charge state");
+
+ /* Get Options */
+ ION_TYPE_T ion_type;
+ string_to_ion_type(Params::GetString("primary-ions"), &ion_type);
+ bool use_precursor_ions = Params::GetBool("precursor-ions");
+ int isotope_count = Params::GetInt("isotope");
+ bool is_flanking = Params::GetBool("flanking");
+ string max_ion_charge = Params::GetString("max-ion-charge");
+
+ int nh3_count = Params::GetInt("nh3");
+ int h2o_count = Params::GetInt("h2o");
+
+ int neutral_loss_count[MAX_MODIFICATIONS];
+ bool is_modification = false;
+
+ // check peptide sequence
+ if (!valid_peptide_sequence(peptide_sequence)) {
+ carp(CARP_FATAL, "The peptide sequence '%s' is not valid", peptide_sequence.c_str());
+ }
+
+ // neutral_losses
+ // initialize
+ int modification_idx = 0;
+ for(; modification_idx < MAX_MODIFICATIONS; ++modification_idx) {
+ neutral_loss_count[modification_idx] = 0;
+ }
+
+ is_modification = (nh3_count || h2o_count || isotope_count || is_flanking);
+
+ neutral_loss_count[NH3] = nh3_count;
+ neutral_loss_count[H2O] = h2o_count;
+ neutral_loss_count[FLANK] = (int)is_flanking;
+ neutral_loss_count[ISOTOPE] = isotope_count;
+
+ // create ion_constraint
+ MASS_TYPE_T frag_masses = get_mass_type_parameter("fragment-mass");
+
+ IonConstraint* ion_constraint =
+ // new_ion_constraint(MONO, max_charge, ion_type, use_precursor_ions);
+ new IonConstraint(frag_masses, charge_state, ion_type, use_precursor_ions);
+
+
+ // set ion_constraint3 modification counts, if modifications should occur
+ if (is_modification) {
+ ion_constraint->setModification(NH3, neutral_loss_count[NH3]);
+ ion_constraint->setModification(H2O, neutral_loss_count[H2O]);
+ ion_constraint->setModification(ISOTOPE, neutral_loss_count[ISOTOPE]);
+ ion_constraint->setModification(FLANK, neutral_loss_count[FLANK]);
+ }
+
+ // create ion_series
+ IonSeries* ion_series = new IonSeries(peptide_sequence, charge_state, ion_constraint);
+
+ // now predict ions
+ ion_series->predictIons();
+
+ // print settings
+ printf("# PEPTIDE: %s\n", peptide_sequence.c_str());
+ printf("# AVERAGE: %f MONO:%f\n",
+ Peptide::calcSequenceMass(peptide_sequence, AVERAGE),
+ Peptide::calcSequenceMass(peptide_sequence, MONO));
+ printf("# CHARGE: %d\n", charge_state);
+ printf("# MAX-ION-CHARGE: %s\n", max_ion_charge.c_str());
+ printf("# NH3 modification: %d\n", neutral_loss_count[NH3]);
+ printf("# H2O modification: %d\n", neutral_loss_count[H2O]);
+ printf("# ISOTOPE modification: %d\n", neutral_loss_count[ISOTOPE]);
+ printf("# FLANK modification: %d\n", neutral_loss_count[FLANK]);
+ // print ions
+ ion_series->print(stdout);
+
+ // free
+ IonConstraint::free(ion_constraint);
+
+ delete ion_series;
+
+ return 0;
+}
+
+/**
+ * \returns The command name for PredictPeptideIons.
+ */
+string PredictPeptideIons::getName() const {
+ return "predict-peptide-ions";
+}
+
+/**
+ * \returns The description for PredictPeptideIons.
+ */
+string PredictPeptideIons::getDescription() const {
+ return
+ "[[nohtml:Given a peptide and a charge state, predict the m/z values of "
+ "the resulting fragment ions.]]"
+ "[[html:<p>Given a peptide and a charge state, predict the corresponding "
+ "fragment ions according to the provided options.</p>]]";
+}
+
+/**
+ * \returns The command arguments
+ */
+vector<string> PredictPeptideIons::getArgs() const {
+ string arr[] = {
+ "peptide sequence",
+ "charge state"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns The command options
+ */
+vector<string> PredictPeptideIons::getOptions() const {
+ string arr[] = {
+ "primary-ions",
+ "precursor-ions",
+ "isotope",
+ "flanking",
+ "max-ion-charge",
+ "fragment-mass",
+ "nh3",
+ "h2o"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns The command outputs
+ */
+vector< pair<string, string> > PredictPeptideIons::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "a series of lines, describing how the ions were predicted. <blockquote "
+ "style=\"font-family: monospace;\"># PEPTIDE: <peptide sequence><br>"
+ "# CHARGE: <peptide charge></blockquote>"
+ "The program then prints a one-"
+ "line header that labels the tab-delimited columns, followed by one line "
+ "per ion:<blockquote style=\"font-family: monospace;\">m/z mass "
+ "charge ion-series peptide-bond-index nh3 h2o "
+ "isotope flank</blockquote>"
+ "<p>The columns contain the following values:"
+ "<ul><li><m/z> is the ion's mass-to-charge</li>"
+ "<li><mass> is the ion's (charged) mass</li>"
+ "<li><charge> is the ion's charge e.g. 1,2,3</li>"
+ "<li><ion-type> is a string representing the series 'a', 'b', 'c', "
+ "'x', 'y', 'z', and 'p'</li>"
+ "<li><peptide-bond-index> is in [1...n), where n is "
+ "peptide-length. Consistent with standard mass spec terminology, b-1 "
+ "corresponds to a prefix ion of a single amino acid, and y-1 "
+ "corresponds to a suffix ion of a single amino acid.<li>"
+ "<li><nh3> is the number of NH3 modifications</li>"
+ "<li><h2o> is the number of H2O Modifications</li>"
+ "<li><isotope> is the number of adjacent isotopic peaks</li>"
+ "<li><flank> is the number of flanking ions</li>"
+ "</ul></p>"));
+ return outputs;
+}
+
+/**
+ * \returns The enum of the application, default PREDICT_PEPTIDE_IONS_COMMAND.
+ */
+COMMAND_T PredictPeptideIons::getCommand() const {
+ return PREDICT_PEPTIDE_IONS_COMMAND;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/PredictPeptideIons.h b/src/app/PredictPeptideIons.h
new file mode 100644
index 0000000..6739fdc
--- /dev/null
+++ b/src/app/PredictPeptideIons.h
@@ -0,0 +1,78 @@
+/**
+ * \file PredictPeptideIons.h
+ *
+ * AUTHOR: Manijeh Naseri
+ * CREATE DATE: January 27, 2012
+ * DESCRIPTION: Main method for the predict-peptide-ions.
+ * Given a peptide sequence, and a charge state, predict
+ * the fragmentation ions.
+ */
+#ifndef PREDICTPEPTIDEIONS_H
+#define PREDICTPEPTIDEIONS_H
+
+#include "CruxApplication.h"
+#include "util/crux-utils.h"
+#include "io/carp.h"
+#include "parameter.h"
+
+class PredictPeptideIons: public CruxApplication {
+
+ public:
+ /**
+ * \returns A blank PredictPeptideIons object.
+ */
+ PredictPeptideIons();
+
+ /**
+ * Destructor
+ */
+ ~PredictPeptideIons();
+
+ /**
+ * Main method for PredictPeptideIons.
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns The command name for PredictPeptideIons.
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns The description for PredictPeptideIons.
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns The command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns The command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns The command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns The enum of the application, PREDICT_PEPTIDE_IONS_COMMAND.
+ */
+ virtual COMMAND_T getCommand() const;
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/app/PrintProcessedSpectra.cpp b/src/app/PrintProcessedSpectra.cpp
new file mode 100644
index 0000000..4adb9e3
--- /dev/null
+++ b/src/app/PrintProcessedSpectra.cpp
@@ -0,0 +1,183 @@
+/**
+ * \file PrintProcessedSpectra.cpp
+ *
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: September 18, 2009
+ *
+ * DESCRIPTION: Main method for the print-processed-spectra command.
+ * For every spectrum in an ms2 file, process as for
+ * xcorr and print peaks in ms2 format to new file.
+ */
+
+#include "PrintProcessedSpectra.h"
+#include "io/SpectrumCollectionFactory.h"
+#include "util/Params.h"
+#include "util/GlobalParams.h"
+
+using namespace std;
+
+/**
+ * \returns a blank PrintProcessedSpectra object
+ */
+PrintProcessedSpectra::PrintProcessedSpectra() {
+
+}
+
+/**
+ * Destructor
+ */
+PrintProcessedSpectra::~PrintProcessedSpectra() {
+}
+
+/**
+ * main method for PrintProcessedSpectra
+ */
+int PrintProcessedSpectra::main(int argc, char** argv) {
+ // Get arguments and options
+ string input_ms2_name = Params::GetString("ms2 file");
+ string output_ms2_name = Params::GetString("output file");
+ output_ms2_name = prefix_fileroot_to_name(output_ms2_name);
+ string output_dir = Params::GetString("output-dir");
+ bool overwrite = Params::GetBool("overwrite");
+ OBSERVED_PREPROCESS_STEP_T stop_after = GlobalParams::getStopAfter();
+
+ // open output file
+ create_output_directory(output_dir, overwrite);
+ FILE* output_ms2 = create_file_in_path(output_ms2_name, output_dir, overwrite);
+ // open input file
+ Crux::SpectrumCollection* spectra =
+ SpectrumCollectionFactory::create(input_ms2_name);
+ if (spectra == NULL) {
+ carp(CARP_FATAL, "Could not read spectra from %s.", input_ms2_name.c_str());
+ }
+
+ spectra->parse();
+ carp(CARP_DEBUG, "Found %d spectra in file.",
+ spectra->getNumSpectra());
+
+ // write header to output file
+ //const char* header = spectra->getComment();
+ //fprintf(output_ms2, "%s", header);
+ fprintf(output_ms2, "H\tComment\tSpectra processed as for Xcorr\n");
+
+ // create iterator for getting spectra
+ FilteredSpectrumChargeIterator* spectrum_iterator =
+ new FilteredSpectrumChargeIterator(spectra);
+
+ if (spectrum_iterator == NULL) {
+ carp(CARP_FATAL, "Could create spectrum iterator");
+ }
+
+ // loop over all spectra, process, print
+ while (spectrum_iterator->hasNext()) {
+ SpectrumZState cur_zstate;
+ int cur_charge = 0;
+ Crux::Spectrum* cur_spectrum =
+ spectrum_iterator->next(cur_zstate);
+
+ cur_charge = cur_zstate.getCharge();
+ carp(CARP_DETAILED_INFO, "Processing spectrum %d charge %d.",
+ cur_spectrum->getFirstScan(), cur_charge);
+
+ // change the peak values
+ FLOAT_T* intensities = NULL;
+ int max_mz_bin = 0;
+ Scorer::getProcessedPeaks(cur_spectrum, cur_charge, XCORR,
+ &intensities, &max_mz_bin, stop_after);
+
+ // print processed spectrum
+ cur_spectrum->printProcessedPeaks(cur_zstate,
+ intensities, max_mz_bin, output_ms2);
+ }
+
+ // close output file
+ delete spectra;
+ fclose(output_ms2);
+
+ return(0);
+}
+
+/**
+ * \returns the command name for PrintProcessedSpectra
+ */
+string PrintProcessedSpectra::getName() const {
+ return "print-processed-spectra";
+}
+
+/**
+ * \returns the description for PrintProcessedSpectra
+ */
+string PrintProcessedSpectra::getDescription() const {
+ return
+ "[[nohtml:Process spectra as for scoring xcorr and print the results to a "
+ "file.]]"
+ "[[html:<p>Pre-process each spectrum in a given file in preparation for "
+ "computing XCorr. The pre-processing steps are described in detail in this "
+ "paper:</p><blockquote>J. K. Eng, B. Fischer, J. Grossman and M. J. "
+ "MacCoss. <a href=\"http://pubs.acs.org/doi/abs/10.1021/pr800420s\">"A "
+ "fast SEQUEST cross correlation algorithm process the peaks as for "
+ "computing."</a> <em>Journal of Proteome Research</em>. "
+ "7(10):4598-4602, 2008.</blockquote><p>The output of this program is "
+ "equivalent to the spectrum shown in Figure 1D of the above paper.</p>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> PrintProcessedSpectra::getArgs() const {
+ string arr[] = {
+ "ms2 file",
+ "output file"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> PrintProcessedSpectra::getOptions() const {
+ string arr[] = {
+ "stop-after",
+ "output-units",
+ "spectrum-parser",
+ "use-z-line",
+ "verbosity",
+ "parameter-file",
+ "overwrite"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > PrintProcessedSpectra::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("output file",
+ "The name of the file in which the processed spectra will be printed in "
+ "MS2 format."));
+ return outputs;
+}
+
+/**
+ * \returns the file stem of the application, default getName.
+ */
+string PrintProcessedSpectra::getFileStem() const {
+ return "processed-spectra";
+}
+
+COMMAND_T PrintProcessedSpectra::getCommand() const {
+ return PROCESS_SPEC_COMMAND;
+}
+
+bool PrintProcessedSpectra::needsOutputDirectory() const {
+ return true;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/PrintProcessedSpectra.h b/src/app/PrintProcessedSpectra.h
new file mode 100644
index 0000000..57d0b53
--- /dev/null
+++ b/src/app/PrintProcessedSpectra.h
@@ -0,0 +1,93 @@
+/**
+ * \file PrintProcessedSpectra.h
+ *
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: September 18, 2009
+ * DESCRIPTION: Main method for the print-processed-spectra command.
+ * For every spectrum in an ms2 file, process as for
+ * xcorr and print peaks in ms2 format to new file.
+ * REVISION:
+ */
+#ifndef PRINTPROCESSEDSPECTRA_H
+#define PRINTPROCESSEDSPECTRA_H
+#include "CruxApplication.h"
+
+
+#include "util/crux-utils.h"
+#include "io/carp.h"
+#include "parameter.h"
+#include "io/SpectrumCollection.h"
+#include "model/FilteredSpectrumChargeIterator.h"
+#include "model/Scorer.h"
+
+#include <string>
+
+class PrintProcessedSpectra: public CruxApplication {
+
+ public:
+ /**
+ * \returns a blank PrintProcessedSpectra object
+ */
+ PrintProcessedSpectra();
+
+ /**
+ * Destructor
+ */
+ ~PrintProcessedSpectra();
+
+ /**
+ * main method for PrintProcessedSpectra
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for PrintProcessedSpectra
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for PrintProcessedSpectra
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns the file stem of the application, default getName.
+ */
+ virtual std::string getFileStem() const;
+
+ /**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+ virtual COMMAND_T getCommand() const;
+
+ virtual bool needsOutputDirectory() const;
+
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/app/PrintVersion.cpp b/src/app/PrintVersion.cpp
new file mode 100644
index 0000000..5754e6a
--- /dev/null
+++ b/src/app/PrintVersion.cpp
@@ -0,0 +1,72 @@
+/**
+ * \file PrintVersion.cpp
+ * \brief Object for printing the crux version number.
+ *****************************************************************************/
+#include "PrintVersion.h"
+#include "crux_version.h"
+#include "pwiz/Version.hpp"
+#include "Caller.h"
+#include "CometSearch/Common.h"
+#include "boost/version.hpp"
+using namespace std;
+
+/**
+ * \returns a blank PrintVersion object
+ */
+PrintVersion::PrintVersion() {
+
+}
+
+/**
+ * Destructor
+ */
+PrintVersion::~PrintVersion() {
+}
+
+/**
+ * main method for PrintVersion
+ */
+int PrintVersion::main(int argc, char** argv) {
+ (void)argc;
+ (void)argv;
+
+ printf("====================\n");
+ printf("Crux version %s\n", CRUX_VERSION);
+
+ printf("====================\n");
+ string proteowizard_version = pwiz::Version::str();
+ printf("Proteowizard version %s\n", proteowizard_version.c_str());
+
+ printf("====================\n");
+ string percolator_version = Caller::greeter();
+ printf("%s", percolator_version.c_str());
+
+ printf("====================\n");
+ printf("Comet version %s\n", comet_version);
+
+ printf("====================\n");
+ printf("Boost version %s\n", BOOST_LIB_VERSION);
+ printf("====================\n");
+
+ return 0;
+}
+
+/**
+ * \returns the command name for PrintVersion
+ */
+string PrintVersion::getName() const {
+ return "version";
+}
+
+/**
+ * \returns the description for PrintVersion
+ */
+string PrintVersion::getDescription() const {
+ return
+ "Print the Crux version number to standard output, "
+ "then exit.";
+}
+
+COMMAND_T PrintVersion::getCommand() const {
+ return VERSION_COMMAND;
+}
diff --git a/src/app/PrintVersion.h b/src/app/PrintVersion.h
new file mode 100644
index 0000000..b6b194f
--- /dev/null
+++ b/src/app/PrintVersion.h
@@ -0,0 +1,57 @@
+/**
+ * \file PrintVersion.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Object for printing the crux version number.
+ *****************************************************************************/
+#ifndef PRINTVERSION_H
+#define PRINTVERSION_H
+
+#include "CruxApplication.h"
+
+#include <string>
+
+class PrintVersion: public CruxApplication {
+
+ public:
+ /**
+ * \returns a blank PrintVersion object
+ */
+ PrintVersion();
+
+ /**
+ * Destructor
+ */
+ ~PrintVersion();
+
+ /**
+ * main method for PrintVersion
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for PrintVersion
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for PrintVersion
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+ virtual COMMAND_T getCommand() const;
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ReadSpectrumRecordsApplication.cpp b/src/app/ReadSpectrumRecordsApplication.cpp
new file mode 100644
index 0000000..d4e810c
--- /dev/null
+++ b/src/app/ReadSpectrumRecordsApplication.cpp
@@ -0,0 +1,91 @@
+#include "ReadSpectrumRecordsApplication.h"
+
+#include "io/carp.h"
+#include "util/Params.h"
+
+ReadSpectrumRecordsApplication::ReadSpectrumRecordsApplication() {
+}
+
+ReadSpectrumRecordsApplication::~ReadSpectrumRecordsApplication() {
+}
+
+int ReadSpectrumRecordsApplication::main(int argc, char** argv) {
+ carp(CARP_INFO, "Running read-spectrumrecords...");
+
+ string records_file = Params::GetString("spectrum records file");
+
+ pb::Header header;
+ HeadedRecordReader reader(records_file, &header);
+ if (!reader.OK()) {
+ carp(CARP_FATAL, "Error reading spectrum records file");
+ }
+
+ show(reader);
+
+ if (!reader.OK()) {
+ carp(CARP_FATAL, "Error reading spectrum records file");
+ }
+
+ return 0;
+}
+
+void ReadSpectrumRecordsApplication::show(
+ HeadedRecordReader& reader
+) {
+ int count = 0;
+ pb::Spectrum pb_spectrum;
+ cout << setprecision(10);
+ while (!reader.Done()) {
+ reader.Read(&pb_spectrum);
+ Spectrum spectrum(pb_spectrum);
+
+ cout << "Spectrum Number: " << spectrum.SpectrumNumber();
+ if (spectrum.PrecursorMZ() > 0)
+ cout << " Precursor m/z: " << spectrum.PrecursorMZ();
+ cout << endl;
+
+ if (spectrum.NumChargeStates() > 0) {
+ cout << "Charge states: " << spectrum.ChargeState(0);
+ for (int i = 1; i < spectrum.NumChargeStates(); ++i)
+ cout << ", " << spectrum.ChargeState(i);
+ cout << endl;
+ }
+
+ for (int i = 0; i < spectrum.Size(); ++i)
+ cout << spectrum.M_Z(i) << " " << spectrum.Intensity(i) << endl;
+ }
+}
+
+string ReadSpectrumRecordsApplication::getName() const {
+ return "read-spectrumrecords";
+}
+
+string ReadSpectrumRecordsApplication::getDescription() const {
+ return "Runs read-spectrumrecords";
+}
+
+vector<string> ReadSpectrumRecordsApplication::getArgs() const {
+ string arr[] = {
+ "spectrum records file"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+bool ReadSpectrumRecordsApplication::needsOutputDirectory() const {
+ return false;
+}
+
+COMMAND_T ReadSpectrumRecordsApplication::getCommand() const {
+ return READ_SPECTRUMRECORDS_COMMAND;
+}
+
+bool ReadSpectrumRecordsApplication::hidden() const {
+ return true;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ReadSpectrumRecordsApplication.h b/src/app/ReadSpectrumRecordsApplication.h
new file mode 100644
index 0000000..fb3e348
--- /dev/null
+++ b/src/app/ReadSpectrumRecordsApplication.h
@@ -0,0 +1,70 @@
+#ifndef READSPECTRUMRECORDSAPPLICATION_H
+#define READSPECTRUMRECORDSAPPLICATION_H
+
+#include "CruxApplication.h"
+
+#include <stdio.h>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <string>
+#include <gflags/gflags.h>
+#include "tide/spectrum_collection.h"
+#include "tide/records.h"
+
+using namespace std;
+
+class ReadSpectrumRecordsApplication : public CruxApplication {
+
+ protected:
+
+ void show(HeadedRecordReader& reader);
+
+ public:
+
+ /**
+ * Constructor
+ */
+ ReadSpectrumRecordsApplication();
+
+ /**
+ * Destructor
+ */
+ ~ReadSpectrumRecordsApplication();
+
+ /**
+ * Main method
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * Returns the command name
+ */
+ virtual string getName() const;
+
+ /**
+ * Returns the command description
+ */
+ virtual string getDescription() const;
+
+ virtual vector<string> getArgs() const;
+
+ /**
+ * Returns whether the application needs the output directory or not. (default false)
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual COMMAND_T getCommand() const;
+
+ virtual bool hidden() const;
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ReadTideIndex.cpp b/src/app/ReadTideIndex.cpp
new file mode 100644
index 0000000..e22ce40
--- /dev/null
+++ b/src/app/ReadTideIndex.cpp
@@ -0,0 +1,153 @@
+#include "ReadTideIndex.h"
+
+#include "TideMatchSet.h"
+#include "io/carp.h"
+#include "parameter.h"
+#include "app/tide/records_to_vector-inl.h"
+#include "app/tide/peptide.h"
+#include "util/Params.h"
+#include <vector>
+
+using namespace std;
+
+ReadTideIndex::ReadTideIndex() {
+}
+
+ReadTideIndex::~ReadTideIndex() {
+}
+
+int ReadTideIndex::main(int argc, char** argv) {
+ carp(CARP_INFO, "Running read-tide-index...");
+
+ string index_dir = Params::GetString("tide database");
+ string peptides_file = index_dir + "/pepix";
+ string proteins_file = index_dir + "/protix";
+ string auxlocs_file = index_dir + "/auxlocs";
+
+ // Read proteins index file
+ carp(CARP_INFO, "Reading proteins...");
+ ProteinVec proteins;
+ pb::Header protein_header;
+ if (!ReadRecordsToVector<pb::Protein, const pb::Protein>(&proteins,
+ proteins_file, &protein_header)) {
+ carp(CARP_FATAL, "Error reading index (%s)", proteins_file.c_str());
+ }
+ carp(CARP_DEBUG, "Read %d proteins", proteins.size());
+
+ // Read auxlocs index file
+ carp(CARP_INFO, "Reading auxiliary locations...");
+ vector<const pb::AuxLocation*> locations;
+ if (!ReadRecordsToVector<pb::AuxLocation>(&locations, auxlocs_file)) {
+ carp(CARP_FATAL, "Error reading index (%s)", auxlocs_file.c_str());
+ }
+ carp(CARP_DEBUG, "Read %d auxlocs", locations.size());
+
+ // Read peptides index file
+ carp(CARP_INFO, "Reading peptides...");
+ pb::Header peptides_header;
+ HeadedRecordReader peptide_reader(peptides_file, &peptides_header);
+ if (peptides_header.file_type() != pb::Header::PEPTIDES ||
+ !peptides_header.has_peptides_header()) {
+ carp(CARP_FATAL, "Error reading index (%s)", peptides_file.c_str());
+ }
+
+ const pb::Header::PeptidesHeader& pepHeader = peptides_header.peptides_header();
+ MassConstants::Init(&pepHeader.mods(), &pepHeader.nterm_mods(), &pepHeader.cterm_mods(),
+ Params::GetDouble("mz-bin-width"),
+ Params::GetDouble("mz-bin-offset"));
+
+ // Set up output file
+ string output_file = make_file_path(getName() + ".peptides.txt");
+ ofstream* output_stream = create_stream_in_path(
+ output_file.c_str(), NULL, Params::GetBool("overwrite"));
+ *output_stream << get_column_header(SEQUENCE_COL) << '\t'
+ << get_column_header(PROTEIN_ID_COL) << endl;
+
+ RecordReader* reader = peptide_reader.Reader();
+ while (!reader->Done()) {
+ // Read peptide
+ pb::Peptide pb_peptide;
+ reader->Read(&pb_peptide);
+ if (Params::GetBool("skip-decoys") && pb_peptide.is_decoy()) {
+ continue;
+ }
+ Peptide peptide(pb_peptide, proteins);
+
+ // Output to file
+ *output_stream << peptide.SeqWithMods() << '\t'
+ << proteins[peptide.FirstLocProteinId()]->name();
+ if (peptide.HasAuxLocationsIndex()) {
+ const pb::AuxLocation* aux_loc = locations[peptide.AuxLocationsIndex()];
+ for (int i = 0; i < aux_loc->location_size(); i++) {
+ const pb::Protein* protein = proteins[aux_loc->location(i).protein_id()];
+ if (protein->has_name()) {
+ *output_stream << ';' << protein->name();
+ }
+ }
+ }
+ *output_stream << endl;
+ }
+
+ output_stream->close();
+ delete output_stream;
+
+ return 0;
+}
+
+string ReadTideIndex::getName() const {
+ return "read-tide-index";
+}
+
+string ReadTideIndex::getDescription() const {
+ return "Reads an index generated by tide-index and outputs information about "
+ "the peptides it contains.";
+}
+
+vector<string> ReadTideIndex::getArgs() const {
+ string arr[] = {
+ "tide database"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> ReadTideIndex::getOptions() const {
+ string arr[] = {
+ "skip-decoys"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > ReadTideIndex::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("read-tide-index.peptides.txt",
+ "a tab-delimited file containing two columns with headers: the peptide, and "
+ "a semicolon-delimited list of IDs of the proteins that peptide occurs in."));
+ outputs.push_back(make_pair("read-tide-index.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("read-tide-index.log.txt",
+ "a log file containing a copy of all messages that were printed to the "
+ "screen during execution."));
+ return outputs;
+}
+
+bool ReadTideIndex::needsOutputDirectory() const {
+ return true;
+}
+
+COMMAND_T ReadTideIndex::getCommand() const {
+ return READ_SPECTRUMRECORDS_COMMAND;
+}
+
+bool ReadTideIndex::hidden() const {
+ return true;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/ReadTideIndex.h b/src/app/ReadTideIndex.h
new file mode 100644
index 0000000..0f0fa5e
--- /dev/null
+++ b/src/app/ReadTideIndex.h
@@ -0,0 +1,81 @@
+#ifndef READTIDEINDEX_H
+#define READTIDEINDEX_H
+
+#include "CruxApplication.h"
+
+#include <stdio.h>
+#include <iostream>
+#include <iomanip>
+#include <fstream>
+#include <string>
+#include <gflags/gflags.h>
+#include "tide/spectrum_collection.h"
+#include "tide/records.h"
+
+using namespace std;
+
+class ReadTideIndex : public CruxApplication {
+
+ public:
+
+ /**
+ * Constructor
+ */
+ ReadTideIndex();
+
+ /**
+ * Destructor
+ */
+ ~ReadTideIndex();
+
+ /**
+ * Main method
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * Returns the command name
+ */
+ virtual string getName() const;
+
+ /**
+ * Returns the command description
+ */
+ virtual string getDescription() const;
+
+ /**
+ * \returns the arguments of the application
+ */
+ virtual vector<string> getArgs() const;
+
+ /**
+ * \returns the options of the application
+ */
+ virtual vector<string> getOptions() const;
+
+ /**
+ * \returns the outputs of the application as name -> description
+ */
+ virtual vector< pair<string, string> > getOutputs() const;
+
+ /**
+ * Returns whether the application needs the output directory or not.
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual COMMAND_T getCommand() const;
+
+ virtual bool hidden() const;
+
+ protected:
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/SortColumn.cpp b/src/app/SortColumn.cpp
new file mode 100644
index 0000000..fafbded
--- /dev/null
+++ b/src/app/SortColumn.cpp
@@ -0,0 +1,369 @@
+/**
+ * \file SortColumn.cpp
+ * \brief Given a delimited file and a column-name, sort the
+ * file.
+ *****************************************************************************/
+#include "SortColumn.h"
+
+#include "io/DelimitedFile.h"
+
+#include "fdstream.hpp"
+
+#include <errno.h>
+#include "util/WinCrux.h"
+#include "util/Params.h"
+
+using namespace std;
+
+
+/**
+ * \returns a blank SortColumn object
+ */
+SortColumn::SortColumn() {
+
+}
+
+/**
+ * Destructor
+ */
+SortColumn::~SortColumn() {
+}
+
+/**
+ * main method for SortColumn
+ */
+int SortColumn::main(int argc, char** argv) {
+ /* Get parameters */
+ delimited_filename_ = Params::GetString("tsv file");
+ column_name_string_ = Params::GetString("column name");
+ column_type_ = get_column_type_parameter("column-type");
+ ascending_ = Params::GetBool("ascending");
+ delimiter_ = get_delimiter_parameter("delimiter");
+ header_ = Params::GetBool("header");
+
+ DelimitedFileReader delimited_file(delimited_filename_, true, delimiter_);
+
+ int col_sort_idx = delimited_file.findColumn(column_name_string_);
+
+ if (col_sort_idx == -1) {
+ carp(CARP_ERROR, "column not found:%s\n\n%s",
+ column_name_string_.c_str(),
+ delimited_file.getAvailableColumnsString().c_str());
+ return -1;
+ }
+
+ col_sort_idx_ = (unsigned int)col_sort_idx;
+
+ /*
+ * So to be able to handle sorting large files without reading the
+ * whole file into memory, we implement a divide-then-merge approach.
+ * Meaning that we read in a maximum number of rows, sort these,
+ * then write out the sorted delimited file to a temporary file.
+ * After processing all of the rows in the original file, we then
+ * merge all the temporary files created, printing out the full sorted file.
+ */
+ vector<int> temp_file_descriptors;
+ vector<boost::fdostream*> temp_file_streams;
+ vector<string> temp_filenames;
+
+ DelimitedFile* temp_delimited = new DelimitedFile(delimiter_);
+ for (unsigned int col_idx=0;col_idx < delimited_file.numCols();col_idx++) {
+ temp_delimited->addColumn(delimited_file.getColumnName(col_idx));
+ }
+
+ //Maximum number of rows to read before sorting then saving to a temporary file.
+ //In the future, we can set this number to be based upon how much memory
+ //is available on the system. We want to make it large enough so that we
+ //don't have to create/merge too many temporary files, but small enough so
+ //that sort-by-column doesn't crash from not enough memory or affect the
+ //other processes on the computer.
+ int max_rows = 200000;
+
+ int current_count = 0;
+
+ while(delimited_file.hasNext()) {
+
+ unsigned int new_row = temp_delimited->addRow();
+ for (unsigned int col_idx = 0;col_idx < delimited_file.numCols();col_idx++) {
+ temp_delimited->setString(col_idx, new_row, delimited_file.getString(col_idx));
+ }
+
+ current_count++;
+
+ if (current_count >= max_rows) {
+ carp(CARP_DEBUG, "Sorting %i rows", max_rows);
+ sortDelimited(temp_delimited);
+
+ char ctemp_filename[50] = "SortColumn_XXXXXX";
+
+ int fd = mkstemp(ctemp_filename);
+ if (fd == -1) {
+ carp(CARP_ERROR, "Error creating temp file!\n "
+ "Error: %s", strerror(errno));
+ return(-1);
+ }
+
+ string temp_filename(ctemp_filename);
+
+ boost::fdostream* out = new boost::fdostream(fd);
+
+ (*out) << (*temp_delimited);
+ temp_file_streams.push_back(out);
+ temp_file_descriptors.push_back(fd);
+ temp_filenames.push_back(temp_filename);
+ delete(temp_delimited);
+
+ //create a new delimited file.
+ temp_delimited = new DelimitedFile(delimiter_);
+
+ for (unsigned int col_idx = 0;col_idx < delimited_file.numCols();col_idx++) {
+ temp_delimited->setString(col_idx, new_row, delimited_file.getString(col_idx));
+ }
+ //reset to count so that we can read in the next batch of rows.
+ current_count = 0;
+
+ }
+
+ delimited_file.next();
+ }
+
+ //done reading the file, now print out the sorted version.
+
+ if (temp_file_descriptors.size() == 0) {
+
+ //no temporary files used, print out the sorted output.
+ sortDelimited(temp_delimited);
+ cout << (*temp_delimited);
+ delete temp_delimited;
+ } else {
+
+ //sort the current and save to a temporary file.
+ sortDelimited(temp_delimited);
+ char ctemp_filename[50] = "SortColumn_XXXXXX";
+
+ int fd = mkstemp(ctemp_filename);
+
+ if (fd == -1) {
+ carp(CARP_ERROR, "Error creating temp file!\n "
+ "Error: %s", strerror(errno));
+ return(-1);
+ }
+
+ string temp_filename(ctemp_filename);
+
+ boost::fdostream* out = new boost::fdostream(fd);
+ (*out) << (*temp_delimited);
+ temp_file_streams.push_back(out);
+ temp_file_descriptors.push_back(fd);
+ temp_filenames.push_back(temp_filename);
+ delete(temp_delimited);
+
+ //flush everything.
+ for (unsigned int i=0; i < temp_file_descriptors.size(); i++) {
+ temp_file_streams[i]->flush();
+ }
+
+ //merge the temporary files together, printing out the merged output.
+ mergeDelimitedFiles(temp_filenames);
+ }
+
+ //clean everything up
+ for (unsigned int idx=0; idx < temp_file_descriptors.size(); idx++) {
+ delete temp_file_streams[idx];
+ close(temp_file_descriptors[idx]);
+ remove(temp_filenames[idx].c_str());
+ }
+
+ return 0;
+
+}
+
+/**
+ * \returns the command name for SortColumn
+ */
+string SortColumn::getName() const {
+ return "sort-by-column";
+}
+
+/**
+ * \returns the description for SortColumn
+ */
+string SortColumn::getDescription() const {
+ return
+ "[[nohtml:Sorts a tab-delimited file by a column.]]"
+ "[[html:<p>Sort the rows of a tab-delimited file according to the values "
+ "in a specified column.</p>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> SortColumn::getArgs() const {
+ string arr[] = {
+ "tsv file",
+ "column name"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> SortColumn::getOptions() const {
+ string arr[] = {
+ "delimiter",
+ "header",
+ "column-type",
+ "ascending",
+ "verbosity"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > SortColumn::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "a copy of the given file, with rows sorted according to the values in the "
+ "specified column."));
+ return outputs;
+}
+
+/**
+ * sorts the delimited file based upon the column type parameter
+ */
+void SortColumn::sortDelimited(
+ DelimitedFile* delimited ///< delimited file to sort.
+ ) {
+
+ switch(column_type_) {
+
+ case COLTYPE_STRING:
+ delimited->sortByStringColumn(column_name_string_, ascending_);
+ break;
+ case COLTYPE_INT:
+ delimited->sortByIntegerColumn(column_name_string_, ascending_);
+ break;
+ case COLTYPE_REAL:
+ delimited->sortByFloatColumn(column_name_string_, ascending_);
+ break;
+ case NUMBER_COLTYPES:
+ case COLTYPE_INVALID:
+ carp(CARP_FATAL, "Unknow column type");
+ }
+}
+
+/**
+ * merges a list of sorted delimited files and prints
+ * out the resulting sorted file. This method accomplishes this
+ * by testing the current row of each temporary file against
+ * the others. If it's compare value is the smallest (or largest when descending)
+ * then printout that temporary file's row and advance the next row.
+ * Keep iterating until all rows for all temporary files are printed out.
+ */
+void SortColumn::mergeDelimitedFiles(
+ vector<string>& temp_filenames
+ ) {
+
+ //open the temporary delimited files using a reader.
+ vector<DelimitedFileReader*> delimited_files;
+ for (unsigned int idx=0;idx < temp_filenames.size();idx++) {
+ delimited_files.push_back(new DelimitedFileReader(temp_filenames[idx], delimiter_));
+ }
+
+ //print out the header if requested.
+ if (header_) {
+ cout << delimited_files[0]->getHeaderString() << endl;
+ }
+
+ int best_idx = -1;
+
+ do {
+ best_idx = -1;
+ //find the temporary file whose current row's column value is the
+ //smallest or largest.
+ for (unsigned int idx = 0;idx < delimited_files.size();idx++) {
+ if (delimited_files[idx]->hasNext()) {
+ if (best_idx == -1) {
+ best_idx = idx;
+ } else {
+ int compare_result = compare(delimited_files[idx], delimited_files[best_idx]);
+ if ((ascending_) && (compare_result == -1)) {
+ best_idx = idx;
+ } else if ((!ascending_) && (compare_result == 1)) {
+ best_idx = idx;
+ }
+ }
+ }
+
+ //if a best was found, print out the row and advance to the
+ //next row.
+ if (best_idx != -1) {
+ cout << delimited_files[best_idx]->getString() << endl;
+ delimited_files[best_idx]->next();
+ }
+ }
+ //iterate until all rows of all temporary files are printed out.
+ } while (best_idx != -1);
+
+ for (unsigned int idx = 0; idx < temp_filenames.size(); idx++) {
+ delete delimited_files[idx];
+ }
+}
+
+/**
+ * \returns the result of comparing two file(s) current row and column:
+ * 1 : file1 > file2
+ * -1 : file1 < file2
+ * 0 : file1 = file2
+ */
+int SortColumn::compare(
+ DelimitedFileReader* file1,
+ DelimitedFileReader* file2
+ ) {
+
+ bool isless = false;
+ bool isequal = false;
+
+ switch (column_type_) {
+ case COLTYPE_STRING:
+ isless = file1->getString(col_sort_idx_) < file2->getString(col_sort_idx_);
+ if (!isless) {
+ isequal = file1->getString(col_sort_idx_) == file2->getString(col_sort_idx_);
+ }
+ break;
+ case COLTYPE_REAL:
+ isless = file1->getDouble(col_sort_idx_) < file2->getDouble(col_sort_idx_);
+ if (!isless) {
+ isequal = file1->getDouble(col_sort_idx_) == file2->getDouble(col_sort_idx_);
+ }
+ break;
+ case COLTYPE_INT:
+ isless = file1->getInteger(col_sort_idx_) < file2->getInteger(col_sort_idx_);
+ if (!isless) {
+ isequal = file1->getInteger(col_sort_idx_) == file2->getInteger(col_sort_idx_);
+ }
+ break;
+ case NUMBER_COLTYPES:
+ case COLTYPE_INVALID:
+ carp(CARP_FATAL, "Column type invalid!");
+
+ }
+
+ if (isless) {
+ return -1;
+ } else if (isequal) {
+ return 0;
+ } else {
+ return 1;
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/SortColumn.h b/src/app/SortColumn.h
new file mode 100644
index 0000000..f0cd023
--- /dev/null
+++ b/src/app/SortColumn.h
@@ -0,0 +1,109 @@
+/**
+ * \file SortColumn.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Given a delimited file and a column-name, sort the
+ * file.
+ *****************************************************************************/
+#ifndef SORTCOLUMN_H
+#define SORTCOLUMN_H
+
+#include "CruxApplication.h"
+#include "io/DelimitedFileReader.h"
+
+#include <string>
+#include <vector>
+
+class SortColumn: public CruxApplication {
+
+ protected:
+ //parameters
+ std::string delimited_filename_; ///<delimited filename to sort
+ std::string column_name_string_; ///<column name to sort by
+ COLTYPE_T column_type_; ///<column's type (int, real, string).
+ bool ascending_; ///<ascending/descending order?
+ char delimiter_; ///<file's delimiter
+ bool header_; ///<print out the header?
+ unsigned int col_sort_idx_; ///<column index to sort by
+
+ //private methods.
+ /**
+ * sorts the delimited file based upon the column type parameter
+ */
+ void sortDelimited(
+ DelimitedFile* delimited
+ );
+
+ /**
+ * merges a list of sorted delimited files and prints
+ * out the resulting sorted file.
+ */
+ void mergeDelimitedFiles(
+ std::vector<std::string>& temp_filenames
+ );
+
+ /**
+ * /returns the result of comparing two file(s) current row and column:
+ * 1 : file1 > file2
+ * -1 : file1 < file2
+ * 0 : file1 = file2
+ */
+ int compare(
+ DelimitedFileReader* file1,
+ DelimitedFileReader* file2
+ );
+
+
+ public:
+
+ /**
+ * \returns a blank SortColumn object
+ */
+ SortColumn();
+
+ /**
+ * Destructor
+ */
+ ~SortColumn();
+
+ /**
+ * main method for SortColumn
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for SortColumn
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for SortColumn
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/SpectralCounts.cpp b/src/app/SpectralCounts.cpp
new file mode 100644
index 0000000..7a17b8d
--- /dev/null
+++ b/src/app/SpectralCounts.cpp
@@ -0,0 +1,1148 @@
+#include <iterator>
+#include "SpectralCounts.h"
+#include "util/crux-utils.h"
+#include "util/Params.h"
+#include "io/OutputFiles.h"
+#include "model/Peptide.h"
+#include "model/ProteinPeptideIterator.h"
+#include "io/SpectrumCollectionFactory.h"
+
+using namespace std;
+using namespace Crux;
+/**
+ * Default constructor.
+ */
+SpectralCounts::SpectralCounts()
+ : output_(NULL),
+ threshold_(0),
+ unique_mapping_(false),
+ quantitation_(PROTEIN_QUANT_LEVEL),
+ parsimony_(PARSIMONY_NONE),
+ measure_(MEASURE_SIN),
+ bin_width_(0),
+ peptide_scores_(Peptide::lessThan),
+ peptide_scores_unique_(Peptide::lessThan),
+ peptide_scores_shared_(Peptide::lessThan),
+ protein_scores_(protein_id_less_than),
+ protein_scores_unique_(protein_id_less_than),
+ protein_scores_shared_(protein_id_less_than),
+ protein_supporting_peptides_(protein_id_less_than),
+ protein_meta_protein_(protein_id_less_than),
+ meta_mapping_(comparePeptideSets),
+ meta_protein_scores_(compareMetaProteins),
+ meta_protein_ranks_(compareMetaProteins) {
+}
+
+/**
+ * Default destructor.
+ */
+SpectralCounts::~SpectralCounts() {
+ delete output_;
+}
+
+/**
+ * Given a collection of scored PSMs, print a list of proteins
+ * ranked by their a specified score. Spectral-counts supports two
+ * types of quantification: Raw counts (RAW),
+ * Normalized Spectral Abundance Factor (NSAF),
+ * Distributed Normalized Spectral Abundance Factor (dNSAF),
+ * EMPAI,
+ * and Normalized Spectral Index (SIN).
+ * \returns 0 on successful completion.
+ */
+int SpectralCounts::main(int argc, char** argv) {
+ getParameterValues(); // all the get_<type>_parameter calls here
+
+ // open output files
+ output_ = new OutputFiles(this);
+ output_->writeHeaders();
+
+ // get a set of matches that pass the threshold
+ filterMatches();
+ carp(CARP_INFO, "Number of matches passed the threshold %i",
+ matches_.size());
+
+ if (matches_.empty()) {
+ carp(CARP_FATAL, "No matches passed the threshold!");
+ }
+
+ // get a set of peptides
+ getPeptideScores();
+ if (unique_mapping_) {
+ makeUniqueMapping();
+ }
+ carp(CARP_INFO, "Number of peptides %i", peptide_scores_.size());
+
+ // quantify at either the peptide or protein level
+ if (quantitation_ == PEPTIDE_QUANT_LEVEL) { // peptide level
+ if (measure_ != MEASURE_RAW) {
+ normalizePeptideScores();
+ }
+ writeRankedPeptides();
+
+ } else if (quantitation_ == PROTEIN_QUANT_LEVEL) { // protein level
+
+ getProteinScores();
+ if (measure_ != MEASURE_RAW) {
+ normalizeProteinScores();
+ checkProteinNormalization();
+ }
+ carp(CARP_INFO, "Number of proteins %i", protein_scores_.size());
+
+ if (parsimony_ != PARSIMONY_NONE) { //if parsimony is not none
+ getProteinToPeptides();
+ getMetaMapping();
+ getProteinToMetaProtein();
+ carp(CARP_INFO, "Number of meta proteins %i", meta_mapping_.size());
+
+ if (parsimony_ == PARSIMONY_GREEDY) { //if parsimony is greedy
+ performParsimonyAnalysis();
+ }
+ getMetaScores();
+ getMetaRanks();
+ }
+ writeRankedProteins();
+ } else {
+ carp(CARP_FATAL, "Invalid quantification level.");
+ }
+
+ return 0;
+}
+
+/**
+ * Collect all the parameter/option values we will need and store them
+ * as member variables.
+ */
+void SpectralCounts::getParameterValues() {
+ psm_file_ = Params::GetString("input PSMs");
+ threshold_ = Params::GetDouble("threshold");
+ database_name_ = Params::GetString("protein-database");
+ unique_mapping_ = Params::GetBool("unique-mapping");
+ quantitation_ = string_to_quant_level_type(Params::GetString("quant-level"));
+ parsimony_ = string_to_parsimony_type(Params::GetString("parsimony"));
+ measure_ = string_to_measure_type(Params::GetString("measure"));
+
+ if (measure_ == MEASURE_SIN && Params::GetString("input-ms2").empty()) {
+ carp(CARP_FATAL, "The SIN computation for spectral-counts requires "
+ "that the --input-ms2 option specify a file.");
+ }
+
+ bin_width_ = Params::GetDouble("mz-bin-width");
+
+ threshold_type_ = get_threshold_type_parameter("threshold-type");
+ custom_threshold_name_ = Params::GetString("custom-threshold-name");
+ threshold_min_ = Params::GetBool("custom-threshold-min");
+}
+
+/**
+ * For every protein that can be mapped from the set of
+ * peptides in PeptideToScore map, enter the protein and
+ * the set of identified peptides it maps to, into
+ * ProteinToPeptide
+ */
+void SpectralCounts::getProteinToPeptides() {
+ for (PeptideToScore::iterator pep_it = peptide_scores_.begin();
+ pep_it != peptide_scores_.end(); ++pep_it) {
+ Peptide* peptide = pep_it->first;
+ for(PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter!= peptide->getPeptideSrcEnd();
+ ++iter) {
+ PeptideSrc* peptide_src = *iter;
+ Protein* protein = peptide_src->getParentProtein();
+ if (protein_supporting_peptides_.find(protein) ==
+ protein_supporting_peptides_.end()) {
+ PeptideSet newset(Peptide::lessThan);
+ protein_supporting_peptides_.insert(make_pair(protein, newset));
+ }
+ protein_supporting_peptides_[protein].insert(peptide);
+ }
+ }
+}
+
+
+/**
+ * Enters the mapping of protein to its metaProtein
+ * into ProteinToMetaProtein. MetaProteins are retreieved
+ * from MetaMapping
+ *
+ */
+void SpectralCounts::getProteinToMetaProtein() {
+ // for every meta protein
+ for (MetaMapping::iterator meta_protein_it = meta_mapping_.begin();
+ meta_protein_it != meta_mapping_.end(); ++meta_protein_it) {
+ MetaProtein proteins = meta_protein_it->second;
+ // for every protein in the meta protein
+ for (MetaProtein::iterator proteins_it = proteins.begin();
+ proteins_it != proteins.end(); ++proteins_it) {
+ // create a mapping of protein to meta protein
+ protein_meta_protein_.insert(make_pair((*proteins_it), proteins));
+ }
+ }
+}
+
+/**
+ * calculates the protein scores based upon the dNSAF metric. First,
+ * the spectral counts for the peptides unique to each protein is added,
+ * then the spectral counts for the peptide shared amongst the proteins
+ * are added with a distribution factor based upon the number of unique
+ * counts that each protein is assigned
+ */
+void SpectralCounts::getProteinScoresDNSAF() {
+
+ //calculate unique scores (unique peptides).
+ for (PeptideToScore::iterator pep_it = peptide_scores_unique_.begin();
+ pep_it != peptide_scores_unique_.end();
+ ++pep_it) {
+
+ Peptide* peptide = pep_it->first;
+ FLOAT_T pep_score = pep_it->second;
+ for (PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter != peptide->getPeptideSrcEnd();
+ ++iter) {
+ PeptideSrc* peptide_src = *iter;
+ Protein* protein = peptide_src->getParentProtein();
+ if (protein_scores_unique_.find(protein) == protein_scores_unique_.end()) {
+ protein_scores_unique_[protein] = 0;
+ protein_scores_shared_[protein] = 0;
+ }
+
+ protein_scores_unique_[protein] += pep_score;
+ }
+ }
+
+ //Handle shared peptides
+ //For each peptide that is shared across multiple proteins,
+ //we calculate a distribution factor based upon the unique
+ //peptides assigned to each protein that is sharing this peptide
+ //we then add the shared peptide count * the protein's distribution
+ //to each protein that is sharing that peptide.
+ //There is a wierd feature that a protein with no unique peptide will
+ //have a dNSAF score of zero... I don't know if we should include the
+ //zero score in the list of proteins...
+ for (PeptideToScore::iterator pep_it = peptide_scores_shared_.begin();
+ pep_it != peptide_scores_shared_.end();
+ ++pep_it) {
+ Peptide* peptide = pep_it->first;
+ FLOAT_T shared_pep_score = pep_it->second;
+
+ double unique_sum = 0.0;
+
+ for (PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter != peptide->getPeptideSrcEnd();
+ ++iter) {
+ PeptideSrc* peptide_src = *iter;
+
+ Protein* protein = peptide_src->getParentProtein();
+ if (protein_scores_unique_.find(protein) != protein_scores_unique_.end()) {
+ unique_sum += protein_scores_unique_[protein];
+ }
+
+ }
+
+ if (unique_sum != 0) {
+ for (PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter != peptide->getPeptideSrcEnd();
+ ++iter) {
+ PeptideSrc* peptide_src = *iter;
+ Protein* protein = peptide_src->getParentProtein();
+ if (protein_scores_unique_.find(protein) != protein_scores_unique_.end()) {
+ FLOAT_T d_factor = protein_scores_unique_[protein] / unique_sum;
+ protein_scores_shared_[protein] += d_factor * shared_pep_score;
+ }
+ }
+ }
+ }
+
+ //add up shared and unique scores to get final score
+ for (ProteinToScore::iterator prot_iter = protein_scores_unique_.begin();
+ prot_iter != protein_scores_unique_.end();
+ ++prot_iter) {
+ Protein* protein = prot_iter->first;
+ FLOAT_T unique_score = prot_iter->second;
+ protein_scores_[protein] = unique_score;
+ }
+
+ for (ProteinToScore::iterator prot_iter = protein_scores_shared_.begin();
+ prot_iter != protein_scores_shared_.end();
+ ++prot_iter) {
+ Protein *protein = prot_iter->first;
+ FLOAT_T shared_score = prot_iter->second;
+ protein_scores_[protein] += shared_score;
+ }
+}
+
+/**
+ * A score for each protein is calculated by summing
+ * the scores of each peptide that belongs to a protein
+ */
+void SpectralCounts::getProteinScores() {
+
+ if (measure_ == MEASURE_DNSAF) {
+ getProteinScoresDNSAF();
+ } else {
+
+ // iterate through each peptide
+ for (PeptideToScore::iterator pep_it = peptide_scores_.begin();
+ pep_it != peptide_scores_.end(); ++pep_it) {
+ Peptide* peptide = pep_it->first;
+ FLOAT_T pep_score = pep_it->second;
+ for (PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter != peptide->getPeptideSrcEnd();
+ ++iter) {
+ PeptideSrc* peptide_src =*iter;
+ Protein* protein = peptide_src->getParentProtein();
+ if (protein_scores_.find(protein) == protein_scores_.end()) {
+ protein_scores_.insert(make_pair(protein, 0.0));
+ }
+ protein_scores_[protein] += pep_score;
+ }
+ }
+ }
+}
+
+/**
+ * Takes the PeptideToScores map and updates all
+ * values with normalized values. Normalized by sum
+ * of all scores and then by the peptide length
+ *
+ */
+void SpectralCounts::normalizePeptideScores() {
+ carp(CARP_DEBUG, "Normalizing peptide scores");
+ FLOAT_T total = 0.0;
+
+ // calculate sum of all scores
+ for (PeptideToScore::iterator it = peptide_scores_.begin();
+ it != peptide_scores_.end(); ++it) {
+ FLOAT_T score = it->second;
+ total += score;
+ }
+
+ // normalize by sum of scores and length
+ for (PeptideToScore::iterator it = peptide_scores_.begin();
+ it != peptide_scores_.end(); ++it) {
+ FLOAT_T score = it->second;
+ Peptide* peptide = it->first;
+ it->second = score / total / (FLOAT_T)peptide->getLength();
+
+ }
+
+}
+
+
+/**
+ * Changes the scores in protien_scores_ to either be divided by the
+ * sum of all scores times the peptide length (SIN, NSAF) or to be the
+ * final emPAI score.
+ */
+void SpectralCounts::normalizeProteinScores() {
+ if (measure_ == MEASURE_EMPAI) {
+ computeEmpai();
+ }
+
+ carp(CARP_DEBUG, "Normalizing protein scores");
+ FLOAT_T total = 0.0;
+
+ // calculate sum of all scores
+ for (ProteinToScore::iterator it = protein_scores_.begin();
+ it != protein_scores_.end(); ++it) {
+
+ FLOAT_T score = it->second;
+ Protein* protein = it->first;
+ if ( (measure_ == MEASURE_NSAF) || (measure_ == MEASURE_DNSAF)) {
+ score = score / (FLOAT_T)protein->getLength();
+ }
+ total += score;
+ }
+
+ // normalize by sum of all scores
+ for (ProteinToScore::iterator it = protein_scores_.begin();
+ it != protein_scores_.end(); ++it) {
+
+ FLOAT_T score = it->second;
+ Protein* protein = it->first;
+ score = score / total;
+ // normalize by length
+ if (measure_ == MEASURE_NSAF ||
+ measure_ == MEASURE_DNSAF ||
+ measure_ == MEASURE_SIN ) {
+ score = score / (FLOAT_T)protein->getLength();
+ }
+ it->second = score;
+ }
+}
+
+/**
+ * Checks that the normalized scores add up to one
+ */
+void SpectralCounts::checkProteinNormalization() {
+
+ FLOAT_T sum = 0;
+
+ for (ProteinToScore::iterator iter = protein_scores_.begin();
+ iter != protein_scores_.end();
+ ++iter) {
+
+ FLOAT_T score = iter->second;
+ if (measure_ == MEASURE_SIN) {
+ //The normalized values of sin do not add up to 1, but they
+ //should if you multiply the length back in...
+ Protein* protein = iter->first;
+ score = score * (FLOAT_T)protein->getLength();
+ }
+
+ sum += score;
+ }
+
+ if (fabs(sum-1.0) > 0.0001) {
+ carp(CARP_WARNING, "Normalized protein scores do not add up to one!:%f", sum);
+ for (ProteinToScore::iterator iter = protein_scores_.begin();
+ iter != protein_scores_.end();
+ ++iter) {
+
+ carp(CARP_DEBUG, "%s %f", iter->first->getIdPointer().c_str(), iter->second);
+ }
+ }
+}
+
+/**
+ * Computes the 10^(observed/total) - 1 score for each protein. Assumes
+ * that protein_scores_ has been populated with the count of observed
+ * unique peptides for each protein.
+ */
+void SpectralCounts::computeEmpai() {
+ PeptideConstraint* constraint = PeptideConstraint::newFromParameters();
+
+ ProteinToScore::iterator it = protein_scores_.begin();;
+ for (; it != protein_scores_.end(); ++it) {
+ FLOAT_T observed_peptides = it->second;
+ Protein* protein = it->first;
+ ProteinPeptideIterator* iter = new ProteinPeptideIterator(protein,
+ constraint);
+ FLOAT_T possible_peptides = iter->getTotalPeptides();
+
+ it->second = pow(10, (observed_peptides / possible_peptides)) - 1.0;
+
+ delete iter;
+ }
+ PeptideConstraint::free(constraint);
+}
+
+/**
+ * For the spectrum associated with the match, sum the intensities of
+ * all b and y ions that are not modified.
+ * \return The sum of unmodified b and y ions.
+ */
+FLOAT_T SpectralCounts::sumMatchIntensity(Match* match,
+ Crux::SpectrumCollection* spectra) {
+ FLOAT_T match_intensity = 0;
+ char* peptide_seq = match->getSequence();
+ MODIFIED_AA_T* modified_sequence = match->getModSequence();
+ int charge = match->getCharge();
+ Spectrum* temp = match->getSpectrum();
+ int scan = temp->getFirstScan();
+
+ Spectrum* spectrum = spectra->getSpectrum(scan);
+
+ if (spectrum == NULL) {
+ carp(CARP_FATAL, "scan: %d doesn't exist or not found!");
+ return 0.0;
+ }
+
+ Ion* ion;
+ SCORER_TYPE_T score_type = XCORR;
+ IonConstraint* ion_constraint =
+ IonConstraint::newIonConstraintSmart(score_type, charge);
+ IonSeries* ion_series = new IonSeries(ion_constraint, charge);
+ ion_series->update(peptide_seq, modified_sequence);
+ ion_series->predictIons();
+ for (IonIterator ion_it = ion_series->begin();
+ ion_it != ion_series->end(); ++ion_it) {
+ ion = (*ion_it);
+ if (ion -> getType() == B_ION || ion -> getType() == Y_ION) {
+ if (!ion->isModified()) {
+ Peak * peak = spectrum->getNearestPeak(ion->getMassZ(),
+ bin_width_);
+ if (peak != NULL) {
+ match_intensity += peak->getIntensity();
+ }
+ }
+ }
+ }
+ delete ion_series;
+ free(peptide_seq);
+
+ return match_intensity;
+}
+
+
+/**
+ * Generate a score for each peptide in the set of matches. Populate
+ * peptide_scores_ which becomes a unique set of peptides, each with a
+ * score.
+ *
+ * For SIN the score is the sum of intensites of b and y ions (without
+ * H2O modifications). Intensites are taken from the .ms2 file.
+ *
+ * For NSAF, the score is the number of matches (spectra) for each peptide.
+ * For EMPAI, the score is 1 as it only reqires the number of peptides
+ * observed per protein.
+ */
+void SpectralCounts::getPeptideScores() {
+ Crux::SpectrumCollection* spectra = NULL;
+
+ // for SIN, parse out spectrum collection from ms2 fiel
+ if( measure_ == MEASURE_SIN ) {
+ spectra = SpectrumCollectionFactory::create(Params::GetString("input-ms2"));
+ }
+
+ for(set<Match*>::iterator match_it = matches_.begin();
+ match_it != matches_.end(); ++match_it) {
+
+ FLOAT_T match_intensity = 1; // for NSAF just count each for the peptide/
+
+ Match* match = (*match_it);
+ // for sin, calculate total ion intensity for match by
+ // summing up peak intensities
+ if (measure_ == MEASURE_SIN) {
+ match_intensity = sumMatchIntensity(match, spectra);
+ }
+
+ // add ion_intensity to peptide scores
+ Peptide* peptide = match->getPeptide();
+
+ if ( measure_ == MEASURE_DNSAF) {
+ //keep track of unique and shared mappings.
+ if (peptide->getNumPeptideSrc() > 1) {
+ if (peptide_scores_shared_.find(peptide) == peptide_scores_shared_.end()) {
+ peptide_scores_shared_.insert(make_pair(peptide, 0.0));
+ }
+ peptide_scores_shared_[peptide] += match_intensity;
+ } else {
+ if (peptide_scores_unique_.find(peptide) == peptide_scores_unique_.end()) {
+ peptide_scores_unique_.insert(make_pair(peptide, 0.0));
+ }
+ peptide_scores_unique_[peptide] += match_intensity;
+ }
+ }
+
+ if (peptide_scores_.find(peptide) == peptide_scores_.end()) {
+ peptide_scores_.insert(make_pair(peptide, 0.0));
+ }
+ peptide_scores_[peptide] += match_intensity;
+
+ }
+
+ if (measure_ == MEASURE_SIN) {
+ delete spectra;
+ }
+
+ // for emPAI we just need a count of unique peptides
+ if (measure_ == MEASURE_EMPAI) {
+ PeptideToScore::iterator itr = peptide_scores_.begin();
+ for(; itr != peptide_scores_.end(); ++itr) {
+ itr->second = 1; // count each unique peptide once
+ }
+ }
+}
+
+
+/**
+ * Create a set of matches, all with an XCORR rank == 1 and all of which
+ * have a qvalue score lower than user-specified threshold.
+ */
+void SpectralCounts::filterMatches() {
+
+ match_collection_ = parser_.create(
+ psm_file_.c_str(),
+ database_name_.c_str());
+ carp(CARP_INFO, "Number of matches:%d", match_collection_->getMatchTotal());
+
+ switch(threshold_type_) {
+ case THRESHOLD_NONE:
+ filterMatchesNone();
+ break;
+ case THRESHOLD_QVALUE:
+ filterMatchesQValue();
+ break;
+ case THRESHOLD_CUSTOM:
+ filterMatchesCustom();
+ break;
+ case THRESHOLD_INVALID:
+ case NUMBER_THRESHOLD_TYPES:
+ carp(CARP_FATAL, "Invalid threshold type");
+ }
+
+}
+
+void SpectralCounts::filterMatchesNone() {
+
+ MatchIterator match_iterator(match_collection_);
+
+ while(match_iterator.hasNext()) {
+ Match* current_match = match_iterator.next();
+ if (!current_match->isDecoy()) {
+ matches_.insert(current_match);
+ }
+ }
+
+}
+
+void SpectralCounts::invalidCustomScore() {
+
+ ostringstream oss;
+
+ oss << "Need valid name for custom threshold. Available ones are:";
+
+ //print out custom names
+ for (int idx=0;idx < NUMBER_SCORER_TYPES;idx++) {
+
+ if (match_collection_->getScoredType((SCORER_TYPE_T)idx)) {
+ oss << endl << "\t" << scorer_type_to_string((SCORER_TYPE_T)idx);
+ }
+
+ }
+
+
+ vector<string> custom_score_names;
+ match_collection_->getCustomScoreNames(custom_score_names);
+
+ for (int idx=0;idx < custom_score_names.size();idx++) {
+ oss << endl << "\t" << custom_score_names[idx];
+ }
+
+ string die_str = oss.str();
+ carp(CARP_FATAL, die_str);
+}
+
+
+/**
+ * filters matches based upon a custom threshold (not q-value)
+ */
+void SpectralCounts::filterMatchesCustom() {
+
+ if (custom_threshold_name_.empty()) {
+ invalidCustomScore();
+ }
+
+
+ //first try to map from tab delimited headers
+ SCORER_TYPE_T scorer;
+ bool tab_header = string_to_scorer_type(custom_threshold_name_.c_str(), &scorer);
+
+ if (tab_header) {
+ //must be a custom field, this can happen with pep xml or mzid.
+ filterMatchesScore(scorer);
+ } else {
+ filterMatchesCustomScore();
+ }
+
+
+}
+
+/**
+ * filters matches based upon a SCORER_TYPE_T
+ */
+void SpectralCounts::filterMatchesScore(
+ SCORER_TYPE_T scorer ///< scorer to use
+ ) {
+
+ MatchIterator match_iterator(match_collection_, scorer, false);
+
+ while (match_iterator.hasNext()) {
+ Match* match = match_iterator.next();
+ if (!match->isDecoy()) {
+ if (threshold_min_) {
+ if (match->getScore(scorer) <= threshold_) {
+ matches_.insert(match);
+ }
+ } else {
+ if (match->getScore(scorer) >= threshold_) {
+ matches_.insert(match);
+ }
+ }
+ }
+ }
+}
+
+/**
+ * filters matches based upon a custom score that is not SCORER_TYPE_T
+ */
+void SpectralCounts::filterMatchesCustomScore() {
+
+ MatchIterator match_iterator(match_collection_);
+
+ while(match_iterator.hasNext()) {
+ Match* match = match_iterator.next();
+ if (!match->isDecoy()) {
+ FLOAT_T score;
+ bool success = match->getCustomScore(custom_threshold_name_, score);
+
+ if (!success) {
+ invalidCustomScore();
+ }
+ if (threshold_min_) {
+ if (score <= threshold_) {
+ matches_.insert(match);
+ }
+ } else {
+ if (score >= threshold_) {
+ matches_.insert(match);
+ }
+ }
+ }
+ }
+}
+
+void SpectralCounts::filterMatchesQValue() {
+ //assume we are using
+ // figure out which qvalue we are using
+ SCORER_TYPE_T qval_type = get_qval_type(match_collection_);
+ if (qval_type == INVALID_SCORER_TYPE) {
+ carp(CARP_FATAL, "The matches in %s do not have q-values.\n"
+ "Please either provide a file with q-values or "
+ "set threshold-type to \"none\" or \"custom.\"",
+ psm_file_.c_str());
+ }
+
+ carp(CARP_DETAILED_DEBUG,
+ "filterMatches(): Getting match iterator for %s",
+ scorer_type_to_string(qval_type));
+
+ MatchIterator* match_iterator = new MatchIterator(match_collection_, qval_type, true);
+
+ while (match_iterator->hasNext()) {
+ Match* match = match_iterator->next();
+
+ carp(CARP_DEBUG, "xcorr rank:%d q-value:%f", match->getRank(XCORR), match->getScore(qval_type));
+ if (match->isDecoy()) {
+ continue;
+ }
+ if ((qval_type == DECOY_XCORR_QVALUE || qval_type == LOGP_QVALUE_WEIBULL_XCORR) &&
+ (match->getRank(XCORR) != 1)) {
+ continue;
+ }
+
+ // find a qvalue score lower than threshold
+ if (match->getScore(qval_type) != FLT_MIN &&
+ match->getScore(qval_type) <= threshold_) {
+ matches_.insert(match);
+ }
+ } // next match
+ delete match_iterator;
+}
+
+/**
+ * Figures out which kind of q-value was scored for this match collection.
+ * \returns PERCOLATOR_QVALUE, QRANKER_QVALUE, or DECOY_XCORR_QVALUE
+ * if any of those were scored or INVALID_SCORER_TYPE if none were scored.
+ */
+SCORER_TYPE_T SpectralCounts::get_qval_type(
+ MatchCollection* match_collection) {
+ SCORER_TYPE_T scored_type = INVALID_SCORER_TYPE;
+
+ if (match_collection->getScoredType(PERCOLATOR_QVALUE)) {
+ scored_type = PERCOLATOR_QVALUE;
+ } else if (match_collection->getScoredType(QRANKER_QVALUE)) {
+ scored_type = QRANKER_QVALUE;
+ } else if (match_collection->getScoredType(DECOY_XCORR_QVALUE)) {
+ scored_type = DECOY_XCORR_QVALUE;
+ } else if(match_collection->getScoredType(BARISTA_QVALUE)) {
+ scored_type = BARISTA_QVALUE;
+ }
+
+ return scored_type;
+}
+
+void SpectralCounts::writeRankedPeptides() {
+ // rearrange pairs to sort by score
+ vector<pair<FLOAT_T, Peptide*> > scoreToPeptide;
+ for (PeptideToScore::iterator it = peptide_scores_.begin();
+ it != peptide_scores_.end(); ++it) {
+ scoreToPeptide.push_back(make_pair(it->second, it->first));
+ }
+
+ sort(scoreToPeptide.begin(), scoreToPeptide.end(), sortRankedPeptides);
+ output_->writeRankedPeptides(scoreToPeptide);
+}
+
+void SpectralCounts::writeRankedProteins() {
+ bool isParsimony = !protein_meta_protein_.empty();
+ // reorganize the protein,score pairs to sort by score
+ vector<boost::tuple<FLOAT_T, Protein*, int> > proteins;
+ for (ProteinToScore::iterator it = protein_scores_.begin();
+ it != protein_scores_.end(); ++it) {
+ int rank = -1;
+ if (isParsimony) {
+ MetaToRank::const_iterator lookup =
+ meta_protein_ranks_.find(protein_meta_protein_[it->first]);
+ if (lookup != meta_protein_ranks_.end()) {
+ rank = lookup->second;
+ }
+ }
+ proteins.push_back(boost::make_tuple(it->second, it->first, rank));
+ }
+
+ sort(proteins.begin(), proteins.end(), sortRankedProteins);
+ output_->writeRankedProteins(proteins, isParsimony);
+}
+
+bool SpectralCounts::sortRankedPeptides(
+ const pair<FLOAT_T, Peptide*>& x,
+ const pair<FLOAT_T, Peptide*>& y) {
+ return x.first != y.first ? x.first > y.first : !Peptide::lessThan(y.second, x.second);
+}
+
+bool SpectralCounts::sortRankedProteins(
+ const boost::tuple<FLOAT_T, Protein*, int>& x,
+ const boost::tuple<FLOAT_T, Protein*, int>& y) {
+ FLOAT_T xScore = x.get<0>();
+ FLOAT_T yScore = y.get<0>();
+ if (xScore != yScore) {
+ return xScore > yScore;
+ }
+ int xRank = x.get<2>();
+ int yRank = y.get<2>();
+ if (xRank != yRank) {
+ return xRank <= yRank;
+ }
+ return y.get<1>()->getIdPointer().compare(x.get<1>()->getIdPointer()) > 0;
+}
+
+/**
+ * Fills in the MetaMapping with entries of set of
+ * peptides that can be found in every protein in
+ * the meta protein
+ *
+ */
+void SpectralCounts::getMetaMapping() {
+ carp(CARP_DEBUG, "Creating a mapping of meta protein to peptides");
+ int count = 0;
+ for(ProteinToPeptides::iterator prot_it = protein_supporting_peptides_.begin();
+ prot_it != protein_supporting_peptides_.end(); ++prot_it) {
+ Protein* protein = prot_it->first;
+ PeptideSet pep_set = prot_it->second;
+
+ if (meta_mapping_.find(pep_set) == meta_mapping_.end()) {
+ MetaProtein meta_protein(protein_id_less_than);
+ count++;
+ meta_mapping_.insert(make_pair(pep_set, meta_protein));
+ }
+ meta_mapping_[pep_set].insert(protein);
+ }
+
+}
+
+/**
+ * Takes a mapping of set of peptides to meta proteins and
+ * a mapping of protein to scores, and finds the largest score
+ * of the meta proteins for each protein. The object returned
+ * is a mapping of MetaProteins to the highest score
+ *
+ */
+void SpectralCounts::getMetaScores() {
+ carp(CARP_DEBUG, "Finding scores of meta proteins");
+ for (MetaMapping::iterator meta_it = meta_mapping_.begin();
+ meta_it != meta_mapping_.end(); ++meta_it) {
+ MetaProtein proteins = (*meta_it).second;
+ FLOAT_T top_score = -1.0;
+ for (MetaProtein::iterator protein_it = proteins.begin();
+ protein_it != proteins.end(); ++protein_it) {
+ Protein* protein = (*protein_it);
+ FLOAT_T score = protein_scores_[protein];
+ top_score = max(score, top_score);
+ }
+ meta_protein_scores_.insert(make_pair(proteins, top_score));
+ }
+
+}
+
+/**
+ * Takes a mapping of MetaProteins to scores and returns
+ * a mapping of set of peptides to rank
+ *
+ */
+void SpectralCounts::getMetaRanks() {
+ carp(CARP_DEBUG, "Finding ranks of meta proteins");
+ vector< pair<FLOAT_T, MetaProtein> > metaVector;
+ for (MetaToScore::iterator meta_it = meta_protein_scores_.begin();
+ meta_it != meta_protein_scores_.end(); ++meta_it) {
+ MetaProtein proteins = (*meta_it).first;
+ FLOAT_T score = (*meta_it).second;
+ metaVector.push_back(make_pair(score, proteins));
+ }
+ sort(metaVector.begin(), metaVector.end(), compareMetaScorePair);
+
+ int cur_rank = 1;
+ for (vector< pair<FLOAT_T, MetaProtein> >::iterator
+ vector_it = metaVector.begin();
+ vector_it != metaVector.end(); ++vector_it) {
+ MetaProtein proteins = (*vector_it).second;
+ meta_protein_ranks_.insert(make_pair(proteins, cur_rank));
+ cur_rank++;
+ }
+
+}
+
+/**
+ * Greedily finds a peptide-to-protein mapping where each
+ * peptide is only mapped to a single meta-protein.
+ *
+ * Would of been better to implement with priority queue w/
+ * adjancency lists: O(n*log(n)) but input size should be
+ * small enough that performance should not be an issue.
+ */
+void SpectralCounts::performParsimonyAnalysis() {
+ carp(CARP_DEBUG, "Performing Greedy Parsimony analysis");
+ MetaMapping result(comparePeptideSets);
+ vector< pair<PeptideSet, MetaProtein > > peps_vector;
+
+ // get all meta mappings into a vector
+ for (MetaMapping::iterator meta_iter = meta_mapping_.begin();
+ meta_iter != meta_mapping_.end(); ++meta_iter) {
+ peps_vector.push_back((*meta_iter));
+ }
+
+
+ // greedy algorithm to pick off the meta proteins with
+ // most peptide mappings
+ while (!peps_vector.empty()) {
+ sort(peps_vector.begin(), peps_vector.end(), setsAreEqualSize);
+ pair<PeptideSet, MetaProtein> node = peps_vector.back();
+ peps_vector.pop_back();
+ if (node.first.size() == 0) { break; }// do not enter anything without peptide sizes
+ result.insert(node);
+ PeptideSet cur_peptides = node.first;
+ // update the peptide sets for the rest of meta proteins
+ for (vector< pair<PeptideSet, MetaProtein > >::iterator
+ iter = peps_vector.begin();
+ iter != peps_vector.end(); ++iter) {
+ PeptideSet peptides = (*iter).first;
+ PeptideSet difference(Peptide::lessThan);
+ set_difference(peptides.begin(), peptides.end(),
+ cur_peptides.begin(), cur_peptides.end(),
+ inserter(difference, difference.end()),
+ Peptide::lessThan);
+ (*iter).first = difference;
+ }
+ }
+ meta_mapping_ = result;
+}
+
+/**
+ * Removes peptides from the map if the peptide
+ * sequence belongs in more than one protein
+ */
+void SpectralCounts::makeUniqueMapping() {
+
+ if (measure_ == MEASURE_DNSAF) {
+ carp(CARP_WARNING, "--unique-mapping ignored for dNSAF!");
+ } else {
+ carp(CARP_DEBUG, "Filtering peptides that have more"
+ "than one protein source");
+ for (PeptideToScore::iterator it = peptide_scores_.begin();
+ it != peptide_scores_.end(); ++it) {
+ Peptide* peptide = it->first;
+ int num_proteins = peptide->getNumPeptideSrc();
+ if (num_proteins > 1) {
+ peptide_scores_.erase(it);
+ }
+ }
+ }
+}
+
+
+/**
+ * \returns The name of the command.
+ */
+string SpectralCounts::getName() const {
+ return "spectral-counts";
+}
+
+/**
+ * \returns The help string to be included in the crux usage statement.
+ */
+string SpectralCounts::getDescription() const {
+ return
+ "[[nohtml:Quantify peptides or proteins using one of three spectral "
+ "counting methods.]]"
+ "[[html:<p>Given a collection of scored PSMs, produce a list of proteins "
+ "or peptides ranked by a quantification score. Spectral-counts supports "
+ "four types of quantification: Normalized Spectral Abundance Factor "
+ "(NSAF), Distributed Normalized Spectral Abundance (dNSAF), Normalized "
+ "Spectral Index (SI<sub>N</sub>) and Exponentially Modified Protein "
+ "Abundance Index (emPAI). The NSAF method is from <a href=\""
+ "http://www.ncbi.nlm.nih.gov/pubmed/17138671\">Paoletti et "
+ "al. (2006)</a>. The SI<sub>N</sub> method is from <a href=\""
+ "http://www.nature.com/nbt/journal/v28/n1/abs/nbt.1592.html\">Griffin et "
+ "al. (2010)</a>. The emPAI method was first described in <a href=\""
+ "http://www.mcponline.org/content/4/9/1265\">Ishihama et al (2005)</a>. "
+ "The quantification methods are defined below and in the following "
+ "paper:<blockquote>S McIlwain, M Mathews, M Bereman, EW Rubel, MJ "
+ "MacCoss, and WS Noble. "
+ "<a href=\"http://www.biomedcentral.com/1471-2105/13/308/abstract\">"
+ "\"Estimating relative abundances of proteins from shotgun proteomics "
+ "data.\"</a> <em>BMC Bioinformatics</em>. 13:308, 2012.</blockquote>"
+ "</p><h3>Protein Quantification</h3>"
+ "<ol><li>For each protein in a given database, the NSAF "
+ "score is:<br>$$NSAF_N=\\frac{S_N/L_N}{\\sum_{i=1}^ns_i/L_i}$$<br>where:"
+ "<ul><li>N is protein index</li><li>S<sub>N</sub> is the number of peptide "
+ "spectra matched to the protein</li><li>L<sub>N</sub> is the length of "
+ "protein N</li><li>n is the total number of proteins in the input "
+ "database</li></ul></li><li>For each protein in a given database, the dNSAF "
+ "score is:<br>$$NSAF_N=\\frac{\\frac{uSpc_N+(d)sSpc_N}{uL_N+sL_N}}{\\frac"
+ "{uSpc_i+(d)sSpc_i}{uL_i+sL_i}}$$<br>where:<ul><li>N is the protein "
+ "index</li><li>uSpc<sub>N</sub> is the unique number spectra matched to the "
+ "protein index</li><li>sSpc<sub>N</sub> is the shared number peptide "
+ "spectra matched to the protein index</li><li>L<sub>N</sub> is the length "
+ "of protein N</li><li>n is the total number of proteins in the input "
+ "database</li><li>d is the distribution factor of peptide K to protein N, "
+ "given by<br>$$d=\\frac{uSpc_N}{\\sum_{i=1}^nuSpc_i}$$</li></ul></li><li>"
+ "For each protein in a given database, the SI<sub>N</sub> score is:<br>"
+ "$$SI_N=\\frac{\\sum_{j=1}^{p_N}(\\sum_{k=1}^{s_j}i_k)}{L_N(\\sum_{j=1}^n"
+ "SI_j)}$$<br>where:<ul><li>N is protein index</li><li>p<sub>n</sub> is the "
+ "number of unique peptides in protein N</li><li>s<sub>j</sub> is the "
+ "number of spectra assigned to peptide j</li><li>i<sub>k</sub> is the "
+ "total fragment ion intensity of spectrum k</li><li>L<sub>N</sub> is the "
+ "length of protein N</li></ul></li><li>For each protein in a given database, "
+ "the emPAI score is:<br>$$emPAI=10^{\\frac{N_{observed}}{N_{observable}}}-1"
+ "$$<br>where:<ul><li>N<sub>observed</sub> is the number of experimentally "
+ "observed peptides with scores above a specified threshold.</li><li>N<sub>"
+ "observable</sub> is the calculated number of observable peptides for the "
+ "protein given the search constraints.</li></ul></li></ol><h3>Peptide "
+ "Quantification</h3><ol><li>For each peptide in a given database, the NSAF "
+ "score is:<br>$$NSAF_N=\\frac{S_N/L_N}{\\sum_{i=1}^ns_i/L_i}$$<br>where: "
+ "<ul><li>N is the peptide index</li><li>S<sub>N</sub> is the number "
+ "spectra matched to peptide N</li><li>L<sub>N</sub> is the length of "
+ "peptide N</li><li>n is the total number of peptides in the input "
+ "database</li></ul></li><li>For each peptide in a given database, the "
+ "SI<sub>N</sub> score is:<br>$$SI_N=\\frac{(\\sum_{k=1}^{S_N}i_k)}{L_N("
+ "\\sum_{j=1}^nSI_J)}$$<br>where:<ul><li>N is the peptide index</li><li>"
+ "S<sub>N</sub> is the number of spectra assigned to peptide N</li><li>"
+ "i<sub>k</sub> is the total fragment ion intensity of spectrum k</li><li>"
+ "L<sub>N</sub> is the length of peptide N</li></ul></li></ol>]]";
+}
+
+vector<string> SpectralCounts::getArgs() const {
+ string arr[] = {
+ "input PSMs"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> SpectralCounts::getOptions() const {
+ string arr[] = {
+ "verbosity",
+ "parameter-file",
+ "parsimony",
+ "threshold",
+ "threshold-type",
+ "input-ms2",
+ "spectrum-parser",
+ "fileroot",
+ "output-dir",
+ "overwrite",
+ "unique-mapping",
+ "quant-level",
+ "measure",
+ "custom-threshold-name",
+ "custom-threshold-min",
+ "mzid-use-pass-threshold",
+ "protein-database"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > SpectralCounts::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("spectral-counts.target.txt",
+ "a tab-delimited text file containing the protein IDs and their "
+ "corresponding scores, in sorted order."));
+ outputs.push_back(make_pair("spectral-counts.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other Crux programs."));
+ outputs.push_back(make_pair("spectral-counts.log.txt",
+ "All messages written to standard error."));
+ return outputs;
+}
+
+COMMAND_T SpectralCounts::getCommand() const {
+ return SPECTRAL_COUNTS_COMMAND;
+}
+
+bool SpectralCounts::needsOutputDirectory() const {
+ return true;
+}
+
+
+// static comparison functions
+
+/**
+ * Compare two sets of peptides and return true if the first unshared
+ * peptide sequence in set one is lexically less than that in set
+ * two.
+ */
+bool SpectralCounts::comparePeptideSets(PeptideSet set_one,
+ PeptideSet set_two) {
+
+ // compare each peptides in the two (sorted) sets
+ PeptideSet::iterator iter1 = set_one.begin();
+ PeptideSet::iterator iter2 = set_two.begin();
+
+ while( iter1 != set_one.end() && iter2 != set_two.end() ) {
+ int diff = Peptide::triCompareSequence(*iter1, *iter2);
+ if (diff != 0) {
+ return diff < 0;
+ }
+ // else they are equal, compare the next
+ ++iter1;
+ ++iter2;
+ }
+
+ // all peptides were the same; are the sets the same size?
+ return set_one.size() < set_two.size();
+}
+
+/**
+ * Comparison function for MetaProteins. MetaProtein one is less than
+ * MetaProtein two if the first non-matching protein id of one is less than
+ * that of two.
+ * \returns True if one < two, false if one == two or one > two.
+ */
+bool SpectralCounts::compareMetaProteins(MetaProtein set_one,
+ MetaProtein set_two) {
+ // compare each protein in the two (sorted) sets
+ MetaProtein::iterator iter1 = set_one.begin();
+ MetaProtein::iterator iter2 = set_two.begin();
+
+ while (iter1 != set_one.end() && iter2 != set_two.end()) {
+ // different proteins one is less than the other
+ if (protein_id_less_than(*iter1, *iter2)) {
+ return true;
+ }
+ // else, they are the same, keep comparing
+ ++iter1;
+ ++iter2;
+ }
+
+ // all proteins were the same, are the sets the same size?
+ return set_one.size() < set_two.size();
+}
+
+/**
+ * Compare the size of the PeptideSets in the two given pairs.
+ * \returns True if the PeptideSets are the same size, else false.
+ */
+bool SpectralCounts::setsAreEqualSize(
+ const pair<PeptideSet, MetaProtein>& peps_one ,
+ const pair<PeptideSet, MetaProtein>& peps_two) {
+ return ((peps_one).first.size() < (peps_two).first.size());
+}
+
+bool SpectralCounts::compareMetaScorePair(
+ const std::pair<FLOAT_T, MetaProtein>& x,
+ const std::pair<FLOAT_T, MetaProtein>& y) {
+ return (x.first != y.first) ? x.first > y.first : !compareMetaProteins(x.second, y.second);
+}
+
diff --git a/src/app/SpectralCounts.h b/src/app/SpectralCounts.h
new file mode 100644
index 0000000..aa2ab00
--- /dev/null
+++ b/src/app/SpectralCounts.h
@@ -0,0 +1,189 @@
+/**
+ * \file SpectralCounts.h
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: 8 March 2011
+ * \brief Object for running the spectral-counts command.
+ */
+#ifndef SPECRAL_COUNTS_H
+#define SPECRAL_COUNTS_H
+
+#include "CruxApplication.h"
+#include <string>
+#include <vector>
+#include <map>
+#include <set>
+#include "util/utils.h"
+#include "io/MatchCollectionParser.h"
+#include "model/objects.h"
+#include "model/Peptide.h"
+#include "io/SpectrumCollection.h"
+#include "io/OutputFiles.h"
+
+#include "boost/tuple/tuple.hpp"
+
+class SpectralCounts: public CruxApplication {
+
+ public:
+
+ SpectralCounts();
+ ~SpectralCounts();
+ virtual int main(int argc, char** argv);
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+ virtual COMMAND_T getCommand() const;
+ virtual bool needsOutputDirectory() const;
+
+ private:
+ // internally-used types
+ /**
+ * \typedef PeptideSet
+ * \brief Collection of peptide objects (not a meta-peptide)
+ */
+ typedef std::set<Crux::Peptide*, bool(*)(Crux::Peptide*, Crux::Peptide*)> PeptideSet;
+ /**
+ * \typedef MetaMapping
+ * \brief Mapping of peptideSet to MetaProtein
+ * Each entry is a set of peptides mapped to a set of proteins of which
+ * all contain the set of peptides
+ */
+ typedef std::map<PeptideSet, MetaProtein,
+ bool(*)(PeptideSet, PeptideSet) > MetaMapping;
+ /**
+ * \typedef ProteinToPeptides
+ * Mapping of Protein objects to a set of peptides that are part
+ * of the protein sequence
+ */
+ typedef std::map<Crux::Protein*, PeptideSet ,
+ bool(*)(Crux::Protein*, Crux::Protein*)> ProteinToPeptides;
+ /**
+ * \typedef MetaToScore
+ * \brief Mapping of MetaProtein to the score assigned to it
+ */
+ typedef std::map<MetaProtein, FLOAT_T,
+ bool(*)(MetaProtein, MetaProtein)> MetaToScore;
+ /**
+ * \typedef ProteinToMeta
+ * \brief Mapping of Protein to MetaProtein to which it belongs
+ */
+ typedef std::map<Crux::Protein*, MetaProtein,
+ bool(*)(Crux::Protein*, Crux::Protein*)> ProteinToMetaProtein;
+
+ // private functions
+ void getParameterValues();
+ void filterMatches();
+ void getPeptideScores();
+
+ /**
+ * calculates the protein scores based upon the dNSAF metric. First,
+ * the spectral counts for the peptides unique to each protein is added,
+ * then the spectral counts for the peptide shared amongst the proteins
+ * are added with a distribution factor based upon the number of unique
+ * counts that each protein is assigned
+ */
+ void getProteinScoresDNSAF();
+
+ void getProteinScores();
+ void getProteinToPeptides();
+ void getProteinToMetaProtein();
+ void getMetaMapping();
+ void getMetaRanks();
+ void getMetaScores();
+ void performParsimonyAnalysis();
+ void normalizePeptideScores();
+ void normalizeProteinScores();
+ /**
+ * Checks that the normalized scores add up to one
+ */
+ void checkProteinNormalization();
+
+ void computeEmpai();
+ void makeUniqueMapping();
+ FLOAT_T sumMatchIntensity(Crux::Match* match,
+ Crux::SpectrumCollection* spectra);
+ SCORER_TYPE_T get_qval_type(MatchCollection* match_collection);
+
+ void writeRankedPeptides();
+ void writeRankedProteins();
+ static bool sortRankedPeptides(
+ const std::pair<FLOAT_T, Crux::Peptide*>& x,
+ const std::pair<FLOAT_T, Crux::Peptide*>& y);
+ static bool sortRankedProteins(
+ const boost::tuple<FLOAT_T, Crux::Protein*, int>& x,
+ const boost::tuple<FLOAT_T, Crux::Protein*, int>& y);
+
+ /**
+ * adds all matches
+ */
+ void filterMatchesNone();
+
+ /**
+ * filters matches based upon a custom threshold (not q-value)
+ */
+ void filterMatchesCustom();
+
+ /**
+ * filters matches based upon q-value
+ */
+ void filterMatchesQValue();
+
+ /**
+ * filters matches based upon a SCORER_TYPE_T
+ */
+ void filterMatchesScore(
+ SCORER_TYPE_T scorer ///< scorer to use
+ );
+
+ /**
+ * filters matches based upon a custom score that is not SCORER_TYPE_T
+ */
+ void filterMatchesCustomScore();
+
+ void invalidCustomScore();
+
+ // member variables
+ OutputFiles* output_;
+ std::string psm_file_;
+ FLOAT_T threshold_;
+ std::string database_name_;
+ bool unique_mapping_;
+ THRESHOLD_T threshold_type_;
+ QUANT_LEVEL_TYPE_T quantitation_;
+ PARSIMONY_TYPE_T parsimony_;
+ MEASURE_TYPE_T measure_;
+ FLOAT_T bin_width_;
+ std::set<Crux::Match*> matches_;
+ MatchCollection* match_collection_;
+ // For custom thresholding fields
+ bool threshold_min_;
+ std::string custom_threshold_name_;
+ MatchCollectionParser parser_;
+
+ PeptideToScore peptide_scores_;
+ PeptideToScore peptide_scores_unique_;
+ PeptideToScore peptide_scores_shared_;
+
+ ProteinToScore protein_scores_;
+ ProteinToScore protein_scores_unique_;
+ ProteinToScore protein_scores_shared_;
+
+ ProteinToPeptides protein_supporting_peptides_;
+ ProteinToMetaProtein protein_meta_protein_;
+ MetaMapping meta_mapping_;
+ MetaToScore meta_protein_scores_;
+ MetaToRank meta_protein_ranks_;
+
+ // comparison function declarations
+ static bool comparePeptideSets(PeptideSet, PeptideSet);
+ static bool compareMetaProteins(MetaProtein, MetaProtein);
+ static bool setsAreEqualSize(const std::pair<PeptideSet, MetaProtein>&,
+ const std::pair<PeptideSet, MetaProtein>&);
+ static bool compareMetaScorePair(const std::pair<FLOAT_T, MetaProtein>&,
+ const std::pair<FLOAT_T, MetaProtein>&);
+
+}; // class
+
+
+#endif
diff --git a/src/app/StatColumn.cpp b/src/app/StatColumn.cpp
new file mode 100644
index 0000000..7fb1a2b
--- /dev/null
+++ b/src/app/StatColumn.cpp
@@ -0,0 +1,178 @@
+/**
+ * \file StatColumn.cpp
+ * \brief Given a delimited file and a column-name, print out statistics
+ * for that column (n, min, max, sum, average, stddev, median).
+ *****************************************************************************/
+#include "StatColumn.h"
+
+#include "io/DelimitedFile.h"
+#include "util/Params.h"
+
+using namespace std;
+
+
+/**
+ * \returns a blank StatColumn object
+ */
+StatColumn::StatColumn() {
+
+}
+
+/**
+ * Destructor
+ */
+StatColumn::~StatColumn() {
+}
+
+/**
+ * main method for StatColumn
+ */
+int StatColumn::main(int argc, char** argv) {
+ delimited_filename_ = Params::GetString("tsv file");
+ column_name_string_ = Params::GetString("column name");
+ delimiter_ = get_delimiter_parameter("delimiter");
+
+ DelimitedFileReader delimited_file(delimited_filename_, true, delimiter_);
+
+ int col_idx = delimited_file.findColumn(column_name_string_);
+
+ if (col_idx == -1) {
+ carp(CARP_ERROR, "column not found:%s\n\n%s",
+ column_name_string_.c_str(),
+ delimited_file.getAvailableColumnsString().c_str());
+ return(-1);
+ }
+
+ vector<FLOAT_T> data;
+
+ FLOAT_T sum = 0;
+
+ while (delimited_file.hasNext()) {
+
+ FLOAT_T current = delimited_file.getFloat(col_idx);
+ data.push_back(current);
+ sum += current;
+ delimited_file.next();
+
+ }
+
+ sort(data.begin(), data.end(), less<FLOAT_T>());
+
+ unsigned int num_points = data.size();
+
+ FLOAT_T min = data.front();
+ FLOAT_T max = data.back();
+
+ FLOAT_T average = sum / (FLOAT_T)num_points;
+
+ FLOAT_T std_dev = 0.0;
+
+ if (num_points >= 2) {
+
+ for (unsigned int idx = 0 ; idx < num_points ; idx++) {
+ FLOAT_T temp = data.at(idx) - average;
+ std_dev += temp * temp;
+ }
+ std_dev = std_dev / (1.0 / (double)(num_points - 1));
+ std_dev = sqrt(std_dev);
+ }
+
+
+
+
+ FLOAT_T median = 0.0;
+
+ if (data.size() == 0) {
+ carp(CARP_WARNING, "Warning no data!");
+ } else {
+ int half = data.size() / 2;
+ if (data.size() % 2 == 0) {
+ median = (data[half] + data[half-1]) / 2.0;
+ } else {
+ median = data[half];
+ }
+ }
+
+ //print out the header
+
+ if (header_) {
+ cout << "N\tMin\tMax\tSum\tAverage\tStdDev\tMedian" << endl;
+ }
+
+ cout << std::setprecision(Params::GetInt("precision"));
+ cout << num_points << delimiter_;
+ cout << min << delimiter_;
+ cout << max << delimiter_;
+ cout << sum << delimiter_;
+ cout << average << delimiter_;
+ if (num_points >= 2) {
+ cout << std_dev << delimiter_;
+ } else {
+ cout << "N/A" << delimiter_;
+ }
+ cout << median << endl;
+
+ return 0;
+}
+
+/**
+ * \returns the command name for StatColumn
+ */
+string StatColumn::getName() const {
+ return "stat-column";
+}
+
+/**
+ * \returns the description for StatColumn
+ */
+string StatColumn::getDescription() const {
+ return
+ "[[nohtml:Collect summary statistics from a column in a tab-delimited "
+ "file.]]"
+ "[[html:<p>Given a tab-delimited file, collect summary statistics on the "
+ "values within a specified column. The specified column must contain "
+ "numeric values.</p>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> StatColumn::getArgs() const {
+ string arr[] = {
+ "tsv file",
+ "column name"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> StatColumn::getOptions() const {
+ string arr[] = {
+ "delimiter",
+ "header",
+ "precision",
+ "verbosity"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > StatColumn::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "The program prints to standard output the following statistics for "
+ "the specified column: number of rows, minimum, maximum, sum, average, "
+ "and median of the data values."));
+ return outputs;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/StatColumn.h b/src/app/StatColumn.h
new file mode 100644
index 0000000..9113774
--- /dev/null
+++ b/src/app/StatColumn.h
@@ -0,0 +1,77 @@
+/**
+ * \file StatColumn.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Given a delimited file and a column-name, print out statistics
+ * for that column (n, min, max, sum, average, median).
+ *****************************************************************************/
+#ifndef STATCOLUMN_H
+#define STATCOLUMN_H
+
+#include "CruxApplication.h"
+#include "io/DelimitedFileReader.h"
+
+#include <string>
+
+class StatColumn: public CruxApplication {
+
+ protected:
+ std::string delimited_filename_;
+ std::string column_name_string_;
+ char delimiter_;
+ bool header_;
+
+
+ public:
+
+ /**
+ * \returns a blank StatColumn object
+ */
+ StatColumn();
+
+ /**
+ * Destructor
+ */
+ ~StatColumn();
+
+ /**
+ * main method for StatColumn
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for StatColumn
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for StatColumn
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/SubtractIndexApplication.cpp b/src/app/SubtractIndexApplication.cpp
new file mode 100755
index 0000000..f42f19a
--- /dev/null
+++ b/src/app/SubtractIndexApplication.cpp
@@ -0,0 +1,288 @@
+/**
+ * \file SubtractIndexApplication.cpp
+ * \brief Iterative PSM meta-search via Cascade protocol
+ ************************************************************/
+#include "SubtractIndexApplication.h"
+#include "io/OutputFiles.h"
+#include "AssignConfidenceApplication.h"
+#include "TideSearchApplication.h"
+#include "TideIndexApplication.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "util/FileUtils.h"
+#include "io/carp.h"
+#include "app/tide/abspath.h"
+#include "app/tide/records_to_vector-inl.h"
+
+#define CHECK(x) GOOGLE_CHECK(x)
+
+using namespace std;
+
+/**
+ * \returns a blank SubtractIndexApplication object
+ */
+SubtractIndexApplication::SubtractIndexApplication() {
+}
+
+/**
+ * Destructor
+ */
+SubtractIndexApplication::~SubtractIndexApplication() {
+}
+
+/**
+ * main method for SubtractIndexApplication
+ */
+int SubtractIndexApplication::main(int argc, char** argv) {
+ carp(CARP_INFO, "Running subtract-index...");
+
+ bool overwrite = Params::GetBool("overwrite");
+ bool has_decoys = false;
+
+ //open tide index 1
+ const string index1 = Params::GetString("tide index 1");
+ bool write_peptides = FileUtils::Exists(index1 + "/tide-index.peptides.target.txt");
+ string peptides_file1 = index1 + "/pepix";
+ string proteins_file1 = index1 + "/protix";
+ string auxlocs_file1 = index1 + "/auxlocs";
+
+ carp(CARP_INFO, "Reading index %s", index1.c_str());
+ ProteinVec proteins1;
+ pb::Header protein_header1;
+ if (!ReadRecordsToVector<pb::Protein, const pb::Protein>(&proteins1,
+ proteins_file1, &protein_header1)) {
+ carp(CARP_FATAL, "Error reading index (%s)", proteins_file1.c_str());
+ }
+ carp(CARP_DEBUG, "Read %d proteins", proteins1.size());
+
+ pb::Header peptides_header1;
+ HeadedRecordReader peptide_reader1(peptides_file1, &peptides_header1);
+ if (peptides_header1.file_type() != pb::Header::PEPTIDES ||
+ !peptides_header1.has_peptides_header()) {
+ carp(CARP_FATAL, "Error reading index (%s)", peptides_file1.c_str());
+ }
+ const pb::Header::PeptidesHeader& pepHeader1 = peptides_header1.peptides_header();
+ DECOY_TYPE_T headerDecoyType = (DECOY_TYPE_T)pepHeader1.decoys();
+ if (headerDecoyType != NO_DECOYS) {
+ has_decoys = true;
+ if (headerDecoyType == PROTEIN_REVERSE_DECOYS) {
+ TideSearchApplication::PROTEIN_LEVEL_DECOYS = true;
+ }
+ }
+ MassConstants::Init(&peptides_header1.peptides_header().mods(),
+ &peptides_header1.peptides_header().nterm_mods(),
+ &peptides_header1.peptides_header().cterm_mods(), 0.0, 0.0);
+
+ //open tide index 2
+ const string index2 = Params::GetString("tide index 2");
+ string peptides_file2 = index2 + "/pepix";
+ string proteins_file2 = index2 + "/protix";
+ carp(CARP_INFO, "Reading index %s", index2.c_str());
+ pb::Header peptides_header2;
+ HeadedRecordReader peptide_reader2(peptides_file2, &peptides_header2);
+ ProteinVec proteins2;
+ pb::Header protein_header2;
+ if (!ReadRecordsToVector<pb::Protein, const pb::Protein>(&proteins2,
+ proteins_file2, &protein_header2)) {
+ carp(CARP_FATAL, "Error reading index (%s)", proteins_file2.c_str());
+ }
+ carp(CARP_DEBUG, "Read %d proteins", proteins2.size());
+
+ //output files;
+ const string index_out = Params::GetString("output index");
+ string out_proteins = index_out + "/" + "protix";
+ string out_peptides = index_out + "/" + "pepix";
+ string out_aux = index_out + "/" + "auxlocs";
+
+ if (create_output_directory(index_out.c_str(), overwrite) != 0) {
+ carp(CARP_FATAL, "Error creating index directory");
+ } else if (FileUtils::Exists(out_proteins) ||
+ FileUtils::Exists(out_peptides) ||
+ FileUtils::Exists(out_aux)) {
+ if (overwrite) {
+ carp(CARP_DEBUG, "Cleaning old index file(s)");
+ remove(out_proteins.c_str());
+ remove(out_peptides.c_str());
+ remove(out_aux.c_str());
+ } else {
+ carp(CARP_FATAL, "Index file(s) already exist, use --overwrite T or a "
+ "different index name");
+ }
+ }
+ ofstream* out_target_list = NULL;
+ ofstream* out_decoy_list = NULL;
+ if (write_peptides) {
+ out_target_list = create_stream_in_path(make_file_path(
+ "tide-index.peptides.target.txt").c_str(), NULL, overwrite);
+ if (has_decoys) {
+ out_decoy_list = create_stream_in_path(make_file_path(
+ "tide-index.peptides.decoy.txt").c_str(), NULL, overwrite);
+ }
+ }
+ //copy aux and protein files;
+ FileUtils::Copy(auxlocs_file1, out_aux);
+ FileUtils::Copy(proteins_file1, out_proteins);
+
+ pb::Header new_header;
+ CHECK(peptides_header1.file_type() == pb::Header::PEPTIDES);
+ CHECK(peptides_header1.has_peptides_header());
+ new_header.set_file_type(pb::Header::PEPTIDES);
+ pb::Header_PeptidesHeader* subheader = new_header.mutable_peptides_header();
+ subheader->CopyFrom(peptides_header1.peptides_header());
+ subheader->set_has_peaks(true);
+ pb::Header_Source* source = new_header.add_source();
+ source->mutable_header()->CopyFrom(peptides_header1);
+ HeadedRecordWriter writer(out_peptides, new_header);
+ CHECK(peptide_reader1.OK());
+ CHECK(peptide_reader2.OK());
+ CHECK(writer.OK());
+
+ pb::Peptide pb_peptide1, pb_peptide2;
+ double pep_mass1, pre_pep_mass1, pep_mass2, pre_pep_mass2;
+ string pep_str1, pep_str2;
+
+ vector<pb::Peptide> peptide_container;
+ pep_mass2 = pre_pep_mass2 = 0.0;
+ pre_pep_mass1 = 0.0;
+ bool found;
+
+ while (!peptide_reader1.Done()) {
+ peptide_reader1.Read(&pb_peptide1);
+ pep_mass1 = pb_peptide1.mass();
+ found = false;
+
+ if (pre_pep_mass1 < pep_mass1) {
+ peptide_container.clear();
+ pre_pep_mass1 = pep_mass1;
+ }
+
+ while (pep_mass2 < pep_mass1) {
+ if (!peptide_reader2.Done()) {
+ peptide_reader2.Read(&pb_peptide2);
+ pep_mass2 = pb_peptide2.mass();
+ } else {
+ break;
+ }
+ }
+ while (pep_mass2 == pep_mass1) {
+ peptide_container.push_back(pb_peptide2);
+ if (!peptide_reader2.Done()) {
+ peptide_reader2.Read(&pb_peptide2);
+ pep_mass2 = pb_peptide2.mass();
+ } else {
+ break;
+ }
+ }
+ pep_str1 = getModifiedPeptideSeq(&pb_peptide1, &proteins1);
+ for (vector<pb::Peptide>::iterator it = peptide_container.begin(); it != peptide_container.end(); ++it) {
+ pep_str2 = getModifiedPeptideSeq(&(*it), &proteins2);
+ if (pep_str1 == pep_str2) {
+ found = true;
+ break;
+ }
+ }
+ if (!found) {
+ CHECK(writer.Write(&pb_peptide1));
+ carp(CARP_DEBUG, "%s\t%lf\n", pep_str1.c_str(), pep_mass1);
+
+ if (write_peptides) {
+ if (!pb_peptide1.is_decoy()) {
+ *out_target_list << pep_str1 << '\t' << pb_peptide1.mass() << endl;
+ } else {
+ *out_decoy_list << pep_str1 << '\t' << pb_peptide1.mass() << endl;
+ }
+ }
+ }
+ }
+
+ return 0;
+}
+
+/**
+ * \returns the command name for SubtractIndexApplication
+ */
+string SubtractIndexApplication::getName() const {
+ return "subtract-index";
+}
+
+/**
+ * \returns the description for SubtractIndexApplication
+ */
+string SubtractIndexApplication::getDescription() const {
+ return "[[html:<p>This command takes two peptide indices, created by the tide-index "
+ "command, and subtracts the second index from the first. The result is an output "
+ "index that contains peptides that appear in the first index but not the second.</p>]]"
+ "[[nohtml:This command takes two peptide indices, created by the tide-index command, "
+ "and subtracts the second index from the first. The result is an output index "
+ "that contains peptides that appear in the first index but not the second.]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> SubtractIndexApplication::getArgs() const {
+ string arr[] = {
+ "tide index 1",
+ "tide index 2",
+ "output index"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+
+/**
+ * \returns the command options
+ */
+vector<string> SubtractIndexApplication::getOptions() const {
+ string arr[] = {
+ "verbosity",
+ "parameter-file",
+ "overwrite",
+ "peptide-list",
+ "output-dir"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > SubtractIndexApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("subtract-index.target.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited text file</a> containing the "
+ "target peptides."));
+ outputs.push_back(make_pair("subtract-index.decoy.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited text file</a> containing the "
+ "decoy peptides."));
+ outputs.push_back(make_pair("subtract-index.log.txt",
+ "a log file containing a copy of all messages that were printed to stderr."));
+ outputs.push_back(make_pair("subtract-index.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ return outputs;
+}
+
+/**
+ * \returns the filestem for SubtractIndexApplication
+ */
+string SubtractIndexApplication::getFileStem() const {
+ return "subtract-index";
+}
+
+COMMAND_T SubtractIndexApplication::getCommand() const {
+ return CASCADE_COMMAND;
+}
+
+/**
+ * \returns whether the application needs the output directory or not.
+ */
+bool SubtractIndexApplication::needsOutputDirectory() const {
+ return true;
+}
+
+void SubtractIndexApplication::processParams() {
+
+}
diff --git a/src/app/SubtractIndexApplication.h b/src/app/SubtractIndexApplication.h
new file mode 100755
index 0000000..6cdd921
--- /dev/null
+++ b/src/app/SubtractIndexApplication.h
@@ -0,0 +1,88 @@
+/**
+ * \file CascadeSearchApplication.h
+ * AUTHOR: Attila Kertesz-Farkas
+ * CREATE DATE: 30 May 2015
+ * \brief Iterative PSM meta-search via Cascade protocol
+ ***********************************************************/
+#ifndef SUBTRACTINDEXAPPLICATION_H
+#define SUBTRACTINDEXAPPLICATION_H
+
+#include "CruxApplication.h"
+#include "peptides.pb.h"
+#include "TideSearchApplication.h"
+#include <string>
+
+
+
+class SubtractIndexApplication: public CruxApplication {
+
+ public:
+
+ /**
+ * \returns a blank CascadeSearchApplication object
+ */
+ SubtractIndexApplication();
+
+ /**
+ * Destructor
+ */
+ ~SubtractIndexApplication();
+
+ /**
+ * main method for CascadeSearchApplication
+ */
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for CascadeSearchApplication
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for CascadeSearchApplication
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns the filestem for CascadeSearchApplication
+ */
+ virtual std::string getFileStem() const;
+
+ /**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+ virtual COMMAND_T getCommand() const;
+
+ /**
+ * \returns whether the application needs the output directory or not.
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual void processParams();
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/TideIndexApplication.cpp b/src/app/TideIndexApplication.cpp
new file mode 100644
index 0000000..065c067
--- /dev/null
+++ b/src/app/TideIndexApplication.cpp
@@ -0,0 +1,938 @@
+#include <cstdio>
+#include <fstream>
+#include "io/carp.h"
+#include "util/CarpStreamBuf.h"
+#include "util/AminoAcidUtil.h"
+#include "util/Params.h"
+#include "util/FileUtils.h"
+#include "util/StringUtils.h"
+#include "GeneratePeptides.h"
+#include "TideIndexApplication.h"
+#include "TideMatchSet.h"
+#include "app/tide/modifications.h"
+#include "app/tide/records_to_vector-inl.h"
+
+#ifdef _MSC_VER
+#include <io.h>
+#endif
+
+extern void AddTheoreticalPeaks(const vector<const pb::Protein*>& proteins,
+ const string& input_filename,
+ const string& output_filename);
+extern void AddMods(HeadedRecordReader* reader,
+ string out_file,
+ string tmpDir,
+ const pb::Header& header,
+ const vector<const pb::Protein*>& proteins, VariableModTable& var_mod_table);
+DECLARE_int32(max_mods);
+DECLARE_int32(min_mods);
+
+TideIndexApplication::TideIndexApplication() {
+}
+
+TideIndexApplication::~TideIndexApplication() {
+}
+
+int TideIndexApplication::main(int argc, char** argv) {
+ return main(Params::GetString("protein fasta file"),
+ Params::GetString("index name"),
+ StringUtils::Join(vector<string>(argv, argv + argc), ' '));
+}
+
+int TideIndexApplication::main(
+ const string& fasta,
+ const string& index,
+ string cmd_line
+) {
+ carp(CARP_INFO, "Running tide-index...");
+
+ if (cmd_line.empty()) {
+ cmd_line = "crux tide-index " + fasta + " " + index;
+ }
+
+ // Reroute stderr
+ CarpStreamBuf buffer;
+ streambuf* old = cerr.rdbuf();
+ cerr.rdbuf(&buffer);
+
+ // Get options
+ double min_mass = Params::GetDouble("min-mass");
+ double max_mass = Params::GetDouble("max-mass");
+ int min_length = Params::GetInt("min-length");
+ int max_length = Params::GetInt("max-length");
+ bool monoisotopic_precursor = Params::GetString("isotopic-mass") != "average";
+ FLAGS_max_mods = Params::GetInt("max-mods");
+ FLAGS_min_mods = Params::GetInt("min-mods");
+ bool allowDups = Params::GetBool("allow-dups");
+ if (FLAGS_min_mods > FLAGS_max_mods) {
+ carp(CARP_FATAL, "The value for 'min-mods' cannot be greater than the value "
+ "for 'max-mods'");
+ }
+ MASS_TYPE_T mass_type = (monoisotopic_precursor) ? MONO : AVERAGE;
+ int missed_cleavages = Params::GetInt("missed-cleavages");
+ DIGEST_T digestion = get_digest_type_parameter("digestion");
+ ENZYME_T enzyme_t = get_enzyme_type_parameter("enzyme");
+ const char* enzymePtr = enzyme_type_to_string(enzyme_t);
+ string enzyme(enzymePtr);
+ if ((enzyme != "no-enzyme") &&
+ (digestion != FULL_DIGEST && digestion != PARTIAL_DIGEST)) {
+ carp(CARP_FATAL, "'digestion' must be 'full-digest' or 'partial-digest'");
+ }
+
+ VariableModTable var_mod_table;
+ var_mod_table.ClearTables();
+ //parse regular amino acid modifications
+ string mods_spec = Params::GetString("mods-spec");
+ carp(CARP_DEBUG, "mods_spec='%s'", mods_spec.c_str());
+ if (!var_mod_table.Parse(mods_spec.c_str())) {
+ carp(CARP_FATAL, "Error parsing mods");
+ }
+ //parse terminal modifications
+ mods_spec = Params::GetString("cterm-peptide-mods-spec");
+ if (!mods_spec.empty() && !var_mod_table.Parse(mods_spec.c_str(), CTPEP)) {
+ carp(CARP_FATAL, "Error parsing c-terminal peptide mods");
+ }
+ mods_spec = Params::GetString("nterm-peptide-mods-spec");
+ if (!mods_spec.empty() && !var_mod_table.Parse(mods_spec.c_str(), NTPEP)) {
+ carp(CARP_FATAL, "Error parsing n-terminal peptide mods");
+ }
+ mods_spec = Params::GetString("cterm-protein-mods-spec");
+ if (!mods_spec.empty() && !var_mod_table.Parse(mods_spec.c_str(), CTPRO)) {
+ carp(CARP_FATAL, "Error parsing c-terminal protein mods");
+ }
+ mods_spec = Params::GetString("nterm-protein-mods-spec");
+ if (!mods_spec.empty() && !var_mod_table.Parse(mods_spec.c_str(), NTPRO)) {
+ carp(CARP_FATAL, "Error parsing n-terminal protein mods");
+ }
+
+ var_mod_table.SerializeUniqueDeltas();
+
+ if (!MassConstants::Init(var_mod_table.ParsedModTable(),
+ var_mod_table.ParsedNtpepModTable(),
+ var_mod_table.ParsedCtpepModTable(), 0, 0)) {
+ carp(CARP_FATAL, "Error in MassConstants::Init");
+ }
+
+ DECOY_TYPE_T decoy_type = get_tide_decoy_type_parameter("decoy-format");
+ string decoyPrefix = Params::GetString("decoy-prefix");
+
+ // Set up output paths
+ bool overwrite = Params::GetBool("overwrite");
+
+ if (!FileUtils::Exists(fasta)) {
+ carp(CARP_FATAL, "Fasta file %s does not exist", fasta.c_str());
+ }
+
+ string out_proteins = FileUtils::Join(index, "protix");
+ string out_peptides = FileUtils::Join(index, "pepix");
+ string out_aux = FileUtils::Join(index, "auxlocs");
+ string modless_peptides = out_peptides + ".nomods.tmp";
+ string peakless_peptides = out_peptides + ".nopeaks.tmp";
+ ofstream* out_target_list = NULL;
+ ofstream* out_decoy_list = NULL;
+ if (Params::GetBool("peptide-list")) {
+ out_target_list = create_stream_in_path(make_file_path(
+ "tide-index.peptides.target.txt").c_str(), NULL, overwrite);
+ if (decoy_type != NO_DECOYS) {
+ out_decoy_list = create_stream_in_path(make_file_path(
+ "tide-index.peptides.decoy.txt").c_str(), NULL, overwrite);
+ }
+ }
+ ofstream* out_decoy_fasta = GeneratePeptides::canGenerateDecoyProteins() ?
+ create_stream_in_path(make_file_path(
+ "tide-index.decoy.fasta").c_str(), NULL, overwrite) : NULL;
+
+ if (create_output_directory(index.c_str(), overwrite) != 0) {
+ carp(CARP_FATAL, "Error creating index directory");
+ } else if (FileUtils::Exists(out_proteins) ||
+ FileUtils::Exists(out_peptides) ||
+ FileUtils::Exists(out_aux)) {
+ if (overwrite) {
+ carp(CARP_DEBUG, "Cleaning old index file(s)");
+ FileUtils::Remove(out_proteins);
+ FileUtils::Remove(out_peptides);
+ FileUtils::Remove(out_aux);
+ FileUtils::Remove(modless_peptides);
+ FileUtils::Remove(peakless_peptides);
+ } else {
+ carp(CARP_FATAL, "Index file(s) already exist, use --overwrite T or a "
+ "different index name");
+ }
+ }
+
+ // Start tide-index
+ carp(CARP_INFO, "Reading %s and computing unmodified peptides...",
+ fasta.c_str());
+ pb::Header proteinPbHeader;
+ vector<TideIndexPeptide> peptideHeap;
+ vector<string*> proteinSequences;
+ fastaToPb(cmd_line, enzyme_t, digestion, missed_cleavages, min_mass, max_mass,
+ min_length, max_length, allowDups, mass_type, decoy_type, fasta, out_proteins,
+ proteinPbHeader, peptideHeap, proteinSequences, out_decoy_fasta);
+
+ pb::Header header_with_mods;
+
+ // Set up peptides header
+ pb::Header_PeptidesHeader& pep_header = *(header_with_mods.mutable_peptides_header());
+ pep_header.Clear();
+ pep_header.set_min_mass(min_mass);
+ pep_header.set_max_mass(max_mass);
+ pep_header.set_min_length(min_length);
+ pep_header.set_max_length(max_length);
+ pep_header.set_monoisotopic_precursor(monoisotopic_precursor);
+ pep_header.set_enzyme(enzyme);
+ if (enzyme != "no-enzyme") {
+ pep_header.set_full_digestion(digestion == FULL_DIGEST);
+ pep_header.set_max_missed_cleavages(missed_cleavages);
+ }
+ pep_header.mutable_mods()->CopyFrom(*(var_mod_table.ParsedModTable()));
+ pep_header.mutable_nterm_mods()->CopyFrom(*(var_mod_table.ParsedNtpepModTable()));
+ pep_header.mutable_cterm_mods()->CopyFrom(*(var_mod_table.ParsedCtpepModTable()));
+
+ header_with_mods.set_file_type(pb::Header::PEPTIDES);
+ header_with_mods.set_command_line(cmd_line);
+ pb::Header_Source* source = header_with_mods.add_source();
+ source->mutable_header()->CopyFrom(proteinPbHeader);
+ source->set_filename(AbsPath(out_proteins));
+
+ pb::Header header_no_mods;
+ header_no_mods.CopyFrom(header_with_mods);
+ pb::ModTable* del = header_no_mods.mutable_peptides_header()->mutable_mods();
+ del->mutable_variable_mod()->Clear();
+ del->mutable_unique_deltas()->Clear();
+
+ bool need_mods = var_mod_table.Unique_delta_size() > 0;
+
+ string basic_peptides = need_mods ? modless_peptides : peakless_peptides;
+ carp(CARP_DETAILED_DEBUG, "basic_peptides=%s", basic_peptides.c_str());
+
+ writePeptidesAndAuxLocs(peptideHeap, basic_peptides, out_aux, header_no_mods);
+ // Do some clean up
+ for (vector<string*>::iterator i = proteinSequences.begin();
+ i != proteinSequences.end();
+ ++i) {
+ delete *i;
+ }
+ vector<TideIndexPeptide>().swap(peptideHeap);
+ ProteinVec proteins;
+ if (!ReadRecordsToVector<pb::Protein>(&proteins, out_proteins)) {
+ carp(CARP_FATAL, "Error reading proteins file");
+ }
+
+ if (need_mods) {
+ carp(CARP_INFO, "Computing modified peptides...");
+ HeadedRecordReader reader(modless_peptides, NULL, 1024 << 10); // 1024kb buffer
+ AddMods(&reader, peakless_peptides, Params::GetString("temp-dir"), header_with_mods, proteins, var_mod_table);
+ }
+
+ if (out_target_list) {
+ // Write peptide lists
+ carp(CARP_INFO, "Writing peptide lists...");
+
+ // This set holds target peptide strings
+ set<string> targetPepStrs;
+ // This vector holds decoy peptide strings and masses
+ vector< pair<string, double> > decoyPepStrs;
+ // Read peptides protocol buffer file
+ vector<const pb::AuxLocation*> locations;
+ if (!ReadRecordsToVector<pb::AuxLocation>(&locations, out_aux)) {
+ carp(CARP_FATAL, "Error reading auxlocs file");
+ }
+ // Iterate over all protocol buffer peptides
+ unsigned int writeCountTargets = 0, writeCountDecoys = 0;
+ HeadedRecordReader reader(peakless_peptides, NULL);
+ while (!reader.Done()) {
+ pb::Peptide* protobuf = new pb::Peptide;
+ reader.Read(protobuf);
+ pb::Peptide* peptide = protobuf;
+ bool writeTarget = true;
+ bool writeDecoy = false;
+
+ if (out_decoy_list) {
+ writeDecoy = peptide->is_decoy();
+ writeTarget = !writeDecoy;
+ }
+ string pep_str = getModifiedPeptideSeq(peptide, &proteins);
+
+ if (writeTarget) {
+ // This is a target, output it
+ targetPepStrs.insert(pep_str);
+ *out_target_list << pep_str << '\t' << peptide->mass() << endl;
+ ++writeCountTargets;
+ }
+ if (writeDecoy) {
+ // This is a decoy, save it to output later
+ decoyPepStrs.push_back(make_pair(pep_str, peptide->mass()));
+ ++writeCountDecoys;
+ }
+ delete peptide;
+ }
+
+ // Iterate over saved decoys and output them
+ for (vector< pair<string, double> >::iterator i = decoyPepStrs.begin();
+ i != decoyPepStrs.end();
+ ++i) {
+ *out_decoy_list << i->first << '\t' << i->second;
+ if (targetPepStrs.find(i->first) != targetPepStrs.end()) {
+ *out_decoy_list << "\t*";
+ }
+ *out_decoy_list << endl;
+ }
+
+ // Close and clean up streams
+ if (out_decoy_list) {
+ out_decoy_list->close();
+ delete out_decoy_list;
+ }
+ out_target_list->close();
+ delete out_target_list;
+
+ carp(CARP_DEBUG, "Wrote %d targets and %d decoys to peptide list",
+ writeCountTargets, writeCountDecoys);
+ }
+
+ carp(CARP_INFO, "Precomputing theoretical spectra...");
+ AddTheoreticalPeaks(proteins, peakless_peptides, out_peptides);
+
+ // Clean up
+ for (vector<const pb::Protein*>::iterator i = proteins.begin();
+ i != proteins.end();
+ ++i) {
+ delete *i;
+ }
+
+ // clean up out_decoy_fasta
+ if (out_decoy_fasta) {
+ delete out_decoy_fasta;
+ }
+
+ // Recover stderr
+ cerr.rdbuf(old);
+ FileUtils::Remove(modless_peptides);
+ FileUtils::Remove(peakless_peptides);
+
+ return 0;
+}
+
+string TideIndexApplication::getName() const {
+ return "tide-index";
+}
+
+string TideIndexApplication::getDescription() const {
+ return
+ "[[nohtml:Create an index for all peptides in a fasta file, for use in "
+ "subsequent calls to tide-search.]]"
+ "[[html:<p>Tide is a tool for identifying peptides from tandem mass "
+ "spectra. It is an independent reimplementation of the SEQUEST<sup>®"
+ "</sup> algorithm, which assigns peptides to spectra by comparing the "
+ "observed spectra to a catalog of theoretical spectra derived from a "
+ "database of known proteins. Tide's primary advantage is its speed. Our "
+ "published paper provides more detail on how Tide works. If you use Tide "
+ "in your research, please cite:</p><blockquote>Benjamin J. Diament and "
+ "William Stafford Noble. "<a href=\""
+ "http://dx.doi.org/10.1021/pr101196n\">Faster SEQUEST Searching for "
+ "Peptide Identification from Tandem Mass Spectra.</a>" <em>Journal of "
+ "Proteome Research</em>. 10(9):3871-9, 2011.</blockquote><p>The <code>"
+ "tide-index</code> command performs an optional pre-processing step on the "
+ "protein database, converting it to a binary format suitable for input to "
+ "the <code>tide-search</code> command.</p><p>Tide considers only the "
+ "standard set of 20 amino acids. Peptides containing non-amino acid "
+ "alphanumeric characters (BJOUXZ) are skipped. Non-alphanumeric characters "
+ "are ignored completely.</p>]]";
+}
+
+vector<string> TideIndexApplication::getArgs() const {
+ string arr[] = {
+ "protein fasta file",
+ "index name"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> TideIndexApplication::getOptions() const {
+ string arr[] = {
+ "decoy-format",
+ "keep-terminal-aminos",
+ "decoy-prefix",
+ "enzyme",
+ "custom-enzyme",
+ "digestion",
+ "missed-cleavages",
+ "max-length",
+ "max-mass",
+ "min-length",
+ "min-mass",
+ "isotopic-mass",
+ "mods-spec",
+ "cterm-peptide-mods-spec",
+ "nterm-peptide-mods-spec",
+ "max-mods",
+ "min-mods",
+ "output-dir",
+ "overwrite",
+ "peptide-list",
+ "parameter-file",
+ "seed",
+ "clip-nterm-methionine",
+ "verbosity",
+ "allow-dups",
+ "temp-dir"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > TideIndexApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("index",
+ "A binary index, using the name specified on the command line."));
+ outputs.push_back(make_pair("tide-index.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("tide-index.log.txt",
+ "a log file containing a copy of all messages that were printed to the "
+ "screen during execution."));
+ return outputs;
+}
+
+bool TideIndexApplication::needsOutputDirectory() const {
+ return true;
+}
+
+COMMAND_T TideIndexApplication::getCommand() const {
+ return TIDE_INDEX_COMMAND;
+}
+
+void TideIndexApplication::fastaToPb(
+ const string& commandLine,
+ const ENZYME_T enzyme,
+ const DIGEST_T digestion,
+ int missedCleavages,
+ FLOAT_T minMass,
+ FLOAT_T maxMass,
+ int minLength,
+ int maxLength,
+ bool allowDups,
+ MASS_TYPE_T massType,
+ DECOY_TYPE_T decoyType,
+ const string& fasta,
+ const string& proteinPbFile,
+ pb::Header& outProteinPbHeader,
+ vector<TideIndexPeptide>& outPeptideHeap,
+ vector<string*>& outProteinSequences,
+ ofstream* decoyFasta
+) {
+ typedef GeneratePeptides::CleavedPeptide PeptideInfo;
+
+ string decoyPrefix = Params::GetString("decoy-prefix");
+ outProteinPbHeader.Clear();
+ outProteinPbHeader.set_file_type(pb::Header::RAW_PROTEINS);
+ outProteinPbHeader.set_command_line(commandLine);
+ pb::Header_Source* headerSource = outProteinPbHeader.add_source();
+ headerSource->set_filename(AbsPath(fasta));
+ headerSource->set_filetype("fasta");
+ unsigned int invalidPepCnt = 0;
+ unsigned int failedDecoyCnt = 0;
+
+ outPeptideHeap.clear();
+ outProteinSequences.clear();
+
+ HeadedRecordWriter proteinWriter(proteinPbFile, outProteinPbHeader);
+ ifstream fastaStream(fasta.c_str(), ifstream::in);
+ pb::Protein pbProtein;
+ string proteinName;
+ string* proteinSequence = new string;
+ int curProtein = -1;
+ vector< pair< ProteinInfo, vector<PeptideInfo> > > cleavedPeptideInfo;
+ set<string> setTargets, setDecoys;
+ map<const string*, TargetInfo> targetInfo;
+
+ // Iterate over all proteins in FASTA file
+ unsigned int targetsGenerated = 0, decoysGenerated = 0;
+ while (GeneratePeptides::getNextProtein(fastaStream, &proteinName, proteinSequence)) {
+ outProteinSequences.push_back(proteinSequence);
+ cleavedPeptideInfo.push_back(make_pair(
+ ProteinInfo(proteinName, proteinSequence), vector<PeptideInfo>()));
+ const ProteinInfo& proteinInfo = cleavedPeptideInfo.back().first;
+ vector<PeptideInfo>& cleavedPeptides = cleavedPeptideInfo.back().second;
+ // Write pb::Protein
+ getPbProtein(++curProtein, proteinName, *proteinSequence, pbProtein);
+ proteinWriter.Write(&pbProtein);
+ cleavedPeptides = GeneratePeptides::cleaveProtein(
+ *proteinSequence, enzyme, digestion, missedCleavages, minLength, maxLength);
+ // Iterate over all generated peptides for this protein
+ for (vector<PeptideInfo>::iterator i = cleavedPeptides.begin();
+ i != cleavedPeptides.end(); ) {
+ FLOAT_T pepMass = calcPepMassTide(i->Sequence(), massType);
+ if (pepMass < 0.0) {
+ // Sequence contained some invalid character
+ carp(CARP_DEBUG, "Ignoring invalid sequence <%s>", i->Sequence().c_str());
+ ++invalidPepCnt;
+ i = cleavedPeptides.erase(i);
+ continue;
+ } else if (pepMass < minMass || pepMass > maxMass) {
+ // Skip to next peptide if not in mass range
+ ++i;
+ continue;
+ }
+ // Add target to heap
+ TideIndexPeptide pepTarget(
+ pepMass, i->Length(), proteinSequence, curProtein, i->Position(), false);
+ outPeptideHeap.push_back(pepTarget);
+ push_heap(outPeptideHeap.begin(), outPeptideHeap.end(), greater<TideIndexPeptide>());
+ if (!allowDups && decoyType != NO_DECOYS) {
+ const string* setTarget = &*(setTargets.insert(i->Sequence()).first);
+ targetInfo.insert(make_pair(setTarget, TargetInfo(proteinInfo, i->Position(), pepMass)));
+ }
+ ++targetsGenerated;
+ ++i;
+ }
+ proteinSequence = new string;
+ }
+ delete proteinSequence;
+ if (targetsGenerated == 0) {
+ carp(CARP_FATAL, "No target sequences generated. Is \'%s\' a FASTA file?",
+ fasta.c_str());
+ }
+
+ // Generate decoys
+ map<const string, const string*> targetToDecoy;
+ if (decoyType == PROTEIN_REVERSE_DECOYS) {
+ if (decoyFasta) {
+ carp(CARP_INFO, "Writing reverse-protein fasta and decoys...");
+ }
+ for (vector< pair< ProteinInfo, vector<PeptideInfo> > >::const_iterator i =
+ cleavedPeptideInfo.begin(); i != cleavedPeptideInfo.end(); ++i) {
+ string decoyProtein = *(i->first.sequence);
+ reverse(decoyProtein.begin(), decoyProtein.end());
+ if (decoyFasta) {
+ (*decoyFasta) << ">"<< decoyPrefix << i->first.name << endl
+ << decoyProtein << endl;
+ }
+ vector<PeptideInfo> cleavedReverse = GeneratePeptides::cleaveProtein(
+ decoyProtein, enzyme, digestion, missedCleavages, minLength, maxLength);
+ // Iterate over all generated peptides for this protein
+ for (vector<PeptideInfo>::iterator j = cleavedReverse.begin();
+ j != cleavedReverse.end();
+ ++j) {
+ FLOAT_T pepMass = calcPepMassTide(j->Sequence(), massType);
+ if (pepMass < 0.0) {
+ // Sequence contained some invalid character
+ carp(CARP_DEBUG, "Ignoring invalid sequence in decoy fasta <%s>",
+ j->Sequence().c_str());
+ ++invalidPepCnt;
+ continue;
+ } else if (pepMass < minMass || pepMass > maxMass) {
+ // Skip to next peptide if not in mass range
+ continue;
+ } else if (!allowDups && setTargets.find(j->Sequence()) != setTargets.end()) {
+ // Sequence already exists as a target
+ continue;
+ }
+ string* decoySequence = new string(j->Sequence());
+ outProteinSequences.push_back(decoySequence);
+
+ // Write pb::Protein
+ getDecoyPbProtein(++curProtein, ProteinInfo(i->first.name, &decoyProtein),
+ *decoySequence, j->Position(), pbProtein);
+ proteinWriter.Write(&pbProtein);
+ // Add decoy to heap
+ TideIndexPeptide pepDecoy(pepMass, j->Length(), decoySequence,
+ curProtein, (j->Position() > 0) ? 1 : 0, true);
+ outPeptideHeap.push_back(pepDecoy);
+ push_heap(outPeptideHeap.begin(), outPeptideHeap.end(),
+ greater<TideIndexPeptide>());
+ ++decoysGenerated;
+ }
+ }
+ } else if (!allowDups) {
+ for (set<string>::const_iterator i = setTargets.begin();
+ i != setTargets.end();
+ ++i) {
+ const string* setTarget = &*i;
+ const map<const string*, TargetInfo>::iterator targetLookup =
+ targetInfo.find(setTarget);
+ const ProteinInfo& proteinInfo = (targetLookup->second.proteinInfo);
+ const int startLoc = targetLookup->second.start;
+ FLOAT_T pepMass = targetLookup->second.mass;
+ if(generateDecoy(*setTarget, targetToDecoy, &setTargets, &setDecoys, decoyType, allowDups, failedDecoyCnt,
+ decoysGenerated, curProtein, proteinInfo, startLoc, pbProtein,
+ pepMass, outPeptideHeap, outProteinSequences)) {
+ proteinWriter.Write(&pbProtein);
+ } else {
+ continue;
+ }
+ }
+
+ } else { // allow dups
+ for (vector<pair<ProteinInfo, vector<PeptideInfo> > >::const_iterator i = cleavedPeptideInfo.begin();
+ i != cleavedPeptideInfo.end();
+ ++i) {
+ for (vector<PeptideInfo>::const_iterator j = i->second.begin();
+ j != i->second.end();
+ ++j) {
+ const string setTarget = j->Sequence();
+ const ProteinInfo& proteinInfo = i->first;
+ const int startLoc = j->Position();
+ FLOAT_T pepMass = calcPepMassTide(j->Sequence(), massType);
+ if(generateDecoy(setTarget, targetToDecoy, NULL, NULL, decoyType, allowDups, failedDecoyCnt,
+ decoysGenerated, curProtein, proteinInfo, startLoc, pbProtein,
+ pepMass, outPeptideHeap, outProteinSequences)) {
+ proteinWriter.Write(&pbProtein);
+ } else {
+ continue;
+ }
+ }
+ }
+
+ }
+ if (invalidPepCnt > 0) {
+ carp(CARP_INFO, "Ignoring %d peptide sequences containing unrecognized characters", invalidPepCnt);
+ }
+ if (failedDecoyCnt > 0) {
+ carp(CARP_INFO, "Failed to generate decoys for %d low complexity peptides", failedDecoyCnt);
+ }
+ carp(CARP_DEBUG, "FASTA produced %d targets and %d decoys",
+ targetsGenerated, decoysGenerated);
+
+ // Write to decoy fasta if necessary (if protein-reverse, we already wrote it)
+ if (decoyFasta && decoyType != PROTEIN_REVERSE_DECOYS) {
+ carp(CARP_INFO, "Writing decoy fasta...");
+ // Iterate over all (protein, peptides from that protein)
+ for (vector< pair< ProteinInfo, vector<PeptideInfo> > >::const_iterator i =
+ cleavedPeptideInfo.begin(); i != cleavedPeptideInfo.end(); ++i) {
+ string decoyProtein = *(i->first.sequence);
+ // Iterate over all peptides from the protein
+ for (vector<PeptideInfo>::const_iterator j = i->second.begin();
+ j != i->second.end();
+ ++j) {
+ // In the protein sequence, replace the target peptide with its decoy
+ const string setTarget = j->Sequence();
+ const map<const string, const string*>::const_iterator decoyCheck = targetToDecoy.find(setTarget);
+ if (decoyCheck != targetToDecoy.end()) {
+ decoyProtein.replace(j->Position(), j->Length(), *(decoyCheck->second));
+ }
+ }
+ // Write out the final protein
+ (*decoyFasta) << ">" << decoyPrefix << i->first.name << endl
+ << decoyProtein << endl;
+ }
+ }
+}
+
+void TideIndexApplication::writePeptidesAndAuxLocs(
+ vector<TideIndexPeptide>& peptideHeap,
+ const string& peptidePbFile,
+ const string& auxLocsPbFile,
+ pb::Header& pbHeader
+) {
+ // Check header
+ if (pbHeader.source_size() != 1) {
+ carp(CARP_FATAL, "pbHeader had a number of sources other than 1");
+ }
+ pb::Header_Source& headerSource = *(pbHeader.mutable_source(0));
+ if (!headerSource.has_filename() || headerSource.has_filetype()) {
+ carp(CARP_FATAL, "pbHeader source invalid");
+ }
+
+ string proteinsFile = headerSource.filename();
+ vector<const pb::Protein*> proteins;
+ pb::Header proteinsHeader;
+ carp(CARP_INFO, "Reading proteins");
+ if (!ReadRecordsToVector<pb::Protein>(&proteins, proteinsFile,
+ &proteinsHeader)) {
+ carp(CARP_FATAL, "Error reading proteins from %s", proteinsFile.c_str());
+ } else if (proteinsHeader.file_type() != pb::Header::RAW_PROTEINS) {
+ carp(CARP_FATAL, "Proteins file %s had invalid type", proteinsFile.c_str());
+ }
+ // Clean up
+ for (vector<const pb::Protein*>::iterator i = proteins.begin();
+ i != proteins.end();
+ ++i) {
+ delete *i;
+ }
+ // The raw proteins file is read in. It's a valid source file;
+ // remember it as such:
+ headerSource.mutable_header()->CopyFrom(proteinsHeader);
+
+ // Now check other desired settings
+ if (!pbHeader.has_peptides_header()) {
+ carp(CARP_FATAL, "!pbHeader->has_peptideHeapheader()");
+ }
+ const pb::Header_PeptidesHeader& settings = pbHeader.peptides_header();
+ //if (!Peptide::SetMinMaxMassAndLength(settings)) {
+ // carp(CARP_FATAL, "Error setting min/max mass/length");
+ if (!settings.has_enzyme() || settings.enzyme().empty()) {
+ carp(CARP_FATAL, "Enzyme settings error");
+ }
+
+ pbHeader.set_file_type(pb::Header::PEPTIDES);
+ pbHeader.mutable_peptides_header()->set_has_peaks(false);
+ pbHeader.mutable_peptides_header()->set_decoys(
+ get_tide_decoy_type_parameter("decoy-format"));
+ HeadedRecordWriter peptideWriter(peptidePbFile, pbHeader); // put header in outfile
+
+ // Create the auxiliary locations header and writer
+ pb::Header auxLocsHeader;
+ auxLocsHeader.set_file_type(pb::Header::AUX_LOCATIONS);
+ pb::Header_Source* auxLocsSource = auxLocsHeader.add_source();
+ auxLocsSource->set_filename(peptidePbFile);
+ auxLocsSource->mutable_header()->CopyFrom(pbHeader);
+ HeadedRecordWriter auxLocWriter(auxLocsPbFile, auxLocsHeader);
+
+ pb::Peptide pbPeptide;
+ pb::AuxLocation pbAuxLoc;
+ int auxLocIdx = -1;
+ carp(CARP_DEBUG, "%d peptides in heap", peptideHeap.size());
+ int count = 0;
+ sort_heap(peptideHeap.begin(), peptideHeap.end(),
+ greater<TideIndexPeptide>());
+ while (!peptideHeap.empty()) {
+ TideIndexPeptide curPeptide(peptideHeap.back());
+ peptideHeap.pop_back();
+ // For duplicate peptides we only record the location
+ while (!peptideHeap.empty() && peptideHeap.back() == curPeptide) {
+ pb::Location* location = pbAuxLoc.add_location();
+ location->set_protein_id(peptideHeap.back().getProteinId());
+ location->set_pos(peptideHeap.back().getProteinPos());
+ peptideHeap.pop_back();
+ }
+ getPbPeptide(count, curPeptide, pbPeptide);
+ // Not all peptides have aux locations associated with them. Check to see
+ // if GetGroup added any locations to aux_location. If yes, only then
+ // assign the corresponding array index to the peptide and write it out.
+ if (pbAuxLoc.location_size() > 0) {
+ pbPeptide.set_aux_locations_index(++auxLocIdx);
+ auxLocWriter.Write(&pbAuxLoc);
+ pbAuxLoc.Clear();
+ }
+
+ // Write the peptide AFTER the aux_locations check, in case we added an
+ // aux_locations_index to the peptide.
+ peptideWriter.Write(&pbPeptide);
+
+ if (++count % 100000 == 0) {
+ carp(CARP_INFO, "Wrote %d peptides", count);
+ }
+ }
+}
+
+FLOAT_T TideIndexApplication::calcPepMassTide(
+ const string& sequence,
+ MASS_TYPE_T massType
+) {
+ FixPt mass;
+ FixPt aaMass;
+ if (massType == AVERAGE) {
+ mass = MassConstants::fixp_avg_h2o;
+ for (size_t i = 0; i < sequence.length(); ++i) {
+ if (i == 0) {
+ aaMass = MassConstants::fixp_nterm_avg_table[sequence[i]];
+ } else if (i == sequence.length() - 1) {
+ aaMass = MassConstants::fixp_cterm_avg_table[sequence[i]];
+ } else {
+ aaMass = MassConstants::fixp_avg_table[sequence[i]];
+ }
+ if (aaMass == 0) {
+ return -1;
+ }
+ mass += aaMass;
+ }
+ } else if (massType == MONO) {
+ mass = MassConstants::fixp_mono_h2o;
+ for (size_t i = 0; i < sequence.length(); ++i) {
+ if (i == 0) {
+ aaMass = MassConstants::fixp_nterm_mono_table[sequence[i]];
+ } else if (i == sequence.length() - 1) {
+ aaMass = MassConstants::fixp_cterm_mono_table[sequence[i]];
+ } else {
+ aaMass = MassConstants::fixp_mono_table[sequence[i]];
+ }
+ if (aaMass == 0) {
+ return -1;
+ }
+ mass += aaMass;
+ }
+ } else {
+ carp(CARP_FATAL, "Invalid mass type");
+ }
+ return MassConstants::ToDouble(mass);
+}
+
+void TideIndexApplication::getPbProtein(
+ int id,
+ const string& name,
+ const string& residues,
+ pb::Protein& outPbProtein
+) {
+ outPbProtein.Clear();
+ outPbProtein.set_id(id);
+ outPbProtein.set_name(name);
+ outPbProtein.set_residues(residues);
+}
+
+void TideIndexApplication::getDecoyPbProtein(
+ int id,
+ const ProteinInfo& targetProteinInfo,
+ string decoyPeptideSequence,
+ int startLoc,
+ pb::Protein& outPbProtein
+) {
+ const string* proteinSequence = targetProteinInfo.sequence;
+ const int pepLen = decoyPeptideSequence.length();
+
+ // Add N term to decoySequence, if it exists
+ if (startLoc > 0) {
+ decoyPeptideSequence.insert(0, 1, proteinSequence->at(startLoc - 1));
+ }
+ // Add C term to decoySequence, if it exists
+ size_t cTermLoc = startLoc + pepLen;
+ decoyPeptideSequence.push_back((cTermLoc < proteinSequence->length()) ?
+ proteinSequence->at(cTermLoc) : '-');
+ // Append original target sequence, unless using protein level decoys
+ if (get_tide_decoy_type_parameter("decoy-format") != PROTEIN_REVERSE_DECOYS) {
+ decoyPeptideSequence.append(targetProteinInfo.sequence->substr(startLoc, pepLen));
+ }
+
+ getPbProtein(id, Params::GetString("decoy-prefix") + targetProteinInfo.name,
+ decoyPeptideSequence, outPbProtein);
+ outPbProtein.set_target_pos(startLoc);
+}
+
+void TideIndexApplication::getPbPeptide(
+ int id,
+ const TideIndexPeptide& peptide,
+ pb::Peptide& outPbPeptide
+) {
+ outPbPeptide.Clear();
+ outPbPeptide.set_id(id);
+ outPbPeptide.set_mass(peptide.getMass());
+ outPbPeptide.set_length(peptide.getLength());
+ outPbPeptide.mutable_first_location()->set_protein_id(peptide.getProteinId());
+ outPbPeptide.mutable_first_location()->set_pos(peptide.getProteinPos());;
+ outPbPeptide.set_is_decoy(peptide.isDecoy());
+}
+
+void TideIndexApplication::addAuxLoc(
+ int proteinId,
+ int proteinPos,
+ pb::AuxLocation& outAuxLoc
+) {
+ pb::Location* location = outAuxLoc.add_location();
+ location->set_protein_id(proteinId);
+ location->set_pos(proteinPos);
+}
+
+void TideIndexApplication::processParams() {
+ // Update mods-spec parameter for default cysteine mod
+ string default_cysteine = "C+" + StringUtils::ToString(CYSTEINE_DEFAULT);
+ string mods_spec = Params::GetString("mods-spec");
+ if (mods_spec.find('C') == string::npos) {
+ mods_spec = mods_spec.empty() ?
+ default_cysteine : default_cysteine + ',' + mods_spec;
+ carp(CARP_DEBUG, "Using default cysteine mod '%s' ('%s')",
+ default_cysteine.c_str(), mods_spec.c_str());
+ }
+ Params::Set("mods-spec", mods_spec);
+}
+
+
+string getModifiedPeptideSeq(const pb::Peptide* peptide,
+ const ProteinVec* proteins) {
+ int mod_index;
+ double mod_delta;
+ stringstream mod_stream;
+ const pb::Location& location = peptide->first_location();
+ const pb::Protein* protein = proteins->at(location.protein_id());
+ // Get peptide sequence without mods
+ string pep_str = protein->residues().substr(location.pos(), peptide->length());
+
+ // Store all mod indices/deltas
+ map<int, double> mod_map;
+ set<int> mod_indices;
+ for (int j = 0; j < peptide->modifications_size(); ++j) {
+ // var_mod_table.DecodeMod(ModCoder::Mod(peptide->modifications(j)), &mod_index, &mod_delta);
+ MassConstants::DecodeMod(ModCoder::Mod(peptide->modifications(j)),
+ &mod_index, &mod_delta);
+ mod_indices.insert(mod_index);
+ mod_map[mod_index] = mod_delta;
+ }
+ for (set<int>::const_reverse_iterator j = mod_indices.rbegin();
+ j != mod_indices.rend();
+ ++j) {
+ // Insert the modification string into the peptide sequence
+ mod_stream << '[' << mod_map[*j] << ']';
+ pep_str.insert(*j + 1, mod_stream.str());
+ mod_stream.str("");
+ }
+ return pep_str;
+}
+
+bool TideIndexApplication::generateDecoy(
+ const string& setTarget,
+ std::map<const string, const string*>& targetToDecoy,
+ set<string>* setTargets,
+ set<string>* setDecoys,
+ DECOY_TYPE_T decoyType,
+ bool allowDups,
+ unsigned int& failedDecoyCnt,
+ unsigned int& decoysGenerated,
+ int& curProtein,
+ const ProteinInfo& proteinInfo,
+ const int startLoc,
+ pb::Protein& pbProtein,
+ FLOAT_T pepMass,
+ vector<TideIndexPeptide>& outPeptideHeap,
+ vector<string*>& outProteinSequences
+) {
+ const map<const string, const string*>::const_iterator decoyCheck =
+ targetToDecoy.find(setTarget);
+ string* decoySequence = new string;
+ if (decoyCheck != targetToDecoy.end()) {
+ // Decoy already generated for this sequence
+ *decoySequence = *(decoyCheck->second);
+ } else {
+ // Try to generate decoy
+ if(allowDups) {
+ set<string> targets, decoys;
+ setTargets = &targets;
+ setDecoys = &decoys;
+ }
+ if (!GeneratePeptides::makeDecoy(setTarget, *setTargets, *setDecoys,
+ decoyType == PEPTIDE_SHUFFLE_DECOYS,
+ *decoySequence)) {
+ carp(CARP_DETAILED_INFO, "Failed to generate decoy for sequence %s",
+ setTarget.c_str());
+ ++failedDecoyCnt;
+ delete decoySequence;
+ return false;
+ } else if(!allowDups) {
+ targetToDecoy[setTarget] = &*(setDecoys->insert(*decoySequence).first);
+ } else {
+ targetToDecoy[setTarget] = decoySequence;
+ }
+ }
+
+ outProteinSequences.push_back(decoySequence);
+
+ // Write pb::Protein
+ getDecoyPbProtein(++curProtein, proteinInfo, *decoySequence,
+ startLoc, pbProtein);
+ // Add decoy to heap
+ TideIndexPeptide pepDecoy(
+ pepMass, setTarget.length(), decoySequence, curProtein, (startLoc > 0) ? 1 : 0, true);
+ outPeptideHeap.push_back(pepDecoy);
+ push_heap(outPeptideHeap.begin(), outPeptideHeap.end(),
+ greater<TideIndexPeptide>());
+ ++decoysGenerated;
+ return true;
+}
+
+
+/*
+* Local Variables:
+* mode: c
+* c-basic-offset: 2
+* End:
+*/
diff --git a/src/app/TideIndexApplication.h b/src/app/TideIndexApplication.h
new file mode 100644
index 0000000..815e5f1
--- /dev/null
+++ b/src/app/TideIndexApplication.h
@@ -0,0 +1,245 @@
+#ifndef TIDEINDEXAPPLICATION_H
+#define TIDEINDEXAPPLICATION_H
+
+#include "CruxApplication.h"
+
+#include <sys/stat.h>
+
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include <errno.h>
+#include <gflags/gflags.h>
+#include "header.pb.h"
+#include "tide/records.h"
+#include "tide/peptide.h"
+#include "tide/theoretical_peak_set.h"
+#include "tide/abspath.h"
+#include "TideSearchApplication.h"
+#include "util/crux-utils.h"
+
+using namespace std;
+
+std::string getModifiedPeptideSeq(const pb::Peptide* peptide, const ProteinVec* proteins);
+
+class TideIndexApplication : public CruxApplication {
+
+ friend class TideSearchApplication;
+
+ public:
+
+ /**
+ * Constructor
+ */
+ TideIndexApplication();
+
+ /**
+ * Destructor
+ */
+ ~TideIndexApplication();
+
+ /**
+ * Main method
+ */
+ virtual int main(int argc, char** argv);
+
+ int main(const string& fasta, const string& index, string cmd_line = "");
+
+ /**
+ * Returns the command name
+ */
+ virtual string getName() const;
+
+ /**
+ * Returns the command description
+ */
+ virtual string getDescription() const;
+
+ /**
+ * Returns the command arguments
+ */
+ virtual vector<string> getArgs() const;
+
+ /**
+ * Returns the command options
+ */
+ virtual vector<string> getOptions() const;
+
+ /**
+ * Returns the command outputs
+ */
+ virtual vector< pair<string, string> > getOutputs() const;
+
+ /**
+ * Returns whether the application needs the output directory or not. (default false)
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual COMMAND_T getCommand() const;
+
+ protected:
+
+ class TideIndexPeptide {
+ private:
+ double mass_;
+ int length_;
+ int proteinId_;
+ int proteinPos_;
+ const char* residues_; // points at protein sequence
+ bool decoy_;
+ public:
+ TideIndexPeptide() {}
+ TideIndexPeptide(double mass, int length, string* proteinSeq,
+ int proteinId, int proteinPos, bool decoy) {
+ mass_ = mass;
+ length_ = length;
+ proteinId_ = proteinId;
+ proteinPos_ = proteinPos;
+ residues_ = proteinSeq->data() + proteinPos;
+ decoy_ = decoy;
+ }
+ TideIndexPeptide(const TideIndexPeptide& other) {
+ mass_ = other.mass_;
+ length_ = other.length_;
+ proteinId_ = other.proteinId_;
+ proteinPos_ = other.proteinPos_;
+ residues_ = other.residues_;
+ decoy_ = other.decoy_;
+ }
+ double getMass() const { return mass_; }
+ int getLength() const { return length_; }
+ int getProteinId() const { return proteinId_; }
+ int getProteinPos() const { return proteinPos_; }
+ string getSequence() const { return string(residues_, length_); }
+ bool isDecoy() const { return decoy_; }
+
+ friend bool operator >(
+ const TideIndexPeptide& lhs, const TideIndexPeptide& rhs) {
+ if (&lhs == &rhs) {
+ return false;
+ } else if (lhs.mass_ != rhs.mass_) {
+ return lhs.mass_ > rhs.mass_;
+ } else if (lhs.length_ != rhs.length_) {
+ return lhs.length_ > rhs.length_;
+ } else {
+ int strncmpResult = strncmp(lhs.residues_, rhs.residues_, lhs.length_);
+ if (strncmpResult != 0) {
+ return strncmpResult > 0;
+ }
+ }
+ return false;
+ }
+ friend bool operator ==(
+ const TideIndexPeptide& lhs, const TideIndexPeptide& rhs) {
+ return (lhs.mass_ == rhs.mass_ && lhs.length_ == rhs.length_ &&
+ strncmp(lhs.residues_, rhs.residues_, lhs.length_) == 0);
+ }
+ };
+
+ struct ProteinInfo {
+ string name;
+ const string* sequence;
+ ProteinInfo(const string& proteinName, const string* proteinSequence)
+ : name(proteinName), sequence(proteinSequence) {}
+ };
+
+ struct TargetInfo {
+ ProteinInfo proteinInfo;
+ int start;
+ FLOAT_T mass;
+ TargetInfo(const ProteinInfo& protein, int startLoc, FLOAT_T pepMass)
+ : proteinInfo(protein), start(startLoc), mass(pepMass) {}
+ };
+
+ static void fastaToPb(
+ const std::string& commandLine,
+ const ENZYME_T enzyme,
+ const DIGEST_T digestion,
+ int missedCleavages,
+ FLOAT_T minMass,
+ FLOAT_T maxMass,
+ int minLength,
+ int maxLength,
+ bool dups,
+ MASS_TYPE_T massType,
+ DECOY_TYPE_T decoyType,
+ const std::string& fasta,
+ const std::string& proteinPbFile,
+ pb::Header& outProteinPbHeader,
+ std::vector<TideIndexPeptide>& outPeptideHeap,
+ std::vector<string*>& outProteinSequences,
+ std::ofstream* decoyFasta
+ );
+
+ static void writePeptidesAndAuxLocs(
+ std::vector<TideIndexPeptide>& peptideHeap, // will be destroyed.
+ const std::string& peptidePbFile,
+ const std::string& auxLocsPbFile,
+ pb::Header& pbHeader
+ );
+
+ static FLOAT_T calcPepMassTide(
+ const std::string& sequence,
+ MASS_TYPE_T massType
+ );
+
+ static void getPbProtein(
+ int id,
+ const std::string& name,
+ const std::string& residues,
+ pb::Protein& outPbProtein
+ );
+
+ static void getDecoyPbProtein(
+ int id,
+ const ProteinInfo& targetProteinInfo,
+ std::string decoyPeptideSequence,
+ int startLoc,
+ pb::Protein& outPbProtein
+ );
+
+ static void getPbPeptide(
+ int id,
+ const TideIndexPeptide& peptide,
+ pb::Peptide& outPbPeptide
+ );
+
+ static void addAuxLoc(
+ int proteinId,
+ int proteinPos,
+ pb::AuxLocation& outAuxLoc
+ );
+
+ /**
+ * Generates decoy for the target peptide, writes the decoy protein to pbProtein
+ * and adds decoy to the heap.
+ */
+ static bool generateDecoy(
+ const string& setTarget,
+ std::map<const string, const string*>& targetToDecoy,
+ set<string>* setTargets,
+ set<string>* setDecoys,
+ DECOY_TYPE_T decoyType,
+ bool allowDups,
+ unsigned int& failedDecoyCnt,
+ unsigned int& decoysGenerated,
+ int& curProtein,
+ const ProteinInfo& proteinInfo,
+ const int startLoc,
+ pb::Protein& pbProtein,
+ FLOAT_T pepMass,
+ vector<TideIndexPeptide>& outPeptideHeap,
+ vector<string*>& outProteinSequences
+ );
+
+ virtual void processParams();
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/TideMatchSet.cpp b/src/app/TideMatchSet.cpp
new file mode 100644
index 0000000..54cdc98
--- /dev/null
+++ b/src/app/TideMatchSet.cpp
@@ -0,0 +1,647 @@
+/*
+ * There are two versions of the report function, which writes matches to output
+ * files. The first version, which takes ofstreams as arguments, is used when
+ * only tab-delimited output is required. It does not perform any object
+ * conversions. The second version takes an OutputFiles object as an argument
+ * and is used when any non-tab-delimited output is required. It must convert
+ * the data from Tide into Crux objects, which increases runtime.
+ */
+
+#include <fstream>
+#include <iomanip>
+
+#include "TideIndexApplication.h"
+#include "TideMatchSet.h"
+#include "TideSearchApplication.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+string TideMatchSet::CleavageType;
+char TideMatchSet::match_collection_loc_[] = {0};
+char TideMatchSet::decoy_match_collection_loc_[] = {0};
+
+TideMatchSet::TideMatchSet(Arr* matches, double max_mz)
+ : matches_(matches), max_mz_(max_mz), exact_pval_search_(false), elution_window_(0) {
+}
+
+TideMatchSet::TideMatchSet(Peptide* peptide, double max_mz)
+ : peptide_(peptide), max_mz_(max_mz), exact_pval_search_(false), elution_window_(0) {
+}
+
+TideMatchSet::~TideMatchSet() {
+}
+
+/**
+ * Write peptide centric matches to output files
+ * This is for writing tab-delimited only
+ */
+void TideMatchSet::report(
+ ofstream* target_file, ///< target file to write to
+ ofstream* decoy_file, ///< decoy file to write to
+ int top_matches,
+ const ActivePeptideQueue* peptides, ///< peptide queue
+ const ProteinVec& proteins, ///< proteins corresponding with peptides
+ const vector<const pb::AuxLocation*>& locations, ///< auxiliary locations
+ bool compute_sp ///< whether to compute sp or not
+) {
+ if (peptide_->spectrum_matches_array.size() == 0) {
+ return;
+ }
+
+ carp(CARP_DETAILED_DEBUG, "TideMatchSet reporting top %d of %d peptide centric matches",
+ top_matches, peptide_->spectrum_matches_array.size());
+
+ int charge;
+ double score;
+ double d_cn = 0.0;
+ int nHit = peptide_->spectrum_matches_array.size();
+
+ if (nHit < top_matches) {
+ top_matches = nHit;
+ }
+ if (exact_pval_search_) {
+ sort(peptide_->spectrum_matches_array.begin(),
+ peptide_->spectrum_matches_array.end(),
+ Peptide::spectrum_matches::compPV);
+ } else {
+ sort(peptide_->spectrum_matches_array.begin(),
+ peptide_->spectrum_matches_array.end(),
+ Peptide::spectrum_matches::compSC);
+ }
+
+ for (int cnt = 0; cnt < nHit; ++cnt) {
+ d_cn = 0.0;
+ if (exact_pval_search_ == true) {
+ score = peptide_->spectrum_matches_array[cnt].score1_;
+ if (cnt < nHit-1) {
+ d_cn = (double)((log10(peptide_->spectrum_matches_array[cnt+1].score1_)
+ - log10(peptide_->spectrum_matches_array[cnt].score1_))
+ /max((FLOAT_T)(-1*log10(peptide_->spectrum_matches_array[cnt].score1_)), FLOAT_T(1)));
+ }
+ } else {
+ score = (double)(peptide_->spectrum_matches_array[cnt].score1_ / 100000000.0);
+ if (cnt < nHit-1) {
+ d_cn = (double)( score
+ - (double)(peptide_->spectrum_matches_array[cnt+1].score1_ / 100000000.0)
+ / (double)max((FLOAT_T)score , FLOAT_T(1)));
+ }
+ }
+ peptide_->spectrum_matches_array[cnt].score1_ = score;
+ peptide_->spectrum_matches_array[cnt].d_cn_ = d_cn;
+ peptide_->spectrum_matches_array[cnt].score3_ = nHit;
+ }
+ //smoothing primary scores in the elution window, only in DIA mode.
+ if (elution_window_ > 0) {
+ sort(peptide_->spectrum_matches_array.begin(),
+ peptide_->spectrum_matches_array.end(),
+ Peptide::spectrum_matches::compRT);
+ int cnt;
+ double mean = 1.0;
+
+ //initialize sliding window
+ int flank = (int)((double)((elution_window_)/2) + 1);
+ flank = flank > nHit ? nHit : flank;
+
+ for (cnt = 0; cnt < flank; ++cnt) {
+ mean *= peptide_->spectrum_matches_array[cnt].score1_;
+ }
+ int top = flank;
+ int bottom = 0;
+ for (cnt = 0; cnt < nHit; ++cnt) {
+ peptide_->spectrum_matches_array[cnt].elution_score_ = pow(mean, 1.0/(top-bottom));
+ if (top < nHit) {
+ mean *= peptide_->spectrum_matches_array[top].score1_;
+ ++top;
+ }
+ if (cnt >= flank-1) {
+ mean /= peptide_->spectrum_matches_array[bottom].score1_;
+ ++bottom;
+ }
+ }
+ //reorder PSMs according to the smoothed p-value
+ sort(peptide_->spectrum_matches_array.begin(),
+ peptide_->spectrum_matches_array.end(),
+ Peptide::spectrum_matches::compES);
+ }
+ peptide_->spectrum_matches_array.resize(top_matches);
+ if (compute_sp) {
+ vector<pair<double, int> > spScoreRank;
+ spScoreRank.reserve(top_matches);
+ for (int cnt = 0; cnt < top_matches; ++cnt) {
+ SpScorer sp_scorer(proteins, *peptide_->spectrum_matches_array[cnt].spectrum_,
+ peptide_->spectrum_matches_array[cnt].charge_, max_mz_);
+ pb::Peptide* pb_peptide = getPbPeptide(*peptide_);
+ sp_scorer.Score(*pb_peptide, peptide_->spectrum_matches_array[cnt].spData_);
+ spScoreRank.push_back(make_pair(-1*peptide_->spectrum_matches_array[cnt].spData_.sp_score, cnt));
+ }
+ sort(spScoreRank.begin(), spScoreRank.end());
+ for (size_t i = 0; i < spScoreRank.size(); ++i) {
+ peptide_->spectrum_matches_array[spScoreRank[i].second].spData_.sp_rank = i;
+ }
+ }
+ // target peptide or concat search
+ ofstream* file =
+ (Params::GetBool("concat") || !peptide_->IsDecoy()) ? target_file : decoy_file;
+ writeToFile(file, peptides, proteins, locations, compute_sp);
+}
+
+/**
+ * Helper function for tab delimited report function for peptide centric search
+ */
+void TideMatchSet::writeToFile(
+ ofstream* file,
+ const ActivePeptideQueue* peptides,
+ const ProteinVec& proteins,
+ const vector<const pb::AuxLocation*>& locations,
+ bool compute_sp ///< whether to compute sp or not
+) {
+ if (!file) {
+ return;
+ }
+ int cur = 0;
+
+ const Peptide* peptide = peptides->GetPeptide(0);
+ const pb::Protein* protein = proteins[peptide->FirstLocProteinId()];
+ int pos = peptide->FirstLocPos();
+ string proteinNames = getProteinName(*protein,
+ (!protein->has_target_pos()) ? pos : protein->target_pos());
+ string flankingAAs, n_term, c_term;
+ getFlankingAAs(peptide, protein, pos, &n_term, &c_term);
+ flankingAAs = n_term + c_term;
+
+ int precision = Params::GetInt("precision");
+
+ // look for other locations
+ if (peptide->HasAuxLocationsIndex()) {
+ const pb::AuxLocation* aux = locations[peptide->AuxLocationsIndex()];
+ for (int i = 0; i < aux->location_size(); ++i) {
+ const pb::Location& location = aux->location(i);
+ protein = proteins[location.protein_id()];
+ pos = location.pos();
+ proteinNames += "," + getProteinName(*protein,
+ (!protein->has_target_pos()) ? pos : protein->target_pos());
+ getFlankingAAs(peptide, protein, pos, &n_term, &c_term);
+ flankingAAs += "," + n_term + c_term;
+ }
+ }
+
+ Crux::Peptide cruxPep = getCruxPeptide(peptide);
+ for (vector<Peptide::spectrum_matches>::const_iterator
+ i = peptide_->spectrum_matches_array.begin();
+ i != peptide_->spectrum_matches_array.end();
+ ++i) {
+ Spectrum* spectrum = i->spectrum_;
+
+ *file << spectrum->SpectrumNumber() << '\t'
+ << i->charge_ << '\t'
+ << spectrum->PrecursorMZ() << '\t'
+ << (spectrum->PrecursorMZ() - MASS_PROTON) * i->charge_ << '\t'
+ << cruxPep.calcModifiedMass() << '\t'
+ << i->d_cn_ << '\t';
+ SpScorer::SpScoreData spData;
+ if (compute_sp) {
+ *file << i->spData_.sp_score << '\t'
+ << i->spData_.sp_rank << '\t';
+ }
+
+ // Use scientific notation for exact p-value, but not refactored XCorr.
+ if (exact_pval_search_) {
+ *file << StringUtils::ToString(i->score1_, precision, false) << '\t';
+ *file << StringUtils::ToString(i->score2_, precision, true) << '\t';
+ } else {
+ *file << StringUtils::ToString(i->score1_, precision, true) << '\t';
+ }
+
+ if (elution_window_ ) {
+ *file << i->elution_score_ << '\t';
+ }
+
+ *file << ++cur << '\t';
+ if (compute_sp) {
+ *file << i->spData_.matched_ions << '\t'
+ << i->spData_.total_ions << '\t';
+ }
+ *file << i->score3_ << '\t';
+
+ if (Params::GetBool("concat")) {
+ *file << peptides->ActiveTargets() + peptides->ActiveDecoys() << '\t';
+ } else {
+ *file << (!peptide->IsDecoy() ? peptides->ActiveTargets() : peptides->ActiveDecoys()) << '\t';
+ }
+ *file << cruxPep.getModifiedSequenceWithMasses() << '\t'
+ << cruxPep.getModsString() << '\t'
+ << CleavageType << '\t'
+ << proteinNames << '\t'
+ << flankingAAs;
+ if (peptide->IsDecoy() && !TideSearchApplication::proteinLevelDecoys()) {
+ // write target sequence
+ const string& residues = protein->residues();
+ *file << '\t'
+ << residues.substr(residues.length() - peptide->Len());
+ } else if (Params::GetBool("concat") && !TideSearchApplication::proteinLevelDecoys()) {
+ *file << '\t'
+ << cruxPep.getUnshuffledSequence();
+ }
+ *file << endl;
+ }
+}
+
+/**
+ * Write matches to output files
+ * This is for writing tab-delimited only
+ */
+void TideMatchSet::report(
+ ofstream* target_file, ///< target file to write to
+ ofstream* decoy_file, ///< decoy file to write to
+ int top_n, ///< number of matches to report
+ const string& spectrum_filename, ///< name of spectrum file
+ const Spectrum* spectrum, ///< spectrum for matches
+ int charge, ///< charge for matches
+ const ActivePeptideQueue* peptides, ///< peptide queue
+ const ProteinVec& proteins, ///< proteins corresponding with peptides
+ const vector<const pb::AuxLocation*>& locations, ///< auxiliary locations
+ bool compute_sp, ///< whether to compute sp or not
+ bool highScoreBest, //< indicates semantics of score magnitude
+ boost::mutex * rwlock
+) {
+ if (matches_->size() == 0) {
+ return;
+ }
+
+ carp(CARP_DETAILED_DEBUG, "Tide MatchSet reporting top %d of %d matches",
+ top_n, matches_->size());
+
+ vector<Arr::iterator> targets, decoys;
+ gatherTargetsAndDecoys(peptides, proteins, targets, decoys, top_n, highScoreBest);
+
+ map<Arr::iterator, FLOAT_T> delta_cn_map;
+ map<Arr::iterator, FLOAT_T> delta_lcn_map;
+ computeDeltaCns(targets, &delta_cn_map, &delta_lcn_map);
+ computeDeltaCns(decoys, &delta_cn_map, &delta_lcn_map);
+
+ map<Arr::iterator, pair<const SpScorer::SpScoreData, int> > sp_map;
+ if (compute_sp) {
+ SpScorer sp_scorer(proteins, *spectrum, charge, max_mz_);
+ computeSpData(targets, &sp_map, &sp_scorer, peptides);
+ computeSpData(decoys, &sp_map, &sp_scorer, peptides);
+ }
+ writeToFile(target_file, top_n, targets, spectrum_filename, spectrum, charge,
+ peptides, proteins, locations, delta_cn_map, delta_lcn_map, compute_sp ? &sp_map : NULL, rwlock);
+ writeToFile(decoy_file, top_n, decoys, spectrum_filename, spectrum, charge,
+ peptides, proteins, locations, delta_cn_map, delta_lcn_map, compute_sp ? &sp_map : NULL, rwlock);
+}
+
+/**
+ * Helper function for tab delimited report function
+ */
+void TideMatchSet::writeToFile(
+ ofstream* file,
+ int top_n,
+ const vector<Arr::iterator>& vec,
+ const string& spectrum_filename,
+ const Spectrum* spectrum,
+ int charge,
+ const ActivePeptideQueue* peptides,
+ const ProteinVec& proteins,
+ const vector<const pb::AuxLocation*>& locations,
+ const map<Arr::iterator, FLOAT_T>& delta_cn_map,
+ const map<Arr::iterator, FLOAT_T>& delta_lcn_map,
+ const map<Arr::iterator, pair<const SpScorer::SpScoreData, int> >* sp_map,
+ boost::mutex * rwlock
+) {
+ if (!file) {
+ return;
+ }
+
+ int massPrecision = Params::GetInt("mass-precision");
+ int precision = Params::GetInt("precision");
+
+ int cur = 0;
+ int concatDistinctMatches = peptides->ActiveTargets() + peptides->ActiveDecoys();
+
+ const vector<Arr::iterator>::const_iterator cutoff =
+ (vec.size() >= top_n) ? vec.begin() + top_n : vec.end();
+
+ for (vector<Arr::iterator>::const_iterator i = vec.begin(); i != cutoff; ++i) {
+ const Peptide* peptide = peptides->GetPeptide((*i)->rank);
+ const pb::Protein* protein = proteins[peptide->FirstLocProteinId()];
+ int pos = peptide->FirstLocPos();
+ string proteinNames = getProteinName(*protein,
+ (!protein->has_target_pos()) ? pos : protein->target_pos());
+ string flankingAAs, n_term, c_term;
+ getFlankingAAs(peptide, protein, pos, &n_term, &c_term);
+ flankingAAs = n_term + c_term;
+
+ // look for other locations
+ if (peptide->HasAuxLocationsIndex()) {
+ const pb::AuxLocation* aux = locations[peptide->AuxLocationsIndex()];
+ for (int i = 0; i < aux->location_size(); ++i) {
+ const pb::Location& location = aux->location(i);
+ protein = proteins[location.protein_id()];
+ pos = location.pos();
+ proteinNames += "," + getProteinName(*protein,
+ (!protein->has_target_pos()) ? pos : protein->target_pos());
+ getFlankingAAs(peptide, protein, pos, &n_term, &c_term);
+ flankingAAs += "," + n_term + c_term;
+ }
+ }
+
+ Crux::Peptide cruxPep = getCruxPeptide(peptide);
+ const SpScorer::SpScoreData* sp_data = sp_map ? &(sp_map->at(*i).first) : NULL;
+
+ rwlock->lock();
+ if (Params::GetBool("file-column")) {
+ *file << spectrum_filename << '\t';
+ }
+ *file << spectrum->SpectrumNumber() << '\t'
+ << charge << '\t'
+ << StringUtils::ToString(spectrum->PrecursorMZ(), massPrecision) << '\t'
+ << StringUtils::ToString((spectrum->PrecursorMZ() - MASS_PROTON) * charge, massPrecision) << '\t'
+ << StringUtils::ToString(cruxPep.calcModifiedMass(), massPrecision) << '\t'
+ << delta_cn_map.at(*i) << '\t'
+ << delta_lcn_map.at(*i) << '\t';
+ if (sp_map) {
+ *file << StringUtils::ToString(sp_data->sp_score, precision) << '\t'
+ << sp_map->at(*i).second << '\t';
+ }
+
+ // Use scientific notation for exact p-value, but not refactored XCorr.
+ if (exact_pval_search_) {
+ *file << StringUtils::ToString((*i)->xcorr_pval, precision, false) << '\t';
+ *file << StringUtils::ToString((*i)->xcorr_score, precision, true) << '\t';
+ } else {
+ *file << StringUtils::ToString((*i)->xcorr_score, precision, true) << '\t';
+ }
+ *file << ++cur << '\t';
+ if (sp_map) {
+ *file << sp_data->matched_ions << '\t'
+ << sp_data->total_ions << '\t';
+ }
+
+ if (Params::GetBool("concat")) {
+ *file << concatDistinctMatches << '\t';
+ } else {
+ *file << (!peptide->IsDecoy() ? peptides->ActiveTargets() : peptides->ActiveDecoys()) << '\t';
+ }
+
+ *file << cruxPep.getModifiedSequenceWithMasses() << '\t'
+ << cruxPep.getModsString() << '\t'
+ << CleavageType << '\t'
+ << proteinNames << '\t'
+ << flankingAAs;
+ if (peptide->IsDecoy() && !TideSearchApplication::proteinLevelDecoys()) {
+ // write target sequence
+ const string& residues = protein->residues();
+ *file << '\t'
+ << residues.substr(residues.length() - peptide->Len());
+ } else if (Params::GetBool("concat") && !TideSearchApplication::proteinLevelDecoys()) {
+ *file << '\t'
+ << cruxPep.getUnshuffledSequence();
+ }
+ *file << endl;
+ rwlock->unlock();
+ }
+}
+
+/**
+ * Write headers for tab delimited file
+ */
+void TideMatchSet::writeHeaders(ofstream* file, bool decoyFile, bool sp) {
+ if (!file) {
+ return;
+ }
+ const int headers[] = {
+ FILE_COL, SCAN_COL, CHARGE_COL, SPECTRUM_PRECURSOR_MZ_COL, SPECTRUM_NEUTRAL_MASS_COL,
+ PEPTIDE_MASS_COL, DELTA_CN_COL, DELTA_LCN_COL, SP_SCORE_COL, SP_RANK_COL,
+ XCORR_SCORE_COL, XCORR_RANK_COL, BY_IONS_MATCHED_COL, BY_IONS_TOTAL_COL,
+ DISTINCT_MATCHES_SPECTRUM_COL, SEQUENCE_COL, MODIFICATIONS_COL, CLEAVAGE_TYPE_COL,
+ PROTEIN_ID_COL, FLANKING_AA_COL, ORIGINAL_TARGET_SEQUENCE_COL
+ };
+ size_t numHeaders = sizeof(headers) / sizeof(int);
+ bool writtenHeader = false;
+ for (size_t i = 0; i < numHeaders; ++i) {
+ int header = headers[i];
+ if (!sp &&
+ (header == SP_SCORE_COL || header == SP_RANK_COL ||
+ header == BY_IONS_MATCHED_COL || header == BY_IONS_TOTAL_COL)) {
+ continue;
+ } else if (header == ORIGINAL_TARGET_SEQUENCE_COL &&
+ (TideSearchApplication::proteinLevelDecoys() ||
+ (!decoyFile && !Params::GetBool("concat")))) {
+ continue;
+ }
+ if (writtenHeader) {
+ *file << '\t';
+ }
+ if (header == FILE_COL &&
+ (!Params::GetBool("file-column") || Params::GetBool("peptide-centric-search"))) {
+ continue;
+ }
+ if (header == XCORR_SCORE_COL && Params::GetBool("exact-p-value")) {
+ *file << get_column_header(EXACT_PVALUE_COL) << '\t'
+ << get_column_header(REFACTORED_SCORE_COL);
+ if (Params::GetInt("elution-window-size") > 0) {
+ *file << '\t' << get_column_header(ELUTION_WINDOW_COL);
+ }
+ writtenHeader = true;
+ continue;
+ }
+ if (header == DISTINCT_MATCHES_SPECTRUM_COL) {
+ if (Params::GetBool("peptide-centric-search")) {
+ *file << get_column_header(DISTINCT_MATCHES_PEPTIDE_COL) << '\t';
+ *file << get_column_header(DISTINCT_MATCHES_SPECTRUM_COL);
+ } else {
+ *file << get_column_header(DISTINCT_MATCHES_SPECTRUM_COL);
+ }
+ writtenHeader = true;
+ continue;
+ }
+ *file << get_column_header(header);
+ writtenHeader = true;
+ }
+ *file << endl;
+}
+
+void TideMatchSet::initModMap(const pb::ModTable& modTable, ModPosition position) {
+ for (int i = 0; i < modTable.variable_mod_size(); i++) {
+ const pb::Modification& mod = modTable.variable_mod(i);
+ if (mod.has_delta() && mod.has_amino_acids()) {
+ ModificationDefinition::NewVarMod(mod.amino_acids(), mod.delta(), position);
+ }
+ }
+ for (int i = 0; i < modTable.static_mod_size(); i++) {
+ const pb::Modification& mod = modTable.static_mod(i);
+ if (mod.has_delta() && mod.has_amino_acids()) {
+ ModificationDefinition::NewStaticMod(mod.amino_acids(), mod.delta(), position);
+ }
+ }
+}
+
+Crux::Peptide TideMatchSet::getCruxPeptide(const Peptide* peptide) {
+ return Crux::Peptide(peptide->Seq(), getMods(peptide));
+}
+
+vector<Crux::Modification> TideMatchSet::getMods(const Peptide* peptide) {
+ vector<Crux::Modification> modVector;
+ string seq(peptide->Seq());
+ const ModCoder::Mod* mods;
+ int pep_mods = peptide->Mods(&mods);
+ for (int i = 0; i < pep_mods; i++) {
+ int mod_index;
+ double mod_delta;
+ MassConstants::DecodeMod(mods[i], &mod_index, &mod_delta);
+ const ModificationDefinition* modDef = ModificationDefinition::Find(mod_delta, false);
+ if (modDef == NULL) {
+ carp(CARP_ERROR, "Could not find modification with delta %f", mod_delta);
+ continue;
+ }
+ modVector.push_back(Crux::Modification(modDef, mod_index));
+ }
+ return modVector;
+}
+
+void TideMatchSet::gatherTargetsAndDecoys(
+ const ActivePeptideQueue* peptides,
+ const ProteinVec& proteins,
+ vector<Arr::iterator>& targetsOut,
+ vector<Arr::iterator>& decoysOut,
+ int top_n,
+ bool highScoreBest // indicates semantics of score magnitude
+) {
+ if (exact_pval_search_) {
+ make_heap(matches_->begin(), matches_->end(), highScoreBest ? lessXcorrPvalScore : moreXcorrPvalScore);
+ } else {
+ make_heap(matches_->begin(), matches_->end(), highScoreBest ? lessXcorrScore : moreXcorrScore);
+ }
+
+ if (!Params::GetBool("concat") && TideSearchApplication::hasDecoys()) {
+ for (Arr::iterator i = matches_->end(); i != matches_->begin(); ) {
+ if (exact_pval_search_) {
+ pop_heap(matches_->begin(), i--, highScoreBest ? lessXcorrPvalScore : moreXcorrPvalScore);
+ } else {
+ pop_heap(matches_->begin(), i--, highScoreBest ? lessXcorrScore : moreXcorrScore);
+ }
+
+ const Peptide& peptide = *(peptides->GetPeptide(i->rank));
+ const pb::Protein& protein = *(proteins[peptide.FirstLocProteinId()]);
+ vector<Arr::iterator>* vec_ptr = !peptide.IsDecoy() ? &targetsOut : &decoysOut;
+ if (vec_ptr->size() < top_n + 1) {
+ vec_ptr->push_back(i);
+ }
+ }
+ } else {
+ int toAdd = min(top_n + 1, matches_->size());
+ for (int i = 0; i < toAdd; ) {
+ if (exact_pval_search_) {
+ pop_heap(matches_->begin(), matches_->end() - i, highScoreBest ? lessXcorrPvalScore : moreXcorrPvalScore);
+ } else {
+ pop_heap(matches_->begin(), matches_->end() - i, highScoreBest ? lessXcorrScore : moreXcorrScore);
+ }
+ targetsOut.push_back(matches_->end() - (++i));
+ }
+ }
+}
+
+/**
+ * Create a pb peptide from Tide peptide
+ */
+pb::Peptide* TideMatchSet::getPbPeptide(const Peptide& peptide) {
+ pb::Peptide* pb_peptide = new pb::Peptide();
+ pb_peptide->set_id(peptide.Id());
+ pb_peptide->set_mass(peptide.Mass());
+ pb_peptide->set_length(peptide.Len());
+ if (peptide.HasAuxLocationsIndex()) {
+ pb_peptide->set_aux_locations_index(peptide.AuxLocationsIndex());
+ }
+
+ // Copy over all the modifications for this Peptide
+ const ModCoder::Mod* mods;
+ int pep_mods = peptide.Mods(&mods);
+ for (int i = 0; i < pep_mods; ++i) {
+ pb_peptide->add_modifications(mods[i]);
+ }
+
+ // Copy over the Peptide's first location within the first protein
+ pb::Location* first_location = pb_peptide->mutable_first_location();
+ first_location->set_protein_id(peptide.FirstLocProteinId());
+ first_location->set_pos(peptide.FirstLocPos());
+
+ return pb_peptide;
+}
+
+/**
+ * Gets the protein name with the index appended.
+ */
+string TideMatchSet::getProteinName(const pb::Protein& protein, int pos) {
+ stringstream proteinNameStream;
+ proteinNameStream << protein.name() << '(' << pos + 1 << ')';
+ return proteinNameStream.str();
+}
+
+/**
+ * Gets the flanking AAs for a Tide peptide sequence
+ */
+void TideMatchSet::getFlankingAAs(
+ const Peptide* peptide, ///< Tide peptide to get flanking AAs for
+ const pb::Protein* protein, ///< Tide protein for the peptide
+ int pos, ///< location of peptide within protein
+ string* out_n, ///< out parameter for n flank
+ string* out_c ///< out parameter for c flank
+) {
+ int idx_n = pos - 1;
+ int idx_c = pos + peptide->Len();
+ const string& seq = protein->residues();
+
+ *out_n = (idx_n >= 0) ? seq.substr(idx_n, 1) : "-";
+ *out_c = (idx_c < seq.length()) ? seq.substr(idx_c, 1) : "-";
+}
+
+void TideMatchSet::computeDeltaCns(
+ const vector<Arr::iterator>& vec, // xcorr*100000000.0, high to low
+ map<Arr::iterator, FLOAT_T>* delta_cn_map, // map to add delta cn scores to
+ map<Arr::iterator, FLOAT_T>* delta_lcn_map // map to add delta cn scores to
+) {
+ vector<FLOAT_T> scores;
+ for (vector<Arr::iterator>::const_iterator i = vec.begin(); i != vec.end(); i++) {
+ if (Params::GetBool("exact-p-value")) {
+ scores.push_back((*i)->xcorr_pval);
+ } else {
+ scores.push_back((*i)->xcorr_score);
+ }
+ }
+ vector< pair<FLOAT_T, FLOAT_T> > deltaCns = MatchCollection::calculateDeltaCns(
+ scores, !Params::GetBool("exact-p-value") ? XCORR : TIDE_SEARCH_EXACT_PVAL);
+ for (int i = 0; i < vec.size(); i++) {
+ delta_cn_map->insert(make_pair(vec[i], deltaCns[i].first));
+ delta_lcn_map->insert(make_pair(vec[i], deltaCns[i].second));
+ }
+}
+
+void TideMatchSet::computeSpData(
+ const vector<Arr::iterator>& vec,
+ map<Arr::iterator, pair<const SpScorer::SpScoreData, int> >* sp_rank_map,
+ SpScorer* sp_scorer,
+ const ActivePeptideQueue* peptides
+) {
+ vector< pair<Arr::iterator, SpScorer::SpScoreData> > spData;
+ spData.reserve(vec.size());
+ for (vector<Arr::iterator>::const_iterator i = vec.begin(); i != vec.end(); ++i) {
+ spData.push_back(make_pair(*i, SpScorer::SpScoreData()));
+ const Peptide& peptide = *(peptides->GetPeptide((*i)->rank));
+ pb::Peptide* pb_peptide = getPbPeptide(peptide);
+ sp_scorer->Score(*pb_peptide, spData.back().second);
+ delete pb_peptide;
+ }
+ sort(spData.begin(), spData.end(), spGreater());
+ for (size_t i = 0; i < spData.size(); ++i) {
+ sp_rank_map->insert(make_pair(
+ spData[i].first, make_pair(spData[i].second, i + 1)));
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/TideMatchSet.h b/src/app/TideMatchSet.h
new file mode 100644
index 0000000..ac6716d
--- /dev/null
+++ b/src/app/TideMatchSet.h
@@ -0,0 +1,221 @@
+#ifndef TIDE_MATCH_SET_H
+#define TIDE_MATCH_SET_H
+
+#include <boost/thread.hpp>
+#include <vector>
+#include "raw_proteins.pb.h"
+#include "tide/records.h"
+#include "tide/active_peptide_queue.h" // no include guard
+#include "tide/fixed_cap_array.h"
+#include "tide/peptide.h"
+#include "tide/sp_scorer.h"
+#include "tide/spectrum_collection.h"
+
+#include "model/Modification.h"
+#include "model/PostProcessProtein.h"
+
+using namespace std;
+
+typedef vector<const pb::Protein*> ProteinVec;
+
+class TideMatchSet {
+
+ public:
+ bool exact_pval_search_;
+ int elution_window_;
+
+ typedef pair<int, int> Pair2;
+ typedef FixedCapacityArray<Pair2> Arr2;
+
+// typedef pair<pair<double, double>, int> Pair; //store results for exact_pval calculations
+// typedef FixedCapacityArray<Pair> Arr;
+
+ struct Scores {
+ double xcorr_score;
+ double xcorr_pval;
+ int resEv_score;
+ double resEv_pval;
+ double combinedPval;
+ int rank;
+ };
+ typedef FixedCapacityArray<Scores> Arr;
+
+ // Matches will be an array of pairs, (score, counter), where counter refers
+ // to the index within the ActivePeptideQueue, counting from the back. This
+ // slight complication is due to the way the generated machine code fills the
+ // counter in the matches buffer by decrementing the counter.
+ TideMatchSet(
+ Arr* matches,
+ double max_mz
+ );
+ TideMatchSet(
+ Peptide* peptide,
+ double max_mz
+ );
+
+ ~TideMatchSet();
+
+ /**
+ * Write peptide centric matches to output files
+ */
+ void report(
+ ofstream* target_file, ///< target file to write to
+ ofstream* decoy_file, ///< decoy file to write to
+ int top_matches,
+ const ActivePeptideQueue* peptides, ///< peptide queue
+ const ProteinVec& proteins, ///< proteins corresponding with peptides
+ const vector<const pb::AuxLocation*>& locations, ///< auxiliary locations
+ bool compute_sp ///< whether to compute sp or not
+ );
+
+ /**
+ * Write spectrum centric to output files
+ */
+ void report(
+ ofstream* target_file, ///< target file to write to
+ ofstream* decoy_file, ///< decoy file to write to
+ int top_n, ///< number of matches to report
+ const string& spectrum_filename, ///< name of spectrum file
+ const Spectrum* spectrum, ///< spectrum for matches
+ int charge, ///< charge for matches
+ const ActivePeptideQueue* peptides, ///< peptide queue
+ const ProteinVec& proteins, ///< proteins corresponding with peptides
+ const vector<const pb::AuxLocation*>& locations, ///< auxiliary locations
+ bool compute_sp, ///< whether to compute sp or not
+ bool highScoreBest, //< indicates semantics of score magnitude
+ boost::mutex * rwlock
+ );
+
+ static void writeHeaders(
+ ofstream* file,
+ bool decoyFile,
+ bool sp
+ );
+
+ static void initModMap(const pb::ModTable& modTable, ModPosition position);
+
+ static string CleavageType;
+
+ protected:
+ Arr* matches_;
+ Arr2* matches2_;
+ Peptide* peptide_;
+ double max_mz_;
+
+ // For allocation
+ static char match_collection_loc_[sizeof(MatchCollection)];
+ static char decoy_match_collection_loc_[sizeof(MatchCollection)];
+
+ static bool lessXcorrScore(const Scores& x, const Scores& y) {
+ return x.xcorr_score < y.xcorr_score;
+ }
+
+ static bool moreXcorrScore(const Scores& x, const Scores& y) {
+ return x.xcorr_score > y.xcorr_score;
+ }
+
+ static bool lessXcorrPvalScore(const Scores& x, const Scores& y) {
+ return x.xcorr_pval < y.xcorr_pval;
+ }
+
+ static bool moreXcorrPvalScore(const Scores& x, const Scores& y) {
+ return x.xcorr_pval > y.xcorr_pval;
+ }
+
+/**
+ * Helper function for tab delimited report function for peptide centric
+ */
+ void writeToFile(
+ ofstream* file,
+ const ActivePeptideQueue* peptides,
+ const ProteinVec& proteins,
+ const vector<const pb::AuxLocation*>& locations,
+ bool compute_sp ///< whether to compute sp or not
+ );
+
+ /**
+ * Helper function for tab delimited report function
+ */
+ void writeToFile(
+ ofstream* file,
+ int top_n,
+ const vector<Arr::iterator>& vec,
+ const string& spectrum_filename,
+ const Spectrum* spectrum,
+ int charge,
+ const ActivePeptideQueue* peptides,
+ const ProteinVec& proteins,
+ const vector<const pb::AuxLocation*>& locations,
+ const map<Arr::iterator, FLOAT_T>& delta_cn_map,
+ const map<Arr::iterator, FLOAT_T>& delta_lcn_map,
+ const map<Arr::iterator, pair<const SpScorer::SpScoreData, int> >* sp_map,
+ boost::mutex * rwlock
+ );
+
+ Crux::Peptide getCruxPeptide(const Peptide* peptide);
+ std::vector<Crux::Modification> getMods(const Peptide* peptide);
+
+ void gatherTargetsAndDecoys(
+ const ActivePeptideQueue* peptides,
+ const ProteinVec& proteins,
+ vector<Arr::iterator>& targetsOut,
+ vector<Arr::iterator>& decoysOut,
+ int top_n,
+ bool highScoreBest // indicates semantics of score magnitude
+ );
+
+ /**
+ * Create a pb peptide from Tide peptide
+ */
+ static pb::Peptide* getPbPeptide(
+ const Peptide& peptide
+ );
+
+ /**
+ * Gets the protein name with the index appended.
+ */
+ static string getProteinName(
+ const pb::Protein& protein,
+ int pos
+ );
+
+ /**
+ * Gets the flanking AAs for a Tide peptide sequence
+ */
+ static void getFlankingAAs(
+ const Peptide* peptide, ///< Tide peptide to get flanking AAs for
+ const pb::Protein* protein, ///< Tide protein for the peptide
+ int pos, ///< location of peptide within protein
+ string* out_n, ///< out parameter for n flank
+ string* out_c ///< out parameter for c flank
+ );
+
+ static void computeDeltaCns(
+ const vector<Arr::iterator>& vec, // xcorr*100000000.0, high to low
+ map<Arr::iterator, FLOAT_T>* delta_cn_map, // map to add delta cn scores to
+ map<Arr::iterator, FLOAT_T>* delta_lcn_map
+ );
+
+ static void computeSpData(
+ const vector<Arr::iterator>& vec,
+ map<Arr::iterator, pair<const SpScorer::SpScoreData, int> >* sp_rank_map,
+ SpScorer* sp_scorer,
+ const ActivePeptideQueue* peptides
+ );
+
+ struct spGreater {
+ inline bool operator() (const pair<Arr::iterator, SpScorer::SpScoreData>& lhs,
+ const pair<Arr::iterator, SpScorer::SpScoreData>& rhs) {
+ return lhs.second.sp_score > rhs.second.sp_score;
+ }
+ };
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/TideSearchApplication.cpp b/src/app/TideSearchApplication.cpp
new file mode 100644
index 0000000..73325da
--- /dev/null
+++ b/src/app/TideSearchApplication.cpp
@@ -0,0 +1,1409 @@
+#include <cstdio>
+#include "app/tide/abspath.h"
+#include "app/tide/records_to_vector-inl.h"
+
+#include "io/carp.h"
+#include "parameter.h"
+#include "io/SpectrumRecordWriter.h"
+#include "TideIndexApplication.h"
+#include "TideSearchApplication.h"
+#include "ParamMedicApplication.h"
+#include "PSMConvertApplication.h"
+#include "tide/mass_constants.h"
+#include "TideMatchSet.h"
+#include "util/Params.h"
+#include "util/FileUtils.h"
+#include "util/StringUtils.h"
+
+bool TideSearchApplication::HAS_DECOYS = false;
+bool TideSearchApplication::PROTEIN_LEVEL_DECOYS = false;
+
+/* This constant is the product of the original "magic number" (10000,
+ * on line 4622 of search28.c) that was used to rescale the XCorr
+ * score, and the integerization constant used by Benjamin Diament in
+ * Tide. In the Tide publication, that constant was reported as 10^7.
+ * However, here it appears to be only 10^4.
+ *
+ * --WSN, 10 March 2015 */
+const double TideSearchApplication::XCORR_SCALING = 100000000.0;
+
+/* This constant is used to put the refactored XCorr back into the
+ * same range as the original XCorr score. It is the XCorr "magic
+ * number" (10000) divided by the EVIDENCE_SCALE_INT (defined in
+ * tide/spectrum_preprocess2.cc). */
+const double TideSearchApplication::RESCALE_FACTOR = 20.0;
+
+TideSearchApplication::TideSearchApplication():
+ exact_pval_search_(false), remove_index_(""), spectrum_flag_(NULL) {
+}
+
+TideSearchApplication::~TideSearchApplication() {
+ if (!remove_index_.empty()) {
+ carp(CARP_DEBUG, "Removing temp index '%s'", remove_index_.c_str());
+ FileUtils::Remove(remove_index_);
+ }
+}
+
+int TideSearchApplication::main(int argc, char** argv) {
+ return main(Params::GetStrings("tide spectra file"));
+}
+int TideSearchApplication::main(const vector<string>& input_files) {
+ return main(input_files, Params::GetString("tide database"));
+}
+
+int TideSearchApplication::main(const vector<string>& input_files, const string input_index) {
+ carp(CARP_INFO, "Running tide-search...");
+
+ // prevent different output formats from using threading
+ if (Params::GetBool("peptide-centric-search") == true) {
+ NUM_THREADS = 1;
+ carp(CARP_INFO, "Threading for peptide-centric formats are not supported yet");
+ } else {
+ NUM_THREADS = Params::GetInt("num-threads");
+ }
+ if (NUM_THREADS < 1) {
+ NUM_THREADS = boost::thread::hardware_concurrency(); // MINIMUM # = 1.
+ // (Meaning just main thread) Do not make this value below 1.
+ // make sure that number of threads are reasonable, e.g. user did not specify millions of threads...
+ } else if (NUM_THREADS > 64) {
+ carp(CARP_INFO, "Requested Threads > 64, Will not thread.");
+ NUM_THREADS = 1;
+ }
+ carp(CARP_INFO, "Number of Threads: %d", NUM_THREADS); // prints the number of threads
+
+ const string index = input_index;
+ string peptides_file = FileUtils::Join(index, "pepix");
+ string proteins_file = FileUtils::Join(index, "protix");
+ string auxlocs_file = FileUtils::Join(index, "auxlocs");
+
+ double window = Params::GetDouble("precursor-window");
+ WINDOW_TYPE_T window_type = string_to_window_type(Params::GetString("precursor-window-type"));
+
+ // Check spectrum-charge parameter
+ string charge_string = Params::GetString("spectrum-charge");
+ int charge_to_search;
+ if (charge_string == "all") {
+ carp(CARP_DEBUG, "Searching all charge states");
+ charge_to_search = 0;
+ } else {
+ charge_to_search = atoi(charge_string.c_str());
+ if (charge_to_search < 1 || charge_to_search > 6) {
+ carp(CARP_FATAL, "Invalid spectrum-charge value %s", charge_string.c_str());
+ }
+ carp(CARP_DEBUG, "Searching charge state %d", charge_to_search);
+ }
+
+ // Check scan-number parameter
+ string scan_range = Params::GetString("scan-number");
+ int min_scan, max_scan;
+ if (scan_range.empty()) {
+ min_scan = 0;
+ max_scan = BILLION;
+ carp(CARP_DEBUG, "Searching all scans");
+ } else if (scan_range.find('-') == string::npos) {
+ // Single scan
+ min_scan = max_scan = atoi(scan_range.c_str());
+ carp(CARP_DEBUG, "Searching single scan %d", min_scan);
+ } else {
+ if (!get_range_from_string(scan_range.c_str(), min_scan, max_scan)) {
+ carp(CARP_FATAL, "The scan number range '%s' is invalid. "
+ "Must be of the form <first>-<last>", scan_range.c_str());
+ } else {
+ if (min_scan > max_scan) {
+ int tmp_scan = min_scan;
+ min_scan = max_scan;
+ max_scan = tmp_scan;
+ carp(CARP_DEBUG, "Switched scan range min and max");
+ }
+ carp(CARP_DEBUG, "Searching scan range %d-%d", min_scan, max_scan);
+ }
+ }
+ //check to compute exact p-value
+ exact_pval_search_ = Params::GetBool("exact-p-value");
+ bin_width_ = Params::GetDouble("mz-bin-width");
+ bin_offset_ = Params::GetDouble("mz-bin-offset");
+ // for now don't allow XCorr p-value searches with variable bin width
+ if (exact_pval_search_ && !Params::IsDefault("mz-bin-width")) {
+ carp(CARP_FATAL, "Tide-search with XCorr p-values and variable bin width "
+ "is not allowed in this version of Crux.");
+ }
+
+ // Check concat parameter
+ bool concat = Params::GetBool("concat");
+
+ // Check compute-sp parameter
+ bool compute_sp = Params::GetBool("compute-sp");
+ if (Params::GetBool("sqt-output") && !compute_sp) {
+ compute_sp = true;
+ carp(CARP_INFO, "Enabling parameter compute-sp since SQT output is enabled "
+ "(this will increase runtime).");
+ }
+
+ // Check isotope-error parameter
+ string isotope_errors_string = Params::GetString("isotope-error");
+ if (isotope_errors_string[0] == ',') {
+ carp(CARP_FATAL, "Error in isotope_error parameter formatting: (%s)", isotope_errors_string.c_str());
+ }
+ for (int i = 0; isotope_errors_string[i] != '\0'; ++i) {
+ if (isotope_errors_string[i] == ',' && (isotope_errors_string[i+1] == ',' || isotope_errors_string[i+1] == '\0')) {
+ carp(CARP_FATAL, "Error in isotope_error parameter formatting: (%s) ", isotope_errors_string.c_str());
+ }
+ }
+
+ vector<int>* negative_isotope_errors = new vector<int>();
+ negative_isotope_errors->push_back(0);
+
+ if (isotope_errors_string != "") {
+ vector<int> isotope_errors = StringUtils::Split<int>(Params::GetString("isotope-error"), ',');
+ for (vector<int>::iterator it = isotope_errors.begin(); it != isotope_errors.end(); ++it) {
+ if (*it < 0) {
+ carp(CARP_FATAL, "Found a negative isotope error: %d. There should not be any legitimate reasons to use negative isotope errors. Try modeling with a modification instead.", *it);
+ } else if (find(negative_isotope_errors->begin(), negative_isotope_errors->end(), -1 * *it) != negative_isotope_errors->end()) {
+ carp(CARP_FATAL, "Found duplicate when parsing isotope_error parameter: %d", *it);
+ }
+ negative_isotope_errors->push_back(-1 * *it);
+ }
+ }
+
+ sort(negative_isotope_errors->begin(), negative_isotope_errors->end());
+
+ carp(CARP_INFO, "Reading index %s", index.c_str());
+ // Read proteins index file
+ ProteinVec proteins;
+ pb::Header protein_header;
+ if (!ReadRecordsToVector<pb::Protein, const pb::Protein>(&proteins,
+ proteins_file, &protein_header)) {
+ carp(CARP_FATAL, "Error reading index (%s)", proteins_file.c_str());
+ }
+ carp(CARP_DEBUG, "Read %d proteins", proteins.size());
+
+ //open a copy of peptide buffer for Amino Acid Frequency (AAF) calculation.
+ double* aaFreqN = NULL;
+ double* aaFreqI = NULL;
+ double* aaFreqC = NULL;
+ int* aaMass = NULL;
+ int nAA = 0;
+
+ if (exact_pval_search_) {
+ pb::Header aaf_peptides_header;
+ HeadedRecordReader aaf_peptide_reader(peptides_file, &aaf_peptides_header);
+
+ if ((aaf_peptides_header.file_type() != pb::Header::PEPTIDES) ||
+ !aaf_peptides_header.has_peptides_header()) {
+ carp(CARP_FATAL, "Error reading index (%s)", peptides_file.c_str());
+ }
+ MassConstants::Init(&aaf_peptides_header.peptides_header().mods(),
+ &aaf_peptides_header.peptides_header().nterm_mods(),
+ &aaf_peptides_header.peptides_header().cterm_mods(),
+ bin_width_, bin_offset_);
+ ActivePeptideQueue* active_peptide_queue =
+ new ActivePeptideQueue(aaf_peptide_reader.Reader(), proteins);
+ nAA = active_peptide_queue->CountAAFrequency(bin_width_, bin_offset_,
+ &aaFreqN, &aaFreqI, &aaFreqC, &aaMass);
+ delete active_peptide_queue;
+ } // End calculation AA frequencies
+
+ // Read auxlocs index file
+ vector<const pb::AuxLocation*> locations;
+ if (!ReadRecordsToVector<pb::AuxLocation>(&locations, auxlocs_file)) {
+ carp(CARP_FATAL, "Error reading index (%s)", auxlocs_file.c_str());
+ }
+ carp(CARP_DEBUG, "Read %d auxlocs", locations.size());
+
+ // Read peptides index file
+ pb::Header peptides_header;
+
+ vector<HeadedRecordReader*> peptide_reader;
+ for (int i = 0; i < NUM_THREADS; i++) {
+ peptide_reader.push_back(new HeadedRecordReader(peptides_file, &peptides_header));
+ }
+
+ if ((peptides_header.file_type() != pb::Header::PEPTIDES) ||
+ !peptides_header.has_peptides_header()) {
+ carp(CARP_FATAL, "Error reading index (%s)", peptides_file.c_str());
+ }
+
+ const pb::Header::PeptidesHeader& pepHeader = peptides_header.peptides_header();
+ DECOY_TYPE_T headerDecoyType = (DECOY_TYPE_T)pepHeader.decoys();
+ if (headerDecoyType != NO_DECOYS) {
+ HAS_DECOYS = true;
+ if (headerDecoyType == PROTEIN_REVERSE_DECOYS) {
+ PROTEIN_LEVEL_DECOYS = true;
+ }
+ }
+
+ MassConstants::Init(&pepHeader.mods(), &pepHeader.nterm_mods(),
+ &pepHeader.cterm_mods(), bin_width_, bin_offset_);
+ ModificationDefinition::ClearAll();
+ TideMatchSet::initModMap(pepHeader.mods(), ANY);
+ TideMatchSet::initModMap(pepHeader.nterm_mods(), PEPTIDE_N);
+ TideMatchSet::initModMap(pepHeader.cterm_mods(), PEPTIDE_C);
+
+ ofstream* target_file = NULL;
+ ofstream* decoy_file = NULL;
+
+ carp(CARP_DEBUG, "Using TideMatchSet to write matches");
+ bool overwrite = Params::GetBool("overwrite");
+ stringstream ss;
+ ss << Params::GetString("enzyme") << '-' << Params::GetString("digestion");
+ TideMatchSet::CleavageType = ss.str();
+ if (!concat) {
+ string target_file_name = make_file_path("tide-search.target.txt");
+ target_file = create_stream_in_path(target_file_name.c_str(), NULL, overwrite);
+ output_file_name_ = target_file_name;
+ if (HAS_DECOYS) {
+ string decoy_file_name = make_file_path("tide-search.decoy.txt");
+ decoy_file = create_stream_in_path(decoy_file_name.c_str(), NULL, overwrite);
+ }
+ } else {
+ string concat_file_name = make_file_path("tide-search.txt");
+ target_file = create_stream_in_path(concat_file_name.c_str(), NULL, overwrite);
+ output_file_name_ = concat_file_name;
+ }
+
+ if (target_file) {
+ TideMatchSet::writeHeaders(target_file, false, compute_sp);
+ TideMatchSet::writeHeaders(decoy_file, true, compute_sp);
+ }
+
+ // Try to read all spectrum files as spectrumrecords, convert those that fail
+ vector<InputFile> input_sr;
+ for (vector<string>::const_iterator f = input_files.begin(); f != input_files.end(); f++) {
+ SpectrumCollection spectra;
+ pb::Header spectrum_header;
+ string spectrumrecords = *f;
+ bool keepSpectrumrecords = true;
+ if (!spectra.ReadSpectrumRecords(spectrumrecords, &spectrum_header)) {
+ // Failed, try converting to spectrumrecords file
+ carp(CARP_INFO, "Converting %s to spectrumrecords format", f->c_str());
+ carp(CARP_INFO, "Elapsed time starting conversion: %.3g s", wall_clock() / 1e6);
+ spectrumrecords = Params::GetString("store-spectra");
+ keepSpectrumrecords = !spectrumrecords.empty();
+ if (!keepSpectrumrecords) {
+ spectrumrecords = make_file_path(FileUtils::BaseName(*f) + ".spectrumrecords.tmp");
+ } else if (input_files.size() > 1) {
+ carp(CARP_FATAL, "Cannot use store-spectra option with multiple input "
+ "spectrum files");
+ }
+ carp(CARP_DEBUG, "New spectrumrecords filename: %s", spectrumrecords.c_str());
+ if (!SpectrumRecordWriter::convert(*f, spectrumrecords)) {
+ carp(CARP_FATAL, "Error converting %s to spectrumrecords format", f->c_str());
+ }
+ carp(CARP_DEBUG, "Reading converted spectra file %s", spectrumrecords.c_str());
+ // Re-read converted file as spectrumrecords file
+ if (!spectra.ReadSpectrumRecords(spectrumrecords, &spectrum_header)) {
+ carp(CARP_DEBUG, "Deleting %s", spectrumrecords.c_str());
+ remove(spectrumrecords.c_str());
+ carp(CARP_FATAL, "Error reading spectra file %s", spectrumrecords.c_str());
+ }
+ }
+ input_sr.push_back(InputFile(*f, spectrumrecords, keepSpectrumrecords));
+ }
+
+ // Loop through spectrum files
+ for (vector<InputFile>::const_iterator f = input_sr.begin();
+ f != input_sr.end();
+ f++) {
+
+ if (!peptide_reader[0]) {
+ for (int i = 0; i < NUM_THREADS; i++) {
+ peptide_reader[i] = new HeadedRecordReader(peptides_file, &peptides_header);
+ }
+ }
+
+ vector<ActivePeptideQueue*> active_peptide_queue;
+ for (int i = 0; i < NUM_THREADS; i++) {
+ active_peptide_queue.push_back(new ActivePeptideQueue(peptide_reader[i]->Reader(), proteins));
+ active_peptide_queue[i]->SetBinSize(bin_width_, bin_offset_);
+ }
+
+ string spectra_file = f->SpectrumRecords;
+ carp(CARP_INFO, "Reading spectra file %s", spectra_file.c_str());
+ // Try to read file as spectrumrecords file
+ SpectrumCollection spectra;
+ pb::Header spectrum_header;
+ if (!spectra.ReadSpectrumRecords(spectra_file, &spectrum_header)) {
+ // This should never happen since we would have failed earlier
+ carp(CARP_FATAL, "Error reading spectra file %s", spectra_file.c_str());
+ }
+
+ carp(CARP_INFO, "Sorting spectra");
+ if (window_type != WINDOW_MZ) {
+ spectra.Sort();
+ } else {
+ spectra.Sort<ScSortByMz>(ScSortByMz(window));
+ }
+
+ double highest_mz = spectra.FindHighestMZ();
+ unsigned int spectrum_num = spectra.SpecCharges()->size();
+ if (spectrum_num > 0 && exact_pval_search_) {
+ highest_mz = spectra.SpecCharges()->at(spectrum_num - 1).neutral_mass;
+ }
+ carp(CARP_DEBUG, "Max m/z %f", highest_mz);
+ MaxBin::SetGlobalMax(highest_mz);
+ // Do the search
+ carp(CARP_INFO, "Running search");
+ if (spectrum_flag_ == NULL) {
+ resetMods();
+ }
+ search(f->OriginalName, spectra.SpecCharges(), active_peptide_queue, proteins,
+ locations, window, window_type, Params::GetDouble("spectrum-min-mz"),
+ Params::GetDouble("spectrum-max-mz"), min_scan, max_scan,
+ Params::GetInt("min-peaks"), charge_to_search,
+ Params::GetInt("top-match"), spectra.FindHighestMZ(),
+ target_file, decoy_file, compute_sp,
+ nAA, aaFreqN, aaFreqI, aaFreqC, aaMass, negative_isotope_errors);
+
+ PSMConvertApplication converter;
+
+ // convert tab delimited to other file formats.
+ if (!concat) {
+ string target_file_name = make_file_path("tide-search.target.txt");
+ if (Params::GetBool("pin-output")) {
+ converter.convertFile("tsv", "pin", target_file_name, "tide-search.target.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("pepxml-output")) {
+ converter.convertFile("tsv", "pepxml", target_file_name, "tide-search.target.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("mzid-output")) {
+ converter.convertFile("tsv", "mzidentml", target_file_name, "tide-search.target.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("sqt-output")) {
+ converter.convertFile("tsv", "sqt", target_file_name, "tide-search.target.", Params::GetString("protein-database"), true);
+ }
+
+ if (HAS_DECOYS) {
+ string decoy_file_name = make_file_path("tide-search.decoy.txt");
+ if (Params::GetBool("pin-output")) {
+ converter.convertFile("tsv", "pin", decoy_file_name, "tide-search.decoy.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("pepxml-output")) {
+ converter.convertFile("tsv", "pepxml", decoy_file_name, "tide-search.decoy.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("mzid-output")) {
+ converter.convertFile("tsv", "mzidentml", decoy_file_name, "tide-search.decoy.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("sqt-output")) {
+ converter.convertFile("tsv", "sqt", decoy_file_name, "tide-search.decoy.", Params::GetString("protein-database"), true);
+ }
+ }
+ } else {
+ string concat_file_name = make_file_path("tide-search.txt");
+ if (Params::GetBool("pin-output")) {
+ converter.convertFile("tsv", "pin", concat_file_name, "tide-search.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("pepxml-output")) {
+ converter.convertFile("tsv", "pepxml", concat_file_name, "tide-search.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("mzid-output")) {
+ converter.convertFile("tsv", "mzidentml", concat_file_name, "tide-search.", Params::GetString("protein-database"), true);
+ }
+ if (Params::GetBool("sqt-output")) {
+ converter.convertFile("tsv", "sqt", concat_file_name, "tide-search.", Params::GetString("protein-database"), true);
+ }
+ }
+
+ // Delete temporary spectrumrecords file
+ if (!f->Keep) {
+ carp(CARP_DEBUG, "Deleting %s", spectra_file.c_str());
+ remove(spectra_file.c_str());
+ }
+
+ // Clean up
+ for (int i = 0; i < NUM_THREADS; i++) {
+ delete active_peptide_queue[i];
+ delete peptide_reader[i];
+ peptide_reader[i] = NULL;
+ }
+
+ } // End of spectrum file loop
+
+ delete negative_isotope_errors;
+
+ for (ProteinVec::iterator i = proteins.begin(); i != proteins.end(); ++i) {
+ delete *i;
+ }
+ if (target_file) {
+ delete target_file;
+ if (decoy_file) {
+ delete decoy_file;
+ }
+ }
+ delete[] aaFreqN;
+ delete[] aaFreqI;
+ delete[] aaFreqC;
+ delete[] aaMass;
+
+ return 0;
+}
+
+void TideSearchApplication::search(void* threadarg) {
+ struct thread_data *my_data = (struct thread_data *) threadarg;
+
+ const string& spectrum_filename = my_data->spectrum_filename;
+ const vector<SpectrumCollection::SpecCharge>* spec_charges = my_data->spec_charges;
+ ActivePeptideQueue* active_peptide_queue = my_data->active_peptide_queue;
+ ProteinVec& proteins = my_data->proteins;
+ vector<const pb::AuxLocation*>& locations = my_data->locations;
+ double precursor_window = my_data->precursor_window;
+ WINDOW_TYPE_T window_type = my_data->window_type;
+ double spectrum_min_mz = my_data->spectrum_min_mz;
+ double spectrum_max_mz = my_data->spectrum_max_mz;
+ int min_scan = my_data->min_scan;
+ int max_scan = my_data->max_scan;
+ int min_peaks = my_data->min_peaks;
+ int search_charge = my_data->search_charge;
+ int top_matches = my_data->top_matches;
+ double highest_mz = my_data->highest_mz;
+ ofstream* target_file = my_data -> target_file;
+ ofstream* decoy_file = my_data->decoy_file;
+ bool compute_sp = my_data->compute_sp;
+ int64_t thread_num = my_data->thread_num;
+ int64_t num_threads = my_data->num_threads;
+ int nAA = my_data->nAA;
+ double* aaFreqN = my_data->aaFreqN;
+ double* aaFreqI = my_data->aaFreqI;
+ double* aaFreqC = my_data->aaFreqC;
+ int* aaMass = my_data->aaMass;
+ vector<boost::mutex*> locks_array = my_data->locks_array;
+ vector<int>* negative_isotope_errors = my_data->negative_isotope_errors;
+
+ double bin_width = my_data->bin_width;
+ double bin_offset = my_data->bin_offset;
+ bool exact_pval_search = my_data->exact_pval_search;
+ map<pair<string, unsigned int>, bool>* spectrum_flag = my_data->spectrum_flag;
+
+ int* sc_index = my_data->sc_index;
+ int* total_candidate_peptides = my_data->total_candidate_peptides;
+
+ // params
+ bool peptide_centric = Params::GetBool("peptide-centric-search");
+ bool use_neutral_loss_peaks = Params::GetBool("use-neutral-loss-peaks");
+ bool use_flanking_peaks = Params::GetBool("use-flanking-peaks");
+ int max_charge = Params::GetInt("max-precursor-charge");
+
+ // This is the main search loop.
+ ObservedPeakSet observed(bin_width, bin_offset,
+ use_neutral_loss_peaks,
+ use_flanking_peaks);
+
+ // cycle through spectrum-charge pairs, sorted by neutral mass
+ FLOAT_T sc_total = (FLOAT_T)spec_charges->size();
+ int print_interval = Params::GetInt("print-search-progress");
+
+ for (vector<SpectrumCollection::SpecCharge>::const_iterator sc = spec_charges->begin()+thread_num;
+ sc < spec_charges->begin() + (spec_charges->size());
+ sc = sc + num_threads) {
+
+ locks_array[3]->lock();
+ ++(*sc_index);
+ if (print_interval > 0 && *sc_index % print_interval == 0) {
+ carp(CARP_INFO, "%d spectrum-charge combinations searched, %.0f%% complete",
+ *sc_index, *sc_index / sc_total * 100);
+ }
+ locks_array[3]->unlock();
+
+ Spectrum* spectrum = sc->spectrum;
+ double precursor_mz = spectrum->PrecursorMZ();
+ int charge = sc->charge;
+ int scan_num = spectrum->SpectrumNumber();
+ if (spectrum_flag != NULL) {
+ locks_array[1]->lock();
+ map<pair<string, unsigned int>, bool>::iterator spectrum_id;
+ spectrum_id = spectrum_flag->find(pair<string, unsigned int>(
+ spectrum_filename, scan_num * 10 + charge));
+ if (spectrum_id != spectrum_flag->end()) {
+ locks_array[1]->unlock();
+ continue;
+ }
+ locks_array[1]->unlock();
+ }
+
+ if (precursor_mz < spectrum_min_mz || precursor_mz > spectrum_max_mz ||
+ scan_num < min_scan || scan_num > max_scan ||
+ spectrum->Size() < min_peaks ||
+ (search_charge != 0 && charge != search_charge) || charge > max_charge) {
+ continue;
+ }
+
+ // The active peptide queue holds the candidate peptides for spectrum.
+ // Calculate and set the window, depending on the window type.
+ vector<double>* min_mass = new vector<double>();
+ vector<double>* max_mass = new vector<double>();
+ vector<bool>* candidatePeptideStatus = new vector<bool>();
+ double min_range, max_range;
+ computeWindow(*sc, window_type, precursor_window, max_charge, negative_isotope_errors, min_mass, max_mass, &min_range, &max_range);
+ if (!exact_pval_search) { //execute original tide-search program
+
+ // Normalize the observed spectrum and compute the cache of
+ // frequently-needed values for taking dot products with theoretical
+ // spectra.
+ observed.PreprocessSpectrum(*spectrum, charge);
+ int nCandPeptide = active_peptide_queue->SetActiveRange(min_mass, max_mass, min_range, max_range, candidatePeptideStatus);
+ if (nCandPeptide == 0) {
+ continue;
+ }
+ locks_array[2]->lock();
+ (*total_candidate_peptides) += nCandPeptide;
+ locks_array[2]->unlock();
+
+ int candidatePeptideStatusSize = candidatePeptideStatus->size();
+ TideMatchSet::Arr2 match_arr2(candidatePeptideStatusSize); // Scored peptides will go here.
+
+ // Programs for taking the dot-product with the observed spectrum are laid
+ // out in memory managed by the active_peptide_queue, one program for each
+ // candidate peptide. The programs will store the results directly into
+ // match_arr. We now pass control to those programs.
+ collectScoresCompiled(active_peptide_queue, spectrum, observed, &match_arr2,
+ candidatePeptideStatusSize, charge);
+
+ // matches will arrange the results in a heap by score, return the top
+ // few, and recover the association between counter and peptide. We output
+ // the top matches.
+ if (peptide_centric) {
+ deque<Peptide*>::const_iterator iter_ = active_peptide_queue->iter_;
+ TideMatchSet::Arr2::iterator it = match_arr2.begin();
+ for (; it != match_arr2.end(); ++iter_, ++it) {
+ int peptide_idx = candidatePeptideStatusSize - (it->second);
+ if ((*candidatePeptideStatus)[peptide_idx]) {
+ (*iter_)->AddHit(spectrum, it->first,0.0,it->second,charge);
+ }
+ }
+ } else { //spectrum centric match report.
+ TideMatchSet::Arr match_arr(nCandPeptide);
+ for (TideMatchSet::Arr2::iterator it = match_arr2.begin();
+ it != match_arr2.end();
+ ++it) {
+ int peptide_idx = candidatePeptideStatusSize - (it->second);
+ if ((*candidatePeptideStatus)[peptide_idx]) {
+ TideMatchSet::Scores curScore;
+ curScore.xcorr_score = (double)(it->first / XCORR_SCALING);
+ curScore.rank = it->second;
+ match_arr.push_back(curScore);
+ }
+ }
+
+ TideMatchSet matches(&match_arr, highest_mz);
+ matches.exact_pval_search_ = exact_pval_search;
+
+ matches.report(target_file, decoy_file, top_matches, spectrum_filename,
+ spectrum, charge, active_peptide_queue, proteins,
+ locations, compute_sp, true, locks_array[0]);
+ } //end peptide_centric == true
+ } else { // execute exact-pval-search
+
+ const int minDeltaMass = aaMass[0];
+ const int maxDeltaMass = aaMass[nAA - 1];
+
+ int maxPrecurMass = floor(MaxBin::Global().CacheBinEnd() + 50.0); // TODO works, but is this the best way to get?
+ int nCandPeptide = active_peptide_queue->SetActiveRangeBIons(min_mass, max_mass, min_range, max_range, candidatePeptideStatus);
+ int candidatePeptideStatusSize = candidatePeptideStatus->size();
+ locks_array[2]->lock();
+ (*total_candidate_peptides) += nCandPeptide;
+ locks_array[2]->unlock();
+
+ TideMatchSet::Arr match_arr(nCandPeptide); //scored peptides will go here
+
+ // iterators needed at multiple places in following code
+ deque<Peptide*>::const_iterator iter_ = active_peptide_queue->iter_;
+ deque<TheoreticalPeakSetBIons>::const_iterator iter1_ = active_peptide_queue->iter1_;
+ vector<int>::const_iterator iter_int;
+ vector<unsigned int>::const_iterator iter_uint;
+
+ //************************************************************************
+ /* For one observed spectrum, calculates:
+ * - vector of cleavage evidence
+ * - score count vectors for a range of integer masses
+ * - p-values of XCorr match scores between spectrum and all selected candidate target and decoy peptides
+ * Written by Jeff Howbert, October, 2013.
+ * Ported to and integrated with Tide by Jeff Howbert, November, 2013.
+ */
+ int peidx;
+ int pe;
+ int ma;
+ int pepMaInt;
+ int* pepMassInt = new int[nCandPeptide];
+ vector<int> pepMassIntUnique;
+ pepMassIntUnique.reserve(nCandPeptide);
+
+ peidx = 0;
+ pe = 0;
+ for (iter_ = active_peptide_queue->iter_;
+ iter_ != active_peptide_queue->end_;
+ ++iter_) {
+ if ((*candidatePeptideStatus)[peidx]) {
+ double pepMass = (*iter_)->Mass();
+ pepMaInt = MassConstants::mass2bin(pepMass);
+ pepMassInt[pe] = pepMaInt;
+ pepMassIntUnique.push_back(pepMaInt);
+ pe++;
+ }
+ peidx++;
+ }
+ std::sort(pepMassIntUnique.begin(), pepMassIntUnique.end());
+ vector<int>::iterator last = std::unique(pepMassIntUnique.begin(),
+ pepMassIntUnique.end());
+ pepMassIntUnique.erase(last, pepMassIntUnique.end());
+ int nPepMassIntUniq = (int)pepMassIntUnique.size();
+
+ int** evidenceObs = new int*[nPepMassIntUniq];
+ int* scoreOffsetObs = new int[nPepMassIntUniq];
+ double** pValueScoreObs = new double*[nPepMassIntUniq];
+ int* intensArrayTheor = new int[maxPrecurMass]; // initialized later in loop
+ for (pe = 0; pe < nPepMassIntUniq; pe++) { // TODO should probably instead use iterator over pepMassIntUnique
+ evidenceObs[pe] = new int[maxPrecurMass];
+ for (ma = 0; ma < maxPrecurMass; ma++) {
+ evidenceObs[pe][ma] = 0;
+ }
+ scoreOffsetObs[pe] = 0;
+ pepMaInt = pepMassIntUnique[pe]; // TODO should be accessed with an iterator
+ // preprocess to create one integerized evidence vector for each cluster of masses among selected peptides
+ double pepMassMonoMean = (pepMaInt - 0.5 + bin_offset) * bin_width;
+ observed.CreateEvidenceVector(*spectrum, bin_width, bin_offset, charge,
+ pepMassMonoMean, maxPrecurMass, evidenceObs[pe]);
+ // NOTE: will have to go back to separate dynamic programming for
+ // target and decoy if they have different probNI and probC
+ int maxEvidence = *std::max_element(evidenceObs[pe], evidenceObs[pe] + maxPrecurMass);
+ int minEvidence = *std::min_element(evidenceObs[pe], evidenceObs[pe] + maxPrecurMass);
+ // estimate maxScore and minScore
+ int maxNResidue = (int)floor((double)pepMaInt / (double)minDeltaMass);
+ vector<int> sortEvidenceObs (evidenceObs[pe], evidenceObs[pe] + maxPrecurMass);
+ std::sort(sortEvidenceObs.begin(), sortEvidenceObs.end(), greater<int>());
+ int maxScore = 0;
+ int minScore = 0;
+ for (int sc = 0; sc < maxNResidue; sc++) {
+ maxScore += sortEvidenceObs[sc];
+ }
+ for (int sc = maxPrecurMass - maxNResidue; sc < maxPrecurMass; sc++) {
+ minScore += sortEvidenceObs[sc];
+ }
+ int bottomRowBuffer = maxEvidence + 1;
+ int topRowBuffer = -minEvidence;
+ int nRowDynProg = bottomRowBuffer - minScore + 1 + maxScore + topRowBuffer;
+ pValueScoreObs[pe] = new double[nRowDynProg];
+
+ scoreOffsetObs[pe] = calcScoreCount(maxPrecurMass, evidenceObs[pe], pepMaInt,
+ maxEvidence, minEvidence, maxScore, minScore,
+ nAA, aaFreqN, aaFreqI, aaFreqC, aaMass,
+ pValueScoreObs[pe]);
+ }
+
+ // ***** calculate p-values for peptide-spectrum matches ***********************************
+ iter_ = active_peptide_queue -> iter_;
+ iter1_ = active_peptide_queue -> iter1_;
+ pe = 0;
+ for (peidx = 0; peidx < candidatePeptideStatusSize; peidx++) { // TODO should probably use iterator instead
+ if ((*candidatePeptideStatus)[peidx]) {
+ int pepMassIntIdx = 0;
+ for (ma = 0; ma < nPepMassIntUniq; ma++) { // TODO should probably use iterator instead
+ if (pepMassIntUnique[ma] == pepMassInt[pe]) { // TODO pepMassIntUnique should be accessed with an iterator
+ pepMassIntIdx = ma;
+ break;
+ }
+ }
+ // score XCorr for target peptide with integerized evidenceObs array
+ for (ma = 0; ma < maxPrecurMass; ma++) {
+ intensArrayTheor[ma] = 0;
+ }
+ for (iter_uint = iter1_->unordered_peak_list_.begin();
+ iter_uint != iter1_->unordered_peak_list_.end();
+ iter_uint++) {
+ intensArrayTheor[*iter_uint] = 1;
+ }
+
+ int scoreRefactInt = 0;
+ for (ma = 0; ma < maxPrecurMass; ma++) {
+ scoreRefactInt += evidenceObs[pepMassIntIdx][ma] * intensArrayTheor[ma];
+ }
+ int scoreCountIdx = scoreRefactInt + scoreOffsetObs[pepMassIntIdx];
+ double pValue = pValueScoreObs[pepMassIntIdx][scoreCountIdx];
+ if (peptide_centric) {
+ (*iter_)->AddHit(spectrum, pValue, (double)scoreRefactInt, candidatePeptideStatusSize - peidx, charge);
+ } else {
+ TideMatchSet::Scores curScores;
+ curScores.xcorr_pval = pValue;
+ curScores.xcorr_score = (double)scoreRefactInt / RESCALE_FACTOR;
+ curScores.rank = candidatePeptideStatusSize - peidx; // TODO ugly hack to conform with the way these indices are generated in standard tide-search
+ match_arr.push_back(curScores);
+ }
+ ++pe;
+ }
+
+ // move to next peptide and b ion queue
+ ++iter_; // TODO need to add test to make sure haven't gone past available peptides
+ ++iter1_; // TODO need to add test to make sure haven't gone past available b ion queues
+ }
+ // clean up
+ delete [] pepMassInt;
+ delete [] scoreOffsetObs;
+ for (pe = 0; pe < nPepMassIntUniq; pe++) {
+ delete [] evidenceObs[pe];
+ delete [] pValueScoreObs[pe];
+ }
+ delete [] evidenceObs;
+ delete [] pValueScoreObs;
+ delete [] intensArrayTheor;
+ if (!peptide_centric) {
+ // matches will arrange the results in a heap by score, return the top
+ // few, and recover the association between counter and peptide. We output
+ // the top matches.
+ TideMatchSet matches(&match_arr, highest_mz);
+ matches.exact_pval_search_ = exact_pval_search;
+
+ matches.report(target_file, decoy_file, top_matches, spectrum_filename,
+ spectrum, charge, active_peptide_queue, proteins,
+ locations, compute_sp, false, locks_array[0]);
+
+ } // end peptide_centric == true
+ } // end exact-pval-search
+ delete min_mass;
+ delete max_mass;
+ delete candidatePeptideStatus;
+ }
+}
+
+void TideSearchApplication::search(
+ const string& spectrum_filename,
+ const vector<SpectrumCollection::SpecCharge>* spec_charges,
+ vector<ActivePeptideQueue*> active_peptide_queue,
+ ProteinVec& proteins,
+ vector<const pb::AuxLocation*>& locations,
+ double precursor_window,
+ WINDOW_TYPE_T window_type,
+ double spectrum_min_mz,
+ double spectrum_max_mz,
+ int min_scan,
+ int max_scan,
+ int min_peaks,
+ int search_charge,
+ int top_matches,
+ double highest_mz,
+ ofstream* target_file,
+ ofstream* decoy_file,
+ bool compute_sp,
+ int nAA,
+ double* aaFreqN,
+ double* aaFreqI,
+ double* aaFreqC,
+ int* aaMass,
+ vector<int>* negative_isotope_errors
+) {
+ // Create an array of 4 locks.
+ // Lock #0: Results file output
+ // Lock #1: Only used by cascade-search on spectrum_flag (map)
+ // Lock #2: Updating # of candidate peptides
+ // Lock #3: Updating sc_index and reporting progress
+ int num_locks = 4;
+ vector<boost::mutex *> locks_array;
+
+ for (int i = 0; i < num_locks; i++) {
+ locks_array.push_back(new boost::mutex());
+ }
+
+ int elution_window = Params::GetInt("elution-window-size");
+ bool peptide_centric = Params::GetBool("peptide-centric-search");
+
+ // initialize fields required for output
+ int* sc_index = new int(-1);
+ int* total_candidate_peptides = new int(0);
+ FLOAT_T sc_total = (FLOAT_T)spec_charges->size();
+
+ if (peptide_centric == false) {
+ elution_window = 0;
+ }
+
+ for (int i = 0; i < NUM_THREADS; i++) {
+ active_peptide_queue[i]->setElutionWindow(elution_window);
+ active_peptide_queue[i]->setPeptideCentric(peptide_centric);
+ }
+
+ if (elution_window > 0 && elution_window % 2 == 0) {
+ for (int i = 0; i < NUM_THREADS; i++) {
+ active_peptide_queue[i]->setElutionWindow(elution_window+1);
+ }
+ }
+
+ if (!peptide_centric || !exact_pval_search_) {
+ for (int i = 0; i < NUM_THREADS; i++) {
+ active_peptide_queue[i]->setElutionWindow(0);
+ }
+ }
+
+ for (int i = 0; i < NUM_THREADS; i++) {
+ active_peptide_queue[i]->SetOutputs(NULL, &locations, top_matches, compute_sp, target_file, decoy_file, highest_mz);
+ }
+
+ // Creating structs to hold information required for each thread to search through
+ // a spec charge
+
+ vector<thread_data> thread_data_array;
+ for (int i= 0; i < NUM_THREADS; i++) {
+ thread_data_array.push_back(thread_data(spectrum_filename, spec_charges, active_peptide_queue[i],
+ proteins, locations, precursor_window, window_type, spectrum_min_mz,
+ spectrum_max_mz, min_scan, max_scan, min_peaks, search_charge, top_matches,
+ highest_mz, target_file, decoy_file, compute_sp,
+ i, NUM_THREADS, nAA, aaFreqN, aaFreqI, aaFreqC, aaMass, locks_array,
+ bin_width_, bin_offset_, exact_pval_search_, spectrum_flag_, sc_index, total_candidate_peptides, negative_isotope_errors));
+ }
+
+ boost::thread_group threadgroup;
+
+ // Launch threads
+ for (int64_t t = 1; t < NUM_THREADS; t++) {
+ boost::thread * currthread = new boost::thread(boost::bind(&TideSearchApplication::search, this, (void *) &(thread_data_array[t])));
+ threadgroup.add_thread(currthread);
+ }
+
+ // Searches through part of the spec charge vector while waiting for threads are busy
+ search( (void *) &(thread_data_array[0]) );
+
+ // Join threads
+ threadgroup.join_all();
+
+ carp(CARP_INFO, "Time per spectrum-charge combination: %lf s.", wall_clock() / (1e6*sc_total));
+ carp(CARP_INFO, "Average number of candidates per spectrum-charge combination: %lf ",
+ (*total_candidate_peptides) / sc_total);
+ for (int i = 0; i < num_locks; i++) {
+ delete locks_array[i];
+ }
+ delete sc_index;
+ delete total_candidate_peptides;
+
+}
+
+void TideSearchApplication::collectScoresCompiled(
+ ActivePeptideQueue* active_peptide_queue,
+ const Spectrum* spectrum,
+ const ObservedPeakSet& observed,
+ TideMatchSet::Arr2* match_arr,
+ int queue_size,
+ int charge
+) {
+ if (!active_peptide_queue->HasNext()) {
+ return;
+ }
+ // prog gets the address of the dot-product program for the first peptide
+ // in the active queue.
+ const void* prog = active_peptide_queue->NextPeptide()->Prog(charge);
+ const int* cache = observed.GetCache();
+ // results will get (score, counter) pairs, where score is the dot product
+ // of the observed peak set with a candidate peptide. The candidate
+ // peptide is given by counter, which refers to the index within the
+ // ActivePeptideQueue, counting from the back. This complication
+ // simplifies the generated programs, which now simply dump the counter.
+ pair<int, int>* results = match_arr->data();
+
+ // See compiler.h for a description of the programs beginning at prog and
+ // how they are generated. Here we initialize certain registers to the
+ // values expected by the programs and call the first one (*prog).
+ //
+ // See gnu assembler format for more on this format. We tell the compiler
+ // to set these registers:
+ // edx/rdx points to the cache.
+ // eax/rax points to the first program.
+ // ecx/rcx is the counter and gets the size of the active queue.
+ // edi/rdi points to the results buffer.
+ //
+ // The push and pop operations are a workaround for a compiler that
+ // doesn't understand that %ecx and %edi (or %rcx and %rdi) get
+ // clobbered. Since they're already input registers, they can't be
+ // included in the clobber list.
+
+#ifdef _MSC_VER
+#ifdef _WIN64
+ DWORD64 rcx;
+ DWORD64 rdi;
+
+ volatile bool restored = false;
+ CONTEXT context;
+ RtlCaptureContext(&context);
+ if (!restored) {
+ rcx = context.Rcx;
+ rdi = context.Rdi;
+
+ context.Rdx = (DWORD64)cache;
+ context.Rax = (DWORD64)prog;
+ context.Rcx = (DWORD64)queue_size;
+ context.Rdi = (DWORD64)results;
+
+ restored = true;
+ RtlRestoreContext(&context, NULL);
+ } else {
+ ((void(*)(void))prog)();
+ }
+
+ restored = false;
+ RtlCaptureContext(&context);
+ if (!restored) {
+ context.Rcx = rcx;
+ context.Rdi = rdi;
+
+ restored = true;
+ RtlRestoreContext(&context, NULL);
+ }
+#else
+ __asm {
+ cld
+ push ecx
+ push edi
+ mov edx, cache
+ mov eax, prog
+ mov ecx, queue_size
+ mov edi, results
+ call eax
+ pop edi
+ pop ecx
+ }
+#endif
+#else
+ __asm__ __volatile__("cld\n" // stos operations increment edi
+#ifdef __x86_64__
+ "push %%rcx\n"
+ "push %%rdi\n"
+ "call *%%rax\n"
+ "pop %%rdi\n"
+ "pop %%rcx\n"
+#else
+ "push %%ecx\n"
+ "push %%edi\n"
+ "call *%%eax\n"
+ "pop %%edi\n"
+ "pop %%ecx\n"
+#endif
+ : // no outputs
+ : "d" (cache),
+ "a" (prog),
+ "c" (queue_size),
+ "D" (results)
+ );
+#endif
+
+ // match_arr is filled by the compiled programs, not by calls to
+ // push_back(). We have to set the final size explicitly.
+ match_arr->set_size(queue_size);
+}
+
+void TideSearchApplication::computeWindow(
+ const SpectrumCollection::SpecCharge& sc,
+ WINDOW_TYPE_T window_type,
+ double precursor_window,
+ int max_charge,
+ vector<int>* negative_isotope_errors,
+ vector<double>* out_min,
+ vector<double>* out_max,
+ double* min_range,
+ double* max_range
+) {
+
+ double unit_dalton = BIN_WIDTH;
+
+ switch (window_type) {
+ case WINDOW_MASS:
+ for (vector<int>::const_iterator ie = negative_isotope_errors->begin(); ie != negative_isotope_errors->end(); ++ie) {
+ out_min->push_back(sc.neutral_mass + (*ie * unit_dalton) - precursor_window);
+ out_max->push_back(sc.neutral_mass + (*ie * unit_dalton) + precursor_window);
+ }
+ *min_range = (sc.neutral_mass + (negative_isotope_errors->front() * unit_dalton)) - precursor_window;
+ *max_range = (sc.neutral_mass + (negative_isotope_errors->back() * unit_dalton)) + precursor_window;
+ break;
+ case WINDOW_MZ: {
+ double mz_minus_proton = sc.spectrum->PrecursorMZ() - MASS_PROTON;
+ for (vector<int>::const_iterator ie = negative_isotope_errors->begin(); ie != negative_isotope_errors->end(); ++ie) {
+ out_min->push_back((mz_minus_proton - precursor_window) * sc.charge + (*ie * unit_dalton));
+ out_max->push_back((mz_minus_proton + precursor_window) * sc.charge + (*ie * unit_dalton));
+ }
+ *min_range = (mz_minus_proton*sc.charge + (negative_isotope_errors->front() * unit_dalton)) - precursor_window*max_charge;
+ *max_range = (mz_minus_proton*sc.charge + (negative_isotope_errors->back() * unit_dalton)) + precursor_window*max_charge;
+ break;
+ }
+ case WINDOW_PPM: {
+ double tiny_precursor = precursor_window * 1e-6;
+ for (vector<int>::const_iterator ie = negative_isotope_errors->begin(); ie != negative_isotope_errors->end(); ++ie) {
+ out_min->push_back((sc.neutral_mass + (*ie * unit_dalton)) * (1.0 - tiny_precursor));
+ out_max->push_back((sc.neutral_mass + (*ie * unit_dalton)) * (1.0 + tiny_precursor));
+ }
+ *min_range = (sc.neutral_mass + (negative_isotope_errors->front() * unit_dalton)) * (1.0 - tiny_precursor);
+ *max_range = (sc.neutral_mass + (negative_isotope_errors->back() * unit_dalton)) * (1.0 + tiny_precursor);
+ break;
+ }
+ default:
+ carp(CARP_FATAL, "Invalid window type");
+ }
+ carp(CARP_DETAILED_DEBUG, "Scan %d.%d mass window is [%f, %f]",
+ sc.spectrum->SpectrumNumber(), sc.charge, (*out_min)[0], (*out_max)[0]);
+}
+
+bool TideSearchApplication::hasDecoys() {
+ return HAS_DECOYS;
+}
+
+bool TideSearchApplication::proteinLevelDecoys() {
+ return PROTEIN_LEVEL_DECOYS;
+}
+
+string TideSearchApplication::getName() const {
+ return "tide-search";
+}
+
+string TideSearchApplication::getDescription() const {
+ return
+ "[[nohtml:Search a collection of spectra against a sequence database, "
+ "returning a collection of peptide-spectrum matches (PSMs). This is a "
+ "fast search engine but requires that you first build an index with "
+ "tide-index.]]"
+ "[[html:<p>Tide is a tool for identifying peptides from tandem mass "
+ "spectra. It is an independent reimplementation of the SEQUEST<sup>®"
+ "</sup> algorithm, which assigns peptides to spectra by comparing the "
+ "observed spectra to a catalog of theoretical spectra derived from a "
+ "database of known proteins. Tide's primary advantage is its speed. Our "
+ "published paper provides more detail on how Tide works. If you use Tide "
+ "in your research, please cite:</p><blockquote>Benjamin J. Diament and "
+ "William Stafford Noble. <a href=\"http://dx.doi.org/10.1021/pr101196n\">"
+ ""Faster SEQUEST Searching for Peptide Identification from Tandem "
+ "Mass Spectra"</a>. <em>Journal of Proteome Research</em>. "
+ "10(9):3871-9, 2011.</blockquote> "
+ "<p>When <code>tide-search</code> runs, it performs "
+ "several intermediate steps, as follows:</p><ol>"
+ "<li>If a FASTA file was provided, convert it to an index using "
+ "<code>tide-index</code>.</li>"
+ "<li>Convert the given "
+ "fragmentation spectra to a binary format.</li><li>Search the spectra "
+ "against the database and store the results in binary format.</li><li>"
+ "Convert the results to one or more requested output formats.</li></ol><p>"
+ "By default, the intermediate binary files are stored in the output "
+ "directory and deleted when Tide finishes execution. If you plan to search "
+ "against given database more than once or search a given set of spectra "
+ "more than once, then you can direct Tide to save the binary spectrum "
+ "files using the <code>--store-index</code> and "
+ "<code>--store-spectra</code> options. "
+ "Subsequent runs of the program will go faster "
+ "if provided with inputs in binary format.</p>]]";
+}
+
+vector<string> TideSearchApplication::getArgs() const {
+ string arr[] = {
+ "tide spectra file+",
+ "tide database"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> TideSearchApplication::getOptions() const {
+ string arr[] = {
+ "precursor-window",
+ "auto-precursor-window",
+ "precursor-window-type",
+ "spectrum-min-mz",
+ "spectrum-max-mz",
+ "min-peaks",
+ "spectrum-charge",
+ "scan-number",
+ "top-match",
+ "store-spectra",
+ "store-index",
+ "concat",
+ "compute-sp",
+ "remove-precursor-peak",
+ "remove-precursor-tolerance",
+ "print-search-progress",
+ "spectrum-parser",
+ "use-z-line",
+ "txt-output",
+ "sqt-output",
+ "pepxml-output",
+ "mzid-output",
+ "pin-output",
+ "fileroot",
+ "file-column",
+ "output-dir",
+ "overwrite",
+ "parameter-file",
+ "exact-p-value",
+ "use-neutral-loss-peaks",
+ "use-flanking-peaks",
+ "mz-bin-width",
+ "auto-mz-bin-width",
+ "mz-bin-offset",
+ "max-precursor-charge",
+ "peptide-centric-search",
+ "isotope-error",
+ "skip-preprocessing",
+ "elution-window-size",
+ "num-threads",
+ "verbosity",
+ "pm-min-precursor-mz",
+ "pm-max-precursor-mz",
+ "pm-min-frag-mz",
+ "pm-max-frag-mz",
+ "pm-min-scan-frag-peaks",
+ "pm-max-precursor-delta-ppm",
+ "pm-charge",
+ "pm-top-n-frag-peaks",
+ "pm-pair-top-n-frag-peaks",
+ "pm-min-common-frag-peaks",
+ "pm-max-scan-separation",
+ "pm-min-peak-pairs"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > TideSearchApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("tide-search.target.txt",
+ "a tab-delimited text file containing the target PSMs. See <a href=\""
+ "../file-formats/txt-format.html\">txt file format</a> for a list of the fields."));
+ outputs.push_back(make_pair("tide-search.decoy.txt",
+ "a tab-delimited text file containing the decoy PSMs. This file will only "
+ "be created if the index was created with decoys."));
+ outputs.push_back(make_pair("tide-search.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other Crux programs."));
+ outputs.push_back(make_pair("tide-search.log.txt",
+ "a log file containing a copy of all messages that were printed to the "
+ "screen during execution."));
+ return outputs;
+}
+bool TideSearchApplication::needsOutputDirectory() const {
+ return true;
+}
+
+COMMAND_T TideSearchApplication::getCommand() const {
+ return TIDE_SEARCH_COMMAND;
+}
+
+/* Calculates counts of peptides with various XCorr scores, given a preprocessed
+ * MS2 spectrum, using dynamic programming.
+ * Written by Jeff Howbert, October, 2012 (as function calcScoreCount).
+ * Ported to and integrated with Tide by Jeff Howbert, November, 2013.
+ */
+int TideSearchApplication::calcScoreCount(
+ int numelEvidenceObs,
+ int* evidenceObs,
+ int pepMassInt,
+ int maxEvidence,
+ int minEvidence,
+ int maxScore,
+ int minScore,
+ int nAA,
+ double* aaFreqN,
+ double* aaFreqI,
+ double* aaFreqC,
+ int* aaMass,
+ double* pValueScoreObs
+) {
+ const int nDeltaMass = nAA;
+ int minDeltaMass = aaMass[0];
+ int maxDeltaMass = aaMass[nDeltaMass - 1];
+
+ // internal variables
+ int row;
+ int col;
+ int ma;
+ int evidence;
+ int de;
+ int evidenceRow;
+ double sumScore;
+
+ int bottomRowBuffer = maxEvidence + 1;
+ int topRowBuffer = -minEvidence;
+ int colBuffer = maxDeltaMass;
+ int colStart = MassConstants::mass2bin(MassConstants::mono_h);
+ int scoreOffsetObs = bottomRowBuffer - minScore;
+
+ int nRow = bottomRowBuffer - minScore + 1 + maxScore + topRowBuffer;
+ int nCol = colBuffer + pepMassInt;
+ int rowFirst = bottomRowBuffer;
+ int rowLast = rowFirst - minScore + maxScore;
+ int colFirst = colStart + MassConstants::mass2bin(MassConstants::mono_h);
+ int colLast = MassConstants::mass2bin(MassConstants::bin2mass(pepMassInt)
+ - MassConstants::mono_oh
+ );
+ int initCountRow = bottomRowBuffer - minScore;
+ int initCountCol = maxDeltaMass + colStart;
+
+ double** dynProgArray = new double*[nRow];
+ for (row = 0; row < nRow; row++) {
+ dynProgArray[row] = new double[nCol];
+ for (col = 0; col < nCol; col++) {
+ dynProgArray[row][col] = 0.0;
+ }
+ }
+ double* scoreCountBinAdjust = 0;
+ scoreCountBinAdjust = new double[nRow];
+ for (row = 0; row < nRow; row++) {
+ scoreCountBinAdjust[row] = 0.0;
+ }
+
+ dynProgArray[initCountRow][initCountCol] = 1.0; // initial count of peptides with mass = 1
+ vector<int> deltaMassCol(nDeltaMass);
+ // populate matrix with scores for first (i.e. N-terminal) amino acid in sequence
+ for (de = 0; de < nDeltaMass; de++) {
+ ma = aaMass[de];
+ row = initCountRow + evidenceObs[ma + colStart];
+ col = initCountCol + ma;
+ if (col <= maxDeltaMass + colLast) {
+ dynProgArray[row][col] += dynProgArray[initCountRow][initCountCol] * aaFreqN[de];
+ }
+ }
+ // set to zero now that score counts for first amino acid are in matrix
+ dynProgArray[initCountRow][initCountCol] = 0.0;
+ // populate matrix with score counts for non-terminal amino acids in sequence
+ for (ma = colFirst; ma < colLast; ma++) {
+ col = maxDeltaMass + ma;
+ evidence = evidenceObs[ma];
+ for (de = 0; de < nDeltaMass; de++) {
+ deltaMassCol[de] = col - aaMass[de];
+ }
+ for (row = rowFirst; row <= rowLast; row++) {
+ evidenceRow = row - evidence;
+ sumScore = dynProgArray[row][col];
+ for (de = 0; de < nDeltaMass; de++) {
+ sumScore += dynProgArray[evidenceRow][deltaMassCol[de]] * aaFreqI[de];
+ }
+ dynProgArray[row][col] = sumScore;
+ }
+ }
+ // populate matrix with score counts for last (i.e. C-terminal) amino acid in sequence
+ ma = colLast;
+ col = maxDeltaMass + ma;
+ evidence = 0; // no evidence should be added for last amino acid in sequence
+ for (de = 0; de < nDeltaMass; de++) {
+ deltaMassCol[de] = col - aaMass[de];
+ }
+ for (row = rowFirst; row <= rowLast; row++) {
+ evidenceRow = row - evidence;
+ sumScore = 0.0;
+ for (de = 0; de < nDeltaMass; de++) {
+ sumScore += dynProgArray[evidenceRow][deltaMassCol[de]] * aaFreqC[de]; // C-terminal residue
+ }
+ dynProgArray[row][col] = sumScore;
+ }
+
+ int colScoreCount = maxDeltaMass + colLast;
+ double totalCount = 0.0;
+ for (row = 0; row < nRow; row++) {
+ // at this point pValueScoreObs just holds counts from last column of dynamic programming array
+ pValueScoreObs[row] = dynProgArray[row][colScoreCount];
+ totalCount += pValueScoreObs[row];
+ scoreCountBinAdjust[row] = pValueScoreObs[row] / 2.0;
+ }
+ // convert from counts to cumulative sum of counts
+ for (row = nRow - 2; row >= 0; row--) {
+ pValueScoreObs[row] += pValueScoreObs[row + 1];
+ }
+ double logTotalCount = log(totalCount);
+ for (row = 0; row < nRow; row++) {
+ // adjust counts to reflect center of bin, not edge
+ pValueScoreObs[row] -= scoreCountBinAdjust[row];
+ // normalize distribution; use exp( log ) to avoid potential underflow
+ pValueScoreObs[row] = exp(log(pValueScoreObs[row]) - logTotalCount);
+ }
+
+ // clean up
+ for (row = 0; row < nRow; row++) {
+ delete [] dynProgArray[row];
+ }
+ delete [] dynProgArray;
+ delete [] scoreCountBinAdjust;
+
+ return scoreOffsetObs;
+}
+
+void TideSearchApplication::processParams() {
+ const string index = Params::GetString("tide database");
+ if (!FileUtils::Exists(index)) {
+ carp(CARP_FATAL, "'%s' does not exist", index.c_str());
+ } else if (FileUtils::IsRegularFile(index)) {
+ // Index is FASTA file
+ carp(CARP_INFO, "Creating index from '%s'", index.c_str());
+ string targetIndexName = Params::GetString("store-index");
+ if (targetIndexName.empty()) {
+ targetIndexName = FileUtils::Join(Params::GetString("output-dir"),
+ "tide-search.tempindex");
+ remove_index_ = targetIndexName;
+ }
+ TideIndexApplication indexApp;
+ indexApp.processParams();
+ if (indexApp.main(index, targetIndexName) != 0) {
+ carp(CARP_FATAL, "tide-index failed.");
+ }
+ Params::Set("tide database", targetIndexName);
+ } else {
+ // Index is Tide index directory
+ pb::Header peptides_header;
+ string peptides_file = FileUtils::Join(index, "pepix");
+ HeadedRecordReader peptide_reader(peptides_file, &peptides_header);
+ if ((peptides_header.file_type() != pb::Header::PEPTIDES) ||
+ !peptides_header.has_peptides_header()) {
+ carp(CARP_FATAL, "Error reading index (%s)", peptides_file.c_str());
+ }
+
+ const pb::Header::PeptidesHeader& pepHeader = peptides_header.peptides_header();
+
+ Params::Set("enzyme", pepHeader.enzyme());
+ const char* digestString =
+ digest_type_to_string(pepHeader.full_digestion() ? FULL_DIGEST : PARTIAL_DIGEST);
+ Params::Set("digestion", digestString);
+ Params::Set("isotopic-mass", pepHeader.monoisotopic_precursor() ? "mono" : "average");
+ }
+ // run param-medic?
+ const string autoPrecursor = Params::GetString("auto-precursor-window");
+ const string autoFragment = Params::GetString("auto-mz-bin-width");
+ if (autoPrecursor != "false" || autoFragment != "false") {
+ if (autoPrecursor != "false" && Params::GetString("precursor-window-type") != "ppm") {
+ carp(CARP_FATAL, "Automatic peptide mass tolerance detection is only supported with ppm "
+ "units. Please rerun with either auto-precursor-window set to 'false' or "
+ "precursor-window-type set to 'ppm'.");
+ }
+ ParamMedicErrorCalculator errCalc;
+ errCalc.processFiles(Params::GetStrings("tide spectra file"));
+ string precursorFailure, fragmentFailure;
+ double precursorSigmaPpm = 0;
+ double fragmentSigmaPpm = 0;
+ double fragmentSigmaTh = 0;
+ double precursorPredictionPpm = 0;
+ double fragmentPredictionPpm = 0;
+ double fragmentPredictionTh = 0;
+ errCalc.calcMassErrorDist(&precursorFailure, &fragmentFailure,
+ &precursorSigmaPpm, &fragmentSigmaPpm,
+ &precursorPredictionPpm, &fragmentPredictionTh);
+
+ if (autoPrecursor != "false") {
+ if (precursorFailure.empty()) {
+ carp(CARP_INFO, "precursor ppm standard deviation: %f", precursorSigmaPpm);
+ carp(CARP_INFO, "Precursor error estimate (ppm): %.2f", precursorPredictionPpm);
+ Params::Set("precursor-window", precursorPredictionPpm);
+ } else {
+ carp(autoPrecursor == "fail" ? CARP_FATAL : CARP_ERROR,
+ "failed to calculate precursor error: %s", precursorFailure.c_str());
+ }
+ }
+ if (autoFragment != "false") {
+ if (fragmentFailure.empty()) {
+ carp(CARP_INFO, "fragment standard deviation (ppm): %f", fragmentSigmaPpm);
+ carp(CARP_INFO, "Fragment bin size estimate (Th): %.4f", fragmentPredictionTh);
+ Params::Set("mz-bin-width", fragmentPredictionTh);
+ } else {
+ carp(autoFragment == "fail" ? CARP_FATAL : CARP_ERROR,
+ "failed to calculate fragment error: %s", fragmentFailure.c_str());
+ }
+ }
+ }
+}
+
+void TideSearchApplication::setSpectrumFlag(map<pair<string, unsigned int>, bool>* spectrum_flag) {
+ spectrum_flag_ = spectrum_flag;
+}
+
+string TideSearchApplication::getOutputFileName() {
+ return output_file_name_;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/TideSearchApplication.h b/src/app/TideSearchApplication.h
new file mode 100644
index 0000000..eff1f10
--- /dev/null
+++ b/src/app/TideSearchApplication.h
@@ -0,0 +1,278 @@
+#ifndef TIDESEARCHAPPLICATION_H
+#define TIDESEARCHAPPLICATION_H
+
+#include "CruxApplication.h"
+#include "TideMatchSet.h"
+
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+#include <gflags/gflags.h>
+#include "peptides.pb.h"
+#include "spectrum.pb.h"
+#include "tide/theoretical_peak_set.h"
+#include "tide/max_mz.h"
+
+using namespace std;
+
+class TideSearchApplication : public CruxApplication {
+
+ friend class SubtractIndexApplication;
+
+ protected:
+ /**
+ brief This variable is used with Cascade Search.
+ This map contains a flag for each spectrum whether
+ a spectrum has not been identified in a prior cycle (0) or not (1).
+ The spectrum ID is a pair containing the ordinal number of the
+ input file in the first component and a scanId-charge-state in the second component.
+ The scanID and the charge state is combined into a single number
+ as scanID*10 + charge_state. Charge state is required to be less than 10.
+ */
+ map<pair<string, unsigned int>, bool>* spectrum_flag_;
+ string output_file_name_;
+
+ static bool HAS_DECOYS;
+ static bool PROTEIN_LEVEL_DECOYS;
+
+ /**
+ * Function that contains the search algorithm and performs the search
+ */
+ void search(void *threadarg);
+
+ /**
+ * Calls search(threadarg), and if threading, creates threads calling
+ * search(threadarg)
+ *
+ * Call structure:
+ * main -> [this function] -> search(void* threadarg)
+ * |
+ * (if threading)|
+ * |
+ * -> Per Thread:
+ * -> search(void* threadarg)
+ */
+ void search(
+ const string& spectrum_filename,
+ const vector<SpectrumCollection::SpecCharge>* spec_charges,
+ vector<ActivePeptideQueue*> active_peptide_queue,
+ ProteinVec& proteins,
+ vector<const pb::AuxLocation*>& locations,
+ double precursor_window,
+ WINDOW_TYPE_T window_type,
+ double spectrum_min_mz,
+ double spectrum_max_mz,
+ int min_scan,
+ int max_scan,
+ int min_peaks,
+ int search_charge,
+ int top_matches,
+ double highest_mz,
+ ofstream* target_file,
+ ofstream* decoy_file,
+ bool compute_sp,
+ int nAA,
+ double* aaFreqN,
+ double* aaFreqI,
+ double* aaFreqC,
+ int* aaMass,
+ vector<int>* negative_isotope_errors
+ );
+
+ void collectScoresCompiled(
+ ActivePeptideQueue* active_peptide_queue,
+ const Spectrum* spectrum,
+ const ObservedPeakSet& observed,
+ TideMatchSet::Arr2* match_arr,
+ int queue_size,
+ int charge
+ );
+
+ void computeWindow(
+ const SpectrumCollection::SpecCharge& sc,
+ WINDOW_TYPE_T window_type,
+ double precursor_window,
+ int max_charge,
+ vector<int>* negative_isotope_errors,
+ vector<double>* out_min,
+ vector<double>* out_max,
+ double* min_range,
+ double* max_range
+ );
+
+ struct ScSortByMz {
+ explicit ScSortByMz(double precursor_window) { precursor_window_ = precursor_window; }
+ bool operator() (const SpectrumCollection::SpecCharge x,
+ const SpectrumCollection::SpecCharge y) {
+ return (x.spectrum->PrecursorMZ() - MASS_PROTON - precursor_window_) * x.charge <
+ (y.spectrum->PrecursorMZ() - MASS_PROTON - precursor_window_) * y.charge;
+ }
+ double precursor_window_;
+ };
+ double bin_width_;
+ double bin_offset_;
+
+ std::string remove_index_;
+
+ struct InputFile {
+ std::string OriginalName;
+ std::string SpectrumRecords;
+ bool Keep;
+ InputFile(const std::string& name,
+ const std::string& spectrumrecords,
+ bool keep):
+ OriginalName(name), SpectrumRecords(spectrumrecords), Keep(keep) {}
+ };
+
+ public:
+
+ // See TideSearchApplication.cpp for descriptions of these two constants
+ static const double XCORR_SCALING;
+ static const double RESCALE_FACTOR;
+
+ bool exact_pval_search_;
+
+ /**
+ * Constructor
+ */
+ TideSearchApplication();
+
+ /**
+ * Destructor
+ */
+ ~TideSearchApplication();
+
+ unsigned int NUM_THREADS;
+
+ /**
+ * Main method
+ */
+ virtual int main(int argc, char** argv);
+
+ int main(const vector<string>& input_files);
+
+ int main(const vector<string>& input_files, const string input_index);
+
+ static bool hasDecoys();
+ static bool proteinLevelDecoys();
+
+ /**
+ * Returns the command name
+ */
+ virtual string getName() const;
+
+ /**
+ * Returns the command description
+ */
+ virtual string getDescription() const;
+
+ /**
+ * Returns the command arguments
+ */
+ virtual vector<string> getArgs() const;
+
+ /**
+ * Returns the command options
+ */
+ virtual vector<string> getOptions() const;
+
+ /**
+ * Returns the command outputs
+ */
+ virtual vector< pair<string, string> > getOutputs() const;
+
+ /**
+ * Returns whether the application needs the output directory or not. (default false)
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual COMMAND_T getCommand() const;
+
+ /**
+ * Struct holding necessary information for each thread to run.
+ */
+ struct thread_data {
+
+ string spectrum_filename;
+ const vector<SpectrumCollection::SpecCharge>* spec_charges;
+ ActivePeptideQueue* active_peptide_queue;
+ ProteinVec proteins;
+ vector<const pb::AuxLocation*> locations;
+ double precursor_window;
+ WINDOW_TYPE_T window_type;
+ double spectrum_min_mz;
+ double spectrum_max_mz;
+ int min_scan;
+ int max_scan;
+ int min_peaks;
+ int search_charge;
+ int top_matches;
+ double highest_mz;
+ ofstream* target_file;
+ ofstream* decoy_file;
+ bool compute_sp;
+ int64_t thread_num;
+ int64_t num_threads;
+ int nAA;
+ double* aaFreqN;
+ double* aaFreqI;
+ double* aaFreqC;
+ int* aaMass;
+ vector<boost::mutex*> locks_array;
+ double bin_width;
+ double bin_offset;
+ bool exact_pval_search;
+ map<pair<string, unsigned int>, bool>* spectrum_flag;
+ int* sc_index;
+ int* total_candidate_peptides;
+ vector<int>* negative_isotope_errors;
+
+ thread_data (const string& spectrum_filename_, const vector<SpectrumCollection::SpecCharge>* spec_charges_,
+ ActivePeptideQueue* active_peptide_queue_, ProteinVec proteins_,
+ vector<const pb::AuxLocation*> locations_, double precursor_window_,
+ WINDOW_TYPE_T window_type_, double spectrum_min_mz_, double spectrum_max_mz_,
+ int min_scan_, int max_scan_, int min_peaks_, int search_charge_, int top_matches_,
+ double highest_mz_, ofstream* target_file_,
+ ofstream* decoy_file_, bool compute_sp_, int64_t thread_num_, int64_t num_threads_, int nAA_,
+ double* aaFreqN_, double* aaFreqI_, double* aaFreqC_, int* aaMass_, vector<boost::mutex*> locks_array_,
+ double bin_width_, double bin_offset_, bool exact_pval_search_, map<pair<string, unsigned int>, bool>* spectrum_flag_,
+ int* sc_index_, int* total_candidate_peptides_, vector<int>* negative_isotope_errors_) :
+ spectrum_filename(spectrum_filename_), spec_charges(spec_charges_), active_peptide_queue(active_peptide_queue_),
+ proteins(proteins_), locations(locations_), precursor_window(precursor_window_), window_type(window_type_),
+ spectrum_min_mz(spectrum_min_mz_), spectrum_max_mz(spectrum_max_mz_), min_scan(min_scan_), max_scan(max_scan_),
+ min_peaks(min_peaks_), search_charge(search_charge_), top_matches(top_matches_), highest_mz(highest_mz_),
+ target_file(target_file_), decoy_file(decoy_file_), compute_sp(compute_sp_),
+ thread_num(thread_num_), num_threads(num_threads_), nAA(nAA_), aaFreqN(aaFreqN_), aaFreqI(aaFreqI_), aaFreqC(aaFreqC_),
+ aaMass(aaMass_), locks_array(locks_array_), bin_width(bin_width_), bin_offset(bin_offset_), exact_pval_search(exact_pval_search_),
+ spectrum_flag(spectrum_flag_), sc_index(sc_index_), total_candidate_peptides(total_candidate_peptides_), negative_isotope_errors(negative_isotope_errors_) {}
+ };
+
+ int calcScoreCount(
+ int numelEvidenceObs,
+ int* evidenceObs,
+ int pepMassInt,
+ int maxEvidence,
+ int minEvidence,
+ int maxScore,
+ int minScore,
+ int nAA,
+ double* aaFreqN,
+ double* aaFreqI,
+ double* aaFreqC,
+ int* aaMass,
+ double* pValueScoreObs
+ );
+
+ void setSpectrumFlag(map<pair<string, unsigned int>, bool>* spectrum_flag);
+ virtual void processParams();
+ string getOutputFileName();
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/bullseye/CKronik2.cpp b/src/app/bullseye/CKronik2.cpp
new file mode 100644
index 0000000..7cc326a
--- /dev/null
+++ b/src/app/bullseye/CKronik2.cpp
@@ -0,0 +1,797 @@
+#include "CKronik2.h"
+
+//-------------------------------------
+// Constructors and Destructors
+//-------------------------------------
+CKronik2::CKronik2(){
+ dPPMTol = 10.0;
+ iGapTol = 1;
+ iMatchTol = 3;
+}
+CKronik2::~CKronik2(){
+}
+
+CKronik2::CKronik2(const CKronik2& c){
+ dPPMTol=c.dPPMTol;
+ iGapTol=c.iGapTol;
+ iMatchTol=c.iMatchTol;
+ iPercent=c.iPercent;
+ vPeps.clear();
+ for(unsigned int i=0;i<c.vPeps.size();i++) vPeps.push_back(c.vPeps[i]);
+ hkData.clear();
+ for(unsigned int i=0;i<c.hkData.size();i++) hkData.push_back(c.hkData[i]);
+}
+
+
+//-------------------------------------
+// Operator Overloads
+//-------------------------------------
+CKronik2& CKronik2::operator=(const CKronik2& c){
+ if(this!=&c){
+ dPPMTol=c.dPPMTol;
+ iGapTol=c.iGapTol;
+ iMatchTol=c.iMatchTol;
+ iPercent=c.iPercent;
+ vPeps.clear();
+ for(unsigned int i=0;i<c.vPeps.size();i++) vPeps.push_back(c.vPeps[i]);
+ hkData.clear();
+ for(unsigned int i=0;i<c.hkData.size();i++) hkData.push_back(c.hkData[i]);
+ }
+ return *this;
+}
+sPepProfile& CKronik2::operator[ ](const unsigned int& i){
+ return vPeps[i];
+}
+
+//-------------------------------------
+// Data Manipulation
+//-------------------------------------
+void CKronik2::add(sPepProfile &p){
+ vPeps.push_back(p);
+}
+
+sPepProfile& CKronik2::at(unsigned int i){
+ return vPeps[i];
+}
+
+void CKronik2::clear(){
+ vPeps.clear();
+ hkData.clear();
+}
+
+void CKronik2::clearHK(){
+ hkData.clear();
+}
+
+void CKronik2::erase(unsigned int i){
+ vPeps.erase(vPeps.begin()+i);
+}
+
+//------------------------------
+// Automation
+//------------------------------
+int CKronik2::getPercent(){
+ return iPercent;
+}
+bool CKronik2::loadHK(char* in){
+ FILE *hkr;
+ sScan scan;
+ sPep pep;
+ double td;
+ char tag;
+ bool firstScan;
+ char line[256];
+ char* tok;
+
+ int pepCount=0;
+
+ sPepProfile s;
+ sProfileData p;
+
+ //Read in the Hardklor results
+ firstScan=true;
+ hkr = fopen(in,"rt");
+ if(hkr==NULL) {
+ cout << "Problem reading file." << endl;
+ return false;
+ }
+
+ hkData.clear();
+ while(!feof(hkr)){
+
+ tag=fgetc(hkr);
+
+ if(tag=='S') {
+ if(firstScan) firstScan=false;
+ else hkData.push_back(scan);
+ scan.clear();
+ fgets(line,256,hkr);
+ tok=strtok(line,"\t\n");
+ scan.scanNum=atoi(tok);
+ tok=strtok(NULL,"\t\n");
+ scan.rTime=(float)atof(tok);
+ tok=strtok(NULL,"\t\n");
+ strcpy(scan.file,tok);
+ //fscanf(hkr,"\t%d\t%f%s\n",&scan.scanNum,&scan.rTime,scan.file);
+ } else {
+ pepCount++;
+ fscanf(hkr,"\t%lf\t%d\t%f\t%lf\t%lf-%lf\t%lf\t%s\t%lf\n", &pep.monoMass,&pep.charge,&pep.intensity,&pep.basePeak,&td,&td,&td,pep.mods,&pep.xCorr);
+ scan.vPep->push_back(pep);
+ }
+ }
+ hkData.push_back(scan);
+ fclose(hkr);
+
+ cout << pepCount << " peptides from " << hkData.size() << " scans." << endl;
+ return true;
+}
+
+bool CKronik2::processHK(char* in, char* out) {
+ FILE *hkr;
+ sScan scan;
+ sPep pep;
+ double td;
+ char tag;
+ bool firstScan;
+ int sIndex,pIndex;
+ int i,j,k,k1,k2;
+
+ char line[256];
+ char* tok;
+
+ int pepCount=0;
+ vector<sScan> allScans;
+
+ double mass;
+ double ppm;
+ int charge;
+ int gap;
+ int matchCount;
+ bool bMatch;
+
+ sPepProfile s;
+ sProfileData p;
+
+ //for tracking which peptides
+ iTwo t;
+ vector<iTwo> vLeft;
+ vector<iTwo> vRight;
+
+ //clear data
+ vPeps.clear();
+
+ //Read in the Hardklor results
+ firstScan=true;
+ hkr = fopen(in,"rt");
+ if(hkr==NULL) {
+ cout << "Problem reading file." << endl;
+ return false;
+ }
+
+ while(!feof(hkr)){
+
+ tag=fgetc(hkr);
+
+ if(tag=='S') {
+ if(firstScan) firstScan=false;
+ else allScans.push_back(scan);
+ scan.clear();
+ fgets(line,256,hkr);
+ tok=strtok(line,"\t\n");
+ scan.scanNum=atoi(tok);
+ tok=strtok(NULL,"\t\n");
+ scan.rTime=(float)atof(tok);
+ tok=strtok(NULL,"\t\n");
+ strcpy(scan.file,tok);
+ //fscanf(hkr,"\t%d\t%f%s\n",&scan.scanNum,&scan.rTime,scan.file);
+ } else {
+ pepCount++;
+ fscanf(hkr,"\t%lf\t%d\t%f\t%lf\t%lf-%lf\t%lf\t%s\t%lf\n", &pep.monoMass,&pep.charge,&pep.intensity,&pep.basePeak,&td,&td,&td,pep.mods,&pep.xCorr);
+ scan.vPep->push_back(pep);
+ }
+ }
+ allScans.push_back(scan);
+ fclose(hkr);
+
+ cout << pepCount << " peptides from " << allScans.size() << " scans." << endl;
+
+ for(i=0;i<allScans.size();i++) allScans[i].sortIntRev();
+
+ cout << "Finding persistent peptide signals:" << endl;
+
+ int startCount=pepCount;
+ int lastPercent=0;
+
+ cerr << lastPercent;
+
+ //Perform the Kronik analysis
+ while(pepCount>0){
+ if(!findMax(allScans,sIndex,pIndex)) break;
+
+ mass=allScans[sIndex].vPep->at(pIndex).monoMass;
+ charge=allScans[sIndex].vPep->at(pIndex).charge;
+ matchCount=1;
+
+ //look left
+ vLeft.clear();
+ gap=0;
+ i=sIndex-1;
+ while(i>-1 && gap<=iGapTol){
+ bMatch=false;
+ t.scan=i;
+ t.pep=-1;
+ for(j=0;j<allScans[i].vPep->size();j++){
+ //if(allScans[i].vPep->at(j).intensity<0.0) continue;
+ ppm=(allScans[i].vPep->at(j).monoMass-mass)/mass*1000000;
+ if(fabs(ppm)<dPPMTol && allScans[i].vPep->at(j).charge==charge){
+ t.pep=j;
+ gap=0;
+ bMatch=true;
+ matchCount++;
+ break;
+ }
+ }
+ if(!bMatch) gap++;
+ vLeft.push_back(t);
+ i--;
+ }
+
+ //look right
+ vRight.clear();
+ gap=0;
+ i=sIndex+1;
+ while(i<allScans.size() && gap<=iGapTol){
+ bMatch=false;
+ t.scan=i;
+ t.pep=-1;
+ for(j=0;j<allScans[i].vPep->size();j++){
+ //if(allScans[i].vPep->at(j).intensity<0.0) continue;
+ ppm=(allScans[i].vPep->at(j).monoMass-mass)/mass*1000000;
+ if(fabs(ppm)<dPPMTol && allScans[i].vPep->at(j).charge==charge){
+ t.pep=j;
+ gap=0;
+ bMatch=true;
+ matchCount++;
+ break;
+ }
+ }
+ if(!bMatch) gap++;
+ vRight.push_back(t);
+ i++;
+ }
+
+ //Only keep sufficient matches
+ if(matchCount>=iMatchTol){
+ //trim gaps
+ while(vLeft.size()>0 && vLeft[vLeft.size()-1].pep<0) vLeft.pop_back();
+ while(vRight.size()>0 && vRight[vRight.size()-1].pep<0) vRight.pop_back();
+
+ //apply basic information
+ s.rTime=allScans[sIndex].rTime;
+ s.basePeak=allScans[sIndex].vPep->at(pIndex).basePeak;
+ s.bestScan=allScans[sIndex].scanNum;
+ s.charge=allScans[sIndex].vPep->at(pIndex).charge;
+ s.intensity=allScans[sIndex].vPep->at(pIndex).intensity;
+ s.monoMass=allScans[sIndex].vPep->at(pIndex).monoMass;
+ strcpy(s.mods,allScans[sIndex].vPep->at(pIndex).mods);
+ s.xCorr=allScans[sIndex].vPep->at(pIndex).xCorr;
+ s.setPoints(vLeft.size()+vRight.size()+1);
+ if(vLeft.size()==0) {
+ s.lowScan=allScans[sIndex].scanNum;
+ s.firstRTime=allScans[sIndex].rTime;
+ } else {
+ s.lowScan=allScans[vLeft[vLeft.size()-1].scan].scanNum;
+ s.firstRTime=allScans[vLeft[vLeft.size()-1].scan].rTime;
+ }
+ if(vRight.size()==0) {
+ s.highScan=allScans[sIndex].scanNum;
+ s.lastRTime=allScans[sIndex].rTime;
+ } else {
+ s.highScan=allScans[vRight[vRight.size()-1].scan].scanNum;
+ s.lastRTime=allScans[vRight[vRight.size()-1].scan].rTime;
+ }
+
+ //apply datapoints
+ s.profile[0].intensity=allScans[sIndex].vPep->at(pIndex).intensity;
+ s.profile[0].interpolated=false;
+ s.profile[0].monoMass=allScans[sIndex].vPep->at(pIndex).monoMass;
+ s.profile[0].rTime=allScans[sIndex].rTime;
+ s.profile[0].scanNum=allScans[sIndex].scanNum;
+ s.profile[0].xCorr=allScans[sIndex].vPep->at(pIndex).xCorr;
+
+ i=1;
+ j=0;
+ while(j<vLeft.size()){
+ //Handle interpolated data
+ if(vLeft[j].pep<0) {
+ k=0;
+ while(vLeft[j+k].pep<0) k++;
+ k2=j+k;
+ if(j==0){
+ s.profile[i].intensity=interpolate(s.profile[0].scanNum,allScans[vLeft[k2].scan].scanNum,(double)s.profile[0].intensity,(double)allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).intensity,allScans[vLeft[j].scan].scanNum);
+ s.profile[i].monoMass =interpolate(s.profile[0].scanNum,allScans[vLeft[k2].scan].scanNum,s.profile[0].monoMass, allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).monoMass, allScans[vLeft[j].scan].scanNum);
+ } else {
+ k=0;
+ while(j+k>=0 && vLeft[j+k].pep<0) k--;
+ k1=j+k;
+ if(k1<0){
+ s.profile[i].intensity=interpolate(s.profile[0].scanNum,allScans[vLeft[k2].scan].scanNum,(double)s.profile[0].intensity,(double)allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).intensity,allScans[vLeft[j].scan].scanNum);
+ s.profile[i].monoMass =interpolate(s.profile[0].scanNum,allScans[vLeft[k2].scan].scanNum,s.profile[0].monoMass, allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).monoMass, allScans[vLeft[j].scan].scanNum);
+ } else {
+ s.profile[i].intensity=interpolate(allScans[vLeft[k1].scan].scanNum,allScans[vLeft[k2].scan].scanNum,(double)allScans[vLeft[k1].scan].vPep->at(vLeft[k1].pep).intensity,(double)allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).intensity,allScans[vLeft[j].scan].scanNum);
+ s.profile[i].monoMass =interpolate(allScans[vLeft[k1].scan].scanNum,allScans[vLeft[k2].scan].scanNum,allScans[vLeft[k1].scan].vPep->at(vLeft[k1].pep).monoMass, allScans[vLeft[k2].scan].vPep->at(vLeft[k2].pep).monoMass, allScans[vLeft[j].scan].scanNum);
+ }
+ }
+ s.profile[i].interpolated=true;
+ s.profile[i].rTime=allScans[vLeft[j].scan].rTime;
+ s.profile[i].scanNum=allScans[vLeft[j].scan].scanNum;
+ s.profile[i].xCorr=0.0;
+ } else {
+ s.profile[i].intensity=allScans[vLeft[j].scan].vPep->at(vLeft[j].pep).intensity;
+ s.profile[i].interpolated=false;
+ s.profile[i].monoMass=allScans[vLeft[j].scan].vPep->at(vLeft[j].pep).monoMass;
+ s.profile[i].rTime=allScans[vLeft[j].scan].rTime;
+ s.profile[i].scanNum=allScans[vLeft[j].scan].scanNum;
+ s.profile[i].xCorr=allScans[vLeft[j].scan].vPep->at(vLeft[j].pep).xCorr;
+ }
+ i++;
+ j++;
+ }
+
+ j=0;
+ while(j<vRight.size()){
+ //Handle interpolated data
+ if(vRight[j].pep<0) {
+ k=0;
+ while(vRight[j+k].pep<0)k++;
+ k2=j+k;
+ if(j==0){
+ s.profile[i].intensity=interpolate(s.profile[0].scanNum,allScans[vRight[k2].scan].scanNum,s.profile[0].intensity,allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).intensity,allScans[vRight[j].scan].scanNum);
+ s.profile[i].monoMass =interpolate(s.profile[0].scanNum,allScans[vRight[k2].scan].scanNum,s.profile[0].monoMass, allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).monoMass, allScans[vRight[j].scan].scanNum);
+ } else {
+ k=0;
+ while((j+k>-1) && vRight[j+k].pep<0)k--;
+ k1=j+k;
+ if(k1<0){
+ s.profile[i].intensity=interpolate(s.profile[0].scanNum,allScans[vRight[k2].scan].scanNum,s.profile[0].intensity,allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).intensity,allScans[vRight[j].scan].scanNum);
+ s.profile[i].monoMass =interpolate(s.profile[0].scanNum,allScans[vRight[k2].scan].scanNum,s.profile[0].monoMass, allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).monoMass, allScans[vRight[j].scan].scanNum);
+ } else {
+ s.profile[i].intensity=interpolate(allScans[vRight[k1].scan].scanNum,allScans[vRight[k2].scan].scanNum,allScans[vRight[k1].scan].vPep->at(vRight[k1].pep).intensity,allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).intensity,allScans[vRight[j].scan].scanNum);
+ s.profile[i].monoMass =interpolate(allScans[vRight[k1].scan].scanNum,allScans[vRight[k2].scan].scanNum,allScans[vRight[k1].scan].vPep->at(vRight[k1].pep).monoMass, allScans[vRight[k2].scan].vPep->at(vRight[k2].pep).monoMass, allScans[vRight[j].scan].scanNum);
+ }
+ }
+ s.profile[i].interpolated=true;
+ s.profile[i].rTime=allScans[vRight[j].scan].rTime;
+ s.profile[i].scanNum=allScans[vRight[j].scan].scanNum;
+ s.profile[i].xCorr=0.0;
+ } else {
+ s.profile[i].intensity=allScans[vRight[j].scan].vPep->at(vRight[j].pep).intensity;
+ s.profile[i].interpolated=false;
+ s.profile[i].monoMass=allScans[vRight[j].scan].vPep->at(vRight[j].pep).monoMass;
+ s.profile[i].rTime=allScans[vRight[j].scan].rTime;
+ s.profile[i].scanNum=allScans[vRight[j].scan].scanNum;
+ s.profile[i].xCorr=allScans[vRight[j].scan].vPep->at(vRight[j].pep).xCorr;
+ }
+ i++;
+ j++;
+ }
+
+ //Add this peptide
+ s.sortScanNum();
+
+ //summed intensity (including interpolation)
+ s.sumIntensity=0.0f;
+ for(i=0;i<s.datapoints;i++) s.sumIntensity+=s.profile[i].intensity;
+
+ vPeps.push_back(s);
+
+ //Erase datapoints already used
+ for(i=0;i<vLeft.size();i++){
+ if(vLeft[i].pep<0) continue;
+ allScans[vLeft[i].scan].vPep->erase(allScans[vLeft[i].scan].vPep->begin()+vLeft[i].pep);
+ pepCount--;
+ }
+ for(i=0;i<vRight.size();i++){
+ if(vRight[i].pep<0) continue;
+ allScans[vRight[i].scan].vPep->erase(allScans[vRight[i].scan].vPep->begin()+vRight[i].pep);
+ pepCount--;
+ }
+ }
+
+ //erase the one we're looking at
+ allScans[sIndex].vPep->erase(allScans[sIndex].vPep->begin()+pIndex);
+ pepCount--;
+
+ //update percent
+ iPercent=100-(int)((float)pepCount/(float)startCount*100.0);
+ if(iPercent>lastPercent){
+ cerr << "\b\b\b" << iPercent;
+ lastPercent=iPercent;
+ }
+
+ }
+ cerr << endl;
+
+ if(out[0]!='\0'){
+ FILE* f;
+ f=fopen(out,"wt");
+
+ //Heading line
+ fprintf(f,"File\tFirst Scan\tLast Scan\tNum of Scans\tCharge\tMonoisotopic Mass\tBase Isotope Peak\t");
+ fprintf(f,"Best Intensity\tSummed Intensity\tFirst RTime\tLast RTime\tBest RTime\tBest Correlation\tModifications\n");
+
+ for(i=0;i<vPeps.size();i++){
+ fprintf(f,"%s\t%d\t%d\t%d\t%d\t%lf\t%lf\t%f\t%f\t%f\t%f\t%f\t%lf\t%s\n","NULL",
+ vPeps[i].lowScan,
+ vPeps[i].highScan,
+ vPeps[i].datapoints,
+ vPeps[i].charge,
+ vPeps[i].monoMass,
+ vPeps[i].basePeak,
+ vPeps[i].intensity,
+ vPeps[i].sumIntensity,
+ vPeps[i].firstRTime,
+ vPeps[i].lastRTime,
+ vPeps[i].rTime,
+ vPeps[i].xCorr,
+ vPeps[i].mods);
+ }
+
+ fclose(f);
+ }
+
+ return true;
+}
+
+
+
+bool CKronik2::findMax(vector<sScan>& v, int& s, int& p){
+ bool found = false;
+ float max=0;
+ unsigned int i;
+ p=0;
+ for(i=0;i<v.size();i++){
+ if(v[i].vPep->size()==0) continue;
+ if(v[i].vPep->at(0).intensity>max){
+ max=v[i].vPep->at(0).intensity;
+ s=i;
+ found = true;
+ }
+ }
+ return found;
+}
+
+
+//-----------------------------------------
+// Tools
+//-----------------------------------------
+bool CKronik2::getRT(int scanNum, float& rt){
+
+ unsigned int i;
+ for(i=0;i<hkData.size();i++){
+ if(hkData[i].scanNum==scanNum){
+ rt=hkData[i].rTime;
+ return true;
+ }
+ }
+
+ rt=0.0f;
+ return false;
+}
+
+//-----------------------------------------
+// Filters
+//-----------------------------------------
+void CKronik2::filterRT(float rt1, float rt2){
+ unsigned int i;
+ vector<sPepProfile> temp;
+
+ for(i=0;i<vPeps.size();i++){
+ if(vPeps[i].rTime>=rt1 && vPeps[i].rTime<=rt2){
+ temp.push_back(vPeps[i]);
+ }
+ }
+
+ vPeps.clear();
+ for(i=0;i<temp.size();i++) vPeps.push_back(temp[i]);
+}
+
+void CKronik2::removeContaminants(float rt){
+ unsigned int i;
+ vector<sPepProfile> temp;
+
+ for(i=0;i<vPeps.size();i++){
+ if((vPeps[i].lastRTime-vPeps[i].firstRTime)<rt){
+ temp.push_back(vPeps[i]);
+ }
+ }
+
+ vPeps.clear();
+ for(i=0;i<temp.size();i++) vPeps.push_back(temp[i]);
+}
+
+void CKronik2::removeMass(double m1, double m2){
+ unsigned int i;
+ vector<sPepProfile> temp;
+
+ for(i=0;i<vPeps.size();i++){
+ if( vPeps[i].monoMass>=m1 && vPeps[i].monoMass<=m2 ){
+ temp.push_back(vPeps[i]);
+ }
+ }
+
+ vPeps.clear();
+ for(i=0;i<temp.size();i++) vPeps.push_back(temp[i]);
+}
+
+//-----------------------------------------
+// Parameter accessors and modifiers
+//-----------------------------------------
+void CKronik2::setPPMTol(double d){
+ dPPMTol=d;
+}
+
+void CKronik2::setMatchTol(int i){
+ iMatchTol=i;
+}
+
+void CKronik2::setGapTol(int i){
+ iGapTol=i;
+}
+
+unsigned int CKronik2::size(){
+ return vPeps.size();
+}
+
+
+//------------------------------------------------------
+// STATISTICS FUNCTIONS (adapted from numerical recipes)
+//------------------------------------------------------
+bool CKronik2::pearson(int i1, int i2, bool byScan, bool interpolate, double& rval, double& pval, double& slope, double& intercept, float& sum1, float& sum2){
+
+ int i,j;
+ double sxx=0.0,syy=0.0,sxy=0.0;
+ double ax=0.0,ay=0.0;
+ double sumx=0.0,sumy=0.0,sumxy=0.0,sumxx=0.0;
+ double yt,xt,t,df;
+ double TINY=1.0e-20;
+ double lrval;
+
+ pval=1.0;
+ rval=0.0;
+
+ vector<float> p1;
+ vector<float> p2;
+
+ if(byScan){
+ i=0;
+ j=0;
+ while(true){
+ if(i==vPeps[i1].datapoints) return false;
+ if(j==vPeps[i2].datapoints) return false;
+ if(vPeps[i1].profile[i].scanNum<vPeps[i2].profile[j].scanNum){
+ i++;
+ continue;
+ } else if(vPeps[i1].profile[i].scanNum>vPeps[i2].profile[j].scanNum){
+ j++;
+ continue;
+ } else {
+ break;
+ }
+ }
+ while(i<vPeps[i1].datapoints && j<vPeps[i2].datapoints){
+ //Build correlation vectors
+ p1.push_back(vPeps[i1].profile[i++].intensity);
+ p2.push_back(vPeps[i2].profile[j++].intensity);
+ }
+ } else {
+
+ //Find center for each peptide
+ float max;
+ int max1, max2;
+
+ max=0.0f;
+ for(i=0;i<vPeps[i1].datapoints;i++){
+ if(vPeps[i1].profile[i].intensity>max){
+ max=vPeps[i1].profile[i].intensity;
+ max1=i;
+ }
+ }
+
+ max=0.0f;
+ for(i=0;i<vPeps[i2].datapoints;i++){
+ if(vPeps[i2].profile[i].intensity>max){
+ max=vPeps[i2].profile[i].intensity;
+ max2=i;
+ }
+ }
+
+ //Build correlation vectors
+ p1.push_back(vPeps[i1].profile[max1].intensity);
+ p2.push_back(vPeps[i2].profile[max2].intensity);
+
+ j=0;
+ while((max1-j)>0 && (max2-j)>0){
+ j++;
+ if(vPeps[i1].profile[max1-j].interpolated && !interpolate) p1.push_back(0.0f);
+ else p1.push_back(vPeps[i1].profile[max1-j].intensity);
+ if(vPeps[i2].profile[max2-j].interpolated && !interpolate) p2.push_back(0.0f);
+ else p2.push_back(vPeps[i2].profile[max2-j].intensity);
+ }
+
+ j=1;
+ while((max1+j)<vPeps[i1].datapoints && (max2+j)<vPeps[i2].datapoints ){
+ if(vPeps[i1].profile[max1+j].interpolated && !interpolate) p1.push_back(0.0f);
+ else p1.push_back(vPeps[i1].profile[max1+j].intensity);
+ if(vPeps[i2].profile[max2+j].interpolated && !interpolate) p2.push_back(0.0f);
+ else p2.push_back(vPeps[i2].profile[max2+j].intensity);
+ j++;
+ }
+ }
+
+ //Get totals
+ for(i=0;i<p1.size();i++){
+ sumx+=p1[i];
+ sumy+=p2[i];
+ sumxy+=p1[i]*p2[i];
+ sumxx+=p1[i]*p1[i];
+ }
+
+ //Pearsons
+ ax=sumx/p1.size();
+ ay=sumy/p2.size();
+ for(i=0;i<p1.size();i++){
+ xt=p1[i]-ax;
+ yt=p2[i]-ay;
+ sxx+=xt*xt;
+ syy+=yt*yt;
+ sxy+=xt*yt;
+ }
+ rval=sxy/(sqrt(sxx*syy)+TINY);
+ if(rval<0.0) lrval=0.0; //negative correlations are false hits in this analysis
+ else lrval=rval;
+
+ df=p1.size()-2;
+ if(df<1) {
+ pval=1.0;
+ } else {
+ t=lrval*sqrt(df/((1-lrval+TINY)*(1+lrval+TINY)));
+ pval=betai(0.5*df,0.5,df/(df+t*t));
+ }
+
+ //Line of best fit
+ slope = (sumx*sumy - p1.size()*sumxy) / (sumx*sumx - p1.size()*sumxx);
+ intercept = (sumx*sumxy - sumy*sumxx) / (sumx*sumx - p1.size()*sumxx);
+
+ sum1=(float)sumx;
+ sum2=(float)sumy;
+
+ return true;
+
+}
+
+double CKronik2::betai(double a, double b, double x){
+ double bt;
+ if(x<0.0 || x>1.0) return 0.0;
+ if(x==0.0 || x==1.0) {
+ bt=0.0;
+ } else {
+ bt=exp(gammaln(a+b)-gammaln(a)-gammaln(b)+a*log(x)+b*log(1.0-x));
+ }
+ if(x<(a+1.0)/(a+b+2.0)) return bt*betacf(a,b,x)/a;
+ else return 1.0-bt*betacf(b,a,1.0-x)/b;
+}
+
+double CKronik2::betacf(double a, double b, double x){
+ int MAXIT = 100;
+ double EPS = 3.0e-7;
+ double FPMIN = 1.0e-30;
+
+ int m,m2;
+ double aa,c,d,del,h,qab,qam,qap;
+
+ qab=a+b;
+ qap=a+1.0;
+ qam=a-1.0;
+ c=1.0;
+ d=1.0-qab*x/qap;
+ if(fabs(d)<FPMIN) d=FPMIN;
+ d=1.0/d;
+ h=d;
+ for(m=1;m<=MAXIT;m++){
+ m2=2*m;
+ aa=m*(b-m)*x/((qam+m2)*(a+m2));
+ d=1.0+aa*d;
+ if(fabs(d)<FPMIN) d=FPMIN;
+ c=1.0+aa/c;
+ if(fabs(c)<FPMIN) c=FPMIN;
+ d=1.0/d;
+ h*=d*c;
+ aa=-(a+m)*(qab+m)*x/((a+m2)*(qap+m2));
+ d=1.0+aa*d;
+ if(fabs(d)<FPMIN) d=FPMIN;
+ c=1.0+aa/c;
+ if(fabs(c)<FPMIN) c=FPMIN;
+ d=1.0/d;
+ del=d*c;
+ h*=del;
+ if(fabs(del-1.0)<EPS) break;
+ }
+ if(m>MAXIT) return 0.0;
+ return h;
+}
+
+double CKronik2::gammaln(double xx){
+ double x,y,tmp,ser;
+ static double cof[6]={76.18009172947146,-86.50532032941677,24.01409824083091,-1.231739572450155,0.1208650973866179e-2,-0.5395239384953e-5};
+ int j;
+
+ y=x=xx;
+ tmp=x+5.5;
+ tmp-=(x+0.5)*log(tmp);
+ ser=1.000000000190015;
+ for(j=0;j<=5;j++) ser+=cof[j]/++y;
+ return -tmp+log(2.5066282746310005*ser/x);
+}
+
+double CKronik2::interpolate(int x1, int x2, double y1, double y2, int x){
+ double m;
+ double b;
+
+ m=(y2-y1)/(x2-x1);
+ b=y2-m*x2;
+ return m*x+b;
+
+}
+
+//--------------------------------
+// Sorting Functions
+//--------------------------------
+void CKronik2::sortBasePeak(){
+ qsort(&vPeps[0],vPeps.size(),sizeof(sPepProfile),compareBP);
+}
+
+void CKronik2::sortMonoMass(){
+ qsort(&vPeps[0],vPeps.size(),sizeof(sPepProfile),compareMM);
+}
+
+void CKronik2::sortFirstRTime(){
+ qsort(&vPeps[0],vPeps.size(),sizeof(sPepProfile),compareFRT);
+}
+
+void CKronik2::sortIntensityRev(){
+ qsort(&vPeps[0],vPeps.size(),sizeof(sPepProfile),compareIRev);
+}
+
+int CKronik2::compareBP(const void *p1, const void *p2){
+ const sPepProfile d1 = *(sPepProfile *)p1;
+ const sPepProfile d2 = *(sPepProfile *)p2;
+ if(d1.basePeak<d2.basePeak) return -1;
+ else if(d1.basePeak>d2.basePeak) return 1;
+ else return 0;
+}
+
+int CKronik2::compareMM(const void *p1, const void *p2){
+ const sPepProfile d1 = *(sPepProfile *)p1;
+ const sPepProfile d2 = *(sPepProfile *)p2;
+ if(d1.monoMass<d2.monoMass) return -1;
+ else if(d1.monoMass>d2.monoMass) return 1;
+ else return 0;
+}
+
+int CKronik2::compareFRT(const void *p1, const void *p2){
+ const sPepProfile d1 = *(sPepProfile *)p1;
+ const sPepProfile d2 = *(sPepProfile *)p2;
+ if(d1.firstRTime<d2.firstRTime) return -1;
+ else if(d1.firstRTime>d2.firstRTime) return 1;
+ else return 0;
+}
+
+int CKronik2::compareIRev(const void *p1, const void *p2){
+ const sPepProfile d1 = *(sPepProfile *)p1;
+ const sPepProfile d2 = *(sPepProfile *)p2;
+ //cout << d1.intensity << " " << d2.intensity << endl;
+ if(d1.intensity>d2.intensity) return -1;
+ else if(d1.intensity<d2.intensity) return 1;
+ else return 0;
+}
diff --git a/src/app/bullseye/CKronik2.h b/src/app/bullseye/CKronik2.h
new file mode 100644
index 0000000..7e2e13d
--- /dev/null
+++ b/src/app/bullseye/CKronik2.h
@@ -0,0 +1,340 @@
+#pragma once
+
+#include <iostream>
+#include <vector>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+#include <cstdio>
+
+using namespace std;
+
+typedef struct sPep{
+ int charge;
+ float intensity;
+ double monoMass;
+ double basePeak;
+ double xCorr;
+ char mods[32];
+} sPep;
+
+typedef struct sScan {
+ vector<sPep> *vPep;
+ int scanNum;
+ char file[256];
+ float rTime;
+
+ //Constructors & Destructor
+ sScan(){vPep = new vector<sPep>;}
+ sScan(const sScan& s){
+ vPep = new vector<sPep>;
+ for(unsigned int i=0;i<s.vPep->size();i++) vPep->push_back(s.vPep->at(i));
+ scanNum = s.scanNum;
+ strcpy(file,s.file);
+ rTime=s.rTime;
+ }
+ ~sScan(){delete vPep;}
+
+ //Copy operator
+ sScan& operator=(const sScan& s){
+ if(this!=&s){
+ delete vPep;
+ vPep = new vector<sPep>;
+ for(unsigned int i=0;i<s.vPep->size();i++) vPep->push_back(s.vPep->at(i));
+ scanNum = s.scanNum;
+ strcpy(file,s.file);
+ rTime=s.rTime;
+ }
+ return *this;
+ }
+
+ //Clear
+ void clear(){
+ delete vPep;
+ vPep = new vector<sPep>;
+ }
+
+ static int compareIntRev(const void *p1, const void *p2){
+ const sPep d1 = *(sPep *)p1;
+ const sPep d2 = *(sPep *)p2;
+ if(d1.intensity>d2.intensity) return -1;
+ else if(d1.intensity<d2.intensity) return 1;
+ else return 0;
+ }
+
+ void sortIntRev(){
+ if(vPep->size()==0) return;
+ qsort(&vPep->at(0),vPep->size(),sizeof(sPep),compareIntRev);
+ }
+
+} sScan;
+
+typedef struct sProfileData {
+ bool interpolated;
+
+ int scanNum;
+
+ float intensity;
+ float rTime;
+
+ double monoMass;
+ double xCorr;
+
+ //Constructor
+ sProfileData(){
+ interpolated=false;
+ scanNum=0;
+ intensity=0.0f;
+ rTime=0.0f;
+ monoMass=0.0;
+ xCorr=0.0;
+ }
+} sProfileData;
+
+typedef struct sPepProfile {
+ int lowScan;
+ int highScan;
+ int bestScan;
+ int charge;
+ int MS2Events;
+
+ unsigned int datapoints;
+
+ float rTime;
+ float firstRTime;
+ float lastRTime;
+ float intensity;
+ float sumIntensity;
+
+ double monoMass;
+ double basePeak;
+ double xCorr;
+
+ char mods[32];
+ char gene[32];
+ char sequence[64];
+
+ sProfileData* profile;
+ //sProfileData* gaussProfile;
+
+ //Constructors
+ sPepProfile() {
+ profile = new sProfileData[1];
+ //gaussProfile = new sProfileData[1];
+ sProfileData d;
+ profile[0]=d;
+ //gaussProfile[0]=d;
+ datapoints=0;
+ lowScan=0;
+ highScan=0;
+ bestScan=0;
+ MS2Events=0;
+ charge=0;
+ rTime=0.0f;
+ firstRTime=0.0f;
+ lastRTime=0.0f;
+ intensity=0.0f;
+ sumIntensity=0.0f;
+ monoMass=0.0;
+ basePeak=0.0;
+ xCorr=0.0;
+ strcpy(mods,"");
+ strcpy(sequence,"");
+ strcpy(gene,"");
+ }
+ sPepProfile(const unsigned int i) {
+ profile = new sProfileData[i];
+ //gaussProfile = new sProfileData[i];
+ sProfileData d;
+ unsigned int j;
+ for(j=0;j<i;j++) profile[j]=d;
+ datapoints=i;
+ lowScan=0;
+ highScan=0;
+ bestScan=0;
+ charge=0;
+ MS2Events=0;
+ rTime=0.0f;
+ firstRTime=0.0f;
+ lastRTime=0.0f;
+ intensity=0.0f;
+ sumIntensity=0.0f;
+ monoMass=0.0;
+ basePeak=0.0;
+ xCorr=0.0;
+ strcpy(mods,"");
+ strcpy(sequence,"");
+ strcpy(gene,"");
+ }
+ sPepProfile(const sPepProfile& p){
+ unsigned int i;
+ profile = new sProfileData[p.datapoints];
+ for(i=0;i<p.datapoints;i++) profile[i]=p.profile[i];
+ lowScan = p.lowScan;
+ highScan = p.highScan;
+ bestScan = p.bestScan;
+ charge = p.charge;
+ MS2Events = p.MS2Events;
+ datapoints = p.datapoints;
+ rTime = p.rTime;
+ firstRTime = p.firstRTime;
+ lastRTime = p.lastRTime;
+ intensity = p.intensity;
+ sumIntensity = p.sumIntensity;
+ monoMass = p.monoMass;
+ basePeak = p.basePeak;
+ xCorr = p.xCorr;
+ strcpy(mods,p.mods);
+ strcpy(sequence,p.sequence);
+ strcpy(gene,p.gene);
+ }
+
+ //Destructor
+ ~sPepProfile(){
+ delete [] profile;
+ }
+
+ //Copy operator
+ sPepProfile& operator=(const sPepProfile& p){
+ if(this!=&p){
+ unsigned int i;
+ delete [] profile;
+ profile = new sProfileData[p.datapoints];
+ for(i=0;i<p.datapoints;i++) profile[i]=p.profile[i];
+ lowScan = p.lowScan;
+ highScan = p.highScan;
+ bestScan = p.bestScan;
+ MS2Events = p.MS2Events;
+ charge = p.charge;
+ datapoints = p.datapoints;
+ rTime = p.rTime;
+ firstRTime = p.firstRTime;
+ lastRTime = p.lastRTime;
+ intensity = p.intensity;
+ sumIntensity = p.sumIntensity;
+ monoMass = p.monoMass;
+ basePeak = p.basePeak;
+ xCorr = p.xCorr;
+ strcpy(mods,p.mods);
+ strcpy(sequence,p.sequence);
+ strcpy(gene,p.gene);
+ }
+ return *this;
+ }
+
+ void setPoints(const unsigned int& i){
+ delete [] profile;
+ profile = new sProfileData[i];
+ datapoints=i;
+ sProfileData d;
+ for(unsigned int j=0;j<i;j++) profile[j]=d;
+ }
+
+ static int compareScanNum(const void *p1, const void *p2){
+ const sProfileData d1 = *(sProfileData *)p1;
+ const sProfileData d2 = *(sProfileData *)p2;
+ if(d1.scanNum<d2.scanNum) return -1;
+ else if(d1.scanNum>d2.scanNum) return 1;
+ else return 0;
+ }
+
+ static int compareIntRev(const void *p1, const void *p2){
+ const sProfileData d1 = *(sProfileData *)p1;
+ const sProfileData d2 = *(sProfileData *)p2;
+ if(d1.intensity>d2.intensity) return -1;
+ else if(d1.intensity<d2.intensity) return 1;
+ else return 0;
+ }
+
+ void sortIntRev(){
+ if(datapoints==0) return;
+ qsort(profile,datapoints,sizeof(sProfileData),compareIntRev);
+ }
+
+ void sortScanNum(){
+ if(datapoints==0) return;
+ qsort(profile,datapoints,sizeof(sProfileData),compareScanNum);
+ }
+
+} sPepProfile;
+
+typedef struct iTwo{
+ int scan;
+ int pep;
+} iTwo;
+
+class CKronik2 {
+public:
+
+ //Constructors and destructors
+ CKronik2();
+ CKronik2(const CKronik2& c);
+ ~CKronik2();
+
+ //Operator overrides
+ CKronik2& operator=(const CKronik2& c);
+ sPepProfile& operator[ ](const unsigned int& i);
+
+ //Statistics functions
+ bool pearson(int i1, int i2, bool byScan, bool interpolate, double& rval, double& pval, double& slope, double& intercept, float& sum1, float& sum2);
+
+ //Parameter accessors and modifiers
+ void setPPMTol(double d);
+ void setMatchTol(int i);
+ void setGapTol(int i);
+
+ //Automation
+ int getPercent();
+ bool loadHK(char* in);
+ bool processHK(char* in, char* out="\0");
+
+ //Tools
+ bool getRT(int scanNum, float& rt);
+
+ //Filters
+ void filterRT(float rt1, float rt2);
+ void removeContaminants(float rt);
+ void removeMass(double m1, double m2);
+
+ //Data manipulation functions
+ sPepProfile& at(unsigned int i);
+ void add(sPepProfile& p);
+ void clear();
+ void clearHK();
+ void erase(unsigned int i);
+ unsigned int size();
+
+ //Sorting functions
+ void sortBasePeak();
+ void sortMonoMass();
+ void sortFirstRTime();
+ void sortIntensityRev();
+
+protected:
+private:
+ bool findMax(vector<sScan>& v, int& s, int& p);
+ double interpolate(int x1, int x2, double y1, double y2, int x);
+
+ //Statistics functions
+ double betai(double a, double b, double x);
+ double betacf(double a, double b, double x);
+ double gammaln(double xx);
+
+ //Data Members: data analysis
+ vector<sPepProfile> vPeps;
+ vector<sScan> hkData;
+
+ //Data Members: parameters
+ double dPPMTol; //default 10.0
+ int iGapTol; //default 1
+ int iMatchTol; //Default 3
+ int iPercent;
+
+ //Sorting Functions
+ void sortPeptide();
+ static int compareBP(const void *p1, const void *p2);
+ static int compareMM(const void *p1, const void *p2);
+ static int compareFRT(const void *p1, const void *p2);
+ static int compareIRev(const void *p1, const void *p2);
+
+};
diff --git a/src/app/bullseye/CMakeLists.txt b/src/app/bullseye/CMakeLists.txt
new file mode 100644
index 0000000..13f35db
--- /dev/null
+++ b/src/app/bullseye/CMakeLists.txt
@@ -0,0 +1,48 @@
+project(bullseye)
+
+cmake_minimum_required(VERSION 2.8.1)
+cmake_policy(VERSION 2.8.1)
+
+include_directories(${CMAKE_SOURCE_DIR}/src)
+include_directories(${CMAKE_SOURCE_DIR}/src/app/hardklor)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_1_56_0)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_aux)
+include_directories(${CMAKE_BINARY_DIR}/ext/include)
+include_directories(${CMAKE_BINARY_DIR}/ext/include/MSToolkit)
+if (WIN32 AND NOT Cygwin)
+ # Needed to put DLL containing type libraries
+ # in include path for Windows
+ include_directories(${CMAKE_BINARY_DIR}/ext/lib)
+endif (WIN32 AND NOT Cygwin)
+
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _CRT_SECURE_NO_WARNINGS
+ CRUX
+ SEARCH_ENABLED
+ )
+else (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _LARGEFILE_SOURCE
+ _FILE_OFFSET_BITS=64
+ _GNU_SOURCE
+ CRUX
+ GCC
+ HAVE_EXPAT_CONFIG_H
+ SEARCH_ENABLED
+ )
+endif (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+add_library(
+ bullseye
+ STATIC
+ bullseye.cpp
+ CKronik2.cpp
+ CruxBullseyeApplication.cpp
+)
diff --git a/src/app/bullseye/CruxBullseyeApplication.cpp b/src/app/bullseye/CruxBullseyeApplication.cpp
new file mode 100644
index 0000000..8284114
--- /dev/null
+++ b/src/app/bullseye/CruxBullseyeApplication.cpp
@@ -0,0 +1,263 @@
+/**
+ * \file CruxBullseyeApplication.cpp
+ * \brief Given a ms1 and ms2 file, run hardklor followed by the bullseye algorithm.
+ *****************************************************************************/
+#include "CruxBullseyeApplication.h"
+#include "app/hardklor/CruxHardklorApplication.h"
+#include "util/CarpStreamBuf.h"
+#include "io/DelimitedFileWriter.h"
+
+#include "util/crux-utils.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+
+/**
+ * \returns a blank CruxBullseyeApplication object
+ */
+CruxBullseyeApplication::CruxBullseyeApplication() {
+}
+
+/**
+ * Destructor
+ */
+CruxBullseyeApplication::~CruxBullseyeApplication() {
+}
+
+int CruxBullseyeApplication::main(int argc, char** argv) {
+ string out_format = Params::GetString("spectrum-format");
+ if (out_format.empty()) {
+ out_format = "ms2";
+ } else if (out_format != "ms2" && out_format != "bms2" &&
+ out_format != "cms2" && out_format != "mgf") {
+ carp(CARP_FATAL, "spectrum-format must be ms2, bms2, cms2, or mgf, but was %s",
+ out_format.c_str());
+ }
+ return main(
+ Params::GetString("MS1 spectra"),
+ Params::GetString("MS2 spectra"),
+ make_file_path("bullseye.pid." + out_format),
+ make_file_path("bullseye.no-pid." + out_format)
+ );
+}
+
+/**
+ * main method for CruxBullseyeApplication
+ */
+int CruxBullseyeApplication::main(
+ const string& input_ms1,
+ const string& input_ms2,
+ const string& match_ms2,
+ const string& nomatch_ms2
+) {
+ /* Get parameters. */
+ string hardklor_output = Params::GetString("hardklor-file");
+ if (hardklor_output.empty()) {
+ hardklor_output = make_file_path("hardklor.mono.txt");
+ if (Params::GetBool("overwrite") || (!FileUtils::Exists(hardklor_output))) {
+ carp(CARP_DEBUG, "Calling hardklor");
+ bool ret = CruxHardklorApplication::main(input_ms1);
+ if (ret != 0) {
+ carp(CARP_WARNING, "Hardklor failed:%d", ret);
+ return ret;
+ }
+ }
+ }
+
+ /* build argument list */
+ vector<string> be_args_vec;
+ be_args_vec.push_back("bullseye");
+
+ /* add flags */
+
+ be_args_vec.push_back("-c");
+ be_args_vec.push_back(Params::GetString("max-persist"));
+
+ if (Params::GetBool("exact-match")) {
+ be_args_vec.push_back("-e");
+ be_args_vec.push_back("-p");
+ be_args_vec.push_back(Params::GetString("exact-tolerance"));
+ }
+
+ be_args_vec.push_back("-g");
+ be_args_vec.push_back(Params::GetString("gap-tolerance"));
+
+ be_args_vec.push_back("-r");
+ be_args_vec.push_back(Params::GetString("persist-tolerance"));
+
+ be_args_vec.push_back("-n");
+ be_args_vec.push_back(Params::GetString("bullseye-min-mass"));
+
+ be_args_vec.push_back("-m");
+ be_args_vec.push_back(Params::GetString("bullseye-max-mass"));
+
+ be_args_vec.push_back("-s");
+ be_args_vec.push_back(
+ //TODO- I don't know why bullseye.cpp adds 1 to the value passed in...
+ StringUtils::ToString(Params::GetInt("scan-tolerance") - 1));
+
+ be_args_vec.push_back("-t");
+ be_args_vec.push_back(Params::GetString("retention-tolerance"));
+
+
+
+ /* add arguments */
+ be_args_vec.push_back(hardklor_output);
+ be_args_vec.push_back(input_ms2);
+ be_args_vec.push_back(match_ms2);
+ be_args_vec.push_back(nomatch_ms2);
+
+
+ /* build argv line */
+ int be_argc = be_args_vec.size();
+
+ char** be_argv = new char*[be_argc];
+
+ be_argv[0] = (char*)be_args_vec[0].c_str();
+ for (int idx = 1;idx < be_argc ; idx++) {
+ be_argv[idx] = (char*)be_args_vec[idx].c_str();
+ carp(CARP_DEBUG, "be_argv[%d]=%s", idx, be_argv[idx]);
+ }
+
+ // Re-route stream to log file
+ CarpStreamBuf buffer;
+ streambuf* old = cout.rdbuf();
+ cout.rdbuf(&buffer);
+
+ /* Call bullseyeMain */
+ int ret = bullseyeMain(be_argc, be_argv);
+
+ // Recover stream
+ cout.rdbuf(old);
+
+ delete []be_argv;
+
+ return ret;
+}
+
+/**
+ * \returns the command name for CruxBullseyeApplication
+ */
+string CruxBullseyeApplication::getName() const {
+ return "bullseye";
+}
+
+/**
+ * \returns the description for CruxBullseyeApplication
+ */
+string CruxBullseyeApplication::getDescription() const {
+ return
+ "[[nohtml:Assign high resolution precursor m/z values to MS/MS data using "
+ "the Hardklör algorithm.]]"
+ "[[html:<p>Bullseye assigns high resolution precursor m/z values to "
+ "fragmentation (MS2) spectra. Bullseye uses the Hardklör algorithm to "
+ "identify persistent isotope distributions (PPIDs) in precursor (MS1) "
+ "scans. For each PPID, MS2 scans that occur within a specified time and "
+ "m/z range are assigned the average monoisotopic m/z from the PPID "
+ "assigned as the precursor m/z. A detailed description of the Bullseye "
+ "algorithm is given in </p><quote>Hsieh EJ, Hoopmann MR, Maclean B, "
+ "MacCoss MJ. <a href=\"http://pubs.acs.org/doi/abs/10.1021/pr900816a\">"
+ ""Comparison of Database Search Strategies for High Precursor Mass "
+ "Accuracy MS/MS Data"</a>. <em>Journal of Proteome Research</em>. "
+ "9(2):1138-43, 2010.</quote><p>Note that, in complex samples, it is not "
+ "unusual for multiple PPIDs to be found near an MS2 spectrum. In those "
+ "cases, Bullseye will assign both mass measurements to the spectrum. In a "
+ ".ms2 file, multiple Z line entries will be made for the scan number.</p>"
+ "<p>It is possible to reduce the number of scans that receive multiple "
+ "PPIDs by adjusting Bullseye's parameters. For example, reducing the "
+ "retention time tolerance ("--retention-tolerance") or reducing "
+ "the tolerance for persistent peptides ("--persist-tolerance") "
+ "will reduce the chances of multiple PPIDs being assigned.</p><p>Bullseye "
+ "uses Hardklör, so all of the <a href=\"hardklor.html\">Hardklör "
+ "parameters</a> may also be used with Bullseye. For users familiar with "
+ "the standalone version of Bullseye, the parameter mapping is "
+ "<a href=\"bullseye_standalone_to_crux.html\">here</a>.</p>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> CruxBullseyeApplication::getArgs() const {
+ string arr[] = {
+ "MS1 spectra",
+ "MS2 spectra"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> CruxBullseyeApplication::getOptions() const {
+ string arr[] = {
+ "fileroot",
+ "output-dir",
+ "overwrite",
+ "max-persist",
+ "exact-match",
+ "exact-tolerance",
+ "persist-tolerance",
+ "gap-tolerance",
+ "scan-tolerance",
+ "bullseye-max-mass",
+ "bullseye-min-mass",
+ "retention-tolerance",
+ "spectrum-format",
+ "parameter-file",
+ "verbosity"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > CruxBullseyeApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("bullseye.pid.<format>",
+ "a file containing the fragmentation spectra for which accurate masses "
+ "were successfully inferred. Unless otherwise specified (with the "
+ "--spectrum-format option), the output file format is \".ms2\". Note that "
+ "if the output format is \".ms2,\" then a single spectrum may have "
+ "multiple \"Z\" lines, each indicating a charge state and accurate mass. "
+ "In addition, Bullseye inserts an \"I\" line (for charge-dependent "
+ "analysis) corresponding to each \"Z\" line. The \"I\" line contains "
+ "\"EZ\" in the second column, the charge and mass from the associated "
+ "\"Z\" line in the third and fourth colummns, followed by the "
+ "chromatographic apex and the intensity at the chromatographic apex."));
+ outputs.push_back(make_pair("bullseye.no-pid.<format>",
+ "a file containing the fragmentation spectra for which accurate masses "
+ "were not inferred."));
+ outputs.push_back(make_pair("hardklor.mono.txt",
+ "a tab-delimited text file containing one line for each isotope "
+ "distribution, as described <a href=\"hardklor.html\">here</a>."));
+ outputs.push_back(make_pair("bullseye.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("bullseye.log.txt",
+ "a log file containing a copy of all messages that were printed to "
+ "standard error."));
+ return outputs;
+}
+
+/**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+bool CruxBullseyeApplication::needsOutputDirectory() const {
+ return true;
+}
+
+COMMAND_T CruxBullseyeApplication::getCommand() const {
+ return BULLSEYE_COMMAND;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/bullseye/CruxBullseyeApplication.h b/src/app/bullseye/CruxBullseyeApplication.h
new file mode 100644
index 0000000..a83afea
--- /dev/null
+++ b/src/app/bullseye/CruxBullseyeApplication.h
@@ -0,0 +1,85 @@
+/**
+ * \file CruxBullseyeApplication.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 4 November 2011
+ * \brief Interface for calling hardklor.
+ *****************************************************************************/
+#ifndef CRUXBULLSEYEAPPLICATION_H
+#define CRUXBULLSEYEAPPLICATION_H
+
+#include "app/CruxApplication.h"
+
+#include <string>
+#include <fstream>
+
+class CruxBullseyeApplication: public CruxApplication {
+
+ protected:
+
+ //Calls the main method in bullseye
+ int bullseyeMain(int argc, char* argv[]);
+
+ public:
+
+ /**
+ * \returns a blank CruxBullseyeApplication object
+ */
+ CruxBullseyeApplication();
+
+ /**
+ * Destructor
+ */
+ ~CruxBullseyeApplication();
+
+ /**
+ * main method for CruxBullseyeApplication
+ */
+ virtual int main(int argc, char** argv);
+
+ int main(const std::string& input_ms1,
+ const std::string& input_ms2,
+ const std::string& match_ms2,
+ const std::string& nomatch_ms2);
+
+ /**
+ * \returns the command name for CruxBullseyeApplication
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for CruxBullseyeApplication
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+ virtual bool needsOutputDirectory() const;
+
+ virtual COMMAND_T getCommand() const;
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/bullseye/Makefile b/src/app/bullseye/Makefile
new file mode 100644
index 0000000..ab47d90
--- /dev/null
+++ b/src/app/bullseye/Makefile
@@ -0,0 +1,288 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
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+all: cmake_check_build_system
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+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 src/app/bullseye/all
+ $(CMAKE_COMMAND) -E cmake_progress_start /data/TeamCity/buildAgent/work/779d99b0241b2175/CMakeFiles 0
+.PHONY : all
+
+# The main clean target
+clean:
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+.PHONY : clean
+
+# The main clean target
+clean/fast: clean
+.PHONY : clean/fast
+
+# Prepare targets for installation.
+preinstall: all
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 src/app/bullseye/preinstall
+.PHONY : preinstall
+
+# Prepare targets for installation.
+preinstall/fast:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 src/app/bullseye/preinstall
+.PHONY : preinstall/fast
+
+# clear depends
+depend:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
+.PHONY : depend
+
+# Convenience name for target.
+src/app/bullseye/CMakeFiles/bullseye.dir/rule:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 src/app/bullseye/CMakeFiles/bullseye.dir/rule
+.PHONY : src/app/bullseye/CMakeFiles/bullseye.dir/rule
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+.PHONY : bullseye/fast
+
+CKronik2.o: CKronik2.cpp.o
+.PHONY : CKronik2.o
+
+# target to build an object file
+CKronik2.cpp.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/CKronik2.cpp.o
+.PHONY : CKronik2.cpp.o
+
+CKronik2.i: CKronik2.cpp.i
+.PHONY : CKronik2.i
+
+# target to preprocess a source file
+CKronik2.cpp.i:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/CKronik2.cpp.i
+.PHONY : CKronik2.cpp.i
+
+CKronik2.s: CKronik2.cpp.s
+.PHONY : CKronik2.s
+
+# target to generate assembly for a file
+CKronik2.cpp.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/CKronik2.cpp.s
+.PHONY : CKronik2.cpp.s
+
+CruxBullseyeApplication.o: CruxBullseyeApplication.cpp.o
+.PHONY : CruxBullseyeApplication.o
+
+# target to build an object file
+CruxBullseyeApplication.cpp.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/CruxBullseyeApplication.cpp.o
+.PHONY : CruxBullseyeApplication.cpp.o
+
+CruxBullseyeApplication.i: CruxBullseyeApplication.cpp.i
+.PHONY : CruxBullseyeApplication.i
+
+# target to preprocess a source file
+CruxBullseyeApplication.cpp.i:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/CruxBullseyeApplication.cpp.i
+.PHONY : CruxBullseyeApplication.cpp.i
+
+CruxBullseyeApplication.s: CruxBullseyeApplication.cpp.s
+.PHONY : CruxBullseyeApplication.s
+
+# target to generate assembly for a file
+CruxBullseyeApplication.cpp.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/CruxBullseyeApplication.cpp.s
+.PHONY : CruxBullseyeApplication.cpp.s
+
+bullseye.o: bullseye.cpp.o
+.PHONY : bullseye.o
+
+# target to build an object file
+bullseye.cpp.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/bullseye.cpp.o
+.PHONY : bullseye.cpp.o
+
+bullseye.i: bullseye.cpp.i
+.PHONY : bullseye.i
+
+# target to preprocess a source file
+bullseye.cpp.i:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/bullseye.cpp.i
+.PHONY : bullseye.cpp.i
+
+bullseye.s: bullseye.cpp.s
+.PHONY : bullseye.s
+
+# target to generate assembly for a file
+bullseye.cpp.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/bullseye/CMakeFiles/bullseye.dir/build.make src/app/bullseye/CMakeFiles/bullseye.dir/bullseye.cpp.s
+.PHONY : bullseye.cpp.s
+
+# Help Target
+help:
+ @echo "The following are some of the valid targets for this Makefile:"
+ @echo "... all (the default if no target is provided)"
+ @echo "... clean"
+ @echo "... depend"
+ @echo "... bullseye"
+ @echo "... edit_cache"
+ @echo "... install"
+ @echo "... install/local"
+ @echo "... install/strip"
+ @echo "... list_install_components"
+ @echo "... package"
+ @echo "... package_source"
+ @echo "... rebuild_cache"
+ @echo "... CKronik2.o"
+ @echo "... CKronik2.i"
+ @echo "... CKronik2.s"
+ @echo "... CruxBullseyeApplication.o"
+ @echo "... CruxBullseyeApplication.i"
+ @echo "... CruxBullseyeApplication.s"
+ @echo "... bullseye.o"
+ @echo "... bullseye.i"
+ @echo "... bullseye.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+
diff --git a/src/app/bullseye/Makefile.bullseye b/src/app/bullseye/Makefile.bullseye
new file mode 100644
index 0000000..ee29b92
--- /dev/null
+++ b/src/app/bullseye/Makefile.bullseye
@@ -0,0 +1,18 @@
+#Set these variables if needed
+C = gcc
+CC = g++
+FLAGS = -O3 -static -D_NOSQLITE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC
+MSTOOLKIT = ../mstoolkit-read-only/
+INCLUDE = -I$(MSTOOLKIT)/include -I$(MSTOOLKIT)/mzParser/include
+PEP = CKronik2.o
+
+
+bullseye : bullseye.cpp $(PEP)
+ $(CC) $(FLAGS) $(INCLUDE) $(PEP) bullseye.cpp -L$(MSTOOLKIT) -lmstoolkitlite -o bullseye
+
+#PEP objects
+CKronik2.o : CKronik2.cpp
+ $(CC) $(FLAGS) CKronik2.cpp -c
+
+clean:
+ rm -f *.o bullseye
diff --git a/src/app/bullseye/bullseye.cpp b/src/app/bullseye/bullseye.cpp
new file mode 100644
index 0000000..c98cc87
--- /dev/null
+++ b/src/app/bullseye/bullseye.cpp
@@ -0,0 +1,465 @@
+#include "CKronik2.h"
+#include "Spectrum.h"
+#include "MSReader.h"
+#ifdef CRUX
+#include "CruxBullseyeApplication.h"
+#endif
+#include <iostream>
+#include <iomanip>
+#include <vector>
+
+using namespace MSToolkit;
+
+MSFileFormat getFileFormat(char* c);
+void matchMS2(CKronik2& p, char* ms2File, char* outFile, char* outFile2);
+void usage();
+
+double mean,stD;
+double ppmTolerance;
+double rtTolerance;
+bool bMatchPrecursorOnly;
+
+#ifdef CRUX
+int CruxBullseyeApplication::bullseyeMain(int argc, char* argv[]){
+#else
+int main(int argc, char* argv[]){
+#endif
+ int i;
+ CKronik2 p1;
+
+ cout << "Bullseye, v1.30, Apr 20, 2011" << endl;
+ cout << "Copyright 2008-2011 Mike Hoopmann, Ed Hsieh, Mike MacCoss" << endl;
+ cout << "University of Washington" << endl;
+
+ //Set global variables
+ ppmTolerance=10.0;
+ rtTolerance=0.5;
+ bMatchPrecursorOnly=false;
+
+ //Set default parameters for some options
+ double contam=2.0;
+ double maxMass=8000.0;
+ double minMass=600.0;
+
+ if(argc<5){
+ usage();
+ exit(0);
+ }
+
+ if(argc>5){
+ for(i=1;i<argc-4;i+=2){
+ if(argv[i][0]!='-') {
+ cout << "Invalid flag!\n" << endl;
+ usage();
+ exit(0);
+ }
+ switch(argv[i][1]){
+ case 'c':
+ contam=atof(argv[i+1]);
+ break;
+ case 'e':
+ bMatchPrecursorOnly=true;
+ i--;
+ break;
+ case 'g':
+ p1.setGapTol(atoi(argv[i+1]));
+ break;
+ case 'm':
+ maxMass=atof(argv[i+1]);
+ break;
+ case 'n':
+ minMass=atof(argv[i+1]);
+ break;
+ case 'p':
+ ppmTolerance=atof(argv[i+1]);
+ break;
+ case 'r':
+ p1.setPPMTol(atof(argv[i+1]));
+ break;
+ case 's':
+ p1.setMatchTol(atoi(argv[i+1])+1);
+ break;
+ case 't':
+ rtTolerance=atof(argv[i+1]);
+ break;
+ default:
+ cout << "Invalid flag!\n" << endl;
+ usage();
+ exit(0);
+ break;
+ }
+ }
+ }
+
+ p1.processHK(argv[argc-4]);
+ if (p1.size() == 0) {
+ cout << "No analysis results, exiting..." << endl;
+ exit(0);
+ }
+
+ //Remove contaminants
+ CKronik2 tKro;
+ for(i=0;i<(int)p1.size();i++){
+ if( (p1[i].lastRTime-p1[i].firstRTime) <= contam) tKro.add(p1[i]);
+ }
+ p1=tKro;
+ cout << "Persistent peptides after removing contaminants: " << p1.size() << endl;
+
+ //Filter based on size
+ tKro.clear();
+ for(i=0;i<(int)p1.size();i++){
+ if( p1[i].monoMass>=minMass && p1[i].monoMass<=maxMass) tKro.add(p1[i]);
+ }
+ p1=tKro;
+ cout << "Persistent peptides from " << minMass << " to " << maxMass << ": " << p1.size() << endl;
+
+ //p1.findPeps();
+ matchMS2(p1,argv[argc-3],argv[argc-2],argv[argc-1]);
+
+ return 0;
+
+}
+
+void matchMS2(CKronik2& p, char* ms2File, char* outFile, char* outFile2){
+
+ Spectrum s;
+ MSReader r,rPos,rNeg;
+ MSObject o,o2;
+ int i,j;
+ int fragCount=0;
+ int lookup[8001];
+ double lowMass, highMass,ppm;
+ int x,z;
+ int a,b;
+ int c=0;
+ int d=0;
+ int iPercent=0;
+ int index;
+ vector<int> vI;
+ vector<int> vHit;
+ MSFileFormat posFF, negFF;
+
+ int ch[10];
+ for(i=0;i<10;i++) ch[i]=0;
+
+ char str1[16];
+ char str2[16];
+
+ //Check file formats for output. Make sure the user specifies the appropriate format
+ posFF=getFileFormat(outFile);
+ negFF=getFileFormat(outFile2);
+
+ switch(posFF){
+ case raw:
+ case mzXML:
+ case zs:
+ case uzs:
+ case ms1:
+ case bms1:
+ case cms1:
+ case dunno:
+ cout << "Output file format (pos set) not acceptable. Choose a different format." << endl;
+ exit(-2);
+ default:
+ break;
+ }
+
+ switch(negFF){
+ case raw:
+ case mzXML:
+ case zs:
+ case uzs:
+ case ms1:
+ case bms1:
+ case cms1:
+ case dunno:
+ cout << "Output file format (neg set) not acceptable. Choose a different format." << endl;
+ exit(-2);
+ default:
+ break;
+ }
+
+ //Hardklor results are sorted and indexed to improve speed of Bullseye
+ cout << "Sorting Hardklor results...";
+ p.sortBasePeak();
+ cout << "Done!" << endl;
+
+ cout << "Building lookup table...";
+ j=0;
+ for(i=0;i<8001;i++){
+ while(p.at(j).basePeak<i){
+ if(j>=p.size()-1) break;
+ j++;
+ }
+ lookup[i]=j;
+ }
+ cout << "Done!" << endl;
+
+ //Read in the data
+ cout << "Matching MS/MS..." << endl;
+ cerr << iPercent;
+
+ b=0;
+ z=0;
+ a=0;
+
+ r.setFilter(MS2);
+ r.readFile(ms2File,s);
+
+ o.setHeader(r.getHeader());
+ o2.setHeader(r.getHeader());
+ o.addToHeader("FileGenerator\tBullseye v1.30\n\0");
+ o2.addToHeader("FileGenerator\tBullseye v1.30\n\0");
+
+ rPos.setPrecisionMZ(4);
+ rNeg.setPrecisionMZ(4);
+ rPos.setHighResMGF(true);
+ rNeg.setHighResMGF(false);
+ rPos.writeFile(outFile,posFF,o);
+ rNeg.writeFile(outFile2,negFF,o2);
+
+ while(s.getScanNumber()>0){
+
+ j=(int)(s.getMZ()+0.5);
+ x=0;
+ vHit.clear();
+
+ //see if we can pick it up on base peak alone
+ for(i=lookup[j-1];i<=lookup[j+1];i++){
+ ppm = (p.at(i).basePeak-s.getMZ())/s.getMZ()*1000000;
+ if( fabs(ppm)<ppmTolerance &&
+ s.getRTime() > p.at(i).firstRTime-rtTolerance &&
+ s.getRTime() < p.at(i).lastRTime+rtTolerance ) {
+ x++;
+ index=i;
+ vHit.push_back(i);
+ }
+ }
+
+ //if base peak wasn't enough, perhaps a different peak was isolated
+ if(!bMatchPrecursorOnly){
+ for(i=0;i<p.size();i++){
+ lowMass = (p.at(i).monoMass+p.at(i).charge*1.00727649)/p.at(i).charge-0.05;
+ switch(p.at(i).charge){
+ case 1:
+ highMass = (p.at(i).monoMass+p.at(i).charge*1.00727649)/p.at(i).charge + 3.10;
+ break;
+ case 2:
+ highMass = (p.at(i).monoMass+p.at(i).charge*1.00727649)/p.at(i).charge + 2.10;
+ break;
+ default:
+ highMass = (p.at(i).monoMass+p.at(i).charge*1.00727649)/p.at(i).charge + 4/p.at(i).charge +0.05;
+ break;
+ }
+ if( s.getMZ() > lowMass &&
+ s.getMZ() < highMass &&
+ s.getRTime() > p.at(i).firstRTime-rtTolerance &&
+ s.getRTime() < p.at(i).lastRTime+rtTolerance ) {
+ x++;
+ index=i;
+ vHit.push_back(i);
+ }
+ }
+ }
+
+ vI.push_back(x);
+ s.setFileType(MS2);
+
+ if(x==0) {
+ z++;
+ o2.add(s);
+ if(o2.size()>500){
+ rNeg.appendFile(outFile2,o2);
+ o2.clear();
+ }
+ ch[0]++;
+ } else if(x==1) {
+ a++;
+ while(s.sizeZ()>0) s.eraseZ(0);
+ if(posFF==mgf){
+ s.addZState(p.at(index).charge,(p.at(index).monoMass+1.00727649*p.at(index).charge)/p.at(index).charge);
+ } else {
+ s.addZState(p.at(index).charge,p.at(index).monoMass+1.00727649);
+ s.addEZState(p.at(index).charge,p.at(index).monoMass+1.00727649,p.at(index).rTime,p.at(index).sumIntensity);
+ }
+ o.add(s);
+ if(o.size()>500){
+ rPos.appendFile(outFile,o);
+ o.clear();
+ }
+ c++;
+ } else {
+ while(s.sizeZ()>0) s.eraseZ(0);
+
+ //erase redundancies in multiple hit list
+ for(i=0;i<vHit.size()-1;i++){
+ for(j=i+1;j<vHit.size();j++){
+ if(p.at(vHit[i]).charge == p.at(vHit[j]).charge) {
+ sprintf(str1,"%.2f\n",p.at(vHit[i]).monoMass+1.00727649);
+ sprintf(str2,"%.2f\n",p.at(vHit[j]).monoMass+1.00727649);
+
+ if(strcmp(str1,str2)==0) {
+ if(p.at(vHit[i]).intensity < p.at(vHit[j]).intensity) vHit[i]=vHit[j];
+ vHit.erase(vHit.begin()+j);
+ j--;
+ }
+
+ }
+ }
+ }
+
+ for(i=0;i<vHit.size();i++) {
+ if(posFF==mgf){
+ s.addZState(p.at(vHit[i]).charge,(p.at(vHit[i]).monoMass+1.00727649*p.at(vHit[i]).charge)/p.at(vHit[i]).charge);
+ } else {
+ s.addZState(p.at(vHit[i]).charge,p.at(vHit[i]).monoMass+1.00727649);
+ s.addEZState(p.at(vHit[i]).charge,p.at(vHit[i]).monoMass+1.00727649,p.at(vHit[i]).rTime,p.at(vHit[i]).sumIntensity);
+ }
+ }
+
+ if(vHit.size()==1) {
+ a++;
+ c++;
+ } else {
+ b++;
+ d+=vHit.size();
+ }
+
+ o.add(s);
+ if(o.size()>500){
+ rPos.appendFile(outFile,o);
+ o.clear();
+ }
+
+ }
+ r.readFile(NULL,s);
+
+ for(i=0;i<vHit.size();i++) ch[p.at(vHit[i]).charge]++;
+
+ //Update file position counter
+ if (r.getPercent() > iPercent){
+ if(iPercent<10) cerr << "\b";
+ else if (iPercent<100) cerr << "\b\b";
+ else cerr << "\b\b\b";
+ cerr.flush();
+ iPercent=r.getPercent();
+ cerr << iPercent;
+ cerr.flush();
+ }
+ }
+
+ rPos.appendFile(outFile,o);
+ rNeg.appendFile(outFile2,o2);
+
+ cerr << endl;
+ cout << "Done!" << endl;
+
+ cout << z << " scans had no visible parental distribution." << endl;
+ cout << a << " scans had a single parental distribution." << endl;
+ cout << b << " scans had multiple possible parental distributions." << endl;
+
+ //Some simple tables of where parental ions are found relative to scan number
+ i=0;
+ a=0;
+ x=0;
+ z=0;
+ b=1;
+ cout << "\nScan:\tNeg\tPos" << endl;
+ while(i<vI.size()){
+ if(vI[i]==0) x++;
+ else z++;
+ a++;
+
+ if(a==1000){
+ cout << b*a << "\t" << x << "\t" << z << endl;
+ x=0;
+ z=0;
+ b++;
+ a=0;
+ }
+
+ i++;
+ }
+
+ cout << b*1000+a << "\t" << x << "\t" << z << endl;
+
+ cout << "\nUnknown charge: " << ch[0] << endl;
+ for(i=1;i<10;i++) cout << "+" << i << ": " << ch[i] << endl;
+
+ cout << c << " singles and " << d << " doubles total." << endl;
+
+}
+
+MSFileFormat getFileFormat(char* c){
+
+ char file[256];
+ char ext[256];
+ char *tok;
+
+ strcpy(file,c);
+ tok=strtok(file,".\n");
+ while(tok!=NULL){
+ strcpy(ext,tok);
+ tok=strtok(NULL,".\n");
+ }
+
+ if(strcmp(ext,"ms1")==0 || strcmp(ext,"MS1")==0) return ms1;
+ if(strcmp(ext,"ms2")==0 || strcmp(ext,"MS2")==0) return ms2;
+ if(strcmp(ext,"bms1")==0 || strcmp(ext,"BMS1")==0) return bms1;
+ if(strcmp(ext,"bms2")==0 || strcmp(ext,"BMS2")==0) return bms2;
+ if(strcmp(ext,"cms1")==0 || strcmp(ext,"CMS1")==0) return cms1;
+ if(strcmp(ext,"cms2")==0 || strcmp(ext,"CMS2")==0) return cms2;
+ if(strcmp(ext,"zs")==0 || strcmp(ext,"ZS")==0) return zs;
+ if(strcmp(ext,"uzs")==0 || strcmp(ext,"UZS")==0) return uzs;
+ if(strcmp(ext,"mgf")==0 || strcmp(ext,"MGF")==0) return mgf;
+ if(strcmp(ext,"mzXML")==0 || strcmp(ext,"MZXML")==0) return mzXML;
+ if(strcmp(ext,"mzML")==0 || strcmp(ext,"MZML")==0) return mzML;
+ if(strcmp(ext,"raw")==0 || strcmp(ext,"RAW")==0) return raw;
+ return dunno;
+
+}
+
+void usage(){
+ cout << "Usage: bullseye [flags] <HK file> <Data file> <Pos file> <Neg file>" << endl;
+ cout << "\n HK files are Hardklor generated results files." << endl;
+ cout << " http://proteome.gs.washington.edu/software/hardklor" << endl;
+ cout << "\n Data files contain the MS/MS data to be used." << endl;
+ cout << " Acceptable formats:" << endl;
+ cout << " Thermo RAW (Windows only), .mzXML" << endl;
+ cout << " .ms2, .bms2, .cms2 (Extracted with MakeMS2)" << endl;
+ cout << " http://proteome.gs.washington.edu/software/makems2/MakeMS2.zip" << endl;
+ cout << "\n Pos and Neg files are output files for matches and non-matches, respectively." << endl;
+ cout << " Acceptable formats (specify with file extension):" << endl;
+ cout << " .ms2, .bms2, .cms2, .mgf" << endl;
+ cout << "\nExample: bullseye -p 5 Peptides.hk RawData.RAW Matches.ms2 NoMatch.ms2" << endl;
+ cout << "\nFlags:" << endl;
+ cout << " -c <num> Ignore peptides that persist for this length in time.\n"
+ << " These peptides are considered contaminants.\n"
+ << " The unit of time is whatever unit is used in your data file.\n"
+ << " Default value: 2\n" << endl;
+ cout << " -e Use exact match to precursor ion. Rather than use wide\n"
+ << " precursor boundaries, this flag forces Bullseye to match\n"
+ << " precursors to the base isotope peak identified in Hardklor.\n"
+ << " The tolerance is set with the -p flag.\n" << endl;
+ cout << " -g <num> Gap size tolerance when checking for peptides across consecutive\n"
+ << " scans.\n"
+ << " Default value: 1\n" << endl;
+ cout << " -m <num> Only consider peptides below this maximum mass in daltons.\n"
+ << " Default value: 8000\n" << endl;
+ cout << " -n <num> Only consider peptides above this minimum mass in daltons.\n"
+ << " Default value: 600\n" << endl;
+ cout << " -p <num> Sets the tolerance (+/- ppm) for exact match searches.\n"
+ << " Default value: 10\n" << endl;
+ cout << " -r <num> Sets the tolerance (+/- ppm) for finding persistent peptides.\n"
+ << " Default value: 5\n" << endl;
+ cout << " -s <num> Number of consecutive scans over which a peptide must be\n"
+ << " observed to be considered real. Gaps in persistence are allowed\n"
+ << " when setting the -g flag.\n"
+ << " Default value: 3\n" << endl;
+ cout << " -t <num> Sets the tolerance (+/- minutes) around the retention\n"
+ << " time over which a peptide can be matched to the MS/MS\n"
+ << " spectrum.\n"
+ << " Default value: 0.5\n" << endl;
+ cout << "\nPlease read the README.txt file for more information on Bullseye." << endl;
+
+}
diff --git a/src/app/bullseye/cmake_install.cmake b/src/app/bullseye/cmake_install.cmake
new file mode 100644
index 0000000..e0c4901
--- /dev/null
+++ b/src/app/bullseye/cmake_install.cmake
@@ -0,0 +1,34 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/bullseye
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
diff --git a/src/app/bullseye/libbullseye.a b/src/app/bullseye/libbullseye.a
new file mode 100644
index 0000000..5fc8940
Binary files /dev/null and b/src/app/bullseye/libbullseye.a differ
diff --git a/src/app/hardklor/CAveragine.cpp b/src/app/hardklor/CAveragine.cpp
new file mode 100644
index 0000000..7132d34
--- /dev/null
+++ b/src/app/hardklor/CAveragine.cpp
@@ -0,0 +1,306 @@
+#include <iomanip>
+#include <iostream>
+#include "CAveragine.h"
+using namespace std;
+
+CAveragine::CAveragine(char* fn, char* fn2){
+ PT = new CPeriodicTable(fn2);
+ atoms = new int[PT->size()];
+ for(int i=0;i<PT->size();i++) atoms[i]=0;
+ enrich = new vector<atomInfo>;
+ loadTable(fn);
+}
+
+CAveragine::~CAveragine(){
+ delete [] atoms;
+ delete enrich;
+}
+
+void CAveragine::calcAveragine(double dMass, CHardklorVariant hv) {
+ int i,j;
+ int iso;
+ int atom;
+ double fixedD = dMass;
+ double units;
+ double *enr;
+ double *abun;
+ double maxAbun;
+ double totAbun;
+ enr = new double[PT->size()];
+ for(i=0;i<PT->size();i++) enr[i]=0;
+
+ for(i=0;i<hv.sizeEnrich();i++){
+
+ atom = hv.atEnrich(i).atomNum;
+ iso = enrich->at(atom).numIsotopes;
+ abun = new double[iso];
+
+ //Set our abundance array and find maximum
+ maxAbun=0;
+ for(j=0;j<iso;j++){
+ abun[j]=enrich->at(atom).abundance->at(j);
+ if(abun[j]>maxAbun) maxAbun=abun[j];
+ }
+
+ //Normalize to 1
+ for(j=0;j<iso;j++) abun[j]/=maxAbun;
+
+ //Normalize, then Calculate enrichment
+ totAbun=0;
+ enr[atom]=0;
+ for(j=0;j<iso;j++){
+ abun[j]/=maxAbun;
+ if(j==hv.atEnrich(i).isotope) abun[j]=(1-hv.atEnrich(i).ape)*abun[j]+hv.atEnrich(i).ape;
+ else abun[j]=(1-hv.atEnrich(i).ape)*abun[j];
+ totAbun+=abun[j];
+ enr[atom]+=abun[j]*enrich->at(atom).mass->at(j);
+ }
+
+ //Calculate average mass
+ enr[atom] /= totAbun;
+ enr[atom] -= PT->at(atom).mass;
+
+ delete [] abun;
+ }
+
+ for(i=0;i<hv.sizeAtom();i++) {
+
+ atoms[hv.atAtom(i).iLower]+=hv.atAtom(i).iUpper;
+ fixedD -= hv.atAtom(i).iUpper*(PT->at(hv.atAtom(i).iLower).mass + enr[hv.atAtom(i).iLower]);
+ }
+
+ units = (fixedD)/(AVE_MASS + enr[1]*AVE_H + enr[6]*AVE_C + enr[7]*AVE_N + enr[8]*AVE_O + enr[16]*AVE_S);
+
+ //Quick fix; assumes complete periodic table
+ atoms[6] += (int)(AVE_C*units+0.5);
+ atoms[8] += (int)(AVE_O*units+0.5);
+ atoms[7] += (int)(AVE_N*units+0.5);
+ atoms[16] += (int)(AVE_S*units+0.5);
+
+ atoms[1] += (int)(fixedD-( ((int)(AVE_C*units+0.5)) * (PT->at(6).mass + enr[6]) +
+ ((int)(AVE_N*units+0.5)) * (PT->at(7).mass + enr[7]) +
+ ((int)(AVE_O*units+0.5)) * (PT->at(8).mass + enr[8]) +
+ ((int)(AVE_S*units+0.5)) * (PT->at(16).mass + enr[16]) )+0.5);
+
+ delete [] enr;
+
+}
+
+void CAveragine::defaultValues(){
+
+ string el[109] = {"X","H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar",
+ "K","Ca","Sc","Ti","V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr","Rb","Sr","Y","Zr",
+ "Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te","I","Xe","Cs","Ba","La","Ce","Pr","Nd","Pm","Sm",
+ "Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu","Hf","Ta","W","Re","Os","Ir","Pt","Au","Hg","Tl","Pb","Bi","Po",
+ "At","Rn","Fr","Ra","Ac","Th","Pa","U","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr","Hx","Cx","Nx",
+ "Ox","Sx"};
+ int sz[109] = {2,2,2,2,1,2,2,2,3,1,3,1,3,1,3,1,4,2,3,3,6,1,5,2,4,1,4,1,5,2,5,2,5,1,6,2,6,2,4,1,5,1,7,1,7,
+ 1,6,2,8,2,10,2,8,1,9,1,7,2,4,1,7,1,7,2,7,1,7,1,6,1,7,2,6,2,5,2,7,2,6,1,7,2,4,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,
+ 1,1,1,1,1,2,2,2,3,4};
+ double m[322] = {1.000000000000,2.000000000000,1.007824600000,2.014102100000,3.016030000000,4.002600000000,
+ 6.015121000000,7.016003000000,9.012182000000,10.012937000000,11.009305000000,12.000000000000,13.003355400000,
+ 14.003073200000,15.000108800000,15.994914100000,16.999132200000,17.999161600000,18.998403200000,
+ 19.992435000000,20.993843000000,21.991383000000,22.989767000000,23.985042000000,24.985837000000,
+ 25.982593000000,26.981539000000,27.976927000000,28.976495000000,29.973770000000,30.973762000000,
+ 31.972070000000,32.971456000000,33.967866000000,35.967080000000,34.968853100000,36.965903400000,
+ 35.967545000000,37.962732000000,39.962384000000,38.963707000000,39.963999000000,40.961825000000,
+ 39.962591000000,41.958618000000,42.958766000000,43.955480000000,45.953689000000,47.952533000000,
+ 44.955910000000,45.952629000000,46.951764000000,47.947947000000,48.947871000000,49.944792000000,
+ 49.947161000000,50.943962000000,49.946046000000,51.940509000000,52.940651000000,53.938882000000,
+ 54.938047000000,53.939612000000,55.934939000000,56.935396000000,57.933277000000,58.933198000000,
+ 57.935346000000,59.930788000000,60.931058000000,61.928346000000,63.927968000000,62.939598000000,
+ 64.927793000000,63.929145000000,65.926034000000,66.927129000000,67.924846000000,69.925325000000,
+ 68.925580000000,70.924700000000,69.924250000000,71.922079000000,72.923463000000,73.921177000000,
+ 75.921401000000,74.921594000000,73.922475000000,75.919212000000,76.919912000000,77.919000000000,
+ 79.916520000000,81.916698000000,78.918336000000,80.916289000000,77.914000000000,79.916380000000,
+ 81.913482000000,82.914135000000,83.911507000000,85.910616000000,84.911794000000,86.909187000000,
+ 83.913430000000,85.909267000000,86.908884000000,87.905619000000,88.905849000000,89.904703000000,
+ 90.905644000000,91.905039000000,93.906314000000,95.908275000000,92.906377000000,91.906808000000,
+ 93.905085000000,94.905840000000,95.904678000000,96.906020000000,97.905406000000,99.907477000000,
+ 98.000000000000,95.907599000000,97.905287000000,98.905939000000,99.904219000000,100.905582000000,
+ 101.904348000000,103.905424000000,102.905500000000,101.905634000000,103.904029000000,104.905079000000,
+ 105.903478000000,107.903895000000,109.905167000000,106.905092000000,108.904757000000,105.906461000000,
+ 107.904176000000,109.903005000000,110.904182000000,111.902758000000,112.904400000000,113.903357000000,
+ 115.904754000000,112.904061000000,114.903880000000,111.904826000000,113.902784000000,114.903348000000,
+ 115.901747000000,116.902956000000,117.901609000000,118.903310000000,119.902200000000,121.903440000000,
+ 123.905274000000,120.903821000000,122.904216000000,119.904048000000,121.903054000000,122.904271000000,
+ 123.902823000000,124.904433000000,125.903314000000,127.904463000000,129.906229000000,126.904473000000,
+ 123.905894000000,125.904281000000,127.903531000000,128.904780000000,129.903509000000,130.905072000000,
+ 131.904144000000,133.905395000000,135.907214000000,132.905429000000,129.906282000000,131.905042000000,
+ 133.904486000000,134.905665000000,135.904553000000,136.905812000000,137.905232000000,137.907110000000,
+ 138.906347000000,135.907140000000,137.905985000000,139.905433000000,141.909241000000,140.907647000000,
+ 141.907719000000,142.909810000000,143.910083000000,144.912570000000,145.913113000000,147.916889000000,
+ 149.920887000000,145.000000000000,143.911998000000,146.914895000000,147.914820000000,148.917181000000,
+ 149.917273000000,151.919729000000,153.922206000000,150.919847000000,152.921225000000,151.919786000000,
+ 153.920861000000,154.922618000000,155.922118000000,156.923956000000,157.924099000000,159.927049000000,
+ 158.925342000000,155.925277000000,157.924403000000,159.925193000000,160.926930000000,161.926795000000,
+ 162.928728000000,163.929171000000,164.930319000000,161.928775000000,163.929198000000,165.930290000000,
+ 166.932046000000,167.932368000000,169.935461000000,168.934212000000,167.933894000000,169.934759000000,
+ 170.936323000000,171.936378000000,172.938208000000,173.938859000000,175.942564000000,174.940770000000,
+ 175.942679000000,173.940044000000,175.941406000000,176.943217000000,177.943696000000,178.945812000000,
+ 179.946545000000,179.947462000000,180.947992000000,179.946701000000,181.948202000000,182.950220000000,
+ 183.950928000000,185.954357000000,184.952951000000,186.955744000000,183.952488000000,185.953830000000,
+ 186.955741000000,187.955860000000,188.958137000000,189.958436000000,191.961467000000,190.960584000000,
+ 192.962917000000,189.959917000000,191.961019000000,193.962655000000,194.964766000000,195.964926000000,
+ 197.967869000000,196.966543000000,195.965807000000,197.966743000000,198.968254000000,199.968300000000,
+ 200.970277000000,201.970617000000,203.973467000000,202.972320000000,204.974401000000,203.973020000000,
+ 205.974440000000,206.975872000000,207.976627000000,208.980374000000,209.000000000000,210.000000000000,
+ 222.000000000000,223.000000000000,226.025000000000,227.028000000000,232.038054000000,231.035900000000,
+ 234.040946000000,235.043924000000,238.050784000000,237.048000000000,244.000000000000,243.000000000000,
+ 247.000000000000,247.000000000000,251.000000000000,252.000000000000,257.000000000000,258.000000000000,
+ 259.000000000000,260.000000000000,1.007824600000,2.014102100000,12.000000000000,13.003355400000,
+ 14.003073200000,15.000108800000,15.994914100000,16.999132200000,17.999161600000,31.972070000000,
+ 32.971456000000,33.967866000000,35.967080000000};
+ double r[322] = {0.900000000000,0.100000000000,0.999855000000,0.000145000000,0.000001380000,0.999998620000,
+ 0.075000000000,0.925000000000,1.000000000000,0.199000000000,0.801000000000,0.989160000000,0.010840000000,
+ 0.996330000000,0.003660000000,0.997576009706,0.000378998479,0.002044991815,1.000000000000,0.904800000000,
+ 0.002700000000,0.092500000000,1.000000000000,0.789900000000,0.100000000000,0.110100000000,1.000000000000,
+ 0.922300000000,0.046700000000,0.031000000000,1.000000000000,0.950210000000,0.007450000000,0.042210000000,
+ 0.000130000000,0.755290000000,0.244710000000,0.003370000000,0.000630000000,0.996000000000,0.932581000000,
+ 0.000117000000,0.067302000000,0.969410000000,0.006470000000,0.001350000000,0.020860000000,0.000040000000,
+ 0.001870000000,1.000000000000,0.080000000000,0.073000000000,0.738000000000,0.055000000000,0.054000000000,
+ 0.002500000000,0.997500000000,0.043450000000,0.837900000000,0.095000000000,0.023650000000,1.000000000000,
+ 0.059000000000,0.917200000000,0.021000000000,0.002800000000,1.000000000000,0.682700000000,0.261000000000,
+ 0.011300000000,0.035900000000,0.009100000000,0.691700000000,0.308300000000,0.486000000000,0.279000000000,
+ 0.041000000000,0.188000000000,0.006000000000,0.601080000000,0.398920000000,0.205000000000,0.274000000000,
+ 0.078000000000,0.365000000000,0.078000000000,1.000000000000,0.009000000000,0.091000000000,0.076000000000,
+ 0.236000000000,0.499000000000,0.089000000000,0.506900000000,0.493100000000,0.003500000000,0.022500000000,
+ 0.116000000000,0.115000000000,0.570000000000,0.173000000000,0.721700000000,0.278300000000,0.005600000000,
+ 0.098600000000,0.070000000000,0.825800000000,1.000000000000,0.514500000000,0.112200000000,0.171500000000,
+ 0.173800000000,0.028000000000,1.000000000000,0.148400000000,0.092500000000,0.159200000000,0.166800000000,
+ 0.095500000000,0.241300000000,0.096300000000,1.000000000000,0.055400000000,0.018600000000,0.127000000000,
+ 0.126000000000,0.171000000000,0.316000000000,0.186000000000,1.000000000000,0.010200000000,0.111400000000,
+ 0.223300000000,0.273300000000,0.264600000000,0.117200000000,0.518390000000,0.481610000000,0.012500000000,
+ 0.008900000000,0.124900000000,0.128000000000,0.241300000000,0.122200000000,0.287300000000,0.074900000000,
+ 0.043000000000,0.957000000000,0.009700000000,0.006500000000,0.003600000000,0.145300000000,0.076800000000,
+ 0.242200000000,0.085800000000,0.325900000000,0.046300000000,0.057900000000,0.574000000000,0.426000000000,
+ 0.000950000000,0.025900000000,0.009050000000,0.047900000000,0.071200000000,0.189300000000,0.317000000000,
+ 0.338700000000,1.000000000000,0.001000000000,0.000900000000,0.019100000000,0.264000000000,0.041000000000,
+ 0.212000000000,0.269000000000,0.104000000000,0.089000000000,1.000000000000,0.001060000000,0.001010000000,
+ 0.024200000000,0.065930000000,0.078500000000,0.112300000000,0.717000000000,0.000900000000,0.999100000000,
+ 0.001900000000,0.002500000000,0.884300000000,0.111300000000,1.000000000000,0.271300000000,0.121800000000,
+ 0.238000000000,0.083000000000,0.171900000000,0.057600000000,0.056400000000,1.000000000000,0.031000000000,
+ 0.150000000000,0.113000000000,0.138000000000,0.074000000000,0.267000000000,0.227000000000,0.478000000000,
+ 0.522000000000,0.002000000000,0.021800000000,0.148000000000,0.204700000000,0.156500000000,0.248400000000,
+ 0.218600000000,1.000000000000,0.000600000000,0.001000000000,0.023400000000,0.189000000000,0.255000000000,
+ 0.249000000000,0.282000000000,1.000000000000,0.001400000000,0.016100000000,0.336000000000,0.229500000000,
+ 0.268000000000,0.149000000000,1.000000000000,0.001300000000,0.030500000000,0.143000000000,0.219000000000,
+ 0.161200000000,0.318000000000,0.127000000000,0.974100000000,0.025900000000,0.001620000000,0.052060000000,
+ 0.186060000000,0.272970000000,0.136290000000,0.351000000000,0.000120000000,0.999880000000,0.001200000000,
+ 0.263000000000,0.142800000000,0.307000000000,0.286000000000,0.374000000000,0.626000000000,0.000200000000,
+ 0.015800000000,0.016000000000,0.133000000000,0.161000000000,0.264000000000,0.410000000000,0.373000000000,
+ 0.627000000000,0.000100000000,0.007900000000,0.329000000000,0.338000000000,0.253000000000,0.072000000000,
+ 1.000000000000,0.001500000000,0.100000000000,0.169000000000,0.231000000000,0.132000000000,0.298000000000,
+ 0.068500000000,0.295240000000,0.704760000000,0.014000000000,0.241000000000,0.221000000000,0.524000000000,
+ 1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,0.000055000000,0.007200000000,0.992745000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,0.999855000000,0.000145000000,0.989160000000,0.010840000000,0.996330000000,
+ 0.003660000000,0.997576009706,0.000378998479,0.002044991815,0.950210000000,0.007450000000,0.042210000000,
+ 0.000130000000};
+
+ int i=0;
+ int j=0;
+ int k;
+ atomInfo a;
+
+ for(k=0;k<109;k++){
+ strcpy(a.symbol,&el[k][0]);
+ a.numIsotopes=sz[k];
+ a.mass->clear();
+ a.abundance->clear();
+ for(j=0;j<a.numIsotopes;j++){
+ a.mass->push_back(m[i]);
+ a.abundance->push_back(r[i]);
+ i++;
+ }
+ enrich->push_back(a);
+ }
+
+}
+
+void CAveragine::clear(){
+ delete [] atoms;
+ atoms = new int[PT->size()];
+ for(int i=0;i<PT->size();i++) atoms[i]=0;
+}
+
+int CAveragine::getElement(int i){
+ return atoms[i];
+}
+
+void CAveragine::getAveragine(char *str){
+ char tstr[10];
+ int i;
+ str[0]=0;
+
+ //Create formula string
+ for(i=0;i<PT->size();i++){
+ if(atoms[i]>0){
+ sprintf(tstr,"%s%i",PT->at(i).symbol,atoms[i]);
+ strcat(str,tstr);
+ }
+ }
+
+}
+
+double CAveragine::getMonoMass(){
+ double d=0;
+ int i;
+
+ for(i=0;i<PT->size();i++) d+=atoms[i]*PT->at(i).mass;
+ return d;
+
+}
+
+CPeriodicTable* CAveragine::getPT(){
+ return PT;
+}
+
+void CAveragine::loadTable(char* c){
+
+ FILE *f;
+ int j;
+ atomInfo a;
+ double d1,d2;
+
+ if(c==NULL || strlen(c)==0){
+ defaultValues();
+ return;
+ }
+
+ f = fopen(c,"rt");
+ if(f==NULL) {
+ cout << "Cannot read " << c << endl;
+ exit(-1);
+ }
+
+ while(!feof(f)){
+
+ fscanf(f,"%2s\t%d\n",&a.symbol,&a.numIsotopes);
+ a.mass->clear();
+ a.abundance->clear();
+
+ for(j=0;j<a.numIsotopes;j++){
+ fscanf(f,"%lf\t%lf\n",&d1,&d2);
+ a.mass->push_back(d1);
+ a.abundance->push_back(d2);
+ }
+
+ enrich->push_back(a);
+ fscanf(f," \n");
+
+ }
+
+ fclose(f);
+
+}
+
+//This is not to be used normally - just here to make my life easier.
+void CAveragine::setAveragine(int C, int H, int N, int O, int S){
+ atoms[1]=H;
+ atoms[6]=C;
+ atoms[7]=N;
+ atoms[8]=O;
+ atoms[16]=S;
+}
diff --git a/src/app/hardklor/CAveragine.h b/src/app/hardklor/CAveragine.h
new file mode 100644
index 0000000..3f90b78
--- /dev/null
+++ b/src/app/hardklor/CAveragine.h
@@ -0,0 +1,101 @@
+#ifndef _CAVERAGINE_H
+#define _CAVERAGINE_H
+
+#include "CHardklorVariant.h"
+#include "CPeriodicTable.h"
+
+#include <cstdlib>
+#include <fstream>
+#include <vector>
+#include <cstring>
+
+using namespace std;
+
+/*
+const double AVE_MASS = 111.1254;
+const double AVE_C = 4.9384;
+const double AVE_H = 7.7583;
+const double AVE_N = 1.3577;
+const double AVE_O = 1.4773;
+const double AVE_S = 0.0417;
+*/
+
+const double AVE_MASS = 111.2137;
+const double AVE_C = 4.9558;
+const double AVE_H = 7.8241;
+const double AVE_N = 1.3571;
+const double AVE_O = 1.4716;
+const double AVE_S = 0.0390;
+
+typedef struct atomInfo {
+ char symbol[3];
+ int numIsotopes;
+ vector<double> *mass;
+ vector<double> *abundance;
+ atomInfo(){
+ strcpy(symbol,"X");
+ numIsotopes=0;
+ mass = new vector<double>;
+ abundance = new vector<double>;
+ }
+ atomInfo(const atomInfo& a){
+ strcpy(symbol,a.symbol);
+ numIsotopes=a.numIsotopes;
+ mass = new vector<double>;
+ abundance = new vector<double>;
+ unsigned int i;
+ for(i=0;i<a.mass->size();i++) mass->push_back(a.mass->at(i));
+ for(i=0;i<a.abundance->size();i++) abundance->push_back(a.abundance->at(i));
+ }
+ ~atomInfo(){
+ delete mass;
+ delete abundance;
+ }
+ atomInfo& operator=(const atomInfo& a){
+ if(&a!=this){
+ strcpy(symbol,a.symbol);
+ numIsotopes=a.numIsotopes;
+ delete mass;
+ delete abundance;
+ mass = new vector<double>;
+ abundance = new vector<double>;
+ unsigned int i;
+ for(i=0;i<a.mass->size();i++) mass->push_back(a.mass->at(i));
+ for(i=0;i<a.abundance->size();i++) abundance->push_back(a.abundance->at(i));
+ }
+ return *this;
+ }
+
+} atomInfo;
+
+class CAveragine {
+
+ public:
+ //Constructors & Destructors
+ //CAveragine();
+ CAveragine(char* fn="ISOTOPE.DAT", char* fn2="Hardklor.dat");
+ ~CAveragine();
+
+ //Methods:
+ void calcAveragine(double,CHardklorVariant);
+ void clear();
+ void defaultValues();
+ void getAveragine(char*);
+ void setAveragine(int,int,int,int,int);
+ int getElement(int);
+ double getMonoMass();
+ CPeriodicTable* getPT();
+ void loadTable(char*);
+
+ protected:
+
+ private:
+ //Data Members:
+ //double monoMass;
+ int *atoms;
+ CPeriodicTable *PT;
+ vector<atomInfo> *enrich;
+
+};
+
+#endif
diff --git a/src/app/hardklor/CHardklor.cpp b/src/app/hardklor/CHardklor.cpp
new file mode 100644
index 0000000..8da5d21
--- /dev/null
+++ b/src/app/hardklor/CHardklor.cpp
@@ -0,0 +1,2280 @@
+
+/*
+ Hardkl�r - Thanks to Aaron Klammer (Klezmer) and
+ Greg Finney for the name suggestions.
+
+ This program scans through high resolution mass spectra,
+ predicts the monoisotopic mass and charge state of any potential
+ peptides (or proteins), generates predicted isotope distributions
+ of averagine and modified averagine molecules matching the mass
+ of each distribution, then correlates the various combinations of each
+ distribution with the spectrum data to find a best match.
+
+ This application was first designed to identify chlorinated peptides,
+ hence the name Hardkl�r. Due to the distinguishing characteristics of
+ a chlorinated distribution, this application makes it possible to predict
+ if the observed distribution is in fact chlorinated. The application
+ has since been extended to differentiate any measurable atomic or
+ enrichment modification.
+
+ The application utilizes an object model, so components may
+ be used in other applications. Furthermore, the design was made
+ to be extended, or possibly embedded in other software.
+
+ Version 1.0 is the first public release.
+*/
+
+#include "CHardklor.h"
+#include "CAveragine.h"
+#include "CMercury8.h"
+#include "CSpecAnalyze.h"
+#include "Smooth.h"
+#include <iomanip>
+using namespace std;
+
+
+SSObject::SSObject(){
+ pepVar = new vector<sInt>;
+ corr=0;
+}
+
+SSObject::SSObject(const SSObject& c){
+ corr = c.corr;
+ pepVar = new vector<sInt>;
+ for(unsigned int i=0;i<c.pepVar->size();i++) pepVar->push_back(c.pepVar->at(i));
+}
+
+SSObject::~SSObject(){
+ delete pepVar;
+}
+
+SSObject& SSObject::operator=(const SSObject& c){
+ if (this != &c) {
+ corr = c.corr;
+ delete pepVar;
+ pepVar = new vector<sInt>;
+ for(unsigned int i=0;i<c.pepVar->size();i++) pepVar->push_back(c.pepVar->at(i));
+ }
+ return *this;
+}
+
+void SSObject::addVar(int a, int b){
+ sInt s;
+ s.iLower = a;
+ s.iUpper = b;
+ pepVar->push_back(s);
+}
+
+void SSObject::clear(){
+ delete pepVar;
+ pepVar = new vector<sInt>;
+ corr = 0;
+}
+
+CHardklor::CHardklor(){
+ averagine=NULL;
+ mercury=NULL;
+ bEcho=true;
+ bMem=false;
+}
+
+CHardklor::CHardklor(CAveragine *a, CMercury8 *m){
+ averagine=a;
+ mercury=m;
+ sa.setAveragine(averagine);
+ sa.setMercury(mercury);
+ bEcho=true;
+ bMem=false;
+}
+
+CHardklor::~CHardklor(){
+ averagine=NULL;
+ mercury=NULL;
+}
+
+void CHardklor::Echo(bool b){
+ bEcho=b;
+}
+
+void CHardklor::SetAveragine(CAveragine *a){
+ averagine=a;
+ sa.setAveragine(averagine);
+}
+
+void CHardklor::SetMercury(CMercury8 *m){
+ mercury=m;
+ sa.setMercury(mercury);
+}
+
+int CHardklor::GoHardklor(CHardklorSetting sett, Spectrum* s){
+ cs = sett;
+ Analyze(s);
+ return 0;
+}
+
+//sorts vector of Results from high to low
+int CHardklor::compareData(const void *p1, const void *p2){
+ const Result d1 = *(Result *)p1;
+ const Result d2 = *(Result *)p2;
+ if(d1.data<d2.data) return 1;
+ else if(d1.data>d2.data) return -1;
+ else return 0;
+}
+
+void CHardklor::Analyze(Spectrum* s) {
+
+ //Objects
+ MSReader r;
+ CNoiseReduction nr(&r,cs);
+ PT=averagine->getPT();
+
+ //iterators
+ unsigned int k; //counters for loops
+
+ int TotalIterations=0;
+ int TotalScans=0;
+ int i;
+
+ //Variables for file and clock management
+ int minutes, seconds;
+ loadTime=0;
+ analysisTime=0;
+ splitTime=0;
+
+ //placeholders for data output to file
+ //int pepID;
+ //int varID;
+
+ //Variables for some basic information output.
+ int iPercent;
+ int zeroPep=0; //Stores the number of spectra from which no potential peptides could be identified
+ int manyPep=0; //Stores the number of spectra from which the number of potential peptides
+ //exceeds the user-defined threshold.
+ int lowSigPep=0; //Stores the number of spectra whose max intensity was below the user defined threshold.
+
+
+ //Build variants (modifications) used in the analysis
+ pepVariants.clear();
+ if(!cs.noBase) {
+ CHardklorVariant hkv;
+ pepVariants.push_back(hkv);
+ }
+ for(k=0;k<cs.variant->size();k++) pepVariants.push_back(cs.variant->at(k));
+
+ //Our temporary spectrum
+ Spectrum curSpec;
+ Spectrum cutSpec;
+
+ //These are for splitting large spectra
+ bool bCutMe=false;
+ bool ReadScan=false;
+ bool bFirst=true;
+ CSplitSpectrum* cSS;
+ int winCount=0;
+
+ vResults.clear();
+
+ //Ouput file info to user
+ if(bEcho){
+ if(s==NULL) cout << "Reading from file: " << cs.inFile << endl;
+ if(!bMem) cout << "Writing to file: " << cs.outFile << endl;
+ }
+
+ if(cs.fileFormat==dunno) {
+ cout << "Unknown file format or bad extension." << endl;
+ return;
+ }
+
+ //Start of algorithm here.
+ getTimerFrequency(timerFrequency);
+ getExactTime(startTime);
+
+ //Read in the initial spectrum
+ r.setFilter(cs.mzXMLFilter);
+ r.setRawFilter(cs.rawFilter);
+ if(s!=NULL){
+ curSpec=*s;
+ } else {
+ if(cs.boxcar==0){
+ if((cs.scan.iLower>0) && (cs.scan.iLower==cs.scan.iUpper)) r.readFile(&cs.inFile[0],curSpec,cs.scan.iLower);
+ else if(cs.scan.iLower>0) r.readFile(&cs.inFile[0],curSpec,cs.scan.iLower);
+ else r.readFile(&cs.inFile[0],curSpec);
+
+ //this is the command to filter by persistence without boxcar averaging
+ // if(!nr.DeNoise(curSpec)) curSpec.setScanNumber(0);
+
+ } else {
+ if(cs.boxcarFilter>0){
+ if(!nr.DeNoiseC(curSpec)) curSpec.setScanNumber(0);
+ } else {
+ if(!nr.DeNoiseD(curSpec)) curSpec.setScanNumber(0);
+ }
+ }
+ }
+
+ TotalScans++;
+
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ loadTime=tmpTime1-tmpTime2;
+
+ //Check that file was read
+ if(curSpec.getScanNumber()==0) {
+ if(s!=NULL) {
+ cout << "Spectrum is invalid." << endl;
+ return;
+ }
+ if(cs.scan.iLower>0) cout << cs.inFile << " is invalid, or requested scan number is of incorrect format." << endl;
+ else cout << cs.inFile << " is invalid, or contains no spectrum." << endl;
+ return;
+ }
+ currentScanNumber = curSpec.getScanNumber();
+
+ //Open a file for output. Results will be written on the fly as they come out of the algorithm.
+ if(!bMem){
+ fptr.open(&cs.outFile[0],ios::out|ios::app);
+ if(!fptr.good()) cout << "Output file error" << endl;
+ fptr << setiosflags(ios::fixed) << setprecision(4);
+ }
+
+ if(!bMem && cs.xml){
+ fptr << "<Hardklor>" << endl;
+ fptr << "<File InputFilename=\"" << cs.inFile << "\" OutputFilename=\"" << cs.outFile << "\">" << endl;
+ WriteParams(fptr,1);
+ }
+
+ //Reset some basic stat counters
+ manyPep=0;
+ zeroPep=0;
+ lowSigPep=0;
+
+ //Set and display on screen percentage counter
+ iPercent=0;
+ if(bEcho) cout << iPercent;
+
+ //While there is still data to read in the file.
+ while(true){
+
+ //Load next spectrum to analyze
+ if(!bFirst){
+
+ //close out xml tag for previous spectrum
+ if(!bMem && cs.xml) fptr << "</Spectrum>" << endl;
+
+ if(s!=NULL) break;
+
+ //track load time
+ getExactTime(startTime);
+ if(cs.boxcar==0){
+ r.readFile(NULL,curSpec);
+ //case 1: nr.DeNoise(curSpec); break;
+ } else {
+ if(cs.boxcarFilter>0) nr.DeNoiseC(curSpec);
+ else nr.DeNoiseD(curSpec);
+ }
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ loadTime+=tmpTime1-tmpTime2;
+
+ } else {
+
+ bFirst=false; //mark that the first scan has been processed
+
+ }
+
+ //Write scan information to output file.
+ if(curSpec.getScanNumber()!=0){
+ if(!bMem){
+ if(cs.scan.iUpper>0 && curSpec.getScanNumber()>cs.scan.iUpper) break;
+ if(cs.reducedOutput) WriteScanLine(curSpec,fptr,2);
+ else if(cs.xml) WriteScanLine(curSpec,fptr,1);
+ else WriteScanLine(curSpec,fptr,0);
+ } else {
+ currentScanNumber = curSpec.getScanNumber();
+ }
+ } else {
+ break; //exit if there is no spectrum left to analyze
+ }
+ TotalScans++;
+
+ //Preprocess spectrum
+ //If we have an empty spectrum, go on to the next one
+ if(curSpec.size()==0) continue;
+
+ getExactTime(startTime);
+ if(cs.smooth>0) SG_Smooth(curSpec,cs.smooth,4);
+ //if(curSpec.getScanNumber()==1999){
+ // for(int xx=0;xx<curSpec.size();xx++) cout << curSpec[xx].mz << "\t" << curSpec[xx].intensity << endl;
+ //}
+
+ //Check our spectrum for file type. Zoom and UltraZoom scans do not
+ //need splitting.
+ if(cs.fileFormat==zs || cs.fileFormat==uzs){
+
+ sa.clear();
+ sa.setParams(cs);
+ sa.setSpectrum(curSpec);
+ sa.FindPeaks();
+ sa.PredictPeptides();
+
+ //do not analyze spectrum with 0 predicted peaks; Keep count of these occurrances.
+ if(sa.predPeak->size()==0){
+ zeroPep++;
+ continue;
+ }
+
+ AnalyzePeaks(sa);
+
+ } else {
+
+ //Reinitialize our split spectrum
+ cSS=new CSplitSpectrum(&curSpec,cs);
+ cSS->SetAveragine(averagine);
+ cSS->SetMercury(mercury);
+
+ //Check if data already centroided
+ if(cs.centroid) {
+ if(cs.chargeMode=='F' || cs.chargeMode=='P' || cs.chargeMode=='S'){
+ cout << "-cdm settings of F, P, and S (FFT, Patterson, Senko) only work on profile data." << endl;
+ cout << "Please choose settings of Q or C (QuickCharge, Complete)" << endl;
+ exit(5);
+ }
+ //This function directly copies the already centroided spectra to the CSS object
+ cSS->Centroid(curSpec);
+
+ //if not, process the data here (ultimately includes centroiding)
+ } else {
+ if(cs.boxcarFilter>0){ //TODO: Figure out how filtering interferes here
+ cs.sn=0;
+ cSS->Centroid(curSpec);
+ } else if(cs.staticSN) {
+ if(cs.sn==0) cSS->NoSplitAnalysis();
+ else cSS->NewSNPass(cs.snWindow);
+ } else {
+ cSS->OverlappingAnalysis(cs.snWindow);
+ if(cs.iAnalysis) cSS->IntersectionAnalysis();
+ else cSS->UnionAnalysis();
+ }
+ }
+
+ //Split the spectrum
+ cSS->MakeAnalysis(cs.winSize);
+
+ //Analyze each window
+ for(winCount=0;winCount<cSS->getNumWindows();winCount++){
+ sa = cSS->getWindow(winCount);
+ sa.setParams(cs);
+ sa.PredictPeptides();
+
+ //do not analyze spectrum with 0 predicted peaks; Keep count of these occurrances.
+ if(sa.predPeak->size()==0){
+ zeroPep++;
+ continue;
+ }
+
+ AnalyzePeaks(sa);
+
+ }
+
+ //clean up cSS object
+ delete cSS;
+
+ }
+
+ //Update the percentage indicator
+ if(bEcho){
+ if (r.getPercent() > iPercent){
+ if(iPercent<10) cout << "\b";
+ else cout << "\b\b";
+ cout.flush();
+ iPercent=r.getPercent();
+ cout << iPercent;
+ cout.flush();
+ }
+ }
+
+ if(!bMem && cs.xml) {
+ fptr << "</Spectrum>" << endl;
+ fptr << "</File>" << endl;
+ fptr << "</Hardklor>" << endl;
+ }
+
+ } //loop to next spectrum (while)
+
+ //Close the output file and clear it so it can be reused.
+ if(!bMem){
+ fptr.close();
+ fptr.clear();
+ }
+
+ if(bEcho) {
+ cout << "\n" << endl;
+
+ switch(cs.algorithm){
+ case SemiComplete:
+ cout << "SemiComplete analysis:" << endl;
+ break;
+ case SemiCompleteFast:
+ cout << "SemiCompleteFast analysis:" << endl;
+ break;
+ case Dynamic:
+ cout << "Dynamic analysis:" << endl;
+ break;
+ case DynamicSemiComplete:
+ cout << "DynamicSemiComplete analysis:" << endl;
+ break;
+ case SemiSubtractive:
+ cout << "SemiSubtractive analysis:" << endl;
+ break;
+ case FewestPeptides:
+ cout << "FewestPeptides analysis:" << endl;
+ break;
+ case FewestPeptidesChoice:
+ cout << "FewestPeptidesChoice analysis:" << endl;
+ break;
+ case FastFewestPeptides:
+ cout << "FastFewestPeptides analysis:" << endl;
+ break;
+ case FastFewestPeptidesChoice:
+ cout << "FastFewestPeptidesChoice analysis:" << endl;
+ break;
+ case Basic:
+ default:
+ cout << "Basic analysis:" << endl;
+ break;
+ }
+ }
+
+ //Output the simple statistics
+ if(bEcho) cout << " Total number of scans analyzed: " << TotalScans << endl;
+ //cout << " Number of (sub)scans not analyzed:" << endl;
+ //cout << " No Peptides Predicted: " << zeroPep << endl;
+ //cout << " Intensity Below Limit: " << lowSigPep << endl;
+ //cout << " Number of scans with more predicted peptides than were analyzed: " << manyPep << endl;
+ //cout << " Total Correlations Made: " << TotalIterations << endl;
+
+ //Output the time to analyze this file.
+ if(bEcho){
+ i=(int)timeToSec(loadTime,timerFrequency);
+ minutes = (int)(i/60);
+ seconds = i - (60*minutes);
+ cout << "\nFile access time: " << minutes << " minutes, " << seconds << " seconds." << endl;
+ i=(int)timeToSec(splitTime,timerFrequency);
+ minutes = (int)(i/60);
+ seconds = i - (60*minutes);
+ cout << "Split Time: " << minutes << " minutes, " << seconds << " seconds." << endl;
+ i=(int)timeToSec(analysisTime,timerFrequency);
+ minutes = (int)(i/60);
+ seconds = i - (60*minutes);
+ cout << "Analysis Time: " << minutes << " minutes, " << seconds << " seconds." << endl;
+
+ if (minutes==0 && seconds==0){
+ cout << "IMPOSSIBLE!!!" << endl;
+ } else if(minutes <=2){
+ cout << "HOLY FRIJOLE!!" << endl;
+ } else if(minutes<=5) {
+ cout << "Like lightning!" << endl;
+ } else if(minutes<=10){
+ cout << "That's pretty damn fast!" << endl;
+ } else if(minutes<=20){
+ cout << "Monkeys calculate faster than that!" << endl;
+ } else if(minutes<=30){
+ cout << "You should have taken a lunch break." << endl;
+ } else if(minutes<=40){
+ cout << "Oi! Too freakin' slow!!" << endl;
+ } else {
+ cout << "You might be able to eek out some better performance by adjusting your parameters." << endl;
+ }
+ }
+
+ PT=NULL;
+
+}
+
+bool CHardklor::AnalyzePeaks(CSpecAnalyze& sa){
+
+ int i;
+ SSObject bsso;
+
+ //Arrays for combinatorial analysis
+ float *match;
+ float *mismatch;
+
+ //Track analysis times
+ getExactTime(startTime);
+
+ //Make an averagine distribution for every variant specified in the conf file.
+ sa.MakePredictions(pepVariants);
+
+ //if there are no possible peptides, stop the analysis here.
+ if(sa.predPep->size()==0) {
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ analysisTime+=tmpTime1-tmpTime2;
+ return false;
+ }
+
+ //Restructure mismatch arrays for faster correlation analysis
+ sa.BuildMismatchArrays();
+
+ //Send the distributions, and the observed data points from the spectrum to a recursive
+ //algorithm that will sum up every combination of every peptide in each of its chlorinated
+ //forms to find the combination that best fits the data.
+
+ //Dimension our arrays
+ match = new float[sa.peaks.size()];
+ for(i=0;i<sa.peaks.size();i++) match[i]=0;
+
+ if(sa.mismatchSize>0){
+ mismatch = new float[sa.mismatchSize];
+ for(i=0;i<sa.mismatchSize;i++) mismatch[i]=0;
+ } else {
+ mismatch = new float[1];
+ mismatch[0] = 0;
+ }
+
+ //clear prior data and select analysis algorithm
+ bsso.clear();
+ switch(cs.algorithm){
+ case SemiComplete:
+ SemiCompleteMethod(match,mismatch,&bsso,1,cs.depth,0);
+ break;
+ case SemiCompleteFast:
+ SemiCompleteFastMethod(match,mismatch,&bsso,1,cs.depth,0);
+ break;
+ case Dynamic:
+ DynamicMethod(match,mismatch,&bsso,1,cs.depth,0,0);
+ break;
+ case DynamicSemiComplete:
+ DynamicSemiCompleteMethod(match,mismatch,&bsso,1,cs.depth,0,0);
+ break;
+ case SemiSubtractive:
+ SemiSubtractiveMethod(&bsso,cs.depth);
+ break;
+ case FewestPeptides:
+ FewestPeptidesMethod(&bsso,cs.depth);
+ break;
+ case FewestPeptidesChoice:
+ FewestPeptidesChoiceMethod(&bsso,cs.depth);
+ break;
+ case FastFewestPeptides:
+ FastFewestPeptidesMethod(&bsso,cs.depth);
+ break;
+ case FastFewestPeptidesChoice:
+ FastFewestPeptidesChoiceMethod(&bsso,cs.depth);
+ break;
+ case Basic:
+ default:
+ BasicMethod(match,mismatch,&bsso,1,cs.depth,sa.predPep->size()-1);
+ break;
+ }
+
+ //Clean up memory
+ delete [] match;
+ delete [] mismatch;
+
+ //Track analysis times
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ analysisTime+=tmpTime1-tmpTime2;
+
+ //if we exceeded our threshold, output the data to file or store it in memoryt
+ if(bsso.corr > cs.corr) {
+ if(!bMem){
+ if(cs.reducedOutput) WritePepLine(bsso,PT,fptr,2);
+ else if(cs.xml) WritePepLine(bsso,PT,fptr,1);
+ else WritePepLine(bsso,PT,fptr,0);
+ } else {
+ ResultToMem(bsso,PT);
+ }
+ }
+
+ return true;
+}
+
+double CHardklor::LinReg(float *match, float *mismatch){
+
+ int i,sz;
+ double sxx=0,syy=0,sxy=0;
+ vector<sFloat> v;
+ sFloat tmp;
+
+ //Correlate matches
+ for(i=0;i<sa.peaks.size();i++){
+ tmp.fLower = sa.peaks.at(i).intensity;
+ tmp.fUpper = match[i];
+ v.push_back(tmp);
+ }
+
+ //Correlate mismatches with 0
+ for(i=0;i<sa.mismatchSize;i++){
+ if(mismatch[i]>0){
+ tmp.fLower = 0;
+ tmp.fUpper = mismatch[i];
+ v.push_back(tmp);
+ }
+ }
+
+ //Cosine angle correlation
+ sxy=0;
+ sxx=0;
+ syy=0;
+ sz=(int)v.size();
+ for(i=0;i<sz;i++){
+ sxy += (v.at(i).fLower*v.at(i).fUpper);
+ sxx += (v.at(i).fLower*v.at(i).fLower);
+ syy += (v.at(i).fUpper*v.at(i).fUpper);
+ }
+
+ if(sxx>0 && syy>0 && sxy>0) return sxy/sqrt(sxx*syy);
+ else return 0;
+
+}
+
+
+void CHardklor::BasicMethod(float *match, float *mismatch,SSObject *combo,
+ int depth, int maxDepth, int start){
+
+ SSObject bestCombo = *combo;
+ SSObject recCombo;
+
+ double RCorr;
+ double bestRCorr = combo->corr;
+ int a,k,n;
+ float intensity;
+
+ float *sumMatch;
+ float *sumMismatch;
+
+ sumMatch = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0){
+ sumMismatch = new float[sa.mismatchSize];
+ } else {
+ sumMismatch = new float[1];
+ };
+
+ //Iterate through all predicted peptides
+ for(k=start; k>-1; k--) {
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ intensity = sa.predPep->at(k).GetIntensity() - match[sa.predPep->at(k).GetMaxPeakIndex()];
+
+ if(intensity<0) {
+ //This predicted peptide cannot contribute to the analysis, so don't go
+ //any deeper
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ return;
+ };
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity*intensity + match[a];
+ };
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity*intensity + mismatch[a];
+ };
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ RCorr = LinReg(sumMatch,sumMismatch);
+
+ //cout << RCorr << endl;
+
+ recCombo = *combo;
+ recCombo.addVar(k,n);
+ recCombo.corr = RCorr;
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ //Check recursions
+ if(depth<maxDepth){
+ BasicMethod(sumMatch,sumMismatch,&recCombo,depth+1,maxDepth,k-1);
+ };
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ };
+ };
+
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ *combo = bestCombo;
+
+};
+
+void CHardklor::SemiCompleteMethod(float *match, float *mismatch,SSObject *combo,
+ int depth, int maxDepth, int start){
+
+ SSObject bestCombo = *combo;
+ SSObject recCombo;
+
+ double RCorr;
+ double bestRCorr = combo->corr;
+ int a,n;
+ unsigned int k;
+
+ float *sumMatch;
+ float *sumMismatch;
+
+ sumMatch = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0){
+ sumMismatch = new float[sa.mismatchSize];
+ } else {
+ sumMismatch = new float[1];
+ };
+
+ //Iterate through all predicted peptides
+ for(k=start; k<sa.predPep->size(); k++) {
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity + match[a];
+ };
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity + mismatch[a];
+ };
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ RCorr = LinReg(sumMatch,sumMismatch);
+
+ recCombo = *combo;
+ recCombo.addVar(k,n);
+ recCombo.corr = RCorr;
+
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ }
+ }
+
+ //If we reached threshold, stop here without recursion
+ if(bestCombo.corr>cs.corr) {
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ *combo = bestCombo;
+ return;
+ }
+
+ if(depth<maxDepth){
+
+ //Iterate through all predicted peptides
+ for(k=start; k<sa.predPep->size(); k++) {
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity + match[a];
+ }
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity + mismatch[a];
+ }
+
+ recCombo = *combo;
+ recCombo.addVar(k,n);
+ recCombo.corr = RCorr;
+
+ //Check recursions
+ SemiCompleteMethod(sumMatch,sumMismatch,&recCombo,depth+1,maxDepth,k+1);
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ }
+ }
+ }
+
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ *combo = bestCombo;
+
+}
+
+void CHardklor::SemiCompleteFastMethod(float *match, float *mismatch,SSObject *combo,
+ int depth, int maxDepth, int start){
+
+ SSObject bestCombo = *combo;
+ SSObject recCombo;
+
+ double RCorr;
+ double bestRCorr = combo->corr;
+ int a,b,n;
+ unsigned int k;
+
+ int numArrays=0;
+ for(k=start;k<sa.predPep->size();k++){
+ numArrays+=sa.predPep->at(k).VariantListSize();
+ }
+
+ float **sumMatch;
+ float **sumMismatch;
+
+ sumMatch = new float* [numArrays];
+ sumMismatch = new float* [numArrays];
+ for(n=0;n<numArrays;n++){
+ sumMatch[n] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0){
+ sumMismatch[n] = new float[sa.mismatchSize];
+ } else {
+ sumMismatch[n] = new float[1];
+ }
+ }
+
+ b=0;
+ //Iterate through all predicted peptides
+ for(k=start; k<sa.predPep->size(); k++) {
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[b][a]=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity + match[a];
+ }
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[b][a]=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity + mismatch[a];
+ }
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ RCorr = LinReg(sumMatch[b],sumMismatch[b]);
+
+ recCombo = *combo;
+ recCombo.addVar(k,n);
+ recCombo.corr = RCorr;
+
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ b++;
+ }
+ }
+
+ //If we reached threshold, stop here without recursion
+ if(bestCombo.corr>cs.corr) {
+ for(n=0;n<numArrays;n++) {
+ delete [] sumMatch[n];
+ delete [] sumMismatch[n];
+ };
+ delete [] sumMatch;
+ delete [] sumMismatch;
+
+ *combo = bestCombo;
+ return;
+ }
+
+ if(depth<maxDepth){
+
+ //Iterate through all predicted peptides
+ b=0;
+ for(k=start; k<sa.predPep->size(); k++) {
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ recCombo = *combo;
+ recCombo.addVar(k,n);
+ recCombo.corr = RCorr;
+
+ //Check recursions
+ SemiCompleteFastMethod(sumMatch[b],sumMismatch[b],&recCombo,depth+1,maxDepth,k+1);
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ b++;
+ }
+ }
+ }
+
+ for(n=0;n<numArrays;n++) {
+ delete [] sumMatch[n];
+ delete [] sumMismatch[n];
+ }
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ *combo = bestCombo;
+
+}
+
+
+void CHardklor::DynamicMethod(float *match, float *mismatch,SSObject *combo,
+ int depth, int maxDepth, int start, double corr){
+
+ SSObject bestCombo = *combo;
+ SSObject recCombo;
+
+ double RCorr;
+ double bestRCorr = combo->corr;
+ int a,n;
+ unsigned int k;
+
+ float *sumMatch;
+ float *sumMismatch;
+
+ sumMatch = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0){
+ sumMismatch = new float[sa.mismatchSize];
+ } else {
+ sumMismatch = new float[1];
+ };
+
+ //Iterate through all predicted peptides
+ for(k=start; k<sa.predPep->size(); k++) {
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity + match[a];
+ };
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity + mismatch[a];
+ };
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ RCorr = LinReg(sumMatch,sumMismatch);
+
+ //cout << "RCorr = " << RCorr << endl;
+
+ recCombo = *combo;
+ recCombo.addVar(k,n);
+ recCombo.corr = RCorr;
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ //Check recursions if better than previously
+ if(depth < maxDepth && RCorr > corr){
+ DynamicMethod(sumMatch,sumMismatch,&recCombo,depth+1,maxDepth,k+1,RCorr);
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+ };
+
+ };
+ };
+
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ *combo = bestCombo;
+
+};
+
+
+void CHardklor::DynamicSemiCompleteMethod(float *match, float *mismatch,SSObject *combo,
+ int depth, int maxDepth, int start, double corr){
+
+ SSObject bestCombo = *combo;
+ SSObject recCombo;
+
+ double RCorr;
+ double bestRCorr = combo->corr;
+ int a,b,n;
+ unsigned int k;
+
+ vector<double> vecCorr;
+
+ float *sumMatch;
+ float *sumMismatch;
+
+ sumMatch = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0){
+ sumMismatch = new float[sa.mismatchSize];
+ } else {
+ sumMismatch = new float[1];
+ }
+
+ //Iterate through all predicted peptides
+ b=0;
+ for(k=start; k<sa.predPep->size(); k++) {
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity + match[a];
+ }
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity + mismatch[a];
+ }
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ RCorr = LinReg(sumMatch,sumMismatch);
+
+ recCombo = *combo;
+ recCombo.addVar(k,n);
+ recCombo.corr = RCorr;
+
+ vecCorr.push_back(RCorr);
+ b++;
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ }
+ }
+
+ //If we reached threshold, stop here without recursion
+ if(bestCombo.corr>cs.corr) {
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ *combo = bestCombo;
+ return;
+ }
+
+
+ //Otherwise, if we're not at the maximum depth, iterate
+ b=0;
+ if(depth < maxDepth) {
+
+ //Iterate through all predicted peptides
+ for(k=start; k<sa.predPep->size(); k++) {
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ if(vecCorr.at(b) > corr) {
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity + match[a];
+ }
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity + mismatch[a];
+ }
+
+ recCombo = *combo;
+ recCombo.addVar(k,n);
+ recCombo.corr = vecCorr.at(b);
+
+ //Check recursions
+ DynamicSemiCompleteMethod(sumMatch,sumMismatch,&recCombo,depth+1,maxDepth,k+1,vecCorr.at(b));
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ }
+ b++;
+
+ }
+ }
+
+ }
+
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ *combo = bestCombo;
+
+};
+
+void CHardklor::SemiSubtractiveMethod(SSObject *combo, int maxDepth){
+
+ SSObject bestCombo = *combo;
+ SSObject recCombo;
+ SSObject depthCombo;
+
+ double RCorr;
+ int a,n;
+ unsigned int k;
+ bool bSkip;
+
+ int depth=0;
+
+ float *sumMatch;
+ float *sumMismatch;
+ float *sumMatchMem;
+ float *sumMismatchMem;
+
+ sumMatch = new float[sa.peaks.size()];
+ sumMatchMem = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0){
+ sumMismatch = new float[sa.mismatchSize];
+ sumMismatchMem = new float[sa.mismatchSize];
+ } else {
+ sumMismatch = new float[1];
+ sumMismatchMem = new float[1];
+ }
+
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatchMem[a]=0;
+ }
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatchMem[a]=0;
+ }
+
+ while(depth < maxDepth) {
+
+ cout << "Depth: " << depth << " of " << maxDepth << endl;
+
+ depthCombo = bestCombo;
+
+ //Iterate through all predicted peptides
+ for(k=0; k<sa.predPep->size(); k++) {
+
+ //Skip peptides we have already analyzed.
+ bSkip=false;
+ for(n=0;n<(int)bestCombo.pepVar->size();n++){
+ if(bestCombo.pepVar->at(n).iLower==k) {
+ bSkip=true;
+ break;
+ }
+ }
+ if(bSkip) continue;
+
+ //check each variant
+ for(n=0; n<sa.predPep->at(k).VariantListSize(); n++){
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity + sumMatchMem[a];
+ }
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity + sumMismatchMem[a];
+ }
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ RCorr = LinReg(sumMatch,sumMismatch);
+ cout << RCorr << endl;
+
+ recCombo = depthCombo;
+ recCombo.addVar(k,n);
+ recCombo.corr = RCorr;
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ }
+
+ }
+
+ //If we reached threshold, stop here without recursion
+ if(bestCombo.corr>cs.corr) {
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ delete [] sumMatchMem;
+ delete [] sumMismatchMem;
+ *combo = bestCombo;
+ return;
+ }
+
+ if(bestCombo.corr>0) {
+ //Copy the best correlated data for the next iteration
+ k = bestCombo.pepVar->at(bestCombo.pepVar->size()-1).iLower;
+ n = bestCombo.pepVar->at(bestCombo.pepVar->size()-1).iUpper;
+
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatchMem[a]+=sa.predPep->at(k).GetVariant(n).GetMatch(a).intensity;
+ }
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatchMem[a]+=sa.predPep->at(k).GetVariant(n).GetMismatch(a).intensity;
+ }
+ }
+
+ depth++;
+
+ }
+
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ delete [] sumMatchMem;
+ delete [] sumMismatchMem;
+ *combo = bestCombo;
+
+}
+
+
+void CHardklor::FewestPeptidesMethod(SSObject *combo, int maxDepth){
+
+ SSObject recCombo;
+ SSObject bestCombo = *combo;
+
+ double RCorr;
+ int a,b,j,k,n,pos;
+ int pepID,varID;
+
+ int depth=0;
+ int countDown=0;
+ int comboListCounter=0;
+
+ float intensity;
+
+ float *sumMatch;
+ float *sumMismatch;
+ float *priorMatch;
+ float *priorMismatch;
+
+ sumMatch = new float[sa.peaks.size()];
+ priorMatch = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0){
+ sumMismatch = new float[sa.mismatchSize];
+ priorMismatch = new float[sa.mismatchSize];
+ } else {
+ sumMismatch = new float[1];
+ priorMismatch = new float[1];
+ };
+
+ vector<SSObject> comboList;
+ comboList.push_back(*combo);
+ comboListCounter++;
+
+ /*
+ for(j=0;j<sa.peaks.size();j++){
+ cout << sa.peaks.at(j).mz << " " << sa.peaks.at(j).intensity << endl;
+ };
+ */
+
+ while(depth < maxDepth && depth < (int)sa.predPep->size()) {
+
+ countDown=comboListCounter;
+ comboListCounter=0;
+ pos=0;
+
+ //scan through current list of combos
+ while(pos < countDown){
+
+ //cout << depth+1 << " of " << maxDepth << "\t" << pos << " of " << countDown << " with " << sa.predPep->size() << endl;
+
+ //clear old priors data
+ for(a=0;a<sa.peaks.size();a++) priorMatch[a]=0;
+ for(a=0;a<sa.mismatchSize;a++) priorMismatch[a]=0;
+
+ //recreate prior match and mismatch data
+ for(n=0;n<(int)comboList.at(pos).pepVar->size();n++){
+ pepID = comboList.at(pos).pepVar->at(n).iLower;
+ varID = comboList.at(pos).pepVar->at(n).iUpper;
+
+ intensity = sa.predPep->at(pepID).GetIntensity() - priorMatch[sa.predPep->at(pepID).GetMaxPeakIndex()];
+
+ for(a=0;a<sa.peaks.size();a++){
+ priorMatch[a]+=sa.predPep->at(pepID).GetVariant(varID).GetMatch(a).intensity*intensity;
+ };
+ for(a=0;a<sa.mismatchSize;a++){
+ priorMismatch[a]+=sa.predPep->at(pepID).GetVariant(varID).GetMismatch(a).intensity*intensity;
+ };
+ };
+
+ if(comboList.at(pos).pepVar->size()>0){
+ b = comboList.at(pos).pepVar->at(comboList.at(pos).pepVar->size()-1).iLower - 1;
+ } else {
+ b = sa.predPep->size()-1;
+ };
+
+ //add every peptide & every variant
+ for(j=b;j>-1;j--){
+
+ intensity = sa.predPep->at(j).GetIntensity() - priorMatch[sa.predPep->at(j).GetMaxPeakIndex()];
+
+ if(intensity<0) {
+ //This predicted peptide cannot contribute to the analysis, so don't go
+ //any deeper
+ continue;
+ };
+
+ //iterate through variants now
+ for(k=0;k<sa.predPep->at(j).VariantListSize();k++){
+
+ //sum matches and mismatches
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity*intensity + priorMatch[a];
+ };
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity*intensity + priorMismatch[a];
+ };
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ RCorr = LinReg(sumMatch,sumMismatch);
+ //cout << RCorr << endl;
+
+ recCombo = comboList.at(0);
+ recCombo.addVar(j,k);
+ recCombo.corr = RCorr;
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ //Add to our list of combos to analyze in the future
+ if(depth<maxDepth-1){
+ comboList.push_back(recCombo);
+ comboListCounter++;
+ };
+
+ };//for k
+
+ };//for j
+
+ //delete our prior combo from the list
+ //comboList.erase(comboList.begin());
+ //countDown--;
+ pos++;
+
+ };//while countDown
+
+ comboList.erase(comboList.begin(),comboList.begin()+countDown);
+
+ //check best to see if it exceeded threshold
+ if(bestCombo.corr>cs.corr) {
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ delete [] priorMatch;
+ delete [] priorMismatch;
+ *combo = bestCombo;
+ return;
+ };
+
+ //otherwise, we iterate
+ depth++;
+
+ };//while depth
+
+ //return the best we got
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ delete [] priorMatch;
+ delete [] priorMismatch;
+ *combo = bestCombo;
+
+};
+
+void CHardklor::FewestPeptidesChoiceMethod(SSObject *combo, int maxDepth){
+
+ SSObject recCombo;
+ SSObject bestCombo = *combo;
+
+ double RCorr;
+ int a,j,k,n;
+ int pepID,varID;
+
+ int depth=0;
+ int countDown=0;
+ int comboListCounter=0;
+ int start;
+
+ float intensity;
+
+ float *sumMatch;
+ float *sumMismatch;
+ float *priorMatch;
+ float *priorMismatch;
+
+ sumMatch = new float[sa.peaks.size()];
+ priorMatch = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0){
+ sumMismatch = new float[sa.mismatchSize];
+ priorMismatch = new float[sa.mismatchSize];
+ } else {
+ sumMismatch = new float[1];
+ priorMismatch = new float[1];
+ };
+
+ vector<SSObject> comboList;
+ comboList.push_back(*combo);
+ comboListCounter++;
+
+ while(depth < maxDepth && depth < (int)sa.predPep->size()) {
+
+ countDown=comboListCounter;
+ comboListCounter=0;
+
+ //scan through current list of combos
+ while(countDown>0){
+
+ //clear old priors data
+ for(a=0;a<sa.peaks.size();a++) priorMatch[a]=0;
+ for(a=0;a<sa.mismatchSize;a++) priorMismatch[a]=0;
+
+ //recreate prior match and mismatch data
+ for(n=0;n<(int)comboList.at(0).pepVar->size();n++){
+ pepID = comboList.at(0).pepVar->at(n).iLower;
+ varID = comboList.at(0).pepVar->at(n).iUpper;
+
+ intensity = sa.predPep->at(pepID).GetIntensity() - priorMatch[sa.predPep->at(pepID).GetMaxPeakIndex()];
+
+ for(a=0;a<sa.peaks.size();a++){
+ priorMatch[a]+=sa.predPep->at(pepID).GetVariant(varID).GetMatch(a).intensity*intensity;
+ };
+ for(a=0;a<sa.mismatchSize;a++){
+ priorMismatch[a]+=sa.predPep->at(pepID).GetVariant(varID).GetMismatch(a).intensity*intensity;
+ };
+ };
+
+ if(comboList.at(0).pepVar->size()>0) start = comboList.at(0).pepVar->at(comboList.at(0).pepVar->size()-1).iLower-1;
+ else start = sa.predPep->size()-1;
+
+ //add every peptide & every variant
+ for(j=start;j>-1;j--){
+
+ intensity = sa.predPep->at(j).GetIntensity() - priorMatch[sa.predPep->at(j).GetMaxPeakIndex()];
+ if(intensity<0) {
+ //This predicted peptide cannot contribute to the analysis, so don't go
+ //any deeper
+ continue;
+ };
+
+ //iterate through variants now
+ for(k=0;k<sa.predPep->at(j).VariantListSize();k++){
+
+ //Add the variant to the distribution being analyzed
+ //Do matches first
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatch[a]=sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity*intensity + priorMatch[a];
+ };
+
+ //Now add mismatches
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatch[a]=sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity*intensity + priorMismatch[a];
+ };
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ RCorr = LinReg(sumMatch,sumMismatch);
+ //cout << RCorr << endl;
+
+ recCombo = comboList.at(0);
+ recCombo.addVar(j,k);
+ recCombo.corr = RCorr;
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ //Add to our list of combos to analyze in the future if above a lower threshhold
+ if(RCorr > (cs.corr/2)) {
+ comboList.push_back(recCombo);
+ comboListCounter++;
+ };
+
+ };//for k
+
+ };//for j
+
+ //delete our prior combo from the list
+ comboList.erase(comboList.begin());
+ countDown--;
+
+ };//while countDown
+
+ //check best to see if it exceeded threshold
+ if(bestCombo.corr>cs.corr) {
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ delete [] priorMatch;
+ delete [] priorMismatch;
+ *combo = bestCombo;
+ return;
+ };
+
+ //otherwise, we iterate
+ depth++;
+
+ };//while depth
+
+ //return the best we got
+ delete [] sumMatch;
+ delete [] sumMismatch;
+ delete [] priorMatch;
+ delete [] priorMismatch;
+ *combo = bestCombo;
+
+};
+
+
+void CHardklor::FastFewestPeptidesMethod(SSObject *combo, int maxDepth){
+
+ SSObject recCombo;
+ SSObject bestCombo = *combo;
+
+ vector<SSObject> *comboListA;
+ vector<SSObject> *comboListB;
+ comboListA = new vector<SSObject>;
+ comboListB = new vector<SSObject>;
+ comboListA->push_back(*combo);
+ comboListB->push_back(*combo);
+
+ double RCorr;
+ int a,b,j,k;
+ //int x;
+
+ int depth=0;
+ float intensity=0.0f;
+
+ float **sumMatchA;
+ float **sumMismatchA;
+ float **sumMatchB;
+ float **sumMismatchB;
+
+ float *sumMatchC;
+ float *sumMismatchC;
+
+ //Initialize arrays
+ sumMatchA = new float* [1];
+ sumMismatchA = new float* [1];
+ sumMatchA[0] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchA[0] = new float[sa.mismatchSize];
+ else sumMismatchA[0] = new float[1];
+
+ sumMatchB = new float* [1];
+ sumMismatchB = new float* [1];
+ sumMatchB[0] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchB[0] = new float[sa.mismatchSize];
+ else sumMismatchB[0] = new float[1];
+
+ sumMatchC = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchC = new float[sa.mismatchSize];
+ else sumMismatchC = new float[1];
+
+ for(a=0;a<sa.peaks.size();a++) sumMatchB[0][a]=0;
+ for(a=0;a<sa.mismatchSize;a++) sumMismatchB[0][a]=0;
+
+ bool storeA=true;
+ int widthA, widthB, widthC, sizeA, sizeB;
+ int count,lastCount;
+ widthA=1;
+ widthB=1;
+ widthC=1;
+ sizeA=1;
+ sizeB=1;
+
+ //cout << "In method, everything initialized" << endl;
+
+ while(depth < maxDepth && depth < sa.predPep->size()) {
+
+ if(storeA){
+ if(depth < maxDepth-1) {
+ for(a=0;a<widthA;a++){
+ delete [] sumMatchA[a];
+ delete [] sumMismatchA[a];
+ }
+ delete [] sumMatchA;
+ delete [] sumMismatchA;
+ widthA=calcDepth(0,depth+1);
+ sumMatchA = new float* [widthA];
+ sumMismatchA = new float* [widthA];
+ for(a=0;a<widthA;a++){
+ sumMatchA[a] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchA[a] = new float[sa.mismatchSize];
+ else sumMismatchA[a] = new float[1];
+ }
+ delete comboListA;
+ comboListA = new vector<SSObject>;
+ //cout << "Done re-initializing A" << endl;
+ } else {
+ widthC=calcDepth(0,depth+1);
+ }
+ } else {
+ if(depth < maxDepth-1) {
+ for(a=0;a<widthB;a++){
+ delete [] sumMatchB[a];
+ delete [] sumMismatchB[a];
+ }
+ delete [] sumMatchB;
+ delete [] sumMismatchB;
+ //cout << "Deleted B ok" << endl;
+ widthB=calcDepth(0,depth+1);
+ //cout << "WidthB: " << widthB << endl;
+ sumMatchB = new float* [widthB];
+ sumMismatchB = new float* [widthB];
+ for(a=0;a<widthB;a++){
+ sumMatchB[a] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchB[a] = new float[sa.mismatchSize];
+ else sumMismatchB[a] = new float[1];
+ }
+ delete comboListB;
+ comboListB = new vector<SSObject>;
+ //cout << "Done re-initializing B" << endl;
+ } else {
+ widthC=calcDepth(0,depth+1);
+ }
+ }
+
+ //scan through current list of combos
+ lastCount=0;
+ count=0;
+ while(true){
+
+ if(storeA){
+ if(depth==maxDepth-1) {
+ if(count==widthC) break;
+ } else {
+ if(count==widthA) break;
+ }
+ if(lastCount==sizeB) break;
+ if(comboListB->at(lastCount).pepVar->size()==0) {
+ b=sa.predPep->size()-1;
+ } else {
+ b = comboListB->at(lastCount).pepVar->at(comboListB->at(lastCount).pepVar->size()-1).iLower-1;
+ //cout << "B: " << b << endl;
+ }
+ } else {
+ if(depth==maxDepth-1) {
+ if(count==widthC) break;
+ } else {
+ if(count==widthB) break;
+ }
+ if(lastCount==sizeA) break;
+ if(comboListA->at(lastCount).pepVar->size()==0) {
+ b=sa.predPep->size()-1;
+ } else {
+ b = comboListA->at(lastCount).pepVar->at(comboListA->at(lastCount).pepVar->size()-1).iLower-1;
+ //cout << "B: " << b << endl;
+ }
+ }
+
+ //add every peptide & every variant
+ for(j=b;j>-1;j--){
+
+ if(storeA){
+ //cout << sumMatchB[lastCount][sa.predPep->at(j).GetMaxPeakIndex()] << ", " << sa.predPep->at(j).GetIntensity() << ", " << sa.predPep->at(j).GetMaxPeakIndex() << endl;
+ intensity = sa.predPep->at(j).GetIntensity() - sumMatchB[lastCount][sa.predPep->at(j).GetMaxPeakIndex()];
+ } else {
+ //cout << sumMatchA[lastCount][sa.predPep->at(j).GetMaxPeakIndex()] << ", " << sa.predPep->at(j).GetIntensity() << ", " << sa.predPep->at(j).GetMaxPeakIndex() << endl;
+ intensity = sa.predPep->at(j).GetIntensity() - sumMatchA[lastCount][sa.predPep->at(j).GetMaxPeakIndex()];
+ }
+
+ //cout << j << ": " << intensity << endl;
+
+ //if intensity is less than zero, this is an invalid summation
+ if(intensity>0) {
+
+ //iterate through variants now
+ for(k=0;k<sa.predPep->at(j).VariantListSize();k++){
+
+ //cout << sa.predPep->at(j).GetMZ() << " " << sa.predPep->at(j).GetVariant(k).GetFormula() << " " << sa.predPep->at(j).GetVariant(k).GetCharge() << endl;
+ //cout << "MISMATCH SIZE: " << sa.mismatchSize << endl;
+
+ //sum matches and mismatches
+ if(storeA){
+ for(a=0;a<sa.peaks.size();a++){
+ //cout << "Match: " << sa.peaks.at(a).mz << " " << sa.peaks.at(a).intensity << " " << sa.predPep->at(j).GetVariant(k).GetMatch(a).mz << " " << sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity << endl;
+ if(depth == maxDepth-1){
+ sumMatchC[a]=sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity*intensity + sumMatchB[lastCount][a];
+ } else {
+ sumMatchA[count][a]=sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity*intensity + sumMatchB[lastCount][a];
+ }
+ }
+ for(a=0;a<sa.mismatchSize;a++){
+ //cout << "Mismatch: " << sa.predPep->at(j).GetVariant(k).GetMismatch(a).mz << " " << sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity << endl;
+ if(depth == maxDepth-1) {
+ sumMismatchC[a]=sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity*intensity + sumMismatchB[lastCount][a];
+ } else {
+ sumMismatchA[count][a]=sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity*intensity + sumMismatchB[lastCount][a];
+ }
+ }
+ } else {
+ for(a=0;a<sa.peaks.size();a++){
+ if(depth == maxDepth-1){
+ sumMatchC[a]=sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity*intensity + sumMatchA[lastCount][a];
+ } else {
+ sumMatchB[count][a]=sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity*intensity + sumMatchA[lastCount][a];
+ }
+ }
+ for(a=0;a<sa.mismatchSize;a++){
+ if(depth == maxDepth-1){
+ sumMismatchC[a]=sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity*intensity + sumMismatchA[lastCount][a];
+ } else {
+ sumMismatchB[count][a]=sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity*intensity + sumMismatchA[lastCount][a];
+ }
+ }
+ }
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ if(depth == maxDepth-1){
+ RCorr = LinReg(sumMatchC,sumMismatchC);
+ } else {
+ if(storeA) RCorr = LinReg(sumMatchA[count],sumMismatchA[count]);
+ else RCorr = LinReg(sumMatchB[count],sumMismatchB[count]);
+ }
+
+ //cout << RCorr << endl;
+
+ if(storeA) recCombo = comboListB->at(lastCount);
+ else recCombo = comboListA->at(lastCount);
+ recCombo.addVar(j,k);
+ recCombo.corr = RCorr;
+
+ /*
+ for(x=0;x<recCombo.pepVar->size();x++) {
+
+ a=recCombo.pepVar->at(x).iLower;
+ b=recCombo.pepVar->at(x).iUpper;
+
+ cout << "(" << a << "," << b << ")" << sa.predPep->at(a).GetMZ() << "\t";
+ cout << sa.predPep->at(a).GetVariant(b).GetCharge() << "\t";
+ };
+ cout << "\n--------" << endl;
+ */
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ count++;
+ if(depth < maxDepth-1){
+ if(storeA) comboListA->push_back(recCombo);
+ else comboListB->push_back(recCombo);
+ }
+
+
+
+ }//for k
+
+ }//end if(intensity>0)
+
+ }//for j
+
+ //iterate to the next stored array
+ lastCount++;
+
+ }//while(true)
+
+ if(storeA) sizeA=count;
+ else sizeB=count;
+
+ //check best to see if it exceeded threshold
+ if(bestCombo.corr>cs.corr) {
+ for(a=0;a<widthA;a++){
+ delete [] sumMatchA[a];
+ delete [] sumMismatchA[a];
+ }
+ delete [] sumMatchA;
+ delete [] sumMismatchA;
+ for(a=0;a<widthB;a++){
+ delete [] sumMatchB[a];
+ delete [] sumMismatchB[a];
+ }
+ delete [] sumMatchB;
+ delete [] sumMismatchB;
+ delete [] sumMatchC;
+ delete [] sumMismatchC;
+ delete comboListA;
+ delete comboListB;
+ *combo = bestCombo;
+ return;
+ }
+
+ //otherwise, we iterate
+ if(storeA) storeA=false;
+ else storeA=true;
+ depth++;
+
+ //This is here for the complete method. It is a failsafe to kill the routine
+ //if there is little hope that combining distributions will produce a real result
+ if(depth==1 && bestCombo.corr<0.05) break;
+
+ }//while depth
+
+ //return the best we got
+ for(a=0;a<widthA;a++){
+ delete [] sumMatchA[a];
+ delete [] sumMismatchA[a];
+ }
+ delete [] sumMatchA;
+ delete [] sumMismatchA;
+ for(a=0;a<widthB;a++){
+ delete [] sumMatchB[a];
+ delete [] sumMismatchB[a];
+ }
+ delete [] sumMatchB;
+ delete [] sumMismatchB;
+ delete [] sumMatchC;
+ delete [] sumMismatchC;
+ delete comboListA;
+ delete comboListB;
+ *combo = bestCombo;
+
+ //cout << "Done! " << bestCombo.corr << " " << SSIterations << endl;
+
+}
+
+void CHardklor::FastFewestPeptidesChoiceMethod(SSObject *combo, int maxDepth){
+
+ SSObject recCombo;
+ SSObject bestCombo = *combo;
+
+ vector<SSObject> *comboListA;
+ vector<SSObject> *comboListB;
+ comboListA = new vector<SSObject>;
+ comboListB = new vector<SSObject>;
+ comboListA->push_back(*combo);
+ comboListB->push_back(*combo);
+
+ double RCorr;
+ int a,b,j,k;
+
+ int depth=0;
+ float intensity;
+
+ float **sumMatchA;
+ float **sumMismatchA;
+ float **sumMatchB;
+ float **sumMismatchB;
+
+ //Initialize arrays
+ sumMatchA = new float* [1];
+ sumMismatchA = new float* [1];
+ sumMatchA[0] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchA[0] = new float[sa.mismatchSize];
+ else sumMismatchA[0] = new float[1];
+
+ sumMatchB = new float* [1];
+ sumMismatchB = new float* [1];
+ sumMatchB[0] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchB[0] = new float[sa.mismatchSize];
+ else sumMismatchB[0] = new float[1];
+
+ for(a=0;a<sa.peaks.size();a++) sumMatchB[0][a]=0;
+ for(a=0;a<sa.mismatchSize;a++) sumMismatchB[0][a]=0;
+
+ bool storeA=true;
+ int widthA, widthB, sizeA, sizeB;
+ int count,lastCount;
+ widthA=1;
+ widthB=1;
+ sizeA=1;
+ sizeB=1;
+
+ //cout << "In method, everything initialized" << endl;
+
+ while(depth < maxDepth && depth < sa.predPep->size()) {
+
+ if(storeA){
+ for(a=0;a<widthA;a++){
+ delete [] sumMatchA[a];
+ delete [] sumMismatchA[a];
+ };
+ delete [] sumMatchA;
+ delete [] sumMismatchA;
+ //cout << "Deleted A ok" << endl;
+ widthA=calcDepth(0,depth+1);
+ //cout << "WidthA: " << widthA << endl;
+ sumMatchA = new float* [widthA];
+ sumMismatchA = new float* [widthA];
+ for(a=0;a<widthA;a++){
+ sumMatchA[a] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchA[a] = new float[sa.mismatchSize];
+ else sumMismatchA[a] = new float[1];
+ };
+ delete comboListA;
+ comboListA = new vector<SSObject>;
+ //cout << "Done re-initializing A" << endl;
+ } else {
+ for(a=0;a<widthB;a++){
+ delete [] sumMatchB[a];
+ delete [] sumMismatchB[a];
+ };
+ delete [] sumMatchB;
+ delete [] sumMismatchB;
+ //cout << "Deleted B ok" << endl;
+ widthB=calcDepth(0,depth+1);
+ //cout << "WidthB: " << widthB << endl;
+ sumMatchB = new float* [widthB];
+ sumMismatchB = new float* [widthB];
+ for(a=0;a<widthB;a++){
+ sumMatchB[a] = new float[sa.peaks.size()];
+ if(sa.mismatchSize>0) sumMismatchB[a] = new float[sa.mismatchSize];
+ else sumMismatchB[a] = new float[1];
+ };
+ delete comboListB;
+ comboListB = new vector<SSObject>;
+ //cout << "Done re-initializing B" << endl;
+ };
+
+ //scan through current list of combos
+ count=0;
+ lastCount=0;
+ while(true){
+
+ if(storeA){
+ if(lastCount==sizeB) break;
+ if(count==widthA) break;
+ if(comboListB->at(lastCount).pepVar->size()==0) b=sa.predPep->size()-1;
+ else b = comboListB->at(lastCount).pepVar->at(comboListB->at(lastCount).pepVar->size()-1).iLower-1;
+ //cout << "Checking ";
+ //for(a=0;a<comboListB->at(lastCount).pepVar->size();a++){
+ // cout << comboListB->at(lastCount).pepVar->at(a).iLower << "." << comboListB->at(lastCount).pepVar->at(a).iUpper << "-";
+ //};
+ //cout << endl;
+ } else {
+ if(lastCount==sizeA) break;
+ if(count==widthB) break;
+ if(comboListA->at(lastCount).pepVar->size()==0) b=sa.predPep->size()-1;
+ else b = comboListA->at(lastCount).pepVar->at(comboListA->at(lastCount).pepVar->size()-1).iLower-1;
+ //cout << "Checking ";
+ //for(a=0;a<comboListA->at(lastCount).pepVar->size();a++){
+ // cout << comboListA->at(lastCount).pepVar->at(a).iLower << "." << comboListA->at(lastCount).pepVar->at(a).iUpper << "-";
+ //};
+ //cout << endl;
+ };
+
+ //add every peptide & every variant
+ for(j=b;j>-1;j--){
+
+ if(storeA){
+ intensity = sa.predPep->at(j).GetIntensity() - sumMatchB[lastCount][sa.predPep->at(j).GetMaxPeakIndex()];
+ } else {
+ intensity = sa.predPep->at(j).GetIntensity() - sumMatchA[lastCount][sa.predPep->at(j).GetMaxPeakIndex()];
+ };
+
+ //if intensity is less than zero, this is an invalid summation
+ if(intensity>0) {
+
+ //iterate through variants now
+ for(k=0;k<sa.predPep->at(j).VariantListSize();k++){
+
+ //sum matches and mismatches
+ if(storeA){
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatchA[count][a]=sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity*intensity + sumMatchB[lastCount][a];
+ };
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatchA[count][a]=sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity*intensity + sumMismatchB[lastCount][a];
+ };
+ } else {
+ for(a=0;a<sa.peaks.size();a++){
+ sumMatchB[count][a]=sa.predPep->at(j).GetVariant(k).GetMatch(a).intensity*intensity + sumMatchA[lastCount][a];
+ };
+ for(a=0;a<sa.mismatchSize;a++){
+ sumMismatchB[count][a]=sa.predPep->at(j).GetVariant(k).GetMismatch(a).intensity*intensity + sumMismatchA[lastCount][a];
+ };
+ };
+
+ //Correlate this combined distribution with the mass spec data.
+ //SSIterations++;
+ if(storeA) RCorr = LinReg(sumMatchA[count],sumMismatchA[count]);
+ else RCorr = LinReg(sumMatchB[count],sumMismatchB[count]);
+
+ if(storeA) recCombo = comboListB->at(lastCount);
+ else recCombo = comboListA->at(lastCount);
+ recCombo.addVar(j,k);
+ recCombo.corr = RCorr;
+
+ //Check if it is the best, if so, mark it
+ if(recCombo.corr>bestCombo.corr) bestCombo = recCombo;
+
+ if(RCorr>cs.corr/2){
+ count++;
+ if(storeA) comboListA->push_back(recCombo);
+ else comboListB->push_back(recCombo);
+ };
+
+ };//for k
+
+ };//end if(intensity>0)
+
+ };//for j
+
+ //iterate to the next stored array
+ lastCount++;
+
+ };//while countDown
+
+ if(storeA) sizeA=count;
+ else sizeB=count;
+
+ //check best to see if it exceeded threshold
+ if(bestCombo.corr>cs.corr) {
+ for(a=0;a<widthA;a++){
+ delete [] sumMatchA[a];
+ delete [] sumMismatchA[a];
+ };
+ delete [] sumMatchA;
+ delete [] sumMismatchA;
+ for(a=0;a<widthB;a++){
+ delete [] sumMatchB[a];
+ delete [] sumMismatchB[a];
+ };
+ delete [] sumMatchB;
+ delete [] sumMismatchB;
+ delete comboListA;
+ delete comboListB;
+ *combo = bestCombo;
+ return;
+ };
+
+ //otherwise, we iterate
+ if(storeA) storeA=false;
+ else storeA=true;
+ depth++;
+
+ };//while depth
+
+ //return the best we got
+ for(a=0;a<widthA;a++){
+ delete [] sumMatchA[a];
+ delete [] sumMismatchA[a];
+ };
+ delete [] sumMatchA;
+ delete [] sumMismatchA;
+ for(a=0;a<widthB;a++){
+ delete [] sumMatchB[a];
+ delete [] sumMismatchB[a];
+ };
+ delete [] sumMatchB;
+ delete [] sumMismatchB;
+ delete comboListA;
+ delete comboListB;
+ *combo = bestCombo;
+
+ //cout << "Done! " << bestCombo.corr << " " << SSIterations << endl;
+
+};
+
+int CHardklor::calcDepth(int start, int max, int depth, int count) {
+ int i,j,n;
+ int total=0;
+ int sz=(int)sa.predPep->size();
+
+ if(max==1) {
+ for(i=start;i<sz;i++) total+=sa.predPep->at(i).VariantListSize();
+ return total;
+ }
+
+ for(i=start;i<sz-max+depth;i++) {
+
+ if(depth==max) {
+ return sa.predPep->at(i).VariantListSize()*count;
+ } else {
+ for(j=i+1;j<sz;j++){
+ n = calcDepth(j,max,depth+1,sa.predPep->at(i).VariantListSize()*count);
+ total+=n;
+ }
+ }
+ if(depth>1) return total;
+ }
+
+ return total;
+
+}
+
+void CHardklor::ResultToMem(SSObject& obj, CPeriodicTable* PT){
+ int j,k;
+ int pepID;
+ int varID;
+ int sz=(int)obj.pepVar->size();
+ char mods[32];
+ char tmp[16];
+
+ //Each peptide in a window is designated with a P
+ for(k=0;k<sz;k++) {
+
+ pepID=obj.pepVar->at(k).iLower;
+ varID=obj.pepVar->at(k).iUpper;
+
+ hkm.monoMass = sa.predPep->at(pepID).GetVariant(varID).GetMonoMass();
+ hkm.charge = sa.predPep->at(pepID).GetVariant(varID).GetCharge();
+ if(cs.distArea) hkm.intensity = sa.predPep->at(pepID).GetIntensity()*(float)sa.predPep->at(pepID).GetVariant(varID).GetArea();
+ else hkm.intensity = sa.predPep->at(pepID).GetIntensity();
+ hkm.scan = currentScanNumber;
+ hkm.mz = sa.predPep->at(pepID).GetMZ();
+ hkm.corr = obj.corr;
+
+ //Add mods
+ strcpy(mods,"");
+ for(j=0;j<sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().sizeAtom();j++){
+ strcat(mods,PT->at(sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atAtom(j).iLower).symbol);
+ sprintf(tmp,"%d",sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atAtom(j).iUpper);
+ strcat(mods,tmp);
+ }
+ strcat(mods,"_");
+ for(j=0;j<sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().sizeEnrich();j++){
+ sprintf(tmp,"%.2lf",sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).ape);
+ strcat(mods,tmp);
+ strcat(mods,PT->at(sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).atomNum).symbol);
+ sprintf(tmp,"%d",sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).isotope);
+ strcat(mods,tmp);
+ }
+ strcpy(hkm.mods,mods);
+ vResults.push_back(hkm);
+
+ }
+
+}
+
+void CHardklor::WritePepLine(SSObject& obj, CPeriodicTable* PT, fstream& fptr, int format){
+ int j,k;
+ int pepID;
+ int varID;
+ int sz=(int)obj.pepVar->size();
+
+ //Each peptide in a window is designated with a P
+ for(k=0;k<sz;k++) {
+
+ pepID=obj.pepVar->at(k).iLower;
+ varID=obj.pepVar->at(k).iUpper;
+
+ if(format==0){
+ fptr << "P\t" << sa.predPep->at(pepID).GetVariant(varID).GetMonoMass();
+ fptr << "\t" << sa.predPep->at(pepID).GetVariant(varID).GetCharge();
+ if(cs.distArea) fptr << "\t" << sa.predPep->at(pepID).GetIntensity()*sa.predPep->at(pepID).GetVariant(varID).GetArea();
+ else fptr << "\t" << sa.predPep->at(pepID).GetIntensity();
+ fptr << "\t" << sa.predPep->at(pepID).GetMZ();
+ fptr << "\t" << sa.peaks.at(0).mz << "-" << sa.peaks.at(sa.peaks.size()-1).mz;
+ fptr << "\t" << sa.S2NCutoff;
+
+ //Add mods
+ fptr << "\t";
+ for(j=0;j<sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().sizeAtom();j++){
+ fptr << PT->at(sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atAtom(j).iLower).symbol;
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atAtom(j).iUpper;
+ }
+ fptr << "_";
+ for(j=0;j<sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().sizeEnrich();j++){
+ fptr << setiosflags(ios::fixed) << setprecision(2);
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).ape;
+ fptr << setiosflags(ios::fixed) << setprecision(4);
+ fptr << PT->at(sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).atomNum).symbol;
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).isotope;
+ fptr << "_";
+ }
+
+ fptr << "\t" << obj.corr;
+ fptr << endl;
+
+ } else if(format==1) {
+ fptr << "<Peak Mass=\"" << sa.predPep->at(pepID).GetVariant(varID).GetMonoMass() << "\" ";
+ fptr << "ChargeState=\"" << sa.predPep->at(pepID).GetVariant(varID).GetCharge() << "\" ";
+ if(cs.distArea) fptr << "Area=\"" << sa.predPep->at(pepID).GetIntensity()*sa.predPep->at(pepID).GetVariant(varID).GetArea() << "\" ";
+ else fptr << "Intensity=\"" << sa.predPep->at(pepID).GetIntensity() << "\" ";
+ fptr << "MZ=\"" << sa.predPep->at(pepID).GetMZ() << "\" ";
+ fptr << "Window=\"" << sa.peaks.at(0).mz << "-" << sa.peaks.at(sa.peaks.size()-1).mz << "\" ";
+ fptr << "SN=\"" << sa.S2NCutoff << "\" ";
+
+ //Add mods
+ fptr << "Mod=\"";
+ for(j=0;j<sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().sizeAtom();j++){
+ fptr << PT->at(sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atAtom(j).iLower).symbol;
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atAtom(j).iUpper;
+ }
+ fptr << "_";
+ for(j=0;j<sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().sizeEnrich();j++){
+ fptr << setiosflags(ios::fixed) << setprecision(2);
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).ape;
+ fptr << setiosflags(ios::fixed) << setprecision(4);
+ fptr << PT->at(sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).atomNum).symbol;
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).isotope;
+ fptr << "_";
+ }
+ fptr << "\" ";
+
+ fptr << "Score=\"" << obj.corr << "\"/>" << endl;
+ } else if(format==2){
+ fptr << (sa.predPep->at(pepID).GetVariant(varID).GetMonoMass()+sa.predPep->at(pepID).GetVariant(varID).GetCharge()*1.007276466)/sa.predPep->at(pepID).GetVariant(varID).GetCharge();
+ if(cs.distArea) fptr << "\t" << sa.predPep->at(pepID).GetIntensity()*sa.predPep->at(pepID).GetVariant(varID).GetArea();
+ else fptr << "\t" << sa.predPep->at(pepID).GetIntensity();
+ fptr << "\t" << sa.predPep->at(pepID).GetVariant(varID).GetCharge();
+ fptr << endl;
+ }
+ }
+}
+
+void CHardklor::WriteScanLine(Spectrum& s, fstream& fptr, int format){
+ //int i;
+
+ if(format==0) {
+ fptr << "S\t" << s.getScanNumber() << "\t" << s.getRTime() << "\t" << cs.inFile;
+
+ //For Alex Panchaud, special ZS case
+ if(s.getFileType()==ZS || s.getFileType()==UZS){
+ if(s.sizeZ()>0){
+ for(int i=0;i<s.sizeZ();i++) fptr << "\t" << s.atZ(i).z << "," << s.atZ(i).mh;
+ }
+ } else {
+
+ //otherwise output precursor info if it exists
+ if(s.sizeZ()==1){
+ fptr << "\t" << s.atZ(0).mh-1.00727649 << "\t" << s.atZ(0).z << "\t" << s.getMZ();
+ } else if(s.sizeZ()>1){
+ fptr << "\t0.0\t0\t" << s.getMZ();
+ } else {
+ fptr << "\t0.0\t0\t0.0";
+ }
+ }
+ fptr << endl;
+ } else if(format==1){
+ fptr << "<Spectrum Scan=\"" << s.getScanNumber() << "\" ";
+ fptr << "RetentionTime=\"" << s.getRTime() << "\" ";
+ fptr << "Filename=\"" << cs.inFile << "\"";
+ if(s.getFileType()==ZS || s.getFileType()==UZS){
+ if(s.sizeZ()>0){
+ for(int i=0;i<s.sizeZ();i++) fptr << " PeptideSignal" << i << "=\"" << s.atZ(i).z << "," << s.atZ(i).mh << "\"";
+ }
+ } else {
+ if(s.sizeZ()==1){
+ fptr << " AccMonoMass=\"" << s.atZ(0).mh-1.00727649 << "\" PrecursorCharge=\"" << s.atZ(0).z << "\" PrecursorMZ=\"" << s.getMZ() << "\"";
+ } else if(s.sizeZ()>1){
+ fptr << " AccMonoMass=\"0.0\" PrecursorCharge=\"0\" PrecursorMZ=\"" << s.getMZ() << "\"";
+ } else {
+ fptr << " AccMonoMass=\"0.0\" PrecursorCharge=\"0\" PrecursorMZ=\"0.0\"";
+ }
+ }
+ fptr << ">" << endl;
+ } else if(format==2) {
+ fptr << "Scan = " << s.getScanNumber();
+ fptr << endl;
+ }
+}
+
+void CHardklor::WriteParams(fstream& fptr, int format){
+
+}
+
+int CHardklor::Size(){
+ return vResults.size();
+}
+
+void CHardklor::SetResultsToMemory(bool b){
+ bMem=b;
+}
+
+hkMem& CHardklor::operator[](const int& index){
+ return vResults[index];
+}
+
diff --git a/src/app/hardklor/CHardklor.h b/src/app/hardklor/CHardklor.h
new file mode 100644
index 0000000..fdff775
--- /dev/null
+++ b/src/app/hardklor/CHardklor.h
@@ -0,0 +1,153 @@
+#ifndef _CHARDKLOR_H
+#define _CHARDKLOR_H
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "HardklorTypes.h"
+//#include "CHardklorProtein.h"
+#include "CHardklorSetting.h"
+#include "CHardklorVariant.h"
+#include "CPeriodicTable.h"
+#include "CSplitSpectrum.h"
+#include "MSObject.h"
+#include "MSReader.h"
+#include "Spectrum.h"
+#include "CNoiseReduction.h"
+//#include "CHardklorFileReader.h"
+
+#ifdef _MSC_VER
+
+#else
+#include <sys/time.h>
+#endif
+
+using namespace std;
+
+#define PminusE 1.00672791
+
+class SSObject {
+public:
+ //Data members
+ vector<sInt> *pepVar;
+ double corr;
+
+ //Constructors & Destructors
+ SSObject();
+ SSObject(const SSObject& c);
+ ~SSObject();
+
+ //Overloaded operators
+ SSObject& operator=(const SSObject& c);
+
+ //Functions
+ void addVar(int a, int b);
+ void clear();
+
+};
+
+class CHardklor{
+
+ public:
+ //Constructors & Destructors:
+ CHardklor();
+ CHardklor(CAveragine *a, CMercury8 *m);
+ ~CHardklor();
+
+ //Operators
+ hkMem& operator[](const int& index);
+
+ //Methods:
+ void Echo(bool b);
+ int GoHardklor(CHardklorSetting sett, Spectrum* s=NULL);
+ void SetAveragine(CAveragine *a);
+ void SetMercury(CMercury8 *m);
+ void SetResultsToMemory(bool b);
+ int Size();
+
+ protected:
+
+ private:
+ //Methods:
+ void Analyze(Spectrum* s=NULL);
+ bool AnalyzePeaks(CSpecAnalyze& sa);
+ int compareData(const void*, const void*);
+ double LinReg(float *match, float *mismatch);
+ void ResultToMem(SSObject& obj, CPeriodicTable* PT);
+ void WriteParams(fstream& fptr, int format=1);
+ void WritePepLine(SSObject& obj, CPeriodicTable* PT, fstream& fptr, int format=0);
+ void WriteScanLine(Spectrum& s, fstream& fptr, int format=0);
+
+ //Finished analysis algorithms
+ void BasicMethod(float *match, float *mismatch,SSObject* combo, int depth, int maxDepth, int start);
+ void DynamicMethod(float *match, float *mismatch,SSObject* combo, int depth, int maxDepth, int start, double corr);
+ void DynamicSemiCompleteMethod(float *match, float *mismatch,SSObject* combo, int depth, int maxDepth, int start, double corr);
+ void FewestPeptidesMethod(SSObject *combo, int maxDepth);
+ void FewestPeptidesChoiceMethod(SSObject *combo, int maxDepth);
+ void SemiCompleteMethod(float *match, float *mismatch,SSObject* combo, int depth, int maxDepth, int start);
+ void SemiCompleteFastMethod(float *match, float *mismatch,SSObject* combo, int depth, int maxDepth, int start);
+ void SemiSubtractiveMethod(SSObject *combo, int maxDepth);
+ void FastFewestPeptidesMethod(SSObject *combo, int maxDepth);
+ void FastFewestPeptidesChoiceMethod(SSObject *combo, int maxDepth);
+
+ //Analysis algorithm support methods
+ int calcDepth(int start, int max, int depth=1, int count=1);
+
+ //Data Members:
+ CSpecAnalyze sa;
+ CHardklorSetting cs;
+ CAveragine *averagine;
+ CMercury8 *mercury;
+ CPeriodicTable *PT;
+ hkMem hkm;
+ bool bEcho;
+ bool bMem;
+ int currentScanNumber;
+ fstream fptr; //TODO: Get rid of this and use FILE* instead.
+
+ //Vector for holding peptide list of distribution
+ vector<CHardklorVariant> pepVariants;
+
+ //Vector for holding results in memory should that be needed
+ vector<hkMem> vResults;
+
+ //Temporary Data Members:
+ char bestCh[200];
+ double BestCorr;
+ int CorrMatches;
+ int ExtraPre;
+ int ExtraObs;
+
+ //For accurate timing of Hardklor
+ #ifdef _MSC_VER
+ __int64 startTime;
+ __int64 stopTime;
+ __int64 loadTime;
+ __int64 splitTime;
+ __int64 analysisTime;
+ __int64 timerFrequency;
+ __int64 tmpTime1;
+ __int64 tmpTime2;
+ #define getExactTime(a) QueryPerformanceCounter((LARGE_INTEGER*)&a)
+ #define getTimerFrequency(a) QueryPerformanceFrequency((LARGE_INTEGER*)&a)
+ #define toMicroSec(a) (a)
+ #define timeToSec(a,b) (a/b)
+ #else
+ timeval startTime;
+ timeval stopTime;
+ uint64_t loadTime;
+ uint64_t splitTime;
+ uint64_t analysisTime;
+ uint64_t tmpTime1;
+ uint64_t tmpTime2;
+ int timerFrequency;
+ #define getExactTime(a) gettimeofday(&a,NULL)
+ #define toMicroSec(a) a.tv_sec*1000000+a.tv_usec
+ #define getTimerFrequency(a) (a)=1
+ #define timeToSec(a,b) (a/1000000)
+ #endif
+
+};
+
+#endif
diff --git a/src/app/hardklor/CHardklor2.cpp b/src/app/hardklor/CHardklor2.cpp
new file mode 100644
index 0000000..c817bd0
--- /dev/null
+++ b/src/app/hardklor/CHardklor2.cpp
@@ -0,0 +1,1484 @@
+#include "CHardklor2.h"
+
+CHardklor2::CHardklor2(CAveragine *a, CMercury8 *m, CModelLibrary *lib){
+ averagine=a;
+ mercury=m;
+ models=lib;
+ bEcho=true;
+ bMem=false;
+ PT=NULL;
+}
+
+CHardklor2::~CHardklor2(){
+ averagine=NULL;
+ mercury=NULL;
+ models=NULL;
+ if(PT!=NULL) {
+ PT=NULL;
+ }
+}
+
+hkMem& CHardklor2::operator[](const int& index){
+ return vResults[index];
+}
+
+void CHardklor2::Echo(bool b){
+ bEcho=b;
+}
+
+int CHardklor2::GoHardklor(CHardklorSetting sett, Spectrum* s){
+
+ //Member variables
+ MSReader r;
+ Spectrum curSpec,c;
+ vector<int> v;
+ FILE* fout;
+ int TotalScans;
+ int manyPep, zeroPep, lowSigPep;
+ int iPercent;
+ int minutes, seconds;
+ int i;
+ vector<pepHit> vPeps;
+
+ //initialize variables
+ cs=sett;
+ loadTime=0;
+ analysisTime=0;
+ TotalScans=0;
+ manyPep=0;
+ zeroPep=0;
+ lowSigPep=0;
+ iPercent=0;
+ getTimerFrequency(timerFrequency);
+
+ vResults.clear();
+
+ //For noise reduction
+ CNoiseReduction nr(&r,cs);
+
+ //Signature
+ //if(bEcho) cout << "\n\nHardklor, v2.06, Mike Hoopmann, Mike MacCoss\nCopyright 2007-2012\nUniversity of Washington\n" << endl;
+
+ //Set the periodic table
+ if(PT==NULL) PT=averagine->getPT();
+
+ //Ouput file info to user
+ if(bEcho){
+ if(s==NULL) cout << "Reading from file: " << cs.inFile << endl;
+ if(!bMem) cout << "Writing to file: " << cs.outFile << endl;
+ }
+ if(cs.fileFormat==dunno) {
+ cout << "Unknown file format or bad extension." << endl;
+ return -1;
+ }
+
+ if(!bMem) fout=fopen(cs.outFile,"wt");
+
+ //read a spectrum
+ getExactTime(startTime);
+
+ //Read in the initial spectrum
+ r.setFilter(cs.mzXMLFilter);
+ r.setRawFilter(cs.rawFilter);
+ if(s!=NULL){
+ curSpec=*s;
+ } else {
+ if(cs.boxcar==0){
+ if((cs.scan.iLower>0) && (cs.scan.iLower==cs.scan.iUpper)) r.readFile(&cs.inFile[0],curSpec,cs.scan.iLower);
+ else if(cs.scan.iLower>0) r.readFile(&cs.inFile[0],curSpec,cs.scan.iLower);
+ else r.readFile(&cs.inFile[0],curSpec);
+ } else {
+ if(cs.boxcarFilter==0){
+ if(!nr.DeNoiseD(curSpec)) curSpec.setScanNumber(0);
+ //if(!nr.DeNoise(curSpec)) curSpec.setScanNumber(0);
+ //do something about this...
+
+ } else {
+ if(!nr.DeNoiseC(curSpec)) curSpec.setScanNumber(0);
+ }
+ }
+ }
+
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ loadTime+=(tmpTime1-tmpTime2);
+
+ //Check that file was read
+ if(curSpec.getScanNumber()==0) {
+ if(s!=NULL) {
+ cout << "Spectrum is invalid." << endl;
+ return -2;
+ }
+ if(cs.scan.iLower>0) cout << cs.inFile << " is invalid, or requested scan number is of incorrect format." << endl;
+ else cout << cs.inFile << " is invalid, or contains no spectrum." << endl;
+ return -2;
+ }
+
+ //Write scan information to output file.
+ if(!bMem){
+ if(cs.reducedOutput) WriteScanLine(curSpec,fout,2);
+ else if(cs.xml) WriteScanLine(curSpec,fout,1);
+ else WriteScanLine(curSpec,fout,0);
+ } else {
+ currentScanNumber = curSpec.getScanNumber();
+ }
+
+ //Output progress indicator
+ if(bEcho) cout << iPercent;
+
+ //While there is still data to read in the file.
+ while(true){
+
+ getExactTime(startTime);
+ TotalScans++;
+
+ //Smooth if requested
+ if(cs.smooth>0) SG_Smooth(curSpec,cs.smooth,4);
+
+ //Centroid if needed; notice that this copy wastes a bit of time.
+ //TODO: make this more efficient
+ if(cs.boxcar==0 && !cs.centroid) Centroid(curSpec,c);
+ else c=curSpec;
+
+ //There is a bug when using noise reduction that results in out of order m/z values
+ //TODO: fix noise reduction so sorting isn't needed
+ if(c.size()>0) c.sortMZ();
+
+ //Analyze
+ QuickHardklor(c,vPeps);
+
+ //export results
+ for(i=0;i<(int)vPeps.size();i++){
+ if(!bMem){
+ if(cs.reducedOutput) WritePepLine(vPeps[i],c,fout,2);
+ else if(cs.xml) WritePepLine(vPeps[i],c,fout,1);
+ else WritePepLine(vPeps[i],c,fout,0);
+ } else {
+ ResultToMem(vPeps[i],c);
+ }
+ }
+
+ //Update progress
+ if(bEcho){
+ if (r.getPercent() > iPercent){
+ if(iPercent<10) cout << "\b";
+ else cout << "\b\b";
+ cout.flush();
+ iPercent=r.getPercent();
+ cout << iPercent;
+ cout.flush();
+ }
+ }
+
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ analysisTime+=tmpTime1-tmpTime2;
+
+ if(s!=NULL) break;
+
+ //Check if any user limits were made and met
+ if( (cs.scan.iUpper == cs.scan.iLower) && (cs.scan.iLower != 0) ){
+ break;
+ } else if( (cs.scan.iLower < cs.scan.iUpper) && (curSpec.getScanNumber() >= cs.scan.iUpper) ){
+ break;
+ }
+
+ //Read next spectrum from file.
+ getExactTime(startTime);
+ if(cs.boxcar==0) {
+ r.readFile(NULL,curSpec);
+ } else {
+ if(cs.boxcarFilter==0){
+ //possible to not filter?
+ nr.DeNoiseD(curSpec);
+ } else {
+ //case 5: nr.DeNoise(curSpec); break; //this is for filtering without boxcar
+ nr.DeNoiseC(curSpec);
+ }
+ }
+
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ loadTime+=(tmpTime1-tmpTime2);
+
+ if(curSpec.getScanNumber()!=0){
+ //Write scan information to output file.
+ if(cs.reducedOutput){
+ WriteScanLine(curSpec,fout,2);
+ } else if(cs.xml) {
+ fprintf(fout,"</Spectrum>\n");
+ WriteScanLine(curSpec,fout,1);
+ } else {
+ WriteScanLine(curSpec,fout,0);
+ }
+ } else {
+ break;
+ }
+ }
+
+ if(!bMem) fclose(fout);
+
+ if(bEcho) {
+ cout << "\n" << endl;
+ cout << " Total number of scans analyzed: " << TotalScans << endl;
+
+ i=(int)timeToSec(loadTime,timerFrequency);
+ minutes = (int)(i/60);
+ seconds = i - (60*minutes);
+ cout << "\nFile access time: " << minutes << " minutes, " << seconds << " seconds." << endl;
+ i=(int)timeToSec(analysisTime,timerFrequency);
+ minutes = (int)(i/60);
+ seconds = i - (60*minutes);
+ cout << "Analysis Time: " << minutes << " minutes, " << seconds << " seconds." << endl;
+
+ if (minutes==0 && seconds==0){
+ cout << "IMPOSSIBLE!!!" << endl;
+ } else if(minutes <=2){
+ cout << "HOLY FRIJOLE!!" << endl;
+ } else if(minutes<=5) {
+ cout << "Like lightning!" << endl;
+ } else if(minutes<=10){
+ cout << "That's pretty damn fast!" << endl;
+ } else if(minutes<=20){
+ cout << "Monkeys calculate faster than that!" << endl;
+ } else if(minutes<=30){
+ cout << "You should have taken a lunch break." << endl;
+ } else if(minutes<=40){
+ cout << "Oi! Too freakin' slow!!" << endl;
+ } else {
+ cout << "You might be able to eek out some better performance by adjusting your parameters." << endl;
+ }
+ }
+ return 1;
+
+}
+
+int CHardklor2::BinarySearch(Spectrum& s, double mz, bool floor){
+
+ int mid=s.size()/2;
+ int upper=s.size();
+ int lower=0;
+
+ if(mz>=s[s.size()-1].mz) return s.size()-1;
+ if(mz<=s[0].mz) return 0;
+
+ while(s[mid].mz!=mz){
+ if(lower>=upper) break;
+ if(s[mid].mz>mz){
+ upper=mid-1;
+ mid=(lower+upper)/2;
+ } else {
+ lower=mid+1;
+ mid=(lower+upper)/2;
+ }
+ }
+
+ if(floor && s[mid].mz>mz && mid>0) return mid-1;
+ else if(!floor && s[mid].mz<mz && mid<s.size()) return mid+1;
+ else return mid;
+
+}
+
+//Calculates the resolution (FWHM) of a peak
+double CHardklor2::CalcFWHM(double mz,double res,int iType){
+ double deltaM;
+ switch(iType){
+ case 0: //Orbitrap
+ deltaM = mz * sqrt(mz) / (20*res); //sqare root of 400
+ break;
+ case 1: //TOF
+ deltaM = mz / res;
+ break;
+ case 2: //QIT
+ deltaM = res / 5000.0;
+ break;
+ case 3: //FTICR
+ default:
+ deltaM = mz * mz / (400*res);
+ break;
+ }
+ return deltaM;
+}
+
+//First derivative method, returns base peak intensity of the set
+void CHardklor2::Centroid(Spectrum& s, Spectrum& out){
+ int i,j;
+ float maxIntensity;
+ int bestPeak;
+ bool bLastPos;
+
+ int nextBest;
+ double FWHM;
+ Peak_T centroid;
+
+ out.clear();
+
+ bLastPos=false;
+ for(i=0;i<s.size()-1;i++){
+
+ if(s[i].intensity<s[i+1].intensity) {
+ bLastPos=true;
+ continue;
+ } else {
+ if(bLastPos){
+ bLastPos=false;
+
+ //find max and add peak
+ maxIntensity=0;
+ for(j=i;j<i+1;j++){
+ if (s[j].intensity>maxIntensity){
+ maxIntensity=s[j].intensity;
+ bestPeak = j;
+ }
+ }
+
+ //Best estimate of Gaussian centroid
+ //Get 2nd highest point of peak
+ if(bestPeak==s.size()){
+ nextBest=bestPeak-1;
+ } else if(s[bestPeak-1].intensity > s[bestPeak+1].intensity){
+ nextBest=bestPeak-1;
+ } else {
+ nextBest=bestPeak+1;
+ }
+
+ //Get FWHM
+ FWHM = CalcFWHM(s[bestPeak].mz,cs.res400,cs.msType);
+
+ //Calc centroid MZ (in three lines for easy reading)
+ centroid.mz = (FWHM*FWHM*log(s[bestPeak].intensity/s[nextBest].intensity));
+ centroid.mz /= (GAUSSCONST*(s[bestPeak].mz-s[nextBest].mz));
+ centroid.mz += ((s[bestPeak].mz+s[nextBest].mz)/2);
+
+ //Calc centroid intensity
+ centroid.intensity=(float)(s[bestPeak].intensity/exp(-pow((s[bestPeak].mz-centroid.mz)/FWHM,2)*GAUSSCONST));
+
+ //some peaks are funny shaped and have bad gaussian fit.
+ //if error is more than 10%, keep existing intensity
+ if( fabs((s[bestPeak].intensity - centroid.intensity) / centroid.intensity * 100) > 10 ||
+ //not a good check for infinity
+ centroid.intensity>999999999999.9 ||
+ centroid.intensity < 0 ) {
+ centroid.intensity=s[bestPeak].intensity;
+ }
+
+ //Hack until I put in mass ranges
+ if(centroid.mz<0 || centroid.mz>2000) {
+ //do nothing if invalid mz
+ } else {
+ out.add(centroid);
+ }
+
+ }
+
+ }
+ }
+
+}
+
+//returns whether or not the peak is still valid. true if peak still exists, false if peak was solved already.
+bool CHardklor2::CheckForPeak(vector<Result>& vMR, Spectrum& s, int index){
+ double dif=100.0;
+ double massDif;
+ bool match=false;
+
+ int mid=s.size()/2;
+ int upper=s.size();
+ int lower=0;
+
+ double FWHM=CalcFWHM(vMR[index].mass,cs.res400,cs.msType);
+
+ if(vMR[index].mass>=s[s.size()-1].mz) {
+ mid=s.size()-1;
+ } else if(vMR[index].mass<=s[0].mz) {
+ mid=0;
+ } else {
+
+ while(s[mid].mz!=vMR[index].mass){
+ if(lower>=upper) break;
+ if(s[mid].mz>vMR[index].mass){
+ upper=mid-1;
+ mid=(lower+upper)/2;
+ } else {
+ lower=mid+1;
+ mid=(lower+upper)/2;
+ }
+ }
+ }
+
+ dif=fabs(s[mid].mz-vMR[index].mass);
+ if(mid>0){
+ massDif=fabs(s[mid-1].mz-vMR[index].mass);
+ if(massDif<dif) {
+ dif=massDif;
+ mid--;
+ }
+ }
+ if(mid<s.size()-1){
+ massDif=fabs(s[mid+1].mz-vMR[index].mass);
+ if(massDif<dif) {
+ dif=massDif;
+ mid++;
+ }
+ }
+
+ if(dif<FWHM){
+ if(mask[mid].intensity>1.0) return false;
+ else return true;
+ }
+ return false;
+
+}
+
+int CHardklor2::CompareBPI(const void *p1, const void *p2){
+ const pepHit d1 = *(pepHit *)p1;
+ const pepHit d2 = *(pepHit *)p2;
+ if(d1.basePeakIndex<d2.basePeakIndex) return -1;
+ else if(d1.basePeakIndex>d2.basePeakIndex) return 1;
+ else return 0;
+}
+
+double CHardklor2::LinReg(vector<float>& mer, vector<float>& obs){
+
+ int i,sz;
+ double sxx=0,syy=0,sxy=0;
+
+ //Cosine angle correlation
+ sxy=0;
+ sxx=0;
+ syy=0;
+ sz=(int)mer.size();
+ for(i=0;i<sz;i++){
+ sxy += (mer[i]*obs[i]);
+ sxx += (mer[i]*mer[i]);
+ syy += (obs[i]*obs[i]);
+ }
+
+ if(sxx>0 && syy>0 && sxy>0) return sxy/sqrt(sxx*syy);
+ else return 0;
+
+}
+
+bool CHardklor2::MatchSubSpectrum(Spectrum& s, int peakIndex, pepHit& pep){
+
+ int i,k,n;
+ unsigned int varCount;
+ unsigned int v;
+ float max=s[peakIndex].intensity;
+ int maxMercuryIndex[3];
+ vector<int> charges;
+ double dif;
+ vector<float> obs;
+ vector<float> mer;
+ vector<int> vMatchIndex;
+ vector<float> vMatchPeak;
+ vector<Result> vMR;
+ Result r;
+ double corr;
+ double da;
+
+ //keep track of best hits
+ double bestCorr;
+ double bestDA;
+ int bestCharge;
+ double bestMass;
+ vector<int> bestMatchIndex;
+ vector<float> bestMatchPeak;
+ int matchCount;
+ int bestMatchCount;
+ int thisMaxIndex=0;
+ int bestVariant;
+
+ mercuryModel* model=NULL;
+
+ double deltaM = CalcFWHM(s[peakIndex].mz,cs.res400,cs.msType);
+ QuickCharge(s,peakIndex,charges);
+
+ bestCorr=0.0;
+ bestMatchCount=0;
+
+ //Mark number of variants to analyze
+ if(cs.noBase) varCount=cs.variant->size();
+ else varCount=cs.variant->size()+1;
+
+ //iterate through all charge states
+ for(i=0;i<(int)charges.size();i++){
+
+ for(v=0;v<varCount;v++){
+
+ //get model from library
+ dif=0;
+ model=models->getModel(charges[i],v,s[peakIndex].mz);
+ for(k=0; k<model->size; k++) {
+ if(model->peaks[k].intensity>dif){
+ dif = model->peaks[k].intensity;
+ maxMercuryIndex[0]=k;
+ }
+ }
+ if(k==0) maxMercuryIndex[1]=-1;
+ else maxMercuryIndex[1]=maxMercuryIndex[0]-1; //allow right shift
+ maxMercuryIndex[2]=maxMercuryIndex[0]+1; //allow left shift
+
+ //Apply shift and find mz boundaries
+ n=0;
+ while(n<3){
+
+ if(maxMercuryIndex[n]<0) {
+ n++;
+ continue;
+ }
+
+ //Align the mercury distribution (MD) to the observed peak. The MD can shift in
+ //either direction for one peak to adjust for system noise. The width of the MD
+ //determines the boundaries for correlation to the observed data.
+ double lower=5000.0;
+ double upper=0.0;
+ double shft = s[peakIndex].mz - model->peaks[maxMercuryIndex[n]].mz;
+
+ vMR.clear();
+ for(k=0; k<model->size; k++) {
+ r.data=model->peaks[k].intensity;
+ r.mass=model->peaks[k].mz+shft;
+ vMR.push_back(r);
+ if(model->peaks[k].intensity>99.999) thisMaxIndex=vMR.size()-1;
+
+ if(r.mass<lower) lower=r.mass;
+ if(r.mass>upper) upper=r.mass;
+ }
+ da=model->area;
+
+ //Add a little buffer to the bounds
+ lower-=0.1;
+ upper+=0.1;
+
+ //Match predictions to the observed peaks and record them in the proper array.
+ corr=PeakMatcherB(vMR,s,lower,upper,deltaM/2,peakIndex,matchCount,vMatchIndex,vMatchPeak);
+ //cout << "\tMSS: " << s[peakIndex].mz << " " << s[peakIndex].intensity << "\t" << charges[i] << "\t" << matchCount << "\t" << corr << endl;
+
+ if(corr>bestCorr || (corr>cs.corr && corr+0.025*(matchCount-bestMatchCount)>bestCorr) ){
+ bestMatchIndex=vMatchIndex;
+ bestMatchPeak=vMatchPeak;
+ bestMatchCount=matchCount;
+ bestCorr=corr;
+ bestMass=model->zeroMass+shft*charges[i];
+ bestCharge=charges[i];
+ bestDA=da;
+ bestVariant=v;
+ }
+
+ n++;
+
+ }//while
+
+ }//for v (variant)
+
+ }//for i (charge)
+ model=NULL;
+
+ //if above threshold, erase peaks.
+ if(bestCorr>cs.corr){
+
+ pep.area=(float)bestDA;
+ strcpy(pep.averagine,"");
+ pep.basePeakIndex=0;
+ pep.charge=bestCharge;
+ pep.corr=bestCorr;
+ pep.highMZ=0;
+ pep.lowMZ=0;
+ pep.massShift=0;
+ pep.monoMass=bestMass;
+ pep.intensity=s[peakIndex].intensity;
+ pep.variantIndex=bestVariant;
+
+ //mark which peaks contributed to this analysis
+ for(k=0;k<(int)bestMatchIndex.size();k++){
+ if(bestMatchPeak[k]*max/s[bestMatchIndex[k]].intensity>0.5) s[bestMatchIndex[k]].intensity=-s[bestMatchIndex[k]].intensity;
+ else s[bestMatchIndex[k]].intensity-=bestMatchPeak[k]*max;
+ }
+
+ return true;
+ }
+
+ return false;
+
+}
+
+double CHardklor2::PeakMatcher(vector<Result>& vMR, Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, int& indexOverlap, vector<int>& vMatchIndex, vector<float>& vMatchIntensity){
+
+ vMatchIndex.clear();
+ vMatchIntensity.clear();
+
+ vector<float> obs;
+ vector<float> mer;
+
+ bool match;
+ bool bMax=false;
+ double corr=0.0;
+ double dif;
+ double massDif;
+
+ matchCount=0;
+ indexOverlap=-1;
+
+ int j,k;
+ for(k=0;k<(int)vMR.size();k++) {
+ if(vMR[k].data>99.9) bMax=true;
+
+ match=false;
+ dif=deltaM;
+
+ //look left
+ j=matchIndex;
+ while(j>-1 && s[j].mz>=lower){
+ massDif=s[j].mz-vMR[k].mass;
+ if(massDif<-deltaM) break;
+ if(fabs(massDif)<dif){
+ dif=fabs(massDif);
+ match=true;
+ matchIndex=j;
+ }
+ j--;
+ }
+
+ //look right
+ j=matchIndex+1;
+ while(j<s.size() && s[j].mz<=upper){
+ massDif=s[j].mz-vMR[k].mass;
+ if(massDif>deltaM) break;
+ if(fabs(massDif)<dif){
+ dif=fabs(massDif);
+ match=true;
+ matchIndex=j;
+ }
+ j++;
+ }
+
+ if(!match) {
+ //if expected peak is significant (above 50 rel abun) and has no match, match it to 0.
+ if(vMR[k].data>50.0) {
+ //cout << "xM: " << vMR[k].mass << "\t0" << endl;
+ mer.push_back((float)vMR[k].data);
+ obs.push_back(0.0f);
+ if(bMax) break;
+ }
+
+ } else {
+ mer.push_back((float)vMR[k].data);
+ //cout << "xM: " << vMR[k].mass << "\t" << s[matchIndex].mz << endl;
+ if(mask[matchIndex].intensity>1.0 && vMR[k].data>50) {
+ if(indexOverlap<0) indexOverlap=matchIndex;
+ }
+ if(s[matchIndex].intensity<1.0) {
+ obs.push_back(0.0f);
+ } else {
+ matchCount++;
+ obs.push_back(s[matchIndex].intensity);
+ }
+ vMatchIndex.push_back(matchIndex);
+ vMatchIntensity.push_back((float)vMR[k].data/100.0f);
+ }
+ }
+
+ if(matchCount<2) corr=0.0;
+ else corr=LinReg(mer,obs);
+
+ //for(j=0;j<mer.size();j++){
+ // cout << "M:" << mer[j] << "\t" << "O:" << obs[j] << endl;
+ //}
+ //cout << "Corr: " << corr << "(" << matchCount << ")" << endl;
+
+ //remove last matched peaks (possibly overlap with other peaks) but only if they are of low abundance.
+ int tmpCount=matchCount;
+ while(corr<0.90 && matchCount>2 && mer[mer.size()-1]<50.0){
+ mer.pop_back();
+ obs.pop_back();
+ matchCount--;
+ double corr2=LinReg(mer,obs);
+ //cout << "Old corr: " << corr << "(" << matchCount+1 << ")" << " New corr: " << corr2 << endl;
+ if(corr2>corr) {
+ corr=corr2;
+ tmpCount=matchCount;
+ }
+ }
+ matchCount=tmpCount;
+
+ return corr;
+}
+
+double CHardklor2::PeakMatcherB(vector<Result>& vMR, Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, vector<int>& vMatchIndex, vector<float>& vMatchIntensity){
+
+ vMatchIndex.clear();
+ vMatchIntensity.clear();
+
+ vector<float> obs;
+ vector<float> mer;
+
+ bool match;
+ bool bMax=false;
+ double corr=0.0;
+ double dif;
+ double massDif;
+
+ matchCount=0;
+
+ int j,k;
+ for(k=0;k<(int)vMR.size();k++) {
+ if(vMR[k].data>99.9) bMax=true;
+ else bMax=false;
+
+ match=false;
+ dif=deltaM;
+
+ //look left
+ j=matchIndex;
+ while(j>-1 && s[j].mz>=lower){
+ massDif=s[j].mz-vMR[k].mass;
+ if(massDif<-deltaM) break;
+ if(fabs(massDif)<dif){
+ dif=fabs(massDif);
+ match=true;
+ matchIndex=j;
+ }
+ j--;
+ }
+
+ //look right
+ j=matchIndex+1;
+ while(j<s.size() && s[j].mz<=upper){
+ massDif=s[j].mz-vMR[k].mass;
+ if(massDif>deltaM) break;
+ if(fabs(massDif)<dif){
+ dif=fabs(massDif);
+ match=true;
+ matchIndex=j;
+ }
+ j++;
+ }
+
+ if(!match) {
+ break;
+ } else {
+ mer.push_back((float)vMR[k].data);
+ if(s[matchIndex].intensity<1.0) {
+ obs.push_back(0.0f);
+ } else {
+ matchCount++;
+ obs.push_back(s[matchIndex].intensity);
+ }
+ vMatchIndex.push_back(matchIndex);
+ vMatchIntensity.push_back((float)vMR[k].data/100.0f);
+ }
+ }
+
+ if(matchCount<2) corr=0.0;
+ else corr=LinReg(mer,obs);
+
+ int tmpCount=matchCount;
+ while(corr<0.90 && matchCount>2){
+ mer.pop_back();
+ obs.pop_back();
+ matchCount--;
+ double corr2=LinReg(mer,obs);
+ if(corr2>corr) {
+ corr=corr2;
+ tmpCount=matchCount;
+ }
+ }
+ matchCount=tmpCount;
+
+ return corr;
+}
+
+void CHardklor2::QuickCharge(Spectrum& s, int index, vector<int>& v){
+
+ int i,j;
+ double dif;
+ double rawCh;
+ double rawChR;
+ int ch;
+ int charge[1000];
+
+ for(i=cs.minCharge;i<=cs.maxCharge;i++) charge[i]=0;
+
+ //check forward
+ for(j=index+1;j<s.size();j++){
+ //if(s[j].intensity<1.0f) continue;
+
+ dif = s[j].mz - s[index].mz;
+ if(dif > 1.1) break;
+
+ rawCh=1/dif;
+ ch = (int)(rawCh+0.5);
+ rawChR=rawCh-(int)rawCh;
+ if(rawChR>0.2 && rawChR<0.8) continue;
+ if(ch<cs.minCharge || ch>cs.maxCharge) continue;
+ charge[ch]=1;
+ }
+ //if no forward charge, exit now.
+ bool bMatch=false;
+ for(i=cs.minCharge;i<=cs.maxCharge;i++){
+ if(charge[i]>0) {
+ bMatch=true;
+ break;
+ }
+ }
+ if(!bMatch) {
+ v.clear();
+ return;
+ }
+
+ //check backward
+ for(j=index-1;j>=0;j--){
+ //if(s[j].intensity<=0.0f) continue;
+
+ dif = s[index].mz - s[j].mz;
+ if(dif > 1.1) break;
+
+ rawCh=1/dif;
+ ch = (int)(rawCh+0.5);
+ rawChR=rawCh-(int)rawCh;
+ if(rawChR>0.2 && rawChR<0.8) continue;
+ if(ch<cs.minCharge || ch>cs.maxCharge) continue;
+ charge[ch]=1;
+ }
+
+ v.clear();
+ for(i=cs.minCharge;i<=cs.maxCharge;i++){
+ if(charge[i]>0) v.push_back(i);
+ }
+
+}
+
+void CHardklor2::QuickHardklor(Spectrum& s, vector<pepHit>& vPeps) {
+
+ //iterators
+ int i,j,k,n,m,x;
+ unsigned int varCount;
+ unsigned int v;
+
+ //tracking spectrum peak intensities
+ float maxHeight=9999999999999.9f;
+ float max=0.0f;
+ float lowPoint=9999999999999.9f;
+
+ //Mercury storage and variables aligning mercury data (including 1 da shifts)
+ mercuryModel* model;
+ vector<Result> vMR;
+ Result r;
+ int maxIndex;
+ int thisMaxIndex;
+ int maxMercuryIndex[3];
+ double da;
+ double lower;
+ double upper;
+ double shft;
+
+ //peak variables
+ vector<int> charges;
+ double deltaM;
+ double dif;
+ double corr;
+ vector<float> obs;
+ vector<float> mer;
+ vector<int> vMatchIndex;
+ vector<float> vMatchPeak;
+ vector<int> vMatchIndex2;
+ vector<float> vMatchPeak2;
+ int matchCount,matchCount2;
+ int indexOverlap;
+ double top3[3];
+
+ //refinement variables
+ bool keepPH;
+ pepHit ph2;
+ //pepHit bestKeepPH;
+ int lowIndex;
+ int highIndex;
+ bool corr2;
+ double corr3;
+
+ //best hit variables
+ double bestCorr;
+ double bestLow;
+ double bestHigh;
+ double bestDA;
+ int bestCharge;
+ double bestMass;
+ vector<int> bestMatchIndex;
+ vector<float> bestMatchPeak;
+ int bestMatchCount;
+ pepHit bestPH;
+ bool bestKeepPH;
+ int bestOverlap;
+ int bestLowIndex;
+ int bestHighIndex;
+ int bestVariant;
+
+ //Results
+ pepHit ph;
+
+ //Spectrum variables
+ Spectrum origSpec=s;
+ Spectrum refSpec=s;
+ Spectrum tmpSpec;
+
+ //create mask
+ mask.clear();
+ for(i=0;i<s.size();i++) mask.add(s[i].mz,0);
+
+ //find lowest intensity;
+ for(i=0;i<s.size();i++){
+ //printf("%.6lf\t%.1f\n",s[i].mz, s[i].intensity);
+ if(s[i].intensity<lowPoint) lowPoint=s[i].intensity;
+ }
+
+ //clear results vector
+ vPeps.clear();
+
+ //Mark number of variants to analyze
+ if(cs.noBase) varCount=cs.variant->size();
+ else varCount=cs.variant->size()+1;
+
+ //start the loop through all peaks
+ while(true){
+
+ //Find most intense peak. Note that sorting is not possible because
+ //peaks change in intensity as they are deconvolved. Also it is advantageous
+ //to keep peaks in m/z order
+ max=0.0f;
+ for(i=0;i<s.size();i++){
+ if(s[i].intensity<maxHeight && s[i].intensity>max){
+ max=s[i].intensity;
+ maxIndex=i;
+ }
+ }
+
+ //stop searching when we reach lowest original point
+ //this prevents overfitting with lots of partial noise peaks
+ if(max<lowPoint) break;
+
+ //Get the FWHM estimate for the peak we are at.
+ deltaM = CalcFWHM(s[maxIndex].mz,cs.res400,cs.msType);
+
+ //Get the charge states. Note that only remaining peaks are used in the estimate.
+ //I'm not sure this is best, but it is simpler and faster
+ QuickCharge(s,maxIndex,charges);
+
+ //Reset our correlation and matchcount scores. Then iterate through each charge state and find best
+ //match to the peaks.
+ bestCorr=0.0;
+ bestMatchCount=0;
+ for(i=0;i<(int)charges.size();i++){
+
+ //cout << s[maxIndex].mz << "\t" << charges[i] << endl;
+
+ //check all variants
+ for(v=0;v<varCount;v++){
+
+ //cout << "Variant: " << v << endl;
+
+ //use model library, align to top 3 peaks
+ dif=0;
+ top3[0]=top3[1]=top3[2]=0;
+ maxMercuryIndex[0]=maxMercuryIndex[1]=maxMercuryIndex[2]=-1;
+ model=models->getModel(charges[i],v,s[maxIndex].mz);
+ for(k=0; k<model->size; k++) {
+ //cout << "i\t" << model->peaks[k].mz << "\t" << model->peaks[k].intensity << endl;
+ //if(model->peaks[k].intensity>dif){
+ if(model->peaks[k].intensity>top3[0]){
+ //dif = model->peaks[k].intensity;
+ top3[2]=top3[1];
+ top3[1]=top3[0];
+ top3[0]=model->peaks[k].intensity;
+ maxMercuryIndex[2]=maxMercuryIndex[1];
+ maxMercuryIndex[1]=maxMercuryIndex[0];
+ maxMercuryIndex[0]=k;
+ } else if(model->peaks[k].intensity>top3[1]) {
+ top3[2]=top3[1];
+ top3[1]=model->peaks[k].intensity;
+ maxMercuryIndex[2]=maxMercuryIndex[1];
+ maxMercuryIndex[1]=k;
+ } else if(model->peaks[k].intensity>top3[2]) {
+ top3[2]=model->peaks[k].intensity;
+ maxMercuryIndex[2]=k;
+ }
+ }
+ //if(k==0) maxMercuryIndex[1]=-1;
+ //else maxMercuryIndex[1]=maxMercuryIndex[0]-1; //allow right shift
+ //maxMercuryIndex[2]=maxMercuryIndex[0]+1; //allow left shift
+
+ //Test all three positions for the model. Note that if the first peak is the base peak, then
+ //no left shift is tested.
+ n=0;
+ while(n<3){
+
+ //skip the left shift if already at leftmost peak.
+ if(maxMercuryIndex[n]<0) {
+ n++;
+ continue;
+ }
+
+ //cout << "ii\tShift #" << n << endl;
+
+ //Align the mercury distribution (MD) to the observed peak. The MD can shift in
+ //either direction for one peak to adjust for system noise. The width of the MD
+ //determines the boundaries for correlation to the observed data.
+ lower=5000.0;
+ upper=0.0;
+ shft = s[maxIndex].mz - model->peaks[maxMercuryIndex[n]].mz;
+ vMR.clear();
+ thisMaxIndex=0;
+ da=0.0f;
+
+ //use model library
+ for(k=0; k<model->size; k++) {
+
+ r.data=model->peaks[k].intensity;
+ r.mass=model->peaks[k].mz+shft;
+ vMR.push_back(r);
+ if(model->peaks[k].intensity>99.999) thisMaxIndex=vMR.size()-1;
+
+ if(r.mass<lower) lower=r.mass;
+ if(r.mass>upper) upper=r.mass;
+ }
+ da=model->area;
+
+ //Add a little buffer to the m/z boundaries
+ lower-=0.1;
+ upper+=0.1;
+
+ //Narrow the search to just the area of the spectrum we need
+ lowIndex=BinarySearch(s,lower,true);
+ highIndex=BinarySearch(s,upper,false);
+
+ //if max peak shifts to already solved peak, skip
+ if(!CheckForPeak(vMR,s,thisMaxIndex)){
+ n++;
+ continue;
+ }
+
+ //Match predictions to the observed peaks and record them in the proper array.
+ corr=PeakMatcher(vMR,s,lower,upper,deltaM/2,maxIndex,matchCount,indexOverlap,vMatchIndex,vMatchPeak);
+ //cout << "ii.i\t" << s[maxIndex].mz << " " << s[maxIndex].intensity << "\t" << charges[i] << "\t" << matchCount << "\t" << corr << "\t" << indexOverlap << "\t" << maxIndex << "\tn" << n << endl;
+
+ //check any overlap with observed peptides. Overlap indicates deconvolution may be necessary.
+ //Deconvolution is at best a rough estimate and is not used if it does not improve the correlation
+ //scores.
+ keepPH=false;
+ if(indexOverlap>-1 /*&& indexOverlap>maxIndex*/){
+
+ //cout << "iii\tChecking overlap: " << indexOverlap << "\t" << maxIndex << endl;
+
+ //Find overlapping peptide
+ for(m=0;m<(int)vPeps.size();m++){
+ if(vPeps[m].basePeakIndex==indexOverlap) break;
+ }
+
+ //break out subspectrum; this is done using the original spectrum peak heights, not
+ //the current peak heights. The peak heights are then adjusted to account for the currently
+ //overlapping peptide model.
+ tmpSpec.clear();
+ x=0;
+ int subIndex=-1;
+ for(j=vPeps[m].lowIndex;j<=vPeps[m].highIndex;j++){
+
+ while(x<(int)vMatchIndex.size() && j>vMatchIndex[x]) x++;
+
+ //generate temporary subspectrum with peak heights reduced for overlapping model
+ if(x<(int)vMatchIndex.size() && j==vMatchIndex[x]){
+ tmpSpec.add(origSpec[j].mz,origSpec[j].intensity-vMatchPeak[x]*max);
+ x++;
+ } else {
+ tmpSpec.add(origSpec[j]);
+ }
+
+ //get the base peak index of the subspectrum
+ if(j==indexOverlap) subIndex=tmpSpec.size()-1;
+ }
+
+ //Re-Solve subspectrum and see if it has better correlation
+ corr2=MatchSubSpectrum(tmpSpec,subIndex,ph2);
+ //cout << "iii.i\tCorr2: " << corr2 << "\t" << ph2.corr << "\t" << origSpec[vPeps[m].basePeakIndex].mz << "\t" << vPeps[m].charge << endl;
+
+ //If correlation is better (or close), go back and try the
+ //newly adjusted peaks.
+ if(corr2 && ph2.corr+0.025>vPeps[m].corr){
+ x=0;
+
+ for(j=lowIndex;j<=highIndex;j++){
+ if(x<tmpSpec.size() && s[j].mz==tmpSpec[x].mz){
+ refSpec[j].intensity=(origSpec[j].intensity+tmpSpec[x].intensity);
+ x++;
+ } else {
+ refSpec[j].intensity=s[j].intensity;
+ }
+ }
+
+ //solve merged models
+ corr3=PeakMatcher(vMR,refSpec,lower,upper,deltaM/2,maxIndex,matchCount2,indexOverlap,vMatchIndex2,vMatchPeak2);
+ //cout << "iii.ii\tCorr3: " << s[maxIndex].mz << " " << s[maxIndex].intensity << "\t" << charges[i] << "\t" << matchCount2 << "\t" << corr3 << "\t" << indexOverlap << endl;
+
+ //keep the new model if it is better than the old one.
+ if(corr3>corr) {
+
+ corr=corr3;
+ vMatchIndex=vMatchIndex2;
+ vMatchPeak=vMatchPeak2;
+ matchCount=matchCount2;
+
+ //refine the overlapping one.
+ keepPH=true;
+
+ } else {
+
+ //it failed, do nothing and move on.
+ keepPH=false;
+
+ }
+
+ }
+
+ }//if indexOverlap>-1
+ double tCorr;
+ if(bestMatchCount==0) tCorr=0;
+ else tCorr=0.025*(matchCount-bestMatchCount)/bestMatchCount;
+ //cout << "Old best corr: " << bestCorr << "(" << bestMatchCount << ") This corr: " << corr << "," << corr+tCorr << "(" << matchCount << ")" << endl;
+ if(/*corr>bestCorr ||*/ (corr>cs.corr && corr+tCorr>bestCorr) ){
+ bestMatchIndex=vMatchIndex;
+ bestMatchPeak=vMatchPeak;
+ bestMatchCount=matchCount;
+ bestCorr=corr;
+ bestMass=model->zeroMass+shft*charges[i];
+ bestCharge=charges[i];
+ bestDA=da;
+ bestLow=lower;
+ bestHigh=upper;
+ bestKeepPH=keepPH;
+ bestPH=ph2;
+ bestOverlap=m;
+ bestLowIndex=lowIndex;
+ bestHighIndex=highIndex;
+ bestVariant=v;
+ }
+
+ n++;
+ }//while
+
+ }//for v (variants)
+
+ }//for i (charges)
+
+ //if above threshold, erase peaks.
+ if(bestCorr>cs.corr){
+ ph.area=(float)bestDA;
+ ph.basePeakIndex=maxIndex;
+ ph.charge=bestCharge;
+ ph.corr=bestCorr;
+ ph.highMZ=bestHigh;
+ ph.intensity=max;
+ ph.lowMZ=bestLow;
+ ph.massShift=0.0;
+ ph.monoMass=bestMass;
+ ph.lowIndex=bestLowIndex;
+ ph.highIndex=bestHighIndex;
+ ph.variantIndex=bestVariant;
+ if(bestKeepPH){
+ vPeps[bestOverlap].area=bestPH.area;
+ vPeps[bestOverlap].intensity=bestPH.intensity;
+ vPeps[bestOverlap].corr=bestPH.corr;
+ vPeps[bestOverlap].charge=bestPH.charge;
+ vPeps[bestOverlap].monoMass=bestPH.monoMass;
+ vPeps[bestOverlap].variantIndex=bestPH.variantIndex;
+ }
+ vPeps.push_back(ph);
+ mask[maxIndex].intensity=100.0f;
+
+ for(k=0;k<(int)bestMatchIndex.size();k++){
+ if(bestMatchPeak[k]*max/s[bestMatchIndex[k]].intensity>0.5){
+ s[bestMatchIndex[k]].intensity=-s[bestMatchIndex[k]].intensity;
+ } else {
+ s[bestMatchIndex[k]].intensity-=bestMatchPeak[k]*max;
+ }
+ //cout << "iv\t" << s[bestMatchIndex[k]].mz << " is now " << s[bestMatchIndex[k]].intensity << endl;
+ }
+ }
+
+ //set new maximum
+ maxHeight=max;
+
+ }
+
+ //Sort results by base peak
+ //This sort is expensive. Instead, try sorting before exporting to file. Make sure RefineHits below is not
+ //order dependent.
+ if(vPeps.size()>0) qsort(&vPeps[0],vPeps.size(),sizeof(pepHit),CompareBPI);
+
+ //Refine overfitting based on density
+ RefineHits(vPeps,origSpec);
+
+}
+
+//Reduces the number of features (cs.depth) per 1 Da window. This removes a lot
+//of false hits resulting from jagged tails on really large peaks. Criteria for
+//removal is lowest peak intensity
+void CHardklor2::RefineHits(vector<pepHit>& vPeps, Spectrum& s){
+
+ unsigned int i;
+ int j;
+ double lowp,highp;
+ bool bRestart=true;
+ vector<pepHit> vTmpHit;
+ vector<int> vPepMask;
+ list<int> vList;
+ list<int>::iterator it;
+
+ //generate an index of the peptides to keep or throw away
+ for(i=0;i<vPeps.size();i++) vPepMask.push_back(0);
+
+ //iterate through all hits
+ for(i=0;i<vPeps.size();i++){
+
+ //skip anything already marked for removal
+ if(vPepMask[i]>0) continue;
+
+ //put a tolerance around each peak
+ lowp=s[vPeps[i].basePeakIndex].mz-0.5;
+ highp=s[vPeps[i].basePeakIndex].mz+0.5;
+
+ //put the current hit in the list
+ vList.clear();
+ vList.push_front(i);
+
+ //find all other hits in the tolerance window
+ //look left first
+ j=i-1;
+ while(j>-1){
+
+ //break out when boundary is reached
+ if(s[vPeps[j].basePeakIndex].mz<lowp) break;
+
+ //skip anything marked for removal.
+ if(vPepMask[j]>0){
+ j--;
+ continue;
+ }
+
+ //add to list from high to low
+ for(it=vList.begin();it!=vList.end();it++){
+ if(s[vPeps[j].basePeakIndex].intensity > s[vPeps[*it].basePeakIndex].intensity) break;
+ }
+ vList.insert(it,j);
+
+ j--;
+ }
+
+ //look right
+ j=i+1;
+ while(j<(int)vPeps.size()){
+
+ //break out when boundary is reached
+ if(s[vPeps[j].basePeakIndex].mz>highp) break;
+
+ //skip anything marked for removal.
+ if(vPepMask[j]>0){
+ j++;
+ continue;
+ }
+
+ //add to list from high to low
+ for(it=vList.begin();it!=vList.end();it++){
+ if(s[vPeps[j].basePeakIndex].intensity > s[vPeps[*it].basePeakIndex].intensity) break;
+ }
+ vList.insert(it,j);
+
+ j++;
+ }
+
+ //remove the lowest peptides below threshold (user specified depth)
+ if((int)vList.size()>cs.depth){
+ it=vList.begin();
+ for(j=0;j<cs.depth;j++) it++;
+ for(it=it;it!=vList.end();it++) vPepMask[*it]=1;
+ }
+
+ }
+
+ //copy over the keepers
+ for(i=0;i<vPeps.size();i++){
+ if(vPepMask[i]) continue;
+ vTmpHit.push_back(vPeps[i]);
+ }
+ vPeps.clear();
+ for(i=0;i<vTmpHit.size();i++)vPeps.push_back(vTmpHit[i]);
+
+}
+
+void CHardklor2::ResultToMem(pepHit& ph, Spectrum& s){
+ int i,j;
+ char mods[32];
+ char tmp[16];
+
+ hkm.monoMass = ph.monoMass;
+ hkm.charge = ph.charge;
+ if(cs.distArea) hkm.intensity = ph.area*ph.intensity;
+ else hkm.intensity = ph.intensity;
+ hkm.scan = currentScanNumber;
+ hkm.mz = s[ph.basePeakIndex].mz;
+ hkm.corr = ph.corr;
+
+ //Add mods
+ if(!cs.noBase) i=ph.variantIndex-1;
+ else i=ph.variantIndex;
+ strcpy(mods,"");
+ if(i<0) {
+ strcat(mods,"_");
+ } else {
+ for(j=0;j<cs.variant->at(i).sizeAtom();j++){
+ strcat(mods,PT->at(cs.variant->at(i).atAtom(j).iLower).symbol);
+ sprintf(tmp,"%d",cs.variant->at(i).atAtom(j).iUpper);
+ strcat(mods,tmp);
+ }
+ strcat(mods,"_");
+ for(j=0;j<cs.variant->at(i).sizeEnrich();j++){
+ sprintf(tmp,"%.2lf",cs.variant->at(i).atEnrich(j).ape);
+ strcat(mods,tmp);
+ strcat(mods,PT->at(cs.variant->at(i).atEnrich(j).atomNum).symbol);
+ sprintf(tmp,"%d_",cs.variant->at(i).atEnrich(j).isotope);
+ strcat(mods,tmp);
+ }
+ }
+ strcpy(hkm.mods,mods);
+ vResults.push_back(hkm);
+}
+
+void CHardklor2::SetResultsToMemory(bool b){
+ bMem=b;
+}
+
+int CHardklor2::Size(){
+ return vResults.size();
+}
+
+void CHardklor2::WritePepLine(pepHit& ph, Spectrum& s, FILE* fptr, int format){
+ int i,j;
+
+ if(format==0){
+ fprintf(fptr,"P\t%.4lf",ph.monoMass);
+ fprintf(fptr,"\t%d",ph.charge);
+ if(cs.distArea) fprintf(fptr,"\t%.0f",ph.area*ph.intensity);
+ else fprintf(fptr,"\t%.0f",ph.intensity);
+ fprintf(fptr,"\t%.4lf",s[ph.basePeakIndex].mz);
+ fprintf(fptr,"\t%.4lf-%.4lf",s[ph.lowIndex].mz,s[ph.highIndex].mz);
+ fprintf(fptr,"\t0.0000");
+
+ //Add mods
+ if(!cs.noBase) i=ph.variantIndex-1;
+ else i=ph.variantIndex;
+ if(i<0) {
+ fprintf(fptr,"\t_");
+ } else {
+ fprintf(fptr,"\t");
+ for(j=0;j<cs.variant->at(i).sizeAtom();j++){
+ fprintf(fptr,"%s",PT->at(cs.variant->at(i).atAtom(j).iLower).symbol);
+ fprintf(fptr,"%d",cs.variant->at(i).atAtom(j).iUpper);
+ }
+ fprintf(fptr,"_");
+ for(j=0;j<cs.variant->at(i).sizeEnrich();j++){
+ fprintf(fptr,"%.2lf",cs.variant->at(i).atEnrich(j).ape);
+ fprintf(fptr,"%s",PT->at(cs.variant->at(i).atEnrich(j).atomNum).symbol);
+ fprintf(fptr,"%d_",cs.variant->at(i).atEnrich(j).isotope);
+ }
+ }
+
+ fprintf(fptr,"\t%.4lf\n",ph.corr);
+
+ } else if(format==1) {
+ /*
+ fptr << "<Peak Mass=\"" << sa.predPep->at(pepID).GetVariant(varID).GetMonoMass() << "\" ";
+ fptr << "ChargeState=\"" << sa.predPep->at(pepID).GetVariant(varID).GetCharge() << "\" ";
+ if(cs.distArea) fptr << "Area=\"" << sa.predPep->at(pepID).GetIntensity()*sa.predPep->at(pepID).GetVariant(varID).GetArea() << "\" ";
+ else fptr << "Intensity=\"" << sa.predPep->at(pepID).GetIntensity() << "\" ";
+ fptr << "MZ=\"" << sa.predPep->at(pepID).GetMZ() << "\" ";
+ fptr << "Window=\"" << sa.peaks.at(0).mz << "-" << sa.peaks.at(sa.peaks.size()-1).mz << "\" ";
+ fptr << "SN=\"" << sa.S2NCutoff << "\" ";
+
+ //Add mods
+ fptr << "Mod=\"";
+ for(j=0;j<sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().sizeAtom();j++){
+ fptr << PT->at(sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atAtom(j).iLower).symbol;
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atAtom(j).iUpper;
+ }
+ fptr << "_";
+ for(j=0;j<sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().sizeEnrich();j++){
+ fptr << setiosflags(ios::fixed) << setprecision(2);
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).ape;
+ fptr << setiosflags(ios::fixed) << setprecision(4);
+ fptr << PT->at(sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).atomNum).symbol;
+ fptr << sa.predPep->at(pepID).GetVariant(varID).GetHKVariant().atEnrich(j).isotope;
+ fptr << "_";
+ }
+ fptr << "\" ";
+
+ fptr << "Score=\"" << obj.corr << "\"/>" << endl;
+ */
+
+ //reduced output
+ } else if(format==2){
+ fprintf(fptr,"%.4lf",(ph.monoMass+ph.charge*1.007276466)/ph.charge);
+ if(cs.distArea) fprintf(fptr,"\t%.0f",ph.area*ph.intensity);
+ else fprintf(fptr,"\t%.0f",ph.intensity);
+ fprintf(fptr,"\t%d\n",ph.charge);
+ }
+}
+
+void CHardklor2::WriteScanLine(Spectrum& s, FILE* fptr, int format){
+
+ if(format==0) {
+ fprintf(fptr,"S\t%d\t%.4f\t%s",s.getScanNumber(),s.getRTime(),cs.inFile);
+
+ //For Alex Panchaud, special ZS case
+ if(s.getFileType()==ZS || s.getFileType()==UZS){
+ if(s.sizeZ()>0){
+ for(int i=0;i<s.sizeZ();i++) fprintf(fptr,"\t%d,%.6lf",s.atZ(i).z,s.atZ(i).mh);
+ }
+ } else {
+
+ //otherwise output precursor info if it exists
+ if(s.sizeZ()==1){
+ fprintf(fptr,"\t%.4lf\t%d\t%.4lf",s.atZ(0).mh-1.00727649,s.atZ(0).z,s.getMZ());
+ } else if(s.sizeZ()>1){
+ fprintf(fptr,"\t0.0\t0\t%.4lf",s.getMZ());
+ } else {
+ fprintf(fptr,"\t0.0\t0\t0.0");
+ }
+ }
+ fprintf(fptr,"\n");
+
+ //For XML output
+ } else if(format==1){
+ fprintf(fptr,"<Spectrum Scan=\"%d\" ",s.getScanNumber());
+ fprintf(fptr,"RetentionTime=\"%.4f\" ",s.getRTime());
+ fprintf(fptr,"Filename=\"%s\"",cs.inFile);
+ if(s.getFileType()==ZS || s.getFileType()==UZS){
+ if(s.sizeZ()>0){
+ for(int i=0;i<s.sizeZ();i++) fprintf(fptr," PeptideSignal%d=\"%d,%.4lf\"",i,s.atZ(i).z,s.atZ(i).mh);
+ }
+ } else {
+ if(s.sizeZ()==1){
+ fprintf(fptr," AccMonoMass=\"%.4lf\" PrecursorCharge=\"%d\" PrecursorMZ=\"%.4lf\"",s.atZ(0).mh-1.00727649,s.atZ(0).z,s.getMZ());
+ } else if(s.sizeZ()>1){
+ fprintf(fptr," AccMonoMass=\"0.0\" PrecursorCharge=\"0\" PrecursorMZ=\"%.4lf\"",s.getMZ());
+ } else {
+ fprintf(fptr," AccMonoMass=\"0.0\" PrecursorCharge=\"0\" PrecursorMZ=\"0.0\"");
+ }
+ }
+ fprintf(fptr,">\n");
+
+ //For reduced output
+ } else if(format==2) {
+ fprintf(fptr, "Scan=%d RT=%.4f\n", s.getScanNumber(),s.getRTime());
+ }
+}
\ No newline at end of file
diff --git a/src/app/hardklor/CHardklor2.h b/src/app/hardklor/CHardklor2.h
new file mode 100644
index 0000000..da94d15
--- /dev/null
+++ b/src/app/hardklor/CHardklor2.h
@@ -0,0 +1,119 @@
+#ifndef _CHARDKLOR2_H
+#define _CHARDKLOR2_H
+
+#include <iostream>
+#include <string>
+#include <vector>
+#include <list>
+#include <cmath>
+
+#include "MSObject.h"
+#include "MSReader.h"
+#include "Spectrum.h"
+#include "HardklorTypes.h"
+#include "CAveragine.h"
+#include "CMercury8.h"
+#include "CHardklor.h"
+#include "CModelLibrary.h"
+
+#ifdef _MSC_VER
+
+#else
+#include <sys/time.h>
+#endif
+
+using namespace std;
+
+class CHardklor2{
+
+ public:
+ //Constructors & Destructors:
+ CHardklor2(CAveragine *a, CMercury8 *m, CModelLibrary *lib);
+ ~CHardklor2();
+
+ //Operators
+ hkMem& operator[](const int& index);
+
+ //Methods:
+ void Echo(bool b);
+ int GoHardklor(CHardklorSetting sett, Spectrum* s=NULL);
+ void QuickCharge(Spectrum& s, int index, vector<int>& v);
+ void SetResultsToMemory(bool b);
+ int Size();
+
+ protected:
+
+ private:
+ //Methods:
+ int BinarySearch(Spectrum& s, double mz, bool floor);
+ double CalcFWHM(double mz,double res,int iType);
+ void Centroid(Spectrum& s, Spectrum& out);
+ bool CheckForPeak(vector<Result>& vMR, Spectrum& s, int index);
+ int CompareData(const void*, const void*);
+ double LinReg(vector<float>& mer, vector<float>& obs);
+ bool MatchSubSpectrum(Spectrum& s, int peakIndex, pepHit& pep);
+ double PeakMatcher(vector<Result>& vMR, Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, int& indexOverlap, vector<int>& vMatchIndex, vector<float>& vMatchIntensity);
+ double PeakMatcherB(vector<Result>& vMR, Spectrum& s, double lower, double upper, double deltaM, int matchIndex, int& matchCount, vector<int>& vMatchIndex, vector<float>& vMatchIntensity);
+ void QuickHardklor(Spectrum& s, vector<pepHit>& vPeps);
+ void RefineHits(vector<pepHit>& vPeps, Spectrum& s);
+ void ResultToMem(pepHit& ph, Spectrum& s);
+ void WritePepLine(pepHit& ph, Spectrum& s, FILE* fptr, int format=0);
+ void WriteScanLine(Spectrum& s, FILE* fptr, int format=0);
+
+ static int CompareBPI(const void *p1, const void *p2);
+
+ //Data Members:
+ CHardklorSetting cs;
+ CAveragine* averagine;
+ CMercury8* mercury;
+ CModelLibrary* models;
+ CPeriodicTable* PT;
+ Spectrum mask;
+ hkMem hkm;
+ bool bEcho;
+ bool bMem;
+ int currentScanNumber;
+
+ //Vector for holding results in memory should that be needed
+ vector<hkMem> vResults;
+
+ //Temporary Data Members:
+ char bestCh[200];
+ double BestCorr;
+ int CorrMatches;
+ int ExtraPre;
+ int ExtraObs;
+
+ int SSIterations;
+
+ //For accurate timing of Hardklor
+ #ifdef _MSC_VER
+ __int64 startTime;
+ __int64 stopTime;
+ __int64 loadTime;
+ __int64 analysisTime;
+ __int64 timerFrequency;
+ __int64 tmpTime1;
+ __int64 tmpTime2;
+ #define getExactTime(a) QueryPerformanceCounter((LARGE_INTEGER*)&a)
+ #define getTimerFrequency(a) QueryPerformanceFrequency((LARGE_INTEGER*)&a)
+ #define toMicroSec(a) (a)
+ #define timeToSec(a,b) (a/b)
+ #else
+ timeval startTime;
+ timeval stopTime;
+ uint64_t loadTime;
+ uint64_t splitTime;
+ uint64_t analysisTime;
+ uint64_t tmpTime1;
+ uint64_t tmpTime2;
+ int timerFrequency;
+ #define getExactTime(a) gettimeofday(&a,NULL)
+ #define toMicroSec(a) a.tv_sec*1000000+a.tv_usec
+ #define getTimerFrequency(a) (a)=1
+ #define timeToSec(a,b) (a/1000000)
+ #endif
+
+};
+
+#endif
diff --git a/src/app/hardklor/CHardklorParser.cpp b/src/app/hardklor/CHardklorParser.cpp
new file mode 100644
index 0000000..79fc80d
--- /dev/null
+++ b/src/app/hardklor/CHardklorParser.cpp
@@ -0,0 +1,547 @@
+#include "CHardklorParser.h"
+
+using namespace std;
+
+CHardklorParser::CHardklorParser(){
+ vQueue = new vector<CHardklorSetting>;
+}
+
+CHardklorParser::~CHardklorParser(){
+ delete vQueue;
+}
+
+//Takes a command line and breaks it into tokens
+//Tokens are then read and used to set global and local parameters
+void CHardklorParser::parse(char* cmd) {
+
+ int j;
+ bool isGlobal=true;
+ sMolecule m;
+ char *tok;
+ char tmpstr[256];
+ char upStr[64];
+ string tstr;
+ vector<string> vs;
+
+ /*
+ //For modifications
+ CHardklorVariant v;
+ CPeriodicTable* PT;
+ int j,k;
+ string atom;
+ string isotope;
+ string percent;
+ bool badMod;
+ int atomNum;
+ bool bNew;
+ */
+
+ bool bFile;
+ char param[32];
+
+ CHardklorSetting hs;
+
+ //Replace first # with a terminator
+ tok=strstr(cmd,"#");
+ if(tok!=NULL) strncpy(tok,"\0",1);
+
+ //if we have only white space, exit here
+ strcpy(tmpstr,cmd);
+ tok=strtok(tmpstr," \t\n");
+ if(tok==NULL) return;
+
+ //Check if we have a parameter (has '=' in it) or a file request.
+ tok=strstr(cmd,"=");
+ if(tok==NULL) bFile=true;
+ else bFile=false;
+
+ //Read file and return, if needed
+ if(bFile){
+
+ hs=global;
+
+ //on systems that allow a space in the path, require quotes (") to capture
+ //complete file name
+ strcpy(tmpstr,cmd);
+
+ //Check for quote
+ if(tmpstr[0]=='\"'){
+
+ //continue reading tokens until another quote is found
+ j=1;
+ while(true){
+ if(j==strlen(tmpstr)){
+ cout << "Invalid input file." << endl;
+ exit(-1);
+ }
+ if(tmpstr[j]=='\"') break;
+ }
+ tmpstr[j]='\0';
+ strcpy(hs.inFile,&tmpstr[1]);
+ j++;
+ } else {
+ tok=strtok(tmpstr," \t\n");
+ strcpy(hs.inFile,tmpstr);
+ j=strlen(tmpstr);
+ }
+
+ //Find first non-whitespace
+ while(true){
+ if(j>=(int)strlen(cmd)){
+ cout << "Invalid output file." << endl;
+ exit(-1);
+ }
+ if(cmd[j]!=' ' && cmd[j]!='\t') break;
+ j++;
+ }
+
+ strcpy(tmpstr,&cmd[j]);
+
+ //Check for quote
+ if(tmpstr[0]=='\"'){
+
+ //continue reading tokens until another quote is found
+ j=1;
+ while(true){
+ if(j==strlen(tmpstr)){
+ cout << "Invalid output file." << endl;
+ exit(-1);
+ }
+ if(tmpstr[j]=='\"') break;
+ }
+ tmpstr[j]='\0';
+ strcpy(hs.outFile,&tmpstr[1]);
+ j++;
+ } else {
+ tok=strtok(tmpstr," \t\n");
+ strcpy(hs.outFile,tmpstr);
+ j=strlen(tmpstr);
+ }
+
+ //cout << hs.inFile << "\t" << hs.outFile << endl;
+
+ hs.fileFormat = getFileFormat(hs.inFile);
+ vQueue->push_back(hs);
+ return;
+ }
+
+ //Read parameter
+ tok=strtok(cmd," \t=\n");
+ if(tok==NULL) return;
+ strcpy(param,tok);
+ tok=strtok(NULL," \t=\n");
+ if(tok==NULL) {
+ warn(param,0);
+ return;
+ }
+
+ //process parameter
+ if(strcmp(param,"algorithm")==0){
+ for(j=0;j<(int)strlen(tok);j++) upStr[j]=toupper(tok[j]);
+ upStr[j]='\0';
+ if(strcmp(upStr,"BASIC")==0) global.algorithm=Basic;
+ else if (strcmp(upStr,"VERSION1")==0) global.algorithm=FastFewestPeptides;
+ else if (strcmp(upStr,"VERSION2")==0) global.algorithm=Version2;
+ else {
+ global.algorithm=Version2;
+ warn("Unknown algorithm. Defaulting to Version2.",2);
+ }
+
+ } else if(strcmp(param,"averagine_mod")==0){
+ if(strlen(tok)==1 && tok[0]=='0') global.variant->clear();
+ else {
+ tstr=tok;
+ tok=strtok(NULL," \t\n");
+ while(tok!=NULL){
+ tstr+=" ";
+ tstr+=tok;
+ tok=strtok(NULL," \t\n");
+ }
+ if(!makeVariant(&tstr[0])) warn("Invalid averagine_mod value. Skipping averagine_mod.",2);
+ }
+
+ } else if(strcmp(param,"boxcar_averaging")==0){
+ global.boxcar=atoi(tok);
+ if(global.boxcar>0 && global.boxcar%2==0) {
+ global.boxcar++;
+ warn("boxcar_averaging value is even number. Incrementing by 1.",2);
+ }
+
+ } else if(strcmp(param,"boxcar_filter")==0){
+ global.boxcarFilter=atoi(tok);
+
+ } else if(strcmp(param,"boxcar_filter_ppm")==0){
+ global.ppm=atof(tok);
+
+ } else if(strcmp(param,"centroided")==0){
+ if(atoi(tok)!=0) global.centroid=true;
+ else global.centroid=false;
+
+ } else if(strcmp(param,"charge_algorithm")==0){
+ for(j=0;j<(int)strlen(tok);j++) upStr[j]=toupper(tok[j]);
+ upStr[j]='\0';
+ if(strcmp(upStr,"QUICK")==0) global.chargeMode='Q';
+ else if (strcmp(upStr,"FFT")==0) global.chargeMode='F';
+ else if (strcmp(upStr,"PATTERSON")==0) global.chargeMode='P';
+ else if (strcmp(upStr,"SENKO")==0) global.chargeMode='S';
+ else if (strcmp(upStr,"NONE")==0) global.chargeMode='B';
+ else {
+ global.chargeMode='Q';
+ warn("Unknown charge algorithm. Defaulting to Quick.",2);
+ }
+
+ } else if(strcmp(param,"charge_max")==0){
+ global.maxCharge=atoi(tok);
+
+ } else if(strcmp(param,"charge_min")==0){
+ global.minCharge=atoi(tok);
+
+ } else if(strcmp(param,"correlation")==0){
+ global.corr=atof(tok);
+
+ } else if(strcmp(param,"depth")==0){
+ global.depth=atoi(tok);
+
+ } else if(strcmp(param,"distribution_area")==0){
+ if(atoi(tok)!=0) global.distArea=true;
+ else global.distArea=false;
+
+ } else if(strcmp(param,"hardklor_data")==0){
+ strcpy(global.HardklorFile,tok);
+
+ } else if(strcmp(param,"instrument")==0){
+ for(j=0;j<(int)strlen(tok);j++) upStr[j]=toupper(tok[j]);
+ upStr[j]='\0';
+ if(strcmp(upStr,"FTICR")==0) global.msType=FTICR;
+ else if (strcmp(upStr,"ORBITRAP")==0) global.msType=OrbiTrap;
+ else if (strcmp(upStr,"TOF")==0) global.msType=TOF;
+ else if (strcmp(upStr,"QIT")==0) global.msType=QIT;
+ else {
+ global.msType=OrbiTrap;
+ warn("Unknown instrument type. Defaulting to Orbitrap.",2);
+ }
+
+ } else if(strcmp(param,"isotope_data")==0){
+ strcpy(global.MercuryFile,tok);
+
+ } else if(strcmp(param,"max_features")==0){
+ } else if(strcmp(param,"ms_level")==0){
+ if(atoi(tok)==3){
+ global.mzXMLFilter=MS3;
+ global.msLevel=3;
+ } else if(atoi(tok)==2) {
+ global.mzXMLFilter=MS2;
+ global.msLevel=2;
+ } else {
+ global.mzXMLFilter=MS1;
+ global.msLevel=1;
+ }
+
+ } else if(strcmp(param,"mz_max")==0){
+ global.window.dUpper=atof(tok);
+
+ } else if(strcmp(param,"mz_min")==0){
+ global.window.dLower=atof(tok);
+
+ } else if(strcmp(param,"mz_window")==0){
+ global.winSize=atof(tok);
+
+ } else if(strcmp(param,"resolution")==0){
+ global.res400=atof(tok);
+
+ } else if(strcmp(param,"scan_range_max")==0){
+ global.scan.iUpper=atoi(tok);
+
+ } else if(strcmp(param,"scan_range_min")==0){
+ global.scan.iLower=atoi(tok);
+
+ } else if(strcmp(param,"sensitivity")==0){
+ } else if(strcmp(param,"signal_to_noise")==0){
+ global.sn=atof(tok);
+
+ } else if(strcmp(param,"smooth")==0){
+ global.smooth=atoi(tok);
+
+ } else if(strcmp(param,"sn_window")==0){
+ global.snWindow=atof(tok);
+
+ } else if(strcmp(param,"static_sn")==0){
+ if(atoi(tok)!=0) global.staticSN=true;
+ else global.staticSN=false;
+
+ } else if(strcmp(param,"xml")==0){
+ if(atoi(tok)!=0) global.xml=true;
+ else global.xml=false;
+
+ } else {
+ warn(param,1);
+ }
+
+}
+
+bool CHardklorParser::parseCMD(int argc, char* argv[]){
+
+ int i=2;
+ char tstr[512];
+
+ while(i<argc-2){
+ if(argv[i][0]=='-'){
+ strcpy(tstr,&argv[i][1]);
+ strcat(tstr," = ");
+ strcat(tstr,argv[i+1]);
+ parse(tstr);
+ } else {
+ cout << "There was an error with your command line parameters." << endl;
+ return false;
+ }
+ i+=2;
+ }
+
+ strcpy(tstr,argv[argc-2]);
+ strcat(tstr," ");
+ strcat(tstr,argv[argc-1]);
+ parse(tstr);
+
+ return true;
+
+}
+
+
+//Reads in a config file and passes it to the parser
+bool CHardklorParser::parseConfig(char* c){
+ fstream fptr;
+ char tstr[512];
+
+ fptr.open(c,ios::in);
+ if(!fptr.good()){
+ cout << "Cannot open config file!" << endl;
+ return false;
+ }
+
+ while(!fptr.eof()) {
+ fptr.getline(tstr,512);
+ if(tstr[0]==0) continue;
+ if(tstr[0]=='#') continue;
+ parse(tstr);
+ }
+
+ fptr.close();
+ return true;
+}
+
+CHardklorSetting& CHardklorParser::queue(int i){
+ return vQueue->at(i);
+}
+
+int CHardklorParser::size(){
+ return vQueue->size();
+}
+
+//Identifies file format from extension - Must conform to these conventions
+MSFileFormat CHardklorParser::getFileFormat(char* c){
+
+ char file[256];
+ char ext[256];
+ char *tok;
+
+ strcpy(file,c);
+ tok=strtok(file,".\n");
+ while(tok!=NULL){
+ strcpy(ext,tok);
+ tok=strtok(NULL,".\n");
+ }
+
+ if(strcmp(ext,"ms1")==0 || strcmp(ext,"MS1")==0) return ms1;
+ if(strcmp(ext,"ms2")==0 || strcmp(ext,"MS2")==0) return ms2;
+ if(strcmp(ext,"bms1")==0 || strcmp(ext,"BMS1")==0) return bms1;
+ if(strcmp(ext,"bms2")==0 || strcmp(ext,"BMS2")==0) return bms2;
+ if(strcmp(ext,"cms1")==0 || strcmp(ext,"CMS1")==0) return cms1;
+ if(strcmp(ext,"cms2")==0 || strcmp(ext,"CMS2")==0) return cms2;
+ if(strcmp(ext,"zs")==0 || strcmp(ext,"ZS")==0) return zs;
+ if(strcmp(ext,"uzs")==0 || strcmp(ext,"UZS")==0) return uzs;
+ if(strcmp(ext,"mzML")==0 || strcmp(ext,"MZML")==0) return mzML;
+ if(strcmp(ext,"mzXML")==0 || strcmp(ext,"MZXML")==0) return mzXML;
+ if(strcmp(ext,"mgf")==0 || strcmp(ext,"MGF")==0) return mgf;
+ if(strcmp(ext,"mz5")==0 || strcmp(ext,"MZ5")==0) return mz5;
+ if(strcmp(ext,"raw")==0 || strcmp(ext,"RAW")==0) return raw;
+ return dunno;
+
+}
+
+void CHardklorParser::warn(char* c, int i){
+ switch(i){
+ case 0:
+ cout << "Parameter " << c << " has no value." << endl;
+ break;
+ case 1:
+ cout << "Unknown parameter: " << c << endl;
+ break;
+ case 2:
+ default:
+ cout << c << endl;
+ break;
+ }
+}
+
+bool CHardklorParser::makeVariant(char* c){
+
+ //For modifications
+ CHardklorVariant v;
+ CPeriodicTable* PT;
+ int j,k;
+ string atom;
+ string isotope;
+ string percent;
+ int atomNum;
+ bool bNew;
+
+ char str[256];
+ char* tok;
+ strcpy(str,c);
+
+ v.clear();
+ PT = new CPeriodicTable(global.HardklorFile);
+
+ tok=strtok(str," \n");
+ while(tok!=NULL){
+ if(isdigit(tok[0]) || tok[0]=='.'){
+ //we have enrichment
+ percent="";
+ atom="";
+ isotope="";
+
+ //Get the APE
+ for(j=0;j<(int)strlen(tok);j++){
+ if(isdigit(tok[j]) || tok[j]=='.') {
+ if(percent.size()==15){
+ warn("Bad averagine_mod: Malformed modification flag, too many digits.",2);
+ return false;
+ }
+ percent+=tok[j];
+ } else {
+ break;
+ }
+ }
+
+ //Get the atom
+ for(j=j;j<(int)strlen(tok);j++){
+ if(isalpha(tok[j])) {
+ if(atom.size()==2){
+ warn("Bad averagine_mod: Malformed modification flag, invalid atom",2);
+ return false;
+ }
+ atom+=tok[j];
+ } else {
+ break;
+ }
+ }
+
+ //Get the isotope
+ for(j=j;j<(int)strlen(tok);j++){
+ if(isotope.size()==2){
+ warn("Bad averagine_mod: Malformed modification flag, bad isotope",2);
+ return false;
+ }
+ isotope+=tok[j];
+ }
+
+ //format the atom properly
+ atom.at(0)=toupper(atom.at(0));
+ if(atom.size()==2) atom.at(1)=tolower(atom.at(1));
+
+ //Get the array number for the atom
+ atomNum=-1;
+ for(j=0;j<PT->size();j++){
+ if(strcmp(PT->at(j).symbol,&atom[0])==0){
+ atomNum=j;
+ break;
+ }
+ }
+
+ if(atomNum==-1){
+ warn("Bad averagine_mod: Malformed modification flag, atom not in periodic table",2);
+ return false;
+ }
+
+ v.addEnrich(atomNum,atoi(&isotope[0]),atof(&percent[0]));
+
+ } else {
+ //we have molecule
+ percent="";
+ atom="";
+ bNew=true;
+
+ //Get the atom
+ for(j=0;j<(int)strlen(tok);j++){
+
+ //Check for an atom symbol
+ if(isalpha(tok[j])) {
+
+ //Check if we were working on the count of the previous atom
+ if(!bNew) {
+ bNew=true;
+
+ //Make sure the atom has uppercase-lowercase letter format;
+ atom.at(0)=toupper(atom.at(0));
+ if(atom.size()==2) atom.at(1)=tolower(atom.at(1));
+
+ //Look up the new atom
+ for(k=0;k<PT->size();k++){
+ if(strcmp(PT->at(k).symbol,&atom[0])==0){
+ //Add the new atom to the variant
+ v.addAtom(k,atoi(&percent[0]));
+ break;
+ }
+ }
+
+ //Clear the fields
+ percent="";
+ atom="";
+ }
+
+ //Add this letter to the atom symbol
+ if(atom.size()==2){
+ warn("Bad averagine_mod: Malformed modification flag, invalid atom",2);
+ return false;
+ }
+ atom+=tok[j];
+
+ } else if(isdigit(tok[j])){
+
+ //Whenever we find a digit, we have already found an atom symbol
+ bNew=false;
+
+ //Add this letter to the atom count
+ if(percent.size()==12){
+ warn("Bad averagine_mod: Malformed modification flag, unreasonable atom count",2);
+ return false;
+ }
+ percent+=tok[j];
+
+ }
+ }
+
+ //process the last atom
+ //Make sure the atom has uppercase-lowercase letter format;
+ atom.at(0)=toupper(atom.at(0));
+ if(atom.size()==2) atom.at(1)=tolower(atom.at(1));
+
+ //Look up the new atom
+ for(k=0;k<PT->size();k++){
+ if(strcmp(PT->at(k).symbol,&atom[0])==0){
+
+ //Add the new atom to the variant
+ v.addAtom(k,atoi(&percent[0]));
+ break;
+
+ }
+ }
+ }
+ tok=strtok(NULL," \n");
+ }
+
+ global.variant->push_back(v);
+ delete PT;
+ return true;
+
+}
\ No newline at end of file
diff --git a/src/app/hardklor/CHardklorParser.h b/src/app/hardklor/CHardklorParser.h
new file mode 100644
index 0000000..9650a72
--- /dev/null
+++ b/src/app/hardklor/CHardklorParser.h
@@ -0,0 +1,42 @@
+#ifndef _CHARDKLORPARSER_H
+#define _CHARDKLORPARSER_H
+
+#include <fstream>
+#include <iostream>
+#include <vector>
+
+#include "CHardklorSetting.h"
+#include "CPeriodicTable.h"
+#include "MSToolkitTypes.h"
+
+using namespace std;
+
+class CHardklorParser {
+
+ public:
+ //Constructors & Destructors
+ CHardklorParser();
+ ~CHardklorParser();
+
+ //Methods
+ void parse(char*);
+ bool parseCMD(int argc, char* argv[]);
+ bool parseConfig(char*);
+ MSFileFormat getFileFormat(char* c);
+ CHardklorSetting& queue(int);
+ int size();
+
+ protected:
+
+ private:
+ //Methods
+ bool makeVariant(char* c);
+ void warn(char*, int);
+
+ //Data Members
+ CHardklorSetting global;
+ vector<CHardklorSetting> *vQueue;
+};
+
+
+#endif
diff --git a/src/app/hardklor/CHardklorProtein.cpp b/src/app/hardklor/CHardklorProtein.cpp
new file mode 100644
index 0000000..a1030c1
--- /dev/null
+++ b/src/app/hardklor/CHardklorProtein.cpp
@@ -0,0 +1,73 @@
+#include "CHardklorProtein.h"
+#include <cstring>
+
+using namespace std;
+
+CHardklorProtein::CHardklorProtein(){
+ enrich = new vector<sEnrichMercury>;
+}
+
+CHardklorProtein::CHardklorProtein(const CHardklorProtein& c){
+ int i;
+
+ enrich = new vector<sEnrichMercury>;
+ for(i=0;i<c.enrich->size();i++) enrich->push_back(c.enrich->at(i));
+
+ ID = c.ID;
+ mz = c.mz;
+ monoMass = c.monoMass;
+ shft = c.shft;
+ abun = c.abun;
+ charge = c.charge;
+ C = c.C;
+ rTime = c.rTime;
+ strcpy(seq,c.seq);
+
+}
+
+CHardklorProtein::~CHardklorProtein(){
+ delete enrich;
+}
+
+CHardklorProtein& CHardklorProtein::operator=(const CHardklorProtein& c){
+ int i;
+
+ if(this != &c){
+ delete enrich;
+ enrich = new vector<sEnrichMercury>;
+ for(i=0;i<c.enrich->size();i++) enrich->push_back(c.enrich->at(i));
+
+ ID = c.ID;
+ mz = c.mz;
+ monoMass = c.monoMass;
+ shft = c.shft;
+ abun = c.abun;
+ charge = c.charge;
+ C = c.C;
+ rTime = c.rTime;
+ strcpy(seq,c.seq);
+ }
+ return *this;
+
+}
+
+void CHardklorProtein::add(int a, int c, double b){
+ sEnrichMercury s;
+ s.atomNum = a;
+ s.isotope = c;
+ s.ape = b;
+ enrich->push_back(s);
+}
+
+sEnrichMercury& CHardklorProtein::at(int i){
+ return enrich->at(i);
+}
+
+void CHardklorProtein::clear(){
+ delete enrich;
+ enrich = new vector<sEnrichMercury>;
+}
+
+int CHardklorProtein::size(){
+ return enrich->size();
+}
diff --git a/src/app/hardklor/CHardklorProtein.h b/src/app/hardklor/CHardklorProtein.h
new file mode 100644
index 0000000..81f4fde
--- /dev/null
+++ b/src/app/hardklor/CHardklorProtein.h
@@ -0,0 +1,42 @@
+#ifndef _CHARDKLORPROTEIN_H
+#define _CHARDKLORPROTEIN_H
+
+#include <vector>
+
+#include "HardklorTypes.h"
+
+using namespace std;
+
+class CHardklorProtein {
+ public:
+ //Constructors & Destructors:
+ CHardklorProtein();
+ CHardklorProtein(const CHardklorProtein&);
+ ~CHardklorProtein();
+
+ //Functions:
+ CHardklorProtein& operator=(const CHardklorProtein&);
+ void add(int, int, double);
+ sEnrichMercury& at(int);
+ void clear();
+ int size();
+
+ //Data Members:
+ sInt ID;
+ double mz;
+ double monoMass;
+ double shft;
+ double abun;
+ double rTime;
+ int charge;
+ int C;
+ char seq[64];
+
+ protected:
+ private:
+ //Data Members:
+ vector<sEnrichMercury> *enrich;
+
+};
+
+#endif
diff --git a/src/app/hardklor/CHardklorSetting.cpp b/src/app/hardklor/CHardklorSetting.cpp
new file mode 100644
index 0000000..6fb6baa
--- /dev/null
+++ b/src/app/hardklor/CHardklorSetting.cpp
@@ -0,0 +1,198 @@
+#include "CHardklorSetting.h"
+
+using namespace std;
+
+CHardklorSetting::CHardklorSetting(){
+ noBase=false;
+ iAnalysis=false;
+ maxCharge=5;
+ minCharge=1;
+ msLevel=1;
+ depth=3;
+ peptide=10;
+ smooth=0;
+ corr=0.85;
+ sn=1.0;
+ scan.iLower=0;
+ scan.iUpper=0;
+ window.dLower=0;
+ window.dUpper=0;
+ strcpy(inFile,"");
+ strcpy(outFile,"");
+ strcpy(MercuryFile,"");
+ strcpy(HardklorFile,"");
+ algorithm=FastFewestPeptides;
+ variant = new vector<CHardklorVariant>;
+
+ msType=FTICR;
+ res400=100000;
+ winSize=4.0;
+
+ chargeMode='Q';
+ snWindow=250.0;
+ skipZero=true;
+ noSplit=false;
+ sl=2;
+ fileFormat=dunno;
+ mzXMLFilter=MS1;
+ distArea=false;
+ strcpy(formula,"");
+
+ centroid=false;
+ staticSN=true;
+ xml=false;
+ reducedOutput=false;
+
+ //ppMatch=1;
+ //ppWin=1;
+ //noiseMatch=1;
+ //noiseWindow=3;
+ ppm=10.0;
+ //sna=0;
+ boxcar=0;
+ boxcarFilter=0;
+
+ //rawAvg=false;
+ //rawAvgWidth=1;
+ //rawAvgCutoff=1000;
+
+ strcpy(rawFilter,"");
+}
+
+CHardklorSetting::CHardklorSetting(const CHardklorSetting& c){
+ int i;
+
+ //Copy variant list
+ variant = new vector<CHardklorVariant>;
+ for(i=0;i<c.variant->size();i++) variant->push_back(c.variant->at(i));
+
+ //Copy other data memebers
+ noBase=c.noBase;
+ iAnalysis=c.iAnalysis;
+ maxCharge=c.maxCharge;
+ minCharge=c.minCharge;
+ msLevel=c.msLevel;
+ depth=c.depth;
+ peptide=c.peptide;
+ smooth=c.smooth;
+ corr=c.corr;
+ sn=c.sn;
+ scan.iLower=c.scan.iLower;
+ scan.iUpper=c.scan.iUpper;
+ window.dLower=c.window.dLower;
+ window.dUpper=c.window.dUpper;
+ strcpy(inFile,c.inFile);
+ strcpy(outFile,c.outFile);
+ strcpy(MercuryFile,c.MercuryFile);
+ strcpy(HardklorFile,c.HardklorFile);
+ algorithm=c.algorithm;
+ msType=c.msType;
+ res400=c.res400;
+ winSize=c.winSize;
+
+ chargeMode=c.chargeMode;
+ snWindow=c.snWindow;
+ skipZero=c.skipZero;
+ noSplit=c.noSplit;
+ sl=c.sl;
+ fileFormat=c.fileFormat;
+ mzXMLFilter=c.mzXMLFilter;
+ distArea=c.distArea;
+ strcpy(formula,c.formula);
+
+ centroid = c.centroid;
+ staticSN = c.staticSN;
+ xml = c.xml;
+ reducedOutput = c.reducedOutput;
+
+ //ppMatch=c.ppMatch;
+ //ppWin=c.ppWin;
+ //noiseMatch=c.noiseMatch;
+ //noiseWindow=c.noiseWindow;
+ ppm=c.ppm;
+ //sna=c.sna;
+ boxcar=c.boxcar;
+ boxcarFilter=c.boxcarFilter;
+
+ //rawAvg=c.rawAvg;
+ //rawAvgWidth=c.rawAvgWidth;
+ //rawAvgCutoff=c.rawAvgCutoff;
+ strcpy(rawFilter,c.rawFilter);
+}
+
+CHardklorSetting::~CHardklorSetting(){
+ delete variant;
+}
+
+CHardklorSetting& CHardklorSetting::operator=(const CHardklorSetting& c){
+ int i;
+ if (this!=&c){
+ delete variant;
+ variant = new vector<CHardklorVariant>;
+ for(i=0;i<c.variant->size();i++){
+ variant->push_back(c.variant->at(i));
+ }
+ noBase=c.noBase;
+ iAnalysis=c.iAnalysis;
+ maxCharge=c.maxCharge;
+ minCharge=c.minCharge;
+ msLevel=c.msLevel;
+ depth=c.depth;
+ peptide=c.peptide;
+ smooth=c.smooth;
+ corr=c.corr;
+ sn=c.sn;
+ scan.iLower=c.scan.iLower;
+ scan.iUpper=c.scan.iUpper;
+ window.dLower=c.window.dLower;
+ window.dUpper=c.window.dUpper;
+ strcpy(inFile,c.inFile);
+ strcpy(outFile,c.outFile);
+ strcpy(MercuryFile,c.MercuryFile);
+ strcpy(HardklorFile,c.HardklorFile);
+ algorithm=c.algorithm;
+ msType=c.msType;
+ res400=c.res400;
+ winSize=c.winSize;
+
+ chargeMode=c.chargeMode;
+ snWindow=c.snWindow;
+ skipZero=c.skipZero;
+ noSplit=c.noSplit;
+ sl=c.sl;
+ fileFormat=c.fileFormat;
+ mzXMLFilter=c.mzXMLFilter;
+ distArea=c.distArea;
+ strcpy(formula,c.formula);
+
+ centroid = c.centroid;
+ staticSN = c.staticSN;
+ xml = c.xml;
+ reducedOutput = c.reducedOutput;
+
+ //ppMatch=c.ppMatch;
+ //ppWin=c.ppWin;
+ //noiseMatch=c.noiseMatch;
+ //noiseWindow=c.noiseWindow;
+ ppm=c.ppm;
+ //sna=c.sna;
+ boxcar=c.boxcar;
+ boxcarFilter=c.boxcarFilter;
+
+ //rawAvg=c.rawAvg;
+ //rawAvgWidth=c.rawAvgWidth;
+ //rawAvgCutoff=c.rawAvgCutoff;
+
+ strcpy(rawFilter,c.rawFilter);
+ }
+ return *this;
+}
+
+void CHardklorSetting::clearVariant(){
+ delete variant;
+ variant = new vector<CHardklorVariant>;
+}
+
+void CHardklorSetting::out(char *s){
+ sprintf(s,"minCh:%d maxCh:%d d:%d p:%d s:%d corr:%lf sn:%lf res:%d,%lf win:%lf sl:%d v:%d\n",minCharge,maxCharge,depth,peptide,smooth,corr,sn,msType,res400,winSize,sl,variant->size());
+}
diff --git a/src/app/hardklor/CHardklorSetting.h b/src/app/hardklor/CHardklorSetting.h
new file mode 100644
index 0000000..9fe9bee
--- /dev/null
+++ b/src/app/hardklor/CHardklorSetting.h
@@ -0,0 +1,90 @@
+#ifndef _CHARDKLORSETTING_H
+#define _CHARDKLORSETTING_H
+
+#include <cstdio>
+#include <cstring>
+#include <string>
+#include <vector>
+
+#include "HardklorTypes.h"
+#include "CHardklorVariant.h"
+
+using namespace std;
+
+/*
+ Defined as a class instead of a struct so
+ that default parameters are used. Data access
+ will be identical to that of a struct.
+*/
+class CHardklorSetting {
+
+ public:
+ //Constructors & Destructors:
+ CHardklorSetting();
+ CHardklorSetting(const CHardklorSetting&);
+ ~CHardklorSetting();
+
+ //Methods:
+ CHardklorSetting& operator=(const CHardklorSetting&);
+ void clearVariant();
+ void out(char *s);
+
+ //Data Mebers:
+ bool centroid; //spectrum data is centroided
+ bool distArea; //report distribution area instead of base peak intensity
+ bool iAnalysis; //intersect analysis(true) or union analysis(false)
+ bool noBase; //No base molecule - perform analysis with only averagine variant models
+ bool noSplit; //analyze entire spectrum at once
+ //bool rawAvg; //use averaged raw scans
+ bool reducedOutput; //output m/z, intensity, and charge only (de-isotoped peaks)
+ bool skipZero; //ignore zero intensity data points
+ bool staticSN; //for sna=THRASH; assume one noise level for entire spectrum
+ bool xml; //output is in xml
+
+ int boxcar; //number of scans to average together
+ int boxcarFilter; //value to meet or exceed to keep peak in boxcar averaged data
+ int depth; //maximum number of overlapping peptides
+ int maxCharge; //max charge state to search for
+ int minCharge; //min charge state to search for
+ int msLevel; //integer representation of the scan level
+ int peptide; //maximum peptide models to analyze at a single time
+ //int ppMatch; //pre-processing matches. m/z must be observed this amount across ppWin
+ //int ppWin; //pre-processing window size (1 = +/-1 scan)
+ //int noiseMatch; //for sna=PP; number of matches required for real peaks
+ //int noiseWindow; //for sna=PP; Size of window over which scans are analyzed
+ //int rawAvgCutoff; //Noise cutoff intensity for averaged raw scans
+ //int rawAvgWidth; //Number of scans on either side of target to average (1 = +/-1 scan)
+ int sl; //sensitivity level
+ int smooth; //Savitsky-Golay smoothing window size
+ //int sna; //Signal-to-noise algorithm; 0=THRASH, 1=Persistent peaks (PP)
+
+ double corr; //correlation threshold
+ double ppm; //ppm tolerance of m/z values to match across scans
+ double res400; //resolution at m/z 400
+ double sn; //for sna=THRASH; signal-to-noise ratio threshold
+ double snWindow; //for sna=THRASH; bin size over which local noise is computed
+ double winSize; //maximum window size for analysis
+
+ sInt scan; //scan range to analyze
+ sDouble window; //m/z range to analyze
+
+ char chargeMode; //charge determination function to use
+ char formula[64]; //non-averagine model formula
+ char inFile[256]; //input file name
+ char outFile[256]; //output file name
+ char rawFilter[256]; //Filter which spectra from raw files are analyzed
+ char MercuryFile[256]; //mercury data file to use
+ char HardklorFile[256]; //hardklor data file to use
+
+ specType msType; //Type of mass spectrometer used to acquire data
+ hkAlgorithm algorithm; //Deconvolving algorithm to use
+ vector<CHardklorVariant> *variant; //Variants to make to averagine
+ MSFileFormat fileFormat; //File format
+ MSSpectrumType mzXMLFilter; //Filter for mzXML files
+
+ protected:
+ private:
+
+};
+
+#endif
diff --git a/src/app/hardklor/CHardklorVariant.cpp b/src/app/hardklor/CHardklorVariant.cpp
new file mode 100644
index 0000000..01bff2a
--- /dev/null
+++ b/src/app/hardklor/CHardklorVariant.cpp
@@ -0,0 +1,100 @@
+#include "CHardklorVariant.h"
+
+using namespace std;
+
+CHardklorVariant::CHardklorVariant(){
+ ID=0;
+ atoms = new vector<sInt>;
+ enrich = new vector<sEnrichMercury>;
+};
+
+CHardklorVariant::CHardklorVariant(const CHardklorVariant& c){
+ int i;
+
+ atoms = new vector<sInt>;
+ enrich = new vector<sEnrichMercury>;
+
+ for(i=0;i<c.atoms->size();i++){
+ atoms->push_back(c.atoms->at(i));
+ };
+
+ for(i=0;i<c.enrich->size();i++){
+ enrich->push_back(c.enrich->at(i));
+ };
+
+ ID = c.ID;
+
+};
+
+CHardklorVariant::~CHardklorVariant(){
+ delete atoms;
+ delete enrich;
+};
+
+CHardklorVariant& CHardklorVariant::operator=(const CHardklorVariant& c){
+ int i;
+ if(this!=&c){
+ delete atoms;
+ delete enrich;
+ atoms = new vector<sInt>;
+ enrich = new vector<sEnrichMercury>;
+
+ for(i=0;i<c.atoms->size();i++){
+ atoms->push_back(c.atoms->at(i));
+ };
+
+ for(i=0;i<c.enrich->size();i++){
+ enrich->push_back(c.enrich->at(i));
+ };
+
+ ID = c.ID;
+
+ };
+ return *this;
+};
+
+void CHardklorVariant::addAtom(const sInt& a){
+ atoms->push_back(a);
+};
+
+void CHardklorVariant::addAtom(const int& a, const int& b){
+ sInt s;
+ s.iLower = a;
+ s.iUpper = b;
+ atoms->push_back(s);
+};
+
+void CHardklorVariant::addEnrich(const sEnrichMercury& a){
+ enrich->push_back(a);
+};
+
+void CHardklorVariant::addEnrich(const int& a, const int& c, const double& b){
+ sEnrichMercury s;
+ s.atomNum = a;
+ s.isotope = c;
+ s.ape = b;
+ enrich->push_back(s);
+};
+
+sInt& CHardklorVariant::atAtom(int i){
+ return atoms->at(i);
+};
+
+sEnrichMercury& CHardklorVariant::atEnrich(int i){
+ return enrich->at(i);
+};
+
+void CHardklorVariant::clear(){
+ delete atoms;
+ delete enrich;
+ atoms = new vector<sInt>;
+ enrich = new vector<sEnrichMercury>;
+};
+
+int CHardklorVariant::sizeAtom(){
+ return atoms->size();
+};
+
+int CHardklorVariant::sizeEnrich(){
+ return enrich->size();
+};
diff --git a/src/app/hardklor/CHardklorVariant.h b/src/app/hardklor/CHardklorVariant.h
new file mode 100644
index 0000000..f924265
--- /dev/null
+++ b/src/app/hardklor/CHardklorVariant.h
@@ -0,0 +1,43 @@
+#ifndef _CHARDKLORVARIANT_H
+#define _CHARDKLORVARIANT_H
+
+#include <vector>
+
+#include "HardklorTypes.h"
+
+using namespace std;
+
+class CHardklorVariant {
+ public:
+ //Constructors & Destructors:
+ CHardklorVariant();
+ CHardklorVariant(const CHardklorVariant&);
+ ~CHardklorVariant();
+
+ //Operators:
+ CHardklorVariant& operator=(const CHardklorVariant&);
+
+ //Methods:
+ void addAtom(const sInt&);
+ void addAtom(const int&, const int&);
+ void addEnrich(const sEnrichMercury&);
+ void addEnrich(const int&, const int&, const double&);
+ sInt& atAtom(int);
+ sEnrichMercury& atEnrich(int);
+ void clear();
+ int sizeAtom();
+ int sizeEnrich();
+
+ //Data Members
+ int ID;
+
+ protected:
+
+ private:
+ //Data Members:
+ vector<sInt> *atoms;
+ vector<sEnrichMercury> *enrich;
+
+};
+
+#endif
diff --git a/src/app/hardklor/CMakeLists.txt b/src/app/hardklor/CMakeLists.txt
new file mode 100644
index 0000000..f3011fb
--- /dev/null
+++ b/src/app/hardklor/CMakeLists.txt
@@ -0,0 +1,60 @@
+project(hardklor)
+
+cmake_minimum_required(VERSION 2.8.1)
+cmake_policy(VERSION 2.8.1)
+
+include_directories(${CMAKE_SOURCE_DIR}/src)
+include_directories(${CMAKE_BINARY_DIR}/ext/include)
+include_directories(${CMAKE_BINARY_DIR}/ext/include/MSToolkit)
+if (WIN32 AND NOT Cygwin)
+ # Needed to put DLL containing type libraries
+ # in include path for Windows
+ include_directories(${CMAKE_BINARY_DIR}/ext/lib)
+endif (WIN32 AND NOT Cygwin)
+
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _CRT_SECURE_NO_WARNINGS
+ CRUX
+ NOMINMAX
+ )
+else (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _FILE_OFFSET_BITS=64
+ _GNU_SOURCE
+ _LARGEFILE_SOURCE
+ CRUX
+ GCC
+ HAVE_EXPAT_CONFIG_H
+ )
+endif (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+add_library(
+ hardklor
+ STATIC
+ CAveragine.cpp
+ CHardklor.cpp
+ CHardklor2.cpp
+ CHardklorParser.cpp
+ CHardklorProtein.cpp
+ CHardklorSetting.cpp
+ CHardklorVariant.cpp
+ CMercury8.cpp
+ CModelLibrary.cpp
+ CNoiseReduction.cpp
+ CPeriodicTable.cpp
+ CSpecAnalyze.cpp
+ CSplitSpectrum.cpp
+ FFT.cpp
+ FFT-HK.cpp
+ S2N.cpp
+ Smooth.cpp
+ SpecAnalyzeSupport.cpp
+ CruxHardklorApplication.cpp
+)
diff --git a/src/app/hardklor/CMercury8.cpp b/src/app/hardklor/CMercury8.cpp
new file mode 100644
index 0000000..25eb97b
--- /dev/null
+++ b/src/app/hardklor/CMercury8.cpp
@@ -0,0 +1,1112 @@
+/*=====================================================================*/
+/* Program MERCURY2.C */
+/* */
+/* MERCURY5 is a version of MERCURY2 using (mostly) double percision. */
+/* instead of floating point arithmatic. It gives more accurate */
+/* intensity values than MERCURY2. */
+/* MERCURY2 is an integer based version of MERCURY, although most of */
+/* the arithmetic is floating point. Using integer (changed to float) */
+/* values for isotopic masses, the calculation can be performed with */
+/* a much smaller data set and is extremely fast. The ASCII output */
+/* file is a stick representation of the mass spectrum. There is no */
+/* ultrahigh resolution mode in this program. */
+/* */
+/* Algorithm by Alan L. Rockwood */
+/* Programming by Steve Van Orden */
+/*=====================================================================*/
+
+/*=====================================================================*/
+/* C++ implementation (CMercury5) by Michael Hoopmann, 2004 */
+/* */
+/* To use: */
+/* 1. Create CMercury5 object. */
+/* 2. Call GoMercury(formula, [optional] charge, [optional] filename)*/
+/* 3. Optionally call Echo(true) to display output to screen. */
+/* */
+/* Example: */
+/* #include "CMercury5.h" */
+/* using namespace std; */
+/* int main(){ */
+/* CMercury5 dist; */
+/* dist.Echo(true); */
+/* dist.GoMercury("C6H12O6",1); */
+/* return 0; */
+/* }; */
+/* */
+/* Including the optional filename to GoMercury outputs the */
+/* distribution to file. The data can be manipulated in code in the */
+/* FixedData vector. See the header files CMercury5.h and mercury.h */
+/* for struct type. */
+/*=====================================================================*/
+
+#include "CMercury8.h"
+#include <cmath>
+#include <iostream>
+using namespace std;
+
+CMercury8::CMercury8(){
+ InitializeData();
+ showOutput = false;
+ bAccMass = false;
+ bRelAbun = true;
+ zeroMass=0;
+}
+
+CMercury8::CMercury8(char* fn){
+ InitializeData(fn);
+ showOutput = false;
+ bAccMass = false;
+ bRelAbun = true;
+ zeroMass=0;
+}
+
+CMercury8::~CMercury8(){
+ int Z;
+
+ for (Z=0; Z<=MAXAtomNo; Z++) {
+
+ delete [] Element[Z].IsoMass;
+ delete [] Element[Z].IntMass;
+ delete [] Element[Z].IsoProb;
+ //if(Element[Z].WrapMass!=NULL) delete [] Element[Z].WrapMass;
+
+ delete [] Orig[Z].IsoMass;
+ delete [] Orig[Z].IntMass;
+ delete [] Orig[Z].IsoProb;
+ //if(Orig[Z].WrapMass!=NULL) delete [] Orig[Z].WrapMass;
+ }
+}
+
+void CMercury8::Echo(bool b){
+ showOutput = b;
+}
+
+//quick hack for N-enrichment
+//This needs to be expanded to be universal for all elements
+void CMercury8::Enrich(int c,int e,double d){
+ int i=0;
+ int j=0;
+ double ab=0;
+ float f=(float)d;
+
+ //c++;
+ if(showOutput) cout << "Enrich: " << Element[c].Symbol << " " << c << "\t" << d << endl;
+
+ //Find highest probability
+ for(i=0;i<Element[c].NumIsotopes;i++){
+ if(Element[c].IsoProb[i]>ab){
+ j=i;
+ ab=Element[c].IsoProb[i];
+ }
+ }
+
+ //Normalize all isotope abundances
+ for(i=0;i<Element[c].NumIsotopes;i++){
+ Element[c].IsoProb[i]/=Element[c].IsoProb[j];
+ }
+
+ //Calculate enrichment
+ for(i=0;i<Element[c].NumIsotopes;i++){
+ if(i==e) Element[c].IsoProb[i]=(1-f)*Element[c].IsoProb[i]+f;
+ else Element[c].IsoProb[i]=(1-f)*Element[c].IsoProb[i];
+ }
+
+ EnrichAtoms.push_back(c);
+
+}
+
+
+/*************************************************/
+/* FUNCTION Intro - called by main() */
+/*************************************************/
+void CMercury8::Intro() {
+ printf("*********************************************************************\n");
+ printf("* M E R C U R Y V I I I *\n");
+ printf("* *\n");
+ printf("* An Integer based Fourier transform isotopic distibution program *\n");
+ printf("* Now capable of calculating accurate masses! *\n");
+ printf("*********************************************************************\n");
+ printf("\n");
+ printf(" Algorithm by : Alan L. Rockwood\n\n");
+ printf(" Program by : Steven L. Van Orden - 1\n");
+ printf(" Michael R. Hoopmann - 2\n\n");
+ printf(" Developed at : 1 - Pacific Northwest Laboratories / \n");
+ printf(" Battelle Northwest\n");
+ printf(" in the laboratory of Richard D. Smith\n");
+ printf(" 2 - University of Washington\n");
+ printf(" Department of Genome Science\n");
+ printf(" Michael J. MacCoss laboratory\n\n\n");
+
+} /* End of Intro() */
+
+/***************************************************/
+/* FUNCTION InitializeData - called by constructor */
+/***************************************************/
+//This function reads the ISOTOPE.DAT file that must be in the same
+//folder as the application.
+void CMercury8::InitializeData(char* fn) {
+
+ FILE *ElementFile;
+ int i, Z;
+
+ //Use default values if an isotope file is not provided
+ if(fn==NULL || strlen(fn)==0){
+ DefaultValues();
+ return;
+ }
+
+ if ((ElementFile = fopen(fn, "rt")) == NULL) {
+ printf("\nError - Cannot open File: ISOTOPE.DAT\n");
+ exit(-1);
+ }
+
+ for (Z=0; Z<=MAXAtomNo; Z++) {
+ Element[Z].Symbol[0]=Element[Z].Symbol[1]=Element[Z].Symbol[2]=0;
+
+ fscanf(ElementFile,"%2s %d\n", &Element[Z].Symbol,&Element[Z].NumIsotopes);
+ strcpy(Orig[Z].Symbol,Element[Z].Symbol);
+ Orig[Z].NumIsotopes = Element[Z].NumIsotopes;
+
+ Element[Z].IsoMass = new float[Element[Z].NumIsotopes+1];
+ Element[Z].IntMass = new int[Element[Z].NumIsotopes+1];
+ Element[Z].IsoProb = new float[Element[Z].NumIsotopes+1];
+ //Element[Z].WrapMass = NULL;
+
+ Orig[Z].IsoMass = new float[Orig[Z].NumIsotopes+1];
+ Orig[Z].IntMass = new int[Orig[Z].NumIsotopes+1];
+ Orig[Z].IsoProb = new float[Orig[Z].NumIsotopes+1];
+ //Orig[Z].WrapMass = NULL;
+
+ for (i=0; i<Element[Z].NumIsotopes; i++) {
+ fscanf(ElementFile, "%f \n", &Element[Z].IsoMass[i]);
+ fscanf(ElementFile, "%f \n", &Element[Z].IsoProb[i]);
+ Element[Z].IntMass[i] = (int)(Element[Z].IsoMass[i]+0.5);
+ Orig[Z].IsoMass[i]=Element[Z].IsoMass[i];
+ Orig[Z].IsoProb[i]=Element[Z].IsoProb[i];
+ Orig[Z].IntMass[i]=Element[Z].IntMass[i];
+ }
+
+ Element[Z].NumAtoms = 0;
+ Element[Z].IsoMass[Element[Z].NumIsotopes] = 0;
+ Element[Z].IsoProb[Element[Z].NumIsotopes] = 0;
+ Orig[Z].NumAtoms = 0;
+ Orig[Z].IsoMass[Orig[Z].NumIsotopes] = 0;
+ Orig[Z].IsoProb[Orig[Z].NumIsotopes] = 0;
+
+ fscanf(ElementFile, " \n");
+ }
+
+ fclose(ElementFile);
+
+}
+
+/*************************************************/
+/* FUNCTION CalcVariances - called by main() */
+/*************************************************/
+void CMercury8::CalcVariances(double *MolVar, double *IntMolVar, int NumElements){
+ int i, j, Z;
+ double Var, IntVar;
+ double avemass, intavemass;
+
+ *MolVar = *IntMolVar = 0;
+ for (i=0; i<NumElements; i++) {
+ Z = AtomicNum[i];
+ avemass = intavemass = 0;
+ for (j=0; j<Element[Z].NumIsotopes; j++){
+ avemass += Element[Z].IsoMass[j] * Element[Z].IsoProb[j];
+ intavemass += Element[Z].IntMass[j] * Element[Z].IsoProb[j];
+ };
+ Var = IntVar = 0;
+ for (j=0; j<Element[Z].NumIsotopes; j++){
+ Var += (Element[Z].IsoMass[j] - avemass) * (Element[Z].IsoMass[j] - avemass) * Element[Z].IsoProb[j];
+ IntVar += (Element[Z].IntMass[j] - intavemass) * (Element[Z].IntMass[j] - intavemass) * Element[Z].IsoProb[j];
+ };
+ *MolVar += Element[Z].NumAtoms * Var;
+ *IntMolVar += Element[Z].NumAtoms * IntVar;
+ };
+
+ //monoisotopic mass (zero mass, EXACT)
+ zeroMass=0;
+ for (i=0; i<NumElements; i++) {
+ Z = AtomicNum[i];
+ zeroMass+=(Element[Z].IsoMass[0] * Element[Z].NumAtoms);
+ };
+ monoMass=zeroMass;
+
+}; /* End of CalcVariances() */
+
+/*************************************************/
+/* FUNCTION CalcMassRange - called by main() */
+/*************************************************/
+void CMercury8::CalcMassRange(int *MassRange, double MolVar, int charge, int type) {
+ int i;
+ double dPoints;
+
+ //This is insufficient without adding the one to the end
+ if ((type == 1) || (charge == 0)) dPoints = (sqrt(1+MolVar)*10);
+ else dPoints = (sqrt(1+MolVar)*10/charge); /* +/- 5 sd's : Multiply charged */
+
+ /* Set to nearest (upper) power of 2 */
+ for (i=1024; i>0; i/=2) {
+ if (i < dPoints) {
+ *MassRange = i * 2 * 2; //MRH: Added extra power of 2 since this rule is often insufficient
+ i = 0;
+ };
+ };
+
+} /* End of CalcMassRange() */
+
+/*************************************************/
+/* FUNCTION AddElement - called by ParseMF() */
+/*************************************************/
+
+//Atom is the atomic abbreviation, Ecount is nth element in the formula
+//Acount is the number of atoms of the element in the formula
+void CMercury8::AddElement(char Atom[3], int Ecount, int Acount) {
+
+ int Z, FOUND=0;
+
+ for (Z=1; Z<=MAXAtomNo; Z++) {
+
+ if (strcmp(Atom,Element[Z].Symbol) == 0) {
+
+ if (Element[Z].NumAtoms != 0) {
+
+ printf("\nError - the element %s has been entered twice in molecular formula\n", Element[Z].Symbol);
+ exit(-1);
+
+ } else {
+
+ AtomicNum[Ecount] = Z;
+ Element[Z].NumAtoms = Acount;
+ //Element[Z].WrapMass = new int[Element[Z].NumIsotopes+1];
+ //Element[Z].WrapMass[Element[Z].NumIsotopes] = 0;
+ FOUND=1;
+ break;
+
+ };
+
+ };
+ };
+
+ if (!FOUND) {
+ printf("\nError - Unknown element in Molecular Formula\n");
+ exit(-1);
+ };
+
+}
+
+/*************************************************/
+/* FUNCTION ParseMF - called by main() */
+/*************************************************/
+//Return codes
+// 0: Success
+// -1: Invalid character
+int CMercury8::ParseMF(char MF[], int *elementcount) {
+ int COND, ERRFLAG;
+ int atomcount;
+ char Atom[3], errorch;
+
+ atomcount=0; COND=0; ERRFLAG=0;
+ Atom[0] = Atom[1] = Atom[2] = '\0';
+
+ unsigned int pos=0;
+ unsigned int peek=0;
+ unsigned int count=0;
+ char digit[2];
+ bool bFirst=true;
+ atomcount=0;
+ *elementcount=0;
+ while(pos<strlen(MF) && ERRFLAG==0){
+ if(isupper(MF[pos])){
+ //Add the last atom
+ if(!bFirst) {
+ AddElement(Atom,(*elementcount)++,atomcount);
+ atomcount=0;
+ } else {
+ bFirst=false;
+ }
+
+ peek=pos+1;
+ if(peek==strlen(MF)){
+ //reached end of string, add this single atom
+ Atom[0]=MF[pos];
+ Atom[1]=Atom[2]='\0';
+ atomcount=1;
+ pos++;
+ continue;
+ }
+
+ if(isupper(MF[peek])){
+ //This is a single atom
+ Atom[0]=MF[pos];
+ Atom[1]=Atom[2]='\0';
+ atomcount=1;
+ pos++;
+ } else if(islower(MF[peek])){
+ //Set the atom name
+ Atom[0]=MF[pos];
+ Atom[1]=MF[peek];
+ Atom[2]='\0';
+ atomcount=0;
+ pos+=2;
+ } else if(isdigit(MF[peek])){
+ //Set the atom name
+ Atom[0]=MF[pos];
+ Atom[1]=Atom[2]='\0';
+ atomcount=0;
+ pos++;
+ } else {
+ errorch=MF[peek];
+ ERRFLAG=1;
+ }
+
+ } else if(isdigit(MF[pos])){
+ digit[0]=MF[pos];
+ digit[1]='\0';
+ atomcount*=10;
+ atomcount+=atoi(digit);
+ pos++;
+ } else {
+ errorch=MF[pos];
+ ERRFLAG=1;
+ }
+ }
+
+ if(ERRFLAG==0) AddElement(Atom,(*elementcount)++,atomcount);
+ else printf("There was an error\n");
+
+ if (ERRFLAG) {
+ printf("\nError in format of input... The character '%c' is invalid\n",errorch);
+ return -1;
+ } else {
+ return 0;
+ }
+
+}
+
+/*************************************************/
+/* FUNCTION CalcFreq - called by main() */
+/* Could be done with less code, but this */
+/* saves a few operations. */
+/*************************************************/
+void CMercury8::CalcFreq(complex* FreqData, int Ecount, int NumPoints, int MassRange, int MassShift) {
+
+ int i, j, k, Z;
+ double real, imag, freq, X, theta, r, tempr;
+ double a, b, c, d;
+
+ /* Calculate first half of Frequency Domain (+)masses */
+ for (i=0; i<NumPoints/2; i++) {
+
+ freq = (double)i/MassRange;
+ r = 1;
+ theta = 0;
+ for (j=0; j<Ecount; j++) {
+ Z = AtomicNum[j];
+ real = imag = 0;
+ for (k=0; k<Element[Z].NumIsotopes; k++) {
+ X = TWOPI * Element[Z].IntMass[k] * freq;
+ real += Element[Z].IsoProb[k] * cos(X);
+ imag += Element[Z].IsoProb[k] * sin(X);
+ }
+
+ /* Convert to polar coordinates, r then theta */
+ tempr = sqrt(real*real+imag*imag);
+ r *= pow(tempr,Element[Z].NumAtoms);
+ if (real > 0) theta += Element[Z].NumAtoms * atan(imag/real);
+ else if (real < 0) theta += Element[Z].NumAtoms * (atan(imag/real) + PI);
+ else if (imag > 0) theta += Element[Z].NumAtoms * HALFPI;
+ else theta += Element[Z].NumAtoms * -HALFPI;
+
+ } /* end for(j) */
+
+ /* Convert back to real:imag coordinates and store */
+ a = r * cos(theta);
+ b = r * sin(theta);
+ c = cos(TWOPI*MassShift*freq);
+ d = sin(TWOPI*MassShift*freq);
+ FreqData[i].real = a*c - b*d;
+ FreqData[i].imag = b*c + a*d;
+
+ } /* end for(i) */
+
+ /* Calculate second half of Frequency Domain (-)masses */
+ for (i=NumPoints/2; i<NumPoints; i++) {
+
+ freq = (double)(i-NumPoints)/MassRange;
+ r = 1;
+ theta = 0;
+ for (j=0; j<Ecount; j++) {
+ Z = AtomicNum[j];
+ real = imag = 0;
+ for (k=0; k<Element[Z].NumIsotopes; k++) {
+ X = TWOPI * Element[Z].IntMass[k] * freq;
+ real += Element[Z].IsoProb[k] * cos(X);
+ imag += Element[Z].IsoProb[k] * sin(X);
+ }
+
+ /* Convert to polar coordinates, r then theta */
+ tempr = sqrt(real*real+imag*imag);
+ r *= pow(tempr,Element[Z].NumAtoms);
+ if (real > 0) theta += Element[Z].NumAtoms * atan(imag/real);
+ else if (real < 0) theta += Element[Z].NumAtoms * (atan(imag/real) + PI);
+ else if (imag > 0) theta += Element[Z].NumAtoms * HALFPI;
+ else theta += Element[Z].NumAtoms * -HALFPI;
+
+ } /* end for(j) */
+
+ /* Convert back to real:imag coordinates and store */
+ a = r * cos(theta);
+ b = r * sin(theta);
+ c = cos(TWOPI*MassShift*freq);
+ d = sin(TWOPI*MassShift*freq);
+ FreqData[i].real = a*c - b*d;
+ FreqData[i].imag = b*c + a*d;
+
+ } /* end of for(i) */
+
+} /* End of CalcFreq() */
+
+
+/*************************************************/
+/* FUNCTION main() - main block of FFTISO */
+/*************************************************/
+//Return Codes:
+// 0: Success
+// 1: Invalid molecular formula
+// 2: Cannot write to file
+int CMercury8::GoMercury(char* MolForm, int Charge, char* filename) {
+
+ unsigned int i;
+ int NumElements=0; /* Number of elements in molecular formula */
+ FILE *outfile; /* output file pointer */
+
+ //MolForm is the only required data
+ if (strlen(MolForm) == 0) {
+ //printf("\nNo molecular formula!\n");
+ return 1;
+ }
+
+ //Parse the formula, check for validity
+ if (ParseMF(MolForm,&NumElements) == -1) {
+ MolForm[0] = '\0';
+ NumElements = 0;
+ return 1;
+ }
+
+ //Run the user requested Mercury
+ if(bAccMass) AccurateMass(NumElements,Charge);
+ else Mercury(NumElements,Charge);
+
+ //If the user requested relative abundance, convert data
+ if(bRelAbun) RelativeAbundance(FixedData);
+
+ //If the user requested the data to file, output it here.
+ if (filename[0]!=0){
+ if ((outfile = fopen(filename,"w")) == NULL) {
+ printf("\nError - Cannot create file %s\n",filename);
+ return 2;
+ }
+ for(i=0;i<FixedData.size();i++){
+ fprintf(outfile,"%lf %lf\n",FixedData[i].mass,FixedData[i].data);
+ }
+ fclose(outfile);
+
+ }
+
+ //If the user wants the data on the screen, let it be so.
+ if(showOutput){
+ for(i=0;i<FixedData.size();i++){
+ printf("%.4f\t%.5f\n",FixedData[i].mass,FixedData[i].data);
+ }
+ }
+
+ //Clear all non-user input so object can be reused:
+ Reset();
+
+ //Output a final, useful message
+ if(showOutput) printf("Mercury successful!\n");
+
+ return 0;
+
+}
+
+
+//This function resets all atomic states to those at initialization.
+//This is so the same object can be reused after performing a calculation
+//or after user intervention, such as Enrich().
+void CMercury8::Reset(){
+ unsigned int i;
+ int j;
+
+ for (i=0;i<20;i++) AtomicNum[i]=0;
+ for (i=0; i<=MAXAtomNo; i++) Element[i].NumAtoms = 0;
+
+ for (i=0;i<(int)EnrichAtoms.size();i++){
+ for (j=0;j<Element[EnrichAtoms[i]].NumIsotopes;j++){
+ Element[EnrichAtoms[i]].IsoProb[j] = Orig[EnrichAtoms[i]].IsoProb[j];
+ }
+ }
+ EnrichAtoms.clear();
+
+}
+
+//This function calculates the accurate mass. It's a bit slower, and it performs poorly
+//on the fringes of large proteins because of the estimation of MassRange algorithm, and the
+//fact that abundances would be so small as to be nearly indistinguishable from zero.
+void CMercury8::AccurateMass(int NumElements, int Charge){
+ int i,j, k;
+ int MassRange;
+ int PtsPerAmu;
+ int NumPoints; /* Working # of datapoints (real:imag) */
+ complex *FreqData; /* Array of real:imaginary frequency values for FFT */
+ double MW;
+ double MIMW, tempMW, MolVar, IntMolVar;
+ int intMW, MIintMW;
+ int dummyLong;
+ int dummyInt;
+
+
+ complex *AltData;
+ complex *AltData2;
+ int MaxIntMW;
+ int PMIintMW;
+ int IsoShift;
+
+ Result r;
+ vector<Result> vParent;
+ vector<Result> vProduct;
+
+ //If we made it this far, we have valid input, so calculate molecular weight
+ CalcWeights(MW, MIMW, tempMW, intMW, MIintMW, MaxIntMW, IsoShift, NumElements);
+
+ //If the user specified an Echo, output the data now.
+ if (showOutput){
+ if (Charge != 0) {
+ printf("Average Molecular Weight: %.3lf, at m/z: %.3f\n",MW,MW/fabs((double)Charge));
+ printf("Average Integer MW: %ld, at m/z: %.3f\n\n",intMW,(float)intMW/fabs((double)Charge));
+ } else {
+ printf("Average Molecular Weight: %.3lf\n",MW);
+ printf("Average Integer MW: %ld\n\n",intMW);
+ }
+ }
+
+ //Set our parental molecular weight. This will be used as the lower bounds.
+ //PMIintMW = (int)round(MIMW);
+ PMIintMW = (int)(MIMW+0.5);
+
+ //Calculate mass range to use based on molecular variance
+ CalcVariances(&MolVar,&IntMolVar,NumElements);
+ CalcMassRange(&MassRange,MolVar,1,1);
+ PtsPerAmu = 1;
+
+ //Allocate memory for Axis arrays
+ NumPoints = MassRange * PtsPerAmu;
+ FreqData = new complex[NumPoints];
+
+ //Start isotope distribution calculation
+ //MH notes: How is this different from using -MW instead of -intMW?
+ CalcFreq(FreqData,NumElements,NumPoints,MassRange,-intMW);
+ FFT(FreqData,NumPoints,false);
+
+ //Converts complex numbers back to masses
+ ConvertMass(FreqData,NumPoints,PtsPerAmu,MW,tempMW,intMW,MIintMW,1,MolVar,IntMolVar);
+
+ //Put our data in the global array
+ FixedData.clear();
+ for(j=NumPoints/2; j<NumPoints; j++){
+ r.data=FreqData[j].real;
+ r.mass=FreqData[j].imag;
+ FixedData.push_back(r);
+ };
+
+ for(j=0; j<NumPoints/2; j++){
+ r.data=FreqData[j].real;
+ r.mass=FreqData[j].imag;
+ FixedData.push_back(r);
+ };
+
+ //Convert the data to integers
+ MassToInt(FreqData,NumPoints);
+
+ //Shift the lower bound to reflect the range of points that will be in common
+ //with all product variants. This is necessary for proteins in which the monoisotopic
+ //mass is not visible, thus we must adjust for the first data point in each product
+ //if(FixedData.at(0).mass > (PMIintMW+IsoShift)) PMIintMW=(int)round(FixedData.at(0).mass)+IsoShift;
+ if(FixedData[0].mass > (PMIintMW+IsoShift)) PMIintMW=(int)(FixedData[0].mass+0.5)+IsoShift;
+
+ //Reduce the parent set to this new boundary
+ GetPeaks(FreqData,NumPoints,vParent,PMIintMW,MaxIntMW);
+
+ //Set the upper bound to the max determined in the parent distribution
+ //MaxIntMW = (int)round(vParent.at(vParent.size()-1).mass);
+ MaxIntMW = (int)(vParent[vParent.size()-1].mass+0.5);
+
+ //set parental masses to 0
+ for(i=0;i<(int)vParent.size();i++) vParent[i].mass=0;
+
+ //We have now completed the analysis on the actual protein.
+ //Next we compute compositions for each element and each isotope
+ for(i=0;i<NumElements;i++){
+
+ //Subtract one atom
+ Element[AtomicNum[i]].NumAtoms--;
+
+ //Calculate the product masses and variances
+ //However, use the same mass range as the parent (calculated above)
+ CalcWeights(MW, MIMW, tempMW, intMW, MIintMW, dummyLong, dummyInt, NumElements);
+ CalcVariances(&MolVar,&IntMolVar,NumElements);
+
+ //Allocate memory for Axis arrays
+ AltData = new complex[NumPoints];
+ AltData2 = new complex[NumPoints];
+
+ //Start isotope distribution calculation
+ CalcFreq(AltData,NumElements,NumPoints,MassRange,-intMW);
+ FFT(AltData,NumPoints,false);
+
+ ConvertMass(AltData,NumPoints,PtsPerAmu,MW,tempMW,intMW,MIintMW,1,MolVar,IntMolVar);
+ MassToInt(AltData,NumPoints);
+
+
+ //Add the integer isotope mass
+ for(j=0;j<Element[AtomicNum[i]].NumIsotopes;j++){
+
+ //add mass to each point
+ for(k=0;k<NumPoints;k++) {
+ AltData2[k].imag=AltData[k].imag+Element[AtomicNum[i]].IntMass[j];
+ AltData2[k].real=AltData[k].real;
+ }
+
+ GetPeaks(AltData2,NumPoints,vProduct,PMIintMW,MaxIntMW);
+
+ //find ratio of abundances, multiply by abundance & number of atoms
+ for(k=0;k<(int)vProduct.size();k++){
+ vProduct[k].data/=vParent[k].data;
+ vProduct[k].data*=Element[AtomicNum[i]].IsoProb[j];
+ vProduct[k].data*=(Element[AtomicNum[i]].NumAtoms+1);
+
+ //Add to the real mass for the parent
+ vParent[k].mass += vProduct[k].data * Element[AtomicNum[i]].IsoMass[j];
+ }
+
+ }
+
+ delete [] AltData;
+ delete [] AltData2;
+
+ //Add back the atom
+ Element[AtomicNum[i]].NumAtoms++;
+
+ }
+
+ //output accurate masses:
+ FixedData.clear();
+ for(i=0;i<(int)vParent.size();i++){
+ if(vParent[i].data < 0.000001) continue;
+ vParent[i].mass=(vParent[i].mass+ProtonMass*Charge)/Charge;
+ FixedData.push_back(vParent[i]);
+ }
+
+ delete [] FreqData;
+
+}
+
+
+void CMercury8::ConvertMass(complex* Data, int NumPoints, int PtsPerAmu,
+ double MW, double tempMW, int intMW, int MIintMW, int charge,
+ double MolVar, double IntMolVar) {
+
+ int i;
+ double mass, ratio, CorrIntMW;
+
+ if (IntMolVar == 0) ratio = 1;
+ else ratio = sqrt(MolVar) / sqrt(IntMolVar);
+
+ CorrIntMW = tempMW * ratio;
+ for (i=NumPoints/2; i<NumPoints; i++) {
+ mass = (double)(i-NumPoints)/PtsPerAmu + intMW;
+ mass *= ratio;
+ mass += MW - CorrIntMW;
+ //mass /= charge;
+ Data[i].imag = mass;
+ };
+
+ for (i=0; i<NumPoints/2; i++) {
+ mass = (double)i/PtsPerAmu + intMW;
+ mass *= ratio;
+ mass += MW - CorrIntMW;
+ //mass /= charge;
+ Data[i].imag = mass;
+ };
+
+};
+
+void CMercury8::MassToInt(complex* Data, int NumPoints) {
+
+ int i, mass;
+
+ for (i=NumPoints/2; i<NumPoints; i++) {
+
+ //Since rounding poses problems, adjust when deviant values occur
+ //This assumes that the average width >1
+ mass = (int)(Data[i].imag+0.5);
+ if(i>NumPoints/2){
+ if(mass == Data[i-1].imag) mass++;
+
+ };
+
+ Data[i].imag = mass;
+ };
+
+ for (i=0; i<NumPoints/2; i++) {
+
+ //Since rounding poses problems, adjust when deviant values occur
+ //This assumes that the average width >1
+ mass = (int)(Data[i].imag+0.5);
+ if(i>0){
+ if(mass == Data[i-1].imag) mass++;
+ };
+
+ Data[i].imag = mass;
+ };
+
+};
+
+
+void CMercury8::GetPeaks(complex* Data, int NumPoints, vector<Result>& v,
+ int lower, int upper){
+ int i;
+ Result r;
+ v.clear();
+
+ for(i=NumPoints/2; i<NumPoints; i++){
+ if(Data[i].imag>=lower && Data[i].imag<=upper){
+ r.data=Data[i].real;
+ r.mass=Data[i].imag;
+ v.push_back(r);
+ };
+ };
+
+ for(i=0; i<NumPoints/2; i++){
+ if(Data[i].imag>=lower && Data[i].imag<=upper){
+ r.data=Data[i].real;
+ r.mass=Data[i].imag;
+ v.push_back(r);
+ };
+ };
+
+};
+
+void CMercury8::RelativeAbundance(vector<Result>& v){
+
+ unsigned int i;
+ double max=0;
+ double sum=0;
+
+ FracAbunData.clear();
+
+ /* Normalize intensity to 0%-100% scale */
+ for (i=0; i<v.size(); i++) {
+ if (v[i].data > max) max = v[i].data;
+ //also, store fractional abundances anyway (useful for Hardklor, which uses both);
+ FracAbunData.push_back(v[i]);
+ sum+=v[i].data;
+ }
+ for (i=0; i<v.size(); i++) {
+ v[i].data = 100 * v[i].data/max;
+ FracAbunData[i].data/=sum;
+ }
+
+}
+
+void CMercury8::CalcWeights(double& MW, double& MIMW, double& tempMW, int& intMW,
+ int& MIintMW, int& MaxIntMW, int& IsoShift, int NumElements){
+
+ int j, k, Z;
+
+ MW = MIMW = tempMW = 0; intMW = MIintMW = MaxIntMW = 0;
+ IsoShift=0;
+
+ for (j=0; j<NumElements; j++) {
+ Z = AtomicNum[j];
+ for (k=0; k<Element[Z].NumIsotopes; k++) {
+ MW += Element[Z].NumAtoms * Element[Z].IsoMass[k] * Element[Z].IsoProb[k];
+ tempMW += Element[Z].NumAtoms * Element[Z].IntMass[k] * Element[Z].IsoProb[k];
+ if (k==0) {
+ MIMW += Element[Z].NumAtoms * Element[Z].IsoMass[k];
+ MIintMW += Element[Z].NumAtoms * Element[Z].IntMass[k];
+ }
+ if(k==Element[Z].NumIsotopes-1){
+
+ //IsoShift is only used for accurate masses as an indication of how
+ //much each product distribution will differ in mass range from the
+ //parent distribution.
+ if((Element[Z].IntMass[k]-Element[Z].IntMass[0]) > IsoShift){
+ IsoShift = Element[Z].IntMass[k]-Element[Z].IntMass[0];
+ }
+
+ MaxIntMW += Element[Z].NumAtoms * Element[Z].IntMass[k];
+ }
+ }
+ }
+
+ MW -= ElectronMass;
+ tempMW -= ElectronMass;
+ MIMW -= ElectronMass;
+ intMW = (int)(tempMW+0.5);
+
+};
+
+//Calculates Mercury as done originally
+void CMercury8::Mercury(int NumElements, int Charge) {
+
+ int j;
+ int MassRange;
+ int PtsPerAmu;
+ int NumPoints; // Working # of datapoints (real:imag)
+ complex *FreqData; // Array of real:imaginary frequency values for FFT
+ double MW;
+ double MIMW, tempMW, MolVar, IntMolVar;
+ int intMW, MIintMW, MaxIntMW;
+ clock_t start, end;
+ float timex, seconds;
+ int minutes, dummyInt;
+ Result r;
+
+ //Calculate molecular weight
+ CalcWeights(MW, MIMW, tempMW, intMW, MIintMW, MaxIntMW, dummyInt, NumElements);
+
+ //If the user specified an Echo, output the data now.
+ if (showOutput){
+ if (Charge != 0) {
+ printf("Average Molecular Weight: %.3lf, at m/z: %.3f\n",MW,MW/fabs((double)Charge));
+ printf("Average Integer MW: %ld, at m/z: %.3f\n\n",intMW,(float)intMW/fabs((double)Charge));
+ } else {
+ printf("Average Molecular Weight: %.3lf\n",MW);
+ printf("Average Integer MW: %ld\n\n",intMW);
+ }
+ }
+
+ //Calculate mass range to use based on molecular variance
+ CalcVariances(&MolVar,&IntMolVar,NumElements);
+ CalcMassRange(&MassRange,MolVar,Charge,1);
+ PtsPerAmu = 1;
+
+ monoMass+=(Charge*(ProtonMass));
+ monoMass/=Charge;
+ if(showOutput) printf("True MonoMass: %.8lf\n",monoMass);
+
+ //Allocate memory for Axis arrays
+ NumPoints = MassRange * PtsPerAmu;
+ FreqData = new complex[NumPoints];
+
+ //Start isotope distribution calculation
+ //MH notes: How is this different from using -MW instead of -intMW?
+ start = clock();
+ CalcFreq(FreqData,NumElements,NumPoints,MassRange,-intMW);
+ FFT(FreqData,NumPoints,false);
+ end = clock();
+
+ //Output the results if the user requested an Echo.
+ if(showOutput){
+ timex = (float)(end - start) / CLOCKS_PER_SEC;
+ minutes = (int)(timex/60);
+ seconds = timex - (60*minutes);
+ printf("Calculation performed in %d min %.3f sec\n",minutes,seconds);
+ }
+
+ //Not sure why we do this...
+ if (Charge == 0) Charge = 1;
+
+ //Convert complex numbers to masses
+ ConvertMass(FreqData,NumPoints,PtsPerAmu,MW,tempMW,intMW,MIintMW,(int)fabs((double)Charge),MolVar,IntMolVar);
+
+ //Put our data in the global array
+ //This performs a bit of computation to eliminate meaningless data.
+ FixedData.clear();
+ for(j=NumPoints/2; j<NumPoints; j++){
+ if((int)(FreqData[j].imag+0.5)<MIintMW) continue;
+ r.data=FreqData[j].real;
+ r.mass=(FreqData[j].imag+(ProtonMass)*Charge)/Charge;
+ if( (monoMass-r.mass)*Charge > 0.5 ) continue;
+ r.data=FreqData[j].real;
+ r.mass=(FreqData[j].imag+ProtonMass*Charge)/Charge;
+ FixedData.push_back(r);
+ };
+
+ for(j=0; j<NumPoints/2; j++){
+ if((int)(FreqData[j].imag+0.5)>MaxIntMW) continue;
+ if(FreqData[j].real<0) break;
+ r.data=FreqData[j].real;
+ r.mass=(FreqData[j].imag+ProtonMass*Charge)/Charge;
+ FixedData.push_back(r);
+ };
+
+ //Clean up the memory
+ delete [] FreqData;
+
+};
+
+
+void CMercury8::AccMass(bool b) {
+ bAccMass = b;
+}
+
+void CMercury8::RelAbun(bool b) {
+ bRelAbun = b;
+}
+
+double CMercury8::getZeroMass(){
+ return zeroMass;
+}
+
+double CMercury8::getMonoMass(){
+ return monoMass;
+}
+
+void CMercury8::DefaultValues(){
+
+ string el[MAXAtomNo+1] = {"X","H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar",
+ "K","Ca","Sc","Ti","V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr","Rb","Sr","Y","Zr",
+ "Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te","I","Xe","Cs","Ba","La","Ce","Pr","Nd","Pm","Sm",
+ "Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu","Hf","Ta","W","Re","Os","Ir","Pt","Au","Hg","Tl","Pb","Bi","Po",
+ "At","Rn","Fr","Ra","Ac","Th","Pa","U","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr","Hx","Cx","Nx",
+ "Ox","Sx"};
+ int sz[MAXAtomNo+1] = {2,2,2,2,1,2,2,2,3,1,3,1,3,1,3,1,4,2,3,3,6,1,5,2,4,1,4,1,5,2,5,2,5,1,6,2,6,2,4,1,5,1,7,1,7,
+ 1,6,2,8,2,10,2,8,1,9,1,7,2,4,1,7,1,7,2,7,1,7,1,6,1,7,2,6,2,5,2,7,2,6,1,7,2,4,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,
+ 1,1,1,1,1,2,2,2,3,4};
+ double m[322] = {1.000000000000,2.000000000000,1.007824600000,2.014102100000,3.016030000000,4.002600000000,
+ 6.015121000000,7.016003000000,9.012182000000,10.012937000000,11.009305000000,12.000000000000,13.003355400000,
+ 14.003073200000,15.000108800000,15.994914100000,16.999132200000,17.999161600000,18.998403200000,
+ 19.992435000000,20.993843000000,21.991383000000,22.989767000000,23.985042000000,24.985837000000,
+ 25.982593000000,26.981539000000,27.976927000000,28.976495000000,29.973770000000,30.973762000000,
+ 31.972070000000,32.971456000000,33.967866000000,35.967080000000,34.968853100000,36.965903400000,
+ 35.967545000000,37.962732000000,39.962384000000,38.963707000000,39.963999000000,40.961825000000,
+ 39.962591000000,41.958618000000,42.958766000000,43.955480000000,45.953689000000,47.952533000000,
+ 44.955910000000,45.952629000000,46.951764000000,47.947947000000,48.947871000000,49.944792000000,
+ 49.947161000000,50.943962000000,49.946046000000,51.940509000000,52.940651000000,53.938882000000,
+ 54.938047000000,53.939612000000,55.934939000000,56.935396000000,57.933277000000,58.933198000000,
+ 57.935346000000,59.930788000000,60.931058000000,61.928346000000,63.927968000000,62.939598000000,
+ 64.927793000000,63.929145000000,65.926034000000,66.927129000000,67.924846000000,69.925325000000,
+ 68.925580000000,70.924700000000,69.924250000000,71.922079000000,72.923463000000,73.921177000000,
+ 75.921401000000,74.921594000000,73.922475000000,75.919212000000,76.919912000000,77.919000000000,
+ 79.916520000000,81.916698000000,78.918336000000,80.916289000000,77.914000000000,79.916380000000,
+ 81.913482000000,82.914135000000,83.911507000000,85.910616000000,84.911794000000,86.909187000000,
+ 83.913430000000,85.909267000000,86.908884000000,87.905619000000,88.905849000000,89.904703000000,
+ 90.905644000000,91.905039000000,93.906314000000,95.908275000000,92.906377000000,91.906808000000,
+ 93.905085000000,94.905840000000,95.904678000000,96.906020000000,97.905406000000,99.907477000000,
+ 98.000000000000,95.907599000000,97.905287000000,98.905939000000,99.904219000000,100.905582000000,
+ 101.904348000000,103.905424000000,102.905500000000,101.905634000000,103.904029000000,104.905079000000,
+ 105.903478000000,107.903895000000,109.905167000000,106.905092000000,108.904757000000,105.906461000000,
+ 107.904176000000,109.903005000000,110.904182000000,111.902758000000,112.904400000000,113.903357000000,
+ 115.904754000000,112.904061000000,114.903880000000,111.904826000000,113.902784000000,114.903348000000,
+ 115.901747000000,116.902956000000,117.901609000000,118.903310000000,119.902200000000,121.903440000000,
+ 123.905274000000,120.903821000000,122.904216000000,119.904048000000,121.903054000000,122.904271000000,
+ 123.902823000000,124.904433000000,125.903314000000,127.904463000000,129.906229000000,126.904473000000,
+ 123.905894000000,125.904281000000,127.903531000000,128.904780000000,129.903509000000,130.905072000000,
+ 131.904144000000,133.905395000000,135.907214000000,132.905429000000,129.906282000000,131.905042000000,
+ 133.904486000000,134.905665000000,135.904553000000,136.905812000000,137.905232000000,137.907110000000,
+ 138.906347000000,135.907140000000,137.905985000000,139.905433000000,141.909241000000,140.907647000000,
+ 141.907719000000,142.909810000000,143.910083000000,144.912570000000,145.913113000000,147.916889000000,
+ 149.920887000000,145.000000000000,143.911998000000,146.914895000000,147.914820000000,148.917181000000,
+ 149.917273000000,151.919729000000,153.922206000000,150.919847000000,152.921225000000,151.919786000000,
+ 153.920861000000,154.922618000000,155.922118000000,156.923956000000,157.924099000000,159.927049000000,
+ 158.925342000000,155.925277000000,157.924403000000,159.925193000000,160.926930000000,161.926795000000,
+ 162.928728000000,163.929171000000,164.930319000000,161.928775000000,163.929198000000,165.930290000000,
+ 166.932046000000,167.932368000000,169.935461000000,168.934212000000,167.933894000000,169.934759000000,
+ 170.936323000000,171.936378000000,172.938208000000,173.938859000000,175.942564000000,174.940770000000,
+ 175.942679000000,173.940044000000,175.941406000000,176.943217000000,177.943696000000,178.945812000000,
+ 179.946545000000,179.947462000000,180.947992000000,179.946701000000,181.948202000000,182.950220000000,
+ 183.950928000000,185.954357000000,184.952951000000,186.955744000000,183.952488000000,185.953830000000,
+ 186.955741000000,187.955860000000,188.958137000000,189.958436000000,191.961467000000,190.960584000000,
+ 192.962917000000,189.959917000000,191.961019000000,193.962655000000,194.964766000000,195.964926000000,
+ 197.967869000000,196.966543000000,195.965807000000,197.966743000000,198.968254000000,199.968300000000,
+ 200.970277000000,201.970617000000,203.973467000000,202.972320000000,204.974401000000,203.973020000000,
+ 205.974440000000,206.975872000000,207.976627000000,208.980374000000,209.000000000000,210.000000000000,
+ 222.000000000000,223.000000000000,226.025000000000,227.028000000000,232.038054000000,231.035900000000,
+ 234.040946000000,235.043924000000,238.050784000000,237.048000000000,244.000000000000,243.000000000000,
+ 247.000000000000,247.000000000000,251.000000000000,252.000000000000,257.000000000000,258.000000000000,
+ 259.000000000000,260.000000000000,1.007824600000,2.014102100000,12.000000000000,13.003355400000,
+ 14.003073200000,15.000108800000,15.994914100000,16.999132200000,17.999161600000,31.972070000000,
+ 32.971456000000,33.967866000000,35.967080000000};
+ double r[322] = {0.900000000000,0.100000000000,0.999855000000,0.000145000000,0.000001380000,0.999998620000,
+ 0.075000000000,0.925000000000,1.000000000000,0.199000000000,0.801000000000,0.989160000000,0.010840000000,
+ 0.996330000000,0.003660000000,0.997576009706,0.000378998479,0.002044991815,1.000000000000,0.904800000000,
+ 0.002700000000,0.092500000000,1.000000000000,0.789900000000,0.100000000000,0.110100000000,1.000000000000,
+ 0.922300000000,0.046700000000,0.031000000000,1.000000000000,0.950210000000,0.007450000000,0.042210000000,
+ 0.000130000000,0.755290000000,0.244710000000,0.003370000000,0.000630000000,0.996000000000,0.932581000000,
+ 0.000117000000,0.067302000000,0.969410000000,0.006470000000,0.001350000000,0.020860000000,0.000040000000,
+ 0.001870000000,1.000000000000,0.080000000000,0.073000000000,0.738000000000,0.055000000000,0.054000000000,
+ 0.002500000000,0.997500000000,0.043450000000,0.837900000000,0.095000000000,0.023650000000,1.000000000000,
+ 0.059000000000,0.917200000000,0.021000000000,0.002800000000,1.000000000000,0.682700000000,0.261000000000,
+ 0.011300000000,0.035900000000,0.009100000000,0.691700000000,0.308300000000,0.486000000000,0.279000000000,
+ 0.041000000000,0.188000000000,0.006000000000,0.601080000000,0.398920000000,0.205000000000,0.274000000000,
+ 0.078000000000,0.365000000000,0.078000000000,1.000000000000,0.009000000000,0.091000000000,0.076000000000,
+ 0.236000000000,0.499000000000,0.089000000000,0.506900000000,0.493100000000,0.003500000000,0.022500000000,
+ 0.116000000000,0.115000000000,0.570000000000,0.173000000000,0.721700000000,0.278300000000,0.005600000000,
+ 0.098600000000,0.070000000000,0.825800000000,1.000000000000,0.514500000000,0.112200000000,0.171500000000,
+ 0.173800000000,0.028000000000,1.000000000000,0.148400000000,0.092500000000,0.159200000000,0.166800000000,
+ 0.095500000000,0.241300000000,0.096300000000,1.000000000000,0.055400000000,0.018600000000,0.127000000000,
+ 0.126000000000,0.171000000000,0.316000000000,0.186000000000,1.000000000000,0.010200000000,0.111400000000,
+ 0.223300000000,0.273300000000,0.264600000000,0.117200000000,0.518390000000,0.481610000000,0.012500000000,
+ 0.008900000000,0.124900000000,0.128000000000,0.241300000000,0.122200000000,0.287300000000,0.074900000000,
+ 0.043000000000,0.957000000000,0.009700000000,0.006500000000,0.003600000000,0.145300000000,0.076800000000,
+ 0.242200000000,0.085800000000,0.325900000000,0.046300000000,0.057900000000,0.574000000000,0.426000000000,
+ 0.000950000000,0.025900000000,0.009050000000,0.047900000000,0.071200000000,0.189300000000,0.317000000000,
+ 0.338700000000,1.000000000000,0.001000000000,0.000900000000,0.019100000000,0.264000000000,0.041000000000,
+ 0.212000000000,0.269000000000,0.104000000000,0.089000000000,1.000000000000,0.001060000000,0.001010000000,
+ 0.024200000000,0.065930000000,0.078500000000,0.112300000000,0.717000000000,0.000900000000,0.999100000000,
+ 0.001900000000,0.002500000000,0.884300000000,0.111300000000,1.000000000000,0.271300000000,0.121800000000,
+ 0.238000000000,0.083000000000,0.171900000000,0.057600000000,0.056400000000,1.000000000000,0.031000000000,
+ 0.150000000000,0.113000000000,0.138000000000,0.074000000000,0.267000000000,0.227000000000,0.478000000000,
+ 0.522000000000,0.002000000000,0.021800000000,0.148000000000,0.204700000000,0.156500000000,0.248400000000,
+ 0.218600000000,1.000000000000,0.000600000000,0.001000000000,0.023400000000,0.189000000000,0.255000000000,
+ 0.249000000000,0.282000000000,1.000000000000,0.001400000000,0.016100000000,0.336000000000,0.229500000000,
+ 0.268000000000,0.149000000000,1.000000000000,0.001300000000,0.030500000000,0.143000000000,0.219000000000,
+ 0.161200000000,0.318000000000,0.127000000000,0.974100000000,0.025900000000,0.001620000000,0.052060000000,
+ 0.186060000000,0.272970000000,0.136290000000,0.351000000000,0.000120000000,0.999880000000,0.001200000000,
+ 0.263000000000,0.142800000000,0.307000000000,0.286000000000,0.374000000000,0.626000000000,0.000200000000,
+ 0.015800000000,0.016000000000,0.133000000000,0.161000000000,0.264000000000,0.410000000000,0.373000000000,
+ 0.627000000000,0.000100000000,0.007900000000,0.329000000000,0.338000000000,0.253000000000,0.072000000000,
+ 1.000000000000,0.001500000000,0.100000000000,0.169000000000,0.231000000000,0.132000000000,0.298000000000,
+ 0.068500000000,0.295240000000,0.704760000000,0.014000000000,0.241000000000,0.221000000000,0.524000000000,
+ 1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,0.000055000000,0.007200000000,0.992745000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,0.999855000000,0.000145000000,0.989160000000,0.010840000000,0.996330000000,
+ 0.003660000000,0.997576009706,0.000378998479,0.002044991815,0.950210000000,0.007450000000,0.042210000000,
+ 0.000130000000};
+
+ int j=0;
+ for (int Z=0; Z<=MAXAtomNo; Z++) {
+ strcpy(Element[Z].Symbol,&el[Z][0]);
+ strcpy(Orig[Z].Symbol,Element[Z].Symbol);
+ Orig[Z].NumIsotopes = Element[Z].NumIsotopes = sz[Z];
+
+ Element[Z].IsoMass = new float[sz[Z]+1];
+ Element[Z].IntMass = new int[sz[Z]+1];
+ Element[Z].IsoProb = new float[sz[Z]+1];
+
+ Orig[Z].IsoMass = new float[sz[Z]+1];
+ Orig[Z].IntMass = new int[sz[Z]+1];
+ Orig[Z].IsoProb = new float[sz[Z]+1];
+
+ for (int i=0; i<Element[Z].NumIsotopes; i++) {
+ Orig[Z].IsoMass[i]=Element[Z].IsoMass[i] = (float)m[j];
+ Orig[Z].IsoProb[i]=Element[Z].IsoProb[i] = (float)r[j];
+ Orig[Z].IntMass[i]=Element[Z].IntMass[i] = (int)(Element[Z].IsoMass[i]+0.5);
+ j++;
+ }
+
+ Element[Z].NumAtoms = 0;
+ Element[Z].IsoMass[Element[Z].NumIsotopes] = 0;
+ Element[Z].IsoProb[Element[Z].NumIsotopes] = 0;
+ Orig[Z].NumAtoms = 0;
+ Orig[Z].IsoMass[Orig[Z].NumIsotopes] = 0;
+ Orig[Z].IsoProb[Orig[Z].NumIsotopes] = 0;
+ }
+
+}
+
diff --git a/src/app/hardklor/CMercury8.h b/src/app/hardklor/CMercury8.h
new file mode 100644
index 0000000..3d6c6fc
--- /dev/null
+++ b/src/app/hardklor/CMercury8.h
@@ -0,0 +1,77 @@
+#ifndef _CMercury8_H
+#define _CMercury8_H
+
+#include <cstdio>
+#include <cstdlib>
+#include <cmath>
+#include <cstring>
+#include "ctype.h"
+#include <ctime>
+#include "mercury.h"
+#include "FFT.h"
+using namespace std;
+
+typedef struct
+{
+ char Symbol[3]; /* Elemental symbol */
+ int NumIsotopes; /* Number of stable isotopes */
+ float *IsoMass; /* Array of isotopic masses */
+ int *IntMass; /* Array of integer isotopic masses */
+ float *IsoProb; /* Array of isotopic probabilities */
+ int NumAtoms; /* Number of occurances of element in molecular formula */
+
+} Atomic5;
+
+class CMercury8 {
+ private:
+ //Data Members:
+ Atomic5 Element[MAXAtomNo+1]; /* 104 elements allows for Z=103 or Lr */
+ Atomic5 Orig[MAXAtomNo+1];
+ int AtomicNum[MAXIsotopes]; /* Atomic numbers of elements parsed from molecular formula */
+ bool showOutput;
+ bool bAccMass;
+ bool bRelAbun;
+ vector<int> EnrichAtoms;
+ double monoMass;
+ double zeroMass;
+
+ //Functions:
+ void AccurateMass(int,int);
+ void AddElement(char[],int,int);
+ void CalcFreq(complex*, int, int, int, int);
+ void CalcMassRange(int*, double, int, int);
+ void CalcVariances(double*, double*, int);
+ void CalcWeights(double&,double&,double&,int&,int&,int&,int&,int);
+ void ConvertMass(complex*, int, int, double, double, int, int, int, double, double);
+ void DefaultValues();
+ void GetPeaks(complex*, int, vector<Result>&, int, int);
+ void InitializeData(char* fn="ISOTOPE.DAT");
+ void MassToInt(complex*, int);
+ void Mercury(int,int);
+ int ParseMF(char[], int*);
+ void RelativeAbundance(vector<Result>&);
+
+ public:
+ //Data Members:
+ vector<Result> FixedData;
+ vector<Result> FracAbunData;
+
+ //Constructors & Destructors:
+ CMercury8();
+ CMercury8(char *fn);
+ ~CMercury8();
+
+ //Functions:
+ void AccMass(bool);
+ void Echo(bool);
+ void Enrich(int,int,double d=0.99);
+ double getMonoMass();
+ double getZeroMass();
+ int GoMercury(char*, int=1, char* filename="\0");
+ void Intro();
+ void RelAbun(bool);
+ void Reset();
+
+};
+
+#endif
diff --git a/src/app/hardklor/CModelLibrary.cpp b/src/app/hardklor/CModelLibrary.cpp
new file mode 100644
index 0000000..5a0955d
--- /dev/null
+++ b/src/app/hardklor/CModelLibrary.cpp
@@ -0,0 +1,119 @@
+#include "CModelLibrary.h"
+
+CModelLibrary::CModelLibrary(CAveragine* avg, CMercury8* mer){
+ averagine=avg;
+ mercury=mer;
+ libModel=NULL;
+
+ chargeMin=0;
+ chargeCount=0;
+ varCount=0;
+ merCount=0;
+}
+
+CModelLibrary::~CModelLibrary(){
+ averagine=NULL;
+ mercury=NULL;
+ if(libModel!=NULL) {
+ eraseLibrary();
+ libModel=NULL;
+ }
+}
+
+bool CModelLibrary::buildLibrary(int lowCharge, int highCharge, vector<CHardklorVariant>& pepVariants){
+
+ int i,j,k;
+ unsigned int n;
+
+ vector<Peak_T> vMR;
+ Peak_T p;
+ float da;
+ double mass;
+ char av[64];
+
+ if(libModel!=NULL) {
+ cout << "library memory already in use." << endl;
+ return false;
+ }
+
+ //Fill in boundaries
+ chargeMin=lowCharge;
+ chargeCount=highCharge+1;
+ varCount=pepVariants.size();
+ merCount=1000;
+
+ libModel = new mercuryModel**[chargeCount];
+ for(i=chargeMin;i<chargeCount;i++){
+
+ libModel[i] = new mercuryModel*[varCount];
+ for(j=0;j<varCount;j++){
+
+ libModel[i][j] = new mercuryModel[merCount];
+ libModel[i][j][0].area=0.0f;
+ libModel[i][j][0].size=0;
+ libModel[i][j][0].zeroMass=0.0;
+ libModel[i][j][0].peaks=NULL;
+ for(k=1;k<merCount;k++){
+
+ mass=k*5*i-(1.007276466*i);
+ averagine->clear();
+ averagine->calcAveragine(mass,pepVariants[j]);
+ averagine->getAveragine(&av[0]);
+ //cout << mass << "\t" << pepVariants[j].sizeAtom() << "\t" << pepVariants[j].sizeEnrich() << "\t" << av << endl;
+ for(n=0;n<(unsigned int)pepVariants[j].sizeEnrich();n++){
+ mercury->Enrich(pepVariants[j].atEnrich(n).atomNum,pepVariants[j].atEnrich(n).isotope,pepVariants[j].atEnrich(n).ape);
+ }
+ mercury->GoMercury(&av[0],i);
+
+ vMR.clear();
+ da=0.0f;
+ for(n=0; n<mercury->FixedData.size(); n++) {
+ if(mercury->FixedData[n].data<1.0) continue;
+ p.intensity=(float)mercury->FixedData[n].data;
+ p.mz=mercury->FixedData[n].mass;
+ da+=p.intensity;
+ vMR.push_back(p);
+ }
+ da/=100.0f;
+
+ libModel[i][j][k].area = da;
+ libModel[i][j][k].size = vMR.size();
+ libModel[i][j][k].peaks = new Peak_T[vMR.size()];
+ libModel[i][j][k].zeroMass = mercury->getZeroMass();
+
+ for(n=0;n<vMR.size();n++) libModel[i][j][k].peaks[n]=vMR[n];
+ }
+ }
+ }
+
+ return true;
+
+}
+
+void CModelLibrary::eraseLibrary(){
+
+ int i,j,k;
+
+ if(libModel==NULL) return;
+
+ for(i=chargeMin;i<chargeCount;i++){
+ for(j=0;j<varCount;j++){
+ for(k=0;k<merCount;k++){
+ delete [] libModel[i][j][k].peaks;
+ }
+ delete [] libModel[i][j];
+ }
+ delete [] libModel[i];
+ }
+ delete [] libModel;
+
+ libModel=NULL;
+
+}
+
+mercuryModel* CModelLibrary::getModel(int charge, int var, double mz){
+
+ int intMZ=(int)(mz/5);
+ return &libModel[charge][var][intMZ];
+
+}
\ No newline at end of file
diff --git a/src/app/hardklor/CModelLibrary.h b/src/app/hardklor/CModelLibrary.h
new file mode 100644
index 0000000..188b342
--- /dev/null
+++ b/src/app/hardklor/CModelLibrary.h
@@ -0,0 +1,40 @@
+#ifndef _CMODELLIBRARY_H
+#define _CMODELLIBRARY_H
+
+#include "HardklorTypes.h"
+#include "CAveragine.h"
+#include "CMercury8.h"
+#include "CHardklorVariant.h"
+#include <vector>
+
+using namespace std;
+
+class CModelLibrary {
+public:
+
+ //Constructors & Destructors
+ CModelLibrary(CAveragine* avg, CMercury8* mer);
+ ~CModelLibrary();
+
+ //User functions
+ bool buildLibrary(int lowCharge, int highCharge, vector<CHardklorVariant>& pepVariants);
+ void eraseLibrary();
+ mercuryModel* getModel(int charge, int var, double mz);
+
+protected:
+
+private:
+
+ //Data Members
+ int chargeMin;
+ int chargeCount;
+ int varCount;
+ int merCount;
+
+ CAveragine* averagine;
+ CMercury8* mercury;
+ mercuryModel*** libModel;
+
+};
+
+#endif
\ No newline at end of file
diff --git a/src/app/hardklor/CNoiseReduction.cpp b/src/app/hardklor/CNoiseReduction.cpp
new file mode 100644
index 0000000..9a7d9ce
--- /dev/null
+++ b/src/app/hardklor/CNoiseReduction.cpp
@@ -0,0 +1,1626 @@
+#include "CNoiseReduction.h"
+
+CNoiseReduction::CNoiseReduction(){
+ pos=0;
+ posA=0;
+ strcpy(lastFile,"");
+}
+
+CNoiseReduction::CNoiseReduction(MSReader* msr, CHardklorSetting& hs){
+ r=msr;
+ cs=hs;
+ pos=0;
+ posA=0;
+ strcpy(lastFile,"");
+}
+
+CNoiseReduction::~CNoiseReduction(){
+ r=NULL;
+}
+
+//Calculates the resolution (FWHM) of a peak
+double CNoiseReduction::calcFWHM(double mz){
+ double deltaM;
+ switch(cs.msType){
+ case OrbiTrap:
+ deltaM = mz * sqrt(mz) / (20*cs.res400); //(20*userParams.res400); //sqare root of 400
+ break;
+ case TOF:
+ deltaM = mz / cs.res400;
+ break;
+ case QIT:
+ deltaM = cs.res400 / 5000.0;
+ break;
+ case FTICR:
+ default:
+ deltaM = mz * mz / (400*cs.res400);
+ break;
+ }
+ return deltaM;
+}
+
+bool CNoiseReduction::DeNoise(Spectrum& sp){
+
+ double ppm;
+ int i,j,k;
+ int index;
+ int matchCount;
+ char cFilter1[256];
+ char cFilter2[256];
+
+ Spectrum tmpSpec;
+ vector<int> v;
+
+ sp.clear();
+
+ if(pos==0){
+ if((cs.scan.iLower>0)) {
+ k=cs.scan.iLower;
+ r->readFile(&cs.inFile[0],tmpSpec,cs.scan.iLower);
+ } else {
+ r->readFile(&cs.inFile[0],tmpSpec);
+ k=tmpSpec.getScanNumber();
+ }
+ if(tmpSpec.getScanNumber()==0) return false;
+ tmpSpec.getRawFilter(cFilter1,256);
+
+ //Gather left side of scan
+ i=1;
+ j=0;
+ while( k-i > 0){
+ r->readFile(&cs.inFile[0],tmpSpec,cs.scan.iLower-i);
+ if(tmpSpec.getScanNumber()==0) {
+ i++;
+ continue;
+ }
+ tmpSpec.getRawFilter(cFilter2,256);
+
+ //Assume High resolution data at all times
+ if(!cs.centroid) {
+ FirstDerivativePeaks(tmpSpec,1);
+ tmpSpec.setRawFilter(cFilter2);
+ }
+
+ s.push_front(tmpSpec);
+ if(strcmp(cFilter1,cFilter2)==0){
+ j++;
+ if(j==(int)(cs.boxcar/2)) break;
+ }
+ i++;
+ }
+
+ //cout << "Done left " << s.size() << " " << cs.rawAvgWidth << endl;
+
+ //Get our position again
+ r->readFile(&cs.inFile[0],tmpSpec,k);
+
+ //Assume High resolution data at all times
+ if(!cs.centroid) {
+ FirstDerivativePeaks(tmpSpec,1);
+ tmpSpec.setRawFilter(cFilter1);
+ }
+
+ //Add first target scan
+ s.push_back(tmpSpec);
+ pos=s.size()-1;
+
+ //Add right side of scan
+ i=1;
+ j=0;
+ while(true){
+ r->readFile(NULL,tmpSpec);
+ if(tmpSpec.getScanNumber()==0) break;
+ tmpSpec.getRawFilter(cFilter2,256);
+
+ //Assume High resolution data at all times
+ if(!cs.centroid) {
+ FirstDerivativePeaks(tmpSpec,1);
+ tmpSpec.setRawFilter(cFilter2);
+ }
+
+ s.push_back(tmpSpec);
+ //cout << tmpSpec.getScanNumber() << " " << cFilter1 << " xx " << cFilter2 << endl;
+ if(strcmp(cFilter1,cFilter2)==0){
+ j++;
+ if(j==(int)(cs.boxcar/2)) break;
+ }
+ i++;
+ }
+
+ }
+
+ //return false if we reached the end
+ if(pos>=(int)s.size()) return false;
+
+ //Because Deque may have mixed spectra, create list of Deque indexes to compare
+ //Shrink Deque on the left if some spectra are not needed
+ //Expand Deque to the right if needed and possible
+ //cout << "Checking scan " << s[pos].getScanNumber() << endl;
+ v.clear();
+ s[pos].getRawFilter(cFilter1,256);
+
+ //look left
+ for(i=pos-1;i>=0;i--){
+ s[i].getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ v.push_back(i);
+ if(v.size()==(int)(cs.boxcar/2)) break;
+ }
+ }
+
+ //erase unneeded left items
+ while(i>0){
+ s.pop_front();
+ i--;
+ for(j=0;j<(int)v.size();j++) v[j]--;
+ pos--;
+ }
+
+ //look right
+ j=0;
+ for(i=pos+1;i<(int)s.size();i++){
+ s[i].getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ v.push_back(i);
+ j++;
+ if(j==(int)(cs.boxcar/2)) break;
+ }
+ }
+
+ //extend right side if needed
+ while(j<(int)(cs.boxcar/2)){
+ r->readFile(NULL,tmpSpec);
+ if(tmpSpec.getScanNumber()==0) break;
+ tmpSpec.getRawFilter(cFilter2,256);
+
+ //Assume High resolution data at all times
+ if(!cs.centroid) {
+ FirstDerivativePeaks(tmpSpec,1);
+ tmpSpec.setRawFilter(cFilter2);
+ }
+
+ s.push_back(tmpSpec);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ v.push_back(s.size()-1);
+ j++;
+ }
+ }
+
+ //if there is nothing to compare to, exit now
+ if(v.size()==0) return false;
+
+ //compare peaks
+ //cout << "Checking " << s[pos].size() << " peaks." << endl;
+ for(i=0;i<s[pos].size();i++){
+ matchCount=1;
+ for(j=0;j<(int)v.size();j++){
+ if(s[v[j]].size()<1) continue;
+ index = NearestPeak(s[v[j]],s[pos].at(i).mz);
+ ppm=fabs( (s[v[j]].at(index).mz-s[pos].at(i).mz)/s[pos].at(i).mz * 1000000);
+ if(ppm<cs.ppm) matchCount++;
+ }
+ if(matchCount>=cs.boxcarFilter || matchCount==v.size()) sp.add(s[pos].at(i));
+ }
+ sp.setScanNumber(s[pos].getScanNumber());
+ sp.setScanNumber(s[pos].getScanNumber(true),true);
+ sp.setRTime(s[pos].getRTime());
+ pos++;
+
+ //cout << sp.getScanNumber() << endl;
+
+ //cout << "Done! " << sp.size() << " " << pos << endl;
+ return true;
+
+}
+
+//Overloaded function allows user to just pass an array of spectra to be compared.
+//No file reading/parsing is performed.
+/*
+bool CNoiseReduction::DeNoise(Spectrum& sp, vector<Spectrum>& vs, int pivot, bool findPeaks){
+
+ double ppm;
+ int i,j;
+ int index;
+ int matchCount;
+
+ Spectrum tmpSpec;
+ vector<int> v;
+
+ sp.clear();
+
+ //Find peaks (centroid) for all scans (assume high res data)
+ if(findPeaks) {
+ for(i=0;i<vs.size();i++) FirstDerivativePeaks(vs[i],1);
+ }
+
+ //compare peaks
+ for(i=0;i<vs[pivot].size();i++){
+ matchCount=1;
+ for(j=0;j<vs.size();j++){
+ if(j==pivot) continue;
+ if(vs[j].size()<1) continue;
+ index = NearestPeak(vs[j],vs[pivot].at(i).mz);
+ ppm=fabs( (vs[j].at(index).mz-vs[pivot].at(i).mz)/vs[pivot].at(i).mz * 1000000);
+ if(ppm<cs.ppm) matchCount++;
+ }
+ if(matchCount>=cs.ppMatch || matchCount==v.size()) sp.add(vs[pivot].at(i));
+ }
+ sp.setScanNumber(vs[pivot].getScanNumber());
+ sp.setScanNumber(vs[pivot].getScanNumber(true),true);
+ sp.setRTime(vs[pivot].getRTime());
+
+ //cout << "Done! " << sp.size() << " " << pivot << endl;
+ return true;
+
+}
+
+//Overloaded function allows user to just pass an array of spectra to be compared.
+//No file reading/parsing is performed.
+bool CNoiseReduction::DeNoise(Spectrum& sp, deque<Spectrum>& vs, int pivot, bool findPeaks){
+
+ double ppm;
+ int i,j;
+ int index;
+ int matchCount;
+
+ Spectrum tmpSpec;
+ vector<int> v;
+
+ sp.clear();
+
+ //Find peaks (centroid) for all scans (assume high res data)
+ if(findPeaks) {
+ for(i=0;i<vs.size();i++) FirstDerivativePeaks(vs[i],1);
+ }
+
+ //compare peaks
+ for(i=0;i<vs[pivot].size();i++){
+ matchCount=1;
+ for(j=0;j<vs.size();j++){
+ if(j==pivot) continue;
+ if(vs[j].size()<1) continue;
+ index = NearestPeak(vs[j],vs[pivot].at(i).mz);
+ ppm=fabs( (vs[j].at(index).mz-vs[pivot].at(i).mz)/vs[pivot].at(i).mz * 1000000);
+ if(ppm<cs.ppm) matchCount++;
+ }
+ if(matchCount>=cs.ppMatch || matchCount==v.size()) sp.add(vs[pivot].at(i));
+ }
+ sp.setScanNumber(vs[pivot].getScanNumber());
+ sp.setScanNumber(vs[pivot].getScanNumber(true),true);
+ sp.setRTime(vs[pivot].getRTime());
+
+ //cout << "Done! " << sp.size() << " " << pos << endl;
+ return true;
+
+}
+*/
+
+//First derivative method taken from CSpecAnalyze, returns base peak intensity of the set
+void CNoiseReduction::FirstDerivativePeaks(Spectrum& sp, int winSize){
+ int i,j;
+ float maxIntensity;
+ int bestPeak;
+ bool bLastPos;
+ Spectrum gp;
+
+ int nextBest;
+ double FWHM;
+ Peak_T centroid;
+
+ bLastPos=false;
+ for(i=0;i<sp.size()-winSize;i++){
+
+ if(sp.at(i).intensity<sp.at(i+winSize).intensity) {
+ bLastPos=true;
+ continue;
+ } else {
+ if(bLastPos){
+ bLastPos=false;
+
+ //find max and add peak
+ maxIntensity=0;
+ for(j=i;j<i+winSize;j++){
+ if (sp.at(j).intensity>maxIntensity){
+ maxIntensity=sp.at(j).intensity;
+ bestPeak = j;
+ }
+ }
+
+ //Best estimate of Gaussian centroid
+ //Get 2nd highest point of peak
+ if(bestPeak==sp.size()-1){
+ nextBest=bestPeak-1;
+ } else if(sp.at(bestPeak-1).intensity > sp.at(bestPeak+1).intensity){
+ nextBest=bestPeak-1;
+ } else {
+ nextBest=bestPeak+1;
+ }
+
+ //Get FWHM
+ FWHM = calcFWHM(sp.at(bestPeak).mz);
+
+ //Calc centroid MZ (in three lines for easy reading)
+ centroid.mz = pow(FWHM,2)*log(sp.at(bestPeak).intensity/sp.at(nextBest).intensity);
+ centroid.mz /= GC*(sp.at(bestPeak).mz-sp.at(nextBest).mz);
+ centroid.mz += (sp.at(bestPeak).mz+sp.at(nextBest).mz)/2;
+
+ //Calc centroid intensity
+ centroid.intensity=(float)(sp.at(bestPeak).intensity/exp(-pow((sp.at(bestPeak).mz-centroid.mz)/FWHM,2)*GC));
+
+ //some peaks are funny shaped and have bad gaussian fit.
+ //if error is more than 10%, keep existing intensity
+ if( fabs((sp.at(bestPeak).intensity - centroid.intensity) / centroid.intensity * 100) > 10 ||
+ //not a good check for infinity
+ centroid.intensity>999999999999.9 ||
+ centroid.intensity < 0 ) {
+ centroid.intensity=sp.at(bestPeak).intensity;
+ }
+
+ //Hack until I put in mass ranges
+ if(centroid.mz<0 || centroid.mz>2000) {
+ //do nothing if invalid mz
+ } else {
+ gp.add(centroid);
+ }
+ i+=winSize-1;
+ }
+
+ }
+ }
+
+ int scanNumber=sp.getScanNumber();
+ int scanNumber2=sp.getScanNumber(false);
+ float rTime=sp.getRTime();
+ sp = gp;
+ sp.setRTime(rTime);
+ sp.setScanNumber(scanNumber);
+ sp.setScanNumber(scanNumber2,true);
+
+}
+
+
+
+//Binary search to quickly find the nearest peak
+int CNoiseReduction::NearestPeak(Spectrum& sp, double mz){
+ int pivot=0;
+ int width=0;
+ int lastWidth=0;
+ int best=0;
+ double dif=9999999.9;
+ double d;
+
+ pivot=sp.size()/2;
+ width=(int)(pivot/2.0+0.5);
+ while(width!=lastWidth && pivot<sp.size() && pivot>-1){
+ d=fabs(sp.at(pivot).mz-mz);
+ if(d<dif){
+ dif=d;
+ best=pivot;
+ }
+ if(sp.at(pivot).mz==mz){
+ return pivot;
+ } else if(sp.at(pivot).mz > mz){
+ pivot-=width;
+ lastWidth=width;
+ width=(int)(width/2.0+0.5);
+ } else {
+ pivot+=width;
+ lastWidth=width;
+ width=(int)(width/2.0+0.5);
+ }
+ }
+ if(pivot<sp.size() && pivot>-1){
+ d=fabs(sp.at(pivot).mz-mz);
+ if(d<dif) best=pivot;
+ }
+ return best;
+}
+
+bool CNoiseReduction::ScanAverage(Spectrum& sp, char* file, int width, float cutoff){
+
+ Spectrum ts;
+ Spectrum ps=sp;
+ MSReader r;
+
+ int i;
+ int j;
+ int k;
+ int widthCount=0;
+ int numScans=1;
+ double dif;
+ double prec;
+ double dt;
+ double c=CParam(ps,3);
+
+ bool bLeft=true;
+ int posLeft=ps.getScanNumber()-1;
+ int posRight=ps.getScanNumber()+1;
+ char cFilter1[256];
+ char cFilter2[256];
+
+ ps.getRawFilter(cFilter1,256);
+
+ while(widthCount<(width*2)){
+
+ //Alternate looking left and right
+ if(bLeft){
+ bLeft=false;
+ widthCount++;
+ while(posLeft>0){
+ r.readFile(file,ts,posLeft);
+ if(ts.getScanNumber()==0) break;
+ ts.getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) break;
+ posLeft--;
+ }
+ } else {
+ bLeft=true;
+ widthCount++;
+ while(true){
+ r.readFile(file,ts,posRight);
+ if(ts.getScanNumber()==0) break;
+ ts.getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) break;
+ posRight++;
+ }
+ }
+ if(ts.getScanNumber()==0) continue;
+
+ numScans++;
+
+ //Match peaks between pivot scan and temp scan
+ k=0;
+ for(i=0;i<ps.size();i++){
+ dif=100000.0;
+ prec = c * ps.at(i).mz * ps.at(i).mz / 2;
+
+ for(j=k;j<ts.size();j++){
+ dt=fabs(ps.at(i).mz-ts.at(j).mz);
+ if(dt<=dif) {
+ if(dt<prec) {
+ ps.at(i).intensity+=ts.at(j).intensity;
+ ts.at(j).mz=-1.0;
+ k=j+1;
+ break;
+ }
+ dif=dt;
+ } else {
+ k=j-1;
+ break;
+ }
+ }
+ }
+
+ //Add unmatched peaks from temp scan
+ for(i=0;i<ts.size();i++){
+ if(ts.at(i).mz>-1.0) ps.add(ts.at(i));
+ }
+
+ //Sort pivot scan peaks for fast traversal against next temp scan
+ ps.sortMZ();
+
+ }
+
+ //Average points and apply cutoff
+ sp.clear();
+ for(i=0;i<ps.size();i++) {
+ ps.at(i).intensity/=numScans;
+ if(ps.at(i).intensity>=cutoff) sp.add(ps.at(i));
+ }
+
+ sp.setScanNumber(ps.getScanNumber());
+ sp.setScanNumber(ps.getScanNumber(true),true);
+ sp.setRTime(ps.getRTime());
+
+ return true;
+}
+
+bool CNoiseReduction::NewScanAverage(Spectrum& sp, char* file, int width, float cutoff, int scanNum){
+
+ Spectrum ts;
+
+ vector<int> vPos;
+
+ int i;
+ int j;
+ int k;
+ int m;
+ int widthCount=0;
+ int numScans=1;
+ double dif;
+ double prec;
+ double dt;
+ double c;
+
+ bool bLeft=true;
+ int posLeft;
+ int posRight;
+ int index;
+ char cFilter1[256];
+ //char cFilter2[256];
+
+ //double slope;
+ //double intercept;
+
+ sp.clear();
+ Spectrum* specs;
+ specs = new Spectrum[width*2+1];
+
+ //if file is not null, create new buffer
+ if(file!=NULL){
+ strcpy(lastFile,file);
+ bs.clear();
+ if(scanNum>0) r->readFile(file,ts,scanNum);
+ else r->readFile(file,ts);
+ if(ts.getScanNumber()==0) {
+ delete [] specs;
+ return false;
+ }
+ bs.push_back(ts);
+ specs[0]=bs[0];
+ c=CParam(specs[0],3);
+ posA=0;
+ } else {
+ posA++;
+ if(posA>=(int)bs.size()) { //end of buffer, no more data
+ delete [] specs;
+ return false;
+ }
+ specs[0]=bs[posA];
+ c=CParam(specs[0],3);
+ }
+
+ specs[0].getRawFilter(cFilter1,256);
+
+ posLeft=posA;
+ posRight=posA;
+ while(widthCount<(width*2)){
+
+ index=-1;
+
+ //Alternate looking left and right
+ if(bLeft){
+ bLeft=false;
+ widthCount++;
+
+ while(true){
+ posLeft--;
+ if(posLeft<0) { //buffer is too short on left, add spectra
+ i=bs[0].getScanNumber();
+ while(true){
+ i--;
+ if(i==0) break;
+ r->readFile(lastFile,ts,i);
+ if(ts.getScanNumber()==0) continue;
+ else break;
+ }
+ if(i==0) break;
+ bs.push_front(ts);
+ posA++;
+ posRight++;
+ posLeft=0;
+ //ts.getRawFilter(cFilter2,256);
+ if(ts.getMsLevel()==cs.msLevel) {
+ index=posLeft;
+ break;
+ }
+ } else {
+ //bs[posLeft].getRawFilter(cFilter2,256);
+ if(bs[posLeft].getMsLevel()==cs.msLevel) {
+ index=posLeft;
+ break;
+ }
+ }
+ }
+
+ } else {
+ bLeft=true;
+ widthCount++;
+
+ while(true){
+ posRight++;
+ if(posRight>=(int)bs.size()) { //buffer is too short on right, add spectra
+ r->readFile(lastFile,ts,bs[bs.size()-1].getScanNumber());
+ r->readFile(NULL,ts);
+ if(ts.getScanNumber()==0) {
+ posRight--;
+ break;
+ }
+ bs.push_back(ts);
+ //ts.getRawFilter(cFilter2,256);
+ if(ts.getMsLevel()==cs.msLevel) {
+ index=posRight;
+ break;
+ }
+ } else {
+ //bs[posRight].getRawFilter(cFilter2,256);
+ if(bs[posRight].getMsLevel()==cs.msLevel) {
+ index=posRight;
+ break;
+ }
+ }
+ }
+ }
+
+ if(index==-1) continue;
+ specs[numScans++]=bs[index];
+
+ }
+
+ double tmz;
+ int mzcount=0;
+
+ /* Ledford equation correction
+ double freq;
+ double conA=0.0;
+ double conB=0.0;
+
+ for(m=0;m<numScans;m++){
+ conA+=specs[m].getConversionA();
+ conB+=specs[m].getConversionB();
+ }
+ conA/=numScans;
+ conB/=numScans;
+
+ printf("%.10lf, %.10lf\n",conA,conB);
+ for(k=0;k<numScans;k++){
+ for(j=0;j<specs[k].size();j++){
+ freq = sqrt(specs[k].getConversionA()*specs[k].getConversionA() - (4*specs[k].at(j).mz*(-specs[k].getConversionB())));
+ freq += specs[k].getConversionA();
+ freq /= (2*specs[k].at(j).mz);
+
+ specs[k].at(j).mz = conA/freq + conB/(freq*freq);
+ }
+ }
+ */
+
+ //Match peaks between pivot scan (0) and neighbors (the rest)
+ for(m=0;m<numScans;m++){
+
+ vPos.clear();
+ for(i=0;i<numScans;i++) vPos.push_back(0);
+
+ for(i=0;i<specs[m].size();i++){ //iterate all points
+ if(specs[m].at(i).intensity<0.1) continue;
+ tmz=specs[m].at(i).mz;
+ mzcount=1;
+ prec = c * tmz * tmz / 2;
+
+ for(k=m+1;k<numScans;k++){ //iterate all neighbors
+ dif=100000.0;
+
+ for(j=vPos[k];j<specs[k].size();j++){ //check if point is a match
+ if(specs[k].at(j).intensity<0.1) continue; //skip meaningless datapoints to speed along
+ dt=fabs(tmz-specs[k].at(j).mz);
+
+ if(dt<=dif) {
+ if(dt<prec) {
+ //linear interpolate
+ //if(specs[k].at(j).mz<tmz && j<specs[k].size()-1){
+ // slope=(specs[k].at(j+1).intensity-specs[k].at(j).intensity)/(specs[k].at(j+1).mz-specs[k].at(j).mz);
+ // intercept=specs[k].at(j).intensity-specs[k].at(j).mz*slope;
+ // specs[m].at(i).intensity+=(tmz*slope+intercept);
+ //} else if(specs[k].at(j).mz>tmz && j>0) {
+ // slope=(specs[k].at(j).intensity-specs[k].at(j-1).intensity)/(specs[k].at(j).mz-specs[k].at(j-1).mz);
+ // intercept=specs[k].at(j).intensity-specs[k].at(j).mz*slope;
+ // specs[m].at(i).intensity+=(tmz*slope+intercept);
+ //} else {
+ specs[m].at(i).intensity += specs[k].at(j).intensity;
+ //}
+
+ //Averaging the mz values appears equivalent to realigning all spectra against
+ //an average Ledford correction.
+ specs[m].at(i).mz += specs[k].at(j).mz;
+ vPos[k]=j+1;
+ specs[k].at(j).intensity=-1.0;
+ mzcount++;
+ break;
+ }
+ dif=dt;
+ } else {
+ vPos[k]=j-1;
+ break;
+ }
+ }
+ }//for k
+
+ sp.add(specs[m].at(i).mz/mzcount,specs[m].at(i).intensity/numScans);
+
+ } //next i
+ } //next m
+
+ if(sp.size()>0) sp.sortMZ();
+ sp.setScanNumber(specs[0].getScanNumber());
+ sp.setScanNumber(specs[0].getScanNumber(true),true);
+ sp.setRTime(specs[0].getRTime());
+ sp.setRawFilter(cFilter1);
+
+ if(posLeft>0){
+ while(posLeft>0){
+ bs.pop_front();
+ posLeft--;
+ posA--;
+ }
+ }
+ delete [] specs;
+ return true;
+}
+
+/*
+bool CNoiseReduction::ScanAverage(Spectrum& sp, vector<Spectrum>& vs, int pivot, float cutoff, double cp){
+
+ int i;
+ int j;
+ int k;
+ int ts;
+ int widthCount=0;
+ int numScans=1;
+ double dif;
+ double prec;
+ double dt;
+ double c;
+ if(cp==0.0) c=CParam(vs[pivot],1);
+ else c=cp;
+
+ bool bLeft=true;
+ int posLeft=pivot-1;
+ int posRight=pivot+1;
+
+
+ cout << "PIVOT: " << vs[pivot].getScanNumber() << endl;
+ cout << c << endl;
+
+ while(numScans<vs.size()){
+
+ //Alternate looking left and right
+ if(bLeft){
+ bLeft=false;
+ if(posLeft<0) continue;
+ ts=posLeft;
+ posLeft--;
+ } else {
+ bLeft=true;
+ if(posRight>=vs.size()) continue;
+ ts=posRight;
+ posRight++;
+ }
+
+ numScans++;
+
+ cout << "TS: " << ts << " " << vs[ts].getScanNumber() << endl;
+ for(i=0;i<vs[ts].size();i++) cout << vs[ts].at(i).mz << " " << vs[ts].at(i).intensity << endl;
+
+ //Match peaks between pivot scan and temp scan
+ k=0;
+ for(i=0;i<vs[pivot].size();i++){
+ dif=100000.0;
+ prec = c * vs[pivot].at(i).mz * vs[pivot].at(i).mz / 2;
+
+ for(j=k;j<vs[ts].size();j++){
+ dt=fabs(vs[pivot].at(i).mz-vs[ts].at(j).mz);
+ if(dt<=dif) {
+ if(dt<prec) {
+ cout << "MATCH: " << vs[pivot].at(i).mz << " to " << vs[ts].at(j).mz << " was " << vs[pivot].at(i).intensity;
+ vs[pivot].at(i).intensity+=vs[ts].at(j).intensity;
+ cout << " is now " << vs[pivot].at(i).intensity << endl;
+ vs[ts].at(j).mz=-1.0;
+ k=j+1;
+ break;
+ }
+ dif=dt;
+ } else {
+ k=j-1;
+ break;
+ }
+ }
+ }
+
+ //Add unmatched peaks from temp scan
+ for(i=0;i<vs[ts].size();i++){
+ if(vs[ts].at(i).mz>-1.0) {
+ vs[pivot].add(vs[ts].at(i));
+ cout << "Adding " << vs[ts].at(i).mz << endl;
+ }
+ }
+
+ //Sort pivot scan peaks for fast traversal against next temp scan
+ vs[pivot].sortMZ();
+
+ }
+
+ cout << "NUMSCANS: " << numScans << endl;
+
+ //Average points and apply cutoff
+ sp.clear();
+ for(i=0;i<vs[pivot].size();i++) {
+ vs[pivot].at(i).intensity/=numScans;
+ if(vs[pivot].at(i).intensity>=cutoff) sp.add(vs[pivot].at(i));
+ }
+
+ sp.setScanNumber(vs[pivot].getScanNumber());
+ sp.setScanNumber(vs[pivot].getScanNumber(true),true);
+ sp.setRTime(vs[pivot].getRTime());
+
+ return true;
+}
+
+bool CNoiseReduction::ScanAverage(Spectrum& sp, deque<Spectrum>& vs, int pivot, float cutoff){
+
+ int i;
+ int j;
+ int k;
+ int ts;
+ int widthCount=0;
+ int numScans=1;
+ double dif;
+ double prec;
+ double dt;
+ double c=CParam(vs[pivot],1);
+
+ bool bLeft=true;
+ int posLeft=pivot-1;
+ int posRight=pivot+1;
+
+ while(numScans<vs.size()){
+
+ //Alternate looking left and right
+ if(bLeft){
+ bLeft=false;
+ if(posLeft<0) continue;
+ ts=posLeft;
+ posLeft--;
+ } else {
+ bLeft=true;
+ if(posRight>=vs.size()) continue;
+ ts=posRight;
+ posRight++;
+ }
+
+ numScans++;
+
+ //Match peaks between pivot scan and temp scan
+ k=0;
+ for(i=0;i<vs[pivot].size();i++){
+ dif=100000.0;
+ prec = c * vs[pivot].at(i).mz * vs[pivot].at(i).mz / 2;
+
+ for(j=k;j<vs[ts].size();j++){
+ dt=fabs(vs[pivot].at(i).mz-vs[ts].at(j).mz);
+ if(dt<=dif) {
+ if(dt<prec) {
+ vs[pivot].at(i).intensity+=vs[ts].at(j).intensity;
+ vs[ts].at(j).mz=-1.0;
+ k=j+1;
+ break;
+ }
+ dif=dt;
+ } else {
+ k=j-1;
+ break;
+ }
+ }
+ }
+
+ //Add unmatched peaks from temp scan
+ for(i=0;i<vs[ts].size();i++){
+ if(vs[ts].at(i).mz>-1.0) vs[pivot].add(vs[ts].at(i));
+ }
+
+ //Sort pivot scan peaks for fast traversal against next temp scan
+ vs[pivot].sortMZ();
+
+ }
+
+ //Average points and apply cutoff
+ sp.clear();
+ for(i=0;i<vs[pivot].size();i++) {
+ vs[pivot].at(i).intensity/=numScans;
+ if(vs[pivot].at(i).intensity>=cutoff) sp.add(vs[pivot].at(i));
+ }
+
+ sp.setScanNumber(vs[pivot].getScanNumber());
+ sp.setScanNumber(vs[pivot].getScanNumber(true),true);
+ sp.setRTime(vs[pivot].getRTime());
+
+ return true;
+}
+*/
+
+/*
+bool CNoiseReduction::ScanAverageBuffered(Spectrum& sp, char* file, int width, float cutoff, int scanNum){
+
+ Spectrum ts;
+ Spectrum ps;
+ //MSReader r;
+
+ int i;
+ int j;
+ int k;
+ int widthCount=0;
+ int numScans=1;
+ double dif;
+ double prec;
+ double dt;
+ double c;
+
+ bool bLeft=true;
+ int posLeft=ps.getScanNumber()-1;
+ int posRight=ps.getScanNumber()+1;
+ int index;
+ char cFilter1[256];
+ char cFilter2[256];
+
+ sp.clear();
+
+ //if file is not null, create new buffer
+ if(file!=NULL){
+ strcpy(lastFile,file);
+ bs.clear();
+ if(scanNum>0) r->readFile(file,ts,scanNum);
+ else r->readFile(file,ts);
+ if(ts.getScanNumber()==0) return false;
+ bs.push_back(ts);
+ ps=bs[0];
+ c=CParam(ps,3);
+ posA=0;
+ } else {
+ posA++;
+ //cout << "ER: " << posA << " " << bs.size() << endl;
+ if(posA>=bs.size()) return false; //end of buffer, no more data
+ ps=bs[posA];
+ c=CParam(ps,3);
+ }
+
+ //set our pivot spectrum
+ //ps=bs[posA];
+ ps.getRawFilter(cFilter1,256);
+ //cout << "Averaging: " << ps.getScanNumber() << endl;
+
+ posLeft=posA;
+ posRight=posA;
+ while(widthCount<(width*2)){
+
+ index=-1;
+
+ //Alternate looking left and right
+ if(bLeft){
+ bLeft=false;
+ widthCount++;
+
+ while(true){
+ posLeft--;
+ if(posLeft<0) { //buffer is too short on left, add spectra
+ i=bs[0].getScanNumber()-1;
+ if(i==0) break;
+ r->readFile(lastFile,ts,i);
+ if(ts.getScanNumber()==0) continue;
+ bs.push_front(ts);
+ posLeft=0;
+ posA++;
+ posRight++;
+ ts.getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ index=posLeft;
+ break;
+ }
+ } else {
+ bs[posLeft].getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ index=posLeft;
+ break;
+ }
+ }
+ }
+
+ } else {
+ bLeft=true;
+ widthCount++;
+
+ while(true){
+ posRight++;
+ //cout << "PR: " << posRight << " " << bs.size() << endl;
+ if(posRight>=bs.size()) { //buffer is too short on right, add spectra
+ r->readFile(lastFile,ts,bs[bs.size()-1].getScanNumber());
+ //cout << ts.getScanNumber() << endl;
+ r->readFile(NULL,ts);
+ //cout << ts.getScanNumber() << endl;
+ //cout << "Full on right: next scan is " << ts.getScanNumber() << " after " << bs[bs.size()-1].getScanNumber() << endl;
+ if(ts.getScanNumber()==0) {
+ posRight--;
+ break;
+ }
+ bs.push_back(ts);
+ ts.getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ index=posRight;
+ break;
+ }
+ } else {
+ bs[posRight].getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ index=posRight;
+ break;
+ }
+ }
+ }
+ }
+
+ if(index==-1) {
+ //cout << "No match " << widthCount << endl;
+ continue;
+ }
+ ts=bs[index];
+ //cout << " with: " << ts.getScanNumber() << " " << numScans+1 << endl;
+
+ numScans++;
+
+ //Match peaks between pivot scan and temp scan
+ k=0;
+ for(i=0;i<ps.size();i++){
+ dif=100000.0;
+ prec = c * ps.at(i).mz * ps.at(i).mz / 2;
+
+ for(j=k;j<ts.size();j++){
+ dt=fabs(ps.at(i).mz-ts.at(j).mz);
+ if(dt<=dif) {
+ if(dt<prec) {
+ ps.at(i).intensity+=ts.at(j).intensity;
+ ts.at(j).mz=-1.0;
+ k=j+1;
+ break;
+ }
+ dif=dt;
+ } else {
+ k=j-1;
+ break;
+ }
+ }
+ }
+
+ //Add unmatched peaks from temp scan
+ for(i=0;i<ts.size();i++){
+ if(ts.at(i).mz>-1.0) ps.add(ts.at(i));
+ }
+
+ //Sort pivot scan peaks for fast traversal against next temp scan
+ ps.sortMZ();
+
+ }
+
+ //Average points and apply cutoff
+ sp.clear();
+ for(i=0;i<ps.size();i++) {
+ ps.at(i).intensity/=numScans;
+ if(ps.at(i).intensity>=cutoff) sp.add(ps.at(i));
+ }
+
+ sp.setScanNumber(ps.getScanNumber());
+ sp.setScanNumber(ps.getScanNumber(true),true);
+ sp.setRTime(ps.getRTime());
+ sp.setRawFilter(cFilter1);
+
+ //clear unused buffer
+ if(posLeft>0){
+ while(posLeft>0){
+ bs.pop_front();
+ posLeft--;
+ posA--;
+ }
+ }
+
+ //cout << "Done averaging" << endl;
+
+ return true;
+}
+*/
+
+bool CNoiseReduction::ScanAveragePlusDeNoise(Spectrum& sp, char* file, int width, float cutoff, int scanNum){
+
+ Spectrum ts;
+ Spectrum ps;
+ //MSReader r;
+
+ vector<int> v;
+ vector<int> vPos;
+
+ int i;
+ int j;
+ int k;
+ int widthCount=0;
+ int numScans=1;
+ int match;
+ double dif;
+ double prec;
+ double dt;
+ double c;
+
+ bool bLeft=true;
+ int posLeft=ps.getScanNumber()-1;
+ int posRight=ps.getScanNumber()+1;
+ int index;
+ char cFilter1[256];
+ //char cFilter2[256];
+
+ sp.clear();
+
+ //if file is not null, create new buffer
+ if(file!=NULL){
+ strcpy(lastFile,file);
+ bs.clear();
+ if(scanNum>0) r->readFile(file,ts,scanNum);
+ else r->readFile(file,ts);
+ if(ts.getScanNumber()==0) return false;
+ bs.push_back(ts);
+ ps=bs[0];
+ c=CParam(ps,3);
+ posA=0;
+ } else {
+ posA++;
+ //cout << "ER: " << posA << " " << bs.size() << endl;
+ if(posA>=(int)bs.size()) return false; //end of buffer, no more data
+ ps=bs[posA];
+ c=CParam(ps,3);
+ }
+
+ //set our pivot spectrum
+ //ps=bs[posA];
+ ps.getRawFilter(cFilter1,256);
+ //cout << "Averaging: " << ps.getScanNumber() << endl;
+
+ posLeft=posA;
+ posRight=posA;
+ while(widthCount<(width*2)){
+
+ index=-1;
+
+ //Alternate looking left and right
+ if(bLeft){
+ bLeft=false;
+ widthCount++;
+
+ while(true){
+ posLeft--;
+ //cout << posLeft << endl;
+ if(posLeft<0) { //buffer is too short on left, add spectra
+ i=bs[0].getScanNumber();
+ while(true){
+ i--;
+ //cout << "I: " << i << endl;
+ if(i==0) break;
+ r->readFile(lastFile,ts,i);
+ if(ts.getScanNumber()==0) continue;
+ else break;
+ }
+ if(i==0) break;
+ bs.push_front(ts);
+ for(i=0;i<(int)v.size();i++)v[i]++;
+ posA++;
+ posRight++;
+ posLeft=0;
+ //ts.getRawFilter(cFilter2,256);
+ if(ts.getMsLevel()==cs.msLevel) {
+ index=posLeft;
+ break;
+ }
+ } else {
+ //bs[posLeft].getRawFilter(cFilter2,256);
+ if(bs[posLeft].getMsLevel()==cs.msLevel) {
+ index=posLeft;
+ break;
+ }
+ }
+ }
+
+ } else {
+ bLeft=true;
+ widthCount++;
+
+ while(true){
+ posRight++;
+ if(posRight>=(int)bs.size()) { //buffer is too short on right, add spectra
+ r->readFile(lastFile,ts,bs[bs.size()-1].getScanNumber());
+ r->readFile(NULL,ts);
+ if(ts.getScanNumber()==0) {
+ posRight--;
+ break;
+ }
+ bs.push_back(ts);
+ //ts.getRawFilter(cFilter2,256);
+ if(ts.getMsLevel()==cs.msLevel) {
+ index=posRight;
+ break;
+ }
+ } else {
+ //bs[posRight].getRawFilter(cFilter2,256);
+ if(bs[posRight].getMsLevel()==cs.msLevel) {
+ index=posRight;
+ break;
+ }
+ }
+ }
+ }
+
+ if(index==-1) continue;
+
+ //ts=bs[index];
+ v.push_back(index);
+
+ numScans++;
+ }
+
+ //cout << "Still Averaging: " << ps.getScanNumber() << endl;
+ //cout << " with: ";
+ //for(i=0;i<v.size();i++) cout << bs[v[i]].getScanNumber() << " ";
+ //cout << endl;
+
+ //cout << numScans << " " << v.size() << endl;
+
+ //Match peaks between pivot scan and neighbors
+ for(i=0;i<(int)v.size();i++) vPos.push_back(0);
+ for(i=0;i<(int)ps.size();i++){ //iterate all points
+ prec = c * ps.at(i).mz * ps.at(i).mz / 2;
+ match=1;
+
+ for(k=0;k<(int)v.size();k++){ //iterate all neighbors
+ dif=100000.0;
+ //cout << "Checking " << bs[v[k]].getScanNumber() << " pos " << vPos[k] << endl;
+
+ for(j=vPos[k];j<bs[v[k]].size();j++){ //check if point is a match
+ dt=fabs(ps.at(i).mz-bs[v[k]].at(j).mz);
+ if(dt<=dif) {
+ if(dt<prec) {
+ ps.at(i).intensity+=bs[v[k]].at(j).intensity;
+ vPos[k]=j+1;
+ match++;
+ break;
+ }
+ dif=dt;
+ } else {
+ vPos[k]=j-1;
+ break;
+ }
+ }
+
+ }
+
+ //if data point was not visible across enough scans, set it to 0
+ if(match<cs.boxcarFilter && match<(int)v.size()) ps.at(i).intensity=0.0;
+
+ }
+
+
+ //Average points and apply cutoff
+ for(i=0;i<ps.size();i++) {
+ ps.at(i).intensity/=numScans;
+ sp.add(ps.at(i));
+ //if(ps.at(i).intensity>=cutoff) sp.add(ps.at(i));
+ }
+
+ sp.setScanNumber(ps.getScanNumber());
+ sp.setScanNumber(ps.getScanNumber(true),true);
+ sp.setRTime(ps.getRTime());
+ sp.setRawFilter(cFilter1);
+
+ //clear unused buffer
+ if(posLeft>0){
+ while(posLeft>0){
+ bs.pop_front();
+ posLeft--;
+ posA--;
+ }
+ }
+
+ //cout << "Done averaging" << endl;
+
+ return true;
+}
+
+bool CNoiseReduction::DeNoiseB(Spectrum& sp){
+
+ Spectrum tmpSpec;
+ vector<int> v;
+
+ sp.clear();
+
+ if(pos==0){
+ if((cs.scan.iLower>0)) {
+ if(!ScanAveragePlusDeNoise(sp,&cs.inFile[0],(int)(cs.boxcar/2),0.1f,cs.scan.iLower)) return false;
+ } else {
+ ScanAveragePlusDeNoise(sp,&cs.inFile[0],(int)(cs.boxcar/2),0.1f);
+ }
+ pos=1;
+ } else {
+ ScanAveragePlusDeNoise(sp,NULL,(int)(cs.boxcar/2),0.1f);
+ }
+
+ if(sp.getScanNumber()==0) return false;
+ FirstDerivativePeaks(sp,1);
+ return true;
+
+}
+
+bool CNoiseReduction::DeNoiseC(Spectrum& sp){
+
+ Spectrum tmpSpec;
+ vector<int> v;
+
+ sp.clear();
+
+ if(pos==0){
+ if(cs.scan.iLower>0) {
+ if(!NewScanAveragePlusDeNoise(sp,cs.inFile,(int)(cs.boxcar/2),0.1f,cs.scan.iLower)) return false;
+ } else {
+ NewScanAveragePlusDeNoise(sp,cs.inFile,(int)(cs.boxcar/2),0.1f);
+ }
+ pos=1;
+ } else {
+ NewScanAveragePlusDeNoise(sp,NULL,(int)(cs.boxcar/2),0.1f);
+ }
+
+ if(sp.getScanNumber()==0) return false;
+ FirstDerivativePeaks(sp,1);
+ return true;
+
+}
+
+bool CNoiseReduction::DeNoiseD(Spectrum& sp){
+
+ Spectrum tmpSpec;
+ vector<int> v;
+
+ sp.clear();
+
+ if(pos==0){
+ if(cs.scan.iLower>0) {
+ if(!NewScanAverage(sp,cs.inFile,(int)(cs.boxcar/2),0.1f,cs.scan.iLower)) return false;
+ } else {
+ NewScanAverage(sp,cs.inFile,(int)(cs.boxcar/2),0.1f);
+ }
+ pos=1;
+ } else {
+ NewScanAverage(sp,NULL,(int)(cs.boxcar/2),0.1f);
+ }
+
+ if(sp.getScanNumber()==0) return false;
+ FirstDerivativePeaks(sp,1);
+ return true;
+
+}
+
+double CNoiseReduction::CParam(Spectrum& sp, int tot){
+ int i;
+ int j=0;
+ double d=0.0;
+
+ if(sp.size()<10) i=1;
+ else i=sp.size()/2;
+
+ while(i<sp.size()-1){
+ if(sp.at(i).intensity > sp.at(i-1).intensity && sp.at(i).intensity > sp.at(i+1).intensity) {
+ d+= ((1/sp.at(i).mz) - (1/sp.at(i+1).mz));
+ j++;
+ i++;
+ if(j==tot) break;
+ } else {
+ i++;
+ }
+ }
+
+ if(j==0) return 0.0;
+ else return d/j;
+}
+
+bool CNoiseReduction::NewScanAveragePlusDeNoise(Spectrum& sp, char* file, int width, float cutoff, int scanNum){
+
+ Spectrum ts;
+
+ vector<int> vPos;
+
+ int i;
+ int j;
+ int k;
+ int m;
+ int widthCount=0;
+ int numScans=1;
+ int match;
+ double dif;
+ double prec;
+ double dt;
+ double c;
+
+ bool bLeft=true;
+ int posLeft;
+ int posRight;
+ int index;
+ char cFilter1[256];
+ char cFilter2[256];
+
+ sp.clear();
+
+ Spectrum* specs;
+ specs = new Spectrum[width*2+1];
+
+ //if file is not null, create new buffer
+ if(file!=NULL){
+ strcpy(lastFile,file);
+ bs.clear();
+ if(scanNum>0) r->readFile(file,ts,scanNum);
+ else r->readFile(file,ts);
+ if(ts.getScanNumber()==0) {
+ delete [] specs;
+ return false;
+ }
+ bs.push_back(ts);
+ specs[0]=bs[0];
+ c=CParam(specs[0],3);
+ posA=0;
+ } else {
+ posA++;
+ if(posA>=(int)bs.size()) { //end of buffer, no more data
+ delete [] specs;
+ return false;
+ }
+ specs[0]=bs[posA];
+ c=CParam(specs[0],3);
+ }
+
+ //set our pivot spectrum
+ specs[0].getRawFilter(cFilter1,256);
+
+ posLeft=posA;
+ posRight=posA;
+ while(widthCount<(width*2)){
+
+ index=-1;
+
+ //Alternate looking left and right
+ if(bLeft){
+ bLeft=false;
+ widthCount++;
+
+ while(true){
+ posLeft--;
+ if(posLeft<0) { //buffer is too short on left, add spectra
+ i=bs[0].getScanNumber();
+ while(true){
+ i--;
+ if(i==0) break;
+ r->readFile(lastFile,ts,i);
+ if(ts.getScanNumber()==0) continue;
+ else break;
+ }
+ if(i==0) break;
+ bs.push_front(ts);
+ posA++;
+ posRight++;
+ posLeft=0;
+ ts.getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ index=posLeft;
+ break;
+ }
+ } else {
+ bs[posLeft].getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ index=posLeft;
+ break;
+ }
+ }
+ }
+
+ } else {
+ bLeft=true;
+ widthCount++;
+
+ while(true){
+ posRight++;
+ if(posRight>=(int)bs.size()) { //buffer is too short on right, add spectra
+ r->readFile(lastFile,ts,bs[bs.size()-1].getScanNumber());
+ r->readFile(NULL,ts);
+ if(ts.getScanNumber()==0) {
+ posRight--;
+ break;
+ }
+ bs.push_back(ts);
+ ts.getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ index=posRight;
+ break;
+ }
+ } else {
+ bs[posRight].getRawFilter(cFilter2,256);
+ if(strcmp(cFilter1,cFilter2)==0) {
+ index=posRight;
+ break;
+ }
+ }
+ }
+ }
+
+ if(index==-1) continue;
+
+ //ts=bs[index];
+ specs[numScans++]=bs[index];
+
+ //cout << "NumScans: " << numScans << endl;
+
+ }
+
+ //Match peaks between pivot scan (0) and neighbors (the rest)
+ //for(m=0;m<cs.ppMatch && m<numScans;m++){
+ for(m=0;m<1;m++){
+
+ //cout << "m " << m << " = " << specs[m].getScanNumber() << endl;
+
+ vPos.clear();
+ for(i=0;i<numScans;i++) vPos.push_back(0);
+ //cout << "Checking " << m << " of " << numScans << " points remaining: " << specs[m].size() << endl;
+
+ for(i=0;i<specs[m].size();i++){ //iterate all points
+ if(specs[m].at(i).intensity<0.1) continue;
+ prec = c * specs[m].at(i).mz * specs[m].at(i).mz / 2;
+ match=1;
+
+ for(k=m+1;k<numScans;k++){ //iterate all neighbors
+ dif=100000.0;
+
+ for(j=vPos[k];j<specs[k].size();j++){ //check if point is a match
+ //cout << "Checking " << j << " of " << specs[k].size() << endl;
+ if(specs[k].at(j).intensity<0.1) continue; //skip meaningless datapoints to speed along
+ dt=fabs(specs[m].at(i).mz-specs[k].at(j).mz);
+ //dt=specs[m].at(i).mz-specs[k].at(j).mz;
+ //if(dt<0.0)dt=-dt;
+ if(dt<=dif) {
+ if(dt<prec) {
+ specs[m].at(i).intensity+=specs[k].at(j).intensity;
+ vPos[k]=j+1;
+ specs[k].at(j).intensity=-1.0;
+ match++;
+ break;
+ }
+ dif=dt;
+ } else {
+ vPos[k]=j-1;
+ break;
+ }
+ }
+
+ }//for k
+
+ //if data point was not visible across enough scans, set it to 0
+ if(match<cs.boxcarFilter && match<numScans) {
+ //ignore point
+ //cout << "BAH! " << specs[m].at(i).mz << " has " << match << " matches." << endl;
+ } else {
+ //add to temp spectrum
+ //cout << specs[m].at(i).mz << " has " << match << " matches." << endl;
+ //sp.add(specs[m].at(i).mz,specs[m].at(i).intensity/numScans);
+ sp.add(specs[m].at(i).mz,specs[m].at(i).intensity/match);
+ }
+
+ } //next i
+
+ } //next m
+
+ //sort
+ //cout << "Done " << sp.size() << endl;
+ if(sp.size()>0) sp.sortMZ();
+ sp.setScanNumber(specs[0].getScanNumber());
+ sp.setScanNumber(specs[0].getScanNumber(true),true);
+ sp.setRTime(specs[0].getRTime());
+ sp.setRawFilter(cFilter1);
+
+ //clear unused buffer
+ if(posLeft>0){
+ while(posLeft>0){
+ bs.pop_front();
+ posLeft--;
+ posA--;
+ }
+ }
+
+ delete [] specs;
+
+ return true;
+}
+
diff --git a/src/app/hardklor/CNoiseReduction.h b/src/app/hardklor/CNoiseReduction.h
new file mode 100644
index 0000000..eaac0c9
--- /dev/null
+++ b/src/app/hardklor/CNoiseReduction.h
@@ -0,0 +1,73 @@
+#ifndef _CNOISEREDUCTION_H
+#define _CNOISEREDUCTION_H
+
+#include "MSReader.h"
+#include "Spectrum.h"
+#include "CHardklorSetting.h"
+#include <cmath>
+#include <iostream>
+#include <deque>
+
+#define GC 5.5451774444795623
+
+class CNoiseReduction {
+
+public:
+
+ //Constructors and Destructors
+ CNoiseReduction();
+ CNoiseReduction(MSReader* msr, CHardklorSetting& hs);
+ ~CNoiseReduction();
+
+ //Functions
+ double CParam(Spectrum& sp, int tot=1);
+ double calcFWHM(double mz);
+ void FirstDerivativePeaks(Spectrum& sp, int winSize);
+ bool DeNoise(Spectrum& sp);
+ //bool DeNoise(Spectrum& sp, vector<Spectrum>& vs, int pivot, bool findPeaks=false);
+ //bool DeNoise(Spectrum& sp, deque<Spectrum>& vs, int pivot, bool findPeaks=false);
+ bool DeNoiseB(Spectrum& sp);
+ bool DeNoiseC(Spectrum& sp);
+ bool DeNoiseD(Spectrum& sp);
+ int NearestPeak(Spectrum& sp, double mz);
+ bool ScanAverage(Spectrum& sp, char* file, int width, float cutoff);
+ bool NewScanAverage(Spectrum& sp, char* file, int width, float cutoff, int scanNum=0);
+ //bool ScanAverage(Spectrum& sp, vector<Spectrum>& vs, int pivot, float cutoff, double cp=0.0);
+ //bool ScanAverage(Spectrum& sp, deque<Spectrum>& vs, int pivot, float cutoff);
+ //bool ScanAverageBuffered(Spectrum& sp, char* file, int width, float cutoff, int scanNum=0);
+ bool ScanAveragePlusDeNoise(Spectrum& sp, char* file, int width, float cutoff, int scanNum=0);
+ bool NewScanAveragePlusDeNoise(Spectrum& sp, char* file, int width, float cutoff, int scanNum=0);
+
+ int pos;
+
+private:
+ //Functions
+
+
+ //Data Members
+ //int pos;
+ int posA;
+ char lastFile[256];
+ CHardklorSetting cs;
+ MSReader* r;
+ deque<Spectrum> s;
+ deque<Spectrum> bs;
+
+ /*
+ __int64 startTime;
+ __int64 stopTime;
+ __int64 loadTime;
+ __int64 analysisTime;
+ __int64 timerFrequency;
+ __int64 tmpTime1;
+ __int64 tmpTime2;
+ #define getExactTime(a) QueryPerformanceCounter((LARGE_INTEGER*)&a)
+ #define getTimerFrequency(a) QueryPerformanceFrequency((LARGE_INTEGER*)&a)
+ #define toMicroSec(a) (a)
+ #define timeToSec(a,b) (a/b)
+ */
+
+};
+
+#endif
+
diff --git a/src/app/hardklor/CPeriodicTable.cpp b/src/app/hardklor/CPeriodicTable.cpp
new file mode 100644
index 0000000..87cb169
--- /dev/null
+++ b/src/app/hardklor/CPeriodicTable.cpp
@@ -0,0 +1,94 @@
+#include "CPeriodicTable.h"
+
+using namespace std;
+
+/*
+CPeriodicTable::CPeriodicTable(){
+ table = new vector<element>;
+ loadTable("Hardklor.dat");
+}
+*/
+
+CPeriodicTable::CPeriodicTable(char* c){
+ loadTable(c);
+}
+
+CPeriodicTable::~CPeriodicTable(){
+}
+
+element& CPeriodicTable::at(int i){
+ return table.at(i);
+}
+
+void CPeriodicTable::defaultValues(){
+ string s[109]={"X","H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar","K",
+ "Ca","Sc","Ti","V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr","Rb","Sr","Y","Zr",
+ "Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te","I","Xe","Cs","Ba","La","Ce","Pr","Nd","Pm",
+ "Sm","Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu","Hf","Ta","W","Re","Os","Ir","Pt","Au","Hg","Tl","Pb",
+ "Bi","Po","At","Rn","Fr","Ra","Ac","Th","Pa","U","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr",
+ "Hx","Cx","Nx","Ox","Sx"};
+ double m[109]={0.000000000000,1.007824600000,3.016030000000,6.015121000000,9.012182000000,10.012937000000,
+ 12.000000000000,14.003073200000,15.994914100000,18.998403200000,19.992435000000,22.989767000000,
+ 23.985042000000,26.981539000000,27.976927000000,30.973762000000,31.972070000000,34.968853100000,
+ 35.967545000000,38.963707000000,39.962591000000,44.955910000000,45.952629000000,49.947161000000,
+ 49.946046000000,54.938047000000,53.939612000000,58.933198000000,57.935346000000,62.939598000000,
+ 63.929145000000,68.925580000000,69.924250000000,74.921594000000,73.922475000000,78.918336000000,
+ 77.914000000000,84.911794000000,83.913430000000,88.905849000000,89.904703000000,92.906377000000,
+ 91.906808000000,98.000000000000,95.907599000000,102.905500000000,101.905634000000,106.905092000000,
+ 105.906461000000,112.904061000000,111.904826000000,120.903821000000,119.904048000000,126.904473000000,
+ 123.905894000000,132.905429000000,129.906282000000,137.907110000000,135.907140000000,140.907647000000,
+ 141.907719000000,145.000000000000,143.911998000000,150.919847000000,151.919786000000,158.925342000000,
+ 155.925277000000,164.930319000000,161.928775000000,168.934212000000,167.933894000000,174.940770000000,
+ 173.940044000000,179.947462000000,179.946701000000,184.952951000000,183.952488000000,190.960584000000,
+ 189.959917000000,196.966543000000,195.965807000000,202.972320000000,203.973020000000,208.980374000000,
+ 209.000000000000,210.000000000000,222.000000000000,223.000000000000,226.025000000000,227.028000000000,
+ 232.038054000000,231.035900000000,234.040946000000,237.048000000000,244.000000000000,243.000000000000,
+ 247.000000000000,247.000000000000,251.000000000000,252.000000000000,257.000000000000,258.000000000000,
+ 259.000000000000,260.000000000000,1.007824600000,12.000000000000,14.003073200000,15.994914100000,
+ 31.972070000000};
+
+ element e;
+ unsigned int i;
+ for(i=0;i<109;i++){
+ e.atomicNum=i;
+ strcpy(e.symbol,&s[i][0]);
+ e.mass=m[i];
+ table.push_back(e);
+ }
+
+}
+
+void CPeriodicTable::loadTable(char* c){
+ FILE* fptr;
+ element e;
+
+ if(c==NULL || strlen(c)==0) {
+ defaultValues();
+ return;
+ }
+
+ fptr = fopen(c,"rt");
+ if(fptr==NULL) {
+ cout << "Cannot open periodic table! " << c << "." << endl;
+ return;
+ }
+
+ /*
+ This loop reads in table entries, line by line.
+ It has basic error detection (missing data), but additional
+ checks should be made to confirm the content of data
+ */
+ while(!feof(fptr)){
+
+ fscanf(fptr,"%d\t%s\t%lf\n",&e.atomicNum,e.symbol,&e.mass);
+ table.push_back(e);
+
+ }
+
+ fclose(fptr);
+
+}
+
+int CPeriodicTable::size(){
+ return table.size();
+}
diff --git a/src/app/hardklor/CPeriodicTable.h b/src/app/hardklor/CPeriodicTable.h
new file mode 100644
index 0000000..989b54a
--- /dev/null
+++ b/src/app/hardklor/CPeriodicTable.h
@@ -0,0 +1,40 @@
+#ifndef _CPERIODICTABLE_H
+#define _CPERIODICTABLE_H
+
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
+#include <iostream>
+#include <vector>
+
+using namespace std;
+
+typedef struct {
+ int atomicNum;
+ char symbol[3];
+ double mass;
+} element;
+
+class CPeriodicTable {
+ public:
+ //Constructors & Destructors
+ //CPeriodicTable();
+ CPeriodicTable(char* c="Hardklor.dat");
+ ~CPeriodicTable();
+
+ //Methods:
+ element& at(int);
+ int size();
+
+ protected:
+ private:
+ //Methods:
+ void defaultValues();
+ void loadTable(char*);
+
+ //Data Members:
+ vector<element> table;
+
+};
+
+#endif
diff --git a/src/app/hardklor/CSettings.cpp b/src/app/hardklor/CSettings.cpp
new file mode 100644
index 0000000..2878576
--- /dev/null
+++ b/src/app/hardklor/CSettings.cpp
@@ -0,0 +1,169 @@
+#include "CSettings.h"
+#include <iostream>
+#include <cstdlib>
+#include <cstdio>
+#include <fstream>
+using namespace std;
+
+CSettings::CSettings(){
+ chlor=0;
+ selen=0;
+ maxPep=5;
+ maxCharge=0;
+ maxDepth=100;
+ smooth=0;
+ signal=0;
+ scan=0;
+ S2N=0;
+ windowLower=0;
+ windowUpper=0;
+ enrichAtom[0]='\0';
+ enrich=0;
+ enrichTimes=0;
+ QAR = false;
+ ROC = false;
+ readFile("settings.conf");
+};
+
+CSettings::CSettings(char *c){
+ chlor=0;
+ selen=0;
+ maxPep=5;
+ maxCharge=0;
+ maxDepth=100;
+ smooth=0;
+ signal=0;
+ scan=0;
+ S2N=0;
+ windowLower=0;
+ windowUpper=0;
+ enrichAtom[0]='\0';
+ enrich=0;
+ enrichTimes=0;
+ QAR = false;
+ ROC = false;
+ readFile(c);
+};
+
+void CSettings::readFile(char* c) {
+ fstream fptr;
+ FileName* f;
+ char tstr[256];
+ char *tok;
+ int i;
+ varType v;
+
+ fptr.open(c,ios::in);
+ if(!fptr.good()){
+ cout << "Cannot read settings file: " << c << endl;
+ fptr.close();
+ return;
+ };
+
+ while(!fptr.eof()){
+ fptr.getline(tstr,100);
+ if(tstr[0]=='#' || tstr[0]==0) continue;
+
+ tok = strtok(tstr," \n\t\r");
+ if(tok==0) continue;
+ if(tok[0]=='#') continue;
+
+ if(strcmp(tok,"[CHLORINE]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ chlor = atoi(tok);
+ for(i=0;i<chlor;i++){
+ v.code=1;
+ v.value=i+1;
+ variants.push_back(v);
+ };
+ } else if(strcmp(tok,"[SELENIUM]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ selen = atoi(tok);
+ for(i=0;i<selen;i++){
+ v.code=2;
+ v.value=i+1;
+ variants.push_back(v);
+ };
+ } else if(strcmp(tok,"[ENRICH]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ strcpy(enrichAtom,tok);
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ enrich = atof(tok);
+ if(strcmp(enrichAtom,"N")==0){
+ v.code=3;
+ v.value=enrich;
+ variants.push_back(v);
+ };
+ enrichTimes=1;
+ } else if(strcmp(tok,"[SMOOTH]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ smooth = atoi(tok);
+ } else if(strcmp(tok,"[CORR]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ corrThresh = atof(tok);
+ } else if(strcmp(tok,"[S2N]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ S2N = atof(tok);
+ } else if(strcmp(tok,"[WINDOW]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ windowLower = atof(tok);
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ windowUpper = atof(tok);
+ } else if(strcmp(tok,"[MAXPEP]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ maxPep = atoi(tok);
+ } else if(strcmp(tok,"[MAXCHARGE]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ maxCharge = atoi(tok);
+ } else if(strcmp(tok,"[MAXDEPTH]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ maxDepth = atoi(tok);
+ } else if(strcmp(tok,"[QAR]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ if(atoi(tok)!=0) QAR = true;
+ } else if(strcmp(tok,"[ROC]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ if(atoi(tok)!=0) ROC = true;
+ } else if(strcmp(tok,"[SCAN]")==0) {
+ tok = strtok(NULL, " \n\t\r");
+ if(tok==NULL) continue;
+ scan = atoi(tok);
+ } else if(strcmp(tok,"[FILE]")==0){
+ f = new FileName;
+ tok = strtok(NULL,"\t\n\r");
+ if(tok==NULL) continue;
+ if(strcmp(tok,"Zoom")==0) f->st=Zoom;
+ else if(strcmp(tok,"UltraZoom")==0) f->st=UltraZoom;
+ else if(strcmp(tok,"IonSpec")==0) f->st=IonSpec2;
+ else if(strcmp(tok,"Other")==0) f->st=Other;
+ tok = strtok(NULL,"\t\n\r");
+ if(tok==NULL) continue;
+ else strcpy(f->infile,tok);
+ tok = strtok(NULL,"\t\n\r");
+ if(tok==NULL) continue;
+ else strcpy(f->outfile,tok);
+ files.push_back(f);
+ } else if(strcmp(tok,"[SIGNAL]")==0){
+ tok = strtok(NULL," \t\n\r");
+ if(tok==NULL) continue;
+ signal = atof(tok);
+ };
+ };
+
+};
+
+
diff --git a/src/app/hardklor/CSettings.h b/src/app/hardklor/CSettings.h
new file mode 100644
index 0000000..f89c0a0
--- /dev/null
+++ b/src/app/hardklor/CSettings.h
@@ -0,0 +1,56 @@
+#ifndef _CSETTINGS_H
+#define _CSETTINGS_H
+
+#include <vector>
+
+using namespace std;
+
+enum ScanType{
+ Zoom,
+ UltraZoom,
+ IonSpec2,
+ Other
+};
+
+typedef struct {
+ int code;
+ double value;
+} varType;
+
+typedef struct {
+ char infile[256];
+ char outfile[256];
+ ScanType st;
+} FileName;
+
+class CSettings {
+ public:
+ bool QAR;
+ bool ROC;
+ int chlor;
+ int selen;
+ int smooth;
+ int maxPep;
+ int maxCharge;
+ int scan;
+ int maxDepth;
+ double S2N;
+ double signal;
+ double corrThresh;
+ double windowLower;
+ double windowUpper;
+ vector<FileName*> files;
+ vector<varType> variants;
+ CSettings();
+ CSettings(char*);
+ char enrichAtom[3];
+ double enrich;
+ int enrichTimes;
+ protected:
+ private:
+ void readFile(char*);
+};
+
+
+
+#endif
diff --git a/src/app/hardklor/CSpecAnalyze.cpp b/src/app/hardklor/CSpecAnalyze.cpp
new file mode 100644
index 0000000..a5ec257
--- /dev/null
+++ b/src/app/hardklor/CSpecAnalyze.cpp
@@ -0,0 +1,858 @@
+#include "CSpecAnalyze.h"
+#include <iostream>
+#include <algorithm>
+using namespace std;
+
+//Default constructor
+CSpecAnalyze::CSpecAnalyze(){
+ basePeak = 0;
+ manyPeps = false;
+ S2NCutoff = 0;
+ predPeak = new vector<CPeakPrediction>;
+ predPep = new vector<CPeptidePrediction>;
+ charges = new vector<int>;
+ mismatchSize = 0;
+ averagine=NULL;
+ mercury=NULL;
+ spec=NULL;
+}
+
+//Copy constructor
+CSpecAnalyze::CSpecAnalyze(const CSpecAnalyze& c){
+ unsigned int i;
+
+ basePeak = c.basePeak;
+ manyPeps = c.manyPeps;
+ peaks = c.peaks;
+ peptide = c.peptide;
+ userParams = c.userParams;
+ mismatchSize = c.mismatchSize;
+ S2NCutoff = c.S2NCutoff;
+ spec = c.spec;
+ averagine = c.averagine;
+ mercury = c.mercury;
+ spec = c.spec;
+
+ predPeak = new vector<CPeakPrediction>;
+ for(i=0;i<c.predPeak->size();i++) predPeak->push_back(c.predPeak->at(i));
+
+ predPep = new vector<CPeptidePrediction>;
+ for(i=0;i<c.predPep->size();i++) predPep->push_back(c.predPep->at(i));
+
+ charges = new vector<int>;
+ for(i=0;i<c.charges->size();i++) charges->push_back(c.charges->at(i));
+}
+
+//Destructor
+CSpecAnalyze::~CSpecAnalyze(){
+ delete predPeak;
+ delete predPep;
+ delete charges;
+ averagine = NULL;
+ mercury = NULL;
+ spec = NULL;
+}
+
+//Overloaded operator
+CSpecAnalyze& CSpecAnalyze::operator=(const CSpecAnalyze& c){
+ unsigned int i;
+
+ if(this!=&c){
+ basePeak = c.basePeak;
+ manyPeps = c.manyPeps;
+ peaks = c.peaks;
+ peptide = c.peptide;
+ userParams = c.userParams;
+ mismatchSize = c.mismatchSize;
+ S2NCutoff = c.S2NCutoff;
+ spec = c.spec;
+ averagine = c.averagine;
+ mercury = c.mercury;
+ spec = c.spec;
+
+ delete predPeak;
+ predPeak = new vector<CPeakPrediction>;
+ for(i=0;i<c.predPeak->size();i++) predPeak->push_back(c.predPeak->at(i));
+
+ delete predPep;
+ predPep = new vector<CPeptidePrediction>;
+ for(i=0;i<c.predPep->size();i++) predPep->push_back(c.predPep->at(i));
+
+ delete charges;
+ charges = new vector<int>;
+ for(i=0;i<c.charges->size();i++) charges->push_back(c.charges->at(i));
+ }
+ return *this;
+}
+
+//Builds arrays of all the modeled peaks that do not match observed peaks.
+//Overlapping mismatched peaks are binned together for simplicity
+void CSpecAnalyze::BuildMismatchArrays(){
+
+ int i,j,k,m;
+ bool match;
+ vector<double> mz;
+ double deltaM;
+ double tmp;
+ Peak_T extraMZ;
+
+ //Create master mismatch set of datapoints.
+ //Essentially, this creates dynamic bins for all mismatched points
+
+ //Iterate through each predicted peptide
+ for(i=0;i<(int)predPep->size();i++) {
+
+ //get resolution
+ deltaM = calcFWHM(predPep->at(i).GetMZ());
+
+ //Iterate through each variant
+ for(j=0;j<predPep->at(i).VariantListSize();j++) {
+
+ //Iterate through each extra data point
+ for(k=0;k<predPep->at(i).GetVariant(j).SizeExtra();k++) {
+ extraMZ = predPep->at(i).GetVariant(j).GetExtra(k);
+
+ //Check mz of every extra data point against the current list
+ match=false;
+ for(m=0;m<(int)mz.size();m++){
+ if( fabs(mz.at(m) - extraMZ.mz) < deltaM ) {
+ match=true;
+ break;
+ }
+ }
+ if(!match) mz.push_back(extraMZ.mz);
+
+ }
+ }
+ }
+
+ //The list is built, sort it
+ if(mz.size()>1) {
+ for(i=0;i<(int)mz.size()-1;i++){
+ for(j=i+1;j<(int)mz.size();j++){
+ if(mz.at(j)<mz.at(i)){
+ tmp = mz.at(i);
+ mz.at(i) = mz.at(j);
+ mz.at(j) = tmp;
+ }
+ }
+ }
+ }
+
+ mismatchSize = mz.size();
+
+ //Recheck all peptide specific mismatches against the master list. This will adjust the mz values of the mismatches
+ //to fit the master bins.
+
+ //Iterate through every predicted peptide
+ for(i=0;i<(int)predPep->size();i++) {
+
+ //get resolution
+ deltaM = calcFWHM(predPep->at(i).GetMZ());
+
+ //Iterate through every variant
+ for(j=0;j<predPep->at(i).VariantListSize();j++) {
+
+ //Resize the mismatch list
+ predPep->at(i).GetVariant(j).SetMismatchSize(mismatchSize);
+
+ //Convert extra data points to mismatches
+ for(k=0;k<predPep->at(i).GetVariant(j).SizeExtra();k++) {
+
+ extraMZ = predPep->at(i).GetVariant(j).GetExtra(k);
+
+ //Check mz of every extra data point against the current list
+ match=false;
+ for(m=0;m<mismatchSize;m++){
+ if( fabs(mz.at(m) - extraMZ.mz) < deltaM ) {
+ predPep->at(i).GetVariant(j).AddMismatch(m,extraMZ.mz,extraMZ.intensity);
+ match=true;
+ break;
+ }
+ }
+
+ if(!match) {
+ //This shouldn't happen. Perhaps error checking should go here.
+ //cout << "Houston, we have a problem" << endl;
+ //cout << extraMZ.mz << " DM:" << deltaM << endl;
+ //for(m=0;m<mismatchSize;m++) cout << mz.at(m) << endl;
+ //exit(-1);
+ }
+ }
+
+ //Delete extra data points
+ predPep->at(i).GetVariant(j).DeleteExtra();
+
+ }
+ }
+
+}
+
+//Calculates the resolution (FWHM) of a peak
+double CSpecAnalyze::calcFWHM(double mz){
+ double deltaM;
+ switch(userParams.msType){
+ case OrbiTrap:
+ deltaM = mz * sqrt(mz) / (20*userParams.res400); //sqare root of 400
+ break;
+ case TOF:
+ deltaM = mz / userParams.res400;
+ break;
+ case QIT:
+ deltaM = userParams.res400 / 5000.0;
+ break;
+ case FTICR:
+ default:
+ deltaM = mz * mz / (400*userParams.res400);
+ break;
+ }
+ return deltaM;
+}
+
+//The QuickCharge algorithm. Simply assign charge based on inverse distance
+void CSpecAnalyze::chargeState(){
+ int i,j,k;
+ double dif;
+ int ch;
+ bool hasState;
+ CPeakPrediction p;
+
+ for(i=0;i<peaks.size()-1;i++){
+ p.Clear();
+ p.SetMZ(peaks.at(i).mz);
+ p.SetIntensity(peaks.at(i).intensity);
+
+ for(j=i+1;j<peaks.size();j++){
+
+ dif = peaks.at(j).mz - peaks.at(i).mz;
+ if(dif > 1.1) break;
+
+ ch = (int)(1/dif+0.5);
+ if(ch<userParams.minCharge || ch>userParams.maxCharge) continue;
+ hasState=false;
+ for(k=0;k<p.Size();k++){
+ if(p.GetCharge(k)==ch) {
+ hasState=true;
+ break;
+ }
+ }
+ if(!hasState) p.AddCharge(ch);
+
+ }
+
+ if(p.Size()>0) predPeak->push_back(p);
+ }
+
+}
+
+void CSpecAnalyze::clear(){
+ //spec=NULL;
+ peaks.clear();
+ peptide.clear();
+ delete predPeak;
+ delete predPep;
+ predPeak = new vector<CPeakPrediction>;
+ predPep = new vector<CPeptidePrediction>;
+ delete charges;
+ charges = new vector<int>;
+ manyPeps=false;
+ S2NCutoff = 0;
+ mismatchSize = 0;
+ basePeak = 0;
+}
+
+//Method for predicting peptides to analyze
+// 5/1/09 Most likely not used - commenting
+/*
+void CSpecAnalyze::FindPeptides(){
+ // split the results into overlapping ranges
+ peaks = signalToNoise(spec,0,spec.size()-1,userParams.sn,&S2NCutoff);
+ FirstDerivativePeaks(peaks,1); //10 for zoomscan, 4 for UZS
+
+ //if there is more than two peaks, find a charge state.
+ if(peaks.size()>2) chargeState();
+
+}
+*/
+
+//Quickest ways to find all spectrum peaks without making any predictions
+int CSpecAnalyze::FindPeaks(){
+
+ /*
+ if(userParams.chargeMode == 'F' ||
+ userParams.chargeMode == 'P' ||
+ userParams.chargeMode == 'S') TraditionalCharges();
+ */
+
+ if(userParams.fileFormat == zs) {
+ peaks = *spec;
+ FirstDerivativePeaks(peaks,10);
+ } else if(userParams.fileFormat == uzs) {
+ peaks = *spec;
+ FirstDerivativePeaks(peaks,4);
+ } else {
+ FirstDerivativePeaks(peaks,1); //10 for zoomscan, 4 for UZS
+ }
+
+ return peaks.size();
+
+}
+
+//Find all spectrum peaks in a given range (by data point array index)
+int CSpecAnalyze::FindPeaks(Spectrum& s, int start, int stop){
+
+ /*
+ if(userParams.chargeMode == 'F' ||
+ userParams.chargeMode == 'P' ||
+ userParams.chargeMode == 'S') TraditionalCharges();
+ */
+
+ if(userParams.fileFormat == zs) {
+ FirstDerivativePeaks(s,start,stop,10);
+ } else if(userParams.fileFormat == uzs) {
+ FirstDerivativePeaks(s,start,stop,4);
+ } else {
+ //intercept low res TOF data here?
+ FirstDerivativePeaks(s,start,stop,1); //10 for zoomscan, 4 for UZS
+ }
+
+ return peaks.size();
+
+}
+
+//First derivative method, returns base peak intensity of the set
+void CSpecAnalyze::FirstDerivativePeaks(Spectrum& s, int winSize){
+ FirstDerivativePeaks(s,0,s.size()-1,winSize);
+}
+
+//First derivative method, returns base peak intensity of the set
+void CSpecAnalyze::FirstDerivativePeaks(Spectrum& s, int start, int stop, int winSize){
+ //cout << "Start centroid " << s.getScanNumber() << " " << start << " " << stop << " " << winSize << endl;
+ int i,j;
+ float maxIntensity;
+ int bestPeak;
+ bool bLastPos;
+ Spectrum gp;
+
+ int nextBest;
+ double FWHM;
+ Peak_T centroid;
+
+ basePeak=0;
+ bLastPos=false;
+ for(i=start;i<stop+1-winSize;i++){
+
+ if(s.at(i).intensity<s.at(i+winSize).intensity) {
+ bLastPos=true;
+ continue;
+ } else {
+ if(bLastPos){
+ bLastPos=false;
+
+ //Possible ways to improve this:
+ //1. check FWHM - arg! what a computational disaster.
+ //2. account for noise - another disaster.
+
+ //find max and add peak
+ maxIntensity=0;
+ for(j=i;j<i+winSize;j++){
+ if (s.at(j).intensity>maxIntensity){
+ maxIntensity=s.at(j).intensity;
+ bestPeak = j;
+ }
+ }
+
+ //Best estimate of Gaussian centroid
+ //Get 2nd highest point of peak
+ if(bestPeak==stop){
+ nextBest=bestPeak-1;
+ } else if(s.at(bestPeak-1).intensity > s.at(bestPeak+1).intensity){
+ nextBest=bestPeak-1;
+ } else {
+ nextBest=bestPeak+1;
+ }
+
+ //Get FWHM
+ FWHM = calcFWHM(s.at(bestPeak).mz);
+
+ //Calc centroid MZ (in three lines for easy reading)
+ centroid.mz = pow(FWHM,2)*log(s.at(bestPeak).intensity/s.at(nextBest).intensity);
+ centroid.mz /= GAUSSCONST*(s.at(bestPeak).mz-s.at(nextBest).mz);
+ centroid.mz += (s.at(bestPeak).mz+s.at(nextBest).mz)/2;
+
+ //Calc centroid intensity
+ centroid.intensity=(float)(s.at(bestPeak).intensity/exp(-pow((s.at(bestPeak).mz-centroid.mz)/FWHM,2)*GAUSSCONST));
+
+ //some peaks are funny shaped and have bad gaussian fit.
+ //if error is more than 10%, keep existing intensity
+ if( fabs((s.at(bestPeak).intensity - centroid.intensity) / centroid.intensity * 100) > 10 ||
+ //not a good check for infinity
+ centroid.intensity>999999999999.9 ||
+ centroid.intensity < 0 ) {
+ centroid.intensity=s.at(bestPeak).intensity;
+ }
+
+ //Hack until I put in mass ranges
+ if(centroid.mz<0 || centroid.mz>2000) {
+ //do nothing if invalid mz
+ } else {
+ gp.add(centroid);
+ if(centroid.intensity > basePeak) {
+ basePeak = centroid.intensity;
+ }
+ }
+ i+=winSize-1;
+ }
+
+ }
+ }
+
+ //cout << "centroid ok" << endl;
+ peaks = gp;
+
+}
+
+double CSpecAnalyze::InterpolateMZ(Peak_T& p1, Peak_T& p2, double halfMax){
+
+ double slope;
+ double xDif;
+ double yDif;
+ double intercept;
+
+ //linear interpolation
+ yDif = (double)(p2.intensity - p1.intensity);
+ xDif = (double)(p2.mz - p1.mz);
+ slope = yDif/xDif;
+ intercept = (double)p1.intensity;
+
+ return (halfMax - intercept)/slope+p1.mz;
+
+}
+
+//5/1/09 - No longer used? Commenting out
+/*
+void CSpecAnalyze::FindCharge(){
+ int i,j,k,n;
+ double monoMass;
+ double shft;
+ double closest=0.0;
+ int closestIndex;
+ double dif=0.0;
+ double deltaM;
+ int maxPeak;
+
+ CPeakPrediction p;
+ CHardklorVariant var;
+ char v[64];
+
+ if(predPeak->size()==0) return;
+
+ //Sort peaks from high to low intensity;
+ for(i=0;i<predPeak->size()-1;i++){
+ for(j=i+1;j<predPeak->size();j++){
+ if(predPeak->at(j).GetIntensity() > predPeak->at(i).GetIntensity()) {
+ p = predPeak->at(j);
+ predPeak->at(j) = predPeak->at(i);
+ predPeak->at(i) = p;
+ };
+ };
+ };
+
+ //Profile every charge state of every peak, from most to least intense
+ for(i=0;i<predPeak->size();i++){
+
+ deltaM = calcFWHM(predPeak->at(i).GetMZ());
+
+ for(j=0;j<predPeak->at(i).Size();j++) {
+
+ //Calc monoisotopic mass
+ monoMass = predPeak->at(i).GetMZ() * predPeak->at(i).GetCharge(j) -
+ predPeak->at(i).GetCharge(j) * (ProtonMass);
+
+ //Create averagine
+ averagine->clear();
+ averagine->calcAveragine(monoMass,var);
+ averagine->getAveragine(&v[0]);
+
+ //Make mercury distribution
+ mercury->GoMercury(&v[0],predPeak->at(i).GetCharge(j));
+
+ //Align to max peak
+ dif=0;
+ for(k=0; k<mercury->FixedData.size(); k++) {
+ if(mercury->FixedData.at(k).data>dif){
+ dif = mercury->FixedData.at(k).data;
+ maxPeak=k;
+ };
+ };
+ shft = predPeak->at(i).GetMZ() - mercury->FixedData.at(maxPeak).mass;
+ for(k=0; k<mercury->FixedData.size(); k++) mercury->FixedData.at(k).mass += shft;
+
+ //Remove charge states of peaks where mercury intensity > 10%
+ for(k=0;k<mercury->FixedData.size();k++){
+ closest=userParams.winSize;
+ closestIndex=-1;
+ if(mercury->FixedData.at(k).data < 10) continue;
+ if(k == maxPeak) continue;
+ for(n=0;n<predPeak->size();n++){
+ if(n == i) continue;
+ dif = (double)fabs(predPeak->at(n).GetMZ()-mercury->FixedData.at(k).mass);
+ if(dif < closest) {
+ closest = dif;
+ closestIndex = n;
+ };
+ };
+
+ //If matching peak was found, erase same charge state at that peak
+ //But only if intensity is lower!!!
+ if(closestIndex > -1 && closest < deltaM) {
+ for(n=0;n<predPeak->at(closestIndex).Size();n++){
+ if(predPeak->at(closestIndex).GetCharge(n) == predPeak->at(i).GetCharge(j) &&
+ predPeak->at(closestIndex).GetIntensity() < predPeak->at(i).GetIntensity()){
+ //cout << "Remove: " << predPeak->at(closestIndex).GetMZ() << " +" << predPeak->at(closestIndex).GetCharge(n) << endl;
+ predPeak->at(closestIndex).EraseCharge(n);
+ break;
+ };
+ };
+ };
+
+ };
+
+ };
+
+ //Iterate predictions
+ };
+};
+*/
+
+//Builds Mercury distribution models for all predicted peptides. Keeps only
+//the ones that align to a user defined (sensitivity level param) number of observed peaks
+void CSpecAnalyze::MakePredictions(vector<CHardklorVariant>& var){
+ int i,j,k,n,q;
+ bool match;
+ double monoMass;
+ double shft;
+ double deltaM;
+ double dif=0;
+ double fracAbun;
+ char v[64];
+ float intensity;
+
+ int maxPeak;
+ int matchMaxPeak;
+ int matchIndex;
+
+ int matchCount;
+ int mismatchCount;
+
+ double distArea;
+ double predMonoMass;
+
+ CPeakPrediction pk;
+ CPeptidePrediction p;
+ CPeptideVariant pv;
+
+ i=peaks.size();
+ pv.SetMatchSize(i);
+
+ //Sort peaks from high to low intensity;
+ for(i=0;i<(int)predPeak->size()-1;i++){
+ for(j=i+1;j<(int)predPeak->size();j++){
+ if(predPeak->at(j).GetIntensity() > predPeak->at(i).GetIntensity()) {
+ pk = predPeak->at(j);
+ predPeak->at(j) = predPeak->at(i);
+ predPeak->at(i) = pk;
+ }
+ }
+ }
+
+ //Go through every peak prediction
+ for(i=0;i<(int)predPeak->size();i++) {
+
+ //Clear any prior peptide prediction data
+ p.Clear();
+
+ //Set some basic data
+ p.SetMZ(predPeak->at(i).GetMZ());
+ p.SetIntensity(predPeak->at(i).GetIntensity());
+
+ //Get the resolution
+ deltaM = calcFWHM(predPeak->at(i).GetMZ());
+
+ //Iterate through every charge state
+ for(j=0;j<predPeak->at(i).Size();j++){
+
+ //Iterate through every variant
+ for(q=0;q<(int)var.size();q++){
+
+ //Clear prior data
+ pv.Clear();
+
+ //Calc monoisotopic mass
+ monoMass = predPeak->at(i).GetMZ() * predPeak->at(i).GetCharge(j) - predPeak->at(i).GetCharge(j) * (ProtonMass);
+
+ //Create averagine
+ if(strcmp(userParams.formula,"")==0){
+ averagine->clear();
+ averagine->calcAveragine(monoMass,var.at(q));
+ averagine->getAveragine(&v[0]);
+ } else {
+ strcpy(v,userParams.formula);
+ }
+
+ //Make mercury distribution
+ for(k=0;k<var.at(q).sizeEnrich();k++){
+ mercury->Enrich(var.at(q).atEnrich(k).atomNum,var.at(q).atEnrich(k).isotope,var.at(q).atEnrich(k).ape);
+ }
+ mercury->GoMercury(&v[0],predPeak->at(i).GetCharge(j));
+
+ //Align to max peak
+ dif=0;
+ for(k=0; k<(int)mercury->FixedData.size(); k++) {
+ if(mercury->FixedData.at(k).data>dif){
+ dif = mercury->FixedData.at(k).data;
+ maxPeak=k;
+ }
+ }
+
+ shft = predPeak->at(i).GetMZ() - mercury->FixedData.at(maxPeak).mass;
+ //for fixed formulas, skip large mass differences.
+ //currently set at 10 ppm, this is only good for FT-Ultra and Orbitrap
+ if(strcmp(userParams.formula,"")!=0){
+ if( fabs(shft/mercury->FixedData[maxPeak].mass*1000000) > 10) continue;
+ }
+ for(k=0; k<(int)mercury->FixedData.size(); k++) {
+ mercury->FixedData.at(k).mass += shft;
+ }
+
+ matchCount=0;
+ mismatchCount=0;
+ fracAbun=0;
+ distArea=0;
+
+ //Match predictions to the observed peaks and record them in the proper array.
+ for(k=0;k<(int)mercury->FixedData.size();k++) {
+ if(mercury->FixedData.at(k).data<S2NCutoff) continue;
+ if(mercury->FixedData.at(k).data<0.1) continue;
+
+ match=false;
+ dif=userParams.winSize;
+ for(n=0;n<peaks.size();n++){
+ if(fabs(peaks.at(n).mz-mercury->FixedData.at(k).mass)<dif){
+ dif=fabs(peaks.at(n).mz-mercury->FixedData.at(k).mass);
+ matchIndex=n;
+ }
+ }
+ if(dif<deltaM){
+ if(k==maxPeak) matchMaxPeak=matchIndex;
+ intensity = (float)mercury->FixedData.at(k).data/100;
+ pv.AddMatch(matchIndex,mercury->FixedData.at(k).mass,intensity);
+ fracAbun+=mercury->FracAbunData.at(k).data;
+ //distArea+=peaks.at(matchIndex).intensity;
+ distArea+=mercury->FixedData.at(k).data/100;
+ matchCount++;
+ } else {
+ intensity = (float)mercury->FixedData.at(k).data/100;
+ distArea+=mercury->FixedData.at(k).data/100;
+ pv.AddExtra(mercury->FixedData.at(k).mass,intensity);
+ mismatchCount++;
+ }
+ }
+
+ if(strcmp(userParams.formula,"")==0) predMonoMass=averagine->getMonoMass();
+ else predMonoMass=mercury->getZeroMass();
+
+ //Record additional information
+ pv.SetCharge(predPeak->at(i).GetCharge(j));
+ pv.SetMonoMass(predMonoMass+(shft*predPeak->at(i).GetCharge(j)));
+ pv.SetFormula(v);
+ pv.SetVariant(var.at(q));
+ pv.SetArea(distArea);
+
+ //Add this variant to our list for this peptide.
+ switch(userParams.sl){
+ case 1:
+ if(fracAbun>0.75) p.AddVariant(pv);
+ break;
+ case 2:
+ if(fracAbun>0.50) p.AddVariant(pv);
+ break;
+ case 3:
+ if(matchCount>1) p.AddVariant(pv);
+ break;
+ default:
+ if(matchCount>mismatchCount) p.AddVariant(pv);
+ break;
+ }
+
+ }
+ }
+
+ //Add peptide prediction to the list.
+ if(p.VariantListSize()>0) {
+ p.SetIntensity(predPeak->at(i).GetIntensity());
+ p.SetMaxPeakIndex(matchMaxPeak);
+ predPep->push_back(p);
+ }
+
+ //if we reach the maximum peptides allowed, stop making predictions
+ if(predPep->size() == userParams.peptide) {
+ return;
+ }
+ }
+
+ return;
+
+}
+
+//This function looks at the peaks, determines which ones might be part of a distribution
+//and creates an array of m/z values, intensities, and charges that will later be made
+//into peptide models
+int CSpecAnalyze::PredictPeptides(){
+ int i,j;
+ CPeakPrediction p;
+ Spectrum s;
+
+ if(peaks.size()>1){
+
+ /*
+ if(peaks.size()>25){
+ peaks.sortIntensity();
+ for(i=0;i<25;i++) s.add(peaks.at(i));
+ peaks=s;
+ peaks.sortMZ();
+ }
+ */
+
+ switch(userParams.chargeMode){
+ case 'C':
+ for(i=0;i<peaks.size();i++){
+ if(peaks.at(i).intensity==0) continue;
+ p.SetMZ(peaks.at(i).mz);
+ p.SetIntensity(peaks.at(i).intensity);
+ for(j=userParams.minCharge;j<=userParams.maxCharge;j++) p.AddCharge(j);
+ predPeak->push_back(p);
+ }
+ break;
+ case 'F':
+ case 'P':
+ case 'S':
+ TraditionalCharges();
+ if(charges->size()==0) break;
+ for(i=0;i<peaks.size();i++){
+ if(peaks.at(i).intensity==0) continue;
+ p.SetMZ(peaks.at(i).mz);
+ p.SetIntensity(peaks.at(i).intensity);
+ for(j=0;j<(int)charges->size();j++) p.AddCharge(charges->at(j));
+ predPeak->push_back(p);
+ }
+ break;
+ case 'Q':
+ default:
+ chargeState();
+ break;
+ }
+ }
+
+ return predPeak->size();
+
+}
+
+//Reduces the peaks to only those we will be using
+void CSpecAnalyze::removePeaksBelowSN(){
+ int i;
+
+ //cout << "BasePeakSN: " << basePeak << endl;
+ //Note: The FirstDerivativePeaks function sets a new basePeak intensity based on a gaussian fit
+ //The SNCutoff, however, is based on the RAW value.
+ //They are different (by no more than 10%), and thus the cutoff has changed.
+
+ /* Old method uses erase function. New method avoids this to gain a little speed
+ for(i=0;i<peaks.size();i++){
+ if( (peaks.at(i).intensity / basePeak * 100) < S2NCutoff) {
+ peaks.erase(i);
+ i--;
+ }
+ }
+ */
+
+ Spectrum s;
+ for(i=0;i<peaks.size();i++){
+ if( (peaks.at(i).intensity / basePeak * 100) >= S2NCutoff) s.add(peaks.at(i));
+ }
+ peaks=s;
+}
+void CSpecAnalyze::setAveragine(CAveragine *a){
+ averagine=a;
+}
+
+void CSpecAnalyze::setMercury(CMercury8 *m){
+ mercury=m;
+}
+
+void CSpecAnalyze::setParams(const CHardklorSetting& sett){
+ userParams=sett;
+}
+
+void CSpecAnalyze::setSpectrum(Spectrum& s){
+ spec=&s;
+}
+
+//For using FFT or Patterson for charge states
+void CSpecAnalyze::TraditionalCharges(){
+
+ if(spec->size()==0) {
+ cout << "Cannot find charge state(s) because spectrum is empty." << endl;
+ exit(6);
+ }
+
+ //Find left and right boundaries in original spectrum
+ double lowMz=peaks[0].mz-0.25;
+ double highMz=peaks[peaks.size()-1].mz+0.25;
+ int lowIndex=binarySearch(lowMz);
+ int highIndex=binarySearch(highMz);
+
+ //fix resolution
+ double mz = peaks.at(peaks.size()/2).mz;
+ double deltaM = calcFWHM(mz);
+ deltaM/=4;
+
+ //Find the charges
+ SenkoCharge(charges,*spec,lowIndex,highIndex,userParams.minCharge,userParams.maxCharge,deltaM,userParams.chargeMode);
+
+}
+
+int CSpecAnalyze::binarySearch(double mz){
+ int lower,mid,upper;
+ int sz=spec->size();
+ double dif;
+
+ mid=sz/2;
+ lower=0;
+ upper=sz;
+
+ while(true){
+ if(lower>=upper) break;
+ if(mz<spec->at(mid).mz){
+ upper=mid-1;
+ mid=(lower+upper)/2;
+ } else {
+ lower=mid+1;
+ mid=(lower+upper)/2;
+ }
+ if(mid==sz) {
+ mid--;
+ break;
+ }
+ }
+
+ if(mid==0 || mid==sz-1) return mid;
+ if(mz<spec->at(mid).mz){
+ dif=spec->at(mid).mz-mz;
+ if(mz-spec->at(mid-1).mz < dif) return mid-1;
+ } else {
+ dif=mz-spec->at(mid).mz;
+ if(spec->at(mid+1).mz-mz < dif) return mid+1;
+ }
+ return mid;
+}
diff --git a/src/app/hardklor/CSpecAnalyze.h b/src/app/hardklor/CSpecAnalyze.h
new file mode 100644
index 0000000..d062831
--- /dev/null
+++ b/src/app/hardklor/CSpecAnalyze.h
@@ -0,0 +1,77 @@
+#ifndef _CSPECANALYZE_H
+#define _CSPECANALYZE_H
+
+#include "CAveragine.h"
+#include "CMercury8.h"
+#include "HardklorTypes.h"
+#include "SpecAnalyzeSupport.h"
+#include "Spectrum.h"
+#include "S2N.h"
+#include "CHardklorSetting.h"
+#include "FFT-HK.h"
+#include <vector>
+#include <cmath>
+using namespace std;
+
+//the following is 8*ln(2)
+#define GAUSSCONST 5.5451774444795623
+
+class CSpecAnalyze {
+ public:
+ //Constructors & Destructors
+ CSpecAnalyze();
+ CSpecAnalyze(const CSpecAnalyze&);
+ ~CSpecAnalyze();
+
+ //Overloaded operators
+ CSpecAnalyze& operator=(const CSpecAnalyze&);
+
+ //Functions
+ void BuildMismatchArrays();
+ void chargeState();
+ void clear();
+ //void FindCharge();
+ int FindPeaks();
+ int FindPeaks(Spectrum& s, int start, int stop);
+ //void FindPeptides();
+ void MakePredictions(vector<CHardklorVariant>& var);
+ int PredictPeptides();
+ void removePeaksBelowSN();
+ void setSpectrum(Spectrum& s);
+ void setAveragine(CAveragine *a);
+ void setMercury(CMercury8 *m);
+ void setParams(const CHardklorSetting& sett);
+ void TraditionalCharges();
+
+ //Data Members
+ float basePeak; //most intense peak in peaks spectrum; used for SN cutoff
+ vector<int> *charges;
+ bool manyPeps;
+ int mismatchSize;
+ Spectrum peaks; //peaks found in the spectrum
+ Spectrum peptide; //peaks that are potential peptides
+ vector<CPeakPrediction> *predPeak;
+ vector<CPeptidePrediction> *predPep;
+ float S2NCutoff;
+
+ protected:
+ private:
+
+ //Functions
+ int binarySearch(double mz);
+ double calcFWHM(double mz);
+ void FirstDerivativePeaks(Spectrum&,int);
+ void FirstDerivativePeaks(Spectrum&,int,int,int);
+ double InterpolateMZ(Peak_T& p1, Peak_T& p2, double halfMax);
+
+ //Data members
+ CAveragine *averagine;
+ CMercury8 *mercury;
+ Spectrum *spec;
+ CHardklorSetting userParams;
+
+};
+
+
+#endif
+
diff --git a/src/app/hardklor/CSplitSpectrum.cpp b/src/app/hardklor/CSplitSpectrum.cpp
new file mode 100644
index 0000000..c283f26
--- /dev/null
+++ b/src/app/hardklor/CSplitSpectrum.cpp
@@ -0,0 +1,812 @@
+#include "CSplitSpectrum.h"
+#include <iostream>
+using namespace std;
+
+CSplitSpectrum::CSplitSpectrum(Spectrum* spec, CHardklorSetting& sett) {
+ wholeSpec=spec;
+ userParams=sett;
+ setA = new vector<CSpecAnalyze>;
+ setB = new vector<CSpecAnalyze>;
+ finalAnalysis = new vector<CSpecAnalyze>;
+ s2n = new vector<float>;
+ aIndex = new vector<int>;
+ bIndex = new vector<int>;
+}
+
+CSplitSpectrum::~CSplitSpectrum(){
+ delete setA;
+ delete setB;
+ delete finalAnalysis;
+ delete s2n;
+ delete aIndex;
+ delete bIndex;
+ wholeSpec=NULL;
+ averagine=NULL;
+ mercury=NULL;
+}
+
+int CSplitSpectrum::getNumWindows(){
+ return finalAnalysis->size();
+}
+
+//Needs function description
+void CSplitSpectrum::NoSplitAnalysis(){
+ int i;
+
+ goodPeaks.clear();
+ delete s2n;
+ s2n = new vector<float>;
+
+ goodPeaks.setParams(userParams);
+ if(userParams.sn>0) {
+
+ //need to add window restrictions
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ goodPeaks.peaks = signalToNoise(*wholeSpec,0,wholeSpec->size()-1,(float)userParams.sn,&goodPeaks.S2NCutoff,true,true);
+ } else {
+ goodPeaks.peaks = signalToNoise(*wholeSpec,0,wholeSpec->size()-1,(float)userParams.sn,&goodPeaks.S2NCutoff);
+ }
+ for(i=0;i<goodPeaks.peaks.size();i++) s2n->push_back(goodPeaks.S2NCutoff);
+ } else {
+
+ goodPeaks.S2NCutoff=0;
+ for(i=0;i<wholeSpec->size();i++){
+ if(userParams.window.dLower>0 || userParams.window.dUpper>0){
+ if(wholeSpec->at(i).mz<userParams.window.dLower || wholeSpec->at(i).mz>userParams.window.dUpper) continue;
+ }
+ goodPeaks.peaks.add(wholeSpec->at(i));
+ s2n->push_back(0);
+ }
+ }
+ goodPeaks.FindPeaks();
+
+}
+
+
+/*
+ This function creates two overlapping arrays of CSpecAnalyze objects with a width
+ of gapSize. The overlap is exactly in the middle of each object. The two arrays are
+ stored as vectors for future analysis.
+*/
+void CSplitSpectrum::OverlappingAnalysis(double gapSize){
+
+ int startA, endA;
+ int startB, endB;
+ double mzStartA, mzEndA;
+ double mzStartB, mzEndB;
+ double mz=0.0;
+
+ int i=0;
+
+ CSpecAnalyze sa;
+ sa.setParams(userParams);
+ sa.setAveragine(averagine);
+ sa.setMercury(mercury);
+
+ delete setA;
+ delete setB;
+ setA = new vector<CSpecAnalyze>;
+ setB = new vector<CSpecAnalyze>;
+
+ startA = -1;
+ startB = -1;
+
+ mzStartA = wholeSpec->at(0).mz;
+ mzEndA = mzStartA + gapSize;
+ mzStartB = mzStartA + (gapSize/2);
+ mzEndB = mzStartB + gapSize;
+
+ while(true){
+
+ if(i==wholeSpec->size()){
+ endA=i-1;
+ endB=i-1;
+ break;
+ }
+
+ mz = wholeSpec->at(i).mz;
+
+ if(mz >= mzStartA && startA == -1) startA=i;
+ if(mz >= mzStartB && startB == -1) startB=i;
+
+ //Check A windows
+ if(mz >= mzEndA) {
+ endA=i;
+
+ if(endA-startA>1){
+
+ //Clear the CSpecAnalyze object and find the peaks
+ sa.clear();
+ if(userParams.sn>0){
+ sa.S2NCutoff = findSNCutoff(*wholeSpec,startA,endA,(float)userParams.sn);
+ } else {
+ sa.S2NCutoff=0;
+ }
+ sa.FindPeaks(*wholeSpec,startA,endA);
+ if(userParams.sn>0) sa.removePeaksBelowSN();
+ setA->push_back(sa);
+ }
+
+ startA=-1;
+ endA=0;
+ mzStartA = mzEndA + 0.000000001;
+ mzEndA = mzEndA + gapSize;
+
+ }
+
+ //Check B windows
+ if(wholeSpec->at(i).mz >= mzEndB) {
+ endB=i;
+
+ if(endB-startB>1){
+
+ //Clear the CSpecAnalyze object and find the peaks
+ sa.clear();
+
+ if(userParams.sn>0){
+ sa.S2NCutoff = findSNCutoff(*wholeSpec,startB,endB,(float)userParams.sn);
+ } else {
+ sa.S2NCutoff=0;
+ }
+ sa.FindPeaks(*wholeSpec,startB,endB);
+ if(userParams.sn>0) sa.removePeaksBelowSN();
+ setB->push_back(sa);
+ }
+
+ startB=-1;
+ endB=0;
+ mzStartB = mzEndB + 0.000000001;
+ mzEndB = mzEndB + gapSize;
+ }
+
+ i++;
+
+ }
+
+}
+
+void CSplitSpectrum::SinglePassAnalysis(double gapSize){
+
+ int startA, endA;
+ double mzStartA, mzEndA;
+
+ int i=0;
+ int j;
+
+ CSpecAnalyze sa;
+ sa.setParams(userParams);
+ sa.setAveragine(averagine);
+ sa.setMercury(mercury);
+
+ goodPeaks.clear();
+ delete s2n;
+ s2n = new vector<float>;
+
+ startA = -1;
+
+ mzStartA = userParams.window.dLower;
+ mzEndA = mzStartA + gapSize;
+
+ while(true){
+
+ if(i==wholeSpec->size()){
+ endA=i-1;
+ break;
+ }
+
+ if(wholeSpec->at(i).mz >= userParams.window.dUpper && userParams.window.dUpper>0){
+ endA=i;
+ break;
+ }
+
+ if(wholeSpec->at(i).mz >= mzStartA && startA == -1) startA=i;
+
+ //Check the window
+ if(wholeSpec->at(i).mz >= mzEndA) {
+ endA=i;
+
+ if(endA-startA>1){
+
+ //Clear the CSpecAnalyze object and find the peaks
+ sa.clear();
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ sa.peaks = signalToNoise(*wholeSpec,startA,endA,(float)userParams.sn,&sa.S2NCutoff,true,true);
+ } else {
+ sa.peaks = signalToNoise(*wholeSpec,startA,endA,(float)userParams.sn,&sa.S2NCutoff);
+ }
+ sa.FindPeaks();
+
+ for(j=0;j<sa.peaks.size();j++) {
+ goodPeaks.peaks.add(sa.peaks.at(j));
+ s2n->push_back(sa.S2NCutoff);
+ }
+
+ }
+
+ startA=-1;
+ endA=0;
+ mzStartA = mzEndA + 0.000000001;
+ mzEndA = mzEndA + gapSize;
+
+ }
+
+ }
+
+ //Check last window
+ if(endA-startA>1){
+
+ //Clear the CSpecAnalyze object and find the peaks
+ sa.clear();
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ sa.peaks = signalToNoise(*wholeSpec,startA,endA,(float)userParams.sn,&sa.S2NCutoff,true,true);
+ } else {
+ sa.peaks = signalToNoise(*wholeSpec,startA,endA,(float)userParams.sn,&sa.S2NCutoff);
+ }
+ sa.FindPeaks();
+
+ for(j=0;j<sa.peaks.size();j++) {
+ goodPeaks.peaks.add(sa.peaks.at(j));
+ s2n->push_back(sa.S2NCutoff);
+ }
+
+ }
+
+}
+
+/*
+ This function sums (in m/z order) the A and B peak sets. At each peak, it records the
+ signal to noise ratio. When there are two ratios, it keeps the lowest.
+*/
+void CSplitSpectrum::UnionAnalysis(){
+
+ unsigned int aCount,apCount,bCount,bpCount;
+
+ aCount=0;
+ bCount=0;
+ apCount=0;
+ bpCount=0;
+
+ goodPeaks.clear();
+ delete s2n;
+ s2n = new vector<float>;
+
+ bool bSkip;
+
+ while(aCount<setA->size() || bCount<setB->size()){
+
+ //Keep iterating through sets until a peak is found
+ while(true){
+
+ //Check A set for next peak
+ if(aCount<setA->size()){
+ if(setA->at(aCount).peaks.size()==0 || apCount>=(unsigned int)setA->at(aCount).peaks.size()) {
+ aCount++;
+ apCount=0;
+ continue;
+ };
+ };
+ //Check B set for next peak
+ if(bCount<setB->size()){
+ if(setB->at(bCount).peaks.size()==0 || bpCount>=(unsigned int)setB->at(bCount).peaks.size()) {
+ bCount++;
+ bpCount=0;
+ continue;
+ };
+ };
+ break;
+ };
+
+ //Compare the peaks between sets. Either both have the same peak, or set A or set B
+ //has an extra peak.
+ if(aCount<setA->size() && bCount<setB->size()){
+ if(setA->at(aCount).peaks.at(apCount).mz == setB->at(bCount).peaks.at(bpCount).mz){
+
+ //check if within user specified bounds
+ bSkip=false;
+ if(userParams.window.dLower>0 || userParams.window.dUpper > 0){
+ if(setA->at(aCount).peaks.at(apCount).mz < userParams.window.dLower || setA->at(aCount).peaks.at(apCount).mz > userParams.window.dUpper) {
+ bSkip=true;
+ };
+ };
+
+ if(!bSkip){
+ goodPeaks.peaks.add(setA->at(aCount).peaks.at(apCount));
+ if(setA->at(aCount).S2NCutoff<=setB->at(bCount).S2NCutoff) {
+ s2n->push_back(setA->at(aCount).S2NCutoff);
+ } else {
+ s2n->push_back(setB->at(bCount).S2NCutoff);
+ };
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ aIndex->push_back(aCount);
+ bIndex->push_back(bCount);
+ };
+ };
+ apCount++;
+ bpCount++;
+
+ } else if(setA->at(aCount).peaks.at(apCount).mz < setB->at(bCount).peaks.at(bpCount).mz) {
+
+ //check if within user specified bounds
+ bSkip=false;
+ if(userParams.window.dLower>0 || userParams.window.dUpper > 0){
+ if(setA->at(aCount).peaks.at(apCount).mz < userParams.window.dLower || setA->at(aCount).peaks.at(apCount).mz > userParams.window.dUpper) {
+ bSkip=true;
+ };
+ };
+
+ if(!bSkip){
+ goodPeaks.peaks.add(setA->at(aCount).peaks.at(apCount));
+ s2n->push_back(setA->at(aCount).S2NCutoff);
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ aIndex->push_back(aCount);
+ bIndex->push_back(-1);
+ };
+ };
+ apCount++;
+
+ } else {
+
+ //check if within user specified bounds
+ bSkip=false;
+ if(userParams.window.dLower>0 || userParams.window.dUpper > 0){
+ if(setB->at(bCount).peaks.at(bpCount).mz < userParams.window.dLower || setB->at(bCount).peaks.at(bpCount).mz > userParams.window.dUpper) {
+ bSkip=true;
+ };
+ };
+
+ if(!bSkip){
+ goodPeaks.peaks.add(setB->at(bCount).peaks.at(bpCount));
+ s2n->push_back(setB->at(bCount).S2NCutoff);
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ aIndex->push_back(-1);
+ bIndex->push_back(bCount);
+ };
+ };
+ bpCount++;
+
+ };
+ continue;
+ };
+
+ //Add any leftover peaks from set A
+ if(aCount<setA->size()){
+
+ //check if within user specified bounds
+ bSkip=false;
+ if(userParams.window.dLower>0 || userParams.window.dUpper > 0){
+ if(setA->at(aCount).peaks.at(apCount).mz < userParams.window.dLower || setA->at(aCount).peaks.at(apCount).mz > userParams.window.dUpper) {
+ bSkip=true;
+ };
+ };
+
+ if(!bSkip){
+ goodPeaks.peaks.add(setA->at(aCount).peaks.at(apCount));
+ s2n->push_back(setA->at(aCount).S2NCutoff);
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ aIndex->push_back(aCount);
+ bIndex->push_back(-1);
+ };
+ };
+ apCount++;
+
+ };
+
+ //Add any leftover peaks from set B
+ if(bCount<setB->size()){
+
+ //check if within user specified bounds
+ bSkip=false;
+ if(userParams.window.dLower>0 || userParams.window.dUpper > 0){
+ if(setB->at(bCount).peaks.at(bpCount).mz < userParams.window.dLower || setB->at(bCount).peaks.at(bpCount).mz > userParams.window.dUpper) {
+ bSkip=true;
+ };
+ };
+
+ if(!bSkip){
+ goodPeaks.peaks.add(setB->at(bCount).peaks.at(bpCount));
+ s2n->push_back(setB->at(bCount).S2NCutoff);
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ aIndex->push_back(-1);
+ bIndex->push_back(bCount);
+ };
+ };
+ bpCount++;
+
+ };
+
+ };
+
+};
+
+/*
+ This function is similar to UnionAnalysis, but differs in that it only accepts peaks
+ when found in both sets. The lowest signal to noise cutoff is kept.
+*/
+void CSplitSpectrum::IntersectionAnalysis(){
+ unsigned int aCount,apCount,bCount,bpCount;
+
+ aCount=0;
+ bCount=0;
+ apCount=0;
+ bpCount=0;
+
+ goodPeaks.clear();
+ delete s2n;
+ s2n = new vector<float>;
+
+ bool bSkip;
+
+ while(aCount<setA->size() && bCount<setB->size()){
+
+ //Keep iterating through sets until a peak is found
+ while(true){
+ //Check set A
+ if(aCount<setA->size()){
+ if(setA->at(aCount).peaks.size()==0 || apCount>=(unsigned int)setA->at(aCount).peaks.size()) {
+ aCount++;
+ apCount=0;
+ continue;
+ }
+ }
+ //Check set B
+ if(bCount<setB->size()){
+ if(setB->at(bCount).peaks.size()==0 || bpCount>=(unsigned int)setB->at(bCount).peaks.size()) {
+ bCount++;
+ bpCount=0;
+ continue;
+ }
+ }
+ break;
+ }
+
+ //Keep peaks found in both sets only.
+ if(aCount<setA->size() && bCount<setB->size()){
+ if(setA->at(aCount).peaks.at(apCount).mz == setB->at(bCount).peaks.at(bpCount).mz){
+
+ //check if within user specified bounds
+ bSkip=false;
+ if(userParams.window.dLower>0 || userParams.window.dUpper > 0){
+ if(setA->at(aCount).peaks.at(apCount).mz < userParams.window.dLower || setA->at(aCount).peaks.at(apCount).mz > userParams.window.dUpper) {
+ bSkip=true;
+ }
+ }
+
+ if(!bSkip){
+ goodPeaks.peaks.add(setA->at(aCount).peaks.at(apCount));
+ if(setA->at(aCount).S2NCutoff<=setB->at(bCount).S2NCutoff) {
+ s2n->push_back(setA->at(aCount).S2NCutoff);
+ } else {
+ s2n->push_back(setB->at(bCount).S2NCutoff);
+ }
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S'){
+ aIndex->push_back(aCount);
+ bIndex->push_back(bCount);
+ }
+ }
+
+ apCount++;
+ bpCount++;
+ } else if(setA->at(aCount).peaks.at(apCount).mz < setB->at(bCount).peaks.at(bpCount).mz) {
+ apCount++;
+ } else {
+ bpCount++;
+ }
+ }
+ }
+
+}
+
+/*
+ This funciton scans through all the good peaks and divides them into sets with a maximum
+ distance between the first and last peak of winSize. When winSize is exceeded, the set
+ of peaks is cut between the two peaks that have a maximum distance from each other.
+*/
+void CSplitSpectrum::MakeAnalysis(double winSize){
+ int i,j;
+ CSpecAnalyze sa;
+
+ double startMZ;
+ double maxDif;
+ int peakCount;
+ int cutPoint;
+ int startPoint;
+ float lowS2N;
+
+ sa.setAveragine(averagine);
+ sa.setMercury(mercury);
+
+ //For optimum window splitting
+ vector<sSplit> split;
+ sSplit tmpSplit;
+ //double tmpDouble;
+ float lowIntensity;
+
+ //For testing purposes:
+ /*
+ cout << "Winsize: " << winSize << endl;
+ for(i=0;i<goodPeaks.peaks.size();i++){
+ cout << goodPeaks.peaks.at(i).mz << " " << goodPeaks.peaks.at(i).intensity << endl;
+ };
+ */
+
+ cutPoint=0;
+ peakCount=0;
+ while(peakCount<goodPeaks.peaks.size()-1){
+ startPoint=peakCount;
+ startMZ=goodPeaks.peaks.at(peakCount).mz;
+ maxDif=0.0;
+
+ //Continue while we are less than winSize and there are still peaks
+ while( ((goodPeaks.peaks.at(peakCount).mz - startMZ) < winSize) && (peakCount<goodPeaks.peaks.size()-1) && (maxDif<1.05) ) {
+ peakCount++;
+
+ //keep track of the maximum distance between consecutive peaks in this window
+ if( (goodPeaks.peaks.at(peakCount).mz - goodPeaks.peaks.at(peakCount-1).mz) > maxDif){
+ cutPoint = peakCount-1;
+ maxDif = goodPeaks.peaks.at(peakCount).mz - goodPeaks.peaks.at(peakCount-1).mz;
+ }
+ }
+
+ //cout << "The CutPoint: " << goodPeaks.peaks[cutPoint].mz << " " << maxDif << endl;
+
+ //if the cutpoint might sever a valid distribution, find a less damaging
+ //location to cut the data.
+ if(maxDif<0.525) {
+ split.clear();
+ for(i=startPoint;i<=peakCount;i++){
+ tmpSplit.index=i;
+ tmpSplit.mz=goodPeaks.peaks.at(i).mz;
+ tmpSplit.intensity=goodPeaks.peaks.at(i).intensity;
+ split.push_back(tmpSplit);
+ //cout << tmpSplit.mz << "," << tmpSplit.intensity << endl;
+ }
+
+ //cout << "Would be CutPoint: " << goodPeaks.peaks[cutPoint].mz << " " << maxDif << endl;
+
+ while(maxDif<0.53) {
+
+ //remove the least intensity peak;
+ lowIntensity=9999999999999.0f;
+ for(i=1;i<(int)split.size();i++){
+ if(split[i].intensity<lowIntensity){
+ lowIntensity=split[i].intensity;
+ j=i;
+ }
+ }
+
+ //Slow method - think of better approach
+ //cout << "Erase: " << split[j].mz << "," << split[j].intensity << endl;
+ split.erase(split.begin()+j);
+
+ //if we trimmed the end of the window, stop now.
+ if( (split[split.size()-1].mz-split[0].mz) < (winSize-1.03)){
+ maxDif=666;
+ cutPoint=split[split.size()-1].index;
+ break;
+ }
+
+
+ //compute the new max difference between peaks
+ maxDif=0.0;
+ for(i=1;i<(int)split.size();i++){
+ if( (split[i].mz-split[i-1].mz) > maxDif){
+ maxDif = split[i].mz-split[i-1].mz;
+ cutPoint = split[i-1].index;
+ }
+ }
+
+ //cout << "New Best dif: " << maxDif << " - " << cutPoint << "," << goodPeaks.peaks[cutPoint].mz << endl;
+
+ }
+
+ }
+
+ /* For checking which peaks appear in a window
+ cout << "For: " << goodPeaks.peaks[startPoint].mz << " - " << goodPeaks.peaks[peakCount].mz << endl;
+ for(i=startPoint;i<=peakCount;i++){
+ cout << " Peak: " << goodPeaks.peaks[i].mz << " " << goodPeaks.peaks[i].intensity << endl;
+ }
+ cout << "CutPoint: " << goodPeaks.peaks[cutPoint].mz << " " << maxDif << endl;
+ */
+
+ //I think this sanity check is for when the distance to the last peak is less than the window size.
+ //if(goodPeaks.peaks.at(peakCount).mz - startMZ < winSize) cutPoint=goodPeaks.peaks.size()-1;
+ if(peakCount==goodPeaks.peaks.size()-1) cutPoint=goodPeaks.peaks.size()-1;
+
+ //Create our optimal window that is less than winsize
+ if(startPoint!=cutPoint) {
+ sa.clear();
+ lowS2N=100;
+
+ //create peaks and find lowest signal to noise cutoff across those peaks
+ for(i=startPoint;i<=cutPoint;i++){
+ sa.peaks.add(goodPeaks.peaks.at(i));
+ if(s2n->at(i)<lowS2N) lowS2N=s2n->at(i);
+ }
+ sa.S2NCutoff=lowS2N;
+
+ //For checking what the cut window is
+ //cout << " Cut point: " << goodPeaks.peaks.at(startPoint).mz << " - " << goodPeaks.peaks.at(cutPoint).mz << endl;
+
+ //Find charges (FFT & Patterson ONLY)
+ /*
+ if(userParams.chargeMode=='F' ||
+ userParams.chargeMode=='P' ||
+ userParams.chargeMode=='S') {
+
+ cout << "hehe: " << startPoint << " " << cutPoint << endl;
+ cout << aIndex->size() << endl;
+ cout << setA->size() << endl;
+
+ //Iterate through all peak indeces in this analysis
+ for(i=startPoint;i<=cutPoint;i++){
+
+ //only add charges from setA if it contributed to the peak
+ if(aIndex->at(i) != -1) {
+
+ for(k=0;k<(int)setA->at(aIndex->at(i)).charges->size();k++){
+ bFound=false;
+ for(j=0;j<(int)sa.charges->size();j++){
+ if(sa.charges->at(j) == setA->at(aIndex->at(i)).charges->at(k)){
+ bFound=true;
+ break;
+ }
+ }
+ if(!bFound) {
+ sa.charges->push_back(setA->at(aIndex->at(i)).charges->at(k));
+ }
+ }
+ }
+
+ //only add charges from SetB if it contributed to the peak
+ if(bIndex->at(i) != -1) {
+ for(k=0;k<(int)setB->at(bIndex->at(i)).charges->size();k++){
+ bFound=false;
+ for(j=0;j<(int)sa.charges->size();j++){
+ if(sa.charges->at(j) == setB->at(bIndex->at(i)).charges->at(k)){
+ bFound=true;
+ break;
+ }
+ }
+ if(!bFound) {
+ sa.charges->push_back(setB->at(bIndex->at(i)).charges->at(k));
+ }
+ }
+ }
+
+ }//i
+
+ }//end charge mode block
+ */
+
+ sa.setSpectrum(*wholeSpec);
+ finalAnalysis->push_back(sa);
+
+ }
+ peakCount=cutPoint+1;
+ }
+
+}
+
+CSpecAnalyze CSplitSpectrum::getWindow(int index){
+ return finalAnalysis->at(index);
+}
+
+void CSplitSpectrum::SetAveragine(CAveragine *a){
+ averagine=a;
+ goodPeaks.setAveragine(averagine);
+}
+
+void CSplitSpectrum::SetMercury(CMercury8 *m){
+ mercury=m;
+ goodPeaks.setMercury(mercury);
+}
+
+void CSplitSpectrum::Centroid(Spectrum& s){
+ goodPeaks.clear();
+ goodPeaks.setParams(userParams);
+ delete s2n;
+ s2n = new vector<float>;
+ for(int i=0;i<s.size();i++){
+ goodPeaks.peaks.add(s.at(i));
+ s2n->push_back(0);
+ }
+}
+
+//This funciton is for calculating S/N thresholds when using Noise reduced data,
+//such as data found on Thermo FT or Orbitrap instruments
+//Make only one pass and set the noise threshold at the lowest point
+void CSplitSpectrum::NewSNPass(double gapSize){
+ int startA, endA;
+ float S2NCutoff;
+ double mzStartA, mzEndA;
+ double mz=0.0;
+ double maxIntensity=0.0;
+ double max;
+ double lowPoint=99999999999;
+
+ unsigned int i=0;
+
+ CSpecAnalyze sa;
+ sa.setParams(userParams);
+ sa.setAveragine(averagine);
+ sa.setMercury(mercury);
+
+ delete setA;
+ setA = new vector<CSpecAnalyze>;
+
+ startA = -1;
+
+ mzStartA = wholeSpec->at(0).mz;
+ mzEndA = mzStartA + gapSize;
+
+ while(true){
+
+ if(i==wholeSpec->size()){
+ endA=i-1;
+ break;
+ }
+
+ mz = wholeSpec->at(i).mz;
+
+ if(mz >= mzStartA && startA == -1) startA=i;
+
+ if(mz >= mzEndA) {
+ endA=i;
+
+ if(endA-startA>1){
+
+ S2NCutoff = findSNCutoff2(*wholeSpec,startA,endA,(float)userParams.sn,max);
+
+ if( (S2NCutoff/100*max) < lowPoint ) lowPoint = S2NCutoff/100*max;
+ if( max > maxIntensity ) maxIntensity = max;
+
+ }
+
+ startA=-1;
+ endA=0;
+ mzStartA = mzEndA + 0.000000001;
+ mzEndA = mzEndA + gapSize;
+
+ }
+
+ i++;
+
+ }
+
+ sa.clear();
+ sa.S2NCutoff = (float)(lowPoint/maxIntensity*100);
+ sa.FindPeaks(*wholeSpec,0,wholeSpec->size()-1);
+
+ if(userParams.sn>0) sa.removePeaksBelowSN();
+
+ goodPeaks.clear();
+ delete s2n;
+ s2n = new vector<float>;
+ for(i=0;i<(unsigned int)sa.peaks.size();i++){
+ if(userParams.window.dLower>0 || userParams.window.dUpper > 0){
+ if(sa.peaks.at(i).mz < userParams.window.dLower || sa.peaks.at(i).mz > userParams.window.dUpper) continue;
+ }
+ goodPeaks.peaks.add(sa.peaks.at(i));
+ s2n->push_back(sa.S2NCutoff);
+ }
+
+}
diff --git a/src/app/hardklor/CSplitSpectrum.h b/src/app/hardklor/CSplitSpectrum.h
new file mode 100644
index 0000000..ab20ca4
--- /dev/null
+++ b/src/app/hardklor/CSplitSpectrum.h
@@ -0,0 +1,56 @@
+#ifndef _CSPLITSPECTRUM_H
+#define _CSPLITSPECTRUM_H
+
+#include "CHardklorSetting.h"
+#include "CSpecAnalyze.h"
+#include "Spectrum.h"
+#include <vector>
+
+using namespace std;
+
+class CSplitSpectrum {
+ public:
+ //Constructors & Destructors
+ CSplitSpectrum(Spectrum *spec, CHardklorSetting& sett);
+ ~CSplitSpectrum();
+
+ //Fuctions
+ int getNumWindows();
+ CSpecAnalyze getWindow(int index);
+ void IntersectionAnalysis();
+ void MakeAnalysis(double winSize);
+ void NoSplitAnalysis();
+ void OverlappingAnalysis(double gapSize);
+ void SinglePassAnalysis(double gapSize);
+ void UnionAnalysis();
+
+ void SetAveragine(CAveragine *a);
+ void SetMercury(CMercury8 *m);
+
+ void Centroid(Spectrum& s);
+
+ void NewSNPass(double gapSize);
+
+
+ private:
+ //Data members
+ Spectrum *wholeSpec;
+ CHardklorSetting userParams;
+
+ CSpecAnalyze goodPeaks;
+ CAveragine *averagine;
+ CMercury8 *mercury;
+
+ vector<CSpecAnalyze> *setA;
+ vector<CSpecAnalyze> *setB;
+ vector<CSpecAnalyze> *finalAnalysis;
+
+ vector<float> *s2n;
+
+ vector<int> *aIndex;
+ vector<int> *bIndex;
+
+};
+
+#endif
+
diff --git a/src/app/hardklor/CruxHardklorApplication.cpp b/src/app/hardklor/CruxHardklorApplication.cpp
new file mode 100644
index 0000000..b8e2edf
--- /dev/null
+++ b/src/app/hardklor/CruxHardklorApplication.cpp
@@ -0,0 +1,308 @@
+/**
+ * \file CruxHardklorApplication.cpp
+ * \brief Runs hardklor
+ *****************************************************************************/
+#include "CruxHardklorApplication.h"
+#include "CAveragine.h"
+#include "CHardklor.h"
+#include "CHardklor2.h"
+#include "CMercury8.h"
+#include "CModelLibrary.h"
+#include "CHardklorParser.h"
+#include "util/CarpStreamBuf.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "io/DelimitedFileWriter.h"
+
+using namespace std;
+
+CruxHardklorApplication::CruxHardklorApplication() {
+}
+
+CruxHardklorApplication::~CruxHardklorApplication() {
+}
+
+int CruxHardklorApplication::main(int argc, char** argv) {
+ return main(Params::GetString("spectra"));
+}
+
+int CruxHardklorApplication::main(const string& ms1) {
+ carp(CARP_INFO, "Hardklor v2.19, April 10 2015");
+ carp(CARP_INFO, "Mike Hoopmann, Mike MacCoss");
+ carp(CARP_INFO, "Copyright 2007-2015");
+ carp(CARP_INFO, "University of Washington");
+
+ string cdm = Params::GetString("cdm");
+ if (cdm == "B") {
+ cdm = "none";
+ } else if (cdm == "F") {
+ cdm = "fft";
+ } else if (cdm == "P") {
+ cdm = "patterson";
+ } else if (cdm == "Q") {
+ cdm = "quick";
+ } else if (cdm == "s") {
+ cdm = "senko";
+ }
+ bool xmlOutput = Params::GetBool("hardklor-xml-output");
+
+ vector<char*> hardklorArgs;
+ addArg(&hardklorArgs, "hardklor");
+ addArg(&hardklorArgs, "-cmd");
+ addArg(&hardklorArgs, "algorithm", Params::GetString("hardklor-algorithm"));
+ addArg(&hardklorArgs, "averagine_mod", Params::GetString("averagine-mod"));
+ addArg(&hardklorArgs, "boxcar_averaging", Params::GetString("boxcar-averaging"));
+ addArg(&hardklorArgs, "boxcar_filter", Params::GetString("boxcar-filter"));
+ addArg(&hardklorArgs, "boxcar_filter_ppm", Params::GetString("boxcar-filter-ppm"));
+ addArg(&hardklorArgs, "centroided", Params::GetBool("centroided"));
+ addArg(&hardklorArgs, "charge_algorithm", cdm);
+ addArg(&hardklorArgs, "charge_max", Params::GetString("max-charge"));
+ addArg(&hardklorArgs, "charge_min", Params::GetString("min-charge"));
+ addArg(&hardklorArgs, "correlation", Params::GetString("corr"));
+ addArg(&hardklorArgs, "depth", Params::GetString("depth"));
+ addArg(&hardklorArgs, "distribution_area", Params::GetBool("distribution-area"));
+ addArg(&hardklorArgs, "hardklor_data", Params::GetString("hardklor-data-file"));
+ addArg(&hardklorArgs, "instrument", Params::GetString("instrument"));
+ addArg(&hardklorArgs, "isotope_data", Params::GetString("isotope-data-file"));
+ addArg(&hardklorArgs, "max_features", Params::GetString("max-features"));
+ addArg(&hardklorArgs, "ms_level", Params::GetString("mzxml-filter"));
+ addArg(&hardklorArgs, "mz_max", Params::GetString("mz-max"));
+ addArg(&hardklorArgs, "mz_min", Params::GetString("mz-min"));
+ addArg(&hardklorArgs, "mz_window", Params::GetString("mz-window"));
+ addArg(&hardklorArgs, "resolution", Params::GetString("resolution"));
+ addArg(&hardklorArgs, "scan_range_max", Params::GetString("scan-range-max"));
+ addArg(&hardklorArgs, "scan_range_min", Params::GetString("scan-range-min"));
+ addArg(&hardklorArgs, "sensitivity", Params::GetString("sensitivity"));
+ addArg(&hardklorArgs, "signal_to_noise", Params::GetString("signal-to-noise"));
+ addArg(&hardklorArgs, "smooth", Params::GetString("smooth"));
+ addArg(&hardklorArgs, "sn_window", Params::GetString("sn-window"));
+ addArg(&hardklorArgs, "static_sn", Params::GetBool("static-sn"));
+ addArg(&hardklorArgs, "xml", xmlOutput);
+
+ addArg(&hardklorArgs, ms1);
+
+ string outputFile = "hardklor.mono.";
+ outputFile += xmlOutput ? "xml" : "txt";
+ outputFile = make_file_path(outputFile);
+ addArg(&hardklorArgs, outputFile);
+
+ CHardklorParser hp;
+ hp.parseCMD(hardklorArgs.size(), &hardklorArgs[0]);
+
+ for (vector<char*>::iterator i = hardklorArgs.begin(); i != hardklorArgs.end(); i++) {
+ delete *i;
+ }
+
+ // Create all the output files that will be used
+ for (int i = 0; i< hp.size(); i++) {
+ const char* out = &hp.queue(i).outFile[0];
+ if (FileUtils::Exists(out) && !Params::GetBool("overwrite")) {
+ carp(CARP_FATAL, "The file '%s' already exists and cannot be overwritten. "
+ "Use --overwrite T to replace or choose a different output file name",
+ out);
+ }
+ fstream fptr(out, ios::out);
+ }
+
+ // Re-route stdout/stderr
+ CarpStreamBuf buffer;
+ streambuf* oldCout = cout.rdbuf();
+ streambuf* oldCerr = cerr.rdbuf();
+ cout.rdbuf(&buffer);
+ cerr.rdbuf(&buffer);
+
+ CAveragine* averagine = new CAveragine(hp.queue(0).MercuryFile, hp.queue(0).HardklorFile);
+ CMercury8* mercury = new CMercury8(hp.queue(0).MercuryFile);
+ CModelLibrary* models = new CModelLibrary(averagine, mercury);
+
+ CHardklor h(averagine, mercury);
+ CHardklor2 h2(averagine, mercury, models);
+ vector<CHardklorVariant> pepVariants;
+ CHardklorVariant hkv;
+
+ for (int i = 0; i < hp.size(); i++) {
+ if (hp.queue(i).algorithm == Version2) {
+ pepVariants.clear();
+ if (!hp.queue(i).noBase) {
+ pepVariants.push_back(hkv);
+ }
+ for (unsigned j = 0; j < hp.queue(i).variant->size(); j++) {
+ pepVariants.push_back(hp.queue(i).variant->at(j));
+ }
+ models->eraseLibrary();
+ models->buildLibrary(hp.queue(i).minCharge, hp.queue(i).maxCharge, pepVariants);
+ h2.GoHardklor(hp.queue(i));
+ } else {
+ h.GoHardklor(hp.queue(i));
+ }
+ }
+
+ // Recover stdout/stderr
+ cout.rdbuf(oldCout);
+ cerr.rdbuf(oldCerr);
+
+ delete models;
+ delete averagine;
+ delete mercury;
+
+ return 0;
+}
+
+void CruxHardklorApplication::addArg(
+ vector<char*>* args,
+ const string& arg
+) {
+ char* toAdd = new char[arg.length() + 1];
+ strcpy(toAdd, arg.c_str());
+ args->push_back(toAdd);
+}
+
+void CruxHardklorApplication::addArg(
+ vector<char*>* args,
+ const string& name,
+ const string& value) {
+ if (!value.empty()) {
+ addArg(args, "-" + name);
+ addArg(args, value);
+ }
+}
+
+void CruxHardklorApplication::addArg(
+ vector<char*>* args,
+ const string& name,
+ bool value) {
+ addArg(args, name, string(value ? "1" : "0"));
+}
+
+/**
+ * \returns the command name for CruxHardklorApplication
+ */
+string CruxHardklorApplication::getName() const {
+ return "hardklor";
+}
+
+/**
+ * \returns the description for CruxHardklorApplication
+ */
+string CruxHardklorApplication::getDescription() const {
+ return
+ "[[nohtml:Identify isotopic distributions from high-resolution mass "
+ "spectra.]]"
+ "[[html:<p>Hardklör analyzes high-resolution mass spectra, "
+ "identifying protein or peptide isotope distributions and determining the "
+ "corresponding monoisotopic masses and charge states. The algorithm aims "
+ "to identify persistence peptide isotope distribution (PPIDs), i.e., "
+ "isotope distributions that recur over multiple scans. Hardklör is "
+ "specifically designed to handle overlapping isotope distributions in a "
+ "single spectrum. A detailed description of the Hardklör algorithm is "
+ "given in</p><blockquote>Hoopmann MR, Finney GL and MacCoss MJ. <a href=\""
+ "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556510/\">"High speed "
+ "data reduction, feature selection, and MS/MS spectrum quality assessment "
+ "of shotgun proteomics datasets using high resolution mass spectrometry."
+ ""</a> <em>Analytical Chemistry</em>. 79:5630-5632 (2007)."
+ "</blockquote>]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> CruxHardklorApplication::getArgs() const {
+ string arr[] = {
+ "spectra"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> CruxHardklorApplication::getOptions() const {
+ string arr[] = {
+ "fileroot",
+ "output-dir",
+ "overwrite",
+ "hardklor-algorithm",
+ "averagine-mod",
+ "boxcar-averaging",
+ "boxcar-filter",
+ "boxcar-filter-ppm",
+ "centroided",
+ "cdm",
+ "min-charge",
+ "max-charge",
+ "corr",
+ "depth",
+ "distribution-area",
+ "hardklor-data-file",
+ "instrument",
+ "isotope-data-file",
+ "max-features",
+ "mzxml-filter",
+ "mz-max",
+ "mz-min",
+ "mz-window",
+ "resolution",
+ "scan-range-max",
+ "scan-range-min",
+ "sensitivity",
+ "signal-to-noise",
+ "smooth",
+ "sn-window",
+ "static-sn",
+ "parameter-file",
+ "verbosity"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > CruxHardklorApplication::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("hardklor.mono.txt",
+ "a tab-delimited text file containing one line for each isotope "
+ "distribution. The columns appear in the following order:<ol><li><strong>"
+ "scan</strong>: The scan number assigned to this spectrum in the input file."
+ "</li><li><strong>retention time</strong>: The time (in seconds) at which the "
+ "spectrum was collected.</li><li><strong>mass</strong>: The uncharged "
+ "monoisotopic mass of the protein or peptide.</li><li><strong>charge</strong>: "
+ "The inferred charge state of the protein or peptide.</li><li><strong>intensity"
+ "</strong>: The intensity of the base isotope peak of the model used to predict "
+ "the protein or peptide.</li><li><strong>m/z</strong>: The m/z of the base peak."
+ "</li><li><strong>s/n</strong>: The signal-to-noise threshold, i.e., the relative "
+ "abundance a peak must exceed in the spectrum window to be considered in the "
+ "scoring algorithm. Note that this is a local noise threshold for the area of "
+ "the spectrum that the peptide was identified in.</li><li><strong>modifications"
+ "</strong>: Deviations to the averagine model. Only modifications specified by "
+ "the user are considered. If no modifications are found in a particular PPID, "
+ "then the column is marked with an underscore.</li><li><strong>dotp</strong>: "
+ "The dot product score applies to all predictions in a given spectrum window. "
+ "Thus, if two protein or peptide predictions share the same spectrum window, "
+ "then they have a single dot product score that is the score of their combined "
+ "peaks.</li></ol>"));
+ outputs.push_back(make_pair("hardklor.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("hardklor.log.txt",
+ "a log file containing a copy of all messages that were printed to "
+ "stderr."));
+ return outputs;
+}
+
+/**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+bool CruxHardklorApplication::needsOutputDirectory() const {
+ return true;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/hardklor/CruxHardklorApplication.h b/src/app/hardklor/CruxHardklorApplication.h
new file mode 100644
index 0000000..2a25324
--- /dev/null
+++ b/src/app/hardklor/CruxHardklorApplication.h
@@ -0,0 +1,88 @@
+/**
+ * \file CruxHardklorApplication.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 4 November 2011
+ * \brief Interface for calling hardklor.
+ *****************************************************************************/
+#ifndef CRUXHARDKLORAPPLICATION_H
+#define CRUXHARDKLORAPPLICATION_H
+
+#include "app/CruxApplication.h"
+
+#include <string>
+#include <fstream>
+
+class CruxHardklorApplication: public CruxApplication {
+
+ public:
+ CruxHardklorApplication();
+ ~CruxHardklorApplication();
+
+ virtual int main(int argc, char** argv);
+
+ /**
+ * \returns the command name for CruxHardklorApplication
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for CruxHardklorApplication
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns whether the application needs the output directory or not. (default false).
+ */
+ virtual bool needsOutputDirectory() const;
+
+ /**
+ * \brief runs hardklor on the input spectra
+ * \returns whether hardklor was successful or not
+ */
+ static int main(
+ const std::string& ms1 ///< file path of spectra to process
+ );
+
+ protected:
+ static void addArg(
+ std::vector<char*>* args,
+ const std::string& arg
+ );
+
+ static void addArg(
+ std::vector<char*>* args,
+ const std::string& name,
+ const std::string& value
+ );
+
+ static void addArg(
+ std::vector<char*>* args,
+ const std::string& name,
+ bool value
+ );
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/hardklor/FFT-HK.cpp b/src/app/hardklor/FFT-HK.cpp
new file mode 100644
index 0000000..fdc0499
--- /dev/null
+++ b/src/app/hardklor/FFT-HK.cpp
@@ -0,0 +1,227 @@
+#include "FFT-HK.h"
+#include <iostream>
+
+using namespace std;
+
+void FFTCharge(double *f, Spectrum& s, unsigned int start, unsigned int stop,
+ unsigned int lowCharge, unsigned int highCharge, double interval, bool bSpline){
+
+ Spectrum fft;
+ Peak_T p;
+ double mz = s.at(start).mz;
+ p.mz = s.at(start).mz;
+ p.intensity = s.at(start).intensity;
+ double maxIntensity = 0;
+
+ int i;
+ int power;
+ int size = (highCharge - lowCharge + 1) * 3;
+ double *in;
+ complex *out;
+
+ //Find out how many points are needed and dimension arrays.
+ power=2;
+ while(power<(s.size()/2)) power*=2;
+ out = new complex[power];
+ in = new double[power];
+
+ //Build the input array.
+ for(i=0;i<power;i++) {
+ if(i<(s.size()/2)) {
+ out[i].real=s.at(i*2).intensity;
+ out[i].imag=s.at(i*2+1).intensity;
+ } else {
+ out[i].real=0;
+ out[i].imag=0;
+ }
+
+ }
+
+ FFTreal(out,power);
+
+ //Create a spectrum of charge states and frequencies
+ for(i=0;i<power;i++){
+ p.mz = (double)i/(power*2*interval);
+ if(p.mz < (double)lowCharge - 0.5) continue;
+ if(p.mz > (double)highCharge + 0.5) break;
+ p.intensity = (float)sqrt(out[i].real*out[i].real+out[i].imag*out[i].imag);
+ fft.add(p);
+ }
+
+ //Linear interpolation of charge range at 1/3 intervals.
+ for(i=0;i<size;i++){
+ mz = (double)(i+2)/3 + (double)(lowCharge - 1);
+ f[i] = GetIntensity(fft,0,fft.size()-1,mz);
+ if(f[i]>maxIntensity) maxIntensity = f[i];
+ }
+
+ //Normalize
+ for(i=0;i<size;i++) {
+ f[i]/=maxIntensity;
+ if(f[i]<0) f[i]=0;
+ if(f[i]>1) f[i]=1;
+ //cout << (double)(i+2)/3 + (double)(lowCharge - 1) << "\t" << f[i] << endl;
+ }
+
+ //Clean up memory
+ delete [] out;
+ delete [] in;
+
+ //cout << "FFT done" << endl;
+
+}
+
+void Patterson(double *f, Spectrum& s, unsigned int start, unsigned int stop,
+ unsigned int lowCharge, unsigned int highCharge, double interval){
+
+ int i,j;
+ int size = (highCharge - lowCharge + 1) * 3;
+ double ch;
+ double shift = (double)(lowCharge-1);
+ double maxIntensity = 0;
+
+ double mz1,mz2;
+
+ if(f==NULL) f = new double[size];
+
+ for(i=0;i<size;i++){
+ f[i]=0;
+ ch = (double)(i+2)/3 + shift;
+ ch = 1/ch;
+ ch /= 2;
+ for(j=start;j<=stop;j++){
+ mz1 = s.at(j).mz - ch;
+ mz2 = s.at(j).mz + ch;
+ f[i]+= (GetIntensity(s,start,stop,mz1) * GetIntensity(s,start,stop,mz2));
+ }
+ if(f[i]>maxIntensity) maxIntensity = f[i];
+ }
+
+ //Normalize
+ if(maxIntensity>0){
+ for(i=0;i<size;i++) {
+ f[i]/=maxIntensity;
+ if(f[i]<0)f[i]=0;
+ if(f[i]>1)f[i]=1;
+
+ //cout << (double)(i+2)/3 + shift << "\t" << f[i] << endl;
+ }
+ }
+ //exit(1);
+
+}
+
+double GetIntensity(Spectrum& s, unsigned int start, unsigned int stop, double mz){
+
+ int index;
+ int lower=start+1;
+ int upper=stop;
+
+ double slope;
+ double xDif;
+ float yDif;
+ float intercept;
+ double newX;
+
+ if(start+1>stop) return 0;
+
+ //binary search for correct point
+ while(true){
+ index = (lower + upper) / 2;
+ if(index==start) return 0;
+
+ if(s.at(index-1).mz < mz && s.at(index).mz > mz) {
+
+ //linear interpolation
+ yDif = s.at(index).intensity - s.at(index-1).intensity;
+ xDif = s.at(index).mz - s.at(index-1).mz;
+ slope = yDif/xDif;
+ intercept = s.at(index-1).intensity;
+ newX = mz - s.at(index-1).mz;
+ return slope * newX + intercept;
+
+ } else if(lower > upper) {
+ return 0;
+ } else {
+ if(s.at(index).mz < mz) {
+ lower = index + 1;
+ } else {
+ upper = index - 1;
+ }
+ }
+ }
+
+}
+
+void SenkoCharge(vector<int> *charges, Spectrum& s, unsigned int start, unsigned int stop,
+ unsigned int lowCharge, unsigned int highCharge, double interval, char method) {
+
+ charges->clear();
+ double *array1;
+ double *array2;
+ float ch;
+ float maxPeak = 0;
+ int i,c;
+ unsigned int j;
+ int size = (highCharge - lowCharge + 1) * 3;
+ bool bFound;
+
+ /* use linear interpolation (splines do not perform well over large
+ spaces that have 0 intensity).
+ */
+ Spectrum spl;
+ Peak_T p;
+ double mz = s.at(start).mz;
+ p.mz = s.at(start).mz;
+ p.intensity = s.at(start).intensity;
+ spl.add(p);
+ while(true){
+ p.mz += interval;
+ if(p.mz > s.at(stop).mz) break;
+ p.intensity=(float)GetIntensity(s,start,stop,p.mz);
+ if(p.intensity<0) p.intensity=0;
+ spl.add(p);
+ }
+
+ switch(method){
+ case 'F':
+ array1 = new double[size];
+ FFTCharge(array1,spl,0,spl.size()-1,lowCharge,highCharge,interval);
+ break;
+ case 'P':
+ array1 = new double[size];
+ Patterson(array1,spl,0,spl.size()-1,lowCharge,highCharge,interval);
+ break;
+ case 'S':
+ default:
+ array1 = new double[size];
+ array2 = new double[size];
+ Patterson(array1,spl,0,spl.size()-1,lowCharge,highCharge,interval);
+ FFTCharge(array2,spl,0,spl.size()-1,lowCharge,highCharge,interval);
+ for(i=0;i<size;i++) array1[i]*=array2[i];
+ delete [] array2;
+ break;
+ }
+
+ //keep all charges that greater than 50% max peak
+ for(i=0;i<size-2;i++){
+ if( (array1[i+1] > array1[i]) && (array1[i+1] > array1[i+2]) &&
+ (array1[i+1] > 0.5) ) {
+ ch = (float)(i+3)/3 + (float)(lowCharge - 1);
+ c = (int)(ch+0.5);
+
+ //check if charge already exists in list. If not, add it to the list.
+ bFound = false;
+ for(j=0;j<charges->size();j++){
+ if(charges->at(j)==c) {
+ bFound = true;
+ break;
+ }
+ }
+ if(!bFound) charges->push_back(c);
+ }
+ }
+
+ delete [] array1;
+
+}
diff --git a/src/app/hardklor/FFT-HK.h b/src/app/hardklor/FFT-HK.h
new file mode 100644
index 0000000..ebac5ac
--- /dev/null
+++ b/src/app/hardklor/FFT-HK.h
@@ -0,0 +1,20 @@
+#ifndef _FFT_HK_H
+#define _FFT_HK_H
+
+#include "MSReader.h"
+#include "FFT.h"
+#include <cmath>
+#include <vector>
+
+using namespace std;
+using namespace MSToolkit;
+
+void FFTCharge(double *f, Spectrum& s, unsigned int start, unsigned int stop,
+ unsigned int lowCharge, unsigned int highCharge, double interval, bool bSpline=false);
+double GetIntensity(Spectrum& s, unsigned int start, unsigned int stop, double mz);
+void Patterson(double *f, Spectrum& s, unsigned int start, unsigned int stop,
+ unsigned int lowCharge, unsigned int highCharge, double interval);
+void SenkoCharge(vector<int> *charges, Spectrum& s, unsigned int start, unsigned int stop,
+ unsigned int lowCharge, unsigned int highCharge, double interval, char method);
+
+#endif
diff --git a/src/app/hardklor/FFT.cpp b/src/app/hardklor/FFT.cpp
new file mode 100644
index 0000000..f96d6bd
--- /dev/null
+++ b/src/app/hardklor/FFT.cpp
@@ -0,0 +1,121 @@
+#include "FFT.h"
+
+void BitReverse(complex* data, int size){
+
+ complex swap;
+ int i,j,k;
+ j=0;
+ k=0;
+
+ for (i=0; i<size; i++) {
+
+ if (j > i) {
+ swap = data[i];
+ data[i] = data[j];
+ data[j] = swap;
+ };
+
+ k = size >> 1;
+ while ( k>1 && j>k-1 ) {
+ j -= k;
+ k >>= 1;
+ };
+ j += k;
+
+ };
+
+};
+
+void FFT(complex* data, int size, bool forward){
+
+ int dir;
+ int jump;
+ int level=1;
+ int i,j,k;
+ double a,b,c,d,e,f;
+ complex swap;
+
+ if(forward) dir=1;
+ else dir=-1;
+
+ BitReverse(data,size);
+
+ while (size > level) {
+
+ jump = level << 1;
+ a = dir*PI/level;
+ b = sin(a);
+ c = sin(0.5*a);
+ d = -2.0*c*c;
+ e = 1.0;
+ f = 0.0;
+
+ for (i=0; i<level; i++){
+ for (j=i; j<size; j+=jump) {
+ k = j + level;
+ swap.real = (e*data[k].real) - (f*data[k].imag);
+ swap.imag = (e*data[k].imag) + (f*data[k].real);
+ data[k].real = data[j].real - swap.real;
+ data[k].imag = data[j].imag - swap.imag;
+ data[j].real += swap.real;
+ data[j].imag += swap.imag;
+ };
+ c = e;
+ e += (c*d) - (f*b);
+ f += (f*d) + (c*b);
+ };
+ level = jump;
+ };
+
+ /* Normalization - adapted from Mercury */
+ /*
+ if(forward) {
+ for (i=0; i<size; i++) {
+ data[i].real /= size;
+ data[i].imag /= size;
+ };
+ };
+ */
+
+};
+
+void FFTreal(complex* data, int size){
+
+ int i,n;
+ double a,b,c,d,e,f;
+ complex x,x2;
+
+ FFT(data,size,true);
+ n=size>>1;
+
+ a = PI/size;
+ b = sin(a);
+ c = sin(0.5*a);
+ d = -2.0*c*c;
+ e = 1.0+d;
+ f = b;
+
+ for(i=1;i<n;i++) {
+
+ x.real=0.5*(data[i].real+data[size-i].real);
+ x.imag=0.5*(data[i].imag-data[size-i].imag);
+ x2.real=0.5*(data[i].imag+data[size-i].imag);
+ x2.imag=-0.5*(data[i].real-data[size-i].real);
+
+ data[i].real = x.real + e * x2.real - f * x2.imag;
+ data[i].imag = x.imag + e * x2.imag + f * x2.real;
+ data[size-i].real = x.real - e * x2.real + f * x2.imag;
+ data[size-i].imag = -x.imag + e * x2.imag + f * x2.real;
+
+ c = e;
+ e += (c*d) - (f*b);
+ f += (f*d) + (c*b);
+
+ };
+
+ d=data[0].real;
+ data[0].real=d+data[0].imag;
+ data[0].imag=d-data[0].imag;
+
+
+};
diff --git a/src/app/hardklor/FFT.h b/src/app/hardklor/FFT.h
new file mode 100644
index 0000000..495f591
--- /dev/null
+++ b/src/app/hardklor/FFT.h
@@ -0,0 +1,20 @@
+#ifndef _FFT_H
+#define _FFT_H
+
+#include <cmath>
+
+#ifndef PI
+#define PI 3.14159265358979323846
+#endif
+
+typedef struct complex{
+ double real;
+ double imag;
+} complex;
+
+
+void BitReverse(complex* data, int size);
+void FFT(complex* data, int size, bool forward);
+void FFTreal(complex* data, int size);
+
+#endif
diff --git a/src/app/hardklor/Hardklor.dat b/src/app/hardklor/Hardklor.dat
new file mode 100644
index 0000000..fb68620
--- /dev/null
+++ b/src/app/hardklor/Hardklor.dat
@@ -0,0 +1,109 @@
+0 X 0
+1 H 1.0078246
+2 He 3.01603
+3 Li 6.015121
+4 Be 9.012182
+5 B 10.012937
+6 C 12.0000000
+7 N 14.0030732
+8 O 15.9949141
+9 F 18.9984032
+10 Ne 19.992435
+11 Na 22.989767
+12 Mg 23.985042
+13 Al 26.981539
+14 Si 27.976927
+15 P 30.973762
+16 S 31.972070
+17 Cl 34.9688531
+18 Ar 35.967545
+19 K 38.963707
+20 Ca 39.962591
+21 Sc 44.955910
+22 Ti 45.952629
+23 V 49.947161
+24 Cr 49.946046
+25 Mn 54.938047
+26 Fe 53.939612
+27 Co 58.933198
+28 Ni 57.935346
+29 Cu 62.939598
+30 Zn 63.929145
+31 Ga 68.925580
+32 Ge 69.924250
+33 As 74.921594
+34 Se 73.922475
+35 Br 78.918336
+36 Kr 77.914
+37 Rb 84.911794
+38 Sr 83.913430
+39 Y 88.905849
+40 Zr 89.904703
+41 Nb 92.906377
+42 Mo 91.906808
+43 Tc 98.0
+44 Ru 95.907599
+45 Rh 102.905500
+46 Pd 101.905634
+47 Ag 106.905092
+48 Cd 105.906461
+49 In 112.904061
+50 Sn 111.904826
+51 Sb 120.903821
+52 Te 119.904048
+53 I 126.904473
+54 Xe 123.905894
+55 Cs 132.905429
+56 Ba 129.906282
+57 La 137.90711
+58 Ce 135.907140
+59 Pr 140.907647
+60 Nd 141.907719
+61 Pm 145.0
+62 Sm 143.911998
+63 Eu 150.919847
+64 Gd 151.919786
+65 Tb 158.925342
+66 Dy 155.925277
+67 Ho 164.930319
+68 Er 161.928775
+69 Tm 168.934212
+70 Yb 167.933894
+71 Lu 174.940770
+72 Hf 173.940044
+73 Ta 179.947462
+74 W 179.946701
+75 Re 184.952951
+76 Os 183.952488
+77 Ir 190.960584
+78 Pt 189.959917
+79 Au 196.966543
+80 Hg 195.965807
+81 Tl 202.972320
+82 Pb 203.973020
+83 Bi 208.980374
+84 Po 209.0
+85 At 210.0
+86 Rn 222.0
+87 Fr 223.0
+88 Ra 226.025
+89 Ac 227.028
+90 Th 232.038054
+91 Pa 231.0359
+92 U 234.040946
+93 Np 237.048
+94 Pu 244.0
+95 Am 243.0
+96 Cm 247.0
+97 Bk 247.0
+98 Cf 251.0
+99 Es 252.0
+100 Fm 257.0
+101 Md 258.0
+102 No 259.0
+103 Lr 260.0
+104 Hx 1.0078246
+105 Cx 12.0000000
+106 Nx 14.0030732
+107 Ox 15.9949141
+108 Sx 31.972070
diff --git a/src/app/hardklor/Hardklor2008.aps b/src/app/hardklor/Hardklor2008.aps
new file mode 100644
index 0000000..35b897b
Binary files /dev/null and b/src/app/hardklor/Hardklor2008.aps differ
diff --git a/src/app/hardklor/Hardklor2008.rc b/src/app/hardklor/Hardklor2008.rc
new file mode 100644
index 0000000..00fc8fd
--- /dev/null
+++ b/src/app/hardklor/Hardklor2008.rc
@@ -0,0 +1,55 @@
+// Microsoft Visual C++ generated resource script.
+//
+#include "resource1.h"
+
+
+
+/////////////////////////////////////////////////////////////////////////////
+//
+// Icon
+//
+
+// Icon with lowest ID value placed first to ensure application icon
+// remains consistent on all systems.
+IDI_ICON2 ICON "Images\\Hardklor5.ico"
+
+/////////////////////////////////////////////////////////////////////////////
+//
+// Version
+//
+
+VS_VERSION_INFO VERSIONINFO
+ FILEVERSION 2,0,4,0
+ PRODUCTVERSION 2,0,4,0
+ FILEFLAGSMASK 0x17L
+#ifdef _DEBUG
+ FILEFLAGS 0x1L
+#else
+ FILEFLAGS 0x0L
+#endif
+ FILEOS 0x4L
+ FILETYPE 0x1L
+ FILESUBTYPE 0x0L
+BEGIN
+ BLOCK "StringFileInfo"
+ BEGIN
+ BLOCK "040904b0"
+ BEGIN
+ VALUE "Comments", "Michael R. Hoopmann, Michael J. MacCoss, Build Date: June 11, 2012"
+ VALUE "CompanyName", "University of Washington, Department of Genome Sciences"
+ VALUE "FileDescription", "Hardkl�r"
+ VALUE "FileVersion", "2, 0, 6, 0"
+ VALUE "InternalName", "Hardkl�r"
+ VALUE "LegalCopyright", "Copyright (C) 2007-2012"
+ VALUE "OriginalFilename", "Hardklor.exe"
+ VALUE "ProductName", "Hardkl�r"
+ VALUE "ProductVersion", "2, 0, 6, 0"
+ END
+ END
+ BLOCK "VarFileInfo"
+ BEGIN
+ VALUE "Translation", 0x409, 1200
+ END
+END
+
+
diff --git a/src/app/hardklor/Hardklor2008.vcproj b/src/app/hardklor/Hardklor2008.vcproj
new file mode 100644
index 0000000..408cc0b
--- /dev/null
+++ b/src/app/hardklor/Hardklor2008.vcproj
@@ -0,0 +1,370 @@
+<?xml version="1.0" encoding="Windows-1252"?>
+<VisualStudioProject
+ ProjectType="Visual C++"
+ Version="9.00"
+ Name="Hardklor2008"
+ ProjectGUID="{34E42C02-DB3A-4486-AF3D-F889F9F2C592}"
+ RootNamespace="Hardklor2008"
+ Keyword="Win32Proj"
+ TargetFrameworkVersion="196613"
+ >
+ <Platforms>
+ <Platform
+ Name="Win32"
+ />
+ </Platforms>
+ <ToolFiles>
+ </ToolFiles>
+ <Configurations>
+ <Configuration
+ Name="Debug|Win32"
+ OutputDirectory="$(SolutionDir)$(ConfigurationName)"
+ IntermediateDirectory="$(ConfigurationName)"
+ ConfigurationType="1"
+ CharacterSet="1"
+ >
+ <Tool
+ Name="VCPreBuildEventTool"
+ />
+ <Tool
+ Name="VCCustomBuildTool"
+ />
+ <Tool
+ Name="VCXMLDataGeneratorTool"
+ />
+ <Tool
+ Name="VCWebServiceProxyGeneratorTool"
+ />
+ <Tool
+ Name="VCMIDLTool"
+ />
+ <Tool
+ Name="VCCLCompilerTool"
+ Optimization="0"
+ AdditionalIncludeDirectories="..\MSToolkit\RAMP;..\zlib;..\MSToolkit"
+ PreprocessorDefinitions="WIN32;_DEBUG;_CONSOLE"
+ MinimalRebuild="true"
+ BasicRuntimeChecks="3"
+ RuntimeLibrary="3"
+ UsePrecompiledHeader="0"
+ WarningLevel="3"
+ DebugInformationFormat="4"
+ />
+ <Tool
+ Name="VCManagedResourceCompilerTool"
+ />
+ <Tool
+ Name="VCResourceCompilerTool"
+ />
+ <Tool
+ Name="VCPreLinkEventTool"
+ />
+ <Tool
+ Name="VCLinkerTool"
+ AdditionalDependencies="MSToolkitLite.lib zLib.lib"
+ OutputFile="$(OutDir)\Hardklor.exe"
+ LinkIncremental="2"
+ AdditionalLibraryDirectories="..\MSToolkit\Release;..\zlib\zlib\Release"
+ GenerateDebugInformation="true"
+ SubSystem="1"
+ TargetMachine="1"
+ />
+ <Tool
+ Name="VCALinkTool"
+ />
+ <Tool
+ Name="VCManifestTool"
+ />
+ <Tool
+ Name="VCXDCMakeTool"
+ />
+ <Tool
+ Name="VCBscMakeTool"
+ />
+ <Tool
+ Name="VCFxCopTool"
+ />
+ <Tool
+ Name="VCAppVerifierTool"
+ />
+ <Tool
+ Name="VCPostBuildEventTool"
+ />
+ </Configuration>
+ <Configuration
+ Name="Release|Win32"
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+ Name="VCMIDLTool"
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+ Name="VCCLCompilerTool"
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+ Optimization="2"
+ EnableIntrinsicFunctions="true"
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+ PreprocessorDefinitions="WIN32;NDEBUG;_CONSOLE;_ATL_MIXED;_CRT_SECURE_NO_WARNINGS;_NOSQLITE"
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+ EnableCOMDATFolding="2"
+ TargetMachine="1"
+ />
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+ Name="VCALinkTool"
+ />
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+ Name="VCManifestTool"
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+ Name="VCXDCMakeTool"
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diff --git a/src/app/hardklor/HardklorTypes.h b/src/app/hardklor/HardklorTypes.h
new file mode 100644
index 0000000..3ed9ebf
--- /dev/null
+++ b/src/app/hardklor/HardklorTypes.h
@@ -0,0 +1,140 @@
+#ifndef _HARDKLORTYPES_H
+#define _HARDKLORTYPES_H
+
+#include "MSToolkitTypes.h"
+
+#include <string>
+#include <vector>
+
+using namespace std;
+using namespace MSToolkit;
+
+enum specType {
+ OrbiTrap,
+ TOF,
+ QIT,
+ FTICR
+};
+
+enum hkAlgorithm {
+ Basic,
+ SemiComplete,
+ SemiCompleteFast,
+ Dynamic,
+ DynamicSemiComplete,
+ SemiSubtractive,
+ FewestPeptides,
+ FewestPeptidesChoice,
+ FastFewestPeptides,
+ FastFewestPeptidesChoice,
+ Version2
+};
+
+enum hkOutputFormat{
+ hk,
+ pepXML
+};
+
+typedef struct {
+ char atom[3];
+ int isotope;
+ double ape;
+} sEnrich;
+
+typedef struct {
+ string molecule;
+ int iLower;
+ int iUpper;
+} sMolecule;
+
+typedef struct {
+ int iLower;
+ int iUpper;
+} sInt;
+
+typedef struct{
+ double dLower;
+ double dUpper;
+} sDouble;
+
+typedef struct{
+ float fLower;
+ float fUpper;
+} sFloat;
+
+typedef struct{
+ int iValue;
+ double dValue;
+} sID;
+
+typedef struct{
+ int atomNum;
+ int isotope;
+ double ape;
+} sEnrichMercury;
+
+typedef struct{
+ double mz;
+ float intensity;
+ int index;
+} sSplit;
+
+//Do this better
+enum ScanType{
+ Zoom,
+ UltraZoom,
+ IonSpec2,
+ Other
+};
+
+typedef struct {
+ char id[5];
+ double mz;
+ double monoMass;
+ double shft;
+ double abun;
+ int charge;
+ char seq[31];
+ int C;
+ int H;
+ int O;
+ int N;
+ int S;
+ vector<sID> *enrich;
+} peps;
+
+typedef struct pepHit{
+ int basePeakIndex;
+ int charge;
+ int lowIndex;
+ int highIndex;
+ int variantIndex;
+ float intensity;
+ float area;
+ double massShift;
+ double lowMZ;
+ double highMZ;
+ double monoMass;
+ double corr;
+ char averagine[32];
+} pepHit;
+
+typedef struct mercuryModel{
+ float area;
+ int size;
+ double zeroMass;
+ Peak_T* peaks;
+} mercuryModel;
+
+//for storing results to memory for modular Hardklor runs
+typedef struct hkMem{
+ int charge;
+ int scan;
+ float intensity; //or area depending on settings.
+ double corr;
+ double monoMass;
+ double mz;
+ char mods[32];
+} hkMem;
+
+#endif
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new file mode 100644
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@@ -0,0 +1,720 @@
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+# Help Target
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+ @echo "The following are some of the valid targets for this Makefile:"
+ @echo "... all (the default if no target is provided)"
+ @echo "... clean"
+ @echo "... depend"
+ @echo "... edit_cache"
+ @echo "... hardklor"
+ @echo "... install"
+ @echo "... install/local"
+ @echo "... install/strip"
+ @echo "... list_install_components"
+ @echo "... package"
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+ @echo "... rebuild_cache"
+ @echo "... CAveragine.o"
+ @echo "... CAveragine.i"
+ @echo "... CAveragine.s"
+ @echo "... CHardklor.o"
+ @echo "... CHardklor.i"
+ @echo "... CHardklor.s"
+ @echo "... CHardklor2.o"
+ @echo "... CHardklor2.i"
+ @echo "... CHardklor2.s"
+ @echo "... CHardklorParser.o"
+ @echo "... CHardklorParser.i"
+ @echo "... CHardklorParser.s"
+ @echo "... CHardklorProtein.o"
+ @echo "... CHardklorProtein.i"
+ @echo "... CHardklorProtein.s"
+ @echo "... CHardklorSetting.o"
+ @echo "... CHardklorSetting.i"
+ @echo "... CHardklorSetting.s"
+ @echo "... CHardklorVariant.o"
+ @echo "... CHardklorVariant.i"
+ @echo "... CHardklorVariant.s"
+ @echo "... CMercury8.o"
+ @echo "... CMercury8.i"
+ @echo "... CMercury8.s"
+ @echo "... CModelLibrary.o"
+ @echo "... CModelLibrary.i"
+ @echo "... CModelLibrary.s"
+ @echo "... CNoiseReduction.o"
+ @echo "... CNoiseReduction.i"
+ @echo "... CNoiseReduction.s"
+ @echo "... CPeriodicTable.o"
+ @echo "... CPeriodicTable.i"
+ @echo "... CPeriodicTable.s"
+ @echo "... CSpecAnalyze.o"
+ @echo "... CSpecAnalyze.i"
+ @echo "... CSpecAnalyze.s"
+ @echo "... CSplitSpectrum.o"
+ @echo "... CSplitSpectrum.i"
+ @echo "... CSplitSpectrum.s"
+ @echo "... CruxHardklorApplication.o"
+ @echo "... CruxHardklorApplication.i"
+ @echo "... CruxHardklorApplication.s"
+ @echo "... FFT-HK.o"
+ @echo "... FFT-HK.i"
+ @echo "... FFT-HK.s"
+ @echo "... FFT.o"
+ @echo "... FFT.i"
+ @echo "... FFT.s"
+ @echo "... S2N.o"
+ @echo "... S2N.i"
+ @echo "... S2N.s"
+ @echo "... Smooth.o"
+ @echo "... Smooth.i"
+ @echo "... Smooth.s"
+ @echo "... SpecAnalyzeSupport.o"
+ @echo "... SpecAnalyzeSupport.i"
+ @echo "... SpecAnalyzeSupport.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
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diff --git a/src/app/hardklor/Makefile.hardklor b/src/app/hardklor/Makefile.hardklor
new file mode 100644
index 0000000..95eebec
--- /dev/null
+++ b/src/app/hardklor/Makefile.hardklor
@@ -0,0 +1,94 @@
+#Set these variables if needed
+C = gcc
+CC = g++
+FLAGS = -O3 -static -D_NOSQLITE -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DGCC
+
+#Path to MSToolkit
+
+LIBPATH = ../MSToolkit
+LIBS = -lmstoolkitlite
+
+#INCLUDE = -I$(LIBPATH) -I$(LIBPATH)/mzParser
+INCLUDE=-I$(LIBPATH)/include
+
+#Do not touch these variables
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+HARDKLOR = CHardklor.o \
+ CHardklor2.o \
+ CAveragine.o \
+ CPeriodicTable.o \
+ CHardklorVariant.o \
+ CHardklorSetting.o \
+ CHardklorParser.o \
+ CModelLibrary.o \
+ CNoiseReduction.o \
+ CSplitSpectrum.o CMercury8.o CSpecAnalyze.o CHardklorProtein.o SpecAnalyzeSupport.o FFT-HK.o
+
+
+#Make statements
+hardklor : HardklorApp.cpp $(HARDKLOR) $(SUPPORT)
+ $(CC) $(FLAGS) $(INCLUDE) $(SUPPORT) $(HARDKLOR) HardklorApp.cpp -L$(LIBPATH) $(LIBS) -o hardklor
+
+clean:
+ rm *.o hardklor
+
+
+#Hardklor objects
+
+
+
+S2N.o : S2N.cpp
+ $(CC) $(FLAGS) $(INCLUDE) S2N.cpp -c
+
+Smooth.o : Smooth.cpp
+ $(CC) $(FLAGS) $(INCLUDE) Smooth.cpp -c
+
+FFT.o : FFT.cpp
+ $(CC) $(FLAGS) $(INCLUDE) FFT.cpp -c
+
+CHardklor.o : CHardklor.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CHardklor.cpp -c
+
+CHardklor2.o : CHardklor2.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CHardklor2.cpp -c
+
+
+CAveragine.o : CAveragine.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CAveragine.cpp -c
+
+CPeriodicTable.o : CPeriodicTable.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CPeriodicTable.cpp -c
+
+CHardklorVariant.o : CHardklorVariant.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CHardklorVariant.cpp -c
+
+CHardklorSetting.o : CHardklorSetting.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CHardklorSetting.cpp -c
+
+CHardklorParser.o : CHardklorParser.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CHardklorParser.cpp -c
+
+CModelLibrary.o : CModelLibrary.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CModelLibrary.cpp -c
+
+CSplitSpectrum.o : CSplitSpectrum.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CSplitSpectrum.cpp -c
+
+CMercury8.o : CMercury8.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CMercury8.cpp -c
+
+CSpecAnalyze.o : CSpecAnalyze.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CSpecAnalyze.cpp -c
+ $(CC) $(FLAGS) $(INCLUDE) CSplitSpectrum.cpp -c
+ $(CC) $(FLAGS) $(INCLUDE) SpecAnalyzeSupport.cpp -c
+ $(CC) $(FLAGS) $(INCLUDE) FFT-HK.cpp -c
+
+CHardklorProtein.o : CHardklorProtein.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CHardklorProtein.cpp -c
+
+SpecAnalyzeSupport.o : SpecAnalyzeSupport.cpp
+ $(CC) $(FLAGS) $(INCLUDE) SpecAnalyzeSupport.cpp -c
+
+CNoiseReduction.o : CNoiseReduction.cpp
+ $(CC) $(FLAGS) $(INCLUDE) CNoiseReduction.cpp -c
+
diff --git a/src/app/hardklor/README.txt b/src/app/hardklor/README.txt
new file mode 100644
index 0000000..a7e501b
--- /dev/null
+++ b/src/app/hardklor/README.txt
@@ -0,0 +1,53 @@
+App: Hardklor
+Purpose: Analyze mass spectra
+
+Version History
+------------------------------------------
+1.0 - Apr 17 2007 - Stable release
+1.01 - May 17 2007 - Recompiled with latest MSToolkit(1.1)
+1.02 - Jun 15 2007 - Fixed monoisotopic mass bug
+1.03 - Aug 29 2007 - Added sensitivity level parameter - much better low abundance peptide performance. Some changes made to Mercury
+
+1.1 - Sep 29 2007 - Added mzXML file support and compressed .cms1 & .cms2 support. Several bugfixes, including better S/N processing.
+
+1.11 - Jan 16 2008 - Fixed bugs in MSToolkit 64-bit file support. Modified default Hardklor settings.
+
+1.20 - Feb 6 2008
+ * Fixed user-defined scan window bug.
+ * Allows reading of centroid data (-c). No signal-to-noise processing is done for this option.
+ * Can set a static S/N cutoff for entire scan. This optimizes Orbitrap and LTQ-FT data analysis. See documentation.
+ * Allows substitution of a user-defined molecule for averagine (-mol). Note: still in testing stages.
+ * Toggle isotope distribution area for output in place of base isotope peak instensity (-da).
+ * Minor speed improvements.
+
+1.22 - Apr 24 2008
+ * Minor Bug Fixes
+ * Upgraded MSToolkit software to 2.42
+
+1.23 - Oct 24 2008
+ * Improvements to spectrum dividing functions
+
+1.24 - Dec 11 2008
+ * Bugfixes for zoomscan and ultrazoomscan files
+
+1.25 - Mar 3 2009
+ * Additional support for ms2 file format
+ * Bugfix to MSToolkit (forked from SVN)
+
+1.26 - Apr 30 2009
+ * Upgraded MSToolkit
+ * Bugfix for rare S/N ratio calculation error
+ * Potentially fixed rare, irregular, and odd 64-bit linux behavior
+
+1.27 - Aug 13 2009
+ * Filenames and their paths can have spaces if entire path and filename is contained in quotes
+
+1.28 - Sep 2 2009
+ * Writes results in XML format with the following parameter: -xml true
+
+1.30 - Sep 13 2009
+ * Bugfix to QuickCharge algorithm
+
+1.31 - Oct 1 2009
+ * Added new signal detection algorithm. It operates on the assumption valid signal peaks persist over multiple adjacent spectra.
+ Detailed description of its usage can be found in the online documentation.
\ No newline at end of file
diff --git a/src/app/hardklor/S2N.cpp b/src/app/hardklor/S2N.cpp
new file mode 100644
index 0000000..655147b
--- /dev/null
+++ b/src/app/hardklor/S2N.cpp
@@ -0,0 +1,340 @@
+#include "S2N.h"
+#include <iostream>
+
+// Adapted from THRASH
+Spectrum signalToNoise(Spectrum& s, int start, int stop, float sig, float* cutoff, bool skipZero, bool subtract){
+
+ int i;
+ int c;
+ double d;
+ int a[100];
+ float b[100];
+ float FWHM;
+ float maxIntensity;
+ float baseIntensity;
+ Spectrum newSpec;
+
+ if(s.size()==0) return newSpec;
+
+ if(skipZero){
+ //count only non-zero values in spectrum
+ c=0;
+ for(i=start;i<stop+1;i++){
+ if(s.at(i).intensity>0)c++;
+ };
+ } else {
+ //accept all values
+ c=stop-start+1;
+ };
+
+ if(c==0) return newSpec;
+
+ float *sortD = new float[c];
+
+ //Set initial array values
+ for(i=0;i<100;i++) {
+ a[i]=0;
+ b[i]=0;
+ };
+
+ //Copy abundances to an array that can be sorted
+ maxIntensity=0;
+ c=0;
+ for(i=start;i<stop+1;i++) {
+ if(skipZero) {
+ if(s.at(i).intensity > 0) sortD[c++] = s.at(i).intensity;
+ } else {
+ sortD[c++] = s.at(i).intensity;
+ };
+ if(s.at(i).intensity > maxIntensity) maxIntensity = s.at(i).intensity;
+ };
+
+ //Sort the array
+ sort(sortD,sortD+c);
+
+ //Find the number of relative abundances at 1% intervals
+ c=0;
+ for(i=0;i<100;i++){
+ while(sortD[c]*100/maxIntensity < i) c++;
+ a[i] = c;
+ };
+
+ //Get the derivative
+ for(i=1;i<100;i++) {
+ b[i]=(float)(a[i]-a[i-1]);
+ };
+
+ //Smooth the derivative
+ SG_SmoothD(&b[0],100,20,2);
+
+ //Find the most intense point in the derivative
+ c=0;
+ for(i=0;i<100;i++){
+ if(b[i]>=b[c]) c=i;
+ };
+ baseIntensity=(float)c;
+
+ //find FWHM (this is a hack - I don't know the proper way to do this)
+ i=c;
+ d=b[c]/2;
+ while(i<100){
+ if(b[i]>d)i++;
+ else break;
+ };
+ FWHM = (float)(i-c);
+
+ i=c;
+ while(i>0){
+ if(b[i]>d)i--;
+ else break;
+ };
+
+ FWHM += (float)(c-i);
+
+
+ //Clean up the memory
+ delete [] sortD;
+
+ //Go find the peaks using the baseIntensity and FWHM
+ if(subtract) newSpec = SNSubtracted(s,start,stop,sig,FWHM,maxIntensity,baseIntensity);
+ else newSpec = SNPeaks(s,start,stop,sig,FWHM,maxIntensity,baseIntensity);
+
+ *cutoff = sig*FWHM+baseIntensity;
+
+ return newSpec;
+
+};
+
+Spectrum SNPeaks(Spectrum& s, int start, int stop, float SN, float FWHM, float max, float base){
+ int i;
+ double sig;
+ Spectrum newSpec;
+
+ //Scan all data. Keep data that exceed the signal to noise threshold.
+ for(i=start;i<stop+1;i++){
+ sig = (s.at(i).intensity*100/max - base) / FWHM;
+ if(sig > SN) newSpec.add(s.at(i));
+ };
+
+ return newSpec;
+
+};
+
+Spectrum SNSubtracted(Spectrum& s, int start, int stop, float SN, float FWHM, float max, float base){
+ int i;
+ double sig;
+ Spectrum newSpec;
+ Peak_T p;
+
+ //Scan all data. Keep data that exceed the signal to noise threshold.
+ for(i=start;i<stop+1;i++){
+ sig = (s.at(i).intensity*100/max - base) / FWHM;
+ if(sig > SN) newSpec.add(s.at(i));
+ else {
+ p=s.at(i);
+ p.intensity=0;
+ newSpec.add(p);
+ };
+ };
+
+ return newSpec;
+
+};
+
+
+// Adapted from THRASH
+float findSNCutoff(Spectrum& s, int start, int stop, float sig, bool skipZero){
+
+ int i;
+ int c;
+ double d;
+ int a[100];
+ float b[100];
+ float FWHM;
+ float maxIntensity;
+ float baseIntensity;
+ Spectrum newSpec;
+
+ if(s.size()==0) 0;
+
+ if(skipZero){
+ //count only non-zero values in spectrum
+ c=0;
+ for(i=start;i<stop+1;i++){
+ if(s.at(i).intensity>0)c++;
+ };
+ } else {
+ //accept all values
+ c=stop-start+1;
+ };
+
+ if(c==0) return 0;
+
+ float *sortD = new float[c];
+
+ //Set initial array values
+ for(i=0;i<100;i++) {
+ a[i]=0;
+ b[i]=0;
+ };
+
+ //Copy abundances to an array that can be sorted
+ maxIntensity=0;
+ c=0;
+ for(i=start;i<stop+1;i++) {
+ if(skipZero) {
+ if(s.at(i).intensity > 0) sortD[c++] = s.at(i).intensity;
+ } else {
+ sortD[c++] = s.at(i).intensity;
+ };
+ if(s.at(i).intensity > maxIntensity) maxIntensity = s.at(i).intensity;
+ };
+
+ //Sort the array
+ sort(sortD,sortD+c);
+
+ //Find the number of relative abundances at 1% intervals
+ c=0;
+ for(i=0;i<100;i++){
+ while(sortD[c]*100/maxIntensity < i) c++;
+ a[i] = c;
+ };
+
+ //Get the derivative
+ for(i=1;i<100;i++) {
+ b[i]=(float)(a[i]-a[i-1]);
+ };
+
+ //Smooth the derivative
+ SG_SmoothD(&b[0],100,20,2);
+
+ //Find the most intense point in the derivative
+ c=0;
+ for(i=0;i<100;i++){
+ if(b[i]>=b[c]) c=i;
+ };
+ baseIntensity=(float)c;
+
+ //find FWHM (this is a hack - I don't know the proper way to do this)
+ i=c;
+ d=b[c]/2;
+ while(i<100){
+ if(b[i]>d)i++;
+ else break;
+ };
+ FWHM = (float)(i-c);
+
+ i=c;
+ while(i>0){
+ if(b[i]>d)i--;
+ else break;
+ };
+
+ FWHM += (float)(c-i);
+
+
+ //Clean up the memory
+ delete [] sortD;
+
+ return sig*FWHM+baseIntensity;
+
+};
+
+float findSNCutoff2(Spectrum& s, int start, int stop, float sig, double& max, bool skipZero){
+
+ int i;
+ int c;
+ double d;
+ int a[100];
+ float b[100];
+ float FWHM;
+ float maxIntensity;
+ float baseIntensity;
+ Spectrum newSpec;
+
+ if(s.size()==0) 0;
+
+ if(skipZero){
+ //count only non-zero values in spectrum
+ c=0;
+ for(i=start;i<stop+1;i++){
+ if(s.at(i).intensity>0)c++;
+ };
+ } else {
+ //accept all values
+ c=stop-start+1;
+ };
+
+ if(c==0) return 0;
+
+ float *sortD = new float[c];
+
+ //Set initial array values
+ for(i=0;i<100;i++) {
+ a[i]=0;
+ b[i]=0;
+ };
+
+ //Copy abundances to an array that can be sorted
+ maxIntensity=0;
+ c=0;
+ for(i=start;i<stop+1;i++) {
+ if(skipZero) {
+ if(s.at(i).intensity > 0) sortD[c++] = s.at(i).intensity;
+ } else {
+ sortD[c++] = s.at(i).intensity;
+ };
+ if(s.at(i).intensity > maxIntensity) maxIntensity = s.at(i).intensity;
+ };
+
+ //Sort the array
+ sort(sortD,sortD+c);
+
+ //Find the number of relative abundances at 1% intervals
+ c=0;
+ for(i=0;i<100;i++){
+ while(sortD[c]*100/maxIntensity < i) c++;
+ a[i] = c;
+ };
+
+ //Get the derivative
+ for(i=1;i<100;i++) {
+ b[i]=(float)(a[i]-a[i-1]);
+ };
+
+ //Smooth the derivative
+ SG_SmoothD(&b[0],100,20,2);
+
+ //Find the most intense point in the derivative
+ c=0;
+ for(i=0;i<100;i++){
+ if(b[i]>=b[c]) c=i;
+ };
+ baseIntensity=(float)c;
+
+ //find FWHM (this is a hack - I don't know the proper way to do this)
+ i=c;
+ d=b[c]/2;
+ while(i<100){
+ if(b[i]>d)i++;
+ else break;
+ };
+ FWHM = (float)(i-c);
+
+ i=c;
+ while(i>0){
+ if(b[i]>d)i--;
+ else break;
+ };
+
+ FWHM += (float)(c-i);
+
+
+ //Clean up the memory
+ delete [] sortD;
+
+ max = maxIntensity;
+ return sig*FWHM+baseIntensity;
+
+};
+
diff --git a/src/app/hardklor/S2N.h b/src/app/hardklor/S2N.h
new file mode 100644
index 0000000..597bd3a
--- /dev/null
+++ b/src/app/hardklor/S2N.h
@@ -0,0 +1,16 @@
+#ifndef _S2N_H
+#define _S2N_H
+
+#include "Spectrum.h"
+#include "Smooth.h"
+#include <algorithm>
+
+using namespace std;
+
+Spectrum signalToNoise(Spectrum& s, int start, int stop, float sig, float* cutoff, bool skipZero=true, bool subtract=false);
+Spectrum SNPeaks(Spectrum& s, int start, int stop, float SN, float FWHM, float max, float base);
+Spectrum SNSubtracted(Spectrum& s, int start, int stop, float SN, float FWHM, float max, float base);
+float findSNCutoff(Spectrum& s, int start, int stop, float sig, bool skipZero=true);
+float findSNCutoff2(Spectrum& s, int start, int stop, float sig, double& max, bool skipZero=true);
+
+#endif
diff --git a/src/app/hardklor/Smooth.cpp b/src/app/hardklor/Smooth.cpp
new file mode 100644
index 0000000..edf25d2
--- /dev/null
+++ b/src/app/hardklor/Smooth.cpp
@@ -0,0 +1,179 @@
+#include "Smooth.h"
+#include <iostream>
+
+//Savitzky-Golay smoothing algorithm
+void SG_Smooth(Spectrum& sp, int m, int p){
+
+ if(2*m<p) {
+ cout << "Invalid Smoothing Parameters == Smoothing Skipped!" << endl;
+ return;
+ }
+
+ int t,i,s;
+ int k;
+ int c1,c2,c3;
+ double weightSum;
+ double *weight, *holder;
+ weight = new double[2*m+1];
+ holder = new double[sp.size()];
+
+ s = 0; // Derivative order s = 0 for smooth
+
+ //copy intensities to holder array and set to 0
+ for(i=0;i<sp.size();i++){
+ holder[i] = sp.at(i).intensity;
+ sp.at(i).intensity=0;
+ }
+
+ //Calculate the Savitzky-Golay Weights for t = 0
+ c1 = 0;
+ weightSum=0;
+ for(i=-m; i<=m; i++){
+ weight[c1] = SG_Weight(i, 0, m, p, s);
+ weightSum+=weight[c1];
+ c1++;
+ }
+
+ c1 = 0;
+ t = -m;
+ // Smoothing for the points 0 to m-1
+ for(k=0; k<m; k++){
+ c3 = 0;
+ for(i=-m; i<=m; i++){
+ sp.at(k).intensity += (float)(SG_Weight(i, t, m, p, s) * holder[k + c3]);
+ c3++;
+ }
+ t++;
+ }
+
+ // Smoothing for the bulk of the chromatogram at t = 0
+ for(k=m;k<sp.size()-m;k++){
+ c2=-m;
+ for(i=0; i<2*m+1; i++){
+ sp.at(k).intensity += (float)(weight[i] * holder[k+c2]);
+ c2++;
+ }
+ }
+
+ // Smoothing for the points end-m+1 to end
+ t = 1;
+ for(k=sp.size()-m; k<sp.size(); k++){
+ c3 = -(2*m+1);
+ for(i=-m; i<=m; i++){
+ sp.at(k).intensity += (float)(SG_Weight(i, t, m, p, s) * holder[k + c3]);
+ c3++;
+ }
+ t++;
+ }
+
+ delete [] weight;
+ delete [] holder;
+}
+
+//Savitzky-Golay smoothing with an array instead of spectrum object
+void SG_SmoothD(float *d, int sz, int m, int p){
+
+ int t,i,s;
+ int k;
+ int c1,c2,c3;
+ float *weight,*holder;
+ weight = new float[sz];
+ holder = new float[sz];
+
+ s = 0; // Derivative order s = 0 for smooth
+
+ for(i=0;i<sz;i++){
+ holder[i] = d[i];
+ d[i]=0;
+ }
+
+ //Calculate the Savitsky-Golay Weights for t = 0
+ c1 = 0;
+ for(i=-m; i<=m; i++){
+ weight[c1] = (float)SG_Weight(i, 0, m , p, s);
+ c1++;
+ }
+
+ c1 = 0;
+ // Smoothing for the points 0 to m-1
+ t = -m;
+ for(k=0; k<m; k++){
+ c3 = 0;
+ for(i=-m; i<=m; i++){
+ d[k] += (float)(SG_Weight(i, t, m, p, s) * holder[k + c3]);
+ c3++;
+ }
+ t++;
+ }
+
+ // Smoothing for the bulk of the chromatogram at t = 0
+ for(k=m;k<sz-m;k++){
+ c2=-m;
+ for(i=0; i<(2*m+1); i++){
+ d[k] += weight[i] * holder[k+c2];
+ c2++;
+ }
+ }
+
+ // Smoothing for the points end-m+1 to end
+ t = 1;
+ for(k=sz-m; k<sz; k++){
+ c3 = -(2*m+1);
+ for(i=-m; i<=m; i++){
+ d[k] += (float)(SG_Weight(i, t, m, p, s) * holder[k + c3]);
+ c3++;
+ }
+ t++;
+ }
+
+ delete [] weight;
+ delete [] holder;
+
+}
+
+// Calculates the Savitsky-Golay weight of the i'th data point
+// for the t'th Least-Square point of the s'th derivative
+// over 2m+1 points, order n.
+double SG_Weight(int i, int t, int m, int n, int s){
+
+ int k;
+ double sum;
+
+ sum = 0;
+ for(k=0;k<=n;k++){
+ sum += (double)(2 * k + 1) *
+ (SG_GenFact(2 * m, k) / SG_GenFact(2 * m + k + 1, k + 1)) *
+ SG_GramPoly(i, m, k, 0) *
+ SG_GramPoly(t, m, k, s);
+ }
+
+ return sum;
+}
+
+// Calculates the Savitsky-Golay Gram Polynomial (s = 0) or it's s'th
+// derivative evaluated at i, order k, over 2m+1 points.
+double SG_GramPoly(int i, int m, int k, int s){
+
+ if(k>0){
+ return (double)(4*k-2) / (double)(k*(2*m-k+1)) *
+ (i*SG_GramPoly(i,m,k-1,s) + s*SG_GramPoly(i,m,k-1,s-1)) -
+ (double)((k-1) * (2*m+k)) / (double)(k*(2*m-k+1)) *
+ SG_GramPoly(i,m,k-2,s);
+ } else if(k==0 && s==0) {
+ return 1;
+ } else {
+ return 0;
+ }
+
+}
+
+double SG_GenFact(int a, int b) {
+ int j;
+ int c;
+ double gf;
+
+ gf = 1;
+ c = a-b+1;
+ for(j=c; j<=a; j++) gf *= j;
+ return gf;
+}
diff --git a/src/app/hardklor/Smooth.h b/src/app/hardklor/Smooth.h
new file mode 100644
index 0000000..8f7b933
--- /dev/null
+++ b/src/app/hardklor/Smooth.h
@@ -0,0 +1,15 @@
+#ifndef _SMOOTH_H
+#define _SMOOTH_H
+
+#include "Spectrum.h"
+
+using namespace std;
+using namespace MSToolkit;
+
+double SG_GenFact(int, int);
+double SG_GramPoly(int, int, int, int);
+void SG_Smooth(Spectrum&, int, int);
+void SG_SmoothD(float*, int, int, int);
+double SG_Weight(int, int, int, int, int);
+
+#endif
diff --git a/src/app/hardklor/SpecAnalyzeSupport.cpp b/src/app/hardklor/SpecAnalyzeSupport.cpp
new file mode 100644
index 0000000..e7bcf25
--- /dev/null
+++ b/src/app/hardklor/SpecAnalyzeSupport.cpp
@@ -0,0 +1,266 @@
+#include "SpecAnalyzeSupport.h"
+
+/* ******************************************************* */
+/* CPeakPrediction */
+/* ******************************************************* */
+
+//Constructors & Destructors
+CPeakPrediction::CPeakPrediction() {
+ mz=0;
+ intensity=0;
+ charges = new vector<int>;
+}
+CPeakPrediction::CPeakPrediction(const CPeakPrediction& p) {
+ mz = p.mz;
+ intensity = p.intensity;
+ charges = new vector<int>;
+ for(unsigned int i=0;i<p.charges->size();i++) charges->push_back(p.charges->at(i));
+}
+CPeakPrediction::~CPeakPrediction() {
+ delete charges;
+}
+
+//Overloaded operators
+CPeakPrediction& CPeakPrediction::operator=(const CPeakPrediction& p){
+ if(this!=&p){
+ mz = p.mz;
+ intensity = p.intensity;
+ delete charges;
+ charges = new vector<int>;
+ for(unsigned int i=0;i<p.charges->size();i++) charges->push_back(p.charges->at(i));
+ }
+ return *this;
+}
+
+//Functions
+void CPeakPrediction::AddCharge(int charge){ charges->push_back(charge); }
+void CPeakPrediction::Clear(){ charges->clear(); }
+void CPeakPrediction::EraseCharge(int index){ charges->erase(charges->begin()+index); }
+int CPeakPrediction::GetCharge(int index){ return charges->at(index); }
+float CPeakPrediction::GetIntensity(){ return intensity; }
+double CPeakPrediction::GetMZ(){ return mz; }
+void CPeakPrediction::SetIntensity(float newIntens){ intensity=newIntens; }
+void CPeakPrediction::SetMZ(double newMZ){ mz=newMZ; }
+int CPeakPrediction::Size(){ return charges->size(); }
+
+
+
+
+/* ******************************************************* */
+/* CPeptideVariant */
+/* ******************************************************* */
+
+//Constructors & Destructors
+CPeptideVariant::CPeptideVariant(){
+ match = new Peak_T[1];
+ matchSize=1;
+ mismatch = new Peak_T[1];
+ mismatchSize=1;
+ extra = new vector<Peak_T>;
+ charge=1;
+ monoMass=0;
+ distArea=0;
+}
+
+CPeptideVariant::CPeptideVariant(const CPeptideVariant& p){
+ int i;
+
+ matchSize = p.matchSize;
+ mismatchSize = p.mismatchSize;
+ charge = p.charge;
+ monoMass = p.monoMass;
+ variant = p.variant;
+ distArea = p.distArea;
+ strcpy(formula,p.formula);
+
+ match = new Peak_T[matchSize];
+ mismatch = new Peak_T[mismatchSize];
+ extra = new vector<Peak_T>;
+
+ for(i=0;i<p.matchSize;i++) match[i]=p.match[i];
+ for(i=0;i<p.mismatchSize;i++) mismatch[i]=p.mismatch[i];
+ for(i=0;i<(int)p.extra->size();i++) extra->push_back(p.extra->at(i));
+}
+
+CPeptideVariant::~CPeptideVariant(){
+ delete [] match;
+ delete [] mismatch;
+ delete extra;
+}
+
+//Overloaded Operators
+CPeptideVariant& CPeptideVariant::operator=(const CPeptideVariant& p) {
+ int i;
+
+ if(this!=&p){
+ matchSize = p.matchSize;
+ mismatchSize = p.mismatchSize;
+ charge = p.charge;
+ monoMass = p.monoMass;
+ variant = p.variant;
+ distArea = p.distArea;
+ strcpy(formula,p.formula);
+
+ delete [] match;
+ delete [] mismatch;
+ delete extra;
+
+ match = new Peak_T[matchSize];
+ mismatch = new Peak_T[mismatchSize];
+ extra = new vector<Peak_T>;
+
+ for(i=0;i<p.matchSize;i++) match[i]=p.match[i];
+ for(i=0;i<p.mismatchSize;i++) mismatch[i]=p.mismatch[i];
+ for(i=0;i<(int)p.extra->size();i++) extra->push_back(p.extra->at(i));
+ }
+ return *this;
+}
+
+//Functions
+void CPeptideVariant::AddExtra(double& mz, float& intensity) {
+ Peak_T p;
+ p.mz=mz;
+ p.intensity=intensity;
+ extra->push_back(p);
+}
+void CPeptideVariant::AddMatch(int& index, double& mz, float& intensity) {
+ Peak_T p;
+ p.mz=mz;
+ p.intensity=intensity;
+ match[index]=p;
+}
+void CPeptideVariant::AddMismatch(int& index, double& mz, float& intensity) {
+ Peak_T p;
+ p.mz=mz;
+ p.intensity=intensity;
+ mismatch[index]=p;
+}
+void CPeptideVariant::Clear(){
+ int i;
+ CHardklorVariant v;
+ delete [] match;
+ delete [] mismatch;
+ delete extra;
+ match = new Peak_T[matchSize];
+ for(i=0;i<matchSize;i++) {
+ match[i].mz=0;
+ match[i].intensity=0;
+ }
+ mismatch = new Peak_T[mismatchSize];
+ for(i=0;i<mismatchSize;i++) {
+ mismatch[i].mz=0;
+ mismatch[i].intensity=0;
+ }
+ extra = new vector<Peak_T>;
+ charge=0;
+ monoMass=0;
+ variant=v;
+ distArea=0;
+ strcpy(formula,"");
+}
+void CPeptideVariant::DeleteExtra(){
+ delete extra;
+ extra = new vector<Peak_T>;
+}
+double& CPeptideVariant::GetArea() { return distArea; }
+int& CPeptideVariant::GetCharge() { return charge; }
+Peak_T& CPeptideVariant::GetExtra(int& index) { return extra->at(index); }
+char* CPeptideVariant::GetFormula() { return formula; }
+CHardklorVariant& CPeptideVariant::GetHKVariant() { return variant; }
+Peak_T& CPeptideVariant::GetMatch(int& index) { return match[index]; }
+Peak_T& CPeptideVariant::GetMismatch(int& index) { return mismatch[index]; }
+double& CPeptideVariant::GetMonoMass() { return monoMass; }
+void CPeptideVariant::SetArea(double& d) { distArea=d; }
+void CPeptideVariant::SetCharge(int ch) { charge=ch; }
+void CPeptideVariant::SetFormula(char form[64]) { strcpy(formula,form); }
+void CPeptideVariant::SetMatchSize(int& num) {
+ delete [] match;
+ match = new Peak_T[num];
+ for(int i=0;i<num;i++) {
+ match[i].mz=0;
+ match[i].intensity=0;
+ }
+ matchSize = num;
+}
+void CPeptideVariant::SetMismatchSize(int& num) {
+ delete [] mismatch;
+ mismatch = new Peak_T[num];
+ for(int i=0;i<num;i++) {
+ mismatch[i].mz=0;
+ mismatch[i].intensity=0;
+ }
+ mismatchSize = num;
+}
+void CPeptideVariant::SetMonoMass(double mass) { monoMass=mass; }
+void CPeptideVariant::SetVariant(CHardklorVariant &v) { variant=v; }
+int CPeptideVariant::SizeExtra() { return extra->size(); }
+
+
+
+
+
+
+/* ******************************************************* */
+/* CPeptidePrediction */
+/* ******************************************************* */
+
+//Constructors & Destructors
+CPeptidePrediction::CPeptidePrediction(){
+ variantList = new vector<CPeptideVariant>;
+ mz=0;
+ intensity=0;
+ bestVar=0;
+ maxPeakIndex=0;
+}
+CPeptidePrediction::CPeptidePrediction(const CPeptidePrediction& p){
+ mz=p.mz;
+ intensity=p.intensity;
+ bestVar=p.bestVar;
+ maxPeakIndex=p.maxPeakIndex;
+ variantList = new vector<CPeptideVariant>;
+ for(unsigned int i=0;i<p.variantList->size();i++){
+ variantList->push_back(p.variantList->at(i));
+ }
+}
+CPeptidePrediction::~CPeptidePrediction(){
+ delete variantList;
+}
+
+//Overloaded operators
+CPeptidePrediction& CPeptidePrediction::operator=(const CPeptidePrediction& p){
+ if(this!=&p){
+ mz=p.mz;
+ intensity=p.intensity;
+ bestVar=p.bestVar;
+ maxPeakIndex=p.maxPeakIndex;
+ delete variantList;
+ variantList = new vector<CPeptideVariant>;
+ for(unsigned int i=0;i<p.variantList->size();i++){
+ variantList->push_back(p.variantList->at(i));
+ }
+ }
+ return *this;
+}
+
+//Functions
+void CPeptidePrediction::AddVariant(CPeptideVariant& var) { variantList->push_back(var); }
+void CPeptidePrediction::Clear() {
+ delete variantList;
+ variantList = new vector<CPeptideVariant>;
+ mz=0;
+ intensity=0;
+ bestVar=0;
+}
+float CPeptidePrediction::GetIntensity() { return intensity; }
+int CPeptidePrediction::GetMaxPeakIndex() { return maxPeakIndex; }
+double CPeptidePrediction::GetMZ() { return mz; }
+CPeptideVariant& CPeptidePrediction::GetVariant(int& index) { return variantList->at(index); }
+void CPeptidePrediction::SetIntensity(float intens) { intensity = intens; }
+void CPeptidePrediction::SetMaxPeakIndex(int index) { maxPeakIndex = index; }
+void CPeptidePrediction::SetMZ(double mass) { mz = mass; }
+int CPeptidePrediction::VariantListSize() { return variantList->size(); }
+
+float& CPeptidePrediction::GetIntensityAt(int& variant, int& mz) {
+ return variantList->at(variant).GetMatch(mz).intensity;
+}
+
diff --git a/src/app/hardklor/SpecAnalyzeSupport.h b/src/app/hardklor/SpecAnalyzeSupport.h
new file mode 100644
index 0000000..36117af
--- /dev/null
+++ b/src/app/hardklor/SpecAnalyzeSupport.h
@@ -0,0 +1,136 @@
+#ifndef _SPECANALYZESUPPORT_H
+#define _SPECANALYZESUPPORT_H
+
+#include <vector>
+#include "CAveragine.h"
+#include "CMercury8.h"
+#include "HardklorTypes.h"
+
+using namespace std;
+
+/* ******************************************************* */
+/* CPeakPrediction */
+/* ******************************************************* */
+class CPeakPrediction{
+ private:
+ //Data Members
+ double mz; //Peak m/z in spectrum
+ float intensity; //Peak intensity in spectrum
+ vector<int> *charges; //All charge state predictions for this peak
+ protected:
+ public:
+ //Constructors and Destructors
+ CPeakPrediction();
+ CPeakPrediction(const CPeakPrediction& p);
+ ~CPeakPrediction();
+
+ //Overloaded operators
+ CPeakPrediction& operator=(const CPeakPrediction& p);
+
+ //Functions
+ void AddCharge(int charge); //Add charge state to the vector
+ void Clear(); //Clear all information
+ void EraseCharge(int index); //Remove charge state
+ int GetCharge(int index); //Get charge state from index
+ float GetIntensity(); //Return intensity
+ double GetMZ(); //Return m/z
+ void SetIntensity(float newIntens); //Set intensity
+ void SetMZ(double newMZ); //Set m/z
+ int Size(); //Get number of charge state predictions
+};
+
+
+/* ******************************************************* */
+/* CPeptideVariant */
+/* ******************************************************* */
+class CPeptideVariant {
+ private:
+ Peak_T *match; //Array of mz and intensities that match the peak list at index n
+ int matchSize;
+ Peak_T *mismatch; //Array of mz and intensities that do not match the peak list at index n
+ int mismatchSize;
+
+ vector<Peak_T> *extra; //Temporary storage of mismatch data until mismatch array size is determined
+
+ int charge; //Charge state of variant
+ char formula[64]; //Molecular formula (averagine-based)
+ double monoMass; //monoisotopic mass
+ double distArea; //distribution area (sum of centroided peaks)
+ CHardklorVariant variant; //Variant settings
+ protected:
+ public:
+ //Constructors & Destructors
+ CPeptideVariant();
+ CPeptideVariant(const CPeptideVariant& p);
+ ~CPeptideVariant();
+
+ //Operator overloads
+ CPeptideVariant& operator=(const CPeptideVariant& p);
+
+ //Functions
+ void AddExtra(double& mz, float& intensity);
+ void AddMatch(int& index, double& mz, float& intensity);
+ void AddMismatch(int& index, double& mz, float& intensity);
+ void Clear();
+ void DeleteExtra();
+ double& GetArea();
+ int& GetCharge();
+ Peak_T& GetExtra(int& index);
+ char* GetFormula();
+ CHardklorVariant& GetHKVariant();
+ Peak_T& GetMatch(int& index);
+ Peak_T& GetMismatch(int& index);
+ double& GetMonoMass();
+ void SetArea(double& d);
+ void SetCharge(int ch);
+ void SetFormula(char form[64]);
+ void SetMatchSize(int& num);
+ void SetMismatchSize(int& num);
+ void SetMonoMass(double mass);
+ void SetVariant(CHardklorVariant& v);
+ int SizeExtra();
+
+};
+
+
+/* ******************************************************* */
+/* CPeptidePrediction */
+/* ******************************************************* */
+class CPeptidePrediction {
+ private:
+ vector<CPeptideVariant> *variantList; //vector of all variants for this peptide
+ double mz; //mz peak from which variants are derived
+ float intensity; //intensity of mz peak
+ int bestVar; //Index to variant with best match/mismatch score
+ int maxPeakIndex;
+ protected:
+ public:
+ //Make variants here?
+ /* Pass vector of variants (CHardklorVariant) and make Mercury distributions */
+ /* Or calculate the variant externally and add it. */
+
+ //Constructors & Destructors
+ CPeptidePrediction();
+ CPeptidePrediction(const CPeptidePrediction& p);
+ ~CPeptidePrediction();
+
+ //Overloaded operators
+ CPeptidePrediction& operator=(const CPeptidePrediction& p);
+
+ //Functions
+ void AddVariant(CPeptideVariant& var);
+ void Clear();
+ float GetIntensity();
+ int GetMaxPeakIndex();
+ double GetMZ();
+ CPeptideVariant& GetVariant(int& index);
+ void SetIntensity(float intens);
+ void SetMaxPeakIndex(int index);
+ void SetMZ(double mass);
+ int VariantListSize();
+
+ float& GetIntensityAt(int& variant, int& mz);
+};
+
+#endif
+
diff --git a/src/app/hardklor/cmake_install.cmake b/src/app/hardklor/cmake_install.cmake
new file mode 100644
index 0000000..bbbdc26
--- /dev/null
+++ b/src/app/hardklor/cmake_install.cmake
@@ -0,0 +1,34 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/hardklor
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
diff --git a/src/app/hardklor/libhardklor.a b/src/app/hardklor/libhardklor.a
new file mode 100644
index 0000000..293469d
Binary files /dev/null and b/src/app/hardklor/libhardklor.a differ
diff --git a/src/app/hardklor/mercury.h b/src/app/hardklor/mercury.h
new file mode 100644
index 0000000..b5c3ca4
--- /dev/null
+++ b/src/app/hardklor/mercury.h
@@ -0,0 +1,27 @@
+#ifndef _MERCURY_H
+#define _MERCURY_H
+
+#include <vector>
+
+#define PI 3.14159265358979323846
+#define TWOPI 6.28318530717958647
+#define HALFPI 1.57079632679489666
+#define GAUSSIAN 1
+#define LORENTZIAN 2
+#define ProtonMass 1.00727649
+#define ElectronMass 0.00054858
+#define MAXAtomNo 108 /* allows for elements H - Lr */
+#define MAXIsotopes 20 /* allows for 20 elements in molecular formula */
+#define EZS Element[Z].Symbol
+#define EZNI Element[Z].NumIsotopes
+#define EZM Element[Z].IsoMass
+#define EZP Element[Z].IsoProb
+#define EZW Element[Z].WrapMass
+#define EZNA Element[Z].NumAtoms
+
+struct Result {
+ double mass;
+ double data;
+};
+
+#endif
diff --git a/src/app/hardklor/resource.h b/src/app/hardklor/resource.h
new file mode 100644
index 0000000..cad4c03
--- /dev/null
+++ b/src/app/hardklor/resource.h
@@ -0,0 +1,17 @@
+//{{NO_DEPENDENCIES}}
+// Microsoft Developer Studio generated include file.
+// Used by Hardklor.rc
+//
+#define IDI_ICON1 101
+#define IDI_ICON2 122
+
+// Next default values for new objects
+//
+#ifdef APSTUDIO_INVOKED
+#ifndef APSTUDIO_READONLY_SYMBOLS
+#define _APS_NEXT_RESOURCE_VALUE 123
+#define _APS_NEXT_COMMAND_VALUE 40001
+#define _APS_NEXT_CONTROL_VALUE 1000
+#define _APS_NEXT_SYMED_VALUE 101
+#endif
+#endif
diff --git a/src/app/hardklor/resource1.h b/src/app/hardklor/resource1.h
new file mode 100644
index 0000000..ef0340e
--- /dev/null
+++ b/src/app/hardklor/resource1.h
@@ -0,0 +1,16 @@
+//{{NO_DEPENDENCIES}}
+// Microsoft Visual C++ generated include file.
+// Used by Hardklor2008.rc
+//
+#define IDI_ICON2 102
+
+// Next default values for new objects
+//
+#ifdef APSTUDIO_INVOKED
+#ifndef APSTUDIO_READONLY_SYMBOLS
+#define _APS_NEXT_RESOURCE_VALUE 103
+#define _APS_NEXT_COMMAND_VALUE 40001
+#define _APS_NEXT_CONTROL_VALUE 1001
+#define _APS_NEXT_SYMED_VALUE 101
+#endif
+#endif
diff --git a/src/app/q-value.cpp b/src/app/q-value.cpp
new file mode 100644
index 0000000..7015b4f
--- /dev/null
+++ b/src/app/q-value.cpp
@@ -0,0 +1,31 @@
+/*******************************************************************************
+ * \file q-value.cpp
+ * AUTHOR: Chris Park
+ * CREATE DATE: Jan 03 2007
+ * \brief Given as input a directory containing binary psm files,
+ * a protein database, and an optional parameter file, analyze the
+ * matches (with percolator or q-value) and return scores indicating
+ * how good the matches are.
+ *
+ * Handles at most 4 files (target and decoy). Expects psm files to
+ * start with <fileroot>.se and
+ * end with the extension '.txt' and decoys to end with
+ * '-decoy#.txt'. Multiple target files in the given directory are
+ * concatinated together and presumed to be non-overlaping parts of
+ * the same ms2 file.
+ ****************************************************************************/
+
+#include "q-value.h"
+#include "io/MatchCollectionParser.h"
+#include "PosteriorEstimator.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+
+#include <map>
+#include <utility>
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/q-value.h b/src/app/q-value.h
new file mode 100644
index 0000000..44907ce
--- /dev/null
+++ b/src/app/q-value.h
@@ -0,0 +1,56 @@
+#ifndef QVALUE_H
+#define QVALUE_H
+
+/**
+ * \file q-value.h
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: November 24, 2008
+ ****************************************************************************/
+#include <stdlib.h>
+#include <stdio.h>
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "model/objects.h"
+#include "parameter.h"
+#include "model/Protein.h"
+#include "model/Peptide.h"
+#include "model/Spectrum.h"
+#include "io/SpectrumCollection.h"
+#include "model/Scorer.h"
+#include "model/Match.h"
+#include "model/MatchCollection.h"
+#include "io/OutputFiles.h"
+
+
+
+FLOAT_T* compute_decoy_qvalues_tdc(
+ FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool reverse);
+
+FLOAT_T* compute_qvalues_from_pvalues(
+ FLOAT_T* pvalues,
+ int num_pvals,
+ FLOAT_T pi_zero);
+
+FLOAT_T estimate_pi0( FLOAT_T* target_scores,
+ int num_targets,
+ FLOAT_T* decoy_scores,
+ int num_decoys,
+ bool ascending );
+
+MatchCollection* run_qvalue(
+ const vector<string>& input_files,
+ OutputFiles& output,
+ COMMAND_T command );
+
+void peptide_level_filtering(
+ MatchCollection* match_collection,
+ std::map<string, FLOAT_T>* BestPeptideScore,
+ SCORER_TYPE_T score_type,
+ bool ascending);
+
+#endif //QVALUE_H
+
diff --git a/src/app/qranker-barista/Barista.cpp b/src/app/qranker-barista/Barista.cpp
new file mode 100644
index 0000000..e9a6059
--- /dev/null
+++ b/src/app/qranker-barista/Barista.cpp
@@ -0,0 +1,2895 @@
+#include "Barista.h"
+#include "model/objects.h"
+#include "app/ComputeQValues.h"
+#include "util/Params.h"
+
+using namespace std;
+double Barista :: check_gradients_hinge_one_net(int protind, int label){
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ max_psm_inds.erase(max_psm_inds.begin(),max_psm_inds.end());
+ max_psm_scores.erase(max_psm_scores.begin(),max_psm_scores.end());
+ for (int i = 0; i < num_pep; i++){
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+ int max_ind = 0;
+ for (int j = 0; j < num_psms; j++){
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = net.fprop(feat);
+ if(sc[0] > max_sc){
+ max_sc = sc[0];
+ max_ind = j;
+ }
+ }
+ max_psm_inds.push_back(max_ind);
+ max_psm_scores.push_back(max_sc);
+ }
+ assert((int)max_psm_inds.size() == num_pep);
+ assert((int)max_psm_scores.size() == num_pep);
+
+ double sm = 0.0;
+ double n = pow(num_pep,alpha);
+ for(unsigned int i = 0; i < max_psm_inds.size() ; i++)
+ sm+= max_psm_scores[i];
+ sm /= n;
+
+ net.clear_gradients();
+ double *gc = new double[1];
+ gc[0] = -label/n;
+ for(int i = 0; i < num_pep; i++){
+ int pepind = pepinds[i];
+ int *psminds = d.pepind2psminds(pepind);
+ int max_psm_ind = psminds[max_psm_inds[i]];
+ double *feat = d.psmind2features(max_psm_ind);
+ net.fprop(feat);
+ net.bprop(gc);
+ }
+
+ double h = 0.000001;
+ double diff = -(1-sm*label);
+ double err = 0.0;
+ double *w = net.get_weights(1);
+ double *dw = net.get_dweights(1);
+ for (int k = 0; k < d.get_num_features(); k++){
+ w[k] += h;
+ max_psm_inds.erase(max_psm_inds.begin(),max_psm_inds.end());
+ max_psm_scores.erase(max_psm_scores.begin(),max_psm_scores.end());
+ for (int i = 0; i < num_pep; i++){
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+ int max_ind = 0;
+ for (int j = 0; j < num_psms; j++){
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = net.fprop(feat);
+ if(sc[0] > max_sc){
+ max_sc = sc[0];
+ max_ind = j;
+ }
+ }
+ max_psm_inds.push_back(max_ind);
+ max_psm_scores.push_back(max_sc);
+ }
+ double sm1 = 0.0;
+ double n = pow(num_pep,alpha);
+ for(unsigned int i = 0; i < max_psm_inds.size() ; i++)
+ sm1 += max_psm_scores[i];
+ sm1 /= n;
+
+ diff += (1-sm1*label);
+ err += dw[k]-diff/h;
+ w[k]-=h;
+ diff -= (1-sm1*label);
+ }
+
+
+ double *bias = net.get_bias(1);
+ double *dbias = net.get_dbias(1);
+ for (int k = 0; k < num_hu; k++)
+ {
+ bias[k] += h;
+ max_psm_inds.erase(max_psm_inds.begin(),max_psm_inds.end());
+ max_psm_scores.erase(max_psm_scores.begin(),max_psm_scores.end());
+ for (int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+ int max_ind = 0;
+ for (int j = 0; j < num_psms; j++)
+ {
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = net.fprop(feat);
+ if(sc[0] > max_sc)
+ {
+ max_sc = sc[0];
+ max_ind = j;
+ }
+ }
+ max_psm_inds.push_back(max_ind);
+ max_psm_scores.push_back(max_sc);
+ }
+ double sm1 = 0.0;
+ double n = pow(num_pep,alpha);
+ for(unsigned int i = 0; i < max_psm_inds.size() ; i++)
+ sm1 += max_psm_scores[i];
+ sm1 /= n;
+
+ diff += 1-sm1*label;
+ err += dbias[k]-diff/h;
+ bias[k]-=h;
+ diff -= 1-sm1*label;
+ }
+
+ w = net.get_weights(2);
+ dw = net.get_dweights(2);
+ for (int k = 0; k < num_hu; k++)
+ {
+ w[k] += h;
+ max_psm_inds.erase(max_psm_inds.begin(),max_psm_inds.end());
+ max_psm_scores.erase(max_psm_scores.begin(),max_psm_scores.end());
+ for (int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+ int max_ind = 0;
+ for (int j = 0; j < num_psms; j++)
+ {
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = net.fprop(feat);
+ if(sc[0] > max_sc)
+ {
+ max_sc = sc[0];
+ max_ind = j;
+ }
+ }
+ max_psm_inds.push_back(max_ind);
+ max_psm_scores.push_back(max_sc);
+ }
+ double sm1 = 0.0;
+ double n = pow(num_pep,alpha);
+ for(unsigned int i = 0; i < max_psm_inds.size() ; i++)
+ sm1 += max_psm_scores[i];
+ sm1 /= n;
+
+ diff += 1-sm1*label;
+ err += dw[k]-diff/h;
+ w[k]-=h;
+ diff -= 1-sm1*label;
+ }
+
+ bias = net.get_bias(2);
+ dbias = net.get_dbias(2);
+ for (int k = 0; k < 1; k++)
+ {
+ bias[k] += h;
+ max_psm_inds.erase(max_psm_inds.begin(),max_psm_inds.end());
+ max_psm_scores.erase(max_psm_scores.begin(),max_psm_scores.end());
+ for (int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+ int max_ind = 0;
+ for (int j = 0; j < num_psms; j++)
+ {
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = net.fprop(feat);
+ if(sc[0] > max_sc)
+ {
+ max_sc = sc[0];
+ max_ind = j;
+ }
+ }
+ max_psm_inds.push_back(max_ind);
+ max_psm_scores.push_back(max_sc);
+ }
+ double sm1 = 0.0;
+ double n = pow(num_pep,alpha);
+ for(unsigned int i = 0; i < max_psm_inds.size() ; i++)
+ sm1 += max_psm_scores[i];
+ sm1 /= n;
+
+ diff += 1-sm1*label;
+ err += dbias[k]-diff/h;
+ bias[k]-=h;
+ diff -= 1-sm1*label;
+ }
+ return err;
+}
+
+double Barista :: check_gradients_hinge_clones(int protind, int label)
+{
+ double sm = get_protein_score(protind);
+ net.clear_gradients();
+ calc_gradients(protind,label);
+
+ double h = 0.0000001;
+ double diff = -(1-sm*label);
+ double err = 0.0;
+ double *w = net.get_weights(1);
+ double *dw = net.get_dweights(1);
+ for (int k = 0; k < d.get_num_features(); k++)
+ {
+ w[k] += h;
+ double sm1 = get_protein_score(protind);
+ diff += (1-sm1*label);
+ err += dw[k]-diff/h;
+ w[k]-=h;
+ diff -= (1-sm1*label);
+ }
+
+ double *bias = net.get_bias(1);
+ double *dbias = net.get_dbias(1);
+ for (int k = 0; k < num_hu; k++)
+ {
+ bias[k] += h;
+ double sm1 = get_protein_score(protind);
+ diff += 1-sm1*label;
+ err += dbias[k]-diff/h;
+ bias[k]-=h;
+ diff -= 1-sm1*label;
+ }
+
+ w = net.get_weights(2);
+ dw = net.get_dweights(2);
+ for (int k = 0; k < num_hu; k++)
+ {
+ w[k] += h;
+ double sm1 = get_protein_score(protind);
+ diff += 1-sm1*label;
+ err += dw[k]-diff/h;
+ w[k]-=h;
+ diff -= 1-sm1*label;
+ }
+
+ bias = net.get_bias(2);
+ dbias = net.get_dbias(2);
+ for (int k = 0; k < 1; k++)
+ {
+ bias[k] += h;
+ double sm1 = get_protein_score(protind);
+ diff += 1-sm1*label;
+ err += dbias[k]-diff/h;
+ bias[k]-=h;
+ diff -= 1-sm1*label;
+ }
+
+ net.update(mu);
+
+ return err;
+}
+
+/**********************************************************/
+int Barista :: getOverFDRPSM(PSMScores &s, NeuralNet &n,double fdr)
+{
+ double* featVec;
+ for(int i = 0; i < s.size(); i++)
+ {
+ featVec = d.psmind2features(s[i].psmind);
+ double *r = n.fprop(featVec);
+ s[i].score = r[0];
+ }
+
+ int overFDR = s.calcOverFDR(fdr);
+
+ if(verbose > 1)
+ {
+ cout << "psm over fdr: num psms " << overFDR << endl;
+ int cn = 0;
+ set<int> peptides;
+ for(int i = 0; i < s.size(); i++)
+ {
+ if(s[i].label == 1)
+ cn++;
+ peptides.insert(d.psmind2pepind(s[i].psmind));
+ if(cn >= overFDR)
+ break;
+ }
+ cout << "psm over fdr: num peptides " << peptides.size() << endl;
+ }
+ return overFDR;
+}
+
+double Barista :: get_peptide_score(int pepind, NeuralNet &n)
+{
+ int num_psm = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -100000000.0;
+ int max_ind = 0;
+ for(int i = 0; i < num_psm; i++)
+ {
+ int psmind = psminds[i];
+ double *feat = d.psmind2features(psmind);
+ double *sc = n.fprop(feat);
+ if(max_sc < sc[0])
+ {
+ max_sc = sc[0];
+ max_ind = i;
+ }
+ }
+ if((int)pepind_to_max_psmind.size() == d.get_num_peptides())
+ pepind_to_max_psmind[pepind] = psminds[max_ind];
+ return max_sc;
+}
+
+
+int Barista :: getOverFDRPep(PepScores &s, NeuralNet &n,double fdr)
+{
+ int pepind = 0;
+ int label = 0;
+ for(int i = 0; i < s.size(); i++)
+ {
+ pepind = s[i].pepind;
+ double sc = get_peptide_score(pepind,n);
+ s[i].score = sc;
+ }
+
+ int overFDR = s.calcOverFDR(fdr);
+
+ if(verbose > 1)
+ {
+ int cn = 0;
+ set<int> proteins_pos;
+ set<int> proteins_neg;
+ int pep_pos = 0;
+ int pep_neg = 0;
+ for(int i = 0; i < s.size(); i++)
+ {
+ label = s[i].label;
+ if(label == 1)
+ cn++;
+
+ if(label == 1)
+ pep_pos++;
+ else
+ pep_neg++;
+
+ int pepind = s[i].pepind;
+ int num_prot = d.pepind2num_prot(pepind);
+ int *protinds = d.pepind2protinds(pepind);
+ for(int j=0; j < num_prot;j++)
+ {
+ if(label == 1)
+ proteins_pos.insert(protinds[j]);
+ else
+ proteins_neg.insert(protinds[j]);
+ }
+ if(cn >= overFDR)
+ break;
+ }
+ cout << "over FDR peptides:\n";
+ cout << "num pos proteins " << proteins_pos.size() << " num neg proteins " << proteins_neg.size() << " num pos peptides " << pep_pos << " num neg peptides " << pep_neg << endl;
+
+ }
+ return overFDR;
+}
+
+/*****************************************************/
+void Barista :: clear()
+{
+ trainset.clear();
+ testset.clear();
+ peptrainset.clear();
+ peptestset.clear();
+ psmtrainset.clear();
+ psmtestset.clear();
+ delete[] net_clones; net_clones = 0;
+ max_psm_inds.clear();
+ max_psm_scores.clear();
+ used_peptides.clear();
+ pepind_to_max_psmind.clear();
+ if (parser)
+ {
+ delete parser;
+ }
+}
+
+
+double Barista :: get_protein_score_parsimonious(int protind, NeuralNet &n)
+{
+ int num_pep = d.protind2num_pep(protind);
+ int num_all_pep = d.protind2num_all_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ double sm = 0.0;
+ double div = pow(num_all_pep,alpha);
+
+ for (int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+
+ if(used_peptides[pepind] == 0)
+ {
+ used_peptides[pepind] = 1;
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+
+ for (int j = 0; j < num_psms; j++)
+ {
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = n.fprop(feat);
+ if(sc[0] > max_sc)
+ {
+ max_sc = sc[0];
+ }
+ }
+ sm += max_sc;
+ }
+ }
+
+ sm /= div;
+ return sm;
+}
+
+int Barista :: getOverFDRProtParsimonious(ProtScores &set, NeuralNet &n, double fdr)
+{
+
+ int total_num_pep = d.get_num_peptides();
+ used_peptides.clear();
+ used_peptides.resize(total_num_pep,0);
+ double r = 0.0;
+ for(int i = 0; i < set.size(); i++)
+ {
+ int protind = set[i].protind;
+ r = get_protein_score_parsimonious(protind,n);
+ set[i].score = r;
+ }
+ return set.calcOverFDR(fdr);
+}
+
+void Barista :: write_results_prot(string &out_dir, int fdr)
+{
+ ostringstream fn;
+ fn << out_dir <<"/barista.target.proteins.txt";
+ carp(CARP_INFO, "write_results to %s", fn.str().c_str());
+ ofstream f_res(fn.str().c_str());
+
+ int cn = 0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ if(trainset[i].label == 1)
+ {
+ //write out proteins
+ f_res << "protein group " << cn+1 << " q=" << trainset[i].q << endl;
+ int protind = trainset[i].protind;
+ f_res << d.ind2prot(protind) << " ";
+ for(unsigned int j = 0; j < trainset[i].subset_protinds.size(); j++)
+ {
+ int ind = trainset[i].subset_protinds[j];
+ if(d.protind2label(ind) == 1)
+ f_res << d.ind2prot(ind) << " ";
+ }
+ f_res << endl;
+
+ //write out peptides
+ f_res << "peptides\n";
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ for( int j = 0; j < num_pep; j++)
+ {
+ int pepind = pepinds[j];
+ f_res << d.ind2pep(pepind);
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ f_res << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ carp(CARP_DEBUG, "warning: did not assign peptide a max psm index");
+ f_res << " ";
+ }
+ f_res << endl << endl;
+ cn++;
+ }
+ if(cn >= fdr)
+ break;
+ }
+ f_res.close();
+}
+
+
+void Barista :: report_all_results()
+{
+ trainset.clear();
+ testset.clear();
+ ProtScores::fillProteinsFull(trainset, d);
+ carp(CARP_INFO, "finished training, making parsimonious protein set");
+ trainset.make_meta_set(d);
+ int fdr_trn = getOverFDRProtParsimonious(trainset,max_net_prot,selectionfdr);
+ carp(CARP_INFO, "total proteins parsimonious at q<%.2f: %d", selectionfdr, fdr_trn);
+
+ int fdr_trn_psm = getOverFDRPSM(psmtrainset, max_net_psm, selectionfdr);
+ carp(CARP_INFO, "peptides at q<%.2f: %d", selectionfdr, getOverFDRPep(peptrainset, max_net_pep, selectionfdr));
+ carp(CARP_INFO, "psms at q<%.2f: %d", selectionfdr, fdr_trn_psm);
+
+ write_results_prot(out_dir, fdr_trn);
+}
+
+void Barista :: get_pep_seq(string &pep, string &seq, string &n, string &c)
+{
+ string tmp;
+ int pos;
+ pos = pep.find('.');
+ n = pep.at(pos-1);
+ tmp = pep.substr(pos+1, pep.size());
+
+ pos = tmp.rfind('.');
+ c = tmp.at(pos+1);
+ seq = tmp.substr(0, pos);
+}
+
+void Barista :: get_tab_delim_proteins(string protein_str, vector<string> &proteins)
+{
+ proteins.clear();
+ string str = protein_str;
+ size_t pos = str.find("\t");
+ while(pos != string::npos){
+ if(pos == 0){
+ str = str.substr(1,str.size()-1);
+ } else{
+ string prot = str.substr(0,pos);
+ str = str.substr(pos+1,str.size()-1);
+ proteins.push_back(prot);
+ }
+ pos = str.find("\t");
+ }
+ proteins.push_back(str);
+}
+
+
+void Barista :: write_protein_special_case_xml(ofstream &os, int i)
+{
+
+ string protein_str;
+ vector<string> tab_delim_proteins;
+
+ int protind = trainset[i].protind;
+ int group = trainset[i].group_number;
+ os << " <protein_group group_id=" << "\"" << group << "\"" << ">" << endl;
+ os << " <q_value>" << trainset[i].q << "</q_value>" << endl;
+ os << " <score>" << trainset[i].score << "</score>" << endl;
+ os << " <protein_ids>" << endl;
+ protein_str = d.ind2prot(protind);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+
+ vector<int> complement = trainset[i].protind2complement[protind];
+ if(complement.size() != 0)
+ {
+ for(unsigned int k = 0; k < complement.size(); k++)
+ {
+ int pepind = complement[k];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <alternative_peptide_id>" << seq << "</alternative_peptide_id>"<< endl;
+ }
+ }
+
+ for(unsigned int j = 0; j < trainset[i].indistinguishable_protinds.size(); j++)
+ {
+ int ind = trainset[i].indistinguishable_protinds[j];
+ if(d.protind2label(ind) == 1)
+ {
+ //os << " <protein_id>" << d.ind2prot(ind) << "</protein_id> " << endl;;
+ protein_str = d.ind2prot(ind);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+
+ vector<int> complement = trainset[i].protind2complement[ind];
+ if(complement.size() != 0)
+ {
+ for(unsigned int k = 0; k < complement.size(); k++)
+ {
+ int pepind = complement[k];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <alternative_peptide_id>" << seq << "</alternative_peptide_id>"<< endl;
+ }
+ }
+ }
+ }
+ os << " </protein_ids>" << endl;
+
+ //write out peptides
+ os << " <peptide_ids>" << endl;
+ vector<int> intersection = trainset[i].intersection;
+ for( unsigned int j = 0; j < intersection.size(); j++)
+ {
+ int pepind = intersection[j];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <peptide_id>" << seq << "</peptide_id>"<< endl;
+ }
+ os << " </peptide_ids>" << endl;
+ os << " </protein_group>" << endl;
+}
+
+
+void Barista :: write_results_prot_xml(ofstream &os)
+{
+ string protein_str;
+ vector<string> tab_delim_proteins;
+ os << "<proteins>" <<endl;
+ int cn = 0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ int protind = trainset[i].protind;
+ int group = trainset[i].group_number;
+ if(d.protind2label(protind) == 1)
+ {
+ cn++;
+ if(trainset[i].has_complement == 1)
+ {
+ write_protein_special_case_xml(os, i);
+ continue;
+ }
+ //write out proteins
+ os << " <protein_group group_id=" << "\"" << group << "\"" << ">" << endl;
+ os << " <q_value>" << trainset[i].q << "</q_value>" << endl;
+ os << " <score>" << trainset[i].score << "</score>" << endl;
+ os << " <nsaf>" << trainset[i].nsaf << "</nsaf>" << endl;
+ os<<"<barista PEP>"<<trainset[i].PEP<<"</barista PEP>"<<endl;
+ os << " <protein_ids>" << endl;
+ protein_str = d.ind2prot(protind);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+
+ for(unsigned int j = 0; j < trainset[i].indistinguishable_protinds.size(); j++)
+ {
+ int ind = trainset[i].indistinguishable_protinds[j];
+ if(d.protind2label(ind) == 1)
+ {
+ protein_str = d.ind2prot(ind);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+ }
+ }
+ os << " </protein_ids>" << endl;
+
+ //write out peptides
+
+ os << " <peptide_ids>" << endl;
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ for( int j = 0; j < num_pep; j++)
+ {
+ int pepind = pepinds[j];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <peptide_id>" << seq << "</peptide_id>"<< endl;
+ }
+ os << " </peptide_ids>" << endl;
+ os << " </protein_group>" << endl;
+ }
+
+ }
+ os << "</proteins>" << endl;
+}
+
+void Barista :: write_subset_protein_special_case_xml(ofstream &os, int i)
+{
+ string protein_str;
+ vector<string> tab_delim_proteins;
+
+ //write out proteins
+ int protind = trainset.get_subset_prot(i).protind;
+ int group = trainset.get_subset_prot(i).group_number;
+ os << " <protein_group group_id=" << "\"" << group << "\"";
+ vector<int> parent_groups = trainset.get_subset_prot(i).parent_groups;
+ if(parent_groups.size() == 0)
+ cout << "problem: no parent groups" << endl;
+ os << " parent_group_ids=" << "\"";
+ for(unsigned int k = 0; k < parent_groups.size()-1; k++)
+ os << parent_groups[k] << ",";
+ os << parent_groups[parent_groups.size()-1] << "\"";
+ os << ">" << endl;
+
+ os << " <protein_ids>" << endl;
+ protein_str = d.ind2prot(protind);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+
+ vector<int> complement = trainset.get_subset_prot(i).protind2complement[protind];
+ if(complement.size() != 0)
+ {
+ for(unsigned int k = 0; k < complement.size(); k++)
+ {
+ int pepind = complement[k];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <alternative_peptide_id>" << seq << "</alternative_peptide_id>"<< endl;
+ }
+ }
+
+ for(unsigned int j = 0; j < trainset.get_subset_prot(i).indistinguishable_protinds.size(); j++)
+ {
+ int ind = trainset.get_subset_prot(i).indistinguishable_protinds[j];
+ if(d.protind2label(ind) == 1)
+ {
+ protein_str = d.ind2prot(ind);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+
+ vector<int> complement = trainset.get_subset_prot(i).protind2complement[ind];
+ if(complement.size() != 0)
+ {
+ for(unsigned int k = 0; k < complement.size(); k++)
+ {
+ int pepind = complement[k];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <alternative_peptide_id>" << seq << "</alternative_peptide_id>"<< endl;
+ }
+ }
+
+ }
+ }
+ os << " </protein_ids>" << endl;
+
+ //write out peptides
+ os << " <peptide_ids>" << endl;
+ vector<int> intersection = trainset.get_subset_prot(i).intersection;
+ for( unsigned int j = 0; j < intersection.size(); j++)
+ {
+ int pepind = intersection[j];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <peptide_id>" << seq << "</peptide_id>"<< endl;
+ }
+ os << " </peptide_ids>" << endl;
+ os << " </protein_group>" << endl;
+
+}
+
+
+
+void Barista :: write_results_subset_prot_xml(ofstream &os)
+{
+ string protein_str;
+ vector<string> tab_delim_proteins;
+ os << "<subset_proteins>" <<endl;
+
+ int num_subset_prot = trainset.get_num_subsets();
+
+ int cn = 0;
+ for(int i = 0; i < num_subset_prot; i++)
+ {
+ int protind = trainset.get_subset_prot(i).protind;
+ int group = trainset.get_subset_prot(i).group_number;
+ if(d.protind2label(protind) == 1)
+ {
+ cn++;
+
+ if(trainset.get_subset_prot(i).has_complement == 1)
+ {
+ write_subset_protein_special_case_xml(os, i);
+ continue;
+ }
+
+ //write out proteins
+ os << " <protein_group group_id=" << "\"" << group << "\"";
+ vector<int> parent_groups = trainset.get_subset_prot(i).parent_groups;
+ if(parent_groups.size() == 0)
+ cout << "problem: no parent groups" << endl;
+ os << " parent_group_ids=" << "\"";
+ for(unsigned int k = 0; k < parent_groups.size()-1; k++)
+ os << parent_groups[k] << ",";
+ os << parent_groups[parent_groups.size()-1] << "\"";
+ os << ">" << endl;
+ os << " <protein_ids>" << endl;
+ protein_str = d.ind2prot(protind);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+
+ for(unsigned int j = 0; j < trainset.get_subset_prot(i).indistinguishable_protinds.size(); j++)
+ {
+ int ind = trainset.get_subset_prot(i).indistinguishable_protinds[j];
+ if(d.protind2label(ind) == 1)
+ {
+ protein_str = d.ind2prot(ind);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+ }
+ }
+ os << " </protein_ids>" << endl;
+
+ //write out peptides
+ os << " <peptide_ids>" << endl;
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ for( int j = 0; j < num_pep; j++)
+ {
+ int pepind = pepinds[j];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <peptide_id>" << seq << "</peptide_id>"<< endl;
+ }
+ os << " </peptide_ids>" << endl;
+ os << " </protein_group>" << endl;
+ }
+ }
+ os << "</subset_proteins>" << endl;
+}
+
+
+void Barista :: write_results_peptides_xml(ofstream &os)
+{
+ string protein_str;
+ vector<string> tab_delim_proteins;
+ os << "<peptides>" <<endl;
+ int cn = 0;
+ for(int i = 0; i < peptrainset.size(); i++)
+ {
+ int pepind = peptrainset[i].pepind;
+ if(peptrainset[i].label == 1)
+ {
+ cn++;
+ //write out proteins
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <peptide peptide_id=\"" << seq << "\">" << endl;
+ os << " <q_value>" << peptrainset[i].q << "</q_value>" << endl;
+ os << " <score>" << peptrainset[i].score << "</score>" << endl;
+ os << " <nsaf>" << peptrainset[i].nsaf << "</nsaf>" << endl;
+ os << " <barista PEP>" <<peptrainset[i].PEP<<"</barista PEP>"<<endl;
+ //write out peptides
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << " <main_psm_id>"<< psmind << "</main_psm_id>" << endl;
+ else
+ carp(CARP_DEBUG,"warning: did not assign peptide %s and index %d a max"
+ "psm index", pep.c_str(), psmind);
+ //print out all the psms in which this peptide is present
+ int num_psm = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ os << " <psm_ids>" << endl;
+ for(int j = 0; j < num_psm; j++)
+ os << " <psm_id>" << psminds[j] << "</psm_id>" << endl;
+ os << " </psm_ids>" << endl;
+
+ //print out all the proteins
+ int num_prot = d.pepind2num_prot(pepind);
+ int *protinds = d.pepind2protinds(pepind);
+ os << " <protein_ids>" << endl;
+ for(int j = 0; j < num_prot; j++)
+ {
+ protein_str = d.ind2prot(protinds[j]);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>"
+ <<endl;
+ }
+ os << " </protein_ids>" << endl;
+ os << " </peptide>" << endl;
+ }
+
+ }
+ os << "</peptides>" << endl;
+}
+
+void Barista :: write_results_psm_xml(ofstream &os)
+{
+ os << "<psms>" <<endl;
+ int cn = 0;
+ for(int i = 0; i < psmtrainset.size(); i++)
+ {
+ int psmind = psmtrainset[i].psmind;
+ if(psmtrainset[i].label == 1)
+ {
+ cn++;
+ //write out proteins
+ os << " <psm psm_id=" << "\"" << psmind << "\"" << ">" << endl;
+ os << " <q_value>" << psmtrainset[i].q << "</q_value>" << endl;
+ os << " <score>" << psmtrainset[i].score << "</score>" << endl;
+ os << " <scan>" << d.psmind2scan(psmind) << "</scan>" << endl;
+ os << " <charge>" << d.psmind2charge(psmind) << "</charge>" << endl;
+ os << " <precursor_mass>" << d.psmind2precursor_mass(psmind) << "</precursor_mass>" << endl;
+ int pepind = d.psmind2pepind(psmind);
+ string pep = d.ind2pep(pepind);
+ string seq, n,c;
+ get_pep_seq(pep,seq,n,c);
+ os << " <peptide_seq n =\"" << n << "\" c=\"" << c << "\" seq=\"" << seq << "\"/>" << endl;
+ os << " <file_name>" << d.psmind2fname(psmind) << "</file_name>" << endl;
+ os << " </psm>" << endl;
+ }
+ }
+ os << "</psms>" << endl;
+}
+
+
+void Barista :: write_results_pep_xml(PepXMLWriter& xmlfile)
+{
+ xmlfile.writeHeader();
+
+ bool* scores_to_print = new bool[NUMBER_SCORER_TYPES];
+ for(int score_idx = 0; score_idx < NUMBER_SCORER_TYPES; score_idx++){
+ scores_to_print[score_idx] = false;
+ }
+ scores_to_print[SP] = true;
+ scores_to_print[XCORR] = true;
+ scores_to_print[BARISTA_SCORE] = true;
+ scores_to_print[BARISTA_QVALUE] = true;
+ scores_to_print[BARISTA_PEP] = true;
+ scores_to_print[DELTA_CN] = true;
+ scores_to_print[BY_IONS_MATCHED] = true;
+ scores_to_print[BY_IONS_TOTAL] = true;
+
+ double* scores = new double[NUMBER_SCORER_TYPES];
+
+ for(int i = 0; i < psmtrainset.size(); i++) {
+ // only print target psms
+ if( psmtrainset[i].label == -1 ){
+ continue;
+ }
+
+ int psmind = psmtrainset[i].psmind;
+
+ // spectrum info
+ int scan = d.psmind2scan(psmind);
+ const char* filename = d.psmind2fname(psmind).c_str();
+ char** path_name = parse_filename_path_extension(filename, NULL);
+ filename = path_name[0];
+ double spectrum_mass = d.psmind2precursor_mass(psmind);
+ int charge = d.psmind2charge(psmind);
+
+ // peptide info
+ int pepind = d.psmind2pepind(psmind);
+ string pep = d.ind2pep(pepind);
+ string modified_sequence, n,c;
+ get_pep_seq(pep, modified_sequence, n, c);
+ char* sequence = unmodify_sequence(modified_sequence.c_str());
+ string flanking_aas = n + c;
+ double peptide_mass = d.psmind2peptide_mass(psmind);
+
+ // protein info
+ int num_proteins = d.pepind2num_prot(pepind);
+ int* protein_indexes = d.pepind2protinds(pepind);
+ vector<string> protein_names;
+ vector<string> protein_descriptions;
+ for(int prot_idx = 0; prot_idx < num_proteins; prot_idx++){
+ string protein_name = d.ind2prot(protein_indexes[prot_idx]);
+ protein_names.push_back(protein_name);
+ protein_descriptions.push_back("");
+ flanking_aas += "," + n + c; // todo
+ }
+
+ // psm info
+ int* psm_ranks = new int[NUMBER_SCORER_TYPES];
+ double delta_cn = d.psmind2deltaCn(psmind);
+
+ scores[XCORR] = d.psmind2xcorr(psmind);
+ scores[SP] = d.psmind2spscore(psmind);
+ scores[QRANKER_SCORE] = psmtrainset[i].score;
+ scores[QRANKER_QVALUE] = psmtrainset[i].q;
+ scores[QRANKER_PEP] = psmtrainset[i].PEP;
+ scores[DELTA_CN] = delta_cn;
+ scores[BY_IONS_MATCHED] = d.psmind2by_ions_matched(psmind);
+ scores[BY_IONS_TOTAL] = d.psmind2by_ions_total(psmind);
+ psm_ranks[SP]=d.psmind2sp_rank(psmind);
+ psm_ranks[XCORR]=d.psmind2xcorr_rank(psmind);
+ xmlfile.writePSM(scan, filename, spectrum_mass, charge, psm_ranks,
+ sequence, modified_sequence.c_str(),
+ peptide_mass, num_proteins,
+ flanking_aas.c_str(), protein_names,
+ protein_descriptions, scores_to_print, scores,
+ d.psmind2matches_spectrum(psmind));
+
+ free(sequence);
+ if( path_name[0] ){
+ free(path_name[0]);
+ }
+ if( path_name[1] ){
+ free(path_name[1]);
+ }
+ free(path_name);
+ }
+
+ xmlfile.writeFooter();
+}
+
+
+
+/*************************************************************************/
+
+void Barista :: write_results_prot_special_case_tab(ofstream &os, int i)
+{
+ //write out protein
+ int protind = trainset[i].protind;
+ int group = trainset[i].group_number;
+ os << group << "\t";
+ os << trainset[i].q << "\t";
+ os << trainset[i].score << "\t";
+ os << d.ind2prot(protind);
+ vector<int> complement = trainset[i].protind2complement[protind];
+ if(complement.size() != 0)
+ {
+ os << "(";
+ int pepind = complement[0];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << pep;
+ for(unsigned int k = 1; k < complement.size(); k++)
+ {
+ pepind = complement[k];
+ pep = d.ind2pep(pepind);
+ get_pep_seq(pep, seq, n, c);
+ os << "," << pep;
+ }
+ os << ")";
+ }
+
+ for(unsigned int j = 0; j < trainset[i].indistinguishable_protinds.size(); j++)
+ {
+ int ind = trainset[i].indistinguishable_protinds[j];
+ if(d.protind2label(ind) == 1)
+ {
+ os << "," << d.ind2prot(ind);
+ vector<int> complement = trainset[i].protind2complement[protind];
+ if(complement.size() != 0)
+ {
+ os << "(";
+ int pepind = complement[0];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << "," << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ for(unsigned int k = 1; k < complement.size(); k++)
+ {
+ pepind = complement[k];
+ pep = d.ind2pep(pepind);
+ get_pep_seq(pep, seq, n, c);
+ psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << "," << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ }
+ os << ")";
+ }
+ }
+ }
+ os << "\t";
+
+ //write out peptides
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ //write the first one
+ int pepind = pepinds[0];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ {
+ carp(CARP_DEBUG,"warning: did not assign peptide max psm index");
+ }
+ for( int j = 1; j < num_pep; j++)
+ {
+ pepind = pepinds[j];
+ pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << "," << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ {
+ carp(CARP_DEBUG,"warning: did not assign peptide %s and index %d a max"
+ "psm index", pep.c_str(), psmind);
+ }
+ }
+ os << endl;
+
+
+}
+
+void Barista :: write_results_prot_tab(ofstream &os)
+{
+ os << "group number" << "\t" << "q-value" << "\t" << "barista score" << "\t" << "NSAF score" << "\t";
+ os<<"barista PEP\t";
+ os << "proteins" << "\t" << "peptides-scan.charge"<<endl;
+
+ int cn = 0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ if(trainset[i].label == 1)
+ {
+ cn++;
+ if(trainset[i].has_complement == 1)
+ {
+ write_results_prot_special_case_tab(os, i);
+ continue;
+ }
+ //write out proteins
+ int protind = trainset[i].protind;
+ int group = trainset[i].group_number;
+ os << group << "\t";
+ os << trainset[i].q << "\t";
+ os << trainset[i].score << "\t";
+ os << trainset[i].nsaf << "\t";
+ os<<trainset[i].PEP<<"\t";
+ os << d.ind2prot(protind);
+ for(unsigned int j = 0; j < trainset[i].indistinguishable_protinds.size(); j++)
+ {
+ int ind = trainset[i].indistinguishable_protinds[j];
+ if(d.protind2label(ind) == 1)
+ {
+ os << "," << d.ind2prot(ind);
+ }
+ }
+ os << "\t";
+
+ //write out peptides
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ //write the first one
+ int pepind = pepinds[0];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ {
+ carp(CARP_DEBUG,"warning: did not assign peptide a max psm index");
+ }
+ for( int j = 1; j < num_pep; j++)
+ {
+ pepind = pepinds[j];
+ pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << "," << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ {
+ carp(CARP_DEBUG, "warning: did not assign peptide %s and index %d a"
+ "max psm index", pep.c_str(), psmind);
+ }
+ }
+ os << endl;
+ }
+ }
+}
+
+
+void Barista :: write_subset_protein_special_case_tab(ofstream &os, int i)
+{
+ //write out protein
+ int protind = trainset[i].protind;
+ int group = trainset[i].group_number;
+ os << group << "\t";
+
+ vector<int> parent_groups = trainset.get_subset_prot(i).parent_groups;
+ if(parent_groups.size() > 0)
+ {
+ os << parent_groups[0];
+ for(unsigned int k = 1; k < parent_groups.size(); k++)
+ os << "," << parent_groups[k];
+ }
+ os << "\t";
+
+ os << d.ind2prot(protind);
+ vector<int> complement = trainset[i].protind2complement[protind];
+ if(complement.size() != 0)
+ {
+ os << "(";
+ int pepind = complement[0];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << pep;
+ for(unsigned int k = 1; k < complement.size(); k++)
+ {
+ pepind = complement[k];
+ pep = d.ind2pep(pepind);
+ get_pep_seq(pep, seq, n, c);
+ os << "," << pep;
+ }
+ os << ")";
+ }
+
+ for(unsigned int j = 0; j < trainset[i].indistinguishable_protinds.size(); j++)
+ {
+ int ind = trainset[i].indistinguishable_protinds[j];
+ if(d.protind2label(ind) == 1)
+ {
+ os << "," << d.ind2prot(ind);
+ vector<int> complement = trainset[i].protind2complement[protind];
+ if(complement.size() != 0)
+ {
+ os << "(";
+ int pepind = complement[0];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << "," << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ for(unsigned int k = 1; k < complement.size(); k++)
+ {
+ pepind = complement[k];
+ pep = d.ind2pep(pepind);
+ get_pep_seq(pep, seq, n, c);
+ psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << "," << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ }
+ os << ")";
+ }
+ }
+ }
+ os << "\t";
+
+ //write out peptides
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ //write the first one
+ int pepind = pepinds[0];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ {
+ carp(CARP_DEBUG, "warning: did not assign peptide a max psm index");
+ }
+ for( int j = 1; j < num_pep; j++)
+ {
+ pepind = pepinds[j];
+ pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << "," << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ {
+ carp(CARP_DEBUG,"warning: did not assign peptide %s and index %d a max"
+ "psm index", pep.c_str(), psmind);
+ }
+ }
+ os << endl;
+
+
+}
+
+
+void Barista :: write_results_subset_prot_tab(ofstream &os)
+{
+ string protein_str;
+ vector<string> tab_delim_proteins;
+
+ os << "group number" << "\t" << "parent group numbers" << "\t";
+ os << "proteins" << "\t" << "peptides-scan.charge" << endl;
+
+ int num_subset_prot = trainset.get_num_subsets();
+
+ int cn = 0;
+ for(int i = 0; i < num_subset_prot; i++)
+ {
+ int protind = trainset.get_subset_prot(i).protind;
+ int group = trainset.get_subset_prot(i).group_number;
+ if(d.protind2label(protind) == 1)
+ {
+ cn++;
+
+ if(trainset.get_subset_prot(i).has_complement == 1)
+ {
+ write_subset_protein_special_case_tab(os, i);
+ continue;
+ }
+
+ os << group << "\t";
+ vector<int> parent_groups = trainset.get_subset_prot(i).parent_groups;
+ if(parent_groups.size() > 0)
+ {
+ os << parent_groups[0];
+ for(unsigned int k = 1; k < parent_groups.size(); k++)
+ os << "," << parent_groups[k];
+ }
+ os << "\t";
+
+ //write out proteins
+ os << d.ind2prot(protind);
+ for(unsigned int j = 0; j < trainset[i].indistinguishable_protinds.size(); j++)
+ {
+ int ind = trainset[i].indistinguishable_protinds[j];
+ if(d.protind2label(ind) == 1)
+ {
+ os << "," << d.ind2prot(ind);
+ }
+ }
+ os << "\t";
+
+ //write out peptides
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ //write the first one
+ int pepind = pepinds[0];
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ {
+ carp(CARP_DEBUG, "warning: did not assign peptide a max psm index");
+ }
+ for( int j = 1; j < num_pep; j++)
+ {
+ pepind = pepinds[j];
+ pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << "," << pep << "-" << d.psmind2scan(psmind) << "." << d.psmind2charge(psmind);
+ else
+ {
+ carp(CARP_DEBUG, "warning: did not assign peptide %s and index %d a"
+ " max psm index", pep.c_str(), psmind);
+ }
+ }
+
+ os << endl;
+ }
+ }
+
+}
+
+
+
+void Barista :: write_results_peptides_tab(ofstream &os)
+{
+ int ps = pepind_to_max_psmind[peptrainset[0].pepind];
+ os<< "q-value" << "\t" << "barista score" << "\t";
+ os << "NSAF score" << "\t";
+ os<<"barista PEP\t";
+ os << "scan" << "\t" ;
+ os<< "charge" << "\t";
+ os<<"spectrum precursor m/z"<<"\t";
+ os<<"spectrum neutral mass"<<"\t";
+ os<<"peptide mass"<<"\t";
+ os<< "delta_cn"<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"sp score"<<"\t";
+ os<<"sp rank\t";
+ }
+ os<<"xcorr score"<<"\t";
+ os<<"xcorr rank"<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"b/y ions matched"<<"\t";
+ os<<"b/y ions total"<<"\t";
+ }
+ os<<"distinct matches/spectrum"<<"\t";
+ os<<"sequence\t";
+ os<<"cleavage type"<<"\t";
+ os<<"protein id"<<"\t";
+ os<<"flanking_aa"<<endl;
+ int cn = 0;
+ for(int i = 0; i < peptrainset.size(); i++){
+ if(peptrainset[i].label == 1){
+ cn++;
+ //write out proteins
+ int pepind = peptrainset[i].pepind;
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ //q-value
+ os << peptrainset[i].q << "\t";
+ //score
+ os << peptrainset[i].score << "\t";
+ ///nsaf
+ os<<peptrainset[i].nsaf<<"\t";
+ //PEP
+ os<<peptrainset[i].PEP<<"\t";
+
+ //write out peptides
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1){
+ //scan
+ os << d.psmind2scan(psmind) << "\t" ;
+ //charge
+ os<< d.psmind2charge(psmind)<<"\t";
+ //mass-to-charge ratio
+ os<<(d.psmind2precursor_mass(psmind)+
+ d.psmind2charge(psmind)*MASS_PROTON)/
+ d.psmind2charge(psmind)<<"\t";
+ //Spectrum Neutral Mass
+ os<<d.psmind2precursor_mass(psmind)<<"\t";
+ //Peptide Mass
+ os<<d.psmind2peptide_mass(psmind)<<"\t";
+ //DELTA CN
+ os <<d.psmind2deltaCn(psmind)<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //Sp Score
+ os<<d.psmind2spscore(psmind)<<"\t";
+ //Sp Rank
+ os<<d.psmind2sp_rank(psmind)<<"\t";
+ }
+ //xcorr Score
+ os<<d.psmind2xcorr(psmind)<<"\t";
+ //xcorr rank
+ os<<d.psmind2xcorr_rank(psmind)<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //by ions match
+ os<<d.psmind2by_ions_matched(psmind)<<"\t";
+ //by ions total
+ os<<d.psmind2by_ions_total(psmind)<<"\t";
+ }
+ //Distinct matches/Spectrum
+ os<<d.psmind2matches_spectrum(psmind)<<"\t";
+ //sequence
+ os<<seq<<"\t";
+ //cleavage type
+ os<<cleavage_type<<"\t";
+ //protein id
+ vector<string> prots;
+ get_protein_id(pepind,prots);
+ print_protein_ids(prots,os,psmind);
+ //Flanking_aa
+ os<<n<<c<<endl;
+ }else{
+ cout<< "waning: did not assign peptide max psmind\n";
+ os<<"not assignd\t";
+ }
+
+ }
+ }
+}
+
+void Barista :: write_results_psm_tab(ofstream &os)
+{
+ int ps= psmtrainset[0].psmind;
+ os << "scan" << "\t" << "charge" << "\t";
+ os << "barista q-value" << "\t" << "barista score" << "\t";
+ os << "barista PEP\t";
+ os<<"spectrum precursor m/z"<<"\t";
+ os<<"spectrum neutral mass"<<"\t";
+ os<<"peptide mass"<<"\t";
+ os<< "delta_cn"<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"sp score"<<"\t";
+ os<<"sp rank\t";
+ }
+ os<<"xcorr score"<<"\t";
+ os<<"xcorr rank"<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"b/y ions matched"<<"\t";
+ os<<"b/y ions total"<<"\t";
+ }
+ os<<"distinct matches/spectrum"<<"\t";
+ os<<"sequence"<<"\t";
+ os<<"cleavage type"<<"\t";
+ os<<"protein id"<<"\t";
+ os<<"flanking aa"<<"\t";
+ os << "filename" << endl;
+ int cn = 0;
+ for(int i = 0; i < psmtrainset.size(); i++)
+ {
+ if(psmtrainset[i].label == 1)
+ {
+ cn++;
+ //write out proteins
+ int psmind = psmtrainset[i].psmind;
+ int pepind = d.psmind2pepind(psmind);
+ string pep = d.ind2pep(pepind);
+ string seq, n,c;
+ get_pep_seq(pep,seq,n,c);
+ //os << psmind << "\t";
+ os << d.psmind2scan(psmind) << "\t";
+ os << d.psmind2charge(psmind) << "\t";
+ os << psmtrainset[i].q << "\t";
+ os << psmtrainset[i].score << "\t";
+ os << psmtrainset[i].PEP << "\t";
+ //mass-to-charge ratio
+ os<<(d.psmind2precursor_mass(psmind)+
+ d.psmind2charge(psmind)*MASS_PROTON)/
+ d.psmind2charge(psmind)<<"\t";
+ //Spectrum Neutral Mass
+ os<<d.psmind2precursor_mass(psmind)<<"\t";
+ //Peptide Mass
+ os<<d.psmind2peptide_mass(psmind)<<"\t";
+ //DELTA CN
+ os <<d.psmind2deltaCn(psmind)<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //Sp Score
+ os<<d.psmind2spscore(psmind)<<"\t";
+ //Sp Rank
+ os<<d.psmind2sp_rank(psmind)<<"\t";
+ }
+ //xcorr Score
+ os<<d.psmind2xcorr(psmind)<<"\t";
+ //xcorr rank
+ os<<d.psmind2xcorr_rank(psmind)<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //by ions match
+ os<<d.psmind2by_ions_matched(psmind)<<"\t";
+ //by ions total
+ os<<d.psmind2by_ions_total(psmind)<<"\t";
+ }
+ //Distinct matches/Spectrum
+ os<<d.psmind2matches_spectrum(psmind)<<"\t";
+ get_pep_seq(pep,seq,n,c);
+ //Sequence
+ os<<seq<<"\t";
+ //cleavage type
+ os<<cleavage_type<<"\t";
+ //protein id
+ vector<string> prots;
+ get_protein_id(pepind,prots);
+ print_protein_ids(prots,os,psmind);
+ //Flanking_aa
+ os<<n<<c<<"\t";
+ os << d.psmind2fname(psmind) << endl;
+ }
+ }
+}
+
+
+
+void Barista :: report_all_results_xml()
+{
+ ostringstream fname;
+ fname << out_dir << "/" << fileroot << "barista.xml";
+ ofstream of(fname.str().c_str());
+ of << "<barista_output>" << endl;
+ of << endl;
+
+ write_results_prot_xml(of);
+ write_results_subset_prot_xml(of);
+
+ write_results_peptides_xml(of);
+
+ write_results_psm_xml(of);
+
+ if (Params::GetBool("pepxml-output")) {
+ ostringstream xml_file_name;
+ xml_file_name << out_dir << "/" << fileroot << "barista.target.pep.xml";
+ PepXMLWriter xmlfile;
+ xmlfile.openFile(xml_file_name.str().c_str(), overwrite_flag);
+ write_results_pep_xml(xmlfile);
+
+ xmlfile.closeFile();
+ }
+
+
+ of << endl;
+ of << "</barista_output>" << endl;
+ of.close();
+
+}
+
+
+void Barista :: report_all_results_tab()
+{
+ ofstream of;
+ ostringstream fname;
+
+ fname << out_dir << "/" << fileroot << "barista.target.proteins.txt";
+ of.open(fname.str().c_str());
+ write_results_prot_tab(of);
+ of.close();
+ fname.str("");
+
+ fname << out_dir << "/" << fileroot << "barista.target.subset-proteins.txt";
+ of.open(fname.str().c_str());
+ write_results_subset_prot_tab(of);
+ of.close();
+ fname.str("");
+
+ fname << out_dir << "/" << fileroot << "barista.target.peptides.txt";
+ of.open(fname.str().c_str());
+ write_results_peptides_tab(of);
+ of.close();
+ fname.str("");
+
+ fname << out_dir << "/" << fileroot << "barista.target.psms.txt";
+ of.open(fname.str().c_str());
+ write_results_psm_tab(of);
+ of.close();
+ fname.str("");
+
+}
+
+
+void Barista :: report_all_results_xml_tab()
+{
+ setup_for_reporting_results();
+ stringstream fname;
+ report_all_results_xml();
+ if (Params::GetBool("txt-output")) {
+ report_all_results_tab();
+ }
+ d.clear_data_all_results();
+
+}
+
+void Barista :: setup_for_reporting_results()
+{
+ d.load_labels_prot_training();
+ trainset.clear();
+ testset.clear();
+
+ ProtScores::fillProteinsFull(trainset, d);
+
+ carp(CARP_INFO, "finished training, making parsimonious protein set");
+
+ trainset.make_meta_set(d);
+
+ psmtrainset.clear();
+ psmtestset.clear();
+ PSMScores::fillFeaturesFull(psmtrainset, d);
+ peptrainset.clear();
+ peptestset.clear();
+ PepScores::fillFeaturesFull(peptrainset, d);
+ d.clear_labels_prot_training();
+
+ int fdr_trn = getOverFDRProt(trainset,max_net_prot,selectionfdr);
+ fdr_trn = getOverFDRProtParsimonious(trainset,max_net_prot,selectionfdr);
+
+ carp(CARP_INFO, "total proteins parsimonious at q<%.2f: %d", selectionfdr, fdr_trn);
+
+ int fdr_trn_psm = getOverFDRPSM(psmtrainset, max_net_psm, selectionfdr);
+
+ pepind_to_max_psmind.clear();
+ pepind_to_max_psmind.resize(d.get_num_peptides(),-1);
+ int fdr_trn_pep = getOverFDRPep(peptrainset, max_net_pep, selectionfdr);
+
+ carp(CARP_INFO, "peptides at q<%.2f: %d", selectionfdr, fdr_trn_pep);
+ carp(CARP_INFO, "psms at q<%.2f: %d", selectionfdr, fdr_trn_psm);
+
+ d.clear_labels_psm_training();
+
+ d.clear_data_prot_training();
+ d.load_data_all_results();
+
+ computeNSAF();
+ computePepNSAF();
+ computePEP();
+
+}
+
+int Barista :: computeNSAF()
+{
+ //check that the lengths of the proteins are available
+ int cnt = 0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ if(trainset[i].label == 1)
+ {
+ int protind = trainset[i].protind;
+ int len = d.protind2length(protind);
+ if(len < 0)
+ cnt++;
+ }
+ }
+ if(cnt > 0)
+ return 0;
+
+ //create auxiliary psmind_to_ind index
+ vector<int>psmind_to_ind;
+ psmind_to_ind.resize(psmtrainset.size(),0);
+ for(int i = 0; i < psmtrainset.size(); i++)
+ psmind_to_ind[psmtrainset[i].psmind] = i;
+
+ //compute NSAF for each protein
+ double sum = 0.0;
+ for(int k = 0; k < trainset.size(); k++)
+ {
+ if(trainset[k].label == 1)
+ {
+ int protind = trainset[k].protind;
+ int len = d.protind2length(protind);
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ int cnt = 0;
+ for (int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ for (int j = 0; j < num_psms; j++)
+ {
+ int psmind = psminds[j];
+ int ind = psmind_to_ind[psmind];
+ assert(psmtrainset[ind].psmind == psmind);
+ if(psmtrainset[ind].q <= 0.01)
+ cnt++;
+ }
+ }
+ //compute NSAF for this protein
+ double nsaf = 0.0;
+ if(len != 0)
+ nsaf = (double)cnt/(double)len;
+ trainset[k].nsaf = nsaf;
+ sum += nsaf;
+ }
+ }
+
+ if(sum > 0)
+ {
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ if(trainset[i]. label == 1)
+ trainset[i].nsaf /= sum;
+ }
+ }
+ else
+ return 0;
+
+ psmind_to_ind.clear();
+ return 1;
+}
+
+int Barista :: computePepNSAF()
+{
+
+ //create auxiliary psmind_to_ind index
+ vector<int>psmind_to_ind;
+ psmind_to_ind.resize(psmtrainset.size(),0);
+ for(int i = 0; i < psmtrainset.size(); i++)
+ psmind_to_ind[psmtrainset[i].psmind] = i;
+
+ //compute NSAF for each peptide
+ double sum = 0.0;
+ for(int k = 0; k < peptrainset.size(); k++)
+ {
+ if(peptrainset[k].label == 1)
+ {
+ int pepind = peptrainset[k].pepind;
+ string pep = d.ind2pep(pepind);
+ string seq, n,c;
+ get_pep_seq(pep,seq,n,c);
+ int len = seq.size();
+
+ int cnt = 0;
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ for (int j = 0; j < num_psms; j++)
+ {
+ int psmind = psminds[j];
+ int ind = psmind_to_ind[psmind];
+ assert(psmtrainset[ind].psmind == psmind);
+ if(psmtrainset[ind].q <= 0.01)
+ cnt++;
+ }
+
+ //compute NSAF for this protein
+ double nsaf = 0.0;
+ if(len != 0)
+ nsaf = (double)cnt/(double)len;
+ peptrainset[k].nsaf = nsaf;
+ sum += nsaf;
+ }
+ }
+
+ if(sum > 0)
+ {
+ for(int i = 0; i < peptrainset.size(); i++)
+ {
+ if(peptrainset[i]. label == 1)
+ peptrainset[i].nsaf /= sum;
+ }
+ }
+ else
+ return 0;
+
+ psmind_to_ind.clear();
+ return 1;
+}
+
+
+void Barista :: computePEP(){
+ carp(CARP_DEBUG, "Computing PEPs");
+ vector<double> target_scores_vect;
+ vector<double> decoy_scores_vect;
+
+ // pull out the target and decoy scores
+ for(int i = 0; i < psmtrainset.size(); i++){
+ if( psmtrainset[i].label == 1 ){
+ target_scores_vect.push_back(psmtrainset[i].score);
+ } else { // == -1
+ decoy_scores_vect.push_back(psmtrainset[i].score);
+ }
+ }
+
+ int num_targets = target_scores_vect.size();
+ int num_decoys = decoy_scores_vect.size();
+ carp(CARP_DEBUG, "Found %d targets and %d decoys", num_targets, num_decoys);
+
+ // copy them to an array as required by the compute_PEP method
+ double* target_scores = new double[num_targets];
+ copy(target_scores_vect.begin(), target_scores_vect.end(), target_scores);
+ double* decoy_scores = new double[num_decoys];
+ copy(decoy_scores_vect.begin(), decoy_scores_vect.end(), decoy_scores);
+
+ double* PEPs = ComputeQValues::compute_PEP(target_scores, num_targets,
+ decoy_scores, num_decoys);
+
+ // fill in the data set with the new scores for the targets
+ int target_idx = 0;
+ for(int full_idx = 0; full_idx < psmtrainset.size(); full_idx++){
+ if( psmtrainset[full_idx].label == 1 ){
+ psmtrainset[full_idx].PEP = PEPs[target_idx];
+ target_idx++;
+ } // else, skip decoys
+ }
+
+ delete[] target_scores;
+ delete[] decoy_scores;
+ delete[] PEPs;
+
+ /**
+ * Calculate Peptide PEPs
+ */
+ target_scores_vect.clear();
+ decoy_scores_vect.clear();
+
+ //pull out the target and decoy scores for peptide PEPs
+ for(int i=0;i<peptrainset.size();i++){
+ if(peptrainset[i].label==1)
+ target_scores_vect.push_back(peptrainset[i].score);
+ else
+ decoy_scores_vect.push_back(peptrainset[i].score);
+ }
+ num_targets = target_scores_vect.size();
+ num_decoys = decoy_scores_vect.size();
+ carp(CARP_DEBUG, "Found %d targets and %d decoys", num_targets, num_decoys);
+
+ // copy them to an array as required by the compute_PEP method
+ target_scores = new double[num_targets];
+ copy(target_scores_vect.begin(), target_scores_vect.end(), target_scores);
+ decoy_scores = new double[num_decoys];
+ copy(decoy_scores_vect.begin(), decoy_scores_vect.end(), decoy_scores);
+ PEPs = ComputeQValues::compute_PEP(target_scores, num_targets,
+ decoy_scores, num_decoys);
+
+ // fill in the data set with the new scores for the targets
+ target_idx = 0;
+ for(int full_idx = 0; full_idx < peptrainset.size(); full_idx++){
+ if( peptrainset[full_idx].label == 1 ){
+ peptrainset[full_idx].PEP = PEPs[target_idx];
+ target_idx++;
+ } // else, skip decoys
+ }
+
+ delete[] target_scores;
+ delete[] decoy_scores;
+ delete[] PEPs;
+
+
+ /**
+ * Calculate Protein PEPs
+ */
+ target_scores_vect.clear();
+ decoy_scores_vect.clear();
+
+ //pull out the target and decoy scores for peptide PEPs
+ for(int i=0;i<trainset.size();i++){
+ if(trainset[i].label==1)
+ target_scores_vect.push_back(trainset[i].score);
+ else
+ decoy_scores_vect.push_back(trainset[i].score);
+ }
+ num_targets = target_scores_vect.size();
+ num_decoys = decoy_scores_vect.size();
+ carp(CARP_DEBUG, "Found %d targets and %d decoys of Protein", num_targets, num_decoys);
+
+ // copy them to an array as required by the compute_PEP method
+ target_scores = new double[num_targets];
+ copy(target_scores_vect.begin(), target_scores_vect.end(), target_scores);
+ decoy_scores = new double[num_decoys];
+ copy(decoy_scores_vect.begin(), decoy_scores_vect.end(), decoy_scores);
+ PEPs = ComputeQValues::compute_PEP(target_scores, num_targets,
+ decoy_scores, num_decoys);
+
+ // fill in the data set with the new scores for the targets
+ target_idx = 0;
+ for(int full_idx = 0; full_idx < trainset.size(); full_idx++){
+ if( trainset[full_idx].label == 1 ){
+ trainset[full_idx].PEP = PEPs[target_idx];
+ target_idx++;
+ } // else, skip decoys
+ }
+
+ delete[] target_scores;
+ delete[] decoy_scores;
+ delete[] PEPs;
+
+
+}
+
+/*************************************************************************/
+void Barista :: report_prot_fdr_counts(vector<double> &qvals, ofstream &of)
+{
+ for(unsigned int count = 0; count < qvals.size(); count++)
+ {
+ double q = qvals[count];
+ if(trainset.size() > 0)
+ {
+ int fdr_trn = getOverFDRProtParsimonious(trainset,max_net_prot,q);
+ of << q << " " << fdr_trn;
+ cout << q << " " << fdr_trn;
+ }
+
+ if(testset.size() > 0)
+ {
+ int fdr_tst = getOverFDRProtParsimonious(testset,max_net_prot,q);
+ of << " " << fdr_tst;
+ cout << " " << fdr_tst;
+ }
+ of << endl;
+ cout << endl;
+ }
+}
+
+void Barista :: report_psm_fdr_counts(vector<double> &qvals, ofstream &of)
+{
+ for(unsigned int count = 0; count < qvals.size(); count++)
+ {
+ double q = qvals[count];
+ if(psmtrainset.size() > 0)
+ {
+ int fdr_trn = getOverFDRPSM(psmtrainset,max_net_prot,q);
+ of << q << " " << fdr_trn;
+ cout << q << " " << fdr_trn;
+ }
+
+ if(psmtestset.size() > 0)
+ {
+ int fdr_tst = getOverFDRPSM(psmtestset,max_net_prot,q);
+ of << " " << fdr_tst;
+ cout << " " << fdr_tst;
+ }
+ of << endl;
+ cout << endl;
+ }
+}
+
+
+void Barista :: report_pep_fdr_counts(vector<double> &qvals, ofstream &of)
+{
+ for(unsigned int count = 0; count < qvals.size(); count++)
+ {
+ double q = qvals[count];
+ if(peptrainset.size() > 0)
+ {
+ int fdr_trn = getOverFDRPep(peptrainset,max_net_prot,q);
+ of << q << " " << fdr_trn;
+ cout << q << " " << fdr_trn;
+ }
+
+ if(psmtestset.size() > 0)
+ {
+ int fdr_tst = getOverFDRPep(peptestset,max_net_prot,q);
+ of << " " << fdr_tst;
+ cout << " " << fdr_tst;
+ }
+ of << endl;
+ cout << endl;
+ }
+}
+
+
+
+void Barista :: report_all_fdr_counts()
+{
+ int num_qvals = 14;
+ vector<double> qvals;
+ qvals.resize(num_qvals,0.0);
+ double q = 0.0;
+ for(int count = 0; count < num_qvals; count++)
+ {
+ qvals[count] = q;
+ if(q < 0.01)
+ q+=0.0025;
+ else
+ q+=0.01;
+ }
+
+ ostringstream fname;
+ fname << out_dir << "/barista_prot_m7" << ".txt";
+ ofstream of(fname.str().c_str());
+ if(trainset.size() > 0)
+ trainset.make_meta_set(d);
+ if(testset.size() > 0)
+ testset.make_meta_set(d);
+ report_prot_fdr_counts(qvals,of);
+ of.close();
+
+ fname.str("");
+ fname << out_dir << "/barista_psm_m7" << ".txt";
+ ofstream ofpsm(fname.str().c_str());
+ report_psm_fdr_counts(qvals,ofpsm);
+ ofpsm.close();
+
+ fname.str("");
+ fname << out_dir << "/barista_pep_m7" << ".txt";
+ ofstream ofpep(fname.str().c_str());
+ report_pep_fdr_counts(qvals,ofpep);
+ ofpep.close();
+
+
+}
+
+
+
+/*******************************************************************************/
+double Barista :: get_protein_score(int protind, NeuralNet &n)
+{
+ int num_pep = d.protind2num_pep(protind);
+ int num_all_pep = d.protind2num_all_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ double sm = 0.0;
+ double div = pow(num_all_pep,alpha);
+
+ for (int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+
+ for (int j = 0; j < num_psms; j++)
+ {
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = n.fprop(feat);
+ if(sc[0] > max_sc)
+ {
+ max_sc = sc[0];
+
+ }
+ }
+ sm += max_sc;
+ }
+ sm /= div;
+ return sm;
+}
+
+int Barista :: getOverFDRProt(ProtScores &set, NeuralNet &n, double fdr)
+{
+ double r = 0.0;
+ for(int i = 0; i < set.size(); i++)
+ {
+ int protind = set[i].protind;
+ r = get_protein_score(protind,n);
+ set[i].score = r;
+ }
+ return set.calcOverFDR(fdr);
+
+}
+
+int Barista :: getOverFDRProt(ProtScores &set, double fdr)
+{
+ double r = 0.0;
+ for(int i = 0; i < set.size(); i++)
+ {
+ int protind = set[i].protind;
+ r = get_protein_score(protind);
+ set[i].score = r;
+ }
+ return set.calcOverFDR(fdr);
+
+}
+
+double Barista :: get_protein_score(int protind)
+{
+ int num_pep = d.protind2num_pep(protind);
+ int num_all_pep = d.protind2num_all_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ max_psm_inds.erase(max_psm_inds.begin(),max_psm_inds.end());
+ max_psm_scores.erase(max_psm_scores.begin(),max_psm_scores.end());
+ int psm_count = 0;
+ for (int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+ int max_ind = 0;
+ for (int j = 0; j < num_psms; j++)
+ {
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = net_clones[psm_count].fprop(feat);
+ if(sc[0] > max_sc)
+ {
+ max_sc = sc[0];
+ max_ind = j;
+ }
+ psm_count++;
+ }
+ max_psm_inds.push_back(max_ind);
+ max_psm_scores.push_back(max_sc);
+ }
+ assert((int)max_psm_inds.size() == num_pep);
+ assert((int)max_psm_scores.size() == num_pep);
+
+ double sm = 0.0;
+ double n = pow(num_all_pep,alpha);
+ for(unsigned int i = 0; i < max_psm_inds.size() ; i++)
+ sm+= max_psm_scores[i];
+ sm /= n;
+ return sm;
+}
+
+void Barista :: calc_gradients(int protind, int label)
+{
+ int num_pep = d.protind2num_pep(protind);
+ int num_all_pep = d.protind2num_all_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ double n = pow(num_all_pep,alpha);
+
+ double *gc = new double[1];
+ gc[0] = -label/n;
+ int psm_count = 0;
+ for(int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+ int num_psms = d.pepind2num_psm(pepind);
+ int clone_ind = psm_count+max_psm_inds[i];
+ net_clones[clone_ind].bprop(gc);
+ psm_count += num_psms;
+ }
+ delete[] gc;
+}
+
+double Barista :: train_hinge(int protind, int label)
+{
+ double sm = get_protein_score(protind);
+
+ double err = max(0.0,1.0-sm*label);
+
+ if(sm*label < 1)
+ {
+ net.clear_gradients();
+ calc_gradients(protind,label);
+ net.update(mu);
+ }
+ return err;
+}
+
+
+double Barista :: train_hinge_psm(int psmind, int label)
+{
+ double *x = d.psmind2features(psmind);
+ double *c = net.fprop(x);
+ double err = 1.0-c[0]*label;
+
+ if(c[0]*label < 1)
+ {
+ double *gc = new double[1];
+ gc[0] = -1*label;
+ net.clear_gradients();
+ net.bprop(gc);
+ net.update(mu);
+ delete[] gc;
+ }
+ return err;
+}
+
+void Barista :: train_net(double selectionfdr)
+{
+ for (int k = 0; k < nepochs; k++)
+ {
+ if(verbose > 0)
+ cout << "epoch " << k << endl;
+ double err_sum = 0.0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ int ind = myrandom_limit(trainset.size());
+ int protind = trainset[ind].protind;
+ int label = trainset[ind].label;
+ err_sum += train_hinge(protind,label);
+ }
+ int fdr_trn = getOverFDRProt(trainset,selectionfdr);
+
+ if(verbose > 0)
+ {
+ cout << "err " << err_sum << " ";
+ cout << selectionfdr << " " << fdr_trn;
+ if(testset.size() > 0)
+ cout << " " << getOverFDRProt(testset,net,selectionfdr);
+ cout << endl;
+ }
+ if(fdr_trn > max_fdr)
+ {
+ max_net_prot = net;
+ max_fdr = fdr_trn;
+ if(verbose == 0)
+ {
+
+ if(testset.size() > 0)
+ carp(CARP_INFO, "q<%.2f: max non-parsimonious so far %d %d",
+ selectionfdr, max_fdr,
+ getOverFDRProt(testset,max_net_prot,selectionfdr));
+ else
+ carp(CARP_INFO, "q<%.2f: max non-parsimonious so far %d",
+ selectionfdr, max_fdr);
+ }
+ }
+ if(verbose > 0)
+ {
+ cout << "q< " << selectionfdr << ": max non-parsimonious so far " << max_fdr;
+ if(testset.size() > 0)
+ cout << " " << getOverFDRProt(testset,max_net_prot,selectionfdr);
+ cout << endl;
+ }
+ if(1)
+ {
+ int fdr_trn_psm = getOverFDRPSM(psmtrainset, net, selectionfdr);
+ if(fdr_trn_psm > max_fdr_psm)
+ {
+ max_net_psm = net;
+ max_fdr_psm = fdr_trn_psm;
+ }
+ }
+ if(1)
+ {
+ int fdr_trn_pep = getOverFDRPep(peptrainset, net, selectionfdr);
+ if(fdr_trn_pep > max_fdr_pep)
+ {
+ max_net_pep = net;
+ max_fdr_pep = fdr_trn_pep;
+ }
+ }
+ }
+ if(verbose > 0)
+ {
+ cout << "max peptides so far at q< " << selectionfdr << ": " << getOverFDRPep(peptrainset, max_net_psm, selectionfdr) << endl;
+ cout << "max psms so far at q<" << selectionfdr << ": " << max_fdr_psm << endl;
+ }
+}
+
+
+
+void Barista :: train_net_multi_task(double selectionfdr, int interval)
+{
+ for (int k = 0; k < nepochs; k++)
+ {
+ if(verbose > 0)
+ cout << "epoch " << k << endl;
+ double err_sum = 0.0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ int ind = myrandom_limit(trainset.size());
+ int protind = trainset[ind].protind;
+ int label = trainset[ind].label;
+ err_sum += train_hinge(protind,label);
+
+ ind = myrandom_limit(interval);
+ int psmind = psmtrainset[ind].psmind;
+ label = psmtrainset[ind].label;
+ train_hinge_psm(psmind,label);
+ }
+ int fdr_trn = getOverFDRProt(trainset,selectionfdr);
+
+ if(verbose > 0)
+ {
+ if(interval == trainset.size())
+ cout << "err " << err_sum << " ";
+ cout << selectionfdr << " " << fdr_trn;
+ if(testset.size() > 0)
+ cout << " " << getOverFDRProt(testset,net,selectionfdr);
+ cout << endl;
+ }
+ if(fdr_trn > max_fdr)
+ {
+ max_net_prot = net;
+ max_fdr = fdr_trn;
+ if(verbose == 0)
+ {
+ if(testset.size() > 0)
+ carp(CARP_INFO, "q<%.2f: max non-parsimonious so far %d %d",
+ selectionfdr, max_fdr,
+ getOverFDRProt(testset,max_net_prot,selectionfdr));
+ else
+ carp(CARP_INFO, "q<%.2f: max non-parsimonious so far %d",
+ selectionfdr, max_fdr);
+ }
+ }
+ if(verbose > 0)
+ {
+ cout << "q< " << selectionfdr << ": max non-parsimonious so far " << max_fdr;
+ if(testset.size() > 0)
+ cout << " " << getOverFDRProt(testset,max_net_prot,selectionfdr);
+ cout << endl;
+ }
+ if(1)
+ {
+ int fdr_trn_psm = getOverFDRPSM(psmtrainset, net, selectionfdr);
+ if(fdr_trn_psm > max_fdr_psm)
+ {
+ max_net_psm = net;
+ max_fdr_psm = fdr_trn_psm;
+ }
+ }
+ if(1)
+ {
+ int fdr_trn_pep = getOverFDRPep(peptrainset, net, selectionfdr);
+ if(fdr_trn_pep > max_fdr_pep)
+ {
+ max_net_pep = net;
+ max_fdr_pep = fdr_trn_pep;
+ }
+ }
+ }
+ if(verbose > 0)
+ {
+ cout << "max peptides so far at q< " << selectionfdr << ": " << getOverFDRPep(peptrainset, max_net_psm, selectionfdr) << endl;
+ cout << "max psms so far at q<" << selectionfdr << ": " << max_fdr_psm << endl;
+ }
+}
+
+
+
+void Barista :: setup_for_training(int trn_to_tst)
+{
+ carp(CARP_INFO, "loading and normalizing data");
+
+ d.load_data_prot_training();
+ d.load_labels_prot_training();
+
+ if(trn_to_tst)
+ {
+ carp(CARP_INFO, "splitting data into training and testing sets");
+ ProtScores::fillProteinsSplit(trainset, testset, d, trn_to_tst);
+ carp(CARP_INFO, "trainset size %d testset size %d", trainset.size(),
+ testset.size());
+ }
+ else
+ {
+ ProtScores::fillProteinsFull(trainset, d);
+ carp(CARP_INFO, "trainset size %d", trainset.size());
+ }
+ thresholdset = trainset;
+
+
+ if(trn_to_tst)
+ PSMScores::fillFeaturesSplit(psmtrainset, psmtestset, d, 0.5);
+ else
+ PSMScores::fillFeaturesFull(psmtrainset, d);
+ if(trn_to_tst)
+ PepScores::fillFeaturesSplit(peptrainset, peptestset, d, 0.5);
+ else
+ PepScores::fillFeaturesFull(peptrainset, d);
+ d.clear_labels_prot_training();
+
+ if(feature_file_flag)
+ {
+ string str = feature_file_name.str();
+ if(!d.print_features(str))
+ carp(CARP_INFO, "could not open file %s for writing features. Feature file will not be written", feature_file_name.str().c_str());
+ }
+
+ d.normalize_psms();
+
+ num_features = d.get_num_features();
+ int has_bias = 1;
+ int is_lin = 1;
+ if(is_lin)
+ num_hu = 1;
+ net.initialize(num_features, num_hu, is_lin, has_bias);
+ max_net_prot = net;
+ max_net_psm = net;
+ max_net_pep = net;
+
+ //get the max num peptides
+ max_peptides = 0;
+ max_psms_in_prot = 0;
+ for (int i = 0; i < d.get_num_proteins();i++)
+ {
+ int num_pep = d.protind2num_pep(i);
+ if(num_pep > max_peptides)
+ max_peptides = num_pep;
+ int *pepinds = d.protind2pepinds(i);
+ int sum_num_psms = 0;
+ for(int j = 0; j < num_pep; j++)
+ {
+ int pepind = pepinds[j];
+ sum_num_psms += d.pepind2num_psm(pepind);
+ }
+ if(max_psms_in_prot < sum_num_psms)
+ max_psms_in_prot = sum_num_psms;
+ }
+ max_psm_inds.reserve(max_peptides);
+ max_psm_scores.reserve(max_peptides);
+
+ //create the net clones
+ net_clones = new NeuralNet[max_psms_in_prot];
+ for (int i = 0; i < max_psms_in_prot;i++)
+ net_clones[i].clone(net);
+}
+
+
+int Barista :: run()
+{
+ setup_for_training(0);
+
+ train_net(selectionfdr);
+
+ return 0;
+
+}
+
+
+int Barista :: run_tries()
+{
+ setup_for_training(0);
+
+ int tries = 3;
+ vector<double> mu_choices;
+ mu_choices.resize(3,0.0);
+ mu_choices[0] = 0.005;
+ mu_choices[1] = 0.01;
+ mu_choices[2] = 0.05;
+ for(int k = 0; k < tries; k++)
+ {
+ mu = mu_choices[k];
+ net.make_random();
+ train_net(selectionfdr);
+ }
+
+ report_all_results_xml_tab();
+
+ return 0;
+
+}
+
+int Barista :: run_tries_multi_task()
+{
+ setup_for_training(0);
+
+ carp(CARP_INFO, "training the model");
+
+ int tries = 3;
+ vector<double> mu_choices;
+ mu_choices.resize(3,0.0);
+ mu_choices[0] = 0.005;
+ mu_choices[1] = 0.01;
+ mu_choices[2] = 0.05;
+ for(int k = 1; k < tries; k++)
+ {
+ mu = mu_choices[k];
+ net.make_random();
+ train_net_multi_task(selectionfdr, psmtrainset.size());
+ }
+
+ int interval= getOverFDRPSM(psmtrainset,max_net_psm,0.01)*2;
+ if(interval > psmtrainset.size())
+ interval = psmtrainset.size()/4;
+ if(interval < 50)
+ interval = psmtrainset.size()/4;
+ train_net_multi_task(selectionfdr, interval);
+
+ report_all_results_xml_tab();
+ return 0;
+
+}
+
+
+
+void Barista :: print_description()
+{
+ cout << endl;
+ cout << "\t crux barista [options] <protein database> <spectra> <search results>" << endl <<endl;
+ cout << "REQUIRED ARGUMENTS:" << endl << endl;
+ cout << "\t <protein database> Directory with FASTA files , list of FASTA files or a single FASTA file with the protein database used for the search." << endl;
+ cout << "\t <spectra> Directory with ms2 files, list of ms2 files or a single ms2 file used for database search." << endl;
+ cout << "\t <search results> Directory with sqt files, list of sqt files or a single sqt file with psms generated during search." << endl;
+ cout << endl;
+
+ cout << "OPTIONAL ARGUMENTS:" << endl << endl;
+ cout << "\t [--enzyme <string>] \n \t The enzyme used to digest the proteins in the experiment. Default trypsin." << endl;
+ cout << "\t [--decoy-prefix <string>] \n \t Specifies the prefix of the protein names that indicates a decoy. Default decoy_" << endl;
+ cout << "\t [--optimization <string>] \n \t Specifies whether to do optimization at the protein, peptide or psm level Default protein" << endl;
+ cout << "\t [--separate-searches <string>] \n \t If the target and decoy searches were run separately, the option then allows the user to specify the location of the decoy search results, the target database search should be provided as required argument." << endl;
+ cout << "\t [--fileroot <string>] \n \t The fileroot string will be added as a prefix to all output file names. Default = none." <<endl;
+ cout << "\t [--output-dir <directory>] \n \t The name of the directory where output files will be created. Default = crux-output." << endl;
+ cout << "\t [--overwrite <T/F>] \n \t Replace existing files (T) or exit if attempting to overwrite (F). Default=F." << endl;
+ cout << "\t [--skip-cleanup <T/F>] \n \t When set to T, prevents the deletion of lookup tables created during the preprocessing step. Default = F." << endl;
+ cout << "\t [--re-run <directory>] \n \t Re-run Barista analysis using a previously computed set of lookup tables." <<endl;
+ cout << "\t [--use-spec-features <T/F>] \n \t When set to F, use minimal feature set. Default T." <<endl;
+ cout<< "\t [--list-of-files <T/F>] \n \t When set to T,there is a list of files for search result. Default= F." <<endl;
+ cout << endl;
+
+}
+
+int Barista :: crux_set_command_line_options(int argc, char *argv[])
+{
+ string db_source;
+ string sqt_source;
+ string ms2_source;
+ string sqt_decoy_source;
+ int separate_search_flag;
+ string output_directory;
+
+ string enzyme;
+ string decoy_prefix;
+
+ string dir_with_tables;
+ int found_dir_with_tables;
+ bool list_of_files_flag;
+ bool spec_features_flag;
+
+ opt_type = Params::GetString("optimization");
+
+ fileroot = Params::GetString("fileroot");
+ if(!fileroot.empty()) {
+ fileroot.append(".");
+ }
+ if(opt_type.compare("psm") == 0)
+ qr.set_fileroot(fileroot);
+ else if(opt_type.compare("peptide") == 0)
+ pr.set_fileroot(fileroot);
+
+ overwrite_flag = Params::GetBool("overwrite");
+ if(opt_type.compare("psm") == 0)
+ qr.set_overwrite_flag(overwrite_flag);
+ if(opt_type.compare("peptide") == 0)
+ pr.set_overwrite_flag(overwrite_flag);
+
+ //options for the parser
+ decoy_prefix = Params::GetString("decoy-prefix");
+
+ enzyme = Params::GetString("enzyme");
+
+ spec_features_flag = Params::GetBool("use-spec-features");
+
+ skip_cleanup_flag = Params::GetBool("skip-cleanup");
+
+ dir_with_tables = Params::GetString("re-run");
+ if(!dir_with_tables.empty()) {
+ found_dir_with_tables = 1;
+ } else {
+ found_dir_with_tables = 0;
+ }
+
+ output_directory = Params::GetString("output-dir");
+
+ feature_file_flag = Params::GetBool("feature-file-out");
+ feature_file_name << output_directory << "/" << fileroot << "barista.features.txt";
+
+ if(found_dir_with_tables){
+ parser= new SQTParser();
+ //set input and output dirs
+ parser->set_output_dir(dir_with_tables);
+ if(opt_type.compare("psm") == 0)
+ {
+ qr.set_input_dir(dir_with_tables);
+ qr.set_output_dir(output_directory);
+ }
+ else if(opt_type.compare("peptide") == 0)
+ {
+ pr.set_input_dir(dir_with_tables);
+ pr.set_output_dir(output_directory);
+ }
+ set_input_dir(dir_with_tables);
+ set_output_dir(output_directory);
+
+ carp(CARP_INFO, "directory with tables: %s", dir_with_tables.c_str());
+ carp(CARP_INFO, "output_directory: %s", output_directory.c_str());
+ }else{
+ db_source = Params::GetString("database");
+ ms2_source = Params::GetString("fragmentation spectra");
+ sqt_source = Params::GetString("search results");
+ sqt_decoy_source = Params::GetString("separate-searches");
+ list_of_files_flag = Params::GetBool("list-of-files");
+ vector<string> files;
+ string files_list;
+
+ if(list_of_files_flag==1){
+ ifstream f(sqt_source.c_str());
+ f>>files_list;
+ while(!f.eof()){
+ files.push_back(files_list);
+ f>> files_list;
+ }
+ }else{
+ files.push_back(sqt_source);
+ }
+
+ for(unsigned i=0; i<files.size();i++){
+ FILE_FORMAT_T format=check_file_format(files[i]);
+ //sqt_source
+ switch (format) {
+ case SQT_FORMAT:
+ file_format_="sqt";
+ parser = new SQTParser();
+ break;
+ case DELIMITED_FORMAT:
+ file_format_="txt";
+ parser = new CruxParser();
+ break;
+ case INVALID_FORMAT:
+ default:
+ carp(CARP_FATAL, "Please enter .sqt or .txt search results");
+ }
+
+ parser->set_decoy_prefix(decoy_prefix);
+ parser->set_enzyme(enzyme);
+ if(enzyme.find("elastase") != string::npos){
+ cleavage_type="elastase-full-digest";
+ }else if (enzyme.find("chymotrypsin") != string::npos){
+ cleavage_type="chymotrypsin-full-digest";
+ }else if (enzyme.find("trypsin") != string::npos){
+ cleavage_type="trypsin-full-digest";
+ }else{
+ cleavage_type="Null";
+ }
+
+ //num of spec features
+ if(spec_features_flag)
+ parser->set_num_spec_features(3);
+ else
+ parser->set_num_spec_features(0);
+
+ if(!sqt_decoy_source.empty()) {
+ separate_search_flag = 1;
+ } else {
+ separate_search_flag = 0;
+ }
+
+ parser->write_features_header();
+ if(opt_type.compare("protein") == 0)
+ parser->set_use_quadratic_features(1);
+ if(parser->get_use_quadratic_features())
+ parser->add_quadratic_features_header();
+ d.get_features_header(parser->get_final_features_header());
+ //set the output directory for the parser
+ if(!parser->set_output_dir(output_directory))
+ return 0;
+ //set input and output for the leaning algo (in and out are the same as the out for the parser)
+
+ if(opt_type.compare("psm") == 0)
+ {
+ qr.set_input_dir(output_directory);
+ qr.set_output_dir(output_directory);
+ }
+ else if(opt_type.compare("peptide") == 0)
+ {
+ pr.set_input_dir(output_directory);
+ pr.set_output_dir(output_directory);
+ }
+ set_input_dir(output_directory);
+ set_output_dir(output_directory);
+
+ if(!parser->set_database_source(db_source))
+ carp(CARP_FATAL, "could not find the database");
+
+ if(separate_search_flag){
+ if(!parser->set_input_sources(ms2_source, sqt_source, sqt_decoy_source))
+ carp(CARP_FATAL, "could not extract features for training");
+ parser->set_num_hits_per_spectrum(1);
+ }else{
+ if(!parser->set_input_sources(ms2_source, sqt_source))
+ carp(CARP_FATAL, "could not extract features for training");
+ }
+ //print some info
+ carp(CARP_INFO, "database source: %s", db_source.c_str());
+ carp(CARP_INFO, "sqt source: %s", sqt_source.c_str());
+ carp(CARP_INFO, "ms2 source: %s", ms2_source.c_str());
+ carp(CARP_INFO, "output_directory: %s", output_directory.c_str());
+ carp(CARP_INFO, "enzyme: %s", enzyme.c_str());
+ carp(CARP_INFO, "decoy prefix: %s", decoy_prefix.c_str());
+
+
+ if(!parser->run())
+ carp(CARP_FATAL, "Could not proceed with training.");
+ parser->clear();
+ }
+ }
+
+
+ if(!parser->check_input_dir(in_dir))
+ carp(CARP_FATAL, "Please re-run with database, ms2 input and sqt input.");
+
+ return 1;
+
+}
+
+int Barista::main(int argc, char **argv) {
+ if(!crux_set_command_line_options(argc,argv))
+ return 1;
+
+ if(opt_type.compare("psm") == 0)
+ qr.run();
+ else if(opt_type.compare("peptide") == 0)
+ pr.run();
+ else
+ {
+ run_tries();
+ }
+ if(skip_cleanup_flag != 1)
+ parser->clean_up(out_dir);
+
+ return 0;
+}
+
+bool Barista :: needsOutputDirectory() const
+{
+ return true;
+}
+
+
+string Barista::getName() const {
+ return "barista";
+}
+
+string Barista::getDescription() const {
+ return
+ "[[nohtml:Rank PSMs, peptides and proteins, assigning a confidence measure "
+ "to each identification.]]"
+ "[[html:<p>Barista is a protein identification algorithm that combines two "
+ "different tasks–peptide-spectrum match (PSM) verification and "
+ "protein inference–into a single learning algorithm. The program "
+ "requires three inputs: a set of MS2 spectra, a protein database, and the "
+ "results of searching the spectra against the database. Barista produces "
+ "as output three ranked lists of proteins, peptides and PSMs, based on how "
+ "likely the proteins and peptides are to be present in the sample and how "
+ "likely the PSMs are to be correct. Barista can jointly analyze the "
+ "results of multiple shotgun proteomics experiments, corresponding to "
+ "different experiments or replicate runs.</p><p>Barista uses a machine "
+ "learning strategy that requires that the database search be carried out "
+ "on target and decoy proteins. The searches may be carried out on a "
+ "concatenated database or, using the <code>--separate-searches</code> "
+ "option, separate target and decoy databases. The <code>crux tide-index"
+ "</code> command can be used to generate a decoy database.</p><p>Barista "
+ "assigns two types of statistical confidence estimates, q-values and "
+ "posterior error probabilities, to identified PSMs, peptides and proteins. "
+ "For more information about these values, see the documentation for <a "
+ "href=\"assign-confidence.html\">assign-confidence</a>.</p>"
+ "<p>More details on the Barista algorithm are provided in</p>"
+ "<blockquote>Marina Spivak, Jason Weston, Michael J. MacCoss and "
+ "William Stafford Noble. <a href=\"http://www.mcponline.org/content/"
+ "11/2/M111.012161.long\">\"Direct maximization of protein identifications "
+ "from tandem mass spectra.\"</a> <i>Molecular and Cellular "
+ "Proteomics</i>. 11(2):M111.012161, 2012.</blockquote>]]";
+}
+
+vector<string> Barista::getArgs() const {
+ string arr[] = {
+ "database",
+ "fragmentation spectra",
+ "search results"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> Barista::getOptions() const {
+ string arr[] = {
+ "enzyme",
+ "decoy-prefix",
+ "separate-searches",
+ "fileroot",
+ "output-dir",
+ "overwrite",
+ "pepxml-output",
+ "txt-output",
+ "skip-cleanup",
+ "re-run",
+ "use-spec-features",
+ "parameter-file",
+ "verbosity",
+ "list-of-files",
+ "feature-file-out",
+ "optimization",
+ "spectrum-parser"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > Barista::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("barista.xml",
+ "an <a href=\"../file-formats/barista-xml-format.html\">XML file</a> that contains "
+ "four information about proteins, subset proteins, peptides, and PSMs."));
+ outputs.push_back(make_pair("barista.target.proteins.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited file</a> containing a ranked "
+ "list of groups of indistinguishable target proteins with associated Barista scores "
+ "and q-values and with peptides that contributed to the identification of the "
+ "protein group."));
+ outputs.push_back(make_pair("barista.target.subset-proteins.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited file</a> containing groups of "
+ "indistinguishable proteins."));
+ outputs.push_back(make_pair("barista.target.peptides.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited file</a> containing a ranked list "
+ "of target peptides with the associated Barista scores and q-values."));
+ outputs.push_back(make_pair("barista.target.psm.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited file format</a> containing a ranked list "
+ "of target peptide-spectrum matches with the associated Barista scores and q-values."));
+ outputs.push_back(make_pair("barista.log.txt",
+ "a file where the program reports its progress."));
+ outputs.push_back(make_pair("barista.params.txt",
+ "a file with the values of all the options given to the current run."));
+ return outputs;
+}
+
+COMMAND_T Barista::getCommand() const {
+ return BARISTA_COMMAND;
+}
+
+// returns file extension
+string Barista:: file_extension (string str){
+ return str.substr(str.rfind('.')+1);
+}
+
+
+//determins which parser to be called
+FILE_FORMAT_T Barista:: check_file_format(string source){
+ string ext = file_extension(source);
+ if (ext=="sqt")
+ return SQT_FORMAT;
+ else if(ext=="txt")
+ return DELIMITED_FORMAT;
+ else
+ carp(CARP_DEBUG,"The file format is invalid");
+ return INVALID_FORMAT;
+}
+
+void Barista :: get_protein_id(int pepind, vector<string> &prot){
+ int * protinds= d.pepind2protinds(pepind) ;
+ unsigned prot_length=d.pepind2num_prot(pepind);
+ for (unsigned k=0;k<prot_length;k++){
+ string protein_str= d.ind2prot( protinds[k]);
+ prot.push_back(protein_str);
+ }
+}
+
+void Barista :: print_protein_ids(vector<string> &prots, ofstream &os, int psmind){
+ if(file_format_=="txt"){
+ for (unsigned int j=0;j<prots.size();j++){
+ if(j==prots.size()-1)
+ os<<prots[j]<<"("<<d.psmind2peptide_position(psmind)<<")\t";
+ else
+ os<<prots[j]<<"("<<d.psmind2peptide_position(psmind)<<")"<<",";
+ }
+ }else if(file_format_=="sqt"){
+ for (unsigned int j=0;j<prots.size();j++){
+ if(j==prots.size()-1)
+ os<<prots[j]<<"\t";
+ else
+ os<<prots[j]<<",";
+ }
+ }
+ prots.clear();
+}
+
+/*
+*Local Variables:
+*mode: c
+*c-basic-offset: 2
+*End:
+*/
diff --git a/src/app/qranker-barista/Barista.h b/src/app/qranker-barista/Barista.h
new file mode 100644
index 0000000..d5b3485
--- /dev/null
+++ b/src/app/qranker-barista/Barista.h
@@ -0,0 +1,200 @@
+#ifndef BARISTA_H
+#define BARISTA_H
+
+#include <sys/types.h>
+#ifndef _MSC_VER
+#include <dirent.h>
+#endif
+
+#include <iostream>
+#include <sstream>
+#include <set>
+#include <algorithm>
+#include <assert.h>
+#include <cstdio>
+#include <iomanip>
+#include "app/CruxApplication.h"
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+#include "io/PepXMLWriter.h"
+#include "DataSetCrux.h"
+#include "ProtScores.h"
+#include "PSMScores.h"
+#include "PepScores.h"
+#include "NeuralNet.h"
+#include "SQTParser.h"
+#include "CruxParser.h"
+#include "QRanker.h"
+#include "PepRanker.h"
+using namespace std;
+#include "util/mass.h"
+
+class Barista : public CruxApplication
+{
+ public:
+ Barista()
+ : verbose(0),
+ skip_cleanup_flag(0),
+ overwrite_flag(0),
+ feature_file_flag(0),
+ list_of_files_flag(0),
+ in_dir(""),
+ out_dir(""),
+ fileroot(""),
+ seed(0),
+ selectionfdr(0.01),
+ nepochs(20),
+ num_features(0),
+ num_hu(3),
+ mu(0.05),
+ weightDecay(0.0),
+ alpha(0.3),
+ max_psms_in_prot(0),
+ net_clones(0),
+ max_fdr(0),
+ max_peptides(0),
+ max_fdr_psm(0),
+ max_fdr_pep(0),
+ parser(NULL){}
+ ~Barista(){clear();}
+ void clear();
+ void print_description();
+ int crux_set_command_line_options(int argc, char *argv[]);
+ int set_command_line_options(int argc, char *argv[]);
+ void setup_for_training(int trn_to_tst);
+ void setup_for_reporting_results();
+ int run();
+
+ int run_tries();
+ int run_tries_multi_task();
+ double train_hinge(int protind, int label);
+ double train_hinge_psm(int psmind, int label);
+ void train_net(double selectionfdr);
+ void train_net_multi_task(double selectionfdr, int interval);
+
+ void calc_gradients(int protind, int label);
+
+ int getOverFDRProt(ProtScores &set, NeuralNet &n, double fdr);
+ int getOverFDRProt(ProtScores &set, double fdr);
+
+ double get_protein_score(int protind);
+ double get_protein_score(int protind, NeuralNet &n);
+ double get_protein_score_parsimonious(int protind, NeuralNet &n);
+ int getOverFDRProtParsimonious(ProtScores &set, NeuralNet &n, double fdr);
+ void computePEP();
+ int computeNSAF();
+ int computePepNSAF();
+
+ void write_results_prot(string &out_dir, int fdr);
+ void report_all_results();
+ void get_pep_seq(string &pep, string &seq, string &n, string &c);
+ void get_tab_delim_proteins(string protein_str, vector<string> &proteins);
+ void write_protein_special_case_xml(ofstream &os, int i);
+ void write_results_prot_xml(ofstream &os);
+ void write_subset_protein_special_case_xml(ofstream &os, int i);
+ void write_results_subset_prot_xml(ofstream &os);
+ void write_results_peptides_xml(ofstream &os);
+ void write_results_psm_xml(ofstream &os);
+ void write_results_pep_xml(PepXMLWriter& xmlfile);
+ void report_all_results_xml();
+ void write_results_prot_special_case_tab(ofstream &os, int i);
+ void write_results_prot_tab(ofstream &os);
+ void write_subset_protein_special_case_tab(ofstream &os, int i);
+ void write_results_subset_prot_tab(ofstream &os);
+ void write_results_peptides_tab(ofstream &os);
+ void write_results_psm_tab(ofstream &os);
+ void report_all_results_tab();
+ void report_all_results_xml_tab();
+ void report_prot_fdr_counts(vector<double> &qvals, ofstream &of);
+ void report_psm_fdr_counts(vector<double> &qvals, ofstream &of);
+ void report_pep_fdr_counts(vector<double> &qvals, ofstream &of);
+ void report_all_fdr_counts();
+ void clean_up();
+ void get_protein_id(int pepind, vector<string> &prots);
+ void print_protein_ids(vector<string> &proteins,ofstream &os,int psmind);
+
+ int getOverFDRPSM(PSMScores &set, NeuralNet &n, double fdr);
+ double get_peptide_score(int pepind, NeuralNet &n);
+ int getOverFDRPep(PepScores &set, NeuralNet &n, double fdr);
+
+ inline void set_input_dir(string input_dir) {in_dir = input_dir; d.set_input_dir(input_dir);}
+ inline void set_output_dir(string output_dir){out_dir = output_dir;}
+
+ /* CruxApplication Methods */
+ virtual int main(int argc, char** argv);
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+ virtual bool needsOutputDirectory() const;
+ virtual COMMAND_T getCommand() const;
+
+
+ double check_gradients_hinge_one_net(int protind, int label);
+ double check_gradients_hinge_clones(int protind, int label);
+
+ FILE_FORMAT_T check_file_format(string filename);
+ string file_extension(string str);
+ protected:
+ SQTParser* parser;
+ int verbose;
+ int skip_cleanup_flag;
+ int overwrite_flag;
+ int feature_file_flag;
+ ostringstream feature_file_name;
+ int list_of_files_flag;
+
+ Dataset d;
+ string in_dir;
+ string out_dir;
+ string fileroot;
+
+ string cleavage_type;
+
+ int seed;
+ double selectionfdr;
+ int nepochs;
+
+ NeuralNet net;
+ int num_features;
+ int num_hu;
+ double mu;
+ double weightDecay;
+ double alpha;
+
+
+ int max_psms_in_prot;
+ NeuralNet *net_clones;
+ NeuralNet max_net_prot;
+ int max_fdr;
+ ProtScores trainset, thresholdset, testset;
+
+ int max_peptides;
+ vector<int> max_psm_inds;
+ vector<double> max_psm_scores;
+
+ //for parsimony counts
+ vector<int> used_peptides;
+ vector<int> pepind_to_max_psmind;
+
+ PSMScores psmtrainset, psmtestset;
+ NeuralNet max_net_psm;
+ int max_fdr_psm;
+
+ PepScores peptrainset,peptestset;
+ NeuralNet max_net_pep;
+ int max_fdr_pep;
+
+ string file_format_;
+ ofstream fdebug;
+
+ string opt_type;
+ QRanker qr;
+ PepRanker pr;
+
+};
+
+
+#endif
diff --git a/src/app/qranker-barista/BipartiteGraph.cpp b/src/app/qranker-barista/BipartiteGraph.cpp
new file mode 100644
index 0000000..0a42707
--- /dev/null
+++ b/src/app/qranker-barista/BipartiteGraph.cpp
@@ -0,0 +1,106 @@
+#include "BipartiteGraph.h"
+
+void BipartiteGraph::create_bipartite_graph(map<int, set<int> > data)
+{
+ int n = data.size();
+ //allocate the range array
+ ranges = new Range[n];
+ nranges = 0;
+ nindices = 0;
+ int max_len = 0;
+ for(map <int, set<int> >::iterator it = data.begin(); it != data.end(); it++)
+ {
+ int len = 0;
+ for(set<int>::iterator itp = (it->second).begin(); itp != (it->second).end(); itp++)
+ {
+ len++;
+ nindices++;
+ }
+ if(len > max_len)
+ max_len = len;
+ int ind = it->first;
+ ranges[ind].len = len;
+ nranges++;
+ }
+ indices = new int[nindices];
+
+ vector<int> t;
+ t.reserve(max_len);
+ set<int> s;
+ int pos = 0;
+ for (int i = 0; i < nranges; i++)
+ {
+ s = data[i];
+ t.erase(t.begin(),t.end());
+ for(set<int>::iterator itp = s.begin(); itp != s.end(); itp++)
+ t.push_back(*itp);
+ sort(t.begin(),t.end());
+ assert((int)t.size() == ranges[i].len);
+ ranges[i].p = pos;
+ for (unsigned int k = 0; k < t.size(); k++)
+ {
+ indices[pos] = t[k];
+ pos++;
+ }
+ }
+}
+
+
+void BipartiteGraph::save(ofstream &os)
+{
+ os.write((char*)(&nranges),sizeof(int));
+ os.write((char*)(&nindices),sizeof(int));
+ os.write((char*)ranges,sizeof(Range)*nranges);
+ os.write((char*)indices,sizeof(int)*nindices);
+}
+
+void BipartiteGraph::load(ifstream &is)
+{
+ is.read((char*)(&nranges),sizeof(int));
+ is.read((char*)(&nindices),sizeof(int));
+ ranges = new Range[nranges];
+ indices = new int[nindices];
+ is.read((char*)ranges,sizeof(Range)*nranges);
+ is.read((char*)indices,sizeof(int)*nindices);
+
+}
+
+
+bool BipartiteGraph::is_index_in_range(int index, int range)
+{
+ assert(range < nranges);
+ for(int i = 0; i < ranges[range].len; i++)
+ {
+ int ofst = ranges[range].p+i;
+ if(indices[ofst] == index)
+ return true;
+ }
+ return false;
+}
+
+bool BipartiteGraph :: is_subset(int r1, int r2)
+{
+ assert(r1 < nranges);
+ assert(r2 < nranges);
+ int len1 = ranges[r1].len;
+ int len2 = ranges[r2].len;
+ int *inds1 = indices+ranges[r1].p;
+ int *inds2 = indices+ranges[r2].p;
+ int i1 = 0;
+ int i2 = 0;
+
+ while(i1 < len1 && i2 < len2)
+ {
+ if(inds1[i1] == inds2[i2])
+ {
+ i1++;
+ i2++;
+ }
+ else if(inds1[i1] < inds2[i2])
+ i1++;
+ else
+ return false;
+ }
+ return true;
+}
+
diff --git a/src/app/qranker-barista/BipartiteGraph.h b/src/app/qranker-barista/BipartiteGraph.h
new file mode 100644
index 0000000..249ccd8
--- /dev/null
+++ b/src/app/qranker-barista/BipartiteGraph.h
@@ -0,0 +1,38 @@
+#ifndef BIPARTITEGRAPH_H
+#define BIPARTITEGRAPH_H
+#include<iostream>
+#include<fstream>
+#include <set>
+#include <map>
+#include <vector>
+#include <algorithm>
+#include <assert.h>
+using namespace std;
+
+class BipartiteGraph{
+ public:
+ struct Range {int p; int len;};
+ BipartiteGraph():nranges(0),nindices(0), ranges((Range*)0), indices((int*)0){}
+ ~BipartiteGraph(){clear();}
+ void clear(){delete[] ranges; ranges = 0; delete[] indices; indices = 0; nranges=0; nindices=0;}
+ void create_bipartite_graph(map<int, set<int> > data);
+
+ bool is_index_in_range(int index, int range);
+ //assumes that inds are sorted
+ bool is_subset(int r1, int r2);
+ int get_nranges() const {return nranges;}
+ int get_nindices() const {return nindices;}
+ int get_range_length(int r){return ranges[r].len;}
+ int* get_range_indices(int r){return (indices+ranges[r].p);}
+
+ void save(ofstream &os);
+ void load(ifstream &is);
+ private:
+ int nranges; //how many ranges
+ int nindices; //size of the index array
+ Range* ranges;
+ int* indices;
+};
+
+
+#endif //BIPARTITEGRAPH_H
diff --git a/src/app/qranker-barista/CMakeLists.txt b/src/app/qranker-barista/CMakeLists.txt
new file mode 100644
index 0000000..e1e4e3e
--- /dev/null
+++ b/src/app/qranker-barista/CMakeLists.txt
@@ -0,0 +1,53 @@
+project(barista)
+
+cmake_minimum_required(VERSION 2.8.4)
+cmake_policy(VERSION 2.8.4)
+
+include_directories(${CMAKE_SOURCE_DIR}/src)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_1_56_0)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_aux)
+include_directories(${CMAKE_BINARY_DIR}/ext/include)
+
+if (WIN32 AND NOT CYGWIN)
+ add_definitions(-DBOOST_ALL_NO_LIB)
+endif (WIN32 AND NOT CYGWIN)
+
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _CRT_SECURE_NO_WARNINGS
+ _SCL_SECURE_NO_WARNINGS
+ CRUX
+ SEARCH_ENABLED
+ )
+else (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _FILE_OFFSET_BITS=64
+ _GNU_SOURCE
+ _LARGEFILE_SOURCE
+ GCC
+ )
+endif (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+add_library(
+ barista
+ STATIC
+ Barista.cpp
+ BipartiteGraph.cpp
+ CruxParser.cpp
+ DataSetCrux.cpp
+ NeuralNet.cpp
+ PepRanker.cpp
+ PepScores.cpp
+ ProtScores.cpp
+ PSMScores.cpp
+ QRanker.cpp
+ SpecFeatures.cpp
+ SQTParser.cpp
+ TabDelimParser.cpp
+)
diff --git a/src/app/qranker-barista/CruxParser.cpp b/src/app/qranker-barista/CruxParser.cpp
new file mode 100644
index 0000000..521a8db
--- /dev/null
+++ b/src/app/qranker-barista/CruxParser.cpp
@@ -0,0 +1,177 @@
+/*************************************************************************//**
+ * \file CruxParser.cpp
+ * AUTHOR: Manijeh Naseri and Sean McIlwain
+ * CREATE DATE: 06/06/2012
+ * \brief Parses tab-delimited search result files
+ ****************************************************************************/
+#include "CruxParser.h"
+#include "model/Peptide.h"
+#include "io/MatchFileReader.h"
+#include "model/PeptideSrc.h"
+#include "model/Match.h"
+#include "io/MatchColumns.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+/******************************/
+
+
+/**
+ * Default constructor
+ */
+CruxParser :: CruxParser()
+ : SQTParser(){
+}
+
+/**
+ * Default destructor
+ */
+CruxParser :: ~CruxParser(){
+}
+
+
+/**
+ * Parse tab delimited file.
+ * Generates the same QRanker internal tables.
+ * Set the matches in the tab delimited file.
+ */
+void CruxParser ::readMatches(
+ MatchFileReader& reader, ///< Reader for the delimited file.
+ int final_hits, ///< Total number of matches
+ enzyme enz, ///< Enzyme used in search
+ bool decoy ///< Are all the matches decoy?
+ ) {
+
+ //set the matches to zero
+ int hits_read = 0;
+
+ // read file line by line and set the variables
+ while (reader.hasNext()) {
+
+ int current_scan = reader.getInteger(SCAN_COL);
+ int current_charge = reader.getInteger(CHARGE_COL);
+ sqt_match matches;
+ matches.scan = current_scan;
+ matches.charge = current_charge;
+ matches.precursor_mass = reader.getDouble(SPECTRUM_NEUTRAL_MASS_COL);
+
+ if (!reader.empty(DISTINCT_MATCHES_SPECTRUM_COL)) {
+ matches.num_sequence_comparisons = reader.getInteger(DISTINCT_MATCHES_SPECTRUM_COL);
+ } else if (!reader.empty(MATCHES_SPECTRUM_COL)) {
+ matches.num_sequence_comparisons = reader.getInteger(MATCHES_SPECTRUM_COL);
+ } else {
+ carp_once(CARP_WARNING, "Empty Matches/Spectrum col");
+ matches.num_sequence_comparisons = 0;
+ }
+ hits_read = 0;
+
+ //iterate over all rows in delimited file, fill-in sqt match structure.
+ while (reader.hasNext() &&
+ reader.getInteger(SCAN_COL) == current_scan &&
+ reader.getInteger(CHARGE_COL) == current_charge) {
+
+ //fill in sqt_match structure with correct fields from delimited file.
+ matches.xcorr_rank.push_back(reader.getInteger(XCORR_RANK_COL));
+ matches.sp_rank.push_back(reader.getInteger(SP_RANK_COL));
+ matches.delta_cn.push_back(reader.getDouble(DELTA_CN_COL));
+ matches.sp_score.push_back(reader.getDouble(SP_SCORE_COL));
+ matches.calc_mass.push_back(reader.getDouble(PEPTIDE_MASS_COL));
+ matches.xcorr_score.push_back(reader.getDouble(XCORR_SCORE_COL));
+ matches.num_ions_matched.push_back(reader.getInteger(BY_IONS_MATCHED_COL));
+ matches.num_total_ions.push_back(reader.getFloat(BY_IONS_TOTAL_COL));
+
+ //set sequence_id
+ string sequence = reader.getString(SEQUENCE_COL);
+ //set flanking_aa
+ string flanking_aa = reader.getString(FLANKING_AA_COL);
+
+ if (flanking_aa.length() != 2)
+ {
+ carp(CARP_DEBUG,
+ "Flanking AA value length is expected to be 2, "
+ "but was %d", flanking_aa.length());
+ }
+
+ ostringstream oss;
+
+ oss << flanking_aa[0] << "." << sequence << "." << flanking_aa[1];
+ string sqt_sequence = oss.str();
+ matches.peptides.push_back(sqt_sequence);
+
+ //read protein Id from search result
+ vector<string> protein_ids = StringUtils::Split(reader.getString(PROTEIN_ID_COL), ',');
+ matches.num_proteins_in_match.push_back(protein_ids.size());
+ for (size_t idx = 0;idx < protein_ids.size(); idx++) {
+ string protein_id = protein_ids.at(idx);
+ //change the format of protein_id to be same as SQTParser
+ size_t protein_idx_pos = protein_id.rfind('(');
+ if (protein_idx_pos != string::npos) {
+ string pep_pos= protein_id.substr(protein_idx_pos);
+ pep_pos=pep_pos.substr(1,pep_pos.size()-2);
+ matches.peptide_pos.push_back(atoi(pep_pos.c_str()));
+ protein_id.erase(protein_idx_pos);
+ } else {
+ matches.peptide_pos.push_back(-1);
+ }
+ matches.proteins.push_back(protein_id);
+ }
+ hits_read++;
+ reader.next();
+ }
+
+ //call SQTParser method to generate internal tables
+ add_matches_to_tables(
+ matches,
+ decoy_prefix,
+ hits_read,
+ final_hits,
+ decoy
+ );
+
+ //call SQTParser method to generate feature vectors
+ extract_features(
+ matches,
+ hits_read,
+ final_hits,
+ enz
+ );
+
+ }
+}
+
+ /*
+ *gets the path of delimited file
+ *\returns true if it can open the file
+ */
+bool CruxParser :: read_search_results(
+ string& cur_fname, /// < current file path to parse
+ bool decoy ///< is this a file of decoys?
+ ) {
+
+ //read file
+ MatchFileReader reader(cur_fname);
+
+ //TODO (SJM) - test to see if we opened the file, if not, WARNING, then return false
+
+ readMatches(
+ reader,
+ fhps,
+ e,
+ decoy
+ );
+ return true;
+}
+
+/**
+ *\returns txt file extension
+ */
+std::string CruxParser::get_parser_extension() {
+ return ".txt";
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/qranker-barista/CruxParser.h b/src/app/qranker-barista/CruxParser.h
new file mode 100644
index 0000000..a925c54
--- /dev/null
+++ b/src/app/qranker-barista/CruxParser.h
@@ -0,0 +1,78 @@
+/*************************************************************************//**
+ * \file CruxParser.cpp
+ * AUTHOR: Manijeh Naseri and Sean McIlwain
+ * CREATE DATE: 06/06/2012
+ * \brief Parses tab-delimited search result files
+ ****************************************************************************/
+#ifndef CRUXPARSER_H
+#define CRUXPARSER_H
+
+#include <sys/stat.h>
+#ifndef _MSC_VER
+#include <dirent.h>
+#endif
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <assert.h>
+#include <vector>
+#include <string>
+#include <math.h>
+#include <map>
+#include <set>
+#include <cstring>
+#include "SpecFeatures.h"
+#include "BipartiteGraph.h"
+#include "SQTParser.h"
+#include "app/CruxApplication.h"
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+
+using namespace std;
+
+class CruxParser:public SQTParser{
+ public:
+
+ CruxParser();
+ virtual ~CruxParser();
+
+
+/**
+ * Parse tab delimited file.
+ * Generates the same QRanker internal tables.
+ * Set the matches in the tab delimited file.
+ */
+ void readMatches(
+ MatchFileReader& reader,///<Reader for the delimted file.
+ int final_hits,///<Total number of matches
+ enzyme enz, ///<Enzyme in used on search
+ bool decoy ///< Are all the matches decoy?
+ );
+
+ /*
+ *gets the path of delimited file
+ *\returns true if it can open the file
+ */
+ virtual bool read_search_results(
+ string& cur_fname, ///< current delimited file path tp parse
+ bool decoy ///< Are all the matches decoy?
+ );
+ virtual string get_parser_extension();
+
+
+ protected:
+ ofstream f_pepind2flanking_aa;
+ ofstream f_psmind2xcorr_rank;
+ ofstream f_psmind2match_spectrum;
+ ofstream f_psmind2cleavage_type;
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/qranker-barista/DataSetCrux.cpp b/src/app/qranker-barista/DataSetCrux.cpp
new file mode 100644
index 0000000..b18319a
--- /dev/null
+++ b/src/app/qranker-barista/DataSetCrux.cpp
@@ -0,0 +1,1369 @@
+#include "DataSetCrux.h"
+#include "SQTParser.h"
+
+Dataset::Dataset()
+ : num_psms(0), num_pos_psms(0), num_neg_psms(0),
+ psmind_to_features((double*)0),
+ psmind_to_label((int*)0),
+ psmind_to_pepind((int*)0),
+ psmind_to_scan(0),
+ psmind_to_charge(0),
+ psmind_to_precursor_mass(0),
+ psmind_to_fileind(0),
+ num_pep(0), num_pos_pep(0), num_neg_pep(0),
+ pepind_to_label(0),
+ num_prot(0), num_pos_prot(0), num_neg_prot(0),
+ protind_to_label(0),
+ protind_to_num_all_pep(0),
+ psmind_to_sp_rank((int*)0),
+ protind_to_length(0),
+ psmind_to_xcorr_rank((int*)0),
+ psmind_to_matches_spectrum((int*)0),
+ psmind_to_by_ions_matched((double*)0),
+ psmind_to_by_ions_total((double*)0),
+ psmind_to_peptide_position((int*)0)
+{
+}
+
+Dataset::~Dataset()
+{
+ delete[] psmind_to_features; psmind_to_features = (double*)0;
+ delete[] psmind_to_label; psmind_to_label = (int*)0;
+ delete[] psmind_to_pepind; psmind_to_pepind = (int*)0;
+ delete[] psmind_to_scan; psmind_to_scan = (int*)0;
+ delete[] psmind_to_charge; psmind_to_charge = (int*)0;
+ delete[] psmind_to_precursor_mass; psmind_to_precursor_mass = (double*)0;
+ delete[] psmind_to_sp_rank; psmind_to_sp_rank=(int*)0;//Sp Rank
+ delete[] psmind_to_xcorr_rank; psmind_to_xcorr_rank=(int*)0;//xcorr Rank
+ // distinct matches/spectrum
+ delete[] psmind_to_matches_spectrum; psmind_to_matches_spectrum=(int*)0;
+ delete[] psmind_to_by_ions_matched; psmind_to_by_ions_matched=(double*)0;// b/y ions matched
+ delete[] psmind_to_by_ions_total; psmind_to_by_ions_total=(double*)0;// b/y ions total
+ delete[] psmind_to_peptide_position; psmind_to_peptide_position=(int*)0;//peptide position in protein
+ fileind_to_fname.clear();
+
+ ind_to_pep.clear();
+ pepind_to_psminds.clear();
+ pepind_to_protinds.clear();
+ delete [] pepind_to_label; pepind_to_label = (int*)0;
+
+ delete [] psmind_to_fileind; psmind_to_fileind = (int*)0;
+ delete[] protind_to_label; protind_to_label = (int*)0;
+ delete[] protind_to_num_all_pep; protind_to_num_all_pep = (int*)0;
+ delete[] protind_to_length; protind_to_length = (int*)0;
+ protind_to_pepinds.clear();
+ ind_to_prot.clear();
+
+}
+
+
+/****************************************************************************/
+
+void Dataset :: load_data_psm_training()
+{
+
+ ostringstream fname;
+ fname << in_dir << "/summary";
+ ifstream f_summary(fname.str().c_str());
+ f_summary >> num_features;
+ f_summary >> num_psms;
+ f_summary >> num_pos_psms;
+ f_summary >> num_neg_psms;
+ f_summary.close();
+ fname.str("");
+
+ //psm features
+ fname << in_dir << "/" << "psm";
+ ifstream f_psm_feat(fname.str().c_str(),ios::binary);
+ if(!f_psm_feat.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_features = new double[num_psms*num_features];
+ f_psm_feat.read((char*)psmind_to_features,sizeof(double)*num_psms*num_features);
+ f_psm_feat.close();
+ fname.str("");
+}
+
+void Dataset :: clear_data_psm_training()
+{
+ delete [] psmind_to_features; psmind_to_features = (double*)0;
+}
+
+void Dataset :: load_labels_psm_training()
+{
+ ostringstream fname;
+ fname << in_dir << "/summary";
+ ifstream f_summary(fname.str().c_str());
+ f_summary >> num_features;
+ f_summary >> num_psms;
+ f_summary >> num_pos_psms;
+ f_summary >> num_neg_psms;
+ f_summary.close();
+ fname.str("");
+
+ //psmind_to_label
+ fname << in_dir << "/psmind_to_label";
+ ifstream f_psmind_to_label(fname.str().c_str(),ios::binary);
+ psmind_to_label = new int[num_psms];
+ f_psmind_to_label.read((char*)psmind_to_label,sizeof(int)*num_psms);
+ f_psmind_to_label.close();
+ fname.str("");
+}
+
+void Dataset :: clear_labels_psm_training()
+{
+ delete [] psmind_to_label; psmind_to_label = (int*)0;
+}
+
+void Dataset :: load_data_psm_results()
+{
+
+ ostringstream fname;
+ fname << in_dir << "/summary";
+ ifstream f_summary(fname.str().c_str());
+ f_summary >> num_features;
+ f_summary >> num_psms;
+ f_summary >> num_pos_psms;
+ f_summary >> num_neg_psms;
+ f_summary.close();
+ fname.str("");
+
+ //psmind_to_pepind
+ fname << in_dir << "/psmind_to_pepind";
+ ifstream f_psmind_to_pepind(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_pepind.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_pepind = new int[num_psms];
+ f_psmind_to_pepind.read((char*)psmind_to_pepind,sizeof(int)*num_psms);
+ f_psmind_to_pepind.close();
+ fname.str("");
+
+ //psmind_to_scan
+ fname << in_dir << "/psmind_to_scan";
+ ifstream f_psmind_to_scan(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_scan.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_scan = new int[num_psms];
+ f_psmind_to_scan.read((char*)psmind_to_scan,sizeof(int)*num_psms);
+ f_psmind_to_scan.close();
+ fname.str("");
+
+ //psmind_to_charge
+ fname << in_dir << "/psmind_to_charge";
+ ifstream f_psmind_to_charge(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_charge.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_charge = new int[num_psms];
+ f_psmind_to_charge.read((char*)psmind_to_charge,sizeof(int)*num_psms);
+ f_psmind_to_charge.close();
+ fname.str("");
+
+ //psmind_to_xcorr
+ fname << in_dir << "/psmind_to_xcorr";
+ ifstream f_psmind_to_xcorr(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_xcorr.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_xcorr = new double[num_psms];
+ f_psmind_to_xcorr.read((char*)psmind_to_xcorr,sizeof(double)*num_psms);
+ f_psmind_to_xcorr.close();
+ fname.str("");
+
+ //psmind_to_deltaCn
+ fname << in_dir << "/psmind_to_deltaCn";
+ ifstream f_psmind_to_deltaCn(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_deltaCn.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_deltaCn = new double[num_psms];
+ f_psmind_to_deltaCn.read((char*)psmind_to_deltaCn,sizeof(double)*num_psms);
+ f_psmind_to_deltaCn.close();
+ fname.str("");
+
+ //psmind_to_spscore
+ fname << in_dir << "/psmind_to_spscore";
+ ifstream f_psmind_to_spscore(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_spscore.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_spscore = new double[num_psms];
+ f_psmind_to_spscore.read((char*)psmind_to_spscore,sizeof(double)*num_psms);
+ f_psmind_to_spscore.close();
+ fname.str("");
+
+ //psmind_to_calculated_mass
+ fname << in_dir << "/psmind_to_calculated_mass";
+ ifstream f_psmind_to_calculated_mass(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_calculated_mass.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_calculated_mass = new double[num_psms];
+ f_psmind_to_calculated_mass.read((char*)psmind_to_calculated_mass,sizeof(double)*num_psms);
+ f_psmind_to_calculated_mass.close();
+ fname.str("");
+
+ //psmind_to_precursor_mass
+ fname << in_dir << "/psmind_to_precursor_mass";
+ ifstream f_psmind_to_precursor_mass(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_precursor_mass.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_precursor_mass = new double[num_psms];
+ f_psmind_to_precursor_mass.read((char*)psmind_to_precursor_mass,sizeof(double)*num_psms);
+ f_psmind_to_precursor_mass.close();
+ fname.str("");
+
+ //fileind_to_fname
+ fname << in_dir << "/fileind_to_fname";
+ ifstream f_fileind_to_fname(fname.str().c_str(),ios::binary);
+ if(!f_fileind_to_fname.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ int ind;
+ string filename;
+ f_fileind_to_fname >> ind;
+ f_fileind_to_fname >> filename;
+ while(!f_fileind_to_fname.eof())
+ {
+ fileind_to_fname[ind] = filename;
+ f_fileind_to_fname >> ind;
+ f_fileind_to_fname >> filename;
+ }
+ f_fileind_to_fname.close();
+ fname.str("");
+
+ //psmind_to_filename
+ fname << in_dir << "/psmind_to_fileind";
+ ifstream f_psmind_to_fileind(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_fileind.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_fileind = new int[num_psms];
+ f_psmind_to_fileind.read((char*)psmind_to_fileind,sizeof(int)*num_psms);
+ f_psmind_to_fileind.close();
+ fname.str("");
+
+ //ind_to_pep
+ fname << in_dir << "/ind_to_pep";
+ ifstream f_ind_to_pep(fname.str().c_str(),ios::binary);
+ string pep;
+ f_ind_to_pep >> ind;
+ f_ind_to_pep >> pep;
+ while(!f_ind_to_pep.eof())
+ {
+ ind_to_pep[ind] = pep;
+ f_ind_to_pep >> ind;
+ f_ind_to_pep >> pep;
+ }
+ f_ind_to_pep.close();
+ fname.str("");
+
+ //ind_to_prot
+ fname << in_dir << "/ind_to_prot";
+ ifstream f_ind_to_prot(fname.str().c_str(),ios::binary);
+
+ string prot;
+ f_ind_to_prot >> ind;
+ f_ind_to_prot >> prot;
+ while(!f_ind_to_prot.eof())
+ {
+ ind_to_prot[ind] = prot;
+ f_ind_to_prot >> ind;
+ f_ind_to_prot >> prot;
+ }
+ f_ind_to_prot.close();
+ fname.str("");
+
+ //pepind_to_protinds
+ fname << in_dir << "/pepind_to_protinds";
+ ifstream f_pepind_to_protinds(fname.str().c_str(),ios::binary);
+ if(!f_pepind_to_protinds.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ pepind_to_protinds.load(f_pepind_to_protinds);
+ f_pepind_to_protinds.close();
+ fname.str("");
+
+ //psmind_to_Sp_rank
+ fname << in_dir << "/psmind_to_sp_rank";
+ ifstream f_psmind_to_sp_rank(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_sp_rank.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+
+ psmind_to_sp_rank = new int[num_psms];
+ f_psmind_to_sp_rank.read((char*)psmind_to_sp_rank,sizeof(int)*num_psms);
+ f_psmind_to_sp_rank.close();
+ fname.str("");
+
+ //psmind_to_xcorr_rank
+ fname << in_dir << "/psmind_to_xcorr_rank";
+ ifstream f_psmind_to_xcorr_rank(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_xcorr_rank.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_xcorr_rank = new int[num_psms];
+ f_psmind_to_xcorr_rank.read((char*)psmind_to_xcorr_rank,sizeof(int)*num_psms);
+ f_psmind_to_xcorr_rank.close();
+ fname.str("");
+
+ //psmind_to_by_ions_matched
+ fname << in_dir << "/psmind_to_by_ions_matched";
+ ifstream f_psmind_to_by_ions_matched(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_by_ions_matched.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_by_ions_matched = new double[num_psms];
+ f_psmind_to_by_ions_matched.read((char*)psmind_to_by_ions_matched,sizeof(double)*num_psms);
+ f_psmind_to_by_ions_matched.close();
+ fname.str("");
+
+ //psmind_to_by_ions_total
+ fname << in_dir << "/psmind_to_by_ions_total";
+ ifstream f_psmind_to_by_ions_total(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_by_ions_total.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_by_ions_total= new double[num_psms];
+ f_psmind_to_by_ions_total.read((char*)psmind_to_by_ions_total,sizeof(double)*num_psms);
+ f_psmind_to_by_ions_total.close();
+ fname.str("");
+
+ //psmind_to_matches_spectrum
+ fname << in_dir << "/psmind_to_matches_spectrum";
+ ifstream f_psmind_to_matches_spectrum(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_matches_spectrum.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_matches_spectrum = new int[num_psms];
+ f_psmind_to_matches_spectrum.read((char*)psmind_to_matches_spectrum,sizeof(int)*num_psms);
+ f_psmind_to_matches_spectrum.close();
+ fname.str("");
+
+ //psmind_to_peptide_position
+ fname << in_dir << "/psmind_to_peptide_position";
+ ifstream f_psmind_to_peptide_position(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_peptide_position.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_peptide_position= new int[num_psms];
+ f_psmind_to_peptide_position.read((char*)psmind_to_peptide_position,sizeof(int)*num_psms);
+ f_psmind_to_peptide_position.close();
+ fname.str("");
+
+}
+
+void Dataset :: clear_data_psm_results()
+{
+ delete [] psmind_to_label; psmind_to_label = (int*)0;
+ delete [] psmind_to_pepind; psmind_to_pepind = (int*)0;
+ delete [] psmind_to_scan; psmind_to_scan = (int*)0;
+ delete [] psmind_to_charge; psmind_to_charge = (int*)0;
+ delete [] psmind_to_xcorr; psmind_to_xcorr = (double*)0;
+ delete [] psmind_to_precursor_mass; psmind_to_precursor_mass = (double*)0;
+ fileind_to_fname.clear();
+ delete [] psmind_to_fileind; psmind_to_fileind = (int*)0;
+ delete [] psmind_to_sp_rank; psmind_to_sp_rank=(int*)0;//sp rank
+ delete [] psmind_to_xcorr_rank; psmind_to_xcorr_rank=(int*)0;//xcorr rank
+ // distinct matches/spectrum
+ delete[] psmind_to_matches_spectrum; psmind_to_matches_spectrum=(int*)0;
+ delete [] psmind_to_by_ions_total; psmind_to_by_ions_total=(double*)0; //b/y ions total
+ delete [] psmind_to_by_ions_matched; psmind_to_by_ions_matched=(double*)0; //by ions matched
+ delete [] psmind_to_peptide_position; psmind_to_peptide_position=(int*)0; //position of peptide in
+ //the begining of protein
+ ind_to_pep.clear();
+ ind_to_prot.clear();
+ pepind_to_protinds.clear();
+}
+
+string& Dataset :: psmind2fname(int psmind)
+{
+ int fileind = psmind_to_fileind[psmind];
+ return fileind_to_fname[fileind];
+}
+
+
+/************************************************************/
+void Dataset :: load_data_prot_training()
+{
+
+ ostringstream fname;
+ fname << in_dir << "/summary";
+ ifstream f_summary(fname.str().c_str());
+ if(!f_summary.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ f_summary >> num_features;
+ f_summary >> num_psms;
+ f_summary >> num_pos_psms;
+ f_summary >> num_neg_psms;
+ f_summary >> num_pep;
+ f_summary >> num_pos_pep;
+ f_summary >> num_neg_pep;
+ f_summary >> num_prot;
+ f_summary >> num_pos_prot;
+ f_summary >> num_neg_prot;
+ f_summary.close();
+ fname.str("");
+
+ //psm features
+ fname << in_dir << "/" << "psm";
+ ifstream f_psm_feat(fname.str().c_str(),ios::binary);
+ if(!f_psm_feat.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_features = new double[num_psms*num_features];
+ f_psm_feat.read((char*)psmind_to_features,sizeof(double)*num_psms*num_features);
+ f_psm_feat.close();
+ fname.str("");
+
+
+ //pepind_to_psminds
+ fname << in_dir << "/pepind_to_psminds";
+ ifstream f_pepind_to_psminds(fname.str().c_str(),ios::binary);
+ if(!f_pepind_to_psminds.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ pepind_to_psminds.load(f_pepind_to_psminds);
+ f_pepind_to_psminds.close();
+ fname.str("");
+
+ //protind_to_num_all_pep
+ fname << in_dir << "/protind_to_num_all_pep";
+ ifstream f_protind_to_num_all_pep(fname.str().c_str(),ios::binary);
+ if(!f_protind_to_num_all_pep.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ protind_to_num_all_pep = new int[num_prot];
+ f_protind_to_num_all_pep.read((char*)protind_to_num_all_pep,sizeof(int)*num_prot);
+ f_protind_to_num_all_pep.close();
+ fname.str("");
+
+ //protind_to_pepinds
+ fname << in_dir << "/protind_to_pepinds";
+ ifstream f_protind_to_pepinds(fname.str().c_str(),ios::binary);
+ if(!f_protind_to_pepinds.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ protind_to_pepinds.load(f_protind_to_pepinds);
+ f_protind_to_pepinds.close();
+ fname.str("");
+
+ //pepind_to_protinds
+ fname << in_dir << "/pepind_to_protinds";
+ ifstream f_pepind_to_protinds(fname.str().c_str(),ios::binary);
+ if(!f_pepind_to_protinds.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ pepind_to_protinds.load(f_pepind_to_protinds);
+ f_pepind_to_protinds.close();
+ fname.str("");
+
+}
+
+void Dataset :: clear_data_prot_training()
+{
+ delete [] psmind_to_features; psmind_to_features = (double*)0;
+ delete [] protind_to_num_all_pep; protind_to_num_all_pep = (int*)0;
+}
+
+void Dataset :: load_labels_prot_training()
+{
+
+ ostringstream fname;
+ fname << in_dir << "/summary";
+ ifstream f_summary(fname.str().c_str());
+ if(!f_summary.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ f_summary >> num_features;
+ f_summary >> num_psms;
+ f_summary >> num_pos_psms;
+ f_summary >> num_neg_psms;
+ f_summary >> num_pep;
+ f_summary >> num_pos_pep;
+ f_summary >> num_neg_pep;
+ f_summary >> num_prot;
+ f_summary >> num_pos_prot;
+ f_summary >> num_neg_prot;
+ f_summary.close();
+ fname.str("");
+
+ //psmind_to_label
+ fname << in_dir << "/psmind_to_label";
+ ifstream f_psmind_to_label(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_label.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_label = new int[num_psms];
+ f_psmind_to_label.read((char*)psmind_to_label,sizeof(int)*num_psms);
+ f_psmind_to_label.close();
+ fname.str("");
+
+ //pepind_to_label
+ fname << in_dir << "/pepind_to_label";
+ ifstream f_pepind_to_label(fname.str().c_str(),ios::binary);
+ if(!f_pepind_to_label.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ pepind_to_label = new int[num_pep];
+ f_pepind_to_label.read((char*)pepind_to_label,sizeof(int)*num_pep);
+ f_pepind_to_label.close();
+ fname.str("");
+
+ //protind_to_label
+ fname << in_dir << "/protind_to_label";
+ ifstream f_protind_to_label(fname.str().c_str(),ios::binary);
+ if(!f_protind_to_label.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ protind_to_label = new int[num_prot];
+ f_protind_to_label.read((char*)protind_to_label,sizeof(int)*num_prot);
+ f_protind_to_label.close();
+ fname.str("");
+
+ //ind_to_pep
+ fname << in_dir << "/ind_to_pep";
+ ifstream f_ind_to_pep(fname.str().c_str(),ios::binary);
+ int ind;
+ string pep;
+ f_ind_to_pep >> ind;
+ f_ind_to_pep >> pep;
+ while(!f_ind_to_pep.eof()){
+ ind_to_pep[ind] = pep;
+ f_ind_to_pep >> ind;
+ f_ind_to_pep >> pep;
+ }
+ f_ind_to_pep.close();
+ fname.str("");
+
+
+}
+
+void Dataset :: clear_labels_prot_training()
+{
+ delete [] psmind_to_label; psmind_to_label = (int*)0;
+ delete [] pepind_to_label; pepind_to_label = (int*)0;
+ delete [] protind_to_label; protind_to_label = (int*)0;
+ ind_to_pep.clear();
+}
+
+
+void Dataset :: load_data_all_results(){
+
+ ostringstream fname;
+
+ //ind_to_pep
+ fname << in_dir << "/ind_to_pep";
+ ifstream f_ind_to_pep(fname.str().c_str(),ios::binary);
+ int ind;
+ string pep;
+ f_ind_to_pep >> ind;
+ f_ind_to_pep >> pep;
+ while(!f_ind_to_pep.eof()){
+ ind_to_pep[ind] = pep;
+ f_ind_to_pep >> ind;
+ f_ind_to_pep >> pep;
+ }
+ f_ind_to_pep.close();
+ fname.str("");
+
+ //ind_to_prot
+ fname << in_dir << "/ind_to_prot";
+ ifstream f_ind_to_prot(fname.str().c_str(),ios::binary);
+
+ string prot;
+ f_ind_to_prot >> ind;
+ f_ind_to_prot >> prot;
+ while(!f_ind_to_prot.eof()){
+ ind_to_prot[ind] = prot;
+ f_ind_to_prot >> ind;
+ f_ind_to_prot >> prot;
+ }
+ f_ind_to_prot.close();
+ fname.str("");
+
+ //protind_to_length
+ fname << in_dir << "/protind_to_length";
+ ifstream f_protind_to_length(fname.str().c_str(),ios::binary);
+ if(!f_protind_to_length.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ protind_to_length = new int[num_prot];
+ f_protind_to_length.read((char*)protind_to_length,sizeof(int)*num_prot);
+ f_protind_to_length.close();
+ fname.str("");
+
+
+ //protind_to_label
+ fname << in_dir << "/protind_to_label";
+ ifstream f_protind_to_label(fname.str().c_str(),ios::binary);
+ if(!f_protind_to_label.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ protind_to_label = new int[num_prot];
+ f_protind_to_label.read((char*)protind_to_label,sizeof(int)*num_prot);
+ f_protind_to_label.close();
+ fname.str("");
+
+ //psm data
+
+ //psmind_to_pepind
+ fname << in_dir << "/psmind_to_pepind";
+ ifstream f_psmind_to_pepind(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_pepind.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_pepind = new int[num_psms];
+ f_psmind_to_pepind.read((char*)psmind_to_pepind,sizeof(int)*num_psms);
+ f_psmind_to_pepind.close();
+ fname.str("");
+
+ //psmind_to_scan
+ fname << in_dir << "/psmind_to_scan";
+ ifstream f_psmind_to_scan(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_scan.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_scan = new int[num_psms];
+ f_psmind_to_scan.read((char*)psmind_to_scan,sizeof(int)*num_psms);
+ f_psmind_to_scan.close();
+ fname.str("");
+
+ //psmind_to_charge
+ fname << in_dir << "/psmind_to_charge";
+ ifstream f_psmind_to_charge(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_charge.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_charge = new int[num_psms];
+ f_psmind_to_charge.read((char*)psmind_to_charge,sizeof(int)*num_psms);
+ f_psmind_to_charge.close();
+ fname.str("");
+
+ //psmind_to_xcorr
+ fname << in_dir << "/psmind_to_xcorr";
+ ifstream f_psmind_to_xcorr(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_xcorr.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_xcorr = new double[num_psms];
+ f_psmind_to_xcorr.read((char*)psmind_to_xcorr,sizeof(double)*num_psms);
+ f_psmind_to_xcorr.close();
+ fname.str("");
+
+ //psmind_to_deltaCn
+ fname << in_dir << "/psmind_to_deltaCn";
+ ifstream f_psmind_to_deltaCn(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_deltaCn.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_deltaCn = new double[num_psms];
+ f_psmind_to_deltaCn.read((char*)psmind_to_deltaCn,sizeof(double)*num_psms);
+ f_psmind_to_deltaCn.close();
+ fname.str("");
+
+ //psmind_to_sp_score
+ fname << in_dir << "/psmind_to_spscore";
+ ifstream f_psmind_to_spscore(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_spscore.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_spscore = new double[num_psms];
+ f_psmind_to_spscore.read((char*)psmind_to_spscore,sizeof(double)*num_psms);
+ f_psmind_to_spscore.close();
+ fname.str("");
+
+ //psmind_to_calculated_mass
+ fname << in_dir << "/psmind_to_calculated_mass";
+ ifstream f_psmind_to_calculated_mass(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_calculated_mass.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_calculated_mass = new double[num_psms];
+ f_psmind_to_calculated_mass.read((char*)psmind_to_calculated_mass,sizeof(double)*num_psms);
+ f_psmind_to_calculated_mass.close();
+ fname.str("");
+
+ //psmind_to_precursor_mass
+ fname << in_dir << "/psmind_to_precursor_mass";
+ ifstream f_psmind_to_precursor_mass(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_precursor_mass.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_precursor_mass = new double[num_psms];
+ f_psmind_to_precursor_mass.read((char*)psmind_to_precursor_mass,sizeof(double)*num_psms);
+ f_psmind_to_precursor_mass.close();
+ fname.str("");
+
+ //fileind_to_fname
+ fname << in_dir << "/fileind_to_fname";
+ ifstream f_fileind_to_fname(fname.str().c_str(),ios::binary);
+ if(!f_fileind_to_fname.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+
+ string filename;
+ f_fileind_to_fname >> ind;
+ f_fileind_to_fname >> filename;
+ while(!f_fileind_to_fname.eof()){
+ fileind_to_fname[ind] = filename;
+ f_fileind_to_fname >> ind;
+ f_fileind_to_fname >> filename;
+ }
+ f_fileind_to_fname.close();
+ fname.str("");
+
+ //psmind_to_filename
+ fname << in_dir << "/psmind_to_fileind";
+ ifstream f_psmind_to_fileind(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_fileind.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_fileind = new int[num_psms];
+ f_psmind_to_fileind.read((char*)psmind_to_fileind,sizeof(int)*num_psms);
+ f_psmind_to_fileind.close();
+ fname.str("");
+
+ //psmind_to_sp_rank
+ fname << in_dir << "/psmind_to_sp_rank";
+ ifstream f_psmind_to_sp_rank(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_sp_rank.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_sp_rank = new int[num_psms];
+ f_psmind_to_sp_rank.read((char*)psmind_to_sp_rank,sizeof(int)*num_psms);
+ f_psmind_to_sp_rank.close();
+ fname.str("");
+
+ //psmind_to_xcorr_rank
+ fname << in_dir << "/psmind_to_xcorr_rank";
+ ifstream f_psmind_to_xcorr_rank(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_xcorr_rank.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_xcorr_rank = new int[num_psms];
+ f_psmind_to_xcorr_rank.read((char*)psmind_to_xcorr_rank,sizeof(int)*num_psms);
+ f_psmind_to_xcorr_rank.close();
+ fname.str("");
+
+ //psmind_to_match_spectrum
+ fname << in_dir << "/psmind_to_matches_spectrum";
+ ifstream f_psmind_to_matches_spectrum(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_matches_spectrum.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_matches_spectrum = new int[num_psms];
+ f_psmind_to_matches_spectrum.read((char*)psmind_to_matches_spectrum,sizeof(int)*num_psms);
+ f_psmind_to_matches_spectrum.close();
+ fname.str("");
+
+ //psmind_to_by_ions_matched
+ fname << in_dir << "/psmind_to_by_ions_matched";
+ ifstream f_psmind_to_by_ions_matched(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_by_ions_matched.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_by_ions_matched = new double[num_psms];
+ f_psmind_to_by_ions_matched.read((char*)psmind_to_by_ions_matched,sizeof(double)*num_psms);
+ f_psmind_to_by_ions_matched.close();
+ fname.str("");
+
+ //psmind_to_by_ions_total
+ fname << in_dir << "/psmind_to_by_ions_total";
+ ifstream f_psmind_to_by_ions_total(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_by_ions_total.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_by_ions_total = new double[num_psms];
+ f_psmind_to_by_ions_total.read((char*)psmind_to_by_ions_total,sizeof(double)*num_psms);
+ f_psmind_to_by_ions_total.close();
+ fname.str("");
+
+ //psmind_to_peptide_position
+ fname << in_dir << "/psmind_to_peptide_position";
+ ifstream f_psmind_to_peptide_position(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_peptide_position.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_peptide_position = new int[num_psms];
+ f_psmind_to_peptide_position.read((char*)psmind_to_peptide_position,sizeof(int)*num_psms);
+ f_psmind_to_peptide_position.close();
+ fname.str("");
+}
+
+void Dataset :: clear_data_all_results()
+{
+ clear_data_psm_results();
+ delete [] protind_to_label; protind_to_label = (int*)0;
+ delete [] protind_to_length; protind_to_length = (int*)0;
+ protind_to_pepinds.clear();
+}
+
+
+
+
+/******************************************************/
+
+void Dataset :: normalize_psms()
+{
+ for (int i = 0; i < num_features; i++)
+ {
+ double mean = 0;
+ for (int j = 0; j < num_psms; j++)
+ mean += psmind_to_features[num_features*j+i];
+ mean /= num_psms;
+
+ double std = 0;
+ for (int j = 0; j < num_psms; j++)
+ {
+ psmind_to_features[num_features*j+i] -= mean;
+ std += psmind_to_features[num_features*j+i]*psmind_to_features[num_features*j+i];
+ }
+ std = sqrt(std/num_psms);
+
+ for (int j = 0; j < num_psms; j++)
+ {
+ if(std > 0)
+ psmind_to_features[num_features*j+i] /= std;
+ }
+
+ double sm = 0;
+ for (int j = 0; j < num_psms; j++)
+ {
+ sm += psmind_to_features[num_features*j+i]*psmind_to_features[num_features*j+i];
+ }
+ //cout << i << " " << sm/num_psms << endl;
+ }
+}
+
+
+int Dataset :: print_features(string &filename)
+{
+ ofstream os(filename.c_str());
+ if(!os.is_open())
+ return 0;
+
+ delete [] psmind_to_label; psmind_to_label = (int*)0;
+ delete [] psmind_to_scan; psmind_to_scan = (int*)0;
+
+ ostringstream fname;
+ //psmind_to_label
+ fname << in_dir << "/psmind_to_label";
+ ifstream f_psmind_to_label(fname.str().c_str(),ios::binary);
+ psmind_to_label = new int[num_psms];
+ f_psmind_to_label.read((char*)psmind_to_label,sizeof(int)*num_psms);
+ f_psmind_to_label.close();
+ fname.str("");
+
+ //psmind_to_scan
+ fname << in_dir << "/psmind_to_scan";
+ ifstream f_psmind_to_scan(fname.str().c_str(),ios::binary);
+ psmind_to_scan = new int[num_psms];
+ f_psmind_to_scan.read((char*)psmind_to_scan,sizeof(int)*num_psms);
+ f_psmind_to_scan.close();
+ fname.str("");
+ //print features header
+ os<<"scan\t"<<"label\t";
+ for(unsigned i=0;i<features_header_.size()-1;i++)
+ os<<features_header_[i]<<"\t";
+ os<<features_header_[features_header_.size()-1]<<endl;
+
+ for (int j = 0; j < num_psms; j++){
+ os << psmind_to_scan[j] << "\t";
+ os << psmind_to_label[j] << "\t";
+ for (int i = 0; i < num_features-1; i++){
+ os << psmind_to_features[num_features*j+i] << "\t";
+ }
+ os << psmind_to_features[num_features*j+(num_features-1)] << endl;
+ }
+ os.close();
+
+ delete [] psmind_to_label; psmind_to_label = (int*)0;
+ delete [] psmind_to_scan; psmind_to_scan = (int*)0;
+ return 1;
+}
+
+/*****************************************************/
+void Dataset :: load_data_pep_training()
+{
+
+ ostringstream fname;
+ fname << in_dir << "/summary";
+ ifstream f_summary(fname.str().c_str());
+ if(!f_summary.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ f_summary >> num_features;
+ f_summary >> num_psms;
+ f_summary >> num_pos_psms;
+ f_summary >> num_neg_psms;
+ f_summary >> num_pep;
+ f_summary >> num_pos_pep;
+ f_summary >> num_neg_pep;
+ f_summary >> num_prot;
+ f_summary >> num_pos_prot;
+ f_summary >> num_neg_prot;
+ f_summary.close();
+ fname.str("");
+
+ //psm features
+ fname << in_dir << "/" << "psm";
+ ifstream f_psm_feat(fname.str().c_str(),ios::binary);
+ if(!f_psm_feat.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_features = new double[num_psms*num_features];
+ f_psm_feat.read((char*)psmind_to_features,sizeof(double)*num_psms*num_features);
+ f_psm_feat.close();
+ fname.str("");
+
+
+ //pepind_to_psminds
+ fname << in_dir << "/pepind_to_psminds";
+ ifstream f_pepind_to_psminds(fname.str().c_str(),ios::binary);
+ if(!f_pepind_to_psminds.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ pepind_to_psminds.load(f_pepind_to_psminds);
+ f_pepind_to_psminds.close();
+ fname.str("");
+
+}
+
+
+void Dataset :: clear_data_pep_training()
+{
+ delete [] psmind_to_features; psmind_to_features = (double*)0;
+}
+
+void Dataset :: load_labels_pep_training()
+{
+
+ ostringstream fname;
+ fname << in_dir << "/summary";
+ ifstream f_summary(fname.str().c_str());
+ if(!f_summary.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ f_summary >> num_features;
+ f_summary >> num_psms;
+ f_summary >> num_pos_psms;
+ f_summary >> num_neg_psms;
+ f_summary >> num_pep;
+ f_summary >> num_pos_pep;
+ f_summary >> num_neg_pep;
+ f_summary >> num_prot;
+ f_summary >> num_pos_prot;
+ f_summary >> num_neg_prot;
+ f_summary.close();
+ fname.str("");
+
+ //psmind_to_label
+ fname << in_dir << "/psmind_to_label";
+ ifstream f_psmind_to_label(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_label.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_label = new int[num_psms];
+ f_psmind_to_label.read((char*)psmind_to_label,sizeof(int)*num_psms);
+ f_psmind_to_label.close();
+ fname.str("");
+
+ //pepind_to_label
+ fname << in_dir << "/pepind_to_label";
+ ifstream f_pepind_to_label(fname.str().c_str(),ios::binary);
+ if(!f_pepind_to_label.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ pepind_to_label = new int[num_pep];
+ f_pepind_to_label.read((char*)pepind_to_label,sizeof(int)*num_pep);
+ f_pepind_to_label.close();
+ fname.str("");
+}
+
+void Dataset :: clear_labels_pep_training()
+{
+ delete [] psmind_to_label; psmind_to_label = (int*)0;
+ delete [] pepind_to_label; pepind_to_label = (int*)0;
+}
+
+void Dataset :: load_data_pep_results()
+{
+
+ ostringstream fname;
+
+ //ind_to_pep
+ fname << in_dir << "/ind_to_pep";
+ ifstream f_ind_to_pep(fname.str().c_str(),ios::binary);
+ int ind;
+ string pep;
+ f_ind_to_pep >> ind;
+ f_ind_to_pep >> pep;
+ while(!f_ind_to_pep.eof()){
+ ind_to_pep[ind] = pep;
+ f_ind_to_pep >> ind;
+ f_ind_to_pep >> pep;
+ }
+ f_ind_to_pep.close();
+ fname.str("");
+
+ //pepind_to_protinds
+ fname << in_dir << "/pepind_to_protinds";
+ ifstream f_pepind_to_protinds(fname.str().c_str(),ios::binary);
+ if(!f_pepind_to_protinds.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ pepind_to_protinds.load(f_pepind_to_protinds);
+ f_pepind_to_protinds.close();
+ fname.str("");
+
+ //ind_to_prot
+ fname << in_dir << "/ind_to_prot";
+ ifstream f_ind_to_prot(fname.str().c_str(),ios::binary);
+
+ string prot;
+ f_ind_to_prot >> ind;
+ f_ind_to_prot >> prot;
+ while(!f_ind_to_prot.eof()){
+ ind_to_prot[ind] = prot;
+ f_ind_to_prot >> ind;
+ f_ind_to_prot >> prot;
+ }
+ f_ind_to_prot.close();
+ fname.str("");
+
+ //protind_to_length
+ fname << in_dir << "/protind_to_length";
+ ifstream f_protind_to_length(fname.str().c_str(),ios::binary);
+ if(!f_protind_to_length.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ protind_to_length = new int[num_prot];
+ f_protind_to_length.read((char*)protind_to_length,sizeof(int)*num_prot);
+ f_protind_to_length.close();
+ fname.str("");
+
+
+ //protind_to_label
+ fname << in_dir << "/protind_to_label";
+ ifstream f_protind_to_label(fname.str().c_str(),ios::binary);
+ if(!f_protind_to_label.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ protind_to_label = new int[num_prot];
+ f_protind_to_label.read((char*)protind_to_label,sizeof(int)*num_prot);
+ f_protind_to_label.close();
+ fname.str("");
+
+
+
+ //psm data
+
+ //psmind_to_pepind
+ fname << in_dir << "/psmind_to_pepind";
+ ifstream f_psmind_to_pepind(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_pepind.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_pepind = new int[num_psms];
+ f_psmind_to_pepind.read((char*)psmind_to_pepind,sizeof(int)*num_psms);
+ f_psmind_to_pepind.close();
+ fname.str("");
+
+ //psmind_to_scan
+ fname << in_dir << "/psmind_to_scan";
+ ifstream f_psmind_to_scan(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_scan.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_scan = new int[num_psms];
+ f_psmind_to_scan.read((char*)psmind_to_scan,sizeof(int)*num_psms);
+ f_psmind_to_scan.close();
+ fname.str("");
+
+ //psmind_to_charge
+ fname << in_dir << "/psmind_to_charge";
+ ifstream f_psmind_to_charge(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_charge.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_charge = new int[num_psms];
+ f_psmind_to_charge.read((char*)psmind_to_charge,sizeof(int)*num_psms);
+ f_psmind_to_charge.close();
+ fname.str("");
+
+ //psmind_to_xcorr
+ fname << in_dir << "/psmind_to_xcorr";
+ ifstream f_psmind_to_xcorr(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_xcorr.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_xcorr = new double[num_psms];
+ f_psmind_to_xcorr.read((char*)psmind_to_xcorr,sizeof(double)*num_psms);
+ f_psmind_to_xcorr.close();
+ fname.str("");
+
+ //psmind_to_deltaCn
+ fname << in_dir << "/psmind_to_deltaCn";
+ ifstream f_psmind_to_deltaCn(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_deltaCn.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_deltaCn = new double[num_psms];
+ f_psmind_to_deltaCn.read((char*)psmind_to_deltaCn,sizeof(double)*num_psms);
+ f_psmind_to_deltaCn.close();
+ fname.str("");
+
+ //psmind_to_sp_score
+ fname << in_dir << "/psmind_to_spscore";
+ ifstream f_psmind_to_spscore(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_spscore.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_spscore = new double[num_psms];
+ f_psmind_to_spscore.read((char*)psmind_to_spscore,sizeof(double)*num_psms);
+ f_psmind_to_spscore.close();
+ fname.str("");
+
+ //psmind_to_calculated_mass
+ fname << in_dir << "/psmind_to_calculated_mass";
+ ifstream f_psmind_to_calculated_mass(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_calculated_mass.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_calculated_mass = new double[num_psms];
+ f_psmind_to_calculated_mass.read((char*)psmind_to_calculated_mass,sizeof(double)*num_psms);
+ f_psmind_to_calculated_mass.close();
+ fname.str("");
+
+ //psmind_to_precursor_mass
+ fname << in_dir << "/psmind_to_precursor_mass";
+ ifstream f_psmind_to_precursor_mass(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_precursor_mass.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_precursor_mass = new double[num_psms];
+ f_psmind_to_precursor_mass.read((char*)psmind_to_precursor_mass,sizeof(double)*num_psms);
+ f_psmind_to_precursor_mass.close();
+ fname.str("");
+
+ //fileind_to_fname
+ fname << in_dir << "/fileind_to_fname";
+ ifstream f_fileind_to_fname(fname.str().c_str(),ios::binary);
+ if(!f_fileind_to_fname.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+
+ string filename;
+ f_fileind_to_fname >> ind;
+ f_fileind_to_fname >> filename;
+ while(!f_fileind_to_fname.eof()){
+ fileind_to_fname[ind] = filename;
+ f_fileind_to_fname >> ind;
+ f_fileind_to_fname >> filename;
+ }
+ f_fileind_to_fname.close();
+ fname.str("");
+
+ //psmind_to_filename
+ fname << in_dir << "/psmind_to_fileind";
+ ifstream f_psmind_to_fileind(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_fileind.is_open())
+ {
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_fileind = new int[num_psms];
+ f_psmind_to_fileind.read((char*)psmind_to_fileind,sizeof(int)*num_psms);
+ f_psmind_to_fileind.close();
+ fname.str("");
+
+ //psmind_to_sp_rank
+ fname << in_dir << "/psmind_to_sp_rank";
+ ifstream f_psmind_to_sp_rank(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_sp_rank.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_sp_rank = new int[num_psms];
+ f_psmind_to_sp_rank.read((char*)psmind_to_sp_rank,sizeof(int)*num_psms);
+ f_psmind_to_sp_rank.close();
+ fname.str("");
+
+ //psmind_to_xcorr_rank
+ fname << in_dir << "/psmind_to_xcorr_rank";
+ ifstream f_psmind_to_xcorr_rank(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_xcorr_rank.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_xcorr_rank = new int[num_psms];
+ f_psmind_to_xcorr_rank.read((char*)psmind_to_xcorr_rank,sizeof(int)*num_psms);
+ f_psmind_to_xcorr_rank.close();
+ fname.str("");
+
+ //psmind_to_match_spectrum
+ fname << in_dir << "/psmind_to_matches_spectrum";
+ ifstream f_psmind_to_matches_spectrum(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_matches_spectrum.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_matches_spectrum = new int[num_psms];
+ f_psmind_to_matches_spectrum.read((char*)psmind_to_matches_spectrum,sizeof(int)*num_psms);
+ f_psmind_to_matches_spectrum.close();
+ fname.str("");
+
+ //psmind_to_by_ions_matched
+ fname << in_dir << "/psmind_to_by_ions_matched";
+ ifstream f_psmind_to_by_ions_matched(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_by_ions_matched.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_by_ions_matched = new double[num_psms];
+ f_psmind_to_by_ions_matched.read((char*)psmind_to_by_ions_matched,sizeof(double)*num_psms);
+ f_psmind_to_by_ions_matched.close();
+ fname.str("");
+
+ //psmind_to_by_ions_total
+ fname << in_dir << "/psmind_to_by_ions_total";
+ ifstream f_psmind_to_by_ions_total(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_by_ions_total.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_by_ions_total = new double[num_psms];
+ f_psmind_to_by_ions_total.read((char*)psmind_to_by_ions_total,sizeof(double)*num_psms);
+ f_psmind_to_by_ions_total.close();
+ fname.str("");
+
+ //psmind_to_peptide_position
+ fname << in_dir << "/psmind_to_peptide_position";
+ ifstream f_psmind_to_peptide_position(fname.str().c_str(),ios::binary);
+ if(!f_psmind_to_peptide_position.is_open()){
+ cout << "could not open file " << fname.str() << " for reading data\n";
+ return;
+ }
+ psmind_to_peptide_position = new int[num_psms];
+ f_psmind_to_peptide_position.read((char*)psmind_to_peptide_position,sizeof(int)*num_psms);
+ f_psmind_to_peptide_position.close();
+ fname.str("");
+}
+
+void Dataset :: clear_data_pep_results()
+{
+ clear_data_psm_results();
+}
+
+
+
+/*
+ * Local Variable
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+/*
+int main()
+{
+ Dataset* d = new Dataset();
+
+ d->set_input_dir("yeast");
+ d->load_prot_data();
+ //d->normalize_psms();
+ return 0;
+}
+*/
diff --git a/src/app/qranker-barista/DataSetCrux.h b/src/app/qranker-barista/DataSetCrux.h
new file mode 100644
index 0000000..2ffa9d8
--- /dev/null
+++ b/src/app/qranker-barista/DataSetCrux.h
@@ -0,0 +1,141 @@
+#ifndef DATASET_H_
+#define DATASET_H_
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <assert.h>
+#include <cmath>
+#include <map>
+#include "BipartiteGraph.h"
+using namespace std;
+
+
+
+class Dataset
+{
+ public:
+
+ Dataset();
+ ~Dataset();
+
+ void load_data_psm_training();
+ void clear_data_psm_training();
+ void load_labels_psm_training();
+ void clear_labels_psm_training();
+ void load_data_psm_results();
+ void clear_data_psm_results();
+
+ void load_data_prot_training();
+ void clear_data_prot_training();
+ void load_labels_prot_training();
+ void clear_labels_prot_training();
+ void load_data_all_results();
+ void clear_data_all_results();
+ void load_data_pep_training();
+ void clear_data_pep_training();
+ void load_labels_pep_training();
+ void clear_labels_pep_training();
+ void load_data_pep_results();
+ void clear_data_pep_results();
+
+ inline void set_input_dir(string input_dir){in_dir = input_dir;}
+ void normalize_psms();
+ int print_features(string &filename);
+
+ inline double* psmind2features(int psmind){return (psmind_to_features+num_features*psmind);}
+ inline int psmind2label(int psmind){return psmind_to_label[psmind];}
+ inline int psmind2scan(int psmind){return psmind_to_scan[psmind];}
+ inline int psmind2charge(int psmind){return psmind_to_charge[psmind];}
+ inline int psmind2pepind(int psmind){return psmind_to_pepind[psmind];}
+ inline double psmind2precursor_mass(int psmind){return psmind_to_precursor_mass[psmind];}
+ inline double psmind2xcorr(int psmind){return psmind_to_xcorr[psmind];}
+ inline double psmind2spscore(int psmind){return psmind_to_spscore[psmind];}
+ inline double psmind2deltaCn(int psmind){return psmind_to_deltaCn[psmind];}
+ inline double psmind2peptide_mass(int psmind){return psmind_to_calculated_mass[psmind];}
+ string& psmind2fname(int psmind);
+ inline string& ind2pep(int ind){return ind_to_pep[ind];}
+ inline int get_num_psms(){return num_psms;}
+ inline int get_num_features(){return num_features;}
+
+ inline int get_num_peptides(){return num_pep;}
+ inline int pepind2label(int pepind){return pepind_to_label[pepind];}
+ inline int pepind2num_psm(int pepind){return pepind_to_psminds.get_range_length(pepind);}
+ inline int* pepind2psminds(int pepind){return pepind_to_psminds.get_range_indices(pepind);}
+ inline int pepind2num_prot(int pepind){return pepind_to_protinds.get_range_length(pepind);}
+ inline int* pepind2protinds(int pepind){return pepind_to_protinds.get_range_indices(pepind);}
+
+ inline int get_num_proteins(){return num_prot;}
+ inline string& ind2prot(int ind){return ind_to_prot[ind];}
+ inline int protind2label(int protind){return protind_to_label[protind];}
+ inline int protind2num_pep(int protind){return protind_to_pepinds.get_range_length(protind);}
+ inline int* protind2pepinds(int protind){return protind_to_pepinds.get_range_indices(protind);}
+ inline int protind2num_all_pep(int protind){return protind_to_num_all_pep[protind];}
+ inline int protind2length(int protind){return protind_to_length[protind];}
+ //returns false if not subset, true if yes, subset
+ inline bool is_prot_subset(int protind1, int protind2){return protind_to_pepinds.is_subset(protind1, protind2);}
+ inline int psmind2sp_rank(int psmind){return psmind_to_sp_rank[psmind];}//Sp rank
+ inline int psmind2xcorr_rank(int psmind){return psmind_to_xcorr_rank[psmind];}//xcorr rank
+ inline double psmind2by_ions_matched(int psmind){return psmind_to_by_ions_matched[psmind];}//b/y ions matched
+ inline double psmind2by_ions_total(int psmind){return psmind_to_by_ions_total[psmind];}//b/y ions total
+ inline int psmind2matches_spectrum(int psmind) {
+ return psmind_to_matches_spectrum[psmind];
+ }// Distinct matchs/spectrum
+ inline int psmind2peptide_position(int psmind){return psmind_to_peptide_position[psmind];}///<peptide position in protein
+
+ inline void get_features_header(vector<string> str){features_header_.swap(str);}
+
+
+ protected:
+ int num_psms;
+ int num_pos_psms;
+ int num_neg_psms;
+ int num_features;
+ double* psmind_to_features;
+ int* psmind_to_label;
+ int *psmind_to_pepind;
+ int *psmind_to_scan;
+ int *psmind_to_charge;
+ double *psmind_to_xcorr;
+ double *psmind_to_spscore;
+ double *psmind_to_deltaCn;
+ double *psmind_to_calculated_mass;
+ double *psmind_to_precursor_mass;
+ int *psmind_to_fileind;
+ int num_pep;
+ int num_pos_pep;
+ int num_neg_pep;
+ int *pepind_to_label;
+ int num_prot;
+ int num_pos_prot;
+ int num_neg_prot;
+ int *protind_to_label;
+ int *protind_to_num_all_pep;
+ int* psmind_to_sp_rank;//Sp rank
+ int *protind_to_length;
+ int* psmind_to_xcorr_rank;//xcorr rank
+ int *psmind_to_matches_spectrum; // distinct matches/spectrum
+ double* psmind_to_by_ions_matched; //b/y ions matched
+ double* psmind_to_by_ions_total; //b/y ions total
+ int* psmind_to_peptide_position;//<pepetide position in protein
+
+ map <int, string> fileind_to_fname;
+
+ vector <string> features_header_;
+
+ BipartiteGraph pepind_to_psminds;
+ BipartiteGraph pepind_to_protinds;
+ map <int, string> ind_to_pep;
+
+
+
+
+ BipartiteGraph protind_to_pepinds;
+
+ map <int, string> ind_to_prot;
+
+ string in_dir;
+};
+
+
+
+#endif /*DATASET_H */
diff --git a/src/app/qranker-barista/Makefile b/src/app/qranker-barista/Makefile
new file mode 100644
index 0000000..732ca0d
--- /dev/null
+++ b/src/app/qranker-barista/Makefile
@@ -0,0 +1,558 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canonical targets will work.
+.SUFFIXES:
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+# A target that is always out of date.
+cmake_force:
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake
+
+# The command to remove a file.
+RM = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/cmake -E remove -f
+
+# Escaping for special characters.
+EQUALS = =
+
+# The program to use to edit the cache.
+CMAKE_EDIT_COMMAND = /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /data/TeamCity/buildAgent/work/779d99b0241b2175
+
+#=============================================================================
+# Targets provided globally by CMake.
+
+# Special rule for the target edit_cache
+edit_cache:
+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake cache editor..."
+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : edit_cache
+
+# Special rule for the target edit_cache
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+ @echo "... package"
+ @echo "... package_source"
+ @echo "... rebuild_cache"
+ @echo "... Barista.o"
+ @echo "... Barista.i"
+ @echo "... Barista.s"
+ @echo "... BipartiteGraph.o"
+ @echo "... BipartiteGraph.i"
+ @echo "... BipartiteGraph.s"
+ @echo "... CruxParser.o"
+ @echo "... CruxParser.i"
+ @echo "... CruxParser.s"
+ @echo "... DataSetCrux.o"
+ @echo "... DataSetCrux.i"
+ @echo "... DataSetCrux.s"
+ @echo "... NeuralNet.o"
+ @echo "... NeuralNet.i"
+ @echo "... NeuralNet.s"
+ @echo "... PSMScores.o"
+ @echo "... PSMScores.i"
+ @echo "... PSMScores.s"
+ @echo "... PepRanker.o"
+ @echo "... PepRanker.i"
+ @echo "... PepRanker.s"
+ @echo "... PepScores.o"
+ @echo "... PepScores.i"
+ @echo "... PepScores.s"
+ @echo "... ProtScores.o"
+ @echo "... ProtScores.i"
+ @echo "... ProtScores.s"
+ @echo "... QRanker.o"
+ @echo "... QRanker.i"
+ @echo "... QRanker.s"
+ @echo "... SQTParser.o"
+ @echo "... SQTParser.i"
+ @echo "... SQTParser.s"
+ @echo "... SpecFeatures.o"
+ @echo "... SpecFeatures.i"
+ @echo "... SpecFeatures.s"
+ @echo "... TabDelimParser.o"
+ @echo "... TabDelimParser.i"
+ @echo "... TabDelimParser.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+
diff --git a/src/app/qranker-barista/NeuralNet.cpp b/src/app/qranker-barista/NeuralNet.cpp
new file mode 100644
index 0000000..b92ee3e
--- /dev/null
+++ b/src/app/qranker-barista/NeuralNet.cpp
@@ -0,0 +1,809 @@
+#include "NeuralNet.h"
+#include "util/utils.h"
+
+/*****************Sigmoid**********************/
+
+void Sigmoid :: resize(int m)
+{
+ num_neurons = m;
+}
+
+
+Sigmoid& Sigmoid :: operator=(Sigmoid &S)
+{
+ num_neurons = S.num_neurons;
+ return *this;
+}
+
+void Sigmoid :: clone(Sigmoid &S)
+{
+ num_neurons = S.num_neurons;
+}
+
+void Sigmoid :: fprop(State& down, State &up)
+{
+ for(int k = 0; k < num_neurons; k++)
+ up.x[k] = 1.0/(1.0+exp(-down.x[k]));
+}
+
+void Sigmoid :: bprop(State &down, State &up)
+{
+ for(int k = 0; k < num_neurons; k++)
+ down.dx[k] = up.dx[k]*(1.0-up.x[k])*up.x[k];
+}
+
+
+/******************** Linear*************************/
+void Linear :: make_random()
+{
+ if(num_neurons > 0 && num_features > 0)
+ {
+ for(int k = 0; k < num_neurons; k++)
+ {
+ for(int j = 0; j < num_features; j++)
+ w[k*num_features+j] = ((double)myrandom()/UNIFORM_INT_DISTRIBUTION_MAX - 0.5)/(num_features*num_neurons);
+ if(has_bias)
+ bias[k] = ((double)myrandom()/UNIFORM_INT_DISTRIBUTION_MAX - 0.5)/(num_features*num_neurons);;
+ }
+ }
+}
+
+void Linear :: resize(int m, int n, int has_b)
+{
+ if(num_neurons != m || num_features != n)
+ {
+ clear();
+ num_neurons = m;
+ num_features = n;
+ has_bias = has_b;
+ w = new double[num_neurons*num_features];
+ bias = new double[num_neurons];
+ dw = new double[num_neurons*num_features];
+ dbias = new double[num_neurons];
+ num_refs = new int[1];
+ num_refs[0] = 1;
+ }
+ for(int k = 0; k < num_neurons; k++)
+ {
+ for(int j = 0; j < num_features; j++)
+ w[k*num_features+j] = ((double)myrandom()/UNIFORM_INT_DISTRIBUTION_MAX - 0.5)/(num_features*num_neurons);
+ if(has_bias)
+ bias[k] = ((double)myrandom()/UNIFORM_INT_DISTRIBUTION_MAX - 0.5)/(num_features*num_neurons);;
+ }
+ memset(dw,0,sizeof(double)*num_neurons*num_features);
+ if(has_bias)
+ memset(dbias, 0, sizeof(double)*num_neurons);
+
+}
+
+
+void Linear :: clear()
+{
+ if(num_refs)
+ {
+ num_refs[0]--;
+ if(num_refs[0] < 1)
+ {
+ delete[] w; w = 0;
+ delete[] bias; bias = 0;
+ delete[] dw; dw = 0;
+ delete[] dbias; dbias = 0;
+ delete[] num_refs; num_refs = 0;
+ num_neurons = 0;
+ num_features = 0;
+ }
+ }
+}
+
+Linear& Linear :: operator=(Linear &L)
+{
+ resize(L.num_neurons, L.num_features, L.has_bias);
+ for(int k = 0; k < num_neurons; k++)
+ {
+ for(int j = 0; j < num_features; j++)
+ w[k*num_features+j] = L.w[k*num_features+j];
+ if(has_bias)
+ bias[k] = L.bias[k];
+ }
+ return *this;
+}
+
+void Linear :: copy(Linear &L)
+{
+ assert(L.num_neurons == num_neurons);
+ assert(L.num_features == num_features);
+ for(int k = 0; k < num_neurons; k++)
+ {
+ for(int j = 0; j < num_features; j++)
+ w[k*num_features+j] = L.w[k*num_features+j];
+ if(has_bias)
+ bias[k] = L.bias[k];
+ }
+}
+
+
+void Linear :: clone(Linear &L)
+{
+ clear();
+ num_neurons = L.num_neurons;
+ num_features = L.num_features;
+ has_bias = L.has_bias;
+ w = L.w;
+ dw = L.dw;
+ bias = L.bias;
+ dbias = L.dbias;
+ num_refs = L.num_refs;
+ num_refs[0]++;
+}
+
+
+void Linear :: clear_gradients()
+{
+ memset(dw,0,sizeof(double)*num_neurons*num_features);
+ if(has_bias)
+ memset(dbias,0,sizeof(double)*num_neurons);
+}
+
+void Linear :: fprop(State &down, State &up)
+{
+ for(int k = 0; k < num_neurons; k++)
+ {
+ double d = 0.0;
+ for(int j = 0; j < num_features; j++)
+ d += w[k*num_features+j]*down.x[j];
+ //if there is a bias
+ if(has_bias)
+ d += bias[k];
+ up.x[k] = d;
+ }
+}
+
+
+void Linear :: bprop(State &down, State &up)
+{
+ memset(down.dx,0,sizeof(double)*num_features);
+ for(int j = 0; j < num_features; j++)
+ for(int k = 0; k < num_neurons; k++)
+ down.dx[j] += up.dx[k]*w[k*num_features+j];
+
+ for(int k = 0; k < num_neurons; k++)
+ {
+ for(int j = 0; j < num_features; j++)
+ dw[k*num_features+j] += up.dx[k]*down.x[j];
+ //if there is a bias
+ if(has_bias)
+ dbias[k] += up.dx[k];
+ }
+}
+
+void Linear :: update(double mu, double weight_decay)
+{
+ for(int k = 0; k < num_neurons; k++)
+ {
+ for(int j = 0; j < num_features; j++)
+ {
+ if(weight_decay > 0.0)
+ dw[k*num_features+j] += weight_decay*w[k*num_features+j];
+ w[k*num_features+j] -= mu*dw[k*num_features+j];
+ }
+ //if there is a bias
+ if(has_bias)
+ {
+ if(weight_decay > 0.0)
+ dbias[k] += weight_decay*bias[k];
+ bias[k] -= mu*dbias[k];
+ }
+ }
+}
+
+void Linear :: update1(double mu, double weight_decay)
+{
+ for(int k = 0; k < num_neurons; k++)
+ {
+ for(int j = 0; j < num_features; j++)
+ {
+ if(weight_decay > 0.0)
+ dw[k*num_features+j] += weight_decay*w[k*num_features+j];
+ w[k*num_features+j] -= (mu/(num_features*num_neurons))*dw[k*num_features+j];
+ }
+ //if there is a bias
+ if(has_bias)
+ {
+ if(weight_decay > 0.0)
+ dbias[k] += weight_decay*bias[k];
+ bias[k] -= (mu/(num_features*num_neurons))*dbias[k];
+ }
+ }
+}
+
+/**************** Neural Net ********************/
+void NeuralNet :: make_random()
+{
+ lin1.make_random();
+ if(!is_linear)
+ lin2.make_random();
+}
+
+void NeuralNet :: resize_states()
+{
+ int num_features = lin1.get_num_features();
+ int num_neurons1 = lin1.get_num_neurons();
+
+ //first state
+ start.resize_dx(num_features);
+ if(!is_linear)
+ {
+ assert(num_neurons1 == sigm1.get_num_neurons());
+ s1.resize(num_neurons1);
+ assert(num_neurons1 == lin2.get_num_features());
+ s2.resize(num_neurons1);
+ }
+ //last state
+ finish.resize_x(1);
+}
+
+void NeuralNet :: initialize(int nfeatures, int num_hu, int is_lin, int has_bias)
+{
+ is_linear = is_lin;
+ //cout << "initializing net " << nfeatures << " " << num_hu << endl;
+ lin1.resize(num_hu, nfeatures, has_bias);
+ if(!is_linear)
+ {
+ sigm1.resize(num_hu);
+ lin2.resize(1,num_hu, has_bias);
+ }
+ resize_states();
+}
+
+NeuralNet& NeuralNet :: operator=(NeuralNet &N)
+{
+ is_linear = N.is_linear;
+ lin1 = N.lin1;
+ if(!is_linear)
+ {
+ sigm1 = N.sigm1;
+ lin2 = N.lin2;
+ }
+ resize_states();
+ return *this;
+}
+
+void NeuralNet :: copy(NeuralNet &N)
+{
+ assert(is_linear == N.is_linear);
+ lin1.copy(N.lin1);
+ if(!is_linear)
+ {
+ lin2.copy(N.lin2);
+ }
+}
+
+
+void NeuralNet :: clone(NeuralNet &N)
+{
+ is_linear = N.is_linear;
+ lin1.clone(N.lin1);
+ if(!is_linear)
+ {
+ sigm1.clone(N.sigm1);
+ lin2.clone(N.lin2);
+ }
+ resize_states();
+}
+
+
+double* NeuralNet :: fprop(double *x)
+{
+ start.x = x;
+ if(is_linear)
+ lin1.fprop(start,finish);
+ else
+ {
+ lin1.fprop(start,s1);
+ sigm1.fprop(s1,s2);
+ lin2.fprop(s2,finish);
+ }
+ return finish.x;
+
+}
+
+
+void NeuralNet :: clear_gradients()
+{
+ lin1.clear_gradients();
+ if(!is_linear)
+ lin2.clear_gradients();
+}
+
+
+double* NeuralNet :: bprop(double *dx)
+{
+ finish.dx = dx;
+ if(is_linear)
+ lin1.bprop(start,finish);
+ else
+ {
+ lin2.bprop(s2,finish);
+ sigm1.bprop(s1,s2);
+ lin1.bprop(start,s1);
+ }
+
+ return start.dx;
+}
+
+void NeuralNet :: update(double mu, double weight_decay)
+{
+ lin1.update(mu, weight_decay);
+ if(!is_linear)
+ lin2.update(mu, weight_decay);
+}
+
+void NeuralNet :: update1(double mu, double weight_decay)
+{
+ lin1.update1(mu, weight_decay);
+ if(!is_linear)
+ lin2.update1(mu, weight_decay);
+}
+
+
+double* NeuralNet :: get_weights(int mod)
+{
+ if(mod == 1)
+ return lin1.get_weights();
+ else if(mod == 2)
+ {
+ if(is_linear)
+ {
+ cout << "neural net was initialized with only 1 layer, layer " << mod << " does not exits" << endl;
+ return 0;
+ }
+ return lin2.get_weights();
+ }
+ else
+ {
+ if(is_linear)
+ cout << "neural net was initialized with only 1 layer, ";
+ else
+ cout << "neural net was initialized with 2 layers, ";
+ cout << "layer " << mod << "does not exist" << endl;
+ return 0;
+ }
+
+}
+
+double* NeuralNet :: get_dweights(int mod)
+{
+ if(mod == 1)
+ return lin1.get_dweights();
+ else if(mod == 2)
+ {
+ if(is_linear)
+ {
+ cout << "neural net was initialized with only 1 layer, layer " << mod << " does not exits" << endl;
+ return 0;
+ }
+ return lin2.get_dweights();
+ }
+ else
+ {
+ if(is_linear)
+ cout << "neural net was initialized with only 1 layer, ";
+ else
+ cout << "neural net was initialized with 2 layers, ";
+ cout << "layer " << mod << "does not exist" << endl;
+ return 0;
+ }
+}
+
+double* NeuralNet :: get_bias(int mod)
+{
+ if(mod == 1)
+ return lin1.get_bias();
+ else if(mod == 2)
+ {
+ if(is_linear)
+ {
+ cout << "neural net was initialized with only 1 layer, layer " << mod << " does not exits" << endl;
+ return 0;
+ }
+ return lin2.get_bias();
+ }
+ else
+ {
+ if(is_linear)
+ cout << "neural net was initialized with only 1 layer, ";
+ else
+ cout << "neural net was initialized with 2 layers, ";
+ cout << "layer " << mod << "does not exist" << endl;
+ return 0;
+ }
+}
+
+double* NeuralNet :: get_dbias(int mod)
+{
+ if(mod == 1)
+ return lin1.get_dbias();
+ if(mod == 2)
+ {
+ if(is_linear)
+ {
+ cout << "neural net was initialized with only 1 layer, layer " << mod << " does not exits" << endl;
+ return 0;
+ }
+ return lin2.get_dbias();
+ }
+ else
+ {
+ if(is_linear)
+ cout << "neural net was initialized with only 1 layer, ";
+ else
+ cout << "neural net was initialized with 2 layers, ";
+ cout << "layer " << mod << "does not exist" << endl;
+ return 0;
+ }
+}
+
+/********************************************************************/
+
+double check_gradients(NeuralNet &n, double *x)
+{
+ double sum = 0.0;
+
+ double h = 10e-6;
+
+ double *c = n.fprop(x);
+ double cbefore = c[0];
+
+ double *gc = new double[1];
+ gc[0] = 1;
+ n.clear_gradients();
+ n.bprop(gc);
+
+ double *w = n.get_weights(1);
+ double *dw = n.get_dweights(1);
+ for (int j = 0; j < n.get_num_hu(); j++)
+ for (int i = 0; i < n.get_num_features(); i++)
+ {
+ int ii = j*n.get_num_features()+i;
+ double ww = w[ii];
+ w[ii] += h;
+ c = n.fprop(x);
+ double d = c[0]-cbefore;
+ sum += fabs(dw[ii]-d/h);
+ w[ii]=ww;
+ }
+
+ double *bias = n.get_bias(1);
+ double *dbias = n.get_dbias(1);
+ for (int i = 0; i < n.get_num_hu();i++)
+ {
+ double bb = bias[i];
+ bias[i] +=h;
+ c = n.fprop(x);
+ double d = c[0]-cbefore;
+ sum += fabs(dbias[i]-d/h);
+ bias[i] =bb;
+ }
+
+ if(n.get_num_layers() > 1)
+ {
+ double *w = n.get_weights(2);
+ double *dw = n.get_dweights(2);
+ for (int i = 0; i < n.get_num_hu(); i++)
+ {
+ double ww = w[i];
+ w[i] += h;
+ c = n.fprop(x);
+ double d = c[0]-cbefore;
+ sum += fabs(dw[i]-d/h);
+ w[i]=ww;
+ }
+
+ double *bias = n.get_bias(2);
+ double *dbias = n.get_dbias(2);
+ for (int i = 0; i < 1;i++)
+ {
+ double bb = bias[i];
+ bias[i] +=h;
+ c = n.fprop(x);
+ double d = c[0]-cbefore;
+ sum += fabs(dbias[i]-d/h);
+ bias[i] =bb;
+ }
+ }
+
+ n.update(0.005);
+ return sum;
+}
+
+double check_gradients_hinge(NeuralNet &n, double *x, int y)
+{
+ double sum = 0.0;
+
+ double h = 10e-6;
+
+ double *c = n.fprop(x);
+ double cbefore = 1.0-c[0]*y;
+
+ double *gc = new double[1];
+ gc[0] = -1*y;
+ n.clear_gradients();
+ n.bprop(gc);
+
+ double *w = n.get_weights(1);
+ double *dw = n.get_dweights(1);
+ for (int j = 0; j < n.get_num_hu(); j++)
+ for (int i = 0; i < n.get_num_features(); i++)
+ {
+ int ii = j*n.get_num_features()+i;
+ double ww = w[ii];
+ w[ii] += h;
+ c = n.fprop(x);
+ double d = (1.0-c[0]*y)-cbefore;
+ sum += fabs(dw[ii]-d/h);
+ w[ii]=ww;
+ }
+
+
+ double *bias = n.get_bias(1);
+ double *dbias = n.get_dbias(1);
+ for (int i = 0; i < n.get_num_hu();i++)
+ {
+ double bb = bias[i];
+ bias[i] +=h;
+ c = n.fprop(x);
+ double d = (1.0-c[0]*y)-cbefore;
+ sum += fabs(dbias[i]-d/h);
+ bias[i] =bb;
+ }
+
+ if(n.get_num_layers() > 1)
+ {
+ double *w = n.get_weights(2);
+ double *dw = n.get_dweights(2);
+ for (int i = 0; i < n.get_num_hu(); i++)
+ {
+ double ww = w[i];
+ w[i] += h;
+ c = n.fprop(x);
+ double d = (1.0-c[0]*y)-cbefore;
+ sum += fabs(dw[i]-d/h);
+ w[i]=ww;
+ }
+
+ double *bias = n.get_bias(2);
+ double *dbias = n.get_dbias(2);
+ for (int i = 0; i < 1;i++)
+ {
+ double bb = bias[i];
+ bias[i] +=h;
+ c = n.fprop(x);
+ double d = (1.0-c[0]*y)-cbefore;
+ sum += fabs(dbias[i]-d/h);
+ bias[i] =bb;
+ }
+ }
+
+ //n.update(0.005);
+ return sum;
+}
+
+
+double check_gradients_sigmoid(NeuralNet &n, double *x, int y)
+{
+ double sum = 0.0;
+
+ double h = 10e-6;
+
+ double *c = n.fprop(x);
+ double a = exp(y*c[0]);
+ double cbefore = (1/(1+a));
+
+ double *gc = new double[1];
+ gc[0] = -a/((1+a)*(1+a))*y;
+ n.clear_gradients();
+ n.bprop(gc);
+
+ double *w = n.get_weights(1);
+ double *dw = n.get_dweights(1);
+ for (int j = 0; j < n.get_num_hu(); j++)
+ for (int i = 0; i < n.get_num_features(); i++)
+ {
+ int ii = j*n.get_num_features()+i;
+ double ww = w[ii];
+ w[ii] += h;
+ c = n.fprop(x);
+ double aa = exp(y*c[0]);
+ double cafter = (1/(1+aa));
+ double d = cafter-cbefore;
+ sum += fabs(dw[ii]-d/h);
+ w[ii]=ww;
+ }
+
+
+ double *bias = n.get_bias(1);
+ double *dbias = n.get_dbias(1);
+ for (int i = 0; i < n.get_num_hu();i++)
+ {
+ double bb = bias[i];
+ bias[i] +=h;
+ c = n.fprop(x);
+ double aa = exp(y*c[0]);
+ double cafter = (1/(1+aa));
+ double d = cafter-cbefore;
+ sum += fabs(dbias[i]-d/h);
+ bias[i] =bb;
+ }
+
+ if(n.get_num_layers() > 1)
+ {
+ double *w = n.get_weights(2);
+ double *dw = n.get_dweights(2);
+ for (int i = 0; i < n.get_num_hu(); i++)
+ {
+ double ww = w[i];
+ w[i] += h;
+ c = n.fprop(x);
+ double aa = exp(y*c[0]);
+ double cafter = (1/(1+aa));
+ double d = cafter-cbefore;
+ sum += fabs(dw[i]-d/h);
+ w[i]=ww;
+ }
+
+ double *bias = n.get_bias(2);
+ double *dbias = n.get_dbias(2);
+ for (int i = 0; i < 1;i++)
+ {
+ double bb = bias[i];
+ bias[i] +=h;
+ c = n.fprop(x);
+ double aa = exp(y*c[0]);
+ double cafter = (1/(1+aa));
+ double d = cafter-cbefore;
+ sum += fabs(dbias[i]-d/h);
+ bias[i] =bb;
+ }
+ }
+
+ //n.update();
+ return sum;
+}
+
+
+/*
+void check_gradients_rank(NeuralNet &n, NeuralNet *nets, double *x1, int y1, double *x2, int y2)
+{
+
+ double diff = 0;
+ double h = 0.0001;
+
+ double *c1 = nets[0].fprop(x1);
+ double *c2 = nets[1].fprop(x2);
+
+ double d = c1[0]-c2[0];
+ diff -= d;
+
+ double *gc = new double[1];
+
+ n.clear_gradients();
+ gc[0] = 1.0;
+ nets[0].bprop(gc);
+ gc[0] = -1.0;
+ nets[1].bprop(gc);
+
+ double *w = n.get_weights(1);
+ double *dw = n.get_dweights(1);
+ for (int j = 0; j < n.get_num_hu(); j++)
+ {
+ for (int i = 0; i < n.get_num_features(); i++)
+ {
+ int ii = j*n.get_num_features()+i;
+ double ww = w[ii];
+ w[ii] += h;
+ c1 = nets[0].fprop(x1);
+ c2 = nets[1].fprop(x2);
+ d = c1[0]-c2[0];
+
+ diff += d;
+ cout << dw[i] << " " << diff/h << " " << dw[i]-diff/h << endl;
+ w[ii]=w;
+ diff -= d;
+ }
+ }
+
+}
+*/
+/******************************************************/
+/*
+int main()
+{
+ int num_features = 17;
+ int num_hu = 5;
+ int has_bias = 1;
+ int is_lin = 0;
+
+ NeuralNet n;
+ n.initialize(num_features, num_hu, is_lin, has_bias);
+
+ double sm = 0;
+ int nexamples = 10000;
+
+ for( int k = 0; k < nexamples; k++)
+ {
+ double *x = new double[num_features];
+ for (int i = 0; i < num_features; i++)
+ {
+ x[i] = (double)rand()/(double)RAND_MAX;
+ }
+ int label = 1;
+ sm += check_gradients_hinge(n, x,label);
+ }
+ cout << sm/(double)nexamples << endl;
+
+ sm = 0;
+ nexamples = 100;
+ for( int k = 0; k < nexamples; k++)
+ {
+ double *x = new double[num_features];
+ for (int i = 0; i < num_features; i++)
+ {
+ x[i] = (double)rand()/(double)RAND_MAX;
+ }
+ int label = 1;
+ sm += check_gradients_sigmoid(n, x,label);
+ }
+ cout << sm/(double)nexamples << endl;
+
+*/
+
+ /*
+ NeuralNet *nets = new NeuralNet[2];
+
+ nets[0].clone(n);
+ nets[1].clone(n);
+
+ double *x1 = new double[num_features];
+ for (int i = 0; i < num_features; i++)
+ {
+ x1[i] = (double)rand()/(double)RAND_MAX;
+ }
+ int label1 = 1;
+
+ double *x2 = new double[num_features];
+ for (int i = 0; i < num_features; i++)
+ {
+ x2[i] = (double)rand()/(double)RAND_MAX;
+ }
+ int label2 = -1;
+
+ check_gradients_rank(n ,nets, x1, label1, x2, label2);
+
+ x1 = new double[num_features];
+ for (int i = 0; i < num_features; i++)
+ {
+ x1[i] = (double)rand()/(double)RAND_MAX;
+ }
+ label1 = 1;
+
+
+ for (int i = 0; i < num_features; i++)
+ {
+ x2[i] = (double)rand()/(double)RAND_MAX;
+ }
+ label2 = -1;
+
+ check_gradients_rank(n, nets, x1, label1, x2, label2);
+ */
+
+
+
+
+ //double *out = n.fprop(x);
+ //cout << out[0] << endl;
+ //double *gc = new double(1);
+ //gc[0] = -1*(double)label;
+ //n.bprop(gc);
+
+ //}
+
diff --git a/src/app/qranker-barista/NeuralNet.h b/src/app/qranker-barista/NeuralNet.h
new file mode 100644
index 0000000..a3fbec9
--- /dev/null
+++ b/src/app/qranker-barista/NeuralNet.h
@@ -0,0 +1,152 @@
+#ifndef NEURAL_NET_H
+#define NEURAL_NET_H
+
+#include <iostream>
+#include <fstream>
+#include <cstdlib>
+#include <assert.h>
+#include <cstring>
+#include <math.h>
+#include <vector>
+using namespace std;
+
+
+class State
+{
+ public:
+ State()
+ : len_x(0),
+ len_dx(0),
+ x((double*)0),
+ dx((double*)0) {}
+ inline void resize(int n) {clear(); x = new double[n]; len_x=n; dx = new double[n]; len_dx = n;}
+ inline void resize_dx(int n) {clear(); dx = new double[n]; len_dx = n;}
+ inline void resize_x(int n) {clear(); x = new double[n]; len_x = n;}
+ inline void clear(){if(len_x) delete[] x; if(len_dx) delete[] dx; len_x = 0; len_dx=0;}
+ ~State(){clear();}
+
+ int len_x;
+ int len_dx;
+ double *x;
+ double *dx;
+
+};
+
+class Sigmoid
+{
+public:
+ Sigmoid():num_neurons(0){}
+ ~Sigmoid() {}
+ void clear(){num_neurons = 0;}
+ void resize(int m);
+ Sigmoid& operator=(Sigmoid &S);
+ void clone(Sigmoid &S);
+
+ inline int get_num_neurons(){return num_neurons;}
+
+ void write_to_file(ofstream &outfile);
+ void read_from_file(ifstream &infile);
+
+ void fprop(State& down, State &up);
+ void bprop(State &down, State &up);
+
+ protected:
+ int num_neurons;
+};
+
+
+
+class Linear
+{
+ public:
+ Linear():
+ num_neurons(0),
+ num_features(0),
+ has_bias(1),
+ num_refs(0),
+ w(0),
+ bias(0),
+ dw(0),
+ dbias(0) {}
+ ~Linear() {clear();}
+ void init(int m, int n, int has_b);
+ void resize(int m, int n, int has_b);
+ void clear();
+ Linear& operator=(Linear &L);
+ void copy(Linear &L);
+ void clone(Linear &L);
+ void make_random();
+
+ inline void set_num_features(int nf) {num_features = nf;}
+ inline int get_num_features() const {return num_features;}
+ inline void set_num_neurons(int nr) {num_neurons = nr;}
+ inline int get_num_neurons() const{return num_neurons;}
+
+ inline double* get_weights() {return w;}
+ inline double* get_dweights() {return dw;}
+ inline double* get_bias() {return bias;}
+ inline double* get_dbias() {return dbias;}
+
+ void write_to_file(ofstream &outfile);
+ void read_from_file(ifstream &infile);
+
+ void fprop(State &down, State &up);
+ void bprop(State &down, State &up);
+ void clear_gradients();
+ void update(double mu, double weight_decay=0.0);
+ void update1(double mu, double weight_decay = 0.0);
+
+ protected:
+ int num_neurons;
+ int num_features;
+ int has_bias;
+
+ int *num_refs;
+ double *w;
+ double *bias;
+ double *dw;
+ double *dbias;
+
+};
+
+/************************NeuralNet******************************************/
+class NeuralNet {
+ public:
+ NeuralNet():is_linear(0){}
+ ~NeuralNet(){}
+ void clear();
+ void resize_states();
+ void initialize(int nfeatures, int num_hu, int is_lin, int has_bias);
+ NeuralNet& operator=(NeuralNet &N);
+ void clone(NeuralNet &N);
+ void copy(NeuralNet &N);
+ void make_random();
+
+ double* fprop(double *down);
+ void clear_gradients();
+ double* bprop(double *up);
+ void update(double mu, double weight_decay=0.0);
+ void update1(double mu, double weight_decay=0.0);
+
+ double* get_weights(int mod);
+ double* get_dweights(int mod);
+ double* get_bias(int mod);
+ double* get_dbias(int mod);
+ inline int get_num_features(){return lin1.get_num_features();}
+ inline int get_num_hu(){return lin1.get_num_neurons();}
+ inline int get_num_layers(){if (is_linear) return 1; else return 2;}
+
+ protected:
+ int is_linear;
+
+ State start;
+ Linear lin1;
+ State s1;
+ Sigmoid sigm1;
+ State s2;
+ Linear lin2;
+ State finish;
+};
+
+
+#endif /*NEURAL_NET_H*/
diff --git a/src/app/qranker-barista/PSMScores.cpp b/src/app/qranker-barista/PSMScores.cpp
new file mode 100644
index 0000000..9ad444c
--- /dev/null
+++ b/src/app/qranker-barista/PSMScores.cpp
@@ -0,0 +1,225 @@
+#include <assert.h>
+#include <iostream>
+#include <fstream>
+#include <utility>
+#include <algorithm>
+#include <set>
+#include <vector>
+#include <string>
+#include <math.h>
+using namespace std;
+#include "PSMScores.h"
+#include "util/utils.h"
+
+inline bool operator>(const PSMScoreHolder &one, const PSMScoreHolder &other)
+ {return (one.score>other.score);}
+
+inline bool operator<(const PSMScoreHolder &one, const PSMScoreHolder &other)
+ {return (one.score<other.score);}
+
+
+
+PSMScores::PSMScores()
+{
+ factor=1;
+ neg=0;
+ pos=0;
+ posNow=0;
+}
+
+PSMScores::~PSMScores()
+{
+
+}
+
+void PSMScores::clear()
+{
+ scores.clear();
+ pos=neg=posNow = 0;
+}
+
+
+/**
+ * Percentage of target scores that are drawn according to the null.
+ */
+double PSMScores::pi0 = 0.9;
+
+
+/**
+ * Calculate the number of targets that score above a specified FDR.
+ */
+int PSMScores::calcOverFDR(double fdr) {
+
+ vector<PSMScoreHolder>::iterator it = scores.begin();
+
+ sort(scores.begin(),scores.end());
+ reverse(scores.begin(),scores.end());
+
+ int positives=0,nulls=0;
+ double efp=0.0,q;
+ posNow = 0;
+ register unsigned int ix=0;
+ for(it=scores.begin();it!=scores.end();it++) {
+ if (it->label!=-1)
+ positives++;
+ if (it->label==-1) {
+ nulls++;
+ efp=pi0*nulls*factor;
+ }
+ if (positives)
+ q=efp/(double)positives;
+ else
+ q=pi0;
+ if (q>pi0)
+ q=pi0;
+ it->q=q;
+ if (fdr>=q)
+ posNow = positives;
+ }
+ for (ix=scores.size();--ix;) {
+ if (scores[ix-1].q > scores[ix].q)
+ scores[ix-1].q = scores[ix].q;
+ }
+ return posNow;
+}
+
+
+void PSMScores::calcMultiOverFDR(vector<double> &fdr, vector<int> &overFDR) {
+
+ vector<PSMScoreHolder>::iterator it = scores.begin();
+
+ sort(scores.begin(),scores.end());
+ reverse(scores.begin(),scores.end());
+
+ int positives=0,nulls=0;
+ double efp=0.0,q;
+ register unsigned int ix=0;
+
+ for(it=scores.begin();it!=scores.end();it++) {
+ if (it->label==1)
+ positives++;
+ if (it->label==-1) {
+ nulls++;
+ efp=pi0*nulls*factor;
+ }
+ if (positives)
+ q=efp/(double)positives;
+ else
+ q=pi0;
+ it->q=q;
+ if (q>pi0)
+ q=pi0;
+
+ for(unsigned int ct = 0; ct < fdr.size(); ct++)
+ if (fdr[ct]>=q)
+ overFDR[ct] = positives;
+ }
+ for (ix=scores.size();--ix;) {
+ if (scores[ix-1].q > scores[ix].q)
+ scores[ix-1].q = scores[ix].q;
+ }
+}
+
+
+
+
+void PSMScores::fillFeaturesSplit(PSMScores& train,PSMScores& test, Dataset& d, double ratio) {
+
+ int num_psms = d.get_num_psms();
+ set<string> peptides_train;
+ set<string> peptides_test;
+
+ assert(ratio>0 && ratio < 1);
+ int n = num_psms;
+ int k = (int)(n*ratio);
+ int l = n-k;
+
+ PSMScoreHolder s;
+
+ //collect everybody
+ vector<PSMScoreHolder> all_examples;
+ all_examples.resize(n,s);
+ for (int i = 0; i < num_psms; i++)
+ {
+ all_examples[i].psmind = i;
+ all_examples[i].label = d.psmind2label(i);
+ }
+
+ //mix up the examples
+ for(int i = 0; i < n; i++)
+ {
+ int p1 = (int)((double)myrandom()/UNIFORM_INT_DISTRIBUTION_MAX*(n-1));
+ int p2 = (int)((double)myrandom()/UNIFORM_INT_DISTRIBUTION_MAX*(n-1));
+ s = all_examples[p1];
+ all_examples[p1] = all_examples[p2];
+ all_examples[p2] = s;
+ }
+
+ train.scores.resize(k,s);
+ test.scores.resize(l,s);
+
+
+ int num_pos_train = 0;
+ int num_neg_train = 0;
+ int num_pos_test = 0;
+ int num_neg_test = 0;
+ //distribute the normal set between train and test
+ for (int i = 0; i < k; i++)
+ {
+ train.scores[i] = all_examples[i];
+ if (train.scores[i].label == 1)
+ num_pos_train++;
+ else
+ num_neg_train++;
+ }
+ for(int i=0; i < l; i++)
+ {
+ test.scores[i] = all_examples[i+k];
+ if (test.scores[i].label == 1)
+ num_pos_test++;
+ else
+ num_neg_test++;
+ }
+ //cout << num_pos_train << " " << num_neg_train << " " << num_pos_test << " " << num_neg_test << "\n";
+ train.pos=num_pos_train;
+ test.pos=num_pos_test;
+ train.neg=num_neg_train;
+ test.neg=num_neg_test;
+ train.factor = train.pos/(double)train.neg;
+ test.factor = train.pos/(double)train.neg;
+
+}
+
+
+void PSMScores::fillFeaturesFull(PSMScores& full, Dataset& d) {
+
+ int n = d.get_num_psms();
+
+ PSMScoreHolder s;
+ full.scores.resize(n,s);
+ int num_pos = 0;
+ int num_neg = 0;
+
+ for (int i = 0; i < n; i++)
+ {
+ full.scores[i].psmind = i;
+ full.scores[i].label = d.psmind2label(i);
+ if (full.scores[i].label == 1)
+ num_pos++;
+ else
+ num_neg++;
+ }
+
+ full.pos=num_pos;
+ full.neg=num_neg;
+ full.factor = full.pos/(double)full.neg;
+}
+
+
+
+
+
+
+
+
+
diff --git a/src/app/qranker-barista/PSMScores.h b/src/app/qranker-barista/PSMScores.h
new file mode 100644
index 0000000..46bdf2f
--- /dev/null
+++ b/src/app/qranker-barista/PSMScores.h
@@ -0,0 +1,44 @@
+#ifndef PSMSCORES_H_
+#define PSMSCORES_H_
+#include <vector>
+#include <algorithm>
+using namespace std;
+#include "DataSetCrux.h"
+
+
+class PSMScoreHolder{
+public:
+ double score;
+ int psmind;
+ double q;
+ double PEP;
+ int label;
+ PSMScoreHolder():score(0.0),psmind(0),q(0.0),PEP(0.0),label(0){;}
+ virtual ~PSMScoreHolder() {;}
+};
+
+class PSMScores
+{
+public:
+ PSMScores();
+ ~PSMScores();
+ void clear();
+ vector<PSMScoreHolder>::iterator begin() {return scores.begin();}
+ vector<PSMScoreHolder>::iterator end() {return scores.end();}
+ static double pi0;
+ double factor;
+
+ int calcOverFDR(double fdr);
+ void calcMultiOverFDR(vector<double> &fdr, vector<int> &overFDR);
+ inline PSMScoreHolder& operator[](int ix){return scores[ix];}
+ void static fillFeaturesSplit(PSMScores& train,PSMScores& test,Dataset &d, double ratio);
+ void static fillFeaturesFull(PSMScores& full,Dataset &d);
+ inline int size(){return scores.size();}
+protected:
+ int neg,pos,posNow;
+ vector<PSMScoreHolder> scores;
+};
+
+
+
+#endif /*PSMSCORES_H_*/
diff --git a/src/app/qranker-barista/PepRanker.cpp b/src/app/qranker-barista/PepRanker.cpp
new file mode 100644
index 0000000..d8c78d3
--- /dev/null
+++ b/src/app/qranker-barista/PepRanker.cpp
@@ -0,0 +1,1431 @@
+#include "PepRanker.h"
+#include "util/modifications.h"
+#include "util/Params.h"
+#include "app/ComputeQValues.h"
+
+PepRanker::PepRanker() :
+ seed(0),
+ selectionfdr(0.01),
+ num_hu(4),
+ mu(0.01),
+ weightDecay(0.000),
+ max_net_gen(NULL),
+ max_net_targ(NULL),
+ net_clones(NULL),
+ psm_count(0),
+ in_dir(""),
+ out_dir(""),
+ skip_cleanup_flag(0),
+ overwrite_flag(0),
+ fileroot(""),
+ feature_file_flag(0),
+ file_format_("")
+{
+}
+
+PepRanker::~PepRanker()
+{
+ delete [] max_net_gen;
+ delete [] max_net_targ;
+ delete [] net_clones;
+}
+
+int PepRanker :: getOverFDRPSM(PSMScores &set, NeuralNet &n, double fdr)
+{
+ double *r;
+ double* featVec;
+
+ for(int i = 0; i < set.size(); i++)
+ {
+ featVec = d.psmind2features(set[i].psmind);
+ r = n.fprop(featVec);
+ set[i].score = r[0];
+
+ }
+ return set.calcOverFDR(fdr);
+}
+
+/***********************************************************/
+
+double PepRanker :: get_peptide_score_xcorr(int pepind)
+{
+ int num_psm = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -100000000.0;
+ int max_ind = 0;
+ for(int i = 0; i < num_psm; i++)
+ {
+ int psmind = psminds[i];
+ double *featVec = d.psmind2features(psmind);
+ double sc = featVec[3];
+ if(max_sc < sc)
+ {
+ max_sc = sc;
+ max_ind = i;
+ }
+ }
+ return max_sc;
+}
+
+void PepRanker :: getMultiFDRXCorr(PepScores &set, vector<double> &qvalues)
+{
+ int pepind = 0;
+ for(int i = 0; i < set.size(); i++)
+ {
+ pepind = set[i].pepind;
+ double sc = get_peptide_score_xcorr(pepind);
+ set[i].score = sc;
+ }
+
+ for(unsigned int ct = 0; ct < qvalues.size(); ct++)
+ overFDRmulti[ct] = 0;
+ set.calcMultiOverFDR(qvalues, overFDRmulti);
+}
+
+
+double PepRanker :: get_peptide_score(int pepind, NeuralNet &n)
+{
+ int num_psm = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -100000000.0;
+ int max_ind = 0;
+ for(int i = 0; i < num_psm; i++)
+ {
+ int psmind = psminds[i];
+ double *feat = d.psmind2features(psmind);
+ double *sc = n.fprop(feat);
+ if(max_sc < sc[0])
+ {
+ max_sc = sc[0];
+ max_ind = i;
+ }
+ }
+ if((int)pepind_to_max_psmind.size() == d.get_num_peptides())
+ pepind_to_max_psmind[pepind] = psminds[max_ind];
+ return max_sc;
+}
+
+
+int PepRanker :: getOverFDR(PepScores &s, NeuralNet &n,double fdr)
+{
+ int pepind = 0;
+ for(int i = 0; i < s.size(); i++)
+ {
+ pepind = s[i].pepind;
+ double sc = get_peptide_score(pepind,n);
+ s[i].score = sc;
+ }
+
+ int overFDR = s.calcOverFDR(fdr);
+
+ return overFDR;
+}
+
+void PepRanker :: getMultiFDR(PepScores &set, NeuralNet &n, vector<double> &qvalues)
+{
+ int pepind = 0;
+ for(int i = 0; i < set.size(); i++)
+ {
+ pepind = set[i].pepind;
+ double sc = get_peptide_score(pepind,n);
+ set[i].score = sc;
+ }
+
+ for(unsigned int ct = 0; ct < qvalues.size(); ct++)
+ overFDRmulti[ct] = 0;
+ set.calcMultiOverFDR(qvalues, overFDRmulti);
+}
+
+void PepRanker :: write_max_nets(string filename, NeuralNet* max_net)
+{
+ ofstream f1(filename.c_str());
+ f1 << "FDR thresh" << "\t" << "PSMs trn" << "\t" << "PSMs tst" << endl;
+ for(int count = 0; count < num_qvals; count++)
+ {
+ net = max_net[count];
+ int r = getOverFDR(testset,net, qvals[count]);
+ int r1 = getOverFDR(trainset,net, qvals[count]);
+ f1 << qvals[count] << "\t" << r1 << "\t" << r << "\n";
+
+ double qn;
+ if(qvals[count] < 0.01)
+ qn = 0.0012;
+ else
+ qn = 0.005;
+ r = getOverFDR(testset,net, qvals[count]+qn);
+ r1 = getOverFDR(trainset,net, qvals[count]+qn);
+ f1 << qvals[count]+qn << "\t" << r1 << "\t" << r << "\n";
+
+ }
+ f1.close();
+}
+
+/***************************************************************************/
+
+double PepRanker :: get_protein_score(int pepind)
+{
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ double max_sc = -1000000.0;
+ int max_ind = 0;
+ for (int j = 0; j < num_psms; j++)
+ {
+ double *feat = d.psmind2features(psminds[j]);
+ double *sc = net_clones[psm_count].fprop(feat);
+ if(sc[0] > max_sc)
+ {
+ max_sc = sc[0];
+ max_ind = j;
+ }
+ psm_count++;
+ }
+ max_psm_inds.push_back(max_ind);
+
+ return max_sc;
+}
+
+void PepRanker :: calc_gradients(int pepind, int label, int i)
+{
+ double *gc = new double[1];
+ gc[0] = -label;
+ int num_psms = d.pepind2num_psm(pepind);
+ int clone_ind = psm_count+max_psm_inds[i];
+ net_clones[clone_ind].bprop(gc);
+ psm_count += num_psms;
+ delete[] gc;
+}
+
+
+
+void PepRanker :: train_net_ranking(PepScores &set, int interval)
+{
+ double r1;
+ double r2;
+ double diff = 0;
+ int label = 1;
+ double *gc = new double[1];
+
+
+ for(int i = 0; i < set.size(); i++)
+ {
+ int ind1, ind2;
+ int label_flag = 1;
+ //get the first index
+ if(interval == 0)
+ ind1 = 0;
+ else
+ ind1 = myrandom_limit(interval);
+ if(ind1>set.size()-1) continue;
+ if(set[ind1].label == 1)
+ label_flag = -1;
+ else
+ label_flag = 1;
+
+ int cn = 0;
+ while(1)
+ {
+ ind2 = myrandom_limit(interval);
+ if(ind2>set.size()-1) continue;
+ if(set[ind2].label == label_flag) break;
+ if(cn > 1000)
+ {
+ ind2 = myrandom_limit(set.size());
+ break;
+ }
+ cn++;
+ }
+
+ //get the scores
+ max_psm_inds.erase(max_psm_inds.begin(),max_psm_inds.end());
+ psm_count = 0;
+ //pass both through the net
+ r1 = get_protein_score(set[ind1].pepind);
+ assert(psm_count == d.pepind2num_psm(set[ind1].pepind));
+ r2 = get_protein_score(set[ind2].pepind);;
+ assert((int)max_psm_inds.size() == 2);
+
+
+ diff = r1-r2;
+
+
+ label=0;
+ if( set[ind1].label==1 && set[ind2].label==-1)
+ label=1;
+ if( set[ind1].label==-1 && set[ind2].label==1)
+ label=-1;
+
+ if(label != 0)
+ {
+ if(label*diff<1)
+ {
+ net.clear_gradients();
+ psm_count = 0;
+ calc_gradients(set[ind1].pepind, label, 0);
+ calc_gradients(set[ind2].pepind, -1.0*label, 1);
+ net.update(mu,weightDecay);
+ }
+
+ }
+ }
+ delete[] gc;
+
+}
+
+void PepRanker :: train_many_target_nets()
+{
+
+ int thr_count = num_qvals-1;
+ while (thr_count > 0)
+ {
+ net.copy(max_net_gen[thr_count]);
+
+ carp(CARP_INFO, "training threshold %d", thr_count);
+ interval = max_overFDR[thr_count];
+ for(int i=switch_iter;i<niter;i++) {
+ //sorts the examples in the training set according to the current net scores
+ getMultiFDR(trainset,net,qvals);
+ train_net_ranking(trainset, interval);
+
+ for(int count = 0; count < num_qvals;count++)
+ {
+ if(overFDRmulti[count] > max_overFDR[count])
+ {
+ max_overFDR[count] = overFDRmulti[count];
+ max_net_targ[count] = net;
+ }
+ }
+
+ if((i % 3) == 0)
+ {
+ carp(CARP_INFO, "Iteration %d :", i);
+ getMultiFDR(trainset,net,qvals);
+ carp(CARP_INFO, "trainset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+ getMultiFDR(testset,net,qvals);
+ carp(CARP_INFO, "testset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d\n ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+
+ }
+
+ }
+ thr_count -= 3;
+ }
+}
+
+
+void PepRanker :: train_many_general_nets()
+{
+ interval = trainset.size();
+ for(int i=0;i<switch_iter;i++) {
+ train_net_ranking(trainset, interval);
+
+ //record the best result
+ getMultiFDR(thresholdset,net,qvals);
+ for(int count = 0; count < num_qvals;count++)
+ {
+ if(overFDRmulti[count] > max_overFDR[count])
+ {
+ max_overFDR[count] = overFDRmulti[count];
+ max_net_gen[count] = net;
+ }
+ }
+ if((i % 10) == 0)
+ {
+ carp(CARP_INFO, "Iteration %d :", i);
+ getMultiFDR(trainset,net,qvals);
+ carp(CARP_INFO, "trainset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+ getMultiFDR(testset,net,qvals);
+ carp(CARP_INFO, "testset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d\n ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+ }
+ }
+
+}
+
+void PepRanker::train_many_nets()
+{
+ carp(CARP_INFO, "Before Iterating");
+ getMultiFDRXCorr(trainset,qvals);
+ carp(CARP_INFO, "trainset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+ getMultiFDRXCorr(testset,qvals);
+ carp(CARP_INFO, "trainset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d \n",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+
+ train_many_general_nets();
+
+ //copy the general net into target nets;
+ for(int count = 0; count < num_qvals; count++)
+ max_net_targ[count] = max_net_gen[count];
+
+ train_many_target_nets();
+
+ ostringstream fname;
+ fname << out_dir << "/" << fileroot << "pep-ranker.peps.at.fdr.thresholds.txt";;
+ write_max_nets(fname.str(), max_net_targ);
+
+}
+
+void PepRanker :: setup_for_training()
+{
+ //mysrandom(seed); This is set by CruxApplication::initialize()
+ carp(CARP_INFO, "reading data");
+
+ ostringstream res;
+ res << out_dir << "/qranker_output";
+ res_prefix = res.str();
+
+ d.load_data_pep_training();
+ if(feature_file_flag)
+ {
+ string str = feature_file_name.str();
+ if(!d.print_features(str))
+ carp(CARP_INFO, "could not open file %s for writing features. Feature file will not be written", feature_file_name.str().c_str());
+ }
+ d.normalize_psms();
+ d.load_labels_pep_training();
+ PepScores::fillFeaturesSplit(trainset, testset, d, 0.75);
+ thresholdset = trainset;
+ d.clear_labels_pep_training();
+
+ int max_psm = 0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ int pepind = trainset[i].pepind;
+ int num_psm = d.pepind2num_psm(pepind);
+ if(num_psm > max_psm)
+ max_psm=num_psm;
+ }
+
+ switch_iter =30;
+ niter = 40;
+
+ num_qvals = 14;
+ qvals.resize(num_qvals,0.0);
+ overFDRmulti.resize(num_qvals,0);
+ max_overFDR.resize(num_qvals,0);
+
+ //initialize q-value arrays
+ double q = 0.0;
+ for(int count = 0; count < num_qvals; count++)
+ {
+ qvals[count] = q;
+ if(q < 0.01)
+ q+=0.0025;
+ else
+ q+=0.01;
+ }
+
+ max_net_gen = new NeuralNet[num_qvals];
+ max_net_targ = new NeuralNet[num_qvals];
+ //set the linear flag: 1 if linear, 0 otherwise
+ int lf = 0; num_hu = 3;
+ if(num_hu == 1)
+ lf = 1;
+ //set whether there is bias in the linear units: 1 if yes, 0 otherwise
+ int bs = 0;
+
+ net.initialize(d.get_num_features(),num_hu,lf,bs);
+ for(int count = 0; count < num_qvals; count++){
+ max_net_gen[count] = net;
+ }
+
+ //create the net clones
+ net_clones = new NeuralNet[2*max_psm];
+ for (int i = 0; i < 2*max_psm;i++)
+ net_clones[i].clone(net);
+
+}
+
+
+int PepRanker::run( ) {
+
+ setup_for_training();
+ train_many_nets();
+ report_results_xml_tab();
+ return 0;
+}
+
+/**************************************************************************/
+
+void PepRanker :: get_pep_seq(string &pep, string &seq, string &n, string &c)
+{
+ string tmp;
+ int pos;
+ pos = pep.find('.');
+ n = pep.at(pos-1);
+ tmp = pep.substr(pos+1, pep.size());
+
+ pos = tmp.find('.');
+ c = tmp.at(pos+1);
+ seq = tmp.substr(0, pos);
+}
+
+void PepRanker :: get_tab_delim_proteins(string protein_str, vector<string> &proteins)
+{
+ proteins.clear();
+ string str = protein_str;
+ size_t pos = str.find("\t");
+ while(pos != string::npos){
+ if(pos == 0){
+ str = str.substr(1,str.size()-1);
+ } else{
+ string prot = str.substr(0,pos);
+ str = str.substr(pos+1,str.size()-1);
+ proteins.push_back(prot);
+ }
+ pos = str.find("\t");
+ }
+ proteins.push_back(str);
+}
+
+
+void PepRanker :: setup_for_reporting_results()
+{
+ d.load_labels_pep_training();
+ trainset.clear();
+ testset.clear();
+ thresholdset.clear();
+ PepScores::fillFeaturesFull(trainset, d);
+ psmtrainset.clear();
+ psmtestset.clear();
+ PSMScores::fillFeaturesFull(psmtrainset, d);
+ d.clear_labels_pep_training();
+
+ //choose the best net for the selectionfdr
+ int max_fdr = 0;
+ int fdr = 0;
+ int ind = 0;
+ for(unsigned int count = 0; count < qvals.size();count++)
+ {
+ fdr = getOverFDR(trainset, max_net_targ[count], selectionfdr);
+ if(fdr > max_fdr) {
+ max_fdr = fdr;
+ ind = count;
+ }
+ }
+ net = max_net_targ[ind];
+ pepind_to_max_psmind.clear();
+ pepind_to_max_psmind.resize(d.get_num_peptides(),-1);
+ int fdr_trn = getOverFDR(trainset,net, selectionfdr);
+ carp(CARP_INFO, "total peptides at q<%.2f: %d", selectionfdr, fdr_trn);
+ getOverFDRPSM(psmtrainset, net, selectionfdr);
+ d.clear_data_pep_training();
+ d.load_data_pep_results();
+
+ computePepNSAF();
+ computePEP();
+
+}
+
+/*****************************************************/
+
+void PepRanker :: write_results_peptides_xml(ofstream &os)
+{
+ string protein_str;
+ vector<string> tab_delim_proteins;
+ os << "<peptides>" <<endl;
+ int cn = 0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ int pepind = trainset[i].pepind;
+ if(trainset[i].label == 1)
+ {
+ cn++;
+ //write out proteins
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ os << " <peptide peptide_id=\"" << seq << "\">" << endl;
+ os << " <q_value>" << trainset[i].q << "</q_value>" << endl;
+ os << " <score>" << trainset[i].score << "</score>" << endl;
+ os << " <nsaf>" << trainset[i].nsaf << "</nsaf>" << endl;
+ os << " <barista PEP>" <<trainset[i].PEP<<"</barista PEP>"<<endl;
+ //write out peptides
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1)
+ os << " <main_psm_id>"<< psmind << "</main_psm_id>" << endl;
+ else
+ cout << "warning: did not assign peptide" << pep << " ind " << pepind << " max psmind\n";
+
+ //print out all the psms in which this peptide is present
+ int num_psm = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ os << " <psm_ids>" << endl;
+ for(int j = 0; j < num_psm; j++)
+ os << " <psm_id>" << psminds[j] << "</psm_id>" << endl;
+ os << " </psm_ids>" << endl;
+
+
+ //print out all the proteins
+ int num_prot = d.pepind2num_prot(pepind);
+ int *protinds = d.pepind2protinds(pepind);
+ os << " <protein_ids>" << endl;
+ for(int j = 0; j < num_prot; j++)
+ {
+ protein_str = d.ind2prot(protinds[j]);
+ get_tab_delim_proteins(protein_str, tab_delim_proteins);
+ for(unsigned int k = 0; k < tab_delim_proteins.size(); k++)
+ os << " <protein_id>" << tab_delim_proteins[k] << "</protein_id>" <<endl;
+ //os << " <protein_id>" << d.ind2prot(protinds[j]) << "</protein_id>" << endl;
+ }
+
+ os << " </protein_ids>" << endl;
+ os << " </peptide>" << endl;
+ }
+
+ }
+ os << "</peptides>" << endl;
+}
+
+void PepRanker :: write_results_psm_xml(ofstream &os)
+{
+ os << "<psms>" <<endl;
+ int cn = 0;
+ for(int i = 0; i < psmtrainset.size(); i++)
+ {
+ int psmind = psmtrainset[i].psmind;
+ if(psmtrainset[i].label == 1)
+ {
+ cn++;
+ //write out proteins
+ os << " <psm psm_id=" << "\"" << psmind << "\"" << ">" << endl;
+ os << " <q_value>" << psmtrainset[i].q << "</q_value>" << endl;
+ os << " <score>" << psmtrainset[i].score << "</score>" << endl;
+ os << " <scan>" << d.psmind2scan(psmind) << "</scan>" << endl;
+ os << " <charge>" << d.psmind2charge(psmind) << "</charge>" << endl;
+ os << " <precursor_mass>" << d.psmind2precursor_mass(psmind) << "</precursor_mass>" << endl;
+ int pepind = d.psmind2pepind(psmind);
+ string pep = d.ind2pep(pepind);
+ string seq, n,c;
+ get_pep_seq(pep,seq,n,c);
+ os << " <peptide_seq n =\"" << n << "\" c=\"" << c << "\" seq=\"" << seq << "\"/>" << endl;
+ os << " <file_name>" << d.psmind2fname(psmind) << "</file_name>" << endl;
+ os << " </psm>" << endl;
+ }
+ }
+ os << "</psms>" << endl;
+}
+
+
+void PepRanker :: report_results_xml()
+{
+
+ ostringstream fname;
+ fname << out_dir << "/" << fileroot << "barista.xml";
+ ofstream of(fname.str().c_str());
+ of << "<barista_output>" << endl;
+ of << endl;
+
+ write_results_peptides_xml(of);
+
+ write_results_psm_xml(of);
+
+ ostringstream xml_file_name;
+ xml_file_name << out_dir << "/" << fileroot << "barista.target.pep.xml";
+ PepXMLWriter xmlfile;
+ xmlfile.openFile(xml_file_name.str().c_str(), overwrite_flag);
+
+ //...
+ xmlfile.closeFile();
+ write_results_pep_xml(xmlfile);
+
+
+ of << endl;
+ of << "</barista_output>" << endl;
+ of.close();
+
+}
+
+/***********************************************************************************/
+
+void PepRanker :: write_results_peptides_tab(ofstream &os)
+{
+ int ps = pepind_to_max_psmind[trainset[0].pepind];
+ os<< "q-value" << "\t" << "barista score" << "\t";
+ os << "NSAF score" << "\t";
+ os<<"barista PEP\t";
+ os << "scan" << "\t" ;
+ os<< "charge" << "\t";
+ os<<"spectrum precursor m/z"<<"\t";
+ os<<"spectrum neutral mass"<<"\t";
+ os<<"peptide mass"<<"\t";
+ os<< "delta_cn"<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"sp score"<<"\t";
+ os<<"sp rank\t";
+ }
+ os<<"xcorr score"<<"\t";
+ os<<"xcorr rank"<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"b/y ions matched"<<"\t";
+ os<<"b/y ions total"<<"\t";
+ }
+ os<<"distinct matches/spectrum"<<"\t";
+ os<<"sequence\t";
+ os<<"cleavage type"<<"\t";
+ os<<"protein id"<<"\t";
+ os<<"flanking_aa"<<endl;
+ int cn = 0;
+ for(int i = 0; i < trainset.size(); i++){
+ if(trainset[i].label == 1){
+ cn++;
+ //write out proteins
+ int pepind = trainset[i].pepind;
+ string pep = d.ind2pep(pepind);
+ string seq, n, c;
+ get_pep_seq(pep, seq, n, c);
+ //q-value
+ os << trainset[i].q << "\t";
+ //score
+ os << trainset[i].score << "\t";
+ ///nsaf
+ os<<trainset[i].nsaf<<"\t";
+ //PEP
+ os<<trainset[i].PEP<<"\t";
+
+ //write out peptides
+ int psmind = pepind_to_max_psmind[pepind];
+ if(psmind > -1){
+ //scan
+ os << d.psmind2scan(psmind) << "\t" ;
+ //charge
+ os<< d.psmind2charge(psmind)<<"\t";
+ //mass-to-charge ratio
+ os<<(d.psmind2precursor_mass(psmind)+
+ d.psmind2charge(psmind)*MASS_PROTON)/
+ d.psmind2charge(psmind)<<"\t";
+ //Spectrum Neutral Mass
+ os<<d.psmind2precursor_mass(psmind)<<"\t";
+ //Peptide Mass
+ os<<d.psmind2peptide_mass(psmind)<<"\t";
+ //DELTA CN
+ os <<d.psmind2deltaCn(psmind)<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //Sp Score
+ os<<d.psmind2spscore(psmind)<<"\t";
+ //Sp Rank
+ os<<d.psmind2sp_rank(psmind)<<"\t";
+ }
+ //xcorr Score
+ os<<d.psmind2xcorr(psmind)<<"\t";
+ //xcorr rank
+ os<<d.psmind2xcorr_rank(psmind)<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //by ions match
+ os<<d.psmind2by_ions_matched(psmind)<<"\t";
+ //by ions total
+ os<<d.psmind2by_ions_total(psmind)<<"\t";
+ }
+ //Matches/Spectrum
+ os<<d.psmind2matches_spectrum(psmind)<<"\t";
+ //sequence
+ os<<seq<<"\t";
+ //cleavage type
+ os<<cleavage_type<<"\t";
+ //protein id
+ vector<string> prots;
+ get_protein_id(pepind,prots);
+ print_protein_ids(prots,os,psmind);
+ //Flanking_aa
+ os<<n<<c<<endl;
+ }else{
+ cout<< "waning: did not assign peptide max psmind\n";
+ os<<"not assignd\t";
+ }
+
+ }
+ }
+}
+
+void PepRanker :: write_results_psm_tab(ofstream &os)
+{
+ int ps= psmtrainset[0].psmind;
+ os << "scan" << "\t" << "charge" << "\t";
+ os << "q-value" << "\t" << "barista score" << "\t";
+ os << "barista PEP\t";
+ os<<"spectrum precursor m/z"<<"\t";
+ os<<"spectrum neutral mass"<<"\t";
+ os<<"peptide mass"<<"\t";
+ os<< "delta_cn"<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"sp score"<<"\t";
+ os<<"sp rank\t";
+ }
+ os<<"xcorr score"<<"\t";
+ os<<"xcorr rank"<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"b/y ions matched"<<"\t";
+ os<<"b/y ions total"<<"\t";
+ }
+ os<<"distinct matches/spectrum"<<"\t";
+ os<<"sequence"<<"\t";
+ os<<"cleavage type"<<"\t";
+ os<<"protein id"<<"\t";
+ os<<"flanking aa"<<"\t";
+ os << "filename" << endl;
+ int cn = 0;
+ for(int i = 0; i < psmtrainset.size(); i++)
+ {
+ if(psmtrainset[i].label == 1)
+ {
+ cn++;
+ //write out proteins
+ int psmind = psmtrainset[i].psmind;
+ int pepind = d.psmind2pepind(psmind);
+ string pep = d.ind2pep(pepind);
+ string seq, n,c;
+ get_pep_seq(pep,seq,n,c);
+ //os << psmind << "\t";
+ os << d.psmind2scan(psmind) << "\t";
+ os << d.psmind2charge(psmind) << "\t";
+ os << psmtrainset[i].q << "\t";
+ os << psmtrainset[i].score << "\t";
+ os << psmtrainset[i].PEP << "\t";
+ //mass-to-charge ratio
+ os<<(d.psmind2precursor_mass(psmind)+
+ d.psmind2charge(psmind)*MASS_PROTON)/
+ d.psmind2charge(psmind)<<"\t";
+ //Spectrum Neutral Mass
+ os<<d.psmind2precursor_mass(psmind)<<"\t";
+ //Peptide Mass
+ os<<d.psmind2peptide_mass(psmind)<<"\t";
+ //DELTA CN
+ os <<d.psmind2deltaCn(psmind)<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //Sp Score
+ os<<d.psmind2spscore(psmind)<<"\t";
+ //Sp Rank
+ os<<d.psmind2sp_rank(psmind)<<"\t";
+ }
+ //xcorr Score
+ os<<d.psmind2xcorr(psmind)<<"\t";
+ //xcorr rank
+ os<<d.psmind2xcorr_rank(psmind)<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //by ions match
+ os<<d.psmind2by_ions_matched(psmind)<<"\t";
+ //by ions total
+ os<<d.psmind2by_ions_total(psmind)<<"\t";
+ }
+ //Distinct matches/Spectrum
+ os<<d.psmind2matches_spectrum(psmind)<<"\t";
+ get_pep_seq(pep,seq,n,c);
+ //Sequence
+ os<<seq<<"\t";
+ //cleavage type
+ os<<cleavage_type<<"\t";
+ //protein id
+ vector<string> prots;
+ get_protein_id(pepind,prots);
+ print_protein_ids(prots,os,psmind);
+ //Flanking_aa
+ os<<n<<c<<"\t";
+ os << d.psmind2fname(psmind) << endl;
+ }
+ }
+}
+
+
+void PepRanker :: report_results_tab()
+{
+ ofstream of;
+ ostringstream fname;
+
+ fname << out_dir << "/" << fileroot << "barista.target.peptides.txt";
+ of.open(fname.str().c_str());
+ write_results_peptides_tab(of);
+ of.close();
+ fname.str("");
+
+ fname << out_dir << "/" << fileroot << "barista.target.psms.txt";
+ of.open(fname.str().c_str());
+ write_results_psm_tab(of);
+ of.close();
+ fname.str("");
+
+}
+/******************************************************************/
+
+
+void PepRanker :: report_results_xml_tab()
+{
+ setup_for_reporting_results();
+ report_results_xml();
+ report_results_tab();
+ d.clear_data_pep_results();
+
+}
+
+
+void PepRanker :: print_description()
+{
+ cout << endl;
+ cout << "\t crux q-ranker [options] <spectra> <search results>" << endl <<endl;
+ cout << "REQUIRED ARGUMENTS:" << endl << endl;
+ cout << "\t <spectra> Directory with ms2 files, list of ms2 files or a single ms2 file used for database search." << endl;
+ cout << "\t <search results> Directory with sqt files, list of sqt files or a single sqt file with psms generated during search." << endl;
+ cout << endl;
+
+ cout << "OPTIONAL ARGUMENTS:" << endl << endl;
+ cout << "\t [--enzyme <string>] \n \t The enzyme used to digest the proteins in the experiment. Default trypsin." << endl;
+ cout << "\t [--decoy-prefix <string>] \n \t Specifies the prefix of the protein names that indicates a decoy. Default decoy_" << endl;
+ cout << "\t [--separate-searches <string>] \n \t If the target and decoy searches were run separately, the option then allows the user to specify the location of the decoy search results, the target database search should be provided as required argument." << endl;
+ cout << "\t [--fileroot <string>] \n \t The fileroot string will be added as a prefix to all output file names. Default = none." <<endl;
+ cout << "\t [--output-dir <directory>] \n \t The name of the directory where output files will be created. Default = crux-output." << endl;
+ cout << "\t [--overwrite <T/F>] \n \t Replace existing files (T) or exit if attempting to overwrite (F). Default=F." << endl;
+ cout << "\t [--skip-cleanup <T/F>] \n \t When set to T, prevents the deletion of lookup tables created during the preprocessing step. Default = F." << endl;
+ cout << "\t [--re-run <directory>] \n \t Re-run PepRanker analysis using a previously computed set of lookup tables." <<endl;
+ cout << "\t [--use-spec-features <T/F>] \n \t When set to F, use minimal feature set. Default T." <<endl;
+ cout << endl;
+
+}
+string PepRanker:: file_extension (string str){
+ string file_exten= str.substr(str.rfind('.')+1);
+ return file_exten;
+}
+
+
+FILE_FORMAT_T PepRanker::check_file_format(string& source) {
+ string ext = file_extension(source);
+
+ if (ext=="sqt")
+ return SQT_FORMAT;
+ else if (ext=="txt")
+ return DELIMITED_FORMAT;
+ return INVALID_FORMAT;
+}
+
+int PepRanker :: crux_set_command_line_options(int argc, char *argv[])
+{
+ string sqt_source;
+ string ms2_source;
+ string sqt_decoy_source;
+ int separate_search_flag;
+ string output_directory;
+ string enzyme;
+ string decoy_prefix;
+
+ string dir_with_tables;
+ int found_dir_with_tables;
+
+ bool spec_features_flag;
+ bool list_of_files_flag;
+ overwrite_flag = Params::GetBool("overwrite");
+
+ fileroot = Params::GetString("fileroot");
+ if(!fileroot.empty()) {
+ fileroot.append(".");
+ }
+
+ decoy_prefix = Params::GetString("decoy-prefix");
+
+
+ enzyme = Params::GetString("enzyme");
+
+ spec_features_flag = Params::GetBool("use-spec-features");
+
+ skip_cleanup_flag = Params::GetBool("skip-cleanup");
+
+
+ dir_with_tables = Params::GetString("re-run");
+ if(!dir_with_tables.empty()) {
+ found_dir_with_tables = 1;
+ } else {
+ found_dir_with_tables = 0;
+ }
+
+ output_directory = Params::GetString("output-dir");
+
+ feature_file_flag = Params::GetBool("feature-file-out");
+ feature_file_name << output_directory << "/" << fileroot << "q-ranker.features.txt";
+
+ if(found_dir_with_tables)
+ {
+ //set input and output dirs
+ parser = new SQTParser();
+ parser -> set_output_dir(dir_with_tables);
+ set_input_dir(dir_with_tables);
+ set_output_dir(output_directory);
+
+ carp(CARP_INFO, "directory with tables: %s", dir_with_tables.c_str());
+ carp(CARP_INFO, "output_directory: %s", output_directory.c_str());
+ }else{
+ ms2_source = Params::GetString("fragmentation spectra");
+ sqt_source = Params::GetString("search results");
+ list_of_files_flag = Params::GetBool("list-of-files");
+ //check file format
+
+ vector<string> files;
+ string files_list;
+ if(list_of_files_flag==1){
+ ifstream f(sqt_source.c_str());
+ f>>files_list;
+ while(!f.eof()){
+ files.push_back(files_list);
+ f>> files_list;
+ }
+ }else{
+ files.push_back(sqt_source);
+ }
+
+ for(unsigned i=0; i<files.size();i++){
+ FILE_FORMAT_T format = check_file_format(files[i]);
+ switch (format) {
+ case SQT_FORMAT:
+ file_format_="sqt";
+ parser = new SQTParser();
+ break;
+ case DELIMITED_FORMAT:
+ file_format_="txt";
+ parser = new CruxParser();
+ break;
+ case INVALID_FORMAT:
+ file_format_="NULL";
+ default:
+ carp(CARP_FATAL, "Please enter .sqt or .txt search results");
+ }
+
+ parser->set_decoy_prefix(decoy_prefix);
+ parser->set_enzyme(enzyme);
+ if(enzyme.find("elastase") != string::npos){
+ cleavage_type="elastase-full-digest";
+ }else if (enzyme.find("chymotrypsin") != string::npos){
+ cleavage_type="chymotrypsin-full-digest";
+ }else if (enzyme.find("trypsin") != string::npos){
+ cleavage_type="trypsin-full-digest";
+ }else{
+ cleavage_type="Null";
+ }
+
+ //num of spec features
+ if(spec_features_flag)
+ parser->set_num_spec_features(3);
+ else
+ parser->set_num_spec_features(0);
+ parser->write_features_header();
+
+ if(parser->get_use_quadratic_features())
+ parser->add_quadratic_features_header();
+ d.get_features_header(parser->get_final_features_header());
+ sqt_decoy_source = Params::GetString("separate-searches");
+ if(!sqt_decoy_source.empty()) {
+ separate_search_flag = 1;
+ } else {
+ separate_search_flag = 0;
+ }
+
+ //set the output directory for the parser
+ if(!parser->set_output_dir(output_directory))
+ return 0;
+ //set input and output for the leaning algo (in and out are the same as the out for the parser)
+ set_input_dir(output_directory);
+ set_output_dir(output_directory);
+
+ if(separate_search_flag){
+ if(!parser->set_input_sources(ms2_source, sqt_source, sqt_decoy_source)){
+ carp(CARP_FATAL, "could not extract features for training");
+ }
+ parser->set_num_hits_per_spectrum(1);
+ }else{
+ if(!parser->set_input_sources(ms2_source, sqt_source)){
+ carp(CARP_FATAL, "could not extract features for training");
+ }
+ }
+
+ //print some info
+ if(format==SQT_FORMAT)
+ carp(CARP_INFO, "sqt source: %s", sqt_source.c_str());
+ if(format==DELIMITED_FORMAT)
+ carp(CARP_INFO, "delmited source: %s", sqt_source.c_str());
+ carp(CARP_INFO, "ms2 source: %s", ms2_source.c_str());
+ carp(CARP_INFO, "output_directory: %s", output_directory.c_str());
+ carp(CARP_INFO, "enzyme: %s", enzyme.c_str());
+ carp(CARP_INFO, "decoy prefix: %s", decoy_prefix.c_str());
+
+ if(!parser->run())
+ carp(CARP_FATAL, "Could not proceed with training.");
+ parser->clear();
+ }
+ }
+
+ if(!parser->check_input_dir(in_dir))
+ carp(CARP_FATAL, "Please re-run with ms2 input and txt input.");
+
+ return 1;
+
+
+}
+
+
+
+int PepRanker :: computePepNSAF()
+{
+
+ //create auxiliary psmind_to_ind index
+ vector<int>psmind_to_ind;
+ psmind_to_ind.resize(psmtrainset.size(),0);
+ for(int i = 0; i < psmtrainset.size(); i++)
+ psmind_to_ind[psmtrainset[i].psmind] = i;
+
+ //compute NSAF for each peptide
+ double sum = 0.0;
+ for(int k = 0; k < trainset.size(); k++)
+ {
+ if(trainset[k].label == 1)
+ {
+ int pepind = trainset[k].pepind;
+ string pep = d.ind2pep(pepind);
+ string seq, n,c;
+ get_pep_seq(pep,seq,n,c);
+ int len = seq.size();
+
+ int cnt = 0;
+ int num_psms = d.pepind2num_psm(pepind);
+ int *psminds = d.pepind2psminds(pepind);
+ for (int j = 0; j < num_psms; j++)
+ {
+ int psmind = psminds[j];
+ int ind = psmind_to_ind[psmind];
+ assert(psmtrainset[ind].psmind == psmind);
+ if(psmtrainset[ind].q <= 0.01)
+ cnt++;
+ }
+
+ //compute NSAF for this protein
+ double nsaf = 0.0;
+ if(len != 0)
+ nsaf = (double)cnt/(double)len;
+ trainset[k].nsaf = nsaf;
+ sum += nsaf;
+ }
+ }
+
+ if(sum > 0)
+ {
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ if(trainset[i]. label == 1)
+ trainset[i].nsaf /= sum;
+ }
+ }
+ else
+ return 0;
+
+ /*
+ double check = 0.0;
+ for(int i = 0; i < trainset.size(); i++)
+ {
+ if(trainset[i]. label == 1)
+ check += trainset[i].nsaf;
+ }
+ cout << check << endl;
+ */
+ psmind_to_ind.clear();
+ return 1;
+}
+
+
+void PepRanker :: computePEP(){
+ carp(CARP_DEBUG, "Computing PEPs");
+ vector<double> target_scores_vect;
+ vector<double> decoy_scores_vect;
+
+ // pull out the target and decoy scores
+ for(int i = 0; i < psmtrainset.size(); i++){
+ if( psmtrainset[i].label == 1 ){
+ target_scores_vect.push_back(psmtrainset[i].score);
+ } else { // == -1
+ decoy_scores_vect.push_back(psmtrainset[i].score);
+ }
+ }
+
+ int num_targets = target_scores_vect.size();
+ int num_decoys = decoy_scores_vect.size();
+ carp(CARP_DEBUG, "Found %d targets and %d decoys", num_targets, num_decoys);
+
+ // copy them to an array as required by the compute_PEP method
+ double* target_scores = new double[num_targets];
+ copy(target_scores_vect.begin(), target_scores_vect.end(), target_scores);
+ double* decoy_scores = new double[num_decoys];
+ copy(decoy_scores_vect.begin(), decoy_scores_vect.end(), decoy_scores);
+
+ double* PEPs = ComputeQValues::compute_PEP(target_scores, num_targets,
+ decoy_scores, num_decoys);
+
+ // fill in the data set with the new scores for the targets
+ int target_idx = 0;
+ for(int full_idx = 0; full_idx < psmtrainset.size(); full_idx++){
+ if( psmtrainset[full_idx].label == 1 ){
+ psmtrainset[full_idx].PEP = PEPs[target_idx];
+ target_idx++;
+ } // else, skip decoys
+ }
+
+ delete target_scores;
+ delete decoy_scores;
+ delete PEPs;
+
+ /**
+ * Calculate Peptide PEPs
+ */
+ target_scores_vect.clear();
+ decoy_scores_vect.clear();
+
+ //pull out the target and decoy scores for peptide PEPs
+ for(int i=0;i<trainset.size();i++){
+ if(trainset[i].label==1)
+ target_scores_vect.push_back(trainset[i].score);
+ else
+ decoy_scores_vect.push_back(trainset[i].score);
+ }
+ num_targets = target_scores_vect.size();
+ num_decoys = decoy_scores_vect.size();
+ carp(CARP_DEBUG, "Found %d targets and %d decoys", num_targets, num_decoys);
+
+ // copy them to an array as required by the compute_PEP method
+ target_scores = new double[num_targets];
+ copy(target_scores_vect.begin(), target_scores_vect.end(), target_scores);
+ decoy_scores = new double[num_decoys];
+ copy(decoy_scores_vect.begin(), decoy_scores_vect.end(), decoy_scores);
+ PEPs = ComputeQValues::compute_PEP(target_scores, num_targets,
+ decoy_scores, num_decoys);
+
+ // fill in the data set with the new scores for the targets
+ target_idx = 0;
+ for(int full_idx = 0; full_idx < trainset.size(); full_idx++){
+ if( trainset[full_idx].label == 1 ){
+ trainset[full_idx].PEP = PEPs[target_idx];
+ target_idx++;
+ } // else, skip decoys
+ }
+
+ delete target_scores;
+ delete decoy_scores;
+ delete PEPs;
+
+}
+
+
+void PepRanker :: write_results_pep_xml(PepXMLWriter& xmlfile)
+{
+ xmlfile.writeHeader();
+
+ bool* scores_to_print = new bool[NUMBER_SCORER_TYPES];
+ for(int score_idx = 0; score_idx < NUMBER_SCORER_TYPES; score_idx++){
+ scores_to_print[score_idx] = false;
+ }
+ scores_to_print[SP] = true;
+ scores_to_print[XCORR] = true;
+ scores_to_print[BARISTA_SCORE] = true;
+ scores_to_print[BARISTA_QVALUE] = true;
+ scores_to_print[BARISTA_PEP] = true;
+ scores_to_print[DELTA_CN] = true;
+ scores_to_print[BY_IONS_MATCHED] = true;
+ scores_to_print[BY_IONS_TOTAL] = true;
+
+ double* scores = new double[NUMBER_SCORER_TYPES];
+
+ for(int i = 0; i < psmtrainset.size(); i++) {
+ // only print target psms
+ if( psmtrainset[i].label == -1 ){
+ continue;
+ }
+
+ int psmind = psmtrainset[i].psmind;
+
+ // spectrum info
+ int scan = d.psmind2scan(psmind);
+ const char* filename = d.psmind2fname(psmind).c_str();
+ char** path_name = parse_filename_path_extension(filename, NULL);
+ filename = path_name[0];
+ double spectrum_mass = d.psmind2precursor_mass(psmind);
+ int charge = d.psmind2charge(psmind);
+
+ // peptide info
+ int pepind = d.psmind2pepind(psmind);
+ string pep = d.ind2pep(pepind);
+ string modified_sequence, n,c;
+ get_pep_seq(pep, modified_sequence, n, c);
+ char* sequence = unmodify_sequence(modified_sequence.c_str());
+ string flanking_aas = n + c;
+ double peptide_mass = d.psmind2peptide_mass(psmind);
+
+ // protein info
+ int num_proteins = d.pepind2num_prot(pepind);
+ int* protein_indexes = d.pepind2protinds(pepind);
+ vector<string> protein_names;
+ vector<string> protein_descriptions;
+ for(int prot_idx = 0; prot_idx < num_proteins; prot_idx++){
+ string protein_name = d.ind2prot(protein_indexes[prot_idx]);
+ protein_names.push_back(protein_name);
+ protein_descriptions.push_back("");
+ flanking_aas += "," + n + c; // todo
+ }
+
+ // psm info
+ int* psm_rank=new int[NUMBER_SCORER_TYPES] ;
+ psm_rank[XCORR]=1;
+ scores[XCORR] = d.psmind2xcorr(psmind);
+ scores[SP] = d.psmind2spscore(psmind);
+ scores[QRANKER_SCORE] = psmtrainset[i].score;
+ scores[QRANKER_QVALUE] = psmtrainset[i].q;
+ scores[QRANKER_PEP] = psmtrainset[i].PEP;
+ scores[DELTA_CN] = d.psmind2deltaCn(psmind);
+ scores[BY_IONS_MATCHED] = d.psmind2by_ions_matched(psmind);
+ scores[BY_IONS_TOTAL] = d.psmind2by_ions_total(psmind);
+
+ xmlfile.writePSM(scan, filename, spectrum_mass, charge, psm_rank,
+ sequence, modified_sequence.c_str(),
+ peptide_mass, num_proteins,
+ flanking_aas.c_str(), protein_names,
+ protein_descriptions, scores_to_print, scores,
+ d.psmind2matches_spectrum(psmind));
+
+ free(sequence);
+ if( path_name[0] ){
+ free(path_name[0]);
+ }
+ if( path_name[1] ){
+ free(path_name[1]);
+ }
+ free(path_name);
+ }
+
+ xmlfile.writeFooter();
+}
+
+
+
+int PepRanker::main(int argc, char **argv) {
+
+
+ if(!crux_set_command_line_options(argc, argv))
+ return 1;
+
+ run();
+ if(skip_cleanup_flag != 1)
+ parser->clean_up(out_dir);
+
+ return 0;
+}
+
+bool PepRanker :: needsOutputDirectory() const
+{
+ return true;
+}
+
+
+string PepRanker::getName() const {
+ return "q-ranker";
+}
+string PepRanker::getDescription() const {
+ return
+ "Analyze a collection of PSMs to target and decoy "
+ "sequences using the new q-ranker algorithm.";
+}
+
+vector<string> PepRanker::getArgs() const {
+ string arr[] = {
+ "fragmentation spectra",
+ "search results"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> PepRanker::getOptions() const {
+ string arr[] = {
+ "enzyme",
+ "decoy-prefix",
+ "separate-searches",
+ "fileroot",
+ "output-dir",
+ "overwrite",
+ "skip-cleanup",
+ "re-run",
+ "use-spec-features",
+ "parameter-file",
+ "verbosity",
+ "list-of-files",
+ "feature-file-out"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+COMMAND_T PepRanker::getCommand() const {
+ return QRANKER_COMMAND;
+}
+
+
+void PepRanker :: get_protein_id(int pepind, vector<string> &prot){
+ int * protinds= d.pepind2protinds(pepind) ;
+ unsigned prot_length=d.pepind2num_prot(pepind);
+ for (unsigned k=0;k<prot_length;k++){
+ string protein_str= d.ind2prot( protinds[k]);
+ prot.push_back(protein_str);
+ }
+}
+
+
+void PepRanker :: print_protein_ids(vector<string> &prots, ofstream &os, int psmind){
+
+ // TODO: find peptide position in SQT files
+ //sqt files do not return peptide position in the protein.
+ //if the search result file is txt we can find file peptide_pos and print it
+ // in front of protein, else do not print anything
+
+ if(file_format_=="txt"){
+ for (unsigned int j=0;j<prots.size();j++){
+ os << prots[j];
+ if (d.psmind2peptide_position(psmind) > -1) {
+ os << "("<<d.psmind2peptide_position(psmind)<<")";
+ }
+ if (j == prots.size() - 1) {
+ os << "\t";
+ } else {
+ os << ",";
+ }
+ }
+ }else if(file_format_=="sqt"){
+ for (unsigned int j=0;j<prots.size();j++){
+ if(j==prots.size()-1)
+ os<<prots[j]<<"\t";
+ else
+ os<<prots[j]<<",";
+ }
+ }
+ prots.clear();
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/qranker-barista/PepRanker.h b/src/app/qranker-barista/PepRanker.h
new file mode 100644
index 0000000..587ead2
--- /dev/null
+++ b/src/app/qranker-barista/PepRanker.h
@@ -0,0 +1,149 @@
+#ifndef PEPRANKER_H_
+#define PEPRANKER_H_
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <time.h>
+#include <cstdlib>
+#include <vector>
+#include <set>
+#include <map>
+#include <string>
+#include <math.h>
+using namespace std;
+
+#include "app/CruxApplication.h"
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+
+#include "io/PepXMLWriter.h"
+#include "NeuralNet.h"
+#include "DataSetCrux.h"
+#include "PSMScores.h"
+#include "PepScores.h"
+#include "SQTParser.h"
+#include "CruxParser.h"
+#include "TabDelimParser.h"
+#include "app/CruxApplication.h"
+#include "util/mass.h"
+#include "model/objects.h"
+
+class PepRanker: public CruxApplication
+{
+
+public:
+ PepRanker();
+ virtual ~PepRanker();
+
+ int run();
+ int getOverFDRPSM(PSMScores &set, NeuralNet &n, double fdr);
+ double get_peptide_score_xcorr(int pepind);
+ void getMultiFDRXCorr(PepScores &set, vector<double> &qvalues);
+ double get_peptide_score(int pepind, NeuralNet &n);
+ int getOverFDR(PepScores &set, NeuralNet &n, double fdr);
+ void getMultiFDR(PepScores &set, NeuralNet &n, vector<double> &qvalues);
+ void write_max_nets(string filename, NeuralNet *max_net);
+ double get_protein_score(int pepind);
+ void calc_gradients(int pepind, int label, int i);
+ void train_net_ranking(PepScores &set, int interval);
+ void train_many_general_nets();
+ void train_many_target_nets();
+ void train_many_nets();
+ void setup_for_training();
+ void setup_for_reporting_results();
+ void report_results_xml_tab();
+
+ void get_tab_delim_proteins(string protein_str, vector<string> &proteins);
+ void get_pep_seq(string &pep, string &seq, string &n, string &c);
+ void write_results_psm_xml(PepXMLWriter& os);
+ void computePEP();
+ int computePepNSAF();
+
+ void write_results_peptides_tab(ofstream &os);
+ void write_results_psm_tab(ofstream &os);
+ void report_results_tab();
+ void write_results_pep_xml(PepXMLWriter& xmlfile);
+ void write_results_peptides_xml(ofstream &os);
+ void write_results_psm_xml(ofstream &os);
+ void report_results_xml();
+
+ inline void set_fileroot(string &fl){fileroot = fl;}
+ inline void set_overwrite_flag(int flag) {overwrite_flag = flag;}
+ inline void set_input_dir(string &input_dir) {in_dir = input_dir; d.set_input_dir(input_dir);}
+ inline void set_output_dir(string &output_dir){out_dir = output_dir;}
+ void print_description();
+ int set_command_line_options(int argc, char **argv);
+ int crux_set_command_line_options(int argc, char *argv[]);
+
+ virtual int main(int argc, char** argv);
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual bool needsOutputDirectory() const;
+ virtual COMMAND_T getCommand() const;
+ FILE_FORMAT_T check_file_format(string &filePath);
+ string file_extension(string filename);
+ void get_protein_id(int pepind, vector<string> &prot);
+ void print_protein_ids(vector<string> &prots, ofstream &os, int psmind);
+
+protected:
+
+ Dataset d;
+ string res_prefix;
+
+ PepScores fullset;
+ PepScores trainset,testset,thresholdset;
+
+ PSMScores psmfullset;
+ PSMScores psmtrainset, psmtestset;
+
+ int seed;
+ double selectionfdr;
+
+ int num_features;
+ NeuralNet net;
+ int num_hu;
+ double mu;
+ double weightDecay;
+ string cleavage_type;
+ int ind_low;
+ int interval;
+ int niter;
+ int switch_iter;
+ double loss;
+
+ int num_qvals;
+ vector<double> qvals;
+ vector<int> overFDRmulti;
+ vector<int> max_overFDR;
+
+ NeuralNet* max_net_gen;
+ NeuralNet* max_net_targ;
+ NeuralNet *net_clones;
+
+ int psm_count;
+ vector<int> max_psm_inds;
+ vector<int> pepind_to_max_psmind;
+
+
+ string in_dir;
+ string out_dir;
+ int skip_cleanup_flag;
+ int overwrite_flag;
+ string fileroot;
+ int feature_file_flag;
+ ostringstream feature_file_name;
+
+ string file_format_;
+
+ TabDelimParser pars;
+ SQTParser* parser;
+
+
+};
+
+
+
+#endif /*QRANKER_H_*/
diff --git a/src/app/qranker-barista/PepScores.cpp b/src/app/qranker-barista/PepScores.cpp
new file mode 100644
index 0000000..ccad2e6
--- /dev/null
+++ b/src/app/qranker-barista/PepScores.cpp
@@ -0,0 +1,226 @@
+#include <assert.h>
+#include <iostream>
+#include <fstream>
+#include <utility>
+#include <algorithm>
+#include <set>
+#include <vector>
+#include <string>
+#include <math.h>
+using namespace std;
+#include "PepScores.h"
+#include "util/utils.h"
+
+inline bool operator>(const PepScoreHolder &one, const PepScoreHolder &other)
+ {return (one.score>other.score);}
+
+inline bool operator<(const PepScoreHolder &one, const PepScoreHolder &other)
+ {return (one.score<other.score);}
+
+
+
+PepScores::PepScores()
+{
+ factor=1;
+ neg=0;
+ pos=0;
+ posNow=0;
+}
+
+PepScores::~PepScores()
+{
+
+}
+
+void PepScores::clear()
+{
+ scores.clear();
+ pos=neg=posNow = 0;
+}
+
+
+/**
+ * Percentage of target scores that are drawn according to the null.
+ */
+double PepScores::pi0 = 0.9;
+
+
+/**
+ * Calculate the number of targets that score above a specified FDR.
+ */
+int PepScores::calcOverFDR(double fdr) {
+
+ vector<PepScoreHolder>::iterator it = scores.begin();
+
+ sort(scores.begin(),scores.end());
+ reverse(scores.begin(),scores.end());
+
+ int positives=0,nulls=0;
+ double efp=0.0,q;
+ posNow = 0;
+ register unsigned int ix=0;
+ for(it=scores.begin();it!=scores.end();it++) {
+ if (it->label!=-1)
+ positives++;
+ if (it->label==-1) {
+ nulls++;
+ efp=pi0*nulls*factor;
+ }
+ if (positives)
+ q=efp/(double)positives;
+ else
+ q=pi0;
+ if (q>pi0)
+ q=pi0;
+ it->q=q;
+ if (fdr>=q)
+ posNow = positives;
+ }
+ for (ix=scores.size();--ix;) {
+ if (scores[ix-1].q > scores[ix].q)
+ scores[ix-1].q = scores[ix].q;
+ }
+ return posNow;
+}
+
+
+void PepScores::calcMultiOverFDR(vector<double> &fdr, vector<int> &overFDR) {
+
+ vector<PepScoreHolder>::iterator it = scores.begin();
+
+ sort(scores.begin(),scores.end());
+ reverse(scores.begin(),scores.end());
+
+ int positives=0,nulls=0;
+ double efp=0.0,q;
+ register unsigned int ix=0;
+
+ for(it=scores.begin();it!=scores.end();it++) {
+ if (it->label==1)
+ positives++;
+ if (it->label==-1) {
+ nulls++;
+ efp=pi0*nulls*factor;
+ }
+ if (positives)
+ q=efp/(double)positives;
+ else
+ q=pi0;
+ it->q=q;
+ if (q>pi0)
+ q=pi0;
+
+ for(unsigned int ct = 0; ct < fdr.size(); ct++)
+ if (fdr[ct]>=q)
+ overFDR[ct] = positives;
+ }
+ for (ix=scores.size();--ix;) {
+ if (scores[ix-1].q > scores[ix].q)
+ scores[ix-1].q = scores[ix].q;
+ }
+
+}
+
+
+
+void PepScores::fillFeaturesFull(PepScores& full, Dataset& d) {
+
+ int n = d.get_num_peptides();
+
+ PepScoreHolder s;
+ full.scores.resize(n,s);
+ int num_pos = 0;
+ int num_neg = 0;
+
+ for (int i = 0; i < n; i++)
+ {
+ full.scores[i].pepind = i;
+ int label = d.pepind2label(i);
+ full.scores[i].label = label;
+ if (full.scores[i].label == 1)
+ num_pos++;
+ else
+ num_neg++;
+ }
+
+ full.pos=num_pos;
+ full.neg=num_neg;
+ full.factor = full.pos/(double)full.neg;
+}
+
+
+void PepScores::fillFeaturesSplit(PepScores& train,PepScores& test, Dataset& d, double ratio) {
+
+ int num_pep = d.get_num_peptides();
+
+ assert(ratio>0 && ratio < 1);
+ int n = num_pep;
+ int k = (int)(n*ratio);
+ int l = n-k;
+
+ PepScoreHolder s;
+
+ //collect everybody
+ vector<PepScoreHolder> all_examples;
+ all_examples.resize(n,s);
+ for (int i = 0; i < num_pep; i++)
+ {
+ all_examples[i].pepind = i;
+ int label = d.pepind2label(i);
+ all_examples[i].label = label;
+ }
+
+ //mix up the examples
+ for(int i = 0; i < n; i++)
+ {
+ int p1 = (int)((double)myrandom()/UNIFORM_INT_DISTRIBUTION_MAX*(n-1));
+ int p2 = (int)((double)myrandom()/UNIFORM_INT_DISTRIBUTION_MAX*(n-1));
+ s = all_examples[p1];
+ all_examples[p1] = all_examples[p2];
+ all_examples[p2] = s;
+ }
+
+ train.scores.resize(k,s);
+ test.scores.resize(l,s);
+
+
+ int num_pos_train = 0;
+ int num_neg_train = 0;
+ int num_pos_test = 0;
+ int num_neg_test = 0;
+ //distribute the normal set between train and test
+ for (int i = 0; i < k; i++)
+ {
+ train.scores[i] = all_examples[i];
+
+ if (train.scores[i].label == 1)
+ num_pos_train++;
+ else
+ num_neg_train++;
+ }
+ for(int i=0; i < l; i++)
+ {
+ test.scores[i] = all_examples[i+k];
+ if (test.scores[i].label == 1)
+ num_pos_test++;
+ else
+ num_neg_test++;
+ }
+ //cout << num_pos_train << " " << num_neg_train << " " << num_pos_test << " " << num_neg_test << "\n";
+ train.pos=num_pos_train;
+ test.pos=num_pos_test;
+ train.neg=num_neg_train;
+ test.neg=num_neg_test;
+ train.factor = train.pos/(double)train.neg;
+ test.factor = train.pos/(double)train.neg;
+
+}
+
+
+
+
+
+
+
+
+
diff --git a/src/app/qranker-barista/PepScores.h b/src/app/qranker-barista/PepScores.h
new file mode 100644
index 0000000..9403c6b
--- /dev/null
+++ b/src/app/qranker-barista/PepScores.h
@@ -0,0 +1,45 @@
+#ifndef PEPSCORES_H_
+#define PEPSCORES_H_
+#include <vector>
+#include <algorithm>
+using namespace std;
+#include "DataSetCrux.h"
+
+
+class PepScoreHolder{
+public:
+ double score;
+ int pepind;
+ double q;
+ int label;
+ double nsaf;
+ double PEP;
+ PepScoreHolder():score(0.0),pepind(0),q(0.0),label(0),nsaf(0.0),PEP(0.0){;}
+ virtual ~PepScoreHolder() {;}
+};
+
+class PepScores
+{
+public:
+ PepScores();
+ ~PepScores();
+ vector<PepScoreHolder>::iterator begin() {return scores.begin();}
+ vector<PepScoreHolder>::iterator end() {return scores.end();}
+ static double pi0;
+ double factor;
+ void clear();
+
+ int calcOverFDR(double fdr);
+ void calcMultiOverFDR(vector<double> &fdr, vector<int> &overFDR);
+ inline PepScoreHolder& operator[](int ix){return scores[ix];}
+ void static fillFeaturesSplit(PepScores& train,PepScores& test,Dataset &d, double ratio);
+ void static fillFeaturesFull(PepScores& full,Dataset &d);
+ inline int size(){return scores.size();}
+protected:
+ int neg,pos,posNow;
+ vector<PepScoreHolder> scores;
+};
+
+
+
+#endif /*PEPSCORES_H_*/
diff --git a/src/app/qranker-barista/ProtScores.cpp b/src/app/qranker-barista/ProtScores.cpp
new file mode 100644
index 0000000..e65049e
--- /dev/null
+++ b/src/app/qranker-barista/ProtScores.cpp
@@ -0,0 +1,917 @@
+#include "ProtScores.h"
+
+
+//inline bool operator<(const ProtScoreHolder &one, const ProtScoreHolder &other)
+//{return (one.score<other.score);}
+
+inline bool operator<(const ProtScoreHolder &one, const ProtScoreHolder &other)
+{return (one.score<other.score) || (one.score == other.score && one.protind < other.protind);}
+
+
+
+ProtScores::ProtScores()
+{
+ factor=1;
+ neg=0;
+ pos=0;
+ posNow=0;
+}
+
+ProtScores::~ProtScores()
+{
+}
+
+
+void ProtScores::clear()
+{
+ scores.clear();
+ pos=neg=posNow = 0;
+}
+
+/**
+ * Percentage of target scores that are drawn according to the null.
+ */
+double ProtScores::pi0 = 0.9;
+
+void ProtScores :: fillProteinsFull(ProtScores& fullset, Dataset &d)
+{
+ int n = d.get_num_proteins();
+ ProtScoreHolder s;
+ fullset.scores.resize(n,s);
+ int num_pos = 0;
+ int num_neg = 0;
+ for(int i = 0; i < n; i++)
+ {
+ fullset[i].protind = i;
+ int label = d.protind2label(i);
+ fullset[i].label = label;
+ if(label == 1)
+ num_pos++;
+ else
+ num_neg++;
+ }
+
+ fullset.pos = num_pos;
+ fullset.neg = num_neg;
+ fullset.factor = (double)num_pos/(double)num_neg;
+}
+
+
+int ProtScores :: traverse_peptide(Dataset &d, int pepind, int trn_tst, vector<int> &assignment_array)
+{
+ int num_added = 0;
+ int num_prot = d.pepind2num_prot(pepind);
+ int *protinds = d.pepind2protinds(pepind);
+ for (int i = 0; i < num_prot;i++)
+ {
+ int protind = protinds[i];
+ if(assignment_array[protind] == 0)
+ {
+ assignment_array[protind] = trn_tst;
+ int num = traverse_protein(d,protind,trn_tst,assignment_array);
+ num_added+=num;
+ }
+ else
+ {
+ if(assignment_array[protind] != trn_tst)
+ cout << "warning: conflict spliting into trn-tst " << assignment_array[protind] << endl;
+ }
+ }
+ return num_added;
+}
+
+int ProtScores :: traverse_protein(Dataset &d, int protind, int trn_tst, vector<int> &assignment_array)
+{
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ int num_added = 0;
+ for(int i = 0; i < num_pep; i++)
+ {
+ int pepind = pepinds[i];
+ int num = traverse_peptide(d,pepind,trn_tst, assignment_array);
+ num_added += num;
+ }
+ return num_added+1;
+}
+
+void ProtScores :: fillProteinsSplit(ProtScores& train,ProtScores& test,Dataset &d, double ratio)
+{
+ int n = d.get_num_proteins();
+ vector<int> assignment_array;
+ assignment_array.resize(n,0);
+ int num_trn = 0;
+ int num_tst = 0;
+ int trn_tst = 0;
+ int max_num = 0;
+ for(int i = 0; i < n; i++)
+ {
+ if(assignment_array[i] == 0)
+ {
+ if (num_trn >= ratio*num_tst)
+ trn_tst = 2;
+ else
+ trn_tst = 1;
+ assignment_array[i] = trn_tst;
+ int num = traverse_protein(d, i, trn_tst, assignment_array);
+ if(num > max_num)
+ {
+ max_num = num;
+ //cout << "max_num " << max_num << endl;
+ }
+
+ if (trn_tst == 1)
+ num_trn += num;
+ else
+ num_tst += num;
+ }
+ }
+ //cout << "total proteins " << num_trn+num_tst << " trainset size " << num_trn << " testeset size " << num_tst << " ratio " << (double)num_trn/(double)num_tst << endl;
+ //cout << "total proteins " << num_trn+num_tst << " trainset size " << num_trn << " testeset size " << num_tst << endl;
+
+ int trn= 0;
+ int tst= 0;
+ int num_pos_trn = 0;
+ int num_neg_trn = 0;
+ int num_pos_tst = 0;
+ int num_neg_tst = 0;
+
+ ProtScoreHolder s;
+ train.scores.resize(num_trn,s);
+ test.scores.resize(num_tst,s);
+
+ for(unsigned int i = 0; i < assignment_array.size();i++)
+ {
+ if(assignment_array[i] == 1)
+ {
+ train[trn].protind = i;
+ int label = d.protind2label(i);
+ train[trn].label = label;
+ if(label == 1)
+ num_pos_trn++;
+ else
+ num_neg_trn++;
+ trn++;
+ }
+ else if (assignment_array[i] == 2)
+ {
+ test[tst].protind = i;
+ int label = d.protind2label(i);
+ test[tst].label = label;
+ if(label == 1)
+ num_pos_tst++;
+ else
+ num_neg_tst++;
+ tst++;
+ }
+ else
+ cout << "protein_not assigned!\n";
+ }
+
+ train.pos=num_pos_trn;
+ test.pos=num_pos_tst;
+ train.neg=num_neg_trn;
+ test.neg=num_neg_tst;
+ train.factor = (double)train.pos/(double)train.neg;
+ test.factor = (double)train.pos/(double)train.neg;
+
+}
+
+
+int ProtScores::calcOverFDR(double fdr) {
+
+ vector<ProtScoreHolder>::iterator it = scores.begin();
+
+ sort(scores.begin(),scores.end());
+ reverse(scores.begin(),scores.end());
+
+ /*
+ ProtScoreHolder s;
+ for(int i = scores.size()-1; i > 0; i--)
+ {
+ if(scores[i].score == scores[i-1].score)
+ {
+ if(scores[i].protind < scores[i-1].protind)
+ {
+ s = scores[i];
+ scores[i] = scores[i-1];
+ scores[i-1] = scores[i];
+ }
+ }
+ }
+ */
+
+ int positives=0,nulls=0;
+ double efp=0.0,q;
+ posNow = 0;
+ register unsigned int ix=0;
+ for(it=scores.begin();it!=scores.end();it++) {
+ if (it->label!=-1)
+ positives++;
+ if (it->label==-1) {
+ nulls++;
+ efp=pi0*nulls*factor;
+ }
+ if (positives)
+ q=efp/(double)positives;
+ else
+ q=pi0;
+ if (q>pi0)
+ q=pi0;
+ it->q=q;
+ if (fdr>=q)
+ posNow = positives;
+ }
+
+ for (ix=scores.size();--ix;) {
+ if (scores[ix-1].q > scores[ix].q)
+ scores[ix-1].q = scores[ix].q;
+ }
+ return posNow;
+}
+
+
+
+void ProtScores :: get_pep_seq(string &pep, string &seq)
+{
+ string tmp;
+ size_t pos = pep.find('.');
+ if(pos > 0 && pos != string::npos)
+ tmp = pep.substr(pos+1,pep.size());
+ pos = tmp.rfind('.');
+ if(pos > 0 && pos != string::npos)
+ tmp = tmp.substr(0,pos);
+ seq = tmp;
+}
+
+int ProtScores :: is_equivalent_pep(Dataset &d, int protind1, string &pep2)
+{
+
+ int num_pep1 = d.protind2num_pep(protind1);
+ int *pepinds1 = d.protind2pepinds(protind1);
+
+ string p2;
+ get_pep_seq(pep2,p2);
+
+ for(int j = 0; j < num_pep1; j++)
+ {
+ string pep1 = d.ind2pep(pepinds1[j]);
+
+ int flag = 1;
+ if(pep1.size() != pep2.size())
+ flag = 0;
+
+ string p1;
+ get_pep_seq(pep1, p1);
+
+ unsigned int ix1 = 0; unsigned int ix2 = 0;
+ while((flag == 1) && (ix1 < p1.size()) && (ix2 < p2.size()))
+ {
+ char c1 = p1.at(ix1);
+ char c2 = p2.at(ix2);
+
+ if(c1 != c2)
+ {
+ flag = 0;
+
+ if(c1 == 'L' && c2 =='I')
+ flag = 1;
+
+ if(c1 == 'I' && c2 =='L')
+ flag = 1;
+ if(c1 == 'T' && c2 =='S')
+ flag = 1;
+ if(c1 == 'S' && c2 =='T')
+ flag = 1;
+ }
+ ix1++; ix2++;
+ }
+ if(flag == 1)
+ return pepinds1[j];
+
+ }
+ return 0;
+
+}
+
+bool ProtScores :: is_equivalent(Dataset &d, int protind1, vector<int> &pep_set)
+{
+
+ for(unsigned int i = 0; i < pep_set.size(); i++)
+ {
+ string pep2 = d.ind2pep(pep_set[i]);
+ if(is_equivalent_pep(d, protind1, pep2) == 0)
+ return false;
+ }
+ return true;
+}
+
+
+
+bool ProtScores :: is_subset(Dataset &d, int protind1, int protind2)
+{
+ int num_pep1 = d.protind2num_pep(protind1);
+ int *pepinds1 = d.protind2pepinds(protind1);
+ int num_pep2 = d.protind2num_pep(protind2);
+ int *pepinds2 = d.protind2pepinds(protind2);
+
+ vector<int> only2;
+
+ int ix1 = 0;
+ int ix2 = 0;
+
+ while(ix1 < num_pep1 && ix2 < num_pep2)
+ {
+ if(pepinds1[ix1] == pepinds2[ix2])
+ {
+ ix1++; ix2++;
+ }
+ else if(pepinds1[ix1] < pepinds2[ix2])
+ ix1++;
+ else
+ {
+ only2.push_back(pepinds2[ix2]); ix2++;
+ }
+ }
+ while(ix2 < num_pep2)
+ {
+ only2.push_back(pepinds2[ix2]);
+ ix2++;
+ }
+ if(only2.size() == 0)
+ return true;
+ else
+ return is_equivalent(d, protind1, only2);
+}
+
+bool ProtScores :: are_equal(Dataset &d, int protind1, int protind2, vector<int> &overlap, vector<int> &only1, vector<int> &only2)
+{
+ int num_pep1 = d.protind2num_pep(protind1);
+ int *pepinds1 = d.protind2pepinds(protind1);
+ int num_pep2 = d.protind2num_pep(protind2);
+ int *pepinds2 = d.protind2pepinds(protind2);
+
+ int ix1 = 0;
+ int ix2 = 0;
+ overlap.clear();
+ only1.clear();
+ only2.clear();
+
+ while(ix1 < num_pep1 && ix2 < num_pep2)
+ {
+ if(pepinds1[ix1] == pepinds2[ix2])
+ {
+ overlap.push_back(pepinds1[ix1]);
+ ix1++; ix2++;
+
+ }
+ else if(pepinds1[ix1] < pepinds2[ix2])
+ {
+ only1.push_back(pepinds1[ix1]);
+ ix1++;
+ }
+ else
+ {
+ only2.push_back(pepinds2[ix2]); ix2++;
+ }
+ }
+ while(ix1 < num_pep1)
+ {
+ only1.push_back(pepinds1[ix1]);
+ ix1++;
+ }
+ while(ix2 < num_pep2)
+ {
+ only2.push_back(pepinds2[ix1]);
+ ix2++;
+ }
+
+ if(only1.size() == 0 && only2.size() == 0)
+ return true;
+ else
+ //return (is_equivalent(d, protind1, only2) && is_equivalent(d, protind2, only1));
+ return false;
+}
+
+void ProtScores :: get_intersection(vector<int> &set1, vector<int> &set2, vector<int> &result)
+{
+ result.clear();
+ unsigned int ix1 = 0;
+ unsigned int ix2 = 0;
+ while(ix1 < set1.size() && ix2 < set2.size())
+ {
+ if(set1[ix1] == set2[ix2])
+ {
+ result.push_back(set1[ix1]);
+ ix1++; ix2++;
+
+ }
+ else if(set1[ix1] < set2[ix2])
+ {
+ ix1++;
+ }
+ else
+ {
+ ix2++;
+ }
+ }
+}
+
+
+void ProtScores :: get_complement(Dataset &d, int protind1, vector<int> &set2, vector<int> &result)
+{
+ int num_pep1 = d.protind2num_pep(protind1);
+ int *pepinds1 = d.protind2pepinds(protind1);
+
+ result.clear();
+ int ix1 = 0;
+ unsigned int ix2 = 0;
+ while(ix1 < num_pep1 && ix2 < set2.size())
+ {
+ if(pepinds1[ix1] == set2[ix2])
+ {
+ ix1++; ix2++;
+ }
+ else if(pepinds1[ix1] < set2[ix2])
+ {
+ result.push_back(pepinds1[ix1]);
+ ix1++;
+ }
+ else
+ {
+ ix2++;
+ }
+ }
+ while(ix1 < num_pep1)
+ {
+ result.push_back(pepinds1[ix1]);
+ ix1++;
+ }
+}
+
+
+void ProtScores :: make_meta_set(Dataset &d)
+{
+ map<int,int>protind2pos_in_array;
+ for(unsigned int i = 0; i < scores.size(); i++)
+ {
+ int protind = scores[i].protind;
+ protind2pos_in_array[protind] = i;
+ }
+
+ vector<int> processed;
+ processed.resize(d.get_num_proteins(),0);
+
+ int group_num = 0;
+ for(unsigned int i = 0; i < scores.size();i++)
+ {
+ int protind1 = scores[i].protind;
+ if(processed[protind1] == 1)
+ continue;
+ processed[protind1] = 1;
+ group_num++;
+ scores[i].group_number = group_num;
+
+ int num_pep1 = d.protind2num_pep(protind1);
+ int *pepinds = d.protind2pepinds(protind1);
+ int flag = 0;
+ for(int j = 0; j < num_pep1; j++)
+ {
+ int pepind = pepinds[j];
+ int num_prot = d.pepind2num_prot(pepind);
+ int *protinds = d.pepind2protinds(pepind);
+
+ for(int k = 0; k < num_prot; k++)
+ {
+ int protind2 = protinds[k];
+ int pos_in_array = protind2pos_in_array[protind2];
+ assert(scores[pos_in_array].protind == protind2);
+ if(protind2 == protind1)
+ {
+ flag = 1;
+ continue;
+ }
+ else if (processed[protind2] == 1)
+ continue;
+ else
+ {
+ if(is_subset(d,protind1, protind2) && is_subset(d,protind2,protind1))
+ {
+ processed[protind2] = 1;
+ (scores[i].indistinguishable_protinds).push_back(protind2);
+ scores[pos_in_array].group_number = group_num;
+ scores[pos_in_array].indistinguishable_prot = 1;
+ }
+ }
+ }
+ }
+ assert(flag == 1);
+ }
+
+ cout << "number of meta groups " << group_num <<endl;
+
+ //do some checks
+ map<int, set<int> > protind2group;
+ map<int, set<int> > group2protind;
+ int count = 0;
+ for(unsigned int i = 0; i < scores.size(); i++)
+ {
+ int protind = scores[i].protind;
+ int group = scores[i].group_number;
+ //protind2group[protind].insert(group);
+ //group2protind[group].insert(protind);
+ if(scores[i].indistinguishable_prot == 0)
+ {
+ count++;
+ vector<int> same_prot_list = scores[i].indistinguishable_protinds;
+ if(same_prot_list.size() > 0)
+ {
+ vector<int> same_prot_list = scores[i].indistinguishable_protinds;
+
+ for(unsigned int k = 0; k < same_prot_list.size(); k++)
+ {
+ int protind2 = same_prot_list[k];
+ int pos_in_array = protind2pos_in_array[protind2];
+ assert(scores[pos_in_array].protind == protind2);
+ assert(scores[pos_in_array].indistinguishable_prot == 1);
+ assert(scores[pos_in_array].group_number == group);
+
+ vector<int> overlap;
+ vector<int> only1;
+ vector<int> only2;
+ if(!are_equal(d, protind, protind2, overlap, only1, only2))
+ scores[i].has_complement = 1;
+ }
+ }
+ }
+ }
+
+ //make sure that each protein belongs only to a single group
+ //for(map<int, set<int> > :: iterator it = protind2group.begin(); it != protind2group.end(); it++)
+ //assert((it->second).size() == 1);
+
+ for(unsigned int i = 0; i < scores.size(); i++)
+ {
+ if(scores[i].indistinguishable_prot == 1)
+ continue;
+
+ int protind = scores[i].protind;
+ //int group = scores[i].group_number;
+ vector<int> same_prot_list = scores[i].indistinguishable_protinds;
+
+ //do a couple more checks
+ //if(same_prot_list.size() > 0)
+ //{
+ // set<int> protinds_in_group = group2protind[group];
+ // assert(same_prot_list.size()+1 == protinds_in_group.size());
+ //}
+
+ if(scores[i].has_complement == 1)
+ {
+ vector<int> intersection;
+ int num_pep = d.protind2num_pep(protind);
+ int *pepinds = d.protind2pepinds(protind);
+ for(int k = 0; k < num_pep; k++)
+ intersection.push_back(pepinds[k]);
+ vector<int> complement;
+ map<int, vector<int> > protind2complement;
+ for(unsigned int k = 0; k < same_prot_list.size(); k++)
+ {
+ vector<int> overlap;
+ vector<int> only1;
+ vector<int> only2;
+ int protind2 = same_prot_list[k];
+ are_equal(d, protind, protind2, overlap, only1, only2);
+ vector<int> result;
+ get_intersection(intersection, overlap, result);
+ intersection = result;
+ }
+
+ for(unsigned int k = 0; k < same_prot_list.size(); k++)
+ {
+ int protind2 = same_prot_list[k];
+ get_complement(d, protind2, intersection, complement);
+ protind2complement[protind2] = complement;
+ }
+
+ get_complement(d, protind, intersection, complement);
+ protind2complement[protind] = complement;
+
+ scores[i].intersection = intersection;
+ scores[i].protind2complement = protind2complement;
+ }
+ }
+
+
+ //now find the subsets
+ for(unsigned int i = 0; i < scores.size();i++)
+ {
+ //if this is a protein that is indistinguishable from some other, don't consider it
+ if(scores[i].indistinguishable_prot == 1)
+ continue;
+
+ int protind1 = scores[i].protind;
+ int num_pep1 = d.protind2num_pep(protind1);
+ int *pepinds = d.protind2pepinds(protind1);
+
+ int flag = 0;
+ for(int j = 0; j < num_pep1; j++)
+ {
+ int pepind = pepinds[j];
+ int num_prot = d.pepind2num_prot(pepind);
+ int *protinds = d.pepind2protinds(pepind);
+
+ for(int k = 0; k < num_prot; k++)
+ {
+ int protind2 = protinds[k];
+ int pos_in_array = protind2pos_in_array[protind2];
+ assert(protind2 == scores[pos_in_array].protind);
+ int group = scores[pos_in_array].group_number;
+ int found = 0;
+ for(unsigned int k = 0; k < scores[i].parent_groups.size(); k++)
+ {
+ if(scores[i].parent_groups[k] == group)
+ {
+ found = 1;
+ break;
+ }
+ }
+ if(found == 1)
+ continue;
+ else if(protind2 == protind1)
+ {
+ flag = 1;
+ continue;
+ }
+ else if (scores[pos_in_array].indistinguishable_prot == 1)
+ continue;
+ else
+ {
+ // is protind1 subset of protind2
+ if(is_subset(d,protind2,protind1))
+ {
+ (scores[i].parent_groups).push_back(group);
+ scores[i].subset_prot=1;
+ (scores[pos_in_array].subset_protinds).push_back(protind1);
+ }
+
+ }
+ }
+ }
+ assert(flag == 1);
+ }
+
+
+ //do some checking
+ int num_unique = 0;
+ int num_same = 0;
+ int num_subset = 0;
+ for(unsigned int i = 0; i < scores.size(); i++)
+ {
+ if(scores[i].indistinguishable_prot == 1)
+ num_same++;
+ else if(scores[i].subset_prot == 1)
+ num_subset++;
+ else
+ {
+ num_unique++;
+
+ //int protind = scores[i].protind;
+ //int group = scores[i].group_number;
+ //if(scores[i].subset_protinds.size() > 0)
+ //{
+ // for(int j = 0; j < scores[i].subset_protinds.size(); j++)
+ //{
+ // int protind2 = scores[i].subset_protinds[j];
+ // assert(is_subset(d,protind, protind2));
+ // int pos_in_array = protind2pos_in_array[protind2];
+ // assert(scores[pos_in_array].subset_prot == 1);
+ // int flag = 0;
+ // for(int k = 0; k < scores[pos_in_array].parent_groups.size(); k++)
+ // {
+ // if(scores[pos_in_array].parent_groups[k] == group)
+ // flag = 1;
+ // }
+ // assert(flag == 1);
+ //}
+ }
+
+ }
+
+ cout << "number of subset groups " << num_subset << endl;
+
+ ProtScoreHolder s;
+ scores_meta.resize(num_unique,s);
+ scores_same.resize(num_same,s);
+ scores_subset.resize(num_subset,s);
+
+ int idx_unique = 0;
+ int idx_same = 0;
+ int idx_subset = 0;
+
+ for(unsigned int i = 0; i < scores.size(); i++)
+ {
+ if(scores[i].indistinguishable_prot == 1)
+ {
+ scores_same[idx_same] = scores[i];
+ idx_same++;
+ }
+ else if(scores[i].subset_prot == 1)
+ {
+ scores_subset[idx_subset] = scores[i];
+ idx_subset++;
+ }
+ else
+ {
+ scores_meta[idx_unique] = scores[i];
+ idx_unique++;
+ }
+ }
+
+ assert((idx_unique+idx_subset) == group_num);
+ assert((idx_unique+idx_subset+idx_same) == (int)scores.size());
+
+ scores.clear();
+ scores = scores_meta;
+ scores_meta.clear();
+
+}
+
+
+
+/*
+bool ProtScores :: is_subset(Dataset &d, int protind1, int protind2)
+{
+ int num_pep1 = d.protind2num_pep(protind1);
+ int *pepinds1 = d.protind2pepinds(protind1);
+ int num_pep2 = d.protind2num_pep(protind2);
+ int *pepinds2 = d.protind2pepinds(protind2);
+
+ int ix1 = 0;
+ int ix2 = 0;
+ vector<int> overlap;
+ vector<int> only1;
+ vector<int> only2;
+
+ while(ix1 < num_pep1 && ix2 < num_pep2)
+ {
+ if(pepinds1[ix1] == pepinds2[ix2])
+ {
+ ix1++; ix2++;
+ }
+ else if(pepinds1[ix1] < pepinds2[ix2])
+ ix1++;
+ else
+ {
+ only2.push_back(pepinds2[ix2]); ix2++;
+ }
+ }
+ if(only2.size() == 0)
+ return true;
+ for(unsigned int i = 0; i < only2.size(); i++)
+ {
+ string pep2 = d.ind2pep(only2[i]);
+ string p2;
+ size_t pos = pep2.find('.');
+ if(pos > 0 && pos != string::npos)
+ p2 = pep2.substr(pos+1,pep2.size());
+ pos = p2.find('.');
+ if(pos > 0 && pos != string::npos)
+ p2 = p2.substr(0,pos);
+
+ for(int j = 0; j < num_pep1; j++)
+ {
+ string pep1 = d.ind2pep(pepinds1[j]);
+ string p1;
+ pos = pep1.find('.');
+ if(pos > 0 && pos != string::npos)
+ p1 = pep1.substr(pos+1,pep1.size());
+ pos = p1.find('.');
+ if(pos > 0 && pos != string::npos)
+ p1 = p1.substr(0,pos);
+
+ unsigned int ix1 = 0; unsigned int ix2 = 0;
+ while(ix1 < p1.size() && ix2 < p2.size())
+ {
+ char c1 = p1.at(ix1);
+ char c2 = p2.at(ix2);
+ if(c1 != c2)
+ {
+ if(c1 == 'L' || c1 =='I')
+ {
+ if(c2 != 'L' && c2 !='I')
+ return false;
+ }
+ else if (c1 == 'T' || c1 =='S')
+ {
+ if(c2 != 'T' && c2 !='S')
+ return false;
+ }
+ else
+ return false;
+ }
+ ix1++; ix2++;
+ }
+ }
+ }
+ return true;
+}
+
+
+
+void ProtScores :: make_meta_set(Dataset &d)
+{
+ for(unsigned int i = 0; i < scores.size(); i++)
+ {
+ int protind = scores[i].protind;
+ int num_pep = d.protind2num_pep(protind);
+ scores[i].score = (double) num_pep;
+ }
+ sort(scores.begin(),scores.end());
+ reverse(scores.begin(),scores.end());
+
+ vector<int> used_prot;
+ used_prot.resize(d.get_num_proteins(),0);
+
+ vector<int> processed;
+ processed.resize(d.get_num_proteins(),0);
+
+ for(unsigned int i = 0; i < scores.size();i++)
+ {
+ int protind1 = scores[i].protind;
+ if(processed[protind1] == 1)
+ continue;
+ processed[protind1] = 1;
+
+ int num_pep = d.protind2num_pep(protind1);
+ int *pepinds = d.protind2pepinds(protind1);
+
+ int flag = 0;
+ for(int j = 0; j < num_pep; j++)
+ {
+ int pepind = pepinds[j];
+ int num_prot = d.pepind2num_prot(pepind);
+ int *protinds = d.pepind2protinds(pepind);
+
+ for(int k = 0; k < num_prot; k++)
+ {
+ int protind2 = protinds[k];
+ if(protind2 == protind1)
+ flag = 1;
+ else if (used_prot[protind2] == 1)
+ continue;
+ else if (processed[protind2] == 1)
+ continue;
+ else
+ {
+ //if(d.is_prot_subset(protind1, protind2))
+ if(is_subset(d,protind1, protind2))
+ {
+ processed[protind2] = 1;
+ used_prot[protind2] = 1;
+ (scores[i].subset_protinds).push_back(protind2);
+ }
+ }
+ }
+ }
+ assert(flag == 1);
+ }
+
+ for(unsigned int i = 0; i < scores.size(); i++)
+ {
+ int protind = scores[i].protind;
+ if(used_prot[protind] == 1)
+ {
+ //if(scores[i].subset_protinds.size()!=0)
+ //cout << " here " << scores[i].subset_protinds.size() << " " << i << " " << scores[i].subset_protinds[0]<< endl;
+ scores[i].in_meta_prot = 1;
+ }
+ }
+
+ for(unsigned int i = 0; i < scores.size(); i++)
+ {
+ for(unsigned int k = 0; k < scores[i].subset_protinds.size(); k++)
+ {
+ int protind = scores[i].subset_protinds[k];
+ assert(used_prot[protind] == 1);
+ assert(d.is_prot_subset(scores[i].protind, protind));
+
+ }
+ }
+
+ if(0)
+ {
+ ProtScoreHolder s;
+ //mix up the examples
+ int n = scores.size();
+ for(int i = 0; i < n; i++)
+ {
+ int p1 = (int)((double)rand()/RAND_MAX*(n-1));
+ int p2 = (int)((double)rand()/RAND_MAX*(n-1));
+ s = scores[p1];
+ scores[p1] = scores[p2];
+ scores[p2] = s;
+ }
+ }
+
+}
+*/
diff --git a/src/app/qranker-barista/ProtScores.h b/src/app/qranker-barista/ProtScores.h
new file mode 100644
index 0000000..27a08aa
--- /dev/null
+++ b/src/app/qranker-barista/ProtScores.h
@@ -0,0 +1,78 @@
+#ifndef PROTSCORES_H_
+#define PROTSCORES_H_
+#include <vector>
+#include <algorithm>
+#include <string>
+using namespace std;
+#include "DataSetCrux.h"
+
+class ProtScoreHolder{
+public:
+ double score;
+ int protind;
+ int label;
+ double q;
+ double nsaf;
+ double PEP;
+ //meta group number
+ int group_number;
+ //flag indicating that it is protein identical to some other protein in terms of peptide composition
+ int indistinguishable_prot;
+ int subset_prot;
+ //inds of identical prots in terms of their peptide composition
+ vector<int> indistinguishable_protinds;
+ vector<int> subset_protinds;
+ vector<int> parent_groups;
+
+ int has_complement;
+ //intersection of peptides in a group
+ vector<int> intersection;
+ map<int, vector<int> > protind2complement;
+ ProtScoreHolder():score(0.0),protind(0),q(0.0),nsaf(0.0),PEP(0.0),group_number(0),indistinguishable_prot(0),subset_prot(0), has_complement(0){;}
+ ~ProtScoreHolder() {;}
+};
+
+
+class ProtScores
+{
+public:
+ ProtScores();
+ ~ProtScores();
+ void clear();
+ vector<ProtScoreHolder>::iterator begin() {return scores.begin();}
+ vector<ProtScoreHolder>::iterator end() {return scores.end();}
+ static double pi0;
+ double factor;
+
+ int calcOverFDR(double fdr);
+ void calcMultiOverFDR(vector<double> &fdr, vector<int> &overFDR);
+ inline ProtScoreHolder& operator[](int ix){return scores[ix];}
+ void static fillProteinsFull(ProtScores& fullset, Dataset &d);
+ int static traverse_peptide(Dataset &d, int pepind, int trn_tst, vector<int> &assignment_array);
+ int static traverse_protein(Dataset &d, int protind, int trn_tst, vector<int> &assignment_array);
+ void static fillProteinsSplit(ProtScores& train,ProtScores& test,Dataset &d, double ratio);
+ void make_meta_set(Dataset &d);
+ bool is_subset(Dataset &d, int protind1, int protind2);
+ bool are_equal(Dataset &d, int protind1, int protind2, vector<int> &overlap, vector<int> &only1, vector<int> &only2);
+ void get_pep_seq(string &pep, string &seq);
+ int is_equivalent_pep(Dataset &d, int protind1, string &pep2);
+ bool is_equivalent(Dataset &d, int protind1, vector<int> &pep_set);
+ void get_intersection(vector<int> &set1, vector<int> &set2, vector<int> &result);
+ void get_complement(Dataset &d, int protind1, vector<int> &set2, vector<int> &result);
+
+ inline int get_num_subsets(){return scores_subset.size();}
+ inline ProtScoreHolder& get_subset_prot(int i){return scores_subset[i];}
+
+ inline int size(){return scores.size();}
+protected:
+ int neg,pos,posNow;
+ vector<ProtScoreHolder> scores;
+ vector<ProtScoreHolder> scores_meta;
+ vector<ProtScoreHolder> scores_same;
+ vector<ProtScoreHolder> scores_subset;
+
+};
+
+
+
+#endif /*PROTSCORES_H_*/
diff --git a/src/app/qranker-barista/QRanker.cpp b/src/app/qranker-barista/QRanker.cpp
new file mode 100644
index 0000000..cfa4d8f
--- /dev/null
+++ b/src/app/qranker-barista/QRanker.cpp
@@ -0,0 +1,1281 @@
+#include "QRanker.h"
+#include "util/modifications.h"
+#include "util/Params.h"
+#include "app/ComputeQValues.h"
+
+QRanker::QRanker() :
+ seed(0),
+ selectionfdr(0.01),
+ num_hu(4),
+ mu(0.01),
+ weightDecay(0.000),
+ max_net_gen(NULL),
+ max_net_targ(NULL),
+ nets(NULL),
+ in_dir(""),
+ out_dir(""),
+ skip_cleanup_flag(0),
+ overwrite_flag(0),
+ fileroot(""),
+ feature_file_flag(0),
+ file_format_("")
+{
+}
+
+QRanker::~QRanker()
+{
+ delete [] max_net_gen;
+ delete [] max_net_targ;
+ delete [] nets;
+}
+
+int QRanker :: getOverFDR(PSMScores &set, NeuralNet &n, double fdr)
+{
+ double *r;
+ double* featVec;
+
+ for(int i = 0; i < set.size(); i++)
+ {
+ featVec = d.psmind2features(set[i].psmind);
+ r = n.fprop(featVec);
+ set[i].score = r[0];
+
+ }
+ return set.calcOverFDR(fdr);
+}
+
+
+void QRanker :: getMultiFDR(PSMScores &set, NeuralNet &n, vector<double> &qvalues)
+{
+ double *r;
+ double* featVec;
+
+ for(int i = 0; i < set.size(); i++)
+ {
+ featVec = d.psmind2features(set[i].psmind);
+ r = n.fprop(featVec);
+ set[i].score = r[0];
+ }
+
+ for(unsigned int ct = 0; ct < qvalues.size(); ct++)
+ overFDRmulti[ct] = 0;
+ set.calcMultiOverFDR(qvalues, overFDRmulti);
+}
+
+void QRanker :: getMultiFDRXCorr(PSMScores &set, vector<double> &qvalues)
+{
+ double r;
+ double* featVec;
+
+ for(int i = 0; i < set.size(); i++)
+ {
+ featVec = d.psmind2features(set[i].psmind);
+ r = featVec[3];
+ set[i].score = r;
+ }
+
+ for(unsigned int ct = 0; ct < qvalues.size(); ct++)
+ overFDRmulti[ct] = 0;
+ set.calcMultiOverFDR(qvalues, overFDRmulti);
+}
+
+
+void QRanker :: printNetResults(vector<int> &scores)
+{
+ double qv; int fdr;
+ cerr << "QVALS SCORES:: ";
+ for(unsigned int count = 0; count < qvals.size();count++)
+ {
+ qv=qvals[count];
+ fdr = scores[count];
+ cerr << qv << ":" << fdr << " ";
+ }
+ cerr << endl;
+}
+
+
+
+
+void QRanker :: write_results()
+{
+ //write out the results of the general net
+ trainset.clear();
+ testset.clear();
+ thresholdset.clear();
+ d.load_labels_psm_training();
+ PSMScores::fillFeaturesFull(fullset, d);
+ d.clear_labels_psm_training();
+
+ //choose the best net for the selectionfdr
+ int max_fdr = 0;
+ int fdr = 0;
+ int ind = 0;
+ for(unsigned int count = 0; count < qvals.size();count++)
+ {
+ fdr = getOverFDR(fullset, max_net_targ[count], selectionfdr);
+ if(fdr > max_fdr) {
+ max_fdr = fdr;
+ ind = count;
+ }
+ }
+ net = max_net_targ[ind];
+ getOverFDR(fullset,net, selectionfdr);
+ d.clear_data_psm_training();
+
+ d.load_data_psm_results();
+ computePEP();
+
+ ostringstream fname;
+ if (Params::GetBool("txt-output")) {
+ fname << out_dir << "/" << fileroot << "q-ranker.target.psms.txt";
+ ofstream f1(fname.str().c_str());
+ fname.str("");
+ fname << out_dir << "/" << fileroot << "q-ranker.decoy.psms.txt";
+ ofstream f2(fname.str().c_str());
+ write_results_psm_tab(f1, f2);
+ f1.close();
+ f2.close();
+ fname.str("");
+ }
+
+ if (Params::GetBool("pepxml-output")) {
+ fname << out_dir << "/" << fileroot << "q-ranker.target.pep.xml";
+ PepXMLWriter xmlfile1;
+ xmlfile1.openFile(fname.str().c_str(), overwrite_flag);
+ fname.str("");
+ fname << out_dir << "/" << fileroot << "q-ranker.decoy.pep.xml";
+ PepXMLWriter xmlfile2;
+ xmlfile2.openFile(fname.str().c_str(), overwrite_flag);
+ write_results_psm_xml(xmlfile1, xmlfile2);
+ xmlfile1.closeFile();
+ xmlfile2.closeFile();
+ }
+ d.clear_data_psm_results();
+}
+
+void QRanker :: write_results_psm_tab(ofstream &osTarget, ofstream &osDecoy)
+{
+ int ps =fullset[0].psmind;
+ ofstream* streams[2] = {&osTarget, &osDecoy};
+ for (size_t i = 0; i < 2; ++i) {
+ ofstream& os = *streams[i];
+ os << "scan" << "\t" << "charge" << "\t" << "q-ranker q-value" << "\t" ;
+ os<< "q-ranker score" << "\t" << "q-ranker PEP\t";
+ os<<"spectrum precursor m/z"<<"\t";
+ os<<"spectrum neutral mass"<<"\t";
+ os<<"peptide mass"<<"\t";
+ os<< "delta_cn"<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"sp score"<<"\t";
+ os<<"sp rank\t";
+ }
+ os<<"xcorr score"<<"\t";
+ os<<"xcorr rank"<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ os<<"b/y ions matched"<<"\t";
+ os<<"b/y ions total"<<"\t";
+ }
+ os<<"distinct matches/spectrum"<<"\t";
+ os<<"sequence"<<"\t";
+ os<<"cleavage type"<<"\t";
+ os<<"protein id"<<"\t";
+ os<<"flanking aa"<<"\t";
+ os<< "filename" << endl;
+ }
+ for(int i = 0; i < fullset.size(); i++){
+ ofstream& os = (fullset[i].label == 1) ? osTarget : osDecoy;
+ int psmind = fullset[i].psmind;
+ int pepind = d.psmind2pepind(psmind);
+ string pep = d.ind2pep(pepind);
+ string seq, n,c;
+ os << d.psmind2scan(psmind) << "\t" ;
+ os<< d.psmind2charge(psmind) << "\t";
+ os<< fullset[i].q << "\t" ;
+ os<< fullset[i].score << "\t";
+ os<< fullset[i].PEP << "\t";
+ //mass-to-charge ratio
+ os<<(d.psmind2precursor_mass(psmind)+
+ d.psmind2charge(psmind)*MASS_PROTON)/
+ d.psmind2charge(psmind)<<"\t";
+ //Spectrum Neutral Mass
+ os<<d.psmind2precursor_mass(psmind)<<"\t";
+ //Peptide Mass
+ os<<d.psmind2peptide_mass(psmind)<<"\t";
+ //DELTA CN
+ os <<d.psmind2deltaCn(psmind)<< "\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //Sp Score
+ os<<d.psmind2spscore(psmind)<<"\t";
+ //Sp Rank
+ os<<d.psmind2sp_rank(psmind)<<"\t";
+ }
+ //xcorr Score
+ os<<d.psmind2xcorr(psmind)<<"\t";
+ //xcorr rank
+ os<<d.psmind2xcorr_rank(psmind)<<"\t";
+ if(d.psmind2spscore(ps)!=-1){
+ //by ions match
+ os<<d.psmind2by_ions_matched(psmind)<<"\t";
+ //by ions total
+ os<<d.psmind2by_ions_total(psmind)<<"\t";
+ }
+ //Matches/Spectrum
+ os<<d.psmind2matches_spectrum(psmind)<<"\t";
+ get_pep_seq(pep,seq,n,c);
+ //Sequence
+ os<<seq<<"\t";
+ //cleavage type
+ os<<cleavage_type<<"\t";
+ //protein id
+ vector<string> prots;
+ get_protein_id(pepind,prots);
+
+ // TODO: find peptide position in SQT files
+ //sqt files do not return peptide position in the protein.
+ //if the search result file is txt we can find file peptide_pos and print it
+ // in front of protein, else do not print anything
+ if(file_format_=="txt"){
+ for (unsigned int j=0;j<prots.size();j++){
+ os << prots[j];
+ if (d.psmind2peptide_position(psmind) > -1) {
+ os << "("<<d.psmind2peptide_position(psmind)<<")";
+ }
+ if (j == prots.size() - 1) {
+ os << "\t";
+ } else {
+ os << ",";
+ }
+ }
+ }else if(file_format_=="sqt"){
+
+ for (unsigned int j=0;j<prots.size();j++){
+ if(j==prots.size()-1)
+ os<<prots[j]<<"\t";
+ else
+ os<<prots[j]<<",";
+ }
+ }
+ //Flanking_aa
+ os<<n<<c;
+ //TODO temp fix to write a set of flanking AAs per protein
+ for(unsigned int j=1;j<prots.size();j++)
+ os<<','<<n<<c;
+ os<<'\t';
+ os<< d.psmind2fname(psmind) << endl;
+ }
+}
+
+
+void QRanker :: get_pep_seq(string &pep, string &seq, string &n, string &c)
+{
+ string tmp;
+ int pos;
+ pos = pep.find('.');
+ n = pep.at(pos-1);
+ tmp = pep.substr(pos+1, pep.size());
+
+ pos = tmp.rfind('.');
+ c = tmp.at(pos+1);
+ seq = tmp.substr(0, pos);
+}
+
+
+void QRanker ::write_results_psm_xml(
+ PepXMLWriter& xmlfileTarget,
+ PepXMLWriter& xmlfileDecoy)
+{
+ xmlfileTarget.writeHeader();
+ xmlfileDecoy.writeHeader();
+
+ bool* scores_to_print = new bool[NUMBER_SCORER_TYPES];
+ for(int score_idx = 0; score_idx < NUMBER_SCORER_TYPES; score_idx++){
+ scores_to_print[score_idx] = false;
+ }
+ scores_to_print[SP] = true;
+ scores_to_print[XCORR] = true;
+ scores_to_print[QRANKER_SCORE] = true;
+ scores_to_print[QRANKER_QVALUE] = true;
+ scores_to_print[QRANKER_PEP] = true;
+ scores_to_print[DELTA_CN] = true;
+ scores_to_print[BY_IONS_MATCHED] = true;
+ scores_to_print[BY_IONS_TOTAL] = true;
+
+ double* scores = new double[NUMBER_SCORER_TYPES];
+
+ for(int i = 0; i < fullset.size(); i++)
+ {
+ int psmind = fullset[i].psmind;
+
+ // spectrum info
+ int scan = d.psmind2scan(psmind);
+ const char* filename = d.psmind2fname(psmind).c_str();
+ char** path_name = parse_filename_path_extension(filename, NULL);
+ filename = path_name[0];
+ double spectrum_mass = d.psmind2precursor_mass(psmind);
+ int charge = d.psmind2charge(psmind);
+
+ // peptide info
+ int pepind = d.psmind2pepind(psmind);
+ string pep = d.ind2pep(pepind);
+ string modified_sequence, n,c;
+ get_pep_seq(pep, modified_sequence, n, c);
+ char* sequence = unmodify_sequence(modified_sequence.c_str());
+ string flanking_aas = n + c;
+ double peptide_mass = d.psmind2peptide_mass(psmind);
+
+ // protein info
+ int num_proteins = d.pepind2num_prot(pepind);
+ int* protein_indexes = d.pepind2protinds(pepind);
+ vector<string> protein_names;
+ vector<string> protein_descriptions;
+ for(int prot_idx = 0; prot_idx < num_proteins; prot_idx++){
+ string protein_name = d.ind2prot(protein_indexes[prot_idx]);
+ protein_names.push_back(protein_name);
+ protein_descriptions.push_back("");
+ flanking_aas += "," + n + c; // todo
+ }
+
+ // psm info
+ int* psm_ranks = new int[NUMBER_SCORER_TYPES];
+ psm_ranks[XCORR]=1;
+ double delta_cn = d.psmind2deltaCn(psmind);
+
+ scores[XCORR] = d.psmind2xcorr(psmind);
+
+ scores[SP] = d.psmind2spscore(psmind);
+ scores[QRANKER_SCORE] = fullset[i].score;
+ scores[QRANKER_QVALUE] = fullset[i].q;
+ scores[QRANKER_PEP] = fullset[i].PEP;
+ scores[DELTA_CN] = delta_cn;
+ scores[BY_IONS_MATCHED] = d.psmind2by_ions_matched(psmind);
+ scores[BY_IONS_TOTAL] = d.psmind2by_ions_total(psmind);
+ psm_ranks[SP] = d.psmind2sp_rank(psmind);
+ psm_ranks[XCORR]=d.psmind2xcorr_rank(psmind);
+
+ PepXMLWriter& xmlfile = (fullset[i].label == 1) ? xmlfileTarget : xmlfileDecoy;
+ xmlfile.writePSM(scan, filename, spectrum_mass, charge, psm_ranks,
+ sequence, modified_sequence.c_str(),
+ peptide_mass, num_proteins,
+ flanking_aas.c_str(), protein_names,
+ protein_descriptions, scores_to_print, scores,
+ d.psmind2matches_spectrum(psmind));
+
+ free(sequence);
+ if( path_name[0] ){
+ free(path_name[0]);
+ }
+ if( path_name[1] ){
+ free(path_name[1]);
+ }
+ free(path_name);
+
+ }
+
+ xmlfileTarget.writeFooter();
+ xmlfileDecoy.writeFooter();
+}
+
+
+
+void QRanker :: write_max_nets(string filename, NeuralNet* max_net)
+{
+ //write out the results of the general net
+
+ ofstream f1(filename.c_str());
+ f1 << "FDR thresh" << "\t" << "PSMs trn" << "\t" << "PSMs tst" << endl;
+ for(int count = 0; count < num_qvals; count++)
+ {
+ net = max_net[count];
+ int r = getOverFDR(testset,net, qvals[count]);
+ int r1 = getOverFDR(trainset,net, qvals[count]);
+ f1 << qvals[count] << "\t" << r1 << "\t" << r << "\n";
+
+ double qn;
+ if(qvals[count] < 0.01)
+ qn = 0.0012;
+ else
+ qn = 0.005;
+ r = getOverFDR(testset,net, qvals[count]+qn);
+ r1 = getOverFDR(trainset,net, qvals[count]+qn);
+ f1 << qvals[count]+qn << "\t" << r1 << "\t" << r << "\n";
+
+ }
+ f1.close();
+}
+
+
+
+
+void QRanker :: write_unique_peptides(string filename, NeuralNet* max_net)
+{
+ //write out the results of the general net
+ ostringstream s1;
+ s1 << filename << ".txt";
+ ofstream f1(s1.str().c_str());
+
+ for(int count = 0; count < num_qvals; count++)
+ {
+ net = max_net[count];
+ int r = getOverFDR(testset,net, qvals[count]);
+ set<int> peps;
+ int cn = 0;
+ for(int i = 0; i < testset.size();i++)
+ {
+ if(testset[i].label == 1)
+ {
+ cn++;
+ int pepind = d.psmind2pepind(testset[i].psmind);
+ peps.insert(pepind);
+ }
+ if(cn > r) break;
+ }
+ int num_tst = 0;
+ for(set<int>::iterator it = peps.begin(); it != peps.end(); it++)
+ num_tst++;
+ peps.clear();
+
+ int r1 = getOverFDR(trainset,net, qvals[count]);
+ cn = 0;
+ for(int i = 0; i < trainset.size();i++)
+ {
+ if(trainset[i].label == 1)
+ {
+ cn++;
+ int pepind = d.psmind2pepind(trainset[i].psmind);
+ peps.insert(pepind);
+ }
+ if(cn > r1) break;
+ }
+ int num_trn = 0;
+ for(set<int>::iterator it = peps.begin(); it != peps.end(); it++)
+ num_trn++;
+ peps.clear();
+ f1 << qvals[count] << " " << num_trn << " " << num_tst << "\n";
+ }
+
+ f1.close();
+}
+
+
+void QRanker :: write_num_psm_per_spectrum(NeuralNet* max_net)
+{
+ //write out the results of the general net
+ //ostringstream s1;
+ //s1 << filename << ".txt";
+ //ofstream f1(s1.str().c_str());
+
+ int count = 5;
+ net = max_net[count];
+ int r = getOverFDR(trainset,net, qvals[count]);
+
+ map<int,set<int> > scan_to_pepinds;
+ int cn = 0;
+ for(int i = 0; i < trainset.size();i++)
+ {
+ if(trainset[i].label == 1)
+ {
+ cn++;
+ int pepind = d.psmind2pepind(trainset[i].psmind);
+ int scan = d.psmind2scan(trainset[i].psmind);
+ if(scan_to_pepinds.find(scan) == scan_to_pepinds.end())
+ {
+ set<int> peps;
+ scan_to_pepinds[scan] = peps;
+ }
+ (scan_to_pepinds[scan]).insert(pepind);
+
+ }
+ if(cn > r) break;
+ }
+
+ vector<int> counts;
+ counts.resize(11,0);
+
+ for(map<int,set<int> >::iterator it = scan_to_pepinds.begin();
+ it != scan_to_pepinds.end(); it++)
+ {
+ int cnt = (it->second).size();
+ counts[cnt]++;
+ }
+ for(unsigned int i = 0; i < counts.size();i++)
+ cout << i << " " << counts[i] << endl;
+
+ //f1.close();
+}
+
+
+
+/*********************** training net functions*******************************************/
+
+void QRanker :: train_net_sigmoid(PSMScores &set, int interval)
+{
+ double *r;
+ int label;
+ double *gc = new double[1];
+ for(int i = 0; i < set.size(); i++)
+ {
+ unsigned int ind;
+ ind = myrandom_limit(interval);
+ //pass both through the net
+ r = net.fprop(d.psmind2features(set[ind].psmind));
+ label = set[ind].label;
+ double a = exp(label*r[0]);
+ net.clear_gradients();
+ gc[0] = -a/((1+a)*(1+a))*label;
+ net.bprop(gc);
+ net.update(mu,weightDecay);
+
+ }
+ delete[] gc;
+}
+
+void QRanker :: train_net_hinge(PSMScores &set, int interval)
+{
+ double *r;
+ int label;
+ double *gc = new double[1];
+ for(int i = 0; i < set.size(); i++)
+ {
+ unsigned int ind;
+ ind = myrandom_limit(interval);
+ //pass both through the net
+ r = net.fprop(d.psmind2features(set[ind].psmind));
+ label = set[ind].label;
+ if(label*r[0]<1)
+ {
+ net.clear_gradients();
+ gc[0] = -1.0*label;
+ net.bprop(gc);
+ net.update(mu,weightDecay);
+ }
+ }
+ delete[] gc;
+}
+
+
+void QRanker :: train_net_ranking(PSMScores &set, int interval)
+{
+ double *r1;
+ double *r2;
+ double diff = 0;
+ int label = 1;
+ double *gc = new double[1];
+
+
+ for(int i = 0; i < set.size(); i++)
+ {
+ int ind1, ind2;
+ int label_flag = 1;
+ //get the first index
+ if(interval == 0)
+ ind1 = 0;
+ else
+ ind1 = myrandom_limit(interval);
+ if(ind1>set.size()-1) continue;
+ if(set[ind1].label == 1)
+ label_flag = -1;
+ else
+ label_flag = 1;
+
+ int cn = 0;
+ while(1)
+ {
+ ind2 = myrandom_limit(interval);
+ if(ind2>set.size()-1) continue;
+ if(set[ind2].label == label_flag) break;
+ if(cn > 1000)
+ {
+ ind2 = myrandom_limit(set.size());
+ break;
+ }
+ cn++;
+ }
+
+ //pass both through the net
+ r1 = nets[0].fprop(d.psmind2features(set[ind1].psmind));
+ r2 = nets[1].fprop(d.psmind2features(set[ind2].psmind));
+ diff = r1[0]-r2[0];
+
+
+ label=0;
+ if( set[ind1].label==1 && set[ind2].label==-1)
+ label=1;
+ if( set[ind1].label==-1 && set[ind2].label==1)
+ label=-1;
+
+ if(label != 0)
+ {
+ if(label*diff<1)
+ {
+ net.clear_gradients();
+ gc[0] = -1.0*label;
+ nets[0].bprop(gc);
+ gc[0] = 1.0*label;
+ nets[1].bprop(gc);
+ net.update(mu,weightDecay);
+ }
+
+ }
+ }
+ delete[] gc;
+
+}
+
+
+void QRanker :: count_pairs(PSMScores &set, int interval)
+{
+ double *r1;
+ double *r2;
+ double diff = 0;
+ int label = 1;
+ double err = 0.0;
+
+ for(int i = 0; i < set.size()*100; i++)
+ {
+ int ind1, ind2;
+ int label_flag = 1;
+ //get the first index
+ if(interval == 0)
+ ind1 = 0;
+ else
+ ind1 = myrandom_limit(interval);
+ if(ind1>set.size()-1) continue;
+ if(set[ind1].label == 1)
+ label_flag = -1;
+ else
+ label_flag = 1;
+
+ int cn = 0;
+ while(1)
+ {
+ ind2 = myrandom_limit(interval);
+ if(ind2>set.size()-1) continue;
+ if(set[ind2].label == label_flag) break;
+ if(cn > 1000)
+ {
+ ind2 = myrandom_limit(set.size());
+ break;
+ }
+ cn++;
+ }
+
+ //pass both through the net
+ r1 = nets[0].fprop(d.psmind2features(set[ind1].psmind));
+ r2 = nets[1].fprop(d.psmind2features(set[ind2].psmind));
+ diff = r1[0]-r2[0];
+
+
+ label=0;
+ if( set[ind1].label==1 && set[ind2].label==-1)
+ label=1;
+ if( set[ind1].label==-1 && set[ind2].label==1)
+ label=-1;
+
+ if(label != 0)
+ {
+ if(label*diff<1)
+ {
+ err += 1-label*diff;
+
+ }
+
+ }
+ }
+
+ cout << "er" << err/trainset.size() << endl;
+}
+
+
+
+void QRanker :: train_many_general_nets()
+{
+ interval = trainset.size();
+ for(int i=0;i<switch_iter;i++) {
+ //train_net_hinge(trainset, interval);
+ train_net_ranking(trainset, interval);
+ //train_net_sigmoid(trainset, interval);
+
+
+ //record the best result
+ getMultiFDR(thresholdset,net,qvals);
+ for(int count = 0; count < num_qvals;count++)
+ {
+ if(overFDRmulti[count] > max_overFDR[count])
+ {
+ max_overFDR[count] = overFDRmulti[count];
+ max_net_gen[count] = net;
+ }
+ }
+ if((i % 10) == 0)
+ {
+ carp(CARP_INFO, "Iteration %d :", i);
+ getMultiFDR(trainset,net,qvals);
+ carp(CARP_INFO, "trainset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+ getMultiFDR(testset,net,qvals);
+ carp(CARP_INFO, "testset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d\n ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+ }
+ }
+
+}
+
+void QRanker :: train_many_target_nets()
+{
+
+ int thr_count = num_qvals-1;
+ while (thr_count > 0)
+ {
+ net.copy(max_net_gen[thr_count]);
+
+ carp(CARP_INFO, "training threshold %d", thr_count);
+ //cout << "training thresh " << thr_count << "\n";
+ //interval = getOverFDR(trainset, net, qvals[thr_count]);
+ interval = max_overFDR[thr_count];
+ for(int i=switch_iter;i<niter;i++) {
+
+ //sorts the examples in the training set according to the current net scores
+ getMultiFDR(trainset,net,qvals);
+ train_net_ranking(trainset, interval);
+
+ for(int count = 0; count < num_qvals;count++)
+ {
+ if(overFDRmulti[count] > max_overFDR[count])
+ {
+ max_overFDR[count] = overFDRmulti[count];
+ max_net_targ[count] = net;
+ }
+ }
+
+ if((i % 3) == 0)
+ {
+ carp(CARP_INFO, "Iteration %d :", i);
+ getMultiFDR(trainset,net,qvals);
+ carp(CARP_INFO, "trainset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+ getMultiFDR(testset,net,qvals);
+ carp(CARP_INFO, "testset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d\n ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+
+ /*
+ cout << "Iteration " << i << " : \n";
+ getMultiFDR(testset,net,qvals);
+ cout << "testset: ";
+ printNetResults(overFDRmulti);
+ cout << "\n";
+ */
+ }
+
+ }
+ thr_count -= 3;
+ }
+}
+
+
+
+void QRanker::train_many_nets()
+{
+ switch_iter =30;
+ niter = 40;
+
+ num_qvals = 14;
+ qvals.resize(num_qvals,0.0);
+ qvals1.resize(num_qvals,0.0);
+ qvals2.resize(num_qvals,0.0);
+
+ overFDRmulti.resize(num_qvals,0);
+ ave_overFDR.resize(num_qvals,0);
+ max_overFDR.resize(num_qvals,0);
+ max_net_gen = new NeuralNet[num_qvals];
+ max_net_targ = new NeuralNet[num_qvals];
+
+ double q = 0.0;
+ for(int count = 0; count < num_qvals; count++)
+ {
+ qvals[count] = q;
+ if (count < 2)
+ qvals1[count] = q;
+ else
+ qvals1[count] = q-0.005;
+ qvals2[count] = q+0.005;
+
+ if(q < 0.01)
+ q+=0.0025;
+ else
+ q+=0.01;
+ }
+
+ //set the linear flag: 1 if linear, 0 otherwise
+ int lf = 0; num_hu = 3;
+ if(num_hu == 1)
+ lf = 1;
+ //set whether there is bias in the linear units: 1 if yes, 0 otherwise
+ int bs = 0;
+
+ net.initialize(d.get_num_features(),num_hu,lf,bs);
+ for(int count = 0; count < num_qvals; count++){
+ max_net_gen[count] = net;
+ }
+
+ nets = new NeuralNet[2];
+ nets[0].clone(net);
+ nets[1].clone(net);
+
+ carp(CARP_INFO, "Before Iterating");
+ getMultiFDRXCorr(trainset,qvals);
+ carp(CARP_INFO, "trainset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d ",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+ getMultiFDRXCorr(testset,qvals);
+ carp(CARP_INFO, "trainset %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d %.2f:%d \n",
+ qvals[0], overFDRmulti[0], qvals[1], overFDRmulti[1], qvals[2], overFDRmulti[2],
+ qvals[3], overFDRmulti[3], qvals[4], overFDRmulti[4], qvals[5], overFDRmulti[5],
+ qvals[6], overFDRmulti[6], qvals[7], overFDRmulti[7], qvals[8], overFDRmulti[8],
+ qvals[9], overFDRmulti[9], qvals[10], overFDRmulti[10], qvals[11], overFDRmulti[11],
+ qvals[12], overFDRmulti[12], qvals[13], overFDRmulti[13]);
+
+ train_many_general_nets();
+
+ //copy the general net into target nets;
+ for(int count = 0; count < num_qvals; count++)
+ max_net_targ[count] = max_net_gen[count];
+
+ train_many_target_nets();
+
+ ostringstream fname;
+ fname << out_dir << "/" << fileroot << "q-ranker.psms.at.fdr.thresholds.txt";;
+ write_max_nets(fname.str(), max_net_targ);
+
+
+}
+
+int QRanker::run( ) {
+ //mysrandom(seed); This is set by CruxApplication::initialize()
+ carp(CARP_INFO, "reading data");
+
+ ostringstream res;
+ res << out_dir << "/qranker_output";
+ res_prefix = res.str();
+
+ d.load_data_psm_training();
+ if(feature_file_flag)
+ {
+ string str = feature_file_name.str();
+ if(!d.print_features(str))
+ carp(CARP_INFO, "could not open file %s for writing features. Feature file will not be written", feature_file_name.str().c_str());
+ }
+ d.normalize_psms();
+ d.load_labels_psm_training();
+ PSMScores::fillFeaturesSplit(trainset, testset, d, 0.75);
+ thresholdset = trainset;
+ d.clear_labels_psm_training();
+ train_many_nets();
+ write_results();
+
+ return 0;
+}
+
+void QRanker :: print_description()
+{
+ cout << endl;
+ cout << "\t crux q-ranker [options] <spectra> <search results>" << endl <<endl;
+ cout << "REQUIRED ARGUMENTS:" << endl << endl;
+ cout << "\t <spectra> Directory with ms2 files, list of ms2 files or a single ms2 file used for database search." << endl;
+ cout << "\t <search results> Directory with sqt files, list of sqt files or a single sqt file with psms generated during search." << endl;
+ cout << endl;
+
+ cout << "OPTIONAL ARGUMENTS:" << endl << endl;
+ cout << "\t [--enzyme <string>] \n \t The enzyme used to digest the proteins in the experiment. Default trypsin." << endl;
+ cout << "\t [--decoy-prefix <string>] \n \t Specifies the prefix of the protein names that indicates a decoy. Default decoy_" << endl;
+ cout << "\t [--separate-searches <string>] \n \t If the target and decoy searches were run separately, the option then allows the user to specify the location of the decoy search results, the target database search should be provided as required argument." << endl;
+ cout << "\t [--fileroot <string>] \n \t The fileroot string will be added as a prefix to all output file names. Default = none." <<endl;
+ cout << "\t [--output-dir <directory>] \n \t The name of the directory where output files will be created. Default = crux-output." << endl;
+ cout << "\t [--overwrite <T/F>] \n \t Replace existing files (T) or exit if attempting to overwrite (F). Default=F." << endl;
+ cout << "\t [--skip-cleanup <T/F>] \n \t When set to T, prevents the deletion of lookup tables created during the preprocessing step. Default = F." << endl;
+ cout << "\t [--re-run <directory>] \n \t Re-run QRanker analysis using a previously computed set of lookup tables." <<endl;
+ cout << "\t [--use-spec-features <T/F>] \n \t When set to F, use minimal feature set. Default T." <<endl;
+ cout << endl;
+
+}
+string QRanker:: file_extension (string str){
+ string file_exten= str.substr(str.rfind('.')+1);
+ return file_exten;
+}
+
+
+FILE_FORMAT_T QRanker::check_file_format(string& source) {
+ string ext = file_extension(source);
+
+ if (ext=="sqt")
+ return SQT_FORMAT;
+ else if (ext=="txt")
+ return DELIMITED_FORMAT;
+ return INVALID_FORMAT;
+}
+
+int QRanker :: crux_set_command_line_options(int argc, char *argv[])
+{
+ string sqt_source;
+ string ms2_source;
+ string sqt_decoy_source;
+ int separate_search_flag;
+ string output_directory;
+ string enzyme;
+ string decoy_prefix;
+
+ string dir_with_tables;
+ int found_dir_with_tables;
+
+ bool spec_features_flag;
+ bool list_of_files_flag;
+ overwrite_flag = Params::GetBool("overwrite");
+
+ fileroot = Params::GetString("fileroot");
+ if (!fileroot.empty()) {
+ fileroot.append(".");
+ }
+
+ decoy_prefix = Params::GetString("decoy-prefix");
+
+
+ enzyme = Params::GetString("enzyme");
+
+ spec_features_flag = Params::GetBool("use-spec-features");
+
+ skip_cleanup_flag = Params::GetBool("skip-cleanup");
+
+
+ dir_with_tables = Params::GetString("re-run");
+ if(!dir_with_tables.empty()) {
+ found_dir_with_tables = 1;
+ } else {
+ found_dir_with_tables = 0;
+ }
+
+ output_directory = Params::GetString("output-dir");
+
+ feature_file_flag = Params::GetBool("feature-file-out");
+ feature_file_name << output_directory << "/" << fileroot << "q-ranker.features.txt";
+
+ if(found_dir_with_tables)
+ {
+ //set input and output dirs
+ parser = new SQTParser();
+ parser -> set_output_dir(dir_with_tables);
+ set_input_dir(dir_with_tables);
+ set_output_dir(output_directory);
+
+ carp(CARP_INFO, "directory with tables: %s", dir_with_tables.c_str());
+ carp(CARP_INFO, "output_directory: %s", output_directory.c_str());
+ }else{
+ ms2_source = Params::GetString("fragmentation spectra");
+ sqt_source = Params::GetString("search results");
+ list_of_files_flag = Params::GetBool("list-of-files");
+ //check file format
+
+ vector<string> files;
+ string files_list;
+ if(list_of_files_flag==1){
+ ifstream f(sqt_source.c_str());
+ f>>files_list;
+ while(!f.eof()){
+ files.push_back(files_list);
+ f>> files_list;
+ }
+ }else{
+ files.push_back(sqt_source);
+ }
+
+ for(unsigned i=0; i<files.size();i++){
+ FILE_FORMAT_T format = check_file_format(files[i]);
+ switch (format) {
+ case SQT_FORMAT:
+ file_format_="sqt";
+ parser = new SQTParser();
+ break;
+ case DELIMITED_FORMAT:
+ file_format_="txt";
+ parser = new CruxParser();
+ break;
+ case INVALID_FORMAT:
+ file_format_="NULL";
+ default:
+ carp(CARP_FATAL, "Please enter .sqt or .txt search results");
+ }
+
+ parser->set_decoy_prefix(decoy_prefix);
+ parser->set_enzyme(enzyme);
+ if(enzyme.find("elastase") != string::npos){
+ cleavage_type="elastase-full-digest";
+ }else if (enzyme.find("chymotrypsin") != string::npos){
+ cleavage_type="chymotrypsin-full-digest";
+ }else if (enzyme.find("trypsin") != string::npos){
+ cleavage_type="trypsin-full-digest";
+ }else{
+ cleavage_type="Null";
+ }
+
+ //num of spec features
+ if(spec_features_flag)
+ parser->set_num_spec_features(3);
+ else
+ parser->set_num_spec_features(0);
+ parser->write_features_header();
+
+ if(parser->get_use_quadratic_features())
+ parser->add_quadratic_features_header();
+ d.get_features_header(parser->get_final_features_header());
+ sqt_decoy_source = Params::GetString("separate-searches");
+ if(!sqt_decoy_source.empty()) {
+ separate_search_flag = 1;
+ } else {
+ separate_search_flag = 0;
+ }
+
+ //set the output directory for the parser
+ if(!parser->set_output_dir(output_directory))
+ return 0;
+ //set input and output for the leaning algo (in and out are the same as the out for the parser)
+ set_input_dir(output_directory);
+ set_output_dir(output_directory);
+
+ if(separate_search_flag){
+ if(!parser->set_input_sources(ms2_source, sqt_source, sqt_decoy_source)){
+ carp(CARP_FATAL, "could not extract features for training");
+ }
+ parser->set_num_hits_per_spectrum(1);
+ }else{
+ if(!parser->set_input_sources(ms2_source, sqt_source)){
+ carp(CARP_FATAL, "could not extract features for training");
+ }
+ }
+
+ //print some info
+ if(format==SQT_FORMAT)
+ carp(CARP_INFO, "sqt source: %s", sqt_source.c_str());
+ if(format==DELIMITED_FORMAT)
+ carp(CARP_INFO, "delmited source: %s", sqt_source.c_str());
+ carp(CARP_INFO, "ms2 source: %s", ms2_source.c_str());
+ carp(CARP_INFO, "output_directory: %s", output_directory.c_str());
+ carp(CARP_INFO, "enzyme: %s", enzyme.c_str());
+ carp(CARP_INFO, "decoy prefix: %s", decoy_prefix.c_str());
+
+ if(!parser->run())
+ carp(CARP_FATAL, "Could not proceed with training.");
+ parser->clear();
+ }
+ }
+
+ if(!parser->check_input_dir(in_dir))
+ carp(CARP_FATAL, "Please re-run with ms2 input and txt input.");
+
+ return 1;
+
+
+}
+
+/**
+ * Uses the target and decoy scores to compute posterior error
+ * probabilities.
+ */
+void QRanker::computePEP(){
+ vector<double> target_scores_vect;
+ vector<double> decoy_scores_vect;
+
+ // pull out the target and decoy scores
+ for(int i = 0; i < fullset.size(); i++){
+ if( fullset[i].label == 1 ){
+ target_scores_vect.push_back(fullset[i].score);
+ } else { // == -1
+ decoy_scores_vect.push_back(fullset[i].score);
+ }
+ }
+
+ int num_targets = target_scores_vect.size();
+ int num_decoys = decoy_scores_vect.size();
+
+ // copy them to an array as required by the compute_PEP method
+ double* target_scores = new double[num_targets];
+ copy(target_scores_vect.begin(), target_scores_vect.end(), target_scores);
+ double* decoy_scores = new double[num_decoys];
+ copy(decoy_scores_vect.begin(), decoy_scores_vect.end(), decoy_scores);
+
+ double* PEPs = ComputeQValues::compute_PEP(target_scores, num_targets,
+ decoy_scores, num_decoys);
+
+ // fill in the data set with the new scores for the targets
+ int target_idx = 0;
+ for(int full_idx = 0; full_idx < fullset.size(); full_idx++){
+ if( fullset[full_idx].label == 1 ){
+ fullset[full_idx].PEP = PEPs[target_idx];
+ target_idx++;
+ } // else, skip decoys
+ }
+
+ delete target_scores;
+ delete decoy_scores;
+ delete PEPs;
+}
+
+
+int QRanker::main(int argc, char **argv) {
+
+
+ if(!crux_set_command_line_options(argc, argv))
+ return 1;
+
+ run();
+ if(skip_cleanup_flag != 1)
+ parser->clean_up(out_dir);
+
+ return 0;
+}
+
+bool QRanker :: needsOutputDirectory() const
+{
+ return true;
+}
+
+
+string QRanker::getName() const {
+ return "q-ranker";
+}
+string QRanker::getDescription() const {
+ return
+ "[[nohtml:Re-rank a collection of PSMs using the Q-ranker algorithm.]]"
+ "[[html:<p>Q-ranker dynamically learns to separate target from decoy PSMs. "
+ "The algorithm is described in this article:</p><blockquote>Marina Spivak, "
+ "Jason Weston, Leon Bottou and William Stafford Noble. <a href=\""
+ "http://noble.gs.washington.edu/papers/spivak2009improvements.html\">"
+ ""Direct <em>q</em> value optimization methods for peptide "
+ "identification from shotgun proteomics data sets."</a> <em>Journal "
+ "of Proteome Research</em>. 8(7):3737-3745, 2009.</blockquote><p>For more "
+ "on q-values and posterior error probabilities (PEP), see the "
+ "documentation for <a href=\"assign-confidence.html\">assign-confidence</a>."
+ "</p>]]";
+}
+
+vector<string> QRanker::getArgs() const {
+ string arr[] = {
+ "fragmentation spectra",
+ "search results"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> QRanker::getOptions() const {
+ string arr[] = {
+ "enzyme",
+ "decoy-prefix",
+ "separate-searches",
+ "fileroot",
+ "output-dir",
+ "overwrite",
+ "pepxml-output",
+ "txt-output",
+ "skip-cleanup",
+ "re-run",
+ "use-spec-features",
+ "parameter-file",
+ "verbosity",
+ "list-of-files",
+ "feature-file-out",
+ "spectrum-parser"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > QRanker::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("qranker.target.pep.xml",
+ "An xml file containing ranked list of target peptide-spectrum matches. The"
+ "following entries are included: scan, charge, psm_id, q-value, score, "
+ "precursor_mass, peptide, filename."));
+ outputs.push_back(make_pair("qranker.decoy.pep.xml",
+ "An xml file containing ranked list of decoy peptide-spectrum matches."));
+ outputs.push_back(make_pair("qranker.target.psm.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited text format</a> containing a "
+ "ranked list of target peptide-spectrum matches with the associated Q-ranker "
+ "scores and q-values."));
+ outputs.push_back(make_pair("qranker.decoy.psm.txt",
+ "a <a href=\"../file-formats/txt-format.html\">tab-delimited text format</a> containing a "
+ "ranked list of decoy peptide-spectrum matches with the associated Q-ranker "
+ "scores and q-values."));
+ outputs.push_back(make_pair("qranker.log.txt",
+ "a file where the program reports its progress."));
+ outputs.push_back(make_pair("qranker.params.txt",
+ "a file with the values of all the options given to the current run."));
+ return outputs;
+}
+
+COMMAND_T QRanker::getCommand() const {
+ return QRANKER_COMMAND;
+}
+
+
+void QRanker :: get_protein_id(int pepind, vector<string> &prot){
+ int * protinds= d.pepind2protinds(pepind) ;
+ unsigned prot_length=d.pepind2num_prot(pepind);
+ for (unsigned k=0;k<prot_length;k++){
+ string protein_str= d.ind2prot( protinds[k]);
+ prot.push_back(protein_str);
+ }
+}
+
+
+void QRanker :: print_protein_ids(vector<string> &prots, ofstream &os, int psmind){
+
+ // TODO: find peptide position in SQT files
+ //sqt files do not return peptide position in the protein.
+ //if the search result file is txt we can find file peptide_pos and print it
+ // in front of protein, else do not print anything
+
+ if(file_format_=="txt"){
+ for (unsigned int j=0;j<prots.size();j++){
+ os << prots[j];
+ if (d.psmind2peptide_position(psmind) > -1) {
+ os << "("<<d.psmind2peptide_position(psmind)<<")";
+ }
+ if (j == prots.size() - 1) {
+ os << "\t";
+ } else {
+ os << ",";
+ }
+ }
+ }else if(file_format_=="sqt"){
+ for (unsigned int j=0;j<prots.size();j++){
+ if(j==prots.size()-1)
+ os<<prots[j]<<"\t";
+ else
+ os<<prots[j]<<",";
+ }
+ }
+ prots.clear();
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/qranker-barista/QRanker.h b/src/app/qranker-barista/QRanker.h
new file mode 100644
index 0000000..490d5d1
--- /dev/null
+++ b/src/app/qranker-barista/QRanker.h
@@ -0,0 +1,143 @@
+#ifndef QRANKER_H_
+#define QRANKER_H_
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <time.h>
+#include <cstdlib>
+#include <vector>
+#include <set>
+#include <map>
+#include <string>
+#include <math.h>
+using namespace std;
+
+#include "app/CruxApplication.h"
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+
+#include "io/PepXMLWriter.h"
+#include "NeuralNet.h"
+#include "DataSetCrux.h"
+#include "PSMScores.h"
+#include "SQTParser.h"
+#include "CruxParser.h"
+#include "TabDelimParser.h"
+#include "app/CruxApplication.h"
+#include "util/mass.h"
+#include "model/objects.h"
+
+double* compute_PEP(double* target_scores, ///< scores for target matches
+ int num_targets, ///< size of target_scores
+ double* decoy_scores, ///< scores for decoy matches
+ int num_decoys, ///< size of decoy_scores
+ bool ascending ///< are the scores ascending or descending
+ );
+
+class QRanker: public CruxApplication
+{
+
+public:
+ QRanker();
+ virtual ~QRanker();
+
+ int run();
+ void train_net_sigmoid(PSMScores &set, int interval);
+ void train_net_ranking(PSMScores &set, int interval);
+ void train_net_hinge(PSMScores &set, int interval);
+ void count_pairs(PSMScores &set, int interval);
+ void train_many_general_nets();
+ void train_many_target_nets();
+ void train_many_nets();
+
+ int getOverFDR(PSMScores &set, NeuralNet &n, double fdr);
+ void getMultiFDR(PSMScores &set, NeuralNet &n, vector<double> &qval);
+ void getMultiFDRXCorr(PSMScores &set, vector<double> &qval);
+ void printNetResults(vector<int> &scores);
+ void write_results();
+ void write_results_psm_tab(ofstream &osTarget, ofstream &osDecoy);
+ void get_pep_seq(string &pep, string &seq, string &n, string &c);
+ void write_results_psm_xml(PepXMLWriter& osTarget, PepXMLWriter& osDecoy);
+ void computePEP();
+
+ void write_max_nets(string filename, NeuralNet *max_net);
+ void write_unique_peptides(string filename, NeuralNet* max_net);
+ void write_num_psm_per_spectrum(NeuralNet* max_net);
+
+ inline void set_fileroot(string &fl){fileroot = fl;}
+ inline void set_overwrite_flag(int flag) {overwrite_flag = flag;}
+ inline void set_input_dir(string &input_dir) {in_dir = input_dir; d.set_input_dir(input_dir);}
+ inline void set_output_dir(string &output_dir){out_dir = output_dir;}
+ void print_description();
+ int set_command_line_options(int argc, char **argv);
+ int crux_set_command_line_options(int argc, char *argv[]);
+
+
+ virtual int main(int argc, char** argv);
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+ virtual bool needsOutputDirectory() const;
+ virtual COMMAND_T getCommand() const;
+ FILE_FORMAT_T check_file_format(string &filePath);
+ string file_extension(string filename);
+ void get_protein_id(int pepind, vector<string> &prot);
+ void print_protein_ids(vector<string> &prots, ofstream &os, int psmind);
+
+protected:
+
+ Dataset d;
+ string res_prefix;
+
+ PSMScores fullset;
+ PSMScores trainset,testset,thresholdset;
+
+ int seed;
+ double selectionfdr;
+
+ int num_features;
+ NeuralNet net;
+ int num_hu;
+ double mu;
+ double weightDecay;
+ string cleavage_type;
+ int ind_low;
+ int interval;
+ int niter;
+ int switch_iter;
+ double loss;
+
+ int num_qvals;
+ vector<double> qvals;
+ vector<double> qvals1;
+ vector<double> qvals2;
+
+ vector<int> overFDRmulti;
+ vector<int> max_overFDR;
+ vector<int> ave_overFDR;
+ NeuralNet* max_net_gen;
+ NeuralNet* max_net_targ;
+ NeuralNet* nets;
+
+ string in_dir;
+ string out_dir;
+ int skip_cleanup_flag;
+ int overwrite_flag;
+ string fileroot;
+ int feature_file_flag;
+ ostringstream feature_file_name;
+
+ string file_format_;
+
+ TabDelimParser pars;
+ SQTParser* parser;
+
+
+};
+
+
+
+#endif /*QRANKER_H_*/
diff --git a/src/app/qranker-barista/SQTParser.cpp b/src/app/qranker-barista/SQTParser.cpp
new file mode 100644
index 0000000..0fcd4f5
--- /dev/null
+++ b/src/app/qranker-barista/SQTParser.cpp
@@ -0,0 +1,2156 @@
+#include "SQTParser.h"
+
+/******************************/
+
+SQTParser :: SQTParser()
+ : database_exists(0),
+ num_prot_not_found_in_db(0),
+ num_pos_prot_not_found_in_db(0),
+ num_neg_prot_not_found_in_db(0),
+ num_mixed_labels(0),
+ num_features(0),
+ num_spec_features(0),
+ num_total_features(0),
+ use_quadratic_features(0),
+ num_spectra(0),
+ num_psm(0),
+ num_pos_psm(0),
+ num_neg_psm(0),
+ num_pep(0),
+ num_pos_pep(0),
+ num_neg_pep(0),
+ num_prot(0),
+ num_pos_prot(0),
+ num_neg_prot(0),
+ num_cur_psm(0),
+ num_cur_prot(0), prot_offset(0),
+ x(0),
+ xs(0),
+ protind_to_num_all_pep(0),
+ protind_to_length(0),
+ cur_fileind(0)
+{
+
+ int capacity = 11;
+ m.xcorr_rank.reserve(capacity);
+ m.sp_rank.reserve(capacity);
+ m.calc_mass.reserve(capacity);
+ m.delta_cn.reserve(capacity);
+ m.xcorr_score.reserve(capacity);
+ m.sp_score.reserve(capacity);
+ m.num_ions_matched.reserve(capacity);
+ m.num_total_ions.reserve(capacity);
+ m.peptides.reserve(capacity);
+ m.num_proteins_in_match.reserve(capacity);
+ m.proteins.reserve(capacity);
+ m.peptide_pos.reserve(capacity);
+
+ //num_psm_features
+ num_features = 17;
+ //num_spec_features
+ num_spec_features = 3;
+
+ //final_hits_per_spectrum
+ fhps = 3;
+ //enzyme
+ e = TRYPSIN_ENZ;
+ //decoy prefix
+ decoy_prefix = "rand_";
+ //max peptide length to be considered
+ max_len = 50;
+ //min peptide length to be considered
+ min_len = 7;
+
+ //feature header
+ features_header_.push_back("sp rank");
+ features_header_.push_back("delta lcn");
+ features_header_.push_back("delta cn");
+ features_header_.push_back("xcorr score");
+ features_header_.push_back("sp score");
+ features_header_.push_back("matched ions/predicted ions");
+ features_header_.push_back("observed mass");
+ features_header_.push_back("peptide length");
+ features_header_.push_back("charge 1");
+ features_header_.push_back("charge 2");
+ features_header_.push_back("charge 3");
+ features_header_.push_back("n-term enz");
+ features_header_.push_back("c-term enz");
+ features_header_.push_back("missed cleavage");
+ features_header_.push_back("number of sequence_comparison");
+ features_header_.push_back("delta mass");
+ features_header_.push_back("abs(delta mass)");
+
+ //spec_features_header_3
+ spec_features_header_3_.push_back("b ions");
+ spec_features_header_3_.push_back("y ions");
+ spec_features_header_3_.push_back("flanking");
+
+ //spec features 7
+ spec_features_header_7_.push_back("b ions");
+ spec_features_header_7_.push_back("y ions");
+ spec_features_header_7_.push_back("flanking");
+ spec_features_header_7_.push_back("H2O-nl");
+ spec_features_header_7_.push_back("CO2-nl");
+ spec_features_header_7_.push_back("NH3-nl");
+ spec_features_header_7_.push_back("NH3-nl-y");
+
+ // set specturm file extensions
+ spectrumExts_.push_back(".ms2");
+ spectrumExts_.push_back(".mzXML");
+ spectrumExts_.push_back(".mgf");
+}
+
+
+SQTParser :: ~SQTParser()
+{
+ clear();
+}
+
+void SQTParser :: clear()
+{
+ clear_matches();
+ delete[] x;
+ x = (double*)0;
+ delete[] xs; xs = (double*)0;
+ delete[] protind_to_num_all_pep; protind_to_num_all_pep = (int*)0;
+ delete[] protind_to_length; protind_to_length = (int*)0;
+
+ pep_to_ind.clear();
+ ind_to_pep.clear();
+ pepind_to_protinds.clear();
+ pepind_to_protinds_map.clear();
+ pepind_to_psminds.clear();
+ pepind_to_psminds_map.clear();
+
+ prot_to_ind.clear();
+ ind_to_prot.clear();
+ protind_to_pepinds_map.clear();
+ protind_to_pepinds.clear();
+ protein_to_num_all_pep_map.clear();
+ protind_to_num_all_pep_map.clear();
+ protein_to_length_map.clear();
+ protind_to_length_map.clear();
+
+ spec_features_header_3_.clear();
+ spec_features_header_7_.clear();
+ features_header_.clear();
+ final_features_header_.clear();
+
+ num_features = 0;
+ num_spec_features = 0;
+ num_spectra = 0;
+ num_psm = 0;
+ num_pos_psm = 0;
+ num_neg_psm = 0;
+ num_pep = 0;
+ num_pos_pep = 0;
+ num_neg_pep = 0;
+ num_prot = 0;
+ num_pos_prot = 0;
+ num_neg_prot = 0;
+ num_cur_prot = 0;
+ prot_offset = 0;
+
+}
+
+void SQTParser :: set_enzyme(string &enz)
+{
+
+ if(enz.find("elastase") != string::npos)
+ {
+ e = ELASTASE_ENZ;
+ }
+ else if (enz.find("chymotrypsin") != string::npos)
+ {
+ e = CHYMOTRYPSIN_ENZ;
+ }
+ else if (enz.find("trypsin") != string::npos)
+ {
+ e = TRYPSIN_ENZ;
+ }
+ else
+ {
+ carp(CARP_WARNING, "could not determine enzyme, will assume trypsin");
+ }
+}
+
+
+
+void SQTParser :: clear_matches()
+{
+ m.xcorr_rank.clear();
+ m.sp_rank.clear();
+ m.calc_mass.clear();
+ m.delta_cn.clear();
+ m.xcorr_score.clear();
+ m.sp_score.clear();
+ m.num_ions_matched.clear();
+ m.num_total_ions.clear();
+ m.peptides.clear();
+ m.num_proteins_in_match.clear();
+ m.proteins.clear();
+ m.peptide_pos.clear();
+}
+
+
+void SQTParser :: erase_matches()
+{
+ m.xcorr_rank.erase(m.xcorr_rank.begin(),m.xcorr_rank.end());
+ m.sp_rank.erase(m.sp_rank.begin(),m.sp_rank.end());
+ m.calc_mass.erase(m.calc_mass.begin(),m.calc_mass.end());
+ m.delta_cn.erase(m.delta_cn.begin(),m.delta_cn.end());
+ m.xcorr_score.erase(m.xcorr_score.begin(),m.xcorr_score.end());
+ m.sp_score.erase(m.sp_score.begin(),m.sp_score.end());
+ m.num_ions_matched.erase(m.num_ions_matched.begin(),m.num_ions_matched.end());
+ m.num_total_ions.erase(m.num_total_ions.begin(),m.num_total_ions.end());
+ m.peptides.erase(m.peptides.begin(),m.peptides.end());
+ m.num_proteins_in_match.erase(m.num_proteins_in_match.begin(),m.num_proteins_in_match.end());
+ m.proteins.erase(m.proteins.begin(),m.proteins.end());
+ m.peptide_pos.erase(m.peptide_pos.begin(),m.peptide_pos.end());
+}
+
+
+void SQTParser :: add_matches_to_tables(sqt_match &m, string &decoy_prefix, int hits_read, int final_hits, bool decoy)
+{
+ int protein_pos = 0;
+ for (int i = 0; i < min(hits_read,final_hits); i++){
+ set<string> proteins;
+ int label = 1; //not decoy by default
+ // go through the proteins of the match
+
+ for (int j = 0; j < m.num_proteins_in_match[i]; j++){
+ string prot = m.proteins[protein_pos];
+ proteins.insert(prot);
+
+ if(prot.find(decoy_prefix) != string::npos || decoy) {
+ label = -1;
+ }
+ protein_pos++;
+ }
+
+
+
+ //record the psm label
+ f_psmind_to_label.write((char*)(&label),sizeof(int));
+
+ string pep = m.peptides[i];
+ int pep_ind = -1;
+ //add peptide to pep_to_ind and ind_to_pep maps
+ if(pep_to_ind.find(pep) == pep_to_ind.end()){
+ pep_ind = num_pep;
+ //add a new peptide
+ pep_to_ind[pep] = pep_ind;
+ ind_to_pep[pep_ind] = pep;
+ //start a pepind_to_psminds entry for the new peptide
+ set<int> tpsm;
+ pepind_to_psminds_map[pep_ind] = tpsm;
+ //start a pepind_to_protinds entry for the new peptide
+ set<int> t;
+ pepind_to_protinds_map[pep_ind] = t;
+ //set the label of the new peptide
+ f_pepind_to_label.write((char*)(&label),sizeof(int));
+ //augment num_pep count
+ num_pep++;
+ if(label == 1)
+ num_pos_pep++;
+ else
+ num_neg_pep++;
+ }else{
+ pep_ind = pep_to_ind[pep];
+ string p = ind_to_pep[pep_ind];
+ //if(pep.compare(p) != 0)
+ // cout << "warning : did not find peptide index in ind_to_pep_table\n";
+ }
+ //augment the pepinds_to_psminds table
+ pepind_to_psminds_map[pep_ind].insert(num_psm);
+
+ for(set<string>::iterator it = proteins.begin(); it != proteins.end();it++){
+ string prot = *it;
+ //if the label is -1 but the protein name does not contain decoy_prefix_,
+ // we don't include it
+ //add prot to tables
+ if((prot.find(decoy_prefix) == string::npos) && (label == -1))
+ num_mixed_labels++;
+ else{
+ int prot_ind = -1;
+ if(prot_to_ind.find(prot) == prot_to_ind.end()){
+ prot_ind = num_prot;
+ //add new protein
+ prot_to_ind[prot] = prot_ind;
+ ind_to_prot[prot_ind] = prot;
+ //start a protind_to_pepinds entry for the new protein
+ set<int> t;
+ protind_to_pepinds_map[prot_ind] = t;
+ //set the prot label
+ f_protind_to_label.write((char*)(&label),sizeof(int));
+ num_prot++; num_cur_prot++;
+ if(label == 1)
+ num_pos_prot++;
+ else
+ num_neg_prot++;
+
+ //find the prot in the prot_to_num_all_pep
+ if(database_exists){
+ int cnt = 0;
+ int len = 0;
+ if(protein_to_num_all_pep_map.find(prot) == protein_to_num_all_pep_map.end()){
+ /*
+ for(map<string,int>::iterator itt = protein_to_num_all_pep_map.begin();
+ itt != protein_to_num_all_pep_map.end(); itt++)
+ {
+ string protein = itt->first;
+ if(protein.find(prot) != string :: npos)
+ cnt = itt->second;
+ }
+ */
+ }else{
+ cnt = protein_to_num_all_pep_map[prot];
+ len = protein_to_length_map[prot];
+
+ }
+
+ //add the cnt to protind_to_num_all_pep_map
+ if(cnt == 0){
+ num_prot_not_found_in_db++;
+ if(label == 1)
+ num_pos_prot_not_found_in_db++;
+ else
+ num_neg_prot_not_found_in_db++;
+ //carp(CARP_WARNING, "did not find protein %s from sqt file in the database ", prot.c_str());
+ }else{
+ protind_to_num_all_pep_map[prot_ind] = cnt;
+ protind_to_length_map[prot_ind] = len;
+ }
+ }
+ }else
+ prot_ind = prot_to_ind[prot];
+ //augment the pepind_to_protinds table
+ (pepind_to_protinds_map[pep_ind]).insert(prot_ind);
+ //augment to protind_to_pepinds table
+ protind_to_pepinds_map[prot_ind].insert(pep_ind);
+ }
+ } //augment num psms
+ num_psm++;
+ if(label == 1)
+ num_pos_psm++;
+ else
+ num_neg_psm++;
+ }
+ num_spectra++;
+}
+
+
+void SQTParser :: allocate_feature_space()
+{
+ //space for feature vector
+ x = new double[num_features];
+
+
+ memset(x,0,sizeof(double)*num_features);
+ //space for spec feature vector
+ if (num_spec_features > 0)
+ {
+ xs = new double[num_spec_features];
+ memset(xs,0,sizeof(double)*num_spec_features);
+ }
+}
+
+
+void SQTParser :: fill_graphs_and_save_data(string &out_dir)
+{
+ ostringstream fname;
+
+ //space for prot to number of all peptides info
+ protind_to_num_all_pep = new int[num_cur_prot];
+ memset(protind_to_num_all_pep,0,sizeof(int)*num_cur_prot);
+ protind_to_length = new int[num_cur_prot];
+ memset(protind_to_length,0,sizeof(int)*num_cur_prot);
+ for(map<int,string>::iterator it = ind_to_prot.begin(); it != ind_to_prot.end(); it++)
+ {
+ int protind = it->first;
+ if(protind < prot_offset)
+ continue;
+ //if database does not exist
+ if(!database_exists)
+ {
+ int cnt = (protind_to_pepinds_map[protind]).size();
+ protind_to_num_all_pep[protind-prot_offset] = cnt;
+ protind_to_length[protind-prot_offset] = -1;
+ }
+ //if did not see any decoy proteins in the database or did not see half of the total proteins in the database
+ else if ( ((double)num_prot_not_found_in_db > (double)num_prot/3.0))
+ {
+ int cnt = (protind_to_pepinds_map[protind]).size();
+ protind_to_num_all_pep[protind-prot_offset] = cnt;
+ protind_to_length[protind-prot_offset] = -1;
+ }
+ else
+ {
+ //if did not find the protein in the count of all proteins, then just get the count of observed proteins
+ if(protind_to_num_all_pep_map.find(protind) == protind_to_num_all_pep_map.end())
+ {
+ int cnt = (protind_to_pepinds_map[protind]).size();
+ protind_to_num_all_pep[protind-prot_offset] = cnt;
+ protind_to_length[protind-prot_offset] = -1;
+ }
+ else
+ {
+ int cnt = protind_to_num_all_pep_map[protind];
+ protind_to_num_all_pep[protind-prot_offset] = cnt;
+ int len = protind_to_length_map[protind];
+ protind_to_length[protind-prot_offset] = len;
+ }
+ }
+ }
+
+ //protind_to_num_all_pep
+ protein_to_num_all_pep_map.clear();
+ protind_to_num_all_pep_map.clear();
+ protein_to_length_map.clear();
+ protind_to_length_map.clear();
+ fname << out_dir << "/protind_to_num_all_pep";
+ f_protind_to_num_all_pep.write((char*)protind_to_num_all_pep,sizeof(int)*num_cur_prot);
+ fname.str("");
+ delete[] protind_to_num_all_pep; protind_to_num_all_pep = (int*)0;
+ fname << out_dir << "/protind_to_length";
+ f_protind_to_length.write((char*)protind_to_length,sizeof(int)*num_cur_prot);
+ fname.str("");
+ delete[] protind_to_length; protind_to_length = (int*)0;
+
+
+ //ind_to_pep
+ fname << out_dir << "/ind_to_pep";
+ ofstream f_ind_to_pep(fname.str().c_str());
+ for(map<int,string>::iterator it = ind_to_pep.begin(); it != ind_to_pep.end(); it++)
+ f_ind_to_pep << it->first << " " << it->second << "\n";
+ f_ind_to_pep.close();
+ fname.str("");
+ ind_to_pep.clear();
+
+ //pep_to_ind
+ fname << out_dir << "/pep_to_ind";
+ ofstream f_pep_to_ind(fname.str().c_str());
+ for(map<string,int>::iterator it = pep_to_ind.begin(); it != pep_to_ind.end(); it++)
+ f_pep_to_ind << it->first << " " << it->second << "\n";
+ f_pep_to_ind.close();
+ fname.str("");
+ pep_to_ind.clear();
+
+ //prot_to_ind
+ fname << out_dir << "/prot_to_ind";
+ ofstream f_prot_to_ind(fname.str().c_str(),ios::binary);
+ for(map<string,int>::iterator it = prot_to_ind.begin(); it != prot_to_ind.end(); it++)
+ f_prot_to_ind << it->first << " " << it->second << "\n";
+ f_prot_to_ind.close();
+ fname.str("");
+ prot_to_ind.clear();
+
+ //ind_to_prot
+ fname << out_dir << "/ind_to_prot";
+ ofstream f_ind_to_prot(fname.str().c_str(),ios::binary);
+ for(map<int,string>::iterator it = ind_to_prot.begin(); it != ind_to_prot.end(); it++)
+ f_ind_to_prot << it->first << " " << it->second << "\n";
+ f_ind_to_prot.close();
+ fname.str("");
+ ind_to_prot.clear();
+
+ //pepind_to_psminds
+ pepind_to_psminds.create_bipartite_graph(pepind_to_psminds_map);
+ pepind_to_psminds_map.clear();
+ fname << out_dir << "/pepind_to_psminds";
+ ofstream f_pepind_to_psminds(fname.str().c_str(),ios::binary);
+ pepind_to_psminds.save(f_pepind_to_psminds);
+ f_pepind_to_psminds.close();
+ fname.str("");
+ pepind_to_psminds.clear();
+
+ //pepind_to_protinds
+ pepind_to_protinds.create_bipartite_graph(pepind_to_protinds_map);
+ pepind_to_protinds_map.clear();
+ fname << out_dir << "/pepind_to_protinds";
+ ofstream f_pepind_to_protinds(fname.str().c_str(),ios::binary);
+ pepind_to_protinds.save(f_pepind_to_protinds);
+ f_pepind_to_protinds.close();
+ fname.str("");
+ pepind_to_protinds.clear();
+
+ //protind_to_pepinds
+ protind_to_pepinds.create_bipartite_graph(protind_to_pepinds_map);
+ protind_to_pepinds_map.clear();
+ fname << out_dir << "/protind_to_pepinds";
+ ofstream f_protind_to_pepinds(fname.str().c_str(),ios::binary);
+ protind_to_pepinds.save(f_protind_to_pepinds);
+ f_protind_to_pepinds.close();
+ fname.str("");
+ protind_to_pepinds.clear();
+
+ //write out data summary
+ fname << out_dir << "/summary";
+ ofstream f_summary(fname.str().c_str());
+ //psm info
+ f_summary << num_total_features << " " << num_psm << " " << num_pos_psm << " " << num_neg_psm << endl;
+ //peptide info
+ f_summary << num_pep << " " << num_pos_pep << " " << num_neg_pep << endl;
+ //protein info
+ f_summary << num_prot << " " << num_pos_prot << " " << num_neg_prot << endl;
+ f_summary.close();
+ fname.str("");
+
+}
+
+
+/********* extracting features **********************************************************/
+int SQTParser::cntEnz(const string& peptide,enzyme enz) {
+ unsigned int pos=2, cnt=0;
+ char n = peptide.at(pos++);
+ while (pos<peptide.size()-2) {
+ char c = peptide.at(pos++);
+ if (isEnz(n,c,enz))
+ cnt++;
+ n=c;
+ }
+ return cnt;
+}
+
+double SQTParser::isTryptic(const char n,const char c) {
+ return (
+ (((n=='K' || n=='R') && c != 'P') ||
+ n=='-' || c=='-')
+ ?1.0:0.0);
+}
+// [FHWYLM].[^P]
+double SQTParser::isChymoTryptic(const char n,const char c) {
+ return (
+ (((n=='F' || n=='H' || n=='W' || n=='Y' || n=='L' || n=='M') && c!= 'P') ||
+ n=='-' || c=='-')
+ ?1.0:0.0);
+}
+
+// [LVAG].[^P]
+double SQTParser::isElastasic(const char n,const char c) {
+ return (
+ (((n=='L' || n=='V' || n=='A' || n=='G' ) && c!= 'P') ||
+ n=='-' || c=='-')
+ ?1.0:0.0);
+}
+
+double SQTParser::isEnz(const char n,const char c, enzyme enz) {
+ switch(enz) {
+ case TRYPSIN_ENZ:
+ return isTryptic(n,c);
+ case CHYMOTRYPSIN_ENZ:
+ return isChymoTryptic(n,c);
+ case ELASTASE_ENZ:
+ return isElastasic(n,c);
+ default:
+ return 0;
+ }
+}
+
+void SQTParser :: extract_psm_features(sqt_match &m, enzyme enz, double *x, int i)
+{
+ string pep = m.peptides[i];
+ memset(x,0,sizeof(double)*num_features);
+ //log rank by Sp
+ if (m.sp_rank[i] > 0)
+ x[0] = log((double) m.sp_rank[i]);
+ else
+ x[0] = 0.0;
+ //deltaLCN
+ x[1] = 0.0;
+ //deltaCN
+ x[2] = m.delta_cn[i];
+ //xcorr score
+ x[3] = m.xcorr_score[i];
+ //sp score
+ x[4] = m.sp_score[i];
+ //matched ions/predicted ions
+ if(m.num_total_ions[i] > 0)
+ x[5] = m.num_ions_matched[i]/m.num_total_ions[i];
+ else
+ x[5] = 0.0;
+ //observed mass
+ x[6] = m.precursor_mass;
+ //peptide length
+ x[7] = pep.size();
+ //charge
+ x[8] = 0.0; x[9] = 0.0; x[10] = 0.0;
+ if (m.charge == 1)
+ x[8] = 1.0;
+ if(m.charge == 2)
+ x[9] = 1.0;
+ if(m.charge == 3)
+ x[10] = 1.0;
+ //whether n-terminus and c-terminus have proper cleavage sites
+ x[11]=isEnz(pep.at(0),pep.at(2),enz);
+ x[12]=isEnz(pep.at(pep.size()-3),pep.at(pep.size()-1),enz);
+ // missed cleavages
+ x[13]=(double)cntEnz(pep,enz);
+ // number of sequence_comparisons
+ x[14] = log((FLOAT_T) m.num_sequence_comparisons);
+ //x[14] = m.num_sequence_comparisons;
+ //difference between measured and calculated mass
+ x[15] = m.precursor_mass-m.calc_mass[i];
+ // absolute value of difference between measured and calculated mass
+ x[16] = m.precursor_mass-m.calc_mass[i];
+}
+
+void SQTParser :: extract_psm_features(sqt_match &m, enzyme enz, double *x, int i, int hits_read)
+{
+ string pep = m.peptides[i];
+ memset(x,0,sizeof(double)*num_features);
+
+ //log rank by Sp
+ if (m.sp_rank[i] > 0)
+ x[0] = log((double) m.sp_rank[i]);
+ else
+ x[0] = 0.0;
+
+ //deltaLCN
+ x[1] = 0.0;
+
+ //deltaCN
+ x[2] = 0.0;
+ if(i < hits_read-1)
+ {
+ double xs = fabs(m.xcorr_score[i]);
+ if(xs > 0.00001)
+ x[2] = (m.xcorr_score[i] - m.xcorr_score[i+1])/m.xcorr_score[i];
+ }
+ //x[2] = m.delta_cn[i];
+
+ //xcorr score
+ x[3] = m.xcorr_score[i];
+
+ //sp score
+ x[4] = m.sp_score[i];
+
+ //matched ions/predicted ions
+ if(m.num_total_ions[i] > 0)
+ x[5] = m.num_ions_matched[i]/m.num_total_ions[i];
+ else
+ x[5] = 0.0;
+
+ //observed mass
+ x[6] = m.precursor_mass;
+
+ //peptide length
+ x[7] = pep.size();
+
+ //charge
+ x[8] = 0.0; x[9] = 0.0; x[10] = 0.0;
+ if (m.charge == 1)
+ x[8] = 1.0;
+ if(m.charge == 2)
+ x[9] = 1.0;
+ if(m.charge == 3)
+ x[10] = 1.0;
+
+ //whether n-terminus and c-terminus have proper cleavage sites
+ x[11]=isEnz(pep.at(0),pep.at(2),enz);
+ x[12]=isEnz(pep.at(pep.size()-3),pep.at(pep.size()-1),enz);
+ // missed cleavages
+ x[13]=(double)cntEnz(pep,enz);
+
+ // number of sequence_comparisons
+ //x[14] = log(m.num_sequence_comparisons);
+ //x[14] = m.num_sequence_comparisons;
+
+ //difference between measured and calculated mass
+ x[15] = m.precursor_mass-m.calc_mass[i];
+ // absolute value of difference between measured and calculated mass
+ x[16] = fabs(m.precursor_mass-m.calc_mass[i]);
+
+}
+
+void SQTParser :: extract_features(sqt_match &m, int hits_read, int final_hits,enzyme enz)
+{
+
+ for (int i = 0; i < min(hits_read,final_hits); i++){
+ //write the feature vector out to file
+ //extract_psm_features(m, enz, x, i);
+ extract_psm_features(m, enz, x, i, hits_read);
+
+ if (num_spec_features > 0){
+
+ if(num_cur_psm % 5000 == 0)
+ carp(CARP_INFO, "PSM number %d", num_cur_psm);
+ string peptide = m.peptides[i];
+ int pos = peptide.find('.');
+ string pept = peptide.substr(pos+1,peptide.size());
+ pos = pept.rfind('.');
+ pept = pept.substr(0,pos);
+
+ if (pept.find('[') != string::npos) {
+ carp(CARP_FATAL, "Modification detected in peptide %s. Barista does not "
+ "support modifications when use-spec-features=T.", pept.c_str());
+ }
+
+ if(num_spec_features == 3)
+ sfg.get_spec_features_m3(m.scan, m.charge,pept,xs);
+ if(num_spec_features == 7)
+ sfg.get_spec_features_m7(m.scan, m.charge,pept,xs);
+
+ //write out features
+ f_psm.write((char*)x, sizeof(double)*num_features);
+ f_psm.write((char*)xs, sizeof(double)*num_spec_features);
+ }else
+ f_psm.write((char*)x, sizeof(double)*num_features);
+
+ num_total_features = num_features+num_spec_features;
+
+ if(use_quadratic_features){
+ //for(int i = 0; i < num_features; i++)
+ //x[i] *= x[i];
+ //f_psm.write((char*)x, sizeof(double)*num_features);
+ //num_total_features += num_features;
+ double *b = new double[1];
+ for(int i = 0; i < num_features; i++){
+ for(int j = i; j < num_features; j++){
+ b[0] = x[i]*x[j];
+ f_psm.write((char*)b, sizeof(double));
+ num_total_features++;
+ }
+ }
+ if(num_spec_features > 0){
+ for(int i = 0; i < num_spec_features; i++){
+ for(int j = i; j < num_spec_features; j++){
+ b[0] = xs[i]*xs[j];
+ f_psm.write((char*)b, sizeof(double));
+ num_total_features++;
+ }
+ }
+ }
+
+ }
+
+
+ //write psm tables
+ double deltaCN = m.delta_cn[i];
+ f_psmind_to_deltaCn.write((char*)(&deltaCN),sizeof(double));
+
+ double xcorr = m.xcorr_score[i];
+ f_psmind_to_xcorr.write((char*)(&xcorr),sizeof(double));
+
+ double sp = m.sp_score[i];
+ f_psmind_to_spscore.write((char*)(&sp),sizeof(double));
+
+ double calc_mass = m.calc_mass[i];
+ f_psmind_to_calculated_mass.write((char*)(&calc_mass),sizeof(double));
+
+ int scan = m.scan;
+ f_psmind_to_scan.write((char*)(&scan),sizeof(int));
+
+ int charge = m.charge;
+ f_psmind_to_charge.write((char*)(&charge),sizeof(int));
+
+ double precursor_mass = m.precursor_mass;
+ f_psmind_to_precursor_mass.write((char*)(&precursor_mass),sizeof(double));
+
+ //Sp rank
+ int sp_rank=m.sp_rank[i];
+ f_psmind_to_sp_rank.write((char*)(&sp_rank),sizeof(int));
+
+ //xcorr rank
+ int xc_rank=m.xcorr_rank[i];
+ f_psmind_to_xcorr_rank.write((char*)(&xc_rank),sizeof(int));
+
+ //matches_spectrum
+ int matches_spectrum = m.num_sequence_comparisons;
+ f_pmsind_to_matches_spectrum.write((char*)(&matches_spectrum),sizeof(int));
+
+ //b/y ions matched
+ double by_ions_matched=m.num_ions_matched[i];
+ f_psmind_to_by_ions_matched.write((char*)(&by_ions_matched),sizeof(double));
+
+ //b/y ions total
+ double by_ions_total=m.num_total_ions[i];
+ f_psmind_to_by_ions_total.write((char*)(&by_ions_total),sizeof(double));
+
+ // peptide position
+ int peptide_position=m.peptide_pos[i];
+ f_psmind_to_peptide_position.write((char*)(&peptide_position),sizeof(int));
+
+ //get the pepind of the peptide
+ string pep = m.peptides[i];
+ int pepind = pep_to_ind[pep];
+ f_psmind_to_pepind.write((char*)(&pepind),sizeof(int));
+
+ f_psmind_to_fileind.write((char*)(&cur_fileind),sizeof(int));
+
+ num_cur_psm++;
+ }
+}
+
+
+
+/************ parsing sqt file*******************************/
+
+void SQTParser :: read_M_line(ifstream &is, sqt_match &m)
+{
+ //rank by scorr
+ int xcorr_rank;
+ is >> xcorr_rank;
+ m.xcorr_rank.push_back(xcorr_rank);
+
+ //rank by Sp
+ int sp_rank;
+ is >> sp_rank;
+ m.sp_rank.push_back(sp_rank);
+
+ //calculated mass
+ double calc_mass;
+ is >> calc_mass;
+ m.calc_mass.push_back(calc_mass);
+
+ //delta cn
+ double delta_cn;
+ is >> delta_cn;
+ m.delta_cn.push_back(delta_cn);
+
+ //xcorr
+ double xcorr;
+ is >> xcorr;
+ m.xcorr_score.push_back(xcorr);
+
+ //sp_score
+ double sp;
+ is >> sp;
+ m.sp_score.push_back(sp);
+
+ //number of matched ions
+ int num_ions_matched;
+ is >> num_ions_matched;
+ m.num_ions_matched.push_back(num_ions_matched);
+
+ //number of total ions;
+ double num_total_ions;
+ is >> num_total_ions;
+ m.num_total_ions.push_back(num_total_ions);
+
+ //peptide
+ string peptide;
+ is >> peptide;
+ m.peptides.push_back(peptide);
+}
+
+
+void SQTParser :: read_S_line(ifstream &is, sqt_match &m)
+{
+ string tempstr;
+ //scan begin
+ is >> m.scan;
+ //scan end
+ is >> tempstr;
+ //charge
+ is >> m.charge;
+ is >> tempstr;
+ is >> tempstr;
+ //precursor ion mass
+ is >> m.precursor_mass;
+ is >> tempstr;
+ is >> tempstr;
+ //number of matches considered
+ is >> m.num_sequence_comparisons;
+}
+
+int SQTParser :: parse_sqt_spectrum_matches(ifstream &is, sqt_match &m)
+{
+ string tempstr;
+ read_S_line(is,m);
+ erase_matches();
+ int num_hits = 0;
+ int num_proteins_in_match = 0;
+ while (!is.eof())
+ {
+ is >> tempstr;
+ if (tempstr.compare("M") == 0)
+ {
+ read_M_line(is,m);
+ if (num_hits > 0)
+ m.num_proteins_in_match.push_back(num_proteins_in_match);
+ num_proteins_in_match = 0;
+ num_hits++;
+ }
+ if(tempstr.compare("L") == 0)
+ {
+ string prot;
+ is >> prot;
+ m.proteins.push_back(prot);
+ num_proteins_in_match++;
+ tempstr = "";
+ }
+ if(tempstr.compare("S") == 0)
+ break;
+ }
+ if (num_hits > 0)
+ m.num_proteins_in_match.push_back(num_proteins_in_match);
+ assert(num_hits == (int)m.num_proteins_in_match.size());
+ return num_hits;
+
+
+}
+
+void SQTParser :: read_sqt_file(ifstream &is, string &decoy_prefix, int final_hits, enzyme enz, bool decoy)
+{
+ int cn = 0;
+ string line;
+ string tempstr;
+ is >> tempstr;
+ while(!is.eof())
+ {
+ if (tempstr.compare("H") != 0)
+ break;
+ getline(is, line);
+ is >> tempstr;
+ }
+ int num_hits;
+ while(!is.eof())
+ {
+ assert(tempstr.compare("S") == 0);
+ num_hits = parse_sqt_spectrum_matches(is,m);
+ add_matches_to_tables(m, decoy_prefix, num_hits, final_hits, decoy);
+ extract_features(m, num_hits, final_hits,enz);
+ cn++;
+ //if(cn > 10)
+ //break;
+ }
+
+}
+
+int SQTParser :: check_file(ostringstream &fname)
+{
+ ifstream f(fname.str().c_str());
+ if(!f.is_open())
+ {
+ carp(CARP_INFO,"could not open %s", fname.str().c_str());
+ return 0;
+ }
+ f.close();
+ fname.str("");
+ return 1;
+}
+
+
+int SQTParser :: check_input_dir(string &in_dir)
+{
+
+ ostringstream fname;
+
+ fname << in_dir << "/summary";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ fname << in_dir << "/psm";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_label
+ fname << in_dir << "/psmind_to_label";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_pepind
+ fname << in_dir << "/psmind_to_pepind";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_scan
+ fname << in_dir << "/psmind_to_scan";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_charge
+ fname << in_dir << "/psmind_to_charge";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_precursor_mass
+ fname << in_dir << "/psmind_to_precursor_mass";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_fileind
+ fname << in_dir << "/psmind_to_fileind";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //fileind_to_fname
+ fname << in_dir << "/fileind_to_fname";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_xcorr
+ fname << in_dir << "/psmind_to_xcorr";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_spscore
+ fname << in_dir << "/psmind_to_spscore";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_spscore
+ fname << in_dir << "/psmind_to_deltaCn";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_calculated_mass
+ fname << in_dir << "/psmind_to_calculated_mass";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //pepind_to_label
+ fname << in_dir << "/pepind_to_label";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //protind_to_label
+ fname << in_dir << "/protind_to_label";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ fname << in_dir << "/protind_to_num_all_pep";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ fname << in_dir << "/protind_to_length";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //ind_to_pep
+ fname << in_dir << "/ind_to_pep";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //pep_to_ind
+ fname << in_dir << "/pep_to_ind";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //ind_to_prot
+ fname << in_dir << "/ind_to_prot";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //prot_to_ind
+ fname << in_dir << "/prot_to_ind";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //pepind_to_protinds
+ fname << in_dir << "/pepind_to_protinds";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //pepind_to_psminds
+ fname << in_dir << "/pepind_to_psminds";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_sp_rank
+ fname << in_dir << "/psmind_to_sp_rank";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_xcorr_rank
+ fname << in_dir << "/psmind_to_xcorr_rank";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_by_ions_matched
+ fname << in_dir << "/psmind_to_by_ions_matched";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_to_by_ions_total
+ fname << in_dir << "/psmind_to_by_ions_total";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //psmind_matches_spectrum
+ fname << in_dir << "/psmind_to_matches_spectrum";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+ //pepind_peptide_position
+ fname << in_dir << "/psmind_to_peptide_position";
+ if(!check_file(fname))
+ return 0;
+ fname.str("");
+
+
+ return 1;
+}
+
+
+void SQTParser :: clean_up(string dir)
+{
+
+ ostringstream fname;
+
+ fname << out_dir << "/summary";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ fname << dir << "/psm";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_pepind
+ fname << out_dir << "/psmind_to_pepind";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_scan
+ fname << out_dir << "/psmind_to_scan";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_charge
+ fname << out_dir << "/psmind_to_charge";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_precursor_mass
+ fname << out_dir << "/psmind_to_precursor_mass";
+ remove(fname.str().c_str());
+ fname.str("");
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_sp_rank
+ fname << out_dir << "/psmind_to_sp_rank";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_xcorr_rank
+ fname << out_dir << "/psmind_to_xcorr_rank";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_label
+ fname << out_dir << "/psmind_to_label";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_fileind
+ fname << out_dir << "/psmind_to_fileind";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //fileind_to_fname
+ fname << out_dir << "/fileind_to_fname";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_calculated_mass
+ fname << out_dir << "/psmind_to_calculated_mass";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_xcorr
+ fname << out_dir << "/psmind_to_xcorr";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_spscore
+ fname << out_dir << "/psmind_to_spscore";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_deltaCn
+ fname << out_dir << "/psmind_to_deltaCn";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //pepind_to_label
+ fname << out_dir << "/pepind_to_label";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //pepind_to_psminds
+ fname << out_dir << "/pepind_to_psminds";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //pepind_to_protinds
+ fname << out_dir << "/pepind_to_protinds";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //ind_to_pep
+ fname << out_dir << "/ind_to_pep";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //pep_to_ind
+ fname << out_dir << "/pep_to_ind";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //protind_to_label
+ fname << out_dir << "/protind_to_label";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //protind_to_num_all_pep
+ fname << out_dir << "/protind_to_num_all_pep";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //protind_to_length
+ fname << out_dir << "/protind_to_length";
+ remove(fname.str().c_str());
+ fname.str("");
+
+
+ //protind_to_pepinds
+ fname << out_dir << "/protind_to_pepinds";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //ind_to_prot
+ fname << out_dir << "/ind_to_prot";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //prot_to_ind
+ fname << out_dir << "/prot_to_ind";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_sp_rank
+ fname << out_dir << "/psmind_to_sp_rank";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_xcorr_rank
+ fname << out_dir << "/psmind_to_xcorr_rank";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_by_ions_matched
+ fname << out_dir << "/psmind_to_by_ions_matched";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_by_ions_total
+ fname << out_dir << "/psmind_to_by_ions_total";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_matches_spectrum
+ fname << out_dir << "/psmind_to_matches_spectrum";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_peptide_position
+ fname << out_dir << "/psmind_to_peptide_position";
+ remove(fname.str().c_str());
+ fname.str("");
+
+}
+
+
+
+void SQTParser :: open_files(string &out_dir)
+{
+
+ ostringstream fname;
+
+ fname << out_dir << "/psm";
+ f_psm.open(fname.str().c_str(), ios::binary);
+ fname.str("");
+
+ //psmind_to_label
+ fname << out_dir << "/psmind_to_label";
+ f_psmind_to_label.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+ //psmind_to_pepind
+ fname << out_dir << "/psmind_to_pepind";
+ f_psmind_to_pepind.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+ //psmind_to_scan
+ fname << out_dir << "/psmind_to_scan";
+ f_psmind_to_scan.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+ //psmind_to_charge
+ fname << out_dir << "/psmind_to_charge";
+ f_psmind_to_charge.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_precursor_mass
+ fname << out_dir << "/psmind_to_precursor_mass";
+ f_psmind_to_precursor_mass.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_sp_rank
+ fname << out_dir << "/psmind_to_sp_rank";
+ f_psmind_to_sp_rank.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_xcorr_rank
+ fname << out_dir << "/psmind_to_xcorr_rank";
+ f_psmind_to_xcorr_rank.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_matches_spectrum
+ fname << out_dir << "/psmind_to_matches_spectrum";
+ f_pmsind_to_matches_spectrum.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+ ///additional info
+ //psmind_to_xcorr
+ fname << out_dir << "/psmind_to_xcorr";
+ f_psmind_to_xcorr.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_spscore
+ fname << out_dir << "/psmind_to_spscore";
+ f_psmind_to_spscore.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_deltaCn
+ fname << out_dir << "/psmind_to_deltaCn";
+ f_psmind_to_deltaCn.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_calculated_mass
+ fname << out_dir << "/psmind_to_calculated_mass";
+ f_psmind_to_calculated_mass.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_by_ions_matched
+ fname << out_dir << "/psmind_to_by_ions_matched";
+ f_psmind_to_by_ions_matched.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_by_ions_total
+ fname << out_dir << "/psmind_to_by_ions_total";
+ f_psmind_to_by_ions_total.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //psmind_to_peptide_position
+ fname << out_dir << "/psmind_to_peptide_position";
+ f_psmind_to_peptide_position.open(fname.str().c_str(),ios::binary );
+ fname.str("");
+
+ //end of additional info
+
+ //pepind_to_label
+ fname << out_dir << "/pepind_to_label";
+ f_pepind_to_label.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+ //protind_to_label
+ fname << out_dir << "/protind_to_label";
+ f_protind_to_label.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+ fname << out_dir << "/protind_to_num_all_pep";
+ f_protind_to_num_all_pep.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+ fname << out_dir << "/protind_to_length";
+ f_protind_to_length.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+ fname << out_dir << "/fileind_to_fname";
+ f_fileind_to_fname.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+ fname << out_dir << "/psmind_to_fileind";
+ f_psmind_to_fileind.open(fname.str().c_str(),ios::binary);
+ fname.str("");
+
+}
+
+void SQTParser :: close_files()
+{
+
+ ostringstream fname;
+
+ f_psm.close();
+ f_psmind_to_label.close();
+ f_psmind_to_pepind.close();
+ f_psmind_to_scan.close();
+ f_psmind_to_charge.close();
+ f_psmind_to_precursor_mass.close();
+
+ f_psmind_to_xcorr.close();
+ f_psmind_to_spscore.close();
+ f_psmind_to_deltaCn.close();
+ f_psmind_to_calculated_mass.close();
+
+ f_pepind_to_label.close();
+ f_protind_to_label.close();
+ f_protind_to_num_all_pep.close();
+ f_protind_to_length.close();
+ f_fileind_to_fname.close();
+ f_psmind_to_fileind.close();
+ f_psmind_to_sp_rank.close();//sp rank
+ f_psmind_to_xcorr_rank.close();//xcorr rank
+ f_pmsind_to_matches_spectrum.close();// distinct matches/spectrum
+ f_psmind_to_by_ions_matched.close();// b/y ions match
+ f_psmind_to_by_ions_total.close();//b/y ions total
+ f_psmind_to_peptide_position.close();//peptide position
+}
+
+
+int SQTParser::cntEnzConstraints(string& seq,enzyme enz) {
+ int cnt = 0;
+ unsigned int pos=0;
+ unsigned int pos1 = pos;
+ char n = seq.at(pos);
+ pos++;
+ while (pos<seq.size()-1) {
+ char c = seq.at(pos);
+ if (isEnz(n,c,enz))
+ {
+ int pep_len = pos-pos1;
+ if(pep_len <= max_len && pep_len >= min_len)
+ {
+ cnt++;
+ pos1 = pos;
+ }
+ }
+ n=c;
+ pos++;
+ }
+ return cnt;
+}
+
+void SQTParser :: digest_database(ifstream &f_db, enzyme e)
+{
+ string tempstr;
+ string prot;
+ ostringstream seq;
+ int num_prot_read = 0;
+ while(!f_db.eof())
+ {
+ f_db >> tempstr;
+ if(tempstr[0] == '>')
+ {
+ if(num_prot_read > 0)
+ {
+ string sequence = seq.str();
+ int cnt = cntEnzConstraints(sequence,e);
+ protein_to_num_all_pep_map[prot] = cnt+1;
+ protein_to_length_map[prot] = sequence.size();
+ seq.str("");
+ }
+ prot = tempstr.substr(1,tempstr.size());
+ num_prot_read++;
+
+ getline(f_db, tempstr);
+ }
+ else
+ {
+ seq << tempstr;
+ }
+ }
+ if(num_prot_read > 0)
+ {
+ string sequence = seq.str();
+ int cnt = cntEnzConstraints(sequence,e);
+ protein_to_num_all_pep_map[prot] = cnt;
+ seq.str("");
+ }
+}
+
+
+bool SQTParser :: read_search_results(string& cur_fname, bool decoy) {
+ ifstream f_sqt(cur_fname.c_str());
+ if(!f_sqt.is_open()){
+ carp(CARP_WARNING, "could not open sqt file: %s", cur_fname.c_str());
+ return false;
+ }
+ read_sqt_file(f_sqt, decoy_prefix, fhps,e, decoy);
+ f_sqt.close();
+ return true;
+}
+
+int SQTParser :: run()
+{
+ //parse database
+ if(database_exists)
+ {
+ for(unsigned int i = 0; i < db_file_names.size(); i++)
+ {
+ db_name = db_file_names[i];
+ ifstream f_db(db_name.c_str());
+ if(!f_db.is_open())
+ {
+ carp(CARP_WARNING, "could not open database file: %s", db_name.c_str());
+ return 0;
+ }
+ carp(CARP_INFO,"digesting database %s", db_name.c_str());
+ digest_database(f_db, e);
+ f_db.close();
+ }
+ }
+
+ allocate_feature_space();
+ open_files(out_dir);
+ carp(CARP_INFO, "parsing files:");
+ int num_files_read = 0;
+ string ms2_fn = "";
+ string last_ms2 = "";
+ if(num_spec_features > 0)
+ sfg.initialize_aa_tables();
+ for(unsigned int i = 0; i < sqt_file_names.size(); i++)
+ {
+ if(num_spec_features>0)
+ {
+ ms2_fn = ms2_file_names[i];
+ if(ms2_fn.compare(last_ms2) != 0)
+ {
+ //prepare to generate spectrum features
+ sfg.clear();
+ carp(CARP_INFO, "reading file %s", ms2_fn.c_str());
+ sfg.read_ms2_file(ms2_fn);
+ }
+ last_ms2 = ms2_fn;
+ }
+
+ cur_fname = sqt_file_names[i];
+ cur_fileind = i;
+ carp(CARP_INFO, "parsing file %s", cur_fname.c_str());
+ f_fileind_to_fname << i << " " << cur_fname << endl;
+ if(read_search_results(cur_fname, i != 0))
+ num_files_read++;
+ }
+ if(num_files_read < 1)
+ {
+ carp(CARP_WARNING, "Could not parse any search result files");
+ return 0;
+ }
+
+ carp(CARP_INFO, "Number of spectra: %d", num_spectra);
+ carp(CARP_INFO, "Number of PSMs: total %d positives %d negatives %d", num_psm, num_pos_psm, num_neg_psm);
+ carp(CARP_INFO, "Number of peptides: total %d positives %d negatives %d", num_pep, num_pos_pep, num_neg_pep);
+ carp(CARP_INFO, "Number of proteins: total %d positives %d negatives %d", num_prot, num_pos_prot, num_neg_prot);
+
+ if(database_exists)
+ {
+ if( (double)num_prot_not_found_in_db > (double)num_prot/3.0)
+ {
+ if( num_neg_prot_not_found_in_db == num_neg_prot && (double)num_pos_prot_not_found_in_db < (double)num_pos_prot/2.0)
+ carp(CARP_WARNING, "The database did not contain any of the decoy proteins that were found in the search result files. This might mean that only target but the decoy database was provided.");
+ else
+ carp(CARP_WARNING, "The database did not contain %d of the % d proteins that were found in the search result files. This might mean that the database does not match search result files.", num_prot_not_found_in_db, num_prot);
+ }
+ }
+
+ if(num_neg_prot == 0)
+ {
+ carp(CARP_WARNING, "Found %d decoy proteins in the search result files.", num_neg_prot);
+ //return 0;
+ //TODO SJM, how decoys are represented in the search results using a
+ //fasta or index search is different for crux.
+ //This temporary fix will work
+ //for q-ranker.
+ }
+
+ //save the data
+ fill_graphs_and_save_data(out_dir);
+ close_files();
+
+ return 1;
+}
+
+
+void SQTParser :: read_list_of_files(string &list, vector<string> &fnames)
+{
+ ifstream f(list.c_str());
+ string str;
+ f >> str;
+ while(!f.eof())
+ {
+ fnames.push_back(str);
+ f >> str;
+ }
+ f.close();
+}
+
+
+int SQTParser :: set_output_dir(string &output_dir, int overwrite_flag)
+{
+ int intStat;
+ struct stat stFileInfo;
+ intStat = stat(output_dir.c_str(), &stFileInfo);
+
+ if (intStat == 0)
+ {
+ //is this a directory?
+ if(!((stFileInfo.st_mode & S_IFMT) == S_IFDIR))
+ {
+ //it is not a directory
+ cout << "WARNING: File " << output_dir << " already exists, but it is not a directory" << endl;
+ if(overwrite_flag == 1)
+ {
+ cout << "INFO: Creating output directory " << output_dir << endl;
+ remove(output_dir.c_str());
+ int dir_access = S_IRWXU + S_IRWXG + S_IRWXO;
+ if (mkdir(output_dir.c_str(), dir_access)) {
+ // mkdir failed
+ cout << "FATAL: Unable to create output directory " << output_dir << endl;
+ return 0;
+ }
+ }
+ else
+ {
+ cout << "FATAL: File " << output_dir << " cannot be overwritten. Please use --overwrite T to replace or specify a different output directory." << endl;
+ return 0;
+ }
+ }
+ }
+ else
+ {
+ cout << "INFO: creating output directory " << output_dir << endl;
+ int dir_access = S_IRWXU + S_IRWXG + S_IRWXO;
+ if (mkdir(output_dir.c_str(), dir_access)) {
+ // mkdir failed
+ cout << "FATAL: unable to create output directory " << output_dir << endl;
+ return 0;
+ }
+ }
+
+ out_dir = output_dir;
+ return 1;
+}
+
+int SQTParser :: is_ending(string &name, const string &ext)
+{
+ int len = ext.size();
+ int pos = name.size()-len-1;
+ string lowerName(name);
+ string lowerExt(ext);
+ transform(lowerName.begin() + pos, lowerName.end(),
+ lowerName.begin() + pos, ::tolower);
+ transform(lowerExt.begin(), lowerExt.end(),
+ lowerExt.begin(), ::tolower);
+ if(lowerName.find(lowerExt,pos) != string::npos)
+ return pos;
+ else
+ return 0;
+}
+
+int SQTParser :: is_spectrum_file(string &fname)
+{
+ for (vector<string>::const_iterator i = spectrumExts_.begin();
+ i != spectrumExts_.end();
+ ++i) {
+ int pos = is_ending(fname, *i);
+ if (pos != 0) {
+ return pos;
+ }
+ }
+ return 0;
+}
+
+int SQTParser :: is_fasta(string &fname)
+{
+ string ext1 = ".fasta";
+ string ext2 = ".fsa";
+ string ext3 = ".fa";
+ if(is_ending(fname, ext1) || is_ending(fname, ext2) || is_ending(fname, ext3))
+ return 1;
+ return 0;
+}
+
+int SQTParser :: set_database_source(string &db_source)
+{
+ DIR *dp;
+ struct dirent *dirp;
+
+ int intStat;
+ struct stat stFileInfo;
+ intStat = stat(db_source.c_str(), &stFileInfo);
+ if(intStat != 0)
+ {
+ carp(CARP_WARNING, "%s does not exist", db_source.c_str());
+ return 0;
+ }
+ //is this a directory?
+ if((stFileInfo.st_mode & S_IFMT) == S_IFDIR)
+ {
+ //try to open it
+ if((dp = opendir(db_source.c_str())) == NULL)
+ {
+ carp(CARP_WARNING, "openning directory %s failed ", db_source.c_str());
+ return 0;
+ }
+ int cn = 0;
+ while ((dirp = readdir(dp)) != NULL)
+ {
+ string fname = string(dirp->d_name);
+ if(is_fasta(fname))
+ {
+ ostringstream fstr;
+ fstr << db_source;
+ if(db_source.at(db_source.size()-1) != '/')
+ fstr <<"/";
+ fstr << fname;
+ string dbname = fstr.str();
+ db_file_names.push_back(dbname);
+ cn++;
+ }
+ }
+ closedir(dp);
+ if(cn<1)
+ {
+ carp(CARP_WARNING, "did not find any .fasta files in %s directory", db_source.c_str());
+ return 0;
+ }
+ }
+ else
+ {
+ if(is_fasta(db_source))
+ db_file_names.push_back(db_source);
+ else
+ read_list_of_files(db_source, db_file_names);
+ }
+
+ database_exists = 1;
+
+ return 1;
+}
+
+string SQTParser::get_parser_extension() {
+
+ return ".sqt";
+}
+
+int SQTParser :: match_file_to_ms2(string &sqt_source, string &prefix)
+{
+ DIR *dp;
+ struct dirent *dirp;
+ //try openning the directory
+ if((dp = opendir(sqt_source.c_str())) == NULL)
+ {
+ carp(CARP_WARNING, "openning directory %s failed ", sqt_source.c_str());
+ return 0;
+ }
+ int cn = 0;
+ //read sqt files in the directory
+ while ((dirp = readdir(dp)) != NULL)
+ {
+ string ext_sqt = get_parser_extension();
+ string fname = string(dirp->d_name);
+ int pos = is_ending(fname, ext_sqt);
+ if((pos != 0) && (fname.find(prefix,0) != string::npos))
+ {
+ ostringstream fstr;
+ fstr << sqt_source;
+ if(sqt_source.at(sqt_source.size()-1) != '/')
+ fstr << "/";
+ fstr << fname;
+ string sqtname = fstr.str();
+ fstr.str("");
+ sqt_file_names.push_back(sqtname);
+ cn++;
+ }
+ }
+ closedir(dp);
+ return cn;
+}
+
+
+int SQTParser :: collect_ms2_files(string &ms2_source, string & sqt_source)
+{
+ DIR *dp;
+ struct dirent *dirp;
+ //try openning the directory
+ if((dp = opendir(ms2_source.c_str())) == NULL)
+ {
+ carp(CARP_WARNING, "openning directory %s failed ", ms2_source.c_str());
+ return 0;
+ }
+ int cn = 0;
+ int total_matched = 0;
+ //read ms2 files in the directory
+ while ((dirp = readdir(dp)) != NULL)
+ {
+ string fname = string(dirp->d_name);
+ int pos = is_spectrum_file(fname);
+ if(pos != 0)
+ {
+ string prefix = fname.substr(0,pos+1);
+ //collect the file
+ ostringstream fstr;
+ fstr << ms2_source;
+ if(ms2_source.at(ms2_source.size()-1) != '/')
+ fstr << "/";
+ fstr << fname;
+ string ms2name = fstr.str();
+ fstr.str("");
+ int num_matched = match_file_to_ms2(sqt_source, prefix);
+ total_matched += num_matched;
+ if(!num_matched)
+ carp(CARP_WARNING, "could not find %s*.sqt in directory %s to match %s, skipping", prefix.c_str(), sqt_source.c_str(), ms2name.c_str());
+ else
+ {
+ for(int i = 0; i < num_matched; i++)
+ ms2_file_names.push_back(ms2name);
+ }
+ cn++;
+ }
+ }
+ closedir(dp);
+
+ if(cn<1)
+ {
+ carp(CARP_WARNING, "did not find any .ms2 files in %s directory", ms2_source.c_str());
+ return 0;
+ }
+ if(total_matched<1)
+ {
+ carp(CARP_WARNING, "did not find any .sqt files in %s directory to match the .ms2 files in %s directory", sqt_source.c_str(), ms2_source.c_str());
+ return 0;
+ }
+
+
+ return 1;
+}
+
+
+int SQTParser :: set_input_sources(string &ms2_source, string &sqt_source)
+{
+
+ int intStat;
+ struct stat stFileInfo;
+ intStat = stat(ms2_source.c_str(), &stFileInfo);
+ if(intStat != 0)
+ {
+ carp(CARP_WARNING, "%s does not exist", ms2_source.c_str());
+ return 0;
+ }
+ if((stFileInfo.st_mode & S_IFMT) == S_IFDIR)
+ {
+ if(!collect_ms2_files(ms2_source, sqt_source))
+ return 0;
+ }
+ else
+ {
+ string ext_sqt = get_parser_extension();
+ if(is_spectrum_file(ms2_source))
+ {
+ if(!is_ending(sqt_source, ext_sqt))
+ {
+ carp(CARP_WARNING, "expecting search file to accompany the ms2 file");
+ return 0;
+ }
+ ms2_file_names.push_back(ms2_source);
+ sqt_file_names.push_back(sqt_source);
+ }
+ else
+ {
+ read_list_of_files(ms2_source, ms2_file_names);
+ read_list_of_files(sqt_source, sqt_file_names);
+ if(ms2_file_names.size() != sqt_file_names.size())
+ {
+ carp(CARP_WARNING, " the number of search and ms2 files does not match: each search file should be accompaned by ms2 file");
+ return 0;
+ }
+ }
+ }
+
+ return 1;
+}
+
+/*************** for separate searches ********************************************************/
+
+int SQTParser :: match_target_file_to_ms2(string &sqt_source, string &prefix)
+{
+ DIR *dp;
+ struct dirent *dirp;
+ //try openning the directory
+ if((dp = opendir(sqt_source.c_str())) == NULL)
+ {
+ carp(CARP_WARNING, "openning directory %s failed ", sqt_source.c_str());
+ return 0;
+ }
+ int cn = 0;
+ //read sqt files in the directory
+ ostringstream oss;
+ oss << ".target" << get_parser_extension();
+ string ext_sqt = oss.str();
+ while ((dirp = readdir(dp)) != NULL)
+ {
+ string fname = string(dirp->d_name);
+ int pos = is_ending(fname, ext_sqt);
+ if((pos != 0) && (fname.find(prefix,0) != string::npos))
+ {
+ ostringstream fstr;
+ fstr << sqt_source;
+ if(sqt_source.at(sqt_source.size()-1) != '/')
+ fstr << "/";
+ fstr << fname;
+ string sqtname = fstr.str();
+ fstr.str("");
+ sqt_file_names.push_back(sqtname);
+ cn++;
+ }
+ }
+ closedir(dp);
+ return cn;
+}
+
+
+int SQTParser :: match_decoy_file_to_ms2(string &sqt_source, string &prefix)
+{
+ DIR *dp;
+ struct dirent *dirp;
+ //try openning the directory
+ if((dp = opendir(sqt_source.c_str())) == NULL)
+ {
+ carp(CARP_WARNING, "openning directory %s failed ", sqt_source.c_str());
+ return 0;
+ }
+ int cn = 0;
+ //read sqt files in the directory
+ ostringstream oss;
+ oss << ".decoy" << get_parser_extension();
+ string ext_sqt = oss.str();
+ while ((dirp = readdir(dp)) != NULL)
+ {
+ string fname = string(dirp->d_name);
+ int pos = is_ending(fname, ext_sqt);
+ if((pos != 0) && (fname.find(prefix,0) != string::npos))
+ {
+ ostringstream fstr;
+ fstr << sqt_source;
+ if(sqt_source.at(sqt_source.size()-1) != '/')
+ fstr << "/";
+ fstr << fname;
+ string sqtname = fstr.str();
+ fstr.str("");
+ sqt_file_names.push_back(sqtname);
+ cn++;
+ }
+ }
+ closedir(dp);
+ return cn;
+}
+
+
+int SQTParser :: collect_ms2_files(string &ms2_source, string &sqt_target_source, string &sqt_decoy_source)
+{
+ DIR *dp;
+ struct dirent *dirp;
+ //try openning the directory
+ if((dp = opendir(ms2_source.c_str())) == NULL)
+ {
+ carp(CARP_WARNING, "openning directory %s failed ", ms2_source.c_str());
+ return 0;
+ }
+ int cn = 0;
+ //read ms2 files in the directory
+ while ((dirp = readdir(dp)) != NULL)
+ {
+ string fname = string(dirp->d_name);
+ int pos = is_spectrum_file(fname);
+ if(pos != 0)
+ {
+ string prefix = fname.substr(0,pos+1);
+ //collect the file
+ ostringstream fstr;
+ fstr << ms2_source;
+ if(ms2_source.at(ms2_source.size()-1) != '/')
+ fstr << "/";
+ fstr << fname;
+ string ms2name = fstr.str();
+ fstr.str("");
+ int num_matched_targets = match_target_file_to_ms2(sqt_target_source, prefix);
+ int num_matched_decoys = match_decoy_file_to_ms2(sqt_decoy_source, prefix);
+
+ if(!num_matched_targets)
+ {
+ carp(CARP_WARNING, "could not find %s*.target.sqt in directory %s to match %s, skipping", prefix.c_str(), sqt_target_source.c_str(), ms2name.c_str());
+ continue;
+ }
+ if(!num_matched_decoys)
+ {
+ carp(CARP_WARNING, "could not find %s*.decoy.sqt in directory %s to match %s, skipping", prefix.c_str(), sqt_decoy_source.c_str(), ms2name.c_str());
+ continue;
+ }
+ for(int i = 0; i < (num_matched_targets+num_matched_decoys); i++)
+ ms2_file_names.push_back(ms2name);
+
+ cn++;
+ }
+ }
+ closedir(dp);
+
+ if(cn<1)
+ {
+ carp(CARP_WARNING, "did not find any .ms2 files in %s directory or did not find any sqt files matching the ms2 files by name", ms2_source.c_str());
+ return 0;
+ }
+
+ return 1;
+}
+
+
+int SQTParser :: set_input_sources(string &ms2_source, string &sqt_target_source, string &sqt_decoy_source)
+{
+ int intStat;
+ struct stat stFileInfo;
+ intStat = stat(ms2_source.c_str(), &stFileInfo);
+ if(intStat != 0)
+ {
+ carp(CARP_WARNING, "%s does not exist", ms2_source.c_str());
+ return 0;
+ }
+ if((stFileInfo.st_mode & S_IFMT) == S_IFDIR)
+ {
+ if(!collect_ms2_files(ms2_source, sqt_target_source, sqt_decoy_source))
+ return 0;
+ }
+ else
+ {
+ string ext_sqt = get_parser_extension();
+
+ if(is_spectrum_file(ms2_source))
+ {
+ if(!is_ending(sqt_target_source, ext_sqt))
+ {
+ carp(CARP_WARNING, "expecting target search file to accompany the ms2 file");
+ return 0;
+ }
+ if(!is_ending(sqt_decoy_source, ext_sqt))
+ {
+ carp(CARP_WARNING, "expecting decoy search file to accompany the ms2 file and the target search file for the separate searches");
+ return 0;
+ }
+
+ sqt_file_names.push_back(sqt_target_source);
+ ms2_file_names.push_back(ms2_source);
+ sqt_file_names.push_back(sqt_decoy_source);
+ ms2_file_names.push_back(ms2_source);
+ }
+ else
+ {
+ read_list_of_files(sqt_target_source, sqt_file_names);
+ read_list_of_files(ms2_source, ms2_file_names);
+ read_list_of_files(sqt_decoy_source, sqt_file_names);
+ read_list_of_files(ms2_source, ms2_file_names);
+ if(ms2_file_names.size() != sqt_file_names.size())
+ {
+ carp(CARP_WARNING, " the number of sqt and ms2 files does not match: each sqt file should be accompaned by ms2 file");
+ return 0;
+ }
+ }
+ }
+
+ return 1;
+}
+void SQTParser :: write_features_header(){
+ //file features header
+ final_features_header_.insert(
+ final_features_header_.begin(),
+ features_header_.begin(),
+ features_header_.end()
+ );
+ if(num_spec_features==3){
+ final_features_header_.insert(
+ final_features_header_.end(),
+ spec_features_header_3_.begin(),
+ spec_features_header_3_.end()
+ );
+ }else if(num_spec_features==7){
+ final_features_header_.insert(
+ final_features_header_.end(),
+ spec_features_header_7_.begin(),
+ spec_features_header_7_.end()
+ );
+ }
+ }
+void SQTParser::add_quadratic_features_header(){
+
+ for(unsigned int i=0;i<features_header_.size();i++){
+ for(unsigned int j=i;j<features_header_.size();j++){
+
+ final_features_header_.push_back(
+ "("
+ +features_header_[i]
+ +")"
+ +"*"
+ +"("
+ +features_header_[j]
+ +")"
+ );
+ }
+ }
+
+ if(num_spec_features==3){
+ for(unsigned int i=0;i<spec_features_header_3_.size();i++){
+ for(unsigned int j=i;j<spec_features_header_3_.size();j++){
+ final_features_header_.push_back(
+ "("
+ +spec_features_header_3_[i]
+ +")"
+ +"*"
+ +"("
+ +spec_features_header_3_[j]
+ +")"
+ );
+ }
+ }
+ }
+ if(num_spec_features==7){
+ for(unsigned int i=0;i<spec_features_header_7_.size();i++){
+ for(unsigned int j=i;j<spec_features_header_7_.size();j++){
+ final_features_header_.push_back(
+ "("
+ +spec_features_header_7_[i]
+ +")"
+ +"*"
+ +"("
+ +spec_features_header_7_[j]
+ +")"
+ );
+ }
+ }
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/qranker-barista/SQTParser.h b/src/app/qranker-barista/SQTParser.h
new file mode 100644
index 0000000..4842775
--- /dev/null
+++ b/src/app/qranker-barista/SQTParser.h
@@ -0,0 +1,250 @@
+#ifndef SQTPARSER_H
+#define SQTPARSER_H
+
+#include <sys/stat.h>
+#ifndef _MSC_VER
+#include <dirent.h>
+#else
+#include "util/WinCrux.h"
+#endif
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <assert.h>
+#include <vector>
+#include <string>
+#include <math.h>
+#include <map>
+#include <set>
+#include <cstring>
+#include "SpecFeatures.h"
+#include "BipartiteGraph.h"
+
+#include "app/CruxApplication.h"
+#include "io/carp.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+
+using namespace std;
+
+typedef enum {TRYPSIN_ENZ,CHYMOTRYPSIN_ENZ,ELASTASE_ENZ} enzyme;
+
+class SQTParser{
+ public:
+ struct sqt_match{
+ int scan;
+ int charge;
+ double precursor_mass;
+ int num_sequence_comparisons;
+ vector <int> xcorr_rank;
+ vector<int> sp_rank;
+ vector<double> calc_mass;
+ vector<double> delta_cn;
+ vector<double> xcorr_score;
+ vector<double> sp_score;
+ vector <int> num_ions_matched;
+ vector<double> num_total_ions;
+ vector<string> peptides;
+ vector<int> num_proteins_in_match;
+ vector<string> proteins;
+ vector<int> peptide_pos;
+
+ };
+ /*
+ SQTParser() : num_spectra(0),num_psm(0),num_pos_psm(0),num_neg_psm(0),num_features(0),
+ num_spec_features(0), num_pep(0),num_pos_pep(0), num_neg_pep(0),num_prot(0),num_pos_prot(0),num_neg_prot(0),
+ num_mixed_labels(0),psmind(0){}
+ */
+ SQTParser();
+ virtual ~SQTParser();
+ void clear();
+ virtual int run();
+ void clear_matches();
+ void erase_matches();
+ inline void set_num_features(int nf) {num_features = nf;}
+ inline void set_num_spec_features(int nsf) {num_spec_features = nsf;}
+ inline int get_num_features() const {return num_features;}
+ inline void set_use_quadratic_features(int use){use_quadratic_features = use;}
+ inline int get_use_quadratic_features()const {return use_quadratic_features;}
+ int set_output_dir(string &output_dir, int overwrite_flag);
+ int set_output_dir(string &output_dir){out_dir = output_dir; return 1;}
+ inline string& get_output_dir(){return out_dir;}
+ inline void set_input_dir(string input_dir){in_dir = input_dir;}
+ inline void set_input_dir_ms2(string input_dir){in_dir_ms2 = input_dir;}
+ inline string& get_input_dir(){return in_dir;}
+ inline void set_db_name(string database){db_name = database;}
+ inline void set_decoy_prefix(string prefix){decoy_prefix = prefix;}
+ inline void set_num_hits_per_spectrum(int hits_per_spectrum){fhps = hits_per_spectrum;}
+ inline vector<string> get_final_features_header(){return final_features_header_;}
+ void set_enzyme(string &enz);
+ int is_ending(string &name, const string &ext);
+ int is_spectrum_file(string &fname);
+ int is_fasta(string &fname);
+ int set_database_source(string &db_source);
+ virtual int match_file_to_ms2(string &sqt_source, string &prefix);
+ int collect_ms2_files(string &ms2_source, string &sqt_source);
+ virtual int set_input_sources(string &ms2_source, string &sqt_source);
+ void read_list_of_files(string &list, vector<string> &fnames);
+
+ /********* for separate database searches ********************************************/
+ virtual int match_target_file_to_ms2(string &sqt_source, string &prefix);
+ virtual int match_decoy_file_to_ms2(string &sqt_source, string &prefix);
+ int collect_ms2_files(string &ms2_source, string &sqt_target_source, string &sqt_decoy_source);
+ virtual int set_input_sources(string &ms2_source, string &sqt_target_source, string &sqt_decoy_source);
+ /*************************************************************************************/
+
+
+ void read_sqt_file(ifstream &is, string &decoy_prefix, int final_hits_per_spectrum, enzyme enz, bool decoy);
+ int parse_sqt_spectrum_matches(ifstream &is, sqt_match &m);
+ void read_S_line(ifstream &is, sqt_match &m);
+ void read_M_line(ifstream &is, sqt_match &m);
+ void digest_database(ifstream &f_db, enzyme e);
+ int cntEnzConstraints(string& seq,enzyme enz);
+
+ static int cntEnz(const string& peptide, enzyme enz);
+ static double isTryptic(const char n,const char c);
+ static double isChymoTryptic(const char n,const char c);
+ static double isElastasic(const char n,const char c);
+ static double isEnz(const char n,const char c, enzyme enz);
+ void extract_psm_features(sqt_match &m, enzyme enz, double *x, int i);
+ void extract_psm_features(sqt_match &m, enzyme enz, double *x, int i, int hits_read);
+ void extract_features(sqt_match &m, int hits_read, int final_hits,enzyme enz);
+ void add_matches_to_tables(sqt_match &m, string &decoy_prefix, int hits_read, int final_hits, bool decoy);
+ void allocate_feature_space();
+ void fill_graphs_and_save_data(string &out_dir);
+
+ void open_files(string &out_dir);
+ void close_files();
+ void clean_up(string dir);
+ int check_file(ostringstream &fname);
+ int check_input_dir(string &in_dir);
+
+ //spec features generator
+ SpecFeaturesGenerator sfg;
+
+ void write_features_header();
+ void add_quadratic_features_header();
+ //void write_quad_features_header();
+
+ protected:
+ //auxiliary variables
+ int database_exists;
+ int num_prot_not_found_in_db;
+ int num_pos_prot_not_found_in_db;
+ int num_neg_prot_not_found_in_db;
+
+ vector<string> features_header_;
+ vector<string> spec_features_header_3_;
+ vector<string> spec_features_header_7_;
+ vector<string> final_features_header_;
+ sqt_match m;
+ int num_mixed_labels;
+ map<int,set<int> > pepind_to_protinds_map;
+ map<int,set<int> > protind_to_pepinds_map;
+ map<int,set<int> > pepind_to_psminds_map;
+
+ //summary of the dataset
+ int num_features;
+ int num_spec_features;
+ int num_total_features;
+ int use_quadratic_features;
+ int num_spectra;
+ int num_psm;
+ int num_pos_psm;
+ int num_neg_psm;
+ int num_pep;
+ int num_pos_pep;
+ int num_neg_pep;
+ int num_prot;
+ int num_pos_prot;
+ int num_neg_prot;
+
+ int num_cur_psm;
+ int num_cur_prot;
+ int prot_offset;
+
+
+
+ //psm feature vector
+ double *x;
+ //spec feature vector
+ double *xs;
+
+ //peptide info
+ map<string,int> pep_to_ind;
+ map<int,string> ind_to_pep;
+ BipartiteGraph pepind_to_protinds;
+ BipartiteGraph pepind_to_psminds;
+
+ //protein info
+ map<string,int> prot_to_ind;
+ map<int,string> ind_to_prot;
+ BipartiteGraph protind_to_pepinds;
+
+ //digested database info
+ map<string,int> protein_to_num_all_pep_map;
+ map<int,int> protind_to_num_all_pep_map;
+ map<string,int> protein_to_length_map;
+ map<int,int> protind_to_length_map;
+ int *protind_to_num_all_pep;
+ int *protind_to_length;
+
+ //writing out data
+ string in_dir;
+ string in_dir_ms2;
+ string out_dir;
+ string db_name;
+ vector<string> sqt_file_names;
+ vector<string> ms2_file_names;
+ vector<string> db_file_names;
+
+ string cur_fname;
+ int cur_fileind;
+
+ //files for writing out data
+ ofstream f_psm;
+ ofstream f_psmind_to_label;
+ ofstream f_psmind_to_scan;
+ ofstream f_psmind_to_charge;
+ ofstream f_psmind_to_precursor_mass;
+ ofstream f_psmind_to_pepind;
+ ofstream f_pepind_to_label;
+ ofstream f_protind_to_label;
+ ofstream f_protind_to_num_all_pep;
+ ofstream f_protind_to_length;
+ ofstream f_fileind_to_fname;
+ ofstream f_psmind_to_fileind;
+
+ ofstream f_psmind_to_xcorr;
+ ofstream f_psmind_to_spscore;
+ ofstream f_psmind_to_deltaCn;
+ ofstream f_psmind_to_calculated_mass;
+
+ ofstream f_psmind_to_sp_rank;//sp rank
+ ofstream f_pmsind_to_matches_spectrum; //matches_spectrum
+ ofstream f_psmind_to_xcorr_rank;//xcorr rank
+ ofstream f_psmind_to_by_ions_matched;// b/y ions match
+ ofstream f_psmind_to_by_ions_total; //b/y ions total
+ ofstream f_psmind_to_peptide_position; //peptide position
+
+ //final hits per spectrum
+ int fhps;
+ //decoy prefix
+ string decoy_prefix;
+ //enzyme
+ enzyme e;
+ //max peptide length to be considered
+ int max_len;
+ //min peptide length to be considered
+ int min_len;
+
+
+ virtual bool read_search_results(string& cur_fname, bool decoy);
+ virtual string get_parser_extension();
+
+ vector<string> spectrumExts_; // spectrum file extensions
+
+};
+
+#endif
diff --git a/src/app/qranker-barista/SpecFeatures.cpp b/src/app/qranker-barista/SpecFeatures.cpp
new file mode 100644
index 0000000..1e6242b
--- /dev/null
+++ b/src/app/qranker-barista/SpecFeatures.cpp
@@ -0,0 +1,499 @@
+#include "SpecFeatures.h"
+
+const double SpecFeaturesGenerator::mass_h2o_mono = 18.01056;
+const double SpecFeaturesGenerator::mass_nh3_mono = 17.02655;
+const double SpecFeaturesGenerator::mass_co_mono = 27.9949;
+const double SpecFeaturesGenerator::proton_mass = 1.00727646688;
+const double SpecFeaturesGenerator::bin_width_mono = 1.0005079;
+
+SpecFeaturesGenerator :: SpecFeaturesGenerator():
+ max_mz_(1025),
+ ts_m3_(NULL), ts_m7_(NULL),
+ spectra_(NULL), spectrum_(NULL)
+{
+ mz_values_.reserve(1000);
+ intens_values_.reserve(1000);
+ peaks_.resize(max_mz_, 0.0);
+}
+
+SpecFeaturesGenerator :: ~SpecFeaturesGenerator()
+{
+ if (spectra_) {
+ delete spectra_;
+ }
+ if (spectrum_) {
+ delete spectrum_;
+ }
+ clear();
+}
+
+void SpecFeaturesGenerator :: clear()
+{
+ max_mz_ = 0;
+ clear_tspec(ts_m3_, 3); ts_m3_ = NULL;
+ clear_tspec(ts_m7_, 7); ts_m7_ = NULL;
+}
+
+void SpecFeaturesGenerator :: read_spectrum()
+{
+ precursor_mz_ = spectrum_->getPrecursorMz();
+
+ mz_values_.clear();
+ intens_values_.clear();
+
+ for (PeakIterator i = spectrum_->begin(); i != spectrum_->end(); ++i) {
+ Peak* peak = *i;
+ FLOAT_T mz = peak->getLocation();
+ mz_values_.push_back(mz);
+ intens_values_.push_back(peak->getIntensity());
+ /*int mz_bin = (int)(mz / bin_width_mono + 0.5);
+ if (mz_bin >= max_mz_) {
+ max_mz_ = mz_bin + 1;
+ }*/
+ }
+}
+
+
+void SpecFeaturesGenerator :: shift_peaks()
+{
+#if 1
+ int n = peaks_.size();
+ vector<double> sums(n);
+ vector<double> integral(n+1);
+ integral[0] = 0;
+ for (int i=0; i<n; i++)
+ integral[i+1] = integral[i] + peaks_[i];
+ for (int i=0; i<n; i++)
+ {
+ int ilo = i - max_xcorr_offset;
+ int ihi = i + max_xcorr_offset+1;
+ sums[i] = integral[ihi<=n ? ihi : n] - integral[ilo>=0 ? ilo : 0];
+ }
+#else
+ vector<double> sums;
+ sums.resize(peaks_.size(),0.0);
+
+ for(unsigned int idx = 0; idx < peaks_.size(); idx++)
+ {
+ for(int sub_idx = idx-max_xcorr_offset; sub_idx <= idx+max_xcorr_offset; sub_idx++)
+ if(sub_idx > -1 && sub_idx < peaks_.size())
+ sums[idx] += peaks_[sub_idx];
+ }
+#endif
+ for(unsigned int idx = 0; idx < peaks_.size(); idx++)
+ peaks_[idx] -= (sums[idx]/(max_xcorr_offset*2.0+1));
+
+}
+
+void SpecFeaturesGenerator :: normalize_each_region(double max_intensity_overall, vector<double> &max_intensity_per_region,
+ int region_selector)
+{
+ int region_idx = 0;
+ double max_intensity = max_intensity_per_region[region_idx];
+ for (int i = 0; i < (int)peaks_.size(); i++)
+ {
+
+ if(i >= (region_idx+1)*region_selector && (region_idx+1)<num_regions)
+ {
+ region_idx++;
+ max_intensity = max_intensity_per_region[region_idx];
+ }
+ // Don't normalize if no peaks in region, and for compatibility
+ // with SEQUEST drop peaks with intensity less than 1/20 of
+ // the overall max intensity.
+ if((max_intensity != 0)
+ && (peaks_[i] > 0.05 * max_intensity_overall))
+ {
+ // normalize intensity to max 50
+ peaks_[i] = (peaks_[i] /max_intensity) * max_per_region;
+ }
+ // no more peaks beyond the 10 regions mark, exit
+ if(i > num_regions * region_selector){
+ return;
+ }
+ }
+}
+
+
+void SpecFeaturesGenerator :: process_observed_spectrum()
+{
+ double experimental_mass_cut_off = precursor_mz_ * charge_ + 50.0;
+
+ if ((int)peaks_.size() != max_mz_)
+ peaks_.resize(max_mz_);
+ peaks_.assign(peaks_.size(), 0.0);
+
+ assert(mz_values_.size() == intens_values_.size());
+ double max_peak_location = 0.0;
+ double max_peak_intensity = 0.0;
+ for (unsigned int i = 0; i < mz_values_.size(); i++) {
+ double peak_location = mz_values_[i];
+ if (peak_location < experimental_mass_cut_off &&
+ peak_location > max_peak_location)
+ max_peak_location = peak_location;
+ }
+ int region_selector = (int)max_peak_location / num_regions;
+ vector<double> max_peak_intensity_per_region;
+ max_peak_intensity_per_region.resize(num_regions,0.0);
+
+ for (unsigned int i = 0; i < mz_values_.size(); i++)
+ {
+ double peak_location = mz_values_[i];
+ double peak_intensity = intens_values_[i];
+ //if above experimental mass, skip
+ if (peak_location > experimental_mass_cut_off)
+ continue;
+ // skip all peaks within precursor ion mz +/- 15
+ if (peak_location < precursor_mz_ + 15 &&
+ peak_location > precursor_mz_ - 15)
+ continue;
+
+ //get the bin and the region
+ int mz = (int)(peak_location / bin_width_mono + 0.5);
+
+ int region = mz / region_selector;
+ // don't let index beyond array
+ if (region >= num_regions) {
+ continue;
+ }
+
+ //update max mz over all spectra
+ /*if (mz >= max_mz_) {
+ max_mz_ = mz + 1;
+ peaks_.resize(max_mz_,0.0);
+ }*/
+ // sqrt the original intensity
+ peak_intensity = sqrt(peak_intensity);
+ if (peak_intensity > max_peak_intensity)
+ max_peak_intensity = peak_intensity;
+ if (peaks_[mz] < peak_intensity) {
+ peaks_[mz] = peak_intensity;
+ // check if this peak is max intensity in the region(one out of 10)
+ if (max_peak_intensity_per_region[region] < peak_intensity) {
+ max_peak_intensity_per_region[region] = peak_intensity;
+ }
+ }
+ }
+ normalize_each_region(max_peak_intensity, max_peak_intensity_per_region,
+ region_selector);
+ shift_peaks();
+}
+
+void SpecFeaturesGenerator :: read_ms2_file(const string& filename)
+{
+ spectra_ = SpectrumCollectionFactory::create(filename.c_str());
+ spectra_->parse();
+
+ // TODO hack for finding max m/z out of all spectra
+ for (SpectrumIterator i = spectra_->begin(); i != spectra_->end(); ++i) {
+ int mz_bin = (int)((*i)->getMaxPeakMz() / bin_width_mono + 0.5);
+ if (mz_bin >= max_mz_) {
+ max_mz_ = mz_bin + 1;
+ }
+ }
+}
+
+/*************************************************************************************/
+
+void SpecFeaturesGenerator :: get_observed_spectrum(int scan)
+{
+ if (spectrum_) {
+ delete spectrum_;
+ spectrum_ = NULL;
+ }
+
+ for (SpectrumIterator i = spectra_->begin(); i != spectra_->end(); ++i) {
+ if (scan == (*i)->getFirstScan()) {
+ spectrum_ = new Crux::Spectrum();
+ spectrum_->copyFrom(*i);
+ break;
+ }
+ }
+ // TODO this doesn't work because subclasses of spectrumcollection override
+ //spectrum_ = spectra_->getSpectrum(scan);
+
+ // not found in MS2 file
+ if (!spectrum_)
+ carp(CARP_FATAL, "Spectrum \"%d\" not found in MS2 file", scan);
+
+ read_spectrum();
+ process_observed_spectrum();
+}
+
+
+void SpecFeaturesGenerator :: clear_tspec(double **tspec, int num_features)
+{
+ if (tspec) {
+ for (int i = 0; i < num_features; i++)
+ if (tspec[i]) {
+ delete [] tspec[i];
+ tspec[i] = NULL;
+ }
+ delete [] tspec;
+ tspec = NULL;
+ }
+}
+
+void SpecFeaturesGenerator :: allocate_tspec(double ***tspec, int num_features)
+{
+ (*tspec) = new double*[num_features];
+ for(int i = 0; i < num_features; i++)
+ (*tspec)[i] = new double[max_mz_];
+}
+
+void SpecFeaturesGenerator :: zero_out_tspec(double **tspec, int num_features)
+{
+ for(int i = 0; i < num_features; i++)
+ memset(tspec[i], 0, sizeof(double) * max_mz_);
+}
+
+void SpecFeaturesGenerator :: add_intensity(double *tspec, int idx, double intensity)
+{
+ if(idx > -1 && idx < max_mz_ &&
+ tspec[idx] < intensity) {
+ tspec[idx] = intensity;
+ }
+}
+
+double SpecFeaturesGenerator :: sproduct(double *tspec)
+{
+ double sm = 0;
+ for (unsigned int i = 0; i < peaks_.size(); i++)
+ sm += tspec[i] * peaks_[i];
+ return sm;
+}
+
+void SpecFeaturesGenerator :: get_spec_features_m3(int scan, int ch, string &peptide, double *features)
+{
+ charge_ = ch;
+ get_observed_spectrum(scan);
+
+ //allocate the theoretical spectrum if necessary
+ if (!ts_m3_)
+ allocate_tspec(&ts_m3_, 3);
+ zero_out_tspec(ts_m3_, 3);
+
+ double mz = 0;
+ int idx = 0;
+ double fragment_mass;
+
+ //start from the beginning of the peptide and do the B-ION
+ fragment_mass = 0.0;
+ for(unsigned int i = 0; i < peptide.size()-1;i++)
+ {
+ char aa = peptide.at(i);
+ if(aa != '.')
+ {
+ //do the B-ION
+ fragment_mass += aa_masses_mono[aa-'A'];
+ //add the fragment
+ for (int charg = 1; charg < ch; charg++)
+ {
+ //add the ion itself
+ mz = (fragment_mass+charg*proton_mass)/charg;
+ idx = (int)(mz/bin_width_mono+0.5);
+ add_intensity(ts_m3_[0], idx, 1.0);
+
+ //add its flanking peaks
+ add_intensity(ts_m3_[1], idx-1, 1.0);
+ add_intensity(ts_m3_[1], idx+1, 1.0);
+
+ //add its neutral losses nh3 and h2o
+ double mz_nh3 = mz-(mass_nh3_mono/charg);
+ idx = (int)(mz_nh3/bin_width_mono+0.5);
+ add_intensity(ts_m3_[2], idx, 1.0);
+ double mz_h2o = mz-(mass_h2o_mono/charg);
+ idx = (int)(mz_h2o/bin_width_mono+0.5);
+ add_intensity(ts_m3_[2], idx, 1.0);
+
+ //add neutral loss co
+ double mz_co = mz-(mass_co_mono/charg);
+ idx = (int)(mz_co/bin_width_mono+0.5);
+ add_intensity(ts_m3_[2], idx, 1.0);
+ }
+ }
+ }
+
+ //do the Y-ION
+ fragment_mass = mass_h2o_mono;
+ for(unsigned int i = peptide.size(); i > 1;i--)
+ {
+ char aa = peptide.at(i-1);
+ if(aa != '.')
+ {
+ fragment_mass += aa_masses_mono[aa-'A'];
+ //add the fragment
+ for (int charg = 1; charg < ch; charg++)
+ {
+ //add the ion itself
+ mz = (fragment_mass+charg*proton_mass)/charg;
+ idx = (int)(mz/bin_width_mono+0.5);
+ add_intensity(ts_m3_[0], idx, 1.0);
+
+ //add its flanking peaks
+ add_intensity(ts_m3_[1], idx-1, 1.0);
+ add_intensity(ts_m3_[1], idx+1, 1.0);
+
+ //add its neutral losses
+ double mz_nh3 = mz-(mass_nh3_mono/charg);
+ idx = (int)(mz_nh3/bin_width_mono+0.5);
+ add_intensity(ts_m3_[2], idx, 1.0);
+ //double mz_h2o = mz-(mass_h2o_mono/charg);
+ //idx = (int)(mz_h2o/bin_width_mono+0.5);
+ //add_intensity(ts_m3[2], idx, 1.0);
+ }
+ }
+ }
+
+ features[0] = sproduct(ts_m3_[0]);
+ features[1] = sproduct(ts_m3_[1]);
+ features[2] = sproduct(ts_m3_[2]);
+
+ //cout << features[0] << " " << features[1] << " " << features[2] << endl;
+
+}
+
+void SpecFeaturesGenerator :: get_spec_features_m7(int scan, int ch, string &peptide, double *features)
+{
+ charge_ = ch;
+ get_observed_spectrum(scan);
+
+ //allocate the theoretical spectrum if necessary
+ if (!ts_m7_)
+ allocate_tspec(&ts_m7_, 7);
+ zero_out_tspec(ts_m7_, 7);
+
+ /*
+ * 0. b-ion
+ * 1. y_ion
+ * 2. flanking
+ * 3. h2o_nl
+ * 4. co2_nl
+ * 5. nh3_nl_b
+ * 6. nh3_nl_y
+ */
+
+ double mz = 0;
+ int idx = 0;
+ double fragment_mass;
+
+ //start from the beginning of the peptide and do the B-ION
+ fragment_mass = 0.0;
+ for(unsigned int i = 0; i < peptide.size()-1;i++)
+ {
+ char aa = peptide.at(i);
+ if(aa != '.')
+ {
+ //do the B-ION
+ fragment_mass += aa_masses_mono[aa-'A'];
+ //add the fragment
+ for (int charg = 1; charg < ch; charg++)
+ {
+ //add the ion itself
+ mz = (fragment_mass+charg*proton_mass)/charg;
+ idx = (int)(mz/bin_width_mono+0.5);
+ //0 in array
+ add_intensity(ts_m7_[0], idx, 1.0);
+
+ //add its flanking peaks (2 in array)
+ add_intensity(ts_m7_[2], idx-1, 1.0);
+ add_intensity(ts_m7_[2], idx+1, 1.0);
+
+ //add its neutral losses nh3(5 in array)
+ double mz_nh3 = mz-(mass_nh3_mono/charg);
+ idx = (int)(mz_nh3/bin_width_mono+0.5);
+ add_intensity(ts_m7_[5], idx, 1.0);
+
+ //add h2o (3 in array)
+ double mz_h2o = mz-(mass_h2o_mono/charg);
+ idx = (int)(mz_h2o/bin_width_mono+0.5);
+ add_intensity(ts_m7_[3], idx, 1.0);
+
+ //add neutral loss co (4 in array)
+ double mz_co = mz-(mass_co_mono/charg);
+ idx = (int)(mz_co/bin_width_mono+0.5);
+ add_intensity(ts_m7_[4], idx, 1.0);
+ }
+ }
+ }
+
+ //do the Y-ION
+ fragment_mass = mass_h2o_mono;
+ for(unsigned int i = peptide.size(); i > 1;i--)
+ {
+ char aa = peptide.at(i-1);
+ if(aa != '.')
+ {
+ fragment_mass += aa_masses_mono[aa-'A'];
+ //add the fragment
+ for (int charg = 1; charg < ch; charg++)
+ {
+ //add the ion itself ( 1 in array)
+ mz = (fragment_mass+charg*proton_mass)/charg;
+ idx = (int)(mz/bin_width_mono+0.5);
+ add_intensity(ts_m7_[1], idx, 1.0);
+
+ //add its flanking peaks ( 2 in array)
+ add_intensity(ts_m7_[2], idx-1, 1.0);
+ add_intensity(ts_m7_[2], idx+1, 1.0);
+
+ //add its neutral losses (6 in array)
+ double mz_nh3 = mz-(mass_nh3_mono/charg);
+ idx = (int)(mz_nh3/bin_width_mono+0.5);
+ add_intensity(ts_m7_[6], idx, 1.0);
+ }
+ }
+ }
+
+ features[0] = sproduct(ts_m7_[0]);
+ features[1] = sproduct(ts_m7_[1]);
+ features[2] = sproduct(ts_m7_[2]);
+ features[3] = sproduct(ts_m7_[3]);
+ features[4] = sproduct(ts_m7_[4]);
+ features[5] = sproduct(ts_m7_[5]);
+ features[6] = sproduct(ts_m7_[6]);
+
+ //cout << features[0] << " " << features[1] << " " << features[2] << " " << features[3] << " " << features[4] << " " << features[5] << " " << features[6] << endl;
+
+}
+
+
+
+
+
+void SpecFeaturesGenerator :: initialize_aa_tables()
+{
+ aa_masses_mono.resize(NUM_AA,0.0);
+ aa_masses_mono['A' - 'A'] = 71.03711;
+ aa_masses_mono['B' - 'A'] = 114.53494;
+ aa_masses_mono['C' - 'A'] = 103.00919;
+ aa_masses_mono['D' - 'A'] = 115.02694;
+ aa_masses_mono['E' - 'A'] = 129.04259;
+ aa_masses_mono['F' - 'A'] = 147.06841;
+ aa_masses_mono['G' - 'A'] = 57.02146;
+ aa_masses_mono['H' - 'A'] = 137.05891;
+ aa_masses_mono['I' - 'A'] = 113.08406;
+ aa_masses_mono['K' - 'A'] = 128.09496;
+ aa_masses_mono['L' - 'A'] = 113.08406;
+ aa_masses_mono['M' - 'A'] = 131.04049;
+ aa_masses_mono['N' - 'A'] = 114.04293;
+ aa_masses_mono['O' - 'A'] = 114.07931;
+ aa_masses_mono['P' - 'A'] = 97.05276;
+ aa_masses_mono['Q' - 'A'] = 128.05858;
+ aa_masses_mono['R' - 'A'] = 156.10111;
+ aa_masses_mono['S' - 'A'] = 87.03203;
+ aa_masses_mono['T' - 'A'] = 101.04768;
+ aa_masses_mono['U' - 'A'] = 150.04344;
+ aa_masses_mono['V' - 'A'] = 99.06841;
+ aa_masses_mono['W' - 'A'] = 186.07931;
+ aa_masses_mono['X' - 'A'] = 113.08406;
+ aa_masses_mono['Y' - 'A'] = 163.06333;
+ aa_masses_mono['Z' - 'A'] = 128.55059;
+
+ //nl_masses_mono.resize(NUM_NL,0.0);
+ //nl_masses_mono[H2O] = mass_h2o_mono;
+ //nl_masses_mono[NH3] = mass_nh3_mono;
+ //nl_masses_mono[CO] = mass_co_mono;
+
+}
+
diff --git a/src/app/qranker-barista/SpecFeatures.h b/src/app/qranker-barista/SpecFeatures.h
new file mode 100644
index 0000000..c81030f
--- /dev/null
+++ b/src/app/qranker-barista/SpecFeatures.h
@@ -0,0 +1,97 @@
+#ifndef SPECFEATURES_H
+#define SPECFEATURES_H
+
+#include<iostream>
+#include<fstream>
+#include <map>
+#include <sstream>
+#include <vector>
+#include <assert.h>
+#include <cstring>
+#include <math.h>
+#include "io/carp.h"
+#include "io/SpectrumCollectionFactory.h"
+
+using namespace std;
+
+#define NUM_IONS 2
+//typedef enum {B_ION, Y_ION} ion_type;
+//number of flanking peaks
+#define NUM_FL 2
+#define NUM_NL 3
+
+//typedef enum {H2O,NH3,CO} nl_type;
+#define NUM_AA 26
+
+
+class SpecFeaturesGenerator
+{
+ public:
+ SpecFeaturesGenerator();
+ ~SpecFeaturesGenerator();
+ void clear();
+ void read_ms2_file(const string& filename);
+ void initialize_aa_tables();
+
+ /*
+ * model m3 consists of 3 features:
+ * by-ions
+ * all flanking peaks
+ * all neutral losses
+ */
+ void get_spec_features_m3(int scan, int ch, string &peptide, double *features);
+ void get_spec_features_m7(int scan, int ch, string &peptide, double *features);
+
+ protected:
+ void read_spectrum();
+ void process_observed_spectrum();
+ void normalize_each_region(
+ double max_intensity_overall,
+ vector<double> &max_intensity_per_region,
+ int region_selector
+ );
+ void shift_peaks();
+ void get_observed_spectrum(int scan);
+ void clear_tspec(double **tspec,int num_features);
+ void allocate_tspec(double ***tspec, int num_features);
+ void zero_out_tspec(double **tspec, int num_features);
+ void add_intensity(double *tspec, int bin, double intensity);
+ double sproduct(double *tspec);
+
+ Crux::SpectrumCollection* spectra_;
+ Crux::Spectrum* spectrum_;
+
+ double precursor_mz_;
+ int charge_;
+
+ //for the processed spectrum
+ int max_mz_;
+ vector<double> peaks_;
+ //for the raw spectrum
+ vector<double> mz_values_;
+ vector<double> intens_values_;
+
+ double **ts_m3_;
+ double **ts_m7_;
+
+ //mass info for neutral losses
+ // While GNU g++ implements an extension that
+ // allows intializing static const doubles, this
+ // is not allowed by the strict C++ standard, so we
+ // have to initialze the doubles in the implementation
+ // to support compilers other than g++.
+ static const double mass_h2o_mono;
+ static const double mass_nh3_mono;
+ static const double mass_co_mono;
+ static const double proton_mass;
+ static const double bin_width_mono;
+ static const int num_regions = 10;
+ static const int max_per_region = 50;
+ static const int max_xcorr_offset = 75;
+
+ vector<double> aa_masses_mono;
+ vector<double> nl_masses_mono;
+
+};
+
+#endif //SPECFEATURES_H
diff --git a/src/app/qranker-barista/TabDelimParser.cpp b/src/app/qranker-barista/TabDelimParser.cpp
new file mode 100644
index 0000000..a9268bf
--- /dev/null
+++ b/src/app/qranker-barista/TabDelimParser.cpp
@@ -0,0 +1,777 @@
+#include "TabDelimParser.h"
+
+/******************************/
+
+TabDelimParser :: TabDelimParser()
+ : num_mixed_labels(0),
+ psmind_to_scan(0),
+ psmind_to_charge(0),
+ psmind_to_label(0),
+ psmind_to_num_pep(0),
+ psmind_to_ofst(0),
+ psmind_to_pepind(0),
+ psmind_to_neutral_mass(0),
+ psmind_to_peptide_mass(0),
+ num_features(0),
+ num_psm(0),
+ num_pos_psm(0),
+ num_neg_psm(0),
+ num_pep(0),
+ num_pep_in_all_psms(0),
+ curr_ofst(0),
+ psmind(0),
+ x(0),
+ num_xlink_features(0)
+{
+
+ //num_psm_features
+ num_features = 17;
+ //num_xlink_features
+ num_xlink_features = 17;
+
+
+ //final_hits_per_spectrum
+ fhps = 3;
+ //decoy prefix
+ decoy_prefix = "random_";
+ //max peptide length to be considered
+ max_len = 50;
+ //min peptide length to be considered
+ min_len = 7;
+
+}
+
+void TabDelimParser :: clear()
+{
+ delete[] x; x = (double*)0;
+ delete[] psmind_to_scan; psmind_to_scan = (int*)0;
+ delete[] psmind_to_charge; psmind_to_charge = (int*)0;
+ delete[] psmind_to_label; psmind_to_label = (int*)0;
+ delete[] psmind_to_num_pep; psmind_to_num_pep = (int*)0;
+ delete[] psmind_to_ofst; psmind_to_ofst = (int*)0;
+ delete[] psmind_to_pepind; psmind_to_pepind = (int*)0;
+ delete[] psmind_to_neutral_mass; psmind_to_neutral_mass = (double*)0;
+ delete[] psmind_to_peptide_mass; psmind_to_peptide_mass = (double*)0;
+}
+
+
+
+TabDelimParser :: ~TabDelimParser()
+{
+ clear();
+}
+
+/* tokens are
+0. scan
+1. charge
+2. spectrum precursor mz
+3. spectrum neutral mass
+4. peptide mass
+5. delta_cn
+6. sp score
+7. xcorr score
+8. xcorr rank
+9. distinct matches/spectrum
+10. sequence
+11. cleavage type
+12. protein id
+13. flanking aa
+14. nzstates
+15. rtime max diff
+16. peptides/spectrum
+17. xcorr sum diff
+18. xcorr max diff
+*/
+
+
+
+void TabDelimParser :: get_tokens(string &line, vector<string>&tokens, string &delim)
+{
+ tokens.erase(tokens.begin(), tokens.end());
+ string tmp = line;
+ string tok;
+ size_t pos = tmp.find(delim);
+ while(pos != string::npos)
+ {
+ tok = tmp.substr(0,pos);
+ tokens.push_back(tok);
+ tmp = tmp.substr(pos+1, tmp.size());
+ pos = tmp.find(delim);
+ }
+ //last token
+ tokens.push_back(tmp);
+}
+
+void TabDelimParser :: first_pass(ifstream &fin)
+{
+ string line;
+ vector<string> tokens;
+ vector<string> peptides;
+ string delim1 = "\t";
+ string delim2 = ",";
+ while(!fin.eof())
+ {
+ getline(fin,line);
+ get_tokens(line, tokens, delim1);
+
+ if(tokens.size() > 1)
+ {
+ //get all peptides and fill pep_to_ind tables
+ string peps = tokens[10];
+ get_tokens(peps,peptides,delim2);
+
+ for(unsigned int i = 0; i < peptides.size(); i++)
+ {
+ string pep = peptides[i];
+ int pep_ind = -1;
+ //add peptide to pep_to_ind and ind_to_pep maps
+ if(pep_to_ind.find(pep) == pep_to_ind.end())
+ {
+ pep_ind = num_pep;
+ //add a new peptide
+ pep_to_ind[pep] = pep_ind;
+ ind_to_pep[pep_ind] = pep;
+ num_pep++;
+ }
+ else
+ {
+ pep_ind = pep_to_ind[pep];
+ string p = ind_to_pep[pep_ind];
+ if(pep.compare(p) != 0)
+ cout << "warning : did not find peptide in ind_to_pep_table\n";
+ }
+ }
+ num_pep_in_all_psms += peptides.size();
+ num_psm++;
+ }
+
+ }
+}
+
+
+void TabDelimParser :: allocate_feature_space()
+{
+ //space for feature vector
+ x = new double[num_features];
+ memset(x,0,sizeof(double)*num_features);
+
+ //space for psminfo
+ psmind_to_pepind = new int[num_pep_in_all_psms];
+ memset(psmind_to_pepind,0,sizeof(int)*num_pep_in_all_psms);
+ psmind_to_num_pep = new int[num_psm];
+ memset(psmind_to_num_pep,0,sizeof(int)*num_psm);
+ psmind_to_ofst = new int[num_psm];
+ memset(psmind_to_ofst,0,sizeof(int)*num_psm);
+ psmind_to_charge = new int[num_pep_in_all_psms];
+ memset(psmind_to_charge,0,sizeof(int)*num_pep_in_all_psms);
+
+ psmind_to_neutral_mass = new double[num_pep_in_all_psms];
+ memset(psmind_to_neutral_mass,0,sizeof(double)*num_pep_in_all_psms);
+ psmind_to_peptide_mass = new double[num_pep_in_all_psms];
+ memset(psmind_to_peptide_mass,0,sizeof(double)*num_pep_in_all_psms);
+
+ psmind_to_scan = new int[num_psm];
+ memset(psmind_to_scan,0,sizeof(int)*num_psm);
+ psmind_to_label = new int[num_psm];
+ memset(psmind_to_label,0,sizeof(int)*num_psm);
+
+}
+
+
+void TabDelimParser :: extract_psm_features(vector<string> & tokens, double *x)
+{
+ memset(x,0,sizeof(double)*num_features);
+ //log rank by Sp
+
+ //deltaLCN
+
+ //deltaCN
+
+ //xcorr score
+ x[3] = atof(tokens[7].c_str());
+ //sp score
+
+ //matched ions/predicted ions
+
+ //observed mass
+
+ //peptide length
+
+ //charge
+
+ //whether n-terminus and c-terminus have proper cleavage sites
+
+ // missed cleavages
+
+ // number of sequence_comparisons
+
+ //difference between measured and calculated mass
+
+ // absolute value of difference between measured and calculated mass
+
+}
+
+
+
+void TabDelimParser :: second_pass(ifstream &fin, int label)
+{
+ string line;
+ vector<string> tokens;
+
+ vector<string> peptides;
+ vector<string> charge_str;
+ vector<string> spectrum_neutral_mass_str;
+ vector<string> peptide_mass_str;
+ string delim1 = "\t";
+ string delim2 = ",";
+ while(!fin.eof())
+ {
+ getline(fin,line);
+ get_tokens(line, tokens, delim1);
+
+ if(tokens.size() > 1)
+ {
+ //extract features
+ extract_psm_features(tokens, x);
+ f_psm.write((char*)x, sizeof(double)*num_features);
+
+ //fill in tables
+
+ //get the scan
+ int scan = atoi(tokens[0].c_str());
+ psmind_to_scan[psmind] = scan;
+
+ //get charges
+ string ch = tokens[1];
+ get_tokens(ch, charge_str,delim2);
+ for(unsigned int i = 0; i < charge_str.size(); i++)
+ psmind_to_charge[curr_ofst+i] = atoi(charge_str[i].c_str());
+
+ //get spectrum neutral mass
+ string neut_mass = tokens[3];
+ get_tokens(neut_mass, spectrum_neutral_mass_str,delim2);
+ for(unsigned int i = 0; i < spectrum_neutral_mass_str.size(); i++)
+ psmind_to_neutral_mass[curr_ofst+i] = atof(spectrum_neutral_mass_str[i].c_str());
+
+ //get peptide mass
+ string pep_mass = tokens[4];
+ get_tokens(pep_mass, peptide_mass_str,delim2);
+ vector<double> peptide_mass;
+ peptide_mass.resize(peptide_mass_str.size(),0);
+ for(unsigned int i = 0; i < peptide_mass_str.size(); i++)
+ psmind_to_peptide_mass[curr_ofst+i] = atof(peptide_mass_str[i].c_str());
+
+ //get all peptides
+ string peps = tokens[10];
+ get_tokens(peps,peptides,delim2);
+ for(unsigned int i = 0; i < peptides.size(); i++)
+ {
+ string pep = peptides[i];
+ int pep_ind = -1;
+ //add peptide to pep_to_ind and ind_to_pep maps
+ if(pep_to_ind.find(pep) == pep_to_ind.end())
+ cout << "warning : did not find peptide in ind_to_pep_table\n";
+ else
+ pep_ind = pep_to_ind[pep];
+ psmind_to_pepind[curr_ofst+i] = pep_ind;
+ }
+ psmind_to_num_pep[psmind] = peptides.size();
+ psmind_to_ofst[psmind] = curr_ofst;
+
+ psmind_to_label[psmind] = label;
+ if(label == 1)
+ num_pos_psm++;
+ else
+ num_neg_psm++;
+
+ //augment counters
+ curr_ofst+= peptides.size();
+ psmind++;
+ }
+ }
+}
+
+/*****************************************************************************************/
+
+void TabDelimParser :: save_data_in_binary(string out_dir)
+{
+ ostringstream fname;
+ //write out data summary
+ fname << out_dir << "/summary.txt";
+ ofstream f_summary(fname.str().c_str());
+ //psm info
+ f_summary << num_features << " " << num_psm << " " << num_pos_psm << " " << num_neg_psm << endl;
+ //peptide info
+ f_summary << num_pep << endl;
+ f_summary.close();
+ fname.str("");
+
+ //psmind_to_pepind
+ fname << out_dir << "/psmind_to_pepind.txt";
+ ofstream f_psmind_to_pepind(fname.str().c_str(),ios::binary);
+ f_psmind_to_pepind.write((char*)psmind_to_pepind,sizeof(int)*num_pep_in_all_psms);
+ f_psmind_to_pepind.close();
+ fname.str("");
+
+ //psmind_to_num_pep
+ fname << out_dir << "/psmind_to_num_pep.txt";
+ ofstream f_psmind_to_num_pep(fname.str().c_str(),ios::binary);
+ f_psmind_to_num_pep.write((char*)psmind_to_num_pep,sizeof(int)*num_psm);
+ f_psmind_to_num_pep.close();
+ fname.str("");
+
+ //psmind_to_ofst
+ fname << out_dir << "/psmind_to_ofst.txt";
+ ofstream f_psmind_to_ofst(fname.str().c_str(),ios::binary);
+ f_psmind_to_ofst.write((char*)psmind_to_ofst,sizeof(int)*num_psm);
+ f_psmind_to_ofst.close();
+ fname.str("");
+
+ //psmind_to_scan
+ fname << out_dir << "/psmind_to_scan.txt";
+ ofstream f_psmind_to_scan(fname.str().c_str(),ios::binary);
+ f_psmind_to_scan.write((char*)psmind_to_scan,sizeof(int)*num_psm);
+ f_psmind_to_scan.close();
+ fname.str("");
+
+ //psmind_to_charge
+ fname << out_dir << "/psmind_to_charge.txt";
+ ofstream f_psmind_to_charge(fname.str().c_str(),ios::binary);
+ f_psmind_to_charge.write((char*)psmind_to_charge,sizeof(int)*num_pep_in_all_psms);
+ f_psmind_to_charge.close();
+ fname.str("");
+
+ //psmind_to_label
+ fname << out_dir << "/psmind_to_label.txt";
+ ofstream f_psmind_to_label(fname.str().c_str(),ios::binary);
+ f_psmind_to_label.write((char*)psmind_to_label,sizeof(int)*num_psm);
+ f_psmind_to_label.close();
+ fname.str("");
+
+ //ind_to_pep
+ fname << out_dir << "/ind_to_pep.txt";
+ ofstream f_ind_to_pep(fname.str().c_str(),ios::binary);
+ for(map<int,string>::iterator it = ind_to_pep.begin(); it != ind_to_pep.end(); it++)
+ f_ind_to_pep << it->first << " " << it->second << "\n";
+ f_ind_to_pep.close();
+ fname.str("");
+
+ //pep_to_ind
+ fname << out_dir << "/pep_to_ind.txt";
+ ofstream f_pep_to_ind(fname.str().c_str(),ios::binary);
+ for(map<string,int>::iterator it = pep_to_ind.begin(); it != pep_to_ind.end(); it++)
+ f_pep_to_ind << it->first << " " << it->second << "\n";
+ f_pep_to_ind.close();
+ fname.str("");
+
+}
+
+void TabDelimParser :: clean_up(string dir)
+{
+
+ ostringstream fname;
+
+ //fname << out_dir << "/summary.txt";
+ //ofstream f_summary(fname.str().c_str());
+
+ fname << dir << "/psm.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_pepind
+ fname << out_dir << "/psmind_to_pepind.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_num_pep
+ fname << out_dir << "/psmind_to_num_pep.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_num_pep
+ fname << out_dir << "/psmind_to_ofst.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_scan
+ fname << out_dir << "/psmind_to_scan.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_charge
+ fname << out_dir << "/psmind_to_charge.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_label
+ fname << out_dir << "/psmind_to_label.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //ind_to_pep
+ fname << out_dir << "/ind_to_pep.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //pep_to_ind
+ fname << out_dir << "/pep_to_ind.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+}
+
+
+
+/******************************************************************************************/
+
+
+int TabDelimParser :: run(vector<string> &filenames)
+{
+ string line;
+ for(unsigned int i = 0; i < filenames.size(); i++)
+ {
+ string fname = filenames[i];
+ cout << fname << endl;
+ ifstream fin(fname.c_str());
+ if(!fin.is_open())
+ {
+ cout << "could not open " << fname << " for reading" << endl;
+ return 0;
+ }
+ getline(fin,line);
+ first_pass(fin);
+ fin.close();
+ }
+ cout << num_psm << " " << num_pep << " " << num_pep_in_all_psms << endl;
+ allocate_feature_space();
+
+ ostringstream fname;
+ fname << out_dir << "/psm.txt";
+ f_psm.open(fname.str().c_str());
+ fname.str("");
+
+ int label = 0;
+ for(unsigned int i = 0; i < filenames.size(); i++)
+ {
+ string fname = filenames[i];
+ cout << fname << endl;
+ ifstream fin(fname.c_str());
+ if(!fin.is_open())
+ {
+ cout << "could not open " << fname << " for reading" << endl;
+ return 0;
+ }
+ getline(fin,line);
+ if(i == 0)
+ label = 1;
+ else
+ label = -1;
+ second_pass(fin,label);
+ fin.close();
+ }
+ f_psm.close();
+ cout << psmind << " " << num_pos_psm << " " << num_neg_psm << endl;
+ save_data_in_binary(out_dir);
+ return 1;
+}
+
+/*******************************************xlinking functions*************************************/
+
+
+/* xlink tokens
+ * 0. scan
+ * 1. charge
+ * 2. spectrum precursor m/z
+ * 3. spectrum neutral mass
+ * 4. peptide mass mono
+ * 5. peptide mass average
+ * 6. mass error(ppm)
+ * 7. sp score
+ * 8. sp rank
+ * 9. b/y ions matched
+ * 10. b/y ions total
+ * 11. xcorr score
+ * 12. xcorr rank
+ * 13. p-value
+ * 14. distinct matches/spectrum
+ * 15. sequence
+ * 16. protein id(loc) 1
+ * 17. protein id(loc) 2
+ */
+
+
+void TabDelimParser :: first_pass_xlink(ifstream &fin)
+{
+ string line;
+ vector<string> tokens;
+ vector<string> subtokens;
+ vector<string> peptides;
+ string delim1 = "\t";
+ string delim2 = ",";
+ string delim3 = " ";
+ while(!fin.eof())
+ {
+ getline(fin,line);
+ get_tokens(line, tokens, delim1);
+
+ if(tokens.size() > 1)
+ {
+ //get all peptides and fill tables
+ string pep_and_loc = tokens[15];
+ get_tokens(pep_and_loc,subtokens,delim3);
+ string peps = subtokens[0];
+ get_tokens(peps,peptides,delim2);
+ psmind_to_peptide1[num_psm] = peptides[0];
+ psmind_to_peptide2[num_psm] = peptides[1];
+ psmind_to_loc[num_psm] = subtokens[1];
+ //proteins
+ psmind_to_protein1[num_psm] = tokens[16];
+ psmind_to_protein2[num_psm] = tokens[17];
+
+ num_psm++;
+ }
+ }
+}
+
+
+void TabDelimParser :: allocate_feature_space_xlink()
+{
+ //space for feature vector
+ x = new double[num_xlink_features];
+ memset(x,0,sizeof(double)*num_xlink_features);
+
+ psmind_to_label = new int[num_psm];
+ memset(psmind_to_label,0,sizeof(int)*num_psm);
+
+}
+
+
+void TabDelimParser :: extract_xlink_features(vector<string> & tokens, double *x)
+{
+ memset(x,0,sizeof(double)*num_xlink_features);
+ //log rank by Sp
+ x[0]=atof(tokens[8].c_str());
+ //deltaLCN
+
+ //deltaCN
+
+ //xcorr score
+ x[3] = atof(tokens[11].c_str());
+ //sp score
+ x[4] = atof(tokens[7].c_str());
+ //matched ions/predicted ions
+
+ //observed mass
+
+ //peptide length
+
+ //charge
+
+ //whether n-terminus and c-terminus have proper cleavage sites
+
+ // missed cleavages
+
+ // number of sequence_comparisons
+
+ //difference between measured and calculated mass
+
+ // absolute value of difference between measured and calculated mass
+
+}
+
+
+
+void TabDelimParser :: second_pass_xlink(ifstream &fin, int label)
+{
+ string line;
+ vector<string> tokens;
+
+ vector<string> peptides;
+ vector<string> charge_str;
+ vector<string> spectrum_neutral_mass_str;
+ vector<string> peptide_mass_str;
+ string delim1 = "\t";
+ string delim2 = ",";
+ while(!fin.eof())
+ {
+ getline(fin,line);
+ get_tokens(line, tokens, delim1);
+
+ if(tokens.size() > 1)
+ {
+ //extract features
+ extract_xlink_features(tokens, x);
+ f_psm.write((char*)x, sizeof(double)*num_features);
+
+ psmind_to_label[psmind] = label;
+ if(label == 1)
+ num_pos_psm++;
+ else
+ num_neg_psm++;
+
+ //augment counters
+ psmind++;
+ }
+ }
+}
+
+
+void TabDelimParser :: save_data_in_binary_xlink(string out_dir)
+{
+ ostringstream fname;
+ //write out data summary
+ fname << out_dir << "/summary.txt";
+ ofstream f_summary(fname.str().c_str());
+ //psm info
+ f_summary << num_xlink_features << " " << num_psm << " " << num_pos_psm << " " << num_neg_psm << endl;
+ f_summary.close();
+ fname.str("");
+
+ //psmind_to_label
+ fname << out_dir << "/psmind_to_label.txt";
+ ofstream f_psmind_to_label(fname.str().c_str(),ios::binary);
+ f_psmind_to_label.write((char*)psmind_to_label,sizeof(int)*num_psm);
+ f_psmind_to_label.close();
+ fname.str("");
+
+ //psmind_to_peptide1
+ fname << out_dir << "/psmind_to_peptide1.txt";
+ ofstream f_psmind_to_peptide1(fname.str().c_str(),ios::binary);
+ for(map<int,string>::iterator it = psmind_to_peptide1.begin(); it != psmind_to_peptide1.end(); it++)
+ f_psmind_to_peptide1 << it->first << " " << it->second << "\n";
+ f_psmind_to_peptide1.close();
+ fname.str("");
+
+ //psmind_to_peptide2
+ fname << out_dir << "/psmind_to_peptide2.txt";
+ ofstream f_psmind_to_peptide2(fname.str().c_str(),ios::binary);
+ for(map<int,string>::iterator it = psmind_to_peptide2.begin(); it != psmind_to_peptide2.end(); it++)
+ f_psmind_to_peptide2 << it->first << " " << it->second << "\n";
+ f_psmind_to_peptide2.close();
+ fname.str("");
+
+ //psmind_to_loc
+ fname << out_dir << "/psmind_to_loc.txt";
+ ofstream f_psmind_to_loc(fname.str().c_str(),ios::binary);
+ for(map<int,string>::iterator it = psmind_to_loc.begin(); it != psmind_to_loc.end(); it++)
+ f_psmind_to_loc << it->first << " " << it->second << "\n";
+ f_psmind_to_loc.close();
+ fname.str("");
+
+ //psmind_to_peptide1
+ fname << out_dir << "/psmind_to_protein1.txt";
+ ofstream f_psmind_to_protein1(fname.str().c_str(),ios::binary);
+ for(map<int,string>::iterator it = psmind_to_protein1.begin(); it != psmind_to_protein1.end(); it++)
+ f_psmind_to_protein1 << it->first << " " << it->second << "\n";
+ f_psmind_to_protein1.close();
+ fname.str("");
+
+ //psmind_to_peptide2
+ fname << out_dir << "/psmind_to_protein2.txt";
+ ofstream f_psmind_to_protein2(fname.str().c_str(),ios::binary);
+ for(map<int,string>::iterator it = psmind_to_protein2.begin(); it != psmind_to_protein2.end(); it++)
+ f_psmind_to_protein2 << it->first << " " << it->second << "\n";
+ f_psmind_to_protein2.close();
+ fname.str("");
+
+}
+
+
+void TabDelimParser :: clean_up_xlink(string dir)
+{
+
+ ostringstream fname;
+
+ //fname << out_dir << "/summary.txt";
+ //ofstream f_summary(fname.str().c_str());
+
+ fname << dir << "/psm.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_label
+ fname << out_dir << "/psmind_to_label.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_peptide1
+ fname << out_dir << "/psmind_to_peptide1.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_peptide2
+ fname << out_dir << "/psmind_to_peptide2.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_loc
+ fname << out_dir << "/psmind_to_loc.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_protein1
+ fname << out_dir << "/psmind_to_protein1.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+ //psmind_to_protein2
+ fname << out_dir << "/psmind_to_protein2.txt";
+ remove(fname.str().c_str());
+ fname.str("");
+
+}
+
+
+
+int TabDelimParser :: run_on_xlink(vector<string> &filenames)
+{
+ string line;
+ for(unsigned int i = 0; i < filenames.size(); i++)
+ {
+ string fname = filenames[i];
+ cout << fname << endl;
+ ifstream fin(fname.c_str());
+ if(!fin.is_open())
+ {
+ cout << "could not open " << fname << " for reading" << endl;
+ return 0;
+ }
+ getline(fin,line);
+ first_pass_xlink(fin);
+ fin.close();
+
+ }
+ cout << num_psm << endl;
+ allocate_feature_space_xlink();
+
+ ostringstream fname;
+ fname << out_dir << "/psm.txt";
+ f_psm.open(fname.str().c_str());
+ fname.str("");
+
+ int label = 0;
+ for(unsigned int i = 0; i < filenames.size(); i++)
+ {
+ string fname = filenames[i];
+ cout << fname << endl;
+ ifstream fin(fname.c_str());
+ if(!fin.is_open())
+ {
+ cout << "could not open " << fname << " for reading" << endl;
+ return 0;
+ }
+ getline(fin,line);
+ if(i == 0)
+ label = 1;
+ else
+ label = -1;
+ second_pass_xlink(fin,label);
+ fin.close();
+ }
+ f_psm.close();
+ cout << psmind << " " << num_pos_psm << " " << num_neg_psm << endl;
+ save_data_in_binary_xlink(out_dir);
+ return 1;
+}
+
+
diff --git a/src/app/qranker-barista/TabDelimParser.h b/src/app/qranker-barista/TabDelimParser.h
new file mode 100644
index 0000000..d534470
--- /dev/null
+++ b/src/app/qranker-barista/TabDelimParser.h
@@ -0,0 +1,105 @@
+#ifndef TABDELIMPARSER_H
+#define TABDELIMPARSER_H
+
+#include <sys/types.h>
+#ifndef _MSC_VER
+#include <dirent.h>
+#endif
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <assert.h>
+#include <vector>
+#include <string>
+#include <math.h>
+#include <map>
+#include <set>
+#include <cstring>
+#include <stdlib.h>
+#include "SpecFeatures.h"
+#include "BipartiteGraph.h"
+using namespace std;
+
+class TabDelimParser{
+ public:
+
+ TabDelimParser();
+ ~TabDelimParser();
+ void clear();
+ inline void set_output_dir(string &dir){out_dir = dir;}
+ inline string& get_output_dir(){return out_dir;}
+ int run(vector<string> &filenames);
+
+ void get_tokens(string &line, vector<string>&tokens, string &delim);
+ void first_pass(ifstream &fin);
+ void second_pass(ifstream &fin, int label);
+ void allocate_feature_space();
+ void extract_psm_features(vector<string> & tokens, double *x);
+ void save_data_in_binary(string out_dir);
+ void clean_up(string dir);
+ /*******************************************************/
+ int run_on_xlink(vector<string> &filenames);
+ void first_pass_xlink(ifstream &fin);
+ void second_pass_xlink(ifstream &fin, int label);
+ void allocate_feature_space_xlink();
+ void extract_xlink_features(vector<string> & tokens, double *x);
+ void save_data_in_binary_xlink(string out_dir);
+ void clean_up_xlink(string dir);
+ protected:
+ //auxiliary variables
+ int num_mixed_labels;
+
+ //psm info
+ int* psmind_to_scan;
+ int* psmind_to_charge;
+ int* psmind_to_label;
+ int* psmind_to_num_pep;
+ int* psmind_to_ofst;
+ int* psmind_to_pepind;
+ double *psmind_to_neutral_mass;
+ double *psmind_to_peptide_mass;
+
+ //peptide info
+ map<string,int> pep_to_ind;
+ map<int,string> ind_to_pep;
+
+ //summary of the dataset
+ int num_features;
+ int num_psm;
+ int num_pos_psm;
+ int num_neg_psm;
+ int num_pep;
+ int num_pep_in_all_psms;
+ int curr_ofst;
+
+ int psmind;
+
+ //psm feature vector
+ double *x;
+
+ //writing out data
+ string out_dir;
+ ofstream f_psm;
+
+ //final hits per spectrum
+ int fhps;
+ //decoy prefix
+ string decoy_prefix;
+ //enzyme
+ // enzyme e;
+ //max peptide length to be considered
+ int max_len;
+ //min peptide length to be considered
+ int min_len;
+
+ /************xlink-specific*************/
+ int num_xlink_features;
+ map<int,string> psmind_to_peptide1;
+ map<int,string> psmind_to_peptide2;
+ map<int,string> psmind_to_loc;
+ map<int,string> psmind_to_protein1;
+ map<int,string> psmind_to_protein2;
+
+};
+
+#endif
diff --git a/src/app/qranker-barista/barista.html b/src/app/qranker-barista/barista.html
new file mode 100644
index 0000000..bf76a5e
--- /dev/null
+++ b/src/app/qranker-barista/barista.html
@@ -0,0 +1,215 @@
+<html>
+<title>crux barista</title>
+<link href="./crux.css" rel="styleSheet" type="text/css">
+</head>
+<body>
+<blockquote>
+
+<H1 ALIGN=CENTER>crux barista</H1>
+
+
+<p>
+<b>Description:</b></p>
+
+<p>
+Barista is a protein identification algorithm that combines two
+different tasks—peptide-spectrum match (PSM) verification and
+protein inference—into a single learning algorithm. The program
+requires two inputs: the results of a database search and a database
+of proteins. Barista produces as output a ranking of proteins based
+on how likely they are to be present in the sample. Barista also
+re-ranks the peptide identifications to more accurately distinguish
+between correct and incorrect identifications. Barista uses a machine
+learning strategy that requires that the database search be carried
+out on target and decoy proteins.</p>
+
+<p>
+<b>Usage:</b></p>
+
+<blockquote>
+<code>crux barista [options] <protein database folder> <sqt folder> <ms2 folder></p>
+<code>crux barista [options] <list of protein database files> <list of sqt files> <list of ms2 files> </p>
+<code>crux barista [options] <protein database file> <sqt file> <ms2 file>
+
+</code>
+</blockquote>
+
+
+<p>
+<b>Required Input:</b></p>
+
+<ul>
+
+<li>
+protein database – The program requires the protein database
+files against which the search was performed. The protein database
+input may be a concatenated database or separate target and decoy
+databases. However, in both cases, the program distinguishes between
+target and decoy proteins based on the decoy prefix. There is an
+option to specify the prefix to the protein name that indicates a
+decoy, the default is "random_".
+
+</p>
+The format of the input can be a directory containing the database
+files, a text file with a list of protein database files or a single
+database file. If the protein database input contains suffix "fasta",
+the program assumes a single-file input. Otherwise it checks whether
+the input is a directory or a text file.
+</li>
+</p>
+<li>
+psm input – Barista recognizes sqt format for psm input. The psm
+input can be specified as a single file with suffix "sqt" and should
+be accompanied by the corresponding ms2 file as a third required
+argument. Alternatively, psm input can be given as a text file containing
+the list of all the "sqt" files and should be accompanied by the text
+file with the list of the corresponding ms2 files as a third required
+argument.
+</p>
+Finally, the psm input can be specified as a directory in which all
+the database search results are located. In this case, the program
+collects all the files with prefix "sqt" contained in the directory and
+analyses them jointly. As it finds each sqt file, it simultaneously
+searches the ms2 input directory for an ms2 file with the same name,
+but with the suffix "sqt" replaced with suffix the "ms2".
+
+</p>
+The multiple files can be results of many different experiments or of
+multiple duplicate runs. They can also be the result of separate
+target and decoy searches. All such files in the given directory are
+analyzed jointly.
+</p>
+<li>
+ms2 input – The ms2 input can be specified as a single file with
+suffix "ms2" and as a text file containing the list of all the ms2
+files and or as a directory where all the ms2 files corresponding to
+the psm input in the second argument can be found.
+
+</ul>
+
+<B>Output:</B>
+
+<UL>
+<p>
+The program writes files to the folder <code>crux-output</code> by
+default. The name of the output folder can be set by the user using
+the <code>--output-dir</code> option. The following files will be
+created:</p>
+
+<li>
+<b>barista.target.html</b>: an HTML file that summarizes the protein
+ranking in a human-readable format. Sets of indistinguishable
+proteins are grouped together, and their IDs are printed along with
+the Barista q-value. Along with each protein group is a list of the
+corresponding peptides. The information about each peptide includes its
+amino acid sequence, scan and charge of the peptide, its position in
+the protein, the q-value and score assigned by Barista. Following is a
+portion of a sample output file, showing the identification of a pair
+of proteins:</li>
+
+<hr></hr>
+
+<p>
+<table cellpadding="10">
+
+<tr><td><b>q-value</b></td><td><b>score</b></td><td><b>ID</b></td>
+<td><b>Peptides</b></td><td><b>Matched</b></td>
+<td><b>Description</b></td></tr>
+
+<tr><td>0.001</td><td>1.25</td><td>foo</td><td>12</td><td>3</td>
+<td>Phosphotyrosine glutamate transporter</td></tr>
+<tr><td></td><td></td><td>foobar</td><td>7</td><td>3</td>
+<td>Phosphotyrosine glutamate transporter (N-terminal domain)</td></tr>
+</table>
+
+<ul>
+<table cellpadding="5" border="1">
+<tr><td>EAMPK</td><td>scan=000230</td><td>charge=2</td><td>20-24</td><td>q=0.07</td><td>score=1.27</td></tr>
+<tr><td>YRMLK</td><td>scan=004870</td><td>charge=2</td><td>27-31</td><td>q=0.09</td><td>score=1.05</td></tr>
+<tr><td>NLMMRPPK</td><td>scan=006790</td><td>charge=3</td><td>54-61</td><td>q=0.59</td><td>score=-0.09</td></tr>
+</table>
+</ul>
+
+<hr></hr>
+
+<li>
+<b>barista.target.proteins.txt</b>: a tab-delimited file containing a
+ranked list of groups of indistinguishable target proteins with
+associated Barista scores and q-values and with peptides that
+contributed to the identification of the protein group). The
+following columns are included: proteins in group, Barista score,
+decoy q-value, peptides with scan and charge (for example,
+EAMPK-001285.2). The semantics of these columns are explained
+in <a href="txt-format.html">this document</a>.</li>
+
+<li>
+<b>barista.target.peptides.txt</b>: a tab-delimited file containing a
+ranked list of target peptides with the associated Barista scores and
+q-values. The following columns are included: peptide, scan of
+spectrum in the peptide-spectrum match, charge of spectrum in the
+peptide-spectrum match, Barista score, decoy q-value. The semantics
+of these columns are explained in <a href="txt-format.html">this
+document</a>.</li>
+
+<li>
+<b>barista.target.psm.txt</b>: a tab-delimited file containing a
+ranked list of target peptide-spectrum matches with the associated
+Barista scores and q-values. The following columns are included: scan
+of spectrum in the peptide-spectrum match, charge of spectrum in the
+peptide-spectrum match, peptide in the peptide-spectrum match, Barista
+score, decoy q-value, the filename where each psm was found. The
+semantics of these columns are explained
+in <a href="txt-format.html">this document</a>.</li>
+
+</ul>
+
+<b>Options:</b>
+
+<ul>
+
+<li>
+<code>--enzyme trypsin|chymotrypsin|elastase</code> – The enzyme
+used to digest the proteins in the experiment. Default =
+trypsin.</li>
+
+<li>
+<code>--decoy-prefix <string></code> – specifies the
+prefix of the protein names that indicates a decoy.
+</li>
+
+<li>
+<code>--fileroot <string></code> –
+The <code>fileroot</code> string will be added as a prefix to all
+output file names. Default = none.
+</li>
+
+
+<li>
+<code>--output-dir <filename></code> –
+The name of the directory where output files will be created.
+Default = crux-output.
+</li>
+
+<li>
+<code>--skip-cleanup <T/F></code> – Barista analysis
+consists of preprocessing data and creating lookup tables which are
+then used during training. This option allows keeping the tables after
+the analysis and doing training directly by specifying the
+--dir-with-tables option (see below). Default = F.
+</li>
+
+
+<li>
+<code>--dir-with-tables <filename></code> – The name of
+the directory where the lookup tables with preprocessed data are
+located. Default = none.
+</li>
+
+
+<hr></hr>
+
+<a href="crux.html">Crux home</a>
+
+</blockquote>
+</body>
+</html>
diff --git a/src/app/qranker-barista/cmake_install.cmake b/src/app/qranker-barista/cmake_install.cmake
new file mode 100644
index 0000000..709781a
--- /dev/null
+++ b/src/app/qranker-barista/cmake_install.cmake
@@ -0,0 +1,34 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/qranker-barista
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
diff --git a/src/app/qranker-barista/libbarista.a b/src/app/qranker-barista/libbarista.a
new file mode 100644
index 0000000..7564322
Binary files /dev/null and b/src/app/qranker-barista/libbarista.a differ
diff --git a/src/app/tide/CMakeLists.txt b/src/app/tide/CMakeLists.txt
new file mode 100644
index 0000000..da1cdc9
--- /dev/null
+++ b/src/app/tide/CMakeLists.txt
@@ -0,0 +1,126 @@
+cmake_minimum_required(VERSION 2.8.4)
+cmake_policy(VERSION 2.8.4)
+
+###### Set up include and link directories ######
+if (WIN32 AND NOT CYGWIN)
+include_directories(
+ ${CMAKE_SOURCE_DIR}/src
+ ${CMAKE_BINARY_DIR}/ext/include
+ ${CMAKE_CURRENT_BINARY_DIR}/protoobj
+ ${CMAKE_BINARY_DIR}/ext/build/src/protobuf-2.5.0/src
+ ${CMAKE_BINARY_DIR}/ext/build/src/google-gflags/src/windows
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_1_56_0
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_aux
+)
+else (WIN32 AND NOT CYGWIN)
+include_directories(
+ ${CMAKE_SOURCE_DIR}/src
+ ${CMAKE_BINARY_DIR}/ext/include
+ ${CMAKE_CURRENT_BINARY_DIR}/protoobj
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProtocolBuffers/src
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_1_56_0
+ ${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_aux
+)
+endif (WIN32 AND NOT CYGWIN)
+
+link_directories(
+ ${CMAKE_BINARY_DIR}/ext/lib
+)
+
+set_directory_properties(
+ PROPERTIES
+ ADDITIONAL_MAKE_CLEAN_FILES
+ protoobj
+)
+
+########### For compiling proto files ###########
+set(
+ proto_files_compiled
+ ${CMAKE_CURRENT_BINARY_DIR}/protoobj/header.pb.cc
+ ${CMAKE_CURRENT_BINARY_DIR}/protoobj/peptides.pb.cc
+ ${CMAKE_CURRENT_BINARY_DIR}/protoobj/raw_proteins.pb.cc
+ ${CMAKE_CURRENT_BINARY_DIR}/protoobj/results.pb.cc
+ ${CMAKE_CURRENT_BINARY_DIR}/protoobj/spectrum.pb.cc
+)
+set(
+ proto_files
+ ${CMAKE_CURRENT_SOURCE_DIR}/protobuf/header.proto
+ ${CMAKE_CURRENT_SOURCE_DIR}/protobuf/peptides.proto
+ ${CMAKE_CURRENT_SOURCE_DIR}/protobuf/raw_proteins.proto
+ ${CMAKE_CURRENT_SOURCE_DIR}/protobuf/results.proto
+ ${CMAKE_CURRENT_SOURCE_DIR}/protobuf/spectrum.proto
+)
+add_custom_command(
+ OUTPUT ${proto_files_compiled}
+ DEPENDS ${proto_files}
+ COMMAND ${CMAKE_COMMAND} -E make_directory protoobj
+ COMMAND
+ ${CMAKE_BINARY_DIR}/ext/bin/protoc
+ --proto_path=${CMAKE_CURRENT_SOURCE_DIR}/protobuf/
+ --cpp_out=${CMAKE_CURRENT_BINARY_DIR}/protoobj
+ --python_out=${CMAKE_CURRENT_BINARY_DIR}/protoobj
+ ${proto_files}
+ WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+)
+
+########## Set up tide-support library ##########
+if (WIN32 AND NOT CYGWIN)
+ set(
+ tide_lib_files
+ ${proto_files_compiled}
+ abspath.cc
+ active_peptide_queue.cc
+ crux_sp_spectrum.cc
+ fifo_alloc.cc
+ index_settings.cc
+ make_peptides.cc
+ mass_constants.cc
+ max_mz.cc
+ mman.c
+ peptide.cc
+ peptide_mods3.cc
+ peptide_peaks.cc
+ sp_scorer.cc
+ spectrum_collection.cc
+ spectrum_preprocess2.cc
+ )
+else (WIN32 AND NOT CYGWIN)
+ set(
+ tide_lib_files
+ ${proto_files_compiled}
+ abspath.cc
+ active_peptide_queue.cc
+ crux_sp_spectrum.cc
+ fifo_alloc.cc
+ index_settings.cc
+ make_peptides.cc
+ mass_constants.cc
+ max_mz.cc
+ peptide.cc
+ peptide_mods3.cc
+ peptide_peaks.cc
+ sp_scorer.cc
+ spectrum_collection.cc
+ spectrum_preprocess2.cc
+ )
+endif (WIN32 AND NOT CYGWIN)
+add_library(tide-support STATIC ${tide_lib_files})
+
+if (WIN32 AND NOT CYGWIN)
+ set_property(
+ TARGET tide-support
+ PROPERTY
+ COMPILE_DEFINITIONS
+ GFLAGS_DLL_DECL=
+ GFLAGS_DLL_DECLARE_FLAG=
+ GFLAGS_DLL_DEFINE_FLAG=
+ )
+elseif (APPLE)
+ set_property(
+ TARGET tide-support
+ PROPERTY
+ COMPILE_DEFINITIONS
+ DARWIN
+ )
+endif (WIN32 AND NOT CYGWIN)
+
diff --git a/src/app/tide/Makefile b/src/app/tide/Makefile
new file mode 100644
index 0000000..84b0460
--- /dev/null
+++ b/src/app/tide/Makefile
@@ -0,0 +1,720 @@
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+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
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+
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+
+# The top-level source directory on which CMake was run.
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+
+# The top-level build directory on which CMake was run.
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+
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+ /net/gs/vol3/software/modules-sw/cmake/2.8.12.2/Linux/RHEL6/x86_64/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
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+ @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
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+.PHONY : list_install_components
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+all: cmake_check_build_system
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+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f CMakeFiles/Makefile2 src/app/tide/all
+ $(CMAKE_COMMAND) -E cmake_progress_start /data/TeamCity/buildAgent/work/779d99b0241b2175/CMakeFiles 0
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+
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+depend:
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+abspath.s: abspath.cc.s
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+peptide_mods3.s: peptide_mods3.cc.s
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+# target to generate assembly for a file
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+peptide_peaks.i: peptide_peaks.cc.i
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+# target to preprocess a source file
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+
+peptide_peaks.s: peptide_peaks.cc.s
+.PHONY : peptide_peaks.s
+
+# target to generate assembly for a file
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+
+# target to build an object file
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+# target to preprocess a source file
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+protoobj/header.pb.s: protoobj/header.pb.cc.s
+.PHONY : protoobj/header.pb.s
+
+# target to generate assembly for a file
+protoobj/header.pb.cc.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/protoobj/header.pb.cc.s
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+.PHONY : protoobj/peptides.pb.o
+
+# target to build an object file
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+.PHONY : protoobj/peptides.pb.i
+
+# target to preprocess a source file
+protoobj/peptides.pb.cc.i:
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+protoobj/peptides.pb.s: protoobj/peptides.pb.cc.s
+.PHONY : protoobj/peptides.pb.s
+
+# target to generate assembly for a file
+protoobj/peptides.pb.cc.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/protoobj/peptides.pb.cc.s
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+protoobj/raw_proteins.pb.o: protoobj/raw_proteins.pb.cc.o
+.PHONY : protoobj/raw_proteins.pb.o
+
+# target to build an object file
+protoobj/raw_proteins.pb.cc.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/protoobj/raw_proteins.pb.cc.o
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+protoobj/raw_proteins.pb.i: protoobj/raw_proteins.pb.cc.i
+.PHONY : protoobj/raw_proteins.pb.i
+
+# target to preprocess a source file
+protoobj/raw_proteins.pb.cc.i:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/protoobj/raw_proteins.pb.cc.i
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+protoobj/raw_proteins.pb.s: protoobj/raw_proteins.pb.cc.s
+.PHONY : protoobj/raw_proteins.pb.s
+
+# target to generate assembly for a file
+protoobj/raw_proteins.pb.cc.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/protoobj/raw_proteins.pb.cc.s
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+protoobj/results.pb.o: protoobj/results.pb.cc.o
+.PHONY : protoobj/results.pb.o
+
+# target to build an object file
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+protoobj/results.pb.i: protoobj/results.pb.cc.i
+.PHONY : protoobj/results.pb.i
+
+# target to preprocess a source file
+protoobj/results.pb.cc.i:
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+protoobj/results.pb.s: protoobj/results.pb.cc.s
+.PHONY : protoobj/results.pb.s
+
+# target to generate assembly for a file
+protoobj/results.pb.cc.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/protoobj/results.pb.cc.s
+.PHONY : protoobj/results.pb.cc.s
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+protoobj/spectrum.pb.o: protoobj/spectrum.pb.cc.o
+.PHONY : protoobj/spectrum.pb.o
+
+# target to build an object file
+protoobj/spectrum.pb.cc.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/protoobj/spectrum.pb.cc.o
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+protoobj/spectrum.pb.i: protoobj/spectrum.pb.cc.i
+.PHONY : protoobj/spectrum.pb.i
+
+# target to preprocess a source file
+protoobj/spectrum.pb.cc.i:
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+protoobj/spectrum.pb.s: protoobj/spectrum.pb.cc.s
+.PHONY : protoobj/spectrum.pb.s
+
+# target to generate assembly for a file
+protoobj/spectrum.pb.cc.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/protoobj/spectrum.pb.cc.s
+.PHONY : protoobj/spectrum.pb.cc.s
+
+sp_scorer.o: sp_scorer.cc.o
+.PHONY : sp_scorer.o
+
+# target to build an object file
+sp_scorer.cc.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/sp_scorer.cc.o
+.PHONY : sp_scorer.cc.o
+
+sp_scorer.i: sp_scorer.cc.i
+.PHONY : sp_scorer.i
+
+# target to preprocess a source file
+sp_scorer.cc.i:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/sp_scorer.cc.i
+.PHONY : sp_scorer.cc.i
+
+sp_scorer.s: sp_scorer.cc.s
+.PHONY : sp_scorer.s
+
+# target to generate assembly for a file
+sp_scorer.cc.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/sp_scorer.cc.s
+.PHONY : sp_scorer.cc.s
+
+spectrum_collection.o: spectrum_collection.cc.o
+.PHONY : spectrum_collection.o
+
+# target to build an object file
+spectrum_collection.cc.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/spectrum_collection.cc.o
+.PHONY : spectrum_collection.cc.o
+
+spectrum_collection.i: spectrum_collection.cc.i
+.PHONY : spectrum_collection.i
+
+# target to preprocess a source file
+spectrum_collection.cc.i:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/spectrum_collection.cc.i
+.PHONY : spectrum_collection.cc.i
+
+spectrum_collection.s: spectrum_collection.cc.s
+.PHONY : spectrum_collection.s
+
+# target to generate assembly for a file
+spectrum_collection.cc.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/spectrum_collection.cc.s
+.PHONY : spectrum_collection.cc.s
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+spectrum_preprocess2.o: spectrum_preprocess2.cc.o
+.PHONY : spectrum_preprocess2.o
+
+# target to build an object file
+spectrum_preprocess2.cc.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/spectrum_preprocess2.cc.o
+.PHONY : spectrum_preprocess2.cc.o
+
+spectrum_preprocess2.i: spectrum_preprocess2.cc.i
+.PHONY : spectrum_preprocess2.i
+
+# target to preprocess a source file
+spectrum_preprocess2.cc.i:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/spectrum_preprocess2.cc.i
+.PHONY : spectrum_preprocess2.cc.i
+
+spectrum_preprocess2.s: spectrum_preprocess2.cc.s
+.PHONY : spectrum_preprocess2.s
+
+# target to generate assembly for a file
+spectrum_preprocess2.cc.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/tide/CMakeFiles/tide-support.dir/build.make src/app/tide/CMakeFiles/tide-support.dir/spectrum_preprocess2.cc.s
+.PHONY : spectrum_preprocess2.cc.s
+
+# Help Target
+help:
+ @echo "The following are some of the valid targets for this Makefile:"
+ @echo "... all (the default if no target is provided)"
+ @echo "... clean"
+ @echo "... depend"
+ @echo "... edit_cache"
+ @echo "... install"
+ @echo "... install/local"
+ @echo "... install/strip"
+ @echo "... list_install_components"
+ @echo "... package"
+ @echo "... package_source"
+ @echo "... rebuild_cache"
+ @echo "... tide-support"
+ @echo "... abspath.o"
+ @echo "... abspath.i"
+ @echo "... abspath.s"
+ @echo "... active_peptide_queue.o"
+ @echo "... active_peptide_queue.i"
+ @echo "... active_peptide_queue.s"
+ @echo "... crux_sp_spectrum.o"
+ @echo "... crux_sp_spectrum.i"
+ @echo "... crux_sp_spectrum.s"
+ @echo "... fifo_alloc.o"
+ @echo "... fifo_alloc.i"
+ @echo "... fifo_alloc.s"
+ @echo "... index_settings.o"
+ @echo "... index_settings.i"
+ @echo "... index_settings.s"
+ @echo "... make_peptides.o"
+ @echo "... make_peptides.i"
+ @echo "... make_peptides.s"
+ @echo "... mass_constants.o"
+ @echo "... mass_constants.i"
+ @echo "... mass_constants.s"
+ @echo "... max_mz.o"
+ @echo "... max_mz.i"
+ @echo "... max_mz.s"
+ @echo "... peptide.o"
+ @echo "... peptide.i"
+ @echo "... peptide.s"
+ @echo "... peptide_mods3.o"
+ @echo "... peptide_mods3.i"
+ @echo "... peptide_mods3.s"
+ @echo "... peptide_peaks.o"
+ @echo "... peptide_peaks.i"
+ @echo "... peptide_peaks.s"
+ @echo "... protoobj/header.pb.o"
+ @echo "... protoobj/header.pb.i"
+ @echo "... protoobj/header.pb.s"
+ @echo "... protoobj/peptides.pb.o"
+ @echo "... protoobj/peptides.pb.i"
+ @echo "... protoobj/peptides.pb.s"
+ @echo "... protoobj/raw_proteins.pb.o"
+ @echo "... protoobj/raw_proteins.pb.i"
+ @echo "... protoobj/raw_proteins.pb.s"
+ @echo "... protoobj/results.pb.o"
+ @echo "... protoobj/results.pb.i"
+ @echo "... protoobj/results.pb.s"
+ @echo "... protoobj/spectrum.pb.o"
+ @echo "... protoobj/spectrum.pb.i"
+ @echo "... protoobj/spectrum.pb.s"
+ @echo "... sp_scorer.o"
+ @echo "... sp_scorer.i"
+ @echo "... sp_scorer.s"
+ @echo "... spectrum_collection.o"
+ @echo "... spectrum_collection.i"
+ @echo "... spectrum_collection.s"
+ @echo "... spectrum_preprocess2.o"
+ @echo "... spectrum_preprocess2.i"
+ @echo "... spectrum_preprocess2.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+
diff --git a/src/app/tide/abspath.cc b/src/app/tide/abspath.cc
new file mode 100644
index 0000000..7400aa8
--- /dev/null
+++ b/src/app/tide/abspath.cc
@@ -0,0 +1,12 @@
+#include "abspath.h"
+#include <boost/filesystem.hpp>
+
+using namespace std;
+
+// Compute an absolute path from the parameter by prepending the current
+// working directory when the given path is a relative path.
+// Although the result is correct (according to 'man path_resolution')
+// no effort is made to decode symlinks or normalize /. and /..
+string AbsPath(const string& path) {
+ return boost::filesystem::absolute(path).string();
+}
diff --git a/src/app/tide/abspath.h b/src/app/tide/abspath.h
new file mode 100644
index 0000000..1ea0faf
--- /dev/null
+++ b/src/app/tide/abspath.h
@@ -0,0 +1,8 @@
+#ifndef ABSPATH_H
+#define ABSPATH_H
+
+#include <string>
+
+std::string AbsPath(const std::string& rel_path);
+
+#endif
diff --git a/src/app/tide/active_peptide_queue.cc b/src/app/tide/active_peptide_queue.cc
new file mode 100644
index 0000000..204e81d
--- /dev/null
+++ b/src/app/tide/active_peptide_queue.cc
@@ -0,0 +1,347 @@
+// original author: Benjamin Diament
+// subsequently modified by Attila Kertesz-Farkas, Jeff Howbert
+#include <deque>
+#include <gflags/gflags.h>
+#include "records.h"
+#include "peptides.pb.h"
+#include "peptide.h"
+#include "active_peptide_queue.h"
+#include "records_to_vector-inl.h"
+#include "theoretical_peak_set.h"
+#include "compiler.h"
+#include "app/TideMatchSet.h"
+#define CHECK(x) GOOGLE_CHECK((x))
+
+DEFINE_int32(fifo_page_size, 1, "Page size for FIFO allocator, in megs");
+
+ActivePeptideQueue::ActivePeptideQueue(RecordReader* reader,
+ const vector<const pb::Protein*>&
+ proteins)
+ : reader_(reader),
+ proteins_(proteins),
+ theoretical_peak_set_(2000), // probably overkill, but no harm
+ theoretical_b_peak_set_(200), // probably overkill, but no harm
+ active_targets_(0), active_decoys_(0),
+ fifo_alloc_peptides_(FLAGS_fifo_page_size << 20),
+ fifo_alloc_prog1_(FLAGS_fifo_page_size << 20),
+ fifo_alloc_prog2_(FLAGS_fifo_page_size << 20) {
+ CHECK(reader_->OK());
+ compiler_prog1_ = new TheoreticalPeakCompiler(&fifo_alloc_prog1_);
+ compiler_prog2_ = new TheoreticalPeakCompiler(&fifo_alloc_prog2_);
+ peptide_centric_ = false;
+ elution_window_ = 0;
+}
+
+ActivePeptideQueue::~ActivePeptideQueue() {
+ deque<Peptide*>::iterator i = queue_.begin();
+ // for (; i != queue_.end(); ++i)
+ // delete (*i)->PB();
+ fifo_alloc_peptides_.ReleaseAll();
+ fifo_alloc_prog1_.ReleaseAll();
+ fifo_alloc_prog2_.ReleaseAll();
+
+ delete compiler_prog1_;
+ delete compiler_prog2_;
+}
+
+// Compute the theoretical peaks of the peptide in the "back" of the queue
+// (i.e. the one most recently read from disk -- the heaviest).
+void ActivePeptideQueue::ComputeTheoreticalPeaksBack() {
+ theoretical_peak_set_.Clear();
+ Peptide* peptide = queue_.back();
+ peptide->ComputeTheoreticalPeaks(&theoretical_peak_set_, current_pb_peptide_,
+ compiler_prog1_, compiler_prog2_);
+}
+
+bool ActivePeptideQueue::isWithinIsotope(vector<double>* min_mass, vector<double>* max_mass, double mass, int* isotope_idx) {
+ for (int i = *isotope_idx; i < min_mass->size(); ++i) {
+ if (mass >= (*min_mass)[i] && mass <= (*max_mass)[i]) {
+ if (i > *isotope_idx) {
+ *isotope_idx = i;
+ }
+ return true;
+ }
+ }
+ return false;
+}
+
+int ActivePeptideQueue::SetActiveRange(vector<double>* min_mass, vector<double>* max_mass, double min_range, double max_range, vector<bool>* candidatePeptideStatus) {
+ //min_range and max_range have been introduced to fix a bug
+ //introduced by m/z selection. see #222 in sourceforge
+ //this has to be true:
+ // min_range <= min_mass <= max_mass <= max_range
+
+ // queue front() is lightest; back() is heaviest
+
+ // delete anything already loaded that falls below min_range
+ while (!queue_.empty() && queue_.front()->Mass() < min_range) {
+ Peptide* peptide = queue_.front();
+ //print hits in peptide-centric search
+ ReportPeptideHits(peptide);
+ peptide->spectrum_matches_array.clear();
+ vector<Peptide::spectrum_matches>().swap(peptide->spectrum_matches_array);
+ // would delete peptide's underlying pb::Peptide;
+ queue_.pop_front();
+// delete peptide;
+ }
+ if (queue_.empty()) {
+ //cerr << "Releasing All\n";
+ fifo_alloc_peptides_.ReleaseAll();
+ fifo_alloc_prog1_.ReleaseAll();
+ fifo_alloc_prog2_.ReleaseAll();
+ //cerr << "Prog1: ";
+ //fifo_alloc_prog1_.Show();
+ //cerr << "Prog2: ";
+ //fifo_alloc_prog2_.Show();
+ } else {
+ Peptide* peptide = queue_.front();
+ // Free all peptides up to, but not including peptide.
+ fifo_alloc_peptides_.Release(peptide);
+ peptide->ReleaseFifo(&fifo_alloc_prog1_, &fifo_alloc_prog2_);
+ }
+
+ // Enqueue all peptides that are not yet queued but are lighter than
+ // max_range. For each new enqueued peptide compute the corresponding
+ // theoretical peaks. Data associated with each peptide is allocated by
+ // fifo_alloc_peptides_.
+ bool done = false;
+ if (queue_.empty() || queue_.back()->Mass() <= max_range) {
+ if (!queue_.empty()) {
+ ComputeTheoreticalPeaksBack();
+ }
+ while (!(done = reader_->Done())) {
+ // read all peptides lighter than max_range
+ reader_->Read(¤t_pb_peptide_);
+ if (current_pb_peptide_.mass() < min_range) {
+ // we would delete current_pb_peptide_;
+ continue; // skip peptides that fall below min_range
+ }
+ Peptide* peptide = new(&fifo_alloc_peptides_)
+ Peptide(current_pb_peptide_, proteins_, &fifo_alloc_peptides_);
+ queue_.push_back(peptide);
+ if (peptide->Mass() > max_range) {
+ break;
+ }
+ ComputeTheoreticalPeaksBack();
+ }
+ }
+ // by now, if not EOF, then the last (and only the last) enqueued
+ // peptide is too heavy
+ assert(!queue_.empty() || done);
+
+ // Set up iterator for use with HasNext(),
+ // GetPeptide(), and NextPeptide(). Return the number of enqueued peptides.
+ if (queue_.empty()) {
+ return 0;
+ }
+
+ iter_ = queue_.begin();
+ while (iter_ != queue_.end() && (*iter_)->Mass() < min_mass->front() ){
+ ++iter_;
+ }
+
+ int* isotope_idx = new int(0);
+ end_ = iter_;
+ int active = 0;
+ active_targets_ = active_decoys_ = 0;
+ while (end_ != queue_.end() && (*end_)->Mass() < max_mass->back() ){
+ if (isWithinIsotope(min_mass, max_mass, (*end_)->Mass(), isotope_idx)) {
+ ++active;
+ candidatePeptideStatus->push_back(true);
+ if (!(*end_)->IsDecoy()) {
+ ++active_targets_;
+ } else {
+ ++active_decoys_;
+ }
+ } else {
+ candidatePeptideStatus->push_back(false);
+ }
+ ++end_;
+ }
+ delete isotope_idx;
+ if (active == 0) {
+ return 0;
+ }
+
+ return active;
+
+}
+
+// Compute the b ion only theoretical peaks of the peptide in the "back" of the queue
+// (i.e. the one most recently read from disk -- the heaviest).
+void ActivePeptideQueue::ComputeBTheoreticalPeaksBack() {
+ theoretical_b_peak_set_.Clear();
+ Peptide* peptide = queue_.back();
+ peptide->ComputeBTheoreticalPeaks(&theoretical_b_peak_set_);
+ b_ion_queue_.push_back(theoretical_b_peak_set_);
+}
+
+int ActivePeptideQueue::SetActiveRangeBIons(vector<double>* min_mass, vector<double>* max_mass, double min_range, double max_range, vector<bool>* candidatePeptideStatus) {
+ exact_pval_search_ = true;
+ // queue front() is lightest; back() is heaviest
+
+ // delete anything already loaded that falls below min_range
+ while (!queue_.empty() && queue_.front()->Mass() < min_range) {
+ Peptide* peptide = queue_.front();
+ // would delete peptide's underlying pb::Peptide;
+ ReportPeptideHits(peptide);
+ peptide->spectrum_matches_array.clear();
+ vector<Peptide::spectrum_matches>().swap(peptide->spectrum_matches_array);
+ queue_.pop_front();
+ b_ion_queue_.pop_front();
+// delete peptide;
+ }
+ if (queue_.empty()) {
+ fifo_alloc_peptides_.ReleaseAll();
+ } else {
+ Peptide* peptide = queue_.front();
+ // Free all peptides up to, but not including peptide.
+ fifo_alloc_peptides_.Release(peptide);
+ }
+
+ // Enqueue all peptides that are not yet queued but are lighter than
+ // max_range. For each new enqueued peptide compute the corresponding
+ // theoretical peaks. Data associated with each peptide is allocated by
+ // fifo_alloc_peptides_.
+ bool done;
+ if (queue_.empty() || queue_.back()->Mass() <= max_range) {
+ while (!(done = reader_->Done())) {
+ // read all peptides lighter than max_range
+ reader_->Read(¤t_pb_peptide_);
+ if (current_pb_peptide_.mass() < min_range) {
+ // we would delete current_pb_peptide_;
+ continue; // skip peptides that fall below min_range
+ }
+ Peptide* peptide = new(&fifo_alloc_peptides_)
+ Peptide(current_pb_peptide_, proteins_, &fifo_alloc_peptides_);
+ queue_.push_back(peptide);
+ ComputeBTheoreticalPeaksBack();
+ if (peptide->Mass() > max_range) {
+ break;
+ }
+ }
+ }
+ // by now, if not EOF, then the last (and only the last) enqueued
+ // peptide is too heavy
+ assert(!queue_.empty() || done);
+
+ iter1_ = b_ion_queue_.begin();
+ iter_ = queue_.begin();
+ while (iter_ != queue_.end() && (*iter_)->Mass() < min_mass->front() ){
+ ++iter_;
+ ++iter1_;
+ }
+
+ int* isotope_idx = new int(0);
+ end_ = iter_;
+ end1_ = iter1_;
+ int active = 0;
+ active_targets_ = active_decoys_ = 0;
+ while (end_ != queue_.end() && (*end_)->Mass() < max_mass->back() ){
+ if (isWithinIsotope(min_mass, max_mass, (*end_)->Mass(), isotope_idx)) {
+ ++active;
+ candidatePeptideStatus->push_back(true);
+ if (!(*end_)->IsDecoy()) {
+ ++active_targets_;
+ } else {
+ ++active_decoys_;
+ }
+ } else {
+ candidatePeptideStatus->push_back(false);
+ }
+ ++end_;
+ ++end1_;
+ }
+ delete isotope_idx;
+ if (active == 0) {
+ return 0;
+ }
+
+ return active;
+}
+
+int ActivePeptideQueue::CountAAFrequency(
+ double binWidth,
+ double binOffset,
+ double** dAAFreqN,
+ double** dAAFreqI,
+ double** dAAFreqC,
+ int** dAAMass
+) {
+
+ unsigned int i = 0;
+ unsigned int cntTerm = 0;
+ unsigned int cntInside = 0;
+ const unsigned int MaxModifiedAAMassBin = 2000 / binWidth; //2000 is the maximum size of a modified amino acid
+ unsigned int* nvAAMassCounterN = new unsigned int[MaxModifiedAAMassBin]; //N-terminal amino acids
+ unsigned int* nvAAMassCounterC = new unsigned int[MaxModifiedAAMassBin]; //C-terminal amino acids
+ unsigned int* nvAAMassCounterI = new unsigned int[MaxModifiedAAMassBin]; //inner amino acids in the peptides
+ memset(nvAAMassCounterN, 0, MaxModifiedAAMassBin * sizeof(unsigned int));
+ memset(nvAAMassCounterC, 0, MaxModifiedAAMassBin * sizeof(unsigned int));
+ memset(nvAAMassCounterI, 0, MaxModifiedAAMassBin * sizeof(unsigned int));
+
+ while (!(reader_->Done())) { // read all peptides in index
+ reader_->Read(¤t_pb_peptide_);
+ Peptide* peptide = new(&fifo_alloc_peptides_) Peptide(current_pb_peptide_, proteins_, &fifo_alloc_peptides_);
+
+ double* dAAResidueMass = peptide->getAAMasses(); //retrieves the amino acid masses, modifications included
+
+ int nLen = peptide->Len(); //peptide length
+ ++nvAAMassCounterN[(unsigned int)(dAAResidueMass[0] / binWidth + 1.0 - binOffset)];
+ for (i = 1; i < nLen-1; ++i) {
+ ++nvAAMassCounterI[(unsigned int)(dAAResidueMass[i] / binWidth + 1.0 - binOffset)];
+ ++cntInside;
+ }
+ ++nvAAMassCounterC[(unsigned int)(dAAResidueMass[nLen - 1] / binWidth + 1.0 - binOffset)];
+ ++cntTerm;
+
+ delete[] dAAResidueMass;
+ fifo_alloc_peptides_.ReleaseAll();
+ }
+
+ //calculate the unique masses
+ unsigned int uiUniqueMasses = 0;
+ for (i = 0; i < MaxModifiedAAMassBin; ++i) {
+ if (nvAAMassCounterN[i] || nvAAMassCounterI[i] || nvAAMassCounterC[i]) {
+ ++uiUniqueMasses;
+ }
+ }
+
+ //calculate the unique amino acid masses
+ *dAAMass = new int[uiUniqueMasses]; //a vector for the unique (integerized) amino acid masses present in the sample
+ *dAAFreqN = new double[uiUniqueMasses]; //a vector for the amino acid frequencies at the N-terminus
+ *dAAFreqI = new double[uiUniqueMasses]; //a vector for the amino acid frequencies inside the peptide
+ *dAAFreqC = new double[uiUniqueMasses]; //a vector for the amino acid frequencies at the C-terminus
+ unsigned int cnt = 0;
+ for (i = 0; i < MaxModifiedAAMassBin; ++i) {
+ if (nvAAMassCounterN[i] || nvAAMassCounterI[i] || nvAAMassCounterC[i]) {
+ (*dAAFreqN)[cnt] = (double)nvAAMassCounterN[i] / cntTerm;
+ (*dAAFreqI)[cnt] = (double)nvAAMassCounterI[i] / cntInside;
+ (*dAAFreqC)[cnt] = (double)nvAAMassCounterC[i] / cntTerm;
+ (*dAAMass)[cnt] = i;
+ cnt++;
+ }
+ }
+
+ delete[] nvAAMassCounterN;
+ delete[] nvAAMassCounterI;
+ delete[] nvAAMassCounterC;
+ return uiUniqueMasses;
+}
+
+void ActivePeptideQueue::ReportPeptideHits(Peptide* peptide) {
+ if (!peptide_centric_) {
+ return;
+ }
+
+ current_peptide_ = peptide;
+ TideMatchSet matches(peptide, highest_mz_);
+ matches.exact_pval_search_ = exact_pval_search_;
+ matches.elution_window_ = elution_window_;
+
+ if (!output_files_) { //only tab-delimited output is supported
+ matches.report(target_file_, decoy_file_, top_matches_,
+ this, proteins_, *locations_, compute_sp_);
+ }
+}
+
diff --git a/src/app/tide/active_peptide_queue.h b/src/app/tide/active_peptide_queue.h
new file mode 100644
index 0000000..78b7ed2
--- /dev/null
+++ b/src/app/tide/active_peptide_queue.h
@@ -0,0 +1,158 @@
+// Benjamin Diament
+//
+// An ActivePeptideQueue is constructed with a file of peptides of
+// non-decreasing neutral mass, and a correpsonding set of proteins. With
+// successive call to SetActiveRange(min_mass, max_mass) the ActivePeptideQueue
+// reads in peptides and initializes them. It also discards any peptides in
+// memory lighter than min_mass.
+//
+// The ActivePeptideQueue maintains in memory a window of peptides that fall
+// within a given mass range. The window to maintain (the "active peptides")
+// is set by a call to SetActiveRange(). Successive values
+// of min_mass and max_mass must be non-decreasing. After the call to
+// SetActiveRange() the client may use the iterator interface HasNext() and
+// NextPeptide() to iterate over the window. The client may also use
+// GetPeptide() to get a specific peptide in the window.
+
+#include <deque>
+#include "peptides.pb.h"
+#include "peptide.h"
+#include "theoretical_peak_set.h"
+#include "fifo_alloc.h"
+#include "spectrum_collection.h"
+#include "io/OutputFiles.h"
+
+//#include "sp_scorer.h"
+#ifndef ACTIVE_PEPTIDE_QUEUE_H
+#define ACTIVE_PEPTIDE_QUEUE_H
+
+class TheoreticalPeakCompiler;
+
+class ActivePeptideQueue {
+ public:
+ ActivePeptideQueue(RecordReader* reader,
+ const vector<const pb::Protein*>& proteins);
+
+ ~ActivePeptideQueue();
+
+ bool isWithinIsotope(vector<double>* min_mass, vector<double>* max_mass, double mass, int* isotope_idx);
+
+ // See above for usage and .cc for implementation details.
+ int SetActiveRange(vector<double>* min_mass, vector<double>* max_mass, double min_range, double max_range, vector<bool>* candidatePeptideStatus);
+ int SetActiveRangeBIons(vector<double>* min_mass, vector<double>* max_mass, double min_range, double max_range, vector<bool>* candidatePeptideStatus);
+
+ bool HasNext() const { return iter_ != end_; }
+ Peptide* NextPeptide() { return *iter_; }
+ const Peptide* GetPeptide(int back_index) const {
+ return peptide_centric_ ? current_peptide_ : *(end_ - back_index);
+ }
+ void SetBinSize(double binWidth, double binOffset) {
+ theoretical_b_peak_set_.binWidth_ = binWidth;
+ theoretical_b_peak_set_.binOffset_ = binOffset;
+ }
+
+ deque<TheoreticalPeakSetBIons> b_ion_queue_;
+ deque<TheoreticalPeakSetBIons>::const_iterator iter1_, end1_;
+
+ int CountAAFrequency(double binWidth, double binOffset, double** dAAFreqN,
+ double** dAAFreqI, double** dAAFreqC, int** dAAMass);
+
+ int ActiveTargets() const { return active_targets_; }
+ int ActiveDecoys() const { return active_decoys_; }
+
+ void ReportPeptideHits(Peptide* peptide);
+ void SetOutputs(OutputFiles* output_files, const vector<const pb::AuxLocation*>* locations, int top_matches,
+ bool compute_sp, ofstream* target_file, ofstream* decoy_file, double highest_mz) {
+ locations_ = locations;
+ output_files_ = output_files;
+ top_matches_ = top_matches;
+ compute_sp_ = compute_sp;
+ target_file_ = target_file;
+ decoy_file_ = decoy_file;
+ highest_mz_ = highest_mz;
+ }
+ void setPeptideCentric(bool peptide_centric) {
+ peptide_centric_ = peptide_centric;
+ }
+
+ void setElutionWindow(int elution_window) {
+ elution_window_ = elution_window;
+ }
+ // iter_ points to the current peptide. Client access is by HasNext(),
+ // GetPeptide(), and NextPeptide(). end_ points just beyond the last active
+ // peptide.
+ deque<Peptide*>::const_iterator iter_, end_;
+
+// const ProteinVec& proteins_;
+ private:
+ const vector<const pb::AuxLocation*>* locations_;
+ OutputFiles* output_files_;
+ int top_matches_;
+ bool compute_sp_;
+ ofstream* target_file_;
+ ofstream* decoy_file_;
+ double highest_mz_;
+ Peptide* current_peptide_;
+ bool exact_pval_search_;
+ bool peptide_centric_;
+ int elution_window_;
+
+
+// Spectrum* spectrum_;
+ // IMPLEMENTATION DETAILS
+
+ // See .cc file.
+ void ComputeTheoreticalPeaksBack();
+ void ComputeBTheoreticalPeaksBack();
+
+ RecordReader* reader_;
+ pb::Peptide current_pb_peptide_;
+
+ // All amino acid sequences from which the peptides are drawn.
+ const vector<const pb::Protein*>& proteins_;
+
+ // Workspace for computing theoretical peaks for a single peptide.
+ // Gets reused for each new peptide.
+ ST_TheoreticalPeakSet theoretical_peak_set_;
+ TheoreticalPeakSetBIons theoretical_b_peak_set_;
+
+ // The active peptides. Lighter peptides are enqueued before heavy ones.
+ // queue_ maintains only the peptides that fall within the range specified
+ // by the last call to SetActiveRange().
+ deque<Peptide*> queue_;
+
+ // Set by most recent call to SetActiveRange()
+ double min_mass_, max_mass_;
+
+ // While we maintain a window of active peptides, we allocate and relase them
+ // on a first-in, first-out basis. We use FifoAllocators
+ // (see fifo_alloc.{h,cc}) to manage memory efficiently for this usage
+ // pattern. As we read in peptides and compute the theoretical peaks, we
+ // use compiler_prog1 and compiler_prog2 to generate code on the fly for
+ // taking dot products with the theoretical peak set for each peptide.
+ // FifoAllocators allow us to execute the code thus generated,
+ // since they set the proper permissions. The set of theoretical peaks for
+ // "dotting" with charge 1 and charge 2 spectra, have different
+ // FifoAllocators and TheoreticalPeakCompilers.
+ FifoAllocator fifo_alloc_peptides_;
+ FifoAllocator fifo_alloc_prog1_;
+ FifoAllocator fifo_alloc_prog2_;
+ TheoreticalPeakCompiler* compiler_prog1_;
+ TheoreticalPeakCompiler* compiler_prog2_;
+
+ // Number of targets and decoys in active range
+ int active_targets_, active_decoys_;
+};
+
+/*
+CONSIDER:
+Make 3 subclasses:
+ Read-as-you-go (below)
+ Preread into memory (as current operation)
+ Threaded reads (!!)
+
+pb::Peptide* pb_peptide = new pb::Peptide;
+CHECK(reader_->Read(pb_peptide));
+!reader_->Done()
+*/
+#endif //ACTIVE_PEPTIDE_QUEUE_H
diff --git a/src/app/tide/cmake_install.cmake b/src/app/tide/cmake_install.cmake
new file mode 100644
index 0000000..82e33ea
--- /dev/null
+++ b/src/app/tide/cmake_install.cmake
@@ -0,0 +1,34 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/tide
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
diff --git a/src/app/tide/compiler.h b/src/app/tide/compiler.h
new file mode 100644
index 0000000..ed960f2
--- /dev/null
+++ b/src/app/tide/compiler.h
@@ -0,0 +1,208 @@
+// Benjamin Diament
+
+// We want to be able to compute a dot product between a theoretical peak set
+// and an observed peak set. Under the assumption (borne out by use cases seen
+// in many test sets) that the same peptide may be a candidate for many
+// different observed spectra, we generate machine code, on the fly, for taking
+// the dot product between a fixed theoretical peak set and a variable observed
+// peak set.
+//
+// That is, the generated code is specific to the theoretical peak set, but not
+// to the observed peak set. A program is generated for a given peptide's
+// theoretical peak set and remains fixed. This program may be run on many
+// different inputs representing many different observed spectra. The input to
+// the generated program consists of the cached vectors for an observed peak set
+// (as described in spectrum_preprocess.h).
+//
+// The generated program has a very simple form: it simply adds together certain
+// specific cache entries specified by an index, and subtracts others. The
+// correct cache index is given by a specific theoretical peak. The cache
+// contents will have been determined during spectrum preprocessing (see
+// spectrum_preprocess.h).
+//
+// The programs for all peptides in the ActivePeptideQueue appear
+// consecutively in memory, (but see caveat about FifoAllocator below) and are
+// all run, one right after the other, on the same input. The input is a
+// buffer pointing to the cache for the observed spectrum. Each program writes
+// an entry to an output buffer with a pair (score, counter). A counter is
+// initialized with the number of candidate peptides to score.
+//
+// The generated code is roughly equivalent to the following C code (the array
+// indices are for illustration, the actual values are determined by the code
+// generator for the particluar candidate peptide's theoretical peak set):
+//
+// *outputbuf++ = cache[72] + cache[195] - cache[546] + ...
+// *outputbuf++ = counter;
+// if (--counter == 0) return;
+// *outputbuf++ = cache[90] + cache[108] + cache[125] + ...
+// *outputbuf++ = counter;
+// if (--counter == 0) return;
+// *outputbuf++ = cache[32]] - cache[42] - cache[321] + ...
+// *outputbuf++ = counter;
+// if (--counter == 0) return;
+// ...
+//
+// As new peptides enter the ActivePeptideQueue the above program is extended.
+// As "older" (lighter) peptides are dequeued and discarded corresponding
+// early lines of the generated program are discarded. Each Peptide maintains
+// a pointer to begining of its corresponding line of generated code. A
+// FifoAllocator manages memory for the generated instructions. When the end
+// of a FifoAllocator page is reached, a jump instruction is inserted to
+// continue execution at the next FifoAllocator page.
+//
+// The compiler here generates x86 code, and assumes cache entries are 32-bit
+// integers. Each program assumes the following upon entry:
+//
+// Register ECX contains the counter i.e. the number of peptides yet to be
+// scored. When ECX = 0 control returns to the caller.
+//
+// Register EDI (RDI on 64-bit machines) points to a buffer where the
+// output of the current program will go (outputbuf in the illustrative C
+// code above).
+//
+// Register EDX points to the cached vectors for an observed peak set
+// (cache in the illustrative C code above).
+//
+// For illustration the first three lines of the above C code would be compiled as follows:
+//
+// mov (%edx+288), %eax // EAX = cache[72] (since 288 == 72 * 4)
+// add (%edx+780), %eax // EAX += cache[195] (since 780 == 195 * 4)
+// sub (%edx+2184), %eax // EAX -= cache[546] (since 2184 == 546 * 4)
+// ...
+// stosl // equivalent to mov %eax, (%edi); inc %edi; (*outputbuf++=%eax)
+// mov %ecx, %eax
+// stosl // equivalent to mov %eax, (%edi); inc %edi; (*outputbuf++=%ecx)
+// loop +1 // equivalent to dec %ecx; if (ecx != 0) skip one instruction
+// ret
+// ... (next program here)
+
+#ifndef COMPILER_H
+#define COMPILER_H
+
+#include <stdint.h>
+
+class TheoreticalPeakCompiler {
+ public:
+ explicit TheoreticalPeakCompiler(FifoAllocator* fifo_alloc)
+ : fifo_alloc_(fifo_alloc), last_alloc_end_(NULL) {
+ // fifo_alloc_ will make room for generated programs.
+ }
+
+ void* Init(int pos_size, int neg_size) {
+ // Init() gets called once per candidate peptide.
+ // pos_size is the number of cache entries to be added together, neg_size
+ // is the number to be subtracted.
+ // add or sub instructions take six bytes. The coda (containing the
+ // storage of results etc.) takes seven bytes.
+ int total_size = 6*(pos_size + neg_size) + 7;
+ pos_ = (unsigned char*) fifo_alloc_->New(total_size);
+ // last_alloc_end points just beyond the last allocated program. By the
+ // end of this block, we will ensure that there is enough room for a five
+ // byte jump instruction in case current program didn't end up being
+ // allocated right after the old.
+ if (pos_ == last_alloc_end_) { // Are programs consecutive?
+ last_alloc_end_ = pos_ + total_size;
+ pos_ -= jmp_size; // Last prog. didn't need room for jump instruction.
+ } else { // Progs. not consecutive. Old prog. needs to jump to new prog.
+ // Above allocation wasn't enough. Need room for jump.
+ fifo_alloc_->Unalloc(total_size);
+ total_size += jmp_size;
+ pos_ = (unsigned char*) fifo_alloc_->New(total_size);
+ if (last_alloc_end_ != NULL)
+ AddJump(last_alloc_end_ - jmp_size, pos_);
+ last_alloc_end_ = pos_ + total_size;
+ }
+ first_ = true; // first theoretical peak gets handled a bit differently.
+ return pos_;
+ }
+
+ // The following three functions assume peaks unsorted, and check that each peak
+ // doesn't point past end of cache.
+
+ void AddPositive(const TheoreticalPeakArr& peaks) {
+ // Write an add instruction for each entry in peaks.
+ int end = MaxBin::Global().CacheBinEnd() * NUM_PEAK_TYPES;
+ for (int i = 0; i < peaks.size(); ++i)
+ if (peaks[i].Code() < end)
+ AddPositive(peaks[i].Code());
+ }
+
+ void AddPositive(const google::protobuf::RepeatedField<int>& peaks) {
+ // Write an add instruction for each entry in peaks.
+ int end = MaxBin::Global().CacheBinEnd() * NUM_PEAK_TYPES;
+ int total = 0;
+ google::protobuf::RepeatedField<int>::const_iterator i = peaks.begin();
+ for (; i != peaks.end(); ++i) {
+ if ((total += *i) >= end)
+ break;
+ AddPositive(total);
+ }
+ }
+
+ void AddNegative(const google::protobuf::RepeatedField<int>& peaks) {
+ // Write a sub instruction for each entry in peaks.
+ int end = MaxBin::Global().CacheBinEnd() * NUM_PEAK_TYPES;
+ int total = 0;
+ google::protobuf::RepeatedField<int>::const_iterator i = peaks.begin();
+ for (; i != peaks.end(); ++i) {
+ if ((total += *i) >= end)
+ break;
+ AddNegative(total);
+ }
+ }
+
+ void Done() {
+ // Write the coda instructions which will store results and update
+ // counter. See comments above.
+ // Poke machine code into the next 7 bytes at pos_.
+ // (int*) pos_ must be a four byte pointer!
+ *((int*) pos_) = 0xc889ab; // stosl; mov %ecx, %eax
+ *((int*) (pos_+3)) = 0xc301e2ab; // stosl; loop +1; ret
+ assert(pos_ + 7 + jmp_size <= last_alloc_end_); // There should still be room
+ // for a jump if needed
+ last_alloc_end_ = pos_ + 7 + jmp_size;
+ fifo_alloc_->Unalloc(last_alloc_end_);
+ }
+
+ private:
+ // Various x86 instructions we need.
+ static const uint16_t add_to_eax_at_edx_plus = 33283;
+ static const uint16_t mov_to_eax_at_edx_plus = 33419;
+ static const uint16_t sub_from_eax_at_edx_plus = 33323;
+ static const unsigned char ret = 195;
+ static const unsigned char jmp_relative = 233;
+
+ static const int jmp_size = 5;
+
+ void AddPositive(int peak) {
+ if (first_) { // First theoretical peak uses a 'mov' rather than an 'add'
+ *((uint16_t*) pos_) = mov_to_eax_at_edx_plus;
+ } else {
+ *((uint16_t*) pos_) = add_to_eax_at_edx_plus;
+ }
+ first_ = false;
+ pos_ += 2;
+ *((int*) pos_) = peak << 2; // Store 4 * the peak position.
+ pos_ += 4;
+ }
+
+ void AddNegative(int peak) {
+ *((uint16_t*) pos_) = sub_from_eax_at_edx_plus;
+ pos_ += 2;
+ *((int*) pos_) = peak << 2; // Store 4 * the peak position.
+ pos_ += 4;
+ }
+
+ static void AddJump(unsigned char* pos, unsigned char* whereto) {
+ int diff = whereto - (pos + jmp_size);
+ *pos++ = jmp_relative;
+ *((int*) pos) = diff;
+ }
+
+ FifoAllocator* fifo_alloc_;
+ unsigned char* last_alloc_end_;
+ unsigned char* pos_; // "cursor position" as we write out instructions.
+ bool first_;
+};
+
+#endif // COMPILER_H
diff --git a/src/app/tide/crux_sp_spectrum.cc b/src/app/tide/crux_sp_spectrum.cc
new file mode 100644
index 0000000..6afba4f
--- /dev/null
+++ b/src/app/tide/crux_sp_spectrum.cc
@@ -0,0 +1,283 @@
+// Tahmina Baker
+//
+// This file contains implementations for the classes defined in
+// crux_sp_spectrum.h. Please see the header file for details.
+
+#include <math.h>
+#include "crux_sp_spectrum.h"
+
+SpSpectrum::SpSpectrum(const Spectrum& spectrum, int charge, double max_mz)
+ : beta_(0.075), max_intensity_(0.0), last_idx_(0) {
+ max_mz_ = MassConstants::mass2bin(max_mz);
+ intensity_array_ = new double[IntensityArraySize()];
+ memset(intensity_array_, 0, sizeof(double)*IntensityArraySize());
+
+ PreprocessSpectrum(spectrum, charge);
+}
+
+SpSpectrum::~SpSpectrum() {
+ delete [] intensity_array_;
+}
+
+void SpSpectrum::PreprocessSpectrum(const Spectrum& spectrum, int charge) {
+ double precursor_mz = spectrum.PrecursorMZ();
+ double experimental_mass_cut_off = precursor_mz*charge + 50;
+ double max_intensity = 0;
+
+ for (int i = 0; i < spectrum.Size(); ++i) {
+ double peak_location = spectrum.M_Z(i);
+
+ // skip all peaks larger than experimental mass
+ if(peak_location > experimental_mass_cut_off)
+ continue;
+
+ // skip all peaks within precursor ion mz +/- 15
+ if((peak_location < precursor_mz + 15) &&
+ (peak_location > precursor_mz - 15))
+ continue;
+
+ // map peak location to bin
+ int bin = MassConstants::mass2bin(peak_location);
+ double intensity = sqrt(spectrum.Intensity(i));
+
+ // set intensity in array with correct mz, only if max peak in the bin
+ if(intensity_array_[bin] < intensity) {
+ intensity_array_[bin] = intensity;
+
+ // check if max_intensity
+ if(intensity > max_intensity)
+ max_intensity = intensity;
+ }
+
+ // set last idx to the largest added peak mz value
+ if(last_idx_ < bin)
+ last_idx_ = bin;
+ }
+
+ // set max_intensity
+ max_intensity_ = max_intensity;
+
+ NormalizeIntensityArray(100);
+
+ SmoothPeaks();
+
+ ZeroPeaks();
+
+ // Sequest28 modifications.
+ // Determine number of top peaks to select based on the experimental mass
+ // In Sequest27, the top peaks were always selected as 200.
+ // Keep top ions of square-root(16*experimental mass) ranking, but not
+ // exceeding 200 ions.
+ int top_bins = 200;
+ if(experimental_mass_cut_off-50 < 3200){
+ // top bins are sqrt of 16* experimental mass
+ top_bins = (int)(sqrt((experimental_mass_cut_off-50)*16) + 0.5);
+ // however cannot exceed 200
+ if(top_bins > 200){
+ top_bins = 200;
+ }
+ }
+ else{
+ top_bins = (int)((experimental_mass_cut_off-50)/14.00);
+ }
+
+ // extract the top ions
+ ExtractPeaks(top_bins);
+
+ // equalize peaks
+ EqualizePeaks();
+}
+
+void SpSpectrum::NormalizeIntensityArray(double threshold) {
+ // return if max_intensity is 0
+ if(max_intensity_ < 0.00001)
+ return;
+
+ // normalize all peaks
+ for(int mz_idx = 0; mz_idx < last_idx_ + 1; ++mz_idx) {
+ intensity_array_[mz_idx] = intensity_array_[mz_idx] *
+ threshold / max_intensity_;
+ }
+}
+
+void SpSpectrum::SmoothPeaks() {
+ // create a new array, which will replace the original intensity array
+ double* new_array = new double[IntensityArraySize()];
+ memset(new_array, 0, sizeof(double)*IntensityArraySize());
+
+ // iterate over all peaks
+ for(int idx = 2; idx < IntensityArraySize()-2; ++idx) {
+ // smooooth
+ new_array[idx] = (intensity_array_[idx-2] + 4*intensity_array_[idx-1] +
+ 6*intensity_array_[idx] + 4*intensity_array_[idx+1] +
+ intensity_array_[idx+2])/16;
+
+ // set last idx in the array
+ if(last_idx_ < idx && new_array[idx] == 0) {
+ last_idx_ = idx -1;
+ break;
+ }
+ }
+
+ delete [] intensity_array_;
+ intensity_array_ = new_array;
+}
+
+void SpSpectrum::ZeroPeaks() {
+ // create a new array, which will replace the original intensity array
+ double* new_array = new double[IntensityArraySize()];
+ memset(new_array, 0, sizeof(double)*IntensityArraySize());
+
+ // step 1,
+ ZeroPeakMeanStdev(1, new_array);
+
+ // step 2,
+ ZeroPeakMeanStdev(2, new_array);
+
+ delete[] intensity_array_;
+ intensity_array_ = new_array;
+}
+
+void SpSpectrum::ExtractPeaks(int top_rank) {
+ // copy all peaks to temp_array
+ double* temp_array = new double[IntensityArraySize()];
+ memset(temp_array, 0, sizeof(double)*IntensityArraySize());
+ int temp_idx = 0;
+ for(int idx = 0; idx < IntensityArraySize(); ++idx){
+ if(intensity_array_[idx] > 0){
+ temp_array[temp_idx] = intensity_array_[idx];
+ ++temp_idx;
+ }
+ }
+
+ // if there's over top_rank peaks, keep only top_rank peaks
+ // quick sort
+ QuickSort(temp_array, temp_idx);
+
+ // set max and cut_off
+ double max_intensity = temp_array[0];
+ double cut_off = temp_array[top_rank-1];
+
+ // remove peaks bellow cut_off
+ // also, normalize peaks to max_intensity to 100
+ for(int idx = 0; idx < IntensityArraySize(); ++idx) {
+ if(intensity_array_[idx] > 0) {
+ if(intensity_array_[idx] < cut_off) {
+ // If it's below cutoff, remove peak
+ intensity_array_[idx] = 0;
+ } else {
+ // nomalize peak to max 100
+ intensity_array_[idx] = intensity_array_[idx] / max_intensity * 100;
+ }
+ }
+ }
+
+ delete [] temp_array;
+}
+
+void SpSpectrum::EqualizePeaks()
+{
+ // equalize peaks to it's greatest intensity
+ // should use array size, but sequest seems to have a bug
+ // last idx is thus, modification to fit sequest
+ // consequences are we will not equalize the very last peak.
+ double max_intensity = 0;
+ int end_idx = 0;
+ int last_idx = IntensityArraySize();
+ for(int idx = 0; idx < last_idx; ++idx) {
+ // are we inside a continous block?
+ if(intensity_array_[idx] > 0){
+ max_intensity = intensity_array_[idx];
+ end_idx = idx + 1;
+
+ // loop to find the largest peak in the continuous block
+ while(end_idx < last_idx && intensity_array_[end_idx] > 0) {
+ // reset max intensity
+ if(intensity_array_[end_idx] > max_intensity)
+ max_intensity = intensity_array_[end_idx];
+
+ ++end_idx;
+ }
+
+ // set all peaks in block to max_intensity
+ for(; idx < end_idx; ++idx)
+ intensity_array_[idx] = max_intensity;
+ }
+ }
+}
+
+double SpSpectrum::GetIntensityArrayMean(int peak_idx, int* peak_count) {
+ // set upper bound
+ int end_idx = peak_idx + 50;
+ if(peak_idx + 50 >= IntensityArraySize())
+ end_idx = IntensityArraySize()-1;
+
+ // set start index
+ int start_idx = peak_idx - 50;
+ if(peak_idx - 50 <= 0)
+ start_idx = 0;
+
+ // sum up the intensities
+ double total_intensity = 0;
+ for(; start_idx <= end_idx; ++start_idx) {
+ ++*peak_count;
+ total_intensity += intensity_array_[start_idx];
+ }
+
+ // BUG! it should divide by 101 but Sequest uses 100
+ return (total_intensity / (*peak_count-1));
+}
+
+double SpSpectrum::GetIntensityArrayStdev(int peak_idx, double mean,
+ int peak_count) {
+ // set upper bound
+ int end_idx = peak_idx + 50;
+ if(peak_idx + 50 >= IntensityArraySize())
+ end_idx = IntensityArraySize()-1;
+
+ // set start index
+ int start_idx = peak_idx - 50;
+ if(peak_idx - 50 <= 0)
+ start_idx = 0;
+
+ // sum up the intensities
+ double variance = 0;
+ double dev = 0;
+ for(; start_idx <= end_idx; ++start_idx){
+ // sum up all deviations squared
+ dev = intensity_array_[start_idx] - mean;
+ variance += (dev*dev);
+ }
+
+ // return the stdev
+ return sqrt(variance/peak_count);
+}
+
+void SpSpectrum::ZeroPeakMeanStdev(int step, double* new_array) {
+ // iterate over all peaks
+ double mean = 0;
+ double stdev = 0;
+ int peak_count = 0;
+ for(int idx = 0; idx < IntensityArraySize(); ++idx){
+ peak_count = 0;
+
+ // get mean
+ mean = GetIntensityArrayMean(idx, &peak_count);
+
+ // get stdev
+ stdev = GetIntensityArrayStdev(idx, mean, peak_count);
+
+ // iterate over all positions and extract peaks
+ if(intensity_array_[idx] > (mean + step*stdev)) {
+ new_array[idx] = intensity_array_[idx] - (mean - stdev);
+
+ // reset the last idx
+ if(last_idx_ < idx)
+ last_idx_ = idx;
+
+ // for only step 1, zero out original peak
+ if(step == 1)
+ intensity_array_[idx] = 0;
+ }
+ }
+}
diff --git a/src/app/tide/crux_sp_spectrum.h b/src/app/tide/crux_sp_spectrum.h
new file mode 100644
index 0000000..4c30eea
--- /dev/null
+++ b/src/app/tide/crux_sp_spectrum.h
@@ -0,0 +1,149 @@
+// Tahmina Baker
+//
+// The code in this file is pretty much a direct copy of the 2009 version of
+// crux's "create_intensity_array_sp" and related functions in scorer.c.
+//
+// The code preprocesses a spectrum for sp calculations as follows:
+// 1. Create an intensity array for the spectrum to be indexed via m/z bin
+// 2. Normalize the array so that maximum peak equals 100
+// 3. Smooth the peaks in the array
+// 4. Extract peaks that are larger than mean + #step*stdev into new array,
+// zero out the peaks that have been extracted, repeat twice, then replace
+// old array with extracted peak array
+// 5. Extract peaks up to top rank peaks remove other peaks, do second
+// normalization on the top peaks back to max 100 intensity, and replace old
+// array with normalized top peak array.
+// 6. Equalize all peaks in a continous region to the largest peak within the
+// continous bins from left to right.
+//
+// The following major modifications were made when the code was ported over:
+// 1. Functions were renamed to follow Tide conventions.
+// E.g. "PreprocessSpectrum" performs the same function as crux's
+// "create_intensity_array_sp".
+// 2. Crux uses the data structure SCORER_T to calculate different types of
+// scores represented by SCORER_TYPE_T, whereas the code here is specific
+// to sp calculations. The SpSpectrum class is equivalent to a crux SCORER_T
+// struct of SCORER_TYPE_T=SP, with only the following subset of data:
+// sp_beta, sp_max_mz, intensity_array, max_intensity, last_idx.
+// 3. SpSpectrum is a private class that preprocesses a given spectrum on
+// creation using private methods, then ONLY exposes the pieces of
+// information needed by the creator. In crux, the static function
+// "create_intensity_array_sp" processes a given spectrum with other static
+// helper functions, then populates an SCORER_T public struct.
+// 4. Tide stores spectrum peak information slightly differently than crux;
+// changes were made to the code to traverse peaks and access peak data.
+// 5. SpSpectrum::SmoothPeaks() is specific to SP calculations while crux's
+// "smooth_peaks" function can handle various types of scores represented
+// by SCORER_TYPE_T.
+// 6. The "double" data type was used in place of crux's "FLOAT_T".
+
+
+#ifndef CRUX_SP_SPECTRUM_H
+#define CRUX_SP_SPECTRUM_H
+
+#include "mass_constants.h"
+#include "spectrum_collection.h"
+#include "spectrum_preprocess.h"
+#include "util/utils.h"
+
+
+class SpSpectrum {
+ public:
+ SpSpectrum(const Spectrum& spectrum, int charge, double max_mz);
+ ~SpSpectrum();
+
+ double Intensity(int index) const { return intensity_array_[index]; }
+ double Beta() const { return beta_; }
+ double TotalIonIntensity() {
+ double total_ion_intensity = 0.0;
+ for (int i = 0; i < IntensityArraySize(); i++)
+ total_ion_intensity += intensity_array_[i];
+ return total_ion_intensity;
+ }
+
+ private:
+
+ void PreprocessSpectrum(const Spectrum& spectrum, int charge);
+
+ // Normalizes array so that maximum peak equals threshold
+ void NormalizeIntensityArray(double threshold);
+
+ // Smooth all peaks in intensity array and replace the original array with
+ // the newly smooothed array.
+ void SmoothPeaks();
+
+ // Zero and extract peaks:
+ // Extract peaks that are larger than mean + #step*stdev into new array
+ // Zero out the peaks that have been extracted
+ // Repeat twice, then replace old array with extracted peak array
+ void ZeroPeaks();
+
+ // Keep only the peaks up to top rank peaks remove other peaks.
+ // Do second normalization on the top peaks back to max 100 intensity.
+ // Replace old array with normalized top peak array.
+ void ExtractPeaks(int top_rank);
+
+ // Equalize all peaks in a continous region to the largest peak within the
+ // continous bins from left to right
+ void EqualizePeaks();
+
+ // Get the mean of intensity in array within +/- 50 mz of the working peak.
+ double GetIntensityArrayMean(int peak_idx, int* peak_count);
+
+ // Get the stdev of intensity in array within +/- 50 mz of the working peak
+ double GetIntensityArrayStdev(int peak_idx, double mean, int peak_count);
+
+ // Helper to "zero and extract peaks". The fact that a peak has removed will
+ // affect the following peaks.
+ void ZeroPeakMeanStdev(int step, double* new_array);
+
+ int IntensityArraySize() {
+ return (int)max_mz_ + 1;
+ }
+
+ void SwapQuick(double* a, int idx, int jdx) {
+ double temp = 0;
+ temp = a[idx];
+ a[idx] = a[jdx];
+ a[jdx] = temp;
+ }
+
+ int Random(int i, int j) {
+ return i + myrandom_limit(j-i+1);
+ }
+
+ void QuickSort(double a[], int left, int right) {
+ int last = left, i;
+
+ if (left >= right) return;
+
+ SwapQuick(a, left, Random(left, right));
+ for (i = left + 1; i <= right; i++)
+ if (a[i] > a[left]) /// CHECK THIS!!
+ SwapQuick(a, ++last, i);
+ SwapQuick(a, left, last);
+ QuickSort(a, left, last-1);
+ QuickSort(a, last+1, right);
+ }
+
+ void QuickSort(double a[], int array_size) {
+ QuickSort(a, 0, array_size-1);
+ }
+
+ // The beta variable = 0.075
+ double beta_;
+
+ // The max mz for the intensity array
+ double max_mz_;
+
+ // Intensity array that can be indexed using the m/z bin
+ double* intensity_array_;
+
+ // the max intensity in the intensity array
+ double max_intensity_;
+
+ // the last index in the array, the data size of the array
+ int last_idx_;
+};
+
+#endif // CRUX_SP_SPECTRUM_H
diff --git a/src/app/tide/fifo_alloc.cc b/src/app/tide/fifo_alloc.cc
new file mode 100644
index 0000000..4a36bac
--- /dev/null
+++ b/src/app/tide/fifo_alloc.cc
@@ -0,0 +1,172 @@
+// Benjamin Diament
+//
+// A FifoPage represents a large block of memory allocated at the system level.
+// We currently use mmap and munmap to get system memory.
+// FifoPage also contains a pointer to "next page" which induces a circular linked list
+// (i.e. the last page points to the first).
+// Schematically, we have the following,
+//
+// FreePage1-->FreePage2-->...-->FreePageM-->UsedPage1-->UsedPage2-->...-->UsedPageN--+
+// ^ |
+// +-------------------------------------<------------------------------------------+
+//
+// current_page_ points to UsedPageN, and first_page_ points to UsedPage1.
+//
+// A system call to obtain new memory will occur whenever total allocations
+// exceed a page's worth.
+// Pages become available for reuse when all contents are Release()'d.
+//
+// On Linux we use mmap to allocate memory and we mark the page as executable
+// to provide run-time compilation of dot product calculations.
+
+#include <sys/types.h>
+#ifdef _MSC_VER
+#include "mman.h"
+#else
+#include <sys/mman.h>
+#endif
+#include<stdlib.h>
+#include<assert.h>
+#include<iostream>
+#include "fifo_alloc.h"
+
+using namespace std;
+
+#ifndef MAP_ANONYMOUS
+#define MAP_ANONYMOUS MAP_ANON
+#endif
+
+#ifdef MMAP_SENTINEL_CHECK
+#undef NASSERT
+#define SENTINEL_DATA_SIZE 100
+#define SENTINEL_VALUE 0xAF
+
+void FillSentinel(void* p, size_t size) {
+ memset(p, SENTINEL_VALUE, size);
+}
+
+void CheckSentinel(void* p, size_t size) {
+ for (size_t i = 0; i < size; ++i)
+ CHECK(((char *) p)[i] == (char) SENTINEL_VALUE);
+}
+
+void* FifoPage::GetPage(size_t size) {
+ // protections to allow exec (see above)
+ int mmap_prot_mode = PROT_READ | PROT_WRITE | PROT_EXEC;
+ // for sentinel data before and after
+ size_t size_with_sentinels = size + 2 * SENTINEL_DATA_SIZE;
+ void* p = mmap(0, size_with_sentinels, mmap_prot_mode,
+ MAP_PRIVATE | MAP_ANONYMOUS, -1, 0);
+ if (p == NULL) {
+ cerr << "Failed to allocate FifoPage of size " << size << ". Aborting\n";
+ abort();
+ }
+ FillSentinel(p, SENTINEL_DATA_SIZE);
+ FillSentinel((char *) p + size + SENTINEL_DATA_SIZE, SENTINEL_DATA_SIZE);
+ void* tmp = (char *) p + SENTINEL_DATA_SIZE;
+ // return (char *) p + SENTINEL_DATA_SIZE;
+ cerr << "mmap'ed page at " << tmp << endl;
+ return tmp;
+}
+
+void FifoPage::DeletePage(void* page, size_t size) {
+ CheckSentinel((char *) page - SENTINEL_DATA_SIZE, SENTINEL_DATA_SIZE);
+ CheckSentinel((char *) page + size, SENTINEL_DATA_SIZE);
+ cerr << "munmap'ed " << page << endl;
+ munmap((char *) page - SENTINEL_DATA_SIZE, size + 2 * SENTINEL_DATA_SIZE);
+}
+#else // MMAP_SENTINEL_CHECK
+void* FifoPage::GetPage(size_t size) {
+ // protections to allow exec (see above)
+ int mmap_prot_mode = PROT_READ | PROT_WRITE | PROT_EXEC;
+ void* p = mmap(0, size, mmap_prot_mode, MAP_PRIVATE | MAP_ANONYMOUS, -1, 0);
+ if (p == NULL) {
+ cerr << "Failed to allocate FifoPage of size " << size << ". Aborting\n";
+ abort();
+ }
+ return p;
+}
+
+void FifoPage::DeletePage(void* page, size_t size) {
+ munmap(page, size);
+}
+#endif // MMAP_SENTINEL_CHECK
+
+void* FifoAllocator::FallbackNew(size_t amount) {
+ // Check if a free page is already in our linked list.
+ FifoPage* free_page = current_page_->Next();
+ if (free_page == first_page_) { // No free page in linked list
+ FifoPage* new_page = new FifoPage(page_size_);
+ current_page_->InsertPage(new_page);
+ current_page_ = new_page;
+ } else {
+ current_page_ = free_page;
+ }
+ assert(current_page_->Empty());
+
+ if (amount > page_size_) { // CONSIDER: eliminate this restriction.
+ cerr << "Requested " << amount << " bytes from FifoAllocator, "
+ << "but page size is " << page_size_ << ". Aborting\n";
+ abort();
+ return NULL;
+ }
+
+ void* result = current_page_->New(amount);
+ assert(result != NULL);
+ return result;
+}
+
+void FifoAllocator::Release(void* first_used) {
+ // Release everything up to, but not including, first_used.
+ while (!first_page_->InPage(first_used)) {
+ if (first_page_ == current_page_) {
+ if (first_page_->AtEnd(first_used)) {
+ first_page_->Clear();
+ return;
+ }
+ // Show();
+ cerr << "Attempted release of address not in FifoAllocator range.\n";
+ abort();
+ }
+ first_page_->Clear();
+ first_page_ = first_page_->Next();
+ }
+ if (first_page_->AtEnd(first_used)) {
+ first_page_->Clear();
+ first_page_ = first_page_->Next();
+ }
+}
+
+void FifoAllocator::ReleaseAll() {
+ while (true) {
+ first_page_->Clear();
+ if (first_page_ == current_page_)
+ break;
+ first_page_ = first_page_->Next();
+ }
+}
+
+FifoAllocator::~FifoAllocator() {
+ FifoPage* page = current_page_;
+ do {
+ FifoPage* next = page->Next();
+ delete page;
+ page = next;
+ } while (page != current_page_);
+}
+
+void FifoAllocator::Show() {
+ FifoPage* page = first_page_;
+ while(true) {
+ page->Show();
+ if (page == current_page_)
+ break;
+ fprintf(stderr, " --> ");
+ page = page->Next();
+ }
+ fprintf(stderr, "\n");
+}
+
+#ifdef MEM_STATS
+size_t FifoAllocator::total_ = 0;
+#endif
diff --git a/src/app/tide/fifo_alloc.h b/src/app/tide/fifo_alloc.h
new file mode 100644
index 0000000..80d9e7c
--- /dev/null
+++ b/src/app/tide/fifo_alloc.h
@@ -0,0 +1,152 @@
+// Benjamin Diament
+//
+// Memory allocator for FIFO usage pattern: client may allocate arbitrarily
+// sized blocks sequentially. A pointer p is returned to each new block.
+// Subsequently a call to Release(p) frees all allocations prior to (not including)
+// allocation of p. It's not possible to free blocks in any order other than that
+// in which they were allocated. This prevents fragmentation but is only appropriate
+// for FIFO usage patterns, e.g. data assocatied with a queue.
+//
+// A page size, S, is supplied to the FifoAllocator constructor.
+// At most 2 * S extra memory will be allocated.
+//
+// Not thread safe! (TODO 254)
+//
+// Unalloc() allows you to deallocate the most recently allocated pointer.
+//
+// Example usage:
+// FifoAllocator alloc(1 << 20); // 1MB page size
+// void* a = alloc.New(15); // Allocate 15 bytes
+// void* b = alloc.New(27000); // Allocate 27000 bytes
+// void* c = alloc.New(150); // Allocate 150 bytes
+// void* d = alloc.New(150); // Allocate 150 bytes
+// void* e = alloc.New(150); // Allocate 150 bytes
+// alloc.Release(c); // Release a and b, but preserve c, d, e.
+// alloc.Unalloc(e); // Free from e onward. (c, d still intact)
+
+#ifndef FIFO_ALLOC_H
+#define FIFO_ALLOC_H
+
+//#define MEM_STATS 1
+
+#include<assert.h>
+#include<stdio.h>
+
+// Used by FifoAllocator; probably not useful alone. See .cc file.
+class FifoPage {
+ public:
+ explicit FifoPage(size_t size)
+ : size_(size),
+ page_((char*) GetPage(size)),
+ end_(page_ + size_),
+ next_(this),
+ end_used_(page_),
+ last_amt_(0) {
+ }
+
+ ~FifoPage() { DeletePage(page_, size_); }
+
+ void Clear() { end_used_ = page_; }
+ bool Empty() const { return end_used_ == page_; }
+
+ void* New(size_t amount) {
+ assert(amount >= 0);
+ if (end_used_ + amount > end_)
+ return NULL;
+ void* pos = end_used_;
+ end_used_ += amount;
+ last_amt_ = amount;
+ return pos;
+ }
+
+ void Unalloc(size_t amount) {
+ assert(amount <= last_amt_);
+ last_amt_ -= amount;
+ end_used_ -= amount;
+ }
+
+ void Unalloc(void* pos) {
+ assert(pos <= end_used_);
+ Unalloc(end_used_ - (char*) pos);
+ }
+
+ void InsertPage(FifoPage* succ) {
+ succ->next_ = next_;
+ next_ = succ;
+ }
+
+ FifoPage* Next() { return next_; }
+
+ bool InPage(void* ptr) {
+ return ((char*) ptr >= page_ && (char*) ptr < end_used_);
+ }
+
+ bool AtEnd(void* ptr) {
+ return ((char*) ptr == end_used_);
+ }
+
+ // For debugging
+ void Show() {
+ fprintf(stderr, "page[%p, )%p %p]", page_, end_used_, end_);
+ }
+
+ private:
+ size_t size_;
+ char* page_;
+ char* end_;
+ FifoPage* next_;
+ char* end_used_;
+ size_t last_amt_;
+
+ static void* GetPage(size_t size);
+ static void DeletePage(void* page, size_t size);
+};
+
+
+class FifoAllocator {
+ public:
+ explicit FifoAllocator(size_t page_size) : page_size_(page_size) {
+ current_page_ = new FifoPage(page_size_);
+ first_page_ = current_page_;
+ }
+
+ ~FifoAllocator();
+
+ void* New(size_t amount) {
+#ifdef MEM_STATS
+ total_ += amount;
+#endif
+ void* result = current_page_->New(amount);
+ if (result != NULL)
+ return result;
+
+ // No more room in current page, get another page.
+ return FallbackNew(amount);
+ }
+
+ void Release(void* first_used);
+ void ReleaseAll();
+
+ void Unalloc(size_t amount) { current_page_->Unalloc(amount); }
+ void Unalloc(void* pos) { current_page_->Unalloc(pos); }
+
+ void Show();
+
+#ifdef MEM_STATS
+ static size_t Total() { return total_; }
+#endif
+
+ private:
+ // Called when current page full
+ void* FallbackNew(size_t amount);
+
+ size_t page_size_;
+ FifoPage* first_page_;
+ FifoPage* current_page_;
+
+#ifdef MEM_STATS
+ static size_t total_;
+#endif
+};
+
+#endif // FIFO_ALLOC_H
diff --git a/src/app/tide/fixed_cap_array.h b/src/app/tide/fixed_cap_array.h
new file mode 100644
index 0000000..ae32e86
--- /dev/null
+++ b/src/app/tide/fixed_cap_array.h
@@ -0,0 +1,80 @@
+// Benjamin Diament
+
+// Class to represent a sized array, but with constant capacity, for
+// speed. No bounds checking or other checking is performed.
+//
+// In FixedCapacityArray size_ always represents the client's interpretation
+// of the number of elements in the array while capacity supplied to Init()
+// never changes.
+// The vector<> template has the problem that if you shrink the size then the
+// the excess capacity will be freed. If later the array grows an allocation
+// is performed. I couldn't find another way around this inefficiency.
+//
+// iterator supplied to match vector<> template usage.
+//
+// Init() will permit optional use of a FifoAllocator for allocation.
+
+#ifndef FIXED_CAP_ARRAY_H
+#define FIXED_CAP_ARRAY_H
+
+#include "fifo_alloc.h"
+
+template <class C>
+class FixedCapacityArray {
+ public:
+ explicit FixedCapacityArray(int capacity)
+ : data_(new C[capacity]), size_(0), del_(true) {
+ }
+
+ // must call Init before use
+ FixedCapacityArray()
+ : data_(NULL),
+ size_(0),
+ del_(true) {
+ }
+
+ void Init(int capacity) { data_ = new C[capacity]; }
+
+ void Init(FifoAllocator* fifo_alloc, int capacity) {
+ if (fifo_alloc == NULL) {
+ Init(capacity);
+ return;
+ }
+ void* buffer = fifo_alloc->New(capacity * sizeof(C));
+ data_ = (C*) buffer;
+ del_ = false;
+ }
+
+ ~FixedCapacityArray() { if (del_) delete[] data_; }
+
+ void clear() { size_ = 0; }
+
+ bool empty() const { return size_ == 0; }
+
+ C operator[](int index) const { return data_[index]; }
+ C& operator[](int index) { return data_[index]; }
+
+ C* data() { return data_; }
+ int size() const { return size_; }
+ void set_size(int size) { size_ = size; }
+
+ void push_back(const C& elt) { data_[size_++] = elt; }
+ C back() { return data_[size_-1]; }
+
+ typedef C* iterator;
+ typedef const C* const_iterator;
+
+ iterator begin() { return data_; }
+ iterator end() { return data_ + size_; }
+ const_iterator begin() const { return data_; }
+ const_iterator end() const { return data_ + size_; }
+
+ private:
+ C* data_;
+ int size_;
+
+ bool del_; // True if new/delete used. False if FifoAllocator used,
+ // in which case client deallocates.
+};
+
+#endif // FIXED_CAP_ARRAY_H
diff --git a/src/app/tide/index_settings.cc b/src/app/tide/index_settings.cc
new file mode 100644
index 0000000..ba988d6
--- /dev/null
+++ b/src/app/tide/index_settings.cc
@@ -0,0 +1,75 @@
+#include <string>
+#include <gflags/gflags.h>
+#include "header.pb.h"
+#include "records.h"
+#include "modifications.h"
+#include "mass_constants.h"
+
+using namespace std;
+
+#define CHECK(x) GOOGLE_CHECK(x)
+
+DEFINE_double(min_mass, 200, "Peptide mass inclusion threshold");
+DEFINE_double(max_mass, 7200, "Peptide mass inclusion threshold");
+DEFINE_int32(min_length, 6, "Peptide length inclusion threshold");
+DEFINE_int32(max_length, 50, "Peptide length inclusion threshold");
+
+DEFINE_string(enzyme, "none", "Digestion enzyme. May be none, trypsin, "
+ "chymotrypsin, elastase, clostripain, cyanogen-bromide, "
+ "idosobenzoate, proline-endopeptidase, staph-protease, "
+ "modified-chymotrypsin, elastase-trypsin-chymotrypsin, "
+ "aspn.");
+DEFINE_string(digestion, "full-digest", "Digestion completeness. "
+ "May be full-digest or partial-digest.");
+DEFINE_int32(max_missed_cleavages, 0, "Maximum number of missed cleavages to "
+ "allow in enzymatic digestion.");
+DEFINE_bool(monoisotopic_precursor, false, "Use monoisotopic precursor masses "
+ "rather than average masses for residues.");
+
+DEFINE_string(mods_spec, "", "Expression for static modifications to include. "
+ "Specify a comma-separated list of the form --mods=C+57.0,...");
+DEFINE_string(mods_table, "", "Modification specification filename. May be "
+ "given instead of --mods_spec.");
+
+void SettingsFromFlags(pb::Header* header) {
+ // Fill in header as PeptidesHeader, according to command-line flags
+
+ pb::Header_PeptidesHeader& pep_header = *header->mutable_peptides_header();
+ pep_header.Clear();
+ pep_header.set_min_mass(FLAGS_min_mass);
+ pep_header.set_max_mass(FLAGS_max_mass);
+ pep_header.set_min_length(FLAGS_min_length);
+ pep_header.set_max_length(FLAGS_max_length);
+ pep_header.set_monoisotopic_precursor(FLAGS_monoisotopic_precursor);
+ pep_header.set_enzyme(FLAGS_enzyme);
+ CHECK(!FLAGS_enzyme.empty());
+ if (FLAGS_enzyme != "none") {
+ CHECK(FLAGS_digestion == "full-digest"
+ || FLAGS_digestion == "partial-digest");
+ pep_header.set_full_digestion(FLAGS_digestion == "full-digest");
+ pep_header.set_max_missed_cleavages(FLAGS_max_missed_cleavages);
+ }
+
+ CHECK(FLAGS_mods_table.empty() || FLAGS_mods_spec.empty())
+ << "Can't specify both --mods_table and --mods_spec";
+
+ VariableModTable var_mod_table;
+ if (!FLAGS_mods_table.empty()) {
+ pb::Header mods_header;
+ pb::ModTable mod_table;
+ HeadedRecordReader mods_reader(FLAGS_mods_table, &mods_header);
+ CHECK(mods_header.file_type() == pb::Header::MOD_TABLE);
+ CHECK(!mods_reader.Done());
+ CHECK(mods_reader.Read(&mod_table));
+ CHECK(mods_reader.Done());
+
+ CHECK(var_mod_table.Init(mod_table));
+ CHECK(var_mod_table.SerializeUniqueDeltas(&mod_table));
+ pep_header.mutable_mods()->CopyFrom(mod_table);
+// CHECK(MassConstants::Init(&mod_table));
+ } else {
+ CHECK(var_mod_table.Parse(FLAGS_mods_spec.c_str()));
+ pep_header.mutable_mods()->CopyFrom(*var_mod_table.ParsedModTable());
+// CHECK(MassConstants::Init(var_mod_table.ParsedModTable()));
+ }
+}
diff --git a/src/app/tide/libtide-support.a b/src/app/tide/libtide-support.a
new file mode 100644
index 0000000..9b28868
Binary files /dev/null and b/src/app/tide/libtide-support.a differ
diff --git a/src/app/tide/make_peptides.cc b/src/app/tide/make_peptides.cc
new file mode 100644
index 0000000..e79ce2d
--- /dev/null
+++ b/src/app/tide/make_peptides.cc
@@ -0,0 +1,765 @@
+// Benjamin Diament
+//
+// Generate peptides (enzymatic or non-enzymatic) from a set of proteins.
+//
+// Example command-line:
+// make_peptides [ options ] --proteins=<raw_proteins.proto input file> \
+// --peptides=<peptides.proto output file>
+// See other command-line options below.
+//
+// Implementation overview
+//
+// We do not wish to write an unsorted list of all the Peptides and then sort
+// them separately, as we expect this would be slow. Instead, we use a heap to
+// write the peptides in sorted order as we generate them. We do this as
+// follows.
+//
+// All proteins sequences are stored in memory (This isn't scalable, but the
+// same work could be done in chunks that fit in memory and then merged
+// later. Such merging is not implemented. TODO 246)
+//
+// To each amino acid in all the protein sequences we assign a Peptide (see
+// class definition below) beginning at that position. This Peptide's length
+// will be incremented over the course of the run until either the maximum
+// peptide mass or length is exceeded. Barring exceeding the mass and length
+// limits, therefore, there are always as many Peptides in memory as there are
+// amino acids.
+//
+// We always maintain a heap of all these Peptides, arranged by mass.
+// We think of identical Peptides (the same amino acid sequence) as a group.
+// We ensure that a group of identical Peptides will come off the heap
+// consecutively, ordered by protein_id and position within the protein.
+// To guarantee this we must use a multi-critereon comparator for the heap.
+// (See Peptide::Compare()).
+//
+// Until there are no Peptides remaining, we repeatedly remove the lightest
+// group of Peptides from the heap, create a protocol buffer representing that
+// peptide and all its locations, and store it to disk as a record. Then we
+// grow each Peptide in the group by one amino acid and insert it back into the
+// heap (assuming it hasn't exceeded the mass and length limits).
+
+#include <stdio.h>
+#include <iostream>
+#include <string>
+#include <climits>
+#include <vector>
+#include <algorithm>
+#include <bitset>
+#include <gflags/gflags.h>
+#include "records.h"
+#include "records_to_vector-inl.h"
+#include "header.pb.h"
+#include "raw_proteins.pb.h"
+#include "peptides.pb.h"
+#include "mass_constants.h"
+
+using namespace std;
+
+#define CHECK(x) GOOGLE_CHECK(x)
+typedef pb::Header_PeptidesHeader Settings;
+
+///////////////////////////////////////////////////////////////////////////////
+// Represents a peptide begining at a fixed position. One instance appears on
+// the heap for each position. The length varies over the course of the run.
+// (See comments above.)
+//
+// After construction, call Init(), which will return true if the peptide
+// should enter the heap. (It might not if it can't be extended to meet
+// the minimum mass and length threshold.)
+//
+// Subclasses may override Advance().
+class Peptide {
+ public:
+ Peptide(const pb::Protein& protein, int pos, int max_len = INT_MAX)
+ : protein_id_(protein.id()),
+ pos_(pos),
+ residues_(protein.residues().data() + pos),
+ protein_end_(min(max_len, int(protein.residues().length() - pos))),
+ length_(0),
+ mass_(monoisotopic_precursor_ ? MassConstants::fixp_mono_h2o
+ : MassConstants::fixp_avg_h2o) {
+ assert(protein_end_ >= 0);
+ }
+
+ int Compare(const Peptide& other, bool allow_equal) const {
+ // To ensure that identical Peptides come off the heap consecutively and
+ // ordered by protein and position.
+ // Return -1 if this < other, return 1 if this > other.
+ // If allow_equal, return 0 when Peptides are identical.
+
+ // mass first
+ if (mass_ > other.mass_)
+ return 1;
+ if (mass_ < other.mass_)
+ return -1;
+ // then length
+ if (length_ < other.length_)
+ return -1;
+ if (length_ > other.length_)
+ return 1;
+ // if all shortcuts fail, have to check the chars
+ const char* u = residues_;
+ const char* v = other.residues_;
+ for (int i = 0; i < length_; ++i, ++u, ++v) {
+ int diff = int(*u) - int(*v);
+ if (diff != 0)
+ return diff;
+ }
+ if (allow_equal)
+ return 0;
+
+ if (protein_id_ < other.protein_id_)
+ return -1;
+ if (protein_id_ > other.protein_id_)
+ return 1;
+ return pos_ - other.pos_;
+ }
+
+ virtual bool Advance() {
+ // Increment length. Return false if limits exceeded.
+ if (protein_end_ == 0 || length_ >= max_length_)
+ return false;
+ --protein_end_;
+ mass_ += AAMass(residues_[length_++]);
+ return mass_ <= max_mass_;
+ }
+
+ int StartPos() { return pos_; }
+ int EndPos() { return pos_ + length_; }
+
+ bool Init() {
+ while (length_ < min_length_ || mass_ < min_mass_)
+ if (!Advance())
+ return false;
+ return true;
+ }
+
+ void Print() {
+ // Debugging
+ cerr << mass_ << "\t len:" << length_ << "\t prot:"
+ << protein_id_ << "\t pos:" << pos_ << "\n";
+ }
+
+ void StartPB(pb::Peptide* pb_peptide) {
+ // Initialize a protocol buffer with the first Peptide in a group.
+ pb_peptide->set_id(peptide_count_++);
+ pb_peptide->set_mass(MassConstants::ToDouble(mass_));
+ pb_peptide->set_length(length_);
+ pb_peptide->mutable_first_location()->set_protein_id(protein_id_);
+ pb_peptide->mutable_first_location()->set_pos(pos_);
+ }
+
+ void BuildAuxLocationsPB(pb::AuxLocation* aux_location) {
+ // Add another location to a protocol buffer representing a group of
+ // locations for the current peptide.
+ pb::Location* location = aux_location->add_location();
+ location->set_protein_id(protein_id_);
+ location->set_pos(pos_);
+ }
+
+ static bool SetMinMaxMassAndLength(const Settings& settings) {
+ // Returns true if successful (settings are valid).
+ if (!settings.has_min_length() ||
+ !settings.has_max_length() ||
+ !settings.has_min_mass() ||
+ !settings.has_max_mass())
+ return false;
+ min_length_ = settings.min_length();
+ max_length_ = settings.max_length();
+ min_mass_ = MassConstants::ToFixPt(settings.min_mass());
+ max_mass_ = MassConstants::ToFixPt(settings.max_mass());
+ monoisotopic_precursor_ = (settings.has_monoisotopic_precursor() &&
+ settings.monoisotopic_precursor());
+ return true;
+ }
+
+ protected:
+ static FixPt AAMass(char aa) {
+ return monoisotopic_precursor_ ? MassConstants::fixp_mono_table[aa]
+ : MassConstants::fixp_avg_table[aa];
+ }
+
+ static int peptide_count_;
+ static int min_length_, max_length_;
+ static FixPt min_mass_, max_mass_;
+ static bool monoisotopic_precursor_;
+
+ int protein_id_;
+ unsigned short int pos_;
+ const char* residues_; // points into protein sequence
+ unsigned short int protein_end_; // remaining residues in protein
+ unsigned short int length_;
+ FixPt mass_;
+};
+
+int Peptide::peptide_count_ = 0;
+int Peptide::min_length_;
+int Peptide::max_length_;
+FixPt Peptide::min_mass_;
+FixPt Peptide::max_mass_;
+bool Peptide::monoisotopic_precursor_;
+
+struct greater_peptide : public binary_function<Peptide*, Peptide*, bool> {
+ bool operator()(Peptide* x, Peptide* y) {
+ if (x == y)
+ return false;
+ return x->Compare(*y, false) > 0;
+ }
+};
+
+class ReversePeptide : public Peptide {
+ public:
+ // pos should be given at the *beginning* of the peptide. max_len must be
+ // provided accurately (not e.g. INT_MAX). As for Peptide, pos + max_len
+ // points just beyond where the peptide ends.
+ ReversePeptide(const pb::Protein& protein, int pos, int max_len)
+ : Peptide(protein, pos + max_len, 0) {
+ CHECK(protein.residues().length() - pos >= max_len);
+ protein_end_ = max_len;
+ }
+
+ virtual bool Advance() {
+ // Same as parent, but move backwards
+ if (protein_end_ == 0 || length_ >= max_length_)
+ return false;
+ --protein_end_;
+ mass_ += AAMass(*--residues_);
+ ++length_;
+ --pos_;
+ return mass_ <= max_mass_;
+ }
+};
+
+// Make only one peptide (if within limits) of length len (or up to protein end)
+class WholePeptide : public Peptide {
+ public:
+ WholePeptide(const pb::Protein& protein, int pos, int len = INT_MAX)
+ : Peptide(protein, pos, len) {
+ }
+
+ virtual bool Advance() {
+ while (Peptide::Advance())
+ if (protein_end_ == 0)
+ return true;
+ return false;
+ }
+};
+
+class SelectivePeptide : public Peptide {
+ public:
+ SelectivePeptide(const pb::Protein& protein, const vector<bool>& mask,
+ int pos, int len = INT_MAX)
+ : Peptide(protein, pos, len), mask_(mask) {
+ }
+
+ virtual bool Advance() {
+ while (true) {
+ if (!Peptide::Advance())
+ return false;
+ if (mask_[EndPos()])
+ return true;
+ }
+ }
+
+ private:
+ const vector<bool>& mask_;
+};
+
+///////////////////////////////////////////////////////////////////////////////
+// Cleaves a protein according to the specification of an enzyme as described in
+// the construction parameters. Returns a vector<int> of the start positions of
+// the resulting peptides.
+class Enzyme {
+ public:
+ // 'left' and 'right' are sets of amino acids. A cleavage will occur at a
+ // given site if, to the left is an amino acid in 'left' and to the right is
+ // an amino acid in 'right'. If invert_XXX is true, then the cleavage occurs
+ // *unless* there is an amino acid in the corresponding set.
+ Enzyme(const char* left, bool invert_left,
+ const char* right, bool invert_right) {
+ Init(left, invert_left, &left_);
+ Init(right, invert_right, &right_);
+ }
+
+ bool Left(char c) const { return left_[Index(c)]; }
+ bool Right(char c) const { return right_[Index(c)]; }
+
+ // Digest protein to find cleavage points.
+ void Cleave(const pb::Protein& protein, vector<int>* result) const {
+ // marks FIRST position of peptides resulting from digestion but excludes
+ // (implicit) position 0 from list. A final entry is inserted marking the
+ // end of the last peptide, just beyond its last amino acid.
+ result->clear();
+ int len = protein.residues().length();
+ for (int i = 0; i < len - 1; ++i)
+ if (Left(protein.residues()[i]) && Right(protein.residues()[i+1]))
+ result->push_back(i+1);
+ result->push_back(len);
+ }
+
+ static vector<bool>* AsBitVec(vector<int>* cleavages) {
+ // caller will own result (and must delete it).
+ int len = cleavages->back() + 1;
+ vector<bool>* bitvec = new vector<bool>(len, false);
+ bitvec->clear();
+ vector<int>::iterator i = cleavages->begin();
+ for (; i != cleavages->end(); ++i)
+ (*bitvec)[*i] = true;
+ return bitvec;
+ }
+
+ // Map enzyme names to variables
+ static const Enzyme* FromName(const string& name);
+
+ private:
+ void Init(const char* chars, bool invert, bitset<26>* bits) {
+ bits->reset();
+ if (invert)
+ bits->set();
+ bool val = !invert;
+ for (; *chars; ++chars)
+ (*bits)[Index(*chars)] = val;
+ }
+
+ static int Index(char c) {
+ CHECK(c >= 'A' && c <= 'Z');
+ return c - 'A';
+ }
+
+ bitset<26> left_;
+ bitset<26> right_;
+
+ // We predefine the following enzymes:
+ static Enzyme trypsin;
+ static Enzyme chymotrypsin;
+ static Enzyme elastase;
+ static Enzyme clostripain;
+ static Enzyme cyanogen_bromide;
+ static Enzyme idosobenzoate;
+ static Enzyme proline_endopeptidase;
+ static Enzyme staph_protease;
+ static Enzyme modified_chymotrypsin;
+ static Enzyme elastase_trypsin_chymotrypsin;
+ static Enzyme aspn;
+};
+
+Enzyme Enzyme::trypsin("KR", false, "P", true);
+Enzyme Enzyme::chymotrypsin("FWY", false, "P", true);
+Enzyme Enzyme::elastase("ALIV", false, "P", true);
+Enzyme Enzyme::clostripain("R", false, "", true);
+Enzyme Enzyme::cyanogen_bromide("M", false, "", true);
+Enzyme Enzyme::idosobenzoate("W", false, "", true);
+Enzyme Enzyme::proline_endopeptidase("P", false, "", true);
+Enzyme Enzyme::staph_protease("E", false, "", true);
+Enzyme Enzyme::modified_chymotrypsin("FWYL", false, "P", true);
+Enzyme Enzyme::elastase_trypsin_chymotrypsin("ALIVKRWFY", false, "P", true);
+Enzyme Enzyme::aspn("", true, "D", false);
+
+// Map enzyme names to variables
+const Enzyme* Enzyme::FromName(const string& name) {
+ if (name == "trypsin")
+ return &trypsin;
+ if (name == "chymotrypsin")
+ return &chymotrypsin;
+ if (name == "elastase")
+ return &elastase;
+ if (name == "clostripain")
+ return &clostripain;
+ if (name == "cyanogen-bromide")
+ return &cyanogen_bromide;
+ if (name == "idosobenzoate")
+ return &idosobenzoate;
+ if (name == "proline-endopeptidase")
+ return &proline_endopeptidase;
+ if (name == "staph-protease")
+ return &staph_protease;
+ if (name == "modified-chymotrypsin")
+ return &modified_chymotrypsin;
+ if (name == "elastase-trypsin-chymotrypsin")
+ return &elastase_trypsin_chymotrypsin;
+ if (name == "aspn")
+ return &aspn;
+ return NULL; // No match
+}
+
+///////////////////////////////////////////////////////////////////////////////
+// Create and manage the heap of peptides; write out the peptide file.
+// Subclasses should override AddProtein() to initialize the heap by calling
+// AddPeptide() for each peptide in the initial heap.
+class PeptideHeap {
+ public:
+ virtual ~PeptideHeap() {}
+
+ void MakePeptides(const vector<const pb::Protein*>& proteins,
+ HeadedRecordWriter* peptide_writer,
+ HeadedRecordWriter* aux_loc_writer);
+
+ protected:
+ bool AddPeptide(Peptide* new_peptide) {
+ if (new_peptide->Init()) {
+ peptides_.push_back(new_peptide);
+ return true;
+ }
+ delete new_peptide;
+ return false;
+ }
+
+ private:
+ typedef vector<Peptide*> PepVec;
+ typedef PepVec::iterator PepIter;
+
+ virtual void AddProtein(const pb::Protein& protein) = 0;
+
+ void GetGroup(pb::Peptide* pb_peptide, pb::AuxLocation* aux_location);
+ void PrintHeap(const string& name, PepIter iter, PepIter end);
+
+ PepVec peptides_;
+};
+
+void PeptideHeap::PrintHeap(const string& name, PepIter iter, PepIter end) {
+ // Debugging
+ cerr << "========= " << name << " =========\n";
+ for (; iter != end; ++iter) {
+ cerr << " ";
+ (*iter)->Print();
+ }
+}
+
+void PeptideHeap::GetGroup(pb::Peptide* pb_peptide, pb::AuxLocation* aux_location) {
+ pb_peptide->Clear();
+ aux_location->Clear();
+
+ // PrintHeap("Start", peptides_.begin(), peptides_.end());
+
+ // Pop a group off the heap.
+ // The group will sit at the end of the peptides_ vector in reverse order.
+ // (STL's pop_heap() operation puts the smallest heap element at the end of
+ // the heap range so we call pop_heap() once for each peptide in the group).
+ Peptide* peptide = peptides_.front(); // smallest heap element
+ vector<Peptide*>::iterator group_begin = peptides_.end();
+ pop_heap(peptides_.begin(), group_begin--, greater_peptide());
+
+ while ((group_begin != peptides_.begin()) &&
+ (peptide->Compare(*peptides_.front(), true) == 0))
+ pop_heap(peptides_.begin(), group_begin--, greater_peptide());
+
+
+ // PrintHeap("Heap Portion", peptides_.begin(), group_begin);
+ // PrintHeap("Group", group_begin, peptides_.end());
+
+ // Fill in pb_peptide with group
+ vector<Peptide*>::iterator iter = peptides_.end() - 1;
+ (*iter)->StartPB(pb_peptide);
+
+ // Add the auxiliary locations
+ for (--iter; iter != group_begin - 1; --iter)
+ (*iter)->BuildAuxLocationsPB(aux_location);
+
+ // Advance all group members, deleting any that are done.
+ iter = group_begin;
+ vector<Peptide*>::iterator end = peptides_.end();
+ while (iter != end) {
+ if ((*iter)->Advance()) {
+ // re-push still-valid peptides and advance iterator
+ push_heap(peptides_.begin(), ++iter, greater_peptide());
+ } else { // Peptide has exceeded mass or length bounds.
+ delete *iter;
+ *iter = *(--end);
+ // don't advance iterator
+ }
+ }
+
+ // PrintHeap("After Advance", peptides_.begin(), end);
+
+ peptides_.resize(end - peptides_.begin()); // remove deleted peptides
+}
+
+void PeptideHeap::MakePeptides(const vector<const pb::Protein*>& proteins,
+ HeadedRecordWriter* peptide_writer,
+ HeadedRecordWriter* aux_loc_writer) {
+ CHECK(peptide_writer->OK());
+ CHECK(aux_loc_writer->OK());
+
+ cerr << "Creating Peptide Array" << endl;
+ vector<const pb::Protein*>::const_iterator i = proteins.begin();
+ for (; i != proteins.end(); ++i) {
+ if (!(*i)->residues().empty())
+ AddProtein(**i);
+ }
+
+ cerr << "heapifying" << endl;
+ make_heap(peptides_.begin(), peptides_.end(), greater_peptide());
+
+ pb::Peptide pb_peptide;
+ pb::AuxLocation aux_location;
+ int aux_loc_idx = 0;
+ for (int count = 1; !peptides_.empty(); ++count) {
+ GetGroup(&pb_peptide, &aux_location);
+
+ // Not all peptides have aux locations associated with them. Check to see
+ // if GetGroup added any locations to aux_location. If yes, only then
+ // assign the corresponding array index to the peptide and write it out.
+ if (aux_location.location_size() > 0) {
+ pb_peptide.set_aux_locations_index(aux_loc_idx++);
+ aux_loc_writer->Write(&aux_location);
+ }
+
+ // Write the peptide AFTER the aux_locations check, in case we added an
+ // aux_locations_index to the peptide.
+ peptide_writer->Write(&pb_peptide);
+
+ if (count % 100000 == 0)
+ cerr << "Wrote " << count << " peptides\n";
+ }
+}
+
+///////////////////////////////////////////////////////////////////////////////
+// Subclasses of PeptideHeap for various peptide restrictions
+
+class NonEnzymaticPeptideHeap : public PeptideHeap {
+ private:
+ virtual void AddProtein(const pb::Protein& protein) {
+ for (int pos = 0; AddPeptide(new Peptide(protein, pos)); ++pos);
+ }
+};
+
+class NonEnzymaticPeptideHeapReverse : public PeptideHeap {
+ // testing only; should give exact same results as NonEnzymaticPeptideHeap
+ private:
+ virtual void AddProtein(const pb::Protein& protein) {
+ for (int len = protein.residues().length();
+ AddPeptide(new ReversePeptide(protein, 0, len)); --len);
+ }
+};
+
+class FullyEnzymaticPeptideHeap : public PeptideHeap {
+ public:
+ FullyEnzymaticPeptideHeap(const Enzyme* enzyme) : enzyme_(enzyme) {}
+
+ virtual ~FullyEnzymaticPeptideHeap() {}
+
+ private:
+ virtual void AddProtein(const pb::Protein& protein) {
+ vector<int> cleavages;
+ enzyme_->Cleave(protein, &cleavages);
+ int begin_pos = 0;
+ vector<int>::iterator end_pos = cleavages.begin();
+ while (end_pos != cleavages.end()) {
+ AddPeptide(new WholePeptide(protein, begin_pos, *end_pos - begin_pos));
+ begin_pos = *end_pos++; // get next peptide
+ }
+ }
+
+ const Enzyme* enzyme_;
+};
+
+class PartiallyEnzymaticPeptideHeap : public PeptideHeap {
+ public:
+ PartiallyEnzymaticPeptideHeap(const Enzyme* enzyme) : enzyme_(enzyme) {}
+
+ virtual ~PartiallyEnzymaticPeptideHeap() {}
+
+ private:
+ virtual void AddProtein(const pb::Protein& protein) {
+ vector<int> cleavages;
+ enzyme_->Cleave(protein, &cleavages);
+ int begin_pos = 0;
+ vector<int>::iterator end_pos = cleavages.begin();
+ while (end_pos != cleavages.end()) {
+ int max_len = *end_pos - begin_pos;
+ AddPeptide(new ReversePeptide(protein, begin_pos, max_len));
+ AddPeptide(new Peptide(protein, begin_pos, max_len - 1));
+ begin_pos = *end_pos++; // get next peptide
+ }
+ }
+
+ const Enzyme* enzyme_;
+};
+
+class AllowMissedCleavagesPeptideHeap : public PeptideHeap {
+ public:
+ AllowMissedCleavagesPeptideHeap(const Enzyme* enzyme, int max_cleavages)
+ : enzyme_(enzyme), max_cleavages_(max_cleavages) {
+ }
+
+ virtual ~AllowMissedCleavagesPeptideHeap() {
+ vector<vector<bool>*>::iterator i = masks_.begin();
+ for (; i != masks_.end(); ++i)
+ delete *i;
+ }
+
+ protected:
+ vector<int> cleavages_; // current set of cleavages
+ vector<bool>* mask_; // current mask
+
+ private:
+ virtual void FlipMaskIfNeeded() {}
+ virtual void AddFwdPeptide(const pb::Protein& protein, int pos, int len) = 0;
+ virtual void AddRevPeptide(const pb::Protein& protein, int pos, int len) {}
+
+ virtual void AddProtein(const pb::Protein& protein) {
+ GetCleavages(protein);
+ FlipMaskIfNeeded();
+ vector<int>::iterator next_pos = cleavages_.begin();
+ vector<int>::iterator last_pos = cleavages_.end() - 1;
+ vector<int>::iterator end_pos = next_pos + max_cleavages_;
+ if (max_cleavages_ >= cleavages_.size())
+ end_pos = last_pos;
+ for (int pos = 0; next_pos != cleavages_.end(); pos = *next_pos++) {
+ AddFwdPeptide(protein, pos, *end_pos - pos);
+ if (end_pos != last_pos)
+ end_pos++;
+ }
+ next_pos = cleavages_.begin();
+ end_pos = cleavages_.begin();
+ int pos = 0;
+ for (; end_pos != cleavages_.end(); ++end_pos) {
+ AddRevPeptide(protein, pos, *end_pos - pos);
+ if (end_pos - cleavages_.begin() >= max_cleavages_)
+ pos = *next_pos++;
+ }
+ }
+
+ virtual void GetCleavages(const pb::Protein& protein) {
+ enzyme_->Cleave(protein, &cleavages_);
+ mask_ = Enzyme::AsBitVec(&cleavages_);
+ masks_.push_back(mask_);
+ }
+
+ vector<vector<bool>*> masks_;
+ const Enzyme* enzyme_;
+ int max_cleavages_;
+};
+
+class FullyEnzymaticAllowMissedCleavagesPeptideHeap
+ : public AllowMissedCleavagesPeptideHeap {
+ public:
+ FullyEnzymaticAllowMissedCleavagesPeptideHeap(const Enzyme* enzyme,
+ int max_cleavages)
+ : AllowMissedCleavagesPeptideHeap(enzyme, max_cleavages) {
+ }
+
+ virtual ~FullyEnzymaticAllowMissedCleavagesPeptideHeap() {}
+
+ private:
+ virtual void AddFwdPeptide(const pb::Protein& protein, int pos, int len) {
+ AddPeptide(new SelectivePeptide(protein, *mask_, pos, len));
+ }
+};
+
+class PartiallyEnzymaticAllowMissedCleavagesPeptideHeap
+ : public AllowMissedCleavagesPeptideHeap {
+ public:
+ PartiallyEnzymaticAllowMissedCleavagesPeptideHeap(const Enzyme* enzyme,
+ int max_cleavages)
+ : AllowMissedCleavagesPeptideHeap(enzyme, max_cleavages) {
+ }
+
+ virtual ~PartiallyEnzymaticAllowMissedCleavagesPeptideHeap() {}
+
+ private:
+ virtual void FlipMaskIfNeeded() { mask_->flip(); }
+
+ virtual void AddFwdPeptide(const pb::Protein& protein, int pos, int len) {
+ AddPeptide(new SelectivePeptide(protein, *mask_, pos, len));
+ }
+
+ virtual void AddRevPeptide(const pb::Protein& protein, int pos, int len) {
+ AddPeptide(new ReversePeptide(protein, pos, len));
+ }
+};
+
+#define CHECK_SETTINGS(x) do { \
+ if (!(x)) { \
+ fprintf(stderr, "SETTINGS CHECK FAILED: %s\n", #x); \
+ return false; \
+ } \
+} while (false)
+
+bool MakePeptides(pb::Header* header, const string& peptides_file,
+ const string& aux_locs_file) {
+
+ // header is passed in as the settings desiderata.
+ // Returns true if settings specified in header are valid.
+
+ // First, collect the source file of raw proteins, read it and check validity
+ CHECK_SETTINGS(header->source_size() == 1);
+ pb::Header_Source& source = *header->mutable_source(0);
+ CHECK_SETTINGS(source.has_filename());
+ CHECK_SETTINGS(!source.has_filetype()); // source.header() is given instead
+ string proteins_filename = source.filename();
+ vector<const pb::Protein*> proteins;
+ pb::Header prot_header;
+ cerr << "Reading Proteins" << endl;
+ CHECK_SETTINGS(ReadRecordsToVector<pb::Protein>(&proteins, proteins_filename,
+ &prot_header));
+ CHECK_SETTINGS(prot_header.file_type() == pb::Header::RAW_PROTEINS);
+ // TODO: reinstate this. CHECK_SETTINGS(prot_header.has_raw_proteins_header());
+ // The raw proteins file is read in. It's a valid source file;
+ // remember it as such:
+ source.mutable_header()->CopyFrom(prot_header);
+
+ // Now check other desired settings
+ CHECK_SETTINGS(header->has_peptides_header());
+ const Settings& settings = header->peptides_header();
+ CHECK_SETTINGS(Peptide::SetMinMaxMassAndLength(settings));
+
+ CHECK_SETTINGS(settings.has_enzyme() && !settings.enzyme().empty());
+
+// CHECK_SETTINGS(MassConstants::Init(&settings.mods()));
+
+ // Determine what type of PeptideHeap to create from settings indicated
+ // in header->
+ PeptideHeap* heap = NULL;
+ if (settings.enzyme() == "none") {
+ CHECK_SETTINGS(!settings.has_full_digestion() &&
+ !settings.has_max_missed_cleavages());
+ heap = new NonEnzymaticPeptideHeap;
+ } else {
+ CHECK_SETTINGS(settings.has_full_digestion() &&
+ settings.has_max_missed_cleavages());
+ int max_missed_cleavages = settings.max_missed_cleavages();
+ if (max_missed_cleavages < 0)
+ max_missed_cleavages = INT_MAX;
+
+ const Enzyme* enzyme = Enzyme::FromName(settings.enzyme());
+ CHECK_SETTINGS(enzyme != NULL); // Unrecognized enzyme name
+
+ if (settings.full_digestion()) {
+ if (max_missed_cleavages != 0) {
+ heap = new FullyEnzymaticAllowMissedCleavagesPeptideHeap(
+ enzyme, max_missed_cleavages);
+ } else {
+ heap = new FullyEnzymaticPeptideHeap(enzyme);
+ }
+ } else { // Partial digest
+ if (max_missed_cleavages != 0) {
+ heap = new PartiallyEnzymaticAllowMissedCleavagesPeptideHeap(
+ enzyme, max_missed_cleavages);
+ } else {
+ heap = new PartiallyEnzymaticPeptideHeap(enzyme);
+ }
+ }
+ }
+ assert(heap != NULL);
+
+ header->set_file_type(pb::Header::PEPTIDES);
+ header->mutable_peptides_header()->set_has_peaks(false);
+ HeadedRecordWriter peptide_writer(peptides_file, *header); // put header in outfile
+
+ // Create the auxiliary locations header and writer
+ pb::Header aux_locs_header;
+ aux_locs_header.set_file_type(pb::Header::AUX_LOCATIONS);
+ pb::Header_Source* aux_locs_source = aux_locs_header.add_source();
+ aux_locs_source->set_filename(peptides_file);
+ aux_locs_source->mutable_header()->CopyFrom(*header);
+ HeadedRecordWriter aux_loc_writer(aux_locs_file, aux_locs_header);
+
+ heap->MakePeptides(proteins, &peptide_writer, &aux_loc_writer);
+ delete heap;
+
+ for (int i = 0; i < proteins.size(); ++i)
+ delete proteins[i];
+
+ return true;
+}
diff --git a/src/app/tide/mass_constants.cc b/src/app/tide/mass_constants.cc
new file mode 100644
index 0000000..c0bedab
--- /dev/null
+++ b/src/app/tide/mass_constants.cc
@@ -0,0 +1,272 @@
+#include <limits>
+#include "io/carp.h"
+#include "mass_constants.h"
+#include "header.pb.h"
+#include "stdio.h"
+
+using namespace std;
+
+double const MassConstants::proton = 1.00727646688;
+double const MassConstants::kFixedPointScalar = 1e5;
+
+const double MassConstants::elts_mono[] = {
+ 1.007825035, // H
+ 12.0, // C
+ 14.003074, // N
+ 15.99491463, // O
+ 30.973762, // P
+ 31.9720707 // S
+};
+
+const double MassConstants::elts_avg[] = {
+ 1.00794, // H
+ 12.0107, // C
+ 14.0067, // N
+ 15.9994, // O
+ 30.973761, // P
+ 32.065 // S
+};
+
+double MassConstants::mono_table[256];
+double MassConstants::avg_table[256];
+double MassConstants::nterm_mono_table[256];
+double MassConstants::cterm_mono_table[256];
+double MassConstants::nterm_avg_table[256];
+double MassConstants::cterm_avg_table[256];
+//double* MassConstants::aa_mass_table = NULL;
+//double MassConstants::aa_bin_1[256];
+//double MassConstants::aa_bin_2[256];
+
+const double MassConstants::mono_h2o = 2*MassConstants::elts_mono[0] + MassConstants::elts_mono[3];
+const double MassConstants::avg_h2o = 2*MassConstants::elts_avg[0] + MassConstants::elts_avg[3];
+const double MassConstants::mono_nh3 = 3*MassConstants::elts_mono[0] + MassConstants::elts_mono[2];
+const double MassConstants::mono_co = MassConstants::elts_mono[1] + MassConstants::elts_mono[3];
+const double MassConstants::mono_oh = MassConstants::elts_mono[0] + MassConstants::elts_mono[3];
+const double MassConstants::mono_h = MassConstants::elts_mono[0] ;
+const double MassConstants::A = 0 - 28.0;
+//const double MassConstants::B_H2O = 0 - MassConstants::mono_h2o;
+//const double MassConstants::B_NH3 = 0 - MassConstants::mono_nh3;
+const double MassConstants::B = 0.0;
+//const double MassConstants::Y_H2O = MassConstants::mono_h2o - 18.0;
+//const double MassConstants::Y_NH3 = MassConstants::mono_h2o - 17.0;
+const double MassConstants::Y = MassConstants::mono_h2o;
+/*const double MassConstants::BIN_SHIFT_A_ION_CHG_1 = 28;
+const double MassConstants::BIN_SHIFT_A_ION_CHG_2 = 14;
+const double MassConstants::BIN_SHIFT_H2O_CHG_1 = 18;
+const double MassConstants::BIN_SHIFT_H2O_CHG_2 = 9;
+const double MassConstants::BIN_SHIFT_NH3_CHG_1 = 17;
+const double MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A = 9;
+const double MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B = 8;
+*/
+double MassConstants::BIN_H2O = 18;
+double MassConstants::BIN_NH3 = 17;
+
+
+//default parameter settings, will be changed during parameter parsing
+double MassConstants::bin_width_ = BIN_WIDTH; // 1.0005079;
+double MassConstants::bin_offset_ = BIN_OFFSET; //0.40;
+
+FixPt MassConstants::fixp_mono_table[256];
+FixPt MassConstants::fixp_avg_table[256];
+FixPt MassConstants::fixp_nterm_mono_table[256];
+FixPt MassConstants::fixp_cterm_mono_table[256];
+FixPt MassConstants::fixp_nterm_avg_table[256];
+FixPt MassConstants::fixp_cterm_avg_table[256];
+
+const FixPt MassConstants::fixp_mono_h2o = ToFixPt(MassConstants::mono_h2o);
+const FixPt MassConstants::fixp_avg_h2o = ToFixPt(MassConstants::avg_h2o);
+const FixPt MassConstants::fixp_mono_nh3 = ToFixPt(MassConstants::mono_nh3);
+const FixPt MassConstants::fixp_mono_co = ToFixPt(MassConstants::mono_co);
+const FixPt MassConstants::fixp_proton = ToFixPt(MassConstants::proton);
+
+ModCoder MassConstants::mod_coder_;
+vector<double> MassConstants::unique_deltas_;
+//double* MassConstants::unique_deltas_bin_;
+
+static bool CheckModTable(const pb::ModTable& mod_table);
+
+void MassConstants::FillMassTable(const double* elements, double* table) {
+ const double* e = elements;
+ double H = e[0], C = e[1], N = e[2], O = e[3], P = e[4], S = e[5];
+
+ for (int i = 0; i < 256; ++i)
+ table[i] = numeric_limits<double>::signaling_NaN();
+
+ table['A'] = C*3 + H*5 + N + O ;
+ table['C'] = C*3 + H*5 + N + O + S ;
+ table['D'] = C*4 + H*5 + N + O*3 ;
+ table['E'] = C*5 + H*7 + N + O*3 ;
+ table['F'] = C*9 + H*9 + N + O ;
+ table['G'] = C*2 + H*3 + N + O ;
+ table['H'] = C*6 + H*7 + N*3 + O ;
+ table['I'] = C*6 + H*11 + N + O ;
+ table['K'] = C*6 + H*12 + N*2 + O ;
+ table['L'] = C*6 + H*11 + N + O ;
+ table['M'] = C*5 + H*9 + N + O + S ;
+ table['N'] = C*4 + H*6 + N*2 + O*2 ;
+ table['P'] = C*5 + H*7 + N + O ;
+ table['Q'] = C*5 + H*8 + N*2 + O*2 ;
+ table['R'] = C*6 + H*12 + N*4 + O ;
+ table['S'] = C*3 + H*5 + N + O*2 ;
+ table['T'] = C*4 + H*7 + N + O*2 ;
+ table['V'] = C*5 + H*9 + N + O ;
+ table['W'] = C*11 + H*10 + N*2 + O ;
+ table['Y'] = C*9 + H*9 + N + O*2 ;
+
+ table['w'] = H*2 + O ; // water
+ table['a'] = H*3 + N ; // ammonia
+ table['c'] = C + O ; // carbon monoxide
+}
+
+
+bool MassConstants::Init(const pb::ModTable* mod_table,
+ const pb::ModTable* n_mod_table,
+ const pb::ModTable* c_mod_table,
+ const double bin_width, const double bin_offset) {
+
+ if (mod_table && !CheckModTable(*mod_table))
+ return false;
+
+ if (!n_mod_table || !c_mod_table) {
+ carp(CARP_FATAL, "We could not find nterm or cterm mod tables. "
+ "This is a [relatively] new requirement in attempt to fix static "
+ "mod discrepancies - 5/19/2015.");
+ }
+
+ if (n_mod_table && !CheckModTable(*n_mod_table))
+ return false;
+
+ if (c_mod_table && !CheckModTable(*c_mod_table))
+ return false;
+
+ for (int i = 0; i < 256; ++i) {
+ mono_table[i] = avg_table[i] = nterm_mono_table[i] =
+ cterm_mono_table[i] = nterm_avg_table[i] = cterm_avg_table[i] = 0;
+ }
+
+ FillMassTable(elts_mono, mono_table);
+ FillMassTable(elts_avg, avg_table);
+ FillMassTable(elts_mono, nterm_mono_table);
+ FillMassTable(elts_mono, cterm_mono_table);
+ FillMassTable(elts_avg, nterm_avg_table);
+ FillMassTable(elts_avg, cterm_avg_table);
+
+ if (mod_table) {
+ // TODO: consider handling average and monoisotopic masses
+ // differently (e.g. with different mod tables). We're deferring
+ // this for now, since we haven't sorted out how to handle average
+ // vs. monoisotopic masses generally.
+ for (int i = 0; i < mod_table->static_mod_size(); ++i) {
+ char aa = mod_table->static_mod(i).amino_acids()[0];
+ double delta = mod_table->static_mod(i).delta();
+ mono_table[aa] += delta;
+ avg_table[aa] += delta;
+ nterm_mono_table[aa] += delta;
+ cterm_mono_table[aa] += delta;
+ nterm_avg_table[aa] += delta;
+ cterm_avg_table[aa] += delta;
+ }
+ carp(CARP_DEBUG, "Number of unique modification masses: %d\n", mod_table->unique_deltas_size());
+
+ mod_coder_.Init(mod_table->unique_deltas_size());
+ unique_deltas_.clear();
+ unique_deltas_.reserve(mod_table->unique_deltas_size());
+ for (int i = 0; i < mod_table->unique_deltas_size(); ++i) {
+ unique_deltas_.push_back(mod_table->unique_deltas(i));
+ }
+ }
+
+ ApplyTerminusStaticMods(n_mod_table, nterm_mono_table, nterm_avg_table);
+ ApplyTerminusStaticMods(c_mod_table, cterm_mono_table, cterm_avg_table);
+
+ SetFixPt(mono_table, avg_table, fixp_mono_table, fixp_avg_table);
+ SetFixPt(nterm_mono_table, nterm_avg_table, fixp_nterm_mono_table, fixp_nterm_avg_table);
+ SetFixPt(cterm_mono_table, cterm_avg_table, fixp_cterm_mono_table, fixp_cterm_avg_table);
+
+ bin_width_ = bin_width;
+ bin_offset_ = bin_offset;
+ BIN_H2O = mass2bin(mono_h2o,1);
+ BIN_NH3 = mass2bin(mono_nh3,1);
+
+ return true;
+}
+
+/* Updates the masses for the respective table to include the
+static mod information from the mod table. */
+void MassConstants::ApplyTerminusStaticMods(const pb::ModTable* mod_table,
+ double* mono_table, double* avg_table) {
+
+ for (int i = 0; i < mod_table->static_mod_size(); ++i) {
+ char aa = (mod_table->static_mod(i).amino_acids())[0];
+ double delta = mod_table->static_mod(i).delta();
+ if (aa == 'X') {
+ const char* AA = "ACDEFGHIKLMNPQRSTVWY";
+ for (int currAA = 0; AA[currAA] != '\0'; currAA++) {
+ mono_table[AA[currAA]] += delta;
+ avg_table[AA[currAA]] += delta;
+ }
+ } else {
+ mono_table[aa] += delta;
+ avg_table[aa] += delta;
+ }
+ }
+}
+
+/* Sets the fixpt for the given mono and avg tables */
+void MassConstants::SetFixPt(double* mono_table, double* avg_table,
+ FixPt* fixp_mono_table, FixPt* fixp_avg_table) {
+ for (int i = 0; i < 256; ++i) {
+ if (mono_table[i] == 0) {
+ mono_table[i] = avg_table[i]/* = aa_bin_1[i] = aa_bin_2[i]*/
+ = numeric_limits<double>::signaling_NaN();
+ fixp_mono_table[i] = fixp_avg_table[i] = 0;
+ } else {
+ fixp_mono_table[i] = ToFixPt(mono_table[i]);
+ fixp_avg_table[i] = ToFixPt(avg_table[i]);
+ }
+ }
+}
+
+static bool CheckModification(const pb::Modification& mod,
+ bool* repeats = NULL) {
+ string aa_str = mod.amino_acids();
+ if (aa_str.length() != 1)
+ return false;
+ char aa = aa_str[0];
+ const char* AA = "ACDEFGHIKLMNPQRSTVWY";
+ for (; (*AA != '\0') && (*AA != aa); ++AA); // find aa in AA
+ if (*AA == '\0')
+ return false;
+ if (repeats != NULL) {
+ if (repeats[aa])
+ return false;
+ repeats[aa] = true;
+ }
+ return true;
+}
+
+static bool CheckModTable(const pb::ModTable& mod_table) {
+ // static mods table should not have repeated amino acids
+ bool repeats[256];
+ for (int i = 0; i < 256; ++i)
+ repeats[i] = false;
+ bool usingXMod = false;
+ for (int i = 0; i < mod_table.static_mod_size(); ++i) {
+ const pb::Modification& mod = mod_table.static_mod(i);
+ string aa_str = mod.amino_acids();
+ if (aa_str.length() != 1) {
+ return false;
+ } else if (aa_str[0] == 'X') {
+ usingXMod = true;
+ } else if (!CheckModification(mod, repeats)) {
+ carp(CARP_FATAL, "Multiple static mods on same residue detected");
+ return false;
+ }
+ }
+ if (usingXMod && mod_table.static_mod_size() > 1) {
+ carp(CARP_FATAL, "We are using X static mod, but we have detected "
+ "other static mods as well. Only one static mod is allowed.");
+ }
+
+ return true;
+}
diff --git a/src/app/tide/mass_constants.h b/src/app/tide/mass_constants.h
new file mode 100644
index 0000000..457d963
--- /dev/null
+++ b/src/app/tide/mass_constants.h
@@ -0,0 +1,118 @@
+// Benjamin Diament
+//
+// Wrapper for all mass constants. Arrays, where they appear,
+// are of length 256, and are indexed by an upper-case letter
+// symbolizing the amino acid.
+//
+// Unused array entries are filled with signaling_NaN, which is
+// supposed to generate an error if touched, but seems to fail silently
+// on Intel. Oh well. :(
+
+#ifndef MASS_CONSTANTS_H
+#define MASS_CONSTANTS_H
+
+#include "mod_coder.h"
+#include <vector>
+
+#define BIN_WIDTH 1.0005079
+#define BIN_OFFSET 0.68
+typedef unsigned int FixPt; // 32-bit fixed-point arithmetic
+ // ALTERNATIVE unsigned long long int; // 64 bits
+ // ALTERNATIVE unsigned long int; // machine register size
+
+namespace pb { class ModTable; }
+
+class MassConstants {
+ public:
+ // Elemental mass values are from www.unimod.org/masses.html.
+ static const double elts_mono[];
+ static const double elts_avg[];
+
+ static const double proton;
+
+ static bool Init(const pb::ModTable* mod_table,
+ const pb::ModTable* n_mod_table,
+ const pb::ModTable* c_mod_table,
+ const double bin_width, const double bin_offset);
+
+ static void ApplyTerminusStaticMods(const pb::ModTable* mod_table,
+ double* mono_table, double* avg_table);
+
+ static void SetFixPt(double* mono_table, double* avg_table,
+ FixPt* fixp_mono_table, FixPt* fixp_avg_table);
+
+ static double mono_table[];
+ static double avg_table[];
+ static double nterm_mono_table[];
+ static double cterm_mono_table[];
+ static double nterm_avg_table[];
+ static double cterm_avg_table[];
+ static const double mono_h2o;
+ static const double avg_h2o;
+ static const double mono_nh3;
+ static const double mono_co;
+ static const double mono_oh;
+ static const double mono_h;
+ static const double A;
+// static const double B_H2O;
+// static const double B_NH3;
+ static const double B;
+// static const double Y_H2O;
+// static const double Y_NH3;
+ static const double Y;
+ static double BIN_H2O;
+ static double BIN_NH3;
+/* static const double BIN_SHIFT_A_ION_CHG_1;
+ static const double BIN_SHIFT_A_ION_CHG_2;
+ static const double BIN_SHIFT_H2O_CHG_1;
+ static const double BIN_SHIFT_H2O_CHG_2;
+ static const double BIN_SHIFT_NH3_CHG_1;
+ static const double BIN_SHIFT_NH3_CHG_2_CASE_A;
+ static const double BIN_SHIFT_NH3_CHG_2_CASE_B;
+*/ // Fixed-Point Versions
+ static const double kFixedPointScalar;
+ static FixPt ToFixPt(double x) {
+ return FixPt(x * kFixedPointScalar + 0.5);
+ }
+ static double ToDouble(FixPt x) {
+ return x/kFixedPointScalar;
+ }
+
+ static FixPt fixp_mono_table[];
+ static FixPt fixp_avg_table[];
+ static FixPt fixp_nterm_mono_table[];
+ static FixPt fixp_cterm_mono_table[];
+ static FixPt fixp_nterm_avg_table[];
+ static FixPt fixp_cterm_avg_table[];
+
+ static const FixPt fixp_mono_h2o;
+ static const FixPt fixp_avg_h2o;
+
+ static const FixPt fixp_mono_nh3;
+ static const FixPt fixp_mono_co;
+
+ static const FixPt fixp_proton;
+
+ static void DecodeMod(int code, int* aa_index, double* delta) {
+ int unique_delta_index;
+ mod_coder_.DecodeMod(code, aa_index, &unique_delta_index);
+ *delta = unique_deltas_[unique_delta_index];
+ }
+ static unsigned int mass2bin(double mass, int charge = 1) {
+ return (unsigned int)((mass + (charge - 1)*proton)/(charge*bin_width_) + 1.0 - bin_offset_);
+ }
+ static double bin2mass(int bin, int charge = 1) {
+ return (bin - 1.0 + bin_offset_) * charge*bin_width_ + (charge - 1)*proton;
+ }
+
+ static double bin_width_;
+ static double bin_offset_;
+ private:
+ static void FillMassTable(const double* elements, double* table);
+
+ static ModCoder mod_coder_;
+ static std::vector<double> unique_deltas_;
+
+};
+
+#endif
diff --git a/src/app/tide/max_mz.cc b/src/app/tide/max_mz.cc
new file mode 100644
index 0000000..a18dea5
--- /dev/null
+++ b/src/app/tide/max_mz.cc
@@ -0,0 +1,9 @@
+// Benjamin Diament
+#include <gflags/gflags.h>
+#include "max_mz.h"
+
+DEFINE_double(max_bin, 0, "During search, ignore peaks with higher m/z than "
+ "this. Zero means use all peaks in the dataset. During indexing,"
+ " 0 means to include all theoretical peaks.");
+
+MaxBin MaxBin::global;
diff --git a/src/app/tide/max_mz.h b/src/app/tide/max_mz.h
new file mode 100644
index 0000000..580440a
--- /dev/null
+++ b/src/app/tide/max_mz.h
@@ -0,0 +1,75 @@
+// Benjamin Diament
+// For handling the arcana and complexity of limiting m/z.
+// Most of this comes up in an effort to mimic Crux's results prefectly, and
+// generally concerns at which m/z value we should stop loops. If there is any
+// theme to draw from these arcana it seems that 0's are implicitly tacked on to the
+// high-end of a spectrum after a cut-off is programatically selected.
+//
+// Many of the methods of the class MaxMZ concern converting back and forth
+// between m/z values (in daltons/charge) to buckets.
+//
+// Once a MaxMZ is Init()'d the following three functions return
+// appropriate calculated values for the spectrum under consideration:
+// MaxBin() : highest bin value that will be returned by MaxMZ::Bin().
+// BackgroundBinEnd() : one bin beyond where background subtraction should end.
+// CacheBinEnd() : one bin beyond where the cache lookups can extend.
+
+
+// This new class called MZX_BIN is to replace the old MAX_MZ class.
+//written by Attila Kertesz-Farkas
+
+#ifndef MAX_BIN_H
+#define MAX_BIN_H
+
+#include <assert.h>
+#include <gflags/gflags.h>
+#include "mass_constants.h"
+
+DECLARE_double(max_bin);
+
+// Maximum offset in the denominator of the XCorr function.
+const int MAX_XCORR_OFFSET = 75;
+
+class MaxBin {
+ public:
+ MaxBin() : max_bin_(0), background_bin_end_(0), cache_bin_end_(0) {}
+
+ //MassConstants has to be initialized before this call.
+ void InitBin(int highest_mz) {
+ max_bin_ = MassConstants::mass2bin(highest_mz, 1);
+ background_bin_end_ = MassConstants::mass2bin(highest_mz + MAX_XCORR_OFFSET + 1, 1);
+ // room for diff between main ion and losses, A ion being most
+ // distant, and 29 bins being as far away as an A-ion can be
+ cache_bin_end_ = MassConstants::mass2bin(highest_mz + MAX_XCORR_OFFSET + 30, 1);
+ }
+
+ int MaxBinEnd() const { return max_bin_; }
+ int BackgroundBinEnd() const { return background_bin_end_; }
+ int CacheBinEnd() const { return cache_bin_end_; }
+
+ static const MaxBin& Global() {
+ // during indexing (as opposed to searching), Global().MaxBin() may be 0,
+ // which indicates we should index all theoretical peaks, regardless of
+ // m/z
+ return global;
+ }
+
+ static void SetGlobalMax(double highest_mz) {
+ global.InitBin(highest_mz);
+ FLAGS_max_bin = global.MaxBinEnd();
+ }
+
+ static void SetGlobalMaxFromFlag() {
+ if (FLAGS_max_bin > 0)
+ SetGlobalMax(FLAGS_max_bin);
+ }
+
+ private:
+ int max_bin_;
+ int background_bin_end_;
+ int cache_bin_end_;
+
+ static MaxBin global;
+};
+
+#endif // MAX_BIN_H
diff --git a/src/app/tide/mman.c b/src/app/tide/mman.c
new file mode 100644
index 0000000..5b0bc78
--- /dev/null
+++ b/src/app/tide/mman.c
@@ -0,0 +1,180 @@
+
+#include <windows.h>
+#include <errno.h>
+#include <io.h>
+
+#include "mman.h"
+
+#ifndef FILE_MAP_EXECUTE
+#define FILE_MAP_EXECUTE 0x0020
+#endif /* FILE_MAP_EXECUTE */
+
+static int __map_mman_error(const DWORD err, const int deferr)
+{
+ if (err == 0)
+ return 0;
+ //TODO: implement
+ return err;
+}
+
+static DWORD __map_mmap_prot_page(const int prot)
+{
+ DWORD protect = 0;
+
+ if (prot == PROT_NONE)
+ return protect;
+
+ if ((prot & PROT_EXEC) != 0)
+ {
+ protect = ((prot & PROT_WRITE) != 0) ?
+ PAGE_EXECUTE_READWRITE : PAGE_EXECUTE_READ;
+ }
+ else
+ {
+ protect = ((prot & PROT_WRITE) != 0) ?
+ PAGE_READWRITE : PAGE_READONLY;
+ }
+
+ return protect;
+}
+
+static DWORD __map_mmap_prot_file(const int prot)
+{
+ DWORD desiredAccess = 0;
+
+ if (prot == PROT_NONE)
+ return desiredAccess;
+
+ if ((prot & PROT_READ) != 0)
+ desiredAccess |= FILE_MAP_READ;
+ if ((prot & PROT_WRITE) != 0)
+ desiredAccess |= FILE_MAP_WRITE;
+ if ((prot & PROT_EXEC) != 0)
+ desiredAccess |= FILE_MAP_EXECUTE;
+
+ return desiredAccess;
+}
+
+void* mmap(void *addr, size_t len, int prot, int flags, int fildes, off_t off)
+{
+ HANDLE fm, h;
+
+ void * map = MAP_FAILED;
+
+#ifdef _MSC_VER
+#pragma warning(push)
+#pragma warning(disable: 4293)
+#endif
+
+ const DWORD dwFileOffsetLow = (sizeof(off_t) <= sizeof(DWORD)) ?
+ (DWORD)off : (DWORD)(off & 0xFFFFFFFFL);
+ const DWORD dwFileOffsetHigh = (sizeof(off_t) <= sizeof(DWORD)) ?
+ (DWORD)0 : (DWORD)((off >> 32) & 0xFFFFFFFFL);
+ const DWORD protect = __map_mmap_prot_page(prot);
+ const DWORD desiredAccess = __map_mmap_prot_file(prot);
+
+ const off_t maxSize = off + (off_t)len;
+
+ const DWORD dwMaxSizeLow = (sizeof(off_t) <= sizeof(DWORD)) ?
+ (DWORD)maxSize : (DWORD)(maxSize & 0xFFFFFFFFL);
+ const DWORD dwMaxSizeHigh = (sizeof(off_t) <= sizeof(DWORD)) ?
+ (DWORD)0 : (DWORD)((maxSize >> 32) & 0xFFFFFFFFL);
+
+#ifdef _MSC_VER
+#pragma warning(pop)
+#endif
+
+ errno = 0;
+
+ if (len == 0
+ /* Unsupported flag combinations */
+ || (flags & MAP_FIXED) != 0
+ /* Usupported protection combinations */
+ || prot == PROT_EXEC)
+ {
+ errno = EINVAL;
+ return MAP_FAILED;
+ }
+
+ h = ((flags & MAP_ANONYMOUS) == 0) ?
+ (HANDLE)_get_osfhandle(fildes) : INVALID_HANDLE_VALUE;
+
+ if ((flags & MAP_ANONYMOUS) == 0 && h == INVALID_HANDLE_VALUE)
+ {
+ errno = EBADF;
+ return MAP_FAILED;
+ }
+
+ fm = CreateFileMapping(h, NULL, protect, dwMaxSizeHigh, dwMaxSizeLow, NULL);
+
+ if (fm == NULL)
+ {
+ errno = __map_mman_error(GetLastError(), EPERM);
+ return MAP_FAILED;
+ }
+
+ map = MapViewOfFile(fm, desiredAccess, dwFileOffsetHigh, dwFileOffsetLow, len);
+
+ CloseHandle(fm);
+
+ if (map == NULL)
+ {
+ errno = __map_mman_error(GetLastError(), EPERM);
+ return MAP_FAILED;
+ }
+
+ return map;
+}
+
+int munmap(void *addr, size_t len)
+{
+ if (UnmapViewOfFile(addr))
+ return 0;
+
+ errno = __map_mman_error(GetLastError(), EPERM);
+
+ return -1;
+}
+
+int mprotect(void *addr, size_t len, int prot)
+{
+ DWORD newProtect = __map_mmap_prot_page(prot);
+ DWORD oldProtect = 0;
+
+ if (VirtualProtect(addr, len, newProtect, &oldProtect))
+ return 0;
+
+ errno = __map_mman_error(GetLastError(), EPERM);
+
+ return -1;
+}
+
+int msync(void *addr, size_t len, int flags)
+{
+ if (FlushViewOfFile(addr, len))
+ return 0;
+
+ errno = __map_mman_error(GetLastError(), EPERM);
+
+ return -1;
+}
+
+int mlock(const void *addr, size_t len)
+{
+ if (VirtualLock((LPVOID)addr, len))
+ return 0;
+
+ errno = __map_mman_error(GetLastError(), EPERM);
+
+ return -1;
+}
+
+int munlock(const void *addr, size_t len)
+{
+ if (VirtualUnlock((LPVOID)addr, len))
+ return 0;
+
+ errno = __map_mman_error(GetLastError(), EPERM);
+
+ return -1;
+}
diff --git a/src/app/tide/mman.h b/src/app/tide/mman.h
new file mode 100644
index 0000000..1957bf5
--- /dev/null
+++ b/src/app/tide/mman.h
@@ -0,0 +1,55 @@
+/*
+ * sys/mman.h
+ * mman-win32
+ */
+
+#ifndef _SYS_MMAN_H_
+#define _SYS_MMAN_H_
+
+#ifndef _WIN32_WINNT // Allow use of features specific to Windows XP or later.
+#define _WIN32_WINNT 0x0501 // Change this to the appropriate value to target other versions of Windows.
+#endif
+
+/* All the headers include this file. */
+#ifndef _MSC_VER
+#include <_mingw.h>
+#endif
+
+#include <sys/types.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define PROT_NONE 0
+#define PROT_READ 1
+#define PROT_WRITE 2
+#define PROT_EXEC 4
+
+#define MAP_FILE 0
+#define MAP_SHARED 1
+#define MAP_PRIVATE 2
+#define MAP_TYPE 0xf
+#define MAP_FIXED 0x10
+#define MAP_ANONYMOUS 0x20
+#define MAP_ANON MAP_ANONYMOUS
+
+#define MAP_FAILED ((void *)-1)
+
+/* Flags for msync. */
+#define MS_ASYNC 1
+#define MS_SYNC 2
+#define MS_INVALIDATE 4
+
+void* mmap(void *addr, size_t len, int prot, int flags, int fildes, off_t off);
+int munmap(void *addr, size_t len);
+int mprotect(void *addr, size_t len, int prot);
+int msync(void *addr, size_t len, int flags);
+int mlock(const void *addr, size_t len);
+int munlock(const void *addr, size_t len);
+
+#ifdef __cplusplus
+};
+#endif
+
+#endif /* _SYS_MMAN_H_ */
diff --git a/src/app/tide/mod_coder.h b/src/app/tide/mod_coder.h
new file mode 100644
index 0000000..1e23d8d
--- /dev/null
+++ b/src/app/tide/mod_coder.h
@@ -0,0 +1,38 @@
+// Benjamin Diament
+
+#ifndef MOD_CODER_H
+#define MOD_CODER_H
+
+class ModCoder {
+ public:
+ typedef int Mod;
+
+ void Init(int num_unique_deltas) {
+ log_unique_deltas_ = IntLog(num_unique_deltas);
+ mask_ = (1 << log_unique_deltas_) - 1;
+ }
+
+ int EncodeMod(int aa_index, int unique_delta_index) {
+ return (aa_index << log_unique_deltas_) + unique_delta_index;
+ }
+
+ void DecodeMod(int code, int* aa_index, int* unique_delta_index) {
+ *aa_index = code >> log_unique_deltas_;
+ *unique_delta_index = code & mask_;
+ }
+
+ private:
+ static int IntLog(int x) {
+ if (x <= 1)
+ return x;
+ int res = 0;
+ for (--x; x > 0; x >>= 1)
+ ++res;
+ return res;
+ }
+
+ int log_unique_deltas_;
+ int mask_;
+};
+
+#endif // MOD_CODER_H
diff --git a/src/app/tide/modifications.h b/src/app/tide/modifications.h
new file mode 100644
index 0000000..47fd9fd
--- /dev/null
+++ b/src/app/tide/modifications.h
@@ -0,0 +1,352 @@
+// Benjamin Diament
+
+#include<climits>
+#include<algorithm>
+#include<iostream>
+#include<stdio.h>
+#if defined ( _MSC_VER ) || defined ( DARWIN )
+#include<unordered_map>
+#else
+#include<tr1/unordered_map>
+#endif
+#include "mod_coder.h"
+#include "io/carp.h"
+
+using namespace std;
+
+#define SHOW_ONE(x) { cout << (#x) << ": " << (x) << "\n"; }
+#define SHOW_PAIR(x) ((x).first) << ", " << ((x).second)
+
+enum mods_spec_type {
+ MOD_SPEC, //table for regular amino acid modifications
+ NTPEP, //type for n-terminal peptide modifications
+ CTPEP, //type for c-terminal peptide modifications
+ NTPRO, //type for n-terminal protein modifications
+ CTPRO //type for c-terminal protein modifications
+};
+
+typedef enum mods_spec_type MODS_SPEC_TYPE_T;
+
+template<typename T> inline void ShowAll(const T& x) {
+ for (typename T::const_iterator it = x.begin(); it != x.end(); ++it)
+ cout << " " << (*it);
+ cout << "\n";
+}
+
+#define SHOW_ALL(x) { cout << (#x) << ":"; ShowAll((x)); }
+
+
+struct first_eq : public binary_function<pair<int, int>, pair<int, int>, bool> {
+ bool operator()(pair<int, int> x, pair<int, int> y) {
+ return x.first == y.first;
+ }
+};
+
+static bool IsAA(char c) {
+ const char* AA = "ACDEFGHIKLMNPQRSTVWYX";
+ for (; (*AA != '\0') && (*AA != c); ++AA);
+ return (*AA == c);
+}
+
+class VariableModTable {
+ public:
+ VariableModTable() { offset_ = 0;}
+
+ bool Init(const pb::ModTable& pb_mod_table) {
+ IntPairVec *possibles;
+ if (&pb_mod_table == &pb_mod_table_)
+ possibles = possibles_;
+ if (&pb_mod_table == &pb_ntpep_mod_table_)
+ possibles = possibles_ntpe_;
+ if (&pb_mod_table == &pb_ctpep_mod_table_)
+ possibles = possibles_ctpe_;
+ if (&pb_mod_table == &pb_ntpro_mod_table_)
+ possibles = possibles_ntpr_;
+ if (&pb_mod_table == &pb_ctpro_mod_table_)
+ possibles = possibles_ctpr_;
+
+ if (pb_mod_table.variable_mod_size() == 0)
+ return true;
+ vector<double>& UD = unique_delta_;
+
+#if defined _MSC_VER || defined DARWIN
+ unordered_map<double, int> deltas;
+#else
+ tr1::unordered_map<double, int> deltas;
+#endif
+ for (int i = 0; i < UD.size(); ++i)
+ deltas[UD[i]] = i;
+
+ for (int i = 0; i < pb_mod_table.variable_mod_size(); ++i) {
+ const pb::Modification& mod = pb_mod_table.variable_mod(i);
+ const string& aa = mod.amino_acids();
+ for (int j = 0; j < aa.size(); ++j) {
+ possibles[aa[j]].push_back(make_pair(deltas[mod.delta()], i + offset_));
+ }
+ }
+ offset_ += pb_mod_table.variable_mod_size();
+
+ // Check possibles lists
+ for (int i = 0; i < 256; ++i) {
+ vector<pair<int, int> >& p = possibles[i];
+ if (!IsAA(char(i)) && p.size() > 0) {
+ return false;
+ }
+ sort(p.begin(), p.end());
+ vector<pair<int, int> >::iterator dup = adjacent_find(p.begin(), p.end(), first_eq());
+ if (dup != p.end()) {
+ carp(CARP_FATAL,
+ "Amino acid modification %c+%g appears more than once in modifications table.",
+ char(i), unique_delta_[dup->first]);
+ return false;
+ }
+ }
+ return true;
+ }
+
+ bool Parse(const char* spec_text, MODS_SPEC_TYPE_T mod_table = MOD_SPEC) {
+ pb::ModTable* pb_mod_table_ptr = NULL;
+ switch (mod_table) {
+ case MOD_SPEC:
+ pb_mod_table_ptr = &pb_mod_table_;
+ break;
+ case NTPEP:
+ pb_mod_table_ptr = &pb_ntpep_mod_table_;
+ break;
+ case CTPEP:
+ pb_mod_table_ptr = &pb_ctpep_mod_table_;
+ break;
+ case NTPRO:
+ pb_mod_table_ptr = &pb_ntpro_mod_table_;
+ break;
+ case CTPRO:
+ pb_mod_table_ptr = &pb_ntpro_mod_table_;
+ break;
+ }
+ if (pb_mod_table_ptr == NULL)
+ return false;
+
+ int pos = 0;
+ while (true) {
+ char c;
+ int next_pos = -1;
+ sscanf(spec_text + pos, " %c%n", &c, &next_pos);
+ if (next_pos == -1)
+ return Error(spec_text, pos, "Expected modification specification.");
+ pos += next_pos - 1;
+ unsigned int limit = 0;
+ if (c >= '1' && c <= '9') {
+ sscanf(spec_text + pos, "%u%n", &limit, &next_pos);
+ if (limit == UINT_MAX) {
+ return Error(spec_text, pos, "Limit too big.");
+ }
+ pos += next_pos;
+ }
+ int aa_len = -1, plus_pos = -1, delta_pos = -1, end_pos = -1;
+ if (mod_table == MOD_SPEC)
+ sscanf(spec_text + pos, "%*[ACDEFGHIKLMNPQRSTVWY]%n%n%*[+-]%n%*[0-9.]%n",
+ &aa_len, &plus_pos, &delta_pos, &end_pos);
+ else
+ sscanf(spec_text + pos, "%*[ACDEFGHIKLMNPQRSTVWYX]%n%n%*[+-]%n%*[0-9.]%n",
+ &aa_len, &plus_pos, &delta_pos, &end_pos);
+
+ if (aa_len == -1)
+ return Error(spec_text, pos, "Expected amino acid symbol.");
+ assert(plus_pos != -1);
+ if (delta_pos == -1)
+ return Error(spec_text, pos + plus_pos, "Expected '+' 'or' - and modification amount.");
+ if (end_pos == -1)
+ return Error(spec_text, pos + delta_pos, "Expected modification amount.");
+ if ((limit == 0) && (aa_len != 1))
+ return Error(spec_text, pos, "Static modifications must be specified "
+ "for one amino acid at a time.");
+ int confirm_end_pos = -1;
+ double delta;
+ sscanf(spec_text + pos + delta_pos, "%lg%n", &delta, &confirm_end_pos);
+ if (delta_pos + confirm_end_pos != end_pos)
+ return Error(spec_text, pos + delta_pos, "Cannot parse modification "
+ "amount.");
+ if (*(spec_text + pos + plus_pos) == '-')
+ delta *= -1;
+
+ pb::Modification* mod;
+ if (limit > 1 && pb_mod_table_ptr != &pb_mod_table_)
+ limit = 1;
+
+ if (limit == 0) {
+ mod = pb_mod_table_ptr->add_static_mod();
+ } else {
+ mod = pb_mod_table_ptr->add_variable_mod();
+ mod->set_max_count(limit);
+ unique_delta_.push_back(delta);
+ max_counts_.push_back(limit);
+ }
+ mod->set_amino_acids(string(spec_text + pos, aa_len));
+ mod->set_delta(delta);
+
+ pos += end_pos;
+ if (spec_text[pos] == '\0')
+ break;
+
+ if (spec_text[pos] == ',')
+ ++pos;
+ }
+ return true;
+ }
+ void ClearTables() {
+ pb_mod_table_.Clear();
+ pb_ntpep_mod_table_.Clear();
+ pb_ctpep_mod_table_.Clear();
+ pb_ntpro_mod_table_.Clear();
+ pb_ctpro_mod_table_.Clear();
+ }
+
+ int NumPoss(char aa, MODS_SPEC_TYPE_T mod_table = MOD_SPEC) const {
+ switch (mod_table) {
+ case MOD_SPEC:
+ return possibles_[aa].size();
+ case NTPEP:
+ return possibles_ntpe_[aa].size();
+ case CTPEP:
+ return possibles_ctpe_[aa].size();
+ case NTPRO:
+ return possibles_ntpr_[aa].size();
+ case CTPRO:
+ return possibles_ctpr_[aa].size();
+ }
+ return 0;
+ }
+
+ int PossMaxCt(char aa, int index, MODS_SPEC_TYPE_T mod_table = MOD_SPEC) const {
+ switch (mod_table) {
+ case MOD_SPEC:
+ return possibles_[aa][index].second;
+ case NTPEP:
+ return possibles_ntpe_[aa][index].second;
+ case CTPEP:
+ return possibles_ctpe_[aa][index].second;
+ case NTPRO:
+ return possibles_ntpr_[aa][index].second;
+ case CTPRO:
+ return possibles_ctpr_[aa][index].second;
+ }
+ return 0;
+ }
+
+ int PossDeltIx(char aa, int index, MODS_SPEC_TYPE_T mod_table = MOD_SPEC) const {
+ switch (mod_table) {
+ case MOD_SPEC:
+ return possibles_[aa][index].first;
+ case NTPEP:
+ return possibles_ntpe_[aa][index].first;
+ case CTPEP:
+ return possibles_ctpe_[aa][index].first;
+ case NTPRO:
+ return possibles_ntpr_[aa][index].first;
+ case CTPRO:
+ return possibles_ctpr_[aa][index].first;
+ }
+ return 0;
+ }
+
+ double PossDelta(char aa, int index) const {
+ return unique_delta_[PossDeltIx(aa, index)];
+ }
+
+#if 0
+ const IntPairVec* Possibles(char aa) const {
+ return &possibles_[aa];
+ }
+#endif
+ bool SerializeUniqueDeltas() {
+ if (unique_delta_.size() == 0)
+ return(0);
+ original_deltas_.resize(unique_delta_.size());
+ copy(unique_delta_.begin(), unique_delta_.end(), original_deltas_.begin());
+ sort(unique_delta_.begin(), unique_delta_.end());
+ unique_delta_.resize(unique(unique_delta_.begin(), unique_delta_.end()) - unique_delta_.begin());
+ coder_.Init(unique_delta_.size());
+
+ //The following these need to be in exactly the same order as parsed in the TideIndexApplication.cpp
+ Init(pb_mod_table_);
+ Init(pb_ctpep_mod_table_);
+ Init(pb_ntpep_mod_table_);
+ Init(pb_ctpro_mod_table_);
+ Init(pb_ntpro_mod_table_);
+ SerializeUniqueDeltas(&pb_mod_table_);
+ SerializeUniqueDeltas(&pb_ctpep_mod_table_);
+ SerializeUniqueDeltas(&pb_ntpep_mod_table_);
+ SerializeUniqueDeltas(&pb_ctpro_mod_table_);
+ SerializeUniqueDeltas(&pb_ntpro_mod_table_);
+ return(1);
+ }
+
+ bool SerializeUniqueDeltas(pb::ModTable* pb_mod_table) {
+ if (pb_mod_table->unique_deltas_size() == 0) {
+ vector<double>::iterator iter = unique_delta_.begin();
+ for (; iter != unique_delta_.end(); ++iter)
+ pb_mod_table->add_unique_deltas(*iter);
+ return true;
+ }
+ // if unique deltas already specified, just confirm equality
+ if (pb_mod_table->unique_deltas_size() != unique_delta_.size())
+ return false;
+ for (int i = 0; i < unique_delta_.size(); ++i)
+ if (unique_delta_[i] != pb_mod_table->unique_deltas(i))
+ return false;
+ return true;
+ }
+
+ const pb::ModTable* ParsedModTable() const { return &pb_mod_table_; }
+ const pb::ModTable* ParsedNtpepModTable() const { return &pb_ntpep_mod_table_; }
+ const pb::ModTable* ParsedCtpepModTable() const { return &pb_ctpep_mod_table_; }
+ const vector<int>* MaxCounts() const { return &max_counts_; }
+ const vector<double>* OriginalDeltas() const { return &original_deltas_; }
+
+ int EncodeMod(int aa_index, int unique_delta_index) {
+ return coder_.EncodeMod(aa_index, unique_delta_index);
+ }
+
+ void Show() {
+ SHOW_ONE(unique_delta_.size());
+ SHOW_ALL(unique_delta_);
+ SHOW_ONE(max_counts_.size());
+ SHOW_ALL(max_counts_);
+ const char* aa = "ACDEFGHIKLMNPQRSTVWYX";
+ for (const char* c = aa; *c; ++c) {
+ cout << "possibles_[" << (*c) << "] = ";
+ for (IntPairVec::iterator i = possibles_[*c].begin();
+ i != possibles_[*c].end(); ++i) {
+ cout << "delta: " << i->first << "(" << unique_delta_[i->first] << ")"
+ << " max_count: " << i->second << "(" << max_counts_[i->second]
+ << ") ";
+ }
+ cout << "\n";
+ }
+ }
+ int Unique_delta_size() { return unique_delta_.size(); }
+ private:
+ bool Error(const char* spec_text, int err_pos, const char* msg) {
+ cerr << "Error: couldn't parse modification specification:\n" << spec_text
+ << "\n" << string(err_pos, ' ') << "^\n" << msg << "\n";
+ pb_mod_table_.Clear();
+ return false;
+ }
+
+ typedef vector<pair<int, int> > IntPairVec;
+ IntPairVec possibles_[256]; // unique_delta_, max_count_
+ IntPairVec possibles_ctpe_[256]; // unique_delta_, max_count_ cterminal peptide
+ IntPairVec possibles_ntpe_[256]; // unique_delta_, max_count_ nterminal peptide
+ IntPairVec possibles_ctpr_[256]; // unique_delta_, max_count_ cterminal protein
+ IntPairVec possibles_ntpr_[256]; // unique_delta_, max_count_ nterminal protein
+ vector<double> unique_delta_, original_deltas_;
+ vector<int> max_counts_;
+ int offset_;
+ ModCoder coder_;
+ pb::ModTable pb_mod_table_; //modification table for regular amino acid modifications
+ pb::ModTable pb_ntpep_mod_table_; //modification table for n-terminal peptide modifications
+ pb::ModTable pb_ctpep_mod_table_; //modification table for c-terminal peptide modifications
+ pb::ModTable pb_ntpro_mod_table_; //modification table for n-terminal protein modifications
+ pb::ModTable pb_ctpro_mod_table_; //modification table for c-terminal protein modifications
+};
+
diff --git a/src/app/tide/peptide.cc b/src/app/tide/peptide.cc
new file mode 100644
index 0000000..d2304e6
--- /dev/null
+++ b/src/app/tide/peptide.cc
@@ -0,0 +1,281 @@
+// Benjamin Diament
+
+#include <iostream>
+#include <limits>
+#include <gflags/gflags.h>
+#include "mass_constants.h"
+#include "max_mz.h"
+#include "fifo_alloc.h"
+#include "fixed_cap_array.h"
+#include "theoretical_peak_set.h"
+#include "peptide.h"
+#include "compiler.h"
+
+#ifdef DEBUG
+DEFINE_int32(debug_peptide_id, -1, "Peptide id to debug.");
+#endif
+
+#if 0
+DEFINE_bool(flanks, true, "Include flanking peaks.");
+DEFINE_bool(dups_ok, false, "Don't remove duplicate peaks");
+#endif
+
+string Peptide::SeqWithMods() const {
+ vector<char> buf(Len() + num_mods_ * 30 + 1);
+ int residue_pos = 0;
+ char* buf_pos = &(buf[0]);
+ for (int i = 0; i < num_mods_; ++i) {
+ int index;
+ double delta;
+ MassConstants::DecodeMod(mods_[i], &index, &delta);
+ while (residue_pos <= index)
+ *buf_pos++ = residues_[residue_pos++];
+ buf_pos += sprintf(buf_pos, "[+%.1f]", delta);
+ }
+ while (residue_pos < Len())
+ *buf_pos++ = residues_[residue_pos++];
+ *buf_pos = '\0';
+ return &(buf[0]);
+}
+
+void Peptide::Show() {
+#ifdef DEBUG
+ if (Id() == FLAGS_debug_peptide_id) {
+ cout << Seq() << endl;
+ cout << "Charge 1 Pos" << endl;
+ for (int i = 0; i < peaks_charge_1_.size(); ++i)
+ cout << "Theoretical Peak[" << peaks_charge_1_[i].Bin() << "] = "
+ << peaks_charge_1_[i].Type() << endl;
+ cout << "Charge 1 Neg" << endl;
+ for (int i = 0; i < negs_charge_1_.size(); ++i)
+ cout << "Theoretical Peak[" << negs_charge_1_[i].Bin() << "] = "
+ << negs_charge_1_[i].Type() << endl;
+ cout << "Charge 2 Pos" << endl;
+ for (int i = 0; i < peaks_charge_2_.size(); ++i)
+ cout << "Theoretical Peak[" << peaks_charge_2_[i].Bin() << "] = "
+ << peaks_charge_2_[i].Type() << endl;
+ cout << "Charge 2 Neg" << endl;
+ for (int i = 0; i < negs_charge_2_.size(); ++i)
+ cout << "Theoretical Peak[" << negs_charge_2_[i].Bin() << "] = "
+ << negs_charge_2_[i].Type() << endl;
+ cout << endl;
+ }
+#endif
+}
+
+template<class W>
+void Peptide::AddIons(W* workspace) const {
+ // Use workspace to assemble all B and Y ions. workspace will determine
+ // which, if any, associated ions will be represented.
+ double max_possible_peak = numeric_limits<double>::infinity();
+ if (MaxBin::Global().MaxBinEnd() > 0)
+ max_possible_peak = MaxBin::Global().CacheBinEnd();
+
+ vector<double> aa_masses(Len());
+ const char* residue = residues_;
+ // Collect m/z values for each residue, for z = 1, 2.
+ for (int i = 0; i < Len(); ++i, ++residue) {
+ if (i == 0) { // nterm static pep
+ aa_masses[i] = MassConstants::nterm_mono_table[*residue];
+ } else if (i == Len() - 1) { // cterm static pep
+ aa_masses[i] = MassConstants::cterm_mono_table[*residue];
+ } else { // all other mods
+ aa_masses[i] = MassConstants::mono_table[*residue];
+ }
+ }
+
+ for (int i = 0; i < num_mods_; ++i) {
+ int index;
+ double delta;
+ MassConstants::DecodeMod(mods_[i], &index, &delta);
+ aa_masses[index] += delta;
+ }
+
+ // Add all charge 1 B ions.
+ double total = aa_masses[0];
+ for (int i = 1; i < Len() && total <= max_possible_peak; ++i) {
+ workspace->AddBIon(total, 1);
+ total += aa_masses[i];
+ }
+
+ // Add all charge 1 Y ions.
+ total = aa_masses[Len() - 1];
+ for (int i = Len()-2; i >= 0 && total <= max_possible_peak; --i) {
+ workspace->AddYIon(total, 1);
+ total += aa_masses[i];
+ }
+
+ // Add all charge 2 B ions.
+ max_possible_peak = max_possible_peak*2 + 2; //adjust for larger charge
+ total = aa_masses[0];
+ for (int i = 1; i < Len() && total <= max_possible_peak; ++i) {
+ workspace->AddBIon(total, 2);
+ total += aa_masses[i];
+ }
+
+ // Add all charge 2 Y ions.
+ total = aa_masses[Len() - 1];
+ for (int i = Len()-2; i >= 0 && total <= max_possible_peak; --i) {
+ workspace->AddYIon(total, 2);
+ total += aa_masses[i];
+ }
+}
+
+template<class W>
+void Peptide::AddBIonsOnly(W* workspace) const {
+ // Use workspace to assemble b ions only.
+ // Intended primarily to support XCorr p-value calculations.
+ double max_possible_peak = numeric_limits<double>::infinity();
+ if (MaxBin::Global().MaxBinEnd() > 0) {
+ max_possible_peak = MaxBin::Global().CacheBinEnd();
+ }
+
+ vector<double> aa_masses(Len());
+ const char* residue = residues_;
+ // Collect m/z values for each residue, for z = 1.
+ for (int i = 0; i < Len(); ++i, ++residue) {
+ if (i == 0) { // nterm static pep
+ aa_masses[i] = MassConstants::nterm_mono_table[*residue];
+ } else if (i == Len() - 1) { // cterm static pep
+ aa_masses[i] = MassConstants::cterm_mono_table[*residue];
+ } else { // all other mods
+ aa_masses[i] = MassConstants::mono_table[*residue];
+ }
+ }
+
+ //Add modifications to amino acids
+ for (int i = 0; i < num_mods_; ++i) {
+ int index;
+ double delta;
+ MassConstants::DecodeMod(mods_[i], &index, &delta);
+ aa_masses[index] += delta;
+ }
+
+ // Add all charge 1 B ions.
+ double total = MassConstants::proton + aa_masses[0];
+ for (int i = 1; i < Len() && total <= max_possible_peak; ++i) {
+ workspace -> AddBIon(total);
+ total += aa_masses[i];
+ }
+}
+
+#ifdef DEBUG
+void DisAsm(const void* prog) {
+ unsigned char* pos = (unsigned char*) prog;
+ while (true) {
+ switch(*pos) {
+ case 3: assert(pos[1] == 130); cout << "add " << *((int*) (void*) (pos+2)) << "(%edx), %eax\n"; pos += 6; break;
+ case 43: assert(pos[1] == 130); cout << "sub " << *((int*) (void*) (pos+2)) << "(%edx), %eax\n"; pos += 6; break;
+ case 195: cout << "ret" << endl; goto out;
+ default: assert(false);
+ }
+ }
+ out:
+ return;
+}
+#endif
+
+void Peptide::Compile(const TheoreticalPeakArr* peaks,
+ const pb::Peptide& pb_peptide,
+ TheoreticalPeakCompiler* compiler_prog1,
+ TheoreticalPeakCompiler* compiler_prog2) {
+ int pos_size = peaks[0].size();
+ prog1_ = compiler_prog1->Init(pos_size, 0);
+ compiler_prog1->AddPositive(peaks[0]);
+// compiler_prog1->AddPositive(pb_peptide.peak1());
+// compiler_prog1->AddNegative(pb_peptide.neg_peak1());
+ compiler_prog1->Done();
+
+ pos_size = peaks[0].size() + peaks[1].size();
+ prog2_ = compiler_prog2->Init(pos_size, 0);
+ compiler_prog2->AddPositive(peaks[0]);
+ compiler_prog2->AddPositive(peaks[1]);
+// compiler_prog2->AddPositive(pb_peptide.peak2());
+// compiler_prog2->AddNegative(pb_peptide.neg_peak2());
+ compiler_prog2->Done();
+/* cout << Seq() << endl;
+ for (int i = 0; i < peaks[0].size(); ++i)
+ cout << "Theoretical Peak[" << peaks[0][i].Bin() << "] = "
+ << peaks[0][i].Type() << endl;
+ for (int i = 0; i < peaks[1].size(); ++i)
+ cout << "Theoretical Peak[" << peaks[1][i].Bin() << "] = "
+ << peaks[1][i].Type() << endl;
+*/
+// exit(1);
+}
+
+void Peptide::ComputeTheoreticalPeaks(TheoreticalPeakSet* workspace) const {
+ AddIons<TheoreticalPeakSet>(workspace); // Generic workspace
+#ifdef DEBUG
+ Show();
+#endif
+}
+
+void Peptide::ComputeBTheoreticalPeaks(TheoreticalPeakSetBIons* workspace) const {
+ AddBIonsOnly<TheoreticalPeakSetBIons>(workspace); // workspace for b ion only peak set
+#ifdef DEBUG
+ Show();
+#endif
+}
+
+void Peptide::ComputeTheoreticalPeaks(ST_TheoreticalPeakSet* workspace,
+ const pb::Peptide& pb_peptide,
+ TheoreticalPeakCompiler* compiler_prog1,
+ TheoreticalPeakCompiler* compiler_prog2) {
+ // Search-time fast workspace
+ AddIons<ST_TheoreticalPeakSet>(workspace);
+
+#if 0
+ TheoreticalPeakArr peaks[2];
+ peaks[0].Init(2000);
+ peaks[1].Init(2000);
+ workspace->GetPeaks(&peaks[0], NULL, &peaks[1], NULL, NULL);
+ Compile(peaks, pb_peptide, compiler_prog1, compiler_prog2);
+#endif
+
+ Compile(workspace->GetPeaks(), pb_peptide, compiler_prog1, compiler_prog2);
+#ifdef DEBUG
+ if (Id() == FLAGS_debug_peptide_id) {
+ cout << "Prog1:" << endl;
+ DisAsm(prog1_);
+ cout << "Prog2:" << endl;
+ DisAsm(prog2_);
+ }
+#endif
+}
+
+// return the amino acid masses in the current peptide
+double* Peptide::getAAMasses(){
+ double* masses_charge = new double[Len()];
+ const char* residue = residues_;
+ for (int i = 0; i < Len(); ++i, ++residue) {
+ if (i == 0) { // nterm static pep
+ masses_charge[i] = MassConstants::nterm_mono_table[*residue];
+ } else if (i == Len() - 1) { // cterm static pep
+ masses_charge[i] = MassConstants::cterm_mono_table[*residue];
+ } else { // all other mods
+ masses_charge[i] = MassConstants::mono_table[*residue];
+ }
+ }
+ for (int i = 0; i < num_mods_; ++i) {
+ int index;
+ double delta;
+ MassConstants::DecodeMod(mods_[i], &index, &delta);
+ masses_charge[index] += delta;
+ }
+ return masses_charge;
+}
+
+// Probably defunct, uses old calling format.
+int NoInlineDotProd(Peptide* peptide, const int* cache, int charge) {
+ const void* prog = peptide->Prog(charge);
+ int result;
+#ifdef _MSC_VER
+ // FIXME CEG add Windows compatible inline assembly
+#else
+ __asm__ __volatile__("call *%[prog]\n"
+ : "=a" (result)
+ : "d" (cache), [prog] "abcSD" (prog));
+#endif
+ return result;
+}
diff --git a/src/app/tide/peptide.h b/src/app/tide/peptide.h
new file mode 100644
index 0000000..b3c0352
--- /dev/null
+++ b/src/app/tide/peptide.h
@@ -0,0 +1,244 @@
+// Benjamin Diament
+
+// Peptide is a class for managing the representation of a peptide and its
+// associated theoretical peaks for use at search time. It encapsulates a
+// diverse set of functions, interacting closely with TheoreticalPeakSet,
+// TheoreticalPeakCompiler, ActivePeptideQueue, and DotProd() (defined in
+// search.cc). At indexing time this class is used with TheoreticalPeakSet to
+// store peaks to a protocol buffer.
+//
+// TODO 255: the intractions with other classes are complicated, and the various
+// functionalities here could probably be encapsulated with cleaner interfaces.
+// Perhaps one way to clean this up would be to make two different Peptide
+// classes: one for indexing and another for searching.
+//
+// At search time, ActivePeptideQueue (see active_peptide_queue.{h,cc})
+// manages the task of reading Peptides from storage and keeping current
+// candidate Peptides in memory. Each Peptide knows how to take the dot
+// product of its theoretical peaks with a given observed spectrum.
+// Specifically, ComputeTheoreticalPeaks() generates a compiled program for
+// doing so. A different version of the generated program exists for charge 1
+// and charge 2.
+
+#ifndef PEPTIDE_H
+#define PEPTIDE_H
+
+#include <iostream>
+#include <vector>
+#include "raw_proteins.pb.h"
+#include "peptides.pb.h"
+#include "theoretical_peak_pair.h"
+#include "fifo_alloc.h"
+#include "mod_coder.h"
+#include "sp_scorer.h"
+
+#include "spectrum_collection.h"
+//#include "TideMatchSet.h"
+
+using namespace std;
+
+class FifoAllocator;
+class TheoreticalPeakSet;
+class TheoreticalPeakSetBIons;
+class SpScorer;
+
+
+// This is the TheoreticalPeakSet we are using at search time. We may use a
+// different subclass of TheoreticalPeakSet in a final version, pending more
+// tests. See Bugzilla #253.
+class TheoreticalPeakSetBYSparse;
+typedef TheoreticalPeakSetBYSparse ST_TheoreticalPeakSet; // ST="search time"
+// This is an alternative TheoreticalPeakSet
+// class TheoreticalPeakSetBYSparseOrdered;
+// typedef TheoreticalPeakSetBYSparseOrdered ST_TheoreticalPeakSet;
+// This alternative TheoreticalPeakSet is slow but slightly more flexible.
+// class TheoreticalPeakSetMakeAll;
+// typedef TheoreticalPeakSetMakeAll ST_TheoreticalPeakSet; // ST="search time"
+
+class TheoreticalPeakCompiler;
+
+// BIG CAUTION: At search time, you CANNOT expect even the IMPLICIT destructor
+// to get called!! We actually RELY on the fact that when we use FIFO
+// allocation, the destructor won't get called. We expect the destructor to
+// get called only when the object is created using the normal system memory
+// allocation. This way, we can use the destructor to clean up the system
+// memory allocated for mods_ when FIFO allocation is NOT used.
+class Peptide {
+ public:
+ // The proteins parameter is presumed to live in memory all the while the
+ // Peptide exists, so that residues_ can refer to the amino acid sequence.
+ Peptide(const pb::Peptide& peptide,
+ const vector<const pb::Protein*>& proteins,
+ FifoAllocator* fifo_alloc = NULL)
+ : len_(peptide.length()), mass_(peptide.mass()), id_(peptide.id()),
+ first_loc_protein_id_(peptide.first_location().protein_id()),
+ first_loc_pos_(peptide.first_location().pos()),
+ has_aux_locations_index_(peptide.has_aux_locations_index()),
+ aux_locations_index_(peptide.aux_locations_index()),
+ mods_(NULL), num_mods_(0), decoy_(peptide.is_decoy()),
+ prog1_(NULL), prog2_(NULL) {
+ // Set residues_ by pointing to the first occurrence in proteins.
+ residues_ = proteins[first_loc_protein_id_]->residues().data()
+ + first_loc_pos_;
+ if (peptide.modifications_size() > 0) {
+ num_mods_ = peptide.modifications_size();
+ if (fifo_alloc) {
+ mods_ = (ModCoder::Mod*) fifo_alloc->New(sizeof(mods_[0]) * num_mods_);
+ } else {
+ mods_ = new ModCoder::Mod[num_mods_];
+ }
+ for (int i = 0; i < num_mods_; ++i)
+ mods_[i] = ModCoder::Mod(peptide.modifications(i));
+ }
+ }
+ class spectrum_matches {
+ public:
+ spectrum_matches(Spectrum* spectrum, double score1, double score2,
+ int score3, int charge) {
+ spectrum_ = spectrum;
+ score1_ = score1;
+ score2_ = score2;
+ score3_ = score3;
+ charge_ = charge;
+ d_cn_ = 0.0;
+ elution_score_ = 0.0;
+ }
+ spectrum_matches() {
+ spectrum_ = NULL;
+ score1_ = 0.0;
+ score2_ = 0.0;
+ score3_ = 0.0;
+ charge_ = 0;
+ d_cn_ = 0.0;
+ elution_score_ = 0.0;
+ }
+ Spectrum* spectrum_;
+ double score1_;
+ double score2_;
+ int score3_;
+ int charge_;
+ double d_cn_;
+ double elution_score_;
+ SpScorer::SpScoreData spData_;
+
+ static bool compPV(const spectrum_matches &a, const spectrum_matches &b) {
+ return a.score1_ < b.score1_;
+ }
+ static bool compSC(const spectrum_matches &a, const spectrum_matches &b) {
+ return a.score1_ > b.score1_;
+ }
+ static bool compRT(const spectrum_matches &a, const spectrum_matches &b) {
+ return a.spectrum_->RTime() < b.spectrum_->RTime();
+ }
+ static bool compES(const spectrum_matches &a, const spectrum_matches &b) {
+ return a.elution_score_ < b.elution_score_;
+ }
+ };
+ vector<spectrum_matches> spectrum_matches_array;
+ void AddHit(Spectrum* spectrum, double score1, double score2,
+ int score3, int charge) {
+
+ spectrum_matches_array.push_back(spectrum_matches(spectrum,
+ score1, score2, score3, charge));
+ }
+
+ // CAUTION: We do NOT expect this destructor to get called when FIFO
+ // allocation is used. It will get called only when normal system memory
+ // is used for allocation. Please see the BIG CAUTION message at the top
+ // of the class definition for details.
+ ~Peptide() {
+ delete[] mods_;
+ }
+
+ // Allocation by FifoAllocator
+ void* operator new(size_t size, FifoAllocator* fifo_alloc) {
+ return fifo_alloc->New(size);
+ }
+
+ string Seq() const { return string(residues_, Len()); } // For display
+
+ string SeqWithMods() const;
+
+ // Compute and cache set of theoretical peaks using the provided workspace.
+ // Workspace exists for efficiency: it can be reused by another Peptide
+ // without reallocating memory. The pb_peptide should be the same as supplied
+ // during construction, but this class doesn't own or store the underlying
+ // pb::Peptide, as it is probably not FifoAllocated.
+ // The first version takes a generic workspace (good for index generation and
+ // testing). The second version is intended to be faster at search time: a
+ // specific subclass of TheoreticalPeakSet is given, which should avoid
+ // associated virtual method calls. (TODO 256: are virtual method calls indeed
+ // avoided?). The second version also produces the compiled programs for
+ // taking dot products.
+ void ComputeTheoreticalPeaks(TheoreticalPeakSet* workspace) const;
+ void ComputeTheoreticalPeaks(ST_TheoreticalPeakSet* workspace,
+ const pb::Peptide& pb_peptide,
+ TheoreticalPeakCompiler* compiler_prog1,
+ TheoreticalPeakCompiler* compiler_prog2);
+ void ComputeBTheoreticalPeaks(TheoreticalPeakSetBIons* workspace) const;
+
+ // Return the appropriate program depending on the precursor charge.
+ // TODO 257: fix the unfortunate use of max_charge.
+ const void* Prog(int max_charge) const {
+ return max_charge <= 2 ? prog1_ : prog2_;
+ }
+
+ void ReleaseFifo(FifoAllocator* fifo_alloc_prog1,
+ FifoAllocator* fifo_alloc_prog2) {
+ // TODO 258: this code should probably move to ActivePeptideQueue
+ if (prog1_ != NULL) {
+ fifo_alloc_prog1->Release(prog1_);
+ } else {
+ fifo_alloc_prog1->ReleaseAll();
+ }
+ if (prog2_ != NULL) {
+ fifo_alloc_prog2->Release(prog2_);
+ } else {
+ fifo_alloc_prog2->ReleaseAll();
+ }
+ }
+
+ int Len() const { return len_; }
+ double Mass() const { return mass_; }
+ int Id() const { return id_; }
+ int FirstLocProteinId() const { return first_loc_protein_id_; }
+ int FirstLocPos() const { return first_loc_pos_; }
+ bool HasAuxLocationsIndex() const { return has_aux_locations_index_; }
+ int AuxLocationsIndex() const { return aux_locations_index_; }
+ int Mods(const ModCoder::Mod** mods) const {
+ *mods = mods_;
+ return num_mods_;
+ }
+ ModCoder::Mod* Mods() const { return mods_; }
+ bool IsDecoy() const { return decoy_; }
+ double* getAAMasses();
+
+ private:
+ template<class W> void AddIons(W* workspace) const;
+ template<class W> void AddBIonsOnly(W* workspace) const;
+
+ void Compile(const TheoreticalPeakArr* peaks,
+ const pb::Peptide& pb_peptide,
+ TheoreticalPeakCompiler* compiler_prog1,
+ TheoreticalPeakCompiler* compiler_prog2);
+
+
+ void Show();
+
+ int len_;
+ double mass_;
+ int id_;
+ int first_loc_protein_id_;
+ int first_loc_pos_;
+ bool has_aux_locations_index_;
+ int aux_locations_index_;
+ const char* residues_;
+ int num_mods_;
+ ModCoder::Mod* mods_;
+ bool decoy_;
+
+ void* prog1_;
+ void* prog2_;
+};
+
+#endif // PEPTIDE_H
diff --git a/src/app/tide/peptide_mods3.cc b/src/app/tide/peptide_mods3.cc
new file mode 100644
index 0000000..f1bb13e
--- /dev/null
+++ b/src/app/tide/peptide_mods3.cc
@@ -0,0 +1,498 @@
+// Benjamin Diament
+//
+
+#include <stdio.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#else
+#include <windows.h>
+#endif
+#include <string>
+#include <vector>
+#include <algorithm>
+#include <numeric>
+#include <gflags/gflags.h>
+#include "abspath.h"
+#include "records.h"
+#include "records_to_vector-inl.h"
+#include "header.pb.h"
+#include "raw_proteins.pb.h"
+#include "peptides.pb.h"
+#include "mass_constants.h"
+#include "modifications.h"
+#include "util/FileUtils.h"
+#include "io/carp.h"
+
+using namespace std;
+
+#define CHECK(x) GOOGLE_CHECK(x)
+
+DEFINE_int32(buf_size, 1024, "Buffer size for files, in KBytes.");
+DEFINE_int32(max_mods, 255, "Maximum number of modifications that can be applied "
+ "to a single peptide.");
+DEFINE_int32(min_mods, 0, "Minimum number of modifications that can be applied "
+ "to a single peptide.");
+
+static string GetTempName(string tmpDir, int filenum) {
+ char buf[36];
+ sprintf(buf, "modified_peptides_partial_%d", filenum);
+ if (tmpDir != "") {
+ return FileUtils::Join(tmpDir, buf);
+ }
+#ifdef _MSC_VER
+ char buf2[261];
+ GetTempPath(261, buf2);
+ return FileUtils::Join(string(buf2), buf);
+#else
+ return FileUtils::Join(string("/tmp/"), buf);
+#endif
+}
+
+class ModsOutputter {
+ public:
+ unsigned long modpeptidecnt_;
+ ModsOutputter(string tmpDir,
+ const vector<const pb::Protein*>& proteins,
+ VariableModTable* var_mod_table,
+ HeadedRecordWriter* final_writer)
+ : proteins_(proteins),
+ mod_table_(var_mod_table),
+ max_counts_(*mod_table_->MaxCounts()),
+ counts_mapper_vec_(max_counts_.size(), 0),
+ final_writer_(final_writer),
+ count_(0) {
+ InitCountsMapper(tmpDir);
+ }
+
+ ~ModsOutputter() {
+ for (int i = 0; i < writers_.size(); ++i)
+ delete writers_[i];
+ Merge();
+ }
+
+ void Output(pb::Peptide* peptide) {
+ peptide_ = peptide;
+ const pb::Location& loc = peptide->first_location();
+ residues_ = proteins_[loc.protein_id()]->residues().data() + loc.pos();
+ vector<int> counts(max_counts_.size(), 0);
+ OutputNtermMods(0, counts);
+ }
+
+ private:
+ string tmpDir_;
+ void OutputMods(int pos, vector<int>& counts);
+ void OutputNtermMods(int pos, vector<int>& counts);
+ void OutputCtermMods(int pos, vector<int>& counts);
+ void Merge();
+
+ void InitCountsMapper(string tmpDir) {
+ tmpDir_ = tmpDir;
+
+ int prod = 1;
+ for (int i = 0; i < max_counts_.size(); ++i) {
+ counts_mapper_vec_[i] = prod;
+ if (max_counts_[i] == 0)
+ prod *= (max_counts_[i]+2);
+ else
+ prod *= (max_counts_[i]+1);
+ }
+
+ writers_.resize(prod);
+ if (prod > 100) {
+ carp(CARP_INFO, "Opening %d files for modifications.", prod);
+ }
+
+ for (int i = 0; i < prod; ++i) {
+ writers_[i] = new RecordWriter(GetTempName(tmpDir, i), FLAGS_buf_size << 10);
+ if (!writers_[i]->OK()) {
+ // delete temporary files
+ for (int j = 0; j < i; ++j)
+ unlink(GetTempName(tmpDir, j).c_str());
+ CHECK(writers_[i]->OK());
+ }
+ }
+
+ const vector<double>& deltas = *mod_table_->OriginalDeltas();
+ delta_by_file_.resize(prod);
+ for (int i = 0; i < prod; ++i) {
+ double total_delta = 0;
+ int x = i;
+ for (int j = max_counts_.size() - 1; j >= 0; --j) {
+ int digit = x / counts_mapper_vec_[j];
+ x %= counts_mapper_vec_[j];
+ total_delta += deltas[j] * digit;
+ }
+ delta_by_file_[i] = total_delta;
+ }
+ }
+
+ int TotalMods(const vector<int>& counts) {
+ return accumulate(counts.begin(), counts.end(), 0);
+ }
+
+ int DotProd(const vector<int>& counts) {
+ int dot = 0;
+ for (int i = 0; i < counts.size(); ++i)
+ dot += counts_mapper_vec_[i] * counts[i];
+ return dot;
+ }
+
+ RecordWriter* Write(const vector<int>& counts) {
+ ++modpeptidecnt_;
+ int index = DotProd(counts);
+ double mass = peptide_->mass();
+ peptide_->set_mass(delta_by_file_[index] + mass);
+ if (!writers_[index]->Write(peptide_)) {
+ carp(CARP_FATAL, "I/O error writing modifications");
+ }
+ peptide_->set_mass(mass);
+ return writers_[index];
+ }
+
+ const vector<const pb::Protein*>& proteins_;
+ VariableModTable* mod_table_;
+ const vector<int>& max_counts_;
+ vector<int> counts_mapper_vec_;
+ vector<RecordWriter*> writers_;
+ vector<double> delta_by_file_;
+ HeadedRecordWriter* final_writer_;
+ int count_;
+
+ pb::Peptide* peptide_;
+ const char* residues_;
+};
+
+//terminal modifications count as a modification and hence
+//it is taken into account the modification limit.
+void ModsOutputter::OutputMods(int pos, vector<int>& counts) {
+ if (TotalMods(counts) > FLAGS_max_mods) {
+ return;
+ }
+ if (pos == peptide_->length()) {
+ OutputCtermMods(pos-1, counts);
+ } else {
+ if (pos == peptide_->length()-1){
+ OutputCtermMods(pos, counts);
+ } else {
+ char aa = residues_[pos];
+ int num_poss = mod_table_->NumPoss(aa);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i);
+ if (counts[poss_max_ct] < max_counts_[poss_max_ct]) {
+ ++counts[poss_max_ct];
+ int delta_index = mod_table_->PossDeltIx(aa, i);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+ OutputMods(pos+1, counts);
+ peptide_->mutable_modifications()->RemoveLast();
+ --counts[poss_max_ct];
+ }
+ }
+ // Having this call to OutputMods come last is, in fact, correct, but it's
+ // tricky to see why. When modified peptides have equal mass, we want
+ // modified positions toward the front of the peptide to appear before those
+ // that come toward the end of the peptide. Having this call at the end
+ // achieves that.
+ OutputMods(pos+1, counts); // without further mods
+ }
+ }
+}
+
+void ModsOutputter::OutputNtermMods(int pos, vector<int>& counts) {
+ if (TotalMods(counts) > FLAGS_max_mods) {
+ return;
+ }
+ bool any_term_modification = false;
+
+ //add static N-terminal modifications
+ char aa = residues_[0];
+ int num_poss = mod_table_->NumPoss(aa, NTPEP);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i, NTPEP);
+ if (max_counts_[poss_max_ct] == 0) {
+ int delta_index = mod_table_->PossDeltIx(aa, i, NTPEP);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+ OutputMods(1, counts);
+ peptide_->mutable_modifications()->RemoveLast();
+ any_term_modification = true;
+ }
+ }
+ aa = 'X';
+ num_poss = mod_table_->NumPoss(aa, NTPEP);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i, NTPEP);
+ if (max_counts_[poss_max_ct] == 0) {
+ int delta_index = mod_table_->PossDeltIx(aa, i, NTPEP);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+ OutputMods(1, counts);
+ peptide_->mutable_modifications()->RemoveLast();
+ any_term_modification = true;
+ }
+ }
+ if (any_term_modification == false){
+ //if there were no static modificatinos add variable terminal modifications
+ aa = residues_[0];
+ num_poss = mod_table_->NumPoss(aa, NTPEP);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i, NTPEP);
+ if (max_counts_[poss_max_ct] == 1) {
+ ++counts[poss_max_ct];
+ int delta_index = mod_table_->PossDeltIx(aa, i, NTPEP);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+ OutputMods(1, counts);
+ peptide_->mutable_modifications()->RemoveLast();
+ --counts[poss_max_ct];
+ any_term_modification = true;
+ }
+ }
+ aa = 'X';
+ num_poss = mod_table_->NumPoss(aa, NTPEP);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i, NTPEP);
+ if (max_counts_[poss_max_ct] == 1) {
+ ++counts[poss_max_ct];
+ int delta_index = mod_table_->PossDeltIx(aa, i, NTPEP);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+ OutputMods(1, counts);
+ peptide_->mutable_modifications()->RemoveLast();
+ --counts[poss_max_ct];
+ any_term_modification = true;
+ }
+ }
+ OutputMods(0, counts);
+ }
+}
+
+void ModsOutputter::OutputCtermMods(int pos, vector<int>& counts) {
+ int total = TotalMods(counts);
+ if (total > FLAGS_max_mods) {
+ return;
+ } else if (total == FLAGS_max_mods) {
+ if (total >= FLAGS_min_mods) {
+ peptide_->set_id(count_++);
+ Write(counts);
+ }
+ return;
+ }
+
+ bool any_term_modification = false;
+ char aa = residues_[pos];
+ int num_poss = mod_table_->NumPoss(aa, CTPEP);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i, CTPEP);
+ if (max_counts_[poss_max_ct] == 0) {
+ int delta_index = mod_table_->PossDeltIx(aa, i, CTPEP);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+
+ if (TotalMods(counts) >= FLAGS_min_mods) {
+ peptide_->set_id(count_++);
+ Write(counts);
+ }
+
+ peptide_->mutable_modifications()->RemoveLast();
+ any_term_modification = true;
+ }
+ }
+ aa = 'X';
+ num_poss = mod_table_->NumPoss(aa, CTPEP);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i, CTPEP);
+ if (max_counts_[poss_max_ct] == 0) {
+ int delta_index = mod_table_->PossDeltIx(aa, i, CTPEP);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+
+ if (TotalMods(counts) >= FLAGS_min_mods) {
+ peptide_->set_id(count_++);
+ Write(counts);
+ }
+
+ peptide_->mutable_modifications()->RemoveLast();
+ any_term_modification = true;
+ }
+ }
+ if (any_term_modification == false){
+ //if there were no static modifications add amino acid mods
+ char aa = residues_[pos];
+ int num_poss = mod_table_->NumPoss(aa);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i);
+ if (counts[poss_max_ct] < max_counts_[poss_max_ct]) {
+ ++counts[poss_max_ct];
+ int delta_index = mod_table_->PossDeltIx(aa, i);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+
+ if (TotalMods(counts) >= FLAGS_min_mods) {
+ peptide_->set_id(count_++);
+ Write(counts);
+ }
+
+ peptide_->mutable_modifications()->RemoveLast();
+ --counts[poss_max_ct];
+ }
+ }
+
+ //add variable c-terminal mods
+ aa = residues_[pos];
+ num_poss = mod_table_->NumPoss(aa, CTPEP);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i, CTPEP);
+ if (max_counts_[poss_max_ct] == 1) {
+ ++counts[poss_max_ct];
+ int delta_index = mod_table_->PossDeltIx(aa, i, CTPEP);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+
+ if (TotalMods(counts) >= FLAGS_min_mods) {
+ peptide_->set_id(count_++);
+ Write(counts);
+ }
+
+ peptide_->mutable_modifications()->RemoveLast();
+ --counts[poss_max_ct];
+ any_term_modification = true;
+ }
+ }
+ aa = 'X';
+ num_poss = mod_table_->NumPoss(aa, CTPEP);
+ for (int i = 0; i < num_poss; ++i) {
+ int poss_max_ct = mod_table_->PossMaxCt(aa, i, CTPEP);
+ if (max_counts_[poss_max_ct] == 1) {
+ ++counts[poss_max_ct];
+ int delta_index = mod_table_->PossDeltIx(aa, i, CTPEP);
+ peptide_->add_modifications(mod_table_->EncodeMod(pos, delta_index));
+
+ if (TotalMods(counts) >= FLAGS_min_mods) {
+ peptide_->set_id(count_++);
+ Write(counts);
+ }
+
+ peptide_->mutable_modifications()->RemoveLast();
+ --counts[poss_max_ct];
+ any_term_modification = true;
+ }
+ }
+ if (TotalMods(counts) >= FLAGS_min_mods) {
+ peptide_->set_id(count_++);
+ Write(counts);
+ }
+ }
+}
+
+class PepReader {
+ public:
+ PepReader(const string& filename)
+ : reader_(filename, FLAGS_buf_size << 10) {
+ CHECK(reader_.OK());
+ }
+
+ bool operator<(const PepReader& other) {
+ double mass = current_.mass();
+ double other_mass = other.current_.mass();
+ if (mass < other_mass)
+ return true;
+ if (mass > other_mass)
+ return false;
+ return current_.id() < other.current_.id();
+ }
+
+ bool Advance() {
+ if (reader_.Done())
+ return false;
+ reader_.Read(¤t_);
+ CHECK(reader_.OK());
+ return true;
+ }
+
+ pb::Peptide* Current() { return ¤t_; }
+
+ private:
+ RecordReader reader_;
+ pb::Peptide current_;
+};
+
+struct greater_pepreader
+ : public binary_function<PepReader*, PepReader*, bool> {
+ bool operator()(PepReader* x, PepReader* y) {
+ if (x == y)
+ return false;
+ return *y < *x;
+ }
+};
+
+void ModsOutputter::Merge() {
+ int num_files = writers_.size();
+ vector<PepReader*> readers(num_files);
+ for (int i = 0; i < num_files; ++i)
+ readers[i] = new PepReader(GetTempName(tmpDir_, i));
+
+ // initialize heap
+ PepReader** heap_end = &(readers[0]) + num_files;
+ for (PepReader** reader = &(readers[0]); reader < heap_end; ++reader)
+ if (!(*reader)->Advance())
+ swap(*reader--, *--heap_end);
+ make_heap(&(readers[0]), heap_end, greater_pepreader());
+
+ // do heap merge
+ int id = 0;
+#ifndef NDEBUG
+ double last_mass = 0.0;
+#endif
+ while (heap_end > &(readers[0])) {
+ pop_heap(&(readers[0]), heap_end, greater_pepreader());
+ pb::Peptide* current = (*(heap_end-1))->Current();
+ current->set_id(id++);
+#ifndef NDEBUG
+ assert(current->mass() >= last_mass);
+ last_mass = current->mass();
+#endif
+ final_writer_->Write(current);
+ CHECK(final_writer_->OK());
+ if ((*(heap_end-1))->Advance()) {
+ push_heap(&(readers[0]), heap_end, greater_pepreader());
+ } else {
+ --heap_end;
+ }
+ }
+
+ // delete temporary files
+ for (int i = 0; i < num_files; ++i) {
+ delete readers[i];
+ unlink(GetTempName(tmpDir_, i).c_str());
+ }
+}
+
+void AddMods(HeadedRecordReader* reader, string out_file,
+ string tmpDir,
+ const pb::Header& header,
+ const vector<const pb::Protein*>& proteins,
+ VariableModTable& var_mod_table) {
+ CHECK(reader->OK());
+ HeadedRecordWriter writer(out_file, header, FLAGS_buf_size << 10);
+ CHECK(writer.OK());
+ ModsOutputter outputter(tmpDir, proteins, &var_mod_table, &writer);
+ outputter.modpeptidecnt_ = 0;
+ pb::Peptide peptide;
+ while (!reader->Done()) {
+ CHECK(reader->Read(&peptide));
+ outputter.Output(&peptide);
+ }
+ carp(CARP_INFO, "Created %d peptides.", outputter.modpeptidecnt_);
+ CHECK(reader->OK());
+}
+
+void AddMods(HeadedRecordReader* reader, string out_file,
+ string tmpDir,
+ const pb::Header& header,
+ const vector<const pb::Protein*>& proteins) {
+ VariableModTable var_mod_table;
+ var_mod_table.Init(header.peptides_header().mods());
+ CHECK(reader->OK());
+ HeadedRecordWriter writer(out_file, header, FLAGS_buf_size << 10);
+ CHECK(writer.OK());
+ ModsOutputter outputter(tmpDir, proteins, &var_mod_table, &writer);
+
+ pb::Peptide peptide;
+ while (!reader->Done()) {
+ CHECK(reader->Read(&peptide));
+ outputter.Output(&peptide);
+ }
+ CHECK(reader->OK());
+}
diff --git a/src/app/tide/peptide_peaks.cc b/src/app/tide/peptide_peaks.cc
new file mode 100644
index 0000000..8630186
--- /dev/null
+++ b/src/app/tide/peptide_peaks.cc
@@ -0,0 +1,97 @@
+// Benjamin Diament
+//
+// Add to the index of peptide records the pre-computed theoretical peaks.
+// We store the TheoreticalPeakSetDiff (q.v.) for each peptide.
+//
+// Example command-line:
+// peptide_peaks --proteins=<raw_proteins.proto input file> \
+// --in_peptides=<peptides.proto input file> \
+// --out_peptides=<peptides.proto output file> \
+//
+// Rather than store the code for each peak in the diff set, we store the
+// delta between each pair. This gives us a bit of compression since the
+// values are stored as varint. The peak locations then have to be restored
+// at search time.
+//
+// TODO 248: We're only doing this to guarantee the exact same results as Crux
+// used to return, but perhaps the diffs don't really add useful info, in which
+// case we could eliminate them.
+
+#include <stdio.h>
+#include <iostream>
+#include <string>
+#include <vector>
+#include "records.h"
+#include "peptide.h"
+#include "theoretical_peak_set.h"
+#include "abspath.h"
+
+using namespace std;
+
+#define CHECK(x) GOOGLE_CHECK(x)
+/*
+static void AddPeaksToPB(pb::Peptide* peptide, const TheoreticalPeakArr* peaks,
+ int charge, bool neg) {
+ int last_code = 0;
+ TheoreticalPeakArr::const_iterator i = peaks->begin();
+ for (; i != peaks->end(); ++i) {
+ int delta = i->Code() - last_code;
+ last_code = i->Code();
+ if (neg) {
+ if (charge == 1) {
+ peptide->add_neg_peak1(delta);
+ } else {
+ peptide->add_neg_peak2(delta);
+ }
+ } else {
+ if (charge == 1) {
+ peptide->add_peak1(delta);
+ } else {
+ peptide->add_peak2(delta);
+ }
+ }
+ }
+}
+*/
+
+void AddTheoreticalPeaks(const vector<const pb::Protein*>& proteins,
+ const string& input_filename,
+ const string& output_filename) {
+ pb::Header orig_header, new_header;
+ HeadedRecordReader reader(input_filename, &orig_header);
+ CHECK(orig_header.file_type() == pb::Header::PEPTIDES);
+ CHECK(orig_header.has_peptides_header());
+// MassConstants::Init(&orig_header.peptides_header().mods());
+ new_header.set_file_type(pb::Header::PEPTIDES);
+ pb::Header_PeptidesHeader* subheader = new_header.mutable_peptides_header();
+ subheader->CopyFrom(orig_header.peptides_header());
+ subheader->set_has_peaks(true);
+ pb::Header_Source* source = new_header.add_source();
+ source->mutable_header()->CopyFrom(orig_header);
+ source->set_filename(AbsPath(input_filename));
+ HeadedRecordWriter writer(output_filename, new_header);
+ CHECK(reader.OK());
+ CHECK(writer.OK());
+
+ pb::Peptide pb_peptide;
+// const int workspace_size = 2000; // More than sufficient for theor. peaks.
+// TheoreticalPeakSetDiff workspace(workspace_size);
+ while (!reader.Done()) {
+ reader.Read(&pb_peptide);
+/* Peptide peptide(pb_peptide, proteins);
+ workspace.Clear();
+ peptide.ComputeTheoreticalPeaks(&workspace);
+ TheoreticalPeakArr peaks_charge_1(2000);
+ TheoreticalPeakArr peaks_charge_2(2000);
+ TheoreticalPeakArr negs_charge_1(2000);
+ TheoreticalPeakArr negs_charge_2(2000);
+ workspace.GetPeaks(&peaks_charge_1, &negs_charge_1,
+ &peaks_charge_2, &negs_charge_2, NULL);
+ AddPeaksToPB(&pb_peptide, &peaks_charge_1, 1, false);
+ AddPeaksToPB(&pb_peptide, &peaks_charge_2, 2, false);
+ AddPeaksToPB(&pb_peptide, &negs_charge_1, 1, true);
+ AddPeaksToPB(&pb_peptide, &negs_charge_2, 2, true);
+*/ CHECK(writer.Write(&pb_peptide));
+ }
+ CHECK(reader.OK());
+}
diff --git a/src/app/tide/protobuf/header.proto b/src/app/tide/protobuf/header.proto
new file mode 100644
index 0000000..5348dd6
--- /dev/null
+++ b/src/app/tide/protobuf/header.proto
@@ -0,0 +1,81 @@
+// Benjamin Diament
+// We place a header record at the top of every Tide-generated file
+// to indicate the settings and sources used to generate it.
+
+package pb;
+
+message Modification {
+ optional string amino_acids = 1;
+ optional double delta = 2;
+ optional int32 max_count = 3;
+}
+
+message ModTable {
+ repeated Modification variable_mod = 1;
+ repeated Modification static_mod = 2;
+ repeated double unique_deltas = 10;
+}
+
+message Header {
+ enum FileType {
+ RAW_PROTEINS = 0;
+ PEPTIDES = 1;
+ SPECTRA = 2;
+ PARAMS = 3;
+ MOD_TABLE = 4;
+ RESULTS = 5;
+ AUX_LOCATIONS = 6;
+ }
+
+ message Source { // represents a source file used in building current file.
+ optional string filename = 1;
+ optional Header header = 2; // either header or filetype should be given.
+ optional string filetype = 3;
+ }
+
+ message RawProteinsHeader {
+ }
+
+ message PeptidesHeader {
+ optional double min_mass = 3;
+ optional double max_mass = 4;
+ optional int32 min_length = 5;
+ optional int32 max_length = 6;
+ optional string enzyme = 7;
+ optional bool full_digestion = 8;
+ optional int32 max_missed_cleavages = 14;
+ optional bool monoisotopic_precursor = 13;
+
+ optional bool has_peaks = 10;
+ optional double downselect_fraction = 11;
+ optional ModTable mods = 12;
+ optional ModTable nterm_mods = 15;
+ optional ModTable cterm_mods = 16;
+ optional int32 decoys = 9;
+ }
+
+ message SpectraHeader {
+ optional bool sorted = 2;
+ }
+
+ message ResultsHeader {
+ optional double mass_window = 1;
+ optional int32 top_matches = 2;
+ optional PeptidesHeader peptides_header = 3;
+ }
+
+ message AuxLocationsHeader {
+ }
+
+ repeated Source source = 1;
+
+ // The FileType should be indicated and one of the three header subfields
+ // should be included to correspond to the type.
+ required FileType file_type = 2;
+ optional RawProteinsHeader raw_proteins_header = 3;
+ optional PeptidesHeader peptides_header = 4;
+ optional SpectraHeader spectra_header = 5;
+ optional ResultsHeader results_header = 6;
+ optional AuxLocationsHeader aux_locs_header = 7;
+ optional string command_line = 8;
+}
diff --git a/src/app/tide/protobuf/peptides.proto b/src/app/tide/protobuf/peptides.proto
new file mode 100644
index 0000000..f622852
--- /dev/null
+++ b/src/app/tide/protobuf/peptides.proto
@@ -0,0 +1,50 @@
+option optimize_for = SPEED;
+package pb;
+
+import "raw_proteins.proto";
+
+message Location {
+ optional int32 protein_id = 1;
+ // Typically, the id numbers in the file of proteins are expected to be
+ // numbered sequentially, so that this field can be treated as a pointer.
+ optional int32 pos = 2; // Start position within protein.
+}
+
+message Peptide {
+ // Comments below refer to usual practice when peptides appear in a file of
+ // records sorted by mass.
+ optional int32 id = 1; // Numbered sequentially.
+ optional double mass = 2; // Neutral mass.
+ optional int32 length = 3; // Number of amino acids.
+ optional Location first_location = 4; // First location within protein
+
+ enum Series { // Not used.
+ Y = 0;
+ B = 1;
+ }
+
+ // These fields represent the symetric vector difference between the
+ // correctly computed set of theoretical peaks and the approximate set
+ // set of theoretical peaks. peak1 and peak2 refer to positive values;
+ // neg_peak1 and neg_peak2 refer to negative values. See
+ // theoretical_peak_set.h
+ // peak1 and neg_peak1 refer to charge 1 ions, and peak2 and neg_peak2
+ // refer to charge 2 ions.
+ repeated int32 peak1 = 5 [packed = true];
+ repeated int32 peak2 = 6 [packed = true];
+ repeated int32 neg_peak1 = 7 [packed = true];
+ repeated int32 neg_peak2 = 8 [packed = true];
+
+ // array of (index << log_num_unique_deltas + mod), where index is the amino
+ // acid with the mod, which is an entry into unique_deltas in the ModTable.
+ repeated int32 modifications = 9 [packed = true];
+
+ optional int32 aux_locations_index = 10; // Array index into AuxLocation
+ optional bool is_decoy = 11;
+
+}
+
+message AuxLocation {
+ repeated Location location = 1;
+}
+
diff --git a/src/app/tide/protobuf/raw_proteins.proto b/src/app/tide/protobuf/raw_proteins.proto
new file mode 100644
index 0000000..b670f86
--- /dev/null
+++ b/src/app/tide/protobuf/raw_proteins.proto
@@ -0,0 +1,10 @@
+option optimize_for = SPEED;
+package pb;
+
+message Protein {
+ optional string name = 1;
+ optional int32 id = 2; // In a file of records of type Protein ids will
+ // usually be numbered sequentially.
+ optional string residues = 3;
+ optional int32 target_pos = 5; // Index in target protein that this decoy protein is from
+}
diff --git a/src/app/tide/protobuf/results.proto b/src/app/tide/protobuf/results.proto
new file mode 100644
index 0000000..051f9b9
--- /dev/null
+++ b/src/app/tide/protobuf/results.proto
@@ -0,0 +1,30 @@
+option optimize_for = SPEED;
+package pb;
+
+import "peptides.proto";
+import "spectrum.proto";
+
+
+// The Results message consists of an experimental spectrum and a repeated
+// field corresponding to the top n matching peptides, each represented by
+// the Match message. Each Match message contains a reference to the Peptide,
+// the charge and the xcorr score for the match.
+
+message Match {
+ optional double xcorr = 1;
+ optional Peptide peptide = 2;
+}
+
+message Stats {
+ optional int32 count = 1;
+ optional double sum = 2;
+ optional double sum_squares = 3;
+}
+
+message Results {
+ optional Spectrum spectrum = 1;
+ optional int32 charge = 2;
+ repeated Match matches = 3;
+ optional int32 spectrum_index = 4;
+ optional Stats stats = 5;
+}
diff --git a/src/app/tide/protobuf/spectrum.proto b/src/app/tide/protobuf/spectrum.proto
new file mode 100644
index 0000000..03dbeee
--- /dev/null
+++ b/src/app/tide/protobuf/spectrum.proto
@@ -0,0 +1,25 @@
+option optimize_for = SPEED;
+package pb;
+
+message Spectrum {
+ // For compactness, store m_z and intensity arrays separately, which allows
+ // [packed = true]. Conceptually, each peak has an m_z and a corresponding
+ // intensity. The arrays are expected to be the same size.
+
+ // Peaks are stored as ints, which are more compact than doubles, especially
+ // when small. They are interpreted as numerators of a fraction; the common
+ // denominator fields are given once for each spectrum, based on the precision
+ // of the data. Example: m/z value of 123.45 is represented as 12345/100.
+
+ // Actual peak_m_z values are expected to be strictly increasing, so we store
+ // the deltas of the numerators to keep the numbers smaller.
+ repeated int64 peak_m_z = 1 [packed = true];
+ repeated int64 peak_intensity = 2 [packed = true];
+ optional int32 peak_m_z_denominator = 3; // common denominator for all m_z's
+ optional int32 peak_intensity_denominator = 4; // common for all intensities
+
+ optional int32 spectrum_number = 5;
+ optional double precursor_m_z = 6;
+ optional double rtime = 8;
+ repeated int32 charge_state = 7 [packed = true]; // may as well use packed
+}
diff --git a/src/app/tide/protobuf/view_ms1_cmds.proto b/src/app/tide/protobuf/view_ms1_cmds.proto
new file mode 100644
index 0000000..b81652d
--- /dev/null
+++ b/src/app/tide/protobuf/view_ms1_cmds.proto
@@ -0,0 +1,12 @@
+option optimize_for = SPEED;
+package pb;
+
+message ViewMS1Command {
+ optional string load = 1;
+ optional double bucket = 2;
+ optional double min_mz = 3;
+ optional double max_mz = 4;
+ optional double min_rtime = 5;
+ optional double max_rtime = 6;
+ optional string write_matrix = 7;
+}
diff --git a/src/app/tide/protoobj/header.pb.cc b/src/app/tide/protoobj/header.pb.cc
new file mode 100644
index 0000000..f1b2e2a
--- /dev/null
+++ b/src/app/tide/protoobj/header.pb.cc
@@ -0,0 +1,3408 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: header.proto
+
+#define INTERNAL_SUPPRESS_PROTOBUF_FIELD_DEPRECATION
+#include "header.pb.h"
+
+#include <algorithm>
+
+#include <google/protobuf/stubs/common.h>
+#include <google/protobuf/stubs/once.h>
+#include <google/protobuf/io/coded_stream.h>
+#include <google/protobuf/wire_format_lite_inl.h>
+#include <google/protobuf/descriptor.h>
+#include <google/protobuf/generated_message_reflection.h>
+#include <google/protobuf/reflection_ops.h>
+#include <google/protobuf/wire_format.h>
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+namespace {
+
+const ::google::protobuf::Descriptor* Modification_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Modification_reflection_ = NULL;
+const ::google::protobuf::Descriptor* ModTable_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ ModTable_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Header_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Header_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Header_Source_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Header_Source_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Header_RawProteinsHeader_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Header_RawProteinsHeader_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Header_PeptidesHeader_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Header_PeptidesHeader_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Header_SpectraHeader_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Header_SpectraHeader_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Header_ResultsHeader_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Header_ResultsHeader_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Header_AuxLocationsHeader_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Header_AuxLocationsHeader_reflection_ = NULL;
+const ::google::protobuf::EnumDescriptor* Header_FileType_descriptor_ = NULL;
+
+} // namespace
+
+
+void protobuf_AssignDesc_header_2eproto() {
+ protobuf_AddDesc_header_2eproto();
+ const ::google::protobuf::FileDescriptor* file =
+ ::google::protobuf::DescriptorPool::generated_pool()->FindFileByName(
+ "header.proto");
+ GOOGLE_CHECK(file != NULL);
+ Modification_descriptor_ = file->message_type(0);
+ static const int Modification_offsets_[3] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Modification, amino_acids_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Modification, delta_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Modification, max_count_),
+ };
+ Modification_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Modification_descriptor_,
+ Modification::default_instance_,
+ Modification_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Modification, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Modification, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Modification));
+ ModTable_descriptor_ = file->message_type(1);
+ static const int ModTable_offsets_[3] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(ModTable, variable_mod_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(ModTable, static_mod_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(ModTable, unique_deltas_),
+ };
+ ModTable_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ ModTable_descriptor_,
+ ModTable::default_instance_,
+ ModTable_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(ModTable, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(ModTable, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(ModTable));
+ Header_descriptor_ = file->message_type(2);
+ static const int Header_offsets_[8] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, source_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, file_type_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, raw_proteins_header_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, peptides_header_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, spectra_header_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, results_header_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, aux_locs_header_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, command_line_),
+ };
+ Header_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Header_descriptor_,
+ Header::default_instance_,
+ Header_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Header));
+ Header_Source_descriptor_ = Header_descriptor_->nested_type(0);
+ static const int Header_Source_offsets_[3] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_Source, filename_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_Source, header_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_Source, filetype_),
+ };
+ Header_Source_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Header_Source_descriptor_,
+ Header_Source::default_instance_,
+ Header_Source_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_Source, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_Source, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Header_Source));
+ Header_RawProteinsHeader_descriptor_ = Header_descriptor_->nested_type(1);
+ static const int Header_RawProteinsHeader_offsets_[1] = {
+ };
+ Header_RawProteinsHeader_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Header_RawProteinsHeader_descriptor_,
+ Header_RawProteinsHeader::default_instance_,
+ Header_RawProteinsHeader_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_RawProteinsHeader, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_RawProteinsHeader, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Header_RawProteinsHeader));
+ Header_PeptidesHeader_descriptor_ = Header_descriptor_->nested_type(2);
+ static const int Header_PeptidesHeader_offsets_[14] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, min_mass_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, max_mass_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, min_length_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, max_length_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, enzyme_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, full_digestion_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, max_missed_cleavages_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, monoisotopic_precursor_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, has_peaks_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, downselect_fraction_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, mods_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, nterm_mods_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, cterm_mods_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, decoys_),
+ };
+ Header_PeptidesHeader_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Header_PeptidesHeader_descriptor_,
+ Header_PeptidesHeader::default_instance_,
+ Header_PeptidesHeader_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_PeptidesHeader, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Header_PeptidesHeader));
+ Header_SpectraHeader_descriptor_ = Header_descriptor_->nested_type(3);
+ static const int Header_SpectraHeader_offsets_[1] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_SpectraHeader, sorted_),
+ };
+ Header_SpectraHeader_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Header_SpectraHeader_descriptor_,
+ Header_SpectraHeader::default_instance_,
+ Header_SpectraHeader_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_SpectraHeader, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_SpectraHeader, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Header_SpectraHeader));
+ Header_ResultsHeader_descriptor_ = Header_descriptor_->nested_type(4);
+ static const int Header_ResultsHeader_offsets_[3] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_ResultsHeader, mass_window_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_ResultsHeader, top_matches_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_ResultsHeader, peptides_header_),
+ };
+ Header_ResultsHeader_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Header_ResultsHeader_descriptor_,
+ Header_ResultsHeader::default_instance_,
+ Header_ResultsHeader_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_ResultsHeader, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_ResultsHeader, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Header_ResultsHeader));
+ Header_AuxLocationsHeader_descriptor_ = Header_descriptor_->nested_type(5);
+ static const int Header_AuxLocationsHeader_offsets_[1] = {
+ };
+ Header_AuxLocationsHeader_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Header_AuxLocationsHeader_descriptor_,
+ Header_AuxLocationsHeader::default_instance_,
+ Header_AuxLocationsHeader_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_AuxLocationsHeader, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Header_AuxLocationsHeader, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Header_AuxLocationsHeader));
+ Header_FileType_descriptor_ = Header_descriptor_->enum_type(0);
+}
+
+namespace {
+
+GOOGLE_PROTOBUF_DECLARE_ONCE(protobuf_AssignDescriptors_once_);
+inline void protobuf_AssignDescriptorsOnce() {
+ ::google::protobuf::GoogleOnceInit(&protobuf_AssignDescriptors_once_,
+ &protobuf_AssignDesc_header_2eproto);
+}
+
+void protobuf_RegisterTypes(const ::std::string&) {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Modification_descriptor_, &Modification::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ ModTable_descriptor_, &ModTable::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Header_descriptor_, &Header::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Header_Source_descriptor_, &Header_Source::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Header_RawProteinsHeader_descriptor_, &Header_RawProteinsHeader::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Header_PeptidesHeader_descriptor_, &Header_PeptidesHeader::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Header_SpectraHeader_descriptor_, &Header_SpectraHeader::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Header_ResultsHeader_descriptor_, &Header_ResultsHeader::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Header_AuxLocationsHeader_descriptor_, &Header_AuxLocationsHeader::default_instance());
+}
+
+} // namespace
+
+void protobuf_ShutdownFile_header_2eproto() {
+ delete Modification::default_instance_;
+ delete Modification_reflection_;
+ delete ModTable::default_instance_;
+ delete ModTable_reflection_;
+ delete Header::default_instance_;
+ delete Header_reflection_;
+ delete Header_Source::default_instance_;
+ delete Header_Source_reflection_;
+ delete Header_RawProteinsHeader::default_instance_;
+ delete Header_RawProteinsHeader_reflection_;
+ delete Header_PeptidesHeader::default_instance_;
+ delete Header_PeptidesHeader_reflection_;
+ delete Header_SpectraHeader::default_instance_;
+ delete Header_SpectraHeader_reflection_;
+ delete Header_ResultsHeader::default_instance_;
+ delete Header_ResultsHeader_reflection_;
+ delete Header_AuxLocationsHeader::default_instance_;
+ delete Header_AuxLocationsHeader_reflection_;
+}
+
+void protobuf_AddDesc_header_2eproto() {
+ static bool already_here = false;
+ if (already_here) return;
+ already_here = true;
+ GOOGLE_PROTOBUF_VERIFY_VERSION;
+
+ ::google::protobuf::DescriptorPool::InternalAddGeneratedFile(
+ "\n\014header.proto\022\002pb\"E\n\014Modification\022\023\n\013am"
+ "ino_acids\030\001 \001(\t\022\r\n\005delta\030\002 \001(\001\022\021\n\tmax_co"
+ "unt\030\003 \001(\005\"o\n\010ModTable\022&\n\014variable_mod\030\001 "
+ "\003(\0132\020.pb.Modification\022$\n\nstatic_mod\030\002 \003("
+ "\0132\020.pb.Modification\022\025\n\runique_deltas\030\n \003"
+ "(\001\"\322\010\n\006Header\022!\n\006source\030\001 \003(\0132\021.pb.Heade"
+ "r.Source\022&\n\tfile_type\030\002 \002(\0162\023.pb.Header."
+ "FileType\0229\n\023raw_proteins_header\030\003 \001(\0132\034."
+ "pb.Header.RawProteinsHeader\0222\n\017peptides_"
+ "header\030\004 \001(\0132\031.pb.Header.PeptidesHeader\022"
+ "0\n\016spectra_header\030\005 \001(\0132\030.pb.Header.Spec"
+ "traHeader\0220\n\016results_header\030\006 \001(\0132\030.pb.H"
+ "eader.ResultsHeader\0226\n\017aux_locs_header\030\007"
+ " \001(\0132\035.pb.Header.AuxLocationsHeader\022\024\n\014c"
+ "ommand_line\030\010 \001(\t\032H\n\006Source\022\020\n\010filename\030"
+ "\001 \001(\t\022\032\n\006header\030\002 \001(\0132\n.pb.Header\022\020\n\010fil"
+ "etype\030\003 \001(\t\032\023\n\021RawProteinsHeader\032\342\002\n\016Pep"
+ "tidesHeader\022\020\n\010min_mass\030\003 \001(\001\022\020\n\010max_mas"
+ "s\030\004 \001(\001\022\022\n\nmin_length\030\005 \001(\005\022\022\n\nmax_lengt"
+ "h\030\006 \001(\005\022\016\n\006enzyme\030\007 \001(\t\022\026\n\016full_digestio"
+ "n\030\010 \001(\010\022\034\n\024max_missed_cleavages\030\016 \001(\005\022\036\n"
+ "\026monoisotopic_precursor\030\r \001(\010\022\021\n\thas_pea"
+ "ks\030\n \001(\010\022\033\n\023downselect_fraction\030\013 \001(\001\022\032\n"
+ "\004mods\030\014 \001(\0132\014.pb.ModTable\022 \n\nnterm_mods\030"
+ "\017 \001(\0132\014.pb.ModTable\022 \n\ncterm_mods\030\020 \001(\0132"
+ "\014.pb.ModTable\022\016\n\006decoys\030\t \001(\005\032\037\n\rSpectra"
+ "Header\022\016\n\006sorted\030\002 \001(\010\032m\n\rResultsHeader\022"
+ "\023\n\013mass_window\030\001 \001(\001\022\023\n\013top_matches\030\002 \001("
+ "\005\0222\n\017peptides_header\030\003 \001(\0132\031.pb.Header.P"
+ "eptidesHeader\032\024\n\022AuxLocationsHeader\"r\n\010F"
+ "ileType\022\020\n\014RAW_PROTEINS\020\000\022\014\n\010PEPTIDES\020\001\022"
+ "\013\n\007SPECTRA\020\002\022\n\n\006PARAMS\020\003\022\r\n\tMOD_TABLE\020\004\022"
+ "\013\n\007RESULTS\020\005\022\021\n\rAUX_LOCATIONS\020\006", 1311);
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedFile(
+ "header.proto", &protobuf_RegisterTypes);
+ Modification::default_instance_ = new Modification();
+ ModTable::default_instance_ = new ModTable();
+ Header::default_instance_ = new Header();
+ Header_Source::default_instance_ = new Header_Source();
+ Header_RawProteinsHeader::default_instance_ = new Header_RawProteinsHeader();
+ Header_PeptidesHeader::default_instance_ = new Header_PeptidesHeader();
+ Header_SpectraHeader::default_instance_ = new Header_SpectraHeader();
+ Header_ResultsHeader::default_instance_ = new Header_ResultsHeader();
+ Header_AuxLocationsHeader::default_instance_ = new Header_AuxLocationsHeader();
+ Modification::default_instance_->InitAsDefaultInstance();
+ ModTable::default_instance_->InitAsDefaultInstance();
+ Header::default_instance_->InitAsDefaultInstance();
+ Header_Source::default_instance_->InitAsDefaultInstance();
+ Header_RawProteinsHeader::default_instance_->InitAsDefaultInstance();
+ Header_PeptidesHeader::default_instance_->InitAsDefaultInstance();
+ Header_SpectraHeader::default_instance_->InitAsDefaultInstance();
+ Header_ResultsHeader::default_instance_->InitAsDefaultInstance();
+ Header_AuxLocationsHeader::default_instance_->InitAsDefaultInstance();
+ ::google::protobuf::internal::OnShutdown(&protobuf_ShutdownFile_header_2eproto);
+}
+
+// Force AddDescriptors() to be called at static initialization time.
+struct StaticDescriptorInitializer_header_2eproto {
+ StaticDescriptorInitializer_header_2eproto() {
+ protobuf_AddDesc_header_2eproto();
+ }
+} static_descriptor_initializer_header_2eproto_;
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int Modification::kAminoAcidsFieldNumber;
+const int Modification::kDeltaFieldNumber;
+const int Modification::kMaxCountFieldNumber;
+#endif // !_MSC_VER
+
+Modification::Modification()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Modification::InitAsDefaultInstance() {
+}
+
+Modification::Modification(const Modification& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Modification::SharedCtor() {
+ _cached_size_ = 0;
+ amino_acids_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ delta_ = 0;
+ max_count_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Modification::~Modification() {
+ SharedDtor();
+}
+
+void Modification::SharedDtor() {
+ if (amino_acids_ != &::google::protobuf::internal::kEmptyString) {
+ delete amino_acids_;
+ }
+ if (this != default_instance_) {
+ }
+}
+
+void Modification::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Modification::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Modification_descriptor_;
+}
+
+const Modification& Modification::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+Modification* Modification::default_instance_ = NULL;
+
+Modification* Modification::New() const {
+ return new Modification;
+}
+
+void Modification::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (has_amino_acids()) {
+ if (amino_acids_ != &::google::protobuf::internal::kEmptyString) {
+ amino_acids_->clear();
+ }
+ }
+ delta_ = 0;
+ max_count_ = 0;
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Modification::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional string amino_acids = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ DO_(::google::protobuf::internal::WireFormatLite::ReadString(
+ input, this->mutable_amino_acids()));
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->amino_acids().data(), this->amino_acids().length(),
+ ::google::protobuf::internal::WireFormat::PARSE);
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(17)) goto parse_delta;
+ break;
+ }
+
+ // optional double delta = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_delta:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &delta_)));
+ set_has_delta();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(24)) goto parse_max_count;
+ break;
+ }
+
+ // optional int32 max_count = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_max_count:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &max_count_)));
+ set_has_max_count();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Modification::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional string amino_acids = 1;
+ if (has_amino_acids()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->amino_acids().data(), this->amino_acids().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ ::google::protobuf::internal::WireFormatLite::WriteString(
+ 1, this->amino_acids(), output);
+ }
+
+ // optional double delta = 2;
+ if (has_delta()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(2, this->delta(), output);
+ }
+
+ // optional int32 max_count = 3;
+ if (has_max_count()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(3, this->max_count(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Modification::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional string amino_acids = 1;
+ if (has_amino_acids()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->amino_acids().data(), this->amino_acids().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ target =
+ ::google::protobuf::internal::WireFormatLite::WriteStringToArray(
+ 1, this->amino_acids(), target);
+ }
+
+ // optional double delta = 2;
+ if (has_delta()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(2, this->delta(), target);
+ }
+
+ // optional int32 max_count = 3;
+ if (has_max_count()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(3, this->max_count(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Modification::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional string amino_acids = 1;
+ if (has_amino_acids()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::StringSize(
+ this->amino_acids());
+ }
+
+ // optional double delta = 2;
+ if (has_delta()) {
+ total_size += 1 + 8;
+ }
+
+ // optional int32 max_count = 3;
+ if (has_max_count()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->max_count());
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Modification::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Modification* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Modification*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Modification::MergeFrom(const Modification& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_amino_acids()) {
+ set_amino_acids(from.amino_acids());
+ }
+ if (from.has_delta()) {
+ set_delta(from.delta());
+ }
+ if (from.has_max_count()) {
+ set_max_count(from.max_count());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Modification::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Modification::CopyFrom(const Modification& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Modification::IsInitialized() const {
+
+ return true;
+}
+
+void Modification::Swap(Modification* other) {
+ if (other != this) {
+ std::swap(amino_acids_, other->amino_acids_);
+ std::swap(delta_, other->delta_);
+ std::swap(max_count_, other->max_count_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Modification::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Modification_descriptor_;
+ metadata.reflection = Modification_reflection_;
+ return metadata;
+}
+
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int ModTable::kVariableModFieldNumber;
+const int ModTable::kStaticModFieldNumber;
+const int ModTable::kUniqueDeltasFieldNumber;
+#endif // !_MSC_VER
+
+ModTable::ModTable()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void ModTable::InitAsDefaultInstance() {
+}
+
+ModTable::ModTable(const ModTable& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void ModTable::SharedCtor() {
+ _cached_size_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+ModTable::~ModTable() {
+ SharedDtor();
+}
+
+void ModTable::SharedDtor() {
+ if (this != default_instance_) {
+ }
+}
+
+void ModTable::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* ModTable::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return ModTable_descriptor_;
+}
+
+const ModTable& ModTable::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+ModTable* ModTable::default_instance_ = NULL;
+
+ModTable* ModTable::New() const {
+ return new ModTable;
+}
+
+void ModTable::Clear() {
+ variable_mod_.Clear();
+ static_mod_.Clear();
+ unique_deltas_.Clear();
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool ModTable::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // repeated .pb.Modification variable_mod = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_variable_mod:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, add_variable_mod()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(10)) goto parse_variable_mod;
+ if (input->ExpectTag(18)) goto parse_static_mod;
+ break;
+ }
+
+ // repeated .pb.Modification static_mod = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_static_mod:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, add_static_mod()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(18)) goto parse_static_mod;
+ if (input->ExpectTag(81)) goto parse_unique_deltas;
+ break;
+ }
+
+ // repeated double unique_deltas = 10;
+ case 10: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_unique_deltas:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ 1, 81, input, this->mutable_unique_deltas())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_LENGTH_DELIMITED) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitiveNoInline<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, this->mutable_unique_deltas())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(81)) goto parse_unique_deltas;
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void ModTable::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // repeated .pb.Modification variable_mod = 1;
+ for (int i = 0; i < this->variable_mod_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 1, this->variable_mod(i), output);
+ }
+
+ // repeated .pb.Modification static_mod = 2;
+ for (int i = 0; i < this->static_mod_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 2, this->static_mod(i), output);
+ }
+
+ // repeated double unique_deltas = 10;
+ for (int i = 0; i < this->unique_deltas_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(
+ 10, this->unique_deltas(i), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* ModTable::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // repeated .pb.Modification variable_mod = 1;
+ for (int i = 0; i < this->variable_mod_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 1, this->variable_mod(i), target);
+ }
+
+ // repeated .pb.Modification static_mod = 2;
+ for (int i = 0; i < this->static_mod_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 2, this->static_mod(i), target);
+ }
+
+ // repeated double unique_deltas = 10;
+ for (int i = 0; i < this->unique_deltas_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteDoubleToArray(10, this->unique_deltas(i), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int ModTable::ByteSize() const {
+ int total_size = 0;
+
+ // repeated .pb.Modification variable_mod = 1;
+ total_size += 1 * this->variable_mod_size();
+ for (int i = 0; i < this->variable_mod_size(); i++) {
+ total_size +=
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->variable_mod(i));
+ }
+
+ // repeated .pb.Modification static_mod = 2;
+ total_size += 1 * this->static_mod_size();
+ for (int i = 0; i < this->static_mod_size(); i++) {
+ total_size +=
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->static_mod(i));
+ }
+
+ // repeated double unique_deltas = 10;
+ {
+ int data_size = 0;
+ data_size = 8 * this->unique_deltas_size();
+ total_size += 1 * this->unique_deltas_size() + data_size;
+ }
+
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void ModTable::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const ModTable* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const ModTable*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void ModTable::MergeFrom(const ModTable& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ variable_mod_.MergeFrom(from.variable_mod_);
+ static_mod_.MergeFrom(from.static_mod_);
+ unique_deltas_.MergeFrom(from.unique_deltas_);
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void ModTable::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void ModTable::CopyFrom(const ModTable& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool ModTable::IsInitialized() const {
+
+ return true;
+}
+
+void ModTable::Swap(ModTable* other) {
+ if (other != this) {
+ variable_mod_.Swap(&other->variable_mod_);
+ static_mod_.Swap(&other->static_mod_);
+ unique_deltas_.Swap(&other->unique_deltas_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata ModTable::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = ModTable_descriptor_;
+ metadata.reflection = ModTable_reflection_;
+ return metadata;
+}
+
+
+// ===================================================================
+
+const ::google::protobuf::EnumDescriptor* Header_FileType_descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Header_FileType_descriptor_;
+}
+bool Header_FileType_IsValid(int value) {
+ switch(value) {
+ case 0:
+ case 1:
+ case 2:
+ case 3:
+ case 4:
+ case 5:
+ case 6:
+ return true;
+ default:
+ return false;
+ }
+}
+
+#ifndef _MSC_VER
+const Header_FileType Header::RAW_PROTEINS;
+const Header_FileType Header::PEPTIDES;
+const Header_FileType Header::SPECTRA;
+const Header_FileType Header::PARAMS;
+const Header_FileType Header::MOD_TABLE;
+const Header_FileType Header::RESULTS;
+const Header_FileType Header::AUX_LOCATIONS;
+const Header_FileType Header::FileType_MIN;
+const Header_FileType Header::FileType_MAX;
+const int Header::FileType_ARRAYSIZE;
+#endif // _MSC_VER
+#ifndef _MSC_VER
+const int Header_Source::kFilenameFieldNumber;
+const int Header_Source::kHeaderFieldNumber;
+const int Header_Source::kFiletypeFieldNumber;
+#endif // !_MSC_VER
+
+Header_Source::Header_Source()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Header_Source::InitAsDefaultInstance() {
+ header_ = const_cast< ::pb::Header*>(&::pb::Header::default_instance());
+}
+
+Header_Source::Header_Source(const Header_Source& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Header_Source::SharedCtor() {
+ _cached_size_ = 0;
+ filename_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ header_ = NULL;
+ filetype_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Header_Source::~Header_Source() {
+ SharedDtor();
+}
+
+void Header_Source::SharedDtor() {
+ if (filename_ != &::google::protobuf::internal::kEmptyString) {
+ delete filename_;
+ }
+ if (filetype_ != &::google::protobuf::internal::kEmptyString) {
+ delete filetype_;
+ }
+ if (this != default_instance_) {
+ delete header_;
+ }
+}
+
+void Header_Source::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Header_Source::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Header_Source_descriptor_;
+}
+
+const Header_Source& Header_Source::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+Header_Source* Header_Source::default_instance_ = NULL;
+
+Header_Source* Header_Source::New() const {
+ return new Header_Source;
+}
+
+void Header_Source::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (has_filename()) {
+ if (filename_ != &::google::protobuf::internal::kEmptyString) {
+ filename_->clear();
+ }
+ }
+ if (has_header()) {
+ if (header_ != NULL) header_->::pb::Header::Clear();
+ }
+ if (has_filetype()) {
+ if (filetype_ != &::google::protobuf::internal::kEmptyString) {
+ filetype_->clear();
+ }
+ }
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Header_Source::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional string filename = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ DO_(::google::protobuf::internal::WireFormatLite::ReadString(
+ input, this->mutable_filename()));
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->filename().data(), this->filename().length(),
+ ::google::protobuf::internal::WireFormat::PARSE);
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(18)) goto parse_header;
+ break;
+ }
+
+ // optional .pb.Header header = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_header:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_header()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(26)) goto parse_filetype;
+ break;
+ }
+
+ // optional string filetype = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_filetype:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadString(
+ input, this->mutable_filetype()));
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->filetype().data(), this->filetype().length(),
+ ::google::protobuf::internal::WireFormat::PARSE);
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Header_Source::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional string filename = 1;
+ if (has_filename()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->filename().data(), this->filename().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ ::google::protobuf::internal::WireFormatLite::WriteString(
+ 1, this->filename(), output);
+ }
+
+ // optional .pb.Header header = 2;
+ if (has_header()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 2, this->header(), output);
+ }
+
+ // optional string filetype = 3;
+ if (has_filetype()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->filetype().data(), this->filetype().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ ::google::protobuf::internal::WireFormatLite::WriteString(
+ 3, this->filetype(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Header_Source::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional string filename = 1;
+ if (has_filename()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->filename().data(), this->filename().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ target =
+ ::google::protobuf::internal::WireFormatLite::WriteStringToArray(
+ 1, this->filename(), target);
+ }
+
+ // optional .pb.Header header = 2;
+ if (has_header()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 2, this->header(), target);
+ }
+
+ // optional string filetype = 3;
+ if (has_filetype()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->filetype().data(), this->filetype().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ target =
+ ::google::protobuf::internal::WireFormatLite::WriteStringToArray(
+ 3, this->filetype(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Header_Source::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional string filename = 1;
+ if (has_filename()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::StringSize(
+ this->filename());
+ }
+
+ // optional .pb.Header header = 2;
+ if (has_header()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->header());
+ }
+
+ // optional string filetype = 3;
+ if (has_filetype()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::StringSize(
+ this->filetype());
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Header_Source::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Header_Source* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Header_Source*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Header_Source::MergeFrom(const Header_Source& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_filename()) {
+ set_filename(from.filename());
+ }
+ if (from.has_header()) {
+ mutable_header()->::pb::Header::MergeFrom(from.header());
+ }
+ if (from.has_filetype()) {
+ set_filetype(from.filetype());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Header_Source::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Header_Source::CopyFrom(const Header_Source& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Header_Source::IsInitialized() const {
+
+ if (has_header()) {
+ if (!this->header().IsInitialized()) return false;
+ }
+ return true;
+}
+
+void Header_Source::Swap(Header_Source* other) {
+ if (other != this) {
+ std::swap(filename_, other->filename_);
+ std::swap(header_, other->header_);
+ std::swap(filetype_, other->filetype_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Header_Source::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Header_Source_descriptor_;
+ metadata.reflection = Header_Source_reflection_;
+ return metadata;
+}
+
+
+// -------------------------------------------------------------------
+
+#ifndef _MSC_VER
+#endif // !_MSC_VER
+
+Header_RawProteinsHeader::Header_RawProteinsHeader()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Header_RawProteinsHeader::InitAsDefaultInstance() {
+}
+
+Header_RawProteinsHeader::Header_RawProteinsHeader(const Header_RawProteinsHeader& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Header_RawProteinsHeader::SharedCtor() {
+ _cached_size_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Header_RawProteinsHeader::~Header_RawProteinsHeader() {
+ SharedDtor();
+}
+
+void Header_RawProteinsHeader::SharedDtor() {
+ if (this != default_instance_) {
+ }
+}
+
+void Header_RawProteinsHeader::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Header_RawProteinsHeader::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Header_RawProteinsHeader_descriptor_;
+}
+
+const Header_RawProteinsHeader& Header_RawProteinsHeader::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+Header_RawProteinsHeader* Header_RawProteinsHeader::default_instance_ = NULL;
+
+Header_RawProteinsHeader* Header_RawProteinsHeader::New() const {
+ return new Header_RawProteinsHeader;
+}
+
+void Header_RawProteinsHeader::Clear() {
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Header_RawProteinsHeader::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ }
+ return true;
+#undef DO_
+}
+
+void Header_RawProteinsHeader::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Header_RawProteinsHeader::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Header_RawProteinsHeader::ByteSize() const {
+ int total_size = 0;
+
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Header_RawProteinsHeader::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Header_RawProteinsHeader* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Header_RawProteinsHeader*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Header_RawProteinsHeader::MergeFrom(const Header_RawProteinsHeader& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Header_RawProteinsHeader::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Header_RawProteinsHeader::CopyFrom(const Header_RawProteinsHeader& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Header_RawProteinsHeader::IsInitialized() const {
+
+ return true;
+}
+
+void Header_RawProteinsHeader::Swap(Header_RawProteinsHeader* other) {
+ if (other != this) {
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Header_RawProteinsHeader::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Header_RawProteinsHeader_descriptor_;
+ metadata.reflection = Header_RawProteinsHeader_reflection_;
+ return metadata;
+}
+
+
+// -------------------------------------------------------------------
+
+#ifndef _MSC_VER
+const int Header_PeptidesHeader::kMinMassFieldNumber;
+const int Header_PeptidesHeader::kMaxMassFieldNumber;
+const int Header_PeptidesHeader::kMinLengthFieldNumber;
+const int Header_PeptidesHeader::kMaxLengthFieldNumber;
+const int Header_PeptidesHeader::kEnzymeFieldNumber;
+const int Header_PeptidesHeader::kFullDigestionFieldNumber;
+const int Header_PeptidesHeader::kMaxMissedCleavagesFieldNumber;
+const int Header_PeptidesHeader::kMonoisotopicPrecursorFieldNumber;
+const int Header_PeptidesHeader::kHasPeaksFieldNumber;
+const int Header_PeptidesHeader::kDownselectFractionFieldNumber;
+const int Header_PeptidesHeader::kModsFieldNumber;
+const int Header_PeptidesHeader::kNtermModsFieldNumber;
+const int Header_PeptidesHeader::kCtermModsFieldNumber;
+const int Header_PeptidesHeader::kDecoysFieldNumber;
+#endif // !_MSC_VER
+
+Header_PeptidesHeader::Header_PeptidesHeader()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Header_PeptidesHeader::InitAsDefaultInstance() {
+ mods_ = const_cast< ::pb::ModTable*>(&::pb::ModTable::default_instance());
+ nterm_mods_ = const_cast< ::pb::ModTable*>(&::pb::ModTable::default_instance());
+ cterm_mods_ = const_cast< ::pb::ModTable*>(&::pb::ModTable::default_instance());
+}
+
+Header_PeptidesHeader::Header_PeptidesHeader(const Header_PeptidesHeader& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Header_PeptidesHeader::SharedCtor() {
+ _cached_size_ = 0;
+ min_mass_ = 0;
+ max_mass_ = 0;
+ min_length_ = 0;
+ max_length_ = 0;
+ enzyme_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ full_digestion_ = false;
+ max_missed_cleavages_ = 0;
+ monoisotopic_precursor_ = false;
+ has_peaks_ = false;
+ downselect_fraction_ = 0;
+ mods_ = NULL;
+ nterm_mods_ = NULL;
+ cterm_mods_ = NULL;
+ decoys_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Header_PeptidesHeader::~Header_PeptidesHeader() {
+ SharedDtor();
+}
+
+void Header_PeptidesHeader::SharedDtor() {
+ if (enzyme_ != &::google::protobuf::internal::kEmptyString) {
+ delete enzyme_;
+ }
+ if (this != default_instance_) {
+ delete mods_;
+ delete nterm_mods_;
+ delete cterm_mods_;
+ }
+}
+
+void Header_PeptidesHeader::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Header_PeptidesHeader::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Header_PeptidesHeader_descriptor_;
+}
+
+const Header_PeptidesHeader& Header_PeptidesHeader::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+Header_PeptidesHeader* Header_PeptidesHeader::default_instance_ = NULL;
+
+Header_PeptidesHeader* Header_PeptidesHeader::New() const {
+ return new Header_PeptidesHeader;
+}
+
+void Header_PeptidesHeader::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ min_mass_ = 0;
+ max_mass_ = 0;
+ min_length_ = 0;
+ max_length_ = 0;
+ if (has_enzyme()) {
+ if (enzyme_ != &::google::protobuf::internal::kEmptyString) {
+ enzyme_->clear();
+ }
+ }
+ full_digestion_ = false;
+ max_missed_cleavages_ = 0;
+ monoisotopic_precursor_ = false;
+ }
+ if (_has_bits_[8 / 32] & (0xffu << (8 % 32))) {
+ has_peaks_ = false;
+ downselect_fraction_ = 0;
+ if (has_mods()) {
+ if (mods_ != NULL) mods_->::pb::ModTable::Clear();
+ }
+ if (has_nterm_mods()) {
+ if (nterm_mods_ != NULL) nterm_mods_->::pb::ModTable::Clear();
+ }
+ if (has_cterm_mods()) {
+ if (cterm_mods_ != NULL) cterm_mods_->::pb::ModTable::Clear();
+ }
+ decoys_ = 0;
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Header_PeptidesHeader::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional double min_mass = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &min_mass_)));
+ set_has_min_mass();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(33)) goto parse_max_mass;
+ break;
+ }
+
+ // optional double max_mass = 4;
+ case 4: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_max_mass:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &max_mass_)));
+ set_has_max_mass();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(40)) goto parse_min_length;
+ break;
+ }
+
+ // optional int32 min_length = 5;
+ case 5: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_min_length:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &min_length_)));
+ set_has_min_length();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(48)) goto parse_max_length;
+ break;
+ }
+
+ // optional int32 max_length = 6;
+ case 6: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_max_length:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &max_length_)));
+ set_has_max_length();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(58)) goto parse_enzyme;
+ break;
+ }
+
+ // optional string enzyme = 7;
+ case 7: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_enzyme:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadString(
+ input, this->mutable_enzyme()));
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->enzyme().data(), this->enzyme().length(),
+ ::google::protobuf::internal::WireFormat::PARSE);
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(64)) goto parse_full_digestion;
+ break;
+ }
+
+ // optional bool full_digestion = 8;
+ case 8: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_full_digestion:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ bool, ::google::protobuf::internal::WireFormatLite::TYPE_BOOL>(
+ input, &full_digestion_)));
+ set_has_full_digestion();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(72)) goto parse_decoys;
+ break;
+ }
+
+ // optional int32 decoys = 9;
+ case 9: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_decoys:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &decoys_)));
+ set_has_decoys();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(80)) goto parse_has_peaks;
+ break;
+ }
+
+ // optional bool has_peaks = 10;
+ case 10: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_has_peaks:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ bool, ::google::protobuf::internal::WireFormatLite::TYPE_BOOL>(
+ input, &has_peaks_)));
+ set_has_has_peaks();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(89)) goto parse_downselect_fraction;
+ break;
+ }
+
+ // optional double downselect_fraction = 11;
+ case 11: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_downselect_fraction:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &downselect_fraction_)));
+ set_has_downselect_fraction();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(98)) goto parse_mods;
+ break;
+ }
+
+ // optional .pb.ModTable mods = 12;
+ case 12: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_mods:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_mods()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(104)) goto parse_monoisotopic_precursor;
+ break;
+ }
+
+ // optional bool monoisotopic_precursor = 13;
+ case 13: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_monoisotopic_precursor:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ bool, ::google::protobuf::internal::WireFormatLite::TYPE_BOOL>(
+ input, &monoisotopic_precursor_)));
+ set_has_monoisotopic_precursor();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(112)) goto parse_max_missed_cleavages;
+ break;
+ }
+
+ // optional int32 max_missed_cleavages = 14;
+ case 14: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_max_missed_cleavages:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &max_missed_cleavages_)));
+ set_has_max_missed_cleavages();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(122)) goto parse_nterm_mods;
+ break;
+ }
+
+ // optional .pb.ModTable nterm_mods = 15;
+ case 15: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_nterm_mods:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_nterm_mods()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(130)) goto parse_cterm_mods;
+ break;
+ }
+
+ // optional .pb.ModTable cterm_mods = 16;
+ case 16: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_cterm_mods:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_cterm_mods()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Header_PeptidesHeader::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional double min_mass = 3;
+ if (has_min_mass()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(3, this->min_mass(), output);
+ }
+
+ // optional double max_mass = 4;
+ if (has_max_mass()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(4, this->max_mass(), output);
+ }
+
+ // optional int32 min_length = 5;
+ if (has_min_length()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(5, this->min_length(), output);
+ }
+
+ // optional int32 max_length = 6;
+ if (has_max_length()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(6, this->max_length(), output);
+ }
+
+ // optional string enzyme = 7;
+ if (has_enzyme()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->enzyme().data(), this->enzyme().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ ::google::protobuf::internal::WireFormatLite::WriteString(
+ 7, this->enzyme(), output);
+ }
+
+ // optional bool full_digestion = 8;
+ if (has_full_digestion()) {
+ ::google::protobuf::internal::WireFormatLite::WriteBool(8, this->full_digestion(), output);
+ }
+
+ // optional int32 decoys = 9;
+ if (has_decoys()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(9, this->decoys(), output);
+ }
+
+ // optional bool has_peaks = 10;
+ if (has_has_peaks()) {
+ ::google::protobuf::internal::WireFormatLite::WriteBool(10, this->has_peaks(), output);
+ }
+
+ // optional double downselect_fraction = 11;
+ if (has_downselect_fraction()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(11, this->downselect_fraction(), output);
+ }
+
+ // optional .pb.ModTable mods = 12;
+ if (has_mods()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 12, this->mods(), output);
+ }
+
+ // optional bool monoisotopic_precursor = 13;
+ if (has_monoisotopic_precursor()) {
+ ::google::protobuf::internal::WireFormatLite::WriteBool(13, this->monoisotopic_precursor(), output);
+ }
+
+ // optional int32 max_missed_cleavages = 14;
+ if (has_max_missed_cleavages()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(14, this->max_missed_cleavages(), output);
+ }
+
+ // optional .pb.ModTable nterm_mods = 15;
+ if (has_nterm_mods()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 15, this->nterm_mods(), output);
+ }
+
+ // optional .pb.ModTable cterm_mods = 16;
+ if (has_cterm_mods()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 16, this->cterm_mods(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Header_PeptidesHeader::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional double min_mass = 3;
+ if (has_min_mass()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(3, this->min_mass(), target);
+ }
+
+ // optional double max_mass = 4;
+ if (has_max_mass()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(4, this->max_mass(), target);
+ }
+
+ // optional int32 min_length = 5;
+ if (has_min_length()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(5, this->min_length(), target);
+ }
+
+ // optional int32 max_length = 6;
+ if (has_max_length()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(6, this->max_length(), target);
+ }
+
+ // optional string enzyme = 7;
+ if (has_enzyme()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->enzyme().data(), this->enzyme().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ target =
+ ::google::protobuf::internal::WireFormatLite::WriteStringToArray(
+ 7, this->enzyme(), target);
+ }
+
+ // optional bool full_digestion = 8;
+ if (has_full_digestion()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteBoolToArray(8, this->full_digestion(), target);
+ }
+
+ // optional int32 decoys = 9;
+ if (has_decoys()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(9, this->decoys(), target);
+ }
+
+ // optional bool has_peaks = 10;
+ if (has_has_peaks()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteBoolToArray(10, this->has_peaks(), target);
+ }
+
+ // optional double downselect_fraction = 11;
+ if (has_downselect_fraction()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(11, this->downselect_fraction(), target);
+ }
+
+ // optional .pb.ModTable mods = 12;
+ if (has_mods()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 12, this->mods(), target);
+ }
+
+ // optional bool monoisotopic_precursor = 13;
+ if (has_monoisotopic_precursor()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteBoolToArray(13, this->monoisotopic_precursor(), target);
+ }
+
+ // optional int32 max_missed_cleavages = 14;
+ if (has_max_missed_cleavages()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(14, this->max_missed_cleavages(), target);
+ }
+
+ // optional .pb.ModTable nterm_mods = 15;
+ if (has_nterm_mods()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 15, this->nterm_mods(), target);
+ }
+
+ // optional .pb.ModTable cterm_mods = 16;
+ if (has_cterm_mods()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 16, this->cterm_mods(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Header_PeptidesHeader::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional double min_mass = 3;
+ if (has_min_mass()) {
+ total_size += 1 + 8;
+ }
+
+ // optional double max_mass = 4;
+ if (has_max_mass()) {
+ total_size += 1 + 8;
+ }
+
+ // optional int32 min_length = 5;
+ if (has_min_length()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->min_length());
+ }
+
+ // optional int32 max_length = 6;
+ if (has_max_length()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->max_length());
+ }
+
+ // optional string enzyme = 7;
+ if (has_enzyme()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::StringSize(
+ this->enzyme());
+ }
+
+ // optional bool full_digestion = 8;
+ if (has_full_digestion()) {
+ total_size += 1 + 1;
+ }
+
+ // optional int32 max_missed_cleavages = 14;
+ if (has_max_missed_cleavages()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->max_missed_cleavages());
+ }
+
+ // optional bool monoisotopic_precursor = 13;
+ if (has_monoisotopic_precursor()) {
+ total_size += 1 + 1;
+ }
+
+ }
+ if (_has_bits_[8 / 32] & (0xffu << (8 % 32))) {
+ // optional bool has_peaks = 10;
+ if (has_has_peaks()) {
+ total_size += 1 + 1;
+ }
+
+ // optional double downselect_fraction = 11;
+ if (has_downselect_fraction()) {
+ total_size += 1 + 8;
+ }
+
+ // optional .pb.ModTable mods = 12;
+ if (has_mods()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->mods());
+ }
+
+ // optional .pb.ModTable nterm_mods = 15;
+ if (has_nterm_mods()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->nterm_mods());
+ }
+
+ // optional .pb.ModTable cterm_mods = 16;
+ if (has_cterm_mods()) {
+ total_size += 2 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->cterm_mods());
+ }
+
+ // optional int32 decoys = 9;
+ if (has_decoys()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->decoys());
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Header_PeptidesHeader::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Header_PeptidesHeader* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Header_PeptidesHeader*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Header_PeptidesHeader::MergeFrom(const Header_PeptidesHeader& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_min_mass()) {
+ set_min_mass(from.min_mass());
+ }
+ if (from.has_max_mass()) {
+ set_max_mass(from.max_mass());
+ }
+ if (from.has_min_length()) {
+ set_min_length(from.min_length());
+ }
+ if (from.has_max_length()) {
+ set_max_length(from.max_length());
+ }
+ if (from.has_enzyme()) {
+ set_enzyme(from.enzyme());
+ }
+ if (from.has_full_digestion()) {
+ set_full_digestion(from.full_digestion());
+ }
+ if (from.has_max_missed_cleavages()) {
+ set_max_missed_cleavages(from.max_missed_cleavages());
+ }
+ if (from.has_monoisotopic_precursor()) {
+ set_monoisotopic_precursor(from.monoisotopic_precursor());
+ }
+ }
+ if (from._has_bits_[8 / 32] & (0xffu << (8 % 32))) {
+ if (from.has_has_peaks()) {
+ set_has_peaks(from.has_peaks());
+ }
+ if (from.has_downselect_fraction()) {
+ set_downselect_fraction(from.downselect_fraction());
+ }
+ if (from.has_mods()) {
+ mutable_mods()->::pb::ModTable::MergeFrom(from.mods());
+ }
+ if (from.has_nterm_mods()) {
+ mutable_nterm_mods()->::pb::ModTable::MergeFrom(from.nterm_mods());
+ }
+ if (from.has_cterm_mods()) {
+ mutable_cterm_mods()->::pb::ModTable::MergeFrom(from.cterm_mods());
+ }
+ if (from.has_decoys()) {
+ set_decoys(from.decoys());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Header_PeptidesHeader::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Header_PeptidesHeader::CopyFrom(const Header_PeptidesHeader& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Header_PeptidesHeader::IsInitialized() const {
+
+ return true;
+}
+
+void Header_PeptidesHeader::Swap(Header_PeptidesHeader* other) {
+ if (other != this) {
+ std::swap(min_mass_, other->min_mass_);
+ std::swap(max_mass_, other->max_mass_);
+ std::swap(min_length_, other->min_length_);
+ std::swap(max_length_, other->max_length_);
+ std::swap(enzyme_, other->enzyme_);
+ std::swap(full_digestion_, other->full_digestion_);
+ std::swap(max_missed_cleavages_, other->max_missed_cleavages_);
+ std::swap(monoisotopic_precursor_, other->monoisotopic_precursor_);
+ std::swap(has_peaks_, other->has_peaks_);
+ std::swap(downselect_fraction_, other->downselect_fraction_);
+ std::swap(mods_, other->mods_);
+ std::swap(nterm_mods_, other->nterm_mods_);
+ std::swap(cterm_mods_, other->cterm_mods_);
+ std::swap(decoys_, other->decoys_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Header_PeptidesHeader::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Header_PeptidesHeader_descriptor_;
+ metadata.reflection = Header_PeptidesHeader_reflection_;
+ return metadata;
+}
+
+
+// -------------------------------------------------------------------
+
+#ifndef _MSC_VER
+const int Header_SpectraHeader::kSortedFieldNumber;
+#endif // !_MSC_VER
+
+Header_SpectraHeader::Header_SpectraHeader()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Header_SpectraHeader::InitAsDefaultInstance() {
+}
+
+Header_SpectraHeader::Header_SpectraHeader(const Header_SpectraHeader& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Header_SpectraHeader::SharedCtor() {
+ _cached_size_ = 0;
+ sorted_ = false;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Header_SpectraHeader::~Header_SpectraHeader() {
+ SharedDtor();
+}
+
+void Header_SpectraHeader::SharedDtor() {
+ if (this != default_instance_) {
+ }
+}
+
+void Header_SpectraHeader::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Header_SpectraHeader::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Header_SpectraHeader_descriptor_;
+}
+
+const Header_SpectraHeader& Header_SpectraHeader::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+Header_SpectraHeader* Header_SpectraHeader::default_instance_ = NULL;
+
+Header_SpectraHeader* Header_SpectraHeader::New() const {
+ return new Header_SpectraHeader;
+}
+
+void Header_SpectraHeader::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ sorted_ = false;
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Header_SpectraHeader::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional bool sorted = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ bool, ::google::protobuf::internal::WireFormatLite::TYPE_BOOL>(
+ input, &sorted_)));
+ set_has_sorted();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Header_SpectraHeader::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional bool sorted = 2;
+ if (has_sorted()) {
+ ::google::protobuf::internal::WireFormatLite::WriteBool(2, this->sorted(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Header_SpectraHeader::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional bool sorted = 2;
+ if (has_sorted()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteBoolToArray(2, this->sorted(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Header_SpectraHeader::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional bool sorted = 2;
+ if (has_sorted()) {
+ total_size += 1 + 1;
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Header_SpectraHeader::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Header_SpectraHeader* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Header_SpectraHeader*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Header_SpectraHeader::MergeFrom(const Header_SpectraHeader& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_sorted()) {
+ set_sorted(from.sorted());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Header_SpectraHeader::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Header_SpectraHeader::CopyFrom(const Header_SpectraHeader& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Header_SpectraHeader::IsInitialized() const {
+
+ return true;
+}
+
+void Header_SpectraHeader::Swap(Header_SpectraHeader* other) {
+ if (other != this) {
+ std::swap(sorted_, other->sorted_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Header_SpectraHeader::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Header_SpectraHeader_descriptor_;
+ metadata.reflection = Header_SpectraHeader_reflection_;
+ return metadata;
+}
+
+
+// -------------------------------------------------------------------
+
+#ifndef _MSC_VER
+const int Header_ResultsHeader::kMassWindowFieldNumber;
+const int Header_ResultsHeader::kTopMatchesFieldNumber;
+const int Header_ResultsHeader::kPeptidesHeaderFieldNumber;
+#endif // !_MSC_VER
+
+Header_ResultsHeader::Header_ResultsHeader()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Header_ResultsHeader::InitAsDefaultInstance() {
+ peptides_header_ = const_cast< ::pb::Header_PeptidesHeader*>(&::pb::Header_PeptidesHeader::default_instance());
+}
+
+Header_ResultsHeader::Header_ResultsHeader(const Header_ResultsHeader& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Header_ResultsHeader::SharedCtor() {
+ _cached_size_ = 0;
+ mass_window_ = 0;
+ top_matches_ = 0;
+ peptides_header_ = NULL;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Header_ResultsHeader::~Header_ResultsHeader() {
+ SharedDtor();
+}
+
+void Header_ResultsHeader::SharedDtor() {
+ if (this != default_instance_) {
+ delete peptides_header_;
+ }
+}
+
+void Header_ResultsHeader::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Header_ResultsHeader::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Header_ResultsHeader_descriptor_;
+}
+
+const Header_ResultsHeader& Header_ResultsHeader::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+Header_ResultsHeader* Header_ResultsHeader::default_instance_ = NULL;
+
+Header_ResultsHeader* Header_ResultsHeader::New() const {
+ return new Header_ResultsHeader;
+}
+
+void Header_ResultsHeader::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ mass_window_ = 0;
+ top_matches_ = 0;
+ if (has_peptides_header()) {
+ if (peptides_header_ != NULL) peptides_header_->::pb::Header_PeptidesHeader::Clear();
+ }
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Header_ResultsHeader::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional double mass_window = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &mass_window_)));
+ set_has_mass_window();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(16)) goto parse_top_matches;
+ break;
+ }
+
+ // optional int32 top_matches = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_top_matches:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &top_matches_)));
+ set_has_top_matches();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(26)) goto parse_peptides_header;
+ break;
+ }
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_peptides_header:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_peptides_header()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Header_ResultsHeader::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional double mass_window = 1;
+ if (has_mass_window()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(1, this->mass_window(), output);
+ }
+
+ // optional int32 top_matches = 2;
+ if (has_top_matches()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(2, this->top_matches(), output);
+ }
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 3;
+ if (has_peptides_header()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 3, this->peptides_header(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Header_ResultsHeader::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional double mass_window = 1;
+ if (has_mass_window()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(1, this->mass_window(), target);
+ }
+
+ // optional int32 top_matches = 2;
+ if (has_top_matches()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(2, this->top_matches(), target);
+ }
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 3;
+ if (has_peptides_header()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 3, this->peptides_header(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Header_ResultsHeader::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional double mass_window = 1;
+ if (has_mass_window()) {
+ total_size += 1 + 8;
+ }
+
+ // optional int32 top_matches = 2;
+ if (has_top_matches()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->top_matches());
+ }
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 3;
+ if (has_peptides_header()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->peptides_header());
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Header_ResultsHeader::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Header_ResultsHeader* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Header_ResultsHeader*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Header_ResultsHeader::MergeFrom(const Header_ResultsHeader& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_mass_window()) {
+ set_mass_window(from.mass_window());
+ }
+ if (from.has_top_matches()) {
+ set_top_matches(from.top_matches());
+ }
+ if (from.has_peptides_header()) {
+ mutable_peptides_header()->::pb::Header_PeptidesHeader::MergeFrom(from.peptides_header());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Header_ResultsHeader::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Header_ResultsHeader::CopyFrom(const Header_ResultsHeader& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Header_ResultsHeader::IsInitialized() const {
+
+ return true;
+}
+
+void Header_ResultsHeader::Swap(Header_ResultsHeader* other) {
+ if (other != this) {
+ std::swap(mass_window_, other->mass_window_);
+ std::swap(top_matches_, other->top_matches_);
+ std::swap(peptides_header_, other->peptides_header_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Header_ResultsHeader::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Header_ResultsHeader_descriptor_;
+ metadata.reflection = Header_ResultsHeader_reflection_;
+ return metadata;
+}
+
+
+// -------------------------------------------------------------------
+
+#ifndef _MSC_VER
+#endif // !_MSC_VER
+
+Header_AuxLocationsHeader::Header_AuxLocationsHeader()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Header_AuxLocationsHeader::InitAsDefaultInstance() {
+}
+
+Header_AuxLocationsHeader::Header_AuxLocationsHeader(const Header_AuxLocationsHeader& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Header_AuxLocationsHeader::SharedCtor() {
+ _cached_size_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Header_AuxLocationsHeader::~Header_AuxLocationsHeader() {
+ SharedDtor();
+}
+
+void Header_AuxLocationsHeader::SharedDtor() {
+ if (this != default_instance_) {
+ }
+}
+
+void Header_AuxLocationsHeader::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Header_AuxLocationsHeader::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Header_AuxLocationsHeader_descriptor_;
+}
+
+const Header_AuxLocationsHeader& Header_AuxLocationsHeader::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+Header_AuxLocationsHeader* Header_AuxLocationsHeader::default_instance_ = NULL;
+
+Header_AuxLocationsHeader* Header_AuxLocationsHeader::New() const {
+ return new Header_AuxLocationsHeader;
+}
+
+void Header_AuxLocationsHeader::Clear() {
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Header_AuxLocationsHeader::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ }
+ return true;
+#undef DO_
+}
+
+void Header_AuxLocationsHeader::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Header_AuxLocationsHeader::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Header_AuxLocationsHeader::ByteSize() const {
+ int total_size = 0;
+
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Header_AuxLocationsHeader::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Header_AuxLocationsHeader* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Header_AuxLocationsHeader*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Header_AuxLocationsHeader::MergeFrom(const Header_AuxLocationsHeader& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Header_AuxLocationsHeader::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Header_AuxLocationsHeader::CopyFrom(const Header_AuxLocationsHeader& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Header_AuxLocationsHeader::IsInitialized() const {
+
+ return true;
+}
+
+void Header_AuxLocationsHeader::Swap(Header_AuxLocationsHeader* other) {
+ if (other != this) {
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Header_AuxLocationsHeader::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Header_AuxLocationsHeader_descriptor_;
+ metadata.reflection = Header_AuxLocationsHeader_reflection_;
+ return metadata;
+}
+
+
+// -------------------------------------------------------------------
+
+#ifndef _MSC_VER
+const int Header::kSourceFieldNumber;
+const int Header::kFileTypeFieldNumber;
+const int Header::kRawProteinsHeaderFieldNumber;
+const int Header::kPeptidesHeaderFieldNumber;
+const int Header::kSpectraHeaderFieldNumber;
+const int Header::kResultsHeaderFieldNumber;
+const int Header::kAuxLocsHeaderFieldNumber;
+const int Header::kCommandLineFieldNumber;
+#endif // !_MSC_VER
+
+Header::Header()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Header::InitAsDefaultInstance() {
+ raw_proteins_header_ = const_cast< ::pb::Header_RawProteinsHeader*>(&::pb::Header_RawProteinsHeader::default_instance());
+ peptides_header_ = const_cast< ::pb::Header_PeptidesHeader*>(&::pb::Header_PeptidesHeader::default_instance());
+ spectra_header_ = const_cast< ::pb::Header_SpectraHeader*>(&::pb::Header_SpectraHeader::default_instance());
+ results_header_ = const_cast< ::pb::Header_ResultsHeader*>(&::pb::Header_ResultsHeader::default_instance());
+ aux_locs_header_ = const_cast< ::pb::Header_AuxLocationsHeader*>(&::pb::Header_AuxLocationsHeader::default_instance());
+}
+
+Header::Header(const Header& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Header::SharedCtor() {
+ _cached_size_ = 0;
+ file_type_ = 0;
+ raw_proteins_header_ = NULL;
+ peptides_header_ = NULL;
+ spectra_header_ = NULL;
+ results_header_ = NULL;
+ aux_locs_header_ = NULL;
+ command_line_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Header::~Header() {
+ SharedDtor();
+}
+
+void Header::SharedDtor() {
+ if (command_line_ != &::google::protobuf::internal::kEmptyString) {
+ delete command_line_;
+ }
+ if (this != default_instance_) {
+ delete raw_proteins_header_;
+ delete peptides_header_;
+ delete spectra_header_;
+ delete results_header_;
+ delete aux_locs_header_;
+ }
+}
+
+void Header::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Header::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Header_descriptor_;
+}
+
+const Header& Header::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_header_2eproto();
+ return *default_instance_;
+}
+
+Header* Header::default_instance_ = NULL;
+
+Header* Header::New() const {
+ return new Header;
+}
+
+void Header::Clear() {
+ if (_has_bits_[1 / 32] & (0xffu << (1 % 32))) {
+ file_type_ = 0;
+ if (has_raw_proteins_header()) {
+ if (raw_proteins_header_ != NULL) raw_proteins_header_->::pb::Header_RawProteinsHeader::Clear();
+ }
+ if (has_peptides_header()) {
+ if (peptides_header_ != NULL) peptides_header_->::pb::Header_PeptidesHeader::Clear();
+ }
+ if (has_spectra_header()) {
+ if (spectra_header_ != NULL) spectra_header_->::pb::Header_SpectraHeader::Clear();
+ }
+ if (has_results_header()) {
+ if (results_header_ != NULL) results_header_->::pb::Header_ResultsHeader::Clear();
+ }
+ if (has_aux_locs_header()) {
+ if (aux_locs_header_ != NULL) aux_locs_header_->::pb::Header_AuxLocationsHeader::Clear();
+ }
+ if (has_command_line()) {
+ if (command_line_ != &::google::protobuf::internal::kEmptyString) {
+ command_line_->clear();
+ }
+ }
+ }
+ source_.Clear();
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Header::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // repeated .pb.Header.Source source = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_source:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, add_source()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(10)) goto parse_source;
+ if (input->ExpectTag(16)) goto parse_file_type;
+ break;
+ }
+
+ // required .pb.Header.FileType file_type = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_file_type:
+ int value;
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ int, ::google::protobuf::internal::WireFormatLite::TYPE_ENUM>(
+ input, &value)));
+ if (::pb::Header_FileType_IsValid(value)) {
+ set_file_type(static_cast< ::pb::Header_FileType >(value));
+ } else {
+ mutable_unknown_fields()->AddVarint(2, value);
+ }
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(26)) goto parse_raw_proteins_header;
+ break;
+ }
+
+ // optional .pb.Header.RawProteinsHeader raw_proteins_header = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_raw_proteins_header:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_raw_proteins_header()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(34)) goto parse_peptides_header;
+ break;
+ }
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 4;
+ case 4: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_peptides_header:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_peptides_header()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(42)) goto parse_spectra_header;
+ break;
+ }
+
+ // optional .pb.Header.SpectraHeader spectra_header = 5;
+ case 5: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_spectra_header:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_spectra_header()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(50)) goto parse_results_header;
+ break;
+ }
+
+ // optional .pb.Header.ResultsHeader results_header = 6;
+ case 6: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_results_header:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_results_header()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(58)) goto parse_aux_locs_header;
+ break;
+ }
+
+ // optional .pb.Header.AuxLocationsHeader aux_locs_header = 7;
+ case 7: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_aux_locs_header:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_aux_locs_header()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(66)) goto parse_command_line;
+ break;
+ }
+
+ // optional string command_line = 8;
+ case 8: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_command_line:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadString(
+ input, this->mutable_command_line()));
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->command_line().data(), this->command_line().length(),
+ ::google::protobuf::internal::WireFormat::PARSE);
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Header::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // repeated .pb.Header.Source source = 1;
+ for (int i = 0; i < this->source_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 1, this->source(i), output);
+ }
+
+ // required .pb.Header.FileType file_type = 2;
+ if (has_file_type()) {
+ ::google::protobuf::internal::WireFormatLite::WriteEnum(
+ 2, this->file_type(), output);
+ }
+
+ // optional .pb.Header.RawProteinsHeader raw_proteins_header = 3;
+ if (has_raw_proteins_header()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 3, this->raw_proteins_header(), output);
+ }
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 4;
+ if (has_peptides_header()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 4, this->peptides_header(), output);
+ }
+
+ // optional .pb.Header.SpectraHeader spectra_header = 5;
+ if (has_spectra_header()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 5, this->spectra_header(), output);
+ }
+
+ // optional .pb.Header.ResultsHeader results_header = 6;
+ if (has_results_header()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 6, this->results_header(), output);
+ }
+
+ // optional .pb.Header.AuxLocationsHeader aux_locs_header = 7;
+ if (has_aux_locs_header()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 7, this->aux_locs_header(), output);
+ }
+
+ // optional string command_line = 8;
+ if (has_command_line()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->command_line().data(), this->command_line().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ ::google::protobuf::internal::WireFormatLite::WriteString(
+ 8, this->command_line(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Header::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // repeated .pb.Header.Source source = 1;
+ for (int i = 0; i < this->source_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 1, this->source(i), target);
+ }
+
+ // required .pb.Header.FileType file_type = 2;
+ if (has_file_type()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteEnumToArray(
+ 2, this->file_type(), target);
+ }
+
+ // optional .pb.Header.RawProteinsHeader raw_proteins_header = 3;
+ if (has_raw_proteins_header()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 3, this->raw_proteins_header(), target);
+ }
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 4;
+ if (has_peptides_header()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 4, this->peptides_header(), target);
+ }
+
+ // optional .pb.Header.SpectraHeader spectra_header = 5;
+ if (has_spectra_header()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 5, this->spectra_header(), target);
+ }
+
+ // optional .pb.Header.ResultsHeader results_header = 6;
+ if (has_results_header()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 6, this->results_header(), target);
+ }
+
+ // optional .pb.Header.AuxLocationsHeader aux_locs_header = 7;
+ if (has_aux_locs_header()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 7, this->aux_locs_header(), target);
+ }
+
+ // optional string command_line = 8;
+ if (has_command_line()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->command_line().data(), this->command_line().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ target =
+ ::google::protobuf::internal::WireFormatLite::WriteStringToArray(
+ 8, this->command_line(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Header::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[1 / 32] & (0xffu << (1 % 32))) {
+ // required .pb.Header.FileType file_type = 2;
+ if (has_file_type()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::EnumSize(this->file_type());
+ }
+
+ // optional .pb.Header.RawProteinsHeader raw_proteins_header = 3;
+ if (has_raw_proteins_header()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->raw_proteins_header());
+ }
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 4;
+ if (has_peptides_header()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->peptides_header());
+ }
+
+ // optional .pb.Header.SpectraHeader spectra_header = 5;
+ if (has_spectra_header()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->spectra_header());
+ }
+
+ // optional .pb.Header.ResultsHeader results_header = 6;
+ if (has_results_header()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->results_header());
+ }
+
+ // optional .pb.Header.AuxLocationsHeader aux_locs_header = 7;
+ if (has_aux_locs_header()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->aux_locs_header());
+ }
+
+ // optional string command_line = 8;
+ if (has_command_line()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::StringSize(
+ this->command_line());
+ }
+
+ }
+ // repeated .pb.Header.Source source = 1;
+ total_size += 1 * this->source_size();
+ for (int i = 0; i < this->source_size(); i++) {
+ total_size +=
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->source(i));
+ }
+
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Header::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Header* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Header*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Header::MergeFrom(const Header& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ source_.MergeFrom(from.source_);
+ if (from._has_bits_[1 / 32] & (0xffu << (1 % 32))) {
+ if (from.has_file_type()) {
+ set_file_type(from.file_type());
+ }
+ if (from.has_raw_proteins_header()) {
+ mutable_raw_proteins_header()->::pb::Header_RawProteinsHeader::MergeFrom(from.raw_proteins_header());
+ }
+ if (from.has_peptides_header()) {
+ mutable_peptides_header()->::pb::Header_PeptidesHeader::MergeFrom(from.peptides_header());
+ }
+ if (from.has_spectra_header()) {
+ mutable_spectra_header()->::pb::Header_SpectraHeader::MergeFrom(from.spectra_header());
+ }
+ if (from.has_results_header()) {
+ mutable_results_header()->::pb::Header_ResultsHeader::MergeFrom(from.results_header());
+ }
+ if (from.has_aux_locs_header()) {
+ mutable_aux_locs_header()->::pb::Header_AuxLocationsHeader::MergeFrom(from.aux_locs_header());
+ }
+ if (from.has_command_line()) {
+ set_command_line(from.command_line());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Header::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Header::CopyFrom(const Header& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Header::IsInitialized() const {
+ if ((_has_bits_[0] & 0x00000002) != 0x00000002) return false;
+
+ for (int i = 0; i < source_size(); i++) {
+ if (!this->source(i).IsInitialized()) return false;
+ }
+ return true;
+}
+
+void Header::Swap(Header* other) {
+ if (other != this) {
+ source_.Swap(&other->source_);
+ std::swap(file_type_, other->file_type_);
+ std::swap(raw_proteins_header_, other->raw_proteins_header_);
+ std::swap(peptides_header_, other->peptides_header_);
+ std::swap(spectra_header_, other->spectra_header_);
+ std::swap(results_header_, other->results_header_);
+ std::swap(aux_locs_header_, other->aux_locs_header_);
+ std::swap(command_line_, other->command_line_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Header::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Header_descriptor_;
+ metadata.reflection = Header_reflection_;
+ return metadata;
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+// @@protoc_insertion_point(global_scope)
diff --git a/src/app/tide/protoobj/header.pb.h b/src/app/tide/protoobj/header.pb.h
new file mode 100644
index 0000000..af56961
--- /dev/null
+++ b/src/app/tide/protoobj/header.pb.h
@@ -0,0 +1,2404 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: header.proto
+
+#ifndef PROTOBUF_header_2eproto__INCLUDED
+#define PROTOBUF_header_2eproto__INCLUDED
+
+#include <string>
+
+#include <google/protobuf/stubs/common.h>
+
+#if GOOGLE_PROTOBUF_VERSION < 2005000
+#error This file was generated by a newer version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please update
+#error your headers.
+#endif
+#if 2005000 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
+#error This file was generated by an older version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please
+#error regenerate this file with a newer version of protoc.
+#endif
+
+#include <google/protobuf/generated_message_util.h>
+#include <google/protobuf/message.h>
+#include <google/protobuf/repeated_field.h>
+#include <google/protobuf/extension_set.h>
+#include <google/protobuf/generated_enum_reflection.h>
+#include <google/protobuf/unknown_field_set.h>
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+// Internal implementation detail -- do not call these.
+void protobuf_AddDesc_header_2eproto();
+void protobuf_AssignDesc_header_2eproto();
+void protobuf_ShutdownFile_header_2eproto();
+
+class Modification;
+class ModTable;
+class Header;
+class Header_Source;
+class Header_RawProteinsHeader;
+class Header_PeptidesHeader;
+class Header_SpectraHeader;
+class Header_ResultsHeader;
+class Header_AuxLocationsHeader;
+
+enum Header_FileType {
+ Header_FileType_RAW_PROTEINS = 0,
+ Header_FileType_PEPTIDES = 1,
+ Header_FileType_SPECTRA = 2,
+ Header_FileType_PARAMS = 3,
+ Header_FileType_MOD_TABLE = 4,
+ Header_FileType_RESULTS = 5,
+ Header_FileType_AUX_LOCATIONS = 6
+};
+bool Header_FileType_IsValid(int value);
+const Header_FileType Header_FileType_FileType_MIN = Header_FileType_RAW_PROTEINS;
+const Header_FileType Header_FileType_FileType_MAX = Header_FileType_AUX_LOCATIONS;
+const int Header_FileType_FileType_ARRAYSIZE = Header_FileType_FileType_MAX + 1;
+
+const ::google::protobuf::EnumDescriptor* Header_FileType_descriptor();
+inline const ::std::string& Header_FileType_Name(Header_FileType value) {
+ return ::google::protobuf::internal::NameOfEnum(
+ Header_FileType_descriptor(), value);
+}
+inline bool Header_FileType_Parse(
+ const ::std::string& name, Header_FileType* value) {
+ return ::google::protobuf::internal::ParseNamedEnum<Header_FileType>(
+ Header_FileType_descriptor(), name, value);
+}
+// ===================================================================
+
+class Modification : public ::google::protobuf::Message {
+ public:
+ Modification();
+ virtual ~Modification();
+
+ Modification(const Modification& from);
+
+ inline Modification& operator=(const Modification& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Modification& default_instance();
+
+ void Swap(Modification* other);
+
+ // implements Message ----------------------------------------------
+
+ Modification* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Modification& from);
+ void MergeFrom(const Modification& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional string amino_acids = 1;
+ inline bool has_amino_acids() const;
+ inline void clear_amino_acids();
+ static const int kAminoAcidsFieldNumber = 1;
+ inline const ::std::string& amino_acids() const;
+ inline void set_amino_acids(const ::std::string& value);
+ inline void set_amino_acids(const char* value);
+ inline void set_amino_acids(const char* value, size_t size);
+ inline ::std::string* mutable_amino_acids();
+ inline ::std::string* release_amino_acids();
+ inline void set_allocated_amino_acids(::std::string* amino_acids);
+
+ // optional double delta = 2;
+ inline bool has_delta() const;
+ inline void clear_delta();
+ static const int kDeltaFieldNumber = 2;
+ inline double delta() const;
+ inline void set_delta(double value);
+
+ // optional int32 max_count = 3;
+ inline bool has_max_count() const;
+ inline void clear_max_count();
+ static const int kMaxCountFieldNumber = 3;
+ inline ::google::protobuf::int32 max_count() const;
+ inline void set_max_count(::google::protobuf::int32 value);
+
+ // @@protoc_insertion_point(class_scope:pb.Modification)
+ private:
+ inline void set_has_amino_acids();
+ inline void clear_has_amino_acids();
+ inline void set_has_delta();
+ inline void clear_has_delta();
+ inline void set_has_max_count();
+ inline void clear_has_max_count();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::std::string* amino_acids_;
+ double delta_;
+ ::google::protobuf::int32 max_count_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(3 + 31) / 32];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static Modification* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class ModTable : public ::google::protobuf::Message {
+ public:
+ ModTable();
+ virtual ~ModTable();
+
+ ModTable(const ModTable& from);
+
+ inline ModTable& operator=(const ModTable& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const ModTable& default_instance();
+
+ void Swap(ModTable* other);
+
+ // implements Message ----------------------------------------------
+
+ ModTable* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const ModTable& from);
+ void MergeFrom(const ModTable& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // repeated .pb.Modification variable_mod = 1;
+ inline int variable_mod_size() const;
+ inline void clear_variable_mod();
+ static const int kVariableModFieldNumber = 1;
+ inline const ::pb::Modification& variable_mod(int index) const;
+ inline ::pb::Modification* mutable_variable_mod(int index);
+ inline ::pb::Modification* add_variable_mod();
+ inline const ::google::protobuf::RepeatedPtrField< ::pb::Modification >&
+ variable_mod() const;
+ inline ::google::protobuf::RepeatedPtrField< ::pb::Modification >*
+ mutable_variable_mod();
+
+ // repeated .pb.Modification static_mod = 2;
+ inline int static_mod_size() const;
+ inline void clear_static_mod();
+ static const int kStaticModFieldNumber = 2;
+ inline const ::pb::Modification& static_mod(int index) const;
+ inline ::pb::Modification* mutable_static_mod(int index);
+ inline ::pb::Modification* add_static_mod();
+ inline const ::google::protobuf::RepeatedPtrField< ::pb::Modification >&
+ static_mod() const;
+ inline ::google::protobuf::RepeatedPtrField< ::pb::Modification >*
+ mutable_static_mod();
+
+ // repeated double unique_deltas = 10;
+ inline int unique_deltas_size() const;
+ inline void clear_unique_deltas();
+ static const int kUniqueDeltasFieldNumber = 10;
+ inline double unique_deltas(int index) const;
+ inline void set_unique_deltas(int index, double value);
+ inline void add_unique_deltas(double value);
+ inline const ::google::protobuf::RepeatedField< double >&
+ unique_deltas() const;
+ inline ::google::protobuf::RepeatedField< double >*
+ mutable_unique_deltas();
+
+ // @@protoc_insertion_point(class_scope:pb.ModTable)
+ private:
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::google::protobuf::RepeatedPtrField< ::pb::Modification > variable_mod_;
+ ::google::protobuf::RepeatedPtrField< ::pb::Modification > static_mod_;
+ ::google::protobuf::RepeatedField< double > unique_deltas_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(3 + 31) / 32];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static ModTable* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Header_Source : public ::google::protobuf::Message {
+ public:
+ Header_Source();
+ virtual ~Header_Source();
+
+ Header_Source(const Header_Source& from);
+
+ inline Header_Source& operator=(const Header_Source& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Header_Source& default_instance();
+
+ void Swap(Header_Source* other);
+
+ // implements Message ----------------------------------------------
+
+ Header_Source* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Header_Source& from);
+ void MergeFrom(const Header_Source& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional string filename = 1;
+ inline bool has_filename() const;
+ inline void clear_filename();
+ static const int kFilenameFieldNumber = 1;
+ inline const ::std::string& filename() const;
+ inline void set_filename(const ::std::string& value);
+ inline void set_filename(const char* value);
+ inline void set_filename(const char* value, size_t size);
+ inline ::std::string* mutable_filename();
+ inline ::std::string* release_filename();
+ inline void set_allocated_filename(::std::string* filename);
+
+ // optional .pb.Header header = 2;
+ inline bool has_header() const;
+ inline void clear_header();
+ static const int kHeaderFieldNumber = 2;
+ inline const ::pb::Header& header() const;
+ inline ::pb::Header* mutable_header();
+ inline ::pb::Header* release_header();
+ inline void set_allocated_header(::pb::Header* header);
+
+ // optional string filetype = 3;
+ inline bool has_filetype() const;
+ inline void clear_filetype();
+ static const int kFiletypeFieldNumber = 3;
+ inline const ::std::string& filetype() const;
+ inline void set_filetype(const ::std::string& value);
+ inline void set_filetype(const char* value);
+ inline void set_filetype(const char* value, size_t size);
+ inline ::std::string* mutable_filetype();
+ inline ::std::string* release_filetype();
+ inline void set_allocated_filetype(::std::string* filetype);
+
+ // @@protoc_insertion_point(class_scope:pb.Header.Source)
+ private:
+ inline void set_has_filename();
+ inline void clear_has_filename();
+ inline void set_has_header();
+ inline void clear_has_header();
+ inline void set_has_filetype();
+ inline void clear_has_filetype();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::std::string* filename_;
+ ::pb::Header* header_;
+ ::std::string* filetype_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(3 + 31) / 32];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static Header_Source* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Header_RawProteinsHeader : public ::google::protobuf::Message {
+ public:
+ Header_RawProteinsHeader();
+ virtual ~Header_RawProteinsHeader();
+
+ Header_RawProteinsHeader(const Header_RawProteinsHeader& from);
+
+ inline Header_RawProteinsHeader& operator=(const Header_RawProteinsHeader& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Header_RawProteinsHeader& default_instance();
+
+ void Swap(Header_RawProteinsHeader* other);
+
+ // implements Message ----------------------------------------------
+
+ Header_RawProteinsHeader* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Header_RawProteinsHeader& from);
+ void MergeFrom(const Header_RawProteinsHeader& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // @@protoc_insertion_point(class_scope:pb.Header.RawProteinsHeader)
+ private:
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[1];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static Header_RawProteinsHeader* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Header_PeptidesHeader : public ::google::protobuf::Message {
+ public:
+ Header_PeptidesHeader();
+ virtual ~Header_PeptidesHeader();
+
+ Header_PeptidesHeader(const Header_PeptidesHeader& from);
+
+ inline Header_PeptidesHeader& operator=(const Header_PeptidesHeader& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Header_PeptidesHeader& default_instance();
+
+ void Swap(Header_PeptidesHeader* other);
+
+ // implements Message ----------------------------------------------
+
+ Header_PeptidesHeader* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Header_PeptidesHeader& from);
+ void MergeFrom(const Header_PeptidesHeader& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional double min_mass = 3;
+ inline bool has_min_mass() const;
+ inline void clear_min_mass();
+ static const int kMinMassFieldNumber = 3;
+ inline double min_mass() const;
+ inline void set_min_mass(double value);
+
+ // optional double max_mass = 4;
+ inline bool has_max_mass() const;
+ inline void clear_max_mass();
+ static const int kMaxMassFieldNumber = 4;
+ inline double max_mass() const;
+ inline void set_max_mass(double value);
+
+ // optional int32 min_length = 5;
+ inline bool has_min_length() const;
+ inline void clear_min_length();
+ static const int kMinLengthFieldNumber = 5;
+ inline ::google::protobuf::int32 min_length() const;
+ inline void set_min_length(::google::protobuf::int32 value);
+
+ // optional int32 max_length = 6;
+ inline bool has_max_length() const;
+ inline void clear_max_length();
+ static const int kMaxLengthFieldNumber = 6;
+ inline ::google::protobuf::int32 max_length() const;
+ inline void set_max_length(::google::protobuf::int32 value);
+
+ // optional string enzyme = 7;
+ inline bool has_enzyme() const;
+ inline void clear_enzyme();
+ static const int kEnzymeFieldNumber = 7;
+ inline const ::std::string& enzyme() const;
+ inline void set_enzyme(const ::std::string& value);
+ inline void set_enzyme(const char* value);
+ inline void set_enzyme(const char* value, size_t size);
+ inline ::std::string* mutable_enzyme();
+ inline ::std::string* release_enzyme();
+ inline void set_allocated_enzyme(::std::string* enzyme);
+
+ // optional bool full_digestion = 8;
+ inline bool has_full_digestion() const;
+ inline void clear_full_digestion();
+ static const int kFullDigestionFieldNumber = 8;
+ inline bool full_digestion() const;
+ inline void set_full_digestion(bool value);
+
+ // optional int32 max_missed_cleavages = 14;
+ inline bool has_max_missed_cleavages() const;
+ inline void clear_max_missed_cleavages();
+ static const int kMaxMissedCleavagesFieldNumber = 14;
+ inline ::google::protobuf::int32 max_missed_cleavages() const;
+ inline void set_max_missed_cleavages(::google::protobuf::int32 value);
+
+ // optional bool monoisotopic_precursor = 13;
+ inline bool has_monoisotopic_precursor() const;
+ inline void clear_monoisotopic_precursor();
+ static const int kMonoisotopicPrecursorFieldNumber = 13;
+ inline bool monoisotopic_precursor() const;
+ inline void set_monoisotopic_precursor(bool value);
+
+ // optional bool has_peaks = 10;
+ inline bool has_has_peaks() const;
+ inline void clear_has_peaks();
+ static const int kHasPeaksFieldNumber = 10;
+ inline bool has_peaks() const;
+ inline void set_has_peaks(bool value);
+
+ // optional double downselect_fraction = 11;
+ inline bool has_downselect_fraction() const;
+ inline void clear_downselect_fraction();
+ static const int kDownselectFractionFieldNumber = 11;
+ inline double downselect_fraction() const;
+ inline void set_downselect_fraction(double value);
+
+ // optional .pb.ModTable mods = 12;
+ inline bool has_mods() const;
+ inline void clear_mods();
+ static const int kModsFieldNumber = 12;
+ inline const ::pb::ModTable& mods() const;
+ inline ::pb::ModTable* mutable_mods();
+ inline ::pb::ModTable* release_mods();
+ inline void set_allocated_mods(::pb::ModTable* mods);
+
+ // optional .pb.ModTable nterm_mods = 15;
+ inline bool has_nterm_mods() const;
+ inline void clear_nterm_mods();
+ static const int kNtermModsFieldNumber = 15;
+ inline const ::pb::ModTable& nterm_mods() const;
+ inline ::pb::ModTable* mutable_nterm_mods();
+ inline ::pb::ModTable* release_nterm_mods();
+ inline void set_allocated_nterm_mods(::pb::ModTable* nterm_mods);
+
+ // optional .pb.ModTable cterm_mods = 16;
+ inline bool has_cterm_mods() const;
+ inline void clear_cterm_mods();
+ static const int kCtermModsFieldNumber = 16;
+ inline const ::pb::ModTable& cterm_mods() const;
+ inline ::pb::ModTable* mutable_cterm_mods();
+ inline ::pb::ModTable* release_cterm_mods();
+ inline void set_allocated_cterm_mods(::pb::ModTable* cterm_mods);
+
+ // optional int32 decoys = 9;
+ inline bool has_decoys() const;
+ inline void clear_decoys();
+ static const int kDecoysFieldNumber = 9;
+ inline ::google::protobuf::int32 decoys() const;
+ inline void set_decoys(::google::protobuf::int32 value);
+
+ // @@protoc_insertion_point(class_scope:pb.Header.PeptidesHeader)
+ private:
+ inline void set_has_min_mass();
+ inline void clear_has_min_mass();
+ inline void set_has_max_mass();
+ inline void clear_has_max_mass();
+ inline void set_has_min_length();
+ inline void clear_has_min_length();
+ inline void set_has_max_length();
+ inline void clear_has_max_length();
+ inline void set_has_enzyme();
+ inline void clear_has_enzyme();
+ inline void set_has_full_digestion();
+ inline void clear_has_full_digestion();
+ inline void set_has_max_missed_cleavages();
+ inline void clear_has_max_missed_cleavages();
+ inline void set_has_monoisotopic_precursor();
+ inline void clear_has_monoisotopic_precursor();
+ inline void set_has_has_peaks();
+ inline void clear_has_has_peaks();
+ inline void set_has_downselect_fraction();
+ inline void clear_has_downselect_fraction();
+ inline void set_has_mods();
+ inline void clear_has_mods();
+ inline void set_has_nterm_mods();
+ inline void clear_has_nterm_mods();
+ inline void set_has_cterm_mods();
+ inline void clear_has_cterm_mods();
+ inline void set_has_decoys();
+ inline void clear_has_decoys();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ double min_mass_;
+ double max_mass_;
+ ::google::protobuf::int32 min_length_;
+ ::google::protobuf::int32 max_length_;
+ ::std::string* enzyme_;
+ ::google::protobuf::int32 max_missed_cleavages_;
+ bool full_digestion_;
+ bool monoisotopic_precursor_;
+ bool has_peaks_;
+ double downselect_fraction_;
+ ::pb::ModTable* mods_;
+ ::pb::ModTable* nterm_mods_;
+ ::pb::ModTable* cterm_mods_;
+ ::google::protobuf::int32 decoys_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(14 + 31) / 32];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static Header_PeptidesHeader* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Header_SpectraHeader : public ::google::protobuf::Message {
+ public:
+ Header_SpectraHeader();
+ virtual ~Header_SpectraHeader();
+
+ Header_SpectraHeader(const Header_SpectraHeader& from);
+
+ inline Header_SpectraHeader& operator=(const Header_SpectraHeader& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Header_SpectraHeader& default_instance();
+
+ void Swap(Header_SpectraHeader* other);
+
+ // implements Message ----------------------------------------------
+
+ Header_SpectraHeader* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Header_SpectraHeader& from);
+ void MergeFrom(const Header_SpectraHeader& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional bool sorted = 2;
+ inline bool has_sorted() const;
+ inline void clear_sorted();
+ static const int kSortedFieldNumber = 2;
+ inline bool sorted() const;
+ inline void set_sorted(bool value);
+
+ // @@protoc_insertion_point(class_scope:pb.Header.SpectraHeader)
+ private:
+ inline void set_has_sorted();
+ inline void clear_has_sorted();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ bool sorted_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(1 + 31) / 32];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static Header_SpectraHeader* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Header_ResultsHeader : public ::google::protobuf::Message {
+ public:
+ Header_ResultsHeader();
+ virtual ~Header_ResultsHeader();
+
+ Header_ResultsHeader(const Header_ResultsHeader& from);
+
+ inline Header_ResultsHeader& operator=(const Header_ResultsHeader& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Header_ResultsHeader& default_instance();
+
+ void Swap(Header_ResultsHeader* other);
+
+ // implements Message ----------------------------------------------
+
+ Header_ResultsHeader* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Header_ResultsHeader& from);
+ void MergeFrom(const Header_ResultsHeader& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional double mass_window = 1;
+ inline bool has_mass_window() const;
+ inline void clear_mass_window();
+ static const int kMassWindowFieldNumber = 1;
+ inline double mass_window() const;
+ inline void set_mass_window(double value);
+
+ // optional int32 top_matches = 2;
+ inline bool has_top_matches() const;
+ inline void clear_top_matches();
+ static const int kTopMatchesFieldNumber = 2;
+ inline ::google::protobuf::int32 top_matches() const;
+ inline void set_top_matches(::google::protobuf::int32 value);
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 3;
+ inline bool has_peptides_header() const;
+ inline void clear_peptides_header();
+ static const int kPeptidesHeaderFieldNumber = 3;
+ inline const ::pb::Header_PeptidesHeader& peptides_header() const;
+ inline ::pb::Header_PeptidesHeader* mutable_peptides_header();
+ inline ::pb::Header_PeptidesHeader* release_peptides_header();
+ inline void set_allocated_peptides_header(::pb::Header_PeptidesHeader* peptides_header);
+
+ // @@protoc_insertion_point(class_scope:pb.Header.ResultsHeader)
+ private:
+ inline void set_has_mass_window();
+ inline void clear_has_mass_window();
+ inline void set_has_top_matches();
+ inline void clear_has_top_matches();
+ inline void set_has_peptides_header();
+ inline void clear_has_peptides_header();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ double mass_window_;
+ ::pb::Header_PeptidesHeader* peptides_header_;
+ ::google::protobuf::int32 top_matches_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(3 + 31) / 32];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static Header_ResultsHeader* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Header_AuxLocationsHeader : public ::google::protobuf::Message {
+ public:
+ Header_AuxLocationsHeader();
+ virtual ~Header_AuxLocationsHeader();
+
+ Header_AuxLocationsHeader(const Header_AuxLocationsHeader& from);
+
+ inline Header_AuxLocationsHeader& operator=(const Header_AuxLocationsHeader& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Header_AuxLocationsHeader& default_instance();
+
+ void Swap(Header_AuxLocationsHeader* other);
+
+ // implements Message ----------------------------------------------
+
+ Header_AuxLocationsHeader* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Header_AuxLocationsHeader& from);
+ void MergeFrom(const Header_AuxLocationsHeader& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // @@protoc_insertion_point(class_scope:pb.Header.AuxLocationsHeader)
+ private:
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[1];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static Header_AuxLocationsHeader* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Header : public ::google::protobuf::Message {
+ public:
+ Header();
+ virtual ~Header();
+
+ Header(const Header& from);
+
+ inline Header& operator=(const Header& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Header& default_instance();
+
+ void Swap(Header* other);
+
+ // implements Message ----------------------------------------------
+
+ Header* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Header& from);
+ void MergeFrom(const Header& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ typedef Header_Source Source;
+ typedef Header_RawProteinsHeader RawProteinsHeader;
+ typedef Header_PeptidesHeader PeptidesHeader;
+ typedef Header_SpectraHeader SpectraHeader;
+ typedef Header_ResultsHeader ResultsHeader;
+ typedef Header_AuxLocationsHeader AuxLocationsHeader;
+
+ typedef Header_FileType FileType;
+ static const FileType RAW_PROTEINS = Header_FileType_RAW_PROTEINS;
+ static const FileType PEPTIDES = Header_FileType_PEPTIDES;
+ static const FileType SPECTRA = Header_FileType_SPECTRA;
+ static const FileType PARAMS = Header_FileType_PARAMS;
+ static const FileType MOD_TABLE = Header_FileType_MOD_TABLE;
+ static const FileType RESULTS = Header_FileType_RESULTS;
+ static const FileType AUX_LOCATIONS = Header_FileType_AUX_LOCATIONS;
+ static inline bool FileType_IsValid(int value) {
+ return Header_FileType_IsValid(value);
+ }
+ static const FileType FileType_MIN =
+ Header_FileType_FileType_MIN;
+ static const FileType FileType_MAX =
+ Header_FileType_FileType_MAX;
+ static const int FileType_ARRAYSIZE =
+ Header_FileType_FileType_ARRAYSIZE;
+ static inline const ::google::protobuf::EnumDescriptor*
+ FileType_descriptor() {
+ return Header_FileType_descriptor();
+ }
+ static inline const ::std::string& FileType_Name(FileType value) {
+ return Header_FileType_Name(value);
+ }
+ static inline bool FileType_Parse(const ::std::string& name,
+ FileType* value) {
+ return Header_FileType_Parse(name, value);
+ }
+
+ // accessors -------------------------------------------------------
+
+ // repeated .pb.Header.Source source = 1;
+ inline int source_size() const;
+ inline void clear_source();
+ static const int kSourceFieldNumber = 1;
+ inline const ::pb::Header_Source& source(int index) const;
+ inline ::pb::Header_Source* mutable_source(int index);
+ inline ::pb::Header_Source* add_source();
+ inline const ::google::protobuf::RepeatedPtrField< ::pb::Header_Source >&
+ source() const;
+ inline ::google::protobuf::RepeatedPtrField< ::pb::Header_Source >*
+ mutable_source();
+
+ // required .pb.Header.FileType file_type = 2;
+ inline bool has_file_type() const;
+ inline void clear_file_type();
+ static const int kFileTypeFieldNumber = 2;
+ inline ::pb::Header_FileType file_type() const;
+ inline void set_file_type(::pb::Header_FileType value);
+
+ // optional .pb.Header.RawProteinsHeader raw_proteins_header = 3;
+ inline bool has_raw_proteins_header() const;
+ inline void clear_raw_proteins_header();
+ static const int kRawProteinsHeaderFieldNumber = 3;
+ inline const ::pb::Header_RawProteinsHeader& raw_proteins_header() const;
+ inline ::pb::Header_RawProteinsHeader* mutable_raw_proteins_header();
+ inline ::pb::Header_RawProteinsHeader* release_raw_proteins_header();
+ inline void set_allocated_raw_proteins_header(::pb::Header_RawProteinsHeader* raw_proteins_header);
+
+ // optional .pb.Header.PeptidesHeader peptides_header = 4;
+ inline bool has_peptides_header() const;
+ inline void clear_peptides_header();
+ static const int kPeptidesHeaderFieldNumber = 4;
+ inline const ::pb::Header_PeptidesHeader& peptides_header() const;
+ inline ::pb::Header_PeptidesHeader* mutable_peptides_header();
+ inline ::pb::Header_PeptidesHeader* release_peptides_header();
+ inline void set_allocated_peptides_header(::pb::Header_PeptidesHeader* peptides_header);
+
+ // optional .pb.Header.SpectraHeader spectra_header = 5;
+ inline bool has_spectra_header() const;
+ inline void clear_spectra_header();
+ static const int kSpectraHeaderFieldNumber = 5;
+ inline const ::pb::Header_SpectraHeader& spectra_header() const;
+ inline ::pb::Header_SpectraHeader* mutable_spectra_header();
+ inline ::pb::Header_SpectraHeader* release_spectra_header();
+ inline void set_allocated_spectra_header(::pb::Header_SpectraHeader* spectra_header);
+
+ // optional .pb.Header.ResultsHeader results_header = 6;
+ inline bool has_results_header() const;
+ inline void clear_results_header();
+ static const int kResultsHeaderFieldNumber = 6;
+ inline const ::pb::Header_ResultsHeader& results_header() const;
+ inline ::pb::Header_ResultsHeader* mutable_results_header();
+ inline ::pb::Header_ResultsHeader* release_results_header();
+ inline void set_allocated_results_header(::pb::Header_ResultsHeader* results_header);
+
+ // optional .pb.Header.AuxLocationsHeader aux_locs_header = 7;
+ inline bool has_aux_locs_header() const;
+ inline void clear_aux_locs_header();
+ static const int kAuxLocsHeaderFieldNumber = 7;
+ inline const ::pb::Header_AuxLocationsHeader& aux_locs_header() const;
+ inline ::pb::Header_AuxLocationsHeader* mutable_aux_locs_header();
+ inline ::pb::Header_AuxLocationsHeader* release_aux_locs_header();
+ inline void set_allocated_aux_locs_header(::pb::Header_AuxLocationsHeader* aux_locs_header);
+
+ // optional string command_line = 8;
+ inline bool has_command_line() const;
+ inline void clear_command_line();
+ static const int kCommandLineFieldNumber = 8;
+ inline const ::std::string& command_line() const;
+ inline void set_command_line(const ::std::string& value);
+ inline void set_command_line(const char* value);
+ inline void set_command_line(const char* value, size_t size);
+ inline ::std::string* mutable_command_line();
+ inline ::std::string* release_command_line();
+ inline void set_allocated_command_line(::std::string* command_line);
+
+ // @@protoc_insertion_point(class_scope:pb.Header)
+ private:
+ inline void set_has_file_type();
+ inline void clear_has_file_type();
+ inline void set_has_raw_proteins_header();
+ inline void clear_has_raw_proteins_header();
+ inline void set_has_peptides_header();
+ inline void clear_has_peptides_header();
+ inline void set_has_spectra_header();
+ inline void clear_has_spectra_header();
+ inline void set_has_results_header();
+ inline void clear_has_results_header();
+ inline void set_has_aux_locs_header();
+ inline void clear_has_aux_locs_header();
+ inline void set_has_command_line();
+ inline void clear_has_command_line();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::google::protobuf::RepeatedPtrField< ::pb::Header_Source > source_;
+ ::pb::Header_RawProteinsHeader* raw_proteins_header_;
+ ::pb::Header_PeptidesHeader* peptides_header_;
+ ::pb::Header_SpectraHeader* spectra_header_;
+ ::pb::Header_ResultsHeader* results_header_;
+ ::pb::Header_AuxLocationsHeader* aux_locs_header_;
+ ::std::string* command_line_;
+ int file_type_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(8 + 31) / 32];
+
+ friend void protobuf_AddDesc_header_2eproto();
+ friend void protobuf_AssignDesc_header_2eproto();
+ friend void protobuf_ShutdownFile_header_2eproto();
+
+ void InitAsDefaultInstance();
+ static Header* default_instance_;
+};
+// ===================================================================
+
+
+// ===================================================================
+
+// Modification
+
+// optional string amino_acids = 1;
+inline bool Modification::has_amino_acids() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Modification::set_has_amino_acids() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Modification::clear_has_amino_acids() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Modification::clear_amino_acids() {
+ if (amino_acids_ != &::google::protobuf::internal::kEmptyString) {
+ amino_acids_->clear();
+ }
+ clear_has_amino_acids();
+}
+inline const ::std::string& Modification::amino_acids() const {
+ return *amino_acids_;
+}
+inline void Modification::set_amino_acids(const ::std::string& value) {
+ set_has_amino_acids();
+ if (amino_acids_ == &::google::protobuf::internal::kEmptyString) {
+ amino_acids_ = new ::std::string;
+ }
+ amino_acids_->assign(value);
+}
+inline void Modification::set_amino_acids(const char* value) {
+ set_has_amino_acids();
+ if (amino_acids_ == &::google::protobuf::internal::kEmptyString) {
+ amino_acids_ = new ::std::string;
+ }
+ amino_acids_->assign(value);
+}
+inline void Modification::set_amino_acids(const char* value, size_t size) {
+ set_has_amino_acids();
+ if (amino_acids_ == &::google::protobuf::internal::kEmptyString) {
+ amino_acids_ = new ::std::string;
+ }
+ amino_acids_->assign(reinterpret_cast<const char*>(value), size);
+}
+inline ::std::string* Modification::mutable_amino_acids() {
+ set_has_amino_acids();
+ if (amino_acids_ == &::google::protobuf::internal::kEmptyString) {
+ amino_acids_ = new ::std::string;
+ }
+ return amino_acids_;
+}
+inline ::std::string* Modification::release_amino_acids() {
+ clear_has_amino_acids();
+ if (amino_acids_ == &::google::protobuf::internal::kEmptyString) {
+ return NULL;
+ } else {
+ ::std::string* temp = amino_acids_;
+ amino_acids_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ return temp;
+ }
+}
+inline void Modification::set_allocated_amino_acids(::std::string* amino_acids) {
+ if (amino_acids_ != &::google::protobuf::internal::kEmptyString) {
+ delete amino_acids_;
+ }
+ if (amino_acids) {
+ set_has_amino_acids();
+ amino_acids_ = amino_acids;
+ } else {
+ clear_has_amino_acids();
+ amino_acids_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ }
+}
+
+// optional double delta = 2;
+inline bool Modification::has_delta() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Modification::set_has_delta() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Modification::clear_has_delta() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Modification::clear_delta() {
+ delta_ = 0;
+ clear_has_delta();
+}
+inline double Modification::delta() const {
+ return delta_;
+}
+inline void Modification::set_delta(double value) {
+ set_has_delta();
+ delta_ = value;
+}
+
+// optional int32 max_count = 3;
+inline bool Modification::has_max_count() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Modification::set_has_max_count() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Modification::clear_has_max_count() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Modification::clear_max_count() {
+ max_count_ = 0;
+ clear_has_max_count();
+}
+inline ::google::protobuf::int32 Modification::max_count() const {
+ return max_count_;
+}
+inline void Modification::set_max_count(::google::protobuf::int32 value) {
+ set_has_max_count();
+ max_count_ = value;
+}
+
+// -------------------------------------------------------------------
+
+// ModTable
+
+// repeated .pb.Modification variable_mod = 1;
+inline int ModTable::variable_mod_size() const {
+ return variable_mod_.size();
+}
+inline void ModTable::clear_variable_mod() {
+ variable_mod_.Clear();
+}
+inline const ::pb::Modification& ModTable::variable_mod(int index) const {
+ return variable_mod_.Get(index);
+}
+inline ::pb::Modification* ModTable::mutable_variable_mod(int index) {
+ return variable_mod_.Mutable(index);
+}
+inline ::pb::Modification* ModTable::add_variable_mod() {
+ return variable_mod_.Add();
+}
+inline const ::google::protobuf::RepeatedPtrField< ::pb::Modification >&
+ModTable::variable_mod() const {
+ return variable_mod_;
+}
+inline ::google::protobuf::RepeatedPtrField< ::pb::Modification >*
+ModTable::mutable_variable_mod() {
+ return &variable_mod_;
+}
+
+// repeated .pb.Modification static_mod = 2;
+inline int ModTable::static_mod_size() const {
+ return static_mod_.size();
+}
+inline void ModTable::clear_static_mod() {
+ static_mod_.Clear();
+}
+inline const ::pb::Modification& ModTable::static_mod(int index) const {
+ return static_mod_.Get(index);
+}
+inline ::pb::Modification* ModTable::mutable_static_mod(int index) {
+ return static_mod_.Mutable(index);
+}
+inline ::pb::Modification* ModTable::add_static_mod() {
+ return static_mod_.Add();
+}
+inline const ::google::protobuf::RepeatedPtrField< ::pb::Modification >&
+ModTable::static_mod() const {
+ return static_mod_;
+}
+inline ::google::protobuf::RepeatedPtrField< ::pb::Modification >*
+ModTable::mutable_static_mod() {
+ return &static_mod_;
+}
+
+// repeated double unique_deltas = 10;
+inline int ModTable::unique_deltas_size() const {
+ return unique_deltas_.size();
+}
+inline void ModTable::clear_unique_deltas() {
+ unique_deltas_.Clear();
+}
+inline double ModTable::unique_deltas(int index) const {
+ return unique_deltas_.Get(index);
+}
+inline void ModTable::set_unique_deltas(int index, double value) {
+ unique_deltas_.Set(index, value);
+}
+inline void ModTable::add_unique_deltas(double value) {
+ unique_deltas_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< double >&
+ModTable::unique_deltas() const {
+ return unique_deltas_;
+}
+inline ::google::protobuf::RepeatedField< double >*
+ModTable::mutable_unique_deltas() {
+ return &unique_deltas_;
+}
+
+// -------------------------------------------------------------------
+
+// Header_Source
+
+// optional string filename = 1;
+inline bool Header_Source::has_filename() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Header_Source::set_has_filename() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Header_Source::clear_has_filename() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Header_Source::clear_filename() {
+ if (filename_ != &::google::protobuf::internal::kEmptyString) {
+ filename_->clear();
+ }
+ clear_has_filename();
+}
+inline const ::std::string& Header_Source::filename() const {
+ return *filename_;
+}
+inline void Header_Source::set_filename(const ::std::string& value) {
+ set_has_filename();
+ if (filename_ == &::google::protobuf::internal::kEmptyString) {
+ filename_ = new ::std::string;
+ }
+ filename_->assign(value);
+}
+inline void Header_Source::set_filename(const char* value) {
+ set_has_filename();
+ if (filename_ == &::google::protobuf::internal::kEmptyString) {
+ filename_ = new ::std::string;
+ }
+ filename_->assign(value);
+}
+inline void Header_Source::set_filename(const char* value, size_t size) {
+ set_has_filename();
+ if (filename_ == &::google::protobuf::internal::kEmptyString) {
+ filename_ = new ::std::string;
+ }
+ filename_->assign(reinterpret_cast<const char*>(value), size);
+}
+inline ::std::string* Header_Source::mutable_filename() {
+ set_has_filename();
+ if (filename_ == &::google::protobuf::internal::kEmptyString) {
+ filename_ = new ::std::string;
+ }
+ return filename_;
+}
+inline ::std::string* Header_Source::release_filename() {
+ clear_has_filename();
+ if (filename_ == &::google::protobuf::internal::kEmptyString) {
+ return NULL;
+ } else {
+ ::std::string* temp = filename_;
+ filename_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ return temp;
+ }
+}
+inline void Header_Source::set_allocated_filename(::std::string* filename) {
+ if (filename_ != &::google::protobuf::internal::kEmptyString) {
+ delete filename_;
+ }
+ if (filename) {
+ set_has_filename();
+ filename_ = filename;
+ } else {
+ clear_has_filename();
+ filename_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ }
+}
+
+// optional .pb.Header header = 2;
+inline bool Header_Source::has_header() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Header_Source::set_has_header() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Header_Source::clear_has_header() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Header_Source::clear_header() {
+ if (header_ != NULL) header_->::pb::Header::Clear();
+ clear_has_header();
+}
+inline const ::pb::Header& Header_Source::header() const {
+ return header_ != NULL ? *header_ : *default_instance_->header_;
+}
+inline ::pb::Header* Header_Source::mutable_header() {
+ set_has_header();
+ if (header_ == NULL) header_ = new ::pb::Header;
+ return header_;
+}
+inline ::pb::Header* Header_Source::release_header() {
+ clear_has_header();
+ ::pb::Header* temp = header_;
+ header_ = NULL;
+ return temp;
+}
+inline void Header_Source::set_allocated_header(::pb::Header* header) {
+ delete header_;
+ header_ = header;
+ if (header) {
+ set_has_header();
+ } else {
+ clear_has_header();
+ }
+}
+
+// optional string filetype = 3;
+inline bool Header_Source::has_filetype() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Header_Source::set_has_filetype() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Header_Source::clear_has_filetype() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Header_Source::clear_filetype() {
+ if (filetype_ != &::google::protobuf::internal::kEmptyString) {
+ filetype_->clear();
+ }
+ clear_has_filetype();
+}
+inline const ::std::string& Header_Source::filetype() const {
+ return *filetype_;
+}
+inline void Header_Source::set_filetype(const ::std::string& value) {
+ set_has_filetype();
+ if (filetype_ == &::google::protobuf::internal::kEmptyString) {
+ filetype_ = new ::std::string;
+ }
+ filetype_->assign(value);
+}
+inline void Header_Source::set_filetype(const char* value) {
+ set_has_filetype();
+ if (filetype_ == &::google::protobuf::internal::kEmptyString) {
+ filetype_ = new ::std::string;
+ }
+ filetype_->assign(value);
+}
+inline void Header_Source::set_filetype(const char* value, size_t size) {
+ set_has_filetype();
+ if (filetype_ == &::google::protobuf::internal::kEmptyString) {
+ filetype_ = new ::std::string;
+ }
+ filetype_->assign(reinterpret_cast<const char*>(value), size);
+}
+inline ::std::string* Header_Source::mutable_filetype() {
+ set_has_filetype();
+ if (filetype_ == &::google::protobuf::internal::kEmptyString) {
+ filetype_ = new ::std::string;
+ }
+ return filetype_;
+}
+inline ::std::string* Header_Source::release_filetype() {
+ clear_has_filetype();
+ if (filetype_ == &::google::protobuf::internal::kEmptyString) {
+ return NULL;
+ } else {
+ ::std::string* temp = filetype_;
+ filetype_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ return temp;
+ }
+}
+inline void Header_Source::set_allocated_filetype(::std::string* filetype) {
+ if (filetype_ != &::google::protobuf::internal::kEmptyString) {
+ delete filetype_;
+ }
+ if (filetype) {
+ set_has_filetype();
+ filetype_ = filetype;
+ } else {
+ clear_has_filetype();
+ filetype_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ }
+}
+
+// -------------------------------------------------------------------
+
+// Header_RawProteinsHeader
+
+// -------------------------------------------------------------------
+
+// Header_PeptidesHeader
+
+// optional double min_mass = 3;
+inline bool Header_PeptidesHeader::has_min_mass() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_min_mass() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Header_PeptidesHeader::clear_has_min_mass() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Header_PeptidesHeader::clear_min_mass() {
+ min_mass_ = 0;
+ clear_has_min_mass();
+}
+inline double Header_PeptidesHeader::min_mass() const {
+ return min_mass_;
+}
+inline void Header_PeptidesHeader::set_min_mass(double value) {
+ set_has_min_mass();
+ min_mass_ = value;
+}
+
+// optional double max_mass = 4;
+inline bool Header_PeptidesHeader::has_max_mass() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_max_mass() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Header_PeptidesHeader::clear_has_max_mass() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Header_PeptidesHeader::clear_max_mass() {
+ max_mass_ = 0;
+ clear_has_max_mass();
+}
+inline double Header_PeptidesHeader::max_mass() const {
+ return max_mass_;
+}
+inline void Header_PeptidesHeader::set_max_mass(double value) {
+ set_has_max_mass();
+ max_mass_ = value;
+}
+
+// optional int32 min_length = 5;
+inline bool Header_PeptidesHeader::has_min_length() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_min_length() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Header_PeptidesHeader::clear_has_min_length() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Header_PeptidesHeader::clear_min_length() {
+ min_length_ = 0;
+ clear_has_min_length();
+}
+inline ::google::protobuf::int32 Header_PeptidesHeader::min_length() const {
+ return min_length_;
+}
+inline void Header_PeptidesHeader::set_min_length(::google::protobuf::int32 value) {
+ set_has_min_length();
+ min_length_ = value;
+}
+
+// optional int32 max_length = 6;
+inline bool Header_PeptidesHeader::has_max_length() const {
+ return (_has_bits_[0] & 0x00000008u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_max_length() {
+ _has_bits_[0] |= 0x00000008u;
+}
+inline void Header_PeptidesHeader::clear_has_max_length() {
+ _has_bits_[0] &= ~0x00000008u;
+}
+inline void Header_PeptidesHeader::clear_max_length() {
+ max_length_ = 0;
+ clear_has_max_length();
+}
+inline ::google::protobuf::int32 Header_PeptidesHeader::max_length() const {
+ return max_length_;
+}
+inline void Header_PeptidesHeader::set_max_length(::google::protobuf::int32 value) {
+ set_has_max_length();
+ max_length_ = value;
+}
+
+// optional string enzyme = 7;
+inline bool Header_PeptidesHeader::has_enzyme() const {
+ return (_has_bits_[0] & 0x00000010u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_enzyme() {
+ _has_bits_[0] |= 0x00000010u;
+}
+inline void Header_PeptidesHeader::clear_has_enzyme() {
+ _has_bits_[0] &= ~0x00000010u;
+}
+inline void Header_PeptidesHeader::clear_enzyme() {
+ if (enzyme_ != &::google::protobuf::internal::kEmptyString) {
+ enzyme_->clear();
+ }
+ clear_has_enzyme();
+}
+inline const ::std::string& Header_PeptidesHeader::enzyme() const {
+ return *enzyme_;
+}
+inline void Header_PeptidesHeader::set_enzyme(const ::std::string& value) {
+ set_has_enzyme();
+ if (enzyme_ == &::google::protobuf::internal::kEmptyString) {
+ enzyme_ = new ::std::string;
+ }
+ enzyme_->assign(value);
+}
+inline void Header_PeptidesHeader::set_enzyme(const char* value) {
+ set_has_enzyme();
+ if (enzyme_ == &::google::protobuf::internal::kEmptyString) {
+ enzyme_ = new ::std::string;
+ }
+ enzyme_->assign(value);
+}
+inline void Header_PeptidesHeader::set_enzyme(const char* value, size_t size) {
+ set_has_enzyme();
+ if (enzyme_ == &::google::protobuf::internal::kEmptyString) {
+ enzyme_ = new ::std::string;
+ }
+ enzyme_->assign(reinterpret_cast<const char*>(value), size);
+}
+inline ::std::string* Header_PeptidesHeader::mutable_enzyme() {
+ set_has_enzyme();
+ if (enzyme_ == &::google::protobuf::internal::kEmptyString) {
+ enzyme_ = new ::std::string;
+ }
+ return enzyme_;
+}
+inline ::std::string* Header_PeptidesHeader::release_enzyme() {
+ clear_has_enzyme();
+ if (enzyme_ == &::google::protobuf::internal::kEmptyString) {
+ return NULL;
+ } else {
+ ::std::string* temp = enzyme_;
+ enzyme_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ return temp;
+ }
+}
+inline void Header_PeptidesHeader::set_allocated_enzyme(::std::string* enzyme) {
+ if (enzyme_ != &::google::protobuf::internal::kEmptyString) {
+ delete enzyme_;
+ }
+ if (enzyme) {
+ set_has_enzyme();
+ enzyme_ = enzyme;
+ } else {
+ clear_has_enzyme();
+ enzyme_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ }
+}
+
+// optional bool full_digestion = 8;
+inline bool Header_PeptidesHeader::has_full_digestion() const {
+ return (_has_bits_[0] & 0x00000020u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_full_digestion() {
+ _has_bits_[0] |= 0x00000020u;
+}
+inline void Header_PeptidesHeader::clear_has_full_digestion() {
+ _has_bits_[0] &= ~0x00000020u;
+}
+inline void Header_PeptidesHeader::clear_full_digestion() {
+ full_digestion_ = false;
+ clear_has_full_digestion();
+}
+inline bool Header_PeptidesHeader::full_digestion() const {
+ return full_digestion_;
+}
+inline void Header_PeptidesHeader::set_full_digestion(bool value) {
+ set_has_full_digestion();
+ full_digestion_ = value;
+}
+
+// optional int32 max_missed_cleavages = 14;
+inline bool Header_PeptidesHeader::has_max_missed_cleavages() const {
+ return (_has_bits_[0] & 0x00000040u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_max_missed_cleavages() {
+ _has_bits_[0] |= 0x00000040u;
+}
+inline void Header_PeptidesHeader::clear_has_max_missed_cleavages() {
+ _has_bits_[0] &= ~0x00000040u;
+}
+inline void Header_PeptidesHeader::clear_max_missed_cleavages() {
+ max_missed_cleavages_ = 0;
+ clear_has_max_missed_cleavages();
+}
+inline ::google::protobuf::int32 Header_PeptidesHeader::max_missed_cleavages() const {
+ return max_missed_cleavages_;
+}
+inline void Header_PeptidesHeader::set_max_missed_cleavages(::google::protobuf::int32 value) {
+ set_has_max_missed_cleavages();
+ max_missed_cleavages_ = value;
+}
+
+// optional bool monoisotopic_precursor = 13;
+inline bool Header_PeptidesHeader::has_monoisotopic_precursor() const {
+ return (_has_bits_[0] & 0x00000080u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_monoisotopic_precursor() {
+ _has_bits_[0] |= 0x00000080u;
+}
+inline void Header_PeptidesHeader::clear_has_monoisotopic_precursor() {
+ _has_bits_[0] &= ~0x00000080u;
+}
+inline void Header_PeptidesHeader::clear_monoisotopic_precursor() {
+ monoisotopic_precursor_ = false;
+ clear_has_monoisotopic_precursor();
+}
+inline bool Header_PeptidesHeader::monoisotopic_precursor() const {
+ return monoisotopic_precursor_;
+}
+inline void Header_PeptidesHeader::set_monoisotopic_precursor(bool value) {
+ set_has_monoisotopic_precursor();
+ monoisotopic_precursor_ = value;
+}
+
+// optional bool has_peaks = 10;
+inline bool Header_PeptidesHeader::has_has_peaks() const {
+ return (_has_bits_[0] & 0x00000100u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_has_peaks() {
+ _has_bits_[0] |= 0x00000100u;
+}
+inline void Header_PeptidesHeader::clear_has_has_peaks() {
+ _has_bits_[0] &= ~0x00000100u;
+}
+inline void Header_PeptidesHeader::clear_has_peaks() {
+ has_peaks_ = false;
+ clear_has_has_peaks();
+}
+inline bool Header_PeptidesHeader::has_peaks() const {
+ return has_peaks_;
+}
+inline void Header_PeptidesHeader::set_has_peaks(bool value) {
+ set_has_has_peaks();
+ has_peaks_ = value;
+}
+
+// optional double downselect_fraction = 11;
+inline bool Header_PeptidesHeader::has_downselect_fraction() const {
+ return (_has_bits_[0] & 0x00000200u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_downselect_fraction() {
+ _has_bits_[0] |= 0x00000200u;
+}
+inline void Header_PeptidesHeader::clear_has_downselect_fraction() {
+ _has_bits_[0] &= ~0x00000200u;
+}
+inline void Header_PeptidesHeader::clear_downselect_fraction() {
+ downselect_fraction_ = 0;
+ clear_has_downselect_fraction();
+}
+inline double Header_PeptidesHeader::downselect_fraction() const {
+ return downselect_fraction_;
+}
+inline void Header_PeptidesHeader::set_downselect_fraction(double value) {
+ set_has_downselect_fraction();
+ downselect_fraction_ = value;
+}
+
+// optional .pb.ModTable mods = 12;
+inline bool Header_PeptidesHeader::has_mods() const {
+ return (_has_bits_[0] & 0x00000400u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_mods() {
+ _has_bits_[0] |= 0x00000400u;
+}
+inline void Header_PeptidesHeader::clear_has_mods() {
+ _has_bits_[0] &= ~0x00000400u;
+}
+inline void Header_PeptidesHeader::clear_mods() {
+ if (mods_ != NULL) mods_->::pb::ModTable::Clear();
+ clear_has_mods();
+}
+inline const ::pb::ModTable& Header_PeptidesHeader::mods() const {
+ return mods_ != NULL ? *mods_ : *default_instance_->mods_;
+}
+inline ::pb::ModTable* Header_PeptidesHeader::mutable_mods() {
+ set_has_mods();
+ if (mods_ == NULL) mods_ = new ::pb::ModTable;
+ return mods_;
+}
+inline ::pb::ModTable* Header_PeptidesHeader::release_mods() {
+ clear_has_mods();
+ ::pb::ModTable* temp = mods_;
+ mods_ = NULL;
+ return temp;
+}
+inline void Header_PeptidesHeader::set_allocated_mods(::pb::ModTable* mods) {
+ delete mods_;
+ mods_ = mods;
+ if (mods) {
+ set_has_mods();
+ } else {
+ clear_has_mods();
+ }
+}
+
+// optional .pb.ModTable nterm_mods = 15;
+inline bool Header_PeptidesHeader::has_nterm_mods() const {
+ return (_has_bits_[0] & 0x00000800u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_nterm_mods() {
+ _has_bits_[0] |= 0x00000800u;
+}
+inline void Header_PeptidesHeader::clear_has_nterm_mods() {
+ _has_bits_[0] &= ~0x00000800u;
+}
+inline void Header_PeptidesHeader::clear_nterm_mods() {
+ if (nterm_mods_ != NULL) nterm_mods_->::pb::ModTable::Clear();
+ clear_has_nterm_mods();
+}
+inline const ::pb::ModTable& Header_PeptidesHeader::nterm_mods() const {
+ return nterm_mods_ != NULL ? *nterm_mods_ : *default_instance_->nterm_mods_;
+}
+inline ::pb::ModTable* Header_PeptidesHeader::mutable_nterm_mods() {
+ set_has_nterm_mods();
+ if (nterm_mods_ == NULL) nterm_mods_ = new ::pb::ModTable;
+ return nterm_mods_;
+}
+inline ::pb::ModTable* Header_PeptidesHeader::release_nterm_mods() {
+ clear_has_nterm_mods();
+ ::pb::ModTable* temp = nterm_mods_;
+ nterm_mods_ = NULL;
+ return temp;
+}
+inline void Header_PeptidesHeader::set_allocated_nterm_mods(::pb::ModTable* nterm_mods) {
+ delete nterm_mods_;
+ nterm_mods_ = nterm_mods;
+ if (nterm_mods) {
+ set_has_nterm_mods();
+ } else {
+ clear_has_nterm_mods();
+ }
+}
+
+// optional .pb.ModTable cterm_mods = 16;
+inline bool Header_PeptidesHeader::has_cterm_mods() const {
+ return (_has_bits_[0] & 0x00001000u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_cterm_mods() {
+ _has_bits_[0] |= 0x00001000u;
+}
+inline void Header_PeptidesHeader::clear_has_cterm_mods() {
+ _has_bits_[0] &= ~0x00001000u;
+}
+inline void Header_PeptidesHeader::clear_cterm_mods() {
+ if (cterm_mods_ != NULL) cterm_mods_->::pb::ModTable::Clear();
+ clear_has_cterm_mods();
+}
+inline const ::pb::ModTable& Header_PeptidesHeader::cterm_mods() const {
+ return cterm_mods_ != NULL ? *cterm_mods_ : *default_instance_->cterm_mods_;
+}
+inline ::pb::ModTable* Header_PeptidesHeader::mutable_cterm_mods() {
+ set_has_cterm_mods();
+ if (cterm_mods_ == NULL) cterm_mods_ = new ::pb::ModTable;
+ return cterm_mods_;
+}
+inline ::pb::ModTable* Header_PeptidesHeader::release_cterm_mods() {
+ clear_has_cterm_mods();
+ ::pb::ModTable* temp = cterm_mods_;
+ cterm_mods_ = NULL;
+ return temp;
+}
+inline void Header_PeptidesHeader::set_allocated_cterm_mods(::pb::ModTable* cterm_mods) {
+ delete cterm_mods_;
+ cterm_mods_ = cterm_mods;
+ if (cterm_mods) {
+ set_has_cterm_mods();
+ } else {
+ clear_has_cterm_mods();
+ }
+}
+
+// optional int32 decoys = 9;
+inline bool Header_PeptidesHeader::has_decoys() const {
+ return (_has_bits_[0] & 0x00002000u) != 0;
+}
+inline void Header_PeptidesHeader::set_has_decoys() {
+ _has_bits_[0] |= 0x00002000u;
+}
+inline void Header_PeptidesHeader::clear_has_decoys() {
+ _has_bits_[0] &= ~0x00002000u;
+}
+inline void Header_PeptidesHeader::clear_decoys() {
+ decoys_ = 0;
+ clear_has_decoys();
+}
+inline ::google::protobuf::int32 Header_PeptidesHeader::decoys() const {
+ return decoys_;
+}
+inline void Header_PeptidesHeader::set_decoys(::google::protobuf::int32 value) {
+ set_has_decoys();
+ decoys_ = value;
+}
+
+// -------------------------------------------------------------------
+
+// Header_SpectraHeader
+
+// optional bool sorted = 2;
+inline bool Header_SpectraHeader::has_sorted() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Header_SpectraHeader::set_has_sorted() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Header_SpectraHeader::clear_has_sorted() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Header_SpectraHeader::clear_sorted() {
+ sorted_ = false;
+ clear_has_sorted();
+}
+inline bool Header_SpectraHeader::sorted() const {
+ return sorted_;
+}
+inline void Header_SpectraHeader::set_sorted(bool value) {
+ set_has_sorted();
+ sorted_ = value;
+}
+
+// -------------------------------------------------------------------
+
+// Header_ResultsHeader
+
+// optional double mass_window = 1;
+inline bool Header_ResultsHeader::has_mass_window() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Header_ResultsHeader::set_has_mass_window() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Header_ResultsHeader::clear_has_mass_window() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Header_ResultsHeader::clear_mass_window() {
+ mass_window_ = 0;
+ clear_has_mass_window();
+}
+inline double Header_ResultsHeader::mass_window() const {
+ return mass_window_;
+}
+inline void Header_ResultsHeader::set_mass_window(double value) {
+ set_has_mass_window();
+ mass_window_ = value;
+}
+
+// optional int32 top_matches = 2;
+inline bool Header_ResultsHeader::has_top_matches() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Header_ResultsHeader::set_has_top_matches() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Header_ResultsHeader::clear_has_top_matches() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Header_ResultsHeader::clear_top_matches() {
+ top_matches_ = 0;
+ clear_has_top_matches();
+}
+inline ::google::protobuf::int32 Header_ResultsHeader::top_matches() const {
+ return top_matches_;
+}
+inline void Header_ResultsHeader::set_top_matches(::google::protobuf::int32 value) {
+ set_has_top_matches();
+ top_matches_ = value;
+}
+
+// optional .pb.Header.PeptidesHeader peptides_header = 3;
+inline bool Header_ResultsHeader::has_peptides_header() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Header_ResultsHeader::set_has_peptides_header() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Header_ResultsHeader::clear_has_peptides_header() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Header_ResultsHeader::clear_peptides_header() {
+ if (peptides_header_ != NULL) peptides_header_->::pb::Header_PeptidesHeader::Clear();
+ clear_has_peptides_header();
+}
+inline const ::pb::Header_PeptidesHeader& Header_ResultsHeader::peptides_header() const {
+ return peptides_header_ != NULL ? *peptides_header_ : *default_instance_->peptides_header_;
+}
+inline ::pb::Header_PeptidesHeader* Header_ResultsHeader::mutable_peptides_header() {
+ set_has_peptides_header();
+ if (peptides_header_ == NULL) peptides_header_ = new ::pb::Header_PeptidesHeader;
+ return peptides_header_;
+}
+inline ::pb::Header_PeptidesHeader* Header_ResultsHeader::release_peptides_header() {
+ clear_has_peptides_header();
+ ::pb::Header_PeptidesHeader* temp = peptides_header_;
+ peptides_header_ = NULL;
+ return temp;
+}
+inline void Header_ResultsHeader::set_allocated_peptides_header(::pb::Header_PeptidesHeader* peptides_header) {
+ delete peptides_header_;
+ peptides_header_ = peptides_header;
+ if (peptides_header) {
+ set_has_peptides_header();
+ } else {
+ clear_has_peptides_header();
+ }
+}
+
+// -------------------------------------------------------------------
+
+// Header_AuxLocationsHeader
+
+// -------------------------------------------------------------------
+
+// Header
+
+// repeated .pb.Header.Source source = 1;
+inline int Header::source_size() const {
+ return source_.size();
+}
+inline void Header::clear_source() {
+ source_.Clear();
+}
+inline const ::pb::Header_Source& Header::source(int index) const {
+ return source_.Get(index);
+}
+inline ::pb::Header_Source* Header::mutable_source(int index) {
+ return source_.Mutable(index);
+}
+inline ::pb::Header_Source* Header::add_source() {
+ return source_.Add();
+}
+inline const ::google::protobuf::RepeatedPtrField< ::pb::Header_Source >&
+Header::source() const {
+ return source_;
+}
+inline ::google::protobuf::RepeatedPtrField< ::pb::Header_Source >*
+Header::mutable_source() {
+ return &source_;
+}
+
+// required .pb.Header.FileType file_type = 2;
+inline bool Header::has_file_type() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Header::set_has_file_type() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Header::clear_has_file_type() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Header::clear_file_type() {
+ file_type_ = 0;
+ clear_has_file_type();
+}
+inline ::pb::Header_FileType Header::file_type() const {
+ return static_cast< ::pb::Header_FileType >(file_type_);
+}
+inline void Header::set_file_type(::pb::Header_FileType value) {
+ assert(::pb::Header_FileType_IsValid(value));
+ set_has_file_type();
+ file_type_ = value;
+}
+
+// optional .pb.Header.RawProteinsHeader raw_proteins_header = 3;
+inline bool Header::has_raw_proteins_header() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Header::set_has_raw_proteins_header() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Header::clear_has_raw_proteins_header() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Header::clear_raw_proteins_header() {
+ if (raw_proteins_header_ != NULL) raw_proteins_header_->::pb::Header_RawProteinsHeader::Clear();
+ clear_has_raw_proteins_header();
+}
+inline const ::pb::Header_RawProteinsHeader& Header::raw_proteins_header() const {
+ return raw_proteins_header_ != NULL ? *raw_proteins_header_ : *default_instance_->raw_proteins_header_;
+}
+inline ::pb::Header_RawProteinsHeader* Header::mutable_raw_proteins_header() {
+ set_has_raw_proteins_header();
+ if (raw_proteins_header_ == NULL) raw_proteins_header_ = new ::pb::Header_RawProteinsHeader;
+ return raw_proteins_header_;
+}
+inline ::pb::Header_RawProteinsHeader* Header::release_raw_proteins_header() {
+ clear_has_raw_proteins_header();
+ ::pb::Header_RawProteinsHeader* temp = raw_proteins_header_;
+ raw_proteins_header_ = NULL;
+ return temp;
+}
+inline void Header::set_allocated_raw_proteins_header(::pb::Header_RawProteinsHeader* raw_proteins_header) {
+ delete raw_proteins_header_;
+ raw_proteins_header_ = raw_proteins_header;
+ if (raw_proteins_header) {
+ set_has_raw_proteins_header();
+ } else {
+ clear_has_raw_proteins_header();
+ }
+}
+
+// optional .pb.Header.PeptidesHeader peptides_header = 4;
+inline bool Header::has_peptides_header() const {
+ return (_has_bits_[0] & 0x00000008u) != 0;
+}
+inline void Header::set_has_peptides_header() {
+ _has_bits_[0] |= 0x00000008u;
+}
+inline void Header::clear_has_peptides_header() {
+ _has_bits_[0] &= ~0x00000008u;
+}
+inline void Header::clear_peptides_header() {
+ if (peptides_header_ != NULL) peptides_header_->::pb::Header_PeptidesHeader::Clear();
+ clear_has_peptides_header();
+}
+inline const ::pb::Header_PeptidesHeader& Header::peptides_header() const {
+ return peptides_header_ != NULL ? *peptides_header_ : *default_instance_->peptides_header_;
+}
+inline ::pb::Header_PeptidesHeader* Header::mutable_peptides_header() {
+ set_has_peptides_header();
+ if (peptides_header_ == NULL) peptides_header_ = new ::pb::Header_PeptidesHeader;
+ return peptides_header_;
+}
+inline ::pb::Header_PeptidesHeader* Header::release_peptides_header() {
+ clear_has_peptides_header();
+ ::pb::Header_PeptidesHeader* temp = peptides_header_;
+ peptides_header_ = NULL;
+ return temp;
+}
+inline void Header::set_allocated_peptides_header(::pb::Header_PeptidesHeader* peptides_header) {
+ delete peptides_header_;
+ peptides_header_ = peptides_header;
+ if (peptides_header) {
+ set_has_peptides_header();
+ } else {
+ clear_has_peptides_header();
+ }
+}
+
+// optional .pb.Header.SpectraHeader spectra_header = 5;
+inline bool Header::has_spectra_header() const {
+ return (_has_bits_[0] & 0x00000010u) != 0;
+}
+inline void Header::set_has_spectra_header() {
+ _has_bits_[0] |= 0x00000010u;
+}
+inline void Header::clear_has_spectra_header() {
+ _has_bits_[0] &= ~0x00000010u;
+}
+inline void Header::clear_spectra_header() {
+ if (spectra_header_ != NULL) spectra_header_->::pb::Header_SpectraHeader::Clear();
+ clear_has_spectra_header();
+}
+inline const ::pb::Header_SpectraHeader& Header::spectra_header() const {
+ return spectra_header_ != NULL ? *spectra_header_ : *default_instance_->spectra_header_;
+}
+inline ::pb::Header_SpectraHeader* Header::mutable_spectra_header() {
+ set_has_spectra_header();
+ if (spectra_header_ == NULL) spectra_header_ = new ::pb::Header_SpectraHeader;
+ return spectra_header_;
+}
+inline ::pb::Header_SpectraHeader* Header::release_spectra_header() {
+ clear_has_spectra_header();
+ ::pb::Header_SpectraHeader* temp = spectra_header_;
+ spectra_header_ = NULL;
+ return temp;
+}
+inline void Header::set_allocated_spectra_header(::pb::Header_SpectraHeader* spectra_header) {
+ delete spectra_header_;
+ spectra_header_ = spectra_header;
+ if (spectra_header) {
+ set_has_spectra_header();
+ } else {
+ clear_has_spectra_header();
+ }
+}
+
+// optional .pb.Header.ResultsHeader results_header = 6;
+inline bool Header::has_results_header() const {
+ return (_has_bits_[0] & 0x00000020u) != 0;
+}
+inline void Header::set_has_results_header() {
+ _has_bits_[0] |= 0x00000020u;
+}
+inline void Header::clear_has_results_header() {
+ _has_bits_[0] &= ~0x00000020u;
+}
+inline void Header::clear_results_header() {
+ if (results_header_ != NULL) results_header_->::pb::Header_ResultsHeader::Clear();
+ clear_has_results_header();
+}
+inline const ::pb::Header_ResultsHeader& Header::results_header() const {
+ return results_header_ != NULL ? *results_header_ : *default_instance_->results_header_;
+}
+inline ::pb::Header_ResultsHeader* Header::mutable_results_header() {
+ set_has_results_header();
+ if (results_header_ == NULL) results_header_ = new ::pb::Header_ResultsHeader;
+ return results_header_;
+}
+inline ::pb::Header_ResultsHeader* Header::release_results_header() {
+ clear_has_results_header();
+ ::pb::Header_ResultsHeader* temp = results_header_;
+ results_header_ = NULL;
+ return temp;
+}
+inline void Header::set_allocated_results_header(::pb::Header_ResultsHeader* results_header) {
+ delete results_header_;
+ results_header_ = results_header;
+ if (results_header) {
+ set_has_results_header();
+ } else {
+ clear_has_results_header();
+ }
+}
+
+// optional .pb.Header.AuxLocationsHeader aux_locs_header = 7;
+inline bool Header::has_aux_locs_header() const {
+ return (_has_bits_[0] & 0x00000040u) != 0;
+}
+inline void Header::set_has_aux_locs_header() {
+ _has_bits_[0] |= 0x00000040u;
+}
+inline void Header::clear_has_aux_locs_header() {
+ _has_bits_[0] &= ~0x00000040u;
+}
+inline void Header::clear_aux_locs_header() {
+ if (aux_locs_header_ != NULL) aux_locs_header_->::pb::Header_AuxLocationsHeader::Clear();
+ clear_has_aux_locs_header();
+}
+inline const ::pb::Header_AuxLocationsHeader& Header::aux_locs_header() const {
+ return aux_locs_header_ != NULL ? *aux_locs_header_ : *default_instance_->aux_locs_header_;
+}
+inline ::pb::Header_AuxLocationsHeader* Header::mutable_aux_locs_header() {
+ set_has_aux_locs_header();
+ if (aux_locs_header_ == NULL) aux_locs_header_ = new ::pb::Header_AuxLocationsHeader;
+ return aux_locs_header_;
+}
+inline ::pb::Header_AuxLocationsHeader* Header::release_aux_locs_header() {
+ clear_has_aux_locs_header();
+ ::pb::Header_AuxLocationsHeader* temp = aux_locs_header_;
+ aux_locs_header_ = NULL;
+ return temp;
+}
+inline void Header::set_allocated_aux_locs_header(::pb::Header_AuxLocationsHeader* aux_locs_header) {
+ delete aux_locs_header_;
+ aux_locs_header_ = aux_locs_header;
+ if (aux_locs_header) {
+ set_has_aux_locs_header();
+ } else {
+ clear_has_aux_locs_header();
+ }
+}
+
+// optional string command_line = 8;
+inline bool Header::has_command_line() const {
+ return (_has_bits_[0] & 0x00000080u) != 0;
+}
+inline void Header::set_has_command_line() {
+ _has_bits_[0] |= 0x00000080u;
+}
+inline void Header::clear_has_command_line() {
+ _has_bits_[0] &= ~0x00000080u;
+}
+inline void Header::clear_command_line() {
+ if (command_line_ != &::google::protobuf::internal::kEmptyString) {
+ command_line_->clear();
+ }
+ clear_has_command_line();
+}
+inline const ::std::string& Header::command_line() const {
+ return *command_line_;
+}
+inline void Header::set_command_line(const ::std::string& value) {
+ set_has_command_line();
+ if (command_line_ == &::google::protobuf::internal::kEmptyString) {
+ command_line_ = new ::std::string;
+ }
+ command_line_->assign(value);
+}
+inline void Header::set_command_line(const char* value) {
+ set_has_command_line();
+ if (command_line_ == &::google::protobuf::internal::kEmptyString) {
+ command_line_ = new ::std::string;
+ }
+ command_line_->assign(value);
+}
+inline void Header::set_command_line(const char* value, size_t size) {
+ set_has_command_line();
+ if (command_line_ == &::google::protobuf::internal::kEmptyString) {
+ command_line_ = new ::std::string;
+ }
+ command_line_->assign(reinterpret_cast<const char*>(value), size);
+}
+inline ::std::string* Header::mutable_command_line() {
+ set_has_command_line();
+ if (command_line_ == &::google::protobuf::internal::kEmptyString) {
+ command_line_ = new ::std::string;
+ }
+ return command_line_;
+}
+inline ::std::string* Header::release_command_line() {
+ clear_has_command_line();
+ if (command_line_ == &::google::protobuf::internal::kEmptyString) {
+ return NULL;
+ } else {
+ ::std::string* temp = command_line_;
+ command_line_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ return temp;
+ }
+}
+inline void Header::set_allocated_command_line(::std::string* command_line) {
+ if (command_line_ != &::google::protobuf::internal::kEmptyString) {
+ delete command_line_;
+ }
+ if (command_line) {
+ set_has_command_line();
+ command_line_ = command_line;
+ } else {
+ clear_has_command_line();
+ command_line_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ }
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+#ifndef SWIG
+namespace google {
+namespace protobuf {
+
+template <>
+inline const EnumDescriptor* GetEnumDescriptor< ::pb::Header_FileType>() {
+ return ::pb::Header_FileType_descriptor();
+}
+
+} // namespace google
+} // namespace protobuf
+#endif // SWIG
+
+// @@protoc_insertion_point(global_scope)
+
+#endif // PROTOBUF_header_2eproto__INCLUDED
diff --git a/src/app/tide/protoobj/header_pb2.py b/src/app/tide/protoobj/header_pb2.py
new file mode 100644
index 0000000..ee5f274
--- /dev/null
+++ b/src/app/tide/protoobj/header_pb2.py
@@ -0,0 +1,570 @@
+# Generated by the protocol buffer compiler. DO NOT EDIT!
+# source: header.proto
+
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import message as _message
+from google.protobuf import reflection as _reflection
+from google.protobuf import descriptor_pb2
+# @@protoc_insertion_point(imports)
+
+
+
+
+DESCRIPTOR = _descriptor.FileDescriptor(
+ name='header.proto',
+ package='pb',
+ serialized_pb='\n\x0cheader.proto\x12\x02pb\"E\n\x0cModification\x12\x13\n\x0b\x61mino_acids\x18\x01 \x01(\t\x12\r\n\x05\x64\x65lta\x18\x02 \x01(\x01\x12\x11\n\tmax_count\x18\x03 \x01(\x05\"o\n\x08ModTable\x12&\n\x0cvariable_mod\x18\x01 \x03(\x0b\x32\x10.pb.Modification\x12$\n\nstatic_mod\x18\x02 \x03(\x0b\x32\x10.pb.Modification\x12\x15\n\runique_deltas\x18\n \x03(\x01\"\xd2\x08\n\x06Header\x12!\n\x06source\x18\x01 \x03(\x0b\x32\x11.pb.Header.Source\x12&\n\tfile_type\x18\x02 \x02(\x0e [...]
+
+
+
+_HEADER_FILETYPE = _descriptor.EnumDescriptor(
+ name='FileType',
+ full_name='pb.Header.FileType',
+ filename=None,
+ file=DESCRIPTOR,
+ values=[
+ _descriptor.EnumValueDescriptor(
+ name='RAW_PROTEINS', index=0, number=0,
+ options=None,
+ type=None),
+ _descriptor.EnumValueDescriptor(
+ name='PEPTIDES', index=1, number=1,
+ options=None,
+ type=None),
+ _descriptor.EnumValueDescriptor(
+ name='SPECTRA', index=2, number=2,
+ options=None,
+ type=None),
+ _descriptor.EnumValueDescriptor(
+ name='PARAMS', index=3, number=3,
+ options=None,
+ type=None),
+ _descriptor.EnumValueDescriptor(
+ name='MOD_TABLE', index=4, number=4,
+ options=None,
+ type=None),
+ _descriptor.EnumValueDescriptor(
+ name='RESULTS', index=5, number=5,
+ options=None,
+ type=None),
+ _descriptor.EnumValueDescriptor(
+ name='AUX_LOCATIONS', index=6, number=6,
+ options=None,
+ type=None),
+ ],
+ containing_type=None,
+ options=None,
+ serialized_start=1197,
+ serialized_end=1311,
+)
+
+
+_MODIFICATION = _descriptor.Descriptor(
+ name='Modification',
+ full_name='pb.Modification',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='amino_acids', full_name='pb.Modification.amino_acids', index=0,
+ number=1, type=9, cpp_type=9, label=1,
+ has_default_value=False, default_value=unicode("", "utf-8"),
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='delta', full_name='pb.Modification.delta', index=1,
+ number=2, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='max_count', full_name='pb.Modification.max_count', index=2,
+ number=3, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=20,
+ serialized_end=89,
+)
+
+
+_MODTABLE = _descriptor.Descriptor(
+ name='ModTable',
+ full_name='pb.ModTable',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='variable_mod', full_name='pb.ModTable.variable_mod', index=0,
+ number=1, type=11, cpp_type=10, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='static_mod', full_name='pb.ModTable.static_mod', index=1,
+ number=2, type=11, cpp_type=10, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='unique_deltas', full_name='pb.ModTable.unique_deltas', index=2,
+ number=10, type=1, cpp_type=5, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=91,
+ serialized_end=202,
+)
+
+
+_HEADER_SOURCE = _descriptor.Descriptor(
+ name='Source',
+ full_name='pb.Header.Source',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='filename', full_name='pb.Header.Source.filename', index=0,
+ number=1, type=9, cpp_type=9, label=1,
+ has_default_value=False, default_value=unicode("", "utf-8"),
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='header', full_name='pb.Header.Source.header', index=1,
+ number=2, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='filetype', full_name='pb.Header.Source.filetype', index=2,
+ number=3, type=9, cpp_type=9, label=1,
+ has_default_value=False, default_value=unicode("", "utf-8"),
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=579,
+ serialized_end=651,
+)
+
+_HEADER_RAWPROTEINSHEADER = _descriptor.Descriptor(
+ name='RawProteinsHeader',
+ full_name='pb.Header.RawProteinsHeader',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=653,
+ serialized_end=672,
+)
+
+_HEADER_PEPTIDESHEADER = _descriptor.Descriptor(
+ name='PeptidesHeader',
+ full_name='pb.Header.PeptidesHeader',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='min_mass', full_name='pb.Header.PeptidesHeader.min_mass', index=0,
+ number=3, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='max_mass', full_name='pb.Header.PeptidesHeader.max_mass', index=1,
+ number=4, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='min_length', full_name='pb.Header.PeptidesHeader.min_length', index=2,
+ number=5, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='max_length', full_name='pb.Header.PeptidesHeader.max_length', index=3,
+ number=6, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='enzyme', full_name='pb.Header.PeptidesHeader.enzyme', index=4,
+ number=7, type=9, cpp_type=9, label=1,
+ has_default_value=False, default_value=unicode("", "utf-8"),
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='full_digestion', full_name='pb.Header.PeptidesHeader.full_digestion', index=5,
+ number=8, type=8, cpp_type=7, label=1,
+ has_default_value=False, default_value=False,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='max_missed_cleavages', full_name='pb.Header.PeptidesHeader.max_missed_cleavages', index=6,
+ number=14, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='monoisotopic_precursor', full_name='pb.Header.PeptidesHeader.monoisotopic_precursor', index=7,
+ number=13, type=8, cpp_type=7, label=1,
+ has_default_value=False, default_value=False,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='has_peaks', full_name='pb.Header.PeptidesHeader.has_peaks', index=8,
+ number=10, type=8, cpp_type=7, label=1,
+ has_default_value=False, default_value=False,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='downselect_fraction', full_name='pb.Header.PeptidesHeader.downselect_fraction', index=9,
+ number=11, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='mods', full_name='pb.Header.PeptidesHeader.mods', index=10,
+ number=12, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='nterm_mods', full_name='pb.Header.PeptidesHeader.nterm_mods', index=11,
+ number=15, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='cterm_mods', full_name='pb.Header.PeptidesHeader.cterm_mods', index=12,
+ number=16, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='decoys', full_name='pb.Header.PeptidesHeader.decoys', index=13,
+ number=9, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=675,
+ serialized_end=1029,
+)
+
+_HEADER_SPECTRAHEADER = _descriptor.Descriptor(
+ name='SpectraHeader',
+ full_name='pb.Header.SpectraHeader',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='sorted', full_name='pb.Header.SpectraHeader.sorted', index=0,
+ number=2, type=8, cpp_type=7, label=1,
+ has_default_value=False, default_value=False,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=1031,
+ serialized_end=1062,
+)
+
+_HEADER_RESULTSHEADER = _descriptor.Descriptor(
+ name='ResultsHeader',
+ full_name='pb.Header.ResultsHeader',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='mass_window', full_name='pb.Header.ResultsHeader.mass_window', index=0,
+ number=1, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='top_matches', full_name='pb.Header.ResultsHeader.top_matches', index=1,
+ number=2, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='peptides_header', full_name='pb.Header.ResultsHeader.peptides_header', index=2,
+ number=3, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=1064,
+ serialized_end=1173,
+)
+
+_HEADER_AUXLOCATIONSHEADER = _descriptor.Descriptor(
+ name='AuxLocationsHeader',
+ full_name='pb.Header.AuxLocationsHeader',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=1175,
+ serialized_end=1195,
+)
+
+_HEADER = _descriptor.Descriptor(
+ name='Header',
+ full_name='pb.Header',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='source', full_name='pb.Header.source', index=0,
+ number=1, type=11, cpp_type=10, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='file_type', full_name='pb.Header.file_type', index=1,
+ number=2, type=14, cpp_type=8, label=2,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='raw_proteins_header', full_name='pb.Header.raw_proteins_header', index=2,
+ number=3, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='peptides_header', full_name='pb.Header.peptides_header', index=3,
+ number=4, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='spectra_header', full_name='pb.Header.spectra_header', index=4,
+ number=5, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='results_header', full_name='pb.Header.results_header', index=5,
+ number=6, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='aux_locs_header', full_name='pb.Header.aux_locs_header', index=6,
+ number=7, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='command_line', full_name='pb.Header.command_line', index=7,
+ number=8, type=9, cpp_type=9, label=1,
+ has_default_value=False, default_value=unicode("", "utf-8"),
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[_HEADER_SOURCE, _HEADER_RAWPROTEINSHEADER, _HEADER_PEPTIDESHEADER, _HEADER_SPECTRAHEADER, _HEADER_RESULTSHEADER, _HEADER_AUXLOCATIONSHEADER, ],
+ enum_types=[
+ _HEADER_FILETYPE,
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=205,
+ serialized_end=1311,
+)
+
+_MODTABLE.fields_by_name['variable_mod'].message_type = _MODIFICATION
+_MODTABLE.fields_by_name['static_mod'].message_type = _MODIFICATION
+_HEADER_SOURCE.fields_by_name['header'].message_type = _HEADER
+_HEADER_SOURCE.containing_type = _HEADER;
+_HEADER_RAWPROTEINSHEADER.containing_type = _HEADER;
+_HEADER_PEPTIDESHEADER.fields_by_name['mods'].message_type = _MODTABLE
+_HEADER_PEPTIDESHEADER.fields_by_name['nterm_mods'].message_type = _MODTABLE
+_HEADER_PEPTIDESHEADER.fields_by_name['cterm_mods'].message_type = _MODTABLE
+_HEADER_PEPTIDESHEADER.containing_type = _HEADER;
+_HEADER_SPECTRAHEADER.containing_type = _HEADER;
+_HEADER_RESULTSHEADER.fields_by_name['peptides_header'].message_type = _HEADER_PEPTIDESHEADER
+_HEADER_RESULTSHEADER.containing_type = _HEADER;
+_HEADER_AUXLOCATIONSHEADER.containing_type = _HEADER;
+_HEADER.fields_by_name['source'].message_type = _HEADER_SOURCE
+_HEADER.fields_by_name['file_type'].enum_type = _HEADER_FILETYPE
+_HEADER.fields_by_name['raw_proteins_header'].message_type = _HEADER_RAWPROTEINSHEADER
+_HEADER.fields_by_name['peptides_header'].message_type = _HEADER_PEPTIDESHEADER
+_HEADER.fields_by_name['spectra_header'].message_type = _HEADER_SPECTRAHEADER
+_HEADER.fields_by_name['results_header'].message_type = _HEADER_RESULTSHEADER
+_HEADER.fields_by_name['aux_locs_header'].message_type = _HEADER_AUXLOCATIONSHEADER
+_HEADER_FILETYPE.containing_type = _HEADER;
+DESCRIPTOR.message_types_by_name['Modification'] = _MODIFICATION
+DESCRIPTOR.message_types_by_name['ModTable'] = _MODTABLE
+DESCRIPTOR.message_types_by_name['Header'] = _HEADER
+
+class Modification(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _MODIFICATION
+
+ # @@protoc_insertion_point(class_scope:pb.Modification)
+
+class ModTable(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _MODTABLE
+
+ # @@protoc_insertion_point(class_scope:pb.ModTable)
+
+class Header(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+
+ class Source(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _HEADER_SOURCE
+
+ # @@protoc_insertion_point(class_scope:pb.Header.Source)
+
+ class RawProteinsHeader(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _HEADER_RAWPROTEINSHEADER
+
+ # @@protoc_insertion_point(class_scope:pb.Header.RawProteinsHeader)
+
+ class PeptidesHeader(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _HEADER_PEPTIDESHEADER
+
+ # @@protoc_insertion_point(class_scope:pb.Header.PeptidesHeader)
+
+ class SpectraHeader(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _HEADER_SPECTRAHEADER
+
+ # @@protoc_insertion_point(class_scope:pb.Header.SpectraHeader)
+
+ class ResultsHeader(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _HEADER_RESULTSHEADER
+
+ # @@protoc_insertion_point(class_scope:pb.Header.ResultsHeader)
+
+ class AuxLocationsHeader(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _HEADER_AUXLOCATIONSHEADER
+
+ # @@protoc_insertion_point(class_scope:pb.Header.AuxLocationsHeader)
+ DESCRIPTOR = _HEADER
+
+ # @@protoc_insertion_point(class_scope:pb.Header)
+
+
+# @@protoc_insertion_point(module_scope)
diff --git a/src/app/tide/protoobj/peptides.pb.cc b/src/app/tide/protoobj/peptides.pb.cc
new file mode 100644
index 0000000..f42851a
--- /dev/null
+++ b/src/app/tide/protoobj/peptides.pb.cc
@@ -0,0 +1,1389 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: peptides.proto
+
+#define INTERNAL_SUPPRESS_PROTOBUF_FIELD_DEPRECATION
+#include "peptides.pb.h"
+
+#include <algorithm>
+
+#include <google/protobuf/stubs/common.h>
+#include <google/protobuf/stubs/once.h>
+#include <google/protobuf/io/coded_stream.h>
+#include <google/protobuf/wire_format_lite_inl.h>
+#include <google/protobuf/descriptor.h>
+#include <google/protobuf/generated_message_reflection.h>
+#include <google/protobuf/reflection_ops.h>
+#include <google/protobuf/wire_format.h>
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+namespace {
+
+const ::google::protobuf::Descriptor* Location_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Location_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Peptide_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Peptide_reflection_ = NULL;
+const ::google::protobuf::EnumDescriptor* Peptide_Series_descriptor_ = NULL;
+const ::google::protobuf::Descriptor* AuxLocation_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ AuxLocation_reflection_ = NULL;
+
+} // namespace
+
+
+void protobuf_AssignDesc_peptides_2eproto() {
+ protobuf_AddDesc_peptides_2eproto();
+ const ::google::protobuf::FileDescriptor* file =
+ ::google::protobuf::DescriptorPool::generated_pool()->FindFileByName(
+ "peptides.proto");
+ GOOGLE_CHECK(file != NULL);
+ Location_descriptor_ = file->message_type(0);
+ static const int Location_offsets_[2] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Location, protein_id_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Location, pos_),
+ };
+ Location_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Location_descriptor_,
+ Location::default_instance_,
+ Location_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Location, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Location, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Location));
+ Peptide_descriptor_ = file->message_type(1);
+ static const int Peptide_offsets_[11] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, id_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, mass_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, length_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, first_location_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, peak1_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, peak2_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, neg_peak1_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, neg_peak2_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, modifications_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, aux_locations_index_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, is_decoy_),
+ };
+ Peptide_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Peptide_descriptor_,
+ Peptide::default_instance_,
+ Peptide_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Peptide, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Peptide));
+ Peptide_Series_descriptor_ = Peptide_descriptor_->enum_type(0);
+ AuxLocation_descriptor_ = file->message_type(2);
+ static const int AuxLocation_offsets_[1] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(AuxLocation, location_),
+ };
+ AuxLocation_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ AuxLocation_descriptor_,
+ AuxLocation::default_instance_,
+ AuxLocation_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(AuxLocation, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(AuxLocation, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(AuxLocation));
+}
+
+namespace {
+
+GOOGLE_PROTOBUF_DECLARE_ONCE(protobuf_AssignDescriptors_once_);
+inline void protobuf_AssignDescriptorsOnce() {
+ ::google::protobuf::GoogleOnceInit(&protobuf_AssignDescriptors_once_,
+ &protobuf_AssignDesc_peptides_2eproto);
+}
+
+void protobuf_RegisterTypes(const ::std::string&) {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Location_descriptor_, &Location::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Peptide_descriptor_, &Peptide::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ AuxLocation_descriptor_, &AuxLocation::default_instance());
+}
+
+} // namespace
+
+void protobuf_ShutdownFile_peptides_2eproto() {
+ delete Location::default_instance_;
+ delete Location_reflection_;
+ delete Peptide::default_instance_;
+ delete Peptide_reflection_;
+ delete AuxLocation::default_instance_;
+ delete AuxLocation_reflection_;
+}
+
+void protobuf_AddDesc_peptides_2eproto() {
+ static bool already_here = false;
+ if (already_here) return;
+ already_here = true;
+ GOOGLE_PROTOBUF_VERIFY_VERSION;
+
+ ::pb::protobuf_AddDesc_raw_5fproteins_2eproto();
+ ::google::protobuf::DescriptorPool::InternalAddGeneratedFile(
+ "\n\016peptides.proto\022\002pb\032\022raw_proteins.proto"
+ "\"+\n\010Location\022\022\n\nprotein_id\030\001 \001(\005\022\013\n\003pos\030"
+ "\002 \001(\005\"\217\002\n\007Peptide\022\n\n\002id\030\001 \001(\005\022\014\n\004mass\030\002 "
+ "\001(\001\022\016\n\006length\030\003 \001(\005\022$\n\016first_location\030\004 "
+ "\001(\0132\014.pb.Location\022\021\n\005peak1\030\005 \003(\005B\002\020\001\022\021\n\005"
+ "peak2\030\006 \003(\005B\002\020\001\022\025\n\tneg_peak1\030\007 \003(\005B\002\020\001\022\025"
+ "\n\tneg_peak2\030\010 \003(\005B\002\020\001\022\031\n\rmodifications\030\t"
+ " \003(\005B\002\020\001\022\033\n\023aux_locations_index\030\n \001(\005\022\020\n"
+ "\010is_decoy\030\013 \001(\010\"\026\n\006Series\022\005\n\001Y\020\000\022\005\n\001B\020\001\""
+ "-\n\013AuxLocation\022\036\n\010location\030\001 \003(\0132\014.pb.Lo"
+ "cationB\002H\001", 410);
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedFile(
+ "peptides.proto", &protobuf_RegisterTypes);
+ Location::default_instance_ = new Location();
+ Peptide::default_instance_ = new Peptide();
+ AuxLocation::default_instance_ = new AuxLocation();
+ Location::default_instance_->InitAsDefaultInstance();
+ Peptide::default_instance_->InitAsDefaultInstance();
+ AuxLocation::default_instance_->InitAsDefaultInstance();
+ ::google::protobuf::internal::OnShutdown(&protobuf_ShutdownFile_peptides_2eproto);
+}
+
+// Force AddDescriptors() to be called at static initialization time.
+struct StaticDescriptorInitializer_peptides_2eproto {
+ StaticDescriptorInitializer_peptides_2eproto() {
+ protobuf_AddDesc_peptides_2eproto();
+ }
+} static_descriptor_initializer_peptides_2eproto_;
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int Location::kProteinIdFieldNumber;
+const int Location::kPosFieldNumber;
+#endif // !_MSC_VER
+
+Location::Location()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Location::InitAsDefaultInstance() {
+}
+
+Location::Location(const Location& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Location::SharedCtor() {
+ _cached_size_ = 0;
+ protein_id_ = 0;
+ pos_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Location::~Location() {
+ SharedDtor();
+}
+
+void Location::SharedDtor() {
+ if (this != default_instance_) {
+ }
+}
+
+void Location::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Location::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Location_descriptor_;
+}
+
+const Location& Location::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_peptides_2eproto();
+ return *default_instance_;
+}
+
+Location* Location::default_instance_ = NULL;
+
+Location* Location::New() const {
+ return new Location;
+}
+
+void Location::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ protein_id_ = 0;
+ pos_ = 0;
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Location::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional int32 protein_id = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &protein_id_)));
+ set_has_protein_id();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(16)) goto parse_pos;
+ break;
+ }
+
+ // optional int32 pos = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_pos:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &pos_)));
+ set_has_pos();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Location::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional int32 protein_id = 1;
+ if (has_protein_id()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(1, this->protein_id(), output);
+ }
+
+ // optional int32 pos = 2;
+ if (has_pos()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(2, this->pos(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Location::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional int32 protein_id = 1;
+ if (has_protein_id()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(1, this->protein_id(), target);
+ }
+
+ // optional int32 pos = 2;
+ if (has_pos()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(2, this->pos(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Location::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional int32 protein_id = 1;
+ if (has_protein_id()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->protein_id());
+ }
+
+ // optional int32 pos = 2;
+ if (has_pos()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->pos());
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Location::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Location* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Location*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Location::MergeFrom(const Location& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_protein_id()) {
+ set_protein_id(from.protein_id());
+ }
+ if (from.has_pos()) {
+ set_pos(from.pos());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Location::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Location::CopyFrom(const Location& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Location::IsInitialized() const {
+
+ return true;
+}
+
+void Location::Swap(Location* other) {
+ if (other != this) {
+ std::swap(protein_id_, other->protein_id_);
+ std::swap(pos_, other->pos_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Location::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Location_descriptor_;
+ metadata.reflection = Location_reflection_;
+ return metadata;
+}
+
+
+// ===================================================================
+
+const ::google::protobuf::EnumDescriptor* Peptide_Series_descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Peptide_Series_descriptor_;
+}
+bool Peptide_Series_IsValid(int value) {
+ switch(value) {
+ case 0:
+ case 1:
+ return true;
+ default:
+ return false;
+ }
+}
+
+#ifndef _MSC_VER
+const Peptide_Series Peptide::Y;
+const Peptide_Series Peptide::B;
+const Peptide_Series Peptide::Series_MIN;
+const Peptide_Series Peptide::Series_MAX;
+const int Peptide::Series_ARRAYSIZE;
+#endif // _MSC_VER
+#ifndef _MSC_VER
+const int Peptide::kIdFieldNumber;
+const int Peptide::kMassFieldNumber;
+const int Peptide::kLengthFieldNumber;
+const int Peptide::kFirstLocationFieldNumber;
+const int Peptide::kPeak1FieldNumber;
+const int Peptide::kPeak2FieldNumber;
+const int Peptide::kNegPeak1FieldNumber;
+const int Peptide::kNegPeak2FieldNumber;
+const int Peptide::kModificationsFieldNumber;
+const int Peptide::kAuxLocationsIndexFieldNumber;
+const int Peptide::kIsDecoyFieldNumber;
+#endif // !_MSC_VER
+
+Peptide::Peptide()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Peptide::InitAsDefaultInstance() {
+ first_location_ = const_cast< ::pb::Location*>(&::pb::Location::default_instance());
+}
+
+Peptide::Peptide(const Peptide& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Peptide::SharedCtor() {
+ _cached_size_ = 0;
+ id_ = 0;
+ mass_ = 0;
+ length_ = 0;
+ first_location_ = NULL;
+ aux_locations_index_ = 0;
+ is_decoy_ = false;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Peptide::~Peptide() {
+ SharedDtor();
+}
+
+void Peptide::SharedDtor() {
+ if (this != default_instance_) {
+ delete first_location_;
+ }
+}
+
+void Peptide::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Peptide::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Peptide_descriptor_;
+}
+
+const Peptide& Peptide::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_peptides_2eproto();
+ return *default_instance_;
+}
+
+Peptide* Peptide::default_instance_ = NULL;
+
+Peptide* Peptide::New() const {
+ return new Peptide;
+}
+
+void Peptide::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ id_ = 0;
+ mass_ = 0;
+ length_ = 0;
+ if (has_first_location()) {
+ if (first_location_ != NULL) first_location_->::pb::Location::Clear();
+ }
+ }
+ if (_has_bits_[9 / 32] & (0xffu << (9 % 32))) {
+ aux_locations_index_ = 0;
+ is_decoy_ = false;
+ }
+ peak1_.Clear();
+ peak2_.Clear();
+ neg_peak1_.Clear();
+ neg_peak2_.Clear();
+ modifications_.Clear();
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Peptide::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional int32 id = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &id_)));
+ set_has_id();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(17)) goto parse_mass;
+ break;
+ }
+
+ // optional double mass = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_mass:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &mass_)));
+ set_has_mass();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(24)) goto parse_length;
+ break;
+ }
+
+ // optional int32 length = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_length:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &length_)));
+ set_has_length();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(34)) goto parse_first_location;
+ break;
+ }
+
+ // optional .pb.Location first_location = 4;
+ case 4: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_first_location:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_first_location()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(42)) goto parse_peak1;
+ break;
+ }
+
+ // repeated int32 peak1 = 5 [packed = true];
+ case 5: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_peak1:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, this->mutable_peak1())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitiveNoInline<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ 1, 42, input, this->mutable_peak1())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(50)) goto parse_peak2;
+ break;
+ }
+
+ // repeated int32 peak2 = 6 [packed = true];
+ case 6: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_peak2:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, this->mutable_peak2())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitiveNoInline<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ 1, 50, input, this->mutable_peak2())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(58)) goto parse_neg_peak1;
+ break;
+ }
+
+ // repeated int32 neg_peak1 = 7 [packed = true];
+ case 7: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_neg_peak1:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, this->mutable_neg_peak1())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitiveNoInline<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ 1, 58, input, this->mutable_neg_peak1())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(66)) goto parse_neg_peak2;
+ break;
+ }
+
+ // repeated int32 neg_peak2 = 8 [packed = true];
+ case 8: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_neg_peak2:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, this->mutable_neg_peak2())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitiveNoInline<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ 1, 66, input, this->mutable_neg_peak2())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(74)) goto parse_modifications;
+ break;
+ }
+
+ // repeated int32 modifications = 9 [packed = true];
+ case 9: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_modifications:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, this->mutable_modifications())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitiveNoInline<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ 1, 74, input, this->mutable_modifications())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(80)) goto parse_aux_locations_index;
+ break;
+ }
+
+ // optional int32 aux_locations_index = 10;
+ case 10: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_aux_locations_index:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &aux_locations_index_)));
+ set_has_aux_locations_index();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(88)) goto parse_is_decoy;
+ break;
+ }
+
+ // optional bool is_decoy = 11;
+ case 11: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_is_decoy:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ bool, ::google::protobuf::internal::WireFormatLite::TYPE_BOOL>(
+ input, &is_decoy_)));
+ set_has_is_decoy();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Peptide::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional int32 id = 1;
+ if (has_id()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(1, this->id(), output);
+ }
+
+ // optional double mass = 2;
+ if (has_mass()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(2, this->mass(), output);
+ }
+
+ // optional int32 length = 3;
+ if (has_length()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(3, this->length(), output);
+ }
+
+ // optional .pb.Location first_location = 4;
+ if (has_first_location()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 4, this->first_location(), output);
+ }
+
+ // repeated int32 peak1 = 5 [packed = true];
+ if (this->peak1_size() > 0) {
+ ::google::protobuf::internal::WireFormatLite::WriteTag(5, ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED, output);
+ output->WriteVarint32(_peak1_cached_byte_size_);
+ }
+ for (int i = 0; i < this->peak1_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32NoTag(
+ this->peak1(i), output);
+ }
+
+ // repeated int32 peak2 = 6 [packed = true];
+ if (this->peak2_size() > 0) {
+ ::google::protobuf::internal::WireFormatLite::WriteTag(6, ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED, output);
+ output->WriteVarint32(_peak2_cached_byte_size_);
+ }
+ for (int i = 0; i < this->peak2_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32NoTag(
+ this->peak2(i), output);
+ }
+
+ // repeated int32 neg_peak1 = 7 [packed = true];
+ if (this->neg_peak1_size() > 0) {
+ ::google::protobuf::internal::WireFormatLite::WriteTag(7, ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED, output);
+ output->WriteVarint32(_neg_peak1_cached_byte_size_);
+ }
+ for (int i = 0; i < this->neg_peak1_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32NoTag(
+ this->neg_peak1(i), output);
+ }
+
+ // repeated int32 neg_peak2 = 8 [packed = true];
+ if (this->neg_peak2_size() > 0) {
+ ::google::protobuf::internal::WireFormatLite::WriteTag(8, ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED, output);
+ output->WriteVarint32(_neg_peak2_cached_byte_size_);
+ }
+ for (int i = 0; i < this->neg_peak2_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32NoTag(
+ this->neg_peak2(i), output);
+ }
+
+ // repeated int32 modifications = 9 [packed = true];
+ if (this->modifications_size() > 0) {
+ ::google::protobuf::internal::WireFormatLite::WriteTag(9, ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED, output);
+ output->WriteVarint32(_modifications_cached_byte_size_);
+ }
+ for (int i = 0; i < this->modifications_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32NoTag(
+ this->modifications(i), output);
+ }
+
+ // optional int32 aux_locations_index = 10;
+ if (has_aux_locations_index()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(10, this->aux_locations_index(), output);
+ }
+
+ // optional bool is_decoy = 11;
+ if (has_is_decoy()) {
+ ::google::protobuf::internal::WireFormatLite::WriteBool(11, this->is_decoy(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Peptide::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional int32 id = 1;
+ if (has_id()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(1, this->id(), target);
+ }
+
+ // optional double mass = 2;
+ if (has_mass()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(2, this->mass(), target);
+ }
+
+ // optional int32 length = 3;
+ if (has_length()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(3, this->length(), target);
+ }
+
+ // optional .pb.Location first_location = 4;
+ if (has_first_location()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 4, this->first_location(), target);
+ }
+
+ // repeated int32 peak1 = 5 [packed = true];
+ if (this->peak1_size() > 0) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteTagToArray(
+ 5,
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED,
+ target);
+ target = ::google::protobuf::io::CodedOutputStream::WriteVarint32ToArray(
+ _peak1_cached_byte_size_, target);
+ }
+ for (int i = 0; i < this->peak1_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteInt32NoTagToArray(this->peak1(i), target);
+ }
+
+ // repeated int32 peak2 = 6 [packed = true];
+ if (this->peak2_size() > 0) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteTagToArray(
+ 6,
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED,
+ target);
+ target = ::google::protobuf::io::CodedOutputStream::WriteVarint32ToArray(
+ _peak2_cached_byte_size_, target);
+ }
+ for (int i = 0; i < this->peak2_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteInt32NoTagToArray(this->peak2(i), target);
+ }
+
+ // repeated int32 neg_peak1 = 7 [packed = true];
+ if (this->neg_peak1_size() > 0) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteTagToArray(
+ 7,
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED,
+ target);
+ target = ::google::protobuf::io::CodedOutputStream::WriteVarint32ToArray(
+ _neg_peak1_cached_byte_size_, target);
+ }
+ for (int i = 0; i < this->neg_peak1_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteInt32NoTagToArray(this->neg_peak1(i), target);
+ }
+
+ // repeated int32 neg_peak2 = 8 [packed = true];
+ if (this->neg_peak2_size() > 0) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteTagToArray(
+ 8,
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED,
+ target);
+ target = ::google::protobuf::io::CodedOutputStream::WriteVarint32ToArray(
+ _neg_peak2_cached_byte_size_, target);
+ }
+ for (int i = 0; i < this->neg_peak2_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteInt32NoTagToArray(this->neg_peak2(i), target);
+ }
+
+ // repeated int32 modifications = 9 [packed = true];
+ if (this->modifications_size() > 0) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteTagToArray(
+ 9,
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED,
+ target);
+ target = ::google::protobuf::io::CodedOutputStream::WriteVarint32ToArray(
+ _modifications_cached_byte_size_, target);
+ }
+ for (int i = 0; i < this->modifications_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteInt32NoTagToArray(this->modifications(i), target);
+ }
+
+ // optional int32 aux_locations_index = 10;
+ if (has_aux_locations_index()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(10, this->aux_locations_index(), target);
+ }
+
+ // optional bool is_decoy = 11;
+ if (has_is_decoy()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteBoolToArray(11, this->is_decoy(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Peptide::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional int32 id = 1;
+ if (has_id()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->id());
+ }
+
+ // optional double mass = 2;
+ if (has_mass()) {
+ total_size += 1 + 8;
+ }
+
+ // optional int32 length = 3;
+ if (has_length()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->length());
+ }
+
+ // optional .pb.Location first_location = 4;
+ if (has_first_location()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->first_location());
+ }
+
+ }
+ if (_has_bits_[9 / 32] & (0xffu << (9 % 32))) {
+ // optional int32 aux_locations_index = 10;
+ if (has_aux_locations_index()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->aux_locations_index());
+ }
+
+ // optional bool is_decoy = 11;
+ if (has_is_decoy()) {
+ total_size += 1 + 1;
+ }
+
+ }
+ // repeated int32 peak1 = 5 [packed = true];
+ {
+ int data_size = 0;
+ for (int i = 0; i < this->peak1_size(); i++) {
+ data_size += ::google::protobuf::internal::WireFormatLite::
+ Int32Size(this->peak1(i));
+ }
+ if (data_size > 0) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(data_size);
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _peak1_cached_byte_size_ = data_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ total_size += data_size;
+ }
+
+ // repeated int32 peak2 = 6 [packed = true];
+ {
+ int data_size = 0;
+ for (int i = 0; i < this->peak2_size(); i++) {
+ data_size += ::google::protobuf::internal::WireFormatLite::
+ Int32Size(this->peak2(i));
+ }
+ if (data_size > 0) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(data_size);
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _peak2_cached_byte_size_ = data_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ total_size += data_size;
+ }
+
+ // repeated int32 neg_peak1 = 7 [packed = true];
+ {
+ int data_size = 0;
+ for (int i = 0; i < this->neg_peak1_size(); i++) {
+ data_size += ::google::protobuf::internal::WireFormatLite::
+ Int32Size(this->neg_peak1(i));
+ }
+ if (data_size > 0) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(data_size);
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _neg_peak1_cached_byte_size_ = data_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ total_size += data_size;
+ }
+
+ // repeated int32 neg_peak2 = 8 [packed = true];
+ {
+ int data_size = 0;
+ for (int i = 0; i < this->neg_peak2_size(); i++) {
+ data_size += ::google::protobuf::internal::WireFormatLite::
+ Int32Size(this->neg_peak2(i));
+ }
+ if (data_size > 0) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(data_size);
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _neg_peak2_cached_byte_size_ = data_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ total_size += data_size;
+ }
+
+ // repeated int32 modifications = 9 [packed = true];
+ {
+ int data_size = 0;
+ for (int i = 0; i < this->modifications_size(); i++) {
+ data_size += ::google::protobuf::internal::WireFormatLite::
+ Int32Size(this->modifications(i));
+ }
+ if (data_size > 0) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(data_size);
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _modifications_cached_byte_size_ = data_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ total_size += data_size;
+ }
+
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Peptide::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Peptide* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Peptide*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Peptide::MergeFrom(const Peptide& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ peak1_.MergeFrom(from.peak1_);
+ peak2_.MergeFrom(from.peak2_);
+ neg_peak1_.MergeFrom(from.neg_peak1_);
+ neg_peak2_.MergeFrom(from.neg_peak2_);
+ modifications_.MergeFrom(from.modifications_);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_id()) {
+ set_id(from.id());
+ }
+ if (from.has_mass()) {
+ set_mass(from.mass());
+ }
+ if (from.has_length()) {
+ set_length(from.length());
+ }
+ if (from.has_first_location()) {
+ mutable_first_location()->::pb::Location::MergeFrom(from.first_location());
+ }
+ }
+ if (from._has_bits_[9 / 32] & (0xffu << (9 % 32))) {
+ if (from.has_aux_locations_index()) {
+ set_aux_locations_index(from.aux_locations_index());
+ }
+ if (from.has_is_decoy()) {
+ set_is_decoy(from.is_decoy());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Peptide::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Peptide::CopyFrom(const Peptide& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Peptide::IsInitialized() const {
+
+ return true;
+}
+
+void Peptide::Swap(Peptide* other) {
+ if (other != this) {
+ std::swap(id_, other->id_);
+ std::swap(mass_, other->mass_);
+ std::swap(length_, other->length_);
+ std::swap(first_location_, other->first_location_);
+ peak1_.Swap(&other->peak1_);
+ peak2_.Swap(&other->peak2_);
+ neg_peak1_.Swap(&other->neg_peak1_);
+ neg_peak2_.Swap(&other->neg_peak2_);
+ modifications_.Swap(&other->modifications_);
+ std::swap(aux_locations_index_, other->aux_locations_index_);
+ std::swap(is_decoy_, other->is_decoy_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Peptide::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Peptide_descriptor_;
+ metadata.reflection = Peptide_reflection_;
+ return metadata;
+}
+
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int AuxLocation::kLocationFieldNumber;
+#endif // !_MSC_VER
+
+AuxLocation::AuxLocation()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void AuxLocation::InitAsDefaultInstance() {
+}
+
+AuxLocation::AuxLocation(const AuxLocation& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void AuxLocation::SharedCtor() {
+ _cached_size_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+AuxLocation::~AuxLocation() {
+ SharedDtor();
+}
+
+void AuxLocation::SharedDtor() {
+ if (this != default_instance_) {
+ }
+}
+
+void AuxLocation::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* AuxLocation::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return AuxLocation_descriptor_;
+}
+
+const AuxLocation& AuxLocation::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_peptides_2eproto();
+ return *default_instance_;
+}
+
+AuxLocation* AuxLocation::default_instance_ = NULL;
+
+AuxLocation* AuxLocation::New() const {
+ return new AuxLocation;
+}
+
+void AuxLocation::Clear() {
+ location_.Clear();
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool AuxLocation::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // repeated .pb.Location location = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_location:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, add_location()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(10)) goto parse_location;
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void AuxLocation::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // repeated .pb.Location location = 1;
+ for (int i = 0; i < this->location_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 1, this->location(i), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* AuxLocation::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // repeated .pb.Location location = 1;
+ for (int i = 0; i < this->location_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 1, this->location(i), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int AuxLocation::ByteSize() const {
+ int total_size = 0;
+
+ // repeated .pb.Location location = 1;
+ total_size += 1 * this->location_size();
+ for (int i = 0; i < this->location_size(); i++) {
+ total_size +=
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->location(i));
+ }
+
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void AuxLocation::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const AuxLocation* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const AuxLocation*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void AuxLocation::MergeFrom(const AuxLocation& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ location_.MergeFrom(from.location_);
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void AuxLocation::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void AuxLocation::CopyFrom(const AuxLocation& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool AuxLocation::IsInitialized() const {
+
+ return true;
+}
+
+void AuxLocation::Swap(AuxLocation* other) {
+ if (other != this) {
+ location_.Swap(&other->location_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata AuxLocation::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = AuxLocation_descriptor_;
+ metadata.reflection = AuxLocation_reflection_;
+ return metadata;
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+// @@protoc_insertion_point(global_scope)
diff --git a/src/app/tide/protoobj/peptides.pb.h b/src/app/tide/protoobj/peptides.pb.h
new file mode 100644
index 0000000..f0bd254
--- /dev/null
+++ b/src/app/tide/protoobj/peptides.pb.h
@@ -0,0 +1,843 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: peptides.proto
+
+#ifndef PROTOBUF_peptides_2eproto__INCLUDED
+#define PROTOBUF_peptides_2eproto__INCLUDED
+
+#include <string>
+
+#include <google/protobuf/stubs/common.h>
+
+#if GOOGLE_PROTOBUF_VERSION < 2005000
+#error This file was generated by a newer version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please update
+#error your headers.
+#endif
+#if 2005000 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
+#error This file was generated by an older version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please
+#error regenerate this file with a newer version of protoc.
+#endif
+
+#include <google/protobuf/generated_message_util.h>
+#include <google/protobuf/message.h>
+#include <google/protobuf/repeated_field.h>
+#include <google/protobuf/extension_set.h>
+#include <google/protobuf/generated_enum_reflection.h>
+#include <google/protobuf/unknown_field_set.h>
+#include "raw_proteins.pb.h"
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+// Internal implementation detail -- do not call these.
+void protobuf_AddDesc_peptides_2eproto();
+void protobuf_AssignDesc_peptides_2eproto();
+void protobuf_ShutdownFile_peptides_2eproto();
+
+class Location;
+class Peptide;
+class AuxLocation;
+
+enum Peptide_Series {
+ Peptide_Series_Y = 0,
+ Peptide_Series_B = 1
+};
+bool Peptide_Series_IsValid(int value);
+const Peptide_Series Peptide_Series_Series_MIN = Peptide_Series_Y;
+const Peptide_Series Peptide_Series_Series_MAX = Peptide_Series_B;
+const int Peptide_Series_Series_ARRAYSIZE = Peptide_Series_Series_MAX + 1;
+
+const ::google::protobuf::EnumDescriptor* Peptide_Series_descriptor();
+inline const ::std::string& Peptide_Series_Name(Peptide_Series value) {
+ return ::google::protobuf::internal::NameOfEnum(
+ Peptide_Series_descriptor(), value);
+}
+inline bool Peptide_Series_Parse(
+ const ::std::string& name, Peptide_Series* value) {
+ return ::google::protobuf::internal::ParseNamedEnum<Peptide_Series>(
+ Peptide_Series_descriptor(), name, value);
+}
+// ===================================================================
+
+class Location : public ::google::protobuf::Message {
+ public:
+ Location();
+ virtual ~Location();
+
+ Location(const Location& from);
+
+ inline Location& operator=(const Location& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Location& default_instance();
+
+ void Swap(Location* other);
+
+ // implements Message ----------------------------------------------
+
+ Location* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Location& from);
+ void MergeFrom(const Location& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional int32 protein_id = 1;
+ inline bool has_protein_id() const;
+ inline void clear_protein_id();
+ static const int kProteinIdFieldNumber = 1;
+ inline ::google::protobuf::int32 protein_id() const;
+ inline void set_protein_id(::google::protobuf::int32 value);
+
+ // optional int32 pos = 2;
+ inline bool has_pos() const;
+ inline void clear_pos();
+ static const int kPosFieldNumber = 2;
+ inline ::google::protobuf::int32 pos() const;
+ inline void set_pos(::google::protobuf::int32 value);
+
+ // @@protoc_insertion_point(class_scope:pb.Location)
+ private:
+ inline void set_has_protein_id();
+ inline void clear_has_protein_id();
+ inline void set_has_pos();
+ inline void clear_has_pos();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::google::protobuf::int32 protein_id_;
+ ::google::protobuf::int32 pos_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(2 + 31) / 32];
+
+ friend void protobuf_AddDesc_peptides_2eproto();
+ friend void protobuf_AssignDesc_peptides_2eproto();
+ friend void protobuf_ShutdownFile_peptides_2eproto();
+
+ void InitAsDefaultInstance();
+ static Location* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Peptide : public ::google::protobuf::Message {
+ public:
+ Peptide();
+ virtual ~Peptide();
+
+ Peptide(const Peptide& from);
+
+ inline Peptide& operator=(const Peptide& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Peptide& default_instance();
+
+ void Swap(Peptide* other);
+
+ // implements Message ----------------------------------------------
+
+ Peptide* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Peptide& from);
+ void MergeFrom(const Peptide& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ typedef Peptide_Series Series;
+ static const Series Y = Peptide_Series_Y;
+ static const Series B = Peptide_Series_B;
+ static inline bool Series_IsValid(int value) {
+ return Peptide_Series_IsValid(value);
+ }
+ static const Series Series_MIN =
+ Peptide_Series_Series_MIN;
+ static const Series Series_MAX =
+ Peptide_Series_Series_MAX;
+ static const int Series_ARRAYSIZE =
+ Peptide_Series_Series_ARRAYSIZE;
+ static inline const ::google::protobuf::EnumDescriptor*
+ Series_descriptor() {
+ return Peptide_Series_descriptor();
+ }
+ static inline const ::std::string& Series_Name(Series value) {
+ return Peptide_Series_Name(value);
+ }
+ static inline bool Series_Parse(const ::std::string& name,
+ Series* value) {
+ return Peptide_Series_Parse(name, value);
+ }
+
+ // accessors -------------------------------------------------------
+
+ // optional int32 id = 1;
+ inline bool has_id() const;
+ inline void clear_id();
+ static const int kIdFieldNumber = 1;
+ inline ::google::protobuf::int32 id() const;
+ inline void set_id(::google::protobuf::int32 value);
+
+ // optional double mass = 2;
+ inline bool has_mass() const;
+ inline void clear_mass();
+ static const int kMassFieldNumber = 2;
+ inline double mass() const;
+ inline void set_mass(double value);
+
+ // optional int32 length = 3;
+ inline bool has_length() const;
+ inline void clear_length();
+ static const int kLengthFieldNumber = 3;
+ inline ::google::protobuf::int32 length() const;
+ inline void set_length(::google::protobuf::int32 value);
+
+ // optional .pb.Location first_location = 4;
+ inline bool has_first_location() const;
+ inline void clear_first_location();
+ static const int kFirstLocationFieldNumber = 4;
+ inline const ::pb::Location& first_location() const;
+ inline ::pb::Location* mutable_first_location();
+ inline ::pb::Location* release_first_location();
+ inline void set_allocated_first_location(::pb::Location* first_location);
+
+ // repeated int32 peak1 = 5 [packed = true];
+ inline int peak1_size() const;
+ inline void clear_peak1();
+ static const int kPeak1FieldNumber = 5;
+ inline ::google::protobuf::int32 peak1(int index) const;
+ inline void set_peak1(int index, ::google::protobuf::int32 value);
+ inline void add_peak1(::google::protobuf::int32 value);
+ inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+ peak1() const;
+ inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+ mutable_peak1();
+
+ // repeated int32 peak2 = 6 [packed = true];
+ inline int peak2_size() const;
+ inline void clear_peak2();
+ static const int kPeak2FieldNumber = 6;
+ inline ::google::protobuf::int32 peak2(int index) const;
+ inline void set_peak2(int index, ::google::protobuf::int32 value);
+ inline void add_peak2(::google::protobuf::int32 value);
+ inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+ peak2() const;
+ inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+ mutable_peak2();
+
+ // repeated int32 neg_peak1 = 7 [packed = true];
+ inline int neg_peak1_size() const;
+ inline void clear_neg_peak1();
+ static const int kNegPeak1FieldNumber = 7;
+ inline ::google::protobuf::int32 neg_peak1(int index) const;
+ inline void set_neg_peak1(int index, ::google::protobuf::int32 value);
+ inline void add_neg_peak1(::google::protobuf::int32 value);
+ inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+ neg_peak1() const;
+ inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+ mutable_neg_peak1();
+
+ // repeated int32 neg_peak2 = 8 [packed = true];
+ inline int neg_peak2_size() const;
+ inline void clear_neg_peak2();
+ static const int kNegPeak2FieldNumber = 8;
+ inline ::google::protobuf::int32 neg_peak2(int index) const;
+ inline void set_neg_peak2(int index, ::google::protobuf::int32 value);
+ inline void add_neg_peak2(::google::protobuf::int32 value);
+ inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+ neg_peak2() const;
+ inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+ mutable_neg_peak2();
+
+ // repeated int32 modifications = 9 [packed = true];
+ inline int modifications_size() const;
+ inline void clear_modifications();
+ static const int kModificationsFieldNumber = 9;
+ inline ::google::protobuf::int32 modifications(int index) const;
+ inline void set_modifications(int index, ::google::protobuf::int32 value);
+ inline void add_modifications(::google::protobuf::int32 value);
+ inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+ modifications() const;
+ inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+ mutable_modifications();
+
+ // optional int32 aux_locations_index = 10;
+ inline bool has_aux_locations_index() const;
+ inline void clear_aux_locations_index();
+ static const int kAuxLocationsIndexFieldNumber = 10;
+ inline ::google::protobuf::int32 aux_locations_index() const;
+ inline void set_aux_locations_index(::google::protobuf::int32 value);
+
+ // optional bool is_decoy = 11;
+ inline bool has_is_decoy() const;
+ inline void clear_is_decoy();
+ static const int kIsDecoyFieldNumber = 11;
+ inline bool is_decoy() const;
+ inline void set_is_decoy(bool value);
+
+ // @@protoc_insertion_point(class_scope:pb.Peptide)
+ private:
+ inline void set_has_id();
+ inline void clear_has_id();
+ inline void set_has_mass();
+ inline void clear_has_mass();
+ inline void set_has_length();
+ inline void clear_has_length();
+ inline void set_has_first_location();
+ inline void clear_has_first_location();
+ inline void set_has_aux_locations_index();
+ inline void clear_has_aux_locations_index();
+ inline void set_has_is_decoy();
+ inline void clear_has_is_decoy();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ double mass_;
+ ::google::protobuf::int32 id_;
+ ::google::protobuf::int32 length_;
+ ::pb::Location* first_location_;
+ ::google::protobuf::RepeatedField< ::google::protobuf::int32 > peak1_;
+ mutable int _peak1_cached_byte_size_;
+ ::google::protobuf::RepeatedField< ::google::protobuf::int32 > peak2_;
+ mutable int _peak2_cached_byte_size_;
+ ::google::protobuf::RepeatedField< ::google::protobuf::int32 > neg_peak1_;
+ mutable int _neg_peak1_cached_byte_size_;
+ ::google::protobuf::RepeatedField< ::google::protobuf::int32 > neg_peak2_;
+ mutable int _neg_peak2_cached_byte_size_;
+ ::google::protobuf::RepeatedField< ::google::protobuf::int32 > modifications_;
+ mutable int _modifications_cached_byte_size_;
+ ::google::protobuf::int32 aux_locations_index_;
+ bool is_decoy_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(11 + 31) / 32];
+
+ friend void protobuf_AddDesc_peptides_2eproto();
+ friend void protobuf_AssignDesc_peptides_2eproto();
+ friend void protobuf_ShutdownFile_peptides_2eproto();
+
+ void InitAsDefaultInstance();
+ static Peptide* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class AuxLocation : public ::google::protobuf::Message {
+ public:
+ AuxLocation();
+ virtual ~AuxLocation();
+
+ AuxLocation(const AuxLocation& from);
+
+ inline AuxLocation& operator=(const AuxLocation& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const AuxLocation& default_instance();
+
+ void Swap(AuxLocation* other);
+
+ // implements Message ----------------------------------------------
+
+ AuxLocation* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const AuxLocation& from);
+ void MergeFrom(const AuxLocation& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // repeated .pb.Location location = 1;
+ inline int location_size() const;
+ inline void clear_location();
+ static const int kLocationFieldNumber = 1;
+ inline const ::pb::Location& location(int index) const;
+ inline ::pb::Location* mutable_location(int index);
+ inline ::pb::Location* add_location();
+ inline const ::google::protobuf::RepeatedPtrField< ::pb::Location >&
+ location() const;
+ inline ::google::protobuf::RepeatedPtrField< ::pb::Location >*
+ mutable_location();
+
+ // @@protoc_insertion_point(class_scope:pb.AuxLocation)
+ private:
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::google::protobuf::RepeatedPtrField< ::pb::Location > location_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(1 + 31) / 32];
+
+ friend void protobuf_AddDesc_peptides_2eproto();
+ friend void protobuf_AssignDesc_peptides_2eproto();
+ friend void protobuf_ShutdownFile_peptides_2eproto();
+
+ void InitAsDefaultInstance();
+ static AuxLocation* default_instance_;
+};
+// ===================================================================
+
+
+// ===================================================================
+
+// Location
+
+// optional int32 protein_id = 1;
+inline bool Location::has_protein_id() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Location::set_has_protein_id() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Location::clear_has_protein_id() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Location::clear_protein_id() {
+ protein_id_ = 0;
+ clear_has_protein_id();
+}
+inline ::google::protobuf::int32 Location::protein_id() const {
+ return protein_id_;
+}
+inline void Location::set_protein_id(::google::protobuf::int32 value) {
+ set_has_protein_id();
+ protein_id_ = value;
+}
+
+// optional int32 pos = 2;
+inline bool Location::has_pos() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Location::set_has_pos() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Location::clear_has_pos() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Location::clear_pos() {
+ pos_ = 0;
+ clear_has_pos();
+}
+inline ::google::protobuf::int32 Location::pos() const {
+ return pos_;
+}
+inline void Location::set_pos(::google::protobuf::int32 value) {
+ set_has_pos();
+ pos_ = value;
+}
+
+// -------------------------------------------------------------------
+
+// Peptide
+
+// optional int32 id = 1;
+inline bool Peptide::has_id() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Peptide::set_has_id() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Peptide::clear_has_id() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Peptide::clear_id() {
+ id_ = 0;
+ clear_has_id();
+}
+inline ::google::protobuf::int32 Peptide::id() const {
+ return id_;
+}
+inline void Peptide::set_id(::google::protobuf::int32 value) {
+ set_has_id();
+ id_ = value;
+}
+
+// optional double mass = 2;
+inline bool Peptide::has_mass() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Peptide::set_has_mass() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Peptide::clear_has_mass() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Peptide::clear_mass() {
+ mass_ = 0;
+ clear_has_mass();
+}
+inline double Peptide::mass() const {
+ return mass_;
+}
+inline void Peptide::set_mass(double value) {
+ set_has_mass();
+ mass_ = value;
+}
+
+// optional int32 length = 3;
+inline bool Peptide::has_length() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Peptide::set_has_length() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Peptide::clear_has_length() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Peptide::clear_length() {
+ length_ = 0;
+ clear_has_length();
+}
+inline ::google::protobuf::int32 Peptide::length() const {
+ return length_;
+}
+inline void Peptide::set_length(::google::protobuf::int32 value) {
+ set_has_length();
+ length_ = value;
+}
+
+// optional .pb.Location first_location = 4;
+inline bool Peptide::has_first_location() const {
+ return (_has_bits_[0] & 0x00000008u) != 0;
+}
+inline void Peptide::set_has_first_location() {
+ _has_bits_[0] |= 0x00000008u;
+}
+inline void Peptide::clear_has_first_location() {
+ _has_bits_[0] &= ~0x00000008u;
+}
+inline void Peptide::clear_first_location() {
+ if (first_location_ != NULL) first_location_->::pb::Location::Clear();
+ clear_has_first_location();
+}
+inline const ::pb::Location& Peptide::first_location() const {
+ return first_location_ != NULL ? *first_location_ : *default_instance_->first_location_;
+}
+inline ::pb::Location* Peptide::mutable_first_location() {
+ set_has_first_location();
+ if (first_location_ == NULL) first_location_ = new ::pb::Location;
+ return first_location_;
+}
+inline ::pb::Location* Peptide::release_first_location() {
+ clear_has_first_location();
+ ::pb::Location* temp = first_location_;
+ first_location_ = NULL;
+ return temp;
+}
+inline void Peptide::set_allocated_first_location(::pb::Location* first_location) {
+ delete first_location_;
+ first_location_ = first_location;
+ if (first_location) {
+ set_has_first_location();
+ } else {
+ clear_has_first_location();
+ }
+}
+
+// repeated int32 peak1 = 5 [packed = true];
+inline int Peptide::peak1_size() const {
+ return peak1_.size();
+}
+inline void Peptide::clear_peak1() {
+ peak1_.Clear();
+}
+inline ::google::protobuf::int32 Peptide::peak1(int index) const {
+ return peak1_.Get(index);
+}
+inline void Peptide::set_peak1(int index, ::google::protobuf::int32 value) {
+ peak1_.Set(index, value);
+}
+inline void Peptide::add_peak1(::google::protobuf::int32 value) {
+ peak1_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+Peptide::peak1() const {
+ return peak1_;
+}
+inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+Peptide::mutable_peak1() {
+ return &peak1_;
+}
+
+// repeated int32 peak2 = 6 [packed = true];
+inline int Peptide::peak2_size() const {
+ return peak2_.size();
+}
+inline void Peptide::clear_peak2() {
+ peak2_.Clear();
+}
+inline ::google::protobuf::int32 Peptide::peak2(int index) const {
+ return peak2_.Get(index);
+}
+inline void Peptide::set_peak2(int index, ::google::protobuf::int32 value) {
+ peak2_.Set(index, value);
+}
+inline void Peptide::add_peak2(::google::protobuf::int32 value) {
+ peak2_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+Peptide::peak2() const {
+ return peak2_;
+}
+inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+Peptide::mutable_peak2() {
+ return &peak2_;
+}
+
+// repeated int32 neg_peak1 = 7 [packed = true];
+inline int Peptide::neg_peak1_size() const {
+ return neg_peak1_.size();
+}
+inline void Peptide::clear_neg_peak1() {
+ neg_peak1_.Clear();
+}
+inline ::google::protobuf::int32 Peptide::neg_peak1(int index) const {
+ return neg_peak1_.Get(index);
+}
+inline void Peptide::set_neg_peak1(int index, ::google::protobuf::int32 value) {
+ neg_peak1_.Set(index, value);
+}
+inline void Peptide::add_neg_peak1(::google::protobuf::int32 value) {
+ neg_peak1_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+Peptide::neg_peak1() const {
+ return neg_peak1_;
+}
+inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+Peptide::mutable_neg_peak1() {
+ return &neg_peak1_;
+}
+
+// repeated int32 neg_peak2 = 8 [packed = true];
+inline int Peptide::neg_peak2_size() const {
+ return neg_peak2_.size();
+}
+inline void Peptide::clear_neg_peak2() {
+ neg_peak2_.Clear();
+}
+inline ::google::protobuf::int32 Peptide::neg_peak2(int index) const {
+ return neg_peak2_.Get(index);
+}
+inline void Peptide::set_neg_peak2(int index, ::google::protobuf::int32 value) {
+ neg_peak2_.Set(index, value);
+}
+inline void Peptide::add_neg_peak2(::google::protobuf::int32 value) {
+ neg_peak2_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+Peptide::neg_peak2() const {
+ return neg_peak2_;
+}
+inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+Peptide::mutable_neg_peak2() {
+ return &neg_peak2_;
+}
+
+// repeated int32 modifications = 9 [packed = true];
+inline int Peptide::modifications_size() const {
+ return modifications_.size();
+}
+inline void Peptide::clear_modifications() {
+ modifications_.Clear();
+}
+inline ::google::protobuf::int32 Peptide::modifications(int index) const {
+ return modifications_.Get(index);
+}
+inline void Peptide::set_modifications(int index, ::google::protobuf::int32 value) {
+ modifications_.Set(index, value);
+}
+inline void Peptide::add_modifications(::google::protobuf::int32 value) {
+ modifications_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+Peptide::modifications() const {
+ return modifications_;
+}
+inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+Peptide::mutable_modifications() {
+ return &modifications_;
+}
+
+// optional int32 aux_locations_index = 10;
+inline bool Peptide::has_aux_locations_index() const {
+ return (_has_bits_[0] & 0x00000200u) != 0;
+}
+inline void Peptide::set_has_aux_locations_index() {
+ _has_bits_[0] |= 0x00000200u;
+}
+inline void Peptide::clear_has_aux_locations_index() {
+ _has_bits_[0] &= ~0x00000200u;
+}
+inline void Peptide::clear_aux_locations_index() {
+ aux_locations_index_ = 0;
+ clear_has_aux_locations_index();
+}
+inline ::google::protobuf::int32 Peptide::aux_locations_index() const {
+ return aux_locations_index_;
+}
+inline void Peptide::set_aux_locations_index(::google::protobuf::int32 value) {
+ set_has_aux_locations_index();
+ aux_locations_index_ = value;
+}
+
+// optional bool is_decoy = 11;
+inline bool Peptide::has_is_decoy() const {
+ return (_has_bits_[0] & 0x00000400u) != 0;
+}
+inline void Peptide::set_has_is_decoy() {
+ _has_bits_[0] |= 0x00000400u;
+}
+inline void Peptide::clear_has_is_decoy() {
+ _has_bits_[0] &= ~0x00000400u;
+}
+inline void Peptide::clear_is_decoy() {
+ is_decoy_ = false;
+ clear_has_is_decoy();
+}
+inline bool Peptide::is_decoy() const {
+ return is_decoy_;
+}
+inline void Peptide::set_is_decoy(bool value) {
+ set_has_is_decoy();
+ is_decoy_ = value;
+}
+
+// -------------------------------------------------------------------
+
+// AuxLocation
+
+// repeated .pb.Location location = 1;
+inline int AuxLocation::location_size() const {
+ return location_.size();
+}
+inline void AuxLocation::clear_location() {
+ location_.Clear();
+}
+inline const ::pb::Location& AuxLocation::location(int index) const {
+ return location_.Get(index);
+}
+inline ::pb::Location* AuxLocation::mutable_location(int index) {
+ return location_.Mutable(index);
+}
+inline ::pb::Location* AuxLocation::add_location() {
+ return location_.Add();
+}
+inline const ::google::protobuf::RepeatedPtrField< ::pb::Location >&
+AuxLocation::location() const {
+ return location_;
+}
+inline ::google::protobuf::RepeatedPtrField< ::pb::Location >*
+AuxLocation::mutable_location() {
+ return &location_;
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+#ifndef SWIG
+namespace google {
+namespace protobuf {
+
+template <>
+inline const EnumDescriptor* GetEnumDescriptor< ::pb::Peptide_Series>() {
+ return ::pb::Peptide_Series_descriptor();
+}
+
+} // namespace google
+} // namespace protobuf
+#endif // SWIG
+
+// @@protoc_insertion_point(global_scope)
+
+#endif // PROTOBUF_peptides_2eproto__INCLUDED
diff --git a/src/app/tide/protoobj/peptides_pb2.py b/src/app/tide/protoobj/peptides_pb2.py
new file mode 100644
index 0000000..c5b236c
--- /dev/null
+++ b/src/app/tide/protoobj/peptides_pb2.py
@@ -0,0 +1,242 @@
+# Generated by the protocol buffer compiler. DO NOT EDIT!
+# source: peptides.proto
+
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import message as _message
+from google.protobuf import reflection as _reflection
+from google.protobuf import descriptor_pb2
+# @@protoc_insertion_point(imports)
+
+
+import raw_proteins_pb2
+
+
+DESCRIPTOR = _descriptor.FileDescriptor(
+ name='peptides.proto',
+ package='pb',
+ serialized_pb='\n\x0epeptides.proto\x12\x02pb\x1a\x12raw_proteins.proto\"+\n\x08Location\x12\x12\n\nprotein_id\x18\x01 \x01(\x05\x12\x0b\n\x03pos\x18\x02 \x01(\x05\"\x8f\x02\n\x07Peptide\x12\n\n\x02id\x18\x01 \x01(\x05\x12\x0c\n\x04mass\x18\x02 \x01(\x01\x12\x0e\n\x06length\x18\x03 \x01(\x05\x12$\n\x0e\x66irst_location\x18\x04 \x01(\x0b\x32\x0c.pb.Location\x12\x11\n\x05peak1\x18\x05 \x03(\x05\x42\x02\x10\x01\x12\x11\n\x05peak2\x18\x06 \x03(\x05\x42\x02\x10\x01\x12\x15\n\tneg_peak1\x18\ [...]
+
+
+
+_PEPTIDE_SERIES = _descriptor.EnumDescriptor(
+ name='Series',
+ full_name='pb.Peptide.Series',
+ filename=None,
+ file=DESCRIPTOR,
+ values=[
+ _descriptor.EnumValueDescriptor(
+ name='Y', index=0, number=0,
+ options=None,
+ type=None),
+ _descriptor.EnumValueDescriptor(
+ name='B', index=1, number=1,
+ options=None,
+ type=None),
+ ],
+ containing_type=None,
+ options=None,
+ serialized_start=337,
+ serialized_end=359,
+)
+
+
+_LOCATION = _descriptor.Descriptor(
+ name='Location',
+ full_name='pb.Location',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='protein_id', full_name='pb.Location.protein_id', index=0,
+ number=1, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='pos', full_name='pb.Location.pos', index=1,
+ number=2, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=42,
+ serialized_end=85,
+)
+
+
+_PEPTIDE = _descriptor.Descriptor(
+ name='Peptide',
+ full_name='pb.Peptide',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='id', full_name='pb.Peptide.id', index=0,
+ number=1, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='mass', full_name='pb.Peptide.mass', index=1,
+ number=2, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='length', full_name='pb.Peptide.length', index=2,
+ number=3, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='first_location', full_name='pb.Peptide.first_location', index=3,
+ number=4, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='peak1', full_name='pb.Peptide.peak1', index=4,
+ number=5, type=5, cpp_type=1, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')),
+ _descriptor.FieldDescriptor(
+ name='peak2', full_name='pb.Peptide.peak2', index=5,
+ number=6, type=5, cpp_type=1, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')),
+ _descriptor.FieldDescriptor(
+ name='neg_peak1', full_name='pb.Peptide.neg_peak1', index=6,
+ number=7, type=5, cpp_type=1, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')),
+ _descriptor.FieldDescriptor(
+ name='neg_peak2', full_name='pb.Peptide.neg_peak2', index=7,
+ number=8, type=5, cpp_type=1, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')),
+ _descriptor.FieldDescriptor(
+ name='modifications', full_name='pb.Peptide.modifications', index=8,
+ number=9, type=5, cpp_type=1, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')),
+ _descriptor.FieldDescriptor(
+ name='aux_locations_index', full_name='pb.Peptide.aux_locations_index', index=9,
+ number=10, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='is_decoy', full_name='pb.Peptide.is_decoy', index=10,
+ number=11, type=8, cpp_type=7, label=1,
+ has_default_value=False, default_value=False,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ _PEPTIDE_SERIES,
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=88,
+ serialized_end=359,
+)
+
+
+_AUXLOCATION = _descriptor.Descriptor(
+ name='AuxLocation',
+ full_name='pb.AuxLocation',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='location', full_name='pb.AuxLocation.location', index=0,
+ number=1, type=11, cpp_type=10, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=361,
+ serialized_end=406,
+)
+
+_PEPTIDE.fields_by_name['first_location'].message_type = _LOCATION
+_PEPTIDE_SERIES.containing_type = _PEPTIDE;
+_AUXLOCATION.fields_by_name['location'].message_type = _LOCATION
+DESCRIPTOR.message_types_by_name['Location'] = _LOCATION
+DESCRIPTOR.message_types_by_name['Peptide'] = _PEPTIDE
+DESCRIPTOR.message_types_by_name['AuxLocation'] = _AUXLOCATION
+
+class Location(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _LOCATION
+
+ # @@protoc_insertion_point(class_scope:pb.Location)
+
+class Peptide(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _PEPTIDE
+
+ # @@protoc_insertion_point(class_scope:pb.Peptide)
+
+class AuxLocation(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _AUXLOCATION
+
+ # @@protoc_insertion_point(class_scope:pb.AuxLocation)
+
+
+DESCRIPTOR.has_options = True
+DESCRIPTOR._options = _descriptor._ParseOptions(descriptor_pb2.FileOptions(), 'H\001')
+_PEPTIDE.fields_by_name['peak1'].has_options = True
+_PEPTIDE.fields_by_name['peak1']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')
+_PEPTIDE.fields_by_name['peak2'].has_options = True
+_PEPTIDE.fields_by_name['peak2']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')
+_PEPTIDE.fields_by_name['neg_peak1'].has_options = True
+_PEPTIDE.fields_by_name['neg_peak1']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')
+_PEPTIDE.fields_by_name['neg_peak2'].has_options = True
+_PEPTIDE.fields_by_name['neg_peak2']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')
+_PEPTIDE.fields_by_name['modifications'].has_options = True
+_PEPTIDE.fields_by_name['modifications']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')
+# @@protoc_insertion_point(module_scope)
diff --git a/src/app/tide/protoobj/raw_proteins.pb.cc b/src/app/tide/protoobj/raw_proteins.pb.cc
new file mode 100644
index 0000000..c864320
--- /dev/null
+++ b/src/app/tide/protoobj/raw_proteins.pb.cc
@@ -0,0 +1,467 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: raw_proteins.proto
+
+#define INTERNAL_SUPPRESS_PROTOBUF_FIELD_DEPRECATION
+#include "raw_proteins.pb.h"
+
+#include <algorithm>
+
+#include <google/protobuf/stubs/common.h>
+#include <google/protobuf/stubs/once.h>
+#include <google/protobuf/io/coded_stream.h>
+#include <google/protobuf/wire_format_lite_inl.h>
+#include <google/protobuf/descriptor.h>
+#include <google/protobuf/generated_message_reflection.h>
+#include <google/protobuf/reflection_ops.h>
+#include <google/protobuf/wire_format.h>
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+namespace {
+
+const ::google::protobuf::Descriptor* Protein_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Protein_reflection_ = NULL;
+
+} // namespace
+
+
+void protobuf_AssignDesc_raw_5fproteins_2eproto() {
+ protobuf_AddDesc_raw_5fproteins_2eproto();
+ const ::google::protobuf::FileDescriptor* file =
+ ::google::protobuf::DescriptorPool::generated_pool()->FindFileByName(
+ "raw_proteins.proto");
+ GOOGLE_CHECK(file != NULL);
+ Protein_descriptor_ = file->message_type(0);
+ static const int Protein_offsets_[4] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Protein, name_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Protein, id_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Protein, residues_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Protein, target_pos_),
+ };
+ Protein_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Protein_descriptor_,
+ Protein::default_instance_,
+ Protein_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Protein, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Protein, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Protein));
+}
+
+namespace {
+
+GOOGLE_PROTOBUF_DECLARE_ONCE(protobuf_AssignDescriptors_once_);
+inline void protobuf_AssignDescriptorsOnce() {
+ ::google::protobuf::GoogleOnceInit(&protobuf_AssignDescriptors_once_,
+ &protobuf_AssignDesc_raw_5fproteins_2eproto);
+}
+
+void protobuf_RegisterTypes(const ::std::string&) {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Protein_descriptor_, &Protein::default_instance());
+}
+
+} // namespace
+
+void protobuf_ShutdownFile_raw_5fproteins_2eproto() {
+ delete Protein::default_instance_;
+ delete Protein_reflection_;
+}
+
+void protobuf_AddDesc_raw_5fproteins_2eproto() {
+ static bool already_here = false;
+ if (already_here) return;
+ already_here = true;
+ GOOGLE_PROTOBUF_VERIFY_VERSION;
+
+ ::google::protobuf::DescriptorPool::InternalAddGeneratedFile(
+ "\n\022raw_proteins.proto\022\002pb\"I\n\007Protein\022\014\n\004n"
+ "ame\030\001 \001(\t\022\n\n\002id\030\002 \001(\005\022\020\n\010residues\030\003 \001(\t\022"
+ "\022\n\ntarget_pos\030\005 \001(\005B\002H\001", 103);
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedFile(
+ "raw_proteins.proto", &protobuf_RegisterTypes);
+ Protein::default_instance_ = new Protein();
+ Protein::default_instance_->InitAsDefaultInstance();
+ ::google::protobuf::internal::OnShutdown(&protobuf_ShutdownFile_raw_5fproteins_2eproto);
+}
+
+// Force AddDescriptors() to be called at static initialization time.
+struct StaticDescriptorInitializer_raw_5fproteins_2eproto {
+ StaticDescriptorInitializer_raw_5fproteins_2eproto() {
+ protobuf_AddDesc_raw_5fproteins_2eproto();
+ }
+} static_descriptor_initializer_raw_5fproteins_2eproto_;
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int Protein::kNameFieldNumber;
+const int Protein::kIdFieldNumber;
+const int Protein::kResiduesFieldNumber;
+const int Protein::kTargetPosFieldNumber;
+#endif // !_MSC_VER
+
+Protein::Protein()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Protein::InitAsDefaultInstance() {
+}
+
+Protein::Protein(const Protein& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Protein::SharedCtor() {
+ _cached_size_ = 0;
+ name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ id_ = 0;
+ residues_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ target_pos_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Protein::~Protein() {
+ SharedDtor();
+}
+
+void Protein::SharedDtor() {
+ if (name_ != &::google::protobuf::internal::kEmptyString) {
+ delete name_;
+ }
+ if (residues_ != &::google::protobuf::internal::kEmptyString) {
+ delete residues_;
+ }
+ if (this != default_instance_) {
+ }
+}
+
+void Protein::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Protein::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Protein_descriptor_;
+}
+
+const Protein& Protein::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_raw_5fproteins_2eproto();
+ return *default_instance_;
+}
+
+Protein* Protein::default_instance_ = NULL;
+
+Protein* Protein::New() const {
+ return new Protein;
+}
+
+void Protein::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (has_name()) {
+ if (name_ != &::google::protobuf::internal::kEmptyString) {
+ name_->clear();
+ }
+ }
+ id_ = 0;
+ if (has_residues()) {
+ if (residues_ != &::google::protobuf::internal::kEmptyString) {
+ residues_->clear();
+ }
+ }
+ target_pos_ = 0;
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Protein::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional string name = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ DO_(::google::protobuf::internal::WireFormatLite::ReadString(
+ input, this->mutable_name()));
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->name().data(), this->name().length(),
+ ::google::protobuf::internal::WireFormat::PARSE);
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(16)) goto parse_id;
+ break;
+ }
+
+ // optional int32 id = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_id:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &id_)));
+ set_has_id();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(26)) goto parse_residues;
+ break;
+ }
+
+ // optional string residues = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_residues:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadString(
+ input, this->mutable_residues()));
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->residues().data(), this->residues().length(),
+ ::google::protobuf::internal::WireFormat::PARSE);
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(40)) goto parse_target_pos;
+ break;
+ }
+
+ // optional int32 target_pos = 5;
+ case 5: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_target_pos:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &target_pos_)));
+ set_has_target_pos();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Protein::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional string name = 1;
+ if (has_name()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->name().data(), this->name().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ ::google::protobuf::internal::WireFormatLite::WriteString(
+ 1, this->name(), output);
+ }
+
+ // optional int32 id = 2;
+ if (has_id()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(2, this->id(), output);
+ }
+
+ // optional string residues = 3;
+ if (has_residues()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->residues().data(), this->residues().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ ::google::protobuf::internal::WireFormatLite::WriteString(
+ 3, this->residues(), output);
+ }
+
+ // optional int32 target_pos = 5;
+ if (has_target_pos()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(5, this->target_pos(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Protein::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional string name = 1;
+ if (has_name()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->name().data(), this->name().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ target =
+ ::google::protobuf::internal::WireFormatLite::WriteStringToArray(
+ 1, this->name(), target);
+ }
+
+ // optional int32 id = 2;
+ if (has_id()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(2, this->id(), target);
+ }
+
+ // optional string residues = 3;
+ if (has_residues()) {
+ ::google::protobuf::internal::WireFormat::VerifyUTF8String(
+ this->residues().data(), this->residues().length(),
+ ::google::protobuf::internal::WireFormat::SERIALIZE);
+ target =
+ ::google::protobuf::internal::WireFormatLite::WriteStringToArray(
+ 3, this->residues(), target);
+ }
+
+ // optional int32 target_pos = 5;
+ if (has_target_pos()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(5, this->target_pos(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Protein::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional string name = 1;
+ if (has_name()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::StringSize(
+ this->name());
+ }
+
+ // optional int32 id = 2;
+ if (has_id()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->id());
+ }
+
+ // optional string residues = 3;
+ if (has_residues()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::StringSize(
+ this->residues());
+ }
+
+ // optional int32 target_pos = 5;
+ if (has_target_pos()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->target_pos());
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Protein::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Protein* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Protein*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Protein::MergeFrom(const Protein& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_name()) {
+ set_name(from.name());
+ }
+ if (from.has_id()) {
+ set_id(from.id());
+ }
+ if (from.has_residues()) {
+ set_residues(from.residues());
+ }
+ if (from.has_target_pos()) {
+ set_target_pos(from.target_pos());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Protein::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Protein::CopyFrom(const Protein& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Protein::IsInitialized() const {
+
+ return true;
+}
+
+void Protein::Swap(Protein* other) {
+ if (other != this) {
+ std::swap(name_, other->name_);
+ std::swap(id_, other->id_);
+ std::swap(residues_, other->residues_);
+ std::swap(target_pos_, other->target_pos_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Protein::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Protein_descriptor_;
+ metadata.reflection = Protein_reflection_;
+ return metadata;
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+// @@protoc_insertion_point(global_scope)
diff --git a/src/app/tide/protoobj/raw_proteins.pb.h b/src/app/tide/protoobj/raw_proteins.pb.h
new file mode 100644
index 0000000..981029b
--- /dev/null
+++ b/src/app/tide/protoobj/raw_proteins.pb.h
@@ -0,0 +1,367 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: raw_proteins.proto
+
+#ifndef PROTOBUF_raw_5fproteins_2eproto__INCLUDED
+#define PROTOBUF_raw_5fproteins_2eproto__INCLUDED
+
+#include <string>
+
+#include <google/protobuf/stubs/common.h>
+
+#if GOOGLE_PROTOBUF_VERSION < 2005000
+#error This file was generated by a newer version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please update
+#error your headers.
+#endif
+#if 2005000 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
+#error This file was generated by an older version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please
+#error regenerate this file with a newer version of protoc.
+#endif
+
+#include <google/protobuf/generated_message_util.h>
+#include <google/protobuf/message.h>
+#include <google/protobuf/repeated_field.h>
+#include <google/protobuf/extension_set.h>
+#include <google/protobuf/unknown_field_set.h>
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+// Internal implementation detail -- do not call these.
+void protobuf_AddDesc_raw_5fproteins_2eproto();
+void protobuf_AssignDesc_raw_5fproteins_2eproto();
+void protobuf_ShutdownFile_raw_5fproteins_2eproto();
+
+class Protein;
+
+// ===================================================================
+
+class Protein : public ::google::protobuf::Message {
+ public:
+ Protein();
+ virtual ~Protein();
+
+ Protein(const Protein& from);
+
+ inline Protein& operator=(const Protein& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Protein& default_instance();
+
+ void Swap(Protein* other);
+
+ // implements Message ----------------------------------------------
+
+ Protein* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Protein& from);
+ void MergeFrom(const Protein& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional string name = 1;
+ inline bool has_name() const;
+ inline void clear_name();
+ static const int kNameFieldNumber = 1;
+ inline const ::std::string& name() const;
+ inline void set_name(const ::std::string& value);
+ inline void set_name(const char* value);
+ inline void set_name(const char* value, size_t size);
+ inline ::std::string* mutable_name();
+ inline ::std::string* release_name();
+ inline void set_allocated_name(::std::string* name);
+
+ // optional int32 id = 2;
+ inline bool has_id() const;
+ inline void clear_id();
+ static const int kIdFieldNumber = 2;
+ inline ::google::protobuf::int32 id() const;
+ inline void set_id(::google::protobuf::int32 value);
+
+ // optional string residues = 3;
+ inline bool has_residues() const;
+ inline void clear_residues();
+ static const int kResiduesFieldNumber = 3;
+ inline const ::std::string& residues() const;
+ inline void set_residues(const ::std::string& value);
+ inline void set_residues(const char* value);
+ inline void set_residues(const char* value, size_t size);
+ inline ::std::string* mutable_residues();
+ inline ::std::string* release_residues();
+ inline void set_allocated_residues(::std::string* residues);
+
+ // optional int32 target_pos = 5;
+ inline bool has_target_pos() const;
+ inline void clear_target_pos();
+ static const int kTargetPosFieldNumber = 5;
+ inline ::google::protobuf::int32 target_pos() const;
+ inline void set_target_pos(::google::protobuf::int32 value);
+
+ // @@protoc_insertion_point(class_scope:pb.Protein)
+ private:
+ inline void set_has_name();
+ inline void clear_has_name();
+ inline void set_has_id();
+ inline void clear_has_id();
+ inline void set_has_residues();
+ inline void clear_has_residues();
+ inline void set_has_target_pos();
+ inline void clear_has_target_pos();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::std::string* name_;
+ ::std::string* residues_;
+ ::google::protobuf::int32 id_;
+ ::google::protobuf::int32 target_pos_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(4 + 31) / 32];
+
+ friend void protobuf_AddDesc_raw_5fproteins_2eproto();
+ friend void protobuf_AssignDesc_raw_5fproteins_2eproto();
+ friend void protobuf_ShutdownFile_raw_5fproteins_2eproto();
+
+ void InitAsDefaultInstance();
+ static Protein* default_instance_;
+};
+// ===================================================================
+
+
+// ===================================================================
+
+// Protein
+
+// optional string name = 1;
+inline bool Protein::has_name() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Protein::set_has_name() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Protein::clear_has_name() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Protein::clear_name() {
+ if (name_ != &::google::protobuf::internal::kEmptyString) {
+ name_->clear();
+ }
+ clear_has_name();
+}
+inline const ::std::string& Protein::name() const {
+ return *name_;
+}
+inline void Protein::set_name(const ::std::string& value) {
+ set_has_name();
+ if (name_ == &::google::protobuf::internal::kEmptyString) {
+ name_ = new ::std::string;
+ }
+ name_->assign(value);
+}
+inline void Protein::set_name(const char* value) {
+ set_has_name();
+ if (name_ == &::google::protobuf::internal::kEmptyString) {
+ name_ = new ::std::string;
+ }
+ name_->assign(value);
+}
+inline void Protein::set_name(const char* value, size_t size) {
+ set_has_name();
+ if (name_ == &::google::protobuf::internal::kEmptyString) {
+ name_ = new ::std::string;
+ }
+ name_->assign(reinterpret_cast<const char*>(value), size);
+}
+inline ::std::string* Protein::mutable_name() {
+ set_has_name();
+ if (name_ == &::google::protobuf::internal::kEmptyString) {
+ name_ = new ::std::string;
+ }
+ return name_;
+}
+inline ::std::string* Protein::release_name() {
+ clear_has_name();
+ if (name_ == &::google::protobuf::internal::kEmptyString) {
+ return NULL;
+ } else {
+ ::std::string* temp = name_;
+ name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ return temp;
+ }
+}
+inline void Protein::set_allocated_name(::std::string* name) {
+ if (name_ != &::google::protobuf::internal::kEmptyString) {
+ delete name_;
+ }
+ if (name) {
+ set_has_name();
+ name_ = name;
+ } else {
+ clear_has_name();
+ name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ }
+}
+
+// optional int32 id = 2;
+inline bool Protein::has_id() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Protein::set_has_id() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Protein::clear_has_id() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Protein::clear_id() {
+ id_ = 0;
+ clear_has_id();
+}
+inline ::google::protobuf::int32 Protein::id() const {
+ return id_;
+}
+inline void Protein::set_id(::google::protobuf::int32 value) {
+ set_has_id();
+ id_ = value;
+}
+
+// optional string residues = 3;
+inline bool Protein::has_residues() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Protein::set_has_residues() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Protein::clear_has_residues() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Protein::clear_residues() {
+ if (residues_ != &::google::protobuf::internal::kEmptyString) {
+ residues_->clear();
+ }
+ clear_has_residues();
+}
+inline const ::std::string& Protein::residues() const {
+ return *residues_;
+}
+inline void Protein::set_residues(const ::std::string& value) {
+ set_has_residues();
+ if (residues_ == &::google::protobuf::internal::kEmptyString) {
+ residues_ = new ::std::string;
+ }
+ residues_->assign(value);
+}
+inline void Protein::set_residues(const char* value) {
+ set_has_residues();
+ if (residues_ == &::google::protobuf::internal::kEmptyString) {
+ residues_ = new ::std::string;
+ }
+ residues_->assign(value);
+}
+inline void Protein::set_residues(const char* value, size_t size) {
+ set_has_residues();
+ if (residues_ == &::google::protobuf::internal::kEmptyString) {
+ residues_ = new ::std::string;
+ }
+ residues_->assign(reinterpret_cast<const char*>(value), size);
+}
+inline ::std::string* Protein::mutable_residues() {
+ set_has_residues();
+ if (residues_ == &::google::protobuf::internal::kEmptyString) {
+ residues_ = new ::std::string;
+ }
+ return residues_;
+}
+inline ::std::string* Protein::release_residues() {
+ clear_has_residues();
+ if (residues_ == &::google::protobuf::internal::kEmptyString) {
+ return NULL;
+ } else {
+ ::std::string* temp = residues_;
+ residues_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ return temp;
+ }
+}
+inline void Protein::set_allocated_residues(::std::string* residues) {
+ if (residues_ != &::google::protobuf::internal::kEmptyString) {
+ delete residues_;
+ }
+ if (residues) {
+ set_has_residues();
+ residues_ = residues;
+ } else {
+ clear_has_residues();
+ residues_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
+ }
+}
+
+// optional int32 target_pos = 5;
+inline bool Protein::has_target_pos() const {
+ return (_has_bits_[0] & 0x00000008u) != 0;
+}
+inline void Protein::set_has_target_pos() {
+ _has_bits_[0] |= 0x00000008u;
+}
+inline void Protein::clear_has_target_pos() {
+ _has_bits_[0] &= ~0x00000008u;
+}
+inline void Protein::clear_target_pos() {
+ target_pos_ = 0;
+ clear_has_target_pos();
+}
+inline ::google::protobuf::int32 Protein::target_pos() const {
+ return target_pos_;
+}
+inline void Protein::set_target_pos(::google::protobuf::int32 value) {
+ set_has_target_pos();
+ target_pos_ = value;
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+#ifndef SWIG
+namespace google {
+namespace protobuf {
+
+
+} // namespace google
+} // namespace protobuf
+#endif // SWIG
+
+// @@protoc_insertion_point(global_scope)
+
+#endif // PROTOBUF_raw_5fproteins_2eproto__INCLUDED
diff --git a/src/app/tide/protoobj/raw_proteins_pb2.py b/src/app/tide/protoobj/raw_proteins_pb2.py
new file mode 100644
index 0000000..f2f07ab
--- /dev/null
+++ b/src/app/tide/protoobj/raw_proteins_pb2.py
@@ -0,0 +1,80 @@
+# Generated by the protocol buffer compiler. DO NOT EDIT!
+# source: raw_proteins.proto
+
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import message as _message
+from google.protobuf import reflection as _reflection
+from google.protobuf import descriptor_pb2
+# @@protoc_insertion_point(imports)
+
+
+
+
+DESCRIPTOR = _descriptor.FileDescriptor(
+ name='raw_proteins.proto',
+ package='pb',
+ serialized_pb='\n\x12raw_proteins.proto\x12\x02pb\"I\n\x07Protein\x12\x0c\n\x04name\x18\x01 \x01(\t\x12\n\n\x02id\x18\x02 \x01(\x05\x12\x10\n\x08residues\x18\x03 \x01(\t\x12\x12\n\ntarget_pos\x18\x05 \x01(\x05\x42\x02H\x01')
+
+
+
+
+_PROTEIN = _descriptor.Descriptor(
+ name='Protein',
+ full_name='pb.Protein',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='name', full_name='pb.Protein.name', index=0,
+ number=1, type=9, cpp_type=9, label=1,
+ has_default_value=False, default_value=unicode("", "utf-8"),
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='id', full_name='pb.Protein.id', index=1,
+ number=2, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='residues', full_name='pb.Protein.residues', index=2,
+ number=3, type=9, cpp_type=9, label=1,
+ has_default_value=False, default_value=unicode("", "utf-8"),
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='target_pos', full_name='pb.Protein.target_pos', index=3,
+ number=5, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=26,
+ serialized_end=99,
+)
+
+DESCRIPTOR.message_types_by_name['Protein'] = _PROTEIN
+
+class Protein(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _PROTEIN
+
+ # @@protoc_insertion_point(class_scope:pb.Protein)
+
+
+DESCRIPTOR.has_options = True
+DESCRIPTOR._options = _descriptor._ParseOptions(descriptor_pb2.FileOptions(), 'H\001')
+# @@protoc_insertion_point(module_scope)
diff --git a/src/app/tide/protoobj/results.pb.cc b/src/app/tide/protoobj/results.pb.cc
new file mode 100644
index 0000000..564bfc4
--- /dev/null
+++ b/src/app/tide/protoobj/results.pb.cc
@@ -0,0 +1,1077 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: results.proto
+
+#define INTERNAL_SUPPRESS_PROTOBUF_FIELD_DEPRECATION
+#include "results.pb.h"
+
+#include <algorithm>
+
+#include <google/protobuf/stubs/common.h>
+#include <google/protobuf/stubs/once.h>
+#include <google/protobuf/io/coded_stream.h>
+#include <google/protobuf/wire_format_lite_inl.h>
+#include <google/protobuf/descriptor.h>
+#include <google/protobuf/generated_message_reflection.h>
+#include <google/protobuf/reflection_ops.h>
+#include <google/protobuf/wire_format.h>
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+namespace {
+
+const ::google::protobuf::Descriptor* Match_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Match_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Stats_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Stats_reflection_ = NULL;
+const ::google::protobuf::Descriptor* Results_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Results_reflection_ = NULL;
+
+} // namespace
+
+
+void protobuf_AssignDesc_results_2eproto() {
+ protobuf_AddDesc_results_2eproto();
+ const ::google::protobuf::FileDescriptor* file =
+ ::google::protobuf::DescriptorPool::generated_pool()->FindFileByName(
+ "results.proto");
+ GOOGLE_CHECK(file != NULL);
+ Match_descriptor_ = file->message_type(0);
+ static const int Match_offsets_[2] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Match, xcorr_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Match, peptide_),
+ };
+ Match_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Match_descriptor_,
+ Match::default_instance_,
+ Match_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Match, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Match, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Match));
+ Stats_descriptor_ = file->message_type(1);
+ static const int Stats_offsets_[3] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Stats, count_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Stats, sum_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Stats, sum_squares_),
+ };
+ Stats_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Stats_descriptor_,
+ Stats::default_instance_,
+ Stats_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Stats, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Stats, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Stats));
+ Results_descriptor_ = file->message_type(2);
+ static const int Results_offsets_[5] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Results, spectrum_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Results, charge_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Results, matches_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Results, spectrum_index_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Results, stats_),
+ };
+ Results_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Results_descriptor_,
+ Results::default_instance_,
+ Results_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Results, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Results, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Results));
+}
+
+namespace {
+
+GOOGLE_PROTOBUF_DECLARE_ONCE(protobuf_AssignDescriptors_once_);
+inline void protobuf_AssignDescriptorsOnce() {
+ ::google::protobuf::GoogleOnceInit(&protobuf_AssignDescriptors_once_,
+ &protobuf_AssignDesc_results_2eproto);
+}
+
+void protobuf_RegisterTypes(const ::std::string&) {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Match_descriptor_, &Match::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Stats_descriptor_, &Stats::default_instance());
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Results_descriptor_, &Results::default_instance());
+}
+
+} // namespace
+
+void protobuf_ShutdownFile_results_2eproto() {
+ delete Match::default_instance_;
+ delete Match_reflection_;
+ delete Stats::default_instance_;
+ delete Stats_reflection_;
+ delete Results::default_instance_;
+ delete Results_reflection_;
+}
+
+void protobuf_AddDesc_results_2eproto() {
+ static bool already_here = false;
+ if (already_here) return;
+ already_here = true;
+ GOOGLE_PROTOBUF_VERIFY_VERSION;
+
+ ::pb::protobuf_AddDesc_peptides_2eproto();
+ ::pb::protobuf_AddDesc_spectrum_2eproto();
+ ::google::protobuf::DescriptorPool::InternalAddGeneratedFile(
+ "\n\rresults.proto\022\002pb\032\016peptides.proto\032\016spe"
+ "ctrum.proto\"4\n\005Match\022\r\n\005xcorr\030\001 \001(\001\022\034\n\007p"
+ "eptide\030\002 \001(\0132\013.pb.Peptide\"8\n\005Stats\022\r\n\005co"
+ "unt\030\001 \001(\005\022\013\n\003sum\030\002 \001(\001\022\023\n\013sum_squares\030\003 "
+ "\001(\001\"\207\001\n\007Results\022\036\n\010spectrum\030\001 \001(\0132\014.pb.S"
+ "pectrum\022\016\n\006charge\030\002 \001(\005\022\032\n\007matches\030\003 \003(\013"
+ "2\t.pb.Match\022\026\n\016spectrum_index\030\004 \001(\005\022\030\n\005s"
+ "tats\030\005 \001(\0132\t.pb.StatsB\002H\001", 305);
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedFile(
+ "results.proto", &protobuf_RegisterTypes);
+ Match::default_instance_ = new Match();
+ Stats::default_instance_ = new Stats();
+ Results::default_instance_ = new Results();
+ Match::default_instance_->InitAsDefaultInstance();
+ Stats::default_instance_->InitAsDefaultInstance();
+ Results::default_instance_->InitAsDefaultInstance();
+ ::google::protobuf::internal::OnShutdown(&protobuf_ShutdownFile_results_2eproto);
+}
+
+// Force AddDescriptors() to be called at static initialization time.
+struct StaticDescriptorInitializer_results_2eproto {
+ StaticDescriptorInitializer_results_2eproto() {
+ protobuf_AddDesc_results_2eproto();
+ }
+} static_descriptor_initializer_results_2eproto_;
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int Match::kXcorrFieldNumber;
+const int Match::kPeptideFieldNumber;
+#endif // !_MSC_VER
+
+Match::Match()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Match::InitAsDefaultInstance() {
+ peptide_ = const_cast< ::pb::Peptide*>(&::pb::Peptide::default_instance());
+}
+
+Match::Match(const Match& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Match::SharedCtor() {
+ _cached_size_ = 0;
+ xcorr_ = 0;
+ peptide_ = NULL;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Match::~Match() {
+ SharedDtor();
+}
+
+void Match::SharedDtor() {
+ if (this != default_instance_) {
+ delete peptide_;
+ }
+}
+
+void Match::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Match::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Match_descriptor_;
+}
+
+const Match& Match::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_results_2eproto();
+ return *default_instance_;
+}
+
+Match* Match::default_instance_ = NULL;
+
+Match* Match::New() const {
+ return new Match;
+}
+
+void Match::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ xcorr_ = 0;
+ if (has_peptide()) {
+ if (peptide_ != NULL) peptide_->::pb::Peptide::Clear();
+ }
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Match::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional double xcorr = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &xcorr_)));
+ set_has_xcorr();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(18)) goto parse_peptide;
+ break;
+ }
+
+ // optional .pb.Peptide peptide = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_peptide:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_peptide()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Match::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional double xcorr = 1;
+ if (has_xcorr()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(1, this->xcorr(), output);
+ }
+
+ // optional .pb.Peptide peptide = 2;
+ if (has_peptide()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 2, this->peptide(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Match::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional double xcorr = 1;
+ if (has_xcorr()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(1, this->xcorr(), target);
+ }
+
+ // optional .pb.Peptide peptide = 2;
+ if (has_peptide()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 2, this->peptide(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Match::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional double xcorr = 1;
+ if (has_xcorr()) {
+ total_size += 1 + 8;
+ }
+
+ // optional .pb.Peptide peptide = 2;
+ if (has_peptide()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->peptide());
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Match::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Match* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Match*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Match::MergeFrom(const Match& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_xcorr()) {
+ set_xcorr(from.xcorr());
+ }
+ if (from.has_peptide()) {
+ mutable_peptide()->::pb::Peptide::MergeFrom(from.peptide());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Match::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Match::CopyFrom(const Match& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Match::IsInitialized() const {
+
+ return true;
+}
+
+void Match::Swap(Match* other) {
+ if (other != this) {
+ std::swap(xcorr_, other->xcorr_);
+ std::swap(peptide_, other->peptide_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Match::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Match_descriptor_;
+ metadata.reflection = Match_reflection_;
+ return metadata;
+}
+
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int Stats::kCountFieldNumber;
+const int Stats::kSumFieldNumber;
+const int Stats::kSumSquaresFieldNumber;
+#endif // !_MSC_VER
+
+Stats::Stats()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Stats::InitAsDefaultInstance() {
+}
+
+Stats::Stats(const Stats& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Stats::SharedCtor() {
+ _cached_size_ = 0;
+ count_ = 0;
+ sum_ = 0;
+ sum_squares_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Stats::~Stats() {
+ SharedDtor();
+}
+
+void Stats::SharedDtor() {
+ if (this != default_instance_) {
+ }
+}
+
+void Stats::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Stats::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Stats_descriptor_;
+}
+
+const Stats& Stats::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_results_2eproto();
+ return *default_instance_;
+}
+
+Stats* Stats::default_instance_ = NULL;
+
+Stats* Stats::New() const {
+ return new Stats;
+}
+
+void Stats::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ count_ = 0;
+ sum_ = 0;
+ sum_squares_ = 0;
+ }
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Stats::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional int32 count = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &count_)));
+ set_has_count();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(17)) goto parse_sum;
+ break;
+ }
+
+ // optional double sum = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_sum:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &sum_)));
+ set_has_sum();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(25)) goto parse_sum_squares;
+ break;
+ }
+
+ // optional double sum_squares = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_sum_squares:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &sum_squares_)));
+ set_has_sum_squares();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Stats::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional int32 count = 1;
+ if (has_count()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(1, this->count(), output);
+ }
+
+ // optional double sum = 2;
+ if (has_sum()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(2, this->sum(), output);
+ }
+
+ // optional double sum_squares = 3;
+ if (has_sum_squares()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(3, this->sum_squares(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Stats::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional int32 count = 1;
+ if (has_count()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(1, this->count(), target);
+ }
+
+ // optional double sum = 2;
+ if (has_sum()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(2, this->sum(), target);
+ }
+
+ // optional double sum_squares = 3;
+ if (has_sum_squares()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(3, this->sum_squares(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Stats::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional int32 count = 1;
+ if (has_count()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->count());
+ }
+
+ // optional double sum = 2;
+ if (has_sum()) {
+ total_size += 1 + 8;
+ }
+
+ // optional double sum_squares = 3;
+ if (has_sum_squares()) {
+ total_size += 1 + 8;
+ }
+
+ }
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Stats::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Stats* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Stats*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Stats::MergeFrom(const Stats& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_count()) {
+ set_count(from.count());
+ }
+ if (from.has_sum()) {
+ set_sum(from.sum());
+ }
+ if (from.has_sum_squares()) {
+ set_sum_squares(from.sum_squares());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Stats::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Stats::CopyFrom(const Stats& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Stats::IsInitialized() const {
+
+ return true;
+}
+
+void Stats::Swap(Stats* other) {
+ if (other != this) {
+ std::swap(count_, other->count_);
+ std::swap(sum_, other->sum_);
+ std::swap(sum_squares_, other->sum_squares_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Stats::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Stats_descriptor_;
+ metadata.reflection = Stats_reflection_;
+ return metadata;
+}
+
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int Results::kSpectrumFieldNumber;
+const int Results::kChargeFieldNumber;
+const int Results::kMatchesFieldNumber;
+const int Results::kSpectrumIndexFieldNumber;
+const int Results::kStatsFieldNumber;
+#endif // !_MSC_VER
+
+Results::Results()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Results::InitAsDefaultInstance() {
+ spectrum_ = const_cast< ::pb::Spectrum*>(&::pb::Spectrum::default_instance());
+ stats_ = const_cast< ::pb::Stats*>(&::pb::Stats::default_instance());
+}
+
+Results::Results(const Results& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Results::SharedCtor() {
+ _cached_size_ = 0;
+ spectrum_ = NULL;
+ charge_ = 0;
+ spectrum_index_ = 0;
+ stats_ = NULL;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Results::~Results() {
+ SharedDtor();
+}
+
+void Results::SharedDtor() {
+ if (this != default_instance_) {
+ delete spectrum_;
+ delete stats_;
+ }
+}
+
+void Results::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Results::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Results_descriptor_;
+}
+
+const Results& Results::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_results_2eproto();
+ return *default_instance_;
+}
+
+Results* Results::default_instance_ = NULL;
+
+Results* Results::New() const {
+ return new Results;
+}
+
+void Results::Clear() {
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (has_spectrum()) {
+ if (spectrum_ != NULL) spectrum_->::pb::Spectrum::Clear();
+ }
+ charge_ = 0;
+ spectrum_index_ = 0;
+ if (has_stats()) {
+ if (stats_ != NULL) stats_->::pb::Stats::Clear();
+ }
+ }
+ matches_.Clear();
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Results::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // optional .pb.Spectrum spectrum = 1;
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_spectrum()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(16)) goto parse_charge;
+ break;
+ }
+
+ // optional int32 charge = 2;
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_charge:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &charge_)));
+ set_has_charge();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(26)) goto parse_matches;
+ break;
+ }
+
+ // repeated .pb.Match matches = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_matches:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, add_matches()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(26)) goto parse_matches;
+ if (input->ExpectTag(32)) goto parse_spectrum_index;
+ break;
+ }
+
+ // optional int32 spectrum_index = 4;
+ case 4: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_spectrum_index:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &spectrum_index_)));
+ set_has_spectrum_index();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(42)) goto parse_stats;
+ break;
+ }
+
+ // optional .pb.Stats stats = 5;
+ case 5: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_stats:
+ DO_(::google::protobuf::internal::WireFormatLite::ReadMessageNoVirtual(
+ input, mutable_stats()));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Results::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // optional .pb.Spectrum spectrum = 1;
+ if (has_spectrum()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 1, this->spectrum(), output);
+ }
+
+ // optional int32 charge = 2;
+ if (has_charge()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(2, this->charge(), output);
+ }
+
+ // repeated .pb.Match matches = 3;
+ for (int i = 0; i < this->matches_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 3, this->matches(i), output);
+ }
+
+ // optional int32 spectrum_index = 4;
+ if (has_spectrum_index()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(4, this->spectrum_index(), output);
+ }
+
+ // optional .pb.Stats stats = 5;
+ if (has_stats()) {
+ ::google::protobuf::internal::WireFormatLite::WriteMessageMaybeToArray(
+ 5, this->stats(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Results::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // optional .pb.Spectrum spectrum = 1;
+ if (has_spectrum()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 1, this->spectrum(), target);
+ }
+
+ // optional int32 charge = 2;
+ if (has_charge()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(2, this->charge(), target);
+ }
+
+ // repeated .pb.Match matches = 3;
+ for (int i = 0; i < this->matches_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 3, this->matches(i), target);
+ }
+
+ // optional int32 spectrum_index = 4;
+ if (has_spectrum_index()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(4, this->spectrum_index(), target);
+ }
+
+ // optional .pb.Stats stats = 5;
+ if (has_stats()) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteMessageNoVirtualToArray(
+ 5, this->stats(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Results::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ // optional .pb.Spectrum spectrum = 1;
+ if (has_spectrum()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->spectrum());
+ }
+
+ // optional int32 charge = 2;
+ if (has_charge()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->charge());
+ }
+
+ // optional int32 spectrum_index = 4;
+ if (has_spectrum_index()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->spectrum_index());
+ }
+
+ // optional .pb.Stats stats = 5;
+ if (has_stats()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->stats());
+ }
+
+ }
+ // repeated .pb.Match matches = 3;
+ total_size += 1 * this->matches_size();
+ for (int i = 0; i < this->matches_size(); i++) {
+ total_size +=
+ ::google::protobuf::internal::WireFormatLite::MessageSizeNoVirtual(
+ this->matches(i));
+ }
+
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Results::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Results* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Results*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Results::MergeFrom(const Results& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ matches_.MergeFrom(from.matches_);
+ if (from._has_bits_[0 / 32] & (0xffu << (0 % 32))) {
+ if (from.has_spectrum()) {
+ mutable_spectrum()->::pb::Spectrum::MergeFrom(from.spectrum());
+ }
+ if (from.has_charge()) {
+ set_charge(from.charge());
+ }
+ if (from.has_spectrum_index()) {
+ set_spectrum_index(from.spectrum_index());
+ }
+ if (from.has_stats()) {
+ mutable_stats()->::pb::Stats::MergeFrom(from.stats());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Results::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Results::CopyFrom(const Results& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Results::IsInitialized() const {
+
+ return true;
+}
+
+void Results::Swap(Results* other) {
+ if (other != this) {
+ std::swap(spectrum_, other->spectrum_);
+ std::swap(charge_, other->charge_);
+ matches_.Swap(&other->matches_);
+ std::swap(spectrum_index_, other->spectrum_index_);
+ std::swap(stats_, other->stats_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Results::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Results_descriptor_;
+ metadata.reflection = Results_reflection_;
+ return metadata;
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+// @@protoc_insertion_point(global_scope)
diff --git a/src/app/tide/protoobj/results.pb.h b/src/app/tide/protoobj/results.pb.h
new file mode 100644
index 0000000..f12d368
--- /dev/null
+++ b/src/app/tide/protoobj/results.pb.h
@@ -0,0 +1,669 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: results.proto
+
+#ifndef PROTOBUF_results_2eproto__INCLUDED
+#define PROTOBUF_results_2eproto__INCLUDED
+
+#include <string>
+
+#include <google/protobuf/stubs/common.h>
+
+#if GOOGLE_PROTOBUF_VERSION < 2005000
+#error This file was generated by a newer version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please update
+#error your headers.
+#endif
+#if 2005000 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
+#error This file was generated by an older version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please
+#error regenerate this file with a newer version of protoc.
+#endif
+
+#include <google/protobuf/generated_message_util.h>
+#include <google/protobuf/message.h>
+#include <google/protobuf/repeated_field.h>
+#include <google/protobuf/extension_set.h>
+#include <google/protobuf/unknown_field_set.h>
+#include "peptides.pb.h"
+#include "spectrum.pb.h"
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+// Internal implementation detail -- do not call these.
+void protobuf_AddDesc_results_2eproto();
+void protobuf_AssignDesc_results_2eproto();
+void protobuf_ShutdownFile_results_2eproto();
+
+class Match;
+class Stats;
+class Results;
+
+// ===================================================================
+
+class Match : public ::google::protobuf::Message {
+ public:
+ Match();
+ virtual ~Match();
+
+ Match(const Match& from);
+
+ inline Match& operator=(const Match& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Match& default_instance();
+
+ void Swap(Match* other);
+
+ // implements Message ----------------------------------------------
+
+ Match* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Match& from);
+ void MergeFrom(const Match& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional double xcorr = 1;
+ inline bool has_xcorr() const;
+ inline void clear_xcorr();
+ static const int kXcorrFieldNumber = 1;
+ inline double xcorr() const;
+ inline void set_xcorr(double value);
+
+ // optional .pb.Peptide peptide = 2;
+ inline bool has_peptide() const;
+ inline void clear_peptide();
+ static const int kPeptideFieldNumber = 2;
+ inline const ::pb::Peptide& peptide() const;
+ inline ::pb::Peptide* mutable_peptide();
+ inline ::pb::Peptide* release_peptide();
+ inline void set_allocated_peptide(::pb::Peptide* peptide);
+
+ // @@protoc_insertion_point(class_scope:pb.Match)
+ private:
+ inline void set_has_xcorr();
+ inline void clear_has_xcorr();
+ inline void set_has_peptide();
+ inline void clear_has_peptide();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ double xcorr_;
+ ::pb::Peptide* peptide_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(2 + 31) / 32];
+
+ friend void protobuf_AddDesc_results_2eproto();
+ friend void protobuf_AssignDesc_results_2eproto();
+ friend void protobuf_ShutdownFile_results_2eproto();
+
+ void InitAsDefaultInstance();
+ static Match* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Stats : public ::google::protobuf::Message {
+ public:
+ Stats();
+ virtual ~Stats();
+
+ Stats(const Stats& from);
+
+ inline Stats& operator=(const Stats& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Stats& default_instance();
+
+ void Swap(Stats* other);
+
+ // implements Message ----------------------------------------------
+
+ Stats* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Stats& from);
+ void MergeFrom(const Stats& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional int32 count = 1;
+ inline bool has_count() const;
+ inline void clear_count();
+ static const int kCountFieldNumber = 1;
+ inline ::google::protobuf::int32 count() const;
+ inline void set_count(::google::protobuf::int32 value);
+
+ // optional double sum = 2;
+ inline bool has_sum() const;
+ inline void clear_sum();
+ static const int kSumFieldNumber = 2;
+ inline double sum() const;
+ inline void set_sum(double value);
+
+ // optional double sum_squares = 3;
+ inline bool has_sum_squares() const;
+ inline void clear_sum_squares();
+ static const int kSumSquaresFieldNumber = 3;
+ inline double sum_squares() const;
+ inline void set_sum_squares(double value);
+
+ // @@protoc_insertion_point(class_scope:pb.Stats)
+ private:
+ inline void set_has_count();
+ inline void clear_has_count();
+ inline void set_has_sum();
+ inline void clear_has_sum();
+ inline void set_has_sum_squares();
+ inline void clear_has_sum_squares();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ double sum_;
+ double sum_squares_;
+ ::google::protobuf::int32 count_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(3 + 31) / 32];
+
+ friend void protobuf_AddDesc_results_2eproto();
+ friend void protobuf_AssignDesc_results_2eproto();
+ friend void protobuf_ShutdownFile_results_2eproto();
+
+ void InitAsDefaultInstance();
+ static Stats* default_instance_;
+};
+// -------------------------------------------------------------------
+
+class Results : public ::google::protobuf::Message {
+ public:
+ Results();
+ virtual ~Results();
+
+ Results(const Results& from);
+
+ inline Results& operator=(const Results& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Results& default_instance();
+
+ void Swap(Results* other);
+
+ // implements Message ----------------------------------------------
+
+ Results* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Results& from);
+ void MergeFrom(const Results& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // optional .pb.Spectrum spectrum = 1;
+ inline bool has_spectrum() const;
+ inline void clear_spectrum();
+ static const int kSpectrumFieldNumber = 1;
+ inline const ::pb::Spectrum& spectrum() const;
+ inline ::pb::Spectrum* mutable_spectrum();
+ inline ::pb::Spectrum* release_spectrum();
+ inline void set_allocated_spectrum(::pb::Spectrum* spectrum);
+
+ // optional int32 charge = 2;
+ inline bool has_charge() const;
+ inline void clear_charge();
+ static const int kChargeFieldNumber = 2;
+ inline ::google::protobuf::int32 charge() const;
+ inline void set_charge(::google::protobuf::int32 value);
+
+ // repeated .pb.Match matches = 3;
+ inline int matches_size() const;
+ inline void clear_matches();
+ static const int kMatchesFieldNumber = 3;
+ inline const ::pb::Match& matches(int index) const;
+ inline ::pb::Match* mutable_matches(int index);
+ inline ::pb::Match* add_matches();
+ inline const ::google::protobuf::RepeatedPtrField< ::pb::Match >&
+ matches() const;
+ inline ::google::protobuf::RepeatedPtrField< ::pb::Match >*
+ mutable_matches();
+
+ // optional int32 spectrum_index = 4;
+ inline bool has_spectrum_index() const;
+ inline void clear_spectrum_index();
+ static const int kSpectrumIndexFieldNumber = 4;
+ inline ::google::protobuf::int32 spectrum_index() const;
+ inline void set_spectrum_index(::google::protobuf::int32 value);
+
+ // optional .pb.Stats stats = 5;
+ inline bool has_stats() const;
+ inline void clear_stats();
+ static const int kStatsFieldNumber = 5;
+ inline const ::pb::Stats& stats() const;
+ inline ::pb::Stats* mutable_stats();
+ inline ::pb::Stats* release_stats();
+ inline void set_allocated_stats(::pb::Stats* stats);
+
+ // @@protoc_insertion_point(class_scope:pb.Results)
+ private:
+ inline void set_has_spectrum();
+ inline void clear_has_spectrum();
+ inline void set_has_charge();
+ inline void clear_has_charge();
+ inline void set_has_spectrum_index();
+ inline void clear_has_spectrum_index();
+ inline void set_has_stats();
+ inline void clear_has_stats();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::pb::Spectrum* spectrum_;
+ ::google::protobuf::RepeatedPtrField< ::pb::Match > matches_;
+ ::google::protobuf::int32 charge_;
+ ::google::protobuf::int32 spectrum_index_;
+ ::pb::Stats* stats_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(5 + 31) / 32];
+
+ friend void protobuf_AddDesc_results_2eproto();
+ friend void protobuf_AssignDesc_results_2eproto();
+ friend void protobuf_ShutdownFile_results_2eproto();
+
+ void InitAsDefaultInstance();
+ static Results* default_instance_;
+};
+// ===================================================================
+
+
+// ===================================================================
+
+// Match
+
+// optional double xcorr = 1;
+inline bool Match::has_xcorr() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Match::set_has_xcorr() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Match::clear_has_xcorr() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Match::clear_xcorr() {
+ xcorr_ = 0;
+ clear_has_xcorr();
+}
+inline double Match::xcorr() const {
+ return xcorr_;
+}
+inline void Match::set_xcorr(double value) {
+ set_has_xcorr();
+ xcorr_ = value;
+}
+
+// optional .pb.Peptide peptide = 2;
+inline bool Match::has_peptide() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Match::set_has_peptide() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Match::clear_has_peptide() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Match::clear_peptide() {
+ if (peptide_ != NULL) peptide_->::pb::Peptide::Clear();
+ clear_has_peptide();
+}
+inline const ::pb::Peptide& Match::peptide() const {
+ return peptide_ != NULL ? *peptide_ : *default_instance_->peptide_;
+}
+inline ::pb::Peptide* Match::mutable_peptide() {
+ set_has_peptide();
+ if (peptide_ == NULL) peptide_ = new ::pb::Peptide;
+ return peptide_;
+}
+inline ::pb::Peptide* Match::release_peptide() {
+ clear_has_peptide();
+ ::pb::Peptide* temp = peptide_;
+ peptide_ = NULL;
+ return temp;
+}
+inline void Match::set_allocated_peptide(::pb::Peptide* peptide) {
+ delete peptide_;
+ peptide_ = peptide;
+ if (peptide) {
+ set_has_peptide();
+ } else {
+ clear_has_peptide();
+ }
+}
+
+// -------------------------------------------------------------------
+
+// Stats
+
+// optional int32 count = 1;
+inline bool Stats::has_count() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Stats::set_has_count() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Stats::clear_has_count() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Stats::clear_count() {
+ count_ = 0;
+ clear_has_count();
+}
+inline ::google::protobuf::int32 Stats::count() const {
+ return count_;
+}
+inline void Stats::set_count(::google::protobuf::int32 value) {
+ set_has_count();
+ count_ = value;
+}
+
+// optional double sum = 2;
+inline bool Stats::has_sum() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Stats::set_has_sum() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Stats::clear_has_sum() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Stats::clear_sum() {
+ sum_ = 0;
+ clear_has_sum();
+}
+inline double Stats::sum() const {
+ return sum_;
+}
+inline void Stats::set_sum(double value) {
+ set_has_sum();
+ sum_ = value;
+}
+
+// optional double sum_squares = 3;
+inline bool Stats::has_sum_squares() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Stats::set_has_sum_squares() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Stats::clear_has_sum_squares() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Stats::clear_sum_squares() {
+ sum_squares_ = 0;
+ clear_has_sum_squares();
+}
+inline double Stats::sum_squares() const {
+ return sum_squares_;
+}
+inline void Stats::set_sum_squares(double value) {
+ set_has_sum_squares();
+ sum_squares_ = value;
+}
+
+// -------------------------------------------------------------------
+
+// Results
+
+// optional .pb.Spectrum spectrum = 1;
+inline bool Results::has_spectrum() const {
+ return (_has_bits_[0] & 0x00000001u) != 0;
+}
+inline void Results::set_has_spectrum() {
+ _has_bits_[0] |= 0x00000001u;
+}
+inline void Results::clear_has_spectrum() {
+ _has_bits_[0] &= ~0x00000001u;
+}
+inline void Results::clear_spectrum() {
+ if (spectrum_ != NULL) spectrum_->::pb::Spectrum::Clear();
+ clear_has_spectrum();
+}
+inline const ::pb::Spectrum& Results::spectrum() const {
+ return spectrum_ != NULL ? *spectrum_ : *default_instance_->spectrum_;
+}
+inline ::pb::Spectrum* Results::mutable_spectrum() {
+ set_has_spectrum();
+ if (spectrum_ == NULL) spectrum_ = new ::pb::Spectrum;
+ return spectrum_;
+}
+inline ::pb::Spectrum* Results::release_spectrum() {
+ clear_has_spectrum();
+ ::pb::Spectrum* temp = spectrum_;
+ spectrum_ = NULL;
+ return temp;
+}
+inline void Results::set_allocated_spectrum(::pb::Spectrum* spectrum) {
+ delete spectrum_;
+ spectrum_ = spectrum;
+ if (spectrum) {
+ set_has_spectrum();
+ } else {
+ clear_has_spectrum();
+ }
+}
+
+// optional int32 charge = 2;
+inline bool Results::has_charge() const {
+ return (_has_bits_[0] & 0x00000002u) != 0;
+}
+inline void Results::set_has_charge() {
+ _has_bits_[0] |= 0x00000002u;
+}
+inline void Results::clear_has_charge() {
+ _has_bits_[0] &= ~0x00000002u;
+}
+inline void Results::clear_charge() {
+ charge_ = 0;
+ clear_has_charge();
+}
+inline ::google::protobuf::int32 Results::charge() const {
+ return charge_;
+}
+inline void Results::set_charge(::google::protobuf::int32 value) {
+ set_has_charge();
+ charge_ = value;
+}
+
+// repeated .pb.Match matches = 3;
+inline int Results::matches_size() const {
+ return matches_.size();
+}
+inline void Results::clear_matches() {
+ matches_.Clear();
+}
+inline const ::pb::Match& Results::matches(int index) const {
+ return matches_.Get(index);
+}
+inline ::pb::Match* Results::mutable_matches(int index) {
+ return matches_.Mutable(index);
+}
+inline ::pb::Match* Results::add_matches() {
+ return matches_.Add();
+}
+inline const ::google::protobuf::RepeatedPtrField< ::pb::Match >&
+Results::matches() const {
+ return matches_;
+}
+inline ::google::protobuf::RepeatedPtrField< ::pb::Match >*
+Results::mutable_matches() {
+ return &matches_;
+}
+
+// optional int32 spectrum_index = 4;
+inline bool Results::has_spectrum_index() const {
+ return (_has_bits_[0] & 0x00000008u) != 0;
+}
+inline void Results::set_has_spectrum_index() {
+ _has_bits_[0] |= 0x00000008u;
+}
+inline void Results::clear_has_spectrum_index() {
+ _has_bits_[0] &= ~0x00000008u;
+}
+inline void Results::clear_spectrum_index() {
+ spectrum_index_ = 0;
+ clear_has_spectrum_index();
+}
+inline ::google::protobuf::int32 Results::spectrum_index() const {
+ return spectrum_index_;
+}
+inline void Results::set_spectrum_index(::google::protobuf::int32 value) {
+ set_has_spectrum_index();
+ spectrum_index_ = value;
+}
+
+// optional .pb.Stats stats = 5;
+inline bool Results::has_stats() const {
+ return (_has_bits_[0] & 0x00000010u) != 0;
+}
+inline void Results::set_has_stats() {
+ _has_bits_[0] |= 0x00000010u;
+}
+inline void Results::clear_has_stats() {
+ _has_bits_[0] &= ~0x00000010u;
+}
+inline void Results::clear_stats() {
+ if (stats_ != NULL) stats_->::pb::Stats::Clear();
+ clear_has_stats();
+}
+inline const ::pb::Stats& Results::stats() const {
+ return stats_ != NULL ? *stats_ : *default_instance_->stats_;
+}
+inline ::pb::Stats* Results::mutable_stats() {
+ set_has_stats();
+ if (stats_ == NULL) stats_ = new ::pb::Stats;
+ return stats_;
+}
+inline ::pb::Stats* Results::release_stats() {
+ clear_has_stats();
+ ::pb::Stats* temp = stats_;
+ stats_ = NULL;
+ return temp;
+}
+inline void Results::set_allocated_stats(::pb::Stats* stats) {
+ delete stats_;
+ stats_ = stats;
+ if (stats) {
+ set_has_stats();
+ } else {
+ clear_has_stats();
+ }
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+#ifndef SWIG
+namespace google {
+namespace protobuf {
+
+
+} // namespace google
+} // namespace protobuf
+#endif // SWIG
+
+// @@protoc_insertion_point(global_scope)
+
+#endif // PROTOBUF_results_2eproto__INCLUDED
diff --git a/src/app/tide/protoobj/results_pb2.py b/src/app/tide/protoobj/results_pb2.py
new file mode 100644
index 0000000..60f4ecb
--- /dev/null
+++ b/src/app/tide/protoobj/results_pb2.py
@@ -0,0 +1,184 @@
+# Generated by the protocol buffer compiler. DO NOT EDIT!
+# source: results.proto
+
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import message as _message
+from google.protobuf import reflection as _reflection
+from google.protobuf import descriptor_pb2
+# @@protoc_insertion_point(imports)
+
+
+import peptides_pb2
+import spectrum_pb2
+
+
+DESCRIPTOR = _descriptor.FileDescriptor(
+ name='results.proto',
+ package='pb',
+ serialized_pb='\n\rresults.proto\x12\x02pb\x1a\x0epeptides.proto\x1a\x0espectrum.proto\"4\n\x05Match\x12\r\n\x05xcorr\x18\x01 \x01(\x01\x12\x1c\n\x07peptide\x18\x02 \x01(\x0b\x32\x0b.pb.Peptide\"8\n\x05Stats\x12\r\n\x05\x63ount\x18\x01 \x01(\x05\x12\x0b\n\x03sum\x18\x02 \x01(\x01\x12\x13\n\x0bsum_squares\x18\x03 \x01(\x01\"\x87\x01\n\x07Results\x12\x1e\n\x08spectrum\x18\x01 \x01(\x0b\x32\x0c.pb.Spectrum\x12\x0e\n\x06\x63harge\x18\x02 \x01(\x05\x12\x1a\n\x07matches\x18\x03 \x03(\x0b\x32 [...]
+
+
+
+
+_MATCH = _descriptor.Descriptor(
+ name='Match',
+ full_name='pb.Match',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='xcorr', full_name='pb.Match.xcorr', index=0,
+ number=1, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='peptide', full_name='pb.Match.peptide', index=1,
+ number=2, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=53,
+ serialized_end=105,
+)
+
+
+_STATS = _descriptor.Descriptor(
+ name='Stats',
+ full_name='pb.Stats',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='count', full_name='pb.Stats.count', index=0,
+ number=1, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='sum', full_name='pb.Stats.sum', index=1,
+ number=2, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='sum_squares', full_name='pb.Stats.sum_squares', index=2,
+ number=3, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=107,
+ serialized_end=163,
+)
+
+
+_RESULTS = _descriptor.Descriptor(
+ name='Results',
+ full_name='pb.Results',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='spectrum', full_name='pb.Results.spectrum', index=0,
+ number=1, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='charge', full_name='pb.Results.charge', index=1,
+ number=2, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='matches', full_name='pb.Results.matches', index=2,
+ number=3, type=11, cpp_type=10, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='spectrum_index', full_name='pb.Results.spectrum_index', index=3,
+ number=4, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='stats', full_name='pb.Results.stats', index=4,
+ number=5, type=11, cpp_type=10, label=1,
+ has_default_value=False, default_value=None,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=166,
+ serialized_end=301,
+)
+
+_MATCH.fields_by_name['peptide'].message_type = peptides_pb2._PEPTIDE
+_RESULTS.fields_by_name['spectrum'].message_type = spectrum_pb2._SPECTRUM
+_RESULTS.fields_by_name['matches'].message_type = _MATCH
+_RESULTS.fields_by_name['stats'].message_type = _STATS
+DESCRIPTOR.message_types_by_name['Match'] = _MATCH
+DESCRIPTOR.message_types_by_name['Stats'] = _STATS
+DESCRIPTOR.message_types_by_name['Results'] = _RESULTS
+
+class Match(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _MATCH
+
+ # @@protoc_insertion_point(class_scope:pb.Match)
+
+class Stats(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _STATS
+
+ # @@protoc_insertion_point(class_scope:pb.Stats)
+
+class Results(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _RESULTS
+
+ # @@protoc_insertion_point(class_scope:pb.Results)
+
+
+DESCRIPTOR.has_options = True
+DESCRIPTOR._options = _descriptor._ParseOptions(descriptor_pb2.FileOptions(), 'H\001')
+# @@protoc_insertion_point(module_scope)
diff --git a/src/app/tide/protoobj/spectrum.pb.cc b/src/app/tide/protoobj/spectrum.pb.cc
new file mode 100644
index 0000000..751948a
--- /dev/null
+++ b/src/app/tide/protoobj/spectrum.pb.cc
@@ -0,0 +1,675 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: spectrum.proto
+
+#define INTERNAL_SUPPRESS_PROTOBUF_FIELD_DEPRECATION
+#include "spectrum.pb.h"
+
+#include <algorithm>
+
+#include <google/protobuf/stubs/common.h>
+#include <google/protobuf/stubs/once.h>
+#include <google/protobuf/io/coded_stream.h>
+#include <google/protobuf/wire_format_lite_inl.h>
+#include <google/protobuf/descriptor.h>
+#include <google/protobuf/generated_message_reflection.h>
+#include <google/protobuf/reflection_ops.h>
+#include <google/protobuf/wire_format.h>
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+namespace {
+
+const ::google::protobuf::Descriptor* Spectrum_descriptor_ = NULL;
+const ::google::protobuf::internal::GeneratedMessageReflection*
+ Spectrum_reflection_ = NULL;
+
+} // namespace
+
+
+void protobuf_AssignDesc_spectrum_2eproto() {
+ protobuf_AddDesc_spectrum_2eproto();
+ const ::google::protobuf::FileDescriptor* file =
+ ::google::protobuf::DescriptorPool::generated_pool()->FindFileByName(
+ "spectrum.proto");
+ GOOGLE_CHECK(file != NULL);
+ Spectrum_descriptor_ = file->message_type(0);
+ static const int Spectrum_offsets_[8] = {
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, peak_m_z_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, peak_intensity_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, peak_m_z_denominator_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, peak_intensity_denominator_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, spectrum_number_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, precursor_m_z_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, rtime_),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, charge_state_),
+ };
+ Spectrum_reflection_ =
+ new ::google::protobuf::internal::GeneratedMessageReflection(
+ Spectrum_descriptor_,
+ Spectrum::default_instance_,
+ Spectrum_offsets_,
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, _has_bits_[0]),
+ GOOGLE_PROTOBUF_GENERATED_MESSAGE_FIELD_OFFSET(Spectrum, _unknown_fields_),
+ -1,
+ ::google::protobuf::DescriptorPool::generated_pool(),
+ ::google::protobuf::MessageFactory::generated_factory(),
+ sizeof(Spectrum));
+}
+
+namespace {
+
+GOOGLE_PROTOBUF_DECLARE_ONCE(protobuf_AssignDescriptors_once_);
+inline void protobuf_AssignDescriptorsOnce() {
+ ::google::protobuf::GoogleOnceInit(&protobuf_AssignDescriptors_once_,
+ &protobuf_AssignDesc_spectrum_2eproto);
+}
+
+void protobuf_RegisterTypes(const ::std::string&) {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedMessage(
+ Spectrum_descriptor_, &Spectrum::default_instance());
+}
+
+} // namespace
+
+void protobuf_ShutdownFile_spectrum_2eproto() {
+ delete Spectrum::default_instance_;
+ delete Spectrum_reflection_;
+}
+
+void protobuf_AddDesc_spectrum_2eproto() {
+ static bool already_here = false;
+ if (already_here) return;
+ already_here = true;
+ GOOGLE_PROTOBUF_VERIFY_VERSION;
+
+ ::google::protobuf::DescriptorPool::InternalAddGeneratedFile(
+ "\n\016spectrum.proto\022\002pb\"\327\001\n\010Spectrum\022\024\n\010pea"
+ "k_m_z\030\001 \003(\003B\002\020\001\022\032\n\016peak_intensity\030\002 \003(\003B"
+ "\002\020\001\022\034\n\024peak_m_z_denominator\030\003 \001(\005\022\"\n\032pea"
+ "k_intensity_denominator\030\004 \001(\005\022\027\n\017spectru"
+ "m_number\030\005 \001(\005\022\025\n\rprecursor_m_z\030\006 \001(\001\022\r\n"
+ "\005rtime\030\010 \001(\001\022\030\n\014charge_state\030\007 \003(\005B\002\020\001B\002"
+ "H\001", 242);
+ ::google::protobuf::MessageFactory::InternalRegisterGeneratedFile(
+ "spectrum.proto", &protobuf_RegisterTypes);
+ Spectrum::default_instance_ = new Spectrum();
+ Spectrum::default_instance_->InitAsDefaultInstance();
+ ::google::protobuf::internal::OnShutdown(&protobuf_ShutdownFile_spectrum_2eproto);
+}
+
+// Force AddDescriptors() to be called at static initialization time.
+struct StaticDescriptorInitializer_spectrum_2eproto {
+ StaticDescriptorInitializer_spectrum_2eproto() {
+ protobuf_AddDesc_spectrum_2eproto();
+ }
+} static_descriptor_initializer_spectrum_2eproto_;
+
+// ===================================================================
+
+#ifndef _MSC_VER
+const int Spectrum::kPeakMZFieldNumber;
+const int Spectrum::kPeakIntensityFieldNumber;
+const int Spectrum::kPeakMZDenominatorFieldNumber;
+const int Spectrum::kPeakIntensityDenominatorFieldNumber;
+const int Spectrum::kSpectrumNumberFieldNumber;
+const int Spectrum::kPrecursorMZFieldNumber;
+const int Spectrum::kRtimeFieldNumber;
+const int Spectrum::kChargeStateFieldNumber;
+#endif // !_MSC_VER
+
+Spectrum::Spectrum()
+ : ::google::protobuf::Message() {
+ SharedCtor();
+}
+
+void Spectrum::InitAsDefaultInstance() {
+}
+
+Spectrum::Spectrum(const Spectrum& from)
+ : ::google::protobuf::Message() {
+ SharedCtor();
+ MergeFrom(from);
+}
+
+void Spectrum::SharedCtor() {
+ _cached_size_ = 0;
+ peak_m_z_denominator_ = 0;
+ peak_intensity_denominator_ = 0;
+ spectrum_number_ = 0;
+ precursor_m_z_ = 0;
+ rtime_ = 0;
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+}
+
+Spectrum::~Spectrum() {
+ SharedDtor();
+}
+
+void Spectrum::SharedDtor() {
+ if (this != default_instance_) {
+ }
+}
+
+void Spectrum::SetCachedSize(int size) const {
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+}
+const ::google::protobuf::Descriptor* Spectrum::descriptor() {
+ protobuf_AssignDescriptorsOnce();
+ return Spectrum_descriptor_;
+}
+
+const Spectrum& Spectrum::default_instance() {
+ if (default_instance_ == NULL) protobuf_AddDesc_spectrum_2eproto();
+ return *default_instance_;
+}
+
+Spectrum* Spectrum::default_instance_ = NULL;
+
+Spectrum* Spectrum::New() const {
+ return new Spectrum;
+}
+
+void Spectrum::Clear() {
+ if (_has_bits_[2 / 32] & (0xffu << (2 % 32))) {
+ peak_m_z_denominator_ = 0;
+ peak_intensity_denominator_ = 0;
+ spectrum_number_ = 0;
+ precursor_m_z_ = 0;
+ rtime_ = 0;
+ }
+ peak_m_z_.Clear();
+ peak_intensity_.Clear();
+ charge_state_.Clear();
+ ::memset(_has_bits_, 0, sizeof(_has_bits_));
+ mutable_unknown_fields()->Clear();
+}
+
+bool Spectrum::MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input) {
+#define DO_(EXPRESSION) if (!(EXPRESSION)) return false
+ ::google::protobuf::uint32 tag;
+ while ((tag = input->ReadTag()) != 0) {
+ switch (::google::protobuf::internal::WireFormatLite::GetTagFieldNumber(tag)) {
+ // repeated int64 peak_m_z = 1 [packed = true];
+ case 1: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitive<
+ ::google::protobuf::int64, ::google::protobuf::internal::WireFormatLite::TYPE_INT64>(
+ input, this->mutable_peak_m_z())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitiveNoInline<
+ ::google::protobuf::int64, ::google::protobuf::internal::WireFormatLite::TYPE_INT64>(
+ 1, 10, input, this->mutable_peak_m_z())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(18)) goto parse_peak_intensity;
+ break;
+ }
+
+ // repeated int64 peak_intensity = 2 [packed = true];
+ case 2: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_peak_intensity:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitive<
+ ::google::protobuf::int64, ::google::protobuf::internal::WireFormatLite::TYPE_INT64>(
+ input, this->mutable_peak_intensity())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitiveNoInline<
+ ::google::protobuf::int64, ::google::protobuf::internal::WireFormatLite::TYPE_INT64>(
+ 1, 18, input, this->mutable_peak_intensity())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(24)) goto parse_peak_m_z_denominator;
+ break;
+ }
+
+ // optional int32 peak_m_z_denominator = 3;
+ case 3: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_peak_m_z_denominator:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &peak_m_z_denominator_)));
+ set_has_peak_m_z_denominator();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(32)) goto parse_peak_intensity_denominator;
+ break;
+ }
+
+ // optional int32 peak_intensity_denominator = 4;
+ case 4: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_peak_intensity_denominator:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &peak_intensity_denominator_)));
+ set_has_peak_intensity_denominator();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(40)) goto parse_spectrum_number;
+ break;
+ }
+
+ // optional int32 spectrum_number = 5;
+ case 5: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_VARINT) {
+ parse_spectrum_number:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, &spectrum_number_)));
+ set_has_spectrum_number();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(49)) goto parse_precursor_m_z;
+ break;
+ }
+
+ // optional double precursor_m_z = 6;
+ case 6: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_precursor_m_z:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &precursor_m_z_)));
+ set_has_precursor_m_z();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(58)) goto parse_charge_state;
+ break;
+ }
+
+ // repeated int32 charge_state = 7 [packed = true];
+ case 7: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED) {
+ parse_charge_state:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPackedPrimitive<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ input, this->mutable_charge_state())));
+ } else if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag)
+ == ::google::protobuf::internal::WireFormatLite::
+ WIRETYPE_VARINT) {
+ DO_((::google::protobuf::internal::WireFormatLite::ReadRepeatedPrimitiveNoInline<
+ ::google::protobuf::int32, ::google::protobuf::internal::WireFormatLite::TYPE_INT32>(
+ 1, 58, input, this->mutable_charge_state())));
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectTag(65)) goto parse_rtime;
+ break;
+ }
+
+ // optional double rtime = 8;
+ case 8: {
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_FIXED64) {
+ parse_rtime:
+ DO_((::google::protobuf::internal::WireFormatLite::ReadPrimitive<
+ double, ::google::protobuf::internal::WireFormatLite::TYPE_DOUBLE>(
+ input, &rtime_)));
+ set_has_rtime();
+ } else {
+ goto handle_uninterpreted;
+ }
+ if (input->ExpectAtEnd()) return true;
+ break;
+ }
+
+ default: {
+ handle_uninterpreted:
+ if (::google::protobuf::internal::WireFormatLite::GetTagWireType(tag) ==
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_END_GROUP) {
+ return true;
+ }
+ DO_(::google::protobuf::internal::WireFormat::SkipField(
+ input, tag, mutable_unknown_fields()));
+ break;
+ }
+ }
+ }
+ return true;
+#undef DO_
+}
+
+void Spectrum::SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const {
+ // repeated int64 peak_m_z = 1 [packed = true];
+ if (this->peak_m_z_size() > 0) {
+ ::google::protobuf::internal::WireFormatLite::WriteTag(1, ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED, output);
+ output->WriteVarint32(_peak_m_z_cached_byte_size_);
+ }
+ for (int i = 0; i < this->peak_m_z_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt64NoTag(
+ this->peak_m_z(i), output);
+ }
+
+ // repeated int64 peak_intensity = 2 [packed = true];
+ if (this->peak_intensity_size() > 0) {
+ ::google::protobuf::internal::WireFormatLite::WriteTag(2, ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED, output);
+ output->WriteVarint32(_peak_intensity_cached_byte_size_);
+ }
+ for (int i = 0; i < this->peak_intensity_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt64NoTag(
+ this->peak_intensity(i), output);
+ }
+
+ // optional int32 peak_m_z_denominator = 3;
+ if (has_peak_m_z_denominator()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(3, this->peak_m_z_denominator(), output);
+ }
+
+ // optional int32 peak_intensity_denominator = 4;
+ if (has_peak_intensity_denominator()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(4, this->peak_intensity_denominator(), output);
+ }
+
+ // optional int32 spectrum_number = 5;
+ if (has_spectrum_number()) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32(5, this->spectrum_number(), output);
+ }
+
+ // optional double precursor_m_z = 6;
+ if (has_precursor_m_z()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(6, this->precursor_m_z(), output);
+ }
+
+ // repeated int32 charge_state = 7 [packed = true];
+ if (this->charge_state_size() > 0) {
+ ::google::protobuf::internal::WireFormatLite::WriteTag(7, ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED, output);
+ output->WriteVarint32(_charge_state_cached_byte_size_);
+ }
+ for (int i = 0; i < this->charge_state_size(); i++) {
+ ::google::protobuf::internal::WireFormatLite::WriteInt32NoTag(
+ this->charge_state(i), output);
+ }
+
+ // optional double rtime = 8;
+ if (has_rtime()) {
+ ::google::protobuf::internal::WireFormatLite::WriteDouble(8, this->rtime(), output);
+ }
+
+ if (!unknown_fields().empty()) {
+ ::google::protobuf::internal::WireFormat::SerializeUnknownFields(
+ unknown_fields(), output);
+ }
+}
+
+::google::protobuf::uint8* Spectrum::SerializeWithCachedSizesToArray(
+ ::google::protobuf::uint8* target) const {
+ // repeated int64 peak_m_z = 1 [packed = true];
+ if (this->peak_m_z_size() > 0) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteTagToArray(
+ 1,
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED,
+ target);
+ target = ::google::protobuf::io::CodedOutputStream::WriteVarint32ToArray(
+ _peak_m_z_cached_byte_size_, target);
+ }
+ for (int i = 0; i < this->peak_m_z_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteInt64NoTagToArray(this->peak_m_z(i), target);
+ }
+
+ // repeated int64 peak_intensity = 2 [packed = true];
+ if (this->peak_intensity_size() > 0) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteTagToArray(
+ 2,
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED,
+ target);
+ target = ::google::protobuf::io::CodedOutputStream::WriteVarint32ToArray(
+ _peak_intensity_cached_byte_size_, target);
+ }
+ for (int i = 0; i < this->peak_intensity_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteInt64NoTagToArray(this->peak_intensity(i), target);
+ }
+
+ // optional int32 peak_m_z_denominator = 3;
+ if (has_peak_m_z_denominator()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(3, this->peak_m_z_denominator(), target);
+ }
+
+ // optional int32 peak_intensity_denominator = 4;
+ if (has_peak_intensity_denominator()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(4, this->peak_intensity_denominator(), target);
+ }
+
+ // optional int32 spectrum_number = 5;
+ if (has_spectrum_number()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteInt32ToArray(5, this->spectrum_number(), target);
+ }
+
+ // optional double precursor_m_z = 6;
+ if (has_precursor_m_z()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(6, this->precursor_m_z(), target);
+ }
+
+ // repeated int32 charge_state = 7 [packed = true];
+ if (this->charge_state_size() > 0) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteTagToArray(
+ 7,
+ ::google::protobuf::internal::WireFormatLite::WIRETYPE_LENGTH_DELIMITED,
+ target);
+ target = ::google::protobuf::io::CodedOutputStream::WriteVarint32ToArray(
+ _charge_state_cached_byte_size_, target);
+ }
+ for (int i = 0; i < this->charge_state_size(); i++) {
+ target = ::google::protobuf::internal::WireFormatLite::
+ WriteInt32NoTagToArray(this->charge_state(i), target);
+ }
+
+ // optional double rtime = 8;
+ if (has_rtime()) {
+ target = ::google::protobuf::internal::WireFormatLite::WriteDoubleToArray(8, this->rtime(), target);
+ }
+
+ if (!unknown_fields().empty()) {
+ target = ::google::protobuf::internal::WireFormat::SerializeUnknownFieldsToArray(
+ unknown_fields(), target);
+ }
+ return target;
+}
+
+int Spectrum::ByteSize() const {
+ int total_size = 0;
+
+ if (_has_bits_[2 / 32] & (0xffu << (2 % 32))) {
+ // optional int32 peak_m_z_denominator = 3;
+ if (has_peak_m_z_denominator()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->peak_m_z_denominator());
+ }
+
+ // optional int32 peak_intensity_denominator = 4;
+ if (has_peak_intensity_denominator()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->peak_intensity_denominator());
+ }
+
+ // optional int32 spectrum_number = 5;
+ if (has_spectrum_number()) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(
+ this->spectrum_number());
+ }
+
+ // optional double precursor_m_z = 6;
+ if (has_precursor_m_z()) {
+ total_size += 1 + 8;
+ }
+
+ // optional double rtime = 8;
+ if (has_rtime()) {
+ total_size += 1 + 8;
+ }
+
+ }
+ // repeated int64 peak_m_z = 1 [packed = true];
+ {
+ int data_size = 0;
+ for (int i = 0; i < this->peak_m_z_size(); i++) {
+ data_size += ::google::protobuf::internal::WireFormatLite::
+ Int64Size(this->peak_m_z(i));
+ }
+ if (data_size > 0) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(data_size);
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _peak_m_z_cached_byte_size_ = data_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ total_size += data_size;
+ }
+
+ // repeated int64 peak_intensity = 2 [packed = true];
+ {
+ int data_size = 0;
+ for (int i = 0; i < this->peak_intensity_size(); i++) {
+ data_size += ::google::protobuf::internal::WireFormatLite::
+ Int64Size(this->peak_intensity(i));
+ }
+ if (data_size > 0) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(data_size);
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _peak_intensity_cached_byte_size_ = data_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ total_size += data_size;
+ }
+
+ // repeated int32 charge_state = 7 [packed = true];
+ {
+ int data_size = 0;
+ for (int i = 0; i < this->charge_state_size(); i++) {
+ data_size += ::google::protobuf::internal::WireFormatLite::
+ Int32Size(this->charge_state(i));
+ }
+ if (data_size > 0) {
+ total_size += 1 +
+ ::google::protobuf::internal::WireFormatLite::Int32Size(data_size);
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _charge_state_cached_byte_size_ = data_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ total_size += data_size;
+ }
+
+ if (!unknown_fields().empty()) {
+ total_size +=
+ ::google::protobuf::internal::WireFormat::ComputeUnknownFieldsSize(
+ unknown_fields());
+ }
+ GOOGLE_SAFE_CONCURRENT_WRITES_BEGIN();
+ _cached_size_ = total_size;
+ GOOGLE_SAFE_CONCURRENT_WRITES_END();
+ return total_size;
+}
+
+void Spectrum::MergeFrom(const ::google::protobuf::Message& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ const Spectrum* source =
+ ::google::protobuf::internal::dynamic_cast_if_available<const Spectrum*>(
+ &from);
+ if (source == NULL) {
+ ::google::protobuf::internal::ReflectionOps::Merge(from, this);
+ } else {
+ MergeFrom(*source);
+ }
+}
+
+void Spectrum::MergeFrom(const Spectrum& from) {
+ GOOGLE_CHECK_NE(&from, this);
+ peak_m_z_.MergeFrom(from.peak_m_z_);
+ peak_intensity_.MergeFrom(from.peak_intensity_);
+ charge_state_.MergeFrom(from.charge_state_);
+ if (from._has_bits_[2 / 32] & (0xffu << (2 % 32))) {
+ if (from.has_peak_m_z_denominator()) {
+ set_peak_m_z_denominator(from.peak_m_z_denominator());
+ }
+ if (from.has_peak_intensity_denominator()) {
+ set_peak_intensity_denominator(from.peak_intensity_denominator());
+ }
+ if (from.has_spectrum_number()) {
+ set_spectrum_number(from.spectrum_number());
+ }
+ if (from.has_precursor_m_z()) {
+ set_precursor_m_z(from.precursor_m_z());
+ }
+ if (from.has_rtime()) {
+ set_rtime(from.rtime());
+ }
+ }
+ mutable_unknown_fields()->MergeFrom(from.unknown_fields());
+}
+
+void Spectrum::CopyFrom(const ::google::protobuf::Message& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+void Spectrum::CopyFrom(const Spectrum& from) {
+ if (&from == this) return;
+ Clear();
+ MergeFrom(from);
+}
+
+bool Spectrum::IsInitialized() const {
+
+ return true;
+}
+
+void Spectrum::Swap(Spectrum* other) {
+ if (other != this) {
+ peak_m_z_.Swap(&other->peak_m_z_);
+ peak_intensity_.Swap(&other->peak_intensity_);
+ std::swap(peak_m_z_denominator_, other->peak_m_z_denominator_);
+ std::swap(peak_intensity_denominator_, other->peak_intensity_denominator_);
+ std::swap(spectrum_number_, other->spectrum_number_);
+ std::swap(precursor_m_z_, other->precursor_m_z_);
+ std::swap(rtime_, other->rtime_);
+ charge_state_.Swap(&other->charge_state_);
+ std::swap(_has_bits_[0], other->_has_bits_[0]);
+ _unknown_fields_.Swap(&other->_unknown_fields_);
+ std::swap(_cached_size_, other->_cached_size_);
+ }
+}
+
+::google::protobuf::Metadata Spectrum::GetMetadata() const {
+ protobuf_AssignDescriptorsOnce();
+ ::google::protobuf::Metadata metadata;
+ metadata.descriptor = Spectrum_descriptor_;
+ metadata.reflection = Spectrum_reflection_;
+ return metadata;
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+// @@protoc_insertion_point(global_scope)
diff --git a/src/app/tide/protoobj/spectrum.pb.h b/src/app/tide/protoobj/spectrum.pb.h
new file mode 100644
index 0000000..370a626
--- /dev/null
+++ b/src/app/tide/protoobj/spectrum.pb.h
@@ -0,0 +1,410 @@
+// Generated by the protocol buffer compiler. DO NOT EDIT!
+// source: spectrum.proto
+
+#ifndef PROTOBUF_spectrum_2eproto__INCLUDED
+#define PROTOBUF_spectrum_2eproto__INCLUDED
+
+#include <string>
+
+#include <google/protobuf/stubs/common.h>
+
+#if GOOGLE_PROTOBUF_VERSION < 2005000
+#error This file was generated by a newer version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please update
+#error your headers.
+#endif
+#if 2005000 < GOOGLE_PROTOBUF_MIN_PROTOC_VERSION
+#error This file was generated by an older version of protoc which is
+#error incompatible with your Protocol Buffer headers. Please
+#error regenerate this file with a newer version of protoc.
+#endif
+
+#include <google/protobuf/generated_message_util.h>
+#include <google/protobuf/message.h>
+#include <google/protobuf/repeated_field.h>
+#include <google/protobuf/extension_set.h>
+#include <google/protobuf/unknown_field_set.h>
+// @@protoc_insertion_point(includes)
+
+namespace pb {
+
+// Internal implementation detail -- do not call these.
+void protobuf_AddDesc_spectrum_2eproto();
+void protobuf_AssignDesc_spectrum_2eproto();
+void protobuf_ShutdownFile_spectrum_2eproto();
+
+class Spectrum;
+
+// ===================================================================
+
+class Spectrum : public ::google::protobuf::Message {
+ public:
+ Spectrum();
+ virtual ~Spectrum();
+
+ Spectrum(const Spectrum& from);
+
+ inline Spectrum& operator=(const Spectrum& from) {
+ CopyFrom(from);
+ return *this;
+ }
+
+ inline const ::google::protobuf::UnknownFieldSet& unknown_fields() const {
+ return _unknown_fields_;
+ }
+
+ inline ::google::protobuf::UnknownFieldSet* mutable_unknown_fields() {
+ return &_unknown_fields_;
+ }
+
+ static const ::google::protobuf::Descriptor* descriptor();
+ static const Spectrum& default_instance();
+
+ void Swap(Spectrum* other);
+
+ // implements Message ----------------------------------------------
+
+ Spectrum* New() const;
+ void CopyFrom(const ::google::protobuf::Message& from);
+ void MergeFrom(const ::google::protobuf::Message& from);
+ void CopyFrom(const Spectrum& from);
+ void MergeFrom(const Spectrum& from);
+ void Clear();
+ bool IsInitialized() const;
+
+ int ByteSize() const;
+ bool MergePartialFromCodedStream(
+ ::google::protobuf::io::CodedInputStream* input);
+ void SerializeWithCachedSizes(
+ ::google::protobuf::io::CodedOutputStream* output) const;
+ ::google::protobuf::uint8* SerializeWithCachedSizesToArray(::google::protobuf::uint8* output) const;
+ int GetCachedSize() const { return _cached_size_; }
+ private:
+ void SharedCtor();
+ void SharedDtor();
+ void SetCachedSize(int size) const;
+ public:
+
+ ::google::protobuf::Metadata GetMetadata() const;
+
+ // nested types ----------------------------------------------------
+
+ // accessors -------------------------------------------------------
+
+ // repeated int64 peak_m_z = 1 [packed = true];
+ inline int peak_m_z_size() const;
+ inline void clear_peak_m_z();
+ static const int kPeakMZFieldNumber = 1;
+ inline ::google::protobuf::int64 peak_m_z(int index) const;
+ inline void set_peak_m_z(int index, ::google::protobuf::int64 value);
+ inline void add_peak_m_z(::google::protobuf::int64 value);
+ inline const ::google::protobuf::RepeatedField< ::google::protobuf::int64 >&
+ peak_m_z() const;
+ inline ::google::protobuf::RepeatedField< ::google::protobuf::int64 >*
+ mutable_peak_m_z();
+
+ // repeated int64 peak_intensity = 2 [packed = true];
+ inline int peak_intensity_size() const;
+ inline void clear_peak_intensity();
+ static const int kPeakIntensityFieldNumber = 2;
+ inline ::google::protobuf::int64 peak_intensity(int index) const;
+ inline void set_peak_intensity(int index, ::google::protobuf::int64 value);
+ inline void add_peak_intensity(::google::protobuf::int64 value);
+ inline const ::google::protobuf::RepeatedField< ::google::protobuf::int64 >&
+ peak_intensity() const;
+ inline ::google::protobuf::RepeatedField< ::google::protobuf::int64 >*
+ mutable_peak_intensity();
+
+ // optional int32 peak_m_z_denominator = 3;
+ inline bool has_peak_m_z_denominator() const;
+ inline void clear_peak_m_z_denominator();
+ static const int kPeakMZDenominatorFieldNumber = 3;
+ inline ::google::protobuf::int32 peak_m_z_denominator() const;
+ inline void set_peak_m_z_denominator(::google::protobuf::int32 value);
+
+ // optional int32 peak_intensity_denominator = 4;
+ inline bool has_peak_intensity_denominator() const;
+ inline void clear_peak_intensity_denominator();
+ static const int kPeakIntensityDenominatorFieldNumber = 4;
+ inline ::google::protobuf::int32 peak_intensity_denominator() const;
+ inline void set_peak_intensity_denominator(::google::protobuf::int32 value);
+
+ // optional int32 spectrum_number = 5;
+ inline bool has_spectrum_number() const;
+ inline void clear_spectrum_number();
+ static const int kSpectrumNumberFieldNumber = 5;
+ inline ::google::protobuf::int32 spectrum_number() const;
+ inline void set_spectrum_number(::google::protobuf::int32 value);
+
+ // optional double precursor_m_z = 6;
+ inline bool has_precursor_m_z() const;
+ inline void clear_precursor_m_z();
+ static const int kPrecursorMZFieldNumber = 6;
+ inline double precursor_m_z() const;
+ inline void set_precursor_m_z(double value);
+
+ // optional double rtime = 8;
+ inline bool has_rtime() const;
+ inline void clear_rtime();
+ static const int kRtimeFieldNumber = 8;
+ inline double rtime() const;
+ inline void set_rtime(double value);
+
+ // repeated int32 charge_state = 7 [packed = true];
+ inline int charge_state_size() const;
+ inline void clear_charge_state();
+ static const int kChargeStateFieldNumber = 7;
+ inline ::google::protobuf::int32 charge_state(int index) const;
+ inline void set_charge_state(int index, ::google::protobuf::int32 value);
+ inline void add_charge_state(::google::protobuf::int32 value);
+ inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+ charge_state() const;
+ inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+ mutable_charge_state();
+
+ // @@protoc_insertion_point(class_scope:pb.Spectrum)
+ private:
+ inline void set_has_peak_m_z_denominator();
+ inline void clear_has_peak_m_z_denominator();
+ inline void set_has_peak_intensity_denominator();
+ inline void clear_has_peak_intensity_denominator();
+ inline void set_has_spectrum_number();
+ inline void clear_has_spectrum_number();
+ inline void set_has_precursor_m_z();
+ inline void clear_has_precursor_m_z();
+ inline void set_has_rtime();
+ inline void clear_has_rtime();
+
+ ::google::protobuf::UnknownFieldSet _unknown_fields_;
+
+ ::google::protobuf::RepeatedField< ::google::protobuf::int64 > peak_m_z_;
+ mutable int _peak_m_z_cached_byte_size_;
+ ::google::protobuf::RepeatedField< ::google::protobuf::int64 > peak_intensity_;
+ mutable int _peak_intensity_cached_byte_size_;
+ ::google::protobuf::int32 peak_m_z_denominator_;
+ ::google::protobuf::int32 peak_intensity_denominator_;
+ double precursor_m_z_;
+ double rtime_;
+ ::google::protobuf::RepeatedField< ::google::protobuf::int32 > charge_state_;
+ mutable int _charge_state_cached_byte_size_;
+ ::google::protobuf::int32 spectrum_number_;
+
+ mutable int _cached_size_;
+ ::google::protobuf::uint32 _has_bits_[(8 + 31) / 32];
+
+ friend void protobuf_AddDesc_spectrum_2eproto();
+ friend void protobuf_AssignDesc_spectrum_2eproto();
+ friend void protobuf_ShutdownFile_spectrum_2eproto();
+
+ void InitAsDefaultInstance();
+ static Spectrum* default_instance_;
+};
+// ===================================================================
+
+
+// ===================================================================
+
+// Spectrum
+
+// repeated int64 peak_m_z = 1 [packed = true];
+inline int Spectrum::peak_m_z_size() const {
+ return peak_m_z_.size();
+}
+inline void Spectrum::clear_peak_m_z() {
+ peak_m_z_.Clear();
+}
+inline ::google::protobuf::int64 Spectrum::peak_m_z(int index) const {
+ return peak_m_z_.Get(index);
+}
+inline void Spectrum::set_peak_m_z(int index, ::google::protobuf::int64 value) {
+ peak_m_z_.Set(index, value);
+}
+inline void Spectrum::add_peak_m_z(::google::protobuf::int64 value) {
+ peak_m_z_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< ::google::protobuf::int64 >&
+Spectrum::peak_m_z() const {
+ return peak_m_z_;
+}
+inline ::google::protobuf::RepeatedField< ::google::protobuf::int64 >*
+Spectrum::mutable_peak_m_z() {
+ return &peak_m_z_;
+}
+
+// repeated int64 peak_intensity = 2 [packed = true];
+inline int Spectrum::peak_intensity_size() const {
+ return peak_intensity_.size();
+}
+inline void Spectrum::clear_peak_intensity() {
+ peak_intensity_.Clear();
+}
+inline ::google::protobuf::int64 Spectrum::peak_intensity(int index) const {
+ return peak_intensity_.Get(index);
+}
+inline void Spectrum::set_peak_intensity(int index, ::google::protobuf::int64 value) {
+ peak_intensity_.Set(index, value);
+}
+inline void Spectrum::add_peak_intensity(::google::protobuf::int64 value) {
+ peak_intensity_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< ::google::protobuf::int64 >&
+Spectrum::peak_intensity() const {
+ return peak_intensity_;
+}
+inline ::google::protobuf::RepeatedField< ::google::protobuf::int64 >*
+Spectrum::mutable_peak_intensity() {
+ return &peak_intensity_;
+}
+
+// optional int32 peak_m_z_denominator = 3;
+inline bool Spectrum::has_peak_m_z_denominator() const {
+ return (_has_bits_[0] & 0x00000004u) != 0;
+}
+inline void Spectrum::set_has_peak_m_z_denominator() {
+ _has_bits_[0] |= 0x00000004u;
+}
+inline void Spectrum::clear_has_peak_m_z_denominator() {
+ _has_bits_[0] &= ~0x00000004u;
+}
+inline void Spectrum::clear_peak_m_z_denominator() {
+ peak_m_z_denominator_ = 0;
+ clear_has_peak_m_z_denominator();
+}
+inline ::google::protobuf::int32 Spectrum::peak_m_z_denominator() const {
+ return peak_m_z_denominator_;
+}
+inline void Spectrum::set_peak_m_z_denominator(::google::protobuf::int32 value) {
+ set_has_peak_m_z_denominator();
+ peak_m_z_denominator_ = value;
+}
+
+// optional int32 peak_intensity_denominator = 4;
+inline bool Spectrum::has_peak_intensity_denominator() const {
+ return (_has_bits_[0] & 0x00000008u) != 0;
+}
+inline void Spectrum::set_has_peak_intensity_denominator() {
+ _has_bits_[0] |= 0x00000008u;
+}
+inline void Spectrum::clear_has_peak_intensity_denominator() {
+ _has_bits_[0] &= ~0x00000008u;
+}
+inline void Spectrum::clear_peak_intensity_denominator() {
+ peak_intensity_denominator_ = 0;
+ clear_has_peak_intensity_denominator();
+}
+inline ::google::protobuf::int32 Spectrum::peak_intensity_denominator() const {
+ return peak_intensity_denominator_;
+}
+inline void Spectrum::set_peak_intensity_denominator(::google::protobuf::int32 value) {
+ set_has_peak_intensity_denominator();
+ peak_intensity_denominator_ = value;
+}
+
+// optional int32 spectrum_number = 5;
+inline bool Spectrum::has_spectrum_number() const {
+ return (_has_bits_[0] & 0x00000010u) != 0;
+}
+inline void Spectrum::set_has_spectrum_number() {
+ _has_bits_[0] |= 0x00000010u;
+}
+inline void Spectrum::clear_has_spectrum_number() {
+ _has_bits_[0] &= ~0x00000010u;
+}
+inline void Spectrum::clear_spectrum_number() {
+ spectrum_number_ = 0;
+ clear_has_spectrum_number();
+}
+inline ::google::protobuf::int32 Spectrum::spectrum_number() const {
+ return spectrum_number_;
+}
+inline void Spectrum::set_spectrum_number(::google::protobuf::int32 value) {
+ set_has_spectrum_number();
+ spectrum_number_ = value;
+}
+
+// optional double precursor_m_z = 6;
+inline bool Spectrum::has_precursor_m_z() const {
+ return (_has_bits_[0] & 0x00000020u) != 0;
+}
+inline void Spectrum::set_has_precursor_m_z() {
+ _has_bits_[0] |= 0x00000020u;
+}
+inline void Spectrum::clear_has_precursor_m_z() {
+ _has_bits_[0] &= ~0x00000020u;
+}
+inline void Spectrum::clear_precursor_m_z() {
+ precursor_m_z_ = 0;
+ clear_has_precursor_m_z();
+}
+inline double Spectrum::precursor_m_z() const {
+ return precursor_m_z_;
+}
+inline void Spectrum::set_precursor_m_z(double value) {
+ set_has_precursor_m_z();
+ precursor_m_z_ = value;
+}
+
+// optional double rtime = 8;
+inline bool Spectrum::has_rtime() const {
+ return (_has_bits_[0] & 0x00000040u) != 0;
+}
+inline void Spectrum::set_has_rtime() {
+ _has_bits_[0] |= 0x00000040u;
+}
+inline void Spectrum::clear_has_rtime() {
+ _has_bits_[0] &= ~0x00000040u;
+}
+inline void Spectrum::clear_rtime() {
+ rtime_ = 0;
+ clear_has_rtime();
+}
+inline double Spectrum::rtime() const {
+ return rtime_;
+}
+inline void Spectrum::set_rtime(double value) {
+ set_has_rtime();
+ rtime_ = value;
+}
+
+// repeated int32 charge_state = 7 [packed = true];
+inline int Spectrum::charge_state_size() const {
+ return charge_state_.size();
+}
+inline void Spectrum::clear_charge_state() {
+ charge_state_.Clear();
+}
+inline ::google::protobuf::int32 Spectrum::charge_state(int index) const {
+ return charge_state_.Get(index);
+}
+inline void Spectrum::set_charge_state(int index, ::google::protobuf::int32 value) {
+ charge_state_.Set(index, value);
+}
+inline void Spectrum::add_charge_state(::google::protobuf::int32 value) {
+ charge_state_.Add(value);
+}
+inline const ::google::protobuf::RepeatedField< ::google::protobuf::int32 >&
+Spectrum::charge_state() const {
+ return charge_state_;
+}
+inline ::google::protobuf::RepeatedField< ::google::protobuf::int32 >*
+Spectrum::mutable_charge_state() {
+ return &charge_state_;
+}
+
+
+// @@protoc_insertion_point(namespace_scope)
+
+} // namespace pb
+
+#ifndef SWIG
+namespace google {
+namespace protobuf {
+
+
+} // namespace google
+} // namespace protobuf
+#endif // SWIG
+
+// @@protoc_insertion_point(global_scope)
+
+#endif // PROTOBUF_spectrum_2eproto__INCLUDED
diff --git a/src/app/tide/protoobj/spectrum_pb2.py b/src/app/tide/protoobj/spectrum_pb2.py
new file mode 100644
index 0000000..176dd1a
--- /dev/null
+++ b/src/app/tide/protoobj/spectrum_pb2.py
@@ -0,0 +1,114 @@
+# Generated by the protocol buffer compiler. DO NOT EDIT!
+# source: spectrum.proto
+
+from google.protobuf import descriptor as _descriptor
+from google.protobuf import message as _message
+from google.protobuf import reflection as _reflection
+from google.protobuf import descriptor_pb2
+# @@protoc_insertion_point(imports)
+
+
+
+
+DESCRIPTOR = _descriptor.FileDescriptor(
+ name='spectrum.proto',
+ package='pb',
+ serialized_pb='\n\x0espectrum.proto\x12\x02pb\"\xd7\x01\n\x08Spectrum\x12\x14\n\x08peak_m_z\x18\x01 \x03(\x03\x42\x02\x10\x01\x12\x1a\n\x0epeak_intensity\x18\x02 \x03(\x03\x42\x02\x10\x01\x12\x1c\n\x14peak_m_z_denominator\x18\x03 \x01(\x05\x12\"\n\x1apeak_intensity_denominator\x18\x04 \x01(\x05\x12\x17\n\x0fspectrum_number\x18\x05 \x01(\x05\x12\x15\n\rprecursor_m_z\x18\x06 \x01(\x01\x12\r\n\x05rtime\x18\x08 \x01(\x01\x12\x18\n\x0c\x63harge_state\x18\x07 \x03(\x05\x42\x02\x10\x01\x42\x0 [...]
+
+
+
+
+_SPECTRUM = _descriptor.Descriptor(
+ name='Spectrum',
+ full_name='pb.Spectrum',
+ filename=None,
+ file=DESCRIPTOR,
+ containing_type=None,
+ fields=[
+ _descriptor.FieldDescriptor(
+ name='peak_m_z', full_name='pb.Spectrum.peak_m_z', index=0,
+ number=1, type=3, cpp_type=2, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')),
+ _descriptor.FieldDescriptor(
+ name='peak_intensity', full_name='pb.Spectrum.peak_intensity', index=1,
+ number=2, type=3, cpp_type=2, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')),
+ _descriptor.FieldDescriptor(
+ name='peak_m_z_denominator', full_name='pb.Spectrum.peak_m_z_denominator', index=2,
+ number=3, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='peak_intensity_denominator', full_name='pb.Spectrum.peak_intensity_denominator', index=3,
+ number=4, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='spectrum_number', full_name='pb.Spectrum.spectrum_number', index=4,
+ number=5, type=5, cpp_type=1, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='precursor_m_z', full_name='pb.Spectrum.precursor_m_z', index=5,
+ number=6, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='rtime', full_name='pb.Spectrum.rtime', index=6,
+ number=8, type=1, cpp_type=5, label=1,
+ has_default_value=False, default_value=0,
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=None),
+ _descriptor.FieldDescriptor(
+ name='charge_state', full_name='pb.Spectrum.charge_state', index=7,
+ number=7, type=5, cpp_type=1, label=3,
+ has_default_value=False, default_value=[],
+ message_type=None, enum_type=None, containing_type=None,
+ is_extension=False, extension_scope=None,
+ options=_descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')),
+ ],
+ extensions=[
+ ],
+ nested_types=[],
+ enum_types=[
+ ],
+ options=None,
+ is_extendable=False,
+ extension_ranges=[],
+ serialized_start=23,
+ serialized_end=238,
+)
+
+DESCRIPTOR.message_types_by_name['Spectrum'] = _SPECTRUM
+
+class Spectrum(_message.Message):
+ __metaclass__ = _reflection.GeneratedProtocolMessageType
+ DESCRIPTOR = _SPECTRUM
+
+ # @@protoc_insertion_point(class_scope:pb.Spectrum)
+
+
+DESCRIPTOR.has_options = True
+DESCRIPTOR._options = _descriptor._ParseOptions(descriptor_pb2.FileOptions(), 'H\001')
+_SPECTRUM.fields_by_name['peak_m_z'].has_options = True
+_SPECTRUM.fields_by_name['peak_m_z']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')
+_SPECTRUM.fields_by_name['peak_intensity'].has_options = True
+_SPECTRUM.fields_by_name['peak_intensity']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')
+_SPECTRUM.fields_by_name['charge_state'].has_options = True
+_SPECTRUM.fields_by_name['charge_state']._options = _descriptor._ParseOptions(descriptor_pb2.FieldOptions(), '\020\001')
+# @@protoc_insertion_point(module_scope)
diff --git a/src/app/tide/records.h b/src/app/tide/records.h
new file mode 100644
index 0000000..ff68d7d
--- /dev/null
+++ b/src/app/tide/records.h
@@ -0,0 +1,249 @@
+// Benjamin Diament
+//
+// Utility routines for reading and writing a file of protocol buffers as
+// records. Each protocol buffer message is encoded into a record which is
+// prepended by its length in the varint format. See protocol buffer
+// documentation:
+// http://code.google.com/apis/protocolbuffers/docs/overview.html.
+// A '\0' is appended to the end of the file.
+// According to the documentation it is inappropriate (also ineffective) to
+// encode a series of records as a protocol buffer containing a single repeated
+// field. Records provide a very basic way to store vastly many messages in
+// a file.
+//
+// The corresponding program records.py can be used to read and write in
+// the same format in Python, provided that all messages are the same type.
+//
+// See peptide_downselect.cc for a very simple example of the use of records.
+//
+// Each file of records is prepended with a 4-byte arbitrarily-chosen string,
+// called a magic number, to provide a check that a given file is indeed a
+// file of records.
+//
+// HeadedRecordReader and HeadedRecordWriter provide an interface for
+// prepending a file of records with a single record of type Header.proto,
+// containing client-provided meta-information about the file.
+// All tide generated files are expected to be HeadedRecords.
+//
+// RecordReader and RecordWriter make use of the classes:
+// google::protobuf::io::FileInputStream
+// google::protobuf::io::FileOutputStream
+// google::protobuf::io::CodedInputStream
+// google::protobuf::io::CodedOutputStream,
+// which are described in the protocol buffer documentation.
+//
+// TODO 259: This class probably should be rewritten, paying more
+// attention to the various idioms for use of ZeroCopyStream and
+// CodedStream! Things could be greatly simplified.
+//
+// Note that CodedInputStream isn't built to handle large streams of
+// input, so it should be reconstructed at each record. Perhaps the
+// underlying ZeroCopyStream should handle EOF determination
+
+
+#ifndef RECORDS_H
+#define RECORDS_H
+
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+#include <fcntl.h>
+#ifdef _MSC_VER
+#include <io.h>
+#else
+#include <unistd.h>
+#endif
+#include <iostream>
+#include <string>
+#include <google/protobuf/message.h>
+#include <google/protobuf/io/zero_copy_stream_impl.h>
+#include <google/protobuf/io/coded_stream.h>
+#include "header.pb.h"
+#include "io/carp.h"
+
+using namespace std;
+
+#ifndef UINT32_MAX
+#define UINT32_MAX 0xfffffffful
+#endif
+#define MAGIC_NUMBER 0xfead1234ul
+
+class RecordWriter {
+ public:
+ explicit RecordWriter(const string& filename, int buf_size = -1)
+ : raw_output_(NULL), coded_output_(NULL) {
+ if ((fd_ = open(filename.c_str(), O_CREAT | O_TRUNC | O_WRONLY, 0644)) < 0) {
+ carp(CARP_FATAL, "Couldn't open file %s for write (errno %d: %s).",
+ filename.c_str(), errno, strerror(errno));
+ return;
+ }
+ raw_output_ = new google::protobuf::io::FileOutputStream(fd_, buf_size);
+ Init();
+ }
+
+ explicit RecordWriter(google::protobuf::io::ZeroCopyOutputStream* raw_output)
+ : fd_(-1), raw_output_(raw_output) {
+ Init();
+ raw_output_ = NULL; // we do not own (and will not delete) raw_output
+ }
+
+ ~RecordWriter() {
+ coded_output_->WriteVarint32(0); // end-of-records marker
+ delete coded_output_;
+ delete raw_output_;
+ if (fd_ > -1)
+ close(fd_);
+ }
+
+ // client should check once after construction
+ bool OK() const { return NULL != coded_output_; }
+
+ bool Write(const google::protobuf::Message* message) {
+ coded_output_->WriteVarint32(message->ByteSize());
+ if (coded_output_->HadError()) {
+ delete coded_output_;
+ coded_output_ = NULL;
+ return false;
+ }
+ message->SerializeWithCachedSizes(coded_output_);
+ return !coded_output_->HadError();
+ }
+
+ private:
+ void Init() {
+ coded_output_ = new google::protobuf::io::CodedOutputStream(raw_output_);
+ coded_output_->WriteLittleEndian32(MAGIC_NUMBER);
+ if (coded_output_->HadError()) {
+ delete coded_output_;
+ coded_output_ = NULL;
+ }
+ }
+
+ int fd_;
+ google::protobuf::io::ZeroCopyOutputStream* raw_output_;
+ google::protobuf::io::CodedOutputStream* coded_output_;
+};
+
+
+class RecordReader {
+ public:
+ explicit RecordReader(const string& filename, int buf_size = -1)
+ : raw_input_(NULL), coded_input_(NULL), size_(UINT32_MAX), valid_(false) {
+ fd_ = open(filename.c_str(), O_RDONLY);
+ if (fd_ < 0)
+ return;
+ raw_input_ = new google::protobuf::io::FileInputStream(fd_, buf_size);
+ google::protobuf::io::CodedInputStream coded_input(raw_input_);
+ google::protobuf::uint32 magic_number;
+ if (coded_input.ReadLittleEndian32(&magic_number)
+ && magic_number == MAGIC_NUMBER)
+ valid_ = true;
+ }
+
+ ~RecordReader() {
+ if (coded_input_)
+ delete coded_input_;
+ delete raw_input_;
+ if (fd_ >= 0)
+ close(fd_);
+ }
+
+ bool OK() const { return valid_; }
+
+ bool Done() {
+ if (!valid_)
+ return true;
+ coded_input_ = new google::protobuf::io::CodedInputStream(raw_input_);
+ if (!coded_input_->ReadVarint32(&size_))
+ return valid_ = false;
+ return (size_ == 0);
+ // TODO 260: there should be an easy way to tell if we're at the end
+ // of the file, but I can't seem to find a reliable way to do that
+ // easily...
+ }
+
+ bool Read(google::protobuf::Message* message) {
+ if (!valid_)
+ return false;
+ assert(size_ != UINT32_MAX);
+ google::protobuf::io::CodedInputStream::Limit limit
+ = coded_input_->PushLimit(size_);
+ if (!message->ParseFromCodedStream(coded_input_))
+ return valid_ = false;
+ if (!coded_input_->ConsumedEntireMessage() ||
+ coded_input_->BytesUntilLimit() != 0)
+ return valid_ = false;
+ coded_input_->PopLimit(limit); // for completeness; perhaps remove
+ delete coded_input_;
+ coded_input_ = NULL;
+ size_ = UINT32_MAX;
+ return true;
+ }
+
+ private:
+ int fd_;
+ google::protobuf::io::ZeroCopyInputStream* raw_input_;
+ google::protobuf::io::CodedInputStream* coded_input_;
+ google::protobuf::uint32 size_;
+ bool valid_;
+};
+
+class HeadedRecordWriter {
+ public:
+ HeadedRecordWriter(const string& filename, const pb::Header& header,
+ int buf_size = -1)
+ : writer_(filename, buf_size) {
+ if (!writer_.OK())
+ carp(CARP_FATAL, "Cannot create the file %s\n", filename.c_str());
+ Write(&header);
+ }
+
+ HeadedRecordWriter(google::protobuf::io::ZeroCopyOutputStream* raw_output,
+ const pb::Header& header)
+ : writer_(raw_output) {
+ Write(&header);
+ }
+
+ RecordWriter* Writer() { return &writer_; }
+
+ // client should check once after construction
+ bool OK() const { return writer_.OK(); }
+
+ bool Write(const google::protobuf::Message* message) {
+ return writer_.Write(message);
+ }
+
+ private:
+ RecordWriter writer_;
+};
+
+class HeadedRecordReader {
+ public:
+ HeadedRecordReader(const string& filename, pb::Header* header = NULL,
+ int buf_size = -1)
+ : reader_(filename, buf_size), header_(header),
+ del_header_(header == NULL) {
+ if (header == NULL)
+ header_ = new pb::Header;
+ if (!Done())
+ Read(header_);
+ }
+ ~HeadedRecordReader() { if (del_header_) delete header_; }
+
+ RecordReader* Reader() { return &reader_; }
+
+ bool OK() const { return reader_.OK(); }
+ bool Done() { return reader_.Done(); }
+ bool Read(google::protobuf::Message* message) {
+ return reader_.Read(message);
+ }
+ const pb::Header* GetHeader() const { return header_; }
+
+ private:
+ void ReadMagicNumber();
+ RecordReader reader_;
+ pb::Header* header_;
+ bool del_header_;
+};
+
+#endif // RECORDS_H
diff --git a/src/app/tide/records_to_vector-inl.h b/src/app/tide/records_to_vector-inl.h
new file mode 100644
index 0000000..85de861
--- /dev/null
+++ b/src/app/tide/records_to_vector-inl.h
@@ -0,0 +1,49 @@
+// Benjamin Diament
+//
+// Templatized function to read a file of records (as in records.{h,cc}) to
+// store in a vector<>.
+//
+// The template parameters are:
+// Protobuf: any protocol buffer message type.
+// VecElement: the type of the vector elements (vector<> actually contains
+// pointers). Usually same as Protobuf, but may be const. Note that
+// VecElement is implicit in the first function parameter.
+//
+// Example:
+//
+// vector<const pb::Protein*> proteins;
+// ReadRecordsToVector<pb::Protein>(&proteins, filename);
+//
+#include "records.h"
+template<class Protobuf, class VecElement>
+bool ReadRecordsToVector(vector<VecElement*>* vec, const string& filename,
+ pb::Header* header = NULL) {
+ HeadedRecordReader reader(filename, header);
+ while (!reader.Done()) {
+ Protobuf* protobuf = new Protobuf;
+ reader.Read(protobuf);
+ vec->push_back(protobuf);
+ }
+ if (!reader.OK()) { // Discard everything if we fail.
+ for (int i = 0; i < vec->size(); ++i)
+ delete (*vec)[i];
+ vec->clear();
+ return false;
+ }
+ return true;
+}
+
+template<class Protobuf>
+int CountRecords(const string& filename) {
+ int count = 0;
+ HeadedRecordReader reader(filename);
+ while (!reader.Done()) {
+ Protobuf protobuf;
+ reader.Read(&protobuf);
+ ++count;
+ }
+ if (!reader.OK())
+ return -1;
+
+ return count;
+}
diff --git a/src/app/tide/sp_scorer.cc b/src/app/tide/sp_scorer.cc
new file mode 100644
index 0000000..1d22732
--- /dev/null
+++ b/src/app/tide/sp_scorer.cc
@@ -0,0 +1,123 @@
+// Tahmina Baker
+//
+// This file contains implementations for classes defined in sp_scorer.h.
+// Please see the header file for details.
+
+#include <list>
+#include "sp_scorer.h"
+#include "peptide.h"
+
+SpScorer::SpScorer(const ProteinVec& proteins, const Spectrum& spectrum,
+ int charge, double max_mz)
+ : proteins_(proteins), spectrum_(spectrum), charge_(charge), max_mz_(max_mz),
+ sp_spectrum_(spectrum, charge, max_mz) {
+}
+
+bool SpScorer::IonLookup(double mass, int charge, bool previous_ion_matched,
+ SpScoreData& sp_score_data) {
+ bool matched = false;
+ sp_score_data.total_ions++;
+ int bin = GetBin(mass, charge);
+ double intensity = 0.0;
+ if (bin < max_mz_)
+ intensity = sp_spectrum_.Intensity(bin);
+ if (intensity > 0) {
+ // We have a match
+ matched = true;
+ sp_score_data.matched_ions++;
+ sp_score_data.intensity_sum += intensity;
+
+ if (previous_ion_matched) {
+ sp_score_data.repeat_count++;
+ }
+ }
+
+ return matched;
+}
+
+void SpScorer::Score(const pb::Peptide& pb_peptide, SpScoreData& sp_score_data) {
+ Peptide peptide(pb_peptide, proteins_);
+ vector<double> m_z(peptide.Len());
+ string sequence = peptide.Seq();
+
+ // Collect m/z values for each residue
+ for (int i = 0; i < sequence.length(); i++)
+ m_z[i] = MassConstants::mono_table[sequence[i]];
+
+ // Account for modifications
+ const ModCoder::Mod* mods;
+ int num_mods = peptide.Mods(&mods);
+ for (int i = 0; i < num_mods; i++) {
+ int index;
+ double delta;
+ MassConstants::DecodeMod(mods[i], &index, &delta);
+ m_z[index] += delta;
+ }
+
+ int precursor_charge = (charge_ == 1) ? 2 : charge_;
+ for (int ion_charge = 1; ion_charge < precursor_charge; ion_charge++) {
+ // Needed for keeping track of repeat_count
+ bool previous_b_ion_matched = false;
+ bool previous_y_ion_matched = false;
+
+ double b_ion = MassConstants::proton;
+ double y_ion = peptide.Mass() + MassConstants::proton;
+
+ for (int i = 0; i < sequence.length(); i++) {
+ // Calculate and look up b-ions
+ if (i < sequence.length()-1) {
+ b_ion += m_z[i];
+ previous_b_ion_matched = IonLookup(b_ion, ion_charge,
+ previous_b_ion_matched,
+ sp_score_data);
+ }
+
+ // Calculate and look up y-ions
+ if (i > 0) {
+ y_ion -= m_z[i-1];
+ previous_y_ion_matched = IonLookup(y_ion, ion_charge,
+ previous_y_ion_matched,
+ sp_score_data);
+ }
+ }
+ }
+
+ sp_score_data.CalculateSpScore(sp_spectrum_.Beta());
+}
+
+void SpScorer::RankSpScores(vector<SpScoreData>& scores,
+ double* smallest_score) {
+
+ if (scores.size() > 0) {
+ *smallest_score = scores[0].sp_score;
+ } else {
+ *smallest_score = 0.0;
+ }
+
+ // We use this list to sort the matches according to sp score, then
+ // use the match id to assign the rankings to the sp scores passed in
+ list<SpScoreMatchPair> sp_score_match_list;
+ for (int match = 0; match < scores.size(); match++) {
+ sp_score_match_list.push_back(make_pair(scores[match].sp_score, match));
+ if (scores[match].sp_score < *smallest_score)
+ *smallest_score = scores[match].sp_score;
+ }
+ sp_score_match_list.sort(CompareBySpScore);
+
+ // Assign rankings to the sp scores passed in
+ list<SpScoreMatchPair>::iterator i;
+ int rank_count = 0;
+ for (i=sp_score_match_list.begin(); i != sp_score_match_list.end(); ++i) {
+ scores[i->second].sp_rank = ++rank_count;
+ }
+
+ if (smallest_score) {
+ if (sp_score_match_list.size() > 0) {
+ // After we go through the loop that assigns the rankings, i is at
+ // list.end(). If we iterate back one, we'll have the lowest sp score.
+ *smallest_score = scores[(--i)->second].sp_score;
+ } else {
+ *smallest_score = 0.0;
+ }
+ }
+}
diff --git a/src/app/tide/sp_scorer.h b/src/app/tide/sp_scorer.h
new file mode 100644
index 0000000..536a4a7
--- /dev/null
+++ b/src/app/tide/sp_scorer.h
@@ -0,0 +1,107 @@
+// Tahmina Baker
+//
+// This file contains classes for calculating the sp score.
+//
+// The sp score is calculated as follows:
+// sp = (intensity_sum*ion_match) * (1+(repeat_count*beta))/num_ions
+//
+// intensity_sum:
+// Convert each ion mz into a bin and use as index into an array of
+// intensities for the spectrum which has been preprocessed for sp
+// calculations (see SpSpectrum for details). This will give us a
+// single_intensity = spectrum_intensity_array[ion.bin]. We then sum up
+// these intensities to get an intensity_sum.
+//
+// ion_match:
+// The total count of ions satisfying the condition (single_intensity > 0)
+//
+// repeat_count:
+// Counts the links between CONSECUTIVE ions matching the spectrum. For example,
+// let's say the following y ion series matched with the spectrum at ion
+// charge 1: y1y2y3y6y12y13. We have consecutive ion matches between y1y2, y2y3
+// and y12y13. The repeat_count then equals 3.
+//
+// beta:
+// Jimmy said this was just some number they came up with. It is simply 0.075.
+// He doesn't know why.
+//
+// num_ions:
+// The total number of ions we tried to match with the spectrum.
+
+
+#ifndef SP_SCORER_H
+#define SP_SCORER_H
+
+#include <vector>
+//#include "peptide.h"
+#include "crux_sp_spectrum.h"
+#include "raw_proteins.pb.h"
+#include "peptides.pb.h"
+
+typedef vector<const pb::Protein*> ProteinVec;
+typedef vector<const pb::AuxLocation*> AuxLocVec;
+
+
+class SpScorer {
+ public:
+ struct SpScoreData {
+ double sp_score;
+ int sp_rank;
+ int matched_ions;
+ int total_ions;
+ double intensity_sum;
+ int repeat_count;
+
+ SpScoreData() : sp_score(0.0), sp_rank(0), matched_ions(0), total_ions(0),
+ intensity_sum(0.0), repeat_count(0) { }
+
+ SpScoreData(double sp_score_in, int sp_rank_in,
+ int matched_ions_in, int total_ions_in,
+ double intensity_sum_in, int repeat_count_in)
+ : sp_score(sp_score_in), sp_rank(sp_rank_in),
+ matched_ions(matched_ions_in), total_ions(total_ions_in),
+ intensity_sum(intensity_sum_in), repeat_count(repeat_count_in) { }
+
+ void CalculateSpScore(double beta) {
+ if (total_ions != 0) {
+ sp_score = (intensity_sum * matched_ions) *
+ (1 + (repeat_count * beta)) / total_ions;
+ }
+ }
+ };
+
+ SpScorer(const ProteinVec& proteins, const Spectrum& spectrum,
+ int charge, double max_mz);
+
+ void Score(const pb::Peptide& pb_peptide, SpScoreData& sp_score_data);
+ void RankSpScores(vector<SpScoreData>& scores,
+ double* smallest_score = NULL);
+ double TotalIonIntensity() {return sp_spectrum_.TotalIonIntensity();}
+
+ private:
+ typedef pair<double, int> SpScoreMatchPair;
+
+ static bool CompareBySpScore(SpScoreMatchPair sp_score_1,
+ SpScoreMatchPair sp_score_2) {
+ if (sp_score_1.first > sp_score_2.first)
+ return true;
+ return false;
+ }
+
+ int GetBin(double mass, int charge) {
+// double mz = (mass + (charge - 1)*MassConstants::proton)/charge;
+ return MassConstants::mass2bin(mass, charge);
+ }
+
+ bool IonLookup(double mass, int charge, bool previous_ion_matched,
+ SpScoreData& sp_score_data);
+
+
+ const ProteinVec& proteins_;
+ const Spectrum& spectrum_;
+ SpSpectrum sp_spectrum_;
+ int charge_;
+ double max_mz_;
+};
+
+#endif // SP_SCORER_H
diff --git a/src/app/tide/spectrum_collection.cc b/src/app/tide/spectrum_collection.cc
new file mode 100644
index 0000000..3c204ae
--- /dev/null
+++ b/src/app/tide/spectrum_collection.cc
@@ -0,0 +1,218 @@
+// Benjamin Diament
+//
+// See .h file.
+
+#include <stdio.h>
+#include <math.h>
+#include <iostream>
+#include <algorithm>
+#include <functional>
+#include "spectrum.pb.h"
+#include "spectrum_collection.h"
+#include "mass_constants.h"
+#include "records.h"
+#include "records_to_vector-inl.h"
+
+using namespace std;
+using google::protobuf::uint64;
+
+#define CHECK(x) GOOGLE_CHECK((x))
+
+Spectrum::Spectrum(const pb::Spectrum& spec) {
+ spectrum_number_ = spec.spectrum_number();
+ precursor_m_z_ = spec.precursor_m_z();
+ rtime_ = spec.rtime();
+ for (int i = 0; i < spec.charge_state_size(); ++i)
+ charge_states_.push_back(spec.charge_state(i));
+ int size = spec.peak_m_z_size();
+ CHECK(size == spec.peak_intensity_size());
+ ReservePeaks(size);
+ uint64 total = 0;
+ double m_z_denom = spec.peak_m_z_denominator();
+ double intensity_denom = spec.peak_intensity_denominator();
+ for (int i = 0; i < size; ++i) {
+ CHECK(spec.peak_m_z(i) > 0);
+ total += spec.peak_m_z(i); // deltas of m/z are stored
+ peak_m_z_.push_back(total / m_z_denom);
+ peak_intensity_.push_back(spec.peak_intensity(i) / intensity_denom);
+ }
+}
+
+static inline bool IsInt(double x) {
+ // See whether x is quite close to an integer (within 0.001).
+ return fabs(x - uint64(x+0.5)) < 0.001;
+}
+
+static inline bool CheckDenom(const vector<double>& vals, int denom) {
+ // See whether all vals can be accommodated by denom when rendered as a
+ // fraction.
+ double d_denom = denom;
+ for (int i = 0; i < vals.size(); ++ i) {
+ if (!IsInt(vals[i] * d_denom))
+ return false;
+ }
+ return true;
+}
+
+static inline int GetDenom(const vector<double>& vals) {
+ // See how much precision is given in the vals array. Not especially fast,
+ // but fast enough. Used only for converting spectrum input format.
+ const int kMaxPrecision = 10000; // store at most 3 digits of precision
+ for (int precision = 1; precision < kMaxPrecision; precision *= 10)
+ if (CheckDenom(vals, precision))
+ return precision;
+ return kMaxPrecision;
+}
+
+void Spectrum::FillPB(pb::Spectrum* spec) {
+ spec->Clear();
+ spec->set_spectrum_number(spectrum_number_);
+ if (precursor_m_z_ > 0)
+ spec->set_precursor_m_z(precursor_m_z_);
+ spec->set_rtime(rtime_);
+ for (int i = 0; i < NumChargeStates(); ++i)
+ spec->add_charge_state(ChargeState(i));
+ int size = peak_m_z_.size();
+ CHECK(size == peak_intensity_.size());
+ int m_z_denom = GetDenom(peak_m_z_);
+ int intensity_denom = GetDenom(peak_intensity_);
+ spec->set_peak_m_z_denominator(m_z_denom);
+ spec->set_peak_intensity_denominator(intensity_denom);
+ uint64 last = 0;
+ for (int i = 0; i < size; ++i) {
+ uint64 val = uint64(peak_m_z_[i]*m_z_denom + 0.5);
+ CHECK(val > last);
+ spec->add_peak_m_z(val - last);
+ last = val;
+ spec->add_peak_intensity(uint64(peak_intensity_[i]*intensity_denom + 0.5));
+ }
+}
+
+void Spectrum::SortIfNecessary() {
+ if (adjacent_find(peak_m_z_.begin(), peak_m_z_.end(), greater<double>())
+ == peak_m_z_.end())
+ return;
+
+ // TODO: eliminate copy operations
+ int size = Size();
+ vector< pair<double, double> > pairs;
+ for (int i = 0; i < size; ++i)
+ pairs[i] = make_pair(peak_m_z_[i], peak_intensity_[i]);
+ sort(pairs.begin(), pairs.begin() + size);
+ for (int i = 0; i < size; ++i) {
+ peak_m_z_[i] = pairs[i].first;
+ peak_intensity_[i] = pairs[i].second;
+ }
+}
+
+void SpectrumCollection::ReadMS(istream& in, bool ms1) {
+ // Parse MS2 file format.
+ // Not very fast: uses scanf. CONSIDER speed-up.
+ static const int kMaxLine = 1000;
+ char line[kMaxLine];
+ Spectrum* spectrum = NULL;
+ while (in.getline(line, kMaxLine)) {
+ switch(line[0]) {
+ case 'S': {
+ if (spectrum)
+ spectra_.push_back(spectrum);
+ int specnum1, specnum2;
+ double precursor_m_z = 0;
+ int ok1 = 0;
+ int ok2 = 0;
+ sscanf(line, "S %d %d%n%lf%n", &specnum1, &specnum2, &ok1,
+ &precursor_m_z, &ok2);
+ CHECK((ok1 > 0) && (ms1 != (ok2 > 0)));
+ CHECK(specnum1 == specnum2);
+ spectrum = new Spectrum(specnum1, precursor_m_z);
+ }
+ break;
+ case 'I': {
+ int pos = 0;
+ double rtime = -1;
+ sscanf(line, "I RTime %n%lf", &pos, &rtime);
+ if (pos > 0) {
+ CHECK(rtime >= 0);
+ spectrum->SetRTime(rtime);
+ }
+ }
+ break;
+ case 'Z':
+ int charge;
+ CHECK(1 == sscanf(line, "Z %d", &charge));
+ spectrum->AddChargeState(charge);
+ break;
+ case '0': case '1': case '2': case '3': case '4':
+ case '5': case '6': case '7': case '8': case '9':
+ double location, intensity;
+ CHECK(2 == sscanf(line, "%lf %lf", &location, &intensity));
+ if (spectrum->Size() > 0) // check that m_z values are increasing.
+ CHECK(location > spectrum->M_Z(spectrum->Size() - 1));
+ if (intensity > 0)
+ spectrum->AddPeak(location, intensity);
+ break;
+ default:
+ break;
+ }
+ }
+ if (spectrum)
+ spectra_.push_back(spectrum);
+}
+
+bool SpectrumCollection::ReadSpectrumRecords(const string& filename,
+ pb::Header* header) {
+ pb::Header tmp_header;
+ if (header == NULL)
+ header = &tmp_header;
+ HeadedRecordReader reader(filename, header);
+ if (header->file_type() != pb::Header::SPECTRA)
+ return false;
+ pb::Spectrum pb_spectrum;
+ while (!reader.Done()) {
+ reader.Read(&pb_spectrum);
+ spectra_.push_back(new Spectrum(pb_spectrum));
+ }
+ if (!reader.OK()) {
+ for (int i = 0; i < spectra_.size(); ++i)
+ delete spectra_[i];
+ spectra_.clear();
+ return false;
+ }
+ return true;
+}
+
+void SpectrumCollection::MakeSpecCharges() {
+ // Create one entry in the spec_charges_ array for each
+ // (spectrum, charge) pair.
+ int spectrum_index = 0;
+ vector<Spectrum*>::iterator i = spectra_.begin();
+ for (; i != spectra_.end(); ++i) {
+ for (int j = 0; j < (*i)->NumChargeStates(); ++j) {
+ int charge = (*i)->ChargeState(j);
+ double neutral_mass = (((*i)->PrecursorMZ() - MassConstants::proton)
+ * charge);
+ spec_charges_.push_back(SpecCharge(neutral_mass, charge, *i,
+ spectrum_index));
+ }
+ spectrum_index++;
+ }
+}
+
+double SpectrumCollection::FindHighestMZ() const {
+ // Return the maximum MZ seen across all input spectra.
+ double highest = 0;
+ vector<Spectrum*>::const_iterator i = spectra_.begin();
+ for (; i != spectra_.end(); ++i) {
+ CHECK((*i)->Size() > 0) << "ERROR: spectrum " << (*i)->SpectrumNumber()
+ << " has no peaks.\n";
+ double last_peak = (*i)->M_Z((*i)->Size() - 1);
+ if (last_peak > highest)
+ highest = last_peak;
+ }
+ return highest;
+}
+
+void SpectrumCollection::Sort() {
+ MakeSpecCharges();
+ sort(spec_charges_.begin(), spec_charges_.end());
+}
diff --git a/src/app/tide/spectrum_collection.h b/src/app/tide/spectrum_collection.h
new file mode 100644
index 0000000..cf8014c
--- /dev/null
+++ b/src/app/tide/spectrum_collection.h
@@ -0,0 +1,122 @@
+// Benjamin Diament
+//
+// The Spectrum class represents a single spectrum, unprocessed. Instances can
+// be read from and to the pb::Spectrum protocol buffer type (q.v.), which is
+// relatively compact.
+//
+// The SpectrumCollection class represents all the spectra in the input.
+// Initialize with ReadMS2() or ReadSpectrumRecords(). ReadMS2() takes an MS2
+// format, ReadSpectrumRecords() takes a file of records of spectrum.proto.
+//
+// SpectrumCollection::Sort() creates one entry in the spec_charges_ array for
+// each (spectrum, charge) pair, e.g. for the case where a spectrum has
+// multiple possible charge states. The spectra have to be sorted by neutral
+// mass in order to perform the rolling-window join. (See
+// active_peptide_queue.{h,cc}.)
+//
+// SpectrumCollection::FindHighestMZ() returns the maximum MZ seen across all
+// input spectra. This is cached by the MaxMZ class.
+
+#ifndef SPECTRUM_COLLECTION_H
+#define SPECTRUM_COLLECTION_H
+
+#include <iostream>
+#include <vector>
+#include "header.pb.h"
+#include "spectrum.pb.h"
+
+using namespace std;
+
+class Spectrum {
+ public:
+ // Manual instantiation and specification
+ Spectrum(int spectrum_number, double precursor_m_z)
+ : spectrum_number_(spectrum_number), precursor_m_z_(precursor_m_z) {
+ }
+ void ReservePeaks(int num) {
+ peak_m_z_.reserve(num);
+ peak_intensity_.reserve(num);
+ }
+ void SetRTime(double rtime) { rtime_ = rtime; }
+ void AddChargeState(int charge_state) {
+ charge_states_.push_back(charge_state);
+ }
+ void AddPeak(double m_z, double intensity) {
+ peak_m_z_.push_back(m_z);
+ peak_intensity_.push_back(intensity);
+ }
+
+ explicit Spectrum(const pb::Spectrum& spec); // Instantiation from PB
+ void FillPB(pb::Spectrum* spec);
+
+ int SpectrumNumber() const { return spectrum_number_; }
+ double PrecursorMZ() const { return precursor_m_z_; }
+ double RTime() const { return rtime_; }
+
+ int NumChargeStates() const { return charge_states_.size(); }
+ int ChargeState(int index) const { return charge_states_[index]; }
+
+ int Size() const { return peak_m_z_.size(); } // number of peaks
+ double M_Z(int index) const { return peak_m_z_[index]; }
+ double Intensity(int index) const { return peak_intensity_[index]; }
+
+ void SortIfNecessary();
+ void InferChargeStatesIfNecessary();
+
+ private:
+ int spectrum_number_;
+ double rtime_;
+ double precursor_m_z_;
+ vector<int> charge_states_;
+
+ vector<double> peak_m_z_;
+ vector<double> peak_intensity_;
+};
+
+class SpectrumCollection {
+ public:
+ ~SpectrumCollection() {
+ for (int i = 0; i < spectra_.size(); ++i)
+ delete spectra_[i];
+ }
+
+ void ReadMS(istream& in, bool ms1);
+ bool ReadSpectrumRecords(const string& filename, pb::Header* header = NULL);
+ void Sort();
+
+ template<typename BinaryPredicate>
+ void Sort(BinaryPredicate Predicate) {
+ MakeSpecCharges();
+ sort(spec_charges_.begin(), spec_charges_.end(), Predicate);
+ }
+
+ double FindHighestMZ() const;
+
+ struct SpecCharge {
+ double neutral_mass;
+ int charge;
+ Spectrum* spectrum;
+ int spectrum_index;
+
+ SpecCharge(double neutral_mass_param, int charge_param,
+ Spectrum* spectrum_param, int spectrum_index_param)
+ : neutral_mass(neutral_mass_param), charge(charge_param),
+ spectrum(spectrum_param), spectrum_index(spectrum_index_param) {
+ }
+
+ bool operator<(const SpecCharge& other) const {
+ return (neutral_mass < other.neutral_mass);
+ }
+ };
+
+ const vector<SpecCharge>* SpecCharges() const { return &spec_charges_; }
+ vector<Spectrum*>* Spectra() { return &spectra_; }
+
+ private:
+ void MakeSpecCharges();
+
+ vector<Spectrum*> spectra_;
+ vector<SpecCharge> spec_charges_;
+};
+
+#endif // SPECTRUM_COLLECTION_H
diff --git a/src/app/tide/spectrum_preprocess.h b/src/app/tide/spectrum_preprocess.h
new file mode 100644
index 0000000..5942bb5
--- /dev/null
+++ b/src/app/tide/spectrum_preprocess.h
@@ -0,0 +1,203 @@
+// Benjamin Diament
+
+// ObservedPeakSet is a workspace for preprocessing an observed spectrum,
+// passed in as a protocol buffer to PreprocessSpectrum().
+//
+// Memory allocated upon construction may be reused for multiple spectra,
+// provided that the spectrum adheres to the limits of MaxMZ::Global().
+// (This guarantee is provided at search time by code that finds the maximimum
+// values as a side effect of sorting. In search.cc the code is this:
+// spectra.Sort();
+// MaxMZ::SetGlobalMax(spectra.HighestMZ());
+// If such a maximumum weren't known in advance the client would construct
+// a fresh ObervedPeakSet.)
+//
+// PreprocessSpectrum() first performs a normalization procedure, then
+// performs some scaling operations and linear combinations and caches the
+// results. The normalization procedure is as described in the XCORR
+// literature: the sqrt of each peak intensity is taken, then peaks are
+// divided into 10 regions and normalized to have a maximum intensity of 50
+// within each region.
+//
+// Notionally what we wish to do is to take a dot product of the normalized peak
+// vector with a potentially large collection of different theoretical peak
+// vectors, one dot product for each candidate peptide. In the interest of
+// efficiency, and because the structure of the theoretical peak vector has some
+// regularities, we can gain efficiency by caching certain results. The cache,
+// accessed by GetCache(), consists of various transformations of the normalized
+// peak vector.
+//
+// These efficiencies are availlable because certain patterns are seen in these
+// theoretical spectra over and over. For instance, whenever we see a Y ion at a
+// particular m/z bin in the theoretical spectrum it will have intensity of 50,
+// and the two bins flanking it will have an intensity of 25. If this Y ion were
+// of charge 1 then a neutral loss of ammonia will almost always appear 17 bins
+// to the left with intensity 10. If this Y ion were of charge 2 then the
+// theoretical spectrum will have a peak of intensity 10 at either 8 or 9 bins
+// to the left -- both versions occur commonly in different theoretical spectra.
+// If this ion were a B ion of charge 1 instead, we would additionally expect a
+// corresponding A ion 28 bins to the left in the theoretical spectrum and a
+// neutral loss of water 18 bins to the left. Because these patterns are so
+// common, it pays very well to compute these transformations and cache the
+// results.
+//
+// Let's call the normalized peak vector u. The cache itself contains several
+// vectors, corresponding to each of the TheoreticalPeakType's (see
+// theoretical_peak_pair.h). The first few are straightforward:
+//
+// PeakMain --> u
+// LossPeak --> 10 * u
+// FlankingPeak --> 25 * u
+// PrimaryPeak --> 50 * u
+//
+// Actually, instead of computing 10 * u, 25 * u, and 50 * u, we compute 2 * u,
+// 5 * u and 10 * u. This results in dot products that are 5 times too small,
+// but the adjustments can be made at the last moment e.g. when results are
+// displayed. These smaller multiplications allow us to use addition operations
+// instead of multiplications.
+//
+// The remaining cache vectors are linear combinations. The idea is that
+// multiplying the ith entry of the appropriate vector below by the ith entry in
+// a theoretical vector of only B and Y ions will capture the contribution of
+// the flanks and the neutral lossses and A ion all in one operation.
+//
+// PeakCombinedB1 represents a charge 1 B ion. u[i-1] and u[i+1] are the two
+// flanking bins. u[i-17] represents the loss of NH3 at charge 1, u[i-18]
+// represents the loss of H2O at charge 1, and u[i-28] represents the A ion at
+// charge 1. It's useful to cache this vector because, most often, a
+// TheoreticalPeakSet will need to represent all six of these peaks at these
+// intensities and relative displacements whenever a B ion of charge 1 is
+// present. Moreover, in the rare case where one or two of these displacements
+// are off by one, say, with respect to the actual TheoreticalPeakSet, a
+// difference vector reprsented by TheoreticalPeakSetDiff (q.v.) accommodates
+// the discrepancy.
+// The ith entry of this cache vector is:
+// 50*u[i] + 25*u[i-1] + 25*u[i+1] + 10*u[i-17] + 10*u[i-18] + 10*u[i-28]
+//
+// Cache vetors for other common theoretical peak conformations are defined
+// similarly:
+//
+// PeakCombinedY1 represents a charge 1 Y ion, its flanks and neutral losses.
+// The ith entry of this cache vector is:
+// 50*u[i] + 25*u[i-1] + 25*u[i+1] + 10*u[i-17]
+//
+// Each of the charge 2 peak types below includes an 'a' version and a 'b'
+// version. In the 'a' version the loss of ammonia is 9 Da. per charge. In the
+// 'b' version the loss of ammonia is 8 Da. per charge. This is because both of
+// these versions occur commonly.
+//
+// PeakCombinedB2a represents a charge 2 B ion, its flanks and neutral losses.
+// The ith entry of this cache vector is:
+// 50*u[i] + 25*u[i-1] + 25*u[i+1] + 10*u[i-9] + 10*u[i-14]
+//
+// PeakCombinedY2a represents a charge 2 Y ion, its flanks and neutral losses.
+// The ith entry of this cache vector is:
+// 50*u[i] + 25*u[i-1] + 25*u[i+1] + 10*u[i-9]
+//
+// PeakCombinedB2b represents a charge 2 B ion, its flanks and neutral losses.
+// The ith entry of this cache vector is:
+// 50*u[i] + 25*u[i-1] + 25*u[i+1] + 10*u[i-8] + 10*u[i-9] + 10*u[i-14]
+//
+// PeakCombinedY2b represents a charge 2 Y ion, its flanks and neutral losses.
+// The ith entry of this cache vector is:
+// 50*u[i] + 25*u[i-1] + 25*u[i+1] + 10*u[i-8]
+#ifndef SPECTRUM_PREPROCESS_H
+#define SPECTRUM_PREPROCESS_H
+
+#include <iostream>
+#include <vector>
+#include "theoretical_peak_pair.h"
+#include "max_mz.h"
+#include "mass_constants.h"
+
+using namespace std;
+
+class Spectrum;
+
+class ObservedPeakSet {
+ public:
+
+ ObservedPeakSet(double bin_width = MassConstants::bin_width_,
+ double bin_offset = MassConstants::bin_width_,
+ bool NL = false, bool FP = false)
+ : peaks_(new double[MaxBin::Global().BackgroundBinEnd()]),
+ cache_(new int[MaxBin::Global().CacheBinEnd()*NUM_PEAK_TYPES]) {
+
+ bin_width_ = bin_width;
+ bin_offset_ = bin_offset;
+ NL_ = NL; //NL means neutral loss
+ FP_ = FP; //FP means flanking peaks
+ }
+
+ ~ObservedPeakSet() { delete[] peaks_; delete[] cache_; }
+
+ const int* GetCache() const { return cache_; } //TODO 261: access restriction?
+
+ // On-the-fly compilation takes the place of this call.
+ int DotProd(const TheoreticalPeakArr& theoretical);
+#ifdef DEBUG
+ int DebugDotProd(const TheoreticalPeakArr& theoretical);
+#endif
+ void PreprocessSpectrum(const Spectrum& spectrum, int charge);
+ void CreateEvidenceVector(const Spectrum& spectrum, double binWidth,
+ double binOffset, int charge, double pepMassMonoMean,
+ int maxPrecurMass, int* evidenceInt);
+
+ // For debugging
+ void Show(const string& name, TheoreticalPeakType peak_type, bool cache_end) {
+ int end = cache_end ? max_mz_.CacheBinEnd() : max_mz_.BackgroundBinEnd();
+ for (int i = 0; i < end; ++i) {
+ double peak = Peak(peak_type, i);
+ if (peak != 0)
+ cout << name << "[" << i << "] = " << peak << endl;
+ }
+ }
+
+#define SHOW(x, y) Show(#x, x, y);
+
+ // For debugging
+ void ShowCache() {
+ SHOW(PeakMain, false);
+ SHOW(LossPeak, false);
+ SHOW(FlankingPeak, false);
+ SHOW(PrimaryPeak, false);
+ SHOW(PeakCombinedB1, true);
+ SHOW(PeakCombinedY1, true);
+ SHOW(PeakCombinedB2, true);
+ SHOW(PeakCombinedY2, true);
+// SHOW(PeakCombinedB2b, true);
+// SHOW(PeakCombinedY2b, true);
+ }
+
+ // For debugging
+ void ShowPeaks() {
+ for (int i = 0; i < max_mz_.BackgroundBinEnd(); ++i)
+ if (peaks_[i] != 0)
+ cout << "peaks_[" << i << "] = " << peaks_[i] << endl;
+ }
+
+ private:
+ int& Peak(TheoreticalPeakType peak_type, int index) {
+ // Note the different order than for TheoreticalPeakPair's constructor.
+ // In context of this class, peak_type feels like the primary selector.
+ return cache_[TheoreticalPeakPair(index, peak_type).Code()];
+ }
+ void MakeInteger();
+ void ComputeCache();
+
+ double* peaks_;
+ int* cache_;
+
+ bool NL_;
+ bool FP_;
+ double bin_width_;
+ double bin_offset_;
+
+ MaxBin max_mz_;
+ int cache_end_;
+
+ friend class ObservedPeakTester;
+};
+
+#endif
+
diff --git a/src/app/tide/spectrum_preprocess2.cc b/src/app/tide/spectrum_preprocess2.cc
new file mode 100644
index 0000000..d317b68
--- /dev/null
+++ b/src/app/tide/spectrum_preprocess2.cc
@@ -0,0 +1,563 @@
+// Benjamin Diament
+//
+// Mostly an implementation of ObservedPeakSet::PreprocessSpectrum(). See .h
+// file.
+//
+// Portions of this code are taken verbatim from Crux, specifically
+// NormalizeEachRegion(). The region-defining code in PreprocessSpectrum() is
+// also from Crux and inherits the attendant arcana. Some of this code is
+// certainly at odds with the published intention of XCORR, but in order to
+// preserve the results from Crux exactly we retain this legacy for now.
+// TODO 251: revisit this.
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <time.h>
+#include <math.h>
+#include <algorithm>
+#include <math.h>
+#include <gflags/gflags.h>
+#include "spectrum_collection.h"
+#include "spectrum_preprocess.h"
+#include "mass_constants.h"
+#include "max_mz.h"
+#include "util/Params.h"
+
+using namespace std;
+
+// Number of m/z regions in XCorr normalization.
+#define NUM_SPECTRUM_REGIONS 10
+
+// Integerization constant for the XCorr p-value calculation.
+#define EVIDENCE_INT_SCALE 500.0
+
+#ifdef DEBUG
+DEFINE_int32(debug_spectrum_id, -1, "Spectrum number to debug");
+DEFINE_int32(debug_charge, 0, "Charge to debug. 0 for all");
+#endif
+
+// This computes that part of the XCORR function where an average value of the
+// peaks within a window surrounding each peak is subtracted from that peak.
+// This version is a linear-time implementation of the subtraction. Linearity is
+// accomplished by computing an array of partial sums.
+static void SubtractBackground(double* observed, int end) {
+ // operation is as follows: new_observed = observed -
+ // average_within_window but average is computed as if the array
+ // extended infinitely: denominator is same throughout array, even
+ // near edges (where fewer elements have been summed)
+ static const double multiplier = 1.0 / (MAX_XCORR_OFFSET * 2);
+
+ double total = 0;
+ vector<double> partial_sums(end+1);
+ for (int i = 0; i < end; ++i)
+ partial_sums[i] = (total += observed[i]);
+ partial_sums[end] = total;
+
+ for (int i = 0; i < end; ++i) {
+ int right_index = min(end, i + MAX_XCORR_OFFSET);
+ int left_index = max(0, i - MAX_XCORR_OFFSET - 1);
+ observed[i] -= multiplier * (partial_sums[right_index] - partial_sums[left_index] - observed[i]);
+ }
+}
+
+void ObservedPeakSet::PreprocessSpectrum(const Spectrum& spectrum,
+ int charge ) {
+#ifdef DEBUG
+ bool debug = (FLAGS_debug_spectrum_id == spectrum.SpectrumNumber()
+ && (FLAGS_debug_charge == 0 || FLAGS_debug_charge == charge));
+ if (debug)
+ debug = true; // allows a breakpoint
+#endif
+ double precursor_mz = spectrum.PrecursorMZ();
+ double proton = MassConstants::proton;
+ double experimental_mass_cut_off = (precursor_mz-proton)*charge+proton + 50;
+ double max_peak_mz = spectrum.M_Z(spectrum.Size()-1);
+
+ assert(MaxBin::Global().MaxBinEnd() > 0);
+
+ max_mz_.InitBin(min(experimental_mass_cut_off, max_peak_mz));
+ cache_end_ = MaxBin::Global().CacheBinEnd() * NUM_PEAK_TYPES;
+
+ memset(peaks_, 0, sizeof(double) * MaxBin::Global().BackgroundBinEnd());
+
+ if (Params::GetBool("skip-preprocessing")) {
+ for (int i = 0; i < spectrum.Size(); ++i) {
+ double peak_location = spectrum.M_Z(i);
+ if (peak_location >= experimental_mass_cut_off) {
+ continue;
+ }
+ int mz = MassConstants::mass2bin(peak_location);
+ double intensity = spectrum.Intensity(i);
+ if (intensity > peaks_[mz]) {
+ peaks_[mz] = intensity;
+ }
+ }
+ } else {
+ bool remove_precursor = Params::GetBool("remove-precursor-peak");
+ double precursor_tolerance = Params::GetDouble("remove-precursor-tolerance");
+
+ // Fill peaks
+ int largest_mz = 0;
+ double highest_intensity = 0;
+ for (int i = 0; i < spectrum.Size(); ++i) {
+ double peak_location = spectrum.M_Z(i);
+ if (peak_location >= experimental_mass_cut_off ||
+ (remove_precursor && fabs(peak_location - precursor_mz) <= precursor_tolerance)) {
+ continue;
+ }
+
+ double intensity = spectrum.Intensity(i);
+ int mz = MassConstants::mass2bin(peak_location);
+ if ((mz > largest_mz) && (intensity > 0)) {
+ largest_mz = mz;
+ }
+
+ intensity = sqrt(intensity);
+ if (intensity > highest_intensity) {
+ highest_intensity = intensity;
+ }
+ if (intensity > peaks_[mz]) {
+ peaks_[mz] = intensity;
+ }
+ }
+
+ double intensity_cutoff = highest_intensity * 0.05;
+
+ double normalizer = 0.0;
+ int region_size = largest_mz / NUM_SPECTRUM_REGIONS + 1;
+ for (int i = 0; i < NUM_SPECTRUM_REGIONS; ++i) {
+ highest_intensity = 0;
+ int high_index = i;
+ for (int j = 0; j < region_size; ++j) {
+ int index = i * region_size + j;
+ if (peaks_[index] <= intensity_cutoff) {
+ peaks_[index] = 0;
+ }
+ if (peaks_[index] > highest_intensity) {
+ highest_intensity = peaks_[index];
+ high_index = index;
+ }
+ }
+ if (highest_intensity == 0) {
+ continue;
+ }
+ normalizer = 50.0 / highest_intensity;
+ for (int j = 0; j < region_size; ++j) {
+ int index = i * region_size + j;
+ if (peaks_[index] != 0) {
+ peaks_[index] *= normalizer;
+ }
+ }
+ }
+
+#ifdef DEBUG
+ if (debug) {
+ cout << "GLOBAL MAX MZ: " << MaxMZ::Global().MaxBin() << ", " << MaxMZ::Global().BackgroundBinEnd()
+ << ", " << MaxMZ::Global().CacheBinEnd() << endl;
+ cout << "MAX MZ: " << max_mz_.MaxBin() << ", " << max_mz_.BackgroundBinEnd()
+ << ", " << max_mz_.CacheBinEnd() << endl;
+ ShowPeaks();
+ cout << "====== SUBTRACTING BACKGROUND ======" << endl;
+ }
+#endif
+ }
+ SubtractBackground(peaks_, max_mz_.BackgroundBinEnd());
+
+#ifdef DEBUG
+ if (debug)
+ ShowPeaks();
+#endif
+ MakeInteger();
+ ComputeCache();
+#ifdef DEBUG
+ if (debug)
+ ShowCache();
+#endif
+}
+
+/* Calculates vector of cleavage evidence for an observed spectrum, using XCorr
+ * b/y/neutral peak sets and heights.
+ *
+ * Written by Jeff Howbert, May, 2013 (as function createEvidenceArrayObserved).
+ * Extended and modified by Jeff Howbert, October, 2013.
+ * Ported to and integrated with Tide by Jeff Howbert, November, 2013.
+ */
+void ObservedPeakSet::CreateEvidenceVector(
+ const Spectrum& spectrum,
+ double binWidth,
+ double binOffset,
+ int charge,
+ double pepMassMonoMean,
+ int maxPrecurMass,
+ int* evidenceInt
+) {
+
+ // TODO preserved from PreprocessSpectrum; may delete in future
+#ifdef DEBUG
+ bool debug = (FLAGS_debug_spectrum_id == spectrum.SpectrumNumber()
+ && (FLAGS_debug_charge == 0 || FLAGS_debug_charge == charge));
+ if (debug) {
+ debug = true; // allows a breakpoint
+ }
+#endif
+ // double experimental_mass_cut_off = (precursor_mz-proton)*charge+proton + 50;
+ // double max_peak_mz = spectrum.M_Z(spectrum.Size()-1);
+ assert(MaxBin::Global().MaxBinEnd() > 0);
+ // max_mz_.Init(min(experimental_mass_cut_off, max_peak_mz));
+ // TODO end preserved
+
+ // TODO need to review these constants, decide which can be moved to parameter file
+ const int nRegion = NUM_SPECTRUM_REGIONS;
+ const double maxIntensPerRegion = 50.0;
+ const double precursorMZExclude = 15.0;
+ const double massNH3Mono = 17.02655; // mass of NH3 (monoisotopic)
+ const double massCOMono = 27.9949; // mass of CO (monoisotopic)
+ const double massH2OMono = 18.010564684; // mass of water (monoisotopic)
+ const double massHMono = 1.0078246; // mass of hydrogen (monoisotopic)
+ const double BYHeight = 50.0;
+ const double NH3LossHeight = 10.0;
+ const double COLossHeight = 10.0; // for creating a ions on the fly from b ions
+ const double H2OLossHeight = 10.0;
+ const double FlankingHeight = BYHeight / 2;;
+ // TODO end need to review
+ bool flanking_peak = Params::GetBool("use-flanking-peaks");
+ bool neutral_loss_peak = Params::GetBool("use-neutral-loss-peaks");
+
+ int ma;
+ int pc;
+ int ionBin;
+ double bIonMass;
+ double yIonMass;
+ double ionMZMultiCharge;
+ double ionMassNH3Loss;
+ double ionMassCOLoss;
+ double ionMassH2OLoss;
+
+ double* evidence = new double[maxPrecurMass];
+ double* intensArrayObs = new double[maxPrecurMass];
+ int* intensRegion = new int[maxPrecurMass];
+
+ for (ma = 0; ma < maxPrecurMass; ma++) {
+ evidence[ma] = 0.0;
+ evidenceInt[ma] = 0;
+ intensArrayObs[ma] = 0.0;
+ intensRegion[ma] = -1;
+ }
+
+ double precurMz = spectrum.PrecursorMZ();
+ int nIon = spectrum.Size();
+ int precurCharge = charge;
+ double experimentalMassCutoff = precurMz * precurCharge + 50.0;
+ double proton = MassConstants::proton;
+
+ // TODO preserved from PreprocessSpectrum only for historical reference; get rid of eventually
+ // // Fill peaks
+ // int largest_mz = 0;
+ // double highest_intensity = 0;
+ // for (int i = 0; i < spectrum.Size(); ++i) {
+ // double peak_location = spectrum.M_Z(i);
+ // if(peak_location >= experimental_mass_cut_off)
+ // continue;
+
+ // double intensity = spectrum.Intensity(i);
+ // int mz = (int)(peak_location / bin_width + 0.5);
+ // if ((mz > largest_mz) && (intensity > 0))
+ // largest_mz = mz;
+
+ // intensity = sqrt(intensity);
+ // if (intensity > highest_intensity)
+ // highest_intensity = intensity;
+ // if (intensity > peaks_[mz])
+ // peaks_[mz] = intensity;
+ // }
+
+ // double intensity_cutoff = highest_intensity * 0.05;
+
+ // int region_size = largest_mz / NUM_SPECTRUM_REGIONS;
+ // for (int i = 0; i < NUM_SPECTRUM_REGIONS; ++i) {
+ // highest_intensity = 0;
+ // for (int j = 0; j < region_size; ++j) {
+ // int index = i * region_size + j;
+ // if (peaks_[index] <= intensity_cutoff)
+ // peaks_[index] = 0;
+ // if (peaks_[index] > highest_intensity)
+ // highest_intensity = peaks_[index];
+ // }
+ // if (highest_intensity == 0)
+ // continue;
+ // double normalizer = 50.0/highest_intensity;
+ // for (int j = 0; j < region_size; ++j) {
+ // int index = i * region_size + j;
+ // if (peaks_[index] != 0)
+ // peaks_[index] *= normalizer;
+ // }
+ // }
+ // TODO end preserved
+
+ double maxIonMass = 0.0;
+ double maxIonIntens = 0.0;
+ for (int ion = 0; ion < nIon; ion++) {
+ double ionMass = spectrum.M_Z(ion);
+ double ionIntens = spectrum.Intensity(ion);
+ if (ionMass >= experimentalMassCutoff) {
+ continue;
+ }
+ if (maxIonMass < ionMass) {
+ maxIonMass = ionMass;
+ }
+ if (maxIonIntens < ionIntens) {
+ maxIonIntens = ionIntens;
+ }
+ }
+ int regionSelector = (int)floor(MassConstants::mass2bin(maxIonMass) / (double)nRegion);
+ for (int ion = 0; ion < nIon; ion++) {
+ double ionMass = spectrum.M_Z(ion);
+ double ionIntens = spectrum.Intensity(ion);
+ if (ionMass >= experimentalMassCutoff) {
+ continue;
+ }
+ if (ionMass > precurMz - precursorMZExclude && ionMass < precurMz + precursorMZExclude) {
+ continue;
+ }
+ ionBin = MassConstants::mass2bin(ionMass);
+ int region = (int)floor((double)(ionBin) / (double)regionSelector);
+ if (region >= nRegion) {
+ region = nRegion - 1;
+ }
+ intensRegion[ionBin] = region;
+ if (intensArrayObs[ionBin] < ionIntens) {
+ intensArrayObs[ionBin] = ionIntens;
+ }
+ }
+
+ maxIonIntens = sqrt(maxIonIntens);
+ for (ma = 0; ma < maxPrecurMass; ma++) {
+ intensArrayObs[ma] = sqrt(intensArrayObs[ma]);
+ if (intensArrayObs[ma] <= 0.05 * maxIonIntens) {
+ intensArrayObs[ma] = 0.0;
+ }
+ }
+
+ double* maxRegion = new double[nRegion];
+ for (int re = 0; re < nRegion; re++) {
+ maxRegion[re] = 0.0;
+ }
+ for (ma = 0; ma < maxPrecurMass; ma++) {
+ int reg = intensRegion[ma];
+ if (reg >= 0 && maxRegion[reg] < intensArrayObs[ma]) {
+ maxRegion[reg] = intensArrayObs[ma];
+ }
+ }
+ for (ma = 0; ma < maxPrecurMass; ma++) {
+ int reg = intensRegion[ma];
+ if (reg >= 0 && maxRegion[reg] > 0.0) {
+ intensArrayObs[ma] *= (maxIntensPerRegion / maxRegion[reg]);
+ }
+ }
+ delete [] maxRegion;
+
+ // ***** Adapted from tide/spectrum_preprocess2.cc.
+ // TODO replace, if possible, with call to
+ // static void SubtractBackground(double* observed, int end).
+ // Note numerous small changes from Tide code.
+ double multiplier = 1.0 / (MAX_XCORR_OFFSET * 2.0 + 1.0);
+ double total = 0.0;
+ double* partial_sums = new double[maxPrecurMass];
+ for (int i = 0; i < maxPrecurMass; ++i) {
+ partial_sums[ i ] = ( total += intensArrayObs[i]);
+ }
+ for (int i = 0; i < maxPrecurMass; ++i) {
+ int right_index = std::min(maxPrecurMass - 1, i + MAX_XCORR_OFFSET);
+ int left_index = std::max(0, i - MAX_XCORR_OFFSET - 1);
+ intensArrayObs[i] -= multiplier * (partial_sums[right_index] - partial_sums[left_index]);
+ }
+ delete [] partial_sums;
+
+ int binFirst = MassConstants::mass2bin(30);
+ int binLast = MassConstants::mass2bin(pepMassMonoMean - 47);
+
+ for (ma = binFirst; ma <= binLast; ma++) {
+ // b ion
+ bIonMass = (ma-0.5+binOffset) * binWidth ;
+ ionBin = MassConstants::mass2bin(bIonMass);
+ evidence[ma] = evidence[ma] + intensArrayObs[ionBin] * BYHeight;
+ for (pc = 2; pc < precurCharge; pc++) {
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(bIonMass, pc)] * BYHeight;
+ }
+ // y ion
+ yIonMass = pepMassMonoMean + 2 * massHMono - bIonMass;
+ ionBin = MassConstants::mass2bin(yIonMass);
+ evidence[ma] = evidence[ma] + intensArrayObs[ionBin] * BYHeight;
+ for (pc = 2; pc < precurCharge; pc++) {
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(yIonMass, pc)] * BYHeight;
+ }
+ if (flanking_peak == true){
+
+ //flanking peaks for b ions
+ ionBin = MassConstants::mass2bin(bIonMass, 1);
+ evidence[ma] = evidence[ma] + intensArrayObs[ionBin + 1] * FlankingHeight;
+ evidence[ma] = evidence[ma] + intensArrayObs[ionBin - 1] * FlankingHeight;
+ for (pc = 2; pc < precurCharge; pc++) {
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(bIonMass, pc) + 1] * FlankingHeight;
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(bIonMass, pc) - 1] * FlankingHeight;
+ }
+ //flanking peaks for b ions
+ ionBin = MassConstants::mass2bin(yIonMass, pc);
+ evidence[ma] = evidence[ma] + intensArrayObs[ionBin + 1] * FlankingHeight;
+ evidence[ma] = evidence[ma] + intensArrayObs[ionBin - 1] * FlankingHeight;
+ for (pc = 2; pc < precurCharge; pc++) {
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(yIonMass, pc) + 1] * FlankingHeight;
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(yIonMass, pc) - 1] * FlankingHeight;
+ }
+ }
+ if (neutral_loss_peak == true){
+ // NH3 loss from b ion
+ ionMassNH3Loss = bIonMass - massNH3Mono;
+ ionBin = MassConstants::mass2bin(ionMassNH3Loss);
+ evidence[ma] = evidence[ma] + intensArrayObs[ionBin] * NH3LossHeight;
+ for (pc = 2; pc < precurCharge; pc++) {
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(ionMassNH3Loss, pc)] * NH3LossHeight;
+ }
+ // NH3 loss from y ion
+ ionMassNH3Loss = yIonMass - massNH3Mono;
+ ionBin = MassConstants::mass2bin(ionMassNH3Loss);//(int)floor(ionMassNH3Loss / binWidth + 1.0 - binOffset);
+ evidence[ma] = evidence[ma] + intensArrayObs[ionBin] * NH3LossHeight;
+ for (pc = 2; pc < precurCharge; pc++) {
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(ionMassNH3Loss, pc)] * NH3LossHeight;
+ }
+ // CO and H2O loss from b ion
+ ionMassCOLoss = bIonMass - massCOMono;
+ ionMassH2OLoss = bIonMass - massH2OMono;
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(ionMassCOLoss)] * COLossHeight;
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(ionMassH2OLoss)] * H2OLossHeight;
+ for (pc = 2; pc < precurCharge; pc++) {
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(ionMassCOLoss, pc)] * COLossHeight;
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(ionMassH2OLoss, pc)] * H2OLossHeight;
+ }
+ // H2O loss from y ion
+ ionMassH2OLoss = yIonMass - massH2OMono;
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(ionMassH2OLoss)] * H2OLossHeight;
+ for (pc = 2; pc < precurCharge; pc++) {
+ evidence[ma] = evidence[ma] + intensArrayObs[MassConstants::mass2bin(ionMassH2OLoss, pc)] * H2OLossHeight;
+ }
+ }
+ }
+
+ // discretize evidence array
+ for (ma = 0; ma < maxPrecurMass; ma++) {
+ evidenceInt[ma] = (int)floor(evidence[ma] / EVIDENCE_INT_SCALE + 0.5);
+ }
+ // clean up
+ delete [] evidence;
+ delete [] intensArrayObs;
+ delete [] intensRegion;
+
+ // TODO preserved from PreprocessSpectrum; may delete in future
+#ifdef DEBUG
+ if (debug) {
+ cout << "GLOBAL MAX MZ: " << MaxMZ::Global().MaxBin() << ", " << MaxMZ::Global().BackgroundBinEnd()
+ << ", " << MaxMZ::Global().CacheBinEnd() << endl;
+ cout << "MAX MZ: " << max_mz_.MaxBin() << ", " << max_mz_.BackgroundBinEnd()
+ << ", " << max_mz_.CacheBinEnd() << endl;
+ ShowPeaks();
+ cout << "====== SUBTRACTING BACKGROUND ======" << endl;
+ }
+#endif
+#ifdef DEBUG
+ if (debug)
+ ShowPeaks();
+#endif
+ // TODO end preserved
+}
+
+inline int round_to_int(double x) {
+ if (x >= 0)
+ return int(x + 0.5);
+ return int(x - 0.5);
+}
+
+void ObservedPeakSet::MakeInteger() {
+ // essentially cheap fixed-point arithmetic for peak intensities
+ for(int i = 0; i < max_mz_.BackgroundBinEnd(); i++)
+ Peak(PeakMain, i) = round_to_int(peaks_[i]*50000);
+}
+
+// See .h file. Computes and stores all transformations of the observed peak
+// set.
+void ObservedPeakSet::ComputeCache() {
+ for (int i = 0; i < max_mz_.BackgroundBinEnd(); ++i) {
+ // Instead of computing 10 * x, 25 * x, and 50 * x, we compute 2 *
+ // x, 5 * x and 10 * x. This results in dot products that are 5
+ // times too small, but the adjustments can be made at the last
+ // moment e.g. when results are displayed. These smaller
+ // multiplications allow us to use addition operations instead of
+ // multiplications.
+ int x = Peak(PeakMain, i);
+ int y = x+x;
+ Peak(LossPeak, i) = y;
+ int z = y+y+x;
+ Peak(FlankingPeak, i) = z;
+ Peak(PrimaryPeak, i) = z+z;
+ }
+
+ for (int i = max_mz_.BackgroundBinEnd() * NUM_PEAK_TYPES; i < cache_end_; ++i) {
+ cache_[i] = 0;
+ }
+
+ for (int i = 0; i < max_mz_.CacheBinEnd(); ++i) {
+ int flanks = Peak(PrimaryPeak, i);
+ if ( FP_ == true) {
+ if (i > 0) {
+ flanks += Peak(FlankingPeak, i-1);
+ }
+ if (i < max_mz_.CacheBinEnd() - 1) {
+ flanks += Peak(FlankingPeak, i+1);
+ }
+ }
+ int Y1 = flanks;
+ if ( NL_ == true) {
+ if (i > MassConstants::BIN_NH3) {
+ Y1 += Peak(LossPeak, i-MassConstants::BIN_NH3);
+ }
+ if (i > MassConstants::BIN_H2O) {
+ Y1 += Peak(LossPeak, i-MassConstants::BIN_H2O);
+ }
+ }
+ Peak(PeakCombinedY1, i) = Y1;
+ int B1 = Y1;
+ Peak(PeakCombinedB1, i) = B1;
+ Peak(PeakCombinedY2, i) = flanks;
+ Peak(PeakCombinedB2, i) = flanks;
+ }
+}
+
+// This dot product is replaced by calls to on-the-fly compiled code.
+int ObservedPeakSet::DotProd(const TheoreticalPeakArr& theoretical) {
+ int total = 0;
+ TheoreticalPeakArr::const_iterator i = theoretical.begin();
+ for (; i != theoretical.end(); ++i) {
+ //if (i->Code() >= cache_end_)
+ // break;
+ total += cache_[i->Code()];
+ }
+ return total;
+}
+
+#if 0
+int ObservedPeakSet::DebugDotProd(const TheoreticalPeakArr& theoretical) {
+ cout << "cache_end_=" << cache_end_ << endl;
+ int total = 0;
+ TheoreticalPeakArr::const_iterator i = theoretical.begin();
+ for (; i != theoretical.end(); ++i) {
+ cout << "DotProd Lookup(" << i->Bin() << "," << i->Type() << "):";
+ if (i->Code() >= cache_end_) {
+ cout << "code=" << i->Code() << "past cache_end_=" << cache_end_ << "; ignoring" << endl;
+ continue;
+ }
+ total += cache_[i->Code()];
+ cout << cache_[i->Code()] << "; total=" << total << endl;
+ }
+ return total;
+}
+#endif
diff --git a/src/app/tide/theoretical_peak_pair.h b/src/app/tide/theoretical_peak_pair.h
new file mode 100644
index 0000000..8a96ef4
--- /dev/null
+++ b/src/app/tide/theoretical_peak_pair.h
@@ -0,0 +1,69 @@
+// Benjamin Diament
+
+// A TheoreticalPeakPair represents the ordered pair (bucket, type) where
+// bucket is an integer refering to a bucketed m/z position in the theoretical
+// spectrum, and type identifies the type of the peak. This type may be
+// LossPeak, FlankingPeak, PrimaryPeak which represents an intensity, or it could be one of
+// the combined peak types (see TheoreticalPeakType below) which represent a
+// linear combination of several peaks.
+#ifndef THEORETICAL_PEAK_PAIR_H
+#define THEORETICAL_PEAK_PAIR_H
+
+#include <utility>
+#include "fixed_cap_array.h"
+
+using namespace std;
+
+enum TheoreticalPeakType {
+ PeakMain = 0,
+ LossPeak = 1,
+ FlankingPeak = 2,
+ PrimaryPeak = 3,
+ PeakCombinedB1 = 4, // Represents charge 1 B ion, its flanks and neutral losses.
+ PeakCombinedY1 = 5, // Represents charge 1 Y ion, its flanks and neutral losses.
+ // Each of the charge 2 peak types below includes an 'a' version and a 'b'
+ // version. In the 'a' version the loss of ammonia is 9 Da. per charge.
+ // In the 'b' version the loss of ammonia is 8 Da. per charge.
+ PeakCombinedB2 = 6, // Represents charge 2 B ion, its flanks and neutral losses.
+ PeakCombinedY2 = 7, // Represents charge 2 Y ion, its flanks and neutral losses.
+// PeakCombinedB2b = 8, // Represents charge 2 B ion, its flanks and neutral losses.
+// PeakCombinedY2b = 9, // Represents charge 2 Y ion, its flanks and neutral losses.
+
+ NUM_PEAK_TYPES = 10 // Total number of peak types.
+};
+
+class TheoreticalPeakPair {
+ public:
+ TheoreticalPeakPair() {} // no intialization; beware.
+
+ explicit TheoreticalPeakPair(int code) : code_(code) {}
+
+ TheoreticalPeakPair(int bin, TheoreticalPeakType peak_type)
+ : code_(bin * NUM_PEAK_TYPES + peak_type) {
+ }
+
+ // Bin() and Type() give the components of the ordered pair as described
+ // above. Code() should be used for serialization to and from a file, and
+ // for indexing into the precomputed cache of transformed observed peaks.
+ // Note that Bin() and Type() are not fast; Code() is fast.
+ int Bin() const { return code_ / NUM_PEAK_TYPES; }
+ int Type() const { return code_ % NUM_PEAK_TYPES; }
+ int Code() const { return code_; }
+
+ bool operator<(const TheoreticalPeakPair& other) const {
+ return code_ < other.code_;
+ }
+
+ bool operator>(const TheoreticalPeakPair& other) const {
+ return code_ > other.code_;
+ }
+
+ private:
+ // code_ represents the bin position and the peak type together. See
+ // constructors and accessors.
+ int code_;
+};
+
+typedef FixedCapacityArray<TheoreticalPeakPair> TheoreticalPeakArr;
+
+#endif // THEORETICAL_PEAK_PAIR_H
diff --git a/src/app/tide/theoretical_peak_set.h b/src/app/tide/theoretical_peak_set.h
new file mode 100644
index 0000000..2928e8a
--- /dev/null
+++ b/src/app/tide/theoretical_peak_set.h
@@ -0,0 +1,790 @@
+// Benjamin Diament
+
+// A TheoreticalPeakSet is an abstract class representing the collection of
+// theoretical peaks corresponding to a peptide. Its memory is designed to be
+// reusable, so it functions as a "workspace" for figuring where the
+// theoretical peaks ought to be. The expected usage pattern is as follows:
+//
+// TheoreticalPeakSet workspace; // Some construction params may be required.
+// Peptide peptide; // Assume already initialized.
+// workspace.Clear(); // Memory gets reused
+// For each left-substring of peptide, call workspace.AddBIon()
+// For each right-substring of peptide, call workspace.AddYIon()
+//
+// After the B and Y ions have been added the client may retreive the
+// TheoreticalPeakArr by a call to workspace.GetPeaks(). Peaks are then written
+// into the provided arrays (specified in the arguments). To avoid unnecessary
+// copying, for most subclasses, GetPeaks() will take the final steps necessary
+// to generate the peaks and write them directly to the client-specified arrays.
+// There are both "positive" peaks and "negative" peaks that may be written,
+// though some subclasses will never write any negative peaks. When present,
+// these negative peaks represent corrections made to the peaks in the positive
+// set. This comes up in cases where the workspace in question actually
+// represents a difference between two TheoreticalPeakSets. See
+// TheoreticalPeakSetDiff for example.
+//
+// Different subclasses of TheoreticalPeakSet have varying characteristics, such
+// as the following:
+//
+// o space requirements (both in memory and on disk)
+// o time required to generate the peak set
+// o sparsity (affects space requirements and dot-product time)
+// o accuracy with respect to the "correct" value of the XCORR function.
+//
+// Here are some the characteristics:
+//
+// TheoreticalPeakSetMakeAll exact, slow, all peaks explicit
+// TheoreticalPeakSetBYSparse inexact, fast, only B and Y explicit,
+// significantly larger than Diff.
+// TheoreticalPeakSetBYSparseOrdered same, slightly slower to generate
+// TheoreticalPeakSetBYAll inexact but same as BYSparse, slow,
+// all peaks explicit
+// TheoreticalPeakSetDiff = MakeAll - BYAll: slow to generate,
+// very sparse, completely different
+// function from MakeAll. Gets stored at
+// indexing and retrieved at search time.
+// TheoreticalPeakSetSparse For testing: very slow, explicitly
+// computes both Diff and BYSparse.
+//
+// Let the following vectors be defined:
+//
+// x is the vector of theoretical peaks created by MakeAll
+// y is the vector of theoretical peaks created by BYSparse
+// z is the vector of theoretical peaks created by Diff
+// w is the vector of theoretical peaks created by BYAll
+// u is the vector of observed peaks with the background subtracted.
+// v is the vector that is a linear combination of shifts of u as computed
+// in ObservedPeakSet::ComputeCache(). E.g. for charge 1 the ith element
+// of v might be (see spectrum_preprocess.h):
+// v[i] = 50*u[i] + 25*u[i-1] + 25*u[i+1] + 10*u[i-17]
+//
+// y is five times sparser than w and includes only the positions of the B and Y
+// ions. BYAll and BYSparse are related as follows: <w, u> = <y, v>. The correct
+// value of the XCORR is <u, x>. But computing with MakeAll is slow. So,
+// instead we do the following: at index time we compute and store z = x - w.
+// At search time we compute <y, v> + <z, u>. This incurs the cost of storing z
+// but generating only y, which can be done quickly. Since both y and z are
+// sparse (though z is much sparser) the above dot products can be computed
+// quickly at search time.
+//
+// The inexactness of BYAll (and BYSparse by extension) is due to two factors.
+// First, an exact rendering of the theoretical peaks such as that in MakeAll
+// would check for duplications (two peaks in the same bin). BYAll simply
+// generates all B and Y peaks without checking for duplications, as this saves
+// time when we generate BYSparse. The duplications get handled by Diff (the z
+// vector above). Second, the peaks generated by BYAll (the w vector above)
+// aren't quite correct: w is not exactly equal to x because the positions of
+// the neutral loss ions at 17 and 18 Da. away may instead be at 18 and 19
+// Da. away after binning. Similarly, at charge 2, neutral loss ions may be
+// either at 8 and 9 m/z away or at 9 and 10 m/z away. All these variations are
+// accounted for when we subtract (x - w) to store the Diff.
+//
+// TODO 253: a final descision on whether to use TheoreticalPeakSetBYSparse or
+// TheoreticalPeakSetBYSparseOrdered at search time is yet to be made. Neither
+// dominated the other in testing done so far.
+
+#ifndef THEORETICAL_PEAK_SET_H
+#define THEORETICAL_PEAK_SET_H
+
+#include <iostream>
+#include <algorithm>
+#include "mass_constants.h"
+//#include "peptide.h"
+#include "peptides.pb.h"
+#include "max_mz.h"
+#include "theoretical_peak_pair.h"
+#include "math.h"
+#include <functional>
+
+using namespace std;
+typedef google::protobuf::RepeatedField<int>::const_iterator FieldIter;
+
+class TheoreticalPeakSet {
+ public:
+ // Sub-classes need to support this interface (see above).
+ // A do-nothing stub is provided for GetNegs().
+ virtual void Clear() = 0;
+ virtual void AddYIon(double mass, int charge) = 0;
+ virtual void AddBIon(double mass, int charge) = 0;
+ virtual void GetPeaks(TheoreticalPeakArr* peaks_charge_1,
+ TheoreticalPeakArr* negs_charge_1,
+ TheoreticalPeakArr* peaks_charge_2,
+ TheoreticalPeakArr* negs_charge_2,
+ const pb::Peptide* peptide = NULL) = 0;
+
+ protected:
+ ////////////////////////////////////////////////////
+ // Utility functions for subclasses
+ //
+ // Many of these fucnctions refer to MaxMZ::Global(). At search time
+ // MaxMZ::Global() will be set at the end of the range of
+ // the observed spectra so we need not calculate theoretical peaks
+ // beyond this limit.
+ ////////////////////////////////////////////////////
+
+ // Copy src to dest, but for each bin copy only the highest intensity peak.
+ static void RemoveDups(const TheoreticalPeakArr& src,
+ TheoreticalPeakArr* dest) {
+ TheoreticalPeakArr::const_iterator i = src.begin();
+ for (; i != src.end(); ++i) {
+ // find last element with current index, that one being the
+ // largest intensity
+ int index = i->Bin();
+ if (MaxBin::Global().MaxBinEnd() > 0
+ && index >= MaxBin::Global().CacheBinEnd())
+ break;
+ for (++i; i != src.end() && i->Bin() == index; ++i);
+ --i;
+ dest->push_back(*i);
+ }
+ }
+
+ static void AddPeak(TheoreticalPeakArr* dest, int index,
+ TheoreticalPeakType intensity) {
+ TheoreticalPeakPair peak(index, intensity);
+ // must insert in nondecreasing order
+ assert(dest->size() == 0 || peak.Code() >= dest->back().Code());
+ dest->push_back(peak);
+ }
+
+/* static void AddPeakUnordered(TheoreticalPeakArr* dest, int index,
+ TheoreticalPeakType intensity) {
+ TheoreticalPeakPair peak(index, intensity);
+ dest->push_back(peak);
+ }
+*/ static void AddPeakUnordered(TheoreticalPeakArr* dest, int index,
+ TheoreticalPeakType intensity, TheoreticalPeakArr* otherset) {
+ TheoreticalPeakPair peak(index, intensity);
+ bool found = false;
+ for (TheoreticalPeakArr::iterator itr = dest->begin(); itr < dest->end(); itr++){
+ if (itr->Bin() == peak.Bin()){
+ found = true;
+ break;
+ }
+ }
+
+ for (TheoreticalPeakArr::iterator itr2 = otherset->begin(); itr2 < otherset->end(); itr2++){
+ if (itr2->Bin() == peak.Bin()){
+ found = true;
+ break;
+ }
+ }
+ if (!found){
+ dest->push_back(peak);
+ }
+ }
+
+ // Append src to dest.
+ static void Copy(const TheoreticalPeakArr& src,
+ TheoreticalPeakArr* dest) {
+ // Confirm that src is already sorted.
+ assert(adjacent_find(src.begin(), src.end(),
+ greater<TheoreticalPeakPair>()) == src.end());
+ TheoreticalPeakArr::const_iterator i = src.begin();
+ if (MaxBin::Global().MaxBinEnd() > 0) {
+ int end = MaxBin::Global().CacheBinEnd() * NUM_PEAK_TYPES;
+ for (; (i != src.end()) && (i->Code() < end); ++i)
+ dest->push_back(*i);
+ } else {
+ for (; i != src.end(); ++i)
+ dest->push_back(*i);
+ }
+ }
+
+ static void CopyUnordered(const TheoreticalPeakArr& src,
+ TheoreticalPeakArr* dest) {
+ TheoreticalPeakArr::const_iterator i = src.begin();
+ if (MaxBin::Global().MaxBinEnd() > 0) {
+ int end = MaxBin::Global().CacheBinEnd() * NUM_PEAK_TYPES;
+ for (; i != src.end(); ++i) {
+ if (i->Code() < end)
+ dest->push_back(*i);
+ }
+ } else {
+ for (; i != src.end(); ++i)
+ dest->push_back(*i);
+ }
+ }
+
+ // Compute x - y as a vector difference. Store positive peaks in pos,
+ // negative peaks in neg. TODO 262: can simply be expressed as symmetric set
+ // difference between x and y.
+ static void Diff(const TheoreticalPeakArr& x,
+ const TheoreticalPeakArr& y,
+ TheoreticalPeakArr* pos,
+ TheoreticalPeakArr* neg) {
+ TheoreticalPeakArr::const_iterator x_iter = x.begin();
+ TheoreticalPeakArr::const_iterator y_iter = y.begin();
+ while (x_iter != x.end() && y_iter != y.end()) {
+ if (*x_iter < *y_iter) {
+ pos->push_back(*x_iter++);
+ } else if (*y_iter < *x_iter) {
+ neg->push_back(*y_iter++);
+ } else {
+ // if equal, they cancel; push nothing!
+ x_iter++; y_iter++;
+ }
+ }
+ for (; x_iter != x.end(); ++x_iter)
+ pos->push_back(*x_iter);
+ for (; y_iter != y.end(); ++y_iter)
+ neg->push_back(*y_iter);
+ }
+
+ // Copy from peaks from protocol buffer to dest.
+ static void CopyExceptions(const google::protobuf::RepeatedField<int>& src,
+ TheoreticalPeakArr* dest) {
+ // dest may be unordered!
+ // The protocol buffer stores deltas between peak values, so we need
+ // to track the total:
+ int total = 0;
+ int end = MaxBin::Global().CacheBinEnd() * NUM_PEAK_TYPES;
+ FieldIter i = src.begin();
+ for (; i != src.end(); ++i) {
+ if ((total += *i) >= end)
+ break;
+ dest->push_back(TheoreticalPeakPair(total));
+ }
+ }
+};
+
+// Utility class for use by subclasses of TheoreticalPeakSet. Contains the
+// actual arrays of B series and Y series ions. The temp[123]_ arrays are
+// spaces for merging sorted arrays of B and Y ions. This class also manages
+// merges with peaks taken from Peptide protocol buffers.
+class OrderedPeakSets {
+ public:
+ void Init(int capacity) {
+ b_series_[0].Init(capacity);
+ b_series_[1].Init(capacity);
+ y_series_[0].Init(capacity);
+ y_series_[1].Init(capacity);
+ temp1_.Init(capacity);
+ temp2_.Init(capacity);
+ temp3_.Init(capacity);
+ }
+
+ void Clear() {
+ b_series_[0].clear();
+ b_series_[1].clear();
+ y_series_[0].clear();
+ y_series_[1].clear();
+ }
+
+ // temp1_ gets the charge 1 peaks. temp3_ gets the combined charge 1 and
+ // charge 2 peaks.
+ void Merge(const pb::Peptide* peptide = NULL) {
+ if (peptide && peptide->peak1_size() > 0) {
+ MergePeaks(&b_series_[0], &y_series_[0], &temp3_);
+ MergeExceptions(temp3_, peptide->peak1(), &temp1_);
+ } else {
+ MergePeaks(&b_series_[0], &y_series_[0], &temp1_);
+ }
+ if (peptide && peptide->peak2_size() > 0) {
+ MergePeaks(&b_series_[1], &y_series_[1], &temp3_);
+ MergeExceptions(temp3_, peptide->peak2(), &temp2_);
+ } else {
+ MergePeaks(&b_series_[1], &y_series_[1], &temp2_);
+ }
+ MergePeaks(&temp1_, &temp2_, &temp3_);
+ }
+
+ TheoreticalPeakArr b_series_[2];
+ TheoreticalPeakArr y_series_[2];
+ TheoreticalPeakArr temp1_, temp2_, temp3_;
+
+ private:
+ static void MergePeaks(TheoreticalPeakArr* a, TheoreticalPeakArr* b,
+ TheoreticalPeakArr* result) {
+ merge(a->begin(), a->end(), b->begin(), b->end(), result->data());
+ result->set_size(a->size() + b->size());
+ }
+
+ static void MergeExceptions(const TheoreticalPeakArr& src,
+ const google::protobuf::RepeatedField<int>& exc,
+ TheoreticalPeakArr* dest) {
+ dest->clear();
+ // The protocol buffer stores deltas between peak values, so we need
+ // to track the total:
+ int total = 0;
+ int end = MaxBin::Global().CacheBinEnd() * NUM_PEAK_TYPES;
+ FieldIter exc_iter = exc.begin();
+ TheoreticalPeakArr::const_iterator src_iter = src.begin();
+
+ if ((exc_iter != exc.end()) && (src_iter != src.end())
+ && ((total = *exc_iter) < end) && (src_iter->Code() < end)) {
+ while (true) {
+ bool advance_src = total >= src_iter->Code();
+ bool advance_exc = total <= src_iter->Code();
+ if (advance_src) {
+ dest->push_back(*src_iter++);
+ if (src_iter == src.end() || (src_iter->Code() >= end))
+ break;
+ }
+ if (advance_exc) {
+ dest->push_back(TheoreticalPeakPair(total));
+ total += *(++exc_iter);
+ if (exc_iter == exc.end() || (total >= end))
+ break;
+ }
+ }
+ }
+
+ if (total < end) {
+ for (; exc_iter != exc.end(); ++exc_iter) {
+ if ((total += *exc_iter) >= end)
+ break;
+ dest->push_back(TheoreticalPeakPair(total));
+ }
+ }
+ for (; src_iter != src.end() && src_iter->Code() < end; ++src_iter) {
+ dest->push_back(*src_iter);
+ }
+#ifdef DEBUG
+ // The last assert here is expensive, so we relegate use to DEBUG mode.
+ assert(exc_iter == exc.end() || total >= end);
+ assert(src_iter == src.end() || src_iter->Code() >= end);
+ assert(dest->size() == (exc_iter - exc.begin()) + (src_iter - src.begin()));
+ assert(adjacent_find(dest->begin(), dest->end(),
+ greater<TheoreticalPeakPair>()) == dest->end());
+#endif
+ }
+};
+
+#if 0
+DECLARE_bool(flanks);
+DECLARE_bool(dups_ok);
+#endif
+
+// Subclass of TheoreticalPeakSet that generates all ions individually and
+// explicitly. The peaks generated will all have type LossPeak, FlankingPeak, or
+// PrimaryPeak.
+/*class TheoreticalPeakSetMakeAll : public TheoreticalPeakSet {
+ public:
+ TheoreticalPeakSetMakeAll(int capacity) {
+ ordered_peak_sets_.Init(capacity);
+ }
+
+ virtual ~TheoreticalPeakSetMakeAll() {}
+
+ void Clear() { ordered_peak_sets_.Clear(); }
+
+ void AddYIon(double mass, int charge) {
+ assert(charge <= 2);
+ AddYIon(mass, charge, &ordered_peak_sets_.y_series_[charge-1]);
+ }
+
+ void AddBIon(double mass, int charge) {
+ assert(charge <= 2);
+ AddBIon(mass, charge, &ordered_peak_sets_.b_series_[charge-1]);
+ }
+
+ void GetPeaks(TheoreticalPeakArr* peaks_charge_1,
+ TheoreticalPeakArr* negs_charge_1,
+ TheoreticalPeakArr* peaks_charge_2,
+ TheoreticalPeakArr* negs_charge_2,
+ const pb::Peptide* peptide = NULL) {
+ assert(peptide == NULL);
+ ordered_peak_sets_.Merge();
+ if (false ) {
+ CopyUnordered(ordered_peak_sets_.temp1_, peaks_charge_1);
+ CopyUnordered(ordered_peak_sets_.temp3_, peaks_charge_2);
+ } else {
+ RemoveDups(ordered_peak_sets_.temp1_, peaks_charge_1);
+ RemoveDups(ordered_peak_sets_.temp3_, peaks_charge_2);
+ }
+ // no negs
+ }
+
+ private:
+ void AddYIon(double mass, int charge, TheoreticalPeakArr* dest) {
+ // H2O
+ int index = MassConstants::mass2bin(mass + MassConstants::Y_H2O, charge);
+ AddPeak(dest, index, LossPeak);
+ // NH3
+ index = MassConstants::mass2bin(mass + MassConstants::Y_NH3, charge);
+ AddPeak(dest, index, LossPeak);
+ index = MassConstants::mass2bin(mass + MassConstants::Y, charge);
+
+ if (true ) AddPeak(dest, index-1, FlankingPeak);
+ AddPeak(dest, index, PrimaryPeak);
+ if (true ) AddPeak(dest, index+1, FlankingPeak);
+ }
+
+ void AddBIon(double mass, int charge, TheoreticalPeakArr* dest) {
+ // A-Ion
+ int index = MassConstants::mass2bin(mass + MassConstants::A, charge);
+
+ AddPeak(dest, index, LossPeak);
+ // H2O
+ index = MassConstants::mass2bin(mass + MassConstants::B_H2O, charge);
+ AddPeak(dest, index, LossPeak);
+ // Rest of peaks are as for Y ion
+ // NH3
+ index = MassConstants::mass2bin(mass + MassConstants::B_NH3, charge);
+ AddPeak(dest, index, LossPeak);
+ index = MassConstants::mass2bin(mass + MassConstants::B, charge);
+
+ if (true ) AddPeak(dest, index-1, FlankingPeak);
+ AddPeak(dest, index, PrimaryPeak);
+ if (true) AddPeak(dest, index+1, FlankingPeak);
+ }
+
+ OrderedPeakSets ordered_peak_sets_;
+};
+*/
+// A subclass of TheoreticalPeakSet that generates a theoretical peak
+// for each B and Y ion at each charge state, 1 and 2. Peak generated
+// will be of type PeakCombinedB1 and PeakCombinedY1 for charge 1
+// ions. Peaks of type PeakCombinedB2a or PeakCombinedB2b will be
+// generated for each B ion of charge 2 depending on whether the
+// corresponding ammonia loss is 8 bins or 9 bins away. Similarly,
+// peaks of type PeakCombinedY2a or PeakCombinedY2b will be generated
+// for each Y ion of charge 2.
+class TheoreticalPeakSetBYSparse : public TheoreticalPeakSet {
+ public:
+ explicit TheoreticalPeakSetBYSparse(int capacity) {
+ peaks_[0].Init(capacity);
+ peaks_[1].Init(capacity);
+ }
+
+ virtual ~TheoreticalPeakSetBYSparse() {}
+
+ void Clear() {
+ peaks_[0].clear();
+ peaks_[1].clear();
+ }
+
+ void AddYIon(double mass, int charge) {
+ assert(charge <= 2);
+ int index_y = MassConstants::mass2bin(mass + MassConstants::Y + MassConstants::proton, charge);
+// cout << "index_y: " << index_y << endl;
+ TheoreticalPeakType series;
+ if (charge == 1) {
+ series = PeakCombinedY1;
+ } else {
+// int nh3_diff = index_y - MassConstants::mass2bin(mass + MassConstants::Y_NH3, charge);
+// assert(nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A ||
+// nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B);
+// series = nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A ? PeakCombinedY2a
+// : PeakCombinedY2b;
+ series = PeakCombinedY2;
+ }
+// AddPeakUnordered(&peaks_[charge-1], index_y, series);
+ if (charge == 1)
+ AddPeakUnordered(&peaks_[charge-1], index_y, series, &peaks_[charge]);
+ else
+ AddPeakUnordered(&peaks_[charge-1], index_y, series, &peaks_[charge-2]);
+ }
+
+ void AddBIon(double mass, int charge) {
+ assert(charge <= 2);
+ int index_b = MassConstants::mass2bin(mass + MassConstants::B + MassConstants::proton, charge);
+// cout << "index_b: " << index_b << endl;
+ TheoreticalPeakType series;
+ if (charge == 1) {
+ series = PeakCombinedB1;
+ } else {
+// int nh3_diff = index_b - MassConstants::mass2bin(mass + MassConstants::B_NH3, charge);
+// assert(nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A ||
+// nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B);
+// series = nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A ? PeakCombinedB2a
+// : PeakCombinedB2b;
+ series = PeakCombinedB2;
+
+ }
+// AddPeakUnordered(&peaks_[charge-1], index_b, series);
+ if (charge == 1)
+ AddPeakUnordered(&peaks_[charge-1], index_b, series, &peaks_[charge]);
+ else
+ AddPeakUnordered(&peaks_[charge-1], index_b, series, &peaks_[charge-2]);
+ }
+
+ // Faster interface needing no copying at all.
+ const TheoreticalPeakArr* GetPeaks() const { return peaks_; }
+
+ void GetPeaks(TheoreticalPeakArr* peaks_charge_1,
+ TheoreticalPeakArr* negs_charge_1,
+ TheoreticalPeakArr* peaks_charge_2,
+ TheoreticalPeakArr* negs_charge_2,
+ const pb::Peptide* peptide = NULL) {
+// CopyUniqueUnordered(peaks_[0], peaks_charge_1);
+// CopyUniqueUnordered(peaks_[0], peaks_charge_2);
+// CopyUniqueUnordered(peaks_[1], peaks_charge_2);
+ CopyUnordered(peaks_[0], peaks_charge_1);
+ CopyUnordered(peaks_[0], peaks_charge_2);
+ CopyUnordered(peaks_[1], peaks_charge_2);
+ if (peptide == NULL)
+ return;
+ CopyExceptions(peptide->peak1(), peaks_charge_1);
+ CopyExceptions(peptide->peak2(), peaks_charge_2);
+ CopyExceptions(peptide->neg_peak1(), negs_charge_1);
+ CopyExceptions(peptide->neg_peak2(), negs_charge_2);
+ }
+
+ private:
+ TheoreticalPeakArr peaks_[2];
+};
+
+// Subclass of TheoreticalPeakSet similar to TheoreticalPeakSetBYSparse
+// (above), but guarantees that peaks will be in increasing order by m/z
+// at the expense of a couple of extra merge operations.
+/*class TheoreticalPeakSetBYSparseOrdered : public TheoreticalPeakSet {
+ public:
+ TheoreticalPeakSetBYSparseOrdered(int capacity) {
+ ordered_peak_sets_.Init(capacity);
+ }
+
+ virtual ~TheoreticalPeakSetBYSparseOrdered() {}
+
+ void Clear() { ordered_peak_sets_.Clear(); }
+
+ void AddYIon(double mass, int charge) {
+ assert(charge <= 2);
+ int index_y = MassConstants::mass2bin(mass + MassConstants::Y, charge);
+ TheoreticalPeakType series;
+ if (charge == 1) {
+ series = PeakCombinedY1;
+ } else {
+ int nh3_diff = index_y - MassConstants::mass2bin(mass + MassConstants::Y_NH3, charge);
+ assert(nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A ||
+ nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B);
+ series = nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A ? PeakCombinedY2a
+ : PeakCombinedY2b;
+ }
+ AddPeak(&ordered_peak_sets_.y_series_[charge-1], index_y, series);
+ }
+
+ void AddBIon(double mass, int charge) {
+ assert(charge <= 2);
+ int index_b = MassConstants::mass2bin(mass + MassConstants::B, charge);
+ TheoreticalPeakType series;
+ if (charge == 1) {
+ series = PeakCombinedB1;
+ } else {
+ int nh3_diff = index_b - MassConstants::mass2bin(mass + MassConstants::B_NH3, charge);
+ assert(nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A ||
+ nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B);
+ series = nh3_diff == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A ? PeakCombinedB2a
+ : PeakCombinedB2b;
+ }
+ AddPeak(&ordered_peak_sets_.b_series_[charge-1], index_b, series);
+ }
+
+
+ void GetPeaks(TheoreticalPeakArr* peaks_charge_1,
+ TheoreticalPeakArr* negs_charge_1,
+ TheoreticalPeakArr* peaks_charge_2,
+ TheoreticalPeakArr* negs_charge_2,
+ const pb::Peptide* peptide = NULL) {
+ ordered_peak_sets_.Merge(peptide);
+ Copy(ordered_peak_sets_.temp1_, peaks_charge_1);
+ Copy(ordered_peak_sets_.temp3_, peaks_charge_2);
+ if (peptide == NULL)
+ return;
+ CopyExceptions(peptide->neg_peak1(), negs_charge_1);
+ CopyExceptions(peptide->neg_peak2(), negs_charge_2);
+ }
+
+ private:
+ OrderedPeakSets ordered_peak_sets_;
+};
+
+// Subclass of TheoreticalPeakSet. This class explicitly generates all ions
+// implicit in the TheoreticalPeakTypes PeakCombinedXXX. See notes above.
+class TheoreticalPeakSetBYAll : public TheoreticalPeakSet {
+ public:
+ TheoreticalPeakSetBYAll(int capacity) {
+ ordered_peak_sets_.Init(capacity);
+ }
+
+ virtual ~TheoreticalPeakSetBYAll() {}
+
+ void Clear() { ordered_peak_sets_.Clear(); }
+
+ void AddYIon(double mass, int charge) {
+ assert(charge <= 2);
+ AddYIon(mass, charge, &ordered_peak_sets_.y_series_[charge-1]);
+ }
+
+ void AddBIon(double mass, int charge) {
+ assert(charge <= 2);
+ AddBIon(mass, charge, &ordered_peak_sets_.b_series_[charge-1]);
+ }
+
+ void GetPeaks(TheoreticalPeakArr* peaks_charge_1,
+ TheoreticalPeakArr* negs_charge_1,
+ TheoreticalPeakArr* peaks_charge_2,
+ TheoreticalPeakArr* negs_charge_2,
+ const pb::Peptide* peptide = NULL) {
+ assert(peptide == NULL);
+ ordered_peak_sets_.Merge();
+ Copy(ordered_peak_sets_.temp1_, peaks_charge_1);
+ Copy(ordered_peak_sets_.temp3_, peaks_charge_2);
+ }
+
+ private:
+ void AddYIon(double mass, int charge, TheoreticalPeakArr* dest) {
+ int index_y = MassConstants::mass2bin(mass + MassConstants::Y, charge);
+ if (charge == 1) {
+ AddPeak(dest, index_y - MassConstants::BIN_SHIFT_H2O_CHG_1, LossPeak);
+ AddPeak(dest, index_y - MassConstants::BIN_SHIFT_NH3_CHG_1, LossPeak);
+ } else {
+ AddPeak(dest, index_y - MassConstants::BIN_SHIFT_H2O_CHG_2, LossPeak);
+ // In case A the NH3 peak will have been added already...
+ assert(MassConstants::BIN_SHIFT_H2O_CHG_2 == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A);
+ // Otherwise (case B), a separate NH3 peak is needed.
+ if (index_y - MassConstants::mass2bin(mass + MassConstants::Y_NH3, charge)
+ == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B)
+ AddPeak(dest, index_y - MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B, LossPeak);
+ }
+ AddPeak(dest, index_y-1, FlankingPeak);
+ AddPeak(dest, index_y, PrimaryPeak);
+ AddPeak(dest, index_y+1, FlankingPeak);
+ }
+
+ void AddBIon(double mass, int charge, TheoreticalPeakArr* dest) {
+ int index_b = MassConstants::mass2bin(mass + MassConstants::B, charge);
+ if (charge == 1) {
+ AddPeak(dest, index_b - MassConstants::BIN_SHIFT_A_ION_CHG_1, LossPeak);
+ AddPeak(dest, index_b - MassConstants::BIN_SHIFT_H2O_CHG_1, LossPeak);
+ AddPeak(dest, index_b - MassConstants::BIN_SHIFT_NH3_CHG_1, LossPeak);
+ } else {
+ AddPeak(dest, index_b - MassConstants::BIN_SHIFT_A_ION_CHG_2, LossPeak);
+ AddPeak(dest, index_b - MassConstants::BIN_SHIFT_H2O_CHG_2, LossPeak);
+ // In case A the NH3 peak will have been added already...
+ assert(MassConstants::BIN_SHIFT_H2O_CHG_2 == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_A);
+ // Otherwise (case B), a separate NH3 peak is needed.
+ if (index_b - MassConstants::mass2bin(mass + MassConstants::B_NH3, charge)
+ == MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B)
+ AddPeak(dest, index_b - MassConstants::BIN_SHIFT_NH3_CHG_2_CASE_B, LossPeak);
+ }
+ AddPeak(dest, index_b-1, FlankingPeak);
+ AddPeak(dest, index_b, PrimaryPeak);
+ AddPeak(dest, index_b+1, FlankingPeak);
+ }
+
+ OrderedPeakSets ordered_peak_sets_;
+};
+
+// Subclass of TheoreticalPeakSet. This class effectively computes
+// the vecotor difference of TheoreticalPeakSetMakeAll and
+// TheoreticalPeakSetBYAll.
+class TheoreticalPeakSetDiff : public TheoreticalPeakSet {
+ public:
+ TheoreticalPeakSetDiff(int capacity)
+ : BY_all_(capacity), make_all_(capacity),
+ make_all_1_(capacity), make_all_2_(capacity),
+ BY_all_1_(capacity), BY_all_2_(capacity) {
+ }
+
+ virtual ~TheoreticalPeakSetDiff() {}
+
+ void Clear() {
+ BY_all_.Clear();
+ make_all_.Clear();
+
+ make_all_1_.clear();
+ make_all_2_.clear();
+ BY_all_1_.clear();
+ BY_all_2_.clear();
+ }
+
+ void AddYIon(double mass, int charge) {
+ BY_all_.AddYIon(mass, charge);
+ make_all_.AddYIon(mass, charge);
+ }
+
+ void AddBIon(double mass, int charge) {
+ BY_all_.AddBIon(mass, charge);
+ make_all_.AddBIon(mass, charge);
+ }
+
+ void GetPeaks(TheoreticalPeakArr* peaks_charge_1,
+ TheoreticalPeakArr* negs_charge_1,
+ TheoreticalPeakArr* peaks_charge_2,
+ TheoreticalPeakArr* negs_charge_2,
+ const pb::Peptide* peptide = NULL) {
+ assert(peptide == NULL);
+
+ make_all_.GetPeaks(&make_all_1_, NULL, &make_all_2_, NULL);
+ BY_all_.GetPeaks(&BY_all_1_, NULL, &BY_all_2_, NULL);
+
+ Diff(make_all_1_, BY_all_1_, peaks_charge_1, negs_charge_1);
+ Diff(make_all_2_, BY_all_2_, peaks_charge_2, negs_charge_2);
+ }
+
+ private:
+ TheoreticalPeakSetBYAll BY_all_;
+ TheoreticalPeakSetMakeAll make_all_;
+
+ // space for partial results, used by GetPeaks() above.
+ TheoreticalPeakArr make_all_1_;
+ TheoreticalPeakArr make_all_2_;
+ TheoreticalPeakArr BY_all_1_;
+ TheoreticalPeakArr BY_all_2_;
+};
+
+// For testing. Bypasses disk storage, doing the combined operations done at
+// indexing and search time. Explicitly represents BYSparse and Diff.
+class TheoreticalPeakSetSparse : public TheoreticalPeakSet {
+ public:
+ TheoreticalPeakSetSparse(int capacity)
+ : BY_sparse_(capacity), diff_(capacity) {
+ }
+
+ virtual ~TheoreticalPeakSetSparse() {}
+
+ void Clear() {
+ BY_sparse_.Clear();
+ diff_.Clear();
+ }
+
+ void AddYIon(double mass, int charge) {
+ BY_sparse_.AddYIon(mass, charge);
+ diff_.AddYIon(mass, charge);
+ }
+
+ void AddBIon(double mass, int charge) {
+ BY_sparse_.AddBIon(mass, charge);
+ diff_.AddBIon(mass, charge);
+ }
+
+ void GetPeaks(TheoreticalPeakArr* peaks_charge_1,
+ TheoreticalPeakArr* negs_charge_1,
+ TheoreticalPeakArr* peaks_charge_2,
+ TheoreticalPeakArr* negs_charge_2,
+ const pb::Peptide* peptide = NULL) {
+ assert(peptide == NULL);
+ BY_sparse_.GetPeaks(peaks_charge_1, NULL, peaks_charge_2, NULL);
+ diff_.GetPeaks(peaks_charge_1, negs_charge_1,
+ peaks_charge_2, negs_charge_2);
+ }
+
+ private:
+ TheoreticalPeakSetBYSparse BY_sparse_;
+ TheoreticalPeakSetDiff diff_;
+};
+
+*/
+
+// This class is used to store theoretical b ions only, with true monoisotopic mass,
+// for use in exact p-value calculations.
+class TheoreticalPeakSetBIons {
+ public:
+ TheoreticalPeakSetBIons() {}
+ explicit TheoreticalPeakSetBIons(int capacity) {
+ unordered_peak_list_.reserve(capacity);
+ }
+ virtual ~TheoreticalPeakSetBIons() {}
+
+ void Clear() { unordered_peak_list_.clear(); }
+ void AddBIon(double mass) {
+ unsigned int index = (unsigned int)floor(mass / binWidth_ + 1.0 - binOffset_);
+ unordered_peak_list_.push_back(index);
+ }
+ vector<unsigned int> unordered_peak_list_;
+ double binWidth_;
+ double binOffset_;
+};
+#endif // THEORETICAL_PEAK_SET_H
diff --git a/src/app/xlink/AccurateMonoMass.cpp b/src/app/xlink/AccurateMonoMass.cpp
new file mode 100644
index 0000000..32a8fa2
--- /dev/null
+++ b/src/app/xlink/AccurateMonoMass.cpp
@@ -0,0 +1,157 @@
+#include "AccurateMonoMass.h"
+
+#include <iostream>
+#include <iomanip>
+#include <cmath>
+
+using namespace std;
+
+
+static bool map_generated_ = false;
+static map<char, MolecularFormula> amino_acid_to_formula_;
+
+#define H 0
+#define C 1
+#define N 2
+#define O 3
+#define P 4
+#define S 5
+
+double mass_table[] = {
+ 1.00782503207, //1H
+ 12.0000000, //12C
+ 14.0030740048, //14N
+ 15.99491461956, //16O
+ 30.97376163, //31P
+ 31.97207100 //32S
+ };
+
+
+MolecularFormula::MolecularFormula() {
+ H_ = 0;
+ C_ = 0;
+ N_ = 0;
+ O_ = 0;
+ P_ = 0;
+ S_ = 0;
+}
+
+MolecularFormula::~MolecularFormula() {
+ ;
+}
+
+MolecularFormula::MolecularFormula(int nH, int nC, int nN, int nO, int nP, int nS) {
+ H_ = nH;
+ C_ = nC;
+ N_ = nN;
+ O_ = nO;
+ P_ = nP;
+ S_ = nS;
+}
+
+void MolecularFormula::add(MolecularFormula& formula) {
+ H_ += formula.H_;
+ C_ += formula.C_;
+ N_ += formula.N_;
+ O_ += formula.O_;
+ P_ += formula.P_;
+ S_ += formula.S_;
+}
+
+double MolecularFormula::calculateMass() {
+ double ans = 0.0;
+
+ ans += mass_table[H] * H_;
+ ans += mass_table[C] * C_;
+ ans += mass_table[N] * N_;
+ ans += mass_table[O] * O_;
+ ans += mass_table[P] * P_;
+ ans += mass_table[S] * S_;
+
+ return ans;
+}
+
+
+static MolecularFormula H2O(2, 0, 0, 1, 0, 0);
+
+void AccurateMonoMass::generateMap() {
+
+ amino_acid_to_formula_['A'] = MolecularFormula(5, 3, 1, 1, 0, 0);
+ amino_acid_to_formula_['C'] = MolecularFormula(5, 3, 1, 1, 0, 1);
+ amino_acid_to_formula_['c'] = MolecularFormula(8, 5, 2, 2, 0, 1); //iodoacetmide adds C2H3NO
+ amino_acid_to_formula_['D'] = MolecularFormula(5, 4, 1, 3, 0, 0);
+ amino_acid_to_formula_['E'] = MolecularFormula(7, 5, 1, 3, 0, 0);
+ amino_acid_to_formula_['F'] = MolecularFormula(9, 9, 1, 1, 0, 0);
+ amino_acid_to_formula_['G'] = MolecularFormula(3, 2, 1, 1, 0, 0);
+ amino_acid_to_formula_['H'] = MolecularFormula(7, 6, 3, 1, 0, 0);
+ amino_acid_to_formula_['I'] = MolecularFormula(11, 6, 1, 1, 0, 0);
+ amino_acid_to_formula_['K'] = MolecularFormula(12, 6, 2, 1, 0, 0);
+ amino_acid_to_formula_['L'] = MolecularFormula(11, 6, 1, 1, 0, 0);
+ amino_acid_to_formula_['M'] = MolecularFormula(9, 5, 1, 1, 0, 1);
+ //amino_acid_to_formula['m'] = MolecularFormula(9, 5, 1, 2, 0, 1); # oxidized methionine
+ amino_acid_to_formula_['N'] = MolecularFormula(6, 4, 2, 2, 0, 0);
+ amino_acid_to_formula_['P'] = MolecularFormula(7, 5, 1, 1, 0, 0);
+ amino_acid_to_formula_['Q'] = MolecularFormula(8, 5, 2, 2, 0, 0);
+ amino_acid_to_formula_['R'] = MolecularFormula(12, 6, 4, 1, 0, 0);
+ amino_acid_to_formula_['S'] = MolecularFormula(5, 3, 1, 2, 0, 0);
+ //amino_acid_to_formula['s'] = MolecularFormula(4, 3, 1, 5, 1, 0); # phosphate
+ amino_acid_to_formula_['T'] = MolecularFormula(7, 4, 1, 2, 0, 0);
+ //amino_acid_to_formula['t'] = MolecularFormula(6, 4, 1, 5, 1, 0); # phosphate
+ amino_acid_to_formula_['V'] = MolecularFormula(9, 5, 1, 1, 0, 0);
+ amino_acid_to_formula_['W'] = MolecularFormula(10, 11, 2, 1, 0, 0);
+ amino_acid_to_formula_['Y'] = MolecularFormula(9, 9, 1, 2, 0, 0);
+ //amino_acid_to_formula['y'] = MolecularFormula(8, 9, 1, 5, 1, 0); # phosphate
+ map_generated_ = true;
+}
+
+double AccurateMonoMass::calculateMass(const string& sequence) {
+
+ if (!map_generated_) generateMap();
+ MolecularFormula formula;
+
+ for (int i=0;i < sequence.length();i++) {
+
+ formula.add(amino_acid_to_formula_[sequence[i]]);
+
+ }
+ formula.add(H2O);
+
+
+ return formula.calculateMass();
+}
+
+int main(int argc, char**argv) {
+
+ AccurateMonoMass::generateMap();
+
+ map<char, MolecularFormula>::iterator iter;
+
+ cout << fixed << setprecision(11);
+
+ for (iter = amino_acid_to_formula_.begin();
+ iter != amino_acid_to_formula_.end();
+ ++iter) {
+ cout << "Mass of :" <<iter -> first << " = " << iter -> second.calculateMass() << endl;
+ }
+
+ double diff = amino_acid_to_formula_['c'].calculateMass() - amino_acid_to_formula_['C'].calculateMass();
+
+ cout << "Diff of acetomide:" << diff << endl;
+
+ cout << "Mass of AA:" << AccurateMonoMass::calculateMass(string("AA")) << endl;
+ cout << "Mass of A + A:" << (AccurateMonoMass::calculateMass(string("A")) + AccurateMonoMass::calculateMass(string("A"))-H2O.calculateMass()) << endl;
+ double massA = AccurateMonoMass::calculateMass("A");
+
+ double massAA = AccurateMonoMass::calculateMass("AAAAAAA");
+
+ double massApA = 7*massA - 6 * H2O.calculateMass();
+
+ double ppm = fabs(massAA - massApA) / massAA * 1e6;
+
+ cout <<" ppm:" << ppm << endl;
+
+ cout <<"H2O:"<< H2O.calculateMass() << endl;
+
+}
+
+
diff --git a/src/app/xlink/CMakeLists.txt b/src/app/xlink/CMakeLists.txt
new file mode 100644
index 0000000..b82e8d3
--- /dev/null
+++ b/src/app/xlink/CMakeLists.txt
@@ -0,0 +1,61 @@
+project(xlink)
+
+cmake_minimum_required(VERSION 2.8.4)
+cmake_policy(VERSION 2.8.4)
+
+include_directories(${CMAKE_SOURCE_DIR}/src)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_1_56_0)
+include_directories(${CMAKE_BINARY_DIR}/ext/build/src/ProteoWizard/libraries/boost_aux)
+include_directories(${CMAKE_BINARY_DIR}/ext/include)
+
+if (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _CRT_SECURE_NO_WARNINGS
+ )
+else (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+ set_property(
+ DIRECTORY
+ PROPERTY
+ COMPILE_DEFINITIONS
+ _FILE_OFFSET_BITS=64
+ _GNU_SOURCE
+ _LARGEFILE_SOURCE
+ GCC
+ )
+endif (${CMAKE_SYSTEM_NAME} MATCHES "Windows")
+
+add_library(
+ xlink
+ STATIC
+ XHHC_Peptide.cpp
+ LinkedPeptide.cpp
+ xhhc.cpp
+ LinkedIonSeries.cpp
+ xhhc_score_peptide_spectrum.cpp
+ xhhc_scorer.cpp
+ xhhc_score_peptide_spectrum.cpp
+ xhhc_scorer.cpp
+ xhhc_search.cpp
+ xlink_assign_ions.cpp
+ xlink_search.cpp
+ SearchForXLinks.cpp
+ xlink_compute_qvalues.cpp
+ LinearPeptide.cpp
+ SelfLoopPeptide.cpp
+ XLinkDatabase.cpp
+ XLinkIonSeriesCache.cpp
+ XLink.cpp
+ XLinkScorer.cpp
+ XLinkSite.cpp
+ XLinkBondMap.cpp
+ XLinkablePeptide.cpp
+ XLinkablePeptideIterator.cpp
+ XLinkablePeptideIteratorTopN.cpp
+ XLinkMatch.cpp
+ XLinkMatchCollection.cpp
+ XLinkPeptide.cpp
+ Weibull.cpp
+)
diff --git a/src/app/xlink/LinearPeptide.cpp b/src/app/xlink/LinearPeptide.cpp
new file mode 100644
index 0000000..088575f
--- /dev/null
+++ b/src/app/xlink/LinearPeptide.cpp
@@ -0,0 +1,245 @@
+
+#include "LinearPeptide.h"
+#include "XLink.h"
+#include "model/ModifiedPeptidesIterator.h"
+#include "model/IonSeries.h"
+#include "util/GlobalParams.h"
+#include "XLinkDatabase.h"
+
+#include <iostream>
+
+using namespace std;
+
+/**
+ * Default constructor
+ */
+LinearPeptide::LinearPeptide() : XLinkMatch() {
+ peptide_ = NULL;
+ sequence_ = NULL;
+}
+
+/**
+ * Constructor with sequence
+ */
+LinearPeptide::LinearPeptide(
+ char* sequence ///< sequence string
+ ) : XLinkMatch() {
+ peptide_ = NULL;
+ sequence_ = sequence;
+}
+
+/**
+ * Constructor from a Crux Peptide
+ */
+LinearPeptide::LinearPeptide(
+ Crux::Peptide* peptide ///< peptide object
+ ) : XLinkMatch() {
+ peptide_ = peptide;
+ sequence_ = NULL;
+ this->setNullPeptide(peptide_->isDecoy());
+}
+
+LinearPeptide::~LinearPeptide() {
+}
+
+
+/**
+ *Add candidates to the XLinkMatchCollection that are linear
+ */
+void LinearPeptide::addCandidates(
+ FLOAT_T min_mass, ///< min mass
+ FLOAT_T max_mass, ///< max mass
+ bool is_decoy, ///< generate decoy canidates
+ XLinkMatchCollection& candidates ///< Vector of candidate -inout
+ ) {
+
+ vector<LinearPeptide>::iterator siter = XLinkDatabase::getLinearBegin(is_decoy, min_mass);
+ if (siter == XLinkDatabase::getLinearEnd(is_decoy) ||
+ siter->getMassConst(GlobalParams::getIsotopicMass()) > max_mass) {
+ return;
+ } else {
+ vector<LinearPeptide>::iterator eiter = XLinkDatabase::getLinearEnd(is_decoy, siter, max_mass);
+
+ while (siter != eiter && siter->getMassConst() <= max_mass) {
+ siter->incrementPointerCount();
+ LinearPeptide& lpeptide = *siter;
+ if (lpeptide.getMassConst() < min_mass || lpeptide.getMassConst() > max_mass) {
+ carp(CARP_DEBUG,
+ "The mass %g of peptide %s is outside the precursor range of %g-%g.",
+ lpeptide.getMass(), lpeptide.getSequenceString().c_str(),
+ min_mass, max_mass);
+ return;
+ } else {
+ //carp(CARP_INFO, "Add linear candidate");
+ candidates.add(&(*siter));
+ ++siter;
+ }
+ }
+ }
+}
+
+/**
+ * returns the candidate type, either a deadlink or a linear candidate
+ */
+XLINKMATCH_TYPE_T LinearPeptide::getCandidateType() {
+ if (isModified()) {
+ return DEADLINK_CANDIDATE;
+ } else {
+ return LINEAR_CANDIDATE;
+ }
+}
+
+/**
+ * \returns the sequence of the peptide in string format
+ */
+string LinearPeptide::getSequenceString() {
+ ostringstream oss;
+ if (peptide_ == NULL) {
+ oss << sequence_;
+
+ } else {
+ oss << peptide_->getModifiedSequenceWithMasses();
+ }
+
+ //oss << " ()";
+ return oss.str();
+
+}
+
+/**
+ * \returns the mass of the peptide
+ */
+FLOAT_T LinearPeptide::calcMass(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ ) {
+
+ if (peptide_ == NULL) {
+ return Crux::Peptide::calcSequenceMass(sequence_, mass_type);
+ } else {
+ return peptide_->calcModifiedMass(mass_type);
+ }
+}
+
+/**
+ *\returns a shuffled version of the peptide
+ */
+void LinearPeptide::shuffle(vector<XLinkMatch*>& decoys) {
+ string seq = getSequenceString();
+ Crux::Peptide* decoy_peptide = new Crux::Peptide(peptide_);
+
+ decoy_peptide->transformToDecoy();
+
+ XLink::addAllocatedPeptide(decoy_peptide);
+
+ LinearPeptide* decoy = new LinearPeptide(decoy_peptide);
+
+ string decoy_seq = decoy->getSequenceString();
+ // carp(CARP_INFO, "Shuffled: %s", decoy_seq.c_str());
+
+ decoy->setNullPeptide(true);
+ decoys.push_back(decoy);
+}
+
+/**
+ * predicts the ions for this peptide
+ */
+void LinearPeptide::predictIons(
+ IonSeries* ion_series, ///< ion series to place the ions
+ int charge ///< charge state of the peptide
+ ) {
+
+ const char* seq = NULL;
+ MODIFIED_AA_T* mod_seq = NULL;
+ if (peptide_ == NULL) {
+ seq = sequence_;
+ convert_to_mod_aa_seq(seq, &mod_seq);
+ } else {
+ seq = peptide_->getSequence();
+ mod_seq = peptide_->getModifiedAASequence();
+ }
+
+ //carp(CARP_INFO, "predicting ions for :%s", seq);
+ /*
+ char* mseq = peptide_->getModifiedSequenceWithMasses(MOD_MASSES_SEPARATE);
+ carp(CARP_INFO, "mod seq:%s", mseq);
+ free(mseq);
+ */
+ ion_series->setCharge(charge);
+ ion_series->update(seq, mod_seq);
+ ion_series->predictIons();
+
+ freeModSeq(mod_seq);
+
+}
+
+/**
+ *\returns the ion sequence as a string
+ */
+string LinearPeptide::getIonSequence(
+ Ion* ion ///< ion object
+ ) {
+
+ string seq_str = string(sequence_);
+
+ int cleavage_idx = ion->getCleavageIdx();
+ if (ion->isForwardType() == B_ION) {
+ return seq_str.substr(0, cleavage_idx);
+ } else {
+ return seq_str.substr(seq_str.length()-cleavage_idx, seq_str.length());
+ }
+}
+
+/**
+ * \returns the peptide for this match
+ */
+Crux::Peptide* LinearPeptide::getPeptide(int peptide_idx) {
+ if (peptide_idx == 0) {
+ return peptide_;
+ } else {
+ return NULL;
+ }
+}
+
+/**
+ *\returns the number of missed cleavages
+ */
+int LinearPeptide::getNumMissedCleavages() {
+ set<int> skip;
+ return peptide_->getMissedCleavageSites(skip);
+}
+
+/**
+ * \returns whether this peptide is modified by a variable mod
+ */
+bool LinearPeptide::isModified() {
+
+ return peptide_->isModified();
+}
+
+bool compareLinearPeptideMass(
+ const LinearPeptide& pep1,
+ const LinearPeptide& pep2) {
+
+ return pep1.getMassConst(MONO) < pep2.getMassConst(MONO);
+
+}
+bool compareLinearPeptideMassToFLOAT(
+ const LinearPeptide& pep1,
+ FLOAT_T mass
+ ) {
+
+ return pep1.getMassConst(MONO) < mass;
+}
+
+bool compareFLOATToLinearPeptideMass(
+ const FLOAT_T& mass,
+ const LinearPeptide& pep1) {
+ return pep1.getMassConst(MONO) > mass;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/LinearPeptide.h b/src/app/xlink/LinearPeptide.h
new file mode 100644
index 0000000..8b759e3
--- /dev/null
+++ b/src/app/xlink/LinearPeptide.h
@@ -0,0 +1,145 @@
+/**
+ * \file LinearPeptide.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Object for Defining a Normal peptide in an xlink search
+ *****************************************************************************/
+#ifndef LINEARPEPTIDE_H_
+#define LINEARPEPTIDE_H_
+
+#include "model/objects.h"
+#include "util/utils.h"
+
+#include "XLinkMatch.h"
+#include "XLinkBondMap.h"
+#include "XLinkablePeptide.h"
+
+#include <vector>
+
+class LinearPeptide : public XLinkMatch {
+ protected:
+
+ Crux::Peptide* peptide_; ///< Peptide this linear peptide referes to
+ char* sequence_; ///< sequence of the peptide
+ public:
+ /**
+ * Default constructor
+ */
+ LinearPeptide();
+
+ /**
+ * Constructor with sequence
+ */
+ LinearPeptide(
+ char* sequence_ ///< sequence string
+ );
+
+ /**
+ * Constructor from a Crux peptide
+ */
+ LinearPeptide(
+ Crux::Peptide* peptide ///< peptide object
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual ~LinearPeptide();
+
+ /**
+ *Add candidates to the XLinkMatchCollection that are linear
+ */
+ static void addCandidates(
+ FLOAT_T min_mass, ///< min mass
+ FLOAT_T max_mass, ///< max mass
+ bool is_decoy,
+ XLinkMatchCollection& candidates ///< Vector of possible candidate -inout
+ );
+
+ /**
+ * returns the candidate type, either a deadlink or a linear candidate
+ */
+ virtual XLINKMATCH_TYPE_T getCandidateType();
+
+ /**
+ * \returns the sequence of the peptide in string format
+ */
+ virtual std::string getSequenceString();
+
+ /**
+ * \returns the mass of the peptide
+ */
+ virtual FLOAT_T calcMass(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ );
+
+ /**
+ *\returns a shuffled version of the peptide
+ */
+ virtual void shuffle(
+ std::vector<XLinkMatch*>& decoys
+ );
+
+ /**
+ * predicts the ions for this peptide
+ */
+ virtual void predictIons(
+ IonSeries* ion_series, ///< ion series to place the ions
+ int charge ///< charge state of the peptide
+ );
+
+ /**
+ * \returns the ion sequence as a string
+ */
+ std::string getIonSequence(
+ Ion* ion ///< ion object
+ );
+
+ /**
+ * \returns the peptide for this match
+ */
+ virtual Crux::Peptide* getPeptide(
+ int peptide_idx ///< should always be zero
+ );
+
+ /**
+ * \returns the number of missed cleavages
+ */
+ virtual int getNumMissedCleavages();
+
+ /**
+ * \returns whether this peptide is modified by a variable mod
+ */
+ virtual bool isModified();
+
+};
+
+/**
+ * Comparison function of two linear peptide masses
+ */
+bool compareLinearPeptideMass(
+ const LinearPeptide& xpep1, ///< linear peptide 1
+ const LinearPeptide& xpep2 ///< linear peptide 2
+ );
+
+/**
+ * Comparison functions for lower_bound and upper_bound
+ */
+bool compareLinearPeptideMassToFLOAT(
+ const LinearPeptide& xpep1,
+ FLOAT_T mass
+ );
+
+
+bool compareFLOATToLinearPeptideMass(
+ const FLOAT_T& mass,
+ const LinearPeptide& pep1);
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/LinkedIonSeries.cpp b/src/app/xlink/LinkedIonSeries.cpp
new file mode 100644
index 0000000..378d0f4
--- /dev/null
+++ b/src/app/xlink/LinkedIonSeries.cpp
@@ -0,0 +1,294 @@
+/**
+ * \file LinkedIonSeries.cpp
+ * AUTHOR: Sean McIlwain and Paul Draghicescu
+ * CREATE DATE: 18 January 2012
+ * \brief Object for keeping track of a (non-)crosslinked peptide ions.
+ *****************************************************************************/
+#include "LinkedIonSeries.h"
+#include "xhhc_scorer.h"
+
+#include "LinkedPeptide.h"
+#include "XHHC_Peptide.h"
+
+#include <iostream>
+
+/**
+ * GLOBALS - TODO GET RID OF THESE!
+ */
+FLOAT_T* mass_matrix = NULL;
+int mass_matrix_size = -1;
+
+
+/**
+ * \returns a blank LinkedIonSeries object
+ */
+LinkedIonSeries::LinkedIonSeries() {
+ charge_ = 0;
+ fragment_mass_type_ = get_mass_type_parameter("fragment-mass");
+}
+
+/**
+ * \returns an ion series object assigning the charge.
+ */
+LinkedIonSeries::LinkedIonSeries(
+ int charge ///< The maximum charge of the ion series.
+ ) {
+
+ charge_ = charge;
+ fragment_mass_type_ = get_mass_type_parameter("fragment-mass");
+}
+
+/**
+ * Default desctructor
+ */
+LinkedIonSeries::~LinkedIonSeries() {
+
+}
+
+/**
+ * \returns charge for this linked ion series
+ */
+int LinkedIonSeries::getCharge() {
+ return charge_;
+}
+
+/**
+ * \returns all the ions in this series
+ */
+vector<LinkedPeptide>& LinkedIonSeries::getIons() {
+ return all_ions_;
+}
+
+/**
+ * \returns the number of ions within this series
+ */
+int LinkedIonSeries::getSize() {
+ return all_ions_.size();
+}
+
+/**
+ * removes all ions from this series
+ */
+void LinkedIonSeries::clear() {
+ all_ions_.clear();
+}
+
+/**
+ * prints out tab delimited information about the ion series
+ */
+void LinkedIonSeries::print() {
+
+ LinkedPeptide::sortByMZ(all_ions_, fragment_mass_type_);
+
+ cout << "m/z\ttype\tcharge\tion" << endl;
+ string ion_type;
+ for (vector<LinkedPeptide>::iterator ion = all_ions_.begin();
+ ion != all_ions_.end();
+ ++ion) {
+
+ if (ion->getIonType() == B_ION)
+ ion_type = "B_ION";
+ else
+ ion_type = "Y_ION";
+
+ cout << ion->getMZ(fragment_mass_type_) << "\t" <<
+ ion_type << "\t" <<
+ ion->getCharge() << "\t" <<
+ *ion << endl;
+ }
+}
+
+/**
+ * cleaves linked_peptide at all positions, adding b and y ions
+ */
+void LinkedIonSeries::addLinkedIons(
+ LinkedPeptide& linked_peptide, ///< The linked peptide
+ SPLITTYPE_T split_type ///< Which peptide to split (A,B, or BOTH)
+ ) {
+
+ linked_peptide.setCharge(charge_);
+
+ fragments_.clear();
+ // split the precursor at every cleavage site
+
+ switch(split_type) {
+ case SPLITTYPE_A:
+ linked_peptide.splitA(fragments_);
+ break;
+ case SPLITTYPE_B:
+ linked_peptide.splitB(fragments_);
+ break;
+ case SPLITTYPE_BOTH:
+ linked_peptide.split(fragments_);
+ break;
+ case SPLITTYPE_INVALID:
+ case NUMBER_SPLITTYPES:
+ carp(CARP_FATAL, "SPLITTYPE invalid:%d", (int)split_type);
+ }
+
+ for (vector<pair<LinkedPeptide, LinkedPeptide> >::iterator ion_pair =
+ fragments_.begin();
+ ion_pair != fragments_.end();
+ ++ion_pair) {
+
+ // if b-ion and not a neutral loss
+ if (ion_pair->first.getCharge() != 0) {
+ ion_pair->first.setIonType(B_ION);
+ ion_pair->first.getMZ(fragment_mass_type_);
+ all_ions_.push_back(ion_pair->first);
+ }
+ // if y-ion and not a neutral loss
+ if (ion_pair->second.getCharge() != 0) {
+ ion_pair->second.setIonType(Y_ION);
+ ion_pair->second.getMZ(fragment_mass_type_);
+ all_ions_.push_back(ion_pair->second);
+ }
+ }
+
+}
+
+/**
+ * gets the Total number of by ions in this series.
+ */
+int LinkedIonSeries::getTotalBYIons() {
+
+ int ans = 0;
+ vector<LinkedPeptide>::iterator ion_iter;
+
+ for (ion_iter = all_ions_.begin();
+ ion_iter != all_ions_.end();
+ ++ion_iter) {
+
+ if (ion_iter -> getIonType() == B_ION || ion_iter -> getIonType() == Y_ION) {
+ ans++;
+ }
+ }
+ return ans;
+}
+
+/**
+ * adds an ion to the observed list, used in conjunction with
+ * getObservableIons
+ */
+void LinkedIonSeries::addIonBin(
+ map<int, bool>& observed, ///< the observed bin vector -in/out
+ int& ions, ///< the number of ions -in/out
+ int& ions_bin, ///< the number of binned ions -in/out
+ FLOAT_T mz, ///< m/z of the ion
+ FLOAT_T bin_width, ///< bin-width
+ FLOAT_T min_mz, ///< max m/z for the range
+ FLOAT_T max_mz, ///< min m/z for the range
+ bool add_flanks ///< add flanks?
+ ) {
+
+ if ((mz >= min_mz) && (mz <= max_mz)) {
+ ions++;
+ int bin_idx = (int)(mz / bin_width + 0.5);
+ if (observed.find(bin_idx) == observed.end()) {
+ observed[bin_idx] = true;
+ ions_bin++;
+ }
+ if (add_flanks) {
+
+ bin_idx = bin_idx - 1;
+ FLOAT_T flank_mz = bin_idx * bin_width;
+ if (flank_mz >= min_mz) {
+ ions++;
+ if (observed.find(bin_idx) == observed.end()) {
+ observed[bin_idx] = true;
+ ions_bin++;
+ }
+ }
+ bin_idx = bin_idx + 2;
+ flank_mz = bin_idx * bin_width;
+ if (flank_mz <= max_mz) {
+ ions++;
+ if (observed.find(bin_idx) == observed.end()) {
+ observed[bin_idx] = true;
+ ions_bin++;
+ }
+ }
+ }
+ }
+}
+
+/**
+ * \returns the total number of ions observable within a binned
+ * range
+ */
+int LinkedIonSeries::getObservableIons(
+ FLOAT_T min_mz, ///< the minimum m/z -in
+ FLOAT_T max_mz, ///< the maximum m/z -in
+ FLOAT_T bin_width, ///< the width of the bins -in
+ int& ions_observable, ///<number of ions observable -out
+ int& ions_observable_bin ///<number of bins observable -out
+ ) {
+
+ ions_observable = 0;
+ ions_observable_bin = 0;
+
+ map<int, bool> observed;
+
+ for (vector<LinkedPeptide>::iterator ion_iter = all_ions_.begin();
+ ion_iter != all_ions_.end();
+ ++ion_iter) {
+
+ double mz = ion_iter -> getMZ(MONO);
+
+ if (ion_iter -> getIonType() == B_ION ||
+ ion_iter -> getIonType() == Y_ION) {
+ addIonBin(observed, ions_observable, ions_observable_bin, mz, bin_width, min_mz, max_mz, true);
+ double h2O_mz = ion_iter -> getMZ(MONO) - (MASS_H2O_MONO/ ion_iter -> getCharge());
+ addIonBin(observed, ions_observable, ions_observable_bin, h2O_mz, bin_width, min_mz, max_mz, false);
+ double nh3_mz = ion_iter -> getMZ(MONO) - (MASS_NH3_MONO/ ion_iter -> getCharge());
+ addIonBin(observed, ions_observable, ions_observable_bin, nh3_mz, bin_width, min_mz, max_mz, false);
+ double co_mz = ion_iter -> getMZ(MONO) - (MASS_CO_MONO / ion_iter -> getCharge());
+ addIonBin(observed, ions_observable, ions_observable_bin, co_mz, bin_width, min_mz, max_mz, false);
+ }
+ }
+ return 0;
+}
+
+/**
+ * \returns the total number of b-y ions observable within a binned
+ * range
+ */
+int LinkedIonSeries::getObservableBYIons(
+ FLOAT_T min_mz, ///< the minimum m/z -in
+ FLOAT_T max_mz, ///< the maximum m/z -in
+ FLOAT_T bin_width, ///< the width of the bins -in
+ int &by_observable, ///<number of ions observable -out
+ int &by_observable_bin ///<number of bins observable -out
+ ) {
+
+ by_observable = 0;
+ by_observable_bin = 0;
+
+ map<int, bool> observed;
+
+ vector<LinkedPeptide>::iterator ion_iter;
+
+ for (ion_iter = all_ions_.begin();
+ ion_iter != all_ions_.end();
+ ++ion_iter) {
+ if (ion_iter -> getMZ(MONO) >= min_mz && ion_iter -> getMZ(MONO) <= max_mz) {
+ if (ion_iter ->getIonType() == B_ION || ion_iter -> getIonType() == Y_ION) {
+ by_observable++;
+ int bin_idx =
+ (int)(ion_iter->getMZ(MONO) / bin_width + 0.5);
+ if (observed.find(bin_idx) == observed.end()) {
+ observed[bin_idx] = true;
+ by_observable_bin++;
+ }
+ }
+ }
+ }
+ return by_observable_bin;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/LinkedIonSeries.h b/src/app/xlink/LinkedIonSeries.h
new file mode 100644
index 0000000..3f63009
--- /dev/null
+++ b/src/app/xlink/LinkedIonSeries.h
@@ -0,0 +1,139 @@
+/**
+ * \file LinkedIonSeries.h
+ * AUTHOR: Sean McIlwain and Paul Draghicescu
+ * CREATE DATE: 18 January 2012
+ * \brief Object for keeping track of a (non-)crosslinked peptide ions.
+ *****************************************************************************/
+#ifndef LINKEDIONSERIES_H
+#define LINKEDIONSERIES_H
+
+#include "xhhc.h"
+
+//CRUX includes
+#include "model/IonSeries.h"
+#include "model/Scorer.h"
+#include "model/Spectrum.h"
+#include "io/SpectrumCollection.h"
+
+class LinkedIonSeries {
+ protected:
+
+ int charge_; ///< maximum charge of the ion series
+ std::vector<LinkedPeptide> all_ions_; ///< list of all ions
+ std::vector<pair<LinkedPeptide, LinkedPeptide> > fragments_; ///< for add linked ions
+ MASS_TYPE_T fragment_mass_type_; ///< mass type of the fragments.
+
+ /**
+ * adds an ion to the observed list, used in conjunction with
+ * getObservableIons
+ */
+ void addIonBin(
+ map<int, bool>& observed, ///< the observed bin vector -in/out
+ int& ions, ///< the number of ions -in/out
+ int& ions_bin, ///< the number of binned ions -in/out
+ FLOAT_T mz, ///< m/z of the ion
+ FLOAT_T bin_width, ///< bin-width
+ FLOAT_T min_mz, ///< max m/z for the range
+ FLOAT_T max_mz, ///< min m/z for the range
+ bool add_flanks ///< add flanks?
+ );
+
+ public:
+
+ /**
+ * \returns a blank LinkedIonSeries object
+ */
+ LinkedIonSeries();
+
+ /**
+ * \returns an ion series object assigning the charge.
+ */
+ LinkedIonSeries(
+ int charge ///< The maximum charge of the ion series.
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual ~LinkedIonSeries();
+
+ /**
+ * \returns charge for this linked ion series
+ */
+ int getCharge();
+
+ /**
+ * \returns all the ions in this series
+ */
+ std::vector<LinkedPeptide>& getIons();
+
+ /**
+ * \returns the number of ions within this series
+ */
+ int getSize();
+
+ /**
+ * \returns the total number of by ions for this series
+ */
+ int getTotalBYIons();
+
+ /**
+ * \returns the total number of ions observable within a binned
+ * range
+ */
+ int getObservableIons(
+ FLOAT_T min_mz, ///< the minimum m/z -in
+ FLOAT_T max_mz, ///< the maximum m/z -in
+ FLOAT_T bin_width, ///< the width of the bins -in
+ int& ions_observable, ///<number of ions observable -out
+ int& ions_observable_bin ///<number of bins observable -out
+ );
+
+ /**
+ * \returns the total number of b-y ions observable within a binned
+ * range
+ */
+ int getObservableBYIons(
+ FLOAT_T min_mz, ///< the minimum m/z -in
+ FLOAT_T max_mz, ///< the maximum m/z -in
+ FLOAT_T bin_width, ///< the width of the bins -in
+ int &by_observable, ///<number of ions observable -out
+ int &by_observable_bin ///<number of bins observable -out
+ );
+
+ /**
+ * sets the charge for this ion series
+ */
+ void setCharge(
+ int charge ///< the charge
+ );
+
+ /**
+ * removes all ions from this series
+ */
+ void clear();
+
+ /**
+ * Adds the linked ions for a linked peptide
+ */
+ void addLinkedIons(
+ LinkedPeptide& linked_peptide, ///< The linked peptide
+ SPLITTYPE_T split_type = SPLITTYPE_BOTH ///< Which peptide to split
+ );
+
+ /**
+ * prints out tab delimited information about the ion series
+ */
+ void print();
+
+
+};
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/xlink/LinkedPeptide.cpp b/src/app/xlink/LinkedPeptide.cpp
new file mode 100644
index 0000000..fe22c9a
--- /dev/null
+++ b/src/app/xlink/LinkedPeptide.cpp
@@ -0,0 +1,459 @@
+/**
+ * \file LinkedPeptide.cpp
+ * AUTHOR: Sean McIlwain and Paul Draghicescu
+ * CREATE DATE: 18 January 2012
+ * \brief Object for keeping track of a (non-)crosslinked peptide.
+ *****************************************************************************/
+//TODO Change cout/cerrs to CARP.
+
+#include "LinkedPeptide.h"
+#include "XHHC_Peptide.h"
+
+using namespace Crux;
+
+/**
+ * mass of the linker
+ */
+FLOAT_T LinkedPeptide::linker_mass_;
+
+/**
+ * Initializes the object
+ */
+void LinkedPeptide::init() {
+
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+ charge_ = 0;
+ type_ = NUMBER_ION_TYPES;
+ mass_[MONO] = 0.0;
+ mass_[AVERAGE] = 0.0;
+ mz_[MONO] = 0.0;
+ mz_[AVERAGE] = 0.0;
+
+}
+
+/**
+ * \returns a blank LinkedPeptide object
+ */
+LinkedPeptide::LinkedPeptide() {
+ init();
+}
+
+/**
+ * \returns a linked peptide object.
+ * constructor for a linked peptide. If A or B null, then
+ * a self link will be created. If an index is -1, a link to nothing
+ * will be created.
+ */
+LinkedPeptide::LinkedPeptide(
+ char* peptide_A, ///< First peptide
+ char* peptide_B, ///< Second peptide (can be NULL)
+ int posA, ///< Index of link on first peptide
+ int posB, ///< Index of link on second peptide
+ int charge ///< charge of product
+ ) {
+
+ init();
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+ charge_ = charge;
+ decoy_ = false;
+ type_ = (ION_TYPE_T)NULL;
+ XHHC_Peptide pepA = XHHC_Peptide(peptide_A);
+ // if a self link or dead end
+ if (peptide_B == NULL) {
+ pepA.addLink(posA);
+ if (posB >= 0)
+ pepA.addLink(posB);
+ peptides_.push_back(pepA);
+ } else {
+ carp(CARP_DETAILED_DEBUG, "adding links at %d and %d", posA, posB);
+ XHHC_Peptide pepB = XHHC_Peptide(peptide_B);
+ pepA.addLink(posA);
+ pepB.addLink(posB);
+ peptides_.push_back(pepA);
+ peptides_.push_back(pepB);
+ }
+ getMZ(MONO);
+ getMZ(AVERAGE);
+}
+
+/**
+ * \returns a blank LinkedPeptide object with
+ * the charge set
+ */
+LinkedPeptide::LinkedPeptide(
+ int charge ///< charge of product
+ ) {
+
+ init();
+ charge_ = charge;
+ decoy_ = false;
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+}
+
+/**
+ * Destructor
+ */
+LinkedPeptide::~LinkedPeptide() {
+}
+
+/**
+ * Sets the linker_mass_ static variable
+ */
+void LinkedPeptide::setLinkerMass(
+ FLOAT_T linker_mass ///< the linker mass
+ ) {
+
+ linker_mass_ = linker_mass;
+}
+
+/**
+ * \returns the linker_mass_ static variable
+ */
+FLOAT_T LinkedPeptide::getLinkerMass() {
+ return linker_mass_;
+}
+
+/**
+ * \returns a reference to the internal
+ * peptides vector
+ */
+vector<XHHC_Peptide>& LinkedPeptide::getPeptides() {
+
+ return peptides_;
+}
+
+/**
+ * \returns the charge of the LinkedPeptide
+ */
+int LinkedPeptide::getCharge() {
+ return charge_;
+}
+
+/**
+ * sets the charge of the LinkedPeptide
+ */
+void LinkedPeptide::setCharge(
+ int charge ///< the charge of the LinkedPeptide
+ ) {
+
+ charge_ = charge;
+}
+
+/**
+ * sets the IonType for the LinkedPeptide
+ */
+void LinkedPeptide::setIonType(
+ ION_TYPE_T type ///< The ion type
+ ) {
+
+ type_ = type;
+}
+
+/**
+ * \returns the ion type for this LinkedPeptide
+ */
+ION_TYPE_T LinkedPeptide::getIonType() {
+ return type_;
+}
+
+/**
+ * \returns the number of peptides in this linked
+ * Peptide (should be 1 or 2)
+ */
+int LinkedPeptide::size() {
+ return peptides_.size();
+}
+
+/**
+ * indicates that this LinkedPeptide is a
+ * decoy
+ */
+void LinkedPeptide::setDecoy() {
+ decoy_ = true;
+}
+
+/**
+ * \returns whether the LinkedPeptide is a
+ * decoy
+ */
+bool LinkedPeptide::isDecoy() {
+ return decoy_;
+}
+
+/**
+ * adds a XHHC_Peptide to the list of peptide
+ * in this LinkedPeptide object
+ */
+void LinkedPeptide::addPeptide(
+ XHHC_Peptide& peptide
+ ) {
+
+ peptides_.push_back(peptide);
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+}
+
+/**
+ * \returns whether the LinkedPeptide is a
+ * crosslinked peptide
+ */
+bool LinkedPeptide::isCrossLinked() {
+ return size() == 2;
+}
+
+/**
+ * \returns whether the Peptide is a normal/linear peptide
+ */
+bool LinkedPeptide::isLinear() {
+ return (peptides_.size() == 1 && peptides_[0].linkSite() == -1);
+}
+
+/**
+ * \returns whether the Peptide is a deadend
+ */
+bool LinkedPeptide::isDeadEnd() {
+ return (peptides_.size() == 1 && peptides_[0].getNumLinks() == 1);
+}
+
+/**
+ * \returns whether the Peptide is a self-loop
+ */
+bool LinkedPeptide::isSelfLoop() {
+ return (peptides_.size() == 1 && peptides_[0].getNumLinks() == 2);
+}
+
+/**
+ * /returns the mass of the LinkedPeptide
+ */
+FLOAT_T LinkedPeptide::getMass(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ ) {
+
+ if (!mass_calculated_[mass_type])
+ calculateMass(mass_type);
+ return mass_[mass_type];
+
+}
+
+/**
+ * calculates the mass of the LinkedPeptide
+ */
+void LinkedPeptide::calculateMass(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ ) {
+
+ // remove H2O from mass if it's a b-ion
+
+ mass_[mass_type] = Peptide::calcSequenceMass((char*)peptides_[0].getSequence().c_str(), mass_type);
+
+ if (peptides_[0].getNumLinks() > 0) {
+ mass_[mass_type] += linker_mass_;
+ }
+
+ if (size() == 2) {
+ mass_[mass_type] += Peptide::calcSequenceMass((char*)peptides_[1].getSequence().c_str(), mass_type);
+ }
+
+ if (type_ == B_ION) {
+ if (mass_type == MONO) {
+ mass_[mass_type] -= MASS_H2O_MONO;
+ } else {
+ mass_[mass_type] -= MASS_H2O_AVERAGE;
+ }
+ }
+ mass_calculated_[mass_type] = true;
+}
+
+/**
+ * \returns the m/z of the LinkedPeptide
+ */
+FLOAT_T LinkedPeptide::getMZ (
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ ) {
+
+ if (mass_type == MONO) {
+ mz_[MONO] = (getMass(MONO) + MASS_PROTON * charge_) / charge_;
+ } else {
+ mz_[AVERAGE] = (getMass(AVERAGE) + MASS_H_AVERAGE * charge_) / charge_;
+ }
+ return mz_[mass_type];
+}
+
+/**
+ * splits the LinkedPeptide into b-y ions
+ */
+void LinkedPeptide::split(
+ vector<pair<LinkedPeptide, LinkedPeptide> >& ion_pairs ///< the b-y ion pairs
+ ) {
+
+ // split between every amino acid on every peptide in the
+ // linked peptide.
+ bool is_loop = false;
+ XHHC_Peptide peptideA = peptides_[0];
+ XHHC_Peptide peptideB = peptides_[0];
+ // dead end
+ if (isDeadEnd()) {
+ peptideB.setSequence("");
+ }
+ // if a loop
+ if (peptideA.getNumLinks() == 2) {
+ is_loop = true;
+ } else if (isCrossLinked()) {
+ peptideB = peptides_[1];
+ }
+ for (int idx = 1; idx < peptideA.getLength(); ++idx) {
+ peptideA.splitAt(idx, ion_pairs, charge_, peptideB, is_loop);
+ }
+
+ if (isCrossLinked()) {
+ for (int idx = 1; idx < peptideB.getLength(); ++idx) {
+ peptideB.splitAt(idx, ion_pairs, charge_, peptideA, is_loop);
+ }
+ }
+}
+
+/**
+ * splits the first LinkedPeptide into b-y ions
+ */
+void LinkedPeptide::splitA(
+ vector<pair<LinkedPeptide, LinkedPeptide> >& ion_pairs ///< the b-y ion pair
+ ) {
+
+ XHHC_Peptide peptideA = peptides_[0];
+ XHHC_Peptide peptideB = peptides_[1];
+
+ for (int idx = 1; idx < peptideA.getLength(); ++idx) {
+ peptideA.splitAt(idx, ion_pairs, charge_, peptideB, false);
+ }
+}
+
+/**
+ * splits the second LinkedPeptide into b-y ions
+ */
+void LinkedPeptide::splitB(
+ vector<pair<LinkedPeptide, LinkedPeptide> >& ion_pairs ///< the b-y ion pair
+ ) {
+
+ XHHC_Peptide peptideA = peptides_[0];
+ XHHC_Peptide peptideB = peptides_[1];
+
+ for (int idx = 1; idx < peptideB.getLength(); ++idx) {
+ peptideB.splitAt(idx, ion_pairs, charge_, peptideA, false);
+ }
+}
+
+/**
+ * used for sorting LinkedPeptides by mass
+ */
+bool operator < (
+ const LinkedPeptide &lp1,
+ const LinkedPeptide &lp2) {
+
+ return lp1.mass_ < lp2.mass_;
+ //return lp1.mz < lp2.mz;
+}
+
+/**
+ * prints the LinkedPeptide to a stream
+ */
+std::ostream &operator<< (std::ostream& os, LinkedPeptide& lp) {
+ vector<XHHC_Peptide> peptides = lp.getPeptides();
+ ostringstream link_positions;
+ link_positions << "(";
+ for (int idx = 0; idx < peptides[0].getLength(); ++idx) {
+ if (peptides[0].hasLinkAt(idx)) link_positions << (idx+1) << "," ;
+ }
+ if (peptides.size() == 2) {
+ for (int idx = 0; idx < peptides[1].getLength(); ++idx) {
+ if (peptides[1].hasLinkAt(idx)) link_positions << (idx+1) << ")";
+ }
+ return os << peptides[0].getSequence() << "," << peptides[1].getSequence() << link_positions.str();// << " +" << lp.charge();
+ }
+ string final = link_positions.str();
+ if (final.length() > 1) final.erase(final.end()-1);
+ return os << peptides[0].getSequence() << final << ")";// +" << lp.charge();
+}
+
+bool compareMassAverage(const LinkedPeptide& lp1, const LinkedPeptide& lp2) {
+ if (lp1.mass_calculated_[AVERAGE] && lp2.mass_calculated_[AVERAGE]) {
+ return lp1.mass_[AVERAGE] < lp2.mass_[AVERAGE];
+ } else {
+ carp(CARP_FATAL, "LinkedPeptide Average mass not calculated!");
+ return false;
+ }
+}
+
+bool compareMassMono(const LinkedPeptide& lp1, const LinkedPeptide& lp2) {
+ if (lp1.mass_calculated_[MONO] && lp2.mass_calculated_[MONO]) {
+ return lp1.mass_[MONO] < lp2.mass_[MONO];
+ } else {
+ carp(CARP_FATAL, "LinkedPeptide Mono mass not calculated!");
+ return false;
+ }
+}
+
+bool compareMZAverage(const LinkedPeptide& lp1, const LinkedPeptide& lp2) {
+
+ return lp1.mz_[AVERAGE] < lp2.mz_[AVERAGE];
+}
+
+bool compareMZMono(const LinkedPeptide& lp1, const LinkedPeptide& lp2) {
+ return lp1.mz_[MONO] < lp2.mz_[MONO];
+}
+
+
+/**
+ * Sorts a vector of LinkedPeptide by mass
+ */
+void LinkedPeptide::sortByMass(
+ vector<LinkedPeptide>& linked_peptides, ///< the LinkedPeptides to sort
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ ) {
+ //TODO : should we put code here to make sure that we have
+ //calculated the all of the masses for a particular mass type?
+
+ if (mass_type == MONO) {
+ sort(linked_peptides.begin(), linked_peptides.end(), compareMassMono);
+ } else {
+ sort(linked_peptides.begin(), linked_peptides.end(), compareMassAverage);
+ }
+}
+
+/**
+ * Sorts a vector of LinkedPeptide by m/z
+ */
+/**
+ * Sorts a vector of LinkedPeptide by mass
+ */
+void LinkedPeptide::sortByMZ(
+ vector<LinkedPeptide>& linked_peptides, ///< the LinkedPeptides to sort
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ ) {
+
+ IF_CARP(CARP_DEBUG,
+ //sanity check
+ for (unsigned int idx=0;idx < linked_peptides.size();idx++) {
+ if (!linked_peptides.at(idx).mass_calculated_[mass_type]) {
+ carp(CARP_ERROR, "mass not calculated for LinkedPeptide!");
+ linked_peptides.at(idx).getMZ(mass_type);
+ }
+ }
+ )
+
+ if (mass_type == MONO) {
+ sort(linked_peptides.begin(), linked_peptides.end(), compareMZMono);
+ } else {
+ sort(linked_peptides.begin(), linked_peptides.end(), compareMZAverage);
+ }
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/LinkedPeptide.h b/src/app/xlink/LinkedPeptide.h
new file mode 100644
index 0000000..61f850d
--- /dev/null
+++ b/src/app/xlink/LinkedPeptide.h
@@ -0,0 +1,255 @@
+/**
+ * \file LinkedPeptide.h
+ * AUTHOR: Sean McIlwain and Paul Draghicescu
+ * CREATE DATE: 18 January 2012
+ * \brief Object for keeping track of a (non-)crosslinked peptide.
+ *****************************************************************************/
+#ifndef LinkedPeptide_H
+#define LinkedPeptide_H
+
+#include "model/objects.h"
+#include "xhhc.h"
+
+
+class LinkedPeptide {
+ protected:
+ bool mass_calculated_[NUMBER_MASS_TYPES]; ///<MONO or AVERAGE.
+ int charge_; ///< charge of the LinkedPeptide
+ bool decoy_; ///< indicates that this LinkedPeptide is a decoy
+ ION_TYPE_T type_; ///<B_ION or Y_ION
+ FLOAT_T mass_[NUMBER_MASS_TYPES]; ///<mass of the LinkedPeptide
+ FLOAT_T mz_[NUMBER_MASS_TYPES]; ///<mz of the LinkedPeptide
+ std::vector<XHHC_Peptide> peptides_; ///<Peptides involved in the LinkedPeptide
+ static FLOAT_T linker_mass_; ///<Mass of the linker
+
+ public:
+
+ /**
+ * Initializes the object
+ */
+ void init();
+
+ /**
+ * \returns a blank LinkedPeptide object
+ */
+ LinkedPeptide();
+
+ /**
+ * \returns a linked peptide object.
+ * constructor for a linked peptide. If A or B null, then
+ * a self link will be created. If an index is -1, a link to nothing
+ * will be created.
+ */
+ LinkedPeptide(
+ char* peptide_A, ///< First peptide
+ char* peptide_B, ///< Second peptide (can be NULL)
+ int posA, ///< Index of link on first peptide
+ int posB, ///< Index of link on second peptide
+ int charge ///< charge of product
+ );
+
+ /**
+ * \returns a blank LinkedPeptide object with
+ * the charge set
+ */
+ LinkedPeptide(
+ int charge ///< charge of product
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~LinkedPeptide();
+
+ /**
+ * adds a XHHC_Peptide to the list of peptide
+ * in this LinkedPeptide object
+ */
+ void addPeptide(
+ XHHC_Peptide& peptide ///< the XHHC_Peptide
+ );
+
+ /**
+ * \returns a reference to the internal
+ * peptides vector
+ */
+ std::vector<XHHC_Peptide>& getPeptides();
+
+ /**
+ * \returns the charge of the LinkedPeptide
+ */
+ int getCharge();
+
+ /**
+ * sets the charge of the LinkedPeptide
+ */
+ void setCharge(
+ int charge ///< the charge of the LinkedPeptide
+ );
+
+ /**
+ * sets the IonType for the LinkedPeptide
+ */
+ void setIonType(
+ ION_TYPE_T type ///<The ion type
+ );
+
+ /**
+ * \returns the ion type for this LinkedPeptide
+ */
+ ION_TYPE_T getIonType();
+
+ /**
+ * \returns the number of peptides in this linked
+ * Peptide (should be 1 or 2)
+ */
+ int size();
+
+ /**
+ * indicates that this LinkedPeptide is a
+ * decoy
+ */
+ void setDecoy();
+
+ /**
+ * \returns whether the LinkedPeptide is a
+ * decoy
+ */
+ bool isDecoy();
+
+ /**
+ * \returns whether the LinkedPeptide is a
+ * crosslinked peptide
+ */
+ bool isCrossLinked();
+
+ /**
+ * \returns whether the Peptide is a deadend
+ */
+ bool isDeadEnd();
+
+ /**
+ * \returns whether the Peptide is a self-loop
+ */
+ bool isSelfLoop();
+
+ /**
+ * \returns whether the Peptide is a normal/linear peptide
+ */
+ bool isLinear();
+
+ /**
+ * \returns the m/z of the LinkedPeptide
+ */
+ FLOAT_T getMZ(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ );
+
+ /**
+ * calculates the mass of the LinkedPeptide
+ */
+ void calculateMass(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ );
+
+ /**
+ * /returns the mass of the LinkedPeptide
+ */
+ FLOAT_T getMass(
+ MASS_TYPE_T mass_type //< Average or Monoisotopic
+ );
+
+ /**
+ * splits the first LinkedPeptide into b-y ions
+ */
+ void splitA(
+ std::vector<std::pair<LinkedPeptide, LinkedPeptide> >& ion_pairs ///<the b-y ion pairs
+ );
+
+ /**
+ * splits the second LinkedPeptide into b-y ions
+ */
+ void splitB(
+ std::vector<std::pair<LinkedPeptide, LinkedPeptide> >& ion_pairs ///< the b-y ion pairs
+ );
+
+ /**
+ * splits the LinkedPeptide into b-y ions
+ */
+ void split(
+ std::vector<std::pair<LinkedPeptide, LinkedPeptide> >& ion_pairs ///< the b-y ion pairs
+ );
+
+ /**
+ * prints the LinkedPeptide to a stream
+ */
+ friend std::ostream &operator<< (
+ std::ostream& os,
+ LinkedPeptide& lp);
+
+ /**
+ * used for sorting LinkedPeptides
+ */
+ friend bool operator< (
+ const LinkedPeptide &lp1,
+ const LinkedPeptide &lp2
+ );
+
+ friend bool compareMassMono(
+ const LinkedPeptide& lp1,
+ const LinkedPeptide& lp2
+ );
+
+ friend bool compareMassAverage(
+ const LinkedPeptide& lp1,
+ const LinkedPeptide& lp2
+ );
+
+ friend bool compareMZMono(
+ const LinkedPeptide& lp1,
+ const LinkedPeptide& lp2
+ );
+
+ friend bool compareMZAverage(
+ const LinkedPeptide& lp1,
+ const LinkedPeptide& lp2
+ );
+
+ /**
+ * Sorts a vector of LinkedPeptide by mass
+ */
+ static void sortByMass(
+ std::vector<LinkedPeptide>& linked_peptides, ///< The LinkedPeptides to sort
+ MASS_TYPE_T mass_type = MONO ///< MONO or AVERAGE
+ );
+
+ /**
+ * Sorts a vector of LinkedPeptide by m/z
+ */
+ static void sortByMZ(
+ std::vector<LinkedPeptide>& linked_peptides, ///< The LinkedPeptides to sort
+ MASS_TYPE_T mass_type = MONO ///< MONO or AVERAGE
+ );
+
+ /**
+ * Sets the linker_mass_ static variable
+ */
+ static void setLinkerMass(
+ FLOAT_T linker_mass ///<the linker mass
+ );
+
+ /**
+ * \returns the linker_mass_ static variable
+ */
+ static FLOAT_T getLinkerMass();
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
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+.PHONY : xlink_assign_ions.i
+
+# target to preprocess a source file
+xlink_assign_ions.cpp.i:
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+.PHONY : xlink_assign_ions.s
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+# target to generate assembly for a file
+xlink_assign_ions.cpp.s:
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+.PHONY : xlink_assign_ions.cpp.s
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+xlink_compute_qvalues.o: xlink_compute_qvalues.cpp.o
+.PHONY : xlink_compute_qvalues.o
+
+# target to build an object file
+xlink_compute_qvalues.cpp.o:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/xlink/CMakeFiles/xlink.dir/build.make src/app/xlink/CMakeFiles/xlink.dir/xlink_compute_qvalues.cpp.o
+.PHONY : xlink_compute_qvalues.cpp.o
+
+xlink_compute_qvalues.i: xlink_compute_qvalues.cpp.i
+.PHONY : xlink_compute_qvalues.i
+
+# target to preprocess a source file
+xlink_compute_qvalues.cpp.i:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/xlink/CMakeFiles/xlink.dir/build.make src/app/xlink/CMakeFiles/xlink.dir/xlink_compute_qvalues.cpp.i
+.PHONY : xlink_compute_qvalues.cpp.i
+
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+.PHONY : xlink_compute_qvalues.s
+
+# target to generate assembly for a file
+xlink_compute_qvalues.cpp.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/xlink/CMakeFiles/xlink.dir/build.make src/app/xlink/CMakeFiles/xlink.dir/xlink_compute_qvalues.cpp.s
+.PHONY : xlink_compute_qvalues.cpp.s
+
+xlink_search.o: xlink_search.cpp.o
+.PHONY : xlink_search.o
+
+# target to build an object file
+xlink_search.cpp.o:
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+
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+
+# target to preprocess a source file
+xlink_search.cpp.i:
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+.PHONY : xlink_search.cpp.i
+
+xlink_search.s: xlink_search.cpp.s
+.PHONY : xlink_search.s
+
+# target to generate assembly for a file
+xlink_search.cpp.s:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(MAKE) -f src/app/xlink/CMakeFiles/xlink.dir/build.make src/app/xlink/CMakeFiles/xlink.dir/xlink_search.cpp.s
+.PHONY : xlink_search.cpp.s
+
+# Help Target
+help:
+ @echo "The following are some of the valid targets for this Makefile:"
+ @echo "... all (the default if no target is provided)"
+ @echo "... clean"
+ @echo "... depend"
+ @echo "... edit_cache"
+ @echo "... install"
+ @echo "... install/local"
+ @echo "... install/strip"
+ @echo "... list_install_components"
+ @echo "... package"
+ @echo "... package_source"
+ @echo "... rebuild_cache"
+ @echo "... xlink"
+ @echo "... LinearPeptide.o"
+ @echo "... LinearPeptide.i"
+ @echo "... LinearPeptide.s"
+ @echo "... LinkedIonSeries.o"
+ @echo "... LinkedIonSeries.i"
+ @echo "... LinkedIonSeries.s"
+ @echo "... LinkedPeptide.o"
+ @echo "... LinkedPeptide.i"
+ @echo "... LinkedPeptide.s"
+ @echo "... SearchForXLinks.o"
+ @echo "... SearchForXLinks.i"
+ @echo "... SearchForXLinks.s"
+ @echo "... SelfLoopPeptide.o"
+ @echo "... SelfLoopPeptide.i"
+ @echo "... SelfLoopPeptide.s"
+ @echo "... Weibull.o"
+ @echo "... Weibull.i"
+ @echo "... Weibull.s"
+ @echo "... XHHC_Peptide.o"
+ @echo "... XHHC_Peptide.i"
+ @echo "... XHHC_Peptide.s"
+ @echo "... XLink.o"
+ @echo "... XLink.i"
+ @echo "... XLink.s"
+ @echo "... XLinkBondMap.o"
+ @echo "... XLinkBondMap.i"
+ @echo "... XLinkBondMap.s"
+ @echo "... XLinkDatabase.o"
+ @echo "... XLinkDatabase.i"
+ @echo "... XLinkDatabase.s"
+ @echo "... XLinkIonSeriesCache.o"
+ @echo "... XLinkIonSeriesCache.i"
+ @echo "... XLinkIonSeriesCache.s"
+ @echo "... XLinkMatch.o"
+ @echo "... XLinkMatch.i"
+ @echo "... XLinkMatch.s"
+ @echo "... XLinkMatchCollection.o"
+ @echo "... XLinkMatchCollection.i"
+ @echo "... XLinkMatchCollection.s"
+ @echo "... XLinkPeptide.o"
+ @echo "... XLinkPeptide.i"
+ @echo "... XLinkPeptide.s"
+ @echo "... XLinkScorer.o"
+ @echo "... XLinkScorer.i"
+ @echo "... XLinkScorer.s"
+ @echo "... XLinkSite.o"
+ @echo "... XLinkSite.i"
+ @echo "... XLinkSite.s"
+ @echo "... XLinkablePeptide.o"
+ @echo "... XLinkablePeptide.i"
+ @echo "... XLinkablePeptide.s"
+ @echo "... XLinkablePeptideIterator.o"
+ @echo "... XLinkablePeptideIterator.i"
+ @echo "... XLinkablePeptideIterator.s"
+ @echo "... XLinkablePeptideIteratorTopN.o"
+ @echo "... XLinkablePeptideIteratorTopN.i"
+ @echo "... XLinkablePeptideIteratorTopN.s"
+ @echo "... xhhc.o"
+ @echo "... xhhc.i"
+ @echo "... xhhc.s"
+ @echo "... xhhc_score_peptide_spectrum.o"
+ @echo "... xhhc_score_peptide_spectrum.i"
+ @echo "... xhhc_score_peptide_spectrum.s"
+ @echo "... xhhc_scorer.o"
+ @echo "... xhhc_scorer.i"
+ @echo "... xhhc_scorer.s"
+ @echo "... xhhc_search.o"
+ @echo "... xhhc_search.i"
+ @echo "... xhhc_search.s"
+ @echo "... xlink_assign_ions.o"
+ @echo "... xlink_assign_ions.i"
+ @echo "... xlink_assign_ions.s"
+ @echo "... xlink_compute_qvalues.o"
+ @echo "... xlink_compute_qvalues.i"
+ @echo "... xlink_compute_qvalues.s"
+ @echo "... xlink_search.o"
+ @echo "... xlink_search.i"
+ @echo "... xlink_search.s"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+ cd /data/TeamCity/buildAgent/work/779d99b0241b2175 && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+
diff --git a/src/app/xlink/README b/src/app/xlink/README
new file mode 100644
index 0000000..3c7095c
--- /dev/null
+++ b/src/app/xlink/README
@@ -0,0 +1,62 @@
+To compile, change the crux_source and crux_lib variables
+in Makefile to point to crux source file and the libcrux.a
+library (after crux has been compiled).
+
+Then run make to compile.
+
+Make a directory called crux-ouput for output files
+
+
+
+Four executables are created:
+
+ xhhc-predict-peptide-ions
+ xhhc-score-peptide-spectrum
+ xhhc-make-histogram
+ xhhc-search
+
+Usage is at the bottom of readme.
+
+There are 7 source files:
+
+ xhhc.cpp
+ xhhc_ion_series.cpp
+ xhhc_scorer.cpp
+
+ xhhc_predict_peptide_ions.cpp
+ xhhc_score_peptide_spectrum.cpp
+ xhhc_make_histogram.cpp
+ xhhc_search.cpp
+
+
+
+
+Things to do:
+
+- fix xhhc-make-histogram
+- fix print_spectrums method in xhhc_scorer
+- fix memory leak in xhhc-search
+- fix get_linkable_peptides method in xhhc.cpp to work for all linkers
+ - implement missed-link-cleavage and num-missed-cleavages options
+
+
+
+
+
+
+Usage: xhhc-score-peptide-spectrum [options] <peptide-sequence-alpha> <peptide-sequence-beta> <position A> <position B> <scan-number> <ms2-filename>
+Optional Arguments:
+ [--charge <int>] The peptide charge. 1|2|3
+ [--parameter-file <string>] The crux parameter file to parse parameter from.
+ [--linker-mass <string>] linker mass and linker modifications. Default 0.
+ [--print-spectrums <int>]
+ [--verbosity <int>] Specify the verbosity of the current processes from 0-100.
+Required Arguments:
+ <peptide-sequence-alpha> The first peptide sequence.
+ <peptide-sequence-beta> The second peptide sequence.
+ <position A> zero based index of linker on peptide A [0, length(A)-1]
+ <position B> zero based index of linker on peptide B [0, length(B)-1]
+ <scan-number> The scan number for the MS-MS spectrum to extract from the ms2 file.
+ This is an integer in the range [1, 100000], and uniquely identifies a particular MS-MS spectrum within an .ms2 file.
+ <ms2-filename> A file containing multiple MS-MS spectra in .ms2 format.
+
diff --git a/src/app/xlink/SearchForXLinks.cpp b/src/app/xlink/SearchForXLinks.cpp
new file mode 100644
index 0000000..6b7b97f
--- /dev/null
+++ b/src/app/xlink/SearchForXLinks.cpp
@@ -0,0 +1,285 @@
+/**
+ * \file SearchForXLinks.cpp
+ * \brief Object for running search-for-xlinks
+ *****************************************************************************/
+#include "SearchForXLinks.h"
+
+#include "xlink_search.h"
+#include "util/mass.h"
+#include "util/Params.h"
+
+using namespace std;
+
+/**
+ * \returns a blank SearchForXLinks object
+ */
+SearchForXLinks::SearchForXLinks() {
+
+}
+
+/**
+ * Destructor
+ */
+SearchForXLinks::~SearchForXLinks() {
+}
+
+/**
+ * main method for SearchForXLinks
+ */
+int SearchForXLinks::main(int argc, char** argv) {
+
+ //The use-old-xlink parameter will determine
+ //which codebase gets called.
+ int ret;
+ if (Params::GetBool("use-old-xlink")) {
+ ret = xhhcSearchMain();
+ } else {
+ ret = xlinkSearchMain();
+ }
+
+ return ret;
+}
+
+void SearchForXLinks::processParams() {
+ for (char c = 'A'; c <= 'Z'; c++) {
+ double deltaMass = Params::GetDouble(string(1, c));
+ increase_amino_acid_mass(c, deltaMass);
+ }
+}
+
+/**
+ * \returns the command name for SearchForXLinks
+ */
+string SearchForXLinks::getName() const {
+ return "search-for-xlinks";
+}
+
+/**
+ * \returns the description for SearchForXLinks
+ */
+string SearchForXLinks::getDescription() const {
+ return
+ "[[nohtml:Search a collection of spectra against a sequence database, "
+ "returning a collection of matches corresponding to linear and "
+ "cross-linked peptides scored by XCorr.]]"
+ "[[html:<p>This command compares a set of spectra to cross-linked "
+ "peptides derived from a protein database in FASTA format. "
+ "For each spectrum, the program generates a list of candidate "
+ "molecules, including linear peptides, dead-end products, self-loop "
+ "products and cross-linked products, with masses that lie within a "
+ "specified range of the spectrum's precursor mass. These candidate "
+ "molecules are ranked using XCorr, and the XCorr scores are assigned "
+ "statistical confidence estimates using an empirical curve fitting procedure."
+ "</p><p>The algorithm is described in more detail in the following article:"
+ "</p><blockquote>Sean McIlwain, Paul Draghicescu, Pragya Singh, David R. "
+ "Goodlett and William Stafford Noble. <a href=\""
+ "http://pubs.acs.org/doi/abs/10.1021/pr901163d\">"
+ ""Detecting cross-linked peptides by searching against a database of "
+ "cross-linked peptide pairs."</a> <em>Journal of Proteome Research"
+ "</em>. 2010.</blockquote>"
+ "<p>In search-for-xlinks, properties of the cross-linker are specified "
+ "using the two required command line arguments, <link sites> and <link "
+ "mass>. In addition, mass shifts associated with mono-links can be "
+ "specified using the --mod option. Below are suggested parameter settings "
+ "for some commonly used cross-linkers:</p>"
+ "<table border=\"1\">"
+ " <tr>"
+ " <td><b>Linker</b></td>"
+ " <td><b>Link Mass</b></td>"
+ " <td><b>Link Sites</b></td>"
+ " <td><b>Mono Link</b></td>"
+ " </tr>"
+ " <tr>"
+ " <td>EDC</td>"
+ " <td>-18.0156</td>"
+ " <td>K:D,E,cterm</td>"
+ " <td> </td>"
+ " </tr>"
+ " <tr>"
+ " <td>BS2</td></td>"
+ " <td>96.0211296</td>"
+ " <td>K,nterm:K,nterm</td>"
+ " <td>--mod 114.0316942,113.0476524:K,nterm:1:T:T</td>"
+ " </tr>"
+ " <tr>"
+ " <td>BS3</td>"
+ " <td>138.0680742</td>"
+ " <td>K,nterm:K,nterm</td>"
+ " <td>--mod 156.0786,155.0946278:K,nterm:1:T:T</td>"
+ " </tr>"
+ /* Need to find out the right parameters for SDA.
+ " <tr>"
+ " <td>SDA</td>"
+ " <td>82.0412979</td>"
+ " <td>K,nterm:X,nterm</td>"
+ " <td>--mod ????</td>"
+ " </tr>"
+ */
+ " <tr>"
+ " <td>DSS</td>"
+ " <td>138.0680796</td>"
+ " <td>K,nterm:K,nterm</td>"
+ " <td>--mod 156.0786,155.0946278:K,nterm:1:T:T</td>"
+ " </tr>"
+ " <tr>"
+ " <td>AMAS</td>"
+ " <td>137.011</td>"
+ " <td>K,nterm:C</td>"
+ " <td>--mod 155.02156:K,nterm,C:1:T:T</td>"
+ " </tr>"
+ " <tr>"
+ " <td>GMBS</td>"
+ " <td>165.0422</td>"
+ " <td>K,nterm:C</td>"
+ " <td>--mod 183.05276:K,nterm,C:1:T:T</td>"
+ " </tr>"
+ " <tr>"
+ " <td>formaldehyde</td>"
+ " <td>9.98435</td>"
+ " <td>K,W,nterm:H,N,Y,K,W,R,nterm</td>"
+ " <td>--mod 12.0,30.010565:K,W,nterm:1:T:T</td>"
+ " </tr>"
+ "</table>"
+ "]]";
+}
+
+/**
+ * \returns the command arguments
+ */
+vector<string> SearchForXLinks::getArgs() const {
+ string arr[] = {
+ "ms2 file",
+ "protein fasta file",
+ "link sites",
+ "link mass"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command options
+ */
+vector<string> SearchForXLinks::getOptions() const {
+ string arr[] = {
+ "use-old-xlink",
+ "xlink-include-linears",
+ "xlink-include-deadends",
+ "xlink-include-selfloops",
+ "xlink-include-inter",
+ "xlink-include-intra",
+ "xlink-include-inter-intra",
+ "xlink-prevents-cleavage",
+ "require-xlink-candidate",
+ "xlink-top-n",
+ "max-xlink-mods",
+ "min-mass",
+ "max-mass",
+ "min-length",
+ "max-length",
+ "mod",
+ "cmod",
+ "nmod",
+ "max-mods",
+ "enzyme",
+ "custom-enzyme",
+ "digestion",
+ "missed-cleavages",
+ "spectrum-min-mz",
+ "spectrum-max-mz",
+ "spectrum-charge",
+ "compute-sp",
+ "precursor-window",
+ "precursor-window-type",
+ "precursor-window-weibull",
+ "precursor-window-type-weibull",
+ "min-weibull-points",
+ "use-a-ions",
+ "use-b-ions",
+ "use-c-ions",
+ "use-x-ions",
+ "use-y-ions",
+ "use-z-ions",
+ "max-ion-charge",
+ "scan-number",
+ "mz-bin-width",
+ "mz-bin-offset",
+ "mod-mass-format",
+ "use-flanking-peaks",
+ "fragment-mass",
+ "isotopic-mass",
+ "isotope-windows",
+ "compute-p-values",
+ "seed",
+ "xlink-print-db",
+ "spectrum-parser",
+ "use-z-line",
+ "top-match",
+ "output-dir",
+ "overwrite",
+ "parameter-file",
+ "verbosity",
+ "A",
+ "C",
+ "D",
+ "E",
+ "F",
+ "G",
+ "H",
+ "I",
+ "K",
+ "L",
+ "M",
+ "N",
+ "P",
+ "Q",
+ "R",
+ "S",
+ "T",
+ "V",
+ "W",
+ "Y",
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+/**
+ * \returns the command outputs
+ */
+vector< pair<string, string> > SearchForXLinks::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("search-for-xlinks.target.txt",
+ "a tab-delimited text file containing the peptide-spectrum matches (PSMs). "
+ "See the <a href=\"../file-formats/txt-format.html\">txt file format</a> for a list of the fields."));
+ outputs.push_back(make_pair("search-for-xlinks.decoy.txt",
+ "a tab-delimited text file containing the decoy PSMs. "
+ "See the <a href=\"../file-formats/txt-format.html\">txt file format</a> for a list of the fields."));
+ outputs.push_back(make_pair("search-for-xlinks.qvalues.txt",
+ "a tab-delimited text file containing the top ranked PSMs with calculated q-values. "
+ "See the <a href=\"../file-formats/txt-format.html\">txt file format</a> for a list of the fields."));
+ outputs.push_back(make_pair("search-for-xlinks.params.txt",
+ "a file containing the name and value of all parameters/options for the "
+ "current operation. Not all parameters in the file may have been used in "
+ "the operation. The resulting file can be used with the --parameter-file "
+ "option for other crux programs."));
+ outputs.push_back(make_pair("search-for-xlinks.log.txt",
+ "a log file containing a copy of all messages that were printed to stderr."));
+ return outputs;
+}
+
+/**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+COMMAND_T SearchForXLinks::getCommand() const {
+ return XLINK_SEARCH_COMMAND;
+}
+
+bool SearchForXLinks::needsOutputDirectory() const {
+ return true;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/SearchForXLinks.h b/src/app/xlink/SearchForXLinks.h
new file mode 100644
index 0000000..8e7a206
--- /dev/null
+++ b/src/app/xlink/SearchForXLinks.h
@@ -0,0 +1,93 @@
+/**
+ * \file SearchForXLinks.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 6 December 2010
+ * \brief Object for running search-for-xlinks
+ *****************************************************************************/
+
+#ifndef SEARCHFORXLINKS_H
+#define SEARCHFORXLINKS_H
+
+#include "app/CruxApplication.h"
+#include "io/DelimitedFileReader.h"
+
+#include <string>
+
+class SearchForXLinks: public CruxApplication {
+
+ protected:
+ /**
+ * The main method for the new xlink search code
+ * \returns return code after execution
+ */
+ int xlinkSearchMain();
+
+ /**
+ * The main method for the old xlink search code
+ * \returns return code after execution
+ */
+ int xhhcSearchMain();
+
+ public:
+
+ /**
+ * \returns a blank SearchForXLinks object
+ */
+ SearchForXLinks();
+
+ /**
+ * Destructor
+ */
+ virtual ~SearchForXLinks();
+
+ /**
+ * main method for SearchForXLinks
+ */
+ virtual int main(int argc, char** argv);
+
+ virtual void processParams();
+
+ /**
+ * \returns the command name for SearchForXLinks
+ */
+ virtual std::string getName() const;
+
+ /**
+ * \returns the description for SearchForXLinks
+ */
+ virtual std::string getDescription() const;
+
+ /**
+ * \returns the command arguments
+ */
+ virtual std::vector<std::string> getArgs() const;
+
+ /**
+ * \returns the command options
+ */
+ virtual std::vector<std::string> getOptions() const;
+
+ /**
+ * \returns the command outputs
+ */
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ /**
+ * \returns the enum of the application, default MISC_COMMAND
+ */
+ virtual COMMAND_T getCommand() const;
+
+ virtual bool needsOutputDirectory() const;
+
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/SelfLoopPeptide.cpp b/src/app/xlink/SelfLoopPeptide.cpp
new file mode 100644
index 0000000..b0e8e60
--- /dev/null
+++ b/src/app/xlink/SelfLoopPeptide.cpp
@@ -0,0 +1,351 @@
+/**
+ * \file SelfLoopPeptide.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Object for Defining a self-loop peptide in an xlink search
+ *****************************************************************************/
+#include "SelfLoopPeptide.h"
+#include "XLinkablePeptide.h"
+#include "XLinkablePeptideIterator.h"
+#include "XLinkPeptide.h"
+#include "XLink.h"
+#include "XLinkDatabase.h"
+#include "util/GlobalParams.h"
+
+#include "model/IonSeries.h"
+#include "model/Ion.h"
+
+#include <iostream>
+#include <sstream>
+
+using namespace std;
+
+/**
+ * Default Constructor
+ */
+SelfLoopPeptide::SelfLoopPeptide() {
+ is_decoy_ = false;
+}
+
+
+/**
+ * Constructor that defines a linkable peptide and the positions
+ */
+SelfLoopPeptide::SelfLoopPeptide(
+ XLinkablePeptide& peptide, ///< linkable peptide
+ int posA, ///< 1st link position on peptide
+ int posB ///< 2nd link position on peptide
+ ) {
+
+ is_decoy_ = false;
+ linked_peptide_ = XLinkablePeptide(peptide);
+ linked_peptide_.clearSites();
+ linked_peptide_.addLinkSite(posA);
+ linked_peptide_.addLinkSite(posB);
+
+ link_pos_idx_.push_back(0);
+ link_pos_idx_.push_back(1);
+
+}
+
+/**
+ * Constructor that defines a linkable peptide and the positions
+ */
+SelfLoopPeptide::SelfLoopPeptide(
+ char* peptide, ///< linkable peptide
+ int posA, ///< 1st link position on peptide
+ int posB ///< 2nd link position on peptide
+ ) {
+
+ linked_peptide_ = peptide;
+ link_pos_idx_.push_back(posA);
+ link_pos_idx_.push_back(posB);
+
+}
+
+/**
+ * Adds Self-loop candidates to the collection
+ */
+void SelfLoopPeptide::addCandidates(
+ FLOAT_T min_mass, ///< min mass
+ FLOAT_T max_mass, ///< max mass
+ bool is_decoy, ///< is decoy.
+ XLinkMatchCollection& candidates ///< collection to add candidates
+ ) {
+
+
+ vector<SelfLoopPeptide>::iterator biter = XLinkDatabase::getSelfLoopBegin(is_decoy, min_mass);
+ if (biter == XLinkDatabase::getSelfLoopEnd(is_decoy) ||
+ biter -> getMassConst(GlobalParams::getIsotopicMass()) > max_mass) {
+ return;
+ } else {
+ vector<SelfLoopPeptide>::iterator eiter = XLinkDatabase::getSelfLoopEnd(is_decoy);
+
+ while (biter != eiter && biter->getMass(GlobalParams::getIsotopicMass()) <= max_mass) {
+ biter->incrementPointerCount();
+ candidates.add(&(*biter));
+ ++biter;
+ }
+ }
+}
+
+/**
+ * \returns the link position
+ */
+int SelfLoopPeptide::getLinkPos(
+ int link_idx ///< link index (0 or 1)
+ ) {
+ return linked_peptide_.getLinkSite(link_pos_idx_[link_idx]);
+}
+
+/**
+ * \returns self-loop candidate
+ */
+XLINKMATCH_TYPE_T SelfLoopPeptide::getCandidateType() {
+ return SELFLOOP_CANDIDATE;
+}
+
+/**
+ * \returns the sequence string, marking the link sites with (X,Y).
+ */
+string SelfLoopPeptide::getSequenceString() {
+
+ string seq = linked_peptide_.getModifiedSequenceString();
+ ostringstream oss;
+ oss << seq << " (" << (getLinkPos(0)+1) << "," << (getLinkPos(1)+1) << ")";
+ string svalue = oss.str();
+
+ return svalue;
+}
+
+/**
+ * \returns the mass of the self-loop peptide
+ */
+FLOAT_T SelfLoopPeptide::calcMass(
+ MASS_TYPE_T mass_type ///< AVERAGE or MONO
+ ) {
+
+ return linked_peptide_.getMass(mass_type) + XLinkPeptide::getLinkerMass();
+}
+
+/**
+ * \returns a shuffled version of self-loop candidate
+ */
+void SelfLoopPeptide::shuffle(vector<XLinkMatch*>& decoys) {
+ carp(CARP_DEBUG, "SelfLoopPeptide::shuffle");
+ SelfLoopPeptide* decoy = new SelfLoopPeptide();
+
+ decoy->linked_peptide_ = linked_peptide_.shuffle();
+ decoy->link_pos_idx_.push_back(link_pos_idx_[0]);
+ decoy->link_pos_idx_.push_back(link_pos_idx_[1]);
+ decoy->is_decoy_ = true;
+ decoy->target_ = this;
+ decoys.push_back(decoy);
+}
+
+SelfLoopPeptide* SelfLoopPeptide::getUnshuffledTarget() {
+ return(target_);
+}
+
+std::string SelfLoopPeptide::getUnshuffledSequence() {
+
+ if (is_decoy_) {
+ //carp(CARP_INFO, "returning unshuffled target");
+ return(getUnshuffledTarget()->getSequenceString());
+ } else {
+ return(getSequenceString());
+ }
+}
+
+/**
+ * Predicts the ions for the self loop candidate
+ */
+void SelfLoopPeptide::predictIons(
+ IonSeries* ion_series, ///< ion vector to place ions in
+ int charge ///< charge state
+ ) {
+
+ const char* seq = linked_peptide_.getSequence();
+ const MODIFIED_AA_T* mod_seq = linked_peptide_.getModifiedSequencePtr();
+ ion_series->setCharge(charge);
+ ion_series->update(seq, mod_seq);
+ ion_series->predictIons();
+
+ unsigned int first_site = min(getLinkPos(0), getLinkPos(1));
+ unsigned int second_site = max(getLinkPos(0), getLinkPos(1));
+ unsigned int N = strlen(seq);
+
+
+ //iterate through the ions and modify the ones that have the linker
+ //attached.
+ vector<Ion*> to_remove;
+
+ for (IonIterator ion_iter = ion_series->begin();
+ ion_iter != ion_series->end();
+ ++ion_iter) {
+
+ Ion* ion = *ion_iter;
+
+ bool keep_ion = false;
+ bool modify_ion = false;
+ unsigned int cleavage_idx = ion->getCleavageIdx();
+
+ if (ion->isForwardType()) {
+ if (cleavage_idx > first_site) {
+ if (cleavage_idx <= second_site) {
+ keep_ion = false;
+ } else {
+ keep_ion = true;
+ modify_ion = true;
+ }
+ } else {
+ keep_ion = true;
+ modify_ion = false;
+ }
+ } else {
+ if (cleavage_idx >= (N-second_site)) {
+ if (cleavage_idx < (N-first_site)) {
+ keep_ion = false;
+ } else {
+ keep_ion = true;
+ modify_ion = true;
+ }
+ } else {
+ keep_ion = true;
+ modify_ion = false;
+ }
+ }
+
+ if (keep_ion) {
+ if (modify_ion) {
+ FLOAT_T mass_z = ion->getMassZ();
+ int charge = ion->getCharge();
+ double mass = (mass_z -MASS_PROTON) * (double)charge;
+ mass += XLinkPeptide::getLinkerMass();
+ mass_z = (mass + MASS_PROTON * (double)charge) / (double)charge;
+ ion->setMassZ(mass_z);
+ if (isnan(ion->getMassZ())) {
+ carp(CARP_FATAL, "NAN5");
+ }
+
+ }
+ } else {
+ to_remove.push_back(ion);
+ }
+ }
+
+ for (unsigned int idx=0;idx < to_remove.size();idx++) {
+ ion_series->removeIon(to_remove[idx]);
+ delete to_remove[idx];
+ }
+
+}
+
+/**
+ * \returns the sequence of ion
+ */
+string SelfLoopPeptide::getIonSequence(
+ Ion* ion ///< ion
+ ) {
+
+ string ion_sequence = ion->getPeptideSequence();
+
+ unsigned int cleavage_idx = ion->getCleavageIdx();
+
+ unsigned int first_site = min(getLinkPos(0), getLinkPos(1));
+ unsigned int second_site = max(getLinkPos(0), getLinkPos(1));
+
+ bool is_linked = false;
+ if (ion->isForwardType()) {
+ is_linked = (cleavage_idx > first_site);
+ } else {
+ is_linked = (cleavage_idx >= (ion_sequence.length() - second_site));
+ }
+
+ string subseq;
+
+ //cerr<<"creating substring"<<endl;
+ if (ion->isForwardType()) {
+ subseq = ion_sequence.substr(0, cleavage_idx);
+ } else {
+ subseq = ion_sequence.substr(ion_sequence.length() - cleavage_idx, ion_sequence.length());
+ }
+
+ if (is_linked) {
+ return subseq + string("*");
+ } else {
+ return subseq;
+ }
+}
+
+/**
+ *\returns the peptide object of self-loop peptide (0 is only valid)
+ */
+Crux::Peptide* SelfLoopPeptide::getPeptide(
+ int peptide_idx
+ ) {
+ if (peptide_idx == 0) {
+ return linked_peptide_.getPeptide();
+ } else {
+ return NULL;
+ }
+}
+
+/**
+ *\returns the number of missed cleavages
+ */
+int SelfLoopPeptide::getNumMissedCleavages() {
+ char missed_cleavage_link_site = 'K';
+
+ int link1_site = getLinkPos(0);
+ int link2_site = getLinkPos(1);
+
+ set<int> skip;
+
+ Crux::Peptide* pep = linked_peptide_.getPeptide();
+
+ char* seq = pep->getSequencePointer();
+
+ if (seq[link1_site] == missed_cleavage_link_site) {
+ skip.insert(link1_site);
+ }
+
+ if (seq[link2_site] == missed_cleavage_link_site) {
+ skip.insert(link2_site);
+ }
+
+ return pep->getMissedCleavageSites(skip);
+
+}
+
+/**
+ *\returns whether the peptide is modified by a variable mod
+ */
+bool SelfLoopPeptide::isModified() {
+
+ return linked_peptide_.isModified();
+}
+
+
+bool compareSelfLoopPeptideMass(
+ const SelfLoopPeptide& spep1,
+ const SelfLoopPeptide& spep2) {
+
+ return spep1.getMassConst(MONO) < spep2.getMassConst(MONO);
+
+}
+
+bool compareSelfLoopPeptideMassToFLOAT(
+ const SelfLoopPeptide& spep1,
+ FLOAT_T mass) {
+
+ return spep1.getMassConst(MONO) < mass;
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/SelfLoopPeptide.h b/src/app/xlink/SelfLoopPeptide.h
new file mode 100644
index 0000000..f4d8918
--- /dev/null
+++ b/src/app/xlink/SelfLoopPeptide.h
@@ -0,0 +1,148 @@
+/**
+ * \file SelfLoopPeptide.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Object for Defining a self-loop peptide in an xlink search
+ *****************************************************************************/
+#ifndef SELFLOOPPEPTIDE_H_
+#define SELFLOOPPEPTIDE_H_
+
+#include "model/objects.h"
+#include "util/utils.h"
+
+#include "XLinkMatch.h"
+#include "XLinkBondMap.h"
+#include "XLinkablePeptide.h"
+
+#include <vector>
+
+class SelfLoopPeptide : public XLinkMatch {
+ protected:
+ SelfLoopPeptide* target_;
+ XLinkablePeptide linked_peptide_; ///< linkable peptide
+ std::vector<int> link_pos_idx_; ///< the two link indices on the peptide
+ public:
+
+ /**
+ * \returns the link position
+ */
+ int getLinkPos(
+ int link_idx ///< link index (0 or 1)
+ );
+
+ /**
+ * Default Constructor
+ */
+ SelfLoopPeptide();
+
+ /**
+ * Constructor that defines a linkable peptide and the positions
+ */
+ SelfLoopPeptide(
+ XLinkablePeptide& peptide, ///< linkable peptide
+ int posA, ///< 1st link position on peptide
+ int posB ///< 2nd link position on peptide
+ );
+
+ /**
+ * Constructor that defines a string peptide with positions
+ */
+ SelfLoopPeptide(
+ char* peptide, ///< character sequence of peptide
+ int posA, ///< 1st link position on peptide
+ int posB ///< 2nd link position on peptide
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual ~SelfLoopPeptide() {}
+
+ /**
+ * Adds Self-loop candidates to the collection
+ */
+ static void addCandidates(
+ FLOAT_T min_mass, ///< min mass
+ FLOAT_T max_mass, ///< max mass
+ bool is_decoy,
+ XLinkMatchCollection& candidates ///< collection to add candidates
+ );
+
+ /**
+ * \returns self-loop candidate
+ */
+ virtual XLINKMATCH_TYPE_T getCandidateType();
+
+ /**
+ * \returns the sequence string, marking the link sites with (X,Y)
+ */
+ virtual std::string getSequenceString();
+
+ /**
+ * \returns the mass of the self-loop peptide
+ */
+ virtual FLOAT_T calcMass(
+ MASS_TYPE_T mass_type ///< AVERAGE or MONO
+ );
+
+ /**
+ * \returns a shuffled version of self-loop candidate
+ */
+ virtual void shuffle(
+ std::vector<XLinkMatch*>& decoys
+ );
+
+ /**
+ * Predictes the ions for the self loop candidate
+ */
+ virtual void predictIons(
+ IonSeries* ion_series, ///< ion vector to place ions in
+ int charge ///< charge state
+ );
+
+ /**
+ * \returns the sequence of the ion
+ */
+ std::string getIonSequence(
+ Ion* ion ///< ion -in
+ );
+
+ /**
+ *\returns the peptide object of self-loop peptide (0 is only valid)
+ */
+ virtual Crux::Peptide* getPeptide(
+ int peptide_idx
+ );
+
+ /**
+ *\returns the number of missed cleavages
+ */
+ virtual int getNumMissedCleavages();
+
+ /**
+ *\returns whether the peptide is modified by a variable mod
+ */
+ virtual bool isModified();
+
+
+ virtual std::string getUnshuffledSequence();
+
+ SelfLoopPeptide* getUnshuffledTarget();
+
+
+};
+
+bool compareSelfLoopPeptideMass(
+ const SelfLoopPeptide& spep1,
+ const SelfLoopPeptide& spep2);
+bool compareSelfLoopPeptideMassToFLOAT(const SelfLoopPeptide& spep1, FLOAT_T mass);
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/Weibull.cpp b/src/app/xlink/Weibull.cpp
new file mode 100644
index 0000000..06cbdd8
--- /dev/null
+++ b/src/app/xlink/Weibull.cpp
@@ -0,0 +1,211 @@
+#include "Weibull.h"
+#include "util/crux-utils.h"
+#include "util/GlobalParams.h"
+#include "model/Scorer.h"
+static const FLOAT_T MIN_XCORR_SHIFT = -3.0;
+static const FLOAT_T MAX_XCORR_SHIFT = 3.0;
+static const FLOAT_T CORR_THRESHOLD = 0.5; //Must achieve this correlation, else punt.
+static const FLOAT_T XCORR_SHIFT = 0.05;
+static const FLOAT_T XCORR_RANGE = MAX_XCORR_SHIFT - MIN_XCORR_SHIFT;
+
+using namespace std;
+
+Weibull::Weibull() {
+ reset();
+}
+
+Weibull::~Weibull() {
+ //
+}
+
+void Weibull::reset() {
+ correlation_ = 0;
+ sequences_.clear();
+ scores_.clear();
+ fit_called_ = false;
+ fit_success_ = false;
+ duplicates_ = 0;
+}
+
+FLOAT_T Weibull::getEta() {
+ return eta_;
+}
+
+FLOAT_T Weibull::getBeta() {
+ return beta_;
+}
+
+FLOAT_T Weibull::getShift() {
+ return shift_;
+}
+
+FLOAT_T Weibull::getCorrelation() {
+ return correlation_;
+}
+
+
+void Weibull::addPoint(
+ const std::string& sequence,
+ FLOAT_T score
+) {
+
+ set<string>::iterator it = sequences_.find(sequence);
+
+ if (it == sequences_.end()) {
+ scores_.push_back(score);
+ sequences_.insert(sequence);
+ fit_called_ = false;
+ } else {
+ duplicates_++;
+ }
+
+}
+
+bool Weibull::fit() {
+
+ int nscores = scores_.size();
+
+ carp(CARP_DEBUG, "Fitting %i scores", nscores);
+ carp(CARP_DEBUG, "There were %i dups detected during insert", duplicates_);
+
+
+ sort(scores_.begin(), scores_.end(), greater<FLOAT_T>());
+ int num_tail_samples = (int)(nscores * GlobalParams::getFractionToFit());
+ carp(CARP_DEBUG, "num tail:%d", num_tail_samples);
+
+ FLOAT_T max_score = scores_[0];
+ FLOAT_T min_score = scores_[nscores-1];
+
+ FLOAT_T xcorr_shift = XCORR_SHIFT * (max_score - min_score) / XCORR_RANGE;
+
+ FLOAT_T max_shift = max_score;
+ FLOAT_T min_shift = min_score - xcorr_shift;
+
+ if (nscores > 29 && xcorr_shift > 0) {
+ carp(CARP_DEBUG, "Fitting weibull n:%d nt:%d "
+ "min:%g max:%g mins:%g maxs:%g shift:%g", nscores,
+ num_tail_samples,
+ min_score,
+ max_score,
+ min_shift,
+ max_shift,
+ xcorr_shift);
+ FLOAT_T* scores_ptr = scores_.data();
+ max_shift = scores_ptr[29];
+ fit_three_parameter_weibull(
+ scores_ptr,
+ num_tail_samples,
+ nscores,
+ min_shift,
+ max_shift,
+ xcorr_shift,
+ 0,
+ &eta_,
+ &beta_,
+ &shift_,
+ &correlation_
+ );
+ if (correlation_ < CORR_THRESHOLD) {
+ carp(CARP_WARNING, "Weibull fit failed corr:%g n:%d nt:%d "
+ "min:%g max:%g mins:%g maxs:%g",
+ correlation_,
+ nscores,
+ num_tail_samples,
+ scores_[nscores-1],
+ scores_[0],
+ min_shift,
+ max_shift
+ );
+ fit_success_ = false;
+ } else {
+ carp(CARP_DEBUG, "Fit succeeded: corr:%g shift:%g eta:%g beta:%g",
+ correlation_,
+ shift_,
+ eta_,
+ beta_);
+ fit_success_ = true;
+ }
+ } else {
+ carp(CARP_WARNING, "Too few scores to fit weibull: n:%d nt:%d "
+ "min:%g max:%g mins:%g maxs:%g shift:%g",
+ nscores,
+ num_tail_samples,
+ min_score,
+ max_score,
+ min_shift,
+ max_shift,
+ xcorr_shift);
+ fit_success_ = false;
+ }
+ //Fit was called.
+ fit_called_ = true;
+ return fit_success_;
+}
+
+FLOAT_T Weibull::getWeibullPValue(FLOAT_T score, bool logp) {
+ if (!fit_called_) {
+ fit();
+ }
+
+ FLOAT_T pvalue = compute_weibull_pvalue(score, eta_, beta_, shift_);
+ if (logp) {
+ pvalue = log10(pvalue);
+ }
+ return(pvalue);
+
+}
+
+FLOAT_T Weibull::getECDFPValue(FLOAT_T score, bool logp) {
+ if (!fit_called_) {
+ fit();
+ }
+
+ FLOAT_T pvalue;
+
+ //end point check, this is probably unstable but a conservative estimate.
+ if (score > scores_[0]) {
+ pvalue = 1.0 / (1.0 + (FLOAT_T)scores_.size());
+ } else {
+ //TODO, use upper/lower bound?
+ int idx = 0;
+ while(idx < scores_.size() && score <= scores_[idx]) {
+ idx++;
+ }
+ pvalue = (FLOAT_T)idx / (FLOAT_T)scores_.size();
+ }
+
+ if (logp) {
+ pvalue = log10(pvalue);
+ }
+ return(pvalue);
+
+
+}
+
+FLOAT_T Weibull::getPValue(FLOAT_T score, bool logp) {
+ if (!fit_called_) {
+ fit();
+ }
+ FLOAT_T pvalue;
+ if (fit_success_) {
+ pvalue = getWeibullPValue(score, logp);
+ }
+ //If the fit failed or the estimated p-value is invalid, then
+ //return the ECDF
+ if (!fit_success_ || pvalue == 0 || pvalue != pvalue) {
+ //x != x should test for NaN.
+ if (!fit_success_) {
+ pvalue = NAN;
+ } else if (pvalue != pvalue) {
+ pvalue = NAN;
+ } else if (pvalue == 0) {
+ pvalue = FLOAT_T_MIN;
+ }
+ }
+
+ return(pvalue);
+}
+
+
+
+
diff --git a/src/app/xlink/Weibull.h b/src/app/xlink/Weibull.h
new file mode 100644
index 0000000..c28efcd
--- /dev/null
+++ b/src/app/xlink/Weibull.h
@@ -0,0 +1,42 @@
+
+#include <set>
+#include <vector>
+#include <string>
+#include "model/objects.h"
+
+class Weibull {
+
+ protected:
+ FLOAT_T correlation_;
+ FLOAT_T eta_;
+ FLOAT_T beta_;
+ FLOAT_T shift_;
+
+ std::set<std::string> sequences_;
+ std::vector<FLOAT_T> scores_;
+
+ bool fit_called_;
+ bool fit_success_;
+
+ int duplicates_;
+
+ public:
+ Weibull();
+ ~Weibull();
+
+ FLOAT_T getEta();
+ FLOAT_T getBeta();
+ FLOAT_T getShift();
+ FLOAT_T getCorrelation();
+
+ void reset();
+ void addPoint(const std::string& sequence, FLOAT_T score);
+ bool fit();
+
+ FLOAT_T getWeibullPValue(FLOAT_T score, bool logp=false);
+ FLOAT_T getECDFPValue(FLOAT_T score, bool logp=false);
+ FLOAT_T getPValue(FLOAT_T score, bool logp=false);
+
+
+
+};
diff --git a/src/app/xlink/XHHC_Peptide.cpp b/src/app/xlink/XHHC_Peptide.cpp
new file mode 100644
index 0000000..099ec72
--- /dev/null
+++ b/src/app/xlink/XHHC_Peptide.cpp
@@ -0,0 +1,238 @@
+/**
+ * \file XHHC_Peptide.cpp
+ * AUTHOR: Sean McIlwain and Paul Draghicescu
+ * CREATE DATE: 19 January 2012
+ * \brief Object for keeping track of the links on a
+ * cross-linkable peptide.
+ *****************************************************************************/
+#include "XHHC_Peptide.h"
+#include "LinkedPeptide.h"
+#include "util/crux-utils.h"
+
+
+using namespace std;
+using namespace Crux;
+/**
+ * \returns a blank XHHC_Peptide object
+ */
+XHHC_Peptide::XHHC_Peptide() {
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+}
+
+/**
+ * \returns XHHC_Peptide object with the sequence initialized
+ */
+XHHC_Peptide::XHHC_Peptide(
+ string sequence
+ ) {
+
+ num_links_ = 0;
+ sequence_ = sequence;
+ length_ = sequence.length();
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+ for (int idx = 0;idx < length_;idx++) {
+ links_.push_back(false);
+ }
+}
+
+/**
+ * Destructor
+ */
+XHHC_Peptide::~XHHC_Peptide() {
+}
+
+/**
+ * \returns whether a link exists at the index
+ */
+bool XHHC_Peptide::hasLinkAt(
+ int index ///< amino acid index
+ ) {
+
+ return links_[index];
+}
+
+/**
+ * \returns the sequence length of the peptide
+ */
+int XHHC_Peptide::getLength() {
+ return length_;
+}
+
+/**
+ * returns whether a link exists
+ */
+bool XHHC_Peptide::hasLink() {
+ return num_links_ > 0;
+}
+
+/**
+ * \returns the peptide sequence
+ */
+string XHHC_Peptide::getSequence() {
+ return sequence_;
+}
+
+/**
+ * \returns whether we have initialized the peptide
+ */
+bool XHHC_Peptide::isEmpty() {
+ return length_ == 0;
+}
+
+/**
+ * \returns the number of links
+ */
+int XHHC_Peptide::getNumLinks() {
+ return num_links_;
+}
+
+/**
+ * sets the peptide sequence
+ */
+void XHHC_Peptide::setSequence(
+ string sequence ///< the sequence of the peptide
+ ) {
+ sequence_ = sequence;
+ length_ = sequence.length();
+}
+
+/**
+ * removes a link from the peptide
+ */
+void XHHC_Peptide::removeLink(
+ int index ///< the amino acid index
+ ) {
+
+ links_[index] = false;
+ num_links_--;
+}
+
+/**
+ * \returns the first index of a link, -1 if none exist
+ */
+int XHHC_Peptide::linkSite() {
+
+ for (int idx = 0; idx < length_; ++idx) {
+ if (hasLinkAt(idx))
+ return idx;
+ }
+ return -1;
+}
+
+/**
+ * \returns the mass of the peptide
+ */
+FLOAT_T XHHC_Peptide::getMass(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ ) {
+
+ if (mass_calculated_[mass_type]) {
+ return mass_[mass_type];
+ } else {
+ mass_[mass_type] = Peptide::calcSequenceMass((char*)sequence_.c_str(), mass_type);
+ mass_calculated_[mass_type] = true;
+ return mass_[mass_type];
+ }
+}
+
+/**
+ * add a link at a amino acid index
+ */
+void XHHC_Peptide::addLink(
+ int index ///< the amino acid index
+ ) {
+ links_[index] = true;
+ num_links_++;
+}
+
+/**
+ * cleaves the peptide at an index, adding b and y ions
+ * skips if a cleave site on self loop between the link
+ */
+void XHHC_Peptide::splitAt(
+ int index, ///< the index to cleave
+ vector<pair<LinkedPeptide, LinkedPeptide> >& pairs, ///< the b-y ion pairs
+ int charge, ///< charge of the peptide
+ XHHC_Peptide& other, ///< the other peptide we are linked to
+ bool is_loop ///< Is this a self loop?
+ ) {
+
+ bool self_flag = false;
+ // for every charge state
+ for (int c = 0; c <= charge; ++c) {
+ XHHC_Peptide pepA = XHHC_Peptide(sequence_.substr(0, index));
+ XHHC_Peptide pepB = XHHC_Peptide(sequence_.substr(index, length_ - index));
+ LinkedPeptide linkedA = LinkedPeptide(c);
+ LinkedPeptide linkedB = LinkedPeptide(charge - c);
+ self_flag = true;
+ // for every position on pepA
+ for (int idx = 0; idx < index; idx++) {
+ if (hasLinkAt(idx)) {
+ pepA.addLink(idx);
+ if (!other.isEmpty() && !is_loop) linkedA.addPeptide(other);
+ // if a loop, skip cleavages in between link sites (same mass as precursor)
+ if (is_loop) {
+ self_flag = !self_flag;
+ }
+ }
+ }
+ if (!self_flag) continue;
+ // for every position on pepB
+ for (int idx = index; idx < length_; idx++) {
+ if (hasLinkAt(idx)) {
+ pepB.addLink(idx - index);
+ if (!other.isEmpty() && !is_loop) {
+ linkedB.addPeptide(other);
+ }
+ }
+ }
+ linkedA.addPeptide(pepA);
+ linkedB.addPeptide(pepB);
+ pairs.push_back(pair<LinkedPeptide, LinkedPeptide> (linkedA, linkedB));
+ }
+}
+
+/**
+ * \returns a shuffled peptide, preserving any links
+ */
+XHHC_Peptide XHHC_Peptide::shuffle() {
+ string shuffled = string(sequence_);
+ XHHC_Peptide shuffled_peptide = XHHC_Peptide(sequence_);
+ for (size_t idx = 0; idx < shuffled.length(); ++idx) {
+ if (hasLinkAt(idx)) shuffled_peptide.addLink(idx);
+ }
+
+ int start_idx = 1;
+ int end_idx = length_ - 2;
+ int switch_idx = 0;
+ char temp_char = 0;
+ while(start_idx <= end_idx) {
+ switch_idx = get_random_number_interval(start_idx, end_idx);
+ temp_char = shuffled[start_idx];
+ shuffled[start_idx] = shuffled[switch_idx];
+ shuffled[switch_idx] = temp_char;
+ if (shuffled_peptide.hasLinkAt(switch_idx)) {
+ //if not a self loop
+ if (!shuffled_peptide.hasLinkAt(start_idx)) {
+ shuffled_peptide.removeLink(switch_idx);
+ shuffled_peptide.addLink(start_idx);
+ }
+ } else if (shuffled_peptide.hasLinkAt(start_idx)) {
+ shuffled_peptide.removeLink(start_idx);
+ shuffled_peptide.addLink(switch_idx);
+ }
+ ++start_idx;
+ }
+ shuffled_peptide.setSequence(shuffled);
+ return shuffled_peptide;
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XHHC_Peptide.h b/src/app/xlink/XHHC_Peptide.h
new file mode 100644
index 0000000..512aead
--- /dev/null
+++ b/src/app/xlink/XHHC_Peptide.h
@@ -0,0 +1,135 @@
+/**
+ * \file XHHC_Peptide.h
+ * AUTHOR: Sean McIlwain and Paul Draghicescu
+ * CREATE DATE: 19 January 2012
+ * \brief Object for keeping track of the links on a
+ * cross-linkable peptide.
+ *****************************************************************************/
+#ifndef XHHC_PEPTIDE_H
+#define XHHC_PEPTIDE_H
+
+#include "model/objects.h"
+
+
+#include <string>
+#include <vector>
+
+class XHHC_Peptide {
+ protected:
+ bool mass_calculated_[NUMBER_MASS_TYPES]; ///< MONO or Average
+ int num_links_; ///< the number of links this peptide has
+ std::vector<bool> links_; ///< vector bools for the aa position of the link
+ std::string sequence_; ///< sequence of the peptide
+ int length_; ///< sequence length
+ FLOAT_T mass_[NUMBER_MASS_TYPES]; ///< mass of the peptide
+
+ public:
+ /**
+ * \returns a blank XHHC_Peptide object
+ */
+ XHHC_Peptide();
+
+ /**
+ * \returns XHHC_Peptide object with the sequence initialized
+ */
+ XHHC_Peptide(
+ std::string sequence ///< the peptide sequence
+ );
+
+
+ /**
+ * Destructor
+ */
+ virtual ~XHHC_Peptide();
+
+ /**
+ * cleaves the peptide at an index, adding b and y ions
+ * skips if a cleave site on self loop between the link
+ */
+ void splitAt(
+ int index, ///< index to cleave
+ std::vector<std::pair<LinkedPeptide, LinkedPeptide> >& pairs, ///< the b-y ion pairs
+ int charge, ///< charge of the peptide
+ XHHC_Peptide& other, ///< the other peptide that we are linked to
+ bool is_loop ///< Is this a self loop?
+ );
+
+ /**
+ * \returns whether a link exists at the index
+ */
+ bool hasLinkAt(
+ int index ///<amino acid index
+ );
+
+ /**
+ * \returns the sequence length of the peptide
+ */
+ int getLength();
+
+ /**
+ * returns whether a link exists
+ */
+ bool hasLink();
+
+ /**
+ * sets the peptide sequence
+ */
+ void setSequence(
+ std::string sequence
+ );
+
+ /**
+ * \returns the peptide sequence
+ */
+ std::string getSequence();
+
+ /**
+ * \returns whether we have initialized the peptide
+ */
+ bool isEmpty();
+
+ /**
+ * \returns the number of links
+ */
+ int getNumLinks();
+
+ /**
+ * add a link at a amino acid index
+ */
+ void addLink(
+ int index ///< the amino acid index
+ );
+
+ /**
+ * removes a link from the peptide
+ */
+ void removeLink(
+ int index ///< the amino acid index
+ );
+
+ /**
+ * \returns the first index of a link, -1 if none exist
+ */
+ int linkSite();
+
+ /**
+ * \returns the mass of the peptide
+ */
+ FLOAT_T getMass(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ );
+
+ /**
+ * \returns a shuffled peptide, preserving any links
+ */
+ XHHC_Peptide shuffle();
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLink.cpp b/src/app/xlink/XLink.cpp
new file mode 100644
index 0000000..af87030
--- /dev/null
+++ b/src/app/xlink/XLink.cpp
@@ -0,0 +1,221 @@
+/**
+ * \file XLink.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Utility functions for search-for-xlinks
+ *****************************************************************************/
+#include "XLink.h"
+#include "util/Params.h"
+
+#include <sstream>
+#include <iostream>
+using namespace std;
+
+namespace XLink {
+
+set<Crux::Peptide*> allocated_peptides_; ///< tracker for allocated peptides
+
+bool testInterIntraKeep(
+ Crux::Peptide *pep1,
+ Crux::Peptide *pep2
+ ) {
+ return(testInterIntraKeep(pep1, pep2, Params::GetBool("xlink-include-intra"),
+ Params::GetBool("xlink-include-inter"),
+ Params::GetBool("xlink-include-inter-intra")));
+}
+
+bool testInterIntraKeep(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2,
+ bool include_intra,
+ bool include_inter,
+ bool include_inter_intra
+ ) {
+ // carp(CARP_INFO, "testInterIntraKeep:start");
+ if (include_intra &&
+ include_inter &&
+ include_inter_intra) {
+ //no need to test
+ return true;
+ }
+
+ XLINKMATCH_TYPE_T cross_link_type = getCrossLinkCandidateType(pep1, pep2);
+
+ if (cross_link_type == XLINK_INTER_INTRA_CANDIDATE && include_inter_intra) {
+ return true;
+ } else if (cross_link_type == XLINK_INTER_CANDIDATE && include_inter) {
+ return true;
+ } else if (cross_link_type == XLINK_INTRA_CANDIDATE && include_intra) {
+ return true;
+ }
+ return false;
+}
+
+XLINKMATCH_TYPE_T getCrossLinkCandidateType(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2
+ ) {
+
+ bool is_intra = false;
+ bool is_inter = false;
+ size_t id1 = -1;
+ size_t id2 = -1;
+
+ for (PeptideSrcIterator src_iterator1 = pep1->getPeptideSrcBegin();
+ src_iterator1 != pep1->getPeptideSrcEnd();
+ ++src_iterator1) {
+ PeptideSrc* src1 = *src_iterator1;
+ size_t id1t = src1->getParentProtein()->getProteinIdx();
+ if (id1 == -1) {
+ id1 = id1t;
+ } else if (id1 != id1t) {
+ return XLINK_INTER_INTRA_CANDIDATE;
+ }
+ for (PeptideSrcIterator src_iterator2 = pep2->getPeptideSrcBegin();
+ src_iterator2 != pep2->getPeptideSrcEnd();
+ ++src_iterator2) {
+ PeptideSrc* src2 = *src_iterator2;
+ size_t id2t = src2->getParentProtein()->getProteinIdx();
+ if (id2 == -1) {
+ id2 = id2t;
+ } else if (id2 != id2t) {
+ return XLINK_INTER_INTRA_CANDIDATE;
+ }
+ if (id1 == id2) {
+ is_intra = true;
+ if (is_inter) {
+ return(XLINK_INTER_INTRA_CANDIDATE);
+ }
+ } else {
+ is_inter = true;
+ if (is_intra) {
+ return(XLINK_INTER_INTRA_CANDIDATE);
+ }
+ }
+ }
+ }
+
+ if (is_intra && !is_inter) {
+ return (XLINK_INTRA_CANDIDATE);
+ } else if (is_inter & !is_intra) {
+ return(XLINK_INTER_CANDIDATE);
+ } else {
+ carp(CARP_FATAL, "Internal error at getCrossLinkCandidateType");
+ }
+ return(INVALID_CANDIDATE);
+}
+
+/**
+ * \returns whether two proposed peptides would contain an intra-protein crosslink
+ */
+bool isCrossLinkIntra(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2
+ ) {
+
+ return(getCrossLinkCandidateType(pep1, pep2) == XLINK_INTRA_CANDIDATE);
+}
+
+/**
+ * \returns whether two proposed peptides would contain an inter-protein crosslink
+ */
+bool isCrossLinkInter(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2
+ ) {
+
+ return(getCrossLinkCandidateType(pep1, pep2) == XLINK_INTER_CANDIDATE);
+}
+
+bool isCrossLinkInterIntra(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2
+ ) {
+
+ return(getCrossLinkCandidateType(pep1, pep2) == XLINK_INTER_INTRA_CANDIDATE);
+}
+
+
+/**
+ * add a peptide to the list of allocated peptides
+ */
+void addAllocatedPeptide(
+ Crux::Peptide* peptide ///< peptide to add
+ ) {
+
+ allocated_peptides_.insert(peptide);
+}
+
+/**
+ * delete all peptides that are allocated
+ */
+void deleteAllocatedPeptides() {
+ carp(CARP_DEBUG, "deleting %d peptides", allocated_peptides_.size());
+ for (set<Crux::Peptide*>::iterator iter =
+ allocated_peptides_.begin();
+ iter != allocated_peptides_.end();
+ ++iter) {
+
+ delete *iter;
+
+ }
+ allocated_peptides_.clear();
+}
+
+
+void get_protein_ids_locations(
+ Crux::Peptide *peptide, ///< peptide
+ set<string>& protein_ids_locations ///< location strings
+ ) {
+
+ std::ostringstream protein_field_stream;
+
+ string prefix = "";
+ if (peptide->isDecoy()) {
+ prefix = Params::GetString("decoy-prefix");
+ }
+
+ for (PeptideSrcIterator peptide_src_iterator =
+ peptide->getPeptideSrcBegin();
+ peptide_src_iterator != peptide->getPeptideSrcEnd();
+ ++peptide_src_iterator) {
+
+ PeptideSrc* peptide_src = *peptide_src_iterator;
+ Crux::Protein* protein = peptide_src->getParentProtein();
+ string& protein_id = protein->getIdPointer();
+ int peptide_loc = peptide_src->getStartIdx();
+ std::ostringstream protein_loc_stream;
+ protein_loc_stream << prefix << protein_id << "(" << peptide_loc << ")";
+ protein_ids_locations.insert(protein_loc_stream.str());
+ }
+
+}
+
+string get_protein_ids_locations(
+ Crux::Peptide* peptide ///< peptide to get protein strings from
+ ) {
+ set<string> protein_ids_locations;
+
+ get_protein_ids_locations(peptide, protein_ids_locations);
+ set<string>::iterator result_iter = protein_ids_locations.begin();
+
+ string protein_field_string = *result_iter;
+
+ while(++result_iter != protein_ids_locations.end()) {
+ protein_field_string += "," + *result_iter;
+ }
+
+ return protein_field_string;
+
+}
+
+} // namespace XLink
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/xlink/XLink.h b/src/app/xlink/XLink.h
new file mode 100644
index 0000000..36ec527
--- /dev/null
+++ b/src/app/xlink/XLink.h
@@ -0,0 +1,107 @@
+/**
+ * \file XLink.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Utility functions for search-for-xlinks
+ *****************************************************************************/
+#ifndef XLINK_H_
+#define XLINK_H_
+#include "model/objects.h"
+#include "XLinkBondMap.h"
+#include "XLinkablePeptide.h"
+
+#include <vector>
+#include <string>
+
+
+class XLinkMatch;
+class XLinkMatchCollection;
+
+
+void get_min_max_mass(
+ FLOAT_T precursor_mz,
+ int charge,
+ bool use_decoy_window,
+ FLOAT_T& min_mass,
+ FLOAT_T& max_mass);
+
+
+
+namespace XLink {
+
+
+/**
+ * \returns whether the proposed xlink peptides would survive the inter/intra filters set by the user
+ */
+bool testInterIntraKeep(Crux::Peptide* pep1, Crux::Peptide* pep2);
+
+bool testInterIntraKeep(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2,
+ bool include_intra,
+ bool include_inter,
+ bool include_inter_intra
+ );
+
+/**
+ * \ returns the crosslink candidate type between two peptides
+ */
+XLINKMATCH_TYPE_T getCrossLinkCandidateType(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2
+ );
+
+/**
+ * \returns whether two proposed peptides would contain an inter-protein crosslink
+ */
+bool isCrossLinkInter(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2
+ );
+
+/**
+ * \returns whether two proposed peptides would contain an intra-protein crosslink
+ */
+bool isCrossLinkIntra(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2
+ );
+
+/**
+ * \returns whether two propsed peptides would contain both an intra and inter protein cross link
+ */
+bool isCrossLinkInterIntra(
+ Crux::Peptide* pep1,
+ Crux::Peptide* pep2
+);
+
+/**
+ * \returns protein ids with start locations marked with (X)
+ */
+std::string get_protein_ids_locations(
+ Crux::Peptide* peptide ///< peptide to get locations from
+ );
+
+/**
+ * add a peptide to the list of allocated peptides
+ */
+void addAllocatedPeptide(
+ Crux::Peptide* peptide ///< peptide to add
+ );
+
+/**
+ * delete all peptides that are allocated
+ */
+void deleteAllocatedPeptides();
+
+} // namespace XLink
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/xlink/XLinkBondMap.cpp b/src/app/xlink/XLinkBondMap.cpp
new file mode 100644
index 0000000..491d1cc
--- /dev/null
+++ b/src/app/xlink/XLinkBondMap.cpp
@@ -0,0 +1,176 @@
+/*************************************************************************
+ * \file XLinkBondMap.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: Febuary 22, 2011
+ * \brief Object for representing the potential cross-links for peptides.
+ ****************************************************************************/
+
+#include "XLinkBondMap.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * Default constructor.
+ */
+XLinkBondMap::XLinkBondMap() {
+ ;
+}
+
+/**
+ * Constructor that initializes XLinkBondMap using the links string.
+ * Format: A:B,C:D,... which means that a link can occur between residue
+ * A and B, or C and D.
+ */
+XLinkBondMap::XLinkBondMap(
+ string& links_string ///<links string
+ ) {
+ init(links_string);
+}
+
+/**
+ * Initializes XLinkBondMap using the links string.
+ * Format: A:B,C:D,... which means that a link can occur between residue
+ * A and B, or C and D.
+ */
+void XLinkBondMap::init(
+ string& links_string ///< links string
+ ) {
+
+ vector<string> bond_strings = StringUtils::Split(links_string, ',');
+
+ for (vector<string>::const_iterator i = bond_strings.begin(); i != bond_strings.end(); i++) {
+ vector<string> link_site_strings = StringUtils::Split(*i, ':');
+
+ if (link_site_strings.size() == 2) {
+ XLinkSite site1(link_site_strings[0]);
+ XLinkSite site2(link_site_strings[1]);
+ (*this)[site1].insert(site2);
+ (*this)[site2].insert(site1);
+ } else {
+ carp(CARP_FATAL,
+ "bad format in %s when parsing %s",
+ links_string.c_str(),
+ i->c_str());
+ }
+ }
+}
+
+/**
+ * Default destructor
+ */
+XLinkBondMap::~XLinkBondMap() {
+}
+
+/**
+ * \returns whether a cross-link can occur at a single position in the
+ * peptide (for deadlinks).
+ */
+bool XLinkBondMap::canLink(
+ Peptide* peptide, ///<peptide object pointer
+ int idx ///<sequence index
+ ) {
+ for (XLinkBondMap::iterator iter = begin();
+ iter != end(); ++iter) {
+
+ if (iter->first.hasSite(peptide, idx)) {
+ return true;
+ }
+ }
+ return false;
+}
+
+/**
+ * \returns whether a cross-link can occur between two positions in the
+ * peptide (for selfloops).
+ */
+bool XLinkBondMap::canLink(
+ Peptide* peptide, ///<peptide object pointer
+ int idx1, ///<1st sequence idx
+ int idx2 ///<2nd sequence idx
+ ) {
+
+ return canLink(peptide, peptide, idx1, idx2);
+}
+
+bool XLinkBondMap::canLink(
+ XLinkablePeptide& pep,
+ int link1_site,
+ int link2_site
+ ) {
+
+ return canLink(
+ pep.getPeptide(),
+ pep.getLinkSite(link1_site),
+ pep.getLinkSite(link2_site));
+}
+
+/**
+ * \returns whether a cross-link can occur between two peptides at their
+ * respective sequence positions (for inter/intra links).
+ */
+bool XLinkBondMap::canLink(
+ Peptide* peptide1, ///<1st peptide object pointer
+ Peptide* peptide2, ///<2nd peptide object pointer
+ int idx1, ///<1st peptide sequence idx
+ int idx2 ///<2nd peptide sequence idx
+ ) { //for inter/intra links
+
+ for (XLinkBondMap::iterator iter1 = begin();
+ iter1 != end(); ++iter1) {
+
+ if (iter1->first.hasSite(peptide1, idx1)) {
+ for (set<XLinkSite>::iterator iter2 = iter1->second.begin();
+ iter2 != iter1->second.end();
+ ++iter2) {
+
+ if (iter2->hasSite(peptide2, idx2)) {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+}
+
+bool XLinkBondMap::canLink(
+ XLinkablePeptide& pep1,
+ XLinkablePeptide& pep2,
+ int link1_site,
+ int link2_site
+ ) {
+
+ return canLink(
+ pep1.getPeptide(),
+ pep2.getPeptide(),
+ pep1.getLinkSite(link1_site),
+ pep2.getLinkSite(link2_site));
+
+}
+
+
+bool XLinkBondMap::canLink(
+ string& protein,
+ int idx) {
+
+
+ for (XLinkBondMap::iterator iter = begin();
+ iter != end(); ++iter) {
+
+ if (iter->first.hasSite(protein, idx)) {
+ return true;
+ }
+ }
+ return false;
+
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/xlink/XLinkBondMap.h b/src/app/xlink/XLinkBondMap.h
new file mode 100644
index 0000000..8f91002
--- /dev/null
+++ b/src/app/xlink/XLinkBondMap.h
@@ -0,0 +1,114 @@
+/**
+ * \file XLinkBondMap.h
+ * $Revision: 1.00 $
+ * \brief Object for representing the potential cross-links for peptides.
+ *************************************************************************/
+#ifndef XLINKBONDMAP_H
+#define XLINKBONDMAP_H
+
+#include "XLinkablePeptide.h"
+#include "XLinkSite.h"
+#include <map>
+#include <set>
+#include <string>
+
+
+/**
+ * \class XLinkBondMap
+ * \brief object representing the potential cross-links for peptides.
+ */
+class XLinkBondMap: public std::map<XLinkSite, std::set<XLinkSite> > {
+
+ public:
+
+ /**
+ * Default constructor.
+ */
+ XLinkBondMap();
+
+ /**
+ * Constructor that initializes XLinkBondMap using the links string.
+ * Format: A:B,C:D,... which means that a link can occur between residue
+ * A and B, or C and D.
+ */
+ XLinkBondMap(
+ std::string& links_string ///<link string
+ );
+
+ /**
+ * Initializes XLinkBondMap using the links string.
+ * Format: A:B,C:D,... which means that a link can occur between residue
+ * A and B, or C and D.
+ */
+ void init(
+ std::string& links_string ///< links string
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual ~XLinkBondMap();
+
+ void setLinkString(
+ std::string& links_string
+ );
+
+ /**
+ * \returns whether a cross-link can occur at a single position in the
+ * peptide (for deadlinks).
+ */
+ bool canLink(
+ Crux::Peptide* peptide, ///<peptide object pointer
+ int idx ///<sequence idx
+ );
+
+ /**
+ * \returns whether a cross-link can occur between two positions in the
+ * peptide (for selfloops).
+ */
+ bool canLink(
+ Crux::Peptide* peptide, ///<peptide object pointer
+ int idx1, ///<1st sequence idx
+ int idx2 ///<2nd sequence idx
+ );
+
+ bool canLink(
+ XLinkablePeptide& pep,
+ int link1_site,
+ int link2_site
+ );
+
+ /**
+ * \returns whether a cross-link can occur between two peptides at their
+ * respective sequence positions (for inter/intra links).
+ */
+ bool canLink(
+ Crux::Peptide* peptide1, ///<1st peptide object pointer
+ Crux::Peptide* peptide2, ///<2nd peptide object pointer
+ int idx1, ///<1st peptide sequence idx
+ int idx2 ///<2nd peptide sequence idx
+ );
+
+ bool canLink(
+ XLinkablePeptide& pep1,
+ XLinkablePeptide& pep2,
+ int link1_site,
+ int link2_site
+ );
+
+ bool canLink(
+ std::string& protein_sequence,
+ int idx);
+
+
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkDatabase.cpp b/src/app/xlink/XLinkDatabase.cpp
new file mode 100644
index 0000000..f7a5610
--- /dev/null
+++ b/src/app/xlink/XLinkDatabase.cpp
@@ -0,0 +1,592 @@
+#include "XLinkDatabase.h"
+#include "util/modifications.h"
+#include "model/ModifiedPeptidesIterator.h"
+#include "util/GlobalParams.h"
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+#include <algorithm>
+
+using namespace std;
+
+Database* XLinkDatabase::protein_database_;
+XLinkBondMap XLinkDatabase::bondmap_;
+
+vector<vector<Crux::Peptide*> > XLinkDatabase::target_peptides_; ///< all peptides generated with no additional missed cleavage;
+
+vector<vector<Crux::Peptide*> > XLinkDatabase::decoy_peptides_;
+
+std::vector<LinearPeptide> XLinkDatabase::target_linear_peptides_;
+std::vector<LinearPeptide> XLinkDatabase::decoy_linear_peptides_;
+
+std::vector<SelfLoopPeptide> XLinkDatabase::target_selfloop_peptides_;
+std::vector<SelfLoopPeptide> XLinkDatabase::decoy_selfloop_peptides_;
+
+std::vector<XLinkablePeptide> XLinkDatabase::target_xlinkable_peptides_;
+std::vector<XLinkablePeptide> XLinkDatabase::decoy_xlinkable_peptides_;
+std::vector<XLinkablePeptide> XLinkDatabase::target_xlinkable_peptides2_; //Peptides that could be selfloops.
+std::vector<XLinkablePeptide> XLinkDatabase::decoy_xlinkable_peptides2_;
+
+std::vector<XLinkablePeptide> XLinkDatabase::target_xlinkable_peptides_flatten_;
+std::vector<XLinkablePeptide> XLinkDatabase::decoy_xlinkable_peptides_flatten_;
+//vector<pair<int, vector<XLinkablePeptide> > > XLinkDatabase::protein_idx_to_xpeptides_;
+
+bool XLinkDatabase::addPeptideToDatabase(Crux::Peptide* peptide) {
+
+ bool added = false;
+ vector<int> link_sites;
+ set<int> skip;
+
+ if (GlobalParams::getXLinkIncludeLinears()) {
+ set<int> skip;
+ if (peptide->getMissedCleavageSites(skip) <= GlobalParams::getMissedCleavages()) {
+ LinearPeptide lpeptide(peptide);
+ lpeptide.getMass(GlobalParams::getIsotopicMass());
+ target_linear_peptides_.push_back(lpeptide);
+ added = true;
+ }
+ }
+
+ if (GlobalParams::getXLinkIncludeInterIntra() ||
+ GlobalParams::getXLinkIncludeInter() ||
+ GlobalParams::getXLinkIncludeIntra() ||
+ GlobalParams::getXLinkIncludeDeadends()) {
+ if (peptide->countModifiedAAs() <= GlobalParams::getMaxXLinkMods()) {
+ XLinkablePeptide::findLinkSites(peptide, bondmap_, link_sites);
+ if (!link_sites.empty()) {
+ XLinkablePeptide xlp(peptide, link_sites);
+ xlp.getMass(GlobalParams::getIsotopicMass());
+ target_xlinkable_peptides_.push_back(xlp);
+ added = true;
+ }
+ }
+ }
+ if (GlobalParams::getXLinkIncludeSelfloops()) {
+ XLinkablePeptide::findLinkSites(peptide, bondmap_, link_sites, 1);
+ if (link_sites.size() > 1) {
+ XLinkablePeptide xlp = XLinkablePeptide(peptide, link_sites);
+ for (size_t link1_idx = 0; link1_idx<xlp.numLinkSites()-1;link1_idx++) {
+ for (size_t link2_idx = link1_idx+1; link2_idx < xlp.numLinkSites();link2_idx++) {
+ if (bondmap_.canLink(xlp, link1_idx, link2_idx)) {
+ //create the candidate.
+ SelfLoopPeptide self_loop(xlp, xlp.getLinkSite(link1_idx), xlp.getLinkSite(link2_idx));
+ if (self_loop.getNumMissedCleavages() <= GlobalParams::getMissedCleavages()) {
+ self_loop.getMass(GlobalParams::getIsotopicMass());
+ target_selfloop_peptides_.push_back(self_loop);
+ added=true;
+ }
+ }
+ }
+ }
+ }
+ }
+ return(added);
+}
+
+
+void XLinkDatabase::initialize() {
+ carp(CARP_INFO, "Initializing database");
+ //Step one, load the database
+ string input_file = Params::GetString("protein fasta file");
+ string link_string = Params::GetString("link sites");
+ bondmap_ = XLinkBondMap(link_string);
+ protein_database_ = NULL;
+ int num_protein = prepare_protein_input(input_file, &protein_database_);
+
+ PEPTIDE_MOD_T** peptide_mods = NULL;
+ int num_peptide_mods = generate_peptide_mod_list( &peptide_mods );
+
+ //Step two create all peptides.
+ int additional_cleavages = 0;
+
+ bool generate_xlinkable = Params::GetBool("xlink-include-inter-intra") ||
+ Params::GetBool("xlink-include-inter") ||
+ Params::GetBool("xlink-include-intra") ||
+ Params::GetBool("xlink-include-deadends");
+
+ if (generate_xlinkable) {
+ additional_cleavages = 1;
+ }
+
+ if (Params::GetBool("xlink-include-selfloops")) {
+ additional_cleavages = 2;
+ }
+
+ int total_missed_cleavages = GlobalParams::getMissedCleavages()+additional_cleavages;
+
+ for (size_t idx=0;idx<=total_missed_cleavages;idx++) {
+ target_peptides_.push_back(vector<Crux::Peptide*>());
+ decoy_peptides_.push_back(vector<Crux::Peptide*>());
+ }
+ //Generate all possible target peptides
+
+ size_t peptide_count = 0;
+ size_t used_count = 0;
+
+ for (int mod_idx=0;mod_idx<num_peptide_mods; mod_idx++) {
+ PEPTIDE_MOD_T* peptide_mod = peptide_mods[mod_idx];
+ double delta_mass = peptide_mod_get_mass_change(peptide_mod);
+ carp(CARP_INFO, "Modification %d has delta mass of %g Da.", mod_idx + 1, delta_mass);
+ //
+ ModifiedPeptidesIterator* peptide_iterator =
+ new ModifiedPeptidesIterator(
+ GlobalParams::getMinMass(),
+ GlobalParams::getMaxMass(),
+ peptide_mod,
+ false,
+ protein_database_,
+ additional_cleavages);
+
+ //add the targets
+ while (peptide_iterator->hasNext()) {
+ peptide_count++;
+ Crux::Peptide* peptide = peptide_iterator->next();
+ int missed_cleavages = peptide->getMissedCleavageSites();
+
+ bool added = addPeptideToDatabase(peptide);
+ if (added) {
+ used_count++;
+ target_peptides_[missed_cleavages].push_back(peptide);
+ } else {
+ delete peptide;
+ }
+ }
+ delete peptide_iterator;
+ }
+
+ carp(CARP_INFO,"Considered linear %d peptides, of which %d were included in the database.", peptide_count, used_count);
+
+ if (Params::GetBool("xlink-include-linears")) {
+ carp(CARP_INFO, " The database contains %d linear peptides.", target_linear_peptides_.size());
+ sort(target_linear_peptides_.begin(), target_linear_peptides_.end(), compareLinearPeptideMass);
+ }
+
+ if (Params::GetBool("xlink-include-selfloops")) {
+ carp(CARP_INFO, " The database contains %d selfloop peptides.", target_selfloop_peptides_.size());
+ sort(target_selfloop_peptides_.begin(), target_selfloop_peptides_.end(), compareSelfLoopPeptideMass);
+ }
+
+ if (generate_xlinkable) {
+ carp(CARP_INFO, " The database contains %d cross-linkable peptides.", target_xlinkable_peptides_.size());
+ sort(target_xlinkable_peptides_.begin(), target_xlinkable_peptides_.end(), compareXLinkablePeptideMass);
+ flattenLinkablePeptides(target_xlinkable_peptides_, target_xlinkable_peptides_flatten_);
+ }
+
+ carp(CARP_INFO, "Done initializing database");
+}
+
+void XLinkDatabase::finalize() {
+ carp(CARP_INFO, "Start to finalize database");
+ target_linear_peptides_.clear();
+ decoy_linear_peptides_.clear();
+ target_selfloop_peptides_.clear();
+ decoy_selfloop_peptides_.clear();
+ target_xlinkable_peptides_.clear();
+ decoy_xlinkable_peptides_.clear();
+ target_xlinkable_peptides_flatten_.clear();
+ for (size_t idx1=0;idx1<target_peptides_.size();idx1++) {
+ for (size_t idx2=0;idx2<target_peptides_[idx1].size();idx2++) {
+ delete target_peptides_[idx1][idx2];
+ }
+ }
+
+ for (size_t idx1=0;idx1<decoy_peptides_.size();idx1++) {
+ for (size_t idx2=0;idx2<decoy_peptides_[idx1].size();idx2++) {
+ delete decoy_peptides_[idx1][idx2];
+ }
+ }
+
+ Database::freeDatabase(protein_database_);
+ carp(CARP_INFO, "Done finalizing database");
+}
+
+void XLinkDatabase::findSelfLoops(
+ vector<XLinkablePeptide>& linkable_peptides,
+ vector<SelfLoopPeptide>& ans) {
+
+ //Loop through all peptides, trying to find peptides with at least two link sites.
+ for (vector<XLinkablePeptide>::iterator iter =
+ linkable_peptides.begin();
+ iter != linkable_peptides.end();
+ ++iter) {
+
+ if (iter->numLinkSites() > 1) {
+ for (size_t link1_idx = 0; link1_idx<iter->numLinkSites()-1;link1_idx++) {
+ for (size_t link2_idx = link1_idx+1; link2_idx < iter->numLinkSites();link2_idx++) {
+ if (bondmap_.canLink(*iter, link1_idx, link2_idx)) {
+ //create the candidate.
+ SelfLoopPeptide self_loop(*iter, iter->getLinkSite(link1_idx), iter->getLinkSite(link2_idx));
+ if (self_loop.getNumMissedCleavages() <= GlobalParams::getMissedCleavages()) {
+ self_loop.getMass(GlobalParams::getIsotopicMass());
+ ans.push_back(self_loop);
+ }
+ }
+ }
+ }
+ }
+ }
+}
+
+void XLinkDatabase::generateAllSelfLoops(bool decoy) {
+
+ int mc = GlobalParams::getMissedCleavages()+2;
+ if (decoy) {
+ findSelfLoops(decoy_xlinkable_peptides_, decoy_selfloop_peptides_);
+ int mc = GlobalParams::getMissedCleavages()+2;
+ generateAllLinkablePeptides(decoy_peptides_[mc], decoy_xlinkable_peptides2_);
+ findSelfLoops(decoy_xlinkable_peptides2_, decoy_selfloop_peptides_);
+ sort(decoy_selfloop_peptides_.begin(),
+ decoy_selfloop_peptides_.end(),
+ compareSelfLoopPeptideMass);
+ } else {
+ findSelfLoops(target_xlinkable_peptides_, target_selfloop_peptides_);
+ generateAllLinkablePeptides(target_peptides_[mc], target_xlinkable_peptides2_);
+ findSelfLoops(target_xlinkable_peptides2_, target_selfloop_peptides_);
+ sort(
+ target_selfloop_peptides_.begin(),
+ target_selfloop_peptides_.end(),
+ compareSelfLoopPeptideMass);
+ }
+}
+
+void XLinkDatabase::findLinearPeptides(vector<Crux::Peptide*> &peptides, vector<LinearPeptide>& linear_peptides) {
+
+ for (vector<Crux::Peptide*>::iterator iter = peptides.begin();
+ iter != peptides.end();
+ ++iter) {
+ LinearPeptide lpeptide(*iter);
+ lpeptide.getMass(GlobalParams::getIsotopicMass());
+ linear_peptides.push_back(lpeptide);
+
+ }
+}
+
+void XLinkDatabase::generateAllLinears(bool decoy) {
+ //NOTE - Right now, we need to call this with decoy=false first.
+
+ for (size_t cleavage_idx = 0;
+ cleavage_idx <= GlobalParams::getMissedCleavages();
+ cleavage_idx++) {
+ findLinearPeptides(target_peptides_[cleavage_idx], target_linear_peptides_);
+ }
+}
+
+
+void XLinkDatabase::flattenLinkablePeptides(vector<XLinkablePeptide>& xpeptides,
+ vector<XLinkablePeptide>& flattened) {
+
+ for (size_t idx=0;idx < xpeptides.size();idx++) {
+ XLinkablePeptide& current = xpeptides[idx];
+ for (size_t link1_idx=0;link1_idx < current.numLinkSites(); link1_idx++) {
+ XLinkablePeptide onelink(current);
+ onelink.getMass(MONO);
+ onelink.clearSites();
+ onelink.addLinkSite(current.getLinkSite(link1_idx));
+ flattened.push_back(onelink);
+ }
+ }
+}
+
+void XLinkDatabase::filterLinkablePeptides(
+ vector<XLinkablePeptide>& xpeptides,
+ vector<XLinkablePeptide>& filtered_xpeptides
+ ) {
+ bool filter1 = !Params::GetBool("xlink-include-inter-intra");
+ bool filter2 = !Params::GetBool("xlink-include-inter") && !Params::GetBool("xlink-include-intra");
+
+ for (size_t idx = 0 ;idx < xpeptides.size();idx++) {
+ //quick check to see if peptide can come from multiple protein sources.
+ //if true, then this should return XLINK_INTER_INTRA_CANDIDATE
+ XLINKMATCH_TYPE_T ctype =
+ XLink::getCrossLinkCandidateType(xpeptides[idx].getPeptide(),
+ xpeptides[idx].getPeptide());
+
+ if ((filter1 && ctype == XLINK_INTER_INTRA_CANDIDATE) ||
+ (filter2 && ctype != XLINK_INTER_INTRA_CANDIDATE)) {
+ } else {
+ filtered_xpeptides.push_back(xpeptides[idx]);
+ }
+ }
+
+ carp(CARP_INFO, "kept %d out of %d", filtered_xpeptides.size(), xpeptides.size());
+
+}
+
+void XLinkDatabase::generateAllLinkablePeptides(
+ vector<Crux::Peptide*>& peptides,
+ vector<XLinkablePeptide>& xpeptides) {
+
+ carp(CARP_DEBUG, "XLinkDatabase::generateAllLinkablePeptides: start()");
+ carp(CARP_DEBUG, "Number of peptides:%d", peptides.size());
+ //Loop through peptides
+ vector<int> link_sites;
+ for (vector<Crux::Peptide*>::iterator iter = peptides.begin();
+ iter != peptides.end();
+ ++iter) {
+ Crux::Peptide* peptide = *iter;
+
+ if (peptide->countModifiedAAs() <= GlobalParams::getMaxXLinkMods()) {
+ XLinkablePeptide::findLinkSites(peptide, bondmap_, link_sites);
+ if (!link_sites.empty()) {
+ XLinkablePeptide xlp(peptide, link_sites);
+ xlp.getMass(MONO);
+ xpeptides.push_back(xlp);
+ }
+ }
+ }
+ carp(CARP_DEBUG, "XLinkDatabase::generateAllLinkablePeptides: done()");
+}
+
+
+void XLinkDatabase::print() {
+
+ string output_directory = Params::GetString("output-dir");
+ if (Params::GetBool("xlink-include-linears")) {
+ ostringstream oss;
+ oss << output_directory << "/" << "xlink_peptides.linear.txt";
+ string temp = oss.str();
+ ofstream peptides_file(temp.c_str());
+
+ peptides_file << setprecision(8);
+
+ peptides_file << "mass\tsequence\tprotein id\tmissed cleavages\tunshuffled sequence"<<endl;
+
+ for (int idx=0;idx < target_linear_peptides_.size();idx++) {
+
+ peptides_file << target_linear_peptides_[idx].getMass(MONO) << "\t";
+ peptides_file << target_linear_peptides_[idx].getSequenceString() << "\t";
+ peptides_file << target_linear_peptides_[idx].getProteinIdString() << "\t";
+ peptides_file << target_linear_peptides_[idx].getNumMissedCleavages() << "\t";
+ peptides_file << "" << endl;
+ }
+
+ for (int idx=0;idx < decoy_linear_peptides_.size();idx++) {
+ peptides_file << decoy_linear_peptides_[idx].getMass(MONO) << "\t";
+ peptides_file << decoy_linear_peptides_[idx].getSequenceString() << "\t";
+ peptides_file << decoy_linear_peptides_[idx].getProteinIdString() << "\t";
+ peptides_file << decoy_linear_peptides_[idx].getNumMissedCleavages() << "\t";
+ peptides_file << decoy_linear_peptides_[idx].getPeptide(0)->getUnshuffledSequence() << endl;
+ }
+
+ peptides_file.flush();
+ }
+
+ if (Params::GetBool("xlink-include-selfloops")) {
+ ostringstream oss;
+ oss << output_directory << "/" << "xlink_peptides.selfloops.txt";
+ string temp = oss.str();
+ ofstream peptides_file(temp.c_str());
+
+ peptides_file << setprecision(8);
+
+ peptides_file << "mass\tsequence\tprotein id\t missed cleavages"<<endl;
+
+ for (int idx=0;idx < target_selfloop_peptides_.size();idx++) {
+
+ peptides_file << target_selfloop_peptides_[idx].getMass(MONO) << "\t";
+ peptides_file << target_selfloop_peptides_[idx].getSequenceString() << "\t";
+ peptides_file << target_selfloop_peptides_[idx].getNumMissedCleavages() << "\t";
+ peptides_file << target_selfloop_peptides_[idx].getProteinIdString() << endl;
+ }
+ peptides_file.flush();
+ }
+
+ ostringstream oss;
+ oss << output_directory << "/" << "xlink_peptides.linkable.txt";
+
+ string temp = oss.str();
+ ofstream peptides_file(temp.c_str());
+
+ peptides_file << setprecision(8);
+
+ peptides_file << "mass\tsequence\tlinks"<<endl;
+
+ for (int idx=0;idx < target_xlinkable_peptides_.size();idx++) {
+
+ peptides_file << target_xlinkable_peptides_[idx].getMass(MONO) << "\t";
+ peptides_file << target_xlinkable_peptides_[idx].getModifiedSequenceString() << "\t";
+ //peptides_file << target_xlinkable_peptides_[idx].getProteinIdString() << endl;
+
+ peptides_file << target_xlinkable_peptides_[idx].getLinkSite(0)+1;
+ for (size_t idx2 = 1;idx2 < target_xlinkable_peptides_[idx].numLinkSites();idx2++) {
+ peptides_file << "," << target_xlinkable_peptides_[idx].getLinkSite(idx2)+1;
+ }
+ peptides_file << endl;
+ }
+ peptides_file.flush();
+}
+
+vector<LinearPeptide>::iterator XLinkDatabase::getLinearBegin(
+ bool decoy
+ ) {
+
+ if (decoy) {
+ return (decoy_linear_peptides_.begin());
+ } else {
+ return (target_linear_peptides_.begin());
+ }
+}
+vector<LinearPeptide>::iterator XLinkDatabase::getLinearBegin(
+ bool decoy,
+ FLOAT_T min_mass
+ ) {
+
+ if (decoy) {
+ return (lower_bound(decoy_linear_peptides_.begin(),
+ decoy_linear_peptides_.end(),
+ min_mass,
+ compareLinearPeptideMassToFLOAT));
+ } else {
+ return (lower_bound(target_linear_peptides_.begin(),
+ target_linear_peptides_.end(),
+ min_mass,
+ compareLinearPeptideMassToFLOAT));
+ }
+}
+
+vector<LinearPeptide>::iterator XLinkDatabase::getLinearEnd(
+ bool decoy
+) {
+
+ if (decoy) {
+ return (decoy_linear_peptides_.end());
+ } else {
+ return (target_linear_peptides_.end());
+ }
+}
+
+vector<LinearPeptide>::iterator XLinkDatabase::getLinearEnd(
+ bool decoy,
+ FLOAT_T max_mass
+ ) {
+ return(std::upper_bound(getLinearBegin(decoy),
+ getLinearEnd(decoy),
+ max_mass,
+ compareFLOATToLinearPeptideMass));
+
+
+}
+
+vector<LinearPeptide>::iterator XLinkDatabase::getLinearEnd(
+ bool decoy,
+ std::vector<LinearPeptide>::iterator& siter,
+ FLOAT_T max_mass
+) {
+ return(std::upper_bound(siter,
+ getLinearEnd(decoy),
+ max_mass,
+ compareFLOATToLinearPeptideMass));
+
+}
+
+vector<SelfLoopPeptide>::iterator XLinkDatabase::getSelfLoopBegin(
+ bool decoy,
+ FLOAT_T min_mass
+ ) {
+
+ if (decoy) {
+ return (lower_bound(decoy_selfloop_peptides_.begin(),
+ decoy_selfloop_peptides_.end(),
+ min_mass,
+ compareSelfLoopPeptideMassToFLOAT));
+ } else {
+
+ return (lower_bound(target_selfloop_peptides_.begin(),
+ target_selfloop_peptides_.end(),
+ min_mass,
+ compareSelfLoopPeptideMassToFLOAT));
+ }
+}
+
+vector<SelfLoopPeptide>::iterator XLinkDatabase::getSelfLoopEnd(
+ bool decoy
+) {
+
+ if (decoy) {
+ return(decoy_selfloop_peptides_.end());
+ } else {
+ return(target_selfloop_peptides_.end());
+ }
+}
+
+vector<XLinkablePeptide>::iterator XLinkDatabase::getXLinkableBegin() {
+ return(target_xlinkable_peptides_.begin());
+
+}
+
+vector<XLinkablePeptide>::iterator XLinkDatabase::getXLinkableBegin(FLOAT_T min_mass) {
+ return (lower_bound(target_xlinkable_peptides_.begin(), target_xlinkable_peptides_.end(),
+ min_mass, compareXLinkablePeptideMassToFLOAT));
+}
+vector<XLinkablePeptide>::iterator XLinkDatabase::getXLinkableEnd() {
+ return(target_xlinkable_peptides_.end());
+}
+
+vector<XLinkablePeptide>& XLinkDatabase::getXLinkablePeptides(
+ bool decoy
+) {
+ if (decoy) {
+ return (decoy_xlinkable_peptides_);
+ } else {
+ return(target_xlinkable_peptides_);
+ }
+}
+
+
+
+XLinkBondMap& XLinkDatabase::getXLinkBondMap() {
+ return bondmap_;
+}
+
+vector<XLinkablePeptide>::iterator XLinkDatabase::getXLinkableFlattenBegin() {
+ return(target_xlinkable_peptides_flatten_.begin());
+}
+
+vector<XLinkablePeptide>::iterator XLinkDatabase::getXLinkableFlattenBegin(
+ bool decoy,
+ FLOAT_T min_mass
+ ) {
+ if (decoy) {
+ return(lower_bound(decoy_xlinkable_peptides_flatten_.begin(),
+ decoy_xlinkable_peptides_flatten_.end(),
+ min_mass, compareXLinkablePeptideMassToFLOAT));
+ } else {
+ return(lower_bound(target_xlinkable_peptides_flatten_.begin(),
+ target_xlinkable_peptides_flatten_.end(),
+ min_mass, compareXLinkablePeptideMassToFLOAT));
+ }
+}
+
+vector<XLinkablePeptide>::iterator XLinkDatabase::getXLinkableFlattenEnd() {
+ return(target_xlinkable_peptides_flatten_.end());
+}
+
+vector<XLinkablePeptide>::iterator XLinkDatabase::getXLinkableFlattenEnd(
+ bool decoy,
+ FLOAT_T max_mass
+ ) {
+
+ if (decoy) {
+ return(std::upper_bound(decoy_xlinkable_peptides_flatten_.begin(),
+ decoy_xlinkable_peptides_flatten_.end(),
+ max_mass,
+ compareXLinkablePeptideMassToFLOAT2));
+ } else {
+
+ return(std::upper_bound(target_xlinkable_peptides_flatten_.begin(),
+ target_xlinkable_peptides_flatten_.end(),
+ max_mass,
+ compareXLinkablePeptideMassToFLOAT2));
+ }
+}
+
+/*
+vector<pair<int, vector<XLinkablePeptide> > >& XLinkDatabase::getTargetProteinIdxToXPeptides() {
+ return protein_idx_to_xpeptides_;
+
+}
+*/
+
+int XLinkDatabase::getNLinkable() {
+ return(target_xlinkable_peptides_.size());
+}
diff --git a/src/app/xlink/XLinkDatabase.h b/src/app/xlink/XLinkDatabase.h
new file mode 100644
index 0000000..acd6006
--- /dev/null
+++ b/src/app/xlink/XLinkDatabase.h
@@ -0,0 +1,144 @@
+#ifndef XLINKDATABASE_H_
+#define XLINKDATABASE_H_
+#include "model/objects.h"
+#include "model/Peptide.h"
+#include "model/Database.h"
+#include "XLinkablePeptide.h"
+#include "SelfLoopPeptide.h"
+#include "LinearPeptide.h"
+
+#include <vector>
+
+class XLinkDatabase {
+
+ protected:
+ static Database* protein_database_;
+ static XLinkBondMap bondmap_;
+
+
+ static std::vector<std::vector<Crux::Peptide*> > target_peptides_;
+ ///< all target peptides generated, indexed by missed cleavages
+
+ static std::vector<std::vector<Crux::Peptide*> > decoy_peptides_;
+ ///< all decoy peptides generated, indexed by missed cleavages
+
+ static std::vector<LinearPeptide> target_linear_peptides_;
+ static std::vector<LinearPeptide> decoy_linear_peptides_;
+
+
+ static std::vector<SelfLoopPeptide> target_selfloop_peptides_;
+ static std::vector<SelfLoopPeptide> decoy_selfloop_peptides_;
+
+ static std::vector<XLinkablePeptide> target_xlinkable_peptides_;
+ static std::vector<XLinkablePeptide> decoy_xlinkable_peptides_;
+
+ static std::vector<XLinkablePeptide> target_xlinkable_peptides_flatten_;
+ static std::vector<XLinkablePeptide> target_xlinkable_peptides2_; //Peptides that could be selfloops.
+ static std::vector<XLinkablePeptide> decoy_xlinkable_peptides2_;
+
+ static std::vector<XLinkablePeptide> decoy_xlinkable_peptides_flatten_;
+
+ static void findLinearPeptides(
+ vector<Crux::Peptide*>& peptides,
+ vector<LinearPeptide>& linears
+ );
+ static void generateAllLinears(bool decoy);
+ static void generateAllLinkablePeptides(
+ std::vector<Crux::Peptide*>& peptides,
+ std::vector<XLinkablePeptide>& xpeptides);
+
+ static void findSelfLoops(
+ std::vector<XLinkablePeptide>& linkable_peptides,
+ std::vector<SelfLoopPeptide>& ans);
+
+ static void generateAllSelfLoops(bool decoy);
+ static void flattenLinkablePeptides(
+ std::vector<XLinkablePeptide>& xpeptides,
+ std::vector<XLinkablePeptide>& flattened
+ );
+
+ static void filterLinkablePeptides(
+ std::vector<XLinkablePeptide>& xpeptides,
+ std::vector<XLinkablePeptide>& filtered_xpeptides
+ );
+
+ static bool addPeptideToDatabase(Crux::Peptide* peptide);
+
+ public:
+ XLinkDatabase() {;}
+ virtual ~XLinkDatabase() {;}
+
+ static void initialize();
+ static void finalize();
+
+ static XLinkBondMap& getXLinkBondMap();
+
+ static std::vector<XLinkablePeptide>::iterator getXLinkableBegin();
+ static std::vector<XLinkablePeptide>::iterator getXLinkableBegin(FLOAT_T min_mass);
+ static std::vector<XLinkablePeptide>::iterator getXLinkableEnd();
+ static int getNLinkable();
+ static std::vector<XLinkablePeptide>& getXLinkablePeptides(
+ bool decoy
+ );
+
+ static XLinkablePeptide& getXLinkablePeptide(
+ bool decoy,
+ int idx
+ );
+
+ static std::vector<XLinkablePeptide>::iterator getXLinkableFlattenBegin();
+ static std::vector<XLinkablePeptide>::iterator getXLinkableFlattenBegin(
+ bool decoy,
+ FLOAT_T min_mass
+ );
+ static std::vector<XLinkablePeptide>::iterator getXLinkableFlattenEnd();
+
+ static std::vector<XLinkablePeptide>::iterator getXLinkableFlattenEnd(
+ bool decoy,
+ FLOAT_T max_mass
+ );
+
+ static std::vector<SelfLoopPeptide>::iterator getSelfLoopBegin(
+ bool decoy
+ );
+
+ static std::vector<SelfLoopPeptide>::iterator getSelfLoopEnd(
+ bool decoy
+ );
+
+ static std::vector<SelfLoopPeptide>::iterator getSelfLoopBegin(
+ bool decoy,
+ FLOAT_T min_mass
+ );
+
+ static std::vector<LinearPeptide>::iterator getLinearBegin(
+ bool decoy
+ );
+
+ static std::vector<LinearPeptide>::iterator getLinearBegin(
+ bool decoy,
+ FLOAT_T min_mass
+ );
+
+ static std::vector<LinearPeptide>::iterator getLinearEnd(
+ bool decoy
+ );
+
+ static std::vector<LinearPeptide>::iterator getLinearEnd(
+ bool decoy,
+ FLOAT_T max_mass
+ );
+
+ static std::vector<LinearPeptide>::iterator getLinearEnd(
+ bool decoy,
+ std::vector<LinearPeptide>::iterator &siter,
+ FLOAT_T max_mass
+ );
+
+ //static std::vector<std::pair<int, vector<XLinkablePeptide> > >& getTargetProteinIdxToXPeptides();
+
+
+ static void print();
+
+};
+#endif
diff --git a/src/app/xlink/XLinkIonSeriesCache.cpp b/src/app/xlink/XLinkIonSeriesCache.cpp
new file mode 100644
index 0000000..30a0960
--- /dev/null
+++ b/src/app/xlink/XLinkIonSeriesCache.cpp
@@ -0,0 +1,141 @@
+#include "XLinkIonSeriesCache.h"
+
+using namespace std;
+
+vector<vector<IonSeries*> > XLinkIonSeriesCache::target_xlinkable_ion_series_;
+
+vector<vector<IonSeries*> > XLinkIonSeriesCache::decoy_xlinkable_ion_series_;
+vector<IonConstraint*> XLinkIonSeriesCache::xcorr_ion_constraint_;
+
+
+IonSeries* XLinkIonSeriesCache::getXLinkablePeptideIonSeries(
+ XLinkablePeptide& xpep,
+ int charge
+ ) {
+
+ IonSeries* ans = NULL;
+ int xpep_idx = xpep.getIndex();
+
+ if (xpep_idx == -1) {
+ //carp(CARP_DEBUG, "Unindexed xlinkable peptide. Returning NULL");
+ return NULL;
+ } else {
+
+ bool decoy = xpep.isDecoy();
+ //carp(CARP_INFO, "decoy %i pep_idx %i charge %i", decoy, xpep_idx, charge);
+ vector<vector<IonSeries*> >* ion_cache = &target_xlinkable_ion_series_;
+ if (decoy) {
+ ion_cache = &decoy_xlinkable_ion_series_;
+ //carp(CARP_INFO, "Getting decoy cache");
+ }
+
+ int charge_idx = charge-1;
+ //carp(CARP_INFO, "getting pepidx:%i",xpep_idx);
+ while(ion_cache->size() <= xpep_idx) {
+ //carp(CARP_INFO, "Adding vector<IonSeries*>():%d", ion_cache->size());
+ ion_cache->push_back(vector<IonSeries*>());
+ }
+
+ vector<IonSeries*>& level1 = (*ion_cache)[xpep_idx];
+
+ if (level1.size() == 0) {
+ IonSeries* ion_series1 = new IonSeries(getXCorrIonConstraint(1), 1);
+ ion_series1->update(xpep.getSequence(), xpep.getModifiedSequencePtr());
+ ion_series1->predictIons();
+ //carp(CARP_INFO, "charge1:%d",ion_series1->getNumIons());
+ level1.push_back(ion_series1);
+ IonSeries* ion_series2 = new IonSeries();
+ IonSeries::copy(ion_series1, ion_series2, false);
+ ion_series2->setCharge(2);
+ ion_series2->setIonConstraint(getXCorrIonConstraint(2));
+ level1.push_back(ion_series2);
+
+ }
+ while(level1.size() <= charge_idx) {
+ IonSeries* next_series = new IonSeries();
+ IonSeries* current_series = level1.back();
+ int next_charge = current_series->getCharge()+1;
+
+ IonSeries::copy(current_series, next_series, false);
+ //carp(CARP_INFO, "copy src:%d dest:%d", current_series->getNumIons(), next_series->getNumIons());
+ next_series->setCharge(next_charge);
+ next_series->setIonConstraint(getXCorrIonConstraint(next_charge));
+
+ for (IonIterator ion_iter = level1[0]->begin();
+ ion_iter != level1[0]->end();
+ ++ion_iter) {
+ Ion* newIon = Ion::newIon();
+ Ion::copy(*ion_iter, newIon, (*ion_iter)->getPeptideSequence());
+ FLOAT_T ion_mass = newIon->getMassFromMassZ();
+ newIon->setCharge(next_charge-1);
+ newIon->setMassZFromMass(ion_mass);
+ next_series->addIon(newIon);
+ }
+ /*
+ IonSeries* test_series = new IonSeries(getXCorrIonConstraint(next_charge), next_charge);
+ test_series->update(xpep.getSequence(), xpep.getModifiedSequencePtr());
+ test_series->predictIons();
+ carp(CARP_INFO, "charge:%d next:%d test:%d", next_charge, next_series->getNumIons(), test_series->getNumIons());
+ delete test_series;
+
+ for (IonIterator iter = test_series->begin();
+ iter != test_series->end();
+ ++iter) {
+ //carp(CARP_INFO, "charge:%d", (*iter)->getCharge());
+ }
+ */
+ level1.push_back(next_series);
+ }
+
+ ans = level1[charge_idx];
+ if (ans == NULL) {
+ carp(CARP_FATAL, "Null ion series?");
+ } else {
+ //carp(CARP_INFO, "using cached ions");
+ }
+ }
+ return ans;
+
+}
+
+IonConstraint* XLinkIonSeriesCache::getXCorrIonConstraint(
+ int charge
+ ) {
+
+ int charge_idx = charge - 1;
+
+ while(xcorr_ion_constraint_.size() <= charge_idx) {
+ xcorr_ion_constraint_.push_back(IonConstraint::newIonConstraintSmart(XCORR, (xcorr_ion_constraint_.size()+1)));
+ }
+ //carp(CARP_INFO, "returning ion_constraint");
+ return(xcorr_ion_constraint_[charge_idx]);
+
+}
+
+
+
+void XLinkIonSeriesCache::finalize() {
+ for (size_t xpep_idx = 0;xpep_idx < target_xlinkable_ion_series_.size(); xpep_idx++) {
+
+ vector<IonSeries*> &level1 = target_xlinkable_ion_series_[xpep_idx];
+ for (size_t charge_idx=0;charge_idx < level1.size(); charge_idx++) {
+ if (level1[charge_idx]) {
+ IonSeries::freeIonSeries(level1[charge_idx]);
+ }
+ }
+ }
+
+ for (size_t xpep_idx = 0;xpep_idx < decoy_xlinkable_ion_series_.size(); xpep_idx++) {
+ vector<IonSeries*>& level1 = decoy_xlinkable_ion_series_[xpep_idx];
+ for (size_t charge_idx=0;charge_idx < level1.size(); charge_idx++) {
+ if (level1[charge_idx]) {
+ IonSeries::freeIonSeries(level1[charge_idx]);
+ }
+ }
+ }
+
+ for (size_t charge_idx=0;charge_idx < xcorr_ion_constraint_.size();charge_idx++) {
+ IonConstraint::free(xcorr_ion_constraint_[charge_idx]);
+ }
+
+}
diff --git a/src/app/xlink/XLinkIonSeriesCache.h b/src/app/xlink/XLinkIonSeriesCache.h
new file mode 100644
index 0000000..5f2802e
--- /dev/null
+++ b/src/app/xlink/XLinkIonSeriesCache.h
@@ -0,0 +1,29 @@
+
+#include "model/IonSeries.h"
+#include "XLinkablePeptide.h"
+#include "model/IonConstraint.h"
+
+#include <vector>
+
+class XLinkIonSeriesCache {
+
+ protected:
+
+ //key is: xpep.getIndex(), charge
+ static std::vector<std::vector<IonSeries*> > target_xlinkable_ion_series_;
+ static std::vector<std::vector<IonSeries*> > decoy_xlinkable_ion_series_;
+
+ static std::vector<IonConstraint*> xcorr_ion_constraint_;
+
+ public:
+
+ static IonSeries* getXLinkablePeptideIonSeries(
+ XLinkablePeptide& xpep,
+ int charge
+ );
+
+ static IonConstraint* getXCorrIonConstraint(int charge);
+
+ static void finalize();
+
+};
diff --git a/src/app/xlink/XLinkMatch.cpp b/src/app/xlink/XLinkMatch.cpp
new file mode 100644
index 0000000..1625289
--- /dev/null
+++ b/src/app/xlink/XLinkMatch.cpp
@@ -0,0 +1,398 @@
+/**
+ * \file XLinkMatch.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Object for Defining a Match in an xlink search
+ *****************************************************************************/
+#include "XLinkMatch.h"
+
+#include "parameter.h"
+#include "model/Scorer.h"
+#include "util/GlobalParams.h"
+#include <sstream>
+#include <ios>
+#include <iomanip>
+#include <iostream>
+#include "XLinkPeptide.h"
+#include "XLinkablePeptide.h"
+#include "io/OutputFiles.h"
+using namespace std;
+
+/**
+ * Constructor for XLinkMatch
+ */
+XLinkMatch::XLinkMatch() : Match() {
+ cached_sequence_ = "";
+ parent_ = NULL;
+ pvalue_= 1;
+ for (int idx = 0;idx < NUMBER_MASS_TYPES;idx++) {
+ mass_calculated_[idx] = false;
+ mass_[idx] = 0;
+ }
+ is_decoy_ = false;
+}
+
+/**
+ * Default destrcutor for XLinkMatch
+ */
+XLinkMatch::~XLinkMatch() {
+ //TODO deleted cached ions
+}
+
+void XLinkMatch::decrementPointerCount() {
+
+ pointer_count_--;
+}
+
+/**
+ * computes the pvalue for this match using the provided weibull paramters
+ */
+void XLinkMatch::computeWeibullPvalue(
+ FLOAT_T shift, ///< shift parameter for weibull
+ FLOAT_T eta, ///< eta parameter for weibull
+ FLOAT_T beta ///< beta parameter for weibull
+ ) {
+
+ pvalue_ = compute_weibull_pvalue(getScore(XCORR), eta, beta, shift);
+}
+
+void XLinkMatch::setPValue(FLOAT_T pvalue) {
+ pvalue_ = pvalue;
+}
+
+FLOAT_T XLinkMatch::getPValue() {
+
+ return(pvalue_);
+
+}
+
+/**
+ * \returns the protein id string for this match
+ * default, can be overridden
+ */
+string XLinkMatch::getProteinIdString() {
+ Crux::Peptide* peptide = this -> getPeptide(0);
+
+ if (peptide == NULL) {
+ return string("");
+ } else {
+ return XLink::get_protein_ids_locations(peptide);
+ }
+}
+
+/**
+ *\returns the protein id for this match
+ */
+string XLinkMatch::getProteinIdXString() {
+ Crux::Peptide* peptide = this -> getPeptide(0);
+ if (peptide == NULL) {
+ return string("");
+ } else {
+ return XLink::get_protein_ids_locations(peptide);
+ }
+
+}
+
+string XLinkMatch::getUnshuffledSequence() {
+ Crux::Peptide* peptide = this->getPeptide(0);
+ if (peptide == NULL) {
+ return string("");
+ } else {
+ return peptide->getUnshuffledSequence();
+ }
+}
+
+
+/**
+ *\returns the flanking amino acids for the match
+ */
+string XLinkMatch::getFlankingAAString() {
+ Crux::Peptide* peptide = this -> getPeptide(0);
+
+ string ans("");
+
+ if (peptide != NULL) {
+ char* flanking_aas = peptide->getFlankingAAs();
+ ans = flanking_aas;
+ free(flanking_aas);
+ }
+ return ans;
+}
+
+/**
+ * \returns the candidate type from a string value
+ */
+XLINKMATCH_TYPE_T XLinkMatch::getCandidateType(std::string& candidate) {
+// cerr << "get candidate type:"<<candidate<<endl;
+ if (candidate == string("linear")) {
+ return LINEAR_CANDIDATE;
+ } else if (candidate == string("dead-link")) {
+ return DEADLINK_CANDIDATE;
+ } else if (candidate == string("self-loop")) {
+ return SELFLOOP_CANDIDATE;
+ } else if (candidate == string("xlink-inter")) {
+ return XLINK_INTER_CANDIDATE;
+ } else if (candidate == string("xlink-intra")) {
+ return XLINK_INTRA_CANDIDATE;
+ } else if (candidate == string("xlink-inter-intra")) {
+ return XLINK_INTER_INTRA_CANDIDATE;
+ } else {
+ return INVALID_CANDIDATE;
+ }
+
+}
+
+/**
+ *\returns the string value for the candidate tyoe of the match
+ */
+string XLinkMatch::getCandidateTypeString() {
+ return getCandidateTypeString(getCandidateType());
+}
+
+const string& XLinkMatch::getSequenceStringConst() {
+ if (cached_sequence_ == "") {
+ cached_sequence_ = getSequenceString();
+ }
+ return(cached_sequence_);
+}
+
+
+/**
+ *\returns the string value of the given candidate type
+ */
+string XLinkMatch::getCandidateTypeString(
+ XLINKMATCH_TYPE_T candidate ///< candidate type to convert
+ ) {
+
+ string ans = "";
+ switch(candidate) {
+ case LINEAR_CANDIDATE:
+ ans = "linear";
+ break;
+ case DEADLINK_CANDIDATE:
+ ans = "dead-link";
+ break;
+ case SELFLOOP_CANDIDATE:
+ ans = "self-loop";
+ break;
+ case XLINK_INTER_CANDIDATE:
+ ans = "xlink-inter";
+ break;
+ case XLINK_INTRA_CANDIDATE:
+ ans = "xlink-intra";
+ break;
+ case XLINK_INTER_INTRA_CANDIDATE:
+ ans = "xlink-inter-intra";
+ break;
+ default:
+ ans = "unknown";
+ }
+
+ return ans;
+
+
+}
+
+vector<IonConstraint*> XLinkMatch::ion_constraint_xcorr_;
+
+IonConstraint* XLinkMatch::getIonConstraintXCORR(int charge) {
+ int idx = charge-1;
+ while(ion_constraint_xcorr_.size() < charge) {
+ ion_constraint_xcorr_.push_back(NULL);
+ }
+ if (ion_constraint_xcorr_[idx] == NULL) {
+ ion_constraint_xcorr_[idx] =
+ IonConstraint::newIonConstraintSmart(XCORR, charge);
+ } else {
+ // carp(CARP_INFO, "IonConstraint cache hit!");
+ }
+ return(ion_constraint_xcorr_[idx]);
+}
+
+IonSeries* XLinkMatch::getIonSeriesXCORR(int charge) {
+
+ int idx = charge-1;
+ while(ion_series_xcorr_.size() < charge) {
+ ion_series_xcorr_.push_back(NULL);
+ }
+
+ if (ion_series_xcorr_[idx] == NULL) {
+ IonSeries* ion_series_xcorr = new IonSeries(getIonConstraintXCORR(charge), charge);
+ predictIons(ion_series_xcorr, charge);
+ ion_series_xcorr_[idx] = ion_series_xcorr;
+ } else {
+ carp(CARP_INFO, "Cache hit!");
+ }
+
+ return(ion_series_xcorr_[idx]);
+
+}
+
+/**
+ * \returns the mass error in part-per-million (ppm)
+ */
+FLOAT_T XLinkMatch::getPPMError() {
+ FLOAT_T mono_mass = getMass(MONO);
+ FLOAT_T obs_mass = parent_->getSpectrumNeutralMass();
+ FLOAT_T isotope;
+
+ if (mono_mass > obs_mass) {
+ isotope = floor((mono_mass - obs_mass) / MASS_NEUTRON + 0.5);
+ } else {
+ isotope = -floor((obs_mass - mono_mass) / MASS_NEUTRON + 0.5);
+ }
+
+
+ obs_mass = obs_mass + isotope * MASS_NEUTRON;
+
+ FLOAT_T ppm = (mono_mass - obs_mass) / obs_mass * 1e6;
+ return ppm;
+
+}
+
+/**
+ * sets the XLinkMatchCollection owner of the match
+ */
+void XLinkMatch::setParent(XLinkMatchCollection* parent) {
+ parent_ = parent;
+}
+
+const vector<XLinkMatch*>& XLinkMatch::getDecoys() {
+ decoys_.clear();
+ shuffle(decoys_);
+ return(decoys_);
+ /*
+ if (decoys_.size() == 0) {
+ shuffle(decoys_);
+ if (decoys_.size() == 0) {
+ carp(CARP_FATAL, "Can't get decoy(s) for XLinkMatch!");
+ }
+ } else {
+ carp(CARP_INFO, "XLinkMatch::Using cached decoys");
+ }
+
+ return(decoys_);
+ */
+}
+
+
+/**
+ * Print one field in the tab-delimited output file, based on column index.
+ */
+void XLinkMatch::printOneMatchField(
+ int column_idx, ///< Index of the column to print. -in
+ MatchCollection* collection, ///< collection holding this match -in
+ MatchFileWriter* output_file, ///< output stream -out
+ Crux::Spectrum* spectrum,
+ int num_target_matches, ///< target matches for this spectrum -in
+ int num_decoy_matches, ///< decoy matches for this spectrum -in
+ int b_y_total, ///< total b/y ions -in
+ int b_y_matched ///< Number of b/y ions matched. -in
+) {
+
+ carp(CARP_DETAILED_DEBUG, "XLinkMatch::printOneMatchField:%s", get_column_header(column_idx));
+
+ switch ((MATCH_COLUMNS_T)column_idx) {
+
+ case PEPTIDE_MASS_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, getMass(GlobalParams::getIsotopicMass()));
+ break;
+ case PVALUE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, pvalue_);
+ break;
+ case SEQUENCE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getSequenceStringConst());
+ break;
+ case PROTEIN_ID_COL:
+ output_file->setColumnCurrentRow(
+ (MATCH_COLUMNS_T)column_idx,
+ getProteinIdString());
+ break;
+ case FLANKING_AA_COL:
+ output_file->setColumnCurrentRow(
+ (MATCH_COLUMNS_T)column_idx,
+ getFlankingAAString());
+ break;
+ case XLINK_PRODUCT_TYPE_COL:
+ output_file->setColumnCurrentRow(
+ (MATCH_COLUMNS_T)column_idx,
+ getCandidateTypeString());
+ break;
+ case PPM_ERROR_COL:
+ output_file->setColumnCurrentRow(
+ (MATCH_COLUMNS_T)column_idx,
+ getPPMError());
+ break;
+ case XCORR_FIRST_COL:
+ if ((Params::GetInt("xlink-top-n") != 0) &&
+ (getCandidateType() == XLINK_INTER_CANDIDATE ||
+ getCandidateType() == XLINK_INTRA_CANDIDATE ||
+ getCandidateType() == XLINK_INTER_INTRA_CANDIDATE)) {
+ XLinkPeptide *xpep = (XLinkPeptide*)this;
+ XLinkablePeptide& lpep = xpep->getXLinkablePeptide(0);
+ output_file->setColumnCurrentRow(
+ (MATCH_COLUMNS_T)column_idx,
+ lpep.getXCorr());
+ } else {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, 0);
+ }
+ break;
+ case XCORR_SECOND_COL:
+ if ((Params::GetInt("xlink-top-n") != 0) &&
+ (getCandidateType() == XLINK_INTER_CANDIDATE ||
+ getCandidateType() == XLINK_INTRA_CANDIDATE ||
+ getCandidateType() == XLINK_INTER_INTRA_CANDIDATE)) {
+ XLinkPeptide *xpep = (XLinkPeptide*)this;
+ XLinkablePeptide& lpep = xpep->getXLinkablePeptide(1);
+ output_file->setColumnCurrentRow(
+ (MATCH_COLUMNS_T)column_idx,
+ lpep.getXCorr());
+ } else {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, 0);
+ }
+ break;
+ case PROTEIN_ID_X_COL:
+ output_file->setColumnCurrentRow(
+ (MATCH_COLUMNS_T)column_idx,
+ getProteinIdXString());
+ break;
+ case XLINK_TYPE_COL:
+ output_file->setColumnCurrentRow(
+ (MATCH_COLUMNS_T)column_idx,
+ getCandidateTypeString());
+ break;
+ case ORIGINAL_TARGET_SEQUENCE_COL:
+ if (null_peptide_ == true || Params::GetBool("concat")) {
+ string seq = getUnshuffledSequence();
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, seq);
+ }
+ break;
+ case MODIFICATIONS_COL:
+ //TODO FIX!
+ break;
+ case ENZ_INT_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, getNumMissedCleavages());
+ break;
+ default:
+ Match::printOneMatchField(column_idx,
+ collection,
+ output_file,
+ spectrum,
+ num_target_matches,
+ num_decoy_matches,
+ b_y_total,
+ b_y_matched
+ );
+ }
+}
+
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/xlink/XLinkMatch.h b/src/app/xlink/XLinkMatch.h
new file mode 100644
index 0000000..3f0e6e3
--- /dev/null
+++ b/src/app/xlink/XLinkMatch.h
@@ -0,0 +1,152 @@
+/**
+ * \file XLinkMatch.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Object for Defining a Match in an xlink search
+ *****************************************************************************/
+#ifndef XLINKMATCH_H_
+#define XLINKMATCH_H_
+
+#include "util/crux-utils.h"
+#include "XLink.h"
+#include "XLinkMatchCollection.h"
+#include <string>
+#include "model/Match.h"
+#include "util/CacheableMass.h"
+
+class XLinkMatch : public Crux::Match, public CacheableMass {
+
+ protected:
+ XLinkMatchCollection* parent_; ///< Owner of this match
+ FLOAT_T pvalue_; ///< p-value of the match
+
+ std::vector<IonSeries*> ion_series_xcorr_;
+ std::vector<IonSeries*> ion_series_sp_;
+ std::vector<XLinkMatch*> decoys_;
+ std::string cached_sequence_;
+
+ static std::vector<IonConstraint*> ion_constraint_xcorr_;
+ static IonConstraint* getIonConstraintXCORR(int charge);
+
+ bool is_decoy_;
+
+ public:
+
+ /**
+ * Constructor for XLinkMatch()
+ */
+ XLinkMatch();
+
+ /**
+ * Default destructor for XLinkMatch
+ */
+ virtual ~XLinkMatch();
+
+ virtual XLINKMATCH_TYPE_T getCandidateType() = 0;
+ virtual int getNumMissedCleavages() = 0;
+ virtual bool isModified() = 0;
+ virtual std::string getSequenceString() = 0;
+ virtual void shuffle(std::vector<XLinkMatch*>& decoys) = 0;
+
+ virtual void predictIons(IonSeries* ion_series, int charge) = 0;
+ virtual std::string getIonSequence(Ion* ion) = 0;
+ virtual Crux::Peptide* getPeptide(int peptide_idx) = 0;
+
+ const std::string& getSequenceStringConst();
+ const std::vector<XLinkMatch*>& getDecoys();
+
+ virtual IonSeries* getIonSeriesXCORR(int charge);
+
+
+ std::string getCandidateTypeString();
+
+
+ void decrementPointerCount();
+
+ /**
+ * computes the pvalue for this match using the provided weibull paramters
+ */
+ void computeWeibullPvalue(
+ FLOAT_T shift, ///< shift parameter for weibull
+ FLOAT_T eta, ///< eta parameter for weibull
+ FLOAT_T beta ///< beta parameter for weibull
+ );
+
+ FLOAT_T getPValue();
+
+ void setPValue(
+ FLOAT_T pvalue
+ );
+
+ /**
+ * \returns the mass error in part-per-million (ppm)
+ */
+ FLOAT_T getPPMError();
+
+ /**
+ * sets the XLinkMatchCollection owner of the match
+ */
+ void setParent(XLinkMatchCollection* parent);
+
+ /**
+ * \returns the protein id string for this match
+ */
+ virtual std::string getProteinIdString();
+
+ /**
+ * \returns the protein id string for this match. In the case
+ * of a xlinked peptide, reportes the position in the protein
+ */
+ virtual std::string getProteinIdXString();
+
+ /**
+ *\returns the flanking amino acids for the match
+ */
+ virtual std::string getFlankingAAString();
+
+ /**
+ *\returns unshuffled version of the sequence
+ */
+ virtual std::string getUnshuffledSequence();
+
+
+ /**
+ * Print one field in the tab-delimited output file, based on column index.
+ * overridden from Match
+ */
+ virtual void printOneMatchField(
+ int column_idx, ///< Index of the column to print. -in
+ MatchCollection* collection, ///< collection holding this match -in
+ MatchFileWriter* output_file, ///< output stream -out
+ Crux::Spectrum* spectrum,
+ int num_target_matches, ///< target matches in spectrum -in
+ int num_decoy_matches, ///< decoy matches (if any) for this spectrum -in
+ int b_y_total, ///< total b/y ions -in
+ int b_y_matched ///< Number of b/y ions matched. -in
+ );
+
+ /**
+ *\returns the string value of the given candidate type
+ */
+ static std::string getCandidateTypeString(
+ XLINKMATCH_TYPE_T candidate ///< candidate
+ );
+
+ /**
+ * \returns the candidate type from a string value
+ */
+ static XLINKMATCH_TYPE_T getCandidateType(
+ std::string& candidate ///< candidate in string format
+ );
+
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkMatchCollection.cpp b/src/app/xlink/XLinkMatchCollection.cpp
new file mode 100644
index 0000000..6a74964
--- /dev/null
+++ b/src/app/xlink/XLinkMatchCollection.cpp
@@ -0,0 +1,444 @@
+/**
+ * \file XLinkMatchCollection.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Collection of possible xlink products
+ *****************************************************************************/
+
+#include "XLinkMatchCollection.h"
+#include "XLinkPeptide.h"
+#include "LinearPeptide.h"
+#include "SelfLoopPeptide.h"
+#include "XLinkScorer.h"
+
+#include "model/Spectrum.h"
+#include "util/GlobalParams.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+#include <iostream>
+
+
+static const FLOAT_T MIN_XCORR_SHIFT = -5.0;
+static const FLOAT_T MAX_XCORR_SHIFT = 5.0;
+//#define CORR_THRESHOLD 0.995 // Must achieve this correlation, else punt.
+static const FLOAT_T CORR_THRESHOLD = 0.5;
+static const FLOAT_T XCORR_SHIFT = 0.05;
+
+using namespace std;
+
+void get_min_max_mass(
+ FLOAT_T precursor_mz,
+ SpectrumZState& zstate,
+ int isotope,
+ FLOAT_T window,
+ WINDOW_TYPE_T precursor_window_type,
+ FLOAT_T& min_mass,
+ FLOAT_T& max_mass,
+ FLOAT_T& precursor_mass) {
+
+ //cerr <<"mz: "
+ // <<precursor_mz
+ // <<" charge:"
+ // <<charge
+ // <<" mass:"<<mass
+ // <<" window:"<<window<<endl;
+
+ precursor_mass = zstate.getNeutralMass() + (double)isotope*MASS_NEUTRON;
+
+ if (precursor_window_type == WINDOW_MASS) {
+ //cerr<<"WINDOW_MASS"<<endl;
+ min_mass = precursor_mass - window;
+ max_mass = precursor_mass + window;
+ } else if (precursor_window_type == WINDOW_MZ) {
+ //cerr<<"WINDOW_MZ"<<endl;
+ double min_mz = precursor_mz - window;
+ double max_mz = precursor_mz + window;
+ min_mass = (min_mz - MASS_PROTON) * (double)zstate.getCharge();
+ max_mass = (max_mz - MASS_PROTON) * (double)zstate.getCharge();
+ } else if (precursor_window_type == WINDOW_PPM) {
+ //cerr<<"WINDOW_PPM"<<endl;
+ min_mass = precursor_mass * (1.0 - window * 1e-6);
+ max_mass = precursor_mass * (1.0 + window * 1e-6);
+ }
+
+ //cerr<<"min:"<<min_mass<<" "<<"max: "<<max_mass<<endl;
+
+}
+
+void get_min_max_mass(
+ FLOAT_T precursor_mz,
+ SpectrumZState& zstate,
+ int isotope,
+ bool use_decoy_window,
+ FLOAT_T& min_mass,
+ FLOAT_T& max_mass,
+ FLOAT_T& precursor_mass) {
+
+ if (use_decoy_window) {
+ get_min_max_mass(precursor_mz,
+ zstate,
+ isotope,
+ Params::GetDouble("precursor-window-weibull"),
+ string_to_window_type(Params::GetString("precursor-window-type-weibull")),
+ min_mass,
+ max_mass, precursor_mass);
+ } else {
+ get_min_max_mass(precursor_mz,
+ zstate,
+ isotope,
+ GlobalParams::getPrecursorWindow(),
+ GlobalParams::getPrecursorWindowType(),
+ min_mass,
+ max_mass,
+ precursor_mass);
+ }
+}
+
+/**
+ * Default constructor
+ */
+XLinkMatchCollection::XLinkMatchCollection() : MatchCollection() {
+ carp(CARP_DEBUG, "XLinkMatchCollection():start");
+ scan_ = 0;
+}
+
+/**
+ * Copy constructor
+ */
+XLinkMatchCollection::XLinkMatchCollection(
+ XLinkMatchCollection& vector ///<collection to copy
+ ) : MatchCollection() {
+
+ carp(CARP_DEBUG, "XLinkMatchCollection(XLinkMatchCollection):start");
+ precursor_mz_ = vector.precursor_mz_;
+ zstate_ = vector.zstate_;
+ scan_ = vector.scan_;
+
+ for (int idx = 0; idx < vector.getMatchTotal(); idx++) {
+ XLinkMatch* currentCandidate = (XLinkMatch*)vector[idx];
+ XLinkMatch* copyCandidate = NULL;
+ switch (currentCandidate -> getCandidateType()) {
+ case LINEAR_CANDIDATE:
+ case DEADLINK_CANDIDATE:
+ copyCandidate =
+ new LinearPeptide(*(LinearPeptide*)currentCandidate);
+ break;
+ case SELFLOOP_CANDIDATE:
+ copyCandidate =
+ new SelfLoopPeptide(*(SelfLoopPeptide*)currentCandidate);
+ break;
+ case XLINK_INTER_CANDIDATE:
+ case XLINK_INTRA_CANDIDATE:
+ case XLINK_INTER_INTRA_CANDIDATE:
+ copyCandidate =
+ new XLinkPeptide(*(XLinkPeptide*)currentCandidate);
+ break;
+ case INVALID_CANDIDATE:
+ carp(CARP_ERROR, "Invalid candidate type.");
+ exit(1);
+ }
+ add(copyCandidate);
+ }
+
+
+}
+
+/**
+ * Constructor that finds all possible candidates
+ */
+/*
+XLinkMatchCollection::XLinkMatchCollection() {
+
+ carp(CARP_DEBUG, "XLinkMatchCollection(...)");
+
+ FLOAT_T min_mass = Params::GetDouble("min-mass");
+ FLOAT_T max_mass = Params::GetDouble("max-mass");
+
+ addCandidates(
+ NULL,
+ 0,
+ 1,
+ min_mass,
+ max_mass,
+ false);
+
+}
+*/
+
+/**
+ * Constructor that finds all candidates within a mass range
+ */
+void XLinkMatchCollection::addCandidates(
+ Crux::Spectrum *spectrum,
+ FLOAT_T precursor_mass,
+ int precursor_charge,
+ FLOAT_T min_mass, ///< min mass
+ FLOAT_T max_mass, ///< max mass
+ bool decoy
+ ) {
+
+ //carp(CARP_INFO, "XLinkMatchCollection.addCandidates() start");
+
+ include_linear_peptides_ = Params::GetBool("xlink-include-linears");
+ include_self_loops_ = Params::GetBool("xlink-include-selfloops");
+
+ if (GlobalParams::getXLinkIncludeInter() ||
+ GlobalParams::getXLinkIncludeIntra() ||
+ GlobalParams::getXLinkIncludeInterIntra()) {
+ int num_xlink_candidates = 0;
+ carp(CARP_DEBUG, "Adding xlink candidates");
+ carp(CARP_DEBUG, "precursor:%g", precursor_mass);
+ carp(CARP_DEBUG, "min:%g", min_mass);
+ carp(CARP_DEBUG, "max:%g", max_mass);
+ num_xlink_candidates = XLinkPeptide::addCandidates(
+ spectrum,
+ precursor_mass,
+ precursor_charge,
+ min_mass,
+ max_mass,
+ decoy,
+ *this);
+ carp(CARP_DETAILED_DEBUG,"Number of xlink candidates:%d", num_xlink_candidates);
+ if (num_xlink_candidates == 0 && Params::GetBool("require-xlink-candidate")) {
+ carp(CARP_DEBUG, "no xlink candidate, returning");
+ return;
+ }
+
+ }
+ if (include_linear_peptides_) {
+
+ LinearPeptide::addCandidates(
+ min_mass,
+ max_mass,
+ decoy,
+ *this);
+
+ }
+
+ if (include_self_loops_) {
+
+ SelfLoopPeptide::addCandidates(
+ min_mass,
+ max_mass,
+ decoy,
+ *this);
+ }
+}
+
+
+/**
+ * Constructor for finding all candidates within a mass range
+ */
+XLinkMatchCollection::XLinkMatchCollection(
+ Crux::Spectrum *spectrum, ///< spectrum
+ SpectrumZState& zstate, ///< z-state
+ bool decoy,
+ bool use_decoy_window
+ ) {
+
+ carp(CARP_DEBUG, "Inside XLinkMatchCollection....");
+
+ precursor_mz_ = spectrum->getPrecursorMz();
+ setZState(zstate);
+
+
+ FLOAT_T min_mass;
+ FLOAT_T max_mass;
+ const vector<int>& isotopes = GlobalParams::getIsotopeWindows();
+ for (int idx = 0; idx < isotopes.size();idx++) {
+ FLOAT_T precursor_mass;
+ get_min_max_mass(precursor_mz_, zstate, isotopes[idx], use_decoy_window, min_mass, max_mass, precursor_mass);
+ carp(CARP_DEBUG, "isotope %i precursor: %g min:%g max:%g", isotopes[idx], precursor_mass, min_mass, max_mass);
+ addCandidates(spectrum, precursor_mass, zstate.getCharge(),
+ min_mass, max_mass, decoy);
+ }
+}
+
+/**
+ * adds a candidate to the list
+ */
+void XLinkMatchCollection::add(
+ XLinkMatch* candidate, ///< candidate to add
+ bool copy
+ ) {
+
+ candidate->setZState(zstate_);
+ candidate->setParent(this);
+ addMatch(candidate);
+ if (!copy) {
+ candidate->decrementPointerCount();
+ }
+ experiment_size_++;
+
+}
+
+void XLinkMatchCollection::add(
+ const vector<XLinkMatch*>& candidates,
+ bool copy
+ ) {
+
+ for (size_t idx = 0;idx < candidates.size();idx++) {
+ //carp(CARP_INFO, "Adding %s", candidates.at(idx)->getSequenceString().c_str());
+ add(candidates.at(idx), copy);
+ }
+
+}
+
+/**
+ * \returns a candidate from the list by index
+ */
+XLinkMatch* XLinkMatchCollection::at(
+ int idx ///< index of the candidate
+ ) {
+ if (idx < 0 || idx >= getMatchTotal()) {
+ carp(CARP_FATAL, "XLinkMatchCollection:index %d out of bounds (0,%d)",
+ idx, getMatchTotal());
+ }
+ return (XLinkMatch*)match_[idx];
+}
+
+/**
+ * \returns a candidate from the list by index
+ */
+XLinkMatch* XLinkMatchCollection::operator[] (
+ int idx ///< index of the candidate
+ ) {
+ return (XLinkMatch*)match_[idx];
+}
+
+
+/**
+ * shuffles the candidates and places the results in a decoy collection
+ */
+void XLinkMatchCollection::shuffle(
+ XLinkMatchCollection& decoy_vector ///< collection to add decoys to
+ ) {
+
+ decoy_vector.precursor_mz_ = precursor_mz_;
+ decoy_vector.zstate_ = zstate_;
+ decoy_vector.scan_ = scan_;
+
+ for (int idx = 0; idx < getMatchTotal(); idx++) {
+ decoy_vector.add(at(idx)->getDecoys());
+ }
+
+}
+
+/**
+ * scores all candidates against the spectrum
+ */
+void XLinkMatchCollection::scoreSpectrum(
+ Crux::Spectrum* spectrum ///< spectrum to score against
+ ) {
+
+ int max_ion_charge = get_max_ion_charge_parameter("max-ion-charge");
+
+ carp(CARP_DEBUG, "Creating scorer");
+ XLinkScorer scorer(
+ spectrum,
+ min(zstate_.getCharge(), max_ion_charge));
+
+ for (int idx = 0; idx < getMatchTotal(); idx++) {
+ carp(CARP_DEBUG, "Scoring candidate:%d", idx);
+ scorer.scoreCandidate(at(idx));
+ }
+
+ // set the match_collection as having been scored
+ scored_type_[XCORR] = true;
+ if (Params::GetBool("compute-sp")) {
+ scored_type_[SP] = true;
+ }
+
+ carp(CARP_DEBUG, "Done scoreSpectrum");
+}
+
+/**
+ * fits a weibull to the collection
+ */
+void XLinkMatchCollection::fitWeibull() {
+
+ //create the array of x's and
+ shift_ = 0;
+ eta_ = 0;
+ beta_ = 0;
+ correlation_ = 0;
+
+ FLOAT_T* xcorrs = extractScores(XCORR);
+// reverse sort the scores
+
+ std::sort(xcorrs, xcorrs + getMatchTotal(), greater<FLOAT_T>());
+
+ double fraction_to_fit = Params::GetDouble("fraction-top-scores-to-fit");
+ int num_tail_samples = (int)(getMatchTotal() * fraction_to_fit);
+
+ fit_three_parameter_weibull(xcorrs,
+ num_tail_samples,
+ getMatchTotal(),
+ MIN_XCORR_SHIFT,
+ MAX_XCORR_SHIFT,
+ XCORR_SHIFT,
+ CORR_THRESHOLD,
+ &eta_,
+ &beta_,
+ &shift_,
+ &correlation_);
+
+ free(xcorrs);
+
+}
+
+/**
+ * computes the p-value for the candidate
+ */
+void XLinkMatchCollection::computeWeibullPValue(
+ int idx ///< candidate
+ ) {
+
+ at(idx)->computeWeibullPvalue(shift_, eta_, beta_);
+}
+
+/**
+ * sets the scan for the collection
+ */
+void XLinkMatchCollection::setScan(
+ unsigned int scan ///< scan number to set
+ ) {
+ scan_ = scan;
+}
+
+/**
+ *\returns the scan number
+ */
+unsigned int XLinkMatchCollection::getScan() {
+ return scan_;
+}
+
+/**
+ *\returns the charge state of the collection
+ */
+int XLinkMatchCollection::getCharge() {
+ return zstate_.getCharge();
+}
+
+/**
+ *\returns the precursor m/z
+ */
+FLOAT_T XLinkMatchCollection::getPrecursorMZ() {
+ return precursor_mz_;
+}
+
+/**
+ * \returns the neutral mass of the collection
+ */
+FLOAT_T XLinkMatchCollection::getSpectrumNeutralMass() {
+ return zstate_.getNeutralMass();
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/xlink/XLinkMatchCollection.h b/src/app/xlink/XLinkMatchCollection.h
new file mode 100644
index 0000000..0934136
--- /dev/null
+++ b/src/app/xlink/XLinkMatchCollection.h
@@ -0,0 +1,169 @@
+/**
+ * \file XLinkMatchCollection.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Collection of possible xlink products
+ *****************************************************************************/
+#ifndef XLINKMATCHCOLLECTION_H_
+#define XLINKMATCHCOLLECTION_H_
+
+/* Crux Includes */
+#include "model/objects.h"
+#include "model/MatchCollection.h"
+#include "model/Database.h"
+#include "model/Spectrum.h"
+#include "util/modifications.h"
+#include "model/SpectrumZState.h"
+
+/* XLink Includes */
+#include "XLink.h"
+#include "XLinkMatch.h"
+
+class XLinkMatchCollection : public MatchCollection {
+ protected:
+
+ bool include_linear_peptides_; ///< Include linear peptides
+ bool include_self_loops_; ///< include self loops
+ int scan_; ///< scan number of the collection
+ FLOAT_T precursor_mz_; ///< precursor m/z
+ Crux::Spectrum* spectrum_; ///< spectrum object
+
+ /**
+ * Adds all of the possible candidates given the mass range
+ */
+ void addCandidates(
+ Crux::Spectrum *spectrum, ///<spectrum
+ FLOAT_T precursor_mass, ///< precursor mass
+ int precursor_charge,
+ FLOAT_T min_mass, ///< minimum mass
+ FLOAT_T max_mass, ///< maximum mass
+ bool decoy ///< decoys?
+ );
+
+ public:
+
+ /**
+ * Default constructor
+ */
+ XLinkMatchCollection();
+
+ /**
+ * Copy constructor
+ */
+ XLinkMatchCollection(
+ XLinkMatchCollection& vector ///< match collection to copy
+ );
+
+ /**
+ * Constructor for finding all candidates within a mass range
+ */
+ XLinkMatchCollection(
+ Crux::Spectrum* spectrum, ///< Spectrum
+ SpectrumZState& zstate, ///< z-state
+ bool decoy,
+ bool use_decoy_window = false ///< decoys?
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual ~XLinkMatchCollection() {}
+
+ /**
+ * adds a candidate to the list
+ */
+ void add(XLinkMatch* candidate, bool copy = false);
+
+ void add(
+ const vector<XLinkMatch*>& candidates,
+ bool copy = false
+ );
+
+ /**
+ *\returns a candidate from the list by index
+ */
+ XLinkMatch* operator[] (
+ int idx ///< index
+ );
+
+ /**
+ *\returns a candidate from the list by index
+ */
+ XLinkMatch* at(
+ int idx ///< index
+ );
+
+ /**
+ * shuffles the candidates and places the results in a decoy collection
+ */
+ void shuffle(
+ XLinkMatchCollection& decoy_vector ///< collection to add decoys to
+ );
+
+ /**
+ * scores all candidates against the spectrum
+ */
+ void scoreSpectrum(
+ Crux::Spectrum* spectrum ///< spectrum to score against
+ );
+
+ /**
+ * sets the ranks for the candidates
+ */
+ void setRanks();
+
+ /**
+ * fits a weibull to the xcorrs in the collection
+ */
+ void fitWeibull();
+
+ FLOAT_T getEta() {return eta_;}
+ FLOAT_T getBeta() {return beta_;}
+ FLOAT_T getShift() {return shift_;}
+ FLOAT_T getCorrelation() {return correlation_;}
+
+
+ /**
+ * computes the p-values for the candidate
+ */
+ void computeWeibullPValue(
+ int idx ///< candidate index
+ );
+
+ /**
+ * sets the scan for the collection
+ */
+ void setScan(
+ unsigned int scan ///< scan number to set
+ );
+
+ /**
+ * \returns the scan number
+ */
+ unsigned int getScan();
+
+ /**
+ * \returns the charge state of the collection
+ */
+ int getCharge();
+
+ /**
+ * \returns the precursor m/z
+ */
+ FLOAT_T getPrecursorMZ();
+
+ /**
+ * \returns the neutral mass of the collection
+ */
+ FLOAT_T getSpectrumNeutralMass();
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkPeptide.cpp b/src/app/xlink/XLinkPeptide.cpp
new file mode 100644
index 0000000..071229d
--- /dev/null
+++ b/src/app/xlink/XLinkPeptide.cpp
@@ -0,0 +1,726 @@
+/**
+ * \file XLinkPeptide.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September 2014
+ * \brief Object for Defining a crosslinked peptide in an xlink search
+ *****************************************************************************/
+#include "XLinkPeptide.h"
+#include "model/ModifiedPeptidesIterator.h"
+#include "model/IonSeries.h"
+#include "model/Ion.h"
+#include "util/Params.h"
+#include "util/GlobalParams.h"
+#include "XLinkDatabase.h"
+#include "XLinkablePeptideIterator.h"
+#include "XLinkablePeptideIteratorTopN.h"
+
+#include <iostream>
+#include <sstream>
+
+using namespace std;
+
+FLOAT_T XLinkPeptide::linker_mass_ = 0;
+set<Crux::Peptide*> XLinkPeptide::allocated_peptides_;
+FLOAT_T XLinkPeptide::pmin_ = 0;
+bool XLinkPeptide::pmin_set_ = false;
+
+XLinkPeptide::XLinkPeptide() : XLinkMatch() {
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+ target_ = NULL;
+}
+
+/**
+ * Constructor using two linkable peptide objects and locations
+ */
+XLinkPeptide::XLinkPeptide(
+ XLinkablePeptide& peptideA, ///< 1st peptide
+ XLinkablePeptide& peptideB, ///< 2nd peptide
+ int posA, ///<link pos1
+ int posB ///<link pos2
+ ) : XLinkMatch() {
+
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+
+ linked_peptides_.push_back(peptideA);
+ linked_peptides_.push_back(peptideB);
+ link_pos_idx_.push_back(posA);
+ link_pos_idx_.push_back(posB);
+
+ doSort();
+
+}
+
+/**
+ * Constructor for using two string peptides and locations
+ */
+XLinkPeptide::XLinkPeptide(
+ char* peptideA, ///< sequence of peptide1
+ char* peptideB, ///< sequence of peptide2
+ int posA, ///< position of crosslink in peptide1
+ int posB ///< position of crosslink in peptide2
+ ) : XLinkMatch() {
+
+ mass_calculated_[MONO] = false;
+ mass_calculated_[AVERAGE] = false;
+
+ XLinkablePeptide A(peptideA);
+ linked_peptides_.push_back(A);
+ XLinkablePeptide B(peptideB);
+ linked_peptides_.push_back(B);
+ A.addLinkSite(posA);
+ link_pos_idx_.push_back(0);
+ B.addLinkSite(posB);
+ link_pos_idx_.push_back(0);
+ doSort();
+}
+
+
+/**
+ * makes sure that sequence1 is smaller in alphanumeric value than
+ * sequence 2
+ */
+void XLinkPeptide::doSort() {
+
+ string seq1 = linked_peptides_[0].getModifiedSequenceString();
+
+ string seq2 = linked_peptides_[1].getModifiedSequenceString();
+
+
+ if (seq1 > seq2) {
+
+ //swap peptides
+ swap(linked_peptides_[0], linked_peptides_[1]);
+ //swap links
+ swap(link_pos_idx_[0], link_pos_idx_[1]);
+ }
+
+ seq1 = linked_peptides_[0].getModifiedSequenceString();
+
+ seq2 = linked_peptides_[1].getModifiedSequenceString();
+
+ assert(seq1 <= seq2);
+
+
+
+}
+
+/**
+ * sets the static linker mass variable
+ */
+void XLinkPeptide::setLinkerMass(
+ FLOAT_T linker_mass ///< linker mass
+ ) {
+ linker_mass_ = linker_mass;
+}
+
+/**
+ * \returns the linker mass
+ */
+FLOAT_T XLinkPeptide::getLinkerMass() {
+ return linker_mass_;
+}
+
+/**
+ * \returns the link position within each peptide
+ */
+int XLinkPeptide::getLinkPos(
+ int peptide_idx ///< 0 - first peptide, 1 - second peptide
+ ) {
+
+ return linked_peptides_.at(peptide_idx).getLinkSite(link_pos_idx_.at(peptide_idx));
+}
+
+int XLinkPeptide::getLinkIdx(
+ int peptide_idx ///< 0 - first peptide, 1 -second peptide
+ ) {
+ return link_pos_idx_[peptide_idx];
+}
+
+bool XLinkPeptide::isDecoy() {
+
+ return linked_peptides_.at(0).isDecoy() || linked_peptides_.at(1).isDecoy();
+
+}
+
+
+/**
+ * \returns whether the cross-link is from peptides from two different
+ * proteins
+ */
+bool XLinkPeptide::isInter() {
+ return XLink::isCrossLinkInter(linked_peptides_.at(0).getPeptide(), linked_peptides_.at(1).getPeptide());
+}
+
+/**
+ * \returns whether the cross-link is from peptides within the same protein
+ */
+bool XLinkPeptide::isIntra() {
+ return XLink::isCrossLinkInter(linked_peptides_[0].getPeptide(), linked_peptides_[1].getPeptide());
+}
+
+/**
+ * \returns whether the cross-link is from peptides that are both within the same protein and from different proteins
+ */
+bool XLinkPeptide::isInterIntra() {
+ return(isInter() && isIntra());
+}
+
+
+
+/***
+ * adds crosslink candidates by iterating through all possible masses
+ */
+int XLinkPeptide::addCandidates(
+ Crux::Spectrum* spectrum,
+ FLOAT_T precursor_mass,
+ int precursor_charge,
+ FLOAT_T min_mass, ///< min mass of crosslink
+ FLOAT_T max_mass, ///< max mass of crosslinks
+ bool decoy,
+ XLinkMatchCollection& candidates ///< candidates in/out
+ ) {
+
+ carp(CARP_DEBUG, "XLinkPeptide::addCandidates - precursor:%g", precursor_mass);
+ carp(CARP_DEBUG, "XLinkPeptide::addCandidates - min:%g", min_mass);
+ carp(CARP_DEBUG, "XLinkPeptide::addCandidates - max:%g", max_mass);
+
+ if (!pmin_set_) {
+ pmin_ = XLinkDatabase::getXLinkableBegin()->getMass(GlobalParams::getIsotopicMass());
+ pmin_set_ = true;
+ }
+ FLOAT_T peptide1_min_mass = pmin_;
+ FLOAT_T peptide1_max_mass = max_mass-pmin_-linker_mass_;
+
+ carp(CARP_DEBUG, "peptide1_min:%g", peptide1_min_mass);
+ carp(CARP_DEBUG, "peptide1_max:%g", peptide1_max_mass);
+
+ if (GlobalParams::getXLinkTopN() > 0) {
+ vector<XLinkablePeptide> xlinkable_peptides;
+ XLinkablePeptideIteratorTopN xlp_iter(spectrum,
+ precursor_mass,
+ peptide1_min_mass,
+ peptide1_max_mass,
+ precursor_charge,
+ decoy);
+ while(xlp_iter.hasNext()) {
+ xlinkable_peptides.push_back(xlp_iter.next());
+ }
+ sort(xlinkable_peptides.begin(), xlinkable_peptides.end(), compareXLinkablePeptideMass);
+ carp(CARP_DEBUG, "get xcorr");
+ for (size_t idx =0;idx<xlinkable_peptides.size();idx++) {
+ carp(CARP_DEBUG, "%f", xlinkable_peptides[idx].getXCorr());
+ }
+ return(addCandidates(min_mass, max_mass, xlinkable_peptides, candidates));
+ } else {
+ return(addCandidates(min_mass, max_mass, XLinkDatabase::getXLinkablePeptides(decoy), candidates));
+ }
+}
+
+int XLinkPeptide::addXLinkPeptides(
+ XLinkablePeptide& pep1,
+ XLinkablePeptide& pep2,
+ XLinkMatchCollection& candidates
+ ) {
+
+ XLinkBondMap& bondmap = XLinkDatabase::getXLinkBondMap();
+ int num_candidates = 0;
+ //for every linkable site, generate the candidate if it is legal.
+ for (unsigned int link1_idx=0;link1_idx < pep1.numLinkSites(); link1_idx++) {
+ for (unsigned int link2_idx=0;link2_idx < pep2.numLinkSites();link2_idx++) {
+ if (bondmap.canLink(pep1, pep2, link1_idx, link2_idx)) {
+ //create the candidate
+ XLinkMatch* newCandidate =
+ new XLinkPeptide(pep1, pep2, link1_idx, link2_idx);
+ candidates.add(newCandidate);
+ num_candidates++;
+ }
+ }
+ }
+ return(num_candidates);
+}
+
+/**
+ * adds crosslink candidates to the XLinkMatchCollection using
+ * the passed in iterator for the 1st peptide
+ */
+int XLinkPeptide::addCandidates(
+ FLOAT_T min_mass, ///< min mass of crosslinks
+ FLOAT_T max_mass, ///< max mass of crosslinks
+ vector<XLinkablePeptide>& linkable_peptides,
+ XLinkMatchCollection& candidates ///< candidates -in/out
+ ) {
+
+ bool include_inter = GlobalParams::getXLinkIncludeInter();
+ bool include_intra = GlobalParams::getXLinkIncludeIntra();
+ bool include_inter_intra = GlobalParams::getXLinkIncludeInterIntra();
+
+ int max_mod_xlink = GlobalParams::getMaxXLinkMods();
+
+ size_t xpeptide_count = linkable_peptides.size();
+ if (xpeptide_count <= 0) { return 0;}
+
+ int num_candidates = 0;
+
+ bool done = false;
+
+ for (size_t pep_idx1=0;pep_idx1 < xpeptide_count-1;pep_idx1++) {
+ XLinkablePeptide& pep1 = linkable_peptides.at(pep_idx1);
+ carp(CARP_DEBUG, "pep_idx1:%d %d %f %s",
+ pep_idx1,
+ xpeptide_count-1,
+ linkable_peptides[pep_idx1].getMassConst(MONO),
+ pep1.getModifiedSequenceString().c_str()
+ );
+ FLOAT_T pep1_mass = pep1.getMassConst(MONO);
+ FLOAT_T pep2_min_mass = min_mass - pep1_mass - linker_mass_;
+ FLOAT_T pep2_max_mass = max_mass - pep1_mass - linker_mass_;
+ int start_idx2 = pep_idx1+1;
+
+ if (pep1_mass + linker_mass_ + linkable_peptides[start_idx2].getMassConst(MONO) > max_mass) {
+ break;
+ }
+ for (size_t pep_idx2=start_idx2;pep_idx2 < xpeptide_count;pep_idx2++) {
+
+ XLinkablePeptide& pep2 = linkable_peptides[pep_idx2];
+ carp(CARP_DEBUG, "pep_idx2:%d %d %f %s",
+ pep_idx2,
+ xpeptide_count,
+ linkable_peptides[pep_idx2].getMassConst(MONO),
+ pep2.getModifiedSequenceString().c_str()
+ );
+ FLOAT_T current_mass = pep2.getMassConst(MONO);
+ if (current_mass > pep2_max_mass) {
+ if (pep_idx2 == start_idx2) {
+ //done = true;
+ }
+ break;
+ }
+ if (current_mass >= pep2_min_mass) {
+ XLINKMATCH_TYPE_T ctype =
+ XLink::getCrossLinkCandidateType(pep1.getPeptide(), pep2.getPeptide());
+
+ if ((include_intra && ctype == XLINK_INTRA_CANDIDATE) ||
+ (include_inter_intra && ctype == XLINK_INTER_INTRA_CANDIDATE) ||
+ (include_inter && ctype == XLINK_INTER_CANDIDATE)) {
+ carp(CARP_DEBUG, "considering %s %s", pep1.getModifiedSequenceString().c_str(), pep2.getModifiedSequenceString().c_str());
+
+ int mods = pep1.getPeptide()->countModifiedAAs() + pep2.getPeptide()->countModifiedAAs();
+ if (mods <= max_mod_xlink) {
+ carp(CARP_DEBUG, "considering2 %s %s", pep1.getModifiedSequenceString().c_str(), pep2.getModifiedSequenceString().c_str());
+ num_candidates += addXLinkPeptides(pep1, pep2, candidates);
+ } // if (mods <= max_mod_xlink ..
+ }
+
+ }
+ }
+ if (done) {
+ break;
+ }
+
+ }
+
+ carp(CARP_DEBUG, "Done searching");
+// delete []tested;
+ return(num_candidates);
+}
+
+
+
+
+/**
+ * \returns the candidate type
+ */
+XLINKMATCH_TYPE_T XLinkPeptide::getCandidateType() {
+
+ return(XLink::getCrossLinkCandidateType(linked_peptides_.at(0).getPeptide(), linked_peptides_.at(1).getPeptide()));
+
+}
+
+/**
+ * \returns the sequence string
+ */
+string XLinkPeptide::getSequenceString() {
+
+ doSort();
+
+ string seq1 = linked_peptides_[0].getModifiedSequenceString();
+
+ string seq2 = linked_peptides_[1].getModifiedSequenceString();
+
+
+
+
+ //assert(seq1 <= seq2);
+
+ ostringstream oss;
+ oss << seq1 << ", " <<
+ seq2 << " (" <<
+ (getLinkPos(0)+1) << "," <<
+ (getLinkPos(1)+1) << ")";
+
+ string svalue = oss.str();
+
+ return svalue;
+}
+
+string XLinkPeptide::getUnshuffledSequence() {
+
+ if (is_decoy_) {
+ if (target_ == NULL) {
+ carp(CARP_FATAL, "null target?!?");
+ }
+ return(target_ -> getSequenceString());
+ } else {
+ return (getSequenceString());
+ }
+}
+
+
+/**
+ * \returns the mass of the xlink peptide
+ */
+FLOAT_T XLinkPeptide::calcMass(MASS_TYPE_T mass_type) {
+ return linked_peptides_[0].getMassConst(mass_type) +
+ linked_peptides_[1].getMassConst(mass_type) +
+ linker_mass_;
+}
+
+/**
+ * \returns a shuffled xlink peptide
+ */
+
+void XLinkPeptide::shuffle(vector<XLinkMatch*>& decoys) {
+
+ //cerr<<"tt:"<<getSequenceString()<<endl;
+
+ XLinkablePeptide d1 = linked_peptides_[0].shuffle();
+ XLinkablePeptide d2 = linked_peptides_[1].shuffle();
+
+ XLinkPeptide* decoy_ff = new XLinkPeptide();
+ decoy_ff->linked_peptides_.push_back(d1);
+ decoy_ff->linked_peptides_.push_back(d2);
+ decoy_ff->link_pos_idx_.push_back(link_pos_idx_[0]);
+ decoy_ff->link_pos_idx_.push_back(link_pos_idx_[1]);
+ decoy_ff->is_decoy_ = true;
+ decoy_ff->target_ = this;
+ decoy_ff->setZState(getZState());
+
+ //cerr<<"decoy_ff:"<<decoy_ff->getSequenceString()<<endl;
+
+ XLinkPeptide* decoy_tf = new XLinkPeptide();
+ decoy_tf->linked_peptides_.push_back(linked_peptides_[0]);
+ decoy_tf->linked_peptides_.push_back(d2);
+ decoy_tf->link_pos_idx_.push_back(link_pos_idx_[0]);
+ decoy_tf->link_pos_idx_.push_back(link_pos_idx_[1]);
+ decoy_tf->is_decoy_ = true;
+ decoy_tf->target_ = this;
+ decoy_tf->setZState(getZState());
+
+ //cerr <<"decoy_tf:"<<decoy_tf->getSequenceString()<<endl;
+
+ XLinkPeptide* decoy_ft = new XLinkPeptide();
+ decoy_ft->linked_peptides_.push_back(d1);
+ decoy_ft->linked_peptides_.push_back(linked_peptides_[1]);
+ decoy_ft->link_pos_idx_.push_back(link_pos_idx_[0]);
+ decoy_ft->link_pos_idx_.push_back(link_pos_idx_[1]);
+ decoy_ft->is_decoy_ = true;
+ decoy_ft->target_ = this;
+ decoy_ft->setZState(getZState());
+
+ //cerr <<"decoy_ft:"<<decoy_ft->getSequenceString()<<endl;
+
+ decoys.push_back(decoy_ff);
+ decoys.push_back(decoy_tf);
+ decoys.push_back(decoy_ft);
+}
+
+/**
+ * fills the ion series with the predicted ions for the cross linked candidate
+ */
+void XLinkPeptide::predictIons(
+ IonSeries* ion_series, ///< IonSeries object to fill
+ int charge, ///< charge state of candidate
+ bool first ///< is this the first peptide?
+ ) {
+ carp(CARP_DEBUG, "predictIons:start %i %i", charge, first?1:0);
+
+ MASS_TYPE_T fragment_mass_type = GlobalParams::getFragmentMass();
+
+ if (first) {
+ linked_peptides_[0].predictIons(
+ ion_series, charge, getLinkIdx(0),
+ linker_mass_ + linked_peptides_[0].getMassConst(fragment_mass_type));
+ } else {
+ linked_peptides_[1].predictIons(
+ ion_series, charge, getLinkIdx(1),
+ linker_mass_ + linked_peptides_[1].getMassConst(fragment_mass_type));
+ }
+}
+
+/**
+ * predicts the ions for xlinked peptide
+ */
+void XLinkPeptide::predictIons(
+ IonSeries* ion_series, ///< IonSeries to fill
+ int charge ///< charge state of the peptide
+ ) {
+
+ MASS_TYPE_T fragment_mass_type = GlobalParams::getFragmentMass();
+ FLOAT_T delta_mass0 = linked_peptides_[0].getMassConst(fragment_mass_type) + linker_mass_;
+ FLOAT_T delta_mass1 = linked_peptides_[1].getMassConst(fragment_mass_type) + linker_mass_;
+
+ //predict the ion_series of the first peptide.
+ linked_peptides_[0].predictIons(ion_series, charge, getLinkIdx(0), delta_mass1, true);
+
+ //predict the ion_series of the second peptide.
+ linked_peptides_[1].predictIons(ion_series, charge, getLinkIdx(1), delta_mass0, false);
+}
+
+/**
+ * \returns the sequence from the ion
+ */
+string XLinkPeptide::getIonSequence(
+ Ion* ion ///< pointer to the ion
+ ) {
+
+ int peptide_idx = 0;
+
+ string ion_sequence = ion->getPeptideSequence();
+
+ if (ion_sequence == linked_peptides_[0].getSequence()) {
+ peptide_idx = 0;
+ } else {
+ peptide_idx = 1;
+ }
+
+ unsigned int cleavage_idx = ion->getCleavageIdx();
+
+ bool is_linked = false;
+
+ if (ion->isForwardType()) {
+ is_linked = (cleavage_idx > (unsigned int)getLinkPos(peptide_idx));
+ } else {
+ is_linked = (cleavage_idx >= (ion_sequence.length() - getLinkPos(peptide_idx)));
+ }
+
+ string subseq;
+ if (ion->isForwardType()) {
+ subseq = ion_sequence.substr(0, cleavage_idx);
+ } else {
+ subseq = ion_sequence.substr(ion_sequence.length() - cleavage_idx, ion_sequence.length());
+ }
+
+ if (!is_linked) {
+ return subseq;
+ } else {
+ string ans;
+ if (peptide_idx == 0) {
+ const char* seq2 = linked_peptides_[1].getSequence();
+ ans = subseq + string(",") + string(seq2);
+ } else {
+ const char* seq1 = linked_peptides_[0].getSequence();
+ ans = string(seq1) + string(",") + subseq;
+ }
+ return ans;
+ }
+}
+
+/**
+ * \returns the Peptide object for the xlinked peptide
+ */
+Crux::Peptide* XLinkPeptide::getPeptide(
+ int peptide_idx ///< 0 or 1
+ ) {
+ return linked_peptides_[peptide_idx].getPeptide();
+}
+XLinkablePeptide& XLinkPeptide::getXLinkablePeptide(
+ int peptide_idx ///< 0 or 1
+ ) {
+ return linked_peptides_[peptide_idx];
+}
+
+/**
+ * \returns the number of missed cleavages for the cross-linked peptide
+ */
+int XLinkPeptide::getNumMissedCleavages() {
+
+ char missed_cleavage_link_site = 'K';
+ set<int> skip;
+
+ int link1_site = getLinkPos(0);
+ int link2_site = getLinkPos(1);
+
+ Crux::Peptide* pep1 = linked_peptides_[0].getPeptide();
+ Crux::Peptide* pep2 = linked_peptides_[1].getPeptide();
+
+ char *seq1 = pep1->getSequencePointer();
+ char *seq2 = pep2->getSequencePointer();
+
+ if (seq1[link1_site] == missed_cleavage_link_site) {
+ skip.insert(link1_site);
+ }
+
+ int missed1 = pep1->getMissedCleavageSites(skip);
+
+ skip.clear();
+
+ if (seq2[link2_site] == missed_cleavage_link_site) {
+ skip.insert(link2_site);
+ }
+
+ int missed2 = pep2->getMissedCleavageSites(skip);
+
+ return max(missed1, missed2);
+
+}
+
+/**
+ *\returns whether the cross-linked peptide is modified
+ */
+bool XLinkPeptide::isModified() {
+
+ return linked_peptides_[0].isModified() || linked_peptides_[1].isModified();
+}
+
+/**
+ *\returns the protein id string for the xlinked peptide
+ */
+string XLinkPeptide::getProteinIdString() {
+
+ doSort();
+
+ ostringstream oss;
+
+ Crux::Peptide* peptide = this -> getPeptide(0);
+ if (peptide == NULL) {
+ carp(CARP_FATAL, "XLinkPeptide : Null first peptide!");
+ }
+
+ vector<string> prot1 = peptide -> getProteinIds();
+ string prefix = "";
+ if (linked_peptides_[0].isDecoy()) {
+ prefix = Params::GetString("decoy-prefix");
+ }
+
+ oss << prefix << prot1[0];
+ for (size_t idx = 1 ; idx < prot1.size() ; idx++) {
+ oss << "," << prefix << prot1[idx];
+ }
+ oss << ";";
+
+ peptide = this -> getPeptide(1);
+
+ if (peptide == NULL) {
+ carp(CARP_FATAL, "XLinkPeptide : Null second peptide!");
+ }
+ vector<string> prot2 = peptide -> getProteinIds();
+ prefix = "";
+ if (linked_peptides_[1].isDecoy()) {
+ prefix = Params::GetString("decoy-prefix");
+ }
+ oss << prefix << prot2[0];
+ for (size_t idx = 1;idx < prot2.size() ; idx++) {
+ oss << "," << prefix << prot2[idx];
+ }
+
+ return oss.str();
+}
+
+/**
+ * \returns the protein id strings where the (X) is the position
+ * within the protein
+ */
+string XLinkPeptide::getProteinIdsXLocations(
+ int idx ///< peptide index (0 or 1)
+ ) {
+
+ Crux::Peptide* peptide = this ->getPeptide(idx);
+
+ ostringstream oss;
+
+ set<string> xlocations;
+
+ int link_pos = getLinkPos(idx);
+
+ for (PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter != peptide->getPeptideSrcEnd();
+ ++iter) {
+ PeptideSrc* peptide_src = *iter;
+ Crux::Protein* protein = peptide_src->getParentProtein();
+ string protein_id = protein->getIdPointer();
+ int peptide_loc = peptide_src->getStartIdx();
+ ostringstream protein_loc_stream;
+ protein_loc_stream << protein_id << "(" << (peptide_loc + link_pos) << ")";
+ xlocations.insert(protein_loc_stream.str());
+ }
+
+ set<string>::iterator result_iter = xlocations.begin();
+ string result_string = *result_iter;
+
+ while (++result_iter != xlocations.end()) {
+ result_string += "," + *result_iter;
+ }
+
+ return result_string;
+}
+
+/**
+ * \returns the protein id string where the (X)s are the positions in
+ * the proteins
+ */
+string XLinkPeptide::getProteinIdXString() {
+ doSort();
+
+ ostringstream oss;
+
+ oss << getProteinIdsXLocations(0);
+ oss << ";";
+ oss << getProteinIdsXLocations(1);
+ return oss.str();
+
+}
+
+/**
+ * \returns the flanking amino acids for both peptides, separated by ;
+ */
+string XLinkPeptide::getFlankingAAString() {
+
+ doSort();
+
+ ostringstream oss;
+
+ Crux::Peptide* peptide = this -> getPeptide(0);
+
+ if (peptide == NULL) {
+ carp(CARP_FATAL, "XLinkPeptide::getFlankingAAString() : Null first peptide!");
+ } else {
+
+ char* flanking_aas = peptide->getFlankingAAs();
+ oss << flanking_aas;
+ std::free(flanking_aas);
+ }
+
+ oss << ";";
+
+ peptide = this->getPeptide(1);
+
+ if (peptide == NULL) {
+ carp(CARP_FATAL, "XLinkPeptide::getFlankingAAString() : Null second peptide!");
+ } else {
+
+ char* flanking_aas = peptide->getFlankingAAs();
+ oss << flanking_aas;
+ std::free(flanking_aas);
+ }
+
+ return oss.str();
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkPeptide.h b/src/app/xlink/XLinkPeptide.h
new file mode 100644
index 0000000..4ecee3e
--- /dev/null
+++ b/src/app/xlink/XLinkPeptide.h
@@ -0,0 +1,252 @@
+/**
+ * \file XLinkPeptide.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September 2014
+ * \brief Object for Defining a crosslinked peptide in an xlink search
+ *****************************************************************************/
+#ifndef XLINKPEPTIDE_H_
+#define XLINKPEPTIDE_H_
+
+#include "model/objects.h"
+#include "util/utils.h"
+
+#include "XLinkMatch.h"
+#include "XLinkBondMap.h"
+#include "XLinkablePeptide.h"
+
+
+#include <set>
+#include <vector>
+
+class XLinkPeptide : public XLinkMatch {
+ protected:
+ static FLOAT_T linker_mass_; ///< contains the link mass
+ static std::set<Crux::Peptide*> allocated_peptides_; ///< tracks the peptides that have been allocated during the candidate finding step
+ std::vector<XLinkablePeptide> linked_peptides_; ///< contains the two peptides in the match
+ std::vector<int> link_pos_idx_; ///< contains the link positions for the two peptides
+
+ XLinkPeptide* target_;
+
+ static FLOAT_T pmin_; ///< contains the minimum mass that a peptide from a crosslink product can take
+ static bool pmin_set_; ///< has the pmin been set?
+ /**
+ * \returns the link position within each peptide
+ */
+ int getLinkPos(
+ int peptide_idx ///< 0 - first peptide, 1 - second peptide
+ );
+
+ /*
+ * Iterates through all linkable sites and adds valid xlink peptide candidates
+ * \returns the number of candidates added.
+ */
+ static int addXLinkPeptides(
+ XLinkablePeptide& pep1, ///< First linkable peptide
+ XLinkablePeptide& pep2, ///< Second linkable peptide
+ XLinkMatchCollection& candidates ///< XLinkable Candidates -out
+ );
+
+ virtual bool isDecoy();
+
+ public:
+
+ /**
+ * Default Constructor
+ */
+ XLinkPeptide();
+
+ /**
+ * Constructor using two linkable peptide objects and locations
+ */
+ XLinkPeptide(
+ XLinkablePeptide& peptideA, ///< 1st peptide
+ XLinkablePeptide& peptideB, ///< 2nd peptide
+ int posA, ///< link pos1
+ int posB ///<link pos2
+ );
+
+ /**
+ * Constructor for using two string peptides and locations
+ */
+ XLinkPeptide(
+ char* peptideA, ///< sequence of peptide1
+ char* peptideB, ///< sequence of peptide2
+ int posA, ///< position of crosslink in peptide1
+ int posB ///< position of crosslink in peptide2
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~XLinkPeptide() {}
+
+ /**
+ * makes sure that sequence1 is smaller in alphanumeric value than
+ * sequence 2
+ */
+ void doSort();
+
+ int getLinkIdx(
+ int peptide_idx ///< 0 - first peptide, 1 -second peptide
+ );
+
+
+
+ /**
+ * \returns whether the cross-link is from peptides from two different
+ * proteins
+ */
+ bool isInter();
+
+ /**
+ * \returns whether the cross-link is from peptides within the same protein
+ */
+ bool isIntra();
+
+ /**
+ * \returns whether the cross-link is from peptides that are both within the same protein and can be from different proteins
+ */
+ bool isInterIntra();
+
+
+
+ /**
+ * sets the static linker mass variable
+ */
+ static void setLinkerMass(
+ FLOAT_T linker_mass ///< linker mass
+ );
+
+ /**
+ * \returns the linker mass from the static variable
+ */
+ static FLOAT_T getLinkerMass();
+
+ /**
+ * adds crosslink candidates to the XLinkMatchCollection using
+ * the passed in iterator for the 1st peptide
+ */
+ static int addCandidates(
+ FLOAT_T min_mass, ///< min mass of crosslinks
+ FLOAT_T max_mass, ///< max mass of crosslinks
+ vector<XLinkablePeptide>&, ///< 1st peptide iterator
+ XLinkMatchCollection& candidates ///< candidates in/out
+ );
+
+ /**
+ * adds crosslink candidates by iterating through all possible masses
+ */
+ static int addCandidates(
+ Crux::Spectrum* spectrum,
+ FLOAT_T precursor_mass,
+ int precursor_charge,
+ FLOAT_T min_mass, ///< min mass of crosslinks
+ FLOAT_T max_mass, ///< max mass of crosslinks
+ bool decoy,
+ XLinkMatchCollection& candidates ///< candidates -in/out
+ );
+
+ /**
+ * \returns the candidate type
+ */
+ virtual XLINKMATCH_TYPE_T getCandidateType();
+
+ /**
+ * \returns the sequence string
+ */
+ virtual std::string getSequenceString();
+
+ virtual std::string getUnshuffledSequence();
+
+ /**
+ * \returns the mass of the xlink peptide
+ */
+ virtual FLOAT_T calcMass(
+ MASS_TYPE_T mass_type ///< MONO or AVERAGE
+ );
+
+ /**
+ * \returns a shuffled xlink peptide
+ */
+ virtual void shuffle(
+ std::vector<XLinkMatch*>& decoys
+ );
+
+ /**
+ * fills the ion series with the predicted ions for the cross linked candidate
+ */
+ virtual void predictIons(
+ IonSeries* ion_series, ///< IonSeries object to fill
+ int charge ///< charge state of the candidate
+ );
+
+ /**
+ * predicts the ions for xlinked peptide
+ */
+ void predictIons(
+ IonSeries* ion_series, ///< IonSeries to fill
+ int charge, ///< charge state of the peptide
+ bool first ///< is this the first peptide?
+ );
+
+ /**
+ * \returns the sequence from the ion
+ */
+ std::string getIonSequence(
+ Ion* ion ///< pointer to the ion object
+ );
+
+ /**
+ * \returns the Peptide object for the xlinked peptide
+ */
+ virtual Crux::Peptide* getPeptide(
+ int peptide_idx ///< 0 or 1
+ );
+
+ XLinkablePeptide& getXLinkablePeptide(
+ int peptide_idx ///<0 or 1
+ );
+ /**
+ * \returns the number of missed cleavages for the cross-linked peptide
+ */
+ virtual int getNumMissedCleavages();
+
+ /**
+ *\returns whether the cross-linked peptide is modified
+ */
+ virtual bool isModified();
+
+ /**
+ *\returns the protein id string for the xlinked peptide
+ */
+ virtual std::string getProteinIdString();
+
+ /**
+ * \returns the protein id strings where the (X) is the position
+ * within the protein
+ */
+ virtual std::string getProteinIdsXLocations(
+ int idx ///< peptide index (0 or 1)
+ );
+
+ /**
+ * \returns the protein id string where the (X)s are the positions in
+ * the proteins
+ */
+ virtual std::string getProteinIdXString();
+
+ /**
+ * \returns the flanking amino acids for both peptides, separated by ;
+ */
+ virtual std::string getFlankingAAString();
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkScorer.cpp b/src/app/xlink/XLinkScorer.cpp
new file mode 100644
index 0000000..fed5405
--- /dev/null
+++ b/src/app/xlink/XLinkScorer.cpp
@@ -0,0 +1,209 @@
+/**
+ * \file XLinkScorer.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Object for scoring xlink products. Tries to optimize the scoring time
+ *****************************************************************************/
+
+#include "XLinkScorer.h"
+#include "model/Scorer.h"
+#include "model/Ion.h"
+#include "model/IonSeries.h"
+#include "util/Params.h"
+#include "XLinkPeptide.h"
+#include "util/GlobalParams.h"
+
+
+#include <iostream>
+
+using namespace std;
+
+/**
+ * initializes the object with the spectrum
+ * charge and appropriate objects
+ */
+void XLinkScorer::init(
+ Crux::Spectrum* spectrum, ///< spectrum to score
+ int charge, ///< charge state
+ bool compute_sp ///< are we scoring sp?
+ ) {
+
+ scorer_xcorr_ = new Scorer(XCORR);
+ scorer_sp_ = new Scorer(SP);
+ spectrum_ = spectrum;
+ charge_ = charge;
+ compute_sp_ = compute_sp;
+
+ if ((spectrum_ != NULL) && (charge_ > 0)) {
+
+ ion_constraint_xcorr_ =
+ IonConstraint::newIonConstraintSmart(XCORR, charge_);
+
+ ion_constraint_sp_ =
+ IonConstraint::newIonConstraintSmart(SP, charge_);
+
+ ion_series_xcorr_ =
+ new IonSeries(ion_constraint_xcorr_, charge_);
+
+ ion_series_sp_ =
+ new IonSeries(ion_constraint_sp_, charge_);
+ } else {
+
+ ion_constraint_xcorr_ = NULL;
+ ion_constraint_sp_ = NULL;
+ ion_series_xcorr_ = NULL;
+ ion_series_sp_ = NULL;
+ }
+}
+
+IonConstraint* XLinkScorer::getIonConstraintXCorr() {
+ return ion_constraint_xcorr_;
+}
+
+
+
+
+/**
+ * default constructor
+ */
+XLinkScorer::XLinkScorer() {
+
+ init(NULL, 0, Params::GetBool("compute-sp"));
+}
+
+/**
+ * Constructor for spectrum and charge
+ */
+XLinkScorer::XLinkScorer(
+ Crux::Spectrum* spectrum, ///< spectrum to score
+ int charge ///< charge state
+ ) {
+
+ init(spectrum, charge, Params::GetBool("compute-sp"));
+}
+
+/**
+ * Constructor for spectrum, charge, and sp
+ */
+XLinkScorer::XLinkScorer(
+ Crux::Spectrum* spectrum, ///<spectrum to score
+ int charge, ///< charge state
+ bool compute_sp ///< computing sp as well?
+ ) {
+
+ init(spectrum, charge, compute_sp);
+}
+
+/**
+ * Destructor
+ */
+XLinkScorer::~XLinkScorer() {
+ //carp(CARP_INFO, "XLinkScorer::~XLinkScorer()");
+ delete ion_series_xcorr_;
+ delete ion_series_sp_;
+ delete ion_constraint_xcorr_;
+ delete ion_constraint_sp_;
+ delete scorer_xcorr_;
+ delete scorer_sp_;
+
+}
+
+/**
+ * \returns the xcorr score for the candidate and sets the sp if requested
+ */
+FLOAT_T XLinkScorer::scoreCandidate(
+ XLinkMatch* candidate ///< candidate to score
+ ) {
+
+ if (compute_sp_) {
+
+ candidate->predictIons(ion_series_sp_, charge_);
+ FLOAT_T sp = scorer_sp_->scoreSpectrumVIonSeries(spectrum_, ion_series_sp_);
+
+ candidate->setScore(SP, sp);
+ candidate->setScore(BY_IONS_MATCHED, scorer_sp_->getSpBYIonMatched());
+ candidate->setScore(BY_IONS_TOTAL, scorer_sp_->getSpBYIonPossible());
+
+ }
+ FLOAT_T xcorr = 0;
+ if (GlobalParams::getXLinkTopN() != 0 &&
+ (candidate->getCandidateType() == XLINK_INTER_CANDIDATE ||
+ candidate->getCandidateType() == XLINK_INTRA_CANDIDATE ||
+ candidate->getCandidateType() == XLINK_INTER_INTRA_CANDIDATE
+ )) {
+
+ XLinkPeptide* xpep = (XLinkPeptide*)candidate;
+ XLinkablePeptide& xpep1 = xpep->getXLinkablePeptide(0);
+ XLinkablePeptide& xpep2 = xpep->getXLinkablePeptide(1);
+ FLOAT_T link_mass = XLinkPeptide::getLinkerMass();
+ FLOAT_T mod_mass1 = xpep1.getMassConst(GlobalParams::getIsotopicMass()) + link_mass;
+ FLOAT_T mod_mass2 = xpep2.getMassConst(GlobalParams::getIsotopicMass()) + link_mass;
+ size_t link_idx1 = xpep->getLinkIdx(0);
+ size_t link_idx2 = xpep->getLinkIdx(1);
+
+ FLOAT_T xcorr1;
+ if (!xpep1.hasXCorr()) {
+ xcorr1 = scoreXLinkablePeptide(xpep1, link_idx1, mod_mass2);
+ xpep1.setXCorr(link_idx1, xcorr1);
+ } else {
+ xcorr1 = xpep1.getXCorr();
+ }
+
+ FLOAT_T xcorr2;
+ if (!xpep2.hasXCorr()) {
+ xcorr2 = scoreXLinkablePeptide(xpep2, link_idx2, mod_mass1);
+ xpep2.setXCorr(link_idx2, xcorr2);
+ } else {
+ xcorr2 = xpep2.getXCorr();
+ }
+
+ xcorr = xcorr1+xcorr2;
+ candidate->setScore(XCORR, xcorr);
+ } else {
+ candidate->predictIons(ion_series_xcorr_, charge_);
+ xcorr = scorer_xcorr_->scoreSpectrumVIonSeries(spectrum_, ion_series_xcorr_);
+ candidate->setScore(XCORR, xcorr);
+ }
+
+
+/*
+ if (candidate->getCandidateType() == XLINK_INTER_CANDIDATE || candidate->getCandidateType() == XLINK_INTRA_CANDIDATE) {
+ carp(CARP_DEBUG, "Scoring xlink peptides individually");
+ XLinkPeptide* xlink_match = (XLinkPeptide*)candidate;
+ carp(CARP_DEBUG, "ions first");
+ xlink_match->predictIons(ion_series_xcorr_, charge_, true);
+ carp(CARP_DEBUG, "scoring first");
+ FLOAT_T xcorr1 = scorer_xcorr_->scoreSpectrumVIonSeries(spectrum_, ion_series_xcorr_);
+ carp(CARP_DEBUG, "first:%f", xcorr1);
+ xlink_match->predictIons(ion_series_xcorr_, charge_, false);
+ carp(CARP_DEBUG, "scoring second");
+ FLOAT_T xcorr2 = scorer_xcorr_->scoreSpectrumVIonSeries(spectrum_, ion_series_xcorr_);
+ carp(CARP_DEBUG, "second:%f", xcorr2);
+ candidate->setScore(XCORR_FIRST, xcorr1);
+ candidate->setScore(XCORR_SECOND, xcorr2);
+ } else {
+
+ candidate->setScore(XCORR_FIRST, xcorr);
+ candidate->setScore(XCORR_SECOND, xcorr);
+ }
+ */
+ return xcorr;
+}
+
+FLOAT_T XLinkScorer::scoreXLinkablePeptide(
+ XLinkablePeptide& xlpeptide,
+ int link_idx,
+ FLOAT_T mod_mass) {
+
+ xlpeptide.predictIons(ion_series_xcorr_, charge_, link_idx, mod_mass);
+ FLOAT_T xcorr = scorer_xcorr_->scoreSpectrumVIonSeries(spectrum_, ion_series_xcorr_);
+ return xcorr;
+
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkScorer.h b/src/app/xlink/XLinkScorer.h
new file mode 100644
index 0000000..ff2f34d
--- /dev/null
+++ b/src/app/xlink/XLinkScorer.h
@@ -0,0 +1,87 @@
+/**
+ * \file XLinkScorer.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Object for scoring xlink products. Tries to optimize the scoring time
+ *****************************************************************************/
+
+#ifndef XLINKSCORER_H_
+#define XLINKSCORER_H_
+#include "model/objects.h"
+#include "XLinkMatch.h"
+
+class XLinkScorer {
+ protected:
+ Crux::Spectrum* spectrum_; ///< spectrum object
+ Scorer* scorer_xcorr_; ///< xcorr scorer object
+ Scorer* scorer_sp_; ///< sp scorer object
+ IonConstraint* ion_constraint_xcorr_; ///< xcorr constraint
+ IonConstraint* ion_constraint_sp_; ///< sp constraint
+ XLinkMatch* candidate_; ///< current candidate
+ int charge_; ///< current charege
+ IonSeries* ion_series_xcorr_; ///< current ion series xcorr
+ IonSeries* ion_series_sp_; ///< current ion series sp
+ bool compute_sp_; ///< calculate sp score
+
+ /**
+ * initializes the object with the spectrum
+ * charge and appropriate objects
+ */
+ void init(
+ Crux::Spectrum* spectrum, ///< spectrum to score
+ int charge, ///< charge state
+ bool compute_sp ///< are we scoring sp?
+ );
+
+ public:
+ /**
+ * default constructor
+ */
+ XLinkScorer();
+
+ /**
+ * Constructor for spectrum and charge
+ */
+ XLinkScorer(
+ Crux::Spectrum* spectrum, ///< spectrum to score
+ int charge ///< charge state
+ );
+
+ /**
+ * Constructor that allows compute sp to be set
+ */
+ XLinkScorer(
+ Crux::Spectrum* spectrum, ///spectrum to score
+ int charge, ///< charge state
+ bool compute_sp ///< scoring sp?
+ );
+
+ /**
+ * destructor, free up the objects
+ */
+ virtual ~XLinkScorer();
+
+ /**
+ * \returns the xcorr score and sets the xcorr and sp scores to the match
+ */
+ FLOAT_T scoreCandidate(XLinkMatch* candidate);
+
+ FLOAT_T scoreXLinkablePeptide(
+ XLinkablePeptide& xlpeptide,
+ int link_idx,
+ FLOAT_T mod_mass
+ );
+
+ IonConstraint* getIonConstraintXCorr();
+
+
+};
+
+
+#endif
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkSite.cpp b/src/app/xlink/XLinkSite.cpp
new file mode 100644
index 0000000..aef2828
--- /dev/null
+++ b/src/app/xlink/XLinkSite.cpp
@@ -0,0 +1,175 @@
+/*************************************************************************
+ * \file XLinkSite.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: Febuary 22, 2011
+ * \brief Object for representing cross-linkable site on a peptide.
+ ****************************************************************************/
+
+#include "XLinkSite.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * Default constructor
+ */
+XLinkSite::XLinkSite() {
+ type_ = XLINKSITE_UNKNOWN;
+ aa_ = 0;
+}
+
+/**
+ * Constructor that determines the type from the supplied site string
+ */
+XLinkSite::XLinkSite(
+ string& site_string ///<string describing the cross-linkable site
+ ) {
+
+ if (site_string == "cterm") {
+
+ type_ = XLINKSITE_CTERM;
+
+ } else if (site_string == "nterm") {
+
+ type_ = XLINKSITE_NTERM;
+
+ } else if (site_string == "*") {
+
+ type_ = XLINKSITE_ALL;
+
+ } else if (site_string.length() == 1) {
+
+ type_ = XLINKSITE_AA;
+ aa_ = site_string[0];
+
+ } else {
+
+ carp(CARP_FATAL, "Unknown link site:%s", site_string.c_str());
+ }
+}
+
+/**
+ * Default destructor
+ */
+XLinkSite::~XLinkSite() {
+}
+
+/**
+ * \returns whether the peptide contains this site at the supplied sequence index.
+ */
+bool XLinkSite::hasSite(
+ Peptide* peptide, ///<peptide object pointer
+ int idx ///<sequence index
+ ) const {
+
+ switch (type_) {
+ case XLINKSITE_CTERM:
+
+ if (idx == peptide->getLength() - 1) {
+ //cerr <<"Cterm peptide:"<<peptide->getSequence()<<" "<<idx<<":"<<(int)peptide->getLength()<<endl;
+ vector<PeptideSrc*>& srcs = peptide->getPeptideSrcVector();
+ for (size_t idx2 = 0 ; idx2 < srcs.size() ; idx2++ ) {
+ int start_idx = srcs[idx2]->getStartIdx();
+ //cerr << "start:"<<start_idx<<" "<<(start_idx+idx)<<" "<<srcs[idx2]->getParentProtein()->getLength()<<endl;
+
+
+ if ((idx + start_idx) >= srcs[idx2]->getParentProtein()->getLength()) {
+ return true;
+ }
+ }
+ }
+ return false;
+ break;
+ case XLINKSITE_NTERM:
+ if (idx == 0) {
+ vector<PeptideSrc*>& srcs = peptide->getPeptideSrcVector();
+ for (size_t idx = 0; idx < srcs.size(); idx++ ) {
+ if (srcs[idx]->getStartIdx() == 1) {
+ return true;
+ }
+ }
+ }
+ return false;
+ break;
+ case XLINKSITE_ALL:
+ return true;
+ break;
+ case XLINKSITE_AA:
+ return peptide->getSequencePointer()[idx] == aa_;
+ break;
+ case XLINKSITE_UNKNOWN:
+ default:
+ carp(CARP_FATAL, "Xlink site not set!");
+ }
+ return false;
+}
+
+bool XLinkSite::hasSite(
+ string& protein_sequence,
+ int idx) const {
+
+ switch(type_) {
+ case XLINKSITE_CTERM:
+ return idx == protein_sequence.length() - 1;
+ case XLINKSITE_NTERM:
+ return idx == 0;
+ break;
+ case XLINKSITE_ALL:
+ return true;
+ break;
+ case XLINKSITE_AA:
+ return protein_sequence.at(idx) == aa_;
+ break;
+ case XLINKSITE_UNKNOWN:
+ default:
+ carp(CARP_FATAL, "XLink site not set!");
+ }
+ return false;
+}
+
+/**
+ * \returns whether this xlinksite is equal to the passed in xlinksite
+ */
+bool XLinkSite::operator == (
+ XLinkSite& xlink_site_obj ///<XLinkSite to compare to
+ ) {
+
+ XLinkSite site1 = *this;
+ XLinkSite site2 = xlink_site_obj;
+
+ if (site1.type_ == site2.type_) {
+ if (site1.type_ == XLINKSITE_AA) {
+ return site1.aa_ == site2.aa_;
+ }
+ return true;
+ } else {
+ return false;
+ }
+}
+
+/**
+ * \returns whether this xlinksite is less than the passed in xlinksite
+ */
+bool XLinkSite::operator < (
+ const XLinkSite& xlink_site_obj ///<XLinkSite to compare to
+ ) const {
+
+ XLinkSite site1 = *this;
+ XLinkSite site2 = xlink_site_obj;
+
+ if (site1.type_ == site2.type_) {
+ if (site1.type_ == XLINKSITE_AA) {
+ return site1.aa_ < site2.aa_;
+ }
+ return false;
+ } else {
+ return site1.type_ < site2.type_;
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkSite.h b/src/app/xlink/XLinkSite.h
new file mode 100644
index 0000000..d14decb
--- /dev/null
+++ b/src/app/xlink/XLinkSite.h
@@ -0,0 +1,79 @@
+/**
+ * \file XLinkSite.h
+ * $Revision: 1.00 $
+ * \brief Object for representing a cross-linkable site on a peptide.
+ *********************************************************************/
+#ifndef XLINKSITE_H
+#define XLINKSITE_H
+
+#include <string>
+
+#include "model/Peptide.h"
+
+/**
+ * \class XLinkSite
+ * \brief object respresneting a cross-linkable site on a peptide.
+ */
+class XLinkSite {
+
+ protected:
+ XLINK_SITE_T type_; ///<The type of the cross-link
+ char aa_; ///<Amino acid type (for XLINKSITE_AA types).
+
+ public:
+
+ /**
+ * Default constructor
+ */
+ XLinkSite();
+
+ /**
+ * Default destructor
+ */
+ virtual ~XLinkSite();
+
+ /**
+ * Constructor that determines the type from the supplied site string
+ */
+ XLinkSite(
+ std::string& site_string ///<string desscribing the cross-linkable site
+ );
+
+ /**
+ * \returns whether the peptide contains this site at the supplied sequence index.
+ */
+ bool hasSite(
+ Crux::Peptide* peptide, ///<peptide object pointer
+ int idx ///<sequence index
+ ) const;
+
+
+ bool hasSite(
+ std::string& protein_sequence,
+ int idx
+ ) const;
+
+ /**
+ * \returns whether this xlinksite is equal to the passed in xlinksite
+ */
+ bool operator == (
+ XLinkSite& xlink_site_obj ///<XLinkSite to compare to
+ );
+
+ /**
+ * \returns whether this xlinksite is less than the passed in xlinksite
+ */
+ bool operator < (
+ const XLinkSite& xlink_site_obj ///<XLinkSite to compare to
+ ) const;
+
+};
+
+#endif
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/app/xlink/XLinkablePeptide.cpp b/src/app/xlink/XLinkablePeptide.cpp
new file mode 100644
index 0000000..6457790
--- /dev/null
+++ b/src/app/xlink/XLinkablePeptide.cpp
@@ -0,0 +1,742 @@
+/*************************************************************************
+ * \file XLinkablePeptide.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: Febuary 22, 2011
+ * \brief Object for finding and defining the link sites on a peptide.
+ ****************************************************************************/
+#include "XLinkablePeptide.h"
+
+#include "XLinkIonSeriesCache.h"
+
+#include "model/objects.h"
+#include "util/modifications.h"
+#include "util/Params.h"
+#include "util/GlobalParams.h"
+#include "model/Ion.h"
+#include "model/IonSeries.h"
+
+#include <iostream>
+
+#include "XLink.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * Initialize object
+ */
+void XLinkablePeptide::init() {
+ peptide_ = NULL;
+ sequence_ = NULL;
+ is_decoy_ = false;
+ link_sites_.clear();
+ xcorr_link_idx_ = -1;
+ predict_ions_call_count_ = 0;
+ index_ = -1;
+ mod_seq_ = NULL;
+}
+
+/**
+ * Default constructor
+ */
+XLinkablePeptide::XLinkablePeptide() {
+ init();
+}
+
+/**
+ * Constructor that defines the peptide as a sequence string
+ */
+XLinkablePeptide::XLinkablePeptide(
+ char* sequence ///< the peptide sequence
+ ) {
+ init();
+ sequence_ = sequence;
+ peptide_ = NULL;
+ is_decoy_ = false;
+}
+
+XLinkablePeptide::XLinkablePeptide(
+ const XLinkablePeptide& xlinkablepeptide
+ ) {
+ init();
+ peptide_ = xlinkablepeptide.peptide_->copyPtr();
+ is_decoy_ = xlinkablepeptide.is_decoy_;
+ link_sites_ = xlinkablepeptide.link_sites_;
+ xcorr_link_idx_ = xlinkablepeptide.xcorr_link_idx_;
+ xcorr_ = xlinkablepeptide.xcorr_;
+ index_ = xlinkablepeptide.index_;
+ for (size_t idx=0;idx<NUMBER_MASS_TYPES;idx++) {
+ if (xlinkablepeptide.mass_calculated_[idx]) {
+ mass_[idx] = xlinkablepeptide.mass_[idx];
+ mass_calculated_[idx] = true;
+ } else {
+ mass_calculated_[idx] = false;
+ }
+ }
+}
+
+XLinkablePeptide::XLinkablePeptide(
+ XLinkablePeptide& xlinkablepeptide
+) {
+ init();
+ peptide_ = xlinkablepeptide.peptide_->copyPtr();
+ is_decoy_ = xlinkablepeptide.is_decoy_;
+ link_sites_ = xlinkablepeptide.link_sites_;
+ xcorr_link_idx_ = xlinkablepeptide.xcorr_link_idx_;
+ xcorr_ = xlinkablepeptide.xcorr_;
+ index_ = xlinkablepeptide.index_;
+ for (size_t idx=0;idx<NUMBER_MASS_TYPES;idx++) {
+ if (xlinkablepeptide.mass_calculated_[idx]) {
+ mass_[idx] = xlinkablepeptide.mass_[idx];
+ mass_calculated_[idx] = true;
+ } else {
+ mass_calculated_[idx] = false;
+ }
+ }
+
+
+}
+
+/**
+ * Constructor that defines the peptide and the linking sites
+ */
+XLinkablePeptide::XLinkablePeptide(
+ Peptide* peptide, ///< the peptide object
+ vector<int>& link_sites ///< the linking sites
+ ) {
+ init();
+ peptide_ = peptide->copyPtr();
+
+ for (unsigned int idx = 0; idx < link_sites.size(); idx++) {
+ addLinkSite(link_sites[idx]);
+ }
+ is_decoy_ = false;
+}
+
+/**
+ * Constructor that generates the possible linking sites
+ * on the peptide using the bondmap object
+ */
+XLinkablePeptide::XLinkablePeptide(
+ Peptide* peptide, ///< the peptide object
+ XLinkBondMap& bondmap, ///< the bond map
+ int additional_cleavages
+ ) {
+ init();
+ peptide_ = peptide->copyPtr();
+ findLinkSites(peptide_, bondmap, link_sites_, additional_cleavages);
+}
+
+XLinkablePeptide::~XLinkablePeptide() {
+ //cerr <<"XLinkablePeptide::~XLinkablePeptide"<<endl;
+ if (mod_seq_ != NULL) {
+ freeModSeq(mod_seq_);
+ }
+}
+
+
+/**
+ * \returns whether a link at this index in the sequence
+ * would prevent cleavage
+ */
+bool XLinkablePeptide::linkSeqPreventsCleavage(
+ int seq_idx) {
+
+ return linkSeqPreventsCleavage(peptide_, seq_idx);
+}
+
+bool XLinkablePeptide::linkSeqPreventsCleavage(
+ Peptide* peptide,
+ int seq_idx
+ ) {
+
+ if (seq_idx >= 0 && seq_idx < peptide->getLength()) {
+
+ if (isCleavageSite(peptide, seq_idx)) {
+
+ char aa = peptide->getSequencePointer()[seq_idx];
+
+ const string& xlink_prevents_cleavage = GlobalParams::getXLinkPreventsCleavage();
+ for (string::const_iterator i = xlink_prevents_cleavage.begin();
+ i != xlink_prevents_cleavage.end();
+ i++) {
+ if (*i == '*' || *i == aa) {
+ return true;
+ }
+ }
+ }
+ }
+ return false;
+}
+
+/**
+ * \returns whether the link site prevents enzymatic
+ * cleavage
+ */
+bool XLinkablePeptide::linkSitePreventsCleavage(
+ size_t link_site_idx
+ ) {
+
+ if (link_site_idx >= numLinkSites()) {
+ return false;
+ }
+
+ return linkSeqPreventsCleavage(getLinkSite(link_site_idx));
+}
+
+
+bool XLinkablePeptide::isMissedCleavageSite(
+ Peptide* peptide,
+ int seq_idx) {
+
+ if (seq_idx == peptide->getLength()-1) {
+ return false;
+ }
+ return isCleavageSite(peptide, seq_idx);
+}
+
+/**
+ * \returns whether the peptide is cleavable at this index
+ */
+bool XLinkablePeptide::isCleavageSite(
+ Peptide* peptide, ///< the peptide
+ int seq_idx ///< the sequence index
+ ) {
+
+ //TODO - make this work for every enzyme
+ if (seq_idx > peptide->getLength()-1) {
+ return false;
+ }
+
+ char* sequence = peptide->getSequencePointer();
+
+ if (sequence[seq_idx] == 'K' || sequence[seq_idx] == 'R') {
+ if (seq_idx == peptide->getLength()-1) {
+ return true;
+ } else {
+ return sequence[seq_idx+1] != 'P';
+ }
+ } else {
+ return false;
+ }
+
+}
+
+/**
+ * given a peptide and a XLinkBondMap object,
+ * generate the possible link sites
+ */
+void XLinkablePeptide::findLinkSites(
+ Peptide* peptide, ///< the peptide object -in
+ XLinkBondMap& bondmap, ///< the bond map -in
+ vector<int>& link_sites, ///< the found link sites -out
+ int additional_cleavages ///< 0 for xlink, 1 for self-loops
+ ) {
+
+ int missed_cleavages = getMissedCleavageSites(peptide);
+ int max_missed_cleavages = GlobalParams::getMissedCleavages() +
+ additional_cleavages; // +1 because a self loop can prevent two cleavages from happening
+
+ link_sites.clear();
+
+ //find all modifications that can prevent xlink.
+ AA_MOD_T** mod_list = NULL;
+ int total_mods = get_all_aa_mod_list(&mod_list);
+ vector<AA_MOD_T*> prevents_xlink;
+
+ for (int mod_idx = 0;mod_idx < total_mods; mod_idx++) {
+ if (aa_mod_get_prevents_xlink(mod_list[mod_idx])) {
+ prevents_xlink.push_back(mod_list[mod_idx]);
+ }
+ }
+
+ //scan through the sequence and find linkable sites.
+ MODIFIED_AA_T* mod_seq = peptide->getModifiedAASequence();
+ int length = peptide->getLength();
+
+ //scan the sequence for linkage sites.
+ for (int seq_idx=0;seq_idx < length;seq_idx++) {
+ if (bondmap.canLink(peptide, seq_idx)) {
+
+ bool link_prevented = false;
+ // 1st test, make sure that we don't link at the c-terminus
+ // if the xlink prevents cleavage and the c-terminus is
+ // a cleavage point.
+ if ((seq_idx == length-1) &&
+ linkSeqPreventsCleavage(peptide, seq_idx)) {
+ link_prevented = true;
+ }
+
+ //2nd test, make sure that there isn't a modification that
+ //prevents the cross-link
+ if (!link_prevented) {
+ //check if the modification prevents xlink.
+ for (unsigned int mod_idx = 0; mod_idx < prevents_xlink.size(); mod_idx++) {
+ //if aa is modified by any modification that can prevent
+ //cross-linking, then don't add the site as a link_site.
+ if (is_aa_modified(mod_seq[seq_idx], prevents_xlink[mod_idx])) {
+ link_prevented = true;
+ break;
+ }
+ }
+ }
+
+ //3rd test make sure that we are within the allowed
+ //number of missed cleavages
+ if (!link_prevented) {
+ //if a link occurs here and prevents a cleavage, then don't
+ //count the number of missed cleavages against the total number
+ //of missed cleavages
+ int total_missed_cleavages = missed_cleavages;
+ if (linkSeqPreventsCleavage(peptide, seq_idx)) {
+ total_missed_cleavages--;
+ }
+
+ if (total_missed_cleavages > max_missed_cleavages) {
+ link_prevented = true;
+ }
+ }
+ //passes all three tests, this is a linkable site.
+ if (!link_prevented) {
+ //if it is a linkable site, then add it to the list.
+ link_sites.push_back(seq_idx);
+ }
+ }
+ }
+ freeModSeq(mod_seq);
+}
+
+/**
+ * \returns the number of link sites on this peptide
+ */
+size_t XLinkablePeptide::numLinkSites() {
+ return link_sites_.size();
+}
+
+/**
+ * \returns whether this peptide is linkable or not
+ */
+bool XLinkablePeptide::isLinkable() {
+ return numLinkSites() > 0;
+}
+
+void XLinkablePeptide::setDecoy(bool is_decoy) {
+
+ is_decoy_ = is_decoy;
+}
+
+/**
+ * \returns whether the peptide is a decoy or not
+ */
+bool XLinkablePeptide::isDecoy() {
+ //return peptide_ -> isDecoy();
+ return is_decoy_;
+}
+
+/**
+ * \returns whether the peptide is linkable using the bond map
+ */
+bool XLinkablePeptide::isLinkable(
+ Peptide* peptide, ///< the peptide object
+ XLinkBondMap& bondmap ///< the bond map
+ ) {
+
+ vector<int> link_sites;
+ findLinkSites(peptide, bondmap, link_sites);
+ return link_sites.size() > 0;
+
+
+}
+
+/**
+ * \returns the number of missed cleavages in the linkable peptide
+ */
+int XLinkablePeptide::getMissedCleavageSites() {
+ return getMissedCleavageSites(peptide_);
+}
+
+int XLinkablePeptide::getMissedCleavageSites(
+ Peptide* peptide ///< the peptide
+) {
+ //TODO - change this to reflect modifications that
+ //prevent cleavage (i.e. deadlinks).
+ return peptide -> getMissedCleavageSites();
+}
+
+/**
+ * \returns the sequence index of a link site
+ */
+int XLinkablePeptide::getLinkSite(
+ int link_site_idx ///< the index of the link site
+ ) {
+
+ return link_sites_.at(link_site_idx);
+}
+
+/**
+ * Adds a link site by sequence index
+ * \returns the index of the added link site
+ */
+int XLinkablePeptide::addLinkSite(
+ int seq_idx ///< the sequence index of the link site
+ ) {
+ link_sites_.push_back(seq_idx);
+ return link_sites_.size()-1;
+}
+
+
+void XLinkablePeptide::clearSites() {
+ link_sites_.clear();
+}
+
+
+/**
+ * \returns the peptide object associated with this XLinkablePeptide
+ */
+Peptide* XLinkablePeptide::getPeptide() {
+ return peptide_;
+}
+
+/**
+ * \returns the mass of the xlinkable peptide
+ */
+FLOAT_T XLinkablePeptide::calcMass(
+ MASS_TYPE_T mass_type
+ ) {
+ if (peptide_ == NULL) {
+ return Peptide::calcSequenceMass(sequence_, mass_type);
+ } else {
+ return peptide_->calcModifiedMass(mass_type);
+ }
+}
+
+/**
+ * \returns an allocated sequence c-string. Must be freed
+ */
+const char* XLinkablePeptide::getSequence() {
+ if (peptide_ == NULL) {
+ return(sequence_);
+ } else {
+ return(peptide_->getSequence());
+ }
+}
+
+/**
+ * \returns the allocated modified sequence. Must be freed.
+ */
+MODIFIED_AA_T* XLinkablePeptide::getModifiedSequence() {
+ MODIFIED_AA_T* mod_seq = NULL;
+
+ if (peptide_ == NULL) {
+ convert_to_mod_aa_seq(sequence_, &mod_seq);
+ } else {
+ mod_seq = peptide_->getModifiedAASequence();
+ }
+
+ return mod_seq;
+}
+const MODIFIED_AA_T* XLinkablePeptide::getModifiedSequencePtr() {
+ if (mod_seq_ == NULL) {
+ mod_seq_ = getModifiedSequence();
+ } else {
+ }
+ return(mod_seq_);
+}
+
+int findLink(vector<int>& link_sites, int link_site) {
+
+ for (unsigned int idx = 0; idx < link_sites.size(); idx++) {
+ if (link_sites[idx] == link_site)
+ return idx;
+ }
+ return -1;
+
+}
+
+void doSwitch(vector<int>& link_sites, int siteA, int siteB) {
+ int siteA_link_idx = findLink(link_sites, siteA);
+ int siteB_link_idx = findLink(link_sites, siteB);
+
+ if (siteA_link_idx != -1 && siteB_link_idx != -1) {
+ int temp_idx = link_sites[siteA_link_idx];
+ link_sites[siteA_link_idx] = link_sites[siteB_link_idx];
+ link_sites[siteB_link_idx] = temp_idx;
+ } else if (siteA_link_idx != -1) {
+ link_sites[siteA_link_idx] = siteB;
+ } else if (siteB_link_idx != -1) {
+ link_sites[siteB_link_idx] = siteA;
+ }
+}
+
+static const int MAX_SHUFFLES = 5;
+
+char* generateShuffledSequence(
+ Peptide* peptide,
+ vector<int>& link_sites
+ ) {
+
+ char* sequence = peptide->getSequence();
+
+ int length = peptide->getLength();
+
+ int num_shuffles = 0;
+ do {
+
+ //Don't move the n-term and c-term amino acids.
+ int start_idx = 1;
+ int end_idx = length - 2;
+
+ while (start_idx < end_idx) {
+ int switch_idx = get_random_number_interval(start_idx, end_idx);
+ char temp_char = sequence[start_idx];
+ sequence[start_idx] = sequence[switch_idx];
+ sequence[switch_idx] = temp_char;
+
+ doSwitch(link_sites, start_idx, switch_idx);
+
+ ++start_idx;
+ }
+
+
+ } while (false /*equal_peptides(sequence, peptide)*/ && (num_shuffles < MAX_SHUFFLES));
+
+ return sequence;
+
+
+}
+
+MODIFIED_AA_T* generateShuffledModSequence(
+ Peptide* peptide,
+ vector<int>& link_sites
+ ) {
+
+ MODIFIED_AA_T* sequence = peptide->getModifiedAASequence();
+ int length = peptide->getLength();
+ int start_idx = 0;
+ int end_idx = length-1;
+ int switch_idx = 0;
+ MODIFIED_AA_T temp_aa = 0;
+
+ // Do not move the first and last residue, regardless of enzyme
+ ++start_idx;
+ --end_idx;
+
+ // shuffle from left to right, using the Knuth algorithm for shuffling.
+ while(start_idx < end_idx) {
+ switch_idx = get_random_number_interval(start_idx, end_idx);
+ temp_aa = sequence[start_idx];
+ sequence[start_idx] = sequence[switch_idx];
+ sequence[switch_idx] = temp_aa;
+ doSwitch(link_sites, start_idx, switch_idx);
+ ++start_idx;
+ }
+
+ return sequence;
+
+}
+
+
+XLinkablePeptide XLinkablePeptide::shuffle() {
+ //cerr <<"XLinkablePeptide::shuffle():start"<<endl;
+ Peptide* peptide = new Peptide(peptide_);
+ XLink::addAllocatedPeptide(peptide);
+ //cerr <<"Linksites"<<endl;
+ vector<int> link_sites;
+ for (unsigned int idx = 0; idx < numLinkSites(); idx++) {
+ link_sites.push_back(getLinkSite(idx));
+ }
+
+ MODIFIED_AA_T* new_mod_seq = NULL;
+
+ if(peptide->isModified()) {
+ //cerr<<"Calling generateShuffledModSequence"<<endl;
+ new_mod_seq = generateShuffledModSequence(peptide, link_sites);
+ peptide->setDecoyModifiedSeq(new_mod_seq);
+ } else {
+ //cerr<<"Calling generateShuffledSequence"<<endl;
+ char* new_seq =
+ generateShuffledSequence(peptide, link_sites);
+ convert_to_mod_aa_seq(new_seq, &new_mod_seq);
+ peptide->setDecoyModifiedSeq(new_mod_seq);
+ free(new_seq);
+ }
+ //cerr<<"Creating new linkable peptide"<<endl;
+ XLinkablePeptide ans(peptide, link_sites);
+ for (size_t idx=0;idx<NUMBER_MASS_TYPES;idx++) {
+ if (mass_calculated_[idx]) {
+ ans.mass_calculated_[idx] = true;
+ ans.mass_[idx] = mass_[idx];
+ }
+ }
+ ans.is_decoy_ = true;
+ return ans;
+}
+
+XLinkablePeptide* XLinkablePeptide::getCachedDecoy() {
+ if (decoy_ == NULL) {
+
+ decoy_ = new XLinkablePeptide(shuffle());
+ }
+ return decoy_;
+}
+
+
+/*
+string getAASequence() {
+ char* seq = get_peptide_sequence(peptide_);
+ string ans(seq);
+ free(seq);
+ return ans;
+}
+*/
+
+/**
+ * \returns the modified sequence string of the xlinkable peptide
+ */
+string XLinkablePeptide::getModifiedSequenceString() {
+ if (peptide_ == NULL) {
+ return string(sequence_);
+ } else {
+ return peptide_->getModifiedSequenceWithMasses();
+ }
+}
+
+bool XLinkablePeptide::isModified() {
+ return peptide_->isModified();
+}
+
+void XLinkablePeptide::setXCorr(size_t link_idx, FLOAT_T xcorr) {
+
+ xcorr_link_idx_ = link_idx;
+ xcorr_ = xcorr;
+
+}
+
+FLOAT_T XLinkablePeptide::getXCorr() const {
+ if (xcorr_link_idx_ != -1) {
+ return xcorr_;
+ }
+ carp(CARP_FATAL, "Xcorr not set!");
+ return 0;
+
+}
+
+bool XLinkablePeptide::hasXCorr() const {
+ //return (xcorr_link_idx_ != -1);
+ return false;
+}
+
+
+bool compareXLinkableXCorr(
+ const XLinkablePeptide& xpep1,
+ const XLinkablePeptide& xpep2
+ ) {
+ return xpep1.getXCorr() > xpep2.getXCorr();
+}
+
+bool compareXLinkableXCorrPtr(
+ const XLinkablePeptide* xpep1,
+ const XLinkablePeptide* xpep2
+ ) {
+ return xpep1 -> getXCorr() > xpep2 -> getXCorr();
+}
+
+
+
+bool compareXLinkablePeptideMass(
+ const XLinkablePeptide& xpep1,
+ const XLinkablePeptide& xpep2
+) {
+
+ return xpep1.getMassConst(MONO) < xpep2.getMassConst(MONO);
+}
+
+bool compareXLinkablePeptideMassToFLOAT(
+ const XLinkablePeptide& xpep1,
+ const FLOAT_T& mass) {
+ return xpep1.getMassConst(MONO) < mass;
+}
+
+bool compareXLinkablePeptideMassToFLOAT2(
+ const FLOAT_T& mass,
+ const XLinkablePeptide& xpep1) {
+ return xpep1.getMassConst(MONO) > mass;
+}
+
+/**
+ * \returns whether the peptide is less than (by lexical modified sequence)
+ */
+bool XLinkablePeptide::operator < (
+ XLinkablePeptide other ///< the other XLinkablePeptide to compare to.
+ ) const {
+
+ XLinkablePeptide xlinkable = *this;
+ return xlinkable.getModifiedSequenceString() < other.getModifiedSequenceString();
+
+}
+
+void XLinkablePeptide::predictIons(
+ IonSeries* ion_series,
+ int charge,
+ int link_idx,
+ FLOAT_T mod_mass,
+ bool clear
+ ) {
+ IonSeries* cached_ions = NULL;
+ bool cached = false;
+ if (GlobalParams::getXLinkUseIonCache()) {
+
+ cached_ions = XLinkIonSeriesCache::getXLinkablePeptideIonSeries(*this, charge);
+ bool cached = cached_ions != NULL;
+ }
+ if (!cached) {
+ cached_ions = new IonSeries(ion_series->getIonConstraint(), charge);
+ cached_ions->update(getSequence(), getModifiedSequencePtr());
+ cached_ions->predictIons();
+ }
+ int link_pos = link_sites_[link_idx];
+ int seq_len = peptide_->getLength();
+ if (clear) {
+ ion_series->clear();
+ }
+ //modify the necessary ions and add to the ion_series
+ IonIterator eiter = cached_ions->end();
+ for (IonIterator ion_iter = cached_ions->begin();
+ ion_iter != eiter;
+ ++ion_iter) {
+ Ion* src_ion = *ion_iter;
+ Ion* ion = src_ion;
+ unsigned int cleavage_idx = ion->getCleavageIdx();
+ if (ion->isForwardType()) {
+ if (cleavage_idx > (unsigned int)link_pos) {
+ ion = Ion::newIon();
+ Ion::copy(src_ion, ion, "");
+ FLOAT_T mass = ion->getMassFromMassZ() + mod_mass;
+ ion->setMassZFromMass(mass);
+ if (isnan(ion->getMassZ())) {
+ carp(CARP_FATAL, "NAN3");
+ }
+ }
+ } else {
+ if (cleavage_idx >= (seq_len-(unsigned int)link_pos)) {
+ ion = Ion::newIon();
+ Ion::copy(src_ion, ion, "");
+ FLOAT_T mass = ion->getMassFromMassZ() + mod_mass;
+ ion->setMassZFromMass(mass);
+ if (isnan(ion->getMassZ())) {
+ carp(CARP_FATAL, "NAN4");
+ }
+ }
+ }
+ ion_series->addIon(ion);
+ }
+ if (!cached) {
+ delete cached_ions;
+ }
+}
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkablePeptide.h b/src/app/xlink/XLinkablePeptide.h
new file mode 100644
index 0000000..431e669
--- /dev/null
+++ b/src/app/xlink/XLinkablePeptide.h
@@ -0,0 +1,284 @@
+/**
+ * \file XLinkablePeptide.h
+ * $Revision: 1.00 $
+ * \brief Object for finding and defining the link sites on a peptide.
+ *************************************************************************/
+#ifndef XLINKABLEPEPTIDE_H_
+#define XLINKABLEPEPTIDE_H_
+
+#include "model/objects.h"
+#include "model/Peptide.h"
+#include "util/CacheableMass.h"
+#include <vector>
+#include <string>
+
+#include "XLinkBondMap.h"
+
+/**
+ * \class XLinkablePeptide
+ * \brief object for finding and defining the link sites on a peptide
+ */
+class XLinkablePeptide : public CacheableMass {
+ protected:
+ Crux::Peptide* peptide_; ///< the peptide object of this XLinkablePeptide (can be null)
+ XLinkablePeptide* decoy_; ///< a saved decoy of the XLinkablePeptide.
+ char* sequence_; ///< the sequence
+ std::vector<int> link_sites_; ///< the sequence indices where linking is possible
+ bool is_decoy_; //Is this from the decoy database?
+ size_t xcorr_link_idx_;
+ FLOAT_T xcorr_;
+ int index_;
+
+ MODIFIED_AA_T* mod_seq_;
+
+ int predict_ions_call_count_;
+ /**
+ * Initialize object
+ */
+ void init();
+
+ public:
+
+ /**
+ * Default constructor
+ */
+ XLinkablePeptide();
+
+ /**
+ * Constructor that defines the peptide as a sequence string
+ */
+ XLinkablePeptide(
+ char* sequence ///< the peptide sequence
+ );
+
+ XLinkablePeptide(
+ const XLinkablePeptide& xlinkablepeptide
+ );
+
+ XLinkablePeptide(
+ XLinkablePeptide& xlinkablepeptide
+ );
+
+ /**
+ * Constructor that defines the peptide and the linking sites
+ */
+ XLinkablePeptide(
+ Crux::Peptide* peptide, ///< the peptide object
+ std::vector<int>& link_sites ///< the linking sites
+ );
+
+ /**
+ * Constructor that generates the possible linking sites
+ * on the peptide using the bondmap object
+ */
+ XLinkablePeptide(
+ Crux::Peptide* peptide, ///< the peptide object
+ XLinkBondMap& bondmap, ///< the bond map
+ int additional_cleavages = 0 ///< 1 - for selfloop peptides
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual ~XLinkablePeptide();
+
+ /**
+ * given a peptide and a XLinkBondMap object,
+ * generate the possible link sites
+ */
+ static void findLinkSites(
+ Crux::Peptide* peptide, ///< the peptide object -in
+ XLinkBondMap& bondmap, ///< the bond map -in
+ std::vector<int>& link_sites, ///< the found link sites -out
+ int additional_cleavages=0 ///< 0 for xlinks, 1 for selfloops
+ );
+
+ void clearSites();
+
+ /**
+ * \returns whether a link at this index in the sequence
+ * would prevent cleavage
+ */
+ bool linkSeqPreventsCleavage(
+ int seq_idx ///< the sequence index
+ );
+
+ static bool linkSeqPreventsCleavage(
+ Crux::Peptide* peptide, ///< the peptide
+ int seq_idx ///< the sequence index
+ );
+
+ /**
+ * \returns whether the link site prevents enzymatic
+ * cleavage
+ */
+ bool linkSitePreventsCleavage(
+ size_t link_site_idx ///< link site
+ );
+
+ /**
+ * \returns whether the peptide is cleavable at this index
+ */
+ static bool isCleavageSite(
+ Crux::Peptide* peptide, ///< the peptide
+ int seq_idx ///< the sequence index
+ );
+
+ /**
+ * \returns whether the aa at this index is a missed cleavage
+ */
+ static bool isMissedCleavageSite(
+ Crux::Peptide* peptide, ///< the peptide
+ int seq_idx ///< the sequence index
+ );
+
+ /**
+ * shuffle the linkable peptide, preserving the link sites
+ * \returns the shuffled XlinkablePeptide
+ */
+ XLinkablePeptide shuffle();
+
+ XLinkablePeptide* getCachedDecoy();
+
+
+ /**
+ * \returns the number of link sites on this peptide
+ */
+ size_t numLinkSites();
+
+ /**
+ * \returns whether this peptide is linkable or not
+ */
+ bool isLinkable();
+
+
+ void setDecoy(bool is_decoy);
+
+ /**
+ * \returns whether the peptide is a decoy or not
+ */
+ bool isDecoy();
+
+
+ /**
+ * \returns whether the peptide is linkable using the bond map
+ */
+ static bool isLinkable(
+ Crux::Peptide* peptide, ///< the peptide object
+ XLinkBondMap& bondmap ///< the bond map
+ );
+
+ /**
+ * Adds a link site by sequence index
+ * \returns the index of the added link site
+ */
+ int addLinkSite(
+ int seq_idx ///< the sequence index of the link site
+ );
+
+ /**
+ * \retuns the sequence index of a link site
+ */
+ int getLinkSite(
+ int link_site_idx ///< the index of the link site
+ );
+
+ /**
+ * \returns the number of missed cleavages in the linkable peptide
+ */
+ int getMissedCleavageSites();
+ static int getMissedCleavageSites(
+ Crux::Peptide* peptide ///< the peptide
+ );
+
+ /**
+ * \returns the peptide object associated with this XLinkablePeptide
+ */
+ Crux::Peptide* getPeptide();
+
+ /**
+ * \returns the mass of the xlinkable peptide
+ */
+ virtual FLOAT_T calcMass(
+ MASS_TYPE_T mass_type=MONO ///< MONO or AVERAGE
+ );
+
+ /**
+ * \returns an allocated sequence c-string. Must be freed
+ */
+ const char* getSequence();
+
+ /**
+ * \returns the allocated modified sequence. Must be freed.
+ */
+ MODIFIED_AA_T* getModifiedSequence();
+
+ const MODIFIED_AA_T* getModifiedSequencePtr();
+ /**
+ * \returns the modified sequence string of the xlinkable peptide
+ */
+ std::string getModifiedSequenceString();
+
+
+ void predictIons(
+ IonSeries* ion_series,
+ int charge,
+ int link_idx,
+ FLOAT_T mod_mass,
+ bool clear = true
+ );
+
+ FLOAT_T getXCorr() const;
+ void setXCorr(
+ size_t link_idx,
+ FLOAT_T xcorr
+ );
+
+ bool hasXCorr() const;
+
+
+ /**
+ * Is the linkable peptide modified?
+ */
+ bool isModified();
+ /**
+ * \returns whether the peptide is less than (by lexical modified sequence)
+ */
+ bool operator < (
+ XLinkablePeptide other ///< the other XLinkablePeptide to compare to.
+ ) const;
+
+ void setIndex(int idx) {index_ = idx;}
+ int getIndex() {return index_;}
+
+
+};
+
+bool compareXLinkablePeptideMass(const XLinkablePeptide& xpep1, const XLinkablePeptide& xpep2);
+bool compareXLinkablePeptideMassToFLOAT(
+ const XLinkablePeptide& xpep1,
+ const FLOAT_T& mass);
+
+bool compareXLinkablePeptideMassToFLOAT2(
+ const FLOAT_T& mass,
+ const XLinkablePeptide& xpep1);
+
+
+bool compareXLinkableXCorr(
+ const XLinkablePeptide& xpep1,
+ const XLinkablePeptide& xpep2
+ );
+
+bool compareXLinkableXCorrPtr(
+ const XLinkablePeptide* xpep1,
+ const XLinkablePeptide* xpep2
+ );
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkablePeptideIterator.cpp b/src/app/xlink/XLinkablePeptideIterator.cpp
new file mode 100644
index 0000000..eb8b0cb
--- /dev/null
+++ b/src/app/xlink/XLinkablePeptideIterator.cpp
@@ -0,0 +1,83 @@
+/**
+ * \file XLinkablePeptideIterator.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Iterator for xlinkable peptides
+ *****************************************************************************/
+
+#include "XLinkablePeptideIterator.h"
+#include "XLink.h"
+#include "LinearPeptide.h"
+#include "util/GlobalParams.h"
+#include <iostream>
+#include "XLinkDatabase.h"
+
+using namespace std;
+
+/**
+ * constructor that sets up the iterator
+ */
+XLinkablePeptideIterator::XLinkablePeptideIterator(
+ double min_mass, ///< min mass of candidates
+ double max_mass, ///< max mass of candidates
+ Database* database, ///< protein database
+ PEPTIDE_MOD_T** peptide_mods, ///<current peptide mod
+ int num_peptide_mods,
+ bool is_decoy, ///< generate decoy candidates
+ XLinkBondMap& bondmap ///< map of valid links
+ ) {
+
+ is_decoy_ = is_decoy;
+
+ iter_ = XLinkDatabase::getXLinkableBegin(min_mass);
+ eiter_ = XLinkDatabase::getXLinkableEnd();
+
+ min_mass_ = min_mass;
+ max_mass_ = max_mass;
+ has_next_ = iter_ != eiter_ && iter_->getMass(GlobalParams::getIsotopicMass()) <= max_mass_;
+}
+
+/**
+ * Destructor
+ */
+XLinkablePeptideIterator::~XLinkablePeptideIterator() {
+ ;
+}
+
+/**
+ * queues the next linkable peptide
+ */
+void XLinkablePeptideIterator::queueNextPeptide() {
+
+ iter_++;
+ has_next_ = iter_ != eiter_ && iter_->getMass(GlobalParams::getIsotopicMass()) <= max_mass_;
+}
+
+/**
+ *\returns whether there is another linkable peptide
+ */
+bool XLinkablePeptideIterator::hasNext() {
+
+ return has_next_;
+}
+
+/**
+ *\returns the next peptide
+ */
+XLinkablePeptide& XLinkablePeptideIterator::next() {
+
+ if (!has_next_) {
+ carp(CARP_WARNING, "next called on empty iterator!");
+ }
+
+ XLinkablePeptide& ans = *iter_;
+ queueNextPeptide();
+ return ans;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkablePeptideIterator.h b/src/app/xlink/XLinkablePeptideIterator.h
new file mode 100644
index 0000000..c7029a9
--- /dev/null
+++ b/src/app/xlink/XLinkablePeptideIterator.h
@@ -0,0 +1,76 @@
+/**
+ * \file XLinkablePeptideIterator.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Iterator for xlinkable peptides
+ *****************************************************************************/
+
+#ifndef XLINKABLEPEPTIDEITERATOR_H
+#define XLINKABLEPEPTIDEITERATOR_H
+
+#include "model/ModifiedPeptidesIterator.h"
+#include "XLinkablePeptide.h"
+#include "XLinkBondMap.h"
+
+class XLinkablePeptideIterator {
+
+ protected:
+ ModifiedPeptidesIterator* peptide_iterator_; ///< peptide iterator to generate peptides
+ XLinkablePeptide current_; ///< current xlinkable peptide
+ XLinkBondMap bondmap_; ///< map of valid links
+ FLOAT_T min_mass_;
+ FLOAT_T max_mass_;
+ bool has_next_; ///< is there a next candidate
+ bool is_decoy_; ///< are we getting decoys
+ std::vector<int> link_sites_; ///< list of links sites
+ std::vector<XLinkablePeptide>::iterator iter_;
+ std::vector<XLinkablePeptide>::iterator eiter_;
+
+ /**
+ * queues the next linkable peptide
+ */
+ void queueNextPeptide();
+
+ public:
+
+ /**
+ * constructor that sets up the iterator
+ */
+ XLinkablePeptideIterator(
+ double min_mass, ///< min mass of candidates
+ double max_mass, ///< max mass of candidates
+ Database* database, ///<peptide index
+ PEPTIDE_MOD_T** peptide_mods, ///< current peptide mod
+ int num_peptide_mods,
+ bool is_decoy, ///< generate decoy candidates
+ XLinkBondMap& bondmap ///< map of valid links
+ );
+
+ XLinkablePeptideIterator() {peptide_iterator_=NULL;}
+
+ /**
+ * Destructor
+ */
+ virtual ~XLinkablePeptideIterator();
+
+ /**
+ * \returns whether there is another linkable peptide
+ */
+ virtual bool hasNext();
+
+ /**
+ *\returns the next linkable peptide
+ */
+ virtual XLinkablePeptide& next();
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkablePeptideIteratorTopN.cpp b/src/app/xlink/XLinkablePeptideIteratorTopN.cpp
new file mode 100644
index 0000000..4f5aa49
--- /dev/null
+++ b/src/app/xlink/XLinkablePeptideIteratorTopN.cpp
@@ -0,0 +1,169 @@
+/**
+ * \file XLinkablePeptideIteratorTopN.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Iterator for xlinkable peptides
+ *****************************************************************************/
+
+#include "XLinkablePeptideIteratorTopN.h"
+#include "XLinkablePeptideIterator.h"
+#include "XLink.h"
+#include "XLinkPeptide.h"
+#include "XLinkScorer.h"
+#include "XLinkDatabase.h"
+#include "util/GlobalParams.h"
+#include <iostream>
+
+
+using namespace std;
+
+/**
+ * constructor that sets up the iterator
+ */
+XLinkablePeptideIteratorTopN::XLinkablePeptideIteratorTopN(
+ Crux::Spectrum* spectrum, ///<spectrum
+ FLOAT_T precursor_mass, ///< Mass of precursor
+ FLOAT_T min_mass, ///< min mass of candidates
+ FLOAT_T max_mass, ///< max mass of candidates
+ int precursor_charge, ///< Charge of precursor
+ bool is_decoy ///< generate decoy candidates
+ ) {
+
+ carp(CARP_DEBUG, "XLinkablePeptideIteratorTopN: start()");
+
+ scored_xlp_.clear();
+
+ XLinkScorer scorer(spectrum, precursor_charge);
+ top_n_ = GlobalParams::getXLinkTopN();
+ //carp(CARP_DEBUG, "top_in:%i", top_n_);
+ //carp(CARP_DEBUG, "precursor:%g", precursor_mass);
+ //carp(CARP_INFO, "min:%g", min_mass);
+ //carp(CARP_INFO, "max:%g", max_mass);
+ vector<XLinkablePeptide>::iterator xlp_biter = XLinkDatabase::getXLinkableFlattenBegin(is_decoy, min_mass);
+ vector<XLinkablePeptide>::iterator xlp_eiter = XLinkDatabase::getXLinkableFlattenEnd(is_decoy, max_mass);
+
+ int nscore = xlp_eiter - xlp_biter;
+// if (nscore > top_n_) {
+ scorePeptides(scorer, precursor_mass, xlp_biter, xlp_eiter);
+// } else {
+// scored_xlp_.insert(scored_xlp_.begin(), xlp_biter, xlp_eiter);
+// }
+
+ //find the begin and end iterators for the given mass range.
+ /*
+ vector<XLinkablePeptide>::iterator target_biter = XLinkDatabase::getXLinkableFlattenBegin(false, min_mass);
+ vector<XLinkablePeptide>::iterator target_eiter = XLinkDatabase::getXLinkableFlattenEnd(false, max_mass);
+ vector<XLinkablePeptide>::iterator decoy_biter = XLinkDatabase::getXLinkableFlattenBegin(true, min_mass);
+ vector<XLinkablePeptide>::iterator decoy_eiter = XLinkDatabase::getXLinkableFlattenEnd(true, max_mass);
+
+
+ int nscore = (target_eiter - target_biter) + (decoy_eiter - decoy_biter);
+ if (nscore > top_n_) {
+ scorePeptides(scorer, precursor_mass, target_biter, target_eiter);
+ scorePeptides(scorer, precursor_mass, decoy_biter, decoy_eiter);
+ sort(scored_xlp_.begin(), scored_xlp_.end(), compareXLinkableXCorr);
+ } else {
+ scored_xlp_.insert(scored_xlp_.begin(), target_biter, target_eiter);
+ scored_xlp_.insert(scored_xlp_.begin(), decoy_biter, decoy_eiter);
+ }
+ */
+
+ current_count_ = 0;
+ queueNextPeptide();
+
+}
+
+void XLinkablePeptideIteratorTopN::scorePeptides(
+ XLinkScorer& scorer,
+ FLOAT_T precursor_mass,
+ vector<XLinkablePeptide>::iterator& biter,
+ vector<XLinkablePeptide>::iterator& eiter
+ ) {
+
+ scored_xlp_.clear();
+ while(biter != eiter) {
+ XLinkablePeptide& pep1 = *biter;
+ FLOAT_T delta_mass = precursor_mass - pep1.getMass(MONO);// - XLinkPeptide::getLinkerMass();
+ FLOAT_T xcorr = scorer.scoreXLinkablePeptide(pep1, 0, delta_mass);
+ pep1.setXCorr(0, xcorr);
+ //pep1.getXCorr();
+ scored_xlp_.push_back(&pep1);
+ biter++;
+ }
+ if (scored_xlp_.size() > 0) {
+ sort(scored_xlp_.begin(), scored_xlp_.end(), compareXLinkableXCorrPtr);
+ }
+
+ IF_CARP(CARP_DETAILED_DEBUG,
+ for (size_t idx = 0;idx < min((size_t)top_n_,scored_xlp_.size());idx++) {
+ string seq = scored_xlp_[idx]->getModifiedSequenceString();
+ carp(CARP_INFO,"%d %g %s", idx, scored_xlp_[idx]->getXCorr(), seq.c_str());
+ }
+ );
+}
+
+/**
+ * Destructor
+ */
+XLinkablePeptideIteratorTopN::~XLinkablePeptideIteratorTopN() {
+}
+
+/**
+ * queues the next linkable peptide
+ */
+void XLinkablePeptideIteratorTopN::queueNextPeptide() {
+ //carp(CARP_DEBUG, "queueNextPeptide()::start");
+
+ if (current_count_ < scored_xlp_.size() && current_count_ < top_n_) {
+ //current_ = scored_xlp_[current_count_];
+ current_count_++;
+ has_next_ = true;
+ } else {
+ has_next_ = false;
+ }
+ //carp(CARP_DEBUG, "queueNextPeptide:%i", has_next_?1:0);
+}
+
+/**
+ *\returns whether there is another linkable peptide
+ */
+bool XLinkablePeptideIteratorTopN::hasNext() {
+ //carp(CARP_DEBUG, "XLinkablePeptideIteratorTopN::hasNext(): %i", has_next_?1:0);
+ return has_next_;
+}
+
+/**
+ *\returns the next peptide
+ */
+XLinkablePeptide& XLinkablePeptideIteratorTopN::next() {
+ //carp(CARP_INFO, "XLinkablePeptideIteratorTopN::next()");
+ if (!has_next_) {
+ carp(CARP_FATAL, "next called on empty iterator!");
+ }
+
+ XLinkablePeptide& ans = *scored_xlp_[current_count_-1];
+ //carp(CARP_INFO, "next peptide:%s %g", ans.getSequence(), ans.getXCorr());
+ queueNextPeptide();
+ //carp(CARP_INFO, "XLinkablePeptideIteratorTopN: returning reference");
+ return ans;
+}
+
+XLinkablePeptide* XLinkablePeptideIteratorTopN::nextPtr() {
+ if (!has_next_) {
+ carp(CARP_FATAL, "next called on empty iterator!");
+ }
+
+ XLinkablePeptide* ans = scored_xlp_[current_count_-1];
+ queueNextPeptide();
+ return ans;
+
+}
+
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/XLinkablePeptideIteratorTopN.h b/src/app/xlink/XLinkablePeptideIteratorTopN.h
new file mode 100644
index 0000000..b7f2117
--- /dev/null
+++ b/src/app/xlink/XLinkablePeptideIteratorTopN.h
@@ -0,0 +1,83 @@
+/**
+ * \file XLinkablePeptideIterator.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 18 September December 2014
+ * \brief Iterator for xlinkable peptides
+ *****************************************************************************/
+
+#ifndef XLINKABLEPEPTIDEITERATORTOPN_H
+#define XLINKABLEPEPTIDEITERATORTOPN_H
+
+#include "XLinkablePeptideIterator.h"
+#include "XLinkablePeptide.h"
+#include "XLinkBondMap.h"
+#include "XLinkScorer.h"
+#include <queue>
+#include <vector>
+
+
+class XLinkablePeptideIteratorTopN: public XLinkablePeptideIterator {
+
+ protected:
+
+ //std::priority_queue<XLinkablePeptide, std::vector<XLinkablePeptide>, CompareXCorr> scored_xlp_;
+ std::vector<XLinkablePeptide*> scored_xlp_; ///< sorted by highest XCorr score.
+ int current_count_;
+ int top_n_; ///<set by kojak-top-n
+ bool has_next_; ///< is there a next candidate
+ bool is_decoy_; ///< are we getting decoys
+
+ /**
+ * queues the next linkable peptide
+ */
+ void queueNextPeptide();
+
+ void scorePeptides(
+ XLinkScorer& scorer,
+ FLOAT_T precursor_mass,
+ std::vector<XLinkablePeptide>::iterator& biter,
+ std::vector<XLinkablePeptide>::iterator& eiter
+ );
+
+ public:
+
+ /**
+ * constructor that sets up the iterator
+ */
+ XLinkablePeptideIteratorTopN(
+ Crux::Spectrum* spectrum,
+ FLOAT_T precursor_mass,
+ FLOAT_T min_mass, ///< min mass of candidates
+ FLOAT_T max_mass, ///< max mass of candidates
+ int precursor_charge, ///< Charge of precursor
+ bool is_decoy ///< generate decoy candidates
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~XLinkablePeptideIteratorTopN();
+
+ /**
+ * \returns whether there is another linkable peptide
+ */
+ bool hasNext();
+
+ /**
+ *\returns the next linkable peptide
+ */
+ XLinkablePeptide& next();
+
+ XLinkablePeptide* nextPtr();
+
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/cmake_install.cmake b/src/app/xlink/cmake_install.cmake
new file mode 100644
index 0000000..5004e1d
--- /dev/null
+++ b/src/app/xlink/cmake_install.cmake
@@ -0,0 +1,34 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/xlink
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
diff --git a/src/app/xlink/libxlink.a b/src/app/xlink/libxlink.a
new file mode 100644
index 0000000..0a68ce4
Binary files /dev/null and b/src/app/xlink/libxlink.a differ
diff --git a/src/app/xlink/spectacle.pl b/src/app/xlink/spectacle.pl
new file mode 100755
index 0000000..9d6bd68
--- /dev/null
+++ b/src/app/xlink/spectacle.pl
@@ -0,0 +1,331 @@
+#!/usr/bin/perl
+#FILE: spectacle
+#AUTHOR: Barbara Frewen
+#CREATE DATE: 01/10/06
+#DESCRIPTION: Read in an annotation file and
+# produce plots of spectra therein
+
+use strict;
+use Getopt::Long;
+use FileHandle;
+
+# !!!!! see TODO items !!!!!!!!
+#TODO label size bigger for png
+#TODO not printing the last peak?
+#TODO mark the precursor m/z
+
+my $usage = "Usage: spectacle [options] <annotations>
+
+Options:
+ -format <eps|fig|png> - format of output file. Default is eps.
+ -html <file> - write an html file with all of the figures.
+ -names <file> - specifiy names of output files. Only enabled for png.
+ -pre-mz - mark the precursor m/z on the x-axis.
+ -title - create a title above the figure of the form
+ <identifier> m/z=<m/z> <comment>.
+ -labeltop - labels at the top of figure
+ -nobox - do not draw a border at top and left of plot
+ -script <file> - print commands to file instead of running
+ gnuplot directly\n";
+
+
+#read the command line
+my $format = "eps";
+my $names_file;
+my $label_up;
+my $html;
+my $premz;
+my $title;
+my $gnuplot_file;
+my $annot_file;
+my $no_box;
+GetOptions("names=s"=>\$names_file,
+ "format=s"=>\$format,
+ "html=s"=>\$html,
+ "pre-mz"=>\$premz,
+ "labeltop"=>\$label_up,
+ "script=s"=>\$gnuplot_file,
+ "title"=>\$title);
+#TODO add verbosity?
+if(@ARGV != 1){
+ print "Missing annotation file or option arguments\n";
+ print $usage;
+ exit;
+}else{
+ $annot_file = $ARGV[0];
+}
+
+#check for option errors...
+
+#format: must be eps png fig; write terminal string
+my $terminal;
+if($format eq "eps"){
+ $terminal = "set terminal postscript eps color solid 24\n";
+}elsif($format eq "png"){
+ #$terminal = "set terminal png medium color\n";
+ $terminal = "set terminal png medium\n";
+}elsif($format eq "fig"){
+ $terminal = "set terminal fig color small 24\n";
+}else{
+ print "Format $format not recognized. Use png, eps, or fig.";
+ exit;
+}
+#print "Format is $format\n";
+
+#check for gnuplot and exit if not present
+if( `which gnuplot` eq "" ){
+ die "Could not find required gnuplot.\n";
+}
+
+#html: change to false and write warning if format!=png
+if($html && $format ne "png" ){
+ print STDERR "Warning: HTML file cannot be created with $format format\n";
+ undef $html;
+}
+
+#names: open and put in a hash (id as key, file name as entry)
+#I haven't checked to see if any names are repeated
+(open NAMES, $names_file or
+ die "Could not open names file $names_file\n") if $names_file;;
+my %spec_names;
+if($names_file){
+ my $line;
+ while($line = <NAMES>){
+ my ($id, $filename) = split /\s/, $line;
+ $spec_names{$id} = $filename;
+ }
+}
+close NAMES;
+
+open ANNOT, $annot_file or die "Couldn't open annotation file $annot_file\n";
+my $line = <ANNOT>;
+
+#open gnuplot and initialize settings for all plots
+($gnuplot_file) ? (open GNUPLOT, ">$gnuplot_file") : (open GNUPLOT, "|gnuplot");
+print GNUPLOT $terminal;
+#print GNUPLOT "set noytics\n"
+print GNUPLOT "set xtics nomirror\n";
+print GNUPLOT "set xlabel \"m/z\"\nset ylabel \"Intensity\"\n";
+print GNUPLOT "set border 3\n" if $no_box;
+#save fig names for html page, temp file names to delete
+my @figNames;
+my @tmpFileNames;
+
+while( $line =~ /^>/){ #each loop is one spectrum
+ #remove > and whitespace
+ chomp $line;
+ $line =~ s/>\s*//;
+ my($id, $mz) = split /\s/, $line;
+ #print "id is $id, mz is $mz\n";
+ my $comment =~ s/$id\s+$mz\s+//;
+
+ #check names
+ my $fig_file_name = "$id.$format";
+ if( $names_file and !$spec_names{$id} ){
+ #print "Don't make fig for $id\n";
+ next;
+ }elsif( $names_file ){
+ $fig_file_name = "$spec_names{$id}.$format";
+ }
+ push @figNames, $fig_file_name;
+
+ #title string
+ if($title){
+ $title = $id." mz: ".$mz." ".$comment;
+ #print "title is $title\n";
+ }
+
+ #list of series, store text to be printed to file
+ my %series; #indexed by color
+ open BLACK, ">black.$id.$$.tmp"
+ or die "Can't create temporary data file\n";
+ push @tmpFileNames, "black.$id.$$.tmp";
+
+ #list of labels
+ my @labels;
+
+ #list of warnings
+ my %warnings;
+
+ #for each peak
+ my $peak_line;
+ #my $max_y = 0;
+ my $max_y = -10;
+ while( ($peak_line = <ANNOT>) !~ /^>/ and (not eof ANNOT)){
+ chomp $peak_line;
+ my($mz, $in, $label, $color) = split /\s+/, $peak_line;
+
+ #print "mz: $mz int: $in label: $label color: $color\n";
+ #keep track of largest intensity for adjusting y-range
+ $max_y = $in if ($in > $max_y);
+
+ #add label to list
+ (push @labels, "$mz $in, $label") if $label;
+
+ #check series, create new if necessary
+ if(!$color){
+ print BLACK "$mz $in\n";
+ }elsif( $series{$color} ){
+ $series{$color} = $series{$color}."$mz $in\n";
+ }else{
+ #check that color is legal
+ #add to list
+ if($color eq "red" or
+ $color eq "green" or
+ $color eq "blue" or
+ $color eq "magenta"){
+ $series{$color} = $series{$color}."$mz $in\n";
+ }else{
+ $warnings{$color} = "Warning: unrecognized color ($color)\n";
+ print BLACK "$mz $in\n";
+ }
+ }
+ }#last peak read
+
+ $line = $peak_line;
+ #print "end of spec, line is $line";
+
+ #close series files
+ close BLACK;
+ #print colors to files
+ foreach my $color (keys %series){
+ open FILE, ">$color.$id.$$.tmp";
+ print FILE $series{$color};
+ close FILE;
+ push @tmpFileNames, "$color.$id.$$.tmp";
+ }
+
+ #print warnings
+ foreach my $color (keys %warnings){
+ print STDERR $warnings{$color};
+ }
+
+ #adjust the labels to be above the peak
+ my $offset = $max_y * 0.04;
+ my $abs_y = $max_y if $label_up;
+ #print "max_y is $max_y, offset is $offset, and abs_y is $abs_y\n";
+ my $label_string;
+ for (@labels){
+ my ($mz, $in, $label) = split /\s/;
+ ($label_up) ? $in = $abs_y : $in +=$offset;
+ $label_string .= "set label \"$label\" at $mz, $in center\n";
+ }
+
+ #clear labels from last plot
+ print GNUPLOT "set nolabel\n";
+ #write filename
+ print GNUPLOT "set output \"$fig_file_name\"\n";
+
+ #set yrange as greater than highest peak
+ $max_y *= 1.1; # if $label_string;
+ #print GNUPLOT "set yrange [-10001:$max_y]\n";
+ #print GNUPLOT "set yrange [-100:10]\n";
+ print GNUPLOT "set yrange [0:$max_y]\n";
+
+ #write title
+ print GNUPLOT "set title \"$title\"\n" if $title;
+
+ #write labels
+ #print GNUPLOT $label_string;
+ #print GNUPLOT "set nolabel\n";
+ #write plot command
+ my $plot = "plot \"black.$id.$$.tmp\" notitle with impulses lt -1, ";
+ foreach my $color (keys %series){
+ my $color_number = get_color_number($color, $format);
+ $plot = $plot.
+ " \"$color.$id.$$.tmp\" notitle with impulses lt $color_number,";
+ }
+ $plot =~ s/,\s*$//; #remove last comma
+ print GNUPLOT $plot."\n";
+
+ #skip over any blank lines between spec
+ while( ($line !~ /^>/) and (not eof ANNOT) ){
+ $line = <ANNOT>;
+ }
+#end while, next spec
+}continue{ #here if a spec was skipped b/c not in names file
+ while( ($line !~ /^>/) and (not eof ANNOT) ){
+ $line = <ANNOT>;
+ }
+}
+
+close GNUPLOT;
+for (@tmpFileNames){
+ #print "temp filename is $_\n";
+ `rm $_`;
+}
+
+#write html file
+if($html){
+ open HTML, ">$html" or die "Couldn't open $html\n";
+ print HTML "<html><body>\n";
+ for (@figNames){
+ print HTML "<p>$_</p><p><img src=\"$_\"></p>\n";
+ }
+ print HTML "</body></html>";
+ close HTML;
+}
+
+########## END OF MAIN #####################
+
+
+#number fig png eps
+#-1 black
+#1 black red red
+#2 blue green green
+#3 green blue blue
+#4 magenta magenta
+#5 red
+#6 magenta
+#7 black
+
+
+sub get_color_number{ #color, format
+ my $color = shift;
+ my $format = shift;
+ my $code = 1;
+
+ if($color eq "black"){
+ if($format eq "png"){
+ $code = -1;
+ }elsif($format eq "eps"){
+ $code = 7;
+ }elsif($format eq "fig"){
+ $code = 1;
+ }
+ }elsif($color eq "red"){
+ if($format eq "png"){
+ $code = 1;
+ }elsif($format eq "eps"){
+ $code = 1;
+ }elsif($format eq "fig"){
+ $code = 5;
+ }
+ }elsif($color eq "green"){
+ if($format eq "png"){
+ $code = 2;
+ }elsif($format eq "eps"){
+ $code = 2;
+ }elsif($format eq "fig"){
+ $code = 3;
+ }
+ }elsif($color eq "blue"){
+ if($format eq "png"){
+ $code = 3;
+ }elsif($format eq "eps"){
+ #$code = 3;
+ $code = 21;
+ }elsif($format eq "fig"){
+ $code = 2;
+ }
+ }elsif($color eq "magenta"){
+ if($format eq "png"){
+ $code = 4;
+ }elsif($format eq "eps"){
+ $code = 4;
+ }elsif($format eq "fig"){
+ $code = 6;
+ }
+ }
+ return $code;
+}
diff --git a/src/app/xlink/xhhc.cpp b/src/app/xlink/xhhc.cpp
new file mode 100644
index 0000000..5c4c8a6
--- /dev/null
+++ b/src/app/xlink/xhhc.cpp
@@ -0,0 +1,405 @@
+#include "xhhc.h"
+#include "XLinkBondMap.h"
+#include "LinkedPeptide.h"
+#include "XHHC_Peptide.h"
+#include "XLinkablePeptide.h"
+#include "XLink.h"
+
+#include "parameter.h"
+#include "model/Peptide.h"
+#include "io/DelimitedFile.h"
+#include "model/DatabaseProteinIterator.h"
+#include "model/ProteinPeptideIterator.h"
+#include "util/Params.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * Global Variable
+ */
+map<string, vector<Peptide*> > sequence_peptide_map; //hack to keep track of peptides.
+
+
+void get_linear_peptides(
+ set<string>& peptides,
+ DatabaseProteinIterator* protein_iterator,
+ PeptideConstraint* peptide_constraint
+ ) {
+
+ int max_missed_cleavages = Params::GetInt("missed-cleavages");
+
+ ProteinPeptideIterator* peptide_iterator = NULL;
+ Protein* protein;
+ Peptide* peptide;
+
+ string sequence = "";
+ string last_sequence = "zz";
+ //bool missed_cleavage = false;
+ // keep track of whether the next peptide contains the previous one or not
+ //size_t index;
+ while (protein_iterator->hasNext()) {
+ protein = protein_iterator->next();
+ peptide_iterator = new ProteinPeptideIterator(protein, peptide_constraint);
+ // missed_cleavages must be all in protein.c for this to work
+ peptide_iterator->prepareMc(500);
+ while (peptide_iterator->hasNext()) {
+ //peptide = database_peptide_iterator_next(peptide_iterator);
+ peptide = peptide_iterator->next();
+ char* seq = peptide->getSequence();
+ sequence = seq;
+ free(seq);
+
+ if (peptide->getMissedCleavageSites() <= max_missed_cleavages) {
+ carp(CARP_DEBUG, "Adding linear peptide:%s", peptide->getSequence());
+ peptides.insert(sequence);
+
+ map<string, vector<Peptide*> >::iterator find_iter;
+
+ find_iter = sequence_peptide_map.find(sequence);
+
+ carp(CARP_DEBUG, "Adding to map:%s,", sequence.c_str());
+
+ if (find_iter == sequence_peptide_map.end()) {
+ vector<Peptide*> peptide_vector;
+ peptide_vector.push_back(peptide);
+ sequence_peptide_map.insert(make_pair(sequence, peptide_vector));
+ } else {
+ find_iter -> second.push_back(peptide);
+ }
+ } else {
+ delete peptide;
+ }
+
+ }
+ delete peptide_iterator;
+ }
+
+
+
+
+}
+
+vector<Peptide*>& get_peptides_from_sequence(string& sequence) {
+ return sequence_peptide_map[sequence];
+}
+
+void free_peptides() {
+ map<string, vector<Peptide*> >::iterator map_iter;
+
+ for (map_iter = sequence_peptide_map.begin();
+ map_iter != sequence_peptide_map.end();
+ ++map_iter) {
+ vector<Peptide*>& peptides = map_iter -> second;
+ for (unsigned int i = 0; i < peptides.size(); i++) {
+ delete peptides[i];
+ }
+ }
+ sequence_peptide_map.clear();
+}
+
+
+void get_linkable_peptides(
+ set<XLinkablePeptide>& peptides,
+ XLinkBondMap& bondmap,
+ DatabaseProteinIterator* protein_iterator,
+ PeptideConstraint* peptide_constraint) {
+
+ ProteinPeptideIterator* peptide_iterator = NULL;
+ Protein* protein;
+ Peptide* peptide;
+ string sequence = "";
+ string last_sequence = "zz";
+ // keep track of whether the next peptide contains the previous one or not
+ while (protein_iterator->hasNext()) {
+ protein = protein_iterator->next();
+ peptide_iterator = new ProteinPeptideIterator(protein, peptide_constraint);
+ // missed_cleavages must be all in protein.c for this to work
+ //TODO either fix this code or make an option to allow all missed cleavages...
+ peptide_iterator->prepareMc(500);
+ while (peptide_iterator->hasNext()) {
+ //peptide = database_peptide_iterator_next(peptide_iterator);
+ peptide = peptide_iterator->next();
+ const char* seq = peptide->getSequence();
+ sequence = seq;
+
+ map<string, vector<Peptide*> >::iterator find_iter;
+
+ find_iter = sequence_peptide_map.find(sequence);
+
+ carp(CARP_DEBUG, "Adding to map:%s", sequence.c_str());
+
+ if (find_iter == sequence_peptide_map.end()) {
+ vector<Peptide*> peptide_vector;
+ peptide_vector.push_back(peptide);
+ sequence_peptide_map.insert(make_pair(sequence, peptide_vector));
+ } else {
+ find_iter -> second.push_back(peptide);
+ }
+
+ XLinkablePeptide xlinkable(peptide, bondmap, 1);
+
+ if (xlinkable.isLinkable()) {
+ peptides.insert(xlinkable);
+ }
+
+ }
+ delete peptide_iterator;
+ }
+}
+
+void print_precursor_count(vector<LinkedPeptide>& all_ions) {
+ int linear_peptides = 0;
+ int self_loop_products = 0;
+ int dead_end_products = 0;
+ int xlink_products = 0;
+
+ for (unsigned int idx = 0; idx < all_ions.size(); idx++) {
+ LinkedPeptide& current = all_ions[idx];
+ if (current.isLinear())
+ linear_peptides++;
+ else if (current.isDeadEnd())
+ dead_end_products++;
+ else if (current.isSelfLoop())
+ self_loop_products++;
+ else if (current.isCrossLinked())
+ xlink_products++;
+ else
+ carp(CARP_ERROR, "Unknown product");
+ }
+
+ carp(CARP_INFO, "Linear Peptides:%d", linear_peptides);
+ carp(CARP_INFO, "Inter/Intra Xlinks:%d", xlink_products);
+ carp(CARP_INFO, "Dead End Products:%d", dead_end_products);
+ carp(CARP_INFO, "Self Loop Products:%d", self_loop_products);
+
+}
+
+// creates an index of all linked peptides from a fasta file
+void find_all_precursor_ions(
+ vector<LinkedPeptide>& all_ions
+ ) {
+
+ string database_file = Params::GetString("protein fasta file");
+
+ carp(CARP_DEBUG, "find_all_precursor_ions: start()");
+ Database* db = new Database(database_file, false);
+ carp(CARP_DEBUG, "peptide constraint");
+ PeptideConstraint* peptide_constraint =
+ PeptideConstraint::newFromParameters();
+ // add two to account for a self loop that prevents two cleavages
+ peptide_constraint->setNumMisCleavage(Params::GetInt("missed-cleavages") + 2);
+
+ carp(CARP_DEBUG, "protein iterator");
+ DatabaseProteinIterator* protein_iterator = new DatabaseProteinIterator(db);
+
+ set<XLinkablePeptide> peptides;
+ carp(CARP_DEBUG, "get_linkable_peptides");
+ string link_string = Params::GetString("link sites");
+ XLinkBondMap bondmap(link_string);
+ get_linkable_peptides(peptides, bondmap, protein_iterator, peptide_constraint);
+ carp(CARP_DEBUG, "add_linked_peptides");
+ add_linked_peptides(all_ions, peptides, bondmap, 1);
+
+ if (Params::GetBool("xlink-include-linears")) {
+ delete protein_iterator;
+ protein_iterator = new DatabaseProteinIterator(db);
+ set<string> linear_peptides;
+ get_linear_peptides(linear_peptides, protein_iterator, peptide_constraint);
+
+ set<string>::iterator iter;
+ for (iter = linear_peptides.begin();
+ iter != linear_peptides.end();
+ ++iter) {
+
+ LinkedPeptide lp = LinkedPeptide(1);
+ XHHC_Peptide p(*iter);
+ lp.addPeptide(p);
+ all_ions.push_back(lp);
+ }
+ }
+
+
+ delete protein_iterator;
+
+
+ carp(CARP_DEBUG, "find_all_precursor_ions: done()");
+
+ //TODO - sort by increasing mass.
+ IF_CARP(CARP_DEBUG, print_precursor_count(all_ions));
+}
+
+
+
+// modified version of crux's estimate_weibull_parameters_from_xcorrs
+bool hhc_estimate_weibull_parameters_from_xcorrs(
+ FLOAT_T* scores,
+ int num_scores,
+ FLOAT_T* eta,
+ FLOAT_T* beta,
+ FLOAT_T* shift,
+ FLOAT_T* correlation,
+ Spectrum* spectrum,
+ int charge
+ ) {
+
+ // check that we have the minimum number of matches
+ if( num_scores < MIN_WEIBULL_MATCHES ) {
+ carp(CARP_DETAILED_INFO, "Too few psms (%i) to estimate "
+ "p-value parameters for spectrum %i, charge %i",
+ num_scores, spectrum->getFirstScan(), charge);
+ // set eta, beta, and shift to something???
+ return false;
+ }
+
+ // reverse sort the first num_samples of them
+ sort(scores, scores + num_scores, greater<FLOAT_T>());
+
+ // use only a fraction of the samples, the high-scoring tail
+ // this parameter is hidden from the user
+ double fraction_to_fit = Params::GetDouble("fraction-top-scores-to-fit");
+ assert( fraction_to_fit >= 0 && fraction_to_fit <= 1 );
+ int num_tail_samples = (int)(num_scores * fraction_to_fit);
+ carp(CARP_DEBUG, "Estimating Weibull params with %d psms (%.2f of %i)",
+ num_tail_samples, fraction_to_fit, num_scores);
+
+ // do the estimation
+ fit_three_parameter_weibull(scores, num_tail_samples, num_scores,
+ MIN_XCORR_SHIFT, MAX_XCORR_SHIFT, XCORR_SHIFT, 0, /*CORR_THRESHOLD*/
+ eta, beta, shift, correlation);
+
+ carp(CARP_DETAILED_DEBUG,
+ "Corr: %.6f Eta: %.6f Beta: %.6f Shift: %.6f",
+ *correlation, *eta, *beta, *shift);
+
+ return true;
+}
+
+// helper function for get_linkable_peptides
+// creates single and cross-linked peptides, considering every pair
+// of peptides and every possible link site
+
+void add_linked_peptides(
+ vector<LinkedPeptide>& all_ions,
+ set<XLinkablePeptide>& peptides,
+ XLinkBondMap& bondmap,
+ int charge) {
+
+ vector<LinkedPeptide> ions;
+
+ // iterate over both sequences, adding linked peptides with correct links
+ for (set<XLinkablePeptide>::iterator iterA = peptides.begin(); iterA != peptides.end(); ++iterA) {
+
+ XLinkablePeptide pepA = *iterA;
+ string seqA = pepA.getModifiedSequenceString();
+
+ // add unlinked precursor
+ LinkedPeptide lp = LinkedPeptide(charge);
+ XHHC_Peptide p = XHHC_Peptide(seqA);
+ lp.addPeptide(p);
+
+ //vector<Peptide*>& crux_peptides = get_peptides_from_sequence(seqA);
+
+ int max_missed_cleavages = Params::GetInt("missed-cleavages");
+ int seqA_missed_cleavages = pepA.getMissedCleavageSites();
+ carp(CARP_DEBUG, "seqA:%s %i %i", seqA.c_str(), pepA.numLinkSites(), seqA_missed_cleavages);
+ if (Params::GetBool("xlink-include-deadends") &&
+ seqA_missed_cleavages <= (max_missed_cleavages+1)) {
+
+ for (size_t link_idx = 0;link_idx < pepA.numLinkSites();link_idx++) {
+ int seq_idx = pepA.getLinkSite(link_idx);
+ int total_cleavages = seqA_missed_cleavages;
+ if (pepA.linkSitePreventsCleavage(link_idx)) {
+ total_cleavages--;
+ }
+ if (total_cleavages <= max_missed_cleavages) {
+ ions.push_back(LinkedPeptide((char*)seqA.c_str(), NULL, seq_idx, -1, charge));
+ }
+ }
+ } /* xlink-include-dead-ends */
+
+ if (Params::GetBool("xlink-include-selfloops") &&
+ (seqA_missed_cleavages <= (max_missed_cleavages+2))) {
+
+ for (size_t link_idx1 = 0;link_idx1 < pepA.numLinkSites()-1;link_idx1++) {
+ for (size_t link_idx2 = link_idx1+1;link_idx2 < pepA.numLinkSites();link_idx2++) {
+ int seq_idx1 = pepA.getLinkSite(link_idx1);
+ int seq_idx2 = pepA.getLinkSite(link_idx2);
+
+ if (bondmap.canLink(pepA.getPeptide(), seq_idx1, seq_idx2)) {
+ int total_missed_cleavages = seqA_missed_cleavages;
+ if (pepA.linkSitePreventsCleavage(link_idx1)) {
+ total_missed_cleavages--;
+ }
+ if (pepA.linkSitePreventsCleavage(link_idx2)) {
+ total_missed_cleavages--;
+ }
+ if (total_missed_cleavages <= max_missed_cleavages) {
+ ions.push_back(LinkedPeptide((char*)seqA.c_str(), NULL, seq_idx1, seq_idx2, charge));
+ }
+ }
+ }
+ }
+ } /* xlink-include-selfloops */
+
+ /* xlink-inter/intra links */
+ if (seqA_missed_cleavages <= max_missed_cleavages+1) {
+
+ for (set<XLinkablePeptide>::iterator iterB = iterA; iterB != peptides.end();++iterB) {
+ XLinkablePeptide pepB = *iterB;
+ string seqB = pepB.getModifiedSequenceString();
+ int seqB_missed_cleavages = pepB.getMissedCleavageSites();
+ if (seqB_missed_cleavages <= (max_missed_cleavages+1) && XLink::testInterIntraKeep(pepA.getPeptide(), pepB.getPeptide())) {
+ for (size_t link_idx1 = 0;link_idx1 < pepA.numLinkSites();link_idx1++) {
+ for (size_t link_idx2 = 0; link_idx2 < pepB.numLinkSites();link_idx2++) {
+ int seq_idx1 = pepA.getLinkSite(link_idx1);
+ int seq_idx2 = pepB.getLinkSite(link_idx2);
+ if (bondmap.canLink(pepA.getPeptide(), pepB.getPeptide(), seq_idx1, seq_idx2)) {
+
+ int totalA = seqA_missed_cleavages;
+ if (pepA.linkSitePreventsCleavage(link_idx1)) {
+ totalA--;
+ }
+
+ int totalB = seqB_missed_cleavages;
+ if (pepB.linkSitePreventsCleavage(link_idx2)) {
+ totalB--;
+ }
+
+ if (totalA <= max_missed_cleavages &&
+ totalB <= max_missed_cleavages) {
+ ions.push_back(LinkedPeptide((char*)seqA.c_str(), (char*)seqB.c_str(), seq_idx1, seq_idx2, charge));
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ } // get next pepA
+ all_ions.insert(all_ions.end(), ions.begin(), ions.end());
+}
+
+// append one shuffled decoy to decoys vector
+void add_decoy(vector<LinkedPeptide>& decoys, LinkedPeptide& lp) {
+ vector<XHHC_Peptide> peptides = lp.getPeptides();
+ LinkedPeptide decoy = LinkedPeptide(lp.getCharge());
+ XHHC_Peptide pepA_shuffled = peptides[0].shuffle();
+ decoy.addPeptide(pepA_shuffled);
+ if (lp.size() == 2) {
+ XHHC_Peptide pepB_shuffled = peptides[1].shuffle();
+ decoy.addPeptide(pepB_shuffled);
+ }
+ decoy.setDecoy();
+ decoy.calculateMass(AVERAGE);
+ decoys.push_back(decoy);
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/app/xlink/xhhc.h b/src/app/xlink/xhhc.h
new file mode 100644
index 0000000..f99c867
--- /dev/null
+++ b/src/app/xlink/xhhc.h
@@ -0,0 +1,111 @@
+/**
+ * \file xhhc.h
+ * $Revision: 1.00$
+ * \brief utility routines for xlinking programs
+ */
+#ifndef XHHC_H
+#define XHHC_H
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string>
+#include <vector>
+#include <map>
+#include <set>
+#include <sstream>
+#include <fstream>
+
+/*Crux Includes*/
+#include "util/utils.h"
+#include "model/Spectrum.h"
+#include "io/carp.h"
+#include "model/PeptideConstraint.h"
+#include "model/Peptide.h"
+#include "model/PeptideSrc.h"
+#include "model/Protein.h"
+#include "model/Database.h"
+#include "model/DatabaseProteinIterator.h"
+#include "parameter.h"
+#include "model/objects.h"
+#include "util/crux-utils.h"
+#include "model/Ion.h"
+
+#include "XLinkBondMap.h"
+#include "XLinkablePeptide.h"
+
+// TODO: get rid of these
+#define MIN_WEIBULL_MATCHES 40
+#define MIN_XCORR_SHIFT -5.0
+#define MAX_XCORR_SHIFT 5.0
+#define XCORR_SHIFT 0.05
+
+// mine
+#define BONFERRONI_CUT_OFF_P 0.0001
+#define BONFERRONI_CUT_OFF_NP 0.01
+#define MIN_WEIBULL_SAMPLES 750
+#define MIN_PRECURSORS 3
+
+/**
+ * \returns the peptide objects from a sequence string
+ * TODO - eliminate this from xlink (this is a HACK)
+ */
+std::vector<Crux::Peptide*>& get_peptides_from_sequence(
+ std::string& sequence ///< the peptide sequence string
+ );
+
+/**
+ * frees allocated peptides
+ */
+void free_peptides();
+
+
+bool hhc_estimate_weibull_parameters_from_xcorrs(
+ FLOAT_T* scores,
+ int num_scores,
+ FLOAT_T* eta,
+ FLOAT_T* beta,
+ FLOAT_T* shift,
+ FLOAT_T* correlation,
+ Crux::Spectrum* spectrum,
+ int charge
+ );
+
+void get_linkable_peptides(
+ std::set<XLinkablePeptide>& peptides,
+ XLinkBondMap& bondmap,
+ DatabaseProteinIterator* protein_iterator,
+ PeptideConstraint* peptide_constraint
+ );
+
+void add_linked_peptides(
+ std::vector<LinkedPeptide>& all_ions,
+ std::set<XLinkablePeptide>& peptides,
+ XLinkBondMap& bondmap,
+ int charge
+ );
+
+/**
+ * appends one shuffled decoy to a vector
+ */
+void add_decoy(
+ std::vector<LinkedPeptide>& decoys, ///< decoy list to add to
+ LinkedPeptide& lp ///< linked peptide to generate decoy from
+ );
+
+
+/**
+ * Generates all of the product precursors for the
+ * search.
+ */
+void find_all_precursor_ions(
+ std::vector<LinkedPeptide>& all_ions ///< all of the precursors found -out
+ );
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/xhhc_all.ms2 b/src/app/xlink/xhhc_all.ms2
new file mode 100644
index 0000000..003897b
--- /dev/null
+++ b/src/app/xlink/xhhc_all.ms2
@@ -0,0 +1,291285 @@
+H CreationDate 8/03/09
+H Extractor Paul Draghicescu
+H ExtractorVersion 1
+H ExtractorOptions 1
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diff --git a/src/app/xlink/xhhc_predict_peptide_ions.cpp b/src/app/xlink/xhhc_predict_peptide_ions.cpp
new file mode 100644
index 0000000..07334a2
--- /dev/null
+++ b/src/app/xlink/xhhc_predict_peptide_ions.cpp
@@ -0,0 +1,121 @@
+#include "LinkedIonSeries.h"
+#include "xhhc_scorer.h"
+#include "LinkedPeptide.h"
+#include "XHHC_Peptide.h"
+#include "util/Params.h"
+
+#include <iostream>
+#include <fstream>
+
+#define NUM_ARGUMENTS 6
+#define NUM_OPTIONS 4
+using namespace std;
+
+int main(int argc, char** argv) {
+
+ char* peptideA = NULL;
+ char* peptideB = NULL;
+ int posA = 0;
+ int posB = 0;
+ FLOAT_T linker_mass = 0;
+ int charge = 1;
+ bool print_spectrum = false;
+
+
+ /* Verbosity level for set-up/command line reading */
+ set_verbosity_level(CARP_ERROR);
+
+ /* Define optional command line arguments */
+ int num_options = NUM_OPTIONS;
+ const char* option_list[NUM_OPTIONS] = {
+ "verbosity",
+ "version",
+ "use-flanking-peaks",
+ "print-theoretical-spectrum"
+ };
+
+ /* Define required command line arguments */
+ int num_arguments = NUM_ARGUMENTS;
+ const char* argument_list[NUM_ARGUMENTS] = {"peptide A",
+ "peptide B",
+ "pos A",
+ "pos B",
+ "charge state",
+ "link mass"};
+
+
+
+ /* for debugging of parameter processing */
+ //set_verbosity_level( CARP_DETAILED_DEBUG );
+ set_verbosity_level( CARP_ERROR );
+
+ /* Set default values for parameters in parameter.c */
+ initialize_parameters();
+
+ /* Define optional and required command line arguments */
+ select_cmd_line_options( option_list, num_options );
+ select_cmd_line_arguments( argument_list, num_arguments);
+
+ /* Parse the command line, including the optional params file */
+ /* does sytnax, type, bounds checking and dies if neccessessary */
+ parse_cmd_line_into_params_hash(argc, argv, "xlink-predict-peptide-ions");
+
+ /* Set verbosity */
+ set_verbosity_level(Params::GetInt("verbosity"));
+
+ /* Get Arguments */
+ linker_mass = Params::GetDouble("link mass");
+ charge = Params::GetInt("charge state");
+
+ peptideA = Params::GetString("peptide A");
+ peptideB = Params::GetString("peptide B");
+
+ posA = Params::GetInt("pos A");
+ posB = Params::GetInt("pos B");
+
+ print_spectrum = Params::GetBool("print-theoretical-spectrum");
+
+ LinkedPeptide::setLinkerMass(linker_mass);
+ LinkedPeptide linked_peptide;
+
+ if (string(peptideB) == "NULL") {
+ linked_peptide = LinkedPeptide(peptideA, NULL, posA-1, posB-1, charge);
+ } else {
+ linked_peptide = LinkedPeptide( peptideA, peptideB, posA-1, posB-1, charge);
+ }
+
+ ostringstream oss;
+ oss << linked_peptide;
+ string precursor_sequence = oss.str();
+ carp(CARP_INFO, "XLink Product:%s", precursor_sequence.c_str());
+ carp(CARP_INFO, "Charge:%i", charge);
+ carp(CARP_INFO, "Linker Mass:%g", linker_mass);
+ carp(CARP_INFO, "Product Mass: %g (MONO) %g (AVERAGE)", linked_peptide.getMass(MONO), linked_peptide.getMass(AVERAGE));
+ carp(CARP_INFO, "====================");
+
+ LinkedIonSeries ion_series(charge);
+ ion_series.addLinkedIons(linked_peptide);
+ ion_series.print();
+
+ if (print_spectrum) {
+ carp(CARP_INFO, "Writing XCORR theoretical spectrum to theoretical.out");
+ map<int, FLOAT_T> theoretical;
+ XHHC_Scorer::xlinkCreateMapTheoretical(ion_series,
+ theoretical);
+
+ ofstream fout("theoretical.out");
+ fout << "> " << linked_peptide << "\t" << linked_peptide.getMZ(MONO) << endl;
+
+ map<int, FLOAT_T>::iterator iter;
+
+ for (iter = theoretical.begin();
+ iter != theoretical.end();
+ ++iter) {
+ fout << iter -> first << "\t";
+ fout << iter -> second << "\t" << endl;
+ }
+
+ fout.close();
+ }
+ return 0;
+}
diff --git a/src/app/xlink/xhhc_score_peptide_spectrum.cpp b/src/app/xlink/xhhc_score_peptide_spectrum.cpp
new file mode 100644
index 0000000..5cce052
--- /dev/null
+++ b/src/app/xlink/xhhc_score_peptide_spectrum.cpp
@@ -0,0 +1,417 @@
+#include "xhhc_score_peptide_spectrum.h"
+#include "xhhc.h"
+#include "LinkedIonSeries.h"
+#include "xhhc_scorer.h"
+#include "LinkedPeptide.h"
+#include "XHHC_Peptide.h"
+
+#include "XLinkPeptide.h"
+#include "SelfLoopPeptide.h"
+#include "XLinkScorer.h"
+
+#include "model/IonConstraint.h"
+#include "model/Scorer.h"
+#include "io/SpectrumCollectionFactory.h"
+#include "util/Params.h"
+
+#include <math.h>
+#include <assert.h>
+#include <ctype.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include <iostream>
+#include <fstream>
+
+using namespace Crux;
+
+XLinkScoreSpectrum::XLinkScoreSpectrum() {
+}
+
+XLinkScoreSpectrum::~XLinkScoreSpectrum() {
+}
+
+int XLinkScoreSpectrum::main(int argc, char** argv) {
+ /* Get Arguments */
+ string peptideAStr = Params::GetString("peptide A");
+ string peptideBStr = Params::GetString("peptide B");
+ char* peptideA = my_copy_string(peptideAStr.c_str());
+ char* peptideB = my_copy_string(peptideBStr.c_str());
+
+ int posA = Params::GetInt("pos A");
+ int posB = Params::GetInt("pos B");
+ int charge = Params::GetInt("charge state");
+ int scan_num = Params::GetInt("scan number");
+
+ string ms2_file = Params::GetString("ms2 file");
+
+ FLOAT_T link_mass = Params::GetDouble("link mass");
+ XLinkPeptide::setLinkerMass(link_mass);
+ string scoremethod(Params::GetString("xlink-score-method"));
+
+
+ XLinkMatch* candidate = NULL;
+
+ // a single peptide linked to itself
+ if (strcmp(peptideB, "NULL") == 0) {
+ cout << "B is null" << endl;
+ if (scoremethod != "composite") {
+ carp(CARP_FATAL, "For composite scoring, provide a linked peptide, "
+ "not a self loop");
+ }
+ candidate = new SelfLoopPeptide(peptideA, posA, posB);
+ } else {
+ candidate = new XLinkPeptide(peptideA, peptideB, posA, posB);
+ }
+
+ // read ms2 file
+ Crux::SpectrumCollection* collection = SpectrumCollectionFactory::create(ms2_file);
+
+ // search for spectrum with correct scan number
+ Spectrum* spectrum = collection->getSpectrum(scan_num);
+ if( spectrum == NULL ) {
+ carp(CARP_ERROR, "Failed to find spectrum with scan_num: %d", scan_num);
+ delete collection;
+ exit(1);
+ }
+
+ XLinkScorer xlink_scorer(spectrum, charge);
+
+ IonConstraint* ion_constraint = xlink_scorer.getIonConstraintXCorr();
+ ion_constraint->setUseIonType(BY_ION, false);
+ ion_constraint->setUseIonType(BYA_ION, false);
+ ion_constraint->setUseIonType(ALL_ION, false);
+ ion_constraint->setUseIonType(A_ION, Params::GetBool("use-a-ions"));
+ ion_constraint->setUseIonType(B_ION, Params::GetBool("use-b-ions"));
+ ion_constraint->setUseIonType(C_ION, Params::GetBool("use-c-ions"));
+ ion_constraint->setUseIonType(X_ION, Params::GetBool("use-x-ions"));
+ ion_constraint->setUseIonType(Y_ION, Params::GetBool("use-y-ions"));
+ ion_constraint->setUseIonType(Z_ION, Params::GetBool("use-z-ions"));
+
+ if (scoremethod == "composite") {
+ FLOAT_T score = xlink_scorer.scoreCandidate(candidate);
+
+ cout << score << endl;
+
+ } else if (scoremethod == "modification") {
+
+ XLinkPeptide* xlp = (XLinkPeptide*)candidate;
+ FLOAT_T deltaB = xlp->getXLinkablePeptide(1).getMass(MONO) + link_mass;
+ FLOAT_T scoreA = xlink_scorer.scoreXLinkablePeptide(xlp->getXLinkablePeptide(0), 0, deltaB);
+
+ FLOAT_T deltaA = xlp->getXLinkablePeptide(0).getMass(MONO) + link_mass;
+ FLOAT_T scoreB = xlink_scorer.scoreXLinkablePeptide(xlp->getXLinkablePeptide(1), 0, deltaA);
+
+ if (scoreA > scoreB)
+ cout << scoreA << "\t" << scoreB << endl;
+ else
+ cout << scoreB << "\t" << scoreA << endl;
+
+ } else if (scoremethod == "concatenation") {
+
+ vector<double> scores;
+ double score1 = get_concat_score(peptideA, peptideB, posA, charge, spectrum);
+ scores.push_back(score1);
+
+ double score2 = get_concat_score(peptideB, peptideA, posB, charge, spectrum);
+ scores.push_back(score2);
+
+ int lengthA = string(peptideA).length();
+ int lengthB = string(peptideB).length();
+
+ double score3 = get_concat_score(peptideA, peptideB, lengthA + posB, charge, spectrum);
+ scores.push_back(score3);
+
+ double score4 = get_concat_score(peptideB, peptideA, lengthB + posA, charge, spectrum);
+ scores.push_back(score4);
+
+ sort(scores.begin(), scores.end(), less<double>());
+ cout <<scores[0];
+ for (int i=1; i < 4; i++) {
+ cout << "\t" << scores[i];
+ }
+
+ cout << endl;
+ } else {
+ carp(CARP_ERROR, "Unknown score method (%s).", scoremethod.c_str());
+ }
+ // free heap
+ delete collection;
+ delete spectrum;
+
+ return 0;
+}
+
+
+double XLinkScoreSpectrum::get_concat_score(char* peptideA, char* peptideB, int link_site, int charge, Spectrum* spectrum) {
+ string lpeptide = string(peptideA) + string(peptideB);
+
+ IonConstraint* ion_constraint = IonConstraint::newIonConstraintSmart(XCORR, charge);
+
+ IonSeries* ion_series = new IonSeries(lpeptide.c_str(), charge, ion_constraint);
+
+ ion_series->predictIons();
+
+ //modify ions.
+
+ //int pepA_begin = 0;
+ int pepB_begin = string(peptideA).length();
+ int llength = lpeptide.length();
+
+ for (IonIterator ion_iterator = ion_series->begin();
+ ion_iterator != ion_series->end();
+ ++ion_iterator) {
+
+ Ion* ion = *ion_iterator;
+ //check to see if if is the cterm of 1st peptide.
+ int ion_charge = ion->getCharge();
+ int cleavage_idx = ion->getCleavageIdx();
+ ION_TYPE_T ion_type = ion->getType();
+
+ //if contains cterm of 1st peptide, modify by -OH
+ carp(CARP_DEBUG, "====================");
+ if (ion_type == B_ION) {
+ carp(CARP_DEBUG, "B-ion");
+ carp(CARP_DEBUG, "%s", lpeptide.substr(0, cleavage_idx).c_str());
+ } else if (ion_type == Y_ION) {
+ carp(CARP_DEBUG, "Y-ion");
+ carp(CARP_DEBUG, "%s", lpeptide.substr(llength-cleavage_idx, llength).c_str());
+ } else {
+ continue;
+ }
+
+ carp(CARP_DEBUG, "cleavage idx:%d", cleavage_idx);
+
+ bool cterm_1st = false;
+ if (ion_type == B_ION) {
+ carp(CARP_DEBUG, "B-Ion");
+ if (cleavage_idx >= pepB_begin) {
+ cterm_1st = true;
+ }
+ } else if (ion_type == Y_ION) {
+ carp(CARP_DEBUG, "Y-ion");
+ if (cleavage_idx > (llength - pepB_begin)) {
+ cterm_1st = true;
+ }
+ }
+
+ bool nterm_2nd = false;
+ if (ion_type == B_ION) {
+ if (cleavage_idx > pepB_begin) {
+ nterm_2nd = true;
+ }
+ } else if (ion_type == Y_ION) {
+ if (cleavage_idx >= (llength-pepB_begin)) {
+ nterm_2nd = true;
+ }
+ }
+
+ bool has_link_site = false;
+ if (ion_type == B_ION) {
+ if (cleavage_idx > link_site) {
+ has_link_site = true;
+ }
+ } else if (ion_type == Y_ION) {
+ if (cleavage_idx >= (llength- link_site)) {
+ has_link_site = true;
+ }
+ }
+
+ carp(CARP_DEBUG, "cterm:%d", cterm_1st);
+ carp(CARP_DEBUG, "nterm:%d", nterm_2nd);
+ carp(CARP_DEBUG, "has site:%d", has_link_site);
+
+
+ //if it contains the cterm of the 1st peptide, modify by -OH
+ if (cterm_1st) {
+ FLOAT_T old_mass = (ion->getMassZ() - MASS_H_MONO) * (FLOAT_T)ion_charge;
+ FLOAT_T new_mass = old_mass + MASS_H2O_MONO - MASS_H_MONO;
+ FLOAT_T new_mz = (new_mass + (FLOAT_T)ion_charge) / (FLOAT_T)ion_charge;
+ ion->setMassZ(new_mz);
+ }
+ //if contains the nterm of 2nd peptide, modify by -H
+ if (nterm_2nd) {
+ FLOAT_T old_mass = (ion->getMassZ() - MASS_H_MONO) * (FLOAT_T)ion_charge;
+ FLOAT_T new_mass = old_mass + MASS_H_MONO;
+ FLOAT_T new_mz = (new_mass + (FLOAT_T)ion_charge) / (FLOAT_T)ion_charge;
+ ion->setMassZ(new_mz);
+ }
+ //if contains the link site, modify by link mass.
+ if (has_link_site) {
+ FLOAT_T old_mass = (ion->getMassZ() - MASS_H_MONO) * (FLOAT_T)ion_charge;
+ FLOAT_T new_mass = old_mass + LinkedPeptide::getLinkerMass();
+ FLOAT_T new_mz = (new_mass + (FLOAT_T)ion_charge) / (FLOAT_T)ion_charge;
+ ion->setMassZ(new_mz);
+ }
+ }
+
+ Scorer* scorer = new Scorer(XCORR);
+
+ // calculate the score
+ FLOAT_T score = scorer->scoreSpectrumVIonSeries(spectrum, ion_series);
+ return score;
+}
+
+FLOAT_T* XLinkScoreSpectrum::get_observed_raw(Spectrum* spectrum, int charge) {
+ FLOAT_T peak_location = 0;
+ int mz = 0;
+ FLOAT_T intensity = 0;
+ FLOAT_T bin_width = BIN_WIDTH_MONO;
+ FLOAT_T precursor_mz = spectrum->getPrecursorMz();
+ FLOAT_T experimental_mass_cut_off = precursor_mz*charge + 50;
+
+ // set max_mz and malloc space for the observed intensity array
+ FLOAT_T sp_max_mz = 512;
+
+ if(experimental_mass_cut_off > 512) {
+ int x = (int)experimental_mass_cut_off / 1024;
+ FLOAT_T y = experimental_mass_cut_off - (1024 * x);
+ sp_max_mz = x * 1024;
+
+ if(y > 0) {
+ sp_max_mz += 1024;
+ }
+ }
+
+ // DEBUG
+ // carp(CARP_INFO, "experimental_mass_cut_off: %.2f sp_max_mz: %.3f", experimental_mass_cut_off, scorer->sp_max_mz);
+ FLOAT_T* observed = (FLOAT_T*)mycalloc((int)sp_max_mz, sizeof(FLOAT_T));
+
+ // DEBUG
+ // carp(CARP_INFO, "max_peak_mz: %.2f, region size: %d",get_spectrum_max_peak_mz(spectrum), region_selector);
+
+ for (PeakIterator peak_iterator = spectrum->begin();
+ peak_iterator != spectrum->end();
+ ++peak_iterator) {
+
+ Peak *peak = *peak_iterator;
+ peak_location = peak->getLocation();
+
+ // skip all peaks larger than experimental mass
+ if(peak_location > experimental_mass_cut_off) {
+ continue;
+ }
+
+ // skip all peaks within precursor ion mz +/- 15
+ if(peak_location < precursor_mz + 15 && peak_location > precursor_mz - 15) {
+ continue;
+ }
+
+ // map peak location to bin
+ mz = (int)(peak_location / bin_width + 0.5);
+
+ // get intensity
+ // sqrt the original intensity
+ intensity = peak->getIntensity();
+
+ // set intensity in array with correct mz, only if max peak in the bin
+ if(observed[mz] < intensity) {
+ observed[mz] = intensity;
+ }
+ }
+
+
+ return observed;
+
+}
+
+
+
+void XLinkScoreSpectrum::print_spectrum(Spectrum* spectrum, LinkedIonSeries& ion_series) {
+
+
+ Scorer* scorer = new Scorer(XCORR);
+ scorer->createIntensityArrayObserved(spectrum, ion_series.getCharge());
+
+ FLOAT_T* observed_raw = get_observed_raw(spectrum, ion_series.getCharge());
+ FLOAT_T* observed_processed = scorer->getIntensityArrayObserved();
+
+
+ FLOAT_T max_mz = scorer->getSpMaxMz();
+
+
+
+
+ XHHC_Scorer xhhc_scorer(max_mz);
+
+ FLOAT_T* theoretical = (FLOAT_T*)mycalloc((size_t)max_mz, sizeof(FLOAT_T));
+ xhhc_scorer.hhcCreateIntensityArrayTheoretical(ion_series, theoretical);
+
+
+
+ ofstream fout("ion_match.out");
+ for (int i = 0; i < max_mz; i++) {
+ fout << i << "\t"
+ << observed_raw[i] << "\t"
+ << observed_processed[i] << "\t"
+ << theoretical[i] << "\t"
+ << (theoretical[i] != 0) << "\t"
+ << (theoretical[i] > 25) << endl;
+ }
+
+ fout.close();
+}
+
+void XLinkScoreSpectrum::processParams() {
+ for (char c = 'A'; c <= 'Z'; c++) {
+ double deltaMass = Params::GetDouble(string(1, c));
+ increase_amino_acid_mass(c, deltaMass);
+ }
+}
+
+string XLinkScoreSpectrum::getName() const {
+ return "xlink-score-spectrum";
+}
+
+string XLinkScoreSpectrum::getDescription() const {
+ return
+ "[[nohtml:Given a cross-linked peptide and a spectrum "
+ "calculate the corresponding XCorr score a number of different ways.]]"
+ "[[html:Given a cross-linked peptide and a spectrum "
+ "calculate the corresponding XCorr score a number of different ways, "
+ "depending upon the xlink-score-method parameter:"
+ "<ul><li>composite – compute a combined XCorr score</li>"
+ "<li>modification - score the two peptides "
+ "separately, treating the second peptide as a variable modification "
+ "on the first peptide</li><li>concatenated - score as the concatenation "
+ "of the two peptides. Note that this mode gives four scores, "
+ "corresponding to the two relative orders of the peptides (AB and BA) "
+ "and the modification appearing on the first or second peptide.</li></ul>]]";
+}
+
+vector<string> XLinkScoreSpectrum::getArgs() const {
+ string arr[] = {
+ "peptide A",
+ "peptide B",
+ "pos A",
+ "pos B",
+ "link mass",
+ "charge state",
+ "scan number",
+ "ms2 file"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> XLinkScoreSpectrum::getOptions() const {
+ string arr[] = {
+ "verbosity",
+ "use-flanking-peaks",
+ "xlink-score-method",
+ "use-a-ions",
+ "use-b-ions",
+ "use-c-ions",
+ "use-x-ions",
+ "use-y-ions",
+ "use-z-ions"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > XLinkScoreSpectrum::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "XCorr score(s) in descending order"));
+ return outputs;
+}
+
diff --git a/src/app/xlink/xhhc_score_peptide_spectrum.h b/src/app/xlink/xhhc_score_peptide_spectrum.h
new file mode 100644
index 0000000..ca4b15f
--- /dev/null
+++ b/src/app/xlink/xhhc_score_peptide_spectrum.h
@@ -0,0 +1,29 @@
+#ifndef XHHC_SCORE_PEPTIDE_SPECTRUM_H
+#define XHHC_SCORE_PEPTIDE_SPECTRUM_H
+
+#include "app/CruxApplication.h"
+#include "model/Spectrum.h"
+#include "LinkedIonSeries.h"
+
+class XLinkScoreSpectrum : public CruxApplication {
+ public:
+ XLinkScoreSpectrum();
+ ~XLinkScoreSpectrum();
+
+ virtual int main(int argc, char** argv);
+ virtual void processParams();
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ private:
+ double get_concat_score(char* peptideA, char* peptideB, int link_site,
+ int charge, Crux::Spectrum* spectrum);
+ FLOAT_T* get_observed_raw(Crux::Spectrum* spectrum, int charge);
+ void print_spectrum(Crux::Spectrum* spectrum, LinkedIonSeries& ion_series);
+};
+
+#endif
+
diff --git a/src/app/xlink/xhhc_scorer.cpp b/src/app/xlink/xhhc_scorer.cpp
new file mode 100644
index 0000000..e41fec9
--- /dev/null
+++ b/src/app/xlink/xhhc_scorer.cpp
@@ -0,0 +1,441 @@
+#include "xhhc_scorer.h"
+#include "xhhc.h"
+#include "LinkedPeptide.h"
+
+#include "model/Spectrum.h"
+#include "model/Scorer.h"
+#include "util/Params.h"
+
+#include <fstream>
+
+// constants for print_spectrums
+#define NORMALIZE 0
+#define MAX_MZ 1200;
+#define MIN_MZ 400;
+#define NO_FLANKS 1
+
+using namespace Crux;
+
+/**
+ * Initializes an empty XHHC_Scorer object
+ */
+void XHHC_Scorer::init() {
+ print_spectrums_ = false;
+ scorer_ = NULL;
+ max_mz_ = 0.0;
+ max_bin_ = 0;
+ current_spectrum_ = NULL;
+
+ bin_width_ = Params::GetDouble("mz-bin-width");
+ bin_offset_ = Params::GetDouble("mz-bin-offset");
+
+}
+
+/**
+ * \returns an empty XHHC_Scorer object
+ */
+XHHC_Scorer::XHHC_Scorer() {
+ init();
+}
+
+/**
+ * Destructor
+ */
+XHHC_Scorer::~XHHC_Scorer() {
+
+ if (scorer_ != NULL) {
+ delete scorer_;
+ }
+
+}
+
+/**
+ * \returns an XHHC_Scorer object with the max_mz initialized
+ */
+XHHC_Scorer::XHHC_Scorer(
+ FLOAT_T max_mz ///< max_mz for the scorer.
+ ) {
+
+ init();
+ max_mz_ = max_mz;
+}
+
+/**
+ * \returns the max_mz
+ */
+FLOAT_T XHHC_Scorer::getMaxMz() {
+
+ return max_mz_;
+}
+
+/*
+ * Sets the print_spectrums_ variable
+ */
+void XHHC_Scorer::setPrint(
+ bool print_spectrums ///< indicator of whether we are printing spectrums
+ ) {
+
+ print_spectrums_ = print_spectrums;
+}
+
+/**
+ * \returns the number of BY ions in the Ionseries that are
+ * matched to peaks in the spectrum
+ */
+int XHHC_Scorer::getMatchedBYIons(
+ Spectrum* spectrum,
+ LinkedIonSeries& ion_series) {
+
+ FLOAT_T bin_width = BIN_WIDTH_MONO;
+ vector<LinkedPeptide>& ions = ion_series.getIons();
+
+ int ans = 0;
+
+ for (vector<LinkedPeptide>::iterator ion = ions.begin(); ion != ions.end(); ++ion) {
+ if (ion -> getMZ(MONO) >= 400 && ion -> getMZ(MONO) <= 1200) {
+ if (ion -> getIonType() == B_ION || ion -> getIonType() == Y_ION) {
+ Peak * peak = spectrum->getNearestPeak(ion->getMZ(AVERAGE),
+ bin_width);
+ if (peak != NULL) {
+ ans++;
+ }
+ }
+ }
+ }
+ return ans;
+}
+
+/**
+ * \returns the xcorr score for the spectrum and the ion_series
+ */
+FLOAT_T XHHC_Scorer::scoreSpectrumVsSeries(
+ Spectrum* spectrum, ///< Spectrum to score
+ LinkedIonSeries& ion_series ///< LinkedIonSeries to score
+ ) {
+
+ FLOAT_T score = 0.0;
+ score = hhcGenScoreXcorr(spectrum, ion_series);
+ return score;
+}
+
+/**
+ * Generates the theoretical/observed arrays and scores the spectrum for xcorr
+ */
+FLOAT_T XHHC_Scorer::hhcGenScoreXcorr(
+ Spectrum* spectrum, ///< the spectrum to score -in
+ LinkedIonSeries& ion_series ///< the ion series to score against the spectrum -in
+ ) {
+
+ FLOAT_T final_score = 0;
+ FLOAT_T* theoretical = NULL;
+
+ if (current_spectrum_ != spectrum) {
+ current_spectrum_ = spectrum;
+ if (scorer_ != NULL) {
+ delete scorer_;
+ scorer_ = NULL;
+ }
+ scorer_ = new Scorer(XCORR);
+ if (!scorer_->createIntensityArrayXcorr(spectrum, ion_series.getCharge())) {
+ carp(CARP_FATAL, "failed to produce XCORR");
+ }
+ }
+
+ max_mz_ = scorer_->getSpMaxMz();
+ max_bin_ = scorer_->getMaxBin();
+ // create theoretical array
+ theoretical = (FLOAT_T*)mycalloc((size_t)max_bin_, sizeof(FLOAT_T));
+
+ if (!hhcCreateIntensityArrayTheoretical(ion_series, theoretical)) {
+ carp(CARP_ERROR, "failed to create theoretical spectrum for Xcorr");
+ return false;
+ }
+
+ // do cross correlation between observed spectrum(in scorer) and theoretical spectrum.
+ // use the two intensity arrays that were created
+ final_score = scorer_->crossCorrelation(theoretical);
+ if (print_spectrums_) {
+ printSpectrums(theoretical, spectrum);
+ }
+ // free theoretical spectrum
+ free(theoretical);
+ return final_score;
+}
+
+/**
+ * adds an intensity in the theoretical map at peak idx
+ */
+void XHHC_Scorer::addIntensityMap(
+ map<int, FLOAT_T>& theoretical, ///< the theoretical map
+ int idx, ///< the idx to add
+ FLOAT_T intensity ///< the corresponding intensity
+ ) {
+
+ map<int, FLOAT_T>::iterator iter = theoretical.find(idx);
+ if (iter == theoretical.end())
+ theoretical[idx] = intensity;
+ else
+ iter -> second = max(intensity, iter -> second);
+}
+
+
+/**
+ * \returns whether create a theoretical map of peak_idx,intensity pairs
+ * is sucessful
+ */
+bool XHHC_Scorer::xlinkCreateMapTheoretical(
+ LinkedIonSeries& ion_series, ///< LinkedIonSeries to create the map from -in
+ map<int, FLOAT_T>& theoretical ///< The theoretical map -out
+ ) {
+
+ theoretical.clear();
+ int intensity_array_idx = 0;
+ FLOAT_T bin_width = BIN_WIDTH_MONO;
+ vector<LinkedPeptide>& ions = ion_series.getIons();
+ // while there are ion's in ion iterator, add matched observed peak intensity
+ for (vector<LinkedPeptide>::iterator ion = ions.begin(); ion != ions.end(); ++ion) {
+ intensity_array_idx = (int)(ion->getMZ(MONO) / bin_width + 0.5);
+ //ion_type = ion->getIonType();
+ //ion_charge = ion->getCharge();
+
+ // is it B, Y ion?
+
+ // neutral loss peak?
+ // Add peaks of intensity 50.0 for B, Y type ions.
+ // In addition, add peaks of intensity of 25.0 to +/- 1 m/z flanking each B, Y ion.
+ // Skip ions that are located beyond max mz limit
+ addIntensityMap(theoretical, intensity_array_idx, 50);
+ if (Params::GetBool("use-flanking-peaks")) {
+ if (intensity_array_idx > 0) {
+ addIntensityMap(theoretical, intensity_array_idx - 1, 25);
+ }
+ addIntensityMap(theoretical, intensity_array_idx + 1, 25);
+
+ }
+
+ // add neutral loss of water and NH3
+ // mass_z + (modification_masses[(int)ion_modification]/(FLOAT_T)charge) * modification_count;
+
+ //TODO put this back in
+ //if(ion_type == B_ION) {
+ int h2o_array_idx = (int)((ion->getMZ(MONO) - (MASS_H2O_MONO/ion->getCharge()) ) / bin_width + 0.5);
+ addIntensityMap(theoretical, h2o_array_idx, 10);
+ //}
+
+ int co_array_idx = (int)((ion -> getMZ(MONO) - (MASS_CO_MONO/ion->getCharge())) / bin_width + 0.5);
+ addIntensityMap(theoretical, co_array_idx, 10);
+
+ int nh3_array_idx = (int)((ion->getMZ(MONO) - (MASS_NH3_MONO/ion->getCharge())) / bin_width + 0.5);
+ addIntensityMap(theoretical, nh3_array_idx, 10);
+ }
+ return true;
+}
+
+/**
+ * Fills in the theoretical array using the LinkedIonSeries
+ */
+bool XHHC_Scorer::hhcCreateIntensityArrayTheoretical(
+ LinkedIonSeries& ion_series, ///< The linked ion series to use -in
+ FLOAT_T* theoretical ///< the empty theoretical spectrum -out
+ ) {
+
+ ION_TYPE_T ion_type;
+ int intensity_array_idx = 0;
+ vector<LinkedPeptide>& ions = ion_series.getIons();
+ // while there are ion's in ion iterator, add matched observed peak intensity
+ for (vector<LinkedPeptide>::iterator ion = ions.begin(); ion != ions.end(); ++ion) {
+ intensity_array_idx = INTEGERIZE(ion->getMZ(MONO), bin_width_, bin_offset_);
+ ion_type = ion->getIonType();
+ //ion_charge = ion->getCharge();
+ // skip ions that are located beyond max mz limit
+ // is it B, Y ion?
+ // neutral loss peak?
+ // Add peaks of intensity 50.0 for B, Y type ions.
+ // In addition, add peaks of intensity of 25.0 to +/- 1 m/z flanking each B, Y ion.
+ // Skip ions that are located beyond max mz limit
+ if((intensity_array_idx)< max_bin_) {
+ //if (ion->type() == Y_ION)
+ //add_intensity(theoretical, intensity_array_idx, 51);
+ Scorer::addIntensity(theoretical, intensity_array_idx, 50);
+ if (Params::GetBool("use-flanking-peaks") &&
+ intensity_array_idx > 0) {
+ Scorer::addIntensity(theoretical, intensity_array_idx - 1, 25);
+ }
+ if(Params::GetBool("use-flanking-peaks") &&
+ ((intensity_array_idx + 1)< max_bin_)) {
+ Scorer::addIntensity(theoretical, intensity_array_idx + 1, 25);
+ }
+ }
+
+ // add neutral loss of water and NH3
+ // mass_z + (modification_masses[(int)ion_modification]/(FLOAT_T)charge) * modification_count;
+
+
+ if(ion_type == B_ION) {
+ int h2o_array_idx =
+ INTEGERIZE((ion->getMZ(MONO) - (MASS_H2O_MONO/ion->getCharge())), bin_width_, bin_offset_);
+
+ if (h2o_array_idx < max_bin_)
+ Scorer::addIntensity(theoretical, h2o_array_idx, 10);
+ }
+
+ int nh3_array_idx =
+ INTEGERIZE((ion->getMZ(MONO) - (MASS_NH3_MONO/ion->getCharge())),
+ bin_width_, bin_offset_);
+ if (nh3_array_idx < max_bin_) {
+ Scorer::addIntensity(theoretical, nh3_array_idx, 10);
+ }
+ }
+ return true;
+}
+
+/**
+ * \returns the sum of the spectrum peak intensities of the by-ions that are matched
+ * to the LinkedIonSeries
+ */
+FLOAT_T XHHC_Scorer::getIonCurrentExplained(
+ LinkedIonSeries& ion_series, ///<The LinkedIonSeries to match
+ Spectrum* spectrum, ///<The spectrum to match
+ FLOAT_T& explained, ///<The ion current explained -out
+ int& by_observed ///<The number of by ions matched
+ ) {
+
+ max_mz_ = spectrum->getMaxPeakMz();
+ FLOAT_T* theoretical = (FLOAT_T*)mycalloc((size_t)max_mz_+1, sizeof(FLOAT_T));
+ hhcCreateIntensityArrayTheoretical(ion_series, theoretical);
+
+ explained = 0.0;
+ by_observed = 0;
+
+ FLOAT_T bin_width = BIN_WIDTH_MONO;
+
+ FLOAT_T ans = 0.0;
+
+ map<int, bool> by_found;
+
+ for (PeakIterator peak_iter = spectrum->begin();
+ peak_iter != spectrum->end();
+ ++peak_iter) {
+
+ Peak * peak = *peak_iter;
+ FLOAT_T spec_mz = peak->getLocation();
+ FLOAT_T spec_intensity = peak->getIntensity();
+ //for each peak in the spectrum, find the array index for the theoretical.
+ int intensity_array_idx = (int)(spec_mz / bin_width + 0.5);
+
+ if (theoretical[intensity_array_idx] >= 45) {
+ //it is a b-y ion that is observed.
+ if (by_found.find(intensity_array_idx) == by_found.end()) {
+ by_found[intensity_array_idx] = true;
+ by_observed++;
+ }
+ ans += spec_intensity;
+ }
+ }
+ free(theoretical);
+
+
+ explained = ans;
+ return ans;
+}
+
+/**
+ * Prints out an annotated spectrum
+ * creates three files for spectacle.pl: spectrums.out,
+ * theoretical.out, observed.out
+ */
+void XHHC_Scorer::printSpectrums(
+ FLOAT_T* theoretical, ///< The theoretical spectrum array
+ Spectrum* spectrum ///< The spectrum to print
+ ) {
+
+ ofstream theoretical_file;
+ ofstream observed_file;
+ ofstream spectrums_file;
+
+ theoretical_file.open("theoretical.out");
+ observed_file.open("observed.out");
+ spectrums_file.open("spectrums.out");
+
+ theoretical_file << "> theoretical" << endl;
+ observed_file << "> observed" << endl;
+ spectrums_file << "> spectrums" << endl;
+ bool noflanks = Params::GetBool("use-flanking-peaks");
+ int normalize = NORMALIZE;
+ int max_mz = MAX_MZ;
+ int min_mz = MIN_MZ;
+ // keep track of colors
+ map<Peak *, string> peak_colors;
+ carp(CARP_DEBUG, "min mz: %d, max mz: %d\n", max_mz);
+ FLOAT_T average = 0;
+
+ for (PeakIterator peak_iter = spectrum->begin();
+ peak_iter != spectrum->end();
+ ++peak_iter) {
+
+ average += (*peak_iter)->getIntensity();
+ }
+
+ average = average / spectrum->getNumPeaks();
+ // make spectacle file for observed peaks
+
+ for (PeakIterator peak_iter = spectrum->begin();
+ peak_iter != spectrum->end();
+ ++peak_iter) {
+
+ Peak * peak = *peak_iter;
+ FLOAT_T location = peak->getLocation();
+ FLOAT_T intensity = peak->getIntensity();
+ if (location > min_mz && location < max_mz) {
+ if (normalize) {
+ peak_colors[peak] = "blue";
+ } else {
+ observed_file << location<< "\t" << intensity << "\tnolabel\tred" << endl;
+ spectrums_file << location<< "\t" << intensity << "\tnolabel\tblue" << endl;
+ }
+ }
+ }
+
+
+ observed_file.close();
+ // make spectacle file for theoretical peaks
+ FLOAT_T* index = theoretical;
+ int i = 0;
+ int match_count = 0;
+ int mismatch_count = 0;
+ while (i <= max_mz) {
+ if (((*index > 1 && !noflanks) || *index > 26) && i >= min_mz) {
+ theoretical_file << i << "\t" << *index << "\tnolabel\tred" << endl;
+ Peak * peak = spectrum->getNearestPeak(i, 1);
+ if (peak != NULL) {
+ ++match_count;
+ peak_colors[peak] = "green";
+ spectrums_file << i << "\t" << -10000 << "\tnolabel\tgreen" << endl;
+ //spectrums_file << get_peak_location(peak) << "\t" << pow (get_peak_intensity(peak) * average * normalize, 0.2) << "\tnolabel\tgreen" << endl;
+ } else {
+ ++mismatch_count;
+ spectrums_file << i << "\t" << -10000 << "\tnolabel\tred" << endl;
+ }
+ }
+ ++i;
+ ++index;
+ }
+ FLOAT_T location;
+ FLOAT_T intensity;
+ for (map<Peak *, string>::iterator it = peak_colors.begin(); it != peak_colors.end(); ++it) {
+ location = it->first->getLocation();
+ intensity = it->first->getIntensity();;
+ //spectrums_file << location << "\t" << pow(intensity * average * normalize, 0.2) << "\tnolabel\t" << it->second << endl;
+ spectrums_file << location << "\t" << intensity << "\tnolabel\t" << it->second << endl;
+ }
+
+ theoretical_file.close();
+ spectrums_file.close();
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/xhhc_scorer.h b/src/app/xlink/xhhc_scorer.h
new file mode 100644
index 0000000..cd57eb1
--- /dev/null
+++ b/src/app/xlink/xhhc_scorer.h
@@ -0,0 +1,146 @@
+/**
+ * \file xhhc_scorer.h
+ * \brief object to score spectrum vs. xlink peptides
+ */
+/*
+ * AUTHOR: Sean McIlwain
+ * $Revision: 1.0 $
+ *****************************************************************************/
+#ifndef XHHC_SCORER_H
+#define XHHC_SCORER_H
+
+#include "model/Scorer.h"
+#include "XHHC_Peptide.h"
+
+#include "LinkedIonSeries.h"
+
+#include <map>
+
+class XHHC_Scorer {
+ private:
+ bool print_spectrums_; ///< Indicator of whether to print the spectrums
+ Scorer* scorer_; ///< The crux scorer
+ Crux::Spectrum* current_spectrum_; ///< Spectrum that this scorer works on
+ FLOAT_T max_mz_; ///< Maximum mz allocated for scorer
+ int max_bin_; ///< Maximum bin idx for scorer.
+ FLOAT_T bin_width_; ///< bin width for scorer
+ FLOAT_T bin_offset_; ///<bin offset for scorer
+
+ static int ion_counter_; ///< Ion counter
+
+ /**
+ * Prints out an annotated spectrum
+ * creates three files for spectacle.pl: spectrums.out,
+ * theoretical.out, observed.out
+ */
+ void printSpectrums(
+ FLOAT_T* theoretical, ///< The theoretical spectrum array
+ Crux::Spectrum* spectrum ///< The spectrum to print
+ );
+
+ /**
+ * Initializes an empty XHHC_Scorer object
+ */
+ void init();
+
+ public:
+
+ /**
+ * \returns an empty XHHC_Scorer object
+ */
+ XHHC_Scorer();
+
+ /**
+ * \returns an XHHC_Scorer object with the max_mz initialized
+ */
+ XHHC_Scorer(
+ FLOAT_T max_mz ///< max_mz for the scorer.
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~XHHC_Scorer();
+
+ /**
+ * \returns the max_mz
+ */
+ FLOAT_T getMaxMz();
+
+ /**
+ * \returns the xcorr score for the spectrum and the ion_series
+ */
+ FLOAT_T scoreSpectrumVsSeries(
+ Crux::Spectrum* spectrum, ///< Spectrum to score
+ LinkedIonSeries& ion_series ///< LinkedIonSeries to score
+ );
+
+ /**
+ * \returns the number of BY ions in the Ionseries that are
+ * matched to peaks in the spectrum
+ */
+ static int getMatchedBYIons(
+ Crux::Spectrum* spectrum, ///< Spectrum to match peaks with
+ LinkedIonSeries& ion_series ///< IonSeries to use
+ );
+
+ /**
+ * adds an intensity in the theoretical map at peak idx
+ */
+ static void addIntensityMap(
+ std::map<int, FLOAT_T>& theoretical, ///< the theoretical map
+ int idx, ///< the idx to add
+ FLOAT_T intensity ///< the corresponding intensity
+ );
+
+ /**
+ * \returns whether create a theoretical map of peak_idx,intensity pairs
+ * is sucessful
+ */
+ static bool xlinkCreateMapTheoretical(
+ LinkedIonSeries& ion_series, ///< LinkedIonSeries to create the map from -in
+ std::map<int, FLOAT_T>& theoretical ///< The theoretical map -out
+ );
+
+ /**
+ * Fills in the theoretical array using the LinkedIonSeries
+ */
+ bool hhcCreateIntensityArrayTheoretical(
+ LinkedIonSeries& ion_series, /// The linked ion series to use -in
+ FLOAT_T* theoretical ///< the empty theoretical spectrum -out
+ );
+
+ /*
+ * Sets the print_spectrums_ variable
+ */
+ void setPrint(
+ bool print_spectrums ///< indicator of whether we are printing spectrums
+ );
+
+ /**
+ * Generates the theoretical/observed arrays and scores the spectrum for xcorr
+ */
+ FLOAT_T hhcGenScoreXcorr(
+ Crux::Spectrum* spectrum, ///< the spectrum to score -in
+ LinkedIonSeries& ion_series ///< the ion series to score against the spectrum -in
+ );
+
+ /**
+ * \returns the sum of the spectrum peak intensities of the by-ions that are matched
+ * to the LinkedIonSeries
+ */
+ FLOAT_T getIonCurrentExplained(
+ LinkedIonSeries& ion_series, ///<The LinkedIonSeries to match
+ Crux::Spectrum* spectrum, ///<The spectrum to match
+ FLOAT_T& explained, ///<The ion current explained -out
+ int& by_observed ///<The number of by ions matched
+ );
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/app/xlink/xhhc_search.cpp b/src/app/xlink/xhhc_search.cpp
new file mode 100644
index 0000000..1769ba3
--- /dev/null
+++ b/src/app/xlink/xhhc_search.cpp
@@ -0,0 +1,580 @@
+/**
+ * \file xhhc_search.cpp
+ * AUTHOR: Sean McIlwain
+ * \brief Main file for crux-search-for-xlinks.
+ *
+ * Given an ms2 file and a fasta file or index, compare all spectra to
+ * peptides and cross-linked products in the fasta file/index and
+ * return high scoring matches.
+ * Products are determined by parameters for length, mass, mass
+ * tolerance, cleavages. Score each spectrum with
+ * respect to all candidates, and rank by score.
+ * tab-delimited file format.
+ */
+
+//XLINK INCLUDES
+#include "xhhc_scorer.h"
+#include "LinkedIonSeries.h"
+#include "xlink_compute_qvalues.h"
+#include "SearchForXLinks.h"
+#include "LinkedPeptide.h"
+#include "XHHC_Peptide.h"
+
+//CRUX INCLUDES
+#include "model/objects.h"
+#include "model/Spectrum.h"
+#include "io/SpectrumCollectionFactory.h"
+#include "model/FilteredSpectrumChargeIterator.h"
+#include "util/GlobalParams.h"
+#include "util/Params.h"
+#include "io/MatchColumns.h"
+//C++ includes
+#include <cmath>
+#include <ctime>
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+
+using namespace std;
+using namespace Crux;
+
+//PRIVATE FUNCTIONS
+
+/**
+ * populate the filtered_ions vector with the products that
+ * fit within the precursor mass window
+ */
+void get_ions_from_window(
+ vector<LinkedPeptide>& filtered_ions, ///< filtered ions -out
+ vector<LinkedPeptide>& all_ions, ///< all ions in the database -in
+ FLOAT_T precursor_mass, ///<precursor mass -in
+ FLOAT_T window, ///< window value -in
+ WINDOW_TYPE_T window_type ///< window type -in
+);
+
+/**
+ * populated the filtered_ions vector with the products that
+ * have mass that is within the (min_mass,max_mass).
+ */
+void get_ions_from_mass_range(
+ vector<LinkedPeptide>& filtered_ions, ///< filtered ions -out
+ vector<LinkedPeptide>& all_ions, ///< all ions in the database -in
+ double min_mass, ///< min mass of ions to select -in
+ double max_mass ///< max mass of ions to select -in
+);
+
+/**
+ * \returns a comma delimited string of protein_id(peptide_start)
+ * locations for the peptides
+ */
+string get_protein_ids_locations(
+ vector<Peptide*>& peptides ///< vector of peptides
+ );
+
+/**
+ * main method for search-for-xlinks using the original code for the paper.
+ */
+int SearchForXLinks::xhhcSearchMain() {
+
+ carp(CARP_INFO, "Beginning crux xlink-search (original)");
+
+ //Get parameters
+ string ms2_file = Params::GetString("ms2 file");
+
+ FLOAT_T precursor_window = Params::GetDouble("precursor-window");
+ FLOAT_T precursor_window_weibull = Params::GetDouble("precursor-window-weibull");
+ WINDOW_TYPE_T precursor_window_type =
+ string_to_window_type(Params::GetString("precursor-window-type"));
+ WINDOW_TYPE_T window_type_weibull =
+ string_to_window_type(Params::GetString("precursor-window-type-weibull"));
+
+ string output_directory = Params::GetString("output-dir");
+
+ unsigned int min_weibull_points =
+ (unsigned int)Params::GetInt("min-weibull-points");
+ int max_ion_charge = get_max_ion_charge_parameter("max-ion-charge");
+ int top_match = Params::GetInt("top-match");
+ FLOAT_T linker_mass = Params::GetDouble("link mass");
+ int scan_num = 0;
+ SpectrumZState zstate;
+
+ //Set the static variable for the linker mass
+ LinkedPeptide::setLinkerMass(linker_mass);
+
+ vector<LinkedPeptide> all_ions;
+ carp(CARP_DETAILED_DEBUG, "Calling find all precursor ions");
+ find_all_precursor_ions(all_ions);
+ carp(CARP_DETAILED_DEBUG, "Sort");
+ // sort filtered ions and decoy ions by mass
+ //sort(all_ions.begin(), all_ions.end());
+ if (Params::GetBool("xlink-print-db")) {
+ ostringstream oss;
+ oss << output_directory << "/" << "xlink_peptides.txt";
+ string temp = oss.str();
+ ofstream peptides_file(temp.c_str());
+ peptides_file << "mass\tsequence" << endl;
+ for (unsigned int idx = 0; idx < all_ions.size(); idx++) {
+ peptides_file << all_ions.at(idx).getMass(MONO) << "\t";
+ peptides_file << all_ions.at(idx) << endl;
+ }
+ peptides_file.flush();
+ carp(CARP_INFO, "outputted database to xlink_peptides.txt");
+ return 0;
+ }
+
+ carp(CARP_INFO, "Loading Spectra");
+ Spectrum* spectrum = NULL;
+ Crux::SpectrumCollection* spectra = SpectrumCollectionFactory::create(ms2_file);
+ spectra->parse();
+
+ FilteredSpectrumChargeIterator* spectrum_iterator =
+ new FilteredSpectrumChargeIterator(spectra);
+
+ FLOAT_T score;
+ // best pvalues
+
+ string target_path = output_directory + "/search-for-xlinks.target.txt";
+ ofstream search_target_file(target_path.c_str());
+ //set precision
+ search_target_file << setprecision(Params::GetInt("precision"));
+ //print header
+ search_target_file << "scan\t";
+ search_target_file << "charge\t";
+ search_target_file << "spectrum precursor m/z\t";
+ search_target_file << "spectrum neutral mass\t";
+ search_target_file << "peptide mass mono\t";
+ search_target_file << "peptide mass average\t";
+ search_target_file << "mass error(ppm)\t";
+ search_target_file << "xcorr score\t";
+ search_target_file << "xcorr rank\t";
+ search_target_file << "p-value\t";
+ search_target_file << get_column_header(DISTINCT_MATCHES_SPECTRUM_COL) << "\t";
+ search_target_file << "sequence\t";
+ search_target_file << "protein id(loc) 1\t";
+ search_target_file << "protein id(loc) 2\t";
+ search_target_file << "by total\t";
+ search_target_file << "by observable (0-1200)\t";
+ search_target_file << "by observable bin (0-1200)\t";
+ search_target_file << "by observable (0-max)\t";
+ search_target_file << "by observable bin (0-max)\t";
+ search_target_file << "by observed bin\t";
+ search_target_file << "ion current total\t";
+ search_target_file << "ion current observed" << "\t";
+ search_target_file << "ions observable bin (0-1200)" << endl;
+
+ string decoy_path = output_directory + "/search-for-xlinks.decoy.txt";
+
+ ofstream search_decoy_file (decoy_path.c_str());
+ //set precision
+ search_decoy_file << setprecision(Params::GetInt("precision"));
+ //print header
+ search_decoy_file << "scan\t";
+ search_decoy_file << "charge\t";
+ search_decoy_file << "spectrum precursor m/z\t";
+ search_decoy_file << "spectrum neutral mass\t";
+ search_decoy_file << "peptide mass mono\t";
+ search_decoy_file << "peptide mass average\t";
+ search_decoy_file << "mass error(ppm)\t";
+ search_decoy_file << "xcorr score\t";
+ search_decoy_file << "xcorr rank\t";
+ search_decoy_file << "p-value\t";
+ search_decoy_file << get_column_header(DISTINCT_MATCHES_SPECTRUM_COL) << "\t";
+ search_decoy_file << "sequence" << endl;
+
+ XHHC_Scorer hhc_scorer;
+ // main loop over spectra in ms2 file
+
+ int search_count = 0;
+
+ // for every observed spectrum
+ while (spectrum_iterator->hasNext()) {
+ int charge;
+ spectrum = spectrum_iterator->next(zstate);
+
+ charge = zstate.getCharge();
+
+ //SCORER_T* scorer = new_scorer(XCORR);
+ scan_num = spectrum->getFirstScan();
+
+ if (search_count % 100 == 0)
+ carp(CARP_INFO, "count %d scan %d charge %d", search_count, scan_num, charge);
+ search_count++;
+
+ //vector<pair<FLOAT_T, LinkedPeptide> > linked_scores;
+ //vector<pair<FLOAT_T, LinkedPeptide> > single_scores;
+ vector<pair<FLOAT_T, LinkedPeptide> > scores;
+
+ vector<LinkedPeptide> target_xpeptides;
+ vector<LinkedPeptide> target_decoy_xpeptides;
+ vector<LinkedPeptide> decoy_train_xpeptides;
+ vector<LinkedPeptide> decoy_xpeptides;
+
+ FLOAT_T precursor_mz = spectrum->getPrecursorMz();
+ FLOAT_T precursor_mass = zstate.getNeutralMass();
+
+
+
+ clock_t start_clock = clock();
+
+
+ carp(CARP_DEBUG, "finding target xpeptides in mass window...%g", precursor_window);
+ get_ions_from_window(
+ target_xpeptides,
+ all_ions,
+ precursor_mass,
+ precursor_window,
+ precursor_window_type
+ );
+
+ if (target_xpeptides.size() < 1) {
+ carp(CARP_INFO, "not enough precursors found in range, skipping scan %d charge %d", scan_num, charge);
+ continue;
+ }
+
+
+ carp(CARP_DEBUG, "finding training xpeptides in decoy precursor window..%g", precursor_window_weibull);
+ get_ions_from_window(
+ target_decoy_xpeptides,
+ all_ions,
+ precursor_mass,
+ precursor_window_weibull,
+ window_type_weibull);
+
+ carp(CARP_DETAILED_DEBUG, "Creating decoys for target window");
+ //create the decoys from the target found in the target_mass_window.
+ for (vector<LinkedPeptide>::iterator ion = target_xpeptides.begin();
+ ion != target_xpeptides.end(); ++ion) {
+ add_decoy(decoy_xpeptides, *ion);
+ }
+
+
+ carp(CARP_DETAILED_DEBUG, "Creating decoys for decoy mass window");
+ //create the decoys from the target found in the decoy_mass_window.
+ while ((decoy_train_xpeptides.size() + target_xpeptides.size()) < min_weibull_points) {
+ for (vector<LinkedPeptide>::iterator ion = target_decoy_xpeptides.begin();
+ ion != target_decoy_xpeptides.end(); ++ion) {
+ add_decoy(decoy_train_xpeptides, *ion);
+ }
+ }
+
+ size_t num_training_points = decoy_train_xpeptides.size() + target_xpeptides.size();
+
+ carp(CARP_DEBUG, "num targets:%d", target_xpeptides.size());
+ carp(CARP_DEBUG, "num decoys:%d", decoy_xpeptides.size());
+ carp(CARP_DEBUG, "num training points:%d", num_training_points);
+
+ clock_t candidate_clock = clock();
+
+ int max_charge = min(max_ion_charge, charge);
+
+ LinkedIonSeries ion_series = LinkedIonSeries(max_charge);
+
+ // for every ion in the mass window
+ carp(CARP_DEBUG, "Scoring targets");
+ for (unsigned int idx = 0; idx < target_xpeptides.size(); idx++) {
+ //LinkedIonSeries ion_series = LinkedIonSeries(links, charge);
+ ion_series.clear();
+ ion_series.addLinkedIons(target_xpeptides[idx]);
+ score = hhc_scorer.scoreSpectrumVsSeries(spectrum, ion_series);
+ scores.push_back(make_pair(score, target_xpeptides[idx]));
+ }
+
+ carp(CARP_DEBUG, "Scoring decoys.");
+ for (unsigned int idx = 0; idx < decoy_xpeptides.size(); idx++) {
+ //LinkedIonSeries ion_series = LinkedIonSeries(links, charge);
+ ion_series.clear();
+ ion_series.addLinkedIons(decoy_xpeptides[idx]);
+ score = hhc_scorer.scoreSpectrumVsSeries(spectrum, ion_series);
+ scores.push_back(make_pair(score, decoy_xpeptides[idx]));
+ }
+
+
+ //use the decoy scores to build the estimator.
+ // create arrays to pass to crux's weibull methods
+ FLOAT_T* linked_decoy_scores_array = new FLOAT_T[num_training_points];
+
+ clock_t decoy_clock = clock();
+ carp(CARP_DEBUG, "scoring training decoys...");
+ // score all training decoys
+ for (unsigned int idx = 0; idx < decoy_train_xpeptides.size(); idx++) {
+ //LinkedIonSeries ion_series = LinkedIonSeries(links, charge);
+ ion_series.clear();
+ ion_series.addLinkedIons(decoy_train_xpeptides[idx]);
+ score = hhc_scorer.scoreSpectrumVsSeries(spectrum, ion_series);
+ linked_decoy_scores_array[idx] = score;
+ }
+
+ clock_t train_decoy_clock = clock();
+
+ for (unsigned int idx = 0; idx < scores.size(); idx++) {
+ if (!scores[idx].second.isDecoy())
+ linked_decoy_scores_array[idx+decoy_train_xpeptides.size()] = scores[idx].first;
+ }
+
+
+ // weibull parameters for candidates
+ FLOAT_T eta_linked = 0.0;
+ FLOAT_T beta_linked = 0.0;
+ FLOAT_T shift_linked = 0.0;
+ FLOAT_T correlation_linked = 0.0;
+
+ // fit weibull to decoys
+
+ carp(CARP_DEBUG, "Fitting weibull to %d scores", num_training_points);
+ hhc_estimate_weibull_parameters_from_xcorrs(linked_decoy_scores_array,
+ num_training_points,
+ &eta_linked, &beta_linked,
+ &shift_linked, &correlation_linked,
+ spectrum, charge);
+
+ //okay we don't need the training peptides/scores anymore
+ delete []linked_decoy_scores_array;
+ vector<LinkedPeptide>().swap(decoy_train_xpeptides);
+
+ // sort scores
+
+ carp(CARP_DEBUG, "sorting %u scores", scores.size());
+ sort(scores.begin(), scores.end(), greater<pair<FLOAT_T, LinkedPeptide> >());
+ carp(CARP_DEBUG, "done sorting");
+ int ndecoys = 0;
+ int ntargets = 0;
+ unsigned int score_index = 0;
+
+ while (score_index < scores.size() && (ndecoys < top_match || ntargets < top_match)) {
+
+
+ double ppm_error = fabs(scores[score_index].second.getMass(MONO) - precursor_mass) /
+ scores[score_index].second.getMass(MONO) * 1e6;
+
+ double pvalue = compute_weibull_pvalue(scores[score_index].first, eta_linked, beta_linked, shift_linked);
+
+ if (pvalue != pvalue) {
+ pvalue = 1;
+ }
+
+ if (scores[score_index].second.isDecoy() && ndecoys < top_match) {
+ ndecoys++;
+ search_decoy_file << scan_num << "\t";
+ search_decoy_file << charge << "\t";
+ search_decoy_file << precursor_mz << "\t";
+ search_decoy_file << precursor_mass << "\t";
+ search_decoy_file << scores[score_index].second.getMass(MONO) << "\t";
+ search_decoy_file << scores[score_index].second.getMass(AVERAGE) << "\t";
+ search_decoy_file << ppm_error << "\t";
+ search_decoy_file << scores[score_index].first <<"\t";
+ search_decoy_file << ndecoys << "\t";
+ search_decoy_file << pvalue << "\t";
+ search_decoy_file << decoy_xpeptides.size() << "\t";
+ search_decoy_file << scores[score_index].second << endl;
+
+ } else if (!scores[score_index].second.isDecoy() && ntargets < top_match) {
+ ntargets++;
+ search_target_file << scan_num << "\t";
+ search_target_file << charge << "\t";
+ search_target_file << precursor_mz << "\t";
+ search_target_file << precursor_mass << "\t";
+ search_target_file << scores[score_index].second.getMass(MONO) << "\t";
+ search_target_file << scores[score_index].second.getMass(AVERAGE) << "\t";
+ search_target_file << ppm_error << "\t";
+ search_target_file << scores[score_index].first <<"\t";
+ search_target_file << ntargets << "\t";
+ search_target_file << pvalue << "\t";
+ search_target_file << target_xpeptides.size() << "\t";
+ search_target_file << scores[score_index].second << "\t";
+
+ //output protein ids/peptide locations. If it is a linear, dead or self loop, only
+ //use the 1st field.
+ string sequence1 = scores[score_index].second.getPeptides()[0].getSequence();
+ vector<Peptide*>& peptides1 = get_peptides_from_sequence(sequence1);
+ string result_string = get_protein_ids_locations(peptides1);
+ search_target_file << result_string << "\t";
+ //if it is cross-linked peptide, use the second field
+ if (scores[score_index].second.isCrossLinked()) {
+ string sequence2 = scores[score_index].second.getPeptides()[1].getSequence();
+ vector<Peptide*>& peptides2 = get_peptides_from_sequence(sequence2);
+ string result_string = get_protein_ids_locations(peptides2);
+ search_target_file << result_string;
+ }
+ search_target_file <<"\t";
+ //get theoretical ions count for (0-1200, with 1Da bins).
+ XHHC_Scorer scorer;
+ LinkedIonSeries ion_series(charge);
+ ion_series.addLinkedIons(scores[score_index].second);
+
+ FLOAT_T ion_current_observed;
+ FLOAT_T ion_current_total = spectrum->getTotalEnergy();
+ int by_total = ion_series.getTotalBYIons();
+ int by_observable;
+ int by_observable2;
+ int by_observable_bin;
+ int by_observable_bin2;
+ int by_observed_bin;
+ int ions_observable;
+ int ions_observable_bin;
+ ion_series.getObservableIons(0, 1200, BIN_WIDTH_MONO, ions_observable, ions_observable_bin);
+ ion_series.getObservableBYIons(0, 1200, BIN_WIDTH_MONO, by_observable, by_observable_bin);
+ ion_series.getObservableBYIons(0, spectrum->getMaxPeakMz(), BIN_WIDTH_MONO, by_observable2, by_observable_bin2);
+ scorer.getIonCurrentExplained(ion_series, spectrum, ion_current_observed, by_observed_bin);
+
+
+
+ search_target_file << by_total << "\t";
+ search_target_file << by_observable << "\t";
+ search_target_file << by_observable_bin << "\t";
+ search_target_file << by_observable2 << "\t";
+ search_target_file << by_observable_bin2 << "\t";
+ search_target_file << by_observed_bin << "\t";
+ search_target_file << ion_current_total << "\t";
+ search_target_file << ion_current_observed << "\t";
+ search_target_file << ions_observable_bin;
+
+ search_target_file << endl;
+
+
+ }
+ score_index++;
+ }
+
+ //free_spectrum(spectrum);
+
+ carp(CARP_DETAILED_DEBUG, "Done with spectrum %d", scan_num);
+ } // get next spectrum
+ search_target_file.close();
+ search_decoy_file.close();
+
+ //Calculate q-values.
+ carp(CARP_INFO, "Computing Q-Values");
+
+ //free memory.
+ xlink_compute_qvalues();
+ delete spectrum_iterator;
+ delete spectra;
+ free_peptides();
+
+ // get list of mods
+ PEPTIDE_MOD_T** peptide_mods = NULL;
+ int num_peptide_mods = generate_peptide_mod_list( &peptide_mods );
+ for(int mod_idx = 0; mod_idx < num_peptide_mods; mod_idx++) {
+ free_peptide_mod(peptide_mods[mod_idx]);
+ }
+ free(peptide_mods);
+
+ carp(CARP_INFO, "Elapsed time: %.3g s", wall_clock() / 1e6);
+ carp(CARP_INFO, "Finished crux search-for-xlinks.");
+
+ return(0);
+}
+
+/**
+ * populate the filtered_ions vector with the ions that
+ * fit within the precursor mass window
+ */
+void get_ions_from_window(
+ vector<LinkedPeptide>& filtered_ions, ///< filtered ions -out
+ vector<LinkedPeptide>& all_ions, ///< all ions in the database -in
+ FLOAT_T precursor_mass, ///<precursor mass -in
+ FLOAT_T window, ///< window value -in
+ WINDOW_TYPE_T window_type ///< window type -in
+ ) {
+
+ double min_mass = 0;
+ double max_mass = 0;
+
+ if (window_type == WINDOW_MASS) {
+ min_mass = precursor_mass - window;
+ max_mass = precursor_mass + window;
+ } else if (window_type == WINDOW_PPM) {
+ min_mass = precursor_mass * (1.0 - window * 1e-6);
+ max_mass = precursor_mass * (1.0 + window * 1e-6);
+ } else {
+ carp(CARP_FATAL, "Precursor m/z window type not supported!");
+ }
+
+ get_ions_from_mass_range(filtered_ions, all_ions, min_mass, max_mass);
+
+}
+
+/**
+ * populated the filtered_ions vector with the products that
+ * have mass that is within the (min_mass,max_mass).
+ */
+void get_ions_from_mass_range(
+ vector<LinkedPeptide>& filtered_ions, ///< filtered ions -out
+ vector<LinkedPeptide>& all_ions, ///< all ions in the database -in
+ double min_mass, ///< min mass of ions to select -in
+ double max_mass ///< max mass of ions to select -in
+ ) {
+
+ MASS_TYPE_T mass_type = GlobalParams::getIsotopicMass();
+
+ filtered_ions.clear();
+ for (vector <LinkedPeptide>::iterator ion = all_ions.begin();
+ ion != all_ions.end();
+ ++ion) {
+ double mass = ion -> getMass(mass_type);
+ if (mass >= min_mass && mass <= max_mass) {
+ filtered_ions.push_back(*ion);
+ }
+ }
+}
+
+/**
+ * given a peptide, populate the protein_ids_locations
+ * with a set of strings that are protein_id(peptide start index).
+ */
+void get_protein_ids_locations(
+ Peptide *peptide, ///< peptide to generate locations from -in
+ set<string>& protein_ids_locations ///< set of protein_id(peptide start index). -out
+ ) {
+
+ std::ostringstream protein_field_stream;
+
+ for (PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter != peptide->getPeptideSrcEnd();
+ ++iter) {
+
+ PeptideSrc* peptide_src = *iter;
+ Protein* protein = peptide_src->getParentProtein();
+ string& protein_id = protein->getIdPointer();
+ int peptide_loc = peptide_src->getStartIdx();
+ std::ostringstream protein_loc_stream;
+ protein_loc_stream << protein_id << "(" << peptide_loc << ")";
+ protein_ids_locations.insert(protein_loc_stream.str());
+
+ }
+
+}
+
+/**
+ * \returns a comma delimited string of protein_id(peptide_start)
+ * locations for the peptides
+ */
+string get_protein_ids_locations(
+ vector<Peptide*>& peptides ///< vector of peptides
+ ) {
+
+ set<string> protein_ids_locations;
+
+ for (unsigned int idx = 0; idx < peptides.size(); idx++) {
+ get_protein_ids_locations(peptides[idx], protein_ids_locations);
+ }
+
+ set<string>::iterator result_iter = protein_ids_locations.begin();
+
+ string protein_field_string = *result_iter;
+
+ while(++result_iter != protein_ids_locations.end()) {
+ protein_field_string += "," + *result_iter;
+ }
+
+ return protein_field_string;
+
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/xlink_assign_ions.cpp b/src/app/xlink/xlink_assign_ions.cpp
new file mode 100644
index 0000000..59fe226
--- /dev/null
+++ b/src/app/xlink/xlink_assign_ions.cpp
@@ -0,0 +1,286 @@
+//TODO - change cerr/couts to carp.
+
+#include "xlink_assign_ions.h"
+
+#include "XLinkMatch.h"
+#include "SelfLoopPeptide.h"
+#include "XLinkPeptide.h"
+
+#include "model/objects.h"
+#include "model/Scorer.h"
+#include "model/IonSeries.h"
+#include "model/Ion.h"
+#include "io/SpectrumCollectionFactory.h"
+#include "io/DelimitedFile.h"
+#include "util/Params.h"
+
+#include <math.h>
+#include <assert.h>
+#include <ctype.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include <iostream>
+#include <fstream>
+
+
+using namespace Crux;
+
+XLinkAssignIons::XLinkAssignIons() {
+}
+
+XLinkAssignIons::~XLinkAssignIons() {
+}
+
+int XLinkAssignIons::main(int argc, char** argv) {
+ /* Get Arguments */
+ string peptideAStr = Params::GetString("peptide A");
+ string peptideBStr = Params::GetString("peptide B");
+ char* peptideA = my_copy_string(peptideAStr.c_str());
+ char* peptideB = my_copy_string(peptideBStr.c_str());
+
+ int posA = Params::GetInt("pos A");
+ int posB = Params::GetInt("pos B");
+ int charge = Params::GetInt("charge state");
+ int scan_num = Params::GetInt("scan number");
+
+ string ms2_file = Params::GetString("ms2 file");
+
+ XLinkPeptide::setLinkerMass(Params::GetDouble("link mass"));
+
+ // create new ion series
+
+ // a single peptide linked to itself
+ if (strcmp(peptideB, "NULL") == 0) {
+ cout << "B is null" << endl;
+ peptideB = NULL;
+ }
+
+ // read ms2 file
+ Crux::SpectrumCollection* collection = SpectrumCollectionFactory::create(ms2_file);
+ collection->parse();
+
+
+ //cout << "lp " << lp << endl;
+ Spectrum* spectrum = NULL;
+ Spectrum* current_spectrum = NULL;
+
+ //TODO allow a binary search on both mgf and ms2 files.
+
+ for (SpectrumIterator spectrum_iterator = collection->begin();
+ spectrum_iterator != collection->end();
+ ++spectrum_iterator) {
+
+ current_spectrum = *spectrum_iterator;
+ if (current_spectrum->getFirstScan() == scan_num) {
+ spectrum = current_spectrum;
+ break;
+ }
+ }
+
+ // search for spectrum with correct scan number
+ if (spectrum == NULL) {
+ carp(CARP_ERROR, "Failed to find spectrum with scan number %d.", scan_num);
+ delete collection;
+ exit(1);
+ }
+
+ //created linked peptide.
+ XLinkMatch* xlp = NULL;
+ if (peptideB != NULL) {
+ xlp = new XLinkPeptide(peptideA, peptideB, posA-1, posB-1);
+ } else {
+ xlp = new SelfLoopPeptide(peptideA, posA-1, posB-1);
+ }
+
+ IonConstraint* ion_constraint = IonConstraint::newIonConstraintSequestXcorr(charge);
+ ion_constraint->setUseIonType(BY_ION, false);
+ ion_constraint->setUseIonType(BYA_ION, false);
+ ion_constraint->setUseIonType(ALL_ION, false);
+ ion_constraint->setUseIonType(A_ION, Params::GetBool("use-a-ions"));
+ ion_constraint->setUseIonType(B_ION, Params::GetBool("use-b-ions"));
+ ion_constraint->setUseIonType(C_ION, Params::GetBool("use-c-ions"));
+ ion_constraint->setUseIonType(X_ION, Params::GetBool("use-x-ions"));
+ ion_constraint->setUseIonType(Y_ION, Params::GetBool("use-y-ions"));
+ ion_constraint->setUseIonType(Z_ION, Params::GetBool("use-z-ions"));
+
+ IonSeries* ion_series = new IonSeries(ion_constraint, charge);
+ xlp->predictIons(ion_series, charge);
+
+ print_spectrum(spectrum, xlp, ion_series);
+
+ // free heap
+ delete collection;
+ delete ion_series;
+ delete ion_constraint;
+ delete xlp;
+ //free_spectrum(spectrum);
+ return 0;
+}
+
+void XLinkAssignIons::print_spectrum(
+ Spectrum* spectrum,
+ XLinkMatch* xlp,
+ IonSeries* ion_series
+ ) {
+
+ carp(CARP_INFO, "Number of peaks = %d", spectrum->getNumPeaks());
+
+ FLOAT_T bin_width = Params::GetDouble("mz-bin-width");
+
+ map<Peak*, Ion*> matched;
+ double matched_intensity = 0;
+
+ for (IonIterator ion_iterator = ion_series->begin();
+ ion_iterator != ion_series->end();
+ ++ion_iterator) {
+
+ Ion* ion = *ion_iterator;
+ Peak* peak = spectrum->getMaxIntensityPeak(ion->getMassZ(), bin_width);
+ if (peak != NULL) {
+ if (matched.find(peak) == matched.end()) {
+ matched_intensity += peak->getIntensity();
+ matched[peak] = ion;
+ } else {
+ carp(CARP_WARNING, "Peak at %g matches more than one theoretical peak.", peak->getLocation());
+ }
+ }
+ }
+
+ double total_intensity = spectrum->getTotalEnergy();
+ double frac_intensity = matched_intensity / total_intensity;
+ carp(CARP_INFO, "Fraction matched intensity = %lf / %lf = %lf",
+ matched_intensity, total_intensity, frac_intensity);
+
+
+ //now print out the spectrum
+
+ DelimitedFile result_file;
+
+ unsigned int mz_obs_col = result_file.addColumn("m/z obs");
+ unsigned int int_col = result_file.addColumn("intensity");
+ unsigned int int_matched_col = result_file.addColumn("matched intensity");
+ unsigned int mz_calc_col = result_file.addColumn("m/z calc");
+ unsigned int mass_obs_col = result_file.addColumn("mass obs");
+ unsigned int mass_calc_col = result_file.addColumn("mass calc");
+ unsigned int ppm_col = result_file.addColumn("ppm(Mass)");
+ unsigned int ion_col = result_file.addColumn("ion");
+ unsigned int seq_col = result_file.addColumn("sequence");
+
+ for (PeakIterator peak_iter = spectrum->begin();
+ peak_iter != spectrum->end();
+ ++peak_iter) {
+
+ Peak * peak = *peak_iter;
+ if (peak->getIntensity() > 0) {
+ unsigned int row_idx = result_file.addRow();
+ result_file.setValue(mz_obs_col, row_idx, peak->getLocation());
+ result_file.setValue(int_col, row_idx, peak->getIntensity());
+ if (matched.find(peak) != matched.end()) {
+ Ion* ion = matched[peak];
+ double mz_calc = ion->getMassZ();
+ double mz_obs = peak->getLocation();
+ int charge = ion->getCharge();
+ double mass_calc = ion->getMassFromMassZ();
+ double mass_obs = (mz_obs - MASS_PROTON) * (double)charge;
+ double ppm = fabs(mass_calc - mass_obs) / mass_calc * 1e6;
+
+ result_file.setValue(int_matched_col, row_idx, peak->getIntensity());
+ result_file.setValue(mz_calc_col, row_idx, mz_calc);
+ result_file.setValue(mass_obs_col, row_idx, mass_obs);
+ result_file.setValue(mass_calc_col, row_idx, mass_calc);
+ result_file.setValue(ppm_col, row_idx, ppm);
+
+ ostringstream ion_string_oss;
+ switch(ion->getType()) {
+ case A_ION:
+ ion_string_oss << "a";
+ break;
+ case B_ION:
+ ion_string_oss << "b";
+ break;
+ case C_ION:
+ ion_string_oss << "c";
+ break;
+ case X_ION:
+ ion_string_oss << "x";
+ break;
+ case Y_ION:
+ ion_string_oss << "y";
+ break;
+ case Z_ION:
+ ion_string_oss << "z";
+ break;
+ default:
+ ion_string_oss << "u";
+ }
+ ion_string_oss << "(+" << charge << ")";
+
+ result_file.setValue(ion_col, row_idx, ion_string_oss.str());
+ result_file.setValue(seq_col, row_idx, xlp->getIonSequence(ion));
+ }
+ }
+ }
+ cout << result_file;
+
+}
+
+void XLinkAssignIons::processParams() {
+ for (char c = 'A'; c <= 'Z'; c++) {
+ double deltaMass = Params::GetDouble(string(1, c));
+ increase_amino_acid_mass(c, deltaMass);
+ }
+}
+
+string XLinkAssignIons::getName() const {
+ return "xlink-assign-ions";
+}
+
+string XLinkAssignIons::getDescription() const {
+ return
+ "Given a spectrum and a pair of cross-linked peptides, assign theoretical "
+ "ion type labels to peaks in the observed spectrum.";
+}
+
+vector<string> XLinkAssignIons::getArgs() const {
+ string arr[] = {
+ "peptide A",
+ "peptide B",
+ "pos A",
+ "pos B",
+ "link mass",
+ "charge state",
+ "scan number",
+ "ms2 file"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector<string> XLinkAssignIons::getOptions() const {
+ string arr[] = {
+ "verbosity",
+ "spectrum-parser",
+ "fragment-mass",
+ "max-ion-charge",
+ "mz-bin-width",
+ "precision"
+ };
+ return vector<string>(arr, arr + sizeof(arr) / sizeof(string));
+}
+
+vector< pair<string, string> > XLinkAssignIons::getOutputs() const {
+ vector< pair<string, string> > outputs;
+ outputs.push_back(make_pair("stdout",
+ "tab-delimited text in which each row is a peak in the observed spectrum, "
+ "and the columns are <ol>"
+ "<li>The m/z value.</li>"
+ "<li>The observed intensity.</li>"
+ "<li>The matched intensity.</li>"
+ "<li>The calculated m/z value of the theoretical peak.</li>"
+ "<li>The mass associated with the observed peak.</li>"
+ "<li>The mass difference (in ppm) between the observed and theoretical peaks.</li>"
+ "<li>The ion type, specified as b or y, followed by the charge state in parentheses.</li>"
+ "<li>The amino acid sequence of the fragment.</li>"));
+ return outputs;
+}
+
diff --git a/src/app/xlink/xlink_assign_ions.h b/src/app/xlink/xlink_assign_ions.h
new file mode 100644
index 0000000..e2ccbe1
--- /dev/null
+++ b/src/app/xlink/xlink_assign_ions.h
@@ -0,0 +1,31 @@
+#ifndef XLINK_ASSIGN_IONS_H
+#define XLINK_ASSIGN_IONS_H
+
+#include "app/CruxApplication.h"
+#include "model/Spectrum.h"
+#include "LinkedIonSeries.h"
+#include "model/objects.h"
+
+class XLinkAssignIons : public CruxApplication {
+ public:
+ XLinkAssignIons();
+ ~XLinkAssignIons();
+
+ virtual int main(int argc, char** argv);
+ virtual void processParams();
+ virtual std::string getName() const;
+ virtual std::string getDescription() const;
+ virtual std::vector<std::string> getArgs() const;
+ virtual std::vector<std::string> getOptions() const;
+ virtual std::vector< std::pair<std::string, std::string> > getOutputs() const;
+
+ private:
+ void print_spectrum(
+ Crux::Spectrum* spectrum,
+ XLinkMatch* xlp,
+ IonSeries* ion_series
+ );
+};
+
+#endif
+
diff --git a/src/app/xlink/xlink_compute_qvalues.cpp b/src/app/xlink/xlink_compute_qvalues.cpp
new file mode 100644
index 0000000..3cf253d
--- /dev/null
+++ b/src/app/xlink/xlink_compute_qvalues.cpp
@@ -0,0 +1,282 @@
+//TODO - change cout/cerrs to carp.
+
+#include "xhhc.h"
+#include "LinkedIonSeries.h"
+#include "xhhc_scorer.h"
+#include "LinkedPeptide.h"
+
+#include "util/crux-utils.h"
+#include "util/Params.h"
+#include "model/objects.h"
+#include "model/Scorer.h"
+#include "io/DelimitedFile.h"
+#include "io/MatchColumns.h"
+
+#include "xlink_compute_qvalues.h"
+
+#include <math.h>
+#include <assert.h>
+#include <ctype.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include <iostream>
+#include <fstream>
+
+void getBestBonf(DelimitedFile& matches, int start, int stop,
+ int& best_index, double& best_bonf) {
+
+ int numScans = stop - start + 1;
+ //if there is only 1 scan, then return it.
+ if (numScans == 1) {
+ best_index = start;
+ double pvalue = matches.getDouble("p-value", best_index);
+ int ntests = matches.getInteger(get_column_header(DISTINCT_MATCHES_SPECTRUM_COL), best_index);
+ best_bonf = bonferroni_correction(pvalue, ntests);
+ } else {
+ map<int, pair<int, double> > charge_best_score;
+ map<int, int> charge_ntests;
+
+ for (int match_idx = start;match_idx <= stop;match_idx++) {
+ int charge = matches.getInteger("charge", match_idx);
+ double pvalue = matches.getDouble("p-value", match_idx);
+
+ if (charge_best_score.find(charge) == charge_best_score.end()) {
+ charge_best_score[charge] = make_pair(match_idx, pvalue);
+ } else if (pvalue < charge_best_score[charge].second) {
+ charge_best_score[charge] = make_pair(match_idx, pvalue);
+ }
+ if (charge_ntests.find(charge) == charge_ntests.end()) {
+ int ntests = matches.getInteger(get_column_header(DISTINCT_MATCHES_SPECTRUM_COL), match_idx);
+ charge_ntests[charge] = ntests;
+ }
+ }
+
+
+ int best_charge = charge_best_score.begin() -> first;
+ double best_charge_pvalue = charge_best_score[best_charge].second;
+ double best_charge_pvalue_bonf =
+ bonferroni_correction(best_charge_pvalue, charge_ntests[best_charge]);
+
+ int best_charge_idx = charge_best_score[best_charge].first;
+
+ for (map<int, pair<int, double> >::iterator iter =
+ charge_best_score.begin();
+ iter != charge_best_score.end();
+ ++iter) {
+
+ double current_charge_pvalue_bonf =
+ bonferroni_correction(iter -> second.second, charge_ntests[iter -> first]);
+ if (current_charge_pvalue_bonf < best_charge_pvalue_bonf) {
+ best_charge = iter -> first;
+ best_charge_pvalue = iter -> second.second;
+ best_charge_pvalue_bonf = current_charge_pvalue_bonf;
+ best_charge_idx = charge_best_score[best_charge].first;
+ }
+
+ }
+
+ int ntests_total = 0;
+ for (map<int, int>::iterator iter =
+ charge_ntests.begin();
+ iter != charge_ntests.end();
+ ++iter) {
+
+ ntests_total += iter -> second;
+ }
+
+ best_bonf = bonferroni_correction(best_charge_pvalue, ntests_total);
+ best_index = best_charge_idx;
+ }
+}
+
+void collapseScans(DelimitedFile& matches_in, DelimitedFile& matches_out) {
+
+ matches_out.clear();
+ //matches_out.addColumns(matches_in.getColumnNames());
+ vector<string>& column_names = matches_in.getColumnNames();
+ for (unsigned int idx = 0; idx < column_names.size(); idx++) {
+ matches_out.addColumn(column_names[idx]);
+ }
+
+ //make sure scans are together.
+ carp(CARP_DETAILED_DEBUG, "Sorting matches by scan");
+ matches_in.sortByIntegerColumn("scan");
+
+ matches_out.addColumn("p-value bonf.");
+
+ if (matches_in.numRows() == 0) {
+ return;
+ }
+
+ int last_scan = matches_in.getInteger("scan", 0);
+ int first_row = 0;
+ int best_row = 0;
+ double best_bonf = 0;
+
+
+ for (unsigned int match_idx = 0;
+ match_idx < matches_in.numRows();
+ match_idx++) {
+
+ int current_scan = matches_in.getInteger("scan", match_idx);
+ if (last_scan != current_scan) {
+ //process the scans between the first and match_idx-1.
+ //find the best row and calculate the bonferroni corrected p-value.
+ carp(CARP_DEBUG, "Collaping %d %d %d", last_scan, first_row, match_idx-1);
+ getBestBonf(matches_in, first_row, match_idx-1, best_row, best_bonf);
+ carp(CARP_DEBUG, "Copying row best: %d %lf", best_row, best_bonf);
+ //update matches out
+ int new_row = matches_out.addRow();
+ matches_in.copyToRow(matches_out, best_row, new_row);
+ carp(CARP_DEBUG, "Adding bonferroni");
+ matches_out.setValue<double>("p-value bonf.", new_row, best_bonf);
+
+
+ //update first_row and last scan.
+ first_row = match_idx;
+ last_scan = current_scan;
+ }
+ }
+
+ carp(CARP_DEBUG, "Doing last entry");
+ //finish the last entry
+ getBestBonf(matches_in, first_row, matches_in.numRows() - 1, best_row, best_bonf);
+ carp(CARP_DEBUG, "best: %d %lf", best_row, best_bonf);
+ int new_row = matches_out.addRow();
+ matches_in.copyToRow(matches_out, best_row, new_row);
+ matches_out.setValue("p-value bonf.", new_row, best_bonf);
+
+
+
+
+}
+
+
+int xlink_compute_qvalues() {
+
+ /* Get Arguments */
+
+ carp(CARP_INFO, "reading targets");
+ string output_dir = Params::GetString("output-dir");
+ string target_filename = "search-for-xlinks.target.txt";
+
+ //Read in targets.
+ string target_path = output_dir + "/" + target_filename;
+ DelimitedFile target_matches(target_path);
+
+ //cout << target_matches << endl;
+
+ //Read in decoys.
+
+ carp(CARP_INFO, "reading decoys");
+
+ string decoy_filename = "search-for-xlinks.decoy.txt";
+ string decoy_path = output_dir + "/" + decoy_filename;
+ DelimitedFile decoy_matches(decoy_path);
+
+ //cout << decoy_matches << endl;
+
+ //Collapse to the best target/decoy and calculate bonferonni corrected p-value.
+
+ carp(CARP_INFO, "collapsing targets");
+ DelimitedFile target_matches_bonf;
+ collapseScans(target_matches, target_matches_bonf);
+
+ carp(CARP_INFO, "collapsing decoys");
+ DelimitedFile decoy_matches_bonf;
+ collapseScans(decoy_matches, decoy_matches_bonf);
+
+ //Sort by increasing p-value.
+ carp(CARP_INFO, "Sorting by p-value bonf.");
+ target_matches_bonf.sortByFloatColumn("p-value bonf.");
+ decoy_matches_bonf.sortByFloatColumn("p-value bonf.");
+
+ //test the decoy p-values for accuracy.
+ for (unsigned int idx = 0; idx < decoy_matches_bonf.numRows(); idx++) {
+ double calc_pvalue = decoy_matches_bonf.getDouble("p-value bonf.", idx);
+ double rank_pvalue = (double)(idx + 1) / (double) decoy_matches_bonf.numRows();
+
+ if ((calc_pvalue > 2 * rank_pvalue) || (calc_pvalue < 0.5 * rank_pvalue)) {
+ carp(CARP_WARNING, "inaccurate p-values!");
+ carp(CARP_WARNING, "scan:%d charge:%d mass: %g rank:%g calc:%g",
+ decoy_matches_bonf.getInteger("scan", idx),
+ decoy_matches_bonf.getInteger("charge", idx),
+ decoy_matches_bonf.getDouble("spectrum neutral mass"),
+ rank_pvalue,
+ calc_pvalue);
+ }
+ }
+
+ carp(CARP_INFO, "Adding q-value column");
+ target_matches_bonf.addColumn("fdr b-h");
+ target_matches_bonf.addColumn("fdr decoy");
+ target_matches_bonf.addColumn("q-value b-h");
+ target_matches_bonf.addColumn("q-value decoy");
+
+ //carp(CARP_INFO,"Calculating q-values");
+ unsigned int decoy_idx = 0;
+ //cout <<"Number of target rows:"<<target_matches_bonf.numRows()<<endl;
+ for (unsigned int target_idx = 0;
+ target_idx < target_matches_bonf.numRows();
+ target_idx++) {
+
+ //calculate q-value by b-h
+ double current_pvalue = target_matches_bonf.getDouble("p-value bonf.", target_idx);
+ //cout <<"Current pvalue:"<<current_pvalue<<endl;
+
+ double fdr_bh = (double) target_matches_bonf.numRows() /
+ (double)(target_idx + 1) *
+ current_pvalue;
+
+ //cout <<"q_value_bh:"<<q_value_bh<<endl;
+
+ while ((decoy_idx < decoy_matches_bonf.numRows()) &&
+ (decoy_matches_bonf.getDouble("p-value bonf.", decoy_idx) <=
+ current_pvalue)) {
+ decoy_idx++;
+ }
+
+ double fdr_decoy = 0;
+ if (decoy_idx != 0) {
+ fdr_decoy = (double)decoy_idx / (double)(target_idx + 1);
+ }
+
+
+
+ //cout <<"Setting row "<<target_idx<<":"<<q_value_bh<<":"<<q_value_decoy<<endl;
+ target_matches_bonf.setValue("fdr b-h", target_idx, fdr_bh);
+ target_matches_bonf.setValue("fdr decoy", target_idx, fdr_decoy);
+ }
+
+ double min_fdr = 1.0;
+ for (int idx = target_matches_bonf.numRows()-1; idx >= 0; idx--) {
+ double cur_fdr = target_matches_bonf.getDouble("fdr b-h", idx);
+ if (cur_fdr < min_fdr) {
+ min_fdr = cur_fdr;
+ }
+ target_matches_bonf.setValue("q-value b-h", idx, min_fdr);
+ }
+
+ min_fdr = 1.0;
+ for (int idx = target_matches_bonf.numRows()-1; idx >= 0; idx--) {
+ double cur_fdr = target_matches_bonf.getDouble("fdr decoy", idx);
+ if (cur_fdr < min_fdr) {
+ min_fdr = cur_fdr;
+ }
+ target_matches_bonf.setValue("q-value decoy", idx, min_fdr);
+ }
+
+
+
+ //sort back by scans? or q-value?
+ //target_matches_bonf.sortByFloatColumn("q-value decoy");
+
+ string result_file = output_dir + "/search-for-xlinks.qvalues..txt";
+ target_matches_bonf.saveData(result_file);
+
+ result_file = output_dir + "/search-for-xlinks.pvalues.decoy.txt";
+ decoy_matches_bonf.saveData(result_file);
+
+ return 0;
+}
diff --git a/src/app/xlink/xlink_compute_qvalues.h b/src/app/xlink/xlink_compute_qvalues.h
new file mode 100644
index 0000000..a8b0d67
--- /dev/null
+++ b/src/app/xlink/xlink_compute_qvalues.h
@@ -0,0 +1,8 @@
+#ifndef XLINK_COMPUTE_QVALUES_H
+#define XLINK_COMPUTE_QVALUES_H
+
+
+int xlink_compute_qvalues();
+
+
+#endif
diff --git a/src/app/xlink/xlink_predict_peptide_ions.cpp b/src/app/xlink/xlink_predict_peptide_ions.cpp
new file mode 100644
index 0000000..9cda46b
--- /dev/null
+++ b/src/app/xlink/xlink_predict_peptide_ions.cpp
@@ -0,0 +1,381 @@
+#include "IonSeries.h"
+#include "XLinkMatch.h"
+#include "XLinkPeptide.h"
+#include "LinearPeptide.h"
+#include "SelfLoopPeptide.h"
+#include "util/Params.h"
+
+#include <iostream>
+#include <fstream>
+
+using namespace std;
+
+int modified_aa_string_length(
+ MODIFIED_AA_T* aa_string) {
+
+ if (aa_string == NULL) {
+ return 0;
+ }
+
+ int ans = 0;
+
+ while (aa_string[ans] != MOD_SEQ_NULL) {
+ ans++;
+ }
+
+ return ans;
+}
+
+
+int main(int argc, char** argv) {
+
+ char* peptideA = NULL;
+ char* peptideB = NULL;
+ int posA = 0;
+ int posB = 0;
+ FLOAT_T linker_mass = 0;
+ int charge = 1;
+ bool print_spectrum = false;
+
+
+ /* Verbosity level for set-up/command line reading */
+ set_verbosity_level(CARP_ERROR);
+
+ /* Define optional command line arguments */
+ const char* option_list[] = {
+ "verbosity",
+ "version",
+ "use-flanking-peaks",
+ "print-theoretical-spectrum",
+ "parameter-file"
+ };
+ int num_options = sizeof(option_list) / sizeof(char*);
+
+ /* Define required command line arguments */
+ const char* argument_list[] = {"peptide A",
+ "peptide B",
+ "pos A",
+ "pos B",
+ "charge state",
+ "link mass"};
+
+ int num_arguments = sizeof(argument_list) / sizeof(char*);
+
+ /* for debugging of parameter processing */
+ //set_verbosity_level( CARP_DETAILED_DEBUG );
+ set_verbosity_level( CARP_ERROR );
+
+ /* Set default values for parameters in parameter.c */
+ initialize_parameters();
+
+ /* Define optional and required command line arguments */
+ select_cmd_line_options( option_list, num_options );
+ select_cmd_line_arguments( argument_list, num_arguments);
+
+ /* Parse the command line, including the optional params file */
+ /* does sytnax, type, bounds checking and dies if neccessessary */
+ parse_cmd_line_into_params_hash(argc, argv, "xlink-predict-peptide-ions");
+
+ /* Set verbosity */
+ set_verbosity_level(Params::GetInt("verbosity"));
+
+ /* Get Arguments */
+ linker_mass = Params::GetDouble("link mass");
+ charge = Params::GetInt("charge state");
+
+ peptideA = Params::GetString("peptide A");
+ peptideB = Params::GetString("peptide B");
+
+ posA = Params::GetInt("pos A");
+ posB = Params::GetInt("pos B");
+
+ print_spectrum = Params::GetBool("print-theoretical-spectrum");
+
+ XLinkPeptide::setLinkerMass(linker_mass);
+
+ XLinkMatch* linked_peptide = NULL;
+
+ cerr << "creating peptide" << endl;
+
+ cerr << "Converting peptideA to MOD_AA" << endl;
+
+ MODIFIED_AA_T* mod_seqA = NULL;
+
+ int len = strlen(peptideA);
+
+ convert_to_mod_aa_seq(peptideA, &mod_seqA);
+
+ cerr << "Length of modified string:" << modified_aa_string_length(mod_seqA) << endl;
+
+ //convert back.
+
+ char* temp =
+ modified_aa_string_to_string_with_masses(mod_seqA, modified_aa_string_length(mod_seqA), MOD_MASS_ONLY);
+
+ cerr << "orig:" << peptideA << ":" << len << " convert:" << temp << ":" << strlen(temp) << endl;
+
+
+ if (string(peptideB) == string("NULL")) {
+ if (posA == -1 || posB == -1) {
+ cout << "Creating linear peptide" << endl;
+ linked_peptide = new LinearPeptide(peptideA);
+ } else {
+ cout << "Creating selfloop peptide" << endl;
+ linked_peptide = new SelfLoopPeptide(peptideA, posA-1, posB-1);
+ }
+ } else {
+ cout << "Creating XLinkPeptide" << endl;
+ linked_peptide = new XLinkPeptide(peptideA, peptideB, posA-1, posB-1);
+ }
+
+ cerr << "Printing stuff" << endl;
+ cerr << "precursor: " << linked_peptide -> getSequenceString() << endl;
+ cerr << "mass:" << linked_peptide -> getMass(MONO) << " " << linked_peptide -> getMass(AVERAGE) <<endl;;
+ cerr << "charge:" << charge << endl;
+ cerr << "link mass:" << linker_mass << endl;
+ cerr << "print_spectrum:" << print_spectrum << endl;
+
+ int max_charge = min(get_max_ion_charge_parameter("max-ion-charge"), charge);
+
+ IonConstraint* ion_constraint = new IonConstraint(MONO, max_charge, BY_ION, false);
+
+ IonSeries* ion_series = new IonSeries(ion_constraint, charge);
+
+ linked_peptide->predictIons(ion_series, charge);
+
+ cout << "mz\t"
+ << "mass\t"
+ << "charge\t"
+ << "cleavage idx\t"
+ << "sequence\t"
+ << "ion type" << endl;
+
+ for (IonIterator ion_iter = ion_series->begin();
+ ion_iter != ion_series->end();
+ ++ion_iter) {
+
+ Ion* ion = *ion_iter;
+ FLOAT_T mz = ion->getMassZ();
+ FLOAT_T mass = ion->getMassFromMassZ();
+ int charge = ion->getCharge();
+ string sequence = linked_peptide->getIonSequence(ion);
+ int cleavage_idx = ion->getCleavageIdx();
+ ION_TYPE_T ion_type = ion->getType();
+
+ string ion_type_string = "";
+ switch (ion_type) {
+ case B_ION:
+ ion_type_string = "b";
+ break;
+ case Y_ION:
+ ion_type_string = "y";
+ break;
+ default:
+ ion_type_string = "u";
+ }
+
+
+ cout << mz << "\t"
+ << mass << "\t"
+ << charge << "\t"
+ << cleavage_idx << "\t"
+ << sequence << "\t"
+ << ion_type_string << endl;
+ }
+
+
+ delete ion_series;
+ delete linked_peptide;
+
+ return 0;
+}
+#include "IonSeries.h"
+#include "XLinkMatch.h"
+#include "XLinkPeptide.h"
+#include "LinearPeptide.h"
+#include "SelfLoopPeptide.h"
+
+#include <iostream>
+#include <fstream>
+
+using namespace std;
+
+int modified_aa_string_length(
+ MODIFIED_AA_T* aa_string) {
+
+ if (aa_string == NULL) {
+ return 0;
+ }
+
+ int ans = 0;
+
+ while (aa_string[ans] != MOD_SEQ_NULL) {
+ ans++;
+ }
+
+ return ans;
+}
+
+
+int main(int argc, char** argv) {
+
+ char* peptideA = NULL;
+ char* peptideB = NULL;
+ int posA = 0;
+ int posB = 0;
+ FLOAT_T linker_mass = 0;
+ int charge = 1;
+ bool print_spectrum = false;
+
+
+ /* Verbosity level for set-up/command line reading */
+ set_verbosity_level(CARP_ERROR);
+
+ /* Define optional command line arguments */
+ const char* option_list[] = {
+ "verbosity",
+ "version",
+ "use-flanking-peaks",
+ "print-theoretical-spectrum",
+ "parameter-file"
+ };
+ int num_options = sizeof(option_list) / sizeof(char*);
+
+ /* Define required command line arguments */
+ const char* argument_list[] = {"peptide A",
+ "peptide B",
+ "pos A",
+ "pos B",
+ "charge state",
+ "link mass"};
+
+ int num_arguments = sizeof(argument_list) / sizeof(char*);
+
+ /* for debugging of parameter processing */
+ //set_verbosity_level( CARP_DETAILED_DEBUG );
+ set_verbosity_level( CARP_ERROR );
+
+ /* Set default values for parameters in parameter.c */
+ initialize_parameters();
+
+ /* Define optional and required command line arguments */
+ select_cmd_line_options( option_list, num_options );
+ select_cmd_line_arguments( argument_list, num_arguments);
+
+ /* Parse the command line, including the optional params file */
+ /* does sytnax, type, bounds checking and dies if neccessessary */
+ parse_cmd_line_into_params_hash(argc, argv, "xlink-predict-peptide-ions");
+
+ /* Set verbosity */
+ set_verbosity_level(Params::GetInt("verbosity"));
+
+ /* Get Arguments */
+ linker_mass = Params::GetDouble("link mass");
+ charge = Params::GetInt("charge state");
+
+ peptideA = Params::GetString("peptide A");
+ peptideB = Params::GetString("peptide B");
+
+ posA = Params::GetInt("pos A");
+ posB = Params::GetInt("pos B");
+
+ print_spectrum = Params::GetBool("print-theoretical-spectrum");
+
+ XLinkPeptide::setLinkerMass(linker_mass);
+
+ XLinkMatch* linked_peptide = NULL;
+
+ cerr << "creating peptide" <<endl;
+
+ cerr << "Converting peptideA to MOD_AA" << endl;
+
+ MODIFIED_AA_T* mod_seqA = NULL;
+
+ int len = strlen(peptideA);
+
+ convert_to_mod_aa_seq(peptideA, &mod_seqA);
+
+ cerr << "Length of modified string:" << modified_aa_string_length(mod_seqA) << endl;
+
+ //convert back.
+
+ char* temp =
+ modified_aa_string_to_string_with_masses(mod_seqA, modified_aa_string_length(mod_seqA), MOD_MASS_ONLY);
+
+ cerr << "orig:" << peptideA << ":" << len << " convert:" << temp << ":" << strlen(temp) << endl;
+
+
+ if (string(peptideB) == string("NULL")) {
+ if (posA == -1 || posB == -1) {
+ cout << "Creating linear peptide" << endl;
+ linked_peptide = new LinearPeptide(peptideA);
+ } else {
+ cout << "Creating selfloop peptide" << endl;
+ linked_peptide = new SelfLoopPeptide(peptideA, posA-1, posB-1);
+ }
+ } else {
+ cout << "Creating XLinkPeptide" << endl;
+ linked_peptide = new XLinkPeptide(peptideA, peptideB, posA-1, posB-1);
+ }
+
+ cerr << "Printing stuff" << endl;
+ cerr << "precursor: " << linked_peptide -> getSequenceString() << endl;
+ cerr << "mass:" << linked_peptide -> getMass(MONO) << " " << linked_peptide -> getMass(AVERAGE) << endl;
+ cerr << "charge:" << charge << endl;
+ cerr << "link mass:"<< linker_mass << endl;
+ cerr << "print_spectrum:"<< print_spectrum << endl;
+
+ int max_charge = min(get_max_ion_charge_parameter("max-ion-charge"), charge);
+
+ IonConstraint* ion_constraint = new IonConstraint(MONO, max_charge, BY_ION, false);
+
+ IonSeries* ion_series = new IonSeries(ion_constraint, charge);
+
+ linked_peptide->predictIons(ion_series, charge);
+
+ cout << "mz\t"
+ << "mass\t"
+ << "charge\t"
+ << "cleavage idx\t"
+ << "sequence\t"
+ << "ion type" << endl;
+
+ for (IonIterator ion_iter = ion_series->begin();
+ ion_iter != ion_series->end();
+ ++ion_iter) {
+
+ Ion* ion = *ion_iter;
+ FLOAT_T mz = ion->getMassZ();
+ FLOAT_T mass = ion->getMassFromMassZ();
+ int charge = ion->getCharge();
+ string sequence = linked_peptide->getIonSequence(ion);
+ int cleavage_idx = ion->getCleavageIdx();
+ ION_TYPE_T ion_type = ion->getType();
+
+ string ion_type_string = "";
+ switch (ion_type) {
+ case B_ION:
+ ion_type_string = "b";
+ break;
+ case Y_ION:
+ ion_type_string = "y";
+ break;
+ default:
+ ion_type_string = "u";
+ }
+
+
+ cout << mz << "\t"
+ << mass << "\t"
+ << charge << "\t"
+ << cleavage_idx << "\t"
+ << sequence << "\t"
+ << ion_type_string << endl;
+ }
+
+
+ delete ion_series;
+ delete linked_peptide;
+
+ return 0;
+}
diff --git a/src/app/xlink/xlink_search.cpp b/src/app/xlink/xlink_search.cpp
new file mode 100644
index 0000000..6a2f2d4
--- /dev/null
+++ b/src/app/xlink/xlink_search.cpp
@@ -0,0 +1,403 @@
+
+/**
+ * \file xlink_search.cpp
+ * \brief Object for running search-for-xlinks (new code)
+ *****************************************************************************/
+#include "SearchForXLinks.h"
+#include "XLinkMatch.h"
+#include "XLinkMatchCollection.h"
+#include "XLinkBondMap.h"
+#include "XLinkPeptide.h"
+#include "XLinkIonSeriesCache.h"
+#include "xlink_compute_qvalues.h"
+
+#include "Weibull.h"
+
+//CRUX INCLUDES
+#include "model/objects.h"
+#include "model/FilteredSpectrumChargeIterator.h"
+#include "io/OutputFiles.h"
+#include "io/SpectrumCollectionFactory.h"
+#include "util/Params.h"
+#include "XLinkDatabase.h"
+
+
+//C++ Includes
+#include <algorithm>
+#include <cmath>
+#include <ctime>
+#include <fstream>
+#include <iomanip>
+#include <iostream>
+
+#include <ctime>
+
+
+
+using namespace std;
+
+void buildArguments(
+ vector<string>& args_vec,
+ int &argc,
+ char** &argv) {
+
+ argc = args_vec.size();
+ argv = new char*[argc];
+
+ argv[0] = (char*)args_vec[0].c_str();
+ carp(CARP_INFO, "argv[0]=%s", argv[0]);
+ for (int idx = 1; idx < argc; idx++) {
+ argv[idx] = (char*)args_vec[idx].c_str();
+ carp(CARP_INFO, "argv[%i]=%s", idx, argv[idx]);
+ }
+
+}
+
+void writeTrainingCandidates(XLinkMatchCollection* training_candidates, int scan_num, Weibull& weibull) {
+ training_candidates->populateMatchRank(XCORR);
+ training_candidates->sort(XCORR);
+ string output_dir = Params::GetString("output-dir");
+
+ string output_file = output_dir + "/" +
+ "scan." + StringUtils::ToString(scan_num) +
+ ".charge." + StringUtils::ToString(training_candidates->getCharge()) +
+ ".training.candidates.txt";
+ //cerr<<"writing "<<output_file<<endl;
+ DelimitedFileWriter writer(output_file.c_str());
+
+
+
+ writer.setColumnName("scan", 0);
+ writer.setColumnName("charge", 1);
+ writer.setColumnName("decoy", 2);
+ writer.setColumnName("sequence", 3);
+ writer.setColumnName("eta", 4);
+ writer.setColumnName("beta", 5);
+ writer.setColumnName("shift", 6);
+ writer.setColumnName("correlation", 7);
+ writer.setColumnName("xcorr score", 8);
+ writer.setColumnName("p-value", 9);
+ writer.setColumnName("p-value ecdf", 10);
+ writer.writeHeader();
+
+ for (size_t idx = 0 ;idx < training_candidates->getMatchTotal();idx++) {
+ writer.setColumnCurrentRow(0, scan_num);
+ writer.setColumnCurrentRow(2, (*training_candidates)[idx]->isDecoy());
+ writer.setColumnCurrentRow(1, (*training_candidates)[idx]->getCharge());
+ writer.setColumnCurrentRow(3, (*training_candidates)[idx]->getSequenceString());
+ writer.setColumnCurrentRow(4, weibull.getEta());
+ writer.setColumnCurrentRow(5, weibull.getBeta());
+ writer.setColumnCurrentRow(6, weibull.getShift());
+ writer.setColumnCurrentRow(7, weibull.getCorrelation());
+ writer.setColumnCurrentRow(8, (*training_candidates)[idx]->getScore(XCORR));
+ FLOAT_T score = (*training_candidates)[idx]->getScore(XCORR);
+ writer.setColumnCurrentRow(9, weibull.getWeibullPValue(score));
+ writer.setColumnCurrentRow(10, weibull.getECDFPValue(score));
+ writer.writeRow();
+ }
+
+}
+
+
+/**
+ * main method for SearchForXLinks that implements to refactored code
+ */
+int SearchForXLinks::xlinkSearchMain() {
+
+ carp(CARP_INFO, "Beginning crux search-for-xlinks (new code)");
+
+ /* Get parameters */
+ carp(CARP_INFO, "Getting parameters");
+ string ms2_file = Params::GetString("ms2 file");
+ string input_file = Params::GetString("protein fasta file");
+ string output_directory = Params::GetString("output-dir");
+ int top_match = Params::GetInt("top-match");
+ XLinkPeptide::setLinkerMass(Params::GetDouble("link mass"));
+ int min_weibull_points = Params::GetInt("min-weibull-points");
+ bool compute_pvalues = Params::GetBool("compute-p-values");
+
+ XLinkBondMap bondmap;
+
+ /* Prepare input fasta */
+ carp(CARP_DEBUG, "Preparing database");
+ XLinkDatabase::initialize();
+ Database* database = NULL;
+ int num_proteins = 0;//prepare_protein_input(input_file, &database);
+ //carp(CARP_DEBUG, "Number of proteins:%d",num_proteins);
+ PEPTIDE_MOD_T** peptide_mods = NULL;
+ int num_peptide_mods = 0;
+
+ /* Usually for debugging purposes, print out the database of canddiates */
+ if (Params::GetBool("xlink-print-db")) {
+ carp(CARP_INFO, "generating and printing xlink database");
+ XLinkDatabase::print();
+ //return 0;
+ }
+
+ int scan_num = 0;
+ int skipped_no_candidates = 0;
+
+ SpectrumZState zstate;
+
+ carp(CARP_DEBUG, "Loading Spectra");
+ Crux::Spectrum* spectrum = NULL;
+ Crux::SpectrumCollection* spectra = SpectrumCollectionFactory::create(ms2_file);
+ spectra->parse();
+
+ FilteredSpectrumChargeIterator* spectrum_iterator =
+ new FilteredSpectrumChargeIterator(spectra);
+
+ /* Prepare output files */
+ carp(CARP_DEBUG, "Preparing output files");
+ OutputFiles output_files(this);
+ output_files.writeHeaders(num_proteins);
+
+ // main loop over spectra in ms2 file
+
+
+ int search_count = 0;
+ FLOAT_T num_spectra = (FLOAT_T)spectra->getNumSpectra();
+ FLOAT_T min_pvalue = 1.0 / num_spectra;
+ //class for estimating pvalues.
+ Weibull weibull;
+
+ // for every observed spectrum
+ carp(CARP_DEBUG, "Searching Spectra");
+
+
+ while (spectrum_iterator->hasNext()) {
+
+ spectrum = spectrum_iterator->next(zstate);
+ scan_num = spectrum->getFirstScan();
+
+ carp(CARP_DEBUG,"count %d scan %d charge %d", search_count, scan_num, zstate.getCharge());
+ if (search_count > 0 && search_count % 1000 == 0) {
+ carp(CARP_INFO,
+ "%d spectrum-charge combinations searched, %.0f%% complete",
+ search_count + spectrum_iterator->numSkipped(),
+ (search_count + spectrum_iterator->numSkipped()) / num_spectra * 100);
+ }
+ search_count++;
+
+ FLOAT_T precursor_mz = spectrum->getPrecursorMz();
+
+ XLinkMatchCollection* target_candidates = new XLinkMatchCollection(
+ spectrum,
+ zstate,
+ false,
+ false
+ );
+
+ carp(CARP_DEBUG, "Scan=%d charge=%d mass=%lg candidates=%d",
+ scan_num,
+ zstate.getCharge(),
+ zstate.getNeutralMass(),
+ target_candidates->getMatchTotal());
+
+ if (target_candidates->getMatchTotal() < 0) {
+ carp(CARP_ERROR, "Scan %d has %d candidates.", scan_num,
+ target_candidates->getMatchTotal());
+ } else if (target_candidates->getMatchTotal() == 0) {
+ skipped_no_candidates++;
+ carp(CARP_DEBUG, "Skipping scan %d charge %d mass %lg",
+ scan_num,
+ zstate.getCharge(),
+ zstate.getNeutralMass()
+ );
+ delete target_candidates;
+ //XLink::deleteAllocatedPeptides();
+ continue;
+ }
+
+ //score targets
+ target_candidates->scoreSpectrum(spectrum);
+
+ carp(CARP_DEBUG, "Getting decoy candidates");
+
+ XLinkMatchCollection* decoy_candidates = new XLinkMatchCollection();
+ target_candidates->shuffle(*decoy_candidates);
+
+
+ /*
+ XLinkMatchCollection* decoy_candidates = new XLinkMatchCollection(
+ spectrum,
+ zstate,
+ true,
+ false);
+
+ */
+ carp(CARP_DEBUG, "scoring decoys");
+ decoy_candidates->scoreSpectrum(spectrum);
+
+ if (compute_pvalues) {
+ weibull.reset();
+ XLinkMatchCollection *target_train_candidates = new XLinkMatchCollection(
+ spectrum,
+ zstate,
+ false,
+ true);
+ XLinkMatchCollection *train_candidates = new XLinkMatchCollection(
+ spectrum,
+ zstate,
+ true,
+ true
+ );
+
+ for (size_t idx=0;idx < target_train_candidates->getMatchTotal();idx++) {
+ train_candidates->add(target_train_candidates->at(idx), true);
+ }
+ while(train_candidates->getMatchTotal() < min_weibull_points) {
+ target_train_candidates->shuffle(*train_candidates);
+ }
+ train_candidates->scoreSpectrum(spectrum);
+ for (int idx = 0;idx < train_candidates->getMatchTotal();idx++) {
+ const string& sequence = (*train_candidates)[idx]->getSequenceStringConst();
+ FLOAT_T score = (*train_candidates)[idx]->getScore(XCORR);
+ weibull.addPoint(sequence, score);
+ }
+ bool write_weibull_points = !weibull.fit();
+ //train_candidates->fitWeibull();
+ //MatchCollection::transferWeibull(train_candidates, target_candidates);
+ //MatchCollection::transferWeibull(train_candidates, decoy_candidates);
+
+
+ target_candidates->sort(XCORR);
+
+
+ int nprint = min(top_match,target_candidates->getMatchTotal());
+
+ carp(CARP_DEBUG, "Calculating %d target p-values", nprint);
+
+ //calculate pvalues.
+ for (int idx=0;idx < nprint;idx++) {
+ FLOAT_T score = (*target_candidates)[idx]->getScore(XCORR);
+ (*target_candidates)[idx]->setPValue(weibull.getPValue(score));
+ //target_candidates->computeWeibullPValue(idx);
+ }
+
+ nprint = min(top_match, (int)decoy_candidates->getMatchTotal());
+
+ carp(CARP_DEBUG, "Calculating %d decoy p-values", nprint);
+
+ decoy_candidates->sort(XCORR);
+
+ for (int idx=0;idx < nprint;idx++) {
+ FLOAT_T score = (*decoy_candidates)[idx]->getScore(XCORR);
+ (*decoy_candidates)[idx]->setPValue(weibull.getPValue(score));
+ FLOAT_T wpvalue = weibull.getWeibullPValue(score);
+ FLOAT_T bpvalue = bonferroni_correction(wpvalue, decoy_candidates->getMatchTotal()) * 2.0;
+ if ((wpvalue == 0) || (wpvalue != wpvalue) || (bpvalue < min_pvalue)) {
+ //If we have a bad fit, 0 or too low pvalue, print out the points.
+ write_weibull_points = true;
+ }
+
+ }
+
+
+ if (write_weibull_points || Params::GetBool("write-weibull-points")) {
+ writeTrainingCandidates(train_candidates, scan_num, weibull);
+ }
+ carp(CARP_DEBUG, "delete train candidates");
+ delete train_candidates;
+ carp(CARP_DEBUG, "delete target train candidates");
+ delete target_train_candidates;
+
+ } // if (compute_p_values)
+
+ //print out
+ target_candidates->setFilePath(ms2_file);
+ decoy_candidates->setFilePath(ms2_file);
+ vector<MatchCollection*> decoy_vec;
+
+ if (Params::GetBool("concat")) {
+ for (size_t idx=0;idx < decoy_candidates->getMatchTotal();idx++) {
+ target_candidates->add(decoy_candidates->at(idx), true);
+ }
+ } else {
+
+ decoy_vec.push_back(decoy_candidates);
+
+ if (decoy_candidates->getScoredType(SP) == true) {
+ decoy_candidates->populateMatchRank(SP);
+ }
+ decoy_candidates->populateMatchRank(XCORR);
+ decoy_candidates->sort(XCORR);
+ }
+
+ carp(CARP_DEBUG, "Ranking");
+
+ if (target_candidates->getScoredType(SP) == true) {
+ target_candidates->populateMatchRank(SP);
+ }
+ target_candidates->populateMatchRank(XCORR);
+ target_candidates->sort(XCORR);
+
+
+ carp(CARP_DEBUG, "Writing results");
+ output_files.writeMatches(
+ (MatchCollection*)target_candidates,
+ decoy_vec,
+ XCORR,
+ spectrum);
+
+ /* Clean up */
+ carp(CARP_DEBUG, "Delete decoy candidates");
+ delete decoy_candidates;
+ carp(CARP_DEBUG, "Delete target candidates");
+ delete target_candidates;
+ XLink::deleteAllocatedPeptides();
+
+ //free_spectrum(spectrum);
+
+ carp(CARP_DEBUG, "Done with spectrum %d", scan_num);
+ carp(CARP_DEBUG, "=====================================");
+ } // get next spectrum
+
+ carp(CARP_INFO, "Skipped %d (%g%%) spectra with 0 candidates.",
+ skipped_no_candidates, skipped_no_candidates / num_spectra * 100);
+
+ carp(CARP_INFO, "Skipped %d (%g%%) spectra with too few peaks.",
+ spectrum_iterator->numSkipped(),
+ spectrum_iterator->numSkipped() / num_spectra * 100);
+
+ output_files.writeFooters();
+
+ // clean up
+
+
+ delete spectrum_iterator;
+ delete spectra;
+ XLink::deleteAllocatedPeptides();
+ for(int mod_idx = 0; mod_idx < num_peptide_mods; mod_idx++) {
+ free_peptide_mod(peptide_mods[mod_idx]);
+ }
+ free(peptide_mods);
+
+ //finalize_weibull();
+ //Scorer::finalize();
+ XLinkIonSeriesCache::finalize();
+ IonSeries::finalize();
+ XLinkDatabase::finalize();
+ //modifications_finalize(); TODO - Figure where to free the modification cache.
+ //Calculate q-values via p-values from weibull fit.
+ if (compute_pvalues) {
+ carp(CARP_DEBUG, "Computing Q-Values using P-values");
+ if (Params::GetBool("concat")) {
+ carp(CARP_WARNING, "Computing Q-Values with concatenated target-decoy files not implemented yet!");
+ } else {
+ xlink_compute_qvalues();
+ }
+ }
+
+ carp(CARP_INFO, "Elapsed time: %.3g s", wall_clock() / 1e6);
+ carp(CARP_INFO, "Finished crux search-for-xlinks (new).");
+
+ return(0);
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/app/xlink/xlink_search.h b/src/app/xlink/xlink_search.h
new file mode 100644
index 0000000..298c451
--- /dev/null
+++ b/src/app/xlink/xlink_search.h
@@ -0,0 +1,15 @@
+#ifndef XLINK_SEARCH_CMD_H
+#define XLINK_SEARCH_CMD_H
+
+/**
+ * \file xlink_search.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: November 19, 2009
+ * \brief Header file for crux search-for-xlinks command.
+ */
+
+int xlink_search_main(int argc, char** argv);
+int xhhc_search_main(int argc, char** argv);
+
+#endif //PERCOLATOR_CMD_H
+
diff --git a/src/cmake_install.cmake b/src/cmake_install.cmake
new file mode 100644
index 0000000..80e7824
--- /dev/null
+++ b/src/cmake_install.cmake
@@ -0,0 +1,62 @@
+# Install script for directory: /data/TeamCity/buildAgent/work/779d99b0241b2175/src
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+ IF(BUILD_TYPE)
+ STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+ CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+ ELSE(BUILD_TYPE)
+ SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+ ENDIF(BUILD_TYPE)
+ MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+ IF(COMPONENT)
+ MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+ SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+ ELSE(COMPONENT)
+ SET(CMAKE_INSTALL_COMPONENT)
+ ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+# Install shared libraries without execute permission?
+IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+ SET(CMAKE_INSTALL_SO_NO_EXE "0")
+ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE)
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+ IF(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/crux" AND
+ NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/crux")
+ FILE(RPATH_CHECK
+ FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/crux"
+ RPATH "")
+ ENDIF()
+ FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/bin" TYPE EXECUTABLE FILES "/data/TeamCity/buildAgent/work/779d99b0241b2175/src/crux")
+ IF(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/crux" AND
+ NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/crux")
+ FILE(RPATH_REMOVE
+ FILE "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/crux")
+ IF(CMAKE_INSTALL_DO_STRIP)
+ EXECUTE_PROCESS(COMMAND "/usr/bin/strip" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/bin/crux")
+ ENDIF(CMAKE_INSTALL_DO_STRIP)
+ ENDIF()
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_LOCAL_ONLY)
+ # Include the install script for each subdirectory.
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/bullseye/cmake_install.cmake")
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/hardklor/cmake_install.cmake")
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/qranker-barista/cmake_install.cmake")
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/xlink/cmake_install.cmake")
+ INCLUDE("/data/TeamCity/buildAgent/work/779d99b0241b2175/src/app/tide/cmake_install.cmake")
+
+ENDIF(NOT CMAKE_INSTALL_LOCAL_ONLY)
+
diff --git a/src/crux b/src/crux
new file mode 100755
index 0000000..636aee2
Binary files /dev/null and b/src/crux differ
diff --git a/src/crux-main.cpp b/src/crux-main.cpp
new file mode 100644
index 0000000..7267bad
--- /dev/null
+++ b/src/crux-main.cpp
@@ -0,0 +1,114 @@
+/**
+ * \file crux-main.cpp
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: November 24, 2008
+ * \brief The starting point for the main crux program.
+ *
+ * Usage is "crux [command] [options] [arguments]" where command
+ * is one of the primary crux commands.
+ **/
+
+#include "crux-main.h"
+#include "util/crux-utils.h" // Need to get definition of NUM_FEATURES.
+
+#include "app/xlink/xlink_assign_ions.h"
+#include "app/xlink/xhhc_score_peptide_spectrum.h"
+#include "app/xlink/xlink_search.h"
+#include "app/CruxApplicationList.h"
+#include "app/ComputeQValues.h"
+#include "app/ComputeQValuesLegacy.h"
+#include "app/CreateDocs.h"
+#include "app/qranker-barista/QRanker.h"
+#include "app/qranker-barista/Barista.h"
+#include "app/PrintProcessedSpectra.h"
+#include "app/GeneratePeptides.h"
+#include "app/GetMs2Spectrum.h"
+#include "app/ParamMedicApplication.h"
+#include "app/Pipeline.h"
+#include "app/PredictPeptideIons.h"
+#include "app/xlink/SearchForXLinks.h"
+#include "app/ExtractColumns.h"
+#include "app/SpectralCounts.h"
+#include "app/ExtractRows.h"
+#include "app/PrintVersion.h"
+#include "app/StatColumn.h"
+#include "app/SortColumn.h"
+#include "app/hardklor/CruxHardklorApplication.h"
+#include "app/bullseye/CruxBullseyeApplication.h"
+#include "app/PercolatorApplication.h"
+#include "app/MakePinApplication.h"
+#include "app/TideIndexApplication.h"
+#include "app/ReadSpectrumRecordsApplication.h"
+#include "app/ReadTideIndex.h"
+#include "app/TideSearchApplication.h"
+#include "app/CometApplication.h"
+#include "app/PSMConvertApplication.h"
+#include "app/CascadeSearchApplication.h"
+#include "app/AssignConfidenceApplication.h"
+#include "app/SubtractIndexApplication.h"
+/**
+ * The starting point for crux. Prints a general usage statement when
+ * given no arguments. Runs one of the crux commands, including
+ * printing the current version number.
+ */
+int main(int argc, char** argv) {
+ try {
+#ifdef _MSC_VER
+ // Turn off auto-tranlation of line-feed to
+ // carriage-return/line-feed
+ _set_fmode(_O_BINARY);
+#endif
+
+ CruxApplicationList applications("crux");
+
+ // Primary commands
+ applications.addMessage(applications.getListName() +
+ " supports the following primary commands:");
+ applications.add(new CruxBullseyeApplication());
+ applications.add(new TideIndexApplication());
+ applications.add(new TideSearchApplication());
+ applications.add(new ReadSpectrumRecordsApplication());
+ applications.add(new ReadTideIndex());
+ applications.add(new CometApplication());
+ applications.add(new PercolatorApplication());
+ applications.add(new QRanker());
+ applications.add(new Barista());
+ applications.add(new SearchForXLinks());
+ applications.add(new SpectralCounts());
+ applications.add(new PipelineApplication());
+ applications.add(new CascadeSearchApplication());
+ applications.add(new AssignConfidenceApplication());
+
+ // Utilities
+ applications.addMessage(applications.getListName() +
+ " supports the following utility commands:");
+ applications.add(new MakePinApplication());
+ applications.add(new PredictPeptideIons());
+ applications.add(new CruxHardklorApplication());
+ applications.add(new ParamMedicApplication());
+ applications.add(new PrintProcessedSpectra());
+ applications.add(new GeneratePeptides());
+ applications.add(new GetMs2Spectrum());
+ applications.add(new CreateDocs());
+ applications.add(new PrintVersion());
+ applications.add(new PSMConvertApplication());
+ applications.add(new SubtractIndexApplication());
+ applications.add(new XLinkAssignIons());
+ applications.add(new XLinkScoreSpectrum());
+
+ // Utilities for processing tab-delimited text files
+ applications.add(new ExtractColumns());
+ applications.add(new ExtractRows());
+ applications.add(new StatColumn());
+ applications.add(new SortColumn());
+
+ int ret = applications.main(argc, argv);
+ google::protobuf::ShutdownProtobufLibrary();
+ return ret;
+ } catch (const std::exception& e) {
+ carp(CARP_FATAL, "An exception occurred: %s", e.what());
+ } catch (...) {
+ carp(CARP_FATAL, "An unknown exception occurred.");
+ }
+}// end main
+
diff --git a/src/crux-main.h b/src/crux-main.h
new file mode 100644
index 0000000..6a3bdfa
--- /dev/null
+++ b/src/crux-main.h
@@ -0,0 +1,17 @@
+/**
+ * \file crux-main.h
+ */
+/*
+ AUTHOR: Barbara Frewen
+ CREATE DATE: November 24, 2008
+ DESCRIPTION: The starting point for what were previously three
+ separate programs: create-index, search-for-matches, analyze-matches.
+ REVISION: $Revision: 1.2 $
+*/
+
+#include "io/carp.h"
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "search.h"
+//#include "PercolatorCInterface.h"
+
diff --git a/src/io/DelimitedFile.cpp b/src/io/DelimitedFile.cpp
new file mode 100644
index 0000000..5c7f193
--- /dev/null
+++ b/src/io/DelimitedFile.cpp
@@ -0,0 +1,825 @@
+/**
+ * \file DelimitedFile.cpp
+ * DATE: Jan 7, 2010
+ * AUTHOR: Sean McIlwain
+ * \brief Object for reading tab-delimited files.
+ *
+ * This class generates a table of values. The default delimiter is tab.
+ * This class is capable of reading string, integers, and floating point
+ * Types from each cell of the table. This class also provides function
+ * for reading a list of integers or string from a cell using a delimiter
+ * that is different from the column delimiter (default is comma ',').
+ ****************************************************************************/
+#include "DelimitedFile.h"
+
+#include <fstream>
+
+#include "carp.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+
+/**
+ * \returns a DelimitedFile object
+ */
+DelimitedFile::DelimitedFile(
+ char delimiter ///< the delimiter to use (default tab)
+ ): delimiter_(delimiter) {
+ clear();
+}
+
+/**
+ * \returns a DelimitedFile object and loads the tab-delimited
+ * data specified by file_name.
+ */
+DelimitedFile::DelimitedFile(
+ const char *file_name, ///< the path of the file to read
+ bool hasHeader, ///< indicate whether header exists
+ char delimiter ///< the delimiter to use (default tab)
+ ) {
+ loadData(file_name, hasHeader, delimiter);
+}
+
+/**
+ * \returns a DelimitedFile object and loads the tab-delimited
+ * data specified by file_name.
+ */
+DelimitedFile::DelimitedFile(
+ const string& file_name, ///< the path of the file to read
+ bool hasHeader, ///< indicates whether header exists
+ char delimiter ///< the delimiter to use (default tab)
+ ) {
+ loadData(file_name, hasHeader, delimiter);
+}
+
+/**
+ * empties the delimited file
+ */
+void DelimitedFile::clear() {
+ for (unsigned int idx=0;idx < data_.size(); idx++) {
+ data_[idx].clear();
+ }
+ data_.clear();
+ column_names_.clear();
+ reset();
+}
+
+/**
+ * Destructor
+ */
+DelimitedFile::~DelimitedFile() {
+ clear();
+}
+
+/**
+ * sets the delimiter
+ */
+void DelimitedFile::setDelimiter(
+ char delimiter ///< the delimiter
+ ) {
+ delimiter_ = delimiter;
+}
+
+/**
+ * /returns the delimiter
+ */
+char DelimitedFile::getDelimiter() const {
+ return delimiter_;
+}
+
+/**
+ *\returns the number of rows, assuming a square matrix
+ */
+unsigned int DelimitedFile::numRows() {
+ if (data_.empty()) {
+ carp(CARP_DEBUG, "DelimitedFile::numRows(): 0x0 matrix");
+ return 0;
+ }
+ return data_[0].size();
+}
+
+/**
+ *\returns the number of rows for a column
+ */
+unsigned int DelimitedFile::numRows(
+ unsigned int col_idx ///<the column index
+ ) {
+ return col_idx < numCols() ? data_[col_idx].size() : 0;
+}
+
+/**
+ *\returns the number of columns
+ */
+unsigned int DelimitedFile::numCols() {
+ return data_.size();
+}
+
+/**
+ * clears the current data and column names,
+ * parses the header if it exists,
+ * reads the file one line at a time while
+ * populating the data matrix with the
+ * strings separated by tabs.
+ */
+void DelimitedFile::loadData(
+ const char *file_name, ///< the file path
+ bool hasHeader, ///< header indicator
+ char delimiter ///< delimiter to use
+ ) {
+ setDelimiter(delimiter);
+ clear();
+
+ fstream file(file_name, ios::in);
+ if (!file.is_open()) {
+ carp(CARP_ERROR, "Opening %s or reading failed", file_name);
+ return;
+ }
+
+ string line;
+
+ if (hasHeader) {
+ if (getline(file, line)) {
+ vector<string> tokens = StringUtils::Split(line, getDelimiter());
+ for (vector<string>::iterator iter = tokens.begin(); iter != tokens.end(); ++iter) {
+ addColumn(*iter);
+ }
+ } else {
+ carp(CARP_WARNING, "No data/headers found!");
+ return;
+ }
+ }
+
+ while (getline(file, line)) {
+ vector<string> tokens = StringUtils::Split(line, getDelimiter());
+ if (!hasHeader && numCols() == 0) {
+ //initialize the number of columns so that addRow won't fail.
+ while (numCols() < tokens.size()) {
+ addColumn();
+ }
+ }
+
+ int row_idx = addRow();
+
+ for (unsigned int col_idx = 0; col_idx < tokens.size(); col_idx++) {
+ if (numCols() <= col_idx) {
+ addColumn();
+ }
+ setString(col_idx, row_idx, tokens[col_idx]);
+ }
+ }
+
+ file.close();
+
+ //reset the iterator.
+ reset();
+}
+
+/**
+ * loads a tab delimited file
+ */
+void DelimitedFile::loadData(
+ const string& file, ///< the file path
+ bool hasHeader, ///< header indicator
+ char delimiter ///< the delimiter to use
+ ) {
+ loadData(file.c_str(), hasHeader, delimiter);
+}
+
+/**
+ * saves a tab delimited file
+ */
+void DelimitedFile::saveData(
+ const string& file ///< the file path
+ ) {
+ saveData(file.c_str());
+}
+
+/**
+ * saves a tab delimited file
+ */
+void DelimitedFile::saveData(
+ const char* file ///< the file path
+ ) {
+ ofstream fout(file);
+
+ //find the maximum number of rows.
+ unsigned int maxRow = 0;
+ for (unsigned int col_idx=0; col_idx < numCols(); col_idx++) {
+ maxRow = max(maxRow, numRows(col_idx));
+ }
+
+ //print out the header if it exists.
+ if (!column_names_.empty()) {
+ fout << column_names_[0];
+ for (unsigned int col_idx=1; col_idx < column_names_.size(); col_idx++) {
+ fout << getDelimiter() << column_names_[col_idx];
+ }
+ fout << endl;
+ }
+
+ //print out all rows, using delimiter_ when
+ //the row goes past the current column
+ //size.
+ for (unsigned int row_idx=0; row_idx < maxRow; row_idx++) {
+ if (row_idx < numRows(0)) {
+ fout << getString((unsigned int)0, row_idx);
+ } else {
+ fout << delimiter_;
+ }
+ for (unsigned int col_idx=1;col_idx < numCols();col_idx++) {
+ fout << getDelimiter();
+ if (row_idx < numRows(col_idx)) {
+ fout << getString(col_idx, row_idx);
+ }
+ }
+ fout << endl;
+ }
+
+ fout.close();
+}
+
+/**
+ * adds a column to the delimited file
+ *\returns the column index.
+ */
+unsigned int DelimitedFile::addColumn(
+ const string& column_name ///< the column name
+ ) {
+ vector<string> new_col;
+ data_.push_back(new_col);
+ column_names_.push_back(column_name);
+ return data_.size()-1;
+}
+
+/**
+ * adds a column to the delimited file
+ *\returns the new column index.
+ */
+unsigned int DelimitedFile::addColumn(
+ const char* column_name ///< the column name
+ ) {
+ string string_name(column_name);
+ return addColumn(string_name);
+}
+
+/**
+ * adds a column to the delimited file
+ *\returns the new column index.
+ */
+unsigned int DelimitedFile::addColumn() {
+ vector<string> new_col;
+ data_.push_back(new_col);
+ return numCols() - 1;
+}
+
+/**
+ * adds a vector of columns to the delimited file
+ */
+void DelimitedFile::addColumns(
+ vector<string>& column_names
+ ) {
+ cout << "Number of columns:" << column_names.size() << endl;
+ for (unsigned int col_idx = 0;col_idx < column_names.size(); col_idx++) {
+ cout << "Adding :" << column_names[col_idx] << endl;
+ //addColumn(column_names[col_idx]);
+ }
+}
+
+
+
+/**
+ * finds the index of a column
+ *\returns the column index, -1 if not found.
+ */
+int DelimitedFile::findColumn(
+ const string& column_name ///< the column name
+ ) {
+ for (unsigned int col_idx=0;col_idx < column_names_.size();col_idx++) {
+ if (column_names_[col_idx] == column_name) {
+ return col_idx;
+ }
+ }
+ return -1;
+}
+
+/**
+ * finds the index of a column
+ *\returns the column index, -1 if not found.
+ */
+int DelimitedFile::findColumn(
+ const char* column_name ///< the column name
+) {
+ string sname = string(column_name);
+ return findColumn(sname);
+}
+
+/**
+ *\returns the string vector corresponding to the column
+ */
+vector<string>& DelimitedFile::getColumn(
+ string column ///< the column name
+ ) {
+ int col_idx = findColumn(column);
+ if (col_idx != -1) {
+ return data_[col_idx];
+ }
+ carp(CARP_ERROR, "column %s not found, returning column 0", column.c_str());
+ return data_[0];
+}
+
+/**
+ *\returns the string vector corresponding to the column
+ */
+vector<string>& DelimitedFile::getColumn(
+ unsigned int col_idx ///< the column index
+ ) {
+ return data_.at(col_idx);
+}
+
+/**
+ *\returns the name of the column
+ */
+string& DelimitedFile::getColumnName(
+ unsigned int col_idx ///< the column index
+ ) {
+ return column_names_.at(col_idx);
+}
+
+/**
+ *\returns the column_names
+ */
+vector<string>& DelimitedFile::getColumnNames() {
+ return column_names_;
+}
+
+
+/**
+ * adds a row to the delimited file
+ *\returns the new row index
+ */
+unsigned int DelimitedFile::addRow() {
+ if (numCols() == 0) {
+ carp(CARP_FATAL, "Must have at least one column before calling add row!");
+ }
+
+ unsigned int row_idx = numRows();
+ for (unsigned int col_idx = 0;col_idx < numCols(); col_idx++) {
+ setString(col_idx, row_idx, "");
+ }
+ return row_idx;
+}
+
+/**
+ *\returns the string value of the cell
+ */
+string& DelimitedFile::getString(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ ) {
+ vector<string>& column = getColumn(col_idx);
+ if (row_idx >= column.size()) {
+ carp(CARP_FATAL, "Row is out of range for column %i:%s row %i:%i",
+ col_idx,
+ getColumnName(col_idx).c_str(),
+ row_idx,
+ column.size());
+ }
+ return getColumn(col_idx).at(row_idx);
+}
+
+/**
+ * gets a string value of the cell.
+ */
+string& DelimitedFile::getString(
+ const char* column_name, ///<the column name
+ unsigned int row_idx ///< the row index
+ ) {
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_ERROR, "Cannot find column %s", column_name);
+ carp(CARP_ERROR, "Available columns");
+ for (unsigned int idx = 0;idx < numCols();idx++) {
+ carp(CARP_ERROR, "%s", getColumnName(idx).c_str());
+ }
+ carp(CARP_FATAL, "Calling FATAL");
+ }
+ return getColumn(col_idx)[row_idx];
+}
+
+/**
+ * gets a string value of the cell
+ * uses the current_row_ as the row index
+ */
+string& DelimitedFile::getString(
+ const char* column_name ///<the column name
+ ) {
+ if (current_row_ >= numRows()) {
+ carp(CARP_FATAL, "Iterated past maximum number of rows!");
+ }
+ return getString(column_name, current_row_);
+}
+
+/**
+ * sets the string value of the cell
+ */
+void DelimitedFile::setString(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx, ///< the row index
+ const string& value ///< the new value
+ ) {
+ //ensure there are enough columns
+ while (col_idx >= numCols()) {
+ addColumn();
+ }
+ vector<string>& col = getColumn(col_idx);
+
+ //ensure there are enough rows
+ while (row_idx >= col.size()) {
+ col.push_back("");
+ }
+
+ col[row_idx] = value;
+}
+
+/**
+ * sets the string value of the cell
+ */
+void DelimitedFile::setString(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx, ///< the row index
+ const char* value ///< the new value
+) {
+ string svalue(value);
+ setString(col_idx, row_idx, svalue);
+}
+
+/**
+ *\returns the data type of the cell
+ */
+template<typename TValue>
+TValue DelimitedFile::getValue(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ ) {
+ return StringUtils::FromString<TValue>(getString(col_idx, row_idx));
+}
+
+/**
+ * gets a double type from cell, checks for infinity.
+ */
+FLOAT_T DelimitedFile::getFloat(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+) {
+ string& string_ans = getString(col_idx, row_idx);
+ if (string_ans == "Inf") {
+ return numeric_limits<FLOAT_T>::infinity();
+ } else if (string_ans == "-Inf") {
+ return -numeric_limits<FLOAT_T>::infinity();
+ }
+ return getValue<FLOAT_T>(col_idx, row_idx);
+}
+
+/**
+ * gets a double type from cell, checks for infinity.
+ */
+FLOAT_T DelimitedFile::getFloat(
+ const char* column_name, ///<the column name
+ unsigned int row_idx ///< the row index
+) {
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_ERROR, "Cannot find column %s", column_name);
+ carp(CARP_ERROR, "Available columns");
+ for (unsigned int idx = 0;idx < numCols();idx++) {
+ carp(CARP_ERROR, "%s", getColumnName(idx).c_str());
+ }
+ carp(CARP_FATAL, "Calling FATAL");
+ }
+ return getFloat(col_idx, row_idx);
+}
+
+/**
+ * gets a double value from cell, checks for infinity
+ * uses the current_row_ as the row index
+ */
+FLOAT_T DelimitedFile::getFloat(
+ const char* column_name ///<the column name
+) {
+ if (current_row_ >= numRows()) {
+ carp(CARP_FATAL, "Iterated past maximum number of rows!");
+ }
+ return getFloat(column_name, current_row_);
+}
+
+/**
+ * gets a double type from cell, checks for infinity.
+ */
+double DelimitedFile::getDouble(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ ) {
+ string& string_ans = getString(col_idx, row_idx);
+ if (string_ans == "Inf") {
+ return numeric_limits<double>::infinity();
+ } else if (string_ans == "-Inf") {
+ return -numeric_limits<double>::infinity();
+ }
+ return getValue<double>(col_idx, row_idx);
+}
+
+/**
+ * gets a double type from cell, checks for infinity.
+ */
+double DelimitedFile::getDouble(
+ const char* column_name, ///<the column name
+ unsigned int row_idx ///<the row index
+) {
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_ERROR, "Cannot find column %s", column_name);
+ carp(CARP_ERROR, "Available columns");
+ for (unsigned int idx = 0;idx < numCols();idx++) {
+ carp(CARP_ERROR, "%s", getColumnName(idx).c_str());
+ }
+ carp(CARP_FATAL, "Calling FATAL");
+ }
+ return getDouble(col_idx, row_idx);
+}
+
+/**
+ * gets a double value from cell, checks for infinity
+ * uses the current_row_ as the row index
+ */
+double DelimitedFile::getDouble(
+ const char* column_name ///<the column name
+) {
+ if (current_row_ >= numRows()) {
+ carp(CARP_FATAL, "Iterated past maximum number of rows!");
+ }
+ return getDouble(column_name, current_row_);
+}
+
+/**
+ * gets an integer type from cell.
+ */
+int DelimitedFile::getInteger(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ ) {
+ //TODO : check the string for a valid integer.
+ return getValue<int>(col_idx, row_idx);
+}
+
+/**
+ * get an integer type from cell, checks for infintiy.
+ */
+int DelimitedFile::getInteger(
+ const char* column_name, ///< the column name
+ unsigned int row_idx ///<the row index
+) {
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_FATAL, "Cannot find column %s", column_name);
+ }
+ return getInteger(col_idx, row_idx);
+}
+
+
+/**
+ * get an integer type from cell, checks for infinity.
+ * uses the current_row_ as the row index.
+ */
+int DelimitedFile::getInteger(
+ const char* column_name ///< the column name
+ ) {
+ if (current_row_ >= numRows()) {
+ carp(CARP_FATAL, "Iterated past maximum number of rows!");
+ }
+ return getInteger(column_name, current_row_);
+}
+
+/**
+ * gets an vector of integers from cell where the
+ * string in the cell are integers which are separated
+ * by a delimiter which is differnt than the column
+ * delimiter. The default delimiter is a comma
+ * uses the current_row_ as the row index.
+ * clears the integer vector before
+ * populating it.
+ */
+void DelimitedFile::getIntegerVectorFromCell(
+ const char* column_name, ///< the column name
+ vector<int>& int_vector, ///<the vector of integers
+ char delimiter ///<the delimiter to use
+ ) {
+ //get the list of strings separated by delimiter
+ vector<string> string_vector_ans = StringUtils::Split(getString(column_name), delimiter);
+
+ //convert each string into an integer.
+ int_vector.clear();
+
+ for (vector<string>::iterator string_iter = string_vector_ans.begin();
+ string_iter != string_vector_ans.end();
+ ++string_iter) {
+ int_vector.push_back(StringUtils::FromString<int>(*string_iter));
+ }
+}
+
+/**
+ * reorders the rows of a delimited file using a built map
+ * of sorted indices.
+ */
+template <typename T>
+void DelimitedFile::reorderRows(
+ multimap<T, unsigned int>& sort_indices, ///<map of indices sorted by type T
+ bool ascending ///<sort in ascending order?
+ ) {
+ vector<vector<string> > newData;
+
+ for (unsigned int col_idx = 0;col_idx < numCols();col_idx++) {
+ vector<string> current_col;
+ unsigned int row_idx;
+ if (ascending) {
+ typename multimap<T, unsigned int>::iterator sort_iter;
+ for (sort_iter = sort_indices.begin();
+ sort_iter != sort_indices.end();
+ ++sort_iter) {
+ row_idx = sort_iter -> second;
+ string current_cell = getString(col_idx, row_idx);
+ current_col.push_back(current_cell);
+ }
+ } else {
+ typename multimap<T, unsigned int>::reverse_iterator sort_iter;
+ for (sort_iter = sort_indices.rbegin();
+ sort_iter != sort_indices.rend();
+ ++sort_iter) {
+ row_idx = sort_iter -> second;
+ string current_cell = getString(col_idx, row_idx);
+ current_col.push_back(current_cell);
+ }
+ }
+ newData.push_back(current_col);
+ }
+ data_.swap(newData);
+}
+
+/**
+ * sorts the delimited file treating the key column as float values
+ */
+void DelimitedFile::sortByFloatColumn(
+ const string& column_name, ///<The name of the key column
+ bool ascending ///<sort in ascending order?
+ ) {
+
+ multimap<FLOAT_T, unsigned int> sort_indices;
+ int sort_col_idx = findColumn(column_name);
+
+ if (sort_col_idx == -1) {
+ carp(CARP_FATAL, "column %s doesn't exist", column_name.c_str());
+ }
+
+ for (unsigned int row_idx=0;row_idx < numRows();row_idx++) {
+ sort_indices.insert(pair<FLOAT_T, unsigned int>(getFloat(sort_col_idx, row_idx), row_idx));
+ }
+
+ reorderRows(sort_indices, ascending);
+}
+
+/**
+ * sorts the delimited file treating the key column as integers
+ */
+void DelimitedFile::sortByIntegerColumn(
+ unsigned int col_idx, ///< the index of the key column
+ bool ascending ///< sort in ascending order?
+ ) {
+ multimap<int, unsigned int> sort_indices;
+ for (unsigned int row_idx=0;row_idx < numRows();row_idx++) {
+ sort_indices.insert(pair<int, unsigned int>(getInteger(col_idx, row_idx), row_idx));
+ }
+ reorderRows(sort_indices, ascending);
+}
+
+
+/**
+ * sorts the delimited file treating the key column as integers
+ */
+void DelimitedFile::sortByIntegerColumn(
+ const string& column_name, ///< the name of the key column
+ bool ascending ///< sort in ascending order?
+ ) {
+ int sort_col_idx = findColumn(column_name);
+ if (sort_col_idx == -1) {
+ carp(CARP_FATAL, "column %s doesn't exist", column_name.c_str());
+ }
+ sortByIntegerColumn(sort_col_idx, ascending);
+}
+
+/**
+ * sorts the delimited file treating the key column as a string
+ */
+void DelimitedFile::sortByStringColumn(
+ const string& column_name, ///< the name of the key column
+ bool ascending ///< sort in ascending order?
+ ) {
+ multimap<string, unsigned int> sort_indices;
+
+ int sort_col_idx = findColumn(column_name);
+
+ if (sort_col_idx == -1) {
+ carp(CARP_FATAL, "column %s doesn't exist", column_name.c_str());
+ }
+
+ for (unsigned int row_idx=0;row_idx < numRows();row_idx++) {
+ sort_indices.insert(pair<string, unsigned int>(getString(sort_col_idx, row_idx), row_idx));
+ }
+
+ reorderRows(sort_indices, ascending);
+}
+
+/**
+ * copies a row to a another DelimitedFile
+ */
+void DelimitedFile::copyToRow(
+ DelimitedFile& dest, ///<The DelimitedFile to copy the row to
+ int src_row_idx, ///<The row index of the source (this)
+ int dest_row_idx ///<The row index of the destination.
+ ) {
+ for (unsigned int src_col_idx=0;src_col_idx < numCols();src_col_idx++) {
+ int dest_col_idx = dest.findColumn(getColumnName(src_col_idx));
+ if (dest_col_idx != -1) {
+ dest.setString(dest_col_idx, dest_row_idx, getString(src_col_idx, src_row_idx));
+ } else {
+ carp(CARP_WARNING, "Column %s not found in destination",
+ getColumnName(src_col_idx).c_str());
+ }
+ }
+}
+
+/*Iterator functions.*/
+/**
+ * resets the current_row_ index to 0.
+ */
+void DelimitedFile::reset() {
+ current_row_ = 0;
+}
+
+/**
+ * increments the current_row_,
+ */
+void DelimitedFile::next() {
+ if (current_row_ < numRows()) {
+ current_row_++;
+ }
+}
+
+/**
+ * \returns whether there are more rows to
+ * iterate through
+ */
+bool DelimitedFile::hasNext() {
+ return current_row_ < numRows();
+}
+
+/**
+ *Allows object to be printed to a stream
+ */
+std::ostream &operator<< (
+ std::ostream& os, ///< The stream to output to
+ DelimitedFile& delimited_file ///< The delimited file to output
+ ) {
+ //find the maximum number of rows.
+ unsigned int maxRow = 0;
+ for (unsigned int col_idx=0; col_idx < delimited_file.numCols(); col_idx++) {
+ maxRow = max(maxRow, delimited_file.numRows(col_idx));
+ }
+
+ //print out the header if it exists.
+ if (delimited_file.column_names_.size() != 0) {
+ os << delimited_file.column_names_[0];
+ for (unsigned int col_idx=1; col_idx < delimited_file.column_names_.size(); col_idx++) {
+ os << delimited_file.getDelimiter() << delimited_file.column_names_[col_idx];
+ }
+ os << endl;
+ }
+
+ //print out all rows, using delimiter_ when
+ //the row goes past the current column
+ //size.
+ for (unsigned int row_idx=0; row_idx < maxRow; row_idx++) {
+ if (row_idx < delimited_file.numRows(0)) {
+ os << delimited_file.getString((unsigned int)0, row_idx);
+ } else {
+ os << delimited_file.getDelimiter();
+ }
+ for (unsigned int col_idx=1;col_idx < delimited_file.numCols();col_idx++) {
+ os <<delimited_file.getDelimiter();
+ if (row_idx < delimited_file.numRows(col_idx))
+ os << delimited_file.getString(col_idx, row_idx);
+ }
+ os << endl;
+ }
+
+ return os;
+}
+
diff --git a/src/io/DelimitedFile.h b/src/io/DelimitedFile.h
new file mode 100644
index 0000000..80ddf94
--- /dev/null
+++ b/src/io/DelimitedFile.h
@@ -0,0 +1,474 @@
+/**
+ * \file DelimitedFile.h
+ * DATE: Jan 7, 2010
+ * AUTHOR: Sean McIlwain
+ * \brief Object for reading tab-delimited files.
+ *
+ * This class generates a table of values. The default delimiter is tab.
+ * This class is capable of reading string, integers, and floating point
+ * Types from each cell of the table. This class also provides function
+ * for reading a list of integers or string from a cell using a delimiter
+ * that is different from the column delimiter (default is comma ',').
+ ****************************************************************************/
+#ifndef DELIMITEDFILE_H
+#define DELIMITEDFILE_H
+
+#include <limits>
+#include <ios>
+#include <iomanip>
+#include <iostream>
+#include <map>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "parameter.h"
+#include "util/Params.h"
+
+class DelimitedFile {
+
+ protected:
+ /** The data vector is indexed by column, then by row
+ * Ex. data_[0][4] means 0th column, 4th row
+ * data_[0] is a string vector of all data in a column.
+ */
+ std::vector<std::vector<std::string> > data_;
+ std::vector<std::string> column_names_;
+ unsigned int current_row_; //used for iterating through the table.
+ char delimiter_;
+
+ /**
+ * reorders the rows of a delimited file using a built map
+ * of sorted indices.
+ */
+ template <typename T>
+ void reorderRows(
+ std::multimap<T, unsigned int>& sort_indices, ///<map of indices sorted by type T
+ bool ascending ///<sort in ascending order?
+ );
+
+ public:
+ /**
+ * \returns a DelimitedFile object
+ */
+ DelimitedFile(
+ char delimiter = '\t' ///< the delimiter to use (default tab)
+ );
+
+ /**
+ * \returns a DelimitedFile object and loads the tab-delimited
+ * data specified by file_name.
+ */
+ DelimitedFile(
+ const char *file_name, ///< the path of the file to read
+ bool hasHeader = true, ///< indicate whether header exists
+ char delimiter = '\t' ///< the delimiter to use (default tab)
+ );
+
+ /**
+ * \returns a DelimitedFile object and loads the tab-delimited
+ * data specified by file_name.
+ */
+ DelimitedFile(
+ const std::string& file_name, ///< the path of the file to read
+ bool hasHeader = true, ///< indicates whether header exists
+ char delimiter = '\t' ///< the delimiter to use (default tab)
+ );
+
+ /**
+ * empties the delimited file
+ */
+ void clear();
+
+ /**
+ * Destructor
+ */
+ virtual ~DelimitedFile();
+
+
+ /**
+ * sets the delimiter
+ */
+ void setDelimiter(
+ char delimiter ///< the delimiter
+ );
+
+ /**
+ * /returns the delimtier
+ */
+ char getDelimiter() const;
+
+ /**
+ *\returns the number of rows, assuming a square matrix
+ */
+ unsigned int numRows();
+
+ /**
+ *\returns the number of columns
+ */
+ unsigned int numCols();
+
+ /**
+ *\returns the number of rows for a column
+ */
+ unsigned int numRows(
+ unsigned int col_idx ///<the column index
+ );
+
+ /**
+ * clears the current data and column names,
+ * parses the header if it exists,
+ * reads the file one line at a time while
+ * populating the data matrix with the
+ * strings separated by tabs.
+ */
+ void loadData(
+ const char *file_name, ///< the file path
+ bool hasHeader = true, ///< header indicator
+ char delimiter = '\t' ///< the delimiter to use (default tab).
+ );
+
+ /**
+ * loads a tab delimited file
+ */
+ void loadData(
+ const std::string& file_name, ///< the file path
+ bool hasHeader = true, ///< header indicator
+ char delimiter = '\t' ///< the delimiter to use (default tab).
+ );
+
+ /**
+ * saves a tab delimited file
+ */
+ void saveData(
+ const char* file_name ///< the file path
+ );
+
+ /**
+ * saves a tab delimited file
+ */
+ void saveData(
+ const std::string& file_name ///< the file path
+ );
+
+ /**
+ * adds a column to the delimited file
+ *\returns the column index.
+ */
+ unsigned int addColumn(
+ const std::string& column_name ///< the column name
+ );
+
+ /**
+ * adds a column to the delimited file
+ *\returns the column index.
+ */
+ unsigned int addColumn(
+ const char* column_name ///< the column name
+ );
+
+ /**
+ * adds a vector of columns to the delimited file
+ */
+ void addColumns(
+ std::vector<std::string>& column_names);
+
+ /**
+ * adds a column to the delimited file
+ */
+ unsigned int addColumn();
+
+ /**
+ * finds the index of a column
+ *\returns the column index, -1 if not found.
+ */
+ int findColumn(
+ const std::string& column_name ///< the column name
+ );
+
+ /**
+ * finds the index of a column
+ *\returns the column index, -1 if not found.
+ */
+ int findColumn(
+ const char* column_name ///< the column name
+ );
+
+ /**
+ * adds a row to the delimited file
+ *\returns the new row index
+ */
+ unsigned int addRow();
+
+ /**
+ *\returns the string vector corresponding to the column
+ */
+ std::vector<std::string>& getColumn(
+ std::string column ///< the column name
+ );
+
+ /**
+ *\returns the string vector corresponding to the column
+ */
+ std::vector<std::string>& getColumn(
+ unsigned int col_idx ///< the column index
+ );
+
+ /**
+ *\returns the name of the column
+ */
+ std::string& getColumnName(
+ unsigned int col_idx ///< the column index
+ );
+
+ /**
+ *\returns the column_names
+ */
+ std::vector<std::string>& getColumnNames();
+
+ /**
+ *\returns the string value of the cell
+ */
+ std::string& getString(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ );
+
+ /**
+ * gets a string value of the cell.
+ */
+ std::string& getString(
+ const char* column_name, ///<the column name
+ unsigned int row_idx ///< the row index
+ );
+
+ /**
+ * gets a string value of the cell
+ * uses the current_row_ as the row index
+ */
+ std::string& getString(
+ const char* column_name ///<the column name
+ );
+
+
+ /**
+ * sets the string value of the cell
+ */
+ void setString(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx, ///< the row index
+ const std::string& value ///< the new value
+ );
+
+ /**
+ * sets the string value of the cell
+ */
+ void setString(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx, ///< the row index
+ const char* value ///< the new value
+ );
+
+ /**
+ *\returns the data of the cell in the specified type
+ */
+ template<typename TValue>
+ TValue getValue(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ );
+
+ /**
+ * sets the cell value with the specified type
+ */
+ template<typename TValue>
+ void setValue(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx, ///< the row index
+ TValue value ///< the new value
+ ) {
+ int precision = Params::GetInt("precision");
+ std::ostringstream ss;
+ ss << std::setprecision(precision) << value;
+ std::string svalue = ss.str();
+ setString(col_idx, row_idx, svalue);
+ }
+
+ template<typename TValue>
+ void setValue(
+ const std::string& column_name, ///< the column index
+ unsigned int row_idx, ///< the row index
+ TValue value ///< the new value
+ ) {
+
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_FATAL, "Column not found %s", column_name.c_str());
+ }
+ setValue(col_idx, row_idx, value);
+ }
+
+ /**
+ * gets a double type from cell, checks for infinity.
+ */
+ FLOAT_T getFloat(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ );
+
+ /**
+ * gets a double type from cell, checks for infinity.
+ */
+ FLOAT_T getFloat(
+ const char* column_name, ///<the column name
+ unsigned int row_idx ///< the row index
+ );
+
+ /**
+ * gets a double value from cell, checks for infinity
+ * uses the current_row_ as the row index
+ */
+ FLOAT_T getFloat(
+ const char* column_name ///<the column name
+ );
+
+ /**
+ * gets a double type from cell, checks for infinity.
+ */
+ double getDouble(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ );
+
+ /**
+ * gets a double type from cell, checks for infinity.
+ */
+ double getDouble(
+ const char* column_name, ///<the column name
+ unsigned int row_idx ///<the row index
+ );
+
+ /**
+ * gets a double value from cell, checks for infinity
+ * uses the current_row_ as the row index
+ */
+ double getDouble(
+ const char* column_name ///<the column name
+ );
+
+
+ /**
+ * gets an integer type from cell, checks for infinity.
+ */
+ int getInteger(
+ unsigned int col_idx, ///< the column index
+ unsigned int row_idx ///< the row index
+ );
+
+ /**
+ * get an integer type from cell, checks for infintiy.
+ */
+ int getInteger(
+ const char* column_name, ///< the column name
+ unsigned int row_idx ///<the row index
+ );
+
+ /**
+ * get an integer type from cell, checks for infinity.
+ * uses the current_row_ as the row index.
+ */
+ int getInteger(
+ const char* column_name ///< the column name
+ );
+
+ /**
+ * gets an vector of integers from cell where the
+ * string in the cell are integers which are separated
+ * by a delimiter which is differnt than the column
+ * delimiter. The default delimiter is a comma
+ * uses the current_row_ as the row index.
+ * clears the integer vector before
+ * populating it.
+ */
+ void getIntegerVectorFromCell(
+ const char* column_name, ///< the column name
+ std::vector<int>& int_vector, ///<the vector of integers
+ char delimiter = ',' ///<the delimiter to use
+ );
+
+ /**
+ * sorts the delimited file treating the key column as float values
+ */
+ void sortByFloatColumn(
+ const std::string& column_name, ///<The name of the key column
+ bool ascending = true ///<sort in ascending order?
+ );
+
+ /**
+ * sorts the delimited file treating the key column as integers
+ */
+ void sortByIntegerColumn(
+ unsigned int col_idx, ///< the index of the key column
+ bool ascending = true ///< sort in ascending order?
+ );
+
+ /**
+ * sorts the delimited file treating the key column as integers
+ */
+ void sortByIntegerColumn(
+ const std::string& column_name, ///< the name of the key column
+ bool ascending = true ///< sort in ascending order?
+ );
+
+ /**
+ * sorts the delimited file treating the key column as a string
+ */
+ void sortByStringColumn(
+ const std::string& column_name, ///< the name of the key column
+ bool ascending = true ///< sort in ascending order?
+ );
+
+ /**
+ * copies a row to a another DelimitedFile
+ */
+ void copyToRow(
+ DelimitedFile& dest, ///<The DelimitedFile to copy the row to
+ int src_row_idx, ///<The row index of the source (this)
+ int dest_row_idx ///<The row index of the destination.
+ );
+
+ /*Iterator functions.*/
+ /**
+ * resets the current_row_ index to 0.
+ */
+ void reset();
+
+ /**
+ * increments the current_row_,
+ */
+ void next();
+
+
+ /**
+ * \returns whether there are more rows to
+ * iterate through
+ */
+ bool hasNext();
+
+ /**
+ * Allows object to be printed to a stream
+ */
+ friend std::ostream &operator<< (
+ std::ostream& os, ///< The stream to output to
+ DelimitedFile& delimited_file ///< The delimited file to output to
+ );
+};
+
+#endif //DELIMITEDFILE_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/DelimitedFileReader.cpp b/src/io/DelimitedFileReader.cpp
new file mode 100644
index 0000000..0d54784
--- /dev/null
+++ b/src/io/DelimitedFileReader.cpp
@@ -0,0 +1,504 @@
+/*************************************************************************
+ * \file DelimitedFileReader.cpp
+ * \brief Object for parsing the tab-delimited files
+ *************************************************************************/
+
+#include "DelimitedFileReader.h"
+
+#include <fstream>
+
+#include <iostream>
+#include <string>
+
+#include "carp.h"
+#include "DelimitedFile.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+
+/**
+ * \returns a DelimitedFileReader object
+ */
+DelimitedFileReader::DelimitedFileReader():
+ num_rows_valid_(false), istream_ptr_(NULL), delimiter_('\t'), owns_stream_(false) {
+}
+
+/**
+ * \returns a DelimitedFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+DelimitedFileReader::DelimitedFileReader(
+ const char *file_name, ///< the path of the file to read
+ bool has_header, ///< indicates whether the header exists (default true).
+ char delimiter ///< the delimiter to use (default tab).
+): istream_ptr_(NULL), num_rows_valid_(false), delimiter_(delimiter) {
+ loadData(file_name, has_header);
+}
+
+/**
+ * \returns a DelimitedFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+DelimitedFileReader::DelimitedFileReader(
+ const std::string& file_name, ///< the path of the file to read
+ bool has_header, ///< indicates whether the header exists (default true).
+ char delimiter ///< the delimiter to use (default tab)
+): istream_ptr_(NULL), delimiter_(delimiter) {
+ loadData(file_name, has_header);
+}
+
+/**
+ * \returns a DelimitedFileReader object and loads the tab-delimted
+ * data specified by istream.
+ */
+DelimitedFileReader::DelimitedFileReader(
+ std::istream* istream_ptr, ///< the stream to be read
+ bool has_header, ///<indicates whether header exists
+ char delimiter ///< the delimiter to use (default tab)
+): istream_ptr_(istream_ptr), istream_begin_(istream_ptr->tellg()), delimiter_(delimiter),
+has_header_(has_header), owns_stream_(false) {
+ loadData();
+}
+
+
+/**
+ * Destructor
+ */
+DelimitedFileReader::~DelimitedFileReader() {
+ if (istream_ptr_ != NULL && owns_stream_) {
+ delete istream_ptr_;
+ }
+}
+
+/**
+ * \returns the number of rows, assuming a square matrix
+ */
+unsigned int DelimitedFileReader::numRows() {
+ if (!num_rows_valid_) {
+ num_rows_ = 0;
+
+ streampos last_pos = istream_ptr_->tellg();
+
+ istream_ptr_->clear();
+ istream_ptr_->seekg(istream_begin_, ios::beg);
+
+ string temp_str;
+
+ while (getline(*istream_ptr_, temp_str)) {
+ num_rows_++;
+ }
+
+ if (has_header_) {
+ num_rows_--;
+ }
+ num_rows_valid_ = true;
+ istream_ptr_->clear();
+ istream_ptr_->seekg(last_pos);
+ }
+ return num_rows_;
+}
+
+/**
+ *\returns the number of columns
+ */
+unsigned int DelimitedFileReader::numCols() {
+ return column_names_.size();
+}
+
+/*
+ *\returns a printable string of the columns available in this file
+ */
+string DelimitedFileReader::getAvailableColumnsString() {
+
+ ostringstream oss;
+ oss << "Available columns:" << endl;
+ for (unsigned int col_idx=0;col_idx < numCols();col_idx++) {
+ oss << col_idx << " " << getColumnName(col_idx) << endl;
+ }
+
+ string ans = oss.str();
+ return ans;
+}
+
+/*
+ *\returns the column name header string
+ */
+string DelimitedFileReader::getHeaderString() {
+ if (numCols() == 0) {
+ return string("");
+ }
+
+ ostringstream oss;
+ oss << getColumnName(0);
+ for (unsigned int col_idx=1;col_idx < numCols();col_idx++) {
+ oss << delimiter_ << getColumnName(col_idx);
+ }
+
+ string ans = oss.str();
+ return ans;
+}
+
+
+void DelimitedFileReader::loadData() {
+ if (!istream_ptr_->good()) {
+ carp(CARP_ERROR, "Stream is not good!");
+ carp(CARP_ERROR, "Filename:%s", file_name_.c_str());
+ carp(CARP_ERROR, "EOF:%i", istream_ptr_ -> eof());
+ carp(CARP_ERROR, "Fail:%i", istream_ptr_ -> fail());
+ carp(CARP_ERROR, "Bad:%i", istream_ptr_ -> bad());
+ carp(CARP_FATAL, "Exiting....");
+ }
+ current_row_ = 0;
+ num_rows_valid_ = false;
+ has_current_ = false;
+ column_mismatch_warned_ = false;
+ istream_begin_ = istream_ptr_->tellg();
+
+ has_next_ = !getline(*istream_ptr_, next_data_string_).fail();
+ next_data_string_ = StringUtils::Trim(next_data_string_);
+ if (has_header_) {
+ if (has_next_) {
+ column_names_ = StringUtils::Split(next_data_string_, delimiter_);
+ has_next_ = !getline(*istream_ptr_, next_data_string_).fail();
+ } else {
+ carp(CARP_WARNING, "No data/headers found!");
+ return;
+ }
+ }
+
+ if (has_next_) {
+ next();
+ }
+}
+
+/**
+ * clears the current data and column names,
+ * parses the header if it exists,
+ * reads the file one line at a time while
+ * populating the data matrix with the
+ * strings separated by tabs.
+ */
+void DelimitedFileReader::loadData(
+ const char *file_name, ///< the file path
+ bool has_header ///< header indicator
+ ) {
+
+ file_name_ = string(file_name);
+ has_header_ = has_header;
+
+ //special case, if filename is '-', then use standard input.
+ if (file_name_ == "-") {
+ istream_ptr_ = &cin;
+ owns_stream_ = false;
+ } else {
+ istream_ptr_ = new ifstream(file_name, ios::in);
+ owns_stream_ = true;
+ }
+ loadData();
+
+}
+
+/**
+ * loads a tab delimited file
+ */
+void DelimitedFileReader::loadData(
+ const string& file, ///< the file path
+ bool has_header ///< header indicator
+ ) {
+ loadData(file.c_str(), has_header);
+}
+
+/**
+ * finds the index of a column
+ *\returns the column index, -1 if not found.
+ */
+int DelimitedFileReader::findColumn(
+ const string& column_name ///< the column name
+ ) {
+ for (unsigned int col_idx=0;col_idx < column_names_.size();col_idx++) {
+ if (column_names_[col_idx] == column_name) {
+ return col_idx;
+ }
+ }
+ return -1;
+}
+
+/**
+ * finds the index of a column
+ *\returns the column index, -1 if not found.
+ */
+int DelimitedFileReader::findColumn(
+ const char* column_name ///< the column name
+) {
+ return findColumn(string(column_name));
+}
+
+/**
+ *\returns the name of the column
+ */
+const string& DelimitedFileReader::getColumnName(
+ unsigned int col_idx ///< the column index
+ ) {
+ return column_names_.at(col_idx);
+}
+
+/**
+ *\returns the column_names
+ */
+const vector<string>& DelimitedFileReader::getColumnNames() {
+ return column_names_;
+}
+
+/**
+ *\returns the current row index
+ */
+int DelimitedFileReader::getCurrentRowIndex() const {
+ return current_row_;
+}
+
+
+/**
+ * \returns the current row string
+ */
+const string& DelimitedFileReader::getString() {
+ if (!has_current_) {
+ carp(CARP_FATAL, "End of file!");
+ }
+ return current_data_string_;
+}
+
+/**
+ *\returns the string value of the cell
+ */
+const string& DelimitedFileReader::getString(
+ unsigned int col_idx ///< the column index
+ ) {
+ if (col_idx >= data_.size()) {
+ carp(CARP_FATAL, "col idx:%i is out of bounds! (0,%i,%i)",
+ col_idx, (column_names_.size()-1), (data_.size()-1));
+ }
+ return data_.at(col_idx);
+}
+
+/**
+ * \returns the string value of the cell.
+ */
+const string& DelimitedFileReader::getString(
+ const char* column_name ///<the column name
+ ) {
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_FATAL, "Cannot find column %s\n" "Available Columns:%s\n",
+ column_name, getAvailableColumnsString().c_str());
+ }
+ return getString(col_idx);
+}
+
+/**
+ * \returns the value of the cell
+ * using the current row
+ */
+template<typename TValue>
+TValue DelimitedFileReader::getValue(
+ unsigned int col_idx ///< the column index
+ ) {
+ return StringUtils::FromString<TValue>(getString(col_idx));
+}
+
+/**
+ * \returns the FLOAT_T value of a cell, checks for infinity
+ */
+FLOAT_T DelimitedFileReader::getFloat(
+ unsigned int col_idx ///< the column index
+ ) {
+ const string& string_ans = getString(col_idx);
+ if (string_ans == "Inf") {
+ return numeric_limits<FLOAT_T>::infinity();
+ } else if (string_ans == "-Inf") {
+ return -numeric_limits<FLOAT_T>::infinity();
+ } else {
+ return getValue<FLOAT_T>(col_idx);
+ }
+}
+
+/**
+ * \returns the FLOAT_T value of a cell, checks for infinity.
+ */
+FLOAT_T DelimitedFileReader::getFloat(
+ const char* column_name ///<the column name
+) {
+
+ carp(CARP_DETAILED_DEBUG, "getFloat for %s", column_name);
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_FATAL, "Cannot find column %s\n"
+ "Available Columns:%s\n",
+ column_name, getAvailableColumnsString().c_str());
+ }
+ return getFloat(col_idx);
+}
+
+/**
+ * \returns the double value of a cell, checks for infinity.
+ */
+double DelimitedFileReader::getDouble(
+ unsigned int col_idx ///< the column index
+ ) {
+ const string& string_ans = getString(col_idx);
+ if (string_ans == "") {
+ return 0.0;
+ } else if (string_ans == "Inf") {
+ return numeric_limits<double>::infinity();
+ } else if (string_ans == "-Inf") {
+ return -numeric_limits<double>::infinity();
+ } else {
+ return getValue<double>(col_idx);
+ }
+}
+
+/**
+ * \returns the double value of a cell, checks for infinity.
+ */
+double DelimitedFileReader::getDouble(
+ const char* column_name ///<the column name
+ ) {
+
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_FATAL, "Cannot find column %s\n"
+ "Available Columns:%s\n",
+ column_name, getAvailableColumnsString().c_str());
+ }
+ return getDouble(col_idx);
+}
+
+/**
+ * \returns the integer value of a cell.
+ */
+int DelimitedFileReader::getInteger(
+ unsigned int col_idx ///< the column index
+ ) {
+ //TODO : check the string for a valid integer.
+ return getValue<int>(col_idx);
+}
+
+/**
+ * \returns the integer value of a cell, checks for infintiy.
+ */
+int DelimitedFileReader::getInteger(
+ const char* column_name ///< the column name
+) {
+
+ int col_idx = findColumn(column_name);
+ if (col_idx == -1) {
+ carp(CARP_FATAL, "Cannot find column %s", column_name);
+ }
+
+ return getInteger(col_idx);
+}
+
+/**
+ * gets an vector of integers from cell where the
+ * string in the cell are integers which are separated
+ * by a delimiter which is differnt than the column
+ * delimiter. The default delimiter is a comma
+ * uses the current_row_ as the row index.
+ * clears the integer vector before
+ * populating it.
+ */
+void DelimitedFileReader::getIntegerVectorFromCell(
+ const char* column_name, ///< the column name
+ vector<int>& int_vector, ///<the vector of integers
+ char delimiter ///<the delimiter to use
+ ) {
+
+ //get the list of strings separated by delimiter
+ vector<string> string_vector_ans = StringUtils::Split(getString(column_name), delimiter);
+
+ //convert each string into an integer.
+ int_vector.clear();
+
+ for (vector<string>::iterator string_iter = string_vector_ans.begin();
+ string_iter != string_vector_ans.end();
+ ++string_iter) {
+ int_vector.push_back(StringUtils::FromString<int>(*string_iter));
+ }
+}
+
+/**
+ * gets an vector of doubles from cell where the
+ * string in the cell are integers which are separated
+ * by a delimiter which is differnt than the column
+ * delimiter. The default delimiter is a comma
+ * uses the current_row_ as the row index.
+ * clears the double vector before
+ * populating it.
+ */
+void DelimitedFileReader::getDoubleVectorFromCell(
+ const char* column_name, ///< the column name
+ std::vector<double>& double_vector, ///<the vector of integers
+ char delimiter ///<the delimiter to use
+) {
+
+ //get the list of strings separated by delimiter
+ vector<string> string_vector_ans = StringUtils::Split(getString(column_name), delimiter);
+
+ //convert each string into an integer.
+ double_vector.clear();
+
+ for (vector<string>::iterator string_iter = string_vector_ans.begin();
+ string_iter != string_vector_ans.end();
+ ++string_iter) {
+ double_vector.push_back(StringUtils::FromString<double>(*string_iter));
+ }
+}
+
+/*Iterator functions.*/
+/**
+ * resets the file pointer to the beginning of the file.
+ */
+void DelimitedFileReader::reset() {
+ istream_ptr_->clear();
+ istream_ptr_->seekg(istream_begin_, ios::beg);
+ loadData();
+}
+
+/**
+ * parses the next line in the file.
+ */
+void DelimitedFileReader::next() {
+ if (has_next_) {
+ current_row_++;
+ current_data_string_ = next_data_string_;
+ //parse next_data_string_ into data_
+ data_ = StringUtils::Split(current_data_string_, delimiter_);
+ //make sure data has the right number of columns for the header.
+ if (data_.size() < column_names_.size()) {
+ if (!column_mismatch_warned_) {
+ carp(CARP_WARNING, "Column count %d for line %d is less than header %d",
+ data_.size(), current_row_, column_names_.size());
+ carp(CARP_WARNING, "%s", current_data_string_.c_str());
+ carp(CARP_WARNING, "Suppressing warnings, other mismatches may exist!");
+ column_mismatch_warned_ = true;
+ }
+ while (data_.size() < column_names_.size()) {
+ data_.push_back("");
+ }
+ }
+
+ //read next line
+ has_next_ = !getline(*istream_ptr_, next_data_string_).fail();
+ has_current_ = true;
+ } else {
+ has_current_ = false;
+ }
+}
+
+/**
+ * \returns whether there are more rows to
+ * iterate through
+ */
+bool DelimitedFileReader::hasNext() {
+ return has_next_ || has_current_;
+}
+
diff --git a/src/io/DelimitedFileReader.h b/src/io/DelimitedFileReader.h
new file mode 100644
index 0000000..6a1d524
--- /dev/null
+++ b/src/io/DelimitedFileReader.h
@@ -0,0 +1,293 @@
+/**
+ * \file DelimitedFileReader.h
+ * $Revision: 1.00 $
+ * DATE: Jan 7, 2010
+ * AUTHOR: Sean McIlwain
+ * \brief Object for reading tab-delimited files.
+ * This class generates a table of values. The default delimiter is tab.
+ * This class is capable of reading string, integers, and floating point
+ * Types from each cell of the table. This class also provides function
+ * for reading a list of integers or string from a cell using a delimiter
+ * that is different from the column delimiter (default is comma ',').
+ * This class reads the data in line by line
+ ****************************************************************************/
+#ifndef DELIMITEDFILEREADER_H
+#define DELIMITEDFILEREADER_H
+
+#include <limits>
+#include <ios>
+#include <iomanip>
+#include <iostream>
+#include <map>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "parameter.h"
+#include "util/Params.h"
+
+class DelimitedFileReader {
+
+ protected:
+ /** The data vector is indexed by column, then by row
+ * Ex. data_[0][4] means 0th column, 4th row
+ * data_[0] is a string vector of all data in a column.
+ */
+
+ std::string next_data_string_; ///<the next data string.
+ std::string current_data_string_; ///<the current data string.
+ std::vector<std::string> data_; ///<the current vectorized data.
+ std::vector<std::string> column_names_; ///<the column names.
+
+ char delimiter_; ///<the delimiter to use.
+
+ unsigned int current_row_; ///<current row count
+ bool has_next_; ///<indicator of whether there is another row to parse
+ bool has_current_; ///<indicator of whether the current row is parsed
+ bool has_header_; ///<indicator of whether there is a header in the file
+
+ bool owns_stream_; ///<indicator of whether the object owns the stream
+
+ std::istream* istream_ptr_; ///<pointer to the stream itself
+
+ std::streampos istream_begin_; ///<position pointer for the beginning of the stream
+
+ std::string file_name_; ///<file name that the stream is open on.
+
+ bool num_rows_valid_; ///<indicator whether the number of rows is valid
+ unsigned int num_rows_; ///<number of rows in the file.
+
+ bool column_mismatch_warned_; ///<indicator of whether the column mismatch warning has been issued
+
+ /**
+ * clears the current data and column names,
+ * parses the header if it exists,
+ * reads the file one line at a time while
+ * populating the data matrix with the
+ * strings separated by delimiter.
+ */
+ void loadData();
+
+ virtual void loadData(
+ const char *file_name, ///< the file path
+ bool has_header = true ///< header indicator
+ );
+
+ virtual void loadData(
+ const std::string& file_name, ///< the file path
+ bool has_header = true ///< header indicator
+ );
+
+ public:
+ /**
+ * \returns a blank DelimitedFileReader object
+ */
+ DelimitedFileReader();
+
+ /**
+ * \returns a DelimitedFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+ DelimitedFileReader(
+ const char *file_name, ///< the path of the file to read
+ bool has_header = true, ///< indicates whether the header exists (default true).
+ char delimiter = '\t' ///< the delimiter to use (default tab).
+ );
+
+ /**
+ * \returns a DelimitedFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+ DelimitedFileReader(
+ const std::string& file_name, ///< the path of the file to read
+ bool has_header = true, ///< indicates whether the header exists (default true).
+ char delimiter = '\t' ///< the delimiter to use (default tab)
+ );
+
+ DelimitedFileReader(
+ std::istream* istream_ptr, ///< the stream to be read
+ bool has_header = true, ///<indicates whether header exists
+ char delimiter = '\t' ///< the delimiter to use (default tab)
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~DelimitedFileReader();
+
+ /**
+ *\returns the number of rows, assuming a square matrix
+ */
+ unsigned int numRows();
+
+ /**
+ *\returns the number of columns
+ */
+ unsigned int numCols();
+
+ /*
+ *\returns a printable string of the columns available in this file
+ */
+ std::string getAvailableColumnsString();
+
+ /*
+ *\returns the column name header string
+ */
+ std::string getHeaderString();
+
+
+ /**
+ * finds the index of a column
+ *\returns the column index, -1 if not found.
+ */
+ int findColumn(
+ const std::string& column_name ///< the column name
+ );
+
+ /**
+ * finds the index of a column
+ *\returns the column index, -1 if not found.
+ */
+ int findColumn(
+ const char* column_name ///< the column name
+ );
+
+ /**
+ *\returns the name of the column
+ */
+ const std::string& getColumnName(
+ unsigned int col_idx ///< the column index
+ );
+
+ /**
+ *\returns the column_names
+ */
+ const std::vector<std::string>& getColumnNames();
+
+ /**
+ *\returns the current row index
+ */
+ int getCurrentRowIndex() const;
+
+ /**
+ * \returns the current row string
+ */
+ const std::string& getString();
+
+ /**
+ * \returns the string value of the cell
+ * using the current row
+ */
+ const std::string& getString(
+ const char* column_name ///<the column name
+ );
+
+ /**
+ * \returns the string value of the cell
+ * using the current row
+ */
+ const std::string& getString(
+ unsigned int col_idx ///< the column index
+ );
+
+ /**
+ * \returns the value of the cell
+ * using the current row
+ */
+ template<typename TValue>
+ TValue getValue(
+ unsigned int col_idx ///< the column index
+ );
+
+ /**
+ * \returns the double value of the cell, checks for infinity
+ * uses the current row
+ */
+ FLOAT_T getFloat(
+ const char* column_name ///<the column name
+ );
+
+ FLOAT_T getFloat(
+ unsigned int col_idx ///<the col index
+ );
+
+ /**
+ * \returns the double value from cell, checks for infinity
+ * uses the current_row_ as the row index
+ */
+ double getDouble(
+ const char* column_name ///<the column name
+ );
+
+ double getDouble(
+ unsigned int col_idx ///<the col index
+ );
+
+ /**
+ * get an integer type from cell, checks for infinity.
+ * uses the current_row_ as the row index.
+ */
+ int getInteger(
+ const char* column_name ///< the column name
+ );
+
+ int getInteger(
+ unsigned int col_idx ///<the col index
+ );
+
+ /**
+ * gets an vector of integers from cell where the
+ * string in the cell are integers which are separated
+ * by a delimiter which is differnt than the column
+ * delimiter. The default delimiter is a comma
+ * uses the current_row_ as the row index.
+ * clears the integer vector before
+ * populating it.
+ */
+ void getIntegerVectorFromCell(
+ const char* column_name, ///< the column name
+ std::vector<int>& int_vector, ///<the vector of integers
+ char delimiter = ',' ///<the delimiter to use
+ );
+
+ /**
+ * gets an vector of doubles from cell where the
+ * string in the cell are integers which are separated
+ * by a delimiter which is differnt than the column
+ * delimiter. The default delimiter is a comma
+ * uses the current_row_ as the row index.
+ * clears the double vector before
+ * populating it.
+ */
+ void getDoubleVectorFromCell(
+ const char* column_name, ///< the column name
+ std::vector<double>& double_vector, ///<the vector of integers
+ char delimiter = ',' ///<the delimiter to use
+ );
+
+ /*Iterator functions.*/
+ /**
+ * resets the file pointer to the beginning of the file.
+ */
+ void reset();
+
+ /**
+ * parses the next line in the file.
+ */
+ void next();
+
+ /**
+ * \returns whether there are more rows to
+ * iterate through
+ */
+ bool hasNext();
+};
+
+#endif //DELIMITEDFILEREADER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/DelimitedFileWriter.cpp b/src/io/DelimitedFileWriter.cpp
new file mode 100644
index 0000000..463773f
--- /dev/null
+++ b/src/io/DelimitedFileWriter.cpp
@@ -0,0 +1,168 @@
+/**
+ * \file DelimitedFileWriter.cpp
+ * $Revision: 1.0 $
+ * DATE: October 19, 2010
+ * AUTHOR: Barbara Frewen
+ * \brief Object for writing tab-delimited files.
+ * This class writes to files one line at a time, creating a table of
+ * data. The values for the current row are set one column at a time
+ * and then the row is written to file, separating columns of data
+ * with the delimiter. The default delimiter is tab, but can be set
+ * to any character. A header row may be defined and printed to the
+ * file at any row in the flile. Once a header has been written,
+ * every row after that will have the same number of fields.
+ */
+
+#include "DelimitedFileWriter.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+
+#include <fstream>
+
+using namespace std;
+
+/**
+ * \returns An empty DelimitedFileWriter object.
+ */
+DelimitedFileWriter::DelimitedFileWriter()
+: file_ptr_(NULL),
+ delimiter_('\t') { // default is tab
+}
+
+/**
+ * \returns A DelimitedFileWriter object with the given file to
+ * write to.
+ */
+DelimitedFileWriter::DelimitedFileWriter
+(const char* filename) // full path of file
+: file_ptr_(NULL),
+ delimiter_('\t') { // default is tab
+ this->openFile(filename);
+}
+
+/**
+ * Destructor
+ */
+DelimitedFileWriter::~DelimitedFileWriter() {
+ if( file_ptr_ ) {
+ file_ptr_->close();
+ delete file_ptr_;
+ }
+}
+
+/**
+ * Writes any existing data, closes any open file and opens the
+ * given file.
+ */
+void DelimitedFileWriter::openFile(const char* filename) {
+ // write any existing data and close file
+ if( file_ptr_ ) {
+ writeRow();
+ file_ptr_->close();
+ delete file_ptr_;
+ }
+
+ // open the file if either it doesn't exist or if we are allowed to overwrite
+ file_ptr_ = FileUtils::GetWriteStream(filename, Params::GetBool("overwrite"));
+ if( file_ptr_ == NULL ) {
+ carp(CARP_FATAL, "Error creating file '%s'.", filename);
+ }
+}
+
+/**
+ * Sets the delimeter to separate columns.
+ */
+void DelimitedFileWriter::setDelimiter(char delimiter) {
+ delimiter_ = delimiter;
+}
+
+/**
+ * Sets the name of the column at the given index, beginning with
+ * zero. Replaces any existing name.
+ */
+void DelimitedFileWriter::setColumnName(const string& name, ///< new name to set
+ unsigned int col_idx) {///< col to name
+ while( column_names_.size() <= col_idx ) {
+ column_names_.push_back("");
+ }
+ column_names_[col_idx] = name;
+}
+
+/**
+ * Sets the names of all columns, clearing any existing names. Pass an
+ * empty vector as the 'names' argument to clear any existing column
+ * names.
+ */
+void DelimitedFileWriter::setColumnNames(const vector<string>& names) {
+ column_names_.clear();
+ column_names_ = names;
+}
+
+/**
+ * Writes the data of the current line to file, clears current data.
+ * If there are column headers set, the line printed will have at
+ * least as many fields as there are column headers.
+ */
+void DelimitedFileWriter::writeRow() {
+ if( current_row_.empty() ) {
+ return;
+ }
+
+ // make the row as long as the header
+ while( current_row_.size() < column_names_.size()) {
+ current_row_.push_back("");
+ }
+ // TODO? warning if row is longer than non-empty header?
+
+ // print each value separated by delimiter
+ *file_ptr_ << current_row_[0];
+ for(size_t idx = 1; idx < current_row_.size(); idx++) {
+ *file_ptr_ << delimiter_ << current_row_[idx];
+ }
+ // end with newline
+ *file_ptr_ << endl;
+
+ // clear the current_row and refill with blanks
+ // if there is a header, that is the min length
+ // if not, each row can be a different length
+ current_row_.assign(column_names_.size(), "");
+
+}
+
+/**
+ * Writes any given column headers to file. For missing column
+ * headers (e.g. if columns 0 and 2 are set, but not 1) print
+ * "column_#".
+ */
+void DelimitedFileWriter::writeHeader() {
+
+ if( column_names_.empty() ) {
+ return;
+ }
+
+ if( file_ptr_ == NULL || !file_ptr_->is_open() ) {
+ carp(CARP_FATAL, "Cannot write to NULL delimited file.");
+ }
+
+ *file_ptr_ << column_names_[0];
+ for(size_t idx = 1; idx < column_names_.size(); idx++) {
+ if( column_names_[idx].empty() ) {
+ *file_ptr_ << delimiter_ << "column_" << (idx+1);
+ } else {
+ *file_ptr_ << delimiter_ << column_names_[idx];
+ }
+ }
+
+ *file_ptr_ << endl;
+
+ // with a header, each line must be that length
+ current_row_.assign(column_names_.size(), "");
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/DelimitedFileWriter.h b/src/io/DelimitedFileWriter.h
new file mode 100644
index 0000000..f3ab26a
--- /dev/null
+++ b/src/io/DelimitedFileWriter.h
@@ -0,0 +1,128 @@
+/**
+ * \file DelimitedFileWriter.h
+ * $Revision: 1.0 $
+ * DATE: October 19, 2010
+ * AUTHOR: Barbara Frewen
+ * \brief Object for writing tab-delimited files.
+ * This class writes to files one line at a time, creating a table of
+ * data. The values for the current row are set one column at a time
+ * and then the row is written to file, separating columns of data
+ * with the delimiter. The default delimiter is tab, but can be set
+ * to any character. A header row may be defined and printed to the
+ * file at any row in the flile. Once a header has been written,
+ * every row after that will have the same number of fields.
+ */
+
+#ifndef DELIMITED_FILE_WRITER_H
+#define DELIMITED_FILE_WRITER_H
+
+#include <vector>
+#include <string>
+#include <algorithm>
+#include <sstream>
+#include <iomanip>
+#include <ios>
+#include "parameter.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+class DelimitedFileWriter {
+
+ protected:
+ std::ofstream* file_ptr_; ///< the file to write to
+ char delimiter_; ///< separate columns with this character
+ std::vector<std::string> column_names_; ///< one entry per column
+ std::vector<std::string> current_row_; ///< values for next row to write
+
+ public:
+ /**
+ * \returns An empty DelimitedFileWriter object.
+ */
+ DelimitedFileWriter();
+
+ /**
+ * \returns A DelimitedFileWriter object with the given file to
+ * write to.
+ */
+ explicit DelimitedFileWriter(const char* filename); // full path of file
+
+ /**
+ * Destructor
+ */
+ virtual ~DelimitedFileWriter();
+
+ /**
+ * Writes any existing data, closes any open file and opens the
+ * given file.
+ */
+ virtual void openFile(const char* filename);
+
+ /**
+ * Sets the delimeter to separate columns.
+ */
+ void setDelimiter(char delimiter);
+
+ /**
+ * Sets the name of the column at the given index, beginning with
+ * zero. Replaces any existing name.
+ */
+ void setColumnName(const std::string& name, ///< new name to set
+ unsigned int col_idx); ///< column to name
+
+ /**
+ * Sets the names of all columns, clearing any existing names.
+ */
+ void setColumnNames(const std::vector<std::string>& names);
+
+ /**
+ * Writes any given column headers to file.
+ */
+ void writeHeader();
+
+ /**
+ * Writes the data of the current line to file, clears current data.
+ */
+ void writeRow();
+
+ // template functions only compile correctly when in the header file
+
+ /**
+ * Sets the value for the current row of the given column.
+ */
+ template<typename ValueType>
+ void setColumnCurrentRow
+ (unsigned int col_idx, ///< set value for this column
+ const ValueType& value, ///< the value to set
+ unsigned int precision, ///<written at this precision
+ bool fixed_float = true) { ///<use fixed float notation?
+
+ // make sure the current_row_ is long enough
+ size_t max_size = std::max((size_t)col_idx + 1, column_names_.size());
+
+ while( current_row_.size() < max_size ) {
+ current_row_.push_back("");
+ }
+
+ current_row_[col_idx] = StringUtils::ToString(value, precision, fixed_float);
+ }
+
+ /**
+ * Sets the value for the current row of the given column.
+ */
+ template<typename ValueType>
+ void setColumnCurrentRow
+ (unsigned int col_idx, ///< set value for this column
+ const ValueType& value) { ///< the value to set
+ // make sure the current_row_ is long enough
+ size_t max_size = std::max((size_t)col_idx + 1, column_names_.size());
+
+ while( current_row_.size() < max_size ) {
+ current_row_.push_back("");
+ }
+
+ current_row_[col_idx] = StringUtils::ToString(value);
+ }
+
+};
+
+#endif //DELIMITED_FILE_WRITER_H
diff --git a/src/io/HTMLWriter.cpp b/src/io/HTMLWriter.cpp
new file mode 100644
index 0000000..0690f12
--- /dev/null
+++ b/src/io/HTMLWriter.cpp
@@ -0,0 +1,14 @@
+#include "HTMLWriter.h"
+
+using namespace Crux;
+using namespace boost;
+using namespace std;
+
+
+HTMLWriter::HTMLWriter() : PMCDelimitedFileWriter() {
+ setWriteHTML(true);
+}
+
+HTMLWriter::~HTMLWriter() {
+ closeFile();
+}
diff --git a/src/io/HTMLWriter.h b/src/io/HTMLWriter.h
new file mode 100644
index 0000000..5abbb06
--- /dev/null
+++ b/src/io/HTMLWriter.h
@@ -0,0 +1,18 @@
+#ifndef HTMLWRITER_H
+#define HTMLWRITER_H
+
+#include <vector>
+
+#include "PMCDelimitedFileWriter.h"
+
+class HTMLWriter : public PMCDelimitedFileWriter {
+
+ public:
+
+ HTMLWriter();
+
+ ~HTMLWriter();
+
+};
+
+#endif
diff --git a/src/io/LineFileReader.cpp b/src/io/LineFileReader.cpp
new file mode 100644
index 0000000..9dac069
--- /dev/null
+++ b/src/io/LineFileReader.cpp
@@ -0,0 +1,156 @@
+/*************************************************************************
+ * \file LineFileReader.cpp
+ * \brief Object for parsing the tab-delimited files
+ *************************************************************************/
+
+#include "LineFileReader.h"
+
+#include <fstream>
+
+#include "carp.h"
+
+using namespace std;
+
+/**
+ * \returns a LineFileReader object
+ */
+LineFileReader::LineFileReader() {
+
+ file_ptr_ = NULL;
+}
+
+/**
+ * \returns a LineFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+LineFileReader::LineFileReader(
+ const char *file_name ///< the path of the file to read
+ ) {
+
+ file_ptr_ = NULL;
+ loadData(file_name);
+}
+
+/**
+ * \returns a LineFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+LineFileReader::LineFileReader(
+ const string& file_name ///< the path of the file to read
+ ) {
+
+ file_ptr_ = NULL;
+ loadData(file_name);
+}
+
+/**
+ * Destructor
+ */
+LineFileReader::~LineFileReader() {
+
+ if (file_ptr_ != NULL) {
+
+ file_ptr_ -> close();
+ delete file_ptr_;
+ }
+}
+
+/**
+ * clears the current data and column names,
+ * parses the header if it exists,
+ * reads the file one line at a time while
+ * populating the data matrix with the
+ * strings separated by tabs.
+ */
+void LineFileReader::loadData(
+ const char *file_name ///< the file path
+ ) {
+
+ file_name_ = string(file_name);
+
+ file_ptr_ = new fstream(file_name, ios::in);
+ current_row_ = 0;
+
+
+ if (!file_ptr_ -> is_open()) {
+ carp(CARP_FATAL, "Opening %s or reading failed", file_name);
+ return;
+ } else {
+ has_next_ = !getline(*file_ptr_, next_data_string_).fail();
+ carp(CARP_DEBUG, "first line:%s", next_data_string_.c_str());
+ if (!has_next_) {
+ carp(CARP_WARNING, "No data found!");
+ }
+ }
+}
+
+/**
+ * loads a tab delimited file
+ */
+void LineFileReader::loadData(
+ const string& file ///< the file path
+ ) {
+
+ loadData(file.c_str());
+}
+
+/**
+ * \returns the current row string
+ */
+const string& LineFileReader::current() {
+ if (!has_current_) {
+ //carp(CARP_FATAL, "End of file!");
+ }
+
+ return current_data_string_;
+}
+
+/*Iterator functions.*/
+
+/**
+ * resets the file pointer to the beginning of the file.
+ */
+void LineFileReader::reset() {
+
+ if (file_ptr_ != NULL) {
+ file_ptr_ -> close();
+ delete file_ptr_;
+ }
+ loadData(file_name_);
+
+}
+
+/**
+ * parses the next line in the file.
+ */
+const string& LineFileReader::next() {
+ //Do we already have a next line ready?
+ if (has_next_) {
+ current_row_++;
+ current_data_string_ = next_data_string_;
+ //read next line
+ has_next_ = !getline(*file_ptr_, next_data_string_).fail();
+ has_current_ = true;
+ } else {
+ has_current_ = false;
+ }
+
+ return current_data_string_;
+}
+
+
+int LineFileReader::getCurrentRow() {
+
+ return current_row_;
+
+}
+
+/**
+ * \returns whether there are more rows to
+ * iterate through
+ */
+bool LineFileReader::hasNext() {
+ return has_next_;
+}
+
+
diff --git a/src/io/LineFileReader.h b/src/io/LineFileReader.h
new file mode 100644
index 0000000..dffc4cd
--- /dev/null
+++ b/src/io/LineFileReader.h
@@ -0,0 +1,97 @@
+/**
+ * \file LineFileReader.h
+ * $Revision: 1.00 $
+ * DATE: Jan 7, 2010
+ * AUTHOR: Sean McIlwain
+ * \brief Object for reading text files line by line.
+ ****************************************************************************/
+#ifndef LINEFILEREADER_H
+#define LINEFILEREADER_H
+
+#include <limits>
+#include <ios>
+#include <iomanip>
+#include <iostream>
+#include <map>
+#include <sstream>
+#include <string>
+#include <vector>
+
+//#include "parameter.h"
+
+
+class LineFileReader {
+
+ protected:
+ /** The data vector is indexed by column, then by row
+ * Ex. data_[0][4] means 0th column, 4th row
+ * data_[0] is a string vector of all data in a column.
+ */
+
+ std::string next_data_string_; //the next data string.
+ std::string current_data_string_; //the current data string.
+ unsigned int current_row_; //current row count
+ bool has_next_;
+ bool has_current_;
+ std::fstream* file_ptr_;
+
+ std::string file_name_;
+
+ bool num_rows_valid_;
+ unsigned int num_rows_;
+
+
+ public:
+ /**
+ * \returns a blank LineFileReader object
+ */
+ LineFileReader();
+
+ /**
+ * \returns a LineFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+ LineFileReader(
+ const char *file_name ///< the path of the file to read
+ );
+
+ /**
+ * \returns a LineFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+ LineFileReader(
+ const std::string& file_name ///< the path of the file to read
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~LineFileReader();
+
+ virtual void loadData(
+ const char *file_name ///< the file path
+ );
+
+ virtual void loadData(
+ const std::string& file_name ///< the file path
+ );
+
+
+ const std::string& current();
+ const std::string& next();
+
+ int getCurrentRow();
+
+ bool hasNext();
+
+ void reset();
+};
+
+#endif //LINEFILEREADER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/MSToolkitSpectrumCollection.cpp b/src/io/MSToolkitSpectrumCollection.cpp
new file mode 100644
index 0000000..0abe0af
--- /dev/null
+++ b/src/io/MSToolkitSpectrumCollection.cpp
@@ -0,0 +1,150 @@
+/**
+ * \file MSToolkitSpectrumCollection.cpp
+ * AUTHOR: Chris Park
+ * CREATE DATE: 28 June 2006
+ * \brief Class to read spectra files using the MSToolkit library.
+ */
+#include "MSReader.h"
+#include "MSToolkitSpectrumCollection.h"
+#include "util/crux-utils.h"
+#include "util/Params.h"
+#include "parameter.h"
+#include "model/Spectrum.h"
+
+/**
+ * Instantiates a new spectrum_collection object from a filename.
+ * Does not parse file.
+ */
+MSToolkitSpectrumCollection::MSToolkitSpectrumCollection(
+ const string& filename ///< The spectrum collection filename.
+) : SpectrumCollection(filename) {
+
+}
+
+/**
+ * Parses all the spectra from file designated by the filename member
+ * variable.
+ * \returns True if the spectra are parsed successfully. False if otherwise.
+ */
+bool MSToolkitSpectrumCollection::parse() {
+
+ // spectrum_collection has already been parsed
+ if(is_parsed_) {
+ return false;
+ }
+
+ // get a list of scans to include if requested
+ string range_string = Params::GetString("scan-number");
+ int first_scan;
+ int last_scan;
+
+ bool success = get_range_from_string(range_string, first_scan, last_scan);
+
+ if( !success ) {
+ carp(CARP_FATAL, "The scan number range '%s' is invalid. "
+ "Must be of the form <first>-<last>.", range_string.c_str());
+ }
+
+ carp(CARP_DEBUG, "Using mstoolkit to parse spectra.");
+
+ MSToolkit::MSReader* mst_reader = new MSToolkit::MSReader();
+ MSToolkit::Spectrum* mst_spectrum = new MSToolkit::Spectrum();
+
+ // only read ms2 scans
+ mst_reader->setFilter(MSToolkit::MS2);
+ // read first spectrum
+ bool ret = mst_reader->readFile(filename_.c_str(), *mst_spectrum);
+
+ if (!ret) {
+ carp(CARP_FATAL, "MSToolkit: Error reading spectra file: %s", filename_.c_str());
+ }
+
+ while(mst_spectrum->getScanNumber() != 0) {
+ // is this a scan to include? if not skip it
+ if( mst_spectrum->getScanNumber() < first_scan ) {
+ mst_reader->readFile(NULL, *mst_spectrum);
+ continue;
+ }
+ // are we past the last scan?
+ if( mst_spectrum->getScanNumber() > last_scan ) {
+ break;
+ }
+ Crux::Spectrum* parsed_spectrum = new Crux::Spectrum();
+ if (parsed_spectrum->parseMstoolkitSpectrum(mst_spectrum, filename_.c_str())) {
+ addSpectrumToEnd(parsed_spectrum);
+ } else {
+ delete parsed_spectrum;
+ }
+
+ mst_reader->readFile(NULL, *mst_spectrum);
+ }
+ delete mst_spectrum;
+ delete mst_reader;
+
+ return true;
+}
+
+/**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan. Removes any existing information in
+ * the given spectrum.
+ * \returns True if the spectrum was allocated, false on error.
+ */
+bool MSToolkitSpectrumCollection::getSpectrum(
+ int first_scan, ///< The first scan of the spectrum to retrieve -in
+ Crux::Spectrum* spectrum ///< Put the spectrum info here
+ ) {
+ carp(CARP_DEBUG, "Using mstoolkit to parse spectrum");
+ MSToolkit::MSReader* mst_reader = new MSToolkit::MSReader();
+ MSToolkit::Spectrum* mst_spectrum = new MSToolkit::Spectrum();
+ bool parsed = false;
+
+ mst_reader->readFile(filename_.c_str(), *mst_spectrum, first_scan);
+
+ if(mst_spectrum->getScanNumber() != 0) {
+ spectrum->parseMstoolkitSpectrum(mst_spectrum,
+ filename_.c_str());
+ parsed = true;
+ } else {
+ carp(CARP_ERROR, "Spectrum %d does not exist in file", first_scan);
+ parsed = false;
+ }
+ delete mst_spectrum;
+ delete mst_reader;
+ return parsed;
+}
+
+/**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan.
+ * \returns The spectrum data from file or NULL.
+ */
+Crux::Spectrum* MSToolkitSpectrumCollection::getSpectrum(
+ int first_scan ///< The first scan of the spectrum to retrieve -in
+ ) {
+ carp(CARP_DEBUG, "Using mstoolkit to parse spectrum");
+ MSToolkit::MSReader* mst_reader = new MSToolkit::MSReader();
+ MSToolkit::Spectrum* mst_spectrum = new MSToolkit::Spectrum();
+ Crux::Spectrum* return_spec = NULL;
+
+ mst_reader->readFile(filename_.c_str(), *mst_spectrum, first_scan);
+
+ if(mst_spectrum->getScanNumber() != 0) {
+ return_spec = new Crux::Spectrum();
+ return_spec->parseMstoolkitSpectrum(mst_spectrum,
+ filename_.c_str());
+ } else {
+ carp(CARP_ERROR, "Spectrum %d does not exist in file", first_scan);
+ return_spec = NULL;
+ }
+ delete mst_spectrum;
+ delete mst_reader;
+ return return_spec;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/MSToolkitSpectrumCollection.h b/src/io/MSToolkitSpectrumCollection.h
new file mode 100644
index 0000000..c22934a
--- /dev/null
+++ b/src/io/MSToolkitSpectrumCollection.h
@@ -0,0 +1,63 @@
+/**
+ * \file MSToolkitSpectrumCollection.h
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: 20 April 2011
+ * \brief Class for accessing spectra using the MSToolkit library.
+ */
+#ifndef MSTOOLKIT_SPECTRUM_COLLECTION_H
+#define MSTOOLKIT_SPECTRUM_COLLECTION_H
+
+#include "SpectrumCollection.h"
+
+/**
+ * \class SpectrumCollection
+ * \brief An abstract class for accessing spectra from a file.
+ */
+class MSToolkitSpectrumCollection : public Crux::SpectrumCollection {
+
+ protected:
+
+ public:
+ /**
+ * Constructor sets filename and initializes member variables.
+ */
+ MSToolkitSpectrumCollection(
+ const std::string& filename ///< The spectrum collection filename. -in
+ );
+
+ /**
+ * Parses all the spectra from file designated by the filename member
+ * variable.
+ * \returns TRUE if the spectra are parsed successfully. FALSE if otherwise.
+ */
+ virtual bool parse();
+
+ /**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan.
+ * \returns The newly allocated Spectrum or NULL if scan number not found.
+ */
+ virtual Crux::Spectrum* getSpectrum(
+ int first_scan ///< The first scan of the spectrum to retrieve -in
+ );
+
+ /**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan. Removes any existing information in the
+ * given spectrum.
+ * \returns True if the spectrum was allocated, false on error.
+ */
+ virtual bool getSpectrum(
+ int first_scan, ///< The first scan of the spectrum to retrieve -in
+ Crux::Spectrum* spectrum ///< Put the spectrum info here
+ );
+
+};
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/MatchCollectionParser.cpp b/src/io/MatchCollectionParser.cpp
new file mode 100644
index 0000000..a3df2b6
--- /dev/null
+++ b/src/io/MatchCollectionParser.cpp
@@ -0,0 +1,211 @@
+/**
+ * \file MatchCollectionParser.cpp
+ * AUTHOR Sean McIlwain
+ * CREATE DATE: 14 June 2011
+ * \brief Return a MatchCollection object of the appropriate
+ * derived class.
+ */
+#include "parameter.h"
+#include "MatchCollectionParser.h"
+#include "MatchFileReader.h"
+#include "PepXMLReader.h"
+#include "SQTReader.h"
+#include "MzIdentMLReader.h"
+#include "model/Protein.h"
+#include "model/PostProcessProtein.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+using namespace Crux;
+
+MatchCollectionParser::MatchCollectionParser() {
+ database_ = NULL;
+ decoy_database_ = NULL;
+}
+
+MatchCollectionParser::~MatchCollectionParser() {
+ Database::freeDatabase(database_);
+ Database::freeDatabase(decoy_database_);
+}
+
+
+/**
+ * Creates database object(s) from fasta or index file
+ */
+void MatchCollectionParser::loadDatabase(
+ const string& fasta_file, ///< fasta or index path -in
+ Database*& database, ///< resulting database -out
+ Database*& decoy_database ///< resulting decoy database -out
+ ) {
+
+ if (fasta_file.empty()) {
+ carp(CARP_DEBUG, "no database provided");
+ database = new Database();
+ database -> setIsParsed(true);
+ decoy_database = new Database();
+ database -> setIsParsed(true);
+ } else {
+ bool use_index = FileUtils::IsDir(fasta_file);
+ // get binary fasta file name with path to crux directory
+ if (use_index == true) {
+ //We aren't supporting search-for-matches anymore, so we won't be
+ //building any indices. We could use tide-indices for this, but
+ //comet doesn't use an index. In the future we can support tide
+ //indices in the post-processing tools if users want that.
+ carp(CARP_FATAL, "Parsing binary index from tide-index is not"
+ " supported.\nPlease use the original fasta file instead.");
+ } else {
+ database = new Database(fasta_file, false);// not memmapped
+ database->transformTextToMemmap(".", true);// is temp
+ decoy_database = new Database();
+ }
+ database->parse();
+ }
+}
+
+
+/**
+ * \returns a Protein object. This function first tries to
+ * find the protein by id in the target or decoy database.
+ * if unsucessful, we then determine whether the protein
+ * is a decoy or not by looking for the "decoy-prefix" in
+ * id. When then create a PostProcessProtein and add it
+ * to the corresponding target or decoy database.
+ */
+Protein* MatchCollectionParser::getProtein(
+ Database* database, ///< target database -in
+ Database* decoy_database, ///< decoy database -in
+ string& protein_id, ///< id of protein to find -in
+ bool& is_decoy ///< is protein a decoy? -out
+ ) {
+
+ //is it in the target database?
+ Protein* protein = database->getProteinByIdString(protein_id.c_str());
+ if (protein != NULL) {
+ is_decoy = false;
+ return protein;
+ }
+
+ //is it in the decoy database?
+ if (decoy_database != NULL) {
+ protein = decoy_database->getProteinByIdString(protein_id.c_str());
+ if (protein != NULL) {
+ is_decoy = true;
+ return protein;
+ }
+ }
+
+ //try creating it and adding it to the database as a postprocess protein
+ carp(CARP_DEBUG, "Creating new protein for %s", protein_id.c_str());
+ protein = new PostProcessProtein();
+ protein->setId(protein_id.c_str());
+ string decoy_prefix = Params::GetString("decoy-prefix");
+ if (protein_id.find(decoy_prefix) != string::npos) {
+ carp(CARP_DEBUG, "adding to decoy database");
+ is_decoy = true;
+ // Fixes segfault in case of NULL decoy database
+ if (decoy_database != NULL) {
+ decoy_database->addProtein(protein);
+ }
+ } else {
+ carp(CARP_DEBUG, "adding to target database");
+ is_decoy = false;
+ database->addProtein(protein);
+ }
+ return protein;
+}
+
+Protein* MatchCollectionParser::getProtein(
+ Database* database, ///< target database -in
+ Database* decoy_database, ///< decoy database -in
+ string& protein_id, ///< id of protein to find -in
+ string& sequence, ///< sequence of the protein -in
+ bool& is_decoy ///< is protein a decoy? -out
+ ) {
+
+ //is it in the target database?
+ Protein* protein = database->getProteinByIdString(protein_id.c_str());
+ if (protein != NULL) {
+ is_decoy = false;
+ return protein;
+ }
+
+ //is it in the decoy database?
+ if (decoy_database != NULL) {
+ protein = decoy_database->getProteinByIdString(protein_id.c_str());
+ if (protein != NULL) {
+ is_decoy = true;
+ return protein;
+ }
+ }
+
+ //try creating it and adding it to the database as a postprocess protein
+ carp(CARP_DEBUG, "Creating new protein for %s", protein_id.c_str());
+ carp(CARP_DEBUG, "Sequence :%s", sequence.c_str());
+
+ protein = new PostProcessProtein();
+
+ protein->setId(protein_id.c_str());
+ protein->setSequence(sequence.c_str());
+ protein->setLength(sequence.length());
+
+
+ string decoy_prefix = Params::GetString("decoy-prefix");
+ if (protein_id.find(decoy_prefix) != string::npos) {
+ is_decoy = true;
+ // Fixes segfault in case of NULL database
+ if (decoy_database != NULL) {
+ decoy_database->addProtein(protein);
+ }
+ } else {
+ is_decoy = false;
+ database->addProtein(protein);
+ }
+ return protein;
+}
+
+/**
+ * \returns a MatchCollection object using the file and protein database
+ */
+MatchCollection* MatchCollectionParser::create(
+ const string& match_path, ///< path to the file of matches
+ const string& fasta_path ///< path to the protein database
+ ) {
+ carp(CARP_DEBUG, "match path:%s", match_path.c_str());
+ if (!fasta_path.empty()) {
+ carp(CARP_DEBUG, "fasta path:%s", fasta_path.c_str());
+ }
+ if (!FileUtils::Exists(match_path)) {
+ carp(CARP_FATAL, "The file %s does not exist. \n", match_path.c_str());
+ }
+
+ if (database_ == NULL || decoy_database_ == NULL) {
+ loadDatabase(fasta_path, database_, decoy_database_);
+ }
+ MatchCollection* collection = NULL;
+
+ if (FileUtils::IsDir(match_path)) {
+ carp(CARP_FATAL, "Internal error");
+ } else if (StringUtils::IEndsWith(match_path, ".xml")) {
+ collection = PepXMLReader::parse(match_path, database_, decoy_database_);
+ } else if (StringUtils::IEndsWith(match_path, ".sqt")) {
+ collection = SQTReader::parse(match_path, database_, decoy_database_);
+ } else if (StringUtils::IEndsWith(match_path, ".mzid")) {
+ collection = MzIdentMLReader::parse(match_path, database_, decoy_database_);
+ } else {
+ collection = MatchFileReader::parse(match_path, database_, decoy_database_);
+ }
+
+ // Test if collection already has file path set, otherwise set it.
+ collection->setFilePath(match_path, false);
+
+ return collection;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/MatchCollectionParser.h b/src/io/MatchCollectionParser.h
new file mode 100644
index 0000000..9c56413
--- /dev/null
+++ b/src/io/MatchCollectionParser.h
@@ -0,0 +1,70 @@
+/**
+ * \file MatchCollectionParser.h
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 14 June 2011
+ * \brief Return a MatchCollection object from the appropriate
+ * file format.
+ */
+#ifndef MATCHCOLLECTIONPARSER_H
+#define MATCHCOLLECTIONPARSER_H
+
+#include "model/MatchCollection.h"
+#include "model/Protein.h"
+
+/**
+ * Instantiates a MatchCollection based on the extension of the
+ * given file.
+ */
+class MatchCollectionParser {
+
+ protected:
+ Database* database_;
+ Database* decoy_database_;
+
+ public:
+
+ MatchCollectionParser();
+ ~MatchCollectionParser();
+
+ /**
+ * \returns a MatchCollection object using the file and protein database
+ */
+ MatchCollection* create(
+ const std::string& match_path, ///< path to the file of matches
+ const std::string& fasta_path ///< path to the protein database
+ );
+
+
+ /**
+ * Creates database object(s) from fasta or index file
+ */
+ static void loadDatabase(
+ const std::string& fasta_file, ///< fasta or index path -in
+ Database*& database, ///< resulting database -out
+ Database*& decoy_database ///< resulting decoy database -out
+ );
+
+ static Crux::Protein* getProtein(
+ Database* database,
+ Database* decoy_database,
+ std::string& protein_id,
+ bool& is_decoy
+ );
+
+ static Crux::Protein* getProtein(
+ Database* database,
+ Database* decoy_database,
+ std::string& protein_id,
+ std::string& sequence,
+ bool& is_decoy
+ );
+
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/io/MatchColumns.cpp b/src/io/MatchColumns.cpp
new file mode 100644
index 0000000..7598908
--- /dev/null
+++ b/src/io/MatchColumns.cpp
@@ -0,0 +1,138 @@
+/*************************************************************************
+ * \file MatchColumns.cpp
+ * \brief Just keeps track of column names for match files.
+ *************************************************************************/
+
+#include "MatchColumns.h"
+#include "io/carp.h"
+#include <string.h>
+
+static const char* match_column_strings[NUMBER_MATCH_COLUMNS] = {
+ "file",
+ "file_idx",
+ "scan",
+ "charge",
+ "spectrum precursor m/z",
+ "spectrum neutral mass",
+ "peptide mass",
+ "delta_cn",
+ "delta_lcn",
+ "sp score",
+ "sp rank",
+ "xcorr score",
+ "xcorr rank",
+ "exact p-value",
+ "refactored xcorr",
+ "Sidak adjusted p-value",
+ "e-value",
+ "p-value",
+ "smoothed p-value",
+ "distinct matches/peptide",
+#ifdef NEW_COLUMNS
+ "Weibull PSM q-value",
+ "Weibull peptide q-value", // NEW
+ "decoy PSM q-value",
+ "decoy peptide q-value", // NEW
+ "percolator score",
+ "percolator rank",
+ "percolator PSM q-value",
+ "percolator peptide q-value", // NEW
+ "q-ranker score",
+ "q-ranker PSM q-value",
+ "q-ranker peptide q-value", // NEW
+#else
+ "Weibull est. q-value",
+ "Weibull est. PEP",
+ "decoy q-value (xcorr)",
+ "decoy PEP (xcorr)",
+ "decoy q-value (e-value)",
+ "decoy PEP (e-value)",
+ "percolator score",
+ "percolator rank",
+ "percolator q-value",
+ "percolator PEP",
+ "q-ranker score",
+ "q-ranker q-value",
+ "q-ranker PEP",
+ "barista score",
+ "barista q-value",
+#endif
+ "tdc q-value",
+ "mix-max q-value",
+ "b/y ions matched",
+ "b/y ions total",
+ "total matches/spectrum",
+ "distinct matches/spectrum",
+ "sequence",
+ "modifications",
+ "cleavage type",
+ "protein id",
+ "peptides",
+ "flanking aa",
+ "original target sequence",
+ "eta",
+ "beta",
+ "shift",
+ "corr",
+ "RAW",
+ "SIN",
+ "NSAF",
+ "dNSAF",
+ "EMPAI",
+ "parsimony rank",
+ "decoy matches/spectrum",
+ "SpecId", // for PinWriter, many of these are repeats with slightly different names, is there better way to do this?
+ "Label",
+ "ScanNr",
+ "ExpMass",
+ "CalcMass",
+ "lnrSp",
+ "deltLCn",
+ "deltCn",
+ "Xcorr",
+ "Sp",
+ "IonFrac",
+ "Mass",
+ "PepLen",
+ "enzN",
+ "enzC",
+ "enzInt",
+ "lnNumSP",
+ "dm",
+ "absdM",
+ "Peptide",
+ "Proteins", // end for PinWriter.
+ "product type",
+ "ppm",
+ "xcorr 1",
+ "xcorr 2",
+ "protein id x",
+ "index name",
+ "xlink type"
+};
+
+/**
+ * Get the name of a given column, by index.
+ */
+const char* get_column_header(
+ int columnIndex
+) {
+ if (columnIndex < 0 || columnIndex >= NUMBER_MATCH_COLUMNS) {
+ carp(CARP_FATAL, "Cannot access output column %d.\n", columnIndex);
+ }
+ carp(CARP_DETAILED_DEBUG, "get_column_header: %d/%d %s",
+ columnIndex, NUMBER_MATCH_COLUMNS - 1, match_column_strings[columnIndex]);
+ return(match_column_strings[columnIndex]);
+}
+
+int get_column_idx(
+ const char* column_name
+) {
+ for (int i = FILE_COL; i < NUMBER_MATCH_COLUMNS; ++i) {
+ if (strcmp(column_name, match_column_strings[i]) == 0) {
+ return i;
+ }
+ }
+ return INVALID_COL;
+}
+
diff --git a/src/io/MatchColumns.h b/src/io/MatchColumns.h
new file mode 100644
index 0000000..7c64c70
--- /dev/null
+++ b/src/io/MatchColumns.h
@@ -0,0 +1,129 @@
+/*************************************************************************
+ * \file MatchColumns.h
+ * \brief Just keeps track of column names for match files.
+ *************************************************************************/
+
+#ifndef MATCHCOLUMNS_H
+#define MATCHCOLUMNS_H
+
+//#define NEW_COLUMNS 1
+
+enum MATCH_COLUMNS_T {
+ FILE_COL,
+ FILE_IDX_COL,
+ SCAN_COL,
+ CHARGE_COL,
+ SPECTRUM_PRECURSOR_MZ_COL,
+ SPECTRUM_NEUTRAL_MASS_COL,
+ PEPTIDE_MASS_COL,
+ DELTA_CN_COL,
+ DELTA_LCN_COL,
+ SP_SCORE_COL,
+ SP_RANK_COL,
+ XCORR_SCORE_COL,
+ XCORR_RANK_COL,
+ EXACT_PVALUE_COL,
+ REFACTORED_SCORE_COL,
+ SIDAK_ADJUSTED_COL,
+ EVALUE_COL,
+ PVALUE_COL,
+ ELUTION_WINDOW_COL,
+ DISTINCT_MATCHES_PEPTIDE_COL,
+#ifdef NEW_COLUMNS
+ WEIBULL_QVALUE_COL,
+ WEIBULL_PEPTIDE_QVALUE_COL, // NEW
+ DECOY_XCORR_QVALUE_COL,
+ DECOY_XCORR_PEPTIDE_QVALUE_COL, // NEW
+ PERCOLATOR_SCORE_COL,
+ PERCOLATOR_RANK_COL,
+ PERCOLATOR_QVALUE_COL,
+ PERCOLATOR_PEPTIDE_QVALUE_COL, // NEW
+ QRANKER_SCORE_COL,
+ QRANKER_QVALUE_COL,
+ QRANKER_PEPTIDE_QVALUE_COL, // NEW
+#else
+ WEIBULL_QVALUE_COL,
+ WEIBULL_PEP_COL,
+ DECOY_XCORR_QVALUE_COL,
+ DECOY_XCORR_PEP_COL,
+ DECOY_EVALUE_QVALUE_COL,
+ DECOY_EVALUE_PEP_COL,
+ PERCOLATOR_SCORE_COL,
+ PERCOLATOR_RANK_COL,
+ PERCOLATOR_QVALUE_COL,
+ PERCOLATOR_PEP_COL,
+ QRANKER_SCORE_COL,
+ QRANKER_QVALUE_COL,
+ QRANKER_PEP_COL,
+ BARISTA_SCORE_COL,
+ BARISTA_QVALUE_COL,
+#endif
+ QVALUE_TDC_COL,
+ QVALUE_MIXMAX_COL,
+ BY_IONS_MATCHED_COL,
+ BY_IONS_TOTAL_COL,
+ MATCHES_SPECTRUM_COL,
+ DISTINCT_MATCHES_SPECTRUM_COL,
+ SEQUENCE_COL,
+ MODIFICATIONS_COL,
+ CLEAVAGE_TYPE_COL,
+ PROTEIN_ID_COL,
+ PEPTIDES_COL,
+ FLANKING_AA_COL,
+ ORIGINAL_TARGET_SEQUENCE_COL,
+ ETA_COL,
+ BETA_COL,
+ SHIFT_COL,
+ CORR_COL,
+ RAW_SCORE_COL,
+ SIN_SCORE_COL,
+ NSAF_SCORE_COL,
+ DNSAF_SCORE_COL,
+ EMPAI_SCORE_COL,
+ PARSIMONY_RANK_COL,
+ DECOY_MATCHES_SPECTRUM_COL,
+ SPEC_ID_COL, // for PinWriter
+ LABEL_COL,
+ SCAN_NR_COL,
+ EXP_MASS_COL,
+ CALC_MASS_COL,
+ LNR_SP_COL,
+ DELT_L_CN_COL,
+ DELT_CN_COL,
+ XCORR_COL,
+ SP_COL,
+ ION_FRAC_COL,
+ MASS_COL,
+ PEP_LEN_COL,
+ ENZ_N_COL,
+ ENZ_C_COL,
+ ENZ_INT_COL,
+ LN_NUM_SP_COL,
+ DM_COL,
+ ABS_DM_COL,
+ PEPTIDE_COL,
+ PROTEINS_COL,
+ XLINK_PRODUCT_TYPE_COL,
+ PPM_ERROR_COL,
+ XCORR_FIRST_COL,
+ XCORR_SECOND_COL,
+ PROTEIN_ID_X_COL,
+ INDEX_NAME_COL,
+ XLINK_TYPE_COL,
+
+ NUMBER_MATCH_COLUMNS,
+ INVALID_COL
+};
+
+/**
+ * Get the name of a given column, by index.
+ */
+const char* get_column_header(
+ int columnIndex
+);
+
+int get_column_idx(
+ const char* column_name
+);
+
+#endif // MATCHCOLUMNS_H
diff --git a/src/io/MatchFileReader.cpp b/src/io/MatchFileReader.cpp
new file mode 100644
index 0000000..e7a4cef
--- /dev/null
+++ b/src/io/MatchFileReader.cpp
@@ -0,0 +1,403 @@
+/*************************************************************************
+ * \file MatchFileReader.cpp
+ * \brief Object for parsing the tab-delimited files
+ *************************************************************************/
+
+#include "MatchColumns.h"
+#include "MatchFileReader.h"
+#include "DelimitedFile.h"
+
+#include "model/MatchCollection.h"
+
+using namespace std;
+
+/**
+ * \returns a blank MatchFileReader object
+ */
+MatchFileReader::MatchFileReader() : DelimitedFileReader(), PSMReader() {
+}
+
+/**
+ * \returns a MatchFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+MatchFileReader::MatchFileReader(const char* file_name) : DelimitedFileReader(file_name, true) {
+ parseHeader();
+}
+
+/**
+ * \returns a MatchFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+MatchFileReader::MatchFileReader(const string& file_name)
+ : DelimitedFileReader(file_name, true), PSMReader(file_name) {
+ parseHeader();
+}
+
+MatchFileReader::MatchFileReader(const string& file_name, Database* database, Database* decoy_database)
+ : DelimitedFileReader(file_name, true), PSMReader(file_name, database, decoy_database) {
+ parseHeader();
+}
+
+MatchFileReader::MatchFileReader(istream* iptr) : DelimitedFileReader(iptr, true, '\t') {
+ parseHeader();
+}
+
+/**
+ * Destructor
+ */
+MatchFileReader::~MatchFileReader() {
+}
+
+/**
+ * Open a new file from an existing MatchFileReader.
+ */
+void MatchFileReader::loadData(
+ const char* file_name, ///< new file to open
+ bool hasHeader
+) {
+ DelimitedFileReader::loadData(file_name, hasHeader);
+ if( hasHeader ) {
+ parseHeader();
+ }
+}
+
+/**
+ * Open a new file from an existing MatchFileReader.
+ */
+void MatchFileReader::loadData(
+ const string& file_name, ///< new file to open
+ bool hasHeader) {
+ DelimitedFileReader::loadData(file_name, hasHeader);
+ if( hasHeader ) {
+ parseHeader();
+ }
+}
+
+/**
+ * parses the header and builds the internal hash table
+ */
+void MatchFileReader::parseHeader() {
+ for (int idx = 0; idx < NUMBER_MATCH_COLUMNS; idx++) {
+ match_indices_[idx] = findColumn(get_column_header(idx));
+ }
+}
+
+/**
+ * \returns the FLOAT_T value of a cell, checks for infinity
+ */
+FLOAT_T MatchFileReader::getFloat(
+ MATCH_COLUMNS_T col_type ///<the column type
+) {
+ int idx = match_indices_[col_type];
+ if (idx == -1) {
+ carp(CARP_DEBUG, "column \"%s\" not found for getFloat", get_column_header(col_type));
+ return -1;
+ }
+ return DelimitedFileReader::getFloat(idx);
+}
+
+/**
+ * \returns the double value of a cell, checks for infinity
+ */
+double MatchFileReader::getDouble(
+ MATCH_COLUMNS_T col_type ///<the column type
+) {
+ carp(CARP_DETAILED_DEBUG, "reading double from column %s", get_column_header(col_type));
+ int idx = match_indices_[col_type];
+ if (idx == -1) {
+ carp(CARP_DEBUG, "column \"%s\" not found for getDouble", get_column_header(col_type));
+ return -1;
+ }
+ return DelimitedFileReader::getDouble(idx);
+}
+
+
+/**
+ * \returns the integer value of a cell, checks for infinity.
+ */
+int MatchFileReader::getInteger(
+ MATCH_COLUMNS_T col_type ///< the column name
+) {
+ carp(CARP_DETAILED_DEBUG, "Reading integer from column %s", get_column_header(col_type));
+ int idx = match_indices_[col_type];
+ if (idx == -1) {
+ carp(CARP_DEBUG, "column \"%s\" not found for getInteger", get_column_header(col_type));
+ return -1;
+ }
+ return DelimitedFileReader::getInteger(idx);
+}
+
+/**
+ * \returns the string value of a cell
+ */
+string MatchFileReader::getString(
+ MATCH_COLUMNS_T col_type ///<the column type
+) {
+ carp(CARP_DETAILED_DEBUG, "Getting string from column %s", get_column_header(col_type));
+ int idx = match_indices_[col_type];
+ if (idx == -1) {
+ carp(CARP_DEBUG, "column \"%s\" not found for getString", get_column_header(col_type));
+ return "";
+ }
+ return DelimitedFileReader::getString(idx);
+}
+
+bool MatchFileReader::empty(
+ MATCH_COLUMNS_T col_type ///<the column type
+) {
+ int idx = match_indices_[col_type];
+ if (idx == -1) {
+ return true;
+ }
+ return DelimitedFileReader::getString(idx).empty();
+}
+
+/**
+ * Fills in the given vector with a bool value indicating if each
+ * MATCH_COLUMN_T type is present in the file being read.
+ * \returns Argument vector has NUM_MATCH_COLUMN_T values if a
+ * valid file is open and header has been parsed, else vector is empty.
+ */
+void MatchFileReader::getMatchColumnsPresent(
+ std::vector<bool>& col_is_present) {
+ col_is_present.clear();
+
+ // has a header been parsed?
+ if( column_names_.empty() ) {
+ return;
+ }
+ col_is_present.assign(NUMBER_MATCH_COLUMNS, false);
+
+ for(int col_idx = 0; col_idx < NUMBER_MATCH_COLUMNS; col_idx++) {
+ col_is_present[col_idx] = (match_indices_[col_idx] > -1);
+ }
+}
+
+MatchCollection* MatchFileReader::parse(
+ const string& file_path,
+ Database* database,
+ Database* decoy_database) {
+ return MatchFileReader(file_path, database, decoy_database).parse();
+}
+
+MatchCollection* MatchFileReader::parse() {
+ MatchCollection* match_collection = new MatchCollection();
+ match_collection->preparePostProcess();
+
+ while (hasNext()) {
+ FLOAT_T ln_experiment_size = 0;
+ if (!empty(DISTINCT_MATCHES_SPECTRUM_COL)) {
+ match_collection->setHasDistinctMatches(true);
+ ln_experiment_size = log(getFloat(DISTINCT_MATCHES_SPECTRUM_COL));
+ } else if (!empty(MATCHES_SPECTRUM_COL)) {
+ ln_experiment_size = log(getFloat(MATCHES_SPECTRUM_COL));
+ }
+
+ match_collection->setScoredType(DELTA_CN, !empty(DELTA_CN_COL));
+ match_collection->setScoredType(DELTA_LCN, !empty(DELTA_LCN_COL));
+ match_collection->setScoredType(SP, !empty(SP_SCORE_COL));
+ match_collection->setScoredType(XCORR, !empty(XCORR_SCORE_COL));
+ match_collection->setScoredType(TIDE_SEARCH_EXACT_PVAL, !empty(EXACT_PVALUE_COL));
+ match_collection->setScoredType(TIDE_SEARCH_REFACTORED_XCORR, !empty(REFACTORED_SCORE_COL));
+ match_collection->setScoredType(EVALUE, !empty(EVALUE_COL));
+ match_collection->setScoredType(DECOY_XCORR_QVALUE, !empty(DECOY_XCORR_QVALUE_COL));
+ match_collection->setScoredType(LOGP_BONF_WEIBULL_XCORR, !empty(PVALUE_COL));
+ match_collection->setScoredType(PERCOLATOR_QVALUE, !empty(PERCOLATOR_QVALUE_COL));
+ match_collection->setScoredType(PERCOLATOR_SCORE, !empty(PERCOLATOR_SCORE_COL));
+ match_collection->setScoredType(LOGP_QVALUE_WEIBULL_XCORR, !empty(WEIBULL_QVALUE_COL));
+ match_collection->setScoredType(QRANKER_SCORE, !empty(QRANKER_SCORE_COL));
+ match_collection->setScoredType(QRANKER_QVALUE, !empty(QRANKER_QVALUE_COL));
+ match_collection->setScoredType(BARISTA_SCORE, !empty(BARISTA_SCORE_COL));
+ match_collection->setScoredType(BARISTA_QVALUE, !empty(BARISTA_QVALUE_COL));
+ match_collection->setScoredType(BY_IONS_MATCHED, !empty(BY_IONS_MATCHED_COL));
+ match_collection->setScoredType(BY_IONS_TOTAL, !empty(BY_IONS_TOTAL_COL));
+
+ // parse match object
+ Crux::Match* match = parseMatch();
+ if (match == NULL) {
+ carp(CARP_ERROR, "Failed to parse tab-delimited PSM match");
+ return NULL;
+ }
+
+ //set all spectrum specific features to parsed match
+ SpectrumZState zState(getFloat(SPECTRUM_NEUTRAL_MASS_COL),
+ getInteger(CHARGE_COL));
+ match->setZState(zState);
+ match->setLnExperimentSize(ln_experiment_size);
+ //add match to match collection.
+ match_collection->addMatchToPostMatchCollection(match);
+ //increment pointer.
+ next();
+ }
+
+ return match_collection;
+}
+
+/**
+ *\returns a match object that is parsed from the tab-delimited result file
+ */
+Crux::Match* MatchFileReader::parseMatch() {
+ // parse spectrum
+ Crux::Spectrum* spectrum = parseSpectrum();
+ if (spectrum == NULL) {
+ carp(CARP_ERROR, "Failed to parse spectrum (tab delimited).");
+ }
+
+ // parse peptide
+ Crux::Peptide* peptide = parsePeptide();
+ if (peptide == NULL) {
+ carp(CARP_ERROR, "Failed to parse peptide (tab delimited)");
+ // FIXME should this exit or return null. I think sometimes we can get
+ // no peptides, which is valid, in which case NULL makes sense.
+ // maybe this should be fixed at the output match level however.
+ return NULL;
+ }
+
+ Crux::Match* match = new Crux::Match(peptide, spectrum, spectrum->getZState(0), false);
+ match->setPostProcess(true);
+ match->setDatabaseIndexName(getString(INDEX_NAME_COL));
+ string path = spectrum->getFullFilename();
+ if (!path.empty()) {
+ match->setFilePath(path);
+ }
+
+ if (!empty(FILE_COL)) {
+ match->setFilePath(getString(FILE_COL));
+ }
+
+ if (empty(SP_SCORE_COL) || empty(SP_RANK_COL)) {
+ match->setScore(SP, NOT_SCORED);
+ match->setRank(SP, 0);
+ } else {
+ match->setScore(SP, getFloat(SP_SCORE_COL));
+ match->setRank(SP, getInteger(SP_RANK_COL));
+ }
+
+ match->setScore(XCORR, getFloat(XCORR_SCORE_COL));
+ match->setRank(XCORR, getInteger(XCORR_RANK_COL));
+
+ if (!empty(DELTA_CN_COL)) {
+ match -> setScore(DELTA_CN, getFloat(DELTA_CN_COL));
+ }
+ if (!empty(DELTA_LCN_COL)) {
+ match -> setScore(DELTA_LCN, getFloat(DELTA_LCN_COL));
+ }
+
+ if (!empty(EXACT_PVALUE_COL)) {
+ match->setScore(TIDE_SEARCH_EXACT_PVAL, getFloat(EXACT_PVALUE_COL));
+ match->setScore(TIDE_SEARCH_REFACTORED_XCORR, getFloat(REFACTORED_SCORE_COL));
+ }
+ if (!empty(DECOY_XCORR_QVALUE_COL)) {
+ match->setScore(DECOY_XCORR_QVALUE, getFloat(DECOY_XCORR_QVALUE_COL));
+ }
+ /* TODO I personally would like access to the raw p-value as well as the bonferonni corrected one (SJM).
+ match -> match_scores[LOGP_WEIBULL_XCORR] = getFloat("logp weibull xcorr");
+ */
+ if (!empty(PVALUE_COL)) {
+ FLOAT_T pval = getFloat(PVALUE_COL);
+ match->setScore(LOGP_BONF_WEIBULL_XCORR,
+ pval > 0 ? -log(pval) : numeric_limits<FLOAT_T>::infinity());
+ }
+ if (!empty(EVALUE_COL)) {
+ match->setScore(EVALUE, getFloat(EVALUE_COL));
+ }
+ if (!empty(PERCOLATOR_QVALUE_COL)) {
+ match->setScore(PERCOLATOR_QVALUE, getFloat(PERCOLATOR_QVALUE_COL));
+ }
+ if (!empty(PERCOLATOR_SCORE_COL)) {
+ match->setScore(PERCOLATOR_SCORE, getFloat(PERCOLATOR_SCORE_COL));
+ match->setRank(PERCOLATOR_SCORE, getInteger(PERCOLATOR_RANK_COL));
+ }
+ if (!empty(WEIBULL_QVALUE_COL)) {
+ match->setScore(LOGP_QVALUE_WEIBULL_XCORR, getFloat(WEIBULL_QVALUE_COL));
+ }
+ if (!empty(QRANKER_SCORE_COL)) {
+ match->setScore(QRANKER_SCORE, getFloat(QRANKER_SCORE_COL));
+ match->setScore(QRANKER_QVALUE, getFloat(QRANKER_QVALUE_COL));
+ }
+ if (!empty(BARISTA_SCORE_COL)) {
+ match->setScore(BARISTA_SCORE, getFloat(BARISTA_SCORE_COL));
+ match->setScore(BARISTA_QVALUE, getFloat(BARISTA_QVALUE_COL));
+ }
+
+ if (!empty(BY_IONS_MATCHED_COL)) {
+ match->setScore(BY_IONS_MATCHED, getInteger(BY_IONS_MATCHED_COL));
+ }
+ if (!empty(BY_IONS_TOTAL_COL)) {
+ match->setScore(BY_IONS_TOTAL, getInteger(BY_IONS_TOTAL_COL));
+ }
+
+ // get experiment size
+ int experimentSize = 0;
+ if (!empty(DISTINCT_MATCHES_SPECTRUM_COL)) {
+ experimentSize = getInteger(DISTINCT_MATCHES_SPECTRUM_COL);
+ } else if (!empty(MATCHES_SPECTRUM_COL)) {
+ experimentSize = getInteger(MATCHES_SPECTRUM_COL);
+ }
+ match->setTargetExperimentSize(experimentSize);
+ if (experimentSize == 0) {
+ carp_once(CARP_WARNING, "num target matches=0, suppressing warning");
+ match->setLnExperimentSize(0);
+ } else {
+ match->setLnExperimentSize(log((FLOAT_T) experimentSize));
+ }
+
+ if (!empty(PROTEIN_ID_COL) &&
+ StringUtils::StartsWith(getString(PROTEIN_ID_COL), Params::GetString("decoy-prefix"))) {
+ match->setNullPeptide(true);
+ }
+
+ return match;
+}
+
+Crux::Peptide* MatchFileReader::parsePeptide() {
+ Crux::Peptide* peptide = new Crux::Peptide();
+ string seq = getString(SEQUENCE_COL);
+ if (!seq.empty()) {
+ //In cases where the sequence is in X.seq.X format, parse out the seq part
+ if (seq.length() > 4 && seq[1] == '.' && seq[seq.length() - 2] == '.') {
+ seq = seq.substr(2, seq.length() - 4);
+ }
+
+ // string length may include mod symbols and be longer than the peptide seq
+ MODIFIED_AA_T* modified_seq;
+ peptide->setLength(convert_to_mod_aa_seq(seq.c_str(), &modified_seq));
+ peptide->setModifiedAASequence(modified_seq, false);
+
+ string modsString = getString(MODIFICATIONS_COL);
+ if (!modsString.empty()) {
+ vector<string> modStrings = StringUtils::Split(getString(MODIFICATIONS_COL), ',');
+ vector<Crux::Modification> mods;
+ for (vector<string>::const_iterator i = modStrings.begin(); i != modStrings.end(); i++) {
+ try {
+ Crux::Modification mod = Crux::Modification::Parse(StringUtils::Trim(*i), peptide);
+ if (!mod.Static()) {
+ mods.push_back(mod);
+ }
+ } catch (runtime_error& e) {
+ carp(CARP_ERROR, "Error parsing modification string: %s", e.what());
+ }
+ }
+ peptide->setMods(mods);
+ }
+
+ if (!PeptideSrc::parseTabDelimited(peptide, *this, database_, decoy_database_)) {
+ carp(CARP_ERROR, "Failed to parse peptide src.");
+ delete peptide;
+ return NULL;
+ }
+ } else {
+ carp(CARP_FATAL, "No peptide sequence (%s).", seq.c_str());
+ }
+ return peptide;
+}
+
+Crux::Spectrum* MatchFileReader::parseSpectrum() {
+ return new Crux::Spectrum(getInteger(SCAN_COL),
+ getInteger(SCAN_COL),
+ getFloat(SPECTRUM_PRECURSOR_MZ_COL),
+ vector<int>(1, getInteger(CHARGE_COL)),
+ getString(FILE_COL));
+}
+
diff --git a/src/io/MatchFileReader.h b/src/io/MatchFileReader.h
new file mode 100644
index 0000000..63f2873
--- /dev/null
+++ b/src/io/MatchFileReader.h
@@ -0,0 +1,146 @@
+/**
+ * \file MatchFileReader.h
+ * $Revision: 1.00 $
+ * DATE: June 10, 2010
+ * AUTHOR: Sean McIlwain
+ * \brief Object for reading tab-delimited files.
+ * This class generates a table of values. The default delimiter is tab.
+ * This class is capable of reading string, integers, and floating point
+ * Types from each cell of the table. This class also provides function
+ * for reading a list of integers or string from a cell using a delimiter
+ * that is different from the column delimiter (default is comma ',').
+ * MatchFileReader hashes the column_id for quick access.
+ **************************************************************************/
+
+#ifndef MATCHFILEREADER_H
+#define MATCHFILEREADER_H
+
+#include "DelimitedFileReader.h"
+#include "MatchColumns.h"
+#include "PSMReader.h"
+
+class MatchFileReader: public DelimitedFileReader, public PSMReader {
+ protected:
+ void parseHeader();
+ Crux::Match* parseMatch();
+ Crux::Peptide* parsePeptide();
+ Crux::Spectrum* parseSpectrum();
+
+ int match_indices_[NUMBER_MATCH_COLUMNS];
+
+ public:
+ /**
+ * \returns a blank MatchFileReader object
+ */
+ MatchFileReader();
+
+ /**
+ * \returns a MatchFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+ MatchFileReader(
+ const char* file_name
+ );
+
+ /**
+ * \returns a MatchFileReader object and loads the tab-delimited
+ * data specified by file_name.
+ */
+ MatchFileReader(
+ const std::string& file_name
+ );
+
+ MatchFileReader(
+ const std::string& file_name,
+ Database* database,
+ Database* decoy_database = NULL);
+
+ /**
+ * \returns a MatchFileReader object and load the tab-delimited
+ * data specified by an input stream
+ */
+ MatchFileReader(
+ std::istream* iptr
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~MatchFileReader();
+
+ /**
+ * Open a new file from an existing MatchFileReader.
+ */
+ virtual void loadData(
+ const char* file_name, ///< new file to open
+ bool hasHeader = true ///< parse first line as header
+ );
+
+ /**
+ * Open a new file from an existing MatchFileReader.
+ */
+ virtual void loadData(
+ const std::string& file_name, ///< new file to open
+ bool hasHeader = true ///< parse first line has header
+ );
+
+ /**
+ * \returns the FLOAT_T value of a cell, checks for infinity
+ */
+ FLOAT_T getFloat(
+ MATCH_COLUMNS_T col_type ///<the column type
+ );
+
+ /**
+ * \returns the double value of a cell, checks for infinity
+ */
+ double getDouble(
+ MATCH_COLUMNS_T col_type ///< the column type
+ );
+
+ /**
+ * \returns the integer value of a cell, checks for infinity.
+ */
+ int getInteger(
+ MATCH_COLUMNS_T col_type ///< the column type
+ );
+
+ /**
+ * gets a string value of the cell
+ */
+ std::string getString(
+ MATCH_COLUMNS_T col_type ///<the column type
+ );
+
+ /**
+ * returns whether the column is empty or not.
+ */
+ bool empty(
+ MATCH_COLUMNS_T col_type ///<the column type
+ );
+
+ /**
+ * Fills in the given vector with a bool value indicating if each
+ * MATCH_COLUMN_T type is present in the file being read.
+ * \returns Argument vector has NUM_MATCH_COLUMN_T values if a
+ * valid file is open and header has been parsed, else vector is empty.
+ */
+ void getMatchColumnsPresent (std::vector<bool>& col_is_present);
+
+ static MatchCollection* parse(
+ const std::string& file_path,
+ Database* database,
+ Database* decoy_database
+ );
+
+ MatchCollection* parse();
+};
+
+#endif //MATCHFILEREADER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/MatchFileWriter.cpp b/src/io/MatchFileWriter.cpp
new file mode 100644
index 0000000..d8af1b0
--- /dev/null
+++ b/src/io/MatchFileWriter.cpp
@@ -0,0 +1,432 @@
+/**
+ * \file MatchFileWriter.cpp
+ * DATE: October 26, 2010
+ * AUTHOR: Barbara Frewen
+ * \brief Object for writing tab-deliminted text files of PSMs (matches).
+ * This class is the extension of DelimitedFileWriter where the
+ * columns are those in MatchColumns. Which columns are written to
+ * file depend on the COMMAND_TYPE_T. For some commands, they also
+ * depend on the columns found in the input file as given by a
+ * MatchFileReader.
+ */
+
+#include "MatchFileWriter.h"
+#include "parameter.h"
+#include "util/Params.h"
+#include "app/TideSearchApplication.h"
+#include <iostream>
+
+using namespace std;
+
+/**
+ * \returns A blank MatchFileWriter object.
+ */
+MatchFileWriter::MatchFileWriter()
+ : DelimitedFileWriter(),
+ num_columns_(0) {
+ for(int col_type = 0; col_type < NUMBER_MATCH_COLUMNS; col_type++) {
+ match_to_print_[col_type] = false;
+ match_precision_[col_type] = 0;
+ match_fixed_float_[col_type] = true;
+ }
+ setPrecision();
+}
+
+/**
+ * \returns A blank MatchFileWriter object and opens a file for
+ * writing.
+ */
+MatchFileWriter::MatchFileWriter(const char* filename)
+ : DelimitedFileWriter(filename),
+ num_columns_(0) {
+ for(int col_type = 0; col_type < NUMBER_MATCH_COLUMNS; col_type++) {
+ match_to_print_[col_type] = false;
+ match_precision_[col_type] = 0;
+ match_fixed_float_[col_type] = true;
+ }
+ setPrecision();
+}
+
+/**
+ * Destructor
+ */
+MatchFileWriter::~MatchFileWriter() {
+}
+
+/**
+ * Set the correct level of precision for each MATCH_COLUMNS_T type.
+ * Also set whether the field should be fixed float or not.
+ */
+void MatchFileWriter::setPrecision() {
+ for(int col_idx = 0; col_idx < NUMBER_MATCH_COLUMNS; col_idx++) {
+ switch(col_idx) {
+ // integer and string fields
+ case FILE_COL:
+ case SCAN_COL:
+ case CHARGE_COL:
+ case SP_RANK_COL:
+ case XCORR_RANK_COL:
+ case PERCOLATOR_RANK_COL:
+ case BY_IONS_MATCHED_COL:
+ case BY_IONS_TOTAL_COL:
+ case DISTINCT_MATCHES_SPECTRUM_COL:
+ case MATCHES_SPECTRUM_COL:
+ case SEQUENCE_COL:
+ case CLEAVAGE_TYPE_COL:
+ case PROTEIN_ID_COL:
+ case FLANKING_AA_COL:
+ case ORIGINAL_TARGET_SEQUENCE_COL:
+ case PARSIMONY_RANK_COL:
+ case RAW_SCORE_COL: //Raw counts should be integral
+ match_precision_[col_idx] = 0;
+ match_fixed_float_[col_idx] = true;
+ break;
+
+ // mass fields
+ case SPECTRUM_PRECURSOR_MZ_COL:
+ case SPECTRUM_NEUTRAL_MASS_COL:
+ case MASS_COL:
+ case DM_COL:
+ case ABS_DM_COL:
+ case PEPTIDE_MASS_COL:
+ match_precision_[col_idx] = Params::GetInt("mass-precision");
+ match_fixed_float_[col_idx] = true;
+ break;
+
+ // score fields
+ case DELTA_CN_COL:
+ case SP_SCORE_COL:
+ case XCORR_SCORE_COL:
+ case XCORR_FIRST_COL:
+ case XCORR_SECOND_COL:
+ case EVALUE_COL:
+ case PVALUE_COL:
+ case WEIBULL_QVALUE_COL:
+ case WEIBULL_PEP_COL:
+ case DECOY_XCORR_QVALUE_COL:
+ case DECOY_XCORR_PEP_COL:
+ case DECOY_EVALUE_QVALUE_COL:
+ case DECOY_EVALUE_PEP_COL:
+ case PERCOLATOR_SCORE_COL:
+ case PERCOLATOR_QVALUE_COL:
+ case PERCOLATOR_PEP_COL:
+ case QRANKER_SCORE_COL:
+ case QRANKER_QVALUE_COL:
+ case QRANKER_PEP_COL:
+ case SIN_SCORE_COL:
+ case NSAF_SCORE_COL:
+ case DNSAF_SCORE_COL:
+ case EMPAI_SCORE_COL:
+ case LNR_SP_COL:
+ case DELT_L_CN_COL:
+ case DELT_CN_COL:
+ case XCORR_COL:
+ case SP_COL:
+ case ION_FRAC_COL:
+ case LN_NUM_SP_COL:
+ case EXACT_PVALUE_COL:
+ case REFACTORED_SCORE_COL:
+ case SIDAK_ADJUSTED_COL:
+ case QVALUE_MIXMAX_COL:
+ case QVALUE_TDC_COL:
+#ifdef NEW_COLUMNS
+ case WEIBULL_PEPTIDE_QVALUE_COL: // NEW
+ case DECOY_XCORR_PEPTIDE_QVALUE_COL: // NEW
+ case PERCOLATOR_PEPTIDE_QVALUE_COL: // NEW
+ case QRANKER_PEPTIDE_QVALUE_COL: // NEW
+#endif
+ match_precision_[col_idx] = Params::GetInt("precision");
+ match_fixed_float_[col_idx] = false;
+ break;
+
+ // special cases
+ case ETA_COL:
+ case BETA_COL:
+ case SHIFT_COL:
+ case CORR_COL:
+ match_precision_[col_idx] = 6;
+ match_fixed_float_[col_idx] = false;
+ break;
+
+ case NUMBER_MATCH_COLUMNS:
+ case INVALID_COL:
+ carp(CARP_FATAL, "Invalid match column type for setting precision.");
+ break;
+ }
+ }
+}
+
+/**
+ * Defines the columns to print based on the vector of flags
+ * indiciating if the MATCH_COLUMN_T should be printed.
+ */
+void MatchFileWriter::addColumnNames(const std::vector<bool>& col_is_printed) {
+ // for each column, if we should print it, mark as true
+ for(size_t col_idx = 0; col_idx < col_is_printed.size(); col_idx++) {
+ bool print_it = col_is_printed[col_idx];
+ if( print_it ) {
+ match_to_print_[col_idx] = true;
+ }
+ }
+}
+
+/**
+ * Adds another columns to print. Printed in order the names are set.
+ */
+void MatchFileWriter::addColumnName(MATCH_COLUMNS_T column_type) {
+ match_to_print_[column_type] = true;
+}
+
+/**
+ * Adds which columns to print based on the COMMAND_TYPE_T. Only for
+ * search-for-matches, sequest-search and spectral-counts.
+ */
+void MatchFileWriter::addColumnNames(CruxApplication* application,
+ bool has_decoys) {
+
+ COMMAND_T command = application->getCommand();
+
+ switch (command) {
+ // commands with no tab files
+ case MISC_COMMAND:
+ case PROCESS_SPEC_COMMAND: ///< print-processed-spectra
+ case GENERATE_PEPTIDES_COMMAND: ///< generate-peptides
+ case GET_MS2_SPECTRUM_COMMAND: ///< get-ms2-spectrum
+ case PREDICT_PEPTIDE_IONS_COMMAND: ///< predict-peptide-ions
+ case VERSION_COMMAND: ///< just print the version number
+ // invalid
+ case NUMBER_COMMAND_TYPES:
+ case INVALID_COMMAND:
+ carp(CARP_FATAL, "Invalid command (%s) for creating a MatchFileWriter.",
+ application->getName().c_str());
+ return;
+
+ // commands that also require list of cols to print
+ case QVALUE_COMMAND: ///< compute-q-values
+ case PERCOLATOR_COMMAND:
+ case QRANKER_COMMAND:
+ case BARISTA_COMMAND:
+ carp(CARP_FATAL,
+ "Post-search command %s requires a list of columns to print.",
+ application->getName().c_str());
+ return;
+
+ // valid commands
+ case TIDE_SEARCH_COMMAND: ///< tide-search
+ if (Params::GetBool("file-column")) {
+ addColumnName(FILE_COL);
+ }
+ if (Params::GetBool("compute-sp") || Params::GetBool("sqt-output")) {
+ if (Params::GetBool("exact-p-value")) {
+ addColumnName(EXACT_PVALUE_COL);
+ addColumnName(REFACTORED_SCORE_COL);
+ } else {
+ addColumnName(SP_SCORE_COL);
+ }
+ addColumnName(SP_RANK_COL);
+ addColumnName(BY_IONS_MATCHED_COL);
+ addColumnName(BY_IONS_TOTAL_COL);
+ }
+ break;
+
+ case XLINK_SEARCH_COMMAND:
+ if (Params::GetBool("compute-p-values")) {
+ addColumnName(PVALUE_COL);
+ addColumnName(ETA_COL);
+ addColumnName(BETA_COL);
+ addColumnName(SHIFT_COL);
+ addColumnName(CORR_COL);
+ }
+ if ((!Params::GetBool("use-old-xlink")) &&
+ (Params::GetInt("xlink-top-n") != 0)) {
+ addColumnName(XCORR_FIRST_COL);
+ addColumnName(XCORR_SECOND_COL);
+ }
+ if (!Params::GetBool("use-old-xlink")) {
+ addColumnName(ENZ_INT_COL);
+ }
+
+ addColumnName(XLINK_TYPE_COL);
+ break;
+
+ case SPECTRAL_COUNTS_COMMAND:
+ // protein or peptide
+ if( string_to_quant_level_type(Params::GetString("quant-level")) == PEPTIDE_QUANT_LEVEL ) {
+ addColumnName(SEQUENCE_COL);
+ } else {
+ addColumnName(PROTEIN_ID_COL);
+ // parsimony?
+ if( string_to_parsimony_type(Params::GetString("parsimony")) != PARSIMONY_NONE ) {
+ addColumnName(PARSIMONY_RANK_COL);
+ }
+ }
+
+ // SIN or NSAF score
+ switch (string_to_measure_type(Params::GetString("measure"))) {
+ case MEASURE_RAW:
+ addColumnName(RAW_SCORE_COL);
+ break;
+ case MEASURE_SIN:
+ addColumnName(SIN_SCORE_COL);
+ break;
+ case MEASURE_NSAF:
+ addColumnName(NSAF_SCORE_COL);
+ break;
+ case MEASURE_DNSAF:
+ addColumnName(DNSAF_SCORE_COL);
+ break;
+ case MEASURE_EMPAI:
+ addColumnName(EMPAI_SCORE_COL);
+ break;
+ default:
+ ;//do nothing
+ }
+
+ return; // do not add additional columns
+ }
+
+ // All search commands have these columns
+ addColumnName(SCAN_COL);
+ addColumnName(CHARGE_COL);
+ addColumnName(SPECTRUM_PRECURSOR_MZ_COL);
+ addColumnName(SPECTRUM_NEUTRAL_MASS_COL);
+ addColumnName(PEPTIDE_MASS_COL);
+ addColumnName(DELTA_CN_COL);
+ if (Params::GetBool("exact-p-value")) {
+ addColumnName(EXACT_PVALUE_COL);
+ addColumnName(REFACTORED_SCORE_COL);
+ } else {
+ addColumnName(XCORR_SCORE_COL);
+ }
+ addColumnName(XCORR_RANK_COL);
+ addColumnName(DISTINCT_MATCHES_SPECTRUM_COL);
+ addColumnName(SEQUENCE_COL);
+ addColumnName(MODIFICATIONS_COL);
+ addColumnName(CLEAVAGE_TYPE_COL);
+ addColumnName(PROTEIN_ID_COL);
+ addColumnName(FLANKING_AA_COL);
+ if ((has_decoys || Params::GetBool("concat")) &&
+ !TideSearchApplication::proteinLevelDecoys()) {
+ addColumnName(ORIGINAL_TARGET_SEQUENCE_COL);
+ }
+
+}
+
+/**
+ * Adds which columns to print based on the COMMAND_TYPE_T and a list
+ * of columns to print. For all post-search commands.
+ */
+void MatchFileWriter::addColumnNames
+ (CruxApplication* application,
+ bool has_decoys,
+ const vector<bool>& cols_to_print) {
+
+ COMMAND_T command = application->getCommand();
+
+ switch (command) {
+ // commands with no tab files
+ case MISC_COMMAND:
+ case PROCESS_SPEC_COMMAND: ///< print-processed-spectra
+ case GENERATE_PEPTIDES_COMMAND: ///< generate-peptides
+ case GET_MS2_SPECTRUM_COMMAND: ///< get-ms2-spectrum
+ case PREDICT_PEPTIDE_IONS_COMMAND: /// predict-peptide-ions
+ case VERSION_COMMAND: ///< just print the version number
+ // invalid
+ case SPECTRAL_COUNTS_COMMAND:
+ case NUMBER_COMMAND_TYPES:
+ case INVALID_COMMAND:
+ carp(CARP_FATAL, "Invalid command (%s) for creating a MatchFileWriter.",
+ application->getName().c_str());
+ return;
+
+ // search commands handled elsewhere
+ case XLINK_SEARCH_COMMAND:
+ addColumnNames(application, has_decoys);
+ return;
+
+ // valid commands
+ case QVALUE_COMMAND: ///< compute-q-values
+ if( cols_to_print[PVALUE_COL] ) {
+ addColumnName(WEIBULL_QVALUE_COL);
+// addColumnName(WEIBULL_PEP_COL);
+ //addColumnName(WEIBULL_PEPTIDE_QVALUE_COL);
+ } else {
+ if ( cols_to_print[EVALUE_COL]) {
+// addColumnName(DECOY_EVALUE_QVALUE_COL);
+// addColumnName(DECOY_EVALUE_PEP_COL);
+ }
+// addColumnName(DECOY_XCORR_QVALUE_COL);
+// addColumnName(DECOY_XCORR_PEP_COL);
+ //addColumnName(DECOY_XCORR_PEPTIDE_QVALUE_COL);
+ }
+ break;
+
+ case PERCOLATOR_COMMAND:
+ addColumnName(PERCOLATOR_SCORE_COL);
+ addColumnName(PERCOLATOR_RANK_COL);
+ addColumnName(PERCOLATOR_QVALUE_COL);
+ addColumnName(PERCOLATOR_PEP_COL);
+ break;
+
+ case QRANKER_COMMAND:
+ addColumnName(QRANKER_SCORE_COL);
+ addColumnName(QRANKER_QVALUE_COL);
+ addColumnName(QRANKER_PEP_COL);
+ break;
+
+ case BARISTA_COMMAND:
+ // place holder
+ break;
+ }
+
+ if( has_decoys ) {
+ addColumnName(ORIGINAL_TARGET_SEQUENCE_COL);
+ }
+
+ // now add remaining columns from the input file
+ addColumnNames(cols_to_print);
+
+ // FIXME (BF 10-27-10): where do these go?
+ // PERCOLATOR_PEPTIDE_QVALUE_COL,
+ // QRANKER_PEPTIDE_QVALUE_COL,
+
+}
+
+/**
+ * Write header to file using column names that have been set.
+ */
+void MatchFileWriter::writeHeader() {
+ num_columns_ = 0;
+ // set file position index for all columns being printed
+ for(unsigned int col_type = 0; col_type < NUMBER_MATCH_COLUMNS; col_type++) {
+ if( match_to_print_[col_type] == true ) {
+ match_indices_[col_type] = num_columns_++;
+ } else {
+ match_indices_[col_type] = -1;
+ }
+ }
+
+ // set all the names for which we have match_indices_
+ column_names_.assign(num_columns_, "");
+ for(unsigned int col_type = 0; col_type < NUMBER_MATCH_COLUMNS; col_type++) {
+ if( match_indices_[col_type] > -1 ) {
+ if (get_column_header(col_type) == NULL) {
+ carp(CARP_FATAL, "Error col type: %d doesn't exist!", col_type);
+ }
+ DelimitedFileWriter::setColumnName(get_column_header(col_type),
+ match_indices_[col_type]);
+ }
+ }
+
+ DelimitedFileWriter::writeHeader();
+
+ // every line will be this length, reserve space in current row for speed
+ current_row_.assign(num_columns_, "");
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/MatchFileWriter.h b/src/io/MatchFileWriter.h
new file mode 100644
index 0000000..3bed2e7
--- /dev/null
+++ b/src/io/MatchFileWriter.h
@@ -0,0 +1,110 @@
+/**
+ * \file MatchFileWriter.h
+ * DATE: October 26, 2010
+ * AUTHOR: Barbara Frewen
+ * \brief Object for writing tab-deliminted text files of PSMs (matches).
+ * This class is the extension of DelimitedFileWriter where the
+ * columns are those in MatchColumns. Which columns are written to
+ * file depend on the COMMAND_TYPE_T. For some commands, they also
+ * depend on the columns found in the input file as given by a
+ * MatchFileReader.
+ */
+
+#ifndef MATCH_FILE_WRITER_H
+#define MATCH_FILE_WRITER_H
+
+#include "app/CruxApplication.h"
+#include "DelimitedFileWriter.h"
+#include "MatchColumns.h"
+#include "model/objects.h"
+#include "util/StringUtils.h"
+#include <iostream>
+
+class MatchFileWriter : public DelimitedFileWriter {
+ protected:
+ bool match_to_print_[NUMBER_MATCH_COLUMNS];///< set before writing header
+ int match_indices_[NUMBER_MATCH_COLUMNS];///<idx of each MATCH_COLUMN in file
+ int match_precision_[NUMBER_MATCH_COLUMNS];///< precision for each column
+ bool match_fixed_float_[NUMBER_MATCH_COLUMNS]; ///< do we use fixed format for the float field?
+ unsigned int num_columns_; ///< number of columns being printed
+
+ void setPrecision();
+
+ public:
+
+ /**
+ * \returns A blank MatchFileWriter object.
+ */
+ MatchFileWriter();
+
+ /**
+ * \returns A MatchFileWriter object and opens a file for writing.
+ */
+ explicit MatchFileWriter(const char* filename);
+
+ /**
+ * Destructor
+ */
+ ~MatchFileWriter();
+
+ // private?
+ /**
+ * Defines the columns to print based on the vector of flags
+ * indiciating if the MATCH_COLUMN_T should be printed.
+ */
+ void addColumnNames(const std::vector<bool>& col_is_printed);
+
+ // private?
+ /**
+ * Adds one column to print.
+ */
+ void addColumnName(MATCH_COLUMNS_T col_type);
+
+ /**
+ * Adds which columns to print based on the COMMAND_TYPE_T. Only for
+ * search-for-matches and sequest-search.
+ */
+ void addColumnNames(CruxApplication* application, bool has_decoys);
+
+ /**
+ * Adds which columns to print based on the COMMAND_TYPE_T and a list
+ * of columns to print. For all post-search commands.
+ */
+ void addColumnNames
+ (CruxApplication* application,
+ bool has_decoys,
+ const std::vector<bool>& cols_to_print);
+
+ /**
+ * Write header to file based on
+ */
+ virtual void writeHeader();
+
+ /**
+ * Set the value in the current row for the given MATCH_COLUMN_T.
+ */
+ template<typename ValueType>
+ void setColumnCurrentRow
+ (MATCH_COLUMNS_T col_type,
+ const ValueType& value) {
+
+ int file_column = match_indices_[col_type];
+ // ignore if this column isn't being printed
+ if( file_column == -1 ) {
+ return;
+ }
+ current_row_.at(file_column) =
+ StringUtils::ToString(value, match_precision_[col_type], match_fixed_float_[col_type]);
+ }
+
+};
+
+#endif // MATCH_FILE_WRITER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/MzIdentMLReader.cpp b/src/io/MzIdentMLReader.cpp
new file mode 100644
index 0000000..2da82d1
--- /dev/null
+++ b/src/io/MzIdentMLReader.cpp
@@ -0,0 +1,361 @@
+/*************************************************************************
+ * \file MzIdentMLReader.cpp
+ * \brief Object for parsing pepxml files
+ *************************************************************************/
+
+#include "MzIdentMLReader.h"
+#include "util/mass.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "expat.h"
+#include "model/Protein.h"
+#include "model/Peptide.h"
+
+#include <cstdio>
+#include <cstring>
+#include <iostream>
+
+#include "DelimitedFile.h"
+#include "parameter.h"
+#include "MatchCollectionParser.h"
+
+using namespace std;
+using namespace Crux;
+using namespace pwiz;
+using namespace identdata;
+
+/**
+ * Initializes the object
+ */
+void MzIdentMLReader::init() {
+ match_collection_ = NULL;
+ use_pass_threshold_ = Params::GetBool("mzid-use-pass-threshold");
+}
+
+/**
+ * \returns an initialized object
+ */
+MzIdentMLReader::MzIdentMLReader() : PSMReader() {
+ init();
+}
+
+/**
+ * \returns an object initialized with the file_path
+ */
+MzIdentMLReader::MzIdentMLReader(
+ const string& file_path ///< the path of the pep.xml file
+ ) : PSMReader(file_path) {
+ init();
+}
+
+/**
+ * \returns an object initialized with the xml path, and the target,decoy databases
+ */
+MzIdentMLReader::MzIdentMLReader(
+ const string& file_path, ///< the path of the pep.xml
+ Database* database, ///< the protein database
+ Database* decoy_database ///< the decoy protein database (can be null)
+ ) : PSMReader(file_path, database, decoy_database) {
+ init();
+}
+
+/**
+ * default destructor
+ */
+MzIdentMLReader::~MzIdentMLReader() {
+}
+
+/**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+
+void MzIdentMLReader::addScores(
+ const SpectrumIdentificationItem& item, ///<proteowizard psm
+ Match* match ///<our psm
+) {
+ FLOAT_T fvalue;
+ int ivalue;
+
+ for (vector<CVParam>::const_iterator i = item.cvParams.begin();
+ i != item.cvParams.end();
+ ++i) {
+ switch (i->cvid) {
+ case MS_SEQUEST_xcorr:
+ fvalue = StringUtils::FromString<FLOAT_T>(i->value);
+ match->setScore(XCORR, fvalue);
+ match_collection_->setScoredType(XCORR, true);
+ break;
+ case MS_SEQUEST_PeptideSp:
+ fvalue = StringUtils::FromString<FLOAT_T>(i->value);
+ match->setScore(SP, fvalue);
+ match_collection_->setScoredType(SP, true);
+ break;
+ case MS_SEQUEST_PeptideRankSp:
+ ivalue = StringUtils::FromString<int>(i->value);
+ match->setRank(SP, ivalue);
+ break;
+ case MS_SEQUEST_deltacn:
+ fvalue = StringUtils::FromString<FLOAT_T>(i->value);
+ match->setScore(DELTA_CN, fvalue);
+ break;
+ case MS_SEQUEST_matched_ions:
+ ivalue = StringUtils::FromString<int>(i->value);
+ match->setScore(BY_IONS_MATCHED, ivalue);
+ break;
+ case MS_SEQUEST_total_ions:
+ ivalue = StringUtils::FromString<int>(i->value);
+ match->setScore(BY_IONS_TOTAL, ivalue);
+ break;
+ case MS_p_value: // exact p-value
+ fvalue = StringUtils::FromString<FLOAT_T>(i->value);
+ match->setScore(TIDE_SEARCH_EXACT_PVAL, fvalue);
+ match_collection_->setScoredType(TIDE_SEARCH_EXACT_PVAL, true);
+ break;
+ default:
+ carp(CARP_DEBUG, "Unknown score type, will be set in custom scores");
+ }
+ //go ahead and set all custom scores to the cvParam names.
+ string name = cvTermInfo(i->cvid).name;
+ fvalue = StringUtils::FromString<FLOAT_T>(i->value);
+ match->setCustomScore(name, fvalue);
+ }
+
+ for (vector<UserParam>::const_iterator i = item.userParams.begin();
+ i != item.userParams.end();
+ ++i) {
+ if (StringUtils::TryFromString(i->value, &fvalue)) {
+ match->setCustomScore(i->name, fvalue);
+ }
+ }
+}
+
+/**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+MatchCollection* MzIdentMLReader::parse(
+ const string& path, ///< path of the xml file
+ Database* database, ///< target protein database
+ Database* decoy_database ///< decoy protein database (can be null)
+ ) {
+ MzIdentMLReader reader(path);
+ reader.setDatabase(database);
+ reader.setDecoyDatabase(decoy_database);
+ MatchCollection* collection = reader.parse();
+ return collection;
+}
+
+/**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+MatchCollection* MzIdentMLReader::parse() {
+ match_collection_ = new MatchCollection();
+ match_collection_ -> preparePostProcess();
+ carp(CARP_DEBUG, "MzIdentMLReader::opening file:%s", file_path_.c_str());
+ pwiz_reader_ = new IdentDataFile(file_path_);
+ parseMods();
+ parseDatabaseSequences();
+ parsePSMs();
+ return match_collection_;
+}
+
+void MzIdentMLReader::parseMods() {
+ AnalysisProtocolCollection& apc = pwiz_reader_->analysisProtocolCollection;
+ for (vector<SpectrumIdentificationProtocolPtr>::const_iterator i = apc.spectrumIdentificationProtocol.begin();
+ i != apc.spectrumIdentificationProtocol.end();
+ i++) {
+ for (vector<SearchModificationPtr>::const_iterator j = (*i)->modificationParams.begin();
+ j != (*i)->modificationParams.end();
+ j++) {
+ const SearchModification& sm = **j;
+ ModPosition position;
+ switch (sm.specificityRules.cvid) {
+ case MS_modification_specificity_peptide_N_term: position = PEPTIDE_N; break;
+ case MS_modification_specificity_peptide_C_term: position = PEPTIDE_C; break;
+ case MS_modification_specificity_protein_N_term: position = PROTEIN_N; break;
+ case MS_modification_specificity_protein_C_term: position = PROTEIN_C; break;
+ default: position = ANY; break;
+ }
+ ModificationDefinition::New(
+ StringUtils::Join(sm.residues), sm.massDelta, position, sm.fixedMod);
+ }
+ }
+}
+
+/**
+ * parses the database sequences from the mzid file
+ */
+void MzIdentMLReader::parseDatabaseSequences() {
+ for (vector<DBSequencePtr>::const_iterator i = pwiz_reader_->sequenceCollection.dbSequences.begin();
+ i != pwiz_reader_->sequenceCollection.dbSequences.end();
+ i++) {
+ DBSequence& db_sequence = (**i);
+ int length = db_sequence.length;
+ string accession = db_sequence.accession;
+ string seq = db_sequence.seq;
+
+ Protein* protein = NULL;
+ bool is_decoy;
+
+ if (seq.empty()) {
+ protein = MatchCollectionParser::getProtein(
+ database_, decoy_database_, accession, is_decoy);
+ } else {
+ protein = MatchCollectionParser::getProtein(
+ database_, decoy_database_, accession, seq, is_decoy);
+ }
+ }
+}
+
+/**
+ * parses the psms from the mzid file
+ */
+void MzIdentMLReader::parsePSMs() {
+ for (vector<SpectrumIdentificationListPtr>::const_iterator i =
+ pwiz_reader_->dataCollection.analysisData.spectrumIdentificationList.begin();
+ i != pwiz_reader_->dataCollection.analysisData.spectrumIdentificationList.end();
+ i++) {
+ for (vector<SpectrumIdentificationResultPtr>::const_iterator j =
+ (*i)->spectrumIdentificationResult.begin();
+ j != (*i)->spectrumIdentificationResult.end();
+ ++j) {
+ SpectrumIdentificationResult& result = **j;
+ string idStr = result.spectrumID;
+ carp(CARP_DEBUG, "idStr:%s", idStr.c_str());
+ //TODO crux requires scan numbers to be integer, where mzid can have
+ //them be strings. I don't know what the appropiate thing to do here.
+ //For now, lets parse as a first_scan-last_scan string, since our
+ //writer outputs it in that format. SJM.
+ int first_scan, last_scan;
+ if (!get_first_last_scan_from_string(idStr, first_scan, last_scan)) {
+ carp(CARP_ERROR, "Cannot find first,last scan from spectrumID:%s",
+ idStr.c_str());
+ }
+
+ //We are not using this yet, but we might.
+ string filename;
+ if (result.spectraDataPtr != NULL) {
+ string filename = result.spectraDataPtr->location;
+ carp(CARP_DEBUG, "filename:%s", filename.c_str());
+ }
+ for (vector<SpectrumIdentificationItemPtr>::const_iterator k =
+ result.spectrumIdentificationItem.begin();
+ k != result.spectrumIdentificationItem.end();
+ k++) {
+ SpectrumIdentificationItem& item = **k;
+ if (use_pass_threshold_ && !item.passThreshold) {
+ continue;
+ }
+ int charge = item.chargeState;
+ FLOAT_T obs_mz = item.experimentalMassToCharge;
+
+ SpectrumZState zstate;
+ zstate.setMZ(obs_mz, charge);
+ vector<int> charge_vec;
+ charge_vec.push_back(charge);
+
+ Spectrum* spectrum = new Spectrum(first_scan, last_scan, obs_mz, charge_vec, "");
+ FLOAT_T calc_mass = (item.calculatedMassToCharge - MASS_PROTON) * (FLOAT_T)charge;
+ string sequence = item.peptidePtr->peptideSequence;
+
+ vector<PeptideEvidencePtr>& peptide_evidences = item.peptideEvidencePtr;
+ PeptideEvidencePtr peptide_evidence_ptr = peptide_evidences.front();
+
+ string protein_id = peptide_evidence_ptr->dbSequencePtr->accession;
+ int start_idx = peptide_evidence_ptr->start;
+
+ carp(CARP_DEBUG, "getting protein %s", protein_id.c_str());
+ bool is_decoy_test;
+ Protein* protein = MatchCollectionParser::getProtein(
+ database_, decoy_database_, protein_id, is_decoy_test);
+
+ if (peptide_evidence_ptr->isDecoy != is_decoy_test) {
+ carp_once(CARP_WARNING, "Protein 0) %s : mzid says isdecoy: %d, "
+ "but database says isdecoy: %d, did you set decoy-prefix?",
+ protein_id.c_str(),
+ peptide_evidence_ptr->isDecoy, is_decoy_test);
+ }
+ //If there is one PeptideEvidence object that is a decoy
+ //then mark the match as a decoy.
+ bool is_decoy = is_decoy || peptide_evidence_ptr->isDecoy || is_decoy_test;
+
+ start_idx = protein->findStart(sequence, "", "");
+
+ if (start_idx == -1) {
+ carp(CARP_FATAL, "can't find sequence %s in first protein %s", sequence.c_str(), protein->getIdPointer().c_str());
+ }
+
+ int length = sequence.length();
+ carp(CARP_DEBUG, "creating peptide %s %f %i", sequence.c_str(), calc_mass, start_idx);
+
+ Crux::Peptide* peptide = new Crux::Peptide(length, protein, start_idx);
+
+ // Add mods to the peptide
+ PeptidePtr pep_ptr = item.peptidePtr;
+ for (vector<ModificationPtr>::const_iterator l = pep_ptr->modification.begin();
+ l != pep_ptr->modification.end();
+ l++) {
+ const ModificationDefinition* mod = ModificationDefinition::Find(
+ (*l)->monoisotopicMassDelta, false);
+ if (mod != NULL) {
+ unsigned char index = (*l)->location;
+ switch (mod->Position()) {
+ case PEPTIDE_N:
+ case PROTEIN_N:
+ index = 0;
+ break;
+ case PEPTIDE_C:
+ case PROTEIN_C:
+ index = length - 1;
+ break;
+ default:
+ index = (*l)->location - 1;
+ }
+ peptide->addMod(mod, index);
+ } else {
+ carp(CARP_ERROR, "Unknown modification: %f", (*l)->monoisotopicMassDelta);
+ }
+ }
+
+ for (int pe_idx = 1; pe_idx < peptide_evidences.size(); pe_idx++) {
+ PeptideEvidencePtr peptide_evidence_ptr = peptide_evidences[pe_idx];
+ int start = peptide_evidence_ptr->start;
+ int end = peptide_evidence_ptr->end;
+ protein_id = peptide_evidence_ptr->dbSequencePtr->accession;
+ carp(CARP_DEBUG, "id: %s start:%i end: %i decoy: %i",
+ protein_id.c_str(), start, end, is_decoy);
+
+ protein = MatchCollectionParser::getProtein(
+ database_, decoy_database_, protein_id, is_decoy_test);
+
+ if (peptide_evidence_ptr->isDecoy != is_decoy_test) {
+ carp_once(CARP_WARNING, "Protein %i) %s: mzid says isdecoy: %i, "
+ "but database says isdecoy: %i, did you set \"decoy-prefix\"?",
+ pe_idx, protein_id.c_str(), peptide_evidence_ptr->isDecoy, is_decoy_test);
+ }
+ is_decoy = is_decoy || peptide_evidence_ptr->isDecoy || is_decoy_test;
+ start_idx = protein->findStart(sequence, "", "");
+ if (start_idx != -1) {
+ PeptideSrc* src = new PeptideSrc((DIGEST_T)0, protein, start_idx);
+ peptide->addPeptideSrc(src);
+ }
+ }
+
+ Match* match = new Match(peptide, spectrum, zstate, is_decoy);
+ // trying to set lnExperimentSize to -1 -> representing unavailable information on distinct matches/spectrum
+ match->setLnExperimentSize(-1);
+ match_collection_->addMatchToPostMatchCollection(match);
+ match->setRank(XCORR, item.rank); // Is it safe to assume this?
+ carp(CARP_DEBUG, "charge: %i obs mz: %f calc mass: %f sequence: %s",
+ charge, obs_mz, calc_mass, sequence.c_str());
+ addScores(item, match);
+ }
+ }
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/MzIdentMLReader.h b/src/io/MzIdentMLReader.h
new file mode 100644
index 0000000..9fd872b
--- /dev/null
+++ b/src/io/MzIdentMLReader.h
@@ -0,0 +1,107 @@
+/**
+ * \file MzIdentMLReader.h
+ * $Revision: 1.00 $
+ * DATE: July 11th, 2012
+ * AUTHOR: Sean McIlwain
+ * \brief Object for reading mzidentml.xml. This object will read a mzidentml file,
+ * creating a matchcollection object. Use proteowizard.
+ *
+ **************************************************************************/
+
+#ifndef MZIDENTMLREADER_H
+#define MZIDENTMLREADER_H
+#include <string>
+#include <vector>
+
+#include "PSMReader.h"
+#include "pwiz/data/identdata/IdentDataFile.hpp"
+#include "model/objects.h"
+
+class MzIdentMLReader : public PSMReader {
+
+ protected:
+
+ pwiz::identdata::IdentDataFile* pwiz_reader_; ///< proteowizard's reader for mzid.
+ MatchCollection* match_collection_; ///<resulting match collection
+ bool use_pass_threshold_; ///<indicator of whether to use the passThreshold attribute
+
+ /**
+ * Initializes the object
+ */
+ void init();
+
+ /**
+ * parses the modifications from the mzid file
+ */
+ void parseMods();
+
+ /**
+ * parses the psms from the mzid file
+ */
+ void parsePSMs();
+
+ /**
+ * parses the database sequences from the mzid file
+ */
+ void parseDatabaseSequences();
+
+ /**
+ * adds the scores for a particular psm from the mzid file to a match object
+ */
+ void addScores(
+ const pwiz::identdata::SpectrumIdentificationItem& item, ///<proteowizard psm
+ Crux::Match* match ///<our psm
+ );
+
+ public:
+
+ /**
+ * \returns an initialized object
+ */
+ MzIdentMLReader();
+
+
+ /**
+ * \returns an object initialized with the file_path
+ */
+ MzIdentMLReader(
+ const std::string& file_path_ ///< the path of the pep.xml file
+ );
+
+ /**
+ * \returns an object initialized with the xml path, and the target,decoy databases
+ */
+ MzIdentMLReader(
+ const std::string& file_path_, ///< the path of the pep.xml
+ Database* database, ///< the protein database
+ Database* decoy_database = NULL ///< the decoy protein database (can be null)
+ );
+
+ /**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+ MatchCollection* parse();
+
+ /**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+ static MatchCollection* parse(
+ const std::string& path, ///< path of the xml file
+ Database* database, ///< target protein database
+ Database* decoy_database ///< decoy protein database (can be null)
+ );
+
+ /**
+ * default destructor
+ */
+ virtual ~MzIdentMLReader();
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/MzIdentMLWriter.cpp b/src/io/MzIdentMLWriter.cpp
new file mode 100644
index 0000000..0a63757
--- /dev/null
+++ b/src/io/MzIdentMLWriter.cpp
@@ -0,0 +1,829 @@
+/**
+ * \file MzIdentMLWriter.cpp
+ * \brief Writes search results in the MzIdentML (mzid) format.
+ */
+#include <iostream>
+#include <fstream>
+#include <string>
+#include "MzIdentMLWriter.h"
+#include "util/crux-utils.h"
+#include "util/MathUtil.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "model/MatchCollection.h"
+#include "model/Modification.h"
+#include "pwiz/data/identdata/Serializer_mzid.hpp"
+#include "model/ProteinMatch.h"
+#include "model/ProteinMatchCollection.h"
+#include "model/PeptideMatch.h"
+#include "model/SpectrumMatch.h"
+
+using namespace std;
+using namespace Crux;
+using namespace pwiz;
+using namespace identdata;
+
+#define calculateMassToCharge(peptide_mass, charge) (FLOAT_T) ((peptide_mass + (charge*MASS_PROTON))/charge)
+
+MzIdentMLWriter::MzIdentMLWriter() : PSMWriter() {
+ //data_ = NULL;
+ fout_ = NULL;
+ sir_idx_ = 0;
+ sil_idx_ = 0;
+ sii_idx_ = 0;
+ peptide_idx_ = 0;
+ peptide_evidence_idx_ = 0;
+ dbs_idx_ = 0;
+ pag_idx_ = 0;
+ pdh_idx_ = 0;
+}
+
+MzIdentMLWriter::~MzIdentMLWriter() {
+ closeFile();
+}
+
+void MzIdentMLWriter::openFile(
+ const char* filename,
+ bool overwrite) {
+ fout_ = create_stream_in_path(filename, NULL, overwrite);
+ mzid_ = IdentDataPtr(new IdentData());
+}
+
+void MzIdentMLWriter::openFile(
+ const string& filename,
+ bool overwrite) {
+ openFile(filename.c_str(), overwrite);
+}
+
+void MzIdentMLWriter::openFile(
+ CruxApplication* application,
+ string filename,
+ MATCH_FILE_TYPE type) {
+ openFile(filename.c_str(), Params::GetBool("overwrite"));
+}
+
+/**
+ * Close the file, if open.
+ */
+void MzIdentMLWriter::closeFile() {
+ if (mzid_ != NULL && fout_ != NULL) {
+ // Add modification information to AnalysisProtocolCollection -> ModificationParams
+ AnalysisProtocolCollection& apc = mzid_->analysisProtocolCollection;
+ SpectrumIdentificationProtocolPtr sipp(new SpectrumIdentificationProtocol());
+ apc.spectrumIdentificationProtocol.push_back(sipp);
+
+ vector<const ModificationDefinition*> mods = ModificationDefinition::AllMods();
+ for (vector<const ModificationDefinition*>::const_iterator i = mods.begin();
+ i != mods.end();
+ i++) {
+ SearchModificationPtr smp(new SearchModification());
+ smp->fixedMod = (*i)->Static();
+ smp->massDelta = MathUtil::Round((*i)->DeltaMass(), Params::GetInt("mod-precision"));
+ smp->residues = vector<char>((*i)->AminoAcids().begin(), (*i)->AminoAcids().end());
+ switch ((*i)->Position()) {
+ case PEPTIDE_N:
+ smp->specificityRules = CVParam(MS_modification_specificity_peptide_N_term);
+ break;
+ case PEPTIDE_C:
+ smp->specificityRules = CVParam(MS_modification_specificity_peptide_C_term);
+ break;
+ case PROTEIN_N:
+ smp->specificityRules = CVParam(MS_modification_specificity_protein_N_term);
+ break;
+ case PROTEIN_C:
+ smp->specificityRules = CVParam(MS_modification_specificity_protein_C_term);
+ break;
+ }
+ sipp->modificationParams.push_back(smp);
+ }
+
+ Serializer_mzIdentML serializer;
+ serializer.write(*fout_, *mzid_);
+ fout_->close();
+ }
+ delete fout_;
+ fout_ = NULL;
+}
+
+/**
+ * \returns the MzIdentML Peptide object, creating it if
+ * it doesn't exist already
+ */
+PeptidePtr MzIdentMLWriter::getPeptide(
+ Crux::Peptide* peptide ///< Peptide -in
+ ) {
+ char* seqTmp = peptide->getSequence();
+ string sequence(seqTmp);
+ free(seqTmp);
+
+ int modPrecision = Params::GetInt("mod-precision");
+
+ vector<Crux::Modification> mods = peptide->getVarMods();
+ for (vector<PeptidePtr>::const_iterator i = mzid_->sequenceCollection.peptides.begin();
+ i != mzid_->sequenceCollection.peptides.end();
+ ++i) {
+ if ((*i)->peptideSequence == sequence && (*i)->modification.size() == mods.size()) {
+ if (mods.empty()) {
+ return *i;
+ }
+ bool match = true;
+ for (vector<ModificationPtr>::const_iterator j = (*i)->modification.begin();
+ j != (*i)->modification.end();
+ ++j) {
+ bool matchCur = false;
+ for (vector<Crux::Modification>::const_iterator k = mods.begin();
+ k != mods.end();
+ k++) {
+ if ((*j)->location == k->Index() &&
+ MathUtil::AlmostEqual((*j)->monoisotopicMassDelta, k->DeltaMass(), modPrecision)) {
+ matchCur = true;
+ break;
+ }
+ }
+ if (!matchCur) {
+ match = false;
+ break;
+ }
+ }
+ //all modifications match, return peptide.
+ if (match) {
+ return *i;
+ }
+ }
+ }
+
+ //Okay, we didn't find a match, so create a new peptide object.
+ PeptidePtr peptide_p(new pwiz::identdata::Peptide(
+ "PEP_" + StringUtils::ToString(peptide_idx_++)));
+ //peptide_p->id = sequence_str;
+ peptide_p->peptideSequence = sequence;
+
+ //add the modifications.
+ for (vector<Crux::Modification>::const_iterator i = mods.begin(); i != mods.end(); i++) {
+ ModificationPtr mod_p(new pwiz::identdata::Modification());
+ switch (i->Position()) {
+ case PEPTIDE_N:
+ case PROTEIN_N:
+ mod_p->location = 0;
+ break;
+ case PEPTIDE_C:
+ case PROTEIN_C:
+ mod_p->location = i->Index() + 2;
+ break;
+ default:
+ mod_p->location = i->Index() + 1;
+ break;
+ }
+ mod_p->monoisotopicMassDelta = MathUtil::Round(i->DeltaMass(), modPrecision);
+ mod_p->residues.push_back(sequence[i->Index()]);
+ mod_p->set(MS_unknown_modification);
+ peptide_p->modification.push_back(mod_p);
+ }
+
+ mzid_->sequenceCollection.peptides.push_back(peptide_p);
+ return peptide_p;
+}
+
+DBSequencePtr MzIdentMLWriter::getDBSequence(std::string& protein_id) {
+ vector<DBSequencePtr>::iterator dbs_iter;
+ for (dbs_iter = mzid_->sequenceCollection.dbSequences.begin();
+ dbs_iter != mzid_->sequenceCollection.dbSequences.end();
+ ++dbs_iter) {
+ DBSequencePtr dbs_ptr = *dbs_iter;
+ if (protein_id == dbs_ptr->accession) {
+ return dbs_ptr;
+ }
+ }
+
+ //I don't know what to do here, there is a problem if we don't have the
+ //protein database, we can't really assign the sequence.
+ //we can fake it as below, but then we have multiple DBSequences for
+ //the same protein. Here we might not have the full sequence.
+ DBSequencePtr dbs_ptr(new DBSequence("DBS_"+boost::lexical_cast<string>(dbs_idx_++)));
+ dbs_ptr->accession = protein_id;
+
+ return (dbs_ptr);
+}
+
+/**
+ * \returns DBSequence for the protein source. If it doesn't exist,
+ * then first create the object in the mzid object
+ */
+DBSequencePtr MzIdentMLWriter::getDBSequence(
+ Crux::Peptide* peptide, ///< peptide -in
+ PeptideSrc* src ///< Source of the peptide -in
+ ) {
+ string protein_id = src->getParentProtein()->getIdPointer();
+ bool is_post_process = src->getParentProtein()->isPostProcess();
+ vector<DBSequencePtr>::iterator dbs_iter;
+
+ string sequence_str;
+ if (is_post_process) {
+ char* seq = peptide->getSequence();
+ sequence_str = seq;
+ free(seq);
+ }
+
+ for (dbs_iter = mzid_->sequenceCollection.dbSequences.begin();
+ dbs_iter != mzid_->sequenceCollection.dbSequences.end();
+ ++dbs_iter) {
+ DBSequencePtr dbs_ptr = *dbs_iter;
+ if (protein_id == dbs_ptr->accession) {
+ if (is_post_process) {
+ //sequence str should be the peptide
+ if (sequence_str == dbs_ptr->seq) {
+ return dbs_ptr;
+ }
+ } else {
+ //we have the full sequence.
+ return dbs_ptr;
+ }
+ }
+ }
+
+ DBSequencePtr dbs_ptr(new DBSequence("DBS_"+boost::lexical_cast<string>(dbs_idx_++)));
+ dbs_ptr->accession = protein_id;
+ if (is_post_process) {
+ dbs_ptr->length = sequence_str.length();
+ dbs_ptr->seq = sequence_str;
+ } else {
+ dbs_ptr->length = src->getParentProtein()->getLength();
+ dbs_ptr->seq = src->getParentProtein()->getSequencePointer();
+ //TODO add description
+ }
+
+ mzid_->sequenceCollection.dbSequences.push_back(dbs_ptr);
+
+ return dbs_ptr;
+}
+
+PeptideEvidencePtr MzIdentMLWriter::getPeptideEvidence(
+ Crux::Peptide* peptide,
+ bool is_decoy,
+ string& protein_id) {
+
+ char* seq = peptide->getSequence();
+ string sequence_str = seq;
+ free(seq);
+
+ //Is there already a peptide evidence ptr?
+ for (vector<PeptideEvidencePtr>::iterator i = mzid_->sequenceCollection.peptideEvidence.begin();
+ i != mzid_->sequenceCollection.peptideEvidence.end();
+ ++i) {
+ PeptideEvidencePtr pe_ptr = *i;
+ if (pe_ptr->peptidePtr->peptideSequence == sequence_str &&
+ pe_ptr->dbSequencePtr->accession == protein_id) {
+ return pe_ptr;
+ }
+ }
+
+ carp(CARP_FATAL, "Couldn't find %s in %s", sequence_str.c_str(), protein_id.c_str());
+ return PeptideEvidencePtr(); // Avoid compiler warning.
+}
+
+/**
+ * \returns PeptideEvidence for the peptide and src.
+ * creates it if it doesn't exist
+ */
+PeptideEvidencePtr MzIdentMLWriter::getPeptideEvidence(
+ Crux::Peptide* peptide, ///< peptide -in
+ bool is_decoy, ///< is this peptide a decoy? -in
+ PeptideSrc* src ///< where to peptide comes from -in
+ ) {
+
+ char* seq = peptide->getSequence();
+ string sequence_str = seq;
+ free(seq);
+
+ string protein_id = src->getParentProtein()->getId();
+
+ //Is there already a peptide evidence ptr?
+ vector<PeptideEvidencePtr>::iterator pe_iter;
+
+ for (vector<PeptideEvidencePtr>::iterator i = mzid_->sequenceCollection.peptideEvidence.begin();
+ i != mzid_->sequenceCollection.peptideEvidence.end();
+ ++i) {
+ PeptideEvidencePtr pe_ptr = *i;
+ if (pe_ptr->peptidePtr->peptideSequence == sequence_str &&
+ pe_ptr->dbSequencePtr->accession == protein_id) {
+ return pe_ptr;
+ }
+ }
+
+ DBSequencePtr dbs_ptr = getDBSequence(peptide, src);
+ PeptideEvidencePtr pe_ptr(new PeptideEvidence(
+ "PE_" + StringUtils::ToString(peptide_evidence_idx_++)));
+
+ if (src->getParentProtein()->isPostProcess()) {
+ pe_ptr->start = 0;
+ pe_ptr->end = peptide->getLength();
+ } else {
+ pe_ptr->start = src->getStartIdx();
+ pe_ptr->end = src->getStartIdx()+peptide->getLength();
+ }
+ pe_ptr->dbSequencePtr = dbs_ptr;
+ pe_ptr->peptidePtr = getPeptide(peptide);
+ pe_ptr->isDecoy = is_decoy;
+
+ mzid_->sequenceCollection.peptideEvidence.push_back(pe_ptr);
+ return pe_ptr;
+}
+
+/**
+ * \returns the SpectrumIdentificationList, creating it if
+ * it doesn't exist yet.
+ */
+SpectrumIdentificationListPtr MzIdentMLWriter::getSpectrumIdentificationList() {
+ SpectrumIdentificationListPtr silp;
+
+ if (mzid_->dataCollection.analysisData.spectrumIdentificationList.size() > 0) {
+ silp = mzid_->dataCollection.analysisData.spectrumIdentificationList.back();
+ } else {
+ silp = SpectrumIdentificationListPtr(new SpectrumIdentificationList(
+ "SIL_" + StringUtils::ToString(sil_idx_++)));
+ mzid_->dataCollection.analysisData.spectrumIdentificationList.push_back(silp);
+ }
+ return silp;
+}
+
+ProteinDetectionListPtr MzIdentMLWriter::getProteinIdentificationList() {
+ ProteinDetectionListPtr pdlp;
+ if (mzid_ -> dataCollection.analysisData.proteinDetectionListPtr != NULL) {
+ pdlp = mzid_->dataCollection.analysisData.proteinDetectionListPtr;
+ } else {
+ pdlp = ProteinDetectionListPtr(
+ new ProteinDetectionList("PDL_1"));
+ mzid_->dataCollection.analysisData.proteinDetectionListPtr = pdlp;
+ }
+ return pdlp;
+}
+
+ProteinAmbiguityGroupPtr MzIdentMLWriter::getProteinAmbiguityGroup(
+ std::string& protein_id
+) {
+ ProteinDetectionListPtr pdlp = getProteinIdentificationList();
+ vector<ProteinAmbiguityGroupPtr>& pag_vec = pdlp->proteinAmbiguityGroup;
+
+ for (size_t pa_idx = 0; pa_idx < pag_vec.size() ;pa_idx++) {
+ std::vector<ProteinDetectionHypothesisPtr>& pdh_vec = pag_vec[pa_idx]->proteinDetectionHypothesis;
+ for (size_t pdh_idx = 0 ; pdh_idx < pdh_vec.size() ; pdh_idx++) {
+ if (pdh_vec[pdh_idx]->dbSequencePtr->accession == protein_id) {
+
+ return pag_vec[pa_idx];
+ }
+ }
+ }
+
+ //not found, create it
+ ProteinAmbiguityGroupPtr pagp = ProteinAmbiguityGroupPtr(
+ new ProteinAmbiguityGroup("PAG_"+boost::lexical_cast<string>(pag_idx_++)));
+
+ ProteinDetectionHypothesisPtr pdhp = getProteinDetectionHypothesis(pagp, protein_id);
+ pag_vec.push_back(pagp);
+ return pagp;
+}
+
+ProteinDetectionHypothesisPtr MzIdentMLWriter::getProteinDetectionHypothesis(
+ ProteinAmbiguityGroupPtr pagp,
+ std::string& protein_id
+ ) {
+ std::vector<ProteinDetectionHypothesisPtr>& pdh_vec = pagp->proteinDetectionHypothesis;
+
+ for (size_t pdh_idx = 0; pdh_idx < pdh_vec.size() ; pdh_idx++) {
+ if (pdh_vec[pdh_idx]->dbSequencePtr->accession == protein_id) {
+ return pdh_vec[pdh_idx];
+ }
+ }
+
+ ProteinDetectionHypothesisPtr pdhp = ProteinDetectionHypothesisPtr(
+ new ProteinDetectionHypothesis("PDH_"+boost::lexical_cast<string>(pdh_idx_++)));
+
+ pdhp->dbSequencePtr = getDBSequence(protein_id);
+ pdh_vec.push_back(pdhp);
+ return pdhp;
+}
+
+ProteinDetectionHypothesisPtr MzIdentMLWriter::getProteinDetectionHypothesis(
+ string& protein_id
+ ) {
+ ProteinAmbiguityGroupPtr pagp = getProteinAmbiguityGroup(protein_id);
+ return getProteinDetectionHypothesis(pagp, protein_id);
+}
+
+PeptideHypothesis& MzIdentMLWriter::getPeptideHypothesis(
+ ProteinMatch* protein_match,
+ PeptideMatch* peptide_match) {
+
+ string protein_id = protein_match->getId();
+ PeptideSrc* src = peptide_match->getSrc(protein_match);
+ ProteinDetectionHypothesisPtr pdhp = getProteinDetectionHypothesis(protein_id);
+ PeptideEvidencePtr pe_ptr = getPeptideEvidence(peptide_match->getPeptide(), true, src);
+
+ for (size_t ph_idx = 0;ph_idx < pdhp->peptideHypothesis.size();ph_idx++) {
+ if (pdhp->peptideHypothesis[ph_idx].peptideEvidencePtr == pe_ptr) {
+ return pdhp->peptideHypothesis[ph_idx];
+ }
+ }
+
+ PeptideHypothesis pep_hyp;
+ pdhp->peptideHypothesis.push_back(pep_hyp);
+ pdhp->peptideHypothesis.back().peptideEvidencePtr = pe_ptr;
+
+ return pdhp->peptideHypothesis.back();
+}
+
+/**
+ * \returns the SpectrumIdentificationResult for the spectrum.
+ * creating it first if it doesn't exist
+ */
+SpectrumIdentificationResultPtr MzIdentMLWriter::getSpectrumIdentificationResult(
+ Crux::Spectrum* spectrum ///< Crux spectrum object -in
+ ) {
+
+ string spectrum_idStr =
+ StringUtils::ToString(spectrum->getFirstScan()) +
+ "-" +
+ StringUtils::ToString(spectrum->getLastScan());
+
+ SpectrumIdentificationListPtr silp = getSpectrumIdentificationList();
+
+ vector<SpectrumIdentificationResultPtr>::iterator sirp_iter;
+
+ for (sirp_iter = silp->spectrumIdentificationResult.begin();
+ sirp_iter != silp->spectrumIdentificationResult.end();
+ ++sirp_iter) {
+
+ SpectrumIdentificationResultPtr sirp = *sirp_iter;
+ if (sirp->spectrumID == spectrum_idStr) {
+ return sirp;
+ }
+ }
+
+ SpectrumIdentificationResultPtr sirp(new SpectrumIdentificationResult());
+
+ sirp->id = "SIR_"+boost::lexical_cast<string>(sir_idx_++);
+ sirp->spectrumID = spectrum_idStr;
+ silp->spectrumIdentificationResult.push_back(sirp);
+ return sirp;
+}
+
+SpectrumIdentificationItemPtr MzIdentMLWriter::getSpectrumIdentificationItem(
+ SpectrumMatch* spectrum_match
+ ) {
+ Crux::Spectrum* spectrum = spectrum_match->getSpectrum();
+ Crux::Peptide* crux_peptide = spectrum_match->getPeptideMatch()->getPeptide();
+ SpectrumZState& zstate = spectrum_match->getZState();
+ int charge_state = zstate.getCharge();
+ double exp_mz = zstate.getMZ();
+
+ PeptidePtr peptide_ptr = getPeptide(crux_peptide);
+ SpectrumIdentificationResultPtr sirp = getSpectrumIdentificationResult(spectrum_match->getSpectrum());
+ vector<SpectrumIdentificationItemPtr>::iterator siip_iter;
+
+ for (siip_iter = sirp->spectrumIdentificationItem.begin(); siip_iter != sirp->spectrumIdentificationItem.end(); ++siip_iter) {
+ SpectrumIdentificationItemPtr siip = *siip_iter;
+ if (siip->peptidePtr == peptide_ptr && siip->chargeState == charge_state && fabs(siip->experimentalMassToCharge - exp_mz) < 0.0001) {
+ return siip;
+ }
+ }
+
+ //wasn't found, create it.
+ SpectrumIdentificationItemPtr siip(new SpectrumIdentificationItem(
+ "SII_"+boost::lexical_cast<string>(sii_idx_++)));
+ siip->chargeState = zstate.getCharge();
+ siip->experimentalMassToCharge = zstate.getMZ();
+
+ siip->calculatedMassToCharge = calculateMassToCharge(crux_peptide->calcModifiedMass(), (FLOAT_T) zstate.getCharge());
+
+ addSpectrumScores(spectrum_match, siip);
+ siip->passThreshold = true;
+ siip->peptidePtr = peptide_ptr;
+ addPeptideEvidences(crux_peptide, false, siip);
+ sirp->spectrumIdentificationItem.push_back(siip);
+ return siip;
+}
+
+void MzIdentMLWriter::addSpectrumScores(
+ SpectrumMatch* spectrum_match,
+ SpectrumIdentificationItemPtr siip) {
+
+ for (ScoreMapIterator iter = spectrum_match->scoresBegin();
+ iter != spectrum_match->scoresEnd();
+ ++iter) {
+ SCORER_TYPE_T score_type = iter->first;
+ FLOAT_T score = iter->second;
+ CVID cvparam_type = getScoreCVID(score_type);
+ if (cvparam_type != CVID_Unknown) {
+ CVParam cvparam(cvparam_type, score);
+ siip->cvParams.push_back(cvparam);
+ } else {
+ carp_once(CARP_WARNING, "Unknown CVPARAM %d", (int)score_type);
+ }
+
+ }
+}
+
+/**
+ * Adds all the peptide evidences to the SpectrumIdentificationItem
+ * using the peptide's protein sources
+ */
+void MzIdentMLWriter::addPeptideEvidences(
+ Crux::Peptide* peptide, ///< peptide to add evidence for
+ bool is_decoy, ///< is peptide a decoy?
+ SpectrumIdentificationItemPtr siip ///< item to add evidences to
+ ) {
+
+ for (PeptideSrcIterator src_iter = peptide->getPeptideSrcBegin();
+ src_iter != peptide->getPeptideSrcEnd();
+ ++src_iter) {
+
+ PeptideEvidencePtr peptide_evidence = getPeptideEvidence(peptide, is_decoy, *src_iter);
+ siip->peptideEvidencePtr.push_back(peptide_evidence);
+ }
+}
+
+/**
+ * \returns the mapping of SCORER_TYPE_T to the cvParam id
+ */
+CVID MzIdentMLWriter::getScoreCVID(
+ SCORER_TYPE_T type ///< type to convert
+ ) {
+ switch(type) {
+ case XCORR:
+ return MS_SEQUEST_xcorr;
+ case SP:
+ return MS_SEQUEST_PeptideSp;
+ case TIDE_SEARCH_EXACT_PVAL:
+ return MS_p_value;
+ case PERCOLATOR_SCORE:
+ return MS_percolator_score;
+ case PERCOLATOR_QVALUE:
+ return MS_percolator_Q_value;
+ case PERCOLATOR_PEP:
+ return MS_percolator_PEP;
+ default:
+ return CVID_Unknown;
+ }
+}
+
+/**
+ * \returns the mapping of SCORER_TYPE_T to cvParam id for ranks
+ */
+CVID MzIdentMLWriter::getRankCVID(
+ SCORER_TYPE_T type ///< type to convert
+ ) {
+ switch(type) {
+ case SP:
+ return MS_SEQUEST_PeptideRankSp;
+ default:
+ return CVID_Unknown;
+ }
+}
+
+/**
+ * Adds the Match scores to the SpectrumIdentificationItem
+ */
+void MzIdentMLWriter::addScores(
+ MatchCollection* match_collection, ///< Parent collection of match
+ Match* match, ///< Match to add
+ SpectrumIdentificationItemPtr item ///< item to add the scores to
+ ) {
+
+ for(int score_idx = (int)SP;
+ score_idx < (int)NUMBER_SCORER_TYPES;
+ score_idx++) {
+ SCORER_TYPE_T score_type = (SCORER_TYPE_T)score_idx;
+ if (match_collection->getScoredType(score_type)) {
+ if (score_type == XCORR && match_collection->exact_pval_search_) {
+ CVParam exactPval(MS_p_value,
+ match->getScore(TIDE_SEARCH_EXACT_PVAL));
+ item->cvParams.push_back(exactPval);
+ CVParam refactXCORR(MS_SEQUEST_xcorr,
+ match->getScore(TIDE_SEARCH_REFACTORED_XCORR));
+ item->cvParams.push_back(refactXCORR);
+ } else {
+ CVID cvparam_type = getScoreCVID(score_type);
+ if (cvparam_type != CVID_Unknown) {
+ CVParam cvparam(cvparam_type, match->getScore(score_type));
+ item->cvParams.push_back(cvparam);
+ }
+ }
+ }
+ }
+
+ if (match_collection->getScoredType(XCORR)) {
+ CVParam delta_cn(MS_SEQUEST_deltacn, match->getScore(DELTA_CN));
+ item->cvParams.push_back(delta_cn);
+ }
+
+ if (match_collection->getScoredType(BY_IONS_MATCHED)) {
+ CVParam matched_ions(MS_SEQUEST_matched_ions, match->getScore(BY_IONS_MATCHED));
+ item->cvParams.push_back(matched_ions);
+ }
+ if (match_collection->getScoredType(BY_IONS_TOTAL)) {
+ CVParam total_ions(MS_SEQUEST_total_ions, match->getScore(BY_IONS_TOTAL));
+ item->cvParams.push_back(total_ions);
+ }
+}
+
+/**
+ * Adds the match ranks to the SpectrumIdentificationItem
+ */
+void MzIdentMLWriter::addRanks(
+ MatchCollection* match_collection, ///< Parent collection of the match
+ Match* match, ///< Match to add
+ SpectrumIdentificationItemPtr item ///< item to add the ranks to
+ ) {
+
+ if (match_collection->getScoredType(SP)) {
+ CVParam sp_rank(getRankCVID(SP), match->getRank(SP));
+ item->cvParams.push_back(sp_rank);
+ }
+}
+
+void MzIdentMLWriter::write(
+ MatchCollection* collection,
+ string database) {
+ addMatches(collection);
+}
+
+/**
+ * Adds the matches in the match collection to
+ * the mzid objects
+ */
+void MzIdentMLWriter::addMatches(
+ MatchCollection* collection ///< matches to add
+ ) {
+ MatchIterator match_iter(collection);
+ while (match_iter.hasNext()) {
+ addMatch(collection, match_iter.next());
+ }
+}
+
+/**
+ * Adds the match to the mzIdentML object
+ */
+void MzIdentMLWriter::addMatch(
+ MatchCollection* collection, ///< parent collection
+ Match* match ///< match to add
+ ) {
+ Crux::Spectrum* spectrum = match->getSpectrum();
+ Crux::Peptide* peptide = match->getPeptide();
+ SpectrumZState zstate = match->getZState();
+
+ SpectrumIdentificationItemPtr siip(new SpectrumIdentificationItem(
+ "SII_"+boost::lexical_cast<string>(sii_idx_++)));
+
+ siip->chargeState = zstate.getCharge();
+ siip->experimentalMassToCharge = zstate.getMZ();
+
+ siip->calculatedMassToCharge = calculateMassToCharge(peptide->calcModifiedMass(), (FLOAT_T) zstate.getCharge());
+
+ if (collection->getScoredType(PERCOLATOR_SCORE)) {
+ siip->rank = match->getRank(PERCOLATOR_SCORE);
+ } else if (collection->getScoredType(XCORR)) {
+ siip->rank = match->getRank(XCORR);
+ }
+ addScores(collection, match, siip);
+ addRanks(collection, match, siip);
+ siip->passThreshold = true;
+ siip->peptidePtr = getPeptide(peptide);
+ addPeptideEvidences(peptide, match->isDecoy(), siip);
+
+ SpectrumIdentificationResultPtr sirp =
+ getSpectrumIdentificationResult(spectrum);
+ sirp->spectrumIdentificationItem.push_back(siip);
+}
+
+void MzIdentMLWriter::addProteinScores(
+ ProteinDetectionHypothesisPtr pdhp,
+ ProteinMatch* protein_match) {
+
+ //TODO should we use these instead?
+ /// q-value for peptides: Peptide identification confidence metric q-value.
+ // MS_q_value_for_peptides = 1001868,
+
+ /// q-value for proteins: Protein identification confidence metric q-value.
+ // MS_q_value_for_proteins = 1001869,
+
+ for (ScoreMapIterator iter = protein_match->scoresBegin();
+ iter != protein_match->scoresEnd();
+ ++iter) {
+
+ SCORER_TYPE_T score_type = iter->first;
+ if (score_type == DELTA_CN || score_type == DELTA_LCN ||
+ score_type == BY_IONS_MATCHED || score_type == BY_IONS_TOTAL) {
+ continue;
+ }
+ FLOAT_T score = iter->second;
+ CVID cvparam_type = getScoreCVID(score_type);
+ if (cvparam_type != CVID_Unknown) {
+ CVParam cvparam(cvparam_type, score);
+ pdhp->cvParams.push_back(cvparam);
+ } else {
+ carp(CARP_WARNING, "Unknown parameter type for score type:%d", score_type);
+ //TODO create a user param.
+ }
+ }
+}
+
+void MzIdentMLWriter::addPeptideScores(
+ PeptideMatch* peptide_match
+ ) {
+ //So PeptideHypothesis doesn't let you add cvparams and they
+ //are not unique, the Peptide tag requires uniqueness, so
+ //I'll add the q-values and scores to those elements (SJM).
+ PeptidePtr peptidep = getPeptide(peptide_match->getPeptide());
+
+ //we already added the scores for this peptide.
+ if (peptidep->cvParams.size() != 0) {
+ return;
+ }
+
+ for (ScoreMapIterator iter = peptide_match->scoresBegin();
+ iter != peptide_match->scoresEnd();
+ ++iter) {
+
+ SCORER_TYPE_T score_type = iter->first;
+ if (score_type == DELTA_CN || score_type == DELTA_LCN ||
+ score_type == BY_IONS_MATCHED || score_type == BY_IONS_TOTAL) {
+ continue;
+ }
+ FLOAT_T score = iter->second;
+ CVID cvparam_type = getScoreCVID(score_type);
+ if (cvparam_type != CVID_Unknown) {
+ CVParam cvparam(cvparam_type, score);
+ peptidep->cvParams.push_back(cvparam);
+ } else {
+ carp(CARP_WARNING, "Unknown parameter type for score type:%d", score_type);
+ //TODO create a user param.
+ }
+ }
+}
+
+void MzIdentMLWriter::addSpectrumMatches(
+ ProteinMatch* protein_match,
+ PeptideMatch* peptide_match
+ ) {
+ PeptideHypothesis& peptide_hypothesis = getPeptideHypothesis(protein_match, peptide_match);
+ for (SpectrumMatchIterator spectrum_iter = peptide_match->spectrumMatchBegin();
+ spectrum_iter != peptide_match->spectrumMatchEnd();
+ ++spectrum_iter) {
+ SpectrumMatch* spectrum_match = *spectrum_iter;
+ SpectrumIdentificationItemPtr sip = getSpectrumIdentificationItem(spectrum_match);
+ peptide_hypothesis.spectrumIdentificationItemPtr.push_back(sip);
+ }
+}
+
+void MzIdentMLWriter::addPeptideMatches(
+ ProteinMatch* protein_match
+ ) {
+ for (PeptideMatchIterator peptide_iter = protein_match->peptideMatchBegin();
+ peptide_iter != protein_match->peptideMatchEnd();
+ ++peptide_iter) {
+ PeptideMatch* peptide_match = *peptide_iter;
+ addPeptideScores(peptide_match);
+ addSpectrumMatches(protein_match, peptide_match);
+ }
+}
+
+/**
+ * Adds the protein matches to the mzid object
+ */
+void MzIdentMLWriter::addProteinMatches(
+ ProteinMatchCollection* protein_match_collection
+) {
+ if (protein_match_collection == NULL) {
+ carp(CARP_FATAL, "ProteinMatchCollection was null");
+ }
+ //now add the protein matches.
+ for (ProteinMatchIterator match_iter = protein_match_collection->proteinMatchBegin();
+ match_iter != protein_match_collection->proteinMatchEnd();
+ match_iter++) {
+ addProteinMatch(*match_iter);
+ }
+}
+
+/**
+ * Adds a protein match to the mzIdentML object
+ */
+void MzIdentMLWriter::addProteinMatch(
+ ProteinMatch* protein_match
+ ) {
+ string protein_id = protein_match->getId();
+
+ //For now, each protein should get its own protein ambiguity group
+ ProteinDetectionHypothesisPtr pdhp = getProteinDetectionHypothesis(protein_id);
+ addProteinScores(pdhp, protein_match);
+ addPeptideMatches(protein_match);
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/io/MzIdentMLWriter.h b/src/io/MzIdentMLWriter.h
new file mode 100644
index 0000000..0a6241d
--- /dev/null
+++ b/src/io/MzIdentMLWriter.h
@@ -0,0 +1,267 @@
+/**
+ * \file MzIdentMLWriter.h
+ * \brief Writes search results in the MzIdentML (mzid) format.
+ */
+#ifndef MZIDENTMLWRITER_H
+#define MZIDENTMLWRITER_H
+
+#include <string>
+#include <vector>
+
+#include "PSMWriter.h"
+#include "model/objects.h"
+#include "model/match_objects.h"
+#include "pwiz/data/identdata/IdentData.hpp"
+
+class MzIdentMLWriter : public PSMWriter {
+
+ protected:
+ std::ofstream* fout_; ///< stream to write the mzid to
+ pwiz::identdata::IdentDataPtr mzid_; ///< structure of mzidentml
+ size_t sir_idx_; ///< counter for SpectrumIdentification results
+ size_t sil_idx_; ///<counter for SpectrumIdentificationList
+ size_t sii_idx_; ///<counter for SpectrumIdentificationItem
+ size_t peptide_idx_; ///<counter for pwiz Peptide
+ size_t peptide_evidence_idx_; ///<counter for PeptideEvidence
+ size_t dbs_idx_; ///< counter for DBSequence
+
+ size_t pag_idx_; ///< counter for ProteinAmbiguityGroups
+ size_t pdh_idx_; ///< counter for ProteinDetectionHypothesis
+
+ /**
+ * \returns DBSequence for the protein source. If it doesn't exist,
+ * then first create the object in the mzid object
+ */
+ pwiz::identdata::DBSequencePtr getDBSequence(
+ Crux::Peptide* peptide, ///< peptide -in
+ PeptideSrc* src ///< Source of the peptide -in
+ );
+
+ /**
+ * \returns PeptideEvidence for the peptide and src.
+ * creates it if it doesn't exist
+ */
+ pwiz::identdata::PeptideEvidencePtr getPeptideEvidence(
+ Crux::Peptide* peptide, ///< peptide -in
+ bool is_decoy, ///< is this peptide a decoy? -in
+ PeptideSrc* src ///< where the peptide is coming from -in
+ );
+
+ pwiz::identdata::PeptideEvidencePtr getPeptideEvidence(
+ Crux::Peptide* peptide,
+ bool is_decoy,
+ std::string& protein_id
+ );
+
+ /**
+ * \returns the MzIdentML Peptide object, creating it if
+ * it doesn't exist already
+ */
+ pwiz::identdata::PeptidePtr getPeptide(
+ Crux::Peptide* peptide ///< peptide -in
+ );
+
+ /**
+ * \returns the SpectrumIdentificationList, creating it if
+ * it doesn't exist yet.
+ */
+ pwiz::identdata::SpectrumIdentificationListPtr getSpectrumIdentificationList();
+
+ /**
+ * \returns the SpectrumIdentificationResult for the spectrum.
+ * creating it first if it doesn't exist
+ */
+ pwiz::identdata::SpectrumIdentificationResultPtr getSpectrumIdentificationResult(
+ Crux::Spectrum* spectrum ///< Crux spectrum object -in
+ );
+
+ /**
+ * \returns the SpectrumIdentificationItem for the SpectrumMatch.
+ * creating it first it it doesn't exist
+ */
+ pwiz::identdata::SpectrumIdentificationItemPtr getSpectrumIdentificationItem(
+ SpectrumMatch* spectrum_match
+ );
+
+ /**
+ * Adds all the peptide evidences to the SpectrumIdentificationItem
+ * using the peptide's protein sources
+ */
+ void addPeptideEvidences(
+ Crux::Peptide* peptide, ///< peptide to add evidence for
+ bool is_decoy, ///< is peptide a decoy?
+ pwiz::identdata::SpectrumIdentificationItemPtr siip ///<item to add evidences to.
+ );
+
+ /**
+ * \returns the mapping of SCORER_TYPE_T to the cvParam id
+ */
+ pwiz::cv::CVID getScoreCVID(
+ SCORER_TYPE_T type ///< type to convert
+ );
+
+ /**
+ * \returns the mapping of SCORER_TYPE_T to the cvPARAM id for ranks
+ */
+ pwiz::cv::CVID getRankCVID(
+ SCORER_TYPE_T type ///< type to convert
+ );
+
+ /**
+ * Adds the Match scores to the SpectrumIdentificationItem
+ */
+ void addScores(
+ MatchCollection* match_collection, ///< Parent collection of match
+ Crux::Match* match, ///< Match to add
+ pwiz::identdata::SpectrumIdentificationItemPtr item ///< item to add the scores to
+ );
+
+ /**
+ * Adds the match ranks to the SpectrumIdentificationItem
+ */
+ void addRanks(
+ MatchCollection* match_collection, ///< Parent collection of the match
+ Crux::Match* match, ///< Match to add
+ pwiz::identdata::SpectrumIdentificationItemPtr item ///< item to add the ranks to
+ );
+
+ pwiz::identdata::ProteinDetectionListPtr getProteinIdentificationList();
+
+ /**
+ * \returns the ProteinAmbiguityGroup for the protein, creating one if
+ * it doesn't exist.
+ */
+ pwiz::identdata::ProteinAmbiguityGroupPtr getProteinAmbiguityGroup(
+ std::string& protein_id
+ );
+
+ pwiz::identdata::ProteinDetectionHypothesisPtr getProteinDetectionHypothesis(
+ pwiz::identdata::ProteinAmbiguityGroupPtr pagp,
+ std::string& protein_id
+ );
+
+ pwiz::identdata::ProteinDetectionHypothesisPtr getProteinDetectionHypothesis(
+ std::string& protein_id
+ );
+
+ pwiz::identdata::PeptideHypothesis& getPeptideHypothesis(
+ ProteinMatch* protein_match,
+ PeptideMatch* peptide_match
+ );
+
+ pwiz::identdata::DBSequencePtr getDBSequence(
+ std::string& protein_id
+ );
+
+ void addProteinScores(
+ pwiz::identdata::ProteinDetectionHypothesisPtr pdhp,
+ ProteinMatch* protein_match
+ );
+
+ void addPeptideMatches(
+ ProteinMatch* protein_match
+ );
+
+ void addSpectrumMatches(
+ ProteinMatch* protein_match,
+ PeptideMatch* peptide_match
+ );
+
+ void addPeptideScores(
+ PeptideMatch* peptide_match
+ );
+
+ void addSpectrumScores(
+ SpectrumMatch* spectrum_match,
+ pwiz::identdata::SpectrumIdentificationItemPtr siip
+ );
+
+
+ public:
+
+ /**
+ * Basic constructor
+ */
+ MzIdentMLWriter();
+
+ /**
+ * Basic destructor
+ */
+ virtual ~MzIdentMLWriter();
+
+ /**
+ * Open a file of the given name. Replace an existing file if
+ * overwrite is true, else exit if an existing file is found.
+ */
+ void openFile(
+ const std::string& filename,
+ bool overwrite
+ );
+
+ void openFile(
+ CruxApplication* application,
+ std::string filename,
+ MATCH_FILE_TYPE type
+ );
+
+ void openFile(
+ const char* filename,
+ bool overwrite
+ );
+
+ /**
+ * Writes out the mzid and frees the memory
+ */
+ void closeFile();
+
+ /**
+ * Adds matches in the match collection to mzid objects [does same thing as "addMatches"]
+ */
+ void write(
+ MatchCollection* collection,
+ std::string database
+ );
+
+ /**
+ * Adds the matches in the match collection to
+ * the mzid objects
+ */
+ void addMatches(
+ MatchCollection* collection ///< matches to add
+ );
+
+ /**
+ * Adds the match to the mzIdentML object
+ */
+ void addMatch(
+ MatchCollection* collection, ///< parent collection
+ Crux::Match* match ///< match to add
+ );
+
+ /**
+ * Adds the protein matches to the mzid object
+ */
+ void addProteinMatches(
+ ProteinMatchCollection* protein_match_collection
+ );
+
+ /**
+ * Adds a protein match to the mzIdentML object
+ */
+ void addProteinMatch(
+ ProteinMatch* protein_match
+ );
+
+
+};
+
+
+#endif // MZIDENTMLWRITER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/OutputFiles.cpp b/src/io/OutputFiles.cpp
new file mode 100644
index 0000000..ddd4143
--- /dev/null
+++ b/src/io/OutputFiles.cpp
@@ -0,0 +1,767 @@
+/**
+ * \file OutputFiles.cpp
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: Aug 24, 2009
+ * PROJECT: crux
+ * \brief A class description for handling all the various
+ * output files, excluding parameter and log files.
+ *
+ * The filenames, locations and overwrite status are taken from
+ * parameter.c.
+ */
+
+#include "OutputFiles.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * Default constructor for OutputFiles. Opens all of the needed
+ * files, naming them based on the values of the parameters output-dir
+ * and fileroot and on the name given (search, percolator, etc.).
+ * Requires that the output directory already exist.
+ */
+OutputFiles::OutputFiles(CruxApplication* program_name)
+: matches_per_spec_(Params::GetInt("top-match")),
+ application_(program_name) {
+
+ delim_file_array_ = NULL;
+ xml_file_array_ = NULL;
+ sqt_file_array_ = NULL;
+ mzid_file_ = NULL;
+ feature_file_ = NULL;
+ pin_file_ = NULL;
+
+ // parameters for all three file types
+ bool overwrite = Params::GetBool("overwrite");
+ const string output_directory = Params::GetString("output-dir");
+ const string fileroot = Params::GetString("fileroot");
+
+ int num_decoy_files = Params::GetInt("num-decoy-files");
+ num_files_ = num_decoy_files + 1; // plus target file
+
+ // TODO (BF oct-21-09): consider moving this logic to parameter.c
+ COMMAND_T command = application_->getCommand();
+ if (Params::GetBool("concat") || command != TIDE_SEARCH_COMMAND) {
+ num_files_ = 1;
+ }
+
+ if (command == XLINK_SEARCH_COMMAND) {
+ if (Params::GetBool("concat")) {
+ num_decoy_files = 0;
+ num_files_ = 1;
+ } else {
+ num_decoy_files = 1;
+ num_files_ = 2;
+ }
+ }
+
+ makeTargetDecoyList();
+
+ carp(CARP_DEBUG,
+ "OutputFiles is opening %d files (%d decoys) in '%s' with root '%s'."
+ " Overwrite: %d.",
+ num_files_, num_decoy_files, output_directory.c_str(), fileroot.c_str(), overwrite);
+
+ // all operations create tab files
+ if( Params::GetBool("txt-output") ) {
+ createFiles(&delim_file_array_,
+ output_directory,
+ fileroot,
+ application_,
+ "txt");
+ }
+
+ // almost all operations create xml files
+ if( command != SPECTRAL_COUNTS_COMMAND &&
+ Params::GetBool("pepxml-output") ) {
+ createFiles(&xml_file_array_,
+ output_directory,
+ fileroot,
+ application_,
+ "pep.xml",
+ overwrite);
+ }
+
+ // sequest and search creates sqt files
+ if( command == TIDE_SEARCH_COMMAND && Params::GetBool("sqt-output") ) {
+ createFiles(&sqt_file_array_,
+ output_directory,
+ fileroot,
+ application_,
+ "sqt",
+ overwrite);
+ }
+
+ //pin
+ if ( command == TIDE_SEARCH_COMMAND && Params::GetBool("pin-output") ) {
+ string filename = makeFileName(
+ fileroot,
+ application_,
+ NULL,// not trget and decoy file
+ "pin"
+ );
+ createFile(
+ &pin_file_,
+ output_directory,
+ filename.c_str(),
+ overwrite
+ );
+ }
+
+ if( Params::GetBool("mzid-output") ) {
+ createFile(&mzid_file_,
+ output_directory,
+ fileroot,
+ application_,
+ "mzid");
+ }
+
+ // only percolator and q-ranker create feature files
+ if( (command == PERCOLATOR_COMMAND
+ || command == QRANKER_COMMAND)
+ && Params::GetBool("feature-file") ) {
+ string filename = makeFileName(fileroot, application_,
+ NULL, // not target or decoy
+ "features.txt");
+ createFile(&feature_file_,
+ output_directory,
+ filename.c_str(),
+ overwrite);
+ }
+ exact_pval_search_ = false;
+}
+
+OutputFiles::~OutputFiles() {
+ for(int file_idx = 0; file_idx < num_files_; file_idx ++) {
+ if( delim_file_array_ ) { delete delim_file_array_[file_idx]; }
+ if( sqt_file_array_ ) { fclose(sqt_file_array_[file_idx]); }
+ if( xml_file_array_ ) { xml_file_array_[file_idx]->closeFile(); }
+ if(pin_file_) {pin_file_->closeFile();}
+ }
+
+ if (mzid_file_) {
+ mzid_file_->closeFile();
+ delete mzid_file_;
+ }
+
+ if( feature_file_ ) { fclose(feature_file_); }
+
+ delete [] delim_file_array_;
+ delete [] sqt_file_array_;
+ delete [] xml_file_array_;
+ delete [] target_decoy_list_;
+ delete pin_file_;
+}
+
+/**
+ * Creates an array of num_files_ strings with the target or decoy
+ * tag that the file in that position should have. The first string
+ * will always be "target", the second will be "decoy" (iff num_files_
+ * = 2) or "decoy-1", the third "decoy-2" and so on.
+ */
+void OutputFiles::makeTargetDecoyList() {
+ target_decoy_list_ = new string[num_files_];
+ target_decoy_list_[0] = "target";
+ if( num_files_ == 2 ) {
+ target_decoy_list_[1] = "decoy";
+ } else {
+ for(int file_idx = 1; file_idx < num_files_; file_idx++) {
+ ostringstream name_builder;
+ name_builder << "decoy-" << file_idx;
+ target_decoy_list_[file_idx] = name_builder.str();
+ }
+ }
+}
+
+/**
+ * \returns A string with all of the parts of the filename
+ * concatenated together as
+ * directory/fileroot.command-name.[target|decoy]extension. Assumes
+ * that extension includes a ".". Either fileroot and/or target_decoy
+ * may be NULL. Directory argument is optional.
+ */
+string OutputFiles::makeFileName(const string& fileroot,
+ CruxApplication* application,
+ const char* target_decoy,
+ const char* extension,
+ const string& directory ) {
+
+ // get command name
+ string basename_str = application->getFileStem();
+ const char* basename = basename_str.c_str();
+
+ ostringstream name_builder;
+ if (!directory.empty()) {
+ name_builder << directory;
+ if (directory[directory.length() - 1] != '/') {
+ name_builder << "/";
+ }
+ }
+ if (!fileroot.empty()) {
+ name_builder << fileroot << ".";
+ }
+ name_builder << basename << "." ;
+ if( target_decoy != NULL && target_decoy[0] != '\0' ) {
+ name_builder << target_decoy << ".";
+ }
+ name_builder << extension;
+ string filename = name_builder.str();
+
+ return filename;
+}
+
+/**
+ * A private function for generating target and decoy files named
+ * according to the given arguments.
+ *
+ * New files are returned via the file_array_ptr argument. When
+ * num_files > 1, exactly one target file is created and the remaining
+ * are decoys. Files are named
+ * "output-dir/fileroot.command_name.target|decoy[-n].extension".
+ * Requires that the output-dir already exist and have write
+ * permissions.
+ * \returns true if num_files new files are created, else false.
+ */
+bool OutputFiles::createFiles(FILE*** file_array_ptr,
+ const string& output_dir,
+ const string& fileroot,
+ CruxApplication* application,
+ const char* extension,
+ bool overwrite) {
+ if( num_files_ == 0 ) {
+ return false;
+ }
+
+ // allocate array
+ *file_array_ptr = new FILE*[num_files_];
+
+ // create each file
+ for(int file_idx = 0; file_idx < num_files_; file_idx++ ) {
+ string filename = makeFileName(fileroot, application,
+ Params::GetBool("concat") ? NULL : target_decoy_list_[file_idx].c_str(),
+ extension);
+ createFile(&(*file_array_ptr)[file_idx],
+ output_dir,
+ filename.c_str(),
+ overwrite);
+
+ }// next file
+
+ return true;
+}
+
+/**
+ * A private function for generating target and decoy pepxml files named
+ * according to the given arguments.
+ *
+ * New files are returned via the file_array_ptr argument. When
+ * num_files > 1, exactly one target file is created and the remaining
+ * are decoys. Files are named
+ * "output-dir/fileroot.command_name.target|decoy[-n].extension".
+ * Requires that the output-dir already exist and have write
+ * permissions.
+ * \returns true if num_files new files are created, else false.
+ */
+bool OutputFiles::createFiles(PepXMLWriter*** xml_writer_array_ptr,
+ const string& output_dir,
+ const string& fileroot,
+ CruxApplication* application,
+ const char* extension,
+ bool overwrite) {
+ if( num_files_ == 0 ) {
+ return false;
+ }
+
+ // allocate array
+ *xml_writer_array_ptr = new PepXMLWriter*[num_files_];
+
+ // create each file
+ for(int file_idx = 0; file_idx < num_files_; file_idx++ ) {
+ string filename = makeFileName(fileroot, application,
+ Params::GetBool("concat") ? NULL : target_decoy_list_[file_idx].c_str(),
+ extension, output_dir);
+ (*xml_writer_array_ptr)[file_idx] = new PepXMLWriter();
+ (*xml_writer_array_ptr)[file_idx]->openFile(filename.c_str(), overwrite);
+
+ }// next file
+
+ return true;
+}
+
+
+/**
+ * A private function for generating target and decoy MatchFileWriters named
+ * according to the given arguments.
+ *
+ * MatchFileWriters are returned via the file_array_ptr argument. When
+ * num_files > 1, exactly one target file is created and the remaining
+ * are decoys. Files are named
+ * "output-dir/fileroot.command_name.target|decoy[-n].extension".
+ * Requires that the output-dir already exist and have write
+ * permissions.
+ * \returns true if num_files new MatchFileWriters are created, else false.
+ */
+bool OutputFiles::createFiles(MatchFileWriter*** file_array_ptr,
+ const string& output_dir,
+ const string& fileroot,
+ CruxApplication* application,
+ const char* extension ) {
+ if( num_files_ == 0 ) {
+ return false;
+ }
+
+ // allocate array
+ *file_array_ptr = new MatchFileWriter*[num_files_];
+
+ // create each file writer
+ for(int file_idx = 0; file_idx < num_files_; file_idx++ ) {
+ string filename = makeFileName(fileroot, application,
+ Params::GetBool("concat") ? NULL : target_decoy_list_[file_idx].c_str(),
+ extension, output_dir);
+ (*file_array_ptr)[file_idx] = new MatchFileWriter(filename.c_str());
+ }
+
+ return true;
+}
+
+
+/**
+ * \brief A private function for opening a file according to the given
+ * arguments.
+ *
+ * New file is returned via the file_ptr argument. File is named
+ * output-dir/fileroot.comand_name[target_decoy].extension. Requires that the
+ * output-dir already exist and have write permissions.
+ * \returns true if the file is created, else false.
+ */
+bool OutputFiles::createFile(FILE** file_ptr,
+ const string& output_dir,
+ const string& filename,
+ bool overwrite) {
+ *file_ptr = create_file_in_path(filename, output_dir, overwrite);
+ return *file_ptr != NULL;
+}
+
+bool OutputFiles::createFile(MzIdentMLWriter** file_ptr,
+ const string& output_dir,
+ const string& fileroot,
+ CruxApplication* application,
+ const char* extension) {
+
+ string filename = makeFileName(fileroot, application, "", extension, output_dir);
+ *file_ptr = new MzIdentMLWriter();
+ (*file_ptr)->openFile(filename, true);
+ return true;
+
+}
+
+/**
+ * \brief A private function for opening a file according to the given
+ * arguments.
+ *
+ * New file is returned via the file_ptr argument. File is named
+ * output-dir/fileroot.pin. Requires that the
+ * output-dir already exist and have write permissions.
+ * \returns true if the file is created, else false.
+ */
+bool OutputFiles::createFile(
+ PinWriter** pin_file_ptr,
+ const string& output_dir,
+ const string& filename,
+ bool overwrite
+) {
+ *pin_file_ptr = new PinWriter();
+ (*pin_file_ptr)->openFile(filename, output_dir, overwrite);
+ return pin_file_ptr != NULL;
+}
+
+
+/**
+ * \brief Write header lines to the .txt, .sqt files, .pep.xml, and .pin
+ * files. Optional num_proteins argument for .sqt files. Use this
+ * for search commands, not post-search.
+ */
+void OutputFiles::writeHeaders(int num_proteins, bool isMixedTargetDecoy) {
+
+ const char* tag = "target";
+
+ // write headers one file at a time for tab and sqt
+ for(int file_idx = 0; file_idx < num_files_; file_idx++) {
+ if( delim_file_array_ ) {
+ bool has_decoy = (bool)file_idx; // only first file (idx 0) is target
+ if( isMixedTargetDecoy ) { // unless it is both
+ has_decoy = true;
+ }
+ delim_file_array_[file_idx]->addColumnNames(application_, has_decoy);
+ delim_file_array_[file_idx]->writeHeader();
+ }
+
+ if( sqt_file_array_ ) {
+ string database = Params::GetString("protein-database");
+ if (!FileUtils::Exists(database.c_str())) {
+ database = Params::GetString("tide database");
+ }
+ MatchCollection::printSqtHeader(sqt_file_array_[file_idx],
+ tag, database, num_proteins, exact_pval_search_);
+ }
+
+ if ( xml_file_array_) {
+ xml_file_array_[file_idx]->writeHeader();
+ }
+
+ tag = "decoy";
+ }
+ //write header at a time for pin file
+ if(pin_file_) {
+ pin_file_->printHeader();
+ }
+}
+
+/**
+ * \brief Write header lines to the .txt and .pep.xml
+ * files. Use this for post-search commands, not search.
+ */
+void OutputFiles::writeHeaders(const vector<bool>& add_this_col) {
+
+
+ // write headers one file at a time for tab and sqt
+ for(int file_idx = 0; file_idx < num_files_; file_idx++) {
+ if( delim_file_array_ ) {
+ delim_file_array_[file_idx]->addColumnNames(application_,
+ (bool)file_idx,
+ add_this_col);
+ delim_file_array_[file_idx]->writeHeader();
+ }
+
+ if ( xml_file_array_) {
+ xml_file_array_[file_idx]->writeHeader();
+ }
+ }
+}
+
+/**
+ * \brief Write header lines to the optional feature file.
+ */
+void OutputFiles::writeFeatureHeader(char** feature_names,
+ int num_names) {
+ // write feature file header
+ if( feature_names && feature_file_ && num_names ) {
+ fprintf(feature_file_, "scan\tlabel");
+ for(int name_idx = 0; name_idx < num_names; name_idx++) {
+ fprintf(feature_file_, "\t%s", feature_names[name_idx]);
+ }
+ fprintf(feature_file_, "\n");
+ }
+}
+
+/**
+ * \brief Write footer lines to .pep.xml files
+ */
+void OutputFiles::writeFooters() {
+ if (xml_file_array_) {
+ for (int file_idx = 0; file_idx < num_files_; file_idx++) {
+ xml_file_array_[file_idx]->writeFooter();
+ }
+ }
+}
+
+/**
+ * \brief Write the given matches to appropriate output files. Limit
+ * the number of matches per spectrum based on top-match parameter
+ * using the ranks from rank_type.
+ */
+void OutputFiles::writeMatches(
+ MatchCollection* target_matches, ///< from real peptides
+ vector<MatchCollection*>& decoy_matches_array,
+ ///< array of collections from shuffled peptides
+ SCORER_TYPE_T rank_type, ///< use ranks for this type
+ Spectrum* spectrum ///< given when all matches are to one spec
+ ) {
+
+ if (!target_matches) {
+ return; // warn?
+ }
+
+ // confirm that there are the expected number of decoy collections
+ if ((int)decoy_matches_array.size() != num_files_ - 1) {
+ carp(CARP_FATAL, "WriteMatches was given %d decoy collections but was expecting %d.",
+ (int)decoy_matches_array.size(), num_files_ - 1);
+ }
+
+ // print to each file type
+ printMatchesTab(target_matches, decoy_matches_array, rank_type, spectrum);
+ printMatchesSqt(target_matches, decoy_matches_array, spectrum);
+ printMatchesXml(target_matches, decoy_matches_array, spectrum, rank_type);
+ printMatchesPin(target_matches, decoy_matches_array);
+ printMatchesMzid(target_matches, decoy_matches_array, rank_type);
+}
+
+// already confirmed that num_files_ = num decoy collections + 1
+void OutputFiles::printMatchesTab(
+ MatchCollection* target_matches, ///< from real peptides
+ vector<MatchCollection*>& decoy_matches_array,
+ SCORER_TYPE_T rank_type,
+ Spectrum* spectrum
+) {
+
+ carp(CARP_DETAILED_DEBUG, "Writing tab delimited results.");
+
+ if (!delim_file_array_) {
+ return;
+ }
+
+ // if a spectrum is given, use one print function
+ if( spectrum ) {
+ MatchCollection* cur_matches = target_matches;
+
+ for(int file_idx = 0; file_idx < num_files_; file_idx++) {
+ cur_matches->calculateDeltaCn();
+ cur_matches->printTabDelimited(delim_file_array_[file_idx],
+ matches_per_spec_, spectrum, rank_type);
+ carp(CARP_DETAILED_DEBUG, "done writing file index %d", file_idx);
+ if( decoy_matches_array.size() > (size_t)file_idx ) {
+ cur_matches = decoy_matches_array[file_idx];
+ }// else if it is NULL, num_files_ == 1 and loop will exit here
+ }
+
+ } else { // use the multi-spectra print function which assumes
+ // targets and decoys are merged
+ target_matches->printMultiSpectra(delim_file_array_[0],
+ (num_files_ > 1) ? delim_file_array_[1] : NULL);
+ }
+
+}
+
+void OutputFiles::printMatchesPin(
+ MatchCollection* target_matches,
+ vector<MatchCollection*>& decoy_matches_array
+ ) {
+ if (pin_file_) {
+ pin_file_->write(target_matches, decoy_matches_array, matches_per_spec_);
+ }
+}
+
+
+void OutputFiles::printMatchesSqt(
+ MatchCollection* target_matches, ///< from real peptides
+ vector<MatchCollection*>& decoy_matches_array,
+ ///< array of collections from shuffled peptides
+ Spectrum* spectrum
+) {
+
+ if( sqt_file_array_ == NULL ) {
+ return;
+ }
+
+ MatchCollection* cur_matches = target_matches;
+
+ for(int file_idx = 0; file_idx < num_files_; file_idx++) {
+
+ cur_matches->printSqt(sqt_file_array_[file_idx],
+ matches_per_spec_,
+ spectrum);
+
+ if( decoy_matches_array.size() > (size_t)file_idx ) {
+ cur_matches = decoy_matches_array[file_idx];
+ } // else if NULL, num_files_==1 and this is last loop
+ }
+
+}
+
+
+void OutputFiles::printMatchesXml(
+ MatchCollection* target_matches, ///< from real peptides
+ vector<MatchCollection*>& decoy_matches_array,
+ ///< array of collections from shuffled peptides
+ Spectrum* spectrum,
+ SCORER_TYPE_T rank_type
+
+) {
+ static int index = 1;
+ if (!xml_file_array_) {
+ return;
+ }
+
+ MatchCollection* cur_matches = target_matches;
+
+ for (int file_idx = 0; file_idx < num_files_; file_idx++) {
+ cur_matches->printXml(xml_file_array_[file_idx], matches_per_spec_, spectrum, rank_type);
+ if( decoy_matches_array.size() > (size_t)file_idx ) {
+ cur_matches = decoy_matches_array[file_idx];
+ } // else if NULL, num_files_==1 and this is last loop
+ }
+ index++;
+}
+
+void OutputFiles::printMatchesMzid(
+ MatchCollection* target_matches,
+ vector<MatchCollection*>& decoy_matches_array,
+ SCORER_TYPE_T rank_type
+ ) {
+ if (!mzid_file_ || !target_matches) {
+ return;
+ }
+
+ printMatchesMzid(target_matches, rank_type);
+
+ for (size_t idx = 0; idx < decoy_matches_array.size();idx++) {
+ printMatchesMzid(decoy_matches_array[idx], rank_type);
+ }
+}
+
+void OutputFiles::printMatchesMzid(
+ MatchCollection* collection,
+ SCORER_TYPE_T rank_type
+ ) {
+ MatchIterator match_iter(collection, rank_type);
+
+ while(match_iter.hasNext()) {
+ Match* current_match = match_iter.next();
+ if (current_match->getRank(rank_type) <= matches_per_spec_) {
+ mzid_file_->addMatch(collection, current_match);
+ } else {
+ break;
+ }
+ }
+}
+
+void OutputFiles::writeMatches(
+ MatchCollection* matches ///< from multiple spectra
+) {
+ matches->printMultiSpectra(delim_file_array_[0], NULL /* no decoy file */);
+ if (xml_file_array_) {
+ matches->printMultiSpectraXml(xml_file_array_[0]);
+ }
+}
+
+/**
+ * \brief Print features from one match to file.
+ */
+void OutputFiles::writeMatchFeatures(
+ Match* match, ///< match to provide scan num, decoy
+ double* features,///< features for this match
+ int num_features) {///< size of features array
+
+ if( feature_file_ == NULL ) { return; }
+
+ // write scan number
+ fprintf(feature_file_, "%i\t",
+ match->getSpectrum()->getFirstScan());
+
+ // decoy or target peptide
+ if (match->getNullPeptide() == false) {
+ fprintf(feature_file_, "1\t");
+ } else {
+ fprintf(feature_file_, "-1\t");
+ }
+
+ // print each feature, end in new-line
+ for(int feature_idx = 0; feature_idx < num_features; feature_idx++) {
+ if (feature_idx < num_features - 1) {
+ fprintf(feature_file_, "%.4f\t", features[feature_idx]);
+ } else {
+ fprintf(feature_file_, "%.4f\n", features[feature_idx]);
+ }
+ }
+
+}
+
+/**
+ * Print the given peptides and their scores in sorted order by score.
+ */
+void OutputFiles::writeRankedPeptides(const vector<pair<FLOAT_T, Peptide*> >& scoreToPeptide) {
+ MatchFileWriter* file = delim_file_array_[0];
+ MATCH_COLUMNS_T score_col = SIN_SCORE_COL;
+
+ MEASURE_TYPE_T measure_type = string_to_measure_type(Params::GetString("measure"));
+ switch (measure_type) {
+ case MEASURE_RAW:
+ score_col = RAW_SCORE_COL;
+ break;
+ case MEASURE_SIN:
+ score_col = SIN_SCORE_COL;
+ break;
+ case MEASURE_NSAF:
+ score_col = NSAF_SCORE_COL;
+ break;
+ case MEASURE_DNSAF:
+ score_col = DNSAF_SCORE_COL;
+ break;
+ case MEASURE_EMPAI:
+ score_col = EMPAI_SCORE_COL;
+ break;
+ default:
+ carp(CARP_FATAL, "Invalid measure type!");
+ }
+
+ // print each pair
+ for(vector<pair<FLOAT_T, Peptide*> >::const_iterator it = scoreToPeptide.begin();
+ it != scoreToPeptide.end(); ++it) {
+ Peptide* peptide = it->second;
+ FLOAT_T score = it->first;
+ const char* seq = peptide->getSequence();
+
+ file->setColumnCurrentRow(SEQUENCE_COL, seq);
+ file->setColumnCurrentRow(score_col, score);
+ file->writeRow();
+ }
+
+}
+
+void OutputFiles::pinSetEnabledStatus(const string& name, bool enabled) {
+ if (pin_file_) {
+ pin_file_->setEnabledStatus(name, enabled);
+ }
+}
+
+/**
+ * Print all of the proteins and their associated scores in sorted
+ * order by score. If there is parsimony information, also print the
+ * parsimony rank.
+ */
+void OutputFiles::writeRankedProteins(const vector<boost::tuple<FLOAT_T, Protein*, int> >& proteins,
+ bool isParsimony) {
+ MatchFileWriter* file = delim_file_array_[0];
+ MATCH_COLUMNS_T score_col = SIN_SCORE_COL;
+
+ switch (string_to_measure_type(Params::GetString("measure"))) {
+ case MEASURE_RAW:
+ score_col = RAW_SCORE_COL;
+ break;
+ case MEASURE_SIN:
+ score_col = SIN_SCORE_COL;
+ break;
+ case MEASURE_NSAF:
+ score_col = NSAF_SCORE_COL;
+ break;
+ case MEASURE_DNSAF:
+ score_col = DNSAF_SCORE_COL;
+ break;
+ case MEASURE_EMPAI:
+ score_col = EMPAI_SCORE_COL;
+ break;
+ default:
+ carp(CARP_FATAL, "Invalid measure type!");
+ }
+
+ // print each protein
+ for(vector<boost::tuple<FLOAT_T, Protein*, int> >::const_iterator it = proteins.begin();
+ it != proteins.end(); ++it) {
+ file->setColumnCurrentRow(score_col, it->get<0>());
+ file->setColumnCurrentRow(PROTEIN_ID_COL, it->get<1>()->getIdPointer());
+ if (isParsimony) {
+ file->setColumnCurrentRow(PARSIMONY_RANK_COL, it->get<2>());
+ }
+ file->writeRow();
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/OutputFiles.h b/src/io/OutputFiles.h
new file mode 100644
index 0000000..7b032c4
--- /dev/null
+++ b/src/io/OutputFiles.h
@@ -0,0 +1,158 @@
+/**
+ * \file OutputFiles.h
+ */
+/*
+ * FILE: OutputFiles.h
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: Aug 24, 2009
+ * PROJECT: crux
+ * DESCRIPTION: A class description for handling all the various
+ * output files, excluding parameter and log files. The filenames,
+ * locations and overwrite status would be taken from parameter.c.
+ */
+#ifndef OUTPUT_FILES_H
+#define OUTPUT_FILES_H
+
+#include <stdio.h>
+#include <string>
+#include <iostream>
+#include <sstream>
+#include "carp.h"
+#include "parameter.h"
+#include "model/objects.h"
+#include "model/MatchCollection.h"
+#include "MatchFileWriter.h"
+#include "PepXMLWriter.h"
+#include "PinWriter.h"
+#include "MzIdentMLWriter.h"
+#include "boost/tuple/tuple.hpp"
+
+class OutputFiles{
+
+ public:
+ explicit OutputFiles(CruxApplication* application);///< command printing files
+
+ ~OutputFiles();
+ void writeHeaders(int num_proteins = 0, bool isMixedTargetDecoy = false);
+ void writeHeaders(const std::vector<bool>& add_this_col);
+ void writeFeatureHeader(char** feature_names = NULL,
+ int num_names = 0);
+ void writeFooters();
+ void writeMatches(MatchCollection* matches,
+ std::vector<MatchCollection*>& decoy_matches_array,
+ SCORER_TYPE_T rank_type = XCORR,
+ Crux::Spectrum* spectrum = NULL);
+ void writeMatches(MatchCollection* matches);
+ void writeMatchFeatures(Crux::Match* match,
+ double* features,
+ int num_features);
+ void writeRankedProteins(const std::vector<boost::tuple<FLOAT_T, Crux::Protein*, int> >& proteins,
+ bool isParsimony);
+ void writeRankedPeptides(const vector<pair<FLOAT_T, Crux::Peptide*> >& scoreToPeptide);
+ void pinSetEnabledStatus(const std::string& name, bool enabled);
+
+ bool exact_pval_search_;
+
+ private:
+ bool createFiles(FILE*** file_array_ptr,
+ const std::string& output_dir,
+ const std::string& fileroot,
+ CruxApplication* application,
+ const char* extension,
+ bool overwrite);
+ bool createFiles(PepXMLWriter*** file_array_ptr,
+ const std::string& output_dir,
+ const std::string& fileroot,
+ CruxApplication* application,
+ const char* extension,
+ bool overwrite);
+ bool createFiles(MatchFileWriter*** file_array_ptr,
+ const std::string& output_dir,
+ const std::string& fileroot,
+ CruxApplication* application,
+ const char* extension);
+
+ bool createFile(MzIdentMLWriter** file_ptr,
+ const std::string& output_dir,
+ const std::string& fileroot,
+ CruxApplication* application,
+ const char* extension);
+
+ bool createFile(FILE** file_ptr,
+ const std::string& output_dir,
+ const std::string& filename,
+ bool overwrite);
+
+ bool createFile(
+ PinWriter** pin_file_ptr,
+ const std::string& output_dir,
+ const std::string& filename,
+ bool overwrite
+ );
+ string makeFileName(const std::string& fileroot,
+ CruxApplication* application,
+ const char* target_decoy,
+ const char* extension,
+ const std::string& directory = "");
+ void makeTargetDecoyList();
+
+ void printMatchesXml(
+ MatchCollection* target_matches,
+ vector<MatchCollection*>& decoy_matches_array,
+ Crux::Spectrum* spectrum,
+ SCORER_TYPE_T rank_type);
+
+
+ void printMatchesTab(
+ MatchCollection* target_matches, ///< from real peptides
+ std::vector<MatchCollection*>& decoy_matches_array,
+ ///< array of collections from shuffled peptides
+ SCORER_TYPE_T rank_type,
+ Crux::Spectrum* spectrum = NULL);
+
+ void printMatchesSqt(
+ MatchCollection* target_matches, ///< from real peptides
+ std::vector<MatchCollection*>& decoy_matches_array,
+ ///< array of collections from shuffled peptides
+ Crux::Spectrum* spectrum = NULL);
+
+ void printMatchesPin(
+ MatchCollection* target_matches, ///< form real peptides
+ std::vector<MatchCollection*>& decoy_maches_array
+ ///< array of collection from shuffled peptides
+ );
+
+ void printMatchesMzid(
+ MatchCollection* target_matches,
+ std::vector<MatchCollection*>& decoy_matches_array,
+ SCORER_TYPE_T rank_type
+ );
+
+ void printMatchesMzid(
+ MatchCollection* collection,
+ SCORER_TYPE_T rank_type
+ );
+
+ int num_files_; ///< num files in each array
+ std::string* target_decoy_list_; ///< target or decoy[-n] string of each file
+ MatchFileWriter** delim_file_array_; ///< array of .txt files
+ FILE** sqt_file_array_; ///< array of .sqt files
+ MzIdentMLWriter* mzid_file_;
+
+ PepXMLWriter** xml_file_array_; ///< array of .pep.xml files
+ FILE* feature_file_; ///< file for percolator/q-ranker to write features to
+ int matches_per_spec_; ///< print this many matches per spec
+ CruxApplication* application_;///< crux application writing these files
+ PinWriter* pin_file_;///< file for inpupt of percolator
+
+};
+
+#endif //OUTPUT_FILES_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/PMCDelimitedFileWriter.cpp b/src/io/PMCDelimitedFileWriter.cpp
new file mode 100644
index 0000000..1f3cbc4
--- /dev/null
+++ b/src/io/PMCDelimitedFileWriter.cpp
@@ -0,0 +1,709 @@
+#include "PMCDelimitedFileWriter.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+using namespace Crux;
+using namespace boost;
+
+/**
+ * Returns an empty PMCDelimitedFileWriter object
+ */
+PMCDelimitedFileWriter::PMCDelimitedFileWriter() : PSMWriter() {
+ write_html_ = false;
+ application_ = NULL;
+}
+
+/**
+ * Destructor
+ */
+PMCDelimitedFileWriter::~PMCDelimitedFileWriter() {
+ closeFile();
+}
+
+/**
+ * Opens a file, writes it, and closes the file
+ */
+void PMCDelimitedFileWriter::writeFile(
+ CruxApplication* application, ///< application writing the file
+ string filename, ///< name of the file to open
+ MATCH_FILE_TYPE type, ///< type of file to be written
+ ProteinMatchCollection* collection ///< collection to be written
+) {
+ openFile(application, filename, type);
+ write(collection);
+ closeFile();
+}
+
+/**
+ * Closes any open file, then opens a file for the specified type of writing
+ */
+void PMCDelimitedFileWriter::openFile(
+ CruxApplication* application, ///< application writing the file
+ string filename, ///< name of the file to open
+ MATCH_FILE_TYPE type ///< type of file to be written
+ ) {
+ closeFile();
+
+ file_ptr_ = FileUtils::GetWriteStream(filename, Params::GetBool("overwrite"));
+ application_ = application;
+ if (!file_ptr_->is_open()) {
+ carp(CARP_FATAL, "Error creating file '%s'.", filename.c_str());
+ }
+
+ // reset columns
+ num_columns_ = 0;
+ for (int i = 0; i < NUMBER_MATCH_COLUMNS; ++i) {
+ match_to_print_[i] = false;
+ match_precision_[i] = false;
+ match_fixed_float_[i] = true;
+ }
+
+ switch (type) {
+ case PROTEINS:
+ setUpProteinsColumns(application);
+ setPrecision();
+ write_function_ = &PMCDelimitedFileWriter::writeProteins;
+ break;
+ case PEPTIDES:
+ setUpPeptidesColumns(application);
+ setPrecision();
+ write_function_ = &PMCDelimitedFileWriter::writePeptides;
+ break;
+ case PSMS:
+ setUpPSMsColumns(application);
+ setPrecision();
+ write_function_ = &PMCDelimitedFileWriter::writePSMs;
+ break;
+ default:
+ carp(CARP_FATAL, "Invalid match file type specified for "
+ "PMCDelimitedFileWriter.");
+ break;
+ }
+}
+
+/**
+ * Closes any open file, if any
+ */
+void PMCDelimitedFileWriter::closeFile() {
+ if (file_ptr_) {
+ file_ptr_->close();
+ delete file_ptr_;
+ file_ptr_ = NULL;
+ }
+}
+
+/**
+ * Write all three file types using the file stem as a base filename
+ */
+void PMCDelimitedFileWriter::writeAll(
+ CruxApplication* application, ///< application writing the files
+ ProteinMatchCollection* collection, ///< collection to be written
+ string stem ///< filestem to be prepended to the filenames
+ ) {
+
+ // write proteins
+ openFile(application, stem + ".proteins.txt", PROTEINS);
+ write(collection);
+ closeFile();
+
+ // write peptides
+ openFile(application, stem + ".peptides.txt", PEPTIDES);
+ write(collection);
+ closeFile();
+
+ // write psms
+ openFile(application, stem + ".psms.txt", PSMS);
+ write(collection);
+ closeFile();
+
+}
+
+void PMCDelimitedFileWriter::write(
+ MatchCollection* collection,
+ string database
+ ) {
+ ProteinMatchCollection protein_collection(collection);
+ write(&protein_collection);
+}
+
+/**
+ * Writes the data in a ProteinMatchCollection to the currently open file
+ */
+void PMCDelimitedFileWriter::write(
+ ProteinMatchCollection* collection ///< collection to be written
+ ) {
+ if (file_ptr_ == NULL) {
+ carp(CARP_FATAL, "No file open to write to.");
+ } else if (collection == NULL) {
+ carp(CARP_FATAL, "ProteinMatchCollection was null");
+ }
+
+ // psm-convert: trying to detect whether additional columns are needed....
+ // Is there a better way to do this or move to setUpPSMSColumns? Seems messy...
+ SpectrumMatchIterator first_spec = collection->spectrumMatchBegin();
+ SpectrumMatch* match = *first_spec;
+
+ if (!match->getFilePath().empty()) {
+ addColumnName(FILE_COL);
+ }
+ addScoreColumnIfExists(match, DELTA_CN, DELTA_CN_COL);
+ addScoreColumnIfExists(match, SP, SP_SCORE_COL);
+ addRankColumnIfExists(match, SP, SP_RANK_COL);
+ addScoreColumnIfExists(match, XCORR, XCORR_SCORE_COL);
+ addRankColumnIfExists(match, XCORR, XCORR_RANK_COL);
+ addScoreColumnIfExists(match, TIDE_SEARCH_EXACT_PVAL, EXACT_PVALUE_COL);
+ addScoreColumnIfExists(match, TIDE_SEARCH_REFACTORED_XCORR, REFACTORED_SCORE_COL);
+ addScoreColumnIfExists(match, BY_IONS_MATCHED, BY_IONS_MATCHED_COL);
+ addScoreColumnIfExists(match, BY_IONS_TOTAL, BY_IONS_TOTAL_COL);
+ if (collection->hasDistinctMatches()) {
+ addColumnName(DISTINCT_MATCHES_SPECTRUM_COL);
+ } else {
+ addColumnName(MATCHES_SPECTRUM_COL);
+ }
+
+ if (!write_html_) {
+ writeHeader();
+ } else {
+ writeHTMLHeader();
+ }
+ (this->*this->PMCDelimitedFileWriter::write_function_)(collection);
+}
+
+// adds score to header and columns if exists
+void PMCDelimitedFileWriter::addScoreColumnIfExists(
+ AbstractMatch* match, ///< match to get score from
+ SCORER_TYPE_T scoreType, ///< score type to get
+ MATCH_COLUMNS_T column ///< column to add the score to
+ ) {
+ if (match->hasScore(scoreType)) {
+ addColumnName(column);
+ }
+}
+
+// adds rank to header and columns if exists
+void PMCDelimitedFileWriter::addRankColumnIfExists(
+ AbstractMatch* match, ///< match to get rank from
+ SCORER_TYPE_T scoreType, ///< rank type to get
+ MATCH_COLUMNS_T column ///< column to add the rank to
+ ) {
+ if (match->hasRank(scoreType)) {
+ addColumnName(column);
+ }
+}
+
+/**
+ * Set up the columns for a protein match file
+ */
+void PMCDelimitedFileWriter::setUpProteinsColumns(
+ CruxApplication* application ///< application writing the file
+) {
+
+ COMMAND_T command = application->getCommand();
+
+ switch(command) {
+ default:
+ carp(CARP_FATAL, "Command (%s) not yet implemented for writing tab "
+ "delimited files.", application->getName().c_str());
+ return;
+ case MISC_COMMAND:
+ case PROCESS_SPEC_COMMAND:
+ case GENERATE_PEPTIDES_COMMAND:
+ case GET_MS2_SPECTRUM_COMMAND:
+ case PREDICT_PEPTIDE_IONS_COMMAND:
+ case VERSION_COMMAND:
+ case NUMBER_COMMAND_TYPES:
+ case INVALID_COMMAND:
+ carp(CARP_FATAL, "Invalid command (%s) for writing tab delimited file.",
+ application->getName().c_str());
+ return;
+ case PERCOLATOR_COMMAND:
+ addColumnName(PERCOLATOR_SCORE_COL);
+ addColumnName(PERCOLATOR_RANK_COL);
+ addColumnName(PERCOLATOR_QVALUE_COL);
+ break;
+ }
+
+ addColumnName(PROTEIN_ID_COL);
+ addColumnName(PEPTIDES_COL);
+}
+
+/**
+ * Write protein match file
+ */
+void PMCDelimitedFileWriter::writeProteins(
+ ProteinMatchCollection* collection ///< collection to be written
+ ) {
+
+ carp(CARP_DEBUG, "Writing proteins");
+
+ MASS_FORMAT_T mass_format_type =
+ get_mass_format_type_parameter("mod-mass-format");
+
+ for (ProteinMatchIterator iter = collection->proteinMatchBegin();
+ iter != collection->proteinMatchEnd();
+ ++iter) {
+ ProteinMatch* match = *iter;
+ Protein* protein = match->getProtein();
+
+ addScoreIfExists(match, PERCOLATOR_SCORE, PERCOLATOR_SCORE_COL);
+ addRankIfExists(match, PERCOLATOR_SCORE, PERCOLATOR_RANK_COL);
+ addScoreIfExists(match, PERCOLATOR_QVALUE, PERCOLATOR_QVALUE_COL);
+ setColumnCurrentRow(PROTEIN_ID_COL, protein->getIdPointer());
+
+ // build peptide list
+ vector<string> peptide_strings;
+ for (PeptideMatchIterator pep_iter = match->peptideMatchBegin();
+ pep_iter != match->peptideMatchEnd();
+ ++pep_iter) {
+ PeptideMatch* pep_match = *pep_iter;
+ Peptide* peptide = pep_match->getPeptide();
+
+ MODIFIED_AA_T* mod_seq = peptide->getModifiedAASequence();
+ char* seq_with_masses = modified_aa_string_to_string_with_masses(
+ mod_seq, peptide->getLength(), mass_format_type);
+ string sequence_str(seq_with_masses);
+ free(seq_with_masses);
+ free(mod_seq);
+
+ for (SpectrumMatchIterator spec_iter = pep_match->spectrumMatchBegin();
+ spec_iter != pep_match->spectrumMatchEnd();
+ ++spec_iter) {
+ SpectrumMatch* spec_match = *spec_iter;
+ Spectrum* spectrum = spec_match->getSpectrum();
+ SpectrumZState& zstate = spec_match->getZState();
+
+ stringstream ss;
+ ss << sequence_str << '-' << spectrum->getFirstScan() << '.'
+ << zstate.getCharge();
+
+ peptide_strings.push_back(ss.str());
+ }
+ }
+ setColumnCurrentRow(PEPTIDES_COL, StringUtils::Join(peptide_strings, ','));
+
+ writeRow();
+ }
+}
+
+/**
+ * Set up the columns for a peptide match file
+ */
+void PMCDelimitedFileWriter::setUpPeptidesColumns(
+ CruxApplication* application ///< application writing the file
+) {
+
+ COMMAND_T command = application->getCommand();
+
+ switch(command) {
+ default:
+ carp(CARP_FATAL, "Command (%s) not yet implemented for writing tab "
+ "delimited files.", application->getName().c_str());
+ return;
+ case MISC_COMMAND:
+ case PROCESS_SPEC_COMMAND:
+ case GENERATE_PEPTIDES_COMMAND:
+ case GET_MS2_SPECTRUM_COMMAND:
+ case PREDICT_PEPTIDE_IONS_COMMAND:
+ case VERSION_COMMAND:
+ case NUMBER_COMMAND_TYPES:
+ case INVALID_COMMAND:
+ carp(CARP_FATAL, "Invalid command (%s) for writing tab delimited file.",
+ application->getName().c_str());
+ return;
+ case PERCOLATOR_COMMAND:
+ addColumnName(PERCOLATOR_SCORE_COL);
+ addColumnName(PERCOLATOR_RANK_COL);
+ addColumnName(PERCOLATOR_QVALUE_COL);
+ addColumnName(PERCOLATOR_PEP_COL);
+ break;
+ }
+
+ addColumnName(SCAN_COL);
+ addColumnName(CHARGE_COL);
+ addColumnName(SPECTRUM_PRECURSOR_MZ_COL);
+ addColumnName(SPECTRUM_NEUTRAL_MASS_COL);
+ addColumnName(PEPTIDE_MASS_COL);
+ //addColumnName(DELTA_CN_COL);
+ //addColumnName(SP_SCORE_COL);
+ //addColumnName(SP_RANK_COL);
+ //addColumnName(XCORR_SCORE_COL);
+ //addColumnName(XCORR_RANK_COL);
+ //addColumnName(BY_IONS_MATCHED_COL);
+ //addColumnName(BY_IONS_TOTAL_COL);
+ //addColumnName(MATCHES_SPECTRUM_COL);
+ addColumnName(SEQUENCE_COL);
+ addColumnName(CLEAVAGE_TYPE_COL);
+ addColumnName(PROTEIN_ID_COL);
+ addColumnName(FLANKING_AA_COL);
+}
+
+/**
+ * Write peptide match file
+ */
+void PMCDelimitedFileWriter::writePeptides(
+ ProteinMatchCollection* collection ///< collection to be written
+ ) {
+
+ carp(CARP_DEBUG, "Writing peptides");
+
+ string cleavage = getCleavageType();
+ MASS_FORMAT_T mass_format_type =
+ get_mass_format_type_parameter("mod-mass-format");
+
+ for (PeptideMatchIterator iter = collection->peptideMatchBegin();
+ iter != collection->peptideMatchEnd();
+ ++iter) {
+ PeptideMatch* match = *iter;
+ Peptide* peptide = match->getPeptide();
+
+ // collect spectra info
+ vector<string> spec_scans;
+ vector<string> spec_charges;
+ vector<string> spec_precursors;
+ vector<string> spec_neutral_masses;
+ for (SpectrumMatchIterator spec_iter = match->spectrumMatchBegin();
+ spec_iter != match->spectrumMatchEnd();
+ ++spec_iter) {
+ SpectrumMatch* spec_match = *spec_iter;
+ Spectrum* spec = spec_match->getSpectrum();
+ SpectrumZState& zstate = spec_match->getZState();
+
+ spec_scans.push_back(lexical_cast<string>(spec->getFirstScan()));
+ spec_charges.push_back(lexical_cast<string>(zstate.getCharge()));
+ spec_precursors.push_back(lexical_cast<string>(spec->getPrecursorMz()));
+ spec_neutral_masses.push_back(lexical_cast<string>(zstate.getNeutralMass()));
+ }
+
+ // collect proteins info
+ vector<string> protein_ids;
+ vector<string> flanking_aas;
+ for (ProteinMatchIterator prot_iter = match->proteinMatchBegin();
+ prot_iter != match->proteinMatchEnd();
+ ++prot_iter) {
+ ProteinMatch* prot_match = *prot_iter;
+ Protein* protein = prot_match->getProtein();
+ protein_ids.push_back(protein->getIdPointer());
+ /** TODO figure out why this works and getFlankingAAs() doesn't **/
+ if (protein->isPostProcess()) {
+ PostProcessProtein* post_process_protein = (PostProcessProtein*)protein;
+ string flanking_str = "";
+ flanking_str += post_process_protein->getNTermFlankingAA();
+ flanking_str += post_process_protein->getCTermFlankingAA();
+ flanking_aas.push_back(flanking_str);
+ }
+ /*****************************************************************/
+ }
+
+ setColumnCurrentRow(SCAN_COL, StringUtils::Join(spec_scans, ','));
+ setColumnCurrentRow(CHARGE_COL, StringUtils::Join(spec_charges, ','));
+ setColumnCurrentRow(SPECTRUM_PRECURSOR_MZ_COL, StringUtils::Join(spec_precursors, ','));
+ setColumnCurrentRow(SPECTRUM_NEUTRAL_MASS_COL, StringUtils::Join(spec_neutral_masses, ','));
+ setColumnCurrentRow(PEPTIDE_MASS_COL, peptide->calcModifiedMass());
+ addScoreIfExists(match, DELTA_CN, DELTA_CN_COL);
+ addScoreIfExists(match, SP, SP_SCORE_COL);
+ addRankIfExists(match, SP, SP_RANK_COL);
+ addScoreIfExists(match, XCORR, XCORR_SCORE_COL);
+ addRankIfExists(match, XCORR, XCORR_RANK_COL);
+ addScoreIfExists(match, PERCOLATOR_SCORE, PERCOLATOR_SCORE_COL);
+ addRankIfExists(match, PERCOLATOR_SCORE, PERCOLATOR_RANK_COL);
+ addScoreIfExists(match, PERCOLATOR_QVALUE, PERCOLATOR_QVALUE_COL);
+ addScoreIfExists(match, PERCOLATOR_PEP, PERCOLATOR_PEP_COL);
+ addScoreIfExists(match, BY_IONS_MATCHED, BY_IONS_MATCHED_COL);
+ addScoreIfExists(match, BY_IONS_TOTAL, BY_IONS_TOTAL_COL);
+ //addScoreIfExists(match, MATCHES_SPECTRUM, MATCHES_SPECTRUM_COL);
+
+ MODIFIED_AA_T* mod_seq = peptide->getModifiedAASequence();
+ char* seq_with_masses = modified_aa_string_to_string_with_masses(
+ mod_seq, peptide->getLength(), mass_format_type);
+ free(mod_seq);
+ setAndFree(SEQUENCE_COL, seq_with_masses);
+
+ setColumnCurrentRow(CLEAVAGE_TYPE_COL, cleavage);
+ setColumnCurrentRow(PROTEIN_ID_COL, StringUtils::Join(protein_ids, ','));
+ //setAndFree(FLANKING_AA_COL, peptide->getFlankingAAs());
+ setColumnCurrentRow(FLANKING_AA_COL, StringUtils::Join(flanking_aas, ','));
+
+ writeRow();
+ }
+}
+
+/**
+ * Set up the columns for a spectrum match file
+ */
+void PMCDelimitedFileWriter::setUpPSMsColumns(
+ CruxApplication* application ///< application writing the file
+) {
+ switch (application->getCommand()) {
+ default:
+ carp(CARP_FATAL, "Command (%s) not yet implemented for writing tab "
+ "delimited files.", application->getName().c_str());
+ return;
+ case MISC_COMMAND:
+ case PROCESS_SPEC_COMMAND:
+ case GENERATE_PEPTIDES_COMMAND:
+ case GET_MS2_SPECTRUM_COMMAND:
+ case PREDICT_PEPTIDE_IONS_COMMAND:
+ case VERSION_COMMAND:
+ case NUMBER_COMMAND_TYPES:
+ case INVALID_COMMAND:
+ carp(CARP_FATAL, "Invalid command (%s) for writing tab delimited file.",
+ application->getName().c_str());
+ return;
+ case PSM_CONVERT_COMMAND:
+ break;
+ case PERCOLATOR_COMMAND:
+ addColumnName(FILE_IDX_COL);
+ addColumnName(FILE_COL);
+ addColumnName(PERCOLATOR_SCORE_COL);
+ addColumnName(PERCOLATOR_RANK_COL);
+ addColumnName(PERCOLATOR_PEP_COL);
+ addColumnName(PERCOLATOR_QVALUE_COL);
+ break;
+ }
+ addColumnName(SCAN_COL);
+ addColumnName(CHARGE_COL);
+ addColumnName(SPECTRUM_PRECURSOR_MZ_COL);
+ addColumnName(SPECTRUM_NEUTRAL_MASS_COL);
+ addColumnName(PEPTIDE_MASS_COL);
+ addColumnName(SEQUENCE_COL);
+ addColumnName(MODIFICATIONS_COL);
+ addColumnName(CLEAVAGE_TYPE_COL);
+ addColumnName(PROTEIN_ID_COL);
+ addColumnName(FLANKING_AA_COL);
+}
+
+/**
+ * Write spectrum match file
+ */
+void PMCDelimitedFileWriter::writePSMs(
+ ProteinMatchCollection* collection ///< collection to be written
+ ) {
+
+ carp(CARP_DEBUG, "Writing PSMs");
+
+ string cleavage = getCleavageType();
+ MASS_FORMAT_T mass_format_type =
+ get_mass_format_type_parameter("mod-mass-format");
+
+ const map<pair<int, int>, int>& spectrum_counts = collection->getMatchesSpectrum();
+
+ bool distinct_matches = collection->hasDistinctMatches();
+ COMMAND_T command = application_->getCommand();
+
+ for (SpectrumMatchIterator iter = collection->spectrumMatchBegin();
+ iter != collection->spectrumMatchEnd();
+ ++iter) {
+ SpectrumMatch* match = *iter;
+ setColumnCurrentRow(FILE_IDX_COL, match->getFileIndex());
+ setColumnCurrentRow(FILE_COL, match->getFilePath());
+
+ Spectrum* spectrum = match->getSpectrum();
+ SpectrumZState& zstate = match->getZState();
+ PeptideMatch* pep_match = match->getPeptideMatch();
+ Peptide* peptide = pep_match->getPeptide();
+
+ if (command == PSM_CONVERT_COMMAND) {
+ addScoreIfExists(match, DELTA_CN, DELTA_CN_COL); // TODO: Figure out difference between match and pep_match,
+ addScoreIfExists(match, BY_IONS_MATCHED, BY_IONS_MATCHED_COL); // since Percolator uses pep_match... While tide-search
+ addScoreIfExists(match, BY_IONS_TOTAL, BY_IONS_TOTAL_COL); // uses match. These are different values, are they supposed to be?
+ // When using pep_match, a lot of things are unknown (-1)
+ setColumnCurrentRow(PROTEIN_ID_COL, peptide->getProteinIdsLocations()); // This was used by an older PMCDelimitedFileWriter and retains the protein id location
+ } else {
+ addScoreIfExists(pep_match, DELTA_CN, DELTA_CN_COL);
+ addScoreIfExists(pep_match, BY_IONS_MATCHED, BY_IONS_MATCHED_COL);
+ addScoreIfExists(pep_match, BY_IONS_TOTAL, BY_IONS_TOTAL_COL);
+ setColumnCurrentRow(PROTEIN_ID_COL, StringUtils::Join(peptide->getProteinIds(), ','));
+ }
+
+ setColumnCurrentRow(SCAN_COL, spectrum->getFirstScan());
+ setColumnCurrentRow(CHARGE_COL, zstate.getCharge());
+ setColumnCurrentRow(SPECTRUM_PRECURSOR_MZ_COL, zstate.getMZ());
+ setColumnCurrentRow(SPECTRUM_NEUTRAL_MASS_COL, zstate.getNeutralMass());
+ setColumnCurrentRow(PEPTIDE_MASS_COL, peptide->calcModifiedMass());
+ addScoreIfExists(match, SP, SP_SCORE_COL);
+ addRankIfExists(match, SP, SP_RANK_COL);
+ addScoreIfExists(match, XCORR, XCORR_SCORE_COL);
+ addRankIfExists(match, XCORR, XCORR_RANK_COL);
+ addScoreIfExists(match, TIDE_SEARCH_EXACT_PVAL, EXACT_PVALUE_COL);
+ addScoreIfExists(match, TIDE_SEARCH_REFACTORED_XCORR, REFACTORED_SCORE_COL);
+ addScoreIfExists(match, PERCOLATOR_SCORE, PERCOLATOR_SCORE_COL);
+ addRankIfExists(match, PERCOLATOR_SCORE, PERCOLATOR_RANK_COL);
+ addScoreIfExists(match, PERCOLATOR_PEP, PERCOLATOR_PEP_COL);
+ addScoreIfExists(match, PERCOLATOR_QVALUE, PERCOLATOR_QVALUE_COL);
+ pair<int, int> scan_charge = make_pair(spectrum->getFirstScan(), zstate.getCharge());
+ map<pair<int, int>, int>::const_iterator lookup = spectrum_counts.find(scan_charge);
+ if (distinct_matches) {
+ setColumnCurrentRow(DISTINCT_MATCHES_SPECTRUM_COL,
+ (lookup != spectrum_counts.end()) ? lookup->second : 0);
+ } else {
+ setColumnCurrentRow(MATCHES_SPECTRUM_COL,
+ (lookup != spectrum_counts.end()) ? lookup->second : 0);
+ }
+ MODIFIED_AA_T* mod_seq = peptide->getModifiedAASequence();
+ char* seq_with_masses = modified_aa_string_to_string_with_masses(
+ mod_seq, peptide->getLength(), mass_format_type);
+ free(mod_seq);
+ setAndFree(SEQUENCE_COL, seq_with_masses);
+ setColumnCurrentRow(MODIFICATIONS_COL, peptide->getModsString());
+
+ setColumnCurrentRow(CLEAVAGE_TYPE_COL, cleavage);
+ setAndFree(FLANKING_AA_COL, peptide->getFlankingAAs());
+
+ if (!write_html_) {
+ writeRow();
+ } else {
+ writeHTMLRow();
+ }
+
+ }
+ if (write_html_) {
+ *file_ptr_ << "</table>" << endl;
+ }
+}
+
+/**
+ * Gets the cleavage type as a string
+ */
+string PMCDelimitedFileWriter::getCleavageType() {
+ ENZYME_T enzyme = get_enzyme_type_parameter("enzyme");
+ const char* enzyme_string = enzyme_type_to_string(enzyme);
+ DIGEST_T digestion = get_digest_type_parameter("digestion");
+ const char* digestion_string = digest_type_to_string(digestion);
+ string cleavage_str = enzyme_string;
+ cleavage_str += "-";
+ cleavage_str += digestion_string;
+ return cleavage_str;
+}
+
+/**
+ * Adds the value of a score to the specified column, if it exists in the match
+ */
+void PMCDelimitedFileWriter::addScoreIfExists(
+ AbstractMatch* match, ///< match to get score from
+ SCORER_TYPE_T scoreType, ///< score type to get
+ MATCH_COLUMNS_T column ///< column to add the score to
+ ) {
+ if (match->hasScore(scoreType)) {
+ setColumnCurrentRow(column, match->getScore(scoreType));
+ } else {
+ setColumnCurrentRow(column, -1);
+ }
+}
+
+/**
+ * Adds the value of a rank to the specified column, if it exists in the match
+ */
+void PMCDelimitedFileWriter::addRankIfExists(
+ AbstractMatch* match, ///< match to get rank from
+ SCORER_TYPE_T scoreType, ///< rank type to get
+ MATCH_COLUMNS_T column ///< column to add the rank to
+ ) {
+ if (match->hasRank(scoreType)) {
+ setColumnCurrentRow(column, match->getRank(scoreType));
+ } else {
+ setColumnCurrentRow(column, -1);
+ }
+}
+
+/**
+ * Sets the value of a char* to the specified column, then frees the pointer
+ */
+void PMCDelimitedFileWriter::setAndFree(
+ MATCH_COLUMNS_T column, ///< column to add the char* to
+ char* value ///< char* to set the column value to
+ ) {
+ if (value != NULL) {
+ setColumnCurrentRow(column, value);
+ free(value);
+ } else {
+ carp(CARP_WARNING, "Cannot set value for column %d", column);
+ }
+}
+
+/**
+ * Sets whether we should write our output in tab delimited or HTML format. Default = false (tab delimited)
+ */
+void PMCDelimitedFileWriter::setWriteHTML(bool write_html) {
+ write_html_ = write_html;
+}
+
+/**
+ * Writes the header in HTML format, this is used for HTMLWriter instead of
+ * DelimitedFileWriter's writeHeader()
+ */
+void PMCDelimitedFileWriter::writeHTMLHeader() {
+
+ num_columns_ = 0;
+ // set file position index for all columns being printed
+ for(unsigned int col_type = 0; col_type < NUMBER_MATCH_COLUMNS; col_type++) {
+ if( match_to_print_[col_type] == true ) {
+ match_indices_[col_type] = num_columns_++;
+ } else {
+ match_indices_[col_type] = -1;
+ }
+ }
+
+ // set all the names for which we have match_indices_
+ column_names_.assign(num_columns_, "");
+ for(unsigned int col_type = 0; col_type < NUMBER_MATCH_COLUMNS; col_type++) {
+ if( match_indices_[col_type] > -1 ) {
+ if (get_column_header(col_type) == NULL) {
+ carp(CARP_FATAL, "Error col type: %d doesn't exist!", col_type);
+ }
+ DelimitedFileWriter::setColumnName(get_column_header(col_type),
+ match_indices_[col_type]);
+ }
+ }
+
+ if( column_names_.empty() ) {
+ return;
+ }
+
+ if( file_ptr_ == NULL || !file_ptr_->is_open() ) {
+ carp(CARP_FATAL, "Cannot write to NULL delimited file.");
+ }
+ *file_ptr_ << "<table border=\"1\">" << "\t<tr>" << endl
+ << "\t\t<td><b>" << column_names_[0] << "</b></td>" << endl;
+ for(size_t idx = 1; idx < column_names_.size(); idx++) {
+ if( !column_names_[idx].empty() ) {
+ *file_ptr_ << "\t\t<td><b>" << column_names_[idx] << "</b></td>" << endl;
+ }
+ }
+
+ *file_ptr_ << "\t</tr>" << endl;
+
+ // with a header, each line must be that length
+ current_row_.assign(column_names_.size(), "");
+}
+
+/**
+ * Writes a row in HTML format, this is used for HTMLWriter instead of
+ * DelimitedFileWriter's writeRow()
+ */
+void PMCDelimitedFileWriter::writeHTMLRow() {
+ if( current_row_.empty() ) {
+ return;
+ }
+
+ // make the row as long as the header
+ while( current_row_.size() < column_names_.size()) {
+ current_row_.push_back("");
+ }
+ // TODO? warning if row is longer than non-empty header?
+
+ // print each value separated by delimiter
+ *file_ptr_ << "\t<tr>" << endl
+ << "\t\t<td>" << current_row_[0] << "</td>" << endl;
+ for(size_t idx = 1; idx < current_row_.size(); idx++) {
+ *file_ptr_ << "\t\t<td>" << current_row_[idx] << "</td>" << endl;
+ }
+ // end with newline
+ *file_ptr_ << "\t</tr>" << endl;
+
+ // clear the current_row and refill with blanks
+ // if there is a header, that is the min length
+ // if not, each row can be a different length
+ current_row_.assign(column_names_.size(), "");
+
+}
diff --git a/src/io/PMCDelimitedFileWriter.h b/src/io/PMCDelimitedFileWriter.h
new file mode 100644
index 0000000..7234d17
--- /dev/null
+++ b/src/io/PMCDelimitedFileWriter.h
@@ -0,0 +1,213 @@
+/**
+ * \file PMCDelimitedFileWriter.h
+ * $Revision$
+ * \brief Writes out delimited files from ProteinMatchCollection objects.
+ */
+
+#ifndef PROTEINMATCHCOLLECTION_DELIMITED_FILE_WRITER_H_
+#define PROTEINMATCHCOLLECTION_DELIMITED_FILE_WRITER_H_
+
+#include <vector>
+
+#include "model/match_objects.h"
+#include "DelimitedFile.h"
+#include "MatchFileWriter.h"
+#include "model/Peptide.h"
+#include "model/PeptideMatch.h"
+#include "model/PostProcessProtein.h"
+#include "model/ProteinMatch.h"
+#include "model/ProteinMatchCollection.h"
+#include "PSMWriter.h"
+#include "model/Spectrum.h"
+#include "model/SpectrumMatch.h"
+
+using namespace std;
+
+class PMCDelimitedFileWriter : public MatchFileWriter, public PSMWriter {
+
+ public:
+ /**
+ * Defines the type of match file being written
+ */
+
+ /**
+ * Returns an empty PMCDelimitedFileWriter object
+ */
+ PMCDelimitedFileWriter();
+
+ /**
+ * Destructor
+ */
+ ~PMCDelimitedFileWriter();
+
+ /**
+ * Opens a file, writes it, and closes the file
+ */
+ void writeFile(
+ CruxApplication* application, ///< application writing the file
+ string filename, ///< name of the file to open
+ MATCH_FILE_TYPE type, ///< type of file to be written
+ ProteinMatchCollection* collection ///< collection to be written
+ );
+
+ /**
+ * Closes any open file, then opens a file for the specified type of writing
+ */
+ void openFile(
+ CruxApplication* application, ///< application writing the file
+ string filename, ///< name of the file to open
+ MATCH_FILE_TYPE type ///< type of file to be written
+ );
+
+ /**
+ * Closes any open file, if any
+ */
+ void closeFile();
+
+ /**
+ * Writes all three file types using the file stem as a base filename
+ */
+ void writeAll(
+ CruxApplication* application, ///< application writing the files
+ ProteinMatchCollection* collection, ///< collection to be written
+ string stem ///< filestem to be prepended to the filenames
+ );
+
+ void write(
+ MatchCollection* collection,
+ string database
+ );
+
+ /**
+ * Writes the data in a ProteinMatchCollection to the currently open file
+ */
+ void write(
+ ProteinMatchCollection* collection ///< collection to be written
+ );
+
+ /**
+ * Sets whether we should write our output in tab delimited or HTML format. Default = false (tab delimited)
+ */
+ void setWriteHTML(bool write_html);
+
+ private:
+
+ bool write_html_; // this determines whether we want to write in html format. Default value = false;
+ CruxApplication* application_; // pointer to the application using this program
+
+ // function pointer to the appropriate writing function for the current file type
+ void (PMCDelimitedFileWriter::*write_function_)(ProteinMatchCollection*);
+
+ /**
+ * Set up the columns for a protein match file
+ */
+ void setUpProteinsColumns(
+ CruxApplication* application ///< application writing the file
+ );
+
+ /**
+ * Write protein match file
+ */
+ void writeProteins(
+ ProteinMatchCollection* collection ///< collection to be written
+ );
+
+ /**
+ * Set up the columns for a peptide match file
+ */
+ void setUpPeptidesColumns(
+ CruxApplication* application ///< application writing the file
+ );
+
+ /**
+ * Write peptide match file
+ */
+ void writePeptides(
+ ProteinMatchCollection* collection ///< collection to be written
+ );
+
+ /**
+ * Set up the columns for a spectrum match file
+ */
+ void setUpPSMsColumns(
+ CruxApplication* application ///< application writing the file
+ );
+
+ /**
+ * Write spectrum match file
+ */
+ void writePSMs(
+ ProteinMatchCollection* collection ///< collection to be written
+ );
+
+ /**
+ * Gets the cleavage type as a string
+ */
+ string getCleavageType();
+
+ /**
+ * Adds a column to the header if match has score
+ */
+ void addScoreColumnIfExists(
+ AbstractMatch* match, ///< match to get score from
+ SCORER_TYPE_T scoreType, ///< score type to get
+ MATCH_COLUMNS_T column ///< column to add the score to
+ );
+
+ /**
+ * Adds a column to the header if match has rank
+ */
+ void addRankColumnIfExists(
+ AbstractMatch* match, ///< match to get rank from
+ SCORER_TYPE_T scoreType, ///< rank type to get
+ MATCH_COLUMNS_T column ///< column to add the rank to
+ );
+
+ /**
+ * Adds the value of a score to the specified column, if it exists in the match
+ */
+ void addScoreIfExists(
+ AbstractMatch* match, ///< match to get score from
+ SCORER_TYPE_T scoreType, ///< score type to get
+ MATCH_COLUMNS_T column ///< column to add the score to
+ );
+
+ /**
+ * Adds the value of a rank to the specified column, if it exists in the match
+ */
+ void addRankIfExists(
+ AbstractMatch* match, ///< match to get rank from
+ SCORER_TYPE_T scoreType, ///< rank type to get
+ MATCH_COLUMNS_T column ///< column to add the rank to
+ );
+
+ /**
+ * Adds the value of a char* to the specified column, then frees the pointer
+ */
+ void setAndFree(
+ MATCH_COLUMNS_T column, ///< column to add the char* to
+ char* value ///< char* to set the column value to
+ );
+
+ /**
+ * Writes the header in HTML format, this is used for HTMLWriter instead of
+ * DelimitedFileWriter's writeHeader()
+ */
+ void writeHTMLHeader();
+
+ /**
+ * Writes a row in HTML format, this is used for HTMLWriter instead of
+ * DelimitedFileWriter's writeRow()
+ */
+ void writeHTMLRow();
+
+};
+
+#endif // PROTEINMATCHCOLLECTION_DELIMITED_FILE_WRITER_H_
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/PMCPepXMLWriter.cpp b/src/io/PMCPepXMLWriter.cpp
new file mode 100644
index 0000000..7233e9a
--- /dev/null
+++ b/src/io/PMCPepXMLWriter.cpp
@@ -0,0 +1,142 @@
+#include "PMCPepXMLWriter.h"
+#include "util/Params.h"
+
+using namespace Crux;
+
+void PMCPepXMLWriter::openFile(
+ string filename,
+ bool overwrite
+) {
+ PepXMLWriter::openFile(filename.c_str(), overwrite);
+}
+
+void PMCPepXMLWriter::openFile(
+ CruxApplication* application,
+ string filename,
+ MATCH_FILE_TYPE type
+) {
+ PepXMLWriter::openFile(filename.c_str(), Params::GetBool("overwrite"));
+}
+
+void PMCPepXMLWriter::write(
+ MatchCollection* collection,
+ string database
+) {
+ ProteinMatchCollection protein_collection(collection);
+ write(&protein_collection);
+}
+
+void PMCPepXMLWriter::closeFile() {
+ PepXMLWriter::closeFile();
+}
+
+/**
+ * Writes the data in a ProteinMatchCollection to the currently open file
+ */
+void PMCPepXMLWriter::write(
+ ProteinMatchCollection* collection ///< collection to be written
+) {
+ if (!file_) {
+ carp(CARP_FATAL, "No file open to write to.");
+ } else if (collection == NULL) {
+ carp(CARP_FATAL, "ProteinMatchCollection was null");
+ }
+
+ writeHeader();
+ writePSMs(collection);
+ writeFooter();
+}
+
+/**
+ * Writes the PSMs in a ProteinMatchCollection to the currently open file
+ */
+void PMCPepXMLWriter::writePSMs(
+ ProteinMatchCollection* collection ///< collection to be written
+) {
+
+ const map<pair<int, int>, int>& spectrum_counts = collection->getMatchesSpectrum();
+
+ // iterate over matches
+ for (SpectrumMatchIterator spec_iter = collection->spectrumMatchBegin();
+ spec_iter != collection->spectrumMatchEnd();
+ ++spec_iter) {
+ SpectrumMatch* spec_match = *spec_iter;
+ PeptideMatch* pep_match = spec_match->getPeptideMatch();
+
+ vector<string> protein_names;
+ vector<string> protein_descriptions;
+ for (ProteinMatchIterator prot_iter = pep_match->proteinMatchBegin();
+ prot_iter != pep_match->proteinMatchEnd();
+ ++prot_iter) {
+ ProteinMatch* prot_match = *prot_iter;
+ Protein* protein = prot_match->getProtein();
+ protein_names.push_back(protein->getIdPointer());
+ protein_descriptions.push_back(protein->getAnnotationPointer());
+ }
+
+ // populate scores
+ double scores[NUMBER_SCORER_TYPES] = { 0 };
+ bool scores_computed[NUMBER_SCORER_TYPES] = { false };
+ for (ScoreMapIterator score_iter = spec_match->scoresBegin();
+ score_iter != spec_match->scoresEnd();
+ ++score_iter) {
+ scores[score_iter->first] = score_iter->second;
+ scores_computed[score_iter->first] = true;
+ }
+
+ // populate ranks
+ int ranks[NUMBER_SCORER_TYPES] = { 0 };
+ for (RankMapIterator rank_iter = spec_match->ranksBegin();
+ rank_iter != spec_match->ranksEnd();
+ ++rank_iter) {
+ ranks[rank_iter->first] = rank_iter->second;
+ }
+
+ Spectrum* spectrum = spec_match->getSpectrum();
+ SpectrumZState zstate = spec_match->getZState();
+ Peptide* peptide = pep_match->getPeptide();
+ int spec_scan = spectrum->getFirstScan();
+ string spec_filename = spectrum->getFilename();
+ FLOAT_T spec_neutral_mass = zstate.getNeutralMass();
+ int spec_charge = zstate.getCharge();
+
+ // get sequence and modified sequence
+ char* seq;
+ seq = peptide->getSequence();
+ string seq_str(seq);
+ free(seq);
+ MODIFIED_AA_T* mod_seq = peptide->getModifiedAASequence();
+ seq =
+ modified_aa_string_to_string_with_masses(mod_seq, peptide->getLength(),
+ get_mass_format_type_parameter("mod-mass-format"));
+ string mod_seq_str(seq);
+ free(seq);
+ free(mod_seq);
+ // get flanking aas
+ char* flanking = peptide->getFlankingAAs();
+ string flanking_str(flanking);
+ free(flanking);
+
+ FLOAT_T peptide_mass = peptide->calcModifiedMass();
+
+ // write psm
+ map<pair<int, int>, int>::const_iterator lookup =
+ spectrum_counts.find(make_pair(spec_scan, spec_charge));
+ writePSM(spec_scan, spec_filename.c_str(),
+ spec_neutral_mass, spec_charge,
+ ranks, seq_str.c_str(), mod_seq_str.c_str(), peptide_mass,
+ protein_names.size(), flanking_str.c_str(),
+ protein_names, protein_descriptions,
+ scores_computed, scores,
+ (lookup != spectrum_counts.end()) ? lookup->second : 0);
+ }
+
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/PMCPepXMLWriter.h b/src/io/PMCPepXMLWriter.h
new file mode 100644
index 0000000..bcbc239
--- /dev/null
+++ b/src/io/PMCPepXMLWriter.h
@@ -0,0 +1,65 @@
+#ifndef PMCPEPXMLWRITER_H
+#define PMCPEPXMLWRITER_H
+
+#include "carp.h"
+#include "model/Peptide.h"
+#include "model/PeptideMatch.h"
+#include "PepXMLWriter.h"
+#include "model/Protein.h"
+#include "model/ProteinMatch.h"
+#include "model/ProteinMatchCollection.h"
+#include "PSMWriter.h"
+#include "model/Spectrum.h"
+#include "model/SpectrumMatch.h"
+
+using namespace std;
+
+class PMCPepXMLWriter : public PepXMLWriter, public PSMWriter {
+
+ public:
+
+ void openFile(
+ string filename,
+ bool overwrite
+ );
+
+ void openFile(
+ CruxApplication* application,
+ string filename,
+ MATCH_FILE_TYPE type
+ );
+
+ void write(
+ MatchCollection* collection,
+ string database
+ );
+
+ void closeFile();
+
+ /**
+ * Writes the data in a ProteinMatchCollection to the currently open file
+ */
+ void write(
+ ProteinMatchCollection* collection ///< collection to be written
+ );
+
+ protected:
+
+ /**
+ * Writes the PSMs in a ProteinMatchCollection to the currently open file
+ */
+ void writePSMs(
+ ProteinMatchCollection* collection ///< collection to be written
+ );
+
+};
+
+#endif // PMCPEPXMLWRITER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/PMCSQTWriter.cpp b/src/io/PMCSQTWriter.cpp
new file mode 100644
index 0000000..3468434
--- /dev/null
+++ b/src/io/PMCSQTWriter.cpp
@@ -0,0 +1,160 @@
+#include "PMCSQTWriter.h"
+
+void PMCSQTWriter::openFile(
+ CruxApplication* application,
+ string filename,
+ MATCH_FILE_TYPE type
+) {
+ SQTWriter::openFile(filename);
+}
+
+void PMCSQTWriter::write(
+ MatchCollection* collection,
+ string database
+) {
+ ProteinMatchCollection protein_collection(collection);
+ write(&protein_collection, database);
+}
+
+void PMCSQTWriter::closeFile() {
+ SQTWriter::closeFile();
+}
+
+/**
+ * Writes the data in a ProteinMatchCollection to the currently open file
+ */
+void PMCSQTWriter::write(
+ ProteinMatchCollection* collection, ///< collection to be written
+ string database ///< the database name
+) {
+ if (!file_) {
+ carp(CARP_FATAL, "No file open to write to.");
+ }
+
+ // count proteins
+ int num_proteins = 0;
+ for (ProteinMatchIterator iter = collection->proteinMatchBegin();
+ iter != collection->proteinMatchEnd();
+ ++iter) {
+ ++num_proteins;
+ }
+
+ writeHeader(database, num_proteins);
+ writePSMs(collection);
+}
+
+/**
+ * Writes the PSMs in a ProteinMatchCollection to the currently open file
+ */
+void PMCSQTWriter::writePSMs(
+ ProteinMatchCollection* collection ///< collection to be written
+) {
+
+ const map<pair<int, int>, int>& spectrum_counts = collection->getMatchesSpectrum();
+
+ string lastPrintedSpectrum = "";
+
+ // iterate over matches
+ for (SpectrumMatchIterator spec_iter = collection->spectrumMatchBegin();
+ spec_iter != collection->spectrumMatchEnd();
+ ++spec_iter) {
+ SpectrumMatch* spec_match = *spec_iter;
+ PeptideMatch* pep_match = spec_match->getPeptideMatch();
+
+ // write spectrum
+ Crux::Spectrum* spectrum = spec_match->getSpectrum();
+ SpectrumZState z_state = spec_match->getZState();
+ map<pair<int, int>, int>::const_iterator lookup =
+ spectrum_counts.find(make_pair(spectrum->getFirstScan(), z_state.getCharge()));
+
+ string spectrum_title = getSpectrumTitle(spectrum->getFirstScan(), z_state.getCharge());
+ if (spectrum_title.compare(lastPrintedSpectrum) != 0) {
+ writeSpectrum(spectrum, z_state, (lookup != spectrum_counts.end()) ?
+ lookup->second : 0);
+ lastPrintedSpectrum = spectrum_title;
+ }
+
+ FLOAT_T xcorr_score = -1.0;
+ int xcorr_rank = -1;
+ FLOAT_T sp_score = -1.0;
+ int sp_rank = -1;
+ FLOAT_T delta_cn = -1.0;
+ FLOAT_T by_ions_matched = -1;
+ FLOAT_T by_ions_total = -1;
+
+ // xcorr
+ if (spec_match->hasScore(XCORR)) {
+ xcorr_score = spec_match->getScore(XCORR);
+ } else {
+ carp_once(CARP_WARNING, "Missing XCorr value writing SQT.");
+ }
+ if (spec_match->hasRank(XCORR)) {
+ xcorr_rank = spec_match->getRank(XCORR);
+ } else {
+ carp_once(CARP_WARNING, "Missing XCorr rank writing SQT.");
+ }
+
+ // sp
+ if (spec_match->hasScore(SP)) {
+ sp_score = spec_match->getScore(SP);
+ } else {
+ carp_once(CARP_WARNING, "Missing SP value writing SQT.");
+ }
+ if (spec_match->hasRank(SP)) {
+ sp_rank = spec_match->getRank(SP);
+ } else {
+ carp_once(CARP_WARNING, "Missing SP rank writing SQT.");
+ }
+
+ // deltacn
+ if (spec_match->hasScore(DELTA_CN)) {
+ delta_cn = spec_match->getScore(DELTA_CN);
+ } else {
+ carp_once(CARP_WARNING, "Missing DeltaCN value writing SQT.");
+ }
+
+ // b/y ions
+ if (spec_match->hasScore(BY_IONS_MATCHED)) {
+ by_ions_matched = spec_match->getScore(BY_IONS_MATCHED);
+ } else {
+ carp_once(CARP_WARNING, "Missing B/Y ions matched value writing SQT.");
+ }
+ if (spec_match->hasScore(BY_IONS_TOTAL)) {
+ by_ions_total = spec_match->getScore(BY_IONS_TOTAL);
+ } else {
+ carp_once(CARP_WARNING, "Missing B/Y ions total value writing SQT.");
+ }
+
+ // checking whether lowest sp and total ion intensity need carp warning
+ if (spectrum->getTotalEnergy() == -1) {
+ carp_once(CARP_WARNING, "Missing Total Energy value writing SQT.");
+ }
+ if (spectrum->getLowestSp() == -1) {
+ carp_once(CARP_WARNING, "Missing Lowest Sp value writing SQT.");
+ }
+
+ bool is_decoy = false; // TODO not sure how to determine
+
+ // write psm
+ writePSM(pep_match->getPeptide(),
+ xcorr_score, xcorr_rank,
+ sp_score, sp_rank,
+ delta_cn,
+ by_ions_matched, by_ions_total,
+ is_decoy);
+ }
+}
+
+string PMCSQTWriter::getSpectrumTitle(int spectrum_scan_number, int charge) {
+ std::ostringstream spectrum_id;
+ spectrum_id << spectrum_scan_number << "." << spectrum_scan_number << "." << charge;
+ return spectrum_id.str();
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/PMCSQTWriter.h b/src/io/PMCSQTWriter.h
new file mode 100644
index 0000000..683da73
--- /dev/null
+++ b/src/io/PMCSQTWriter.h
@@ -0,0 +1,63 @@
+#ifndef PMCSQTWRITER_H
+#define PMCSQTWRITER_H
+
+#include "model/PeptideMatch.h"
+#include "model/ProteinMatchCollection.h"
+#include "PSMWriter.h"
+#include "model/SpectrumMatch.h"
+#include "SQTWriter.h"
+
+using namespace std;
+
+class PMCSQTWriter : public SQTWriter, public PSMWriter {
+
+ public:
+
+ void openFile(
+ CruxApplication* application,
+ string filename,
+ MATCH_FILE_TYPE type
+ );
+
+ void write(
+ MatchCollection* collection,
+ string database
+ );
+
+ void closeFile();
+
+ /**
+ * Writes the data in a ProteinMatchCollection to the currently open file
+ */
+ void write(
+ ProteinMatchCollection* collection, ///< collection to be written
+ string database ///< the database name
+// int top_match ///< the top matches to output
+ );
+
+ string getSpectrumTitle(
+ int spectrum_scan_number,
+ int charge
+ );
+
+ protected:
+
+ /**
+ * Writes the PSMs in a ProteinMatchCollection to the currently open file
+ */
+ void writePSMs(
+ ProteinMatchCollection* collection ///< collection to be written
+// int top_match //< the top matches to output
+ );
+
+};
+
+#endif // PMCSQTWRITER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/PSMReader.cpp b/src/io/PSMReader.cpp
new file mode 100644
index 0000000..e7273ee
--- /dev/null
+++ b/src/io/PSMReader.cpp
@@ -0,0 +1,29 @@
+/*
+Abstract class for a peptide-spectrum match readers
+*/
+
+#include <cstdio>
+#include "PSMReader.h"
+#include "parameter.h"
+
+using namespace std;
+
+PSMReader::PSMReader()
+ : database_(NULL), decoy_database_(NULL) {
+}
+
+PSMReader::PSMReader(const string& file_path, Database* database, Database* decoy_database)
+ : file_path_(file_path), database_(database), decoy_database_(decoy_database) {
+}
+
+PSMReader::~PSMReader() {
+}
+
+void PSMReader::setDatabase(Database* database) {
+ database_ = database;
+}
+
+void PSMReader::setDecoyDatabase(Database* decoy_database) {
+ decoy_database_ = decoy_database;
+}
+
diff --git a/src/io/PSMReader.h b/src/io/PSMReader.h
new file mode 100644
index 0000000..518eddb
--- /dev/null
+++ b/src/io/PSMReader.h
@@ -0,0 +1,40 @@
+/*
+Abstract class for a peptide-spectrum match readers
+*/
+
+#ifndef PSMREADER_H
+#define PSMREADER_H
+
+#include "model/MatchCollection.h"
+
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+#include <string>
+
+class PSMReader {
+
+ public:
+ // Constructors
+ PSMReader();
+ PSMReader(const std::string& file_path,
+ Database* database = NULL,
+ Database* decoy_database = NULL);
+
+ // Destructor
+ virtual ~PSMReader();
+
+ // Pure Virtual Parse Functions
+ virtual MatchCollection* parse() = 0;
+
+ // Methods usable by all Readers
+ void setDatabase(Database* database);
+ void setDecoyDatabase(Database* decoy_database);
+
+ protected:
+ Database* database_;
+ Database* decoy_database_;
+ std::string file_path_;
+};
+
+#endif
diff --git a/src/io/PSMWriter.cpp b/src/io/PSMWriter.cpp
new file mode 100644
index 0000000..313cfd1
--- /dev/null
+++ b/src/io/PSMWriter.cpp
@@ -0,0 +1,11 @@
+/*
+Abstract class for a peptide-spectrum match writers
+*/
+
+#include "PSMWriter.h"
+
+PSMWriter::PSMWriter() {
+}
+
+PSMWriter::~PSMWriter() {
+}
diff --git a/src/io/PSMWriter.h b/src/io/PSMWriter.h
new file mode 100644
index 0000000..548a2b4
--- /dev/null
+++ b/src/io/PSMWriter.h
@@ -0,0 +1,36 @@
+/*
+Abstract class for a peptide-spectrum match writers
+*/
+
+#ifndef PSMWRITER_H
+#define PSMWRITER_H
+
+#include "model/MatchCollection.h"
+#include "parameter.h"
+
+#include <iostream>
+#include <fstream>
+#include <iomanip>
+#include <string>
+
+class PSMWriter {
+
+ public:
+ // Constructor
+ PSMWriter();
+
+ // Destructor
+ virtual ~PSMWriter();
+
+ enum MATCH_FILE_TYPE { NONE, PROTEINS, PEPTIDES, PSMS };
+
+ // Pure virtual write, open file, and close file
+
+ virtual void openFile(CruxApplication* application, std::string filename, MATCH_FILE_TYPE type) = 0;
+
+ virtual void write(MatchCollection* collection, std::string database) = 0;
+
+ virtual void closeFile() = 0;
+};
+
+#endif
diff --git a/src/io/PWIZSpectrumCollection.cpp b/src/io/PWIZSpectrumCollection.cpp
new file mode 100644
index 0000000..39b3cd3
--- /dev/null
+++ b/src/io/PWIZSpectrumCollection.cpp
@@ -0,0 +1,274 @@
+/**
+ * \file PWIZSpectrumCollection.cpp
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: 21 April 2011
+ * \brief Class to read spectra files using the proteowizard library.
+ */
+#include "PWIZSpectrumCollection.h"
+#include "util/crux-utils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "parameter.h"
+#include <iostream>
+#include "pwiz/data/msdata/SpectrumInfo.hpp"
+#if defined (_MSC_VER) && defined(INCLUDE_VENDOR_LIBRARIES)
+#include "pwiz/data/msdata/DefaultReaderList.hpp"
+//#include "pwiz/data/vendor_readers/ABI/Reader_ABI.hpp"
+//#include "pwiz/data/vendor_readers/ABI/T2D/Reader_ABI_T2D.hpp"
+#include "pwiz/data/vendor_readers/Agilent/Reader_Agilent.hpp"
+#include "pwiz/data/vendor_readers/Bruker/Reader_Bruker.hpp"
+#include "pwiz/data/vendor_readers/Shimadzu/Reader_Shimadzu.hpp"
+#include "pwiz/data/vendor_readers/Thermo/Reader_Thermo.hpp"
+#include "pwiz/data/vendor_readers/Waters/Reader_Waters.hpp"
+#endif
+
+
+using namespace std;
+/**
+ * Instantiates a new spectrum_collection object from a filename.
+ * Does not parse file.
+ */
+PWIZSpectrumCollection::PWIZSpectrumCollection(
+ const string& filename ///< The spectrum collection filename.
+) : SpectrumCollection(filename) {
+#if defined(_MSC_VER) && defined(INCLUDE_VENDOR_LIBRARIES)
+ pwiz::msdata::DefaultReaderList readerList;
+ //readerList.push_back(pwiz::msdata::ReaderPtr(new pwiz::msdata::Reader_ABI));
+ //readerList.push_back(pwiz::msdata::ReaderPtr(new pwiz::msdata::Reader_ABI_T2D));
+ readerList.push_back(pwiz::msdata::ReaderPtr(new pwiz::msdata::Reader_Agilent));
+ //readerList.push_back(pwiz::msdata::ReaderPtr(new pwiz::msdata::Reader_Bruker));
+ readerList.push_back(pwiz::msdata::ReaderPtr(new pwiz::msdata::Reader_Shimadzu));
+ readerList.push_back(pwiz::msdata::ReaderPtr(new pwiz::msdata::Reader_Thermo));
+ readerList.push_back(pwiz::msdata::ReaderPtr(new pwiz::msdata::Reader_Waters));
+ carp(CARP_DETAILED_INFO, "Support for vendor specific formats enabled.");
+ try {
+ reader_ = new pwiz::msdata::MSDataFile(filename_, &readerList);
+ } catch (const runtime_error& error) {
+ carp(CARP_FATAL, "Unable to parse spectrum file %s. Error: %s.", filename_.c_str(), error.what());
+ }
+#else
+ carp(CARP_DETAILED_INFO, "Support for vendor specific formats not enabled.");
+ try {
+ reader_ = new pwiz::msdata::MSDataFile(filename_);
+ }
+ catch (const runtime_error& error) {
+ carp(CARP_FATAL, "Unable to parse spectrum file %s. Error: %s.", filename_.c_str(), error.what());
+ }
+#endif
+ if( reader_ == NULL ) {
+ carp(CARP_FATAL, "PWIZSpectrumCollection unable to open '%s'.",
+ filename_.c_str());
+ }
+}
+
+PWIZSpectrumCollection::~PWIZSpectrumCollection() {
+ delete reader_;
+}
+
+/**
+ * Parses the first/last scan from the title
+ * \returns whether this was successful.
+ * For MGF files that place their scan numbers in the title string
+ */
+bool PWIZSpectrumCollection::parseFirstLastScanFromTitle(
+ string& scan_title_str,
+ int& first_scan,
+ int& last_scan
+ ) {
+
+ first_scan = -1;
+ last_scan = -1;
+ vector<string> scan_title_tokens = StringUtils::Split(scan_title_str, '.');
+ bool success = false;
+ //make sure we have enough tokens and that the last token is dta.
+ if ((scan_title_tokens.size() >= 4) && (scan_title_tokens.back().find("dta") == 0)) {
+ carp(CARP_DETAILED_DEBUG, "Attempting to parse title:%s", scan_title_str.c_str());
+ size_t n = scan_title_tokens.size();
+
+ int title_charge;
+ int title_first_scan;
+ int title_last_scan;
+ //try to parse the first scan, last scan, and charge from the title, keeping track
+ //of whether we were successful.
+
+ success = StringUtils::TryFromString(scan_title_tokens[n-2], &title_charge);
+ success &= StringUtils::TryFromString(scan_title_tokens[n-3], &title_last_scan);
+ success &= StringUtils::TryFromString(scan_title_tokens[n-4], &title_first_scan);
+
+ if (success) {
+ //okay we parsed the three numbers, fill in the results.
+ carp(CARP_DETAILED_DEBUG, "Title first scan:%i", title_first_scan);
+ carp(CARP_DETAILED_DEBUG, "Title last scan:%i" , title_last_scan);
+ carp(CARP_DETAILED_DEBUG, "Title charge:%i", title_charge);
+ first_scan = title_first_scan;
+ last_scan = title_last_scan;
+ }
+ }
+ return success;
+}
+
+/**
+ * Parses all the spectra from file designated by the filename member
+ * variable.
+ * \returns True if the spectra are parsed successfully. False if otherwise.
+ */
+bool PWIZSpectrumCollection::parse() {
+
+ // spectrum_collection has already been parsed
+ if(is_parsed_) {
+ return false;
+ }
+
+ carp(CARP_DEBUG, "Using proteowizard to parse spectra.");
+
+ // todo see getFilters() below
+ // pwiz::analysis::SpectrumListFactory::wrap(*reader, spectrum_filters);
+
+ // TODO add first/last scan to base class
+ // get a list of scans to include if requested
+ string range_string = Params::GetString("scan-number");
+ int first_scan = -1;
+ int last_scan = -1;
+
+ get_range_from_string(range_string, first_scan, last_scan);
+
+ if (first_scan == -1 || last_scan == -1) {
+ carp(CARP_FATAL, "The scan number range '%s' is invalid. "
+ "Must be of the form <first>-<last>.", range_string.c_str());
+ }
+
+ // get info for translating identifiers into scan numbers
+ pwiz::msdata::CVID native_id_format =
+ pwiz::msdata::id::getDefaultNativeIDFormat(*reader_);
+
+ // look at all spectra in file
+ pwiz::msdata::SpectrumListPtr all_spectra = reader_->run.spectrumListPtr;
+
+ int num_spec = all_spectra->size();
+ carp(CARP_DEBUG, "PWIZ:Number of spectra:%i", num_spec);
+ bool assign_new_scans = false;
+ int scan_counter = 0;
+ for (int spec_idx = 0; spec_idx < num_spec; spec_idx++) {
+ carp(CARP_DETAILED_DEBUG, "Parsing spectrum index %d.", spec_idx);
+ pwiz::msdata::SpectrumPtr spectrum;
+ try {
+ spectrum = all_spectra->spectrum(spec_idx, true);
+ } catch (boost::bad_lexical_cast) {
+ carp(CARP_FATAL, "boost::bad_lexical_cast occured while parsing spectrum.\n"
+ "Do your spectra contain z-lines?");
+ }
+ // skip if no peaks or not ms2
+ if (spectrum->defaultArrayLength < 1 ||
+ spectrum->cvParam(pwiz::msdata::MS_ms_level).valueAs<int>() != 2) {
+ continue;
+ }
+
+ // check that scan number is in range
+ int scan_number_begin, scan_number_end;
+ if (!assign_new_scans) {
+ string ms_peak_list_scans = spectrum->cvParam(pwiz::msdata::MS_peak_list_scans).value;
+ string ms_spectrum_title = spectrum->cvParam(pwiz::msdata::MS_spectrum_title).value;
+ carp(CARP_DETAILED_DEBUG, "ms_peak_list_scans:%s", ms_peak_list_scans.c_str());
+ carp(CARP_DETAILED_DEBUG, "ms_spectrum_title:%s", ms_spectrum_title.c_str());
+ if (ms_peak_list_scans.empty() || !get_first_last_scan_from_string(ms_peak_list_scans, scan_number_begin, scan_number_end)) {
+ if (ms_spectrum_title.empty() || !parseFirstLastScanFromTitle(ms_spectrum_title, scan_number_begin, scan_number_end)) {
+ string scan_value = pwiz::msdata::id::translateNativeIDToScanNumber(
+ native_id_format, spectrum->id);
+ carp(CARP_DETAILED_DEBUG, "scan_value:%s", scan_value.c_str());
+ if (scan_value.empty() || !get_range_from_string<int>(
+ scan_value.c_str(), scan_number_begin, scan_number_end)) {
+ assign_new_scans = true;
+ carp(CARP_ERROR, "Proteowizard parser could not determine scan numbers "
+ "for this file, assigning new scan numbers.");
+ } else {
+ carp(CARP_DETAILED_DEBUG, "found scan:%i-%i from native id", scan_number_begin, scan_number_end);
+ }
+ } else {
+ carp(CARP_DETAILED_DEBUG, "found scan:%i-%i from ms_spectrum_title", scan_number_begin, scan_number_end);
+ }
+ } else {
+ carp(CARP_DETAILED_DEBUG, "found scan:%i-%i from ms_peak_list_scans", scan_number_begin, scan_number_end);
+ }
+ if (scan_number_begin == 0) {
+ // PWiz assigns scan numbers starting from 0 if they are missing. In this case, we re-assign starting from 1 below.
+ carp_once(CARP_INFO, "Parser could not determine scan numbers for this "
+ "file, using ordinal numbers as scan numbers.");
+ assign_new_scans = true;
+ }
+ }
+ if (assign_new_scans) {
+ carp_once(CARP_WARNING,
+ "Proteowizard parser could not determine scan numbers "
+ "for this file. Assigning new scan numbers.");
+ scan_number_begin = ++scan_counter;
+ scan_number_end = scan_number_begin;
+ }
+ carp(CARP_DETAILED_DEBUG, "found scan:%i %i-%i", scan_number_begin, first_scan, last_scan);
+ if( scan_number_end < first_scan ) {
+ continue;
+ } else if( scan_number_begin > last_scan ) {
+ break;
+ }
+
+ Crux::Spectrum* crux_spectrum = new Crux::Spectrum();
+ if (crux_spectrum->parsePwizSpecInfo(spectrum, scan_number_begin, scan_number_end)) {
+ addSpectrumToEnd(crux_spectrum);
+ } else {
+ delete crux_spectrum;
+ }
+ }
+
+ is_parsed_ = true;
+
+ return true;
+}
+
+/**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan. Removes any existing information in
+ * the given spectrum.
+ * \returns True if the spectrum was allocated, false on error.
+ */
+bool PWIZSpectrumCollection::getSpectrum(
+ int first_scan, ///< The first scan of the spectrum to retrieve -in
+ Crux::Spectrum* spectrum ///< Put the spectrum info here
+ ) {
+ parse();
+ return SpectrumCollection::getSpectrum(first_scan, spectrum);
+}
+
+/**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan.
+ * \returns The spectrum data from file or NULL.
+ */
+Crux::Spectrum* PWIZSpectrumCollection::getSpectrum(
+ int first_scan ///< The first scan of the spectrum to retrieve -in
+ ) {
+
+ parse();
+ return SpectrumCollection::getSpectrum(first_scan);
+}
+
+/*
+void getFilters() {
+ // select only the MS2 level spectra and only those in the given scan range
+ ostringstream string_builder;
+ vector<string> spectrum_filters;
+ spectrum_filters.push_back("msLevel 2");
+
+ string_builder << "scanNumber [";
+ string_builder << first_scan_;
+ string_builder << ",";
+ string_builder << last_scan_;
+ string_buildter << "]";
+ spectrum_filters.push_back(string_builder.c_str());
+ // where filters include scan range, ms2 only
+}
+*/
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/PWIZSpectrumCollection.h b/src/io/PWIZSpectrumCollection.h
new file mode 100644
index 0000000..0c7d86b
--- /dev/null
+++ b/src/io/PWIZSpectrumCollection.h
@@ -0,0 +1,82 @@
+/**
+ * \file PWIZSpectrumCollection.h
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: 21 April 2011
+ * \brief Class for accessing spectra using the proteoewizard library.
+ */
+#ifndef PWIZ_SPECTRUM_COLLECTION_H
+#define PWIZ_SPECTRUM_COLLECTION_H
+
+#include "SpectrumCollection.h"
+
+#include "pwiz/data/msdata/MSDataFile.hpp"
+
+/**
+ * \class SpectrumCollection
+ * \brief An abstract class for accessing spectra from a file.
+ */
+class PWIZSpectrumCollection : public Crux::SpectrumCollection {
+
+ protected:
+ pwiz::msdata::MSDataFile* reader_;
+
+ /**
+ * Parses the first/last scan from the title
+ * \returns whether parse was successful.
+ * For MGF files that place their scan numbers in the title string
+ */
+ bool parseFirstLastScanFromTitle(
+ std::string& scan_title_str, ///< title string to parse -in
+ int& first_scan, ///< first scan -out
+ int& last_scan ///< last scan -out
+ );
+
+ public:
+ /**
+ * Constructor sets filename and initializes member variables.
+ */
+ PWIZSpectrumCollection(
+ const std::string& filename ///< The spectrum collection filename. -in
+ );
+
+ /**
+ * Default Constructor
+ */
+ virtual ~PWIZSpectrumCollection();
+
+ /**
+ * Parses all the spectra from file designated by the filename member
+ * variable.
+ * \returns TRUE if the spectra are parsed successfully. FALSE if otherwise.
+ */
+ virtual bool parse();
+
+ /**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan.
+ * \returns The newly allocated Spectrum or NULL if scan number not found.
+ */
+ virtual Crux::Spectrum* getSpectrum(
+ int first_scan ///< The first scan of the spectrum to retrieve -in
+ );
+
+ /**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan. Removes any existing information in the
+ * given spectrum.
+ * \returns True if the spectrum was allocated, false on error.
+ */
+ virtual bool getSpectrum(
+ int first_scan, ///< The first scan of the spectrum to retrieve -in
+ Crux::Spectrum* spectrum ///< Put the spectrum info here
+ );
+
+};
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/PepXMLReader.cpp b/src/io/PepXMLReader.cpp
new file mode 100644
index 0000000..3cb0b9f
--- /dev/null
+++ b/src/io/PepXMLReader.cpp
@@ -0,0 +1,606 @@
+/*************************************************************************
+ * \file PepXMLReader.cpp
+ * \brief Object for parsing pepxml files
+ *************************************************************************/
+
+#include "expat.h"
+#include "PepXMLReader.h"
+#include "util/mass.h"
+#include "util/AminoAcidUtil.h"
+#include "util/MathUtil.h"
+#include "model/Protein.h"
+#include "model/PostProcessProtein.h"
+#include "model/Peptide.h"
+#include "DelimitedFile.h"
+#include "parameter.h"
+#include "MatchCollectionParser.h"
+
+#include <cstdio>
+#include <cstring>
+#include <iostream>
+
+using namespace std;
+using namespace Crux;
+
+void open_handler(void *data, const char *el, const char **attr) {
+ PepXMLReader* reader = (PepXMLReader*)data;
+ if (strcmp(el, "aminoacid_modification") == 0) {
+ reader->aminoacidModificationOpen(attr);
+ } else if (strcmp(el, "spectrum_query") == 0) {
+ reader->spectrumQueryOpen(attr);
+ } else if (strcmp(el, "search_result") == 0) {
+ reader->searchResultOpen();
+ } else if (strcmp(el, "search_hit") == 0) {
+ reader->searchHitOpen(attr);
+ } else if (strcmp(el, "mod_aminoacid_mass") == 0) {
+ reader->modAminoAcidMassOpen(attr);
+ } else if (strcmp(el, "alternative_protein") == 0) {
+ reader->alternativeProteinOpen(attr);
+ } else if (strcmp(el, "search_score") == 0) {
+ reader->searchScoreOpen(attr);
+ } else if (strcmp(el, "peptideprophet_result") == 0) {
+ reader->peptideProphetResultOpen(attr);
+ } else {
+ carp(CARP_DEBUG, "Unsupported open tag:%s", el);
+ }
+}
+
+void close_handler(void *data, const char *el) {
+ PepXMLReader* reader = (PepXMLReader*)data;
+ if (strcmp(el, "aminoacid_modification") == 0) {
+ reader->aminoacidModificationClose();
+ } else if (strcmp(el, "spectrum_query") == 0) {
+ reader->spectrumQueryClose();
+ } else if (strcmp(el, "search_result") == 0) {
+ reader->searchResultClose();
+ } else if (strcmp(el, "search_hit") == 0) {
+ reader->searchHitClose();
+ } else if (strcmp(el, "mod_aminoacid_mass") == 0) {
+ reader->modAminoAcidMassClose();
+ } else if (strcmp(el, "alternative_protein") == 0) {
+ reader->alternativeProteinClose();
+ } else if (strcmp(el, "search_score") == 0) {
+ reader->searchScoreClose();
+ } else if (strcmp(el, "peptideprophet_result") == 0) {
+ reader->peptideProphetResultClose();
+ } else {
+ carp(CARP_DEBUG, "Unsupported close tag:%s", el);
+ }
+} /* End of end handler */
+
+/**
+ * Initializes the object
+ */
+void PepXMLReader::init() {
+ aminoacid_modification_open_ = false;
+ spectrum_query_open_ = false;
+ search_result_open_ = false;
+ search_hit_open_ = false;
+ alternative_protein_open_ = false;
+ search_score_open_ = false;
+ peptideprophet_result_open_ = false;
+
+ current_spectrum_ = NULL;
+}
+
+/**
+ * \returns an initialized object
+ */
+PepXMLReader::PepXMLReader() : PSMReader() {
+ init();
+}
+
+/**
+ * \returns an object initialized with the file_path
+ */
+PepXMLReader::PepXMLReader(
+ const string& file_path ///< the path of the pep.xml file
+ ) : PSMReader(file_path) {
+ init();
+}
+
+/**
+ * \returns an object initialized with the xml path, and the target,decoy databases
+ */
+PepXMLReader::PepXMLReader(
+ const string& file_path, ///< the path of the pep.xml
+ Database* database, ///< the protein database
+ Database* decoy_database ///< the decoy protein database (can be null)
+ ) : PSMReader(file_path, database, decoy_database) {
+ init();
+}
+
+/**
+ * default destructor
+ */
+PepXMLReader::~PepXMLReader() {
+}
+
+/**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+MatchCollection* PepXMLReader::parse() {
+ FILE* file_ptr = fopen(file_path_.c_str(), "r");
+ if (file_ptr == NULL) {
+ carp(CARP_FATAL, "Opening %s or reading failed", file_path_.c_str());
+ }
+
+ XML_Parser xml_parser = XML_ParserCreate(NULL);
+
+ if (!xml_parser) {
+ carp(CARP_FATAL, "Couldn't allocate memory for parser");
+ }
+
+ current_match_collection_ = new MatchCollection();
+ current_match_collection_->preparePostProcess();
+ XML_SetUserData(xml_parser, this);
+ XML_SetElementHandler(xml_parser, open_handler, close_handler);
+
+ int done = 0;
+ while (!done) {
+ char buf[8192];
+ int len = fread(buf, 1, sizeof(buf), file_ptr);
+ if (ferror(stdin)) {
+ carp(CARP_FATAL, "Read error");
+ }
+ done = feof(file_ptr);
+ if (!XML_Parse(xml_parser, buf, len, done)) {
+ carp(CARP_FATAL, "Parse error at line %d:\n%s\n",
+ (int)XML_GetCurrentLineNumber(xml_parser),
+ XML_ErrorString(XML_GetErrorCode(xml_parser)));
+ }
+ }
+ fclose(file_ptr);
+ return current_match_collection_;
+}
+
+void PepXMLReader::aminoacidModificationOpen(const char** attr) {
+ if (aminoacid_modification_open_) {
+ carp(CARP_FATAL, "aminoacid_modification not closed before another was opened!");
+ }
+ aminoacid_modification_open_ = true;
+
+ ModPosition pos = ANY;
+ char aa = '\0';
+ double mass = 0, dMass = 0;
+ bool variable = false;
+ char symbol = '\0';
+
+ for (int i = 0; attr[i]; i += 2) {
+ if (strcmp(attr[i], "aminoacid") == 0) {
+ aa = attr[i + 1][0];
+ } else if (strcmp(attr[i], "mass") == 0) {
+ mass = atof(attr[i + 1]);
+ } else if (strcmp(attr[i], "massdiff") == 0) {
+ dMass = atof(attr[i + 1]);
+ } else if (strcmp(attr[i], "variable") == 0) {
+ variable = strcmp(attr[i + 1], "Y") == 0;
+ } else if (strcmp(attr[i], "peptide_terminus") == 0) {
+ // TODO: is this protein terminus?
+ if (strcmp(attr[i + 1], "n") == 0) {
+ pos = PEPTIDE_N;
+ } else if (strcmp(attr[i + 1], "c") == 0) {
+ pos = PEPTIDE_C;
+ } else if (strcmp(attr[i + 1], "nc") == 0) {
+ //pos = PEPTIDE_NC; TODO
+ }
+ } else if (strcmp(attr[i], "symbol") == 0) {
+ symbol = attr[i + 1][0];
+ }
+ }
+
+ ModificationDefinition::New(string(1, aa), dMass, pos, !variable);
+}
+
+void PepXMLReader::aminoacidModificationClose() {
+ aminoacid_modification_open_ = false;
+}
+
+/**
+ * Handles the spectrum_query open tag event
+ */
+void PepXMLReader::spectrumQueryOpen(
+ const char** attr ///< attribute array for element
+ ) {
+ if (spectrum_query_open_) {
+ carp(CARP_FATAL, "spectrum_query not closed before another was opened!");
+ }
+ spectrum_query_open_ = true;
+
+ int first_scan = -1;
+ int last_scan = -1;
+ double precursor_mass = -1;
+ int charge = -1;
+
+ for (int i = 0; attr[i]; i += 2) {
+ if (strcmp(attr[i], "start_scan") == 0) {
+ first_scan = atoi(attr[i+1]);
+ } else if (strcmp(attr[i], "end_scan") == 0) {
+ last_scan = atoi(attr[i+1]);
+ } else if (strcmp(attr[i], "precursor_neutral_mass") == 0) {
+ precursor_mass = atof(attr[i+1]);
+ } else if (strcmp(attr[i], "assumed_charge") == 0) {
+ charge = atoi(attr[i+1]);
+ }
+ }
+
+ double precursor_mz = (precursor_mass + (MASS_PROTON * (double) charge)) / (double)charge;
+ vector<int> charge_vec;
+ charge_vec.push_back(charge);
+ current_spectrum_ = new Crux::Spectrum(first_scan, last_scan, precursor_mz, charge_vec, "");
+ current_zstate_.setNeutralMass(precursor_mass, charge);
+}
+
+/**
+ * Handles the spectrum_query close tag event
+ */
+void PepXMLReader::spectrumQueryClose() {
+ spectrum_query_open_ = false;
+}
+
+/**
+ * Handles the search_result open tag event
+ */
+void PepXMLReader::searchResultOpen() {
+ if (search_result_open_) {
+ carp(CARP_FATAL, "search_result not closed before another opened!");
+ }
+ search_result_open_ = true;
+}
+
+/**
+ * Handles the search_result close tag event
+ */
+void PepXMLReader::searchResultClose() {
+ search_result_open_ = false;
+}
+
+/**
+ * /returns the start position of the peptide sequence within the protein
+ */
+int PepXMLReader::findStart(
+ Protein* protein, ///< the protein to find the sequence
+ string peptide_sequence, ///< the peptide sequence to find
+ string prev_aa, ///< the amino acid before the sequence in the protein
+ string next_aa ///< the next amino acid after the sequence in the protein
+ ) {
+ if (protein->getSequencePointer() == NULL) {
+ return -1;
+ }
+ int case_ = -1;
+ int ans = -1;
+
+ if (prev_aa == "-") {
+ case_ = 0;
+ ans = 1;
+ } else if (next_aa == "-") {
+ case_ = 1;
+ ans = protein->getLength() - peptide_sequence.length() + 1;
+ } else {
+ //use the flanking amino acids to further constrain our search in the sequence
+ size_t pos = string::npos;
+ string seq = prev_aa + peptide_sequence + next_aa;
+ string protein_seq = protein->getSequencePointer();
+ pos = protein_seq.find(seq);
+ if (pos == string::npos) {
+ carp(CARP_DEBUG, "could not find %s in protein %s\n%s", seq.c_str(), protein->getIdPointer().c_str(), protein_seq.c_str());
+ //finding the sequence with the flanks failed, try finding without the flanks.
+ seq = peptide_sequence;
+ pos = protein_seq.find(seq);
+ if (pos == string::npos) {
+ carp(CARP_FATAL, "could not find %s in protein %s\n%s",
+ seq.c_str(), protein->getIdPointer().c_str(), protein_seq.c_str());
+ }
+ case_ = 2;
+ ans = (pos+1);
+ } else {
+ case_ = 3;
+ ans = pos+2;
+ }
+ }
+
+ return ans;
+}
+
+/**
+ * Handles the search_hit open tag event
+ */
+void PepXMLReader::searchHitOpen(
+ const char** attr ///< atttribute array for element
+ ) {
+ if (search_hit_open_) {
+ carp(CARP_FATAL, "Search Hit not closed before another open!");
+ }
+ search_hit_open_ = true;
+ int hit_rank = -1;
+ string protein_string, prev_aa, next_aa;
+ unsigned by_ions_matched = 0;
+ unsigned by_ions_total = 0;
+ unsigned current_num_matches = 0;
+
+ for (int i = 0; attr[i]; i += 2) {
+ if (strcmp(attr[i], "hit_rank") == 0) {
+ hit_rank = atoi(attr[i+1]);
+ } else if (strcmp(attr[i], "peptide") == 0) {
+ current_peptide_sequence_ = attr[i+1];
+ } else if (strcmp(attr[i], "protein") == 0) {
+ protein_string = attr[i+1];
+ } else if (strcmp(attr[i], "num_tot_proteins") == 0) {
+ ; // do nothing.
+ } else if (strcmp(attr[i], "num_matched_ions") == 0) {
+ current_match_collection_->setScoredType(BY_IONS_MATCHED, true);
+ by_ions_matched = atoi(attr[i+1]);
+ } else if (strcmp(attr[i], "tot_num_ions") == 0) {
+ current_match_collection_->setScoredType(BY_IONS_TOTAL, true);
+ by_ions_total = atoi(attr[i+1]);
+ } else if (strcmp(attr[i], "peptide_prev_aa") == 0) {
+ prev_aa = attr[i+1];
+ } else if (strcmp(attr[i], "peptide_next_aa") == 0) {
+ next_aa = attr[i+1];
+ } else if (strcmp(attr[i], "num_matched_peptides") == 0) {
+ current_num_matches = atoi(attr[i+1]);
+ }
+ }
+
+ unsigned char length = current_peptide_sequence_.length();
+ bool is_decoy;
+
+ Protein* protein =
+ MatchCollectionParser::getProtein(database_, decoy_database_, protein_string, is_decoy);
+ int start_idx = protein->findStart(current_peptide_sequence_, prev_aa, next_aa);
+ Peptide* peptide = new Crux::Peptide(length, protein, start_idx);
+
+ current_match_ = new Match(peptide, current_spectrum_, current_zstate_, is_decoy);
+ if (is_decoy) {
+ current_match_->setNullPeptide(true);
+ }
+
+ if ((hit_rank > 0) && (current_match_->getRank(XCORR) == 0)) {
+ current_match_->setRank(XCORR, hit_rank);
+ }
+ if (by_ions_total > 0) {
+ current_match_->setScore(BY_IONS_MATCHED, by_ions_matched);
+ current_match_->setScore(BY_IONS_TOTAL, by_ions_total);
+ }
+
+ if (current_num_matches > 0) {
+ current_match_->setLnExperimentSize(logf(current_num_matches));
+ current_match_collection_->setHasDistinctMatches(true);
+ } else {
+ current_match_->setLnExperimentSize(0);
+ }
+}
+
+/**
+ * Handles the search_hit close tag event
+ */
+void PepXMLReader::searchHitClose() {
+ search_hit_open_ = false;
+ //We should have all the information needed to add the match object.
+ current_match_collection_->addMatch(current_match_);
+}
+
+/**
+ * Handles the mod_aminoacid_mass open tag event
+ */
+void PepXMLReader::modAminoAcidMassOpen(
+ const char** attr ///< attribute array for element
+ ) {
+ mod_aminoacid_mass_open_ = true;
+ int position = -1;
+ FLOAT_T mod_mass = 0;
+ bool have_mod_mass = false;
+
+ for (int idx = 0; attr[idx]; idx += 2) {
+ if (strcmp(attr[idx], "position") == 0) {
+ position = atoi(attr[idx+1]);
+ } else if (strcmp(attr[idx], "mass") == 0) {
+ mod_mass = atof(attr[idx+1]);
+ have_mod_mass = true;
+ }
+ }
+
+ if (position > 0 && have_mod_mass) {
+ char* seq = current_match_->getPeptide()->getSequence();
+ ModPosition mod_position = ANY;
+ if (position <= 1) {
+ mod_position = PEPTIDE_N;
+ } else if (position >= strlen(seq)) {
+ mod_position = PEPTIDE_C;
+ }
+ char aa = seq[position - 1];
+ free(seq);
+ double staticDeltaMass = ModificationDefinition::DeltaMass(aa, mod_position);
+ mod_mass -= staticDeltaMass;
+ // mass includes amino acid mass, subtract it
+ mod_mass -= AminoAcidUtil::GetMass(aa, Params::GetString("isotopic-mass") == "mono");
+ if (MathUtil::Round(mod_mass, Params::GetInt("mod-precision")) != 0.0) {
+ // look for a variable mod with this mass
+ const ModificationDefinition* mod = ModificationDefinition::Find(mod_mass, false);
+ if (mod == NULL) {
+ // no variable mod with this mass, try finding a static one
+ mod = ModificationDefinition::Find(staticDeltaMass, true);
+ }
+ if (mod != NULL) {
+ if (!mod->Static()) {
+ current_match_->getPeptide()->addMod(mod, position - 1);
+ }
+ } else {
+ // mod was not defined at top of file, add it as a variable modification
+ mod_mass = MathUtil::Round(mod_mass, Params::GetInt("mod-precision"));
+ mod = ModificationDefinition::NewVarMod(string(1, aa), mod_mass, UNKNOWN);
+ current_match_->getPeptide()->addMod(mod, position - 1);
+ }
+ }
+ } else {
+ carp(CARP_WARNING, "mod_aminoacid_mass error");
+ }
+}
+
+/**
+ * Handles the mod_aminoacid_mass close tag event
+ */
+void PepXMLReader::modAminoAcidMassClose() {
+ mod_aminoacid_mass_open_ = false;
+}
+
+/**
+ * Handles the alternative_protein open tag event
+ */
+void PepXMLReader::alternativeProteinOpen(
+ const char** attr ///< atttribute array for element
+ ) {
+ alternative_protein_open_ = true;
+
+ string protein_string;
+ string prev_aa;
+ string next_aa;
+
+ for (int i = 0; attr[i]; i += 2) {
+ if (strcmp(attr[i], "protein") == 0) {
+ protein_string = attr[i+1];
+ } else if (strcmp(attr[i], "peptide_prev_aa") == 0) {
+ prev_aa = attr[i+1];
+ } else if (strcmp(attr[i], "peptide_next_aa") == 0) {
+ next_aa = attr[i+1];
+ }
+ }
+
+ bool is_decoy;
+
+ Protein* protein =
+ MatchCollectionParser::getProtein(database_, decoy_database_, protein_string, is_decoy);
+ if (is_decoy) {
+ current_match_->setNullPeptide(true);
+ }
+ int start_idx = protein->findStart(current_peptide_sequence_, prev_aa, next_aa);
+
+ PeptideSrc* src = new PeptideSrc(INVALID_DIGEST, protein, start_idx);
+ current_match_->getPeptide()->addPeptideSrc(src);
+}
+
+/**
+ * Handles the alternative_protein close tag event
+ */
+void PepXMLReader::alternativeProteinClose() {
+ alternative_protein_open_ = false;
+}
+
+/**
+ * Handles the search_score open tag event
+ */
+void PepXMLReader::searchScoreOpen(
+ const char** attr ///< attribute array for element
+ ) {
+ search_score_open_ = true;
+ string name;
+ double value = 0.0;
+
+ for (int i = 0; attr[i]; i += 2) {
+ if (strcmp(attr[i], "name") == 0) {
+ name = attr[i+1];
+ } else if (strcmp(attr[i], "value") == 0) {
+ value = atof(attr[i+1]);
+ }
+ }
+
+ if (name == "xcorr_score" || name == "xcorr") {
+ current_match_collection_->setScoredType(XCORR, true);
+ current_match_->setScore(XCORR, value);
+ } else if (name == "xcorr_rank") {
+ current_match_->setRank(XCORR, value);
+ } else if (name == "expect") {
+ current_match_->setScore(EVALUE, value);
+ } else if (name == "delta_cn" || name == "deltacn") {
+ current_match_->setScore(DELTA_CN, value);
+ } else if (name == "sp" || name == "spscore") {
+ current_match_collection_->setScoredType(SP, true);
+ current_match_->setScore(SP, value);
+ } else if (name == "sp_rank" || name == "sprank") {
+ current_match_->setRank(SP, value);
+ } else if (name == "percolator_score") {
+ current_match_collection_->setScoredType(PERCOLATOR_SCORE, true);
+ current_match_->setScore(PERCOLATOR_SCORE, value);
+ } else if (name == "percolator_qvalue") {
+ current_match_collection_->setScoredType(PERCOLATOR_QVALUE, true);
+ current_match_->setScore(PERCOLATOR_QVALUE, value);
+ } else if (name == "percolator_PEP") {
+ current_match_collection_->setScoredType(PERCOLATOR_PEP, true);
+ current_match_->setScore(PERCOLATOR_PEP, value);
+ } else if (name == "qranker_score") {
+ current_match_collection_->setScoredType(QRANKER_SCORE, true);
+ current_match_->setScore(QRANKER_SCORE, value);
+ } else if (name == "qranker_qvalue") {
+ current_match_collection_->setScoredType(QRANKER_QVALUE, true);
+ current_match_->setScore(QRANKER_QVALUE, value);
+ } else if (name == "qranker_PEP") {
+ current_match_collection_->setScoredType(QRANKER_PEP, true);
+ current_match_->setScore(QRANKER_PEP, value);
+ }
+ //set the custom score
+ current_match_->setCustomScore(name, value);
+}
+
+/**
+ * Handles the search_score close tag event
+ */
+void PepXMLReader::searchScoreClose() {
+ search_score_open_ = false;
+}
+
+/**
+ * Handles the peptideprophet_result open tag event
+ */
+void PepXMLReader::peptideProphetResultOpen(
+ const char** attr ///< attribute array for element
+ ) {
+ if (peptideprophet_result_open_) {
+ carp(CARP_FATAL, "peptideprophet_result_open_ before close!");
+ }
+
+ peptideprophet_result_open_ = true;
+
+ FLOAT_T probability = 0;
+ bool probability_parsed = false;
+ for (int idx = 0; attr[idx]; idx += 2) {
+ if (strcmp(attr[idx], "probability") == 0) {
+ probability = atof(attr[idx+1]);
+ probability_parsed = true;
+ }
+ }
+
+ //Place the peptideprophet probability score as a custom score.
+ if (probability_parsed) {
+ current_match_->setCustomScore("peptideprophet", probability);
+ } else {
+ carp_once(CARP_WARNING, "Couldn't parse probability from peptideprophet_result");
+ }
+}
+
+/**
+ * Handles the peptideprophet_result close tag event
+ */
+void PepXMLReader::peptideProphetResultClose() {
+ peptideprophet_result_open_ = false;
+}
+
+/**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+MatchCollection* PepXMLReader::parse(
+ const string& file_path, ///< path of the xml file
+ Database* database, ///< target protein database
+ Database* decoy_database ///< decoy protein database (can be null)
+ ) {
+ PepXMLReader reader(file_path);
+ reader.setDatabase(database);
+ reader.setDecoyDatabase(decoy_database);
+ return reader.parse();
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/PepXMLReader.h b/src/io/PepXMLReader.h
new file mode 100644
index 0000000..b43bc65
--- /dev/null
+++ b/src/io/PepXMLReader.h
@@ -0,0 +1,198 @@
+/**
+ * \file PepXMLReader.h
+ * $Revision: 1.00 $
+ * DATE: July 11th, 2012
+ * AUTHOR: Sean McIlwain
+ * \brief Object for reading pep.xml. This object will read a pepxml file,
+ * creating a matchcollection object. Use the expat library in MSToolkit.
+ *
+ **************************************************************************/
+
+#ifndef PEPXMLREADER_H
+#define PEPXMLREADER_H
+#include <string>
+#include <vector>
+
+#include "PSMReader.h"
+#include "model/Spectrum.h"
+#include "model/Match.h"
+#include "model/MatchCollection.h"
+
+class PepXMLReader : public PSMReader {
+
+ protected:
+
+ SpectrumZState current_zstate_; ///< keeps track of the current zstate
+ Crux::Spectrum* current_spectrum_; ///< Keeps track of the current spectrum object
+ Crux::Match* current_match_; ///< keeps track of the current match object
+ std::string current_peptide_sequence_; ///< keeps track of the current peptide sequence
+ MatchCollection* current_match_collection_; ///< keeps track of the current match collection object
+
+ /*State variable for element tags */
+ bool aminoacid_modification_open_;
+ bool spectrum_query_open_; ///< are we within a spectrum_query?
+ bool search_result_open_; ///< are we within a search_result element
+ bool search_hit_open_; ///< are we within a search
+ bool mod_aminoacid_mass_open_; ///< are we within a mod_aminoacid_mass element?
+ bool alternative_protein_open_; ///< are we within a alternative_protein element
+ bool search_score_open_; ///< are we within a search_score element
+ bool peptideprophet_result_open_; ///< are we within a peptideprophet_result element?
+
+ /**
+ * /returns the start position of the peptide sequence within the protein
+ */
+ int findStart(
+ Crux::Protein* protein, ///< the protein to find the sequence
+ std::string peptide_sequence, ///< the peptide sequence to find
+ std::string prev_aa, ///< the amino acid before the sequence in the protein
+ std::string next_aa ///< the next amino acid after the sequence in the protein
+ );
+
+ /* Specific element tag handler functions */
+
+ void aminoacidModificationOpen(const char** attr);
+ void aminoacidModificationClose();
+
+ /**
+ * Handles the spectrum_query open tag event
+ */
+ void spectrumQueryOpen(
+ const char** attr ///< attribute array for element
+ );
+
+ /**
+ * Handles the spectrum_query close tag event
+ */
+ void spectrumQueryClose();
+
+ /**
+ * Handles the search_result open tag event
+ */
+ void searchResultOpen();
+
+ /**
+ * Handles the search_result close tag event
+ */
+ void searchResultClose();
+
+ /**
+ * Handles the search_hit open tag event
+ */
+ void searchHitOpen(
+ const char** attr ///< atttribute array for element
+ );
+
+ /**
+ * Handles the search_hit close tag event
+ */
+ void searchHitClose();
+
+ /**
+ * Handles the mod_aminoacid_mass open tag event
+ */
+ void modAminoAcidMassOpen(
+ const char** attr ///< attribute array for element
+ );
+
+ /**
+ * Handles the mod_aminoacid_mass close tag event
+ */
+ void modAminoAcidMassClose();
+
+ /**
+ * Handles the alternative_protein open tag event
+ */
+ void alternativeProteinOpen(
+ const char** attr ///< attribute array for element
+ );
+
+ /**
+ * Handles the alternative_protein close tag event
+ */
+ void alternativeProteinClose();
+
+ /**
+ * Handles the search_score open tag event
+ */
+ void searchScoreOpen(const char** attr);
+
+ /**
+ * Handles the search_score close tag event
+ */
+ void searchScoreClose();
+
+ /**
+ * Handles the peptideprophet_result open tag event
+ */
+ void peptideProphetResultOpen(
+ const char** attr ///< attribute array for element
+ );
+
+ /**
+ * Handles the peptideprophet_result close tag event
+ */
+ void peptideProphetResultClose();
+
+ /**
+ * Initializes the object
+ */
+ void init();
+
+
+ public:
+
+ /**
+ * \returns an initialized object
+ */
+ PepXMLReader();
+
+
+ /**
+ * \returns an object initialized with the file_path
+ */
+ PepXMLReader(
+ const std::string& file_path_ ///< the path of the pep.xml file
+ );
+
+ /**
+ * \returns an object initialized with the xml path, and the target,decoy databases
+ */
+ PepXMLReader(
+ const std::string& file_path_, ///< the path of the pep.xml
+ Database* database, ///< the protein database
+ Database* decoy_database = NULL ///< the decoy protein database (can be null)
+ );
+
+ /**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+ MatchCollection* parse();
+
+ /**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+ static MatchCollection* parse(
+ const std::string& path, ///< path of the xml file
+ Database* database, ///< target protein database
+ Database* decoy_database ///< decoy protein database (can be null)
+ );
+
+
+ /*open/close handlers*/
+ friend void open_handler(void* data, const char* element, const char** attr);
+ friend void close_handler(void* data, const char* el);
+
+ /**
+ * default destructor
+ */
+ virtual ~PepXMLReader();
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/PepXMLWriter.cpp b/src/io/PepXMLWriter.cpp
new file mode 100644
index 0000000..3e47a74
--- /dev/null
+++ b/src/io/PepXMLWriter.cpp
@@ -0,0 +1,463 @@
+/**
+ * \file PepXMLWriter.cpp
+ * \brief Writes search results in the TPP-compliant .pep.xml format.
+ */
+#include <iostream>
+#include "PepXMLWriter.h"
+#include "util/AminoAcidUtil.h"
+#include "util/crux-utils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "model/MatchCollection.h"
+
+using namespace std;
+
+PepXMLWriter::PepXMLWriter():
+ file_(NULL), current_index_(1), mass_precision_(Params::GetInt("mass-precision")),
+ enzyme_(get_enzyme_type_parameter("enzyme")),
+ precision_(Params::GetInt("precision")) {
+}
+
+PepXMLWriter::~PepXMLWriter() {
+ closeFile();
+}
+
+/**
+ * Open a file of the given name. Replace an existing file if
+ * overwrite is true, else exit if an existing file is found.
+ */
+void PepXMLWriter::openFile(const char* filename, bool overwrite) {
+ file_ = create_file_in_path(filename, "", overwrite);
+}
+
+/**
+ * Close the file, if open.
+ */
+void PepXMLWriter::closeFile() {
+ if (file_) {
+ fclose(file_);
+ file_ = NULL;
+ }
+}
+
+/**
+ * Write all of the elements that preceed the spectrum_query
+ * elements.
+ * Requires OpenFile has been called without CloseFile.
+ */
+void PepXMLWriter::writeHeader() {
+ MatchCollection::printXmlHeader(file_, "");
+}
+
+/**
+ * Close the msms_run_summaryand msms_pipeline_analysis tags.
+ * Requires OpenFile has been called without CloseFile.
+ */
+void PepXMLWriter::writeFooter() {
+ closeSpectrumElement();
+ MatchCollection::printXmlFooter(file_);
+}
+
+/**
+ * Write the details for a PSM to be contained in a spectrum_query
+ * element.
+ * Begins with the <spectrum_query> element if spectrum_scan_number is
+ * different than in the last writePSM() call. Writes one
+ * <search_hit> in the list of <search_elements>. To add more
+ * <search_hits>, call writePSM() again with the same spectrum_scan_number
+ *
+ * Requires that the arrays pre_aas, post_aas,
+ * protein_names, protein_descriptions are all num_proteins long.
+ * Assumes scores is NUMBER_SCORER_TYPES long.
+ * Requires OpenFile has been called without CloseFile.
+ */
+void PepXMLWriter::writePSM(
+ int spectrum_scan_number, ///< identifier for the spectrum
+ const char* filename, ///< file the spectrum came from
+ double spectrum_neutral_mass, ///< computed mass of the spectrum at this charge state
+ int charge, ///< assumed charge state for the match
+ int* PSM_ranks, ///< rank of this peptide for the spectrum
+ const char* unmodified_peptide_sequence, ///< sequence with no mods
+ const char* modified_peptide_sequence, ///< either with symbols or masses
+ double peptide_mass, ///< mass of the peptide sequence
+ int num_proteins, ///< proteins matched to this peptide
+ const char* flanking_aas, ///< "XY, AB, " X and Y are the preceeding and
+ /// following aas in the first protein
+ vector<string>& protein_names, ///<
+ vector<string>& protein_descriptions, ///<
+ bool* scores_computed,
+ double* scores, ///< indexed by score type
+ unsigned cur_num_matches
+) {
+ string spectrum_title = getSpectrumTitle(spectrum_scan_number, filename, charge);
+ //cerr<<"by_ion_fraction_matched: "<<by_ion_fraction_matched<<endl;
+ // close the last spec element if this is a new spectrum and not the first
+ if (!last_spectrum_printed_.empty() && last_spectrum_printed_ != spectrum_title) {
+ closeSpectrumElement();
+ }
+
+ // print the spec info if this is a new spectrum
+ if (last_spectrum_printed_ != spectrum_title) {
+ printSpectrumElement(spectrum_scan_number, spectrum_title.c_str(),
+ spectrum_neutral_mass, charge);
+ last_spectrum_printed_ = spectrum_title;
+ }
+ // else, just add to the search_result list
+ //cerr<<"3.LnExperimentSize: "<<current_ln_experiment_size<<endl;
+ printPeptideElement(PSM_ranks,
+ unmodified_peptide_sequence,
+ modified_peptide_sequence,
+ peptide_mass,
+ spectrum_neutral_mass,
+ num_proteins,
+ flanking_aas,
+ protein_names,
+ protein_descriptions,
+ scores_computed,
+ scores,
+ cur_num_matches);
+}
+
+/**
+ * Write the <spectrum_query> element and the <search_result> tag.
+ */
+void PepXMLWriter::printSpectrumElement(int spectrum_scan_number,
+ const char* spectrum_title,
+ double spectrum_neutral_mass,
+ int charge) {
+ fprintf(file_, " <spectrum_query spectrum=\"%s\" start_scan=\"%i\""
+ " end_scan=\"%i\" precursor_neutral_mass=\"%.*f\""
+ " assumed_charge=\"%i\" index=\"%i\">\n"
+ " <search_result>\n",
+ spectrum_title,
+ spectrum_scan_number,
+ spectrum_scan_number,
+ Params::GetInt("mass-precision"),
+ spectrum_neutral_mass,
+ charge,
+ current_index_++);
+}
+
+string PepXMLWriter::getSpectrumTitle(int spectrum_scan_number,
+ const char* filename,
+ int charge) {
+ string formatted(filename);
+ if (StringUtils::IEndsWith(formatted, ".pid")) {
+ // Remove bullseye extension if it exists
+ formatted.erase(formatted.length() - 4);
+ }
+ std::ostringstream spectrum_id;
+ spectrum_id << formatted << "." << std::setw(5) << std::setfill('0')
+ << spectrum_scan_number << "." << std::setw(5)
+ << std::setfill('0') << spectrum_scan_number << "." << charge;
+ return spectrum_id.str();
+}
+
+void PepXMLWriter::closeSpectrumElement() {
+ fprintf(file_, " </search_result>\n </spectrum_query>\n");
+}
+
+/**
+ * Print everything between the <search_hit> tags for this match
+ */
+void PepXMLWriter::printPeptideElement(int *ranks,
+ const char* peptide_sequence,
+ const char* modified_peptide_sequence,
+ double peptide_mass,
+ double spectrum_mass,
+ int num_proteins,
+ const char* flanking_aas,
+ vector<string>& protein_names,
+ vector<string>& protein_descriptions,
+ bool* scores_computed,
+ double* scores,
+ unsigned current_num_matches
+) {
+ // get values
+ char flanking_aas_prev = flanking_aas[0];
+ char flanking_aas_next = flanking_aas[1];
+ string protein_id = (!protein_names.empty()) ? protein_names.front() : "";
+ string protein_annotation = (!protein_descriptions.empty()) ?
+ protein_descriptions.front() : "";
+ int num_tol_term = get_num_terminal_cleavage(peptide_sequence,
+ flanking_aas_prev,
+ flanking_aas_next,
+ enzyme_);
+ int num_missed_cleavages = get_num_internal_cleavage(peptide_sequence,
+ enzyme_);
+
+ // print <search_hit> tag
+ fprintf(file_, " <search_hit hit_rank=\"%i\" peptide=\"%s\" "
+ "peptide_prev_aa=\"%c\" peptide_next_aa=\"%c\" protein=\"%s\" "
+ "num_tot_proteins=\"%i\" ",
+ ranks[XCORR], // -1 if unavailable, uses xcorr rank otherwise
+ peptide_sequence,
+ flanking_aas_prev,
+ flanking_aas_next,
+ protein_id.c_str(),
+ num_proteins);
+ if (scores_computed[BY_IONS_MATCHED]) {
+ fprintf(file_, "num_matched_ions=\"%i\" ", (unsigned)scores[BY_IONS_MATCHED]);
+ }
+ if (scores_computed[BY_IONS_TOTAL]) {
+ fprintf(file_, "tot_num_ions=\"%i\" ", (unsigned)scores[BY_IONS_TOTAL]);
+ }
+
+ if (flanking_aas_prev != 'X' && flanking_aas_next != 'X') {
+ fprintf(file_, "calc_neutral_pep_mass=\"%.*f\" "
+ "massdiff=\"%+.*f\" "
+ "num_tol_term=\"%i\" num_missed_cleavages=\"%i\" "
+ "num_matched_peptides=\"%i\""
+ " is_rejected=\"%i\" ",
+ mass_precision_,
+ peptide_mass,
+ mass_precision_,
+ spectrum_mass - peptide_mass,
+ num_tol_term,
+ num_missed_cleavages,
+ current_num_matches,
+ 0);
+ } else {
+ fprintf(file_, "calc_neutral_pep_mass=\"%.*f\" "
+ "massdiff=\"%+.*f\" "
+ "num_tol_term=\"\" num_missed_cleavages=\"%i\" "
+ "num_matched_peptides=\"%i\""
+ " is_rejected=\"%i\" ",
+ mass_precision_,
+ peptide_mass,
+ mass_precision_,
+ spectrum_mass - peptide_mass,
+ num_missed_cleavages,
+ current_num_matches,
+ 0);
+ }
+
+ fprintf(file_, "protein_descr=\"%s\">\n", protein_annotation.c_str());
+
+ // print additonal proteins
+ for(int prot_idx = 1; prot_idx < num_proteins; prot_idx++) {
+ int flank_idx = strlen("XX,") * prot_idx;
+ flanking_aas_prev = flanking_aas[flank_idx];
+ flanking_aas_next = flanking_aas[flank_idx + 1];
+ num_tol_term = get_num_terminal_cleavage(peptide_sequence,
+ flanking_aas_prev,
+ flanking_aas_next,
+ enzyme_);
+ protein_id = protein_names[prot_idx];
+ protein_annotation = protein_descriptions[prot_idx];
+ fprintf(file_,
+ " <alternative_protein protein=\"%s\" "
+ "protein_descr=\"%s\" "
+ "num_tol_term=\"%i\" peptide_prev_aa=\"%c\" "
+ "peptide_next_aa=\"%c\"/> \n",
+ protein_id.c_str(),
+ protein_annotation.c_str(),
+ num_tol_term,
+ flanking_aas_prev,
+ flanking_aas_next);
+ }
+
+ // print modifications
+ print_modifications_xml(modified_peptide_sequence, peptide_sequence, file_);
+
+ // print scores
+ printScores(scores, scores_computed, ranks);
+
+ // print post-search (analysis) fields
+ printAnalysis(scores, scores_computed);
+
+ // close the search_hit tag
+ fprintf(file_, " </search_hit>\n");
+}
+
+void PepXMLWriter::printScores(
+ double* scores,
+ bool* scores_computed,
+ int* ranks
+) {
+ string ranks_to_string[2] = {"sprank", "xcorr_rank"};
+ for (int i = 0; i < NUMBER_SCORER_TYPES; i++) {
+ if (i == BY_IONS_MATCHED || i == BY_IONS_TOTAL) {
+ continue;
+ }
+ if (scores_computed[i]) {
+ fprintf(file_, " <search_score name=\"%s\" value=\"%.*f\" />\n",
+ scorer_type_to_string((SCORER_TYPE_T)i), precision_, scores[i]);
+ if (i < 2) {
+ fprintf(file_, " <search_score name=\"%s\" value=\"%i\" />\n",
+ ranks_to_string[i].c_str(), ranks[i]);
+ }
+ }
+ }
+}
+
+
+void PepXMLWriter::printAnalysis(double* scores,
+ bool* scores_computed) {
+ // only write the analysis_result section for post-search psms
+ bool post_search = false;
+ if( scores_computed[PERCOLATOR_SCORE]
+ || scores_computed[QRANKER_SCORE]
+ || scores_computed[DECOY_XCORR_QVALUE]
+ || scores_computed[LOGP_QVALUE_WEIBULL_XCORR] ) {
+ post_search = true;
+ }
+
+ if( !post_search ) {
+ return;
+ }
+
+ SCORER_TYPE_T score = INVALID_SCORER_TYPE;
+ SCORER_TYPE_T qval = INVALID_SCORER_TYPE;
+ SCORER_TYPE_T pep = INVALID_SCORER_TYPE;
+ string score_name;
+
+ if (scores_computed[PERCOLATOR_SCORE]) {
+ score = PERCOLATOR_SCORE;
+ qval = PERCOLATOR_QVALUE;
+ pep = PERCOLATOR_PEP;
+ score_name = "percolator_score";
+ } else if (scores_computed[QRANKER_SCORE]) {
+ score = QRANKER_SCORE;
+ qval = QRANKER_QVALUE;
+ pep = QRANKER_PEP;
+ score_name = "q-ranker_score";
+ } else if (scores_computed[LOGP_QVALUE_WEIBULL_XCORR]) {
+ qval = LOGP_QVALUE_WEIBULL_XCORR;
+ pep = LOGP_WEIBULL_PEP;
+ }
+
+ fprintf(file_, "<analysis_result analysis=\"peptideprophet\">\n");
+ fprintf(file_, "<peptideprophet_result probability=\"%.*f\">\n",
+ precision_, (1 - scores[pep]));
+ fprintf(file_, "<search_score_summary>\n");
+ if (!score_name.empty()) {
+ fprintf(file_, "<parameter name=\"%s\" value=\"%.*f\"/>\n",
+ score_name.c_str(), precision_, scores[score]);
+ }
+ fprintf(file_, "<parameter name=\"%s\" value=\"%.*f\"/>\n",
+ "qvalue", precision_, scores[qval]);
+ fprintf(file_, "<parameter name=\"%s\" value=\"%.*f\"/>\n",
+ "pep", precision_, scores[pep]);
+ fprintf(file_, "</search_score_summary>\n");
+ fprintf(file_, "</peptideprophet_result>\n");
+ fprintf(file_, "</analysis_result>\n");
+}
+
+/**
+ * \brief prints both variable and static modifications for
+ * peptide sequence in xml format to the specificed output file
+ */
+void PepXMLWriter::print_modifications_xml(
+ const char* mod_seq,
+ const char* pep_seq,
+ FILE* output_file
+) {
+ carp(CARP_DEBUG, "print_modifications_xml:%s %s", mod_seq, pep_seq);
+ // variable modifications
+ int mod_precision = Params::GetInt("mod-precision");
+ map<int, double> var_mods = find_variable_modifications(mod_seq);
+ if (!var_mods.empty()) {
+ fprintf(output_file, "<modification_info modified_peptide=\"%s\">\n", mod_seq);
+ for (map<int, double>::iterator it = var_mods.begin(); it != var_mods.end(); ++it) {
+ fprintf(output_file, "<mod_aminoacid_mass position=\"%i\" mass=\"%.*f\"/>\n",
+ it->first, //index
+ mod_precision, it->second); //mass
+ }
+ fprintf(output_file, "</modification_info>\n");
+ }
+
+ // static modifications
+ map<int, double> static_mods = find_static_modifications(pep_seq);
+ if (!static_mods.empty()) {
+ carp(CARP_DEBUG, "<modification_info modified_peptide=\"%s\">", pep_seq);
+ fprintf(output_file, "<modification_info modified_peptide=\"%s\">\n", pep_seq);
+ for (map<int, double>::iterator it = static_mods.begin(); it != static_mods.end(); ++it) {
+ fprintf(output_file, "<mod_aminoacid_mass position=\"%i\" mass=\"%.*f\"/>\n",
+ it->first, //index
+ mod_precision, it->second); //mass
+ }
+ fprintf(output_file, "</modification_info>\n");
+ }
+}
+
+/**
+ * \brief takes an empty mapping of index to mass
+ * and extract information from mod sequence fill
+ * up map
+ */
+map<int, double> PepXMLWriter::find_variable_modifications(const char* mod_seq) {
+ bool monoisotopic = get_mass_type_parameter("isotopic-mass") != AVERAGE;
+ map<int, double> mods;
+ int seq_index = 1;
+ const char* amino = mod_seq;
+ const char* end = NULL;
+ const char* start = NULL;
+ // Parse returned string to find modifications within brackets
+ while (*(amino) != '\0' && *(amino+1) != '\0') {
+ if (*(amino+1) =='[') {
+ start = amino+2;
+ end = amino+2;
+ while (*end != ']') {
+ end++;
+ }
+ char* mass = (char*)mymalloc(sizeof(char)*(end-start+1));
+ strncpy(mass, start, end-start);
+ mass[end-start] = '\0';
+ mods[seq_index] = atof(mass) + AminoAcidUtil::GetMass(*amino, monoisotopic);
+ amino = end;
+ free(mass);
+ } else if (*(amino+1) < 'A' || *(amino+1) > 'Z') { // a mod symbol
+ double mass = 0; // sum up all adjacent symbols
+ end = amino + 1;
+ while( *end < 'A' || *end > 'Z' ) {
+ mass += get_mod_mass_from_symbol(*end);
+ end++;
+ }
+ mods[seq_index] = mass + AminoAcidUtil::GetMass(*amino, monoisotopic);
+ }
+ seq_index++;
+ amino++;
+ }
+ return mods;
+}
+
+/**
+ * \brief takes an empty mapping of index to mass
+ * of static mods and a full mapping of var mods
+ * to fill up the mapping of static mods
+ */
+map<int, double> PepXMLWriter::find_static_modifications(
+ const char* peptide_sequence
+) {
+ map<int, double> static_mods;
+ const char* seq_iter = peptide_sequence;
+ MASS_TYPE_T isotopic_type = get_mass_type_parameter("isotopic-mass");
+ for (size_t i = 0; peptide_sequence[i] != '\0'; i++) {
+ char aa = peptide_sequence[i];
+ double sum = AminoAcidUtil::GetMass(aa, isotopic_type == MONO);
+ int modCount = 0;
+ vector<const ModificationDefinition*> staticMods = ModificationDefinition::StaticMods(aa);
+ for (vector<const ModificationDefinition*>::const_iterator j = staticMods.begin();
+ j != staticMods.end();
+ j++) {
+ if ((*j)->Position() == ANY ||
+ ((*j)->Position() == PEPTIDE_N && i == 0) ||
+ ((*j)->Position() == PEPTIDE_C && peptide_sequence[i + 1] == '\0')) {
+ ++modCount;
+ sum += (*j)->DeltaMass();
+ }
+ }
+ if (modCount > 0) {
+ static_mods[i + 1] = sum;
+ }
+ }
+ return static_mods;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/PepXMLWriter.h b/src/io/PepXMLWriter.h
new file mode 100644
index 0000000..9220a0c
--- /dev/null
+++ b/src/io/PepXMLWriter.h
@@ -0,0 +1,139 @@
+/**
+ * \file PepXMLWriter.h
+ * \brief Writes search results in the TPP-compliant .pep.xml format.
+ */
+#ifndef PEPXMLWRITER_H
+#define PEPXMLWRITER_H
+
+#include <string>
+#include <vector>
+#include "model/objects.h"
+
+class PepXMLWriter {
+
+ public:
+ PepXMLWriter();
+ ~PepXMLWriter();
+
+ /**
+ * Open a file of the given name. Replace an existing file if
+ * overwrite is true, else exit if an existing file is found.
+ */
+ void openFile(const char* filename, bool overwrite);
+
+ /**
+ * Close the file, if open.
+ */
+ void closeFile();
+
+ /**
+ * Write all of the elements that preceed the spectrum_query
+ * elements.
+ * Requires OpenFile has been called without CloseFile.
+ */
+ void writeHeader();
+
+ /**
+ * Close the msms_run_summaryand msms_pipeline_analysis tags.
+ * Requires OpenFile has been called without CloseFile.
+ */
+ void writeFooter();
+
+ /**
+ * Write the details for a PSM to be contained in a spectrum_query
+ * element. Requires that the arrays pre_aas, post_aas,
+ * protein_names, protein_descriptions are all num_proteins long.
+ * Assumes scores is NUMBER_SCORER_TYPES long.
+ * Requires OpenFile has been called without CloseFile.
+ */
+ void writePSM(
+ int spectrum_scan_number, ///< identifier for the spectrum
+ const char* filename, ///< file that spectrum came from
+ double spectrum_neutral_mass, ///< computed mass of the spectrum
+ ///at this charge state
+ int charge, ///< assumed charge state for the match
+ int* PSM_rank, ///< rank of this peptide for the spectrum
+ const char* unmodified_peptide_sequence, ///< sequence with no mods
+ const char* modified_peptide_sequence, ///< either with symbols or masses
+ double peptide_mass, ///< mass of the peptide sequence
+ int num_proteins, ///< proteins matched to this peptide
+ const char* flanking, ///< "XY, AB, " X and Y are the preceeding and
+ /// following aas in the first protein
+ std::vector<std::string>& protein_names, ///<
+ std::vector<std::string>& protein_descriptions, ///<
+ bool* scores_computed,
+ double* scores, ///< indexed by score type
+ unsigned current_num_matches
+ );
+
+ protected:
+ void initScoreNames();
+ void printSpectrumElement(int spectrum_scan_number,
+ const char* filename,
+ double spectrum_neutral_mass,
+ int charge);
+ void closeSpectrumElement();
+ std::string getSpectrumTitle(int spectrum_scan_number,
+ const char* filename,
+ int charge);
+ void printPeptideElement(int* rank,
+ const char* peptide_sequence,
+ const char* mod_peptide_sequence,
+ double peptide_mass,
+ double spectrum_mass,
+ int num_proteins,
+ const char* flanking_aas,
+ std::vector<std::string>& protein_names,
+ std::vector<std::string>& protein_descriptions,
+ bool* scores_computed,
+ double* scores,
+ unsigned current_num_matches);
+
+ void printScores(
+ double* scores,
+ bool* scores_computed,
+ int* ranks
+ );
+
+ void printAnalysis(double* scores, bool* scores_computed);
+
+ /**
+ * \brief prints both variable and static modifications for
+ * peptide sequence
+ */
+ void print_modifications_xml(const char* mod_seq, const char* sequence, FILE* output_file);
+
+ /**
+ * \brief takes an empty mapping of index to mass
+ * of static mods and a full mapping of var mods
+ * to fill up the mapping of static mods
+ */
+ std::map<int, double> find_static_modifications(
+ const char* sequence
+ );
+
+ /**
+ * \brief takes an empty mapping of index to mass
+ * and extract information from mod sequence fill
+ * up map
+ */
+ std::map<int, double> find_variable_modifications(const char* mod_seq);
+
+ std::string filename_;
+ FILE* file_;
+ std::string last_spectrum_printed_;
+ int current_index_;
+ int mass_precision_;
+ ENZYME_T enzyme_;
+ int precision_;
+};
+
+#endif // PEPXMLWRITER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/PinWriter.cpp b/src/io/PinWriter.cpp
new file mode 100644
index 0000000..1a4bec7
--- /dev/null
+++ b/src/io/PinWriter.cpp
@@ -0,0 +1,295 @@
+/**
+ * \file PinWriter.cpp
+ * \brief Writes search results in the .pin format.
+ */
+#include <iostream>
+#include "PinWriter.h"
+#include "model/MatchCollection.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+#include "MatchCollectionParser.h"
+#include <cctype>
+#include <cstdio>
+#include <cstring>
+#include <sstream>
+#include <vector>
+#include "model/Spectrum.h"
+#include "SQTReader.h"
+#include "model/SpectrumZState.h"
+#include <fstream>
+#include <limits>
+#include <boost/filesystem.hpp>
+#include "util/Params.h"
+#include "util/FileUtils.h"
+#include "util/StringUtils.h"
+#include "MassHandler.h"
+#include <boost/foreach.hpp>
+
+using namespace std;
+using namespace Crux;
+
+#define MAX_LOG_P 100.0 // Needed for handling p-value = 0, which should not happen, but alas does.
+
+PinWriter::PinWriter():
+ out_(NULL),
+ enzyme_(get_enzyme_type_parameter("enzyme")),
+ precision_(Params::GetInt("precision")),
+ mass_precision_(Params::GetInt("mass-precision")) {
+
+ features_.push_back(make_pair("SpecId", true));
+ features_.push_back(make_pair("Label", true));
+ features_.push_back(make_pair("ScanNr", true));
+ features_.push_back(make_pair("ExpMass", true));
+ features_.push_back(make_pair("CalcMass", true));
+ features_.push_back(make_pair("lnrSp", false));
+ features_.push_back(make_pair("deltLCn", true));
+ features_.push_back(make_pair("deltCn", true));
+ features_.push_back(make_pair("XCorr", true));
+ features_.push_back(make_pair("Sp", false));
+ features_.push_back(make_pair("IonFrac", false));
+ features_.push_back(make_pair("RefactoredXCorr", false));
+ features_.push_back(make_pair("NegLog10PValue", false));
+ features_.push_back(make_pair("PepLen", true));
+ for (int i = '1'; i <= '9'; i++) {
+ features_.push_back(make_pair("Charge" + string(1, i), false));
+ }
+ features_.push_back(make_pair("enzN", true));
+ features_.push_back(make_pair("enzC", true));
+ features_.push_back(make_pair("enzInt", true));
+ features_.push_back(make_pair("lnNumSP", true));
+ features_.push_back(make_pair("lnNumDSP", false));
+ features_.push_back(make_pair("dM", true));
+ features_.push_back(make_pair("absdM", true));
+ features_.push_back(make_pair("Peptide", true));
+ features_.push_back(make_pair("Proteins", true));
+}
+
+PinWriter::~PinWriter() {
+ closeFile();
+}
+
+/**
+ * Open a file of the given name. Replace an existing file if
+ * overwrite is true, else exit if an existing file is found.
+ */
+void PinWriter::openFile(const string& filename, const string& output_dir, bool overwrite) {
+ if (!(out_ = create_stream_in_path(filename.c_str(), output_dir.c_str(), overwrite))) {
+ carp(CARP_FATAL, "Can't open file '%s'", filename.c_str());
+ }
+}
+
+void PinWriter::openFile(CruxApplication* application, string filename, MATCH_FILE_TYPE type) {
+ openFile(filename, "", Params::GetBool("overwrite"));
+}
+
+bool PinWriter::getEnabledStatus(const string& name) const {
+ for (vector< pair<string, bool> >::const_iterator i = features_.begin(); i != features_.end(); i++) {
+ if (i->first == name) {
+ return i->second;
+ }
+ }
+ return false;
+}
+
+void PinWriter::setEnabledStatus(const string& name, bool enabled) {
+ IsFeature finder(name);
+ vector< pair<string, bool> >::iterator i =
+ find_if(features_.begin(), features_.end(), finder);
+ if (i != features_.end()) {
+ i->second = enabled;
+ } else {
+ carp(CARP_WARNING, "setEnabledStatus: feature '%s' not found", name.c_str());
+ }
+}
+
+/**
+ * Close the file, if open.
+ */
+void PinWriter::closeFile() {
+ if (out_) {
+ delete out_;
+ out_ = NULL;
+ }
+}
+
+void PinWriter::write(
+ MatchCollection* target_collection,
+ const vector<MatchCollection*>& decoys,
+ int top_rank
+) {
+ vector<MatchCollection*> collections(1, target_collection);
+ collections.insert(collections.end(), decoys.begin(), decoys.end());
+ for (vector<MatchCollection*>::iterator i = collections.begin();
+ i != collections.end();
+ i++) {
+ MatchIterator match_iterator(*i);
+ while (match_iterator.hasNext()) {
+ Match* match = match_iterator.next();
+ if (match->getRank(XCORR) <= top_rank) {
+ printPSM(match);
+ }
+ }
+ }
+}
+
+void PinWriter::write(MatchCollection* collection, string database) {
+ bool sp = collection->getScoredType(SP);
+ bool xcorr = collection->getScoredType(XCORR);
+ bool exact_p = collection->getScoredType(TIDE_SEARCH_REFACTORED_XCORR);
+ setEnabledStatus("lnrSp", sp);
+ setEnabledStatus("deltLCn", collection->getScoredType(DELTA_LCN));
+ setEnabledStatus("deltCn", collection->getScoredType(DELTA_CN));
+ setEnabledStatus("XCorr", xcorr);
+ setEnabledStatus("Sp", sp);
+ setEnabledStatus("IonFrac", sp);
+ setEnabledStatus("RefactoredXCorr", exact_p);
+ setEnabledStatus("NegLog10PValue", exact_p);
+
+ int max_charge = 0;
+ for (MatchIterator i = MatchIterator(collection); i.hasNext();) {
+ max_charge = max(i.next()->getCharge(), max_charge);
+ }
+ for (int i = 1; i <= max_charge; i++) {
+ setEnabledStatus("Charge" + StringUtils::ToString(i), true);
+ }
+
+ vector<MatchCollection*> decoyvec;
+ int top_match = Params::GetInt("top-match");
+ printHeader();
+ write(collection, decoyvec, top_match); // TODO: When top match is greater than default (5) in a given PSM File?
+}
+
+bool PinWriter::isInfinite(FLOAT_T x) {
+ return x == numeric_limits<FLOAT_T>::infinity() || -x == numeric_limits<FLOAT_T>::infinity();
+}
+
+void PinWriter::printHeader() {
+ enabledFeatures_.clear();
+ FeatureCopy copier(&enabledFeatures_);
+ for_each(features_.begin(), features_.end(), copier);
+
+ for (vector< pair<string, bool> >::const_iterator i = features_.begin();
+ i != features_.end();
+ i++) {
+ carp(CARP_DEBUG, "PIN feature: '%s'%s",
+ i->first.c_str(), !i->second ? " (disabled)" : "");
+ }
+ *out_ << StringUtils::Join(enabledFeatures_, '\t') << endl;
+}
+
+void PinWriter::printPSM(
+ Match* match
+) {
+ Peptide* peptide = match->getPeptide();
+ Spectrum* spectrum = match->getSpectrum();
+ int charge = match->getCharge();
+ bool enzC = false;
+ bool enzN = false;
+ double obsMass = match->getZState().getSinglyChargedMass();
+ FLOAT_T calcMass = peptide->calcModifiedMass() + MASS_PROTON;
+ FLOAT_T dM = MassHandler::massDiff(obsMass, calcMass, charge);
+
+ const char* sequence = peptide->getSequence();
+ int missedCleavages = get_num_internal_cleavage(sequence, enzyme_);
+ get_terminal_cleavages(sequence, peptide->getNTermFlankingAA(),
+ peptide->getCTermFlankingAA(), enzyme_, enzN, enzC);
+
+ vector<string> fields;
+ BOOST_FOREACH(const std::string& feature, enabledFeatures_) {
+ if (feature == "SpecId") {
+ fields.push_back(getId(match, spectrum->getFirstScan()));
+ } else if (feature == "Label") {
+ fields.push_back(match->getNullPeptide() ? "-1" : "1");
+ } else if (feature == "ScanNr") {
+ fields.push_back(StringUtils::ToString(spectrum->getFirstScan()));
+ } else if (feature == "ExpMass") {
+ fields.push_back(StringUtils::ToString(obsMass, mass_precision_));
+ } else if (feature == "CalcMass") {
+ fields.push_back(StringUtils::ToString(calcMass, mass_precision_));
+ } else if (feature == "lnrSp") {
+ double sp = match->getRank(SP);
+ fields.push_back(StringUtils::ToString(sp > 0 ? log(sp) : 0, precision_));
+ } else if (feature == "deltLCn") {
+ FLOAT_T delta_lcn = match->getScore(DELTA_LCN);
+ if (isInfinite(delta_lcn) || isnan(delta_lcn)) {
+ delta_lcn = 0;
+ }
+ fields.push_back(StringUtils::ToString(delta_lcn, precision_));
+ } else if (feature == "deltCn") {
+ FLOAT_T delta_cn = match->getScore(DELTA_CN);
+ if (isInfinite(delta_cn) || isnan(delta_cn)) {
+ delta_cn = 0;
+ }
+ fields.push_back(StringUtils::ToString(delta_cn, precision_));
+ } else if (feature == "XCorr") {
+ fields.push_back(StringUtils::ToString(match->getScore(XCORR), precision_));
+ } else if (feature == "Sp") {
+ fields.push_back(StringUtils::ToString(match->getScore(SP), precision_));
+ } else if (feature == "IonFrac") {
+ FLOAT_T ionMatch = match->getScore(BY_IONS_MATCHED);
+ FLOAT_T ionTotal = match->getScore(BY_IONS_TOTAL);
+ FLOAT_T ionFrac = (ionMatch != NOT_SCORED && ionTotal != NOT_SCORED && ionTotal > 0)
+ ? ionMatch / ionTotal
+ : 0;
+ fields.push_back(StringUtils::ToString(ionFrac, precision_));
+ } else if (feature == "RefactoredXCorr") {
+ fields.push_back(
+ StringUtils::ToString(match->getScore(TIDE_SEARCH_REFACTORED_XCORR), precision_));
+ } else if (feature == "NegLog10PValue") {
+ FLOAT_T logP = -log10(match->getScore(TIDE_SEARCH_EXACT_PVAL));
+ fields.push_back(StringUtils::ToString(isInfinite(logP) ? MAX_LOG_P : logP, precision_));
+ } else if (feature == "PepLen") {
+ fields.push_back(StringUtils::ToString((unsigned) peptide->getLength()));
+ } else if (StringUtils::StartsWith(feature, "Charge")) {
+ int chargeFeature = StringUtils::FromString<int>(feature.substr(6));
+ fields.push_back(charge == chargeFeature ? "1" : "0");
+ } else if (feature == "enzN") {
+ fields.push_back(enzN ? "1" : "0");
+ } else if (feature == "enzC") {
+ fields.push_back(enzC ? "1" : "0");
+ } else if (feature == "enzInt") {
+ fields.push_back(StringUtils::ToString(missedCleavages));
+ } else if (feature == "lnNumSP" || feature == "lnNumDSP") {
+ fields.push_back(StringUtils::ToString(match->getLnExperimentSize(), precision_));
+ } else if (feature == "dM") {
+ fields.push_back(StringUtils::ToString(dM, precision_));
+ } else if (feature == "absdM") {
+ fields.push_back(StringUtils::ToString(fabs(dM), precision_));
+ } else if (feature == "Peptide") {
+ fields.push_back(getPeptide(peptide));
+ } else if (feature == "Proteins") {
+ fields.push_back(StringUtils::Join(peptide->getProteinIds(), '\t'));
+ } else {
+ carp(CARP_FATAL, "Unknown feature: '%s'", feature.c_str());
+ }
+ }
+ *out_ << StringUtils::Join(fields, '\t') << endl;
+}
+
+string PinWriter::getPeptide(Peptide* pep) {
+ stringstream sequence;
+ sequence << pep->getNTermFlankingAA() << '.'
+ << (Params::GetBool("mod-symbols")
+ ? pep->getModifiedSequenceWithSymbols()
+ : pep->getModifiedSequenceWithMasses())
+ << '.' << pep->getCTermFlankingAA();
+ return sequence.str();
+}
+
+string PinWriter::getId(Match* match, int scan_number) {
+ string prefix = Params::GetBool("filestem-prefixes")
+ ? FileUtils::Stem(match->getFilePath())
+ : "";
+
+ stringstream psm_id;
+ if (prefix.empty()) {
+ psm_id << (match->getNullPeptide() ? "decoy" : "target")
+ << '_' << match->getFileIndex();
+ } else {
+ psm_id << prefix;
+ }
+ psm_id << '_' << scan_number << '_' << match->getCharge() << '_'
+ << match->getRank(XCORR);
+ return psm_id.str();
+}
+
diff --git a/src/io/PinWriter.h b/src/io/PinWriter.h
new file mode 100644
index 0000000..4d36dcd
--- /dev/null
+++ b/src/io/PinWriter.h
@@ -0,0 +1,90 @@
+/**
+ * \file PinWriter.h
+ * \brief Writes search results in the .pin format.
+ */
+#ifndef PINWRITER_H
+#define PINWRITER_H
+
+#include <set>
+#include <string>
+#include <vector>
+#include "model/objects.h"
+#include "model/Spectrum.h"
+#include "util/mass.h"
+#include "model/Match.h"
+#include "model/MatchCollection.h"
+#include "PSMWriter.h"
+#include "model/SpectrumZState.h"
+#include "model/Spectrum.h"
+#include "model/Peptide.h"
+#include <limits>
+
+class PinWriter : public PSMWriter {
+ public:
+ PinWriter();
+ ~PinWriter();
+ explicit PinWriter(const char* output_file);
+
+ void write(
+ MatchCollection* target_collection,
+ const std::vector<MatchCollection*>& decoys,
+ int top_rank
+ );
+ // PSMWriter write
+ void write(
+ MatchCollection* collection,
+ std::string database
+ );
+
+ void printHeader();
+
+ void closeFile();
+ void openFile(
+ const std::string& filename,
+ const std::string& output_directory,
+ bool overwrite
+ );
+
+ // PSMWriter openfile version
+ void openFile(
+ CruxApplication* application, ///< application writing the file
+ std::string filename, ///< name of the file to open
+ MATCH_FILE_TYPE type ///< type of file to be written
+ );
+
+ bool getEnabledStatus(const std::string& name) const;
+ void setEnabledStatus(const std::string& name, bool enabled);
+
+ protected:
+ std::vector< std::pair<std::string, bool> > features_;
+ std::vector<std::string> enabledFeatures_;
+ std::ofstream* out_;
+ ENZYME_T enzyme_;
+ int precision_;
+ int mass_precision_;
+
+ void printPSM(Crux::Match* match);
+
+ std::string getPeptide(Crux::Peptide* pep);
+ bool isInfinite(FLOAT_T x);
+ std::string getId(Crux::Match* match, int scan_number);
+
+ struct IsFeature : public std::unary_function<const std::pair<std::string, bool>&, bool> {
+ explicit IsFeature(const std::string& name): search_(name) {}
+ bool operator() (const std::pair<std::string, bool>& check) {
+ return search_ == check.first;
+ }
+ std::string search_;
+ };
+
+ struct FeatureCopy {
+ explicit FeatureCopy(std::vector<std::string>* target): target_(target) {}
+ void operator() (const std::pair<std::string, bool>& feature) {
+ if (feature.second) target_->push_back(feature.first);
+ }
+ std::vector<std::string>* target_;
+ };
+};
+
+#endif // PINWRITER_H
+
diff --git a/src/io/SQTReader.cpp b/src/io/SQTReader.cpp
new file mode 100644
index 0000000..e579326
--- /dev/null
+++ b/src/io/SQTReader.cpp
@@ -0,0 +1,407 @@
+/*************************************************************************
+ * \file SQTReader.cpp
+ * \brief Object for parsing sqt files
+ *************************************************************************/
+
+#include <cstdio>
+#include <cstring>
+#include <iostream>
+#include <fstream>
+
+#include "parameter.h"
+#include "LineFileReader.h"
+#include "MatchCollectionParser.h"
+#include "SQTReader.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * Initializes the object
+ */
+void SQTReader::init() {
+ last_parsed_ = SQT_LINE_NONE;
+ current_spectrum_ = NULL;
+ current_match_ = NULL;
+}
+
+/**
+ * \returns an initialized object
+ */
+SQTReader::SQTReader() : PSMReader() {
+ init();
+}
+
+/**
+ * \returns an object initialized with the file_path
+ */
+SQTReader::SQTReader(
+ const string& file_path ///< the path of the pep.xml file
+ ) : PSMReader(file_path) {
+ init();
+}
+
+/**
+ * \returns an object initialized with the xml path, and the target,decoy databases
+ */
+SQTReader::SQTReader(
+ const string& file_path, ///< the path of the sqt
+ Database* database, ///< the protein database
+ Database* decoy_database ///< the decoy protein database (can be null)
+ ) : PSMReader(file_path, database, decoy_database) {
+ init();
+}
+
+/**
+ * default destructor
+ */
+SQTReader::~SQTReader() {
+}
+
+/**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+MatchCollection* SQTReader::parse() {
+ current_match_collection_ = new MatchCollection();
+ current_match_collection_->preparePostProcess();
+ current_match_collection_->setScoredType(XCORR, true);
+ current_match_collection_->setScoredType(SP, true);
+ last_parsed_ = SQT_LINE_NONE;
+
+ LineFileReader line_reader(file_path_);
+ while (line_reader.hasNext()) {
+ string line = line_reader.next();
+ if (!line.empty()) {
+ switch (line[0]) {
+ case 'H':
+ parseHeader(line);
+ break;
+ case 'S':
+ parseSpectrum(line);
+ break;
+ case 'M':
+ parseMatch(line);
+ break;
+ case 'L':
+ parseLocus(line);
+ break;
+ default:
+ carp(CARP_ERROR, "Unknown line %d\n%s", line_reader.getCurrentRow(), line.c_str());
+ }
+ }
+ }
+
+ //add the last match
+ if (current_match_ != NULL) {
+ current_match_collection_->addMatchToPostMatchCollection(current_match_);
+ }
+ return current_match_collection_;
+}
+
+
+void SQTReader::parseHeader(const string& line) {
+ last_parsed_ = SQT_LINE_HEADER;
+ string content = StringUtils::Trim(line.substr(2));
+ if (StringUtils::StartsWith(content, "StaticMod")) {
+ content = StringUtils::Trim(content.substr(10));
+ vector<string> tokens = StringUtils::Split(content, '=');
+ if (tokens.size() == 2) {
+ ModificationDefinition::NewStaticMod(
+ tokens[0], StringUtils::FromString<double>(tokens[1]), UNKNOWN /*TODO*/);
+ }
+ } else if (StringUtils::StartsWith(content, "DiffMod")) {
+ content = StringUtils::Trim(content.substr(8));
+ vector<string> tokens = StringUtils::Split(content, '=');
+ if (tokens.size() == 2) {
+ string t0 = StringUtils::Trim(tokens[0]);
+ string aminoAcids = t0.substr(0, t0.length() - 1);
+ char symbol = t0[t0.length() - 1];
+ double deltaMass = StringUtils::FromString<double>(tokens[1]);
+ ModificationDefinition::NewVarMod(
+ aminoAcids, deltaMass, UNKNOWN /*TODO*/, false, false, symbol);
+ }
+ }
+}
+
+void SQTReader::parseSpectrum(const string& line) {
+ const int spectrum_low_scan_idx = 1;
+ const int spectrum_high_scan_idx = 2;
+ const int spectrum_charge_idx = 3;
+ const int spectrum_observed_mass_idx = 6;
+ const int spectrum_total_ion_intensity_idx = 7;
+ const int spectrum_lowest_sp_idx = 8;
+ const int spectrum_num_matches_idx = 9;
+
+ vector<string> tokens = StringUtils::Split(line, '\t');
+
+ int low_scan = -1;
+ int high_scan = -1;
+ int charge = -1;
+ current_ln_experiment_size_ = 0.0;
+ for (int i = 0; i < tokens.size(); i++) {
+ switch (i) {
+ case spectrum_low_scan_idx:
+ low_scan = StringUtils::FromString<int>(tokens[i]);
+ break;
+ case spectrum_high_scan_idx:
+ high_scan = StringUtils::FromString<int>(tokens[i]);
+ break;
+ case spectrum_charge_idx:
+ charge = StringUtils::FromString<int>(tokens[i]);
+ break;
+ case spectrum_observed_mass_idx: {
+ double observed_mass = StringUtils::FromString<double>(tokens[i]);
+ current_zstate_.setSinglyChargedMass(observed_mass, charge);
+ vector<int> chargeVec(1, charge);
+ current_spectrum_ = new Spectrum(low_scan, high_scan,
+ current_zstate_.getMZ(), chargeVec, "");
+ break;
+ }
+ case spectrum_num_matches_idx: {
+ int current_num_matches = StringUtils::FromString<int>(tokens[i]);
+ if (current_num_matches > 0) {
+ current_match_collection_->setHasDistinctMatches(true);
+ current_ln_experiment_size_ = logf((FLOAT_T)current_num_matches);
+ }
+ break;
+ }
+ case spectrum_total_ion_intensity_idx:
+ if (!tokens[i].empty()) {
+ current_spectrum_->setHasTotalEnergy(true);
+ current_spectrum_->setTotalEnergy(StringUtils::FromString<double>(tokens[i]));
+ }
+ break;
+ case spectrum_lowest_sp_idx:
+ if (!tokens[i].empty()) {
+ current_spectrum_->setHasLowestSp(true);
+ current_spectrum_->setLowestSp(StringUtils::FromString<double>(tokens[i]));
+ }
+ break;
+ }
+ }
+ last_parsed_ = SQT_LINE_SPECTRUM;
+}
+
+void SQTReader::parseMatch(const string& line) {
+ const int match_xcorr_rank_idx = 1;
+ const int match_sp_rank_idx = 2;
+ const int match_calculated_mass_idx = 3;
+ const int match_delta_cn_idx = 4;
+ const int match_xcorr_idx = 5;
+ const int match_sp_idx = 6;
+ const int match_matched_ions_idx = 7;
+ const int match_expected_ions_idx = 8;
+ const int match_sequence_idx = 9;
+ const int match_validation_idx = 10;
+
+ vector<string> tokens = StringUtils::Split(line, '\t');
+
+ int xcorr_rank = StringUtils::FromString<int>(tokens[match_xcorr_rank_idx]);
+ int sp_rank = StringUtils::FromString<int>(tokens[match_sp_rank_idx]);
+ double calculated_mass = StringUtils::FromString<double>(tokens[match_calculated_mass_idx]);
+ double delta_cn = StringUtils::FromString<double>(tokens[match_delta_cn_idx]);
+ double xcorr = StringUtils::FromString<double>(tokens[match_xcorr_idx]);
+ double sp = StringUtils::FromString<double>(tokens[match_sp_idx]);
+ int matched_ions = StringUtils::FromString<int>(tokens[match_matched_ions_idx]);
+ int expected_ions = StringUtils::FromString<int>(tokens[match_expected_ions_idx]);
+
+ string sqt_sequence = tokens[match_sequence_idx];
+ vector<string> sequence_tokens = StringUtils::Split(sqt_sequence, '.');
+
+ current_prev_aa_ = sequence_tokens.front();
+ current_next_aa_ = sequence_tokens.back();
+ sequence_tokens.erase(sequence_tokens.begin());
+ sequence_tokens.pop_back();
+ current_peptide_sequence_ = StringUtils::Join(sequence_tokens, '.');
+ if (current_match_ != NULL) {
+ current_match_collection_->addMatchToPostMatchCollection(current_match_);
+ }
+
+ string unmodifiedSequence;
+ vector<Modification> mods;
+ for (size_t i = 0; i < current_peptide_sequence_.size(); i++) {
+ char c = current_peptide_sequence_[i];
+ if ('A' <= c && c <= 'Z') {
+ unmodifiedSequence.push_back(c);
+ } else {
+ const ModificationDefinition* modDef = ModificationDefinition::Find(c);
+ if (modDef != NULL) {
+ mods.push_back(Modification(modDef, (i > 0) ? i - 1 : 0));
+ } else {
+ carp(CARP_ERROR, "Unknown modification in %s: %c",
+ current_peptide_sequence_.c_str(), c);
+ }
+
+ }
+ }
+ Peptide* peptide = new Peptide(unmodifiedSequence, mods);
+ current_peptide_sequence_ = unmodifiedSequence;
+
+ current_match_ = new Match(peptide, current_spectrum_, current_zstate_, false);
+ current_match_->setScore(XCORR, xcorr);
+ current_match_->setScore(SP, sp);
+ current_match_->setScore(DELTA_CN, delta_cn);
+ current_match_->setRank(XCORR, xcorr_rank);
+ current_match_->setRank(SP, sp_rank);
+
+ current_match_->setScore(BY_IONS_MATCHED, matched_ions);
+ current_match_->setScore(BY_IONS_TOTAL, expected_ions);
+ current_match_->setLnExperimentSize(current_ln_experiment_size_);
+
+ last_parsed_ = SQT_LINE_MATCH;
+}
+
+void SQTReader::parseLocus(const string& line) {
+ const int locus_protein_id_idx = 1;
+ const int locus_protein_desc_idx = 2;
+
+ vector<string> tokens = StringUtils::Split(line, '\t');
+
+ string protein_id = tokens[locus_protein_id_idx];
+ string protein_desc = "";
+ if (tokens.size() > 2) {
+ protein_desc = tokens[locus_protein_desc_idx];
+ }
+ bool is_decoy;
+ Protein* protein =
+ MatchCollectionParser::getProtein(database_, decoy_database_, protein_id, is_decoy);
+
+ int start_idx = protein->findStart(current_peptide_sequence_, current_prev_aa_, current_next_aa_);
+ PeptideSrc* peptide_src = new PeptideSrc((DIGEST_T)0, protein, start_idx);
+ current_match_->getPeptide()->addPeptideSrc(peptide_src);
+ if (is_decoy) {
+ current_match_->setNullPeptide(true);
+ }
+
+ last_parsed_ = SQT_LINE_LOCUS;
+}
+
+/**
+ * /returns the start position of the peptide sequence within the protein
+ */
+int SQTReader::findStart(
+ Protein* protein, ///< the protein to find the sequence
+ string peptide_sequence, ///< the peptide sequence to find
+ string prev_aa, ///< the amino acid before the sequence in the protein
+ string next_aa ///< the next amino acid after the sequence in the protein
+ ) {
+ if (prev_aa == "-") {
+ return 1;
+ } else if (next_aa == "-") {
+ return protein->getLength() - peptide_sequence.length() + 1;
+ } else {
+ //use the flanking amino acids to further constrain our search in the sequence
+ size_t pos = string::npos;
+ string seq = prev_aa + peptide_sequence + next_aa;
+ string protein_seq = protein->getSequencePointer();
+ pos = protein_seq.find(seq);
+ if (pos == string::npos) {
+ carp(CARP_DEBUG, "could not find %s in protein %s\n%s", seq.c_str(), protein->getIdPointer().c_str(), protein_seq.c_str());
+ //finding the sequence with the flanks failed, try finding without the flanks.
+ seq = peptide_sequence;
+ pos = protein_seq.find(seq);
+ if (pos == string::npos) {
+ carp(CARP_FATAL, "could not %s in protein %s\n%s", seq.c_str(), protein->getIdPointer().c_str(), protein_seq.c_str());
+ }
+ return pos+1;
+ }
+ return pos+2;
+ }
+}
+
+/**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+MatchCollection* SQTReader::parse(
+ const string& file_path, ///< path of the xml file
+ Database* database, ///< target protein database
+ Database* decoy_database ///< decoy protein database (can be null)
+ ) {
+ SQTReader* reader = new SQTReader(file_path);
+ reader->setDatabase(database);
+ reader->setDecoyDatabase(decoy_database);
+ return reader->parse();
+}
+
+/**
+ * \use the modification symbols in this SQT file
+ * looks for DiffMod <residues><symbol>=<delta mass.
+ */
+void SQTReader::readSymbols(const string& file, bool append) {
+ ifstream sqt(file.c_str());
+ if (!sqt) {
+ carp(CARP_FATAL, "Could not open '%s' for reading.", file.c_str());
+ }
+
+ bool doneReset = false;
+
+ AA_MOD_T** list_of_mods;
+ int num_mods = get_all_aa_mod_list(&list_of_mods);
+
+ string line;
+ carp(CARP_DEBUG, "Reading modifications from %s", file.c_str());
+ while (std::getline(sqt, line)) {
+ size_t idx;
+ if ((idx = line.find_first_not_of(" \t")) != string::npos &&
+ line[idx] == 'H' &&
+ (idx = line.find("DiffMod", idx + 1)) != string::npos &&
+ (idx = line.find_first_of(" \t", idx + 1)) != string::npos) {
+ if (num_mods == MAX_AA_MODS) {
+ carp(CARP_FATAL, "Too many modifications in file '%s'", file.c_str());
+ }
+ if ((idx = line.find_first_not_of(" \t", idx + 1)) == string::npos) {
+ continue;
+ }
+ char residue = toupper(line[idx]);
+ if (++idx >= line.length()) {
+ continue;
+ }
+ char symbol = line[idx];
+ if ((idx = line.find('=', idx + 1)) == string::npos ||
+ idx >= line.length() - 1) {
+ continue;
+ }
+ FLOAT_T mass = StringUtils::FromString<FLOAT_T>(line.substr(idx + 1));
+
+ if (residue < 'A' || residue > 'Z') {
+ carp(CARP_FATAL, "The DiffMod residue '%c' in file '%s' is invalid",
+ residue, file.c_str());
+ }
+
+ if (!doneReset && !append) {
+ resetMods();
+ doneReset = true;
+ }
+
+ AA_MOD_T* mod = NULL;
+ for (int i = 0; i < num_mods; ++i) {
+ if (aa_mod_get_mass_change(list_of_mods[i]) == mass) {
+ mod = list_of_mods[i];
+ aa_mod_get_aa_list(mod)[residue - 'A'] = true;
+ break;
+ }
+ }
+ if (!mod) {
+ mod = new_aa_mod(num_mods);
+ aa_mod_set_mass_change(mod, mass);
+ aa_mod_set_symbol(mod, symbol);
+ aa_mod_get_aa_list(mod)[residue - 'A'] = true;
+ list_of_mods[num_mods] = mod;
+ incrementNumMods();
+ ++num_mods;
+ }
+
+ carp(CARP_DETAILED_DEBUG, "Read mod %c (symbol %c) with mass %f",
+ residue, symbol, mass);
+ }
+ }
+ carp(CARP_DEBUG, "Read %d modifications from %s", num_mods, file.c_str());
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/SQTReader.h b/src/io/SQTReader.h
new file mode 100644
index 0000000..8688609
--- /dev/null
+++ b/src/io/SQTReader.h
@@ -0,0 +1,126 @@
+/**
+ * \file SQTReader.h
+ * $Revision: 1.00 $
+ * DATE: July 11th, 2012
+ * AUTHOR: Sean McIlwain
+ * \brief Object for reading sqt. This object will read a sqt file,
+ * creating a matchcollection object.
+ *
+ **************************************************************************/
+
+#ifndef SQTREADER_H
+#define SQTREADER_H
+#include <string>
+#include <vector>
+
+#include "PSMReader.h"
+#include "model/Spectrum.h"
+#include "model/Match.h"
+#include "model/MatchCollection.h"
+
+enum SQT_LINE_T {
+ SQT_LINE_NONE,
+ SQT_LINE_HEADER,
+ SQT_LINE_SPECTRUM,
+ SQT_LINE_MATCH,
+ SQT_LINE_LOCUS
+};
+
+
+class SQTReader : public PSMReader {
+
+ protected:
+ SpectrumZState current_zstate_; ///< keeps track of the current zstate
+ Crux::Spectrum* current_spectrum_; ///< Keeps track of the current spectrum object
+ FLOAT_T current_ln_experiment_size_;
+ FLOAT_T ln_experiment_size_;
+ Crux::Match* current_match_; ///< keeps track of the current match object
+ std::string current_peptide_sequence_; ///< keeps track of the current peptide sequence
+ std::string current_prev_aa_; ///< keeps track of the current previous amino acid
+ std::string current_next_aa_; ///< keeps track of the current next amino acid
+
+ MatchCollection* current_match_collection_; ///< keeps track of the current match collection object
+
+ SQT_LINE_T last_parsed_;
+
+ /**
+ * /returns the start position of the peptide sequence within the protein
+ */
+ int findStart(
+ Crux::Protein* protein, ///< the protein to find the sequence
+ std::string peptide_sequence, ///< the peptide sequence to find
+ std::string prev_aa, ///< the amino acid before the sequence in the protein
+ std::string next_aa ///< the next amino acid after the sequence in the protein
+ );
+
+ /**
+ * Initializes the object
+ */
+ void init();
+
+ void parseHeader(const std::string& line);
+ void parseSpectrum(const std::string& line);
+ void parseMatch(const std::string& line);
+ void parseLocus(const std::string& line);
+
+ public:
+
+ /**
+ * \returns an initialized object
+ */
+ SQTReader();
+
+ /**
+ * \returns an object initialized with the file_path
+ */
+ SQTReader(
+ const std::string& file_path_ ///< the path of the pep.xml file
+ );
+
+ /**
+ * \returns an object initialized with the xml path, and the target,decoy databases
+ */
+ SQTReader(
+ const std::string& file_path_, ///< the path of the pep.xml
+ Database* database, ///< the protein database
+ Database* decoy_database = NULL ///< the decoy protein database (can be null)
+ );
+
+ /**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+ MatchCollection* parse();
+
+ /**
+ * \returns the MatchCollection resulting from the parsed xml file
+ */
+ static MatchCollection* parse(
+ const std::string& path, ///< path of the xml file
+ Database* database, ///< target protein database
+ Database* decoy_database ///< decoy protein database (can be null)
+ );
+
+ /**
+ * \use the modification symbols in this SQT file
+ * looks for DiffMod <residues><symbol>=<delta mass.
+ */
+ static void readSymbols(const std::string& file, bool append = true);
+
+ /*open/close handlers*/
+ friend void open_handler(void* data, const char* element, const char** attr);
+ friend void close_handler(void* data, const char* el);
+
+ /**
+ * default destructor
+ */
+ virtual ~SQTReader();
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/SQTWriter.cpp b/src/io/SQTWriter.cpp
new file mode 100644
index 0000000..b20c3a4
--- /dev/null
+++ b/src/io/SQTWriter.cpp
@@ -0,0 +1,239 @@
+#include "SQTWriter.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "util/GlobalParams.h"
+
+using namespace Crux;
+
+SQTWriter::SQTWriter() {
+}
+
+SQTWriter::~SQTWriter() {
+ closeFile();
+}
+
+void SQTWriter::openFile(string filename) {
+ file_ = FileUtils::GetWriteStream(filename, Params::GetBool("overwrite"));
+ if (!file_) {
+ carp(CARP_FATAL, "Error creating file '%s'.", filename.c_str());
+ }
+}
+
+void SQTWriter::closeFile() {
+ if (file_ && file_->is_open()) {
+ file_->close();
+ delete file_;
+ file_ = NULL;
+ }
+}
+
+void SQTWriter::writeHeader(
+ string database,
+ int num_proteins,
+ bool is_decoy
+) {
+ if (!file_->is_open()) {
+ return;
+ }
+
+ streamsize old_precision = file_->precision();
+
+ time_t hold_time = time(0);
+
+ MASS_TYPE_T mass_type = GlobalParams::getIsotopicMass();
+ char precursor_masses[64];
+ mass_type_to_string(mass_type, precursor_masses);
+
+ mass_type = get_mass_type_parameter("fragment-mass");
+ char fragment_masses[64];
+ mass_type_to_string(mass_type, fragment_masses);
+
+ double tol = Params::GetDouble("precursor-window");
+ double frag_mass_tol = Params::GetDouble("mz-bin-width") / 2.0;
+
+ string prelim_score_type = Params::GetString("prelim-score-type");
+ string score_type = Params::GetString("score-type");
+
+ *file_ << "H\tSQTGenerator Crux" << endl
+ << "H\tSQTGeneratorVersion 1.0" << endl
+ << "H\tComment Crux was written by..." << endl
+ << "H\tComment ref..." << endl
+ << "H\tStartTime\t" << string(ctime(&hold_time))
+ << "H\tEndTime " << endl
+ << "H\tDatabase\t" << database << endl;
+
+ if (is_decoy) {
+ *file_ << "H\tComment\tDatabase shuffled; these are decoy matches" << endl;
+ }
+
+ *file_ << "H\tDBSeqLength\t?" << endl
+ << "H\tDBLocusCount\t" << num_proteins << endl
+ << "H\tPrecursorMasses\t" << precursor_masses << endl
+ << "H\tFragmentMasses\t" << fragment_masses << endl //?????????
+ << fixed
+ << "H\tAlg-PreMasTol\t" << setprecision(1) << tol << endl
+ << "H\tAlg-FragMassTol\t" << setprecision(2) << frag_mass_tol << endl
+ << "H\tAlg-XCorrMode\t0" << endl;
+ file_->unsetf(ios_base::fixed);
+ file_->precision(old_precision);
+
+ *file_ << "H\tComment\tpreliminary algorithm " << prelim_score_type << endl
+ << "H\tComment\tfinal algorithm " << score_type << endl;
+
+ for (char aa = 'A'; aa <= 'Z'; aa++) {
+ vector<const ModificationDefinition*> staticMods = ModificationDefinition::StaticMods(aa);
+ for (vector<const ModificationDefinition*>::const_iterator i = staticMods.begin();
+ i != staticMods.end();
+ i++) {
+ *file_ << "H\tStaticMod\t" << aa << '='
+ << StringUtils::ToString((*i)->DeltaMass(), Params::GetInt("mod-precision"))
+ << endl;
+ }
+ }
+
+ // print dynamic mods, if any
+ // format DiffMod <AAs><symbol>=<mass change>
+ vector<const ModificationDefinition*> varMods = ModificationDefinition::VarMods();
+ for (vector<const ModificationDefinition*>::const_iterator i = varMods.begin();
+ i != varMods.end();
+ i++) {
+ char symbol = (*i)->Symbol();
+ *file_ << "H\tDiffMod\t" << StringUtils::Join((*i)->AminoAcids()) << symbol << "=";
+ if ((*i)->DeltaMass() >= 0) {
+ *file_ << '+';
+ }
+ *file_ << StringUtils::ToString((*i)->DeltaMass(), Params::GetInt("mod-precision"))
+ << endl;
+ switch ((*i)->Position()) {
+ case PEPTIDE_N:
+ case PROTEIN_N:
+ *file_ << "H\tComment\tMod " << symbol << " is an N-terminal modification" << endl;
+ break;
+ case PEPTIDE_C:
+ case PROTEIN_C:
+ *file_ << "H\tComment\tMod " << symbol << " is an C-terminal modification" << endl;
+ break;
+ }
+ }
+
+ *file_ << "H\tAlg-DisplayTop\t" << Params::GetInt("top-match") << endl;
+ // this is not correct for an sqt from analzyed matches
+
+ ENZYME_T enzyme = get_enzyme_type_parameter("enzyme");
+ DIGEST_T digestion = get_digest_type_parameter("digestion");
+ const char* enz_str = enzyme_type_to_string(enzyme);
+ const char* dig_str = digest_type_to_string(digestion);
+ string custom_str;
+ if (enzyme == CUSTOM_ENZYME) {
+ string rule = Params::GetString("custom-enzyme");
+ custom_str = ", custom pattern: " + rule;
+ }
+ *file_ << "H\tEnzymeSpec\t" << enz_str << "-" << dig_str << custom_str << endl;
+
+
+ *file_ << "H\tLine fields: S, scan number, scan number, "
+ << "charge, 0, server, experimental mass, total ion intensity, "
+ << "lowest Sp, number of matches" << endl
+ << "H\tLine fields: M, rank by xcorr score, rank by sp score, "
+ << "peptide mass, deltaCn, xcorr score, sp score, number ions matched, "
+ << "total ions compared, sequence, validation status" << endl;
+}
+
+void SQTWriter::writeSpectrum(
+ Spectrum* spectrum,
+ SpectrumZState& z_state,
+ int num_matches
+) {
+ if (!file_->is_open()) {
+ return;
+ }
+
+ *file_ << "S"
+ << "\t" << spectrum->getFirstScan()
+ << "\t" << spectrum->getLastScan()
+ << "\t" << z_state.getCharge()
+ << "\t0.0" // process time
+ << "\tserver"
+ << "\t"
+ << StringUtils::ToString(
+ z_state.getSinglyChargedMass(), Params::GetInt("mass-precision"))
+ << "\t";
+
+ // print total ion intensity if exists...
+ if (spectrum->hasTotalEnergy()) {
+ *file_ << StringUtils::ToString(spectrum->getTotalEnergy(), 2);
+ }
+ *file_ << "\t";
+
+ // print lowest sp if exists
+ if (spectrum->hasLowestSp()) {
+ *file_ << StringUtils::ToString(spectrum->getLowestSp(), Params::GetInt("precision"));
+ }
+ *file_ << "\t";
+
+ if (num_matches != 0) {
+ *file_ << num_matches;
+ }
+ *file_ << endl;
+
+}
+
+void SQTWriter::writePSM(
+ Peptide* peptide,
+ FLOAT_T xcorr_score,
+ int xcorr_rank,
+ FLOAT_T sp_score,
+ int sp_rank,
+ FLOAT_T delta_cn,
+ int b_y_matched,
+ int b_y_total,
+ bool is_decoy
+) {
+ if (!file_->is_open()) {
+ return;
+ }
+
+ int length = peptide->getLength();
+ MODIFIED_AA_T* mod_seq = copy_mod_aa_seq(peptide->getModifiedAASequence(), length);
+ if (!mod_seq) {
+ return;
+ }
+
+ Protein* protein = peptide->getPeptideSrc()->getParentProtein();
+ string seq_str = peptide->getSequenceSqt();
+
+ *file_ << "M"
+ << "\t" << xcorr_rank
+ << "\t" << sp_rank
+ << "\t" << StringUtils::ToString(
+ peptide->calcModifiedMass() + MASS_PROTON, Params::GetInt("mass-precision"))
+ << "\t" << StringUtils::ToString(delta_cn, 2)
+ << "\t" << StringUtils::ToString(xcorr_score, Params::GetInt("precision"))
+ << "\t" << StringUtils::ToString(sp_score, Params::GetInt("precision"))
+ << "\t" << b_y_matched
+ << "\t" << b_y_total
+ << "\t" << seq_str
+ << "\tU"
+ << endl;
+
+ for (PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter != peptide->getPeptideSrcEnd();
+ ++iter) {
+ PeptideSrc* peptide_src = *iter;
+ Protein* protein = peptide_src->getParentProtein();
+ string protein_id_str = protein->getId();
+ if (is_decoy && protein->getDatabase()->getDecoyType() == NO_DECOYS) {
+ protein_id_str = Params::GetString("decoy-prefix") + protein_id_str;
+ }
+ *file_ << "L" << "\t" << protein_id_str << endl;
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/SQTWriter.h b/src/io/SQTWriter.h
new file mode 100644
index 0000000..adfdad5
--- /dev/null
+++ b/src/io/SQTWriter.h
@@ -0,0 +1,59 @@
+#ifndef SQTWRITER_H
+#define SQTWRITER_H
+
+#include "carp.h"
+#include "parameter.h"
+#include "model/PostProcessProtein.h"
+#include "model/Spectrum.h"
+
+#include <iomanip>
+#include <string>
+
+using namespace std;
+
+class SQTWriter {
+
+ public:
+ SQTWriter();
+ ~SQTWriter();
+ void openFile(string filename);
+ void closeFile();
+
+ void writeHeader(
+ string database,
+ int num_proteins,
+ bool is_decoy = false
+ );
+
+ void writeSpectrum(
+ Crux::Spectrum* spectrum,
+ SpectrumZState& z_state,
+ int num_matches
+ );
+
+ void writePSM(
+ Crux::Peptide* peptide,
+ FLOAT_T xcorr_score,
+ int xcorr_rank,
+ FLOAT_T sp_score,
+ int sp_rank,
+ FLOAT_T delta_cn,
+ int b_y_matched,
+ int b_y_total,
+ bool is_decoy
+ );
+
+ protected:
+ ofstream* file_;
+
+};
+
+#endif // SQTWRITER_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/SpectrumCollection.cpp b/src/io/SpectrumCollection.cpp
new file mode 100644
index 0000000..655150d
--- /dev/null
+++ b/src/io/SpectrumCollection.cpp
@@ -0,0 +1,260 @@
+/**
+ * \file SpectrumCollection.cpp
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: 11 April 2011
+ * \brief Abstract class for accessing spectra from a file.
+ */
+#include "SpectrumCollection.h"
+#include "model/ProteinIndex.h"
+#include "model/Peak.h"
+#include "util/utils.h"
+#ifndef _MSC_VER
+#include "unistd.h"
+#endif
+#include "parameter.h"
+#include <cerrno>
+#include <cstring>
+#include "io/carp.h"
+#include "util/WinCrux.h"
+#include <iostream>
+
+using namespace std;
+using namespace Crux;
+
+namespace Crux {
+
+/**
+ * Instantiates a new spectrum_collection object from a filename.
+ * Resolves any relative paths. Confirms that file exists.
+ */
+SpectrumCollection::SpectrumCollection (
+ const string& filename ///< The spectrum collection filename.
+ )
+: filename_(filename), is_parsed_(false), num_charged_spectra_(0) {
+#if DARWIN
+ char path_buffer[PATH_MAX];
+ char* absolute_path_file = realpath(filename.c_str(), path_buffer);
+#else
+ char* absolute_path_file = realpath(filename.c_str(), NULL);
+#endif
+ if (absolute_path_file == NULL) {
+ carp(CARP_FATAL, "Error from spectrum file '%s'. (%s)",
+ filename.c_str(), strerror(errno));
+ }
+
+ if(access(absolute_path_file, F_OK)) {
+ carp(CARP_FATAL, "File %s could not be opened\n", absolute_path_file);
+ }
+ filename_ = absolute_path_file;
+
+#ifndef DARWIN
+ free(absolute_path_file);
+#endif
+}
+
+/**
+ * Copy constructor. Creates copies of each spectrum for the new
+ * collection.
+ */
+SpectrumCollection::SpectrumCollection(
+ SpectrumCollection& old_collection
+ ) : filename_(old_collection.filename_),
+ is_parsed_(old_collection.is_parsed_),
+ num_charged_spectra_(old_collection.num_charged_spectra_) {
+ // copy spectra
+ for (SpectrumIterator spectrum_iterator = old_collection.begin();
+ spectrum_iterator != old_collection.end();
+ ++spectrum_iterator) {
+
+ Spectrum* old_spectrum = *spectrum_iterator;
+ Spectrum* new_spectrum = new Spectrum(*old_spectrum);
+ this->addSpectrumToEnd(new_spectrum);
+ }
+}
+
+/**
+ * Default destructor
+ */
+SpectrumCollection::~SpectrumCollection() {
+
+ for (SpectrumIterator spectrum_iterator = this->begin();
+ spectrum_iterator != this->end();
+ ++spectrum_iterator) {
+ delete *spectrum_iterator;
+ }
+ spectra_.clear();
+}
+
+/**
+ * \returns the begining of the spectra deque
+ */
+SpectrumIterator SpectrumCollection::begin() {
+ return spectra_.begin();
+}
+
+/**
+ * \returns the end of the spectra deque
+ */
+SpectrumIterator SpectrumCollection::end() {
+ return spectra_.end();
+}
+
+/*
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan.
+ * \returns The newly allocated Spectrum or NULL if scan number not found.
+ */
+Spectrum* SpectrumCollection::getSpectrum(
+ int first_scan ///< The first scan of the spectrum to retrieve -in
+ ) {
+
+
+ Spectrum* spectrum = new Spectrum();
+ bool success = getSpectrum(first_scan, spectrum);
+ if (success) {
+ return spectrum;
+ } else {
+ delete spectrum;
+ return NULL;
+ }
+}
+
+/**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan. Removes any existing information in the
+ * given spectrum.
+ * \returns True if the spectrum was allocated, false on error.
+ */
+bool SpectrumCollection::getSpectrum(
+ int first_scan, ///< The first scan of the spectrum to retrieve -in
+ Spectrum* spectrum ///< Put the spectrum info here
+ ) {
+
+ for (SpectrumIterator spectrum_iterator = this->begin();
+ spectrum_iterator != this->end();
+ ++spectrum_iterator) {
+
+ if ((*spectrum_iterator)->getFirstScan() == first_scan) {
+
+ spectrum->copyFrom(*spectrum_iterator);
+ return true;
+ }
+ }
+ return false;
+
+}
+
+
+/**
+ * Adds a spectrum to the spectrum_collection.
+ * adds the spectrum to the end of the spectra array
+ * should only be used when the adding in increasing scan num order
+ * when adding in random order should use add_spectrum
+ * spectrum must be heap allocated
+ */
+void SpectrumCollection::addSpectrumToEnd(
+ Spectrum* spectrum ///< spectrum to add to spectrum_collection -in
+ ) {
+ // set spectrum
+ spectra_.push_back(spectrum);
+ num_charged_spectra_ += spectrum->getNumZStates();
+}
+
+/**
+ * Adds a spectrum to the spectrum_collection.
+ * adds the spectrum in correct order into the spectra array
+ * spectrum must be heap allocated
+ */
+void SpectrumCollection::addSpectrum(
+ Spectrum* spectrum ///< spectrum to add to spectrum_collection -in
+ ) {
+
+ unsigned int add_index = 0;
+
+ // find correct location
+ // TODO -- replace with binary search if necessary.
+ for(; add_index < spectra_.size(); ++add_index) {
+ if(spectra_[add_index]->getFirstScan() >
+ spectrum->getFirstScan()) {
+ break;
+ }
+ }
+
+ spectra_.insert(spectra_.begin()+add_index, spectrum);
+
+ num_charged_spectra_ += spectrum->getNumZStates();
+}
+
+
+// FIXME maybe a faster way? can't perform binary search since we must know the array index
+/**
+ * Removes a spectrum from the spectrum_collection.
+ */
+void SpectrumCollection::removeSpectrum(
+ Spectrum* spectrum ///< spectrum to be removed from spectrum_collection -in
+ ) {
+
+ int scan_num = spectrum->getFirstScan();
+ unsigned int spectrum_index = 0;
+
+ // find where the spectrum is located in the spectrum array
+ for(; spectrum_index < spectra_.size(); ++spectrum_index) {
+ if(scan_num == spectra_[spectrum_index]->getFirstScan() ) {
+ break;
+ }
+ }
+
+ num_charged_spectra_ -= spectrum->getNumZStates();
+
+ delete spectra_[spectrum_index];
+ spectra_[spectrum_index] = NULL;
+ spectra_.erase(spectra_.begin() + spectrum_index);
+
+}
+
+
+
+
+
+/**
+ * \returns A pointer to the name of the file from which the spectra
+ * were parsed.
+ */
+const char* SpectrumCollection::getFilename() {
+ return filename_.c_str();
+}
+
+/**
+ * \returns The current number of spectrum in the
+ * spectrum_collection. Zero if the file has not yet been parsed.
+ */
+int SpectrumCollection::getNumSpectra() {
+ return spectra_.size();
+}
+
+/**
+ * \returns The current number of spectra assuming differnt
+ * charge(i.e. one spectrum with two charge states are counted as two
+ * spectra) in the spectrum_collection. Zero if the file has not been
+ * parsed.
+ */
+int SpectrumCollection::getNumChargedSpectra() {
+ return num_charged_spectra_;
+}
+
+
+/**
+ * \returns True if the spectrum_collection file has been parsed.
+ */
+bool SpectrumCollection::getIsParsed() {
+ return is_parsed_;
+}
+
+} // namespace Crux
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/SpectrumCollection.h b/src/io/SpectrumCollection.h
new file mode 100644
index 0000000..7c97cac
--- /dev/null
+++ b/src/io/SpectrumCollection.h
@@ -0,0 +1,143 @@
+/**
+ * \file SpectrumCollection.h
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: 14 April 2011
+ * \brief An abstract class for accessing spectra from a file.
+ */
+#ifndef CRUX_SPECTRUM_COLLECTION_H
+#define CRUX_SPECTRUM_COLLECTION_H
+
+#include <stdio.h>
+#include "model/objects.h"
+#include "model/Spectrum.h"
+
+#include <deque>
+
+/**
+ * \class SpectrumCollection
+ * \brief An abstract class for accessing spectra from a file.
+ */
+namespace Crux {
+
+class SpectrumCollection {
+
+ friend class ::FilteredSpectrumChargeIterator;
+
+ protected:
+ std::deque<Crux::Spectrum*> spectra_; ///< spectra from the file
+ std::string filename_; ///< filename
+ bool is_parsed_; ///< file has been read and spectra_ populated
+ int num_charged_spectra_; ///< sum of all charge states from all spectra
+
+ /**
+ * Base class constructor is protected. Sets filename and
+ * initializes member variables.
+ */
+ SpectrumCollection(
+ const std::string& filename///< The spectrum collection filename. -in
+ );
+
+ /**
+ * Adds a spectrum to the spectrum_collection.
+ * adds the spectrum in correct order into the spectra array
+ * spectrum must be heap allocated
+ *\returns TRUE if succeed to add, else FALSE
+ */
+ void addSpectrum(
+ Crux::Spectrum* spectrum ///< spectrum to add to spectrum_collection -in
+ );
+
+ /**
+ * Adds a spectrum to the spectrum_collection.
+ * adds the spectrum to the end of the spectra array
+ * should only be used when the adding in increasing scan num order
+ * when adding in random order should use add_spectrum
+ * spectrum must be heap allocated
+ *\returns TRUE if succeed to add, else FALSE
+ */
+ void addSpectrumToEnd(
+ Crux::Spectrum* spectrum ///< spectrum to add to spectrum_collection -in
+ );
+
+ /**
+ * Removes a spectrum from the spectrum_collection.
+ */
+ void removeSpectrum(
+ Crux::Spectrum* spectrum ///< spectrum to be removed from spectrum_collection -in
+ );
+
+ public:
+
+ /**
+ * Copy constructor. Deep copy.
+ */
+ SpectrumCollection(SpectrumCollection& old_collection);
+ /**
+ * Default destructor.
+ */
+ virtual ~SpectrumCollection();
+
+ SpectrumIterator begin();
+ SpectrumIterator end();
+
+ /**
+ * Parses all the spectra from file designated by the filename member
+ * variable.
+ * \returns TRUE if the spectra are parsed successfully. FALSE if otherwise.
+ */
+ virtual bool parse() = 0;
+
+ /**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan.
+ * \returns The newly allocated Spectrum or NULL if scan number not found.
+ */
+ virtual Crux::Spectrum* getSpectrum(
+ int first_scan ///< The first scan of the spectrum to retrieve -in
+ ) = 0;
+
+ /**
+ * Parses a single spectrum from a spectrum_collection with first scan
+ * number equal to first_scan. Removes any existing information in the
+ * given spectrum.
+ * \returns True if the spectrum was allocated, false on error.
+ */
+ virtual bool getSpectrum(
+ int first_scan, ///< The first scan of the spectrum to retrieve -in
+ Crux::Spectrum* spectrum ///< Put the spectrum info here
+ ) = 0;
+
+ /**
+ * \returns A pointer to the name of the file containing these spectra.
+ */
+ const char* getFilename();
+
+ /**
+ * \returns The current number of spectrum in the
+ * spectrum_collection. Assumes it has been parsed.
+ */
+ int getNumSpectra();
+
+ /**
+ * \returns The current number of spectra assuming differnt
+ * charge(i.e. one spectrum with two charge states are counted as
+ * two spectra) in the spectrum_collection. Assumes file has been
+ * parsed.
+ */
+ int getNumChargedSpectra();
+
+ /**
+ * \returns TRUE if the spectrum_collection file has been parsed
+ */
+ bool getIsParsed();
+};
+
+} // namespace Crux
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/io/SpectrumCollectionFactory.cpp b/src/io/SpectrumCollectionFactory.cpp
new file mode 100644
index 0000000..5b53095
--- /dev/null
+++ b/src/io/SpectrumCollectionFactory.cpp
@@ -0,0 +1,46 @@
+/**
+ * \file SpectrumCollectionFactory.cpp
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: 14 June 2011
+ * \brief Return a SpectrumCollection object of the appropriate
+ * derived class.
+ */
+#include "parameter.h"
+#include "SpectrumCollectionFactory.h"
+#include "MSToolkitSpectrumCollection.h"
+#include "PWIZSpectrumCollection.h"
+#include "util/FileUtils.h"
+#include "util/Params.h"
+
+/**
+ * Instantiates a SpectrumCollection based on the extension of the
+ * given file and the use-mstoolkit and msgf options.
+ */
+Crux::SpectrumCollection* SpectrumCollectionFactory::create(const string& filename) {
+ if (!FileUtils::Exists(filename)) {
+ carp(CARP_FATAL, "The file %s does not exist. \n", filename.c_str());
+ }
+ if (FileUtils::IsDir(filename)) {
+ carp(CARP_FATAL, "Path %s is a directory. \n Please enter a spectrum filename\
+(.ms2, .mgf, or .mzXML)", filename.c_str());
+ }
+
+ string parser = Params::GetString("spectrum-parser");
+ if (parser == "pwiz") {
+ carp(CARP_DEBUG, "Using protewizard to parse spectra");
+ return new PWIZSpectrumCollection(filename);
+ } else if (parser == "mstoolkit") {
+ carp(CARP_DEBUG, "Using mstoolkit to parse spectra");
+ return new MSToolkitSpectrumCollection(filename);
+ }
+
+ carp(CARP_FATAL, "Unknown spectrum parser type");
+ return(NULL); // Avoid compiler warning.
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/SpectrumCollectionFactory.h b/src/io/SpectrumCollectionFactory.h
new file mode 100644
index 0000000..61ab5de
--- /dev/null
+++ b/src/io/SpectrumCollectionFactory.h
@@ -0,0 +1,30 @@
+/**
+ * \file SpectrumCollectionFactory.h
+ * AUTHOR: Barbara Frewen
+ * CREATE DATE: 14 June 2011
+ * \brief Return a SpectrumCollection object of the appropriate
+ * derived class.
+ */
+#ifndef SPECTRUM_COLLECTION_FACTORY_H
+#define SPECTRUM_COLLECTION_FACTORY_H
+
+#include "SpectrumCollection.h"
+
+/**
+ * Instantiates a SpectrumCollection based on the extension of the
+ * given file and the use-mstoolkit option.
+ */
+class SpectrumCollectionFactory {
+
+ public:
+ static Crux::SpectrumCollection* create(const std::string& filename);
+
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/io/SpectrumRecordWriter.cpp b/src/io/SpectrumRecordWriter.cpp
new file mode 100644
index 0000000..cbd8716
--- /dev/null
+++ b/src/io/SpectrumRecordWriter.cpp
@@ -0,0 +1,195 @@
+#include <cmath>
+#include <memory>
+#include "app/tide/records.h"
+#include "app/tide/mass_constants.h"
+
+#include "model/Peak.h"
+#include "SpectrumCollectionFactory.h"
+#include "SpectrumRecordWriter.h"
+#include "io/carp.h"
+#include "util/crux-utils.h"
+
+// For printing uint64_t values
+#define __STDC_FORMAT_MACROS
+#ifndef _MSC_VER
+#include <inttypes.h>
+#endif
+
+int SpectrumRecordWriter::scanCounter_ = 0;
+
+/**
+ * Converts a spectra file to spectrumrecords format for use with tide-search.
+ * Spectra file is read by pwiz. Returns true on successful conversion.
+ */
+bool SpectrumRecordWriter::convert(
+ const string& infile, ///< spectra file to convert
+ string outfile ///< spectrumrecords file to output
+) {
+ auto_ptr<Crux::SpectrumCollection> spectra(SpectrumCollectionFactory::create(infile.c_str()));
+
+ // Open infile
+ try {
+ if (!spectra->parse()) {
+ return false;
+ }
+ } catch (const std::exception& e) {
+ carp(CARP_ERROR, "%s", e.what());
+ return false;
+ } catch (...) {
+ return false;
+ }
+
+ // Write outfile
+ pb::Header header;
+ header.set_file_type(pb::Header::SPECTRA);
+
+ pb::Header_Source* source = header.add_source();
+ source->set_filename(infile);
+ size_t pos = infile.rfind('.');
+ string extension = (pos == string::npos) ? "UNKNOWN" : infile.substr(pos + 1);
+ source->set_filetype(extension);
+
+ header.mutable_spectra_header()->set_sorted(false);
+
+ HeadedRecordWriter writer(outfile, header);
+ if (!writer.OK()) {
+ return false;
+ }
+
+ scanCounter_ = 0;
+
+ // Go through the spectrum list and write each spectrum
+ for (SpectrumIterator i = spectra->begin(); i != spectra->end(); ++i) {
+ (*i)->sortPeaks(_PEAK_LOCATION); // Sort by m/z
+ vector<pb::Spectrum> pb_spectra = getPbSpectra(*i);
+ for (vector<pb::Spectrum>::const_iterator j = pb_spectra.begin();
+ j != pb_spectra.end();
+ ++j) {
+ writer.Write(&*j);
+ }
+ }
+
+ return true;
+}
+
+/**
+ * Return a pb::Spectrum from a pwiz SpectrumPtr
+ * If spectrum is ms1, or has no precursors/peaks then return empty pb::Spectrum
+ */
+vector<pb::Spectrum> SpectrumRecordWriter::getPbSpectra(
+ const Crux::Spectrum* s
+) {
+ vector<pb::Spectrum> spectra;
+
+ if (s->getNumZStates() == 0 || s->getNumPeaks() == 0) {
+ return spectra;
+ }
+
+ // Get scan number
+ int scan_num = s->getFirstScan();
+ if (scanCounter_ > 0 || scan_num <= 0) {
+ carp_once(CARP_INFO, "Parser could not determine scan numbers for this "
+ "file, using ordinal numbers as scan numbers.");
+ scan_num = ++scanCounter_;
+ }
+
+ const vector<SpectrumZState>& zStates = s->getZStates();
+ for (vector<SpectrumZState>::const_iterator i = zStates.begin(); i != zStates.end(); ++i) {
+ spectra.push_back(pb::Spectrum());
+ pb::Spectrum& newSpectrum = spectra.back();
+ newSpectrum.set_spectrum_number(scan_num);
+ newSpectrum.set_precursor_m_z(i->getMZ());
+ newSpectrum.mutable_charge_state()->Add(i->getCharge());
+ addPeaks(&newSpectrum, s);
+ if (newSpectrum.peak_m_z_size() == 0) {
+ spectra.pop_back();
+ }
+ }
+
+ return spectra;
+}
+
+/**
+ * Add peaks to a pb::Spectrum
+ */
+void SpectrumRecordWriter::addPeaks(
+ pb::Spectrum* spectrum,
+ const Crux::Spectrum* s
+) {
+ int mz_denom, intensity_denom;
+ getDenoms(s, &mz_denom, &intensity_denom);
+ spectrum->set_peak_m_z_denominator(mz_denom);
+ spectrum->set_peak_intensity_denominator(intensity_denom);
+ uint64_t last = 0;
+ int last_index = -1;
+ uint64_t intensity_sum = 0;
+
+ for (PeakIterator i = s->begin(); i != s->end(); ++i) {
+ FLOAT_T peakMz = (*i)->getLocation();
+ uint64_t mz = peakMz * mz_denom + 0.5;
+ uint64_t intensity = (*i)->getIntensity() * intensity_denom + 0.5;
+ if (mz < last) {
+ // Unsorted peaks, this should never happen since peaks get sorted earlier
+ carp(CARP_FATAL, "Peaks are not sorted");
+ } else if (mz == last) {
+ intensity_sum += intensity;
+ spectrum->set_peak_intensity(last_index, intensity_sum);
+ } else {
+ spectrum->add_peak_m_z(mz - last);
+ spectrum->add_peak_intensity(intensity);
+ last = mz;
+ intensity_sum = intensity;
+ ++last_index;
+ }
+ }
+}
+
+/**
+ * See how much precision is given in the peak data
+ */
+void SpectrumRecordWriter::getDenoms(
+ const Crux::Spectrum* s, ///< spectra with peaks to check
+ int* mzDenom, ///< out parameter for m/z denom
+ int* intensityDenom ///< out parameter for intensity denom
+) {
+ const int kMaxPrecision = 10000; // store at most 4 digits of precision
+ *mzDenom = kMaxPrecision;
+ *intensityDenom = kMaxPrecision;
+ for (int precision = 1; precision < kMaxPrecision; precision *= 10) {
+ bool mzDenomOk = (*mzDenom == kMaxPrecision);
+ bool intensityDenomOk = (*intensityDenom == kMaxPrecision);
+ if (!mzDenomOk && !intensityDenomOk) {
+ return;
+ }
+ for (PeakIterator i = s->begin(); i != s->end(); ++i) {
+ if (mzDenomOk) {
+ double mzX = (*i)->getLocation() * precision;
+ if (fabs(mzX - google::protobuf::uint64(mzX + 0.5)) >= 0.001) {
+ mzDenomOk = false;
+ }
+ }
+ if (intensityDenomOk) {
+ double intensityX = (*i)->getIntensity() * precision;
+ if (fabs(intensityX - google::protobuf::uint64(intensityX + 0.5)) >= 0.001) {
+ intensityDenomOk = false;
+ }
+ }
+ if (!mzDenomOk && !intensityDenomOk) {
+ break;
+ }
+ }
+ if (mzDenomOk) {
+ *mzDenom = precision;
+ }
+ if (intensityDenomOk) {
+ *intensityDenom = precision;
+ }
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/SpectrumRecordWriter.h b/src/io/SpectrumRecordWriter.h
new file mode 100644
index 0000000..f647d62
--- /dev/null
+++ b/src/io/SpectrumRecordWriter.h
@@ -0,0 +1,64 @@
+#ifndef SPECTRUM_RECORD_WRITER_H
+#define SPECTRUM_RECORD_WRITER_H
+
+#include "Spectrum.h"
+#include "spectrum.pb.h"
+
+using namespace std;
+
+/**
+ * A class for converting spectra file to the spectrumrecords format for use
+ * with tide-search.
+ */
+class SpectrumRecordWriter {
+
+ public:
+
+ /**
+ * Converts a spectra file to spectrumrecords format for use with tide-search.
+ * Spectra file is read by pwiz. Returns true on successful conversion.
+ */
+ static bool convert(
+ const string& infile, ///< spectra file to convert
+ string outfile ///< spectrumrecords file to output
+ );
+
+ protected:
+
+ static int scanCounter_;
+
+ /**
+ * Return a pb::Spectrum from a Crux::Spectrum
+ * Returns a default instance if there is a problem
+ */
+ static std::vector<pb::Spectrum> getPbSpectra(
+ const Crux::Spectrum* s
+ );
+
+ /**
+ * Add peaks to a pb::Spectrum
+ */
+ static void addPeaks(
+ pb::Spectrum* spectrum,
+ const Crux::Spectrum* s
+ );
+
+ /**
+ * See how much precision is given in the vals array.
+ */
+ static void getDenoms(
+ const Crux::Spectrum* s, ///< values to check
+ int* mzDenom, ///< out parameter for m/z denom
+ int* intensityDenom ///< out parameter for intensity denom
+ );
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/io/carp.cpp b/src/io/carp.cpp
new file mode 100644
index 0000000..90e9672
--- /dev/null
+++ b/src/io/carp.cpp
@@ -0,0 +1,138 @@
+/*************************************************************************
+ * \file carp.cpp
+ * \brief Object for representing a single protein.
+ *************************************************************************/
+#include <stdio.h>
+#include <stdlib.h>
+#include <stdarg.h>
+#include "carp.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+#include "util/Params.h"
+#include "util/utils.h"
+
+using namespace std;
+
+/**
+ * Constants
+ */
+static int G_verbosity;
+static FILE* log_file = NULL;
+
+unsigned int hash_size_ = 1000;
+
+void set_verbosity_level(int verbosity) {
+ G_verbosity = verbosity;
+}
+
+int get_verbosity_level(void) {
+ return G_verbosity;
+}
+
+/**
+ * Open log file for carp messages.
+ *
+ * Parameters must have been processed before calling this function.
+ */
+void open_log_file(string log_file_name) {
+ string output_dir = Params::GetString("output-dir");
+ bool overwrite = Params::GetBool("overwrite");
+ log_file_name = prefix_fileroot_to_name(log_file_name);
+ log_file = create_file_in_path(log_file_name, output_dir.c_str(), overwrite);
+}
+
+/**
+ * Print command line to log file.
+ *
+ * Parameters must have been processed before calling this function.
+ */
+void log_command_line(int argc, char *argv[]) {
+ // Command line arguments were shifted, shift back.
+ ++argc;
+ --argv;
+ if (log_file != NULL) {
+ fprintf(log_file, "COMMAND LINE: ");
+ int i = 0;
+ for (i = 0; i < argc; ++i) {
+ fprintf(log_file, "%s%c", argv[i], i < (argc - 1) ? ' ' : '\n');
+ }
+ }
+}
+
+static void carp_print(const char *string) {
+ fprintf(stderr, "%s", string);
+ if (log_file != NULL) {
+ fprintf(log_file, "%s", string);
+ }
+}
+
+/**
+ * Print message to log file.
+ *
+ * Print severity level and message to log file.
+ * The term 'carp' is used because 'log' is already used
+ * by the math library.
+ *
+ * Verbosity of CARP_FATAL will cause the
+ * program to exit with status code 1.
+ *
+ */
+void carp( int verbosity, const char* format, ...) {
+ if (verbosity <= G_verbosity) {
+ va_list argp;
+
+ if (verbosity == CARP_WARNING) {
+ carp_print("WARNING: ");
+ } else if (verbosity == CARP_ERROR) {
+ carp_print("ERROR: ");
+ } else if (verbosity == CARP_FATAL) {
+ carp_print("FATAL: ");
+ } else if (verbosity == CARP_INFO) {
+ carp_print("INFO: ");
+ } else if (verbosity == CARP_DETAILED_INFO) {
+ carp_print("DETAILED INFO: ");
+ } else if (verbosity == CARP_DEBUG) {
+ carp_print("DEBUG: ");
+ } else if (verbosity == CARP_DETAILED_DEBUG) {
+ carp_print("DETAILED DEBUG: ");
+ } else {
+ carp_print("UNKNOWN: ");
+ }
+
+ va_start(argp, format);
+ vfprintf(stderr, format, argp);
+ va_end(argp);
+ if (log_file != NULL) {
+ va_start(argp, format); //BF: added to fix segfault
+ vfprintf(log_file, format, argp);
+ va_end(argp);
+ }
+ carp_print("\n");
+ fflush(stderr);
+ if (log_file != NULL) {
+ fflush(log_file);
+ }
+ }
+ if (verbosity == CARP_FATAL) {
+ // Fatal carps cause the program to exit
+#ifdef DEBUG
+ abort(); // Dump core in DEBUG mode. Use 'make CXXFLAGS=-DDEBUG"'
+#else
+ exit(1);
+#endif
+ }
+}
+
+void carp ( int verbosity, string& msg) {
+
+ string carp_msg = msg;
+ carp(verbosity, "%s", carp_msg.c_str());
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/io/carp.h b/src/io/carp.h
new file mode 100644
index 0000000..6aa97c0
--- /dev/null
+++ b/src/io/carp.h
@@ -0,0 +1,153 @@
+/**
+ * \file carp.h
+ * $Revision: 1.6 $
+ * \brief Provides methods for logging error messages, and setting verbosity level.
+ *****************************************************************************/
+#ifndef CARP_H
+#define CARP_H
+
+#include "util/utils.h"
+
+
+/**
+ * Verbosity level for a fatal error (e.g., could not open an input file)
+ */
+static const int CARP_FATAL = 0;
+
+/**
+ * Verbosity level for a serious, not fatal, error
+ * (e.g., could not close a file handle)
+ */
+static const int CARP_ERROR = 10;
+
+/**
+ * Verbosity level for a warning (e.g., a spectrum has no peaks)
+ */
+static const int CARP_WARNING = 20;
+
+/**
+ * Verbosity level for informational message (e.g., processed X lines of file)
+ */
+static const int CARP_INFO = 30;
+
+/**
+ * Verbosity level for detailed informational message (e.g, on spectrum 1000 )
+ */
+static const int CARP_DETAILED_INFO = 40;
+
+/**
+ * Verbosity level for a debugging message
+ */
+static const int CARP_DEBUG = 50;
+
+/**
+ * Verbosity level for very detailed debugging message
+ */
+static const int CARP_DETAILED_DEBUG = 60;
+
+/**
+ * The maximum verbosity level
+ */
+static const int CARP_MAX = 100;
+
+/**
+ * Allow for compilation to remove carp commands in the preprocessor.
+ */
+#define IF_CARP(x, y) if (get_verbosity_level() >= x) {y;}
+#define CRUX_DEBUG
+
+#ifdef CRUX_DEBUG
+/**
+ * Allow for compilation to remove carp commands in the preprocessor.
+ */
+#define IF_CARP_DEBUG(y) IF_CARP(CARP_DEBUG, y)
+/**
+ * Allow for compilation to remove carp commands in the preprocessor.
+ */
+#define IF_CARP_DETAILED_DEBUG(y) IF_CARP(CARP_DETAILED_DEBUG, y)
+#else
+/**
+ * Allow for compilation to remove carp commands in the preprocessor.
+ */
+#define IF_CARP_DEBUG(y) y;
+/**
+ * Allow for compilation to remove carp commands in the preprocessor.
+ */
+#define IF_CARP_DETAILED_DEBUG(y) y;
+#endif
+
+
+#include <stdio.h>
+#include <string>
+#include "util/utils.h"
+
+/**
+ * Sets the global verbosity level. Expects an integer greater than or equal
+ * to CARP_FATAL and less than CARP_MAX
+ */
+void set_verbosity_level(int verbosity);
+
+/**
+ * \returns the current verbosity level.
+ */
+int get_verbosity_level(void);
+
+/**
+ * Open log file for carp messages.
+ *
+ * Parameters must have been processed before calling this function.
+ */
+void open_log_file(std::string log_file_name);
+
+/**
+ * Print command line to log file.
+ *
+ * Parameters must have been processed before calling this function.
+ */
+void log_command_line(int argc, char *argv[]);
+
+/**
+ * Print message to log file.
+ *
+ * Print severity level and message to log file.
+ * The term 'carp' is used because 'log' is already used
+ * by the math library.
+ *
+ * Verbosity of CARP_FATAL will cause the
+ * program to exit with status code 1.
+ *
+ */
+void carp(
+ int verbosity,
+ const char* format,
+ ...
+);
+
+void carp(
+ int verbosity,
+ std::string& msg
+);
+
+/**
+ * \def carp_once( verbosity, msg, ...)
+ *
+ * \brief Print message to log file, just once.
+ *
+ * Similar to the carp function, below, but will only print the message once.
+ */
+#define carp_once( verbosity, msg, ... ) \
+{ \
+ static bool _carp_; \
+ if (!_carp_) carp(verbosity, msg, ## __VA_ARGS__); \
+ _carp_ = 1;\
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
+#endif
diff --git a/src/libcrux-support.a b/src/libcrux-support.a
new file mode 100644
index 0000000..f6d4f9c
Binary files /dev/null and b/src/libcrux-support.a differ
diff --git a/src/model/AbstractMatch.cpp b/src/model/AbstractMatch.cpp
new file mode 100644
index 0000000..55d76a4
--- /dev/null
+++ b/src/model/AbstractMatch.cpp
@@ -0,0 +1,142 @@
+/*************************************************************************//**
+ * \file AbstractMatch.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 1/26 2013
+ * \brief Object for holding match scores.
+ ****************************************************************************/
+#include "AbstractMatch.h"
+#include "io/carp.h"
+
+/**
+ * \returns a new memory allocated abstract match
+ */
+AbstractMatch::AbstractMatch() {
+}
+
+/**
+ * default destructor
+ */
+AbstractMatch::~AbstractMatch() {
+}
+
+
+/**
+ * \returns the match score for a particular score type
+ */
+FLOAT_T AbstractMatch::getScore(
+ SCORER_TYPE_T type ///< score type desired
+ ) const {
+
+ ScoreMap::const_iterator findScore = scores_.find(type);
+ if (findScore == scores_.end()) {
+ carp(CARP_WARNING, "Score not set!");
+ return 0.0;
+ }
+
+ return findScore->second;
+
+}
+
+/**
+ * \returns the match rank for a particular score type
+ */
+int AbstractMatch::getRank(
+ SCORER_TYPE_T type ///< score type desired
+ ) const {
+
+ RankMap::const_iterator findRank = ranks_.find(type);
+ if (findRank == ranks_.end()) {
+ carp(CARP_WARNING, "Rank not set!");
+ return 0;
+ }
+
+ return findRank->second;
+
+}
+
+/**
+ * sets the match score for particular score type
+ */
+void AbstractMatch::setScore(
+ SCORER_TYPE_T type, ///< score to set
+ FLOAT_T score ///< score value
+ ) {
+
+ scores_[type] = score;
+
+}
+
+/**
+ * sets the match rank for particular score type
+ */
+void AbstractMatch::setRank(
+ SCORER_TYPE_T type, ///< rank to set
+ int rank ///< rank value
+ ) {
+
+ ranks_[type] = rank;
+
+}
+
+/**
+ * \returns whether the match has a particular score type assigned
+ */
+bool AbstractMatch::hasScore(
+ SCORER_TYPE_T type ///< score to test
+ ) const {
+
+ return (scores_.find(type) != scores_.end());
+}
+
+/**
+ * \returns whether the match has a particular rank type assigned
+ */
+bool AbstractMatch::hasRank(
+ SCORER_TYPE_T type ///< rank to test
+ ) const {
+
+ return (ranks_.find(type) != ranks_.end());
+}
+
+/**
+ * \returns whether the match is a decoy or not (default false)
+ */
+bool AbstractMatch::isDecoy() {
+
+ return false;
+}
+
+/**
+ * \returns the beginning iterator for all set scores in the match
+ */
+ScoreMapIterator AbstractMatch::scoresBegin() {
+ return scores_.begin();
+}
+
+/**
+ * \returns the end iterator for all set scores in the match
+ */
+ScoreMapIterator AbstractMatch::scoresEnd() {
+ return scores_.end();
+}
+
+/**
+ * \returns the beginning iterator for all set ranks in the match
+ */
+RankMapIterator AbstractMatch::ranksBegin() {
+ return ranks_.begin();
+}
+
+/**
+ * \returns the end iterator for all set ranks in the match
+ */
+RankMapIterator AbstractMatch::ranksEnd() {
+ return ranks_.end();
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/AbstractMatch.h b/src/model/AbstractMatch.h
new file mode 100644
index 0000000..f0fe7ed
--- /dev/null
+++ b/src/model/AbstractMatch.h
@@ -0,0 +1,104 @@
+/**
+ * \file AbstractMatch.h
+ * $Revision: 1.00 $
+ * \brief Object for holding match scores
+ ****************************************************************************/
+#ifndef ABSTRACTMATCH_H_
+#define ABSTRACTMATCH_H_
+
+#include "match_objects.h"
+
+class AbstractMatch {
+
+ protected:
+ ScoreMap scores_; ///< map of scores
+ RankMap ranks_; ///< map of ranks for scores
+
+ public:
+
+ /**
+ * \returns a new memory allocated abstract match
+ */
+ AbstractMatch();
+
+ /**
+ * default destructor
+ */
+ virtual ~AbstractMatch();
+
+ /**
+ * \returns the match score for a particular score type
+ */
+ virtual FLOAT_T getScore(
+ SCORER_TYPE_T type ///<score type desired
+ ) const;
+
+ /**
+ * \returns the match rank for a particular score type
+ */
+ virtual int getRank(
+ SCORER_TYPE_T type ///<score type desired
+ ) const;
+
+ /**
+ * sets the match score for particular score type
+ */
+ virtual void setScore(
+ SCORER_TYPE_T type, ///< score to set
+ FLOAT_T score ///< score value
+ );
+
+ /**
+ * sets the match rank for particular score type
+ */
+ virtual void setRank(
+ SCORER_TYPE_T type, ///< rank to set
+ int rank ///< rank value
+ );
+
+ /**
+ * \returns whether the match has a particular score type assigned
+ */
+ virtual bool hasScore(
+ SCORER_TYPE_T type ///< score to test
+ ) const;
+
+ virtual bool hasRank(
+ SCORER_TYPE_T type ///< rank to test
+ ) const;
+
+ /**
+ * \returns whether the match is a decoy or not (default false).
+ */
+ virtual bool isDecoy();
+
+ /**
+ * \returns the beginning iterator for all set scores in the match
+ */
+ ScoreMapIterator scoresBegin();
+
+ /**
+ * \returns the end iterator for all set scores in the match
+ */
+ ScoreMapIterator scoresEnd();
+
+ /**
+ * \returns the beginning iterator for all set ranks in the match
+ */
+ RankMapIterator ranksBegin();
+
+ /**
+ * \returns the end iterator for all set ranks in the match
+ */
+ RankMapIterator ranksEnd();
+
+};
+
+#endif //ABSTRACTMATCH_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/Database.cpp b/src/model/Database.cpp
new file mode 100644
index 0000000..fc184a0
--- /dev/null
+++ b/src/model/Database.cpp
@@ -0,0 +1,836 @@
+/*************************************************************************//**
+ * \file Database.cpp
+ * \brief Object for representing a database of protein sequences.
+ ****************************************************************************/
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <ctype.h>
+#include <sys/types.h>
+#include <fcntl.h>
+#ifndef _MSC_VER
+#include <sys/mman.h>
+#include <unistd.h>
+#endif
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "Peptide.h"
+#include "Protein.h"
+#include "ProteinPeptideIterator.h"
+#include "Database.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+#include "ProteinIndex.h"
+#include "ProteinIndexIterator.h"
+
+#include "DatabaseProteinIterator.h"
+#include "DatabasePeptideIterator.h"
+
+#include <map>
+#include <vector>
+#include <iostream>
+
+using namespace std;
+using namespace Crux;
+const string Database::binary_suffix = "-binary-fasta";
+const string Database::decoy_binary_suffix = "-binary-fasta-decoy";
+const string Database::decoy_fasta_suffix = "-random.fasta";
+
+/**
+ * intializes a database object
+ */
+void Database::init(){
+ file_ = NULL;
+ is_parsed_ = false;
+ size_ = 0;
+ use_light_protein_ = false;
+ is_memmap_ = false;
+ data_address_ = NULL;
+ pointer_count_ = 1;
+ file_size_ = 0;
+ is_hashed_ = false;
+ proteins_ = new vector<Protein*>();
+ protein_map_ = new map<const char*, Protein*, cmp_str>();
+ decoys_ = NO_DECOYS;
+ binary_is_temp_ = false;
+}
+
+/**
+ * \returns An (empty) database object.
+ */
+Database::Database() {
+ init();
+}
+
+
+/**
+ * \returns A new database object.
+ */
+Database::Database(
+ const string& filename, ///< The file from which to parse the database.
+ ///< either text fasta file or binary fasta file -in
+ bool is_memmap, ///< are we using a memory mapped binary fasta file?
+ ///< If so, all proteins are memory mapped -in
+ DECOY_TYPE_T decoys ///< is this a decoy database
+ )
+{
+ carp(CARP_DEBUG, "Creating new database from '%s'", filename.c_str());
+ init();
+ is_memmap_ = is_memmap;
+ if( is_memmap_ ){
+ binary_filename_ = filename;
+ } else {
+ fasta_filename_ = filename;
+ }
+ decoys_ = decoys;
+}
+
+/**
+ * Frees an allocated protein object.
+ */
+void Database::freeDatabase(
+ Database* database ///< An allocated database -in
+ )
+{
+ if(database == NULL){
+ return;
+ }
+
+ // decrement database pointer counter
+ --database->pointer_count_;
+ carp(CARP_DETAILED_DEBUG, "Database pointer count %i",
+ database->pointer_count_);
+
+ // DEBUG show the databse pointer count
+ // printf("Free: After free: %s: %d\n", database->pointer_count);
+
+ // only free up memory when remaining pointers are from the proteins
+ if((size_t)database->pointer_count_ > database->proteins_->size() ){
+ return;
+ }
+
+ delete database;
+}
+
+Database::~Database() {
+
+ // only free proteins if been parsed and file has been opened
+ if(is_parsed_){
+ carp(CARP_DEBUG, "Freeing database.");
+
+ // free each protein in the array
+ unsigned int protein_idx;
+ for(protein_idx=0; protein_idx < proteins_->size(); ++protein_idx){
+ delete ((*proteins_)[protein_idx]);
+ }
+ delete proteins_;
+ delete protein_map_; // contents already deleted
+
+ // free memory mapped binary file from memory
+ if(is_memmap_){
+ // un map the memory!!
+#ifdef _MSC_VER
+ stub_unmmap(&unmap_info_);
+#else
+ if(munmap(data_address_, file_size_) != 0){
+ carp(CARP_ERROR, "failed to unmap the memory of binary fasta file");
+ }
+#endif
+ }
+ // not memory mapped
+ else if (file_ != NULL) {
+ // close file handle
+ carp(CARP_DEBUG, "Closing database filehandle");
+ fclose(file_);
+ }
+ }
+
+ if( binary_is_temp_ && !binary_filename_.empty() ){
+ carp(CARP_DEBUG, "Deleting temp binary fasta %s.",
+ binary_filename_.c_str());
+ remove(binary_filename_.c_str());
+ }
+}
+
+/**
+ * Prints a database object to file.
+ */
+void Database::print(
+ FILE* file ///< output file stream -out
+ )
+{
+ Protein* protein = NULL;
+
+ if( is_memmap_ ){
+ fprintf(file, "filename:%s\n", binary_filename_.c_str());
+ } else {
+ fprintf(file, "filename:%s\n", fasta_filename_.c_str());
+ }
+ fprintf(file, "is_parsed:");
+
+ // has the database been parsed?
+ if(is_parsed_){
+ fprintf(file, "true\n");
+ DatabaseProteinIterator* iterator
+ = new DatabaseProteinIterator(this);
+
+ while(iterator->hasNext()){
+ protein = iterator->next();
+ // if the database uses light/heavy functionality
+ if(use_light_protein_){
+ protein->toHeavy();
+ }
+ protein->print(stdout);
+
+ // if the database uses light/heavy functionality
+ /**
+ * uncomment this code if you want to restore a protein to
+ * light after converted to heavy
+ if(database->use_light_protein){
+ protein_to_light(protein);
+ }
+ */
+ }
+ delete iterator;
+ }
+ else{
+ fprintf(file, "false\n");
+ }
+}
+
+void Database::addProtein(
+ Protein* protein
+ ) {
+
+ protein->setDatabase(this);
+
+ // add protein to database
+ proteins_->push_back(protein);
+
+ protein->setProteinIdx(proteins_->size()-1);
+
+ if (is_hashed_) {
+ string& id = protein->getIdPointer();
+ protein_map_->insert(make_pair(id.c_str(), protein));
+ }
+}
+
+/**
+ * Parses a database from the text based fasta file in the filename
+ * member variable
+ * reads in all proteins in the fasta file and creates a protein object
+ * and adds them to the database protein array
+ * total proteins in fasta file must not exceed MAX_PROTEIN constant
+ * IF using light_protein functionality will not read in the sequence or id.
+ * \returns true if success. false if failure.
+ */
+bool Database::parseTextFasta()
+{
+ unsigned long working_index;
+ FILE* file = NULL;
+ char* new_line = NULL;
+ int line_length;
+ size_t buf_length = 0;
+ Protein* new_protein;
+ unsigned int protein_idx;
+
+ carp(CARP_DEBUG, "Parsing text fasta file '%s'", fasta_filename_.c_str());
+ // check if already parsed
+ if(is_parsed_){
+ return true;
+ }
+
+ // open file and
+ file = fopen(fasta_filename_.c_str(), "rb");
+
+ // check if succesfully opened file
+ if(file == NULL){
+ carp(CARP_ERROR, "Failed to open fasta file %s", fasta_filename_.c_str());
+ return false;
+ }
+
+ // check if use light protein and parse those proteins from protein index
+ if(use_light_protein_ && ProteinIndex::onDisk(fasta_filename_.c_str(), false)){
+ // let the user know that protein index file is being used
+ carp(CARP_INFO, "using protein index file");
+
+ // create a protein index iterator
+ ProteinIndexIterator* protein_index_iterator =
+ new ProteinIndexIterator(fasta_filename_.c_str());
+
+ // iterate over all proteins in protein index
+ while(protein_index_iterator->hasNext()){
+ // check if there's space for more proteins
+ new_protein = protein_index_iterator->next();
+ new_protein->setDatabase(this);
+
+ // add protein to database
+ proteins_->push_back(new_protein);
+ }
+ // job well done..free iterator
+ delete protein_index_iterator;
+ }
+ else{
+ working_index = ftell(file);
+ // check each line until reach '>' line
+ while((line_length = getline(&new_line, &buf_length, file)) != -1){
+ if(new_line[0] == '>'){
+ // the new protein to be added
+ new_protein = new Protein();
+
+ // do not parse the protein sequence if using light/heavy functionality
+ if(use_light_protein_){
+ // set light and offset
+ new_protein->setOffset(working_index);
+ new_protein->setIsLight(true);
+ }
+ else{
+ // rewind to the beginning of the protein to include ">" line
+ fseek(file, working_index, SEEK_SET);
+
+ // failed to parse the protein from fasta file
+ // protein offset is set in the parse_protein_fasta_file method
+ if(!new_protein->parseProteinFastaFile(file)){
+ fclose(file);
+ delete new_protein;
+ for(protein_idx=0;protein_idx<proteins_->size();protein_idx++){
+ delete (proteins_->at(protein_idx));
+ }
+ proteins_->clear();
+ carp(CARP_ERROR, "Failed to parse fasta file");
+ return false;
+ }
+ new_protein->setIsLight(false);
+ }
+ // add protein to database
+ proteins_->push_back(new_protein);
+ // set protein index, database
+ new_protein->setProteinIdx(proteins_->size()-1);
+ new_protein->setDatabase(this);
+ }
+ working_index = ftell(file);
+ }
+ free(new_line);
+ }
+
+ // yes the database is paresed now..!!
+ is_parsed_ = true;
+ file_ = file;
+ return true;
+}
+
+/**
+ * memory maps the binary fasta file for the database
+ *\return true if successfully memory map binary fasta file, else false
+ */
+bool Database::memoryMap(
+ int file_d ///< file descriptor -in
+ )
+{
+ struct stat file_info;
+
+ // get information of the binary fasta file
+ if (stat(binary_filename_.c_str(), &file_info) == -1) {
+ carp(CARP_ERROR,
+ "Failed to retrieve information of binary fasta file: %s",
+ binary_filename_.c_str());
+ return false;
+ }
+
+ // set size of the binary fasta file in database
+ // this is used later to know how much to unmap
+ file_size_ = file_info.st_size;
+
+ // memory map the entire binary fasta file!
+#ifdef _MSC_VER
+ data_address_ = stub_mmap(binary_filename_.c_str(), &unmap_info_);
+
+#else
+ data_address_ = mmap((caddr_t)0, file_info.st_size,
+ PROT_READ, MAP_PRIVATE /*MAP_SHARED*/, file_d, 0);
+
+ // check if memory mapping has succeeded
+ if ((caddr_t)(data_address_) == (caddr_t)(-1)){
+ carp(CARP_ERROR, "Failed to use mmap function for binary fasta file: %s",
+ binary_filename_.c_str());
+ return false;
+ }
+#endif
+
+ return true;
+}
+
+/**
+ * Assumes that there is a 1 at the very end after all the proteins in
+ * binary file.
+ * \returns True successfully populates the proteins from memory mapped
+ * binary fasta file, else false .
+ */
+bool Database::populateProteinsFromMemmap()
+{
+ Protein* new_protein;
+ unsigned int protein_idx = 0;
+ char* data = (char*)data_address_;
+
+ // parse proteins until the end of list
+ while((int)data[0] != 1){
+
+ // the new protein to be added
+ new_protein = new Protein();
+
+ // parse protein from memory map
+ if(!new_protein->parseProteinBinaryMemmap(&data)){
+ // failed to parse the protein from memmap
+ // free all proteins, and return false
+ delete new_protein;
+ for(; protein_idx < proteins_->size(); ++protein_idx){
+ delete proteins_->at(protein_idx);
+ }
+ proteins_->clear();
+ carp(CARP_ERROR, "Failed to parse fasta file");
+ return false;
+ }
+ new_protein->setIsLight(false);
+
+ // add protein to database
+ proteins_->push_back(new_protein);
+ // set protein index, database
+ new_protein->setProteinIdx(proteins_->size()-1);
+ new_protein->setDatabase(this);
+ }
+
+ return true;
+}
+
+/**
+ * \brief Parses a database from the binary fasta file in the filename
+ * member variable.
+ *
+ * Memory maps the binary fasta file into memory. The protein
+ * sequences are not copied, but just pointed to the memory mapped
+ * location.
+ * \returns true if success. false if failure.
+ */
+bool Database::parseMemmapBinary()
+{
+ int file_d = -1;
+ carp(CARP_DEBUG, "Parsing binary fasta file '%s'", binary_filename_.c_str());
+
+ // check if already parsed
+ if(is_parsed_){
+ return true;
+ }
+
+ // open file and
+ file_d = open(binary_filename_.c_str(), O_RDONLY);
+
+ // check if succesfully opened file
+ if(file_d == -1){
+ carp(CARP_FATAL, "Failed to open file to parse database");
+ return false;
+ }
+
+ // FIXME, if what to use some light protein for binary file change here...
+ // check if user request light protein
+ // When using a binary file in memory map, cannot use light protein
+ // change to false on light protein useage
+ if(use_light_protein_){
+ carp(CARP_WARNING,
+ "memory mapping does not support light protein,changing settings to use heavy protein");
+ use_light_protein_ = false;;
+ }
+
+ // memory map the binary fasta file into memory
+ if(!memoryMap(file_d)){
+ carp(CARP_ERROR, "Failed to memory map binary fasta file into memory");
+ return false;
+ }
+
+ // populate the proteins from the memory mapped fasta file
+ if(!populateProteinsFromMemmap()){
+ carp(CARP_ERROR, "Failed to populate the proteins from memory mapped fasta file");
+ return false;
+ }
+
+ // yes the database is paresed now..!!
+ is_parsed_ = true;
+ return true;
+}
+
+
+/**
+ * Parses a database from the file in the filename member variable
+ * The is_memmap field in the database struct determines whether the
+ * input file is a binary fasta file or normal text fasta file.
+ *
+ * IF is_memmap is true, memory maps the entire binary fasta file into memory
+ * and then creates protein objects that point to the memory mapped binary file
+ *
+ * IF is_memmap is false, uses the traditional text fasta file which
+ * it parses out the various peptides for each protein. Only when
+ * using text fasta file can you use light/heavy protein, in which
+ * if using light_protein functionality will not read in the sequence
+ * or id. Will parse sequence if protein
+ * is needed, lazy parsing.
+ *
+ * For Both cases, reads in all proteins in file and creates a protein object
+ * and adds them to the database protein array
+ * total proteins in fasta file must not exceed MAX_PROTEIN constant
+ *
+ * \returns true if success. false if failure.
+ */
+bool Database::parse()
+{
+ // should we parse the database using memory mapped binary fasta file?
+ if(is_memmap_){
+ return parseMemmapBinary();
+ }
+ else{ // parse database from normal text fasta file, no memory mapping!
+ return parseTextFasta();
+ }
+
+ // succeeded in parsing database
+ return true;
+}
+
+
+/**
+ * \brief Changes a database from one that reads from a fasta file to
+ * one that reads from a binary/memmory mapped protein file.
+ *
+ * If database already has binary source (i.e. is_memmap == true),
+ * returns true.
+ * Opens the fasta file pointed to by filename for reading. Creates an
+ * output file with the name given. Reads in each protein from the
+ * text file and serializes it to the output file. Closes both files.
+ * Changes filename to point to new output file and sets is_memmap to
+ * true. Parses the database.
+ * \returns true if all processes succeed, else false.
+ */
+bool Database::transformTextToMemmap(
+ const char* output_dir,
+ bool binary_is_temp
+ ){
+
+ createBinaryFasta(output_dir, binary_is_temp);
+
+ // set is_memmap to true
+ setMemmap(true);
+
+ // parse the binary fasta
+ bool success = parse();
+
+ return success;
+}
+
+/**
+ * Using the fasta file the Database was instantiated with, write a
+ * binary protein file in the given directory to use for memory
+ * mapping. If is_temp, delete the file on destruction. Warns if
+ * Database was not opened with a text file. If the database is to
+ * contain decoy proteins, randomizes each protein before
+ * serializing. Also prints a new fasta file of the decoy proteins in
+ * the same directory as the binary file.
+ */
+void Database::createBinaryFasta(const char* directory, bool is_temp){
+ binary_is_temp_ = is_temp;
+
+ if( fasta_filename_.empty() ){
+ carp(CARP_WARNING, "No fasta file to transform to binary.");
+ return;
+ }
+
+ // get the name of the new binary file
+ const char* binary_suffix = Database::binary_suffix.c_str();
+ if( decoys_ != NO_DECOYS ){
+ binary_suffix = Database::decoy_binary_suffix.c_str();
+ }
+ char* tmp_name = generate_name_path( fasta_filename_.c_str(), ".fasta",
+ binary_suffix, directory);
+ binary_filename_ = tmp_name;
+ free(tmp_name);
+ carp(CARP_DEBUG, "Transforming text file '%s' to binary file '%s'",
+ fasta_filename_.c_str(), binary_filename_.c_str());
+
+ // open output file
+ FILE* output_file = fopen(binary_filename_.c_str(), "wb");
+ if( output_file == NULL ){
+ carp(CARP_FATAL, "Could not open binary protein file %s",
+ binary_filename_.c_str());
+ }
+ // also open a fasta file if this is a decoy database
+ FILE* output_fasta = NULL;
+ if( decoys_ != NO_DECOYS){
+ vector<const char*> suffixes;
+ suffixes.push_back(".fasta");
+ suffixes.push_back(".fa");
+ suffixes.push_back(".fsa");
+ char* fasta_output_name = generate_name_path( fasta_filename_.c_str(),
+ suffixes,
+ decoy_fasta_suffix.c_str(),
+ directory);
+ output_fasta = fopen(fasta_output_name, "wb");
+ if( output_fasta == NULL ){
+ carp(CARP_FATAL, "Could not open new fasta file %s for decoy proteins.",
+ output_fasta);
+ }
+ free(fasta_output_name);
+ }
+
+
+ // open input file
+ FILE* input_file = fopen(fasta_filename_.c_str(), "rb");
+ if( input_file == NULL ){
+ carp(CARP_FATAL, "Could not open fasta file %s", fasta_filename_.c_str());
+ }
+
+ // for file reading
+ char* new_line = NULL;
+ int line_length = 0;
+ size_t buf_length = 0;
+ unsigned int mod_me = 1000;
+ unsigned int protein_idx = 0;
+
+ // read through the fasta and at each line beginning with >, parse a protein
+ unsigned long working_index = ftell(input_file);
+ while((line_length = getline(&new_line, &buf_length, input_file)) != -1){
+ if(new_line[0] == '>'){
+ // the new protein to be serialize
+ Protein* new_protein = new Protein();
+
+ // rewind to the begining of the protein to include ">" line
+ fseek(input_file, working_index, SEEK_SET);
+ // protein offset is set in the parse_protein_fasta_file method
+ if(!new_protein->parseProteinFastaFile(input_file)){
+ fclose(input_file);
+ delete new_protein;
+ carp(CARP_FATAL, "Failed to parse fasta file");
+ }
+ new_protein->setIsLight(false);
+
+ if( decoys_ != NO_DECOYS ){
+ new_protein->shuffle(decoys_);
+ new_protein->print(output_fasta);
+ }
+
+ // serialize protein as binary to output file
+ new_protein->serialize(output_file);
+
+ // update protein count
+ ++protein_idx;
+
+ // free this protein
+ delete new_protein;
+ }
+
+ // print status
+ if(protein_idx % mod_me == 0){
+ if((protein_idx / 10) == mod_me){
+ mod_me *= 10;
+ }
+ carp(CARP_INFO, "Reached protein %d", protein_idx);
+ }
+
+ working_index = ftell(input_file);
+ } // next line
+
+ // write the end character to binary fasta file
+ char term_char = 1; // use 1 and not '*' as the terminal
+ // character for the file b/c id length is
+ // stored in same field and id len == 42
+ // is the smae as '*'
+ fwrite(&term_char, sizeof(char), 1, output_file);
+
+ // print final status
+ carp(CARP_INFO, "Total proteins found: %d", protein_idx);
+
+ free(new_line);
+ fclose(input_file);
+ fclose(output_file);
+}
+
+/**
+ * Access routines of the form get_<object>_<field> and set_<object>_<field>.
+ */
+
+/**
+ *sets true,false whether the database uses memory mapped
+ */
+void Database::setMemmap(
+ bool is_memmap ///< is the database memory mapped?
+ )
+{
+ is_memmap_ = is_memmap;
+}
+
+/**
+ *\returns the filename of the database
+ * returns a heap allocated new copy of the filename
+ * user must free the return filename
+ */
+char* Database::getFilename()
+{
+ if( is_memmap_ ){
+ return my_copy_string(binary_filename_.c_str());
+ }
+ return my_copy_string(fasta_filename_.c_str());
+}
+
+
+/**
+ *\returns the pointer to the filename of the database
+ * user must not free or change the filename
+ */
+const char* Database::getFilenamePointer()
+{
+ if( is_memmap_ ){
+ return binary_filename_.c_str();
+ }
+ return fasta_filename_.c_str();
+}
+
+/**
+ *\returns true|false whether the database has been parsed?
+ */
+bool Database::getIsParsed()
+{
+ return is_parsed_;
+}
+
+void Database::setIsParsed(
+ bool is_parsed
+ ) {
+ is_parsed_ = is_parsed;
+}
+
+/**
+ * \returns The type of shuffling used on the proteins in this database
+ */
+DECOY_TYPE_T Database::getDecoyType(){
+ return decoys_;
+}
+
+
+/**
+ * sets the use_light_protein of the database
+ */
+void Database::setUseLightProtein(
+ bool use ///< should I use the light/heavy functionality?
+ )
+{
+ use_light_protein_ = use;
+}
+
+/**
+ *\returns true|false whether the database uses light/heavy
+ */
+bool Database::getUseLightProtein()
+{
+ return use_light_protein_;
+}
+
+/**
+ *\returns the total number of proteins of the database
+ */
+unsigned int Database::getNumProteins()
+{
+ return proteins_->size();
+}
+
+/**
+ *\returns the src FILE* of the database
+ */
+FILE* Database::getFile()
+{
+ return file_;
+}
+
+/**
+ * sets the src FILE* of the database
+ */
+void Database::setFile(
+ FILE* file ///< the src file to add -in
+ )
+{
+ file_ = file;
+}
+
+/**
+ * \returns the nth protein of the database
+ *
+ */
+Protein* Database::getProteinAtIdx(
+ unsigned int protein_idx ///< The index of the protein to retrieve -in
+ )
+{
+ //carp(CARP_DETAILED_DEBUG, "Getting db protein idx = %i, num proteins %i",
+ // protein_idx, database->proteins.size());
+ if( protein_idx >= proteins_->size()){
+ carp(CARP_FATAL,
+ "Protein index %i out of bounds. %i proteins in the database",
+ protein_idx, proteins_->size());
+ }
+
+ return proteins_->at(protein_idx);
+}
+
+/**
+ *\returns the protein designated by protein id of the database
+ */
+Protein* Database::getProteinByIdString(
+ const char* protein_id ///< The id string for this protein -in
+ ) {
+
+ //TODO - Implement as a hashtable rather than a map to make
+ //this even faster if needed.
+ Protein* protein = NULL;
+ if (is_hashed_) {
+ map<const char*, Protein*, cmp_str>::iterator find_iter;
+ find_iter = protein_map_->find(protein_id);
+
+ if (find_iter != protein_map_->end()) {
+ protein = find_iter->second;
+ }
+ } else {
+ //create the hashtable of protein ids
+ for (unsigned int protein_idx = 0;
+ protein_idx < proteins_->size();
+ protein_idx++) {
+
+ Protein* current_protein = proteins_->at(protein_idx);
+ string& current_id = current_protein->getIdPointer();
+ protein_map_->insert(make_pair(current_id.c_str(), current_protein));
+
+ if (current_id == protein_id) {
+ protein = current_protein;
+ }
+
+ }
+ is_hashed_ = true;
+ }
+ return protein;
+}
+
+/**
+ * increase the pointer_count produced by this database.
+ * \returns database pointer
+ */
+Database* Database::copyPtr(
+ Database* database ///< the query database -in/out
+ )
+{
+ if( database == NULL ){
+ return NULL;
+ }
+ ++database->pointer_count_;
+ return database;
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/Database.h b/src/model/Database.h
new file mode 100644
index 0000000..fe8bc44
--- /dev/null
+++ b/src/model/Database.h
@@ -0,0 +1,347 @@
+/**
+ * \file Database.h
+ * $Revision: 1.27 $
+ * \brief Object for representing a database of protein sequences.
+ *****************************************************************************/
+#ifndef DATABASE_H
+#define DATABASE_H
+
+#include <stdio.h>
+#include "util/utils.h"
+#include "model/objects.h"
+#include "Peptide.h"
+#include "Protein.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+#include <string>
+#include <map>
+
+#ifdef _MSC_VER
+#include "util/WinCrux.h"
+#endif
+
+//Comparator function for c type strings.
+struct cmp_str {
+
+ bool operator()(char const *a, char const *b) const {
+ return strcmp(a, b) < 0;
+ }
+};
+
+
+class Database {
+ protected:
+ std::string fasta_filename_; ///< Name of the text file.
+ std::string binary_filename_;///< Full path to the binary protein sequence file.
+ FILE* file_; ///< Open filehandle for this database.
+ /// A database has only one associated file.
+ bool is_parsed_; ///< Has this database been parsed yet.
+ std::vector<Crux::Protein*>* proteins_; ///< Proteins in this database.
+ std::map<const char*, Crux::Protein*, cmp_str>* protein_map_; //map for proteins
+ bool is_hashed_; //Indicator of whether the database has been hashed/mapped.
+ unsigned long int size_; ///< The size of the database in bytes (convenience)
+ bool use_light_protein_; ///< should I use the light/heavy protein option
+ bool is_memmap_; ///< Are we using a memory mapped fasta file?
+#ifdef _MSC_VER
+ SIMPLE_UNMMAP unmap_info_;
+#endif
+ void* data_address_; ///< pointer to the beginning of the memory mapped data,
+ unsigned int pointer_count_; ///< number of pointers referencing this database.
+ long file_size_; ///< the size of the binary fasta file, when memory mapping
+ DECOY_TYPE_T decoys_; ///< the type of decoys, none if target db
+ bool binary_is_temp_; ///< should we delete the binary fasta in destructor
+
+ /**
+ * Parses a database from the text based fasta file in the filename
+ * member variable
+ * reads in all proteins in the fasta file and creates a protein object
+ * and adds them to the database protein array
+ * total proteins in fasta file must not exceed MAX_PROTEIN constant
+ * IF using light_protein functionality will not read in the sequence or id.
+ * \returns true if success. false if failure.
+ */
+ bool parseTextFasta();
+
+ /**
+ * memory maps the binary fasta file for the database
+ *\return true if successfully memory map binary fasta file, else false
+ */
+ bool memoryMap(
+ int file_d ///< file descriptor -in
+ );
+
+ /**
+ * Assumes that there is a 1 at the very end after all the proteins in binary file
+ *\return true successfully populates the proteins from memory mapped binary fasta file, else false
+ */
+ bool populateProteinsFromMemmap();
+
+ /**
+ * \brief Parses a database from the binary fasta file in the filename
+ * member variable.
+ *
+ * Memory maps the binary fasta file into memory. The protein
+ * sequences are not copied, but just pointed to the memory mapped
+ * location.
+ * \returns true if success. false if failure.
+ */
+ bool parseMemmapBinary();
+
+ /**
+ * intializes a database object
+ */
+ void init();
+
+ public:
+ /**
+ * The suffix on binary and text fasta files.
+ */
+ static const std::string binary_suffix;
+ static const std::string decoy_binary_suffix;
+ static const std::string decoy_fasta_suffix;
+
+ /**
+ * \returns An (empty) database object.
+ */
+
+ Database();
+
+ /**
+ * \returns A new database object.
+ */
+ Database(
+ const std::string& filename, ///< The file from which to parse the database. either text fasta file or binary fasta file -in
+ bool is_memmap, ///< are we using a memory mapped binary fasta file, thus proteins are all memory mapped -in
+ DECOY_TYPE_T decoys = NO_DECOYS ///< is this to be a decoy database
+ );
+
+ void addProtein(
+ Crux::Protein* protein
+ );
+
+ /**
+ * Frees an allocated protein object.
+ */
+ static void freeDatabase(
+ Database* database ///< An allocated database -in
+ );
+
+ virtual ~Database();
+
+ /**
+ * Prints a database object to file.
+ */
+ void print(
+ FILE* file ///< output file stream -out
+ );
+
+ /**
+ * Parses a database from the file in the filename member variable
+ * reads in all proteins in the fasta file and creates a protein object
+ * and adds them to the database protein array
+ * total proteins in fasta file must not exceed MAX_PROTEIN constant
+ * \returns TRUE if success. FALSE if failure.
+ */
+ bool parse();
+
+ /**
+ * \brief Changes a database from one that reads from a fasta file to
+ * one that reads from a binary/memmory mapped protein file.
+ *
+ * If database already has binary source (i.e. is_memmap == TRUE),
+ * returns TRUE.
+ * Opens the fasta file pointed to by filename for reading. Creates a
+ * file with the name given. Reads in each protein from the text file
+ * and serializes it to the output file. Closes both files. Changes
+ * filename to point to new output file and sets is_memmap to true.
+ * Parses the database.
+ * \returns TRUE if all processes succeed, else FALSE.
+ */
+ bool transformTextToMemmap(
+ const char* binary_protein_filename,
+ bool binary_is_temp
+ );
+
+ /**
+ * \returns FALSE if nth protein cannot be parsed or does not exist
+ */
+ /**
+ bool get_database_protein_at_idx(
+ DATABASE_T* database, ///< A parsed database object -in
+ unsigned int protein_idx, ///< The index of the protein to retrieve -in
+ Protein** protein ///< A pointer to a pointer to a PROTEIN object -out
+ );
+ **/
+
+ /**
+ * Using the fasta file the Database was instantiated with, write a
+ * binary protein file in the given directory to use for memory
+ * mapping. If is_temp, delete the file on destruction. Warns if
+ * Database was not opened with a text file.
+ */
+ void createBinaryFasta(const char* directory, bool is_temp = false);
+
+ /**
+ * Access routines of the form get_<object>_<field> and set_<object>_<field>.
+ */
+
+ /**
+ * Additional get and set methods
+ */
+
+ /**
+ *\returns the filename of the database
+ * returns a heap allocated new copy of the filename
+ * user must free the return filename
+ */
+ char* getFilename();
+
+ /**
+ *\returns the pointer to the filename of the database
+ * user must not free or change the filename
+ */
+ const char* getFilenamePointer();
+
+ /**
+ * sets the filename of the database
+ * protein->sequence must been initiailized
+ */
+ void setFilename(
+ const char* filename ///< the filename to add -in
+ );
+
+ /**
+ *\returns TRUE|FALSE whether the database has been parsed?
+ */
+ bool getIsParsed();
+
+ void setIsParsed(
+ bool is_parsed
+ );
+
+ /**
+ * \returns The type of shuffling used on the proteins in this database
+ */
+ DECOY_TYPE_T getDecoyType();
+
+ /**
+ *\returns the total number of proteins of the database
+ */
+ unsigned int getNumProteins();
+
+ /**
+ *\returns the src FILE* of the database
+ */
+ FILE* getFile();
+
+ /**
+ * sets the src FILE* of the database
+ */
+ void setFile(
+ FILE* file ///< the src file to add -in
+ );
+
+ /**
+ *\returns the nth protein of the database
+ */
+ Crux::Protein* getProteinAtIdx(
+ unsigned int protein_idx ///< The index of the protein to retrieve -in
+ );
+
+ /**
+ *\returns the protein designated by protein id of the database
+ */
+ Crux::Protein* getProteinByIdString(
+ const char* protein_id ///< The id string for this protein -in
+ );
+
+ /**
+ * sets the use_light_protein of the database
+ */
+ void setUseLightProtein(
+ bool use ///< should I use the light/heavy functionality?
+ );
+
+ /**
+ *\returns TRUE|FALSE whether the database uses light/heavy
+ */
+ bool getUseLightProtein();
+
+ /**
+ *sets TRUE,FALSE whether the database uses memory mapped
+ */
+ void setMemmap(
+ bool is_memmap ///< is the database memory mapped?
+ );
+
+ /**
+ * increase the pointer_count produced by this database.
+ * \returns database pointer
+ */
+ static Database* copyPtr(
+ Database* database ///< the query database -in/out
+ );
+
+};
+
+/**
+ * Frees an allocated database_peptide_iterator object.
+ */
+void void_free_database_peptide_iterator(
+ void* database_peptide_iterator ///< the iterator to free -in
+ );
+
+/**
+ * The basic iterator functions.
+ * \returns TRUE if there are additional peptides to iterate over, FALSE if not.
+ */
+bool void_database_peptide_iterator_has_next(
+ void* database_peptide_iterator ///< the iterator of interest -in
+ );
+
+/**
+ * \returns The next peptide in the database.
+ */
+Crux::Peptide* void_database_peptide_iterator_next(
+ void* database_peptide_iterator ///< the iterator of interest -in
+ );
+
+/***********************************
+ * database sorted peptide iterator
+ ***********************************/
+
+/**********************************************************************
+ * wrapper, for generate_peptides_iterator, cast back to original type
+ ***********************************************************************/
+
+/**
+ * Frees an allocated database_sorted_peptide_iterator object.
+ */
+void void_free_database_sorted_peptide_iterator(
+ void* database_peptide_iterator ///< the iterator to free -in
+ );
+
+/**
+ * The basic iterator functions.
+ * \returns TRUE if there are additional peptides to iterate over, FALSE if not.
+ */
+bool void_database_sorted_peptide_iterator_has_next(
+ void* database_peptide_iterator ///< the iterator of interest -in
+ );
+
+/**
+ * returns each peptide in sorted order
+ * \returns The next peptide in the database.
+ */
+Crux::Peptide* void_database_sorted_peptide_iterator_next(
+ void* database_peptide_iterator ///< the iterator of interest -in
+ );
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/DatabasePeptideIterator.cpp b/src/model/DatabasePeptideIterator.cpp
new file mode 100644
index 0000000..bdf18a8
--- /dev/null
+++ b/src/model/DatabasePeptideIterator.cpp
@@ -0,0 +1,342 @@
+/**
+ * \file DatabasePeptideIterator.cpp
+ * \brief Object to iterator over the peptides within a database
+ *****************************************************************************/
+
+#include "DatabasePeptideIterator.h"
+
+using namespace std;
+using namespace Crux;
+
+/***********************************************
+ * database_peptide_Iterators - can use the light protein functionality
+ * to save space
+ ***********************************************/
+
+/**
+ * Instantiates a new database_peptide_iterator from a database.
+ * \returns a DATABASE_PEPTIDE_ITERATOR_T object.
+ */
+
+DatabasePeptideIterator::DatabasePeptideIterator(
+ Database* database,
+ ///< the database of interest -in
+ PeptideConstraint* peptide_constraint,
+ ///< the peptide_constraint with which to filter peptides -in
+ bool store_all_peptides, ///< for removing duplicates
+ bool is_decoy ///< return decoy instead of target peptides
+ )
+{
+ Protein* next_protein = NULL;
+
+ // Initialize
+ database_protein_iterator_ = NULL;
+ cur_protein_peptide_iterator_ = NULL;
+ peptide_constraint_ = NULL;
+ prior_protein_ = NULL;
+ first_passed_ = false;
+ store_all_peptides_ = false;
+ is_decoy_ = is_decoy;
+
+
+ // set up peptide storage
+ store_all_peptides_ = store_all_peptides;
+ peptide_map_ = map<const char*, Peptide*, cmp_str>();
+ cur_map_position_ = peptide_map_.begin();
+
+ // set a new protein iterator
+ database_protein_iterator_ = new DatabaseProteinIterator(database);
+ if( database_protein_iterator_ == NULL){
+ carp(CARP_ERROR,
+ "Could not create protein iterator for database peptide iterator.");
+ }
+
+ // set peptide constraint
+ peptide_constraint_ = PeptideConstraint::copyPtr(peptide_constraint);
+
+ // check if there are any proteins to create peptides from
+ if(database_protein_iterator_->hasNext()){
+
+ next_protein = database_protein_iterator_->next();
+
+ // if using light/heavy functionality parse the light protein
+ if(database->getUseLightProtein() && next_protein->getIsLight()){
+ if(!next_protein->toHeavy()){
+ carp(CARP_FATAL, "failed to create a database_peptide_iterator,"
+ "no proteins in database");
+ }
+ }
+
+ // set new protein peptide iterator
+ cur_protein_peptide_iterator_ =
+ new ProteinPeptideIterator(next_protein, peptide_constraint);
+
+ // if first protein does not contain a match peptide, reinitailize
+ while(!cur_protein_peptide_iterator_->hasNext()) {
+ // covert the heavy back to light
+ /**
+ * uncomment this code if you want to restore a protein to
+ * light after converted to heavy
+ if(database->use_light_protein && !get_protein_is_light(next_protein)){
+ protein_to_light(next_protein);
+ }
+ */
+
+ // end of list of peptides for database_peptide_iterator
+ if(!database_protein_iterator_->hasNext()){
+ break;
+ }
+ else{ // create new protein_peptide_iterator for next protein
+ // free old iterator
+ delete (cur_protein_peptide_iterator_);
+
+ // get next protein
+ next_protein = database_protein_iterator_->next();
+
+ // if using light/heavy functionality parse the light protein
+ if(database->getUseLightProtein() && next_protein->getIsLight()){
+ if(!next_protein->toHeavy()){
+ carp(CARP_FATAL, "failed to create a database_peptide_iterator"
+ " no proteins in database");
+ }
+ }
+ // create new protein_peptide_iterator
+ cur_protein_peptide_iterator_ =
+ new ProteinPeptideIterator(next_protein, peptide_constraint);
+ }
+ }
+ }
+ else{ // no proteins to create peptides from
+ carp(CARP_FATAL, "failed to create a database_peptide_iterator,"
+ "no proteins in database");
+ }
+ // set the current working protein
+ prior_protein_ = next_protein;
+
+ // queue up first peptide
+ if( store_all_peptides ){
+ generateAllPeptides(); // fill the map
+ queueFirstPeptideFromMap();
+
+ } else {
+ next_peptide_ = nextFromFile();
+ }
+ // parent class requires a call to queueNextPeptide via initialize(),
+ // but the first peptide is already queued. This is a lazy way to
+ // get around it.
+ already_initialized_ = false;
+ initialize();
+}
+
+/**
+ * Private function to generate peptides for this iterator, sort them
+ * and remove duplicates before returning them to the caller.
+ * Peptides are stored in the iterator's member variable peptide_map.
+ */
+void DatabasePeptideIterator::generateAllPeptides(){
+
+ Peptide* cur_peptide = NULL;
+ map<const char*, Peptide*, cmp_str>& peptide_map = peptide_map_;
+ map<const char*, Peptide*, cmp_str>::iterator peptide_map_ptr;
+
+ // populate map with all peptides, combining when duplicates found
+ while(hasNextFromFile()){
+ cur_peptide = nextFromFile();
+ char* sequence = cur_peptide->getSequence();
+
+ // does it already exist in the map?
+ peptide_map_ptr = peptide_map.find(sequence);
+ if( peptide_map_ptr == peptide_map.end() ){ // not found, add it
+ peptide_map[(const char*)sequence] = cur_peptide;
+ } else { // already exists, combine new peptide with existing
+ Peptide::mergePeptidesCopySrc(peptide_map_ptr->second, cur_peptide);
+ delete cur_peptide;
+ std::free(sequence);
+ }
+ } // next peptide
+
+}
+
+/**
+ * Once the peptide_map has been populated with peptides, point the
+ * cur_peptide to first in map, point map pointer to second in map.
+ */
+void DatabasePeptideIterator::queueFirstPeptideFromMap(){
+
+ if( peptide_map_.empty() ){ // no peptides to return
+ next_peptide_ = NULL;
+ cur_map_position_ = peptide_map_.end();
+ return;
+ }
+
+ // set cur_peptide to first peptide in map
+ next_peptide_ = peptide_map_.begin()->second;
+ // set map pointer to one past first (i.e. next to return)
+ cur_map_position_ = peptide_map_.begin();
+ ++(cur_map_position_);
+}
+
+/**
+ * Frees an allocated database_peptide_iterator object.
+ */
+DatabasePeptideIterator::~DatabasePeptideIterator() {
+
+ delete cur_protein_peptide_iterator_;
+ delete database_protein_iterator_;
+ PeptideConstraint::free(peptide_constraint_);
+
+ // free seqs in map
+
+ map<const char*, Peptide*, cmp_str>::iterator peptide_iter =
+ peptide_map_.begin();
+ for(; peptide_iter != peptide_map_.end();
+ ++peptide_iter){
+
+ std::free((char*)peptide_iter->first); // free sequence
+ // peptide freed elsewhere? segfault if here
+ }
+ peptide_map_.clear();
+}
+
+/**
+ * The basic iterator functions.
+ * \returns true if there are additional peptides to iterate over,
+ * false if not.
+ */
+bool DatabasePeptideIterator::hasNextFromFile() {
+
+ return (cur_protein_peptide_iterator_->hasNext());
+}
+
+/**
+ * Implementation of PeptideIterator's method to prepare the iterator
+ * to return the next peptide.
+ * \returns True if there is another peptide to return, else false.
+ */
+bool DatabasePeptideIterator::queueNextPeptide() {
+
+ // parent class will make the first call without returning any peptides
+ // but we already queued up the first one in the constructor
+ if( already_initialized_ == false ){
+ already_initialized_ = true;
+ if(is_decoy_ && next_peptide_){
+ next_peptide_->transformToDecoy();
+ }
+ return (next_peptide_ != NULL); // are we starting out with a peptide
+ }
+ bool has_next = false;
+
+ // fetch next peptide either from file or from map
+ if( store_all_peptides_ ){
+ if( cur_map_position_ == peptide_map_.end() ){
+ next_peptide_ = NULL;
+ has_next = false;
+ } else {
+ next_peptide_ = cur_map_position_->second;
+ ++(cur_map_position_);
+ has_next = true;
+ }
+ } else {
+ if( hasNextFromFile() ){
+ next_peptide_ = nextFromFile();
+ has_next = (next_peptide_ != NULL);
+ } else {
+ next_peptide_ = NULL;
+ has_next = false;
+ }
+ }
+
+ // take care of decoys
+ if(is_decoy_ && next_peptide_){
+ next_peptide_->transformToDecoy();
+ }
+
+ return has_next;
+}
+
+/**
+ * \returns The next peptide in the database.
+ */
+Peptide* DatabasePeptideIterator::nextFromFile()
+{
+ /*BF: Could this be simplified? if next peptide, return it
+ if not, look for next protein, if not return NULL
+ */
+
+ // did you reset working protein?
+ bool reset = false;
+
+ // the peptide to return
+ Peptide* next_peptide =
+ cur_protein_peptide_iterator_->next();
+
+ Database* database =
+ database_protein_iterator_->getDatabase();
+
+ // reset database_peptide_iterator if needed
+ while(!cur_protein_peptide_iterator_->hasNext()){
+ reset = true;
+ Protein* next_protein = NULL;
+
+ /**
+ * uncomment this code if you want to restore a protein to
+ * light after converted to heavy
+ // covert the heavy back to light
+ if(database->use_light_protein && next_protein != NULL && !get_protein_is_light(next_protein)){
+ protein_to_light(next_protein);
+ }
+ */
+
+ // end of list of peptides for database_peptide_iterator
+ if(!database_protein_iterator_->hasNext()){
+ break;
+ }
+ else{ // create new protein_peptide_iterator for next protein
+ // free old iterator
+ delete cur_protein_peptide_iterator_;
+
+ // get next protein
+ next_protein =
+ database_protein_iterator_->next();
+
+ // if using light/heavy functionality parse the light protein
+ if(database->getUseLightProtein() && next_protein->getIsLight()){
+ if(!next_protein->toHeavy()){
+ carp(CARP_FATAL, "Failed to create a database_peptide_iterator, "
+ "no proteins in database");
+ }
+ }
+ // create new protein_peptide_iterator
+ cur_protein_peptide_iterator_ =
+ new ProteinPeptideIterator(next_protein, peptide_constraint_);
+ }
+ }
+
+ // are we using the light functionality?
+ if(database->getUseLightProtein()){
+ // get the current working protein
+ Protein* protein_bye = cur_protein_peptide_iterator_->getProtein();
+ // set first passed, shows that we extraced at least one protein since we moved on to the next protein
+ if(!reset && !first_passed_){
+ first_passed_ = true;
+ }
+ // convert prior_protein to light
+ else if(!reset && first_passed_ && (protein_bye != prior_protein_)){
+ /**
+ * uncomment this code if you want to restore a protein to
+ * light after converted to heavy
+ protein_to_light(database_peptide_iterator->prior_protein);
+ */
+ prior_protein_ = protein_bye;
+ }
+ }
+
+ return next_peptide;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/DatabasePeptideIterator.h b/src/model/DatabasePeptideIterator.h
new file mode 100644
index 0000000..98924c0
--- /dev/null
+++ b/src/model/DatabasePeptideIterator.h
@@ -0,0 +1,68 @@
+/**
+ * \file DatabasePeptideIterator.h
+ * $Revision: 1.27 $
+ * \brief Object to iterator over the peptides within a database
+ *****************************************************************************/
+
+#ifndef DATABASEPEPTIDEITERATOR_H
+#define DATABASEPEPTIDEITERATOR_H
+
+#include "model/objects.h"
+#include "DatabaseProteinIterator.h"
+#include "ProteinPeptideIterator.h"
+#include "PeptideConstraint.h"
+#include "PeptideIterator.h"
+
+class DatabasePeptideIterator : public PeptideIterator {
+ protected:
+ DatabaseProteinIterator* database_protein_iterator_;
+ ///< The protein iterator.
+ ProteinPeptideIterator* cur_protein_peptide_iterator_;
+ ///< The peptide iterator for the current protein.
+ PeptideConstraint* peptide_constraint_;
+ ///< The constraint for the kind of peptide to iterate over.
+ Crux::Protein* prior_protein_;
+ ///< the protein that was used before the current working protein
+ bool first_passed_;
+ ///< is it ok to convert prior_protein to light?
+ bool store_all_peptides_; ///< true for search so duplicates are combined
+ std::map<const char*, Crux::Peptide*, cmp_str> peptide_map_; ///< store peptides by sequence
+ std::map<const char*, Crux::Peptide*, cmp_str>::iterator cur_map_position_; ///< next in map to return
+ bool already_initialized_; ///< flag for first call to queueNextPeptide
+ bool is_decoy_; ///< transform all peptides to decoys before returning
+
+ /* Private Functions */
+ Crux::Peptide* nextFromFile();
+ bool hasNextFromFile();
+ void generateAllPeptides();
+ void queueFirstPeptideFromMap();
+
+ public:
+
+ /**
+ * Instantiates a new database_peptide_iterator from a database.
+ * \returns a DATABASE_PEPTIDE_ITERATOR_T object.
+ */
+ DatabasePeptideIterator(
+ Database* database, ///< the database of interest -in
+ PeptideConstraint* peptide_constraint, ///< the peptide_constraint to filter peptides -in
+ bool store_all_peptides, ///< true: parse all (unique) peptides into map
+ bool is_decoy = false ///< return decoy or target peptides
+ );
+
+ /**
+ * Frees an allocated database_peptide_iterator object.
+ */
+ ~DatabasePeptideIterator();
+
+ virtual bool queueNextPeptide();
+
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/DatabaseProteinIterator.cpp b/src/model/DatabaseProteinIterator.cpp
new file mode 100644
index 0000000..75aa8d6
--- /dev/null
+++ b/src/model/DatabaseProteinIterator.cpp
@@ -0,0 +1,81 @@
+/**
+ * \file DatabaseProteinIterator.cpp
+ * $Revision: 1.27 $
+ * \brief Object to iterator over the proteins within a database
+ *****************************************************************************/
+
+#include "DatabaseProteinIterator.h"
+using namespace Crux;
+
+/**
+ * Instantiates a new database_protein_iterator from a database.
+ *
+ * \returns a DATABASE_PROTEIN_ITERATOR_T object.
+ */
+DatabaseProteinIterator::DatabaseProteinIterator(
+ Database* database ///< the database to create a protein iterator -in
+ )
+{
+ // if database is parsed, if not do so..
+ if(!database->getIsParsed()){
+ // failed to parse database
+ if(!database->parse()){
+ carp(CARP_FATAL, "Failed to parse database, cannot create iterator");
+ }
+ }
+
+ database_ = Database::copyPtr(database);
+ cur_protein_ = 0;
+}
+
+
+/**
+ * Frees an allocated database_protein_iterator object.
+ */
+DatabaseProteinIterator::~DatabaseProteinIterator() {
+
+ // subtract pointer count
+ Database::freeDatabase(database_);
+}
+
+/**
+ * The basic iterator functions.
+ * \returns true if there are additional proteins to iterate over, false if not.
+ */
+bool DatabaseProteinIterator::hasNext()
+{
+ return (cur_protein_ < database_->getNumProteins());
+}
+
+
+/**
+ * \returns The next protein in the database.
+ */
+Protein* DatabaseProteinIterator::next()
+{
+ ++cur_protein_;
+
+ // print number of protein generated to STDERR for every 500 protein reached
+ if(cur_protein_ % 500 == 0){
+ carp(CARP_DETAILED_DEBUG, "Reached protein %d out of %d",
+ cur_protein_,
+ database_->getNumProteins());
+ }
+
+ return database_->getProteinAtIdx(cur_protein_-1);
+}
+
+/**
+ * \returns the protein database for this iterator
+ */
+Database* DatabaseProteinIterator::getDatabase() {
+
+ return database_;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/DatabaseProteinIterator.h b/src/model/DatabaseProteinIterator.h
new file mode 100644
index 0000000..663078c
--- /dev/null
+++ b/src/model/DatabaseProteinIterator.h
@@ -0,0 +1,64 @@
+/**
+ * \file DatabaseProteinIterator.h
+ * $Revision: 1.27 $
+ * \brief Object to iterator over the proteins within a database
+ *****************************************************************************/
+
+#ifndef DATABASEPROTEINITERATOR_H
+#define DATABASEPROTEINITERATOR_H
+
+#include "Database.h"
+
+class DatabaseProteinIterator {
+
+ protected:
+ Database* database_; ///< The database whose proteins to iterate over
+ unsigned int cur_protein_; ///< The index of the current protein
+
+ public:
+
+ /**
+ * Instantiates a new database_protein_iterator from a database.
+ * \returns a DATABASE_PROTEIN_ITERATOR_T object.
+ */
+ DatabaseProteinIterator(
+ Database* database ///< the database to create a protein iterator -in
+ );
+
+ /**
+ * Frees an allocated database_protein_iterator object.
+ */
+ virtual ~DatabaseProteinIterator();
+
+ /**
+ * The basic iterator functions.
+ * \returns TRUE if there are additional proteins to iterate over, FALSE if not.
+ */
+ bool hasNext();
+
+ /**
+ * \returns The next protein in the database.
+ */
+ Crux::Protein* next();
+
+ /**
+ * \returns the protein to the corresponding protein_idx in the database.
+ */
+ Crux::Protein* getProtein(
+ unsigned int protein_idx ///< protein_idx to which protein to return -in
+ );
+
+ /**
+ * \returns the protein database for this iterator
+ */
+ Database* getDatabase();
+
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/FilteredSpectrumChargeIterator.cpp b/src/model/FilteredSpectrumChargeIterator.cpp
new file mode 100644
index 0000000..9d32133
--- /dev/null
+++ b/src/model/FilteredSpectrumChargeIterator.cpp
@@ -0,0 +1,145 @@
+/*************************************************************************//**
+ * \file FilteredSpectrumChargeIterator.cpp
+ * AUTHOR: Chris Park
+ * CREATE DATE: 28 June 2006
+ * \brief code to support working with collection of multiple spectra
+ ****************************************************************************/
+#include "FilteredSpectrumChargeIterator.h"
+
+#include "parameter.h"
+#include "util/Params.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * \brief Sets up an iterator with the next spectrum that complies
+ * with the constraints. Sets has_next to FALSE when there are no
+ * more spectra in the collection that pass. Increments
+ * spectrum_index and charge_index.
+ */
+void FilteredSpectrumChargeIterator::queueNextSpectrum() {
+
+ Spectrum* spec = NULL;
+
+ // Are there any more charge states for this spectrum?
+ if( zstate_index_ < (int)zstates_.size()-1 ){
+ zstate_index_++;
+ }
+ // Are there any more spectra?
+ else if( spectrum_index_ < spectrum_collection_->getNumSpectra()-1){
+
+ spectrum_index_++;
+ spec = spectrum_collection_->spectra_[spectrum_index_];
+ // first free any existing zstates in the iterator
+ zstates_.clear();
+ zstates_ = spec->getZStatesToSearch();
+ zstate_index_ = 0;
+ }else{ // none left
+ has_next_ = false;
+ return;
+ }
+
+ // Does the current pass?
+ spec = spectrum_collection_->spectra_[spectrum_index_];
+ int this_charge = -1;
+ if (zstate_index_ < (int)zstates_.size()) {
+ this_charge = zstates_[zstate_index_].getCharge();
+ }
+ double mz = spec->getPrecursorMz();
+ int num_peaks = spec->getNumPeaks();
+
+ // Warn if we skip due to too few peaks.
+ if ( num_peaks < min_peaks_ ) {
+ num_skipped_++;
+ carp(CARP_DEBUG, "Skipping scan %d with %d (< %d) peaks.",
+ spectrum_index_, num_peaks, min_peaks_);
+ }
+
+ if( search_charge_ == 0 || search_charge_ == this_charge ){
+ if( mz >= min_mz_ && mz <= max_mz_
+ && num_peaks >= min_peaks_ ){
+ // passes all tests
+ has_next_ = true;
+ return;
+ }
+ }
+
+ // try the next spectrum
+ queueNextSpectrum();
+
+}
+
+
+ /**
+ * Instantiates a new spectrum_iterator object from
+ * spectrum_collection. This iterator returns unique spectrum-charge
+ * pairs (e.g.a spectrum to be searched as +2 and +3 is returned once
+ * as +2 and once as +3). The charge is returned by setting the int
+ * pointer in the argument list. The iterator also filters spectra by
+ * m/z so that none outside the spectrum-min-mz--spectrum-max-mz
+ * range (as defined in parameter.c). The iterator also filters by
+ * minimum number of peaks.
+ * \returns a SPECTRUM_ITERATOR_T object.
+ */
+FilteredSpectrumChargeIterator::FilteredSpectrumChargeIterator(
+ Crux::SpectrumCollection* spectrum_collection
+) {
+
+ spectrum_collection_ = spectrum_collection;
+ has_next_ = false;
+ spectrum_index_ = -1;
+ num_skipped_ = 0;
+ zstate_index_ = -1;
+ min_mz_ = Params::GetDouble("spectrum-min-mz");
+ max_mz_ = Params::GetDouble("spectrum-max-mz");
+ min_peaks_ = Params::GetInt("min-peaks");
+
+ string charge_str = Params::GetString("spectrum-charge");
+ if (charge_str == "all") {
+ search_charge_ = 0;
+ } else {
+ search_charge_ = atoi(charge_str.c_str());
+ }
+
+ // queue next spectrum
+ carp(CARP_DEBUG,"Queueing next spectrum");
+ queueNextSpectrum();
+ carp(CARP_DEBUG,"Done Queueing next spectrum");
+
+}
+
+FilteredSpectrumChargeIterator::~FilteredSpectrumChargeIterator() {
+
+}
+
+bool FilteredSpectrumChargeIterator::hasNext() {
+ return has_next_;
+}
+
+int FilteredSpectrumChargeIterator::numSkipped() {
+ return num_skipped_;
+}
+
+Spectrum* FilteredSpectrumChargeIterator::next(SpectrumZState& zstate) {
+
+ carp(CARP_DEBUG,"FilteredSpectrumChargeIterator::next()");
+ Spectrum* next_spectrum = NULL;
+ if (has_next_) {
+ next_spectrum =
+ spectrum_collection_->spectra_[spectrum_index_];
+
+ zstate = zstates_[zstate_index_];
+ carp(CARP_DEBUG,"Queueing next spectrum");
+ queueNextSpectrum();
+ carp(CARP_DEBUG,"Done queueing next spectrum");
+ }
+ return next_spectrum;
+
+}
+
+
+
+
+
+
diff --git a/src/model/FilteredSpectrumChargeIterator.h b/src/model/FilteredSpectrumChargeIterator.h
new file mode 100644
index 0000000..98becf5
--- /dev/null
+++ b/src/model/FilteredSpectrumChargeIterator.h
@@ -0,0 +1,81 @@
+/**
+ * \file FilteredSpectrumChargeIterator.h
+ * \brief Object for representing many spectra.
+ *****************************************************************************/
+#ifndef FILTEREDSPECTRUMCHARGEITERATOR_H
+#define FILTEREDSPECTRUMCHARGEITERATOR_H
+
+#include <vector>
+
+#include "Spectrum.h"
+#include "io/SpectrumCollection.h"
+
+class FilteredSpectrumChargeIterator {
+ protected:
+ Crux::SpectrumCollection* spectrum_collection_;///< spectra to iterate over
+ bool has_next_; ///< is there a spec that passes criteria
+ int spectrum_index_; ///< The index of the current spectrum
+ int num_skipped_; ///< Number of scans skipped due to too few peaks.
+ std::vector<SpectrumZState> zstates_; ///< Array of possible zstates to search
+ int zstate_index_; ///< The index of the z-state for the current spectrum
+ double min_mz_; ///< return only spec above this mz
+ double max_mz_; ///< return only spec below this mz
+ int search_charge_; ///< which z to search, 0 for all
+ int min_peaks_; ///< minimum number of peaks a spec must have
+
+ /**
+ * \brief Sets up an iterator with the next spectrum that complies
+ * with the constraints. Sets has_next to FALSE when there are no
+ * more spectra in the collection that pass. Increments
+ * spectrum_index and charge_index.
+ */
+ void queueNextSpectrum();
+
+ public:
+ /**
+ * Instantiates a new spectrum_iterator object from
+ * spectrum_collection. This iterator returns unique spectrum-charge
+ * pairs (e.g.a spectrum to be searched as +2 and +3 is returned once
+ * as +2 and once as +3). The charge is returned by setting the int
+ * pointer in the argument list. The iterator also filters spectra by
+ * mass so that none outside the spectrum-min-mz--spectrum-max-mz
+ * range (as defined in parameter.c). The iterator also filters by
+ * minimum number of peaks.
+ * \returns a SPECTRUM_ITERATOR_T object.
+ */
+ FilteredSpectrumChargeIterator(
+ Crux::SpectrumCollection* spectrum_collection
+ );
+
+ /**
+ * Frees an filtered_spectrum_charge_iterator object.
+ */
+ ~FilteredSpectrumChargeIterator();
+
+ /**
+ * The basic iterator function has_next.
+ */
+ bool hasNext();
+
+ /**
+ * Report number of skipped scans.
+ */
+ int numSkipped();
+
+ /**
+ * The basic iterator function next.
+ */
+ Crux::Spectrum* next(SpectrumZState& zstate);
+
+};
+
+
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/GeneratePeptidesIterator.cpp b/src/model/GeneratePeptidesIterator.cpp
new file mode 100644
index 0000000..e65b04b
--- /dev/null
+++ b/src/model/GeneratePeptidesIterator.cpp
@@ -0,0 +1,63 @@
+/**
+ * \file GeneratePeptidesIterator.h
+ * \brief An object to return candidate peptides from a database.
+ */
+#include <iostream>
+#include "GeneratePeptidesIterator.h"
+#include "DatabasePeptideIterator.h"
+
+using namespace std;
+
+GeneratePeptidesIterator::GeneratePeptidesIterator()
+{}
+
+GeneratePeptidesIterator::GeneratePeptidesIterator(
+ pair<FLOAT_T,FLOAT_T> min_max_mass, ///< precursor m/z of spectrum
+ bool is_decoy, ///< generate target or decoy peptides
+ Database* database, ///< database to provide peptides
+ int additional_missed_cleavages
+ )
+{
+ PeptideConstraint* constraint = PeptideConstraint::newFromParameters();
+ constraint->setMinMass(min_max_mass.first);
+ constraint->setMaxMass(min_max_mass.second);
+ constraint->setNumMisCleavage(constraint->getNumMisCleavage()+additional_missed_cleavages);
+
+
+
+ // Check that database exists
+ if (database == NULL){
+ carp(CARP_FATAL, "Cannot generate peptides when database is NULL.");
+ }
+
+ iterator_ = new DatabasePeptideIterator(database,
+ constraint,
+ true, // store all peptides
+ is_decoy);
+
+ initialize();
+ PeptideConstraint::free(constraint);
+}
+
+GeneratePeptidesIterator::~GeneratePeptidesIterator()
+{
+ delete iterator_;
+}
+
+bool GeneratePeptidesIterator::queueNextPeptide(){
+ if( iterator_ == NULL ){
+ carp(CARP_FATAL,
+ "GeneratePeptidesIterator is missing its database iterator.");
+ }
+
+ if( iterator_->hasNext() ){
+ carp(CARP_DETAILED_DEBUG,
+ "GeneratePeptidesIterator has a peptide, returning true");
+ next_peptide_ = iterator_->next();
+ return true;
+ }
+ // else
+
+ next_peptide_ = NULL;
+ return false;
+}
diff --git a/src/model/GeneratePeptidesIterator.h b/src/model/GeneratePeptidesIterator.h
new file mode 100644
index 0000000..00fabee
--- /dev/null
+++ b/src/model/GeneratePeptidesIterator.h
@@ -0,0 +1,41 @@
+/**
+ * \file GeneratePeptidesIterator.h
+ * \brief An object to return candidate peptides from a database.
+ */
+#ifndef GENERATEPEPTIDESITERATOR_H
+#define GENERATEPEPTIDESITERATOR_H
+
+#include <utility>
+#include "PeptideIterator.h"
+#include "Database.h"
+#include "PeptideConstraint.h"
+
+class GeneratePeptidesIterator : public PeptideIterator
+{
+ protected:
+ PeptideIterator* iterator_;
+
+ virtual bool queueNextPeptide();
+
+ public:
+ GeneratePeptidesIterator();
+
+ GeneratePeptidesIterator(
+ std::pair<FLOAT_T,FLOAT_T> min_max_mass, ///< max target mass of peptides
+ bool is_decoy, ///< generate target or decoy peptides
+ Database* database, ///< database to provide peptides
+ int additional_missed_cleavages = 0
+ );
+
+ ~GeneratePeptidesIterator();
+
+};
+
+#endif
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/Ion.cpp b/src/model/Ion.cpp
new file mode 100644
index 0000000..1b4edbd
--- /dev/null
+++ b/src/model/Ion.cpp
@@ -0,0 +1,1132 @@
+/*************************************************************************//**
+ * \file ion.cpp
+ * \brief Object for representing a single ion.
+ ****************************************************************************/
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "Ion.h"
+#include "util/Alphabet.h"
+#include "Peptide.h"
+#include "Peak.h"
+#include "util/mass.h"
+#include "util/utils.h"
+#include <sys/types.h>
+#ifndef _MSC_VER
+#include <netinet/in.h>
+#include <inttypes.h>
+#else
+#include <Winsock2.h>
+#include "util/WinCrux.h"
+#endif
+
+#include <stack>
+
+using namespace Crux;
+using namespace std;
+
+
+class IonCache {
+ protected:
+ stack<Ion*> cache_;
+ #ifdef DEBUG
+ int ncheckin;
+ int ncheckout;
+ #endif
+ public:
+ IonCache() {
+ #ifdef DEBUG
+ ncheckin = 0;
+ ncheckout = 0;
+ #endif
+ }
+
+ ~IonCache() {
+ while(!cache_.empty()) {
+ Ion* ion = cache_.top();
+ cache_.pop();
+ delete ion;
+ }
+ #ifdef DEBUG
+ carp(CARP_INFO, "Ion cache check in: %d check out:%d", ncheckin, ncheckout);
+ #endif
+ }
+
+ Ion* checkout() {
+ #ifdef DEBUG
+ ncheckout++;
+ #endif
+ if (cache_.empty()) {
+ return (new Ion());
+ } else {
+ Ion* ion = cache_.top();
+ cache_.pop();
+ return(ion);
+ }
+ }
+ void checkin(Ion* ion) {
+ #ifdef DEBUG
+ ncheckin++;
+ #endif
+ cache_.push(ion);
+ }
+};
+
+
+IonCache ion_cache_;
+
+
+// At one point I need to reverse the endianness for pfile_create to work
+ // Apparently that is no longer true. Hence 0 below.
+ static const bool REVERSE_ENDIAN = 0;
+
+ /**
+ * Array to store the modification masses
+ */
+ static FLOAT_T modification_masses[MAX_MODIFICATIONS];
+
+ /**
+ * Have we initialized the modification_masses?
+ */
+ static bool initialized_modification_masses = false;
+
+ static const int DETECTABLE_MZ_MIN = 200;
+ static const int DETECTABLE_MZ_MAX = 2400;
+
+
+/**
+ * initializes the mass array
+ */
+void Ion::initializeModificationMasses(
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+)
+{
+ // set modification mass
+ if(mass_type == MONO){
+ modification_masses[NH3] = -MASS_NH3_MONO;
+ modification_masses[H2O] = -MASS_H2O_MONO ;
+ modification_masses[ISOTOPE] = 1; // FIXME check this!!!
+ modification_masses[FLANK] = 1; // FIXME check this!!!
+ }
+ else if(mass_type == AVERAGE){
+ modification_masses[NH3] = -MASS_NH3_AVERAGE;
+ modification_masses[H2O] = -MASS_H2O_AVERAGE;
+ modification_masses[ISOTOPE] = 1; // FIXME check this!!!
+ modification_masses[FLANK] = 1; // FIXME check this!!!
+ }
+
+ initialized_modification_masses = true;
+}
+
+/**
+ * initializes an Ion object.
+ */
+void Ion::init() {
+ type_ = (ION_TYPE_T)0;
+ cleavage_idx_ = 0;
+ charge_ = 0;
+ peptide_sequence_.clear();
+ memset(modification_counts_,0,sizeof(int)*MAX_MODIFICATIONS);
+ ion_mass_z_ = 0;
+ peak_ = NULL;
+ pointer_count_ = 0;
+ CacheableMass::init();
+}
+
+/**
+ * \returns An (empty) ion object.
+ */
+Ion::Ion() {
+ init();
+}
+
+/**
+ * helper function
+ * only copies the pointer to the peptide sequence
+ * creates an heap allocated ion, ion mass is not calculated.
+ * \returns an ION_T object
+ */
+void Ion::initBasicIon(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const string& peptide ///< location for the new ion -in
+ )
+{
+ // init ion
+ init();
+ type_ = type;
+ cleavage_idx_ = cleavage_idx;
+ charge_ = charge;
+ peptide_sequence_ = peptide;
+ peak_ = NULL;
+}
+
+/**
+ * only copies the pointer to the peptide sequence
+ * ion mass/z with out any modification
+ * \returns an ION_T object
+ */
+Ion::Ion(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ )
+{
+ // get new basic ion
+ initBasicIon(type, cleavage_idx, charge, peptide);
+
+ // calculate and set ion mass/z
+ if(!calcMassZ(mass_type, false)){
+ carp(CARP_ERROR, "failed to calculate ion mass/z");
+ }
+}
+
+/**
+ * only copies the pointer to the peptide sequence
+ * inputs a array of all the modification counts
+ * \returns an ION_T object
+ */
+Ion::Ion(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ int* modification_counts ///< an array of modification counts for each modification -in
+ )
+{
+ // get new basic ion
+ initBasicIon(type, cleavage_idx, charge, peptide);
+
+ // set all modification counts in the ion
+ int modification_idx = 0;
+ for(; modification_idx < MAX_MODIFICATIONS; ++modification_idx){
+ modification_counts_[modification_idx] = modification_counts[modification_idx];
+ }
+
+ // calculate and set ion mass/z
+ if(!calcMassZ(mass_type, true)){
+ carp(CARP_ERROR, "failed to calculate ion mass/z");
+ }
+}
+
+/**
+ * only copies the pointer to the peptide sequence
+ * inputs a array of all the modification counts
+ * inputs the pre modified mass, of just all AA mass summed up.
+ * \returns an ION_T object
+ */
+Ion::Ion(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ FLOAT_T base_mass, ///< the base mass of the ion -in
+ int* modification_counts ///< an array of modification counts for each modification -in
+ )
+{
+ // get new basic ion
+ initBasicIon(type, cleavage_idx, charge, peptide);
+
+ // set all modification counts in the ion
+ int modification_idx = 0;
+ for(; modification_idx < MAX_MODIFICATIONS; ++modification_idx){
+ modification_counts_[modification_idx] = modification_counts[modification_idx];
+ }
+
+ // calculate and set ion mass/z
+ if(!calcMassZWithMass(mass_type, base_mass, true)){
+ carp(CARP_ERROR, "failed to calculate ion mass/z");
+ }
+}
+
+/**
+ * only copies the pointer to the peptide sequence
+ * inputs the pre modified mass, of just all AA mass summed up.
+ * \returns an ION_T object
+ */
+Ion::Ion(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ FLOAT_T base_mass ///< the base mass of the ion -in
+ ) {
+ init(type, cleavage_idx, charge, peptide, mass_type, base_mass);
+}
+
+void Ion::init(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ FLOAT_T base_mass ///< the base mass of the ion -in
+ )
+{
+ // get new basic ion
+ initBasicIon(type, cleavage_idx, charge, peptide);
+
+ // set all modification counts in the ion
+ int modification_idx = 0;
+ for(; modification_idx < MAX_MODIFICATIONS; ++modification_idx){
+ modification_counts_[modification_idx] = 0;
+ }
+
+ // calculate and set ion mass/z
+ if(!calcMassZWithMass(mass_type, base_mass, true)){
+ carp(CARP_ERROR, "failed to calculate ion mass/z");
+ }
+}
+
+
+/**
+ * frees A ION_T object
+ */
+Ion::~Ion() {
+}
+
+/**
+ * decrements the pointer and frees ion
+ */
+void Ion::freeIon(
+ Ion* ion ///< the ion to free
+ ) {
+
+ ion->pointer_count_--;
+
+ if (ion->pointer_count_ <= 0) {
+ ion_cache_.checkin(ion);//delete ion;
+ }
+}
+
+Ion* Ion::newIon() {
+ Ion* ion = ion_cache_.checkout();
+ ion->init();
+ return(ion);
+}
+
+/**
+ * increments the pointer count for the ion
+ */
+void Ion::incrementPointerCount() {
+ pointer_count_++;
+}
+
+
+/**
+ * prints the location and fields of ION_T object to the file, in the
+ * following format:
+ *
+ * m/z \\t mass \\t charge \\t ion-series \\t ...
+ * peptide-bond-index \\t modifications \n
+ *
+ * Where:
+ *
+ * m/z - is the ion's mass-to-charge
+ * mass - is the ion's (charged) mass
+ * charge - is the ion's charge e.g. 1,2,3
+ * ion-series - is one of (b,y,p)
+ * bond-index - is in [1...n), where n is peptide length
+ * modifications - is one of (none|nh3|h2o)
+ *
+ * if the ion has more than one modification, each will be printed on a
+ * separate line, with the necessary number of tabs to right justify
+ */
+void Ion::print(
+ FILE* file ///< to this file -in
+ )
+{
+ // print all fields of ion
+
+
+ char* type_str = ion_type_to_string(type_);
+
+ fprintf(file, "%.2f\t%.2f\t%d\t%s\t%d",
+ ion_mass_z_, (ion_mass_z_)*charge_, charge_,
+ type_str, cleavage_idx_);
+
+ free(type_str);
+
+ // iterate over all modification counts
+ int mod_idx;
+ for(mod_idx=0; mod_idx < MAX_MODIFICATIONS; ++mod_idx){
+ fprintf(file,"\t%d", modification_counts_[mod_idx]);
+ }
+
+ fprintf(file,"\n");
+}
+
+/**
+ * prints the ION_T object to the file, in the
+ * following format for GMTK single-ion models:
+ *
+ * 1. m/z ratio - ratio of the ion's mass-to-charge to the peptide's m/z
+ * 2. raw - raw intensity
+ * 3. rank - the ion rank
+ * 4. proton mobility - always set to 1 (for now) FIXME
+ * 5. m/z ratio int
+ * 6. index of the amide bond cleavage from N-term
+ * 7. index of the amide bond cleavage from C-term
+ * 8. Left amino acid ID
+ * 9. Right amino acid ID
+ * 10. Is this ion possible?
+ * 11. Is this ion detectable?
+ * 12. Is this ion detected?
+ */
+void Ion::printGmtkSingle(
+ FILE* file ///< to this file -in
+ ){
+
+ int has_mobile_proton = 1;
+ int is_detectable = 0;
+ int is_detected = 0;
+ int is_possible = 0;
+
+ FLOAT_T intensity = 0.0;
+ FLOAT_T intensity_rank = 0.0;
+ if (peak_ != NULL){
+ intensity = peak_->getIntensity();
+ intensity_rank = peak_->getIntensityRank();
+ is_detected = 1;
+ }
+
+ if ((ion_mass_z_ >= DETECTABLE_MZ_MIN) &&
+ (ion_mass_z_ <= DETECTABLE_MZ_MAX)){
+ is_detectable = 1;
+ }
+
+ FLOAT_T mz_ratio = (ion_mass_z_)/(getMass(MONO));
+ int mz_int = (int)(mz_ratio * (MZ_INT_MAX - MZ_INT_MIN) + MZ_INT_MIN);
+
+ const char* format = "%.6f\t%.6f\t%.6f\t%i\t%i\t%i\t%i\t%i\t%i\t%i\t%i\t%i\n";
+ fprintf(file, format,
+ mz_ratio, // 1
+ intensity, // 2
+ intensity_rank, // 3
+ has_mobile_proton, // 4
+ mz_int, // 5
+ cleavage_idx_, // 6
+ peptide_sequence_.length() - cleavage_idx_ + 1, // 7
+ Alphabet::aminoToInt(peptide_sequence_[cleavage_idx_-1]),// 8
+ Alphabet::aminoToInt(peptide_sequence_[cleavage_idx_]), // 9
+ is_possible, // 10
+ is_detectable, // 11
+ is_detected // 12
+ );
+}
+
+/*
+ * Same output as above, but in binary
+ *
+ * ints
+ *
+ * 0. m/z ratio - ratio of the ion's mass-to-charge to the peptide's m/z
+ * 1. raw - raw intensity
+ * 2. rank - the ion rank
+ *
+ * floats
+ *
+ * 0. proton mobility - always set to 1 (for now) FIXME
+ * 1. m/z ratio int
+ * 2. index of the amide bond cleavage from N-term
+ * 3. index of the amide bond cleavage from C-term
+ * 4. Left amino acid ID
+ * 5. Right amino acid ID
+ * 6. Is this ion possible?
+ * 7. Is this ion detectable?
+ * 8. Is this ion detected?
+
+ */
+void Ion::printGmtkSingleBinary(
+ FILE* file, ///< to this file -in
+ int sentence_idx,
+ int frame_idx
+ ){
+
+ FLOAT_T* float_array = (FLOAT_T*)mycalloc(sizeof(FLOAT_T), SINGLE_ION_FLOATS);
+ int* int_array = (int*)mycalloc(sizeof(int), SINGLE_ION_INTS);
+
+ FLOAT_T mz_ratio = (ion_mass_z_)/getMass(MONO);
+ float_array[0] = mz_ratio; // 0
+ float_array[1] = 0.0; // 1
+ float_array[2] = 0.0; // 2
+ int is_detected = 0;
+ if (peak_ != NULL){
+ float_array[1] = peak_->getIntensity(); //1
+ float_array[2] = peak_->getIntensityRank(); //2
+ is_detected = 1;
+
+#ifdef LOG_INTENSITY
+ // START
+ // replace the rank intensity with the negative log of the
+ // TIC normalized intensity. A hack, I know
+ float_array[2] = 10.0 + log(float_array[1]);
+#endif
+
+ }
+
+ int mz_int = (int)(mz_ratio * (MZ_INT_MAX - MZ_INT_MIN) + MZ_INT_MIN);
+ int cterm_idx = peptide_sequence_.length() - cleavage_idx_;
+ int left_amino = Alphabet::aminoToInt(peptide_sequence_[cleavage_idx_-1]);
+ int right_amino = Alphabet::aminoToInt(peptide_sequence_[cleavage_idx_]);
+ int is_detectable = 0;
+ if (
+ ((ion_mass_z_ >= DETECTABLE_MZ_MIN)
+ &&
+ (ion_mass_z_ <= DETECTABLE_MZ_MAX))
+
+ ||
+
+ is_detected
+
+ ){
+ is_detectable = 1;
+ }
+
+
+ int_array[0] = 1; // 0
+ int_array[1] = mz_int; // 1
+ int_array[2] = cleavage_idx_; // 2
+ int_array[3] = cterm_idx; // 3
+ int_array[4] = left_amino; // 4
+ int_array[5] = right_amino; // 5
+ int_array[6] = 1; // 6
+ int_array[7] = is_detectable; // 7
+ int_array[8] = is_detected; // 8
+
+ if (REVERSE_ENDIAN){
+
+ int idx;
+ for (idx=0; idx < 9; idx++){
+ int_array[idx] = htonl(int_array[idx]);
+ }
+ for (idx=0; idx < 3; idx++){
+ // htonl does not seem to work on the floats (!!)
+ // so I will reverse the bytes by hand
+ FLOAT_T old_float;
+ FLOAT_T new_float;
+
+ old_float = float_array[idx];
+
+ char *forward_endian = (char*) &old_float;
+ char *reversed_endian = (char*) &new_float;
+
+ reversed_endian[0] = forward_endian[3];
+ reversed_endian[1] = forward_endian[2];
+ reversed_endian[2] = forward_endian[1];
+ reversed_endian[3] = forward_endian[0];
+ float_array[idx] = new_float;
+ }
+
+ int big_end_sentence_idx = htonl(sentence_idx);
+ int big_end_frame_idx = htonl(frame_idx);
+
+ fwrite(&big_end_sentence_idx, sizeof(int), 1, file);
+ fwrite(&big_end_frame_idx, sizeof(int), 1, file);
+
+ } else {
+
+ fwrite(&sentence_idx, sizeof(int), 1, file);
+ fwrite(&frame_idx, sizeof(int), 1, file);
+
+ }
+
+ fwrite(float_array, sizeof(FLOAT_T), 3, file);
+ fwrite(int_array, sizeof(int), 9, file);
+ free(float_array);
+ free(int_array);
+}
+
+/**
+ * A hack routine to print out a null ion if there are none in the series.
+ * For using neutral losses with GMTK.
+ * Come in both binary and ascii versions.
+ */
+void Ion::printNullGmtkSingleBinary(
+ FILE* file,
+ int sentence_idx,
+ int frame_idx
+ ){
+
+ FLOAT_T float_array[3] = {0.0, 0.0, 0.0};
+ int int_array[9] = {0, 0, 0, 0, 0, 0, 0, 0, 0};
+ fwrite(&sentence_idx, sizeof(int), 1, file);
+ fwrite(&frame_idx, sizeof(int), 1, file);
+ fwrite(float_array, sizeof(FLOAT_T), 3, file);
+ fwrite(int_array, sizeof(int), 9, file);
+}
+
+/**
+ * A hack routine to print out a null ion if there are none in the series.
+ * For using neutral losses with GMTK.
+ */
+void Ion::printNullGmtkPairedBinary(
+ FILE* file,
+ int sentence_idx,
+ int frame_idx
+ ){
+
+ // FIX get rid of magic numbers
+ FLOAT_T float_array[6] = {0.0, 0.0, 0.0, 0.0, 0.0, 0.0};
+ int int_array[12] = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0};
+ fwrite(&sentence_idx, sizeof(int), 1, file);
+ fwrite(&frame_idx, sizeof(int), 1, file);
+ fwrite(float_array, sizeof(FLOAT_T), 6, file);
+ fwrite(int_array, sizeof(int), 12, file);
+}
+
+
+/**
+ * A hack routine to print out a null ion if there are none in the series.
+ * For using neutral losses with GMTK.
+ * Come in both binary and ascii versions.
+ */
+void Ion::printNullGmtkSingle(
+ FILE* file
+ ){
+
+ const char* string = "0.0\t0.0\t0.0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n";
+ fprintf(file, "%s", string);
+}
+
+
+/**
+ * prints the location and fields of the two ION_T objects to the file
+ * following format for GMTK paired-ion models:
+ *
+ * ints
+ *
+ * 1. m/z ratio int (from N-term)
+ * 2. m/z ratio int (from C-term)
+ * 3. peptide idx (from N-term)
+ * 4. peptide idx (from C-term)
+ * 5. aa Id (N-term)
+ * 6. aa Id (C-term)
+ * 7. first possible
+ * 8. first detectable
+ * 9. first detected
+ * 10. second possible
+ * 11. second observable
+ * 12. second detected
+ *
+ * floats
+ *
+ * 1. m/z ratio FLOAT_T (from N-term)
+ * 2. m/z ratio FLOAT_T (from C-term)
+ * 3. first raw
+ * 4. second raw
+ * 5. first rank
+ * 6. second rank
+ *
+ */
+void Ion::printGmtkPairedBinary(
+ Ion* first_ion, ///< print this ion -in
+ Ion* second_ion, ///< print this ion -in
+ FILE* file, ///< to this file -in
+ int sentence_idx,
+ int frame_idx
+ ){
+
+ FLOAT_T* float_array = (FLOAT_T*)mycalloc(sizeof(FLOAT_T), PAIRED_ION_FLOATS);
+ int* int_array = (int*)mycalloc(sizeof(int), PAIRED_ION_INTS);
+
+ // start with the floats
+ FLOAT_T n_mz_ratio = (first_ion->ion_mass_z_)/(first_ion->getMass(MONO));
+ float_array[0] = n_mz_ratio; // 0
+ // TODO
+ // subtract from 1.0?
+ FLOAT_T c_mz_ratio = 1.0 - n_mz_ratio; // 1
+ float_array[1] = c_mz_ratio;
+
+ int first_is_detected = 0;
+ if (first_ion->peak_ != NULL){
+ // put in LOG_INTENSITY ?
+ float_array[2] = first_ion->peak_->getIntensity(); //2
+ float_array[4] = first_ion->peak_->getIntensityRank();//4
+ first_is_detected = 1;
+ }
+
+ int second_is_detected = 0;
+ if (second_ion->peak_ != NULL){
+ // put in LOG_INTENSITY ?
+ float_array[3] = second_ion->peak_->getIntensity(); //3
+ float_array[5] = second_ion->peak_->getIntensityRank();//5
+ second_is_detected = 1;
+ }
+
+ // next do the ints
+ int n_mz_int = (int)(n_mz_ratio * (MZ_INT_MAX - MZ_INT_MIN) + MZ_INT_MIN);
+ int c_mz_int = (int)(c_mz_ratio * (MZ_INT_MAX - MZ_INT_MIN) + MZ_INT_MIN);
+ int cterm_idx = first_ion->peptide_sequence_.length()
+ - first_ion->cleavage_idx_;
+ int left_amino = Alphabet::aminoToInt(
+ first_ion->peptide_sequence_[first_ion->cleavage_idx_-1]);
+ int right_amino = Alphabet::aminoToInt(
+ first_ion->peptide_sequence_[first_ion->cleavage_idx_]);
+ int first_is_detectable = 0;
+ if (
+ ((first_ion->ion_mass_z_ >= DETECTABLE_MZ_MIN)
+ &&
+ (first_ion->ion_mass_z_ <= DETECTABLE_MZ_MAX))
+
+ ||
+
+ first_is_detected
+
+ ){
+ first_is_detectable = 1;
+ }
+
+ int second_is_detectable = 0;
+ if (
+ ((second_ion->ion_mass_z_ >= DETECTABLE_MZ_MIN)
+ &&
+ (second_ion->ion_mass_z_ <= DETECTABLE_MZ_MAX))
+
+ ||
+
+ second_is_detected
+
+ ){
+ second_is_detectable = 1;
+ }
+
+ int_array[0] = n_mz_int;
+ int_array[1] = c_mz_int;
+ int_array[2] = first_ion->cleavage_idx_;
+ int_array[3] = cterm_idx;
+ int_array[4] = left_amino;
+ int_array[5] = right_amino;
+ int_array[6] = 1; // TODO is possible always true?
+ int_array[7] = first_is_detectable;
+ int_array[8] = first_is_detected;
+ int_array[9] = 1; // TODO is possible always true?
+ int_array[10] = second_is_detectable;
+ int_array[11] = second_is_detected;
+
+ // account for endian differences
+ if (REVERSE_ENDIAN){
+
+ int idx;
+ for (idx=0; idx < PAIRED_ION_INTS; idx++){
+ int_array[idx] = htonl(int_array[idx]);
+ }
+ for (idx=0; idx < PAIRED_ION_FLOATS; idx++){
+ // htonl does not seem to work on the floats (!!)
+ // so I will reverse the bytes by hand
+ FLOAT_T old_float;
+ FLOAT_T new_float;
+
+ old_float = float_array[idx];
+
+ char *forward_endian = (char*) &old_float;
+ char *reversed_endian = (char*) &new_float;
+
+ reversed_endian[0] = forward_endian[3];
+ reversed_endian[1] = forward_endian[2];
+ reversed_endian[2] = forward_endian[1];
+ reversed_endian[3] = forward_endian[0];
+ float_array[idx] = new_float;
+ }
+
+ sentence_idx = htonl(sentence_idx);
+ frame_idx = htonl(frame_idx);
+ }
+
+ // output to the file
+ fwrite(&sentence_idx, sizeof(int), 1, file);
+ fwrite(&frame_idx, sizeof(int), 1, file);
+ fwrite(float_array, sizeof(FLOAT_T), PAIRED_ION_FLOATS, file);
+ fwrite(int_array, sizeof(int), PAIRED_ION_INTS, file);
+ free(float_array);
+ free(int_array);
+};
+
+/**
+ *\return the modified mass_z accodring to the modification type
+ */
+FLOAT_T Ion::modifyMassZ(
+ FLOAT_T mass_z, ///< the pre-modified ion mass_z -in
+ int modification_count, ///< number of times more the modification occurs -in
+ ION_MODIFICATION_T ion_modification, ///< the type of modification -in
+ int charge, ///< charge of the ion
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ )
+{
+ // initalize the modified masses(average|mono);
+ if(!initialized_modification_masses){
+ initializeModificationMasses(mass_type);
+ }
+
+ return mass_z + (modification_masses[(int)ion_modification]/(float)charge) * modification_count;
+}
+
+
+/**
+ * Adds the given ION_MODIFICATION to this ion
+ */
+void Ion::addModification(
+ ION_MODIFICATION_T modification, ///< add this modification to the ion -in
+ int modification_count, ///< the number of modifications -in
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ )
+{
+ // update modification count
+ modification_counts_[(int)modification] += modification_count;
+ // reset ion mass_z
+ ion_mass_z_ = modifyMassZ(ion_mass_z_,
+ modification_count,
+ modification,
+ charge_,
+ mass_type);
+}
+
+/**
+ * Adds the given ION_MODIFICATION to this ion
+ */
+void Ion::setPeak(
+ Peak * peak ///< peak to add to this ion -in
+ ){
+ peak_ = peak;
+};
+
+/**
+ *\returns the ion's AA mass added all up
+ */
+FLOAT_T Ion::getMass(
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ )
+{
+ FLOAT_T mass = 0;
+ bool reverse = false;
+
+ size_t start_idx = 0;
+ size_t end_idx = 0;
+
+ // get sequence for x,y,z ion
+ if(type_ == X_ION || type_ == Y_ION || type_ == Z_ION){
+ // convert the cleavage index into the actually index that start from the left.
+ end_idx = peptide_sequence_.length();
+ start_idx = end_idx - cleavage_idx_;
+ reverse = true;
+ }
+ // get sequence for a,b,c ion
+ else{
+ end_idx = cleavage_idx_;
+ }
+
+ // add up all AA mass
+ for(int ion_idx = start_idx; ion_idx < end_idx; ++ion_idx){
+ mass += get_mass_amino_acid(peptide_sequence_[ion_idx], mass_type);
+ }
+
+ // if X,Y,Z ion add H2O
+ if(reverse){
+ if(mass_type == AVERAGE){
+ mass += MASS_H2O_AVERAGE;
+ }else{
+ mass += MASS_H2O_MONO;
+ }
+ }
+
+ return mass;
+}
+
+/**
+ *\return the modified mass accodring to the modification type
+ */
+FLOAT_T Ion::modifyMass(
+ FLOAT_T mass, ///< the pre-modified ion mass -in
+ int modification_count, ///< number of times more the modification occurs -in
+ ION_MODIFICATION_T ion_modification, ///< the type of modification -in
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ )
+{
+ // initalize the modified masses(average|mono);
+ if(!initialized_modification_masses){
+ initializeModificationMasses(mass_type);
+ }
+
+ return mass + modification_masses[(int)ion_modification] * modification_count;
+}
+
+/**
+ * is_modified, indiciates if there are any modification to the ion
+ * speeds up the proccess if FALSE.
+ *\returns true if successfully computes the mass/z of the ion, else FALSE
+ */
+bool Ion::calcMassZWithMass(
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ FLOAT_T mass, ///< the basic mass of the ion -in
+ bool is_modified ///< are there any modifications for this ion? -in
+ )
+{
+ FLOAT_T h_mass = MASS_H_MONO;
+
+ // alter mass according to the modification
+ if(is_modified){
+ // iterate over all type of modifications for ion
+ int modification_idx = 0;
+ for(; modification_idx < MAX_MODIFICATIONS; ++modification_idx){
+ // update ion mass if modification is needed
+ if(modification_counts_[modification_idx] != 0){
+ mass = modifyMass(mass, modification_counts_[modification_idx],
+ (ION_MODIFICATION_T)modification_idx, mass_type);
+ }
+ }
+ }
+
+ // reset h mass if needed
+ if(mass_type == AVERAGE){
+ h_mass = MASS_H_AVERAGE;
+ }
+
+ // convert mass to m/z and assigned to ion
+ ion_mass_z_ = (mass + (h_mass*(FLOAT_T)charge_))/(FLOAT_T)charge_;
+
+ return true;
+}
+
+/**
+ * is_modified, indiciates if there are any modification to the ion
+ * speeds up the proccess if FLASE.
+ *\returns true if successfully computes the mass/z of the ion, else FALSE
+ */
+bool Ion::calcMassZ(
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ bool is_modified ///< are there any modifications for this ion? -in
+ )
+{
+ FLOAT_T mass = this->getMass(mass_type);
+ return this->calcMassZWithMass(mass_type, mass, is_modified);
+}
+
+/**
+ * Copies ion object from src to dest.
+ * must pass in a seperate pointer peptide sequence from its own ion_series object
+ * must pass in a memory allocated ION_T* dest
+ */
+void Ion::copy(
+ Ion* src,///< ion to copy from -in
+ Ion* dest,///< ion to copy to -out
+ const string& peptide_sequence ///< the peptide sequence that the dest should refer to -in
+ )
+{
+ dest->type_ = src->type_;
+ dest->cleavage_idx_ = src->cleavage_idx_;
+ dest->charge_ = src->charge_;
+
+ // set all modification counts in the ion
+ int modification_idx = 0;
+ for(; modification_idx < MAX_MODIFICATIONS; ++modification_idx){
+ dest->modification_counts_[modification_idx] = src->modification_counts_[modification_idx];
+ }
+
+ dest->ion_mass_z_ = src->ion_mass_z_;
+ dest->peptide_sequence_ = peptide_sequence;
+ CacheableMass::copy(src, dest);
+
+
+}
+
+/*
+ * Overriden function in CacheableMass
+ */
+FLOAT_T Ion::calcMass(MASS_TYPE_T mass_type) {
+ return Peptide::calcSequenceMass(peptide_sequence_, MONO);
+}
+
+
+/**
+ * \returns true if forward ion_type(A,B,C),
+ * else reverse ion_type(X,Y,Z) FALSE
+ */
+bool Ion::isForwardType()
+{
+ // is ion forward type?
+ if(type_ == B_ION ||
+ type_ == A_ION ||
+ type_ == C_ION)
+ {
+ return true;
+ }
+
+ // reverse type ion
+ return false;
+}
+
+/**
+ *\returns true if the ion has modifications, else FALSE
+ */
+bool Ion::isModified()
+{
+ int by_modification = 0;
+
+ // only add ions with no modifications
+ for(; by_modification < MAX_MODIFICATIONS; ++by_modification){
+ if(modification_counts_[by_modification] != 0){
+ return true;
+ }
+ }
+
+ return false;
+}
+
+/*********************************
+ * get, set methods for ion fields
+ *********************************/
+
+/**
+ * \returns the location of ION_T object
+ */
+FLOAT_T Ion::getMassZ()
+{
+ return ion_mass_z_;
+}
+
+/**
+ * sets the mass/z of the ION_T object
+ * while this can be calculated from the char*, cleavage_idx and
+ * modifications, it allows some optimizations if we allow it to be set
+ * instead
+ */
+void Ion::setMassZ(
+ FLOAT_T mass_z ///< the m/z location -in
+ )
+{
+ ion_mass_z_ = mass_z;
+}
+
+FLOAT_T Ion::getMassFromMassZ() {
+ FLOAT_T ans = (ion_mass_z_ - MASS_PROTON) * (FLOAT_T)charge_;
+ return ans;
+
+}
+
+void Ion::setMassZFromMass(
+ FLOAT_T mass
+ ) {
+
+ FLOAT_T charge = charge_;
+ ion_mass_z_ = (mass + MASS_PROTON * charge) / charge;
+
+}
+
+
+/**
+ * return the cleavage_idx of the ion object
+ */
+int Ion::getCleavageIdx()
+{
+ return cleavage_idx_;
+}
+
+/**
+ * set the cleavage_idx of the ion object
+ */
+void Ion::setCleavageIdx(
+ int cleavage_idx ///< the cleavage index in the peptide -in
+ )
+{
+ cleavage_idx_ = cleavage_idx;
+}
+
+/**
+ * return the charge of the ion object
+ */
+int Ion::getCharge()
+{
+ return charge_;
+}
+
+/**
+ * set the charge of the ion object
+ */
+void Ion::setCharge(
+ int charge ///< the charge of this ion -in
+ )
+{
+ charge_ = charge;
+}
+
+/**
+ * return the ION_TYPE_T of the ion object
+ */
+ION_TYPE_T Ion::getType()
+{
+ return type_;
+}
+
+/**
+ * set the ION_TYPE_T of the ion object
+ */
+void Ion::setType(
+ ION_TYPE_T ion_type ///< the ion type of this ion -in
+ )
+{
+ type_ = ion_type;
+}
+
+/**
+ * return the parent peptide sequence of the ion object
+ * returns a pointer to the sequence, should not free
+ */
+const string& Ion::getPeptideSequence()
+{
+ return peptide_sequence_;
+}
+
+/**
+ * return a pointer to the modification_count array of the ion object
+ */
+int* Ion::getModificationCounts()
+{
+ return modification_counts_;
+}
+
+/**
+ * return the count of in the modification_count array of the ion object
+ */
+int Ion::getSingleModificationCount(
+ ION_MODIFICATION_T mod_type ///< the modification count wanted -in
+ )
+{
+ return modification_counts_[mod_type];
+}
+
+int Ion::getTotalModificationCount() {
+ int total = 0;
+
+ for (int idx=NH3;idx < ALL_MODIFICATION;idx++) {
+ total += modification_counts_[idx];
+ }
+
+ return total;
+
+}
+
+
+/**
+ * set the parent peptide_sequence of the ion object
+ */
+void Ion::setPeptideSequence(
+ char* peptide_sequence ///< the parent peptide's sequence of this ion -in
+ )
+{
+ peptide_sequence_ = peptide_sequence;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/Ion.h b/src/model/Ion.h
new file mode 100644
index 0000000..672c5c6
--- /dev/null
+++ b/src/model/Ion.h
@@ -0,0 +1,473 @@
+/**
+ * \file Ion.h
+ * $Revision: 1.15 $
+ * \brief Object for representing one ion in an ion_series.
+ *
+ */
+#ifndef ION_H
+#define ION_H
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#include "model/objects.h"
+#include "util/utils.h"
+#include "util/mass.h"
+#include "Peak.h"
+#include "util/CacheableMass.h"
+
+static const int MAX_MODIFICATIONS = 4; ///< maximum modifications allowed per ion
+
+class Ion : public CacheableMass {
+
+ protected:
+ ION_TYPE_T type_; ///< type of the ion
+ int cleavage_idx_; ///< index of peptide amide that fragments to form this ion, starting from the N-term end
+ // N.b. this is different than the b1,y1 index, in that it always starts
+ // from the N-term
+ int charge_; ///< the ion charge
+ std::string peptide_sequence_;
+ int modification_counts_[MAX_MODIFICATIONS]; ///< an array of the number of different ion modifications
+ FLOAT_T ion_mass_z_; ///< The mass/z of the ion.
+ Peak * peak_; ///< The assigned peak. NULL if no peak // TODO add ptr count
+ int pointer_count_; ///< count of number of references to this ion.
+
+ static const int MZ_INT_MAX = 10;
+ static const int MZ_INT_MIN = 0;
+ static const int PAIRED_ION_INTS = 12;
+ static const int PAIRED_ION_FLOATS = 6;
+ static const int SINGLE_ION_FLOATS = 3;
+ static const int SINGLE_ION_INTS = 9;
+
+ /**
+ * helper function
+ * only copies the pointer to the peptide sequence
+ * creates an heap allocated ion, ion mass is not calculated.
+ * \returns an ION_T object
+ */
+ void initBasicIon(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const std::string& peptide ///< location for the new ion -in
+ );
+
+
+ // Override calcMass
+ virtual FLOAT_T calcMass(MASS_TYPE_T mass_type);
+
+
+ /**
+ * initializes the mass array
+ */
+ static void initializeModificationMasses(
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ );
+
+ /**
+ *\return the modified mass_z accodring to the modification type
+ */
+ FLOAT_T modifyMassZ(
+ FLOAT_T mass_z, ///< the pre-modified ion mass_z -in
+ int modification_count, ///< number of times more the modification occurs -in
+ ION_MODIFICATION_T ion_modification, ///< the type of modification -in
+ int charge, ///< charge of the ion
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ );
+
+ /**
+ *\return the modified mass accodring to the modification type
+ */
+ FLOAT_T modifyMass(
+ FLOAT_T mass, ///< the pre-modified ion mass -in
+ int modification_count, ///< number of times more the modification occurs -in
+ ION_MODIFICATION_T ion_modification, ///< the type of modification -in
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ );
+
+ /**
+ *\returns the ion's AA mass added all up
+ */
+ FLOAT_T getMass(
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ );
+
+ public:
+
+ /**
+ * initializes an Ion object.
+ */
+ void init();
+ void init(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const std::string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ FLOAT_T base_mass ///< the base mass of the ion -in
+ );
+
+ /**
+ * \returns An (empty) ion object.
+ */
+ Ion();
+
+ /**
+ * The peptide sequence is copied as a pointer.
+ * only copies the pointer to the peptide sequence
+ * cleavage index starts from 0...n (ex 0:A:1:K:2:V:3:..n:L)
+ * \returns an ION_T object
+ */
+ Ion(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const std::string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ );
+
+ /**
+ * only copies the pointer to the peptide sequence
+ * inputs a array of all the modification counts
+ * \returns an ION_T object
+ */
+ Ion(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const std::string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ int* modification_counts ///< an array of modification counts for each modification -in
+ );
+
+ /**
+ * only copies the pointer to the peptide sequence
+ * inputs a array of all the modification counts
+ * inputs the pre modified mass, of just all AA mass summed up.
+ * \returns an ION_T object
+ */
+ Ion(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const std::string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ FLOAT_T base_mass, ///< the base mass of the ion -in
+ int* modification_counts ///< an array of modification counts for each modification -in
+ );
+
+ /**
+ * only copies the pointer to the peptide sequence
+ * inputs the pre modified mass, of just all AA mass summed up.
+ * \returns an ION_T object
+ */
+ Ion(
+ ION_TYPE_T type, ///< intensity for the new ion -in
+ int cleavage_idx, ///< index into the peptide amide bonds of this ion
+ int charge, ///< charge of the ion
+ const std::string& peptide, ///< location for the new ion -in
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ FLOAT_T base_mass ///< the base mass of the ion -in
+ );
+
+ /**
+ * frees A ION_T object
+ */
+ ~Ion();
+
+ static Ion* newIon();
+
+ /**
+ * decrements the pointer and free the ion
+ */
+ static void freeIon(
+ Ion* ion ///< ion to free
+ );
+
+ /**
+ * Increments the pointer count
+ */
+ void incrementPointerCount();
+
+ /**
+ * prints the location and fields of ION_T object to the file, in the
+ * following format:
+ *
+ * m/z \\t mass \\t charge \\t ion-series \\t ...
+ * peptide-bond-index \\t modifications \n
+ *
+ * Where:
+ *
+ * m/z - is the ion's mass-to-charge
+ * mass - is the ion's (charged) mass
+ * charge - is the ion's charge e.g. 1,2,3
+ * ion-series - is one of (b,y,p)
+ * bond-index - is in [1...n), where n is peptide length
+ * modifications - is one of (none|nh3|h2o)
+ *
+ * if the ion has more than one modification, each will be printed on a
+ * separate line, with the necessary number of tabs to right justify
+ */
+ void print(
+ FILE* file ///< to this file -in
+ );
+
+ /**
+ * prints the location and fields of ION_T object to the file, in the
+ * following format for GMTK single-ion models:
+ *
+ * m/z \\t mass \\t charge \\t ion-series \\t ...
+ * peptide-bond-index \\t modifications \n
+ *
+ * Where:
+ *
+ * m/z - is the ion's mass-to-charge
+ * mass - is the ion's (charged) mass
+ * charge - is the ion's charge e.g. 1,2,3
+ * ion-series - is one of (b,y,p)
+ * bond-index - is in [1...n), where n is peptide length
+ * modifications - is one of (none|nh3|h2o)
+ *
+ * if the ion has more than one modification, each will be printed on a
+ * separate line, with the necessary number of tabs to right justify
+ */
+ void printGmtkSingle(
+ FILE* file ///< to this file -in
+ );
+
+ /**
+ * As print_ion_gmtk_single above, but in binary.
+ */
+ void printGmtkSingleBinary(
+ FILE* file, ///< to this file -in
+ int sentence_idx,
+ int frame_idx
+ );
+
+ /**
+ * Some hack routines to print out a null ion if there are none in the series.
+ * For using neutral losses with GMTK.
+ * Come in both binary and ascii versions.
+ */
+ void printNullGmtkSingleBinary(
+ FILE* file,
+ int sentence_idx,
+ int frame_idx
+ );
+
+ void printNullGmtkPairedBinary(
+ FILE* file,
+ int sentence_idx,
+ int frame_idx
+ );
+
+ /**
+ * A hack routine to print out a null ion if there are none in the series.
+ * For using neutral losses with GMTK.
+ * Come in both binary and ascii versions.
+ */
+ void printNullGmtkSingle(
+ FILE* file
+ );
+
+ /**
+ * prints the location and fields of the two ION_T objects to the file
+ * following format for GMTK paired-ion models:
+ *
+ * ints
+ *
+ * 1. m/z ratio int (from N-term)
+ * 2. m/z ratio int (from C-term)
+ * 3. peptide idx (from N-term)
+ * 4. peptide idx (from C-term)
+ * 5. aa Id (N-term)
+ * 6. aa Id (C-term)
+ * 7. first possible
+ * 8. first detectable
+ * 9. first detected
+ * 10. second possible
+ * 11. second observable
+ * 12. second detected
+ *
+ * floats
+ *
+ * 1. m/z ratio FLOAT_T (from N-term)
+ * 2. m/z ratio FLOAT_T (from C-term)
+ * 3. first raw
+ * 4. second raw
+ * 5. first rank
+ * 6. second rank
+ *
+ */
+ static void printGmtkPairedBinary(
+ Ion* first_ion, ///< print this ion -in
+ Ion* second_ion, ///< print this ion -in
+ FILE* file, ///< to this file -in
+ int sentence_idx,
+ int frame_idx
+ );
+
+ /**
+ * Adds the given ION_MODIFICATION to this ion
+ */
+ void addModification(
+ ION_MODIFICATION_T modification, ///< add this modification to the ion -in
+ int modification_count, ///< the number of modifications
+ MASS_TYPE_T mass_type ///< mass type (average, mono) -in
+ );
+
+ /**
+ * Adds the given ION_MODIFICATION to this ion
+ */
+ void setPeak(
+ Peak * peak ///< peak to add to this ion -in
+ );
+
+ /**
+ * Copies ion object from src to dest.
+ * must pass in a seperate pointer peptide sequence from its own ion_series object
+ * must pass in a memory allocated ION_T* dest
+ */
+ static void copy(
+ Ion* src,///< ion to copy from -in
+ Ion* dest,///< ion to copy to -out
+ const std::string& peptide_sequence ///< the peptide sequence that the dest should refer to -in
+ );
+
+ /**
+ *\returns TRUE if forward ion_type(A,B,C), else reverse ion_type(X,Y,Z) FALSE
+ */
+ bool isForwardType();
+
+ /**
+ *\returns TRUE if the ion has modifications, else FALSE
+ */
+ bool isModified();
+
+ /*********************************
+ * get, set methods for ion fields
+ *********************************/
+
+ /**
+ * \returns the location of ION_T object
+ */
+ FLOAT_T getMassZ();
+
+ /**
+ * sets the mass/z of the ION_T object
+ * while this can be calculated from the char*, cleavage_idx and
+ * modifications, it allows some optimizations if we allow it to be set
+ * instead
+ */
+ void setMassZ(
+ FLOAT_T mass_z ///< the m/z location -in
+ );
+
+ FLOAT_T getMassFromMassZ();
+
+ void setMassZFromMass(
+ FLOAT_T mass
+ );
+
+
+ /**
+ * return the cleavage_idx of the ion object
+ */
+ int getCleavageIdx();
+
+ /**
+ * set the cleavage_idx of the ion object
+ */
+ void setCleavageIdx(
+ int cleavage_idx ///< the cleavage index in the peptide -in
+ );
+
+ /**
+ * return the charge of the ion object
+ */
+ int getCharge();
+
+ /**
+ * set the charge of the ion object
+ */
+ void setCharge(
+ int charge ///< the charge of this ion -in
+ );
+
+ /**
+ * return the ION_TYPE_T of the ion object
+ */
+ ION_TYPE_T getType();
+
+ /**
+ * set the ION_TYPE_T of the ion object
+ */
+ void setType(
+ ION_TYPE_T ion_type ///< the ion type of this ion -in
+ );
+
+ /**
+ * return the parent peptide sequence of the ion object
+ * returns a pointer to the sequence, should not free
+ */
+ const std::string& getPeptideSequence();
+
+ /**
+ * return a pointer to the modification_count array of the ion object
+ */
+ int* getModificationCounts();
+
+ /**
+ * return the count of in the modification_count array of the ion object
+ */
+ int getSingleModificationCount(
+ ION_MODIFICATION_T mod_type ///< the modification count wanted -in
+ );
+
+ /**
+ * return the total number of modifications this ion has.
+ */
+ int getTotalModificationCount();
+
+ /**
+ * set the parent peptide_sequence of the ion object
+ */
+ void setPeptideSequence(
+ char* peptide_sequence ///< the parent peptide's sequence of this ion -in
+ );
+
+ /**
+ * is_modified, indiciates if there are any modification to the ion
+ * speeds up the proccess if FLASE.
+ *\returns TRUE if successfully computes the mass/z of the ion, else FALSE
+ */
+ bool calcMassZ(
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ bool is_modified ///< are there any modifications for this ion? -in
+ );
+
+ /**
+ * is_modified, indiciates if there are any modification to the ion
+ * speeds up the proccess if FLASE.
+ *\returns TRUE if successfully computes the mass/z of the ion, else FALSE
+ */
+ bool calcMassZWithMass(
+ MASS_TYPE_T mass_type, ///< mass type (average, mono) -in
+ FLOAT_T mass, ///< the basic mass of the ion -in
+ bool is_modified ///< are there any modifications for this ion? -in
+ );
+
+};
+
+/**
+ *
+ */
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/IonConstraint.cpp b/src/model/IonConstraint.cpp
new file mode 100644
index 0000000..7fa891c
--- /dev/null
+++ b/src/model/IonConstraint.cpp
@@ -0,0 +1,473 @@
+#include "IonConstraint.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include <string>
+#include "util/GlobalParams.h"
+
+using namespace std;
+/*************************
+ * ION_CONSTRAINT methods
+ *************************/
+
+/**
+ *Initializes an IonConstraint object, called from constructor
+ */
+void IonConstraint::init(){
+
+ use_neutral_losses_ = false;
+
+
+ int modification_idx = 0;
+
+ // initialize all modifications count to 0
+ for(; modification_idx < MAX_MODIFICATIONS; ++modification_idx){
+ modifications_[modification_idx] = 0;
+ }
+
+ for (int idx = 0;idx < NUMBER_ION_TYPES; idx++) {
+ ion_types_[idx] = false;
+ }
+
+ mass_type_ = MONO;
+ max_charge_ = 0;
+ ion_type_ = (ION_TYPE_T)0;
+ precursor_ion_ = false;
+ min_charge_ = 0;
+ exact_modifications_ = false;
+ pointer_count_ = 0;
+
+}
+
+/**
+ *\returns an empty heap allocated ion_constraint
+ */
+IonConstraint::IonConstraint() {
+
+ init();
+}
+
+/**
+ * modification, all modifications 0
+ * add more modifications as needed using the set_ion_constraint_modification
+ *\returns a new heap allocated ion_constraint
+ */
+IonConstraint::IonConstraint(
+ MASS_TYPE_T mass_type, ///< the mass_type to use MONO|AVERAGE
+ int max_charge, ///< max charge of the ions <= the parent peptide's charge
+ ION_TYPE_T ion_type, ///< the ion types the peptide series should include
+ bool precursor_ion ///< should include precursor ion?
+ )
+{
+
+ init();
+ use_neutral_losses_ = false;
+
+ // set all fields of constraint
+ mass_type_ = mass_type;
+
+ const string& charge_str = GlobalParams::getMaxIonCharge();
+ //string charge_str = get_string_parameter("max-ion-charge");
+
+ max_charge_ = max(1, max_charge - 1);
+
+ if (charge_str != "peptide") {
+ int charge_val;
+ if (StringUtils::TryFromString(charge_str, &charge_val)) {
+ max_charge_ = min(charge_val, max_charge_);
+ } else {
+ carp_once(CARP_WARNING, "Charge is not valid:%s", charge_str.c_str());
+ }
+ }
+
+ min_charge_ = 0;
+ exact_modifications_ = false;
+ ion_type_ = ion_type;
+ setUseIonType(ion_type, true);
+ precursor_ion_ = precursor_ion;
+ pointer_count_ = 1;
+
+}
+
+/**
+ * \brief Create a new ion constraint based on the score type and the
+ * charge of the peptide to be modeled. Uses other
+ * new_ion_constraint_ methods for some types.
+ *
+ * \returns A newly allocated ion constraint.
+ */
+IonConstraint* IonConstraint::newIonConstraintSmart(
+ SCORER_TYPE_T score_type,
+ int charge
+){
+
+ IonConstraint* new_constraint = NULL;
+
+ switch(score_type){
+ case SP:
+ new_constraint = newIonConstraintSequestSp(charge);
+ break;
+ case XCORR:
+ new_constraint = newIonConstraintSequestXcorr(charge);
+ break;
+ default:
+ // use default type for others
+ ION_TYPE_T ion_type = GlobalParams::getPrimaryIons();
+ //string_to_ion_type(get_string_parameter("primary-ions"), &ion_type);
+ new_constraint = new IonConstraint(
+ GlobalParams::getFragmentMass(),
+ //get_mass_type_parameter("fragment-mass"),
+ charge, ion_type,
+ GlobalParams::getPrecursorIons());
+ //get_boolean_parameter("precursor-ions"));
+ break;
+ }
+ return new_constraint;
+}
+
+
+
+/**
+ * modification, sets all fields for gmtk settings
+ *\returns a new heap allocated ion_constraint
+ */
+IonConstraint* IonConstraint::newIonConstraintGmtk(
+ int charge
+ )
+{
+ IonConstraint* constraint = NULL;
+
+ int max_charge = 1;
+ if(charge > 1){
+ max_charge = charge;
+ }
+ constraint = new IonConstraint(MONO, max_charge, ALL_ION, false);
+
+ // set all modifications count for gmtk
+ constraint->use_neutral_losses_ = true;
+ constraint->min_charge_ = 1;
+ constraint->modifications_[NH3] = -1;
+ constraint->modifications_[H2O] = -1;
+ constraint->modifications_[ISOTOPE] = 0;
+ constraint->modifications_[FLANK] = 0;
+
+ return constraint;
+}
+
+
+/**
+ * modification, sets all fields for sequest settings
+ *\returns a new heap allocated ion_constraint
+ */
+IonConstraint* IonConstraint::newIonConstraintSequest(
+ MASS_TYPE_T mass_type, ///< the mass_type to use MONO|AVERAGE
+ int max_charge, ///< the maximum charge of the ions.
+ ///< cannot exceed the parent peptide's charge
+ ION_TYPE_T ion_type, ///< the ion types the peptide series should include
+ bool precursor_ion ///< should include precursor ion?
+ )
+{
+ IonConstraint* constraint = new IonConstraint(mass_type, max_charge, ion_type, precursor_ion);
+
+ // set
+ constraint->use_neutral_losses_ = true;
+
+ // set all modifications count for sequest
+ constraint->modifications_[NH3] = 1;
+ constraint->modifications_[H2O] = 1;
+ constraint->modifications_[ISOTOPE] = 1;
+ constraint->modifications_[FLANK] = 1;
+
+ return constraint;
+}
+
+/**
+ * modification, sets all fields for sequest Sp scoring settings
+ * make B, Y type ions
+ *\returns a new heap allocated ion_constraint
+ */
+IonConstraint* IonConstraint::newIonConstraintSequestSp(
+ int charge ///< the maximum charge of the ions, cannot exceed the parent peptide's charge
+ )
+{
+ IonConstraint* constraint = NULL;
+ constraint = new IonConstraint(MONO, charge, BY_ION, false);
+
+ // set
+ constraint->use_neutral_losses_ = true;
+
+ // set all modifications count for sequest
+ constraint->modifications_[NH3] = 0;
+ constraint->modifications_[H2O] = 0;
+ constraint->modifications_[ISOTOPE] = 0;
+ constraint->modifications_[FLANK] = 0;
+
+ return constraint;
+}
+
+
+/**
+ * modification, sets all fields for Sequest Xcorr scoring settings
+ * make B, Y, A type ions
+ *\returns a new heap allocated ion_constraint
+ */
+IonConstraint* IonConstraint::newIonConstraintSequestXcorr(
+ int charge ///< the maximum charge of the ions, cannot exceed the parent peptide's charge
+ )
+{
+ IonConstraint* constraint = NULL;
+ constraint = new IonConstraint(MONO, charge, BYA_ION, false);
+
+ // set
+ constraint->use_neutral_losses_ = true;
+
+ // set all modifications count for sequest
+ constraint->modifications_[NH3] = 0;// -1;
+ constraint->modifications_[H2O] = 0;// -1;
+ constraint->modifications_[ISOTOPE] = 0;// not sure
+ constraint->modifications_[FLANK] = 0;
+
+ return constraint;
+}
+
+/**
+ * Frees an allocated ion_constraint object.
+ */
+void IonConstraint::free(IonConstraint* ion_constraint)
+{
+ ion_constraint->pointer_count_--;
+ if (ion_constraint->pointer_count_ == 0) {
+ delete ion_constraint;
+ }
+}
+
+
+IonConstraint::~IonConstraint()
+{
+}
+
+
+/**
+ * copies ion_constraint pointer
+ */
+IonConstraint* IonConstraint::copy(
+ IonConstraint* ion_constraint
+ ){
+
+ ion_constraint->pointer_count_++;
+ return ion_constraint;
+}
+
+
+/**
+ * copies ion_constraint object from src to dest
+ * must pass in a memory allocated ION_CONSTRAINT_T dest
+ */
+void IonConstraint::copy(
+ IonConstraint* src,///< ion_constraint to copy from -in
+ IonConstraint* dest///< ion_constraint to copy to -out
+ )
+{
+ int modification_idx = 0;
+ dest->use_neutral_losses_ = src->use_neutral_losses_;
+
+ // if use natural loss, copy
+ if(src->use_neutral_losses_){
+ // iterate over all modifications a update new constraint
+ for(; modification_idx < MAX_MODIFICATIONS; ++modification_idx){
+ dest->modifications_[modification_idx] = src->modifications_[modification_idx];
+ }
+ }
+
+ dest->mass_type_ = src->mass_type_;
+ dest->max_charge_ = src->max_charge_;
+ dest->ion_type_ = src->ion_type_;
+ dest->precursor_ion_ = src->precursor_ion_;
+}
+
+/** FIXME!!!! double check
+ * Determines if a ion satisfies a ion_constraint.
+ * \returns true if the constraint is satisified. false if not.
+ */
+bool IonConstraint::isSatisfied(
+ Ion* ion ///< query ion -in
+ )
+{
+ int* counts = NULL;
+
+ // TODO Fix
+ bool return_val = true;
+ // print_ion(ion, stderr);
+ // fprintf(stderr, "%i->%i\n", ion_constraint->min_charge, ion_constraint->max_charge);
+ // check ion type
+ ION_TYPE_T ion_type = ion->getType();
+ if(
+ !(ion_type == ion_type_)
+
+ &&
+
+ !((ion_type_ == BY_ION) && (ion_type == B_ION || ion_type == Y_ION))
+
+ &&
+
+ !((ion_type_ == BYA_ION)
+ &&
+ (ion_type == B_ION || ion_type == Y_ION || ion_type == A_ION))
+
+ &&
+
+ !(ion_type_ == ALL_ION)
+
+ ){
+
+ // precursor ion?
+ if(!(precursor_ion_ && ion_type == P_ION)){
+ return_val = false;
+ }
+ }
+
+ // check charge
+ if(ion->getCharge() > max_charge_){
+ return_val = false;
+ }
+
+ if(ion->getCharge() < min_charge_){
+ return_val = false;
+ }
+
+ // check modifications
+ counts = ion->getModificationCounts();
+ int mod_idx;
+ for(mod_idx=0; mod_idx < MAX_MODIFICATIONS; ++mod_idx){
+ if(modifications_[mod_idx] >= 0){
+ if(counts[mod_idx] > modifications_[mod_idx]){
+ return_val = false;
+ break;
+ }
+ }
+ else{
+ if(counts[mod_idx] < modifications_[mod_idx]){
+ return_val = false;
+ break;
+ }
+ }
+ if (exact_modifications_){
+ if(counts[mod_idx] != modifications_[mod_idx]){
+ return_val = false;
+ break;
+ }
+ }
+ }
+
+ // Add more checks here as more contraints are added
+
+ // fprintf(stderr, "r = %i\n", return_val);
+ return return_val;
+}
+
+/**
+ * \returns ION_TYPE for this constraint
+ */
+/*
+ION_TYPE_T IonConstraint::getIonType() {
+ return ion_type_;
+}
+*/
+
+void IonConstraint::setUseIonType(
+ ION_TYPE_T ion_type,
+ bool val
+ ) {
+ ion_types_[ion_type] = val;
+}
+
+bool IonConstraint::getUseIonType(ION_TYPE_T ion_type) {
+ return(ion_types_[ion_type]);
+}
+
+
+
+
+/**
+ * sets the modification count
+ * can only add isotopes
+ */
+void IonConstraint::setModification(
+ ION_MODIFICATION_T mod_type, ///< ion modification type -in
+ int count ///< the count of the modification -in
+ )
+{
+ // set modification count, can only add for isotope
+ if(mod_type != ISOTOPE){
+ modifications_[mod_type] = count;
+ }
+ else{
+ modifications_[mod_type] = abs(count);
+ }
+
+ // set neutral loss to true if needed
+ if(!use_neutral_losses_){
+ use_neutral_losses_ = true;
+ }
+}
+
+/**
+ * sets the exact modification boolean
+ */
+void IonConstraint::setExactness(
+ bool exactness ///< whether to use exact mods or not -in
+ ){
+ exact_modifications_ = exactness;
+ if (exactness){
+ min_charge_ = max_charge_;
+ }
+}
+
+/**
+ * gets the modification count for specific mod_type
+ */
+int IonConstraint::getModification(
+ ION_MODIFICATION_T mod_type ///< ion modification type -in
+ )
+{
+ return modifications_[mod_type];
+}
+
+/**
+ * \returns the modifications array
+ */
+int* IonConstraint::getModifications() {
+ return modifications_;
+}
+
+
+/**
+ * gets the mass type of the ion_constraint
+ */
+MASS_TYPE_T IonConstraint::getMassType()
+{
+ return mass_type_;
+}
+
+/**
+ * get the maximum charge of the IonConstraint
+ */
+int IonConstraint::getMaxCharge()
+{
+ return max_charge_;
+}
+
+/**
+ *\returns precuror_ion_
+ */
+bool IonConstraint::getPrecursorIon() {
+ return precursor_ion_;
+}
+
+/**
+ * get the neutral loss field of the ion constraint.
+ */
+bool IonConstraint::getUseNeutralLosses()
+{
+ return use_neutral_losses_;
+}
+
diff --git a/src/model/IonConstraint.h b/src/model/IonConstraint.h
new file mode 100644
index 0000000..60b92b0
--- /dev/null
+++ b/src/model/IonConstraint.h
@@ -0,0 +1,214 @@
+/**
+ * \file IonConstraint.h
+ * AUTHOR: Chris Park
+ * CREATE DATE: 28 June 2006
+ * \brief Object for defining constraints on an ion series.
+ *****************************************************************************/
+#ifndef IONCONSTRAINT_H
+#define IONCONSTRAINT_H
+
+#include "model/objects.h"
+
+#include "IonSeries.h"
+#include "Ion.h"
+
+/**
+ * \class ion_constraint
+ * \brief An object to represent the contraints which the ions in this
+ * series obey.
+ */
+class IonConstraint {
+ protected:
+ bool use_neutral_losses_; ///< Should ions include neutral losses
+ int modifications_[MAX_MODIFICATIONS];
+ ///< an array to indicate which modifications to perform
+ MASS_TYPE_T mass_type_;
+ ///< the mass_type to use MONO|AVERAGE
+ int max_charge_;
+ ///< maximum charge of the ions, cannot exceed the parent peptide's charge
+ ION_TYPE_T ion_type_;
+ ///< the ion types the peptide series should include
+
+ bool ion_types_[NUMBER_ION_TYPES];
+ bool precursor_ion_;
+ ///< does a precursor-ion satisfy this constraint
+ int min_charge_;
+ bool exact_modifications_;
+ ///< TRUE = ints in modfications array indicate exact number of mods
+ ///< FALSE = ints in modfications array indicate maximum number of mods
+ unsigned int pointer_count_; ///< Number of pointers referencing me
+
+ /**
+ *Initializes an IonConstraint object, called from constructor
+ */
+ void init();
+
+ public:
+
+ /**
+ *\returns an empty heap allocated ion_constraint
+ */
+
+ IonConstraint();
+
+ /**
+ * modification, all modifications 0
+ * add more modifications as needed using the set_ion_constraint_modification
+ *\returns a new heap allocated ion_constraint
+ */
+ IonConstraint(
+ MASS_TYPE_T mass_type, ///< the mass_type to use MONO|AVERAGE
+ int max_charge, ///< the maximum charge of the ions, cannot exceed the parent peptide's charge
+ ION_TYPE_T ion_type, ///< the ion types the peptide series should include
+ bool precursor_ion ///< should include precursor ion?
+ );
+
+ /**
+ * \brief Create a new ion constraint based on the score type and the
+ * charge of the peptide to be modeled. Uses other
+ * new_ion_constraint_ methods for some types.
+ *
+ * \returns A newly allocated ion constraint.
+ */
+ static IonConstraint* newIonConstraintSmart(
+ SCORER_TYPE_T score_type,
+ int charge
+ );
+
+ /**
+ * modification, sets all fields for sequest settings
+ *\returns a new heap allocated ion_constraint
+ */
+ static IonConstraint* newIonConstraintSequest(
+ MASS_TYPE_T mass_type, ///< the mass_type to use MONO|AVERAGE
+ int max_charge, ///< the maximum charge of the ions, cannot exceed the parent peptide's charge
+ ION_TYPE_T ion_type, ///< the ion types the peptide series should include
+ bool precursor_ion ///< should include precursor ion?
+ );
+
+ /**
+ * modification, sets all fields for GMTK settings
+ *\returns a new heap allocated ion_constraint
+ */
+ static IonConstraint* newIonConstraintGmtk(
+ int charge ///< the charge of the peptide for which to predict ions
+ );
+
+ /**
+ * modification, sets all fields for sequest Sp scoring settings
+ *\returns a new heap allocated ion_constraint
+ */
+ static IonConstraint* newIonConstraintSequestSp(
+ int max_charge ///< the maximum charge of the ions, cannot exceed the parent peptide's charge
+ );
+
+ /**
+ * modification, sets all fields for Sequest Xcorr scoring settings
+ * make B, Y, A type ions
+ *\returns a new heap allocated ion_constraint
+ */
+ static IonConstraint* newIonConstraintSequestXcorr(
+ int charge ///< the maximum charge of the ions, cannot exceed the parent peptide's charge
+ );
+
+ /**
+ * Frees an allocated ion_constraint object.
+ */
+ static void free(IonConstraint* ion_constraint);
+
+ virtual ~IonConstraint();
+
+ /**
+ * copies the ion_constraint pointer
+ */
+ static IonConstraint* copy(
+ IonConstraint* ion_constraint
+ );
+
+ /**
+ * copies ion_constraint object from src to dest
+ * must pass in a memory allocated ION_CONSTRAINT_T dest
+ */
+ static void copy(
+ IonConstraint* src,///< ion_constraint to copy from -in
+ IonConstraint* dest///< ion_constraint to copy to -out
+ );
+
+ /**
+ * Determines if a ion satisfies a ion_constraint.
+ * \returns TRUE if the constraint is satisified. FALSE if not.
+ */
+ bool isSatisfied(
+ Ion* ion ///< query ion -in
+ );
+
+ /**
+ * \returns ION_TYPE for this constraint
+ */
+ //ION_TYPE_T getIonType();
+
+ void setUseIonType(
+ ION_TYPE_T ion_type,
+ bool val
+ );
+
+ bool getUseIonType(
+ ION_TYPE_T ion_type
+ );
+
+ /**
+ * Sets the modification count
+ * can only add isotopes
+ */
+ void setModification(
+ ION_MODIFICATION_T mod_type, ///< ion modification type -in
+ int count ///< the count of the modification -in
+ );
+
+ /**
+ * Sets the exact modification boolean to exactness criteria
+ * and if exactness is true sets min_charge = max_charge.
+ * In other words, the constraint is now exact, in that it refers to a
+ * particular ion series, charge states, and modification state, as opposed
+ * to e.g. b-ions of charge state +1 or +2, or with or without NH3 loss
+ */
+ void setExactness(
+ bool exactness ///< whether to be exact or not -in
+ );
+
+ /**
+ * gets the modification count for specific mod_type
+ */
+ int getModification(
+ ION_MODIFICATION_T mod_type ///< ion modification type -in
+ );
+
+ int* getModifications();
+
+ /**
+ * gets the mass type of the ion_constraint
+ */
+ MASS_TYPE_T getMassType();
+
+ /**
+ * get the maximum charge of the IonConstraint
+ */
+ int getMaxCharge();
+
+
+ bool getPrecursorIon();
+
+ /**
+ * get the neutral loss field of the ion constraint.
+ */
+ bool getUseNeutralLosses();
+
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/IonFilteredIterator.cpp b/src/model/IonFilteredIterator.cpp
new file mode 100644
index 0000000..16a7bfc
--- /dev/null
+++ b/src/model/IonFilteredIterator.cpp
@@ -0,0 +1,108 @@
+/**
+ * \file IonFilteredIterator.cpp
+ * \brief An object to iterate over ion objects that meet constraints
+ * in the IonSeries.
+ *****************************************************************************/
+#include "IonFilteredIterator.h"
+
+/**
+ * sets up the iterator for next iteration.
+ *
+ *\returns true if successfully sets up the ion_filtered_iterator for next iteration
+ */
+bool IonFilteredIterator::setup()
+{
+ bool found = false;
+ Ion* current_ion = NULL;
+
+ // iterate over ions until discovers the first ion that meets the ion constraint
+ while((!found) && (ion_iterator_ != ion_iterator_end_)){
+ // get next ion
+ current_ion = *ion_iterator_;
+
+ // check if the current ion satisfies the ion_constraint for the iterator
+ if(constraint_->isSatisfied(current_ion)){
+ found = true;
+ ion_ = current_ion;
+ }
+ ++ion_iterator_;
+ }
+
+ has_next_ = found;
+
+ return true;
+}
+
+/**
+ * Only copies in the constraint as pointer
+ * Instantiates a new ion_filtered_iterator object from ion_series.
+ * \returns a IonFilteredIterator object.
+ */
+IonFilteredIterator::IonFilteredIterator(
+ IonSeries* ion_series, ///< ion_series to iterate -in
+ IonConstraint* constraint ///< ion_constraint which returned ions satisfy
+ )
+{
+
+
+ // set constraint, ion_series
+ constraint_ = constraint;
+ ion_series_ = ion_series;
+ has_next_ = false;
+
+ // set the working array of ions
+ if(constraint_->getUseIonType(ALL_ION) ||
+ constraint_->getUseIonType(BY_ION) ||
+ constraint_->getUseIonType(BYA_ION)) {
+
+ ion_iterator_ = ion_series->begin();
+ ion_iterator_end_ = ion_series->end();
+ }
+ else{
+ carp(CARP_FATAL, "DEPRECATED/FIX!");
+ //ion_iterator_ = ion_series->getSpecificIons(constraint->getIonType()).begin();
+ //ion_iterator_end_ = ion_series->getSpecificIons(constraint->getIonType()).end();
+ }
+
+ // initialize iterator
+ setup();
+
+}
+
+/**
+ * The constraint is NOT freed from the iterator.
+ * Frees an allocated ion_filtered_iterator object.
+ */
+IonFilteredIterator::~IonFilteredIterator()
+{
+
+}
+
+/**
+ * The basic iterator function has_next.
+ */
+bool IonFilteredIterator::hasNext()
+{
+ return has_next_;
+}
+
+/**
+ * The basic iterator function next.
+ */
+Ion* IonFilteredIterator::next()
+{
+
+ Ion* next_ion = NULL;
+
+ // check if a ion is present to return
+ if(!has_next_){
+ carp(CARP_FATAL, "index out of bounds for ion_filtered_iterator");
+ }
+
+ next_ion = ion_;
+
+ // re-initialize iterator
+ setup();
+
+ return next_ion;
+}
diff --git a/src/model/IonFilteredIterator.h b/src/model/IonFilteredIterator.h
new file mode 100644
index 0000000..078a625
--- /dev/null
+++ b/src/model/IonFilteredIterator.h
@@ -0,0 +1,70 @@
+/**
+ * \file IonFilteredIterator.h
+ ****************************************************************************/
+#ifndef IONFILTEREDITERATOR_H
+#define IONFILTEREDITERATOR_H
+
+#include "IonSeries.h"
+#include "IonConstraint.h"
+
+
+/**
+ * \class ion_filtered_iterator
+ * \brief An object to iterate over ion objects that meet constraint in
+ * the ion_series
+ */
+class IonFilteredIterator{
+ protected:
+ IonSeries* ion_series_; ///< the ion series that the ion we are iterating
+ IonConstraint* constraint_; ///< constraints which the ions obey
+ bool has_next_; ///< the boolean which the iterator has a next ion
+ int ion_idx_; ///< the current ion that is being returned
+ Ion* ion_; ///< the next ion to return when called upon
+
+ IonIterator ion_iterator_;
+ IonIterator ion_iterator_end_;
+ /**
+ * sets up the iterator for next iteration.
+ *
+ *\returns true if successfully sets up the ion_filtered_iterator for next iteration
+ */
+ bool setup();
+
+ public:
+
+ /**
+ * Only copies in the constraint as pointer
+ * Instantiates a new ion_filtered_iterator object from ion_series.
+ * \returns an IonFilteredIterator object.
+ */
+ IonFilteredIterator(
+ IonSeries* ion_series, ///< ion_series to iterate -in
+ IonConstraint* constraint ///< ion_constraint which returned ions satisfy
+ );
+
+ /**
+ * The constraint is NOT freed from the iterator.
+ * Frees an allocated ion_filtered_iterator object.
+ */
+ virtual ~IonFilteredIterator();
+
+ /**
+ * The basic iterator function has_next.
+ */
+ bool hasNext();
+
+ /**
+ * The basic iterator function next.
+ */
+ Ion* next();
+
+};
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/IonSeries.cpp b/src/model/IonSeries.cpp
new file mode 100644
index 0000000..6a621b6
--- /dev/null
+++ b/src/model/IonSeries.cpp
@@ -0,0 +1,1231 @@
+/*************************************************************************//**
+ * \file ion_series.cpp
+ * AUTHOR: Chris Park
+ * CREATE DATE: 21 Sep 2006
+ * \brief code to support working with a series of ions
+ ****************************************************************************/
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#include "Ion.h"
+#include "IonSeries.h"
+#include "util/Params.h"
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+#include "Peptide.h"
+#include "util/mass.h"
+#include "util/GlobalParams.h"
+#include "IonFilteredIterator.h"
+#include "Spectrum.h"
+
+#include <stack>
+
+using namespace Crux;
+
+static const int BINARY_GMTK = 1;
+static const int PRINT_NULL_IONS = 1;
+static const int MIN_FRAMES = 3;
+
+FLOAT_T* IonSeries::mass_matrix_ = NULL;
+
+
+/**
+ * \struct loss_limit
+ * \brief An object that specifies the max amount of neutral loss
+ * possible at a given cleavage index.
+ * All numbers are for forward ions(A,B,C) subtract from total to get
+ * reverse limit.
+ */
+struct loss_limit{
+ int nh3; ///< the limit to how many NH3 may be lost
+ int h2o; ///< the limit to how many H2O may be lost
+ // add more if needed for other neutral loss
+ // If change this struct, must also modify update_ion_series method
+};
+
+
+//Test cache for speeding up loss limit allocations
+class LossLimitCache {
+ protected:
+ stack<LOSS_LIMIT_T*> cache_;
+ public:
+ LossLimitCache() {
+ }
+
+ ~LossLimitCache() {
+ while(!cache_.empty()) {
+ LOSS_LIMIT_T *element = cache_.top();
+ cache_.pop();
+ delete []element;
+ }
+ }
+
+ LOSS_LIMIT_T* checkout() {
+ LOSS_LIMIT_T* new_element;
+ if (cache_.empty()) {
+ new_element = new LOSS_LIMIT_T[GlobalParams::getMaxLength()];
+ } else {
+ new_element = cache_.top();
+ cache_.pop();
+ }
+ return (new_element);
+ }
+ void checkin(LOSS_LIMIT_T* array) {
+ cache_.push(array);
+ }
+
+};
+
+static LossLimitCache loss_limit_cache;
+
+
+
+
+/**
+ * Initializes an (empty) ion_series object, only called by constructors.
+ */
+void IonSeries::init() {
+
+ peptide_.clear();
+ modified_aa_seq_ = NULL;
+ modified_aa_seq_owner_ = false;
+ charge_ = 0;
+ constraint_ = NULL;
+ is_predicted_ = false;
+ pointer_count_ = 1;
+ loss_limit_ = NULL;
+ peptide_length_ = 0;
+}
+
+/**
+ * \returns An (empty) ion_series object.
+ */
+IonSeries::IonSeries() {
+ init();
+}
+
+/**
+ * \brief Creates an ion series for a specific peptide, charge state,
+ * and constraint without acutally predicting the ions.
+ *
+ * Creates a copy of the peptide sequence and calcualtes the peptide
+ * mass.
+ * Use this method to create ion_series only when few are needed
+ * because the memory allocation process is expensive. Alternatively,
+ * use "new_ion_series_generic" and "update_ion_series" in combination
+ * to reuse an ion_seires object.
+ * \returns A newly allocated ion_series object from the given
+ * peptide, charge, and constraint.
+ */
+IonSeries::IonSeries(
+ const string& peptide, ///< The peptide for this ion series. -in
+ int charge, ///< The charge for this ion series -in
+ IonConstraint* constraint ///< constraints which these ions obey.
+ )
+{
+
+ init();
+ // copy the peptide sequence
+ peptide_ = peptide;
+ convert_to_mod_aa_seq(peptide_, &(modified_aa_seq_));
+ modified_aa_seq_owner_ = true;
+ charge_ = charge;
+ constraint_ = constraint;
+ peptide_length_ = peptide_.length();
+
+ // create the loss limit array
+ loss_limit_ = loss_limit_cache.checkout();
+ //loss_limit_ = new LOSS_LIMIT_T[GlobalParams::getMaxLength()];
+ memset(loss_limit_, 0, sizeof(LOSS_LIMIT_T) * peptide_length_);
+}
+
+/**
+ * \brief Creates an ion_series object without a specific peptide.
+ * Peptide details are added with the "update_ion_series" method.
+ * \returns A newly allocated ion_series object that must be updated
+ * for each peptide instance.
+ */
+IonSeries::IonSeries(
+ IonConstraint* constraint, ///< constraints which these ions obey.
+ int charge ///< The charge for this ion series -in
+ ) {
+
+ init();
+ constraint_ = constraint;
+ charge_ = charge;
+ loss_limit_ = loss_limit_cache.checkout();
+ //loss_limit_ = new LOSS_LIMIT_T[GlobalParams::getMaxLength()];
+}
+
+/**
+ * \brief Updates an ion_series to a specific instance of a peptide
+ * sequence. If the ion_series has already generated ions, they will
+ * be free-ed. A copy of the peptide sequence is made and all other
+ * variables (except ion_constraint) are also updated for the new
+ * peptide sequence.
+ */
+void IonSeries::update(
+ const char* peptide, ///< The peptide sequence with no mod characters. -in
+ const MODIFIED_AA_T* mod_seq ///< modified version of char* sequence -in
+ )
+{
+ int ion_type_idx = 0;
+
+ // Initialize the ion_series object for the new peptide sequence
+
+ // free old peptide sequence
+
+ if(modified_aa_seq_owner_ && modified_aa_seq_){
+ freeModSeq(modified_aa_seq_);
+ modified_aa_seq_owner_ = false;
+ }
+
+ // iterate over all ions, and free them
+ for (unsigned int idx=0;idx<ions_.size();idx++) {
+ Ion::freeIon(ions_[idx]);
+ }
+ ions_.clear();
+
+ // initialize all specific_ions back to 0
+ int ion_idx;
+
+ for(ion_idx=0; ion_type_idx < MAX_NUM_ION_TYPE; ++ion_type_idx){
+ specific_ions_[ion_type_idx].clear();
+ }
+
+ is_predicted_ = false;
+
+ // set ion_series for new instance of peptide
+
+ // copy the peptide sequence
+ peptide_ = peptide;
+ peptide_length_ = peptide_.length();
+
+ modified_aa_seq_ = (MODIFIED_AA_T*)mod_seq;
+
+ // Initialize the loss limit array for the new peptide
+ //carp(CARP_INFO, "loss_limit_:%d peptide_length:%d", loss_limit_, peptide_length_);
+ memset(loss_limit_, 0, sizeof(LOSS_LIMIT_T) * peptide_length_);
+}
+
+int IonSeries::incrementPointerCount() {
+ pointer_count_++;
+ return (pointer_count_);
+}
+
+void IonSeries::freeIonSeries(IonSeries* ions) {
+
+ ions->pointer_count_--;
+ if (ions->pointer_count_ <= 0) {
+ delete ions;
+ }
+}
+
+void IonSeries::clear() {
+ for (unsigned int idx=0;idx<ions_.size();idx++) {
+ Ion::freeIon(ions_[idx]);
+ }
+ ions_.clear();
+
+ // initialize all specific_ions back to 0
+ for(size_t ion_type_idx=0; ion_type_idx < MAX_NUM_ION_TYPE; ++ion_type_idx){
+ specific_ions_[ion_type_idx].clear();
+ }
+}
+/**
+ * Frees an allocated ion_series object.
+ */
+IonSeries::~IonSeries()
+{
+ if(modified_aa_seq_owner_ && modified_aa_seq_){
+ freeModSeq(modified_aa_seq_);
+ }
+ if(loss_limit_){
+ loss_limit_cache.checkin(loss_limit_);
+ }
+ // free constraint?
+
+ // iterate over all ions, and free them
+
+ for (unsigned int idx=0;idx<ions_.size();idx++) {
+ Ion::freeIon(ions_[idx]);
+ }
+ ions_.clear();
+
+}
+
+void IonSeries::finalize() {
+ delete []mass_matrix_;
+
+}
+
+
+/**
+ * Iterator access
+ */
+IonIterator IonSeries::begin() {
+ return ions_.begin();
+}
+
+IonIterator IonSeries::end() {
+ return ions_.end();
+}
+
+/**
+ * Prints a ion_series object to file.
+ */
+void IonSeries::print(
+ FILE* file ///< file for output -out
+ )
+{
+ // check if the ions has been already predicted
+ if(!is_predicted_){
+ carp(CARP_ERROR, "ion series has not predicted ions");
+ return;
+ }
+
+ // print header
+ fprintf(file, "m/z\tmass\tcharge\tion-series\tpeptide-bond-index\tnh3\th2o\tisotope\tflank\n");
+
+
+ // print each ion in the ion series
+ unsigned int ion_idx;
+ for(ion_idx=0; ion_idx < ions_.size(); ++ion_idx){
+ ions_[ion_idx]->print(file);
+ }
+}
+
+/**
+ * Prints a ion_series object to file, in GMTK single-ion format.
+ */
+void IonSeries::printSingleGmtk(
+ IonConstraint* ion_constraint, ///< ion_constraint to obey -in
+ FILE* file, ///< file output
+ int sentence_idx){
+
+ // create the filtered iterator that will select among the ions
+ IonFilteredIterator ion_iterator(this, ion_constraint);
+
+ // foreach ion in ion iterator, add matched observed peak intensity
+ Ion* ion;
+ int frame_idx = 0;
+ while(ion_iterator.hasNext()) {
+ ion = ion_iterator.next();
+
+#ifdef BINARY_GMTK
+ ion->printGmtkSingleBinary(file, sentence_idx, frame_idx);
+#else
+ ion->printGmtkSingle(file);
+ sentence_idx++; // hack to avoid error for not using sentence_idx
+#endif
+ frame_idx++;
+ }
+
+ // print a null ion if there are none in this ion series
+#ifdef PRINT_NULL_IONS
+ for (; frame_idx < MIN_FRAMES; frame_idx++){
+#ifdef BINARY_GMTK
+ print_null_ion_gmtk_single_binary(file, sentence_idx, frame_idx);
+#else
+ print_null_ion_gmtk_single(file);
+ sentence_idx++; // hack to avoid error for not using sentence_idx
+#endif
+ }
+#endif
+
+}
+
+/**
+ * Prints a ion_series object to file, in GMTK paired-ion format.
+ */
+void IonSeries::printPairedGmtk(
+ IonConstraint* first_ion_constraint, ///< ion_constraint to obey -in
+ IonConstraint* second_ion_constraint, ///< ion_constraint to obey -in
+ FILE* file, ///< file output
+ int sentence_idx
+ )
+{
+
+ // create the filtered iterator that will select among the ions
+ IonFilteredIterator ion_iterator(this, first_ion_constraint);
+
+ // foreach ion in ion iterator, add matched observed peak intensity
+ int frame_idx = 0;
+ while(ion_iterator.hasNext()){
+ Ion* first_ion = ion_iterator.next();
+ int cleavage_idx = first_ion->getCleavageIdx();
+ Ion* second_ion = this->getIon(second_ion_constraint, cleavage_idx);
+ if ( (first_ion == NULL) || (second_ion == NULL) ){
+ continue;
+ }
+ Ion::printGmtkPairedBinary(
+ first_ion,
+ second_ion,
+ file,
+ sentence_idx,
+ frame_idx++);
+ }
+
+#ifdef PRINT_NULL_IONS
+ for (; frame_idx < MIN_FRAMES; frame_idx++){
+ print_null_ion_gmtk_paired_binary(file, sentence_idx, frame_idx);
+ }
+#endif
+
+}
+
+
+/**
+ * \brief Find instances of amino acid which can incur neutral
+ * losses: H2O (S|T|E|D), NH3(R|K|Q|N).
+ * Set the count of those observed so far for each cleavage index.
+ * If no instance of amino acid, the count is assigned to 0
+ * The information is used to determine if how many nh3 or h2o neutral
+ * losses are possible.
+ */
+void IonSeries::scanForAAForNeutralLoss()
+{
+ int peptide_length = peptide_length_;
+ string sequence = peptide_;
+
+ // make sure loss_limit array is the right size
+ if (peptide_length_ != sequence.length()){
+ memset(loss_limit_, 0, sizeof(LOSS_LIMIT_T) * peptide_length_);
+ }
+
+ int h2o_aa = 0;
+ int nh3_aa = 0;
+
+ // search for the first instance of the amino acids
+ int cleavage_idx;
+ for(cleavage_idx=0; cleavage_idx < peptide_length; ++cleavage_idx){
+ LOSS_LIMIT_T* loss_limit_count = &loss_limit_[cleavage_idx];
+ // is the AA (S|T|E|D) ?
+ if(sequence[cleavage_idx] == 'S' ||
+ sequence[cleavage_idx] == 'T' ||
+ sequence[cleavage_idx] == 'E' ||
+ sequence[cleavage_idx] == 'D' )
+ {
+ loss_limit_count->h2o = ++h2o_aa;
+ loss_limit_count->nh3 = nh3_aa;
+ }
+ // is the AA (R|K|Q|N) ?
+ else if(sequence[cleavage_idx] == 'R' ||
+ sequence[cleavage_idx] == 'K' ||
+ sequence[cleavage_idx] == 'Q' ||
+ sequence[cleavage_idx] == 'N' )
+ {
+ loss_limit_count->nh3 = ++nh3_aa;
+ loss_limit_count->h2o = h2o_aa;
+ }
+ else{
+ loss_limit_count->h2o = h2o_aa;
+ loss_limit_count->nh3 = nh3_aa;
+ }
+ }
+
+}
+
+/**
+ * \brief Creates an array in which element i is the sum of the masses
+ * of amino acids 0 to (i-1). At i=0 is stored the length of the
+ * peptide.
+ * \returns an array of ion masses for all sub sequences
+ */
+FLOAT_T* IonSeries::createIonMassMatrix(
+ //char* peptide, ///< The peptide for this ion series. -in
+ MODIFIED_AA_T* modified_seq, ///< the sequence
+ MASS_TYPE_T mass_type, ///< the mass_type to use MONO|AVERAGE
+ int peptide_length ///< the length of the peptide
+ )
+{
+ if( modified_seq == NULL ){
+ //if( peptide == NULL ){
+ carp(CARP_ERROR, "Cannot create mass matrix from NULL seqence");
+ return NULL;
+ }
+
+ if (mass_matrix_ == NULL) {
+ //Allocate the static mass_matrix_
+ mass_matrix_ = new FLOAT_T[sizeof(FLOAT_T)*(GlobalParams::getMaxLength()+1)];
+ }
+
+ FLOAT_T* mass_matrix = mass_matrix_;
+
+ // at index 0, the length of the peptide is stored
+ mass_matrix[0] = peptide_length;
+
+ // add up AA masses
+ int ion_idx = 1;
+ // initialize first to be mass of c-term amino acid
+ // mass_matrix[ion_idx] = get_mass_amino_acid(peptide[ion_idx-1], mass_type);
+ mass_matrix[ion_idx] = get_mass_mod_amino_acid(modified_seq[ion_idx-1], mass_type);
+ //++ion_idx;
+ //for(; ion_idx <= peptide_length; ++ion_idx){
+ for(ion_idx = 2; ion_idx <= peptide_length; ++ion_idx){
+ mass_matrix[ion_idx] = mass_matrix[ion_idx-1] +
+ get_mass_mod_amino_acid(modified_seq[ion_idx-1], mass_type);
+ //get_mass_amino_acid(peptide[ion_idx-1], mass_type);
+ }
+ // DEBUGGING
+ /*
+ fprintf(stderr, "seq:");
+ for(ion_idx = 0; ion_idx < peptide_length; ++ion_idx){
+ fprintf(stderr, "\t%s", modified_aa_to_string(modified_seq[ion_idx]));
+ }
+ fprintf(stderr, "\nmas:");
+ for(ion_idx = 0; ion_idx < peptide_length; ++ion_idx){
+ fprintf(stderr, "\t%.2f", get_mass_mod_amino_acid(modified_seq[ion_idx], MONO));
+ }
+ fprintf(stderr, "\nsum:");
+ for(ion_idx = 0; ion_idx < peptide_length; ++ion_idx){
+ fprintf(stderr, "\t%.2f", mass_matrix[ion_idx+1]);
+ }
+ fprintf(stderr, "\n");
+ */
+ return mass_matrix;
+}
+
+/**
+ * user must ensure that there is enough space for this ion
+ * adds ion to ion_series' master ion_array and if B|Y ion to the specific ion_array
+ */
+void IonSeries::addIon(
+ Ion* ion ///< ion to add -in
+ )
+{
+ // add ion to ion series
+ ions_.push_back(ion);
+
+ // increment the pointer
+ ion->incrementPointerCount();
+
+ // add a pointer of ion to the specific ion_type array
+ specific_ions_[ion->getType()].push_back(ion);
+}
+
+/**
+ * helper function: add_ions
+ * add all the ions to ion_series up to the max charge
+ *\returns true if successfully adds all ions, else false
+ */
+bool IonSeries::addIonsByCharge(
+ FLOAT_T mass, ///< the base mass of the ion to add
+ int cleavage_idx, ///< the absolute cleavage index (A,B,C from left X,Y,Z from right)
+ ION_TYPE_T ion_type ///< the ion type of the ions to be added
+ )
+{
+ IonConstraint* constraint = constraint_;
+ int charge_idx = 1;
+ Ion* ion = NULL;
+ int max_charge;
+
+ // set the max charge, the maximum cannot exceed the precursor ion's charge
+ if(constraint->getMaxCharge() > charge_){
+ max_charge = charge_;
+ }
+ else{
+ max_charge = constraint->getMaxCharge();
+ }
+
+ // iterate over all different charge
+ for(; charge_idx <= max_charge; ++charge_idx){
+ // create ion
+ ion = Ion::newIon();
+ ion->init(ion_type,
+ cleavage_idx,
+ charge_idx,
+ peptide_,
+ constraint->getMassType(),
+ mass);
+ // add ion to ion series
+ this->addIon(ion);
+ }
+
+ return true;
+}
+
+/**
+ * Creates all the ions with no modifications up to the max charge
+ * Adds each ion to ion_series
+ *\returns true if successfully generates all the ions, else false
+ */
+bool IonSeries::generateIonsNoModification(
+ FLOAT_T* mass_matrix ///< the mass matrix that stores the mass
+ )
+{
+ if( mass_matrix == NULL ){
+ carp(CARP_ERROR,
+ "Cannot generate ions from NULL mass matrix");
+ return false;
+ }
+ int cleavage_idx = 1;
+ IonConstraint* constraint = constraint_;
+ FLOAT_T mass = 0;
+
+ // get peptide length
+ int peptide_length = (int)mass_matrix[0];
+
+ // iterate over all cleavage index
+ for(; cleavage_idx < peptide_length; ++cleavage_idx){
+
+ // add A ion
+ if(constraint->getUseIonType(A_ION)
+ || constraint->getUseIonType(BYA_ION)
+ || constraint->getUseIonType(ALL_ION)){
+
+ // set mass
+ mass = mass_matrix[cleavage_idx];
+
+ if(constraint->getMassType() == MONO){
+ mass -= MASS_CO_MONO;
+ }
+ else{ // average
+ mass -= MASS_CO_AVERAGE;
+ }
+
+ // add ions up to max charge
+ if(!this->addIonsByCharge(mass, cleavage_idx, A_ION)){
+ carp(CARP_ERROR, "failed to add ions by different charge for A ion");
+ return false;
+ }
+ }
+
+ // add B ion
+ if(constraint->getUseIonType(ALL_ION)
+ || constraint->getUseIonType(BY_ION)
+ || constraint->getUseIonType(BYA_ION)
+ || constraint->getUseIonType(B_ION)){
+
+ // set mass
+ mass = mass_matrix[cleavage_idx];
+
+ // add ions up to max charge
+ if(!this->addIonsByCharge(mass, cleavage_idx, B_ION)){
+ carp(CARP_ERROR, "failed to add ions by different charge for B ion");
+ return false;
+ }
+
+ }
+
+ // add C ion
+ if(constraint->getUseIonType(C_ION)
+ || constraint->getUseIonType(ALL_ION)){
+ // set mass
+ mass = mass_matrix[cleavage_idx];
+
+ if(constraint->getMassType() == MONO){
+ mass += MASS_NH3_MONO;
+ }
+ else{ // average
+ mass += MASS_NH3_AVERAGE;
+ }
+
+ // add ions up to max charge
+ if(!this->addIonsByCharge(mass, cleavage_idx, C_ION)){
+ carp(CARP_ERROR, "failed to add ions by different charge for C ion");
+ return false;
+ }
+ }
+
+ // add X ion
+ if(constraint->getUseIonType(X_ION)
+ || constraint->getUseIonType(ALL_ION)){
+ // set mass
+ mass = mass_matrix[(int)mass_matrix[0]] - mass_matrix[(int)mass_matrix[0] - cleavage_idx];
+
+ if(constraint->getMassType() == MONO){
+ mass += MASS_CO_MONO + MASS_H2O_MONO;
+ }
+ else{ // average
+ mass += MASS_CO_AVERAGE + MASS_H2O_AVERAGE;
+ }
+
+ // add ions up to max charge
+ if(!this->addIonsByCharge(mass, cleavage_idx, X_ION)){
+ carp(CARP_ERROR, "failed to add ions by different charge for X ion");
+ return false;
+ }
+ }
+
+ // add Y ion
+ if(constraint->getUseIonType(ALL_ION) ||
+ constraint->getUseIonType(BY_ION) ||
+ constraint->getUseIonType(BYA_ION) ||
+ constraint->getUseIonType(Y_ION)){
+
+ // set mass
+ mass = mass_matrix[(int)mass_matrix[0]] - mass_matrix[(int)mass_matrix[0] - cleavage_idx];
+
+ if(constraint->getMassType() == MONO){
+ mass += MASS_H2O_MONO;
+ }
+ else{ // average
+ mass += MASS_H2O_AVERAGE;
+ }
+
+ // add ions up to max charge
+ if(!this->addIonsByCharge(mass, cleavage_idx, Y_ION)){
+ carp(CARP_ERROR, "failed to add ions by different charge Y ion");
+ return false;
+ }
+
+ }
+
+ // add Z ion
+ if(constraint->getUseIonType(Z_ION) ||
+ constraint->getUseIonType(ALL_ION) ){
+
+ // set mass
+ mass = mass_matrix[(int)mass_matrix[0]] - mass_matrix[(int)mass_matrix[0] - cleavage_idx];
+
+ if(constraint->getMassType() == MONO){
+ mass = mass - MASS_NH3_MONO + MASS_H2O_MONO;
+ }
+ else{ // average
+ mass = mass - MASS_NH3_AVERAGE + MASS_H2O_AVERAGE;
+ }
+
+ // add ions up to max charge
+ if(!this->addIonsByCharge(mass, cleavage_idx, Z_ION)){
+ carp(CARP_ERROR, "failed to add ions by different charge Z ion");
+ return false;
+ }
+ }
+ }
+
+ // add P ion(precursor ion)?
+ if(constraint_->getPrecursorIon()){
+
+ // set mass
+ mass = mass_matrix[(int)mass_matrix[0]];
+
+ // mass type
+ if(constraint->getMassType() == MONO){
+ mass += MASS_H2O_MONO;
+ }
+ else{ // average
+ mass += MASS_H2O_AVERAGE;
+ }
+
+ // add ions up to max charge
+ if(!addIonsByCharge(mass, (int)mass_matrix[0], P_ION)){
+ carp(CARP_ERROR, "failed to add ions by different charge P ion");
+ return false;
+ }
+ }
+
+ return true;
+}
+
+/**
+ * The modification depends on the loss/add && if the ion contains RKQN or STED
+ * The number of losses possible cannot exceed the number of RKQN or STED in the ion
+ * The loss_limit array in the ion_series must be populated prior to this method call
+ *\returns true if the ion can lose the mod_type modification, else false
+ */
+bool IonSeries::canIonGenerateModification(
+ Ion* ion, ///< the ion to check if can lose nh3 -in
+ ION_MODIFICATION_T mod_type, ///< generate ions of this modification_type -in/out
+ int increment ///< the add/loss of the modification
+ )
+{
+
+ //Make sure that an ion can have 0 or 1 modifications.
+ if (ion->getTotalModificationCount() == 1) {
+ return false;
+ }
+
+
+ int cleavage_idx = ion->getCleavageIdx();
+
+ // check for NH3 modification
+ if(mod_type == NH3){
+ // adding is ok
+ if(increment >= 0){
+ return true;
+ }
+
+ // is forward ion_type(ABC)?
+ if(ion->isForwardType()){
+ // does this ion contain enough counts of the RKQN
+ if(-increment > (&loss_limit_[cleavage_idx-1])->nh3){
+ return false;
+ }
+ return true;
+ }
+ else{// backward ions XYZ
+ // does this ion contain enough counts of the RKQN
+ if(cleavage_idx == peptide_length_){
+ if(-increment > (&loss_limit_[peptide_length_-1])->nh3){
+ return false;
+ }
+ }
+ else if(-increment >
+ ((&loss_limit_[peptide_length_-1])->nh3 -
+ (&loss_limit_[peptide_length_ - cleavage_idx - 1])->nh3)){
+ return false;
+ }
+ return true;
+ }
+ }
+
+ // check for H2O modification
+ if(mod_type == H2O){
+ // adding is ok
+ if(increment >= 0){
+ return true;
+ }
+
+ // is forward ion_type(ABC)?
+ if(ion->isForwardType()){
+ // does this ion contain enough counts of the STED
+ if(-increment > (&loss_limit_[cleavage_idx-1])->h2o){
+ return false;
+ }
+ return true;
+ }
+ else{// backward ions XYZ
+ // does this ion contain enough counts of the STED
+ if(cleavage_idx == peptide_length_){
+ if(-increment > (&loss_limit_[peptide_length_-1])->h2o){
+ return false;
+ }
+ }
+ else if(-increment >
+ ((&loss_limit_[peptide_length_-1])->h2o -
+ (&loss_limit_[peptide_length_ - cleavage_idx - 1])->h2o)){
+ return false;
+ }
+ return true;
+ }
+ }
+
+ // check for ISOTOPE modification
+ else if(mod_type == ISOTOPE){
+ // adding is ok
+ if(increment >= 0 && ion->getType() != P_ION){
+ return true;
+ }
+ // add more constraint if needed
+ }
+ // check for FLANK modification
+ else if(mod_type == FLANK){
+ // only add flanking ions to type B,Y ions
+ if(ion->getType() == B_ION || ion->getType() == Y_ION){
+ // only add ions with no modifications
+ if(!ion->isModified()){
+ return true;
+ }
+ }
+ }
+
+ return false;
+}
+
+/**
+ * creates all the ions with specific modifications up to the max charge
+ * copies all the existing ions that can be modified,
+ * then applies the different modifications then adds the new modified ions to ion_series
+ *\returns true if successfully generates all the ions with modifications, else false
+ */
+bool IonSeries::generateIons(
+ ION_MODIFICATION_T mod_type ///< generate ions of this modification_type -in/out
+ )
+{
+ int ion_idx = 0;
+ int total_ion = ions_.size();
+ Ion* working_ion = NULL;
+ Ion* new_ion = NULL;
+ int* modifications = constraint_->getModifications();
+
+ // modification index
+ int type_idx = 0;
+ int type_increment = 1;
+
+ // reset modification increment, if mod_type loss
+ if(modifications[mod_type] < 0){
+ type_increment = -1;
+ }
+
+ // iterate over all the ions to determine which ones should be copies and modified
+ for(; ion_idx < total_ion; ++ion_idx){
+ working_ion = ions_[ion_idx];
+
+ // can this ion generate a mod_type modification?, if not skip to next ion
+ if(!(canIonGenerateModification(working_ion, mod_type, type_increment))){
+ continue;
+ }
+
+ // add/sub thorugh all mod_type modifications!!!
+ for(type_idx = type_increment; abs(type_idx) <= abs(modifications[mod_type]); ){
+ // copy the src ion, into new ion
+ new_ion = Ion::newIon();
+ Ion::copy(working_ion, new_ion, working_ion->getPeptideSequence());
+
+ // add the modification to the new ion
+ new_ion->addModification(mod_type, type_idx, constraint_->getMassType());
+
+ // add ion to ion_series
+ addIon(new_ion);
+
+ // can this ion generate a mod_type modification for the next count of modification?,
+ if(!(this->canIonGenerateModification(working_ion, mod_type,
+ (type_idx += type_increment)))){
+ break;
+ }
+ }
+ }
+ return true;
+}
+
+/**
+ * creates all the flanking ions up to the max charge
+ * can only create flanking ions that are B|Y ions and don't have modification
+ * assumes the ions with no modification all are at the begining of the ion[] in ion_series
+ * copies all the existing ions that can be modified,
+ * then applies the different modifications then adds the new modified ions to ion_series
+ *\returns true if successfully generates all the ions with modifications, else false
+ */
+bool IonSeries::generateIonsFlank()
+{
+ int ion_idx = 0;
+ int total_ion = ions_.size();
+ Ion* working_ion = NULL;
+ Ion* new_ion = NULL;
+ Ion* new_ion2 = NULL;
+ int* modifications = constraint_->getModifications();
+
+ // modification index
+ int type_idx = 0;
+ int type_increment = 1;
+
+ // iterate over all the ions to determine which ones should be copies and modified
+ for(; ion_idx < total_ion; ++ion_idx){
+ working_ion = ions_[ion_idx];
+
+ // no more ions that are not modified, thus done
+ if(working_ion->getSingleModificationCount(NH3) != 0){
+ break;
+ }
+
+ // can this ion generate a mod_type modification?, if not skip to next ion
+ if(!canIonGenerateModification(working_ion, FLANK, type_increment)){
+ continue;
+ }
+
+ // add/sub thorugh all mod_type modifications!!!
+ for(type_idx = type_increment; type_idx <= modifications[FLANK]; type_idx += type_increment){
+ // copy the src ion, into new ion
+ new_ion = Ion::newIon();
+ new_ion2 = Ion::newIon();
+ Ion::copy(working_ion, new_ion, working_ion->getPeptideSequence());
+ Ion::copy(working_ion, new_ion2, working_ion->getPeptideSequence());
+
+ // add the modification to the new ion
+ new_ion->addModification(FLANK, type_idx, constraint_->getMassType());
+ new_ion2->addModification(FLANK, -type_idx, constraint_->getMassType());
+
+ // add ion to ion_series
+ addIon(new_ion);
+ addIon(new_ion2);
+ }
+ }
+ return true;
+}
+
+/**
+ * \brief The engine of ion series. Predicts all the ions from the
+ * peptide that meet the ion constraint. All predicted ions are stored
+ * in the ion_series as ion objects.
+ */
+void IonSeries::predictIons()
+{
+ if(is_predicted_){
+ carp(CARP_WARNING, "The ion series has already been predicted and added");
+ return;
+ }
+
+ IonConstraint* constraint = constraint_;
+
+ // create a mass matrix
+ FLOAT_T* mass_matrix =
+ createIonMassMatrix(modified_aa_seq_, constraint->getMassType(), peptide_length_);
+ /*
+ printf("cumulative mass sum is:\n");
+ int idx = 0;
+ for(idx = 0; idx < mass_matrix[0]; idx++){
+ printf("%i\t%f\n", idx, mass_matrix[idx]);
+ }
+ */
+ // scan for the first and last (S, T, E, D) and (R, K, Q, N),
+ // initialize to determine modification is ok.
+ // the first, last of STED, RKQN are stored in ion_series.
+
+ scanForAAForNeutralLoss();
+
+ // generate ions without any modifications
+ if(!generateIonsNoModification(mass_matrix)){
+ carp(CARP_FATAL, "failed to generate ions, no modifications");
+ }
+
+ // create modification ions?
+ if(constraint_->getUseNeutralLosses()){
+
+ // generate ions with nh3 modification
+ if(abs(constraint->getModifications()[NH3]) > 0){
+ if(!generateIons(NH3)){
+ carp(CARP_FATAL, "failed to generate ions, NH3 modifications");
+ }
+ }
+
+ // generate ions with h2o modification
+ if(abs(constraint->getModifications()[H2O]) > 0){
+ if(!generateIons(H2O)){
+ carp(CARP_FATAL, "failed to generate ions, H2O modifications");
+ }
+ }
+
+ // generate ions with isotope modification
+ if(constraint->getModifications()[ISOTOPE] > 0){
+ if(!generateIons(ISOTOPE)){
+ carp(CARP_FATAL, "failed to generate ions, ISOTOPE modifications");
+ }
+ }
+
+ // generate ions with flank modification
+ if(constraint->getModifications()[FLANK] > 0){
+ if(!generateIonsFlank()){
+ carp(CARP_FATAL, "failed to generate ions, FLANK modifications");
+ }
+ }
+
+ // add more modifications here
+
+ }
+
+ // ion series now been predicted
+ is_predicted_ = true;
+
+}
+
+/**
+ * Copies ion_series object from src to dest.
+ * must pass in a memory allocated ION_SERIES_T* dest
+ * does not copy the loss_limit.
+ */
+void IonSeries::copy(
+ IonSeries* src,///< ion to copy from -in
+ IonSeries* dest,///< ion to copy to -out
+ bool create_ions ///< should we create new ions or copy the pointers?
+ )
+{
+ Ion* src_ion = NULL;
+ Ion* dest_ion = NULL;
+
+ dest->peptide_ = src->peptide_;
+ dest->charge_ = src->charge_;
+ dest->peptide_length_ = src->peptide_length_;
+ //mod seq???
+
+ // add copy of pointer ion constraint
+ dest->constraint_ = src->constraint_;
+
+ // add copy ion, add ion_filtered_iterator
+
+ for (IonIterator iterator = src->begin();
+ iterator != src->end();
+ ++iterator) {
+
+ src_ion = *iterator;
+ // add ion
+ if (create_ions) {
+ dest_ion = Ion::newIon();
+ Ion::copy(src_ion, dest_ion, dest->peptide_);
+ } else {
+ dest_ion = src_ion;
+
+ }
+ dest->addIon(dest_ion);
+ }
+
+ dest->is_predicted_ = true;
+}
+
+/**
+ * remove an ion from IonSeries, does not free ion.
+ */
+void IonSeries::removeIon(
+ Ion* ion ///<ion to remove
+ ) {
+
+
+ IonIterator ion_iter;
+
+ for (ion_iter = begin();
+ ion_iter != end();
+ ++ion_iter) {
+
+ if (*ion_iter == ion) {
+ ions_.erase(ion_iter);
+ return;
+ }
+
+
+
+ }
+
+ carp(CARP_ERROR, "Cannot find ion to delete:%i", ion);
+
+}
+
+
+/*************************************
+ * ION_SERIES_T: get and set methods
+ ************************************/
+
+/**
+ * \returns the ion that meets the criteria or NULL
+ * TODO possibly reimplement if linear scan is too slow
+ */
+Ion* IonSeries::getIon(
+ IonConstraint* ion_constraint,
+ int cleavage_idx
+ ){
+
+ IonFilteredIterator ion_iterator(this, ion_constraint);
+ Ion* ion = NULL;
+
+ while(ion_iterator.hasNext()){
+ ion = ion_iterator.next();
+ if(ion->getCleavageIdx() == cleavage_idx){
+ return ion;
+ }
+ }
+ return NULL;
+}
+
+/**
+ *\returns the peptide length of which the ions are made
+ */
+int IonSeries::getPeptideLength()
+{
+ return peptide_length_;
+}
+
+/**
+ * User should not free the peptide sequence seperate from the ion_series
+ *\returns a pointer to the original parent peptide sequence of the ion_series object
+ */
+string& IonSeries::getPeptide()
+{
+ return peptide_;
+}
+
+/**
+ * copies in the peptide sequence to heap allocated sequence.
+ * set the parent peptide sequence of the ion_series object
+ */
+void IonSeries::setPeptide(
+ char* peptide///< the peptide sequence to set -in
+ )
+{
+ peptide_ = peptide;
+}
+
+/**
+ *\returns the charge of the ion_series object
+ */
+int IonSeries::getCharge()
+{
+ return charge_;
+}
+
+/**
+ * set the charge of the ion_series object
+ */
+void IonSeries::setCharge(
+ int charge///< the charge of the ion -in
+ )
+{
+ charge_ = charge;
+}
+
+/**
+ * get the is_predicted field of the ion_series object
+ */
+bool IonSeries::getIsPredicted() {
+ return is_predicted_;
+}
+
+/**
+ * set the is_predicted field of the ion_series object
+ */
+void IonSeries::setIsPredicted(
+ bool is_predicted///< the is_predicted field -in
+ ) {
+ is_predicted_ = is_predicted;
+}
+
+/**
+ * get the modified_aa_seq of the ion_series object
+ */
+MODIFIED_AA_T* IonSeries::getModifiedAASeq()
+{
+ return modified_aa_seq_;
+}
+
+/**
+ *\returns the constraint of the ion_series object
+ */
+IonConstraint* IonSeries::getIonConstraint()
+{
+ return constraint_;
+}
+
+/**
+ * set the of the ion_series object
+ */
+void IonSeries::setIonConstraint(
+ IonConstraint* constraint///< -in
+ )
+{
+ constraint_ = constraint;
+}
+
+/**
+ *\returns the total number of ions in the ion_series object
+ */
+int IonSeries::getNumIons()
+{
+ return ions_.size();
+}
+
+/**
+ *\returns the total number of ion_type in the ion_series object
+ */
+int IonSeries::getNumIonsOneType(
+ ION_TYPE_T ion_type ///< the type of ions -in
+ )
+{
+ return specific_ions_[ion_type].size();
+}
+
+vector<Ion*>& IonSeries::getSpecificIons(
+ ION_TYPE_T ion_type ///< the type of ions -in
+ )
+{
+ return specific_ions_[ion_type];
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/IonSeries.h b/src/model/IonSeries.h
new file mode 100644
index 0000000..2f629dc
--- /dev/null
+++ b/src/model/IonSeries.h
@@ -0,0 +1,354 @@
+/**
+ * \file IonSeries.h
+ * AUTHOR: Chris Park
+ * CREATE DATE: 28 June 2006
+ * \brief Object for a series of ions.
+ *****************************************************************************/
+#ifndef IONSERIES_H
+#define IONSERIES_H
+
+#include <stdio.h>
+#include <vector>
+#include "model/objects.h"
+#include "Peptide.h"
+#include "Ion.h"
+#include "IonConstraint.h"
+
+static const int MAX_NUM_ION_TYPE = 8; // number of different ion_types
+
+/**
+ * \class IonSeries
+ * \brief An object to represent a series of ions, and organize them.
+ * For which additional data structures will be created as needed
+ * loss_limit can be equal to NULL, thus if need to use should always
+ * check that it is not NULL.
+ */
+class IonSeries {
+ friend class XLinkPeptide;
+ friend class XLinkablePeptide;
+ friend class XLinkIonSeriesCache;
+ protected:
+
+ static FLOAT_T* mass_matrix_; /// < Pre-allocated mass matrix
+ // TODO change name to unmodified_char_seq
+ std::string peptide_; ///< The peptide sequence for this ion series
+ MODIFIED_AA_T* modified_aa_seq_; ///< sequence of the peptide
+ bool modified_aa_seq_owner_;
+ int charge_; ///< /<The charge state of the peptide for this ion series
+ IonConstraint* constraint_; ///< The constraints which these ions obey
+ std::vector<Ion*> ions_; ///< The ions in this series
+ int num_ions_; ///< number of ions
+ bool is_predicted_; ///< has this ion_series been predicted already?
+ std::vector<Ion*> specific_ions_[MAX_NUM_ION_TYPE];
+ ///< specific ions in the series, reference to master array of ions
+ LOSS_LIMIT_T* loss_limit_;
+ ///< nh3, h2o loss limit for a given cleavage index,
+ ///< before using this array should always sheck if not NULL
+ int peptide_length_; ///< the length of the peptide
+
+ // ??? what is the difference between peptide_length and num_ions
+
+ int pointer_count_;
+
+ /**
+ * \brief Creates an array in which element i is the sum of the masses
+ * of amino acids 0 to (i-1). At i=0 is stored the length of the
+ * peptide.
+ * \returns an array of ion masses for all sub sequences
+ */
+ FLOAT_T* createIonMassMatrix(
+ //char* peptide, ///< The peptide for this ion series. -in
+ MODIFIED_AA_T* modified_seq, ///< the sequence
+ MASS_TYPE_T mass_type, ///< the mass_type to use MONO|AVERAGE
+ int peptide_length ///< the length of the peptide
+ );
+
+ /**
+ * user must ensure that there is enough space for this ion
+ * adds ion to ion_series' master ion_array and if B|Y ion to the specific ion_array
+ */
+ void addIon(
+ Ion* ion ///< ion to add -in
+ );
+
+ int incrementPointerCount();
+
+ /**
+ * helper function: add_ions
+ * add all the ions to ion_series up to the max charge
+ *\returns TRUE if successfully adds all ions, else FALSE
+ */
+ bool addIonsByCharge(
+ FLOAT_T mass, ///< the base mass of the ion to add
+ int cleavage_idx, ///< the absolute cleavage index (A,B,C from left X,Y,Z from right)
+ ION_TYPE_T ion_type ///< the ion type of the ions to be added
+ );
+
+ /**
+ * The modification depends on the loss/add && if the ion contains RKQN or STED
+ * The number of losses possible cannot exceed the number of RKQN or STED in the ion
+ * The loss_limit array in the ion_series must be populated prior to this method call
+ *\returns TRUE if the ion can lose the mod_type modification, else FALSE
+ */
+ bool canIonGenerateModification(
+ Ion* ion, ///< the ion to check if can lose nh3 -in
+ ION_MODIFICATION_T mod_type, ///< generate ions of this modification_type -in/out
+ int increment ///< the add/loss of the modification
+ );
+
+ /**
+ * Initializes an (empty) ion_series object, only called by constructors.
+ */
+ void init();
+
+ public:
+
+
+
+ /**
+ * \returns An (empty) ion_series object.
+ */
+ IonSeries();
+
+ /**
+ * copies in the peptide sequence
+ * Use this method to create ion_series only when few are needed,
+ * because the memory allocation process is expensive.
+ * If need a repeated new ion-series for different peptides,
+ * use "new_ion_series_generic" & "update_ion_series" combination, thus only allocate one
+ * ion_seires object.
+ *\returns Instantiates a new ion_series object from the given peptide sequence and charge
+ */
+ IonSeries(
+ const std::string& peptide, ///< The peptide for this ion series. -in
+ int charge, ///< The charge for this ion series -in
+ IonConstraint* constraint ///< The constraints which the ions in this series obey.
+ );
+
+ /**
+ * Creates a heap allocated generic ion_series object that must be updated by "update_ion_series" method
+ * to transform the object into a ion-series for a specific instance of a peptide sequence and charge.
+ *\returns Instantiates a new generic ion_series object that must be updated for each peptide instance
+ */
+ IonSeries(
+ IonConstraint* constraint, ///< The constraints which the ions in this series obey.
+ int charge ///< The charge for this ion series -in
+ );
+
+
+/**
+ * Updates an ion_series to a specific instance of a peptide sequence.
+ * If the ion_series has been already generated its ions, will free ions up.
+ * Copies in the peptide sequence.
+ * and re-initialize for the new peptide sequence.
+ */
+ void update(
+ const char* peptide, ///< The peptide sequence for this ion series. -in
+ const MODIFIED_AA_T* mod_seq ///< modified version of seq -in
+ );
+
+
+ /**
+ * Frees an allocated ion_series object.
+ */
+ virtual ~IonSeries();
+
+ static void freeIonSeries(IonSeries* ions);
+
+ static void finalize();
+
+ /**
+ *Iterator access
+ */
+ IonIterator begin();
+ IonIterator end();
+
+
+ /**
+ * Prints a ion_series object to file.
+ */
+ void print(
+ FILE* file ///< file for output -out
+ );
+
+ /**
+ * Prints a ion_series object to file, in GMTK single-ion format.
+ */
+ void printSingleGmtk(
+ IonConstraint* ion_constraint, ///< ion_constraint to obey -in
+ FILE* file, ///< file -out
+ int sentence_idx
+ );
+
+ /**
+ * Prints a ion_series object to file, in GMTK paired-ion format.
+ */
+ void printPairedGmtk(
+ IonConstraint* first_ion_constraint, ///< ion_constraint to obey -in
+ IonConstraint* second_ion_constraint, ///< ion_constraint to obey -in
+ FILE* file, ///< file output
+ int sentence_idx
+ );
+
+ /**
+ * \brief Find instances of amino acid which can incur neutral
+ * losses: H2O (S|T|E|D), NH3(R|K|Q|N).
+ * Set the count of those observed so far for each cleavage index.
+ * If no instance of amino acid, the count is assigned to 0
+ * The information is used to determine if how many nh3 or h2o neutral
+ * losses are possible.
+ */
+ void scanForAAForNeutralLoss();
+
+ /**
+ * Creates all the ions with no modifications up to the max charge
+ * Adds each ion to ion_series
+ *\returns TRUE if successfully generates all the ions, else FALSE
+ */
+ bool generateIonsNoModification(
+ FLOAT_T* mass_matrix ///< the mass matrix that stores the mass
+ );
+
+ /**
+ * creates all the ions with specific modifications up to the max charge
+ * copies all the existing ions that can be modified,
+ * then applies the different modifications then adds the new modified ions to ion_series
+ *\returns TRUE if successfully generates all the ions with modifications, else FALSE
+ */
+ bool generateIons(
+ ION_MODIFICATION_T mod_type ///< generate ions of this modification_type -in/out
+ );
+
+ /**
+ * creates all the flanking ions up to the max charge
+ * can only create flanking ions that are B|Y ions and don't have modification
+ * assumes the ions with no modification all are at the begining of the ion[] in ion_series
+ * copies all the existing ions that can be modified,
+ * then applies the different modifications then adds the new modified ions to ion_series
+ *\returns TRUE if successfully generates all the ions with modifications, else FALSE
+ */
+ bool generateIonsFlank();
+
+ /**
+ * Predict ion series
+ */
+ void predictIons();
+
+ /**
+ * Copies ion_series object from src to dest.
+ * must pass in a memory allocated ION_SERIES_T dest
+ */
+ static void copy(
+ IonSeries* src,///< ion to copy from -in
+ IonSeries* dest,///< ion to copy to -out
+ bool create_ions ///< Create a copy of the ions?
+ );
+
+ /**
+ * remove an ion from IonSeries, does not free ion.
+ */
+ void removeIon(
+ Ion* ion ///<ion to remove
+ );
+
+
+ /*************************************
+ * ION_SERIES_T: get and set methods
+ ************************************/
+
+ /**
+ * \returns the ion that meets the constraint or NULL
+ */
+ Ion* getIon(
+ IonConstraint* ion_constraint,
+ int cleavage_idx
+ );
+
+ /**
+ * User should not free the peptide sequence seperate from the ion_series
+ *\returns a pointer to the original parent peptide sequence of the ion_series object
+ */
+ std::string& getPeptide();
+
+ /**
+ *\returns the peptide length of which the ions are made
+ */
+ int getPeptideLength();
+
+ /**
+ * copies in the peptide sequence to heap allocated sequence.
+ * set the parent peptide sequence of the ion_series object
+ */
+ void setPeptide(
+ char* peptide///< the peptide sequence to set -in
+ );
+
+ /**
+ *\returns the charge of the ion_series object
+ */
+ int getCharge();
+
+ /**
+ * set the charge of the ion_series object
+ */
+ void setCharge(
+ int charge///< the charge of the ion -in
+ );
+
+ /**
+ * get the is_predicted field of the ion_series object
+ */
+ bool getIsPredicted();
+
+ /**
+ * set the is_predicted field of the ion_series object
+ */
+ void setIsPredicted(
+ bool is_predicted///< the is_predicted field -in
+ );
+
+ /**
+ * get the modified_aa_seq of the ion_series object
+ */
+ MODIFIED_AA_T* getModifiedAASeq();
+
+ /**
+ *\returns the constraint of the ion_series object
+ */
+ IonConstraint* getIonConstraint();
+
+ /**
+ * set the of the ion_series object
+ */
+ void setIonConstraint(
+ IonConstraint* constraint///< -in
+ );
+
+ /**
+ *\returns the total number of ions in the ion_series object
+ */
+ int getNumIons();
+
+ /**
+ *\returns the total number of ion_type in the ion_series object
+ */
+ int getNumIonsOneType(
+ ION_TYPE_T ion_type ///< the type of ions -in
+ );
+
+ /**
+ *\returns the ions corresponding to a specific ion type.
+ */
+ std::vector<Ion*>& getSpecificIons(
+ ION_TYPE_T ion_type /// < the type of ions -in
+ );
+ void clear();
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/Match.cpp b/src/model/Match.cpp
new file mode 100644
index 0000000..fdccecf
--- /dev/null
+++ b/src/model/Match.cpp
@@ -0,0 +1,1110 @@
+/*************************************************************************//**
+ * \file Match.cpp
+ * AUTHOR: Chris Park
+ * CREATE DATE: 11/27 2006
+ * \brief Object for matching a peptide and a spectrum, generate
+ * a preliminary score(e.g., Sp)
+ ****************************************************************************/
+#include <math.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include <set>
+#include <map>
+#include "io/carp.h"
+#include "ProteinPeptideIterator.h"
+#include "Spectrum.h"
+#include "Ion.h"
+#include "IonSeries.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+#include "util/GlobalParams.h"
+#include "Scorer.h"
+#include "Match.h"
+#include "MatchCollection.h"
+#include "Peptide.h"
+#include "util/Params.h"
+#include "util/FileUtils.h"
+
+#include <string>
+
+#include "io/MatchFileReader.h"
+
+using namespace std;
+using namespace Crux;
+
+vector<string> Match::file_paths_;
+
+void Match::init() {
+
+ spectrum_=NULL;
+ peptide_=NULL;
+ // initialize score, rank !!!! DEBUG
+ for (unsigned int idx=0;idx<NUMBER_SCORER_TYPES;idx++) {
+ match_scores_[idx] = NOT_SCORED;
+ match_rank_[idx] = 0;
+ }
+ pointer_count_ = 0;
+ // default is not a null peptide match
+ null_peptide_ = false;
+ peptide_sequence_ = NULL;
+ mod_sequence_ = NULL;
+ post_process_match_ = 0;
+ ln_experiment_size_ = 0;
+ num_target_matches_ = 0;
+ best_per_peptide_ = false;
+ file_idx_ = -1;
+}
+
+
+/**
+ * \returns a new memory allocated match
+ */
+Match::Match(){
+ init();
+ ++pointer_count_;
+ exact_pval_search_ = false;
+}
+
+/**
+ * Create a new match with the given members.
+ */
+Match::Match(Peptide* peptide, ///< the peptide for this match
+ Spectrum* spectrum, ///< the spectrum for this match
+ const SpectrumZState& zstate, ///< the charge/mass of the spectrum
+ bool is_decoy)///< is the peptide a decoy or not
+{
+ init();
+ peptide_ = peptide;
+ spectrum_ = spectrum;
+ zstate_ = zstate;
+ null_peptide_ = is_decoy;
+
+ ++pointer_count_;
+ exact_pval_search_ = false;
+}
+
+/**
+ * free the memory allocated match
+ * spectrum is not freed by match
+ */
+void Match::freeMatch(
+ Match* match ///< the match to free -in
+ )
+{
+ --match->pointer_count_;
+
+ // only free match when pointer count reaches
+ if(match->pointer_count_ == 0){
+ delete match;
+ }
+}
+
+Match::~Match() {
+ // but aren't there multiple matches pointing to the same peptide?
+ // if so, create a new free_shallow_match which doesn't touch the members
+ if (peptide_ != NULL){
+ delete peptide_;
+ }
+ if(post_process_match_ && spectrum_ !=NULL){
+ delete spectrum_;
+ }
+ /*
+ if (peptide_sequence_ != NULL){
+ free(peptide_sequence_);
+ }
+ */
+ if (mod_sequence_ != NULL){
+ free(mod_sequence_);
+ }
+}
+
+bool Match::ScoreComparer::operator() (const Match* x, const Match* y) {
+ FLOAT_T scoreX = x->getScore(type_);
+ FLOAT_T scoreY = y->getScore(type_);
+ return less_ ? Match::ScoreLess(scoreX, scoreY) : Match::ScoreGreater(scoreX, scoreY);
+}
+
+bool Match::ScoreLess(FLOAT_T x, FLOAT_T y) {
+ if (isnan(x) || isinf(x)) {
+ x = std::numeric_limits<FLOAT_T>::max();
+ }
+ if (isnan(y) || isinf(y)) {
+ y = std::numeric_limits<FLOAT_T>::max();
+ }
+ return x < y;
+}
+
+bool Match::ScoreGreater(FLOAT_T x, FLOAT_T y) {
+ if (isnan(x) || isinf(x)) {
+ x = -std::numeric_limits<FLOAT_T>::max();
+ }
+ if (isnan(y) || isinf(y)) {
+ y = -std::numeric_limits<FLOAT_T>::max();
+ }
+ return x > y;
+}
+
+/**
+ * \brief Print the match information in sqt format to the given file
+ *
+ * Only crux sequest-search produces sqt files so the two scores
+ * printed are always Sp and xcorr.
+ */
+void Match::printSqt(
+ FILE* file ///< output stream -out
+ ){
+ if (!file) {
+ carp(CARP_ERROR, "Cannot print match to sqt file from null input");
+ return;
+ }
+
+ Peptide* peptide = getPeptide();
+ // this should get the sequence from the match, not the peptide
+ char* sequence = getSequenceSqt();
+
+ int b_y_total = getScore(BY_IONS_TOTAL);
+ if (b_y_total == NOT_SCORED) {
+ b_y_total = 0;
+ }
+ int b_y_matched = getScore(BY_IONS_MATCHED);
+ if (b_y_matched == NOT_SCORED) {
+ b_y_matched = 0;
+ }
+
+ FLOAT_T delta_cn = getScore(DELTA_CN);
+ FLOAT_T score_main = getScore(XCORR);
+
+ // write format string with variable precision
+ int precision = Params::GetInt("precision");
+
+ // print match info
+ if (exact_pval_search_) {
+ fprintf(file, "M\t%i\t%i\t%.*f\t%.2f\t%.*g\t%.*g\t%.*g\t%i\t%i\t%s\tU\n",
+ getRank(XCORR),
+ getRank(SP),
+ Params::GetInt("mass-precision"),
+ peptide->calcModifiedMass() + MASS_PROTON,
+ delta_cn,
+ precision,
+ getScore(TIDE_SEARCH_EXACT_PVAL),
+ precision,
+ getScore(TIDE_SEARCH_REFACTORED_XCORR),
+ precision,
+ getScore(SP),
+ b_y_matched,
+ b_y_total,
+ sequence
+ );
+ } else {
+ fprintf(file, "M\t%i\t%i\t%.*f\t%.2f\t%.*g\t%.*g\t%i\t%i\t%s\tU\n",
+ getRank(XCORR),
+ getRank(SP),
+ Params::GetInt("mass-precision"),
+ peptide->calcModifiedMass() + MASS_PROTON,
+ delta_cn,
+ precision,
+ score_main,
+ precision,
+ getScore(SP),
+ b_y_matched,
+ b_y_total,
+ sequence
+ );
+ }
+ free(sequence);
+
+ PeptideSrc* peptide_src = NULL;
+ string protein_id;
+ Protein* protein = NULL;
+
+ for(PeptideSrcIterator iter = peptide->getPeptideSrcBegin();
+ iter != peptide->getPeptideSrcEnd();
+ ++iter){
+ string rand;
+ peptide_src = *iter;
+ protein = peptide_src->getParentProtein();
+ protein_id = protein->getId();
+
+ // only prepend "decoy-prefix" if we are doing a fasta search
+ Database* database = protein->getDatabase();
+ if( null_peptide_
+ && (database != NULL && database->getDecoyType() == NO_DECOYS) ){
+ rand = Params::GetString("decoy-prefix");
+ }
+
+ // print match info (locus line), add "decoy-prefix" to locus name for decoys
+ fprintf(file, "L\t%s%s\n", rand.c_str(), protein_id.c_str());
+ }
+
+ return;
+}
+
+
+/**
+ * Print one field in the tab-delimited output file, based on column index.
+ */
+void Match::printOneMatchField(
+ int column_idx, ///< Index of the column to print. -in
+ MatchCollection* collection, ///< collection holding this match -in
+ MatchFileWriter* output_file, ///< output stream -out
+ Spectrum* spectrum,
+ int num_target_matches, ///< num matches per spectrum -in
+ int num_decoy_matches, ///< target matches for same spectrum -in
+ int b_y_total, ///< total b/y ions -in
+ int b_y_matched ///< Number of b/y ions matched. -in
+) {
+ switch ((MATCH_COLUMNS_T)column_idx) {
+ case FILE_COL:
+ if (strlen(spectrum->getFullFilename()) == 0) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, getFilePath());
+ }
+ else {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, spectrum->getFullFilename());
+ }
+ break;
+ case SCAN_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ spectrum->getFirstScan());
+ break;
+ case CHARGE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getCharge());
+ break;
+ case SPECTRUM_PRECURSOR_MZ_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ spectrum->getPrecursorMz());
+ break;
+ case SPECTRUM_NEUTRAL_MASS_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getNeutralMass());
+ break;
+ case PEPTIDE_MASS_COL:
+ {
+ Peptide* peptide = getPeptide();
+ double peptide_mass = peptide->calcModifiedMass();
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ peptide_mass);
+ }
+ break;
+ case DELTA_CN_COL:
+ {
+ FLOAT_T delta_cn = getScore(DELTA_CN);
+ if( delta_cn == 0 ){// I hate -0, this prevents it
+ delta_cn = 0.0;
+ }
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, delta_cn);
+ }
+ break;
+ case SP_SCORE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(SP));
+ break;
+ case SP_RANK_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getRank(SP));
+ break;
+ case XCORR_SCORE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(XCORR));
+ break;
+ case EXACT_PVALUE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(TIDE_SEARCH_EXACT_PVAL));
+ break;
+ case REFACTORED_SCORE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(TIDE_SEARCH_REFACTORED_XCORR));
+ break;
+ case SIDAK_ADJUSTED_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(SIDAK_ADJUSTED));
+ break;
+ case XCORR_RANK_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getRank(!Params::GetBool("exact-p-value") ? XCORR : TIDE_SEARCH_EXACT_PVAL));
+ break;
+ case EVALUE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(EVALUE));
+ break;
+ case PVALUE_COL:
+ {
+ double log_pvalue = getScore(LOGP_BONF_WEIBULL_XCORR);
+ if (P_VALUE_NA == log_pvalue) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, "NaN");
+ } else {
+ double p_value = log_pvalue != numeric_limits<FLOAT_T>::infinity() ?
+ exp(-1 * log_pvalue) : 0;
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ p_value);
+ }
+ }
+ break;
+ case WEIBULL_QVALUE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(LOGP_QVALUE_WEIBULL_XCORR));
+ break;
+ case WEIBULL_PEP_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(LOGP_WEIBULL_PEP));
+ break;
+#ifdef NEW_COLUMNS
+ case WEIBULL_PEPTIDE_QVALUE_COL:
+ if ((scores_computed[LOGP_QVALUE_WEIBULL_XCORR] == true) &&
+ (match->best_per_peptide == true)) {
+ double qvalue = getScore(LOGP_PEPTIDE_QVALUE_WEIBULL);
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, qvalue);
+ }
+ break;
+#endif
+ case QVALUE_TDC_COL:
+// if (null_peptide_ == false) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(QVALUE_TDC));
+// }
+ break;
+ case QVALUE_MIXMAX_COL:
+// if (null_peptide_ == false) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(QVALUE_MIXMAX));
+// }
+ break;
+ case DECOY_XCORR_QVALUE_COL:
+ if (null_peptide_ == false) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(DECOY_XCORR_QVALUE));
+ }
+ break;
+ case DECOY_XCORR_PEP_COL:
+ if (null_peptide_ == false) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(DECOY_XCORR_PEP));
+ }
+ break;
+ case DECOY_EVALUE_QVALUE_COL:
+ if (null_peptide_ == false) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(DECOY_EVALUE_QVALUE));
+ }
+ break;
+ case DECOY_EVALUE_PEP_COL:
+ if (null_peptide_ == false) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(DECOY_EVALUE_PEP));
+ }
+ break;
+
+#ifdef NEW_COLUMNS
+ case DECOY_XCORR_PEPTIDE_QVALUE_COL:
+ if ( (null_peptide_ == false) && (best_per_peptide_ == true)) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(DECOY_XCORR_PEPTIDE_QVALUE));
+ }
+ break;
+#endif
+ case PERCOLATOR_SCORE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(PERCOLATOR_SCORE));
+ break;
+ case PERCOLATOR_RANK_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getRank(PERCOLATOR_SCORE));
+ break;
+ case PERCOLATOR_QVALUE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(PERCOLATOR_QVALUE));
+ break;
+ case PERCOLATOR_PEP_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(PERCOLATOR_PEP));
+ break;
+#ifdef NEW_COLUMNS
+ case PERCOLATOR_PEPTIDE_QVALUE_COL:
+ if ( match->best_per_peptide == true) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(PERCOLATOR_PEPTIDE_QVALUE));
+ }
+ break;
+#endif
+ case QRANKER_SCORE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(QRANKER_SCORE));
+ break;
+ case QRANKER_QVALUE_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(QRANKER_QVALUE));
+ break;
+ case QRANKER_PEP_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(QRANKER_PEP));
+ break;
+#ifdef NEW_COLUMNS
+ case QRANKER_PEPTIDE_QVALUE_COL:
+ if (match->best_per_peptide == true) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getScore(QRANKER_PEPTIDE_QVALUE));
+ }
+ break;
+#endif
+ case BY_IONS_MATCHED_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, b_y_matched);
+ break;
+ case BY_IONS_TOTAL_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, b_y_total);
+ break;
+ case DISTINCT_MATCHES_SPECTRUM_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ num_target_matches);
+ break;
+ case MATCHES_SPECTRUM_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ num_target_matches);
+ break;
+ case DECOY_MATCHES_SPECTRUM_COL:
+ if( null_peptide_ ){
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ num_decoy_matches);
+ }
+ break;
+ case SEQUENCE_COL:
+ {
+ // this should get the sequence from the match, not the peptide
+ char* sequence = getModSequenceStrWithMasses(
+ get_mass_format_type_parameter("mod-mass-format"));
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx, sequence);
+ free(sequence);
+ }
+ break;
+ case MODIFICATIONS_COL:
+ {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ getPeptide()->getModsString());
+ }
+ break;
+ case CLEAVAGE_TYPE_COL:
+ {
+ ENZYME_T enzyme = GlobalParams::getEnzyme();
+ const char* enzyme_string = enzyme_type_to_string(enzyme);
+ DIGEST_T digestion = GlobalParams::getDigestion();
+ const char* digestion_string = digest_type_to_string(digestion);
+ string cleavage_str = enzyme_string;
+ cleavage_str += "-";
+ cleavage_str += digestion_string;
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ cleavage_str.c_str() );
+ }
+ break;
+ case PROTEIN_ID_COL:
+ {
+ Peptide* peptide = getPeptide();
+ string protein_ids_string = peptide->getProteinIdsLocations();
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ protein_ids_string.c_str());
+ }
+ break;
+ case FLANKING_AA_COL:
+ {
+ Peptide* peptide = getPeptide();
+ char* flanking_aas = peptide->getFlankingAAs();
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ flanking_aas);
+ free(flanking_aas);
+ }
+ break;
+ case ORIGINAL_TARGET_SEQUENCE_COL:
+ if (null_peptide_ || Params::GetBool("concat")) {
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ peptide_->getUnshuffledSequence());
+ }
+ break;
+ case ETA_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ collection->getCalibrationEta());
+ break;
+ case BETA_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ collection->getCalibrationBeta());
+ break;
+ case SHIFT_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ collection->getCalibrationShift());
+ break;
+ case CORR_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ collection->getCalibrationCorr());
+ break;
+ case INDEX_NAME_COL:
+ output_file->setColumnCurrentRow((MATCH_COLUMNS_T)column_idx,
+ database_index_name_);
+ break;
+ // values only for spectral-counts
+ case RAW_SCORE_COL:
+ case SIN_SCORE_COL:
+ case NSAF_SCORE_COL:
+ case DNSAF_SCORE_COL:
+ case EMPAI_SCORE_COL:
+ case PARSIMONY_RANK_COL:
+ return;
+ case NUMBER_MATCH_COLUMNS:
+ case INVALID_COL:
+ carp(CARP_FATAL, "Error in printing code (match.cpp).");
+ break;
+ }
+}
+
+/**
+ * \brief Print the match information in tab delimited format to the given file
+ *
+ */
+void Match::printTab(
+ MatchCollection* collection, ///< collection holding this match -in
+ MatchFileWriter* output_file, ///< output stream -out
+ Spectrum* spectrum,
+ int num_target_matches, ///< num matches in spectrum -in
+ int num_decoy_matches ///< target matches for same spectrum -in
+ ){
+
+ carp(CARP_DETAILED_DEBUG, "Match::printTab: begin.");
+
+ // Usually because no decoy file to print to.
+ if( output_file == NULL ){
+ return;
+ }
+
+ int b_y_total = getScore(BY_IONS_TOTAL);
+ if (b_y_total == NOT_SCORED) {
+ b_y_total = 0;
+ }
+ int b_y_matched = getScore(BY_IONS_MATCHED);
+ if (b_y_matched == NOT_SCORED) {
+ b_y_matched = 0;
+ }
+
+ // Print tab delimited fields
+ int column_idx;
+ for (column_idx = 0; column_idx < NUMBER_MATCH_COLUMNS; column_idx++) {
+ carp(CARP_DETAILED_DEBUG,"print col:%i",column_idx);
+ carp(CARP_DETAILED_DEBUG, "%s", get_column_header(column_idx));
+ printOneMatchField(column_idx,
+ collection,
+ output_file,
+ spectrum,
+ num_target_matches,
+ num_decoy_matches,
+ b_y_total,
+ b_y_matched);
+ }
+ output_file->writeRow();
+ carp(CARP_DETAILED_DEBUG, "Match::printTab done.");
+}
+
+/****************************
+ * match get, set methods
+ ***************************/
+
+/**
+ * Returns a heap allocated peptide sequence of the PSM
+ * User must free the sequence.
+ *
+ * Go to top README for N,C terminus tryptic feature info.
+ *
+ *\returns the match peptide sequence, returns NULL if no sequence avaliable
+ */
+char* Match::getSequence() {
+ // if post_process_match and has a null peptide you can't get sequence
+ if(post_process_match_ && null_peptide_){
+ carp(CARP_ERROR,
+ "Cannot retrieve null peptide sequence for post_process_match");
+ return NULL;
+ }
+
+ if(peptide_sequence_ == NULL){
+ peptide_sequence_ = peptide_->getSequence();
+ }
+ return my_copy_string(peptide_sequence_);
+}
+
+/**
+ * Returns a heap allocated peptide sequence of the PSM formatted with
+ * the flanking amino acids and modifiation symbols.
+ *
+ * Sequence is in the form of X.SEQ.X where X is the flanking amino
+ * acid or - if peptide is at the end of the protein.
+ * Sequence may not be the same as for the peptide if this is for a
+ * decoy database.
+ *\returns The sqt-formatted peptide sequence for this match.
+ */
+char* Match::getSequenceSqt(){
+
+ // get_match_mod_sequence (use method in case match->mod_seq == NULL)
+ MODIFIED_AA_T* mod_seq = getModSequence();
+ if( mod_seq == NULL ){
+ return NULL;
+ }
+ int length = getPeptide()->getLength();
+
+ // turn it into string
+ char* seq = modified_aa_string_to_string_with_masses(mod_seq, length,
+ get_mass_format_type_parameter("mod-mass-format"));
+
+ // get peptide flanking residues
+ char c_term = peptide_->getCTermFlankingAA();
+ char n_term = peptide_->getNTermFlankingAA();
+
+ // allocate seq + 4 length array
+ char* final_string = (char*)mycalloc((strlen(seq)+5), sizeof(char));
+
+ // copy pieces in
+ final_string[0] = n_term;
+ final_string[1] = '.';
+ strcpy(&final_string[2], seq);
+ final_string[strlen(seq) + 2] = '.';
+ final_string[strlen(seq) + 3] = c_term;
+ final_string[strlen(seq) + 4] = '\0';
+
+ carp(CARP_DETAILED_DEBUG, "start string %s, final %s", seq, final_string);
+
+ // delete mod seq and string version
+ free(seq);
+ free(mod_seq);
+ return final_string;
+}
+
+/**
+ * \brief Returns a newly allocated modified_aa sequence of the PSM.
+ * Sequence is the same as the peptide, if target match or is a
+ * shuffled sequence if a null (decoy) match. If match field
+ * 'mod_sequence' is non NULL, returns a copy of that value, otherwise
+ * fills that field and returns a copy of the value.
+ *
+ * \returns the match peptide sequence, returns NULL if no sequence avaliable
+ */
+MODIFIED_AA_T* Match::getModSequence()
+{
+
+ // if post_process_match and has a null peptide you can't get sequence
+ if(post_process_match_ && null_peptide_){
+ return NULL;
+ }
+
+ if(mod_sequence_ == NULL){
+ mod_sequence_ = peptide_->getModifiedAASequence();
+ }
+
+ return copy_mod_aa_seq(mod_sequence_, peptide_->getLength());
+}
+
+/**
+ * \brief Returns a newly allocated string of sequence including any
+ * modifications represented as symbols (*,@,#, etc) following the
+ * modified residue.
+ * \returns The peptide sequence of the match including modification
+ * characters.
+ */
+char* Match::getModSequenceStrWithSymbols(){
+
+ // if post_process_match and has a null peptide you can't get sequence
+ if(post_process_match_ && null_peptide_){
+ return NULL;
+ }
+
+ if(mod_sequence_ == NULL){
+ mod_sequence_ = peptide_->getModifiedAASequence();
+ }
+
+ return modified_aa_string_to_string_with_symbols(mod_sequence_,
+ peptide_->getLength());
+}
+
+/**
+ * \brief Returns a newly allocated string of sequence including any
+ * modifications represented as mass values in brackets following the
+ * modified residue. If merge_masses is true, the sum of multiple
+ * modifications on one residue are printed. If false, each mass is
+ * printed in a comma-separated list.
+ * \returns The peptide sequence of the match including modification
+ * masses.
+ */
+char* Match::getModSequenceStrWithMasses(
+ MASS_FORMAT_T mass_format)
+{
+ // if post_process_match and has a null peptide you can't get sequence
+ if(post_process_match_ && null_peptide_){
+ return NULL;
+ }
+
+ if(mod_sequence_ == NULL){
+ mod_sequence_ = peptide_->getModifiedAASequence();
+ }
+
+ return modified_aa_string_to_string_with_masses(mod_sequence_,
+ peptide_->getLength(),
+ mass_format);
+}
+/**
+ * Must ask for score that has been computed
+ *\returns the match_mode score in the match object
+ */
+FLOAT_T Match::getScore (
+ SCORER_TYPE_T match_mode ///< the working mode (SP, XCORR) -in
+ ) const
+{
+ return match_scores_[match_mode];
+}
+
+/**
+ * sets the match score
+ */
+void Match::setScore(
+ SCORER_TYPE_T match_mode, ///< the working mode (SP, XCORR) -in
+ FLOAT_T match_score ///< the score of the match -in
+ )
+{
+ match_scores_[match_mode] = match_score;
+}
+
+
+/**
+ * set the custom match score
+ */
+void Match::setCustomScore(
+ const std::string& match_score_name, ///< the name of the score -in
+ FLOAT_T match_score ///< the score of the match -in
+ ) {
+
+ match_custom_scores_[match_score_name] = match_score;
+
+}
+
+/**
+ * get the custom score
+ */
+bool Match::getCustomScore(
+ const std::string& match_score_name, ///< the name of the score -in
+ FLOAT_T& score ///< the value of the score -out
+ ) {
+
+ if (match_custom_scores_.find(match_score_name) == match_custom_scores_.end()) {
+ carp(CARP_ERROR, "custom match score:%s doesn't exist!", match_score_name.c_str());
+ return false;
+ }
+
+ score = match_custom_scores_[match_score_name];
+ return true;
+
+}
+
+void Match::getCustomScoreNames(
+ vector<string>& custom_score_names
+ ) {
+
+ custom_score_names.clear();
+
+ for (map<string,FLOAT_T>::iterator iter = match_custom_scores_.begin();
+ iter != match_custom_scores_.end();
+ ++iter) {
+ custom_score_names.push_back(iter->first);
+ }
+
+}
+
+/**
+ * sets the file index for this match
+ */
+void Match::setFileIndex(
+ int file_idx ///< file index to set
+ ) {
+
+ file_idx_ = file_idx;
+}
+
+/**
+ * \returns the file index for this match
+ */
+int Match::getFileIndex() {
+ return(file_idx_);
+}
+
+int Match::findFileIndex(const string& file_path, bool match_stem) {
+ for (size_t idx = 0; idx < file_paths_.size(); idx++) {
+ if (file_path == file_paths_[idx]) {
+ return idx;
+ }
+ }
+ if (match_stem) {
+ for (size_t idx = 0; idx < file_paths_.size(); idx++) {
+ if (file_path == FileUtils::Stem(file_paths_[idx])) {
+ return idx;
+ }
+ }
+ }
+ return -1;
+}
+
+/**
+ * sets the file path for this match
+ * \returns the associated file index
+ */
+int Match::setFilePath(
+ const string& file_path ///< file path to set
+ ) {
+ file_idx_ = findFileIndex(file_path);
+ if (file_idx_ == -1) {
+ file_idx_ = file_paths_.size();
+ file_paths_.push_back(file_path);
+ }
+ return file_idx_;
+}
+
+/**
+ * \returns the file path for this match
+ */
+string Match::getFilePath() {
+ return(getFilePath(file_idx_));
+}
+
+string Match::getFilePath(int file_idx) {
+ if (file_idx == -1 || file_paths_.empty()) {
+ return "";
+ } else {
+ return(file_paths_[file_idx]);
+ }
+}
+
+
+
+bool Match::isDecoy() {
+
+ return null_peptide_;
+
+}
+
+/**
+ * sets whether the match is post process or not
+ */
+void Match::setPostProcess(
+ bool post_process ///< whether the match is post process or not
+) {
+ post_process_match_ = post_process;
+}
+
+/**
+ * Must ask for score that has been computed
+ *\returns the match_mode rank in the match object
+ */
+int Match::getRank(
+ SCORER_TYPE_T match_mode ///< the working mode (SP, XCORR) -in
+ )
+{
+ return match_rank_[match_mode];
+}
+
+/**
+ * sets the rank of the match
+ */
+void Match::setRank(
+ SCORER_TYPE_T match_mode, ///< the working mode -in
+ int match_rank ///< the rank of the match -in
+ )
+{
+ match_rank_[match_mode] = match_rank;
+}
+
+/**
+ *\returns the spectrum in the match object
+ */
+Spectrum* Match::getSpectrum()
+{
+ return spectrum_;
+}
+
+/**
+ *\returns the peptide in the match object
+ */
+Peptide* Match::getPeptide()
+{
+ return peptide_;
+}
+
+/**
+ * sets whether the match is a null peptide match or not
+ */
+void Match::setNullPeptide(
+ bool null_peptide ///< whether the match is a null peptide match or not
+) {
+ null_peptide_ = null_peptide;
+}
+
+/**
+ * gets the match if it is a null_peptide match
+ *\returns true if match is null peptide, else false
+ */
+bool Match::getNullPeptide()
+{
+ return null_peptide_;
+}
+
+void Match::setZState(
+ SpectrumZState& zstate) {
+
+ zstate_ = zstate;
+
+}
+
+SpectrumZState& Match::getZState() {
+
+ return zstate_;
+
+}
+
+/**
+ * gets the match charge
+ */
+int Match::getCharge() {
+ return getZState().getCharge();
+}
+
+/**
+ * /returns the match neutral mass
+ */
+FLOAT_T Match::getNeutralMass() {
+ return getZState().getNeutralMass();
+}
+
+/**
+ * sets the match ln_experiment_size
+ */
+void Match::setLnExperimentSize(
+ FLOAT_T ln_experiment_size ///< the ln_experiment_size value of PSM -in
+ )
+{
+ ln_experiment_size_ = ln_experiment_size;
+}
+
+/**
+ * gets the match ln_experiment_size
+ */
+FLOAT_T Match::getLnExperimentSize() {
+ return ln_experiment_size_;
+}
+
+/**
+ * Sets the total number of target matches searched for this spectrum.
+ */
+void Match::setTargetExperimentSize(int num_matches){
+ num_target_matches_ = num_matches;
+}
+
+/**
+ * \returns The total number of target matches searched for this spectrum.
+ */
+int Match::getTargetExperimentSize(){
+ return num_target_matches_;
+}
+
+/**
+ *Increments the pointer count to the match object
+ */
+void Match::incrementPointerCount() {
+ ++pointer_count_;
+}
+
+/**
+ * Set the best-per-peptide Boolean to true.
+ */
+void Match::setBestPerPeptide() {
+ best_per_peptide_ = true;
+}
+
+
+/************************************************
+ * TODO: Why are these here?
+ ************************************************/
+
+/**
+ * \brief Counts the number of internal cleavages
+ *
+ */
+int get_num_internal_cleavage(const char* peptide_sequence, ENZYME_T enzyme){
+ // get number of internal cleavages
+ int num_missed_cleavages = 0;
+ const char* seq_iter = peptide_sequence;
+
+ while (*(seq_iter+1) != '\0'){
+ if (ProteinPeptideIterator::validCleavagePosition(seq_iter, enzyme)){
+ num_missed_cleavages++;
+ }
+ seq_iter++;
+ }
+ return num_missed_cleavages;
+}
+
+/**
+ * \brief Returns whether the nterm and cterm of a peptide are proper cleavages
+ */
+void get_terminal_cleavages(
+ const char* peptide_sequence, ///< peptide sequenc
+ const char flanking_aas_prev, ///< amino acid before cleavage (n-term)
+ const char flanking_aas_next, ///< amino acid after cleavage (c-term)
+ ENZYME_T enzyme, ///< Enzyme used in cleavage
+ bool& nterm, ///< -out is nterminus from a proper cleavage
+ bool& cterm ///< -out is cterminus from a proper cleavage?
+ ) {
+ int num_tol_term = 0;
+ char cleavage[3];
+ cleavage[2] = '\0';
+ cleavage[0] = flanking_aas_prev;
+ cleavage[1] = peptide_sequence[0];
+ nterm = flanking_aas_prev == '-' || ProteinPeptideIterator::validCleavagePosition(cleavage, enzyme);
+
+ cleavage[0] = peptide_sequence[strlen(peptide_sequence)-1];
+ cleavage[1] = flanking_aas_next;
+ cterm = flanking_aas_next == '-' || ProteinPeptideIterator::validCleavagePosition(cleavage, enzyme);
+}
+
+/**
+ * \brief Counts the number of terminal cleavage. Either 0, 1, or 2
+ *
+ */
+int get_num_terminal_cleavage(
+ const char* peptide_sequence,
+ const char flanking_aas_prev,
+ const char flanking_aas_next,
+ ENZYME_T enzyme
+ ){
+
+ bool cterm, nterm;
+
+ get_terminal_cleavages(peptide_sequence,
+ flanking_aas_prev,
+ flanking_aas_next,
+ enzyme,
+ nterm, cterm);
+
+ int num_tol_term = 0;
+ if (nterm) {
+ num_tol_term++;
+ }
+ if (cterm) {
+ num_tol_term++;
+ }
+ return num_tol_term;
+}
+
+void Match::setDatabaseIndexName(string index_name){
+ database_index_name_ = index_name;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/Match.h b/src/model/Match.h
new file mode 100644
index 0000000..30287f7
--- /dev/null
+++ b/src/model/Match.h
@@ -0,0 +1,459 @@
+/**
+ * \file Match.h
+ * $Revision: 1.24 $
+ * \brief Object for given a peptide and a spectrum, generate
+ * a preliminary score(ex, Sp)
+ ****************************************************************************/
+#ifndef MATCH_H
+#define MATCH_H
+
+#include "io/MatchFileWriter.h"
+#include <math.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <set>
+#include <map>
+#include <ctype.h>
+#include <float.h>
+#include <string>
+
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include "io/carp.h"
+#include "Spectrum.h"
+#include "io/SpectrumCollection.h"
+#include "Ion.h"
+#include "IonSeries.h"
+#include "util/crux-utils.h"
+#include "model/objects.h"
+#include "parameter.h"
+#include "Scorer.h"
+
+
+/* Global variables */
+static const FLOAT_T NOT_SCORED = FLT_MIN;
+static const FLOAT_T P_VALUE_NA = -1.0;
+
+namespace Crux{
+
+class Match {
+ protected:
+ /**
+ * README!
+ * Issues on the overall_type field in match struct
+ *
+ * Outstanding question: How do you determine the
+ * peptide trypticity for multiple protein sources?
+ *
+ * For example, if one protein src is tryptic while the other is
+ * not tryptic, what is the peptide trypticity used for feature and
+ * shuffling peptide sequence?
+ *
+ * Currently, we use the "Tryptic wins all" approach, where
+ * if N-terminus is tryptic in any of the src proteins we claim it
+ * tryptic on the N terminus. Same applies for C-terminus.
+ * Thus, even if no peptide is tryptic in any of its src protein,
+ * if there are one src protein where it is N tryptic and another where
+ * it is C tryptic, overall we will call the peptide in the match tryptic.
+ *
+ * There are for sure other methods, for example to randomly sample the src
+ * protein and consider that protein as its src or to shuffle the flanking
+ * sequence of the peptide in each of peptide and randomly sample from the
+ * shuffled flanking sequence to determine the shuffled peptide's trypticity.
+ *
+ */
+ Crux::Spectrum* spectrum_; ///< the spectrum we are scoring with
+ Crux::Peptide* peptide_; ///< the peptide we are scoring
+ FLOAT_T match_scores_[NUMBER_SCORER_TYPES];
+ std::map<string,FLOAT_T> match_custom_scores_;
+ ///< array of scores, one for each type (index with SCORER_TYPE_T)
+ int match_rank_[NUMBER_SCORER_TYPES];
+ ///< rank of this match for each type scored (index with SCORER_TYPE_T)
+ int pointer_count_;
+ ///< number of pointers to this match object (when reach 0, free memory)
+ bool null_peptide_; ///< Is the match a null (decoy) peptide match?
+ const char* peptide_sequence_; ///< peptide sequence is that of peptide or shuffled
+ MODIFIED_AA_T* mod_sequence_; ///< seq of peptide or shuffled if null peptide
+ SpectrumZState zstate_;
+ // post_process match object features
+ // only valid when post_process_match is true
+ bool post_process_match_; ///< Is this a post process match object?
+ FLOAT_T ln_experiment_size_;
+ ///< natural log of total number of candidate peptides evaluated
+ int num_target_matches_; ///< total target candidates for this spectrum
+ bool best_per_peptide_; ///< Is this the best scoring PSM for this peptide?
+ int file_idx_; ///< index of where this match came from
+ string database_index_name_;
+ static std::vector<std::string> file_paths_;
+ /**
+ * Print one field in the tab-delimited output file, based on column index.
+ */
+ virtual void printOneMatchField(
+ int column_idx, ///< Index of the column to print. -in
+ MatchCollection* collection, ///< collection holding this match -in
+ MatchFileWriter* output_file, ///< output stream -out
+ Crux::Spectrum* spectrum,
+ int num_target_matches, ///< target matches for this spectrum -in
+ int num_decoy_matches, ///< decoy matches (if any) for this spectrum -in
+ int b_y_total, ///< total b/y ions -in
+ int b_y_matched ///< Number of b/y ions matched. -in
+ );
+
+ void init();
+
+ public:
+ bool exact_pval_search_;
+ /**
+ * \returns a new memory allocated match
+ */
+ Match();
+
+ /**
+ *
+ */
+ Match(Crux::Peptide* peptide, ///< the peptide for this match
+ Crux::Spectrum* spectrum, ///< the spectrum for this match
+ const SpectrumZState& zstate, ///< the charge/mass of the spectrum
+ bool is_decoy);///< is the peptide a decoy or not
+
+ /**
+ * free the memory allocated match
+ */
+ static void freeMatch(
+ Match* match ///< the match to free -in
+ );
+
+ virtual ~Match();
+
+ struct ScoreComparer {
+ public:
+ // If less, sort is from least to greatest
+ ScoreComparer(SCORER_TYPE_T type, bool less): type_(type), less_(less) {}
+ bool operator() (const Match* x, const Match* y);
+
+ private:
+ SCORER_TYPE_T type_;
+ bool less_;
+ };
+ static bool ScoreLess(FLOAT_T x, FLOAT_T y);
+ static bool ScoreGreater(FLOAT_T x, FLOAT_T y);
+
+ /**
+ * print the information of the match
+ */
+ void print(
+ FILE* file, ///< output stream -out
+ bool output_sequence, ///< should I output peptide sequence -in
+ SCORER_TYPE_T output_mode ///< the output mode -in
+ );
+
+ /**
+ * \brief Print the match information in sqt format to the given file
+ *
+ * The main score goes in the position usually holding the xcorr. The other
+ * score goes in the position usually holding the preliminary Sp
+ * score. For searches analyzed by percolator, main and other should
+ * be discriminant score and qvalue.
+ */
+ void printSqt(
+ FILE* file ///< output stream -out
+ );
+
+ /**
+ * \brief Print the match information in tab delimited format to the
+ * given file.
+ *
+ */
+ void printTab(
+ MatchCollection* collection, ///< collection holding this match -in
+ MatchFileWriter* file, ///< output stream -out
+ Spectrum* spectrum,
+ int num_target_matches, ///< target matches for this spectrum -in
+ int num_decoy_matches ///< decoy matches (if any) for this spectrum -in
+ );
+
+ /****************************
+ * match get, set methods
+ ***************************/
+
+ /**
+ * Returns a heap allocated peptide sequence of the PSM
+ * Sequence may not be the same as for the peptide if this is for a
+ * decoy database.
+ * User must free the sequence.
+ *\returns the match peptide sequence
+ */
+ char* getSequence();
+
+ /**
+ * Returns a heap allocated peptide sequence of the PSM formatted with
+ * the flanking amino acids and modifiation symbols.
+ *
+ * Sequence is in the form of X.SEQ.X where X is the flanking amino
+ * acid or - if peptide is at the end of the protein.
+ * Sequence may not be the same as for the peptide if this is for a
+ * decoy database.
+ *\returns The sqt-formatted peptide sequence for this match.
+ */
+ char* getSequenceSqt();
+
+ /**
+ * \brief Returns a newly allocated modified_aa sequence of the PSM
+ * User must free the sequence.
+ *\returns the match peptide sequence
+ */
+ MODIFIED_AA_T* getModSequence();
+
+ /**
+ * \brief Returns a newly allocated string of sequence including any
+ * modifications represented as symbols (*,@,#, etc) following the
+ * modified residue.
+ * \returns The peptide sequence of the match including modification
+ * characters.
+ */
+ char* getModSequenceStrWithSymbols();
+
+ /**
+ * \brief Returns a newly allocated string of sequence including any
+ * modifications represented as mass values in brackets following the
+ * modified residue. If mass_format is MOD_MASS_ONLY, the sum of multiple
+ * modifications on one residue are printed. If MOD_MASSES_SEPARATE,
+ * each mass is printed in a comma-separated list. If AA_PLUS_MOD, then
+ * the mass printed is that of the amino acid plus the modification.
+ * \returns The peptide sequence of the match including modification
+ * masses.
+ */
+ char* getModSequenceStrWithMasses(
+ MASS_FORMAT_T mass_format
+ );
+
+ /**
+ * Must ask for score that has been computed
+ *\returns the match_mode score in the match object
+ */
+ FLOAT_T getScore(
+ SCORER_TYPE_T match_mode ///< the working mode (SP, XCORR) -in
+ ) const;
+
+ /**
+ * sets the match score
+ */
+ void setScore(
+ SCORER_TYPE_T match_mode, ///< the working mode (SP, XCORR) -in
+ FLOAT_T match_score ///< the score of the match -in
+ );
+
+ /**
+ * get the custom score
+ * \retuns the custom score if it exists
+ */
+ FLOAT_T getScore(
+ std::string& match_score_name ///< the name of the score -in
+ );
+
+ /**
+ * set the custom match score
+ */
+ void setCustomScore(
+ const std::string& match_score_name, ///< the name of the score -in
+ FLOAT_T match_score ///< the score of the match -in
+ );
+
+ /**
+ * get the custom score
+ */
+ bool getCustomScore(
+ const std::string& match_score_name, ///< the name of the score -in
+ FLOAT_T& score ///< the value of the score -out
+ );
+
+ void getCustomScoreNames(
+ std::vector<std::string>& custom_score_names
+ );
+
+
+ /**
+ * sets the file index for this match
+ */
+ void setFileIndex(
+ int file_idx ///< file index to set
+ );
+
+ /**
+ *\returns the file index for this match
+ */
+ int getFileIndex();
+
+ static int findFileIndex(const std::string& file_path, bool match_stem = false);
+
+ /**
+ * sets the file path for this match
+ * \returns the associated file index
+ */
+ int setFilePath(
+ const std::string& file_path ///< file path to set
+ );
+
+ /**
+ * \returns the file path for this match
+ */
+ std::string getFilePath();
+
+ static std::string getFilePath(int file_idx);
+
+ virtual bool isDecoy();
+
+ /**
+ * Must ask for score that has been computed
+ *\returns the match_mode rank in the match object
+ */
+ int getRank(
+ SCORER_TYPE_T match_mode ///< the working mode (SP, XCORR) -in
+ );
+
+ /**
+ * sets the rank of the match
+ */
+ void setRank(
+ SCORER_TYPE_T match_mode, ///< the working mode (SP, XCORR) -in
+ int match_rank ///< the rank of the match -in
+ );
+
+ /**
+ *\returns the spectrum in the match object
+ */
+ Crux::Spectrum* getSpectrum();
+
+ /**
+ *\returns the peptide in the match object
+ */
+ Crux::Peptide* getPeptide();
+
+ /**
+ * sets the match charge and mass
+ */
+
+ void setZState(
+ SpectrumZState& zstate
+ );
+
+ SpectrumZState& getZState();
+
+ /**
+ * gets the match charge
+ */
+
+ int getCharge();
+
+ /**
+ * gets the spectrum neutral mass
+ */
+ FLOAT_T getNeutralMass();
+
+ /**
+ * sets the match ln_experiment_size
+ */
+ void setLnExperimentSize(
+ FLOAT_T ln_experiment_size ///< the ln_experiment_size value of PSM -in
+ );
+
+ /**
+ * gets the match ln_experiment_size
+ */
+ FLOAT_T getLnExperimentSize();
+
+ /**
+ * \returns The total number of target matches searched for this spectrum.
+ */
+ int getTargetExperimentSize();
+
+ /**
+ * sets the total number of target matches searched for this spectrum.
+ */
+ void setTargetExperimentSize(int num_matches);
+
+ /**
+ *Increments the pointer count to the match object
+ */
+ void incrementPointerCount();
+
+ /**
+ * sets whether the match is a null peptide match or not
+ */
+ void setNullPeptide(
+ bool null_peptide ///< whether the match is a null peptide match or not
+ );
+
+ /**
+ * gets the match if it is a null_peptide match
+ *\returns true if match is null peptide, else false
+ */
+ bool getNullPeptide();
+
+ /**
+ * sets whether the match is post process or not
+ */
+ void setPostProcess(
+ bool post_process ///< whether the match is post process or not
+ );
+
+ /**
+ * Set the best-per-peptide Boolean to true.
+ */
+ void setBestPerPeptide();
+
+ /**
+ *Set the database index name where the peptide comes from
+ */
+ void setDatabaseIndexName(string index_name);
+
+};
+
+} /* Namespace for Match */
+
+/************************************************
+ * TODO: Why are these here?
+ ************************************************/
+/**
+ * \brief Returns whether the nterm and cterm of a peptide are proper cleavages
+ */
+void get_terminal_cleavages(
+ const char* peptide_sequence, ///< peptide sequence
+ const char flanking_aas_prev, ///< amino acid before cleavage (n-term)
+ const char flanking_aas_next, ///< amino acid after cleavage (c-term)
+ ENZYME_T enzyme, ///< Enzyme used in cleavage
+ bool& nterm, ///< -out is nterminus from a proper cleavage?
+ bool& cterm ///< -out is cterminus from a proper cleavage?
+);
+
+/**
+ * \brief Counts the number of internal cleavages
+ * why is this here?
+ */
+int get_num_internal_cleavage(
+ const char* peptide_sequence,
+ ENZYME_T enzyme
+);
+
+/**
+ * \brief Counts the number of terminal cleavage. Either 0, 1, or 2
+ *
+ */
+int get_num_terminal_cleavage(
+ const char* peptide_sequence,
+ const char flanking_aas_prev,
+ const char flanking_aas_next,
+ ENZYME_T enzyme
+);
+
+#endif //MATCH_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/MatchCollection.cpp b/src/model/MatchCollection.cpp
new file mode 100644
index 0000000..480b4ca
--- /dev/null
+++ b/src/model/MatchCollection.cpp
@@ -0,0 +1,1407 @@
+/*********************************************************************//**
+ * \file MatchCollection.cpp
+ * AUTHOR: Chris Park
+ * CREATE DATE: 11/27 2006
+ * \brief A set of peptide spectrum matches for one spectrum.
+ *
+ * Methods for creating and manipulating match_collections.
+ * Creating a match collection generates all matches (searches a
+ * spectrum against a database.
+ ****************************************************************************/
+#include "MatchCollection.h"
+#include "MatchIterator.h"
+#include <string>
+#include "io/MatchFileReader.h"
+#include "io/SQTReader.h"
+#include "util/AminoAcidUtil.h"
+#include "util/Params.h"
+#include "util/GlobalParams.h"
+#include "util/StringUtils.h"
+#include "util/WinCrux.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * \returns An (empty) match_collection object.
+ */
+void MatchCollection::init() {
+ try {
+ match_.reserve(10 * MILLION);
+ } catch (std::bad_alloc& ba) {
+ carp(CARP_DEBUG, "Bad alloc in reserve: %s", ba.what());
+ }
+ experiment_size_ = 0;
+ target_experiment_size_ = 0;
+ zstate_ = SpectrumZState();
+ null_peptide_collection_ = false;
+
+ // loop over to set all score type to false
+ for(int score_type_idx = 0 ;
+ score_type_idx < NUMBER_SCORER_TYPES ;
+ ++score_type_idx){
+
+ scored_type_[score_type_idx] = false;
+ }
+
+ // set last score to -1, thus nothing has been done yet
+ last_sorted_ = (SCORER_TYPE_T)-1;
+ iterator_lock_ = false;
+ eta_ = 0;
+ beta_ = 0;
+ shift_ = 0;
+ correlation_ = 0;
+ xcorrs_.reserve(10 * MILLION);
+
+ post_process_collection_ = false;
+ top_scoring_sp_ = NULL;
+ exact_pval_search_ = false;
+ has_distinct_matches_ = false;
+}
+
+/**
+ * /brief Free the memory allocated for a match collection
+ * Deep free; each match is freed which, in turn, frees each spectrum
+ * and peptide.
+ */
+MatchCollection::~MatchCollection() {
+ // decrement the pointer count in each match object
+ for (vector<Crux::Match*>::iterator i = match_.begin(); i != match_.end(); i++) {
+ Match::freeMatch(*i);
+ }
+
+ if(top_scoring_sp_){
+ Match::freeMatch(top_scoring_sp_);
+ }
+}
+
+/**
+ * \brief Creates a new match collection with no matches in it. Sets
+ * the member variable indicating if the matches are to real peptides
+ * or to decoy (shuffled) peptides. Other member variables are set to
+ * default values. The method add_matches() can be used to search a
+ * spectrum and store the matches in this collection.
+ *
+ * \returns A newly allocated match collection
+ */
+MatchCollection::MatchCollection(
+ bool is_decoy
+ ){
+ init();
+ null_peptide_collection_ = is_decoy;
+}
+
+void MatchCollection::preparePostProcess() {
+ // prepare the match_collection
+ init();
+ // set this as a post_process match collection
+ post_process_collection_ = true;
+}
+
+/**
+ * Sort the match collection by score type.
+ */
+void MatchCollection::sort(
+ SCORER_TYPE_T score_type ///< the score type to sort by -in
+ )
+{
+ carp(CARP_DETAILED_DEBUG, "Sorting match collection.");
+
+ // check if we are allowed to alter match_collection
+ if (iterator_lock_) {
+ carp(CARP_FATAL,
+ "Cannot sort a match collection when a match iterator is already instantiated");
+ }
+
+ // The order here follows that of the definition in ../objects.h.
+ SCORER_TYPE_T sort_by = score_type;
+ bool smaller_is_better = false;
+ switch (score_type) {
+ case SP:
+ case XCORR:
+ smaller_is_better = false;
+ break;
+ case EVALUE:
+ smaller_is_better = true;
+ break;
+
+ case DECOY_XCORR_QVALUE:
+ case DECOY_XCORR_PEPTIDE_QVALUE:
+ case DECOY_XCORR_PEP:
+ smaller_is_better = false;
+ sort_by = XCORR;
+ break;
+
+ case DECOY_EVALUE_QVALUE:
+ case DECOY_EVALUE_PEPTIDE_QVALUE:
+ case DECOY_EVALUE_PEP:
+ smaller_is_better = true;
+ sort_by = EVALUE;
+ break;
+
+ // N.B. These are actually NEGATIVE log p-values.
+ case LOGP_WEIBULL_XCORR:
+ case LOGP_BONF_WEIBULL_XCORR:
+ case LOGP_QVALUE_WEIBULL_XCORR:
+ case LOGP_WEIBULL_PEP:
+ case LOGP_PEPTIDE_QVALUE_WEIBULL:
+ smaller_is_better = false;
+ sort_by = LOGP_BONF_WEIBULL_XCORR;
+ break;
+
+ case PERCOLATOR_SCORE:
+ case PERCOLATOR_QVALUE:
+ case PERCOLATOR_PEPTIDE_QVALUE:
+ case PERCOLATOR_PEP:
+ smaller_is_better = false;
+ sort_by = PERCOLATOR_SCORE;
+ break;
+
+ case QRANKER_SCORE:
+ case QRANKER_QVALUE:
+ case QRANKER_PEPTIDE_QVALUE:
+ case QRANKER_PEP:
+ smaller_is_better = false;
+ sort_by = QRANKER_SCORE;
+ break;
+
+ case BARISTA_SCORE:
+ case BARISTA_QVALUE:
+ case BARISTA_PEPTIDE_QVALUE:
+ case BARISTA_PEP:
+ smaller_is_better = false;
+ sort_by = BARISTA_SCORE;
+ break;
+
+ case DELTA_CN:
+ case DELTA_LCN:
+ case BY_IONS_MATCHED:
+ case BY_IONS_TOTAL:
+ carp(CARP_FATAL, "Cannot sort by score type %s.",
+ scorer_type_to_string(score_type));
+ break;
+
+ case TIDE_SEARCH_EXACT_PVAL:
+ smaller_is_better = true;
+ break;
+ case TIDE_SEARCH_REFACTORED_XCORR:
+ smaller_is_better = false;
+ break;
+ case SIDAK_ADJUSTED:
+ case TIDE_SEARCH_EXACT_SMOOTHED:
+ smaller_is_better = true;
+ break;
+
+ case XCORR_FIRST:
+ case XCORR_SECOND:
+ carp(CARP_FATAL, "Cannot sort by score type %s.",
+ scorer_type_to_string(score_type));
+
+ case QVALUE_TDC:
+ case QVALUE_MIXMAX:
+ smaller_is_better = true;
+ break;
+
+ case NUMBER_SCORER_TYPES:
+ case INVALID_SCORER_TYPE:
+ carp(CARP_FATAL, "Cannot sort by score type %s.",
+ scorer_type_to_string(score_type));
+ }
+
+ // Don't sort if it's already sorted.
+ if (last_sorted_ == sort_by) {
+ return;
+ }
+
+ if (!scored_type_[sort_by]) {
+ carp(CARP_WARNING, "Cannot sort MatchCollection (does not have %s scores)",
+ scorer_type_to_string(sort_by));
+ return;
+ }
+
+ if (smaller_is_better) {
+ carp(CARP_DEBUG, "Sorting in ascending order by %s.",
+ scorer_type_to_string(score_type));
+ } else {
+ carp(CARP_DEBUG, "Sorting in descending order by %s.",
+ scorer_type_to_string(score_type));
+ }
+
+ // Do the sort.
+ Match::ScoreComparer comparer(sort_by, smaller_is_better);
+ std::sort(match_.begin(), match_.end(), comparer);
+ last_sorted_ = sort_by;
+}
+
+/**
+ * Assigns a rank for the given score type to each match. First sorts
+ * by the score type (if not already sorted). Overwrites any existing
+ * rank values, so it can be performed on a collection with matches
+ * newly added to previously ranked matches. Rank 1 is highest
+ * score. Matches with the same score will be given the same rank.
+ *
+ * \returns true, if populates the match rank in the match collection
+ */
+bool MatchCollection::populateMatchRank(
+ SCORER_TYPE_T score_type ///< score type (SP, XCORR) by which to rank -in
+ )
+{
+ carp(CARP_DETAILED_DEBUG, "Ranking matches by %i.", score_type);
+ carp(CARP_DETAILED_DEBUG, "Collection currently ranked by %d", last_sorted_);
+ // check if the match collection is in the correct sorted order
+ if (last_sorted_ != score_type) {
+ sort(score_type);
+ }
+
+ // set match rank for all match objects that have been scored for
+ // this type
+ int cur_rank = 0;
+ FLOAT_T cur_score = NOT_SCORED;
+ for (vector<Crux::Match*>::iterator i = match_.begin(); i != match_.end(); i++) {
+ FLOAT_T this_score = (*i)->getScore(score_type);
+
+ if( NOT_SCORED == (*i)->getScore(score_type) ){
+ char* seq = (*i)->getModSequenceStrWithMasses(MOD_MASS_ONLY);
+ carp(CARP_WARNING,
+ "PSM spectrum %i charge %i sequence %s was NOT scored for type %i",
+ (*i)->getSpectrum()->getFirstScan(),
+ (*i)->getCharge(), seq,
+ (int)score_type);
+ free(seq);
+ }
+
+ // does this match have a higher score?
+ if( this_score != cur_score ){
+ cur_score = this_score;
+ cur_rank++;
+ }
+
+ // set_match_rank( cur_match, score_type, match_index+1);
+ (*i)->setRank(score_type, cur_rank);
+
+ carp(CARP_DETAILED_DEBUG, "Match rank %i, score %f", cur_rank, cur_score);
+ }
+
+ return true;
+}
+
+/**
+ * For the #top_count ranked peptides, calculate the Weibull parameters
+ *\returns true, if successfully calculates the Weibull parameters
+ */
+static const FLOAT_T MIN_XCORR_SHIFT = -5.0;
+static const FLOAT_T MAX_XCORR_SHIFT = 5.0;
+//#define CORR_THRESHOLD 0.995 // Must achieve this correlation, else punt.
+static const FLOAT_T CORR_THRESHOLD = 0.0; // For now, turn off the threshold.
+static const FLOAT_T XCORR_SHIFT = 0.05;
+static const FLOAT_T MIN_SP_SHIFT = -100.0;
+static const FLOAT_T MAX_SP_SHIFT = 300.0;
+static const FLOAT_T SP_SHIFT = 5.0;
+
+/**
+ * match_collection get, set method
+ */
+
+/**
+ *\returns true, if the match collection has been scored by score_type
+ */
+bool MatchCollection::getScoredType(
+ SCORER_TYPE_T score_type ///< the score_type (MATCH_SP, MATCH_XCORR) -in
+ )
+{
+ return scored_type_[score_type];
+}
+
+/**
+ * sets the score_type to value
+ */
+void MatchCollection::setScoredType(
+ SCORER_TYPE_T score_type, ///< the score_type (MATCH_SP, MATCH_XCORR) -in
+ bool value
+ )
+{
+ scored_type_[score_type] = value;
+}
+
+/**
+ *
+ */
+void MatchCollection::getCustomScoreNames(
+ vector<string>& custom_score_names
+ ) {
+ custom_score_names.clear();
+
+ if (!match_.empty()) {
+ match_.front()->getCustomScoreNames(custom_score_names);
+ }
+}
+
+/**
+ * Set the filepath for all matches in the collection
+ *\returns the associated file idx
+ */
+int MatchCollection::setFilePath(
+ const string& file_path, ///< File path to set
+ bool overwrite ///< Overwrite existing files?
+ ) {
+ int file_idx = -1;
+ for (vector<Crux::Match*>::iterator i = match_.begin(); i != match_.end(); i++) {
+ if (overwrite || (*i)->getFileIndex() == -1) {
+ file_idx = (*i)->setFilePath(file_path);
+ }
+ }
+ return file_idx;
+}
+
+/**
+ *\returns true, if there is a match_iterators instantiated by match collection
+ */
+bool MatchCollection::getIteratorLock() {
+ return iterator_lock_;
+}
+
+/**
+ *\returns the total match objects avaliable in current match_collection
+ */
+int MatchCollection::getMatchTotal() {
+ return match_.size();
+}
+
+bool MatchCollection::getHasDistinctMatches() {
+ return has_distinct_matches_;
+}
+
+void MatchCollection::setHasDistinctMatches(bool distinct) {
+ has_distinct_matches_ = distinct;
+}
+
+
+void MatchCollection::setExperimentSize(int size) {
+ experiment_size_ = size;
+}
+
+/**
+ * \returns The total number of peptides searched for this spectrum,
+ * target peptides for a target collection or decoy peptides for a
+ * decoy collection.
+ */
+int MatchCollection::getExperimentSize() {
+ return experiment_size_;
+}
+
+/**
+ * Sets the total number of target peptides searched for this
+ * spectrum. Only needs to be used by decoy match collections.
+ */
+void MatchCollection::setTargetExperimentSize(int numMatches) {
+ target_experiment_size_ = numMatches;
+}
+
+/**
+ * \returns The number of target matches that this spectrum had.
+ * Different than getExperimentSize() for decoy match collections.
+ */
+int MatchCollection::getTargetExperimentSize() {
+ if( null_peptide_collection_ ){
+ return target_experiment_size_;
+ }
+ return experiment_size_;
+}
+
+/**
+ *\returns the charge of the spectrum that the match collection was created
+ */
+int MatchCollection::getCharge()
+{
+ return zstate_.getCharge();
+}
+
+/**
+ * \brief Transfer the Weibull distribution parameters, including the
+ * correlation from one match_collection to another. No check to see
+ * that the parameters have been estimated.
+ */
+void MatchCollection::transferWeibull(
+ MatchCollection* from_collection,
+ MatchCollection* to_collection
+ ){
+ to_collection->eta_ = from_collection->eta_;
+ to_collection->beta_ = from_collection->beta_;
+ to_collection->shift_ = from_collection->shift_;
+ to_collection->correlation_ = from_collection->correlation_;
+}
+
+/**
+ * \brief Prints out the pepxml header to the output stream
+ * passed in as a parameter.
+ */
+
+void MatchCollection::printXmlHeader(
+ FILE* output,
+ const string& ms2file
+ ){
+ if (output == NULL) {
+ return;
+ }
+ time_t hold_time;
+ ENZYME_T enzyme = GlobalParams::getEnzyme();
+ const char* enz_str = enzyme_type_to_string(enzyme);
+ string database = Params::GetString("protein-database");
+
+ MASS_TYPE_T isotopic_mass_type = GlobalParams::getIsotopicMass();
+ MASS_TYPE_T fragment_mass_type = GlobalParams::getFragmentMass();
+
+ const char* isotopic_mass;
+ const char* fragment_mass;
+ DIGEST_T digest = GlobalParams::getDigestion();
+ int max_num_internal_cleavages;
+ int min_number_termini;
+ int missed_cleavage = GlobalParams::getMissedCleavages();
+ if (missed_cleavage){
+ max_num_internal_cleavages = GlobalParams::getMaxLength();
+ } else {
+ max_num_internal_cleavages = 0;
+ }
+
+ if (digest == FULL_DIGEST){
+ min_number_termini = 2;
+ } else if (digest == PARTIAL_DIGEST){
+ min_number_termini = 1;
+ } else {
+ min_number_termini = 0;
+ }
+
+ if (isotopic_mass_type == AVERAGE){
+ isotopic_mass = "average";
+ } else {
+ isotopic_mass = "monoisotopic";
+ }
+
+ if (fragment_mass_type == AVERAGE){
+ fragment_mass = "average";
+ } else {
+ fragment_mass = "monoisotopic";
+ }
+
+ char* absolute_database_path = NULL;
+ if (!database.empty()) {
+#if DARWIN
+ char path_buffer[PATH_MAX];
+ absolute_database_path = realpath(database.c_str(), path_buffer);
+#else
+ absolute_database_path = realpath(database.c_str(), NULL);
+#endif
+ }
+
+ hold_time = time(0);
+ const char* xsi = "http://www.w3.org/2001/XMLSchema-instance";
+ const char* xmlns = "http://regis-web.systemsbiology.net/pepXML";
+ const char* schema_location = "/usr/local/tpp/schema/pepXML_v110.xsd";
+ fprintf(output, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+ fprintf(output, "<?xml-stylesheet type=\"text/xsl\" href=\"\"?>\n");
+ fprintf(output, "<msms_pipeline_analysis date=\"%s\" xmlns=\"%s\""
+ " xmlns:xsi=\"%s\" xsi:schemaLocation=\"%s %s\""
+ " summary_xml=\"\">\n",
+ StringUtils::RTrim(string(ctime(&hold_time))).c_str(),
+ xmlns, xsi, xmlns, schema_location);
+ fprintf(output, "<msms_run_summary base_name=\"%s\" msManufacturer=\"%s\" "
+ "msModel=\"%s\" msIonization=\"%s\" msAnalyzer=\"%s\" "
+ "msDectector=\"%s\" raw_data_type=\"%s\" raw_data=\"%s\" >\n",
+ "NA", // TODO, dummy value
+ "NA", // TODO, dummy value
+ "NA", // TODO, dummy value
+ "NA", // TODO, dummy value
+ "NA", // TODO, dummy value
+ "NA", // TODO, dummy value
+ "NA", // TODO, dummy value
+ "NA" // TODO, dummy value
+ );
+ fprintf(output, "<sample_enzyme name=\"%s\">\n</sample_enzyme>\n", enz_str);
+ fprintf(output, "<search_summary base_name=\"%s\" search_engine=\"%s\" "
+ "precursor_mass_type=\"%s\" fragment_mass_type=\"%s\" "
+ "out_data_type=\"%s\" out_data=\"%s\" search_id=\"%i\" >\n",
+ "NA", // TODO, dummy value
+ "Crux",
+ isotopic_mass, // isotopic mass type is precursor mass type?
+ fragment_mass,
+ "NA", // TODO, dummy value
+ "NA",
+ 1 // TODO, dummy value
+ );
+ fprintf(output, "<search_database local_path=\"%s\" type=\"%s\" />\n",
+ absolute_database_path,
+ "AA");
+ fprintf(output, "<enzymatic_search_constraint enzyme=\"%s\" "
+ "max_num_internal_cleavages=\"%i\" min_number_termini=\"%i\"/>\n",
+ enz_str,
+ max_num_internal_cleavages,
+ min_number_termini);
+#ifndef DARWIN
+ free(absolute_database_path);
+#endif
+
+
+ char aa_str[2];
+ aa_str[1] = '\0';
+ int alphabet_size = (int)'A'+ ((int)'Z'-(int)'A');
+ MASS_TYPE_T isotopic_type = GlobalParams::getIsotopicMass();
+ int aa = 0;
+
+ // static amino acid modifications
+ for (char aa = 'A'; aa <= 'Z'; aa++) {
+ vector<const ModificationDefinition*> staticMods = ModificationDefinition::StaticMods(aa);
+ double aaMass = AminoAcidUtil::GetMass(aa, isotopic_type == MONO);
+ for (vector<const ModificationDefinition*>::const_iterator i = staticMods.begin();
+ i != staticMods.end();
+ i++) {
+ double modMass = (*i)->DeltaMass();
+ double totalMass = aaMass + modMass;
+ string termString;
+ switch ((*i)->Position()) {
+ case PEPTIDE_N: termString = "peptide_terminus=\"n\" "; break;
+ case PEPTIDE_C: termString = "peptide_terminus=\"c\" "; break;
+ }
+ fprintf(output, "<aminoacid_modification aminoacid=\"%c\" mass=\"%s\" "
+ "massdiff=\"%s\" variable=\"N\" %s/>\n",
+ aa,
+ StringUtils::ToString(totalMass, Params::GetInt("mass-precision")).c_str(),
+ StringUtils::ToString(modMass, Params::GetInt("mod-precision")).c_str(),
+ termString.c_str());
+ }
+ }
+
+ // variable amino acid modifications
+ vector<const ModificationDefinition*> varMods = ModificationDefinition::VarMods();
+ for (vector<const ModificationDefinition*>::const_iterator i = varMods.begin();
+ i != varMods.end();
+ i++) {
+ for (set<char>::const_iterator j = (*i)->AminoAcids().begin();
+ j != (*i)->AminoAcids().end();
+ j++) {
+ double modMass = (*i)->DeltaMass();
+ double aaMass = AminoAcidUtil::GetMass(*j, isotopic_type == MONO);
+ double totalMass = aaMass + modMass;
+ string termString;
+ switch ((*i)->Position()) {
+ case PEPTIDE_N: termString = "peptide_terminus=\"n\" "; break;
+ case PEPTIDE_C: termString = "peptide_terminus=\"c\" "; break;
+ }
+ fprintf(output, "<aminoacid_modification aminoacid=\"%c\" mass=\"%s\" "
+ "massdiff=\"%s\" variable=\"Y\" %s/>\n",
+ *j,
+ StringUtils::ToString(totalMass, Params::GetInt("mass-precision")).c_str(),
+ StringUtils::ToString(modMass, Params::GetInt("mod-precision")).c_str(),
+ termString.c_str());
+ }
+ }
+
+ for (vector<const Param*>::const_iterator i = Params::Begin(); i != Params::End(); i++) {
+ string name = (*i)->GetName();
+ if ((*i)->IsVisible() &&
+ name != "mod" && name != "cmod" && name != "nmod") {
+ fprintf(output, "<parameter name=\"%s\" value=\"%s\"/>\n",
+ name.c_str(), (*i)->GetString().c_str());
+ }
+ }
+ fprintf(output, "</search_summary>\n");
+}
+
+/**
+ * Write header for .sqt file. Assumes only sequest-search is writing
+ * this file type.
+ */
+void MatchCollection::printSqtHeader(
+ FILE* output,
+ const char* type,
+ string database,
+ int num_proteins,
+ bool exact_pval_search){
+ if( output == NULL ){
+ return;
+ }
+
+ time_t hold_time;
+ hold_time = time(0);
+
+ bool decoy = false;
+ if( strcmp(type, "decoy") == 0 ){
+ decoy = true;
+ }
+
+ fprintf(output, "H\tSQTGenerator Crux\n");
+ fprintf(output, "H\tSQTGeneratorVersion 1.0\n");
+ fprintf(output, "H\tComment Crux was written by...\n");
+ fprintf(output, "H\tComment ref...\n");
+ fprintf(output, "H\tStartTime\t%s", ctime(&hold_time));
+ fprintf(output, "H\tEndTime \n");
+
+ fprintf(output, "H\tDatabase\t%s\n", database.c_str());
+
+ if(decoy){
+ fprintf(output, "H\tComment\tDatabase shuffled; these are decoy matches\n");
+ }
+ fprintf(output, "H\tDBSeqLength\t?\n");
+ fprintf(output, "H\tDBLocusCount\t%d\n", num_proteins);
+
+ MASS_TYPE_T mass_type = GlobalParams::getIsotopicMass();
+ char temp_str[64];
+ mass_type_to_string(mass_type, temp_str);
+ fprintf(output, "H\tPrecursorMasses\t%s\n", temp_str);
+
+ mass_type = get_mass_type_parameter("fragment-mass");
+ mass_type_to_string(mass_type, temp_str);
+ fprintf(output, "H\tFragmentMasses\t%s\n", temp_str); //?????????
+
+ double tol = Params::GetDouble("precursor-window");
+ fprintf(output, "H\tAlg-PreMasTol\t%.1f\n",tol);
+ fprintf(output, "H\tAlg-FragMassTol\t%.2f\n",
+ Params::GetDouble("mz-bin-width") / 2.0);
+ fprintf(output, "H\tAlg-XCorrMode\t0\n");
+
+ fprintf(output, "H\tComment\tpreliminary algorithm %s\n",
+ Params::GetString("prelim-score-type").c_str());
+
+ fprintf(output, "H\tComment\tfinal algorithm %s\n",
+ Params::GetString("score-type").c_str());
+
+ int aa = 0;
+ char aa_str[2];
+ aa_str[1] = '\0';
+ int alphabet_size = (int)'A' + ((int)'Z'-(int)'A');
+ MASS_TYPE_T isotopic_type = GlobalParams::getIsotopicMass();
+
+ for(aa = (int)'A'; aa < alphabet_size -1; aa++){
+ aa_str[0] = (char)aa;
+ double mod = Params::GetDouble(aa_str);
+ if( mod != 0 ){
+ // double mass = mod + get_mass_amino_acid(aa, isotopic_type);
+ double mass = get_mass_amino_acid(aa, isotopic_type);
+ fprintf(output, "H\tStaticMod\t%s=%.3f\n", aa_str, mass);
+ }
+ }
+ // print dynamic mods, if any
+ // format DiffMod <AAs><symbol>=<mass change>
+ AA_MOD_T** aa_mod_list = NULL;
+ int num_mods = get_all_aa_mod_list(&aa_mod_list);
+ int mod_idx = 0;
+ for(mod_idx = 0; mod_idx < num_mods; mod_idx++){
+
+ AA_MOD_T* aamod = aa_mod_list[mod_idx];
+ string aa_list_str = aa_mod_get_aa_list_string(aamod);
+ char aa_symbol = aa_mod_get_symbol(aamod);
+ double mass_dif = aa_mod_get_mass_change(aamod);
+
+ fprintf(output, "H\tDiffMod\t%s%c=%+.2f\n", aa_list_str.c_str(),
+ aa_symbol, mass_dif);
+ }
+ num_mods = get_c_mod_list(&aa_mod_list);
+ for(mod_idx = 0; mod_idx < num_mods; mod_idx++){
+ AA_MOD_T* aamod = aa_mod_list[mod_idx];
+ char aa_symbol = aa_mod_get_symbol(aamod);
+
+ fprintf(output, "H\tComment\tMod %c is a C-terminal modification\n",
+ aa_symbol);
+ }
+
+ num_mods = get_n_mod_list(&aa_mod_list);
+ for(mod_idx = 0; mod_idx < num_mods; mod_idx++){
+ AA_MOD_T* aamod = aa_mod_list[mod_idx];
+ char aa_symbol = aa_mod_get_symbol(aamod);
+
+ fprintf(output, "H\tComment\tMod %c is a N-terminal modification\n",
+ aa_symbol);
+ }
+
+
+
+ //for letters in alphabet
+ // double mod = Params::GetDouble(letter);
+ // if mod != 0
+ // double mass = mod + getmass(letter);
+ // fprintf(output, "H\tStaticMod\t%s=%.3f\n", letter, mass);
+ // fprintf(output, "H\tStaticMod\tC=160.139\n");
+ fprintf(output, "H\tAlg-DisplayTop\t%d\n",
+ // Params::GetInt("max-sqt-result"));
+ Params::GetInt("top-match"));
+ // this is not correct for an sqt from analzyed matches
+
+ ENZYME_T enzyme = get_enzyme_type_parameter("enzyme");
+ DIGEST_T digestion = get_digest_type_parameter("digestion");
+ const char* enz_str = enzyme_type_to_string(enzyme);
+ const char* dig_str = digest_type_to_string(digestion);
+ char custom_str[SMALL_BUFFER];
+ if( enzyme == CUSTOM_ENZYME){
+ string rule = Params::GetString("custom-enzyme");
+ sprintf(custom_str, ", custom pattern: %s", rule.c_str());
+ }else{
+ custom_str[0] = 0;
+ }
+ fprintf(output, "H\tEnzymeSpec\t%s-%s%s\n", enz_str, dig_str, custom_str);
+ // write a comment that says what the scores are
+ fprintf(output, "H\tLine fields: S, scan number, scan number, "
+ "charge, 0, server, experimental mass, total ion intensity, "
+ "lowest Sp, number of matches\n");
+ if (exact_pval_search) {
+ fprintf(output, "H\tLine fields: M, rank by xcorr score, rank by sp score, "
+ "peptide mass, deltaCn, exact P-value, recalibrated xcorr, sp score, number ions matched, "
+ "total ions compared, sequence, validation status\n");
+ } else {
+ fprintf(output, "H\tLine fields: M, rank by xcorr score, rank by sp score, "
+ "peptide mass, deltaCn, xcorr score, sp score, number ions matched, "
+ "total ions compared, sequence, validation status\n");
+ }
+}
+
+/**
+ * Print the header line for a tab-delimited file.
+ */
+void MatchCollection::printTabHeader(FILE* output){
+
+ if( output == NULL ){
+ return;
+ }
+
+ int column_idx;
+ for (column_idx = 0; column_idx < NUMBER_MATCH_COLUMNS; column_idx++) {
+ fprintf(output, "%s", get_column_header(column_idx));
+ if (column_idx < NUMBER_MATCH_COLUMNS - 1) {
+ fprintf(output, "\t");
+ } else {
+ fprintf(output, "\n");
+ }
+ }
+}
+
+
+/**
+ * Print Footer lines for xml files
+ */
+void MatchCollection::printXmlFooter(FILE* output){
+ if (output == NULL ){
+ return;
+ }
+
+ fprintf(output, "</msms_run_summary>\n");
+ fprintf(output, "</msms_pipeline_analysis>\n");
+}
+
+
+/**
+ * \brief Print the given match collection for several spectra to
+ * xml files only. Takes the spectrum information from the
+ * matches in the collection. At least for now, prints all matches in
+ * the collection rather than limiting by top-match parameter.
+ */
+void MatchCollection::printMultiSpectraXml(PepXMLWriter* output) {
+ carp(CARP_DETAILED_DEBUG, "Writing matches to xml file");
+ // reuse these for each match
+ vector<string> protein_ids;
+ vector<string> protein_descriptions;
+ double* scores = new double[NUMBER_SCORER_TYPES];
+
+ for (vector<Crux::Match*>::iterator i = match_.begin(); i != match_.end(); i++) {
+ Match* cur_match = *i;
+ bool is_decoy = cur_match->getNullPeptide();
+ Spectrum* spectrum = cur_match->getSpectrum();
+ double cur_ln_experiment_size=0;
+ if (!is_decoy) {
+ int* ranks = new int[NUMBER_SCORER_TYPES];
+ ranks[XCORR] = -1;
+ char* peptide_sequence = cur_match->getSequence();
+ char* mod_peptide_sequence = cur_match->getModSequenceStrWithMasses(
+ get_mass_format_type_parameter("mod-mass-format"));
+ Peptide* peptide = cur_match->getPeptide();
+ char* flanking_aas = peptide->getFlankingAAs();
+ int num_proteins = peptide->getProteinInfo(protein_ids, protein_descriptions);
+ for (int score_idx = 0; score_idx < NUMBER_SCORER_TYPES; score_idx++) {
+ if (scored_type_[score_idx]) {
+ scores[score_idx] = cur_match->getScore((SCORER_TYPE_T)score_idx);
+ ranks[score_idx] = cur_match->getRank((SCORER_TYPE_T)score_idx);
+ }
+ }
+ unsigned num_matches = (!isDecoy()) ? getTargetExperimentSize() : getExperimentSize();
+ output->writePSM(spectrum->getFirstScan(),
+ spectrum->getFilename(),
+ cur_match->getNeutralMass(),
+ cur_match->getCharge(),
+ ranks,
+ peptide_sequence,
+ mod_peptide_sequence,
+ peptide->calcModifiedMass(),
+ num_proteins,
+ flanking_aas,
+ protein_ids,
+ protein_descriptions,
+ scored_type_,
+ scores,
+ num_matches);
+ }
+ }
+
+}
+
+/**
+ * \brief Print the psm features to file in xml format
+ *
+ * Prints a spectrum_query tag which encompasses the search_hit tag
+ * which represents peptide to spectra match.
+ *
+ * returns true, if succesfully printed xml format of PSMs, else false
+ *
+ */
+
+bool MatchCollection::printXml(
+ PepXMLWriter* output,
+ int top_match,
+ Spectrum* spectrum,
+ SCORER_TYPE_T main_score
+ )
+{
+ if ( output == NULL || spectrum == NULL || match_.empty()){
+ return false;
+ }
+
+ // calculate delta_cn and populate fields in the matches
+ calculateDeltaCn();
+
+ // for deciding when to quit
+ int count = 0;
+ int last_rank = 0;
+
+ // reuse these for each match
+ vector<string> protein_ids;
+ vector<string> protein_descriptions;
+ bool* scores_computed = new bool[NUMBER_SCORER_TYPES];
+
+ for(int score_idx = 0; score_idx < NUMBER_SCORER_TYPES; score_idx++){
+ scores_computed[score_idx] = false;
+ }
+ scores_computed[main_score] = true;
+ if (scored_type_[SP]) {
+ scores_computed[SP] = true;
+ }
+ if (scored_type_[DELTA_CN]) {
+ scores_computed[DELTA_CN] = true;
+ }
+ if (scored_type_[BY_IONS_MATCHED]) {
+ scores_computed[BY_IONS_MATCHED] = true;
+ }
+ if (scored_type_[BY_IONS_TOTAL]) {
+ scores_computed[BY_IONS_TOTAL] = true;
+ }
+ scores_computed[TIDE_SEARCH_EXACT_PVAL] = exact_pval_search_;
+ scores_computed[TIDE_SEARCH_REFACTORED_XCORR] = exact_pval_search_;
+ scores_computed[main_score] = !exact_pval_search_;
+
+ double* scores = new double[NUMBER_SCORER_TYPES];
+ int* ranks = new int[NUMBER_SCORER_TYPES];
+
+ Match* match = NULL;
+ // create match iterator
+ // true: return match in sorted order of main_score type
+ MatchIterator* match_iterator = new MatchIterator(this, main_score, true);
+ // iterate over matches
+ while (match_iterator->hasNext()) {
+ match = match_iterator->next();
+ int cur_rank = match->getRank(main_score);
+ if (scored_type_[XCORR]) {
+ ranks[XCORR] = match->getRank(XCORR);
+ }
+ if (scored_type_[SP]) {
+ ranks[SP] = match->getRank(SP);
+ scores[SP] = match->getScore(SP);
+ }
+ if (scored_type_[DELTA_CN]) {
+ scores[DELTA_CN] = match->getScore(DELTA_CN);
+ }
+ if (scored_type_[BY_IONS_MATCHED]) {
+ scores[BY_IONS_MATCHED] = match->getScore(BY_IONS_MATCHED);
+ }
+ if (scored_type_[BY_IONS_TOTAL]) {
+ scores[BY_IONS_TOTAL] = match->getScore(BY_IONS_TOTAL);
+ }
+ // print if we haven't reached the limit
+ // or if we are at the limit but this match is a tie with the last
+ if (count < top_match || last_rank == cur_rank) {
+ char* peptide_sequence = match->getSequence();
+ char* mod_peptide_sequence = match->getModSequenceStrWithMasses(
+ get_mass_format_type_parameter("mod-mass-format"));
+ Peptide* peptide = match->getPeptide();
+ char* flanking_aas = peptide->getFlankingAAs();
+ int num_proteins = peptide->getProteinInfo(protein_ids,
+ protein_descriptions);
+ for(int score_idx=0; score_idx < NUMBER_SCORER_TYPES; score_idx++){
+ if(scored_type_[score_idx]) {
+ scores[score_idx] = match->getScore((SCORER_TYPE_T)score_idx);
+ }
+ }
+ unsigned num_matches = (!isDecoy()) ? getTargetExperimentSize() : getExperimentSize();
+ output->writePSM(spectrum->getFirstScan(),
+ spectrum->getFilename(),
+ zstate_.getNeutralMass(),
+ zstate_.getCharge(),
+ ranks,
+ peptide_sequence,
+ mod_peptide_sequence,
+ peptide->calcModifiedMass(),
+ num_proteins,
+ flanking_aas,
+ protein_ids,
+ protein_descriptions,
+ scores_computed,
+ scores,
+ num_matches);
+ count++;
+ last_rank = cur_rank;
+ free(peptide_sequence);
+ free(mod_peptide_sequence);
+ free(flanking_aas);
+ } else if( count >= top_match && last_rank != cur_rank ) {
+ break;
+ } // else see if there is one more tie to print
+
+ }// next match
+
+ carp(CARP_DETAILED_DEBUG, "printed %d out of %d xml matches",
+ count, match_.size());
+
+ delete match_iterator;
+ delete [] scores_computed;
+ delete [] scores;
+ delete [] ranks;
+
+ return true;
+}
+
+
+/**
+ * \brief Print the psm features to file in sqt format.
+ *
+ * Prints one S line, 'top_match' M lines, and one locus line for each
+ * peptide source of each M line.
+ * Assumes one spectrum per match collection. Only crux
+ * sequset-search produces sqt files so the two scores are always Sp
+ * and xcorr.
+ * Possible side effects: Calculates delta_cn and stores in each match
+ *\returns true, if sucessfully print sqt format of the PSMs, else false
+ */
+bool MatchCollection::printSqt(
+ FILE* output, ///< the output file -out
+ int top_match, ///< the top matches to output -in
+ Spectrum* spectrum ///< the spectrum to print sqt -in
+ )
+{
+
+ if( output == NULL || spectrum == NULL || match_.empty() ){
+ return false;
+ }
+
+ SpectrumZState& zstate = zstate_;
+ int num_matches = experiment_size_;
+
+ // calculate delta_cn and populate fields in the matches
+ calculateDeltaCn();
+
+ // First, print spectrum info
+ spectrum->printSqt(output, num_matches, zstate);
+
+ Match* match = NULL;
+
+ // create match iterator
+ // true: return match in sorted order of main_score type
+ MatchIterator* match_iterator =
+ new MatchIterator(this, XCORR, true);
+
+ // Second, iterate over matches, prints M and L lines
+ while(match_iterator->hasNext()){
+ match = match_iterator->next();
+
+ // print only up to max_rank_result of the matches
+ if( match->getRank(XCORR) > top_match ){
+ break;
+ }// else
+
+ match->printSqt(output);
+
+ }// next match
+
+ // make sure top_scoring_sp_ has been set
+ if( top_scoring_sp_ == NULL){
+ carp(CARP_DEBUG, "Top scoring SP was not set.");
+ } else if( top_scoring_sp_->getRank(XCORR) > top_match ){
+ // print the match with Sp rank==1 if its xcorr rank > top_match rank.
+ top_scoring_sp_->printSqt(output);
+ }
+
+ delete match_iterator;
+
+ return true;
+}
+
+/**
+ * \brief Print the psm features to file in tab delimited format.
+ *
+ * Matches will be sorted by main_score and the ranks of those scores
+ * will be used to determine how many matches are printed for each
+ * spectrum.
+ * \returns true, if sucessfully print tab-delimited format of the
+ * PSMs, else false
+ */
+bool MatchCollection::printTabDelimited(
+ MatchFileWriter* output, ///< the output file -out
+ int top_match, ///< the top matches to output -in
+ Spectrum* spectrum, ///< the spectrum to print sqt -in
+ SCORER_TYPE_T main_score ///< the main score to report -in
+ )
+{
+
+ if( output == NULL || spectrum == NULL || match_.empty() ){
+ return false;
+ }
+ int num_target_matches = getTargetExperimentSize();
+ int num_decoy_matches = getExperimentSize();
+
+ Match* match = NULL;
+
+ // create match iterator
+ // true: return match in sorted order of main_score type
+ MatchIterator* match_iterator =
+ new MatchIterator(this, main_score, true);
+ int count = 0;
+ int last_rank = 0;
+
+ // iterate over matches
+ while(match_iterator->hasNext()){
+ match = match_iterator->next();
+ int cur_rank = match->getRank(main_score);
+
+ // print if we haven't reached the limit
+ // or if we are at the limit but this match is a tie with the last
+ if( count < top_match || last_rank == cur_rank ){
+
+ match->printTab(this, output, spectrum, num_target_matches, num_decoy_matches);
+ count++;
+ last_rank = cur_rank;
+ } else if( count >= top_match && last_rank != cur_rank ) {
+ break;
+ } // else see if there is one more tie to print
+
+ }// next match
+
+ carp(CARP_DETAILED_DEBUG, "printed %d out of %d tab matches",
+ count, num_target_matches);
+
+ delete match_iterator;
+
+ return true;
+}
+
+/**
+ * Retrieve the calibration parameter eta.
+ */
+FLOAT_T MatchCollection::getCalibrationEta()
+{
+ return eta_;
+}
+
+/**
+ * Retrieve the calibration parameter beta.
+ */
+FLOAT_T MatchCollection::getCalibrationBeta()
+{
+ return beta_;
+}
+
+/**
+ * Retrieve the calibration parameter shift.
+ */
+FLOAT_T MatchCollection::getCalibrationShift()
+{
+ return shift_;
+}
+
+/**
+ * Retrieve the calibration correlation.
+ */
+FLOAT_T MatchCollection::getCalibrationCorr()
+{
+ return correlation_;
+}
+
+/**
+ * \brief Print the given match collection for several spectra to
+ * tab-delimited files only. Takes the spectrum information from the
+ * matches in the collection. At least for now, prints all matches in
+ * the collection rather than limiting by top-match parameter. Uses
+ * SP as preliminary score and XCORR as main score.
+ */
+void MatchCollection::printMultiSpectra(
+ MatchFileWriter* tab_file,
+ MatchFileWriter* decoy_tab_file
+) {
+ carp(CARP_DETAILED_DEBUG, "Writing matches to file");
+
+ // if file location is target (i.e. tdc=T), print all to target
+ MatchFileWriter* decoy_file = decoy_tab_file;
+ if (Params::GetString("estimation-method") == "tdc") {
+ decoy_file = tab_file;
+ }
+
+ // for each match, get spectrum info, determine if decoy, print
+ for (vector<Crux::Match*>::iterator i = match_.begin(); i != match_.end(); i++) {
+ Match* cur_match = *i;
+ bool is_decoy = cur_match->getNullPeptide();
+ FLOAT_T num_psm_per_spec = cur_match->getLnExperimentSize();
+ num_psm_per_spec = expf(num_psm_per_spec) + 0.5; // round to nearest int
+ int num_target_psm_per_spec = cur_match->getTargetExperimentSize();
+
+ cur_match->printTab(this, (is_decoy ? decoy_file : tab_file),
+ cur_match->getSpectrum(),
+ (int)num_psm_per_spec, num_target_psm_per_spec);
+ }
+}
+
+/**
+ * \brief Adds the match to match_collection by copying the pointer.
+ *
+ * \returns true if successfully adds the match to the
+ * match_collection, else false
+ */
+bool MatchCollection::addMatch(
+ Match* match ///< the match to add -in
+ )
+{
+ if( match == NULL ){
+ carp(CARP_FATAL, "Cannot add NULL match.");
+ }
+
+ // add a new match to array
+ match_.push_back(match);
+ match->incrementPointerCount();
+
+ return true;
+}
+
+/**
+ * Adds the match object to match_collection
+ * Only for post_process (i.e. post search) match_collections. Keeps
+ * track of all peptides in a hash table.
+ * \returns true if successfully adds the match to the
+ * match_collection, else false
+ */
+// this method renamed so that a more general add_match_to_match_collection could be implemented
+bool MatchCollection::addMatchToPostMatchCollection(
+ Match* match ///< the match to add -in
+ )
+{
+ if( match == NULL ){
+ carp(CARP_FATAL, "Cannot add NULL match to NULL collection.");
+ }
+
+ // only for post_process_collections
+ if(!post_process_collection_){
+ carp(CARP_ERROR, "Must be a post process match collection to add a match.");
+ return false;
+ }
+
+ // add a new match to array
+ match_.push_back(match);
+ match->incrementPointerCount();
+
+ // DEBUG, print total peptided scored so far
+ if(match_.size() % 1000 == 0){
+ carp(CARP_DEBUG, "parsed PSM: %d", match_.size());
+ }
+
+ return true;
+}
+
+/**
+ * \brief Calculate the delta_cn of each match and populate the field.
+ *
+ * Delta_cn is the normalized difference between xcorrs of different ranks.
+ * match[i] = (match[i] - match[i+1]) / match[i].
+ * Sorts match_collection by xcorr, if necessary.
+ *
+ */
+bool MatchCollection::calculateDeltaCn() {
+ if (scored_type_[DELTA_CN] && scored_type_[DELTA_LCN]) {
+ return false;
+ }
+
+ SCORER_TYPE_T type = XCORR;
+ if (!scored_type_[type]) {
+ type = TIDE_SEARCH_EXACT_PVAL;
+ if (!scored_type_[type]) {
+ carp(CARP_WARNING,
+ "Delta_cn not calculated because match collection not scored for xcorr");
+ return false;
+ }
+ }
+
+ vector<FLOAT_T> scores;
+ for (vector<Match*>::iterator i = match_.begin(); i != match_.end(); i++) {
+ scores.push_back((*i)->getScore(type));
+ }
+ vector< pair<FLOAT_T, FLOAT_T> > deltaCns = calculateDeltaCns(scores, type);
+
+ for (size_t i = 0; i < deltaCns.size(); i++) {
+ match_[i]->setScore(DELTA_CN, deltaCns[i].first);
+ match_[i]->setScore(DELTA_LCN, deltaCns[i].second);
+ }
+
+ scored_type_[DELTA_CN] = scored_type_[DELTA_LCN] = true;
+ return true;
+}
+
+vector< pair<FLOAT_T, FLOAT_T> > MatchCollection::calculateDeltaCns(
+ vector<FLOAT_T> scores,
+ SCORER_TYPE_T type
+) {
+ vector< pair<FLOAT_T, FLOAT_T> > deltaCns(scores.size(), make_pair(0, 0));
+ if (scores.empty()) {
+ return deltaCns;
+ }
+
+ map< const FLOAT_T*, pair<FLOAT_T, FLOAT_T>* > scorePtrs;
+ for (size_t i = 0; i < scores.size(); i++) {
+ scorePtrs[&scores[i]] = &deltaCns[i];
+ }
+
+ if (type != TIDE_SEARCH_EXACT_PVAL) {
+ // Higher is better - sort descending
+ std::sort(scores.begin(), scores.end(), std::greater<FLOAT_T>());
+ } else {
+ // Lower is better - sort ascending
+ std::sort(scores.begin(), scores.end(), std::less<FLOAT_T>());
+ }
+
+ int top_match = Params::GetInt("top-match");
+
+// FLOAT_T last = scores.back();
+ FLOAT_T last = scores[min(top_match, (int) scores.size()) - 1];
+ for (vector<FLOAT_T>::const_iterator i = scores.begin(); i != scores.end(); i++) {
+ vector<FLOAT_T>::const_iterator next = (i != scores.end() - 1) ? i + 1 : i;
+ FLOAT_T deltaCn, deltaLCn;
+ switch (type) {
+ default:
+ deltaCn = (*i - *next) / max(*i, (FLOAT_T)1.0);
+ deltaLCn = (*i - last) / max(*i, (FLOAT_T)1.0);
+ break;
+ case TIDE_SEARCH_EXACT_PVAL:
+ deltaCn = -log10(*i) + log10(*next);
+ deltaLCn = -log10(*i) + log10(last);
+ break;
+ }
+ scorePtrs[&*i]->first = deltaCn;
+ scorePtrs[&*i]->second = deltaLCn;
+ }
+ return deltaCns;
+}
+
+/**********************************
+ * match_collection get, set methods
+ **********************************/
+
+/**
+ * \returns true if the match_collection only contains decoy matches,
+ * else (all target or mixed) returns false.
+ */
+bool MatchCollection::isDecoy() {
+ return null_peptide_collection_;
+}
+
+/**
+ * Try setting the match collection's charge. Successful if the
+ * current charge is 0 (i.e. hasn't yet been set) or if the current
+ * charge is the same as the given value. Otherwise, returns false
+ *
+ * \returns true if the match_collection's charge state was changed.
+ */
+
+bool MatchCollection::setZState(
+ SpectrumZState& zstate ///< new zstate
+ ) {
+ if (getCharge() == 0) {
+ zstate_ = zstate;
+ return true;
+ } else {
+ //error
+ carp(CARP_WARNING, "Cannot change the zstate of a match collection "
+ "once it has been set.");
+ return false;
+ }
+}
+
+/**
+ * Extract a given type of score into an array. The array is
+ * allocated here and must be freed by the caller.
+ */
+FLOAT_T* MatchCollection::extractScores(
+ SCORER_TYPE_T score_type ///< Type of score to extract.
+)
+{
+ FLOAT_T* return_value = (FLOAT_T*)mycalloc(match_.size(),
+ sizeof(FLOAT_T));
+
+ MatchIterator* match_iterator =
+ new MatchIterator(this, score_type, false);
+ int idx = 0;
+ while(match_iterator->hasNext()){
+ Match* match = match_iterator->next();
+ return_value[idx] = match->getScore(score_type);
+ idx++;
+ }
+ delete match_iterator;
+
+ return(return_value);
+}
+
+/**
+ * Given a hash table that maps from a score to its q-value, assign
+ * q-values to all of the matches in a given collection.
+ */
+void MatchCollection::assignQValues(
+ const map<FLOAT_T, FLOAT_T>* score_to_qvalue_hash,
+ SCORER_TYPE_T score_type,
+ SCORER_TYPE_T derived_score_type
+){
+
+ // Iterate over the matches filling in the q-values
+ MatchIterator* match_iterator =
+ new MatchIterator(this, score_type, false);
+
+ while(match_iterator->hasNext()){
+ Match* match = match_iterator->next();
+ FLOAT_T score = match->getScore(score_type);
+
+ FLOAT_T qvalue;
+ // If the score is not a number, punt.
+ if ( isinf(score) || isnan(score) ) {
+ carp(CARP_DEBUG, "Found inf or nan score.");
+ qvalue = numeric_limits<double>::quiet_NaN();
+ } else {
+ // Retrieve the corresponding q-value.
+ map<FLOAT_T, FLOAT_T>::const_iterator map_position
+ = score_to_qvalue_hash->find(score);
+ if (map_position == score_to_qvalue_hash->end()) {
+ carp(CARP_FATAL,
+ "Cannot find q-value corresponding to score of %g.",
+ score);
+ }
+ qvalue = map_position->second;
+ }
+ match->setScore(derived_score_type, qvalue);
+ }
+ scored_type_[derived_score_type] = true;
+ delete match_iterator;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/model/MatchCollection.h b/src/model/MatchCollection.h
new file mode 100644
index 0000000..6b13e25
--- /dev/null
+++ b/src/model/MatchCollection.h
@@ -0,0 +1,387 @@
+/**
+ * \file MatchCollection.h
+ * $Revision: 1.38 $
+ * \brief A set of peptide spectrum matches for one spectrum.
+ *
+ * Object for given a database and a spectrum, generate all match objects
+ * Creating a match collection generates all matches (searches a
+ * spectrum against a database.
+ */
+#ifndef MATCH_COLLECTION_H
+#define MATCH_COLLECTION_H
+
+
+#include <algorithm>
+#include <math.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#endif
+#include <map>
+#include <time.h>
+#include "io/carp.h"
+#include "Spectrum.h"
+#include "io/SpectrumCollection.h"
+#include "Ion.h"
+#include "IonSeries.h"
+#include "util/crux-utils.h"
+#include "model/objects.h"
+#include "parameter.h"
+#include "Scorer.h"
+#include "Match.h"
+#include "PeptideSrc.h"
+#include "ProteinIndex.h"
+#include "util/modifications.h"
+#include "ModifiedPeptidesIterator.h"
+#include "io/MatchFileWriter.h"
+#include "MatchIterator.h"
+#include "io/PepXMLWriter.h"
+
+using namespace std;
+
+static const int _PSM_SAMPLE_SIZE = 500;
+///< max number of peptides a single match collection can hold
+
+class MatchCollection {
+ friend class MatchIterator;
+ protected:
+ std::vector<Crux::Match*> match_; ///< array of match object
+ int experiment_size_; ///< total matches before any truncation
+ int target_experiment_size_; ///< total target matches for same spectrum
+ SpectrumZState zstate_; ///< zstate of the associated spectrum
+ bool null_peptide_collection_; ///< are the peptides shuffled
+ bool scored_type_[NUMBER_SCORER_TYPES];
+ ///< TRUE if matches have been scored by the type
+ SCORER_TYPE_T last_sorted_;
+ ///< the last type by which it's been sorted ( -1 if unsorted)
+ bool iterator_lock_;
+ ///< has an itterator been created? if TRUE can't manipulate matches
+
+ bool has_distinct_matches_; ///< does the match collection have distinct matches?
+
+ // Values for fitting the Weibull distribution
+ FLOAT_T eta_; ///< The eta parameter for the Weibull distribution.
+ FLOAT_T beta_; ///< The beta parameter for the Weibull distribution.
+ FLOAT_T shift_; ///< The location parameter for the Weibull distribution.
+ FLOAT_T correlation_; ///< The correlation parameter for the Weibull distribution.
+ vector<FLOAT_T> xcorrs_; ///< xcorrs to be used for weibull
+
+ // The following features (post_*) are only valid when
+ // post_process_collection boolean is true
+ bool post_process_collection_;
+ ///< Is this a post process match_collection?
+ Crux::Match* top_scoring_sp_; ///< the match with Sp rank == 1
+
+ /**
+ * initializes a MatchCollection object
+ */
+ void init();
+
+
+ public:
+ bool exact_pval_search_;
+
+ /**
+ * \brief Creates a new match collection with no matches in it. Sets
+ * member variables from parameter.c. The charge and null_collection
+ * variables are set with the method add_matches(). Search is
+ * conducted in add_matches().
+ *
+ * \returns A newly allocated match collection with member variables set.
+ */
+ MatchCollection(bool is_decoy = false);
+
+ /**
+ * free the memory allocated match collection
+ */
+ virtual ~MatchCollection();
+
+ /**
+ * sort the match collection by score_type(SP, XCORR, ... )
+ *\returns true, if successfully sorts the match_collection
+ */
+ void sort(
+ SCORER_TYPE_T score_type ///< the score type (SP, XCORR) -in
+ );
+
+ /**
+ * Rank matches in a collection based on the given score type.
+ * Requires that match_collection was already scored for that score type.
+ * Rank 1, means highest score
+ * \returns true, if populates the match rank in the match collection
+ */
+ bool populateMatchRank(
+ SCORER_TYPE_T score_type ///< the score type (SP, XCORR) -in
+ );
+
+ /**
+ * match_collection get, set method
+ */
+
+ /**
+ *\returns true, if the match collection has been scored by score_type
+ */
+ bool getScoredType(
+ SCORER_TYPE_T score_type ///< the score_type (MATCH_SP, MATCH_XCORR) -in
+ );
+
+ /**
+ * sets the score_type to value
+ */
+ void setScoredType(
+ SCORER_TYPE_T score_type, ///< the score_type (MATCH_SP, MATCH_XCORR) -in
+ bool value
+ );
+
+ void getCustomScoreNames(
+ std::vector<std::string>& custom_score_names
+ );
+
+ void preparePostProcess();
+
+ /**
+ *\returns true, if there is a match_iterators instantiated by match collection
+ */
+ bool getIteratorLock();
+
+ /**
+ *\returns the total match objects avaliable in current match_collection
+ */
+ int getMatchTotal();
+
+ /**
+ * Sets the total peptides searched in the experiment in match_collection
+ */
+ void setExperimentSize(int size);
+
+ /**
+ *\returns the total peptides searched in the experiment in match_collection
+ */
+ int getExperimentSize();
+
+ /**
+ * Sets the total number of target peptides searched for this
+ * spectrum. Only to be used by decoy match collections.
+ */
+ void setTargetExperimentSize(int numMatches);
+
+ /**
+ * \returns the number of target matches that this spectrum had.
+ * Different than getExperimentSize() for decoy match collections.
+ */
+ int getTargetExperimentSize();
+
+ /**
+ * Set the filepath for all matches in the collection
+ * \returns the associated file idx
+ */
+ int setFilePath(
+ const std::string& file_path, ///< File path to set
+ bool overwrite = false ///< Overwrite existing files?
+ );
+
+ /**
+ * \returns true if the match_collection only contains decoy matches,
+ * else (all target or mixed) returns false.
+ */
+ bool isDecoy();
+
+ /**
+ *\returns the charge of the spectrum that the match collection was created
+ */
+ int getCharge();
+
+ bool calculateDeltaCn();
+
+ // Take a vector of scores and return a vector of <deltaCn, deltaLCn>
+ static std::vector< std::pair<FLOAT_T, FLOAT_T> > calculateDeltaCns(
+ std::vector<FLOAT_T>, SCORER_TYPE_T type);
+
+ /**
+ * \brief Transfer the Weibull distribution parameters, including the
+ * correlation from one match_collection to another. No check to see
+ * that the parameters have been estimated.
+ */
+ static void transferWeibull(
+ MatchCollection* from_collection,
+ MatchCollection* to_collection
+ );
+
+ /**
+ * \brief Add a single match to a collection.
+ * Only puts a copy of the pointer to the match in the
+ * match_collection, does not allocate a new match.
+ */
+ bool addMatch(
+ Crux::Match* match ///< add this match
+ );
+
+ /**
+ * \brief Print the given match collection for one spectrum to all
+ * appropriate files.
+ */
+ void print(
+ Crux::Spectrum* spectrum,
+ bool is_decoy,
+ FILE* psm_file,
+ FILE* sqt_file,
+ FILE* decoy_file,
+ FILE* tab_file,
+ FILE* decoy_tab_file
+ );
+
+ /**
+ * \brief Print the given match collection for several spectra to all
+ * appropriate files. Takes the spectrum information from the matches
+ * in the collection.
+ */
+ void printMultiSpectra(
+ MatchFileWriter* tab_file,
+ MatchFileWriter* decoy_tab_file
+ );
+
+ /**
+ * \brief Print the given match collection for several spectra to
+ * xml files only. Takes the spectrum information from the
+ * matches in the collection. At least for now, prints all matches in
+ * the collection rather than limiting by top-match parameter.
+ */
+ void printMultiSpectraXml(
+ PepXMLWriter* output
+ );
+
+ /*
+ * Print the XML file header
+ */
+ static void printXmlHeader(FILE* outfile, const string& ms2file);
+
+ /*
+ * Print the SQT file header
+ */
+ static void printSqtHeader(
+ FILE* outfile,
+ const char* type,
+ string database,
+ int num_proteins,
+ bool exact_pval_search_ = false
+ );
+
+ /*
+ * Print the tab delimited file header
+ */
+ static void printTabHeader(
+ FILE* outfile
+ );
+
+ /*
+ * Print the XML file footer
+ */
+ static void printXmlFooter(
+ FILE* outfile
+ );
+
+ /**
+ * Print the psm features to output file up to 'top_match' number of
+ * top peptides among the match_collection in xml file format
+ * returns true, if sucessfully print xml format of the PSMs, else false
+ */
+ bool printXml(
+ PepXMLWriter* output,
+ int top_match,
+ Crux::Spectrum* spectrum,
+ SCORER_TYPE_T main_score
+ );
+
+ /**
+ * Print the psm features to output file upto 'top_match' number of
+ * top peptides among the match_collection in sqt file format
+ *\returns true, if sucessfully print sqt format of the PSMs, else false
+ */
+ bool printSqt(
+ FILE* output, ///< the output file -out
+ int top_match, ///< the top matches to output -in
+ Crux::Spectrum* spectrum ///< the spectrum to print sqt -in
+ );
+
+ /**
+ * Print the psm features to output file upto 'top_match' number of
+ * top peptides among the match_collection in tab delimited file format
+ *\returns true, if sucessfully print sqt format of the PSMs, else false
+ */
+ bool printTabDelimited(
+ MatchFileWriter* output, ///< the output file -out
+ int top_match, ///< the top matches to output -in
+ Crux::Spectrum* spectrum, ///< the spectrum to print sqt -in
+ SCORER_TYPE_T main_score ///< the main score to report -in
+ );
+
+ /**
+ * Retrieve the calibration parameter eta.
+ */
+ FLOAT_T getCalibrationEta();
+
+ /**
+ * Retrieve the calibration parameter beta.
+ */
+ FLOAT_T getCalibrationBeta();
+
+ /**
+ * Retrieve the calibration parameter shift.
+ */
+ FLOAT_T getCalibrationShift();
+
+ /**
+ * Retrieve the calibration parameter correlation.
+ */
+ FLOAT_T getCalibrationCorr();
+
+ bool getHasDistinctMatches();
+ void setHasDistinctMatches(bool distinct_matches);
+
+ /**
+ * Try setting the match collection's zstate. Successful if the
+ * current charge is 0 (i.e. hasn't yet been set) or if the current
+ * charge is the same as the given value. Otherwise, returns false
+ *
+ * \returns true if the match_collection's zstate was changed.
+ */
+ bool setZState(
+ SpectrumZState& zstate ///< new zstate
+ );
+
+ /**
+ * Extract a given type of score into an array. The array is
+ * allocated here and must be freed by the caller.
+ */
+ FLOAT_T* extractScores(
+ SCORER_TYPE_T score_type ///< Type of score to extract.
+ );
+
+ /**
+ * Given a hash table that maps from a score to its q-value, assign
+ * q-values to all of the matches in a given collection.
+ */
+ void assignQValues(
+ const map<FLOAT_T, FLOAT_T>* score_to_qvalue_hash,
+ SCORER_TYPE_T score_type,
+ SCORER_TYPE_T derived_score_type
+ );
+
+ /*******************************************
+ * match_collection post_process extension
+ ******************************************/
+ bool addMatchToPostMatchCollection(Crux::Match* match);
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/MatchCollectionIterator.cpp b/src/model/MatchCollectionIterator.cpp
new file mode 100644
index 0000000..e69de29
diff --git a/src/model/MatchCollectionIterator.h b/src/model/MatchCollectionIterator.h
new file mode 100644
index 0000000..e69de29
diff --git a/src/model/MatchIterator.cpp b/src/model/MatchIterator.cpp
new file mode 100644
index 0000000..45fd5f3
--- /dev/null
+++ b/src/model/MatchIterator.cpp
@@ -0,0 +1,133 @@
+/**
+ * \file MatchIterator.cpp
+ * $Revision: 1.38 $
+ * \brief An object that iterates over the match objects in the
+ * specified match_collection for the specified score type (SP, XCORR)
+ */
+#include "MatchIterator.h"
+
+/**
+ * Initializes a match iterator object.
+ */
+void MatchIterator::init() {
+
+ match_collection_ = NULL;
+ match_mode_ = (SCORER_TYPE_T)0;
+ match_idx_ = 0;
+ match_total_ = 0;
+}
+
+MatchIterator::MatchIterator(
+ MatchCollection* match_collection
+ ) {
+ // TODO (BF 06-Feb-08): Could we pass back an iterator with has_next==False
+ if (match_collection == NULL){
+ carp(CARP_FATAL, "Null match collection passed to match iterator");
+ }
+ // is there an existing iterator?
+ if(match_collection->iterator_lock_){
+ carp(CARP_FATAL,
+ "Can only have one match iterator instantiated at a time");
+ }
+
+ init();
+ // set items
+ match_collection_ = match_collection;
+ match_idx_ = 0;
+ match_total_ = match_collection->match_.size();
+
+
+
+ // ok lock up match collection
+ match_collection->iterator_lock_ = true;
+}
+
+
+/**
+ * create a new memory allocated match iterator, which iterates over
+ * match iterator only one iterator is allowed to be instantiated per
+ * match collection at a time
+ *\returns a new memory allocated match iterator
+ */
+MatchIterator::MatchIterator(
+ MatchCollection* match_collection,
+ ///< the match collection to iterate -out
+ SCORER_TYPE_T score_type,
+ ///< the score type to iterate (LOGP_EXP_SP, XCORR) -in
+ bool sort_match ///< should I return the match in sorted order?
+ )
+{
+ // TODO (BF 06-Feb-08): Could we pass back an iterator with has_next==False
+ if (match_collection == NULL){
+ carp(CARP_FATAL, "Null match collection passed to match iterator");
+ }
+ // is there an existing iterator?
+ if(match_collection->iterator_lock_){
+ carp(CARP_FATAL,
+ "Can only have one match iterator instantiated at a time");
+ }
+
+ // has the score type been populated in match collection?
+ if(!match_collection->scored_type_[score_type]){
+ const char* score_str = scorer_type_to_string(score_type);
+ carp(CARP_ERROR, "New match iterator for score type %s.", score_str);
+ carp(CARP_FATAL,
+ "The match collection has not been scored for request score type.");
+ }
+
+ init();
+ // set items
+ match_collection_ = match_collection;
+ match_mode_ = score_type;
+ match_idx_ = 0;
+ match_total_ = match_collection->match_.size();
+
+ // only sort if requested and match collection is not already sorted
+ if(sort_match){
+ match_collection->sort(score_type);
+ }
+
+
+ // ok lock up match collection
+ match_collection->iterator_lock_ = true;
+}
+
+/**
+ * free the memory allocated iterator
+ */
+MatchIterator::~MatchIterator()
+{
+ if (match_collection_ != NULL){
+ match_collection_->iterator_lock_ = false;
+ }
+}
+
+/**
+ * Does the match_iterator have another match struct to return?
+ *\returns true, if match iter has a next match, else False
+ */
+bool MatchIterator::hasNext()
+{
+ return match_idx_ < match_total_;
+}
+
+/**
+ * return the next match struct!
+ *\returns the match in decreasing score order for the match_mode(SCORER_TYPE_T)
+ */
+Crux::Match* MatchIterator::next()
+{
+ return match_collection_->match_[match_idx_++];
+}
+
+
+Crux::Match* MatchIterator::getMatch(int match_idx){
+ return (match_idx_ < match_total_) ? match_collection_->match_[match_idx] : NULL;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/MatchIterator.h b/src/model/MatchIterator.h
new file mode 100644
index 0000000..dbb8b73
--- /dev/null
+++ b/src/model/MatchIterator.h
@@ -0,0 +1,83 @@
+/**
+ * \file MatchIterator.h
+ * $Revision: 1.38 $
+ * \brief An object that iterates over the match objects in the
+ * specified match_collection for the specified score type (SP, XCORR)
+ */
+#ifndef MATCHITERATOR_H
+#define MATCHITERATOR_H
+
+#include "MatchCollection.h"
+
+class MatchIterator {
+ protected:
+ MatchCollection* match_collection_; ///< the match collection to iterate -out
+ SCORER_TYPE_T match_mode_; ///< the current working score (SP, XCORR)
+ int match_idx_; ///< current match to return
+ int match_total_; ///< total_match_count
+
+ /**
+ * Initializes a match iterator object.
+ */
+ void init();
+
+ public:
+
+ MatchIterator(
+ MatchCollection* match_collection ///< the match collection to iterate -in
+ );
+
+ /**
+ * create a new memory allocated match iterator
+ * creates a new the generate_peptides_iterator inside the match_iterator
+ *\returns a new memory allocated match iterator
+ */
+ MatchIterator(
+ MatchCollection* match_collection, ///< the match collection to iterate -in
+ SCORER_TYPE_T match_mode, ///< the mode to set (MATCH_SP, MATCH_XCORR) -in
+ bool sort_match = false ///< should I return the match in sorted order? (default false)
+ );
+
+ /**
+ * \brief Create a match iterator to return matches from a collection
+ * grouped by spectrum and sorted by given score type.
+ *
+ * \returns A heap-allocated match iterator.
+ */
+ /*
+ MatchIterator(
+ MatchCollection* match_collection, ///< match collection to iterate -in
+ SCORER_TYPE_T scorer ///< the score to sort by (MATCH_SP, MATCH_XCORR) -in
+ );
+ */
+ /**
+ * free the memory allocated iterator
+ */
+ ~MatchIterator();
+
+ /**
+ * Does the match_iterator have another match struct to return?
+ * MUST set the iterator to correct mode before calling this method
+ *\returns true, if match iter has a next match, else False
+ */
+ bool hasNext();
+
+ /**
+ * return the next match struct!
+ * MUST set the iterator to correct mode before initialially calling this method
+ *\returns the match in decreasing score order for the match_mode(SCORER_TYPE_T)
+ */
+ Crux::Match* next();
+
+ Crux::Match* getMatch(int match_idx);
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/Modification.cpp b/src/model/Modification.cpp
new file mode 100644
index 0000000..566108a
--- /dev/null
+++ b/src/model/Modification.cpp
@@ -0,0 +1,572 @@
+#include "Modification.h"
+#include "io/carp.h"
+#include "util/AminoAcidUtil.h"
+#include "util/MathUtil.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+
+#include <algorithm>
+#include <cmath>
+#include <cstdio>
+#include <sstream>
+#include <stdexcept>
+
+using namespace std;
+using namespace Crux;
+
+ModificationDefinition::ModificationDefinition(
+ const string& aminoAcids, double deltaMass, ModPosition position,
+ bool preventsCleavage, bool preventsXLink, char symbol)
+ : deltaMass_(deltaMass), position_(position),
+ symbol_(symbol), preventsCleavage_(preventsCleavage), preventsXLink_(preventsXLink) {
+ AddAminoAcids(aminoAcids);
+}
+
+ModificationDefinition::~ModificationDefinition() {
+}
+
+const ModificationDefinition* ModificationDefinition::New(
+ const string& aminoAcids, double deltaMass, ModPosition position,
+ bool isStatic, bool preventsCleavage, bool preventsXLink) {
+ return isStatic
+ ? NewStaticMod(aminoAcids, deltaMass, position, preventsCleavage, preventsXLink)
+ : NewVarMod(aminoAcids, deltaMass, position, preventsCleavage, preventsXLink, '\0');
+}
+
+const ModificationDefinition* ModificationDefinition::NewStaticMod(
+ const string& aminoAcids, double deltaMass, ModPosition position,
+ bool preventsCleavage, bool preventsXLink) {
+ // Look for existing
+ vector<ModificationDefinition*> staticMods = modContainer_.StaticMods();
+ for (vector<ModificationDefinition*>::const_iterator i = staticMods.begin();
+ i != staticMods.end();
+ i++) {
+ if (MathUtil::AlmostEqual((*i)->deltaMass_, deltaMass, Params::GetInt("mod-precision")) &&
+ (position == UNKNOWN || (*i)->position_ == UNKNOWN || (*i)->position_ == position) &&
+ (*i)->preventsCleavage_ == preventsCleavage &&
+ (*i)->preventsXLink_ == preventsXLink) {
+ string added = (*i)->AddAminoAcids(aminoAcids);
+ for (string::const_iterator j = added.begin(); j != added.end(); j++) {
+ modContainer_.staticMods_[*j].push_back(*i);
+ }
+ if (position != UNKNOWN && (*i)->position_ == UNKNOWN) {
+ (*i)->position_ = position;
+ }
+ return *i;
+ }
+ }
+ // Does not exist yet
+ ModificationDefinition* mod = new ModificationDefinition(
+ aminoAcids, deltaMass, position, '\0', preventsCleavage, preventsXLink);
+ modContainer_.Add(mod);
+ return mod;
+}
+
+const ModificationDefinition* ModificationDefinition::NewVarMod(
+ const string& aminoAcids, double deltaMass, ModPosition position,
+ bool preventsCleavage, bool preventsXLink, char symbol) {
+ // Look for existing
+ for (vector<ModificationDefinition*>::const_iterator i = modContainer_.varMods_.begin();
+ i != modContainer_.varMods_.end();
+ i++) {
+ if (MathUtil::AlmostEqual((*i)->deltaMass_, deltaMass, Params::GetInt("mod-precision")) &&
+ (position == UNKNOWN || (*i)->position_ == UNKNOWN || (*i)->position_ == position) &&
+ (*i)->preventsCleavage_ == preventsCleavage &&
+ (*i)->preventsXLink_ == preventsXLink &&
+ (symbol == '\0' || (*i)->symbol_ == symbol)) {
+ (*i)->AddAminoAcids(aminoAcids);
+ if (position != UNKNOWN && (*i)->position_ == UNKNOWN) {
+ (*i)->position_ = position;
+ }
+ return *i;
+ }
+ }
+ // Does not exist yet
+ if (symbol == '\0') {
+ symbol = modContainer_.NextSymbol();
+ } else {
+ modContainer_.ConsumeSymbol(symbol);
+ }
+ ModificationDefinition* mod = new ModificationDefinition(
+ aminoAcids, deltaMass, position, preventsCleavage, preventsXLink, symbol);
+ modContainer_.Add(mod);
+ return mod;
+}
+
+string ModificationDefinition::String() const {
+ // For debugging
+ stringstream ss;
+ ss << '[' << this << ']';
+ if (!aminoAcids_.empty()) {
+ ss << '[' << StringUtils::Join(aminoAcids_) << ']';
+ } else {
+ ss << "[?]";
+ }
+ ss << '[' << DeltaMass() << ']';
+ if (Static()) {
+ ss << "[static]";
+ } else {
+ ss << "[variable " << Symbol() << ']';
+ }
+ ss << '[';
+ switch (Position()) {
+ default: ss << "unknown"; break;
+ case ANY: ss << "any"; break;
+ case PEPTIDE_N: ss << "peptide N"; break;
+ case PEPTIDE_C: ss << "peptide C"; break;
+ case PROTEIN_N: ss << "protein N"; break;
+ case PROTEIN_C: ss << "protein C"; break;
+ }
+ ss << ']';
+ return ss.str();
+}
+
+void ModificationDefinition::ListAll() {
+ // For debugging
+ ListStaticMods();
+ ListVarMods();
+}
+
+void ModificationDefinition::ListStaticMods() {
+ // For debugging
+ carp(CARP_INFO, "Listing static modifications");
+ vector<ModificationDefinition*> staticMods = modContainer_.StaticMods();
+ for (vector<ModificationDefinition*>::const_iterator i = staticMods.begin();
+ i != staticMods.end();
+ i++) {
+ carp(CARP_INFO, "%s", (*i)->String().c_str());
+ }
+}
+
+void ModificationDefinition::ListVarMods() {
+ // For debugging
+ carp(CARP_INFO, "Listing variable modifications");
+ for (vector<ModificationDefinition*>::const_iterator i = modContainer_.varMods_.begin();
+ i != modContainer_.varMods_.end();
+ i++) {
+ carp(CARP_INFO, "%s", (*i)->String().c_str());
+ }
+}
+
+void ModificationDefinition::ClearAll() {
+ modContainer_ = ModificationDefinitionContainer();
+}
+
+void ModificationDefinition::ClearStaticMods() {
+ vector<ModificationDefinition*> staticMods = modContainer_.StaticMods();
+ for (vector<ModificationDefinition*>::const_iterator i = staticMods.begin();
+ i != staticMods.end();
+ i++) {
+ delete *i;
+ }
+ modContainer_.staticMods_.clear();
+}
+
+void ModificationDefinition::ClearVarMods() {
+ for (vector<ModificationDefinition*>::const_iterator i = modContainer_.varMods_.begin();
+ i != modContainer_.varMods_.end();
+ i++) {
+ delete *i;
+ }
+ modContainer_.varMods_.clear();
+ modContainer_.InitSymbolPool();
+}
+
+vector<const ModificationDefinition*> ModificationDefinition::AllMods() {
+ vector<const ModificationDefinition*> mods = StaticMods();
+ vector<const ModificationDefinition*> varMods = VarMods();
+ mods.insert(mods.end(), varMods.begin(), varMods.end());
+ return mods;
+}
+
+vector<const ModificationDefinition*> ModificationDefinition::StaticMods(char c) {
+ vector<ModificationDefinition*> mods = modContainer_.StaticMods(c);
+ vector<const ModificationDefinition*> modsConst;
+ for (vector<ModificationDefinition*>::const_iterator i = mods.begin();
+ i != mods.end();
+ i++) {
+ modsConst.push_back(*i);
+ }
+ return modsConst;
+}
+
+vector<const ModificationDefinition*> ModificationDefinition::VarMods() {
+ vector<const ModificationDefinition*> mods;
+ for (vector<ModificationDefinition*>::const_iterator i = modContainer_.varMods_.begin();
+ i != modContainer_.varMods_.end();
+ i++) {
+ mods.push_back(*i);
+ }
+ return mods;
+}
+
+double ModificationDefinition::DeltaMass(char c, ModPosition position) {
+ double mass = 0.0;
+ vector<const ModificationDefinition*> staticMods = StaticMods(c);
+ for (vector<const ModificationDefinition*>::const_iterator i = staticMods.begin();
+ i != staticMods.end();
+ i++) {
+ if ((*i)->position_ == UNKNOWN || (*i)->position_ == ANY || position == (*i)->position_) {
+ mass += (*i)->DeltaMass();
+ }
+ }
+ return mass;
+}
+
+const set<char>& ModificationDefinition::AminoAcids() const {
+ return aminoAcids_;
+}
+
+double ModificationDefinition::DeltaMass() const {
+ return deltaMass_;
+}
+
+bool ModificationDefinition::Static() const {
+ return symbol_ == '\0';
+}
+
+ModPosition ModificationDefinition::Position() const {
+ return position_;
+}
+
+char ModificationDefinition::Symbol() const {
+ return symbol_;
+}
+
+bool ModificationDefinition::PreventsCleavage() const {
+ return preventsCleavage_;
+}
+
+bool ModificationDefinition::PreventsXLink() const {
+ return preventsXLink_;
+}
+
+const ModificationDefinition* ModificationDefinition::Find(char symbol) {
+ for (vector<ModificationDefinition*>::const_iterator i = modContainer_.varMods_.begin();
+ i != modContainer_.varMods_.end();
+ i++) {
+ if ((*i)->symbol_ == symbol) {
+ return *i;
+ }
+ }
+ return NULL;
+}
+
+const ModificationDefinition* ModificationDefinition::Find(
+ double deltaMass, bool isStatic, ModPosition position) {
+ vector<ModificationDefinition*> staticMods = modContainer_.StaticMods();
+ vector<ModificationDefinition*>* mods = isStatic ? &staticMods : &modContainer_.varMods_;
+ for (vector<ModificationDefinition*>::const_iterator i = mods->begin();
+ i != mods->end();
+ i++) {
+ if ((position == UNKNOWN || position == (*i)->Position()) &&
+ MathUtil::AlmostEqual((*i)->deltaMass_, deltaMass, Params::GetInt("mod-precision"))) {
+ return *i;
+ }
+ }
+ return NULL;
+}
+
+string ModificationDefinition::AddAminoAcids(const string& aminoAcids) {
+ string added;
+ for (string::const_iterator i = aminoAcids.begin(); i != aminoAcids.end(); i++) {
+ if (*i == 'X') {
+ for (char j = 'A'; j <= 'Z'; j++) {
+ if (aminoAcids_.insert(j).second) {
+ added.push_back(j);
+ }
+ }
+ break;
+ }
+ if (aminoAcids_.insert(*i).second) {
+ added.push_back(*i);
+ }
+ }
+ return added;
+}
+
+void swap(Modification& x, Modification& y) {
+ using std::swap;
+ swap(x.index_, y.index_);
+ swap(x.mod_, y.mod_);
+}
+
+ostream& operator<<(ostream& stream, const Modification& mod) {
+ stream << mod.String();
+ return stream;
+}
+
+Modification::Modification(const ModificationDefinition* mod, unsigned char index)
+ : index_(index), mod_(mod) {
+}
+
+Modification::Modification(const Modification& other)
+ : index_(other.index_), mod_(other.mod_) {
+}
+
+Modification::~Modification() {
+}
+
+Modification& Modification::operator=(Modification other) {
+ swap(*this, other);
+ return *this;
+}
+
+bool Modification::operator==(const Modification& other) const {
+ return index_ == other.index_ && mod_ == other.mod_;
+}
+
+bool Modification::operator!=(const Modification& other) const {
+ return !(*this == other);
+}
+
+string Modification::String() const {
+ char buffer[32];
+ string positionStr;
+ switch (mod_->Position()) {
+ case PEPTIDE_N: positionStr = "_n"; break;
+ case PEPTIDE_C: positionStr = "_c"; break;
+ case PROTEIN_N: positionStr = "_N"; break;
+ case PROTEIN_C: positionStr = "_C"; break;
+ }
+ sprintf(buffer, "%d_%c_%.*f%s",
+ index_ + 1,
+ mod_->Static() ? 'S' : 'V',
+ Params::GetInt("mod-precision"), mod_->DeltaMass(),
+ positionStr.c_str());
+ return string(buffer);
+}
+
+Modification Modification::Parse(const string& modString, Peptide* peptide) {
+ vector<string> pieces = StringUtils::Split(modString, '_');
+ if (3 > pieces.size() || pieces.size() > 4) {
+ throw runtime_error("Could not parse modification string '" + modString + "'");
+ }
+ unsigned char index = (unsigned char)StringUtils::FromString<unsigned int>(pieces[0]) - 1;
+ bool isStatic = false;
+ if (StringUtils::IEquals(pieces[1], "S")) {
+ isStatic = true;
+ } else if (!StringUtils::IEquals(pieces[1], "V")) {
+ throw runtime_error("Could not parse modification string '" + modString + "'");
+ }
+ double deltaMass = StringUtils::FromString<double>(pieces[2]);
+ ModPosition position = ANY;
+ if (pieces.size() == 4) {
+ if (pieces[3] == "n") {
+ position = PEPTIDE_N;
+ } else if (pieces[3] == "c") {
+ position = PEPTIDE_C;
+ } else if (pieces[3] == "N") {
+ position = PROTEIN_N;
+ } else if (pieces[3] == "C") {
+ position = PROTEIN_C;
+ } else {
+ throw runtime_error("Could not parse modification string '" + modString + "'");
+ }
+ }
+ const ModificationDefinition* definition =
+ ModificationDefinition::Find(deltaMass, isStatic, position);
+ string aa;
+ if (peptide) {
+ char* seq = peptide->getSequence();
+ aa.push_back(seq[index]);
+ free(seq);
+ }
+ if (definition == NULL) {
+ // Create new modification
+ definition = ModificationDefinition::New(
+ !aa.empty() ? aa : "X", deltaMass, position, isStatic);
+ } else if (!aa.empty() &&
+ definition->AminoAcids().find(aa[0]) == definition->AminoAcids().end()) {
+ definition = ModificationDefinition::New(
+ aa, definition->DeltaMass(), definition->Position(), definition->Static(),
+ definition->PreventsCleavage(), definition->PreventsXLink());
+ }
+
+ return Modification(definition, index);
+}
+
+unsigned char Modification::Index() const {
+ return index_;
+}
+
+const ModificationDefinition* Modification::Definition() const {
+ return mod_;
+}
+
+double Modification::DeltaMass() const {
+ return mod_->DeltaMass();
+}
+
+bool Modification::Static() const {
+ return mod_->Static();
+}
+
+ModPosition Modification::Position() const {
+ return mod_->Position();
+}
+
+char Modification::Symbol() const {
+ return mod_->Symbol();
+}
+
+bool Modification::PreventsCleavage() const {
+ return mod_->PreventsCleavage();
+}
+
+bool Modification::PreventsXLink() const {
+ return mod_->PreventsXLink();
+}
+
+// Turns a MODIFIED_AA_T* and its length into a sequence and vector of Modification
+// TODO Remove this
+void Modification::FromSeq(MODIFIED_AA_T* seq, int length,
+ string* outSeq, vector<Modification>* outMods) {
+ *outSeq = string(length, 'X');
+ if (outMods != NULL) {
+ *outMods = vector<Modification>();
+ }
+ if (seq != NULL && length != 0) {
+ AA_MOD_T** allMods = NULL;
+ int modCount = get_all_aa_mod_list(&allMods);
+ for (int i = 0; i < length; i++) {
+ (*outSeq)[i] = modified_aa_to_char(seq[i]);
+ if (outMods == NULL) {
+ continue;
+ }
+ for (int j = 0; j < modCount; j++) {
+ if (is_aa_modified(seq[i], allMods[j])) {
+ ModPosition position = UNKNOWN;
+ switch (aa_mod_get_position(allMods[j])) {
+ case N_TERM: position = PEPTIDE_N; break;
+ case C_TERM: position = PEPTIDE_C; break;
+ }
+ string aaList = aa_mod_get_aa_list_string(allMods[j]);
+ bool preventsCleavage = aa_mod_get_prevents_cleavage(allMods[j]);
+ bool preventsXLink = aa_mod_get_prevents_xlink(allMods[j]);
+ double massChange = aa_mod_get_mass_change(allMods[j]);
+ const ModificationDefinition* def =
+ ModificationDefinition::Find(massChange, false, position);
+ if (!def) {
+ char symbol = aa_mod_get_symbol(allMods[j]);
+ def = ModificationDefinition::NewVarMod(
+ aaList, massChange, position, preventsCleavage, preventsXLink, symbol);
+ }
+ outMods->push_back(Modification(def, (unsigned char)i));
+ }
+ }
+ }
+ }
+}
+
+// Turns an unmodified sequence and vector of mods into a MODIFIED_AA_T*
+// TODO Remove this
+MODIFIED_AA_T* Modification::ToSeq(const string& seq, const vector<Modification>& mods) {
+
+ MODIFIED_AA_T* modSeq = newModSeq();
+
+ for (unsigned i = 0; i < seq.length(); i++) {
+ modSeq[i] = char_aa_to_modified(seq[i]);
+ }
+ modSeq[seq.length()] = MOD_SEQ_NULL;
+
+ for (vector<Modification>::const_iterator i = mods.begin(); i != mods.end(); i++) {
+ if (!i->Static()) {
+ modify_aa(&modSeq[i->Index()], get_aa_mod_from_mass((FLOAT_T)i->DeltaMass()));
+ }
+ }
+
+ return modSeq;
+}
+
+ModificationDefinitionContainer::ModificationDefinitionContainer() {
+ InitSymbolPool();
+}
+
+ModificationDefinitionContainer::~ModificationDefinitionContainer() {
+ for (vector<ModificationDefinition*>::const_iterator i = varMods_.begin();
+ i != varMods_.end();
+ i++) {
+ delete *i;
+ }
+ vector<ModificationDefinition*> staticMods = StaticMods();
+ for (vector<ModificationDefinition*>::const_iterator i = staticMods.begin();
+ i != staticMods.end();
+ i++) {
+ delete *i;
+ }
+}
+
+void ModificationDefinitionContainer::InitSymbolPool() {
+ symbolPool_.clear();
+ symbolPool_.push_back('*');
+ symbolPool_.push_back('#');
+ symbolPool_.push_back('@');
+ symbolPool_.push_back('^');
+ symbolPool_.push_back('~');
+ symbolPool_.push_back('%');
+ symbolPool_.push_back('$');
+ symbolPool_.push_back('&');
+ symbolPool_.push_back('!');
+ symbolPool_.push_back('?');
+ symbolPool_.push_back('+');
+}
+
+vector<ModificationDefinition*> ModificationDefinitionContainer::StaticMods(char c) {
+ vector<ModificationDefinition*> mods;
+ for (map< char, vector<ModificationDefinition*> >::const_iterator i = staticMods_.begin();
+ i != staticMods_.end();
+ i++) {
+ if (c != '\0' && c != i->first) {
+ continue;
+ }
+ for (vector<ModificationDefinition*>::const_iterator j = i->second.begin();
+ j != i->second.end();
+ j++) {
+ if (find(mods.begin(), mods.end(), *j) == mods.end()) {
+ mods.push_back(*j);
+ }
+ }
+ }
+ return mods;
+}
+
+void ModificationDefinitionContainer::Add(ModificationDefinition* def) {
+ if (def->Static()) {
+ for (set<char>::const_iterator i = def->AminoAcids().begin();
+ i != def->AminoAcids().end();
+ i++) {
+ map< char, vector<ModificationDefinition*> >::const_iterator j = staticMods_.find(*i);
+ if (j == staticMods_.end()) {
+ staticMods_[*i] = vector<ModificationDefinition*>(1, def);
+ } else {
+ staticMods_[*i].push_back(def);
+ }
+ }
+ } else {
+ varMods_.push_back(def);
+ }
+ carp(CARP_DEBUG, "Added new modification [%x]: aa[%s] dM[%f] static[%d] symbol[%c]",
+ def, StringUtils::Join(def->AminoAcids()).c_str(), def->DeltaMass(),
+ def->Static(), def->Symbol());
+}
+
+char ModificationDefinitionContainer::NextSymbol() {
+ if (!symbolPool_.empty()) {
+ char symbol = symbolPool_.front();
+ symbolPool_.pop_front();
+ return symbol;
+ }
+ carp(CARP_WARNING, "No more symbols for variable modifications available");
+ return '+';
+}
+
+void ModificationDefinitionContainer::ConsumeSymbol(char c) {
+ for (deque<char>::iterator i = symbolPool_.begin(); i != symbolPool_.end(); i++) {
+ if (*i == c) {
+ symbolPool_.erase(i);
+ return;
+ }
+ }
+}
+
diff --git a/src/model/Modification.h b/src/model/Modification.h
new file mode 100644
index 0000000..4299515
--- /dev/null
+++ b/src/model/Modification.h
@@ -0,0 +1,131 @@
+#ifndef CRUX_MODIFICATION_H
+#define CRUX_MODIFICATION_H
+
+#include "model/Peptide.h"
+#include "util/modifications.h"
+
+#include <deque>
+#include <ostream>
+#include <set>
+#include <string>
+#include <vector>
+
+enum ModPosition {
+ UNKNOWN, ANY,
+ PEPTIDE_N, PEPTIDE_C,
+ PROTEIN_N, PROTEIN_C
+};
+
+class ModificationDefinition {
+public:
+ ModificationDefinition(
+ const std::string& aminoAcids, double deltaMass, ModPosition position,
+ bool preventsCleavage, bool preventsXLink, char symbol);
+ virtual ~ModificationDefinition();
+
+ static const ModificationDefinition* New(
+ const std::string& aminoAcids, double deltaMass, ModPosition position,
+ bool isStatic, bool preventsCleavage = false, bool preventsXLink = false);
+ static const ModificationDefinition* NewStaticMod(
+ const std::string& aminoAcids, double deltaMass, ModPosition position,
+ bool preventsCleavage = false, bool preventsXLink = false);
+ static const ModificationDefinition* NewVarMod(
+ const std::string& aminoAcids, double deltaMass, ModPosition position,
+ bool preventsCleavage = false, bool preventsXLink = false, char symbol = '\0');
+
+ std::string String() const;
+ static void ListAll();
+ static void ListStaticMods();
+ static void ListVarMods();
+
+ static void ClearAll();
+ static void ClearStaticMods();
+ static void ClearVarMods();
+
+ static std::vector<const ModificationDefinition*> AllMods();
+ static std::vector<const ModificationDefinition*> StaticMods(char c = '\0');
+ static std::vector<const ModificationDefinition*> VarMods();
+ static double DeltaMass(char c, ModPosition position);
+
+ const std::set<char>& AminoAcids() const;
+ double DeltaMass() const;
+ bool Static() const;
+ ModPosition Position() const;
+ char Symbol() const;
+ bool PreventsCleavage() const;
+ bool PreventsXLink() const;
+
+ static const ModificationDefinition* Find(char symbol);
+ static const ModificationDefinition* Find(double deltaMass,
+ bool isStatic, ModPosition position = UNKNOWN);
+protected:
+ std::string AddAminoAcids(const std::string& aminoAcids);
+
+ std::set<char> aminoAcids_;
+ double deltaMass_;
+ ModPosition position_;
+ char symbol_;
+ bool preventsCleavage_;
+ bool preventsXLink_;
+};
+
+namespace Crux { class Modification; }
+void swap(Crux::Modification& x, Crux::Modification& y);
+
+namespace Crux {
+class Modification {
+public:
+ friend void ::swap(Modification& x, Modification& y);
+ friend std::ostream& operator<<(std::ostream& stream, const Modification& mod);
+
+ Modification(const ModificationDefinition* mod, unsigned char index);
+ Modification(const Modification& other);
+ virtual ~Modification();
+
+ Modification& operator=(Modification other);
+ bool operator==(const Modification& other) const;
+ bool operator!=(const Modification& other) const;
+
+ std::string String() const;
+ static Modification Parse(const std::string& modString, Peptide* peptide);
+
+ unsigned char Index() const;
+ const ModificationDefinition* Definition() const;
+ double DeltaMass() const;
+ bool Static() const;
+ ModPosition Position() const;
+ char Symbol() const;
+ bool PreventsCleavage() const;
+ bool PreventsXLink() const;
+
+ static void FromSeq(MODIFIED_AA_T* seq, int length,
+ std::string* outSeq, std::vector<Modification>* outMods);
+ static MODIFIED_AA_T* ToSeq(const std::string& seq, const std::vector<Modification>& mods);
+protected:
+ unsigned char index_; // 0 based position
+ const ModificationDefinition* mod_;
+};
+}
+
+class ModificationDefinitionContainer {
+public:
+ friend class ModificationDefinition;
+
+ ModificationDefinitionContainer();
+ virtual ~ModificationDefinitionContainer();
+protected:
+ void InitSymbolPool();
+ std::vector<ModificationDefinition*> StaticMods(char c = '\0');
+ void Add(ModificationDefinition* def);
+ char NextSymbol();
+ void ConsumeSymbol(char c);
+
+ std::vector<ModificationDefinition*> varMods_;
+ std::map< char, std::vector<ModificationDefinition*> > staticMods_;
+ std::deque<char> symbolPool_;
+};
+
+static ModificationDefinitionContainer modContainer_;
+
+#endif
+
diff --git a/src/model/ModifiedPeptidesIterator.cpp b/src/model/ModifiedPeptidesIterator.cpp
new file mode 100644
index 0000000..84a6fc4
--- /dev/null
+++ b/src/model/ModifiedPeptidesIterator.cpp
@@ -0,0 +1,238 @@
+/**
+ * \file GenerateModifiedPeptidesIterator.h
+ * \brief An object to return candidate peptides from a database.
+ */
+#include "ModifiedPeptidesIterator.h"
+#include "SpectrumZState.h"
+#include "util/GlobalParams.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * Constructor that sets all fields with the given values. Will
+ * return peptides in a window around the given m/z or mass with the
+ * given modifications applied.
+ */
+ModifiedPeptidesIterator::ModifiedPeptidesIterator(
+ double mz, ///< Spectrum precrusor mz
+ SpectrumZState& zstate, ///< Target mz of peptides
+ PEPTIDE_MOD_T* pmod, ///< Peptide mod to apply
+ bool is_decoy, ///< generate decoy peptides
+ Database* dbase ///< Database from which to draw peptides
+)
+{
+ peptide_source_ = new GeneratePeptidesIterator(getMinMaxMass(mz, zstate,
+ pmod),
+ is_decoy, dbase);
+ peptide_modification_ = pmod;
+ temp_peptide_list_ = new_empty_list();
+ max_aas_modified_ = GlobalParams::getMaxAasModified();
+
+ initialize();
+ carp(CARP_DETAILED_DEBUG,
+ "After initialize, has next is %d and next peptide is null? %d",
+ hasNext(), (next_peptide_ == NULL));
+}
+
+/**
+ * Constructor for returning all peptides in the database
+ * that fall within the constraints defined in parameter.cpp.
+ */
+ModifiedPeptidesIterator::ModifiedPeptidesIterator(
+ PEPTIDE_MOD_T* pmod, ///< Peptide mod to apply
+ Database* dbase ///< Database from which to draw peptides
+){
+ peptide_source_ = new GeneratePeptidesIterator(getMinMaxMass(),
+ false, // not decoy
+ dbase);
+
+ peptide_modification_ = pmod;
+ temp_peptide_list_ = new_empty_list();
+ max_aas_modified_ = GlobalParams::getMaxAasModified();
+ initialize();
+}
+
+/**
+ * Constructor for returnign all peptides in the database
+ * that fall within the mass range
+ */
+ModifiedPeptidesIterator::ModifiedPeptidesIterator(
+ double min_mass, ///< min-mass of peptides
+ double max_mass, ///< max-mass of peptides
+ PEPTIDE_MOD_T* pmod, ///< Peptide mod to apply
+ bool is_decoy, ///< generate decoy peptides
+ Database* dbase, ///< Database from which to draw peptides
+ int additional_missed_cleavages
+) {
+
+ peptide_source_ = new GeneratePeptidesIterator(
+ pair<FLOAT_T,FLOAT_T>(min_mass, max_mass),
+ is_decoy,
+ dbase,
+ additional_missed_cleavages);
+
+ peptide_modification_ = pmod;
+ temp_peptide_list_ = new_empty_list();
+ max_aas_modified_ = GlobalParams::getMaxAasModified();
+ initialize();
+}
+
+
+/**
+ * Destructor that frees any peptides not yet returned via next().
+ */
+ModifiedPeptidesIterator::~ModifiedPeptidesIterator(){
+ delete_linked_list(temp_peptide_list_);
+ delete next_peptide_;
+ delete peptide_source_;
+}
+
+/**
+ * Use parameter.cpp values to determine the range of masses to
+ * consider.
+ * \returns A pair with the minimum and maximum mass for generating
+ * peptides.
+ */
+pair<FLOAT_T,FLOAT_T>ModifiedPeptidesIterator::getMinMaxMass()
+{
+ return pair<FLOAT_T,FLOAT_T>(GlobalParams::getMinMass(),
+ GlobalParams::getMaxMass());
+}
+
+/**
+ * Use parameter.cpp for window type and window size to find the mass
+ * window around the given m/z or mass.
+ * \returns A pair with the minimum and maximum masses to search.
+ */
+pair<FLOAT_T,FLOAT_T> ModifiedPeptidesIterator::getMinMaxMass(
+ double mz, ///< precursor mz for peptide window
+ SpectrumZState& zstate, ///< charge/mass pair for peptide window
+ PEPTIDE_MOD_T* pmod) ///< peptide mod with the delta mass for peptides
+{
+ WINDOW_TYPE_T precursor_window_type = GlobalParams::getPrecursorWindowType();
+
+ double window = GlobalParams::getPrecursorWindow();
+ double min_mass = 0;
+ double max_mass = 0;
+
+ // get the mass difference
+ double delta_mass = peptide_mod_get_mass_change(pmod);
+
+ if (precursor_window_type == WINDOW_MASS) {
+ double mass = zstate.getNeutralMass() - delta_mass;
+ min_mass = mass - window;
+ max_mass = mass + window;
+ } else if (precursor_window_type == WINDOW_MZ) {
+ double min_mz = mz - window;
+ double max_mz = mz + window;
+ min_mass = (min_mz - MASS_PROTON) * (double)zstate.getCharge() - delta_mass;
+ max_mass = (max_mz - MASS_PROTON) * (double)zstate.getCharge() - delta_mass;
+ } else if (precursor_window_type == WINDOW_PPM) {
+ double mass = zstate.getNeutralMass() - delta_mass;
+ min_mass = mass * (1.0 - window * 1e-6);
+ max_mass = mass * (1.0 + window * 1e-6);
+ carp(CARP_DEBUG,"mass:%f charge:%i min_mass:%f max_mass:%f",
+ mass, zstate.getCharge(), min_mass, max_mass);
+ } else {
+ carp(CARP_FATAL,"Invalid window type");
+ }
+ pair<FLOAT_T,FLOAT_T> min_max(min_mass, max_mass);
+ return min_max;
+}
+
+/**
+ * \brief Queue next_peptide to be returned.
+ *
+ * Takes unmodified peptides from a base class and applies the
+ * modification to each.
+ *
+ * Filters out peptides that can't be modified. Stores multiple
+ * versions of same peptide that can have the mod applied in more than
+ * one way (ie on different residues) in temp_peptide_list_. Deletes
+ * elements from list as used. Sets next_peptide to NULL when there are
+ * no more to be returned.
+ * \returns True if there is a peptide to return or false if there are
+ * none.
+ */
+bool ModifiedPeptidesIterator::queueNextPeptide(){
+
+ carp(CARP_DETAILED_DEBUG, "ModifiedPeptidesIterator queueNextPeptide");
+
+ // first, try getting next from the temp list
+ if( ! is_empty_linked_list( temp_peptide_list_)){
+ carp(CARP_DETAILED_DEBUG,"Queue is getting next peptide from temp list");
+ next_peptide_ = (Peptide*)pop_front_linked_list(temp_peptide_list_);
+
+ return true;
+ }
+
+ // second, try getting next from iterator
+ if( ! peptide_source_->hasNext() ){
+ carp(CARP_DETAILED_DEBUG,
+ "ModifiedPeptidesIterator queue has no more peptides in the generator");
+ next_peptide_ = NULL;
+ return false; // no more peptides for this iterator
+ }
+
+ // else, get the next unmodified peptide
+ Peptide* unmod_peptide = peptide_source_->next();
+
+ IF_CARP_DETAILED_DEBUG(
+ const char* debugseq = unmod_peptide->getSequence();
+ carp(CARP_DETAILED_DEBUG, "Next peptide in pep_gen is %s", debugseq);
+ )
+
+ // apply modifications, discard peptides that can't be modified
+
+ // keep looking until a peptide can be modified or we run out of peptides
+ carp(CARP_DETAILED_DEBUG, "Queue is looking for modifyable peptide");
+ while( unmod_peptide != NULL &&
+ ! is_peptide_modifiable(unmod_peptide, peptide_modification_) ){
+ delete unmod_peptide;
+ unmod_peptide = peptide_source_->next();
+ }
+
+ if( unmod_peptide == NULL ){
+ // none of the remaining peptides were modifiable
+ carp(CARP_DETAILED_DEBUG, "Skipped all remaining peptides in generator");
+ next_peptide_ = NULL;
+ return false;
+ }
+
+ IF_CARP_DETAILED_DEBUG(
+ const char* umodseq = unmod_peptide->getSequence();
+ carp(CARP_DETAILED_DEBUG, "Iterator is modifying peptide %s",
+ umodseq);
+ )
+ modify_peptide(unmod_peptide,
+ peptide_modification_,
+ temp_peptide_list_,
+ max_aas_modified_ );
+ // this put a copy in the list, get rid of the original
+ delete unmod_peptide;
+
+ if( is_empty_linked_list(temp_peptide_list_) ){
+ carp(CARP_DETAILED_DEBUG, "Modifier didn't return any peptides");
+ next_peptide_ = NULL;
+ return false;
+ }
+
+ // now set next_peptide to the first in the list and move list forward
+ next_peptide_ = (Peptide*)pop_front_linked_list(temp_peptide_list_);
+
+ IF_CARP_DETAILED_DEBUG(
+ string seq = next_peptide_->getModifiedSequenceWithMasses();
+ carp(CARP_DETAILED_DEBUG, "Queue set next peptide as %s", seq.c_str());
+ )
+
+ return true;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/ModifiedPeptidesIterator.h b/src/model/ModifiedPeptidesIterator.h
new file mode 100644
index 0000000..a36136c
--- /dev/null
+++ b/src/model/ModifiedPeptidesIterator.h
@@ -0,0 +1,75 @@
+/**
+ * \file GenerateModifiedPeptidesIterator.h
+ * \brief An object to return candidate peptides from a database.
+ */
+#ifndef MODIFIEDPEPTIDESITERATOR_H
+#define MODIFIEDPEPTIDESITERATOR_H
+
+#include <vector>
+#include "GeneratePeptidesIterator.h"
+#include "util/peptide_modifications.h"
+#include "SpectrumZState.h"
+
+class ModifiedPeptidesIterator : public PeptideIterator
+{
+ protected:
+ GeneratePeptidesIterator* peptide_source_;///< gets unmod peptides from index
+ PEPTIDE_MOD_T* peptide_modification_; ///< the modification to apply
+ LINKED_LIST_T* temp_peptide_list_;///< modified peptides ready to return
+ int max_aas_modified_;///< modify no more than this many aas per peptides
+
+ std::pair<FLOAT_T,FLOAT_T> getMinMaxMass();
+ std::pair<FLOAT_T,FLOAT_T> getMinMaxMass(
+ double mz,
+ SpectrumZState& zstate,
+ PEPTIDE_MOD_T* pmod);
+
+ virtual bool queueNextPeptide();
+
+ public:
+ /**
+ * Constructor for returning peptides in a window around the given
+ * m/z.
+ */
+ ModifiedPeptidesIterator(
+ double mz, ///< Spectrum precrusor mz
+ SpectrumZState& zstate, ///< Target mz of peptides
+ PEPTIDE_MOD_T* pmod, ///< Peptide mod to apply
+ bool is_decoy, ///< generate decoy peptides
+ Database* dbase ///< Database from which to draw peptides
+ );
+
+ /**
+ * Constructor for returning all peptides in the database
+ * that fall within the constraints defined in parameter.cpp.
+ */
+ ModifiedPeptidesIterator(
+ PEPTIDE_MOD_T* pmod, ///< Peptide mod to apply
+ Database* dbase ///< Database from which to draw peptides
+ );
+
+ /**
+ * Constructor for returnign all peptides in the database
+ * that fall within the mass range
+ */
+ ModifiedPeptidesIterator(
+ double min_mass, ///< min-mass of peptides
+ double max_mass, ///< max-mass of peptides
+ PEPTIDE_MOD_T* pmod, ///< Peptide mod to apply
+ bool is_decoy, ///< generate decoy peptides
+ Database* dbase, ///< Database from which to draw peptides
+ int additional_missed_cleavages = 0
+ );
+
+
+ ~ModifiedPeptidesIterator();
+};
+
+#endif
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/Peak.cpp b/src/model/Peak.cpp
new file mode 100644
index 0000000..92ce087
--- /dev/null
+++ b/src/model/Peak.cpp
@@ -0,0 +1,136 @@
+/**
+ * AUTHOR: Kha Nguyen
+ * CREATE DATE: 4/21/2011
+ *
+ * \file Peak.cpp
+ */
+
+#include "Peak.h"
+#include "util/utils.h"
+#include <string.h>
+#include <stdlib.h>
+#include <stdio.h>
+#include "io/carp.h"
+#include <algorithm>
+
+/**
+ * Construct a Peak object
+ * @param intensity: intensity for the new peak
+ * @param location: location for the new peak
+ */
+Peak::Peak(FLOAT_T intensity, FLOAT_T location) {
+ this->intensity_ = intensity;
+ this->intensity_rank_ = 0.0;
+ this->location_ = location;
+}
+
+/**
+ * Return the intensity of this Peak
+ */
+FLOAT_T Peak::getIntensity() const {
+ return this->intensity_;
+}
+
+ /**
+ * Return the intensity rank of this Peak
+ */
+FLOAT_T Peak::getIntensityRank() const {
+ return this->intensity_rank_;
+}
+
+/**
+ * Return the location of this Peak
+ */
+FLOAT_T Peak::getLocation() const {
+ return this->location_;
+}
+
+/**
+ * Set the intensity of this Peak
+ */
+void Peak::setIntensity(FLOAT_T intensity) {
+ this->intensity_ = intensity;
+}
+
+/**
+ * Set the intensity rank of this peak
+ */
+void Peak::setIntensityRank(FLOAT_T intensity_rank) {
+ this->intensity_rank_ = intensity_rank;
+}
+
+/**
+ * Set the location of this Peak
+ */
+void Peak::setLocation(FLOAT_T location) {
+ this->location_ = location;
+}
+
+/**
+ * Print the intensity and location of this peak to stdout
+ */
+void Peak::print() {
+ printf("%.1f %.1f\n",
+ this->location_,
+ this->intensity_);
+}
+
+/**
+ * Compare the intensity of this Peak and another Peak
+ * Return true if this Peak is greater, false otherwise
+ */
+bool Peak::compareByIntensity(Peak other) {
+ return getIntensity() > other.getIntensity();
+}
+
+/**
+ * Compare the mz(location) of this Peak and another Peak
+ * Return true if the other Peak is greater, false otherwise
+ */
+bool Peak::compareByMZ(Peak other) {
+ return getLocation() < other.getLocation();
+}
+
+
+std::vector<Peak*> allocate_peak_vector(unsigned int num_peaks) {
+ std::vector<Peak*> ans;
+
+ for (unsigned int idx = 0; idx < num_peaks; idx++) {
+ ans.push_back(new Peak(0,0));
+ }
+
+ return ans;
+}
+
+void free_peak_vector(std::vector<Peak*> &peaks) {
+ for (unsigned int idx = 0; idx < peaks.size(); idx++) {
+ delete peaks[idx];
+ }
+ peaks.clear();
+}
+
+bool compare_peaks_by_intensity(Peak* peak_one, Peak* peak_two) {
+ return (peak_one->getIntensity() > peak_two->getIntensity());
+}
+
+bool compare_peaks_by_mz(Peak* peak_one, Peak* peak_two) {
+ return (peak_one->getLocation() < peak_two->getLocation());
+}
+
+void sort_peaks(std::vector<Peak*> &peak_array, PEAK_SORT_TYPE_T sort_type) {
+ if (sort_type == _PEAK_INTENSITY) {
+ sort(peak_array.begin(), peak_array.end(), compare_peaks_by_intensity);
+ } else if (sort_type == _PEAK_LOCATION) {
+ sort(peak_array.begin(), peak_array.end(), compare_peaks_by_mz);
+ } else {
+ carp(CARP_ERROR, "no matching peak sort type");
+ }
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/Peak.h b/src/model/Peak.h
new file mode 100644
index 0000000..a71faca
--- /dev/null
+++ b/src/model/Peak.h
@@ -0,0 +1,109 @@
+#ifndef PEAK_H
+#define PEAK_H
+
+/**
+ * AUTHOR: Kha Nguyen
+ * CREATE DATE: 04/21/2011
+ *
+ * Object for representing one peak in a spectrum
+ *
+ * A peak is primarily identified via its intensity (height) and location \
+ * (position on the m/z axis)
+ *
+ * \file Peak.h
+ *
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include "util/utils.h"
+#include <vector>
+#include "model/objects.h"
+
+class Peak {
+public:
+ /**
+ * Construct a Peak object
+ * @param intensity: intensity for the new peak
+ * @param location: location for the new peak
+ */
+ Peak(FLOAT_T intensity, FLOAT_T location);
+
+ /**
+ * Return the intensity of this Peak
+ */
+ FLOAT_T getIntensity() const;
+
+ /**
+ * Return the intensity rank of this Peak
+ */
+ FLOAT_T getIntensityRank() const;
+
+ /**
+ * Return the location of this Peak
+ */
+ FLOAT_T getLocation() const;
+
+ /**
+ * Set the intensity of this Peak
+ */
+ void setIntensity(FLOAT_T intensity);
+
+ /**
+ * Set the intensity rank of this Peak
+ */
+ void setIntensityRank(FLOAT_T intensity_rank);
+
+ /**
+ * Set the location of this Peak
+ */
+ void setLocation(FLOAT_T location);
+
+ /**
+ * Print the intensity and location of this peak to stdout
+ */
+ void print();
+
+ /**
+ * Compare the intensity of this Peak and another Peak
+ * Return true if this Peak is greater, false otherwise
+ */
+ bool compareByIntensity(Peak other);
+
+ /**
+ * Compare the mz(location) of this Peak and another Peak
+ * Return true if the other Peak is greater, false otherwise
+ */
+ bool compareByMZ(Peak other);
+
+private:
+ FLOAT_T intensity_; // The intensity of this peak
+ FLOAT_T intensity_rank_; // The rank intensity of this peak
+ FLOAT_T location_; // The location of this peak
+
+};
+
+/**
+ * Return a vector of allocated Peak pointers
+ */
+std::vector<Peak*> allocate_peak_vector(unsigned int num_peaks);
+
+/**
+ * Free a Peak pointer array
+ */
+void free_peak_vector(std::vector<Peak*> &peaks);
+
+/**
+ * Sort peaks by their intensity or location
+ * Use the lib function sort()
+ */
+void sort_peaks(std::vector<Peak*> &peak_array, PEAK_SORT_TYPE_T sort_type);
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+#endif
diff --git a/src/model/Peptide.cpp b/src/model/Peptide.cpp
new file mode 100644
index 0000000..bb6f832
--- /dev/null
+++ b/src/model/Peptide.cpp
@@ -0,0 +1,1275 @@
+/*************************************************************************//**
+ * \file Peptide.cpp
+ * \brief Object for representing a single peptide.
+ ****************************************************************************/
+#include "Peptide.h"
+#include "PeptideSrc.h"
+#include "PostProcessProtein.h"
+#include <string.h>
+
+#include <numeric>
+#include <set>
+#include <vector>
+#include "io/MatchFileReader.h"
+#include "util/AminoAcidUtil.h"
+#include "util/GlobalParams.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * \struct residue_iterator
+ * \brief Object to iterate over the residues in a peptide, starting at the
+ * first residue of the peptide, and proceeding in order.
+ */
+struct residue_iterator {
+ Peptide* peptide; ///< The peptide whose residues to iterate over.
+ char* sequence; ///< The peptide sequence
+ int residue_idx; ///< The index of the current peak
+};
+
+/* Private functions */
+
+/* Public functions--Allocators/Deallocators */
+
+/**
+ * \returns An (empty) peptide object.
+ */
+Peptide::Peptide() : length_(0), decoy_modified_seq_(NULL) {
+}
+
+Peptide::Peptide(string sequence)
+ : sequence_(sequence), length_(sequence.length()), decoy_modified_seq_(NULL) {
+}
+
+Peptide::Peptide(string sequence, vector<Modification> mods)
+ : sequence_(sequence), varMods_(mods), length_(sequence.length()),
+ decoy_modified_seq_(NULL) {
+}
+
+Peptide* Peptide::copyPtr() {
+ pointer_count_++;
+ return this;
+}
+
+// FIXME association part might be need to change
+/**
+ * \returns A new peptide object, populated with the user specified parameters.
+ */
+Peptide::Peptide(
+ unsigned char length, ///< The length of the peptide -in
+ Protein* parent_protein, ///< the parent_protein of this peptide -in
+ int start_idx ///< the start index of this peptide in the protein sequence -in
+ )
+ : length_(length), decoy_modified_seq_(NULL) {
+ // FIXME: find the level of digest for this specific protein
+ peptide_srcs_.push_back(new PeptideSrc(NON_SPECIFIC_DIGEST, parent_protein, start_idx));
+}
+
+/**
+ * \brief Allocates a new peptide giving it the values of the source
+ * peptide.
+ * \returns A newly allocated peptide identical to the source.
+ */
+Peptide::Peptide(
+ Peptide* src ///< source peptide -in
+) {
+ if (!src) {
+ carp(CARP_ERROR, "Cannot copy null peptide!");
+ } else {
+ length_ = src->length_;
+ PeptideSrc::copy(src->peptide_srcs_,peptide_srcs_);
+ varMods_ = src->varMods_;
+ if( src->decoy_modified_seq_ == NULL ){
+ decoy_modified_seq_ = NULL;
+ } else {
+ decoy_modified_seq_ = copy_mod_aa_seq(src->decoy_modified_seq_, src->length_);
+ }
+ }
+}
+
+/**
+ * Merges two identical peptides by adding the peptide_src of the
+ * second to the first. The second peptide remains unchanged.
+ * Does not comfirm identity of peptides.
+ * \returns true if merge is successfull.
+ */
+bool Peptide::mergePeptidesCopySrc(
+ Peptide* peptide_dest,
+ Peptide* peptide_giver
+ ){
+
+ vector<PeptideSrc*>& dest_srcs = peptide_dest->peptide_srcs_;
+ vector<PeptideSrc*>& giver_srcs = peptide_giver->peptide_srcs_;
+
+ // do both peptides have at least one peptide_src?
+ if(dest_srcs.empty() || giver_srcs.empty()){
+ carp(CARP_ERROR, "failed to merge two peptides");
+ return false;
+ }
+
+ for(vector<PeptideSrc*>::iterator iter=giver_srcs.begin();
+ iter != giver_srcs.end();
+ iter++
+ ){
+ PeptideSrc* new_src = new PeptideSrc(*(*iter));
+ dest_srcs.push_back(new_src);
+ }
+
+ return true;
+}
+
+/**
+ * Frees an allocated peptide object.
+ * Depending on peptide_src implementation determines how to free srcs
+ */
+Peptide::~Peptide() {
+ for (vector<PeptideSrc*>::iterator i = peptide_srcs_.begin();
+ i != peptide_srcs_.end();
+ i++) {
+ delete *i;
+ }
+ if(decoy_modified_seq_){
+ freeModSeq(decoy_modified_seq_);
+ }
+}
+
+// Public functions--Getters and Setters
+
+/* source-related getters and setters */
+
+/**
+ * sets the peptide_src field in the peptide
+ * this method should be ONLY used when the peptide has no existing list of peptide_src
+ * must pass on a heap allocated peptide_srcs_ object
+ * does not copy in the object, just the pointer to the object.
+ */
+void Peptide::setPeptideSrc(
+ PeptideSrc* new_association ///< new peptide_src -in
+ ) {
+ assert(peptide_srcs_.empty());
+ peptide_srcs_.push_back(new_association);
+}
+
+/**
+ * this method adds the new_association to the end of the existing peptide's
+ * if no prior existing list, adds it at the front
+ * must pass on a heap allocated peptide_srcs_ object
+ * does not copy in the object, just the pointer to the object.
+ */
+void Peptide::addPeptideSrc(
+ PeptideSrc* new_association ///< new peptide_src -in
+ ) {
+ peptide_srcs_.push_back(new_association);
+}
+
+// TODO: why do we need both of these?
+/**
+ * returns a pointer to the peptide_protein_association field of the peptide
+ */
+PeptideSrc* Peptide::getPeptideSrc() const {
+ return !peptide_srcs_.empty() ? peptide_srcs_[0] : NULL;
+}
+
+/**
+ *returns the pepide_srcs_
+ */
+vector<PeptideSrc*>& Peptide::getPeptideSrcVector() {
+ return peptide_srcs_;
+}
+
+/**
+ *Return the begining of the peptide_srcs_
+ */
+PeptideSrcIterator Peptide::getPeptideSrcBegin() {
+ return peptide_srcs_.begin();
+}
+
+/**
+ *Return the end of the peptide_srcs_
+ */
+PeptideSrcIterator Peptide::getPeptideSrcEnd() {
+ return peptide_srcs_.end();
+}
+
+/**
+ * \returns The number of peptide sources (i.e. proteins) the peptide has.
+ */
+int Peptide::getNumPeptideSrc(){
+ return peptide_srcs_.size();
+}
+
+/**
+ * get the peptide->first peptide_src->parent protein->database
+ */
+Database* Peptide::getFirstSrcDatabase() {
+ return peptide_srcs_.at(0)->getParentProtein()->getDatabase();
+}
+
+// set by peptide_src?
+/**
+ * returns a pointer to the peptide's first parent protein field of the peptide
+ */
+Protein* Peptide::getParentProtein() {
+ return peptide_srcs_.at(0)->getParentProtein();
+}
+
+/**
+ * sets the sequence length of the peptide
+ * length maximum of 255
+ */
+void Peptide::setLength(
+ unsigned char length ///< the length of sequence -in
+ ) {
+ length_ = length;
+}
+
+/* sequence-related getters and setters */
+/**
+ *\returns the sequence length of the peptide
+ */
+unsigned char Peptide::getLength() {
+ return length_;
+}
+
+/**
+ * \brief Check whether a given sequence is equal to a given peptide.
+ * \returns A Boolean indicating equality or not.
+ */
+static bool equal_peptides(
+ char* peptide_sequence, ///< peptide sequence -in
+ Peptide* peptide_object ///< peptide object -in
+ )
+{
+ char* parent_sequence =
+ peptide_object->getPeptideSrc()->getParentProtein()->getSequencePointer();
+ int start_idx = peptide_object->getPeptideSrc()->getStartIdx();
+
+ int result = strncmp(peptide_sequence,
+ &(parent_sequence[start_idx-1]),
+ peptide_object->getLength());
+
+ // Return true if strncmp returns 0.
+ return((bool)(!result));
+}
+
+/**
+ * \brief Get a string representation of the peptide sequence with no
+ * added modification symbols.
+ * Returns decoy sequence for decoy peptides.
+ * \returns The newly-allocated sequence of peptide
+ */
+char* Peptide::getSequence() const {
+ //Check that the peptide has parent(s)
+ if (!sequence_.empty()) {
+ return copy_string_part(sequence_.c_str(), sequence_.length());
+ }
+
+ if (decoy_modified_seq_ != NULL) {
+ return modified_aa_to_unmodified_string(decoy_modified_seq_, length_);
+ }
+ string unshuffled = getUnshuffledSequence();
+ if (unshuffled.empty()) {
+ return NULL;
+ }
+ return copy_string_part(unshuffled.c_str(), unshuffled.length());
+}
+
+/**
+ * \brief Get a string representation of the target (unshuffled)
+ * peptide sequence with no added modification symbols.
+ * For target peptides, returns the same as get_peptide_sequence.
+ * \returns The newly-allocated sequence of peptide
+ */
+string Peptide::getUnshuffledSequence() const {
+ if (!sequence_.empty()) {
+ return sequence_;
+ }
+ //check parent(s) protein of the peptide not be empty
+ PeptideSrc* src = getPeptideSrc();
+ if (src == NULL) {
+ carp(CARP_ERROR, "Cannot get sequence from peptide with no peptide src.");
+ return "";
+ }
+ char* parent_sequence = src->getParentProtein()->getSequencePointer(src->getStartIdx()-1);
+ return string(parent_sequence, length_);
+}
+
+/**
+ * \brief Get a pointer to the peptide sequence that is NOT null
+ * terminated.
+ * USE WITH CAUTION. Pointer is to the parent protein sequence and
+ * thus is not null-terminated until the end of the protein. Parent
+ * protein is taken from the first protein source.
+ *
+ * \returns A pointer to an existing peptide sequence.
+ */
+char* Peptide::getSequencePointer() {
+ if (peptide_srcs_.empty()) {
+ carp(CARP_FATAL, "ERROR: no peptide_src to retrieve peptide sequence pointer\n");
+ }
+ PeptideSrc* src = getPeptideSrc();
+ return src->getParentProtein()->getSequencePointer(src->getStartIdx()-1);
+}
+
+/**
+ * \returns The sequence of peptide as used in sqt files, namely with
+ * each flanking AA and any modifications
+ *
+ * Format is [AA|-].[peptide_sequence].[AA|-] where AA is a flanking
+ * amino acid and - indicates this is the end of the protein sequence
+ * Gets flanking AAs from the first peptide_src, thus must have at
+ * least one peptide src
+ *
+ * \returns A newly allocated char* with formated peptide sequence
+ */
+string Peptide::getSequenceSqt() {
+ return string(1, getNTermFlankingAA()) + "." +
+ getModifiedSequenceWithSymbols() +
+ "." + string(1, getCTermFlankingAA());
+}
+
+/**
+ * \brief Return a char for the amino acid n-terminal to the peptide
+ * in the peptide src at the given index.
+ *
+ * \returns A char (A-Z) or - if peptide is the first in the protein.
+ */
+char Peptide::getNTermFlankingAA() {
+ PeptideSrc* src = getPeptideSrc();
+ if (src == NULL) {
+ return '-';
+ }
+
+ // get protein seq
+ Protein* protein = src->getParentProtein();
+
+ // get peptide start idx, protein index starts at 1
+ int start_index = src->getStartIdx();
+
+ if (protein->isPostProcess()) {
+ return ((PostProcessProtein*)protein)->getNTermFlankingAA(start_index - 1);
+ }
+ char* protein_seq = protein->getSequencePointer();
+
+ char aa = '-';
+ // if not at beginning, return char
+ if( start_index > 1 ){
+ aa = protein_seq[start_index - 2]; // -1 for 1-based shift
+ // -1 for aa before start
+ }
+ return aa;
+}
+
+/**
+ * \brief Return a char for the amino acid c-terminal to the peptide
+ * in the peptide src at the given index.
+ *
+ * \returns A char (A-Z) or - if peptide is the last in the protein.
+ */
+char Peptide::getCTermFlankingAA() {
+ PeptideSrc* src = getPeptideSrc();
+ if (src == NULL) {
+ return '-';
+ }
+
+ // get protein seq and length
+ Protein* protein = src->getParentProtein();
+
+ // get peptide start idx, protein index starts at 1
+ int start_index = src->getStartIdx();
+
+ if (protein->isPostProcess()) {
+ return ((PostProcessProtein*)protein)->getCTermFlankingAA(start_index - 1);
+ }
+ char* protein_seq = protein->getSequencePointer();
+ int protein_length = protein->getLength();
+
+ // get peptide end idx
+ int end_index = start_index + length_ - 1;
+
+ char aa = '-';
+ // if not at end, return char
+ if( end_index < protein_length ){
+ aa = protein_seq[end_index]; // -1 for 1-based shift, +1 for aa after end
+ }
+ return aa;
+}
+
+void Peptide::addMod(const ModificationDefinition* mod, unsigned char index) {
+ varMods_.push_back(Modification(mod, index));
+}
+
+void Peptide::setMods(const vector<Modification>& mods) {
+ varMods_ = mods;
+}
+
+vector<Modification> Peptide::getMods() const {
+ vector<Modification> mods = varMods_;
+ vector<Modification> staticMods = getStaticMods();
+ mods.insert(mods.end(), staticMods.begin(), staticMods.end());
+ return mods;
+}
+
+vector<Modification> Peptide::getVarMods() const {
+ return varMods_;
+}
+
+vector<Modification> Peptide::getStaticMods() const {
+ char* seq = getSequence();
+ vector<Modification> mods;
+ for (unsigned char i = 0; seq[i] != '\0'; i++) {
+ const vector<const ModificationDefinition*>& staticMods =
+ ModificationDefinition::StaticMods(seq[i]);
+ for (vector<const ModificationDefinition*>::const_iterator j = staticMods.begin();
+ j != staticMods.end();
+ j++) {
+ if ((*j)->Position() == ANY ||
+ ((*j)->Position() == PEPTIDE_N && i == 0) ||
+ ((*j)->Position() == PEPTIDE_C && seq[i + 1] == '\0')) {
+ mods.push_back(Modification(*j, (unsigned char)i));
+ }
+ }
+ }
+ free(seq);
+ return mods;
+}
+
+/**
+ * \brief Add a modification to a peptide.
+ *
+ * Adds the modified sequence to the peptide and changes the peptide
+ * mass based on the mass change in the peptide_mod.
+ * \returns void
+ */
+void Peptide::setMod(
+ MODIFIED_AA_T* mod_seq, ///< modified seq to add
+ PEPTIDE_MOD_T* pep_mod ///< mod that made the seq
+) {
+ if (!mod_seq || !pep_mod) {
+ carp(CARP_ERROR, "Cannot modify peptide. mod, or seq is NULL.");
+ return;
+ }
+ vector<Modification> newMods;
+ Modification::FromSeq(mod_seq, length_, &sequence_, &newMods);
+ for (vector<Modification>::const_iterator i = newMods.begin(); i != newMods.end(); i++) {
+ varMods_.push_back(*i);
+ }
+}
+
+string Peptide::getModsString() const {
+ vector<string> allMods;
+ vector<Modification> staticMods = getStaticMods();
+ for (vector<Modification>::const_iterator i = staticMods.begin(); i != staticMods.end(); i++) {
+ allMods.push_back(i->String());
+ }
+ for (vector<Modification>::const_iterator i = varMods_.begin(); i != varMods_.end(); i++) {
+ allMods.push_back(i->String());
+ }
+ return StringUtils::Join(allMods, ',');
+}
+
+bool Peptide::isModified() {
+ return !varMods_.empty();
+}
+
+bool Peptide::isDecoy() {
+ return decoy_modified_seq_ != NULL;
+}
+
+/**
+ * \brief Get the modified peptide sequence
+ *
+ * If the peptide has no modifications, create a sequence of
+ * MODIFIED_AA_T's in which none of them are actually modified.
+ * \returns A newly allocated copy of the sequence of MODIFIED_AA_Ts.
+ */
+MODIFIED_AA_T* Peptide::getModifiedAASequence() {
+ MODIFIED_AA_T* seq_copy = NULL;
+ char* seq = getSequence();
+ if (!varMods_.empty()) {
+ string seqString(seq);
+ seq_copy = Modification::ToSeq(seqString, varMods_);
+ } else {
+ convert_to_mod_aa_seq(seq, &seq_copy);
+ }
+ std::free(seq);
+ return seq_copy;
+}
+
+/**
+ * sets the modified sequence for the peptide
+ */
+void Peptide::setModifiedAASequence(
+ MODIFIED_AA_T* mod_seq, ///< modified sequence to set
+ bool decoy ///< is the peptide a decoy?
+) {
+ Modification::FromSeq(mod_seq, length_, &sequence_, &varMods_);
+ if (decoy) {
+ if (decoy_modified_seq_) {
+ std::free(decoy_modified_seq_);
+ }
+ decoy_modified_seq_ = copy_mod_aa_seq(mod_seq);
+ }
+}
+
+void Peptide::setDecoyModifiedSeq(MODIFIED_AA_T* decoy_modified_seq) {
+ decoy_modified_seq_ = decoy_modified_seq;
+}
+
+/**
+ * \brief Get the modified aa sequence in string form.
+ *
+ * If the peptide has no modifications, returns same string as
+ * get_peptide_sequence. If modified, adds the mod symbols to the string.
+ * \returns The peptide sequence including any modifications.
+ */
+string Peptide::getModifiedSequenceWithSymbols() {
+ if (decoy_modified_seq_) {
+ char* seqTmp =
+ modified_aa_string_to_string_with_symbols(decoy_modified_seq_, length_);
+ string seqString(seqTmp);
+ free(seqTmp);
+ return seqString;
+ }
+
+ char* seqC = getSequence();
+ string seq(seqC);
+ free(seqC);
+ map<unsigned char, string> symbols;
+ for (vector<Modification>::const_iterator i = varMods_.begin(); i != varMods_.end(); i++) {
+ map<unsigned char, string>::const_iterator j = symbols.find(i->Index());
+ if (j == symbols.end()) {
+ symbols[i->Index()] = i->Symbol();
+ } else {
+ symbols[i->Index()] += i->Symbol();
+ }
+ }
+
+ for (map<unsigned char, string>::const_reverse_iterator i = symbols.rbegin();
+ i != symbols.rend();
+ i++) {
+ seq.insert(i->first + 1, i->second);
+ }
+
+ return seq;
+}
+
+/**
+ * \brief Get the modified aa sequence in string form.
+ *
+ * If the peptide has no modifications, returns same string as
+ * get_peptide_sequence. If modified, adds in brackets the masses of
+ * all modifications. If merge_masses is true, prints the sum of all
+ * modifications for a residue. If false, prints all masses in a
+ * comma separated list.
+ * \returns The peptide sequence including any modifications.
+ */
+string Peptide::getModifiedSequenceWithMasses() {
+ if (decoy_modified_seq_) {
+ char* seqTmp = modified_aa_string_to_string_with_masses(
+ decoy_modified_seq_, length_, GlobalParams::getModMassFormat());
+ string seqString(seqTmp);
+ free(seqTmp);
+ return seqString;
+ }
+
+ char* seqC = getSequence();
+ string seq(seqC);
+ free(seqC);
+ map< int, vector<double> > masses;
+ for (vector<Modification>::const_iterator i = varMods_.begin(); i != varMods_.end(); i++) {
+ map< int, vector<double> >::const_iterator j = masses.find(i->Index());
+ if (j == masses.end()) {
+ masses[i->Index()] = vector<double>(1, i->DeltaMass());
+ } else {
+ masses[i->Index()].push_back(i->DeltaMass());
+ }
+ }
+ int precision = GlobalParams::getModPrecision();
+ MASS_TYPE_T massType = GlobalParams::getIsotopicMass();
+ for (map< int, vector<double> >::const_reverse_iterator i = masses.rbegin();
+ i != masses.rend();
+ i++) {
+ char buffer[64];
+ switch (GlobalParams::getModMassFormat()) {
+ case MOD_MASS_ONLY: {
+ double sum = accumulate(i->second.begin(), i->second.end(), 0.0);
+ sprintf(buffer, "[%.*f]", precision, sum);
+ break;
+ }
+ case AA_PLUS_MOD: {
+ double sum = accumulate(i->second.begin(), i->second.end(),
+ get_mass_amino_acid(seq[i->first], massType));
+ sprintf(buffer, "[%.*f]", precision, sum);
+ break;
+ }
+ case MOD_MASSES_SEPARATE: {
+ vector<string> massStrings;
+ for (vector<double>::const_iterator j = i->second.begin(); j != i->second.end(); j++) {
+ massStrings.push_back(StringUtils::ToString(*j, precision));
+ }
+ sprintf(buffer, "[%s]", StringUtils::Join(massStrings, ',').c_str());
+ break;
+ }
+ }
+ seq.insert(i->first + 1, buffer);
+ }
+
+ return seq;
+}
+
+/* getters requiring calculation */
+
+/**
+ * \brief Count the number of modified amino acids in the
+ * peptide. This number is distnct from the number of aamods in the
+ * peptide mod since one amino acid can have more than one
+ * modification on it.
+ * \returns The number of amino acids in the peptide that have at
+ * least one modification.
+ */
+int Peptide::countModifiedAAs(){
+ set<unsigned char> indices;
+ for (vector<Modification>::const_iterator i = varMods_.begin(); i != varMods_.end(); i++) {
+ indices.insert(i->Index());
+ }
+ return indices.size();
+}
+
+/**
+ * \returns The mass of the given peptide as determined by the aa sequence.
+ */
+FLOAT_T Peptide::calcSequenceMass(
+ const string& peptide, ///< the query peptide -in
+ MASS_TYPE_T mass_type ///< isotopic mass type (AVERAGE, MONO) -in
+ ) {
+ FLOAT_T peptide_mass = 0;
+ for (string::const_iterator i = peptide.begin(); i != peptide.end(); i++) {
+ peptide_mass += get_mass_amino_acid(*i, mass_type);
+ }
+ if(mass_type == AVERAGE){
+ return peptide_mass + MASS_H2O_AVERAGE;
+ }
+ return peptide_mass + MASS_H2O_MONO;
+}
+
+/**
+ * This appears to be the same as calc_sequence_mass??
+ * \returns The mass of the given peptide.
+ */
+FLOAT_T Peptide::calcMass(MASS_TYPE_T mass_type) const {
+ FLOAT_T mass = 0;
+ char* seq = getSequence();
+ for (char* i = seq; *i != '\0'; i++) {
+ mass += AminoAcidUtil::GetMass(*i, mass_type != AVERAGE);
+ }
+ free(seq);
+
+ return mass_type != AVERAGE ? mass + MASS_H2O_MONO : mass + MASS_H2O_AVERAGE;
+}
+
+FLOAT_T Peptide::calcModifiedMass(MASS_TYPE_T mass_type) const {
+ FLOAT_T mass = calcMass(mass_type);
+ for (vector<Modification>::const_iterator i = varMods_.begin(); i != varMods_.end(); i++) {
+ mass += i->DeltaMass();
+ }
+ vector<Modification> staticMods = getStaticMods();
+ for (vector<Modification>::const_iterator i = staticMods.begin(); i != staticMods.end(); i++) {
+ mass += i->DeltaMass();
+ }
+ return mass;
+}
+
+FLOAT_T Peptide::calcModifiedMass() const {
+ return calcModifiedMass(GlobalParams::getIsotopicMass());
+}
+
+/**
+ * Examines the peptide sequence and counts how many tryptic missed
+ * cleavage sites exist.
+ *\returns the number of missed cleavage sites in the peptide
+ */
+int Peptide::getMissedCleavageSites() {
+
+ int missed_count = 0;
+ int aa_idx = 0;
+ char* sequence = getSequencePointer();
+
+ // count the missed cleavage sites
+ for(; aa_idx < length_-1; ++aa_idx){
+ if(sequence[aa_idx] == 'K' ||
+ sequence[aa_idx] == 'R'){
+
+ // skip one that are followed by a P
+ if(sequence[aa_idx+1] == 'P'){
+ continue;
+ }
+ else{
+ ++missed_count;
+ }
+ }
+ }
+
+ return missed_count;
+}
+
+int Peptide::getMissedCleavageSites(
+ set<int> skip ///< skip these amino acid indices.
+) {
+ int missed_count = 0;
+ char* sequence = getSequencePointer();
+
+ // count the missed cleavage sites
+ for (int aa_idx = 0; aa_idx < length_ - 1; ++aa_idx) {
+ if (skip.find(aa_idx) != skip.end()) {
+ continue;
+ }
+
+ bool cleavage_prevented = true;
+ if (sequence[aa_idx] == 'K' || sequence[aa_idx] == 'R') {
+ cleavage_prevented = false;
+ // skip one that are followed by a P
+ if (sequence[aa_idx + 1] == 'P') {
+ cleavage_prevented = true;
+ continue;
+ }
+
+ for (vector<Modification>::const_iterator modIter = varMods_.begin();
+ modIter != varMods_.end();
+ modIter++) {
+ if (modIter->Index() == aa_idx && modIter->PreventsCleavage()) {
+ cleavage_prevented = true;
+ break;
+ }
+ }
+ }
+
+ if (!cleavage_prevented) {
+ ++missed_count;
+ }
+ }
+
+ return missed_count;
+}
+
+
+/**
+ * \brief Find the distance from the c-terminus of the source protein
+ * to the c-terminus of the peptide (seq[0]).
+ * In the case of multiple source proteins, return the smallest
+ * distance.
+ * \returns The distance from the protein c-terminus.
+ */
+int Peptide::getCDistance(){
+
+ int min_index = MAX_PROTEIN_SEQ_LENGTH;
+ for(vector<PeptideSrc*>::iterator iter= peptide_srcs_.begin();
+ iter!= peptide_srcs_.end();
+ ++iter
+ ){
+ PeptideSrc* cur_src = *iter;
+ int index = cur_src->getStartIdx();
+ if( index < min_index ){
+ min_index = index;
+ }
+ }
+ return min_index - 1;
+}
+
+/**
+ * \brief Find the distance from the n-terminus of the source protein
+ * to the n-terminus of the peptide.
+ * In the case of multiple source proteins, return the smallest
+ * distance.
+ * \returns The distance from the protein c-terminus.
+ */
+int Peptide::getNDistance(){
+
+ int min_index = MAX_PROTEIN_SEQ_LENGTH;
+ int peptide_length = getLength();
+
+ for(vector<PeptideSrc*>::iterator iter= peptide_srcs_.begin();
+ iter!= peptide_srcs_.end();
+ ++iter
+ ){
+ PeptideSrc* cur_src = *iter;
+ int protein_length = cur_src->getParentProtein()->getLength();
+ // get index of end
+ int start_index = cur_src->getStartIdx();
+
+ int cidx = protein_length - (start_index + peptide_length - 1);
+ if( cidx < min_index){
+ min_index = cidx;
+ }
+ }
+ return min_index;
+
+}
+
+/**
+ * Change the given target peptide into a decoy by randomizing its sequence.
+ * Uses settings in parameter.c to decide between shuffling and
+ * reversing the sequence. Any modifications that exist will be
+ * maintained on the same amino acids whose position will move. If
+ * the peptide is already a decoy, replaces the existing decoy
+ * sequence.
+ */
+void Peptide::transformToDecoy() {
+ bool reverse_seq = (get_decoy_type_parameter("decoys") == PROTEIN_REVERSE_DECOYS);
+
+ // delete any existing decoy sequence
+ if (decoy_modified_seq_){
+ freeModSeq(decoy_modified_seq_);
+ }
+ // if the peptide is already modified, shuffle the modified sequence
+ if (!varMods_.empty()) {
+ MODIFIED_AA_T* new_seq = NULL;
+ if (reverse_seq) {
+ new_seq = generateReversedModSequence();
+ } else {
+ new_seq = generateShuffledModSequence();
+ }
+ decoy_modified_seq_ = new_seq;
+ } else {// shuffle the unmodified sequence
+ char* new_seq = NULL;
+ if (reverse_seq) {
+ new_seq = generateReversedSequence();
+ } else {
+ new_seq = generateShuffledSequence();
+ }
+ convert_to_mod_aa_seq(new_seq, &(decoy_modified_seq_));
+ std::free(new_seq);
+ }
+}
+
+/**
+ * \brief Return a randomly shuffled version of the given peptide's
+ * sequence, leaving the terminal amino acids in place. Ensures that
+ * the shuffled version is not the same as the given peptide.
+ *
+ * \returns A newly-allocated char array with the shuffled sequence.
+ */
+static const int MAX_SHUFFLES = 5; // Don't bother trying to shuffle more than this.
+char* Peptide::generateShuffledSequence() {
+ // Allocate a copy of the peptide.
+ char* sequence = getSequence();
+ int length = length_;
+
+ // Shuffle from left to right, using the Knuth algorithm for shuffling.
+ int num_shuffles = 0;
+ do {
+
+ // Don't move the n-term and c-term amino acids
+ int start_idx = 1;
+ int end_idx = length - 2;
+
+ while(start_idx < end_idx){
+ int switch_idx = get_random_number_interval(start_idx, end_idx);
+ char temp_char = sequence[start_idx];
+ sequence[start_idx] = sequence[switch_idx];
+ sequence[switch_idx] = temp_char;
+ ++start_idx;
+ }
+ num_shuffles++;
+ } while (equal_peptides(sequence, this) && (num_shuffles < MAX_SHUFFLES));
+
+ return sequence;
+}
+
+/**
+ * \brief Return a reversed version of the given peptide's sequence as
+ * an array of char (A-Z). Leave the first and last residue
+ * unchanged. If the reversed sequence is identical to the target,
+ * shuffle the sequence instead.
+ *
+ * \returns A newly-allocated char array of the reversed sequence.
+ */
+char* Peptide::generateReversedSequence() {
+ char* sequence = getSequence();
+ int length = length_;
+ int start_idx = 1; // leave first ...
+ int end_idx = length -2; // ...and last residue in place
+ char temp_char = 0;
+
+ while(start_idx < end_idx){
+ temp_char = sequence[end_idx];
+ sequence[end_idx] = sequence[start_idx];
+ sequence[start_idx] = temp_char;
+ start_idx++;
+ end_idx--;
+ }
+
+ // check to see if the reversed sequence is the same as original
+ if( strncmp(sequence, getSequencePointer(), length_) == 0 ){
+ carp(CARP_DETAILED_INFO,
+ "Peptide %s is a palindrome and will be shuffled instead of reversed.",
+ sequence);
+ std::free(sequence);
+ sequence = generateShuffledSequence();
+ }
+
+ return sequence;
+}
+
+/**
+ * \brief Return a randomly shuffled version of the given peptide's
+ * sequence as an array of MODIIFIED_AA_T. Based on the peptide type,
+ * will leave the end(s) unchanged to preserve the tryptic property.
+ *
+ *\returns A newly-allcoated MODIFIED_AA_T array of the shuffled sequence.
+ */
+MODIFIED_AA_T* Peptide::generateShuffledModSequence() {
+ //TODO (BF 6-Apr-09): should we warn if seq is len 3 and won't change?
+ MODIFIED_AA_T* sequence = getModifiedAASequence();
+ int length = length_;
+ int start_idx = 1;
+ int end_idx = length - 2;
+ int switch_idx = 0;
+ MODIFIED_AA_T temp_aa = 0;
+
+ // shuffle from left to right, using the Knuth algorithm for shuffling.
+ while (start_idx < end_idx) {
+ switch_idx = get_random_number_interval(start_idx, end_idx);
+ temp_aa = sequence[start_idx];
+ sequence[start_idx] = sequence[switch_idx];
+ sequence[switch_idx] = temp_aa;
+ ++start_idx;
+ }
+
+ return sequence;
+}
+
+/**
+ * \brief Return a reversed version of the given peptide's sequence as
+ * an array of MODIFIED_AA_T. Leave the first and last residue
+ * unchanged. If the reversed sequence is identical to the target,
+ * shuffle the sequence instead.
+ *
+ * \returns A newly-allocated MODIFIED_AA_T array of the reversed sequence.
+ */
+MODIFIED_AA_T* Peptide::generateReversedModSequence() {
+
+ MODIFIED_AA_T* sequence = getModifiedAASequence();
+ int length = length_;
+ int start_idx = 0;
+ int end_idx = length - 1;
+ MODIFIED_AA_T temp_aa = 0;
+
+ // first check to see if it will yield a different seq when reversed
+ if( modified_aa_seq_is_palindrome(sequence, length) == true){
+ return generateShuffledModSequence();
+ }
+
+ // Do not move the first and last residue, regardless of enzyme
+ ++start_idx;
+ --end_idx;
+
+ // reverse
+ while(start_idx < end_idx){
+ temp_aa = sequence[start_idx];
+ sequence[start_idx] = sequence[end_idx];
+ sequence[end_idx] = temp_aa;
+ ++start_idx;
+ end_idx--;
+ }
+
+ return sequence;
+}
+
+
+/* Comparisons for sorting */
+
+/**
+ * Compare two peptide sequences.
+ * \returns Zero (0) if the sequences are identical, -1 if the first
+ * sequence is less than the first and 1 if the first sequence is
+ * greater than teh first.
+ */
+int Peptide::triCompareSequence(
+ Peptide* peptide_one, ///< the peptide sequence to compare -out
+ Peptide* peptide_two ///< the peptide sequence to compare -out
+ )
+{
+ // find the shorter peptide
+ int short_len = 0;
+ if( peptide_one->length_ < peptide_two->length_ ){
+ short_len = peptide_one->length_;
+ } else {
+ short_len = peptide_two->length_;
+ }
+
+ char* seq_one = peptide_one->getPeptideSrc()->getSequencePointer();
+ char* seq_two = peptide_two->getPeptideSrc()->getSequencePointer();
+
+ // stop comparing as soon as they differ
+ int pep_idx = 0;
+ for(pep_idx = 0; pep_idx < short_len; pep_idx++ ){
+ if(seq_one[pep_idx] != seq_two[pep_idx]){
+ pep_idx++; // stop pointing one after the difference
+ break;
+ }
+ }
+
+ // move index back one to the last letter compared
+ pep_idx--;
+
+ // if the seqs are the same up to this point, then compare the lengths
+ if( seq_one[pep_idx] == seq_two[pep_idx] ){
+ if( peptide_one->length_ == peptide_two->length_ ){ // same seq
+ return 0;
+ } else if ( peptide_one->length_ < peptide_two->length_ ){
+ return -1;
+ } else {
+ return 1;
+ }
+ }
+
+ // else, the seqs are different
+ if(seq_one[pep_idx] < seq_two[pep_idx]){
+ return -1;
+ } else {
+ return 1;
+ }
+
+}
+/**
+ * Compare the sequence of two peptides and return true if the first
+ * petpide sequence is less than (in a lexical sort) the second
+ * peptide. Return false if they are idential peptides.
+ */
+bool Peptide::lessThan(
+ Peptide* peptide_one,
+ Peptide* peptide_two
+ ){
+ // find the shorter peptide
+ int short_len = 0;
+ if( peptide_one->length_ < peptide_two->length_ ){
+ short_len = peptide_one->length_;
+ } else {
+ short_len = peptide_two->length_;
+ }
+
+ char* seq_one = peptide_one->getPeptideSrc()->getSequencePointer();
+ char* seq_two = peptide_two->getPeptideSrc()->getSequencePointer();
+
+ // stop comparing as soon as they differ
+ int pep_idx = 0;
+ for(pep_idx = 0; pep_idx < short_len; pep_idx++ ){
+ if(seq_one[pep_idx] != seq_two[pep_idx]){
+ break;
+ }
+ }
+ if( seq_one[pep_idx] == seq_two[pep_idx] ){
+ return (peptide_one->length_ < peptide_two->length_);
+ }
+
+ return (seq_one[pep_idx] < seq_two[pep_idx]);
+}
+
+/* Public functions--Printing / parsing */
+
+/**
+ * Fills the given vectors with the names and descriptions of all
+ * proteins containing this peptide. Makes the descriptions
+ * xml-friendly by swapping double for single quotes and angled braces
+ * for square. Returned in the same order as getFlankingAAs(). Clears
+ * any existing values in the vectors.
+ * Adapted from Match::get_information_of_proteins()
+ * \returns The number of proteins.
+ */
+int Peptide::getProteinInfo(vector<string>& protein_ids,
+ vector<string>& protein_descriptions){
+
+ protein_ids.clear();
+ protein_descriptions.clear();
+
+ for(PeptideSrcIterator iter = getPeptideSrcBegin();
+ iter!=getPeptideSrcEnd();
+ ++iter
+ ){
+ PeptideSrc* peptide_src = *iter;
+ Protein* protein = peptide_src->getParentProtein();
+ protein_ids.push_back(protein->getIdPointer());
+
+ string description = "";
+ const string& annotation_pointer = protein->getAnnotationPointer();
+ if (!annotation_pointer.empty()) {
+ description = protein->getAnnotationPointer();
+ // replace double quotes with single quotes
+ replace(description.begin(), description.end(), '"', '\'');
+ // remove any xml tags in the description by replacing <> with []
+ replace(description.begin(), description.end(), '<', '[');
+ replace(description.begin(), description.end(), '>', ']');
+ }
+ protein_descriptions.push_back(description);
+
+ }
+
+ return protein_ids.size();
+}
+
+/* Public functions--Iterators */
+
+/**
+ * Instantiates a new residue_iterator from a peptide.
+ * \returns a RESIDUE_ITERATOR_T object.
+ */
+RESIDUE_ITERATOR_T* new_residue_iterator(
+ Peptide* peptide ///< peptide sequence to iterate -in
+ )
+{
+ RESIDUE_ITERATOR_T* residue_iterator =
+ (RESIDUE_ITERATOR_T*)mycalloc(1, sizeof(RESIDUE_ITERATOR_T));
+
+ residue_iterator->peptide = peptide;
+ residue_iterator->residue_idx = 0;
+ residue_iterator->sequence = peptide->getSequence();
+ return residue_iterator;
+}
+
+/**
+ * Frees an allocated residue_iterator object.
+ */
+void free_residue_iterator(
+ RESIDUE_ITERATOR_T* residue_iterator ///< free this object -in
+ )
+{
+ free(residue_iterator->sequence);
+ free(residue_iterator);
+}
+
+/**
+ * The basic iterator functions.
+ * \returns true if there are additional residues to iterate over, false if not.
+ */
+bool residue_iterator_has_next(
+ RESIDUE_ITERATOR_T* residue_iterator ///< the query iterator -in
+ )
+{
+ return (residue_iterator->residue_idx < residue_iterator->peptide->getLength());
+}
+
+/**
+ * \returns The next residue (a character) in the peptide.
+ */
+char residue_iterator_next(
+ RESIDUE_ITERATOR_T* residue_iterator ///< the query iterator -in
+ )
+{
+ ++residue_iterator->residue_idx;
+ return residue_iterator->sequence[residue_iterator->residue_idx - 1];
+}
+
+/**
+ * \brief Builds a comma delimited string listing the
+ * protein id(peptide start index) for the sources of
+ * a peptide
+ *
+ * \returns a string of the protein sources for this peptide
+ */
+string Peptide::getProteinIdsLocations() {
+
+ set<string> protein_ids_locations;
+ string protein_field_string;
+
+ std::ostringstream protein_field_stream;
+ if (!peptide_srcs_.empty()) {
+ for( PeptideSrcIterator iter = getPeptideSrcBegin();
+ iter!=getPeptideSrcEnd();++iter){
+
+ PeptideSrc* peptide_src =*iter;
+ Protein* protein = peptide_src->getParentProtein();
+ string& protein_id = protein->getIdPointer();
+ std::ostringstream protein_loc_stream;
+ protein_loc_stream << protein_id;
+
+ if (!protein->isPostProcess()) {
+ int peptide_loc = peptide_src->getStartIdx();
+ protein_loc_stream << "(" << peptide_loc << ")";
+ } else if (peptide_src->getStartIdxOriginal() > 0) {
+ protein_loc_stream << "(" << peptide_src->getStartIdxOriginal() << ")";
+ }
+
+ protein_ids_locations.insert(protein_loc_stream.str());
+ }
+ }
+
+ set<string>::iterator result_iter = protein_ids_locations.begin();
+ protein_field_string = *result_iter;
+
+ while(++result_iter != protein_ids_locations.end()) {
+ protein_field_string += "," + *result_iter;
+ }
+
+ return protein_field_string;
+}
+
+
+/**
+ * \brief Builds a comma delimited string listing the protein ids
+ * for the sources of a peptide.
+ */
+vector<string> Peptide::getProteinIds() {
+ vector<string> ids;
+ for (PeptideSrcIterator iter = getPeptideSrcBegin(); iter != getPeptideSrcEnd(); ++iter) {
+ ids.push_back((*iter)->getParentProtein()->getIdPointer());
+ }
+ return ids;
+}
+
+/**
+ * \brief Builds a comma delimited string listing the flanking amino acids
+ * for the sources of a peptide.
+ *
+ * \returns a pointer to the string. Caller is responsible for freeing memeory.
+ * If peptide has no sources returns NULL.
+ */
+char* Peptide::getFlankingAAs() {
+
+ string flanking_string = "";
+
+ // iterate over all PeptideSrc
+ for (PeptideSrcIterator iter = getPeptideSrcBegin();
+ iter != getPeptideSrcEnd();
+ ++iter) {
+ // add comma if there is already flanking AA(s) in the string
+ if (!flanking_string.empty()) {
+ flanking_string += ',';
+ }
+ PeptideSrc* src = *iter;
+ Protein* protein = src->getParentProtein();
+ int start_idx = src->getStartIdx();
+ if (!protein->isPostProcess()) {
+ // not post process, get flanking AAs from protein sequence
+ int end_idx = start_idx + getLength() - 1;
+ int protein_length = protein->getLength();
+ char* protein_seq = protein->getSequencePointer();
+ flanking_string += (start_idx > 1) ? protein_seq[start_idx - 2] : '-';
+ flanking_string += (end_idx < protein_length) ? protein_seq[end_idx] : '-';
+ } else {
+
+ // post process, get flanking AAs from the protein object
+ PostProcessProtein* post_process_protein = (PostProcessProtein*)protein;
+ flanking_string += post_process_protein->getNTermFlankingAA(start_idx - 1);
+ flanking_string += post_process_protein->getCTermFlankingAA(start_idx - 1);
+ }
+ }
+
+ // convert to c string
+ int length = flanking_string.length();
+ char* flanking_field = (char*)malloc(sizeof(char)*(length + 1));
+ memcpy(flanking_field, flanking_string.c_str(), length);
+ flanking_field[length] = '\0';
+
+ return flanking_field;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/Peptide.h b/src/model/Peptide.h
new file mode 100644
index 0000000..66c27cb
--- /dev/null
+++ b/src/model/Peptide.h
@@ -0,0 +1,490 @@
+/**
+ * \file peptide.h
+ * $Revision: 1.52 $
+ * \brief Object for representing one peptide.
+ */
+#ifndef CRUX_PEPTIDE_H_
+#define CRUX_PEPTIDE_H_
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "util/mass.h"
+#include "Modification.h"
+#include "Protein.h"
+#include "model/objects.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+#include "Database.h"
+#include "util/modifications.h"
+#include "util/peptide_modifications.h"
+
+//these may be elsewhere
+static const int MAX_PEPTIDE_LENGTH = 255;
+
+#include <string>
+
+/**
+ * \class peptide
+ * \brief A subsequence of a protein.
+ */
+
+class ModificationDefinition;
+
+namespace Crux {
+
+class Modification;
+
+class Peptide {
+
+ protected:
+ int pointer_count_;
+ unsigned char length_; ///< The length of the peptide
+ std::vector<PeptideSrc*> peptide_srcs_; ///< a vector of peptide_srcs_
+
+ MODIFIED_AA_T* decoy_modified_seq_; ///< randomized peptide sequence
+ std::string sequence_;
+ std::vector<Modification> varMods_;
+
+ public:
+ /* Allocators/deallocators */
+
+ /**
+ * \returns An (empty) peptide object.
+ */
+ Peptide();
+ Peptide(std::string sequence);
+ Peptide(std::string sequence, std::vector<Modification> mods);
+
+ /**
+ * \returns A new peptide object, populated with the user specified
+ * parameters.
+ */
+ Peptide(
+ unsigned char length, ///< The length of the peptide -in
+ Crux::Protein* parent_protein, ///< The parent_protein of this peptide -in
+ int start_idx ///< Start index of peptide in the protein sequence -in
+ );
+
+ /**
+ * \brief Allocates a new peptide giving it the values of the source
+ * peptide.
+ * \returns A newly allocated peptide identical to the source.
+ */
+ Peptide(
+ Peptide* src ///< source peptide -in
+ );
+
+ /**
+ * Merges two identical peptides by adding the peptide_src of the
+ * second to the first. The second peptide remains unchanged.
+ * Does not comfirm identity of peptides.
+ * \returns true if merge is successfull.
+ */
+ static bool mergePeptidesCopySrc(
+ Peptide* peptide_dest,
+ Peptide* peptide_giver
+ );
+
+ /**
+ * Frees an allocated peptide object.
+ * Depending on peptide_src implementation determines how to free srcs
+ * This decision is made by global variable PEPTIDE_SRC_USE_LINK_LIST
+ */
+ ~Peptide();
+
+ Crux::Peptide* copyPtr();
+
+ /* Getters and Setters */
+
+ /* Get-set: source */
+
+ /**
+ * sets the peptide_src field in the peptide
+ * must pass on a heap allocated peptide_src object
+ * does not copy in the object, just the pointer to the object.
+ */
+ void setPeptideSrc(
+ PeptideSrc* new_association ///< new peptide_src -in
+ );
+
+ /**
+ * this method adds the new_association to the end of the existing peptide's
+ * linklist of peptide_srcs
+ * must pass on a heap allocated peptide_src object
+ * does not copy in the object, just the pointer to the object.
+ */
+ void addPeptideSrc(
+ PeptideSrc* new_association ///< new peptide_src -in
+ );
+
+ /**
+ * this method adds the peptide src array to an EMPTY peptide
+ * only used in index.c, when the peptide src count for peptide is known
+ * Any existing peptide_src will lose it's reference
+ */
+ void addPeptideSrcArray(
+ PeptideSrc* peptide_src_array ///< new peptide_src -in
+ );
+
+ /**
+ * returns a pointer to the first PeptideSrc object of the peptide
+ */
+ PeptideSrc* getPeptideSrc() const;
+
+ /**
+ * returns a point to the peptide_protein_association field of the peptide
+ */
+ std::vector<PeptideSrc*>& getPeptideSrcVector();
+
+ PeptideSrcIterator getPeptideSrcBegin();
+ PeptideSrcIterator getPeptideSrcEnd();
+
+ /**
+ * get the peptide->first peptide_src->parent protein->database
+ */
+ Database* getFirstSrcDatabase();
+
+ /**
+ * \returns The number of peptide sources (i.e. proteins) the peptide has.
+ */
+ int getNumPeptideSrc();
+
+ /**
+ * returns a pointer to the peptide's first parent protein field of the peptide
+ */
+ Crux::Protein* getParentProtein();
+
+ /**
+ * sets the sequence length of the peptide
+ */
+ void setLength(
+ unsigned char length ///< the length of sequence -in
+ );
+
+ /**
+ *\returns the sequence length of the peptide
+ */
+ unsigned char getLength();
+
+ /**
+ * \brief Get the sequence of a peptide.
+ * Goes to the first peptide_src to gain sequence, thus must have at
+ * least one peptide src
+ * \returns A newly allocated copy of the sequence.
+ */
+ char* getSequence() const;
+
+ /**
+ * \brief Get a string representation of the target (unshuffled)
+ * peptide sequence with no added modification symbols.
+ * For target peptides, returns the same as get_peptide_sequence.
+ * \returns The newly-allocated sequence of peptide
+ */
+ std::string getUnshuffledSequence() const;
+
+ /**
+ * \returns a pointer to the start of peptide sequence with in it's protein parent sequence,
+ * thus does not have terminating signe until end of parent protein
+ * goes to the first peptide_src to find the location of start, thus must have at least one peptide src
+ * should not print, will result in printing the entire protein sequence
+ */
+ char* getSequencePointer();
+
+ /**
+ * \brief Formats the sequence of the peptide with each flanking AA.
+ *
+ * Format is "X.peptide_sequence.X", where "X" is a flanking amino acid.
+ * "X", is printed as "-" if there is no flanking sequence.
+ * Goes to the first peptide_src to gain sequence, thus must have at
+ * least one peptide src
+ * \returns A newly allocated string with the sqt-formated peptide sequence.
+ */
+ std::string getSequenceSqt();
+
+ /**
+ * \brief Return a char for the amino acid c-terminal to the peptide
+ * in the peptide src at the given index.
+ *
+ * \returns A char (A-Z) or - if peptide is the first in the protein.
+ */
+ char getCTermFlankingAA();
+
+ /**
+ * \brief Return a char for the amino acid n-terminal to the peptide
+ * in the peptide src at the given index.
+ *
+ * \returns A char (A-Z) or - if peptide is the last in the protein.
+ */
+ char getNTermFlankingAA();
+
+ void addMod(const ModificationDefinition* mod, unsigned char index);
+ void setMods(const std::vector<Modification>& mods);
+ std::vector<Modification> getMods() const;
+ std::vector<Modification> getVarMods() const;
+ std::vector<Modification> getStaticMods() const;
+
+ /**
+ * \brief Add a modification to a peptide.
+ *
+ * Adds the modified sequence to the peptide and changes the peptide
+ * mass based on the mass change in the peptide_mod.
+ * \returns void
+ */
+ void setMod(
+ MODIFIED_AA_T* mod_seq, ///< modified seq to add
+ PEPTIDE_MOD_T* pep_mod ///< mod that made the seq
+ );
+
+ std::string getModsString() const;
+
+ bool isModified();
+
+ bool isDecoy();
+
+ /**
+ * \brief Get the modified aa sequence
+ *
+ * If the peptide has no modifications, create a sequence of
+ * MODIFIED_AA_T's in which none of them are actually modified.
+ * \returns A newly allocated copy of the sequence of MODIFIED_AA_Ts.
+ */
+ //MODIFIED_AA_T* get_peptide_modified_sequence( // why is this not working??!!
+ unsigned short* getModifiedAASequence();
+
+ /**
+ * sets the modified sequence for the peptide
+ */
+ void setModifiedAASequence(
+ MODIFIED_AA_T* mod_seq, ///< modified sequence to set
+ bool decoy ///< is the peptide a decoy?
+ );
+
+ /**
+ * \brief Get the modified aa sequence in string form.
+ *
+ * If the peptide has no modifications, returns same string as
+ * get_peptide_sequence. If modified, adds the mod symbols to the string.
+ * \returns The peptide sequence including any modifications.
+ */
+ std::string getModifiedSequenceWithSymbols();
+
+ /**
+ * \brief Get the modified aa sequence in string form.
+ *
+ * If the peptide has no modifications, returns same string as
+ * get_peptide_sequence. If modified, adds in brackets the masses of
+ * all modifications. If merge_masses is true, prints the sum of all
+ * modifications for a residue. If false, prints all masses in a
+ * comma separated list.
+ * \returns The peptide sequence including any modifications.
+ */
+ std::string getModifiedSequenceWithMasses();
+
+ void setDecoyModifiedSeq(MODIFIED_AA_T* decoy_modified_seq);
+
+ /* Getters requiring calculation */
+ int countModifiedAAs();
+
+ /**
+ * \returns The mass of the given peptide.
+ */
+ static FLOAT_T calcSequenceMass(
+ const std::string& peptide, ///< the query peptide -in
+ MASS_TYPE_T mass_type ///< isotopic mass type (AVERAGE, MONO) -in
+ );
+
+ /**
+ * \returns The mass of the given peptide.
+ */
+ FLOAT_T calcMass(
+ MASS_TYPE_T mass_type ///< isotopic mass type (AVERAGE, MONO) -in
+ ) const;
+
+ /**
+ * \returns the mass of the given peptide, with modifications
+ */
+ FLOAT_T calcModifiedMass(
+ MASS_TYPE_T mass_type ///< isotopic mass type (AVERAGE, MONO) -in
+ ) const;
+
+ FLOAT_T calcModifiedMass() const;
+
+ /**
+ * Examines the peptide sequence and counts how many tryptic missed
+ * cleavage sites exist.
+ *\returns the number of missed cleavage sites in the peptide
+ */
+ int getMissedCleavageSites();
+
+ int getMissedCleavageSites(
+ std::set<int> skip //skip these amino acid indices.
+ );
+
+ /**
+ * \brief Find the distance from the n-terminus of the source protein
+ * to the n-terminus of the peptide.
+ * In the case of multiple source proteins, return the smallest
+ * distance.
+ * \returns The distance from the protein n-terminus.
+ */
+ int getNDistance();
+
+ /**
+ * \brief Find the distance from the c-terminus of the source protein
+ * to the c-terminus of the peptide.
+ * In the case of multiple source proteins, return the smallest
+ * distance.
+ * \returns The distance from the protein c-terminus.
+ */
+ int getCDistance();
+
+ /**
+ * Change the given target peptide into a decoy by randomizing its sequence.
+ * Uses settings in parameter.c to decide between shuffling and
+ * reversing the sequence. Any modifications that exist will be
+ * maintained on the same amino acids whose position will move.
+ */
+ void transformToDecoy();
+
+ /**
+ * \brief Return a randomly shuffled version of the given peptide's
+ * sequence as an array of char (A-Z). Based on the peptide type,
+ * will leave the end(s) unchanged to preserve the tryptic property.
+ *
+ *\returns A newly-allcoated char array of the shuffled sequence.
+ */
+ char* generateShuffledSequence();
+
+ /**
+ * \brief Return a reversed version of the given peptide's sequence as
+ * an array of char (A-Z). Leave the first and last residue
+ * unchanged. If the reversed sequence is identical to the target,
+ * shuffle the sequence instead.
+ *
+ * \returns A newly-allocated char array of the reversed sequence.
+ */
+ char* generateReversedSequence();
+
+ /**
+ * \brief Return a randomly shuffled version of the given peptide's
+ * sequence as an array of MODIIFIED_AA_T. Based on the peptide type,
+ * will leave the end(s) unchanged to preserve the tryptic property.
+ *
+ *\returns A newly-allcoated MODIFIED_AA_T array of the shuffled sequence.
+ */
+ MODIFIED_AA_T* generateShuffledModSequence();
+
+ /**
+ * \brief Return a reversed version of the given peptide's sequence as
+ * an array of MODIFIED_AA_T. Leave the first and last residue
+ * unchanged. If the reversed sequence is identical to the target,
+ * shuffle the sequence instead.
+ *
+ * \returns A newly-allocated MODIFIED_AA_T array of the reversed sequence.
+ */
+ MODIFIED_AA_T* generateReversedModSequence();
+
+ /* Comparisons for sorting */
+
+ /**
+ * Compare two peptide sequences.
+ * \returns Zero (0) if the sequences are identical, -1 if the first
+ * sequence is less than the first and 1 if the first sequence is
+ * greater than the first.
+ */
+ static int triCompareSequence(
+ Peptide* peptide_one, ///< the peptide sequence to compare -out
+ Peptide* peptide_two ///< the peptide sequence to compare -out
+ );
+
+ /**
+ * Compare the sequence of two peptides and return true if the first
+ * peptide sequence is less than (in a lexical sort) the second peptide.
+ */
+ static bool lessThan(
+ Peptide* peptide_one,
+ Peptide* peptide_two
+ );
+
+ /**
+ * \brief Builds a comma delimited string listing the
+ * protein id(peptide start index) for the sources of
+ * a peptide
+ *
+ * \returns a string of the protein sources for this peptide
+ */
+ std::string getProteinIdsLocations();
+
+ /**
+ * \brief Builds a comma delimited string listing the protein ids
+ * for the sources of a peptide.
+ */
+ std::vector<std::string> getProteinIds();
+
+ /**
+ * \brief Builds a comma delimited string listing the flanking amino acids
+ * for the sources of a peptide.
+ *
+ * \returns a pointer to the string. Caller is responsible for freeing memeory.
+ * If peptide has no sources returns NULL.
+ */
+ char* getFlankingAAs();
+
+ /**
+ * Fills the given vectors with the names and descriptions of all
+ * proteins containing this peptide. Returned in the same order as
+ * getFlankingAAs(). Clears any existing data in the vectors.
+ * \returns The number of proteins.
+ */
+ int getProteinInfo(std::vector<std::string>& protein_ids,
+ std::vector<std::string>& protein_descriptions);
+
+}; // class Peptide
+
+}; // namespace Crux
+
+/* Iterators */
+
+/**
+ * Instantiates a new residue_iterator from a peptide.
+ * \returns a RESIDUE_ITERATOR_T object.
+ */
+RESIDUE_ITERATOR_T* new_residue_iterator(
+ Crux::Peptide* peptide ///< peptide sequence to iterate -in
+ );
+
+/**
+ * Frees an allocated residue_iterator object.
+ */
+void free_residue_iterator(
+ RESIDUE_ITERATOR_T* residue_iterator ///< free this object -in
+ );
+
+/**
+ * The basic iterator functions.
+ * \returns true if there are additional residues to iterate over, false if not.
+ */
+bool residue_iterator_has_next(
+ RESIDUE_ITERATOR_T* residue_iterator ///< the query iterator -in
+ );
+
+/**
+ * \returns The next residue (a character) in the peptide.
+ */
+char residue_iterator_next(
+ RESIDUE_ITERATOR_T* residue_iterator ///< the query iterator -in
+ );
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/PeptideConstraint.cpp b/src/model/PeptideConstraint.cpp
new file mode 100644
index 0000000..2039418
--- /dev/null
+++ b/src/model/PeptideConstraint.cpp
@@ -0,0 +1,317 @@
+/*************************************************************************//**
+ * \file PeptideConstraint.cpp
+ * \brief Object for holding the peptide constraint information.
+ ****************************************************************************/
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "util/mass.h"
+#include "util/GlobalParams.h"
+#include "util/Params.h"
+#include "Peptide.h"
+#include "Protein.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+
+using namespace Crux;
+
+/**
+ * Allocates a new (empty) peptide_constraint object.
+ * \returns An allocated PEPTIDE_CONSTRAINT_T object.
+ */
+void PeptideConstraint::init() {
+ carp(CARP_DETAILED_DEBUG, "Initializing peptide constraint");
+ enzyme_ = (ENZYME_T)0;
+ digestion_ = (DIGEST_T)0;
+ min_mass_ = 0;
+ min_length_ = 0;
+ max_length_ = 0;
+ num_mis_cleavage_ = 0;
+ mass_type_ = (MASS_TYPE_T)0;
+ num_pointers_ = 1;
+}
+
+PeptideConstraint::PeptideConstraint() {
+ init();
+}
+
+/**
+ * Instantiates a new peptide_constraint object.
+ * \returns An allocated PEPTIDE_CONSTRAINT_T object.
+ */
+PeptideConstraint::PeptideConstraint(
+ ENZYME_T enzyme,
+ DIGEST_T digest,
+ FLOAT_T min_mass, ///< the minimum mass -in
+ FLOAT_T max_mass, ///< the maximum mass -in
+ int min_length, ///< the minimum length of peptide -in
+ int max_length, ///< the maximum lenth of peptide(max limit = 255) -in
+ int num_mis_cleavage, ///< The maximum mis cleavage of the peptide -in
+ MASS_TYPE_T mass_type ///< isotopic mass type (AVERAGE, MONO) -in
+ )
+{
+ // max length must be less or equal than 255 becuase of the unsigned char limit of 255
+ if(max_length > 255){
+ carp(CARP_FATAL, "ERROR: cannot set max length higer than 255");
+ }
+
+ init();
+
+ setEnzyme(enzyme);
+ setDigest(digest);
+ setMinMass(min_mass);
+ setMaxMass(max_mass);
+ setMinLength(min_length);
+ setMaxLength(max_length);
+ setNumMisCleavage(num_mis_cleavage);
+ setMassType(mass_type);
+}
+
+PeptideConstraint::PeptideConstraint(
+ ENZYME_T enzyme,
+ DIGEST_T digest,
+ int min_length, ///< the minimum length of peptide -in
+ int max_length, ///< the maximum lenth of peptide(max limit = 255) -in
+ int num_mis_cleavage ///< The maximum mis cleavage of the peptide -in
+) {
+ // max length must be less or equal than 255 becuase of the unsigned char limit of 255
+ if (max_length > 255) {
+ carp(CARP_FATAL, "ERROR: cannot set max length higer than 255");
+ }
+
+ init();
+
+ setEnzyme(enzyme);
+ setDigest(digest);
+ setMinLength(min_length);
+ setMaxLength(max_length);
+ setNumMisCleavage(num_mis_cleavage);
+}
+
+/**
+ * \brief Create a new peptide constraint and populate its values
+ * based on those in parameter.c
+ * \returns A newly allocated peptide constraint.
+ */
+PeptideConstraint* PeptideConstraint::newFromParameters() {
+
+ PeptideConstraint* new_constraint = new PeptideConstraint();
+
+ new_constraint->setEnzyme(GlobalParams::getEnzyme());
+ new_constraint->setDigest(GlobalParams::getDigestion());
+ new_constraint->setMinMass(GlobalParams::getMinMass());
+ new_constraint->setMaxMass(GlobalParams::getMaxMass());
+ new_constraint->setMinLength(GlobalParams::getMinLength());
+ new_constraint->setMaxLength(GlobalParams::getMaxLength());
+ // TODO : change this after missed cleavage is an integer parameter
+ // rather than boolean.
+ new_constraint->setNumMisCleavage(GlobalParams::getMissedCleavages());
+ new_constraint->setMassType(GlobalParams::getIsotopicMass());
+
+ return new_constraint;
+}
+
+
+/**
+ * Copy peptide pointer and increment pointer count
+ */
+PeptideConstraint* PeptideConstraint::copyPtr(
+ PeptideConstraint* constraint
+ ) {
+
+ constraint->num_pointers_++;
+ return constraint;
+}
+
+// FIXME check the association..as long as there is one tryptic parent then true
+// num_miss_cleavage is not implemented..add if needed
+/**
+ * Determines if a peptide satisfies a peptide_constraint.
+ * \returns TRUE if the constraint is satisified. FALSE if not.
+ */
+bool PeptideConstraint::isSatisfied(
+ Peptide* peptide ///< the query peptide -in
+ ) {
+
+ return (peptide->getLength() <= getMaxLength() &&
+ peptide->getLength() >= getMinLength() &&
+ peptide->calcModifiedMass() <= getMaxMass() &&
+ peptide->calcModifiedMass() >= getMinMass()
+ );
+}
+
+/**
+ * Frees an allocated peptide_constraint object.
+ */
+void PeptideConstraint::free(
+ PeptideConstraint* peptide_constraint ///< object to free -in
+ ) {
+
+ peptide_constraint->num_pointers_--;
+ if (peptide_constraint->num_pointers_ <= 0) {
+ carp(CARP_DETAILED_DEBUG, "Final free of peptide constraint");
+ delete peptide_constraint;
+ }
+
+}
+
+PeptideConstraint::~PeptideConstraint() {
+
+}
+
+/**
+ * Sets the enzyme used for the in silicos digestion
+ * of the protein sequence into peptides.
+ */
+void PeptideConstraint::setEnzyme(
+ ENZYME_T enzyme
+){
+
+ enzyme_ = enzyme;
+}
+
+/**
+ * \returns The enzyme for this peptide constraint.
+ */
+ENZYME_T PeptideConstraint::getEnzyme()
+{
+ return enzyme_;
+}
+
+/**
+ * Sets the level of digestion for the peptide constraint.
+ */
+void PeptideConstraint::setDigest(
+ DIGEST_T digest
+ ){
+
+ digestion_ = digest;
+}
+
+/**
+ * \returns The level of digestion for the peptide constraint.
+ */
+DIGEST_T PeptideConstraint::getDigest() {
+
+ return digestion_;
+}
+
+
+/**
+ * sets the min mass of the peptide_constraint
+ */
+void PeptideConstraint::setMinMass(
+ FLOAT_T min_mass ///< the min mass of the peptide constraint - in
+ )
+{
+ min_mass_ = min_mass;
+}
+
+/**
+ * \returns the min mass of the peptide_constraint
+ */
+FLOAT_T PeptideConstraint::getMinMass() {
+
+ return min_mass_;
+}
+
+/**
+ * sets the max mass of the peptide_constraint
+ */
+void PeptideConstraint::setMaxMass(
+ FLOAT_T max_mass ///< the max mass of the peptide constraint - in
+ ) {
+
+ max_mass_ = max_mass;
+}
+
+/**
+ * \returns the max mass of the peptide_constraint
+ */
+FLOAT_T PeptideConstraint::getMaxMass() {
+
+ return max_mass_;
+}
+
+/**
+ * sets the min length of the peptide_constraint
+ */
+void PeptideConstraint::setMinLength(
+ int min_length ///< the min length of the peptide constraint - in
+ ) {
+
+ min_length_ = min_length;
+}
+
+/**
+ * \returns the min length of the peptide_constraint
+ */
+int PeptideConstraint::getMinLength() {
+
+ return min_length_;
+}
+
+/**
+ * sets the max length of the peptide_constraint
+ * maximum limit 255
+ */
+void PeptideConstraint::setMaxLength(
+ int max_length ///< the max length of the peptide constraint - in
+ ) {
+
+ // check if maximum length is with in range <= 255
+ if(max_length > 255){
+ carp(CARP_FATAL, "maximum length:%d over limit 255.", max_length);
+ }
+
+ max_length_ = max_length;
+}
+
+/**
+ * \returns the max length of the peptide_constraint
+ */
+int PeptideConstraint::getMaxLength(
+ ) {
+
+ return max_length_;
+}
+
+
+/**
+ * sets the num_mis_cleavage of the peptide_constraint
+ */
+void PeptideConstraint::setNumMisCleavage(
+ int num_mis_cleavage ///< The maximum mis cleavage of the peptide -in
+ ) {
+
+ num_mis_cleavage_ = num_mis_cleavage;
+}
+
+/**
+ * \returns the num_mis_cleavage of the peptide_constraint
+ */
+int PeptideConstraint::getNumMisCleavage() {
+
+ return num_mis_cleavage_;
+}
+
+/**
+ * sets the mass type of the peptide_constraint
+ */
+void PeptideConstraint::setMassType(
+ MASS_TYPE_T mass_type ///< the mass_type for the constraint -in
+ ) {
+
+ mass_type_ = mass_type;
+}
+
+/**
+ * \returns the mass type of the mass_constraint
+ */
+MASS_TYPE_T PeptideConstraint::getMassType() {
+
+ return mass_type_;
+}
diff --git a/src/model/PeptideConstraint.h b/src/model/PeptideConstraint.h
new file mode 100644
index 0000000..02820ad
--- /dev/null
+++ b/src/model/PeptideConstraint.h
@@ -0,0 +1,200 @@
+/**
+ * \file peptide_constraint.h
+ * $Revision: 1.5 $
+ * \brief Object for holding the peptide constraint information.
+ */
+#ifndef PEPTIDE_CONSTRAINT_H
+#define PEPTIDE_CONSTRAINT_H
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "model/objects.h"
+#include "util/mass.h"
+#include "Peptide.h"
+#include "Protein.h"
+#include "io/carp.h"
+
+/**
+ * \class PeptideConstraint
+ * \brief Object to represent constraints which a peptide may or may not
+ * satisfy.
+ *
+ * def TRYPTIC: a protein that ends with either K or R and
+ * any other K and R in the sequence must be followed by a P
+ */
+class PeptideConstraint {
+ protected:
+ ENZYME_T enzyme_;
+ DIGEST_T digestion_;
+ FLOAT_T min_mass_; ///< The minimum mass of the peptide
+ FLOAT_T max_mass_; ///< The maximum mass of the peptide
+ int min_length_; ///< The minimum length of the peptide
+ int max_length_; ///< The maximum length of the peptide
+ int num_mis_cleavage_; ///< The maximum mis cleavage of the peptide
+ MASS_TYPE_T mass_type_; ///< isotopic mass type (AVERAGE, MONO)
+ int num_pointers_; ///< Number of pointers to this constraint
+
+ public:
+
+ void init();
+
+ /**
+ * Allocates a new (empty) peptide_constraint object.
+ * \returns An allocated PeptideConstraint object.
+ */
+ PeptideConstraint();
+
+ /**
+ * Instantiates a new peptide_constraint object.
+ * \returns An allocated PEPTIDE_CONSTRAINT_T object.
+ */
+ PeptideConstraint(
+ ENZYME_T enzyme, ///< the enzyme to use for digestion
+ DIGEST_T digest, ///< the degree of digestion
+ FLOAT_T min_mass, ///< the minimum mass -in
+ FLOAT_T max_mass, ///< the maximum mass -in
+ int min_length, ///< the minimum length of peptide -in
+ int max_length, ///< the maximum lenth of peptide -in
+ int num_mis_cleavage, ///< The maximum mis cleavage of the peptide -in
+ MASS_TYPE_T mass_type ///< isotopic mass type (AVERAGE, MONO) -in
+ );
+
+ PeptideConstraint(
+ ENZYME_T enzyme, ///< the enzyme to use for digestion
+ DIGEST_T digest, ///< the degree of digestion
+ int min_length, ///< the minimum length of peptide -in
+ int max_length, ///< the maximum lenth of peptide -in
+ int num_mis_cleavage ///< The maximum mis cleavage of the peptide -in
+ );
+
+ /**
+ * \brief Create a new peptide constraint and populate its values
+ * based on those in parameter.c
+ * \returns A newly allocated peptide constraint.
+ */
+ static PeptideConstraint* newFromParameters();
+
+ /**
+ * Determines if a peptide satisfies a peptide_constraint.
+ * \returns TRUE if the constraint is satisified. FALSE if not.
+ */
+ bool isSatisfied(
+ Crux::Peptide* peptide ///< the query peptide -in
+ );
+
+ /**
+ * Copies an allocated peptide_constraint object.
+ */
+ static PeptideConstraint* copyPtr(
+ PeptideConstraint* peptide_constraint ///< object to copy -in
+ );
+
+ /**
+ * Frees an allocated peptide_constraint object.
+ */
+ static void free(PeptideConstraint*);
+ virtual ~PeptideConstraint();
+
+ /**
+ * Setters/Getters
+ */
+
+ void setEnzyme(
+ ENZYME_T enzyme
+ );
+
+ ENZYME_T getEnzyme();
+
+
+ void setDigest(
+ DIGEST_T digest
+ );
+
+ DIGEST_T getDigest();
+
+ /**
+ * sets the min mass of the peptide_constraint
+ */
+ void setMinMass(
+ FLOAT_T min_mass ///< the min mass of the peptide constraint - in
+ );
+
+ /**
+ * \returns the min mass of the peptide_constraint
+ */
+ FLOAT_T getMinMass();
+
+ /**
+ * sets the max mass of the peptide_constraint
+ */
+ void setMaxMass(
+ FLOAT_T max_mass ///< the max mass of the peptide constraint - in
+ );
+
+ /**
+ * \returns the max mass of the peptide_constraint
+ */
+ FLOAT_T getMaxMass();
+
+ /**
+ * sets the min length of the peptide_constraint
+ */
+ void setMinLength(
+ int min_length ///< the min length of the peptide constraint - in
+ );
+
+ /**
+ * \returns the min length of the peptide_constraint
+ */
+ int getMinLength();
+
+ /**
+ * sets the max length of the peptide_constraint
+ */
+ void setMaxLength(
+ int max_length ///< the max length of the peptide constraint - in
+ );
+
+ /**
+ * \returns the max length of the peptide_constraint
+ */
+ int getMaxLength();
+
+ /**
+ * sets the num_mis_cleavage of the peptide_constraint
+ */
+ void setNumMisCleavage(
+ int num_mis_cleavage ///< The maximum mis cleavage of the peptide -in
+ );
+
+ /**
+ * \returns the num_mis_cleavage of the peptide_constraint
+ */
+ int getNumMisCleavage();
+
+ /**
+ * sets the mass type of the peptide_constraint
+ */
+ void setMassType(
+ MASS_TYPE_T mass_type ///< the peptide_type for the constraint -in
+ );
+
+ /**
+ * \returns the mass type of the mass_constraint
+ */
+ MASS_TYPE_T getMassType();
+
+};
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/PeptideIterator.h b/src/model/PeptideIterator.h
new file mode 100644
index 0000000..4cfdb65
--- /dev/null
+++ b/src/model/PeptideIterator.h
@@ -0,0 +1,64 @@
+/**
+ * \file PeptideIterator.h
+ * Abstract class for returning peptides from a peptide source.
+ */
+#ifndef PETPIDE_ITERATOR_H
+#define PETPIDE_ITERATOR_H
+
+#include "Peptide.h"
+
+class PeptideIterator{
+
+ private:
+ bool has_next_;
+
+ protected:
+ Crux::Peptide* next_peptide_;
+
+ /**
+ * \brief Prepare the iterator to return the next peptide.
+ * Derived classes must implement this method, pointing
+ * next_peptide_ to the peptide that will be returned next and
+ * returning true. When there are no more peptides, it must set
+ * has_next_ to false, set next_peptide_ to NULL and return false.
+ * \returns true if there are more peptides to fetch or false if we are done
+ */
+ virtual bool queueNextPeptide() = 0;
+
+ /**
+ * Call this method in the constructor to set the first peptide.
+ */
+ void initialize(){
+ has_next_ = queueNextPeptide();
+ }
+
+ public:
+ virtual ~PeptideIterator(){};
+
+ /**
+ * Return the next peptide in the iterator or NULL if none are left.
+ */
+ Crux::Peptide* next(){
+ Crux::Peptide* return_me = next_peptide_;
+ has_next_ = queueNextPeptide();
+ return return_me;
+ }
+
+ /**
+ * Return true if there are more peptides to return or false if not.
+ */
+ bool hasNext(){
+ return has_next_;
+ }
+
+};
+
+#endif //PETPIDE_ITERATOR_H
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/model/PeptideMatch.cpp b/src/model/PeptideMatch.cpp
new file mode 100644
index 0000000..f9d7413
--- /dev/null
+++ b/src/model/PeptideMatch.cpp
@@ -0,0 +1,135 @@
+/**
+ * \file PeptideMatch.cpp
+ * \brief Object for holding peptide scores
+ ********************************/
+#include "PeptideMatch.h"
+#include "SpectrumMatch.h"
+
+using namespace Crux;
+using namespace std;
+
+/**
+ * \returns an empty PeptideMatch
+ */
+PeptideMatch::PeptideMatch() {
+
+}
+
+/**
+ * \returns a PeptideMatch with the peptide set
+ */
+PeptideMatch::PeptideMatch(
+ Peptide* peptide ///< Peptide to set
+ ) {
+
+ setPeptide(peptide);
+
+}
+
+/**
+ * Default destructor
+ */
+PeptideMatch::~PeptideMatch() {
+
+}
+
+/**
+ * sets the peptide for this match
+ */
+void PeptideMatch::setPeptide(
+ Peptide* peptide ///< peptide to set
+ ) {
+
+ peptide_ = peptide;
+
+}
+
+/**
+ * \returns the peptide for the match
+ */
+Peptide* PeptideMatch::getPeptide() {
+
+ return(peptide_);
+}
+
+/**
+ * adds a ProteinMatch to this PeptideMatch
+ */
+void PeptideMatch::addProteinMatch(
+ ProteinMatch* protein_match, ///< ProteinMatch to set
+ PeptideSrc* src ///< PeptideSrc
+ ) {
+ for (deque<ProteinMatch*>::iterator iter = protein_matches_.begin();
+ iter != protein_matches_.end();
+ ++iter) {
+ if (*iter == protein_match) {
+ return;
+ }
+ }
+ protein_matches_.push_back(protein_match);
+ protein_match_to_peptide_src_[protein_match] = src;
+}
+
+/**
+ * \returns the associated PeptideSrc for the ProteinMatch
+ */
+PeptideSrc* PeptideMatch::getSrc(
+ ProteinMatch* protein_match ///< gets the associated PeptideSrc
+ ) {
+
+ return protein_match_to_peptide_src_[protein_match];
+
+}
+
+/**
+ * Sets the spectrum match
+ */
+void PeptideMatch::addSpectrumMatch(
+ SpectrumMatch* spectrum_match ///< SpectrumMatch to add
+ ) {
+ for (deque<SpectrumMatch*>::iterator iter = spectrum_matches_.begin();
+ iter != spectrum_matches_.end();
+ ++iter) {
+ if (*iter == spectrum_match) {
+ return;
+ }
+ }
+ spectrum_matches_.push_back(spectrum_match);
+ spectrum_match->setPeptideMatch(this);
+}
+
+
+/**
+ * \returns the begin iterator of the spectrummatches
+ */
+SpectrumMatchIterator PeptideMatch::spectrumMatchBegin() {
+ return spectrum_matches_.begin();
+}
+
+/**
+ * \returns the begin iterator of the spectrum matches
+ */
+SpectrumMatchIterator PeptideMatch::spectrumMatchEnd() {
+ return spectrum_matches_.end();
+}
+
+/**
+ * \returns the begin iterator of the spectrum matches
+ */
+ProteinMatchIterator PeptideMatch::proteinMatchBegin() {
+ return protein_matches_.begin();
+}
+
+/**
+ * \returns the end iterator of the spectrum matches
+ */
+ProteinMatchIterator PeptideMatch::proteinMatchEnd() {
+ return protein_matches_.end();
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/PeptideMatch.h b/src/model/PeptideMatch.h
new file mode 100644
index 0000000..681ff43
--- /dev/null
+++ b/src/model/PeptideMatch.h
@@ -0,0 +1,102 @@
+/**
+ * \file PeptideMatch.h
+ * $Revision: 1.00 $
+ * \brief Object for holding peptide scores
+ ******************************************************/
+#ifndef PEPTIDEMATCH_H_
+#define PEPTIDEMATCH_H_
+
+#include "AbstractMatch.h"
+#include "match_objects.h"
+#include "Peptide.h"
+
+class PeptideMatch : public AbstractMatch {
+
+ protected:
+ std::deque<ProteinMatch*> protein_matches_; ///< protein matches associated with this peptide match
+ std::map<ProteinMatch*, PeptideSrc*> protein_match_to_peptide_src_; ///< peptide srcs for the protein match
+ std::deque<SpectrumMatch*> spectrum_matches_; ///< spectrum matches for this peptide
+ Crux::Peptide* peptide_; ///< peptide itself
+
+ public:
+ /**
+ * \returns an empty PeptideMatch
+ */
+ PeptideMatch();
+
+ /**
+ * \returns a PeptideMatch with the peptide set
+ */
+ PeptideMatch(
+ Crux::Peptide* peptide ///< Peptide to set
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual ~PeptideMatch();
+
+ /**
+ * Sets the peptide for this match
+ */
+ void setPeptide(
+ Crux::Peptide* peptide ///< peptide to set
+ );
+
+ /**
+ * \returns the peptide for the match
+ */
+ Crux::Peptide* getPeptide();
+
+ /**
+ * adds a ProteinMatch to this PeptideMatch
+ */
+ void addProteinMatch(
+ ProteinMatch* protein_match, ///< ProteinMatch to set
+ PeptideSrc* src ///< Location in protein
+ );
+
+ /**
+ * \returns the associated PeptideSrc from the ProteinMatch
+ */
+ PeptideSrc* getSrc(
+ ProteinMatch* protein_match ///< gets the associated src
+ );
+
+ /**
+ * Adds a spectrumMatch to this PeptideMatch
+ */
+ void addSpectrumMatch(
+ SpectrumMatch* spectrum_match ///<SpectrumMatch to add
+ );
+
+ /**
+ * \returns the begin iterator of the spectrummatches
+ */
+ SpectrumMatchIterator spectrumMatchBegin();
+
+ /**
+ * \returns the end iterator of the spectrum matches
+ */
+ SpectrumMatchIterator spectrumMatchEnd();
+
+ /**
+ * \returns the begin iterator of the spectrum matches
+ */
+ ProteinMatchIterator proteinMatchBegin();
+
+ /**
+ * \returns the end iterator of the spectrum matches
+ */
+ ProteinMatchIterator proteinMatchEnd();
+
+};
+
+#endif //PEPTIDEMATCH_H_
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/PeptideSrc.cpp b/src/model/PeptideSrc.cpp
new file mode 100644
index 0000000..f262418
--- /dev/null
+++ b/src/model/PeptideSrc.cpp
@@ -0,0 +1,514 @@
+/*************************************************************************//**
+ * \file PeptideSrc.cpp
+ * \brief Object for mapping a peptide to its parent protein.
+ ****************************************************************************/
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "io/carp.h"
+#include "util/utils.h"
+#include "util/mass.h"
+#include "util/StringUtils.h"
+#include "DatabasePeptideIterator.h"
+#include "Peptide.h"
+#include "Protein.h"
+#include "PeptideSrc.h"
+#include "PeptideConstraint.h"
+#include "PeptideIterator.h"
+
+#include <vector>
+#include <string>
+
+#include "io/DelimitedFile.h"
+#include "io/MatchFileReader.h"
+#include "io/MatchCollectionParser.h"
+
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * Static variable definitions
+ */
+map<string, Peptide* > PeptideSrc::sequence_to_peptide_; ///< Maps a sequence to a peptide object
+map<string, Peptide* > PeptideSrc::decoy_sequence_to_peptide_; ///< Maps a decoy sequence to a peptide object
+
+
+/**
+ * \returns An (empty) peptide_src object.
+ */
+PeptideSrc::PeptideSrc() {
+ digestion_ = (DIGEST_T)0;
+ parent_protein_ = NULL;
+ start_idx_ = 0;
+ start_idx_original_ = 0;
+}
+
+/**
+ *\returns a PeptideSrc object, populated with user specified parameters
+ */
+PeptideSrc::PeptideSrc(
+ DIGEST_T digest,
+ Protein* parent_protein, ///< the parent of this peptide -in
+ int start_idx ///< start index of the peptide in the protein sequence -in
+ ) {
+ start_idx_original_ = 0;
+ setDigest(digest);
+ setParentProtein(parent_protein);
+ setStartIdx(start_idx);
+}
+
+/**
+ * Frees the an individual allocated peptide_src object
+ * assumes that new_association pointer is NULL or some other pointer exist for the rest of the linklist
+ */
+PeptideSrc::~PeptideSrc() {
+}
+
+/**
+ * Copies the entire linklist of peptide_src object src to dest.
+ * dest must be a heap allocated peptide_src
+ */
+void PeptideSrc::copy(
+ vector<PeptideSrc*>& src, ///< source peptide_src -in
+ vector<PeptideSrc*>& dest ///< destination peptide_src -out
+ )
+{
+
+ for (vector<PeptideSrc*>::iterator iter = src.begin();
+ iter != src.end();
+ ++iter) {
+ PeptideSrc* dest_src = new PeptideSrc(*(*iter));
+ dest.push_back(dest_src);
+
+ }
+}
+
+/**
+ * sets the level of digestion
+ */
+void PeptideSrc::setDigest(
+ DIGEST_T digest ///< the type of the peptide -in
+ ){
+
+ digestion_ = digest;
+}
+
+/**
+ * \returns the level of digestion
+ */
+DIGEST_T PeptideSrc::getDigest() {
+
+ return digestion_;
+}
+
+/**
+ * sets the parent protein
+ */
+void PeptideSrc::setParentProtein(
+ Protein* parent_protein ///< the parent of this preptide -in
+ ) {
+ parent_protein_ = parent_protein;
+}
+
+/**
+ * \returns a pointer to the parent protein
+ */
+Protein* PeptideSrc::getParentProtein() {
+ return parent_protein_;
+}
+
+/**
+ * sets the start index of the peptide in the protein sequence
+ */
+void PeptideSrc::setStartIdx(
+ int start_idx ///< start index of the peptide in the protein sequence -in
+ ) {
+ start_idx_ = start_idx;
+}
+
+/**
+ * \returns the start index of the peptide in the protein sequence
+ */
+int PeptideSrc::getStartIdx() {
+ return start_idx_;
+}
+
+/**
+ * \sets the original start index of the peptide in the protein sequence
+ */
+void PeptideSrc::setStartIdxOriginal(
+ int start_idx ///< start index of the peptide in the original protein sequence -in
+) {
+ start_idx_original_ = start_idx;
+}
+
+/**
+ * \returns the original start index of the peptide in the protein sequence
+ */
+int PeptideSrc::getStartIdxOriginal() {
+ return start_idx_original_;
+}
+
+/**
+ * \returns a pointer to the start of the peptide with in it's parent protein sequence
+ */
+char* PeptideSrc::getSequencePointer() {
+
+ return parent_protein_->getSequencePointer(start_idx_ - 1);
+
+}
+
+/**
+ *\returns the peptide_src strct size, value of sizeof function
+ */
+int PeptideSrc::getSizeOf(){
+ return sizeof(PeptideSrc);
+}
+
+/**
+ * serialize peptide src in binary
+ * The peptide serialization format looks like this:
+ *
+ *<int: protein index><PEPTIDE_TYPE_T: peptide_type><int: peptide start index>
+ * the protein index is the index of the parent protein in the
+ *database Database
+ *
+ */
+void PeptideSrc::serialize(
+ FILE* file ///< output file -in
+ ) {
+
+ // write protein index in database
+ unsigned int protein_idx = parent_protein_->getProteinIdx();
+ carp(CARP_DETAILED_DEBUG, "protein idx to write is %i", protein_idx);
+
+ fwrite(&protein_idx, sizeof(int), 1, file);
+ carp(CARP_DETAILED_DEBUG, "Serializing protein src of index %d",
+ protein_idx);
+
+ // write peptide src type(tryptic, all, ...)
+ fwrite(&(digestion_), sizeof(DIGEST_T), 1, file);
+ // write start index in protein of peptide in this peptide src
+ fwrite(&(start_idx_), sizeof(int), 1, file);
+
+}
+
+/**
+ * Return the number of bytes taken up by one peptide_src when
+ * serialized to file. Used for skipping past peptide_src in an index
+ * file.
+ */
+int PeptideSrc::sizeOfSerialized(){
+
+ return (sizeof(int)*2 + sizeof(DIGEST_T));
+}
+
+/**
+ * \brief Read in the peptide_src objects from the given file and
+ * assosiated them with the given peptide.
+ * Proteins for the pepitde_src are found in the given database. If
+ * database is NULL, does not set proteins. (This option is used for
+ * sorting index files while creating index.)
+ *
+ * \returns true if peptide_src's were successfully parsed, else
+ * returns false.
+ */
+bool PeptideSrc::parseTabDelimited(
+ Peptide* peptide, ///< assign peptide_src(s) to this peptide
+ MatchFileReader& file, ///< file to read from
+ Database* database, ///< database containing proteins
+ Database* decoy_database ///< database containing decoy proteins
+) {
+
+ if( peptide == NULL ){
+ carp(CARP_ERROR, "Cannot parse peptide src with NULL peptide.");
+ return false;
+ }
+
+ carp(CARP_DETAILED_DEBUG,"Parsing id line:%s",
+ file.getString(PROTEIN_ID_COL).c_str());
+
+ //if the protein id field is empty, then we have to search the database...
+ if (file.empty(PROTEIN_ID_COL)) {
+ carp_once(CARP_WARNING, "empty protein id string in tab delimited file. "
+ "searching database to find proteins to match peptide "
+ "sequence");
+
+ //if we haven't done this already, build a map of sequence strings to peptide
+ //objects.
+ if (sequence_to_peptide_.empty()) {
+ fillPeptides(database, decoy_database);
+ }
+
+ string seq_string(peptide->getModifiedSequenceWithSymbols());
+
+ if (sequence_to_peptide_.find(seq_string) == sequence_to_peptide_.end()) {
+ carp(CARP_WARNING, "Cannot find peptide in database!");
+ return false;
+ }
+ Peptide* src_peptide = sequence_to_peptide_[seq_string];
+ vector<PeptideSrc*>& src_peptide_srcs = src_peptide->getPeptideSrcVector();
+
+ for (vector<PeptideSrc*>::iterator iter = src_peptide_srcs.begin();
+ iter != src_peptide_srcs.end();
+ ++iter) {
+ PeptideSrc* new_src = *iter;
+ peptide->addPeptideSrc(new_src);
+ }
+ return true;
+ } else {
+ vector<string> protein_ids = StringUtils::Split(file.getString(PROTEIN_ID_COL), ',');
+
+ if (protein_ids.size() == 0) {
+ carp(CARP_ERROR, "No protein ids found!");
+ return false;
+ }
+
+ vector<string> flanking_aas = StringUtils::Split(file.getString(FLANKING_AA_COL), ',');
+
+ if (protein_ids.size() != flanking_aas.size()) {
+ carp_once(CARP_DEBUG,
+ "Flanking amino acid count (%d) did not match protein count (%d) for protein %s.",
+ flanking_aas.size(),
+ protein_ids.size(),
+ file.getString(PROTEIN_ID_COL).c_str());
+ carp_once(CARP_DEBUG, "Only reporting error once; others may exist")
+ while(flanking_aas.size() < protein_ids.size()) {
+ flanking_aas.push_back("");
+ }
+ }
+
+ //For every protein id source, create the object and add it to the list.
+ for (size_t idx = 0; idx < protein_ids.size(); idx++) {
+ PeptideSrc* peptide_src = new PeptideSrc();
+ DIGEST_T digestion =
+ string_to_digest_type((char*)file.getString(CLEAVAGE_TYPE_COL).c_str());
+
+ Protein* parent_protein = NULL;
+ int start_index = 1;
+
+ string protein_id = protein_ids.at(idx);
+ string flanking_aa = flanking_aas.at(idx);
+ string prev_aa = "", next_aa = "";
+ if (flanking_aa.length() == 2) {
+ prev_aa = flanking_aa[0];
+ next_aa = flanking_aa[1];
+ }
+
+ carp(CARP_DETAILED_DEBUG,"Parsing %s", protein_id.c_str());
+ // get the protein and peptide index e.g. X(10)
+ size_t left_paren_index = protein_id.find('(');
+
+ if (left_paren_index == string::npos) {
+ //protein id is the string.
+ bool is_decoy;
+
+ parent_protein=MatchCollectionParser::getProtein(
+ database, decoy_database, protein_id, is_decoy);
+ if (parent_protein == NULL) {
+ carp(CARP_WARNING, "Can't find protein %s",protein_id.c_str());
+ continue;
+ }
+
+ //find the start index
+ MODIFIED_AA_T* mod_seq;
+ int seq_length = convert_to_mod_aa_seq(file.getString(SEQUENCE_COL).c_str(), &mod_seq);
+ char* unmodified_sequence = modified_aa_to_unmodified_string(mod_seq, seq_length);
+ string sequence = unmodified_sequence;
+ std::free(unmodified_sequence);
+ std::free(mod_seq);
+
+ start_index = parent_protein->findStart(sequence, prev_aa, next_aa);
+ if (start_index == -1) {
+ carp(CARP_FATAL, "Can't find sequence %s in %s:%s",
+ sequence.c_str(),
+ protein_id.c_str());
+ }
+ } else {
+ string protein_id_string = protein_id.substr(0, left_paren_index);
+ string peptide_start_index_string = protein_id.substr(left_paren_index+1,
+ protein_id.length() - left_paren_index - 2);
+ bool is_decoy;
+ // set fields in new peptide src
+ parent_protein = MatchCollectionParser::getProtein(
+ database, decoy_database, protein_id_string, is_decoy);
+
+ MODIFIED_AA_T* mod_seq;
+ int seq_length = convert_to_mod_aa_seq(file.getString(SEQUENCE_COL).c_str(), &mod_seq);
+ char* unmodified_sequence = modified_aa_to_unmodified_string(mod_seq, seq_length);
+ string sequence = unmodified_sequence;
+ std::free(unmodified_sequence);
+ std::free(mod_seq);
+
+
+ if (parent_protein -> isPostProcess()) {
+ // Attempting to store protein_id location in start_idx_original of peptide src [Please check
+ // if this is valid usage, since PMCDelimitedFileWriter uses startidxoriginal to print protein
+ // id location] so I am making an assumption that this is the purpose of start_idx_original.
+ // Also, I'm not sure if I need this for all proteins or just post process ones.
+ int peptide_start_index_int = StringUtils::FromString<int>(peptide_start_index_string);
+ peptide_src->setStartIdxOriginal(peptide_start_index_int);
+ }
+
+ //string sequence = file.getString(SEQUENCE_COL);
+ start_index = parent_protein->findStart(sequence, prev_aa, next_aa);
+ }
+
+ // set parent protein of the peptide src
+ peptide_src->setParentProtein(parent_protein);
+
+ // set digest type of peptide src
+ peptide_src->setDigest(digestion);
+
+ // set start index of peptide src
+ peptide_src->setStartIdx(start_index);
+
+ // add it to the list of protein sources for this peptide
+ peptide->addPeptideSrc(peptide_src);
+
+ }
+ } // next peptide_src in file
+
+ carp(CARP_DETAILED_DEBUG, "Done parsing id line:%s", file.getString(PROTEIN_ID_COL).c_str());
+
+ return true;
+}
+
+
+/**
+ * fills the sequence_to_peptide_ member variable for use in parseTabDelimited
+ * used when the tab delimited file doesn't provide a protein id, but we have
+ * sequences and access to the database.
+ */
+void PeptideSrc::fillPeptides(
+ Database* database, ///< the protein database
+ Database* decoy_database ///< the decoy database
+ ) {
+
+ PeptideConstraint* constraint = PeptideConstraint::newFromParameters();
+ PeptideIterator* iterator = new DatabasePeptideIterator(database, constraint, true, false);
+
+ while (iterator->hasNext()) {
+
+ Peptide* peptide = iterator->next();
+ const char* sequence = peptide->getSequence();
+ string sequence_string = string(sequence);
+
+ if (sequence_to_peptide_.find(sequence_string) == sequence_to_peptide_.end()) {
+ sequence_to_peptide_[sequence_string] = peptide;
+ }
+ }
+ delete iterator;
+ delete constraint;
+
+ //TODO - map the decoy sequences to Peptides if we need them in the future.
+ if (decoy_database == NULL) {
+ carp(CARP_INFO, "decoy database is null");
+ }
+}
+
+
+/**
+ * \brief Read in the peptide_src objects from the given file and
+ * assosiated them with the given peptide.
+ * Proteins for the pepitde_src are found in the given database. If
+ * database is NULL, does not set proteins. (This option is used for
+ * sorting index files while creating index.)
+ * \returns true if peptide_src's were successfully parsed, else
+ * returns false.
+ */
+bool PeptideSrc::parse(
+ Peptide* peptide, ///< assign peptide_src(s) to this peptide
+ FILE* file, ///< file to read from
+ Database* database) ///< database containing proteins
+{
+ if( peptide == NULL || file == NULL ){
+ carp(CARP_ERROR, "Cannot parse peptide src with NULL peptide or file.");
+ return false;
+ }
+
+ // first field in file should be number of src's
+ int num_peptide_src = -1;
+ size_t num_read = fread(&num_peptide_src, sizeof(int), 1, file);
+ if( num_peptide_src < 1 || num_read != 1 ){
+ carp(CARP_ERROR,
+ "Index file corrupted, peptide must have at least one peptide src");
+ return false;
+ }
+
+ // read in each peptide_src (prot index, peptide type, start index)
+ int src_idx = 0;
+ int protein_index = -1;
+ Protein* parent_protein = NULL;
+ DIGEST_T digestion;
+ int start_index = -1;
+ for(src_idx = 0; src_idx < num_peptide_src; src_idx++){
+
+ PeptideSrc* peptide_src = new PeptideSrc();
+
+ // get protein index
+ size_t num_read = fread(&protein_index, (sizeof(int)), 1, file);
+ if( protein_index < 0 || num_read != 1){
+ carp(CARP_ERROR, "Index file corrupted could not read protein index");
+ delete peptide_src;
+ return false;
+ }
+ carp(CARP_DETAILED_DEBUG, "Peptide src %d has protein idx %i",
+ src_idx, protein_index);
+
+ // read peptide type of peptide src
+ /*
+ if(fread(&peptide_type, sizeof(PEPTIDE_TYPE_T), 1, file) != 1){
+ carp(CARP_ERROR, "Index file corrupted, failed to read peptide type.");
+ free(peptide_src);
+ return false;
+ }
+ */
+
+ // read digestion level of peptide src
+ if(fread(&digestion, sizeof(DIGEST_T), 1, file) != 1){
+ carp(CARP_ERROR, "Index file corrupted, failed to read digestion type.");
+ delete peptide_src;
+ return false;
+ }
+
+ // read start index of peptide in parent protein of thsi peptide src
+ if(fread(&start_index, sizeof(int), 1, file) != 1){
+ carp(CARP_ERROR, "Index file corrupted, failed to read start index.");
+ delete peptide_src;
+ return false;
+ }
+
+ // set fields in new peptide src
+ parent_protein =
+ database->getProteinAtIdx(protein_index);
+
+ // set parent protein of the peptide src
+ peptide_src->setParentProtein(parent_protein);
+
+ // set peptide type of peptide src
+ // set_peptide_src_peptide_type(peptide_src, peptide_type);
+ peptide_src->setDigest(digestion);
+
+ // set start index of peptide src
+ peptide_src->setStartIdx(start_index);
+
+ peptide->addPeptideSrc(peptide_src);
+
+ }// next peptide_src in file
+
+ carp(CARP_DETAILED_DEBUG, "Finished parsing peptide src.");
+ return true;
+}
+
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/PeptideSrc.h b/src/model/PeptideSrc.h
new file mode 100644
index 0000000..e2dedee
--- /dev/null
+++ b/src/model/PeptideSrc.h
@@ -0,0 +1,189 @@
+/**
+ * \file PeptideSrch
+ * $Revision: 1.12 $
+ * \brief Object for mapping a peptide to it's parent protein.
+ */
+#ifndef PEPTIDE_SRC_H
+#define PEPTIDE_SRC_H
+#include <map>
+#include <stdio.h>
+#include <string>
+
+#include "util/utils.h"
+#include "util/mass.h"
+#include "model/objects.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+
+
+class PeptideSrc {
+
+ protected:
+ DIGEST_T digestion_; ///< how specific the ends are relative to the enzyme
+ Crux::Protein* parent_protein_; ///< the parent of this preptide
+
+ /*
+ * start_idx_ tracks the index of the peptide within the corresponding protein
+ * start_idx_original_ is for keeping track of the index of the peptide within
+ * the original protein, which we may not have the full sequence of
+ */
+ int start_idx_; ///< start index of the peptide in the protein sequence, first residue is 1
+ int start_idx_original_; ///< start index of the peptide in the original protein sequence
+ static std::map<std::string, Crux::Peptide* > sequence_to_peptide_; ///< Maps a sequence to a peptide object
+ static std::map<std::string, Crux::Peptide* > decoy_sequence_to_peptide_; ///< Maps a decoy sequence to a peptide object
+
+ /**
+ * \brief fills the sequence_to_peptide_ member variable for use in parseTabDelimited
+ * used when the tab delimited file doesn't provide a protein id, but we have
+ * sequences and access to the database.
+ */
+ static void fillPeptides(
+ Database* database, ///< the protein database
+ Database* decoy_database ///< the decoy database
+ );
+
+ public:
+
+ /**
+ * \returns An (empty) peptide_src object.
+ */
+ PeptideSrc();
+
+ /**
+ * \returns a PeptideSrc object, populated with user
+ * specified parameters
+ */
+ PeptideSrc(
+ DIGEST_T digest,
+ Crux::Protein* parent_protein, ///< the parent of this preptide -in
+ int start_idx ///< peptide start index in protein sequence, first is 1 -in
+ );
+
+ /**
+ * Frees the an individual allocated peptide_src object
+ */
+ virtual ~PeptideSrc();
+
+ /**
+ * Copies the entire vector of peptide_src object src to dest.
+ * dest must be a heap allocated peptide_src
+ */
+ static void copy(
+ std::vector<PeptideSrc*>& src, ///< source peptide_src -in
+ std::vector<PeptideSrc*>& dest ///< destination peptide_src -out
+ );
+
+ /**
+ * sets the level of digestion
+ */
+ void setDigest(
+ DIGEST_T digest ///< the type of the peptide -in
+ );
+
+ /**
+ * \returns the level of digestion
+ */
+ DIGEST_T getDigest();
+
+ /**
+ * sets the parent protein
+ */
+ void setParentProtein(
+ Crux::Protein* parent_protein ///< the parent of this preptide -in
+ );
+
+ /**
+ * \returns a pointer to the parent protein
+ */
+ Crux::Protein* getParentProtein();
+
+ /**
+ * sets the start index of the peptide in the protein sequence
+ */
+ void setStartIdx(
+ int start_idx ///< start index of the peptide in the protein sequence -in
+ );
+
+ /**
+ * \returns the start index of the peptide in the protein sequence
+ */
+ int getStartIdx();
+
+ /**
+ * sets the original start index of the peptide in the protein sequence
+ */
+ void setStartIdxOriginal(
+ int start_idx ///< start index of the peptide in the original protein sequence -in
+ );
+
+ /**
+ * \returns the original start index of the peptide in the protein sequence
+ */
+ int getStartIdxOriginal();
+
+ /**
+ * \returns a pointer to the start of the peptide with in it's parent protein sequence
+ */
+ char* getSequencePointer();
+
+ /**
+ *\returns the peptide_src strct size, value of sizeof function
+ */
+ static int getSizeOf(void);
+
+ /**
+ * serialize peptide src in binary
+ */
+ void serialize(
+ FILE* file ///< output file -in
+ );
+
+ /**
+ * Return the number of bytes taken up by one peptide_src when
+ * serialized to file. Used for skipping past peptide_src in an index
+ * file.
+ */
+ static int sizeOfSerialized();
+
+ /**
+ * \brief Read in the peptide_src objects from the given file and
+ * assosiated them with the given peptide.
+ * Proteins for the pepitde_src are found in the given database. If
+ * database is NULL, does not set proteins. (This option is used for
+ * sorting index files while creating index.)
+ *
+ * \returns true if peptide_src's were successfully parsed, else
+ * returns false.
+ */
+ static bool parseTabDelimited(
+ Crux::Peptide* peptide, ///< assign peptide_src(s) to this peptide
+ MatchFileReader& file, ///< file to read from
+ Database* database, ///< database containing proteins
+ Database* decoy_database = NULL ///< optional database with decoy proteins
+ );
+
+ /**
+ * \brief Read in the peptide_src objects from the given file and
+ * assosiated them with the given peptide.
+ *
+ * Proteins for the pepitde_src are found in the given database. If
+ * database is NULL, does not set proteins. (This option used for
+ * sorting index files while creating index.)
+ *
+ * \returns true if peptide_src's were successfully parsed, else
+ * returns false and sets peptide's peptide_src member variable to
+ * NULL.
+ */
+ static bool parse(
+ Crux::Peptide* peptide, ///< assign peptide_src(s) to this peptide
+ FILE* file, ///< file to read from
+ Database* database); ///< database containing proteins
+
+};
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/PostProcessProtein.cpp b/src/model/PostProcessProtein.cpp
new file mode 100644
index 0000000..a0986ba
--- /dev/null
+++ b/src/model/PostProcessProtein.cpp
@@ -0,0 +1,142 @@
+/**
+ * \file PostProcessProtein.cpp
+ * AUTHOR : Sean McIlwain
+ * $Revision: 1.00 $
+ * \brief Object for representing a protein that doesn't exist within the database
+ */
+
+#include "PostProcessProtein.h"
+#include <iostream>
+
+using namespace std;
+
+
+/**
+ * Default constructor
+ */
+PostProcessProtein::PostProcessProtein() : Protein() {
+}
+
+/**
+ * Default destructor
+ */
+PostProcessProtein::~PostProcessProtein() {
+}
+
+
+/**
+ * \returns the index of the sequence in the sequences_ vector and
+ * returns the index. If sequence is not found, then add to the
+ * list of sequences and return the last index
+ */
+int PostProcessProtein::findStart(
+ string sequence, ///< the sequence to find
+ string prev_aa, ///< the previous aa of the sequence
+ string next_aa ///< the next aa of the sequence
+ ) {
+
+ int ans = -1;
+
+ for (int idx = 0; idx < sequences_.size();idx++) {
+
+ if (sequences_[idx] == sequence) {
+ ans = idx+1;
+ break;
+ }
+ }
+
+ if (ans == -1) {
+ sequences_.push_back(sequence);
+ prev_aas_.push_back(prev_aa);
+ next_aas_.push_back(next_aa);
+ ans = sequences_.size();
+ }
+
+ return ans;
+
+}
+
+/**
+ * \returns the ith sequence
+ */
+char* PostProcessProtein::getSequence(
+ int offset ///< The offset (or sequence index) for the sequence
+ ) {
+
+ char* ans = my_copy_string(sequences_[offset].c_str());
+
+ return ans;
+}
+
+/**
+ * \returns the ith sequence pointer
+ */
+char* PostProcessProtein::getSequencePointer(
+ int offset ///< The offset (or sequence index) for the sequence
+ ) {
+ return (char*)(sequences_[offset].c_str());
+
+}
+
+char PostProcessProtein::getNTermFlankingAA(
+ int offset ///< The offset (or sequence index) for the flanking AA
+ ) {
+
+ char ans = '-';
+
+ if ((offset >= prev_aas_.size()) || (prev_aas_.at(offset).length() == 0)) {
+ carp_once(CARP_WARNING, "Missing nterm flanking for protein:%s offset:%d",
+ getIdPointer().c_str(), offset);
+ } else {
+ ans = prev_aas_.at(offset)[0];
+ }
+ carp(CARP_DETAILED_DEBUG, "protein:%s offset:%d pflank:%c(%d)",
+ getIdPointer().c_str(), offset, ans,(int)ans);
+
+ return ans;
+}
+
+char PostProcessProtein::getCTermFlankingAA(
+ int offset ///< The offset (or sequence index) for the flanking AA
+ ) {
+
+ char ans = next_aas_.at(offset)[0];
+ if (ans == '\0') {
+ carp_once(CARP_WARNING, "Missing cterm flanking aa for protein:%s offset:%d",getIdPointer().c_str(), offset);
+ ans = 'X';
+ }
+ carp(CARP_DETAILED_DEBUG, "protein:%s offset:%d nflank:%c(%d)", getIdPointer().c_str(), offset, ans,(int)ans);
+
+ return ans;
+}
+
+/**
+ * \returns true indicating that this is a PostProcessProtein object
+ */
+bool PostProcessProtein::isPostProcess() {
+
+ return true;
+}
+
+/**
+ * ends the program since we can't get the protein length from this
+ * post process protein object
+ */
+unsigned int PostProcessProtein::getLength() {
+
+ if (sequence_ == NULL) {
+ carp_once(CARP_WARNING, "Need protein sequence in order to calculate protein length.\n"
+ " Please provide protein fasta or index using the protein-database parameter\n"
+ " Protein %s doesn't have the full sequence", getIdPointer().c_str());
+
+ return 0;
+ }
+
+ return length_;
+
+}
+
+Database* PostProcessProtein::getDatabase() {
+ return NULL;
+}
+
diff --git a/src/model/PostProcessProtein.h b/src/model/PostProcessProtein.h
new file mode 100644
index 0000000..2d921b5
--- /dev/null
+++ b/src/model/PostProcessProtein.h
@@ -0,0 +1,105 @@
+/**
+ * \file PostProcessProtein.h
+ * AUTHOR : Sean McIlwain
+ * $Revision: 1.00 $
+ * \brief Object for representing a protein that doesn't exist within the database
+ */
+#ifndef POSTPROCESSPROTEIN_H_
+#define POSTPROCESSPROTEIN_H_
+
+#include "Protein.h"
+
+/**
+ * There are cases where the protein database will not be available for the post-process
+ * routines. This class acts as a way to get around that problem. The main difficulty is
+ * that the Peptide object relies on the PeptideSrc object to print out the sequence.
+ * This PeptideSrc object contains a Protein object and the start index of the
+ * peptide's sequence within this protein. Parsing the search results files post-process
+ * without the database, only has the peptide sequence and the protein ids that the peptide
+ * came from. PostProcessProtein keeps track of the peptides associated with a protein by
+ * maintaining a vector. findStart returns the index of the peptide in the vector. If
+ * the peptide doesn't exist in the vector, than findStart will add the peptide to the vector
+ * and return the index.
+ * getSequence and getSequencePointer to return the correct peptide sequence
+ * by using the offset parameter. This way we can still use the Peptide and PeptideSrc objects
+ * together to print out the peptide sequence and the proteins associated with that sequence
+ */
+
+/**
+ * TODO: support the flanking amino acids so that peptide->getFlankingAAs() works correctly.
+ */
+class PostProcessProtein : public Crux::Protein {
+
+ std::vector<std::string> sequences_; ///< sequences that we have seen so far.
+ std::vector<std::string> prev_aas_; ///< previous amino acid to the sequence
+ std::vector<std::string> next_aas_; ///< next amino acid to the sequence
+
+ public:
+
+
+ /**
+ * Default constructor
+ */
+ PostProcessProtein();
+
+ /**
+ * Default destructor
+ */
+ virtual ~PostProcessProtein();
+
+ /**
+ * \returns the index of the sequence in the sequences_ vector and
+ * returns the index. If sequence is not found, then add to the
+ * list of sequences and return the last index
+ */
+ virtual int findStart(
+ std::string sequence, ///< the sequence to find
+ std::string prev_aa, ///< the previous aa of the sequence
+ std::string next_aa ///< the next aa of the sequence
+ );
+
+ /**
+ * \returns the ith sequence
+ */
+ virtual char* getSequence(
+ int offset=0 ///< The offset (or sequence index) for the sequence
+ );
+
+ /**
+ * \returns the ith sequence pointer
+ */
+ virtual char* getSequencePointer(
+ int offset=0 ///< The offset (or sequence index) for the sequence
+ );
+
+ char getNTermFlankingAA(
+ int offset=0 ///< The offset (or sequence index) for the AA
+ );
+
+ char getCTermFlankingAA(
+ int offset=0 ///< The offset (or sequence index) for the AA
+ );
+
+ /**
+ * \returns true indicating that this is a PostProcessProtein object
+ */
+ virtual bool isPostProcess();
+
+ /**
+ * ends the program since we can't get the protein length from this
+ * post process protein object
+ */
+ virtual unsigned int getLength();
+
+ virtual Database* getDatabase();
+
+};
+
+
+#endif
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/Protein.cpp b/src/model/Protein.cpp
new file mode 100644
index 0000000..3c89b87
--- /dev/null
+++ b/src/model/Protein.cpp
@@ -0,0 +1,940 @@
+/*************************************************************************//**
+ * \file protein.cpp
+ * \brief Object for representing a single protein.
+ ****************************************************************************/
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <string.h>
+#include <ctype.h>
+#include <vector>
+#include "util/Params.h"
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "parameter.h"
+#include "util/GlobalParams.h"
+#include "Peptide.h"
+#include "Protein.h"
+#include "PeptideSrc.h"
+#include "Database.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+#include "ProteinPeptideIterator.h"
+
+using namespace std;
+using namespace Crux;
+/**
+ * Constants
+ */
+static const int PROTEIN_ID_LENGTH = 100;
+static const int PROTEIN_SEQUENCE_LENGTH = 40000;
+static const int PROTEIN_ANNOTATION_LENGTH = 100;
+static const int LONGEST_LINE = PROTEIN_ID_LENGTH + PROTEIN_ID_LENGTH;
+static const int FASTA_LINE = 50;
+static const int SMALLEST_MASS = 57;
+static const int LARGEST_MASS = 190;
+
+/**
+ * Set member variables to default values.
+ */
+void Protein::init() {
+ database_ = NULL;
+ offset_ = 0;
+ protein_idx_ = 0;
+ is_light_ = false;
+ is_memmap_ = false;
+ id_.clear();
+ sequence_ = NULL;
+ length_ = 0;
+ annotation_.clear();
+}
+
+/**
+ * \returns An (empty) protein object.
+ */
+Protein::Protein() {
+ init();
+}
+
+/**
+ * \returns A new protein object(heavy).
+ * The protein is does not constain a database, users must provide one.
+ */
+Protein::Protein(
+ const char* id, ///< The protein sequence id. -in
+ const char* sequence, ///< The protein sequence. -in
+ unsigned int length, ///< The length of the protein sequence. -in
+ const char* annotation, ///< Optional protein annotation. -in
+ unsigned long int offset,
+ ///< The file location in the source file in the database -in
+ unsigned int protein_idx, ///< The index of the protein in it's database.-in
+ Database* database ///< the database of its origin
+ )
+{
+ init();
+ setId(id);
+ setSequence(sequence);
+ setLength(length);
+ setAnnotation(annotation);
+ setOffset(offset);
+ setProteinIdx(protein_idx);
+ setIsLight(false);
+ database_ = Database::copyPtr(database);
+ is_memmap_ = false;
+}
+
+
+
+
+/**
+ * \returns A new light protein object.
+ */
+Protein* Protein::newLightProtein(
+ unsigned long int offset,
+ ///< The file location in the source file in the database -in
+ unsigned int protein_idx ///< The index of the protein in it's database. -in
+ )
+{
+ Protein* protein = new Protein();
+ protein->setIsLight(true);
+ protein->setOffset(offset);
+ protein->setProteinIdx(protein_idx);
+ return protein;
+}
+
+
+/**
+ * convert light protein to heavy, by parsing all the sequence from fasta file
+ * \returns TRUE if successfully converts the protein to heavy
+ */
+bool Protein::toHeavy()
+{
+ // protein already heavy
+ if(!is_light_){
+ return true;
+ }
+
+ FILE* file = database_->getFile();
+
+ // rewind to the begining of the protein to include ">" line
+ fseek(file, offset_, SEEK_SET);
+
+ // failed to parse the protein from fasta file
+ // protein offset is set in the parse_protein_fasta_file method
+ if(!parseProteinFastaFile(file)){
+ carp(CARP_ERROR,
+ "failed convert protein to heavy, cannot parse fasta file");
+ return false;
+ }
+
+ is_light_ = false;
+
+ return true;
+}
+
+/**
+ * covert heavy protein back to light
+ * \returns TRUE if successfully converts the protein to light
+ */
+bool Protein::toLight()
+{
+ // protein already light
+ if(is_light_){
+ return true;
+ }
+ // free all char* in protein object
+ free(sequence_);
+ sequence_ = NULL;
+ annotation_.clear();
+ id_.clear();
+ return (is_light_ = true);
+}
+
+/**
+ * Frees an allocated protein object.
+ */
+Protein::~Protein()
+{
+ // FIXME what is the point of checking this?
+ if(!is_memmap_ && !is_light_){
+ if (sequence_ != NULL){
+ free(sequence_);
+ }
+ }
+}
+
+/**
+ * Prints a protein object to file.
+ * if light protein coverts it to heavy protein
+ */
+void Protein::print(
+ FILE* file ///< output stream -out
+ )
+{
+ // covnert to heavy protein
+ if(is_light_){
+ toHeavy();
+ }
+ int sequence_index;
+ int sequence_length = getLength();
+ char* sequence = getSequence();
+ string& id = getIdPointer();
+ string annotation = getAnnotation();
+
+ fprintf(file, ">%s %s\n", id.c_str(), annotation.c_str());
+
+ sequence_index = 0;
+ while (sequence_length - sequence_index > FASTA_LINE) {
+ fprintf(file, "%.*s\n", FASTA_LINE, &(sequence[sequence_index]));
+ sequence_index += FASTA_LINE;
+ }
+ fprintf(file, "%s\n\n", &(sequence[sequence_index]));
+
+ free(sequence);
+}
+
+/**
+ * \returns the starting location of the sequence in a protein. If not found, returns -1
+ */
+int Protein::findStart(
+ string peptide_sequence, ///< the sequence to find
+ string prev_aa, ///< the previous amino acid for the sequence
+ string next_aa ///< the next amino acid for the sequence
+ ) {
+
+ if (getSequencePointer() == NULL) {
+ return -1;
+ }
+
+ if (prev_aa == "-") {
+ return 1;
+ } else if (next_aa == "-") {
+ return getLength() - peptide_sequence.length();
+ } else {
+ //use the flanking amino acids to further constrain our search in the sequence
+ size_t pos = string::npos;
+ string seq = prev_aa + peptide_sequence + next_aa;
+ string protein_seq = getSequencePointer();
+ pos = protein_seq.find(seq);
+ if (pos == string::npos) {
+ carp(CARP_DEBUG, "could not find %s in protein %s\n%s", seq.c_str(), getIdPointer().c_str(), protein_seq.c_str());
+ //finding the sequence with the flanks failed, try finding without the flanks.
+ seq = peptide_sequence;
+ pos = protein_seq.find(seq);
+ if (pos == string::npos) {
+ carp(CARP_ERROR, "could not %s in protein %s\n%s", seq.c_str(), getIdPointer().c_str(), protein_seq.c_str());
+ return -1;
+ }
+ return (pos+1);
+ }
+ return (pos+2);
+ }
+
+}
+
+bool Protein::isPostProcess() {
+
+ return false;
+
+}
+
+/**
+ * prints a binary representation of the protein
+ *
+ * FORMAT (no line break)
+ * <int: id length><char: id><int: annotation length>
+ <char: annotation><int: sequence length><char: sequence>
+ *
+ * Make sure when reading the binary data, add one to the length so
+ * that it will read in the terminating char as well.
+ */
+void Protein::serialize(
+ FILE* file ///< output stream -out
+ )
+{
+ // covnert to heavy protein
+ if(is_light_){
+ toHeavy();
+ }
+
+ int id_length = id_.length();
+ int annotation_length = annotation_.length();
+
+ // write the protein id length
+ fwrite(&id_length, sizeof(int), 1, file);
+
+ // write the protein id
+ // include "/0"
+ fwrite(id_.c_str(), sizeof(char), id_length+1, file);
+
+ // write the protein annotation length
+ fwrite(&annotation_length, sizeof(int), 1, file);
+
+ // write the protein annotation
+ // include "/0"
+ fwrite(annotation_.c_str(), sizeof(char), annotation_length+1, file);
+
+ // write the protein sequence length
+ fwrite(&length_, sizeof(unsigned int), 1, file);
+
+ // write the protein sequence
+ // include "/0"
+ fwrite(sequence_, sizeof(char), length_+1, file);
+}
+
+
+/**
+ * Copies protein object src to dest.
+ * assumes that the protein is heavy
+ * dest must be a heap allocated object
+ */
+void Protein::copy(
+ Protein* src,///< protein to copy -in
+ Protein* dest ///< protein to copy to -out
+ )
+{
+ char* sequence = src->getSequence();
+
+ dest->setId(src->getIdPointer());
+ dest->setSequence(sequence);
+ dest->setLength(src->getLength());
+ dest->setAnnotation(src->getAnnotationPointer());
+ dest->setOffset(src->offset_);
+ dest->setProteinIdx(src->protein_idx_);
+ dest->setIsLight(src->is_light_);
+ dest->database_ = src->database_;
+
+ free(sequence);
+}
+
+
+/**
+ * Parses a protein from an memory mapped binary fasta file
+ * the protein_idx field of the protein must be added before or after
+ * you parse the protein
+ * protein must be a heap allocated
+ *
+ * Assume memmap pointer is set at beginning of protein
+ * Assume protein binary format (no line break)
+ * <int: id length><char: id><int: annotation length>
+ <char: annotation><int: sequence length><char: sequence>
+ *
+ * modifies the *memmap pointer!
+ * \returns TRUE if success. FALSE is failure.
+ */
+bool Protein::parseProteinBinaryMemmap(
+ char** memmap
+ ///< a pointer to a pointer to the memory mapped binary fasta file -in
+ )
+{
+ int id_length = 0;
+ int annotation_length = 0;
+ int sequence_length = 0;
+
+ /* FIXME, maybe use this to check if still within file
+ if(*memmap_as_char[0] == EOF){
+ carp(CARP_ERROR, "end of file");
+ }
+ */
+
+ /***set protein ID***/
+
+ // read id length
+ id_length = *((int *) *memmap);
+
+ // reset pointer to start of id
+ *memmap += sizeof(int);
+
+ // set protein id to mem mapped id
+ id_ = *memmap;
+
+ // reset pointer to move to annotation_length
+ *memmap += (id_length + 1);
+
+
+ /***set protein annotation***/
+
+ // read annotation length
+ annotation_length = *((int *) *memmap);
+
+ // reset pointer to start of annotation
+ *memmap += sizeof(int);
+
+ // set protein annotation to mem mapped annotation
+ annotation_ = *memmap;
+
+ // reset pointer to move to sequence_length
+ *memmap += (annotation_length + 1);
+
+
+ /***set protein sequence***/
+
+ // read sequence length
+ sequence_length = *((int *) *memmap);
+ length_ = sequence_length;
+
+ // reset pointer to start of sequence
+ *memmap += sizeof(int);
+
+ // set protein annotation to mem mapped sequence
+ sequence_ = *memmap;
+
+ // reset pointer to move to start of next protein
+ *memmap += (sequence_length + 1);
+
+ // now this protein has been created from memory mapped!
+ is_memmap_ = true;
+
+ return true;
+}
+
+// FIXME ID line and annotation might need to be fixed
+VERBOSE_T verbosity = NORMAL_VERBOSE;
+/**
+ * Parses a protein from an open (FASTA) file.
+ * the protein_idx field of the protein must be added before or after
+ * you parse the protein
+ * \returns TRUE if success. FALSE is failure.
+ * protein must be a heap allocated
+ */
+bool Protein::parseProteinFastaFile(
+ FILE* file ///< fasta file -in
+ )
+{
+ static char name[LONGEST_LINE]; ///< Just the sequence ID.
+ static char desc[LONGEST_LINE]; ///< Just the comment field.
+ static char buffer[PROTEIN_SEQUENCE_LENGTH];///> The sequence to read in.
+ static unsigned int sequence_length; // the sequence length
+
+ // Read the title line.
+ if (!readTitleLine(file, name, desc)) {
+ return(false);
+ }
+
+ buffer[0] = '\0';
+
+ // Read the sequence.
+ if (!readRawSequence(file, name, PROTEIN_SEQUENCE_LENGTH, buffer, &sequence_length)) {
+ carp(CARP_FATAL, "Sequence %s is too long.\n", name);
+ exit(1);
+ }
+
+ // update the protein object.
+ setLength(sequence_length);
+ setId(name);
+ setSequence(buffer);
+ setAnnotation(desc);
+
+ return(true);
+
+}
+
+/**************************************************/
+
+/**
+ * FASTA file parsing code
+ * AUTHOR: William Stafford Noble
+ * modified by Chris Park
+ */
+
+/**
+ * Find the beginning of the next sequence, and read the sequence ID
+ * and the comment.
+ */
+bool Protein::readTitleLine
+(FILE* fasta_file, ///< file to read -in
+ char* name, ///< write protein name here -out
+ char* description) ///< write description here -out
+{
+ static char id_line[LONGEST_LINE]; // Line containing the ID and comment.
+ int a_char; // The most recently read character.
+
+ // Read until the first occurrence of ">".
+ while ((a_char = getc(fasta_file)) != '>') {
+ // If we hit the end of the file, return FALSE.
+ if (a_char == EOF) {
+ return(false);
+ }
+ }
+ // set protein offset FIXME: might not need to "-1" -CHRIS
+ offset_ = ftell(fasta_file) - 1;
+
+ /**
+ * chris edited, added this block to make sure all of comment line
+ * is read although might not be stored, to ensure the file* is at
+ * start of the sequence
+ */
+
+ {
+ char* new_line = NULL;
+ int line_length;
+ size_t buf_length = 0;
+
+ if((line_length = getline(&new_line, &buf_length, fasta_file)) == -1){
+ carp(CARP_FATAL, "Error reading Fasta file.\n");
+ }
+ strncpy(id_line, new_line, LONGEST_LINE-1);
+ free(new_line);
+ }
+
+ // Remove EOL.
+ id_line[strlen(id_line) - 1] = '\0';
+
+ // Extract the ID from the beginning of the line.
+ if (sscanf(id_line, "%s", name) != 1) {
+ carp(CARP_FATAL, "Error reading sequence ID.\n%s\n", id_line);
+ }
+
+ // Store the rest of the line as the comment.
+ strcpy(description, &(id_line[strlen(name)+1]));
+
+ return(true);
+}
+
+
+/****************************************************************************
+ * Read raw sequence until a '>' is encountered or too many letters
+ * are read. The new sequence is appended to the end of the given
+ * sequence.
+ *
+ * Return: Was the sequence read completely?
+ ****************************************************************************/
+bool Protein::readRawSequence
+ (FILE* fasta_file, // Input Fasta file.
+ char* name, // Sequence ID (used in error messages).
+ unsigned int max_chars, // Maximum number of allowed characters.
+ char* raw_sequence, // Pre-allocated sequence.
+ unsigned int* sequence_length // the sequence length -chris added
+ )
+{
+ int a_char;
+ unsigned int i_seq;
+ bool return_value = true;
+
+ // Start at the end of the given sequence.
+ i_seq = strlen(raw_sequence);
+ assert((unsigned int)strlen(raw_sequence) < max_chars);
+
+ // Read character by character.
+ while ((a_char = getc(fasta_file)) != EOF) {
+
+ // Check for the beginning of the next sequence.
+ if (a_char == '>') {
+ // Put the ">" back onto the stream for the next call to find.
+ ungetc(a_char, fasta_file);
+ break;
+ }
+
+ // Skip non-alphabetic characters.
+ if (!isalpha((int)a_char)) {
+ if ((a_char != ' ') && (a_char != '\t') && (a_char != '\n') && (a_char != '\r')) {
+ carp(CARP_WARNING,"Skipping character %c in sequence %s.",
+ a_char, name);
+ }
+
+ } else {
+
+ // Convert invalid characters to X.
+ a_char = toupper((int)a_char);
+
+ /**
+ * Check the ASCII code. If the char is above or below the
+ * A(65)~Z(90)range, convert the character to an 'X'.
+ */
+ if ( (int)a_char < 65 || (int)a_char > 90 ) {
+ carp(CARP_WARNING, "Converting illegal character %c to X ",
+ a_char);
+ carp(CARP_WARNING, "in sequence %s.", name);
+ a_char = 'X';
+ }
+
+ raw_sequence[i_seq] = a_char;
+ i_seq++;
+ }
+ if (i_seq >= max_chars) {
+ return_value = false;
+ break;
+ }
+ }
+ raw_sequence[i_seq] = '\0';
+ *sequence_length = i_seq; // chris added
+
+ return(return_value);
+}
+
+
+/**
+ * end of FASTA parsing
+ * Thanks Bill!
+ */
+
+/**
+ * Change the sequence of a protein to be a randomized version of
+ * itself. The method of randomization is dependent on the
+ * decoy_type (shuffle or reverse). The name of the protein is also
+ * changed by prefixing with "decoy-prefix"
+ */
+void Protein::shuffle(
+ DECOY_TYPE_T decoy_type){ ///< method for shuffling
+ char* decoy_str = decoy_type_to_string(decoy_type);
+ carp(CARP_DEBUG, "Shuffling protein %s as %s",
+ id_.c_str(), decoy_str);
+ free(decoy_str);
+
+ switch(decoy_type){
+ case NO_DECOYS:
+ return;
+
+ case PROTEIN_REVERSE_DECOYS:
+ reverse(sequence_, sequence_ + strlen(sequence_));
+ break;
+
+ case PROTEIN_SHUFFLE_DECOYS:
+ carp(CARP_DEBUG, "shuffling");
+ shuffle_array(sequence_, strlen(sequence_));
+ break;
+
+ case PEPTIDE_SHUFFLE_DECOYS:
+ peptideShuffleSequence();
+ break;
+
+ case INVALID_DECOY_TYPE:
+ case NUMBER_DECOY_TYPES:
+ carp(CARP_FATAL, "Illegal decoy type for shuffling protein.");
+ break;
+ }
+
+ // change the protein name
+ string prefix = Params::GetString("decoy-prefix");
+ id_ = prefix + id_;
+}
+
+/**
+ * Access routines of the form get_<object>_<field> and set_<object>_<field>.
+ */
+
+/**
+ * Additional get and set methods
+ */
+
+/**
+ *\returns the id of the protein
+ * returns a heap allocated new copy of the id
+ * user must free the return id
+ * assumes that the protein is heavy
+ */
+string Protein::getId()
+{
+
+ if(is_light_){
+ carp(CARP_FATAL, "Cannot get ID from light protein.");
+ }
+
+ return id_;
+
+}
+
+/**
+ *\returns a pointer to the id of the protein
+ * assumes that the protein is heavy
+ */
+string& Protein::getIdPointer()
+{
+ if(is_light_){
+ carp(CARP_FATAL, "Cannot get ID pointer from light protein.");
+ }
+ return id_;
+}
+
+/**
+ * sets the id of the protein
+ */
+void Protein::setId(
+ const string& id ///< the sequence to add -in
+ )
+{
+ id_ = id;
+}
+
+/**
+ *\returns the sequence of the protein
+ * returns a heap allocated new copy of the sequence
+ * user must free the return sequence
+ * assumes that the protein is heavy
+ */
+char* Protein::getSequence(
+ int offset
+) {
+ if(is_light_){
+ carp(CARP_FATAL, "Cannot get sequence from light protein.");
+ }
+ unsigned int sequence_length = strlen(sequence_) +1-offset; // +\0
+ char * copy_sequence =
+ (char *)mymalloc(sizeof(char)*sequence_length);
+ return strncpy(copy_sequence, sequence_+offset, sequence_length);
+}
+
+/**
+ *\returns a pointer to the sequence of the protein
+ * assumes that the protein is heavy
+ */
+char* Protein::getSequencePointer(
+ int offset
+)
+{
+ if(is_light_){
+ carp(CARP_FATAL, "Cannot get sequence pointer from light protein.");
+ }
+ return sequence_+offset;
+}
+
+/**
+ * sets the sequence of the protein
+ */
+void Protein::setSequence(
+ const char* sequence ///< the sequence to add -in
+ )
+{
+
+ free(sequence_);
+ unsigned int sequence_length = strlen(sequence) +1; // +\0
+ char * copy_sequence =
+ (char *)mymalloc(sizeof(char)*sequence_length);
+ sequence_ =
+ strncpy(copy_sequence, sequence, sequence_length);
+}
+
+/**
+ *\returns the length of the protein
+ * assumes that the protein is heavy
+ */
+unsigned int Protein::getLength()
+{
+ return length_;
+}
+
+/**
+ * sets the id of the protein
+ */
+void Protein::setLength(
+ unsigned int length ///< the length to add -in
+ )
+{
+ length_ = length;
+}
+
+/**
+ *\returns the annotation of the protein
+ * returns a heap allocated new copy of the annotation
+ * user must free the return annotation
+ * assumes that the protein is heavy
+ */
+string Protein::getAnnotation()
+{
+ if(is_light_){
+ carp(CARP_FATAL, "Cannot get annotation from light protein.");
+ }
+
+ return annotation_;
+}
+
+/**
+ *\returns A const pointer to the annotation of the protein.
+ */
+const string& Protein::getAnnotationPointer(){
+ return annotation_;
+}
+
+/**
+ * sets the annotation of the protein
+ */
+void Protein::setAnnotation(
+ const string& annotation ///< the sequence to add -in
+ )
+{
+ annotation_ = annotation;
+}
+
+/**
+ * sets the offset of the protein in the fasta file
+ */
+void Protein::setOffset(
+ unsigned long int offset
+ ///< The file location in the source file in the database -in
+ )
+{
+ offset_ = offset;
+}
+
+/**
+ *\returns the offset the protein
+ */
+unsigned long int Protein::getOffset()
+{
+ return offset_;
+}
+
+/**
+ * sets the protein_idx (if, idx=n, nth protein in the fasta file)
+ */
+void Protein::setProteinIdx(
+ unsigned int protein_idx ///< The index of the protein in it's database. -in
+ )
+{
+ // carp(CARP_DETAILED_DEBUG, "set protein idx = %i", protein_idx);
+ protein_idx_ = protein_idx;
+}
+
+/**
+ *\returns the protein_idx field
+ */
+unsigned int Protein::getProteinIdx()
+{
+ return protein_idx_;
+}
+
+/**
+ * sets the is_light field (is the protein a light protein?)
+ */
+void Protein::setIsLight(
+ bool is_light ///< is the protein a light protein? -in
+ )
+{
+ is_light_ = is_light;
+}
+
+/**
+ *\returns TRUE if the protein is light protein
+ */
+bool Protein::getIsLight()
+{
+ return is_light_;
+}
+
+/**
+ * sets the database for protein
+ */
+void Protein::setDatabase(
+ Database* database ///< Which database is this protein part of -in
+ )
+{
+ database_ = Database::copyPtr(database);
+}
+
+/**
+ *\returns Which database is this protein part of
+ */
+Database* Protein::getDatabase()
+{
+ return database_;
+}
+
+/**
+ * Comparison function for sorting proteins by protein id.
+ */
+bool Crux::protein_id_less_than(Protein* protein_one, Protein* protein_two){
+ int compare = protein_one->getIdPointer().compare(protein_two->getIdPointer());
+ return (compare > 0);
+}
+
+/**
+ * Rearrange the sequence_ between cleavage sites, keeping residues
+ * on either side of a cleavage in place. Get enzyme from
+ * parameters. Cases of NO_ENZYME or NON_SPECIFIC_DIGEST are the same
+ * as shuffling the whole protein. Same behavior for full and partial
+ * digest, min/max length/mass and missed cleavages, i.e. shuffle
+ * between every cleavage site.
+ */
+void Protein::peptideShuffleSequence(){
+ if( sequence_ == NULL ){
+ carp(CARP_WARNING, "Cannot shuffle a NULL sequence");
+ return;
+ }
+ if( length_ < 2 ){
+ return;
+ }
+
+ // get the digest rule
+ ENZYME_T enzyme = GlobalParams::getEnzyme();
+ // cases where peptide-shuffle is really protein shuffle
+ if( enzyme == NO_ENZYME
+ || GlobalParams::getDigestion() == NON_SPECIFIC_DIGEST){
+ this->shuffle(PROTEIN_SHUFFLE_DECOYS);
+ return;
+ }
+
+ // store valid cleavage locations
+ vector<int> cleave_after_here;
+
+ // traverse the sequence to penultimate residue
+ for(size_t seq_offset = 0; seq_offset < length_ - 1; seq_offset++){
+ // mark each valid location (mark x for cleavage between x and y)
+ if( ProteinPeptideIterator::validCleavagePosition(sequence_ + seq_offset,
+ enzyme) ){
+ cleave_after_here.push_back(seq_offset);
+ }
+ }
+
+ // shuffle between each cleavage site (leave a and b in place)
+ int start = 0; // shuffle between prot first residue and first site
+ int end = -1;
+ vector<int>::iterator next_position = cleave_after_here.begin();
+ for(; next_position != cleave_after_here.end(); ++next_position){
+ end = *next_position;
+ shuffleRegion(start, end);
+ start = end + 1; // hold in place both sides of the cleavage site
+ }
+
+ // shuffle end of sequence
+ end = length_ - 1;
+ if( start < end ){
+ shuffleRegion(start, end);
+ }
+}
+
+/**
+ * Shuffle the region of the sequence between start and end, leaving
+ * start and end residues in place. Repeat up to three times if the
+ * shuffled sequence doesn't change.
+ */
+void Protein::shuffleRegion(
+ int start, ///< index of peptide start
+ int end){///< index of last residue in peptide
+
+ int sub_seq_length = end - start - 1;
+ char* buf = new char[sub_seq_length + 1];
+ if( sub_seq_length > 1 ){
+ carp(CARP_DETAILED_DEBUG, "Shuffle from %d to %d.", start+1, end);
+
+ // store the sequence before shuffling not including the unmoved residues
+ strncpy(buf, sequence_ + start + 1, sub_seq_length);
+ buf[sub_seq_length] = '\0';
+
+ shuffle_array(sequence_ + start + 1, sub_seq_length);
+
+ // check to see if it changed
+ bool has_changed = strncmp(buf, sequence_ + start, sub_seq_length + 2);
+ // try reshuffling up to three more times
+ int count = 0;
+ while( (count < 3) && (has_changed == false)){
+ shuffle_array(sequence_ + start + 1, sub_seq_length);
+ has_changed = strncmp(buf, sequence_ + start, sub_seq_length + 2);
+ count++;
+ }
+ if( !has_changed ){
+ carp(CARP_WARNING, "Unable to generate a shuffled sequence "
+ "different than the original for sequence %s of protein %s "
+ "at position %d.", buf, id_.c_str(), start);
+ }
+ }
+ delete [] buf;
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/Protein.h b/src/model/Protein.h
new file mode 100644
index 0000000..6f3becc
--- /dev/null
+++ b/src/model/Protein.h
@@ -0,0 +1,347 @@
+/**
+ * \file Protein.h
+ * $Revision: 1.25 $
+ * \brief Object for representing one protein sequence.
+ *****************************************************************************/
+#ifndef CRUX_PROTEIN_H
+#define CRUX_PROTEIN_H
+
+#include <stdio.h>
+#include "util/utils.h"
+#include "model/objects.h"
+#include "Peptide.h"
+#include "PeptideSrc.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+
+namespace Crux {
+
+class Protein {
+ protected:
+ Database* database_; ///< Which database is this protein part of
+ unsigned long int offset_; ///< The file location in the database source file
+ unsigned int protein_idx_; ///< The index of the protein in it's database.
+ bool is_light_; ///< is the protein a light protein?
+ bool is_memmap_; ///< is the protein produced from memory mapped file
+ std::string id_; ///< The protein sequence id.
+ char* sequence_; ///< The protein sequence.
+ unsigned int length_; ///< The length of the protein sequence.
+ std::string annotation_; ///< Optional protein annotation.
+
+ /**
+ * Find the beginning of the next sequence, and read the sequence ID
+ * and the comment.
+ */
+ bool readTitleLine
+ (FILE* fasta_file,///< file to read
+ char* name, ///< put protein name here
+ char* description);///< put protein description here
+
+
+ /**
+ * Read raw sequence until a '>' is encountered or too many letters
+ * are read. The new sequence is appended to the end of the given
+ * sequence.
+ *
+ * Return: Was the sequence read completely?
+ **/
+ static bool readRawSequence
+ (FILE* fasta_file, // Input Fasta file.
+ char* name, // Sequence ID (used in error messages).
+ unsigned int max_chars, // Maximum number of allowed characters.
+ char* raw_sequence, // Pre-allocated sequence.
+ unsigned int* sequence_length // the sequence length -chris added
+ );
+
+ /**
+ * Rearrange the sequence_ between cleavage sites, keeping residues
+ * on either side of a cleavage in place. Get enzyme from
+ * parameters. Same behavior for full and partial digest, min/max
+ * length/mass and missed cleavages, i.e. shuffle between every
+ * cleavage site.
+ */
+ void peptideShuffleSequence();
+
+ /**
+ * Shuffle the region of the sequence between start and end, leaving
+ * start and end residues in place. Repeat up to three times if the
+ * shuffled sequence doesn't change.
+ */
+ void shuffleRegion(
+ int start, ///< index of peptide start
+ int end); ///< index of last residue in peptide
+
+ public:
+
+ /**
+ * Initialize member variables to default values.
+ */
+ void init();
+
+ /**
+ * \returns An (empty) protein object.
+ */
+ Protein();
+
+ /**
+ * \returns A new protein object(heavy).
+ */
+ Protein(
+ const char* id, ///< The protein sequence id.
+ const char* sequence, ///< The protein sequence.
+ unsigned int length, ///< The length of the protein sequence.
+ const char* annotation, ///< Optional protein annotation. -in
+ unsigned long int offset,
+ ///< The file location in the source file in the database -in
+ unsigned int protein_idx,///< The index of the protein in its database. -in
+ Database* database ///< the database of its origin
+ );
+
+ /**
+ * \returns A new light protein object.
+ */
+ static Protein* newLightProtein(
+ unsigned long int offset,
+ ///< The file location in the source file in the database -in
+ unsigned int protein_idx ///< The index of the protein in its database. -in
+ );
+
+ /**
+ * convert light protein to heavy, by parsing all the sequence from fasta file
+ * \returns TRUE if successfully converts the protein to heavy
+ */
+ bool toHeavy();
+
+ /**
+ * covert heavy protein back to light
+ * \returns TRUE if successfully converts the protein to light
+ */
+ bool toLight();
+
+ /**
+ * Frees an allocated protein object.
+ */
+
+ virtual ~Protein();
+
+ /**
+ * Prints a protein object to file.
+ */
+ void print(
+ FILE* file ///< output stream -out
+ );
+
+ /**
+ * Copies protein object src to dest.
+ * dest must be a heap allocated object
+ */
+ static void copy(
+ Protein* src,///< protein to copy -in
+ Protein* dest ///< protein to copy to -out
+ );
+
+ /**
+ * Parses a protein from an open (FASTA) file.
+ * \returns TRUE if success. FALSE is failure.
+ */
+ bool parseProteinFastaFile(
+ FILE* file ///< fasta file -in
+ );
+
+ /**
+ * Parses a protein from an memory mapped binary fasta file
+ * the protein_idx field of the protein must be added before or
+ * after you parse the protein.
+ * \returns TRUE if success. FALSE is failure.
+ * protein must be a heap allocated
+ *
+ * Assume memmap pointer is set at beginning of protein
+ * Assume protein binary format (no line break)
+ * <int: id length><char: id><int: annotation length>
+ <char: annotation><int: sequence length><char: sequence>
+ *
+ * modifies the *memmap pointer!
+ */
+ bool parseProteinBinaryMemmap(
+ char** memmap
+ ///< a pointer to a pointer to the memory mapped binary fasta file -in
+ );
+
+ /**
+ * Change the sequence of a protein to be a randomized version of
+ * itself. The method of randomization is dependent on the
+ * decoy_type (shuffle or reverse). The name of the protein is also
+ * changed by prefixing with "decoy-prefix"
+ */
+ void shuffle(DECOY_TYPE_T decoy_type);
+
+ /**
+ * Additional get and set methods
+ */
+
+ /**
+ *\returns the id of the protein
+ * returns a heap allocated new copy of the id
+ * user must free the return id
+ */
+ std::string getId();
+
+ /**
+ *\returns a pointer to the id of the protein
+ */
+ std::string& getIdPointer();
+
+ /**
+ * sets the id of the protein
+ */
+ void setId(
+ const std::string& id ///< the sequence to add -in
+ );
+
+ /**
+ *\returns the sequence of the protein
+ * returns a heap allocated new copy of the sequence
+ * user must free the return sequence
+ */
+ virtual char* getSequence(
+ int offset=0
+ );
+
+ /**
+ *\returns a pointer to the sequence of the protein
+ */
+ virtual char* getSequencePointer(
+ int offset=0
+ );
+
+ /**
+ * sets the sequence of the protein
+ */
+ void setSequence(
+ const char* sequence ///< the sequence to add -in
+ );
+
+ /**
+ *\returns the length of the protein
+ */
+ virtual unsigned int getLength();
+
+ /**
+ * sets the id of the protein
+ */
+ void setLength(
+ unsigned int length ///< the length to add -in
+ );
+
+ /**
+ *\returns the annotation of the protein
+ * returns a heap allocated new copy of the annotation
+ * user must free the return annotation
+ */
+ std::string getAnnotation();
+
+ /**
+ *\returns A const pointer to the annotation of the protein.
+ */
+ const std::string& getAnnotationPointer();
+
+ /**
+ * sets the annotation of the protein
+ */
+ void setAnnotation(
+ const std::string& annotation ///< the sequence to add -in
+ );
+
+
+ /**
+ * sets the offset of the protein in the fasta file
+ */
+ void setOffset(
+ unsigned long int offset
+ ///< The file location in the source file in the database -in
+ );
+
+ /**
+ *\returns the offset the protein
+ */
+ unsigned long int getOffset();
+
+ /**
+ * sets the protein_idx (if, idx=n, nth protein in the fasta file)
+ */
+ void setProteinIdx(
+ unsigned int protein_idx ///< The index of the protein in its database. -in
+ );
+
+ /**
+ *\returns the protein_idx field
+ */
+ unsigned int getProteinIdx();
+
+ /**
+ * sets the is_light field (is the protein a light protein?)
+ */
+ void setIsLight(
+ bool is_light ///< is the protein a light protein? -in
+ );
+
+ /**
+ *\returns TRUE if the protein is light protein
+ */
+ bool getIsLight();
+
+ /**
+ * sets the database for protein
+ */
+ void setDatabase(
+ Database* database ///< Which database is this protein part of -in
+ );
+
+ /**
+ *\returns Which database is this protein part of
+ */
+ virtual Database* getDatabase();
+
+ /**
+ * prints a binary representation of the protein
+ *
+ * FORMAT (no line break)
+ * <int: id length><char: id><int: annotation length>
+ <char: annotation><int: sequence length><char: sequence>
+ *
+ * make sure when rading the binary data, add one to the length so
+ * that it will read in the terminating char as well.
+ */
+ void serialize(
+ FILE* file ///< output stream -out
+ );
+
+ /**
+ * \returns the start index of the sequence in the protein
+ * tries to use the previous aa and next aa to refine where
+ * this sequence exits
+ */
+ virtual int findStart(
+ std::string sequence,
+ std::string prev_aa,
+ std::string next_aa
+ );
+
+ virtual bool isPostProcess();
+
+};
+
+/**
+ * Comparison function for sorting proteins by protein id.
+ */
+bool protein_id_less_than(Protein* protein_one, Protein* protein_two);
+
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/ProteinIndex.cpp b/src/model/ProteinIndex.cpp
new file mode 100644
index 0000000..475f87b
--- /dev/null
+++ b/src/model/ProteinIndex.cpp
@@ -0,0 +1,174 @@
+/*************************************************************************//**
+ * \file ProteinIndex.cpp
+ * \brief Object for creating a protein index or binary fasta file
+ ****************************************************************************/
+#include <stdio.h>
+#include <stdlib.h>
+#include <assert.h>
+#include <ctype.h>
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "Peptide.h"
+#include "Protein.h"
+#include "Database.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+#include "ProteinIndex.h"
+#include "util/WinCrux.h"
+
+
+/***************/
+
+/**
+ *
+ *\returns the file handler for the output file
+ */
+FILE* get_output_file(
+ char* fasta_file, ///< input fasta file -in
+ bool is_binary_file ///< Are we creating a binary fasta file?
+ )
+{
+ char* name = NULL;
+
+ // create a binary fasta file?
+ if(is_binary_file){
+ name = generate_name(fasta_file, "_binary_fasta", ".fasta", NULL);
+ }
+ else{// create a normal protein index file
+ name = generate_name(fasta_file, "_protein_index", ".fasta", NULL);
+ }
+
+ FILE* file = fopen(name, "wb");
+ free(name);
+ return file;
+}
+
+
+/**
+ * creates a protein index on to the output_file
+ * \returns true if successfully creates a protein index, else false
+ */
+bool ProteinIndex::create(
+ char* fasta_file ///< input fasta file -in
+ )
+{
+ unsigned long working_index;
+ FILE* file = NULL;
+ char* new_line = NULL;
+ int line_length;
+ size_t buf_length = 0;
+ unsigned int protein_idx = 0;
+ FILE* output_file = NULL;
+
+ // open file and
+ file = fopen(fasta_file, "rb");
+
+ // check if succesfully opened file
+ if(file == NULL){
+ carp(CARP_FATAL, "Failed to open fasta file '%s'", fasta_file);
+ return false;
+ }
+
+ // get output file
+ output_file = get_output_file(fasta_file, false);
+
+ // check if succesfully created file
+ if(output_file == NULL){
+ carp(CARP_ERROR, "Failed to create protein index file");
+ fclose(file);
+ return false;
+ }
+
+ working_index = ftell(file);
+ // check each line until reach '>' line
+ while((line_length = getline(&new_line, &buf_length, file)) != -1){
+ if(new_line[0] == '>'){
+ ++protein_idx;
+ fprintf(output_file, "* %d ",protein_idx);
+ fprintf(output_file, "%ld\n", working_index);
+ }
+ working_index = ftell(file);
+ }
+
+ free(new_line);
+ fclose(file);
+ fclose(output_file);
+
+ return true;
+}
+
+/***************************************************************
+ * FIXME, implement this if needed
+ *
+
+**
+ * \returns An (empty) protein_index object.
+ *
+PROTEIN_INDEX_T* allocate_protein_index(void);
+
+**
+ * creates a protein_index that contains the offset and protein index of the protein
+ * in the fasta file.
+ *\returns a new protein_index object
+ *
+PROTEIN_INDEX_T* new_protein_index(
+ unsigned long int offset, ///< The file location in the source file in the database
+ unsigned int protein_idx ///< The index of the protein in it's database.
+ );
+
+**
+ *
+ * free a protein index object
+ *
+void free_protein_index(
+ PROTEIN_INDEX_T* protein_index ///< the protein index to free
+ );
+
+*****************************************************************/
+
+/**
+ * input is the fasta file name which the protein index
+ * should have been created.
+ * or if creating binary fasta file, is that already on disk?
+ *
+ *\returns TRUE if protein index or binary fasta file is on disk, else false
+ */
+bool ProteinIndex::onDisk(
+ const char* fasta_file, ///< input fasta file -in
+ bool is_binary ///< are we looking for the binary fasta file? or preotein index
+ )
+{
+ char* name = NULL;
+
+ // create a binary fasa file?
+ if(is_binary){
+ name = generate_name(fasta_file, "_binary_fasta", ".fasta", NULL);
+ }
+ else{// create a normal protein index file
+ name = generate_name(fasta_file, "_protein_index", ".fasta", NULL);
+ }
+
+ // check if can open file
+ if(access(name, F_OK)){
+ free(name);
+ return false;
+ }
+
+ free(name);
+ return true;
+}
+
+/**
+ * protein index iterator
+ * the protein index iterator parses the protein index file
+ * for each protein index one by one and returns a new light protein.
+ */
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/ProteinIndex.h b/src/model/ProteinIndex.h
new file mode 100644
index 0000000..3df012b
--- /dev/null
+++ b/src/model/ProteinIndex.h
@@ -0,0 +1,75 @@
+/**
+ * \file ProteinIndex.h
+ * $Revision: 1.3 $
+ * \brief Object for creating a protein index
+ *****************************************************************************/
+#ifndef PROTEIN_INDEX_H
+#define PROTEIN_INDEX_H
+
+#include <stdio.h>
+#include "util/utils.h"
+#include "model/objects.h"
+#include "Peptide.h"
+#include "Protein.h"
+#include "io/carp.h"
+#include "PeptideConstraint.h"
+
+
+class ProteinIndex {
+ protected:
+ unsigned long int offset_; ///< The offset of the protein in the fasta file
+ unsigned int protein_idx_; ///< The idx of the protein in the fasta file
+ public:
+
+
+ /**
+ * \returns An (empty) protein_index object.
+ */
+ void init();
+ ProteinIndex();
+
+ /**
+ * Creates a protein_index that contains the offset and protein
+ * index of the protein in the fasta file.
+ */
+ ProteinIndex(
+ unsigned long int offset, ///< The file location in the database source file
+ unsigned int protein_idx ///< The index of the protein in its database.
+ );
+
+ /**
+ * Free a protein index object.
+ */
+ virtual ~ProteinIndex();
+
+ /**
+ * Creates a protein index for the output_file.
+ * \returns True if successfully creates a protein index, else
+ * false.
+ */
+ static bool create(
+ char* fasta_file ///< input fasta file stream -in
+ );
+
+ /**
+ * input is the fasta file name which the protein index
+ * should have been created.
+ * or if creating binary fasta file, is that already on disk?
+ *
+ *\returns TRUE if protein index or binary fasta file is on disk, else FALSE
+ */
+ static bool onDisk(
+ const char* fasta_file, ///< input fasta file -in
+ bool is_binary ///< looking for the binary fasta file or protein index?
+ );
+
+};
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/ProteinIndexIterator.cpp b/src/model/ProteinIndexIterator.cpp
new file mode 100644
index 0000000..644b4d6
--- /dev/null
+++ b/src/model/ProteinIndexIterator.cpp
@@ -0,0 +1,128 @@
+/*************************************************************************//**
+ * \file ProteinIndexIterator.cpp
+ * \brief Object for iterating a protein index file
+ ****************************************************************************/
+#include "ProteinIndexIterator.h"
+
+using namespace Crux;
+
+/**
+ *
+ *\returns TRUE if successfully sets the protein_index_iterator, else FALSE
+ */
+bool ProteinIndexIterator::setup() {
+
+ // used to parse each line from file
+ char* new_line = NULL;
+ int line_length;
+ size_t buf_length = 0;
+ FILE* file = file_;
+
+ // protein fields
+ char star[2] = "";
+ unsigned long int offset;
+ unsigned int protein_idx;
+
+ Protein* protein = NULL;
+ bool found = false;
+
+ while((line_length = getline(&new_line, &buf_length, file)) != -1){
+ // begining of the protein feilds
+ if(new_line[0] == '*'){
+ // read the crux_index_file information
+ if(sscanf(new_line,"%s %d %ld",
+ star, &protein_idx, &offset) < 2){
+ free(new_line);
+ carp(CARP_WARNING, "incorrect file format");
+ fclose(file);
+ return false;
+ }
+ found = true;
+ break;
+ }
+ // skip header lines
+ else if(new_line[0] == '#'){
+ continue;
+ }
+ }
+
+ // there is a next protein to return
+ if(found){
+ protein = Protein::newLightProtein(offset, protein_idx);
+ next_protein_ = protein;
+ has_next_ = true;
+ }
+ // no more proteins..
+ else{
+ has_next_ = false;
+ }
+
+ free(new_line);
+ return true;
+}
+
+/**
+ * There must be the correct protein index file present
+ *\returns a new heap allocated protein index iterator
+ */
+ProteinIndexIterator::ProteinIndexIterator(
+ const char* fasta_file ///< input fasta file -in
+ )
+{
+ char* name = generate_name(fasta_file, "_protein_index", ".fasta", NULL);
+ FILE* file = fopen(name, "rb");
+
+ if(file == NULL){
+ carp(CARP_FATAL, "failed to open protein index file: %s", name);
+ }
+
+ free(name);
+
+ next_protein_ = NULL;
+ has_next_ = false;
+ file_ = file;
+
+ // set up the protein_index_iterator
+ if(!setup()){
+ carp(CARP_FATAL, "failed to setup ProteinIndexIterator");
+ }
+}
+
+/**
+ * Frees the allocated protein index iterator
+ */
+ProteinIndexIterator::~ProteinIndexIterator() {
+
+ // free the file handler
+ fclose(file_);
+
+ // free unused protein
+ if(next_protein_ != NULL){
+ delete (next_protein_);
+ }
+}
+
+/**
+ *
+ *\returns TRUE if there is another protein to return, else FALSE
+ */
+bool ProteinIndexIterator::hasNext() {
+
+ return has_next_;
+}
+
+/**
+ *\return the next protein in the protein index file
+ */
+Protein* ProteinIndexIterator::next() {
+
+ Protein* protein = next_protein_;
+ next_protein_ = NULL;
+
+ // set up the protein_index_iterator
+ if(!setup()){
+ carp(CARP_FATAL, "failed to setup protein_index_iterator");
+ }
+
+ return protein;
+}
diff --git a/src/model/ProteinIndexIterator.h b/src/model/ProteinIndexIterator.h
new file mode 100644
index 0000000..e760b75
--- /dev/null
+++ b/src/model/ProteinIndexIterator.h
@@ -0,0 +1,65 @@
+#ifndef PROTEIN_INDEX_ITERATOR_H
+#define PROTEIN_INDEX_ITERATOR_H
+/**
+ * \file ProteinIndexIterator.h
+ * $Revision: 1.3 $
+ * \brief Object for iterating a protein index file
+ *****************************************************************************/
+
+#include "Protein.h"
+
+/**
+ * protein index iterator
+ * the protein index iterator parses the protein index file
+ * for each protein index one by one and returns a new protein_index object
+ */
+
+class ProteinIndexIterator {
+ protected:
+ FILE* file_; ///< The file handler of the fasta file
+ Crux::Protein* next_protein_; ///< the next protein index to return
+ bool has_next_; ///< is there a new protein to return?
+
+ /**
+ *
+ *\returns true if successfully sets the ProteinIndexIterator, else false
+ */
+ bool setup();
+
+ public:
+
+ /**
+ *
+ *\returns a new heap allocated protein index iterator
+ */
+ ProteinIndexIterator(
+ const char* fasta_file ///< input fasta file -in
+ );
+
+ /**
+ * Frees the allocated protein index iterator
+ */
+ virtual ~ProteinIndexIterator();
+
+ /**
+ *
+ *\returns true if there is another protein index to return, else false
+ */
+ bool hasNext();
+
+ /**
+ *
+ *\return the next protein index in the protein index file
+ */
+ Crux::Protein* next();
+
+};
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/ProteinMatch.cpp b/src/model/ProteinMatch.cpp
new file mode 100644
index 0000000..693e760
--- /dev/null
+++ b/src/model/ProteinMatch.cpp
@@ -0,0 +1,93 @@
+/**
+ * \file ProteinMatch.cpp
+ * \brief Object for holding protein scores
+ ********************************/
+#include "ProteinMatch.h"
+
+#include "Protein.h"
+
+using namespace Crux;
+using namespace std;
+
+/**
+ * \returns an empty ProteinMatch object
+ */
+ProteinMatch::ProteinMatch() {
+ ;
+}
+
+/**
+ * \returns a ProteinMatch object with the protein set
+ */
+ProteinMatch::ProteinMatch(
+ Protein* protein ///< Protein to set
+ ) {
+ protein_ = protein;
+}
+
+/**
+ * Destructor
+ */
+ProteinMatch::~ProteinMatch() {
+
+}
+
+/**
+ * \returns the protein for the match
+ */
+Crux::Protein* ProteinMatch::getProtein() {
+ return protein_;
+}
+
+/**
+ * sets the protein for the match
+ */
+void ProteinMatch::setProtein(
+ Crux::Protein* protein ///< Protein to set
+) {
+ protein_ = protein;
+}
+
+/**
+ * \returns the begining of the peptidematches vector
+ */
+PeptideMatchIterator ProteinMatch::peptideMatchBegin() {
+ return peptide_matches_.begin();
+}
+
+/**
+ * \returns the end of the peptide matches vector
+ */
+PeptideMatchIterator ProteinMatch::peptideMatchEnd() {
+ return peptide_matches_.end();
+}
+
+/**
+ * adds a peptide match to the protein match
+ */
+void ProteinMatch::addPeptideMatch(
+ PeptideMatch* peptide_match ///<PeptideMatch to add
+ ) {
+ for (deque<PeptideMatch*>::iterator iter = peptide_matches_.begin();
+ iter != peptide_matches_.end();
+ ++iter) {
+ if (*iter == peptide_match) {
+ return;
+ }
+ }
+ peptide_matches_.push_back(peptide_match);
+}
+
+/**
+ * \returns the id for this protein
+ */
+string ProteinMatch::getId() const {
+ return string(protein_->getIdPointer());
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/ProteinMatch.h b/src/model/ProteinMatch.h
new file mode 100644
index 0000000..a668fe9
--- /dev/null
+++ b/src/model/ProteinMatch.h
@@ -0,0 +1,84 @@
+/**
+ * \file ProteinMatch.h
+ * $Revision: 1.00 $
+ * \brief Object for holding protein scores
+ ******************************************************/
+#ifndef PROTEINMATCH_H_
+#define PROTEINMATCH_H_
+
+#include "match_objects.h"
+#include "AbstractMatch.h"
+
+#include <map>
+#include <string>
+#include <vector>
+
+class ProteinMatch : public AbstractMatch {
+
+ protected:
+ std::deque<PeptideMatch*> peptide_matches_; ///< PeptideMatches associated with this ProteinMatch
+ Crux::Protein* protein_; ///< Protein
+
+ public:
+
+ /**
+ * \returns an empty ProteinMatch object
+ */
+ ProteinMatch();
+
+ /**
+ * \returns a ProteinMatch object with the protein set
+ */
+ ProteinMatch(
+ Crux::Protein* protein ///< Protein to set
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~ProteinMatch();
+
+ /**
+ * \returns the protein for the match
+ */
+ Crux::Protein* getProtein();
+
+ /**
+ * sets the protein for the match
+ */
+ void setProtein(
+ Crux::Protein* protein ///< Protein to set
+ );
+
+ /**
+ * \returns the begining of the peptidematches vector
+ */
+ PeptideMatchIterator peptideMatchBegin();
+
+ /**
+ * \returns the end of the peptide matches vector
+ */
+ PeptideMatchIterator peptideMatchEnd();
+
+ /**
+ * adds a peptide match to the protein match
+ */
+ void addPeptideMatch(
+ PeptideMatch* peptide_match ///< peptide_match to add
+ );
+
+ /**
+ * \returns the id for this protein
+ */
+ std::string getId() const;
+
+};
+
+#endif //PROTEINMATCH_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/ProteinMatchCollection.cpp b/src/model/ProteinMatchCollection.cpp
new file mode 100644
index 0000000..7ed700e
--- /dev/null
+++ b/src/model/ProteinMatchCollection.cpp
@@ -0,0 +1,279 @@
+/**
+ * \file ProteinMatchCollection.cpp
+ * \brief Object for holding a collection of ProtinMatches, PeptideMatches, and SpectrumMatches
+ ********************************/
+#include "ProteinMatchCollection.h"
+#include "ProteinMatch.h"
+#include "PeptideMatch.h"
+#include "SpectrumMatch.h"
+
+#include "Match.h"
+#include "MatchCollection.h"
+
+using namespace std;
+using namespace Crux;
+
+/**
+ * \returns a blank ProteinMatchCollection
+ */
+ProteinMatchCollection::ProteinMatchCollection() {
+ distinct_matches_ = true;
+}
+
+/**
+ * \returns a ProteinMatchCollection using a MatchCollection
+ * TODO - remove this later
+ */
+ProteinMatchCollection::ProteinMatchCollection(
+ MatchCollection* match_collection ///< matches to add
+ ) {
+ distinct_matches_ = true;
+ addMatches(match_collection);
+
+}
+
+
+/**
+ * Default destructor
+ */
+ProteinMatchCollection::~ProteinMatchCollection() {
+
+ // delete protein matches
+ for (ProteinMatchIterator iter = proteinMatchBegin();
+ iter != proteinMatchEnd();
+ ++iter) {
+ delete *iter;
+ }
+
+ // delete modified aa strings + peptide matches
+ for (map<MODIFIED_AA_T*, PeptideMatch*, cmpSeq>::iterator iter = peptide_match_map_.begin();
+ iter != peptide_match_map_.end();
+ ++iter) {
+ free(iter->first);
+ delete iter->second;
+ }
+
+ // delete spectrum matches
+ for (SpectrumMatchIterator iter = spectrumMatchBegin();
+ iter != spectrumMatchEnd();
+ ++iter) {
+ delete *iter;
+ }
+
+}
+
+/**
+ * \returns the begin iterator for the ProteinMatch objects
+ */
+ProteinMatchIterator ProteinMatchCollection::proteinMatchBegin() {
+
+ return protein_matches_.begin();
+}
+
+/**
+ * \returns the end iterator for the ProteinMatch objects
+ */
+ProteinMatchIterator ProteinMatchCollection::proteinMatchEnd() {
+
+ return protein_matches_.end();
+}
+
+/**
+ * \returns the begin iterator for the PeptideMatch objects
+ */
+PeptideMatchIterator ProteinMatchCollection::peptideMatchBegin() {
+ return peptide_matches_.begin();
+}
+
+/**
+ * \returns the end iterator for the PeptideMatch objects
+ */
+PeptideMatchIterator ProteinMatchCollection::peptideMatchEnd() {
+ return peptide_matches_.end();
+}
+
+/**
+ * \returns the begin iterator for all of the SpectrumMatch objects
+ */
+SpectrumMatchIterator ProteinMatchCollection::spectrumMatchBegin() {
+ return spectrum_matches_.begin();
+}
+
+/**
+ * \returns the end iterator for all of the SpectrumMatch objects
+ */
+SpectrumMatchIterator ProteinMatchCollection::spectrumMatchEnd() {
+ return spectrum_matches_.end();
+}
+
+/**
+ * \returns the ProteinMatch for a Protein, creates a new
+ * one if it is not found and create is true
+ */
+ProteinMatch* ProteinMatchCollection::getProteinMatch(
+ Protein* protein, ///< Protein for which to find the protein match
+ bool create ///< Create the ProteinMatch if it doesn't exist
+ ) {
+
+ string id = protein->getIdPointer();
+
+ ProteinMatch* ans = getProteinMatch(id);
+ if (ans == NULL) {
+ if (create) {
+ ans = new ProteinMatch(protein);
+ protein_matches_.push_back(ans);
+ protein_match_map_.insert(pair<string, ProteinMatch*>(id, ans));
+ } else {
+ carp(CARP_WARNING, "ProteinMatch for %s not found!", protein->getIdPointer().c_str());
+ }
+ }
+ return ans;
+}
+
+/**
+ * \returns the PeptideMatch for a peptide object, creating
+ * if it doesn't exist and create is true
+ */
+PeptideMatch* ProteinMatchCollection::getPeptideMatch(
+ Peptide* peptide, ///< peptide to find
+ bool create ///< create if it doesn't exist?
+ ) {
+
+
+ MODIFIED_AA_T* mod_seq = peptide->getModifiedAASequence();
+
+ PeptideMatch* ans = getPeptideMatch(mod_seq);
+
+ if (ans == NULL) {
+ if (create) {
+ ans = new PeptideMatch(peptide);
+ peptide_matches_.push_back(ans);
+ peptide_match_map_.insert(pair<MODIFIED_AA_T*, PeptideMatch*>(mod_seq, ans));
+ } else {
+ free(mod_seq);
+ carp(CARP_FATAL, "Could not find peptidematch for sequence %s",
+ peptide->getSequence());
+ }
+ } else {
+ free(mod_seq);
+ }
+
+ return ans;
+}
+
+/**
+ * \returns the ProteinMatch for a Protein, null if it doesn't exist
+ */
+ProteinMatch* ProteinMatchCollection::getProteinMatch(
+ const string& id ///< id of the protein
+ ) {
+ map<string, ProteinMatch*>::iterator iter = protein_match_map_.find(id);
+ return (iter != protein_match_map_.end()) ? iter->second : NULL;
+}
+
+/**
+ * \returns the PeptideMatch for the sequence, null if it doesn't exist.
+ */
+PeptideMatch* ProteinMatchCollection::getPeptideMatch(
+ MODIFIED_AA_T* mod_seq ///< Modified Sequence to find
+ ) {
+ map<MODIFIED_AA_T*, PeptideMatch*, cmpSeq>::iterator iter = peptide_match_map_.find(mod_seq);
+ return (iter != peptide_match_map_.end()) ? iter->second : NULL;
+}
+
+
+
+/**
+ * Helper method that adds a Crux match to the ProteinCollection,
+ * creating the SpectrumMatch, PeptideMatch, and ProteinMatch objects.
+ */
+void ProteinMatchCollection::addMatch(
+ MatchCollection* match_collection, ///< Collection from where the match came from
+ Match* match ///< Match to add
+ ){
+
+ //create a spectrum match.
+ Spectrum* spectrum = match->getSpectrum();
+ SpectrumZState z_state = match->getZState();
+ SpectrumMatch* spectrum_match = new SpectrumMatch(spectrum);
+ spectrum_match->setFileIndex(match->getFileIndex());
+ spectrum_match->setZState(z_state);
+ spectrum_matches_.push_back(spectrum_match);
+
+ pair<int, int> scan_charge = make_pair(spectrum->getFirstScan(), z_state.getCharge());
+
+ if (match->getLnExperimentSize() >= 0 &&
+ spectrum_counts_.find(scan_charge) == spectrum_counts_.end()) {
+ spectrum_counts_[scan_charge] = floor(exp(match->getLnExperimentSize()) + 0.5);
+ }
+
+ Peptide* peptide = match->getPeptide();
+ PeptideMatch* peptide_match = getPeptideMatch(peptide);
+
+ //add the spectrum match.
+ peptide_match->addSpectrumMatch(spectrum_match);
+
+ for (int score_idx = (int)SP;
+ score_idx < (int)NUMBER_SCORER_TYPES;
+ score_idx++) {
+
+ SCORER_TYPE_T score_type = (SCORER_TYPE_T)score_idx;
+ if (match_collection->getScoredType(score_type)) {
+ peptide_match->setScore(score_type, match->getScore(score_type));
+ peptide_match->setRank(score_type, match->getRank(score_type));
+ spectrum_match->setScore(score_type, match->getScore(score_type));
+ spectrum_match->setRank(score_type, match->getRank(score_type));
+ }
+ }
+
+ for (PeptideSrcIterator src_iter = peptide->getPeptideSrcBegin();
+ src_iter != peptide->getPeptideSrcEnd();
+ ++src_iter) {
+ PeptideSrc* src = *src_iter;
+ Protein* protein = src->getParentProtein();
+ ProteinMatch* protein_match = getProteinMatch(protein);
+ protein_match->addPeptideMatch(peptide_match);
+ peptide_match->addProteinMatch(protein_match, src);
+ }
+}
+
+/**
+ * Helper method that adds a Crux match to the ProteinMatchCollection,
+ * Adding all SpectrumMatch, PeptideMatch, and ProteinMatches
+ */
+void ProteinMatchCollection::addMatches(
+ MatchCollection* match_collection ///< collection to add
+ ) {
+
+ carp(CARP_DEBUG, "Adding %d matches to ProteinMatchCollection",
+ match_collection->getMatchTotal());
+ distinct_matches_ = match_collection->getHasDistinctMatches();
+
+ MatchIterator match_iter(match_collection);
+ while(match_iter.hasNext()) {
+ addMatch(match_collection, match_iter.next());
+ }
+
+}
+
+/**
+ * Get the matches/spectrum as a map, where the key is <scan, chage>
+ */
+const map<pair<int, int>, int>& ProteinMatchCollection::getMatchesSpectrum() {
+ return spectrum_counts_;
+}
+
+
+/**
+ * \returns whether matches are distinct are not
+ */
+bool ProteinMatchCollection::hasDistinctMatches() {
+ return distinct_matches_;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/ProteinMatchCollection.h b/src/model/ProteinMatchCollection.h
new file mode 100644
index 0000000..af5a0c9
--- /dev/null
+++ b/src/model/ProteinMatchCollection.h
@@ -0,0 +1,161 @@
+/**
+ * \file ProteinMatchCollection.h
+ * $Revision: 1.00 $
+ * \brief Object for holding a collection of ProteinMatches, PeptideMatches, and SpectrumMatches.
+ ************************************************************************************************/
+#ifndef PROTEINMATCHCOLLECTION_H_
+#define PROTEINMATCHCOLLECTION_H_
+#include "PeptideMatch.h"
+#include "ProteinMatch.h"
+#include "match_objects.h"
+
+#include <deque>
+#include <set>
+#include <string>
+
+class ProteinMatchCollection {
+
+ protected:
+
+ struct cmpSeq {
+ bool operator() (const MODIFIED_AA_T* lhs, const MODIFIED_AA_T* rhs) const {
+ size_t idx = -1;
+ MODIFIED_AA_T lhs_aa, rhs_aa;
+ do {
+ ++idx;
+ lhs_aa = lhs[idx];
+ rhs_aa = rhs[idx];
+ if (lhs_aa != rhs_aa) {
+ return lhs_aa < rhs_aa;
+ }
+ } while (lhs_aa != MOD_SEQ_NULL && rhs_aa != MOD_SEQ_NULL);
+ return rhs_aa != MOD_SEQ_NULL;
+ }
+ };
+
+ std::map<std::string, ProteinMatch*> protein_match_map_;
+ std::map<MODIFIED_AA_T*, PeptideMatch*, cmpSeq> peptide_match_map_;
+ std::deque<ProteinMatch*> protein_matches_; ///< All protein matches
+ std::deque<PeptideMatch*> peptide_matches_; ///< All peptide matches
+ std::deque<SpectrumMatch*> spectrum_matches_; ///< All spectrum matches
+
+ std::map<std::pair<int, int>, int> spectrum_counts_; ///< matches/spectrum
+ bool distinct_matches_; ///< are matches distinct?
+ public:
+
+ /**
+ * \returns a blank ProteinMatchCollection
+ */
+ ProteinMatchCollection();
+
+ /**
+ * \returns a ProteinMatchCollection using a MatchCollection
+ * TODO - remove this later
+ */
+ ProteinMatchCollection(
+ MatchCollection* match_collection ///< matches to add
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual~ ProteinMatchCollection();
+
+ /**
+ * \returns the begin iterator for the ProteinMatch objects
+ */
+ ProteinMatchIterator proteinMatchBegin();
+
+ /**
+ * \returns the end iterator for the ProteinMatch objects
+ */
+ ProteinMatchIterator proteinMatchEnd();
+
+ /**
+ * \returns the begin iterator for the PeptideMatch objects
+ */
+ PeptideMatchIterator peptideMatchBegin();
+
+ /**
+ * \returns the end iterator for all of the PeptideMatch objects
+ */
+ PeptideMatchIterator peptideMatchEnd();
+
+ /**
+ * \returns the begin iterator for all of the SpectrumMatch objects
+ */
+ SpectrumMatchIterator spectrumMatchBegin();
+
+ /**
+ * \returns the end iterator for all of the SpectrumMatch objects
+ */
+ SpectrumMatchIterator spectrumMatchEnd();
+
+ /**
+ * \returns the ProteinMatch for a Protein, creates a new
+ * one if it is not found and create is true
+ */
+ ProteinMatch* getProteinMatch(
+ Crux::Protein* protein, ///< Protein for which to find the protein match
+ bool create = true ///< Create the ProteinMatch if it doesn't exist
+ );
+
+ /**
+ * \returns the ProteinMatch for a Protein, null if it doesn't exist
+ */
+ ProteinMatch* getProteinMatch(
+ const std::string& id ///< id of the protein
+ );
+
+ /**
+ * \returns a PeptideMatch for a Peptide object, creating it
+ * if it doesn't exist and create is true
+ */
+ PeptideMatch* getPeptideMatch(
+ Crux::Peptide* peptide, ///< peptide to find
+ bool create=true ///< create if it doesn't exist?
+ );
+
+ /**
+ * \returns the PeptideMatch for the sequence, null if it doesn't exist
+ */
+ PeptideMatch* getPeptideMatch(
+ MODIFIED_AA_T* mod_seq ///< modified sequence to find
+ );
+
+ /**
+ * Helper method that adds a Crux match to the ProteinCollection,
+ * creating the SpectrumMatch, PeptideMatch, and ProteinMatch objects.
+ */
+ void addMatch(
+ MatchCollection* match_collection, ///<Collection from where the match came from
+ Crux::Match* match ///< Match to add
+ );
+
+ /**
+ * Helper method that adds a Crux match to the ProteinMatchCollection,
+ * Adding all SpectrumMatch, PeptideMatch, and ProteinMatch objects.
+ */
+ void addMatches(MatchCollection* match_collection);
+
+ /**
+ * Get the matches/spectrum as a map, where the key is <scan, charge>
+ */
+ const std::map<std::pair<int, int>, int>& getMatchesSpectrum();
+
+ /**
+ * \returns whether matches are distinct are not
+ */
+ bool hasDistinctMatches();
+
+};
+
+#endif // PROTEINMATCHCOLLECTION_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/ProteinPeptideIterator.cpp b/src/model/ProteinPeptideIterator.cpp
new file mode 100644
index 0000000..5a83229
--- /dev/null
+++ b/src/model/ProteinPeptideIterator.cpp
@@ -0,0 +1,525 @@
+/**
+ * \file ProteinPeptideIterator.cpp
+ * $Revision: 0.0 $
+ */
+
+#include "ProteinPeptideIterator.h"
+#include "util/GlobalParams.h"
+#include "util/Params.h"
+
+using namespace std;
+using namespace Crux;
+
+/*
+ * Takes a cumulative distribution of peptide masses (the mass_array) and
+ * the start index and end index and returns a peptide mass
+ */
+FLOAT_T ProteinPeptideIterator::calculateSubsequenceMass (
+ double* mass_array,
+ int start_idx,
+ int cur_length
+ ){
+
+ FLOAT_T mass_h2o = MASS_H2O_AVERAGE;
+ if (GlobalParams::getIsotopicMass() == MONO) {
+ mass_h2o = MASS_H2O_MONO;
+ }
+
+ // carp(CARP_DETAILED_DEBUG, "mass start = %i", start_idx);
+ int end_idx = start_idx + cur_length;
+ // carp(CARP_DETAILED_DEBUG, "mass end = %i", end_idx);
+ FLOAT_T peptide_mass = mass_array[end_idx] - mass_array[start_idx] + mass_h2o;
+
+ return peptide_mass;
+}
+
+/**
+ * \brief Decide if a residue is in an inclusion list or is not in an
+ * exclusion list.
+ *
+ * For use with the user-specified enzyme digestion. Takes an amino
+ * acid, a list of amino acids, and a flag for if it is an inclusion
+ * list or an exclusion list. A cleavage can happen before/after the
+ * given residue if it is either in the inclusion list or is not in
+ * the exculsion list.
+ * \returns true if the residue is in the inclusion list or not in the
+ * exclusion list.
+ */
+bool ProteinPeptideIterator::isResidueLegal(char aa,
+ char* aa_list,
+ int list_size,
+ bool for_inclusion){
+
+ // The logic for returning for_inclusion:
+ // For an inclusion list (true), once we find the aa it passes (true)
+ // For an exclusion list (false), once we find the aa, it fails (false)
+ int idx=0;
+ for(idx=0; idx < list_size; idx++){
+ if( aa == aa_list[idx] ){ return for_inclusion; }
+ }
+ // or if we got to the end of the list and didn't find a match
+ // for inclusion, it fails (!true)
+ // for exclusion, it passes (!false)
+ return ! for_inclusion;
+}
+
+/**
+ * Compares the first and second amino acids in the given sequence to
+ * see if they conform to the cleavage rules of the given enzyme. For
+ * NO_ENZYME, always returns true.
+ *
+ * \returns true if this is a valid cleavage position for the given enzyme.
+ */
+bool ProteinPeptideIterator::validCleavagePosition(
+ const char* sequence,
+ ENZYME_T enzyme
+){
+
+ switch(enzyme){
+
+ case TRYPSIN:
+ return (sequence[0] == 'K' || sequence[0] == 'R') && sequence[1] != 'P';
+ //trypsin/p k or r
+ case TRYPSINP:
+ return sequence[0] == 'K' || sequence[0] == 'R';
+ case ELASTASE:
+ return (sequence[0] == 'A' || sequence[0] == 'L' ||
+ sequence[0] == 'I' || sequence[0] == 'V') && sequence[1] != 'P';
+ case CLOSTRIPAIN:
+ return sequence[0] == 'R';
+ case CYANOGEN_BROMIDE:
+ return sequence[0] == 'M';
+ case IODOSOBENZOATE:
+ return sequence[0] == 'W';
+ case PROLINE_ENDOPEPTIDASE:
+ return sequence[0] == 'P';
+ case STAPH_PROTEASE:
+ return sequence[0] == 'E';
+ case ASPN:
+ return sequence[1] == 'D';
+ case LYSC:
+ return sequence[0] == 'K' && sequence[1] != 'P';
+ case LYSN:
+ return sequence[1] == 'K';
+ case ARGC:
+ return sequence[0] == 'R' && sequence [1] != 'P';
+ case GLUC:
+ return (sequence[0] == 'D' || sequence[0] == 'E') && sequence[1] != 'P';
+ case PEPSINA:
+ return (sequence[0] == 'F' || sequence[0] == 'L') && sequence[1] != 'P';
+ case CHYMOTRYPSIN:
+ return (sequence[0] == 'F' || sequence[0] == 'L' ||
+ sequence[0] == 'W' || sequence[0] == 'Y') && sequence[1] != 'P';
+ case ELASTASE_TRYPSIN_CHYMOTRYPSIN:
+ return (sequence[0] == 'A' || sequence[0] == 'L' ||
+ sequence[0] == 'I' || sequence[0] == 'V' ||
+ sequence[0] == 'K' || sequence[0] == 'R' ||
+ sequence[0] == 'W' || sequence[0] == 'F' ||
+ sequence[0] == 'Y' ) && sequence[1] != 'P';
+ case CUSTOM_ENZYME:
+ //carp(CARP_FATAL, "The custom enzyme is not yet implmented.");
+
+ return ( isResidueLegal(sequence[0],
+ pre_cleavage_list,
+ pre_list_size,
+ pre_for_inclusion)
+ &&
+ isResidueLegal(sequence[1],
+ post_cleavage_list,
+ post_list_size,
+ post_for_inclusion) );
+ break;
+
+ case NO_ENZYME:
+ return true;
+ break;
+
+ case INVALID_ENZYME:
+ case NUMBER_ENZYME_TYPES:
+ carp(CARP_FATAL, "Cannot generate peptides with invalid enzyme: %d", enzyme);
+ break;
+
+ }// end switch
+
+ return false;
+}
+
+/**
+ * \brief Adds peptides to the iterator based on our constraint and
+ * the given possible cleavage positions.
+ *
+ * The allowed cleavages on either end of the peptide are specified
+ * separately so that the ends can obey different cleavage rules
+ * (e.g. tryptic and non). Use the member variable
+ * cumulative_cleavages_ to keep track of skipped enzyme cleavage
+ * sites since the cterm allowed cleavages may be non-tryptic for a partially
+ * tryptic search. Add a peptide to the iterator for each
+ * pair of n- and c-term cleavages that obey all of the peptide
+ * constraints: correct length, mass, and number of internal cleavage
+ * positions.
+ * A small inconsistency:
+ * Allowed cleavages start at 0, while the output cleavages start at 1.
+ */
+void ProteinPeptideIterator::selectPeptides(
+ int* nterm_allowed_cleavages,
+ int nterm_num_cleavages,
+ int* cterm_allowed_cleavages,
+ int cterm_num_cleavages,
+ int int_num_skip_cleavages){
+
+ // to avoid checking a lot of C-term before our current N-term cleavage
+ int previous_cterm_cleavage_start= 0;
+
+ PeptideConstraint* constraint = peptide_constraint_;
+ int nterm_idx, cterm_idx;
+
+ // for each possible n-term (start) position...
+ for (nterm_idx=0; nterm_idx < nterm_num_cleavages; nterm_idx++){
+
+ // check all possible c-term (end) positions
+
+ int next_cterm_cleavage_start = previous_cterm_cleavage_start;
+ bool no_new_cterm_cleavage_start = true;
+ for (cterm_idx = previous_cterm_cleavage_start;
+ cterm_idx < cterm_num_cleavages; cterm_idx++){
+
+ if ((*cumulative_cleavages_)[cterm_allowed_cleavages[cterm_idx]-1] - \
+ (*cumulative_cleavages_)[nterm_allowed_cleavages[nterm_idx]] \
+ > int_num_skip_cleavages) {
+ break;
+ }
+ if (cterm_allowed_cleavages[cterm_idx]
+ <= nterm_allowed_cleavages[nterm_idx]){
+ continue;
+ }
+
+ // check our length constraint
+ int length =
+ cterm_allowed_cleavages[cterm_idx] - nterm_allowed_cleavages[nterm_idx];
+
+ // if too short, try next cterm position
+ if (length < constraint->getMinLength()){
+ continue;
+ // if too long, go to next nterm (start) position
+ } else if (length > constraint->getMaxLength()){
+ break;
+ } else if (no_new_cterm_cleavage_start){
+ next_cterm_cleavage_start = cterm_idx;
+ no_new_cterm_cleavage_start = false;
+ }
+
+ // check our mass constraint
+ FLOAT_T peptide_mass = calculateSubsequenceMass(mass_array_,
+ nterm_allowed_cleavages[nterm_idx], length);
+
+ // TODO: if too small, try next cterm (end), if too large, try
+ // next nterm (start), else in range so add peptide
+ if ((constraint->getMinMass() <= peptide_mass) &&
+ (peptide_mass <= constraint->getMaxMass())){
+
+ // we have found a peptide
+ nterm_cleavage_positions_->push_back(nterm_allowed_cleavages[nterm_idx] + 1);
+
+ peptide_lengths_->push_back(length);
+ peptide_masses_->push_back(peptide_mass);
+ carp(CARP_DETAILED_DEBUG,
+ "New pep: %i (%i)", nterm_allowed_cleavages[nterm_idx], length);
+
+ num_cleavages_++;
+ }
+ }
+ previous_cterm_cleavage_start = next_cterm_cleavage_start;
+
+ }
+}
+
+/**
+ * Creates the data structures in the protein_peptide_iterator object necessary
+ * for creating peptide objects.
+ * - mass_array - cumulative distribution of masses. used to determine
+ * the mass of any peptide subsequence.
+ * - nterm_cleavage_positions - the nterm cleavage positions of the
+ * peptides that satisfy the protein_peptide_iterator contraints
+ * - peptide_lengths - the lengths of the peptides that satisfy the constraints
+ * - cumulative_cleavages - cumulative distribution of cleavage positions
+ * used to determine if a cleavage location has been skipped
+ */
+void ProteinPeptideIterator::prepare()
+{
+ prepareMc(num_mis_cleavage_);
+}
+
+void ProteinPeptideIterator::prepareMc(
+ int missed_cleavages)
+{
+ Protein* protein = protein_;
+ MASS_TYPE_T mass_type = peptide_constraint_->getMassType();
+ double* mass_array = (double*)mycalloc(protein->getLength()+1, sizeof(double));
+
+ ENZYME_T enzyme = peptide_constraint_->getEnzyme();
+
+ // initialize mass matrix and enzyme cleavage positions
+ int* cleavage_positions = (int*) mycalloc(protein->getLength()+1, sizeof(int));
+ int* non_cleavage_positions = (int*)mycalloc(protein->getLength()+1, sizeof(int));
+ int* all_positions = (int*) mycalloc(protein->getLength()+1, sizeof(int));
+
+ // initialize first value in all array except non_cleavage_positions
+ unsigned int start_idx = 0;
+ mass_array[start_idx] = 0.0;
+ int cleavage_position_idx = 0;
+ int non_cleavage_position_idx = 0;
+ cleavage_positions[cleavage_position_idx++] = 0;
+
+ // calculate our cleavage positions and masses
+ for(start_idx = 1; start_idx < protein->getLength()+1; start_idx++){
+ int sequence_idx = start_idx - 1;
+ char amino_acid = protein->getSequencePointer()[sequence_idx];
+ mass_array[start_idx] = mass_array[start_idx-1] +
+ get_mass_amino_acid(amino_acid, mass_type);
+
+ if( amino_acid == 'B' || amino_acid == 'X' || amino_acid == 'Z' ){
+ carp_once(CARP_WARNING,
+ "Ignoring peptides with ambiguous amino acids (B, X, Z).");
+ }
+
+ // increment cumulative cleavages before we check if current position
+ // is a cleavage site because cleavages come *after* the current amino acid
+ cumulative_cleavages_->push_back(cleavage_position_idx);
+
+ //if (valid_cleavage_position(protein->sequence + sequence_idx)){
+ if (validCleavagePosition(protein->getSequencePointer() + sequence_idx, enzyme)){
+ cleavage_positions[cleavage_position_idx++] = sequence_idx + 1;
+ } else {
+ non_cleavage_positions[non_cleavage_position_idx++] = sequence_idx + 1;
+ }
+
+ all_positions[sequence_idx] = sequence_idx;
+ }
+
+ // put in the implicit cleavage at end of protein
+ if (cleavage_positions[cleavage_position_idx-1] != (int)protein->getLength()){
+ cleavage_positions[cleavage_position_idx++] = protein->getLength();
+ }
+
+ all_positions[protein->getLength()] = (int)protein->getLength();
+
+ int num_cleavage_positions = cleavage_position_idx;
+ int num_non_cleavage_positions = non_cleavage_position_idx;
+ if (mass_array_ != NULL) {
+ free(mass_array_);
+ }
+ mass_array_ = mass_array;
+
+ carp(CARP_DETAILED_DEBUG, "num_cleavage_positions = %i", num_cleavage_positions);
+
+ // now determine the cleavage positions that actually match our constraints
+
+ DIGEST_T digestion =
+ peptide_constraint_->getDigest();
+
+ switch (digestion){
+
+ case FULL_DIGEST:
+ this->selectPeptides(
+ cleavage_positions, num_cleavage_positions-1,
+ cleavage_positions+1, num_cleavage_positions-1,
+ missed_cleavages);
+
+ break;
+
+ case PARTIAL_DIGEST:
+ // add the C-term tryptic cleavage positions.
+ this->selectPeptides(
+ all_positions, protein->getLength(),
+ cleavage_positions+1, num_cleavage_positions-1,
+ missed_cleavages);
+
+ // add the N-term tryptic cleavage positions.
+ // no +1 below for non_cleavage_positions below
+ // because it does not include sequence beginning. it is *special*
+ this->selectPeptides(
+ cleavage_positions, num_cleavage_positions-1,
+ non_cleavage_positions, num_non_cleavage_positions-1,
+ missed_cleavages);
+
+ break;
+
+ case NON_SPECIFIC_DIGEST:
+ this->selectPeptides(
+ all_positions, protein->getLength(),
+ all_positions+1, protein->getLength(), // len-1?
+ 500); // for unspecific ends, allow internal cleavage sites
+ break;
+
+ case INVALID_DIGEST:
+ case NUMBER_DIGEST_TYPES:
+ carp(CARP_FATAL, "Invalid digestion type in protein peptide iterator.");
+ }
+
+/*
+ int idx;
+ for (idx=0; idx < iterator->num_cleavages; idx++){
+ carp(CARP_DETAILED_DEBUG, "%i->%i",
+ iterator->nterm_cleavage_positions[idx],
+ //iterator->peptide_lengths[idx],
+ //iterator->peptide_lengths[idx],
+ iterator->protein->sequence[iterator->nterm_cleavage_positions[idx]-1]);
+ }
+*/
+ if (num_cleavages_ > 0){
+ has_next_ = true;
+ } else {
+ has_next_ = false;
+ }
+
+ free(cleavage_positions);
+ free(non_cleavage_positions);
+ free(all_positions);
+}
+
+/**
+ * \brief Estimate the maximum number of peptides a protein can
+ * produce. Counts the number of subsequences of length
+ * min_seq_length, min_seq_length + 1, ..., max_seq_length that can be
+ * formed from a protein of the given length. No enzyme specificity
+ * assumed.
+ */
+unsigned int ProteinPeptideIterator::countMaxPeptides(
+ unsigned int protein_length, ///< length of protein
+ unsigned int min_seq_length, ///< min peptide length
+ unsigned int max_seq_length) ///< max peptide length
+{
+ if( max_seq_length > protein_length ){
+ max_seq_length = protein_length;
+ }
+
+ unsigned int total_peptides = 0;
+ for(unsigned int len = min_seq_length; len <= max_seq_length; len++){
+ total_peptides += protein_length + 1 - len;
+ }
+ return total_peptides;
+}
+
+/**
+ * Instantiates a new peptide_iterator from a protein.
+ * \returns a PROTEIN_PEPTIDE_ITERATOR_T object.
+ * assumes that the protein is heavy
+ */
+ProteinPeptideIterator::ProteinPeptideIterator(
+ Protein* protein, ///< the protein's peptide to iterate -in
+ PeptideConstraint* peptide_constraint ///< the peptide constraints -in
+ )
+{
+
+ // initialize iterator
+ protein_ = NULL;
+ cur_start_ = 0;
+ cur_length_ = 1;
+ peptide_idx_ = 0;
+ peptide_constraint_ = NULL;
+ mass_array_ = NULL;
+ current_cleavage_idx_ = 0;
+ has_next_ = false;
+
+ peptide_idx_ = 0;
+ peptide_constraint_
+ = PeptideConstraint::copyPtr(peptide_constraint);
+ cur_start_ = 0;
+ cur_length_ = 1;
+ num_mis_cleavage_
+ = peptide_constraint_->getNumMisCleavage();
+ protein_ = protein;
+
+ nterm_cleavage_positions_ = new vector<int>();
+ peptide_lengths_ = new vector<int>();
+ peptide_masses_ = new vector<FLOAT_T>();
+ cumulative_cleavages_ = new vector<int>();
+
+ // estimate array size and reserve space to avoid resizing vector
+ int max_peptides = countMaxPeptides(protein->getLength(),
+ GlobalParams::getMinLength(),
+ GlobalParams::getMaxLength());
+ nterm_cleavage_positions_->reserve(max_peptides);
+ peptide_lengths_->reserve(max_peptides);
+ peptide_masses_->reserve(max_peptides);
+ cumulative_cleavages_->reserve(max_peptides);
+ num_cleavages_ = 0;
+
+ // prepare the iterator data structures
+ prepare();
+}
+
+
+/**
+ * Frees an allocated peptide_iterator object.
+ */
+ProteinPeptideIterator::~ProteinPeptideIterator()
+{
+ PeptideConstraint::free(peptide_constraint_);
+ free(mass_array_);
+ delete nterm_cleavage_positions_;
+ delete peptide_lengths_;
+ delete peptide_masses_;
+ delete cumulative_cleavages_;
+}
+
+/**
+ * The basic iterator functions.
+ * \returns true if there are additional peptides, false if not.
+ */
+bool ProteinPeptideIterator::hasNext()
+{
+ return has_next_;
+}
+
+/**
+ * \returns The next peptide in the protein, in an unspecified order
+ * the Peptide is new heap allocated object, user must free it
+ */
+Crux::Peptide* ProteinPeptideIterator::next()
+{
+ if( !has_next_){
+ carp(CARP_DEBUG, "Returning null");
+ return NULL;
+ }
+
+ int cleavage_idx = current_cleavage_idx_;
+ int current_start = (*nterm_cleavage_positions_)[cleavage_idx];
+ int current_length = (*peptide_lengths_)[cleavage_idx];
+
+ // create new peptide
+ Peptide* peptide = new Peptide(current_length, protein_, current_start);
+ // update position of iterator
+ ++current_cleavage_idx_;
+
+ // update has_next field
+ if (current_cleavage_idx_ == num_cleavages_){
+ has_next_ = false;
+ } else {
+ has_next_ = true;
+ }
+ return peptide;
+}
+
+/**
+ *\returns the protein that the iterator was created on
+ */
+Protein* ProteinPeptideIterator::getProtein()
+{
+ return protein_;
+}
+
+/**
+ * \returns The total number of peptides in this protein.
+ */
+int ProteinPeptideIterator::getTotalPeptides(){
+ return num_cleavages_;
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/ProteinPeptideIterator.h b/src/model/ProteinPeptideIterator.h
new file mode 100644
index 0000000..594ad44
--- /dev/null
+++ b/src/model/ProteinPeptideIterator.h
@@ -0,0 +1,180 @@
+/**
+ * \file ProteinPeptideIterator.h
+ * $Revision: 1.25 $
+ * \brief Object to iterate over the peptides within a protein in an
+ * unspecified order. The peptides should satisfy the constraints specified
+ * in the peptide_constraint object.
+ *****************************************************************************/
+#ifndef PROTEINPEPTIDEITERATOR_H
+#define PROTEINPEPTIDEITERATOR_H
+
+#include "Protein.h"
+#include "Peptide.h"
+
+#include <iterator>
+#include <vector>
+
+class ProteinPeptideIterator {
+
+ protected:
+ Crux::Protein* protein_; ///< The protein whose peptides to iterate over.
+ unsigned short int cur_start_; ///< Start in protein of the current peptide.
+ unsigned short int cur_length_; ///< The length of the current peptide.
+ unsigned int peptide_idx_; ///< The index of the current peptide.
+ PeptideConstraint* peptide_constraint_; ///< peptide type to iterate over.
+ double* mass_array_; ///< stores all the peptides' masses
+ std::vector<int>* nterm_cleavage_positions_; ///< nterm cleavages that satisfy
+ ///< constraint. 1st aa is 1.
+ std::vector<int>* peptide_lengths_; ///< all the lengths of valid peptides
+ std::vector<FLOAT_T>* peptide_masses_; ///< all the masses of valid peptides
+ std::vector<int>* cumulative_cleavages_; ///< cumulative number of cleavages so far
+ int current_cleavage_idx_; /// where are we in the cleavage positions?
+ int num_cleavages_; /// how many cleavage positions?
+
+ bool has_next_; ///< is there a next?
+ int num_mis_cleavage_; ///< The maximum mis cleavage of the peptide
+
+ /*
+ * Takes a cumulative distribution of peptide masses (the mass_array) and
+ * the start index and end index and returns a peptide mass
+ */
+ FLOAT_T calculateSubsequenceMass(
+ double* mass_array,
+ int start_idx,
+ int cur_length
+ );
+
+ /**
+ * \brief Decide if a residue is in an inclusion list or is not in an
+ * exclusion list.
+ *
+ * For use with the user-specified enzyme digestion. Takes an amino
+ * acid, a list of amino acids, and a flag for if it is an inclusion
+ * list or an exclusion list. A cleavage can happen before/after the
+ * given residue if it is either in the inclusion list or is not in
+ * the exculsion list.
+ * \returns TRUE if the residue is in the inclusion list or not in the
+ * exclusion list.
+ */
+ static bool isResidueLegal(
+ char aa,
+ char* aa_list,
+ int list_size,
+ bool for_inclusion
+ );
+
+ /**
+ * \brief Adds cleavages to the protein peptide iterator that obey iterator
+ * constraint.
+ *
+ * Uses the allowed cleavages arrays, and whether skipped cleavages
+ * are allowed.
+ * A small inconsistency:
+ * Allowed cleavages start at 0, while the output cleavages start at 1.
+ */
+ void selectPeptides(
+ int* nterm_allowed_cleavages,
+ int nterm_num_cleavages,
+ int* cterm_allowed_cleavages,
+ int cterm_num_cleavages,
+ int num_skip_cleavages);
+
+ /**
+ * Creates the data structures in the protein_peptide_iterator object necessary
+ * for creating peptide objects.
+ * - mass_array - cumulative distribution of masses. used to determine
+ * the mass of any peptide subsequence.
+ * - nterm_cleavage_positions - the nterm cleavage positions of the
+ * peptides that satisfy the protein_peptide_iterator contraints
+ * - peptide_lengths - the lengths of the peptides that satisfy the constraints
+ * - cumulative_cleavages - cumulative distribution of cleavage positions
+ * used to determine if a cleavage location has been skipped
+ */
+ void prepare();
+
+ /**
+ * \brief Estimate the maximum number of peptides a protein can
+ * produce. Counts the number of subsequences of length
+ * min_seq_length, min_seq_length + 1, ..., max_seq_length that can be
+ * formed from a protein of the given length. No enzyme specificity
+ * assumed.
+ */
+ unsigned int countMaxPeptides(
+ unsigned int protein_length, ///< length of protein
+ unsigned int min_seq_length, ///< min peptide length
+ unsigned int max_seq_length); ///< max peptide length
+
+ public:
+ /**
+ * Instantiates a new peptide_iterator from a peptide.
+ * \returns a PROTEIN_PEPTIDE_ITERATOR_T object.
+ */
+ ProteinPeptideIterator(
+ Crux::Protein* protein,
+ PeptideConstraint* peptide_constraint
+ );
+
+ /**
+ * Frees an allocated peptide_iterator object.
+ */
+ ~ProteinPeptideIterator();
+
+ /**
+ * The basic iterator functions.
+ * \returns TRUE if there are additional peptides to iterate over, FALSE if not.
+ */
+ bool hasNext();
+
+ /**
+ * \returns The next peptide in the protein, in an unspecified order
+ */
+ Crux::Peptide* next();
+
+ /**
+ *\returns the protein that the iterator was created on
+ */
+ Crux::Protein* getProtein();
+
+ /**
+ * \returns The total number of peptides in this protein.
+ */
+ int getTotalPeptides();
+
+ /**
+ * Creates the data structures in the protein_peptide_iterator object necessary
+ * for creating peptide objects.
+ * - mass_array - cumulative distribution of masses. used to determine
+ * the mass of any peptide subsequence.
+ * - nterm_cleavage_positions - the nterm cleavage positions of the
+ * peptides that satisfy the protein_peptide_iterator contraints
+ * - peptide_lengths - the lengths of the peptides that satisfy the constraints
+ * - cumulative_cleavages - cumulative distribution of cleavage positions
+ * used to determine if a cleavage location has been skipped
+ */
+ void prepareMc(
+ int missed_cleavages
+ );
+
+ /**
+ * Compares the first and second amino acids in the given sequence to
+ * see if they conform to the cleavage rules of the given enzyme. For
+ * NO_ENZYME, always returns TRUE.
+ *
+ * \returns TRUE if this is a valid cleavage position for the given enzyme.
+ */
+ static bool validCleavagePosition(
+ const char* sequence,
+ ENZYME_T enzyme
+ );
+
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
+#endif
diff --git a/src/model/Scorer.cpp b/src/model/Scorer.cpp
new file mode 100644
index 0000000..d4f625b
--- /dev/null
+++ b/src/model/Scorer.cpp
@@ -0,0 +1,1682 @@
+/*************************************************************************//**
+ * \file Scorer.cpp
+ * AUTHOR: Chris Park
+ * CREATE DATE: 9 Oct 2006
+ * \brief object to score spectrum versus spectrum or spectrum
+ * versus ion_series
+ ****************************************************************************/
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#ifndef _MSC_VER
+#include <dirent.h>
+#include <unistd.h>
+#endif
+#include <ctype.h>
+#include <sys/stat.h>
+#ifdef _MSC_VER
+#include "util/windirent.h"
+#endif
+#include "model/IonConstraint.h"
+#include "model/IonFilteredIterator.h"
+#include "model/IonSeries.h"
+#include "util/crux-utils.h"
+#include "util/GlobalParams.h"
+#include "util/Params.h"
+#include "model/Spectrum.h"
+#include "Scorer.h"
+#include "parameter.h"
+
+using namespace Crux;
+
+/**
+ * Maximum range for cross correlation offset.
+ */
+static const int MAX_XCORR_OFFSET = 75;
+
+// The following two constants are hardware dependent.
+// These values should be good for double precision floating point
+// numbers compatible with the IEEE 754 standard.
+
+/**
+* Constant for EVD p_value calculation
+*/
+static const FLOAT_T DBL_EPSILON_ = 2.2204460492503131e-16;
+/**
+* Constant for EVD p_value calculation
+*/
+static const int DBL_MAX_10_EXP_ = 308;
+
+/**
+ * Cut-off below which the simple Bonferroni calculation can be used.
+ */
+static const FLOAT_T BONFERRONI_CUT_OFF_P = 0.0001;
+/**
+ * Cut-off below which the simple Bonferroni calculation can be used.
+ */
+static const FLOAT_T BONFERRONI_CUT_OFF_NP = 0.01;
+
+static const int GMTK_MAX_ION_FILES = 50;
+static const int GMTK_NUM_CHARGES = 2;
+static const int GMTK_NUM_BASE_IONS = 3;
+static const int GMTK_NUM_NEUTRAL_LOSS = 2;
+static const int GMTK_NUM_ION_SERIES =
+ GMTK_NUM_BASE_IONS * GMTK_NUM_CHARGES * (GMTK_NUM_NEUTRAL_LOSS + 1);
+static const int GMTK_NUM_PAIRED_ION_SERIES = 15;
+
+/**
+ * Relative peak height of b- and y-ions.
+ */
+static const int B_Y_HEIGHT = 50;
+/**
+ * Relative height of flanking peaks.
+ */
+static int FLANK_HEIGHT = 25;
+/**
+ * Relative height of neutral loss peaks.
+ */
+static const int LOSS_HEIGHT = 10;
+
+/**
+ * Number of regions into which the spectrum is divided for normalization.
+ */
+static const int NUM_REGIONS = 10;
+
+/**
+ * Maximum peak height within each region of the spectrum after normalizing.
+ */
+static const int MAX_PER_REGION = 50;
+
+
+int ion_counter=0;
+
+/**
+ * Initializes an empty scorer object
+ */
+void Scorer::init() {
+ type_ = (SCORER_TYPE_T)0;
+ sp_beta_ = 0.0;
+ sp_max_mz_ = 0.0;
+ sp_b_y_ion_matched_ = 0;
+ sp_b_y_ion_possible_ = 0;
+ sp_b_y_ion_fraction_matched_ = 0;
+ intensity_array_ = NULL;
+ initialized_ = false;
+ last_idx_ = 0;
+ bin_width_ = 0;
+ bin_offset_ = 0;
+ observed_ = NULL;
+ theoretical_ = NULL;
+}
+
+/**
+ *\returns An (empty) scorer object.
+ */
+Scorer::Scorer() {
+ init();
+}
+
+
+/**
+ * If not planning to use the default values, must parse the parameter file before.
+ * Instantiates a new scorer object from a filename.
+ * \returns a new scorer object
+ */
+Scorer::Scorer(
+ SCORER_TYPE_T type ///< the type of scorer -in
+ )
+{
+ // initialize
+ init();
+
+ // set score type
+ type_ = type;
+
+ // set bin_width and bin_offset.
+ bin_width_ = Params::GetDouble("mz-bin-width");
+ bin_offset_ = Params::GetDouble("mz-bin-offset");
+
+ // set fields needed for each score type
+ if(type == SP){
+ //sp_beta_ = Params::GetDouble("beta"); TODO what happened to beta? SJM
+ sp_max_mz_ = Params::GetDouble("max-mz");
+ // allocate the intensity array
+ intensity_array_ = (FLOAT_T*)mycalloc(getMaxBin(), sizeof(FLOAT_T));
+ max_intensity_ = 0;
+ last_idx_ = 0;
+ // the scorer as not been initialized yet.
+ initialized_ = false;
+ }
+ else if(type == XCORR){
+ // scorer->sp_max_mz = Params::GetDouble("max-mz");
+ // scorer->observed = (FLOAT_T*)mycalloc((int)scorer->sp_max_mz, sizeof(FLOAT_T));
+ last_idx_ = 0;
+ // the scorer as not been initialized yet.
+ initialized_ = false;
+ }
+ else{
+ // the scorer as not been initialized yet.
+ initialized_ = false;
+ }
+
+ use_flanks_ = Params::GetBool("use-flanking-peaks");
+}
+
+/**
+ * Frees an allocated scorer object.
+ */
+Scorer::~Scorer() {
+ // score type SP?
+ if (intensity_array_ != NULL) {
+ free(intensity_array_);
+ }
+ if (observed_ != NULL) {
+ free(observed_);
+ }
+}
+
+
+/**
+ * normalize array so that maximum peak equals threshold
+ */
+void nomalize_intensity_array(
+ FLOAT_T* intensity_array, ///< the array to normalize -in/out
+ int array_size, ///< size of array -in
+ FLOAT_T max_intensity, ///< the maximum intensity in array -in
+ FLOAT_T threshold ///< the threshold to which the peaks should be normalized -in
+ )
+{
+ int mz_idx = 0;
+
+ // return if max_intensity is 0
+ if(max_intensity < 0.00001){
+ return;
+ }
+
+ // normalize all peaks
+ for(; mz_idx < array_size; ++mz_idx){
+ intensity_array[mz_idx]
+ = intensity_array[mz_idx] * threshold / max_intensity;
+ }
+}
+
+/**
+ * smooth all peaks in intensity array
+ * Replaces the original array with the newly smooothed array
+ */
+void Scorer::smoothPeaks() {
+
+ int idx = 2;
+ FLOAT_T* array = intensity_array_;
+
+ // create a new array, which will replace the original intensity array
+ FLOAT_T* new_array = (FLOAT_T*)mycalloc(getMaxBin(), sizeof(FLOAT_T));
+
+ if (type_ == SP){
+ // iterate over all peaks
+ for(; idx < getMaxBin()-2; ++idx){
+ // smooooth
+ new_array[idx] = (array[idx-2] +
+ (4 * array[idx-1]) +
+ (6 * array[idx]) +
+ (4 * array[idx+1]) + array[idx+2] ) / 16;
+
+ // set last idx in the array
+ if(last_idx_ < idx && new_array[idx] == 0){
+ last_idx_ = idx -1;
+ break;
+ }
+ }
+ }
+ free(intensity_array_);
+ intensity_array_ = new_array;
+}
+
+/**
+ * get the mean of intensity in array within +/- 50 mz of the working peak
+ * \returns the mean +/- 50mz region
+ */
+FLOAT_T get_mean_from_array(
+ FLOAT_T* original_array, ///< the array to normalize -in
+ int array_size, ///< the size of array -in
+ int peak_idx, ///< the peak indx in array -in
+ int* peak_count ///< pointer to peak count, store peak count here -out
+ )
+{
+ FLOAT_T total_intensity = 0;
+ int start_idx = peak_idx - 50;
+ int end_idx = peak_idx + 50;
+
+ // set upper bound
+ if(peak_idx + 50 >= array_size){
+ end_idx = array_size-1;
+ }
+ // set start index
+ if(peak_idx - 50 <= 0){
+ start_idx = 0;
+ }
+
+ // sum up the intensities
+ for(; start_idx <= end_idx; ++start_idx){
+ // printf("%.2f\n", original_array[start_idx]);
+
+ ++*peak_count;
+ total_intensity += original_array[start_idx];
+ }
+
+ // BUG! it should divide by 101 but Sequest uses 100
+ return (total_intensity / (*peak_count-1));
+}
+
+/**
+ * get the stdev of intensity in array within +/- 50 mz of the working peak
+ * \returns the stdev +/- 50mz region
+ */
+FLOAT_T get_stdev_from_array(
+ FLOAT_T* original_array, ///< the array to normalize -in
+ int array_size, ///< the size of array -in
+ int peak_idx, ///< the peak indx in array -ina
+ FLOAT_T mean, ///< the mean in the +/- 50 interval -in
+ int peak_count ///< peak count -in
+ )
+{
+ FLOAT_T variance = 0;
+ int start_idx = peak_idx - 50;
+ int end_idx = peak_idx + 50;
+ FLOAT_T dev = 0;
+
+ // set upper bound
+ if(peak_idx + 50 >= array_size){
+ end_idx = array_size-1;
+ }
+ // set start index
+ if(peak_idx - 50 <= 0){
+ start_idx = 0;
+ }
+
+ // sum up the intensities
+ for(; start_idx <= end_idx; ++start_idx){
+ // sum up all deviations squared
+ dev = original_array[start_idx] - mean;
+ variance += (dev*dev);
+ }
+
+ // return the stdev
+ return sqrt(variance/peak_count);
+}
+
+/***
+ * zero and extract peaks
+ * extract peaks that are larger than mean + #step*stdev into new array
+ * zero out the peaks that have been extracted
+ * yes, the facter that a peak has removed will effect the fallowing peaks
+ */
+void Scorer::zeroPeakMeanStdev(
+ FLOAT_T* original_array, ///< the array to normalize -in/out
+ FLOAT_T* new_array, ///< the array to normalize -in/out
+ int step ///< is this 1 or 2 step -in
+ )
+{
+ int peak_count = 0;
+ int idx = 0;
+ int array_size = getMaxBin();
+ FLOAT_T mean = 0;
+ FLOAT_T stdev = 0;
+
+ // iterate over all peaks
+ for(; idx < array_size; ++idx){
+ peak_count = 0;
+ // get mean
+ mean = get_mean_from_array(original_array, array_size, idx, &peak_count);
+ // get stdev
+ stdev = get_stdev_from_array(original_array, array_size, idx, mean, peak_count);
+
+ // DEBUG
+ // carp(CARP_INFO, "zero idx: %d mean: %.8f, stdev: %.8f", idx, mean, stdev);
+
+ // iterate over all positions and extract peaks
+ if(original_array[idx] > (mean + step*stdev)){
+ new_array[idx] = original_array[idx] - (mean - stdev);
+
+ // DEBUG
+ // carp(CARP_INFO, "extract peak: %.2f at idx: %d", original_array[idx], idx);
+
+ // reset the last idx
+ if(last_idx_ < idx){
+ last_idx_ = idx;
+ }
+
+ // for only step 1,
+ if(step == 1){
+ // zero out original peak
+ original_array[idx] = 0;
+ }
+ }
+ }
+}
+
+/**
+ * \brief Zero and extract peaks
+ *
+ * Extract peaks that are larger than mean + #step*stdev into new
+ * array. Zero out the peaks that have been extracted. Repeat twice,
+ * than replace old array with extracted peak array.
+ */
+void Scorer::zeroPeaks()
+{
+ // create a new array, which will replace the original intensity array
+ FLOAT_T* new_array = (FLOAT_T*)mycalloc(getMaxBin(), sizeof(FLOAT_T));
+
+ // step 1,
+ zeroPeakMeanStdev(intensity_array_, new_array, 1);
+ // step 2,
+ zeroPeakMeanStdev(intensity_array_, new_array, 2);
+
+ // replace intensity_array with new intensity array
+ free(intensity_array_);
+ intensity_array_ = new_array;
+
+ // DEBUG
+ /*
+ int idx = 0;
+ for(; idx < scorer->sp_max_mz; ++idx){
+ carp(CARP_INFO, "extracted peaks: %.2f, at idx %d", new_array[idx], idx);
+ }
+ */
+}
+
+/**
+ * keep only the peaks up to top rank peaks remove other peaks.
+ * do second normalization on the top peaks back to max 100 intensity
+ * replace old array with normalized top peak array
+ */
+void Scorer::extractPeaks(
+ int top_rank ///< keep the top ranking peaks -in
+ ) {
+
+ // create a new array, which will replace the original intensity array
+ FLOAT_T* temp_array = (FLOAT_T*)mycalloc(getMaxBin(), sizeof(FLOAT_T));
+ FLOAT_T* original_array = intensity_array_;
+ int idx = 0;
+ int temp_idx = 0;
+ FLOAT_T cut_off = 0;
+ FLOAT_T max_intensity;
+
+ // copy all peaks to temp_array
+ for(; idx < getMaxBin(); ++idx){
+ if(intensity_array_[idx] > 0){
+ temp_array[temp_idx] = original_array[idx];
+
+ // DEBUG print all temp array values
+ // carp(CARP_INFO, "before sort data[%d]=%.3f",temp_idx, temp_array[temp_idx]);
+
+ ++temp_idx;
+ }
+ }
+
+ // if there's over top_rank peaks, keep only top_rank peaks
+ // quick sort
+ quicksort(temp_array, temp_idx);
+
+ // set max and cut_off
+ max_intensity = temp_array[0];
+ cut_off = temp_array[top_rank-1];
+
+ // remove peaks bellow cut_off
+ // also, normalize peaks to max_intensity to 100
+ for(idx = 0; idx < getMaxBin(); ++idx){
+ // DEBUG print all temp array values
+ // carp(CARP_INFO, "sorted data[%d]=%.3f",idx, temp_array[idx]);
+
+ if(original_array[idx] > 0){
+ // is it bellow cut off?
+ if(original_array[idx] < cut_off){
+ // remove peak
+ original_array[idx] = 0;
+ }
+ else{
+ // nomalize peak to max 100
+ original_array[idx] = original_array[idx] / max_intensity * 100;
+ }
+ }
+ }
+
+ free(temp_array);
+ return;
+}
+
+/**
+ * equalize all peaks in a continous region to the largest peak within the continous bins
+ * start from left to right
+ */
+void Scorer::equalizePeaks() {
+
+ int idx;
+ // int array_size = (int)scorer->sp_max_mz-2;
+
+ FLOAT_T max_intensity = 0;
+ int end_idx = 0;
+ int last_idx = last_idx_;
+
+ // equalize peaks to it's greatest intensity
+ // should use array size, but sequest seems to have a bug
+ // last idx is thus, modification to fit sequest
+ // consequences are we will not equalize the very last peak.
+ for(idx = 0; idx < last_idx/*array_size*/; ++idx){
+ // are we inside a continous block?
+ if(intensity_array_[idx] > 0){
+ max_intensity = intensity_array_[idx];
+ end_idx = idx + 1;
+
+ // loop to find the largest peak in the continous block
+ while(end_idx < last_idx && intensity_array_[end_idx] > 0){
+ // reset max intensity
+ if(intensity_array_[end_idx] > max_intensity){
+ max_intensity = intensity_array_[end_idx];
+ }
+
+ ++end_idx;
+ }
+
+ // set all peaks in block to max_intesity
+ for(; idx < end_idx; ++idx){
+ intensity_array_[idx] = max_intensity;
+ }
+ }
+ }
+}
+
+/**
+ * create the intensity array
+ * SCORER must have been created for SP type
+ * \returns true if successful, else FLASE
+ */
+bool Scorer::createIntensityArraySp(
+ Spectrum* spectrum, ///< the spectrum to score -in
+ int charge ///< the peptide charge -in
+ )
+{
+ Peak * peak = NULL;
+ FLOAT_T peak_location = 0;
+ FLOAT_T max_intensity = 0;
+ int mz = 0;
+ FLOAT_T intensity = 0;
+ FLOAT_T bin_width = bin_width_;
+ FLOAT_T bin_offset = bin_offset_;
+ FLOAT_T precursor_mz = spectrum->getPrecursorMz();
+ FLOAT_T experimental_mass_cut_off = precursor_mz*charge + 50;
+ int top_bins = 200;
+
+ // if score type equals SP
+ if(type_ != SP){
+ carp(CARP_ERROR, "incorrect scorer type, only use this method for SP scorers");
+ return false;
+ }
+
+ // while there are more peaks to iterate over..
+ for (PeakIterator peak_iterator = spectrum->begin();
+ peak_iterator != spectrum->end();
+ ++peak_iterator) {
+
+ peak = *peak_iterator;
+ peak_location = peak->getLocation();
+
+ // skip all peaks larger than experimental mass
+ if(peak_location > experimental_mass_cut_off){
+ continue;
+ }
+
+ // skip all peaks within precursor ion mz +/- 15
+ if(peak_location < precursor_mz + 15 && peak_location > precursor_mz - 15){
+ continue;
+ }
+
+ // map peak location to bin
+ mz = INTEGERIZE(peak_location, bin_width, bin_offset);
+
+ if (mz >= getMaxBin()) {
+ carp_once(CARP_WARNING,
+ "SP Scoring: bin:%i is greater than max:%i\n"
+ " mz:%g bin width:%g bin offset:%g\n"
+ " max mz:%g\n"
+ " This warning will not be repeated",
+ mz, getMaxBin(),
+ peak_location, bin_width, bin_offset,
+ sp_max_mz_);
+ continue;
+ }
+
+ // get intensity
+ intensity = sqrt(peak->getIntensity());
+
+ // set intensity in array with correct mz, only if max peak in the bin
+ if(intensity_array_[mz] < intensity){
+ intensity_array_[mz] = intensity;
+
+ // check if max_intensity
+ if(intensity > max_intensity){
+ max_intensity = intensity;
+ }
+ }
+
+ // set last idx to the largest added peak mz value
+ if(last_idx_ < mz){
+ last_idx_ = mz;
+ }
+ }
+
+ // set max_intensity
+ max_intensity_ = max_intensity;
+
+ // normalize intensity
+ nomalize_intensity_array(intensity_array_, last_idx_+1, max_intensity_, 100);
+
+ // smooth peaks
+ smoothPeaks();
+
+ // zero peaks
+ zeroPeaks();
+
+ /* Sequest28 modifications. Determine number of top peaks to select
+ * based on the experimental mass. In Sequest27, the top peaks were
+ * always selected as 200. Keep top ions of sqrt(16*experimental
+ * mass) ranking, but not exceeding 200 ions. */
+ if(experimental_mass_cut_off-50 < 3200){
+ // top bins are sqrt of 16* experimental mass
+ top_bins = (int)(sqrt((experimental_mass_cut_off-50)*16) + 0.5);
+ // however cannot exceed 200
+ if(top_bins > 200){
+ top_bins = 200;
+ }
+ }
+ else{
+ top_bins = (int)((experimental_mass_cut_off-50)/14.00);
+ }
+
+ // extrace the top ions
+ extractPeaks(top_bins);
+
+ // equalize peaks
+ equalizePeaks();
+
+ // Debug
+ /*
+ int idx; int count = 0;
+ for(idx = 0; idx < scorer->last_idx; ++idx){
+ if(scorer->intensity_array[idx] > 0){
+ // DEBUG
+ carp(CARP_INFO, "scoring array[%d], %d = %.4f", idx, count, scorer->intensity_array[idx]);
+ ++count;
+ }
+ }
+ */
+
+ // scorer now been initialized!, ready to score peptides..
+ initialized_ = true;
+
+ return true;
+}
+
+/**
+ * calculates all the necessay values for Sp score, related to the specfic ion_type
+ * adds to intensity_sum and repeat_count
+ *\returns the number of matches found from the predicted ions
+ */
+int Scorer::calculateIonTypeSp(
+ IonSeries* ion_series, ///< the ion series to score against the spectrum -in
+ FLOAT_T* intensity_sum, ///< the total intensity sum of all matches so far -out
+ ION_TYPE_T ion_type, ///< the ion type to check -in
+ int* repeat_count ///< the repeated count of ions (ex. consecutive b ions) -out
+ )
+{
+ int cleavage_idx = 0;
+ Ion* ion = NULL;
+ FLOAT_T one_intensity = 0;
+ int ion_match = 0;
+ int ion_charge = 0;
+ int intensity_array_idx = 0;
+ int* before_cleavage
+ = (int*)mymalloc(ion_series->getCharge()*sizeof(int));
+ int cleavage_array_idx = 0;
+ FLOAT_T bin_width = bin_width_;
+ FLOAT_T bin_offset = bin_offset_;
+
+ // initialize before cleavage indecies
+ for(; cleavage_array_idx < ion_series->getCharge(); ++cleavage_array_idx){
+ before_cleavage[cleavage_array_idx] = -1;
+ }
+
+ // create ion constraint
+ IonConstraint* ion_constraint =
+ new IonConstraint(ion_series->getIonConstraint()->getMassType(), ion_series->getCharge(), ion_type, false);
+
+ // create the filtered iterator that will select among the ions
+ IonFilteredIterator* ion_iterator = new IonFilteredIterator(ion_series, ion_constraint);
+
+ // while there are ion's in ion iterator, add matched observed peak intensity
+ while(ion_iterator->hasNext()){
+ ion = ion_iterator->next();
+ intensity_array_idx
+ = INTEGERIZE(ion->getMassZ(), bin_width, bin_offset);
+ // get the intensity matching to ion's m/z
+ if(intensity_array_idx < getMaxBin()){
+ one_intensity = intensity_array_[intensity_array_idx];
+ }
+ else{
+ // printf("index out of bounds: %d scorer->sp_max_mz: %.2f ion_mass_z: %.2f\n", intensity_array_idx, scorer->sp_max_mz, get_ion_mass_z(ion));
+ one_intensity = 0;
+ }
+
+ // if there is a match in the observed spectrum
+ if(one_intensity > 0){
+
+ // DEBUG
+ // carp(CARP_INFO, "matched ion: %.2f ion intensity: %.2f", get_ion_mass_z(ion), one_intensity);
+
+ ++ion_match;
+ *intensity_sum = *intensity_sum + one_intensity;
+
+ // get ion charge
+ ion_charge = ion->getCharge() - 1;
+
+ // check if repeated ion b1, b2, ...
+ if((cleavage_idx = ion->getCleavageIdx()) == before_cleavage[ion_charge] + 1){
+ ++*repeat_count;
+ }
+
+ // reset the previous cleavage index
+ before_cleavage[ion_charge] = cleavage_idx;
+ }
+ }
+
+
+ // free ion iterator, ion_constraint
+ free(before_cleavage);
+ IonConstraint::free(ion_constraint);
+ delete ion_iterator;
+
+ return ion_match;
+}
+
+
+/**
+ * given a spectrum and ion series calculates the Sp score
+ *\returns the sp score
+ */
+FLOAT_T Scorer::genScoreSp(
+ Spectrum* spectrum, ///< the spectrum to score -in
+ IonSeries* ion_series ///< the ion series to score against the spectrum -in
+ ) {
+
+ FLOAT_T final_score = 0;
+ FLOAT_T intensity_sum = 0;
+ int ion_match = 0;
+ int repeat_count = 0;
+
+ // initialize the scorer before scoring if necessary
+ if(!initialized_){
+ // create intensity array
+ if(!createIntensityArraySp(spectrum, ion_series->getCharge())){
+ carp(CARP_FATAL, "failed to produce Sp");
+ }
+ }
+
+ // calculate the B_ION and Y_ION portions of the Sp score
+ ion_match =
+ calculateIonTypeSp(ion_series, &intensity_sum, B_ION, &repeat_count) +
+ calculateIonTypeSp(ion_series, &intensity_sum, Y_ION, &repeat_count);
+
+ // set the fraction of b,y ions matched for this ion_series
+ sp_b_y_ion_matched_ = ion_match;
+ sp_b_y_ion_possible_ = ion_series->getNumIons();
+ sp_b_y_ion_fraction_matched_ = (FLOAT_T)ion_match / ion_series->getNumIons();
+
+ //// DEBUG!!!!
+ /*
+ carp(CARP_INFO, "# repeat count: %d ion_match count: %d, total_ion count: %d sum: %.2f",
+ repeat_count, ion_match, get_ion_series_num_ions(ion_series),
+ intensity_sum);
+ */
+ // calculate Sp score.
+ if(ion_match != 0){
+ final_score =
+ (intensity_sum * ion_match) * (1+ (repeat_count * sp_beta_)) / ion_series->getNumIons();
+ }
+
+ // return score
+ return final_score;
+}
+
+
+
+
+
+/*****************************************************
+ * Xcorr related functions
+ *
+ *****************************************************/
+
+/**
+ * Normalize each peak intensity of the observed spectrum to max 50
+ * based on the max intenstiy in each of 10 regions.
+ * .
+ */
+void Scorer::normalizeEachRegion(
+ vector<FLOAT_T>& observed, ///< intensities to normalize
+ const vector<FLOAT_T>& max_intensity_per_region, ///< the max intensity in each 10 regions -in
+ int region_selector ///< the size of each regions -in
+ )
+{
+ int region_idx = 0;
+ int next_region = region_selector;
+ FLOAT_T max_intensity = max_intensity_per_region[region_idx];
+
+ // normalize each region
+ for (int i = 0; i < observed.size(); ++i) {
+ // increment the region index and update max_intensity if this
+ // peak is in the next region
+ if (i >= next_region && region_idx < (NUM_REGIONS - 1)) {
+ max_intensity = max_intensity_per_region[++region_idx];
+ next_region += region_selector;
+ }
+ // normalize intensity to max 50
+ observed[i] = (max_intensity != 0)
+ ? (observed[i] / max_intensity) * MAX_PER_REGION
+ : 0.0;
+ }
+}
+
+FLOAT_T* Scorer::getIntensityArrayObserved() {
+ return observed_;
+}
+
+/**
+ * Create the intensity arrays for observed spectrum.
+ * SCORER must have been created for XCORR type.
+ * \returns true if successful, else false.
+ */
+bool Scorer::createIntensityArrayObserved(
+ Spectrum* spectrum, ///< the spectrum to score(observed) -in
+ int charge, ///< the peptide charge -in
+ OBSERVED_PREPROCESS_STEP_T stop_after
+ ) {
+ FLOAT_T precursor_mz = spectrum->getPrecursorMz();
+ FLOAT_T experimental_mass_cut_off = precursor_mz*charge + 50;
+
+ // set max_mz and malloc space for the observed intensity array
+ FLOAT_T sp_max_mz = 512;
+
+ if(experimental_mass_cut_off > 512){
+ int x = (int)experimental_mass_cut_off / 1024;
+ FLOAT_T y = experimental_mass_cut_off - (1024 * x);
+ sp_max_mz = x * 1024;
+
+ if(y > 0){
+ sp_max_mz += 1024;
+ }
+ }
+
+ sp_max_mz_ = sp_max_mz;
+
+ vector<FLOAT_T> observed(getMaxBin(), 0);
+
+ // Store the max intensity in entire spectrum
+ FLOAT_T max_intensity_overall = 0.0;
+ // store the max intensity in each 10 regions to later normalize
+ vector<FLOAT_T> max_intensity_per_region(NUM_REGIONS, 0);
+
+ // while there are more peaks to iterate over..
+ // find the maximum peak m/z (location)
+ double max_peak = 0.0;
+
+ for (PeakIterator peak_iterator = spectrum->begin();
+ peak_iterator != spectrum->end();
+ ++peak_iterator) {
+ Peak* peak = *peak_iterator;
+ FLOAT_T peak_location = peak->getLocation();
+ if (peak_location < experimental_mass_cut_off && peak_location > max_peak
+ && peak->getIntensity() > 0) {
+ max_peak = peak_location;
+ }
+ }
+ int region_selector = INTEGERIZE(max_peak, bin_width_, bin_offset_) / NUM_REGIONS + 1;
+
+ FLOAT_T tolerance = GlobalParams::getRemovePrecursorTolerance();
+
+ // while there are more peaks to iterate over..
+ // bin peaks, adjust intensties, find max for each region
+ for (PeakIterator peak_iterator = spectrum->begin();
+ peak_iterator != spectrum->end();
+ ++peak_iterator) {
+ Peak* peak = *peak_iterator;
+ FLOAT_T peak_location = peak->getLocation();
+
+ // skip all peaks larger than experimental mass
+ // skip all peaks within precursor ion mz +/- 15
+ if (peak_location > experimental_mass_cut_off ||
+ (stop_after >= REMOVE_PRECURSOR_STEP &&
+ peak_location < precursor_mz + tolerance &&
+ peak_location > precursor_mz - tolerance)) {
+ continue;
+ }
+
+ // map peak location to bin
+ int mz = INTEGERIZE(peak_location, bin_width_, bin_offset_);
+ int region = mz / region_selector;
+
+ // don't let index beyond array
+ if (region == NUM_REGIONS && mz < experimental_mass_cut_off) {
+ // Force peak into lower bin
+ region = NUM_REGIONS - 1;
+ } else if (region >= NUM_REGIONS) {
+ // Skip peak altogether
+ continue;
+ }
+
+ // get intensity
+ // sqrt the original intensity
+ FLOAT_T intensity = (stop_after >= SQUARE_ROOT_STEP)
+ ? sqrt(peak->getIntensity()) : peak->getIntensity();
+
+ // Record the max intensity in the full spectrum
+ if (intensity > max_intensity_overall) {
+ max_intensity_overall = intensity;
+ }
+
+ // set intensity in array with correct mz, only if max peak in the bin
+ if (observed[mz] < intensity) {
+ observed[mz] = intensity;
+ // check if this peak is max intensity in the region(one out of 10)
+ if (max_intensity_per_region[region] < intensity) {
+ max_intensity_per_region[region] = intensity;
+ }
+ }
+ }
+
+ // For compatibility with SEQUEST drop peaks with intensity less than 1/20 of
+ // the overall max intensity.
+ if (stop_after >= REMOVE_GRASS_STEP) {
+ for (vector<FLOAT_T>::iterator i = observed.begin(); i != observed.end(); i++) {
+ if (*i <= 0.05 * max_intensity_overall) {
+ *i = 0.0;
+ }
+ }
+ }
+
+ // normalize each 10 regions to max intensity of 50
+ if (stop_after >= TEN_BIN_STEP) {
+ normalizeEachRegion(observed, max_intensity_per_region, region_selector);
+ }
+
+ observed_ = (FLOAT_T*)mycalloc(observed.size(), sizeof(FLOAT_T));
+ copy(observed.begin(), observed.end(), observed_);
+
+ if (stop_after == XCORR_STEP) {
+ // TODO maybe replace with a faster implementation that uses cum distribution
+ for (int i = 0; i < observed.size(); i++) {
+ for (int j = i - MAX_XCORR_OFFSET; j <= i + MAX_XCORR_OFFSET; j++) {
+ if (j > 0 && j < observed.size()) {
+ observed_[i] -= (observed[j] / (MAX_XCORR_OFFSET * 2.0 + 1));
+ }
+ }
+ }
+ }
+
+ return true;
+}
+
+/**
+ * Generate the processed peaks for the spectrum and return via the
+ * intensities array. It's implemented here so that
+ * create_intensity_array_observed() can remain private and so that
+ * the scorer->observed array can be accessed directly.
+ */
+void Scorer::getProcessedPeaks(
+ Spectrum* spectrum,
+ int charge,
+ SCORER_TYPE_T score_type, // SP, XCORR
+ FLOAT_T** intensities, ///< pointer to array of intensities
+ int* max_mz_bin,
+ OBSERVED_PREPROCESS_STEP_T stop_after){
+ // const string& stop_after){
+
+ // create a scorer
+ Scorer scorer(score_type);
+
+ // call create_intensity_array_observed
+ scorer.createIntensityArrayObserved(spectrum, charge, stop_after);
+
+ // return the observed array and the sp_max_mz
+ *intensities = scorer.observed_;
+ *max_mz_bin = scorer.getMaxBin();
+}
+
+
+
+/**
+ * Score the ion series directly.
+ * \returns the calculated XCORR score.
+ */
+FLOAT_T Scorer::scoreIntensityIonSeries(
+ IonSeries* ion_series ///< the ion series to score against the spectrum (theoretical) -in
+ ) {
+
+
+ FLOAT_T ans = 0.0;
+
+ Ion* ion = NULL;
+ int intensity_array_idx = 0;
+ int ion_charge = 0;
+ ION_TYPE_T ion_type;
+ FLOAT_T ion_mass_z = 0;
+ FLOAT_T bin_width = bin_width_;
+ FLOAT_T bin_offset = bin_offset_;
+ int max_bin = getMaxBin();
+ FLOAT_T B_Y_sum = 0.0;
+ FLOAT_T FLANK_sum = 0.0;
+ FLOAT_T LOSS_sum = 0.0;
+
+ // create the ion iterator that will iterate through the ions
+
+ // while there are ion's in ion iterator, add matched observed peak intensity
+ IonIterator eiter = ion_series->end();
+ for (IonIterator ion_iterator = ion_series->begin();
+ ion_iterator != eiter;
+ ++ion_iterator) {
+
+ ion = *ion_iterator;
+
+ ion_mass_z = ion->getMassZ();
+ intensity_array_idx
+ = INTEGERIZE(ion_mass_z, bin_width, bin_offset);
+
+ // skip ions that are located beyond max mz limit
+ if(intensity_array_idx >= max_bin){
+ continue;
+ }
+ ion_type = ion->getType();
+
+ // is it B, Y ion?
+ if(ion_type == B_ION ||
+ ion_type == Y_ION){
+
+ // if (!ion->isModified()){
+ // Add peaks of intensity 50.0 for B, Y type ions.
+ // In addition, add peaks of intensity of 25.0 to +/- 1 m/z flanking each B, Y ion if requested.
+ // Skip ions that are located beyond max mz limit
+ B_Y_sum += observed_[intensity_array_idx];
+ if (use_flanks_) {
+ FLANK_sum += observed_[intensity_array_idx-1];
+ if ((intensity_array_idx + 1) < max_bin) {
+ FLANK_sum += observed_[intensity_array_idx+1];
+ }
+ }
+
+ // add neutral loss of water and NH3
+ ion_charge = ion->getCharge();
+ if(ion_type == B_ION){
+ int h2o_array_idx =
+ INTEGERIZE((ion_mass_z - (MASS_H2O_MONO/ion_charge)),
+ bin_width, bin_offset);
+ LOSS_sum += observed_[h2o_array_idx];
+ }
+
+ int nh3_array_idx
+ = INTEGERIZE((ion_mass_z - (MASS_NH3_MONO/ion_charge)),
+ bin_width, bin_offset);
+ LOSS_sum += observed_[nh3_array_idx];
+
+ }// is it A ion?
+ else if(ion_type == A_ION){
+ // Add peaks of intensity 10.0 for A type ions.
+ LOSS_sum += observed_[intensity_array_idx];
+ }
+ else{// ERROR!, only should create B, Y, A type ions for xcorr theoreical
+ carp(CARP_ERROR, "only should create B, Y, A type ions for xcorr theoretical spectrum");
+ return 0;
+ }
+ }
+
+ ans = B_Y_sum * B_Y_HEIGHT + FLANK_sum * FLANK_HEIGHT + LOSS_sum * LOSS_HEIGHT;
+ return ans / 10000.0;
+}
+
+/**
+ * create the intensity arrays for both observed and theoretical spectrum
+ * SCORER must have been created for XCORR type
+ * \returns true if successful, else FLASE
+ */
+bool Scorer::createIntensityArrayXcorr(
+ Spectrum* spectrum, ///< the spectrum to score(observed) -in
+ int charge ///< the peptide charge -in
+ )
+{
+
+ // DEBUG
+ // carp(CARP_INFO, "precursor_mz: %.1f", precursor_mz);
+
+ if(type_ != XCORR){
+ carp(CARP_ERROR, "Incorrect scorer type, only use this method for XCORR scorers");
+ return false;
+ }
+
+ // create intensity array for observed spectrum
+ if(!createIntensityArrayObserved(spectrum, charge)){
+ carp(CARP_ERROR, "Failed to preprocess observed spectrum for Xcorr");
+ return false;
+ }
+
+ // scorer now been initialized!, ready to score peptides..
+ initialized_ = true;
+
+ return true;
+}
+
+/**
+ * Uses an iterative cross correlation
+ *
+ *\return the final cross correlation score between the observed and the
+ *theoretical spectra
+ */
+FLOAT_T Scorer::crossCorrelation(
+ FLOAT_T* theoretical ///< the theoretical spectrum to score against the observed spectrum -in
+ )
+{
+
+ int size = getMaxBin();
+ FLOAT_T score_at_zero = 0;
+
+ // compare each location in theoretical spectrum
+ int idx;
+ for(idx = 0; idx < size; ++idx){
+ score_at_zero += observed_[idx] * theoretical[idx];
+ }
+
+ return score_at_zero / 10000.0;
+}
+
+/**
+ * given a spectrum and ion series calculates the xcorr score
+ *\returns the xcorr score
+ */
+FLOAT_T Scorer::genScoreXcorr(
+ Spectrum* spectrum, ///< the spectrum to score -in
+ IonSeries* ion_series ///< the ion series to score against the spectrum -in
+ )
+{
+ FLOAT_T final_score = 0;
+ // initialize the scorer before scoring if necessary
+ // preprocess the observed spectrum in scorer
+ if(!initialized_){
+ // create intensity array for observed spectrum, if already not been done
+ if(!createIntensityArrayXcorr(spectrum, ion_series->getCharge())){
+ carp(CARP_FATAL, "failed to produce XCORR");
+ }
+ }
+ final_score = scoreIntensityIonSeries(ion_series);
+ // debug
+ // carp(CARP_INFO, "xcorr: %.2f", final_score);
+
+ // return score
+ return final_score;
+}
+
+/*****************************************************
+ * General purpose functions
+ *
+ *****************************************************/
+
+/**
+ * Score a spectrum vs. an ion series
+ */
+FLOAT_T Scorer::scoreSpectrumVIonSeries(
+ Spectrum* spectrum, ///< the spectrum to score -in
+ IonSeries* ion_series ///< the ion series to score against the spectrum -in
+ ) {
+
+ FLOAT_T final_score = 0;
+
+ if(type_ == SP){
+ final_score = genScoreSp(spectrum, ion_series);
+ }
+ else if(type_ == XCORR){
+ final_score = genScoreXcorr(spectrum, ion_series);
+ }
+ else{
+ carp(CARP_ERROR, "no scoring method availiable for the scorers' score type");
+ }
+
+ return final_score;
+}
+
+/**
+ * Score a spectrum vs. another spectrum
+ */
+
+FLOAT_T Scorer::scoreSpectrumVSpectrum(
+ Spectrum* first_spectrum, ///< the first spectrum to score
+ Spectrum* second_spectrum ///< the second spectrum to score
+) {
+
+ (void)first_spectrum;
+ (void)second_spectrum;
+ return 0.0;
+}
+
+/**
+ * Creates an array of ion constraints for GMTK models.
+ * 0 - b
+ * 1 - b-nh3
+ * 2 - b-h2o
+ * 3 - b+2
+ * 4 - b-nh3+2
+ * 5 - b-h2o+2
+ * 6 - y
+ * 7 - y-nh3
+ * 8 - y-h2o
+ * 9 - y+2
+ * 10 - y-nh3+2
+ * 11 - y-h2o+2
+ * 12 - a
+ * 13 - a-nh3
+ * 14 - a-h2o
+ * 15 - a+2
+ * 16 - a-nh3+2
+ * 17 - a-h2o+2
+ */
+IonConstraint** Scorer::singleIonConstraints() {
+
+ carp(CARP_INFO, "Num ion series %i", GMTK_NUM_ION_SERIES);
+ IonConstraint** ion_constraints = new IonConstraint*[GMTK_NUM_ION_SERIES];
+
+ ION_TYPE_T ion_types[GMTK_NUM_BASE_IONS] = { B_ION, Y_ION, A_ION };
+ int charges[GMTK_NUM_CHARGES] = { 1, 2 };
+
+ MASS_TYPE_T mass_type = GlobalParams::getFragmentMass();
+
+ int ion_constraint_idx = 0;
+
+ int ion_type_idx;
+ // b and y. NOTE keep in synch with GMTKmodel.py writeIonFilesC
+ for (ion_type_idx=0; ion_type_idx < GMTK_NUM_BASE_IONS; ion_type_idx++){
+
+ int charge_idx;
+ for (charge_idx=0; charge_idx < GMTK_NUM_CHARGES; charge_idx++){
+
+ int neutral_idx;
+ for(neutral_idx=0; neutral_idx< GMTK_NUM_NEUTRAL_LOSS+1; neutral_idx++){
+ IonConstraint* ion_constraint =
+ new IonConstraint( mass_type, charges[charge_idx],
+ ion_types[ion_type_idx], false);
+ ion_constraint->setExactness(true);
+ if (neutral_idx == 0){
+ ;
+ }
+ else if (neutral_idx == 1){
+ ion_constraint->setModification(NH3, -1);
+ } else if (neutral_idx == 2){
+ ion_constraint->setModification(H2O, -1);
+ }
+ ion_constraints[ion_constraint_idx] = ion_constraint;
+ ion_constraint_idx++;
+ }
+ }
+ }
+ return ion_constraints;
+}
+
+/**
+ * Frees the single_ion_constraints array
+ */
+void Scorer::freeSingleIonConstraints(
+ IonConstraint** ion_constraints
+ ){
+
+ int constraint_idx;
+ for (constraint_idx=0; constraint_idx<GMTK_NUM_ION_SERIES; constraint_idx++){
+ IonConstraint::free(ion_constraints[constraint_idx]);
+ }
+ delete ion_constraints;
+}
+
+/**
+ * Creates the an array of ion constraints for GMTK models.
+
+ * TODO do we need one for paired and single? Do we want an iterator?
+ */
+IonConstraint** Scorer::pairedIonConstraints(){
+
+ carp(CARP_INFO, "Num ion series %i", GMTK_NUM_PAIRED_ION_SERIES);
+ IonConstraint** base_ion_constraints = singleIonConstraints();
+ IonConstraint** ion_constraints =
+ new IonConstraint*[2 * GMTK_NUM_PAIRED_ION_SERIES];
+
+ // FIX magic numbers
+ /* 0 - b
+ * 1 - b-nh3
+ * 2 - b-h2o
+ * 3 - b+2
+ * 4 - b-nh3+2
+ * 5 - b-h2o+2
+ * 6 - y
+ * 7 - y-nh3
+ * 8 - y-h2o
+ * 9 - y+2
+ * 10 - y-nh3+2
+ * 11 - y-h2o+2
+ * 12 - a
+ * 13 - a-nh3
+ * 14 - a-h2o
+ * 15 - a+2
+ * 16 - a-nh3+2
+ * 17 - a-h2o+2*/
+
+ int indices[GMTK_NUM_PAIRED_ION_SERIES * 2] = {
+ 0, 6, // b,y
+ 0, 12,// b,a
+ 6, 12,// y,a
+ 0, 2, // b,b-h2o
+ 0, 1, // b,b-nh3
+ 0, 3, // b,b+2
+ 2, 5, // b-h2o,b-h2o+2
+ 1, 4, // b-nh3,b-nh3+2
+ 6, 8, // y,y-h2o
+ 6, 7, // y,y-nh3
+ 6, 9, // y,y+2
+ 8, 11,// y-h2o,y-h2o+2
+ 7, 10,// y-nh3,y-nh3+2
+ 12,15,// a,a+2
+ 3,9 // b+2,y+2
+ };
+
+ int idx;
+ for (idx = 0; idx < GMTK_NUM_PAIRED_ION_SERIES * 2; idx++){
+ ion_constraints[idx] = IonConstraint::copy(
+ base_ion_constraints[indices[idx]]);
+ }
+ return ion_constraints;
+}
+
+/**
+ * Frees the paired ion_constraints array
+ */
+void Scorer::freePairedIonConstraints(
+ IonConstraint** ion_constraints
+ ){
+
+ int constraint_idx;
+ for (constraint_idx=0; constraint_idx<GMTK_NUM_PAIRED_ION_SERIES;
+ constraint_idx++){
+ IonConstraint::free(ion_constraints[constraint_idx]);
+ }
+ delete ion_constraints;
+}
+
+/*******************************
+ * get, set methods for scorer
+ *******************************/
+
+/**
+ *\returns the score type of the scorer
+ */
+SCORER_TYPE_T Scorer::getType() {
+
+ return type_;
+}
+
+/**
+ *sets the scorer type
+ */
+void Scorer::setType(
+ SCORER_TYPE_T type ///< The type of scorer -in
+) {
+ type_ = type;
+}
+
+/**
+ *\returns the beta value of the scorer
+ */
+FLOAT_T Scorer::getSpBeta() {
+
+ return sp_beta_;
+}
+
+/**
+ *sets the scorer beta value
+ */
+void Scorer::setSpBeta(
+ FLOAT_T sp_beta ///< used for Sp: the beta variable -in
+ ) {
+
+ sp_beta_ = sp_beta;
+}
+
+/**
+ *\returns the max_mz value of the scorer
+ */
+FLOAT_T Scorer::getSpMaxMz() {
+
+ return sp_max_mz_;
+}
+
+/**
+ *set the scorer max_mz value
+ */
+void Scorer::setSpMaxMz(
+ FLOAT_T sp_max_mz ///< used for Sp: the max_mz variable -in
+ ) {
+
+ sp_max_mz_ = sp_max_mz;
+}
+
+/**
+ *\returns the max bin index of the scorer array(s).
+ */
+int Scorer::getMaxBin() {
+ return INTEGERIZE(sp_max_mz_, bin_width_, bin_offset_);
+}
+
+/**
+ * adds the intensity at add_idx
+ * if, there already exist a peak at the index, only overwrite if
+ * intensity is larger than the existing peak.
+ */
+void Scorer::addIntensity(
+ FLOAT_T* intensity_array, ///< the intensity array to add intensity at index add_idx -out
+ int add_idx, ///< the idex to add the intensity -in
+ FLOAT_T intensity ///< the intensity to add -in
+ ) {
+
+ assert(add_idx >= 0);
+ ion_counter++;
+ if(intensity_array[add_idx] < intensity){
+ intensity_array[add_idx] = intensity;
+ }
+}
+
+
+FLOAT_T Scorer::scoreIntensity(
+ int add_idx,
+ FLOAT_T intensity
+ ) {
+ if (add_idx >= 0) {
+ return (observed_[add_idx] * intensity);
+ } else {
+ return 0.0;
+ }
+}
+
+
+
+/**
+ *\returns the fraction of b,y ions matched for scoring SP,
+ * the values is valid for the last ion series scored with this scorer object
+ */
+FLOAT_T Scorer::getSpBYIonFractionMatched() {
+
+ return sp_b_y_ion_fraction_matched_;
+}
+
+/**
+ *\returns the number of b,y ions matched for scoring SP
+ */
+int Scorer::getSpBYIonMatched() {
+
+ return sp_b_y_ion_matched_;
+}
+
+/**
+ *\returns the number of b,y ions possible to match for scoring SP
+ */
+int Scorer::getSpBYIonPossible() {
+
+ return sp_b_y_ion_possible_;
+}
+
+/*************************************
+ * Score for LOGP_EXP_SP && LOGP_BONF_EXP_SP
+ *
+ *
+ *
+ ************************************/
+
+/**
+ * Compute a p-value for a given score w.r.t. an exponential with the
+ * given parameters.
+ * \returns the -log(p_value) of the exponential distribution
+ */
+FLOAT_T score_logp_exp_sp(
+ FLOAT_T sp_score, ///< The sp score for the scoring peptide -in
+ FLOAT_T mean ///< The overall mean of the sp scored peptides -in
+ )
+{
+ return -log( exp(-(1/mean) * sp_score) );
+}
+
+/**
+ * Compute a p-value for a given score w.r.t. an exponential with the
+ * given parameters.
+ * \returns the -log(p_value) of the exponential distribution with
+ * Bonferroni correction
+ */
+FLOAT_T score_logp_bonf_exp_sp(
+ FLOAT_T sp_score, ///< The sp score for the scoring peptide -in
+ FLOAT_T mean, ///< The overall mean of the sp scored peptides -in
+ int num_peptide ///< The number of peptides scored for sp
+ )
+{
+ double p_value = exp(-(1/mean) * sp_score);
+
+ // The Bonferroni correction
+ // use original equation 1-(1-p_value)^n when p is not too small
+ if(p_value > BONFERRONI_CUT_OFF_P ||
+ p_value*num_peptide > BONFERRONI_CUT_OFF_NP){
+ return -log(1-pow((1-p_value), num_peptide));
+ }
+ // else, use the approximation
+ else{
+ return -log(p_value*num_peptide);
+ }
+}
+
+/**
+ * Apply a Bonferroni correction to a given p-value.
+ * \returns the corrected p_value.
+ */
+FLOAT_T bonferroni_correction(
+ FLOAT_T p_value, ///< The uncorrected p-value.
+ int num_tests ///< The number of tests performed.
+ )
+{
+ FLOAT_T return_value;
+
+ // use original equation 1-(1-p_value)^n when p is not too small
+ if(p_value > BONFERRONI_CUT_OFF_P ||
+ p_value * num_tests > BONFERRONI_CUT_OFF_NP){
+
+ return_value = 1-pow((1-p_value), num_tests);
+ }
+ // else, use the approximation
+ else {
+ return_value = p_value * num_tests;
+ }
+
+ carp(CARP_DETAILED_DEBUG, "Stat: pvalue after = %.6f", return_value);
+ return return_value;
+}
+
+/**
+ * Compute a p-value for a given score w.r.t. a Weibull with given parameters.
+ *\returns the p_value
+ */
+FLOAT_T compute_weibull_pvalue(
+ FLOAT_T score, ///< The score for the scoring peptide -in
+ FLOAT_T eta, ///< The eta parameter of the Weibull -in
+ FLOAT_T beta, ///< The beta parameter of the Weibull -in
+ FLOAT_T shift ///< The shift parameter of the Weibull -in
+ ){
+ carp(CARP_DETAILED_DEBUG, "Stat: score = %.6f", score);
+
+ FLOAT_T return_value;
+
+ // No Weibull parameter, return NaN.
+ if (eta == 0.0) {
+ carp(CARP_DETAILED_DEBUG, "Failed fit, returning p-value=NaN");
+ return_value = NaN();
+ }
+ // undefined past shift, give lowest possible score.
+ else if (score + shift <= 0) {
+ carp(CARP_DETAILED_DEBUG, "Bad shift, returning p-value=1");
+ return_value = 1.0;
+ }
+ else {
+ return_value = exp(-pow((score + shift) / eta, beta));
+ carp(CARP_DETAILED_DEBUG, "Stat: pvalue before = %g", return_value);
+ }
+ return(return_value);
+}
+
+/**
+ * Compute a p-value for a given score w.r.t. a Weibull with given parameters.
+ *\returns the -log(p_value)
+ */
+double score_logp_bonf_weibull(
+ FLOAT_T score, ///< The score for the scoring peptide -in
+ FLOAT_T eta, ///< The eta parameter of the Weibull
+ FLOAT_T beta, ///< The beta parameter of the Weibull
+ FLOAT_T shift, ///< The shift parameter of the Weibull
+ int num_peptide ///< The number of peptides
+ ){
+ carp(CARP_DETAILED_DEBUG, "Stat: score = %.6f", score);
+
+ double temp = score + shift;
+ if (temp <=0) {
+ //undefined past shift, give lowest possible score (-log(1.0)).
+ carp(CARP_DETAILED_DEBUG,"undefined returning 0");
+ return 0.0;
+ }
+ else {
+ double p_value = exp(-pow((double) temp/eta, (double) beta));
+ carp(CARP_DETAILED_DEBUG, "Stat: pvalue before = %.15f", p_value);
+
+ // The Bonferroni correction
+ // use original equation 1-(1-p_value)^n when p is not too small
+ if(p_value > BONFERRONI_CUT_OFF_P
+ || p_value*num_peptide > BONFERRONI_CUT_OFF_NP){
+
+ double corrected_pvalue = -log(1-pow((1-p_value), num_peptide));
+ carp(CARP_DETAILED_DEBUG, "Stat: pvalue after = %.6f", corrected_pvalue);
+ return corrected_pvalue;
+ }
+ // else, use the approximation
+ else{
+ double corrected_pvalue = -log(p_value*num_peptide);
+ carp(CARP_DETAILED_DEBUG, "Stat: pvalue after = %.6f", corrected_pvalue);
+ return corrected_pvalue;
+ }
+ }
+}
+
+/**
+ * Compute a p-value for a given score w.r.t. an EVD with the given parameters.
+ * Function: ExtremeValueP()
+ *
+ * Purpose: Calculate P(S>x) according to an extreme
+ * value distribution, given x and the parameters
+ * of the distribution (characteristic
+ * value mu, decay constant lambda).
+ *
+ * This function is exquisitely prone to
+ * floating point exceptions if it isn't coded
+ * carefully.
+ *
+ * Args: x = score
+ * mu = characteristic value of extreme value distribution
+ * lambda = decay constant of extreme value distribution
+ *
+ *\returns P(S>x)
+ */
+double compute_evd_pvalue(
+ FLOAT_T score, ///< The xcorr score for the scoring peptide -in
+ FLOAT_T evd_mu, ///< EVD parameter Xcorr(characteristic value of extreme value distribution) -in
+ FLOAT_T evd_lambda ///< EVD parameter Xcorr(decay constant of extreme value distribution) -in
+ )
+{
+ // These constants are hardware dependent.
+ // These values should be good for double precision floating point
+ // numbers compatible with the IEEE 754 standard.
+ // DBL_EPSILON = 2.2204460492503131e-16
+ // DBL_MAX_10_EXP = 308
+
+ double p_value = 0;
+
+ // avoid exceptions near P=1.0
+ if((evd_lambda * (score - evd_mu)) <= -1.0 * log(-1.0 * log(DBL_EPSILON_))){
+ return 1.0;
+ }
+
+ // avoid underflow fp exceptions near P=0.0
+ if((evd_lambda * (score - evd_mu)) >= 2.3 * DBL_MAX_10_EXP_){
+ return 0.0;
+ }
+
+ // a roundoff issue arises; use 1 - e^-x --> x for small x
+ p_value = exp(-1.0 * evd_lambda * (score - evd_mu));
+ if (p_value < 1e-7){
+ return p_value;
+ }
+ else{
+ return (1.0 - exp(-1.0 * p_value));
+ }
+}
+
+/**
+ * Compute a p-value for a given score w.r.t. an EVD with the given parameters.
+ *\returns the -log(p_value) of the EVD distribution
+ */
+FLOAT_T score_logp_evd_xcorr(
+ FLOAT_T xcorr_score, ///< The xcorr score for the scoring peptide -in
+ FLOAT_T mu, ///< EVD parameter Xcorr(characteristic value of extreme value distribution) -in
+ FLOAT_T l_value ///< EVD parameter Xcorr(decay constant of extreme value distribution) -in
+ )
+{
+ return -log(compute_evd_pvalue(xcorr_score, mu, l_value));
+}
+
+/**
+ * Compute a p-value for a given score w.r.t. an EVD with the given parameters.
+ *\returns the -log(p_value) of the EVD distribution with Bonferroni correction
+ */
+FLOAT_T score_logp_bonf_evd_xcorr(
+ FLOAT_T xcorr_score, ///< The xcorr score for the scoring peptide -in
+ FLOAT_T mu, ///< EVD parameter Xcorr(characteristic value of extreme value distribution) -in
+ FLOAT_T l_value, ///< EVD parameter Xcorr(decay constant of extreme value distribution) -in
+ int num_peptide ///< The number of peptides scored for sp -in
+ )
+{
+ double p_value = compute_evd_pvalue(xcorr_score, mu, l_value);
+
+ // DEBUG
+ carp(CARP_DEBUG, "p_value: %E, experiment_size: %d", p_value, num_peptide);
+
+ // The Bonferroni correction
+ // use original equation 1-(1-p_value)^n when p is not too small
+ if(p_value > BONFERRONI_CUT_OFF_P || p_value*num_peptide > BONFERRONI_CUT_OFF_NP){
+ return -log(1-pow((1-p_value), num_peptide));
+ }
+ // else, use the approximation
+ else{
+ return -log(p_value*num_peptide);
+ }
+}
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/Scorer.h b/src/model/Scorer.h
new file mode 100644
index 0000000..de44f32
--- /dev/null
+++ b/src/model/Scorer.h
@@ -0,0 +1,504 @@
+/**
+ * \file Scorer.h
+ * \brief object to score spectrum vs. spectrum or spectrum vs. scorer
+ */
+
+/*
+ * AUTHOR: Chris Park
+ * CREATE DATE: 9 Oct 2006
+ * $Revision: 1.22 $
+ *****************************************************************************/
+#ifndef SCORER_H
+#define SCORER_H
+
+#include <stdio.h>
+#ifndef _MSC_VER
+#include <dirent.h>
+#endif
+#include <string>
+#ifdef _MSC_VER
+#include "util/windirent.h"
+#endif
+#include "model/objects.h"
+#include "model/Spectrum.h"
+#include "model/Peptide.h"
+#include "model/Ion.h"
+
+
+/**
+ * Macro for converting floating point to integers.
+ */
+
+#define INTEGERIZE(VALUE,BIN_SIZE,BIN_OFFSET) \
+ ((int)( ( ( VALUE / BIN_SIZE ) + 1.0 ) - BIN_OFFSET ) )
+
+class Scorer {
+
+ protected:
+ SCORER_TYPE_T type_; ///< The type of scorer
+ FLOAT_T sp_beta_; ///< used for Sp: the beta variable
+ FLOAT_T sp_max_mz_; ///< used for Sp: the max mz for the intensity array
+ int sp_b_y_ion_matched_; ///< The most recent ion_collection number of the b, y ion matched while scoring for SP
+ int sp_b_y_ion_possible_; ///< The most recent ion_collection number of the b, y ion possible while scoring for SP
+ FLOAT_T sp_b_y_ion_fraction_matched_; ///< The ratio of matched and possible.
+
+ FLOAT_T* intensity_array_; ///< used for Sp: the intensity array, which can be indexed using the m/z
+ FLOAT_T max_intensity_; ///< the max intensity in the intensity array
+ bool initialized_; ///< has the scorer been initialized?
+ int last_idx_; ///< the last index in the array, the data size of the array
+
+ FLOAT_T bin_width_; ///< width of the bins to use for arrays
+ FLOAT_T bin_offset_; ///< m/z offset for the bins.
+ bool use_flanks_; ///< use flanking peaks in calculation of XCorr theoretical
+
+ /// used for xcorr
+ FLOAT_T* observed_; ///< used for Xcorr: observed spectrum intensity array
+ FLOAT_T* theoretical_; ///< used for Xcorr: theoretical spectrum intensity array
+
+ /**
+ * Initializes an empty scorer object
+ */
+ void init();
+
+ /**
+ * smooth all peaks in intensity array
+ * Replaces the original array with the newly smooothed array
+ */
+ void smoothPeaks();
+
+ /***
+ * zero and extract peaks
+ * extract peaks that are larger than mean + #step*stdev into new array
+ * zero out the peaks that have been extracted
+ * yes, the facter that a peak has removed will effect the fallowing peaks
+ */
+ void zeroPeakMeanStdev(
+ FLOAT_T* original_array, ///< the array to normalize -in/out
+ FLOAT_T* new_array, ///< the array to normalize -in/out
+ int step ///< is this 1 or 2 step -in
+ );
+
+ /**
+ * \brief Zero and extract peaks
+ *
+ * Extract peaks that are larger than mean + #step*stdev into new
+ * array. Zero out the peaks that have been extracted. Repeat twice,
+ * than replace old array with extracted peak array.
+ */
+ void zeroPeaks();
+
+ /**
+ * keep only the peaks up to top rank peaks remove other peaks.
+ * do second normalization on the top peaks back to max 100 intensity
+ * replace old array with normalized top peak array
+ */
+ void extractPeaks(
+ int top_rank ///< keep the top ranking peaks -in
+ );
+
+ /**
+ * equalize all peaks in a continous region to the largest peak within the continous bins
+ * start from left to right
+ */
+ void equalizePeaks();
+
+ /**
+ * calculates all the necessay values for Sp score, related to the specfic ion_type
+ * adds to intensity_sum and repeat_count
+ *\returns the number of matches found from the predicted ions
+ */
+ int calculateIonTypeSp(
+ IonSeries* ion_series, ///< the ion series to score against the spectrum -in
+ FLOAT_T* intensity_sum, ///< the total intensity sum of all matches so far -out
+ ION_TYPE_T ion_type, ///< the ion type to check -in
+ int* repeat_count ///< the repeated count of ions (ex. consecutive b ions) -out
+ );
+
+ /**
+ * create the intensity array
+ * SCORER must have been created for SP type
+ * \returns true if successful, else FLASE
+ */
+ bool createIntensityArraySp(
+ Crux::Spectrum* spectrum, ///< the spectrum to score -in
+ int charge ///< the peptide charge -in
+ );
+
+ /**
+ * given a spectrum and ion series calculates the Sp score
+ *\returns the sp score
+ */
+ FLOAT_T genScoreSp(
+ Crux::Spectrum* spectrum, ///< the spectrum to score -in
+ IonSeries* ion_series ///< the ion series to score against the spectrum -in
+ );
+
+ /*****************************************************
+ * Xcorr related functions
+ *
+ *****************************************************/
+
+ /**
+ * normalize each 10 regions of the observed spectrum to max 50
+ */
+ void normalizeEachRegion(
+ vector<FLOAT_T>& observed, ///< intensities to normalize
+ const vector<FLOAT_T>& max_intensity_per_region, ///< the max intensity in each 10 regions -in
+ int region_selector ///< the size of each regions -in
+ );
+
+ /**
+ * given a spectrum and ion series calculates the xcorr score
+ *\returns the xcorr score
+ */
+ FLOAT_T genScoreXcorr(
+ Crux::Spectrum* spectrum, ///< the spectrum to score -in
+ IonSeries* ion_series ///< the ion series to score against the spectrum -in
+ );
+
+ /**
+ * Scores the ion series directly against the observed array.
+ */
+ FLOAT_T scoreIntensityIonSeries(
+ IonSeries* ion_series
+ );
+
+ /*****************************************************
+ * General purpose functions
+ *
+ *****************************************************/
+ /**
+ * Creates the an array of ion constraints for GMTK models.
+
+ * TODO do we need one for paired and single? Do we want an iterator?
+ */
+ IonConstraint** pairedIonConstraints();
+
+ /**
+ * Frees the paired ion_constraints array
+ */
+ void freePairedIonConstraints(
+ IonConstraint** ion_constraints
+ );
+
+ public:
+
+ /**
+ * \returns An (empty) scorer object.
+ */
+ Scorer();
+
+ /**
+ * Instantiates a new scorer object from a SCORER_TYPE_T.
+ * \returns a new scorer object
+ */
+ Scorer(
+ SCORER_TYPE_T type ///< the type of scorer -in
+ );
+
+ /**
+ * Frees an allocated scorer object.
+ */
+ ~Scorer();
+
+ /**
+ * Score a spectrum vs. an ion series
+ */
+ FLOAT_T scoreSpectrumVIonSeries(
+ Crux::Spectrum* spectrum, ///< the spectrum to score -in
+ IonSeries* ion_series ///< the ion series to score against the spectrum -in
+ );
+
+ /**
+ * Frees the single_ion_constraints array
+ */
+ void freeSingleIonConstraints(
+ IonConstraint** ion_constraints
+ );
+
+ /**
+ * Creates the an array of ion constraints for GMTK models.
+ * TODO do we need one for paired and single? Do we want an iterator?
+ */
+ IonConstraint** singleIonConstraints();
+
+ /**
+ * Score a spectrum vs. another spectrum
+ */
+ FLOAT_T scoreSpectrumVSpectrum(
+ Crux::Spectrum* first_spectrum, ///< the first spectrum to score -in
+ Crux::Spectrum* second_spectrum ///< the second spectrum to score -in
+ );
+
+ /*******************************
+ * get, set methods for scorer
+ *******************************/
+
+ /**
+ *\returns the score type of the scorer
+ */
+ SCORER_TYPE_T getType();
+
+ /**
+ *sets the scorer type
+ */
+ void setType(
+ SCORER_TYPE_T type ///< The type of scorer -in
+ );
+
+ /**
+ *\returns the beta value of the scorer
+ */
+ FLOAT_T getSpBeta();
+
+ /**
+ *sets the scorer beta value
+ */
+ void setSpBeta(
+ FLOAT_T sp_beta ///< used for Sp: the beta variable -in
+ );
+
+ /**
+ *\returns the gamma value of the scorer
+ */
+ FLOAT_T getSpGamma();
+
+ /**
+ *sets the scorer gamma value
+ */
+ void setSpGamma(
+ FLOAT_T sp_gamma ///< used for Sp: the gamma variable -in
+ );
+
+
+ /**
+ *\returns the min_mz value of the scorer
+ */
+ FLOAT_T getSpMinMz();
+
+ /**
+ *sets the scorer min_mz value
+ */
+ void setSpMinMz(
+ FLOAT_T sp_min_mz ///< used for Sp: the min_mz variable -in
+ );
+
+
+ /**
+ *\returns the max_mz value of the scorer
+ */
+ FLOAT_T getSpMaxMz();
+
+ /**
+ *sets the scorer max_mz value
+ */
+ void setSpMaxMz(
+ FLOAT_T sp_max_mz ///< used for Sp: the max_mz variable -in
+ );
+
+ /**
+ *\returns the max bin index of the scorer array(s).
+ */
+ int getMaxBin();
+
+ /**
+ *\returns the sp_array_resolution value of the scorer
+ */
+ FLOAT_T getSpArrayResolution();
+
+ /**
+ *sets the scorer sp_array_resolution value
+ */
+ void setSpArrayResolution(
+ FLOAT_T sp_array_resolution ///< used for Sp: the sp_array_resolution variable -in
+ );
+
+ /**
+ *\returns the sp_sum_resolution value of the scorer
+ */
+ FLOAT_T getSpSumResolution();
+
+ /**
+ *sets the scorer sp_sum_resolution value
+ */
+ void setSpSumResolution(
+ FLOAT_T sp_sum_resolution ///< used for Sp: the sp_sum_resolution variable -in
+ );
+
+ /**
+ *\returns the equalize_resolution value of the scorer
+ */
+ FLOAT_T getSpEqualizeResolution();
+
+ /**
+ *sets the scorer equalize_resolution value
+ */
+ void setSpEqualizeResolution(
+ FLOAT_T sp_equalize_resolution ///< used for Sp: the equalize_resolution variable -in
+ );
+
+ /**
+ *\returns the fraction of b,y ions matched for scoring SP, the values is valid for the last ion series scored with this scorer object
+ */
+ FLOAT_T getSpBYIonFractionMatched();
+
+ /**
+ *\returns the number of possible matched b,y ions for scoring SP
+ */
+ int getSpBYIonMatched();
+
+ /**
+ *\returns the number of matched b,y ions for scoring SP
+ */
+ int getSpBYIonPossible();
+
+ /**
+ * Generate the processed peaks for the spectrum and return via the
+ * intensities array. It's implemented here so that
+ * create_intensity_array_observed() can remain private and so that
+ * the scorer->observed array can be accessed directly.
+ * .
+ */
+ static void getProcessedPeaks(
+ Crux::Spectrum* spectrum,
+ int charge,
+ SCORER_TYPE_T score_type,
+ FLOAT_T** intensities, ///< pointer to array of intensities
+ int* mz_bins,
+ OBSERVED_PREPROCESS_STEP_T stop_after);
+
+ /**
+ * create the intensity arrays for both observed and theoretical spectrum
+ * SCORER must have been created for XCORR type
+ * \returns true if successful, else false
+ */
+ bool createIntensityArrayXcorr(
+ Crux::Spectrum* spectrum, ///< the spectrum to score(observed) -in
+ int charge ///< the peptide charge -in
+ );
+
+ /**
+ * Uses an iterative cross correlation
+ *
+ *\return the final cross correlation score between the observed and the
+ *theoretical spectra
+ */
+ FLOAT_T crossCorrelation(
+ FLOAT_T* theoretical ///< the theoretical spectrum to score against the observed spectrum -in
+ );
+
+ FLOAT_T* getIntensityArrayObserved();
+
+ bool createIntensityArrayObserved(
+ Crux::Spectrum* spectrum, ///< the spectrum to score(observed) -in
+ int charge, ///< the peptide charge -in
+ OBSERVED_PREPROCESS_STEP_T stop_after = XCORR_STEP ///< the preprocessing step to stop after -in
+ );
+
+ /**
+ * adds the intensity at add_idx
+ * if, there already exist a peak at the index, only overwrite if
+ * intensity is larger than the existing peak.
+ */
+ static void addIntensity(
+ FLOAT_T* intensity_array, ///< the intensity array to add intensity at index add_idx -out
+ int add_idx, ///< the idex to add the intensity -in
+ FLOAT_T intensity ///< the intensity to add -in
+ );
+
+ /**
+ * \return the score using the observed[idx] * intensity
+ */
+ FLOAT_T scoreIntensity(
+ int add_idx,
+ FLOAT_T intensity
+ );
+
+};
+
+
+/*************************************
+ * Score for LOGP_*
+ ************************************/
+
+/**
+ * Compute a p-value for a given score w.r.t. an exponential with the given parameters.
+ *\returns the -log(p_value) of the exponential distribution
+ */
+FLOAT_T score_logp_exp_sp(
+ FLOAT_T sp_score, ///< The sp score for the scoring peptide -in
+ FLOAT_T mean ///< The overall mean of the sp scored peptides -in
+ );
+
+/**
+ * Compute a p-value for a given score w.r.t. an exponential with the given parameters.
+ *\returns the -log(p_value) of the exponential distribution with Bonferroni correction
+ */
+FLOAT_T score_logp_bonf_exp_sp(
+ FLOAT_T sp_score, ///< The sp score for the scoring peptide -in
+ FLOAT_T mean, ///< The overall mean of the sp scored peptides -in
+ int num_peptide ///< The number of peptides scored for sp
+ );
+
+/**
+ * Apply a Bonferroni correction to a given p-value.
+ * \returns the corrected -log(p_value)
+ */
+FLOAT_T bonferroni_correction(
+ FLOAT_T p_value, ///< The uncorrected p-value.
+ int num_tests ///< The number of tests performed.
+ );
+
+/**
+ * Compute a p-value for a given score w.r.t. a Weibull with given parameters.
+ *\returns the p_value
+ */
+FLOAT_T compute_weibull_pvalue(
+ FLOAT_T score, ///< The score for the scoring peptide -in
+ FLOAT_T eta, ///< The eta parameter of the Weibull -in
+ FLOAT_T beta, ///< The beta parameter of the Weibull -in
+ FLOAT_T shift ///< The shift parameter of the Weibull -in
+ );
+
+/**
+ * Compute a p-value for a given score w.r.t. a Weibull with given parameters.
+ *\returns the -log(p_value)
+ */
+double score_logp_bonf_weibull(
+ FLOAT_T score, ///< The score for the scoring peptide -in
+ FLOAT_T eta, ///< The eta parameter of the Weibull
+ FLOAT_T beta, ///< The beta parameter of the Weibull
+ FLOAT_T shift, ///< The shift parameter of the Weibull
+ int num_peptides ///< The number of peptides
+ );
+
+
+/**
+ * Compute a p-value for a given score w.r.t. an EVD with the given parameters.
+ *\returns the -log(p_value) of the EVD distribution
+ */
+FLOAT_T score_logp_evd_xcorr(
+ FLOAT_T xcorr_score, ///< The xcorr score for the scoring peptide -in
+ FLOAT_T mu, ///< EVD parameter Xcorr(characteristic value of extreme value distribution) -in
+ FLOAT_T l_value ///< EVD parameter Xcorr(decay constant of extreme value distribution) -in
+ );
+
+/**
+ * Compute a p-value for a given score w.r.t. an EVD with the given parameters.
+ *\returns the -log(p_value) of the EVD distribution with Bonferroni correction
+ */
+FLOAT_T score_logp_bonf_evd_xcorr(
+ FLOAT_T xcorr_score, ///< The xcorr score for the scoring peptide -in
+ FLOAT_T mu, ///< EVD parameter Xcorr(characteristic value of extreme value distribution) -in
+ FLOAT_T l_value, ///< EVD parameter Xcorr(decay constant of extreme value distribution) -in
+ int num_peptide ///< The number of peptides scored for sp -in
+ );
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/model/Spectrum.cpp b/src/model/Spectrum.cpp
new file mode 100644
index 0000000..e3764d9
--- /dev/null
+++ b/src/model/Spectrum.cpp
@@ -0,0 +1,971 @@
+/*************************************************************************//**
+ * \file Spectrum.cpp
+ * AUTHOR: Chris Park, cpp-ified by Barbara Frewen
+ * CREATE DATE: June 22 2006, turned into a class Sept 21, 2010
+ * \brief code to support working with spectra
+ ****************************************************************************/
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#include "Spectrum.h"
+#include "util/utils.h"
+#include "util/mass.h"
+#include "util/Params.h"
+#include "parameter.h"
+#include "Scorer.h"
+#include "io/carp.h"
+#include <vector>
+#include <string>
+#include "io/DelimitedFile.h"
+#include "io/MatchFileReader.h"
+#include "MSToolkit/Spectrum.h"
+#include "util/FileUtils.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+using namespace Crux;
+namespace pzd = pwiz::msdata;
+
+/**
+ * Default constructor.
+ */
+Spectrum::Spectrum() :
+ first_scan_(0),
+ last_scan_(0),
+ precursor_mz_(0),
+ min_peak_mz_(0),
+ max_peak_mz_(0),
+ total_energy_(0),
+ lowest_sp_(0),
+ has_total_energy_(false),
+ has_lowest_sp_(false),
+ has_peaks_(false),
+ sorted_by_mz_(false),
+ sorted_by_intensity_(false),
+ has_mz_peak_array_(false)
+{
+ mz_peak_array_ = NULL;
+}
+
+/**
+ * Constructor initializes spectrum with given values.
+ */
+Spectrum::Spectrum (
+ int first_scan, ///< The number of the first scan -in
+ int last_scan, ///< The number of the last scan -in
+ FLOAT_T precursor_mz, ///< The m/z of the precursor
+ const vector<int>& possible_z, ///< The possible charge states
+ const string& filename ///< Optional filename
+ ) :
+ first_scan_(first_scan),
+ last_scan_(last_scan),
+ precursor_mz_(precursor_mz),
+ min_peak_mz_(0),
+ max_peak_mz_(0),
+ total_energy_(0),
+ lowest_sp_(0),
+ has_total_energy_(false),
+ has_lowest_sp_(false),
+ filename_(filename),
+ has_peaks_(false),
+ sorted_by_mz_(false),
+ sorted_by_intensity_(false),
+ has_mz_peak_array_(false)
+ {
+ mz_peak_array_ = NULL;
+
+ for (unsigned int idx=0;idx<possible_z.size();idx++) {
+ SpectrumZState zstate;
+ zstate.setMZ(precursor_mz, possible_z.at(idx));
+ zstates_.push_back(zstate);
+ }
+}
+
+/**
+ * Default destructor.
+ */
+Spectrum::~Spectrum()
+{
+ free_peak_vector(peaks_);
+
+ if(has_mz_peak_array_){
+ delete [] mz_peak_array_;
+ }
+}
+
+/**
+ * \returns the peak iterator that signifies the start of the peaks
+ * in the spectrum
+ */
+PeakIterator Spectrum::begin() const {
+ return peaks_.begin();
+}
+
+/**
+ * \returns the peak iterator that signifies the end of the peaks
+ * in the spectrum
+ */
+PeakIterator Spectrum::end() const {
+ return peaks_.end();
+}
+
+/**
+ * Prints a spectrum object to file in ms2 format.
+ */
+void Spectrum::print(FILE* file) ///< output file to print at -out
+{
+ int mass_precision = Params::GetInt("mass-precision");
+ fprintf(file, "S\t%06d\t%06d\t%.*f\n",
+ first_scan_,
+ last_scan_,
+ mass_precision,
+ precursor_mz_);
+
+ // print 'I' line
+ for(size_t line_idx = 0; line_idx < i_lines_v_.size(); line_idx++){
+ fprintf(file, "%s\n", (i_lines_v_[line_idx]).c_str());
+ }
+
+ // print 'Z', 'D' line
+ for(size_t z_idx = 0; z_idx < zstates_.size(); z_idx++){
+ fprintf(file, "Z\t%d\t%.*f\n", zstates_[z_idx].getCharge(), mass_precision,
+ zstates_[z_idx].getSinglyChargedMass());
+ // are there any 'D' lines to print?
+ if(z_idx < d_lines_v_.size() ){
+ fprintf(file, "%s", d_lines_v_[z_idx].c_str());
+ }
+ }
+
+ // print 'EZ' line
+ for (size_t ez_idx = 0; ez_idx < ezstates_.size(); ez_idx++) {
+ fprintf(file, "I\tEZ\t%d\t%.4f\t%.4f\t%.4f\n", ezstates_[ez_idx].getCharge(),
+ ezstates_[ez_idx].getSinglyChargedMass(),
+ ezstates_[ez_idx].getRTime(),
+ ezstates_[ez_idx].getArea());
+ }
+
+ if (zstates_.size() == 0 && ezstates_.size() != 0) {
+ for (size_t ez_idx = 0; ez_idx < ezstates_.size(); ez_idx++) {
+ fprintf(file, "Z\t%d\t%.*f\n", ezstates_[ez_idx].getCharge(), mass_precision,
+ ezstates_[ez_idx].getSinglyChargedMass());
+ }
+ }
+
+ // print peaks
+ for(int peak_idx = 0; peak_idx < (int)peaks_.size(); ++peak_idx){
+ fprintf(file, "%.*f %.4f\n",
+ mass_precision,
+ peaks_[peak_idx]->getLocation(),
+ peaks_[peak_idx]->getIntensity());
+ }
+}
+
+/**
+ * Prints a spectrum in ms2 format with the given intensities instead of the
+ * observed peaks. Assumes intensities are in m/z bins from 0 to
+ * max_mz_bin. Only prints non-zero intensities.
+ */
+void Spectrum::printProcessedPeaks(
+ SpectrumZState& zstate, ///< print at this charge state
+ FLOAT_T* intensities, ///< intensities of new peaks
+ int max_mz_bin, ///< num_bins in intensities
+ FILE* file){ ///< print to this file
+
+ int mass_precision = Params::GetInt("mass-precision");
+
+ // print S line
+ fprintf(file, "S\t%06d\t%06d\t%.*f\n",
+ first_scan_,
+ last_scan_,
+ mass_precision,
+ precursor_mz_);
+
+ // print I line(s)
+ for(size_t line_idx = 0; line_idx < i_lines_v_.size(); line_idx++){
+ fprintf(file, "%s\n", (i_lines_v_[line_idx]).c_str());
+ }
+
+ // print 'Z', 'D' line
+ if( zstate.getCharge() != 0 ){ // print only one charge state
+ fprintf(file, "Z\t%d\t%.*f\n", zstate.getCharge(), mass_precision,
+ zstate.getSinglyChargedMass());
+ // TODO find associated Z line and print
+ } else { // print all charge states
+
+ for(size_t z_idx = 0; z_idx < zstates_.size(); z_idx++){
+ fprintf(file, "Z\t%d\t%.*f\n", zstates_[z_idx].getCharge(), mass_precision,
+ zstates_[z_idx].getSinglyChargedMass());
+ // are there any 'D' lines to print?
+ if(z_idx < d_lines_v_.size()){
+ fprintf(file, "%s", d_lines_v_[z_idx].c_str());
+ }
+ }
+ }
+
+ // print peaks
+ for(int bin_idx = 0; bin_idx < max_mz_bin; bin_idx++){
+ string intensity = StringUtils::ToString(intensities[bin_idx], mass_precision);
+ // Make sure the value has at least one non-zero digit, once it has been
+ // converted to a string with the specified precision
+ if (intensity.find_first_of("123456789") == string::npos) {
+ continue;
+ }
+ if (Params::GetString("output-units") == "mz") {
+ double mz = (bin_idx - 0.5 + Params::GetDouble("mz-bin-offset")) *
+ Params::GetDouble("mz-bin-width");
+ fprintf(file, "%f %s\n", mz, intensity.c_str());
+ } else {
+ fprintf(file, "%d %s\n", bin_idx, intensity.c_str());
+ }
+ }
+ return;
+}
+
+
+/**
+ * Prints a spectrum object to file in sqt format.
+ */
+void Spectrum::printSqt(
+ FILE* file, ///< output file to print to -out
+ int num_matches, ///< number of peptides compared to this spec -in
+ SpectrumZState& zstate ///< charge used for the search -in
+ ){
+
+ fprintf(file,
+ "S\t%d\t%d\t%d\t%.1f\t%s\t%.*f\t%.2f\t%.*f\t%d\n",
+ first_scan_,
+ last_scan_,
+ zstate.getCharge(),
+ 0.0, // FIXME dummy <process time>
+ "server", // FIXME dummy <server>
+ Params::GetInt("mass-precision"),
+ zstate.getSinglyChargedMass(), //this is used in search
+ total_energy_,
+ Params::GetInt("precision"),
+ lowest_sp_,
+ num_matches);
+}
+
+/**
+ * Copy constructor. Deep copy--allocates new peaks for peak vector.
+ */
+ Spectrum::Spectrum(
+ const Spectrum& old_spectrum ///< the spectrum to take values from
+ ) :
+ first_scan_(old_spectrum.first_scan_),
+ last_scan_(old_spectrum.last_scan_),
+ precursor_mz_(old_spectrum.precursor_mz_),
+ zstates_(old_spectrum.zstates_),
+ min_peak_mz_(old_spectrum.min_peak_mz_),
+ max_peak_mz_(old_spectrum.max_peak_mz_),
+ total_energy_(old_spectrum.total_energy_),
+ filename_(old_spectrum.filename_),
+ i_lines_v_(old_spectrum.i_lines_v_),
+ d_lines_v_(old_spectrum.d_lines_v_),
+ has_peaks_(old_spectrum.has_peaks_),
+ sorted_by_mz_(old_spectrum.sorted_by_mz_),
+ sorted_by_intensity_(old_spectrum.sorted_by_intensity_),
+ has_mz_peak_array_(old_spectrum.has_mz_peak_array_)
+{
+
+ // copy each peak
+ for(int peak_idx=0; peak_idx < (int)old_spectrum.peaks_.size(); ++peak_idx){
+ this->addPeak(old_spectrum.peaks_[peak_idx]->getIntensity(),
+ old_spectrum.peaks_[peak_idx]->getLocation());
+ }
+
+ /* Should we do this??
+ if( old_spectrum.mz_peak_array ){
+ populateMzPeakArray();
+ }
+ */
+}
+
+void Spectrum::copyFrom(Spectrum *src) {
+
+ first_scan_ = src->first_scan_;
+ last_scan_ = src->last_scan_;
+ precursor_mz_ = src->precursor_mz_;
+ zstates_ = src->zstates_;
+ min_peak_mz_ = src->min_peak_mz_;
+ max_peak_mz_ = src->max_peak_mz_;
+ filename_ = src->filename_;
+ i_lines_v_ = src->i_lines_v_;
+ d_lines_v_ = src-> d_lines_v_;
+ has_peaks_ = src-> has_peaks_;
+ sorted_by_mz_ = src->sorted_by_mz_;
+ sorted_by_intensity_ = src->sorted_by_intensity_;
+ has_mz_peak_array_ = src->has_mz_peak_array_;
+ // copy each peak
+ for(int peak_idx=0; peak_idx < (int)src->peaks_.size(); ++peak_idx){
+ this->addPeak(src->peaks_[peak_idx]->getIntensity(),
+ src->peaks_[peak_idx]->getLocation());
+ }
+
+ /* Should we do this??
+ if( old_spectrum.mz_peak_array ){
+ populateMzPeakArray();
+ }
+ */
+
+}
+
+/**
+ * Transfer values from an MSToolkit spectrum to the crux Spectrum.
+ * \returns TRUE if success. FALSE is failure.
+ */
+bool Spectrum::parseMstoolkitSpectrum
+ (MSToolkit::Spectrum* mst_spectrum, ///< the input MSToolkit spectrum -in
+ const char* filename ///< filename of the spectrum
+ ) {
+
+ // clear any existing values
+ zstates_.clear();
+
+ free_peak_vector(peaks_);
+ i_lines_v_.clear();
+ d_lines_v_.clear();
+ if( mz_peak_array_ ){ delete [] mz_peak_array_; }
+
+ MSToolkit::Spectrum* mst_real_spectrum = (MSToolkit::Spectrum*)mst_spectrum;
+
+ //set first_scan, last_scan, and precursor_mz.
+ first_scan_ = mst_real_spectrum->getScanNumber();
+ last_scan_ = mst_real_spectrum->getScanNumber();
+ precursor_mz_ = mst_real_spectrum->getMZ();
+
+ // setfilename of empty spectrum
+ filename_ = filename;
+
+ //add all peaks.
+ for(int peak_idx = 0; peak_idx < (int)mst_real_spectrum->size(); peak_idx++){
+ this->addPeak(mst_real_spectrum->at(peak_idx).intensity,
+ mst_real_spectrum->at(peak_idx).mz);
+ }
+
+ //add possible charge states.
+ if( mst_real_spectrum->sizeZ() > 0 ){
+ for (int z_idx = 0; z_idx < mst_real_spectrum -> sizeZ(); z_idx++) {
+ SpectrumZState zstate;
+ zstate.setSinglyChargedMass(
+ mst_real_spectrum->atZ(z_idx).mh,
+ mst_real_spectrum->atZ(z_idx).z);
+ zstates_.push_back(zstate);
+ }
+ } else if (!Params::GetBool("pm-ignore-no-charge")) { // if no charge states detected, decide based on spectrum
+ assignZState();
+ } else {
+ return false;
+ }
+
+ return true;
+}
+
+/**
+ * Transfer values from a proteowizard SpectrumInfo object to the
+ * crux spectrum.
+ */
+bool Spectrum::parsePwizSpecInfo(
+ const pzd::SpectrumPtr& pwiz_spectrum,
+ int firstScan,
+ int lastScan
+){
+ // clear any existing values
+ zstates_.clear();
+ ezstates_.clear();
+ free_peak_vector(peaks_);
+ i_lines_v_.clear();
+ d_lines_v_.clear();
+ if( mz_peak_array_ ){ free(mz_peak_array_); }
+
+ // assign new values
+ first_scan_ = firstScan;
+ last_scan_ = lastScan;
+
+ // get peaks
+ int num_peaks = pwiz_spectrum->defaultArrayLength;
+ vector<double>& mzs = pwiz_spectrum->getMZArray()->data;
+ vector<double>& intensities = pwiz_spectrum->getIntensityArray()->data;
+ for(int peak_idx = 0; peak_idx < num_peaks; peak_idx++){
+ addPeak(intensities[peak_idx], mzs[peak_idx]);
+ }
+ has_peaks_ = true;
+
+ // get precursor m/z and charge
+ // is there exactly one precursor?
+ if( pwiz_spectrum->precursors.size() != 1 ){
+ carp(CARP_FATAL, "Spectrum %d has more than one precursor.", first_scan_);
+ }
+ // get the isolation window as the precursor m/z
+ pzd::IsolationWindow iso_window =
+ pwiz_spectrum->precursors[0].isolationWindow;
+ bool have_precursor_mz = iso_window.hasCVParam(pzd::MS_isolation_window_target_m_z);
+ if (have_precursor_mz) {
+ precursor_mz_ =
+ iso_window.cvParam(pzd::MS_isolation_window_target_m_z).valueAs<double>();
+ }
+
+ // each charge state(s) stored in selectedIon(s)
+ // is there at least one selected ion?
+ vector<pzd::SelectedIon> ions = pwiz_spectrum->precursors[0].selectedIons;
+ if (ions.empty()) {
+ carp(CARP_FATAL, "No selected ions in spectrum %d.", first_scan_);
+ }
+
+ // determined charge states will be stored
+ // one per selected ion
+ if (ions[0].hasCVParam(pzd::MS_charge_state)) {
+ carp(CARP_DEBUG, "MS_charge_state");
+ // get each charge state and possibly the associated mass
+ for(size_t ion_idx = 0; ion_idx < ions.size(); ion_idx++){
+ int charge = ions[ion_idx].cvParam(pzd::MS_charge_state).valueAs<int>();
+ carp(CARP_DEBUG, "Charge:%d", charge);
+ if (ions[ion_idx].hasCVParam(pzd::MS_accurate_mass_OBSOLETE)) {
+ //bullseye-determined charge states
+ FLOAT_T accurate_mass =
+ ions[ion_idx].cvParam(pzd::MS_accurate_mass_OBSOLETE).valueAs<FLOAT_T>();
+ carp(CARP_DEBUG, "accurate mass:%f charge:%i",accurate_mass, charge);
+ SpectrumZState zstate;
+ zstate.setSinglyChargedMass(accurate_mass, charge);
+ ezstates_.push_back(zstate);
+ } else if (ions[ion_idx].hasCVParam(pzd::MS_selected_ion_m_z)) {
+ FLOAT_T mz =
+ ions[ion_idx].cvParam(pzd::MS_selected_ion_m_z).valueAs<FLOAT_T>();
+ carp(CARP_DEBUG, "mz:%g", mz);
+ //if we don't have a precursor set yet, set it now.
+ if (!have_precursor_mz) {
+ precursor_mz_ = mz;
+ }
+ SpectrumZState zstate;
+ zstate.setMZ(mz, charge);
+ zstates_.push_back(zstate);
+ } else {
+ ostringstream oss;
+ oss << "Cannot find precursor mass! CVParams:"<<endl;
+
+ for (vector<pwiz::data::CVParam>::iterator iter = ions[0].cvParams.begin();
+ iter != ions[0].cvParams.end();
+ ++iter) {
+ oss<<"id:"<<(int)iter->cvid<<" value:"<<iter->value;
+ }
+ string err_string = oss.str();
+ carp(CARP_FATAL, err_string);
+ }
+ }
+ } else {
+ if (Params::GetBool("use-z-line")) {
+ const vector<pwiz::data::UserParam>& specUserParams = pwiz_spectrum->userParams;
+ for (vector<pwiz::data::UserParam>::const_iterator i = specUserParams.begin();
+ i != specUserParams.end();
+ ++i) {
+ if (i->name == "ms2 file charge state") {
+ const string& zLine = i->value; // "<charge> <m/z>"
+ size_t separator = zLine.find(" ");
+ SpectrumZState zstate;
+ zstate.setMZ(boost::lexical_cast<double>(zLine.substr(separator + 1)),
+ boost::lexical_cast<int>(zLine.substr(0, separator)));
+ zstates_.push_back(zstate);
+ }
+ }
+ }
+
+ if (zstates_.empty()) {
+ if (ions[0].hasCVParam(pzd::MS_possible_charge_state)) {
+ // possible charge states will all be stored in the first selected ion
+ carp(CARP_DEBUG, "charges stored ion");
+ vector<pzd::CVParam> charges =
+ ions[0].cvParamChildren(pzd::MS_possible_charge_state);
+ for (size_t charge_idx = 0; charge_idx < charges.size(); charge_idx++) {
+ SpectrumZState zstate;
+ zstate.setMZ(precursor_mz_, charges[charge_idx].valueAs<int>());
+ zstates_.push_back(zstate);
+ }
+ } else if (!Params::GetBool("pm-ignore-no-charge")) { // we have no charge information
+ assignZState(); //do choose charge and add +1 or +2,+3
+ } else {
+ return false;
+ }
+ }
+ }
+
+ return true;
+}
+
+/**
+ * Adds a peak to the spectrum given a intensity and location
+ * calls update_spectrum_fields to update num_peaks, min_peak ...
+ */
+void Spectrum::addPeak
+( FLOAT_T intensity, ///< the intensity of peak to add -in
+ FLOAT_T location_mz ///< the location of peak to add -in
+ )
+{
+ Peak *peak = new Peak(intensity, location_mz);
+ peaks_.push_back(peak);
+ updateFields(intensity, location_mz);
+ has_peaks_ = true;
+}
+
+void Spectrum::truncatePeaks(int count) {
+ if (count < 0) {
+ count = 0;
+ }
+ if (peaks_.size() <= count) {
+ return;
+ }
+ min_peak_mz_ = count > 0 ? numeric_limits<FLOAT_T>::max() : 0;
+ max_peak_mz_ = 0;
+ vector<Peak*>::const_iterator removePoint = peaks_.begin() + count;
+ for (vector<Peak*>::const_iterator i = peaks_.begin(); i != peaks_.end(); i++) {
+ if (i < removePoint) {
+ FLOAT_T mz = (*i)->getLocation();
+ if (mz < min_peak_mz_) {
+ min_peak_mz_ = mz;
+ }
+ if (mz > max_peak_mz_) {
+ max_peak_mz_ = mz;
+ }
+ } else {
+ total_energy_ -= (*i)->getIntensity();
+ delete *i;
+ }
+ }
+ peaks_.resize(count);
+}
+
+/**
+ * Creates and fills mz_peak_array_, the array of pointers to peaks
+ * in the Spectrum's vector of peaks. Peaks in the array are
+ * indexed by ???
+ */
+void Spectrum::populateMzPeakArray()
+{
+ if (has_mz_peak_array_ == true){
+ return;
+ }
+
+ int array_length = MZ_TO_PEAK_ARRAY_RESOLUTION * MAX_PEAK_MZ;
+ mz_peak_array_ = new Peak * [array_length];
+ for (int peak_idx = 0; peak_idx < array_length; peak_idx++){
+ mz_peak_array_[peak_idx] = NULL;
+ }
+ for(int peak_idx = 0; peak_idx < (int)peaks_.size(); peak_idx++){
+ Peak * peak = peaks_[peak_idx];
+ FLOAT_T peak_mz = peak->getLocation();
+ int mz_idx = (int) (peak_mz * MZ_TO_PEAK_ARRAY_RESOLUTION);
+ if (mz_peak_array_[mz_idx] != NULL){
+ carp(CARP_INFO, "Peak collision at mz %.3f = %i", peak_mz, mz_idx);
+ if (mz_peak_array_[mz_idx]->getIntensity() < peak->getIntensity()) {
+ mz_peak_array_[mz_idx] = peak;
+ }
+ } else {
+ mz_peak_array_[mz_idx] = peak;
+ }
+ }
+ has_mz_peak_array_ = true;
+}
+
+/**
+ * \returns The closest intensity within 'max' of 'mz' in 'spectrum'
+ * NULL if no peak.
+ * This should lazily create the data structures within the
+ * spectrum object that it needs.
+ * TODO: reimplement with faster peak lookup
+ */
+Peak * Spectrum::getNearestPeak(
+ FLOAT_T mz, ///< the mz of the peak around which to sum intensities -in
+ FLOAT_T max ///< the maximum distance to get intensity -in
+ )
+{
+ this->populateMzPeakArray(); // for rapid peak lookup by mz
+
+ FLOAT_T min_distance = BILLION;
+ int min_mz_idx = (int)((mz - max) * MZ_TO_PEAK_ARRAY_RESOLUTION + 0.5);
+ min_mz_idx = min_mz_idx < 0 ? 0 : min_mz_idx;
+ int max_mz_idx = (int)((mz + max) * MZ_TO_PEAK_ARRAY_RESOLUTION + 0.5);
+ int absolute_max_mz_idx = MAX_PEAK_MZ * MZ_TO_PEAK_ARRAY_RESOLUTION - 1;
+ max_mz_idx = max_mz_idx > absolute_max_mz_idx
+ ? absolute_max_mz_idx : max_mz_idx;
+ Peak * peak = NULL;
+ Peak * nearest_peak = NULL;
+ int peak_idx;
+ for (peak_idx=min_mz_idx; peak_idx < max_mz_idx + 1; peak_idx++){
+ if ((peak = mz_peak_array_[peak_idx]) == NULL){
+ continue;
+ }
+ FLOAT_T peak_mz = peak->getLocation();
+ FLOAT_T distance = fabs(mz - peak_mz);
+ if (distance > max){
+ continue;
+ }
+ if (distance < min_distance){
+ nearest_peak = peak;
+ min_distance = distance;
+ }
+ }
+ return nearest_peak;
+}
+
+/**
+ * \returns The PEAK_T within 'max' of 'mz' in 'spectrum'
+ * that is the maximum intensity.
+ * NULL if no peak within 'max'
+ * This should lazily create the data structures within the
+ * spectrum object that it needs.
+ */
+Peak* Spectrum::getMaxIntensityPeak(
+ FLOAT_T mz, ///< the mz of the peak to find
+ FLOAT_T max ///< the maximum distance to get intensity -in
+ ) {
+
+ FLOAT_T max_intensity = -BILLION;
+ Peak* max_intensity_peak = NULL;
+
+ for (PeakIterator peak_iter = begin();
+ peak_iter != end();
+ ++peak_iter) {
+
+ Peak* peak = *peak_iter;
+ FLOAT_T peak_mz = peak->getLocation();
+ FLOAT_T distance = fabs(mz - peak_mz);
+ FLOAT_T intensity = peak->getIntensity();
+ if ((distance <= max) && (intensity > max_intensity)){
+ max_intensity_peak = peak;
+ max_intensity = intensity;
+ }
+ }
+ return max_intensity_peak;
+}
+
+/**
+ * Updates num_peaks, min_peak_mz, max_peak_mz, total_energy.
+ */
+void Spectrum::updateFields(
+ FLOAT_T intensity, ///< the intensity of the peak that has been added -in
+ FLOAT_T location ///< the location of the peak that has been added -in
+) {
+ // is new peak the smallest peak
+ if(peaks_.size() == 1 || min_peak_mz_ > location){
+ min_peak_mz_ = location;
+ }
+ // is new peak the largest peak
+ if(peaks_.size() == 1 || max_peak_mz_ < location){
+ max_peak_mz_ = location;
+ }
+ // update total_energy
+ total_energy_ += intensity;
+}
+
+/**
+ * \returns The number of the first scan.
+ */
+int Spectrum::getFirstScan() const
+{
+ return first_scan_;
+}
+
+/**
+ * \returns The number of the last scan.
+ */
+int Spectrum::getLastScan() const
+{
+ return last_scan_;
+}
+
+/**
+ * \returns The m/z of the precursor.
+ */
+FLOAT_T Spectrum::getPrecursorMz() const
+{
+ return precursor_mz_;
+}
+
+/**
+ * \returns The minimum m/z of all peaks.
+ */
+FLOAT_T Spectrum::getMinPeakMz()
+{
+ return min_peak_mz_;
+}
+
+/**
+ * \returns The maximum m/z of all peaks.
+ */
+FLOAT_T Spectrum::getMaxPeakMz()
+{
+ return max_peak_mz_;
+}
+
+/**
+ * \returns The number of peaks.
+ */
+int Spectrum::getNumPeaks() const
+{
+ return (int)peaks_.size();
+}
+
+
+/**
+ * \returns The sum of intensities in all peaks.
+ */
+double Spectrum::getTotalEnergy()
+{
+ return total_energy_;
+}
+
+/**
+ * Sets the total ion current.
+ */
+void Spectrum::setTotalEnergy(FLOAT_T tic)
+{
+ total_energy_ = tic;
+}
+
+/**
+ * returns whether there is a total energy
+ */
+bool Spectrum::hasTotalEnergy()
+{
+ return has_total_energy_;
+}
+
+/**
+ * sets whether there is a total energy
+ */
+void Spectrum::setHasTotalEnergy(bool has_total_energy)
+{
+ has_total_energy_ = has_total_energy;
+}
+
+/**
+ * Sets the lowest Sp score.
+ */
+void Spectrum::setLowestSp(FLOAT_T sp)
+{
+ lowest_sp_ = sp;
+}
+
+/**
+ * Returns the lowest Sp score
+ */
+FLOAT_T Spectrum::getLowestSp()
+{
+ return lowest_sp_;
+}
+
+/**
+ * returns whether there is a lowest sp score
+ */
+bool Spectrum::hasLowestSp()
+{
+ return has_lowest_sp_;
+}
+
+/**
+ * sets whether there is a lowest sp score
+ */
+void Spectrum::setHasLowestSp(bool has_lowest_sp)
+{
+ has_lowest_sp_ = has_lowest_sp;
+}
+
+/**
+ * \returns A read-only reference to the vector of possible chare
+ * states for this spectrum. If EZ states are available, return those.
+ */
+const vector<SpectrumZState>& Spectrum::getZStates() const {
+ if (ezstates_.size() != 0) {
+ return ezstates_;
+ } else {
+ return zstates_;
+ }
+}
+
+
+/**
+ * Considers the spectrum-charge parameter and returns the
+ * appropriate charge states that should be searched for this
+ * spectrum: all of them or the one selected by the parameter.
+ * /returns A vector of charge states to consider for this spectrum.
+ */
+vector<SpectrumZState> Spectrum::getZStatesToSearch() {
+ vector<SpectrumZState> select_zstates;
+ string charge_str = Params::GetString("spectrum-charge");
+
+ if (charge_str == "all") { // return full array of charges
+ select_zstates = getZStates();
+ } else { // return a single charge state.
+ int param_charge = atoi(charge_str.c_str());
+
+ if( (param_charge < 1) || (param_charge > MAX_CHARGE) ){
+ carp(CARP_FATAL, "spectrum-charge option must be 1,2,3,.. %d or 'all'. "
+ "'%s' is not valid", MAX_CHARGE, charge_str.c_str());
+ }
+
+ for (unsigned int zstate_idx=0;zstate_idx < getNumZStates();zstate_idx++) {
+ if (getZState(zstate_idx).getCharge() == param_charge) {
+ select_zstates.push_back(getZState(zstate_idx));
+ }
+ }
+ }
+
+ return select_zstates;
+}
+
+/**
+ * \returns the ZState at the requested index
+ */
+const SpectrumZState& Spectrum::getZState(
+ int idx ///< the zstate index
+) {
+ return getZStates().at(idx);
+}
+
+
+/**
+ * \returns The number of possible charge states of this spectrum.
+ */
+unsigned int Spectrum::getNumZStates() const {
+ return getZStates().size();
+}
+
+/**
+ * \returns The intensity of the peak with the maximum intensity.
+ */
+FLOAT_T Spectrum::getMaxPeakIntensity()
+{
+ FLOAT_T max_intensity = -1;
+
+ for(int peak_idx = 0; peak_idx < (int)peaks_.size(); ++peak_idx){
+ if (max_intensity <= peaks_[peak_idx]->getIntensity()) {
+ max_intensity = peaks_[peak_idx]->getIntensity();
+ }
+ }
+ return max_intensity;
+}
+
+/**
+ * Normalize peak intensities so that they sum to unity.
+ */
+void Spectrum::sumNormalize()
+{
+ for(int peak_idx = 0; peak_idx < (int)peaks_.size(); peak_idx++){
+ Peak * peak = peaks_[peak_idx];
+ FLOAT_T new_intensity = peak->getIntensity() / total_energy_;
+ peak->setIntensity(new_intensity);
+ }
+}
+
+/**
+ * Sort peaks
+ */
+void Spectrum::sortPeaks(PEAK_SORT_TYPE_T type)
+{
+ if ((type == _PEAK_LOCATION && sorted_by_mz_) ||
+ (type == _PEAK_INTENSITY && sorted_by_intensity_)) {
+ return;
+ }
+ sort_peaks(peaks_, type);
+ sorted_by_mz_ = (type == _PEAK_LOCATION);
+ sorted_by_intensity_ = (type == _PEAK_INTENSITY);
+}
+
+/**
+ * Populate peaks with rank information.
+ */
+void Spectrum::rankPeaks()
+{
+ sort_peaks(peaks_, _PEAK_INTENSITY);
+ sorted_by_intensity_ = true;
+ sorted_by_mz_ = false;
+ int rank = (int)peaks_.size();
+ for(int peak_idx = 0; peak_idx < (int) peaks_.size(); peak_idx++){
+ Peak * peak = peaks_[peak_idx];
+ FLOAT_T new_rank = rank/(float)peaks_.size();
+ rank--;
+ peak->setIntensityRank(new_rank);
+ }
+
+}
+
+/**
+ * \returns The name of the file (no path or extension) this spectrum
+ * came from or an empty string, if filename is unavailable.
+ */
+const char* Spectrum::getFilename() {
+ return FileUtils::Stem(filename_).c_str();
+}
+
+/**
+ * \Determine charge state for a spectrum without Z line
+ * /return true if it can determine charge state and return false if it can't create z line
+ */
+bool Spectrum::assignZState() {
+ carp_once(CARP_WARNING, "Spectrum %i has no charge state. Calculating charge",
+ first_scan_);
+
+ if (peaks_.empty()) {
+ carp(CARP_INFO, "Cannot determine charge state of spectrum %d with no peaks.",
+ first_scan_);
+ return false;
+ }
+
+ // sum peaks below and above the precursor m/z window separately
+ FLOAT_T left_sum = 0.00001;
+ FLOAT_T right_sum = 0.00001;
+ for (vector<Peak*>::const_iterator i = peaks_.begin(); i != peaks_.end(); i++) {
+ FLOAT_T location = (*i)->getLocation();
+ if (location < precursor_mz_ - 20) {
+ left_sum += (*i)->getIntensity();
+ } else if (location > precursor_mz_ + 20) {
+ right_sum += (*i)->getIntensity();
+ } // else, skip peaks around precursor
+ }
+
+ // What is the justification for this? Ask Mike MacCoss
+ FLOAT_T FractionWindow = 0;
+ FLOAT_T CorrectionFactor = 1;
+ FLOAT_T max_peak_mz = peaks_.back()->getLocation();
+ if ((precursor_mz_ * 2) >= max_peak_mz) {
+ FractionWindow = (precursor_mz_ * 2) - max_peak_mz;
+ CorrectionFactor = fabs((precursor_mz_ - FractionWindow)) / precursor_mz_;
+ }
+
+ // if the ratio of intensities above/below the precursor is small
+ assert(left_sum != 0);
+
+ SpectrumZState zstate;
+ if ((right_sum / left_sum) < (0.2 * CorrectionFactor)) {
+ // +1 spectrum
+ zstate.setMZ(precursor_mz_, 1);
+ zstates_.push_back(zstate);
+ return true;
+ }
+
+ // multiply charged spectrum
+ zstate.setMZ(precursor_mz_, 2);
+ zstates_.push_back(zstate);
+ zstate.setMZ(precursor_mz_, 3);
+ zstates_.push_back(zstate);
+ return true;
+}
+
+const char* Spectrum::getFullFilename(){
+
+ if (filename_.empty()){
+ return "";
+ }
+ return filename_.c_str();
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/model/Spectrum.h b/src/model/Spectrum.h
new file mode 100644
index 0000000..38b2f13
--- /dev/null
+++ b/src/model/Spectrum.h
@@ -0,0 +1,375 @@
+/**
+ * \file spectrum.h
+ * $Revision: 1.43 $
+ * \brief Object for representing one spectrum.
+ *****************************************************************************/
+#ifndef SPECTRUM_H
+#define SPECTRUM_H
+
+#include <stdio.h>
+#include <vector>
+#include <string>
+#include "util/utils.h"
+#include "model/objects.h"
+#include "Peak.h"
+
+#include "Spectrum.h"
+#include "MSToolkit/Spectrum.h"
+#include "pwiz/data/msdata/SpectrumInfo.hpp"
+#include "SpectrumZState.h"
+
+/**
+ * \class Spectrum
+ * \brief A mass spectrum
+
+ * A mass spectrum consists mainly of a list of peak objects along with
+ * some identifying information. A single spectrum is generated from one
+ * or more "scans" of the mass spectrometer; each scan is identified by
+ * a unique increasing positive integer. The range of scans that
+ * generated a particular spectrum are indicated by the member variables
+ * "first_scan" and "last_scan". In addition to scan information,
+ * a tandem fragmentation mass spectrum has information
+ * about the m/z of the intact ion that generated the spectrum, which is
+ * indicated by "precursor_mz" member variable.
+ * Also, while the m/z of particular spectrum is known, the charge state of
+ * the originating ion is unknown; the possible charge states of the
+ * precursor ion is stored "possible_z" and "num_possible_z".
+ * Finally, some summary information that can be derived from the spectrum
+ * peaks but is convenient to have is stored as "min_peak_mz",
+ * "max_peak_mz", and "total_energy".
+ */
+
+namespace Crux {
+
+class Spectrum{
+ protected:
+ // member variables
+ int first_scan_; ///< The number of the first scan
+ int last_scan_; ///< The number of the last scan
+ FLOAT_T precursor_mz_; ///< The m/z of precursor (MS-MS spectra)
+ std::vector<SpectrumZState> zstates_;
+ std::vector<SpectrumZState> ezstates_;
+ std::vector<Peak*> peaks_; ///< The spectrum peaks
+ FLOAT_T min_peak_mz_; ///< The minimum m/z of all peaks
+ FLOAT_T max_peak_mz_; ///< The maximum m/z of all peaks
+ double total_energy_; ///< The sum of intensities in all peaks
+ FLOAT_T lowest_sp_; ///< The lowest Sp score (for writing SQT)
+ bool has_total_energy_;
+ bool has_lowest_sp_;
+ std::string filename_; ///< Optional filename
+ std::vector<std::string> i_lines_v_; ///< store i lines
+ std::vector<std::string> d_lines_v_; ///< store d lines
+ bool has_peaks_; ///< Does the spectrum contain peak information
+ bool sorted_by_mz_; ///< Are the spectrum peaks sorted by m/z...
+ bool sorted_by_intensity_; ///< ... or by intensity?
+ bool has_mz_peak_array_; ///< Is the mz_peak_array populated.
+ Peak **mz_peak_array_; ///< Allows rapid peak retrieval by mz.
+
+ // constants
+ /**
+ * m/z resolution. I.e., 5 == 0.2 m/z units
+ */
+ static const int MZ_TO_PEAK_ARRAY_RESOLUTION = 5;
+ static const int MAX_PEAK_MZ = 5000; ///< Maximum possible m/z value.
+ static const int MAX_CHARGE = 6; ///< Maximum allowed charge.
+
+ // private methods
+ /**
+ * Updates num_peaks, min_peak_mz, max_peak_mz, total_energy fields.
+ */
+ void updateFields
+ (FLOAT_T intensity,///< the intensity of the peak that has been added -in
+ FLOAT_T location ///< the location of the peak that has been added -in
+ );
+
+ public:
+ /**
+ * Default constructor.
+ */
+ Spectrum();
+
+ /**
+ * Constructor initializes spectrum with given values.
+ */
+ Spectrum
+ (int first_scan, ///< number of the first scan -in
+ int last_scan, ///< number of the last scan -in
+ FLOAT_T precursor_mz, ///< m/z of the precursor
+ const std::vector<int>& possible_z, ///< possible charge states
+ const std::string& filename
+ );
+
+ /**
+ * Copy constructor. Deep copy--allocates new peaks peak array.
+ */
+ Spectrum(const Spectrum& old_spec);
+
+ void copyFrom(Spectrum* src);
+
+
+ /**
+ * Default destructor.
+ */
+ ~Spectrum();
+
+ /**
+ * \returns the peak iterator that signifies the start of the peaks
+ * in the spectrum
+ */
+ PeakIterator begin() const;
+
+ /**
+ * \returns the peak iterator that signifies the end of the peaks
+ * in the spectrum
+ */
+ PeakIterator end() const;
+
+ /**
+ * Prints a spectrum object to file.
+ */
+ void print(FILE* file); ///< output file to print at -out
+
+ /**
+ * Prints a spectrum with the given intensities instead of the
+ * observed peaks. Assumes intensities are in m/z bins from 0 to
+ * max_mz_bin. Only prints non-zero intensities.
+ */
+ void printProcessedPeaks
+ (SpectrumZState& zstate, ///< print at this charge state
+ FLOAT_T* intensities, ///< intensities of new peaks
+ int max_mz_bin, ///< num_bins in intensities
+ FILE* file); ///< print to this file
+
+ /**
+ * Prints a spectrum object to file in sqt format.
+ */
+ void printSqt
+ (FILE* file, ///< output file to print at -out
+ int num_matches, ///< number of peptides compared to this spec -in
+ SpectrumZState& zstate ///< charge used for the search -in
+ );
+
+ /**
+ * Transfer values from an MSToolkit spectrum to the crux Spectrum.
+ */
+ bool parseMstoolkitSpectrum(MSToolkit::Spectrum* mst_spectrum,
+ const char* filename = NULL);
+
+ /**
+ * Transfer values from a proteowizard Spectrum object to the
+ * crux spectrum.
+ */
+ bool parsePwizSpecInfo(
+ const pwiz::msdata::SpectrumPtr& pwiz_spectrum,
+ int firstScan,
+ int lastScan
+ );
+
+ /**
+ * Normalize peak intensities so that they sum to unity.
+ */
+ void sumNormalize();
+
+ /**
+ * Sort peaks
+ */
+ void sortPeaks(PEAK_SORT_TYPE_T type);
+
+ /**
+ * Populate peaks with rank information.
+ */
+ void rankPeaks();
+
+ /**
+ * \returns The number of the first scan.
+ */
+ int getFirstScan() const;
+
+ /**
+ * \returns The number of the last scan.
+ */
+ int getLastScan() const;
+
+ /**
+ * \returns The m/z of the precursor.
+ */
+ FLOAT_T getPrecursorMz() const;
+
+ /**
+ * \returns The a const reference to a vector of the possible charge
+ * states of this spectrum. If EZ states are available, return those.
+ */
+ const std::vector<SpectrumZState>& getZStates() const;
+
+ /**
+ * \returns the ZState at the requested index
+ */
+ const SpectrumZState& getZState(int idx);
+
+ /**
+ * Considers the spectrum-charge parameter and returns the
+ * appropriate charge states that should be searched for this
+ * spectrum: all of them or the one selected by the parameter.
+ * /returns A vector of charge states to consider for this spectrum.
+ */
+ //std::vector<int> getChargesToSearch();
+
+ std::vector<SpectrumZState> getZStatesToSearch();
+
+
+ /**
+ * \returns The number of possible charge states of this spectrum.
+ */
+ unsigned int getNumZStates() const;
+
+ /**
+ * \returns The minimum m/z of all peaks.
+ */
+ FLOAT_T getMinPeakMz();
+
+ /**
+ * \returns The maximum m/z of all peaks.
+ */
+ FLOAT_T getMaxPeakMz();
+
+ /**
+ * \returns The number of peaks.
+ */
+ int getNumPeaks() const;
+
+ /**
+ * \returns The closest PEAK_T within 'max' of 'mz' in 'spectrum'
+ * NULL if no peak within 'max'
+ * This should lazily create the data structures within the
+ * spectrum object that it needs.
+ */
+ Peak * getNearestPeak
+ (FLOAT_T mz, ///< the mz of the peak around which to sum intensities -in
+ FLOAT_T max ///< the maximum distance to get intensity -in
+ );
+
+ /**
+ * \returns The PEAK_T within 'max' of 'mz' in 'spectrum'
+ * that is the maximum intensity.
+ * NULL if no peak within 'max'
+ * This should lazily create the data structures within the
+ * spectrum object that it needs.
+ */
+ Peak* getMaxIntensityPeak(
+ FLOAT_T mz, ///< the mz of the peak to find
+ FLOAT_T max ///< the maximum distance to get intensity -in
+ );
+
+
+ /**
+ * \returns The sum of intensities in all peaks.
+ */
+ double getTotalEnergy();
+
+ /**
+ * Sets the total ion current.
+ */
+ void setTotalEnergy(
+ FLOAT_T tic ///< the total ion current
+ );
+
+ /**
+ * returns whether there is a total energy
+ */
+ bool hasTotalEnergy();
+
+ /**
+ * sets whether there is a total energy
+ */
+ void setHasTotalEnergy(
+ bool has_total_energy
+ );
+
+ /**
+ * Sets the lowest Sp score.
+ */
+ void setLowestSp(
+ FLOAT_T sp ///< the lowest Sp score for this spectrum
+ );
+
+ /**
+ * Returns the lowest Sp score
+ */
+ FLOAT_T getLowestSp();
+
+ /**
+ * returns whether there is a lowest sp score
+ */
+ bool hasLowestSp();
+
+ /**
+ * sets whether there is a lowest sp score
+ */
+ void setHasLowestSp(
+ bool has_lowest_sp
+ );
+
+ /**
+ * \returns The intensity of the peak with the maximum intensity.
+ */
+ FLOAT_T getMaxPeakIntensity();
+
+ /**
+ * \returns The mass of the singly charged precursor ion, according
+ * to the formula mass = m/z * charge - (mass_H * (charge - 1))
+ */
+ //FLOAT_T getSinglyChargedMass(int charge); ///< the charge of the precursor ion -in
+
+ /**
+ * Adds a possible charge(z) to the spectrum.
+ */
+ //bool addPossibleZ(int charge); ///< charge to add
+
+ /**
+ * Adds a peak to the spectrum given a intensity and location.
+ * Calls update_fields.
+ */
+ void addPeak
+ (FLOAT_T intensity, ///< the intensity of peak to add -in
+ FLOAT_T location_mz ///< the location of peak to add -in
+ );
+
+ void truncatePeaks(int count);
+
+ /**
+ * Creates and fills mz_peak_array_, the array of pointers to peaks
+ * in the Spectrum's vector of peaks. Peaks in the array are
+ * indexed by ???
+ */
+ void populateMzPeakArray();
+
+ /**
+ *if ms2 file dose not have any Z line then assignZState will create it
+ */
+ bool assignZState();
+
+ /**
+ * \returns The name of the file this spectrum came from or an empty
+ * string, if unavailable.
+ */
+ const char* getFilename();
+ const char* getFullFilename();
+};
+
+}
+
+/**
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+#endif
+
+/** \mainpage The crux API documentation page.
+ * \section Introduction
+ * Welcome to crux, a C software package for analysis of tandem mass
+ * spectrometry data. Click on the links above to see documentation for
+ * crux objects and their user interfaces.
+ */
diff --git a/src/model/SpectrumMatch.cpp b/src/model/SpectrumMatch.cpp
new file mode 100644
index 0000000..aa73b00
--- /dev/null
+++ b/src/model/SpectrumMatch.cpp
@@ -0,0 +1,103 @@
+/**
+ * \file SpectrumMatch.cpp
+ * \brief Object for holding spectrum scores
+ *******************************************/
+#include "SpectrumMatch.h"
+#include "SpectrumZState.h"
+
+#include "Match.h"
+using namespace Crux;
+
+/**
+ * \returns an empty SpectrumMatch
+ */
+SpectrumMatch::SpectrumMatch():
+ file_idx_(-1) {
+}
+
+/**
+ * \returns a SpectrumMatch, setting the spectrum
+ */
+SpectrumMatch::SpectrumMatch(
+ Spectrum* spectrum /// < Spectrum object for this match
+): file_idx_(-1) {
+
+ setSpectrum(spectrum);
+
+}
+
+/**
+ * Destructor
+ */
+SpectrumMatch::~SpectrumMatch() {
+}
+
+/**
+ * sets the peptide match for this spectrummatch
+ */
+void SpectrumMatch::setPeptideMatch(
+ PeptideMatch* peptide_match ///< peptide match to set
+ ) {
+ peptide_match_ = peptide_match;
+}
+
+/**
+ * \returns the associated PeptideMatch
+ */
+PeptideMatch* SpectrumMatch::getPeptideMatch() {
+ return peptide_match_;
+}
+
+/**
+ * sets the spectrum object
+ */
+void SpectrumMatch::setSpectrum(
+ Spectrum* spectrum ///< spectrum to set
+ ) {
+
+ spectrum_ = spectrum;
+}
+
+/**
+ * \returns the Spectrum
+ */
+Spectrum* SpectrumMatch::getSpectrum() {
+ return spectrum_;
+}
+
+/**
+ * sets the zstate
+ */
+void SpectrumMatch::setZState(
+ SpectrumZState& zstate ///< zstate to set
+ ) {
+
+ zstate_ = zstate;
+}
+
+/**
+ * \returns the zstate
+ */
+SpectrumZState& SpectrumMatch::getZState() {
+
+ return zstate_;
+}
+
+void SpectrumMatch::setFileIndex(int file_idx) {
+ file_idx_ = file_idx;
+}
+
+int SpectrumMatch::getFileIndex() {
+ return(file_idx_);
+}
+
+std::string SpectrumMatch::getFilePath() {
+ return(Match::getFilePath(file_idx_));
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/SpectrumMatch.h b/src/model/SpectrumMatch.h
new file mode 100644
index 0000000..88109a1
--- /dev/null
+++ b/src/model/SpectrumMatch.h
@@ -0,0 +1,101 @@
+/**
+ * \file SpectrumMatch.h
+ * $Revision: 1.00 $
+ * \brief Object for holding spectrum scores
+ ******************************************************/
+#ifndef SPECTRUMMATCH_H_
+#define SPECTRUMMATCH_H_
+
+#include "match_objects.h"
+#include "SpectrumZState.h"
+#include "AbstractMatch.h"
+
+class SpectrumMatch : public AbstractMatch {
+
+ protected:
+ PeptideMatch* peptide_match_; ///< PeptideMatch which this SpectrumMatch matches to
+ Crux::Spectrum* spectrum_; ///< Spectrum object
+ SpectrumZState zstate_; ///< Current zstate
+ int file_idx_; /// file index
+ public:
+
+ /**
+ * \returns an empty SpectrumMatch
+ */
+ SpectrumMatch();
+
+ /**
+ * \returns a SpectrumMatch, setting the spectrum
+ */
+ SpectrumMatch(
+ Crux::Spectrum* spectrum_ ///< Spectrum object for this match
+ );
+
+ /**
+ * Destructor
+ */
+ virtual ~SpectrumMatch();
+
+ /**
+ * sets the peptide match for this spectrummatch
+ */
+ void setPeptideMatch(
+ PeptideMatch* peptide_match ///< peptide match to set
+ );
+
+ /**
+ * \returns the associated PeptideMatch
+ */
+ PeptideMatch* getPeptideMatch();
+
+ /**
+ * sets the spectrum object
+ */
+ void setSpectrum(
+ Crux::Spectrum* spectrum ///< spectrum to set
+ );
+
+ /**
+ * \returns the spectrum
+ */
+ Crux::Spectrum* getSpectrum();
+
+ /**
+ * sets the zstate
+ */
+ void setZState(
+ SpectrumZState& zstate ///< zstate to set
+ );
+
+ /**
+ * \returns the zstate
+ */
+ SpectrumZState& getZState();
+
+ /**
+ * sets the file index for this spectrum match
+ */
+ void setFileIndex(int file_idx);
+
+ /**
+ * \returns the file index for this spectrum match
+ */
+ int getFileIndex();
+
+ /**
+ *\returns the file path for this spectrum match
+ */
+ std::string getFilePath();
+
+
+
+};
+
+#endif //SPECTRUMMATCH_H
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/SpectrumZState.cpp b/src/model/SpectrumZState.cpp
new file mode 100644
index 0000000..0811a87
--- /dev/null
+++ b/src/model/SpectrumZState.cpp
@@ -0,0 +1,167 @@
+
+/*************************************************************************//**
+ * \file SpectrumZState.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: January 28, 2011
+ * \brief code to support spectrum precursor z-states.
+ ****************************************************************************/
+#include "SpectrumZState.h"
+
+#include "io/carp.h"
+#include "util/mass.h"
+
+
+/**
+ * Default constructor
+ */
+SpectrumZState::SpectrumZState() {
+ charge_ = 0;
+ neutral_mass_ = 0;
+ rtime_ = 0;
+ area_ = 0;
+}
+
+SpectrumZState::SpectrumZState(
+ double neutral_mass,
+ int charge
+ ) {
+
+ neutral_mass_ = neutral_mass;
+ charge_ = charge;
+ rtime_ = 0;
+ area_ = 0;
+}
+
+/**
+ * copy constructor
+ */
+SpectrumZState::SpectrumZState(
+ const SpectrumZState& other
+) {
+ charge_ = other.charge_;
+ neutral_mass_ = other.neutral_mass_;
+ rtime_ = other.rtime_;
+ area_ = other.area_;
+}
+
+/**
+ * Default destructor
+ */
+SpectrumZState::~SpectrumZState() {
+
+}
+
+/**
+ * \returns The charge for this z-state
+ */
+int SpectrumZState::getCharge() const {
+ return charge_;
+}
+
+/**
+ * Sets the neutral mass and charge for this z-state
+ * using the m/z and charge.
+ */
+
+void SpectrumZState::setMZ(
+ FLOAT_T mz,
+ int charge
+) {
+
+ neutral_mass_ = (mz - MASS_PROTON) * (double)charge;
+ charge_ = charge;
+
+}
+
+FLOAT_T SpectrumZState::getMZ() const {
+
+ return (neutral_mass_ > 0) ?
+ (neutral_mass_ + (FLOAT_T)charge_*MASS_PROTON) / (FLOAT_T)charge_ :
+ 0;
+}
+
+
+/**
+ * Sets the neutral mass and charge for this z-state
+ * using the singly charged mass.
+ */
+void SpectrumZState::setSinglyChargedMass(
+ double mph,
+ int charge
+ ) {
+
+ neutral_mass_ = mph - MASS_PROTON;
+ charge_ = charge;
+}
+
+/**
+ * \returns the m+h charged mass for this z-state
+ */
+double SpectrumZState:: getSinglyChargedMass() const {
+
+ return (neutral_mass_ > 0) ?
+ neutral_mass_ + MASS_PROTON :
+ 0;
+}
+
+/**
+ * Sets the neutral mass for this z-state
+ */
+void SpectrumZState::setNeutralMass(
+ FLOAT_T neutral_mass,
+ int charge
+ ) {
+
+ neutral_mass_ = neutral_mass;
+ charge_ = charge;
+}
+
+/**
+ * \returns The neutral mass for this z-state
+ */
+FLOAT_T SpectrumZState::getNeutralMass() const {
+
+ return (neutral_mass_ > 0) ? neutral_mass_ : 0;
+}
+
+/**
+ * Sets the retention time for this z-state
+ */
+void SpectrumZState::setRTime(
+ FLOAT_T rtime
+ ) {
+
+ rtime_ = rtime;
+}
+
+/**
+ * \returns The retention time for this z-state
+ */
+FLOAT_T SpectrumZState::getRTime() const {
+ return rtime_;
+}
+
+/**
+ * Sets the area for this z-state
+ */
+void SpectrumZState::setArea(
+ FLOAT_T area
+ ) {
+
+ area_ = area;
+}
+
+/**
+ * \returns The area for this z-state
+ */
+FLOAT_T SpectrumZState::getArea() const {
+ return area_;
+}
+
+
+/**
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/SpectrumZState.h b/src/model/SpectrumZState.h
new file mode 100644
index 0000000..8c8d53d
--- /dev/null
+++ b/src/model/SpectrumZState.h
@@ -0,0 +1,134 @@
+/**
+ * \file SpectrumZState.h
+ * $Revision: 1.00 $
+ * \brief Object for representing a MS2 spectrum's charge, and neutral mass.
+ *******************************************************************************/
+#ifndef SPECTRUMZSTATE_H
+#define SPECTRUMZSTATE_H
+
+#include "model/objects.h"
+#include "util/utils.h"
+
+
+/**
+ * \class SpectrumZState
+ * \brief Object for representing a spectrum precursor's
+ * charge and neutral mass.
+ */
+
+class SpectrumZState {
+ protected:
+ int charge_;
+ double neutral_mass_;
+
+ /* EZ State fields */
+ FLOAT_T rtime_;
+ FLOAT_T area_;
+ public:
+
+ /**
+ * Default constructor
+ */
+ SpectrumZState();
+
+ /**
+ * sets the neutral mass and charge
+ */
+ SpectrumZState(
+ double neutral_mass,
+ int charge
+ );
+
+ /**
+ * copy constructor
+ */
+ SpectrumZState(
+ const SpectrumZState& other
+ );
+
+ /**
+ * Default destructor
+ */
+ virtual ~SpectrumZState();
+
+ /**
+ * \returns The charge for this z-state
+ */
+ int getCharge() const;
+
+
+ /**
+ * sets the m/z, charge for this z-state
+ */
+ void setMZ(
+ FLOAT_T mz,
+ int charge);
+
+ FLOAT_T getMZ() const;
+
+
+ /**
+ * Sets the m+h charged mass for this z-state
+ */
+ void setSinglyChargedMass(
+ double mph,
+ int charge
+ );
+
+ /**
+ * \returns the m+h charged mass for this z-state
+ */
+ double getSinglyChargedMass() const;
+
+ /**
+ * Sets the neutral mass for this z-state
+ */
+ void setNeutralMass(
+ FLOAT_T neutral_mass,
+ int charge
+ );
+
+ /**
+ * \returns The neutral mass for this z-state
+ */
+ FLOAT_T getNeutralMass() const;
+
+ /**
+ * Sets the retention time for this z-state
+ */
+ void setRTime(
+ FLOAT_T rtime
+ );
+
+ /**
+ * \returns The retention time for this z-state
+ */
+ FLOAT_T getRTime() const;
+
+ /**
+ * Sets the area for this z-state
+ */
+ void setArea(
+ FLOAT_T area
+ );
+
+ /**
+ * \returns The area for this z-state
+ */
+ FLOAT_T getArea() const;
+
+
+
+
+};
+
+/**
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
+#endif
+
diff --git a/src/model/match_objects.h b/src/model/match_objects.h
new file mode 100644
index 0000000..67b6c5f
--- /dev/null
+++ b/src/model/match_objects.h
@@ -0,0 +1,36 @@
+#ifndef MATCHOBJECTS_H_
+#define MATCHOBJECTS_H_
+
+#include "model/objects.h"
+#include <deque>
+#include <map>
+#include <string>
+
+class ProteinMatchCollection;
+class ProteinMatch;
+class PeptideMatch;
+class SpectrumMatch;
+class AbstractMatch;
+
+typedef std::deque<SpectrumMatch*> SpectrumMatchCollection;
+typedef SpectrumMatchCollection::iterator SpectrumMatchIterator;
+
+typedef std::deque<PeptideMatch*> PeptideMatchCollection;
+typedef PeptideMatchCollection::iterator PeptideMatchIterator;
+
+typedef std::deque<ProteinMatch*>::iterator ProteinMatchIterator;
+
+typedef std::map<SCORER_TYPE_T, FLOAT_T> ScoreMap;
+typedef std::map<SCORER_TYPE_T, int> RankMap;
+typedef ScoreMap::iterator ScoreMapIterator;
+typedef RankMap::iterator RankMapIterator;
+
+#endif //MATCHOBJECTS_H
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/model/objects.h b/src/model/objects.h
new file mode 100644
index 0000000..acffed0
--- /dev/null
+++ b/src/model/objects.h
@@ -0,0 +1,811 @@
+
+/**
+ * \file objects.h
+ * $Revision: 1.62 $
+ * \brief The defined objects
+ *****************************************************************************/
+#ifndef CRUX_OBJECTS_H
+#define CRUX_OBJECTS_H
+
+#include <stdio.h>
+#include <vector>
+#include <deque>
+#include <set>
+#include <map>
+#include "util/utils.h"
+
+#include <stdint.h>
+
+#define QSORT_COMPARE_METHOD int(*)(const void*, const void*)
+
+
+class DelimitedFile;
+class DelimitedFileReader;
+class MatchFileReader;
+class SpectrumZState;
+
+class MatchCandidate;
+/**
+ * Object for defining xlinkable peptides
+ */
+class XLinkablePeptide;
+
+/**
+ * Object for defining valid links
+ */
+class XLinkBondMap;
+
+/**
+ * Object for defining a cross-link product match
+ */
+class XLinkMatch;
+
+/**
+ * Object for define a cross link peptide
+ */
+class XLinkPeptide;
+
+/**
+ * Object for defining the Xlinkable iterator
+ */
+class XLinkablePeptideIterator;
+
+/**
+ * \class Peak
+ * A peak in a spectrum
+ */
+class Peak;
+
+/**
+ * The enum for peak sort type(_PEAK_LOCATION, _PEAK_INTENSITY)
+ */
+enum _peak_sort_type {_PEAK_LOCATION, _PEAK_INTENSITY};
+
+/**
+ * \typedef PEAK_SORT_TYPE_T
+ * \brief The typedef for peak sort type(_PEAK_LOCATION, _PEAK_INTENSITY)
+ */
+typedef enum _peak_sort_type PEAK_SORT_TYPE_T;
+
+/**
+ * \class Spectrum
+ * \brief A spectrum
+ */
+namespace Crux { class Spectrum; }
+
+/**
+ * \typedef PeakIterator
+ * \brief An object to iterate over the peaks in a spectrum
+ */
+typedef std::vector<Peak*>::const_iterator PeakIterator;
+
+/**
+ * \class SpectrumCollection
+ * \brief A collection of spectra
+ */
+namespace Crux { class SpectrumCollection; }
+
+/**
+ * \typedef SpectrumIterator
+ * \brief An object to iterate over the spectra in a SpectrumCollection
+ */
+typedef std::deque<Crux::Spectrum*>::iterator SpectrumIterator;
+
+/**
+ * \class FilteredSpectrumChargeIterator
+ * \brief An object to iterate over the spectra in a spectrum_collection
+ */
+class FilteredSpectrumChargeIterator;
+
+/**
+ * \class Peptide
+ * \brief A peptide subsequence of a protein
+ */
+namespace Crux { class Peptide; };
+
+/**
+ * \class PeptideConstraint
+ * \brief An object representing constraints which a peptide may or may not
+ * satisfy.
+ */
+class PeptideConstraint;
+
+/**
+ * \typedef RESIDUE_ITERATOR_T
+ * \brief An object to iterate over the residues in a peptide
+ */
+typedef struct residue_iterator RESIDUE_ITERATOR_T;
+
+// REPLACE PEPTIDE_TYPE_T with DIGEST_T and ENZYME_T
+/**
+ * \enum _digest_type
+ * The rule governing how a peptide was cleaved from its source
+ * protein sequence.
+ */
+enum _digest_type {
+ INVALID_DIGEST, ///< required invalid value for the enum
+ FULL_DIGEST, ///< c- AND n-term specific to ENZYME_T
+ PARTIAL_DIGEST, ///< c- OR n-term specific to ENZYME_T
+ NON_SPECIFIC_DIGEST, ///< not specific to any enzyme cleavage rules
+ NUMBER_DIGEST_TYPES ///< keep last, number of types
+};
+
+/**
+ * \typedef DIGEST_T
+ * \brief The rule governing how a peptide was digested. Used in
+ * conjunction with ENZYME_T to define how peptides are generated.
+ */
+typedef enum _digest_type DIGEST_T;
+
+/**
+ * \enum _enzyme_type
+ */
+enum _enzyme_type {
+ INVALID_ENZYME, ///< required invalid value for the enum
+ NO_ENZYME, ///< cleave anywhere
+ TRYPSIN, ///< cleave after K or R, not before P
+ TRYPSINP, ///< cleave after K or R
+ CHYMOTRYPSIN, ///< cleave after FWYL, not before P
+ ELASTASE, ///< cleave after ALIV, not before P
+ CLOSTRIPAIN, ///< cleave after R
+ CYANOGEN_BROMIDE, ///< cleave after M
+ IODOSOBENZOATE, ///< cleave after W
+ PROLINE_ENDOPEPTIDASE, ///< cleave after P
+ STAPH_PROTEASE, ///< cleave after E
+ ASPN, ///< cleave before D
+ LYSC, ///< cleave after K , not befor P
+ LYSN, ///< cleave before K
+ ARGC, ///< cleave after R, not before P
+ GLUC, ///< cleave after D or E, not before P
+ PEPSINA, ///< cleave after FL, not before P
+ ELASTASE_TRYPSIN_CHYMOTRYPSIN, ///< cleave after ALIVKRWFY, not before P
+ CUSTOM_ENZYME, ///< cleave after/before user-defined residues
+ NUMBER_ENZYME_TYPES ///< leave last, number of types
+};
+
+/**
+ * \typedef ENZYME_T
+ * \brief The enzyme with which a peptide was digested. Used in
+ * conjunction with DIGEST_T to define how peptides are generated.
+ */
+typedef enum _enzyme_type ENZYME_T;
+
+/**
+ * The enum for isotopic mass type (average, mono)
+ */
+enum _mass_type {AVERAGE, MONO, NUMBER_MASS_TYPES };
+
+/**
+ * \typedef MASS_TYPE_T
+ * \brief The typedef for mass type (average, mono);
+ */
+typedef enum _mass_type MASS_TYPE_T;
+
+
+/**
+ * The enum for window type for selecting peptides or assigning ions.
+ */
+enum _window_type {
+ WINDOW_INVALID,
+ WINDOW_MASS,
+ WINDOW_MZ,
+ WINDOW_PPM,
+ NUMBER_WINDOW_TYPES
+};
+
+
+/**
+ * The enum for measure type for spectral counts
+ */
+enum _measure_type {
+ MEASURE_INVALID,
+ MEASURE_RAW,
+ MEASURE_SIN,
+ MEASURE_NSAF,
+ MEASURE_DNSAF,
+ MEASURE_EMPAI,
+ NUMBER_MEASURE_TYPES
+};
+
+/**
+ * \typedef MEASURE_TYPE_T
+ * \brief The typedef for measure type (sin, nsaf)
+ */
+typedef enum _measure_type MEASURE_TYPE_T;
+
+/**
+ * The quantification level type for spectral counts
+ */
+enum _quant_level_type {
+ QUANT_LEVEL_INVALID,
+ PEPTIDE_QUANT_LEVEL,
+ PROTEIN_QUANT_LEVEL,
+ NUMBER_QUANT_LEVEL_TYPES
+};
+
+/**
+ * The enum of type of threshold to use for spectral counts
+ */
+enum THRESHOLD_T {
+ THRESHOLD_INVALID,
+ THRESHOLD_NONE,
+ THRESHOLD_QVALUE,
+ THRESHOLD_CUSTOM,
+ NUMBER_THRESHOLD_TYPES
+};
+
+/**
+ * \typedef QUANT_LEVEL_TYPE_T
+ * \brief The typdef for quantificaiton level (peptide, protein)
+ */
+typedef enum _quant_level_type QUANT_LEVEL_TYPE_T;
+
+
+/**
+ * The enum for parsimony type for spectral counts
+ */
+enum _parsimony_type {
+ PARSIMONY_INVALID,
+ PARSIMONY_SIMPLE,
+ PARSIMONY_GREEDY,
+ PARSIMONY_NONE,
+ NUMBER_PARSIMONY_TYPES
+};
+
+/*
+ * \typedef PARSIMONY_TYPE_T
+ * \brief The typedef for parsimony type (simple, greedy, none)
+ */
+typedef enum _parsimony_type PARSIMONY_TYPE_T;
+
+/**
+ * \enum DECOY_TYPE_T
+ */
+enum DECOY_TYPE_T {
+ INVALID_DECOY_TYPE,
+ NO_DECOYS,
+ PROTEIN_REVERSE_DECOYS,
+ PROTEIN_SHUFFLE_DECOYS,
+ PEPTIDE_SHUFFLE_DECOYS,
+ PEPTIDE_REVERSE_DECOYS,
+ NUMBER_DECOY_TYPES
+};
+
+/**
+ * \enum MASS_FORMAT_T
+ */
+enum MASS_FORMAT_T {
+ INVALID_MASS_FORMAT,
+ MOD_MASS_ONLY,
+ AA_PLUS_MOD,
+ MOD_MASSES_SEPARATE,
+ NUMBER_MASS_FORMATS
+};
+
+/**
+ * \typedef WINDOW_TYPE_T
+ * \brief The typedef for window type (mass, mz, ppm);
+ */
+typedef enum _window_type WINDOW_TYPE_T;
+
+enum OBSERVED_PREPROCESS_STEP_T {
+ INVALID_STEP,
+ DISCRETIZE_STEP,
+ REMOVE_PRECURSOR_STEP,
+ SQUARE_ROOT_STEP,
+ REMOVE_GRASS_STEP,
+ TEN_BIN_STEP,
+ XCORR_STEP,
+ NUMBER_PREPROCESS_STEPS
+};
+
+
+/**
+ * \class PeptideSrc
+ * \brief object for mapping a peptide to it's parent protein.
+ */
+class PeptideSrc;
+
+
+/**
+ * \class Protein
+ * \brief A protein sequence
+ */
+namespace Crux { class Protein; }
+
+/**
+ * \class ProteinPeptideIterator
+ * \brief An object to iterate over the peptides in a protein sequence
+ */
+class ProteinPeptideIterator;
+
+/**
+ * \class Database
+ * \brief A database of protein sequences.
+ */
+class Database;
+
+/**
+ * \class DatabaseProteinIterator
+ * \brief An object to iterate over the proteins in a database
+ */
+class DatabaseProteinIterator;
+
+/**
+ * \class DatabasePeptideIterator
+ * \brief An object to iterate over the peptides in a database
+ */
+class DatabasePeptideIterator;
+
+/**
+ * The enum for sort type (mass, length, lexical, none)
+ */
+enum SORT_TYPE_T {SORT_NONE,
+ SORT_MASS,
+ SORT_LENGTH,
+ SORT_LEXICAL,
+ NUMBER_SORT_TYPES };
+
+/**
+ * \typedef PEPTIDE_WRAPPER_T
+ * \brief An object to wrap a peptide, allowing a linked list of peptides.
+ */
+typedef struct peptide_wrapper PEPTIDE_WRAPPER_T;
+
+/**
+ * \class Index
+ * \brief An index of a database
+ */
+class Index;
+
+/**
+ * \class IndexPeptideIterator
+ * \brief An object to iterate over the peptides in an index
+ */
+class IndexPeptideIterator;
+
+/**
+ * \brief An iterator to further filter peptides from an
+ * IndexPeptideIterator based on digestion.
+ */
+class IndexFilteredPeptideIterator;
+
+/**
+ * \class Ion
+ * \brief An object to represent a (fragment) ion of a peptide
+ */
+class Ion;
+
+/**
+ * \class ION_SERIES_T
+ * \brief An object to represent a series of ions
+ */
+class IonSeries;
+
+/**
+ * \typedef ION_CONSTRAINT_T
+ * \brief An object to represent a constraint to be applied to ions
+ */
+class IonConstraint;
+
+/**
+ * The enum for index type
+ */
+enum _index_type {DB_INDEX, BIN_INDEX};
+
+/**
+ * \typedef INDEX_TYPE_T
+ * \brief The typedef for index type (db_index, bin_index)
+ */
+typedef enum _index_type INDEX_TYPE_T;
+
+/**
+ * The enum for an ion type (P_ion is the precursor ion)
+ * BY_ION(B & Y ion), BYA_ION(B & Y & A ion)
+ */
+enum _ion_type {A_ION, B_ION, C_ION, X_ION, Y_ION, Z_ION,
+ P_ION, BY_ION, BYA_ION, ALL_ION, NUMBER_ION_TYPES };
+
+/**
+ * \typedef ION_TYPE_T
+ * \brief The typedef for ion type (a,b,c,x,y,z ions)
+ */
+typedef enum _ion_type ION_TYPE_T;
+
+/**
+ * The enum for an ion modification
+ */
+enum _ion_modification {NH3, H2O, ISOTOPE, FLANK, ALL_MODIFICATION};
+
+/**
+ * \typedef ION_MODIFICATION_T
+ * \brief The typedef for ion modification type (NH3, H2O etc.)
+ */
+typedef enum _ion_modification ION_MODIFICATION_T;
+
+/**
+ * \class ProteinIndex
+ * \brief Object to store the protein relation to the fasta file
+ */
+class ProteinIndex;
+
+/**
+ * \class ProteinIndexIterator
+ * \brief Object to iterate over the protein index in the protein index file
+ */
+class ProteinIndexIterator;
+
+/**
+ * \typedef IonIterator
+ * \brief An object to iterate over all ion objects in the ion_series
+ */
+typedef std::vector<Ion*>::iterator IonIterator;
+
+/**
+ * \class IonFilteredIterator
+ * \brief An object to iterate over ion objects that meet constraint in the ion_series
+ */
+class IonFilteredIterator;
+
+/**
+ *\typedef LOSS_LIMIT_T
+ *\brief An object that specifies the max amount of neutral loss possible at a given cleavage index
+ * all numbers are for forward ions(A,B,C) subtract from total to get reverse limit
+ */
+typedef struct loss_limit LOSS_LIMIT_T;
+
+/**
+ * \class Scorer
+ * \brief An object to score a spectrum v. ion_series or spectrum v. spectrum
+ */
+class Scorer;
+
+/**
+ * The enum for scorer type. Scores are indexed by this type in the
+ * Match. If you update this definition, be sure to update the
+ * score() function in model/MatchCollection.cpp.
+ */
+enum _scorer_type {
+ SP, ///< SEQUEST preliminary score
+ XCORR, ///< SEQUEST primary score
+ EVALUE, ///< Comet e-value
+
+ // Scores of individual peptides in cross-linking.
+ XCORR_FIRST,
+ XCORR_SECOND,
+
+ DECOY_XCORR_QVALUE, ///< q-value derived from decoys
+ DECOY_XCORR_PEPTIDE_QVALUE,
+ DECOY_XCORR_PEP, ///< posterior error prob for xcorrs (target/decoy)
+ DECOY_EVALUE_QVALUE, ///< q-value derived from empirical null (decoy)
+ DECOY_EVALUE_PEPTIDE_QVALUE,
+ DECOY_EVALUE_PEP, ///< posterior error prob for e-value (target/decoy)
+
+ // N.B. Despite the name, these are actually NEGATIVE log p-values.
+ LOGP_WEIBULL_XCORR, ///< p-value from Weibull fit
+ LOGP_BONF_WEIBULL_XCORR, ///< Bonferroni adjusted Weibull p-value
+ LOGP_QVALUE_WEIBULL_XCORR, ///< q-value from Weibull p-value
+ LOGP_WEIBULL_PEP, ///< posterior error prob from weibull p-values
+ LOGP_PEPTIDE_QVALUE_WEIBULL, ///< peptide-level q-value for Weibull p-value
+
+ PERCOLATOR_SCORE,
+ PERCOLATOR_QVALUE,
+ PERCOLATOR_PEPTIDE_QVALUE,
+ PERCOLATOR_PEP, ///< posterior error prob from percolator scores
+
+ QRANKER_SCORE,
+ QRANKER_QVALUE,
+ QRANKER_PEPTIDE_QVALUE,
+ QRANKER_PEP, ///< posterior error prob from q-ranker scores
+
+ BARISTA_SCORE,
+ BARISTA_QVALUE,
+ BARISTA_PEPTIDE_QVALUE,
+ BARISTA_PEP, ///< posterior error prob from barista scores
+
+ // Various auxiliary scores.
+ DELTA_CN,
+ DELTA_LCN,
+ BY_IONS_MATCHED,
+ BY_IONS_TOTAL,
+
+ TIDE_SEARCH_EXACT_PVAL, ///< exact p-value from Tide
+ TIDE_SEARCH_REFACTORED_XCORR, ///< raw score corresponding to exact p-value
+
+ // The following are computed by assign-confidence.
+ SIDAK_ADJUSTED, ///< Sidak adjusted p-value
+ TIDE_SEARCH_EXACT_SMOOTHED, ///< smoothed p-value
+ QVALUE_TDC, ///< q-value from target-decoy competition
+ QVALUE_MIXMAX, ///< q-value from mix-max method
+
+ NUMBER_SCORER_TYPES,
+ INVALID_SCORER_TYPE
+};
+
+/**
+ * \typedef SCORER_TYPE_T
+ * \brief The typedef for scorer type.
+ */
+typedef enum _scorer_type SCORER_TYPE_T;
+
+/**
+ * The enum for protein scorer type
+ */
+enum _protein_scorer_type { PROTEIN_SCORER_PVALUE,
+ PROTEIN_SCORER_OLIVER,
+ NUMBER_PROTEIN_SCORER_TYPES };
+
+/**
+ * \typedef PROTEIN_SCORER_TYPE_T
+ * \brief The typedef for protein scorer type
+ */
+typedef enum _protein_scorer_type PROTEIN_SCORER_TYPE_T;
+
+/**
+ *\class Match
+ *\brief An object that contains the information of a peptide and the scoring of multiple types
+ */
+
+namespace Crux { class Match; }
+
+/**
+ *\class MatchCollection
+ *\brief An object that contains mutiple match objects
+ */
+class MatchCollection;
+
+/**
+ *\class MatchIterator
+ *\brief An object that navigates the matches
+ */
+class MatchIterator;
+
+/**
+ *\class MatchCollectionIterator
+ *\brief An object that navigates the match_collection objects
+ */
+class MatchCollectionIterator;
+
+/**
+ *\typedef PeptideSrcIterator
+ *\brief An object to iterate over the PeptideSrc in a peptide
+ */
+typedef std::vector<PeptideSrc*>::iterator PeptideSrcIterator;
+
+/**
+ * The enum for algorithm type (PERCOLATOR, CZAR, ALL)
+ */
+enum _algorithm {PERCOLATOR_ALGORITHM,
+ RCZAR_ALGORITHM,
+ QVALUE_ALGORITHM,
+ NO_ALGORITHM,
+ ALL_ALGORITHM,
+ QRANKER_ALGORITHM,
+ NUMBER_ALGORITHM_TYPES };
+
+/**
+ * \typedef ALGORITHM_TYPE_T
+ * \brief The typedef for _algorithm (PERCOLATOR, CZAR, ALL)
+ */
+typedef enum _algorithm ALGORITHM_TYPE_T;
+
+/**
+ * the enum for hardklor algorithm type
+ */
+enum _hardklor_algorithm {INVALID_HK_ALGORITHM,
+ BASIC_HK_ALGORITHM,
+ FEWEST_PEPTIDES_HK_ALGORITHM,
+ FAST_FEWEST_PEPTIDES_HK_ALGORITHM,
+ FEWEST_PEPTIDES_CHOICE_HK_ALGORITHM,
+ FAST_FEWEST_PEPTIDES_CHOICE_HK_ALGORITHM,
+ NUMBER_HK_ALGORITHM_TYPES };
+
+typedef enum _hardklor_algorithm HARDKLOR_ALGORITHM_T;
+
+/**
+ * One value for each command that can be passed to crux
+ * (e.g. search-for-matches, sequest-search, percolator).
+ */
+enum _command {
+ INVALID_COMMAND, ///< required by coding standards
+ BULLSEYE_COMMAND, ///< bullseye
+ QVALUE_COMMAND, ///< compute-q-values
+ PERCOLATOR_COMMAND, ///< percolator
+ TIDE_INDEX_COMMAND, ///< tide-index
+ TIDE_SEARCH_COMMAND, ///< tide-search
+ COMET_COMMAND, ///< comet
+ PSM_CONVERT_COMMAND, ///< psm-convert
+ READ_SPECTRUMRECORDS_COMMAND, ///< read-spectrumrecords
+ READ_TIDE_INDEX_COMMAND, ///< read-tide-index
+ SPECTRAL_COUNTS_COMMAND, ///< spectral counts
+ QRANKER_COMMAND, ///< q-ranker
+ BARISTA_COMMAND, ///< barista
+ PROCESS_SPEC_COMMAND, ///< print-processed-spectra
+ XLINK_SEARCH_COMMAND, ///< search-for-xlinks
+ GENERATE_PEPTIDES_COMMAND, ///< generate-peptides
+ GET_MS2_SPECTRUM_COMMAND, ///<get-ms2-spectrum
+ PREDICT_PEPTIDE_IONS_COMMAND, ///< predict-peptide-ions
+ PIPELINE_COMMAND, ///< pipeline
+ CASCADE_COMMAND, ///< Cascade Search
+ VERSION_COMMAND, ///< just print the version number
+ MISC_COMMAND, ///< miscellaneous command
+ NUMBER_COMMAND_TYPES ///< always keep this last so the value
+ /// changes as cmds are added
+};
+
+typedef enum _command COMMAND_T;
+
+/**
+ * \typedef MODIFIED_AA_T
+ * \brief The alternate type for encoding a peptide sequence (instead
+ * of char). Allows modifications to be added to each AA. See
+ * modifications.h for more details.
+ */
+// why doesn't this work when I put it in modifications.h????
+//typedef unsigned short MODIFIED_AA_T; ///< letters in the expanded peptide
+typedef uint16_t MODIFIED_AA_T;
+
+/**
+ * \typedef AA_MOD_T
+ * \brief The struct _aa_mod is typdefed as AA_MOD_T
+ */
+typedef struct _aa_mod AA_MOD_T;
+
+/**
+ * \typedef PEPTIDE_MOD_T
+ * \brief The struct _peptide_mod is typdefed as PEPTIDE_MOD_T
+ */
+typedef struct _peptide_mod PEPTIDE_MOD_T;
+
+/**
+ * \enum _mod_position (typedefed as MOD_POSITION_T)
+ * \brief An indication of where an AA_MOD may occur within a peptide.
+ * Default is ANY_POSITION.
+ */
+enum _mod_position{
+ ANY_POSITION, ///< at any position in any peptide
+ C_TERM, ///< only c-terminus of peptide, seq[0]
+ N_TERM ///< only n-terminus of peptide, seq[len]
+};
+
+/**
+ * \typedef MOD_POSITION_T
+ * \brief The typedef of the indicator for where an amino acid
+ * modification can occur within a peptide and/or protein.
+ */
+typedef enum _mod_position MOD_POSITION_T;
+
+/**
+ * \typedef _linked_list_head is typdefed as LINKED_LIST_T*
+ * All list actions can be performed with an object of this type.
+ */
+typedef struct _linked_list_head LINKED_LIST_T;
+
+/**
+ * \typedef _linked_list_node is typdefed as LINKED_LIST_T*
+ * This is an element of a list. Can be used for adding to the end of
+ * list or walking through a list. Cannot allocate a new one.
+ */
+typedef struct _linked_list_node LIST_POINTER_T;
+
+/**
+ * \enum _xlink_site_t (typedefed as XLINK_SITE_T)
+ * \brief An indication of the type of the crosslinking site that
+ * may occur in a peptide.
+ * Default is UNKNOWN.
+ */
+enum XLINK_SITE_T{
+ XLINKSITE_UNKNOWN,
+ XLINKSITE_CTERM,
+ XLINKSITE_NTERM,
+ XLINKSITE_ALL,
+ XLINKSITE_AA,
+ NUMBER_XLINKSITES
+};
+
+enum XLINKMATCH_TYPE_T {
+ INVALID_CANDIDATE,
+ LINEAR_CANDIDATE,
+ DEADLINK_CANDIDATE,
+ SELFLOOP_CANDIDATE,
+ XLINK_INTER_CANDIDATE,
+ XLINK_INTRA_CANDIDATE,
+ XLINK_INTER_INTRA_CANDIDATE};
+
+/**
+ * \class LinkedPeptide
+ * \brief a cross-linked peptide
+ *
+ */
+class LinkedPeptide;
+
+/**
+ * \class XHHC_Peptide
+ * \brief a XHHC Peptide
+ */
+class XHHC_Peptide;
+
+/**
+ * \enum COMPARISON_T
+ */
+enum COMPARISON_T{
+ COMPARISON_INVALID,
+ COMPARISON_LT,
+ COMPARISON_LTE,
+ COMPARISON_EQ,
+ COMPARISON_GTE,
+ COMPARISON_GT,
+ COMPARISON_NEQ,
+ NUMBER_COMPARISONS,
+};
+
+/**
+ * \enum COLTYPE_T
+ */
+enum COLTYPE_T{
+ COLTYPE_INVALID,
+ COLTYPE_INT,
+ COLTYPE_REAL,
+ COLTYPE_STRING,
+ NUMBER_COLTYPES
+};
+
+/**
+ * \enum SPLITTYPE_T
+ * \brief indication of which peptide in a crosslinked peptide to
+ * generate ions for
+ */
+enum SPLITTYPE_T{
+ SPLITTYPE_INVALID,
+ SPLITTYPE_BOTH,
+ SPLITTYPE_A,
+ SPLITTYPE_B,
+ NUMBER_SPLITTYPES
+};
+
+/**
+ * \typedef peptideToScore
+ * \brief Mapping of peptide object to scores
+ */
+typedef std::map<Crux::Peptide*, FLOAT_T, bool(*)(Crux::Peptide*, Crux::Peptide*) > PeptideToScore;
+
+/**
+ * \typedef ProteinToScore
+ * \brief Mapping of protein object to scores
+ */
+typedef std::map<Crux::Protein*, FLOAT_T, bool(*)(Crux::Protein*, Crux::Protein*) > ProteinToScore;
+
+/**
+ * \typedef MetaProtein
+ * \brief Collection of protein objects which contain exactly the same
+ * set of peptides.
+ */
+typedef std::set<Crux::Protein*, bool(*)(Crux::Protein*, Crux::Protein*) > MetaProtein;
+
+/**
+ * \typedef ProteinToMetaProtein
+ * \brief Mapping of Protein to MetaProtein to which it belongs
+ */
+typedef std::map<Crux::Protein*, MetaProtein, bool(*)(Crux::Protein*, Crux::Protein*) > ProteinToMetaProtein;
+
+/**
+ * \typedef MetaToRank
+ * \brief Mapping of MetaProtein to ranks to the rank asigned to it
+ */
+typedef std::map<MetaProtein, int, bool(*)(MetaProtein, MetaProtein) > MetaToRank;
+
+
+/**
+ * \enum FILE_FORMAT_T
+ * \brief indication of which file format is read
+ * by the Barista or QRanker
+ */
+enum FILE_FORMAT_T{
+ INVALID_FORMAT,
+ SQT_FORMAT,
+ XML_FORMAT,
+ DELIMITED_FORMAT
+};
+
+#endif
+
diff --git a/src/parameter.cpp b/src/parameter.cpp
new file mode 100644
index 0000000..f2ee192
--- /dev/null
+++ b/src/parameter.cpp
@@ -0,0 +1,947 @@
+/***********************************************************************//**
+ * \file parameter.cpp
+ * FILE: parameter.cpp
+ * AUTHOR: written by Tobias Mann, CRUXified by Chris Park
+ * Missed-cleavage conversion: Kha Nguyen
+ * \brief General parameter handling utilities. MUST declare ALL
+ * optional command parameters here inside initalialize_parameters.
+ ****************************************************************************/
+
+#include "util/crux-utils.h"
+#include "io/LineFileReader.h"
+#include "parameter.h"
+#include "util/Params.h"
+#include "util/StringUtils.h"
+#include "util/WinCrux.h"
+#include "model/Peptide.h"
+#include <iostream>
+
+using namespace std;
+
+/*
+ * Global variables
+ */
+
+static const char* parameter_type_strings[NUMBER_PARAMETER_TYPES] = {
+ "INT_ARG", "DOUBLE_ARG", "STRING_ARG", "MASS_TYPE_T", "DIGEST_T",
+ "ENZYME_T",
+ "bool", "SCORER_TYPE_T", "ION_TYPE_T",
+ "ALGORITHM_T", "HARDKLOR_ALGORITHM_TYPE_T",
+ "WINDOW_TYPE_T", "MEASURE_TYPE_T", "THRESHOLD_T",
+ "PARSIMONY_TYPE_T", "QUANT_LEVEL_TYPE_T", "DECOY_TYPE_T", "MASS_FORMAT_T"};
+
+//one hash for parameter values, one for usage statements, one for types
+// all hashes keyed on parameter/option name
+
+AA_MOD_T* list_of_mods[MAX_AA_MODS]; // list containing all aa mods
+ // in param file, c-,n-term mods at end
+AA_MOD_T** list_of_variable_mods = NULL; // pointer to first non-fixed mod
+AA_MOD_T** list_of_c_mods = NULL; // pointer to first c_term mod in list
+AA_MOD_T** list_of_n_mods = NULL; //pointer to first n_term mod in list
+int fixed_c_mod = -1; // position in list_of_mods or -1 if not present
+int fixed_n_mod = -1; // position in list_of_mods or -1 if not present
+int num_fixed_mods = 0;
+int num_mods = 0; // ANY_POSITION mods
+int num_c_mods = 0; // variable c-term mods
+int num_n_mods = 0; // variable n-term mods
+//require num_mods + num_c_mods + num_n_mods +
+//(fixed_c_mod > -1) + (fixed_n_mod > -1) <= MAX_AA_MODS
+
+char* pre_cleavage_list;
+char* post_cleavage_list;
+int pre_list_size;
+int post_list_size;
+bool pre_for_inclusion;
+bool post_for_inclusion;
+
+vector<string> comet_enzyme_info_lines_;
+
+/**
+ * \returns the comet enzyme info lines parsed from the file
+ * or generated defaults
+ */
+const std::vector<std::string>& get_comet_enzyme_info_lines() {
+ return comet_enzyme_info_lines_;
+}
+
+/************************************
+ * Private function declarations
+ ************************************
+ */
+
+bool string_to_param_type(const char*, PARAMETER_TYPE_T* );
+
+/************************************
+ * Function definitions
+ ************************************
+ */
+
+/**
+ * initialize parameters
+ * ONLY add optional parameters here!!!
+ * MUST declare ALL optional parameters in array to be used
+ * Every option and its default value for every executable
+ * must be declared here
+ */
+void initialize_parameters(void){
+ /* initialize the list of mods */
+ for (int mod_idx = 0; mod_idx < MAX_AA_MODS; mod_idx++) {
+ //initialize_aa_mod(&list_of_mods[mod_idx], mod_idx);
+ list_of_mods[mod_idx] = new_aa_mod(mod_idx);
+ }
+
+ /* initialize custom enzyme variables */
+ pre_list_size = 0;
+ post_list_size = 0;
+ pre_cleavage_list = NULL;
+ post_cleavage_list = NULL;
+ pre_for_inclusion = true;
+ post_for_inclusion = false;
+
+ // Default comet enzyme lines
+ comet_enzyme_info_lines_.push_back("0. No_enzyme\t\t\t\t0 - -");
+ comet_enzyme_info_lines_.push_back("1. Trypsin\t\t\t\t1 KR P");
+ comet_enzyme_info_lines_.push_back("2. Trypsin/P\t\t\t\t1 KR -");
+ comet_enzyme_info_lines_.push_back("3. Lys_C\t\t\t\t1 K P");
+ comet_enzyme_info_lines_.push_back("4. Lys_N\t\t\t\t0 K -");
+ comet_enzyme_info_lines_.push_back("5. Arg_C\t\t\t\t1 R P");
+ comet_enzyme_info_lines_.push_back("6. Asp_N\t\t\t\t0 D -");
+ comet_enzyme_info_lines_.push_back("7. CNBr\t\t\t\t1 M -");
+ comet_enzyme_info_lines_.push_back("8. Glu_C\t\t\t\t1 DE P");
+ comet_enzyme_info_lines_.push_back("9. PepsinA\t\t\t\t1 FL P");
+ comet_enzyme_info_lines_.push_back("10. Chymotrypsin\t\t\t1 FWYL P");
+}
+
+/**
+ * Read the value given for custom-enzyme and enter values into global
+ * params. Correct syntax is [A-Z]|[A-Z] or {A-Z}|{A-Z}. An X
+ * indicates that any residue is legal. Sets pre/post_list size and
+ * allocates memory for pre/post_cleavage_list. Sets
+ * pre/post_for_inclusion as true if [] encloses list or false if {}
+ * encloses list. For special case of [X], set p_cleavage_list as
+ * empty and inclusion as false.
+ */
+// NOTE (BF mar-11-09): for testing would be nice if this returned
+// error code instead of dying
+void parse_custom_enzyme(const string& rule_str){
+ bool success = true;
+ int len = rule_str.length();
+ int idx = 0;
+ int pipe_idx = 0;
+
+ // 1. find the |
+ for(idx = 0; idx < len; idx++){
+ if( rule_str[idx] == '|' ){
+ pipe_idx = idx;
+ break;
+ }
+ }
+ // check that there isn't a second
+ for(idx = idx+1; idx < len; idx++){
+ if( rule_str[idx] == '|' ){
+ success = false;
+ break;
+ }
+ }
+
+ // 2. set beginning and end of strings relative to pipe, start, end
+ // 0 1 p-1 p p+1 p+2 len-1 len
+ // [ X ] | [ X ] '0'
+ int pre_first_idx = 1;
+ int pre_end_idx = pipe_idx - 1;
+ int post_first_idx = pipe_idx + 2;
+ int post_end_idx = len -1;
+
+ // 3. check that braces match and set inclusion
+ // pre-list
+ if(pipe_idx < 1){
+ success = false;
+ }else if(rule_str[pre_first_idx-1] == '[' &&
+ rule_str[pre_end_idx] == ']'){
+ pre_for_inclusion = true;
+ }else if(rule_str[pre_first_idx-1] == '{' &&
+ rule_str[pre_end_idx] == '}'){
+ pre_for_inclusion = false;
+ }else{
+ success = false;
+ }
+
+ // post list
+ if(pipe_idx + 2 >= len ){
+ success = false;
+ }else if(rule_str[post_first_idx-1] == '[' &&
+ rule_str[post_end_idx] == ']'){
+ post_for_inclusion = true;
+ }else if(rule_str[post_first_idx-1] == '{' &&
+ rule_str[post_end_idx] == '}'){
+ post_for_inclusion = false;
+ }else{
+ success = false;
+ }
+
+ // check that braces aren't empty
+ if(pre_first_idx >= pre_end_idx || post_first_idx >= post_end_idx ){
+ success = false;
+ }
+
+ if( success == false ){
+ carp(CARP_FATAL, "Custom enzyme syntax '%s' is incorrect. "
+ "Must be of the form [AZ]|[AZ] or with [] replaced by {}. "
+ "AZ is a list of residues (letters A-Z) required [] or prohibited {}. "
+ "Use [X] to indicate any reside is legal.",
+ rule_str.c_str());
+ }
+
+ // 4. allocate lists and fill
+ pre_list_size = pre_end_idx - pre_first_idx;
+ pre_cleavage_list = (char*)mycalloc(pre_list_size, sizeof(char));
+ for(idx = 0; idx < pre_list_size; idx++){
+ pre_cleavage_list[idx] = rule_str[pre_first_idx+idx];
+ }
+
+ post_list_size = post_end_idx - post_first_idx;
+ post_cleavage_list = (char*)mycalloc(post_list_size, sizeof(char));
+ for(idx = 0; idx < post_list_size; idx++){
+ post_cleavage_list[idx] = rule_str[post_first_idx+idx];
+ }
+
+
+ // 5. check special case of [X]
+ if(strncmp( rule_str.c_str(), "[X]", pre_list_size+2) == 0){
+ free(pre_cleavage_list);
+ pre_cleavage_list = NULL;
+ pre_list_size = 0;
+ pre_for_inclusion = false;
+ }
+
+ if(strncmp( rule_str.c_str()+post_first_idx-1, "[X]", post_list_size+2) == 0){
+ free(post_cleavage_list);
+ post_cleavage_list = NULL;
+ post_list_size = 0;
+ post_for_inclusion = false;
+ }
+}
+
+/**
+ * Maximum size of the description of a parameter.
+ */
+static const int PARAMETER_BUFFER = 10000;
+
+/**
+ * Print modifications to the given file in the format used in the
+ * parameter file. Expected names are "mod", "cmod", "nmod". The
+ * function to get the list of modifications should correspond to the
+ * mod name. (i.e. for "mod", use get_aa_mod_list(), for "cmod" use
+ * get_c_mod_list(), for "nmod" use get_n_mod_list())
+ */
+void print_mods_parameter_file(ostream* param_file,
+ const char* name,
+ int (*mod_getter)(AA_MOD_T***)){
+ // get mod description
+ char comments[PARAMETER_BUFFER] = "";
+ strcat_formatted(comments, "# ", Params::GetUsage(name).c_str());
+ strcat_formatted(comments, "# ", Params::GetFileNotes(name).c_str());
+ int precision = Params::GetInt("mod-precision");
+
+ // get list of mods to print
+ AA_MOD_T** mod_list = NULL;
+ int total_mods = (*mod_getter)(&mod_list);
+ for( int mod_idx = 0 ; mod_idx < total_mods; mod_idx++){
+ float mass = aa_mod_get_mass_change(mod_list[mod_idx]);
+
+ // standard mods have the format mass:aa_list:max
+ if( strcmp(name, "mod") == 0 ){
+ int max = aa_mod_get_max_per_peptide(mod_list[mod_idx]);
+ bool* aas_modified = aa_mod_get_aa_list(mod_list[mod_idx]);
+ char aa_str[PARAMETER_BUFFER] = "";
+ char* aa_str_ptr = aa_str;
+ for(int aa_idx = 0; aa_idx < AA_LIST_LENGTH; aa_idx++){
+ if( aas_modified[aa_idx] == true ){
+ sprintf(aa_str_ptr, "%c", (aa_idx + 'A'));
+ aa_str_ptr++;
+ }
+ }
+ char buffer[1024];
+ sprintf(buffer, "%s%s=%.*f:%s:%i", comments, name, precision,
+ mass, aa_str, max);
+ *param_file << buffer << endl << endl;
+ } else { // nmod, cmod have the format mass:end_distance
+ int distance = aa_mod_get_max_distance(mod_list[mod_idx]);
+ char buffer[1024];
+ sprintf(buffer, "%s%s=%.*f:%i", comments, name, precision,
+ mass, distance);
+ *param_file << buffer << endl << endl;
+ }
+ }
+
+ // if there were no mods, print placeholder
+ if( total_mods == 0 ){
+ *param_file << Params::ProcessHtmlDocTags(comments) << name << "=NO MODS" << endl << endl;
+ }
+}
+
+/**
+ *
+ * parse the parameter file given the filename
+ */
+void parse_parameter_file(
+ const char* parameter_filename ///< the parameter file to be parsed -in
+ )
+{
+ FILE *file;
+ char *line;
+ int idx;
+
+ carp(CARP_DETAILED_DEBUG, "Parsing parameter file '%s'",parameter_filename);
+
+ /* check if parameter file exists, if not die */
+ if(access(parameter_filename, F_OK)){
+ carp(CARP_FATAL, "Could not open parameter file '%s'", parameter_filename);
+ }
+
+ LineFileReader line_reader(parameter_filename);
+
+ bool found_comet = false;
+
+ while(line_reader.hasNext()) {
+ string line = line_reader.next();
+ bool found_equal = false;
+ if (found_comet) {
+ comet_enzyme_info_lines_.push_back(line);
+ } else {
+ if (line.find("[COMET_ENZYME_INFO]") != string::npos) {
+ comet_enzyme_info_lines_.clear();
+ found_comet = true;
+ } else {
+ size_t comment = line.find('#');
+ if (comment != string::npos) {
+ line = line.substr(0, comment);
+ }
+ size_t equals = line.find('=');
+ if (equals == string::npos) {
+ continue;
+ }
+ string option_name = StringUtils::Trim(line.substr(0, equals));
+ string option_value = StringUtils::Trim(line.substr(equals + 1));
+ if (!Params::Exists(option_name)) {
+ carp(CARP_WARNING, "Read parameter '%s' from parameter file, but no "
+ "such parameter exists.", option_name.c_str());
+ continue;
+ } else if (Params::IsArgument(option_name)) {
+ carp(CARP_WARNING, "Read parameter '%s' from parameter file, but is "
+ "an argument, not an option.", option_name.c_str());
+ continue;
+ }
+ Params::Set(option_name, option_value);
+ }
+ }
+ }
+ if (comet_enzyme_info_lines_.empty()) {
+ carp(CARP_WARNING, "putting in default comet enzyme lines");
+ comet_enzyme_info_lines_.push_back("0. No_enzyme\t\t\t\t0 - -");
+ comet_enzyme_info_lines_.push_back("1. Trypsin\t\t\t\t1 KR P");
+ comet_enzyme_info_lines_.push_back("2. Trypsin/P\t\t\t\t1 KR -");
+ comet_enzyme_info_lines_.push_back("3. Lys_C\t\t\t\t1 K P");
+ comet_enzyme_info_lines_.push_back("4. Lys_N\t\t\t\t0 K -");
+ comet_enzyme_info_lines_.push_back("5. Arg_C\t\t\t\t1 R P");
+ comet_enzyme_info_lines_.push_back("6. Asp_N\t\t\t\t0 D -");
+ comet_enzyme_info_lines_.push_back("7. CNBr\t\t\t\t1 M -");
+ comet_enzyme_info_lines_.push_back("8. Glu_C\t\t\t\t1 DE P");
+ comet_enzyme_info_lines_.push_back("9. PepsinA\t\t\t\t1 FL P");
+ comet_enzyme_info_lines_.push_back("10. Chymotrypsin\t\t\t1 FWYL P");
+ }
+}
+
+/**************************************************
+ * GETTERS (public)
+ **************************************************
+ */
+
+DIGEST_T get_digest_type_parameter( const char* name ){
+ string param = Params::GetString(name);
+ DIGEST_T digest_type = string_to_digest_type(param);
+ if( digest_type == INVALID_DIGEST ){
+ carp(CARP_FATAL, "Digest_type parameter %s has the value %s "
+ "which is not of the correct type.", name, param.c_str());
+ }
+ return digest_type;
+}
+
+ENZYME_T get_enzyme_type_parameter( const char* name ){
+ string param = Params::GetString(name);
+ ENZYME_T enzyme_type = string_to_enzyme_type(param);
+ if( enzyme_type == INVALID_ENZYME ){
+ carp(CARP_FATAL, "Enzyme_type parameter %s has the value %s "
+ "which is not of the correct type.", name, param.c_str());
+ }
+ return enzyme_type;
+}
+
+MASS_TYPE_T get_mass_type_parameter(
+ const char* name
+ ){
+ string param_value_str = Params::GetString(name);
+ MASS_TYPE_T param_value;
+ bool success = string_to_mass_type(param_value_str, ¶m_value);
+
+ if( ! success ){
+ carp(CARP_FATAL,
+ "Mass_type parameter %s has the value %s which is not of "
+ "the correct type", name, param_value_str.c_str());
+ }
+ return param_value;
+}
+
+THRESHOLD_T get_threshold_type_parameter(
+ const char* name
+ ){
+ return string_to_threshold_type(Params::GetString(name));
+}
+
+DECOY_TYPE_T get_decoy_type_parameter(
+ const char* name
+ ){
+ return string_to_decoy_type(Params::GetString(name));
+}
+
+DECOY_TYPE_T get_tide_decoy_type_parameter(
+ const char* name
+) {
+ return string_to_tide_decoy_type(Params::GetString(name));
+}
+
+MASS_FORMAT_T get_mass_format_type_parameter(
+ const char* name
+ ){
+ return string_to_mass_format(Params::GetString(name));
+}
+
+int get_max_ion_charge_parameter(
+ const char* name
+ ){
+ string param_value_str = Params::GetString(name);
+ if (param_value_str == "peptide") {
+ return BILLION; //using this with min function on peptide charge.
+ }
+ int ans = atoi(param_value_str.c_str());
+ if (ans <= 0 || ans > 6) {
+ carp(CARP_FATAL,
+ "Max_ion_charge parameter %s has the value %s which is not a "
+ "legal value", name, param_value_str.c_str());
+ }
+ return ans;
+}
+
+char get_delimiter_parameter(
+ const char* name
+ ) {
+ string param_value_str = Params::GetString(name);
+ if (param_value_str == "tab") {
+ return '\t'; //using this with min function on peptide charge.
+ } else {
+ if (param_value_str.length() != 1) {
+ carp(CARP_FATAL,
+ "delimiter parameter %s with value %s is not a single character or "
+ "'tab'", name, param_value_str.c_str());
+ }
+ return param_value_str[0];
+ }
+}
+
+COLTYPE_T get_column_type_parameter(const char* name){
+ return string_to_column_type(Params::GetString(name));
+}
+
+COMPARISON_T get_comparison_parameter(const char* name) {
+ return string_to_comparison(Params::GetString(name));
+}
+
+
+/**************************************************
+ * SETTERS (private)
+ **************************************************
+ */
+
+/**
+ * Routines that return crux enumerated types.
+ */
+
+bool string_to_param_type(const char* name, PARAMETER_TYPE_T* result ){
+ bool success = true;
+ if( name == NULL ){
+ return false;
+ }
+
+ int param_type = convert_enum_type_str(
+ name, -10, parameter_type_strings, NUMBER_PARAMETER_TYPES);
+ (*result) = (PARAMETER_TYPE_T)param_type;
+
+ if( param_type == -10 ){
+ success = false;
+ }
+ return success;
+}
+
+/**
+ * \brief Get the pointer to the list of AA_MODs requested by the
+ * user. Does NOT include the c- and n-term mods
+ * \returns The number of items pointed to by mods
+ */
+int get_aa_mod_list
+ (AA_MOD_T*** mods) ///< the address of an array of pointers
+{
+ *mods = list_of_variable_mods;
+ return num_mods;
+}
+
+/**
+ * \brief Get the pointer to the list of AA_MODs for the peptide
+ * c-terminus. Return 0 and set mods==NULL if there are no c-term
+ * mods.
+ *
+ * \returns The number of items pointed to by mods
+ */
+int get_c_mod_list
+ (AA_MOD_T*** mods) ///< the address of an array of pointers
+{
+ *mods = list_of_c_mods;
+ return num_c_mods;
+}
+/**
+ * \brief Get the pointer to the list of AA_MODs for the peptide
+ * n-terminus. Return 0 and set mods==NULL if there are no n-term
+ * mods.
+ *
+ * \returns The number of items pointed to by mods
+ */
+int get_n_mod_list
+ (AA_MOD_T*** mods) ///< the address of an array of pointers
+{
+ *mods = list_of_n_mods;
+ return num_n_mods;
+}
+
+/**
+ * \brief Get the pointer to the list of AA_MODs requested by the
+ * user. Includes aa_mods, c- and n-term mods.
+ * \returns The number of items pointed to by mods
+ */
+int get_all_aa_mod_list
+ (AA_MOD_T*** mods) ///< the address of an array of pointers
+{
+ *mods = list_of_mods;
+ return num_mods + num_c_mods + num_n_mods + num_fixed_mods;
+}
+
+/**
+ * \returns The index of the C_TERM or N_TERM fixed modification in
+ * the global list of modifications.
+ */
+int get_fixed_mod_index(MOD_POSITION_T position){
+ int index = -1;
+ switch(position){
+ case N_TERM:
+ index = fixed_n_mod;
+ break;
+ case C_TERM:
+ index = fixed_c_mod;
+ break;
+ case ANY_POSITION:
+ carp(CARP_ERROR, "Getting non-terminal fixed mods not implemented.");
+ break;
+ }
+ return index;
+}
+
+/**
+ * \returns the number of fixed terminal modifications: 0, 1, or 2.
+ */
+int get_num_fixed_mods(){
+ return num_fixed_mods;
+}
+
+/* Helper functions for read_mods_from_file */
+/* TODO: these reads could be made more general as in
+ read_double(&double, char*, char) */
+
+/**
+ * \brief Set the mass_change field in an AA_MOD based on a line from
+ * a parameter file.
+ *
+ * Assumes that the line points to a FLOAT_T followed by separator.
+ * Converts the number and sets the appropriate field in the mod.
+ * Dies with error if line does not point to a number. Returns a
+ * pointer to the character after the first instance of separator or
+ * to the end of the line if separator does not appear.
+ *
+ * \returns A pointer to the next token in the line.
+ */
+char* read_mass_change(AA_MOD_T* mod, char* line, char separator,
+ int& max_precision){
+ //carp(CARP_DEBUG, "token points to %s", line);
+
+ aa_mod_set_mass_change(mod, atof(line));
+ if( aa_mod_get_mass_change(mod) == 0){
+ carp(CARP_FATAL, "The mass change is not valid for mod %s", line);
+ }
+ char* next = line;
+ char* decimal = NULL;
+ // read to end of line, colon, or whitespace
+ while(*next != '\0' && *next != separator && *next != ' ' && *next != '\t'){
+ if(*next == '.'){
+ decimal = next;
+ }
+ next++;
+ }
+ // distance from decimal to separator is number of digits
+ if( decimal != NULL ){
+ int distance = next - decimal -1;
+ if( distance > max_precision ){
+ max_precision = distance;
+ }
+ }
+
+ next++; // point past the separator
+
+ return next;
+}
+/**
+ * \brief Read the line from the parameter file and set the bool vaues
+ * in the mod's aa_list appropriately.
+ *
+ * Assumes that line points to a list of letters, a-Z, followed by
+ * separator. Fails if characters before separator are not a-Z.
+ * Returns a pointer to the character after separator, or to the end
+ * of the line if separator is not found.
+ *
+ * \returns A pointer to the next token in the line.
+ */
+char* set_aa_list(AA_MOD_T* mod, char* line, char separator){
+ carp(CARP_DETAILED_DEBUG, "token points to %s", line);
+
+ bool* aa_list = aa_mod_get_aa_list(mod);
+ while( *line != '\0' && *line != ':'){
+ char aa = toupper( *line );
+ carp(CARP_DETAILED_DEBUG, "aa is %c", aa);
+
+ if( aa < 'A' || aa > 'Z' ){
+ carp(CARP_FATAL, "The letter '%c' in the aa list is invalid.", aa);
+ }
+ carp(CARP_DETAILED_DEBUG, "aa index is %d", aa - 'A');
+ aa_list[aa - 'A'] = true;
+ //mod->aa_list[aa - 'A'] = true;
+ carp(CARP_DETAILED_DEBUG, "Set %c to true index %d", aa, (int)(aa-'A'));
+ line++;
+ }
+
+ if( *line == separator ){
+ line++;
+ }
+ return line;
+}
+
+/**
+ * \brief Set the max_per_peptide field in the mod with the value
+ * pointed to by line.
+ *
+ * Fails if line does not point to a valid integer.
+ * \returns void
+ */
+char* read_max_per_peptide(AA_MOD_T* mod, char* line, char separator){
+ //carp(CARP_DETAILED_DEBUG, "token points to %s", line);
+ if( *line == '\0' ){
+ carp(CARP_FATAL, "Missing maximum mods per peptide for mod %s", line);
+ }
+
+ aa_mod_set_max_per_peptide(mod, atoi(line));
+ if( aa_mod_get_max_per_peptide(mod) == 0 ){
+ carp(CARP_FATAL, "Maximum mods per peptide is invalid for mod %s", line);
+ }
+
+ char* next = line;
+ while(*next != '\0' && *next != separator){
+ next++;
+ }
+ if (*next != '\0') {
+ next++; // point past the separator
+ }
+ return next;
+}
+
+char* read_prevents_cleavage(AA_MOD_T* mod, char* line, char separator) {
+ char* next = line;
+ switch(*line) {
+ case ':':
+ next++;
+ case '\0':
+ carp(CARP_DEBUG, "No prevents_cleavage property found %s",line);
+ break;
+ case 'T':
+ case 't':
+ carp(CARP_DEBUG, "prevents_cleavage set to true %s",line);
+ aa_mod_set_prevents_cleavage(mod, true);
+ break;
+ case 'F':
+ case 'f':
+ carp(CARP_DEBUG, "prevents_cleavage set to false %s", line);
+ aa_mod_set_prevents_cleavage(mod, false);
+ break;
+ }
+
+ while (*next != '\0' && *next != separator) {
+ next++;
+ }
+ if (*next != '\0') {
+ next++; //points past the separator
+ }
+
+ return next;
+}
+
+char* read_prevents_xlink(AA_MOD_T* mod, char* line, char separator) {
+ char* next = line;
+ switch(*line) {
+ case ':':
+ next++;
+ case '\0':
+ carp(CARP_DEBUG, "No prevents_xlink property found %s",line);
+ break;
+ case 'T':
+ case 't':
+ carp(CARP_DEBUG, "prevents_xlink set to true %s",line);
+ aa_mod_set_prevents_xlink(mod, true);
+ break;
+ case 'F':
+ case 'f':
+ carp(CARP_DEBUG, "prevents_xlink set to false %s",line);
+ aa_mod_set_prevents_xlink(mod, false);
+ break;
+ }
+
+ while (*next != '\0' && *next != separator) {
+ next++;
+ }
+ if (*next != '\0') {
+ next++; //points past the separator
+ }
+
+ return next;
+}
+
+/**
+ * \brief Set the max_distance field in the mod with the value
+ * pointed to by line.
+ *
+ * Fails if line does not point to a valid integer.
+ * \returns void
+ */
+void read_max_distance(AA_MOD_T* mod, char* line){
+ int max_distance = atoi(line);
+
+ // make sure it's 0 because the file says 0; if not, default to max
+ if( max_distance == 0 && *line != '0' ){
+ max_distance = MAX_PROTEIN_SEQ_LENGTH;
+ }
+ aa_mod_set_max_distance(mod, max_distance);
+
+ return;
+}
+
+/**
+ * \brief This is the private function, detailed reader used by
+ * read_mods_from_file().
+ *
+ * Reads through whole file looking for lines that start with
+ * line_tag. Parses information into each of those lines putting it
+ * into the list_of_aa_mods, beginning with index cur_index and not
+ * exceeding MAX_AA_MODS. Distinguishes between regular
+ * aa_mods and c-term or n-term mods for which struct fields it
+ * fills.
+ * \returns Returns the index of the next mod in the list.
+ */
+int read_mods(
+ FILE* param_file, ///< file from which to read mod info
+ int cur_index, ///< index of next mod to be entered
+ const char* line_tag,///< text at beginning of mod line (eg mod=)
+ MOD_POSITION_T position,///< type of mod (any, c-, n-term)
+ int& max_precision///< most digits in mass change
+){
+
+ carp(CARP_DEBUG, "Reading mods for %d position", (int)position);
+ char* line = (char*)mycalloc(MAX_LINE_LENGTH, sizeof(char));
+
+
+ // read the whole file looking for mods
+ while(fgets(line, MAX_LINE_LENGTH, param_file)==line){
+ // read line until one starts with tag (mod=, cmod=, nmod=)
+ if( 0 != strncmp(line, line_tag, strlen(line_tag)) ){
+ continue;
+ }
+
+ // check bounds on index
+ if( cur_index == MAX_AA_MODS ){
+ carp(CARP_FATAL, "Too many modifications in parameter file, " \
+ "%d maximum", MAX_AA_MODS);
+ }
+ AA_MOD_T* cur_mod = list_of_mods[cur_index];
+
+ // prepare for reading line
+ carp(CARP_DEBUG, "mod line: %s", line);
+ char* token = line + strlen(line_tag);
+
+ // check for default value "NO MODS" written to default.parameter
+ if( strncmp(token, "NO MODS", strlen("NO MODS")) == 0 ){
+ return cur_index;
+ }
+
+ // get the FLOAT_T and check for ok-ness
+ token = read_mass_change(cur_mod, token, ':', max_precision);
+
+ // fill in values for standard mods
+ if( position == ANY_POSITION ){
+ // read the aa list and set the values in mod
+ token = set_aa_list(cur_mod, token, ':');
+
+ // get max per peptide
+ token = read_max_per_peptide(cur_mod, token, ':');
+
+ // read whether this modification prevents cleavage (OPTIONAL)
+ token = read_prevents_cleavage(cur_mod, token, ':');
+
+ // read whether this modification prevents xlink (OPTIONAL)
+ token = read_prevents_xlink(cur_mod, token, ':');
+
+
+ } else { // fill in values for c- or n-mod
+ // get the max distance
+ read_max_distance(cur_mod, token);
+
+ // set all bools to true
+ int i = 0;
+ bool* aa_list = aa_mod_get_aa_list(cur_mod);
+ for(i=0; i<AA_LIST_LENGTH; i++){
+ aa_list[i] = true;
+ }
+ // set type to c-/n-term and max to 1
+ aa_mod_set_position(cur_mod, position);
+ aa_mod_set_max_per_peptide(cur_mod, 1);
+ }
+
+ // increment counter and get next mod
+ cur_index++;
+
+ }// repeat until end of file
+
+ free(line);
+ return cur_index;
+}
+
+/**
+ * \brief Read the paramter file and populate the static parameter
+ * list of AA_MODS, inlcuding the list of position mods.
+ *
+ * Also updates the array of amino_masses. Dies with an error if the
+ * number of mods in the parameter file is greater than MAX_AA_MODS.
+ * \returns void
+ */
+void read_mods_from_file(const char* param_filename) {
+ carp(CARP_DEBUG, "Reading mods from parameter file '%s'", param_filename);
+
+ // open file
+ FILE* param_file = fopen(param_filename, "rb");
+ if( param_file == NULL ){
+ carp(CARP_FATAL, "Could not open parameter file '%s'", param_filename);
+ }
+
+ // get first mod
+ int total_num_mods = 0;
+ int max_precision = 0; // gets updated with max seen in param file
+
+ // start with fixed terminal mods
+ total_num_mods = read_mods(param_file, 0, "nmod-fixed=",
+ N_TERM, max_precision);
+ // keep track of where we stored the fixed mod
+ if( total_num_mods == 1 ){
+ fixed_n_mod = 0; // first in list
+ } else if (total_num_mods > 1){
+ carp(CARP_FATAL, "Cannot specify more than one fixed n-terminal modification.");
+ }
+ rewind( param_file );
+
+ total_num_mods = read_mods(param_file, total_num_mods, "cmod-fixed=",
+ C_TERM, max_precision);
+ // keep track of where we stored the fixed mod
+ if( total_num_mods == 1 && fixed_n_mod == -1 ){
+ fixed_c_mod = 0; // first in list
+ } else if( total_num_mods == 2 ){
+ fixed_c_mod = 1; // second in list
+ } else if (total_num_mods > 2){
+ carp(CARP_FATAL,
+ "Cannot specify more than one fixed n-terminal modification.");
+ }
+ rewind( param_file );
+ num_fixed_mods = total_num_mods;
+
+ // now get the variable mods
+ list_of_variable_mods = &list_of_mods[total_num_mods];
+ total_num_mods = read_mods(param_file, total_num_mods,
+ "mod=", ANY_POSITION, max_precision);
+ num_mods = total_num_mods - num_fixed_mods; // set global var
+
+ // Read the file again to get the cmods
+ rewind( param_file );
+
+ // set cmod pointer to next in array
+ list_of_c_mods = &list_of_mods[total_num_mods];
+
+ total_num_mods = read_mods(param_file, total_num_mods, "cmod=",
+ C_TERM, max_precision);
+ num_c_mods = total_num_mods - num_mods - num_fixed_mods;
+
+ // if no cmods present, don't point to the list of mods
+ if (num_c_mods == 0) {
+ list_of_c_mods = NULL;
+ }
+
+ // Read the file again to get the nmods
+ rewind( param_file );
+
+ // set nmod pointer to next in array
+ list_of_n_mods = &list_of_mods[total_num_mods];
+
+ total_num_mods = read_mods(param_file, total_num_mods, "nmod=",
+ N_TERM, max_precision);
+ num_n_mods = total_num_mods - num_mods - num_c_mods - num_fixed_mods;
+
+ // if no nmods present, don't point to the list of mods
+ if( num_n_mods == 0){
+ list_of_n_mods = NULL;
+ }
+
+ // set the mod-precision option
+ Params::Set("mod-precision", max_precision);
+
+ // close file
+ fclose(param_file);
+ carp(CARP_DEBUG, "Finished reading mods file");
+}
+
+void incrementNumMods() {
+ num_mods++;
+}
+
+void resetMods() {
+ for (int i = 0; i < MAX_AA_MODS; i++) {
+ free_aa_mod(list_of_mods[i]);
+ list_of_mods[i] = new_aa_mod(i);
+ }
+ num_mods = 0;
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/parameter.h b/src/parameter.h
new file mode 100644
index 0000000..617aae8
--- /dev/null
+++ b/src/parameter.h
@@ -0,0 +1,266 @@
+/**
+ * \file parameter.h
+ * $Revision: 1.37 $
+ * \brief General parameter handling utilities. All values stored here.
+
+ * \detail MUST declare ALL optional command line parameters and
+ * required command line arguments here in initalialize_parameters.
+ * Parameters can only be set via parse_cmd_line_into_params_hash()
+ * which takes values from the command line and from an optional
+ * parameter file (provided on the command line with the --parameter
+ * option). Options are checked for correct type and legal values.
+ * Exits with usage statement on error. Parameter values can be
+ * retrieved with get_<type>_paramter functions.
+ *
+ ****************************************************************************/
+#ifndef PARAMETER_FILE_H
+#define PARAMETER_FILE_H
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <math.h>
+#include <limits.h>
+#include <string>
+#include "util/utils.h"
+#include "util/crux-utils.h"
+#include "io/carp.h"
+#include "model/objects.h"
+
+#include "util/modifications.h"
+
+static const int PARAMETER_LENGTH = 1024;
+///< maximum length of parameter name and value in characters
+static const int NUM_PARAMS = 512; ///< maximum number of parameters allowed
+static const int MAX_LINE_LENGTH = 4096; ///< maximum line length in the parameter file
+static const int MILLION = 1000000;
+static const int BILLION = 1000000000;
+static const int SMALL_BUFFER = 256;
+static const int MAX_SET_PARAMS = 256;
+
+// The size of the bins for discretizing the m/z axis of the
+// observed spectrum. For use with monoisotopic mass.
+static const FLOAT_T BIN_WIDTH_MONO = 1.0005079;
+// The size of the bins for discretizing the m/z axis of the
+// observed spectrum. For use with average mass.
+static const FLOAT_T BIN_WIDTH_AVERAGE = 1.0011413;
+
+// Global variables
+// NOTE (BF mar-10-09): Could be like mod lists, but will require a
+// get_parameter call for each...residue? protein?
+extern char* pre_cleavage_list;
+extern char* post_cleavage_list;
+extern int pre_list_size;
+extern int post_list_size;
+extern bool pre_for_inclusion;
+extern bool post_for_inclusion;
+
+// TODO (BF 1-28-08): these should be private. move to parameter.c
+/**
+ * Data types of parameters. Used for checking valid parameter input
+ * from user.
+ *
+ * To add a new parameter type:
+ * (for NEW types) 1. create enum,
+ * 2. create array of strings,
+ * 3. write string-to-type,
+ * 4. write type-to-string
+ * (for ALL types) 5. add to parameter-type enum and strings
+ * 6. write get-type-parameter
+ * 7. write set-type-parameter
+ * 8. add to the check_type_and_bounds
+ *
+ */
+enum parameter_type {
+ INT_P, ///< parameters of type int
+ DOUBLE_P, ///< parameters of type double
+ STRING_P, ///< parameters of type char*
+ MASS_TYPE_P, ///< parameters of type MASS_TYPE_T
+ DIGEST_TYPE_P, ///< parameters of type DIGEST_T
+ ENZYME_TYPE_P, ///< parameters of type ENZYME_T
+ //PEPTIDE_TYPE_P, ///< parameters of type PEPTIDE_TYPE_T
+ BOOLEAN_P, ///< parameters of type bool
+ SCORER_TYPE_P, ///< parameters of type SCORER_TYPE_T
+ ION_TYPE_P, ///< parameters of type ION_TYPE_T
+ ALGORITHM_TYPE_P, ///< parameters of type ALGORITHM_TYPE_T
+ HARDKLOR_ALGORITHM_TYPE_P, ///< parameters of type HARDKLOR_ALGORITHM_T
+ WINDOW_TYPE_P, ///< parameters of type WINDOW_TYPE_T
+ MEASURE_TYPE_P, ///< parameters of type MEASURE_TYPE_T
+ THRESHOLD_P, ///< parameters of type THRESHOLD_TYPE_T
+ PARSIMONY_TYPE_P, ///< parameters of type PARSIMONY_TYPE_T
+ QUANT_LEVEL_TYPE_P,///< parameters of type QUANT_LEVEL_TYPE_T
+ DECOY_TYPE_P, ///< parameters of type DECOY_TYPE_T
+ MASS_FORMAT_P, ///< parameters of type MASS_FORMAT_T
+
+ NUMBER_PARAMETER_TYPES ///< leave this last, number of types
+};
+typedef enum parameter_type PARAMETER_TYPE_T;
+
+/**
+ * /brief Initialize parameters to default values.
+ *
+ * Every required argument for every executable and every option and
+ * its default value must be declared here. Allocates hash tables for
+ * holding parameter values.
+ */
+void initialize_parameters(void);
+
+void parse_custom_enzyme(const std::string& rule_str);
+
+/**
+ *
+ * parse the parameter file given the filename
+ */
+void parse_parameter_file(
+ const char* parameter_filename ///< the parameter file to be parsed -in
+ );
+
+void read_mods_from_file(const char* param_file);
+
+MASS_TYPE_T get_mass_type_parameter(
+ const char* name
+ );
+
+char get_delimiter_parameter(
+ const char* name
+ );
+
+DIGEST_T get_digest_type_parameter(
+ const char* name
+ );
+
+ENZYME_T get_enzyme_type_parameter(
+ const char* name
+ );
+
+DIGEST_T get_digest_type_parameter(
+ const char* name
+ );
+
+ENZYME_T get_enzyme_type_parameter(
+ const char* name
+ );
+
+THRESHOLD_T get_threshold_type_parameter(
+ const char* name
+ );
+
+QUANT_LEVEL_TYPE_T get_quant_level_type_parameter(
+ const char* name
+ );
+
+DECOY_TYPE_T get_decoy_type_parameter(
+ const char* name
+ );
+
+DECOY_TYPE_T get_tide_decoy_type_parameter(
+ const char* name
+ );
+
+MASS_FORMAT_T get_mass_format_type_parameter(
+ const char* name
+ );
+
+int get_max_ion_charge_parameter(
+ const char* name
+ );
+
+double get_mz_bin_width();
+
+double get_mz_bin_offset();
+
+COLTYPE_T get_column_type_parameter(
+ const char* name
+ );
+
+COMPARISON_T get_comparison_parameter(
+ const char* name
+ );
+
+/**
+ * \returns the comet enzyme info lines parsed from the file
+ * or generated defaults
+ */
+const std::vector<std::string>& get_comet_enzyme_info_lines();
+
+/**
+ * Prints the parameters. If lead_string is not null, preprends it to
+ * each line.
+ */
+void print_parameters(
+ char* first_line, ///< the first line to be printed before the parameter list -in
+ char* parameter_filename, ///< the parameter file name -in
+ char* lead_string, ///< the lead string to be printed before each line -in
+ FILE* outstream ///< the output stream -out
+ );
+
+
+/**
+ * \brief Get the pointer to the list of AA_MODs requested by the
+ * user. Does not include the c- and n-term mods. Argument is a
+ * reference to an array of pointers. Return 0 and set mods == NULL
+ * if there are no aa_mods.
+ * \returns The number of items pointed to by mods
+ */
+int get_aa_mod_list(AA_MOD_T*** mods);
+
+/**
+ * Adds 1 to the number of variable modifications in the
+ * parameters
+ */
+void incrementNumMods();
+
+void resetMods();
+
+/**
+ * \brief Get the pointer to the list of AA_MODs for the peptide
+ * c-terminus. Argument is a reference to an array of
+ * pointers. Return 0 and set mods==NULL if there are no c-term
+ * mods.
+ *
+ * \returns The number of items pointed to by mods
+ */
+int get_c_mod_list(AA_MOD_T*** mods);
+
+/**
+ * \brief Get the pointer to the list of AA_MODs for the peptide
+ * n-terminus. Argument is a reference to an array of
+ * pointers. Return 0 and set mods==NULL if there are no n-term
+ * mods.
+ *
+ * \returns The number of items pointed to by mods
+ */
+int get_n_mod_list(AA_MOD_T*** mods);
+
+/**
+ * \brief Get the pointer to the list of AA_MODs requested by the
+ * user. Includes aa_mods, c- and n-term mods. Argument is a
+ * reference to an array of pointers. Returns 0 and sets mods == NULL
+ * if there are no aa_mods.
+ * \returns The number of items pointed to by mods
+ */
+int get_all_aa_mod_list(AA_MOD_T*** mods);
+
+/**
+ * \returns The index of the C_TERM or N_TERM fixed modification in
+ * the global list of modifications.
+ */
+int get_fixed_mod_index(MOD_POSITION_T p);
+
+/**
+ * \returns the number of fixed terminal modifications: 0, 1, or 2.
+ */
+int get_num_fixed_mods();
+
+/**
+ * Print modifications to the given file in the format used in the
+ * parameter file. Expected names are "mod", "cmod", "nmod". The
+ * function to get the list of modifications should correspond to the
+ * mod name. (i.e. for "mod", use get_aa_mod_list(), for "cmod" use
+ * get_c_mod_list(), for "nmod" use get_n_mod_list())
+ */
+void print_mods_parameter_file(std::ostream* param_file,
+ const char* name,
+ int (*mod_getter)(AA_MOD_T***));
+
+#endif
diff --git a/src/util/Alphabet.cpp b/src/util/Alphabet.cpp
new file mode 100644
index 0000000..a4421d7
--- /dev/null
+++ b/src/util/Alphabet.cpp
@@ -0,0 +1,56 @@
+/*********************************************************************
+ * \file alphabet.cpp
+ * AUTHOR: Unknown
+ * \brief Provide a function for converting amino acids to ints.
+ ********************************************************************/
+#include "Alphabet.h"
+
+int Alphabet::amino_array_[AMINO_ARRAY_CAPACITY] = {0};
+bool Alphabet::amino_array_populated_ = false;
+
+/**
+ * Converts a character into an amino acid
+ */
+void Alphabet::populateAminoArray(void) {
+ if ( amino_array_populated_ ) {
+ return;
+ }
+ amino_array_['A'-'A'] = 0;
+ amino_array_['C'-'A'] = 1;
+ amino_array_['D'-'A'] = 2;
+ amino_array_['E'-'A'] = 3;
+ amino_array_['F'-'A'] = 4;
+ amino_array_['G'-'A'] = 5;
+ amino_array_['H'-'A'] = 6;
+ amino_array_['I'-'A'] = 7;
+ amino_array_['K'-'A'] = 8;
+ amino_array_['L'-'A'] = 9;
+ amino_array_['M'-'A'] = 10;
+ amino_array_['N'-'A'] = 11;
+ amino_array_['P'-'A'] = 12;
+ amino_array_['Q'-'A'] = 13;
+ amino_array_['R'-'A'] = 14;
+ amino_array_['S'-'A'] = 15;
+ amino_array_['T'-'A'] = 16;
+ amino_array_['V'-'A'] = 17;
+ amino_array_['W'-'A'] = 18;
+ amino_array_['Y'-'A'] = 19;
+
+ amino_array_populated_ = true;
+ return;
+}
+
+/**
+ * Converts a character into an int using the global amino_hash
+ */
+int Alphabet::aminoToInt(char amino) {
+ populateAminoArray();
+ int value = amino_array_[amino - 'A'];
+ return value;
+}
+
+
+const char* Alphabet::aminoAcids[] = { "A", "C", "D", "E", "F", "G", "H",
+ "I", "K", "L", "M", "N", "P", "Q",
+ "R", "S", "T", "V", "W", "Y", };
+const int Alphabet::numAminoAcids = sizeof(aminoAcids) / sizeof(char*);
diff --git a/src/util/Alphabet.h b/src/util/Alphabet.h
new file mode 100644
index 0000000..b7c8a80
--- /dev/null
+++ b/src/util/Alphabet.h
@@ -0,0 +1,31 @@
+/**
+ * \file alphabet.h
+ * AUTHOR: Unknown
+ * \brief Provide a function for converting amino acids to ints.
+ ********************************************************************/
+#ifndef ALPHABET_H
+#define ALPHABET_H
+
+
+class Alphabet {
+
+ public:
+ /**
+ * Converts a character into an int using the global amino_hash
+ */
+ static int aminoToInt(char amino);
+
+ /**
+ * Constants for iterating through all amino acids.
+ */
+ static const char* aminoAcids[];
+ static const int numAminoAcids;
+
+ protected:
+ static const int AMINO_ARRAY_CAPACITY = 100;
+ static int amino_array_[AMINO_ARRAY_CAPACITY];
+ static bool amino_array_populated_;
+ static void populateAminoArray();
+
+};
+#endif
diff --git a/src/util/AminoAcidUtil.cpp b/src/util/AminoAcidUtil.cpp
new file mode 100644
index 0000000..3bb29d5
--- /dev/null
+++ b/src/util/AminoAcidUtil.cpp
@@ -0,0 +1,107 @@
+#include "AminoAcidUtil.h"
+
+#include <limits>
+#include <stdexcept>
+
+using namespace std;
+
+string AminoAcidUtil::GetName(char c) {
+ switch (c) {
+ case 'A': return "alanine";
+ case 'B': return "";
+ case 'C': return "cysteine";
+ case 'D': return "aspartic acid";
+ case 'E': return "glutamic acid";
+ case 'F': return "phenylalanine";
+ case 'G': return "glycine";
+ case 'H': return "histidine";
+ case 'I': return "isoleucine";
+ case 'J': return "";
+ case 'K': return "lysine";
+ case 'L': return "leucine";
+ case 'M': return "methionine";
+ case 'N': return "asparagine";
+ case 'O': return "ornithine";
+ case 'P': return "proline";
+ case 'Q': return "glutamine";
+ case 'R': return "arginine";
+ case 'S': return "serine";
+ case 'T': return "threonine";
+ case 'U': return "selenocysteine";
+ case 'V': return "valine";
+ case 'W': return "tryptophan";
+ case 'X': return "";
+ case 'Y': return "tyrosine";
+ case 'Z': return "";
+ }
+ throw runtime_error("'" + string(1, c) + "' is not a valid amino acid");
+}
+
+double AminoAcidUtil::GetMass(char c, bool monoisotopic) {
+ if (monoisotopic) {
+ // Monoisotopic masses
+ switch (c) {
+ case 'A': return 71.03711;
+ case 'B': return numeric_limits<double>::quiet_NaN();
+ case 'C': return 103.00919;
+ case 'D': return 115.02694;
+ case 'E': return 129.04259;
+ case 'F': return 147.06841;
+ case 'G': return 57.02146;
+ case 'H': return 137.05891;
+ case 'I': return 113.08406;
+ case 'J': return 113.08406;
+ case 'K': return 128.09496;
+ case 'L': return 113.08406;
+ case 'M': return 131.04049;
+ case 'N': return 114.04293;
+ case 'O': return 114.07931;
+ case 'P': return 97.05276;
+ case 'Q': return 128.05858;
+ case 'R': return 156.10111;
+ case 'S': return 87.03203;
+ case 'T': return 101.04768;
+ case 'U': return 150.04344;
+ case 'V': return 99.06841;
+ case 'W': return 186.07931;
+ case 'X': return numeric_limits<double>::quiet_NaN();
+ case 'Y': return 163.06333;
+ case 'Z': return numeric_limits<double>::quiet_NaN();
+ }
+ } else {
+ // Average masses
+ switch (c) {
+ case 'A': return 71.0788;
+ case 'B': return numeric_limits<double>::quiet_NaN();
+ case 'C': return 103.1388;
+ case 'D': return 115.0886;
+ case 'E': return 129.1155;
+ case 'F': return 147.1766;
+ case 'G': return 57.0519;
+ case 'H': return 137.1411;
+ case 'I': return 113.1594;
+ case 'J': return 113.1594;
+ case 'K': return 128.1741;
+ case 'L': return 113.1594;
+ case 'M': return 131.1926;
+ case 'N': return 114.1038;
+ case 'O': return 114.1472;
+ case 'P': return 97.1167;
+ case 'Q': return 128.1307;
+ case 'R': return 156.1875;
+ case 'S': return 87.0782;
+ case 'T': return 101.1051;
+ case 'U': return 150.0388;
+ case 'V': return 99.1326;
+ case 'W': return 186.2132;
+ case 'X': return numeric_limits<double>::quiet_NaN();
+ case 'Y': return 163.1760;
+ case 'Z': return numeric_limits<double>::quiet_NaN();
+ }
+ }
+ throw runtime_error("'" + string(1, c) + "' is not a valid amino acid");
+}
+
+AminoAcidUtil::AminoAcidUtil() {}
+AminoAcidUtil::~AminoAcidUtil() {}
+
diff --git a/src/util/AminoAcidUtil.h b/src/util/AminoAcidUtil.h
new file mode 100644
index 0000000..1105d4e
--- /dev/null
+++ b/src/util/AminoAcidUtil.h
@@ -0,0 +1,18 @@
+#ifndef AMINOACIDUTIL_H
+#define AMINOACIDUTIL_H
+
+#include <string>
+
+const double CYSTEINE_DEFAULT = 57.021464;
+
+class AminoAcidUtil {
+ public:
+ static std::string GetName(char c);
+ static double GetMass(char c, bool monoisotopic = true);
+ private:
+ AminoAcidUtil();
+ ~AminoAcidUtil();
+};
+
+#endif
+
diff --git a/src/util/ArgParser.cpp b/src/util/ArgParser.cpp
new file mode 100644
index 0000000..7435b8f
--- /dev/null
+++ b/src/util/ArgParser.cpp
@@ -0,0 +1,127 @@
+#include "ArgParser.h"
+#include "StringUtils.h"
+
+using namespace std;
+
+ArgParser::ArgParser() {
+}
+
+void ArgParser::Parse(int argc, char** argv, const vector<string>& args) {
+ args_.clear();
+ options_.clear();
+
+ vector<ArgSpec> argSpecs = ArgStringsToArgSpecs(args);
+ int multi = -1; // Which argument accepts multiple values?
+ for (size_t i = 0; i < argSpecs.size(); i++) {
+ if (!argSpecs[i].IsMulti()) {
+ continue;
+ } else if (multi != -1) {
+ throw runtime_error("Cannot have multiple arguments that accept "
+ "multiple values.");
+ }
+ multi = i;
+ }
+
+ vector<string> parsedArgs;
+ // Start at 1 to skip the application name
+ for (int i = 1; i < argc; i++) {
+ string arg(argv[i]);
+ if (StringUtils::StartsWith(arg, "--")) {
+ // This is a option name
+ string option = arg.substr(2);
+ if (++i == argc) {
+ throw ArgParserException("No value found for option '" + option + "'");
+ }
+ options_[option] = argv[i];
+ } else {
+ // This is an argument
+ parsedArgs.push_back(arg);
+ }
+ }
+
+ int excess_args = parsedArgs.size() - argSpecs.size();
+ if (multi == -1 && excess_args != 0) {
+ throw ArgParserException("Expected " + StringUtils::ToString(argSpecs.size()) +
+ " arguments, but found " +
+ StringUtils::ToString(parsedArgs.size()),
+ argc == 1);
+ } else if (multi != -1 && excess_args < 0) {
+ throw ArgParserException("Expected at least " +
+ StringUtils::ToString(argSpecs.size()) +
+ " arguments, but found " +
+ StringUtils::ToString(parsedArgs.size()),
+ argc == 1);
+ }
+
+ int curParsedArg = -1;
+ for (vector<ArgSpec>::const_iterator i = argSpecs.begin(); i != argSpecs.end(); i++) {
+ string argName = i->GetName();
+ args_[argName] = vector<string>(1, parsedArgs[++curParsedArg]);
+ if (i->IsMulti()) {
+ for (int j = 0; j < excess_args; j++) {
+ args_[argName].push_back(parsedArgs[++curParsedArg]);
+ }
+ }
+ }
+}
+
+ArgParser::~ArgParser() {
+}
+
+const map< string, vector<string> >& ArgParser::GetArgs() const {
+ return args_;
+}
+
+const map<string, string>& ArgParser::GetOptions() const {
+ return options_;
+}
+
+const string ArgParser::GetArg(const string& name) const {
+ map< string, vector<string> >::const_iterator i = args_.find(name);
+ return (i != args_.end()) ? i->second.front() : "";
+}
+
+const vector<string> ArgParser::GetArgMulti(const string& name) const {
+ map< string, vector<string> >::const_iterator i = args_.find(name);
+ return (i != args_.end()) ? i->second : vector<string>();
+}
+
+const string ArgParser::GetOption(const string& name) const {
+ map<string, string>::const_iterator i = options_.find(name);
+ return (i != options_.end()) ? i->second : "";
+}
+
+ArgParser::ArgSpec::ArgSpec(const string& name, bool multi)
+ : name_(name), multi_(multi) {
+}
+
+string ArgParser::ArgSpec::GetName() const {
+ return name_;
+}
+
+bool ArgParser::ArgSpec::IsMulti() const {
+ return multi_;
+}
+
+vector<ArgParser::ArgSpec> ArgParser::ArgStringsToArgSpecs(const vector<string>& args) {
+ vector<ArgSpec> specs;
+ for (vector<string>::const_iterator i = args.begin(); i != args.end(); i++) {
+ string arg = *i;
+ size_t plus = arg.find('+');
+ if (plus == i->length() - 1) {
+ specs.push_back(ArgSpec(arg.substr(0, plus), true));
+ } else {
+ specs.push_back(ArgSpec(arg, false));
+ }
+ }
+ return specs;
+}
+
+ArgParserException::ArgParserException(const string& what, bool fullUsage)
+ : runtime_error(what), fullUsage_(fullUsage) {
+}
+
+bool ArgParserException::ShowFullUsage() const {
+ return fullUsage_;
+}
+
diff --git a/src/util/ArgParser.h b/src/util/ArgParser.h
new file mode 100644
index 0000000..81157de
--- /dev/null
+++ b/src/util/ArgParser.h
@@ -0,0 +1,47 @@
+#ifndef ARGPARSER_H
+#define ARGPARSER_H
+
+#include <map>
+#include <stdexcept>
+#include <string>
+#include <vector>
+
+class ArgParser {
+ public:
+ ArgParser();
+ ~ArgParser();
+
+ void Parse(int argc, char** argv, const std::vector<std::string>& args);
+ const std::map< std::string, std::vector<std::string> >& GetArgs() const;
+ const std::map<std::string, std::string>& GetOptions() const;
+ const std::string GetArg(const std::string& name) const;
+ const std::vector<std::string> GetArgMulti(const std::string& name) const;
+ const std::string GetOption(const std::string& name) const;
+
+ protected:
+ class ArgSpec {
+ public:
+ explicit ArgSpec(const std::string& name, bool multi = false);
+ std::string GetName() const;
+ bool IsMulti() const;
+ protected:
+ std::string name_;
+ bool multi_;
+ };
+
+ static std::vector<ArgSpec> ArgStringsToArgSpecs(const std::vector<std::string>& args);
+
+ std::map< std::string, std::vector<std::string> > args_;
+ std::map<std::string, std::string> options_;
+};
+
+class ArgParserException : public std::runtime_error {
+ public:
+ explicit ArgParserException(const std::string& what, bool fullUsage = false);
+ bool ShowFullUsage() const;
+ private:
+ bool fullUsage_;
+};
+
+#endif
+
diff --git a/src/util/CacheableMass.cpp b/src/util/CacheableMass.cpp
new file mode 100644
index 0000000..b9efa8b
--- /dev/null
+++ b/src/util/CacheableMass.cpp
@@ -0,0 +1,85 @@
+/*************************************************************************//**
+ * \file CacheableMass.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 28 Oct 2016
+ * \brief abstract object to Store the calculated mass of an instantied object
+ ****************************************************************************/
+
+#include "CacheableMass.h"
+#include "io/carp.h"
+
+/**
+ * Initialized the object
+ */
+void CacheableMass::init() {
+ for (size_t idx=0;idx < NUMBER_MASS_TYPES;idx++) {
+ mass_calculated_[idx] = false;
+ }
+}
+
+/**
+ * Constructor
+ */
+CacheableMass::CacheableMass() {
+ init();
+}
+
+/**
+ * Destructor
+ */
+CacheableMass::~CacheableMass() {
+}
+
+/*
+ * If the mass is already calculated for this mass type, return it
+ * Otherwise call calcMass to set it and return the result.
+ */
+FLOAT_T CacheableMass::getMass(
+ MASS_TYPE_T mass_type ///< Mass type
+ ) {
+
+ if (!mass_calculated_[mass_type]) {
+ //carp(CARP_DEBUG, "Calculating mass");
+ mass_[mass_type] = calcMass(mass_type);
+ mass_calculated_[mass_type] = true;
+ }
+
+ return mass_[mass_type];
+
+}
+
+FLOAT_T CacheableMass::getMassConst(
+ MASS_TYPE_T mass_type
+ ) const {
+
+ if (!mass_calculated_[mass_type]) {
+ carp(CARP_FATAL, "Internal Error: mass not calculated yet! %d", mass_type);
+ }
+ return (mass_[mass_type]);
+}
+
+/*
+ * Copies the calculated mass arrray
+ */
+void CacheableMass::copy(
+ CacheableMass* src,
+ CacheableMass* dest
+ ) {
+
+ for (size_t idx=0;idx < NUMBER_MASS_TYPES;idx++) {
+ if (src->mass_calculated_[idx]) {
+ dest->mass_calculated_[idx] = true;
+ dest->mass_[idx] = src->mass_[idx];
+ } else {
+ dest->mass_calculated_[idx] = false;
+ }
+ }
+
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/util/CacheableMass.h b/src/util/CacheableMass.h
new file mode 100644
index 0000000..53ebc74
--- /dev/null
+++ b/src/util/CacheableMass.h
@@ -0,0 +1,68 @@
+/**
+ * \file CacheableMass.h
+ * \brief abstract object to Store the calculated mass of an instantied object
+ */
+
+/*
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: Oct. 28, 2016
+ * $Revision: 1.00 $
+ *****************************************************************************/
+#ifndef CACHEABLEMASS_H_
+#define CACHEABLEMASS_H_
+
+#include "model/objects.h"
+
+class CacheableMass {
+
+ protected:
+ bool mass_calculated_[NUMBER_MASS_TYPES]; ///< is mass calculated?
+ FLOAT_T mass_[NUMBER_MASS_TYPES]; ///< calculated mass
+
+ public:
+ /*
+ * Initializes the object
+ */
+ void init();
+
+ CacheableMass();
+
+ virtual ~CacheableMass();
+
+ /*
+ * Override this method to return the calculated mass of the object
+ */
+ virtual FLOAT_T calcMass(
+ MASS_TYPE_T mass_type
+ )=0;
+
+
+ /*
+ * If the mass is already calculated for this mass type, return it
+ * Otherwise call calcMass to set it and return the result.
+ */
+ FLOAT_T getMass(
+ MASS_TYPE_T mass_type = MONO ///< Type of mass to return
+ );
+
+ FLOAT_T getMassConst(
+ MASS_TYPE_T mass_type = MONO ///< Type of mass to return
+ ) const;
+
+ /*
+ * Copies the calculated mass arrray
+ */
+ static void copy(
+ CacheableMass* src, ///< Source
+ CacheableMass* dest ///< Dest
+ );
+
+};
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+#endif
diff --git a/src/util/CarpStreamBuf.cpp b/src/util/CarpStreamBuf.cpp
new file mode 100644
index 0000000..b3edacc
--- /dev/null
+++ b/src/util/CarpStreamBuf.cpp
@@ -0,0 +1,101 @@
+/**
+ * \file CarpStreamBuf.cpp
+ * AUTHOR: Sean McIlwain
+ * CREATE DATE: 10/30/2012
+ * $Revision: 1.00 $
+ * \brief streambuffer that routes c++ stream to the carp logging system
+ *************************************************************************/
+#include "CarpStreamBuf.h"
+#include "io/carp.h"
+#include <iostream>
+#include <sstream>
+
+using namespace std;
+
+/**
+ * Handles data being put into the stream. Fills up the buffer_ string
+ * until an endline is encountered, then passes the buffer to carp.
+ */
+int CarpStreamBuf::overflow(
+ int over_char ///< character to put into the stream
+) {
+
+ if (over_char == EOF) {
+ return EOF;
+ } else {
+
+ buffer_.push_back((char)over_char);
+
+ if (buffer_.find(endl_str_) != string::npos) {
+ buffer_.erase(buffer_.length()-endl_str_.length(), endl_str_.length());
+ carp(CARP_INFO, "%s", buffer_.c_str());
+ buffer_.clear();
+ }
+ return over_char;
+ }
+}
+
+/**
+ * Not used, just returns EOF
+ */
+int CarpStreamBuf::underflow() {
+
+ return EOF;
+}
+
+/**
+ * Not used, just returns EOF
+ */
+int CarpStreamBuf::uflow() {
+
+ return EOF;
+}
+
+/**
+ * Not used, just returns EOF
+ */
+int CarpStreamBuf::pbackfail(
+ int c
+ ) {
+
+ return EOF;
+}
+
+/**
+ * Not used, just returns EOF
+ */
+int CarpStreamBuf::sync() {
+
+ return 0;
+}
+
+/**
+ * Constructor
+ */
+CarpStreamBuf::CarpStreamBuf() : streambuf() {
+
+ //An attempt to make endline detection cross-platform.
+ ostringstream oss;
+ oss << endl;
+ endl_str_ = oss.str();
+}
+
+/**
+ * Destructor
+ */
+CarpStreamBuf::~CarpStreamBuf() {
+
+ //If there is any buffer left, then just print it out.
+ if (buffer_.length() != 0) {
+ carp(CARP_INFO, "%s", buffer_.c_str());
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
+
diff --git a/src/util/CarpStreamBuf.h b/src/util/CarpStreamBuf.h
new file mode 100644
index 0000000..d889e43
--- /dev/null
+++ b/src/util/CarpStreamBuf.h
@@ -0,0 +1,72 @@
+/**
+ * \file CarpStreamBuf.h
+ * $Revision: 1.00 $
+ * \brief streambuffer that routes c++ stream to the carp logging system
+ *************************************************************************/
+#ifndef CARPSTREAMBUF_H_
+#define CARPSTREAMBUF_H_
+
+#include <iostream>
+#include <cstdio>
+#include <string>
+
+class CarpStreamBuf : public std::streambuf {
+ private:
+ std::string endl_str_; ///< Definition of endline
+ std::string buffer_; ///< buffer of characters put into the stream
+
+ protected:
+ /*
+ * Overrides for std::streambuf
+ */
+
+ /**
+ * Handles data being put into the stream. Fills up the buffer_ string
+ * until an endline is encountered, then passes the buffer to carp.
+ */
+ virtual int overflow(
+ int over_char = EOF ///< character to put into the stream
+ );
+
+ /**
+ * Not used, just returns EOF
+ */
+ virtual int underflow();
+
+ /**
+ * Not used, just returns EOF
+ */
+ virtual int uflow();
+
+ /**
+ * Not used, just returns EOF
+ */
+ virtual int pbackfail(
+ int pback_char = EOF ///< character to popback
+ );
+
+ /**
+ * Not used, just returns EOF
+ */
+ virtual int sync();
+
+ public:
+ /**
+ * Constructor
+ */
+ CarpStreamBuf();
+
+
+ virtual ~CarpStreamBuf();
+};
+
+
+#endif
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/util/FileUtils.cpp b/src/util/FileUtils.cpp
new file mode 100644
index 0000000..cc05a3d
--- /dev/null
+++ b/src/util/FileUtils.cpp
@@ -0,0 +1,86 @@
+#include "FileUtils.h"
+#include "boost/filesystem.hpp"
+#include <fstream>
+#include <stdexcept>
+
+using namespace std;
+
+bool FileUtils::Exists(const string& path) {
+ return boost::filesystem::exists(path);
+}
+
+bool FileUtils::IsRegularFile(const string& path) {
+ return boost::filesystem::is_regular_file(path);
+}
+
+bool FileUtils::IsDir(const string& path) {
+ return boost::filesystem::is_directory(path);
+}
+
+void FileUtils::Rename(const string& from, const string& to) {
+ if (Exists(from)) {
+ boost::filesystem::rename(from, to);
+ }
+}
+
+void FileUtils::Remove(const string& path) {
+ if (Exists(path)) {
+ boost::filesystem::remove_all(path);
+ }
+}
+
+string FileUtils::Join(const string& path1, const string& path2) {
+ return (boost::filesystem::path(path1) / boost::filesystem::path(path2)).string();
+}
+
+string FileUtils::Read(const string& path) {
+ try {
+ ifstream stream(path.c_str());
+ stream.seekg(0, ios::end);
+ size_t size = stream.tellg();
+ string buffer(size, '\0');
+ stream.seekg(0);
+ stream.read(&buffer[0], size);
+ return buffer;
+ } catch (...) {
+ throw runtime_error("Error reading file '" + path + "'");
+ }
+}
+
+ofstream* FileUtils::GetWriteStream(const string& path, bool overwrite) {
+ if (Exists(path) && !overwrite) {
+ return NULL;
+ }
+ ofstream* stream = new ofstream(path.c_str());
+ if (!stream->good()) {
+ delete stream;
+ return NULL;
+ }
+ return stream;
+}
+
+string FileUtils::BaseName(const string& path) {
+ boost::filesystem::path p(path);
+ return p.has_filename() ? p.filename().string() : "";
+}
+
+string FileUtils::DirName(const string& path) {
+ boost::filesystem::path p(path);
+ return p.has_parent_path() ? p.parent_path().string() : "";
+}
+
+string FileUtils::Stem(const string& path) {
+ boost::filesystem::path p(path);
+ return p.has_stem() ? p.stem().string() : "";
+}
+
+string FileUtils::Extension(const string& path) {
+ boost::filesystem::path p(path);
+ return p.has_extension() ? p.extension().string() : "";
+}
+void FileUtils::Copy(const std::string& orig, const std::string& dest) {
+ if (Exists(orig)) {
+ boost::filesystem::copy(orig, dest);
+ }
+}
+
diff --git a/src/util/FileUtils.h b/src/util/FileUtils.h
new file mode 100644
index 0000000..b4b3eef
--- /dev/null
+++ b/src/util/FileUtils.h
@@ -0,0 +1,28 @@
+#ifndef FILEUTILS_H
+#define FILEUTILS_H
+
+#include <fstream>
+#include <string>
+
+class FileUtils {
+ public:
+ static bool Exists(const std::string& path);
+ static bool IsRegularFile(const std::string& path);
+ static bool IsDir(const std::string& path);
+ static void Rename(const std::string& from, const std::string& to);
+ static void Remove(const std::string& path);
+ static std::string Join(const std::string& path1, const std::string& path2);
+ static std::string Read(const std::string& path);
+ static std::ofstream* GetWriteStream(const std::string& path, bool overwrite);
+ static std::string BaseName(const std::string& path);
+ static std::string DirName(const std::string& path);
+ static std::string Stem(const std::string& path);
+ static std::string Extension(const std::string& path);
+ static void Copy(const std::string& orig, const std::string& dest);
+ private:
+ FileUtils();
+ ~FileUtils();
+};
+
+#endif
+
diff --git a/src/util/GlobalParams.cpp b/src/util/GlobalParams.cpp
new file mode 100644
index 0000000..3ce89ca
--- /dev/null
+++ b/src/util/GlobalParams.cpp
@@ -0,0 +1,197 @@
+#include "GlobalParams.h"
+#include "util/Params.h"
+#include "parameter.h"
+#include "util/StringUtils.h"
+
+using namespace std;
+
+
+MASS_TYPE_T GlobalParams::isotopic_mass_;
+int GlobalParams::missed_cleavages_;
+int GlobalParams::max_aas_modified_;
+FLOAT_T GlobalParams::min_mass_;
+FLOAT_T GlobalParams::max_mass_;
+WINDOW_TYPE_T GlobalParams::precursor_window_type_;
+FLOAT_T GlobalParams::precursor_window_;
+int GlobalParams::min_length_;
+int GlobalParams::max_length_;
+string GlobalParams::xlink_prevents_cleavage_;
+string GlobalParams::max_ion_charge_;
+ION_TYPE_T GlobalParams::primary_ions_;
+MASS_TYPE_T GlobalParams::fragment_mass_;
+bool GlobalParams::precursor_ions_;
+ENZYME_T GlobalParams::enzyme_;
+DIGEST_T GlobalParams::digestion_;
+FLOAT_T GlobalParams::remove_precursor_tolerance_;
+OBSERVED_PREPROCESS_STEP_T GlobalParams::stop_after_;
+bool GlobalParams::xlink_include_inter_;
+bool GlobalParams::xlink_include_intra_;
+bool GlobalParams::xlink_include_inter_intra_;
+bool GlobalParams::xlink_include_deadends_;
+bool GlobalParams::xlink_include_linears_;
+bool GlobalParams::xlink_include_selfloops_;
+int GlobalParams::max_xlink_mods_;
+int GlobalParams::mod_precision_;
+int GlobalParams::xlink_top_n_;
+vector<int> GlobalParams::isotope_windows_;
+FLOAT_T GlobalParams::fraction_to_fit_;
+bool GlobalParams::xlink_use_ion_cache_;
+MASS_FORMAT_T GlobalParams::mod_mass_format_;
+
+void GlobalParams::set() {
+ isotopic_mass_ = get_mass_type_parameter("isotopic-mass");
+ missed_cleavages_ = Params::GetInt("missed-cleavages");
+ max_aas_modified_ = Params::GetInt("max-aas-modified");
+ min_mass_ = Params::GetDouble("min-mass");
+ max_mass_ = Params::GetDouble("max-mass");
+ precursor_window_type_ = string_to_window_type(Params::GetString("precursor-window-type"));
+ precursor_window_ = Params::GetDouble("precursor-window");
+ min_length_ = Params::GetInt("min-length");
+ max_length_ = Params::GetInt("max-length");
+ xlink_prevents_cleavage_ = Params::GetString("xlink-prevents-cleavage");
+ max_ion_charge_ = Params::GetString("max-ion-charge");
+ string_to_ion_type(Params::GetString("primary-ions"), &primary_ions_);
+ fragment_mass_ = get_mass_type_parameter("fragment-mass");
+ precursor_ions_ = Params::GetBool("precursor-ions");
+ enzyme_ = get_enzyme_type_parameter("enzyme");
+ digestion_ = get_digest_type_parameter("digestion");
+ remove_precursor_tolerance_ = Params::GetDouble("remove-precursor-tolerance");
+ stop_after_ = string_to_observed_preprocess_step(Params::GetString("stop-after"));
+ xlink_include_inter_ = Params::GetBool("xlink-include-inter");
+ xlink_include_intra_ = Params::GetBool("xlink-include-intra");
+ xlink_include_inter_intra_ = Params::GetBool("xlink-include-inter-intra");
+ xlink_include_deadends_ = Params::GetBool("xlink-include-deadends");
+ xlink_include_selfloops_ = Params::GetBool("xlink-include-selfloops");
+ xlink_include_linears_ = Params::GetBool("xlink-include-linears");
+ max_xlink_mods_ = Params::GetInt("max-xlink-mods");
+ mod_precision_ = Params::GetInt("mod-precision");
+ xlink_top_n_ = Params::GetInt("xlink-top-n");
+ isotope_windows_ = StringUtils::Split<int>(Params::GetString("isotope-windows"), ',');
+ fraction_to_fit_ = Params::GetDouble("fraction-top-scores-to-fit");
+ xlink_use_ion_cache_ = Params::GetBool("xlink-use-ion-cache");
+ mod_mass_format_ = get_mass_format_type_parameter("mod-mass-format");
+}
+
+const MASS_TYPE_T& GlobalParams::getIsotopicMass() {
+ return isotopic_mass_;
+}
+
+const int& GlobalParams::getMissedCleavages() {
+ return missed_cleavages_;
+}
+
+const int& GlobalParams::getMaxAasModified() {
+ return max_aas_modified_;
+}
+
+const FLOAT_T& GlobalParams::getMinMass() {
+ return min_mass_;
+}
+
+const FLOAT_T& GlobalParams::getMaxMass() {
+ return max_mass_;
+}
+
+const WINDOW_TYPE_T& GlobalParams::getPrecursorWindowType() {
+ return precursor_window_type_;
+}
+
+const FLOAT_T& GlobalParams::getPrecursorWindow() {
+ return precursor_window_;
+}
+
+const int& GlobalParams::getMinLength() {
+ return min_length_;
+}
+
+const int& GlobalParams::getMaxLength() {
+ return max_length_;
+}
+
+const string& GlobalParams::getXLinkPreventsCleavage() {
+ return xlink_prevents_cleavage_;
+}
+
+const string& GlobalParams::getMaxIonCharge() {
+ return max_ion_charge_;
+}
+
+const ION_TYPE_T& GlobalParams::getPrimaryIons() {
+ return primary_ions_;
+}
+
+const MASS_TYPE_T& GlobalParams::getFragmentMass() {
+ return fragment_mass_;
+}
+
+const bool& GlobalParams::getPrecursorIons() {
+ return precursor_ions_;
+}
+
+const ENZYME_T& GlobalParams::getEnzyme() {
+ return enzyme_;
+}
+
+const DIGEST_T& GlobalParams::getDigestion() {
+ return digestion_;
+}
+
+const FLOAT_T& GlobalParams::getRemovePrecursorTolerance() {
+ return remove_precursor_tolerance_;
+}
+
+const OBSERVED_PREPROCESS_STEP_T& GlobalParams::getStopAfter() {
+ return stop_after_;
+}
+
+const bool& GlobalParams::getXLinkIncludeInter() {
+ return xlink_include_inter_;
+}
+
+const bool& GlobalParams::getXLinkIncludeIntra() {
+ return xlink_include_intra_;
+}
+
+const bool& GlobalParams::getXLinkIncludeInterIntra() {
+ return xlink_include_inter_intra_;
+}
+
+const bool& GlobalParams::getXLinkIncludeDeadends() {
+ return xlink_include_deadends_;
+}
+
+const bool& GlobalParams::getXLinkIncludeSelfloops() {
+ return xlink_include_selfloops_;
+}
+
+const bool& GlobalParams::getXLinkIncludeLinears() {
+ return xlink_include_linears_;
+}
+const int& GlobalParams::getMaxXLinkMods() {
+ return max_xlink_mods_;
+}
+
+const int& GlobalParams::getModPrecision() {
+ return mod_precision_;
+}
+
+const int& GlobalParams::getXLinkTopN() {
+ return xlink_top_n_;
+}
+
+const vector<int>& GlobalParams::getIsotopeWindows() {
+ return isotope_windows_;
+}
+
+const FLOAT_T& GlobalParams::getFractionToFit() {
+ return fraction_to_fit_;
+}
+
+const bool& GlobalParams::getXLinkUseIonCache() {
+ return xlink_use_ion_cache_;
+}
+
+const MASS_FORMAT_T& GlobalParams::getModMassFormat() {
+ return mod_mass_format_;
+}
+
diff --git a/src/util/GlobalParams.h b/src/util/GlobalParams.h
new file mode 100644
index 0000000..cd41f51
--- /dev/null
+++ b/src/util/GlobalParams.h
@@ -0,0 +1,97 @@
+/**
+ * \file GlobalParams.h
+ * $Revision: 1.00 $
+ * $Author: sjoemac $
+ * \brief Object for fast loading of parameters
+ */
+#ifndef GLOBAL_PARAMS_H
+#define GLOBAL_PARAMS_H
+
+
+
+#include "model/objects.h"
+#include <string>
+#include <vector>
+
+
+class GlobalParams {
+
+ protected:
+ static MASS_TYPE_T isotopic_mass_;
+ static int missed_cleavages_;
+ static int max_aas_modified_;
+ static FLOAT_T min_mass_;
+ static FLOAT_T max_mass_;
+ static WINDOW_TYPE_T precursor_window_type_;
+ static FLOAT_T precursor_window_;
+ static int min_length_;
+ static int max_length_;
+ static std::string xlink_prevents_cleavage_;
+ static std::string max_ion_charge_;
+ static ION_TYPE_T primary_ions_;
+ static MASS_TYPE_T fragment_mass_;
+ static bool precursor_ions_;
+ static ENZYME_T enzyme_;
+ static DIGEST_T digestion_;
+ static FLOAT_T remove_precursor_tolerance_;
+ static OBSERVED_PREPROCESS_STEP_T stop_after_;
+ static bool xlink_include_inter_;
+ static bool xlink_include_intra_;
+ static bool xlink_include_inter_intra_;
+ static bool xlink_include_deadends_;
+ static bool xlink_include_selfloops_;
+ static bool xlink_include_linears_;
+ static int max_xlink_mods_;
+ static int mod_precision_;
+ static int xlink_top_n_;
+ static std::vector<int> isotope_windows_;
+ static FLOAT_T fraction_to_fit_;
+ static bool xlink_use_ion_cache_;
+ static MASS_FORMAT_T mod_mass_format_;
+
+ public:
+ /**
+ * Set all of the parameters using the Params::Get calls
+ */
+ static void set();
+
+ /**
+ * The following function calls returns the value of the parameter using a saved variable
+ * These call are much faster than using the Params::Get calls
+ */
+ static const MASS_TYPE_T& getIsotopicMass();
+ static const int& getMissedCleavages();
+ static const int& getMaxAasModified();
+ static const FLOAT_T& getMinMass();
+ static const FLOAT_T& getMaxMass();
+ static const WINDOW_TYPE_T& getPrecursorWindowType();
+ static const FLOAT_T& getPrecursorWindow();
+ static const int& getMinLength();
+ static const int& getMaxLength();
+ static const std::string& getXLinkPreventsCleavage();
+ static const std::string& getMaxIonCharge();
+ static const ION_TYPE_T& getPrimaryIons();
+ static const MASS_TYPE_T& getFragmentMass();
+ static const bool& getPrecursorIons();
+ static const ENZYME_T& getEnzyme();
+ static const DIGEST_T& getDigestion();
+ static const FLOAT_T& getRemovePrecursorTolerance();
+ static const OBSERVED_PREPROCESS_STEP_T& getStopAfter();
+ static const bool& getXLinkIncludeInter();
+ static const bool& getXLinkIncludeIntra();
+ static const bool& getXLinkIncludeInterIntra();
+ static const bool& getXLinkIncludeDeadends();
+ static const bool& getXLinkIncludeSelfloops();
+ static const bool& getXLinkIncludeLinears();
+ static const int& getMaxXLinkMods();
+ static const int& getModPrecision();
+ static const int& getXLinkTopN();
+ static const std::vector<int>& getIsotopeWindows();
+ static const FLOAT_T& getFractionToFit();
+ static const bool& getXLinkUseIonCache();
+ static const MASS_FORMAT_T& getModMassFormat();
+};
+
+#endif
+
+
diff --git a/src/util/MathUtil.cpp b/src/util/MathUtil.cpp
new file mode 100644
index 0000000..def3474
--- /dev/null
+++ b/src/util/MathUtil.cpp
@@ -0,0 +1,20 @@
+#include "MathUtil.h"
+
+#include <cmath>
+
+using namespace std;
+
+double MathUtil::Round(double x, int decimals) {
+ double shift = pow(10.0, decimals);
+ return (x >= 0)
+ ? floor(x * shift + 0.5) / shift
+ : ceil(x * shift - 0.5) / shift;
+}
+
+bool MathUtil::AlmostEqual(double x, double y, int precision) {
+ return abs(x - y) < 5*pow(10.0, -(precision + 1));
+}
+
+MathUtil::MathUtil() {}
+MathUtil::~MathUtil() {}
+
diff --git a/src/util/MathUtil.h b/src/util/MathUtil.h
new file mode 100644
index 0000000..c549973
--- /dev/null
+++ b/src/util/MathUtil.h
@@ -0,0 +1,15 @@
+#ifndef MATHUTIL_H
+#define MATHUTIL_H
+
+class MathUtil {
+ public:
+ static double Round(double x, int decimals = 0);
+ static bool AlmostEqual(double x, double y, int precision);
+
+ private:
+ MathUtil();
+ ~MathUtil();
+};
+
+#endif
+
diff --git a/src/util/Params.cpp b/src/util/Params.cpp
new file mode 100644
index 0000000..b554b0c
--- /dev/null
+++ b/src/util/Params.cpp
@@ -0,0 +1,2849 @@
+#include "AminoAcidUtil.h"
+#include "crux_version.h"
+#include "mass.h"
+#include "model/Peptide.h"
+#include "model/objects.h"
+#include "parameter.h"
+#include "Params.h"
+#include "StringUtils.h"
+
+#include <algorithm>
+
+using namespace std;
+
+/**
+ * \file Params.cpp
+ *
+ * This module handles user-level parameters in Crux. Required
+ * arguments are given on the command line; optional parameters can be
+ * specified either on the command line or in a parameter file.
+ * Textual descriptions of each parameter are stored in the source
+ * code, and these are used to automatically generate usage
+ * statements, comments in output parameter files, and HTML
+ * documentation.
+ *
+ * Following are the steps required to add a new argument or parameter
+ * to an existing command:
+ *
+ * - In Params.cpp, inside the constructor Params::Params(), add a
+ * call to Init{Bool,Int,String,Double,Arg}Param. This will specify
+ * things like the parameter name, type, default value, what
+ * commands it works with, and whether it is visible to the end
+ * user.
+ *
+ * - If your parameter is optional, then in Params::Categorize(), add
+ * an "items.insert()" with the name of your new parameter. This
+ * controls what category the parameter gets printed in when the
+ * HTML documentation is created. Note that if the parameter
+ * doesn't get added to a category in Params::Categorize(), it just
+ * appears under a generic category called "<command name> options"
+ *
+ * - In the .cpp file that contains the main() for the command that
+ * uses this parameter, find a call to either getArgs() (if your new
+ * parameter is required) or getOptions() (if it is optional), and
+ * add the name of your new parameter to the list of options there.
+
+ * - In the same file, add a call to
+ * Params::get{Bool,Int,String,Double}() to retrieve the value
+ * associated with the parameter. In general, these methods can be
+ * used anywhere in the source code in order to retrieve parameters.
+ * However, it's good form, when feasible, to access parameters in
+ * the main() and then to pass them as arguments, rather than
+ * accessing them as globals within subroutines.
+ *
+ * - If you need to edit the textual description of the command
+ * itself, search in the same file for a call to getDescription().
+ * Portions of that description enclosed in "[[nohtml: XXX ]]" will
+ * be used for the usage statement, and portions in "[[html: XXX ]]"
+ * will be in the HTML docs.
+ *
+ */
+
+static Params paramContainer_;
+
+Params::Params() : finalized_(false) {
+ /* generate_peptide arguments */
+ InitArgParam("protein fasta file",
+ "The name of the file in FASTA format from which to retrieve proteins.");
+ InitArgParam("index name",
+ "The desired name of the binary index.");
+ InitArgParam("ms2 file",
+ "File containing spectra to be searched.");
+ /* psm-convert arguments */
+ InitArgParam("input PSM file",
+ "The name of a PSM file in tab-delimited text, SQT, pepXML or mzIdentML format");
+ InitArgParam("output format",
+ "The desired format of the output file. Legal values are tsv, html, sqt, pin, "
+ "pepxml, mzidentml.");
+ /* get-ms2-spectrum */
+ InitArgParam("scan number",
+ "Scan number identifying the spectrum.");
+ InitArgParam("output file",
+ "File where spectrum will be written.");
+ /* predict-peptide-ions */
+ InitArgParam("peptide sequence",
+ "The peptide sequence.");
+ InitArgParam("charge state",
+ "The charge state of the peptide.");
+ /* hardklor arguments */
+ InitArgParam("spectra",
+ "The name of a file from which to parse high-resolution spectra. The file "
+ "may be in MS1 (.ms1), binary MS1 (.bms1), compressed MS1 (.cms1), or mzXML "
+ "(.mzXML) format.");
+ /*Percolator arguments*/
+ InitArgParam("peptide-spectrum matches",
+ "A collection of target and decoy peptide-spectrum matches (PSMs). Input may "
+ "be in one of five formats: PIN, SQT, pepXML, [[html:<a href=\"../file-formats/txt-format.html\">]]"
+ "Crux tab-delimited text[[html:</a>]], or a list of files (when list-of-files=T). "
+ "Note that if the input is provided as SQT, pepXML, or Crux "
+ "tab-delimited text, then a PIN file will be generated in the output directory "
+ "prior to execution."
+ "Crux determines the format of the input file by examining its "
+ "filename extension. "
+ "[[html:<br>Decoy PSMs can be provided to Percolator in two "
+ "ways: either as a separate file or embedded within the same file as the target "
+ "PSMs. Percolator will first search for target PSMs in a separate file. The "
+ "decoy file name is constructed from the target name by replacing \"target\" with "
+ "\"decoy\". For example, if search.target.txt is provided as input, then "
+ "Percolator will search for a corresponding file named search.decoy.txt. If no "
+ "decoy file is found, then Percolator will assume that the given input file "
+ "contains a mix of target and decoy PSMs. Within this file, decoys are identified "
+ "using a prefix (specified via --decoy-prefix) on the protein name.]]");
+ /*make-pin arguments*/
+ InitArgParam("psm results",
+ "A collection of target and decoy peptide-spectrum matches (PSMs). Input may be in "
+ "one of four formats: SQT, PepXML (obtained from SEQUEST), [[html:<a href=\""
+ "../file-formats/txt-format.html\">]]Crux tab-delimited text[[html:</a>]], or list of files (when "
+ "list-of-files=T)."
+ "[[html:<br>Decoy PSMs can be provided to make-pin in two ways: either as a separate "
+ "file or embedded within the same file as the target PSMs. make-pin will first search "
+ "for the target PSMs in a separate file. The decoy file name is constructed from the "
+ "target name by replacing \"target\" with \"decoy\". For example, if search.target.txt "
+ "is provided as input, then make-pin will search for a corresponding file named "
+ "search.decoy.txt. If no decoy file is found, then make-pin will assume that the "
+ "given input file contains a mix of target and decoy PSMs. Within this file, decoys "
+ "are identified using a prefix (specified via --decoy-prefix) on the protein name.]]");
+ InitStringParam("decoy input", "",
+ "make-pin can convert any file format in sqt, tab-delimited and pep.xml file "
+ "to pin file ",
+ "Argument, not option for make-pin", false);
+ InitStringParam("output-file", "",
+ "Path where pin file will be written instead of make-pin.pin.",
+ "It is optional for make-pin", true);
+ InitBoolParam("filestem-prefixes", false,
+ "Prefix PSM IDs with filestems instead of target or decoy and file index.",
+ "Available for make-pin", false);
+ InitBoolParam("mod-symbols", false,
+ "Print modification symbols instead of masses in peptide sequences.",
+ "Available for make-pin", false);
+ // q-ranker/barista arguments
+ InitArgParam("fragmentation spectra",
+ "The fragmentation spectra must be provided in [[html:<a href=\"../file-formats/ms2-format.html\">]]"
+ "MS2[[html:</a>]], mzXML, or MGF format.");
+ // pipeline arguments
+ InitArgParam("mass spectra",
+ "The name of the file(s) from which to parse the fragmentation spectra, in any of the "
+ "[[html:<a href=\"http://proteowizard.sourceforge.net/tools.shtml\">]]file formats "
+ "supported by ProteoWizard[[html:</a>]]. Alteratively, with Tide-search, these files "
+ "may be binary spectrum files produced by a previous run of [[html:<code>]]crux "
+ "tide-search[[html:</code>]] using the [[html:<code>]]store-spectra[[html:</code>]] "
+ "parameter.");
+ InitArgParam("peptide source",
+ "Either the name of a file in fasta format from which to retrieve proteins and "
+ "peptides or an index created by a previous run of [[html:<code>]]crux tide-index"
+ "[[html:</code>]] (for Tide searching).");
+ /* *** Initialize Options (command line and param file) *** */
+
+ /* options for all executables */
+ InitIntParam("verbosity", 30, 0, 100,
+ "Specify the verbosity of the current processes. Each level prints the following "
+ "messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-"
+ "fatal errors, 20-warnings, 30-information on the progress of execution, 40-more "
+ "progress information, 50-debug info, 60-detailed debug info.",
+ "Available for all crux programs.", true);
+ InitStringParam("parameter-file", "",
+ "A file containing parameters. [[html: See the "
+ "<a href=\"../file-formats/parameter-file.html\">parameter documentation</a> page for details.]]",
+ "Available for all crux programs. Any options specified on the "
+ "command line will override values in the parameter file.", true);
+ InitBoolParam("overwrite", false,
+ "Replace existing files if true or fail when trying to overwrite a file if false.",
+ "Available for all crux programs. Applies to parameter file "
+ "as well as index, search, and analysis output files.", true);
+ /* generate_peptide parameters */
+ InitIntParam("min-length", 6, 1, MAX_PEPTIDE_LENGTH,
+ "The minimum length of peptides to consider.",
+ "Used from the command line or parameter file by "
+ "crux-generate-peptides, and crux tide-index.", true);
+ InitIntParam("max-length", 50, 1, MAX_PEPTIDE_LENGTH,
+ "The maximum length of peptides to consider.",
+ "Available from command line or parameter file for "
+ "crux-generate-peptides, crux tide-index. ", true);
+ InitDoubleParam("min-mass", 200, 0, BILLION,
+ "The minimum mass (in Da) of peptides to consider.",
+ "Available from command line or parameter file for "
+ "crux-generate-peptides and crux tide-index. ", true);
+ InitDoubleParam("max-mass", 7200, 1, BILLION,
+ "The maximum mass (in Da) of peptides to consider.",
+ "Available from command line or parameter file for "
+ "crux-generate-peptides and crux tide-index. ", true);
+ InitIntParam("min-peaks", 20, 0, BILLION,
+ "The minimum number of peaks a spectrum must have for it to be searched.",
+ "Available for tide-search.", true);
+ InitStringParam("enzyme", "trypsin", "no-enzyme|trypsin|trypsin/p|chymotrypsin|"
+ "elastase|clostripain|cyanogen-bromide|iodosobenzoate|proline-endopeptidase|"
+ "staph-protease|asp-n|lys-c|lys-n|arg-c|glu-c|pepsin-a|"
+ "elastase-trypsin-chymotrypsin|custom-enzyme",
+ "Specify the enzyme used to digest the proteins in silico. Available enzymes "
+ "(with the corresponding digestion rules indicated in parentheses) include "
+ "no-enzyme ([X]|[X]), trypsin ([RK]|{P}), trypsin/p ([RK]|[]), chymotrypsin "
+ "([FWYL]|{P}), elastase ([ALIV]|{P}), clostripain ([R]|[]), cyanogen-bromide "
+ "([M]|[]), iodosobenzoate ([W]|[]), proline-endopeptidase ([P]|[]), staph-protease "
+ "([E]|[]), asp-n ([]|[D]), lys-c ([K]|{P}), lys-n ([]|[K]), arg-c ([R]|{P}), "
+ "glu-c ([DE]|{P}), pepsin-a ([FL]|{P}), elastase-trypsin-chymotrypsin "
+ "([ALIVKRWFY]|{P}). Specifying --enzyme no-enzyme yields a non-enzymatic digest. "
+ "[[html:<strong>]]Warning:[[html:</strong>]] the resulting index may be quite large.",
+ "Available for crux-generate-peptides and crux tide-index.", true);
+ InitStringParam("custom-enzyme", "",
+ "Specify rules for in silico digestion of protein sequences. Overrides the enzyme "
+ "option. Two lists of residues are given enclosed in square brackets or curly "
+ "braces and separated by a |. The first list contains residues required/prohibited "
+ "before the cleavage site and the second list is residues after the cleavage site. "
+ "If the residues are required for digestion, they are in square brackets, '[' and "
+ "']'. If the residues prevent digestion, then they are enclosed in curly braces, "
+ "'{' and '}'. Use X to indicate all residues. For example, trypsin cuts after R or "
+ "K but not before P which is represented as [RK]|{P}. AspN cuts after any residue "
+ "but only before D which is represented as [X]|[D].",
+ "", true);
+ InitStringParam("digestion", "full-digest",
+ "full-digest|partial-digest|non-specific-digest",
+ "Specify whether every peptide in the database must have two enzymatic termini "
+ "(full-digest) or if peptides with only one enzymatic terminus are also included "
+ "(partial-digest).",
+ "Available for crux-generate-peptides and crux tide-index.", true);
+ InitIntParam("missed-cleavages", 0, 0, 500,
+ "Maximum number of missed cleavages per peptide to allow in enzymatic digestion.",
+ "Available from command line or parameter file for crux-generate-peptides. "
+ "When used with enzyme=<trypsin|elastase|chymotrypsin> "
+ "includes peptides containing one or more potential cleavage sites.", true);
+ InitDoubleParam("precursor-window", 3.0, 0, 100,
+ "Tolerance used for matching peptides to spectra. Peptides must be within +/- "
+ "'precursor-window' of the spectrum value. The precursor window units depend upon "
+ "precursor-window-type.",
+ "Available for tide-search and crux-generate-peptides.", true);
+ InitStringParam("precursor-window-type", "mass", "mass|mz|ppm",
+ "Specify the units for the window that is used to select peptides around the precursor "
+ "mass location (mass, mz, ppm). The magnitude of the window is defined by the precursor-"
+ "window option, and candidate peptides must fall within this window. For the mass window-"
+ "type, the spectrum precursor m+h value is converted to mass, and the window is defined "
+ "as that mass +/- precursor-window. If the m+h value is not available, then the mass is "
+ "calculated from the precursor m/z and provided charge. The peptide mass is computed as "
+ "the sum of the average amino acid masses plus 18 Da for the terminal OH group. The mz "
+ "window-type calculates the window as spectrum precursor m/z +/- precursor-window and "
+ "then converts the resulting m/z range to the peptide mass range using the precursor "
+ "charge. For the parts-per-million (ppm) window-type, the spectrum mass is calculated as "
+ "in the mass type. The lower bound of the mass window is then defined as the spectrum "
+ "mass / (1.0 + (precursor-window / 1000000)) and the upper bound is defined as spectrum "
+ "mass / (1.0 - (precursor-window / 1000000)).",
+ "Available for search-for-xlinks and tide-search.", true);
+ InitStringParam("auto-precursor-window", "false", "false|warn|fail",
+ "Automatically estimate optimal value for the precursor-window parameter "
+ "from the spectra themselves. false=no estimation, warn=try to estimate "
+ "but use the default value in case of failure, fail=try to estimate and "
+ "quit in case of failure.",
+ "Available for tide-search.", true);
+ InitStringParam("spectrum-parser", "pwiz", "pwiz|mstoolkit",
+ "Specify the parser to use for reading in MS/MS spectra.[[html: The default, "
+ "ProteoWizard parser can read the MS/MS file formats listed <a href=\""
+ "http://proteowizard.sourceforge.net/formats.shtml\">here</a>. The alternative is "
+ "<a href=\"../mstoolkit.html\">MSToolkit parser</a>. "
+ "If the ProteoWizard parser fails to read your files properly, you may want to try the "
+ "MSToolkit parser instead.]]",
+ "Available for search-for-xlinks.", true);
+ InitBoolParam("use-z-line", true,
+ "Specify whether, when parsing an MS2 spectrum file, Crux obtains the "
+ "precursor mass information from the \"S\" line or the \"Z\" line. ",
+ "Available when spectrum-parser = pwiz.", true);
+ InitStringParam("keep-terminal-aminos", "NC", "N|C|NC|none",
+ "When creating decoy peptides using decoy-format=shuffle or decoy-format="
+ "peptide-reverse, this option specifies whether the N-terminal and "
+ "C-terminal amino acids are kept in place or allowed to be shuffled or "
+ "reversed. For a target peptide \"EAMPK\" with decoy-format=peptide-reverse, setting "
+ "keep-terminal-aminos to \"NC\" will yield \"EPMAK\"; setting it to \"C\" will yield "
+ "\"PMAEK\"; setting it to \"N\" will yield \"EKPMA\"; and setting it to \"none\" will "
+ "yield \"KPMAE\".",
+ "Available for tide-index.", true);
+ InitBoolParam("peptide-list", false,
+ "Create in the output directory a text file listing of all the peptides in the "
+ "database, along with their neutral masses, one per line. If decoys are generated, "
+ "then a second file will be created containing the decoy peptides. Decoys that also "
+ "appear in the target database are marked with an asterisk in a third column.",
+ "Available for tide-index.", true);
+ // print-processed-spectra option
+ InitStringParam("stop-after", "xcorr", "remove-precursor|square-root|"
+ "remove-grass|ten-bin|xcorr",
+ "Stop after the specified pre-processing step.",
+ "Available for print-processed-spectra.", true);
+ InitStringParam("output-units", "bin", "mz|bin",
+ "Specify the output units for processed spectra.",
+ "Available for print-processed-spectra", true);
+ /* more generate_peptide parameters */
+ InitBoolParam("sqt-output", false,
+ "Outputs an SQT results file to the output directory. Note that if sqt-output is "
+ "enabled, then compute-sp is automatically enabled and cannot be overridden.",
+ "Available for tide-search.", true);
+ InitBoolParam("mzid-output", false,
+ "Output an mzIdentML results file to the output directory.",
+ "Available for tide-search, percolator.", true);
+ InitBoolParam("pin-output", false,
+ "Output a Percolator input (PIN) file to the output directory.",
+ "Available for tide-search.", true);
+ InitBoolParam("pout-output", false,
+ "Output a Percolator [[html:<a href=\""
+ "https://github.com/percolator/percolator/blob/master/src/xml/percolator_out.xsd\">]]"
+ "pout.xml[[html:</a>]] format results file to the output directory.",
+ "Available for percolator.", true);
+ InitBoolParam("pepxml-output", false,
+ "Output a pepXML results file to the output directory.",
+ "Available for tide-search, q-ranker, barista, percolator.", true);
+ InitBoolParam("txt-output", true,
+ "Output a tab-delimited results file to the output directory.",
+ "Available for tide-search, percolator, q-ranker, barista.", true);
+ InitStringParam("prelim-score-type", "sp", "sp|xcorr",
+ "Initial scoring (sp, xcorr).",
+ "The score applied to all possible psms for a given spectrum. Typically "
+ "used to filter out the most plausible for further scoring.", false);
+ InitStringParam("score-type", "xcorr", "xcorr|sp|xcorr-pvalue|sp-pvalue",
+ "The primary scoring method to use (xcorr, sp, xcorr-pvalue, sp-pvalue).",
+ "Primary scoring is typically done on a subset (see max-rank-preliminary) of all "
+ "possible psms for each spectrum. Default is the SEQUEST-style xcorr. "
+ "Crux also offers a p-value calculation for each psm based on xcorr "
+ "or sp (xcorr-pvalue, sp-pvalue).", false);
+ InitBoolParam("compute-sp", false,
+ "Compute the preliminary score Sp for all candidate peptides. Report this score in the "
+ "output, along with the corresponding rank, the number of matched ions and the total "
+ "number of ions. This option is recommended if results are to be analyzed by Percolator "
+ "or Barista. If sqt-output is enabled, then compute-sp is automatically enabled and "
+ "cannot be overridden. Note that the Sp computation requires re-processing each "
+ "observed spectrum, so turning on this switch involves significant computational overhead.",
+ "Available for tide-search.", true);
+ InitBoolParam("compute-p-values", false,
+ "Estimate the parameters of the score distribution for each spectrum by fitting to a "
+ "Weibull distribution, and compute a p-value for each xlink product. This option is "
+ "only available when use-old-xlink=F.",
+ "Currently only implemented for XCORR.", true);
+ InitStringParam("scan-number", "",
+ "A single scan number or a range of numbers to be searched. Range should be "
+ "specified as 'first-last' which will include scans 'first' and 'last'.",
+ "The search range x-y is inclusive of x and y.", true);
+ /* N.B. Use NaN to indicate that no user preference was specified.
+ * In this case, the default value depends on the mass type.
+ * S.M. Also prevent a width of 0. */
+ InitDoubleParam("mz-bin-width", 1.0005079, 1e-4, BILLION,
+ "Before calculation of the XCorr score, the m/z axes of the observed and theoretical "
+ "spectra are discretized. This parameter specifies the size of each bin. The exact "
+ "formula for computing the discretized m/z value is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z "
+ "value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms "
+ "0.02 is recommended.",
+ "Available for tide-search and xlink-assign-ions.", true);
+ InitDoubleParam("mz-bin-offset", 0.40, 0.0, 1.0,
+ "In the discretization of the m/z axes of the observed and theoretical spectra, this "
+ "parameter specifies the location of the left edge of the first bin, relative to "
+ "mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be "
+ "located at +0.xx Da).",
+ "Available for tide-search.", true);
+ InitStringParam("auto-mz-bin-width", "false", "false|warn|fail",
+ "Automatically estimate optimal value for the mz-bin-width parameter "
+ "from the spectra themselves. false=no estimation, warn=try to estimate "
+ "but use the default value in case of failure, fail=try to estimate and "
+ "quit in case of failure.",
+ "Available for tide-search.", true);
+ InitBoolParam("use-flanking-peaks", false,
+ "Include flanking peaks around singly charged b and y theoretical ions. Each flanking "
+ "peak occurs in the adjacent m/z bin and has half the intensity of the primary peak.",
+ "Available for the tide-search and search-for-xlinks commands.", true);
+ InitDoubleParam("spectrum-min-mz", 0.0, 0, BILLION,
+ "The lowest spectrum m/z to search in the ms2 file.",
+ "Available for tide-search.", true);
+ InitDoubleParam("spectrum-max-mz", BILLION, 1, BILLION,
+ "The highest spectrum m/z to search in the ms2 file.",
+ "Available for tide-search.", true);
+ InitStringParam("spectrum-charge", "all", "1|2|3|all",
+ "The spectrum charges to search. With 'all' every spectrum will be searched and "
+ "spectra with multiple charge states will be searched once at each charge state. "
+ "With 1, 2, or 3 only spectra with that charge state will be searched.",
+ "Used by tide-search.", true);
+ InitStringParam("fileroot", "",
+ "The fileroot string will be added as a prefix to all output file names.",
+ "Available for all commands that produce an output directory.", true);
+ InitStringParam("output-dir", "crux-output",
+ "The name of the directory where output files will be created.",
+ "Available for most commands.", true);
+ InitStringParam("temp-dir", "",
+ "The name of the directory where temporary files will be created. If this "
+ "parameter is blank, then the system temporary directory will be used",
+ "Available for tide-index.", true);
+ // coder options regarding decoys
+ InitIntParam("num-decoy-files", 1, 0, 10,
+ "Replaces number-decoy-set. Determined by decoy-location"
+ " and num-decoys-per-target",
+ "", false);
+ InitBoolParam("decoy-p-values", false,
+ "Store all decoy p-values in a file",
+ "", false);
+ InitIntParam("top-match", 5, 1, BILLION,
+ "Specify the number of matches to report for each spectrum.",
+ "Available for tide-search and crux percolator", true);
+ InitStringParam("seed", "1",
+ "When given a unsigned integer value seeds the random number generator with that value. "
+ "When given the string \"time\" seeds the random number generator with the system time.",
+ "Available for all Crux commands.", true);
+ InitStringParam("fragment-mass", "mono", "average|mono",
+ "Specify which isotopes to use in calculating fragment ion mass.",
+ "Used by crux-predict-peptide-ions.", true);
+ InitStringParam("isotopic-mass", "mono", "average|mono",
+ "Specify the type of isotopic masses to use when calculating the peptide mass.",
+ "Used from command line or parameter file by crux-generate-peptides.", true);
+ InitStringParam("mod", "NO MODS",
+ "Consider modifications on any amino acid in aa list with at most max-per-peptide in one "
+ "peptide. The parameter takes the form "
+ "[[html:<mass change>:<aa list>:<max per peptide>:<prevents cleavage>:"
+ "<prevents cross-link>]]"
+ "[[nohtml:<mass change>:<aa list>:<max per peptide>:<prevents cleavage>:<prevents cross-link>]]"
+ ". This parameter may be included with different values multiple times so long as "
+ "the total number of mod, cmod, and nmod parameters does not exceed 11. The \"prevents "
+ "cleavage\" and \"prevents cross-link\" arguments are optional T/F arguments for describing whether the "
+ "modification prevents enzymatic cleavage of cross-linking, respectively. This option is "
+ "only available when use-old-xlink=F. "
+ "Note that this parameter only takes effect when specified in the "
+ "parameter file.",
+ "Available for search-for-xlinks.", true);
+ InitStringParam("cmod", "NO MODS",
+ "Specify a variable modification to apply to C-terminus of peptides. "
+ "<mass change>:<max distance from protein c-term (-1 for no max)>. "
+ "Note that this parameter only takes effect when specified in the "
+ "parameter file.",
+ "Available for search-for-xlinks.", true);
+ InitStringParam("nmod", "NO MODS",
+ "Specify a variable modification to apply to N-terminus of peptides. "
+ "<mass change>:<max distance from protein n-term (-1 for no max)> "
+ "Note that this parameter only takes effect when specified in the "
+ "parameter file.",
+ "Available for search-for-xlinks.", true);
+ InitIntParam("min-mods", 0, 0, MAX_PEPTIDE_LENGTH,
+ "The minimum number of modifications that can be applied to a single "
+ "peptide.",
+ "Available for tide-index.", true);
+ InitIntParam("max-mods", MAX_PEPTIDE_LENGTH, 0, MAX_PEPTIDE_LENGTH,
+ "The maximum number of modifications that can be applied to a single "
+ "peptide.",
+ "Available for tide-index.", true);
+ InitIntParam("max-aas-modified", MAX_PEPTIDE_LENGTH, 0, MAX_PEPTIDE_LENGTH,
+ "The maximum number of modified amino acids that can appear in one "
+ "peptide. Each aa can be modified multiple times.",
+ "", true);
+ InitStringParam("mod-mass-format", "mod-only", "mod-only|total|separate",
+ "Specify how sequence modifications are reported in various output files. Each "
+ "modification is reported as a number enclosed in square braces following the "
+ "modified residue; however, the number may correspond to one of three different "
+ "masses: (1) 'mod-only' reports the value of the mass shift induced by the "
+ "modification; (2) 'total' reports the mass of the residue with the modification "
+ "(residue mass plus modification mass); (3) 'separate' is the same as 'mod-only', "
+ "but multiple modifications to a single amino acid are reported as a "
+ "comma-separated list of values. For example, suppose amino acid D has an "
+ "unmodified mass of 115 as well as two moifications of masses +14 and +2. In this "
+ "case, the amino acid would be reported as D[16] with 'mod-only', D[131] with 'total', "
+ "and D[14,2] with 'separate'.",
+ "Available for generate-peptides.", true);
+ InitIntParam("mod-precision", 2, 0, 20,//arbitrary
+ "Set the precision for modifications as written to .txt files.",
+ "Also changes mods written to parameter file. Set internally based on "
+ "the max mod precision in the param file.",
+ false);
+
+ InitBoolParam("use-a-ions", false,
+ "Consider a-ions in the search? Note that an a-ion is equivalent to a "
+ "neutral loss of CO from the b-ion. "
+ "Peak height is 10 (in arbitrary units).",
+ "Available for search-for-xlinks and xlink-score-spectrum.", true);
+ InitBoolParam("use-b-ions", true,
+ "Consider b-ions in the search? Peak height is 50 (in arbitrary units).",
+ "Available for search-for-xlinks and xlink-score-spectrum.", true);
+ InitBoolParam("use-c-ions", false,
+ "Consider c-ions in the search? Peak height is 50 (in arbitrary units).",
+ "Available for search-for-xlinks and xlink-score-spectrum.", true);
+ InitBoolParam("use-x-ions", false,
+ "Consider x-ions in the search? Peak height is 10 (in arbitrary units).",
+ "Available for search-for-xlinks and xlink-score-spectrum.", true);
+ InitBoolParam("use-y-ions", true,
+ "Consider y-ions in the search? Peak height is 50 (in arbitrary units).",
+ "Available for search-for-xlinks and xlink-score-spectrum.", true);
+ InitBoolParam("use-z-ions", false,
+ "Consider z-ions in the search? Peak height is 50 (in arbitrary units).",
+ "Available for search-for-xlinks and xlink-score-spectrum.", true);
+
+ InitIntParam("precision", 8, 1, 100, //max is arbitrary
+ "Set the precision for scores written to sqt and text files.",
+ "Available for all commands.", true);
+ InitIntParam("mass-precision", 4, 1, 100, // max is arbitrary
+ "Set the precision for masses and m/z written to sqt and .txt files. "
+ "Note that this parameter only takes effect when specified in the "
+ "parameter file.",
+ "Available for all commands.", true);
+ InitIntParam("print-search-progress", 1000, 0, BILLION,
+ "Show search progress by printing every n spectra searched. Set to 0 to show no "
+ "search progress.",
+ "Available for tide-search", true);
+ // Sp scoring params
+ InitDoubleParam("max-mz", 4000, 0, BILLION,
+ "Used in scoring sp.",
+ "Hide from users", false);
+ InitDoubleParam("fraction-top-scores-to-fit", 0.55, 0, 1,
+ "The fraction of psms per spectrum to use for estimating the "
+ "score distribution for calculating p-values. "
+ "Not compatible with 'number-top-scores-to-fig'.",
+ "For developers/research only.", false);
+ /* analyze-matches options */
+ InitStringParam("algorithm", "percolator", "percolator|curve-fit|none",
+ "The analysis algorithm to use (percolator, curve-fit, none).",
+ "Available only for crux-analyze-matches. Using 'percolator' will "
+ "assign a q-value to the top-ranking psm for each spectrum based on "
+ "the decoy searches. Using 'curve-fit' will assign a q-value to same "
+ "using the p-values calculated with score-type=<xcorr-pvalue|"
+ "sq-pvalue>. Incorrect combinations of score-type and algorithm cause"
+ " undefined behavior. Using 'none' will turn the binary .csm files "
+ "into text.", false);
+ // **** percolator options. ****
+ InitStringParam("search-input", "auto", "auto|separate|concatenated",
+ "Specify the type of target-decoy search. Using 'auto', percolator attempts "
+ "to detect the search type automatically. Using 'separate' specifies two searches: "
+ "one against target and one against decoy protein db. Using 'concatenated' "
+ "specifies a single search on concatenated target-decoy protein db.",
+ "Available for percolator", true);
+ InitStringParam("percolator-seed", "1",
+ "When given a unsigned integer value seeds the random number generator with that value. "
+ "When given the string \"time\" seeds the random number generator with the system time.",
+ "Available for all percolator", true);
+ InitBoolParam("feature-file-out", false,
+ "Output the computed features in [[html:<a href=\"../file-formats/features.html\">]]tab-delimited "
+ "text format[[html:</a>]].",
+ "Available for percolator and q-ranker.", true);
+ InitBoolParam("decoy-xml-output", false,
+ "Include decoys (PSMs, peptides, and/or proteins) in the XML output.",
+ "Available for crux percolator", true);
+ InitStringParam("decoy-prefix", "decoy_",
+ "Specifies the prefix of the protein names that indicate a decoy.",
+ "Available for percolator", true);
+ InitBoolParam("output-weights", false,
+ "Output final weights to a file named \"percolator.weights.txt\".",
+ "Available for crux percolator", true);
+ InitStringParam("init-weights", "",
+ "Read initial weights from the given file (one per line).",
+ "Available for crux percolator", true);
+ InitIntParam("subset-max-train", 0,
+ "Only train Percolator on a subset of PSMs, and use the resulting score "
+ "vector to evaluate the other PSMs. Recommended when analyzing huge numbers "
+ "(>1 million) of PSMs. When set to 0, all PSMs are used for training as "
+ "normal.",
+ "Available for crux percolator", true);
+ InitDoubleParam("c-pos", 0.00,
+ "Penalty for mistakes made on positive examples. If this value is set to 0, "
+ "then it is set via cross validation over the values {0.1, 1, 10}, selecting the "
+ "value that yields the largest number of PSMs identified at the q-value threshold "
+ "set via the --test-fdr parameter.",
+ "Available for crux percolator", true);
+ InitDoubleParam("c-neg", 0.0, 0.0, 0.90,
+ "Penalty for mistake made on negative examples. If not specified, then "
+ "this value is set by cross validation over {0.1, 1, 10}.",
+ "Available for crux percolator", true);
+ InitDoubleParam("train-fdr", 0.01, 0, BILLION,
+ "False discovery rate threshold to define positive examples in training.",
+ "Available for crux percolator", true);
+ InitDoubleParam("test-fdr", 0.01, 0.0, 1.0,
+ "False discovery rate threshold used in selecting hyperparameters during internal "
+ "cross-validation and for reporting the final results.",
+ "Available for crux percolator.", true);
+ InitDoubleParam("fido-fast-gridsearch", 0.0, 0.0, 1.0,
+ "Apply the specified threshold to PSM, peptide and protein probabilities to "
+ "obtain a faster estimate of the alpha, beta and gamma parameters.",
+ "Available for crux percolator.", true);
+ InitBoolParam("fido-no-split-large-components", false,
+ "Do not approximate the posterior distribution by allowing large graph "
+ "components to be split into subgraphs. The splitting is done by "
+ "duplicating peptides with low probabilities. Splitting continues "
+ "until the number of possible configurations of each subgraph is "
+ "below 2^18",
+ "Available for crux percolator", true);
+ InitDoubleParam("fido-protein-truncation-threshold", 0.01, 0.0, 1.0,
+ "To speed up inference, proteins for which none of the associated "
+ "peptides has a probability exceeding the specified threshold will "
+ "be assigned probability = 0.",
+ "Available for crux percolator", true);
+ InitBoolParam("tdc", true,
+ "Use target-decoy competition to assign q-values and PEPs. When set to F, "
+ "the mix-max method, which estimates the proportion pi0 of incorrect target "
+ "PSMs, is used instead.",
+ "Available for crux percolator", true);
+ InitIntParam("maxiter", 10, 0, 100000000,
+ "Maximum number of iterations for training.",
+ "Available for crux percolator", true);
+ InitBoolParam("quick-validation", false,
+ "Quicker execution by reduced internal cross-validation.",
+ "Available for crux percolator", true);
+ InitStringParam("default-direction", "",
+ "In its initial round of training, Percolator uses one feature to induce a ranking "
+ "of PSMs. By default, Percolator will select the feature that produces the largest "
+ "set of target PSMs at a specified FDR threshold (cf. --train-fdr). This option "
+ "allows the user to specify which feature is used for the initial ranking, using the "
+ "name as a string[[html: from <a href=\"../file-formats/features.html\">this table</a>]]. The name "
+ "can be preceded by a hyphen (e.g. \"-XCorr\") to indicate that a lower value is "
+ "better.",
+ "Available for crux percolator", true);
+ InitBoolParam("unitnorm", false,
+ "Use unit normalization (i.e., linearly rescale each PSM's feature vector to have a "
+ "Euclidean length of 1), instead of standard deviation normalization.",
+ "Available for crux percolator.", true);
+ InitBoolParam("test-each-iteration", false,
+ "Measure performance on test set each iteration.",
+ "Available for crux percolator.", true);
+ InitBoolParam("feature-file-in", false,
+ "When set to T, interpret the input file as a PIN file.",
+ "Available for crux percolator.", true);
+ InitStringParam("picked-protein", "",
+ "Use the picked protein-level FDR to infer protein probabilities, provide the "
+ "fasta file as the argument to this flag.",
+ "Available for crux percolator", true);
+ InitStringParam("protein-enzyme", "trypsin", "no_enzyme|elastase|pepsin|proteinasek|"
+ "thermolysin|trypsinp|chymotrypsin|lys-n|lys-c|arg-c|asp-n|glu-c|trypsin",
+ "Type of enzyme",
+ "Available for crux percolator", true);
+ InitBoolParam("protein-report-fragments", false,
+ "By default, if the peptides associated with protein A are a proper subset "
+ "of the peptides associated with protein B, then protein A is eliminated and "
+ "all the peptides are considered as evidence for protein B. Note that this "
+ "filtering is done based on the complete set of peptides in the database, not "
+ "based on the identified peptides in the search results. Alternatively, if this "
+ "option is set and if all of the identified peptides associated with protein B "
+ "are also associated with protein A, then Percolator will report a comma-"
+ "separated list of protein IDs, where the full-length protein B is first in the "
+ "list and the fragment protein A is listed second. Not available for Fido.",
+ "Available for crux percolator", true);
+ InitBoolParam("protein-report-duplicates", false,
+ "If multiple database proteins contain exactly the same set of peptides, then "
+ "Percolator will randomly discard all but one of the proteins. If this option "
+ "is set, then the IDs of these duplicated proteins will be reported as a comma-"
+ "separated list. Not available for Fido.",
+ "Available for crux percolator", true);
+ InitBoolParam("protein", false,
+ "Use the Fido algorithm to infer protein probabilities. Must be true to use any of the Fido options.",
+ "Available for crux percolator", true);
+ InitDoubleParam("fido-alpha", 0.0, 0.0, 1.0,
+ "Specify the probability with which a present protein emits an associated peptide. "
+ "Set by grid search (see --fido-gridsearch-depth parameter) if not specified.",
+ "Available for crux percolator if --protein T is set.", true);
+ InitDoubleParam("fido-beta", 0.0, 0.0, 10.0,
+ "Specify the probability of the creation of a peptide from noise. Set by grid "
+ "search (see --fido-gridsearch-depth parameter) if not specified.",
+ "Available for crux percolator if --protein T is set.", true);
+ InitDoubleParam("fido-gamma", 0.0, 0.0, 10.0,
+ "Specify the prior probability that a protein is present in the sample. Set by grid "
+ "search (see --fido-gridsearch-depth parameter) if not specified.",
+ "Available for crux percolator if --protein T is set.", true);
+ InitBoolParam("fido-empirical-protein-q", false,
+ "Estimate empirical p-values and q-values for proteins using target-decoy analysis.",
+ "Available for crux percolator if --protein T is set.", true);
+ InitIntParam("fido-gridsearch-depth", 0, 0, 2,
+ "Set depth of the grid search for alpha, beta and gamma estimation.[[html: The values "
+ "considered, for each possible value of the --fido-gridsearch-depth parameter, are as follows:<ul>"
+ "<li>0: alpha = {0.01, 0.04, 0.09, 0.16, 0.25, 0.36, 0.5}; beta = {0.0, 0.01, 0.15, "
+ "0.025, 0.035, 0.05, 0.1}; gamma = {0.1, 0.25, 0.5, 0.75}.</li><li>1: alpha = {0.01, "
+ "0.04, 0.09, 0.16, 0.25, 0.36}; beta = {0.0, 0.01, 0.15, 0.025, 0.035, 0.05}; gamma = "
+ "{0.1, 0.25, 0.5}.</li><li>2: alpha = {0.01, 0.04, 0.16, 0.25, 0.36}; beta = {0.0, "
+ "0.01, 0.15, 0.030, 0.05}; gamma = {0.1, 0.5}.</li><li>3: alpha = {0.01, 0.04, 0.16, "
+ "0.25, 0.36}; beta = {0.0, 0.01, 0.15, 0.030, 0.05}; gamma = {0.5}.</li></ul>]]",
+ "Available for crux percolator if --protein T is set.", true);
+ InitDoubleParam("fido-gridsearch-mse-threshold", 0.05, 0, 1,
+ "Q-value threshold that will be used in the computation of the MSE and ROC AUC "
+ "score in the grid search.",
+ "Available for crux percolator if --protein T is set.", true);
+ InitBoolParam("override", false,
+ "By default, Percolator will examine the learned weights for each feature, and if "
+ "the weight appears to be problematic, then percolator will discard the learned "
+ "weights and instead employ a previously trained, static score vector. This switch "
+ "allows this error checking to be overriden.",
+ "Available for crux percolator.", true);
+ InitBoolParam("klammer", false,
+ "Use retention time features calculated as in \"Improving tandem mass spectrum "
+ "identification using peptide retention time prediction across diverse chromatography "
+ "conditions\" by Klammer AA, Yi X, MacCoss MJ and Noble WS. ([[html:<em>]]Analytical "
+ "Chemistry[[html:</em>]]. 2007 Aug 15;79(16):6111-8.).",
+ "Available for crux percolator", true);
+ InitBoolParam("only-psms", false,
+ "Do not remove redundant peptides; keep all PSMs and exclude peptide level probability.",
+ "Available for crux percolator", true);
+ // **** Tide arguments ****
+ InitArgParam("spectrum records file",
+ "A spectrum records file generated by a previous run of crux tide-search "
+ "using the store-spectra parameter.");
+ InitArgParam("tide spectra file",
+ "The name of one or more files from which to parse the fragmentation spectra, in any "
+ "of the file formats supported by ProteoWizard. Alternatively, the argument "
+ "may be one or more binary spectrum files produced by a previous run of crux "
+ "tide-search using the store-spectra parameter.");
+ InitArgParam("tide database",
+ "Either a FASTA file or a directory containing a database index created by a previous "
+ "run of crux tide-index.");
+ // **** Tide options ****
+ InitStringParam("decoy-format", "shuffle", "none|shuffle|peptide-reverse|protein-reverse",
+ "Include a decoy version of every peptide by shuffling or reversing the "
+ "target sequence or protein. In shuffle or peptide-reverse mode, each peptide is "
+ "either reversed or shuffled, leaving the N-terminal and C-terminal amino acids in "
+ "place. Note that peptides appear multiple times in the target database are only "
+ "shuffled once. In peptide-reverse mode, palindromic peptides are shuffled. Also, if a "
+ "shuffled peptide produces an overlap with the target or decoy database, then the "
+ "peptide is re-shuffled up to 5 times. Note that, despite this repeated shuffling, "
+ "homopolymers will appear in both the target and decoy database. The protein-reverse "
+ "mode reverses the entire protein sequence, irrespective of the composite peptides.",
+ "Available for tide-index", true);
+ InitStringParam("mods-spec", "C+57.02146",
+ "[[nohtml:Expression for static and variable mass modifications to include. "
+ "Specify a comma-separated list of modification sequences of the form: "
+ "C+57.02146,2M+15.9949,1STY+79.966331,...]][[html:The general form of a modification "
+ "specification has three components, as exemplified by <span style=\"color: red;\">1"
+ "</span><span style=\"color: green;\">STY</span>+<span style=\"color: blue\">79.966331"
+ "</span>.<br>The three components are: [<span style=\"color: red;\">max_per_peptide"
+ "</span>]<span style=\"color: green;\">residues</span>[+/-]<span style-\"color: blue;\">"
+ "mass_change</span><br>In the example, <span style=\"color: red;\">max_per_peptide"
+ "</span> is <span style=\"color: red;\">1</span>, <span style=\"color: green;\">"
+ "residues</span> are <span style=\"color: green;\">STY</span>, and "
+ "<span style=\"color: blue;\">mass_change</span> is <span style=\"color: blue;\">"
+ "+79.966331</span>. To specify a static modification, the number preceding the amino "
+ "acid must be omitted; i.e., <span style=\"color: green;\">C</span>+<span "
+ "style=\"color: blue;\">57.02146</span> specifies a static modification of 57.02146 "
+ "Da to cysteine. Note that Tide allows at most one modification per amino "
+ "acid. Also, the default modification (C+57.02146) will be added to "
+ "every mods-spec string unless an explicit C+0 is included.]]",
+ "Available for tide-index", true);
+ InitStringParam("nterm-peptide-mods-spec", "",
+ "[[nohtml:Specifies N-terminal static and variable mass modifications on peptides. "
+ "Specify a comma-separated list of N-terminal modification sequences of the form: "
+ "1E-18.0106,C-17.0265]][[html:Specify peptide n-terminal modifications. Like "
+ "--mods-spec, this specification has three components, but with a slightly different "
+ "syntax. The <span style=\"color: red;\">max_per_peptide</span> can be either \"1\", "
+ "in which case it defines a variable terminal modification, or missing, in which case "
+ "the modification is static. The <span style=\"color: green;\">residues</span> field "
+ "indicates which amino acids are subject to the modification, with the reside <span "
+ "style=\"color: green;\">X</span> corresponding to any amino acid. Finally, <span "
+ "style=\"color: blue;\">added_mass</span> is defined as before.]]",
+ "Available for tide-index", true);
+ InitStringParam("cterm-peptide-mods-spec", "",
+ "[[nohtml:Specifies C-terminal static and variable mass modifications on peptides. "
+ "Specify a comma-separated list of C-terminal modification sequences of the form: "
+ "X+21.9819]][[html:Specify peptide c-terminal modifications. See "
+ "nterm-peptide-mods-spec for syntax.]]",
+ "Available for tide-index", true);
+ InitStringParam("cterm-protein-mods-spec", "",
+ "Specifies C-terminal static and variable mass modifications on proteins. "
+ "Specify a comma-separated list of C-terminal protein modification sequences of the form: "
+ ",...",
+ "Available for tide-index", false);
+ InitStringParam("nterm-protein-mods-spec", "",
+ "Specifies N-terminal static and variable mass modifications on proteins. "
+ "Specify a comma-separated list of N-terminal protein modification sequences of the form: "
+ ",...",
+ "Available for tide-index", false);
+ InitStringParam("store-spectra", "",
+ "Specify the name of the file where the binarized fragmentation spectra "
+ "will be stored. Subsequent runs of crux tide-search will execute more quickly if "
+ "provided with the spectra in binary format. The filename is specified relative to "
+ "the current working directory, not the Crux output directory (as specified by "
+ "--output-dir). This option is not valid if multiple input spectrum files are given.",
+ "Available for tide-search", true);
+ InitBoolParam("exact-p-value", false,
+ "Enable the calculation of exact p-values for the XCorr score[[html: as described in "
+ "<a href=\"http://www.ncbi.nlm.nih.gov/pubmed/24895379\">this article</a>]]. Calculation "
+ "of p-values increases the running time but increases the number of identifications at a "
+ "fixed confidence threshold. The p-values will be reported in a new column with header "
+ "\"exact p-value\", and the \"xcorr score\" column will be replaced with a \"refactored "
+ "xcorr\" column. Note that, currently, p-values can only be computed when the "
+ "mz-bin-width parameter is set to its default value. Variable and static mods are allowed "
+ "on non-terminal residues in conjunction with p-value computation, but currently only "
+ "static mods are allowed on the N-terminus, and no mods on the C-terminus.",
+ "Available for tide-search", true);
+ InitStringParam("store-index", "",
+ "When providing a FASTA file as the index, the generated binary index will be stored at "
+ "the given path. This option has no effect if a binary index is provided as the index.",
+ "Available for tide-search", true);
+ InitBoolParam("concat", false,
+ "When set to T, target and decoy search results are reported in a single file, and only "
+ "the top-scoring N matches (as specified via --top-match) are reported for each spectrum, "
+ "irrespective of whether the matches involve target or decoy peptides.",
+ "Available for tide-search", true);
+ InitBoolParam("file-column", true,
+ "Include the file column in tab-delimited output.",
+ "Available for tide-search", true);
+ // Same as remove_precursor_peak and remove_precursor tolerance in Comet
+ InitBoolParam("remove-precursor-peak", false,
+ "If true, all peaks around the precursor m/z will be removed, within a range "
+ "specified by the --remove-precursor-tolerance option.",
+ "Available for tide-search.", true);
+ InitDoubleParam("remove-precursor-tolerance", 1.5, 0, BILLION,
+ "This parameter specifies the tolerance (in Th) around each precursor m/z that is "
+ "removed when the --remove-precursor-peak option is invoked.",
+ "Available for print-processed spectra and tide-search.", true);
+ InitBoolParam("clip-nterm-methionine", false,
+ "When set to T, for each protein that begins with methionine, tide-index will "
+ "put two copies of the leading peptide into the index, with and without the N-terminal "
+ "methionine.",
+ "Available for tide-index.", true);
+ InitBoolParam("allow-dups", false,
+ "Prevent duplicate peptides between the target and decoy databases. When set to \"F\", "
+ "the program keeps all target and previously generated decoy peptides in memory. A shuffled "
+ "decoy will be re-shuffled multiple times to avoid duplication. If a non-duplicated peptide "
+ "cannot be generated, the decoy is skipped entirely. When set to \"T\", every decoy is added to "
+ "the database without checking for duplication. This option reduces the memory requirements "
+ "significantly.",
+ "Available for tide-index.", true);
+ InitBoolParam("use-neutral-loss-peaks", true,
+ "Controls whether neutral loss ions are considered in the search. "
+ "Two types of neutral losses are included and are applied only to "
+ "singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) "
+ "and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of "
+ "the primary peak.",
+ "Available for tide-search.", true);
+ InitIntParam("max-precursor-charge", 5, 1, BILLION,
+ "The maximum charge state of a spectra to consider in search.",
+ "Available for tide-search.", true);
+ InitBoolParam("peptide-centric-search", false,
+ "Carries out a peptide-centric search. For each peptide the top-scoring spectra "
+ "are reported, in contrast to the standard spectrum-centric search where the top-"
+ "scoring peptides are reported. Note that in this case the \"xcorr rank\" column "
+ "will contain the rank of the given spectrum with respect to the given candidate "
+ "peptide, rather than vice versa (which is the default).",
+ "Available for tide-search.", true);
+ InitIntParam("elution-window-size", 0, 0, 10,
+ "Size of the elution window used in smoothing score in DIA mode. "
+ "Used only with peptide-centric-search if greater than 0. A score of a psms "
+ "centred in the window is substituted by the geometric mean of the scores "
+ "in the window. If windows size is even, then it is increased by 1.",
+ "Available for tide-search.", false);
+ InitBoolParam("skip-decoys", true,
+ "Skips decoys when reading a Tide index.",
+ "Available for read-tide-index", false);
+ InitBoolParam("skip-preprocessing", false,
+ "Skip preprocessing steps on spectra. Default = F.",
+ "Available for tide-search", true);
+ InitStringParam("isotope-error", "",
+ "List of positive, non-zero integers.",
+ "Isotope errors to include. "
+ "Specify a comma-separated list of isotope errors of the form: "
+ "1,2,3,..."
+ "Available for tide-search", true);
+ InitIntParam("num-threads", 0, 0, 64,
+ "0=poll CPU to set num threads; else specify num threads directly.",
+ "Available for tide-search tab-delimited files only.", true);
+ /*
+ * Comet parameters
+ */
+ InitArgParam("input spectra",
+ "The name of the file from which to parse the spectra. Valid formats include mzXML, "
+ "mzML, mz5, raw, ms2, and cms2. Files in mzML or mzXML may be compressed with gzip. "
+ "RAW files can be parsed only under windows and if the appropriate libraries were "
+ "included at compile time.");
+ /* Comet - Database */
+ InitArgParam("database_name",
+ "A full or relative path to the sequence database, "
+ "in FASTA format, to search. Example databases include "
+ "RefSeq or UniProt. The database can contain amino acid "
+ "sequences or nucleic acid sequences. If sequences are "
+ "amino acid sequences, set the parameter \"nucleotide_reading_frame = 0\". "
+ "If the sequences are nucleic acid sequences, you must instruct Comet to "
+ "translate these to amino acid sequences. Do this by setting "
+ "nucleotide_reading_frame\" to a value between 1 and 9.");
+ InitIntParam("decoy_search", 0, 0, 2,
+ "0=no, 1=concatenated search, 2=separate search.",
+ "Available for comet.", true);
+ /* Comet - CPU threads */
+ InitIntParam("num_threads", 0, -64, 64,
+ "0=poll CPU to set num threads; else specify num threads directly.",
+ "Available for comet.", true);
+ /* Comet - Masses */
+ InitDoubleParam("peptide_mass_tolerance", 3.0, 0, BILLION,
+ "Controls the mass tolerance value. The mass tolerance "
+ "is set at +/- the specified number i.e. an entered value "
+ "of \"1.0\" applies a -1.0 to +1.0 tolerance. "
+ "The units of the mass tolerance is controlled by the parameter "
+ "\"peptide_mass_units\". ",
+ "Available for comet.", true);
+ InitIntParam("peptide_mass_units", 0, 0, 2,
+ "0=amu, 1=mmu, 2=ppm.",
+ "Available for comet.", true);
+ InitStringParam("auto_peptide_mass_tolerance", "false", "false|warn|fail",
+ "Automatically estimate optimal value for the peptide_mass_tolerancel parameter "
+ "from the spectra themselves. false=no estimation, warn=try to estimate "
+ "but use the default value in case of failure, fail=try to estimate and "
+ "quit in case of failure.",
+ "Available for comet.", true);
+ InitIntParam("mass_type_parent", 1, 0, 1,
+ "0=average masses, 1=monoisotopic masses.",
+ "Available for comet.", true);
+ InitIntParam("mass_type_fragment", 1, 0, 1,
+ "0=average masses, 1=monoisotopic masses.",
+ "Available for comet.", true);
+ InitIntParam("precursor_tolerance_type", 0, 0, 1,
+ "0=singly charged peptide mass, 1=precursor m/z.",
+ "Available for comet.", true);
+ InitIntParam("isotope_error", 0, 0, 2,
+ "0=off, 1=on -1/0/1/2/3 (standard C13 error), 2=-8/-4/0/4/8 (for +4/+8 labeling).",
+ "Available for comet.", true);
+ /* Comet - Search enzyme */
+ InitIntParam("search_enzyme_number", 1, 0, BILLION,
+ "Specify a search enzyme from the end of the parameter file.",
+ "Available for comet.", true);
+ InitIntParam("num_enzyme_termini", 2, 1, 9,
+ "valid values are 1 (semi-digested), 2 (fully digested), 8 N-term, 9 C-term.",
+ "Available for comet.", true);
+ InitIntParam("allowed_missed_cleavage", 2, 0, 5,
+ "Maximum value is 5; for enzyme search.",
+ "Available for comet.", true);
+ /* Comet - Fragment ions */
+ InitDoubleParam("fragment_bin_tol", 1.000507, 0, BILLION,
+ "Binning to use on fragment ions.",
+ "Available for comet.", true);
+ InitDoubleParam("fragment_bin_offset", 0.40, 0, 1.0,
+ "Offset position to start the binning (0.0 to 1.0).",
+ "Available for comet.", true);
+ InitStringParam("auto_fragment_bin_tol", "false", "false|warn|fail",
+ "Automatically estimate optimal value for the fragment_bin_tol parameter "
+ "from the spectra themselves. false=no estimation, warn=try to estimate "
+ "but use the default value in case of failure, fail=try to estimate and "
+ "quit in case of failure.",
+ "Available for comet.", true);
+ InitIntParam("theoretical_fragment_ions", 1, 0, 1,
+ "0=default peak shape, 1=M peak only.",
+ "Available for comet.", true);
+ InitIntParam("use_A_ions", 0, 0, 1,
+ "Controls whether or not A-ions are considered in the search (0 - no, 1 - yes).",
+ "Available for comet.", true);
+ InitIntParam("use_B_ions", 1, 0, 1,
+ "Controls whether or not B-ions are considered in the search (0 - no, 1 - yes).",
+ "Available for comet.", true);
+ InitIntParam("use_C_ions", 0, 0, 1,
+ "Controls whether or not C-ions are considered in the search (0 - no, 1 - yes).",
+ "Available for comet.", true);
+ InitIntParam("use_X_ions", 0, 0, 1,
+ "Controls whether or not X-ions are considered in the search (0 - no, 1 - yes).",
+ "Available for comet.", true);
+ InitIntParam("use_Y_ions", 1, 0, 1,
+ "Controls whether or not Y-ions are considered in the search (0 - no, 1 - yes).",
+ "Available for comet.", true);
+ InitIntParam("use_Z_ions", 0, 0, 1,
+ "Controls whether or not Z-ions are considered in the search (0 - no, 1 - yes).",
+ "Available for comet.", true);
+ InitIntParam("use_NL_ions", 1, 0, 1,
+ "0=no, 1= yes to consider NH3/H2O neutral loss peak.",
+ "Available for comet.", true);
+ /* Comet - Output */
+ InitIntParam("output_sqtfile", 0, 0, 1,
+ "0=no, 1=yes write sqt file.",
+ "Available for comet.", true);
+ InitIntParam("output_txtfile", 1, 0, 1,
+ "0=no, 1=yes write tab-delimited text file.",
+ "Available for comet.", true);
+ InitIntParam("output_pepxmlfile", 1, 0, 1,
+ "0=no, 1=yes write pep.xml file.",
+ "Available for comet.", true);
+ InitIntParam("output_percolatorfile", 0, 0, 1,
+ "0=no, 1=yes write percolator file.",
+ "Available for comet.", true);
+ InitIntParam("output_outfiles", 0, 0, 1,
+ "0=no, 1=yes write .out files.",
+ "Available for comet.", true);
+ InitIntParam("print_expect_score", 1, 0, 1,
+ "0=no, 1=yes to replace Sp with expect in out & sqt.",
+ "Available for comet.", true);
+ InitIntParam("num_output_lines", 5, 1, BILLION,
+ "num peptide results to show.",
+ "Available for comet.", true);
+ InitIntParam("show_fragment_ions", 0, 0, 1,
+ "0=no, 1=yes for out files only.",
+ "Available for comet.", true);
+ InitIntParam("sample_enzyme_number", 1, 0, 10,
+ "Sample enzyme which is possibly different than the one applied to the search. "
+ "Used to calculate NTT & NMC in pepXML output.",
+ "Available for comet. ", true);
+ /* Comet - mzXML/mzML parameters */
+ InitStringParam("scan_range", "0 0",
+ "Start and scan scan range to search; 0 as first entry ignores parameter.",
+ "Available for comet.", true);
+ InitStringParam("precursor_charge", "0 0",
+ "Precursor charge range to analyze; does not override "
+ "mzXML charge; 0 as first entry ignores parameter.",
+ "Available for comet.", true);
+ InitIntParam("override_charge", 0, 0, 3,
+ "Specifies the whether to override existing precursor charge state information when present "
+ "in the files with the charge range specified by the \"precursor_charge\" parameter.",
+ "Available for comet.", true);
+ InitIntParam("ms_level", 2, 2, 3,
+ "MS level to analyze, valid are levels 2 or 3.",
+ "Available for comet. ", true);
+ InitStringParam("activation_method", "ALL", "ALL|CID|ECD|ETD|PQD|HCD|IRMPD",
+ "Specifies which scan types are searched.",
+ "Available for comet. ", true);
+ /* Comet - Misc. parameters */
+ InitStringParam("digest_mass_range", "600.0 5000.0",
+ "MH+ peptide mass range to analyze.",
+ "Available for comet.", true);
+ InitIntParam("num_results", 50, 0, BILLION,
+ "Number of search hits to store internally.",
+ "Available for comet.", true);
+ InitIntParam("skip_researching", 1, 0, 1,
+ "For '.out' file output only, 0=search everything again, 1=don't search if .out exists.",
+ "Available for comet.", true);
+ InitIntParam("max_fragment_charge", 3, 1, 5,
+ "Set maximum fragment charge state to analyze (allowed max 5).",
+ "Available for comet.", true);
+ InitIntParam("max_precursor_charge", 6, 1, 9,
+ "Set maximum precursor charge state to analyze (allowed max 9).",
+ "Available for comet.", true);
+ InitIntParam("nucleotide_reading_frame", 0, 0, 9,
+ "0=proteinDB, 1-6, 7=forward three, 8=reverse three, 9=all six.",
+ "Available for comet.", true);
+ InitIntParam("clip_nterm_methionine", 0, 0, 1,
+ "0=leave sequences as-is; 1=also consider sequence w/o N-term methionine.",
+ "Available for comet.", true);
+ InitIntParam("spectrum_batch_size", 0, 0, BILLION,
+ "Maximum number of spectra to search at a time; 0 to search the entire scan range in one loop.",
+ "Available for comet.", true);
+ InitStringParam("decoy_prefix", "decoy_",
+ "Specifies the prefix of the protein names that indicates a decoy.",
+ "Available for comet.", true);
+ InitStringParam("output_suffix", "",
+ "Specifies the suffix string that is appended to the base output name "
+ "for the pep.xml, pin.xml, txt and sqt output files.",
+ "Available for comet.", true);
+ InitStringParam("mass_offsets", "",
+ "Specifies one or more mass offsets to apply. This value(s) are effectively "
+ "subtracted from each precursor mass such that peptides that are smaller "
+ "than the precursor mass by the offset value can still be matched to the "
+ "respective spectrum.",
+ "Available for comet.", true);
+ /* Comet - Spectral processing */
+ InitIntParam("minimum_peaks", 10, 1, BILLION,
+ "Minimum number of peaks in spectrum to search.",
+ "Available for comet.", true);
+ InitDoubleParam("minimum_intensity", 0, 0, BILLION,
+ "Minimum intensity value to read in.",
+ "Available for comet. ", true);
+ InitIntParam("remove_precursor_peak", 0, 0, 2,
+ "0=no, 1=yes, 2=all charge reduced precursor peaks (for ETD).",
+ "Available for comet. ", true);
+ InitDoubleParam("remove_precursor_tolerance", 1.5, -BILLION, BILLION,
+ "+- Da tolerance for precursor removal.",
+ "Available for comet. ", true);
+ InitStringParam("clear_mz_range", "0.0 0.0",
+ "For iTRAQ/TMT type data; will clear out all peaks in the specified m/z range.",
+ "Available for comet.", true);
+ /* Comet - Variable modifications */
+ for (int i = 1; i <= 9; i++) {
+ InitStringParam("variable_mod0" + StringUtils::ToString(i), "0.0 null 0 4 -1 0 0",
+ "Up to 9 variable modifications are supported; format: "
+ "\"<mass> <residues> <0=variable/1=binary> <max mods per a peptide>\" "
+ "e.g. 79.966331 STY 0 3.",
+ "Available for comet.", true);
+ }
+ InitIntParam("max_variable_mods_in_peptide", 5, 0, BILLION,
+ "Specifies the total/maximum number of residues that can be modified in a peptide.",
+ "Available for comet.", true);
+ InitIntParam("require_variable_mod", 0, 0, 1,
+ "Controls whether the analyzed peptides must contain at least one variable modification.",
+ "Available for comet.", true);
+ /* Comet - Static modifications */
+ InitDoubleParam("add_Cterm_peptide", 0, 0, BILLION,
+ "Specifiy a static modification to the c-terminus of all peptides.",
+ "Available for comet.", true);
+ InitDoubleParam("add_Nterm_peptide", 0, 0, BILLION,
+ "Specify a static modification to the n-terminus of all peptides.",
+ "Available for comet.", true);
+ InitDoubleParam("add_Cterm_protein", 0, 0, BILLION,
+ "Specify a static modification to the c-terminal peptide of each protein.",
+ "Available for comet.", true);
+ InitDoubleParam("add_Nterm_protein", 0, 0, BILLION,
+ "Specify a static modification to the n-terminal peptide of each protein.",
+ "Available for comet.", true);
+ for (char c = 'A'; c <= 'Z'; c++) {
+ string aaString = string(1, c);
+ string aaName = AminoAcidUtil::GetName(c);
+ aaName = aaName.empty() ? "user_amino_acid" : StringUtils::Replace(aaName, " ", "_");
+ InitDoubleParam("add_" + aaString + "_" + aaName,
+ c != 'C' ? 0 : CYSTEINE_DEFAULT, 0, BILLION,
+ "Specify a static modification to the residue " + aaString + ".",
+ "Available for comet.", true);
+ }
+ // **** q-ranker-barista arguments ****
+ InitArgParam("database",
+ "The program requires the FASTA format protein database files against "
+ "which the search was performed. The protein database input may be a "
+ "concatenated database or separate target and decoy databases; the "
+ "latter is supported with the --separate-searches option, described "
+ "below. In either case, Barista distinguishes between target and decoy "
+ "proteins based on the presence of a decoy prefix on the sequence "
+ "identifiers (see the --decoy-prefix option, below). The database can "
+ "be provided in three different ways: (1) as a a single FASTA file "
+ "with suffix \".fa\", \".fsa\" or \".fasta\", (2) as a text file "
+ "containing a list of FASTA files, one per line, or (3) as a directory "
+ "containing multiple FASTA files (identified via the filename suffixes "
+ "\".fa\", \".fsa\" or \".fasta\").");
+ InitArgParam("search results",
+ "Search results in the [[html:<a href=\"../file-formats/txt-format.html\">]]tab-delimited text format"
+ "[[html:</a>]] produced by Crux or in [[html:<a href=\"../file-formats/sqt-format.html\">]]SQT format[[html:</a>]]. "
+ "Like the spectra, the search results can be provided "
+ "as a single file, a list of files or a directory of files. Note, however, that the "
+ "input mode for spectra and for search results must be the same; i.e., if you provide "
+ "a list of files for the spectra, then you must also provide a list of files "
+ "containing your search results. When the MS2 files and tab-delimited text files are "
+ "provided via a file listing, it is assumed that the order of the MS2 files matches "
+ "the order of the tab-delimited files. Alternatively, when the MS2 files and "
+ "tab-delimited files are provided via directories, the program will search for pairs of "
+ "files with the same root name but different extensions (\".ms2\" and \".txt\").");
+ // **** q-ranker options. ****
+ InitBoolParam("skip-cleanup", false,
+ "Analysis begins with a pre-processsing step that creates a "
+ "set of lookup tables which are then used during training. Normally, "
+ "these lookup tables are deleted at the end of the analysis, "
+ "but setting this option to T prevents the deletion of these tables. "
+ "Subsequently, analyses can be repeated more efficiently "
+ "by specifying the --re-run option.",
+ "Available for q-ranker and barista.", true);
+ InitStringParam("re-run", "",
+ "Re-run a previous analysis using a previously computed set of "
+ "lookup tables. For this option to work, the --skip-cleanup option must have "
+ "been set to true when the program was run the first time.",
+ "Available for q-ranker and barista.", true);
+ InitBoolParam("use-spec-features", true,
+ "Use an enriched feature set, including separate features for each ion type.",
+ "Available for q-ranker and barista.", true);
+ InitStringParam("separate-searches", "",
+ "If the target and decoy searches were run separately, rather than "
+ "using a concatenated database, then the program will assume that the "
+ "database search results provided as a required argument are from the "
+ "target database search. This option then allows the user to specify "
+ "the location of the decoy search results. Like the required arguments, "
+ "these search results can be provided as a single file, a list of files "
+ "or a directory. However, the choice (file, list or directory) must be "
+ "consistent for the MS2 files and the target and decoy tab-delimited files. Also, "
+ "if the MS2 and tab-delimited files are provided in directories, then Q-ranker "
+ "will use the MS2 filename (foo.ms2) to identify corresponding target "
+ "and decoy tab-delimited files with names like foo*.target.txt and "
+ "foo*.decoy.txt. This naming convention allows the target and decoy txt "
+ "files to reside in the same directory.",
+ "Available for q-ranker and barista.", true);
+ //**** Barista and QRanker options. ******
+ InitBoolParam("list-of-files", false,
+ "Specify that the search results are provided as lists of files, rather than as "
+ "individual files.",
+ "Available for barista and percolator.", true);
+ InitStringParam("optimization", "protein", "protein|peptide|psm",
+ "Specifies whether to do optimization at the protein, peptide or psm level.",
+ "Available for barista.", true);
+ /* analyze-matches parameter options */
+ InitArgParam("target input",
+ "One or more files, each containing a collection of peptide-spectrum matches (PSMs) "
+ "in [[html:<a href=\"../file-formats/txt-format.html\">]]tab-delimited text[[html:</a>]], [[html:<a "
+ "href=\"http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML\">]]PepXML"
+ "[[html:</a>]], or [[html:<a href=\"http://www.psidev.info/mzidentml\">]]mzIdentML"
+ "[[html:</a>]] format. In tab-delimited text format, only the specified score column "
+ "is required. However if --estimation-method is tdc, then the columns \"scan\" and "
+ "\"charge\" are required, as well as \"protein ID\" if the search was run with "
+ "concat=F. Furthermore, if the --estimation-method is specified to peptide-level "
+ "is set to T, then the column "
+ "\"peptide\" must be included, and if --sidak is set to T, then the \"distinct "
+ "matches/spectrum\" column must be included.[[html:<br>Note that multiple files can "
+ "also be provided either on the command line or using the --list-of-files option.<br>"
+ "Decoys can be provided in two ways: either as a separate file or embedded within the "
+ "same file as the targets. Crux will first search the given file for decoys using a "
+ "prefix (specified via --decoy-prefix) on the protein name. If no decoys are found, "
+ "then Crux will search for decoys in a separate file. The decoy file name is constructed "
+ "from the target file name by replacing \"target\" with \"decoy\". For example, if "
+ "tide-search.target.txt is provided as input, then Crux will search for a corresponding "
+ "file named \"tide-search.decoy.txt.\"<br>Note that if decoys are provided in a separate "
+ "file, then assign-confidence will first carry out a target-decoy competition, "
+ "identifying corresponding pairs of targets and decoys and eliminating the one with "
+ "the worse score. In this case, the column/tag called \"delta_cn\" will be eliminated "
+ "from the output.]]");
+ InitDoubleParam("pi-zero", 1.0, 0, 1,
+ "The estimated percent of target scores that are drawn from the "
+ "null distribution.",
+ "Used by assign-confidence, percolator and q-ranker", false);
+ InitStringParam("estimation-method", "tdc", "mix-max|tdc|peptide-level",
+ "Specify the method used to estimate q-values. The mix-max procedure or target-decoy "
+ "competition apply to PSMs. The peptide-level option eliminates any PSM for which there "
+ "exists a better scoring PSM involving the same peptide, and then uses decoys to "
+ "assign confidence estimates.",
+ "Used by assign-confidence.", true);
+ InitBoolParam("sidak", false,
+ "Adjust the score using the Sidak adjustment and reports them in a new column in the "
+ "output file. Note that this adjustment only makes sense if the given scores are "
+ "p-values, and that it requires the presence of the \"distinct matches/spectrum\" "
+ "feature for each PSM.",
+ "Used by assign-confidence.", true);
+ InitStringParam("score", "",
+ "Specify the column (for tab-delimited input) or tag (for XML input) "
+ "used as input to the q-value estimation procedure. If this parameter is unspecified, "
+ "then the program searches for \"xcorr score\", \"evalue\" (comet), "
+ "\"exact p-value\" score fields in this order in the input file. ",
+ "Used by assign-confidence.", true);
+ InitBoolParam("combine-charge-states", false,
+ "Specify this parameter to T in order to combine charge states with peptide sequences"
+ "in peptide-centric search. Works only if estimation-method = peptide-level.",
+ "Used by assign-confidence.", true);
+ InitBoolParam("combine-modified-peptides", false,
+ "Specify this parameter to T in order to treat peptides carrying different or "
+ "no modifications as being the same. Works only if estimation = peptide-level.",
+ "Used by assign-confidence.", true);
+ InitStringParam("percolator-intraset-features", "F",
+ "Set a feature for percolator that in later versions is not an option.",
+ "Shouldn't be variable; hide from user.", false);
+ /* Cascade-Search parameters */
+ InitDoubleParam("q-value-threshold", 0.01, 0, 1.0,
+ "The q-value threshold used by cascade search. Each spectrum identified in one search "
+ "with q-value less than this threshold will be excluded from all subsequent searches.",
+ "Used by Cascade-Search", true);
+ InitArgParam("database-series",
+ "A comma-separated list of databases, each generated by tide-index. "
+ "Cascade-search will search the given spectra against these databases in the given order.");
+ /*Subtract-index parameters*/
+ InitArgParam("tide index 1", "A peptide index produced using tide-index");
+ InitArgParam("tide index 2", "A second peptide index, to be subtracted from the first index.");
+ InitArgParam("output index", "A new peptide index containing all peptides that occur in the"
+ "first index but not the second.");
+// InitArgParam("index name", "output tide index");
+ // **** predict-peptide-ions options. ****
+ InitStringParam("primary-ions", "by", "a|b|y|by|bya",
+ "Predict the specified primary ion series. 'a' indicates a-ions only, 'b' indicates "
+ "b-ions only, 'y' indicates y-ions only, 'by' indicates both b and y, 'bya' "
+ "indicates b, y, and a.",
+ "Only available for crux-predict-peptide-ions. Set automatically to "
+ "'by' for searching.", true);
+ InitBoolParam("precursor-ions", false,
+ "Predict the precursor ions, and all associated ions (neutral losses, multiple "
+ "charge states) consistent with the other specified options.",
+ "Only available for crux-predict-peptide-ions.", true);
+ InitIntParam("isotope", 0, 0, 2,
+ "Predict the given number of isotope peaks (0|1|2).",
+ "Only available for crux-predict-peptide-ion. Automatically set to "
+ "0 for Sp scoring and 1 for xcorr scoring.", true);
+ InitBoolParam("flanking", false,
+ "Predict flanking peaks for b- and y ions.",
+ "Only available for crux-predict-peptide-ion.", true);
+ InitStringParam("max-ion-charge", "peptide",
+ "Predict theoretical ions up to max charge state (1, 2, ... ,6) or up to the charge state "
+ "of the peptide (\"peptide\"). If the max-ion-charge is greater than the "
+ "charge state of the peptide, then the maximum is the peptide charge. ",
+ "Available for predict-peptide-ions and search-for-xlinks. "
+ "Set to 'peptide' for search.", true);
+ InitIntParam("nh3", 0, -100, BILLION,
+ "Include among the predicted peaks b/y ions with up to n losses of nh3. For example, "
+ "for --nh3 2, predict a peak for each b- and y-ion with the loss of one nh3 group and "
+ "predict a second peak for each b- and y-ion with the loss of two nh3 groups. These "
+ "peaks will have 1 and 2, respectively, in the NH3 column of the output.",
+ "Only available for crux-predict-peptide-ions.", true);
+ InitIntParam("h2o", 0, -100, BILLION,
+ "Include in the predicted peaks, b/y ions with the loss of 1 to n water molecules. See "
+ "--nh3 for an example.",
+ "Only available for crux-predict-peptide-ions.", true);
+ // ***** spectral-counts aguments *****
+ InitArgParam("input PSMs",
+ "A PSM file in either tab delimited text format (as produced by percolator, "
+ "q-ranker, or barista) or pepXML format.");
+ // also uses "protein-database"
+ // ***** spectral-counts options *****
+ InitStringParam("protein-database", "",
+ "The name of the file in FASTA format.",
+ "Option for spectral-counts", true);
+ InitStringParam("measure", "NSAF", "RAW|NSAF|dNSAF|SIN|EMPAI",
+ "Type of analysis to make on the match results: "
+ "(RAW|NSAF|dNSAF|SIN|EMPAI). With exception of the RAW metric, the database of "
+ "sequences need to be provided using --protein-database.",
+ "Available for spectral-counts. RAW is raw counts, "
+ "NSAF is Normalized Spectral Abundance Factor, "
+ "dNSAF is Distributed Spectral Abundance Factor, "
+ "SIN is Spectral Index Normalized and EMPAI is "
+ "Exponentially Modified Protein Abundance Index", true);
+ InitBoolParam("unique-mapping", false,
+ "Ignore peptides that map to multiple proteins.",
+ "Available for spectral-counts.", true);
+ InitStringParam("quant-level", "protein", "protein|peptide",
+ "Quantification at protein or peptide level.",
+ "Available for spectral-counts and either NSAF and SIN.", true);
+ InitStringParam("parsimony", "none", "none|simple|greedy",
+ "Perform a parsimony analysis on the proteins, and report a \"parsimony rank\" column "
+ "in the output file. This column contains integers indicating the protein's rank in a "
+ "list sorted by spectral counts. If the parsimony analysis results in two proteins "
+ "being merged, then their parsimony rank is the same. In such a case, the rank is "
+ "assigned based on the largest spectral count of any protein in the merged meta-protein. "
+ "The \"simple\" parsimony algorithm only merges two proteins A and B if the peptides "
+ "identified in protein A are the same as or a subset of the peptides identified in "
+ "protein B. The \"greedy\" parsimony algorithm does additional merging, using the "
+ "peptide q-values to greedily assign each peptide to a single protein.",
+ "Available for spectral-counts.", true);
+ InitStringParam("threshold-type", "qvalue", "none|qvalue|custom",
+ "Determines what type of threshold to use when filtering matches. none : read all "
+ "matches, qvalue : use calculated q-value from percolator or q-ranker, custom : use "
+ "--custom-threshold-name and --custom-threshold-min parameters.",
+ "used for crux spectral-counts", true);
+ InitDoubleParam("threshold", 0.01,
+ "Only consider PSMs with a threshold value. By default, q-values "
+ "are thresholded using a specified threshold value. This behavior can be "
+ "changed using the --custom-threshold and --threshold-min "
+ "parameters.",
+ "Available for spectral-counts. All PSMs with higher (or lower) than "
+ "this will be ignored.", true);
+ InitStringParam("custom-threshold-name", "",
+ "Specify which field to apply the threshold to. The direction of the threshold "
+ "(<= or >=) is governed by --custom-threshold-min. By default, the threshold "
+ "applies to the q-value, specified by \"percolator q-value\", \"q-ranker q-value\", "
+ "\"decoy q-value (xcorr)\", or \"barista q-value\".",
+ "Available for spectral-counts.", true);
+ InitBoolParam("custom-threshold-min", true,
+ "When selecting matches with a custom threshold, custom-threshold-min determines "
+ "whether to filter matches with custom-threshold-name values that are greater-than or "
+ "equal (F) or less-than or equal (T) than the threshold.",
+ "Available for spectral-counts.", true);
+ InitStringParam("input-ms2", "",
+ "MS2 file corresponding to the psm file. Required to measure the SIN. Ignored for "
+ "NSAF, dNSAF and EMPAI.",
+ "Available for spectral-counts with measure=SIN.", true);
+ InitBoolParam("mzid-use-pass-threshold", false,
+ "Use mzid's passThreshold attribute to filter matches.",
+ "Used when parsing mzIdentML files.", true);
+ // ***** static mods *****
+ for (char c = 'A'; c <= 'Z'; c++) {
+ double deltaMass = (c != 'C') ? 0 : CYSTEINE_DEFAULT;
+ bool visible = (c != 'B' && c != 'J' && c != 'O' && c != 'U' && c != 'X' && c != 'Z');
+ InitDoubleParam(string(1, c), deltaMass,
+ "Change the mass of all amino acids '" + string(1, c) + "' by the "
+ "given amount.", "", visible);
+ }
+ /* psm-convert options */
+ InitStringParam("input-format", "auto", "auto|tsv|sqt|pepxml|mzidentml",
+ "Legal values are auto, tsv, sqt, pepxml or mzidentml format.",
+ "option, for psm-convert", true);
+ InitBoolParam("distinct-matches", true,
+ "Whether matches/ion are distinct (as opposed to total).",
+ "option, for psm-convert.", true);
+ /* get-ms2-spectrum options */
+ InitBoolParam("stats", false,
+ "Rather than the spectrum, output summary statistics to standard output. Each statistic "
+ "is placed on a separate line, in the format <name>:<value> (e.g. \"TIC:1000.0\")."
+ "[[html:<br>The following statistics are reported for the entire spectrum:<ul><li>"
+ "Precursor m/z</li><li>Total Ion Current</li><li>Base Peak Intensity</li><li>Number of "
+ "peaks</li><li>Minimum m/z</li><li>Maximum m/z</li></ul>In addition, for each possible "
+ "spectrum charge state, the following statistics are reported:<ul><li>Charge state</li>"
+ "<li>Neutral mass</li><li>Charged mass</li><li>M+H+ mass</li></ul>]]",
+ "Available only for crux-get-ms2-spectrum. Does not affect contents "
+ "of the output file.", true);
+
+ InitBoolParam("write-weibull-points", false,
+ "write out the weibull training points for the"
+ "spectrum,charge", "Available for crux search-for-xlinks", true);
+
+ // **** xlink-predict-peptide-ions options ****
+ InitArgParam("peptide A",
+ "The sequence of peptide A.");
+ InitArgParam("peptide B",
+ "The sequence of peptide B.");
+ InitArgParam("pos A",
+ "Position of cross-link on peptide A");
+ InitArgParam("pos B",
+ "Position of cross-link on peptide B");
+ InitBoolParam("print-theoretical-spectrum", false,
+ "Print the theoretical spectrum",
+ "Available for xlink-predict-peptide-ions.", true);
+ InitBoolParam("use-old-xlink", true /* Turn to false later */,
+ "Use the old version of xlink-searching algorithm. When false, a new version of the "
+ "code is run. The new version supports variable modifications and can handle more "
+ "complex databases. This new code is still in development and should be considered a "
+ "beta release.",
+ "Available for search-for-xlinks program.", true);
+ // **** xlink-score-spectrum options ****
+ InitStringParam("xlink-score-method", "composite", "composite|modification|concatenated",
+ "Score method for xlink {composite, modification, concatenated}.",
+ "Available for xlink-score-spectrum.", true);
+ // **** search-xlink options ****
+ InitStringParam("isotope-windows", "0",
+ "Provides a list of isotopic windows to search. For example, -1,0,1 will search in "
+ "three disjoint windows: (1) precursor_mass - neutron_mass +/- window, (2) precursor_mass "
+ "+/- window, and (3) precursor_mass + neutron_mass +/- window. The window size is defined "
+ "from the precursor-window and precursor-window-type parameters. This option is only "
+ "available when use-old-xlink=F.",
+ "Used for crux search-for-xlinks", true);
+
+ InitIntParam("xlink-top-n", 250, 0, BILLION,
+ "Top-n open-mod peptides to consider in the second pass, value of 0 will search all candiates.",
+ "Available for crux search-for-xlinks",
+ true);
+
+ InitBoolParam("xlink-print-db", false,
+ "Prints out the generated database of xlink products to the file xlink_peptides.txt in "
+ "the output directory.",
+ "Used for testing the candidate generatation.", false);
+ InitBoolParam("require-xlink-candidate", false,
+ "If there is no cross-link candidate found, then don't bother looking for linear, "
+ "self-loop, and dead-link candidates.",
+ "Available for crux search-for-xlinks program.", true);
+
+ InitBoolParam("xlink-use-ion-cache", false,
+ "Use an ion cache for the xlinkable peptides",
+ "May not be scalable for large databases", false);
+
+ InitBoolParam("xlink-include-linears", true,
+ "Include linear peptides in the search.",
+ "Available for crux search-for-xlinks program.", true);
+ InitBoolParam("xlink-include-deadends", true,
+ "Include dead-end peptides in the search.",
+ "Available for crux search-for-xlinks program.", true);
+ InitBoolParam("xlink-include-selfloops", true,
+ "Include self-loop peptides in the search.",
+ "Available for crux search-for-xlinks program.", true);
+ InitBoolParam("xlink-include-intra", true,
+ "Include intra-protein cross-link candiates within the search.",
+ "Available for crux search-for-xlinks program.", true);
+ InitBoolParam("xlink-include-inter", true,
+ "Include inter-protein cross-link candidates within the search.",
+ "Available for crux search-for-xlinks program.", true);
+ InitBoolParam("xlink-include-inter-intra", true,
+ "Include crosslink candidates that are both inter and intra.",
+ "Available for crux search-for-xlinks program.", true);
+ InitStringParam("xlink-prevents-cleavage", "K",
+ "List of amino acids for which the cross-linker can prevent cleavage. This option is "
+ "only available when use-old-xlink=F.",
+ "Available for search-for-xlinks program.", true);
+ InitIntParam("max-xlink-mods", 255 , 0, BILLION,
+ "Specify the maximum number of modifications allowed on a crosslinked peptide. This "
+ "option is only available when use-old-xlink=F.",
+ "Available for crux search-for-xlinks", true);
+ InitDoubleParam("precursor-window-weibull", 20.0, 0, 1e6,
+ "Search decoy peptides within +/- precursor-window-weibull of the precursor mass. "
+ "The resulting scores are used only for fitting the Weibull distribution",
+ "Available for crux search-for-xlinks. ", true);
+ InitStringParam("precursor-window-type-weibull", "mass", "mass|mz|ppm",
+ "Window type to use in conjunction with the precursor-window-weibull parameter.",
+ "Available for crux search-for-xlinks", true);
+ InitIntParam("min-weibull-points", 4000, 1, BILLION,
+ "Keep shuffling and collecting XCorr scores until the minimum number of points for "
+ "weibull fitting (using targets and decoys) is achieved.",
+ "Available for crux search-for-xlinks", true);
+ InitArgParam("link sites",
+ "A comma delimited list of the amino acids to allow cross-links with. For example, "
+ "\"A:K,A:D\" means that the cross linker can attach A to K or A to D. Cross-links "
+ "involving the N-terminus of a protein can be specified as a link site by using "
+ "\"nterm\". For example, \"nterm:K\" means that a cross-link can attach a protein's "
+ "N-terminus to a lysine.");
+ InitArgParam("link mass",
+ "The mass modification of the linker when attached to a peptide.");
+ /* hardklor parameters */
+ InitStringParam("hardklor-algorithm", "version1", "basic|version1|version2",
+ "Determines which spectral feature detection algorithm to use. Different results are "
+ "possible with each algorithm, and there are pros and cons to each.[[html: There are "
+ "three algorithms to choose from:<ul><li>basic – Performs unoptimized "
+ "deconvolution and is provided for legacy purposes only.</li><li>version1 – "
+ "Uses the optimizations developed during the 1.0+ series. It is very accurate, but has "
+ "limited sensitivity, and moderate speed improvements.</li><li>version2 – Uses "
+ "the optimizations developed for version 2.0+. It is highly sensitive, but less "
+ "accurate for very low abundance features, and performs exceptionally fast.</li></ul>]]",
+ "Available for crux hardklor", true);
+ InitStringParam("averagine-mod", "",
+ "Defines alternative averagine models in the analysis that incorporate additional "
+ "atoms and/or isotopic enrichments. Modifications are represented as text strings. "
+ "Inclusion of additional atoms in the model is done using by entering an atomic "
+ "formula, such as: PO2 or Cl. Inclusion of isotopic enrichment to the model is done by "
+ "specifying the percent enrichment (as a decimal) followed by the atom being enriched "
+ "and an index of the isotope. For example, 0.75H1 specifies 75% enrichment of the first "
+ "heavy isotope of hydrogen. In other words, 75% deuterium enrichment. Two or more "
+ "modifications can be combined into the same model, and separated by spaces: B2 0.5B1",
+ "Available for crux hardklor", true);
+ InitIntParam("boxcar-averaging", 0, 0, BILLION,
+ "Boxcar averaging is a sliding window that averages n adjacent spectra prior to feature "
+ "detection. Averaging generally improves the signal-to-noise ratio of features in the "
+ "spectra, as well as improving the shape of isotopic envelopes. However, averaging will "
+ "also change the observed peak intensities. Averaging with too wide a window will "
+ "increase the occurrence of overlapping features and broaden the chromatographic "
+ "profiles of observed features. The number specified is the total adjacent scans to be "
+ "combined, centered on the scan being analyzed. Therefore, an odd number is recommended "
+ "to center the boxcar window. For example, a value of 3 would produce an average of the "
+ "scan of interest, plus one scan on each side. A value of 0 disables boxcar averaging.",
+ "Available for crux hardklor", true);
+ InitIntParam("boxcar-filter", 0, 0, BILLION,
+ "This parameter is only functional when boxcar-averaging is used. The filter will "
+ "remove any peaks not seen in n scans in the boxcar window. The effect is to reduce "
+ "peak accumulation due to noise and reduce chromatographic broadening of peaks. Caution "
+ "should be used as over-filtering can occur. The suggested number of scans to set for "
+ "filtering should be equal to or less than the boxcar-averaging window size. A value of "
+ "0 disables filtering.",
+ "Available for crux hardklor", true);
+ InitDoubleParam("boxcar-filter-ppm", 10.0, 0.0, BILLION,
+ "This parameter is only functional when boxcar-filter is used. The value specifies the "
+ "mass tolerance in ppm for declaring a peak the same prior to filtering across all "
+ "scans in the boxcar window.",
+ "Available for crux hardklor", true);
+ InitBoolParam("centroided", false,
+ "Indicates whether the data contain profile or centroided peaks.",
+ "Available for crux hardklor", true);
+ InitStringParam("cdm", "Q", "B|F|P|Q|S",
+ "Choose the charge state determination method.[[html: There are five methods to "
+ "choose from:<ul><li>B – Basic method, assume all charge states are possible."
+ "</li><li>F – Fast Fourier transform.</li><li>P – Patterson algorithm.</li>"
+ "<li>Q – QuickCharge method, uses inverse peak distances.</li><li>S – "
+ "Senko method, or combined Fast Fourier Transform and Patterson algorithm.</li></ul>]]",
+ "Available for crux hardklor", true);
+ InitIntParam("min-charge", 1, 1, BILLION,
+ "Specifies the minimum charge state to allow when finding spectral features. It is "
+ "best to set this value to the lowest assumed charge state to be present. If set higher "
+ "than actual charge states that are present, those features will not be identified or "
+ "incorrectly assigned a different charge state and mass.",
+ "Available for crux hardklor", true);
+ InitIntParam("max-charge", 5, 1, BILLION,
+ "Specifies the maximum charge state to allow when finding spectral features. It is "
+ "best to set this value to a practical number (i.e. do not set it to 20 when doing a "
+ "tryptic shotgun analysis). If set higher than actual charge states that are present, "
+ "the algorithm will perform significantly slower without any improvement in results.",
+ "Available for crux hardklor", true);
+ InitDoubleParam("corr", 0.85, 0, 1.0,
+ "Sets the correlation threshold (cosine similarity) for accepting each predicted "
+ "feature.",
+ "Available for crux hardklor", true);
+ InitIntParam("depth", 3, 1, BILLION,
+ "Sets the depth of combinatorial analysis. For a given set of peaks in a spectrum, "
+ "search for up to this number of combined peptides that explain the observed peaks. "
+ "The analysis stops before depth is reached if the current number of deconvolved "
+ "features explains the observed peaks with a correlation score above the threshold "
+ "defined with the correlation parameter.",
+ "Available for crux hardklor", true);
+ InitBoolParam("distribution-area", false,
+ "When reporting each feature, report abundance as the sum of all isotope peaks. The "
+ "value reported is the estimate of the correct peak heights based on the averagine "
+ "model scaled to the observed peak heights.",
+ "Available for crux hardklor", true);
+ InitStringParam("hardklor-data-file", "",
+ "Specifies an ASCII text file that defines symbols for the periodic table.",
+ "Available for crux hardklor", true);
+ InitStringParam("instrument", "fticr", "fticr|orbitrap|tof|qit",
+ "Indicates the type of instrument used to collect data. This parameter, combined with "
+ "the resolution parameter, define how spectra will be centroided (if you provide "
+ "profile spectra) and the accuracy when aligning observed peaks to the models.",
+ "Available for crux hardklor", true);
+ InitStringParam("isotope-data-file", "",
+ "Specifies an ASCII text file that can be read to override the natural isotope "
+ "abundances for all elements.",
+ "Available for crux hardklor", true);
+ InitIntParam("max-features", 10, 1, BILLION,
+ "Specifies the maximum number of models to build for a set of peaks being analyzed. "
+ "Regardless of the setting, the number of models will never exceed the number of peaks "
+ "in the current set. However, as many of the low abundance peaks are noise or tail ends "
+ "of distributions, defining models for them is detrimental to the analysis.",
+ "Available for crux hardklor", true);
+ InitIntParam("mzxml-filter", 1, 1, 2,
+ "Filters the spectra prior to analysis for the requested MS/MS level. For example, if "
+ "the data contain MS and MS/MS spectra, setting mzxml-filter = 1 will analyze only the "
+ "MS scan events. Setting mzxml-filter = 2 will analyze only the MS/MS scan events.",
+ "Available for crux hardklor", true);
+ InitDoubleParam("mz-max", 0, 0, 10000,
+ "Constrains the search in each spectrum to signals below this value in Thomsons. "
+ "Setting to 0 disables this feature.",
+ "Available for crux hardklor", true);
+ InitDoubleParam("mz-min", 0, 0, 10000,
+ "Constrains the search in each spectrum to signals above this value in Thomsons. "
+ "Setting to 0 disables this feature.",
+ "Available for crux hardklor", true);
+ InitDoubleParam("mz-window", 4.0, 1.0, 20.0,
+ "Only used when algorithm = version1. Defines the maximum window size in Thomsons to "
+ "analyze when deconvolving peaks in a spectrum into features.",
+ "Available for crux hardklor", true);
+ InitDoubleParam("resolution", 100000, 1, BILLION,
+ "Specifies the resolution of the instrument at 400 m/z for the data being analyzed.",
+ "Available for crux hardklor", true);
+ InitIntParam("scan-range-max", 0, 0, BILLION,
+ "Used to restrict analysis to spectra with scan numbers below this parameter value. "
+ "A value of 0 disables this feature.",
+ "Available for crux hardklor", true);
+ InitIntParam("scan-range-min", 0, 0, BILLION,
+ "Used to restrict analysis to spectra with scan numbers above this parameter value. "
+ "A value of 0 disables this feature.",
+ "Available for crux hardklor", true);
+ InitIntParam("sensitivity", 2, 0, 3,
+ "Set the sensitivity level. There are four levels: 0 (low), 1 (moderate), "
+ "2 (high), and 3 (max). Increasing the sensitivity will increase computation time, "
+ "but will also yield more isotope distributions.",
+ "Available for crux hardklor", true);
+ InitDoubleParam("signal-to-noise", 1.0, 0.0, BILLION,
+ "Filters spectra to remove peaks below this signal-to-noise ratio prior to finding "
+ "features.",
+ "Available for crux hardklor", true);
+ InitIntParam("smooth", 0, 0, 21,
+ "Uses Savitzky-Golay smoothing on profile peak data prior to centroiding the spectra. "
+ "This parameter is recommended for low resolution spectra only. Smoothing data causes "
+ "peak depression and broadening. Only use odd numbers for the degree of smoothing (as "
+ "it defines a window centered on each data point). Higher values will produce smoother "
+ "peaks, but with greater depression and broadening. Setting this parameter to 0 disables "
+ "smoothing.",
+ "Available for crux hardklor", true);
+ InitDoubleParam("sn-window", 250.0, 0.0, BILLION,
+ "Set the signal-to-noise window length (in m/z). Because noise may "
+ "be non-uniform across a spectrum, this value adjusts the segment size "
+ "considered when calculating a signal-over-noise ratio.",
+ "Available for crux hardklor", true);
+ InitBoolParam("static-sn", true,
+ "Applies the lowest noise threshold of any sn_window across the entire mass range for a "
+ "spectrum. Setting this parameter to 0 turns off this feature, and different noise "
+ "thresholds will be used for each local mass window in a spectrum.",
+ "Available for crux hardklor", true);
+ InitBoolParam("hardklor-xml-output", false,
+ "Output XML instead of tab-delimited text.",
+ "Available for crux hardklor", false);
+ /* bullseye parameters */
+ InitArgParam("MS1 spectra",
+ "The name of a file from which to parse high-resolution spectra of intact peptides. "
+ "The file may be in MS1 (.ms1), binary MS1 (.bms1), compressed MS1 (.cms1), or "
+ "mzXML (.mzXML) format. Bullseye will search for PPIDs in these spectra.");
+ InitArgParam("MS2 spectra",
+ "The name of a file from which to parse peptide fragmentation spectra. The file may "
+ "be in MS2 (.ms2), binary MS2 (.bms2), compressed MS2 (.cms2) or mzXML (.mzXML) format. "
+ "Bullseye will assign high-resolution precursor masses to these spectra.");
+ InitStringParam("hardklor-file", "",
+ "Input hardklor file into bullseye",
+ "Hidden option for crux bullseye.", false);
+ InitDoubleParam("max-persist", 2.0, 0, BILLION,
+ "Ignore PPIDs that persist for longer than this length of time in the MS1 spectra. The "
+ "unit of time is whatever unit is used in your data file (usually minutes). These PPIDs "
+ "are considered contaminants.",
+ "Available for crux bullseye", true);
+ InitBoolParam("exact-match", false,
+ "When true, require an exact match (as defined by --exact-tolerance) between the "
+ "center of the precursor isolation window in the MS2 scan and the base isotopic "
+ "peak of the PPID. If this option is set to false and no exact match is observed, "
+ "then attempt to match using a wider m/z tolerance. This wider tolerance is calculated "
+ "using the PPID's monoisotopic mass and charge (the higher the charge, the smaller "
+ "the window).",
+ "Available for crux bullseye", true);
+ InitIntParam("gap-tolerance", 1, 0, BILLION,
+ "Allowed gap size when checking for PPIDs across consecutive MS1 scans.",
+ "Available for crux bullseye", true);
+ InitDoubleParam("bullseye-min-mass", 600, 0, BILLION,
+ "Only consider PPIDs above this minimum mass in daltons.",
+ "Available for crux bullseye", true);
+ InitDoubleParam("bullseye-max-mass", 8000, 1, BILLION,
+ "Only consider PPIDs below this maximum mass in daltons.",
+ "Available for crux bullseye", true);
+ InitDoubleParam("exact-tolerance", 10.0, 0, BILLION,
+ "Set the tolerance (+/-ppm) for --exact-match.",
+ "Available for crux bullseye", true);
+ InitDoubleParam("persist-tolerance", 10.0, 0, BILLION,
+ "Set the mass tolerance (+/-ppm) for finding PPIDs in consecutive MS1 scans.",
+ "Available for crux bullseye", true);
+ InitIntParam("scan-tolerance", 3, 0, BILLION,
+ "Total number of MS1 scans over which a PPID must be observed to be considered real. "
+ "Gaps in persistence are allowed by setting --gap-tolerance.",
+ "Available for crux bullseye", true);
+ InitDoubleParam("retention-tolerance", 0.5, 0, BILLION,
+ "Set the tolerance (+/-units) around the retention time over which a PPID can be "
+ "matches to the MS2 spectrum. The unit of time is whatever unit is used in your data "
+ "file (usually minutes).",
+ "Available for crux bullseye", true);
+ InitStringParam("spectrum-format", "", "|ms2|bms2|cms2|mgf",
+ "The format to write the output spectra to. If empty, the spectra will be "
+ "output in the same format as the MS2 input.",
+ "Available for crux bullseye", true);
+ /* crux-util parameters */
+ InitBoolParam("ascending", true,
+ "Sort in ascending (T) or descending (F) order.",
+ "Available for sort-by-column", true);
+ InitArgParam("tsv file",
+ "A tab-delimited file, with column headers in the first row. Use \"-\" to read from "
+ "standard input.");
+ InitStringParam("delimiter", "tab",
+ "Specify the input and output delimiter to use when processing the "
+ "delimited file. The argument can be either a single character or "
+ "the keyword 'tab.'",
+ "Available for the delimited utility programs.", true);
+ InitArgParam("column names",
+ "A comma-delimited list of column names.");
+ InitArgParam("column name",
+ "A column name.");
+ InitArgParam("column value",
+ "A cell value for a column.");
+ InitBoolParam("header", true,
+ "Print the header line of the file, in addition to the columns that match.",
+ "Available for crux extract-columns and extract-rows", true);
+ InitStringParam("column-type", "string", "int|real|string",
+ "Specifies the data type of the column, either an integer (int), a floating point "
+ "number (real), or a string.",
+ "Available for crux extract-rows", true);
+ InitStringParam("comparison", "eq", "eq|gt|gte|lt|lte|neq",
+ "Specify the operator that is used to compare an entry in the specified column to the "
+ "value given on the command line.[[html: Legal values are as follows:<ul><li>eq – "
+ "The two values are equal</li><li>lt – The file value is less than the argument "
+ "value</li><li>lte – The file value is less than or equal to the argument value"
+ "</li><li>gt – The file value is greater than the argument value</li><li>gte "
+ "– The file value is greater than or equal to the argument value</li><li>neq "
+ "– The file value is not equal to the argument value</li></ul>]]",
+ "Available for crux extract-rows", true);
+ // crux pipeline options
+ InitBoolParam("bullseye", false,
+ "Run the Bullseye algorithm on the given MS data, using it to assign high-resolution "
+ "precursor values to the MS/MS data. If a spectrum file ends with .ms2 or .cms2, matching "
+ ".ms1/.cms1 files will be used as the MS1 file. Otherwise, it is assumed that the "
+ "spectrum file contains both MS1 and MS2 scans.",
+ "Available for crux pipeline", true);
+ InitStringParam("search-engine", "tide-search", "comet|tide-search",
+ "Specify which search engine to use.",
+ "Available for crux pipeline", true);
+ InitStringParam("post-processor", "percolator", "percolator|assign-confidence|none",
+ "Specify which post-processor to apply to the search results.",
+ "Available for crux pipeline", true);
+ // create-docs
+ InitArgParam("tool-name",
+ "Specifies the Crux tool to generate documentation for. If the value is "
+ "'list', then a list of available tools will be given. If the value is "
+ "'default-params', then a default parameter file will be given."
+ "If the value is 'param-table' then a table will be printed showing "
+ "which parameters are associated with which commands.");
+ InitStringParam("doc-template", "",
+ "Specifies the main template to be used for generating documentation.",
+ "Available for crux create-docs", false);
+ InitStringParam("doc-input-template", "",
+ "Specifies the template to be used for inputs when generating "
+ "documentation.",
+ "Available for crux create-docs", false);
+ InitStringParam("doc-output-template", "",
+ "Specifies the template to be used for outputs when generating "
+ "documentation.",
+ "Available for crux create-docs", false);
+ InitStringParam("doc-option-category-template", "",
+ "Specifies the template to be used for option categories when generating "
+ "documentation.",
+ "Available for crux create-docs", false);
+ InitStringParam("doc-option-template", "",
+ "Specifies the template to be used for options when generating "
+ "documentation.",
+ "Available for crux create-docs", false);
+ // param-medic
+ InitArgParam("spectrum-file",
+ "File from which to parse fragmentation spectra.");
+ InitBoolParam("pm-ignore-no-charge", false,
+ "When parsing spectra for measurement error estimation, ignore those without charge state information.",
+ "Available for param-medic and tide-search and comet", false);
+ InitDoubleParam("pm-min-precursor-mz", 400,
+ "Minimum precursor m/z value to use in measurement error estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitDoubleParam("pm-max-precursor-mz", 1800,
+ "Minimum precursor m/z value to use in measurement error estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitDoubleParam("pm-min-frag-mz", 150,
+ "Minimum fragment m/z value to use in measurement error estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitDoubleParam("pm-max-frag-mz", 1800,
+ "Maximum fragment m/z value to use in measurement error estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitIntParam("pm-min-scan-frag-peaks", 40,
+ "Minimum fragment peaks an MS/MS scan must contain to be used in measurement error estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitDoubleParam("pm-max-precursor-delta-ppm", 50,
+ "Maximum ppm distance between precursor m/z values to consider two scans "
+ "potentially generated by the same peptide for measurement error estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitIntParam("pm-charge", 2,
+ "Precursor charge state to consider MS/MS spectra from, in measurement error estimation. Ideally, this "
+ "should be the most frequently occurring charge state in the given data.",
+ "Available for param-medic and tide-search and comet", true);
+ InitIntParam("pm-top-n-frag-peaks", 30,
+ "Number of most-intense fragment peaks to consider for measurement error estimation, per MS/MS spectrum.",
+ "Available for param-medic and tide-search and comet", true);
+ InitIntParam("pm-pair-top-n-frag-peaks", 5,
+ "Number of fragment peaks per spectrum pair to be used in fragment error "
+ "estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitIntParam("pm-min-common-frag-peaks", 20,
+ "Number of the most-intense peaks that two spectra must share in order to "
+ "potentially be generated by the same peptide, for measurement error estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitIntParam("pm-max-scan-separation", 1000,
+ "Maximum number of scans two spectra can be separated by in order to be "
+ "considered potentially generated by the same peptide, for measurement error estimation.",
+ "Available for param-medic and tide-search and comet", true);
+ InitIntParam("pm-min-peak-pairs", 100,
+ "Minimum number of peak pairs (for precursor or fragment) that must be "
+ "successfully paired in order to attempt to estimate measurement error distribution.",
+ "Available for param-medic and tide-search and comet", true);
+
+ InitBoolParam("no-analytics", false, "Don't post data to Google Analytics.", "", false);
+
+ Categorize();
+}
+
+Params::~Params() {
+ for (map<string, Param*>::iterator i = params_.begin(); i != params_.end(); i++) {
+ delete i->second;
+ }
+}
+
+void Params::Categorize() {
+ set<string> items;
+
+ items.clear();
+ items.insert("max-persist");
+ items.insert("persist-tolerance");
+ items.insert("scan-tolerance");
+ items.insert("gap-tolerance");
+ items.insert("bullseye-max-mass");
+ items.insert("bullseye-min-mass");
+ AddCategory("Identifying PPIDs in MS1 spectra", items);
+
+ items.clear();
+ items.insert("exact-match");
+ items.insert("exact-tolerance");
+ items.insert("retention-tolerance");
+ AddCategory("Matching PPIDs to MS2 spectra", items);
+
+ items.clear();
+ items.insert("max-length");
+ items.insert("min-length");
+ items.insert("max-mass");
+ items.insert("min-mass");
+ items.insert("isotopic-mass");
+ items.insert("clip-nterm-methionine");
+ AddCategory("Peptide properties", items);
+
+ items.clear();
+ items.insert("mods-spec");
+ items.insert("nterm-peptide-mods-spec");
+ items.insert("cterm-peptide-mods-spec");
+ items.insert("nterm-protein-mods-spec");
+ items.insert("cterm-protein-mods-spec");
+ items.insert("min-mods");
+ items.insert("max-mods");
+ items.insert("mod");
+ for (char c = 'A'; c <= 'Z'; c++) {
+ items.insert(string(1, c));
+ }
+ AddCategory("Amino acid modifications", items);
+
+ items.clear();
+ items.insert("decoy-format");
+ items.insert("keep-terminal-aminos");
+ items.insert("seed");
+ items.insert("allow-dups");
+ AddCategory("Decoy database generation", items);
+
+ items.clear();
+ items.insert("enzyme");
+ items.insert("custom-enzyme");
+ items.insert("digestion");
+ items.insert("missed-cleavages");
+ AddCategory("Enzymatic digestion", items);
+
+ items.clear();
+ items.insert("max-precursor-charge");
+ items.insert("precursor-window");
+ items.insert("auto-precursor-window");
+ items.insert("precursor-window-type");
+ AddCategory("Precursor selection", items);
+
+ items.clear();
+ items.insert("max-ion-charge");
+ items.insert("peptide-centric-search");
+ items.insert("exact-p-value");
+ items.insert("compute-sp");
+ items.insert("spectrum-min-mz");
+ items.insert("spectrum-max-mz");
+ items.insert("min-peaks");
+ items.insert("spectrum-charge");
+ items.insert("scan-number");
+ items.insert("remove-precursor-peak");
+ items.insert("remove-precursor-tolerance");
+ items.insert("use-flanking-peaks");
+ items.insert("use-neutral-loss-peaks");
+ items.insert("mz-bin-width");
+ items.insert("auto-mz-bin-width");
+ items.insert("mz-bin-offset");
+ items.insert("precursor-window-weibull");
+ items.insert("precursor-window-type-weibull");
+ items.insert("min-weibull-points");
+ items.insert("mod-mass-format");
+ items.insert("fragment-mass");
+ items.insert("isotope-windows");
+ items.insert("isotope-error");
+ items.insert("skip-preprocessing");
+ items.insert("compute-p-values");
+ AddCategory("Search parameters", items);
+
+ items.clear();
+ items.insert("use-a-ions");
+ items.insert("use-b-ions");
+ items.insert("use-c-ions");
+ items.insert("use-x-ions");
+ items.insert("use-y-ions");
+ items.insert("use-z-ions");
+ AddCategory("Fragment ion parameters", items);
+
+ items.clear();
+ items.insert("picked-protein");
+ items.insert("protein-enzyme");
+ items.insert("protein-report-fragments");
+ items.insert("protein-report-duplicates");
+ AddCategory("Protein inference options", items);
+
+ items.clear();
+ items.insert("protein");
+ items.insert("fido-alpha");
+ items.insert("fido-beta");
+ items.insert("fido-gamma");
+ items.insert("fido-empirical-protein-q");
+ items.insert("fido-gridsearch-depth");
+ items.insert("fido-gridsearch-mse-threshold");
+ items.insert("fido-fast-gridsearch");
+ items.insert("fido-protein-truncation-threshold");
+ items.insert("fido-no-split-large-components");
+ AddCategory("Fido options", items);
+
+ items.clear();
+ items.insert("use-old-xlink");
+ items.insert("xlink-include-inter");
+ items.insert("xlink-include-intra");
+ items.insert("xlink-include-inter-intra");
+ items.insert("xlink-include-linears");
+ items.insert("xlink-include-deadends");
+ items.insert("xlink-include-selfloops");
+ items.insert("xlink-prevents-cleavage");
+ items.insert("max-xlink-mods");
+ AddCategory("Cross-linking parameters", items);
+
+ items.clear();
+ items.insert("decoy_search");
+ AddCategory("Database", items);
+
+ items.clear();
+ items.insert("num-threads");
+ items.insert("num_threads");
+ AddCategory("CPU threads", items);
+
+ items.clear();
+ items.insert("peptide_mass_tolerance");
+ items.insert("auto_peptide_mass_tolerance");
+ items.insert("peptide_mass_units");
+ items.insert("mass_type_parent");
+ items.insert("mass_type_fragment");
+ items.insert("precursor_tolerance_type");
+ items.insert("isotope_error");
+ AddCategory("Masses", items);
+
+ items.clear();
+ items.insert("search_enzyme_number");
+ items.insert("num_enzyme_termini");
+ items.insert("allowed_missed_cleavage");
+ AddCategory("Search enzyme", items);
+
+ items.clear();
+ items.insert("fragment_bin_tol");
+ items.insert("auto_fragment_bin_tol");
+ items.insert("fragment_bin_offset");
+ items.insert("theoretical_fragment_ions");
+ items.insert("use_A_ions");
+ items.insert("use_B_ions");
+ items.insert("use_C_ions");
+ items.insert("use_X_ions");
+ items.insert("use_Y_ions");
+ items.insert("use_Z_ions");
+ items.insert("use_NL_ions");
+ AddCategory("Fragment ions", items);
+
+ items.clear();
+ items.insert("scan_range");
+ items.insert("precursor_charge");
+ items.insert("override_charge");
+ items.insert("ms_level");
+ items.insert("activation_method");
+ AddCategory("mzXML/mzML parameters", items);
+
+ items.clear();
+ items.insert("digest_mass_range");
+ items.insert("num_results");
+ items.insert("skip_researching");
+ items.insert("max_fragment_charge");
+ items.insert("max_precursor_charge");
+ items.insert("nucleotide_reading_frame");
+ items.insert("clip_nterm_methionine");
+ items.insert("spectrum_batch_size");
+ items.insert("decoy_prefix");
+ items.insert("output_suffix");
+ items.insert("mass_offsets");
+ AddCategory("Miscellaneous parameters", items);
+
+ items.clear();
+ items.insert("minimum_peaks");
+ items.insert("minimum_intensity");
+ items.insert("remove_precursor_peak");
+ items.insert("remove_precursor_tolerance");
+ items.insert("clear_mz_range");
+ AddCategory("Spectral processing", items);
+
+ items.clear();
+ for (int i = 1; i <= 9; i++) {
+ items.insert("variable_mod0" + StringUtils::ToString(i));
+ }
+ items.insert("max_variable_mods_in_peptide");
+ items.insert("require_variable_mod");
+ AddCategory("Variable modifications", items);
+
+ items.clear();
+ items.insert("add_Cterm_peptide");
+ items.insert("add_Nterm_peptide");
+ items.insert("add_Cterm_protein");
+ items.insert("add_Nterm_protein");
+ for (char c = 'A'; c <= 'Z'; c++) {
+ string aaString = string(1, c);
+ string aaName = AminoAcidUtil::GetName(c);
+ aaName = aaName.empty() ? "user_amino_acid" : StringUtils::Replace(aaName, " ", "_");
+ items.insert("add_" + aaString + "_" + aaName);
+ }
+ AddCategory("Static modifications", items);
+
+ items.clear();
+ items.insert("only-psms");
+ items.insert("tdc");
+ items.insert("search-input");
+ AddCategory("General options", items);
+
+ items.clear();
+ items.insert("subset-max-train");
+ items.insert("c-pos");
+ items.insert("c-neg");
+ items.insert("test-fdr");
+ items.insert("train-fdr");
+ items.insert("maxiter");
+ items.insert("quick-validation");
+ items.insert("test-each-iteration");
+ items.insert("percolator-seed");
+ AddCategory("SVM training options", items);
+
+ items.clear();
+ items.insert("override");
+ items.insert("output-weights");
+ items.insert("init-weights");
+ items.insert("default-direction");
+ items.insert("unitnorm");
+ items.insert("klammer");
+ AddCategory("SVM feature input options", items);
+
+ items.clear();
+ items.insert("pm-min-precursor-mz");
+ items.insert("pm-max-precursor-mz");
+ items.insert("pm-min-frag-mz");
+ items.insert("pm-max-frag-mz");
+ items.insert("pm-min-scan-frag-peaks");
+ items.insert("pm-max-precursor-delta-ppm");
+ items.insert("pm-charge");
+ items.insert("pm-top-n-frag-peaks");
+ items.insert("pm-pair-top-n-frag-peaks");
+ items.insert("pm-min-common-frag-peaks");
+ items.insert("pm-max-scan-separation");
+ items.insert("pm-min-peak-pairs");
+ AddCategory("param-medic options", items);
+
+ items.clear();
+ items.insert("spectrum-format");
+ items.insert("spectrum-parser");
+ items.insert("list-of-files");
+ items.insert("print-search-progress");
+ items.insert("use-z-line");
+ items.insert("top-match");
+ items.insert("concat");
+ items.insert("store-spectra");
+ items.insert("store-index");
+ items.insert("xlink-print-db");
+ items.insert("fileroot");
+ items.insert("temp-dir");
+ items.insert("output-dir");
+ items.insert("output-file");
+ items.insert("overwrite");
+ items.insert("txt-output");
+ items.insert("sqt-output");
+ items.insert("pepxml-output");
+ items.insert("mzid-output");
+ items.insert("pin-output");
+ items.insert("pout-output");
+ items.insert("output_sqtfile");
+ items.insert("output_txtfile");
+ items.insert("output_pepxmlfile");
+ items.insert("output_percolatorfile");
+ items.insert("output_outfiles");
+ items.insert("print_expect_score");
+ items.insert("num_output_lines");
+ items.insert("show_fragment_ions");
+ items.insert("sample_enzyme_number");
+ items.insert("feature-file-in");
+ items.insert("feature-file-out");
+ items.insert("decoy-xml-output");
+ items.insert("parameter-file");
+ items.insert("verbosity");
+ items.insert("decoy-prefix");
+ items.insert("precision");
+ items.insert("peptide-list");
+ items.insert("comparison");
+ items.insert("header");
+ items.insert("column-type");
+ items.insert("ascending");
+ items.insert("delimiter");
+ items.insert("file-column");
+ AddCategory("Input and output", items);
+
+}
+
+bool Params::GetBool(const string& name) {
+ return Require(name)->GetBool();
+}
+
+int Params::GetInt(const string& name) {
+ return Require(name)->GetInt();
+}
+
+double Params::GetDouble(const string& name) {
+ return Require(name)->GetDouble();
+}
+
+string Params::GetString(const string& name) {
+ return Require(name)->GetString();
+}
+
+bool Params::GetBoolDefault(const string& name) {
+ return Require(name)->GetBoolDefault();
+}
+
+int Params::GetIntDefault(const string& name) {
+ return Require(name)->GetIntDefault();
+}
+
+double Params::GetDoubleDefault(const string& name) {
+ return Require(name)->GetDoubleDefault();
+}
+
+string Params::GetStringDefault(const string& name) {
+ return Require(name)->GetStringDefault();
+}
+
+const vector<string>& Params::GetStrings(const string& name) {
+ Param* param = Require(name);
+ if (!param->IsArgument()) {
+ throw runtime_error("Parameter '" + name + "' is not an argument");
+ }
+ return ((ArgParam*)param)->GetStrings();
+}
+
+string Params::GetUsage(const string& name) {
+ return Require(name)->GetUsage();
+}
+
+string Params::GetFileNotes(const string& name) {
+ return Require(name)->GetFileNotes();
+}
+
+bool Params::IsVisible(const string& name) {
+ return Require(name)->IsVisible();
+}
+
+bool Params::IsArgument(const string& name) {
+ return Require(name)->IsArgument();
+}
+
+string Params::GetAcceptedValues(const string& name) {
+ return Require(name)->GetAcceptedValues();
+}
+
+bool Params::IsDefault(const string& name) {
+ return Require(name)->IsDefault();
+}
+
+bool Params::Exists(const string& name) {
+ return paramContainer_.Get(name) != NULL;
+}
+
+void Params::Set(const string& name, bool value) {
+ paramContainer_.CanModifyCheck();
+ Param* param = Require(name);
+ param->Set(value);
+ param->ThrowIfInvalid();
+}
+
+void Params::Set(const string& name, int value) {
+ paramContainer_.CanModifyCheck();
+ Param* param = Require(name);
+ param->Set(value);
+ param->ThrowIfInvalid();
+}
+
+void Params::Set(const string& name, double value) {
+ paramContainer_.CanModifyCheck();
+ Param* param = Require(name);
+ param->Set(value);
+ param->ThrowIfInvalid();
+}
+
+void Params::Set(const string& name, const char* value) {
+ Set(name, string(value));
+}
+
+void Params::Set(const string& name, const string& value) {
+ paramContainer_.CanModifyCheck();
+ Param* param = Require(name);
+ param->Set(value);
+ param->ThrowIfInvalid();
+}
+
+void Params::AddArgValue(const string& name, const string& value) {
+ paramContainer_.CanModifyCheck();
+ Param* param = Require(name);
+ if (!param->IsArgument()) {
+ throw runtime_error("Cannot add value to '" + name + "', it is not an argument");
+ }
+ ((ArgParam*)param)->AddValue(value);
+}
+
+void Params::Finalize() {
+ paramContainer_.FinalizeParams();
+}
+
+void Params::Write(ostream* out, bool defaults) {
+ if (out == NULL || !out->good()) {
+ throw runtime_error("Bad file stream for writing parameter file");
+ }
+
+ *out << "# Crux parameter file (generated by Crux version " << CRUX_VERSION << ")" << endl
+ << "# Full documentation available at http://cruxtoolkit.sourceforge.net/" << endl
+ << "# comet_version 2016.01 rev. 1" << endl
+ << "# Everything following the \'#\' symbol is treated as a comment." << endl
+ << endl;
+
+ for (vector<const Param*>::const_iterator i = Begin(); i != End(); i++) {
+ string name = (*i)->GetName();
+ // Print mods and Comet parameters later
+ if (!(*i)->IsVisible() ||
+ name == "mod" || name == "cmod" || name == "nmod" ||
+ name.find('_') != string::npos) {
+ continue;
+ }
+ *out << (*i)->GetParamFileString(defaults) << endl;
+ }
+
+ print_mods_parameter_file(out, "mod", get_aa_mod_list);
+ print_mods_parameter_file(out, "nmod", get_n_mod_list);
+ print_mods_parameter_file(out, "cmod", get_c_mod_list);
+
+ // Print Comet parameters
+ *out << "####################" << endl
+ << "# Comet Parameters #" << endl
+ << "####################" << endl;
+ for (vector<const Param*>::const_iterator i = Begin(); i != End(); i++) {
+ string name = (*i)->GetName();
+ // Print mods and Comet parameters later
+ if (!(*i)->IsVisible() ||
+ name == "mod" || name == "cmod" || name == "nmod" ||
+ name.find('_') == string::npos) {
+ continue;
+ }
+ *out << (*i)->GetParamFileString(defaults) << endl;
+ }
+
+ *out << "#" << endl
+ << "# COMET_ENZYME_INFO _must_ be at the end of this parameters file" << endl
+ << "#" << endl
+ << "[COMET_ENZYME_INFO]" << endl;
+
+ const vector<string>& cometEnzymes = get_comet_enzyme_info_lines();
+ if (cometEnzymes.empty() || defaults) {
+ *out << "0. No_enzyme 0 - -" << endl
+ << "1. Trypsin 1 KR P" << endl
+ << "2. Trypsin/P 1 KR -" << endl
+ << "3. Lys_C 1 K P" << endl
+ << "4. Lys_N 0 K -" << endl
+ << "5. Arg_C 1 R P" << endl
+ << "6. Asp_N 0 D -" << endl
+ << "7. CNBr 1 M -" << endl
+ << "8. Glu_C 1 DE P" << endl
+ << "9. PepsinA 1 FL P" << endl
+ << "10. Chymotrypsin 1 FWYL P" << endl;
+ /*TODO: Put these back in after we figure out what to do with enzyme info
+ *out << "11. Elastase 1 ALIV P" << endl
+ << "12. Clostripain 1 R -" << endl
+ << "13. Iodosobenzoate 1 W -" << endl
+ << "14. Proline_Endopeptidase 1 P -" << endl
+ << "15. Staph_Protease 1 E -" << endl
+ << "16. Modified_Chymotrypsin 1 FWYL P" << endl
+ << "17. Elastase_Trypsin_Chymotrypsin 1 ALIVKRWFY P" << endl;
+ */
+ } else {
+ for (vector<string>::const_iterator i = cometEnzymes.begin();
+ i != cometEnzymes.end();
+ i++) {
+ *out << *i << endl;
+ }
+ }
+}
+
+map<string, Param*>::const_iterator Params::BeginAll() {
+ return paramContainer_.params_.begin();
+}
+
+map<string, Param*>::const_iterator Params::EndAll() {
+ return paramContainer_.params_.end();
+}
+
+vector<const Param*>::const_iterator Params::Begin() {
+ return paramContainer_.paramsOrdered_.begin();
+}
+
+vector<const Param*>::const_iterator Params::End() {
+ return paramContainer_.paramsOrdered_.end();
+}
+
+string Params::ProcessHtmlDocTags(string s, bool html) {
+ // If html is true, instances of [[html:{text}]] become {text} and
+ // instances of [[nohtml:{text}]] are removed.
+ // If html is false, instances of [[nohtml:{text}]] become {text} and
+ // instances of [[html:{text}]] are removed.
+
+ const string OPEN_TAG = "[[";
+ const string CLOSE_TAG = "]]";
+ const string HTML_PREFIX = "html:";
+ const string NO_HTML_PREFIX = "nohtml:";
+
+ size_t pos, endPos = 0;
+ while ((pos = s.find(OPEN_TAG, endPos)) != string::npos) {
+ size_t prefixStart = pos + OPEN_TAG.length();
+ if ((endPos = s.find(CLOSE_TAG, prefixStart)) == string::npos) {
+ return s;
+ }
+
+ string fullOpen = OPEN_TAG;
+ bool fullRemove;
+ if (s.length() >= prefixStart + HTML_PREFIX.length() &&
+ s.compare(prefixStart, HTML_PREFIX.length(), HTML_PREFIX) == 0) {
+ fullOpen += HTML_PREFIX;
+ fullRemove = !html;
+ } else if (s.length() >= prefixStart + NO_HTML_PREFIX.length() &&
+ s.compare(prefixStart, NO_HTML_PREFIX.length(), NO_HTML_PREFIX) == 0) {
+ fullOpen += NO_HTML_PREFIX;
+ fullRemove = html;
+ } else {
+ endPos = prefixStart;
+ continue;
+ }
+
+ if (!fullRemove) {
+ s.erase(pos, fullOpen.length());
+ endPos -= fullOpen.length();
+ s.erase(endPos, CLOSE_TAG.length());
+ } else {
+ s.erase(pos, endPos + CLOSE_TAG.length() - pos);
+ endPos = pos;
+ }
+ }
+ return s;
+}
+
+vector< pair< string, vector<string> > > Params::GroupByCategory(const vector<string>& options) {
+ vector< pair< string, vector<string> > > groups;
+
+ pair< string, vector<string> > uncategorizedPair = make_pair("", vector<string>(options));
+ vector<string>& uncategorized = uncategorizedPair.second;
+
+ // Iterate over all categories
+ for (vector<ParamCategory>::const_iterator i = paramContainer_.categories_.begin();
+ i != paramContainer_.categories_.end();
+ i++) {
+ bool any = false;
+ // Iterate over each given option and check if it is in the category
+ for (vector<string>::const_iterator j = options.begin(); j != options.end(); j++) {
+ Param* param = Require(*j);
+ // This option was in the category
+ if (i->Items.find(param) != i->Items.end()) {
+ if (!any) {
+ any = true;
+ groups.push_back(make_pair(i->Name, vector<string>()));
+ }
+ groups.back().second.push_back(*j);
+ vector<string>::iterator iter;
+ while ((iter = find(uncategorized.begin(), uncategorized.end(), *j)) !=
+ uncategorized.end()) {
+ uncategorized.erase(iter);
+ }
+ }
+ }
+ }
+
+ if (!uncategorized.empty()) {
+ groups.insert(groups.begin(), uncategorizedPair);
+ }
+ return groups;
+}
+
+void Params::InitBoolParam(
+ const string& name,
+ bool value,
+ const string& usage,
+ const string& fileNotes,
+ bool visible
+) {
+ Add(new BoolParam(name, usage, fileNotes, visible, value));
+}
+
+void Params::InitIntParam(
+ const string& name,
+ int value,
+ int min,
+ int max,
+ const string& usage,
+ const string& fileNotes,
+ bool visible
+) {
+ Add(new IntParam(name, usage, fileNotes, visible, value, min, max));
+}
+
+void Params::InitIntParam(
+ const string& name,
+ int value,
+ const string& usage,
+ const string& fileNotes,
+ bool visible
+) {
+ Add(new IntParam(name, usage, fileNotes, visible, value));
+}
+
+void Params::InitDoubleParam(
+ const string& name,
+ double value,
+ double min,
+ double max,
+ const string& usage,
+ const string& fileNotes,
+ bool visible
+) {
+ Add(new DoubleParam(name, usage, fileNotes, visible, value, min, max));
+}
+
+void Params::InitDoubleParam(
+ const string& name,
+ double value,
+ const string& usage,
+ const string& fileNotes,
+ bool visible
+) {
+ Add(new DoubleParam(name, usage, fileNotes, visible, value));
+}
+
+void Params::InitStringParam(
+ const string& name,
+ const string& value,
+ const string& validValues,
+ const string& usage,
+ const string& fileNotes,
+ bool visible
+) {
+ Add(new StringParam(name, usage, fileNotes, visible, value,
+ StringUtils::Split(validValues, '|')));
+}
+
+void Params::InitStringParam(
+ const string& name,
+ const string& value,
+ const string& usage,
+ const string& fileNotes,
+ bool visible
+) {
+ Add(new StringParam(name, usage, fileNotes, visible, value));
+}
+
+void Params::InitArgParam(
+ const string& name,
+ const string& usage
+) {
+ Add(new ArgParam(name, usage));
+}
+
+Param* Params::Require(const string& name) {
+ Param* param = paramContainer_.Get(name);
+ if (param == NULL) {
+ throw runtime_error("Parameter '" + name + "' does not exist");
+ }
+ return param;
+}
+
+Param* Params::Get(const string& name) {
+ map<string, Param*>::iterator i = params_.find(name);
+ return (i == params_.end()) ? NULL : i->second;
+}
+
+void Params::Add(Param* param) {
+ CanModifyCheck();
+ param->ThrowIfInvalid();
+
+ string paramName = param->GetName();
+ if (!params_.insert(make_pair(paramName, param)).second) {
+ throw runtime_error("Parameter '" + paramName + "' already exists");
+ }
+ if (!param->IsArgument()) {
+ paramsOrdered_.push_back(param);
+ }
+}
+
+void Params::AddCategory(const string& name, const set<string>& params) {
+ // Validate passed in set
+ for (set<string>::const_iterator i = params.begin(); i != params.end(); i++) {
+ if (Get(*i) == NULL) {
+ throw runtime_error("Parameter '" + *i + "' does not exist");
+ }
+ }
+
+ ParamCategory* category = NULL;
+ // Check if this category already exists
+ for (vector<ParamCategory>::iterator i = categories_.begin(); i != categories_.end(); i++) {
+ if (i->Name == name) {
+ category = &*i;
+ break;
+ }
+ }
+
+ // Create new category
+ if (!category) {
+ categories_.push_back(ParamCategory(name));
+ category = &(categories_.back());
+ }
+
+ // Loop over parameters and add them to the category if they are in the passed in set
+ for (vector<const Param*>::const_iterator i = Begin(); i != End(); i++) {
+ string paramName = (*i)->GetName();
+ if (params.find(paramName) != params.end()) {
+ // Check if this parameter has already been categorized
+ for (vector<ParamCategory>::const_iterator j = categories_.begin();
+ j != categories_.end();
+ j++) {
+ if (j->Items.find(*i) != j->Items.end()) {
+ throw runtime_error("Parameter '" + paramName + "' has already been categorized");
+ }
+ }
+ // Add parameter to category
+ category->Items.insert(*i);
+ }
+ }
+}
+
+void Params::FinalizeParams() {
+ if (finalized_) {
+ return;
+ }
+
+ for (char c = 'A'; c <= 'Z'; c++) {
+ string aa = string(1, c);
+ double deltaMass = GetDouble(aa);
+ if (deltaMass != 0) {
+ ModificationDefinition::NewStaticMod(aa, deltaMass, ANY);
+ }
+ }
+
+ if (GetString("enzyme") == "no-enzyme") {
+ Set("digestion", "non-specific-digest");
+ Set("missed-cleavages", 500);
+ }
+
+ string customEnzyme = GetString("custom-enzyme");
+ if (!customEnzyme.empty()) {
+ parse_custom_enzyme(customEnzyme);
+ Set("enzyme", "custom-enzyme");
+ }
+
+ if (GetString("enzyme") == "no-enzyme") {
+ Set("digestion", "non-specific-digest");
+ } else if (GetString("digestion") == "non-specific-digest") {
+ Set("enzyme", "no-enzyme");
+ }
+
+ double new_value = GetDouble("mz-bin-width");
+// ***************************
+#ifdef _MSC_VER
+ // Peculiarities of Windows floating point handling
+ // results in us getting 0.0 here rather than Nan
+ // FIXME: is there a more portable way of checking
+ // that a floating point value has not been set?
+ if (new_value == 0.0) {
+#else
+ if (isnan(new_value)) {
+#endif
+ // If no width specified, choose based on mass type.
+ if (get_mass_type_parameter("fragment-mass") == MONO) {
+ new_value = BIN_WIDTH_MONO;
+ } else {
+ new_value = BIN_WIDTH_AVERAGE;
+ }
+
+ Set("mz-bin-width", new_value);
+ }
+// ***************************
+
+ finalized_ = true;
+}
+
+void Params::CanModifyCheck() const {
+ if (finalized_) {
+ throw runtime_error("Parameters have been finalized and cannot be modified");
+ }
+}
+
+// ***** Parameter classes ***** //
+//
+// Param (base class)
+//
+Param::Param(const string& name,
+ const string& usage,
+ const string& fileNotes,
+ bool visible)
+ : name_(name), usage_(usage), fileNotes_(fileNotes), visible_(visible) {}
+Param::~Param() {}
+string Param::GetName() const { return name_; }
+string Param::GetUsage() const { return usage_; }
+string Param::GetFileNotes() const { return fileNotes_; }
+bool Param::IsVisible() const { return visible_; }
+bool Param::IsArgument() const { return false; }
+void Param::ThrowIfInvalid() const {}
+string Param::GetParamFileString(bool defaultValue) const {
+ vector<string> lines =
+ StringUtils::Split(Params::ProcessHtmlDocTags(usage_), '\n');
+ vector<string> noteLines =
+ StringUtils::Split(Params::ProcessHtmlDocTags(fileNotes_), '\n');
+ lines.insert(lines.end(), noteLines.begin(), noteLines.end());
+ stringstream ss;
+ for (vector<string>::const_iterator i = lines.begin(); i != lines.end(); i++) {
+ vector<string> formatted = StringUtils::Split(StringUtils::LineFormat(*i, 78), '\n');
+ for (vector<string>::const_iterator j = formatted.begin(); j != formatted.end(); j++) {
+ ss << "# " << *j << endl;
+ }
+ }
+ ss << name_ << '=' << (defaultValue ? GetStringDefault() : GetString()) << endl;
+ return ss.str();
+}
+void Param::Set(bool value) {
+ throw runtime_error("Cannot set value of '" + name_ + "' from bool");
+}
+void Param::Set(int value) {
+ throw runtime_error("Cannot set value of '" + name_ + "' from int");
+}
+void Param::Set(double value) {
+ throw runtime_error("Cannot set value of '" + name_ + "' from double");
+}
+void Param::Set(const char* value) {
+ Set(string(value));
+}
+void Param::Set(const string& value) {
+ throw runtime_error("Cannot set value of '" + name_ + "' from string");
+}
+//
+// BoolParam
+//
+BoolParam::BoolParam(const string& name,
+ const string& usage,
+ const string& fileNotes,
+ bool visible,
+ bool value)
+ : Param(name, usage, fileNotes, visible), value_(value), original_(value) {}
+string BoolParam::GetAcceptedValues() const { return "T|F"; }
+bool BoolParam::IsDefault() const { return value_ == original_; }
+bool BoolParam::GetBool() const { return value_; }
+int BoolParam::GetInt() const { return IntParam::From(value_); }
+double BoolParam::GetDouble() const { return DoubleParam::From(value_); }
+string BoolParam::GetString() const { return StringParam::From(value_); }
+bool BoolParam::GetBoolDefault() const { return original_; }
+int BoolParam::GetIntDefault() const { return IntParam::From(original_); }
+double BoolParam::GetDoubleDefault() const { return DoubleParam::From(original_); }
+string BoolParam::GetStringDefault() const { return StringParam::From(original_); }
+void BoolParam::Set(bool value) { value_ = value; }
+void BoolParam::Set(int value) { value_ = From(value); }
+void BoolParam::Set(double value) { value_ = From(value); }
+void BoolParam::Set(const string& value) {
+ try {
+ value_ = From(value);
+ } catch (...) {
+ throw runtime_error("Invalid value for '" + name_ + "': " + "'" + value + "' "
+ "(expected boolean)");
+ }
+}
+bool BoolParam::From(int i) { return i != 0; }
+bool BoolParam::From(double d) { return d != 0; }
+bool BoolParam::From(string s) {
+ s = StringUtils::ToLower(s);
+ if (s == "t" || s == "true") {
+ return true;
+ } else if (s == "f" || s == "false") {
+ return false;
+ }
+ throw runtime_error("Cannot convert '" + s + "' to boolean");
+}
+//
+// IntParam
+//
+IntParam::IntParam(const string& name,
+ const string& usage,
+ const string& fileNotes,
+ bool visible,
+ int value,
+ int min,
+ int max)
+ : Param(name, usage, fileNotes, visible),
+ value_(value), original_(value), min_(min), max_(max) {}
+void IntParam::ThrowIfInvalid() const {
+ if (value_ < min_ || value_ > max_) {
+ throw runtime_error("Value of '" + name_ + "' must be between " +
+ StringUtils::ToString(min_) + " and " +
+ StringUtils::ToString(max_));
+ }
+}
+string IntParam::GetAcceptedValues() const { return "<integer>"; }
+bool IntParam::IsDefault() const { return value_ == original_; }
+bool IntParam::GetBool() const { return BoolParam::From(value_); }
+int IntParam::GetInt() const { return value_; }
+double IntParam::GetDouble() const { return DoubleParam::From(value_); }
+string IntParam::GetString() const { return StringParam::From(value_); }
+bool IntParam::GetBoolDefault() const { return BoolParam::From(original_); }
+int IntParam::GetIntDefault() const { return original_; }
+double IntParam::GetDoubleDefault() const { return DoubleParam::From(original_); }
+string IntParam::GetStringDefault() const { return StringParam::From(original_); }
+void IntParam::Set(bool value) { value_ = From(value); }
+void IntParam::Set(int value) { value_ = value; }
+void IntParam::Set(double value) { value_ = From(value); }
+void IntParam::Set(const string& value) {
+ try {
+ value_ = From(value);
+ } catch (...) {
+ throw runtime_error("Invalid value for '" + name_ + "': " + "'" + value + "' "
+ "(expected int)");
+ }
+}
+int IntParam::From(bool b) { return b ? 1 : 0; }
+int IntParam::From(double d) { return (int)d; }
+int IntParam::From(const string& s) { return StringUtils::FromString<int>(s); }
+//
+// DoubleParam
+//
+DoubleParam::DoubleParam(const string& name,
+ const string& usage,
+ const string& fileNotes,
+ bool visible,
+ double value,
+ double min,
+ double max)
+ : Param(name, usage, fileNotes, visible),
+ value_(value), original_(value), min_(min), max_(max) {}
+void DoubleParam::ThrowIfInvalid() const {
+ if (value_ < min_ || value_ > max_) {
+ throw runtime_error("Value of '" + name_ + "' must be between " +
+ StringUtils::ToString(min_) + " and " +
+ StringUtils::ToString(max_));
+ }
+}
+string DoubleParam::GetAcceptedValues() const { return "<float>"; }
+bool DoubleParam::IsDefault() const { return value_ == original_; }
+bool DoubleParam::GetBool() const { return BoolParam::From(value_); }
+int DoubleParam::GetInt() const { return IntParam::From(value_); }
+double DoubleParam::GetDouble() const { return value_; }
+string DoubleParam::GetString() const { return StringParam::From(value_); }
+bool DoubleParam::GetBoolDefault() const { return BoolParam::From(original_); }
+int DoubleParam::GetIntDefault() const { return IntParam::From(original_); }
+double DoubleParam::GetDoubleDefault() const { return original_; }
+string DoubleParam::GetStringDefault() const { return StringParam::From(original_); }
+void DoubleParam::Set(bool value) { value_ = From(value); }
+void DoubleParam::Set(int value) { value_ = From(value); }
+void DoubleParam::Set(double value) { value_ = value; }
+void DoubleParam::Set(const string& value) {
+ try {
+ value_ = From(value);
+ } catch (...) {
+ throw runtime_error("Invalid value for '" + name_ + "': " + "'" + value + "' "
+ "(expected float)");
+ }
+}
+double DoubleParam::From(bool b) { return b ? 1 : 0; }
+double DoubleParam::From(int i) { return (double)i; }
+double DoubleParam::From(const string& s) { return StringUtils::FromString<double>(s); }
+//
+// StringParam
+//
+StringParam::StringParam(const string& name,
+ const string& usage,
+ const string& fileNotes,
+ bool visible,
+ const string& value,
+ const vector<string>& validValues)
+ : Param(name, usage, fileNotes, visible),
+ original_(value), validValues_(validValues) {
+ Set(value);
+}
+void StringParam::ThrowIfInvalid() const {
+ if (!validValues_.empty() &&
+ find(validValues_.begin(), validValues_.end(), value_) == validValues_.end()) {
+ throw runtime_error("Invalid value for '" + name_ + "'; must be one of <" +
+ StringUtils::Join(validValues_, '|') + ">");
+ }
+}
+string StringParam::GetAcceptedValues() const {
+ return validValues_.empty() ? "<string>" : StringUtils::Join(validValues_, '|');
+}
+bool StringParam::IsDefault() const { return value_ == original_; }
+bool StringParam::GetBool() const { return BoolParam::From(value_); }
+int StringParam::GetInt() const { return IntParam::From(value_); }
+double StringParam::GetDouble() const { return DoubleParam::From(value_); }
+string StringParam::GetString() const { return value_; }
+bool StringParam::GetBoolDefault() const { return BoolParam::From(original_); }
+int StringParam::GetIntDefault() const { return IntParam::From(original_); }
+double StringParam::GetDoubleDefault() const { return DoubleParam::From(original_); }
+string StringParam::GetStringDefault() const { return original_; }
+void StringParam::Set(bool value) { value_ = From(value); }
+void StringParam::Set(int value) { value_ = From(value); }
+void StringParam::Set(double value) { value_ = From(value); }
+void StringParam::Set(const string& value) {
+ value_ = value != "__NULL_STR" ? value : "";
+}
+string StringParam::From(bool b) { return b ? "true" : "false"; }
+string StringParam::From(int i) { return StringUtils::ToString(i); }
+string StringParam::From(double d) { return StringUtils::ToString(d); }
+//
+// ArgParam
+//
+ArgParam::ArgParam(const string& name, const string& usage)
+ : Param(name, usage, "", false), values_(vector<string>()) {}
+string ArgParam::GetAcceptedValues() const { return "<string>"; }
+bool ArgParam::IsArgument() const { return true; }
+bool ArgParam::IsDefault() const { return false; }
+bool ArgParam::GetBool() const { return BoolParam::From(GetString()); }
+int ArgParam::GetInt() const { return StringUtils::FromString<int>(GetString()); }
+double ArgParam::GetDouble() const { return StringUtils::FromString<double>(GetString()); }
+string ArgParam::GetString() const {
+ if (values_.empty()) {
+ throw runtime_error("No value for argument '" + name_ + "'");
+ }
+ return values_.front();
+}
+bool ArgParam::GetBoolDefault() const { return false; }
+int ArgParam::GetIntDefault() const { return 0; }
+double ArgParam::GetDoubleDefault() const { return 0; }
+string ArgParam::GetStringDefault() const { return ""; }
+const vector<string>& ArgParam::GetStrings() const { return values_; }
+void ArgParam::Set(bool value) { values_ = vector<string>(1, StringParam::From(value)); }
+void ArgParam::Set(int value) { values_ = vector<string>(1, StringParam::From(value)); }
+void ArgParam::Set(double value) { values_ = vector<string>(1, StringParam::From(value)); }
+void ArgParam::Set(const string& value) { values_ = vector<string>(1, value); }
+void ArgParam::AddValue(const string& value) { values_.push_back(value); }
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/util/Params.h b/src/util/Params.h
new file mode 100644
index 0000000..faa4fe3
--- /dev/null
+++ b/src/util/Params.h
@@ -0,0 +1,399 @@
+#ifndef PARAMS_H
+#define PARAMS_H
+
+#include <ostream>
+#include <limits>
+#include <map>
+#include <set>
+#include <vector>
+
+#ifdef _MSC_VER
+// Turn off Microsoft min and max macros
+#undef max
+#undef min
+#endif
+
+class Param;
+
+class Params {
+ public:
+ Params();
+ ~Params();
+
+ // Get the value of the parameter
+ static bool GetBool(const std::string& name);
+ static int GetInt(const std::string& name);
+ static double GetDouble(const std::string& name);
+ static std::string GetString(const std::string& name);
+
+ // Get the default value of the parameter
+ static bool GetBoolDefault(const std::string& name);
+ static int GetIntDefault(const std::string& name);
+ static double GetDoubleDefault(const std::string& name);
+ static std::string GetStringDefault(const std::string& name);
+
+ // Get the values of an argument that accepts multiple values
+ static const std::vector<std::string>& GetStrings(const std::string& name);
+
+ // Get the usage statement for the parameter
+ static std::string GetUsage(const std::string& name);
+
+ // Get whether the parameter has been modified from its original value or not
+ static std::string GetFileNotes(const std::string& name);
+
+ // Get whether the parameter is visible to the user or not
+ static bool IsVisible(const std::string& name);
+
+ // Get whether the parameter is an argument or an option
+ static bool IsArgument(const std::string& name);
+
+ // Get the accepted values for the parameter
+ static std::string GetAcceptedValues(const std::string& name);
+
+ // Get whether the parameter has been modified from its original value or not
+ static bool IsDefault(const std::string& name);
+
+ // Get whether the parameter exists or not
+ static bool Exists(const std::string& name);
+
+ // Set the value of a parameter after it has been initialized
+ // Throws exception if parameter doesn't exist or parameters have been finalized
+ static void Set(const std::string& name, bool value);
+ static void Set(const std::string& name, int value);
+ static void Set(const std::string& name, double value);
+ static void Set(const std::string& name, const char* value);
+ static void Set(const std::string& name, const std::string& value);
+
+ // Add the value of an argument
+ // Throws exception if parameter has an invalid value, already exists as a non-argument,
+ // or parameters have been finalized
+ static void AddArgValue(const std::string& name, const std::string& value);
+
+ // Lock parameters and prevent them from being modified
+ static void Finalize();
+
+ // Write all contents of the ordered parameter list to file
+ static void Write(std::ostream* out, bool defaults = false);
+
+ // Get iterators for the beginning and end of the entire parameter list
+ static std::map<std::string, Param*>::const_iterator BeginAll();
+ static std::map<std::string, Param*>::const_iterator EndAll();
+
+ // Get iterators for the beginning and end of the ordered parameter list
+ static std::vector<const Param*>::const_iterator Begin();
+ static std::vector<const Param*>::const_iterator End();
+
+ // Process tags in a string
+ static std::string ProcessHtmlDocTags(std::string s, bool html = false);
+
+ // Group the given options by category
+ static std::vector< std::pair< std::string, std::vector<std::string> > > GroupByCategory(
+ const std::vector<std::string>& options);
+
+ private:
+ struct ParamCategory {
+ explicit ParamCategory(std::string name): Name(name), Items(std::set<const Param*>()) {}
+ std::string Name;
+ std::set<const Param*> Items;
+ };
+
+ // Group parameters by category
+ void Categorize();
+
+ // Initialize optional parameters
+ void InitBoolParam(
+ const std::string& name,
+ bool value,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible
+ );
+ void InitIntParam(
+ const std::string& name,
+ int value,
+ int min,
+ int max,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible
+ );
+ void InitIntParam(
+ const std::string& name,
+ int value,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible
+ );
+ void InitDoubleParam(
+ const std::string& name,
+ double value,
+ double min,
+ double max,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible
+ );
+ void InitDoubleParam(
+ const std::string& name,
+ double value,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible
+ );
+ void InitStringParam(
+ const std::string& name,
+ const std::string& value,
+ const std::string& validValues,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible
+ );
+ void InitStringParam(
+ const std::string& name,
+ const std::string& value,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible
+ );
+ void InitArgParam(
+ const std::string& name,
+ const std::string& usage
+ );
+
+ // Get a parameter by name
+ // Throws exception if the parameter doesn't exist
+ static Param* Require(const std::string& name);
+
+ // Get a parameter by name; returns NULL if the parameter doesn't exist
+ Param* Get(const std::string& name);
+
+ // Add a parameter to the container
+ // Throws exception if parameter has an invalid value, already exists,
+ // or parameters have been finalized
+ void Add(Param* param);
+
+ // Add parameter category
+ void AddCategory(const std::string& name, const std::set<std::string>& params);
+
+ // Lock parameters and prevent them from being modified
+ void FinalizeParams();
+
+ // Throw exception if the parameters have been finalized
+ void CanModifyCheck() const;
+
+ std::map<std::string, Param*> params_;
+ std::vector<const Param*> paramsOrdered_;
+ std::vector<ParamCategory> categories_;
+ bool finalized_;
+};
+
+class Param {
+ public:
+ Param(const std::string& name,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible);
+ virtual ~Param();
+
+ // Get the name of the parameter
+ std::string GetName() const;
+
+ // Get the usage statement for the parameter
+ std::string GetUsage() const;
+
+ // Get additional notes about the parameter for the parameter file
+ std::string GetFileNotes() const;
+
+ // Get whether the parameter is visible to the user or not
+ bool IsVisible() const;
+
+ // Get whether the parameter is an argument or an option
+ virtual bool IsArgument() const;
+
+ // Get whether the parameter's value is valid or not
+ virtual void ThrowIfInvalid() const;
+
+ // Get the type of the parameter
+ virtual std::string GetAcceptedValues() const = 0;
+
+ // Get whether the parameter has been modified from its original value or not
+ virtual bool IsDefault() const = 0;
+
+ // Get the value of the parameter
+ virtual bool GetBool() const = 0;
+ virtual int GetInt() const = 0;
+ virtual double GetDouble() const = 0;
+ virtual std::string GetString() const = 0;
+
+ // Get the default value of the parameter
+ virtual bool GetBoolDefault() const = 0;
+ virtual int GetIntDefault() const = 0;
+ virtual double GetDoubleDefault() const = 0;
+ virtual std::string GetStringDefault() const = 0;
+
+ // Set the value of the parameter
+ virtual void Set(bool value);
+ virtual void Set(int value);
+ virtual void Set(double value);
+ virtual void Set(const char* value);
+ virtual void Set(const std::string& value);
+
+ // Get the parameter as a string to write to a parameter file
+ virtual std::string GetParamFileString(bool defaultValue = false) const;
+ protected:
+ std::string name_, usage_, fileNotes_;
+ bool visible_;
+};
+
+class BoolParam : public Param {
+ public:
+ BoolParam(const std::string& name,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible,
+ bool value);
+ std::string GetAcceptedValues() const;
+ bool IsDefault() const;
+ bool GetBool() const;
+ int GetInt() const;
+ double GetDouble() const;
+ std::string GetString() const;
+ bool GetBoolDefault() const;
+ int GetIntDefault() const;
+ double GetDoubleDefault() const;
+ std::string GetStringDefault() const;
+ void Set(bool value);
+ void Set(int value);
+ void Set(double value);
+ void Set(const std::string& value);
+
+ static bool From(int i);
+ static bool From(double d);
+ static bool From(std::string s);
+ protected:
+ bool value_, original_;
+};
+
+class IntParam : public Param {
+ public:
+ IntParam(const std::string& name,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible,
+ int value,
+ int min = -std::numeric_limits<int>::max(),
+ int max = std::numeric_limits<int>::max());
+ std::string GetAcceptedValues() const;
+ void ThrowIfInvalid() const;
+ bool IsDefault() const;
+ bool GetBool() const;
+ int GetInt() const;
+ double GetDouble() const;
+ std::string GetString() const;
+ bool GetBoolDefault() const;
+ int GetIntDefault() const;
+ double GetDoubleDefault() const;
+ std::string GetStringDefault() const;
+ void Set(bool value);
+ void Set(int value);
+ void Set(double value);
+ void Set(const std::string& value);
+
+ static int From(bool b);
+ static int From(double d);
+ static int From(const std::string& s);
+ protected:
+ int value_, min_, max_, original_;
+};
+
+class DoubleParam : public Param {
+ public:
+ DoubleParam(const std::string& name,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible,
+ double value,
+ double min = -std::numeric_limits<double>::max(),
+ double max = std::numeric_limits<double>::max());
+ std::string GetAcceptedValues() const;
+ void ThrowIfInvalid() const;
+ bool IsDefault() const;
+ bool GetBool() const;
+ int GetInt() const;
+ double GetDouble() const;
+ std::string GetString() const;
+ bool GetBoolDefault() const;
+ int GetIntDefault() const;
+ double GetDoubleDefault() const;
+ std::string GetStringDefault() const;
+ void Set(bool value);
+ void Set(int value);
+ void Set(double value);
+ void Set(const std::string& value);
+
+ static double From(bool b);
+ static double From(int i);
+ static double From(const std::string& s);
+ protected:
+ double value_, min_, max_, original_;
+};
+
+class StringParam : public Param {
+ public:
+ StringParam(const std::string& name,
+ const std::string& usage,
+ const std::string& fileNotes,
+ bool visible,
+ const std::string& value,
+ const std::vector<std::string>& validvalues = std::vector<std::string>());
+ std::string GetAcceptedValues() const;
+ void ThrowIfInvalid() const;
+ bool IsDefault() const;
+ bool GetBool() const;
+ int GetInt() const;
+ double GetDouble() const;
+ std::string GetString() const;
+ bool GetBoolDefault() const;
+ int GetIntDefault() const;
+ double GetDoubleDefault() const;
+ std::string GetStringDefault() const;
+ void Set(bool value);
+ void Set(int value);
+ void Set(double value);
+ void Set(const std::string& value);
+
+ static std::string From(bool b);
+ static std::string From(int i);
+ static std::string From(double d);
+ protected:
+ std::string value_, original_;
+ std::vector<std::string> validValues_;
+};
+
+class ArgParam : public Param {
+ public:
+ ArgParam(const std::string& name, const std::string& usage);
+ bool IsArgument() const;
+ std::string GetAcceptedValues() const;
+ bool IsDefault() const;
+ bool GetBool() const;
+ int GetInt() const;
+ double GetDouble() const;
+ std::string GetString() const;
+ bool GetBoolDefault() const;
+ int GetIntDefault() const;
+ double GetDoubleDefault() const;
+ std::string GetStringDefault() const;
+
+ const std::vector<std::string>& GetStrings() const;
+ void Set(bool value);
+ void Set(int value);
+ void Set(double value);
+ void Set(const std::string& value);
+ void AddValue(const std::string& value);
+ protected:
+ std::vector<std::string> values_;
+};
+
+#endif
+
diff --git a/src/util/StringUtils.cpp b/src/util/StringUtils.cpp
new file mode 100644
index 0000000..eb9c17d
--- /dev/null
+++ b/src/util/StringUtils.cpp
@@ -0,0 +1,139 @@
+#include "StringUtils.h"
+
+#include "boost/algorithm/string.hpp"
+
+using namespace std;
+
+const char* StringUtils::WHITESPACE_CHARS = " \t\n\v\f\r";
+
+vector<string> StringUtils::Split(const string& s, char delimiter) {
+ return Split<string>(s, delimiter);
+}
+
+vector<string> StringUtils::Split(const string& s, const string& delimiter) {
+ return Split<string>(s, delimiter);
+}
+
+vector<string> StringUtils::Fields(const string& s) {
+ return Fields<string>(s);
+}
+
+string StringUtils::ToLower(string s) {
+ boost::to_lower(s);
+ return s;
+}
+
+string StringUtils::ToUpper(string s) {
+ boost::to_upper(s);
+ return s;
+}
+
+bool StringUtils::IEquals(const string& x, const string& y) {
+ return boost::iequals(x, y);
+}
+
+string StringUtils::Replace(string s, const string& oldSubstring, const string& newSubstring) {
+ size_t find = 0;
+ while ((find = s.find(oldSubstring, find)) != string::npos) {
+ s.replace(find, oldSubstring.length(), newSubstring);
+ find += newSubstring.length();
+ }
+ return s;
+}
+
+bool StringUtils::StartsWith(const string& s, const string& substring) {
+ return substring.length() <= s.length()
+ ? s.compare(0, substring.length(), substring) == 0
+ : false;
+}
+
+bool StringUtils::IStartsWith(const string& s, const string& substring) {
+ return StartsWith(ToLower(s), ToLower(substring));
+}
+
+bool StringUtils::EndsWith(const string& s, const string& substring) {
+ return substring.length() <= s.length()
+ ? s.compare(s.length() - substring.length(), substring.length(), substring) == 0
+ : false;
+}
+
+bool StringUtils::IEndsWith(const string& s, const string& substring) {
+ return EndsWith(ToLower(s), ToLower(substring));
+}
+
+string StringUtils::Trim(string s) {
+ boost::trim(s);
+ return s;
+}
+
+string StringUtils::LTrim(string s) {
+ boost::trim_left(s);
+ return s;
+}
+
+string StringUtils::RTrim(string s) {
+ boost::trim_right(s);
+ return s;
+}
+
+bool StringUtils::IsNumeric(const string& s, bool allowNegative, bool allowDecimal) {
+ if (s.empty()) {
+ return false;
+ }
+
+ string::const_iterator i = s.begin();
+ if (allowNegative && *i == '-') {
+ ++i;
+ }
+
+ bool foundDecimal = false;
+
+ for (; i != s.end(); ++i) {
+ if (allowDecimal && *i == '.') {
+ if (foundDecimal) {
+ // Found two decimals
+ return false;
+ }
+ foundDecimal = true;
+ } else if (!isdigit(*i)) {
+ // Found non-digit character
+ return false;
+ }
+ }
+
+ // Decimal can't be last character
+ return !foundDecimal || *(--i) == '.';
+}
+
+string StringUtils::LineFormat(string s, unsigned limit, unsigned indentSize) {
+ if (indentSize >= limit) {
+ throw runtime_error("Limit must be greater than indent size");
+ }
+ stringstream lines;
+ string indent(indentSize, ' ');
+ unsigned contentLimit = limit - indentSize;
+
+ while (s.length() > contentLimit) {
+ size_t lineEnd;
+ if (isspace(s[contentLimit])) {
+ lineEnd = s.find_last_not_of(WHITESPACE_CHARS, contentLimit);
+ } else {
+ lineEnd = s.find_last_of(WHITESPACE_CHARS, contentLimit);
+ lineEnd = (lineEnd == string::npos)
+ ? lineEnd = contentLimit - 1
+ : lineEnd = s.find_last_not_of(WHITESPACE_CHARS, lineEnd);
+ }
+ if (lineEnd == string::npos) {
+ s = LTrim(s);
+ continue;
+ }
+ lines << indent << s.substr(0, lineEnd + 1) << endl;
+ s = LTrim(s.substr(lineEnd + 2));
+ }
+ lines << indent << s;
+ return lines.str();
+}
+
+StringUtils::StringUtils() {}
+StringUtils::~StringUtils() {}
+
diff --git a/src/util/StringUtils.h b/src/util/StringUtils.h
new file mode 100644
index 0000000..5e3078b
--- /dev/null
+++ b/src/util/StringUtils.h
@@ -0,0 +1,167 @@
+#ifndef STRINGUTILS_H
+#define STRINGUTILS_H
+
+#include <iomanip>
+#include <string>
+#include <sstream>
+#include <stdexcept>
+#include <vector>
+
+class StringUtils {
+ public:
+ // Convert from a string
+ template<typename T>
+ static T FromString(const std::string& s) {
+ T out;
+ if (!TryFromString(s, &out)) {
+ throw std::runtime_error("Could not convert string '" + s + "'");
+ }
+ return out;
+ }
+
+ //Convert from a string, returning false if conversion fails
+ template<typename T>
+ static bool TryFromString(const std::string& s, T* out) {
+ std::stringstream ss(s);
+ ss >> *out;
+ return ss.eof() && !ss.fail();
+ }
+ static bool TryFromString(const std::string& s, std::string* out) {
+ *out = s;
+ return true;
+ }
+
+ // Convert to a string
+ template<typename T>
+ static std::string ToString(const T& obj, int decimals = -1, bool fixedFloat = true) {
+ std::stringstream converter;
+ if (decimals >= 0) {
+ converter << std::fixed << std::setprecision(decimals);
+ if (fixedFloat) {
+ converter << std::fixed;
+ } else {
+ converter.unsetf(std::ios_base::floatfield);
+ }
+ } else {
+ converter << std::setprecision(8);
+ }
+ converter << obj;
+ return converter.str();
+ }
+
+ // Joins a vector of strings into a single string separated by a delimiter
+ template<typename T>
+ static std::string Join(const T values, const char delimiter ='\0') {
+ std::stringstream ss;
+ for (typename T::const_iterator i = values.begin(); i != values.end(); i++) {
+ if (i != values.begin() && delimiter != '\0') {
+ ss << delimiter;
+ }
+ ss << *i;
+ }
+ return ss.str();
+ }
+
+ // Split a string on a delimiter
+ static std::vector<std::string> Split(const std::string& s, char delimiter);
+ static std::vector<std::string> Split(const std::string& s, const std::string& delimiter);
+
+ template<typename T>
+ static std::vector<T> Split(const std::string& s, char delimiter) {
+ std::vector<T> tokens;
+ std::string::const_iterator from = s.begin();
+ for (std::string::const_iterator i = from; i != s.end(); ++i) {
+ if (*i == delimiter) {
+ tokens.push_back(FromString<T>(std::string(from, i)));
+ from = i + 1;
+ }
+ }
+ tokens.push_back(FromString<T>(std::string(from, s.end())));
+ return tokens;
+ }
+
+ template<typename T>
+ static std::vector<T> Split(const std::string& s, const std::string& delimiter) {
+ std::vector<T> tokens;
+ size_t from = 0;
+ size_t find;
+ while ((find = s.find(delimiter, from)) != std::string::npos) {
+ tokens.push_back(FromString<T>(s.substr(from, find - from)));
+ from = find + delimiter.length();
+ }
+ tokens.push_back(FromString<T>(s.substr(from)));
+ return tokens;
+ }
+
+ static std::vector<std::string> Fields(const std::string& s);
+
+ template<typename T>
+ static std::vector<T> Fields(const std::string& s) {
+ std::vector<T> fields;
+ std::string current;
+ for (std::string::const_iterator i = s.begin(); i != s.end(); i++) {
+ if (*i == ' ' || *i == '\t') {
+ if (!current.empty()) {
+ fields.push_back(FromString<T>(current));
+ current.clear();
+ }
+ } else {
+ current.push_back(*i);
+ }
+ }
+ if (!current.empty()) {
+ fields.push_back(FromString<T>(current));
+ }
+ return fields;
+ }
+
+ // Convert a string to lowercase
+ static std::string ToLower(std::string s);
+
+ // Convert a string to uppercase
+ static std::string ToUpper(std::string s);
+
+ // Compare two strings without case sensitivity
+ static bool IEquals(const std::string& x, const std::string& y);
+
+ // Replace all instances of a substring with a new substring
+ static std::string Replace(
+ std::string s, const std::string& oldSubstring, const std::string& newSubstring);
+
+ // Return whether a string begins with a substring
+ static bool StartsWith(const std::string& s, const std::string& substring);
+
+ // Return whether a string starts with a substring (case insensitive)
+ static bool IStartsWith(const std::string& s, const std::string& substring);
+
+ // Return whether a string ends with a substring
+ static bool EndsWith(const std::string& s, const std::string& substring);
+
+ // Return whether a string ends with a substring (case insensitive)
+ static bool IEndsWith(const std::string& s, const std::string& substring);
+
+ // Trim whitespace from the beginning and end of a string
+ static std::string Trim(std::string s);
+
+ // Trim whitespace from the beginning of a string
+ static std::string LTrim(std::string s);
+
+ // Trim whitespace from the end of a string
+ static std::string RTrim(std::string s);
+
+ // Return whether a string is numeric
+ static bool IsNumeric(
+ const std::string& s, bool allowNegative = true, bool allowDecimal = true);
+
+ // Break a string into lines limited by length
+ static std::string LineFormat(std::string s, unsigned limit, unsigned indentSize = 0);
+
+ private:
+ static const char* WHITESPACE_CHARS;
+
+ StringUtils();
+ ~StringUtils();
+};
+
+#endif
+
diff --git a/src/util/WinCrux.cpp b/src/util/WinCrux.cpp
new file mode 100644
index 0000000..4d871e8
--- /dev/null
+++ b/src/util/WinCrux.cpp
@@ -0,0 +1,193 @@
+/**
+ * \file WinCrux.cpp
+ * \brief Support functions need to compile Crux under native windows.
+ */
+
+#include <stdlib.h>
+#include <time.h>
+#include <Winsock2.h>
+#include "carp.h"
+#include "utils.h"
+#include "WinCrux.h"
+#include <iostream>
+#include <vector>
+
+
+using namespace std;
+
+// Windows GetTimeOfDay() code from http://www.suacommunity.com/dictionary/index.php
+
+#define DELTA_EPOCH_IN_MICROSECS 11644473600000000Ui64
+
+struct timezone {
+ int tz_minuteswest; /* minutes W of Greenwich */
+ int tz_dsttime; /* type of dst correction */
+};
+
+// Definition of a gettimeofday function
+
+int gettimeofday(struct timeval *tv, struct timezone *tz) {
+// Define a structure to receive the current Windows filetime
+ FILETIME ft;
+
+// Initialize the present time to 0 and the timezone to UTC
+ unsigned __int64 tmpres = 0;
+ static int tzflag = 0;
+
+ if (NULL != tv) {
+ GetSystemTimeAsFileTime(&ft);
+
+// The GetSystemTimeAsFileTime returns the number of 100 nanosecond
+// intervals since Jan 1, 1601 in a structure. Copy the high bits to
+// the 64 bit tmpres, shift it left by 32 then or in the low 32 bits.
+ tmpres |= ft.dwHighDateTime;
+ tmpres <<= 32;
+ tmpres |= ft.dwLowDateTime;
+
+// Convert to microseconds by dividing by 10
+ tmpres /= 10;
+
+// The Unix epoch starts on Jan 1 1970. Need to subtract the difference
+// in seconds from Jan 1 1601.
+ tmpres -= DELTA_EPOCH_IN_MICROSECS;
+
+// Finally change microseconds to seconds and place in the seconds value.
+// The modulus picks up the microseconds.
+ tv->tv_sec = (long)(tmpres / 1000000UL);
+ tv->tv_usec = (long)(tmpres % 1000000UL);
+ }
+
+ if (NULL != tz) {
+ if (!tzflag) {
+ _tzset();
+ tzflag++;
+ }
+
+// Adjust for the timezone west of Greenwich
+ tz->tz_minuteswest = _timezone / 60;
+ tz->tz_dsttime = _daylight;
+ }
+
+ return 0;
+}
+
+char *realpath(const char * file_name, char * resolved_name) {
+
+ char * full_path_buffer = (char *) mymalloc(MAX_PATH * sizeof(char));
+ size_t needed_buff_size
+ = GetFullPathName(file_name, MAX_PATH, full_path_buffer, NULL);
+
+ if (needed_buff_size == 0) {
+ // An error occurred.
+ LPSTR lpMsgBuf;
+ FormatMessage(
+ FORMAT_MESSAGE_ALLOCATE_BUFFER
+ | FORMAT_MESSAGE_FROM_SYSTEM
+ | FORMAT_MESSAGE_IGNORE_INSERTS,
+ NULL,
+ GetLastError(),
+ MAKELANGID(LANG_NEUTRAL, SUBLANG_DEFAULT), // Default language
+ (LPTSTR) &lpMsgBuf,
+ 0,
+ NULL
+ );
+ carp(CARP_FATAL, lpMsgBuf);
+
+ }
+
+ if (needed_buff_size > MAX_PATH) {
+ full_path_buffer = (char *) myrealloc(full_path_buffer, needed_buff_size);
+ needed_buff_size
+ = GetFullPathName(file_name, MAX_PATH, full_path_buffer, NULL);
+ }
+
+ return full_path_buffer;
+}
+
+/*
+This code was placed in the public domain by the author,
+Sean Barrett, in November 2007. Do with it as you will.
+(Seee the page for stb_vorbis or the mollyrocket source
+page for a longer description of the public domain non-license).
+*/
+
+// Public domain code from https://mollyrocket.com/forums/viewtopic.php?p=2529
+// map 'filename' and return a pointer to it. fill out *length and *un if not-NULL
+void *stub_mmap(const char *filename, SIMPLE_UNMMAP *un) {
+ HANDLE f = CreateFile(filename, GENERIC_READ, FILE_SHARE_READ, NULL, OPEN_EXISTING, FILE_ATTRIBUTE_NORMAL, NULL);
+ HANDLE m;
+ void *p;
+ if (!f) return NULL;
+ m = CreateFileMapping(f, NULL, PAGE_READONLY, 0, 0, NULL);
+ if (!m) { CloseHandle(f); return NULL; }
+ p = MapViewOfFile(m, FILE_MAP_READ, 0, 0, 0);
+ if (!p) { CloseHandle(m); CloseHandle(f); return NULL; }
+ if (un) {
+ un->f = f;
+ un->m = m;
+ un->p = p;
+ }
+ return p;
+}
+
+void stub_unmmap(SIMPLE_UNMMAP *un) {
+ UnmapViewOfFile(un->p);
+ CloseHandle(un->m);
+ CloseHandle(un->f);
+}
+
+int scandir(
+ const char *dirname,
+ struct dirent ***namelist,
+ int (*select)(struct dirent *),
+ int (*compar)(const void *, const void *)
+) {
+ errno = 0;
+
+ DIR *directory = opendir(dirname);
+ if (!directory) {
+ return -1;
+ }
+
+ struct dirent *entry;
+ vector<struct dirent *> *entries = new vector<struct dirent *>;
+ while(entry = readdir(directory)) {
+ if (!select || select(entry)) {
+ struct dirent *valid_entry = new struct dirent;
+ copy_dirent(entry, valid_entry);
+ entries->push_back(valid_entry);
+ }
+ }
+ if (errno) {
+ return -1;
+ }
+
+ *namelist = static_cast<struct dirent **>(malloc(sizeof(struct dirent *) * entries->size()));
+ copy(entries->begin(), entries->end(), *namelist);
+
+ return entries->size();
+}
+
+int alphasort(const void *d1, const void *d2) {
+
+ // FIXME this is only a stub
+ return 0;
+}
+
+char *mkdtemp(char *temp) {
+
+ // Create temporary file name from template
+ char *dirname = _mktemp(temp);
+
+ if (dirname) {
+ // Create the directory
+ int result = _mkdir(dirname);
+ if (result < 0) {
+ free(dirname);
+ dirname = NULL;
+ }
+ }
+
+ return dirname;
+
+}
diff --git a/src/util/WinCrux.h b/src/util/WinCrux.h
new file mode 100644
index 0000000..e8d49c5
--- /dev/null
+++ b/src/util/WinCrux.h
@@ -0,0 +1,65 @@
+#ifndef WINCRUX_H
+#define WINCRUX_H
+
+#ifdef _MSC_VER
+#define WIN32_LEAN_AND_MEAN
+#include <direct.h>
+#include <fcntl.h>
+#include <io.h>
+#include <string.h>
+#include <windows.h>
+#include "utils.h"
+#include "windirent.h"
+
+// The Windows C runtime has a hard limit on the
+// number of simultaneously opened files
+#define WIN_MAX_OPEN_FILES 2048
+
+// Rename some functions to the windows version
+#define access _access
+#define pclose _pclose
+#define popen _popen
+#define chdir _chdir
+#define getcwd _getcwd
+#define mkdir(a, b) _mkdir(a)
+#define mkstemp _mktemp_s
+#define snprintf _snprintf
+
+#undef NO_ERROR
+// Turn off Microsoft min and max macros
+#undef max
+#undef min
+
+#define R_OK 04
+#define W_OK 02
+#define F_OK 00
+
+#define S_ISDIR(mode) (((mode) & S_IFMT) == S_IFDIR)
+
+int gettimeofday(struct timeval *tv, struct timezone *tz);
+char *realpath(const char * file_name, char * resolved_name);
+
+typedef struct {
+ HANDLE f;
+ HANDLE m;
+ void *p;
+} SIMPLE_UNMMAP;
+
+// map 'filename' and return a pointer to it.
+void *stub_mmap(const char *filename, SIMPLE_UNMMAP *un);
+
+// Release memory mapped file
+void stub_unmmap(SIMPLE_UNMMAP *un);
+
+int scandir(
+ const char *dirname,
+ struct dirent ***namelist,
+ int (*select)(struct dirent *),
+ int (*compar)(const void *, const void *)
+);
+
+int alphasort(const void *d1, const void *d2);
+
+#endif
+#endif
+
diff --git a/src/util/crux-utils.cpp b/src/util/crux-utils.cpp
new file mode 100644
index 0000000..6a1178f
--- /dev/null
+++ b/src/util/crux-utils.cpp
@@ -0,0 +1,1669 @@
+/**
+ * \file crux-utils.cpp
+ * \brief General-use functions for crux
+ */
+
+#include <sys/types.h>
+#include <fstream>
+#include <errno.h>
+#include <sys/stat.h>
+#ifndef _MSC_VER
+#include <unistd.h>
+#include <sys/dir.h>
+#include <dirent.h>
+#endif
+#include <iostream>
+#include "crux-utils.h"
+#include "model/Database.h"
+#include "Params.h"
+#include "parameter.h"
+#include "Params.h"
+#include "StringUtils.h"
+#include "WinCrux.h"
+#include "io/LineFileReader.h"
+#include <boost/filesystem.hpp>
+#include <boost/asio.hpp>
+#include "FileUtils.h"
+#include "crux_version.h"
+
+using namespace std;
+
+/**
+ * PRECISION, determines the precision of the compare float, users
+ * should lower the number if need more precision
+ */
+static const FLOAT_T PRECISION = 0.000000005;
+
+/**
+ * the maximum error in terms of Units in the Last Place.
+ * This specifies how big an error we are willing to accept in terms of the value of the least significant
+ * digit of the floating point numbers representation.
+ * MAX_ULPS can also be interpreted in terms of how many representable floats
+ * we are willing to accept between A and B. This function will allow MAX_ULPS-1 floats between A and B.
+ */
+static const int MAX_ULPS = 2;
+
+static const unsigned int TARGET_STRING_LENGTH = 6; //The length of string "target"
+static const unsigned int DECOY_STRING_LENGTH = 5; // The length of string "decoy"
+
+
+/* Functions for converting custom types to and from strings */
+
+static const int INVALID_ENUM_STRING = -10;
+/**
+ * The string version of the decoy types
+ */
+static const char* decoy_type_strings[NUMBER_DECOY_TYPES] = {
+ "invalid", "none", "reverse", "protein-shuffle",
+ "peptide-shuffle", "peptide-reverse"
+};
+
+DECOY_TYPE_T string_to_decoy_type(const string& name) {
+ int decoy_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ decoy_type_strings,
+ NUMBER_DECOY_TYPES);
+ if (decoy_int < 0) {
+ decoy_int = 0;
+ }
+
+ return (DECOY_TYPE_T)decoy_int;
+}
+
+DECOY_TYPE_T string_to_tide_decoy_type(const string& name) {
+ if (name == "none") {
+ return NO_DECOYS;
+ } else if (name == "shuffle") {
+ return PEPTIDE_SHUFFLE_DECOYS;
+ } else if (name == "peptide-reverse") {
+ return PEPTIDE_REVERSE_DECOYS;
+ } else if (name == "protein-reverse") {
+ return PROTEIN_REVERSE_DECOYS;
+ }
+ carp(CARP_FATAL, "Invalid decoy type %s", name.c_str());
+ return(INVALID_DECOY_TYPE); // Avoid compiler warning.
+}
+
+char* decoy_type_to_string(DECOY_TYPE_T type) {
+ return my_copy_string(decoy_type_strings[type]);
+}
+
+/**
+ * The string version of the mass format types
+ */
+static const char* mass_format_type_strings[NUMBER_MASS_FORMATS] =
+ { "invalid", "mod-only", "total", "separate" };
+
+MASS_FORMAT_T string_to_mass_format(const string& name) {
+ int mass_format_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ mass_format_type_strings,
+ NUMBER_MASS_FORMATS);
+ if (mass_format_int < 0) {
+ mass_format_int = 0;
+ }
+
+ return (MASS_FORMAT_T)mass_format_int;
+}
+
+char* mass_format_type_to_string(MASS_FORMAT_T type) {
+ return my_copy_string(mass_format_type_strings[type]);
+}
+
+/**
+ * The string version of isotopic mass type (average, mono)
+ */
+static const char* mass_type_strings[NUMBER_MASS_TYPES] = {"average", "mono"};
+
+bool string_to_mass_type(const string& name, MASS_TYPE_T* result) {
+ bool success = true;
+ //this is copied from parameter.c::get_peptide_mass_type
+ int mass_type = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ mass_type_strings, NUMBER_MASS_TYPES);
+
+ (*result) = (MASS_TYPE_T)mass_type;
+
+ if (mass_type < 0) {
+ success = false;
+ }
+ return success;
+}
+
+bool mass_type_to_string(MASS_TYPE_T type, char* type_str) {
+ bool success = true;
+ if ((int)type > NUMBER_MASS_TYPES) {
+ success = false;
+ type_str = NULL;
+ }
+
+ // type_str = mass_type_strings[type];
+ strcpy(type_str, mass_type_strings[type]);
+
+ return success;
+}
+
+// replace peptide type
+/**
+ * The string versions of digest types
+ */
+static const char* digest_type_strings[NUMBER_DIGEST_TYPES] =
+ {"invalid", "full-digest", "partial-digest", "non-specific-digest"};
+
+DIGEST_T string_to_digest_type(const string& name) {
+ int clev_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ digest_type_strings,
+ NUMBER_DIGEST_TYPES);
+ if (clev_int < 0) {
+ clev_int = 0;
+ }
+
+ return (DIGEST_T)clev_int;
+}
+
+const char* digest_type_to_string(DIGEST_T type){
+ if( (int)type > NUMBER_DIGEST_TYPES){
+ return NULL;
+ }
+
+ const char* type_str = digest_type_strings[type];
+ return type_str;
+}
+
+/**
+ * The string version of observed preprocessing types
+ */
+static const char* observed_preprocess_step_strings[NUMBER_PREPROCESS_STEPS] =
+ {"invalid", "discretize", "remove-precursor", "square-root", "remove-grass",
+ "ten-bin", "xcorr"};
+
+OBSERVED_PREPROCESS_STEP_T string_to_observed_preprocess_step(const string& name) {
+
+ int obs_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ observed_preprocess_step_strings,
+ NUMBER_PREPROCESS_STEPS);
+ if ( obs_int < 0 ){
+ obs_int = 0;
+ }
+ return (OBSERVED_PREPROCESS_STEP_T)obs_int;
+}
+
+char* observed_preproces_step_to_string(OBSERVED_PREPROCESS_STEP_T type) {
+ if ( (int)type > NUMBER_PREPROCESS_STEPS) {
+ return NULL;
+ }
+ char* obs_str = my_copy_string(observed_preprocess_step_strings[type]);
+ return(obs_str);
+}
+
+/**
+ * The string version of enzyme types
+ */
+static const char* enzyme_type_strings[NUMBER_ENZYME_TYPES] = {
+ "invalid", "no-enzyme", "trypsin", "trypsin/p", "chymotrypsin",
+ "elastase", "clostripain", "cyanogen-bromide", "iodosobenzoate",
+ "proline-endopeptidase", "staph-protease", "asp-n", "lys-c",
+ "lys-n" , "arg-c" , "glu-c" , "pepsin-a", "elastase-trypsin-chymotrypsin",
+ "custom-enzyme"
+};
+
+ENZYME_T string_to_enzyme_type(const string& name) {
+ int enz_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ enzyme_type_strings,
+ NUMBER_ENZYME_TYPES);
+ if (enz_int < 0) {
+ enz_int = 0;
+ }
+
+ return (ENZYME_T)enz_int;
+}
+
+const char* enzyme_type_to_string(ENZYME_T type){
+ if ((int)type > NUMBER_ENZYME_TYPES) {
+ return NULL;
+ }
+ const char* type_str = enzyme_type_strings[type];
+ return type_str;
+}
+
+/**
+ * The string version of mass types
+ */
+static const char* window_type_strings[NUMBER_WINDOW_TYPES] =
+ {"invalid", "mass", "mz", "ppm"};
+
+WINDOW_TYPE_T string_to_window_type(const string& name) {
+ int window_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ window_type_strings,
+ NUMBER_WINDOW_TYPES);
+ if (window_int < 0) {
+ window_int = 0;
+ }
+
+ return (WINDOW_TYPE_T)window_int;
+}
+
+/**
+ * The string version of parsimony types
+ */
+static const char* parsimony_type_strings[NUMBER_PARSIMONY_TYPES] =
+ {"invalid", "simple", "greedy", "none"};
+
+PARSIMONY_TYPE_T string_to_parsimony_type(const string& name) {
+ int parsimony_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ parsimony_type_strings,
+ NUMBER_PARSIMONY_TYPES);
+ if (parsimony_int < 0) {
+ parsimony_int = 0;
+ }
+
+ return (PARSIMONY_TYPE_T)parsimony_int;
+}
+
+/**
+ * The string version of measure types
+ */
+static const char* measure_type_strings[NUMBER_MEASURE_TYPES] =
+ {"invalid", "RAW", "SIN", "NSAF", "dNSAF", "EMPAI"};
+
+MEASURE_TYPE_T string_to_measure_type(const string& name) {
+ int measure_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ measure_type_strings,
+ NUMBER_MEASURE_TYPES);
+ if (measure_int < 0) {
+ measure_int = 0;
+ }
+
+ return (MEASURE_TYPE_T)measure_int;
+}
+
+
+char * measure_type_to_string(MEASURE_TYPE_T type) {
+ if ((int)type > NUMBER_MEASURE_TYPES) {
+ return NULL;
+ }
+
+ char * type_str = my_copy_string(measure_type_strings[type]);
+
+ return type_str;
+}
+
+/**
+ * the string version of threshold type
+ */
+static const char* threshold_type_strings[NUMBER_THRESHOLD_TYPES] = {
+ "invalid", "none", "qvalue", "custom"
+};
+
+THRESHOLD_T string_to_threshold_type(const string& name) {
+
+ int threshold_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ threshold_type_strings,
+ NUMBER_THRESHOLD_TYPES);
+
+ if ( threshold_int < 0) {
+ threshold_int = 0;
+ }
+ return (THRESHOLD_T)threshold_int;
+
+}
+
+char* threshold_type_to_string(THRESHOLD_T type) {
+ if ( (int)type > NUMBER_THRESHOLD_TYPES) {
+ return NULL;
+ }
+
+ char* type_str = my_copy_string(threshold_type_strings[type]);
+
+ return type_str;
+}
+
+/**
+ * The string version of quantification level types
+ */
+static const char* quant_level_type_strings[NUMBER_QUANT_LEVEL_TYPES] =
+ {"invalid", "peptide", "protein"};
+
+QUANT_LEVEL_TYPE_T string_to_quant_level_type(const string& name) {
+ int quant_int = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ quant_level_type_strings,
+ NUMBER_QUANT_LEVEL_TYPES);
+ if (quant_int < 0) {
+ quant_int = 0;
+ }
+ return (QUANT_LEVEL_TYPE_T)quant_int;
+}
+
+/**
+ * The string version of column types
+ */
+static const char* column_type_strings[NUMBER_COLTYPES] =
+ {"invalid", "int", "real", "string"};
+
+COLTYPE_T string_to_column_type(const string& name) {
+ int coltype_int = convert_enum_type_str(
+ name.c_str(),
+ INVALID_ENUM_STRING,
+ column_type_strings,
+ NUMBER_COLTYPES);
+
+ if (coltype_int < 0) {
+ coltype_int = 0;
+ }
+
+ return (COLTYPE_T)coltype_int;
+
+}
+
+/**
+ * The string version of comparison types
+ */
+static const char* comparison_type_strings[NUMBER_COMPARISONS] =
+ {"invalid", "lt", "lte", "eq", "gte", "gt", "neq"};
+
+COMPARISON_T string_to_comparison(const string& name) {
+ int comparison_int = convert_enum_type_str(
+ name.c_str(),
+ INVALID_ENUM_STRING,
+ comparison_type_strings,
+ NUMBER_COMPARISONS);
+
+ if (comparison_int < 0) {
+ comparison_int = 0;
+ }
+
+ return (COMPARISON_T)comparison_int;
+
+}
+
+/*
+ * The string version of ion types
+ */
+static const char* ion_type_strings[NUMBER_ION_TYPES] = {
+ "a", "b", "c", "x", "y", "z", "p", "by", "bya", "all" };
+
+bool string_to_ion_type(const string& name, ION_TYPE_T* result) {
+ bool success = true;
+ int ion_type = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ ion_type_strings, NUMBER_ION_TYPES);
+ (*result) = (ION_TYPE_T)ion_type;
+ if (ion_type < 0) {
+ success = false;
+ }
+ return success;
+}
+
+bool ion_type_to_string(ION_TYPE_T type,
+ char* type_str) {
+ bool success = true;
+ if ((int)type > NUMBER_ION_TYPES) {
+ success = false;
+ type_str = NULL;
+ }
+ strcpy(type_str, ion_type_strings[type]);
+ return success;
+}
+
+/*
+ * The string version of ALGORITHM_TYPE_T
+ */
+static const char* algorithm_type_strings[NUMBER_ALGORITHM_TYPES] = {
+ "percolator", "rczar", "curve-fit",
+ "none", "all", "q-ranker"
+};
+
+bool string_to_algorithm_type(char* name, ALGORITHM_TYPE_T* result) {
+ bool success = true;
+
+ int algorithm_type = convert_enum_type_str(name, INVALID_ENUM_STRING,
+ algorithm_type_strings,
+ NUMBER_ALGORITHM_TYPES);
+ *result = (ALGORITHM_TYPE_T)algorithm_type;
+ if (algorithm_type < 0) {
+ success = false;
+ }
+ return success;
+}
+
+bool algorithm_type_to_string(ALGORITHM_TYPE_T type, char* type_str) {
+ bool success = true;
+ if ((int)type > NUMBER_ALGORITHM_TYPES) {
+ success = false;
+ type_str = NULL;
+ }
+ strcpy(type_str, algorithm_type_strings[type]);
+ return success;
+}
+
+/*
+ * The string version of HARDKLOR_ALGORITHM_T
+ */
+static const char* hardklor_algorithm_type_strings[NUMBER_HK_ALGORITHM_TYPES] = {
+ "invalid", "basic", "fewest-peptides", "fast-fewest-peptides",
+ "fewest-peptides-choice", "fast-fewest-peptides-choice"
+};
+
+static const char* hardklor_hardklor_algorithm_type_strings[NUMBER_HK_ALGORITHM_TYPES] = {
+ "invalid", "Basic", "FewestPeptides", "FastFewestPeptides",
+ "FewestPeptidesChoice", "FastFewestPeptidesChoice"
+};
+
+HARDKLOR_ALGORITHM_T string_to_hardklor_algorithm_type(const string& name) {
+ int hk_algorithm = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ hardklor_algorithm_type_strings, NUMBER_HK_ALGORITHM_TYPES);
+
+ if (hk_algorithm < 0) {
+ hk_algorithm = 0;
+ }
+
+ return (HARDKLOR_ALGORITHM_T)hk_algorithm;
+}
+
+string hardklor_hardklor_algorithm_type_to_string(
+ HARDKLOR_ALGORITHM_T type
+) {
+ return string(hardklor_hardklor_algorithm_type_strings[type]);
+}
+
+char* ion_type_to_string(ION_TYPE_T type) {
+
+ char* type_str = my_copy_string(ion_type_strings[type]);
+ return type_str;
+
+}
+
+
+/*
+ * The string version of SCORER_TYPE_T
+ */
+static const char* scorer_type_strings[NUMBER_SCORER_TYPES] = {
+ "spscore",
+ "xcorr_score",
+ "evalue_score",
+
+ "xcorr first",
+ "xcorr second",
+
+ "decoy_xcorr_qvalue",
+ "decoy_xcorr_peptide_qvalue",
+ "decoy_xcorr_PEP",
+
+ "decoy_evalue_qvalue",
+ "decoy_evalue_peptide_qvalue",
+ "decoy_evalue_pep",
+
+ "logp_weibull_xcorr",
+ "logp_bonf_weibull_xcorr",
+ "logp_qvalue_weibull_xcorr",
+ "logp_weibull_PEP",
+ "logp_peptide_qvalue_weibull",
+
+ "percolator_score",
+ "percolator_qvalue",
+ "percolator_peptide_qvalue",
+ "percolator_PEP",
+
+ "qranker_score",
+ "qranker_qvalue",
+ "qranker_peptide_qvalue",
+ "qranker_PEP",
+
+ "barista_score",
+ "barista_qvalue",
+ "barista_peptide_qvalue",
+ "barista_PEP",
+
+ "deltacn",
+ "deltalcn",
+ "by_ions_matched",
+ "by_ions_total",
+ "exact_pvalue",
+ "refactored_xcorr"
+};
+
+bool string_to_scorer_type(const string& name, SCORER_TYPE_T* result) {
+ bool success = true;
+ int scorer_type = convert_enum_type_str(name.c_str(), INVALID_ENUM_STRING,
+ scorer_type_strings,
+ NUMBER_SCORER_TYPES);
+ *result = (SCORER_TYPE_T)scorer_type;
+ if (scorer_type < 0) {
+ success = false;
+ }
+ return success;
+}
+
+const char* scorer_type_to_string(SCORER_TYPE_T type) {
+ if ((int)type > NUMBER_SCORER_TYPES) {
+ return NULL;
+ }
+ return scorer_type_strings[type];
+}
+
+
+/**
+ * returns a heap allocated copy of the src string
+ */
+char* my_copy_string(const char* src) {
+ if (src == NULL) {
+ return NULL;
+ }
+ int length = strlen(src) +1; // +\0
+ char* copy =
+ (char *)mymalloc(sizeof(char)*length);
+ return strncpy(copy, src, length);
+}
+
+/**
+ * Returns copy of the src string upto the specified length.
+ * Includes a null terminating character.
+ * The string is heap allocated; thus, user must free.
+ */
+char* copy_string_part(const char* src, int length) {
+ char* copy = (char*)mycalloc(length+1, sizeof(char));
+ strncpy(copy, src, length);
+ copy[length] = '\0';
+ return copy;
+}
+
+/**
+ * \returns the 0 if equal, 1 if float_a is larger, -1 if float_b is larger
+ * compare the absolute value of the difference of two numbers with an
+ * appropriate epsilon to get relations.
+ * Multiplying the epsilon by sum of the comparands adjusts the comparison
+ * to the range of the numbers, allowing a single epsilon to be used for many,
+ * or perhaps all compares.
+ */
+/*inline*/ int compare_float(FLOAT_T float_a, FLOAT_T float_b) {
+ FLOAT_T EPSILON = PRECISION;
+ FLOAT_T sum = float_a + float_b;
+ if (fabsf(float_a - float_b) <= fabsf(sum)* EPSILON) { // a == b
+ return 0;
+ } else if ((float_a - float_b) > fabsf(sum)* EPSILON) { // a > b
+ return 1;
+ } else { // a < b
+ return -1;
+ }
+}
+
+/**
+ * Compares two numbers and returns true if when rounded to the given
+ * precision they are equal. Otherwise, returns false.
+ * E.g. is_equal(0.10, 0.14, 1) -> true. is_equal(0.10, 0.15, 1) -> false
+ */
+bool is_equal(FLOAT_T a, FLOAT_T b, int precision) {
+ a = (a * pow((FLOAT_T) 10.0, (FLOAT_T) precision)) + 0.5;
+ b = (b * pow((FLOAT_T) 10.0, (FLOAT_T) precision)) + 0.5;
+ return (int)a == (int)b;
+}
+
+/**
+ * parses the filename and path
+ * returns an array A, with A[0] the filename and A[1] the path to the filename
+ * returns A[1] NULL if only a filename was passed in
+ * ex) ../../file_name => returns filename , ../../
+ * file_name => returns filename, NULL
+ *\returns A heap allocated array of both filename and path
+ */
+char** parse_filename_path(const string& file) {
+ int len = file.length();
+ int end_idx = len;
+ int end_path = -1; // index of where the last "/" is located
+ char* path = NULL;
+ char* filename = NULL;
+ char** result = (char**)mycalloc(2, sizeof(char*));
+
+ for (; end_idx > 0; --end_idx) {
+ if (file[end_idx - 1] == '/') {
+ end_path = end_idx;
+ break;
+ }
+ }
+ // copy path, if there is a "/" in the file
+ if (end_path != -1) {
+ path = copy_string_part(file.c_str(), end_path);
+ }
+ // copy filename
+ filename = copy_string_part(&(file.c_str()[end_idx]), len);
+
+ // set result with filename and path
+ result[0] = filename;
+ result[1] = path;
+
+ return result;
+}
+
+/**
+ * \brief Parses the filename, path, and file extension of given string.
+ *
+ * The array returned, A, contains the filename (A[0]) striped of the
+ * given file extension and the path (A[1]). If extension is NULL,
+ * strips all characters after the last "." from the filename. Use
+ * parse_filename_path() to return filename with extension.
+ * Returned path is NULL if no "/" in given name.
+ * extension. e.g. Given "../../filname.ext" and ".ext" returns
+ * A[0]="filename" A[1]="../../". Given "filename" returns A[0] =
+ * NULL and A[1] = "filename".
+ *
+ * \returns A heap allocated array of filename striped of extension and
+ * path.
+ */
+char** parse_filename_path_extension(
+ const char* file, ///< filename and path to parse -in
+ const char* extension ///< extension to look for (includes leading .) --in
+) {
+
+ carp(CARP_DETAILED_DEBUG, "Given path/file %s and ext %s", file, extension);
+ char** file_path_array = parse_filename_path(file);
+ char* trimmed_filename = file_path_array[0];
+
+ // look for extension
+ if (extension != NULL) {
+ carp(CARP_DETAILED_DEBUG, "File trimmed of path is %s", trimmed_filename);
+ if (!StringUtils::EndsWith(trimmed_filename, extension)) {
+ return file_path_array; // extension not found, don't change filename
+ }
+
+ int file_len = strlen(trimmed_filename);
+ int ext_len = strlen(extension);
+ // after comparing the whole extension, it matched
+ trimmed_filename[file_len - ext_len] = '\0';
+
+ } else { // find the last "."
+ char* dot = strrchr(trimmed_filename, '.');
+ if (dot != NULL) {
+ *dot = '\0';
+ }
+ }
+
+ carp(CARP_DETAILED_DEBUG, "Final trimmed filename %s", trimmed_filename);
+
+
+ return file_path_array;
+}
+
+/**
+ * parses the filename
+ * ex) ../../file_name => returns filename
+ *\returns A heap allocated array of filename
+ */
+char* parse_filename(const char* file) {
+ int len = strlen(file);
+ int end_idx = len;
+ int end_path = -1; // index of where the last "/" is located
+ char* filename = NULL;
+
+ for (; end_idx > 0; --end_idx) {
+ if (strncmp(&file[end_idx - 1], "/", 1) == 0) {
+ end_path = end_idx;
+ break;
+ }
+ }
+
+ // copy filename
+ filename = copy_string_part(&file[end_path], len);
+
+ return filename;
+}
+
+/**
+ * convert the integer into a string
+ * \returns a heap allocated string
+ */
+char* int_to_char(unsigned int i) {
+ unsigned int digit = i / 10;
+ char* int_string = (char*)mycalloc(digit+2, sizeof(char));
+ sprintf(int_string, "%d", i);
+ return int_string;
+}
+
+/**
+ * convert the integer into a string
+ * \returns a heap allocated string
+ */
+char* signed_int_to_char(int i) {
+ int digit = abs(i)/ 10;
+ char* int_string = (char*)mycalloc(digit+2, sizeof(char));
+ sprintf(int_string, "%d", i);
+ return int_string;
+}
+
+/**
+ * given two strings return a concatenated third string
+ * \returns a heap allocated string that concatenates the two inputs
+ */
+char* cat_string(const char* string_one, const char* string_two) {
+ int len_one = strlen(string_one);
+ int len_two = strlen(string_two);
+
+ char* result = (char*)mycalloc(len_one + len_two + 1, sizeof(char));
+ strncpy(result, string_one, len_one);
+ strncpy(&result[len_one], string_two, len_two);
+ return result;
+}
+
+/**
+ * Adds the fileroot parameter to a string as a prefix.
+ */
+string prefix_fileroot_to_name(const string& name) {
+ string fileroot = Params::GetString("fileroot");
+ return (fileroot.empty()) ? name : fileroot + '.' + name;
+}
+
+/**
+ * \returns the filepath 'output_dir'/'fileroot'.'filename'
+ */
+string make_file_path(
+ const string& filename ///< the name of the file
+ ) {
+ string output_directory = Params::GetString("output-dir");
+ string fileroot = Params::GetString("fileroot");
+
+ ostringstream name_builder;
+ name_builder << output_directory;
+
+ if (output_directory[output_directory.length() - 1] != '/' ) {
+ name_builder << "/";
+ }
+
+ if (!fileroot.empty()) {
+ name_builder << fileroot << ".";
+ }
+
+ name_builder << filename;
+
+ return name_builder.str();
+}
+
+/**
+ * Given the path and the filename return a file with path
+ * "path/filename". Returns filename unchanged if path = NULL.
+ * \returns a heap allocated string, "path/filename"
+ */
+char* get_full_filename(const char* path, const char* filename) {
+ char* result = NULL;
+ if (path == NULL || strlen(path) == 0) {
+ result = my_copy_string(filename);
+ } else {
+ // TODO (BF 26-Feb-08) don't add second / if path already ends in /
+ char* ready_path = cat_string(path, "/");
+ result = cat_string(ready_path, filename);
+ free(ready_path);
+ }
+ return result;
+}
+
+/**
+ * returns the file size of the given filename
+ */
+long get_filesize(char *FileName) {
+ struct stat file;
+ // return file size
+ if (!stat(FileName, &file)) {
+ return file.st_size;
+ }
+ return 0;
+}
+
+/**
+ * \brief A function for creating a directory to hold output files from crux.
+ *
+ * Tries to create a the named directory for use as the output directory for crux.
+ * If the overwrite option is true, an existing directory wtih that
+ * name will not cause an error.
+ *
+ * \returns 0 if successful, -1 if an error occured.
+*/
+int create_output_directory(
+ const string& output_folder, // Name of output folder.
+ bool overwrite // Whether or not to overwrite an existing dir
+) {
+ int result = -1;
+ bool path_is_directory = false;
+ bool path_exists = false;
+ struct stat stat_buffer;
+
+ // Does the output directory alredy exist?
+ if (stat(output_folder.c_str(), &stat_buffer)) {
+ if (errno == ENOENT) {
+ // stat failed because the path doesn't exist.
+ path_exists = false;
+ path_is_directory = false;
+ } else {
+ // stat failed for some other reason
+ carp(
+ CARP_ERROR,
+ "Unable to check for status of output directory '%s': %s.\n",
+ output_folder.c_str(),
+ strerror(errno)
+ );
+ result = -1;
+ }
+ } else {
+ path_exists = true;
+ path_is_directory = S_ISDIR(stat_buffer.st_mode);
+ }
+
+ if (path_exists) {
+ if (!path_is_directory) {
+ carp(CARP_ERROR,
+ "A non-directory file named '%s' already exists,\n"
+ "so that name can't be used for an output directory.\n",
+ output_folder.c_str());
+ result = -1;
+ } else {
+ if (!overwrite) {
+ carp(CARP_WARNING,
+ "The output directory '%s' already exists.\nExisting files will not"
+ " be overwritten.", output_folder.c_str());
+ result = 0;
+ } else {
+ carp(CARP_WARNING,
+ "The output directory '%s' already exists.\nExisting files will be overwritten.",
+ output_folder.c_str());
+ result = 0;
+ }
+ }
+ } else {
+ // The directory doesn't exist, so we can create it.
+ // Does this accomodate the case where one or more of the
+ // parent directories doesn't exit?
+ int dir_access = S_IRWXU + S_IRWXG + S_IRWXO;
+ if (!boost::filesystem::create_directories(output_folder)) {
+ // mkdir failed
+ carp(CARP_ERROR, "Unable to create output directory '%s': %s.\n",
+ output_folder.c_str(), strerror(errno));
+ result = -1;
+ } else {
+ result = 0;
+ carp(CARP_INFO, "Writing results to output directory '%s'.", output_folder.c_str());
+ }
+ }
+ return result;
+}
+
+/**
+ * \brief Take a filename, strip its leading path information (if
+ * any) and file extension (if any). Tries all file extensions until
+ * one is found. Add a new path (if given) and a new suffix (exension).
+ *
+ * If given ../dir/filename.ext, [.txt, .ext, t], .new-ext, otherdir
+ * would return otherdir/filename.new-ext
+ * \returns A heap allocated filename
+ */
+char* generate_name_path(
+ const char* filename,
+ vector<const char*> old_suffixes,
+ const char* new_suffix,
+ const char* new_path
+) {
+ // check the filename for the extension. Use the first that matches
+ for (size_t suffix_idx = 0; suffix_idx < old_suffixes.size(); suffix_idx++) {
+ if (StringUtils::IEndsWith(filename, old_suffixes[suffix_idx])) {
+ return generate_name_path(filename, old_suffixes[suffix_idx],
+ new_suffix, new_path);
+ }
+ }
+ // if we got to here, none of the suffixes were found, so it
+ // doesn't matter which we use
+ return generate_name_path(filename, "", new_suffix, new_path);
+
+}
+
+/**
+ * \brief Take a filename, strip its leading path information (if
+ * any) and file extension (if any). Add a new path (if given) and a
+ * new suffix (exension).
+ *
+ * If given ../dir/filename.ext, .new-ext, .ext, otherdir would return
+ * otherdir/filename.new-ext
+ * \returns A heap allocated filename
+ */
+char* generate_name_path(
+ const char* filename,
+ const char* old_suffix,
+ const char* new_suffix,
+ const char* new_path
+) {
+ carp(CARP_DEBUG, "Generate name given filename '%s', old suffix '%s', " \
+ "new suffix '%s', new path '%s'",
+ filename, old_suffix, new_suffix, new_path);
+
+ // parse path, filename, extension
+ char** name_path = parse_filename_path_extension(filename, old_suffix);
+
+ // add the extension
+ char* new_name = cat_string(name_path[0], new_suffix);
+
+ // add path to new filename
+ char* full_new_name = get_full_filename(new_path, new_name);
+
+ // cleanup
+ free(name_path[0]);
+ free(name_path[1]);
+ free(name_path);
+ free(new_name);
+
+ carp(CARP_DEBUG, "Final name is '%s'", full_new_name);
+ return full_new_name;
+}
+/**
+ * given a fasta_file name it returns a name with the name_tag add to the end
+ * Suffix may be NULL
+ * format: suffix_myfasta_nameTag
+ * \returns A heap allocated file name of the given fasta file
+ */
+char* generate_name(
+ const char* fasta_filename,
+ const char* name_tag,
+ const char* file_extension,
+ const char* suffix
+) {
+ int len = strlen(fasta_filename);
+ int end_path = len; // index of where the "." is located in the file
+ char* name = NULL;
+ char* after_suffix = NULL;
+ int suffix_length = 0;
+ char** file_n_path = NULL;
+ int length = 0;
+
+ // cut off the file extension if needed
+ int end_idx;
+ for (end_idx = len; end_idx > 0; --end_idx) {
+ if (strcmp(&fasta_filename[end_idx - 1], file_extension) == 0) {
+ end_path = end_idx - 1;
+ break;
+ }
+ }
+
+ // check suffix
+ if (suffix != NULL) {
+ suffix_length = strlen(suffix);
+ file_n_path = parse_filename_path(fasta_filename);
+ }
+
+ name = (char*)mycalloc(
+ suffix_length + end_path + strlen(name_tag) + 1, sizeof(char));
+ after_suffix = name;
+
+ // if suffix exit add to top
+ if (suffix_length != 0) {
+ length = strlen(file_n_path[1]);
+ if (file_n_path[1] != NULL) {
+ strncpy(name, file_n_path[1], length);
+ after_suffix = &name[length];
+ }
+ strncpy(after_suffix, suffix, suffix_length);
+ after_suffix = &after_suffix[suffix_length];
+
+ length = strlen(file_n_path[0]);
+
+ strncpy(after_suffix, file_n_path[0], (length - (len-end_path)));
+ after_suffix = &after_suffix[(length - (len-end_path))];
+
+ free(file_n_path[0]);
+ free(file_n_path[1]);
+ free(file_n_path);
+ } else {
+ strncpy(after_suffix, fasta_filename, end_path);
+ }
+
+ strcat(after_suffix, name_tag);
+ return name;
+}
+
+/**
+ * checks if each AA is an AA
+ *\returns true if sequence is valid else, false
+ */
+bool valid_peptide_sequence(const string& sequence) {
+ for (string::const_iterator i = sequence.begin(); i != sequence.end(); i++) {
+ if (!isupper(*i)) {
+ return false;
+ }
+ }
+ return true;
+}
+
+/**
+ * \brief Open and create a file of the given name in the given
+ * directory.
+ *
+ * Assumes the directory exists. Fails if file can't be opened or if
+ * file exists and overwrite is false.
+ *\returns A file handle to the newly created file.
+ */
+FILE* create_file_in_path(
+ const string& filename, ///< the filename to create & open -in
+ const string& directory, ///< the directory to open the file in -in
+ bool overwrite ///< replace file (T) or die if exists (F)
+) {
+ char* file_full_path = get_full_filename(directory.c_str(), filename.c_str());
+ // FIXME CEG consider using stat instead
+ FILE* file = fopen(file_full_path, "rb"); //to test if file exists
+ if (file != NULL) {
+ //The file exists, are we allowed to overwrite it?
+ fclose(file);
+ file = NULL;
+ if (!overwrite) {
+ // Not allowed to overwrite, we must die.
+ carp(CARP_FATAL,
+ "The file '%s' already exists and cannot be overwritten. "
+ "Use --overwrite T to replace or choose a different output file name",
+ file_full_path);
+ } else {
+ // Allowed to overwrite, send warning message.
+ carp(CARP_WARNING,
+ "The file '%s' already exists and will be overwritten.", file_full_path);
+ }
+ }
+
+ file = fopen(file_full_path, "wb+"); //read and write, replace existing
+
+ if (file == NULL) {
+ carp(CARP_FATAL, "Failed to create and open file: %s", file_full_path);
+ }
+
+ free(file_full_path);
+
+ return file;
+}
+
+ofstream* create_stream_in_path(
+ const char* filename, ///< the filename to create & open -in
+ const char* directory, ///< the directory to open the file in -in
+ bool overwrite ///< replace file (T) or die if exists (F)
+) {
+ char* file_full_path = get_full_filename(directory, filename);
+ // FIXME CEG consider using stat instead
+ FILE* file = fopen(file_full_path, "rb"); //to test if file exists
+ if (file != NULL) {
+ //The file exists, are we allowed to overwrite it?
+ fclose(file);
+ file = NULL;
+ if (!overwrite) {
+ // Not allowed to overwrite, we must die.
+ carp(CARP_FATAL,
+ "The file '%s' already exists and cannot be overwritten. "
+ "Use --overwrite T to replace or choose a different output file name",
+ file_full_path);
+ } else {
+ // Allowed to overwrite, send warning message.
+ carp(CARP_WARNING,
+ "The file '%s' already exists and will be overwritten.", file_full_path);
+ }
+ }
+
+ ofstream* fout = new ofstream(file_full_path);
+
+ if (fout == NULL) {
+ carp(CARP_FATAL, "Failed to create and open file: %s", file_full_path);
+ }
+ free(file_full_path);
+ return fout;
+}
+
+bool get_first_last_scan_from_string(
+ const std::string& const_scans_string,
+ int& first_scan,
+ int& last_scan
+ ) {
+
+ set<int> scans;
+
+ if (get_scans_from_string(const_scans_string, scans)) {
+ first_scan = *(scans.begin()++);
+ last_scan = *(scans.rbegin()++);
+ carp(CARP_DEBUG, "scan string:%s %i %i", const_scans_string.c_str(), first_scan, last_scan);
+ return true;
+ } else {
+ return false;
+ }
+}
+
+bool get_scans_from_string(
+ const string& const_scans_string,
+ set<int>& scans) {
+ scans.clear();
+
+ //first tokenize by comma.
+ vector<string> tokens_comma = StringUtils::Split(const_scans_string, ',');
+ if (tokens_comma.size() > 1) {
+ carp_once(CARP_WARNING, "Multiple scans detected in line %s. "
+ "Crux currently only handles "
+ "first_scan - last_scan properly", const_scans_string.c_str());
+ }
+ int temp_scan;
+
+ for (size_t idx1 = 0; idx1 < tokens_comma.size(); idx1++) {
+ string current = tokens_comma[idx1];
+ if (current.find("-") == string::npos) {
+ if (StringUtils::TryFromString(current, &temp_scan)) {
+ scans.insert(temp_scan);
+ } else {
+ carp(CARP_ERROR, "Error parsing scans line:%s", const_scans_string.c_str());
+ return false;
+ }
+ } else {
+ vector<string> tokens_dash = StringUtils::Split(tokens_comma[idx1], '-');
+ if (tokens_dash.size() != 2) {
+ carp(CARP_ERROR, "Error parsing scans line:%s here:%s",
+ const_scans_string.c_str(), tokens_comma[idx1].c_str());
+ return false;
+ }
+ int temp_scan2;
+ bool success = StringUtils::TryFromString(tokens_dash[0], &temp_scan);
+ success &= StringUtils::TryFromString(tokens_dash[1], &temp_scan2);
+ if (!success || temp_scan > temp_scan2) {
+ carp(CARP_ERROR, "Error parsing scans line:%s here: %s",
+ const_scans_string.c_str(), tokens_comma[idx1].c_str());
+ }
+ for (int idx3 = temp_scan;idx3 <= temp_scan2 ; idx3++) {
+ scans.insert(idx3);
+ }
+ }
+ }
+ return true;
+}
+
+/**
+ * User define our upper and our lower bounds.
+ * The random number will always be
+ * between low and high, inclusive.
+ * There is no seeding in this function, user must do it for themselves
+ *\returns a random number between the interval user provides
+ */
+int get_random_number_interval(
+ int low, ///< the number for lower bound -in
+ int high ///< the number for higher bound -in
+) {
+ return (myrandom_limit(high - low + 1) + low);
+}
+
+/**
+ *\returns the number of digits in the number
+ */
+int get_number_digits(
+ int number ///< the number to count digits
+) {
+ int idx = 0;
+ for (; number >= 10; ++idx) {
+ number = number/10;
+ }
+ return ++idx;
+}
+
+void swap_quick(
+ FLOAT_T* a,
+ int idx,
+ int jdx
+) {
+ FLOAT_T temp = 0;
+ temp = a[idx];
+ a[idx] = a[jdx];
+ a[jdx] = temp;
+}
+
+long Random(int i, int j) {
+ return i + myrandom_limit(j-i+1);
+}
+
+void quick_sort(FLOAT_T a[], int left, int right) {
+ int last = left, i;
+
+ if (left >= right) return;
+
+ swap_quick(a, left, Random(left, right));
+ for (i = left + 1; i <= right; i++) {
+ if (a[i] > a[left]) { /// CHECK THIS!!
+ swap_quick(a, ++last, i);
+ }
+ }
+ swap_quick(a, left, last);
+ quick_sort(a, left, last-1);
+ quick_sort(a, last+1, right);
+}
+
+void quicksort(FLOAT_T a[], int array_size) {
+ quick_sort(a, 0, array_size - 1);
+}
+
+/**
+ * \brief Shuffle an array of floats. Uses the Knuth algorithm. Uses
+ * get_random_number_interval() to generate random numbers.
+ */
+void shuffle_floats(FLOAT_T* array, int size) {
+ if (array == NULL) {
+ carp(CARP_ERROR, "Cannot shuffle NULL array.");
+ return;
+ }
+ int idx, switch_idx;
+ int last_element_idx = size - 1;
+ FLOAT_T temp_value;
+ for (idx = 0; idx < size; idx++) {
+ switch_idx = get_random_number_interval(idx, last_element_idx);
+ temp_value = array[idx];
+ array[idx] = array[switch_idx];
+ array[switch_idx] = temp_value;
+ }
+}
+
+/**
+ * Fits a three-parameter Weibull distribution to the input data.
+ * Implementation of Weibull distribution parameter estimation from
+ * http:// www.chinarel.com/onlincebook/LifeDataWeb/rank_regression_on_y.htm
+ * \returns eta, beta, c (which in this case is the amount the data should
+ * be shifted by) and the best correlation coefficient
+ */
+void fit_three_parameter_weibull(
+ FLOAT_T* data, ///< the data to be fit -in
+ int fit_data_points, ///< the number of data points to fit -in
+ int total_data_points, ///< the total number of data points to fit -in
+ FLOAT_T min_shift, ///< the minimum shift to allow -in
+ FLOAT_T max_shift, ///< the maximum shift to allow -in
+ FLOAT_T step, ///< step for shift -in
+ FLOAT_T corr_threshold, ///< minimum correlation, else no fit -in
+ FLOAT_T* eta, ///< the eta parameter of the Weibull dist -out
+ FLOAT_T* beta, ///< the beta parameter of the Weibull dist -out
+ FLOAT_T* shift, ///< the best shift -out
+ FLOAT_T* correlation ///< the best correlation -out
+) {
+ FLOAT_T correlation_tolerance = 0.1;
+
+ FLOAT_T best_eta = 0.0;
+ FLOAT_T best_beta = 0.0;
+ FLOAT_T best_shift = 0.0;
+ FLOAT_T best_correlation = 0.0;
+
+ FLOAT_T cur_eta = 0.0;
+ FLOAT_T cur_beta = 0.0;
+ FLOAT_T cur_correlation = 0.0;
+ FLOAT_T cur_shift = 0.0;
+
+ for (cur_shift = max_shift; cur_shift > min_shift ; cur_shift -= step) {
+
+ fit_two_parameter_weibull(data, fit_data_points, total_data_points,
+ cur_shift, &cur_eta, &cur_beta, &cur_correlation);
+ //According to the definition of the weibull distribution,
+ //https://en.wikipedia.org/wiki/Weibull_distribution
+ //the eta and beta parameters both have to be >0.
+ //Put in a check here so that any fit needs to satisfy these constraints
+ //In order to be considered.
+ //SJM 2016_03_03
+ if (cur_beta > 0 && cur_eta > 0 && cur_correlation > best_correlation){
+ best_eta = cur_eta;
+ best_beta = cur_beta;
+ best_shift = cur_shift;
+ best_correlation = cur_correlation;
+ } else if (cur_correlation < best_correlation - correlation_tolerance) {
+ break;
+ }
+ }
+
+ // Only store the parameters if the fit was good enough.
+ *correlation = best_correlation;
+ if (best_correlation >= corr_threshold) {
+ *eta = best_eta;
+ *beta = best_beta;
+ *shift = best_shift;
+ } else {
+ *eta = 0.0;
+ *beta = 0.0;
+ *shift = 0.0;
+ }
+ carp(CARP_DEBUG, "e:%g b:%g s:%g c:%g", *eta, *beta, *shift, *correlation);
+}
+
+/**
+ * Fits a two-parameter Weibull distribution to the input data.
+ *
+ * Called by the three parameter weibull fitting function to see if
+ * the proposed shift gives the best correlation. If there are too
+ * few data points, sets correlation to 0 (minimum value).
+ * http:// www.chinarel.com/onlincebook/LifeDataWeb/rank_regression_on_y.htm
+ * \returns eta, beta and the correlation coefficient.
+ */
+void fit_two_parameter_weibull(
+ FLOAT_T* data, ///< the data to be fit. should be in descending order -in
+ int fit_data_points, ///< the number of data points to fit -in
+ int total_data_points, ///< the total number of data points -in
+ FLOAT_T shift, ///< the amount by which to shift our data -in
+ FLOAT_T* eta, ///< the eta parameter of the Weibull dist -out
+ FLOAT_T* beta, ///< the beta parameter of the Weibull dist -out
+ FLOAT_T* correlation ///< the best correlation -out
+) {
+ FLOAT_T* X = (FLOAT_T*)mymalloc(sizeof(FLOAT_T) * fit_data_points); //hold data here
+
+ // transform data into an array of values for fitting
+ // shift (including only non-neg data values) and take log
+ int idx;
+ for (idx = 0; idx < fit_data_points; idx++) {
+ FLOAT_T score = data[idx] + shift; // move right by shift
+ if (score <= 0.0) {
+ carp(CARP_DEBUG, "Reached negative score at idx %i", idx);
+ fit_data_points = idx;
+ break;
+ }
+ X[idx] = log(score);
+ // carp(CARP_DEBUG, "X[%i]=%.6f=ln(%.6f)", idx, X[idx], score);
+ }
+
+ FLOAT_T* Y = (FLOAT_T*)mymalloc(sizeof(FLOAT_T) * fit_data_points);
+ for (idx = 0; idx < fit_data_points; idx++) {
+ int reverse_idx = total_data_points - idx;
+ FLOAT_T F_T_idx = (reverse_idx - 0.3) / (total_data_points + 0.4);
+ Y[idx] = log( -log(1.0 - F_T_idx) );
+ //carp(CARP_DEBUG, "Y[%i]=%.6f", idx, Y[idx]);
+ }
+
+ int N = fit_data_points; // rename for formula's sake
+ FLOAT_T sum_Y = 0.0;
+ FLOAT_T sum_X = 0.0;
+ FLOAT_T sum_XY = 0.0;
+ FLOAT_T sum_XX = 0.0;
+ for (idx = 0; idx < fit_data_points; idx++) {
+ sum_Y += Y[idx];
+ sum_X += X[idx];
+ sum_XX += X[idx] * X[idx];
+ sum_XY += X[idx] * Y[idx];
+ }
+ carp(CARP_DETAILED_DEBUG, "sum_X=%.6f", sum_X);
+ carp(CARP_DETAILED_DEBUG, "sum_Y=%.6f", sum_Y);
+ carp(CARP_DETAILED_DEBUG, "sum_XX=%.6f", sum_XX);
+ carp(CARP_DETAILED_DEBUG, "sum_XY=%.6f", sum_XY);
+
+ FLOAT_T b_num = sum_XY - (sum_X * sum_Y / N);
+ carp(CARP_DETAILED_DEBUG, "b_num=%.6f", b_num);
+ FLOAT_T b_denom = sum_XX - sum_X * sum_X / N;
+ carp(CARP_DETAILED_DEBUG, "b_denom=%.6f", b_denom);
+ FLOAT_T b_hat = b_num / b_denom;
+
+ FLOAT_T a_hat = (sum_Y - b_hat * sum_X) / N;
+ *beta = b_hat;
+ *eta = exp( - a_hat / *beta );
+
+ FLOAT_T c_num = 0.0;
+ FLOAT_T c_denom_X = 0.0;
+ FLOAT_T c_denom_Y = 0.0;
+ FLOAT_T mean_X = sum_X / N;
+ FLOAT_T mean_Y = sum_Y / N;
+ for (idx = 0; idx < N; idx++) {
+ FLOAT_T X_delta = X[idx] - mean_X;
+ FLOAT_T Y_delta = Y[idx] - mean_Y;
+ c_num += X_delta * Y_delta;
+ c_denom_X += X_delta * X_delta;
+ c_denom_Y += Y_delta * Y_delta;
+ }
+ FLOAT_T c_denom = sqrt(c_denom_X * c_denom_Y);
+ if (c_denom == 0.0) {
+ //carp(CARP_FATAL, "Zero denominator in correlation calculation!");
+ carp(CARP_DETAILED_DEBUG, "Zero denominator in correlation calculation!");
+ *correlation = 0.0; // min value
+ *eta = 0;
+ *beta = 0;
+ } else {
+ *correlation = c_num / c_denom;
+ }
+ carp(CARP_DETAILED_DEBUG, "shift=%.6f", shift);
+ carp(CARP_DETAILED_DEBUG, "eta=%.6f", *eta);
+ carp(CARP_DETAILED_DEBUG, "beta=%.6f", *beta);
+ carp(CARP_DETAILED_DEBUG, "correlation=%.6f", *correlation);
+
+ free(Y);
+ free(X);
+}
+
+
+/**
+ * \brief Open the fasta file and prepare it for
+ * searching. Die if the input file cannot be found or read.
+ * \returns The number of proteins in the file
+ */
+int prepare_protein_input(
+ const string& input_file, ///< name of the fasta file
+ Database** database ///< return new fasta database here
+) {
+ int num_proteins = 0;
+
+ carp(CARP_INFO, "Preparing protein fasta file %s", input_file.c_str());
+ *database = new Database(input_file, false);
+ if (database == NULL) {
+ carp(CARP_FATAL, "Could not create protein database");
+ }
+
+ if (!(*database)->parse()) {
+ carp(CARP_FATAL, "Error with protein database.");
+ }
+ return (*database)->getNumProteins();
+}
+
+/**
+ * Maximum characters per line when printing formatted text.
+ */
+static const int MAX_CHARS_PER_LINE = 70;
+
+/**
+ *\brief Extend a given string with lines not exceeding a specified width,
+ * breaking on spaces.
+ */
+void strcat_formatted(
+ char* string_to_extend,
+ const char* lead_string, // Appears at the start of each line.
+ const char* extension // Text to add.
+) {
+ int i_string = 0;
+ int string_length = strlen(extension);
+ char buffer[MAX_CHARS_PER_LINE + 1];
+
+ while (string_length - i_string > MAX_CHARS_PER_LINE) {
+
+ // Be sure to break on a space.
+ int index_of_last_space = MAX_CHARS_PER_LINE;
+ while (extension[i_string + index_of_last_space] != ' ') {
+ index_of_last_space--;
+ }
+
+ sprintf(buffer, "%.*s", index_of_last_space, &(extension[i_string]));
+
+ strcat(string_to_extend, lead_string);
+ strcat(string_to_extend, buffer);
+ strcat(string_to_extend, "\n");
+
+ i_string += index_of_last_space + 1;
+ }
+ strcat(string_to_extend, lead_string);
+ strcat(string_to_extend, &(extension[i_string]));
+ strcat(string_to_extend, "\n");
+}
+
+/**
+ * \brief Checks if the given input file contains target, decoy PSMs or
+ * concatenated search results.
+ *
+ *\returns corrected file names. It does not check if files are exist.
+ */
+void check_target_decoy_files(
+ string &target, //filename of the target PSMs
+ string &decoy //filename of the decoy PSMs
+) {
+ int target_pos = target.find("target");
+ if (target_pos < 0) {
+ int decoy_pos = decoy.find("decoy");
+ if (decoy_pos < 0) {
+ // user gave concatenated result file
+ decoy = "";
+ } else {
+ // user gave decoy results file
+ target.replace(decoy_pos, DECOY_STRING_LENGTH, "target");
+ }
+ } else {
+ // user gave target results file
+ decoy.replace(target_pos, TARGET_STRING_LENGTH, "decoy");
+ }
+}
+
+void get_search_result_paths(
+ const string &infile, ///< path of the first file.
+ std::vector<std::string> &outpaths ///< paths of all search results -out
+) {
+ outpaths.clear();
+ if (Params::GetBool("list-of-files")) {
+ LineFileReader reader(infile);
+ while(reader.hasNext()) {
+ string current = StringUtils::Trim(reader.next());
+ carp(CARP_INFO, "current is:%s", current.c_str());
+ if (FileUtils::Exists(current)) {
+ outpaths.push_back(current);
+ } else {
+ carp(CARP_ERROR, "Search file '%s' doesn't exist", current.c_str());
+ }
+ }
+ } else {
+ string target = infile;
+ string decoy = infile;
+ check_target_decoy_files(target, decoy);
+ if (!target.empty()) {
+ if (FileUtils::Exists(target)) {
+ outpaths.push_back(target);
+ } else {
+ carp(CARP_ERROR, "Target file '%s' doesn't exist", target.c_str());
+ }
+ }
+ if (!decoy.empty()) {
+ if (FileUtils::Exists(decoy)) {
+ outpaths.push_back(decoy);
+ } else {
+ carp(CARP_ERROR, "Decoy file '%s' doesn't exist", decoy.c_str());
+ }
+ }
+ }
+}
+
+void get_files_from_list(
+ const string &infile, ///< path of the first file.
+ std::vector<std::string> &outpaths ///< paths of all search results -out
+ ) {
+ outpaths.clear();
+ if (Params::GetBool("list-of-files")) {
+ LineFileReader reader(infile);
+ while (reader.hasNext()) {
+ string current = reader.next();
+ carp(CARP_INFO, "current is:%s", current.c_str());
+ if (FileUtils::Exists(current)) {
+ outpaths.push_back(current);
+ } else {
+ carp(CARP_ERROR, "Search file '%s' doesn't exist", current.c_str());
+ }
+ }
+ } else if (FileUtils::Exists(infile)) {
+ outpaths.push_back(infile);
+ }
+}
+
+bool parseUrl(string url, string* host, string* path) {
+ if (!host || !path) {
+ return false;
+ }
+ // find protocol
+ size_t protocolSuffix = url.find("://");
+ if (protocolSuffix != string::npos) {
+ url = url.substr(protocolSuffix + 3);
+ }
+ size_t pathBegin = url.find('/');
+ if (pathBegin == string::npos) {
+ *host = url;
+ *path = "/";
+ } else {
+ *host = url.substr(0, pathBegin);
+ *path = url.substr(pathBegin);
+ }
+ if (host->empty()) {
+ *host = *path = "";
+ return false;
+ }
+ return true;
+}
+
+string httpRequest(const string& url, const std::string& data, bool waitForResponse) {
+ // Parse URL into host and path components
+ string host, path;
+ if (!parseUrl(url, &host, &path)) {
+ carp(CARP_ERROR, "Failed parsing URL %s", url.c_str());
+ return "";
+ }
+
+ using namespace boost::asio;
+
+ // Establish TCP connection to host on port 80
+ io_service service;
+ ip::tcp::resolver resolver(service);
+ ip::tcp::resolver::iterator endpoint = resolver.resolve(ip::tcp::resolver::query(host, "80"));
+ ip::tcp::socket sock(service);
+ connect(sock, endpoint);
+
+ // Determine method (GET if no data; otherwise POST)
+ string method = data.empty() ? "GET" : "POST";
+ string contentLengthHeader = data.empty()
+ ? ""
+ : "Content-Length: " + StringUtils::ToString(data.length()) + "\r\n";
+ // Send the HTTP request
+ string request =
+ method + " " + path + " HTTP/1.1\r\n"
+ "Host: " + host + "\r\n" +
+ contentLengthHeader +
+ "Connection: close\r\n"
+ "\r\n" + data;
+ sock.send(buffer(request));
+
+ if (!waitForResponse) {
+ return "";
+ }
+
+ // Read the response into stringstream
+ stringstream response;
+ boost::system::error_code ec;
+ do {
+ char buf[1024];
+ size_t n = sock.receive(buffer(buf), 0, ec);
+ if (!ec) {
+ response.write(buf, n);
+ }
+ } while (!ec);
+ return response.str();
+}
+
+void postToAnalytics(const string& appName) {
+ // Post data to Google Analytics
+ // For more information, see: https://developers.google.com/analytics/devguides/collection/protocol/v1/devguide
+ try {
+ stringstream paramBuilder;
+ paramBuilder << "v=1" // Protocol verison
+ << "&tid=UA-26136956-1" // Tracking ID
+ // TODO Generate UUID for cid
+ // The Client ID (cid) anonymously identifies a particular user
+ // or device and should be a random UUID
+ << "&cid=35009a79-1a05-49d7-b876-2b884d0f825b"
+ << "&t=event" // Hit type
+ << "&ec=crux" // Event category
+ << "&ea=" << appName // Event action
+ << "&el=" // Event label
+#ifdef _MSC_VER
+ "win"
+#elif __APPLE__
+ "mac"
+#else
+ "linux"
+#endif
+ << '-' << CRUX_VERSION;
+ httpRequest(
+ "http://www.google-analytics.com/collect",
+ paramBuilder.str(),
+ false);
+ } catch (...) {
+ }
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/util/crux-utils.h b/src/util/crux-utils.h
new file mode 100644
index 0000000..af9ef02
--- /dev/null
+++ b/src/util/crux-utils.h
@@ -0,0 +1,483 @@
+/**
+ * \file crux-utils.h
+ * $Revision: 1.41 $
+ * $Author: cegrant $
+ * \brief Utilities for the crux project
+ */
+#ifndef CRUX_UTILS_H
+#define CRUX_UTILS_H
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <ctype.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#ifndef _MSC_VER
+#include <dirent.h>
+#include <unistd.h>
+#endif
+#include <time.h>
+#include <algorithm>
+#include <limits>
+#include "io/carp.h"
+#include "utils.h"
+#include "model/objects.h"
+#include "parameter.h"
+#include "StringUtils.h"
+#include "model/Peak.h"
+#include "app/CruxApplication.h"
+
+#include <set>
+#include <sstream>
+#include <string>
+#include <vector>
+
+/**
+ * The number of features used to represent a PSM for Percolator or q-ranker.
+ */
+const unsigned int NUM_FEATURES = 16;
+
+/**
+ *\returns a heap copy of the given string
+ */
+char* my_copy_string(const char* src);
+
+/**
+ * returns copy of the src string upto the specified length
+ * includes a null terminating `\0' character
+ * the string is heap allocated thus, user must free
+ */
+char* copy_string_part(const char* src, int length);
+
+/**
+ * \returns the 0 if equal, 1 if float_a is larger, -1 if float_b is larger
+ * compare the absolute value of the difference of two numbers with an
+ * appropriate epsilon to get relations.
+ * Multiplying the epsilon by sum of the comparands adjusts the comparison
+ * to the range of the numbers, allowing a single epsilon to be used for many,
+ * or perhaps all compares.
+ */
+int compare_float(FLOAT_T float_a, FLOAT_T float_b);
+
+/**
+ * Compares two numbers and returns TRUE if they are within the given
+ * precision of each other, otherwise returns FALSE. E.g. if
+ * precision is 2, a and b must be equal when rounded to two decimal
+ * places.
+ */
+bool is_equal(FLOAT_T a, FLOAT_T b, int precision);
+
+/**
+ * \brief Parses the filename and path of given string.
+ *
+ * The array returned, A, contains the filename (A[0]) and the path
+ * (A[1]). Path is NULL if no / in given name. e.g. Given
+ * "../../filname" returns A[0]="filename" and A[1]="../../". Given
+ * "filename" returns A[0] = "filename" and A[1] = NULL.
+ *
+ *\returns A heap allocated array of both filename and path
+ */
+char** parse_filename_path(const std::string& file);
+
+/**
+ * \brief Parses the filename, path, and file extension of given string.
+ *
+ * The array returned, A, contains the filename (A[0]) striped of the
+ * given file extension and the path (A[1]). If extension is NULL,
+ * strips all characters after the last "." from the filename. Use
+ * parse_filename_path() to return filename with extension.
+ * Returned path is NULL if no "/" in given name.
+ * extension. e.g. Given "../../filname.ext" and ".ext" returns
+ * A[0]="filename" A[1]="../../". Given "filename" returns A[0] =
+ * NULL and A[1] = "filename".
+ *
+ * \returns A heap allocated array of filename striped of extension and
+ * path.
+ */
+char** parse_filename_path_extension(const char* file, const char* extension);
+
+/**
+ * parses the filename
+ * ex) ../../file_name => returns filename
+ *\returns A heap allocated array of filename
+ */
+char* parse_filename(const char* file);
+
+/**
+ * Examines filename to see if it ends in the given extension
+ * \returns True if filename ends in the extension, else false.
+ */
+bool has_extension(std::string filename, std::string extension);
+
+/**
+ * convert the integer into a string
+ * \returns a heap allocated string
+ */
+char* int_to_char(unsigned int i);
+
+/**
+ * convert the integer into a string
+ * \returns a heap allocated string
+ */
+char* signed_int_to_char(int i);
+
+/**
+ *prints the peptide type given it's enum value
+ */
+//void print_peptide_type(PEPTIDE_TYPE_T peptide_type, FILE* file);
+
+/**
+ * given two strings return a concatenated third string
+ * \returns a heap allocated string that concatenates the two inputs
+ */
+char* cat_string(const char* string_one, const char* string_two);
+
+/**
+ * Adds the fileroot parameter to a string as a prefix.
+ */
+std::string prefix_fileroot_to_name(const std::string& name);
+
+/**
+ * \returns the filepath 'output_dir'/'fileroot'.'filename'
+ */
+std::string make_file_path(
+ const std::string& filename ///< the name of the file
+ );
+
+
+/**
+ * given the path and the filename return a file with path
+ * "path/filename"
+ * \returns a heap allocated string, "path/filename"
+ */
+char* get_full_filename(const char* path, const char* filename);
+
+/**
+ * returns the file size of the given filename
+ */
+long get_filesize(char *FileName);
+
+/**
+ * \brief A function for creating a directory to hold output files from crux.
+ *
+ * Tries to create a the named directory for use as the output directory for crux.
+ * If the overwrite option is true, an existing directory wtih that
+ * name will not cause an error.
+ *
+ * \returns 0 if successful, -1 if an error occured.
+*/
+int create_output_directory(
+ const std::string& output_folder, // Name of output folder.
+ bool overwrite // Whether or not to overwrite an existing dir
+);
+
+/**
+ * given a fasta_file name it returns a name with the name_tag add to the end
+ * format: myfasta_nameTag
+ * \returns A heap allocated file name of the given fasta file
+ */
+char* generate_name(
+ const char* fasta_filename,
+ const char* name_tag,
+ const char* file_extension,
+ const char* suffix
+ );
+/**
+ * \brief Take a filename, strip its leading path information (if
+ * any) and file extension (if any). Tries all file extensions until
+ * one is found. Add a new path (if given) and a new suffix (exension).
+ *
+ * If given ../dir/filename.ext, [.txt, .ext, t], .new-ext, otherdir
+ * would return otherdir/filename.new-ext
+ * \returns A heap allocated filename
+ */
+char* generate_name_path(
+ const char* filename,
+ std::vector<const char*> old_suffixes,
+ const char* new_suffix,
+ const char* new_path
+ );
+
+/**
+ * \brief Take a filename, strip its leading path information (if
+ * any) and file extension (if any). Add a new path (if given) and a
+ * new suffix (exension).
+ *
+ * If given ../dir/filename.ext, .new-ext, .ext, otherdir would return
+ * otherdir/filename.new-ext
+ * \returns A heap allocated filename
+ */
+char* generate_name_path(
+ const char* filename,
+ const char* old_suffix,
+ const char* new_suffix,
+ const char* new_path
+ );
+
+/**
+ * \brief Open and create a file of the given name in the given
+ * directory.
+ *
+ * Assumes the directory exists. Fails if file can't be opened or if
+ * file exists and overwrite is false.
+ *\returns A file handle to the newly created file.
+ */
+FILE* create_file_in_path(
+ const std::string& filename, ///< the filename to create & open -in
+ const std::string& directory, ///< the directory to open the file in -in
+ bool overwrite ///< replace the file (T) or die if exists (F)
+ );
+
+/**
+ * \brief c++ version of create_file_in_path
+ */
+std::ofstream* create_stream_in_path(
+ const char* filename, ///< the filename to create & open -in
+ const char* directory, ///< the directory to open the file in -in
+ bool overwrite ///< replace file (T) or die if exists (F)
+ );
+
+/**
+ * checks if each AA is an AA
+ *\returns TRUE if sequence is valid else, FALSE
+ */
+bool valid_peptide_sequence(const std::string& sequence);
+
+/**
+ * quickSort for FLOAT_Ts
+ */
+void quicksort(FLOAT_T numbers[], int array_size);
+
+/**
+ * User define our upper and our lower bounds.
+ * The random number will always be
+ * between low and high, inclusive.
+ * There is no seeding in this function, user must do it for themselves
+ *\returns a random number between the interval user provides
+ */
+int get_random_number_interval(
+ int low, ///< the number for lower bound -in
+ int high ///< the number for higher bound -in
+ );
+
+/**
+ * \brief Shuffle an array of FLOAT_Ts. Uses the Knuth algorithm. Uses
+ * get_random_number_interval() to generate random numbers.
+ */
+void shuffle_floats(FLOAT_T* array, int size);
+
+/**
+ * \brief Shuffles an array of elements. Uses the Knuth algorithm. Uses
+ * get_random_number_interval() to generate random numbers.
+ */
+template<typename T>
+void shuffle_array(T* array, int size) {
+ if (array == NULL) {
+ carp(CARP_ERROR, "Cannot shuffle NULL array.");
+ return;
+ }
+
+ int idx, switch_idx;
+ int last_element_idx = size - 1;
+ T temp_value;
+ for (idx = 0; idx < size; idx++) {
+ switch_idx = get_random_number_interval(idx, last_element_idx);
+ temp_value = array[idx];
+ array[idx] = array[switch_idx];
+ array[switch_idx] = temp_value;
+ }
+}
+
+/**
+ *\returns the number of digits in the number
+ */
+int get_number_digits(
+ int number ///< the number to count digits
+ );
+
+/**
+ * Fits a three-parameter Weibull distribution to the input data.
+ * \returns eta, beta, c (which in this case is the amount the data should
+ * be shifted by) and the best correlation coefficient
+ */
+
+void fit_three_parameter_weibull(
+ FLOAT_T* data, ///< the data to be fit. should be in descending order -in
+ int fit_data_points, ///< the number of data points to fit -in
+ int total_data_points, ///< the total number of data points -in
+ FLOAT_T min_shift, ///< the minimum shift to allow -in
+ FLOAT_T max_shift, ///< the maximum shift to allow -in
+ FLOAT_T step, ///< the step for shift modification -in
+ FLOAT_T corr_threshold, ///< minimum correlation, else no fit -in
+ FLOAT_T* eta, ///< the eta parameter of the Weibull dist -out
+ FLOAT_T* beta, ///< the beta parameter of the Weibull dist -out
+ FLOAT_T* shift, ///< the best shift -out
+ FLOAT_T* correlation ///< the best correlation -out
+ );
+
+/**
+ * Fits a two-parameter Weibull distribution to the input data.
+ * \returns eta, beta and the correlation coefficient
+ */
+void fit_two_parameter_weibull(
+ FLOAT_T* data, ///< the data to be fit -in
+ int fit_data_points, ///< the number of data points to fit -in
+ int total_data_points, ///< the total number of data points -in
+ FLOAT_T shift, ///< the amount by which to shift our data -in
+ FLOAT_T* eta, ///< the eta parameter of the Weibull dist -out
+ FLOAT_T* beta, ///< the beta parameter of the Weibull dist -out
+ FLOAT_T* correlation ///< the best correlation -out
+ );
+
+bool string_to_mass_type(const std::string& name, MASS_TYPE_T*);
+bool mass_type_to_string(MASS_TYPE_T, char*);
+bool string_to_algorithm_type(char*, ALGORITHM_TYPE_T*);
+bool algorithm_type_to_string(ALGORITHM_TYPE_T, char*);
+bool string_to_scorer_type(const std::string& name, SCORER_TYPE_T*);
+const char* scorer_type_to_string(SCORER_TYPE_T);
+bool string_to_ion_type(const std::string& name, ION_TYPE_T*);
+bool ion_type_to_string(ION_TYPE_T, char*);
+char* ion_type_to_string(ION_TYPE_T type);
+
+// new style of type_to_string and string_to_type functions
+// requires an invalid value for each enum
+DIGEST_T string_to_digest_type(const std::string& name);
+const char* digest_type_to_string(DIGEST_T);
+ENZYME_T string_to_enzyme_type(const std::string& name);
+const char* enzyme_type_to_string(ENZYME_T);
+OBSERVED_PREPROCESS_STEP_T string_to_observed_preprocess_step(const std::string& name);
+char* observed_preprocess_step_to_string(OBSERVED_PREPROCESS_STEP_T type);
+WINDOW_TYPE_T string_to_window_type(const std::string& name);
+PARSIMONY_TYPE_T string_to_parsimony_type(const std::string& name);
+MEASURE_TYPE_T string_to_measure_type(const std::string& name);
+char * measure_type_to_string(MEASURE_TYPE_T type);
+THRESHOLD_T string_to_threshold_type(const std::string& name);
+char * threshold_type_to_string(THRESHOLD_T type);
+QUANT_LEVEL_TYPE_T string_to_quant_level_type(const std::string& name);
+COLTYPE_T string_to_column_type(const std::string& name);
+COMPARISON_T string_to_comparison(const std::string& name);
+DECOY_TYPE_T string_to_decoy_type(const std::string& name);
+DECOY_TYPE_T string_to_tide_decoy_type(const std::string& name);
+char* decoy_type_to_string(DECOY_TYPE_T type);
+MASS_FORMAT_T string_to_mass_format(const std::string& name);
+char* mass_format_type_to_string(MASS_FORMAT_T type);
+
+HARDKLOR_ALGORITHM_T string_to_hardklor_algorithm_type(const std::string& name);
+std::string hardklor_hardklor_algorithm_type_to_string(HARDKLOR_ALGORITHM_T type);
+
+/**
+ * \brief Open the fasta file and prepare it for
+ * searching. Die if the input file cannot be found or read.
+ * \returns The number of proteins in the file
+ */
+int prepare_protein_input(
+ const std::string& input_file, ///< name of the fasta file
+ Database** database);///< return new fasta database here
+
+/**
+ * converts a string in #-# format to
+ * a first and last variable
+ * \returns whether the extraction was successful or not
+ */
+
+bool get_first_last_scan_from_string(
+ const std::string& const_scans_string,
+ int& first_scan,
+ int& last_scan
+ );
+
+bool get_scans_from_string(
+ const std::string& const_scans_string,
+ std::set<int>& scans
+);
+
+
+template<typename TValue>
+static bool get_range_from_string(
+ const std::string& const_range_string, ///< the string to extract
+ TValue& first, ///< the first value
+ TValue& last ///< the last value
+ ) {
+
+ if (const_range_string.empty()) {
+ first = (TValue)0;
+ last = std::numeric_limits<TValue>::max();
+ return true;
+ }
+ char* range_string = my_copy_string(const_range_string.c_str());
+
+ bool ret;
+
+ char* dash = strchr(range_string, '-');
+ if (dash == NULL) { // a single number
+ ret = StringUtils::TryFromString(range_string, &first);
+ last = first;
+ } else {
+ //invalid if more than one dash
+ const char* dash_check = strchr(dash + 1, '-');
+ if (dash_check) {
+ ret = false;
+ } else {
+ *dash = '\0';
+ ret = StringUtils::TryFromString(range_string, &first);
+ *dash = '-';
+ dash++;
+ ret &= StringUtils::TryFromString(dash, &last);
+ }
+ }
+
+ free(range_string);
+ return ret;
+}
+
+/**
+ *\brief Extend a given string with lines not exceeding a specified width,
+ * breaking on spaces.
+ */
+void strcat_formatted(
+ char* string_to_extend,
+ const char* lead_string, // Appears at the start of each line.
+ const char* extension // Text to add.
+);
+
+/**
+ * \brief Checks if the given input file contains target, decoy PSMs or
+ * concatenated search results.
+ *
+ *\returns corrected file names. It does not check if files are exist.
+ */
+void check_target_decoy_files(
+ std::string &target, //filename of the target PSMs
+ std::string &decoy //filename of the decoy PSMs
+);
+
+void get_search_result_paths(
+ const std::string& infile,
+ std::vector<std::string> &outpaths ///< paths of all search results -out
+);
+
+
+/**
+ * \brief Checks if the given input file contains target, decoy PSMs or
+ * concatenated search results.
+ *
+ *\returns corrercted file names. It does not check if files are exist.
+ */
+void check_target_decoy_files(
+ std::string &target, //filename of the target PSMs
+ std::string &decoy //filename of the decoy PSMs
+);
+
+void get_files_from_list(
+ const std::string &infile, ///< path of the first file.
+ std::vector<std::string> &outpaths ///< paths of all search results -out
+);
+
+bool parseUrl(std::string url, std::string* host, std::string* path);
+std::string httpRequest(const std::string& url, const std::string& data = "", bool waitForResponse = true);
+void postToAnalytics(const std::string& appName);
+
+#endif
diff --git a/src/util/linked_list.cpp b/src/util/linked_list.cpp
new file mode 100644
index 0000000..89eb653
--- /dev/null
+++ b/src/util/linked_list.cpp
@@ -0,0 +1,370 @@
+/**
+ * \file linked_list.cpp
+ * \brief Method definitions for a linked list class.
+ */
+
+#include "linked_list.h"
+
+/**
+ * \struct _linked_list_node
+ * \brief A node of a linked list
+ */
+struct _linked_list_node {
+ void* data;
+ struct _linked_list_node *next;
+};
+//typedef struct _linked_list_node LIST_POINTER_T*;
+
+/**
+ * \struct _linked_list_head
+ * \brief The head of a linked list
+ */
+struct _linked_list_head {
+ // TODO change next to head or first
+ struct _linked_list_node *next;
+ struct _linked_list_node *last;
+};
+//typedef struct _linked_list_head LINKED_LIST_T;
+
+/**
+ * \brief Allocate the first element of a new list.
+ * \returns A pointer to the new list.
+ */
+LINKED_LIST_T* new_empty_list() {
+ LINKED_LIST_T* head = (LINKED_LIST_T*)mymalloc(sizeof(LINKED_LIST_T));
+ head->next = NULL;
+ head->last = NULL;
+ return head;
+}
+
+/**
+ * \brief Private function for adding a node to the list.
+ * Allocates the node, sets data field to new_item, sets next to NULL.
+ * \returns A pointer to the newly created node.
+ */
+LIST_POINTER_T* new_node(void* new_item) {
+ LIST_POINTER_T* the_node = (LIST_POINTER_T*)mymalloc(sizeof(LIST_POINTER_T));
+ the_node->data = new_item;
+ the_node->next = NULL;
+ return the_node;
+}
+
+/**
+ * \brief Allocate the first element of a new list.
+ * \returns A pointer to the new list.
+ */
+LINKED_LIST_T* new_list(void* first_item) {
+ LINKED_LIST_T* head = (LINKED_LIST_T*)mymalloc(sizeof(LINKED_LIST_T));
+ head->next = new_node(first_item);
+ head->last = head->next;
+ return head;
+}
+
+/**
+ * \brief Add an item to the end of this list. Traverses to the end
+ * of the list, creates a new list node, and adds it to the end of the list.
+ * \returns A pointer to the last (newly created) element in the list.
+ */
+LIST_POINTER_T* push_back_linked_list(LINKED_LIST_T* list_head, void* add_me) {
+
+ if( list_head == NULL ) {
+ carp(CARP_ERROR, "Cannot add to a NULL list.");
+ return NULL;
+ }
+
+ // adding to an empty list
+ if( list_head->next == NULL ) {
+ list_head->next = new_node(add_me);
+ list_head->last = list_head->next;
+ return list_head->next;
+ }
+
+ // find the end of the list
+ LIST_POINTER_T* last_node = list_head->last;
+ assert( (list_head->last)->next == NULL);
+
+ last_node->next = new_node(add_me);
+ list_head->last = last_node->next;
+ return last_node->next;
+}
+
+/**
+ * \brief Add an item to the beginning of this list. Creates a new
+ * list node, and insersts it between the head and the first node.
+ * \returns A pointer to the first (newly created) element in the list.
+ */
+LIST_POINTER_T* push_front_linked_list(LINKED_LIST_T* list_head, void* add_me) {
+
+ if( list_head == NULL ) {
+ carp(CARP_ERROR, "Cannot add to null list\n");
+ return NULL;
+ }
+
+ LIST_POINTER_T* add_this_node = new_node(add_me);
+ add_this_node->next = list_head->next;
+ list_head->next = add_this_node;
+ if( list_head->last == NULL ) {
+ list_head->last = add_this_node;
+ }
+ return add_this_node;
+}
+
+/**
+ * \brief Remove the element from the end of the list (farthest from
+ * the head) and return a pointer to its data.
+ * Deletes the last list node leaving the data and the rest of the
+ * list intact.
+ * \returns A pointer to the data in the last item in the list, NULL
+ * if list is empty.
+ */
+void* pop_back_linked_list(LINKED_LIST_T* list) {
+
+ if( list == NULL || list->next == NULL ) {
+ return NULL;
+ }
+
+ // find the end of the list
+ LIST_POINTER_T* last_node = list->last;
+ void* data = last_node->data;
+
+ // special case of one item in list
+ if( last_node == list->next ) {
+ list->last = NULL;
+ list->next = NULL;
+ } else {
+ // find the node pointing to last
+ LIST_POINTER_T* second_to_last_node = list->next;
+
+ while( second_to_last_node->next != last_node ) {
+ second_to_last_node = second_to_last_node->next;
+ }
+
+ list->last = second_to_last_node;
+ second_to_last_node->next = NULL;
+ }
+ free(last_node);
+ return data;
+}
+
+/**
+ * \brief Remove the first element from the list, returning a pointer
+ * to the data.
+ * Deletes the first list node leaving the data and the
+ * head of the list intact. Head now points to what was the second
+ * element, if any.
+ * \returns A pointer to the data in the first item in the list, NULL
+ * if list is empty.
+ */
+void* pop_front_linked_list(LINKED_LIST_T* list) {
+
+ if( list == NULL || list->next == NULL ) {
+ return NULL;
+ }
+
+ LIST_POINTER_T* first_node = list->next;
+ void* data = first_node->data;
+ list->next = first_node->next;
+ // if only one node, change last to NULL
+ if( list->next == NULL ) {
+ list->last = NULL;
+ }
+
+ free(first_node);
+ return data;
+}
+
+/**
+ * \brief Get a pointer to the first element in the list. Can be used
+ * to start a traverse of the list.
+ * \returns A pointer to the first list node. NULL if empty list.
+ */
+LIST_POINTER_T* get_first_linked_list(LINKED_LIST_T* head) {
+ if( head == NULL ) {
+ return NULL;
+ }
+ return head->next;
+}
+
+/**
+ * \brief Get the next element in the list. Can be used for
+ * traversing a list.
+ * \returns A pointer to the next list node. NULL if at end of list.
+ */
+LIST_POINTER_T* get_next_linked_list(LIST_POINTER_T* node) {
+ if( node == NULL ) {
+ return NULL;
+ }
+ return node->next;
+}
+
+/**
+ * \brief Get the item pointed to by this node in the list.
+ * \returns Returns a void pointer to the item held at this node.
+ */
+void* get_data_linked_list(LIST_POINTER_T* node) {
+ if( node == NULL ) {
+ return NULL;
+ }
+ return node->data;
+}
+
+/**
+ * \brief Is this list empty?
+ * \returns true if node->next is NULL, else false
+ */
+bool is_empty_linked_list(LINKED_LIST_T* head) {
+ if( head == NULL || head->next == NULL ) {
+ return true;
+ }
+ return false;
+}
+
+/**
+ * \brief Is this list element at the end of the list?
+ * \returns false if node->next is NULL, else true
+ */
+bool has_next_linked_list(LIST_POINTER_T* node) {
+ if( node == NULL || node->next == NULL ) {
+ return false;
+ }
+ return true;
+}
+
+/**
+ * \brief Combines two lists by having the end of the first list point
+ * to the first element of the second. If the first list is null, returns
+ * a pointer to the second list. Does not change the second list.
+ * \returns Returns a pointer to the beginning of the combined lists.
+ */
+LINKED_LIST_T* combine_lists(LINKED_LIST_T* first, LINKED_LIST_T* second) {
+ if( first == NULL ) {
+ return second;
+ }
+ if( second == NULL ) {
+ return first;
+ }
+
+ // check for empty list
+ if( first->next == NULL ) {
+ first->next = second->next;
+ first->last = second->last;
+ } else {
+ // find the end of the first list
+ LIST_POINTER_T* last_node = first->last;
+
+ // set to the beginning of the second list
+ last_node->next = second->next;
+
+ // set the end of the first to the end of the last
+ first->last = second->last;
+ }
+ return first;
+}
+
+/**
+ * \brief Create a copy of each node in the original list, linked in
+ * the same order.
+ * \return A pointer to the head of the new list.
+ */
+LINKED_LIST_T* copy_list(LINKED_LIST_T* original) {
+ if( original == NULL ) {
+ return NULL;
+ }
+
+ LINKED_LIST_T* copy = new_empty_list();
+ // check for empty list
+ if( is_empty_linked_list( original ) ) {
+ return copy;
+ }
+
+ //initialize first element
+ LIST_POINTER_T* cur_original = get_first_linked_list(original);
+ copy->next = new_node( get_data_linked_list(cur_original) );
+
+ LIST_POINTER_T* cur_copy = copy->next;
+ cur_original = cur_original->next;
+
+ while( cur_original != NULL ) {
+ cur_copy->next = new_node( cur_original->data );
+ cur_copy = cur_copy->next;
+ cur_original = cur_original->next;
+ }
+
+ copy->last = cur_copy->next;
+ return copy;
+}
+
+// TODO? delete_only_this_list_node?
+/**
+ * \brief Deletes the given list node and all list nodes after this
+ * one WITHOUT deleting the data pointed to.
+ * \returns void
+ */
+void delete_list_node(LIST_POINTER_T* list) {
+ if( list == NULL ) {
+ return;
+ }
+
+ if( list->next != NULL ) {
+ delete_list_node(list->next);
+ }// else next is null and this is the end of the list
+
+ free(list);
+ return;
+}
+
+/**
+ * \brief Removes all nodes from a list while leaving the data intact.
+ */
+void clear_list(LINKED_LIST_T* list) {
+ if( list == NULL ) {
+ return;
+ }
+ LIST_POINTER_T* first = list->next;
+ delete_list_node(first);
+ list->next = NULL;
+}
+
+
+
+/**
+ * \brief Deletes the given list WITHOUT deleting the data pointed to.
+ * \returns void
+ */
+void delete_linked_list(LINKED_LIST_T* list) {
+ if( list ) {
+ if( list->next != NULL ) {
+ delete_list_node(list->next);
+ }// else next is null and this is the end of the list
+
+ free(list);
+ }
+ return;
+}
+
+/**
+ * \brief Deletes only the node AFTER this one. The given node then
+ * points to what the next node pointed to before. The data remains
+ * untouched.
+ * \returns A pointer to the new list element that follows the given one.
+ */
+LIST_POINTER_T* delete_next_list_node(LIST_POINTER_T* pre_node) {
+
+ if( pre_node == NULL ) {
+ return NULL;
+ }
+ // before: head ....pre-> delete-> next...NULL
+ // after : head ....pre-> next...NULL
+
+ LIST_POINTER_T* delete_node = pre_node->next;
+ if( delete_node == NULL ) {
+ return NULL;
+ }
+ LIST_POINTER_T* next_node = delete_node->next;
+
+ pre_node->next = next_node;
+ free(delete_node);
+
+ return next_node;
+}
+
diff --git a/src/util/linked_list.h b/src/util/linked_list.h
new file mode 100644
index 0000000..9a5b892
--- /dev/null
+++ b/src/util/linked_list.h
@@ -0,0 +1,145 @@
+/**
+ * \file linked_list.h
+ * Header file for a linked list class.
+ */
+#ifndef LINKED_LIST_H
+#define LINKED_LIST_H
+
+#include <assert.h>
+#include "util/utils.h"
+#include "model/objects.h"
+#include "io/carp.h"
+
+/**
+ * \brief Allocate the first element of a new list.
+ * \returns A pointer to the new list.
+ */
+LINKED_LIST_T* new_empty_list();
+
+/**
+ * \brief Allocate the first element of a new list.
+ * \returns A pointer to the new list.
+ */
+LINKED_LIST_T* new_list(void* first_item);
+
+/**
+ * \brief Add an item to the end of this list. Traverses to the end
+ * of the list, creates a new list node, and adds it to the end of the list.
+ * \returns A pointer to the last (newly created) element in the list.
+ */
+LIST_POINTER_T* push_back_linked_list(LINKED_LIST_T* list_head, void* add_me);
+
+/**
+ * \brief Add an item to the beginning of this list. Creates a new
+ * list node, and insersts it between the head and the first node.
+ * \returns A pointer to the first (newly created) element in the list.
+ */
+LIST_POINTER_T* push_front_linked_list(LINKED_LIST_T* list_head, void* add_me);
+
+/**
+ * \brief Remove the element from the end of the list (farthest from
+ * the head) and return a pointer to its data.
+ * Deletes the last list node leaving the data and the rest of the
+ * list intact.
+ * \returns A pointer to the data in the last item in the list, NULL
+ * if list is empty.
+ */
+void* pop_back_linked_list(LINKED_LIST_T* list);
+
+/**
+ * \brief Remove the first element from the list, returning a pointer
+ * to the data.
+ * Deletes the first list node leaving the data and the
+ * head of the list intact. Head now points to what was the second
+ * element, if any.
+ * \returns A pointer to the data in the first item in the list, NULL
+ * if list is empty.
+ */
+void* pop_front_linked_list(LINKED_LIST_T* list);
+
+/**
+ * \brief Get a pointer to the first element in the list. Can be used
+ * to start a traverse of the list.
+ * \returns A pointer to the first list node. NULL if empty list.
+ */
+LIST_POINTER_T* get_first_linked_list(LINKED_LIST_T* head);
+
+/**
+ * \brief Get the next element in the list. Can be used for
+ * traversing a list.
+ * \returns A pointer to the next list node. NULL if at end of list.
+ */
+LIST_POINTER_T* get_next_linked_list(LIST_POINTER_T* node);
+
+/**
+ * \brief Get the item pointed to by this node in the list.
+ * \returns Returns a void pointer to the item held at this node.
+ */
+void* get_data_linked_list(LIST_POINTER_T* list);
+
+/**
+ * \brief Is this list empty?
+ * \returns TRUE if node->next is NULL, else FALSE
+ */
+bool is_empty_linked_list(LINKED_LIST_T* head);
+
+/**
+ * \brief Is this list element at the end of the list?
+ * \returns FALSE if node->next is NULL, else TRUE
+ */
+bool has_next_linked_list(LIST_POINTER_T* node);
+
+/**
+ * \brief Combines two lists by having the end of the first list point
+ * to the beginning of the second. If the first list is null, returns
+ * a pointer to the second list.
+ * \returns Returns a pointer to the beginning of the combined lists.
+ */
+LINKED_LIST_T* combine_lists(LINKED_LIST_T* beginning, LINKED_LIST_T* add_me);
+
+/**
+ * \brief Create a copy of each node in the original list, linked in
+ * the same order.
+ * \return A pointer to the head of the new list.
+ */
+LINKED_LIST_T* copy_list(LINKED_LIST_T* original);
+
+/**
+ * \brief Removes all nodes from a list while leaving the data intact.
+ */
+void clear_list(LINKED_LIST_T* list);
+
+/**
+ * \brief Deletes the given list node and all list nodes after this
+ * one WITHOUT deleting the data pointed to.
+ * \returns void
+ */
+void delete_linked_list(LINKED_LIST_T* list);
+
+/**
+ * \brief Deletes the given list node and all list nodes after this
+ * one WITHOUT deleting the data pointed to.
+ * \returns void
+ */
+void delete_list_node(LIST_POINTER_T* list);
+
+/**
+ * \brief Deletes only the node AFTER this one. The given node then
+ * points to what the next node pointed to before.
+ * \returns A pointer to the new list element that follows the given one.
+ */
+LIST_POINTER_T* delete_next_list_node(LIST_POINTER_T* pre_node);
+
+
+
+
+
+
+
+
+
+
+
+
+
+#endif // LINKED_LIST_H
diff --git a/src/util/mass.cpp b/src/util/mass.cpp
new file mode 100644
index 0000000..cecf9aa
--- /dev/null
+++ b/src/util/mass.cpp
@@ -0,0 +1,307 @@
+/**
+ * \file mass.cpp
+ * \brief Provides constants and methods for calculating mass
+ ****************************************************************************/
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "utils.h"
+#include "model/objects.h"
+#include "mass.h"
+#include "model/Protein.h"
+#include "model/Peptide.h"
+#include "io/carp.h"
+#include "model/Ion.h"
+#include "modifications.h"
+#include "Params.h"
+
+/* Private Variables */
+
+/**
+ * Array to store the amino acid masses
+ */
+FLOAT_T amino_masses[('Z' - 'A')*2 + 2];
+enum {NUM_MOD_MASSES = 2048}; // 2 ^ MAX_AA_MODS = 2^11 = 2048
+FLOAT_T aa_mod_masses[(int)NUM_MOD_MASSES];
+
+
+/**
+ * Have we initialized the amino acid masses?
+ */
+bool initialized_amino_masses = false;
+
+// FIXME need to find the monoisotopic mass for some AA -chris
+/**
+ * initializes the mass array
+ */
+void initialize_amino_masses() {
+ // average mass
+ amino_masses['A' - 'A'] = 71.0788;
+ // set mass high to prevent peptides containing B
+ amino_masses['B' - 'A'] = 7000.0;
+ amino_masses['C' - 'A'] = 103.1388;
+ amino_masses['D' - 'A'] = 115.0886;
+ amino_masses['E' - 'A'] = 129.1155;
+ amino_masses['F' - 'A'] = 147.1766;
+ amino_masses['G' - 'A'] = 57.0519;
+ amino_masses['H' - 'A'] = 137.1411;
+ amino_masses['I' - 'A'] = 113.1594;
+ amino_masses['J' - 'A'] = 113.1594;
+ amino_masses['K' - 'A'] = 128.1741;
+ amino_masses['L' - 'A'] = 113.1594;
+ amino_masses['M' - 'A'] = 131.1926;
+ amino_masses['N' - 'A'] = 114.1038;
+ amino_masses['O' - 'A'] = 114.1472;
+ amino_masses['P' - 'A'] = 97.1167;
+ amino_masses['Q' - 'A'] = 128.1307;
+ amino_masses['R' - 'A'] = 156.1875;
+ amino_masses['S' - 'A'] = 87.0782;
+ amino_masses['T' - 'A'] = 101.1051;
+ amino_masses['U' - 'A'] = 150.0388;
+ amino_masses['V' - 'A'] = 99.1326;
+ amino_masses['W' - 'A'] = 186.2132;
+ // set mass high to prevent peptides containing X
+ amino_masses['X' - 'A'] = 7000.0;
+ amino_masses['Y' - 'A'] = 163.1760;
+ // set mass high to prevent peptides containing Z
+ amino_masses['Z' - 'A'] = 7000.0;
+
+ // monoisotopic mass
+ amino_masses['A' - 'A' + 26] = 71.03711;
+ // set mass high to prevent peptides containing B
+ amino_masses['B' - 'A' + 26] = 7000.0;
+ amino_masses['C' - 'A' + 26] = 103.00919;
+ amino_masses['D' - 'A' + 26] = 115.02694;
+ amino_masses['E' - 'A' + 26] = 129.04259;
+ amino_masses['F' - 'A' + 26] = 147.06841;
+ amino_masses['G' - 'A' + 26] = 57.02146;
+ amino_masses['H' - 'A' + 26] = 137.05891;
+ amino_masses['I' - 'A' + 26] = 113.08406;
+ amino_masses['J' - 'A' + 26] = 113.08406;
+ amino_masses['K' - 'A' + 26] = 128.09496;
+ amino_masses['L' - 'A' + 26] = 113.08406;
+ amino_masses['M' - 'A' + 26] = 131.04049;
+ amino_masses['N' - 'A' + 26] = 114.04293;
+ amino_masses['O' - 'A' + 26] = 114.07931;
+ amino_masses['P' - 'A' + 26] = 97.05276;
+ amino_masses['Q' - 'A' + 26] = 128.05858;
+ amino_masses['R' - 'A' + 26] = 156.10111;
+ amino_masses['S' - 'A' + 26] = 87.03203;
+ amino_masses['T' - 'A' + 26] = 101.04768;
+ amino_masses['U' - 'A' + 26] = 150.04344;
+ amino_masses['V' - 'A' + 26] = 99.06841;
+ amino_masses['W' - 'A' + 26] = 186.07931;
+ // set mass high to prevent peptides containing X
+ amino_masses['X' - 'A' + 26] = 7000.0;
+ amino_masses['Y' - 'A' + 26] = 163.06333;
+ // set mass high to prevent peptides containing Z
+ amino_masses['Z' - 'A' + 26] = 7000.0;
+
+ // modifications
+ initialize_aa_mod_combinations_array();
+
+ initialized_amino_masses = true;
+}
+
+/**
+ * \brief Populates the array aa_mod_masses with the mass change of
+ * all possible combinations of aa_mods. Gets the list of aa_mods
+ * from parameter.c. For example, if mod1 and a mass change of 50 and
+ * mod5 has a mass change of 10, then the entry at index
+ * (binary 00010001 =) 17 is (50 + 10=) 60.
+ */
+void initialize_aa_mod_combinations_array() {
+ // set all to 0
+ int i = 0;
+ for (i = 0; i < NUM_MOD_MASSES; i++) {
+ aa_mod_masses[i] = 0;
+ }
+
+ // get aa mod list
+ AA_MOD_T** amod_list = NULL;
+ int num_mods = get_all_aa_mod_list(&amod_list);
+ int mod_idx = 0;
+
+ // for each aa mod
+ for (mod_idx = 0; mod_idx < num_mods; mod_idx++) {
+ //printf("\nmod#: %i\n", mod_idx);
+ int entry_idx = 0;
+
+ while (entry_idx < NUM_MOD_MASSES) {
+ //printf("skip from %i", entry_idx);
+ // skip 2^i entries for mod_i (first mod is 1)
+ entry_idx += (int)pow(2.0, mod_idx);
+ //printf(" to %i\n", entry_idx);
+
+ // write i entries for mod_i
+ //int write_num = mod_idx+1;
+ int write_num = (int)pow(2.0, mod_idx);
+ while (write_num > 0 && entry_idx < NUM_MOD_MASSES) {
+ //printf("write at %i from %.3f", entry_idx, aa_mod_masses[entry_idx]);
+
+ aa_mod_masses[entry_idx] += aa_mod_get_mass_change(amod_list[mod_idx]);
+ //printf(" to %.3f\n", aa_mod_masses[entry_idx]);
+ entry_idx++;
+ write_num--;
+ }// next write
+ }// next skip
+ }// next mod
+
+ //printf("Initialized mod combinations are:\n");
+ //for (i = 0; i < 36; i++) {
+ //printf("index %i\tmass %.1f\n", i, aa_mod_masses[i]);
+ //}
+}
+
+/**
+ * \returns The mass of the given amino acid.
+ */
+FLOAT_T get_mass_amino_acid(
+ char amino_acid, ///< the query amino acid -in
+ MASS_TYPE_T mass_type ///< the isotopic mass type (AVERAGE, MONO) -in
+) {
+ if (mass_type == AVERAGE) {
+ return get_mass_amino_acid_average(amino_acid);
+ } else if (mass_type == MONO) {
+ return get_mass_amino_acid_monoisotopic(amino_acid);
+ }
+ carp(CARP_FATAL, "ERROR: mass type does not exist\n");
+ // avoid compiler warning
+ return 1;
+}
+
+/**
+ * \returns The mass of the given amino acid.
+ */
+FLOAT_T get_mass_mod_amino_acid(
+ MODIFIED_AA_T amino_acid, ///< the query amino acid -in
+ MASS_TYPE_T mass_type ///< the isotopic mass type (AVERAGE, MONO) -in
+) {
+ switch (mass_type) {
+ case AVERAGE:
+ return get_mass_mod_amino_acid_average(amino_acid);
+ case MONO:
+ return get_mass_mod_amino_acid_monoisotopic(amino_acid);
+ case NUMBER_MASS_TYPES:
+ carp(CARP_FATAL, "Bad mass type.");
+ }
+ return 0;
+}
+
+/**
+ * \returns The average mass of the given amino acid.
+ */
+FLOAT_T get_mass_amino_acid_average(
+ char amino_acid ///< the query amino acid -in
+) {
+ // has the amino_masses array been initialized?
+ if (!initialized_amino_masses) {
+ initialize_amino_masses();
+ initialized_amino_masses = true;
+ }
+ return(amino_masses[(short int)amino_acid - 'A']);
+}
+
+/**
+ * \returns The average mass of the given amino acid.
+ */
+FLOAT_T get_mass_mod_amino_acid_average(
+ MODIFIED_AA_T amino_acid ///< the query amino acid -in
+) {
+ if (!initialized_amino_masses) {
+ initialize_amino_masses();
+ }
+ //printf("aa is %hu, char %c\n", (unsigned short)amino_acid, modified_aa_to_char(amino_acid));
+
+ short int aa = amino_acid & GET_AA_MASK;
+ unsigned short int mod = amino_acid & GET_MOD_MASK;
+ mod = mod >> 5;
+ //printf("aa idx %hi mass %.3f + mod idx %hu mass %.3f\n", aa, amino_masses[aa], mod, aa_mod_masses[mod]);
+ return amino_masses[aa] + aa_mod_masses[mod];
+
+}
+
+/**
+ * Finds the modification identifier associated with the given mass
+ * shift. Can be the identifier from a single modification or from
+ * multiple modifications to the same residue. The returned
+ * identifier can be used to modify a MODIFIED_AA_T so that it has the
+ * given mass shift.
+ */
+MODIFIED_AA_T get_mod_identifier(FLOAT_T mass_shift) {
+ if (!initialized_amino_masses) {
+ initialize_amino_masses();
+ }
+
+ int precision = Params::GetInt("mod-precision");
+ for (int mod_idx = 0; mod_idx < (int)NUM_MOD_MASSES; mod_idx++) {
+ if (is_equal(mass_shift, aa_mod_masses[mod_idx], precision)) {
+ MODIFIED_AA_T identifier = mod_idx;
+ identifier = identifier << 5;
+ return identifier;
+ }
+ }
+
+ // if we got to here, no mod found
+ carp_once(CARP_WARNING, "No modification identifier found for mass shift %.*f."
+ "\nWarning Suppressed, others may exist",
+ precision, mass_shift);
+
+ return 0;
+}
+
+/**
+ * \returns The monoisotopic mass of the given amino acid.
+ */
+FLOAT_T get_mass_amino_acid_monoisotopic(
+ char amino_acid ///< the query amino acid -in
+) {
+ // has the amino_masses array been initialized?
+ if (!initialized_amino_masses) {
+ initialize_amino_masses();
+ initialized_amino_masses = true;
+ }
+ return(amino_masses[(short int)amino_acid - 'A' + 26 ]);
+}
+
+/**
+ * \returns The monoisotopic mass of the given amino acid.
+ */
+FLOAT_T get_mass_mod_amino_acid_monoisotopic(
+ MODIFIED_AA_T amino_acid ///< the query amino acid -in
+) {
+ if (!initialized_amino_masses) {
+ initialize_amino_masses();
+ }
+
+ short int aa = amino_acid & GET_AA_MASK;
+ unsigned short int mod = amino_acid & GET_MOD_MASK;
+ mod = mod >> 5;
+ //printf("mod aa idx %hi mass %.3f + mod idx %hu mass %.3f\n", aa, amino_masses[aa+26], mod, aa_mod_masses[mod]);
+ return amino_masses[aa + 26] + aa_mod_masses[mod];
+
+}
+
+
+/**
+ * increase the amino acid mass for both mono and average
+ */
+void increase_amino_acid_mass(
+ char amino_acid, ///< the query amino acid -in
+ FLOAT_T update_mass ///< the mass amount to update for the amino acid -in
+) {
+ // has the amino_masses array been initialized?
+ if (!initialized_amino_masses) {
+ initialize_amino_masses();
+ initialized_amino_masses = true;
+ }
+
+ // check if amino acid
+ if ((short int)amino_acid < 'A' || (short int)amino_acid > 'Z') {
+ carp(CARP_ERROR, "Cannot update mass, char: %c not an amino acid");
+ }
+
+ amino_masses[(short int)amino_acid - 'A' + 26 ] += update_mass;
+ amino_masses[(short int)amino_acid - 'A'] += update_mass;
+}
diff --git a/src/util/mass.h b/src/util/mass.h
new file mode 100644
index 0000000..18b4ac3
--- /dev/null
+++ b/src/util/mass.h
@@ -0,0 +1,132 @@
+#include "model/objects.h"
+#include "io/carp.h"
+//#include "modifications.h"
+
+/**
+ * \file mass.h
+ * $Revision: 1.18 $
+ * \brief Provides constants and methods for calculating mass
+ *****************************************************************************/
+#ifndef _MASS_H
+#define _MASS_H
+
+/**
+ * Mass of ammonia
+ */
+#define MASS_NH3_MONO 17.02655 ///< Mass of NH3 (monoisotopic)
+#define MASS_NH3_AVERAGE 17.03056 ///< Mass of NH3 (average)
+
+
+// mass of water
+#define MASS_H2O_MONO 18.010564684 ///< Mass of water (monoisotopic)
+#define MASS_H2O_AVERAGE 18.0153 ///< Mass of water (average)
+
+/**
+ * Mass of hydrogen
+ */
+#define MASS_H_MONO 1.0078246 ///< Mass of hydrogen (monoisotopic)
+#define MASS_H_AVERAGE 1.00794 ///< Mass of hydrogen (average)
+
+/* As for the constants, these are for supporting mono-isotopic and
+ * average masses. When I was collaborating with Pragya with
+ * cross-linking code, she wanted more accurate calculations on the
+ * mass of the peptides and the mass of the spectrum neutral mass.
+ * MASS_PROTON was added in order to improve the accuracy of the
+ * calculated spectrum mass and the precision of the mono-isotopic
+ * masses of the amino acids were extended. When we are going to
+ * support accurate masses for the precursor ions, I think that
+ * MASS_PROTON will be the correct one to use for the spectrum
+ * mass. --Sean McIlwain, 8 November 2010 */
+
+// FIXME, change in spectrum, peptide to be able to pick mono, average
+#define MASS_H 1.00782503207 ///< mass of hydrogen
+#define MASS_PROTON 1.00727646677 ///< mass of proton
+#define MASS_NEUTRON 1.00866491600 ///< mass of neutron
+
+/**
+ * Mass of oxygen
+ */
+#define MASS_O 16.0013 ///< mass of oxygen
+
+#define MASS_OH 17.00274
+
+/**
+ * Mass of carbon monoxide
+ */
+#define MASS_CO_MONO 27.9949 ///< Mass of (monoisotopic)
+#define MASS_CO_AVERAGE 28.0101 ///< Mass of (average)
+
+
+/**
+ * \returns The mass of the given amino acid.
+ */
+FLOAT_T get_mass_amino_acid(
+ char amino_acid, ///< the query amino acid -in
+ MASS_TYPE_T mass_type ///< the isotopic mass type (AVERAGE, MONO) -in
+ );
+
+/**
+ * \returns The mass of the given amino acid.
+ */
+FLOAT_T get_mass_mod_amino_acid(
+ MODIFIED_AA_T amino_acid, ///< the query amino acid -in
+ MASS_TYPE_T mass_type ///< the isotopic mass type (AVERAGE, MONO) -in
+ );
+
+
+/**
+ * \returns The average mass of the given amino acid.
+ */
+FLOAT_T get_mass_amino_acid_average(
+ char amino_acid ///< the query amino acid -in
+ );
+
+/**
+ * \returns The average mass of the given amino acid.
+ */
+FLOAT_T get_mass_mod_amino_acid_average(
+ MODIFIED_AA_T amino_acid ///< the query amino acid -in
+ );
+
+/**
+ * \returns The monoisotopic mass of the given amino acid.
+ */
+FLOAT_T get_mass_amino_acid_monoisotopic(
+ char amino_acid ///< the query amino acid -in
+ );
+
+/**
+ * \returns The monoisotopic mass of the given amino acid.
+ */
+FLOAT_T get_mass_mod_amino_acid_monoisotopic(
+ MODIFIED_AA_T amino_acid ///< the query amino acid -in
+ );
+
+/**
+ * Finds the modification identifier associated with the given mass
+ * shift. Can be the identifier from a single modfification or from
+ * multiple modficiations to the same residue. The returned
+ * identifier can be used to modify a MODIFIED_AA_T so that it has the
+ * given mass shift.
+ */
+MODIFIED_AA_T get_mod_identifier(FLOAT_T mass_shift);
+
+/**
+ * increase the amino acid mass for both mono and average
+ */
+void increase_amino_acid_mass(
+ char amino_acid, ///< the query amino acid -in
+ FLOAT_T update_mass ///< the mass amount to update for the amino acid -in
+ );
+
+/**
+ * \brief Populates the array aa_mod_masses with the mass change of
+ * all possible combinations of aa_mods. Gets the list of aa_mods
+ * from parameter.c. For example, if mod1 and a mass change of 50 and
+ * mod5 has a mass change of 10, then the entry at index
+ * (binary 00010001 =) 17 is (50 + 10=) 60.
+ */
+void initialize_aa_mod_combinations_array();
+
+
+#endif
diff --git a/src/util/modifications.cpp b/src/util/modifications.cpp
new file mode 100644
index 0000000..607f632
--- /dev/null
+++ b/src/util/modifications.cpp
@@ -0,0 +1,993 @@
+/**
+ * \file modifications.cpp
+ * \brief Datatypes and methods for amino acid modifications
+ *
+ * Two data structures define modifications. The AA_MOD_T is the most
+ * basic type. It is the information provided by the user: mass
+ * change caused by this mod, amino acids which may be modified in
+ * this way, and the maximum number of this type of modification which
+ * may occur on one peptide. AA_MODs are defined here.
+ * A collection of AA_MODs that may occur
+ * on some peptide are represented as a PEPTIDE_MOD_T. This stores
+ * a list of AA_MODS and the net mass change experienced by the
+ * peptide. PEPTIDE_MODs are defined in peptide_modifications.h
+ * AA_MODs are instantiated once after parsing the parameter file. All
+ * possible PEPTIDE_MODs are calcualted once and reused for each
+ * spectrum search. One PEPTIDE_MOD corresponds to one mass window
+ * that must be searched.
+ *
+ * $Revision: 1.8 $
+ */
+
+#include "modifications.h"
+#include "mass.h"
+#include "GlobalParams.h"
+#include "Params.h"
+#include <stack>
+#include <iostream>
+
+using namespace std;
+
+/**
+ * \brief Keeps a stack of allocated modification sequences
+ */
+class MODIFIED_AA_T_Cache {
+ protected:
+ stack<MODIFIED_AA_T*> cache_; ///< Cache itself
+ public:
+
+ /**
+ * Constructor
+ */
+ MODIFIED_AA_T_Cache() {;}
+
+ /**
+ * Destructor, deletes all objects in cache
+ */
+ ~MODIFIED_AA_T_Cache() {
+ size_t objects_in_cache = cache_.size();
+ while(!cache_.empty()) {
+ MODIFIED_AA_T *element = cache_.top();
+ cache_.pop();
+ delete []element;
+ }
+ }
+
+ /**
+ * checks out a object out of the cache
+ */
+ MODIFIED_AA_T* checkout(bool clear=false) {
+ MODIFIED_AA_T* new_element;
+ if (cache_.empty()) {
+ new_element = new MODIFIED_AA_T[GlobalParams::getMaxLength()+1];
+ } else {
+ new_element = cache_.top();
+ cache_.pop();
+ }
+ if (clear) {
+ memset(new_element, 0, sizeof(MODIFIED_AA_T)*GlobalParams::getMaxLength()+1);
+ }
+ return (new_element);
+ }
+
+
+ /**
+ * checks in a object into the cache
+ */
+ void checkin(
+ MODIFIED_AA_T* array
+ ) {
+ cache_.push(array);
+ }
+
+};
+
+MODIFIED_AA_T_Cache modified_aa_cache; ///< The cache of modified sequences
+
+/**
+ * \return a new modification sequence array. Can be off of already allocated
+ * arrays
+ */
+MODIFIED_AA_T* newModSeq() {
+ MODIFIED_AA_T* ans = modified_aa_cache.checkout();
+ return(ans);
+}
+
+/**
+ * Releases the modification sequence back into the cache
+ */
+void freeModSeq(
+ MODIFIED_AA_T* &seq ///< sequence to release
+ ) {
+ modified_aa_cache.checkin(seq);
+ seq=NULL;
+}
+
+/* Private constants */
+//enum { MAX_PROTEIN_SEQ_LENGTH = 40000 };
+
+/* Private global variables */
+/*
+ Modified sequences need both a textual representation as well as a
+ way to be encoded. A peptide sequence is typically an array of
+ char. A modified sequence will now be an array of MODIFIED_AA_T,
+ which are shorts. Each MODIFIED_AA_T is made up of two parts: the
+ 5 least-significant bits are used to encode the amino acid, and the
+ remaining are used to encode the modifications made to the aa.
+
+ Values 0-26 are used to represent amino acids A-Z. There is a
+ function that will take an MODIFIED_AA_T and return the text
+ representation of the amino acid.
+
+ The value of the most significant bit is used to represent
+ modification by the first AA_MOD_T in the parameter.c list. The
+ second most significant bit represents the second MOD_AA_T in the
+ list and so on. Note that each AA_MOD_T can be applied only once
+ to an amino acid. A MODIFED_AA_T can have between 0 and 11
+ modifications applied to it. There is a function that will take a
+ MODIFIED_AA_T* and the index of an AA_MOD_T and return true if the
+ MODIFIED_AA_T has had the AA_MOD_T applied to it.
+
+ For a textual representation of a modiciation, there are 11
+ non-alpha-numeric characters chosen. There is a function that will
+ take an MODIFIED_AA_T* and return a pointer to an array of
+ characters that begins with the letter of the amino acid and is
+ followed by all of the symbols corresponding to all of the
+ modifications that have been applied to the amino acid.
+ */
+char mod_sqt_symbols[MAX_AA_MODS] = //{'*', '@', '#', '^', '~', '%',
+ {'*', '#', '@', '^', '~', '%', // like sequest
+ '$', '&', '!', '?', '+'};
+
+uint16_t mod_id_masks[MAX_AA_MODS] = {
+ 0x0020, // 0000 0000 0010 0000 *
+ 0x0040, // 0000 0000 0100 0000 #
+ 0x0080, // 0000 0000 1000 0000 @
+ 0x0100, // 0000 0001 0000 0000 ^
+ 0x0200, // 0000 0010 0000 0000 ~
+ 0x0400, // 0000 0100 0000 0000 %
+ 0x0800, // 0000 1000 0000 0000 $
+ 0x1000, // 0001 0000 0000 0000 &
+ 0x2000, // 0010 0000 0000 0000 !
+ 0x4000, // 0100 0000 0000 0000 ?
+ 0x8000 // 1000 0000 0000 0000 +
+};
+
+/* Definitions of public methods */
+
+/**
+ * \brief Allocate an AA_MOD, including the aa_list and initialize all
+ * fields to default values. Symbol and unique identifier are set
+ * according to index.
+ * \returns A heap allocated AA_MOD with default values.
+ */
+AA_MOD_T* new_aa_mod(int mod_idx) {
+
+ assert(mod_idx > -1 && mod_idx < MAX_AA_MODS );
+
+ AA_MOD_T* mod = (AA_MOD_T*)mymalloc(sizeof(AA_MOD_T));
+
+ mod->mass_change = 0;
+ mod->max_per_peptide = 0;
+ mod->position = ANY_POSITION;
+ mod->max_distance = MAX_PROTEIN_SEQ_LENGTH;
+ mod->symbol = mod_sqt_symbols[mod_idx];
+ mod->identifier = mod_id_masks[mod_idx];
+ mod->prevents_cleavage = false;
+ mod->prevents_xlink = false;
+ // allocate the aa lists for mods
+ /*
+ mod->aa_list = // all 0's?
+ (bool*)mycalloc(AA_LIST_LENGTH, sizeof(bool));
+ */
+ // initialize to false
+ int aa_idx = 0;
+ for (aa_idx = 0; aa_idx < AA_LIST_LENGTH; aa_idx++) {
+ mod->aa_list[aa_idx] = false;
+ }
+ return mod;
+}
+
+/**
+ * \brief Free the memory for an AA_MOD including the aa_list.
+ */
+void free_aa_mod(AA_MOD_T* mod) {
+ if (mod) {
+ //if( mod->aa_list ) {free(mod->aa_list);}
+ free(mod);
+ }
+}
+
+/**
+ * \brief Converts a MODIFIED_AA into a char, effectively unmodifying it.
+ * \returns The unmodified char representation of an aa.
+ */
+char modified_aa_to_char(MODIFIED_AA_T aa) {
+ aa = aa & 0x001F; // 0000 0000 0001 1111
+ return (char)aa + 'A';
+}
+
+/**
+ * \brief Converts a char representation of an aa to an unmodified aa
+ * of type MODIFIED_AA_T. Requires 'A' <= char <= 'Z'.
+ * \returns The MODIFIED_AA_T represnetation of an aa.
+ */
+MODIFIED_AA_T char_aa_to_modified(char aa) {
+ assert( aa >= 'A' && aa <= 'Z' );
+ MODIFIED_AA_T mod_aa = (MODIFIED_AA_T)aa - (MODIFIED_AA_T)'A';
+ return mod_aa;
+}
+
+/**
+ * \brief Converts a MODIFIED_AA_T to it's textual representation,
+ * i.e. a letter followed by between 0 and 11 symbols for the
+ * modifications made to the amino acid.
+ * \returns A newly allocated char* with amino acid and modifciation
+ * symbols.
+ */
+char* modified_aa_to_string_with_symbols(MODIFIED_AA_T aa) {
+
+ int modified_by = 0;
+ AA_MOD_T** mod_list = NULL;
+ int total_mods = get_all_aa_mod_list(&mod_list);
+ for (int mod_idx = 0; mod_idx < total_mods; mod_idx++) {
+ if (is_aa_modified(aa, mod_list[mod_idx])) {
+ modified_by++;
+ }
+ }
+ char* return_string = (char*)mymalloc((modified_by+2)*sizeof(char));
+ // 2 = aa + null term
+ int return_idx = 0;
+ return_string[return_idx] = modified_aa_to_char(aa);
+ return_idx++;
+ for (int mod_idx = 0; mod_idx < total_mods; mod_idx++) {
+ if (is_aa_modified(aa, mod_list[mod_idx])) {
+ return_string[return_idx] = aa_mod_get_symbol(mod_list[mod_idx]);
+ return_idx++;
+ }
+ }
+ return_string[return_idx] = '\0';
+ return return_string;
+}
+
+/**
+ * \brief Converts a MODIFIED_AA_T to it's textual representation,
+ * i.e. a letter either alone or followed by square brackets containing
+ * the mass(es) of any modifications. If mass_format is
+ * MOD_MASSES_SEPARATE, all masses are listed in a comma-separated
+ * list. If MOD_MASS_ONLY, they are summed and returned in one
+ * number. If AA_PLUS_MOD, the mass of the residue plus the mass of
+ * the modifciation(s) is printed.
+ *
+ * \returns A newly allocated char* with amino acid and modifciation
+ * masses in square brackets.
+ */
+char* modified_aa_to_string_with_masses(MODIFIED_AA_T aa,
+ MASS_FORMAT_T mass_format,
+ int precision) {
+ int modified_by = 0;
+ AA_MOD_T** mod_list = NULL;
+ int total_mods = get_all_aa_mod_list(&mod_list);
+ for (int mod_idx = 0; mod_idx < total_mods; mod_idx++) {
+ if (is_aa_modified(aa, mod_list[mod_idx])) {
+ modified_by++;
+ }
+ }
+
+ // return the char if no mods
+ if (modified_by == 0) {
+ char* aa_str = (char*)mymalloc(2 * sizeof(char));
+ sprintf(aa_str, "%c", modified_aa_to_char(aa));
+ return aa_str;
+ }
+
+ // go through all mods and sum mass or append to string
+
+ // at most 11 mods, each at most 7 char "000.00,", total 77
+ char* mass_string = (char*)mymalloc(128 * sizeof(char));
+ char* mass_string_ptr = mass_string;
+ FLOAT_T summed_masses = 0;
+ if (mass_format == AA_PLUS_MOD) {
+ summed_masses =
+ get_mass_mod_amino_acid(aa, GlobalParams::getIsotopicMass());
+ } else {
+
+ for (int mod_idx = 0; mod_idx < total_mods; mod_idx++) {
+ if (is_aa_modified(aa, mod_list[mod_idx])) {
+ // either add to the sum or to the string
+ if (mass_format == MOD_MASS_ONLY) {
+ summed_masses += aa_mod_get_mass_change(mod_list[mod_idx]);
+ } else {
+ sprintf(mass_string_ptr, "%.*f,", precision,
+ aa_mod_get_mass_change(mod_list[mod_idx]));
+ mass_string_ptr += strlen(mass_string_ptr);
+ }
+ }
+ }
+ }
+
+ // combine aa and masses
+ char* return_string = NULL;
+ if (mass_format != MOD_MASSES_SEPARATE) { // X[000.00]'/0'
+ return_string = (char*)mymalloc(10 * sizeof(char));
+ sprintf(return_string, "%c[%1.*f]", modified_aa_to_char(aa),
+ precision, summed_masses );
+ } else { // X[000.00,etc]'/0'
+ return_string = (char*)mymalloc((4 + strlen(mass_string)) * sizeof(char));
+ // take off the last comma
+ mass_string[(strlen(mass_string) - 1)] = '\0';
+ sprintf(return_string, "%c[%s]", modified_aa_to_char(aa), mass_string);
+
+ }
+ free(mass_string);
+ return return_string;
+}
+
+/**
+ * \brief Take an array of MODIFIED_AA_T's and return an array of
+ * char's that includes the letter of each aa and the mass change of
+ * any modifications in brackets following the modified residue.
+ * If mass_format is MOD_MASSES_SEPARATE, all masses are listed in a
+ * comma-separated list. If MOD_MASS_ONLY, they are summed and
+ * returned in one number. If AA_PLUS_MOD, the mass of the residue
+ * plus the mass of the modifciation(s) is printed.
+ *
+ * \returns A newly allocated array of characters, a text
+ * representation of the modified sequence.
+ */
+char* modified_aa_string_to_string_with_masses(
+ MODIFIED_AA_T* aa_string, // the modified aa's to translate
+ int length, // length of aa_string
+ MASS_FORMAT_T mass_format // which mass value to print
+) {
+ if (aa_string == NULL || length == 0) {
+ carp(CARP_ERROR, "Cannot print a NULL modified sequence");
+ return NULL;
+ }
+ // get access to the mods
+ AA_MOD_T** global_mod_list = NULL;
+ int mod_list_length = get_all_aa_mod_list(&global_mod_list);
+
+ // count up modifications
+ int count = 0;
+ for (int mod_str_idx = 0; mod_str_idx < length; mod_str_idx++) {
+ // check each mod in list
+ for(int global_idx = 0; global_idx < mod_list_length; global_idx++) {
+ if (is_aa_modified(aa_string[mod_str_idx], global_mod_list[global_idx])) {
+ count++; // count all mods
+ }
+ }
+ }
+
+ int precision = GlobalParams::getModPrecision();
+ // max total length = #aas + ( #mods * (strlen("[000.,]")+precision) ) + '/0'
+ int buffer_size = length + (count * (9 + precision)) + 1;
+ char* return_string = (char*)mymalloc(buffer_size * sizeof(char));
+ char* return_str_ptr = return_string;
+ for (int mod_str_idx = 0; mod_str_idx < length; mod_str_idx++) {
+ char* cur_mod =
+ modified_aa_to_string_with_masses(aa_string[mod_str_idx], mass_format, precision);
+ strcpy( return_str_ptr, cur_mod );
+ return_str_ptr += strlen(cur_mod);
+ free(cur_mod);
+ }
+
+ return return_string;
+}
+
+/**
+ * \brief Take an array of MODIFIED_AA_T's and return an array of
+ * char's that includes the letter of each aa and the symbol for all
+ * applied modifications.
+ *
+ * \returns A newly allocated array of characters, a text
+ * representation of the modified sequence.
+ */
+char* modified_aa_string_to_string_with_symbols(
+ MODIFIED_AA_T* aa_string,
+ int length
+) {
+ if (aa_string == NULL || length == 0) {
+ carp(CARP_ERROR, "Cannot print a NULL modified sequence");
+ return NULL;
+ }
+
+ AA_MOD_T** global_mod_list = NULL;
+ int mod_list_length = get_all_aa_mod_list(&global_mod_list);
+ int global_idx = 0;
+
+ // count up amino acids and modifications
+ int count = 0;
+ int mod_str_idx = 0;
+ // while (aa_string[mod_str_idx] != MOD_SEQ_NULL) {
+ for (mod_str_idx = 0; mod_str_idx < length; mod_str_idx++) {
+ count++; // count the aas
+ for (global_idx = 0; global_idx < mod_list_length; global_idx++) {
+ if (is_aa_modified(aa_string[mod_str_idx], global_mod_list[global_idx])) {
+ count++; // count all mods
+ }
+ }
+ // mod_str_idx++;
+ }
+ // carp(CARP_DETAILED_DEBUG, "Found %d modified aas out of %i",
+ // count - mod_str_idx, count);
+ //int mod_str_len = mod_str_idx; // keep track of aa_string length
+
+ // create a buffer to hold all aas and mod symbols
+ char* return_string = (char*)mymalloc((count+1)*sizeof(char));
+ char* return_str_ptr = return_string;
+
+ // for each mod_aa, get the string representation, copy to return str
+ // for (mod_str_idx = 0; mod_str_idx < mod_str_len; mod_str_idx++) {
+ for (mod_str_idx = 0; mod_str_idx < length; mod_str_idx++) {
+
+ char* cur_mod = modified_aa_to_string_with_symbols(aa_string[mod_str_idx]);
+ strcpy( return_str_ptr, cur_mod );
+ return_str_ptr += strlen(cur_mod);
+ free(cur_mod);
+ }
+
+ return return_string;
+}
+
+/**
+ * \brief Takes an array of MODIFIED_AA_T's and returns an array of
+ * char's, one for each amino acid in the sequence. It DOES NOT
+ * include any modification symbols. Use with caution.
+ * \returns A newly allocated char* with ONLY amino acids, all
+ * modifications are removed.
+ */
+char* modified_aa_to_unmodified_string(MODIFIED_AA_T* aa_string, int length) {
+ if (aa_string == NULL) {
+ carp(CARP_ERROR, "Cannot print a NULL modified sequence");
+ return NULL;
+ }
+
+ char* new_string = (char*)mycalloc(length+1, sizeof(char));
+ for (int aa_idx = 0; aa_idx < length; aa_idx++) {
+ new_string[aa_idx] = modified_aa_to_char(aa_string[aa_idx]);
+ }
+ new_string[length] = '\0';
+
+ return new_string;
+}
+
+/**
+ * \brief Allocates an array of MODIFIED_AA_T's and populates it with
+ * the MODIFIED_AA_T value that corresponds to each sequence char
+ * value and trailing modification symbols or masses. Returns the new
+ * sequence via the mod_sequence argument.
+ *
+ * \returns The length of the mod_sequence array.
+ */
+int convert_to_mod_aa_seq(const string& sequence,
+ MODIFIED_AA_T** mod_sequence,
+ MASS_FORMAT_T mass_format) {
+
+ if( sequence.empty() ){
+ carp(CARP_ERROR, "Cannot convert NULL sequence to modifiable characters");
+ return 0;
+ }
+
+ MASS_TYPE_T mass_type = GlobalParams::getIsotopicMass();
+ const char* csequence = sequence.c_str();
+
+ int seq_len = sequence.length();
+ MODIFIED_AA_T* new_sequence = newModSeq();
+ unsigned int seq_idx = 0; // current position in given sequence
+ unsigned int mod_idx = 0; // current position in the new_sequence
+ for(seq_idx = 0; seq_idx < seq_len; seq_idx++){
+ // is the character a residue?
+ if( csequence[seq_idx] >= 'A' && csequence[seq_idx] <= 'Z' ){
+ // add to the new sequence
+ new_sequence[mod_idx] = char_aa_to_modified( csequence[seq_idx] );
+ mod_idx++;
+ continue;
+ }
+
+ // else it's a modification as symbol or mass
+ const AA_MOD_T* aa_mod = NULL;
+
+ if (sequence[seq_idx] == '[' || sequence[seq_idx] == ',') {//mod mass
+ seq_idx++;
+ FLOAT_T delta_mass = atof(csequence + seq_idx);
+ if (mass_format == AA_PLUS_MOD) {
+ assert(mod_idx > 0);
+ delta_mass -= get_mass_mod_amino_acid(new_sequence[mod_idx - 1],
+ mass_type);
+ }
+ // translate mass into aa_mod
+ aa_mod = get_aa_mod_from_mass(delta_mass);
+
+ // move to next mod or residue
+ while (sequence[seq_idx] != ']' && sequence[seq_idx] != ',') {
+ seq_idx++;
+ }
+ // back up one for the comma
+ if (sequence[seq_idx] == ',') {
+ seq_idx--;
+ }
+ } else { // mod symbol
+ // translate character into aa_mod
+ aa_mod = get_aa_mod_from_symbol(sequence[seq_idx]);
+ }
+ if (mod_idx == 0) {
+ //This can happen with nterminal modifications from comet.
+ seq_idx++;
+ if (seq_idx < seq_len && sequence[seq_idx] >= 'A' && sequence[seq_idx] <= 'Z') {
+ new_sequence[mod_idx] = char_aa_to_modified( sequence[seq_idx] );
+ mod_idx++;
+ } else {
+ carp(CARP_FATAL, "Cannot parse sequence %s", csequence);
+ }
+
+
+ }
+ // apply the modification
+ if (aa_mod == NULL) {
+ carp(CARP_WARNING, "There is an unidentifiable modification in sequence "
+ "<%s> at position %d.", csequence, seq_idx - 1);
+ } else {
+ // apply modification
+ modify_aa(&new_sequence[mod_idx-1], aa_mod);
+ }
+ } // next character in given sequence
+
+ // null terminate
+ new_sequence[mod_idx] = MOD_SEQ_NULL;
+
+ // return new_sequence;
+ *mod_sequence = new_sequence;
+ return mod_idx;
+}
+
+/**
+ * \brief Allocate a new MODIFIED_AA_T array and copy values into it.
+ */
+MODIFIED_AA_T* copy_mod_aa_seq(const MODIFIED_AA_T* source, int length) {
+ if (source == NULL) {
+ carp(CARP_ERROR, "Cannot copy NULL sequence of modified_aa's.");
+ return NULL;
+ }
+
+ MODIFIED_AA_T* new_seq = newModSeq();
+ memcpy( new_seq, source, length * sizeof(MODIFIED_AA_T));
+ new_seq[length] = MOD_SEQ_NULL;
+
+ return new_seq;
+}
+
+/**
+ * \brief Allocate a new MODIFIED_AA_T array and copy values into it.
+ */
+MODIFIED_AA_T* copy_mod_aa_seq(
+ const MODIFIED_AA_T* source ///< Sequence to copy
+ ) {
+ if (source == NULL) {
+ carp(CARP_ERROR, "Cannot copy NULL sequence of modified_aa's.");
+ return NULL;
+ }
+
+ MODIFIED_AA_T* new_seq = newModSeq();
+ size_t length = 0;
+ while (source[length] != MOD_SEQ_NULL) {
+ new_seq[length] = source[length];
+ length++;
+ }
+ new_seq[length] = MOD_SEQ_NULL;
+ return(new_seq);
+
+}
+
+
+
+/**
+ * \brief Remove any characters not A-Z from a peptide sequence.
+ * \returns A newly allocated string with the given sequence less any
+ * modififcation symbols or masses.
+ */
+char* unmodify_sequence(const char* modified_sequence) {
+ if (modified_sequence == NULL) {
+ return NULL;
+ }
+ char* new_seq = my_copy_string(modified_sequence);
+ unmodify_sequence_in_place(new_seq);
+ return new_seq;
+}
+
+/**
+ * \brief Remove any characters that are not A-Z from a given peptide
+ * seqeunce.
+ */
+void unmodify_sequence_in_place(char* sequence) {
+ int seq_len = strlen(sequence);
+ int next_aa_idx = 0;
+ int move_to_here = 0;
+ while (next_aa_idx < seq_len) {
+ if (sequence[next_aa_idx] >= 'A' && sequence[next_aa_idx] <= 'Z') {
+ sequence[move_to_here] = sequence[next_aa_idx];
+ move_to_here++;
+ }
+ next_aa_idx++;
+ }
+ sequence[move_to_here] = '\0';
+}
+
+
+/**
+ * \brief Determine if an array of MODIFIED_AA_T is a palindrome.
+ * Used by reverse_sequence to avoid returning a reversed sequence
+ * that is the same as the target. Ignores the first and last
+ * residues.
+ * \returns true if the reversed sequence would be the same as the
+ * forward, otherwise false.
+ */
+bool modified_aa_seq_is_palindrome(MODIFIED_AA_T* seq, int length) {
+ if (seq == NULL) {
+ return false;
+ }
+
+ int left_idx = 1; // skip first and last residues
+ int right_idx = length - 2;
+
+ while (left_idx < right_idx) {
+ if (seq[left_idx] != seq[right_idx]) {
+ return false;
+ }// else, keep checking
+ left_idx++;
+ right_idx--;
+ }
+
+ // if we got to here, they all matched
+ return true;
+}
+
+// FIXME: implement this
+bool is_aa_modified(MODIFIED_AA_T aa, AA_MOD_T* mod) {
+ return (aa & mod->identifier) != 0;
+}
+
+/**
+ * \brief Determine if this modified amino acid can be modified by
+ * this modification.
+ *
+ * Checks the mod list of modifiable residues to see if aa is in the
+ * list. Also checks to see if aa has already been modified by this
+ * mod.
+ * \returns true if it can be modified, else false
+ */
+bool is_aa_modifiable(
+ MODIFIED_AA_T aa, ///< The sequence amino acid to be modified
+ AA_MOD_T* mod) { ///< The aa_mod to modify it with
+
+ if (is_aa_modified(aa, mod)) {
+ return false;
+ }
+ if (mod->aa_list[(int)modified_aa_to_char(aa) - 'A']) {
+ //if (mod->aa_list[(int)modified_aa_to_char(aa)] && !is_aa_modified(aa, mod)) {
+ return true;
+ }
+ // else not in list or already modified by this mod
+ return false;
+}
+
+/**
+ * \brief Adds a modification to a MODIFIED_AA_T.
+ *
+ * Assumes that the aa is modifiable, no explicit check. If the aa is
+ * already modified for the mod, no change to aa.
+ */
+void modify_aa(MODIFIED_AA_T* aa, const AA_MOD_T* mod) {
+ if (aa == NULL || mod == NULL) {
+ carp(CARP_ERROR, "Cannot modify aa. Either aa or mod is NULL.");
+ return;
+ }
+ *aa = *aa | mod->identifier;
+}
+
+/**
+ * \brief Return the AA_MOD_T associated with the given symbol. If
+ * the symbol does not represent a modification, returns null.
+ * Requires that parameters have been initialized.
+ */
+const AA_MOD_T* get_aa_mod_from_symbol(const char symbol) {
+ AA_MOD_T** mod_list = NULL;
+ int total_mods = get_all_aa_mod_list(&mod_list);
+ for (int mod_idx = 0; mod_idx < total_mods; mod_idx++) {
+ AA_MOD_T* cur_mod = mod_list[mod_idx];
+ if (cur_mod->symbol == symbol) {
+ return cur_mod;
+ }
+ }
+
+ // none of the mods matched the symbol
+ carp(CARP_ERROR, "The modification symbol '%c' is not valid.", symbol);
+ return NULL;
+}
+
+/**
+ * \brief Return the delta mass associated with the given modification
+ * symbol. If the symbol does not represent a modification, returns
+ * 0. Requires that parameters have been initialized.
+ */
+FLOAT_T get_mod_mass_from_symbol(const char symbol) {
+
+ const AA_MOD_T* mod = get_aa_mod_from_symbol(symbol);
+ if (mod == NULL) {
+ return 0;
+ }
+
+ return aa_mod_get_mass_change(mod);
+}
+
+// a temporary AA_MOD_T with identifier and mass for (potentially)
+// more than one modification
+AA_MOD_T multi_mod;
+
+/**
+ * \brief Return the modification identifier that can be used to modify a
+ * MODIFIED_AA_T so that it has the given mass shift.
+ * The mass may either be from a single AA_MOD_T as given by the user
+ * or from any combination of AA_MOD_T's. If no combinations of
+ * AA_MOD_T's can be found for the mass, returns 0.
+ * Requires that parameters have been initialized.
+ */
+const AA_MOD_T* get_aa_mod_from_mass(FLOAT_T mass) {
+ // find the identifier for this mass shift
+ MODIFIED_AA_T id = get_mod_identifier(mass);
+
+ if (id == 0) { // get_mod_id already warned
+ //here we are creating a modification. Hopefully
+ //this will only get used when post-processing search
+ //results, maybe we will need to check that at some point
+ //SJM 2013_10_10.
+ carp(CARP_INFO, "Creating modification for %f", mass);
+ AA_MOD_T** mods = NULL;
+ int num_mods = get_all_aa_mod_list(&mods);
+ mods[num_mods]->mass_change = mass;
+ incrementNumMods();
+ initialize_aa_mod_combinations_array();
+ return get_aa_mod_from_mass(mass);
+ } else {
+ // set multi_mod_identifier to that id and mass
+ multi_mod.identifier = id;
+ }
+ multi_mod.mass_change = mass;
+ carp(CARP_DETAILED_DEBUG, "Returning %i %f", multi_mod.identifier, multi_mod.mass_change);
+ return &multi_mod;
+}
+
+/**
+ * print all fields in aa mod. For debugging
+ */
+void print_a_mod(AA_MOD_T* mod) {
+ printf("AMOD: mass %.2f, max per %d, max dist %d, symb %c, aa list ",
+ mod->mass_change, mod->max_per_peptide, mod->max_distance,
+ mod->symbol);
+
+ int i = 0;
+ for (i = 0; i < AA_LIST_LENGTH; i++) {
+ if (mod->aa_list[i]) {
+ printf("%c", (i + 'A'));
+ }
+ }
+ printf("\n");
+}
+
+/**
+ * \brief Generates a string representation of an aa_mod and returns a
+ * pointer to that newly allocated string.
+ */
+char* aa_mod_to_string(const AA_MOD_T* mod) {
+ const char* format_str =
+ "mass change=%.2f, symbol=%c, max=%d, position=%s, apply to ";
+ char* return_str = (char*)mycalloc( strlen(format_str) + 50, sizeof(char));
+ // add 26 for letters and some more for good measure
+
+ // get position info
+ const char* pos_format = "%c-term most %d from end";
+ char* pos_buffer = (char*)mycalloc(strlen(pos_format) + 9, sizeof(char));
+ switch (mod->position) {
+ case ANY_POSITION:
+ strcpy(pos_buffer, "any");
+ break;
+ case C_TERM:
+ sprintf(pos_buffer, pos_format, 'C', mod->max_distance);
+ break;
+ case N_TERM:
+ sprintf(pos_buffer, pos_format, 'N', mod->max_distance);
+ break;
+ }
+ int length = sprintf(return_str, format_str, mod->mass_change,
+ mod->symbol, mod->max_per_peptide, pos_buffer);
+
+ char* str_ptr = return_str + length;
+ int i = 0;
+ for (i = 0; i < AA_LIST_LENGTH; i++) {
+ if (mod->aa_list[i]) {
+ sprintf(str_ptr, "%c", (i + 'A'));
+ str_ptr++;
+ }
+ }
+ free(pos_buffer);
+ return return_str;
+}
+
+/* Setters and Getters */
+
+/**
+ * \brief Set the symbol used by this modification.
+ * \returns void
+ */
+void aa_mod_set_symbol(AA_MOD_T* mod, char symbol) {
+ mod->symbol = symbol;
+}
+
+/**
+ * \brief Set the mass change caused by this modification.
+ * \returns void
+ */
+void aa_mod_set_mass_change(AA_MOD_T* mod, double mass_change) {
+ mod->mass_change = mass_change;
+}
+
+/**
+ * \brief Get the mass change caused by this modification.
+ * \returns The mass change caused by this modification.
+ */
+double aa_mod_get_mass_change(const AA_MOD_T* mod) {
+ return mod->mass_change;
+}
+
+/**
+ * \brief Access to the aa_list of the AA_MOD_T struct. This pointer
+ * can be used to get or set the list of residues on which this mod
+ * can be placed.
+ * \returns A pointer to the list of amino acids on which this mod can
+ * be placed.
+ */
+bool* aa_mod_get_aa_list(AA_MOD_T* mod) {
+ return mod->aa_list;
+}
+
+/**
+ * \brief Set the maximum number of times this modification can be
+ * placed on one peptide.
+ * \returns void
+ */
+void aa_mod_set_max_per_peptide(AA_MOD_T* mod, int max) {
+ mod->max_per_peptide = max;
+}
+
+/**
+ * \brief Get the maximum number of times this modification can be
+ * placed on one peptide.
+ * \returns The max times per peptide this mod can be placed.
+ */
+int aa_mod_get_max_per_peptide(AA_MOD_T* mod) {
+ return mod->max_per_peptide;
+}
+
+/**
+ * \brief Set the maximum distance from the protein terminus that the
+ * modification can be placed. Which terminus (C or N) is determined
+ * by the position type. To indicate no position restriction, set to
+ * MAX_PROTEIN_SEQ_LENGTH.
+ * \returns void
+ */
+void aa_mod_set_max_distance(AA_MOD_T* mod, int distance) {
+ mod->max_distance = (distance == -1) ? MAX_PROTEIN_SEQ_LENGTH :
+ distance;
+}
+
+/**
+ * \brief Get the maximum distance from the protein end that the
+ * modification can be placed. Will be MAX_PROTEIN_SEQ_LENGTH if
+ * position type is ANY_POSITION.
+ * \returns Maximum distance from protein terminus at which mod can be
+ * placed.
+ */
+int aa_mod_get_max_distance(AA_MOD_T* mod) {
+ return mod->max_distance;
+}
+
+/**
+ * \brief Set the position type of an aa_mod.
+ * \returns void
+ */
+void aa_mod_set_position(AA_MOD_T* mod, MOD_POSITION_T position) {
+ mod->position = position;
+}
+
+/**
+ * \brief Where in the peptide can the modification be placed.
+ * \returns ANY_POSITION for standard mods; C_TERM or N_TERM for those
+ * that can only be placed at the ends of the peptide.
+ */
+MOD_POSITION_T aa_mod_get_position(AA_MOD_T* mod) {
+ return mod->position;
+}
+
+/**
+ * \brief Sets whether the modification can prevent cleavage.
+ * \returns void
+ */
+void aa_mod_set_prevents_cleavage(AA_MOD_T* mod, bool prevents_cleavage) {
+ mod->prevents_cleavage = prevents_cleavage;
+}
+
+/**
+ * \brief gets whether the modification can prevent cleavage
+ * \returns true or false
+ */
+bool aa_mod_get_prevents_cleavage(AA_MOD_T* mod) {
+ return mod->prevents_cleavage;
+}
+
+/**
+ * \brief Sets whether the modifications can prevent cross-linking.
+ * \returns void
+ */
+void aa_mod_set_prevents_xlink(AA_MOD_T* mod, bool prevents_xlink) {
+ mod->prevents_xlink = prevents_xlink;
+}
+
+/**
+ * \brief gets whether the modification can prevent cross-linking.
+ * \returns true or false
+ */
+bool aa_mod_get_prevents_xlink(AA_MOD_T* mod) {
+ return mod->prevents_xlink;
+}
+
+/**
+ * \brief The character used to uniquely identify the mod in the sqt file.
+ * \returns The character identifier.
+ */
+char aa_mod_get_symbol(const AA_MOD_T* mod) {
+ return mod->symbol;
+}
+
+/**
+ * \brief Create a string containing all of the amino acids that can
+ * be modified by this aa_mod. E.g. if S, T, and Y can be modified,
+ * returns "STY".
+ * \returns A newly allocated string.
+ */
+string aa_mod_get_aa_list_string(AA_MOD_T* mod) {
+ string s;
+ for (int i = 0; i < AA_LIST_LENGTH; i++) {
+ if (mod->aa_list[i]) {
+ s += (char)('A' + i);
+ }
+ }
+ return s;
+}
+
+/**
+ * Count the number of modified aas in the string.
+ */
+int count_modified_aas(MODIFIED_AA_T* seq) {
+ if (seq == NULL) {
+ return 0;
+ }
+
+ int count = 0;
+ int aa_idx = 0;
+ while (seq[aa_idx] != MOD_SEQ_NULL) {
+ if (GET_MOD_MASK & seq[aa_idx]) {
+ count++;
+ }
+ aa_idx++;
+ }
+
+ return count;
+
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/util/modifications.h b/src/util/modifications.h
new file mode 100644
index 0000000..ad2a54e
--- /dev/null
+++ b/src/util/modifications.h
@@ -0,0 +1,419 @@
+/**
+ * \file modifications.h
+ * \brief Datatypes and methods for amino acid modifications
+ *
+ * Two data structures define modifications. The AA_MOD_T is the most
+ * basic type. It is the information provided by the user: mass
+ * change caused by this mod, amino acids which may be modified in
+ * this way, and the maximum number of this type of modification which
+ * may occur on one peptide. AA_MODs are defined here.
+ * A collection of AA_MODs that may occur
+ * on some peptide are represented as a PEPTIDE_MOD_T. This stores
+ * a list of AA_MODS and the net mass change experienced by the
+ * peptide. PEPTIDE_MODs are defined in peptide_modifications.h
+ * AA_MODs are instantiated once after parsing the parameter file. All
+ * possible PEPTIDE_MODs are calcualted once and reused for each
+ * spectrum search. One PEPTIDE_MOD corresponds to one mass window
+ * that must be searched.
+ *
+ * $Revision: 1.7 $
+ */
+#ifndef MODIFICATION_FILE_H
+#define MODIFICATION_FILE_H
+
+#include <assert.h>
+#include "utils.h"
+#include "linked_list.h"
+#include "model/objects.h"
+#include "parameter.h"
+
+/* Public constants */
+static const int MAX_AA_MODS = 11;
+static const int MAX_PROTEIN_SEQ_LENGTH = 40000;
+static const int AA_LIST_LENGTH = 26; // A-Z
+static const int MOD_MASS_PRECISION = 2; // printed as X[1.23]X
+#define GET_AA_MASK 0x001F // 0000 0000 0001 1111
+#define GET_MOD_MASK 0xFFE0 // 1111 1111 1110 0000
+
+/**
+ * \struct _aa_mod
+ *
+ * Modification at the amino acid level. A single mass change that can
+ * occur on any of the residues listed. This information is given by
+ * the user in the parameter file. Also stores a character symbol
+ * assigned at runtime to be used in the sqt result file and an
+ * integer bitmask to be used to give each aa_mod a unique identifier.
+ */
+struct _aa_mod{
+ double mass_change; ///< the amount by which the mass of the residue changes
+ bool aa_list[AA_LIST_LENGTH];
+ ///< an array indexed by AA, true if can be modified
+ int max_per_peptide; ///< the maximum number of mods per peptide
+ MOD_POSITION_T position; ///< where the mod can occur in the pep/prot
+ int max_distance; ///< the max distance from the protein terminus
+ char symbol; ///< the character to represent the mod in sqt files
+ bool prevents_cleavage; ///< can modification prevent cleavage?
+ bool prevents_xlink; ///< can modification prevent xlink?
+ MODIFIED_AA_T identifier; ///< the bitmask assigned for unique ID
+};
+
+// this was moved to object.h b/c methods in peptide.h weren't compiling
+//typedef unsigned short MODIFIED_AA_T; ///< letters in the expanded peptide
+ ///alphabet, bits for mod1 mod2...aa
+#define MOD_SEQ_NULL (MODIFIED_AA_T)('Z' - 'A' + 1)
+//enum {MOD_SEQ_NULL = 'Z' - 'A' + 1};
+///< null terminating character of array
+
+/*
+ e.g. There are three aa_mods specified in this run and they are
+ given the masks mod1 1000_0000_0000_0000
+ mod2 0100_0000_0000_0000
+ mod3 0010_0000_0000_0000
+ The amino acid Y has the value
+ Y 0000_0000_0001_0011
+
+ Suppose you set the variable aa to Y. Do stuff. To ask "is aa
+ modified by mod2", do this. answer = mod2 AND aa; answer == 0
+ To change aa to be modified by modcalle2, aa = mod2 NOR aa
+ (i.e. !(mod2 || aa) ) now aa == 0100_0000_0001_0011
+ If we ask again, answer == 0100_0000_0000_0000
+ */
+
+/**
+ * \brief Allocate an AA_MOD, including space for the aa_list and
+ * initialize all fields to default values. Symbol and unique
+ * identifier are set according to index.
+ * \returns A heap allocated AA_MOD with default values.
+ */
+AA_MOD_T* new_aa_mod(int mod_idx);
+
+/**
+ * \brief Free the memory for an AA_MOD including the aa_list.
+ */
+void free_aa_mod(AA_MOD_T* mod);
+
+/**
+ * \brief Converts a MODIFIED_AA into a char, effectively unmodifying it.
+ * \returns The unmodified char representation of an aa.
+ */
+char modified_aa_to_char(MODIFIED_AA_T aa);
+
+/**
+ * \brief Converts a char representation of an aa to an unmodified aa
+ * of type MODIFIED_AA_T. Requires 'A' <= char <= 'Z'.
+ * \returns The MODIFIED_AA_T represnetation of an aa.
+ */
+MODIFIED_AA_T char_aa_to_modified(char aa);
+
+/**
+ * \brief Converts a MODIFIED_AA_T* to it's textual representation,
+ * i.e. a letter followed by between 0 and 11 symbols for the
+ * modifications made to the amino acid.
+ * \returns A newly allocated char* with amino acid and modifciation
+ * symbols.
+ */
+char* modified_aa_to_string_with_symbols(MODIFIED_AA_T aa);
+
+/**
+ * \brief Converts a MODIFIED_AA_T to it's textual representation,
+ * i.e. a letter either alone or followed by square braces containing
+ * the mass(es) of any modifications. If mass_format is
+ * MOD_MASSES_SEPARATE, all masses are listed in a comma-separated
+ * list. If MOD_MASS_ONLY, they are summed and returned in one
+ * number. If AA_PLUS_MOD, the mass of the residue plus the mass of
+ * the modifciation(s) is printed.
+ *
+ * \returns A newly allocated char* with amino acid and modifciation
+ * masses in square brackets.
+ */
+char* modified_aa_to_string_with_masses(MODIFIED_AA_T aa,
+ MASS_FORMAT_T mass_format,
+ int precision);
+/**
+ * \brief Take an array of MODIFIED_AA_T's and return an array of
+ * char's that includes the letter of each aa and the mass change of
+ * any modifications in brackets following the modified residue. If
+ * If is mass_format MOD_MASSES_SEPARATE, all masses are listed in a
+ * comma-separated list. If MOD_MASS_ONLY, they are summed and
+ * returned in one number. If AA_PLUS_MOD, the mass of the residue
+ * plus the mass of the modifciation(s) is printed.
+ *
+ * \returns A newly allocated array of characters, a text
+ * representation of the modified sequence.
+ */
+char* modified_aa_string_to_string_with_masses(
+ MODIFIED_AA_T* aa_string, // the modified aa's to translate
+ int length, // length of aa_string
+ MASS_FORMAT_T mass_format); // which mass value to print
+
+/**
+ * \brief Take an array of MODIFIED_AA_T's and return an array of
+ * char's that includes the letter of each aa and the symbol for all
+ * applied modifications.
+ *
+ * \returns A newly allocated array of characters, a text
+ * representation of the modified sequence.
+ */
+char* modified_aa_string_to_string_with_symbols(
+ MODIFIED_AA_T* aa_string, // modified aa's to translate
+ int length); // length of aa_string
+
+/**
+ * \brief Takes an array of MODIFIED_AA_T's and returns an array of
+ * char's, one for each amino acid in the sequence. It DOES NOT
+ * include any modification symbols. Use with caution.
+ * \returns A newly allocated char* with ONLY amino acids, all
+ * modifications are removed.
+ */
+char* modified_aa_to_unmodified_string(MODIFIED_AA_T* aa_string, int length);
+
+/**
+ * \brief Allocates an array of MODIFIED_AA_T's and populates it with
+ * the MODIFIED_AA_T value that corresponds to each sequence char
+ * value and trailing modification symbols or masses. Returns the new
+ * sequence via the mod_sequence argument.
+ *
+ * \returns The length of the mod_sequence array.
+ */
+int convert_to_mod_aa_seq(const std::string& sequence, MODIFIED_AA_T** mod_sequence,
+ MASS_FORMAT_T mass_format = MOD_MASS_ONLY);
+
+/**
+ * \brief Allocate a new MODIFIED_AA_T array and copy values into it.
+ */
+MODIFIED_AA_T* copy_mod_aa_seq(
+ const MODIFIED_AA_T* source,
+ int length);
+
+/**
+ * \brief Allocate a new MODIFIED_AA_T array and copy values into it.
+ */
+MODIFIED_AA_T* copy_mod_aa_seq(
+ const MODIFIED_AA_T* source ///< Sequence to copy
+ );
+
+/**
+ * \return a new modification sequence array. Can be off of already allocated
+ * arrays
+ */
+MODIFIED_AA_T* newModSeq();
+
+/**
+ * Releases the modification sequence back into the cache
+ */
+void freeModSeq(
+ MODIFIED_AA_T* &mod_seq ///< Sequence to release
+ );
+
+
+/**
+ * \brief Remove any characters not A-Z from a peptide sequence.
+ * \returns A newly allocated string with the given sequence less any
+ * modififcation symbols or masses.
+ */
+char* unmodify_sequence(const char* modified_seqeunce);
+
+/**
+ * \brief Remove any characters not A-Z from a peptide sequence.
+ */
+void unmodify_sequence_in_place(char* modified_seqeunce);
+
+/**
+ * \brief Determine if an array of MODIFIED_AA_T is a palindrome.
+ * Used by reverse_sequence to avoid returning a reversed sequence
+ * that is the same as the target. Ignores the first and last
+ * residues.
+ * \returns TRUE if the reversed sequence would be the same as the
+ * forward, otherwise FALSE.
+ */
+bool modified_aa_seq_is_palindrome(MODIFIED_AA_T* seq, int length);
+
+/**
+ * \brief Frees memory for an array of MODIFIED_AA_Ts. Assumes is
+ * terminated with the MOD_SEQ_NULL value
+ */
+void free_mod_aa_seq(MODIFIED_AA_T* seq);
+
+/**
+ * \brief checks to see if an amino acid is modified by a given mod
+ * \returns TRUE if aa is modified by mod
+ */
+bool is_aa_modified(MODIFIED_AA_T aa, AA_MOD_T* mod);
+
+/**
+ * \brief Determine if this modified amino acid can be modified by
+ * this modification.
+ *
+ * Checks the mod list of modifiable residues to see if aa is in the
+ * list. Also checks to see if aa has already been modified by this
+ * mod.
+ * \returns TRUE if it can be modified, else FALSE
+ */
+bool is_aa_modifiable(MODIFIED_AA_T aa, AA_MOD_T* mod);
+
+/**
+ * \brief Adds a modification to a MODIFIED_AA_T.
+ *
+ * Assumes that the aa is modifiable, no explicit check. If the aa is
+ * already modified for the mod, no change to aa.
+ */
+void modify_aa(MODIFIED_AA_T* aa, const AA_MOD_T* mod);
+
+/**
+ * \brief Return the AA_MOD_T associated with the given symbol. If
+ * the symbol does not represent a modification, returns null.
+ * Requires that parameters have been initialized.
+ */
+const AA_MOD_T* get_aa_mod_from_symbol(const char symbol);
+
+/**
+ * \brief Return the delta mass associated with the given modification
+ * symbol. If the symbol does not represent a modification, returns
+ * 0. Requires that parameters have been initialized.
+ */
+FLOAT_T get_mod_mass_from_symbol(const char symbol);
+
+/**
+ * \brief Return the AA_MOD_T associated with the given mass shift.
+ * The mass may either be from a single AA_MOD_T as given by the user
+ * or from any combination of AA_MOD_T's. If no AA_MOD_T(s) can be
+ * found for the mass, returns null.
+ * Requires that parameters have been initialized.
+ */
+const AA_MOD_T* get_aa_mod_from_mass(FLOAT_T mass);
+
+/**
+ * print all fields in mod. For debugging
+ */
+void print_a_mod(AA_MOD_T* mod);
+
+/* Setters and Getters */
+
+/**
+ * \brief Set the symbol used by this modification.
+ * \returns void
+ */
+void aa_mod_set_symbol(AA_MOD_T* mod, char symbol);
+
+/**
+ * \brief Set the mass change caused by this modification.
+ * \returns void
+ */
+void aa_mod_set_mass_change(AA_MOD_T* mod, double mass_change);
+/**
+ * \brief Get the mass change caused by this modification.
+ * \returns The mass change caused by this modification.
+ */
+double aa_mod_get_mass_change(const AA_MOD_T* mod);
+
+/**
+ * \brief Access to the aa_list of the AA_MOD_T struct. This pointer
+ * can be used to get or set the list of residues on which this mod
+ * can be placed.
+ * \returns A pointer to the list of amino acids on which this mod can
+ * be placed.
+ */
+bool* aa_mod_get_aa_list(AA_MOD_T* mod);
+
+/**
+ * \brief Set the maximum number of times this modification can be
+ * placed on one peptide.
+ * \returns void
+ */
+void aa_mod_set_max_per_peptide(AA_MOD_T* mod, int max);
+/**
+ * \brief Get the maximum number of times this modification can be
+ * placed on one peptide.
+ * \returns The max times per peptide this mod can be placed.
+ */
+int aa_mod_get_max_per_peptide(AA_MOD_T* mod);
+
+/**
+ * \brief Set the maximum distance from the protein terminus that the
+ * modification can be placed. Which terminus (C or N) is determined
+ * by the position type. To indicate no position restriction, set to
+ * MAX_PROTEIN_SEQ_LENGTH.
+ * \returns void
+ */
+void aa_mod_set_max_distance(AA_MOD_T* mod, int distance);
+/**
+ * \brief Get the maximum distance from the protein end that the
+ * modification can be placed. Will be MAX_PROTEIN_SEQ_LENGTH if
+ * position type is ANY_POSITION.
+ * \returns Maximum distance from protein terminus at which mod can be
+ * placed.
+ */
+int aa_mod_get_max_distance(AA_MOD_T* mod);
+
+/**
+ * \brief Set the position type of an aa_mod.
+ * \returns void
+ */
+void aa_mod_set_position(AA_MOD_T* mod, MOD_POSITION_T position);
+
+/**
+ * \brief Where in the peptide can the modification be placed.
+ * \returns ANY_POSITION for standard mods; C_TERM or N_TERM for those
+ * that can only be placed at the ends of the peptide.
+ */
+MOD_POSITION_T aa_mod_get_position(AA_MOD_T* mod);
+
+/**
+ * \brief Sets whether the modification can prevent cleavage.
+ * \returns void
+ */
+void aa_mod_set_prevents_cleavage(AA_MOD_T* mod, bool prevents_cleavage);
+
+/**
+ * \brief gets whether the modification can prevent cleavage
+ * \returns TRUE or FALSE
+ */
+bool aa_mod_get_prevents_cleavage(AA_MOD_T* mod);
+
+/**
+ * \brief Sets whether the modifications can prevent cross-linking.
+ * \returns void
+ */
+void aa_mod_set_prevents_xlink(AA_MOD_T* mod, bool prevents_xlink);
+
+/**
+ * \brief gets whether the modification can prevent cross-linking.
+ * \returns TRUE or FALSE
+ */
+bool aa_mod_get_prevents_xlink(AA_MOD_T* mod);
+
+/**
+ * \brief The character used to uniquely identify the mod in the sqt file.
+ * \returns The character identifier.
+ */
+char aa_mod_get_symbol(const AA_MOD_T* mod);
+
+/**
+ * \brief Generates a string representation of an aa_mod and returns a
+ * pointer to that newly allocated string.
+ */
+char* aa_mod_to_string(const AA_MOD_T* mod);
+
+/**
+ * \brief Create a string containing all of the amino acids that can
+ * be modified by this aa_mod. E.g. if S, T, and Y can be modified,
+ * returns "STY".
+ * \returns A newly allocated string.
+ */
+std::string aa_mod_get_aa_list_string(AA_MOD_T* mod);
+
+/**
+ * Count the number of modified aas in the string.
+ */
+int count_modified_aas(MODIFIED_AA_T* seq);
+
+#endif //MODIFICATION_FILE_H
+
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
+
diff --git a/src/util/peptide_modifications.cpp b/src/util/peptide_modifications.cpp
new file mode 100644
index 0000000..14933f6
--- /dev/null
+++ b/src/util/peptide_modifications.cpp
@@ -0,0 +1,814 @@
+/**
+ * \file modifications.cpp
+ * \brief Datatypes and methods for peptide modifications
+ *
+ * Two data structures define modifications. The AA_MOD_T is the most
+ * basic type. It is the information provided by the user: mass
+ * change caused by this mod, amino acids which may be modified in
+ * this way, and the maximum number of this type of modification which
+ * may occur on one peptide. AA_MODs are defined in modifications.h.
+ * A collection of AA_MODs that may occur
+ * on some peptide are represented as a PEPTIDE_MOD_T. This stores
+ * a list of AA_MODS and the net mass change experienced by the
+ * peptide. PEPTIDE_MODs are defined here.
+ * AA_MODs are instantiated once after parsing the parameter file. All
+ * possible PEPTIDE_MODs are calcualted once and reused for each
+ * spectrum search. One PEPTIDE_MOD corresponds to one mass window
+ * that must be searched.
+ *
+ * $Revision: 1.6 $
+ */
+
+#include "peptide_modifications.h"
+#include "model/Peptide.h"
+#include "Params.h"
+
+using namespace Crux;
+
+/* Private data types, typedefed in objects.h */
+/**
+ * \struct _peptide_mod
+ * A collection of aa modifications that can occur on a single
+ * peptide. Includes the list of aa_mods and the net mass
+ * change of all mods. Each aa_mod is included in the list as many
+ * times at it appears in the collection. There is no information about
+ * which residues in a peptide are modified.
+ */
+struct _peptide_mod{
+ double mass_change; ///< the net mass change for the peptide
+ int num_mods; ///< the number of items in the list_of_mods
+ int aa_mod_counts[MAX_AA_MODS]; ///< the number of each kind of aa mod
+ ///as listed in parameter.c
+};
+
+/* Private functions */
+int apply_mod_to_list(
+ LINKED_LIST_T* mod_seqs, ///< a pointer to a list of seqs
+ AA_MOD_T* mod_to_apply, ///< the specific mod to apply
+ int num_copies,
+ int max_aas_modified
+);
+
+int apply_mod_to_seq(
+ MODIFIED_AA_T* seq, ///< the seq to modify
+ AA_MOD_T* mod, ///< the mod to apply
+ int skip_n, ///< skip over n aas modified by this mod
+ LINKED_LIST_T* return_list); ///< the newly modified versions of
+
+
+/* Definitions of public methods */
+
+/**
+ * \brief Allocate a PEPTIDE_MOD and set all fields to default values
+ * (i.e. no modifications).
+ * \returns A heap allocated PEPTIDE_MOD with default values.
+ */
+PEPTIDE_MOD_T* new_peptide_mod() {
+ PEPTIDE_MOD_T* new_mod = (PEPTIDE_MOD_T*)mymalloc(sizeof(PEPTIDE_MOD_T));
+ new_mod->mass_change = 0;
+ new_mod->num_mods = 0;
+ int i = 0;
+ for (i = 0; i < MAX_AA_MODS; i++) {
+ new_mod->aa_mod_counts[i] = 0;
+ }
+ // add any fixed terminal mods by setting their count to 1
+ int index = get_fixed_mod_index(N_TERM);
+ AA_MOD_T** list = NULL;
+ get_all_aa_mod_list(&list);
+ if( index > -1 ) {
+ new_mod->aa_mod_counts[index] = 1;
+ new_mod->num_mods++;
+ new_mod->mass_change += aa_mod_get_mass_change(list[index]);
+ }
+ index = get_fixed_mod_index(C_TERM);
+ if( index > -1 ) {
+ new_mod->aa_mod_counts[index] = 1;
+ new_mod->num_mods++;
+ new_mod->mass_change += aa_mod_get_mass_change(list[index]);
+ }
+
+ return new_mod;
+}
+
+/**
+ * \brief Allocate a new peptide mod and copy contents of given mod
+ * into it.
+ * \returns A pointer to a new peptide mod which is a copy of the
+ * given one.
+ */
+PEPTIDE_MOD_T* copy_peptide_mod(PEPTIDE_MOD_T* original) {
+ PEPTIDE_MOD_T* copy = new_peptide_mod();
+ copy->mass_change = original->mass_change;
+ copy->num_mods = original->num_mods;
+ int i = 0;
+ for (i = 0; i < MAX_AA_MODS; i++) {
+ copy->aa_mod_counts[i] = original->aa_mod_counts[i];
+ }
+
+ return copy;
+}
+
+/**
+ * \brief Free the memory for a PEPTIDE_MOD including the aa_list.
+ */
+void free_peptide_mod(PEPTIDE_MOD_T* mod) {
+ if(mod) {
+ free(mod);
+ }
+}
+
+/* see below */
+int generate_peptide_mod_list_TESTER(
+ PEPTIDE_MOD_T*** peptide_mod_list,
+ AA_MOD_T** aa_mod_list,
+ int num_aa_mods);
+
+/**
+ * \brief Generate a list of all PEPTIDE_MODs that can be considered
+ * given the list of AA_MODs and POSITION_MODs provided by the user
+ * via the parameter file.
+ *
+ * This only needs to be called once for a search. The list of
+ * PEPTIDE_MODs can be reused for each spectrum. Allows at most one
+ * n-term and one c-term mod and at most mod->max_per_peptide
+ * modifications of one type per peptide. Sorts the list by number of
+ * aa mods and returns only the number of peptide mods that have
+ * between 0 and max-mods aa mods.
+ *
+ * The actual work is done in generate_peptide_mod_list_TESTER() so
+ * that it can be tested without going through parameter.c.
+ *
+ * \returns The number of peptide_mods listed in the
+ * peptide_mod_list argument.
+ */
+int generate_peptide_mod_list(
+ PEPTIDE_MOD_T*** peptide_mod_list ///< return here the list of peptide_mods
+) {
+ AA_MOD_T** aa_mod_list = NULL;
+ int num_aa_mods = get_all_aa_mod_list(&aa_mod_list);
+
+ // continued below
+ int count = generate_peptide_mod_list_TESTER( peptide_mod_list,
+ aa_mod_list, num_aa_mods);
+ return count;
+}
+
+int generate_peptide_mod_list_TESTER(
+ PEPTIDE_MOD_T*** peptide_mod_list,
+ AA_MOD_T** aa_mod_list,
+ int num_aa_mods) {
+
+ // initialize list of peptide mods with one unmodified peptide
+ LINKED_LIST_T* final_list = new_list( new_peptide_mod() );
+ int final_counter = 1;
+
+ // for each non-fixed aa_mod
+ int num_fixed_mods = get_num_fixed_mods();
+ for(int mod_list_idx = num_fixed_mods; mod_list_idx < num_aa_mods;
+ mod_list_idx++) {
+
+ AA_MOD_T* cur_aa_mod = aa_mod_list[mod_list_idx];
+ int cur_mod_max = aa_mod_get_max_per_peptide(cur_aa_mod);
+ char cur_mod_id = aa_mod_get_symbol(cur_aa_mod);
+ carp(CARP_DETAILED_DEBUG, "cur max %d, id %c", cur_mod_max, cur_mod_id);
+
+ // initialize temp list
+ LINKED_LIST_T* temp_list = new_empty_list();
+ int temp_counter = 0;
+
+ int copies = 1;
+ for(copies = 1; copies < cur_mod_max + 1; copies++) {
+
+ // for each pep_mod in final list
+ LIST_POINTER_T* final_ptr = get_first_linked_list(final_list);
+ while( final_ptr != NULL ) {
+ // get the current peptide mod
+ PEPTIDE_MOD_T* cur_pep_mod =
+ (PEPTIDE_MOD_T*)get_data_linked_list(final_ptr);
+ carp(CARP_DETAILED_DEBUG, "cur pep_mod has %d mods",
+ peptide_mod_get_num_aa_mods(cur_pep_mod));
+
+ // copy the peptide_mod and add to it i copies of cur_mod
+ PEPTIDE_MOD_T* mod_copy = copy_peptide_mod(cur_pep_mod);
+ //peptide_mod_add_aa_mod(mod_cpy, cur_aa_mod, copies);
+ peptide_mod_add_aa_mod(mod_copy, mod_list_idx, copies);
+ carp(CARP_DETAILED_DEBUG, "adding %d %c's to temp",
+ copies, cur_mod_id);
+
+ // add to temp list
+ //temp_list_end = add_linked_list(temp_list_end, mod_cpy);
+ push_back_linked_list(temp_list, mod_copy);
+
+ // if this is the first added, set the head of temp list
+ //temp_list = (temp_list == NULL) ? temp_list_end : temp_list;
+ temp_counter++;
+ final_ptr = get_next_linked_list(final_ptr);
+ }// last in final list
+
+ }// max copies
+
+ // append temp list to final list
+ carp(CARP_DETAILED_DEBUG, "adding temp list (%d) to final (%d)",
+ temp_counter, final_counter);
+ combine_lists(final_list, temp_list);
+ free(temp_list);
+ final_counter += temp_counter;
+ }// last aa_mod
+
+ // allocate an array of PEPTIDE_MOD_T* to return
+ PEPTIDE_MOD_T** final_array = (PEPTIDE_MOD_T**)mycalloc(final_counter,
+ sizeof(PEPTIDE_MOD_T*));
+ // fill in the array and delete the list
+ LIST_POINTER_T* final_list_ptr = get_first_linked_list(final_list);
+ int pep_idx = 0;
+ while(final_list_ptr != NULL) {
+ assert(pep_idx < final_counter);
+
+ final_array[pep_idx] =(PEPTIDE_MOD_T*)get_data_linked_list(final_list_ptr);
+ final_list_ptr = get_next_linked_list(final_list_ptr);
+ pep_idx++;
+ }
+
+ delete_linked_list(final_list);
+
+ // sort list
+ qsort(final_array, final_counter, sizeof(PEPTIDE_MOD_T*),
+ (QSORT_COMPARE_METHOD)compare_peptide_mod_num_aa_mods);
+
+ // find the index of the first peptide mod with too many aa mods
+ int max = 1; //Params::GetInt("max-mods");
+ // should use binary search...
+ int mod_idx = 0;
+ for(mod_idx = 0; mod_idx < final_counter; mod_idx++) {
+ if(final_array[mod_idx]->num_mods > max) {
+ break;
+ }
+ }
+
+ carp(CARP_INFO,
+ "Created %d peptide mods, keeping %d with %d or fewer aa mods",
+ final_counter, mod_idx, max);
+ // set return value
+ *peptide_mod_list = final_array;
+ // return final_counter;
+ return mod_idx;
+
+ /*
+ get the number of items in final list
+
+ init final_list to have one unmodified pep
+ init temp_list to empty
+
+ for each mod in aa_mod_list
+ for i 1 to mod_max
+ for each pep_mod in final_list
+ copy the pep_mod and add i aa_mods
+ add to the temp_list
+ end of final_list
+ end i==max
+ add the temp_list to the final_list
+ last mod
+
+ sort by num-mods, fewest to most
+ */
+}
+
+/**
+ * \brief Given the sequence, a modification, and the position for the sequence
+ * modification, determine whether this modification is valid.
+ * \returns true if the modification can be applied.
+ */
+bool is_sequence_position_modifiable(
+ char* sequence,
+ int position,
+ AA_MOD_T* mod) {
+
+ if(is_aa_modifiable(char_aa_to_modified(sequence[position]), mod)) {
+
+ if (aa_mod_get_prevents_cleavage(mod)) {
+ //make sure that position is not the beginning or end.
+ if (position == 0 || sequence[position+1] == '\0') {
+ return false;
+ } else {
+ return true;
+ }
+ } else {
+ //modification doesn't prevent cleavage, return true.
+ return true;
+ }
+ } else {
+ //aa is not modifiable by this modificationa
+ return false;
+ }
+}
+
+/**
+ * \brief Given the sequence, a modification, and the position for the sequence
+ * modification, determine whether this modification is valid.
+ * \returns true if the modification can be applied.
+ */
+bool is_sequence_position_modifiable(
+ MODIFIED_AA_T* sequence,
+ int position,
+ AA_MOD_T* mod) {
+
+ if( is_aa_modifiable( sequence[position], mod )) {
+
+ if (aa_mod_get_prevents_cleavage(mod)) {
+ //make sure that position is not the beginning or end.
+ if (position == 0 || sequence[position+1] == MOD_SEQ_NULL) {
+ return false;
+ } else {
+ return true;
+ }
+ } else {
+ //modification doesn't prevent cleavage, return true.
+ return true;
+ }
+ } else {
+ return false;
+ }
+}
+
+/**
+ * \brief Check a peptide sequence to see if the aa_mods in
+ * peptide_mod can be applied.
+ *
+ * Assumes that an amino acid can be modified by more than one aa_mod,
+ * but not more than once by a sligle aa_mod.
+ * \returns true if the sequence can be modified, else false
+ */
+bool is_peptide_modifiable(
+ Peptide* peptide, ///< The peptide to apply mods to
+ PEPTIDE_MOD_T* peptide_mod) { ///< The mods to apply
+
+ // a NULL peptide cannot be modified
+ if( peptide == NULL ) {
+ return false;
+ }
+ // peptide mods with no aa mods can be applied to any peptide
+ if( peptide_mod == NULL ||
+ peptide_mod_get_num_aa_mods( peptide_mod ) == 0 ) {
+ return true;
+ }
+
+ char* sequence = peptide->getSequence();
+
+ // for each aa_mod (skip those not in peptide_mod)
+
+ AA_MOD_T** all_mods = NULL;
+ int num_aa_mods = get_all_aa_mod_list(&all_mods);
+ assert( num_aa_mods < MAX_AA_MODS );
+
+ bool success = true;
+ for(int amod_idx = 0; amod_idx < num_aa_mods; amod_idx++) {
+
+ // FIRST: check to see if it is included in this pmod
+ if( peptide_mod->aa_mod_counts[amod_idx] == 0 ) {
+ continue;
+ }
+
+ // SECOND: check modifyability based on type
+ AA_MOD_T* cur_aa_mod = all_mods[amod_idx];
+ // for position-based mods, check distance from protein end
+ int max_distance = aa_mod_get_max_distance(cur_aa_mod);
+ int locations_count = 0;
+ int cur_seq_idx = 0;
+ switch( aa_mod_get_position(cur_aa_mod) ) {
+ case C_TERM:
+ if( max_distance < peptide->getCDistance()) {
+ success = false;
+ }
+ break;
+
+ case N_TERM:
+ if( max_distance < peptide->getNDistance()) {
+ success = false;
+ }
+ break;
+
+ // count leagal locations for this aa mod, compare with counts
+ case ANY_POSITION:
+ // look for an aa in the seq where this mod can be placed
+ while(sequence[cur_seq_idx] != '\0' ) {
+ if (is_sequence_position_modifiable(sequence, cur_seq_idx, cur_aa_mod)) {
+ locations_count++;
+ }// else keep looking
+ cur_seq_idx++;
+ }// end of sequence
+
+ if( locations_count < peptide_mod->aa_mod_counts[amod_idx] ) {
+ //return false;
+ success = false;
+ }
+ break;
+
+ }// end of switch
+
+ if( success == false ) {
+ break; // done look at any more aa_mods
+ }
+ }// next in aa_mod list
+
+ free(sequence);
+ return success;
+}
+
+// move this to peptide.c
+/*
+void add_peptide_mod_seq(Peptide* peptide, MODIFIED_AA_T* cur_mod_seq) {
+ if( peptide == NULL || cur_mod_seq == NULL ) {
+ carp(CARP_ERROR, "Cannot add NULL modified sequence to null peptide");
+ }
+
+ // test out that the mod seq is valid
+ int i = 0;
+ while( cur_mod_seq[i] != MOD_SEQ_NULL) {
+ printf("%d(%c) ", cur_mod_seq[i], (char)cur_mod_seq[i] + 'A');
+ i++;
+ }
+ printf("\n");
+}
+ */
+
+
+/**
+ * \brief Take a peptide and a peptide_mod and return via the third
+ * arguement a list of modified peptides.
+ *
+ * The peptide_mod should be guaranteed to be applicable to
+ * the peptide at least once. However, there may not be any modified
+ * forms that pass the max_aas_modified filter. For the peptide_mod to
+ * be successfully
+ * applied, every aa_mod in its list must be applied to the sequence
+ * as many times as its value in the aa_mods_counts array. A single
+ * amino acid can be modified multiple times by different aa_mods, but
+ * only once for a given aa_mod (as defined by modifiable()). The
+ * modified peptides will be added to the end of the modified_peptides
+ * list. Any existing elements in the list will not be removed.
+ *
+ * \returns The number of modified peptides in the list pointed to by
+ * modified_peptides.
+ */
+int modify_peptide(
+ Peptide* peptide, ///< the peptide to modify
+ PEPTIDE_MOD_T* peptide_mod, ///< the set of aa_mods to apply
+ LINKED_LIST_T* modified_peptides,///< the returned modified peptides
+ int max_aas_modified ///< filter out peptides > m_a_m
+) {
+
+ if( peptide == NULL ) {
+ carp(CARP_ERROR, "Cannot modify NULL peptide or use NULL peptide mod");
+ return 0;
+ }
+ if( modified_peptides == NULL ) {
+ carp(CARP_ERROR, "Cannot return modified peptides to NULL list.");
+ return 0;
+ }
+ // in case of no modifications
+ if( peptide_mod == NULL ||
+ peptide_mod_get_num_aa_mods(peptide_mod) == 0 ) {
+ carp(CARP_DETAILED_DEBUG,
+ "Modifying peptide with no aa_mods, return peptide copy");
+ Peptide* peptide_copy = new Peptide(peptide);
+ push_back_linked_list(modified_peptides, peptide_copy);
+ return 1;
+ }
+
+ // get the peptide sequence and convert to MODIFIED_AA_T*
+ char* sequence = peptide->getSequence();
+ MODIFIED_AA_T* pre_modified_seq = NULL;
+ convert_to_mod_aa_seq(sequence, &pre_modified_seq);
+
+ carp(CARP_DETAILED_DEBUG, "Modifying peptide %s", sequence);
+
+ // get the aa_mod info
+ int* aa_mod_counts = peptide_mod->aa_mod_counts;
+ AA_MOD_T** aa_mod_list = NULL;
+ int num_aa_mods = get_all_aa_mod_list(&aa_mod_list);
+
+ // initialize a list of modified seqs with the unmod seq
+ LINKED_LIST_T* modified_seqs = new_list(pre_modified_seq);
+ int aa_mod_idx = 0;
+ int total_count = 0;
+
+ // try applying each aa_mod to the sequence
+ for(aa_mod_idx = 0; aa_mod_idx < num_aa_mods; aa_mod_idx++) {
+
+ //printf("aaidx is %d and mod count is %d\n", aa_mod_idx, aa_mod_counts[aa_mod_idx]);
+ int mod_count = aa_mod_counts[aa_mod_idx];
+ if( mod_count == 0 ) { continue; } // do not apply this aa mod
+
+ //fprintf(stderr, "applying to list, total count is %d\n", total_count);
+ total_count = apply_mod_to_list(modified_seqs,
+ aa_mod_list[aa_mod_idx],
+ mod_count,
+ max_aas_modified);
+
+ //printf("after applying count is %d\n", total_count);
+ // the count should be > 0, but check for error case
+ if( total_count == 0 || is_empty_linked_list(modified_seqs) ) {
+ carp(CARP_DETAILED_DEBUG,
+ "Peptide modification could not be applied to sequence %s",
+ sequence);
+ return total_count; // free things...
+ }
+ } // next aa_mod
+
+ carp(CARP_DETAILED_DEBUG, "Sequence %s has %i modified forms.", sequence, total_count);
+ free(sequence);
+
+ // create a peptide for each sequence and add it to the list
+ // filter out those with more than max_aas_modified
+ total_count = 0;
+ while (!is_empty_linked_list(modified_seqs)) {
+ MODIFIED_AA_T* cur_mod_seq =
+ (MODIFIED_AA_T*)pop_front_linked_list(modified_seqs);
+ if (count_modified_aas(cur_mod_seq) > max_aas_modified) {
+ continue;
+ }
+
+ Peptide* cur_peptide = new Peptide(peptide);
+ cur_peptide->setMod(cur_mod_seq, peptide_mod);
+ freeModSeq(cur_mod_seq);
+ push_back_linked_list(modified_peptides, cur_peptide );
+ total_count++;
+ }
+ carp(CARP_DETAILED_DEBUG, "There were %i modified seqs created", total_count);
+ free(modified_seqs);
+ return total_count;
+}
+
+
+/**
+ * \brief Beginning with a list of modified seqs, apply another
+ * modification to each in as many ways as possible. Update the list
+ * to contain the new seqs.
+ *
+ * To be used for adding multiple modifications to a peptide
+ * sequence. Adding the first aa mod creates one list of seqs. The
+ * second aa mod is then applied to the list. Any seqs that can have
+ * both modifications applied is returned and those that cannot are
+ * removed from the list.
+ *
+ * \returns The number of modified seqs in the list.
+ */
+int apply_mod_to_list(
+ LINKED_LIST_T* apply_mod_to_these, ///< a pointer to a list of seqs
+ AA_MOD_T* mod_to_apply, ///< the specific mod to apply
+ int num_to_apply, ///< how many of this mod to apply
+ int max_aas_modified ///< don't return seqs with more than this many aas moded
+) {
+
+ /* Null cases */
+ if( is_empty_linked_list(apply_mod_to_these) ) { // nothing to apply mod to
+ return 0;
+ }
+
+ if( mod_to_apply == NULL ) { // no modification to add, return as is
+ // get the current count
+ LIST_POINTER_T* cur_seq = get_first_linked_list(apply_mod_to_these);
+ int num_seqs = 0;
+ while( cur_seq != NULL ) {
+ num_seqs++;
+ }
+ return num_seqs;
+ }
+
+ //printf("iterating over seqs in list, applying %d of mod %c\n",
+ // num_to_apply, aa_mod_get_symbol(mod_to_apply));
+
+ // initialize a temp list of seqs to return
+ LINKED_LIST_T* completed_seqs = new_empty_list();
+
+ int return_seq_count = 0;
+ int times_idx = 0;
+
+ // apply the mod num_to_apply times
+ for(times_idx = 0; times_idx < num_to_apply; times_idx++) {
+ // reset count
+ return_seq_count = 0;
+
+ // for each seq
+ while (!is_empty_linked_list(apply_mod_to_these)) {
+ // get modified seq
+ MODIFIED_AA_T* cur_seq =
+ (MODIFIED_AA_T*)pop_front_linked_list(apply_mod_to_these);
+
+ /*
+ char* print_me = modified_aa_string_to_string(cur_seq);
+ printf("Original: %s\n", print_me);
+ free(print_me);
+ */
+ return_seq_count += apply_mod_to_seq(cur_seq,
+ mod_to_apply,
+ times_idx, // skip n modified aas
+ completed_seqs);
+
+ //printf("Now there are %d seqs to return\n", return_seq_count);
+ freeModSeq(cur_seq);
+ }// apply to next seq until list is empty
+
+ // make the collected results the input to the next application
+ combine_lists(apply_mod_to_these, completed_seqs);
+ free(completed_seqs); // just deletes head, not full list
+ completed_seqs = new_empty_list();
+
+ }// apply next time
+
+ free( completed_seqs ); // just the head of the list
+
+ // Check all seqs in list and remove those with too many aas modified
+ // push a dummy onto the front for ease of deleting
+ // in a list nodeA->nodeB, we need nodeA to delete nodeB
+ // call A and B prev and cur
+ push_front_linked_list(apply_mod_to_these, NULL);
+ LIST_POINTER_T* prev_node = get_first_linked_list(apply_mod_to_these);
+ LIST_POINTER_T* cur_node = NULL;
+ MODIFIED_AA_T* cur_seq = NULL;
+
+ while (has_next_linked_list(prev_node)) {
+ cur_node = get_next_linked_list(prev_node);
+ cur_seq = (MODIFIED_AA_T*)get_data_linked_list(cur_node);
+
+ if (count_modified_aas(cur_seq) > max_aas_modified) {
+ // delete cur, set cur to node after prev
+ cur_node = delete_next_list_node(prev_node);
+ freeModSeq(cur_seq); // list delete doesn't remove data
+ } else
+ prev_node = cur_node;
+ cur_node = get_next_linked_list(prev_node);
+ cur_seq = (MODIFIED_AA_T*)get_data_linked_list(cur_node);
+ }// next seq
+ // pop the dummy off the front
+ pop_front_linked_list(apply_mod_to_these);
+
+ return return_seq_count;
+}
+
+/**
+ * \brief Beginning with a peptide sequence (of modified aas) and an
+ * aa_mod, return via the 'return_list' parameter a list of modified
+ * versions of the peptide sequence.
+ *
+ * The initial seq is left untouched. If the seq cannot be modified
+ * by the aa_mod, return_list is unchanged and 0 is returned. If the
+ * mod is NULL the return list is given one item, an unchanged copy of
+ * the seq.
+ *
+ * \returns The number of ways in which the sequence could be
+ * modified, i.e. the number of items added to return_list.
+ */
+// TODO (BF 17-Sep-08): could add seq length to make consistent with
+// other functions with MODIFIED_AA_T array parameters
+int apply_mod_to_seq(
+ MODIFIED_AA_T* seq, ///< the seq to modify
+ AA_MOD_T* mod, ///< the mod to apply
+ int skip_n, ///< pass over n aas modified by this mod
+ LINKED_LIST_T* return_list) { ///< the newly modified versions of the seq
+
+ // Boundry cases
+ if( seq == NULL ) {
+ return 0;
+ }
+ if( return_list == NULL ) {
+ carp(CARP_ERROR, "Cannot add modified sequences to a NULL list.");
+ return 0;
+ }
+
+ // find seq length (see TODO above)
+ int seq_len = 0;
+ while( seq[seq_len] != MOD_SEQ_NULL ) {
+ seq_len++;
+ }
+
+ // no modification to add, return seq as is
+ if( mod == NULL ) {
+ push_back_linked_list( return_list, copy_mod_aa_seq(seq, seq_len) );
+ return 1;
+ }
+
+ // special case: positional mods
+ if( N_TERM == aa_mod_get_position(mod) ) {
+ //MODIFIED_AA_T* seq_copy = copy_mod_aa_seq(seq);
+ MODIFIED_AA_T* seq_copy = copy_mod_aa_seq(seq, seq_len);
+ modify_aa( &seq_copy[0], mod );
+ push_back_linked_list(return_list, seq_copy);
+ return 1; // one added to list
+ }
+ if( C_TERM == aa_mod_get_position(mod)) {
+ //MODIFIED_AA_T* seq_copy = copy_mod_aa_seq(seq);
+ MODIFIED_AA_T* seq_copy = copy_mod_aa_seq(seq, seq_len);
+ /*
+ // find last index
+ int seq_idx = 0;
+ while( seq[seq_idx] != MOD_SEQ_NULL ) {
+ seq_idx++;
+ }
+ */
+ //modify_aa( &seq_copy[seq_idx-1], mod );
+ modify_aa( &seq_copy[seq_len-1], mod );
+ push_back_linked_list(return_list, seq_copy);
+ return 1; // one added to list
+ }
+
+ // first loop, skip over n modified aas in the seq
+ int seq_idx = 0;
+ while( seq[seq_idx] != MOD_SEQ_NULL && skip_n != 0) {
+ if( is_aa_modified( seq[seq_idx], mod ) ) {
+ skip_n--;
+ }
+ seq_idx++;
+ }// nex mod_aa; stop at end of seq or having skipped n
+
+ // second loop, for each aa: check for modifiability, copy and add
+
+ // check each aa
+ // copy seq when modifiable and add to list
+ int count = 0;
+ while( seq[seq_idx] != MOD_SEQ_NULL ) {
+ if (is_sequence_position_modifiable(seq, seq_idx, mod)) {
+ // MODIFIED_AA_T* seq_copy = copy_mod_aa_seq(seq);
+ MODIFIED_AA_T* seq_copy = copy_mod_aa_seq(seq, seq_len);
+ modify_aa( &seq_copy[seq_idx], mod );
+
+ push_back_linked_list(return_list, seq_copy);
+ count++;
+ }
+
+ seq_idx++;
+ }
+
+ return count;
+}
+
+/**
+ * print all fields in peptide mod. For debugging
+ */
+void print_p_mod(PEPTIDE_MOD_T* mod) {
+ printf("PMOD: mass %.2f, num %d, aa mods\n ",
+ mod->mass_change, mod->num_mods);
+ AA_MOD_T** all_mods = NULL;
+ int num_aa_mods = get_all_aa_mod_list( &all_mods );
+ assert( num_aa_mods < MAX_AA_MODS );
+ for(int i = 0; i < num_aa_mods; i++) {
+ print_a_mod( all_mods[i] );
+ printf(" ");
+ }
+ printf("\n");
+}
+
+/* Setters and Getters */
+/**
+ * \brief Add a new aa_mod to the peptide mod. Updates mass_change,
+ * num_mods and list_of_aa_mods. Does not enforce the copy number of
+ * an aa_mod to be less than max_per_peptide.
+ * \returns void
+ */
+void peptide_mod_add_aa_mod(
+ PEPTIDE_MOD_T* pep_mod, ///< The peptide mod being added to
+ int aa_mod_idx, ///< The index into the global list of aa mods
+ int copies ) { ///< How many of the aa_mod to add
+
+ AA_MOD_T** all_mods = NULL;
+ int num_aa_mods = get_all_aa_mod_list( &all_mods );
+ assert( num_aa_mods < MAX_AA_MODS );
+
+ //printf("mass change for amod of index %d is %.2f\n", aa_mod_idx, aa_mod_get_mass_change(all_mods[aa_mod_idx]));
+ pep_mod->mass_change += aa_mod_get_mass_change(all_mods[aa_mod_idx])
+ * copies;
+ //printf("pep mod mass change is now %.2f\n", pep_mod->mass_change );
+ pep_mod->num_mods += copies;
+
+ pep_mod->aa_mod_counts[aa_mod_idx] += copies;
+}
+
+/**
+ * \brief Get the value of the net mass change for this peptide_mod.
+ * \returns The mass change for the peptide mod.
+ */
+double peptide_mod_get_mass_change(PEPTIDE_MOD_T* mod) {
+ return mod->mass_change;
+}
+
+/**
+ * \brief Get the number of aa_mods in this peptide_mod.
+ * \returns The number of aa_mods in this peptide_mod.
+ */
+int peptide_mod_get_num_aa_mods(PEPTIDE_MOD_T* mod) {
+ return mod->num_mods;
+}
+
+/**
+ * \brief Compares the number of aa mods in two peptide mods for
+ * sorting.
+ * \returns Negative int, 0, or positive int if the number of aa_mods
+ * in pmod 1 is less than, equal to or greater than the number of
+ * aa_mods in pmod2, respectively.
+ */
+int compare_peptide_mod_num_aa_mods(const void* pmod1,
+ const void* pmod2) {
+ return (*(PEPTIDE_MOD_T**)pmod1)->num_mods
+ - (*(PEPTIDE_MOD_T**)pmod2)->num_mods;
+}
+
diff --git a/src/util/peptide_modifications.h b/src/util/peptide_modifications.h
new file mode 100644
index 0000000..6068b71
--- /dev/null
+++ b/src/util/peptide_modifications.h
@@ -0,0 +1,160 @@
+/**
+ * \file peptide_modifications.h
+ * \brief Datatypes and methods for peptide modifications
+ *
+ * Two data structures define modifications. The AA_MOD_T is the most
+ * basic type. It is the information provided by the user: mass
+ * change caused by this mod, amino acids which may be modified in
+ * this way, and the maximum number of this type of modification which
+ * may occur on one peptide. AA_MODs are defined in modifications.h.
+ * A collection of AA_MODs that may occur
+ * on some peptide are represented as a PEPTIDE_MOD_T. This stores
+ * a list of AA_MODS and the net mass change experienced by the
+ * peptide. PEPTIDE_MODs are defined here.
+ * AA_MODs are instantiated once after parsing the parameter file. All
+ * possible PEPTIDE_MODs are calcualted once and reused for each
+ * spectrum search. One PEPTIDE_MOD corresponds to one mass window
+ * that must be searched.
+ *
+ * $Revision: 1.5 $
+ */
+#ifndef PEPTIDE_MODIFICATIONS_H
+#define PEPTIDE_MODIFICATIONS_H
+
+#include <assert.h>
+#include "utils.h"
+#include "linked_list.h"
+#include "model/objects.h"
+#include "modifications.h"
+
+/**
+ * \brief Allocate a PEPTIDE_MOD and set all fields to default values
+ * (i.e. no modifications).
+ * \returns A heap allocated PEPTIDE_MOD with default values.
+ */
+PEPTIDE_MOD_T* new_peptide_mod();
+
+/**
+ * \brief Allocate a new peptide mod and copy contents of given mod
+ * into it.
+ * \returns A pointer to a new peptide mod which is a copy of the
+ * given one.
+ */
+PEPTIDE_MOD_T* copy_peptide_mod(PEPTIDE_MOD_T* original);
+
+/**
+ * \brief Free the memory for a PEPTIDE_MOD including the aa_list.
+ */
+void free_peptide_mod(PEPTIDE_MOD_T* mod);
+
+/**
+ * \brief Generate a list of all PEPTIDE_MODs that can be considered
+ * given the list of AA_MODs provided by the user and found in parameter.c.
+ *
+ * This only needs to be called once for a search. The list of
+ * PEPTIDE_MODs can be reused for each spectrum.
+ *
+ * \returns The number of peptide_mods returned in the
+ * peptide_mod_list argument.
+ */
+int generate_peptide_mod_list(
+ PEPTIDE_MOD_T*** peptide_mod_list ///< return here the list of peptide_mods
+);
+
+/**
+ * \brief Check a peptide sequence to see if the aa_mods in
+ * peptide_mod can be applied.
+ *
+ * Assumes that an amino acid can be modified by more than one aa_mod,
+ * but not more than once by a single aa_mod as defined in modifiable().
+ * \returns TRUE if the sequence can be modified, else FALSE
+ */
+bool is_peptide_modifiable( Crux::Peptide* peptide,
+ PEPTIDE_MOD_T* peptide_mod);
+
+
+/**
+ * \brief Take a peptide and a peptide_mod and return via parameters a
+ * list of modified peptides.
+ *
+ * The peptide_mod should be guaranteed to be able to be applied to
+ * the peptide at least once. A single amino acid can be modified
+ * multiple times by different aa_mods, but only once for a given
+ * aa_mod as defined in modifiable().
+ *
+ * \returns The number of modified peptides in the array pointed to by
+ * modified_peptides.
+ */
+int modify_peptide(Crux::Peptide* peptide,
+ PEPTIDE_MOD_T* peptide_mod,
+ LINKED_LIST_T* modified_peptides,
+ int max_aas_modified
+);
+
+/* Setters and Getters */
+/**
+ * \brief Add a new aa_mod to the peptide mod. Updates mass_change,
+ * num_mods and list_of_aa_mods. Does not enforce the copy number of
+ * an aa_mod to be less than max_per_peptide.
+ * \returns void
+ */
+void peptide_mod_add_aa_mod(PEPTIDE_MOD_T* pep_mod,
+ //AA_MOD_T* aa_mod,
+ int aa_mod_idx,
+ int copies );
+
+/**
+ * \brief Get the value of the net mass change for this peptide_mod.
+ * \returns The mass change for the peptide mod.
+ */
+double peptide_mod_get_mass_change(PEPTIDE_MOD_T* mod);
+
+/**
+ * \brief Get the number of aa_mods in this peptide_mod.
+ * \returns The number of aa_mods in this peptide_mod.
+ */
+int peptide_mod_get_num_aa_mods(PEPTIDE_MOD_T* mod);
+
+/**
+ * \brief Get a pointer to the list of aa_mods in this peptide_mod.
+ * The number of elements in the list is given by
+ * peptide_mod_get_num_aa_mods. A unique aa_mod may be listed more
+ * than once. There is no particular order to the aa_mods in the
+ * list.
+ * \returns A pointer to a list of AA_MOD_T pointers.
+ */
+LINKED_LIST_T* peptide_mod_get_aa_mod_list(PEPTIDE_MOD_T* mod);
+
+/**
+ * \brief Compares the number of aa mods in two peptide mods for
+ * sorting.
+ * \returns Negative int, 0, or positive int if the number of aa_mods
+ * in pmod 1 is less than, equal to or greater than the number of
+ * aa_mods in pmod2, respectively.
+ */
+int compare_peptide_mod_num_aa_mods(const void* pmod1,
+ const void* pmod2);
+
+/**
+ * print all fields in peptide mod. For debugging
+ */
+void print_p_mod(PEPTIDE_MOD_T* mod);
+
+
+#endif // PEPTIDE_MODIFICATIONS_H
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/src/util/utils.cpp b/src/util/utils.cpp
new file mode 100644
index 0000000..2b1c7a5
--- /dev/null
+++ b/src/util/utils.cpp
@@ -0,0 +1,469 @@
+/*********************************************************************
+ * \file utils.cpp
+ * AUTHOR: William Stafford Noble
+ * CREATE DATE: 9-8-97
+ * PROJECT: shared
+ * COPYRIGHT: 1997-2001 Columbia University
+ * DESCRIPTION: Various useful generic utilities.
+ ********************************************************************/
+#include <stdarg.h>
+#include <string.h>
+#ifdef _MSC_VER
+#include <Winsock2.h>
+#else
+#include <sys/time.h>
+#include <unistd.h>
+#endif
+#include <assert.h>
+#include <errno.h>
+#include "boost/random/mersenne_twister.hpp"
+#include "boost/random/uniform_int_distribution.hpp"
+#include "utils.h"
+#include "io/carp.h"
+#include "WinCrux.h"
+
+#ifdef INCLUDE_GETLINE
+
+/*********************************************************
+ This function replaces the GNU extension of the same name.
+ Reads a line from the given stream.
+ *********************************************************/
+int getline(char **lineptr, size_t *n, FILE *stream) {
+
+ const size_t BUFFSIZE = 100;
+
+ // Check the input values.
+ if (lineptr == NULL || stream == NULL) {
+ errno = EINVAL;
+ return -1;
+ }
+
+ // Read the first character from the stream.
+ size_t index = 0;
+ int c = fgetc(stream);
+ int e = ferror(stream);
+ if (c == EOF || e) {
+ return -1;
+ }
+
+ // Allocate an buffer if needed.
+ if (*lineptr == NULL) {
+ *lineptr = (char *) mymalloc((*n + BUFFSIZE) * sizeof(char));
+ *n += BUFFSIZE;
+ }
+
+ // Copy from the stream to the buffer until we find a line end.
+ while(c != '\n' && c != EOF && !e) {
+ (*lineptr)[index++] = c;
+ if (index > *n - 1) {
+ // Out of space, expand the buffer.
+ *lineptr = (char *) myrealloc(*lineptr, *n + BUFFSIZE);
+ *n += BUFFSIZE;
+ }
+ c = fgetc(stream);
+ e = ferror(stream);
+ }
+
+ // Reached end of line, end of file, or read error.
+ if (!e) {
+
+ if (c != EOF) {
+ (*lineptr)[index++] = c;
+ if (index > (*n - 1)) {
+ *lineptr = (char *) myrealloc(*lineptr, *n + 1);
+ (*n)++;
+ }
+ }
+
+ // Terminate the string.
+ (*lineptr)[index] = 0;
+
+ // Return the length of the string
+ // without the terminating null.
+ return index;
+ } else {
+ // Some sort of read error
+ return -1;
+ }
+}
+
+#endif
+
+/***********************************************************************
+ * Return the value to replace a missing value -- NaN.
+ ***********************************************************************/
+double NaN(void) {
+ return atof("NaN");
+}
+
+/***********************************************************************
+ * Return elapsed time in microseconds since the last call.
+ ***********************************************************************/
+double wall_clock() {
+ static int first_call = 1;
+ static double first_time;
+ double t;
+ struct timeval tp;
+
+ gettimeofday(&tp, NULL);
+ if (first_call == 1) {
+ first_time = (1E6*((double)tp.tv_sec)+
+ ((double)tp.tv_usec));
+ t = first_time;
+ first_call = 0;
+ } else {
+ t = (1E6*((double)tp.tv_sec)+
+ ((double)tp.tv_usec));
+ t = t - first_time;
+ }
+ return (double) t;
+}
+
+/************************************************************************
+ * See .h file for description.
+ ************************************************************************/
+bool open_file(
+ const char * filename, /* Name of the file to be opened. */
+ const char * file_mode, /* Mode to be passed to fopen. */
+ bool allow_stdin, /* If true, filename "-" is stdin. */
+ const char * file_description,
+ const char * content_description,
+ FILE ** afile /* Pointer to the open file. */
+) {
+ if (filename == NULL) {
+ carp(CARP_ERROR, "No %s filename specified.\n", file_description);
+ return(false);
+ } else if ((allow_stdin) && (strcmp(filename, "-") == 0)) {
+ if (strchr(file_mode, 'r') != NULL) {
+ carp(CARP_INFO, "Reading %s from stdin.\n", content_description);
+ *afile = stdin;
+ } else if (strchr(file_mode, 'w') != NULL) {
+ carp(CARP_INFO, "Writing %s to stdout.\n", content_description);
+ *afile = stdout;
+ } else {
+ carp(CARP_INFO, "Sorry, I can't figure out whether to use stdin ");
+ carp(CARP_INFO, "or stdout for %s.\n", content_description);
+ return(false);
+ }
+ } else if ((*afile = fopen(filename, file_mode)) == NULL) {
+ carp(CARP_INFO, "Error opening file %s.\n", filename);
+ return(false);
+ }
+ return(true);
+}
+
+/********************************************************************
+ * void mymalloc, mycalloc, myrealloc
+ *
+ * See .h file for descriptions.
+ ********************************************************************/
+void *mymalloc(size_t size) {
+ void * temp_ptr;
+
+ if (size == 0)
+ size++;
+
+ temp_ptr = malloc(size);
+
+ if (temp_ptr == NULL) {
+ carp(CARP_FATAL, "Memory exhausted. Cannot allocate %d bytes.", (int)size);
+ }
+
+
+ return(temp_ptr);
+}
+
+void *mycalloc(size_t nelem, size_t size) {
+ void * temp_ptr;
+
+ /* Make sure we allocate something. */
+ if (size == 0) {
+ size = 1;
+ }
+ if (nelem == 0) {
+ nelem = 1;
+ }
+
+ temp_ptr = calloc(nelem, size);
+
+ if (temp_ptr == NULL) {
+ carp(CARP_FATAL, "Memory exhausted. Cannot allocate %d bytes.", (int)size);
+ }
+
+ return(temp_ptr);
+}
+
+void * myrealloc(void * ptr, size_t size) {
+ void * temp_ptr;
+
+ /* Make sure we allocate something. */
+ if (size == 0)
+ size = 1;
+ assert(size > 0);
+
+ /* Some non-ANSI systems complain about reallocating NULL pointers. */
+ if (ptr == NULL) {
+ temp_ptr = malloc(size);
+ } else {
+ temp_ptr = realloc(ptr, size);
+ }
+
+ if (temp_ptr == NULL) {
+ carp(CARP_FATAL, "Memory exhausted. Cannot allocate %d bytes.", (int)size);
+ }
+
+ return(temp_ptr);
+}
+
+/********************************************************************
+ * fwrite with a check to make sure it was successful (useful for NFS problems)
+ ********************************************************************/
+bool myfwrite(
+ const void *ptr,
+ size_t size,
+ size_t nitems,
+ FILE *stream
+) {
+ size_t ret = fwrite(ptr, size, nitems, stream);
+ if (nitems != ret) {
+ carp(CARP_ERROR, "Problem writing %i items", nitems);
+ return false;
+ }
+ return true;
+}
+
+/**********************************************************************
+ * Compute a logarithm.
+ **********************************************************************/
+PROB_T my_log(PROB_T x) {
+ if (x > 0.0) {
+ return(LOG_VALUE(log(x)));
+ } else if (x < 0.0) {
+ carp(CARP_FATAL, "Tried to take the log of a negative value (%g).", x);
+ } /* else if (x == 0.0) */
+ return(LOG_ZERO);
+}
+
+/* The lookup table. */
+static const int LOG_PRECISION = 100000;
+static PROB_T log_table[(int) LOG_PRECISION + 2];
+
+/**********************************************************************
+ * Set up lookup table for log(x), 0 <= x <= 1.
+ **********************************************************************/
+void init_log_prob(void) {
+ int i_table;
+ PROB_T table_value;
+
+ log_table[0] = LOG_ZERO;
+ for (i_table = 1; i_table <= LOG_PRECISION; i_table++) {
+ table_value = (double)(i_table / LOG_PRECISION);
+ log_table[i_table] = log(table_value);
+ }
+ log_table[i_table] = 0; /* For use in iterpolation when x=1 */
+}
+
+/**********************************************************************
+ * Efficiently find log(x), when 0 < x <= 1. Doesn't check bounds.
+ **********************************************************************/
+PROB_T log_prob (PROB_T value) {
+ const PROB_T scaled_value = value * LOG_PRECISION;
+ const int log_index = (int)scaled_value;
+ const PROB_T decimal_part = scaled_value - log_index;
+ const PROB_T lower_value = log_table[log_index];
+ const PROB_T upper_value = log_table[log_index+1];
+ const PROB_T interpolation = decimal_part * (lower_value - upper_value);
+
+ if (value == 0.0) {
+ return(LOG_ZERO);
+ }
+ return(lower_value + interpolation);
+}
+
+
+/**************************************************************************
+ * See .h file for description.
+ **************************************************************************/
+bool is_zero (double value, bool log_form) {
+ if ((log_form) && (value < LOG_SMALL)) {
+ return(true);
+ } else if ((!log_form) && (value == 0.0)) {
+ return(true);
+ } else {
+ return(false);
+ }
+}
+
+/**************************************************************************
+ * See .h file for description.
+ **************************************************************************/
+bool almost_equal(double value1, double value2, double slop) {
+ if ((value1 - slop > value2) || (value1 + slop < value2)) {
+ return(false);
+ } else {
+ return(true);
+ }
+}
+
+/**************************************************************************
+ * Generic functions for converting between integer and string
+ * representations of an enumerated type.
+ *
+ * Assumes that the longest string representation of the enumerated
+ * type does not exceed 100 characters.
+ *
+ * Assumes that the zeroth enumerated type element is invalid.
+ **************************************************************************/
+const char * convert_enum_type (
+ int enum_type, /* The enumerated type object to be converted. */
+ const char * enum_strs[], /* String values associated with this type. */
+ int num_enums /* Number of values of the type. */
+) {
+ if ((enum_type <= 0) || (enum_type >= num_enums)) {
+ carp(CARP_FATAL, "Illegal enumerated type value (%d).", enum_type);
+ }
+
+ return(enum_strs[enum_type]);
+}
+
+int convert_enum_type_str(
+ const char * enum_type_str, /* String to be converted. */
+ int default_value, /* Value to return if string not found. */
+ const char ** enum_strs, /* String values associated with this type. */
+ int num_enums /* Number of values of the type. */
+) {
+ int i_enum;
+
+ /* If no string was given, return the default. */
+ if (enum_type_str == NULL) {
+ return(default_value);
+ }
+
+ /* Search for the value corresponding to the given string. */
+ for (i_enum = 0; i_enum < num_enums; i_enum++) {
+ if (strcmp(enum_type_str, enum_strs[i_enum]) == 0) {
+ return(i_enum);
+ }
+ }
+ // carp(CARP_FATAL, "Illegal value (%s).", enum_type_str);
+ // exit(1);
+ return( default_value );
+}
+
+/*******************************************************************************
+ * \brief Get the name of the CPU.
+ ****************************************************************************/
+static const int MAX_HOST_NAME = 100;
+const char* hostname() {
+ static char the_hostname[MAX_HOST_NAME];
+#ifdef _MSC_VER
+ WSADATA wsaData;
+ WSAStartup(MAKEWORD(2, 2), &wsaData);
+#endif
+ int result = gethostname(the_hostname, MAX_HOST_NAME);
+ if (result != 0) {
+ snprintf(the_hostname, MAX_HOST_NAME, "unknown");
+ }
+
+ return(the_hostname);
+}
+
+/*******************************************************************************
+ * \brief Get the current date and time.
+ ****************************************************************************/
+const char* date_and_time() {
+ FILE * date_stream;
+ static char the_date[MAX_HOST_NAME];
+ static bool first_time = true;
+
+ if (first_time) {
+ // FIXME: we should be able to get the date
+ // from a function call rather than having
+ // to call a shell command.
+#ifdef _MSC_VER
+ date_stream = (FILE *)popen("date /T", "r");
+#else
+ date_stream = (FILE *)popen("date", "r");
+#endif
+ if (fgets(the_date, MAX_HOST_NAME, date_stream) == NULL) {
+ return NULL;
+ }
+ pclose(date_stream);
+ }
+
+ /* Remove the EOL. */
+ assert(the_date[strlen(the_date)-1] == '\n');
+ the_date[strlen(the_date)-1] = '\0';
+
+ first_time = false;
+ return(the_date);
+}
+
+/**
+ * parses a file of length max_lines and returns an array of strings
+ */
+char** parse_file(
+ char* file_name,
+ int max_lines,
+ int* num_lines
+) {
+
+ FILE *infile;
+ if (open_file(file_name, "r", 1, "input", "", &infile) == 0)
+ exit(1);
+
+ size_t buf_length = 1024;
+ char** lines = (char**) mycalloc(max_lines, sizeof(char*));
+ int line_idx = 0;
+ int length = 0;
+ while ((length = getline(&lines[line_idx], &buf_length, infile)) != -1) {
+ char* line = lines[line_idx];
+ if (line[length-2] == '\n' || line[length-2] == '\r') {
+ line[length-2] = '\0';
+ } else if (line[length-1] == '\n' || line[length-1] == '\r') {
+ line[length-1]='\0';
+ }
+ line_idx++;
+ if (line_idx >= max_lines) {
+ carp(CARP_FATAL, "Number of lines in %s exceeds maximum of %i!",
+ file_name, max_lines);
+ }
+ }
+ free(lines[line_idx]);
+ fclose(infile);
+ *num_lines = line_idx;
+
+ return lines;
+}
+
+boost::mt19937& get_mt19937() {
+ static boost::mt19937 mt19937_;
+ return mt19937_;
+}
+
+/**
+ * Returns an integer in the range between 0 and UNIFORM_INT_DISTRIBUTION_MAX
+ */
+int myrandom() {
+ static boost::random::uniform_int_distribution<>
+ uniform_int_distribution_(0, UNIFORM_INT_DISTRIBUTION_MAX);
+ return uniform_int_distribution_(get_mt19937());
+}
+
+/**
+ * Returns an integer in the range [0, max)
+ */
+int myrandom_limit(int max) {
+ return myrandom() % max;
+}
+
+void mysrandom(unsigned seed) {
+ get_mt19937().seed(seed);
+}
+
+/*
+ * Local Variables:
+ * mode: c
+ * c-basic-offset: 2
+ * End:
+ */
diff --git a/src/util/utils.h b/src/util/utils.h
new file mode 100644
index 0000000..2e038fe
--- /dev/null
+++ b/src/util/utils.h
@@ -0,0 +1,247 @@
+/**
+ * \file utils.h
+ * \brief Various useful generic utilities.
+ ********************************************************************/
+// AUTHOR: William Stafford Noble
+// CREATE DATE: 9-8-97
+
+#ifndef UTILS_H
+#define UTILS_H
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <limits>
+
+/*#ifndef linux
+#include <ieeefp.h>
+#endif*/
+
+// Macro allowing us to build using floats or double
+#ifdef USE_DOUBLES
+typedef double FLOAT_T;
+#else
+typedef float FLOAT_T;
+#endif
+
+#define FLOAT_T_MIN numeric_limits<FLOAT_T>::min();
+
+
+typedef int VERBOSE_T;
+static const int INVALID_VERBOSE = 0;
+static const int QUIET_VERBOSE = 1;
+static const int NORMAL_VERBOSE = 2;
+static const int HIGH_VERBOSE = 3;
+static const int HIGHER_VERBOSE = 4;
+static const int DUMP_VERBOSE = 5;
+
+static const int FILENAME_LENGTH = 4096;
+static const int BAD_SCORE = -1;
+static const int IDLENGTH = 256;
+static const int PEPTIDELENGTH = 80;
+static const int LINELENGTH = 4096;
+
+extern int verbosity;
+
+#define UNIFORM_INT_DISTRIBUTION_MAX 2147483647 // Max value of int32
+
+#ifdef DARWIN
+#ifdef PRE_LION
+#define INCLUDE_GETLINE
+#endif
+#endif
+#ifdef _MSC_VER
+#define INCLUDE_GETLINE
+#endif
+
+#ifdef INCLUDE_GETLINE
+/*********************************************************
+ This function replaces the GNU extension of the same name.
+ Reads a line from the given stream.
+ *********************************************************/
+int getline(char **lineptr, size_t *n, FILE *stream);
+#endif
+
+/***********************************************************************
+ * Return a not-a-number.
+ ***********************************************************************/
+double NaN(void);
+
+/***********************************************************************
+ * Return elapsed time in microseconds since the last call.
+ ***********************************************************************/
+double wall_clock(void);
+
+/************************************************************************
+ * int open_file
+ *
+ * Open a file gracefully.
+ *
+ * RETURN: Was the open successful?
+ ************************************************************************/
+bool open_file(
+ const char* filename, // Name of the file to be opened.
+ const char* file_mode, // Mode to be passed to fopen.
+ bool allow_stdin, // If true, filename "-" is stdin.
+ const char* file_description,
+ const char* content_description,
+ FILE** afile); // Pointer to the open file.
+
+/********************************************************************
+ * DEBUG_CODE (macro)
+ *
+ * Allow debugging code to be included or excluded from a compiled
+ * program.
+ ********************************************************************/
+#ifdef DEBUG
+#define DEBUG_CODE( debug_value, code_fragment ) \
+ { if (debug_value) { code_fragment } }
+#else
+#define DEBUG_CODE( debug_value, code_fragment )
+#endif
+
+/********************************************************************
+ * Allocate dynamic memory. Die gracefully if memory is exhausted.
+ ********************************************************************/
+void *mymalloc(size_t size);
+void *mycalloc(size_t nelem, size_t size);
+void *myrealloc(void * ptr, size_t size);
+
+/********************************************************************
+ * fwrite with a check to make sure it was successful (useful for NFS problems)
+ ********************************************************************/
+bool myfwrite(const void *ptr, size_t size, size_t nitems, FILE *stream);
+
+/********************************************************************
+ * Math macros.
+ ********************************************************************/
+/* Note that the following type must be the same as the MTYPE and ATYPE
+ defined in 'matrix.h' and 'array.h'. */
+typedef double PROB_T; // Type definition for probability/frequency.
+#define PROB_SCAN " %lf" // Scanf string for PROB_T.
+
+#define LOG_ZERO (-1.0E10) // Zero on the log scale.
+#define LOG_SMALL (-0.5E10) // Threshold below which everything is zero.
+#define BITS (33.2) // = LOG2(-LOG_ZERO)
+
+#ifndef MIN
+#define MIN(a, b) (((a) < (b)) ? (a) : (b))
+#endif
+#ifndef MAX
+#define MAX(a, b) (((a) > (b)) ? (a) : (b))
+#endif
+
+/***************************************************************************
+ * Find the nearest integer.
+ ***************************************************************************/
+#define nint(x) ((int)((x) >= 0 ? ((x) + 0.5) : ((x) - 0.5)))
+
+/**************************************************************************
+ * Compute the logarithm of x, when 0 <= x <= 1.
+ **************************************************************************/
+void init_log_prob
+ (void);
+
+PROB_T log_prob
+ (PROB_T value);
+
+#define log_prob2(x) (log_prob(x) * 1.44269504)
+
+/**************************************************************************
+ * Compute the logarithm of x. Returns LOG_ZERO if x==0.
+ **************************************************************************/
+PROB_T my_log
+ (PROB_T x);
+
+#define my_log2(x) (my_log(x) * 1.44269504)
+
+#define EXP2(x) \
+( ( (x) < LOG_SMALL) ? \
+ 0.0 : \
+ (exp((x) * 0.69314718 )) \
+)
+
+/**************************************************************************
+ * Given the logs (in base 2) of two numbers, return the log of their
+ * sum.
+ *
+ * This function is optimized based upon the following formula:
+ *
+ * log(x+y) = log(x) + log(1 + exp(log(y) - log(x)))
+ *
+ **************************************************************************/
+#define LOG_VALUE(logx) \
+( ( (logx) < LOG_SMALL ) ? \
+ LOG_ZERO : \
+ (logx) \
+)
+
+#define LOG_SUM1(logx, logy) \
+( \
+ ( ( (logx) - (logy) ) > BITS ) ? \
+ LOG_VALUE(logx) : \
+ (logx) + my_log2( 1 + EXP2((logy) - (logx) ) ) \
+)
+
+#define LOG_SUM(logx, logy) \
+( \
+ ( (logx) > (logy) ) ? \
+ LOG_SUM1( (logx), (logy) ) : \
+ LOG_SUM1( (logy), (logx) ) \
+)
+
+/**************************************************************************
+ * Test for zero on a value that may be either a log or a raw float.
+ **************************************************************************/
+bool is_zero(double value, bool log_form);
+
+/**************************************************************************
+ * Test to see if two values are approximately equal.
+ **************************************************************************/
+bool almost_equal(double value1, double value2, double slop);
+
+/**************************************************************************
+ * Generic functions for converting between integer and string
+ * representations of an enumerated type.
+ *
+ * Assumes that the longest string representation of the enumerated
+ * type does not exceed 100 characters.
+ *
+ * Assumes that the zeroth enumerated type element is invalid.
+ **************************************************************************/
+const char* convert_enum_type(
+ int enum_type, /* The enumerated type object to be converted. */
+ const char* enum_strs[], /* String values associated with this type. */
+ int num_enums); /* Number of values of the type. */
+
+int convert_enum_type_str(
+ const char* enum_type_str, /* String to be converted. */
+ int default_value, /* Value to return if first arg is null. */
+ const char** enum_strs, /* String values associated with this type. */
+ int num_enums); /* Number of values of the type. */
+
+/**************************************************************************
+ * Get the name of the CPU.
+ **************************************************************************/
+const char* hostname(void);
+
+/**************************************************************************
+ * Get the current date and time.
+ **************************************************************************/
+const char* date_and_time(void);
+
+/************************************************************************
+ * parses a file of length max_lines and returns an array of strings
+ ************************************************************************/
+char** parse_file(
+ char* file_name,
+ int max_lines,
+ int* num_lines
+ );
+
+int myrandom();
+int myrandom_limit(int max);
+void mysrandom(unsigned seed);
+
+#endif
+
diff --git a/src/util/windirent.h b/src/util/windirent.h
new file mode 100644
index 0000000..3dbca46
--- /dev/null
+++ b/src/util/windirent.h
@@ -0,0 +1,369 @@
+/*****************************************************************************
+ * dirent.h - dirent API for Microsoft Visual Studio
+ *
+ * Copyright (C) 2006 Toni Ronkko
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining
+ * a copy of this software and associated documentation files (the
+ * ``Software''), to deal in the Software without restriction, including
+ * without limitation the rights to use, copy, modify, merge, publish,
+ * distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject to
+ * the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included
+ * in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED ``AS IS'', WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ * OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ * IN NO EVENT SHALL TONI RONKKO BE LIABLE FOR ANY CLAIM, DAMAGES OR
+ * OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ * ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ *
+ * Aug 11, 2010, Toni Ronkko
+ * Added d_type and d_namlen fields to dirent structure. The former is
+ * especially useful for determining whether directory entry represents a
+ * file or a directory. For more information, see
+ * http://www.delorie.com/gnu/docs/glibc/libc_270.html
+ *
+ * Aug 11, 2010, Toni Ronkko
+ * Improved conformance to the standards. For example, errno is now set
+ * properly on failure and assert() is never used. Thanks to Peter Brockam
+ * for suggestions.
+ *
+ * Aug 11, 2010, Toni Ronkko
+ * Fixed a bug in rewinddir(): when using relative directory names, change
+ * of working directory no longer causes rewinddir() to fail.
+ *
+ * Dec 15, 2009, John Cunningham
+ * Added rewinddir member function
+ *
+ * Jan 18, 2008, Toni Ronkko
+ * Using FindFirstFileA and WIN32_FIND_DATAA to avoid converting string
+ * between multi-byte and unicode representations. This makes the
+ * code simpler and also allows the code to be compiled under MingW. Thanks
+ * to Azriel Fasten for the suggestion.
+ *
+ * Mar 4, 2007, Toni Ronkko
+ * Bug fix: due to the strncpy_s() function this file only compiled in
+ * Visual Studio 2005. Using the new string functions only when the
+ * compiler version allows.
+ *
+ * Nov 2, 2006, Toni Ronkko
+ * Major update: removed support for Watcom C, MS-DOS and Turbo C to
+ * simplify the file, updated the code to compile cleanly on Visual
+ * Studio 2005 with both unicode and multi-byte character strings,
+ * removed rewinddir() as it had a bug.
+ *
+ * Aug 20, 2006, Toni Ronkko
+ * Removed all remarks about MSVC 1.0, which is antiqued now. Simplified
+ * comments by removing SGML tags.
+ *
+ * May 14 2002, Toni Ronkko
+ * Embedded the function definitions directly to the header so that no
+ * source modules need to be included in the Visual Studio project. Removed
+ * all the dependencies to other projects so that this very header can be
+ * used independently.
+ *
+ * May 28 1998, Toni Ronkko
+ * First version.
+ *****************************************************************************/
+#ifndef DIRENT_H
+#define DIRENT_H
+
+#define WIN32_LEAN_AND_MEAN
+#include <windows.h>
+#include <string.h>
+#include <stdlib.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+
+/* File type and permission flags for stat() */
+#if defined(_MSC_VER) && !defined(S_IREAD)
+# define S_IFMT _S_IFMT /* file type mask */
+# define S_IFDIR _S_IFDIR /* directory */
+# define S_IFCHR _S_IFCHR /* character device */
+# define S_IFFIFO _S_IFFIFO /* pipe */
+# define S_IFREG _S_IFREG /* regular file */
+# define S_IREAD _S_IREAD /* read permission */
+# define S_IWRITE _S_IWRITE /* write permission */
+# define S_IEXEC _S_IEXEC /* execute permission */
+#endif
+#define S_IFBLK 0 /* block device */
+#define S_IFLNK 0 /* link */
+#define S_IFSOCK 0 /* socket */
+
+#if defined(_MSC_VER)
+# define S_IRUSR S_IREAD /* read, user */
+# define S_IWUSR S_IWRITE /* write, user */
+# define S_IXUSR 0 /* execute, user */
+# define S_IRGRP 0 /* read, group */
+# define S_IWGRP 0 /* write, group */
+# define S_IXGRP 0 /* execute, group */
+# define S_IROTH 0 /* read, others */
+# define S_IWOTH 0 /* write, others */
+# define S_IXOTH 0 /* execute, others */
+# define S_IRWXU S_IREAD | S_IWRITE | S_IEXEC /* read, write, execute user */
+# define S_IRWXG 0 /* read, write, execute group */
+# define S_IRWXO 0 /* read, write, execute othter */
+#endif
+
+/* Indicates that d_type field is available in dirent structure */
+#define _DIRENT_HAVE_D_TYPE
+
+/* File type flags for d_type */
+#define DT_UNKNOWN 0
+#define DT_REG S_IFREG
+#define DT_DIR S_IFDIR
+#define DT_FIFO S_IFFIFO
+#define DT_SOCK S_IFSOCK
+#define DT_CHR S_IFCHR
+#define DT_BLK S_IFBLK
+
+/* Macros for converting between st_mode and d_type */
+#define IFTODT(mode) ((mode) & S_IFMT)
+#define DTTOIF(type) (type)
+
+/*
+ * File type macros. Note that block devices, sockets and links cannot be
+ * distinguished on Windows and the macros S_ISBLK, S_ISSOCK and S_ISLNK are
+ * only defined for compatibility. These macros should always return false
+ * on Windows.
+ */
+#define S_ISFIFO(mode) (((mode) & S_IFMT) == S_IFFIFO)
+#define S_ISDIR(mode) (((mode) & S_IFMT) == S_IFDIR)
+#define S_ISLNK(mode) (((mode) & S_IFMT) == S_IFLNK)
+#define S_ISSOCK(mode) (((mode) & S_IFMT) == S_IFSOCK)
+#define S_ISCHR(mode) (((mode) & S_IFMT) == S_IFCHR)
+#define S_ISBLK(mode) (((mode) & S_IFMT) == S_IFBLK)
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+
+typedef struct dirent {
+ char d_name[MAX_PATH + 1]; /* File name */
+ size_t d_namlen; /* Length of name without \0 */
+ int d_type; /* File type */
+} dirent;
+
+
+typedef struct DIR {
+ dirent curentry; /* Current directory entry */
+ WIN32_FIND_DATAA find_data; /* Private file data */
+ int cached; /* True if data is valid */
+ HANDLE search_handle; /* Win32 search handle */
+ char patt[MAX_PATH + 3]; /* Initial directory name */
+} DIR;
+
+
+/* Forward declarations */
+static void copy_dirent(struct dirent *src, struct dirent *dest);
+static DIR *opendir(const char *dirname);
+static struct dirent *readdir(DIR *dirp);
+static int closedir(DIR *dirp);
+static void rewinddir(DIR* dirp);
+
+
+/* Use the new safe string functions introduced in Visual Studio 2005 */
+#if defined(_MSC_VER) && _MSC_VER >= 1400
+# define DIRENT_STRNCPY(dest, src, size) strncpy_s((dest), (size), (src), _TRUNCATE)
+#else
+# define DIRENT_STRNCPY(dest, src, size) strncpy((dest), (src), (size))
+#endif
+
+/* Set errno variable */
+#if defined(_MSC_VER)
+#define DIRENT_SET_ERRNO(x) _set_errno (x)
+#else
+#define DIRENT_SET_ERRNO(x) (errno = (x))
+#endif
+
+/*****************************************************************************
+ * Copy a dirent structure.
+ */
+static void copy_dirent(struct dirent *src, struct dirent *dest) {
+ dest->d_type = src->d_type;
+ dest->d_namlen = src->d_namlen;
+ strncpy(dest->d_name, src->d_name, src->d_namlen + 1);
+}
+
+/*****************************************************************************
+ * Open directory stream DIRNAME for read and return a pointer to the
+ * internal working area that is used to retrieve individual directory
+ * entries.
+ */
+static DIR *opendir(const char *dirname) {
+ DIR *dirp;
+
+ /* ensure that the resulting search pattern will be a valid file name */
+ if (dirname == NULL) {
+ DIRENT_SET_ERRNO (ENOENT);
+ return NULL;
+ }
+ if (strlen (dirname) + 3 >= MAX_PATH) {
+ DIRENT_SET_ERRNO (ENAMETOOLONG);
+ return NULL;
+ }
+
+ /* construct new DIR structure */
+ dirp = (DIR*) malloc (sizeof (struct DIR));
+ if (dirp != NULL) {
+ int error;
+
+ /*
+ * Convert relative directory name to an absolute directory one. This
+ * allows rewinddir() to function correctly when the current working
+ * directory is changed between opendir() and rewinddir().
+ */
+ if (GetFullPathNameA (dirname, MAX_PATH, dirp->patt, NULL)) {
+ char *p;
+
+ /* append the search pattern "\\*\0" to the directory name */
+ p = strchr (dirp->patt, '\0');
+ if (dirp->patt < p && *(p-1) != '\\' && *(p-1) != ':') {
+ *p++ = '\\';
+ }
+ *p++ = '*';
+ *p = '\0';
+
+ /* open directory stream and retrieve the first entry */
+ dirp->search_handle = FindFirstFileA (dirp->patt, &dirp->find_data);
+ if (dirp->search_handle != INVALID_HANDLE_VALUE) {
+ /* a directory entry is now waiting in memory */
+ dirp->cached = 1;
+ error = 0;
+ } else {
+ /* search pattern is not a directory name? */
+ DIRENT_SET_ERRNO (ENOENT);
+ error = 1;
+ }
+ } else {
+ /* buffer too small */
+ DIRENT_SET_ERRNO (ENOMEM);
+ error = 1;
+ }
+
+ if (error) {
+ free (dirp);
+ dirp = NULL;
+ }
+ }
+
+ return dirp;
+}
+
+
+/*****************************************************************************
+ * Read a directory entry, and return a pointer to a dirent structure
+ * containing the name of the entry in d_name field. Individual directory
+ * entries returned by this very function include regular files,
+ * sub-directories, pseudo-directories "." and "..", but also volume labels,
+ * hidden files and system files may be returned.
+ */
+static struct dirent *readdir(DIR *dirp) {
+ DWORD attr;
+ if (dirp == NULL) {
+ /* directory stream did not open */
+ DIRENT_SET_ERRNO (EBADF);
+ return NULL;
+ }
+
+ /* get next directory entry */
+ if (dirp->cached != 0) {
+ /* a valid directory entry already in memory */
+ dirp->cached = 0;
+ } else {
+ /* get the next directory entry from stream */
+ if (dirp->search_handle == INVALID_HANDLE_VALUE) {
+ return NULL;
+ }
+ if (FindNextFileA (dirp->search_handle, &dirp->find_data) == FALSE) {
+ /* the very last entry has been processed or an error occured */
+ FindClose (dirp->search_handle);
+ dirp->search_handle = INVALID_HANDLE_VALUE;
+ return NULL;
+ }
+ }
+
+ /* copy as a multibyte character string */
+ DIRENT_STRNCPY ( dirp->curentry.d_name,
+ dirp->find_data.cFileName,
+ sizeof(dirp->curentry.d_name) );
+ dirp->curentry.d_name[MAX_PATH] = '\0';
+
+ /* compute the length of name */
+ dirp->curentry.d_namlen = strlen (dirp->curentry.d_name);
+
+ /* determine file type */
+ attr = dirp->find_data.dwFileAttributes;
+ if ((attr & FILE_ATTRIBUTE_DEVICE) != 0) {
+ dirp->curentry.d_type = DT_CHR;
+ } else if ((attr & FILE_ATTRIBUTE_DIRECTORY) != 0) {
+ dirp->curentry.d_type = DT_DIR;
+ } else {
+ dirp->curentry.d_type = DT_REG;
+ }
+ return &dirp->curentry;
+}
+
+
+/*****************************************************************************
+ * Close directory stream opened by opendir() function. Close of the
+ * directory stream invalidates the DIR structure as well as any previously
+ * read directory entry.
+ */
+static int closedir(DIR *dirp) {
+ if (dirp == NULL) {
+ /* invalid directory stream */
+ DIRENT_SET_ERRNO (EBADF);
+ return -1;
+ }
+
+ /* release search handle */
+ if (dirp->search_handle != INVALID_HANDLE_VALUE) {
+ FindClose (dirp->search_handle);
+ dirp->search_handle = INVALID_HANDLE_VALUE;
+ }
+
+ /* release directory structure */
+ free (dirp);
+ return 0;
+}
+
+
+/*****************************************************************************
+ * Resets the position of the directory stream to which dirp refers to the
+ * beginning of the directory. It also causes the directory stream to refer
+ * to the current state of the corresponding directory, as a call to opendir()
+ * would have done. If dirp does not refer to a directory stream, the effect
+ * is undefined.
+ */
+static void rewinddir(DIR* dirp) {
+ if (dirp != NULL) {
+ /* release search handle */
+ if (dirp->search_handle != INVALID_HANDLE_VALUE) {
+ FindClose (dirp->search_handle);
+ }
+
+ /* open new search handle and retrieve the first entry */
+ dirp->search_handle = FindFirstFileA (dirp->patt, &dirp->find_data);
+ if (dirp->search_handle != INVALID_HANDLE_VALUE) {
+ /* a directory entry is now waiting in memory */
+ dirp->cached = 1;
+ } else {
+ /* failed to re-open directory: no directory entry in memory */
+ dirp->cached = 0;
+ }
+}
+}
+
+
+#ifdef __cplusplus
+}
+#endif
+#endif /*DIRENT_H*/
--
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